url = 'https://' + url;
}
url = new URL(url);
- return db.discoveryDoc({baseURL: url.origin}).map(function() {
+ return m.request(url.origin + '/discovery/v1/apis/arvados/v1/rest').then(function() {
return url.origin + '/';
}).catch(function(err) {
// If url is a Workbench site (and isn't too old),
// discovery doc from a session's API server.
discoveryDoc: function(session) {
var cache = db.discoveryCache[session.baseURL];
- if (!cache) {
+ if (!cache && session) {
db.discoveryCache[session.baseURL] = cache = m.stream();
- m.request(session.baseURL+'discovery/v1/apis/arvados/v1/rest')
+ var baseURL = session.baseURL;
+ if (baseURL[baseURL.length - 1] !== '/') {
+ baseURL += '/';
+ }
+ m.request(baseURL+'discovery/v1/apis/arvados/v1/rest')
.then(function (dd) {
// Just in case we're talking with an old API server.
dd.remoteHosts = dd.remoteHosts || {};
autoLoadRemoteHosts: function() {
var sessions = db.loadAll();
var doc = db.discoveryDoc(db.loadLocal());
+ if (doc === undefined) { return; }
doc.map(function(d) {
Object.keys(d.remoteHosts).map(function(uuidPrefix) {
if (!(sessions[uuidPrefix])) {
end
def render_markup(markup)
- raw RedCloth.new(markup.to_s).to_html(:refs_arvados, :textile) if markup
+ sanitize(raw(RedCloth.new(markup.to_s).to_html(:refs_arvados, :textile))) if markup
end
def human_readable_bytes_html(n)
project = api_fixture('groups')['aproject']
use_token :active
found = Group.find(project['uuid'])
- found.description = '
Textile description with link to home page <a href="/">take me home</a>.'
+ found.description = '
<b>Textile</b> description with link to home page <a href="/">take me home</a>.'
found.save!
get(:show, {id: project['uuid']}, session_for(:active))
- assert_includes @response.body, 'Textile description with link to home page <a href="/">take me home</a>.'
+ assert_includes @response.body, '<b>Textile</b> description with link to home page <a href="/">take me home</a>.'
+ end
+
+ test "find a project and edit description to unsafe html description" do
+ project = api_fixture('groups')['aproject']
+ use_token :active
+ found = Group.find(project['uuid'])
+ found.description = 'Textile description with unsafe script tag <script language="javascript">alert("Hello there")</script>.'
+ found.save!
+ get(:show, {id: project['uuid']}, session_for(:active))
+ assert_includes @response.body, 'Textile description with unsafe script tag alert("Hello there").'
end
test "find a project and edit description to textile description with link to object" do
debian8,debian9,ubuntu1404,ubuntu1604,centos7|rdflib|4.2.2|2|python|all
debian8,debian9,ubuntu1404,centos7|shellescape|3.4.1|2|python|all
debian8,debian9,ubuntu1404,ubuntu1604,centos7|mistune|0.7.3|2|python|all
-debian8,debian9,ubuntu1404,ubuntu1604,centos7|typing|3.5.3.0|2|python|all
+debian8,debian9,ubuntu1404,ubuntu1604,centos7|typing|3.6.4|2|python|all
debian8,debian9,ubuntu1404,ubuntu1604,centos7|avro|1.8.1|2|python|all
debian8,debian9,ubuntu1404,centos7|ruamel.ordereddict|0.4.9|2|python|amd64
debian8,debian9,ubuntu1404,ubuntu1604,centos7|cachecontrol|0.11.7|2|python|all
centos7|pbr|0.11.1|2|python|all
centos7|pyparsing|2.1.10|2|python|all
centos7|keepalive|0.5|2|python|all
+centos7|networkx|1.11|0|python|all
+centos7|psutil|5.0.1|0|python|all
debian8,debian9,ubuntu1404,ubuntu1604,centos7|lockfile|0.12.2|2|python|all|--epoch 1
debian8,debian9,ubuntu1404,ubuntu1604,centos7|subprocess32|3.5.1|2|python|all
all|ruamel.yaml|0.14.12|2|python|amd64|--python-setup-py-arguments --single-version-externally-managed
all|future|0.16.0|2|python|all
all|future|0.16.0|2|python3|all
all|mypy-extensions|0.3.0|1|python|all
+all|prov|1.5.1|0|python|all
+all|bagit|1.6.4|0|python|all
+all|typing-extensions|3.6.5|0|python|all
export ARV_PACKAGES_DIR="/arvados/packages/$target"
-dpkg-deb -x $(ls -t "$ARV_PACKAGES_DIR/$1"_*.deb | head -n1) .
+if [[ -f $(ls -t "$ARV_PACKAGES_DIR/$1"_*.deb | head -n1) ]] ; then
+ debpkg=$(ls -t "$ARV_PACKAGES_DIR/$1"_*.deb | head -n1)
+else
+ debpkg=$(ls -t "$ARV_PACKAGES_DIR/processed/$1"_*.deb | head -n1)
+fi
+
+dpkg-deb -x $debpkg .
while read so && [ -n "$so" ]; do
echo
declare $(format_last_commit_here "git_ts=%ct git_hash=%h")
ARVADOS_BUILDING_VERSION="$(git describe --abbrev=0).$(date -ud "@$git_ts" +%Y%m%d%H%M%S)"
echo "$ARVADOS_BUILDING_VERSION"
-}
+}
nohash_version_from_git() {
if [[ -n "$ARVADOS_BUILDING_VERSION" ]]; then
repo_subdir=${pkgname:0:1}
fi
- repo_pkg_list=$(curl -o - http://apt.arvados.org/pool/${D}/main/${repo_subdir}/)
+ repo_pkg_list=$(curl -s -o - http://apt.arvados.org/pool/${D}/main/${repo_subdir}/)
echo ${repo_pkg_list} |grep -q ${complete_pkgname}
- if [ $? -eq 0 ]; then
+ if [ $? -eq 0 ] ; then
echo "Package $complete_pkgname exists, not rebuilding!"
curl -o ./${complete_pkgname} http://apt.arvados.org/pool/${D}/main/${repo_subdir}/${complete_pkgname}
return 1
+ elif test -f "$WORKSPACE/packages/$TARGET/processed/${complete_pkgname}" ; then
+ echo "Package $complete_pkgname exists, not rebuilding!"
+ return 1
else
echo "Package $complete_pkgname not found, building"
return 0
do_install() {
skipit=false
- if [[ -z "${only_install}" || "${only_install}" == "${1}" ]]; then
+ if [[ -z "${only_install}" || "${only_install}" == "${1}" || "${only_install}" == "${2}" ]]; then
retry do_install_once ${@}
else
skipit=true
- Run a workflow using Workbench:
- user/getting_started/workbench.html.textile.liquid
- user/tutorials/tutorial-workflow-workbench.html.textile.liquid
+ - user/composer/composer.html.textile.liquid
- Access an Arvados virtual machine:
- user/getting_started/vm-login-with-webshell.html.textile.liquid
- user/getting_started/ssh-access-unix.html.textile.liquid
admin:
- Topics:
- admin/index.html.textile.liquid
+ - Upgrading and migrations:
- admin/upgrading.html.textile.liquid
+ - install/migrate-docker19.html.textile.liquid
+ - Users and Groups:
- install/cheat_sheet.html.textile.liquid
- - user/topics/arvados-sync-groups.html.textile.liquid
- - admin/storage-classes.html.textile.liquid
- admin/activation.html.textile.liquid
- - admin/migrating-providers.html.textile.liquid
- admin/merge-remote-account.html.textile.liquid
+ - admin/migrating-providers.html.textile.liquid
+ - user/topics/arvados-sync-groups.html.textile.liquid
+ - Monitoring:
+ - admin/health-checks.html.textile.liquid
+ - admin/metrics.html.textile.liquid
+ - admin/management-token.html.textile.liquid
+ - Cloud:
+ - admin/storage-classes.html.textile.liquid
- admin/spot-instances.html.textile.liquid
- - install/migrate-docker19.html.textile.liquid
installguide:
- Overview:
- install/index.html.textile.liquid
- Core:
- install/install-postgresql.html.textile.liquid
- install/install-api-server.html.textile.liquid
+ - install/install-controller.html.textile.liquid
- Keep:
- install/install-keepstore.html.textile.liquid
- install/configure-fs-storage.html.textile.liquid
--- /dev/null
+---
+layout: default
+navsection: admin
+title: Health checks
+...
+
+{% comment %}
+Copyright (C) The Arvados Authors. All rights reserved.
+
+SPDX-License-Identifier: CC-BY-SA-3.0
+{% endcomment %}
+
+Health check endpoints are found at @/_health/ping@ on many Arvados services. The purpose of the health check is to offer a simple method of determining if a service can be reached and allow the service to self-report any problems, suitable for integrating into operational alert systems.
+
+To access health check endpoints, services must be configured with a "management token":management-token.html .
+
+Health check endpoints return a JSON object with the field @health@. This has a value of either @OK@ or @ERROR@. On error, it may also include a field @error@ with additional information. Examples:
+
+<pre>
+{
+ "health": "OK"
+}
+</pre>
+
+<pre>
+{
+ "health": "ERROR"
+ "error": "Inverted polarity in the warp core"
+}
+</pre>
+
+h2. Healthcheck aggregator
+
+The service @arvados-health@ performs health checks on all configured services and returns a single value of @OK@ or @ERROR@ for the entire cluster. It exposes the endpoint @/_health/all@ .
+
+The healthcheck aggregator uses the @NodeProfile@ section of the cluster-wide @arvados.yml@ configuration file. Here is an example.
+
+<pre>
+Cluster:
+ # The cluster uuid prefix
+ zzzzz:
+ NodeProfile:
+ # For each node, the profile name corresponds to a
+ # locally-resolvable hostname, and describes which Arvados
+ # services are available on that machine.
+ api:
+ arvados-controller:
+ Listen: 8000
+ arvados-api-server:
+ Listen: 8001
+ manage:
+ arvados-node-manager:
+ Listen: 8002
+ workbench:
+ arvados-workbench:
+ Listen: 8003
+ arvados-ws:
+ Listen: 8004
+ keep:
+ keep-web:
+ Listen: 8005
+ keepproxy:
+ Listen: 8006
+ keep0:
+ keepstore:
+ Listen: 25701
+ keep1:
+ keepstore:
+ Listen: 25701
+</pre>
--- /dev/null
+---
+layout: default
+navsection: admin
+title: Management token
+...
+
+{% comment %}
+Copyright (C) The Arvados Authors. All rights reserved.
+
+SPDX-License-Identifier: CC-BY-SA-3.0
+{% endcomment %}
+
+To enable and collect health checks and metrics, services must be configured with a "management token".
+
+Services must have ManagementToken configured. This is used to authorize access monitoring endpoints. If ManagementToken is not configured, monitoring endpoints will return the error @404 disabled@.
+
+To access a monitoring endpoint, the requester must provide the HTTP header @Authorization: Bearer (ManagementToken)@.
+
+h2. API server
+
+Set @ManagementToken@ in the appropriate section of @application.yml@
+
+<pre>
+production:
+ # Token to be included in all healthcheck requests. Disabled by default.
+ # Server expects request header of the format "Authorization: Bearer xxx"
+ ManagementToken: xxx
+</pre>
+
+h2. Node Manager
+
+Set @port@ (the listen port) and @ManagementToken@ in the @Manage@ section of @node-manager.ini@.
+
+<pre>
+[Manage]
+# The management server responds to http://addr:port/status.json with
+# a snapshot of internal state.
+
+# Management server listening address (default 127.0.0.1)
+#address = 0.0.0.0
+
+# Management server port number (default -1, server is disabled)
+#port = 8989
+
+ManagementToken = xxx
+</pre>
+
+h2. Other services
+
+The following services also support monitoring. Set @ManagementToken@ in the respective yaml config file for each service.
+
+* keepstore
+* keep-web
+* keepproxy
+* arv-git-httpd
+* websockets
--- /dev/null
+---
+layout: default
+navsection: admin
+title: Metrics
+...
+
+{% comment %}
+Copyright (C) The Arvados Authors. All rights reserved.
+
+SPDX-License-Identifier: CC-BY-SA-3.0
+{% endcomment %}
+
+Some Arvados services publish Prometheus/OpenMetrics-compatible metrics at @/metrics@, and some provide additional runtime status at @/status.json@. Metrics can help you understand how components perform under load, find performance bottlenecks, and detect and diagnose problems.
+
+To access metrics endpoints, services must be configured with a "management token":management-token.html. When accessing a metrics endpoint, prefix the management token with @"Bearer "@ and supply it in the @Authorization@ request header.
+
+<pre>curl -sfH "Authorization: Bearer your_management_token_goes_here" "https://0.0.0.0:25107/status.json"
+</pre>
+
+h2. Keep-web
+
+Keep-web exports metrics at @/metrics@ -- e.g., @https://collections.zzzzz.arvadosapi.com/metrics@.
+
+table(table table-bordered table-condensed).
+|_. Name|_. Type|_. Description|
+|request_duration_seconds|summary|elapsed time between receiving a request and sending the last byte of the response body (segmented by HTTP request method and response status code)|
+|time_to_status_seconds|summary|elapsed time between receiving a request and sending the HTTP response status code (segmented by HTTP request method and response status code)|
+
+Metrics in the @arvados_keepweb_collectioncache@ namespace report keep-web's internal cache of Arvados collection metadata.
+
+table(table table-bordered table-condensed).
+|_. Name|_. Type|_. Description|
+|arvados_keepweb_collectioncache_requests|counter|cache lookups|
+|arvados_keepweb_collectioncache_api_calls|counter|outgoing API calls|
+|arvados_keepweb_collectioncache_permission_hits|counter|collection-to-permission cache hits|
+|arvados_keepweb_collectioncache_pdh_hits|counter|UUID-to-PDH cache hits|
+|arvados_keepweb_collectioncache_hits|counter|PDH-to-manifest cache hits|
+|arvados_keepweb_collectioncache_cached_manifests|gauge|number of collections in the cache|
+|arvados_keepweb_collectioncache_cached_manifest_bytes|gauge|memory consumed by cached collection manifests|
+
+h2. Keepstore
+
+Keepstore exports metrics at @/status.json@ -- e.g., @http://keep0.zzzzz.arvadosapi.com:25107/status.json@.
+
+h3. Root
+
+table(table table-bordered table-condensed).
+|_. Attribute|_. Type|_. Description|
+|Volumes| array of "volumeStatusEnt":#volumeStatusEnt ||
+|BufferPool| "PoolStatus":#PoolStatus ||
+|PullQueue| "WorkQueueStatus":#WorkQueueStatus ||
+|TrashQueue| "WorkQueueStatus":#WorkQueueStatus ||
+|RequestsCurrent| int ||
+|RequestsMax| int ||
+|Version| string ||
+
+h3(#volumeStatusEnt). volumeStatusEnt
+
+table(table table-bordered table-condensed).
+|_. Attribute|_. Type|_. Description|
+|Label| string||
+|Status| "VolumeStatus":#VolumeStatus ||
+|VolumeStats| "ioStats":#ioStats ||
+
+h3(#VolumeStatus). VolumeStatus
+
+table(table table-bordered table-condensed).
+|_. Attribute|_. Type|_. Description|
+|MountPoint| string||
+|DeviceNum| uint64||
+|BytesFree| uint64||
+|BytesUsed| uint64||
+
+h3(#ioStats). ioStats
+
+table(table table-bordered table-condensed).
+|_. Attribute|_. Type|_. Description|
+|Errors| uint64||
+|Ops| uint64||
+|CompareOps| uint64||
+|GetOps| uint64||
+|PutOps| uint64||
+|TouchOps| uint64||
+|InBytes| uint64||
+|OutBytes| uint64||
+
+h3(#PoolStatus). PoolStatus
+
+table(table table-bordered table-condensed).
+|_. Attribute|_. Type|_. Description|
+|BytesAllocatedCumulative| uint64||
+|BuffersMax| int||
+|BuffersInUse| int||
+
+h3(#WorkQueueStatus). WorkQueueStatus
+
+table(table table-bordered table-condensed).
+|_. Attribute|_. Type|_. Description|
+|InProgress| int||
+|Queued| int||
+
+h3. Example response
+
+<pre>
+{
+ "Volumes": [
+ {
+ "Label": "[UnixVolume /var/lib/arvados/keep0]",
+ "Status": {
+ "MountPoint": "/var/lib/arvados/keep0",
+ "DeviceNum": 65029,
+ "BytesFree": 222532972544,
+ "BytesUsed": 435456679936
+ },
+ "InternalStats": {
+ "Errors": 0,
+ "InBytes": 1111,
+ "OutBytes": 0,
+ "OpenOps": 1,
+ "StatOps": 4,
+ "FlockOps": 0,
+ "UtimesOps": 0,
+ "CreateOps": 0,
+ "RenameOps": 0,
+ "UnlinkOps": 0,
+ "ReaddirOps": 0
+ }
+ }
+ ],
+ "BufferPool": {
+ "BytesAllocatedCumulative": 67108864,
+ "BuffersMax": 20,
+ "BuffersInUse": 0
+ },
+ "PullQueue": {
+ "InProgress": 0,
+ "Queued": 0
+ },
+ "TrashQueue": {
+ "InProgress": 0,
+ "Queued": 0
+ },
+ "RequestsCurrent": 1,
+ "RequestsMax": 40,
+ "Version": "dev"
+}
+</pre>
+
+h2. Node manager
+
+The node manager status end point provides a snapshot of internal status at the time of the most recent wishlist update.
+
+table(table table-bordered table-condensed).
+|_. Attribute|_. Type|_. Description|
+|nodes_booting|int|Number of nodes in booting state|
+|nodes_unpaired|int|Number of nodes in unpaired state|
+|nodes_busy|int|Number of nodes in busy state|
+|nodes_idle|int|Number of nodes in idle state|
+|nodes_fail|int|Number of nodes in fail state|
+|nodes_down|int|Number of nodes in down state|
+|nodes_shutdown|int|Number of nodes in shutdown state|
+|nodes_wish|int|Number of nodes in the current wishlist|
+|node_quota|int|Current node count ceiling due to cloud quota limits|
+|config_max_nodes|int|Configured max node count|
+
+h3. Example
+
+<pre>
+{
+ "actor_exceptions": 0,
+ "idle_times": {
+ "compute1": 0,
+ "compute3": 0,
+ "compute2": 0,
+ "compute4": 0
+ },
+ "create_node_errors": 0,
+ "destroy_node_errors": 0,
+ "nodes_idle": 0,
+ "config_max_nodes": 8,
+ "list_nodes_errors": 0,
+ "node_quota": 8,
+ "Version": "1.1.4.20180719160944",
+ "nodes_wish": 0,
+ "nodes_unpaired": 0,
+ "nodes_busy": 4,
+ "boot_failures": 0
+}
+</pre>
TODO: extract this information based on git commit messages and generate changelogs / release notes automatically.
{% endcomment %}
+h3. 2018-07-31: "#13497":https://dev.arvados.org/issues/13497 "db5107dca":https://dev.arvados.org/projects/arvados/repository/revisions/db5107dca adds a new system service, arvados-controller
+* "Install the controller":../install/install-controller.html after upgrading your system.
+* Verify your setup by confirming that API calls appear in the controller's logs (_e.g._, @journalctl -fu arvados-controller@) while loading a workbench page.
+
h3. 2018-04-05: v1.1.4 regression in arvados-cwl-runner for workflows that rely on implicit discovery of secondaryFiles
h4. Secondary files missing from toplevel workflow inputs
This bug will be fixed in an upcoming release of Arvados.
-h3. 2017-12-08: #11908 commit:8f987a9271 now requires minimum of Postgres 9.4 (previously 9.3)
+h3. 2017-12-08: "#11908":https://dev.arvados.org/issues/11908 "8f987a9271":https://dev.arvados.org/projects/arvados/repository/revisions/8f987a9271 now requires minimum of Postgres 9.4 (previously 9.3)
* Debian 8 (pg 9.4) and Debian 9 (pg 9.6) do not require an upgrade
* Ubuntu 16.04 (pg 9.5) does not require an upgrade
* Ubuntu 14.04 (pg 9.3) requires upgrade to Postgres 9.4: https://www.postgresql.org/download/linux/ubuntu/
*# Install the @rh-postgresql94@ backport package from either Software Collections: http://doc.arvados.org/install/install-postgresql.html or the Postgres developers: https://www.postgresql.org/download/linux/redhat/
*# Restore from the backup using @psql@
-h3. 2017-09-25: #12032 commit:68bdf4cbb now requires minimum of Postgres 9.3 (previously 9.1)
+h3. 2017-09-25: "#12032":https://dev.arvados.org/issues/12032 "68bdf4cbb":https://dev.arvados.org/projects/arvados/repository/revisions/68bdf4cbb now requires minimum of Postgres 9.3 (previously 9.1)
* Debian 8 (pg 9.4) and Debian 9 (pg 9.6) do not require an upgrade
* Ubuntu 16.04 (pg 9.5) does not require an upgrade
* Ubuntu 14.04 (pg 9.3) is compatible, however upgrading to Postgres 9.4 is recommended: https://www.postgresql.org/download/linux/ubuntu/
*# Install the @rh-postgresql94@ backport package from either Software Collections: http://doc.arvados.org/install/install-postgresql.html or the Postgres developers: https://www.postgresql.org/download/linux/redhat/
*# Restore from the backup using @psql@
-h3. 2017-06-30: #11807 commit:55aafbb converts old "jobs" database records from YAML to JSON, making the upgrade process slower than usual.
-* The migration can take some time if your database contains a substantial number of YAML-serialized rows (i.e., you installed Arvados before March 3, 2017 commit:660a614 and used the jobs/pipelines APIs). Otherwise, the upgrade will be no slower than usual.
+h3. 2017-06-30: "#11807":https://dev.arvados.org/issues/11807 "55aafbb":https://dev.arvados.org/projects/arvados/repository/revisions/55aafbb converts old "jobs" database records from YAML to JSON, making the upgrade process slower than usual.
+* The migration can take some time if your database contains a substantial number of YAML-serialized rows (i.e., you installed Arvados before March 3, 2017 "660a614":https://dev.arvados.org/projects/arvados/repository/revisions/660a614 and used the jobs/pipelines APIs). Otherwise, the upgrade will be no slower than usual.
* The conversion runs as a database migration, i.e., during the deb/rpm package upgrade process, while your API server is unavailable.
* Expect it to take about 1 minute per 20K jobs that have ever been created/run.
-h3. 2017-06-05: #9005 commit:cb230b0 reduces service discovery overhead in keep-web requests.
+h3. 2017-06-05: "#9005":https://dev.arvados.org/issues/9005 "cb230b0":https://dev.arvados.org/projects/arvados/repository/revisions/cb230b0 reduces service discovery overhead in keep-web requests.
* When upgrading keep-web _or keepproxy_ to/past this version, make sure to update API server as well. Otherwise, a bad token in a request can cause keep-web to fail future requests until either keep-web restarts or API server gets upgraded.
-h3. 2017-04-12: #11349 commit:2c094e2 adds a "management" http server to nodemanager.
+h3. 2017-04-12: "#11349":https://dev.arvados.org/issues/11349 "2c094e2":https://dev.arvados.org/projects/arvados/repository/revisions/2c094e2 adds a "management" http server to nodemanager.
* To enable it, add to your configuration file: <pre>[Manage]
address = 127.0.0.1
port = 8989</pre> (see example configuration files in source:services/nodemanager/doc or https://doc.arvados.org/install/install-nodemanager.html for more info)
* The server responds to @http://{address}:{port}/status.json@ with a summary of how many nodes are in each state (booting, busy, shutdown, etc.)
-h3. 2017-03-23: #10766 commit:e8cc0d7 replaces puma with arvados-ws as the recommended websocket server.
+h3. 2017-03-23: "#10766":https://dev.arvados.org/issues/10766 "e8cc0d7":https://dev.arvados.org/projects/arvados/repository/revisions/e8cc0d7 replaces puma with arvados-ws as the recommended websocket server.
* See http://doc.arvados.org/install/install-ws.html for install/upgrade instructions.
* Remove the old puma server after the upgrade is complete. Example, with runit: <pre>
$ sudo sv down /etc/sv/puma
$ systemctl stop puma
</pre>
-h3. 2017-03-06: #11168 commit:660a614 uses JSON instead of YAML to encode hashes and arrays in the database.
+h3. 2017-03-06: "#11168":https://dev.arvados.org/issues/11168 "660a614":https://dev.arvados.org/projects/arvados/repository/revisions/660a614 uses JSON instead of YAML to encode hashes and arrays in the database.
* Aside from a slight performance improvement, this should have no externally visible effect.
* Downgrading past this version is not supported, and is likely to cause errors. If this happens, the solution is to upgrade past this version.
* After upgrading, make sure to restart puma and crunch-dispatch-* processes.
-h3. 2017-02-03: #10969 commit:74a9dec introduces a Docker image format compatibility check: the @arv keep docker@ command prevents users from inadvertently saving docker images that compute nodes won't be able to run.
+h3. 2017-02-03: "#10969":https://dev.arvados.org/issues/10969 "74a9dec":https://dev.arvados.org/projects/arvados/repository/revisions/74a9dec introduces a Docker image format compatibility check: the @arv keep docker@ command prevents users from inadvertently saving docker images that compute nodes won't be able to run.
* If your compute nodes run a version of *docker older than 1.10* you must override the default by adding to your API server configuration (@/etc/arvados/api/application.yml@): <pre><code class="yaml">docker_image_formats: ["v1"]</code></pre>
-* Refer to the comments above @docker_image_formats@ in @/var/www/arvados-api/current/config/application.default.yml@ or source:services/api/config/application.default.yml or issue #10969 for more detail.
+* Refer to the comments above @docker_image_formats@ in @/var/www/arvados-api/current/config/application.default.yml@ or source:services/api/config/application.default.yml or issue "#10969":https://dev.arvados.org/issues/10969 for more detail.
* *NOTE:* This does *not* include any support for migrating existing Docker images from v1 to v2 format. This will come later: for now, sites running Docker 1.9 or earlier should still *avoid upgrading Docker further than 1.9.*
-h3. 2016-09-27: several Debian and RPM packages -- keep-balance (commit:d9eec0b), keep-web (commit:3399e63), keepproxy (commit:6de67b6), and arvados-git-httpd (commit:9e27ddf) -- now enable their respective components using systemd. These components prefer YAML configuration files over command line flags (commit:3bbe1cd).
+h3. 2016-09-27: several Debian and RPM packages -- keep-balance ("d9eec0b":https://dev.arvados.org/projects/arvados/repository/revisions/d9eec0b), keep-web ("3399e63":https://dev.arvados.org/projects/arvados/repository/revisions/3399e63), keepproxy ("6de67b6":https://dev.arvados.org/projects/arvados/repository/revisions/6de67b6), and arvados-git-httpd ("9e27ddf":https://dev.arvados.org/projects/arvados/repository/revisions/9e27ddf) -- now enable their respective components using systemd. These components prefer YAML configuration files over command line flags ("3bbe1cd":https://dev.arvados.org/projects/arvados/repository/revisions/3bbe1cd).
* On Debian-based systems using systemd, services are enabled automatically when packages are installed.
* On RedHat-based systems using systemd, unit files are installed but services must be enabled explicitly: e.g., <code>"sudo systemctl enable keep-web; sudo systemctl start keep-web"</code>.
* The new systemd-supervised services will not start up successfully until configuration files are installed in /etc/arvados/: e.g., <code>"Sep 26 18:23:55 62751f5bb946 keep-web[74]: 2016/09/26 18:23:55 open /etc/arvados/keep-web/keep-web.yml: no such file or directory"</code>
** keepproxy - /etc/arvados/keepproxy/keepproxy.yml
** arvados-git-httpd - /etc/arvados/arv-git-httpd/arv-git-httpd.yml
-h3. 2016-05-31: commit:ae72b172c8 and commit:3aae316c25 install Python modules and scripts to different locations on the filesystem.
-* Previous packages installed these files to the distribution's preferred path under @/usr/local@ (or the equivalent location in a Software Collection). Now they get installed to a path under @/usr@. This improves compatibility with other Python packages provided by the distribution. See #9242 for more background.
+h3. 2016-05-31: "ae72b172c8":https://dev.arvados.org/projects/arvados/repository/revisions/ae72b172c8 and "3aae316c25":https://dev.arvados.org/projects/arvados/repository/revisions/3aae316c25 install Python modules and scripts to different locations on the filesystem.
+* Previous packages installed these files to the distribution's preferred path under @/usr/local@ (or the equivalent location in a Software Collection). Now they get installed to a path under @/usr@. This improves compatibility with other Python packages provided by the distribution. See "#9242":https://dev.arvados.org/issues/9242 for more background.
* If you simply import Python modules from scripts, or call Python tools relying on $PATH, you don't need to make any changes. If you have hardcoded full paths to some of these files (e.g., in symbolic links or configuration files), you will need to update those paths after this upgrade.
-h3. 2016-04-25: commit:eebcb5e requires the crunchrunner package to be installed on compute nodes and shell nodes in order to run CWL workflows.
+h3. 2016-04-25: "eebcb5e":https://dev.arvados.org/projects/arvados/repository/revisions/eebcb5e requires the crunchrunner package to be installed on compute nodes and shell nodes in order to run CWL workflows.
* On each Debian-based compute node and shell node, run: @sudo apt-get install crunchrunner@
* On each Red Hat-based compute node and shell node, run: @sudo yum install crunchrunner@
-h3. 2016-04-21: commit:3c88abd changes the Keep permission signature algorithm.
+h3. 2016-04-21: "3c88abd":https://dev.arvados.org/projects/arvados/repository/revisions/3c88abd changes the Keep permission signature algorithm.
* All software components that generate signatures must be upgraded together. These are: keepstore, API server, keep-block-check, and keep-rsync. For example, if keepstore < 0.1.20160421183420 but API server >= 0.1.20160421183420, clients will not be able to read or write data in Keep.
* Jobs and client operations that are in progress during the upgrade (including arv-put's "resume cache") will fail.
-h3. 2015-01-05: commit:e1276d6e disables Workbench's "Getting Started" popup by default.
+h3. 2015-01-05: "e1276d6e":https://dev.arvados.org/projects/arvados/repository/revisions/e1276d6e disables Workbench's "Getting Started" popup by default.
* If you want new users to continue seeing this popup, set @enable_getting_started_popup: true@ in Workbench's @application.yml@ configuration.
-h3. 2015-12-03: commit:5590c9ac makes a Keep-backed writable scratch directory available in crunch jobs (see #7751)
-* All compute nodes must be upgraded to arvados-fuse >= 0.1.2015112518060 because crunch-job uses some new arv-mount flags (--mount-tmp, --mount-by-pdh) introduced in merge commit:346a558
+h3. 2015-12-03: "5590c9ac":https://dev.arvados.org/projects/arvados/repository/revisions/5590c9ac makes a Keep-backed writable scratch directory available in crunch jobs (see "#7751":https://dev.arvados.org/issues/7751)
+* All compute nodes must be upgraded to arvados-fuse >= 0.1.2015112518060 because crunch-job uses some new arv-mount flags (--mount-tmp, --mount-by-pdh) introduced in merge "346a558":https://dev.arvados.org/projects/arvados/repository/revisions/346a558
* Jobs will fail if the API server (in particular crunch-job from the arvados-cli gem) is upgraded without upgrading arvados-fuse on compute nodes.
-h3. 2015-11-11: commit:1e2ace5 changes recommended config for keep-web (see #5824)
+h3. 2015-11-11: "1e2ace5":https://dev.arvados.org/projects/arvados/repository/revisions/1e2ace5 changes recommended config for keep-web (see "#5824":https://dev.arvados.org/issues/5824)
* proxy/dns/ssl config should be updated to route "https://download.uuid_prefix.arvadosapi.com/" requests to keep-web (alongside the existing "collections" routing)
* keep-web command line adds @-attachment-only-host download.uuid_prefix.arvadosapi.com@
* Workbench config adds @keep_web_download_url@
* More info on the (still beta/non-TOC-linked) "keep-web doc page":http://doc.arvados.org/install/install-keep-web.html
-h3. 2015-11-04: commit:1d1c6de removes stopped containers (see #7444)
+h3. 2015-11-04: "1d1c6de":https://dev.arvados.org/projects/arvados/repository/revisions/1d1c6de removes stopped containers (see "#7444":https://dev.arvados.org/issues/7444)
* arvados-docker-cleaner removes _all_ docker containers as soon as they exit, effectively making @docker run@ default to @--rm@. If you run arvados-docker-cleaner on a host that does anything other than run crunch-jobs, and you still want to be able to use @docker start@, read the "new doc page":http://doc.arvados.org/install/install-compute-node.html to learn how to turn this off before upgrading.
-h3. 2015-11-04: commit:21006cf adds a keep-web service (see #5824)
+h3. 2015-11-04: "21006cf":https://dev.arvados.org/projects/arvados/repository/revisions/21006cf adds a keep-web service (see "#5824":https://dev.arvados.org/issues/5824)
* Nothing relies on it yet, but early adopters can install it now by following http://doc.arvados.org/install/install-keep-web.html (it is not yet linked in the TOC).
!(full-width){{site.baseurl}}/images/Crunch_dispatch.svg!
+h2(#RAM). Understanding RAM requests for containers
+
+The @runtime_constraints@ section of a container specifies working RAM (@ram@) and Keep cache (@keep_cache_ram@). If not specified, containers get a default Keep cache (@container_default_keep_cache_ram@, default 256 MiB). The total RAM requested for a container is the sum of working RAM, Keep cache, and an additional RAM reservation configured by the admin (@ReserveExtraRAM@ in the dispatcher configuration, default zero).
+
+The total RAM request is used to schedule containers onto compute nodes. RAM allocation limits are enforced using kernel controls such as cgroups. A container which requests 1 GiB RAM will only be permitted to allocate up to 1 GiB of RAM, even if scheduled on a 4 GiB node. On HPC systems, a multi-core node may run multiple containers at a time.
+
+When running on the cloud, the memory request (along with CPU and disk) is used to select (and possibly boot) an instance type with adequate resources to run the container. Instance type RAM is derated 5% from the published specification to accomodate virtual machine, kernel and system services overhead.
+
+h3. Calculate minimum instance type RAM for a container
+
+ (RAM request + Keep cache + ReserveExtraRAM) * (100/95)
+
+For example, for a 3 GiB request, default Keep cache, and no extra RAM reserved:
+
+ (3072 + 256) * 1.0526 = 3494 MiB
+
+To run this container, the instance type must have a published RAM size of at least 3494 MiB.
+
+h3. Calculate the maximum requestable RAM for an instance type
+
+ (Instance type RAM * (95/100)) - Keep cache - ReserveExtraRAM
+
+For example, for a 3.75 GiB node, default Keep cache, and no extra RAM reserved:
+
+ (3840 * 0.95) - 256 = 3392 MiB
+
+To run on this instance type, the container can request at most 3392 MiB of working RAM.
+
h2. Job API (deprecated)
# To submit work, create a "job":{{site.baseurl}}/api/methods/jobs.html . If the same job has been submitted in the past, it will return an existing job in @Completed@ state.
.userinput {
color: #d14;
}
+
+table.CodeRay {
+ margin-left: 3em;
+ width: calc(100% - 6em);
+}
+
+td.line-numbers {
+ width: 2em;
+}
img.full-width {
width: 100%
}
+
+img.screenshot {
+ max-width: calc(100% - 2em);
+ border: 3px;
+ border-style: solid;
+ margin-left: 2em;
+ margin-bottom: 2em;
+}
---
layout: default
navsection: admin
-title: User management
+title: User management at the CLI
...
{% comment %}
Copyright (C) The Arvados Authors. All rights reserved.
</code></pre>
</notextile>
+h3(#disable_api_methods). disable_api_methods
+
+Set the @disable_api_methods@ configuration option to disable the deprecated @jobs@ API. This will prevent users from accidentally submitting jobs that won't run. "All new installations should use the containers API.":crunch2-slurm/install-prerequisites.html
+
+<notextile>
+<pre><code>
+ disable_api_methods:
+ - jobs.create
+ - pipeline_instances.create
+ - pipeline_templates.create
+ - jobs.get
+ - pipeline_instances.get
+ - pipeline_templates.get
+ - jobs.list
+ - pipeline_instances.list
+ - pipeline_templates.list
+ - jobs.index
+ - pipeline_instances.index
+ - pipeline_templates.index
+ - jobs.update
+ - pipeline_instances.update
+ - pipeline_templates.update
+ - jobs.queue
+ - jobs.queue_size
+ - job_tasks.create
+ - job_tasks.get
+ - job_tasks.list
+ - job_tasks.index
+ - job_tasks.update
+ - jobs.show
+ - pipeline_instances.show
+ - pipeline_templates.show
+ - job_tasks.show
+</code></pre>
+</notextile>
+
h2(#set_up). Set up Nginx and Passenger
The Nginx server will serve API requests using Passenger. It will also be used to proxy SSL requests to other services which are covered later in this guide.
First, "Install Nginx and Phusion Passenger":https://www.phusionpassenger.com/library/walkthroughs/deploy/ruby/ownserver/nginx/oss/install_passenger_main.html.
-Edit the http section of your Nginx configuration to run the Passenger server, and serve SSL requests. Add a block like the following, adding SSL and logging parameters to taste:
+Edit the http section of your Nginx configuration to run the Passenger server. Add a block like the following, adding SSL and logging parameters to taste:
<notextile>
-<pre><code>server {
+<pre><code>
+server {
listen 127.0.0.1:8000;
server_name localhost-api;
default 1;
<span class="userinput">10.20.30.0/24</span> 0;
}
-
-server {
- listen <span class="userinput">[your public IP address]</span>:443 ssl;
- server_name <span class="userinput">uuid_prefix.your.domain</span>;
-
- ssl on;
- ssl_certificate <span class="userinput">/YOUR/PATH/TO/cert.pem</span>;
- ssl_certificate_key <span class="userinput">/YOUR/PATH/TO/cert.key</span>;
-
- index index.html index.htm index.php;
-
- # Refer to the comment about this setting in the server section above.
- client_max_body_size 128m;
-
- location / {
- proxy_pass http://api;
- proxy_redirect off;
- proxy_connect_timeout 90s;
- proxy_read_timeout 300s;
-
- proxy_set_header X-Forwarded-Proto https;
- proxy_set_header Host $http_host;
- proxy_set_header X-External-Client $external_client;
- proxy_set_header X-Real-IP $remote_addr;
- proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for;
- }
-}
</code></pre>
</notextile>
--- /dev/null
+---
+layout: default
+navsection: installguide
+title: Install the controller
+...
+{% comment %}
+Copyright (C) The Arvados Authors. All rights reserved.
+
+SPDX-License-Identifier: CC-BY-SA-3.0
+{% endcomment %}
+
+The arvados-controller service must be installed on your API server node.
+
+On Debian-based systems:
+
+<notextile>
+<pre><code>~$ <span class="userinput">sudo apt-get install arvados-controller</span>
+</code></pre>
+</notextile>
+
+On Red Hat-based systems:
+
+<notextile>
+<pre><code>~$ <span class="userinput">sudo yum install arvados-controller</span>
+</code></pre>
+</notextile>
+
+Verify the @arvados-controller@ program is functional:
+
+<notextile>
+<pre><code>~$ <span class="userinput">arvados-controller -h</span>
+Usage:
+ -config file
+[...]
+</code></pre>
+</notextile>
+
+h3. Configure Nginx to route requests to the controller
+
+Add @upstream@ and @server@ definitions inside the @http@ section of your Nginx configuration using the following template.
+
+{% include 'notebox_begin' %}
+
+If you are adding arvados-controller to an existing system as part of the upgrade procedure, do not add a new "server" part here. Instead, add only the "upstream" part as shown here, and update your existing "server" section by changing its @proxy_pass@ directive from @http://api@ to @http://controller@.
+
+{% include 'notebox_end' %}
+
+<notextile>
+<pre><code>upstream controller {
+ server 127.0.0.1:9004 fail_timeout=10s;
+}
+
+server {
+ listen <span class="userinput">[your public IP address]</span>:443 ssl;
+ server_name <span class="userinput">uuid_prefix.your.domain</span>;
+
+ ssl on;
+ ssl_certificate <span class="userinput">/YOUR/PATH/TO/cert.pem</span>;
+ ssl_certificate_key <span class="userinput">/YOUR/PATH/TO/cert.key</span>;
+
+ # Refer to the comment about this setting in the passenger (arvados
+ # api server) section of your Nginx configuration.
+ client_max_body_size 128m;
+
+ location / {
+ proxy_pass http://controller;
+ proxy_redirect off;
+ proxy_connect_timeout 90s;
+ proxy_read_timeout 300s;
+
+ proxy_set_header X-Forwarded-Proto https;
+ proxy_set_header Host $http_host;
+ proxy_set_header X-External-Client $external_client;
+ proxy_set_header X-Real-IP $remote_addr;
+ proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for;
+ }
+}
+</code></pre>
+</notextile>
+
+Restart Nginx to apply the new configuration.
+
+<notextile>
+<pre><code>~$ <span class="userinput">sudo nginx -s reload</span>
+</code></pre>
+</notextile>
+
+h3. Configure arvados-controller
+
+Create the cluster configuration file @/etc/arvados/config.yml@ using the following template.
+
+<notextile>
+<pre><code>Clusters:
+ <span class="userinput">uuid_prefix</span>:
+ NodeProfiles:
+ apiserver:
+ arvados-controller:
+ Listen: ":<span class="userinput">9004</span>" # must match the "upstream controller" section of your Nginx config
+ arvados-api-server:
+ Listen: ":<span class="userinput">8000</span>" # must match the "upstream api" section of your Nginx config
+ PostgreSQL:
+ ConnectionPool: 128
+ Connection:
+ host: localhost
+ dbname: arvados_production
+ user: arvados
+ password: <span class="userinput">xxxxxxxx</span>
+ sslmode: require
+</code></pre>
+</notextile>
+
+Create the host configuration file @/etc/arvados/environment@.
+
+<notextile>
+<pre><code>ARVADOS_NODE_PROFILE=apiserver
+</code></pre>
+</notextile>
+
+h3. Start the service (option 1: systemd)
+
+If your system does not use systemd, skip this section and follow the "runit instructions":#runit instead.
+
+If your system uses systemd, the arvados-controller service should already be set up. Restart it to load the new configuration file, and check its status:
+
+<notextile>
+<pre><code>~$ <span class="userinput">sudo systemctl restart arvados-controller</span>
+~$ <span class="userinput">sudo systemctl status arvados-controller</span>
+● arvados-controller.service - Arvados controller
+ Loaded: loaded (/lib/systemd/system/arvados-controller.service; enabled; vendor preset: enabled)
+ Active: active (running) since Tue 2018-07-31 13:17:44 UTC; 3s ago
+ Docs: https://doc.arvados.org/
+ Main PID: 25066 (arvados-control)
+ CGroup: /system.slice/arvados-controller.service
+ └─25066 /usr/bin/arvados-controller
+
+Jul 31 13:17:44 zzzzz systemd[1]: Starting Arvados controller...
+Jul 31 13:17:44 zzzzz arvados-controller[25191]: {"Listen":"[::]:9004","Service":"arvados-controller","level":"info","msg":"listening","time":"2018-07-31T13:17:44.521694195Z"}
+Jul 31 13:17:44 zzzzz systemd[1]: Started Arvados controller.
+</code></pre>
+</notextile>
+
+Skip ahead to "confirm the service is working":#confirm.
+
+h3(#runit). Start the service (option 2: runit)
+
+Install runit to supervise the arvados-controller daemon. {% include 'install_runit' %}
+
+Create a supervised service.
+
+<notextile>
+<pre><code>~$ <span class="userinput">sudo mkdir /etc/service/arvados-controller</span>
+~$ <span class="userinput">cd /etc/service/arvados-controller</span>
+~$ <span class="userinput">sudo mkdir log log/main</span>
+~$ <span class="userinput">printf '#!/bin/sh\nset -a\n. /etc/arvados/environment\nexec arvados-controller 2>&1\n' | sudo tee run</span>
+~$ <span class="userinput">printf '#!/bin/sh\nexec svlogd main\n' | sudo tee log/run</span>
+~$ <span class="userinput">sudo chmod +x run log/run</span>
+~$ <span class="userinput">sudo sv exit .</span>
+~$ <span class="userinput">cd -</span>
+</code></pre>
+</notextile>
+
+Use @sv stat@ and check the log file to verify the service is running.
+
+<notextile>
+<pre><code>~$ <span class="userinput">sudo sv stat /etc/service/arvados-controller</span>
+run: /etc/service/arvados-controller: (pid 12520) 2s; run: log: (pid 12519) 2s
+~$ <span class="userinput">tail /etc/service/arvados-controller/log/main/current</span>
+{"Listen":"[::]:9004","Service":"arvados-controller","level":"info","msg":"listening","time":"2018-07-31T13:17:44.521694195Z"}
+</code></pre>
+</notextile>
+
+h3(#confirm). Confirm the service is working
+
+Confirm the service is listening on its assigned port and responding to requests.
+
+<notextile>
+<pre><code>~$ <span class="userinput">curl -X OPTIONS http://0.0.0.0:<b>9004</b>/login</span>
+{"errors":["Forbidden"],"error_token":"1533044555+684b532c"}
+</code></pre>
+</notextile>
--- /dev/null
+---
+layout: default
+navsection: userguide
+title: Create a Workflow with Composer
+...
+{% comment %}
+Copyright (C) The Arvados Authors. All rights reserved.
+
+SPDX-License-Identifier: CC-BY-SA-3.0
+{% endcomment %}
+
+The Arvados Workflow Composer is a graphical interface for building Common Workflow Language (CWL) workflows to run on Arvados.
+
+This tutorial will demonstrate:
+
+# Creating a new git repository through Arvados to store the workflow
+# Creating CommandLineTools for "sort" and "uniq"
+# Creating a Workflow which uses "sort" and "uniq" to remove duplicate lines from a text file
+# Submitting the Workflow to run on Arvados
+
+h3. 1. Access from workbench
+
+!(screenshot)c1.png!
+
+h3. 2. Composer starting page
+
+!(screenshot)c2.png!
+
+h3. 3. Manage git repositories (opens Workbench in new tab)
+
+!(screenshot)c2b.png!
+
+h3. 4. Add a new repository
+
+!(screenshot)c4.png!
+
+!(screenshot)c3.png!
+
+h3. 5. Return to Composer. Use refresh button to discover new repository (may take a few moments to show up).
+
+!(screenshot)c2c.png!
+
+h3. 6. Create a new Command Line Tool
+
+!(screenshot)c5.png!
+
+!(screenshot)c20.png!
+
+h3. 7. Set Docker image, base command, and input port for "sort" tool
+
+The "Docker Repository" is the name:tag of a "Docker image uploaded Arvados.":{{site.baseurl}}/user/topics/arv-docker.html (Use @arv-keepdocker --pull debian:8@) You can also find prepackaged bioinformatics tools on various sites, such as http://dockstore.org and http://biocontainers.pro/ .
+
+!(screenshot)c6.png!
+
+h3. 8. Redirect stdout to a file
+
+!(screenshot)c7.png!
+
+h3. 9. Capture output file
+
+!(screenshot)c8.png!
+
+h3. 10. Save Command Line Tool
+
+!(screenshot)c22.png!
+
+h3. 11. Repeat steps 6-10 for "uniq" tool
+
+Create a new tool with a "base command" of "uniq".
+
+h3. 12. Switch back to "Home" tab and create workflow
+
+!(screenshot)c24.png!
+
+!(screenshot)c9.png!
+
+!(screenshot)c10.png!
+
+h3. 13. Drag and drop tools into Workflow
+
+!(screenshot)c11.png!
+
+h3. 14. Drag from input port of "sort" to empty space to create workflow input
+
+!(screenshot)c21.png!
+
+h3. 15. Drag from output port of "sort" to input port of "uniq"
+
+!(screenshot)c13.png!
+
+h3. 16. Drag from output port of "uniq" to empty space to create workflow output
+
+!(screenshot)c14.png!
+
+h3. 17. Save Workflow
+
+!(screenshot)c23.png!
+
+h3. 18. Click on "Test" tab then click "Run"
+
+!(screenshot)c15.png!
+
+h3. 19. Choose input file
+
+You may need to "upload an input file":{{site.baseurl}}/user/tutorials/tutorial-keep.html
+
+!(screenshot)c16.png!
+
+h3. 20. Run the workflow
+
+!(screenshot)c17.png!
+
+h3. 21. Monitor progress (may take several minutes)
+
+!(screenshot)c18.png!
+
+h3. 22. Get workflow output
+
+!(screenshot)c19.png!
tmpdirMin: 90000
</pre>
+* Available compute nodes types vary over time and across different cloud providers, so try to limit the RAM requirement to what the program actually needs. However, if you need to target a specific compute node type, see this discussion on "calculating RAM request and choosing instance type for containers.":{{site.baseurl}}/api/execution.html#RAM
+
* Instead of scattering separate steps, prefer to scatter over a subworkflow.
With the following pattern, @step1@ has to wait for all samples to complete before @step2@ can start computing on any samples. This means a single long-running sample can prevent the rest of the workflow from moving on:
run: tool3.cwl
</pre>
-* When migrating from crunch v1 API (--api=jobs) to the crunch v2 API (--api=containers) there are a few differences in behavior:
+h2(#migrate). Migrating running CWL on jobs API to containers API
+
+* When migrating from jobs API (--api=jobs) (sometimes referred to as "crunch v1") to the containers API (--api=containers) ("crunch v2") there are a few differences in behavior:
** The tool is limited to accessing only collections which are explicitly listed in the input, and further limited to only the subdirectories of collections listed in input. For example, given an explicit file input @/dir/subdir/file1.txt@, a tool will not be able to implicitly access the file @/dir/file2.txt@. Use @secondaryFiles@ or a @Directory@ input to describe trees of files.
** Files listed in @InitialWorkDirRequirement@ appear in the output directory as normal files (not symlinks) but cannot be moved, renamed or deleted. These files will be added to the output collection but without any additional copies of the underlying data.
** Tools are disallowed network access by default. Tools which require network access must include @arv:APIRequirement: {}@ in their @requirements@ section.
h2. Upload your image
-Finally, we are ready to upload the new Docker image to Arvados. Use @arv keep docker@ with the image repository name to upload the image. Without arguments, @arv keep docker@ will print out the list of Docker images in Arvados that are available to you.
+Finally, we are ready to upload the new Docker image to Arvados. Use @arv-keepdocker@ with the image repository name to upload the image. Without arguments, @arv-keepdocker@ will print out the list of Docker images in Arvados that are available to you.
<notextile>
-<pre><code>$ <span class="userinput">arv keep docker arvados/jobs-with-r</span>
+<pre><code>$ <span class="userinput">arv-keepdocker arvados/jobs-with-r</span>
703M / 703M 100.0%
Collection saved as 'Docker image arvados/jobs-with-r:latest 2818853ff9f9'
qr1hi-4zz18-abcdefghijklmno
-$ <span class="userinput">arv keep docker</span>
+$ <span class="userinput">arv-keepdocker</span>
REPOSITORY TAG IMAGE ID COLLECTION CREATED
arvados/jobs-with-r latest 2818853ff9f9 qr1hi-4zz18-abcdefghijklmno Tue Jan 17 20:35:53 2017
</code></pre>
h2. Share Docker images
-Docker images are subject to normal Arvados permissions. If wish to share your Docker image with others (or wish to share a pipeline template that uses your Docker image) you will need to use @arv keep docker@ with the @--project-uuid@ option to upload the image to a shared project.
+Docker images are subject to normal Arvados permissions. If wish to share your Docker image with others (or wish to share a pipeline template that uses your Docker image) you will need to use @arv-keepdocker@ with the @--project-uuid@ option to upload the image to a shared project.
<notextile>
-<pre><code>$ <span class="userinput">arv keep docker --project-uuid qr1hi-j7d0g-xxxxxxxxxxxxxxx arvados/jobs-with-r</span>
+<pre><code>$ <span class="userinput">arv-keepdocker --project-uuid qr1hi-j7d0g-xxxxxxxxxxxxxxx arvados/jobs-with-r</span>
</code></pre>
</notextile>
h3. Steps
+notextile. <div class="spaced-out">
+
# Start from the *Workbench Dashboard*. You can access the Dashboard by clicking on *<i class="fa fa-lg fa-fw fa-dashboard"></i> Dashboard* in the upper left corner of any Workbench page.
# Click on the <span class="btn btn-sm btn-primary"><i class="fa fa-fw fa-gear"></i> Run a process...</span> button. This will open a dialog box titled *Choose a pipeline or workflow to run*.
# In the search box, type in *Tutorial bwa mem cwl*.
# After the process starts running, you can track the progress by watching log messages from the component(s). This page refreshes automatically. You will see a <span class="label label-success">complete</span> label when the process completes successfully.
# Click on the *Output* link to see the results of the process. This will load a new page listing the output files from this process. You'll see the output SAM file from the alignment tool under the *Files* tab.
# Click on the <span class="btn btn-sm btn-info"><i class="fa fa-download"></i></span> download button to the right of the SAM file to download your results.
+
+notextile. </div>
h2. Developing workflows
-For an introduction and and detailed documentation about writing CWL, see the "CWL User Guide":http://commonwl.org/v1.0/UserGuide.html and the "CWL Specification":http://commonwl.org/v1.0 .
+For an introduction and and detailed documentation about writing CWL, see the "CWL User Guide":https://www.commonwl.org/user_guide and the "CWL Specification":http://commonwl.org/v1.0 .
See "Best Practices for writing CWL":{{site.baseurl}}/user/cwl/cwl-style.html and "Arvados CWL Extensions":{{site.baseurl}}/user/cwl/cwl-extensions.html for additional information about using CWL on Arvados.
+h2. Using Composer
+
+You can create new workflows in the browser using "Arvados Composer":{{site.baseurl}}/user/composer/composer.html
+
h2. Registering a workflow to use in Workbench
Use @--create-workflow@ to register a CWL workflow with Arvados. This enables you to share workflows with other Arvados users, and run them by clicking the <span class="btn btn-sm btn-primary"><i class="fa fa-fw fa-gear"></i> Run a process...</span> button on the Workbench Dashboard and on the command line by UUID.
"os"
"strconv"
"strings"
+ "syscall"
"time"
)
// Interval between samples. Must be positive.
PollPeriod time.Duration
+ // Temporary directory, will be monitored for available, used & total space.
+ TempDir string
+
// Where to write statistics. Must not be nil.
Logger *log.Logger
- reportedStatFile map[string]string
- lastNetSample map[string]ioSample
- lastDiskSample map[string]ioSample
- lastCPUSample cpuSample
+ reportedStatFile map[string]string
+ lastNetSample map[string]ioSample
+ lastDiskIOSample map[string]ioSample
+ lastCPUSample cpuSample
+ lastDiskSpaceSample diskSpaceSample
done chan struct{} // closed when we should stop reporting
flushed chan struct{} // closed when we have made our last report
continue
}
delta := ""
- if prev, ok := r.lastDiskSample[dev]; ok {
+ if prev, ok := r.lastDiskIOSample[dev]; ok {
delta = fmt.Sprintf(" -- interval %.4f seconds %d write %d read",
sample.sampleTime.Sub(prev.sampleTime).Seconds(),
sample.txBytes-prev.txBytes,
sample.rxBytes-prev.rxBytes)
}
r.Logger.Printf("blkio:%s %d write %d read%s\n", dev, sample.txBytes, sample.rxBytes, delta)
- r.lastDiskSample[dev] = sample
+ r.lastDiskIOSample[dev] = sample
}
}
}
}
+type diskSpaceSample struct {
+ hasData bool
+ sampleTime time.Time
+ total uint64
+ used uint64
+ available uint64
+}
+
+func (r *Reporter) doDiskSpaceStats() {
+ s := syscall.Statfs_t{}
+ err := syscall.Statfs(r.TempDir, &s)
+ if err != nil {
+ return
+ }
+ bs := uint64(s.Bsize)
+ nextSample := diskSpaceSample{
+ hasData: true,
+ sampleTime: time.Now(),
+ total: s.Blocks * bs,
+ used: (s.Blocks - s.Bfree) * bs,
+ available: s.Bavail * bs,
+ }
+
+ var delta string
+ if r.lastDiskSpaceSample.hasData {
+ prev := r.lastDiskSpaceSample
+ interval := nextSample.sampleTime.Sub(prev.sampleTime).Seconds()
+ delta = fmt.Sprintf(" -- interval %.4f seconds %d used",
+ interval,
+ int64(nextSample.used-prev.used))
+ }
+ r.Logger.Printf("statfs %d available %d used %d total%s\n",
+ nextSample.available, nextSample.used, nextSample.total, delta)
+ r.lastDiskSpaceSample = nextSample
+}
+
type cpuSample struct {
hasData bool // to distinguish the zero value from real data
sampleTime time.Time
}
r.lastNetSample = make(map[string]ioSample)
- r.lastDiskSample = make(map[string]ioSample)
+ r.lastDiskIOSample = make(map[string]ioSample)
+
+ if len(r.TempDir) == 0 {
+ // Temporary dir not provided, try to get it from the environment.
+ r.TempDir = os.Getenv("TMPDIR")
+ }
+ if len(r.TempDir) > 0 {
+ r.Logger.Printf("notice: monitoring temp dir %s\n", r.TempDir)
+ }
ticker := time.NewTicker(r.PollPeriod)
for {
r.doCPUStats()
r.doBlkIOStats()
r.doNetworkStats()
+ r.doDiskSpaceStats()
select {
case <-r.done:
return
Package: ArvadosR
Type: Package
Title: Arvados R SDK
-Version: 0.0.2
+Version: 0.0.5
Authors@R: person("Fuad", "Muhic", role = c("aut", "cre"), email = "fmuhic@capeannenterprises.com")
Maintainer: Ward Vandewege <wvandewege@veritasgenetics.com>
Description: This is the Arvados R SDK
-# Copyright (C) The Arvados Authors. All rights reserved.
-#
-# SPDX-License-Identifier: Apache-2.0
-
#' users.get
-#'
+#'
#' users.get is a method defined in Arvados class.
-#'
+#'
#' @usage arv$users.get(uuid)
#' @param uuid The UUID of the User in question.
#' @return User object.
NULL
#' users.create
-#'
+#'
#' users.create is a method defined in Arvados class.
-#'
+#'
#' @usage arv$users.create(user, ensure_unique_name = "false")
#' @param user User object.
#' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision.
NULL
#' users.update
-#'
+#'
#' users.update is a method defined in Arvados class.
-#'
+#'
#' @usage arv$users.update(user, uuid)
#' @param user User object.
#' @param uuid The UUID of the User in question.
NULL
#' users.delete
-#'
+#'
#' users.delete is a method defined in Arvados class.
-#'
+#'
#' @usage arv$users.delete(uuid)
#' @param uuid The UUID of the User in question.
#' @return User object.
NULL
#' users.current
-#'
+#'
#' users.current is a method defined in Arvados class.
-#'
+#'
#' @usage arv$users.current(NULL)
#' @return User object.
#' @name users.current
NULL
#' users.system
-#'
+#'
#' users.system is a method defined in Arvados class.
-#'
+#'
#' @usage arv$users.system(NULL)
#' @return User object.
#' @name users.system
NULL
#' users.activate
-#'
+#'
#' users.activate is a method defined in Arvados class.
-#'
+#'
#' @usage arv$users.activate(uuid)
-#' @param uuid
+#' @param uuid
#' @return User object.
#' @name users.activate
NULL
#' users.setup
-#'
+#'
#' users.setup is a method defined in Arvados class.
-#'
+#'
#' @usage arv$users.setup(user = NULL, openid_prefix = NULL,
#' repo_name = NULL, vm_uuid = NULL, send_notification_email = "false")
-#' @param user
-#' @param openid_prefix
-#' @param repo_name
-#' @param vm_uuid
-#' @param send_notification_email
+#' @param user
+#' @param openid_prefix
+#' @param repo_name
+#' @param vm_uuid
+#' @param send_notification_email
#' @return User object.
#' @name users.setup
NULL
#' users.unsetup
-#'
+#'
#' users.unsetup is a method defined in Arvados class.
-#'
+#'
#' @usage arv$users.unsetup(uuid)
-#' @param uuid
+#' @param uuid
#' @return User object.
#' @name users.unsetup
NULL
#' users.update_uuid
-#'
+#'
#' users.update_uuid is a method defined in Arvados class.
-#'
+#'
#' @usage arv$users.update_uuid(uuid, new_uuid)
-#' @param uuid
-#' @param new_uuid
+#' @param uuid
+#' @param new_uuid
#' @return User object.
#' @name users.update_uuid
NULL
+#' users.merge
+#'
+#' users.merge is a method defined in Arvados class.
+#'
+#' @usage arv$users.merge(new_owner_uuid,
+#' new_user_token, redirect_to_new_user = NULL)
+#' @param new_owner_uuid
+#' @param new_user_token
+#' @param redirect_to_new_user
+#' @return User object.
+#' @name users.merge
+NULL
+
#' users.list
-#'
+#'
#' users.list is a method defined in Arvados class.
-#'
+#'
#' @usage arv$users.list(filters = NULL,
#' where = NULL, order = NULL, select = NULL,
#' distinct = NULL, limit = "100", offset = "0",
#' count = "exact")
-#' @param filters
-#' @param where
-#' @param order
-#' @param select
-#' @param distinct
-#' @param limit
-#' @param offset
-#' @param count
+#' @param filters
+#' @param where
+#' @param order
+#' @param select
+#' @param distinct
+#' @param limit
+#' @param offset
+#' @param count
#' @return UserList object.
#' @name users.list
NULL
#' api_client_authorizations.get
-#'
+#'
#' api_client_authorizations.get is a method defined in Arvados class.
-#'
+#'
#' @usage arv$api_client_authorizations.get(uuid)
#' @param uuid The UUID of the ApiClientAuthorization in question.
#' @return ApiClientAuthorization object.
NULL
#' api_client_authorizations.create
-#'
+#'
#' api_client_authorizations.create is a method defined in Arvados class.
-#'
+#'
#' @usage arv$api_client_authorizations.create(apiclientauthorization,
#' ensure_unique_name = "false")
#' @param apiClientAuthorization ApiClientAuthorization object.
NULL
#' api_client_authorizations.update
-#'
+#'
#' api_client_authorizations.update is a method defined in Arvados class.
-#'
+#'
#' @usage arv$api_client_authorizations.update(apiclientauthorization,
#' uuid)
#' @param apiClientAuthorization ApiClientAuthorization object.
NULL
#' api_client_authorizations.delete
-#'
+#'
#' api_client_authorizations.delete is a method defined in Arvados class.
-#'
+#'
#' @usage arv$api_client_authorizations.delete(uuid)
#' @param uuid The UUID of the ApiClientAuthorization in question.
#' @return ApiClientAuthorization object.
NULL
#' api_client_authorizations.create_system_auth
-#'
+#'
#' api_client_authorizations.create_system_auth is a method defined in Arvados class.
-#'
+#'
#' @usage arv$api_client_authorizations.create_system_auth(api_client_id = NULL,
#' scopes = NULL)
-#' @param api_client_id
-#' @param scopes
+#' @param api_client_id
+#' @param scopes
#' @return ApiClientAuthorization object.
#' @name api_client_authorizations.create_system_auth
NULL
#' api_client_authorizations.current
-#'
+#'
#' api_client_authorizations.current is a method defined in Arvados class.
-#'
+#'
#' @usage arv$api_client_authorizations.current(NULL)
#' @return ApiClientAuthorization object.
#' @name api_client_authorizations.current
NULL
#' api_client_authorizations.list
-#'
+#'
#' api_client_authorizations.list is a method defined in Arvados class.
-#'
+#'
#' @usage arv$api_client_authorizations.list(filters = NULL,
#' where = NULL, order = NULL, select = NULL,
#' distinct = NULL, limit = "100", offset = "0",
#' count = "exact")
-#' @param filters
-#' @param where
-#' @param order
-#' @param select
-#' @param distinct
-#' @param limit
-#' @param offset
-#' @param count
+#' @param filters
+#' @param where
+#' @param order
+#' @param select
+#' @param distinct
+#' @param limit
+#' @param offset
+#' @param count
#' @return ApiClientAuthorizationList object.
#' @name api_client_authorizations.list
NULL
#' containers.get
-#'
+#'
#' containers.get is a method defined in Arvados class.
-#'
+#'
#' @usage arv$containers.get(uuid)
#' @param uuid The UUID of the Container in question.
#' @return Container object.
NULL
#' containers.create
-#'
+#'
#' containers.create is a method defined in Arvados class.
-#'
+#'
#' @usage arv$containers.create(container,
#' ensure_unique_name = "false")
#' @param container Container object.
NULL
#' containers.update
-#'
+#'
#' containers.update is a method defined in Arvados class.
-#'
+#'
#' @usage arv$containers.update(container,
#' uuid)
#' @param container Container object.
NULL
#' containers.delete
-#'
+#'
#' containers.delete is a method defined in Arvados class.
-#'
+#'
#' @usage arv$containers.delete(uuid)
#' @param uuid The UUID of the Container in question.
#' @return Container object.
NULL
#' containers.auth
-#'
+#'
#' containers.auth is a method defined in Arvados class.
-#'
+#'
#' @usage arv$containers.auth(uuid)
-#' @param uuid
+#' @param uuid
#' @return Container object.
#' @name containers.auth
NULL
#' containers.lock
-#'
+#'
#' containers.lock is a method defined in Arvados class.
-#'
+#'
#' @usage arv$containers.lock(uuid)
-#' @param uuid
+#' @param uuid
#' @return Container object.
#' @name containers.lock
NULL
#' containers.unlock
-#'
+#'
#' containers.unlock is a method defined in Arvados class.
-#'
+#'
#' @usage arv$containers.unlock(uuid)
-#' @param uuid
+#' @param uuid
#' @return Container object.
#' @name containers.unlock
NULL
#' containers.secret_mounts
-#'
+#'
#' containers.secret_mounts is a method defined in Arvados class.
-#'
+#'
#' @usage arv$containers.secret_mounts(uuid)
-#' @param uuid
+#' @param uuid
#' @return Container object.
#' @name containers.secret_mounts
NULL
#' containers.current
-#'
+#'
#' containers.current is a method defined in Arvados class.
-#'
+#'
#' @usage arv$containers.current(NULL)
#' @return Container object.
#' @name containers.current
NULL
#' containers.list
-#'
+#'
#' containers.list is a method defined in Arvados class.
-#'
+#'
#' @usage arv$containers.list(filters = NULL,
#' where = NULL, order = NULL, select = NULL,
#' distinct = NULL, limit = "100", offset = "0",
#' count = "exact")
-#' @param filters
-#' @param where
-#' @param order
-#' @param select
-#' @param distinct
-#' @param limit
-#' @param offset
-#' @param count
+#' @param filters
+#' @param where
+#' @param order
+#' @param select
+#' @param distinct
+#' @param limit
+#' @param offset
+#' @param count
#' @return ContainerList object.
#' @name containers.list
NULL
#' api_clients.get
-#'
+#'
#' api_clients.get is a method defined in Arvados class.
-#'
+#'
#' @usage arv$api_clients.get(uuid)
#' @param uuid The UUID of the ApiClient in question.
#' @return ApiClient object.
NULL
#' api_clients.create
-#'
+#'
#' api_clients.create is a method defined in Arvados class.
-#'
+#'
#' @usage arv$api_clients.create(apiclient,
#' ensure_unique_name = "false")
#' @param apiClient ApiClient object.
NULL
#' api_clients.update
-#'
+#'
#' api_clients.update is a method defined in Arvados class.
-#'
+#'
#' @usage arv$api_clients.update(apiclient,
#' uuid)
#' @param apiClient ApiClient object.
NULL
#' api_clients.delete
-#'
+#'
#' api_clients.delete is a method defined in Arvados class.
-#'
+#'
#' @usage arv$api_clients.delete(uuid)
#' @param uuid The UUID of the ApiClient in question.
#' @return ApiClient object.
NULL
#' api_clients.list
-#'
+#'
#' api_clients.list is a method defined in Arvados class.
-#'
+#'
#' @usage arv$api_clients.list(filters = NULL,
#' where = NULL, order = NULL, select = NULL,
#' distinct = NULL, limit = "100", offset = "0",
#' count = "exact")
-#' @param filters
-#' @param where
-#' @param order
-#' @param select
-#' @param distinct
-#' @param limit
-#' @param offset
-#' @param count
+#' @param filters
+#' @param where
+#' @param order
+#' @param select
+#' @param distinct
+#' @param limit
+#' @param offset
+#' @param count
#' @return ApiClientList object.
#' @name api_clients.list
NULL
-#' authorized_keys.get
-#'
-#' authorized_keys.get is a method defined in Arvados class.
-#'
-#' @usage arv$authorized_keys.get(uuid)
-#' @param uuid The UUID of the AuthorizedKey in question.
-#' @return AuthorizedKey object.
-#' @name authorized_keys.get
-NULL
-
-#' authorized_keys.create
-#'
-#' authorized_keys.create is a method defined in Arvados class.
-#'
-#' @usage arv$authorized_keys.create(authorizedkey,
-#' ensure_unique_name = "false")
-#' @param authorizedKey AuthorizedKey object.
-#' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision.
-#' @return AuthorizedKey object.
-#' @name authorized_keys.create
-NULL
-
-#' authorized_keys.update
-#'
-#' authorized_keys.update is a method defined in Arvados class.
-#'
-#' @usage arv$authorized_keys.update(authorizedkey,
-#' uuid)
-#' @param authorizedKey AuthorizedKey object.
-#' @param uuid The UUID of the AuthorizedKey in question.
-#' @return AuthorizedKey object.
-#' @name authorized_keys.update
-NULL
-
-#' authorized_keys.delete
-#'
-#' authorized_keys.delete is a method defined in Arvados class.
-#'
-#' @usage arv$authorized_keys.delete(uuid)
-#' @param uuid The UUID of the AuthorizedKey in question.
-#' @return AuthorizedKey object.
-#' @name authorized_keys.delete
-NULL
-
-#' authorized_keys.list
-#'
-#' authorized_keys.list is a method defined in Arvados class.
-#'
-#' @usage arv$authorized_keys.list(filters = NULL,
-#' where = NULL, order = NULL, select = NULL,
-#' distinct = NULL, limit = "100", offset = "0",
-#' count = "exact")
-#' @param filters
-#' @param where
-#' @param order
-#' @param select
-#' @param distinct
-#' @param limit
-#' @param offset
-#' @param count
-#' @return AuthorizedKeyList object.
-#' @name authorized_keys.list
-NULL
-
#' container_requests.get
-#'
+#'
#' container_requests.get is a method defined in Arvados class.
-#'
+#'
#' @usage arv$container_requests.get(uuid)
#' @param uuid The UUID of the ContainerRequest in question.
#' @return ContainerRequest object.
NULL
#' container_requests.create
-#'
+#'
#' container_requests.create is a method defined in Arvados class.
-#'
+#'
#' @usage arv$container_requests.create(containerrequest,
#' ensure_unique_name = "false")
#' @param containerRequest ContainerRequest object.
NULL
#' container_requests.update
-#'
+#'
#' container_requests.update is a method defined in Arvados class.
-#'
+#'
#' @usage arv$container_requests.update(containerrequest,
#' uuid)
#' @param containerRequest ContainerRequest object.
NULL
#' container_requests.delete
-#'
+#'
#' container_requests.delete is a method defined in Arvados class.
-#'
+#'
#' @usage arv$container_requests.delete(uuid)
#' @param uuid The UUID of the ContainerRequest in question.
#' @return ContainerRequest object.
NULL
#' container_requests.list
-#'
+#'
#' container_requests.list is a method defined in Arvados class.
-#'
+#'
#' @usage arv$container_requests.list(filters = NULL,
#' where = NULL, order = NULL, select = NULL,
#' distinct = NULL, limit = "100", offset = "0",
#' count = "exact")
-#' @param filters
-#' @param where
-#' @param order
-#' @param select
-#' @param distinct
-#' @param limit
-#' @param offset
-#' @param count
+#' @param filters
+#' @param where
+#' @param order
+#' @param select
+#' @param distinct
+#' @param limit
+#' @param offset
+#' @param count
#' @return ContainerRequestList object.
#' @name container_requests.list
NULL
+#' authorized_keys.get
+#'
+#' authorized_keys.get is a method defined in Arvados class.
+#'
+#' @usage arv$authorized_keys.get(uuid)
+#' @param uuid The UUID of the AuthorizedKey in question.
+#' @return AuthorizedKey object.
+#' @name authorized_keys.get
+NULL
+
+#' authorized_keys.create
+#'
+#' authorized_keys.create is a method defined in Arvados class.
+#'
+#' @usage arv$authorized_keys.create(authorizedkey,
+#' ensure_unique_name = "false")
+#' @param authorizedKey AuthorizedKey object.
+#' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision.
+#' @return AuthorizedKey object.
+#' @name authorized_keys.create
+NULL
+
+#' authorized_keys.update
+#'
+#' authorized_keys.update is a method defined in Arvados class.
+#'
+#' @usage arv$authorized_keys.update(authorizedkey,
+#' uuid)
+#' @param authorizedKey AuthorizedKey object.
+#' @param uuid The UUID of the AuthorizedKey in question.
+#' @return AuthorizedKey object.
+#' @name authorized_keys.update
+NULL
+
+#' authorized_keys.delete
+#'
+#' authorized_keys.delete is a method defined in Arvados class.
+#'
+#' @usage arv$authorized_keys.delete(uuid)
+#' @param uuid The UUID of the AuthorizedKey in question.
+#' @return AuthorizedKey object.
+#' @name authorized_keys.delete
+NULL
+
+#' authorized_keys.list
+#'
+#' authorized_keys.list is a method defined in Arvados class.
+#'
+#' @usage arv$authorized_keys.list(filters = NULL,
+#' where = NULL, order = NULL, select = NULL,
+#' distinct = NULL, limit = "100", offset = "0",
+#' count = "exact")
+#' @param filters
+#' @param where
+#' @param order
+#' @param select
+#' @param distinct
+#' @param limit
+#' @param offset
+#' @param count
+#' @return AuthorizedKeyList object.
+#' @name authorized_keys.list
+NULL
+
#' collections.get
-#'
+#'
#' collections.get is a method defined in Arvados class.
-#'
+#'
#' @usage arv$collections.get(uuid)
#' @param uuid The UUID of the Collection in question.
#' @return Collection object.
NULL
#' collections.create
-#'
+#'
#' collections.create is a method defined in Arvados class.
-#'
+#'
#' @usage arv$collections.create(collection,
#' ensure_unique_name = "false")
#' @param collection Collection object.
NULL
#' collections.update
-#'
+#'
#' collections.update is a method defined in Arvados class.
-#'
+#'
#' @usage arv$collections.update(collection,
#' uuid)
#' @param collection Collection object.
NULL
#' collections.delete
-#'
+#'
#' collections.delete is a method defined in Arvados class.
-#'
+#'
#' @usage arv$collections.delete(uuid)
#' @param uuid The UUID of the Collection in question.
#' @return Collection object.
NULL
#' collections.provenance
-#'
+#'
#' collections.provenance is a method defined in Arvados class.
-#'
+#'
#' @usage arv$collections.provenance(uuid)
-#' @param uuid
+#' @param uuid
#' @return Collection object.
#' @name collections.provenance
NULL
#' collections.used_by
-#'
+#'
#' collections.used_by is a method defined in Arvados class.
-#'
+#'
#' @usage arv$collections.used_by(uuid)
-#' @param uuid
+#' @param uuid
#' @return Collection object.
#' @name collections.used_by
NULL
#' collections.trash
-#'
+#'
#' collections.trash is a method defined in Arvados class.
-#'
+#'
#' @usage arv$collections.trash(uuid)
-#' @param uuid
+#' @param uuid
#' @return Collection object.
#' @name collections.trash
NULL
#' collections.untrash
-#'
+#'
#' collections.untrash is a method defined in Arvados class.
-#'
+#'
#' @usage arv$collections.untrash(uuid)
-#' @param uuid
+#' @param uuid
#' @return Collection object.
#' @name collections.untrash
NULL
#' collections.list
-#'
+#'
#' collections.list is a method defined in Arvados class.
-#'
+#'
#' @usage arv$collections.list(filters = NULL,
#' where = NULL, order = NULL, select = NULL,
#' distinct = NULL, limit = "100", offset = "0",
#' count = "exact", include_trash = NULL)
-#' @param filters
-#' @param where
-#' @param order
-#' @param select
-#' @param distinct
-#' @param limit
-#' @param offset
-#' @param count
+#' @param filters
+#' @param where
+#' @param order
+#' @param select
+#' @param distinct
+#' @param limit
+#' @param offset
+#' @param count
#' @param include_trash Include collections whose is_trashed attribute is true.
#' @return CollectionList object.
#' @name collections.list
NULL
#' humans.get
-#'
+#'
#' humans.get is a method defined in Arvados class.
-#'
+#'
#' @usage arv$humans.get(uuid)
#' @param uuid The UUID of the Human in question.
#' @return Human object.
NULL
#' humans.create
-#'
+#'
#' humans.create is a method defined in Arvados class.
-#'
+#'
#' @usage arv$humans.create(human, ensure_unique_name = "false")
#' @param human Human object.
#' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision.
NULL
#' humans.update
-#'
+#'
#' humans.update is a method defined in Arvados class.
-#'
+#'
#' @usage arv$humans.update(human, uuid)
#' @param human Human object.
#' @param uuid The UUID of the Human in question.
NULL
#' humans.delete
-#'
+#'
#' humans.delete is a method defined in Arvados class.
-#'
+#'
#' @usage arv$humans.delete(uuid)
#' @param uuid The UUID of the Human in question.
#' @return Human object.
NULL
#' humans.list
-#'
+#'
#' humans.list is a method defined in Arvados class.
-#'
+#'
#' @usage arv$humans.list(filters = NULL,
#' where = NULL, order = NULL, select = NULL,
#' distinct = NULL, limit = "100", offset = "0",
#' count = "exact")
-#' @param filters
-#' @param where
-#' @param order
-#' @param select
-#' @param distinct
-#' @param limit
-#' @param offset
-#' @param count
+#' @param filters
+#' @param where
+#' @param order
+#' @param select
+#' @param distinct
+#' @param limit
+#' @param offset
+#' @param count
#' @return HumanList object.
#' @name humans.list
NULL
#' job_tasks.get
-#'
+#'
#' job_tasks.get is a method defined in Arvados class.
-#'
+#'
#' @usage arv$job_tasks.get(uuid)
#' @param uuid The UUID of the JobTask in question.
#' @return JobTask object.
NULL
#' job_tasks.create
-#'
+#'
#' job_tasks.create is a method defined in Arvados class.
-#'
+#'
#' @usage arv$job_tasks.create(jobtask, ensure_unique_name = "false")
#' @param jobTask JobTask object.
#' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision.
NULL
#' job_tasks.update
-#'
+#'
#' job_tasks.update is a method defined in Arvados class.
-#'
+#'
#' @usage arv$job_tasks.update(jobtask, uuid)
#' @param jobTask JobTask object.
#' @param uuid The UUID of the JobTask in question.
NULL
#' job_tasks.delete
-#'
+#'
#' job_tasks.delete is a method defined in Arvados class.
-#'
+#'
#' @usage arv$job_tasks.delete(uuid)
#' @param uuid The UUID of the JobTask in question.
#' @return JobTask object.
NULL
#' job_tasks.list
-#'
+#'
#' job_tasks.list is a method defined in Arvados class.
-#'
+#'
#' @usage arv$job_tasks.list(filters = NULL,
#' where = NULL, order = NULL, select = NULL,
#' distinct = NULL, limit = "100", offset = "0",
#' count = "exact")
-#' @param filters
-#' @param where
-#' @param order
-#' @param select
-#' @param distinct
-#' @param limit
-#' @param offset
-#' @param count
+#' @param filters
+#' @param where
+#' @param order
+#' @param select
+#' @param distinct
+#' @param limit
+#' @param offset
+#' @param count
#' @return JobTaskList object.
#' @name job_tasks.list
NULL
-#' links.get
-#'
-#' links.get is a method defined in Arvados class.
-#'
-#' @usage arv$links.get(uuid)
-#' @param uuid The UUID of the Link in question.
-#' @return Link object.
-#' @name links.get
+#' jobs.get
+#'
+#' jobs.get is a method defined in Arvados class.
+#'
+#' @usage arv$jobs.get(uuid)
+#' @param uuid The UUID of the Job in question.
+#' @return Job object.
+#' @name jobs.get
NULL
-#' links.create
-#'
-#' links.create is a method defined in Arvados class.
-#'
-#' @usage arv$links.create(link, ensure_unique_name = "false")
-#' @param link Link object.
+#' jobs.create
+#'
+#' jobs.create is a method defined in Arvados class.
+#'
+#' @usage arv$jobs.create(job, ensure_unique_name = "false",
+#' find_or_create = "false", filters = NULL,
+#' minimum_script_version = NULL, exclude_script_versions = NULL)
+#' @param job Job object.
#' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision.
-#' @return Link object.
-#' @name links.create
-NULL
-
-#' links.update
-#'
-#' links.update is a method defined in Arvados class.
-#'
-#' @usage arv$links.update(link, uuid)
-#' @param link Link object.
-#' @param uuid The UUID of the Link in question.
-#' @return Link object.
-#' @name links.update
-NULL
-
-#' links.delete
-#'
-#' links.delete is a method defined in Arvados class.
-#'
-#' @usage arv$links.delete(uuid)
-#' @param uuid The UUID of the Link in question.
-#' @return Link object.
-#' @name links.delete
-NULL
-
-#' links.list
-#'
-#' links.list is a method defined in Arvados class.
-#'
-#' @usage arv$links.list(filters = NULL,
-#' where = NULL, order = NULL, select = NULL,
-#' distinct = NULL, limit = "100", offset = "0",
-#' count = "exact")
-#' @param filters
-#' @param where
-#' @param order
-#' @param select
-#' @param distinct
-#' @param limit
-#' @param offset
-#' @param count
-#' @return LinkList object.
-#' @name links.list
-NULL
-
-#' links.get_permissions
-#'
-#' links.get_permissions is a method defined in Arvados class.
-#'
-#' @usage arv$links.get_permissions(uuid)
-#' @param uuid
-#' @return Link object.
-#' @name links.get_permissions
-NULL
-
-#' jobs.get
-#'
-#' jobs.get is a method defined in Arvados class.
-#'
-#' @usage arv$jobs.get(uuid)
-#' @param uuid The UUID of the Job in question.
-#' @return Job object.
-#' @name jobs.get
-NULL
-
-#' jobs.create
-#'
-#' jobs.create is a method defined in Arvados class.
-#'
-#' @usage arv$jobs.create(job, ensure_unique_name = "false",
-#' find_or_create = "false", filters = NULL,
-#' minimum_script_version = NULL, exclude_script_versions = NULL)
-#' @param job Job object.
-#' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision.
-#' @param find_or_create
-#' @param filters
-#' @param minimum_script_version
-#' @param exclude_script_versions
-#' @return Job object.
-#' @name jobs.create
+#' @param find_or_create
+#' @param filters
+#' @param minimum_script_version
+#' @param exclude_script_versions
+#' @return Job object.
+#' @name jobs.create
NULL
#' jobs.update
-#'
+#'
#' jobs.update is a method defined in Arvados class.
-#'
+#'
#' @usage arv$jobs.update(job, uuid)
#' @param job Job object.
#' @param uuid The UUID of the Job in question.
NULL
#' jobs.delete
-#'
+#'
#' jobs.delete is a method defined in Arvados class.
-#'
+#'
#' @usage arv$jobs.delete(uuid)
#' @param uuid The UUID of the Job in question.
#' @return Job object.
NULL
#' jobs.queue
-#'
+#'
#' jobs.queue is a method defined in Arvados class.
-#'
+#'
#' @usage arv$jobs.queue(filters = NULL,
#' where = NULL, order = NULL, select = NULL,
#' distinct = NULL, limit = "100", offset = "0",
#' count = "exact")
-#' @param filters
-#' @param where
-#' @param order
-#' @param select
-#' @param distinct
-#' @param limit
-#' @param offset
-#' @param count
+#' @param filters
+#' @param where
+#' @param order
+#' @param select
+#' @param distinct
+#' @param limit
+#' @param offset
+#' @param count
#' @return Job object.
#' @name jobs.queue
NULL
#' jobs.queue_size
-#'
+#'
#' jobs.queue_size is a method defined in Arvados class.
-#'
+#'
#' @usage arv$jobs.queue_size(NULL)
#' @return Job object.
#' @name jobs.queue_size
NULL
#' jobs.cancel
-#'
+#'
#' jobs.cancel is a method defined in Arvados class.
-#'
+#'
#' @usage arv$jobs.cancel(uuid)
-#' @param uuid
+#' @param uuid
#' @return Job object.
#' @name jobs.cancel
NULL
#' jobs.lock
-#'
+#'
#' jobs.lock is a method defined in Arvados class.
-#'
+#'
#' @usage arv$jobs.lock(uuid)
-#' @param uuid
+#' @param uuid
#' @return Job object.
#' @name jobs.lock
NULL
#' jobs.list
-#'
+#'
#' jobs.list is a method defined in Arvados class.
-#'
+#'
#' @usage arv$jobs.list(filters = NULL, where = NULL,
#' order = NULL, select = NULL, distinct = NULL,
#' limit = "100", offset = "0", count = "exact")
-#' @param filters
-#' @param where
-#' @param order
-#' @param select
-#' @param distinct
-#' @param limit
-#' @param offset
-#' @param count
+#' @param filters
+#' @param where
+#' @param order
+#' @param select
+#' @param distinct
+#' @param limit
+#' @param offset
+#' @param count
#' @return JobList object.
#' @name jobs.list
NULL
#' keep_disks.get
-#'
+#'
#' keep_disks.get is a method defined in Arvados class.
-#'
+#'
#' @usage arv$keep_disks.get(uuid)
#' @param uuid The UUID of the KeepDisk in question.
#' @return KeepDisk object.
NULL
#' keep_disks.create
-#'
+#'
#' keep_disks.create is a method defined in Arvados class.
-#'
+#'
#' @usage arv$keep_disks.create(keepdisk,
#' ensure_unique_name = "false")
#' @param keepDisk KeepDisk object.
NULL
#' keep_disks.update
-#'
+#'
#' keep_disks.update is a method defined in Arvados class.
-#'
+#'
#' @usage arv$keep_disks.update(keepdisk,
#' uuid)
#' @param keepDisk KeepDisk object.
NULL
#' keep_disks.delete
-#'
+#'
#' keep_disks.delete is a method defined in Arvados class.
-#'
+#'
#' @usage arv$keep_disks.delete(uuid)
#' @param uuid The UUID of the KeepDisk in question.
#' @return KeepDisk object.
NULL
#' keep_disks.ping
-#'
+#'
#' keep_disks.ping is a method defined in Arvados class.
-#'
+#'
#' @usage arv$keep_disks.ping(uuid = NULL,
#' ping_secret, node_uuid = NULL, filesystem_uuid = NULL,
#' service_host = NULL, service_port, service_ssl_flag)
-#' @param uuid
-#' @param ping_secret
-#' @param node_uuid
-#' @param filesystem_uuid
-#' @param service_host
-#' @param service_port
-#' @param service_ssl_flag
+#' @param uuid
+#' @param ping_secret
+#' @param node_uuid
+#' @param filesystem_uuid
+#' @param service_host
+#' @param service_port
+#' @param service_ssl_flag
#' @return KeepDisk object.
#' @name keep_disks.ping
NULL
#' keep_disks.list
-#'
+#'
#' keep_disks.list is a method defined in Arvados class.
-#'
+#'
#' @usage arv$keep_disks.list(filters = NULL,
#' where = NULL, order = NULL, select = NULL,
#' distinct = NULL, limit = "100", offset = "0",
#' count = "exact")
-#' @param filters
-#' @param where
-#' @param order
-#' @param select
-#' @param distinct
-#' @param limit
-#' @param offset
-#' @param count
+#' @param filters
+#' @param where
+#' @param order
+#' @param select
+#' @param distinct
+#' @param limit
+#' @param offset
+#' @param count
#' @return KeepDiskList object.
#' @name keep_disks.list
NULL
+#' nodes.get
+#'
+#' nodes.get is a method defined in Arvados class.
+#'
+#' @usage arv$nodes.get(uuid)
+#' @param uuid The UUID of the Node in question.
+#' @return Node object.
+#' @name nodes.get
+NULL
+
+#' nodes.create
+#'
+#' nodes.create is a method defined in Arvados class.
+#'
+#' @usage arv$nodes.create(node, ensure_unique_name = "false",
+#' assign_slot = NULL)
+#' @param node Node object.
+#' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision.
+#' @param assign_slot assign slot and hostname
+#' @return Node object.
+#' @name nodes.create
+NULL
+
+#' nodes.update
+#'
+#' nodes.update is a method defined in Arvados class.
+#'
+#' @usage arv$nodes.update(node, uuid, assign_slot = NULL)
+#' @param node Node object.
+#' @param uuid The UUID of the Node in question.
+#' @param assign_slot assign slot and hostname
+#' @return Node object.
+#' @name nodes.update
+NULL
+
+#' nodes.delete
+#'
+#' nodes.delete is a method defined in Arvados class.
+#'
+#' @usage arv$nodes.delete(uuid)
+#' @param uuid The UUID of the Node in question.
+#' @return Node object.
+#' @name nodes.delete
+NULL
+
+#' nodes.ping
+#'
+#' nodes.ping is a method defined in Arvados class.
+#'
+#' @usage arv$nodes.ping(uuid, ping_secret)
+#' @param uuid
+#' @param ping_secret
+#' @return Node object.
+#' @name nodes.ping
+NULL
+
+#' nodes.list
+#'
+#' nodes.list is a method defined in Arvados class.
+#'
+#' @usage arv$nodes.list(filters = NULL,
+#' where = NULL, order = NULL, select = NULL,
+#' distinct = NULL, limit = "100", offset = "0",
+#' count = "exact")
+#' @param filters
+#' @param where
+#' @param order
+#' @param select
+#' @param distinct
+#' @param limit
+#' @param offset
+#' @param count
+#' @return NodeList object.
+#' @name nodes.list
+NULL
+
+#' links.get
+#'
+#' links.get is a method defined in Arvados class.
+#'
+#' @usage arv$links.get(uuid)
+#' @param uuid The UUID of the Link in question.
+#' @return Link object.
+#' @name links.get
+NULL
+
+#' links.create
+#'
+#' links.create is a method defined in Arvados class.
+#'
+#' @usage arv$links.create(link, ensure_unique_name = "false")
+#' @param link Link object.
+#' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision.
+#' @return Link object.
+#' @name links.create
+NULL
+
+#' links.update
+#'
+#' links.update is a method defined in Arvados class.
+#'
+#' @usage arv$links.update(link, uuid)
+#' @param link Link object.
+#' @param uuid The UUID of the Link in question.
+#' @return Link object.
+#' @name links.update
+NULL
+
+#' links.delete
+#'
+#' links.delete is a method defined in Arvados class.
+#'
+#' @usage arv$links.delete(uuid)
+#' @param uuid The UUID of the Link in question.
+#' @return Link object.
+#' @name links.delete
+NULL
+
+#' links.list
+#'
+#' links.list is a method defined in Arvados class.
+#'
+#' @usage arv$links.list(filters = NULL,
+#' where = NULL, order = NULL, select = NULL,
+#' distinct = NULL, limit = "100", offset = "0",
+#' count = "exact")
+#' @param filters
+#' @param where
+#' @param order
+#' @param select
+#' @param distinct
+#' @param limit
+#' @param offset
+#' @param count
+#' @return LinkList object.
+#' @name links.list
+NULL
+
+#' links.get_permissions
+#'
+#' links.get_permissions is a method defined in Arvados class.
+#'
+#' @usage arv$links.get_permissions(uuid)
+#' @param uuid
+#' @return Link object.
+#' @name links.get_permissions
+NULL
+
#' keep_services.get
-#'
+#'
#' keep_services.get is a method defined in Arvados class.
-#'
+#'
#' @usage arv$keep_services.get(uuid)
#' @param uuid The UUID of the KeepService in question.
#' @return KeepService object.
NULL
#' keep_services.create
-#'
+#'
#' keep_services.create is a method defined in Arvados class.
-#'
+#'
#' @usage arv$keep_services.create(keepservice,
#' ensure_unique_name = "false")
#' @param keepService KeepService object.
NULL
#' keep_services.update
-#'
+#'
#' keep_services.update is a method defined in Arvados class.
-#'
+#'
#' @usage arv$keep_services.update(keepservice,
#' uuid)
#' @param keepService KeepService object.
NULL
#' keep_services.delete
-#'
+#'
#' keep_services.delete is a method defined in Arvados class.
-#'
+#'
#' @usage arv$keep_services.delete(uuid)
#' @param uuid The UUID of the KeepService in question.
#' @return KeepService object.
NULL
#' keep_services.accessible
-#'
+#'
#' keep_services.accessible is a method defined in Arvados class.
-#'
+#'
#' @usage arv$keep_services.accessible(NULL)
#' @return KeepService object.
#' @name keep_services.accessible
NULL
#' keep_services.list
-#'
+#'
#' keep_services.list is a method defined in Arvados class.
-#'
+#'
#' @usage arv$keep_services.list(filters = NULL,
#' where = NULL, order = NULL, select = NULL,
#' distinct = NULL, limit = "100", offset = "0",
#' count = "exact")
-#' @param filters
-#' @param where
-#' @param order
-#' @param select
-#' @param distinct
-#' @param limit
-#' @param offset
-#' @param count
+#' @param filters
+#' @param where
+#' @param order
+#' @param select
+#' @param distinct
+#' @param limit
+#' @param offset
+#' @param count
#' @return KeepServiceList object.
#' @name keep_services.list
NULL
#' pipeline_templates.get
-#'
+#'
#' pipeline_templates.get is a method defined in Arvados class.
-#'
+#'
#' @usage arv$pipeline_templates.get(uuid)
#' @param uuid The UUID of the PipelineTemplate in question.
#' @return PipelineTemplate object.
NULL
#' pipeline_templates.create
-#'
+#'
#' pipeline_templates.create is a method defined in Arvados class.
-#'
+#'
#' @usage arv$pipeline_templates.create(pipelinetemplate,
#' ensure_unique_name = "false")
#' @param pipelineTemplate PipelineTemplate object.
NULL
#' pipeline_templates.update
-#'
+#'
#' pipeline_templates.update is a method defined in Arvados class.
-#'
+#'
#' @usage arv$pipeline_templates.update(pipelinetemplate,
#' uuid)
#' @param pipelineTemplate PipelineTemplate object.
NULL
#' pipeline_templates.delete
-#'
+#'
#' pipeline_templates.delete is a method defined in Arvados class.
-#'
+#'
#' @usage arv$pipeline_templates.delete(uuid)
#' @param uuid The UUID of the PipelineTemplate in question.
#' @return PipelineTemplate object.
NULL
#' pipeline_templates.list
-#'
+#'
#' pipeline_templates.list is a method defined in Arvados class.
-#'
+#'
#' @usage arv$pipeline_templates.list(filters = NULL,
#' where = NULL, order = NULL, select = NULL,
#' distinct = NULL, limit = "100", offset = "0",
#' count = "exact")
-#' @param filters
-#' @param where
-#' @param order
-#' @param select
-#' @param distinct
-#' @param limit
-#' @param offset
-#' @param count
+#' @param filters
+#' @param where
+#' @param order
+#' @param select
+#' @param distinct
+#' @param limit
+#' @param offset
+#' @param count
#' @return PipelineTemplateList object.
#' @name pipeline_templates.list
NULL
#' pipeline_instances.get
-#'
+#'
#' pipeline_instances.get is a method defined in Arvados class.
-#'
+#'
#' @usage arv$pipeline_instances.get(uuid)
#' @param uuid The UUID of the PipelineInstance in question.
#' @return PipelineInstance object.
NULL
#' pipeline_instances.create
-#'
+#'
#' pipeline_instances.create is a method defined in Arvados class.
-#'
+#'
#' @usage arv$pipeline_instances.create(pipelineinstance,
#' ensure_unique_name = "false")
#' @param pipelineInstance PipelineInstance object.
NULL
#' pipeline_instances.update
-#'
+#'
#' pipeline_instances.update is a method defined in Arvados class.
-#'
+#'
#' @usage arv$pipeline_instances.update(pipelineinstance,
#' uuid)
#' @param pipelineInstance PipelineInstance object.
NULL
#' pipeline_instances.delete
-#'
+#'
#' pipeline_instances.delete is a method defined in Arvados class.
-#'
+#'
#' @usage arv$pipeline_instances.delete(uuid)
#' @param uuid The UUID of the PipelineInstance in question.
#' @return PipelineInstance object.
NULL
#' pipeline_instances.cancel
-#'
+#'
#' pipeline_instances.cancel is a method defined in Arvados class.
-#'
+#'
#' @usage arv$pipeline_instances.cancel(uuid)
-#' @param uuid
+#' @param uuid
#' @return PipelineInstance object.
#' @name pipeline_instances.cancel
NULL
#' pipeline_instances.list
-#'
+#'
#' pipeline_instances.list is a method defined in Arvados class.
-#'
+#'
#' @usage arv$pipeline_instances.list(filters = NULL,
#' where = NULL, order = NULL, select = NULL,
#' distinct = NULL, limit = "100", offset = "0",
#' count = "exact")
-#' @param filters
-#' @param where
-#' @param order
-#' @param select
-#' @param distinct
-#' @param limit
-#' @param offset
-#' @param count
+#' @param filters
+#' @param where
+#' @param order
+#' @param select
+#' @param distinct
+#' @param limit
+#' @param offset
+#' @param count
#' @return PipelineInstanceList object.
#' @name pipeline_instances.list
NULL
-#' nodes.get
-#'
-#' nodes.get is a method defined in Arvados class.
-#'
-#' @usage arv$nodes.get(uuid)
-#' @param uuid The UUID of the Node in question.
-#' @return Node object.
-#' @name nodes.get
-NULL
-
-#' nodes.create
-#'
-#' nodes.create is a method defined in Arvados class.
-#'
-#' @usage arv$nodes.create(node, ensure_unique_name = "false",
-#' assign_slot = NULL)
-#' @param node Node object.
-#' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision.
-#' @param assign_slot assign slot and hostname
-#' @return Node object.
-#' @name nodes.create
-NULL
-
-#' nodes.update
-#'
-#' nodes.update is a method defined in Arvados class.
-#'
-#' @usage arv$nodes.update(node, uuid, assign_slot = NULL)
-#' @param node Node object.
-#' @param uuid The UUID of the Node in question.
-#' @param assign_slot assign slot and hostname
-#' @return Node object.
-#' @name nodes.update
-NULL
-
-#' nodes.delete
-#'
-#' nodes.delete is a method defined in Arvados class.
-#'
-#' @usage arv$nodes.delete(uuid)
-#' @param uuid The UUID of the Node in question.
-#' @return Node object.
-#' @name nodes.delete
-NULL
-
-#' nodes.ping
-#'
-#' nodes.ping is a method defined in Arvados class.
-#'
-#' @usage arv$nodes.ping(uuid, ping_secret)
-#' @param uuid
-#' @param ping_secret
-#' @return Node object.
-#' @name nodes.ping
-NULL
-
-#' nodes.list
-#'
-#' nodes.list is a method defined in Arvados class.
-#'
-#' @usage arv$nodes.list(filters = NULL,
-#' where = NULL, order = NULL, select = NULL,
-#' distinct = NULL, limit = "100", offset = "0",
-#' count = "exact")
-#' @param filters
-#' @param where
-#' @param order
-#' @param select
-#' @param distinct
-#' @param limit
-#' @param offset
-#' @param count
-#' @return NodeList object.
-#' @name nodes.list
-NULL
-
#' repositories.get
-#'
+#'
#' repositories.get is a method defined in Arvados class.
-#'
+#'
#' @usage arv$repositories.get(uuid)
#' @param uuid The UUID of the Repository in question.
#' @return Repository object.
NULL
#' repositories.create
-#'
+#'
#' repositories.create is a method defined in Arvados class.
-#'
+#'
#' @usage arv$repositories.create(repository,
#' ensure_unique_name = "false")
#' @param repository Repository object.
NULL
#' repositories.update
-#'
+#'
#' repositories.update is a method defined in Arvados class.
-#'
+#'
#' @usage arv$repositories.update(repository,
#' uuid)
#' @param repository Repository object.
NULL
#' repositories.delete
-#'
+#'
#' repositories.delete is a method defined in Arvados class.
-#'
+#'
#' @usage arv$repositories.delete(uuid)
#' @param uuid The UUID of the Repository in question.
#' @return Repository object.
NULL
#' repositories.get_all_permissions
-#'
+#'
#' repositories.get_all_permissions is a method defined in Arvados class.
-#'
+#'
#' @usage arv$repositories.get_all_permissions(NULL)
#' @return Repository object.
#' @name repositories.get_all_permissions
NULL
#' repositories.list
-#'
+#'
#' repositories.list is a method defined in Arvados class.
-#'
+#'
#' @usage arv$repositories.list(filters = NULL,
#' where = NULL, order = NULL, select = NULL,
#' distinct = NULL, limit = "100", offset = "0",
#' count = "exact")
-#' @param filters
-#' @param where
-#' @param order
-#' @param select
-#' @param distinct
-#' @param limit
-#' @param offset
-#' @param count
+#' @param filters
+#' @param where
+#' @param order
+#' @param select
+#' @param distinct
+#' @param limit
+#' @param offset
+#' @param count
#' @return RepositoryList object.
#' @name repositories.list
NULL
#' specimens.get
-#'
+#'
#' specimens.get is a method defined in Arvados class.
-#'
+#'
#' @usage arv$specimens.get(uuid)
#' @param uuid The UUID of the Specimen in question.
#' @return Specimen object.
NULL
#' specimens.create
-#'
+#'
#' specimens.create is a method defined in Arvados class.
-#'
+#'
#' @usage arv$specimens.create(specimen,
#' ensure_unique_name = "false")
#' @param specimen Specimen object.
NULL
#' specimens.update
-#'
+#'
#' specimens.update is a method defined in Arvados class.
-#'
+#'
#' @usage arv$specimens.update(specimen,
#' uuid)
#' @param specimen Specimen object.
NULL
#' specimens.delete
-#'
+#'
#' specimens.delete is a method defined in Arvados class.
-#'
+#'
#' @usage arv$specimens.delete(uuid)
#' @param uuid The UUID of the Specimen in question.
#' @return Specimen object.
NULL
#' specimens.list
-#'
+#'
#' specimens.list is a method defined in Arvados class.
-#'
+#'
#' @usage arv$specimens.list(filters = NULL,
#' where = NULL, order = NULL, select = NULL,
#' distinct = NULL, limit = "100", offset = "0",
#' count = "exact")
-#' @param filters
-#' @param where
-#' @param order
-#' @param select
-#' @param distinct
-#' @param limit
-#' @param offset
-#' @param count
+#' @param filters
+#' @param where
+#' @param order
+#' @param select
+#' @param distinct
+#' @param limit
+#' @param offset
+#' @param count
#' @return SpecimenList object.
#' @name specimens.list
NULL
#' logs.get
-#'
+#'
#' logs.get is a method defined in Arvados class.
-#'
+#'
#' @usage arv$logs.get(uuid)
#' @param uuid The UUID of the Log in question.
#' @return Log object.
NULL
#' logs.create
-#'
+#'
#' logs.create is a method defined in Arvados class.
-#'
+#'
#' @usage arv$logs.create(log, ensure_unique_name = "false")
#' @param log Log object.
#' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision.
NULL
#' logs.update
-#'
+#'
#' logs.update is a method defined in Arvados class.
-#'
+#'
#' @usage arv$logs.update(log, uuid)
#' @param log Log object.
#' @param uuid The UUID of the Log in question.
NULL
#' logs.delete
-#'
+#'
#' logs.delete is a method defined in Arvados class.
-#'
+#'
#' @usage arv$logs.delete(uuid)
#' @param uuid The UUID of the Log in question.
#' @return Log object.
NULL
#' logs.list
-#'
+#'
#' logs.list is a method defined in Arvados class.
-#'
+#'
#' @usage arv$logs.list(filters = NULL, where = NULL,
#' order = NULL, select = NULL, distinct = NULL,
#' limit = "100", offset = "0", count = "exact")
-#' @param filters
-#' @param where
-#' @param order
-#' @param select
-#' @param distinct
-#' @param limit
-#' @param offset
-#' @param count
+#' @param filters
+#' @param where
+#' @param order
+#' @param select
+#' @param distinct
+#' @param limit
+#' @param offset
+#' @param count
#' @return LogList object.
#' @name logs.list
NULL
#' traits.get
-#'
+#'
#' traits.get is a method defined in Arvados class.
-#'
+#'
#' @usage arv$traits.get(uuid)
#' @param uuid The UUID of the Trait in question.
#' @return Trait object.
NULL
#' traits.create
-#'
+#'
#' traits.create is a method defined in Arvados class.
-#'
+#'
#' @usage arv$traits.create(trait, ensure_unique_name = "false")
#' @param trait Trait object.
#' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision.
NULL
#' traits.update
-#'
+#'
#' traits.update is a method defined in Arvados class.
-#'
+#'
#' @usage arv$traits.update(trait, uuid)
#' @param trait Trait object.
#' @param uuid The UUID of the Trait in question.
NULL
#' traits.delete
-#'
+#'
#' traits.delete is a method defined in Arvados class.
-#'
+#'
#' @usage arv$traits.delete(uuid)
#' @param uuid The UUID of the Trait in question.
#' @return Trait object.
NULL
#' traits.list
-#'
+#'
#' traits.list is a method defined in Arvados class.
-#'
+#'
#' @usage arv$traits.list(filters = NULL,
#' where = NULL, order = NULL, select = NULL,
#' distinct = NULL, limit = "100", offset = "0",
#' count = "exact")
-#' @param filters
-#' @param where
-#' @param order
-#' @param select
-#' @param distinct
-#' @param limit
-#' @param offset
-#' @param count
+#' @param filters
+#' @param where
+#' @param order
+#' @param select
+#' @param distinct
+#' @param limit
+#' @param offset
+#' @param count
#' @return TraitList object.
#' @name traits.list
NULL
#' virtual_machines.get
-#'
+#'
#' virtual_machines.get is a method defined in Arvados class.
-#'
+#'
#' @usage arv$virtual_machines.get(uuid)
#' @param uuid The UUID of the VirtualMachine in question.
#' @return VirtualMachine object.
NULL
#' virtual_machines.create
-#'
+#'
#' virtual_machines.create is a method defined in Arvados class.
-#'
+#'
#' @usage arv$virtual_machines.create(virtualmachine,
#' ensure_unique_name = "false")
#' @param virtualMachine VirtualMachine object.
NULL
#' virtual_machines.update
-#'
+#'
#' virtual_machines.update is a method defined in Arvados class.
-#'
+#'
#' @usage arv$virtual_machines.update(virtualmachine,
#' uuid)
#' @param virtualMachine VirtualMachine object.
NULL
#' virtual_machines.delete
-#'
+#'
#' virtual_machines.delete is a method defined in Arvados class.
-#'
+#'
#' @usage arv$virtual_machines.delete(uuid)
#' @param uuid The UUID of the VirtualMachine in question.
#' @return VirtualMachine object.
NULL
#' virtual_machines.logins
-#'
+#'
#' virtual_machines.logins is a method defined in Arvados class.
-#'
+#'
#' @usage arv$virtual_machines.logins(uuid)
-#' @param uuid
+#' @param uuid
#' @return VirtualMachine object.
#' @name virtual_machines.logins
NULL
#' virtual_machines.get_all_logins
-#'
+#'
#' virtual_machines.get_all_logins is a method defined in Arvados class.
-#'
+#'
#' @usage arv$virtual_machines.get_all_logins(NULL)
#' @return VirtualMachine object.
#' @name virtual_machines.get_all_logins
NULL
#' virtual_machines.list
-#'
+#'
#' virtual_machines.list is a method defined in Arvados class.
-#'
+#'
#' @usage arv$virtual_machines.list(filters = NULL,
#' where = NULL, order = NULL, select = NULL,
#' distinct = NULL, limit = "100", offset = "0",
#' count = "exact")
-#' @param filters
-#' @param where
-#' @param order
-#' @param select
-#' @param distinct
-#' @param limit
-#' @param offset
-#' @param count
+#' @param filters
+#' @param where
+#' @param order
+#' @param select
+#' @param distinct
+#' @param limit
+#' @param offset
+#' @param count
#' @return VirtualMachineList object.
#' @name virtual_machines.list
NULL
#' workflows.get
-#'
+#'
#' workflows.get is a method defined in Arvados class.
-#'
+#'
#' @usage arv$workflows.get(uuid)
#' @param uuid The UUID of the Workflow in question.
#' @return Workflow object.
NULL
#' workflows.create
-#'
+#'
#' workflows.create is a method defined in Arvados class.
-#'
+#'
#' @usage arv$workflows.create(workflow,
#' ensure_unique_name = "false")
#' @param workflow Workflow object.
NULL
#' workflows.update
-#'
+#'
#' workflows.update is a method defined in Arvados class.
-#'
+#'
#' @usage arv$workflows.update(workflow,
#' uuid)
#' @param workflow Workflow object.
NULL
#' workflows.delete
-#'
+#'
#' workflows.delete is a method defined in Arvados class.
-#'
+#'
#' @usage arv$workflows.delete(uuid)
#' @param uuid The UUID of the Workflow in question.
#' @return Workflow object.
NULL
#' workflows.list
-#'
+#'
#' workflows.list is a method defined in Arvados class.
-#'
+#'
#' @usage arv$workflows.list(filters = NULL,
#' where = NULL, order = NULL, select = NULL,
#' distinct = NULL, limit = "100", offset = "0",
#' count = "exact")
-#' @param filters
-#' @param where
-#' @param order
-#' @param select
-#' @param distinct
-#' @param limit
-#' @param offset
-#' @param count
+#' @param filters
+#' @param where
+#' @param order
+#' @param select
+#' @param distinct
+#' @param limit
+#' @param offset
+#' @param count
#' @return WorkflowList object.
#' @name workflows.list
NULL
#' groups.get
-#'
+#'
#' groups.get is a method defined in Arvados class.
-#'
+#'
#' @usage arv$groups.get(uuid)
#' @param uuid The UUID of the Group in question.
#' @return Group object.
NULL
#' groups.create
-#'
+#'
#' groups.create is a method defined in Arvados class.
-#'
+#'
#' @usage arv$groups.create(group, ensure_unique_name = "false")
#' @param group Group object.
#' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision.
NULL
#' groups.update
-#'
+#'
#' groups.update is a method defined in Arvados class.
-#'
+#'
#' @usage arv$groups.update(group, uuid)
#' @param group Group object.
#' @param uuid The UUID of the Group in question.
NULL
#' groups.delete
-#'
+#'
#' groups.delete is a method defined in Arvados class.
-#'
+#'
#' @usage arv$groups.delete(uuid)
#' @param uuid The UUID of the Group in question.
#' @return Group object.
NULL
#' groups.contents
-#'
+#'
#' groups.contents is a method defined in Arvados class.
-#'
+#'
#' @usage arv$groups.contents(filters = NULL,
#' where = NULL, order = NULL, distinct = NULL,
#' limit = "100", offset = "0", count = "exact",
#' include_trash = NULL, uuid = NULL, recursive = NULL)
-#' @param filters
-#' @param where
-#' @param order
-#' @param distinct
-#' @param limit
-#' @param offset
-#' @param count
+#' @param filters
+#' @param where
+#' @param order
+#' @param distinct
+#' @param limit
+#' @param offset
+#' @param count
#' @param include_trash Include items whose is_trashed attribute is true.
-#' @param uuid
+#' @param uuid
#' @param recursive Include contents from child groups recursively.
#' @return Group object.
#' @name groups.contents
NULL
#' groups.trash
-#'
+#'
#' groups.trash is a method defined in Arvados class.
-#'
+#'
#' @usage arv$groups.trash(uuid)
-#' @param uuid
+#' @param uuid
#' @return Group object.
#' @name groups.trash
NULL
#' groups.untrash
-#'
+#'
#' groups.untrash is a method defined in Arvados class.
-#'
+#'
#' @usage arv$groups.untrash(uuid)
-#' @param uuid
+#' @param uuid
#' @return Group object.
#' @name groups.untrash
NULL
#' groups.list
-#'
+#'
#' groups.list is a method defined in Arvados class.
-#'
+#'
#' @usage arv$groups.list(filters = NULL,
#' where = NULL, order = NULL, select = NULL,
#' distinct = NULL, limit = "100", offset = "0",
#' count = "exact", include_trash = NULL)
-#' @param filters
-#' @param where
-#' @param order
-#' @param select
-#' @param distinct
-#' @param limit
-#' @param offset
-#' @param count
+#' @param filters
+#' @param where
+#' @param order
+#' @param select
+#' @param distinct
+#' @param limit
+#' @param offset
+#' @param count
#' @param include_trash Include items whose is_trashed attribute is true.
#' @return GroupList object.
#' @name groups.list
NULL
#' user_agreements.get
-#'
+#'
#' user_agreements.get is a method defined in Arvados class.
-#'
+#'
#' @usage arv$user_agreements.get(uuid)
#' @param uuid The UUID of the UserAgreement in question.
#' @return UserAgreement object.
NULL
#' user_agreements.create
-#'
+#'
#' user_agreements.create is a method defined in Arvados class.
-#'
+#'
#' @usage arv$user_agreements.create(useragreement,
#' ensure_unique_name = "false")
#' @param userAgreement UserAgreement object.
NULL
#' user_agreements.update
-#'
+#'
#' user_agreements.update is a method defined in Arvados class.
-#'
+#'
#' @usage arv$user_agreements.update(useragreement,
#' uuid)
#' @param userAgreement UserAgreement object.
NULL
#' user_agreements.delete
-#'
+#'
#' user_agreements.delete is a method defined in Arvados class.
-#'
+#'
#' @usage arv$user_agreements.delete(uuid)
#' @param uuid The UUID of the UserAgreement in question.
#' @return UserAgreement object.
NULL
#' user_agreements.signatures
-#'
+#'
#' user_agreements.signatures is a method defined in Arvados class.
-#'
+#'
#' @usage arv$user_agreements.signatures(NULL)
#' @return UserAgreement object.
#' @name user_agreements.signatures
NULL
#' user_agreements.sign
-#'
+#'
#' user_agreements.sign is a method defined in Arvados class.
-#'
+#'
#' @usage arv$user_agreements.sign(NULL)
#' @return UserAgreement object.
#' @name user_agreements.sign
NULL
#' user_agreements.list
-#'
+#'
#' user_agreements.list is a method defined in Arvados class.
-#'
+#'
#' @usage arv$user_agreements.list(filters = NULL,
#' where = NULL, order = NULL, select = NULL,
#' distinct = NULL, limit = "100", offset = "0",
#' count = "exact")
-#' @param filters
-#' @param where
-#' @param order
-#' @param select
-#' @param distinct
-#' @param limit
-#' @param offset
-#' @param count
+#' @param filters
+#' @param where
+#' @param order
+#' @param select
+#' @param distinct
+#' @param limit
+#' @param offset
+#' @param count
#' @return UserAgreementList object.
#' @name user_agreements.list
NULL
#' user_agreements.new
-#'
+#'
#' user_agreements.new is a method defined in Arvados class.
-#'
+#'
#' @usage arv$user_agreements.new(NULL)
#' @return UserAgreement object.
#' @name user_agreements.new
NULL
#' project.get
-#'
+#'
#' projects.get is equivalent to groups.get method.
-#'
+#'
#' @usage arv$projects.get(uuid)
#' @param uuid The UUID of the Group in question.
#' @return Group object.
NULL
#' project.create
-#'
+#'
#' projects.create wrapps groups.create method by setting group_class attribute to "project".
-#'
+#'
#' @usage arv$projects.create(group, ensure_unique_name = "false")
#' @param group Group object.
#' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision.
NULL
#' project.update
-#'
+#'
#' projects.update wrapps groups.update method by setting group_class attribute to "project".
-#'
+#'
#' @usage arv$projects.update(group, uuid)
#' @param group Group object.
#' @param uuid The UUID of the Group in question.
NULL
#' project.delete
-#'
+#'
#' projects.delete is equivalent to groups.delete method.
-#'
+#'
#' @usage arv$project.delete(uuid)
#' @param uuid The UUID of the Group in question.
#' @return Group object.
NULL
#' project.list
-#'
+#'
#' projects.list wrapps groups.list method by setting group_class attribute to "project".
-#'
+#'
#' @usage arv$projects.list(filters = NULL,
#' where = NULL, order = NULL, distinct = NULL,
#' limit = "100", offset = "0", count = "exact",
#' include_trash = NULL, uuid = NULL, recursive = NULL)
-#' @param filters
-#' @param where
-#' @param order
-#' @param distinct
-#' @param limit
-#' @param offset
-#' @param count
+#' @param filters
+#' @param where
+#' @param order
+#' @param distinct
+#' @param limit
+#' @param offset
+#' @param count
#' @param include_trash Include items whose is_trashed attribute is true.
-#' @param uuid
+#' @param uuid
#' @param recursive Include contents from child groups recursively.
#' @return Group object.
#' @name projects.list
#' \item{}{\code{\link{users.delete}}}
#' \item{}{\code{\link{users.get}}}
#' \item{}{\code{\link{users.list}}}
+#' \item{}{\code{\link{users.merge}}}
#' \item{}{\code{\link{users.setup}}}
#' \item{}{\code{\link{users.system}}}
#' \item{}{\code{\link{users.unsetup}}}
{
endPoint <- stringr::str_interp("users/${uuid}")
url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("OAuth2", private$token),
+ headers <- list(Authorization = paste("OAuth2", private$token),
"Content-Type" = "application/json")
queryArgs <- NULL
-
+
body <- NULL
-
+
response <- private$REST$http$exec("GET", url, headers, body,
queryArgs, private$numRetries)
resource <- private$REST$httpParser$parseJSONResponse(response)
-
+
if(!is.null(resource$errors))
stop(resource$errors)
-
+
resource
},
{
endPoint <- stringr::str_interp("users")
url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("OAuth2", private$token),
+ headers <- list(Authorization = paste("OAuth2", private$token),
"Content-Type" = "application/json")
queryArgs <- list(ensure_unique_name = ensure_unique_name)
-
+
if(length(user) > 0)
- body <- jsonlite::toJSON(list(user = user),
+ body <- jsonlite::toJSON(list(user = user),
auto_unbox = TRUE)
else
body <- NULL
-
+
response <- private$REST$http$exec("POST", url, headers, body,
queryArgs, private$numRetries)
resource <- private$REST$httpParser$parseJSONResponse(response)
-
+
if(!is.null(resource$errors))
stop(resource$errors)
-
+
resource
},
{
endPoint <- stringr::str_interp("users/${uuid}")
url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("OAuth2", private$token),
+ headers <- list(Authorization = paste("OAuth2", private$token),
"Content-Type" = "application/json")
queryArgs <- NULL
-
+
if(length(user) > 0)
- body <- jsonlite::toJSON(list(user = user),
+ body <- jsonlite::toJSON(list(user = user),
auto_unbox = TRUE)
else
body <- NULL
-
+
response <- private$REST$http$exec("PUT", url, headers, body,
queryArgs, private$numRetries)
resource <- private$REST$httpParser$parseJSONResponse(response)
-
+
if(!is.null(resource$errors))
stop(resource$errors)
-
+
resource
},
{
endPoint <- stringr::str_interp("users/${uuid}")
url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("OAuth2", private$token),
+ headers <- list(Authorization = paste("OAuth2", private$token),
"Content-Type" = "application/json")
queryArgs <- NULL
-
+
body <- NULL
-
+
response <- private$REST$http$exec("DELETE", url, headers, body,
queryArgs, private$numRetries)
resource <- private$REST$httpParser$parseJSONResponse(response)
-
+
if(!is.null(resource$errors))
stop(resource$errors)
-
+
resource
},
{
endPoint <- stringr::str_interp("users/current")
url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("OAuth2", private$token),
+ headers <- list(Authorization = paste("OAuth2", private$token),
"Content-Type" = "application/json")
queryArgs <- NULL
-
+
body <- NULL
-
+
response <- private$REST$http$exec("GET", url, headers, body,
queryArgs, private$numRetries)
resource <- private$REST$httpParser$parseJSONResponse(response)
-
+
if(!is.null(resource$errors))
stop(resource$errors)
-
+
resource
},
{
endPoint <- stringr::str_interp("users/system")
url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("OAuth2", private$token),
+ headers <- list(Authorization = paste("OAuth2", private$token),
"Content-Type" = "application/json")
queryArgs <- NULL
-
+
body <- NULL
-
+
response <- private$REST$http$exec("GET", url, headers, body,
queryArgs, private$numRetries)
resource <- private$REST$httpParser$parseJSONResponse(response)
-
+
if(!is.null(resource$errors))
stop(resource$errors)
-
+
resource
},
{
endPoint <- stringr::str_interp("users/${uuid}/activate")
url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("OAuth2", private$token),
+ headers <- list(Authorization = paste("OAuth2", private$token),
"Content-Type" = "application/json")
queryArgs <- NULL
-
+
body <- NULL
-
+
response <- private$REST$http$exec("POST", url, headers, body,
queryArgs, private$numRetries)
resource <- private$REST$httpParser$parseJSONResponse(response)
-
+
if(!is.null(resource$errors))
stop(resource$errors)
-
+
resource
},
{
endPoint <- stringr::str_interp("users/setup")
url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("OAuth2", private$token),
+ headers <- list(Authorization = paste("OAuth2", private$token),
"Content-Type" = "application/json")
queryArgs <- list(user = user, openid_prefix = openid_prefix,
repo_name = repo_name, vm_uuid = vm_uuid,
send_notification_email = send_notification_email)
-
+
body <- NULL
-
+
response <- private$REST$http$exec("POST", url, headers, body,
queryArgs, private$numRetries)
resource <- private$REST$httpParser$parseJSONResponse(response)
-
+
if(!is.null(resource$errors))
stop(resource$errors)
-
+
resource
},
{
endPoint <- stringr::str_interp("users/${uuid}/unsetup")
url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("OAuth2", private$token),
+ headers <- list(Authorization = paste("OAuth2", private$token),
"Content-Type" = "application/json")
queryArgs <- NULL
-
+
body <- NULL
-
+
response <- private$REST$http$exec("POST", url, headers, body,
queryArgs, private$numRetries)
resource <- private$REST$httpParser$parseJSONResponse(response)
-
+
if(!is.null(resource$errors))
stop(resource$errors)
-
+
resource
},
{
endPoint <- stringr::str_interp("users/${uuid}/update_uuid")
url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("OAuth2", private$token),
+ headers <- list(Authorization = paste("OAuth2", private$token),
"Content-Type" = "application/json")
queryArgs <- list(new_uuid = new_uuid)
-
+
body <- NULL
-
+
response <- private$REST$http$exec("POST", url, headers, body,
queryArgs, private$numRetries)
resource <- private$REST$httpParser$parseJSONResponse(response)
-
+
if(!is.null(resource$errors))
stop(resource$errors)
+
+ resource
+ },
+ users.merge = function(new_owner_uuid, new_user_token,
+ redirect_to_new_user = NULL)
+ {
+ endPoint <- stringr::str_interp("users/merge")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("OAuth2", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- list(new_owner_uuid = new_owner_uuid,
+ new_user_token = new_user_token, redirect_to_new_user = redirect_to_new_user)
+
+ body <- NULL
+
+ response <- private$REST$http$exec("POST", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
resource
},
{
endPoint <- stringr::str_interp("users")
url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("OAuth2", private$token),
+ headers <- list(Authorization = paste("OAuth2", private$token),
"Content-Type" = "application/json")
queryArgs <- list(filters = filters, where = where,
order = order, select = select, distinct = distinct,
limit = limit, offset = offset, count = count)
-
+
body <- NULL
-
+
response <- private$REST$http$exec("GET", url, headers, body,
queryArgs, private$numRetries)
resource <- private$REST$httpParser$parseJSONResponse(response)
-
+
if(!is.null(resource$errors))
stop(resource$errors)
-
+
resource
},
{
endPoint <- stringr::str_interp("api_client_authorizations/${uuid}")
url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("OAuth2", private$token),
+ headers <- list(Authorization = paste("OAuth2", private$token),
"Content-Type" = "application/json")
queryArgs <- NULL
-
+
body <- NULL
-
+
response <- private$REST$http$exec("GET", url, headers, body,
queryArgs, private$numRetries)
resource <- private$REST$httpParser$parseJSONResponse(response)
-
+
if(!is.null(resource$errors))
stop(resource$errors)
-
+
resource
},
{
endPoint <- stringr::str_interp("api_client_authorizations")
url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("OAuth2", private$token),
+ headers <- list(Authorization = paste("OAuth2", private$token),
"Content-Type" = "application/json")
queryArgs <- list(ensure_unique_name = ensure_unique_name)
-
+
if(length(apiclientauthorization) > 0)
- body <- jsonlite::toJSON(list(apiclientauthorization = apiclientauthorization),
+ body <- jsonlite::toJSON(list(apiclientauthorization = apiclientauthorization),
auto_unbox = TRUE)
else
body <- NULL
-
+
response <- private$REST$http$exec("POST", url, headers, body,
queryArgs, private$numRetries)
resource <- private$REST$httpParser$parseJSONResponse(response)
-
+
if(!is.null(resource$errors))
stop(resource$errors)
-
+
resource
},
{
endPoint <- stringr::str_interp("api_client_authorizations/${uuid}")
url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("OAuth2", private$token),
+ headers <- list(Authorization = paste("OAuth2", private$token),
"Content-Type" = "application/json")
queryArgs <- NULL
-
+
if(length(apiclientauthorization) > 0)
- body <- jsonlite::toJSON(list(apiclientauthorization = apiclientauthorization),
+ body <- jsonlite::toJSON(list(apiclientauthorization = apiclientauthorization),
auto_unbox = TRUE)
else
body <- NULL
-
+
response <- private$REST$http$exec("PUT", url, headers, body,
queryArgs, private$numRetries)
resource <- private$REST$httpParser$parseJSONResponse(response)
-
+
if(!is.null(resource$errors))
stop(resource$errors)
-
+
resource
},
{
endPoint <- stringr::str_interp("api_client_authorizations/${uuid}")
url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("OAuth2", private$token),
+ headers <- list(Authorization = paste("OAuth2", private$token),
"Content-Type" = "application/json")
queryArgs <- NULL
-
+
body <- NULL
-
+
response <- private$REST$http$exec("DELETE", url, headers, body,
queryArgs, private$numRetries)
resource <- private$REST$httpParser$parseJSONResponse(response)
-
+
if(!is.null(resource$errors))
stop(resource$errors)
-
+
resource
},
{
endPoint <- stringr::str_interp("api_client_authorizations/create_system_auth")
url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("OAuth2", private$token),
+ headers <- list(Authorization = paste("OAuth2", private$token),
"Content-Type" = "application/json")
queryArgs <- list(api_client_id = api_client_id,
scopes = scopes)
-
+
body <- NULL
-
+
response <- private$REST$http$exec("POST", url, headers, body,
queryArgs, private$numRetries)
resource <- private$REST$httpParser$parseJSONResponse(response)
-
+
if(!is.null(resource$errors))
stop(resource$errors)
-
+
resource
},
{
endPoint <- stringr::str_interp("api_client_authorizations/current")
url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("OAuth2", private$token),
+ headers <- list(Authorization = paste("OAuth2", private$token),
"Content-Type" = "application/json")
queryArgs <- NULL
-
+
body <- NULL
-
+
response <- private$REST$http$exec("GET", url, headers, body,
queryArgs, private$numRetries)
resource <- private$REST$httpParser$parseJSONResponse(response)
-
+
if(!is.null(resource$errors))
stop(resource$errors)
-
+
resource
},
{
endPoint <- stringr::str_interp("api_client_authorizations")
url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("OAuth2", private$token),
+ headers <- list(Authorization = paste("OAuth2", private$token),
"Content-Type" = "application/json")
queryArgs <- list(filters = filters, where = where,
order = order, select = select, distinct = distinct,
limit = limit, offset = offset, count = count)
-
+
body <- NULL
-
+
response <- private$REST$http$exec("GET", url, headers, body,
queryArgs, private$numRetries)
resource <- private$REST$httpParser$parseJSONResponse(response)
-
+
if(!is.null(resource$errors))
stop(resource$errors)
-
+
resource
},
{
endPoint <- stringr::str_interp("containers/${uuid}")
url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("OAuth2", private$token),
+ headers <- list(Authorization = paste("OAuth2", private$token),
"Content-Type" = "application/json")
queryArgs <- NULL
-
+
body <- NULL
-
+
response <- private$REST$http$exec("GET", url, headers, body,
queryArgs, private$numRetries)
resource <- private$REST$httpParser$parseJSONResponse(response)
-
+
if(!is.null(resource$errors))
stop(resource$errors)
-
+
resource
},
{
endPoint <- stringr::str_interp("containers")
url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("OAuth2", private$token),
+ headers <- list(Authorization = paste("OAuth2", private$token),
"Content-Type" = "application/json")
queryArgs <- list(ensure_unique_name = ensure_unique_name)
-
+
if(length(container) > 0)
- body <- jsonlite::toJSON(list(container = container),
+ body <- jsonlite::toJSON(list(container = container),
auto_unbox = TRUE)
else
body <- NULL
-
+
response <- private$REST$http$exec("POST", url, headers, body,
queryArgs, private$numRetries)
resource <- private$REST$httpParser$parseJSONResponse(response)
-
+
if(!is.null(resource$errors))
stop(resource$errors)
-
+
resource
},
{
endPoint <- stringr::str_interp("containers/${uuid}")
url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("OAuth2", private$token),
+ headers <- list(Authorization = paste("OAuth2", private$token),
"Content-Type" = "application/json")
queryArgs <- NULL
-
+
if(length(container) > 0)
- body <- jsonlite::toJSON(list(container = container),
+ body <- jsonlite::toJSON(list(container = container),
auto_unbox = TRUE)
else
body <- NULL
-
+
response <- private$REST$http$exec("PUT", url, headers, body,
queryArgs, private$numRetries)
resource <- private$REST$httpParser$parseJSONResponse(response)
-
+
if(!is.null(resource$errors))
stop(resource$errors)
-
+
resource
},
{
endPoint <- stringr::str_interp("containers/${uuid}")
url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("OAuth2", private$token),
+ headers <- list(Authorization = paste("OAuth2", private$token),
"Content-Type" = "application/json")
queryArgs <- NULL
-
+
body <- NULL
-
+
response <- private$REST$http$exec("DELETE", url, headers, body,
queryArgs, private$numRetries)
resource <- private$REST$httpParser$parseJSONResponse(response)
-
+
if(!is.null(resource$errors))
stop(resource$errors)
-
+
resource
},
{
endPoint <- stringr::str_interp("containers/${uuid}/auth")
url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("OAuth2", private$token),
+ headers <- list(Authorization = paste("OAuth2", private$token),
"Content-Type" = "application/json")
queryArgs <- NULL
-
+
body <- NULL
-
+
response <- private$REST$http$exec("GET", url, headers, body,
queryArgs, private$numRetries)
resource <- private$REST$httpParser$parseJSONResponse(response)
-
+
if(!is.null(resource$errors))
stop(resource$errors)
-
+
resource
},
{
endPoint <- stringr::str_interp("containers/${uuid}/lock")
url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("OAuth2", private$token),
+ headers <- list(Authorization = paste("OAuth2", private$token),
"Content-Type" = "application/json")
queryArgs <- NULL
-
+
body <- NULL
-
+
response <- private$REST$http$exec("POST", url, headers, body,
queryArgs, private$numRetries)
resource <- private$REST$httpParser$parseJSONResponse(response)
-
+
if(!is.null(resource$errors))
stop(resource$errors)
-
+
resource
},
{
endPoint <- stringr::str_interp("containers/${uuid}/unlock")
url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("OAuth2", private$token),
+ headers <- list(Authorization = paste("OAuth2", private$token),
"Content-Type" = "application/json")
queryArgs <- NULL
-
+
body <- NULL
-
+
response <- private$REST$http$exec("POST", url, headers, body,
queryArgs, private$numRetries)
resource <- private$REST$httpParser$parseJSONResponse(response)
-
+
if(!is.null(resource$errors))
stop(resource$errors)
-
+
resource
},
{
endPoint <- stringr::str_interp("containers/${uuid}/secret_mounts")
url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("OAuth2", private$token),
+ headers <- list(Authorization = paste("OAuth2", private$token),
"Content-Type" = "application/json")
queryArgs <- NULL
-
+
body <- NULL
-
+
response <- private$REST$http$exec("GET", url, headers, body,
queryArgs, private$numRetries)
resource <- private$REST$httpParser$parseJSONResponse(response)
-
+
if(!is.null(resource$errors))
stop(resource$errors)
-
+
resource
},
{
endPoint <- stringr::str_interp("containers/current")
url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("OAuth2", private$token),
+ headers <- list(Authorization = paste("OAuth2", private$token),
"Content-Type" = "application/json")
queryArgs <- NULL
-
+
body <- NULL
-
+
response <- private$REST$http$exec("GET", url, headers, body,
queryArgs, private$numRetries)
resource <- private$REST$httpParser$parseJSONResponse(response)
-
+
if(!is.null(resource$errors))
stop(resource$errors)
-
+
resource
},
{
endPoint <- stringr::str_interp("containers")
url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("OAuth2", private$token),
+ headers <- list(Authorization = paste("OAuth2", private$token),
"Content-Type" = "application/json")
queryArgs <- list(filters = filters, where = where,
order = order, select = select, distinct = distinct,
limit = limit, offset = offset, count = count)
-
+
body <- NULL
-
+
response <- private$REST$http$exec("GET", url, headers, body,
queryArgs, private$numRetries)
resource <- private$REST$httpParser$parseJSONResponse(response)
-
+
if(!is.null(resource$errors))
stop(resource$errors)
-
+
resource
},
{
endPoint <- stringr::str_interp("api_clients/${uuid}")
url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("OAuth2", private$token),
+ headers <- list(Authorization = paste("OAuth2", private$token),
"Content-Type" = "application/json")
queryArgs <- NULL
-
+
body <- NULL
-
+
response <- private$REST$http$exec("GET", url, headers, body,
queryArgs, private$numRetries)
resource <- private$REST$httpParser$parseJSONResponse(response)
-
+
if(!is.null(resource$errors))
stop(resource$errors)
-
+
resource
},
{
endPoint <- stringr::str_interp("api_clients")
url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("OAuth2", private$token),
+ headers <- list(Authorization = paste("OAuth2", private$token),
"Content-Type" = "application/json")
queryArgs <- list(ensure_unique_name = ensure_unique_name)
-
+
if(length(apiclient) > 0)
- body <- jsonlite::toJSON(list(apiclient = apiclient),
+ body <- jsonlite::toJSON(list(apiclient = apiclient),
auto_unbox = TRUE)
else
body <- NULL
-
+
response <- private$REST$http$exec("POST", url, headers, body,
queryArgs, private$numRetries)
resource <- private$REST$httpParser$parseJSONResponse(response)
-
+
if(!is.null(resource$errors))
stop(resource$errors)
-
+
resource
},
{
endPoint <- stringr::str_interp("api_clients/${uuid}")
url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("OAuth2", private$token),
+ headers <- list(Authorization = paste("OAuth2", private$token),
"Content-Type" = "application/json")
queryArgs <- NULL
-
+
if(length(apiclient) > 0)
- body <- jsonlite::toJSON(list(apiclient = apiclient),
+ body <- jsonlite::toJSON(list(apiclient = apiclient),
auto_unbox = TRUE)
else
body <- NULL
-
+
response <- private$REST$http$exec("PUT", url, headers, body,
queryArgs, private$numRetries)
resource <- private$REST$httpParser$parseJSONResponse(response)
-
+
if(!is.null(resource$errors))
stop(resource$errors)
-
+
resource
},
{
endPoint <- stringr::str_interp("api_clients/${uuid}")
url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("OAuth2", private$token),
+ headers <- list(Authorization = paste("OAuth2", private$token),
"Content-Type" = "application/json")
queryArgs <- NULL
-
+
body <- NULL
-
+
response <- private$REST$http$exec("DELETE", url, headers, body,
queryArgs, private$numRetries)
resource <- private$REST$httpParser$parseJSONResponse(response)
-
+
if(!is.null(resource$errors))
stop(resource$errors)
-
+
resource
},
{
endPoint <- stringr::str_interp("api_clients")
url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("OAuth2", private$token),
+ headers <- list(Authorization = paste("OAuth2", private$token),
"Content-Type" = "application/json")
queryArgs <- list(filters = filters, where = where,
order = order, select = select, distinct = distinct,
limit = limit, offset = offset, count = count)
-
+
body <- NULL
-
+
response <- private$REST$http$exec("GET", url, headers, body,
queryArgs, private$numRetries)
resource <- private$REST$httpParser$parseJSONResponse(response)
-
+
if(!is.null(resource$errors))
stop(resource$errors)
-
+
resource
},
- authorized_keys.get = function(uuid)
+ container_requests.get = function(uuid)
{
- endPoint <- stringr::str_interp("authorized_keys/${uuid}")
+ endPoint <- stringr::str_interp("container_requests/${uuid}")
url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("OAuth2", private$token),
+ headers <- list(Authorization = paste("OAuth2", private$token),
"Content-Type" = "application/json")
queryArgs <- NULL
-
+
body <- NULL
-
+
response <- private$REST$http$exec("GET", url, headers, body,
queryArgs, private$numRetries)
resource <- private$REST$httpParser$parseJSONResponse(response)
-
+
if(!is.null(resource$errors))
stop(resource$errors)
-
+
resource
},
- authorized_keys.create = function(authorizedkey,
+ container_requests.create = function(containerrequest,
ensure_unique_name = "false")
{
- endPoint <- stringr::str_interp("authorized_keys")
+ endPoint <- stringr::str_interp("container_requests")
url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("OAuth2", private$token),
+ headers <- list(Authorization = paste("OAuth2", private$token),
"Content-Type" = "application/json")
queryArgs <- list(ensure_unique_name = ensure_unique_name)
-
- if(length(authorizedkey) > 0)
- body <- jsonlite::toJSON(list(authorizedkey = authorizedkey),
+
+ if(length(containerrequest) > 0)
+ body <- jsonlite::toJSON(list(containerrequest = containerrequest),
auto_unbox = TRUE)
else
body <- NULL
-
+
response <- private$REST$http$exec("POST", url, headers, body,
queryArgs, private$numRetries)
resource <- private$REST$httpParser$parseJSONResponse(response)
-
+
if(!is.null(resource$errors))
stop(resource$errors)
-
+
resource
},
- authorized_keys.update = function(authorizedkey, uuid)
+ container_requests.update = function(containerrequest, uuid)
{
- endPoint <- stringr::str_interp("authorized_keys/${uuid}")
+ endPoint <- stringr::str_interp("container_requests/${uuid}")
url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("OAuth2", private$token),
+ headers <- list(Authorization = paste("OAuth2", private$token),
"Content-Type" = "application/json")
queryArgs <- NULL
-
- if(length(authorizedkey) > 0)
- body <- jsonlite::toJSON(list(authorizedkey = authorizedkey),
+
+ if(length(containerrequest) > 0)
+ body <- jsonlite::toJSON(list(containerrequest = containerrequest),
auto_unbox = TRUE)
else
body <- NULL
-
+
response <- private$REST$http$exec("PUT", url, headers, body,
queryArgs, private$numRetries)
resource <- private$REST$httpParser$parseJSONResponse(response)
-
+
if(!is.null(resource$errors))
stop(resource$errors)
-
+
resource
},
- authorized_keys.delete = function(uuid)
+ container_requests.delete = function(uuid)
{
- endPoint <- stringr::str_interp("authorized_keys/${uuid}")
+ endPoint <- stringr::str_interp("container_requests/${uuid}")
url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("OAuth2", private$token),
+ headers <- list(Authorization = paste("OAuth2", private$token),
"Content-Type" = "application/json")
queryArgs <- NULL
-
+
body <- NULL
-
+
response <- private$REST$http$exec("DELETE", url, headers, body,
queryArgs, private$numRetries)
resource <- private$REST$httpParser$parseJSONResponse(response)
-
+
if(!is.null(resource$errors))
stop(resource$errors)
-
+
resource
},
- authorized_keys.list = function(filters = NULL,
+ container_requests.list = function(filters = NULL,
where = NULL, order = NULL, select = NULL,
distinct = NULL, limit = "100", offset = "0",
count = "exact")
{
- endPoint <- stringr::str_interp("authorized_keys")
+ endPoint <- stringr::str_interp("container_requests")
url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("OAuth2", private$token),
+ headers <- list(Authorization = paste("OAuth2", private$token),
"Content-Type" = "application/json")
queryArgs <- list(filters = filters, where = where,
order = order, select = select, distinct = distinct,
limit = limit, offset = offset, count = count)
-
+
body <- NULL
-
+
response <- private$REST$http$exec("GET", url, headers, body,
queryArgs, private$numRetries)
resource <- private$REST$httpParser$parseJSONResponse(response)
-
+
if(!is.null(resource$errors))
stop(resource$errors)
-
+
resource
},
- container_requests.get = function(uuid)
+ authorized_keys.get = function(uuid)
{
- endPoint <- stringr::str_interp("container_requests/${uuid}")
+ endPoint <- stringr::str_interp("authorized_keys/${uuid}")
url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("OAuth2", private$token),
+ headers <- list(Authorization = paste("OAuth2", private$token),
"Content-Type" = "application/json")
queryArgs <- NULL
-
+
body <- NULL
-
+
response <- private$REST$http$exec("GET", url, headers, body,
queryArgs, private$numRetries)
resource <- private$REST$httpParser$parseJSONResponse(response)
-
+
if(!is.null(resource$errors))
stop(resource$errors)
-
+
resource
},
- container_requests.create = function(containerrequest,
+ authorized_keys.create = function(authorizedkey,
ensure_unique_name = "false")
{
- endPoint <- stringr::str_interp("container_requests")
+ endPoint <- stringr::str_interp("authorized_keys")
url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("OAuth2", private$token),
+ headers <- list(Authorization = paste("OAuth2", private$token),
"Content-Type" = "application/json")
queryArgs <- list(ensure_unique_name = ensure_unique_name)
-
- if(length(containerrequest) > 0)
- body <- jsonlite::toJSON(list(containerrequest = containerrequest),
+
+ if(length(authorizedkey) > 0)
+ body <- jsonlite::toJSON(list(authorizedkey = authorizedkey),
auto_unbox = TRUE)
else
body <- NULL
-
+
response <- private$REST$http$exec("POST", url, headers, body,
queryArgs, private$numRetries)
resource <- private$REST$httpParser$parseJSONResponse(response)
-
+
if(!is.null(resource$errors))
stop(resource$errors)
-
+
resource
},
- container_requests.update = function(containerrequest, uuid)
+ authorized_keys.update = function(authorizedkey, uuid)
{
- endPoint <- stringr::str_interp("container_requests/${uuid}")
+ endPoint <- stringr::str_interp("authorized_keys/${uuid}")
url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("OAuth2", private$token),
+ headers <- list(Authorization = paste("OAuth2", private$token),
"Content-Type" = "application/json")
queryArgs <- NULL
-
- if(length(containerrequest) > 0)
- body <- jsonlite::toJSON(list(containerrequest = containerrequest),
+
+ if(length(authorizedkey) > 0)
+ body <- jsonlite::toJSON(list(authorizedkey = authorizedkey),
auto_unbox = TRUE)
else
body <- NULL
-
+
response <- private$REST$http$exec("PUT", url, headers, body,
queryArgs, private$numRetries)
resource <- private$REST$httpParser$parseJSONResponse(response)
-
+
if(!is.null(resource$errors))
stop(resource$errors)
-
+
resource
},
- container_requests.delete = function(uuid)
+ authorized_keys.delete = function(uuid)
{
- endPoint <- stringr::str_interp("container_requests/${uuid}")
+ endPoint <- stringr::str_interp("authorized_keys/${uuid}")
url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("OAuth2", private$token),
+ headers <- list(Authorization = paste("OAuth2", private$token),
"Content-Type" = "application/json")
queryArgs <- NULL
-
+
body <- NULL
-
+
response <- private$REST$http$exec("DELETE", url, headers, body,
queryArgs, private$numRetries)
resource <- private$REST$httpParser$parseJSONResponse(response)
-
+
if(!is.null(resource$errors))
stop(resource$errors)
-
+
resource
},
- container_requests.list = function(filters = NULL,
+ authorized_keys.list = function(filters = NULL,
where = NULL, order = NULL, select = NULL,
distinct = NULL, limit = "100", offset = "0",
count = "exact")
{
- endPoint <- stringr::str_interp("container_requests")
+ endPoint <- stringr::str_interp("authorized_keys")
url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("OAuth2", private$token),
+ headers <- list(Authorization = paste("OAuth2", private$token),
"Content-Type" = "application/json")
queryArgs <- list(filters = filters, where = where,
order = order, select = select, distinct = distinct,
limit = limit, offset = offset, count = count)
-
+
body <- NULL
-
+
response <- private$REST$http$exec("GET", url, headers, body,
queryArgs, private$numRetries)
resource <- private$REST$httpParser$parseJSONResponse(response)
-
+
if(!is.null(resource$errors))
stop(resource$errors)
-
+
resource
},
{
endPoint <- stringr::str_interp("collections/${uuid}")
url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("OAuth2", private$token),
+ headers <- list(Authorization = paste("OAuth2", private$token),
"Content-Type" = "application/json")
queryArgs <- NULL
-
+
body <- NULL
-
+
response <- private$REST$http$exec("GET", url, headers, body,
queryArgs, private$numRetries)
resource <- private$REST$httpParser$parseJSONResponse(response)
-
+
if(!is.null(resource$errors))
stop(resource$errors)
-
+
resource
},
{
endPoint <- stringr::str_interp("collections")
url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("OAuth2", private$token),
+ headers <- list(Authorization = paste("OAuth2", private$token),
"Content-Type" = "application/json")
queryArgs <- list(ensure_unique_name = ensure_unique_name)
-
+
if(length(collection) > 0)
- body <- jsonlite::toJSON(list(collection = collection),
+ body <- jsonlite::toJSON(list(collection = collection),
auto_unbox = TRUE)
else
body <- NULL
-
+
response <- private$REST$http$exec("POST", url, headers, body,
queryArgs, private$numRetries)
resource <- private$REST$httpParser$parseJSONResponse(response)
-
+
if(!is.null(resource$errors))
stop(resource$errors)
-
+
resource
},
{
endPoint <- stringr::str_interp("collections/${uuid}")
url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("OAuth2", private$token),
+ headers <- list(Authorization = paste("OAuth2", private$token),
"Content-Type" = "application/json")
queryArgs <- NULL
-
+
if(length(collection) > 0)
- body <- jsonlite::toJSON(list(collection = collection),
+ body <- jsonlite::toJSON(list(collection = collection),
auto_unbox = TRUE)
else
body <- NULL
-
+
response <- private$REST$http$exec("PUT", url, headers, body,
queryArgs, private$numRetries)
resource <- private$REST$httpParser$parseJSONResponse(response)
-
+
if(!is.null(resource$errors))
stop(resource$errors)
-
+
resource
},
{
endPoint <- stringr::str_interp("collections/${uuid}")
url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("OAuth2", private$token),
+ headers <- list(Authorization = paste("OAuth2", private$token),
"Content-Type" = "application/json")
queryArgs <- NULL
-
+
body <- NULL
-
+
response <- private$REST$http$exec("DELETE", url, headers, body,
queryArgs, private$numRetries)
resource <- private$REST$httpParser$parseJSONResponse(response)
-
+
if(!is.null(resource$errors))
stop(resource$errors)
-
+
resource
},
{
endPoint <- stringr::str_interp("collections/${uuid}/provenance")
url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("OAuth2", private$token),
+ headers <- list(Authorization = paste("OAuth2", private$token),
"Content-Type" = "application/json")
queryArgs <- NULL
-
+
body <- NULL
-
+
response <- private$REST$http$exec("GET", url, headers, body,
queryArgs, private$numRetries)
resource <- private$REST$httpParser$parseJSONResponse(response)
-
+
if(!is.null(resource$errors))
stop(resource$errors)
-
+
resource
},
{
endPoint <- stringr::str_interp("collections/${uuid}/used_by")
url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("OAuth2", private$token),
+ headers <- list(Authorization = paste("OAuth2", private$token),
"Content-Type" = "application/json")
queryArgs <- NULL
-
+
body <- NULL
-
+
response <- private$REST$http$exec("GET", url, headers, body,
queryArgs, private$numRetries)
resource <- private$REST$httpParser$parseJSONResponse(response)
-
+
if(!is.null(resource$errors))
stop(resource$errors)
-
+
resource
},
{
endPoint <- stringr::str_interp("collections/${uuid}/trash")
url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("OAuth2", private$token),
+ headers <- list(Authorization = paste("OAuth2", private$token),
"Content-Type" = "application/json")
queryArgs <- NULL
-
+
body <- NULL
-
+
response <- private$REST$http$exec("POST", url, headers, body,
queryArgs, private$numRetries)
resource <- private$REST$httpParser$parseJSONResponse(response)
-
+
if(!is.null(resource$errors))
stop(resource$errors)
-
+
resource
},
{
endPoint <- stringr::str_interp("collections/${uuid}/untrash")
url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("OAuth2", private$token),
+ headers <- list(Authorization = paste("OAuth2", private$token),
"Content-Type" = "application/json")
queryArgs <- NULL
-
+
body <- NULL
-
+
response <- private$REST$http$exec("POST", url, headers, body,
queryArgs, private$numRetries)
resource <- private$REST$httpParser$parseJSONResponse(response)
-
+
if(!is.null(resource$errors))
stop(resource$errors)
-
+
resource
},
{
endPoint <- stringr::str_interp("collections")
url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("OAuth2", private$token),
+ headers <- list(Authorization = paste("OAuth2", private$token),
"Content-Type" = "application/json")
queryArgs <- list(filters = filters, where = where,
order = order, select = select, distinct = distinct,
limit = limit, offset = offset, count = count,
include_trash = include_trash)
-
+
body <- NULL
-
+
response <- private$REST$http$exec("GET", url, headers, body,
queryArgs, private$numRetries)
resource <- private$REST$httpParser$parseJSONResponse(response)
-
+
if(!is.null(resource$errors))
stop(resource$errors)
-
+
resource
},
{
endPoint <- stringr::str_interp("humans/${uuid}")
url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("OAuth2", private$token),
+ headers <- list(Authorization = paste("OAuth2", private$token),
"Content-Type" = "application/json")
queryArgs <- NULL
-
+
body <- NULL
-
+
response <- private$REST$http$exec("GET", url, headers, body,
queryArgs, private$numRetries)
resource <- private$REST$httpParser$parseJSONResponse(response)
-
+
if(!is.null(resource$errors))
stop(resource$errors)
-
+
resource
},
{
endPoint <- stringr::str_interp("humans")
url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("OAuth2", private$token),
+ headers <- list(Authorization = paste("OAuth2", private$token),
"Content-Type" = "application/json")
queryArgs <- list(ensure_unique_name = ensure_unique_name)
-
+
if(length(human) > 0)
- body <- jsonlite::toJSON(list(human = human),
+ body <- jsonlite::toJSON(list(human = human),
auto_unbox = TRUE)
else
body <- NULL
-
+
response <- private$REST$http$exec("POST", url, headers, body,
queryArgs, private$numRetries)
resource <- private$REST$httpParser$parseJSONResponse(response)
-
+
if(!is.null(resource$errors))
stop(resource$errors)
-
+
resource
},
{
endPoint <- stringr::str_interp("humans/${uuid}")
url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("OAuth2", private$token),
+ headers <- list(Authorization = paste("OAuth2", private$token),
"Content-Type" = "application/json")
queryArgs <- NULL
-
+
if(length(human) > 0)
- body <- jsonlite::toJSON(list(human = human),
+ body <- jsonlite::toJSON(list(human = human),
auto_unbox = TRUE)
else
body <- NULL
-
+
response <- private$REST$http$exec("PUT", url, headers, body,
queryArgs, private$numRetries)
resource <- private$REST$httpParser$parseJSONResponse(response)
-
+
if(!is.null(resource$errors))
stop(resource$errors)
-
+
resource
},
{
endPoint <- stringr::str_interp("humans/${uuid}")
url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("OAuth2", private$token),
+ headers <- list(Authorization = paste("OAuth2", private$token),
"Content-Type" = "application/json")
queryArgs <- NULL
-
+
body <- NULL
-
+
response <- private$REST$http$exec("DELETE", url, headers, body,
queryArgs, private$numRetries)
resource <- private$REST$httpParser$parseJSONResponse(response)
-
+
if(!is.null(resource$errors))
stop(resource$errors)
-
+
resource
},
{
endPoint <- stringr::str_interp("humans")
url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("OAuth2", private$token),
+ headers <- list(Authorization = paste("OAuth2", private$token),
"Content-Type" = "application/json")
queryArgs <- list(filters = filters, where = where,
order = order, select = select, distinct = distinct,
limit = limit, offset = offset, count = count)
-
+
body <- NULL
-
+
response <- private$REST$http$exec("GET", url, headers, body,
queryArgs, private$numRetries)
resource <- private$REST$httpParser$parseJSONResponse(response)
-
+
if(!is.null(resource$errors))
stop(resource$errors)
-
+
resource
},
{
endPoint <- stringr::str_interp("job_tasks/${uuid}")
url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("OAuth2", private$token),
+ headers <- list(Authorization = paste("OAuth2", private$token),
"Content-Type" = "application/json")
queryArgs <- NULL
-
+
body <- NULL
-
+
response <- private$REST$http$exec("GET", url, headers, body,
queryArgs, private$numRetries)
resource <- private$REST$httpParser$parseJSONResponse(response)
-
+
if(!is.null(resource$errors))
stop(resource$errors)
-
+
resource
},
{
endPoint <- stringr::str_interp("job_tasks")
url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("OAuth2", private$token),
+ headers <- list(Authorization = paste("OAuth2", private$token),
"Content-Type" = "application/json")
queryArgs <- list(ensure_unique_name = ensure_unique_name)
-
+
if(length(jobtask) > 0)
- body <- jsonlite::toJSON(list(jobtask = jobtask),
+ body <- jsonlite::toJSON(list(jobtask = jobtask),
auto_unbox = TRUE)
else
body <- NULL
-
+
response <- private$REST$http$exec("POST", url, headers, body,
queryArgs, private$numRetries)
resource <- private$REST$httpParser$parseJSONResponse(response)
-
+
if(!is.null(resource$errors))
stop(resource$errors)
-
+
resource
},
{
endPoint <- stringr::str_interp("job_tasks/${uuid}")
url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("OAuth2", private$token),
+ headers <- list(Authorization = paste("OAuth2", private$token),
"Content-Type" = "application/json")
queryArgs <- NULL
-
+
if(length(jobtask) > 0)
- body <- jsonlite::toJSON(list(jobtask = jobtask),
+ body <- jsonlite::toJSON(list(jobtask = jobtask),
auto_unbox = TRUE)
else
body <- NULL
-
+
response <- private$REST$http$exec("PUT", url, headers, body,
queryArgs, private$numRetries)
resource <- private$REST$httpParser$parseJSONResponse(response)
-
+
if(!is.null(resource$errors))
stop(resource$errors)
-
+
resource
},
{
endPoint <- stringr::str_interp("job_tasks/${uuid}")
url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("OAuth2", private$token),
+ headers <- list(Authorization = paste("OAuth2", private$token),
"Content-Type" = "application/json")
queryArgs <- NULL
-
+
body <- NULL
-
+
response <- private$REST$http$exec("DELETE", url, headers, body,
queryArgs, private$numRetries)
resource <- private$REST$httpParser$parseJSONResponse(response)
-
+
if(!is.null(resource$errors))
stop(resource$errors)
-
+
resource
},
{
endPoint <- stringr::str_interp("job_tasks")
url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("OAuth2", private$token),
+ headers <- list(Authorization = paste("OAuth2", private$token),
"Content-Type" = "application/json")
queryArgs <- list(filters = filters, where = where,
order = order, select = select, distinct = distinct,
limit = limit, offset = offset, count = count)
-
+
body <- NULL
-
+
response <- private$REST$http$exec("GET", url, headers, body,
queryArgs, private$numRetries)
resource <- private$REST$httpParser$parseJSONResponse(response)
-
+
if(!is.null(resource$errors))
stop(resource$errors)
-
+
resource
},
- links.get = function(uuid)
+ jobs.get = function(uuid)
{
- endPoint <- stringr::str_interp("links/${uuid}")
+ endPoint <- stringr::str_interp("jobs/${uuid}")
url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("OAuth2", private$token),
+ headers <- list(Authorization = paste("OAuth2", private$token),
"Content-Type" = "application/json")
queryArgs <- NULL
-
+
body <- NULL
-
+
response <- private$REST$http$exec("GET", url, headers, body,
queryArgs, private$numRetries)
resource <- private$REST$httpParser$parseJSONResponse(response)
-
+
if(!is.null(resource$errors))
stop(resource$errors)
-
+
resource
},
- links.create = function(link, ensure_unique_name = "false")
+ jobs.create = function(job, ensure_unique_name = "false",
+ find_or_create = "false", filters = NULL,
+ minimum_script_version = NULL, exclude_script_versions = NULL)
{
- endPoint <- stringr::str_interp("links")
+ endPoint <- stringr::str_interp("jobs")
url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("OAuth2", private$token),
+ headers <- list(Authorization = paste("OAuth2", private$token),
"Content-Type" = "application/json")
- queryArgs <- list(ensure_unique_name = ensure_unique_name)
-
- if(length(link) > 0)
- body <- jsonlite::toJSON(list(link = link),
+ queryArgs <- list(ensure_unique_name = ensure_unique_name,
+ find_or_create = find_or_create, filters = filters,
+ minimum_script_version = minimum_script_version,
+ exclude_script_versions = exclude_script_versions)
+
+ if(length(job) > 0)
+ body <- jsonlite::toJSON(list(job = job),
auto_unbox = TRUE)
else
body <- NULL
-
+
response <- private$REST$http$exec("POST", url, headers, body,
queryArgs, private$numRetries)
resource <- private$REST$httpParser$parseJSONResponse(response)
-
+
if(!is.null(resource$errors))
stop(resource$errors)
-
+
resource
},
- links.update = function(link, uuid)
+ jobs.update = function(job, uuid)
{
- endPoint <- stringr::str_interp("links/${uuid}")
+ endPoint <- stringr::str_interp("jobs/${uuid}")
url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("OAuth2", private$token),
+ headers <- list(Authorization = paste("OAuth2", private$token),
"Content-Type" = "application/json")
queryArgs <- NULL
-
- if(length(link) > 0)
- body <- jsonlite::toJSON(list(link = link),
+
+ if(length(job) > 0)
+ body <- jsonlite::toJSON(list(job = job),
auto_unbox = TRUE)
else
body <- NULL
-
+
response <- private$REST$http$exec("PUT", url, headers, body,
queryArgs, private$numRetries)
resource <- private$REST$httpParser$parseJSONResponse(response)
-
+
if(!is.null(resource$errors))
stop(resource$errors)
-
+
resource
},
- links.delete = function(uuid)
+ jobs.delete = function(uuid)
{
- endPoint <- stringr::str_interp("links/${uuid}")
+ endPoint <- stringr::str_interp("jobs/${uuid}")
url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("OAuth2", private$token),
+ headers <- list(Authorization = paste("OAuth2", private$token),
"Content-Type" = "application/json")
queryArgs <- NULL
-
+
body <- NULL
-
+
response <- private$REST$http$exec("DELETE", url, headers, body,
queryArgs, private$numRetries)
resource <- private$REST$httpParser$parseJSONResponse(response)
-
+
if(!is.null(resource$errors))
stop(resource$errors)
-
+
resource
},
- links.list = function(filters = NULL, where = NULL,
+ jobs.queue = function(filters = NULL, where = NULL,
order = NULL, select = NULL, distinct = NULL,
limit = "100", offset = "0", count = "exact")
{
- endPoint <- stringr::str_interp("links")
+ endPoint <- stringr::str_interp("jobs/queue")
url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("OAuth2", private$token),
+ headers <- list(Authorization = paste("OAuth2", private$token),
"Content-Type" = "application/json")
queryArgs <- list(filters = filters, where = where,
order = order, select = select, distinct = distinct,
limit = limit, offset = offset, count = count)
-
+
body <- NULL
-
+
response <- private$REST$http$exec("GET", url, headers, body,
queryArgs, private$numRetries)
resource <- private$REST$httpParser$parseJSONResponse(response)
-
+
if(!is.null(resource$errors))
stop(resource$errors)
-
+
resource
},
- links.get_permissions = function(uuid)
+ jobs.queue_size = function()
{
- endPoint <- stringr::str_interp("permissions/${uuid}")
+ endPoint <- stringr::str_interp("jobs/queue_size")
url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("OAuth2", private$token),
+ headers <- list(Authorization = paste("OAuth2", private$token),
"Content-Type" = "application/json")
queryArgs <- NULL
-
+
body <- NULL
-
+
response <- private$REST$http$exec("GET", url, headers, body,
queryArgs, private$numRetries)
resource <- private$REST$httpParser$parseJSONResponse(response)
-
+
if(!is.null(resource$errors))
stop(resource$errors)
-
+
resource
},
- jobs.get = function(uuid)
+ jobs.cancel = function(uuid)
{
- endPoint <- stringr::str_interp("jobs/${uuid}")
+ endPoint <- stringr::str_interp("jobs/${uuid}/cancel")
url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("OAuth2", private$token),
+ headers <- list(Authorization = paste("OAuth2", private$token),
"Content-Type" = "application/json")
queryArgs <- NULL
-
+
body <- NULL
-
- response <- private$REST$http$exec("GET", url, headers, body,
+
+ response <- private$REST$http$exec("POST", url, headers, body,
queryArgs, private$numRetries)
resource <- private$REST$httpParser$parseJSONResponse(response)
-
+
if(!is.null(resource$errors))
stop(resource$errors)
-
+
resource
},
- jobs.create = function(job, ensure_unique_name = "false",
- find_or_create = "false", filters = NULL,
- minimum_script_version = NULL, exclude_script_versions = NULL)
+ jobs.lock = function(uuid)
{
- endPoint <- stringr::str_interp("jobs")
+ endPoint <- stringr::str_interp("jobs/${uuid}/lock")
url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("OAuth2", private$token),
+ headers <- list(Authorization = paste("OAuth2", private$token),
"Content-Type" = "application/json")
- queryArgs <- list(ensure_unique_name = ensure_unique_name,
- find_or_create = find_or_create, filters = filters,
- minimum_script_version = minimum_script_version,
- exclude_script_versions = exclude_script_versions)
-
- if(length(job) > 0)
- body <- jsonlite::toJSON(list(job = job),
- auto_unbox = TRUE)
- else
- body <- NULL
-
+ queryArgs <- NULL
+
+ body <- NULL
+
response <- private$REST$http$exec("POST", url, headers, body,
queryArgs, private$numRetries)
resource <- private$REST$httpParser$parseJSONResponse(response)
-
+
if(!is.null(resource$errors))
stop(resource$errors)
-
+
resource
},
- jobs.update = function(job, uuid)
+ jobs.list = function(filters = NULL, where = NULL,
+ order = NULL, select = NULL, distinct = NULL,
+ limit = "100", offset = "0", count = "exact")
{
- endPoint <- stringr::str_interp("jobs/${uuid}")
+ endPoint <- stringr::str_interp("jobs")
url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("OAuth2", private$token),
+ headers <- list(Authorization = paste("OAuth2", private$token),
"Content-Type" = "application/json")
- queryArgs <- NULL
-
- if(length(job) > 0)
- body <- jsonlite::toJSON(list(job = job),
- auto_unbox = TRUE)
- else
- body <- NULL
-
- response <- private$REST$http$exec("PUT", url, headers, body,
+ queryArgs <- list(filters = filters, where = where,
+ order = order, select = select, distinct = distinct,
+ limit = limit, offset = offset, count = count)
+
+ body <- NULL
+
+ response <- private$REST$http$exec("GET", url, headers, body,
queryArgs, private$numRetries)
resource <- private$REST$httpParser$parseJSONResponse(response)
-
+
if(!is.null(resource$errors))
stop(resource$errors)
-
+
resource
},
- jobs.delete = function(uuid)
+ keep_disks.get = function(uuid)
{
- endPoint <- stringr::str_interp("jobs/${uuid}")
+ endPoint <- stringr::str_interp("keep_disks/${uuid}")
url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("OAuth2", private$token),
+ headers <- list(Authorization = paste("OAuth2", private$token),
"Content-Type" = "application/json")
queryArgs <- NULL
-
+
body <- NULL
-
- response <- private$REST$http$exec("DELETE", url, headers, body,
+
+ response <- private$REST$http$exec("GET", url, headers, body,
queryArgs, private$numRetries)
resource <- private$REST$httpParser$parseJSONResponse(response)
-
+
if(!is.null(resource$errors))
stop(resource$errors)
-
+
resource
},
- jobs.queue = function(filters = NULL, where = NULL,
- order = NULL, select = NULL, distinct = NULL,
- limit = "100", offset = "0", count = "exact")
+ keep_disks.create = function(keepdisk, ensure_unique_name = "false")
{
- endPoint <- stringr::str_interp("jobs/queue")
+ endPoint <- stringr::str_interp("keep_disks")
url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("OAuth2", private$token),
+ headers <- list(Authorization = paste("OAuth2", private$token),
"Content-Type" = "application/json")
- queryArgs <- list(filters = filters, where = where,
- order = order, select = select, distinct = distinct,
- limit = limit, offset = offset, count = count)
-
- body <- NULL
-
- response <- private$REST$http$exec("GET", url, headers, body,
+ queryArgs <- list(ensure_unique_name = ensure_unique_name)
+
+ if(length(keepdisk) > 0)
+ body <- jsonlite::toJSON(list(keepdisk = keepdisk),
+ auto_unbox = TRUE)
+ else
+ body <- NULL
+
+ response <- private$REST$http$exec("POST", url, headers, body,
queryArgs, private$numRetries)
resource <- private$REST$httpParser$parseJSONResponse(response)
-
+
if(!is.null(resource$errors))
stop(resource$errors)
-
+
resource
},
- jobs.queue_size = function()
+ keep_disks.update = function(keepdisk, uuid)
{
- endPoint <- stringr::str_interp("jobs/queue_size")
+ endPoint <- stringr::str_interp("keep_disks/${uuid}")
url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("OAuth2", private$token),
+ headers <- list(Authorization = paste("OAuth2", private$token),
"Content-Type" = "application/json")
queryArgs <- NULL
-
- body <- NULL
-
- response <- private$REST$http$exec("GET", url, headers, body,
+
+ if(length(keepdisk) > 0)
+ body <- jsonlite::toJSON(list(keepdisk = keepdisk),
+ auto_unbox = TRUE)
+ else
+ body <- NULL
+
+ response <- private$REST$http$exec("PUT", url, headers, body,
queryArgs, private$numRetries)
resource <- private$REST$httpParser$parseJSONResponse(response)
-
+
if(!is.null(resource$errors))
stop(resource$errors)
-
+
resource
},
- jobs.cancel = function(uuid)
+ keep_disks.delete = function(uuid)
{
- endPoint <- stringr::str_interp("jobs/${uuid}/cancel")
+ endPoint <- stringr::str_interp("keep_disks/${uuid}")
url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("OAuth2", private$token),
+ headers <- list(Authorization = paste("OAuth2", private$token),
"Content-Type" = "application/json")
queryArgs <- NULL
-
+
body <- NULL
-
- response <- private$REST$http$exec("POST", url, headers, body,
+
+ response <- private$REST$http$exec("DELETE", url, headers, body,
queryArgs, private$numRetries)
resource <- private$REST$httpParser$parseJSONResponse(response)
-
+
if(!is.null(resource$errors))
stop(resource$errors)
-
+
resource
},
- jobs.lock = function(uuid)
+ keep_disks.ping = function(uuid = NULL, ping_secret,
+ node_uuid = NULL, filesystem_uuid = NULL,
+ service_host = NULL, service_port, service_ssl_flag)
{
- endPoint <- stringr::str_interp("jobs/${uuid}/lock")
+ endPoint <- stringr::str_interp("keep_disks/ping")
url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("OAuth2", private$token),
+ headers <- list(Authorization = paste("OAuth2", private$token),
"Content-Type" = "application/json")
- queryArgs <- NULL
-
+ queryArgs <- list(uuid = uuid, ping_secret = ping_secret,
+ node_uuid = node_uuid, filesystem_uuid = filesystem_uuid,
+ service_host = service_host, service_port = service_port,
+ service_ssl_flag = service_ssl_flag)
+
body <- NULL
-
+
response <- private$REST$http$exec("POST", url, headers, body,
queryArgs, private$numRetries)
resource <- private$REST$httpParser$parseJSONResponse(response)
-
+
if(!is.null(resource$errors))
stop(resource$errors)
-
+
resource
},
- jobs.list = function(filters = NULL, where = NULL,
- order = NULL, select = NULL, distinct = NULL,
- limit = "100", offset = "0", count = "exact")
+ keep_disks.list = function(filters = NULL,
+ where = NULL, order = NULL, select = NULL,
+ distinct = NULL, limit = "100", offset = "0",
+ count = "exact")
{
- endPoint <- stringr::str_interp("jobs")
+ endPoint <- stringr::str_interp("keep_disks")
url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("OAuth2", private$token),
+ headers <- list(Authorization = paste("OAuth2", private$token),
"Content-Type" = "application/json")
queryArgs <- list(filters = filters, where = where,
order = order, select = select, distinct = distinct,
limit = limit, offset = offset, count = count)
-
+
body <- NULL
-
+
response <- private$REST$http$exec("GET", url, headers, body,
queryArgs, private$numRetries)
resource <- private$REST$httpParser$parseJSONResponse(response)
-
+
if(!is.null(resource$errors))
stop(resource$errors)
-
+
resource
},
- keep_disks.get = function(uuid)
+ nodes.get = function(uuid)
{
- endPoint <- stringr::str_interp("keep_disks/${uuid}")
+ endPoint <- stringr::str_interp("nodes/${uuid}")
url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("OAuth2", private$token),
+ headers <- list(Authorization = paste("OAuth2", private$token),
"Content-Type" = "application/json")
queryArgs <- NULL
-
+
body <- NULL
-
+
response <- private$REST$http$exec("GET", url, headers, body,
queryArgs, private$numRetries)
resource <- private$REST$httpParser$parseJSONResponse(response)
-
+
if(!is.null(resource$errors))
stop(resource$errors)
-
+
resource
},
- keep_disks.create = function(keepdisk, ensure_unique_name = "false")
+ nodes.create = function(node, ensure_unique_name = "false",
+ assign_slot = NULL)
{
- endPoint <- stringr::str_interp("keep_disks")
+ endPoint <- stringr::str_interp("nodes")
url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("OAuth2", private$token),
+ headers <- list(Authorization = paste("OAuth2", private$token),
"Content-Type" = "application/json")
- queryArgs <- list(ensure_unique_name = ensure_unique_name)
-
- if(length(keepdisk) > 0)
- body <- jsonlite::toJSON(list(keepdisk = keepdisk),
+ queryArgs <- list(ensure_unique_name = ensure_unique_name,
+ assign_slot = assign_slot)
+
+ if(length(node) > 0)
+ body <- jsonlite::toJSON(list(node = node),
auto_unbox = TRUE)
else
body <- NULL
-
+
response <- private$REST$http$exec("POST", url, headers, body,
queryArgs, private$numRetries)
resource <- private$REST$httpParser$parseJSONResponse(response)
-
+
if(!is.null(resource$errors))
stop(resource$errors)
-
+
resource
},
- keep_disks.update = function(keepdisk, uuid)
+ nodes.update = function(node, uuid, assign_slot = NULL)
{
- endPoint <- stringr::str_interp("keep_disks/${uuid}")
+ endPoint <- stringr::str_interp("nodes/${uuid}")
url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("OAuth2", private$token),
+ headers <- list(Authorization = paste("OAuth2", private$token),
"Content-Type" = "application/json")
- queryArgs <- NULL
-
- if(length(keepdisk) > 0)
- body <- jsonlite::toJSON(list(keepdisk = keepdisk),
+ queryArgs <- list(assign_slot = assign_slot)
+
+ if(length(node) > 0)
+ body <- jsonlite::toJSON(list(node = node),
auto_unbox = TRUE)
else
body <- NULL
-
+
response <- private$REST$http$exec("PUT", url, headers, body,
queryArgs, private$numRetries)
resource <- private$REST$httpParser$parseJSONResponse(response)
-
+
if(!is.null(resource$errors))
stop(resource$errors)
-
+
resource
},
- keep_disks.delete = function(uuid)
+ nodes.delete = function(uuid)
{
- endPoint <- stringr::str_interp("keep_disks/${uuid}")
+ endPoint <- stringr::str_interp("nodes/${uuid}")
url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("OAuth2", private$token),
+ headers <- list(Authorization = paste("OAuth2", private$token),
"Content-Type" = "application/json")
queryArgs <- NULL
-
+
body <- NULL
-
+
response <- private$REST$http$exec("DELETE", url, headers, body,
queryArgs, private$numRetries)
resource <- private$REST$httpParser$parseJSONResponse(response)
-
+
if(!is.null(resource$errors))
stop(resource$errors)
-
+
resource
},
- keep_disks.ping = function(uuid = NULL, ping_secret,
- node_uuid = NULL, filesystem_uuid = NULL,
- service_host = NULL, service_port, service_ssl_flag)
+ nodes.ping = function(uuid, ping_secret)
{
- endPoint <- stringr::str_interp("keep_disks/ping")
+ endPoint <- stringr::str_interp("nodes/${uuid}/ping")
url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("OAuth2", private$token),
+ headers <- list(Authorization = paste("OAuth2", private$token),
"Content-Type" = "application/json")
- queryArgs <- list(uuid = uuid, ping_secret = ping_secret,
- node_uuid = node_uuid, filesystem_uuid = filesystem_uuid,
- service_host = service_host, service_port = service_port,
- service_ssl_flag = service_ssl_flag)
-
+ queryArgs <- list(ping_secret = ping_secret)
+
body <- NULL
-
+
response <- private$REST$http$exec("POST", url, headers, body,
queryArgs, private$numRetries)
resource <- private$REST$httpParser$parseJSONResponse(response)
-
+
if(!is.null(resource$errors))
stop(resource$errors)
-
+
resource
},
- keep_disks.list = function(filters = NULL,
- where = NULL, order = NULL, select = NULL,
- distinct = NULL, limit = "100", offset = "0",
- count = "exact")
+ nodes.list = function(filters = NULL, where = NULL,
+ order = NULL, select = NULL, distinct = NULL,
+ limit = "100", offset = "0", count = "exact")
{
- endPoint <- stringr::str_interp("keep_disks")
+ endPoint <- stringr::str_interp("nodes")
url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("OAuth2", private$token),
+ headers <- list(Authorization = paste("OAuth2", private$token),
"Content-Type" = "application/json")
queryArgs <- list(filters = filters, where = where,
order = order, select = select, distinct = distinct,
limit = limit, offset = offset, count = count)
-
+
body <- NULL
-
+
response <- private$REST$http$exec("GET", url, headers, body,
queryArgs, private$numRetries)
resource <- private$REST$httpParser$parseJSONResponse(response)
-
+
if(!is.null(resource$errors))
stop(resource$errors)
-
+
resource
},
- keep_services.get = function(uuid)
+ links.get = function(uuid)
{
- endPoint <- stringr::str_interp("keep_services/${uuid}")
+ endPoint <- stringr::str_interp("links/${uuid}")
url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("OAuth2", private$token),
+ headers <- list(Authorization = paste("OAuth2", private$token),
"Content-Type" = "application/json")
queryArgs <- NULL
-
+
body <- NULL
-
+
response <- private$REST$http$exec("GET", url, headers, body,
queryArgs, private$numRetries)
resource <- private$REST$httpParser$parseJSONResponse(response)
-
+
if(!is.null(resource$errors))
stop(resource$errors)
-
+
resource
},
- keep_services.create = function(keepservice,
- ensure_unique_name = "false")
+ links.create = function(link, ensure_unique_name = "false")
{
- endPoint <- stringr::str_interp("keep_services")
+ endPoint <- stringr::str_interp("links")
url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("OAuth2", private$token),
+ headers <- list(Authorization = paste("OAuth2", private$token),
"Content-Type" = "application/json")
queryArgs <- list(ensure_unique_name = ensure_unique_name)
-
- if(length(keepservice) > 0)
- body <- jsonlite::toJSON(list(keepservice = keepservice),
+
+ if(length(link) > 0)
+ body <- jsonlite::toJSON(list(link = link),
auto_unbox = TRUE)
else
body <- NULL
-
+
response <- private$REST$http$exec("POST", url, headers, body,
queryArgs, private$numRetries)
resource <- private$REST$httpParser$parseJSONResponse(response)
-
+
if(!is.null(resource$errors))
stop(resource$errors)
-
+
resource
},
- keep_services.update = function(keepservice, uuid)
+ links.update = function(link, uuid)
{
- endPoint <- stringr::str_interp("keep_services/${uuid}")
+ endPoint <- stringr::str_interp("links/${uuid}")
url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("OAuth2", private$token),
+ headers <- list(Authorization = paste("OAuth2", private$token),
"Content-Type" = "application/json")
queryArgs <- NULL
-
- if(length(keepservice) > 0)
- body <- jsonlite::toJSON(list(keepservice = keepservice),
+
+ if(length(link) > 0)
+ body <- jsonlite::toJSON(list(link = link),
auto_unbox = TRUE)
else
body <- NULL
-
+
response <- private$REST$http$exec("PUT", url, headers, body,
queryArgs, private$numRetries)
resource <- private$REST$httpParser$parseJSONResponse(response)
-
+
if(!is.null(resource$errors))
stop(resource$errors)
-
+
resource
},
- keep_services.delete = function(uuid)
+ links.delete = function(uuid)
{
- endPoint <- stringr::str_interp("keep_services/${uuid}")
+ endPoint <- stringr::str_interp("links/${uuid}")
url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("OAuth2", private$token),
+ headers <- list(Authorization = paste("OAuth2", private$token),
"Content-Type" = "application/json")
queryArgs <- NULL
-
+
body <- NULL
-
+
response <- private$REST$http$exec("DELETE", url, headers, body,
queryArgs, private$numRetries)
resource <- private$REST$httpParser$parseJSONResponse(response)
-
+
if(!is.null(resource$errors))
stop(resource$errors)
-
+
resource
},
- keep_services.accessible = function()
+ links.list = function(filters = NULL, where = NULL,
+ order = NULL, select = NULL, distinct = NULL,
+ limit = "100", offset = "0", count = "exact")
{
- endPoint <- stringr::str_interp("keep_services/accessible")
+ endPoint <- stringr::str_interp("links")
url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("OAuth2", private$token),
+ headers <- list(Authorization = paste("OAuth2", private$token),
"Content-Type" = "application/json")
- queryArgs <- NULL
-
+ queryArgs <- list(filters = filters, where = where,
+ order = order, select = select, distinct = distinct,
+ limit = limit, offset = offset, count = count)
+
body <- NULL
-
+
response <- private$REST$http$exec("GET", url, headers, body,
queryArgs, private$numRetries)
resource <- private$REST$httpParser$parseJSONResponse(response)
-
+
if(!is.null(resource$errors))
stop(resource$errors)
-
+
resource
},
- keep_services.list = function(filters = NULL,
- where = NULL, order = NULL, select = NULL,
- distinct = NULL, limit = "100", offset = "0",
- count = "exact")
+ links.get_permissions = function(uuid)
{
- endPoint <- stringr::str_interp("keep_services")
+ endPoint <- stringr::str_interp("permissions/${uuid}")
url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("OAuth2", private$token),
+ headers <- list(Authorization = paste("OAuth2", private$token),
"Content-Type" = "application/json")
- queryArgs <- list(filters = filters, where = where,
- order = order, select = select, distinct = distinct,
- limit = limit, offset = offset, count = count)
-
+ queryArgs <- NULL
+
body <- NULL
-
+
response <- private$REST$http$exec("GET", url, headers, body,
queryArgs, private$numRetries)
resource <- private$REST$httpParser$parseJSONResponse(response)
-
+
if(!is.null(resource$errors))
stop(resource$errors)
-
+
resource
},
- pipeline_templates.get = function(uuid)
+ keep_services.get = function(uuid)
{
- endPoint <- stringr::str_interp("pipeline_templates/${uuid}")
+ endPoint <- stringr::str_interp("keep_services/${uuid}")
url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("OAuth2", private$token),
+ headers <- list(Authorization = paste("OAuth2", private$token),
"Content-Type" = "application/json")
queryArgs <- NULL
-
+
body <- NULL
-
+
response <- private$REST$http$exec("GET", url, headers, body,
queryArgs, private$numRetries)
resource <- private$REST$httpParser$parseJSONResponse(response)
-
+
if(!is.null(resource$errors))
stop(resource$errors)
-
+
resource
},
- pipeline_templates.create = function(pipelinetemplate,
+ keep_services.create = function(keepservice,
ensure_unique_name = "false")
{
- endPoint <- stringr::str_interp("pipeline_templates")
+ endPoint <- stringr::str_interp("keep_services")
url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("OAuth2", private$token),
+ headers <- list(Authorization = paste("OAuth2", private$token),
"Content-Type" = "application/json")
queryArgs <- list(ensure_unique_name = ensure_unique_name)
-
- if(length(pipelinetemplate) > 0)
- body <- jsonlite::toJSON(list(pipelinetemplate = pipelinetemplate),
+
+ if(length(keepservice) > 0)
+ body <- jsonlite::toJSON(list(keepservice = keepservice),
auto_unbox = TRUE)
else
body <- NULL
-
+
response <- private$REST$http$exec("POST", url, headers, body,
queryArgs, private$numRetries)
resource <- private$REST$httpParser$parseJSONResponse(response)
-
+
if(!is.null(resource$errors))
stop(resource$errors)
-
+
resource
},
- pipeline_templates.update = function(pipelinetemplate, uuid)
+ keep_services.update = function(keepservice, uuid)
{
- endPoint <- stringr::str_interp("pipeline_templates/${uuid}")
+ endPoint <- stringr::str_interp("keep_services/${uuid}")
url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("OAuth2", private$token),
+ headers <- list(Authorization = paste("OAuth2", private$token),
"Content-Type" = "application/json")
queryArgs <- NULL
-
- if(length(pipelinetemplate) > 0)
- body <- jsonlite::toJSON(list(pipelinetemplate = pipelinetemplate),
+
+ if(length(keepservice) > 0)
+ body <- jsonlite::toJSON(list(keepservice = keepservice),
auto_unbox = TRUE)
else
body <- NULL
-
+
response <- private$REST$http$exec("PUT", url, headers, body,
queryArgs, private$numRetries)
resource <- private$REST$httpParser$parseJSONResponse(response)
-
+
if(!is.null(resource$errors))
stop(resource$errors)
-
+
resource
},
- pipeline_templates.delete = function(uuid)
+ keep_services.delete = function(uuid)
{
- endPoint <- stringr::str_interp("pipeline_templates/${uuid}")
+ endPoint <- stringr::str_interp("keep_services/${uuid}")
url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("OAuth2", private$token),
+ headers <- list(Authorization = paste("OAuth2", private$token),
"Content-Type" = "application/json")
queryArgs <- NULL
-
+
body <- NULL
-
+
response <- private$REST$http$exec("DELETE", url, headers, body,
queryArgs, private$numRetries)
resource <- private$REST$httpParser$parseJSONResponse(response)
-
+
if(!is.null(resource$errors))
stop(resource$errors)
+
+ resource
+ },
+ keep_services.accessible = function()
+ {
+ endPoint <- stringr::str_interp("keep_services/accessible")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("OAuth2", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- NULL
+
+ body <- NULL
+
+ response <- private$REST$http$exec("GET", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
resource
},
- pipeline_templates.list = function(filters = NULL,
+ keep_services.list = function(filters = NULL,
where = NULL, order = NULL, select = NULL,
distinct = NULL, limit = "100", offset = "0",
count = "exact")
{
- endPoint <- stringr::str_interp("pipeline_templates")
+ endPoint <- stringr::str_interp("keep_services")
url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("OAuth2", private$token),
+ headers <- list(Authorization = paste("OAuth2", private$token),
"Content-Type" = "application/json")
queryArgs <- list(filters = filters, where = where,
order = order, select = select, distinct = distinct,
limit = limit, offset = offset, count = count)
-
+
body <- NULL
-
+
response <- private$REST$http$exec("GET", url, headers, body,
queryArgs, private$numRetries)
resource <- private$REST$httpParser$parseJSONResponse(response)
-
+
if(!is.null(resource$errors))
stop(resource$errors)
-
+
resource
},
- pipeline_instances.get = function(uuid)
+ pipeline_templates.get = function(uuid)
{
- endPoint <- stringr::str_interp("pipeline_instances/${uuid}")
+ endPoint <- stringr::str_interp("pipeline_templates/${uuid}")
url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("OAuth2", private$token),
+ headers <- list(Authorization = paste("OAuth2", private$token),
"Content-Type" = "application/json")
queryArgs <- NULL
-
+
body <- NULL
-
+
response <- private$REST$http$exec("GET", url, headers, body,
queryArgs, private$numRetries)
resource <- private$REST$httpParser$parseJSONResponse(response)
-
+
if(!is.null(resource$errors))
stop(resource$errors)
-
+
resource
},
- pipeline_instances.create = function(pipelineinstance,
+ pipeline_templates.create = function(pipelinetemplate,
ensure_unique_name = "false")
{
- endPoint <- stringr::str_interp("pipeline_instances")
+ endPoint <- stringr::str_interp("pipeline_templates")
url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("OAuth2", private$token),
+ headers <- list(Authorization = paste("OAuth2", private$token),
"Content-Type" = "application/json")
queryArgs <- list(ensure_unique_name = ensure_unique_name)
-
- if(length(pipelineinstance) > 0)
- body <- jsonlite::toJSON(list(pipelineinstance = pipelineinstance),
+
+ if(length(pipelinetemplate) > 0)
+ body <- jsonlite::toJSON(list(pipelinetemplate = pipelinetemplate),
auto_unbox = TRUE)
else
body <- NULL
-
+
response <- private$REST$http$exec("POST", url, headers, body,
queryArgs, private$numRetries)
resource <- private$REST$httpParser$parseJSONResponse(response)
-
+
if(!is.null(resource$errors))
stop(resource$errors)
-
+
resource
},
- pipeline_instances.update = function(pipelineinstance, uuid)
+ pipeline_templates.update = function(pipelinetemplate, uuid)
{
- endPoint <- stringr::str_interp("pipeline_instances/${uuid}")
+ endPoint <- stringr::str_interp("pipeline_templates/${uuid}")
url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("OAuth2", private$token),
+ headers <- list(Authorization = paste("OAuth2", private$token),
"Content-Type" = "application/json")
queryArgs <- NULL
-
- if(length(pipelineinstance) > 0)
- body <- jsonlite::toJSON(list(pipelineinstance = pipelineinstance),
+
+ if(length(pipelinetemplate) > 0)
+ body <- jsonlite::toJSON(list(pipelinetemplate = pipelinetemplate),
auto_unbox = TRUE)
else
body <- NULL
-
+
response <- private$REST$http$exec("PUT", url, headers, body,
queryArgs, private$numRetries)
resource <- private$REST$httpParser$parseJSONResponse(response)
-
+
if(!is.null(resource$errors))
stop(resource$errors)
-
+
resource
},
- pipeline_instances.delete = function(uuid)
+ pipeline_templates.delete = function(uuid)
{
- endPoint <- stringr::str_interp("pipeline_instances/${uuid}")
+ endPoint <- stringr::str_interp("pipeline_templates/${uuid}")
url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("OAuth2", private$token),
+ headers <- list(Authorization = paste("OAuth2", private$token),
"Content-Type" = "application/json")
queryArgs <- NULL
-
+
body <- NULL
-
+
response <- private$REST$http$exec("DELETE", url, headers, body,
queryArgs, private$numRetries)
resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- pipeline_instances.cancel = function(uuid)
- {
- endPoint <- stringr::str_interp("pipeline_instances/${uuid}/cancel")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("OAuth2", private$token),
- "Content-Type" = "application/json")
- queryArgs <- NULL
-
- body <- NULL
-
- response <- private$REST$http$exec("POST", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
+
if(!is.null(resource$errors))
stop(resource$errors)
-
+
resource
},
- pipeline_instances.list = function(filters = NULL,
+ pipeline_templates.list = function(filters = NULL,
where = NULL, order = NULL, select = NULL,
distinct = NULL, limit = "100", offset = "0",
count = "exact")
{
- endPoint <- stringr::str_interp("pipeline_instances")
+ endPoint <- stringr::str_interp("pipeline_templates")
url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("OAuth2", private$token),
+ headers <- list(Authorization = paste("OAuth2", private$token),
"Content-Type" = "application/json")
queryArgs <- list(filters = filters, where = where,
order = order, select = select, distinct = distinct,
limit = limit, offset = offset, count = count)
-
+
body <- NULL
-
+
response <- private$REST$http$exec("GET", url, headers, body,
queryArgs, private$numRetries)
resource <- private$REST$httpParser$parseJSONResponse(response)
-
+
if(!is.null(resource$errors))
stop(resource$errors)
-
+
resource
},
- nodes.get = function(uuid)
+ pipeline_instances.get = function(uuid)
{
- endPoint <- stringr::str_interp("nodes/${uuid}")
+ endPoint <- stringr::str_interp("pipeline_instances/${uuid}")
url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("OAuth2", private$token),
+ headers <- list(Authorization = paste("OAuth2", private$token),
"Content-Type" = "application/json")
queryArgs <- NULL
-
+
body <- NULL
-
+
response <- private$REST$http$exec("GET", url, headers, body,
queryArgs, private$numRetries)
resource <- private$REST$httpParser$parseJSONResponse(response)
-
+
if(!is.null(resource$errors))
stop(resource$errors)
-
+
resource
},
- nodes.create = function(node, ensure_unique_name = "false",
- assign_slot = NULL)
+ pipeline_instances.create = function(pipelineinstance,
+ ensure_unique_name = "false")
{
- endPoint <- stringr::str_interp("nodes")
+ endPoint <- stringr::str_interp("pipeline_instances")
url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("OAuth2", private$token),
+ headers <- list(Authorization = paste("OAuth2", private$token),
"Content-Type" = "application/json")
- queryArgs <- list(ensure_unique_name = ensure_unique_name,
- assign_slot = assign_slot)
-
- if(length(node) > 0)
- body <- jsonlite::toJSON(list(node = node),
+ queryArgs <- list(ensure_unique_name = ensure_unique_name)
+
+ if(length(pipelineinstance) > 0)
+ body <- jsonlite::toJSON(list(pipelineinstance = pipelineinstance),
auto_unbox = TRUE)
else
body <- NULL
-
+
response <- private$REST$http$exec("POST", url, headers, body,
queryArgs, private$numRetries)
resource <- private$REST$httpParser$parseJSONResponse(response)
-
+
if(!is.null(resource$errors))
stop(resource$errors)
-
+
resource
},
- nodes.update = function(node, uuid, assign_slot = NULL)
+ pipeline_instances.update = function(pipelineinstance, uuid)
{
- endPoint <- stringr::str_interp("nodes/${uuid}")
+ endPoint <- stringr::str_interp("pipeline_instances/${uuid}")
url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("OAuth2", private$token),
+ headers <- list(Authorization = paste("OAuth2", private$token),
"Content-Type" = "application/json")
- queryArgs <- list(assign_slot = assign_slot)
-
- if(length(node) > 0)
- body <- jsonlite::toJSON(list(node = node),
+ queryArgs <- NULL
+
+ if(length(pipelineinstance) > 0)
+ body <- jsonlite::toJSON(list(pipelineinstance = pipelineinstance),
auto_unbox = TRUE)
else
body <- NULL
-
+
response <- private$REST$http$exec("PUT", url, headers, body,
queryArgs, private$numRetries)
resource <- private$REST$httpParser$parseJSONResponse(response)
-
+
if(!is.null(resource$errors))
stop(resource$errors)
-
+
resource
},
- nodes.delete = function(uuid)
+ pipeline_instances.delete = function(uuid)
{
- endPoint <- stringr::str_interp("nodes/${uuid}")
+ endPoint <- stringr::str_interp("pipeline_instances/${uuid}")
url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("OAuth2", private$token),
+ headers <- list(Authorization = paste("OAuth2", private$token),
"Content-Type" = "application/json")
queryArgs <- NULL
-
+
body <- NULL
-
+
response <- private$REST$http$exec("DELETE", url, headers, body,
queryArgs, private$numRetries)
resource <- private$REST$httpParser$parseJSONResponse(response)
-
+
if(!is.null(resource$errors))
stop(resource$errors)
-
+
resource
},
- nodes.ping = function(uuid, ping_secret)
+ pipeline_instances.cancel = function(uuid)
{
- endPoint <- stringr::str_interp("nodes/${uuid}/ping")
+ endPoint <- stringr::str_interp("pipeline_instances/${uuid}/cancel")
url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("OAuth2", private$token),
+ headers <- list(Authorization = paste("OAuth2", private$token),
"Content-Type" = "application/json")
- queryArgs <- list(ping_secret = ping_secret)
-
+ queryArgs <- NULL
+
body <- NULL
-
+
response <- private$REST$http$exec("POST", url, headers, body,
queryArgs, private$numRetries)
resource <- private$REST$httpParser$parseJSONResponse(response)
-
+
if(!is.null(resource$errors))
stop(resource$errors)
-
+
resource
},
- nodes.list = function(filters = NULL, where = NULL,
- order = NULL, select = NULL, distinct = NULL,
- limit = "100", offset = "0", count = "exact")
+ pipeline_instances.list = function(filters = NULL,
+ where = NULL, order = NULL, select = NULL,
+ distinct = NULL, limit = "100", offset = "0",
+ count = "exact")
{
- endPoint <- stringr::str_interp("nodes")
+ endPoint <- stringr::str_interp("pipeline_instances")
url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("OAuth2", private$token),
+ headers <- list(Authorization = paste("OAuth2", private$token),
"Content-Type" = "application/json")
queryArgs <- list(filters = filters, where = where,
order = order, select = select, distinct = distinct,
limit = limit, offset = offset, count = count)
-
+
body <- NULL
-
+
response <- private$REST$http$exec("GET", url, headers, body,
queryArgs, private$numRetries)
resource <- private$REST$httpParser$parseJSONResponse(response)
-
+
if(!is.null(resource$errors))
stop(resource$errors)
-
+
resource
},
{
endPoint <- stringr::str_interp("repositories/${uuid}")
url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("OAuth2", private$token),
+ headers <- list(Authorization = paste("OAuth2", private$token),
"Content-Type" = "application/json")
queryArgs <- NULL
-
+
body <- NULL
-
+
response <- private$REST$http$exec("GET", url, headers, body,
queryArgs, private$numRetries)
resource <- private$REST$httpParser$parseJSONResponse(response)
-
+
if(!is.null(resource$errors))
stop(resource$errors)
-
+
resource
},
{
endPoint <- stringr::str_interp("repositories")
url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("OAuth2", private$token),
+ headers <- list(Authorization = paste("OAuth2", private$token),
"Content-Type" = "application/json")
queryArgs <- list(ensure_unique_name = ensure_unique_name)
-
+
if(length(repository) > 0)
- body <- jsonlite::toJSON(list(repository = repository),
+ body <- jsonlite::toJSON(list(repository = repository),
auto_unbox = TRUE)
else
body <- NULL
-
+
response <- private$REST$http$exec("POST", url, headers, body,
queryArgs, private$numRetries)
resource <- private$REST$httpParser$parseJSONResponse(response)
-
+
if(!is.null(resource$errors))
stop(resource$errors)
-
+
resource
},
{
endPoint <- stringr::str_interp("repositories/${uuid}")
url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("OAuth2", private$token),
+ headers <- list(Authorization = paste("OAuth2", private$token),
"Content-Type" = "application/json")
queryArgs <- NULL
-
+
if(length(repository) > 0)
- body <- jsonlite::toJSON(list(repository = repository),
+ body <- jsonlite::toJSON(list(repository = repository),
auto_unbox = TRUE)
else
body <- NULL
-
+
response <- private$REST$http$exec("PUT", url, headers, body,
queryArgs, private$numRetries)
resource <- private$REST$httpParser$parseJSONResponse(response)
-
+
if(!is.null(resource$errors))
stop(resource$errors)
-
+
resource
},
{
endPoint <- stringr::str_interp("repositories/${uuid}")
url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("OAuth2", private$token),
+ headers <- list(Authorization = paste("OAuth2", private$token),
"Content-Type" = "application/json")
queryArgs <- NULL
-
+
body <- NULL
-
+
response <- private$REST$http$exec("DELETE", url, headers, body,
queryArgs, private$numRetries)
resource <- private$REST$httpParser$parseJSONResponse(response)
-
+
if(!is.null(resource$errors))
stop(resource$errors)
-
+
resource
},
{
endPoint <- stringr::str_interp("repositories/get_all_permissions")
url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("OAuth2", private$token),
+ headers <- list(Authorization = paste("OAuth2", private$token),
"Content-Type" = "application/json")
queryArgs <- NULL
-
+
body <- NULL
-
+
response <- private$REST$http$exec("GET", url, headers, body,
queryArgs, private$numRetries)
resource <- private$REST$httpParser$parseJSONResponse(response)
-
+
if(!is.null(resource$errors))
stop(resource$errors)
-
+
resource
},
{
endPoint <- stringr::str_interp("repositories")
url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("OAuth2", private$token),
+ headers <- list(Authorization = paste("OAuth2", private$token),
"Content-Type" = "application/json")
queryArgs <- list(filters = filters, where = where,
order = order, select = select, distinct = distinct,
limit = limit, offset = offset, count = count)
-
+
body <- NULL
-
+
response <- private$REST$http$exec("GET", url, headers, body,
queryArgs, private$numRetries)
resource <- private$REST$httpParser$parseJSONResponse(response)
-
+
if(!is.null(resource$errors))
stop(resource$errors)
-
+
resource
},
{
endPoint <- stringr::str_interp("specimens/${uuid}")
url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("OAuth2", private$token),
+ headers <- list(Authorization = paste("OAuth2", private$token),
"Content-Type" = "application/json")
queryArgs <- NULL
-
+
body <- NULL
-
+
response <- private$REST$http$exec("GET", url, headers, body,
queryArgs, private$numRetries)
resource <- private$REST$httpParser$parseJSONResponse(response)
-
+
if(!is.null(resource$errors))
stop(resource$errors)
-
+
resource
},
{
endPoint <- stringr::str_interp("specimens")
url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("OAuth2", private$token),
+ headers <- list(Authorization = paste("OAuth2", private$token),
"Content-Type" = "application/json")
queryArgs <- list(ensure_unique_name = ensure_unique_name)
-
+
if(length(specimen) > 0)
- body <- jsonlite::toJSON(list(specimen = specimen),
+ body <- jsonlite::toJSON(list(specimen = specimen),
auto_unbox = TRUE)
else
body <- NULL
-
+
response <- private$REST$http$exec("POST", url, headers, body,
queryArgs, private$numRetries)
resource <- private$REST$httpParser$parseJSONResponse(response)
-
+
if(!is.null(resource$errors))
stop(resource$errors)
-
+
resource
},
{
endPoint <- stringr::str_interp("specimens/${uuid}")
url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("OAuth2", private$token),
+ headers <- list(Authorization = paste("OAuth2", private$token),
"Content-Type" = "application/json")
queryArgs <- NULL
-
+
if(length(specimen) > 0)
- body <- jsonlite::toJSON(list(specimen = specimen),
+ body <- jsonlite::toJSON(list(specimen = specimen),
auto_unbox = TRUE)
else
body <- NULL
-
+
response <- private$REST$http$exec("PUT", url, headers, body,
queryArgs, private$numRetries)
resource <- private$REST$httpParser$parseJSONResponse(response)
-
+
if(!is.null(resource$errors))
stop(resource$errors)
-
+
resource
},
{
endPoint <- stringr::str_interp("specimens/${uuid}")
url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("OAuth2", private$token),
+ headers <- list(Authorization = paste("OAuth2", private$token),
"Content-Type" = "application/json")
queryArgs <- NULL
-
+
body <- NULL
-
+
response <- private$REST$http$exec("DELETE", url, headers, body,
queryArgs, private$numRetries)
resource <- private$REST$httpParser$parseJSONResponse(response)
-
+
if(!is.null(resource$errors))
stop(resource$errors)
-
+
resource
},
{
endPoint <- stringr::str_interp("specimens")
url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("OAuth2", private$token),
+ headers <- list(Authorization = paste("OAuth2", private$token),
"Content-Type" = "application/json")
queryArgs <- list(filters = filters, where = where,
order = order, select = select, distinct = distinct,
limit = limit, offset = offset, count = count)
-
+
body <- NULL
-
+
response <- private$REST$http$exec("GET", url, headers, body,
queryArgs, private$numRetries)
resource <- private$REST$httpParser$parseJSONResponse(response)
-
+
if(!is.null(resource$errors))
stop(resource$errors)
-
+
resource
},
{
endPoint <- stringr::str_interp("logs/${uuid}")
url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("OAuth2", private$token),
+ headers <- list(Authorization = paste("OAuth2", private$token),
"Content-Type" = "application/json")
queryArgs <- NULL
-
+
body <- NULL
-
+
response <- private$REST$http$exec("GET", url, headers, body,
queryArgs, private$numRetries)
resource <- private$REST$httpParser$parseJSONResponse(response)
-
+
if(!is.null(resource$errors))
stop(resource$errors)
-
+
resource
},
{
endPoint <- stringr::str_interp("logs")
url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("OAuth2", private$token),
+ headers <- list(Authorization = paste("OAuth2", private$token),
"Content-Type" = "application/json")
queryArgs <- list(ensure_unique_name = ensure_unique_name)
-
+
if(length(log) > 0)
- body <- jsonlite::toJSON(list(log = log),
+ body <- jsonlite::toJSON(list(log = log),
auto_unbox = TRUE)
else
body <- NULL
-
+
response <- private$REST$http$exec("POST", url, headers, body,
queryArgs, private$numRetries)
resource <- private$REST$httpParser$parseJSONResponse(response)
-
+
if(!is.null(resource$errors))
stop(resource$errors)
-
+
resource
},
{
endPoint <- stringr::str_interp("logs/${uuid}")
url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("OAuth2", private$token),
+ headers <- list(Authorization = paste("OAuth2", private$token),
"Content-Type" = "application/json")
queryArgs <- NULL
-
+
if(length(log) > 0)
- body <- jsonlite::toJSON(list(log = log),
+ body <- jsonlite::toJSON(list(log = log),
auto_unbox = TRUE)
else
body <- NULL
-
+
response <- private$REST$http$exec("PUT", url, headers, body,
queryArgs, private$numRetries)
resource <- private$REST$httpParser$parseJSONResponse(response)
-
+
if(!is.null(resource$errors))
stop(resource$errors)
-
+
resource
},
{
endPoint <- stringr::str_interp("logs/${uuid}")
url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("OAuth2", private$token),
+ headers <- list(Authorization = paste("OAuth2", private$token),
"Content-Type" = "application/json")
queryArgs <- NULL
-
+
body <- NULL
-
+
response <- private$REST$http$exec("DELETE", url, headers, body,
queryArgs, private$numRetries)
resource <- private$REST$httpParser$parseJSONResponse(response)
-
+
if(!is.null(resource$errors))
stop(resource$errors)
-
+
resource
},
{
endPoint <- stringr::str_interp("logs")
url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("OAuth2", private$token),
+ headers <- list(Authorization = paste("OAuth2", private$token),
"Content-Type" = "application/json")
queryArgs <- list(filters = filters, where = where,
order = order, select = select, distinct = distinct,
limit = limit, offset = offset, count = count)
-
+
body <- NULL
-
+
response <- private$REST$http$exec("GET", url, headers, body,
queryArgs, private$numRetries)
resource <- private$REST$httpParser$parseJSONResponse(response)
-
+
if(!is.null(resource$errors))
stop(resource$errors)
-
+
resource
},
{
endPoint <- stringr::str_interp("traits/${uuid}")
url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("OAuth2", private$token),
+ headers <- list(Authorization = paste("OAuth2", private$token),
"Content-Type" = "application/json")
queryArgs <- NULL
-
+
body <- NULL
-
+
response <- private$REST$http$exec("GET", url, headers, body,
queryArgs, private$numRetries)
resource <- private$REST$httpParser$parseJSONResponse(response)
-
+
if(!is.null(resource$errors))
stop(resource$errors)
-
+
resource
},
{
endPoint <- stringr::str_interp("traits")
url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("OAuth2", private$token),
+ headers <- list(Authorization = paste("OAuth2", private$token),
"Content-Type" = "application/json")
queryArgs <- list(ensure_unique_name = ensure_unique_name)
-
+
if(length(trait) > 0)
- body <- jsonlite::toJSON(list(trait = trait),
+ body <- jsonlite::toJSON(list(trait = trait),
auto_unbox = TRUE)
else
body <- NULL
-
+
response <- private$REST$http$exec("POST", url, headers, body,
queryArgs, private$numRetries)
resource <- private$REST$httpParser$parseJSONResponse(response)
-
+
if(!is.null(resource$errors))
stop(resource$errors)
-
+
resource
},
{
endPoint <- stringr::str_interp("traits/${uuid}")
url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("OAuth2", private$token),
+ headers <- list(Authorization = paste("OAuth2", private$token),
"Content-Type" = "application/json")
queryArgs <- NULL
-
+
if(length(trait) > 0)
- body <- jsonlite::toJSON(list(trait = trait),
+ body <- jsonlite::toJSON(list(trait = trait),
auto_unbox = TRUE)
else
body <- NULL
-
+
response <- private$REST$http$exec("PUT", url, headers, body,
queryArgs, private$numRetries)
resource <- private$REST$httpParser$parseJSONResponse(response)
-
+
if(!is.null(resource$errors))
stop(resource$errors)
-
+
resource
},
{
endPoint <- stringr::str_interp("traits/${uuid}")
url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("OAuth2", private$token),
+ headers <- list(Authorization = paste("OAuth2", private$token),
"Content-Type" = "application/json")
queryArgs <- NULL
-
+
body <- NULL
-
+
response <- private$REST$http$exec("DELETE", url, headers, body,
queryArgs, private$numRetries)
resource <- private$REST$httpParser$parseJSONResponse(response)
-
+
if(!is.null(resource$errors))
stop(resource$errors)
-
+
resource
},
{
endPoint <- stringr::str_interp("traits")
url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("OAuth2", private$token),
+ headers <- list(Authorization = paste("OAuth2", private$token),
"Content-Type" = "application/json")
queryArgs <- list(filters = filters, where = where,
order = order, select = select, distinct = distinct,
limit = limit, offset = offset, count = count)
-
+
body <- NULL
-
+
response <- private$REST$http$exec("GET", url, headers, body,
queryArgs, private$numRetries)
resource <- private$REST$httpParser$parseJSONResponse(response)
-
+
if(!is.null(resource$errors))
stop(resource$errors)
-
+
resource
},
{
endPoint <- stringr::str_interp("virtual_machines/${uuid}")
url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("OAuth2", private$token),
+ headers <- list(Authorization = paste("OAuth2", private$token),
"Content-Type" = "application/json")
queryArgs <- NULL
-
+
body <- NULL
-
+
response <- private$REST$http$exec("GET", url, headers, body,
queryArgs, private$numRetries)
resource <- private$REST$httpParser$parseJSONResponse(response)
-
+
if(!is.null(resource$errors))
stop(resource$errors)
-
+
resource
},
{
endPoint <- stringr::str_interp("virtual_machines")
url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("OAuth2", private$token),
+ headers <- list(Authorization = paste("OAuth2", private$token),
"Content-Type" = "application/json")
queryArgs <- list(ensure_unique_name = ensure_unique_name)
-
+
if(length(virtualmachine) > 0)
- body <- jsonlite::toJSON(list(virtualmachine = virtualmachine),
+ body <- jsonlite::toJSON(list(virtualmachine = virtualmachine),
auto_unbox = TRUE)
else
body <- NULL
-
+
response <- private$REST$http$exec("POST", url, headers, body,
queryArgs, private$numRetries)
resource <- private$REST$httpParser$parseJSONResponse(response)
-
+
if(!is.null(resource$errors))
stop(resource$errors)
-
+
resource
},
{
endPoint <- stringr::str_interp("virtual_machines/${uuid}")
url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("OAuth2", private$token),
+ headers <- list(Authorization = paste("OAuth2", private$token),
"Content-Type" = "application/json")
queryArgs <- NULL
-
+
if(length(virtualmachine) > 0)
- body <- jsonlite::toJSON(list(virtualmachine = virtualmachine),
+ body <- jsonlite::toJSON(list(virtualmachine = virtualmachine),
auto_unbox = TRUE)
else
body <- NULL
-
+
response <- private$REST$http$exec("PUT", url, headers, body,
queryArgs, private$numRetries)
resource <- private$REST$httpParser$parseJSONResponse(response)
-
+
if(!is.null(resource$errors))
stop(resource$errors)
-
+
resource
},
{
endPoint <- stringr::str_interp("virtual_machines/${uuid}")
url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("OAuth2", private$token),
+ headers <- list(Authorization = paste("OAuth2", private$token),
"Content-Type" = "application/json")
queryArgs <- NULL
-
+
body <- NULL
-
+
response <- private$REST$http$exec("DELETE", url, headers, body,
queryArgs, private$numRetries)
resource <- private$REST$httpParser$parseJSONResponse(response)
-
+
if(!is.null(resource$errors))
stop(resource$errors)
-
+
resource
},
{
endPoint <- stringr::str_interp("virtual_machines/${uuid}/logins")
url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("OAuth2", private$token),
+ headers <- list(Authorization = paste("OAuth2", private$token),
"Content-Type" = "application/json")
queryArgs <- NULL
-
+
body <- NULL
-
+
response <- private$REST$http$exec("GET", url, headers, body,
queryArgs, private$numRetries)
resource <- private$REST$httpParser$parseJSONResponse(response)
-
+
if(!is.null(resource$errors))
stop(resource$errors)
-
+
resource
},
{
endPoint <- stringr::str_interp("virtual_machines/get_all_logins")
url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("OAuth2", private$token),
+ headers <- list(Authorization = paste("OAuth2", private$token),
"Content-Type" = "application/json")
queryArgs <- NULL
-
+
body <- NULL
-
+
response <- private$REST$http$exec("GET", url, headers, body,
queryArgs, private$numRetries)
resource <- private$REST$httpParser$parseJSONResponse(response)
-
+
if(!is.null(resource$errors))
stop(resource$errors)
-
+
resource
},
{
endPoint <- stringr::str_interp("virtual_machines")
url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("OAuth2", private$token),
+ headers <- list(Authorization = paste("OAuth2", private$token),
"Content-Type" = "application/json")
queryArgs <- list(filters = filters, where = where,
order = order, select = select, distinct = distinct,
limit = limit, offset = offset, count = count)
-
+
body <- NULL
-
+
response <- private$REST$http$exec("GET", url, headers, body,
queryArgs, private$numRetries)
resource <- private$REST$httpParser$parseJSONResponse(response)
-
+
if(!is.null(resource$errors))
stop(resource$errors)
-
+
resource
},
{
endPoint <- stringr::str_interp("workflows/${uuid}")
url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("OAuth2", private$token),
+ headers <- list(Authorization = paste("OAuth2", private$token),
"Content-Type" = "application/json")
queryArgs <- NULL
-
+
body <- NULL
-
+
response <- private$REST$http$exec("GET", url, headers, body,
queryArgs, private$numRetries)
resource <- private$REST$httpParser$parseJSONResponse(response)
-
+
if(!is.null(resource$errors))
stop(resource$errors)
-
+
resource
},
{
endPoint <- stringr::str_interp("workflows")
url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("OAuth2", private$token),
+ headers <- list(Authorization = paste("OAuth2", private$token),
"Content-Type" = "application/json")
queryArgs <- list(ensure_unique_name = ensure_unique_name)
-
+
if(length(workflow) > 0)
- body <- jsonlite::toJSON(list(workflow = workflow),
+ body <- jsonlite::toJSON(list(workflow = workflow),
auto_unbox = TRUE)
else
body <- NULL
-
+
response <- private$REST$http$exec("POST", url, headers, body,
queryArgs, private$numRetries)
resource <- private$REST$httpParser$parseJSONResponse(response)
-
+
if(!is.null(resource$errors))
stop(resource$errors)
-
+
resource
},
{
endPoint <- stringr::str_interp("workflows/${uuid}")
url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("OAuth2", private$token),
+ headers <- list(Authorization = paste("OAuth2", private$token),
"Content-Type" = "application/json")
queryArgs <- NULL
-
+
if(length(workflow) > 0)
- body <- jsonlite::toJSON(list(workflow = workflow),
+ body <- jsonlite::toJSON(list(workflow = workflow),
auto_unbox = TRUE)
else
body <- NULL
-
+
response <- private$REST$http$exec("PUT", url, headers, body,
queryArgs, private$numRetries)
resource <- private$REST$httpParser$parseJSONResponse(response)
-
+
if(!is.null(resource$errors))
stop(resource$errors)
-
+
resource
},
{
endPoint <- stringr::str_interp("workflows/${uuid}")
url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("OAuth2", private$token),
+ headers <- list(Authorization = paste("OAuth2", private$token),
"Content-Type" = "application/json")
queryArgs <- NULL
-
+
body <- NULL
-
+
response <- private$REST$http$exec("DELETE", url, headers, body,
queryArgs, private$numRetries)
resource <- private$REST$httpParser$parseJSONResponse(response)
-
+
if(!is.null(resource$errors))
stop(resource$errors)
-
+
resource
},
{
endPoint <- stringr::str_interp("workflows")
url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("OAuth2", private$token),
+ headers <- list(Authorization = paste("OAuth2", private$token),
"Content-Type" = "application/json")
queryArgs <- list(filters = filters, where = where,
order = order, select = select, distinct = distinct,
limit = limit, offset = offset, count = count)
-
+
body <- NULL
-
+
response <- private$REST$http$exec("GET", url, headers, body,
queryArgs, private$numRetries)
resource <- private$REST$httpParser$parseJSONResponse(response)
-
+
if(!is.null(resource$errors))
stop(resource$errors)
-
+
resource
},
{
endPoint <- stringr::str_interp("groups/${uuid}")
url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("OAuth2", private$token),
+ headers <- list(Authorization = paste("OAuth2", private$token),
"Content-Type" = "application/json")
queryArgs <- NULL
-
+
body <- NULL
-
+
response <- private$REST$http$exec("GET", url, headers, body,
queryArgs, private$numRetries)
resource <- private$REST$httpParser$parseJSONResponse(response)
-
+
if(!is.null(resource$errors))
stop(resource$errors)
-
+
resource
},
{
endPoint <- stringr::str_interp("groups")
url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("OAuth2", private$token),
+ headers <- list(Authorization = paste("OAuth2", private$token),
"Content-Type" = "application/json")
queryArgs <- list(ensure_unique_name = ensure_unique_name)
-
+
if(length(group) > 0)
- body <- jsonlite::toJSON(list(group = group),
+ body <- jsonlite::toJSON(list(group = group),
auto_unbox = TRUE)
else
body <- NULL
-
+
response <- private$REST$http$exec("POST", url, headers, body,
queryArgs, private$numRetries)
resource <- private$REST$httpParser$parseJSONResponse(response)
-
+
if(!is.null(resource$errors))
stop(resource$errors)
-
+
resource
},
{
endPoint <- stringr::str_interp("groups/${uuid}")
url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("OAuth2", private$token),
+ headers <- list(Authorization = paste("OAuth2", private$token),
"Content-Type" = "application/json")
queryArgs <- NULL
-
+
if(length(group) > 0)
- body <- jsonlite::toJSON(list(group = group),
+ body <- jsonlite::toJSON(list(group = group),
auto_unbox = TRUE)
else
body <- NULL
-
+
response <- private$REST$http$exec("PUT", url, headers, body,
queryArgs, private$numRetries)
resource <- private$REST$httpParser$parseJSONResponse(response)
-
+
if(!is.null(resource$errors))
stop(resource$errors)
-
+
resource
},
{
endPoint <- stringr::str_interp("groups/${uuid}")
url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("OAuth2", private$token),
+ headers <- list(Authorization = paste("OAuth2", private$token),
"Content-Type" = "application/json")
queryArgs <- NULL
-
+
body <- NULL
-
+
response <- private$REST$http$exec("DELETE", url, headers, body,
queryArgs, private$numRetries)
resource <- private$REST$httpParser$parseJSONResponse(response)
-
+
if(!is.null(resource$errors))
stop(resource$errors)
-
+
resource
},
{
endPoint <- stringr::str_interp("groups/contents")
url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("OAuth2", private$token),
+ headers <- list(Authorization = paste("OAuth2", private$token),
"Content-Type" = "application/json")
queryArgs <- list(filters = filters, where = where,
order = order, distinct = distinct, limit = limit,
offset = offset, count = count, include_trash = include_trash,
uuid = uuid, recursive = recursive)
-
+
body <- NULL
-
+
response <- private$REST$http$exec("GET", url, headers, body,
queryArgs, private$numRetries)
resource <- private$REST$httpParser$parseJSONResponse(response)
-
+
if(!is.null(resource$errors))
stop(resource$errors)
-
+
resource
},
{
endPoint <- stringr::str_interp("groups/${uuid}/trash")
url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("OAuth2", private$token),
+ headers <- list(Authorization = paste("OAuth2", private$token),
"Content-Type" = "application/json")
queryArgs <- NULL
-
+
body <- NULL
-
+
response <- private$REST$http$exec("POST", url, headers, body,
queryArgs, private$numRetries)
resource <- private$REST$httpParser$parseJSONResponse(response)
-
+
if(!is.null(resource$errors))
stop(resource$errors)
-
+
resource
},
{
endPoint <- stringr::str_interp("groups/${uuid}/untrash")
url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("OAuth2", private$token),
+ headers <- list(Authorization = paste("OAuth2", private$token),
"Content-Type" = "application/json")
queryArgs <- NULL
-
+
body <- NULL
-
+
response <- private$REST$http$exec("POST", url, headers, body,
queryArgs, private$numRetries)
resource <- private$REST$httpParser$parseJSONResponse(response)
-
+
if(!is.null(resource$errors))
stop(resource$errors)
-
+
resource
},
{
endPoint <- stringr::str_interp("groups")
url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("OAuth2", private$token),
+ headers <- list(Authorization = paste("OAuth2", private$token),
"Content-Type" = "application/json")
queryArgs <- list(filters = filters, where = where,
order = order, select = select, distinct = distinct,
limit = limit, offset = offset, count = count,
include_trash = include_trash)
-
+
body <- NULL
-
+
response <- private$REST$http$exec("GET", url, headers, body,
queryArgs, private$numRetries)
resource <- private$REST$httpParser$parseJSONResponse(response)
-
+
if(!is.null(resource$errors))
stop(resource$errors)
-
+
resource
},
{
endPoint <- stringr::str_interp("user_agreements/${uuid}")
url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("OAuth2", private$token),
+ headers <- list(Authorization = paste("OAuth2", private$token),
"Content-Type" = "application/json")
queryArgs <- NULL
-
+
body <- NULL
-
+
response <- private$REST$http$exec("GET", url, headers, body,
queryArgs, private$numRetries)
resource <- private$REST$httpParser$parseJSONResponse(response)
-
+
if(!is.null(resource$errors))
stop(resource$errors)
-
+
resource
},
{
endPoint <- stringr::str_interp("user_agreements")
url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("OAuth2", private$token),
+ headers <- list(Authorization = paste("OAuth2", private$token),
"Content-Type" = "application/json")
queryArgs <- list(ensure_unique_name = ensure_unique_name)
-
+
if(length(useragreement) > 0)
- body <- jsonlite::toJSON(list(useragreement = useragreement),
+ body <- jsonlite::toJSON(list(useragreement = useragreement),
auto_unbox = TRUE)
else
body <- NULL
-
+
response <- private$REST$http$exec("POST", url, headers, body,
queryArgs, private$numRetries)
resource <- private$REST$httpParser$parseJSONResponse(response)
-
+
if(!is.null(resource$errors))
stop(resource$errors)
-
+
resource
},
{
endPoint <- stringr::str_interp("user_agreements/${uuid}")
url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("OAuth2", private$token),
+ headers <- list(Authorization = paste("OAuth2", private$token),
"Content-Type" = "application/json")
queryArgs <- NULL
-
+
if(length(useragreement) > 0)
- body <- jsonlite::toJSON(list(useragreement = useragreement),
+ body <- jsonlite::toJSON(list(useragreement = useragreement),
auto_unbox = TRUE)
else
body <- NULL
-
+
response <- private$REST$http$exec("PUT", url, headers, body,
queryArgs, private$numRetries)
resource <- private$REST$httpParser$parseJSONResponse(response)
-
+
if(!is.null(resource$errors))
stop(resource$errors)
-
+
resource
},
{
endPoint <- stringr::str_interp("user_agreements/${uuid}")
url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("OAuth2", private$token),
+ headers <- list(Authorization = paste("OAuth2", private$token),
"Content-Type" = "application/json")
queryArgs <- NULL
-
+
body <- NULL
-
+
response <- private$REST$http$exec("DELETE", url, headers, body,
queryArgs, private$numRetries)
resource <- private$REST$httpParser$parseJSONResponse(response)
-
+
if(!is.null(resource$errors))
stop(resource$errors)
-
+
resource
},
{
endPoint <- stringr::str_interp("user_agreements/signatures")
url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("OAuth2", private$token),
+ headers <- list(Authorization = paste("OAuth2", private$token),
"Content-Type" = "application/json")
queryArgs <- NULL
-
+
body <- NULL
-
+
response <- private$REST$http$exec("GET", url, headers, body,
queryArgs, private$numRetries)
resource <- private$REST$httpParser$parseJSONResponse(response)
-
+
if(!is.null(resource$errors))
stop(resource$errors)
-
+
resource
},
{
endPoint <- stringr::str_interp("user_agreements/sign")
url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("OAuth2", private$token),
+ headers <- list(Authorization = paste("OAuth2", private$token),
"Content-Type" = "application/json")
queryArgs <- NULL
-
+
body <- NULL
-
+
response <- private$REST$http$exec("POST", url, headers, body,
queryArgs, private$numRetries)
resource <- private$REST$httpParser$parseJSONResponse(response)
-
+
if(!is.null(resource$errors))
stop(resource$errors)
-
+
resource
},
{
endPoint <- stringr::str_interp("user_agreements")
url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("OAuth2", private$token),
+ headers <- list(Authorization = paste("OAuth2", private$token),
"Content-Type" = "application/json")
queryArgs <- list(filters = filters, where = where,
order = order, select = select, distinct = distinct,
limit = limit, offset = offset, count = count)
-
+
body <- NULL
-
+
response <- private$REST$http$exec("GET", url, headers, body,
queryArgs, private$numRetries)
resource <- private$REST$httpParser$parseJSONResponse(response)
-
+
if(!is.null(resource$errors))
stop(resource$errors)
-
+
resource
},
{
endPoint <- stringr::str_interp("user_agreements/new")
url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("OAuth2", private$token),
+ headers <- list(Authorization = paste("OAuth2", private$token),
"Content-Type" = "application/json")
queryArgs <- NULL
-
+
body <- NULL
-
+
response <- private$REST$http$exec("GET", url, headers, body,
queryArgs, private$numRetries)
resource <- private$REST$httpParser$parseJSONResponse(response)
-
+
if(!is.null(resource$errors))
stop(resource$errors)
-
+
resource
},
#' \item{flush()}{Write connections content to a file (override current content of the file).}
#' \item{remove(name)}{Removes ArvadosFile or Subcollection specified by name from the subcollection.}
#' \item{getSizeInBytes()}{Returns file size in bytes.}
-#' \item{move(newLocation)}{Moves file to a new location inside collection.}
+#' \item{move(destination)}{Moves file to a new location inside collection.}
+#' \item{copy(destination)}{Copies file to a new location inside collection.}
#' }
#'
#' @name ArvadosFile
#' mytable <- read.table(arvConnection)
#'
#' myFile$move("newFolder/myFile")
+#' myFile$copy("newFolder/myFile")
#' }
NULL
fileSize <- REST$getResourceSize(self$getRelativePath(),
private$collection$uuid)
-
fileSize
},
getCollection = function() private$collection,
- setCollection = function(collection)
+ setCollection = function(collection, setRecursively = TRUE)
{
private$collection <- collection
},
writeResult
},
- move = function(newLocation)
+ move = function(destination)
{
if(is.null(private$collection))
- stop("ArvadosFile doesn't belong to any collection")
+ stop("ArvadosFile doesn't belong to any collection.")
- newLocation <- trimFromEnd(newLocation, "/")
- nameAndPath <- splitToPathAndName(newLocation)
+ destination <- trimFromEnd(destination, "/")
+ nameAndPath <- splitToPathAndName(destination)
newParent <- private$collection$get(nameAndPath$path)
if(is.null(newParent))
- {
- stop("Unable to get destination subcollection")
- }
+ stop("Unable to get destination subcollection.")
childWithSameName <- newParent$get(nameAndPath$name)
private$collection$uuid)
private$dettachFromCurrentParent()
- private$attachToNewParent(newParent)
+ private$attachToNewParent(self, newParent)
+ private$parent <- newParent
private$name <- nameAndPath$name
- "Content moved successfully."
+ self
+ },
+
+ copy = function(destination)
+ {
+ if(is.null(private$collection))
+ stop("ArvadosFile doesn't belong to any collection.")
+
+ destination <- trimFromEnd(destination, "/")
+ nameAndPath <- splitToPathAndName(destination)
+
+ newParent <- private$collection$get(nameAndPath$path)
+
+ if(is.null(newParent))
+ stop("Unable to get destination subcollection.")
+
+ childWithSameName <- newParent$get(nameAndPath$name)
+
+ if(!is.null(childWithSameName))
+ stop("Destination already contains content with same name.")
+
+ REST <- private$collection$getRESTService()
+ REST$copy(self$getRelativePath(),
+ paste0(newParent$getRelativePath(), "/", nameAndPath$name),
+ private$collection$uuid)
+
+ newFile <- self$duplicate(nameAndPath$name)
+ newFile$setCollection(self$getCollection())
+ private$attachToNewParent(newFile, newParent)
+ newFile$setParent(newParent)
+
+ newFile
+ },
+
+ duplicate = function(newName = NULL)
+ {
+ name <- if(!is.null(newName)) newName else private$name
+ newFile <- ArvadosFile$new(name)
+ newFile
}
),
collection = NULL,
buffer = NULL,
- attachToNewParent = function(newParent)
+ attachToNewParent = function(content, newParent)
{
- #Note: We temporary set parents collection to NULL. This will ensure that
- # add method doesn't post file on REST.
+ # We temporary set parents collection to NULL. This will ensure that
+ # add method doesn't post this file on REST.
+ # We also need to set content's collection to NULL because
+ # add method throws exception if we try to add content that already
+ # belongs to a collection.
parentsCollection <- newParent$getCollection()
+ content$setCollection(NULL, setRecursively = FALSE)
newParent$setCollection(NULL, setRecursively = FALSE)
-
- newParent$add(self)
-
+ newParent$add(content)
+ content$setCollection(parentsCollection, setRecursively = FALSE)
newParent$setCollection(parentsCollection, setRecursively = FALSE)
-
- private$parent <- newParent
},
dettachFromCurrentParent = function()
{
- #Note: We temporary set parents collection to NULL. This will ensure that
- # remove method doesn't remove this subcollection from REST.
+ # We temporary set parents collection to NULL. This will ensure that
+ # remove method doesn't remove this file from REST.
parent <- private$parent
parentsCollection <- parent$getCollection()
parent$setCollection(NULL, setRecursively = FALSE)
-
parent$remove(private$name)
-
parent$setCollection(parentsCollection, setRecursively = FALSE)
}
),
relativePath <- paste0("/", relativePath)
}
- cat(paste0("Type: ", "\"", "ArvadosFile", "\""), sep = "\n")
- cat(paste0("Name: ", "\"", x$getName(), "\""), sep = "\n")
- cat(paste0("Relative path: ", "\"", relativePath, "\""), sep = "\n")
- cat(paste0("Collection: ", "\"", collection, "\""), sep = "\n")
+ cat(paste0("Type: ", "\"", "ArvadosFile", "\""), sep = "\n")
+ cat(paste0("Name: ", "\"", x$getName(), "\""), sep = "\n")
+ cat(paste0("Relative path: ", "\"", relativePath, "\""), sep = "\n")
+ cat(paste0("Collection: ", "\"", collection, "\""), sep = "\n")
}
#' @section Methods:
#' \describe{
#' \item{add(content)}{Adds ArvadosFile or Subcollection specified by content to the collection.}
-#' \item{create(fileNames, relativePath = "")}{Creates one or more ArvadosFiles and adds them to the collection at specified path.}
+#' \item{create(files)}{Creates one or more ArvadosFiles and adds them to the collection at specified path.}
#' \item{remove(fileNames)}{Remove one or more files from the collection.}
-#' \item{move(content, newLocation)}{Moves ArvadosFile or Subcollection to another location in the collection.}
+#' \item{move(content, destination)}{Moves ArvadosFile or Subcollection to another location in the collection.}
+#' \item{copy(content, destination)}{Copies ArvadosFile or Subcollection to another location in the collection.}
#' \item{getFileListing()}{Returns collections file content as character vector.}
#' \item{get(relativePath)}{If relativePath is valid, returns ArvadosFile or Subcollection specified by relativePath, else returns NULL.}
#' }
#' arv <- Arvados$new("your Arvados token", "example.arvadosapi.com")
#' collection <- Collection$new(arv, "uuid")
#'
-#' newFile <- ArvadosFile$new("myFile")
-#' collection$add(newFile, "myFolder")
-#'
#' createdFiles <- collection$create(c("main.cpp", lib.dll), "cpp/src/")
#'
#' collection$remove("location/to/my/file.cpp")
public = list(
uuid = NULL,
- # api = NULL,
initialize = function(api, uuid)
{
- # self$api <- api
private$REST <- api$getRESTService()
-
self$uuid <- uuid
-
- private$fileContent <- private$REST$getCollectionContent(uuid)
- private$tree <- CollectionTree$new(private$fileContent, self)
},
add = function(content, relativePath = "")
{
if(is.null(private$tree))
- private$genereateCollectionTreeStructure()
+ private$generateCollectionTreeStructure()
if(relativePath == "" ||
relativePath == "." ||
if("ArvadosFile" %in% class(content) ||
"Subcollection" %in% class(content))
{
+ if(!is.null(content$getCollection()))
+ stop("Content already belongs to a collection.")
+
if(content$getName() == "")
stop("Content has invalid name.")
}
},
- create = function(fileNames, relativePath = "")
+ create = function(files)
{
if(is.null(private$tree))
- private$genereateCollectionTreeStructure()
-
- if(relativePath == "" ||
- relativePath == "." ||
- relativePath == "./")
- {
- subcollection <- private$tree$getTree()
- }
- else
- {
- relativePath <- trimFromEnd(relativePath, "/")
- subcollection <- self$get(relativePath)
- }
-
- if(is.null(subcollection))
- stop(paste("Subcollection", relativePath, "doesn't exist."))
+ private$generateCollectionTreeStructure()
- if(is.character(fileNames))
+ if(is.character(files))
{
- arvadosFiles <- NULL
- sapply(fileNames, function(fileName)
+ sapply(files, function(file)
{
- childWithSameName <- subcollection$get(fileName)
+ childWithSameName <- self$get(file)
if(!is.null(childWithSameName))
stop("Destination already contains file with same name.")
- newFile <- ArvadosFile$new(fileName)
- subcollection$add(newFile)
+ newTreeBranch <- private$tree$createBranch(file)
+ private$tree$addBranch(private$tree$getTree(), newTreeBranch)
- arvadosFiles <<- c(arvadosFiles, newFile)
+ private$REST$create(file, self$uuid)
+ newTreeBranch$setCollection(self)
})
- if(length(arvadosFiles) == 1)
- return(arvadosFiles[[1]])
- else
- return(arvadosFiles)
+ "Created"
}
else
{
stop(paste0("Expected character vector, got ",
- paste0("(", paste0(class(fileNames), collapse = ", "), ")"),
+ paste0("(", paste0(class(files), collapse = ", "), ")"),
"."))
}
},
remove = function(paths)
{
if(is.null(private$tree))
- private$genereateCollectionTreeStructure()
+ private$generateCollectionTreeStructure()
if(is.character(paths))
{
}
},
- move = function(content, newLocation)
+ move = function(content, destination)
{
if(is.null(private$tree))
- private$genereateCollectionTreeStructure()
+ private$generateCollectionTreeStructure()
content <- trimFromEnd(content, "/")
if(is.null(elementToMove))
stop("Content you want to move doesn't exist in the collection.")
- elementToMove$move(newLocation)
+ elementToMove$move(destination)
+ },
+
+ copy = function(content, destination)
+ {
+ if(is.null(private$tree))
+ private$generateCollectionTreeStructure()
+
+ content <- trimFromEnd(content, "/")
+
+ elementToCopy <- self$get(content)
+
+ if(is.null(elementToCopy))
+ stop("Content you want to copy doesn't exist in the collection.")
+
+ elementToCopy$copy(destination)
+ },
+
+ refresh = function()
+ {
+ if(!is.null(private$tree))
+ {
+ private$tree$getTree()$setCollection(NULL, setRecursively = TRUE)
+ private$tree <- NULL
+ }
},
getFileListing = function()
{
if(is.null(private$tree))
- private$genereateCollectionTreeStructure()
+ private$generateCollectionTreeStructure()
content <- private$REST$getCollectionContent(self$uuid)
content[order(tolower(content))]
get = function(relativePath)
{
if(is.null(private$tree))
- private$genereateCollectionTreeStructure()
+ private$generateCollectionTreeStructure()
private$tree$getElement(relativePath)
},
- toJSON = function()
- {
- fields <- sapply(private$classFields, function(field)
- {
- self[[field]]
- }, USE.NAMES = TRUE)
-
- jsonlite::toJSON(list("collection" =
- Filter(Negate(is.null), fields)), auto_unbox = TRUE)
- },
-
- isEmpty = function() {
- fields <- sapply(private$classFields,
- function(field) self[[field]])
-
- if(any(sapply(fields, function(field) !is.null(field) && field != "")))
- FALSE
- else
- TRUE
- },
-
getRESTService = function() private$REST,
setRESTService = function(newRESTService) private$REST <- newRESTService
),
REST = NULL,
tree = NULL,
fileContent = NULL,
- classFields = NULL,
- genereateCollectionTreeStructure = function()
+ generateCollectionTreeStructure = function()
{
if(is.null(self$uuid))
stop("Collection uuid is not defined.")
initialize = function(fileContent, collection)
{
self$pathsList <- fileContent
-
- treeBranches <- sapply(fileContent, function(filePath)
- {
- splitPath <- unlist(strsplit(filePath, "/", fixed = TRUE))
- branch <- private$createBranch(splitPath)
- })
-
+ treeBranches <- sapply(fileContent, function(filePath) self$createBranch(filePath))
root <- Subcollection$new("")
-
- sapply(treeBranches, function(branch)
- {
- private$addBranch(root, branch)
- })
-
+ sapply(treeBranches, function(branch) self$addBranch(root, branch))
root$setCollection(collection)
private$tree <- root
},
- getElement = function(relativePath)
- {
- relativePath <- trimFromStart(relativePath, "./")
- relativePath <- trimFromEnd(relativePath, "/")
-
- if(endsWith(relativePath, "/"))
- relativePath <- substr(relativePath, 0, nchar(relativePath) - 1)
-
- splitPath <- unlist(strsplit(relativePath, "/", fixed = TRUE))
- returnElement <- private$tree
-
- for(pathFragment in splitPath)
- {
- returnElement <- returnElement$get(pathFragment)
-
- if(is.null(returnElement))
- return(NULL)
- }
-
- returnElement
- },
-
- getTree = function() private$tree
- ),
-
- private = list(
-
- tree = NULL,
-
- createBranch = function(splitPath)
+ createBranch = function(filePath)
{
+ splitPath <- unlist(strsplit(filePath, "/", fixed = TRUE))
branch <- NULL
lastElementIndex <- length(splitPath)
if(is.null(child))
{
+ # Make sure we are don't make any REST call while adding child
+ collection <- container$getCollection()
+ container$setCollection(NULL, setRecursively = FALSE)
container$add(node)
+ container$setCollection(collection, setRecursively = FALSE)
}
else
{
# If we encounter that same name again we know
# it's a folder so we need to replace ArvadosFile with Subcollection.
if("ArvadosFile" %in% class(child))
- {
child = private$replaceFileWithSubcollection(child)
- }
- private$addBranch(child, node$getFirst())
+ self$addBranch(child, node$getFirst())
}
},
+ getElement = function(relativePath)
+ {
+ relativePath <- trimFromStart(relativePath, "./")
+ relativePath <- trimFromEnd(relativePath, "/")
+
+ if(endsWith(relativePath, "/"))
+ relativePath <- substr(relativePath, 0, nchar(relativePath) - 1)
+
+ splitPath <- unlist(strsplit(relativePath, "/", fixed = TRUE))
+ returnElement <- private$tree
+
+ for(pathFragment in splitPath)
+ {
+ returnElement <- returnElement$get(pathFragment)
+
+ if(is.null(returnElement))
+ return(NULL)
+ }
+
+ returnElement
+ },
+
+ getTree = function() private$tree
+ ),
+
+ private = list(
+
+ tree = NULL,
+
replaceFileWithSubcollection = function(arvadosFile)
{
subcollection <- Subcollection$new(arvadosFile$getName())
initialize = function()
{
self$validContentTypes <- c("text", "raw")
- self$validVerbs <- c("GET", "POST", "PUT", "DELETE", "PROPFIND", "MOVE")
+ self$validVerbs <- c("GET", "POST", "PUT", "DELETE", "PROPFIND", "MOVE", "COPY")
},
exec = function(verb, url, headers = NULL, body = NULL, queryParams = NULL,
{
collectionURL <- paste0(self$getWebDavHostName(), "c=", uuid, "/")
fromURL <- paste0(collectionURL, from)
- toURL <- paste0(collectionURL, to)
+ toURL <- paste0(collectionURL, trimFromStart(to, "/"))
headers <- list("Authorization" = paste("OAuth2", self$token),
- "Destination" = toURL)
+ "Destination" = toURL)
serverResponse <- self$http$exec("MOVE", fromURL, headers,
retryTimes = self$numRetries)
serverResponse
},
+ copy = function(from, to, uuid)
+ {
+ collectionURL <- paste0(self$getWebDavHostName(), "c=", uuid, "/")
+ fromURL <- paste0(collectionURL, from)
+ toURL <- paste0(collectionURL, trimFromStart(to, "/"))
+
+ headers <- list("Authorization" = paste("OAuth2", self$token),
+ "Destination" = toURL)
+
+ serverResponse <- self$http$exec("COPY", fromURL, headers,
+ retryTimes = self$numRetries)
+
+ if(serverResponse$status_code < 200 || serverResponse$status_code >= 300)
+ stop(paste("Server code:", serverResponse$status_code))
+
+ serverResponse
+ },
+
getCollectionContent = function(uuid)
{
collectionURL <- URLencode(paste0(self$getWebDavHostName(),
#' \item{get(relativePath)}{If relativePath is valid, returns ArvadosFile or Subcollection specified by relativePath, else returns NULL.}
#' \item{getFileListing()}{Returns subcollections file content as character vector.}
#' \item{getSizeInBytes()}{Returns subcollections content size in bytes.}
-#' \item{move(newLocation)}{Moves subcollection to a new location inside collection.}
+#' \item{move(destination)}{Moves subcollection to a new location inside collection.}
+#' \item{copy(destination)}{Copies subcollection to a new location inside collection.}
#' }
#'
#' @name Subcollection
#' myFolder$remove("myFile")
#'
#' myFolder$move("newLocation/myFolder")
+#' myFolder$copy("newLocation/myFolder")
#' }
NULL
if("ArvadosFile" %in% class(content) ||
"Subcollection" %in% class(content))
{
+ if(!is.null(content$getCollection()))
+ stop("Content already belongs to a collection.")
+
if(content$getName() == "")
stop("Content has invalid name.")
return(sum(fileSizes))
},
- move = function(newLocation)
+ move = function(destination)
{
if(is.null(private$collection))
- stop("Subcollection doesn't belong to any collection")
+ stop("Subcollection doesn't belong to any collection.")
- newLocation <- trimFromEnd(newLocation, "/")
- nameAndPath <- splitToPathAndName(newLocation)
+ destination <- trimFromEnd(destination, "/")
+ nameAndPath <- splitToPathAndName(destination)
newParent <- private$collection$get(nameAndPath$path)
if(is.null(newParent))
- {
- stop("Unable to get destination subcollection")
- }
+ stop("Unable to get destination subcollection.")
childWithSameName <- newParent$get(nameAndPath$name)
private$collection$uuid)
private$dettachFromCurrentParent()
- private$attachToNewParent(newParent)
+ private$attachToNewParent(self, newParent)
+ private$parent <- newParent
private$name <- nameAndPath$name
- "Content moved successfully."
+ self
+ },
+
+ copy = function(destination)
+ {
+ if(is.null(private$collection))
+ stop("Subcollection doesn't belong to any collection.")
+
+ destination <- trimFromEnd(destination, "/")
+ nameAndPath <- splitToPathAndName(destination)
+
+ newParent <- private$collection$get(nameAndPath$path)
+
+ if(is.null(newParent) || !("Subcollection" %in% class(newParent)))
+ stop("Unable to get destination subcollection.")
+
+ childWithSameName <- newParent$get(nameAndPath$name)
+
+ if(!is.null(childWithSameName))
+ stop("Destination already contains content with same name.")
+
+ REST <- private$collection$getRESTService()
+ REST$copy(self$getRelativePath(),
+ paste0(newParent$getRelativePath(), "/", nameAndPath$name),
+ private$collection$uuid)
+
+ newContent <- self$duplicate(nameAndPath$name)
+ newContent$setCollection(self$getCollection(), setRecursively = TRUE)
+ newContent$setParent(newParent)
+ private$attachToNewParent(newContent, newParent)
+
+ newContent
+ },
+
+ duplicate = function(newName = NULL)
+ {
+ name <- if(!is.null(newName)) newName else private$name
+ root <- Subcollection$new(name)
+ for(child in private$children)
+ root$add(child$duplicate())
+
+ root
},
get = function(name)
}
},
- attachToNewParent = function(newParent)
+ attachToNewParent = function(content, newParent)
{
- #Note: We temporary set parents collection to NULL. This will ensure that
- # add method doesn't post file on REST.
+ # We temporary set parents collection to NULL. This will ensure that
+ # add method doesn't post this subcollection to REST.
+ # We also need to set content's collection to NULL because
+ # add method throws exception if we try to add content that already
+ # belongs to a collection.
parentsCollection <- newParent$getCollection()
+ content$setCollection(NULL, setRecursively = FALSE)
newParent$setCollection(NULL, setRecursively = FALSE)
-
- newParent$add(self)
-
+ newParent$add(content)
+ content$setCollection(parentsCollection, setRecursively = FALSE)
newParent$setCollection(parentsCollection, setRecursively = FALSE)
-
- private$parent <- newParent
},
dettachFromCurrentParent = function()
{
- #Note: We temporary set parents collection to NULL. This will ensure that
- # remove method doesn't remove this subcollection from REST.
+ # We temporary set parents collection to NULL. This will ensure that
+ # remove method doesn't remove this subcollection from REST.
parent <- private$parent
parentsCollection <- parent$getCollection()
parent$setCollection(NULL, setRecursively = FALSE)
-
parent$remove(private$name)
-
parent$setCollection(parentsCollection, setRecursively = FALSE)
},
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: Apache-2.0
+
.onLoad <- function(libName, pkgName)
{
minAllowedRVersion <- "3.3.0"
arvadosFile <- collection$get("location/to/my/file.cpp")
```
- or
+or
```{r}
arvadosSubcollection <- collection$get("location/to/my/directory/")
size <- arvadosFile$getSizeInBytes()
```
- or
+or
```{r}
size <- arvadosSubcollection$getSizeInBytes()
* Create new file in a collection:
```{r}
-collection$create(fileNames, optionalRelativePath)
+collection$create(files)
```
- Example:
+Example:
```{r}
-mainFile <- collection$create("main.cpp", "cpp/src/")
-fileList <- collection$create(c("main.cpp", lib.dll), "cpp/src/")
+mainFile <- collection$create("cpp/src/main.cpp")
+fileList <- collection$create(c("cpp/src/main.cpp", "cpp/src/util.h"))
```
-* Add existing ArvadosFile or Subcollection to a collection:
-
-```{r}
-folder <- Subcollection$new("src")
-file <- ArvadosFile$new("main.cpp")
-folder$add(file)
-```
-
-```{r}
-collection$add(folder, "cpp")
-```
-
-This examples will add file "main.cpp" in "./cpp/src/" folder if folder exists.
-If subcollection contains more files or folders they will be added recursively.
-
* Delete file from a collection:
```{r}
subcollection$remove("folderInsideSubcollection/")
```
-* Move file or folder inside collection:
+* Move or rename a file or folder within a collection (moving between collections is currently not supported):
-Directley from collection
+Directly from collection
```{r}
collection$move("folder/file.cpp", "file.cpp")
Make sure to include new file name in destination.
In second example file$move("newDestination/") will not work.
+* Copy file or folder within a collection (copying between collections is currently not supported):
+
+Directly from collection
+
+```{r}
+collection$copy("folder/file.cpp", "file.cpp")
+```
+
+Or from file
+
+```{r}
+file <- collection$get("location/to/my/file.cpp")
+file$copy("destination/file.cpp")
+```
+
+Or from subcollection
+
+```{r}
+subcollection <- collection$get("location/to/folder")
+subcollection$copy("destination/folder")
+```
+
#### Working with Aravdos projects
* Get a project:
\item{}{\code{\link{users.delete}}}
\item{}{\code{\link{users.get}}}
\item{}{\code{\link{users.list}}}
+ \item{}{\code{\link{users.merge}}}
\item{}{\code{\link{users.setup}}}
\item{}{\code{\link{users.system}}}
\item{}{\code{\link{users.unsetup}}}
\item{flush()}{Write connections content to a file (override current content of the file).}
\item{remove(name)}{Removes ArvadosFile or Subcollection specified by name from the subcollection.}
\item{getSizeInBytes()}{Returns file size in bytes.}
- \item{move(newLocation)}{Moves file to a new location inside collection.}
+ \item{move(destination)}{Moves file to a new location inside collection.}
+ \item{copy(destination)}{Copies file to a new location inside collection.}
}
}
myFile$write("This is new file content")
fileContent <- myFile$read()
fileContent <- myFile$read("text")
-fileContent <- myFile$read("raw", offset = 8, length = 4)
+fileContent <- myFile$read("raw", offset = 8, length = 4)
#Write a table:
arvConnection <- myFile$connection("w")
mytable <- read.table(arvConnection)
myFile$move("newFolder/myFile")
+myFile$copy("newFolder/myFile")
}
}
\describe{
\item{add(content)}{Adds ArvadosFile or Subcollection specified by content to the collection.}
- \item{create(fileNames, relativePath = "")}{Creates one or more ArvadosFiles and adds them to the collection at specified path.}
+ \item{create(files)}{Creates one or more ArvadosFiles and adds them to the collection at specified path.}
\item{remove(fileNames)}{Remove one or more files from the collection.}
- \item{move(content, newLocation)}{Moves ArvadosFile or Subcollection to another location in the collection.}
+ \item{move(content, destination)}{Moves ArvadosFile or Subcollection to another location in the collection.}
+ \item{copy(content, destination)}{Copies ArvadosFile or Subcollection to another location in the collection.}
\item{getFileListing()}{Returns collections file content as character vector.}
\item{get(relativePath)}{If relativePath is valid, returns ArvadosFile or Subcollection specified by relativePath, else returns NULL.}
}
arv <- Arvados$new("your Arvados token", "example.arvadosapi.com")
collection <- Collection$new(arv, "uuid")
-newFile <- ArvadosFile$new("myFile")
-collection$add(newFile, "myFolder")
-
createdFiles <- collection$create(c("main.cpp", lib.dll), "cpp/src/")
collection$remove("location/to/my/file.cpp")
\title{Subcollection}
\description{
Subcollection class represents a folder inside Arvados collection.
-It is essentially a composite of ArvadosFiles and other Subcollections.
+It is essentially a composite of arvadosFiles and other subcollections.
}
\section{Usage}{
\item{get(relativePath)}{If relativePath is valid, returns ArvadosFile or Subcollection specified by relativePath, else returns NULL.}
\item{getFileListing()}{Returns subcollections file content as character vector.}
\item{getSizeInBytes()}{Returns subcollections content size in bytes.}
- \item{move(newLocation)}{Moves subcollection to a new location inside collection.}
+ \item{move(destination)}{Moves subcollection to a new location inside collection.}
+ \item{copy(destination)}{Copies subcollection to a new location inside collection.}
}
}
myFolder$remove("myFile")
myFolder$move("newLocation/myFolder")
+myFolder$copy("newLocation/myFolder")
}
}
--- /dev/null
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/Arvados.R
+\name{users.merge}
+\alias{users.merge}
+\title{users.merge}
+\usage{
+arv$users.merge(new_owner_uuid,
+ new_user_token, redirect_to_new_user = NULL)
+}
+\arguments{
+\item{new_owner_uuid}{}
+
+\item{new_user_token}{}
+
+\item{redirect_to_new_user}{}
+}
+\value{
+User object.
+}
+\description{
+users.merge is a method defined in Arvados class.
+}
numberOfPUTRequests = NULL,
numberOfPOSTRequests = NULL,
numberOfMOVERequests = NULL,
+ numberOfCOPYRequests = NULL,
numberOfgetConnectionCalls = NULL,
initialize = function(expectedURL = NULL,
self$numberOfPUTRequests <- 0
self$numberOfPOSTRequests <- 0
self$numberOfMOVERequests <- 0
+ self$numberOfCOPYRequests <- 0
self$numberOfgetConnectionCalls <- 0
self$numberOfDELETERequests <- self$numberOfDELETERequests + 1
else if(verb == "MOVE")
self$numberOfMOVERequests <- self$numberOfMOVERequests + 1
+ else if(verb == "COPY")
+ self$numberOfCOPYRequests <- self$numberOfCOPYRequests + 1
else if(verb == "PROPFIND")
{
return(self$content)
createCallCount = NULL,
deleteCallCount = NULL,
moveCallCount = NULL,
+ copyCallCount = NULL,
getCollectionContentCallCount = NULL,
getResourceSizeCallCount = NULL,
readCallCount = NULL,
collectionContent = NULL,
returnContent = NULL,
- initialize = function(collectionContent = NULL, returnContent = NULL,
+ initialize = function(collectionContent = NULL, returnContent = NULL,
expectedFilterContent = NULL)
{
self$getResourceCallCount <- 0
self$createCallCount <- 0
self$deleteCallCount <- 0
self$moveCallCount <- 0
+ self$copyCallCount <- 0
self$getCollectionContentCallCount <- 0
self$getResourceSizeCallCount <- 0
self$readCallCount <- 0
self$returnContent
},
+ copy = function(from, to, uuid)
+ {
+ self$copyCallCount <- self$copyCallCount + 1
+ self$returnContent
+ },
+
getCollectionContent = function(uuid)
{
self$getCollectionContentCallCount <- self$getCollectionContentCallCount + 1
self$getResourceSizeCallCount <- self$getResourceSizeCallCount + 1
self$returnContent
},
-
+
read = function(relativePath, uuid, contentType = "text", offset = 0, length = 0)
{
self$readCallCount <- self$readCallCount + 1
test_that("read raises exception offset or length is negative number", {
-
collectionContent <- c("animal", "animal/fish")
fakeREST <- FakeRESTService$new(collectionContent)
test_that("flush sends data stored in a connection to a REST server", {
-
collectionContent <- c("animal", "animal/fish")
fakeREST <- FakeRESTService$new(collectionContent)
animal <- ArvadosFile$new("animal")
expect_that(animal$move("new/location"),
- throws_error("ArvadosFile doesn't belong to any collection"))
+ throws_error("ArvadosFile doesn't belong to any collection."))
})
test_that(paste("move raises exception if newLocationInCollection",
"parameter is invalid"), {
-
collectionContent <- c("animal",
"animal/fish",
"animal/dog",
dog <- collection$get("animal/dog")
expect_that(dog$move("objects/dog"),
- throws_error("Unable to get destination subcollection"))
+ throws_error("Unable to get destination subcollection."))
})
test_that("move raises exception if new location contains content with the same name", {
test_that("move moves arvados file inside collection tree", {
-
collectionContent <- c("animal",
"animal/fish",
"animal/dog",
expect_that(dogIsNullOnOldLocation, is_true())
expect_that(dogExistsOnNewLocation, is_true())
})
+
+test_that(paste("copy raises exception if arvados file",
+ "doesn't belong to any collection"), {
+
+ animal <- ArvadosFile$new("animal")
+
+ expect_that(animal$copy("new/location"),
+ throws_error("ArvadosFile doesn't belong to any collection."))
+})
+
+test_that(paste("copy raises exception if location parameter is invalid"), {
+
+ collectionContent <- c("animal",
+ "animal/fish",
+ "animal/dog",
+ "animal/fish/shark",
+ "ball")
+
+ fakeREST <- FakeRESTService$new(collectionContent)
+
+ api <- Arvados$new("myToken", "myHostName")
+ api$setRESTService(fakeREST)
+
+ collection <- Collection$new(api, "myUUID")
+ dog <- collection$get("animal/dog")
+
+ expect_that(dog$copy("objects/dog"),
+ throws_error("Unable to get destination subcollection."))
+})
+
+test_that("copy raises exception if new location contains content with the same name", {
+
+
+ collectionContent <- c("animal",
+ "animal/fish",
+ "animal/dog",
+ "animal/fish/shark",
+ "dog")
+
+ fakeREST <- FakeRESTService$new(collectionContent)
+
+ api <- Arvados$new("myToken", "myHostName")
+ api$setRESTService(fakeREST)
+ collection <- Collection$new(api, "myUUID")
+ dog <- collection$get("animal/dog")
+
+ expect_that(dog$copy("dog"),
+ throws_error("Destination already contains content with same name."))
+
+})
+
+test_that("copy copies arvados file inside collection tree", {
+
+ collectionContent <- c("animal",
+ "animal/fish",
+ "animal/dog",
+ "animal/fish/shark",
+ "ball")
+
+ fakeREST <- FakeRESTService$new(collectionContent)
+
+ api <- Arvados$new("myToken", "myHostName")
+ api$setRESTService(fakeREST)
+ collection <- Collection$new(api, "myUUID")
+ dog <- collection$get("animal/dog")
+
+ dog$copy("dog")
+ dogExistsOnOldLocation <- !is.null(collection$get("animal/dog"))
+ dogExistsOnNewLocation <- !is.null(collection$get("dog"))
+
+ expect_that(dogExistsOnOldLocation, is_true())
+ expect_that(dogExistsOnNewLocation, is_true())
+})
+
+test_that("duplicate performs deep cloning of Arvados file", {
+ arvFile <- ArvadosFile$new("foo")
+ newFile1 <- arvFile$duplicate()
+ newFile2 <- arvFile$duplicate("bar")
+
+ expect_that(newFile1$getFileListing(), equals(arvFile$getFileListing()))
+ expect_that(newFile2$getFileListing(), equals(c("bar")))
+})
fixed = TRUE))
})
-test_that("create raises exception if relative path is not valid", {
-
- collectionContent <- c("animal",
- "animal/fish",
- "ball")
-
- fakeREST <- FakeRESTService$new(collectionContent)
-
- api <- Arvados$new("myToken", "myHostName")
- api$setRESTService(fakeREST)
- collection <- Collection$new(api, "myUUID")
-
- newPen <- ArvadosFile$new("pen")
-
- expect_that(collection$create(newPen, "objects"),
- throws_error("Subcollection objects doesn't exist.",
- fixed = TRUE))
-})
-
test_that(paste("create adds files specified by fileNames",
"to local tree structure and remote REST service"), {
- collectionContent <- c("animal", "animal/fish", "ball")
- fakeREST <- FakeRESTService$new(collectionContent)
-
+ fakeREST <- FakeRESTService$new()
api <- Arvados$new("myToken", "myHostName")
api$setRESTService(fakeREST)
collection <- Collection$new(api, "myUUID")
- files <- c("dog", "cat")
- collection$create(files, "animal")
+ collection$create(c("animal/dog", "animal/cat"))
dog <- collection$get("animal/dog")
cat <- collection$get("animal/cat")
expect_that(fishIsNotNull, is_true())
expect_that(fish$getName(), equals("fish"))
})
+
+test_that(paste("copy copies content to a new location inside file tree",
+ "and on REST service"), {
+
+ collectionContent <- c("animal", "animal/dog", "ball")
+ fakeREST <- FakeRESTService$new(collectionContent)
+
+ api <- Arvados$new("myToken", "myHostName")
+ api$setRESTService(fakeREST)
+ collection <- Collection$new(api, "myUUID")
+
+ collection$copy("animal/dog", "dog")
+
+ dogExistsOnOldLocation <- !is.null(collection$get("animal/dog"))
+ dogExistsOnNewLocation <- !is.null(collection$get("dog"))
+
+ expect_that(dogExistsOnOldLocation, is_true())
+ expect_that(dogExistsOnNewLocation, is_true())
+ expect_that(fakeREST$copyCallCount, equals(1))
+})
+
+test_that("copy raises exception if new location is not valid", {
+
+ collectionContent <- c("animal", "animal/fish", "ball")
+ fakeREST <- FakeRESTService$new(collectionContent)
+
+ api <- Arvados$new("myToken", "myHostName")
+ api$setRESTService(fakeREST)
+ collection <- Collection$new(api, "myUUID")
+
+ expect_that(collection$copy("fish", "object"),
+ throws_error("Content you want to copy doesn't exist in the collection.",
+ fixed = TRUE))
+})
+
+test_that("refresh invalidates current tree structure", {
+
+ collectionContent <- c("animal", "animal/fish", "ball")
+ fakeREST <- FakeRESTService$new(collectionContent)
+
+ api <- Arvados$new("myToken", "myHostName")
+ api$setRESTService(fakeREST)
+ collection <- Collection$new(api, "aaaaa-j7d0g-ccccccccccccccc")
+
+ # Before refresh
+ fish <- collection$get("animal/fish")
+ expect_that(fish$getName(), equals("fish"))
+ expect_that(fish$getCollection()$uuid, equals("aaaaa-j7d0g-ccccccccccccccc"))
+
+ collection$refresh()
+
+ # After refresh
+ expect_that(fish$getName(), equals("fish"))
+ expect_true(is.null(fish$getCollection()))
+})
throws_error("Server code: 404"))
})
+test_that("copy calls REST service properly", {
+
+ uuid <- "aaaaa-j7d0g-ccccccccccccccc"
+ expectedURL <- "https://webDavHost/c=aaaaa-j7d0g-ccccccccccccccc/file"
+ fakeHttp <- FakeHttpRequest$new(expectedURL)
+ fakeHttpParser <- FakeHttpParser$new()
+
+ REST <- RESTService$new("token", "https://host/",
+ fakeHttp, fakeHttpParser,
+ 0, "https://webDavHost/")
+
+ REST$copy("file", "newDestination/file", uuid)
+
+ expect_that(fakeHttp$URLIsProperlyConfigured, is_true())
+ expect_that(fakeHttp$requestHeaderContainsAuthorizationField, is_true())
+ expect_that(fakeHttp$requestHeaderContainsDestinationField, is_true())
+ expect_that(fakeHttp$numberOfCOPYRequests, equals(1))
+})
+
+test_that("copy raises exception if server response code is not between 200 and 300", {
+
+ uuid <- "aaaaa-j7d0g-ccccccccccccccc"
+ response <- list()
+ response$status_code <- 404
+ fakeHttp <- FakeHttpRequest$new(serverResponse = response)
+
+ REST <- RESTService$new("token", "https://host/",
+ fakeHttp, HttpParser$new(),
+ 0, "https://webDavHost/")
+
+ expect_that(REST$copy("file", "newDestination/file", uuid),
+ throws_error("Server code: 404"))
+})
+
test_that("getCollectionContent retreives correct content from WebDAV server", {
uuid <- "aaaaa-j7d0g-ccccccccccccccc"
fish <- collection$get("animal/fish")
expect_that(fish$move("objects/dog"),
- throws_error("Unable to get destination subcollection"))
+ throws_error("Unable to get destination subcollection."))
})
test_that("move moves subcollection inside collection tree", {
expect_that(resourceSize, equals(100))
})
+
+#########################
+test_that(paste("copy raises exception if subcollection",
+ "doesn't belong to any collection"), {
+
+ animal <- Subcollection$new("animal")
+
+ expect_that(animal$copy("new/location"),
+ throws_error("Subcollection doesn't belong to any collection."))
+})
+
+test_that("copy raises exception if new location contains content with the same name", {
+
+ collectionContent <- c("animal",
+ "animal/fish",
+ "animal/dog",
+ "animal/fish/shark",
+ "fish")
+ fakeREST <- FakeRESTService$new(collectionContent)
+
+ api <- Arvados$new("myToken", "myHostName")
+ api$setRESTService(fakeREST)
+ collection <- Collection$new(api, "myUUID")
+ fish <- collection$get("animal/fish")
+
+ expect_that(fish$copy("fish"),
+ throws_error("Destination already contains content with same name."))
+
+})
+
+test_that(paste("copy raises exception if location parameter is invalid"), {
+
+ collectionContent <- c("animal",
+ "animal/fish",
+ "animal/dog",
+ "animal/fish/shark",
+ "ball")
+ fakeREST <- FakeRESTService$new(collectionContent)
+
+ api <- Arvados$new("myToken", "myHostName")
+ api$setRESTService(fakeREST)
+
+ collection <- Collection$new(api, "myUUID")
+ fish <- collection$get("animal/fish")
+
+ expect_that(fish$copy("objects/dog"),
+ throws_error("Unable to get destination subcollection."))
+})
+
+test_that("copy copies subcollection inside collection tree", {
+
+ collectionContent <- c("animal",
+ "animal/fish",
+ "animal/dog",
+ "animal/fish/shark",
+ "ball")
+ fakeREST <- FakeRESTService$new(collectionContent)
+
+ api <- Arvados$new("myToken", "myHostName")
+ api$setRESTService(fakeREST)
+ collection <- Collection$new(api, "myUUID")
+ fish <- collection$get("animal/fish")
+
+ fish$copy("fish")
+ fishExistsOnOldLocation <- !is.null(collection$get("animal/fish"))
+ fishExistsOnNewLocation <- !is.null(collection$get("fish"))
+
+ expect_that(fishExistsOnOldLocation, is_true())
+ expect_that(fishExistsOnNewLocation, is_true())
+})
+
+test_that("duplicate performs deep cloning of Subcollection", {
+ foo <- ArvadosFile$new("foo")
+ bar <- ArvadosFile$new("bar")
+ sub <- Subcollection$new("qux")
+ sub$add(foo)
+ sub$add(bar)
+
+ newSub1 <- sub$duplicate()
+ newSub2 <- sub$duplicate("quux")
+
+ expect_that(newSub1$getFileListing(), equals(sub$getFileListing()))
+ expect_that(sort(newSub2$getFileListing()), equals(c("quux/bar", "quux/foo")))
+})
s.executables << "arv-crunch-job"
s.executables << "arv-tag"
s.required_ruby_version = '>= 2.1.0'
- s.add_runtime_dependency 'arvados', '~> 0.1', '>= 0.1.20150128223554'
+ s.add_runtime_dependency 'arvados', '~> 1.1.0', '>= 1.1.4'
# Our google-api-client dependency used to be < 0.9, but that could be
# satisfied by the buggy 0.9.pre*. https://dev.arvados.org/issues/9213
s.add_runtime_dependency 'google-api-client', '~> 0.6', '>= 0.6.3', '<0.8.9'
my $cgroup_root = "/sys/fs/cgroup";
my $docker_bin = "docker.io";
my $docker_run_args = "";
+my $srun_sync_timeout = 15*60;
GetOptions('force-unlock' => \$force_unlock,
'git-dir=s' => \$git_dir,
'job=s' => \$jobspec,
'cgroup-root=s' => \$cgroup_root,
'docker-bin=s' => \$docker_bin,
'docker-run-args=s' => \$docker_run_args,
+ 'srun-sync-timeout=i' => \$srun_sync_timeout,
);
if (defined $job_api_token) {
my ($stdout_r, $stdout_w);
pipe $stdout_r, $stdout_w or croak("pipe() failed: $!");
+ my $started_srun = scalar time;
+
my $srunpid = fork();
if ($srunpid == 0)
{
if (!$busy) {
select(undef, undef, undef, 0.1);
}
+ if (($started_srun + $srun_sync_timeout) < scalar time) {
+ # Exceeded general timeout for "srun_sync" operations, likely
+ # means something got stuck on the remote node.
+ Log(undef, "srun_sync exceeded timeout, will fail.");
+ $main::please_freeze = 1;
+ }
killem(keys %proc) if $main::please_freeze;
}
my $exited = $?;
else:
raise Exception("Unsupported API '%s', expected one of %s" % (work_api, expected_api))
+ if self.work_api == "jobs":
+ logger.warn("""
+*******************************
+Using the deprecated 'jobs' API.
+
+To get rid of this warning:
+
+Users: read about migrating at
+http://doc.arvados.org/user/cwl/cwl-style.html#migrate
+and use the option --api=containers
+
+Admins: configure the cluster to disable the 'jobs' API as described at:
+http://doc.arvados.org/install/install-api-server.html#disable_api_methods
+*******************************""")
+
self.loadingContext = ArvLoadingContext(vars(arvargs))
self.loadingContext.fetcher_constructor = self.fetcher_constructor
self.loadingContext.resolver = partial(collectionResolver, self.api, num_retries=self.num_retries)
self.uuid = response["uuid"]
self.arvrunner.process_submitted(self)
- logger.info("%s submitted container %s", self.arvrunner.label(self), response["uuid"])
+ logger.info("%s submitted container_request %s", self.arvrunner.label(self), response["uuid"])
def done(self, record):
try:
p = sp[0]
if p.startswith("keep:") and arvados.util.keep_locator_pattern.match(p[5:]):
pdh = p[5:]
- return (self.collection_cache.get(pdh), sp[1] if len(sp) == 2 else None)
+ return (self.collection_cache.get(pdh), urlparse.unquote(sp[1]) if len(sp) == 2 else None)
else:
return (None, path)
else:
return super(CollectionFsAccess, self).exists(fn)
+ def size(self, fn): # type: (unicode) -> bool
+ collection, rest = self.get_collection(fn)
+ if collection is not None:
+ if rest:
+ arvfile = collection.find(rest)
+ if isinstance(arvfile, arvados.arvfile.ArvadosFile):
+ return arvfile.size()
+ raise IOError(errno.EINVAL, "Not a path to a file %s" % (fn))
+ else:
+ return super(CollectionFsAccess, self).size(fn)
+
def isfile(self, fn): # type: (unicode) -> bool
collection, rest = self.get_collection(fn)
if collection is not None:
sc = []
def only_real(obj):
+ # Only interested in local files than need to be uploaded,
+ # don't include file literals, keep references, etc.
if obj.get("location", "").startswith("file:"):
sc.append(obj)
visit_class(workflowobj, ("CommandLineTool", "Workflow"), discover_default_secondary_files)
- for d in discovered:
- sc.extend(discovered[d])
+ for d in list(discovered.keys()):
+ # Only interested in discovered secondaryFiles which are local
+ # files that need to be uploaded.
+ if d.startswith("file:"):
+ sc.extend(discovered[d])
+ else:
+ del discovered[d]
mapper = ArvPathMapper(arvrunner, sc, "",
"keep:%s",
# Note that arvados/build/run-build-packages.sh looks at this
# file to determine what version of cwltool and schema-salad to build.
install_requires=[
- 'cwltool==1.0.20180615183820',
- 'schema-salad==2.7.20180501211602',
- 'typing >= 3.5.3',
+ 'cwltool==1.0.20180806194258',
+ 'schema-salad==2.7.20180719125426',
+ 'typing >= 3.6.4',
'ruamel.yaml >=0.13.11, <0.15',
'arvados-python-client>=1.1.4.20180607143841',
'setuptools',
--- /dev/null
+fastq1:
+ class: File
+ location: keep:20850f01122e860fb878758ac1320877+71/sample1_S01_R1_001.fastq.gz
\ No newline at end of file
--- /dev/null
+cwlVersion: v1.0
+class: CommandLineTool
+inputs:
+ fastq1: File
+outputs:
+ out: stdout
+baseCommand: echo
+arguments:
+ - $(inputs.fastq1.size)
+stdout: size.txt
\ No newline at end of file
--- /dev/null
+cwlVersion: v1.0
+class: CommandLineTool
+requirements:
+ - class: InlineJavascriptRequirement
+arguments:
+ - ls
+ - -l
+ - $(inputs.hello)
+inputs:
+ hello:
+ type: File
+ default:
+ class: File
+ location: keep:4d8a70b1e63b2aad6984e40e338e2373+69/hello.txt
+ secondaryFiles:
+ - .idx
+outputs: []
\ No newline at end of file
if ! arv-get 4d8a70b1e63b2aad6984e40e338e2373+69 > /dev/null ; then
arv-put --portable-data-hash secondaryFiles/hello.txt*
fi
+if ! arv-get 20850f01122e860fb878758ac1320877+71 > /dev/null ; then
+ arv-put --portable-data-hash samples/sample1_S01_R1_001.fastq.gz
+fi
+
exec cwltest --test arvados-tests.yml --tool arvados-cwl-runner $@ -- --disable-reuse --compute-checksum
tool: 12418-glob-empty-collection.cwl
doc: "Test glob output on empty collection"
+- job: null
+ output:
+ out: null
+ tool: 13976-keepref-wf.cwl
+ doc: "Test issue 13976"
+
- job: null
output:
out: out
out: null
tool: wf-defaults/wf7.cwl
doc: workflow level default in RunInSingleContainer
+
+- job: 13931-size-job.yml
+ output:
+ "out": {
+ "checksum": "sha1$5bf6e5357bd42a6b1d2a3a040e16a91490064d26",
+ "location": "size.txt",
+ "class": "File",
+ "size": 3
+ }
+ tool: 13931-size.cwl
+ doc: Test that size is set for files in Keep
keepdocker.return_value = [("zzzzz-4zz18-zzzzzzzzzzzzzz3", "")]
runner.api.collections().get().execute.return_value = {
- "portable_data_hash": "99999999999999999999999999999993+99"}
+ "portable_data_hash": "99999999999999999999999999999994+99",
+ "manifest_text": ". 99999999999999999999999999999994+99 0:0:file1 0:0:file2"}
document_loader, avsc_names, schema_metadata, metaschema_loader = cwltool.process.get_schema("v1.0")
metadata["cwlVersion"] = tool["cwlVersion"]
mockcollection().portable_data_hash.return_value = "99999999999999999999999999999999+118"
+ mockcollectionreader().find.return_value = arvados.arvfile.ArvadosFile(mock.MagicMock(), "token.txt")
arvtool = arvados_cwl.ArvadosWorkflow(runner, tool, loadingContext)
arvtool.formatgraph = None
"fileblub": {
"basename": "token.txt",
"class": "File",
- "location": "/keep/99999999999999999999999999999999+118/token.txt"
+ "location": "/keep/99999999999999999999999999999999+118/token.txt",
+ "size": 0
},
"sleeptime": 5
}''')])
"listing": [{
"basename": "renamed.txt",
"class": "File",
- "location": "keep:99999999999999999999999999999998+99/file1.txt"
+ "location": "keep:99999999999999999999999999999998+99/file1.txt",
+ "size": 0
}],
'class': 'Directory'
},
{
'basename': 'renamed.txt',
'class': 'File', 'location':
- 'keep:99999999999999999999999999999998+99/file1.txt'
+ 'keep:99999999999999999999999999999998+99/file1.txt',
+ 'size': 0
}
]}},
'cwl:tool': '3fffdeaa75e018172e1b583425f4ebff+60/workflow.cwl#main',
'z': {'basename': 'anonymous', 'class': 'Directory', 'listing': [
{'basename': 'renamed.txt',
'class': 'File',
- 'location': 'keep:99999999999999999999999999999998+99/file1.txt'
+ 'location': 'keep:99999999999999999999999999999998+99/file1.txt',
+ 'size': 0
}
]}
},
@stubs
def test_submit_file_keepref(self, stubs, tm, collectionReader):
capture_stdout = cStringIO.StringIO()
+ collectionReader().find.return_value = arvados.arvfile.ArvadosFile(mock.MagicMock(), "blorp.txt")
exited = arvados_cwl.main(
["--submit", "--no-wait", "--api=containers", "--debug",
"tests/wf/submit_keepref_wf.cwl"],
"class": "File",
"location": "keep:99999999999999999999999999999998+99/file1.txt",
"nameext": ".txt",
- "nameroot": "renamed"
+ "nameroot": "renamed",
+ "size": 0
}
]
},
RUN apt-get update -q && apt-get install -qy git python-pip python-virtualenv python-dev libcurl4-gnutls-dev libgnutls28-dev nodejs python-pyasn1-modules
-RUN pip install -U setuptools
+RUN pip install -U setuptools six
ARG sdk
ARG runner
offset := 0
for {
params["offset"] = offset
+
+ // This list variable must be a new one declared
+ // inside the loop: otherwise, items in the API
+ // response would get deep-merged into the items
+ // loaded in previous iterations.
var list arvados.ContainerList
+
err := d.Arv.List("containers", params, &list)
if err != nil {
log.Printf("Error getting list of containers: %q", err)
// For the metrics to be accurate, the caller must ensure every
// request passed to the Handler also passes through
// LogRequests(logger, ...), and vice versa.
-func Instrument(logger *logrus.Logger, next http.Handler) Handler {
+//
+// If registry is nil, a new registry is created.
+//
+// If logger is nil, logrus.StandardLogger() is used.
+func Instrument(registry *prometheus.Registry, logger *logrus.Logger, next http.Handler) Handler {
if logger == nil {
logger = logrus.StandardLogger()
}
+ if registry == nil {
+ registry = prometheus.NewRegistry()
+ }
reqDuration := prometheus.NewSummaryVec(prometheus.SummaryOpts{
Name: "request_duration_seconds",
Help: "Summary of request duration.",
Name: "time_to_status_seconds",
Help: "Summary of request TTFB.",
}, []string{"code", "method"})
- registry := prometheus.NewRegistry()
registry.MustRegister(timeToStatus)
registry.MustRegister(reqDuration)
m := &metrics{
# SPDX-License-Identifier: Apache-2.0
require 'google/api_client'
+# Monkeypatch google-api-client gem to avoid sending newline characters
+# on headers to make ruby-2.3.7+ happy.
+# See: https://dev.arvados.org/issues/13920
+Google::APIClient::ENV::OS_VERSION.strip!
+
require 'json'
require 'tempfile'
gem 'mocha', require: false
end
+# We need this dependency because of crunchv1
+gem 'arvados-cli'
+
# We'll need to update related code prior to Rails 5.
# See: https://github.com/rails/activerecord-deprecated_finders
gem 'activerecord-deprecated_finders', require: 'active_record/deprecated_finders'
i18n (~> 0)
json (>= 1.7.7, < 3)
jwt (>= 0.1.5, < 2)
+ arvados-cli (1.1.4.20180723133344)
+ activesupport (>= 3.2.13, < 5)
+ andand (~> 1.3, >= 1.3.3)
+ arvados (~> 0.1, >= 0.1.20150128223554)
+ curb (~> 0.8)
+ google-api-client (~> 0.6, >= 0.6.3, < 0.8.9)
+ json (>= 1.7.7, < 3)
+ oj (~> 3.0)
+ trollop (~> 2.0)
autoparse (0.3.3)
addressable (>= 2.3.1)
extlib (>= 0.9.15)
coffee-script-source (1.12.2)
concurrent-ruby (1.0.5)
crass (1.0.4)
+ curb (0.9.6)
database_cleaner (1.7.0)
erubis (2.7.0)
eventmachine (1.2.6)
acts_as_api
andand
arvados (>= 0.1.20150615153458)
+ arvados-cli
coffee-rails (~> 4.0)
database_cleaner
factory_girl_rails
uglifier (~> 2.0)
BUNDLED WITH
- 1.16.2
+ 1.16.3
req_id = "req-" + Random::DEFAULT.rand(2**128).to_s(36)[0..19]
end
response.headers['X-Request-Id'] = Thread.current[:request_id] = req_id
- yield
+ Rails.logger.tagged(req_id) do
+ yield
+ end
Thread.current[:request_id] = nil
end
all_objects = []
@items_available = 0
+ # Reload the orders param, this time without prefixing unqualified
+ # columns ("name" => "groups.name"). Here, unqualified orders
+ # apply to each table being searched, not "groups".
+ load_limit_offset_order_params(fill_table_names: false)
+
# Trick apply_where_limit_order_params into applying suitable
# per-table values. *_all are the real ones we'll apply to the
# aggregate set.
# table_name for the current klass, apply that order.
# Otherwise, order by recency.
request_order =
- request_orders.andand.find { |r| r =~ /^#{klass.table_name}\./i } ||
+ request_orders.andand.find { |r| r =~ /^#{klass.table_name}\./i || r !~ /\./ } ||
klass.default_orders.join(", ")
@select = nil
end
def manifest_files
+ return '' if !self.manifest_text
+
names = ''
- if self.manifest_text
- self.manifest_text.scan(/ \d+:\d+:(\S+)/) do |name|
- names << name.first.gsub('\040',' ') + "\n"
- break if names.length > 2**12
- end
+ self.manifest_text.scan(/ \d+:\d+:(\S+)/) do |name|
+ names << name.first.gsub('\040',' ') + "\n"
end
-
- if self.manifest_text and names.length < 2**12
- self.manifest_text.scan(/^\.\/(\S+)/m) do |stream_name|
- names << stream_name.first.gsub('\040',' ') + "\n"
- break if names.length > 2**12
- end
+ self.manifest_text.scan(/^\.\/(\S+)/m) do |stream_name|
+ names << stream_name.first.gsub('\040',' ') + "\n"
end
-
- names[0,2**12]
+ names
end
def default_empty_manifest
module Server
class Application < Rails::Application
+ # The following is to avoid SafeYAML's warning message
+ SafeYAML::OPTIONS[:default_mode] = :safe
+
# Settings in config/environments/* take precedence over those specified here.
# Application configuration should go into files in config/initializers
# -- all .rb files in that directory are automatically loaded.
--- /dev/null
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: AGPL-3.0
+
+class IndexAllFilenames < ActiveRecord::Migration
+ def up
+ ActiveRecord::Base.connection.execute 'ALTER TABLE collections ALTER COLUMN file_names TYPE text'
+ end
+ def down
+ ActiveRecord::Base.connection.execute 'ALTER TABLE collections ALTER COLUMN file_names TYPE varchar(8192)'
+ end
+end
SET statement_timeout = 0;
SET client_encoding = 'UTF8';
SET standard_conforming_strings = on;
+SELECT pg_catalog.set_config('search_path', '', false);
SET check_function_bodies = false;
SET client_min_messages = warning;
-- COMMENT ON EXTENSION plpgsql IS 'PL/pgSQL procedural language';
-SET search_path = public, pg_catalog;
-
SET default_tablespace = '';
SET default_with_oids = false;
-- Name: api_client_authorizations; Type: TABLE; Schema: public; Owner: -
--
-CREATE TABLE api_client_authorizations (
+CREATE TABLE public.api_client_authorizations (
id integer NOT NULL,
api_token character varying(255) NOT NULL,
api_client_id integer NOT NULL,
-- Name: api_client_authorizations_id_seq; Type: SEQUENCE; Schema: public; Owner: -
--
-CREATE SEQUENCE api_client_authorizations_id_seq
+CREATE SEQUENCE public.api_client_authorizations_id_seq
START WITH 1
INCREMENT BY 1
NO MINVALUE
-- Name: api_client_authorizations_id_seq; Type: SEQUENCE OWNED BY; Schema: public; Owner: -
--
-ALTER SEQUENCE api_client_authorizations_id_seq OWNED BY api_client_authorizations.id;
+ALTER SEQUENCE public.api_client_authorizations_id_seq OWNED BY public.api_client_authorizations.id;
--
-- Name: api_clients; Type: TABLE; Schema: public; Owner: -
--
-CREATE TABLE api_clients (
+CREATE TABLE public.api_clients (
id integer NOT NULL,
uuid character varying(255),
owner_uuid character varying(255),
-- Name: api_clients_id_seq; Type: SEQUENCE; Schema: public; Owner: -
--
-CREATE SEQUENCE api_clients_id_seq
+CREATE SEQUENCE public.api_clients_id_seq
START WITH 1
INCREMENT BY 1
NO MINVALUE
-- Name: api_clients_id_seq; Type: SEQUENCE OWNED BY; Schema: public; Owner: -
--
-ALTER SEQUENCE api_clients_id_seq OWNED BY api_clients.id;
+ALTER SEQUENCE public.api_clients_id_seq OWNED BY public.api_clients.id;
--
-- Name: authorized_keys; Type: TABLE; Schema: public; Owner: -
--
-CREATE TABLE authorized_keys (
+CREATE TABLE public.authorized_keys (
id integer NOT NULL,
uuid character varying(255) NOT NULL,
owner_uuid character varying(255) NOT NULL,
-- Name: authorized_keys_id_seq; Type: SEQUENCE; Schema: public; Owner: -
--
-CREATE SEQUENCE authorized_keys_id_seq
+CREATE SEQUENCE public.authorized_keys_id_seq
START WITH 1
INCREMENT BY 1
NO MINVALUE
-- Name: authorized_keys_id_seq; Type: SEQUENCE OWNED BY; Schema: public; Owner: -
--
-ALTER SEQUENCE authorized_keys_id_seq OWNED BY authorized_keys.id;
+ALTER SEQUENCE public.authorized_keys_id_seq OWNED BY public.authorized_keys.id;
--
-- Name: collections; Type: TABLE; Schema: public; Owner: -
--
-CREATE TABLE collections (
+CREATE TABLE public.collections (
id integer NOT NULL,
owner_uuid character varying(255),
created_at timestamp without time zone NOT NULL,
description character varying(524288),
properties jsonb,
delete_at timestamp without time zone,
- file_names character varying(8192),
+ file_names text,
trash_at timestamp without time zone,
is_trashed boolean DEFAULT false NOT NULL,
storage_classes_desired jsonb DEFAULT '["default"]'::jsonb,
-- Name: collections_id_seq; Type: SEQUENCE; Schema: public; Owner: -
--
-CREATE SEQUENCE collections_id_seq
+CREATE SEQUENCE public.collections_id_seq
START WITH 1
INCREMENT BY 1
NO MINVALUE
-- Name: collections_id_seq; Type: SEQUENCE OWNED BY; Schema: public; Owner: -
--
-ALTER SEQUENCE collections_id_seq OWNED BY collections.id;
+ALTER SEQUENCE public.collections_id_seq OWNED BY public.collections.id;
--
-- Name: commit_ancestors; Type: TABLE; Schema: public; Owner: -
--
-CREATE TABLE commit_ancestors (
+CREATE TABLE public.commit_ancestors (
id integer NOT NULL,
repository_name character varying(255),
descendant character varying(255) NOT NULL,
-- Name: commit_ancestors_id_seq; Type: SEQUENCE; Schema: public; Owner: -
--
-CREATE SEQUENCE commit_ancestors_id_seq
+CREATE SEQUENCE public.commit_ancestors_id_seq
START WITH 1
INCREMENT BY 1
NO MINVALUE
-- Name: commit_ancestors_id_seq; Type: SEQUENCE OWNED BY; Schema: public; Owner: -
--
-ALTER SEQUENCE commit_ancestors_id_seq OWNED BY commit_ancestors.id;
+ALTER SEQUENCE public.commit_ancestors_id_seq OWNED BY public.commit_ancestors.id;
--
-- Name: commits; Type: TABLE; Schema: public; Owner: -
--
-CREATE TABLE commits (
+CREATE TABLE public.commits (
id integer NOT NULL,
repository_name character varying(255),
sha1 character varying(255),
-- Name: commits_id_seq; Type: SEQUENCE; Schema: public; Owner: -
--
-CREATE SEQUENCE commits_id_seq
+CREATE SEQUENCE public.commits_id_seq
START WITH 1
INCREMENT BY 1
NO MINVALUE
-- Name: commits_id_seq; Type: SEQUENCE OWNED BY; Schema: public; Owner: -
--
-ALTER SEQUENCE commits_id_seq OWNED BY commits.id;
+ALTER SEQUENCE public.commits_id_seq OWNED BY public.commits.id;
--
-- Name: container_requests; Type: TABLE; Schema: public; Owner: -
--
-CREATE TABLE container_requests (
+CREATE TABLE public.container_requests (
id integer NOT NULL,
uuid character varying(255),
owner_uuid character varying(255),
-- Name: container_requests_id_seq; Type: SEQUENCE; Schema: public; Owner: -
--
-CREATE SEQUENCE container_requests_id_seq
+CREATE SEQUENCE public.container_requests_id_seq
START WITH 1
INCREMENT BY 1
NO MINVALUE
-- Name: container_requests_id_seq; Type: SEQUENCE OWNED BY; Schema: public; Owner: -
--
-ALTER SEQUENCE container_requests_id_seq OWNED BY container_requests.id;
+ALTER SEQUENCE public.container_requests_id_seq OWNED BY public.container_requests.id;
--
-- Name: containers; Type: TABLE; Schema: public; Owner: -
--
-CREATE TABLE containers (
+CREATE TABLE public.containers (
id integer NOT NULL,
uuid character varying(255),
owner_uuid character varying(255),
-- Name: containers_id_seq; Type: SEQUENCE; Schema: public; Owner: -
--
-CREATE SEQUENCE containers_id_seq
+CREATE SEQUENCE public.containers_id_seq
START WITH 1
INCREMENT BY 1
NO MINVALUE
-- Name: containers_id_seq; Type: SEQUENCE OWNED BY; Schema: public; Owner: -
--
-ALTER SEQUENCE containers_id_seq OWNED BY containers.id;
+ALTER SEQUENCE public.containers_id_seq OWNED BY public.containers.id;
--
-- Name: groups; Type: TABLE; Schema: public; Owner: -
--
-CREATE TABLE groups (
+CREATE TABLE public.groups (
id integer NOT NULL,
uuid character varying(255),
owner_uuid character varying(255),
-- Name: groups_id_seq; Type: SEQUENCE; Schema: public; Owner: -
--
-CREATE SEQUENCE groups_id_seq
+CREATE SEQUENCE public.groups_id_seq
START WITH 1
INCREMENT BY 1
NO MINVALUE
-- Name: groups_id_seq; Type: SEQUENCE OWNED BY; Schema: public; Owner: -
--
-ALTER SEQUENCE groups_id_seq OWNED BY groups.id;
+ALTER SEQUENCE public.groups_id_seq OWNED BY public.groups.id;
--
-- Name: humans; Type: TABLE; Schema: public; Owner: -
--
-CREATE TABLE humans (
+CREATE TABLE public.humans (
id integer NOT NULL,
uuid character varying(255) NOT NULL,
owner_uuid character varying(255) NOT NULL,
-- Name: humans_id_seq; Type: SEQUENCE; Schema: public; Owner: -
--
-CREATE SEQUENCE humans_id_seq
+CREATE SEQUENCE public.humans_id_seq
START WITH 1
INCREMENT BY 1
NO MINVALUE
-- Name: humans_id_seq; Type: SEQUENCE OWNED BY; Schema: public; Owner: -
--
-ALTER SEQUENCE humans_id_seq OWNED BY humans.id;
+ALTER SEQUENCE public.humans_id_seq OWNED BY public.humans.id;
--
-- Name: job_tasks; Type: TABLE; Schema: public; Owner: -
--
-CREATE TABLE job_tasks (
+CREATE TABLE public.job_tasks (
id integer NOT NULL,
uuid character varying(255),
owner_uuid character varying(255),
-- Name: job_tasks_id_seq; Type: SEQUENCE; Schema: public; Owner: -
--
-CREATE SEQUENCE job_tasks_id_seq
+CREATE SEQUENCE public.job_tasks_id_seq
START WITH 1
INCREMENT BY 1
NO MINVALUE
-- Name: job_tasks_id_seq; Type: SEQUENCE OWNED BY; Schema: public; Owner: -
--
-ALTER SEQUENCE job_tasks_id_seq OWNED BY job_tasks.id;
+ALTER SEQUENCE public.job_tasks_id_seq OWNED BY public.job_tasks.id;
--
-- Name: job_tasks_qsequence_seq; Type: SEQUENCE; Schema: public; Owner: -
--
-CREATE SEQUENCE job_tasks_qsequence_seq
+CREATE SEQUENCE public.job_tasks_qsequence_seq
START WITH 1
INCREMENT BY 1
NO MINVALUE
-- Name: job_tasks_qsequence_seq; Type: SEQUENCE OWNED BY; Schema: public; Owner: -
--
-ALTER SEQUENCE job_tasks_qsequence_seq OWNED BY job_tasks.qsequence;
+ALTER SEQUENCE public.job_tasks_qsequence_seq OWNED BY public.job_tasks.qsequence;
--
-- Name: jobs; Type: TABLE; Schema: public; Owner: -
--
-CREATE TABLE jobs (
+CREATE TABLE public.jobs (
id integer NOT NULL,
uuid character varying(255),
owner_uuid character varying(255),
-- Name: jobs_id_seq; Type: SEQUENCE; Schema: public; Owner: -
--
-CREATE SEQUENCE jobs_id_seq
+CREATE SEQUENCE public.jobs_id_seq
START WITH 1
INCREMENT BY 1
NO MINVALUE
-- Name: jobs_id_seq; Type: SEQUENCE OWNED BY; Schema: public; Owner: -
--
-ALTER SEQUENCE jobs_id_seq OWNED BY jobs.id;
+ALTER SEQUENCE public.jobs_id_seq OWNED BY public.jobs.id;
--
-- Name: keep_disks; Type: TABLE; Schema: public; Owner: -
--
-CREATE TABLE keep_disks (
+CREATE TABLE public.keep_disks (
id integer NOT NULL,
uuid character varying(255) NOT NULL,
owner_uuid character varying(255) NOT NULL,
-- Name: keep_disks_id_seq; Type: SEQUENCE; Schema: public; Owner: -
--
-CREATE SEQUENCE keep_disks_id_seq
+CREATE SEQUENCE public.keep_disks_id_seq
START WITH 1
INCREMENT BY 1
NO MINVALUE
-- Name: keep_disks_id_seq; Type: SEQUENCE OWNED BY; Schema: public; Owner: -
--
-ALTER SEQUENCE keep_disks_id_seq OWNED BY keep_disks.id;
+ALTER SEQUENCE public.keep_disks_id_seq OWNED BY public.keep_disks.id;
--
-- Name: keep_services; Type: TABLE; Schema: public; Owner: -
--
-CREATE TABLE keep_services (
+CREATE TABLE public.keep_services (
id integer NOT NULL,
uuid character varying(255) NOT NULL,
owner_uuid character varying(255) NOT NULL,
-- Name: keep_services_id_seq; Type: SEQUENCE; Schema: public; Owner: -
--
-CREATE SEQUENCE keep_services_id_seq
+CREATE SEQUENCE public.keep_services_id_seq
START WITH 1
INCREMENT BY 1
NO MINVALUE
-- Name: keep_services_id_seq; Type: SEQUENCE OWNED BY; Schema: public; Owner: -
--
-ALTER SEQUENCE keep_services_id_seq OWNED BY keep_services.id;
+ALTER SEQUENCE public.keep_services_id_seq OWNED BY public.keep_services.id;
--
-- Name: links; Type: TABLE; Schema: public; Owner: -
--
-CREATE TABLE links (
+CREATE TABLE public.links (
id integer NOT NULL,
uuid character varying(255),
owner_uuid character varying(255),
-- Name: links_id_seq; Type: SEQUENCE; Schema: public; Owner: -
--
-CREATE SEQUENCE links_id_seq
+CREATE SEQUENCE public.links_id_seq
START WITH 1
INCREMENT BY 1
NO MINVALUE
-- Name: links_id_seq; Type: SEQUENCE OWNED BY; Schema: public; Owner: -
--
-ALTER SEQUENCE links_id_seq OWNED BY links.id;
+ALTER SEQUENCE public.links_id_seq OWNED BY public.links.id;
--
-- Name: logs; Type: TABLE; Schema: public; Owner: -
--
-CREATE TABLE logs (
+CREATE TABLE public.logs (
id integer NOT NULL,
uuid character varying(255),
owner_uuid character varying(255),
-- Name: logs_id_seq; Type: SEQUENCE; Schema: public; Owner: -
--
-CREATE SEQUENCE logs_id_seq
+CREATE SEQUENCE public.logs_id_seq
START WITH 1
INCREMENT BY 1
NO MINVALUE
-- Name: logs_id_seq; Type: SEQUENCE OWNED BY; Schema: public; Owner: -
--
-ALTER SEQUENCE logs_id_seq OWNED BY logs.id;
+ALTER SEQUENCE public.logs_id_seq OWNED BY public.logs.id;
--
-- Name: users; Type: TABLE; Schema: public; Owner: -
--
-CREATE TABLE users (
+CREATE TABLE public.users (
id integer NOT NULL,
uuid character varying(255),
owner_uuid character varying(255) NOT NULL,
-- Name: materialized_permission_view; Type: MATERIALIZED VIEW; Schema: public; Owner: -
--
-CREATE MATERIALIZED VIEW materialized_permission_view AS
+CREATE MATERIALIZED VIEW public.materialized_permission_view AS
WITH RECURSIVE perm_value(name, val) AS (
VALUES ('can_read'::text,(1)::smallint), ('can_login'::text,1), ('can_write'::text,2), ('can_manage'::text,3)
), perm_edges(tail_uuid, head_uuid, val, follow, trashed) AS (
((pv.val = 3) OR (groups.uuid IS NOT NULL)) AS follow,
(0)::smallint AS trashed,
(0)::smallint AS followtrash
- FROM ((links
+ FROM ((public.links
LEFT JOIN perm_value pv ON ((pv.name = (links.name)::text)))
- LEFT JOIN groups ON (((pv.val < 3) AND ((groups.uuid)::text = (links.head_uuid)::text))))
+ LEFT JOIN public.groups ON (((pv.val < 3) AND ((groups.uuid)::text = (links.head_uuid)::text))))
WHERE ((links.link_class)::text = 'permission'::text)
UNION ALL
SELECT groups.owner_uuid,
ELSE 0
END AS "case",
1
- FROM groups
+ FROM public.groups
), perm(val, follow, user_uuid, target_uuid, trashed) AS (
SELECT (3)::smallint AS val,
true AS follow,
(users.uuid)::character varying(32) AS user_uuid,
(users.uuid)::character varying(32) AS target_uuid,
(0)::smallint AS trashed
- FROM users
+ FROM public.users
UNION
SELECT (LEAST((perm_1.val)::integer, edges.val))::smallint AS val,
edges.follow,
-- Name: nodes; Type: TABLE; Schema: public; Owner: -
--
-CREATE TABLE nodes (
+CREATE TABLE public.nodes (
id integer NOT NULL,
uuid character varying(255),
owner_uuid character varying(255),
-- Name: nodes_id_seq; Type: SEQUENCE; Schema: public; Owner: -
--
-CREATE SEQUENCE nodes_id_seq
+CREATE SEQUENCE public.nodes_id_seq
START WITH 1
INCREMENT BY 1
NO MINVALUE
-- Name: nodes_id_seq; Type: SEQUENCE OWNED BY; Schema: public; Owner: -
--
-ALTER SEQUENCE nodes_id_seq OWNED BY nodes.id;
+ALTER SEQUENCE public.nodes_id_seq OWNED BY public.nodes.id;
--
-- Name: permission_refresh_lock; Type: TABLE; Schema: public; Owner: -
--
-CREATE TABLE permission_refresh_lock (
+CREATE TABLE public.permission_refresh_lock (
id integer NOT NULL
);
-- Name: permission_refresh_lock_id_seq; Type: SEQUENCE; Schema: public; Owner: -
--
-CREATE SEQUENCE permission_refresh_lock_id_seq
+CREATE SEQUENCE public.permission_refresh_lock_id_seq
START WITH 1
INCREMENT BY 1
NO MINVALUE
-- Name: permission_refresh_lock_id_seq; Type: SEQUENCE OWNED BY; Schema: public; Owner: -
--
-ALTER SEQUENCE permission_refresh_lock_id_seq OWNED BY permission_refresh_lock.id;
+ALTER SEQUENCE public.permission_refresh_lock_id_seq OWNED BY public.permission_refresh_lock.id;
--
-- Name: pipeline_instances; Type: TABLE; Schema: public; Owner: -
--
-CREATE TABLE pipeline_instances (
+CREATE TABLE public.pipeline_instances (
id integer NOT NULL,
uuid character varying(255),
owner_uuid character varying(255),
-- Name: pipeline_instances_id_seq; Type: SEQUENCE; Schema: public; Owner: -
--
-CREATE SEQUENCE pipeline_instances_id_seq
+CREATE SEQUENCE public.pipeline_instances_id_seq
START WITH 1
INCREMENT BY 1
NO MINVALUE
-- Name: pipeline_instances_id_seq; Type: SEQUENCE OWNED BY; Schema: public; Owner: -
--
-ALTER SEQUENCE pipeline_instances_id_seq OWNED BY pipeline_instances.id;
+ALTER SEQUENCE public.pipeline_instances_id_seq OWNED BY public.pipeline_instances.id;
--
-- Name: pipeline_templates; Type: TABLE; Schema: public; Owner: -
--
-CREATE TABLE pipeline_templates (
+CREATE TABLE public.pipeline_templates (
id integer NOT NULL,
uuid character varying(255),
owner_uuid character varying(255),
-- Name: pipeline_templates_id_seq; Type: SEQUENCE; Schema: public; Owner: -
--
-CREATE SEQUENCE pipeline_templates_id_seq
+CREATE SEQUENCE public.pipeline_templates_id_seq
START WITH 1
INCREMENT BY 1
NO MINVALUE
-- Name: pipeline_templates_id_seq; Type: SEQUENCE OWNED BY; Schema: public; Owner: -
--
-ALTER SEQUENCE pipeline_templates_id_seq OWNED BY pipeline_templates.id;
+ALTER SEQUENCE public.pipeline_templates_id_seq OWNED BY public.pipeline_templates.id;
--
-- Name: repositories; Type: TABLE; Schema: public; Owner: -
--
-CREATE TABLE repositories (
+CREATE TABLE public.repositories (
id integer NOT NULL,
uuid character varying(255) NOT NULL,
owner_uuid character varying(255) NOT NULL,
-- Name: repositories_id_seq; Type: SEQUENCE; Schema: public; Owner: -
--
-CREATE SEQUENCE repositories_id_seq
+CREATE SEQUENCE public.repositories_id_seq
START WITH 1
INCREMENT BY 1
NO MINVALUE
-- Name: repositories_id_seq; Type: SEQUENCE OWNED BY; Schema: public; Owner: -
--
-ALTER SEQUENCE repositories_id_seq OWNED BY repositories.id;
+ALTER SEQUENCE public.repositories_id_seq OWNED BY public.repositories.id;
--
-- Name: schema_migrations; Type: TABLE; Schema: public; Owner: -
--
-CREATE TABLE schema_migrations (
+CREATE TABLE public.schema_migrations (
version character varying(255) NOT NULL
);
-- Name: specimens; Type: TABLE; Schema: public; Owner: -
--
-CREATE TABLE specimens (
+CREATE TABLE public.specimens (
id integer NOT NULL,
uuid character varying(255),
owner_uuid character varying(255),
-- Name: specimens_id_seq; Type: SEQUENCE; Schema: public; Owner: -
--
-CREATE SEQUENCE specimens_id_seq
+CREATE SEQUENCE public.specimens_id_seq
START WITH 1
INCREMENT BY 1
NO MINVALUE
-- Name: specimens_id_seq; Type: SEQUENCE OWNED BY; Schema: public; Owner: -
--
-ALTER SEQUENCE specimens_id_seq OWNED BY specimens.id;
+ALTER SEQUENCE public.specimens_id_seq OWNED BY public.specimens.id;
--
-- Name: traits; Type: TABLE; Schema: public; Owner: -
--
-CREATE TABLE traits (
+CREATE TABLE public.traits (
id integer NOT NULL,
uuid character varying(255) NOT NULL,
owner_uuid character varying(255) NOT NULL,
-- Name: traits_id_seq; Type: SEQUENCE; Schema: public; Owner: -
--
-CREATE SEQUENCE traits_id_seq
+CREATE SEQUENCE public.traits_id_seq
START WITH 1
INCREMENT BY 1
NO MINVALUE
-- Name: traits_id_seq; Type: SEQUENCE OWNED BY; Schema: public; Owner: -
--
-ALTER SEQUENCE traits_id_seq OWNED BY traits.id;
+ALTER SEQUENCE public.traits_id_seq OWNED BY public.traits.id;
--
-- Name: users_id_seq; Type: SEQUENCE; Schema: public; Owner: -
--
-CREATE SEQUENCE users_id_seq
+CREATE SEQUENCE public.users_id_seq
START WITH 1
INCREMENT BY 1
NO MINVALUE
-- Name: users_id_seq; Type: SEQUENCE OWNED BY; Schema: public; Owner: -
--
-ALTER SEQUENCE users_id_seq OWNED BY users.id;
+ALTER SEQUENCE public.users_id_seq OWNED BY public.users.id;
--
-- Name: virtual_machines; Type: TABLE; Schema: public; Owner: -
--
-CREATE TABLE virtual_machines (
+CREATE TABLE public.virtual_machines (
id integer NOT NULL,
uuid character varying(255) NOT NULL,
owner_uuid character varying(255) NOT NULL,
-- Name: virtual_machines_id_seq; Type: SEQUENCE; Schema: public; Owner: -
--
-CREATE SEQUENCE virtual_machines_id_seq
+CREATE SEQUENCE public.virtual_machines_id_seq
START WITH 1
INCREMENT BY 1
NO MINVALUE
-- Name: virtual_machines_id_seq; Type: SEQUENCE OWNED BY; Schema: public; Owner: -
--
-ALTER SEQUENCE virtual_machines_id_seq OWNED BY virtual_machines.id;
+ALTER SEQUENCE public.virtual_machines_id_seq OWNED BY public.virtual_machines.id;
--
-- Name: workflows; Type: TABLE; Schema: public; Owner: -
--
-CREATE TABLE workflows (
+CREATE TABLE public.workflows (
id integer NOT NULL,
uuid character varying(255),
owner_uuid character varying(255),
-- Name: workflows_id_seq; Type: SEQUENCE; Schema: public; Owner: -
--
-CREATE SEQUENCE workflows_id_seq
+CREATE SEQUENCE public.workflows_id_seq
START WITH 1
INCREMENT BY 1
NO MINVALUE
-- Name: workflows_id_seq; Type: SEQUENCE OWNED BY; Schema: public; Owner: -
--
-ALTER SEQUENCE workflows_id_seq OWNED BY workflows.id;
+ALTER SEQUENCE public.workflows_id_seq OWNED BY public.workflows.id;
--
-- Name: api_client_authorizations id; Type: DEFAULT; Schema: public; Owner: -
--
-ALTER TABLE ONLY api_client_authorizations ALTER COLUMN id SET DEFAULT nextval('api_client_authorizations_id_seq'::regclass);
+ALTER TABLE ONLY public.api_client_authorizations ALTER COLUMN id SET DEFAULT nextval('public.api_client_authorizations_id_seq'::regclass);
--
-- Name: api_clients id; Type: DEFAULT; Schema: public; Owner: -
--
-ALTER TABLE ONLY api_clients ALTER COLUMN id SET DEFAULT nextval('api_clients_id_seq'::regclass);
+ALTER TABLE ONLY public.api_clients ALTER COLUMN id SET DEFAULT nextval('public.api_clients_id_seq'::regclass);
--
-- Name: authorized_keys id; Type: DEFAULT; Schema: public; Owner: -
--
-ALTER TABLE ONLY authorized_keys ALTER COLUMN id SET DEFAULT nextval('authorized_keys_id_seq'::regclass);
+ALTER TABLE ONLY public.authorized_keys ALTER COLUMN id SET DEFAULT nextval('public.authorized_keys_id_seq'::regclass);
--
-- Name: collections id; Type: DEFAULT; Schema: public; Owner: -
--
-ALTER TABLE ONLY collections ALTER COLUMN id SET DEFAULT nextval('collections_id_seq'::regclass);
+ALTER TABLE ONLY public.collections ALTER COLUMN id SET DEFAULT nextval('public.collections_id_seq'::regclass);
--
-- Name: commit_ancestors id; Type: DEFAULT; Schema: public; Owner: -
--
-ALTER TABLE ONLY commit_ancestors ALTER COLUMN id SET DEFAULT nextval('commit_ancestors_id_seq'::regclass);
+ALTER TABLE ONLY public.commit_ancestors ALTER COLUMN id SET DEFAULT nextval('public.commit_ancestors_id_seq'::regclass);
--
-- Name: commits id; Type: DEFAULT; Schema: public; Owner: -
--
-ALTER TABLE ONLY commits ALTER COLUMN id SET DEFAULT nextval('commits_id_seq'::regclass);
+ALTER TABLE ONLY public.commits ALTER COLUMN id SET DEFAULT nextval('public.commits_id_seq'::regclass);
--
-- Name: container_requests id; Type: DEFAULT; Schema: public; Owner: -
--
-ALTER TABLE ONLY container_requests ALTER COLUMN id SET DEFAULT nextval('container_requests_id_seq'::regclass);
+ALTER TABLE ONLY public.container_requests ALTER COLUMN id SET DEFAULT nextval('public.container_requests_id_seq'::regclass);
--
-- Name: containers id; Type: DEFAULT; Schema: public; Owner: -
--
-ALTER TABLE ONLY containers ALTER COLUMN id SET DEFAULT nextval('containers_id_seq'::regclass);
+ALTER TABLE ONLY public.containers ALTER COLUMN id SET DEFAULT nextval('public.containers_id_seq'::regclass);
--
-- Name: groups id; Type: DEFAULT; Schema: public; Owner: -
--
-ALTER TABLE ONLY groups ALTER COLUMN id SET DEFAULT nextval('groups_id_seq'::regclass);
+ALTER TABLE ONLY public.groups ALTER COLUMN id SET DEFAULT nextval('public.groups_id_seq'::regclass);
--
-- Name: humans id; Type: DEFAULT; Schema: public; Owner: -
--
-ALTER TABLE ONLY humans ALTER COLUMN id SET DEFAULT nextval('humans_id_seq'::regclass);
+ALTER TABLE ONLY public.humans ALTER COLUMN id SET DEFAULT nextval('public.humans_id_seq'::regclass);
--
-- Name: job_tasks id; Type: DEFAULT; Schema: public; Owner: -
--
-ALTER TABLE ONLY job_tasks ALTER COLUMN id SET DEFAULT nextval('job_tasks_id_seq'::regclass);
+ALTER TABLE ONLY public.job_tasks ALTER COLUMN id SET DEFAULT nextval('public.job_tasks_id_seq'::regclass);
--
-- Name: jobs id; Type: DEFAULT; Schema: public; Owner: -
--
-ALTER TABLE ONLY jobs ALTER COLUMN id SET DEFAULT nextval('jobs_id_seq'::regclass);
+ALTER TABLE ONLY public.jobs ALTER COLUMN id SET DEFAULT nextval('public.jobs_id_seq'::regclass);
--
-- Name: keep_disks id; Type: DEFAULT; Schema: public; Owner: -
--
-ALTER TABLE ONLY keep_disks ALTER COLUMN id SET DEFAULT nextval('keep_disks_id_seq'::regclass);
+ALTER TABLE ONLY public.keep_disks ALTER COLUMN id SET DEFAULT nextval('public.keep_disks_id_seq'::regclass);
--
-- Name: keep_services id; Type: DEFAULT; Schema: public; Owner: -
--
-ALTER TABLE ONLY keep_services ALTER COLUMN id SET DEFAULT nextval('keep_services_id_seq'::regclass);
+ALTER TABLE ONLY public.keep_services ALTER COLUMN id SET DEFAULT nextval('public.keep_services_id_seq'::regclass);
--
-- Name: links id; Type: DEFAULT; Schema: public; Owner: -
--
-ALTER TABLE ONLY links ALTER COLUMN id SET DEFAULT nextval('links_id_seq'::regclass);
+ALTER TABLE ONLY public.links ALTER COLUMN id SET DEFAULT nextval('public.links_id_seq'::regclass);
--
-- Name: logs id; Type: DEFAULT; Schema: public; Owner: -
--
-ALTER TABLE ONLY logs ALTER COLUMN id SET DEFAULT nextval('logs_id_seq'::regclass);
+ALTER TABLE ONLY public.logs ALTER COLUMN id SET DEFAULT nextval('public.logs_id_seq'::regclass);
--
-- Name: nodes id; Type: DEFAULT; Schema: public; Owner: -
--
-ALTER TABLE ONLY nodes ALTER COLUMN id SET DEFAULT nextval('nodes_id_seq'::regclass);
+ALTER TABLE ONLY public.nodes ALTER COLUMN id SET DEFAULT nextval('public.nodes_id_seq'::regclass);
--
-- Name: permission_refresh_lock id; Type: DEFAULT; Schema: public; Owner: -
--
-ALTER TABLE ONLY permission_refresh_lock ALTER COLUMN id SET DEFAULT nextval('permission_refresh_lock_id_seq'::regclass);
+ALTER TABLE ONLY public.permission_refresh_lock ALTER COLUMN id SET DEFAULT nextval('public.permission_refresh_lock_id_seq'::regclass);
--
-- Name: pipeline_instances id; Type: DEFAULT; Schema: public; Owner: -
--
-ALTER TABLE ONLY pipeline_instances ALTER COLUMN id SET DEFAULT nextval('pipeline_instances_id_seq'::regclass);
+ALTER TABLE ONLY public.pipeline_instances ALTER COLUMN id SET DEFAULT nextval('public.pipeline_instances_id_seq'::regclass);
--
-- Name: pipeline_templates id; Type: DEFAULT; Schema: public; Owner: -
--
-ALTER TABLE ONLY pipeline_templates ALTER COLUMN id SET DEFAULT nextval('pipeline_templates_id_seq'::regclass);
+ALTER TABLE ONLY public.pipeline_templates ALTER COLUMN id SET DEFAULT nextval('public.pipeline_templates_id_seq'::regclass);
--
-- Name: repositories id; Type: DEFAULT; Schema: public; Owner: -
--
-ALTER TABLE ONLY repositories ALTER COLUMN id SET DEFAULT nextval('repositories_id_seq'::regclass);
+ALTER TABLE ONLY public.repositories ALTER COLUMN id SET DEFAULT nextval('public.repositories_id_seq'::regclass);
--
-- Name: specimens id; Type: DEFAULT; Schema: public; Owner: -
--
-ALTER TABLE ONLY specimens ALTER COLUMN id SET DEFAULT nextval('specimens_id_seq'::regclass);
+ALTER TABLE ONLY public.specimens ALTER COLUMN id SET DEFAULT nextval('public.specimens_id_seq'::regclass);
--
-- Name: traits id; Type: DEFAULT; Schema: public; Owner: -
--
-ALTER TABLE ONLY traits ALTER COLUMN id SET DEFAULT nextval('traits_id_seq'::regclass);
+ALTER TABLE ONLY public.traits ALTER COLUMN id SET DEFAULT nextval('public.traits_id_seq'::regclass);
--
-- Name: users id; Type: DEFAULT; Schema: public; Owner: -
--
-ALTER TABLE ONLY users ALTER COLUMN id SET DEFAULT nextval('users_id_seq'::regclass);
+ALTER TABLE ONLY public.users ALTER COLUMN id SET DEFAULT nextval('public.users_id_seq'::regclass);
--
-- Name: virtual_machines id; Type: DEFAULT; Schema: public; Owner: -
--
-ALTER TABLE ONLY virtual_machines ALTER COLUMN id SET DEFAULT nextval('virtual_machines_id_seq'::regclass);
+ALTER TABLE ONLY public.virtual_machines ALTER COLUMN id SET DEFAULT nextval('public.virtual_machines_id_seq'::regclass);
--
-- Name: workflows id; Type: DEFAULT; Schema: public; Owner: -
--
-ALTER TABLE ONLY workflows ALTER COLUMN id SET DEFAULT nextval('workflows_id_seq'::regclass);
+ALTER TABLE ONLY public.workflows ALTER COLUMN id SET DEFAULT nextval('public.workflows_id_seq'::regclass);
--
-- Name: api_client_authorizations api_client_authorizations_pkey; Type: CONSTRAINT; Schema: public; Owner: -
--
-ALTER TABLE ONLY api_client_authorizations
+ALTER TABLE ONLY public.api_client_authorizations
ADD CONSTRAINT api_client_authorizations_pkey PRIMARY KEY (id);
-- Name: api_clients api_clients_pkey; Type: CONSTRAINT; Schema: public; Owner: -
--
-ALTER TABLE ONLY api_clients
+ALTER TABLE ONLY public.api_clients
ADD CONSTRAINT api_clients_pkey PRIMARY KEY (id);
-- Name: authorized_keys authorized_keys_pkey; Type: CONSTRAINT; Schema: public; Owner: -
--
-ALTER TABLE ONLY authorized_keys
+ALTER TABLE ONLY public.authorized_keys
ADD CONSTRAINT authorized_keys_pkey PRIMARY KEY (id);
-- Name: collections collections_pkey; Type: CONSTRAINT; Schema: public; Owner: -
--
-ALTER TABLE ONLY collections
+ALTER TABLE ONLY public.collections
ADD CONSTRAINT collections_pkey PRIMARY KEY (id);
-- Name: commit_ancestors commit_ancestors_pkey; Type: CONSTRAINT; Schema: public; Owner: -
--
-ALTER TABLE ONLY commit_ancestors
+ALTER TABLE ONLY public.commit_ancestors
ADD CONSTRAINT commit_ancestors_pkey PRIMARY KEY (id);
-- Name: commits commits_pkey; Type: CONSTRAINT; Schema: public; Owner: -
--
-ALTER TABLE ONLY commits
+ALTER TABLE ONLY public.commits
ADD CONSTRAINT commits_pkey PRIMARY KEY (id);
-- Name: container_requests container_requests_pkey; Type: CONSTRAINT; Schema: public; Owner: -
--
-ALTER TABLE ONLY container_requests
+ALTER TABLE ONLY public.container_requests
ADD CONSTRAINT container_requests_pkey PRIMARY KEY (id);
-- Name: containers containers_pkey; Type: CONSTRAINT; Schema: public; Owner: -
--
-ALTER TABLE ONLY containers
+ALTER TABLE ONLY public.containers
ADD CONSTRAINT containers_pkey PRIMARY KEY (id);
-- Name: groups groups_pkey; Type: CONSTRAINT; Schema: public; Owner: -
--
-ALTER TABLE ONLY groups
+ALTER TABLE ONLY public.groups
ADD CONSTRAINT groups_pkey PRIMARY KEY (id);
-- Name: humans humans_pkey; Type: CONSTRAINT; Schema: public; Owner: -
--
-ALTER TABLE ONLY humans
+ALTER TABLE ONLY public.humans
ADD CONSTRAINT humans_pkey PRIMARY KEY (id);
-- Name: job_tasks job_tasks_pkey; Type: CONSTRAINT; Schema: public; Owner: -
--
-ALTER TABLE ONLY job_tasks
+ALTER TABLE ONLY public.job_tasks
ADD CONSTRAINT job_tasks_pkey PRIMARY KEY (id);
-- Name: jobs jobs_pkey; Type: CONSTRAINT; Schema: public; Owner: -
--
-ALTER TABLE ONLY jobs
+ALTER TABLE ONLY public.jobs
ADD CONSTRAINT jobs_pkey PRIMARY KEY (id);
-- Name: keep_disks keep_disks_pkey; Type: CONSTRAINT; Schema: public; Owner: -
--
-ALTER TABLE ONLY keep_disks
+ALTER TABLE ONLY public.keep_disks
ADD CONSTRAINT keep_disks_pkey PRIMARY KEY (id);
-- Name: keep_services keep_services_pkey; Type: CONSTRAINT; Schema: public; Owner: -
--
-ALTER TABLE ONLY keep_services
+ALTER TABLE ONLY public.keep_services
ADD CONSTRAINT keep_services_pkey PRIMARY KEY (id);
-- Name: links links_pkey; Type: CONSTRAINT; Schema: public; Owner: -
--
-ALTER TABLE ONLY links
+ALTER TABLE ONLY public.links
ADD CONSTRAINT links_pkey PRIMARY KEY (id);
-- Name: logs logs_pkey; Type: CONSTRAINT; Schema: public; Owner: -
--
-ALTER TABLE ONLY logs
+ALTER TABLE ONLY public.logs
ADD CONSTRAINT logs_pkey PRIMARY KEY (id);
-- Name: nodes nodes_pkey; Type: CONSTRAINT; Schema: public; Owner: -
--
-ALTER TABLE ONLY nodes
+ALTER TABLE ONLY public.nodes
ADD CONSTRAINT nodes_pkey PRIMARY KEY (id);
-- Name: permission_refresh_lock permission_refresh_lock_pkey; Type: CONSTRAINT; Schema: public; Owner: -
--
-ALTER TABLE ONLY permission_refresh_lock
+ALTER TABLE ONLY public.permission_refresh_lock
ADD CONSTRAINT permission_refresh_lock_pkey PRIMARY KEY (id);
-- Name: pipeline_instances pipeline_instances_pkey; Type: CONSTRAINT; Schema: public; Owner: -
--
-ALTER TABLE ONLY pipeline_instances
+ALTER TABLE ONLY public.pipeline_instances
ADD CONSTRAINT pipeline_instances_pkey PRIMARY KEY (id);
-- Name: pipeline_templates pipeline_templates_pkey; Type: CONSTRAINT; Schema: public; Owner: -
--
-ALTER TABLE ONLY pipeline_templates
+ALTER TABLE ONLY public.pipeline_templates
ADD CONSTRAINT pipeline_templates_pkey PRIMARY KEY (id);
-- Name: repositories repositories_pkey; Type: CONSTRAINT; Schema: public; Owner: -
--
-ALTER TABLE ONLY repositories
+ALTER TABLE ONLY public.repositories
ADD CONSTRAINT repositories_pkey PRIMARY KEY (id);
-- Name: specimens specimens_pkey; Type: CONSTRAINT; Schema: public; Owner: -
--
-ALTER TABLE ONLY specimens
+ALTER TABLE ONLY public.specimens
ADD CONSTRAINT specimens_pkey PRIMARY KEY (id);
-- Name: traits traits_pkey; Type: CONSTRAINT; Schema: public; Owner: -
--
-ALTER TABLE ONLY traits
+ALTER TABLE ONLY public.traits
ADD CONSTRAINT traits_pkey PRIMARY KEY (id);
-- Name: users users_pkey; Type: CONSTRAINT; Schema: public; Owner: -
--
-ALTER TABLE ONLY users
+ALTER TABLE ONLY public.users
ADD CONSTRAINT users_pkey PRIMARY KEY (id);
-- Name: virtual_machines virtual_machines_pkey; Type: CONSTRAINT; Schema: public; Owner: -
--
-ALTER TABLE ONLY virtual_machines
+ALTER TABLE ONLY public.virtual_machines
ADD CONSTRAINT virtual_machines_pkey PRIMARY KEY (id);
-- Name: workflows workflows_pkey; Type: CONSTRAINT; Schema: public; Owner: -
--
-ALTER TABLE ONLY workflows
+ALTER TABLE ONLY public.workflows
ADD CONSTRAINT workflows_pkey PRIMARY KEY (id);
-- Name: api_client_authorizations_search_index; Type: INDEX; Schema: public; Owner: -
--
-CREATE INDEX api_client_authorizations_search_index ON api_client_authorizations USING btree (api_token, created_by_ip_address, last_used_by_ip_address, default_owner_uuid, uuid);
+CREATE INDEX api_client_authorizations_search_index ON public.api_client_authorizations USING btree (api_token, created_by_ip_address, last_used_by_ip_address, default_owner_uuid, uuid);
--
-- Name: api_clients_search_index; Type: INDEX; Schema: public; Owner: -
--
-CREATE INDEX api_clients_search_index ON api_clients USING btree (uuid, owner_uuid, modified_by_client_uuid, modified_by_user_uuid, name, url_prefix);
+CREATE INDEX api_clients_search_index ON public.api_clients USING btree (uuid, owner_uuid, modified_by_client_uuid, modified_by_user_uuid, name, url_prefix);
--
-- Name: authorized_keys_search_index; Type: INDEX; Schema: public; Owner: -
--
-CREATE INDEX authorized_keys_search_index ON authorized_keys USING btree (uuid, owner_uuid, modified_by_client_uuid, modified_by_user_uuid, name, key_type, authorized_user_uuid);
+CREATE INDEX authorized_keys_search_index ON public.authorized_keys USING btree (uuid, owner_uuid, modified_by_client_uuid, modified_by_user_uuid, name, key_type, authorized_user_uuid);
--
-- Name: collection_index_on_properties; Type: INDEX; Schema: public; Owner: -
--
-CREATE INDEX collection_index_on_properties ON collections USING gin (properties);
+CREATE INDEX collection_index_on_properties ON public.collections USING gin (properties);
--
-- Name: collections_full_text_search_idx; Type: INDEX; Schema: public; Owner: -
--
-CREATE INDEX collections_full_text_search_idx ON collections USING gin (to_tsvector('english'::regconfig, (((((((((((((((((COALESCE(owner_uuid, ''::character varying))::text || ' '::text) || (COALESCE(modified_by_client_uuid, ''::character varying))::text) || ' '::text) || (COALESCE(modified_by_user_uuid, ''::character varying))::text) || ' '::text) || (COALESCE(portable_data_hash, ''::character varying))::text) || ' '::text) || (COALESCE(uuid, ''::character varying))::text) || ' '::text) || (COALESCE(name, ''::character varying))::text) || ' '::text) || (COALESCE(description, ''::character varying))::text) || ' '::text) || COALESCE((properties)::text, ''::text)) || ' '::text) || (COALESCE(file_names, ''::character varying))::text)));
+CREATE INDEX collections_full_text_search_idx ON public.collections USING gin (to_tsvector('english'::regconfig, (((((((((((((((((COALESCE(owner_uuid, ''::character varying))::text || ' '::text) || (COALESCE(modified_by_client_uuid, ''::character varying))::text) || ' '::text) || (COALESCE(modified_by_user_uuid, ''::character varying))::text) || ' '::text) || (COALESCE(portable_data_hash, ''::character varying))::text) || ' '::text) || (COALESCE(uuid, ''::character varying))::text) || ' '::text) || (COALESCE(name, ''::character varying))::text) || ' '::text) || (COALESCE(description, ''::character varying))::text) || ' '::text) || COALESCE((properties)::text, ''::text)) || ' '::text) || COALESCE(file_names, (''::character varying)::text))));
--
-- Name: collections_search_index; Type: INDEX; Schema: public; Owner: -
--
-CREATE INDEX collections_search_index ON collections USING btree (owner_uuid, modified_by_client_uuid, modified_by_user_uuid, portable_data_hash, uuid, name);
+CREATE INDEX collections_search_index ON public.collections USING btree (owner_uuid, modified_by_client_uuid, modified_by_user_uuid, portable_data_hash, uuid, name);
--
-- Name: container_requests_full_text_search_idx; Type: INDEX; Schema: public; Owner: -
--
-CREATE INDEX container_requests_full_text_search_idx ON container_requests USING gin (to_tsvector('english'::regconfig, (((((((((((((((((((((((((((((((((((((((((COALESCE(uuid, ''::character varying))::text || ' '::text) || (COALESCE(owner_uuid, ''::character varying))::text) || ' '::text) || (COALESCE(modified_by_client_uuid, ''::character varying))::text) || ' '::text) || (COALESCE(modified_by_user_uuid, ''::character varying))::text) || ' '::text) || (COALESCE(name, ''::character varying))::text) || ' '::text) || COALESCE(description, ''::text)) || ' '::text) || COALESCE((properties)::text, ''::text)) || ' '::text) || (COALESCE(state, ''::character varying))::text) || ' '::text) || (COALESCE(requesting_container_uuid, ''::character varying))::text) || ' '::text) || (COALESCE(container_uuid, ''::character varying))::text) || ' '::text) || COALESCE(runtime_constraints, ''::text)) || ' '::text) || (COALESCE(container_image, ''::character varying))::text) || ' '::text) || COALESCE(environment, ''::text)) || ' '::text) || (COALESCE(cwd, ''::character varying))::text) || ' '::text) || COALESCE(command, ''::text)) || ' '::text) || (COALESCE(output_path, ''::character varying))::text) || ' '::text) || COALESCE(filters, ''::text)) || ' '::text) || COALESCE(scheduling_parameters, ''::text)) || ' '::text) || (COALESCE(output_uuid, ''::character varying))::text) || ' '::text) || (COALESCE(log_uuid, ''::character varying))::text) || ' '::text) || (COALESCE(output_name, ''::character varying))::text)));
+CREATE INDEX container_requests_full_text_search_idx ON public.container_requests USING gin (to_tsvector('english'::regconfig, (((((((((((((((((((((((((((((((((((((((((COALESCE(uuid, ''::character varying))::text || ' '::text) || (COALESCE(owner_uuid, ''::character varying))::text) || ' '::text) || (COALESCE(modified_by_client_uuid, ''::character varying))::text) || ' '::text) || (COALESCE(modified_by_user_uuid, ''::character varying))::text) || ' '::text) || (COALESCE(name, ''::character varying))::text) || ' '::text) || COALESCE(description, ''::text)) || ' '::text) || COALESCE((properties)::text, ''::text)) || ' '::text) || (COALESCE(state, ''::character varying))::text) || ' '::text) || (COALESCE(requesting_container_uuid, ''::character varying))::text) || ' '::text) || (COALESCE(container_uuid, ''::character varying))::text) || ' '::text) || COALESCE(runtime_constraints, ''::text)) || ' '::text) || (COALESCE(container_image, ''::character varying))::text) || ' '::text) || COALESCE(environment, ''::text)) || ' '::text) || (COALESCE(cwd, ''::character varying))::text) || ' '::text) || COALESCE(command, ''::text)) || ' '::text) || (COALESCE(output_path, ''::character varying))::text) || ' '::text) || COALESCE(filters, ''::text)) || ' '::text) || COALESCE(scheduling_parameters, ''::text)) || ' '::text) || (COALESCE(output_uuid, ''::character varying))::text) || ' '::text) || (COALESCE(log_uuid, ''::character varying))::text) || ' '::text) || (COALESCE(output_name, ''::character varying))::text)));
--
-- Name: container_requests_index_on_properties; Type: INDEX; Schema: public; Owner: -
--
-CREATE INDEX container_requests_index_on_properties ON container_requests USING gin (properties);
+CREATE INDEX container_requests_index_on_properties ON public.container_requests USING gin (properties);
--
-- Name: container_requests_search_index; Type: INDEX; Schema: public; Owner: -
--
-CREATE INDEX container_requests_search_index ON container_requests USING btree (uuid, owner_uuid, modified_by_client_uuid, modified_by_user_uuid, name, state, requesting_container_uuid, container_uuid, container_image, cwd, output_path, output_uuid, log_uuid, output_name);
+CREATE INDEX container_requests_search_index ON public.container_requests USING btree (uuid, owner_uuid, modified_by_client_uuid, modified_by_user_uuid, name, state, requesting_container_uuid, container_uuid, container_image, cwd, output_path, output_uuid, log_uuid, output_name);
--
-- Name: containers_search_index; Type: INDEX; Schema: public; Owner: -
--
-CREATE INDEX containers_search_index ON containers USING btree (uuid, owner_uuid, modified_by_client_uuid, modified_by_user_uuid, state, log, cwd, output_path, output, container_image, auth_uuid, locked_by_uuid);
+CREATE INDEX containers_search_index ON public.containers USING btree (uuid, owner_uuid, modified_by_client_uuid, modified_by_user_uuid, state, log, cwd, output_path, output, container_image, auth_uuid, locked_by_uuid);
--
-- Name: group_index_on_properties; Type: INDEX; Schema: public; Owner: -
--
-CREATE INDEX group_index_on_properties ON groups USING gin (properties);
+CREATE INDEX group_index_on_properties ON public.groups USING gin (properties);
--
-- Name: groups_full_text_search_idx; Type: INDEX; Schema: public; Owner: -
--
-CREATE INDEX groups_full_text_search_idx ON groups USING gin (to_tsvector('english'::regconfig, (((((((((((((((COALESCE(uuid, ''::character varying))::text || ' '::text) || (COALESCE(owner_uuid, ''::character varying))::text) || ' '::text) || (COALESCE(modified_by_client_uuid, ''::character varying))::text) || ' '::text) || (COALESCE(modified_by_user_uuid, ''::character varying))::text) || ' '::text) || (COALESCE(name, ''::character varying))::text) || ' '::text) || (COALESCE(description, ''::character varying))::text) || ' '::text) || (COALESCE(group_class, ''::character varying))::text) || ' '::text) || COALESCE((properties)::text, ''::text))));
+CREATE INDEX groups_full_text_search_idx ON public.groups USING gin (to_tsvector('english'::regconfig, (((((((((((((((COALESCE(uuid, ''::character varying))::text || ' '::text) || (COALESCE(owner_uuid, ''::character varying))::text) || ' '::text) || (COALESCE(modified_by_client_uuid, ''::character varying))::text) || ' '::text) || (COALESCE(modified_by_user_uuid, ''::character varying))::text) || ' '::text) || (COALESCE(name, ''::character varying))::text) || ' '::text) || (COALESCE(description, ''::character varying))::text) || ' '::text) || (COALESCE(group_class, ''::character varying))::text) || ' '::text) || COALESCE((properties)::text, ''::text))));
--
-- Name: groups_search_index; Type: INDEX; Schema: public; Owner: -
--
-CREATE INDEX groups_search_index ON groups USING btree (uuid, owner_uuid, modified_by_client_uuid, modified_by_user_uuid, name, group_class);
+CREATE INDEX groups_search_index ON public.groups USING btree (uuid, owner_uuid, modified_by_client_uuid, modified_by_user_uuid, name, group_class);
--
-- Name: humans_search_index; Type: INDEX; Schema: public; Owner: -
--
-CREATE INDEX humans_search_index ON humans USING btree (uuid, owner_uuid, modified_by_client_uuid, modified_by_user_uuid);
+CREATE INDEX humans_search_index ON public.humans USING btree (uuid, owner_uuid, modified_by_client_uuid, modified_by_user_uuid);
--
-- Name: index_api_client_authorizations_on_api_client_id; Type: INDEX; Schema: public; Owner: -
--
-CREATE INDEX index_api_client_authorizations_on_api_client_id ON api_client_authorizations USING btree (api_client_id);
+CREATE INDEX index_api_client_authorizations_on_api_client_id ON public.api_client_authorizations USING btree (api_client_id);
--
-- Name: index_api_client_authorizations_on_api_token; Type: INDEX; Schema: public; Owner: -
--
-CREATE UNIQUE INDEX index_api_client_authorizations_on_api_token ON api_client_authorizations USING btree (api_token);
+CREATE UNIQUE INDEX index_api_client_authorizations_on_api_token ON public.api_client_authorizations USING btree (api_token);
--
-- Name: index_api_client_authorizations_on_expires_at; Type: INDEX; Schema: public; Owner: -
--
-CREATE INDEX index_api_client_authorizations_on_expires_at ON api_client_authorizations USING btree (expires_at);
+CREATE INDEX index_api_client_authorizations_on_expires_at ON public.api_client_authorizations USING btree (expires_at);
--
-- Name: index_api_client_authorizations_on_user_id; Type: INDEX; Schema: public; Owner: -
--
-CREATE INDEX index_api_client_authorizations_on_user_id ON api_client_authorizations USING btree (user_id);
+CREATE INDEX index_api_client_authorizations_on_user_id ON public.api_client_authorizations USING btree (user_id);
--
-- Name: index_api_client_authorizations_on_uuid; Type: INDEX; Schema: public; Owner: -
--
-CREATE UNIQUE INDEX index_api_client_authorizations_on_uuid ON api_client_authorizations USING btree (uuid);
+CREATE UNIQUE INDEX index_api_client_authorizations_on_uuid ON public.api_client_authorizations USING btree (uuid);
--
-- Name: index_api_clients_on_created_at; Type: INDEX; Schema: public; Owner: -
--
-CREATE INDEX index_api_clients_on_created_at ON api_clients USING btree (created_at);
+CREATE INDEX index_api_clients_on_created_at ON public.api_clients USING btree (created_at);
--
-- Name: index_api_clients_on_modified_at; Type: INDEX; Schema: public; Owner: -
--
-CREATE INDEX index_api_clients_on_modified_at ON api_clients USING btree (modified_at);
+CREATE INDEX index_api_clients_on_modified_at ON public.api_clients USING btree (modified_at);
--
-- Name: index_api_clients_on_owner_uuid; Type: INDEX; Schema: public; Owner: -
--
-CREATE INDEX index_api_clients_on_owner_uuid ON api_clients USING btree (owner_uuid);
+CREATE INDEX index_api_clients_on_owner_uuid ON public.api_clients USING btree (owner_uuid);
--
-- Name: index_api_clients_on_uuid; Type: INDEX; Schema: public; Owner: -
--
-CREATE UNIQUE INDEX index_api_clients_on_uuid ON api_clients USING btree (uuid);
+CREATE UNIQUE INDEX index_api_clients_on_uuid ON public.api_clients USING btree (uuid);
--
-- Name: index_authkeys_on_user_and_expires_at; Type: INDEX; Schema: public; Owner: -
--
-CREATE INDEX index_authkeys_on_user_and_expires_at ON authorized_keys USING btree (authorized_user_uuid, expires_at);
+CREATE INDEX index_authkeys_on_user_and_expires_at ON public.authorized_keys USING btree (authorized_user_uuid, expires_at);
--
-- Name: index_authorized_keys_on_owner_uuid; Type: INDEX; Schema: public; Owner: -
--
-CREATE INDEX index_authorized_keys_on_owner_uuid ON authorized_keys USING btree (owner_uuid);
+CREATE INDEX index_authorized_keys_on_owner_uuid ON public.authorized_keys USING btree (owner_uuid);
--
-- Name: index_authorized_keys_on_uuid; Type: INDEX; Schema: public; Owner: -
--
-CREATE UNIQUE INDEX index_authorized_keys_on_uuid ON authorized_keys USING btree (uuid);
+CREATE UNIQUE INDEX index_authorized_keys_on_uuid ON public.authorized_keys USING btree (uuid);
--
-- Name: index_collections_on_created_at; Type: INDEX; Schema: public; Owner: -
--
-CREATE INDEX index_collections_on_created_at ON collections USING btree (created_at);
+CREATE INDEX index_collections_on_created_at ON public.collections USING btree (created_at);
--
-- Name: index_collections_on_delete_at; Type: INDEX; Schema: public; Owner: -
--
-CREATE INDEX index_collections_on_delete_at ON collections USING btree (delete_at);
+CREATE INDEX index_collections_on_delete_at ON public.collections USING btree (delete_at);
--
-- Name: index_collections_on_is_trashed; Type: INDEX; Schema: public; Owner: -
--
-CREATE INDEX index_collections_on_is_trashed ON collections USING btree (is_trashed);
+CREATE INDEX index_collections_on_is_trashed ON public.collections USING btree (is_trashed);
--
-- Name: index_collections_on_modified_at; Type: INDEX; Schema: public; Owner: -
--
-CREATE INDEX index_collections_on_modified_at ON collections USING btree (modified_at);
+CREATE INDEX index_collections_on_modified_at ON public.collections USING btree (modified_at);
--
-- Name: index_collections_on_modified_at_uuid; Type: INDEX; Schema: public; Owner: -
--
-CREATE INDEX index_collections_on_modified_at_uuid ON collections USING btree (modified_at DESC, uuid);
+CREATE INDEX index_collections_on_modified_at_uuid ON public.collections USING btree (modified_at DESC, uuid);
--
-- Name: index_collections_on_owner_uuid; Type: INDEX; Schema: public; Owner: -
--
-CREATE INDEX index_collections_on_owner_uuid ON collections USING btree (owner_uuid);
+CREATE INDEX index_collections_on_owner_uuid ON public.collections USING btree (owner_uuid);
--
-- Name: index_collections_on_owner_uuid_and_name; Type: INDEX; Schema: public; Owner: -
--
-CREATE UNIQUE INDEX index_collections_on_owner_uuid_and_name ON collections USING btree (owner_uuid, name) WHERE (is_trashed = false);
+CREATE UNIQUE INDEX index_collections_on_owner_uuid_and_name ON public.collections USING btree (owner_uuid, name) WHERE (is_trashed = false);
--
-- Name: index_collections_on_portable_data_hash; Type: INDEX; Schema: public; Owner: -
--
-CREATE INDEX index_collections_on_portable_data_hash ON collections USING btree (portable_data_hash);
+CREATE INDEX index_collections_on_portable_data_hash ON public.collections USING btree (portable_data_hash);
--
-- Name: index_collections_on_trash_at; Type: INDEX; Schema: public; Owner: -
--
-CREATE INDEX index_collections_on_trash_at ON collections USING btree (trash_at);
+CREATE INDEX index_collections_on_trash_at ON public.collections USING btree (trash_at);
--
-- Name: index_collections_on_uuid; Type: INDEX; Schema: public; Owner: -
--
-CREATE UNIQUE INDEX index_collections_on_uuid ON collections USING btree (uuid);
+CREATE UNIQUE INDEX index_collections_on_uuid ON public.collections USING btree (uuid);
--
-- Name: index_commit_ancestors_on_descendant_and_ancestor; Type: INDEX; Schema: public; Owner: -
--
-CREATE UNIQUE INDEX index_commit_ancestors_on_descendant_and_ancestor ON commit_ancestors USING btree (descendant, ancestor);
+CREATE UNIQUE INDEX index_commit_ancestors_on_descendant_and_ancestor ON public.commit_ancestors USING btree (descendant, ancestor);
--
-- Name: index_commits_on_repository_name_and_sha1; Type: INDEX; Schema: public; Owner: -
--
-CREATE UNIQUE INDEX index_commits_on_repository_name_and_sha1 ON commits USING btree (repository_name, sha1);
+CREATE UNIQUE INDEX index_commits_on_repository_name_and_sha1 ON public.commits USING btree (repository_name, sha1);
--
-- Name: index_container_requests_on_container_uuid; Type: INDEX; Schema: public; Owner: -
--
-CREATE INDEX index_container_requests_on_container_uuid ON container_requests USING btree (container_uuid);
+CREATE INDEX index_container_requests_on_container_uuid ON public.container_requests USING btree (container_uuid);
--
-- Name: index_container_requests_on_modified_at_uuid; Type: INDEX; Schema: public; Owner: -
--
-CREATE INDEX index_container_requests_on_modified_at_uuid ON container_requests USING btree (modified_at DESC, uuid);
+CREATE INDEX index_container_requests_on_modified_at_uuid ON public.container_requests USING btree (modified_at DESC, uuid);
--
-- Name: index_container_requests_on_owner_uuid; Type: INDEX; Schema: public; Owner: -
--
-CREATE INDEX index_container_requests_on_owner_uuid ON container_requests USING btree (owner_uuid);
+CREATE INDEX index_container_requests_on_owner_uuid ON public.container_requests USING btree (owner_uuid);
--
-- Name: index_container_requests_on_requesting_container_uuid; Type: INDEX; Schema: public; Owner: -
--
-CREATE INDEX index_container_requests_on_requesting_container_uuid ON container_requests USING btree (requesting_container_uuid);
+CREATE INDEX index_container_requests_on_requesting_container_uuid ON public.container_requests USING btree (requesting_container_uuid);
--
-- Name: index_container_requests_on_uuid; Type: INDEX; Schema: public; Owner: -
--
-CREATE UNIQUE INDEX index_container_requests_on_uuid ON container_requests USING btree (uuid);
+CREATE UNIQUE INDEX index_container_requests_on_uuid ON public.container_requests USING btree (uuid);
--
-- Name: index_containers_on_auth_uuid; Type: INDEX; Schema: public; Owner: -
--
-CREATE INDEX index_containers_on_auth_uuid ON containers USING btree (auth_uuid);
+CREATE INDEX index_containers_on_auth_uuid ON public.containers USING btree (auth_uuid);
--
-- Name: index_containers_on_modified_at_uuid; Type: INDEX; Schema: public; Owner: -
--
-CREATE INDEX index_containers_on_modified_at_uuid ON containers USING btree (modified_at DESC, uuid);
+CREATE INDEX index_containers_on_modified_at_uuid ON public.containers USING btree (modified_at DESC, uuid);
--
-- Name: index_containers_on_owner_uuid; Type: INDEX; Schema: public; Owner: -
--
-CREATE INDEX index_containers_on_owner_uuid ON containers USING btree (owner_uuid);
+CREATE INDEX index_containers_on_owner_uuid ON public.containers USING btree (owner_uuid);
--
-- Name: index_containers_on_secret_mounts_md5; Type: INDEX; Schema: public; Owner: -
--
-CREATE INDEX index_containers_on_secret_mounts_md5 ON containers USING btree (secret_mounts_md5);
+CREATE INDEX index_containers_on_secret_mounts_md5 ON public.containers USING btree (secret_mounts_md5);
--
-- Name: index_containers_on_uuid; Type: INDEX; Schema: public; Owner: -
--
-CREATE UNIQUE INDEX index_containers_on_uuid ON containers USING btree (uuid);
+CREATE UNIQUE INDEX index_containers_on_uuid ON public.containers USING btree (uuid);
--
-- Name: index_groups_on_created_at; Type: INDEX; Schema: public; Owner: -
--
-CREATE INDEX index_groups_on_created_at ON groups USING btree (created_at);
+CREATE INDEX index_groups_on_created_at ON public.groups USING btree (created_at);
--
-- Name: index_groups_on_delete_at; Type: INDEX; Schema: public; Owner: -
--
-CREATE INDEX index_groups_on_delete_at ON groups USING btree (delete_at);
+CREATE INDEX index_groups_on_delete_at ON public.groups USING btree (delete_at);
--
-- Name: index_groups_on_group_class; Type: INDEX; Schema: public; Owner: -
--
-CREATE INDEX index_groups_on_group_class ON groups USING btree (group_class);
+CREATE INDEX index_groups_on_group_class ON public.groups USING btree (group_class);
--
-- Name: index_groups_on_is_trashed; Type: INDEX; Schema: public; Owner: -
--
-CREATE INDEX index_groups_on_is_trashed ON groups USING btree (is_trashed);
+CREATE INDEX index_groups_on_is_trashed ON public.groups USING btree (is_trashed);
--
-- Name: index_groups_on_modified_at; Type: INDEX; Schema: public; Owner: -
--
-CREATE INDEX index_groups_on_modified_at ON groups USING btree (modified_at);
+CREATE INDEX index_groups_on_modified_at ON public.groups USING btree (modified_at);
--
-- Name: index_groups_on_modified_at_uuid; Type: INDEX; Schema: public; Owner: -
--
-CREATE INDEX index_groups_on_modified_at_uuid ON groups USING btree (modified_at DESC, uuid);
+CREATE INDEX index_groups_on_modified_at_uuid ON public.groups USING btree (modified_at DESC, uuid);
--
-- Name: index_groups_on_owner_uuid; Type: INDEX; Schema: public; Owner: -
--
-CREATE INDEX index_groups_on_owner_uuid ON groups USING btree (owner_uuid);
+CREATE INDEX index_groups_on_owner_uuid ON public.groups USING btree (owner_uuid);
--
-- Name: index_groups_on_owner_uuid_and_name; Type: INDEX; Schema: public; Owner: -
--
-CREATE UNIQUE INDEX index_groups_on_owner_uuid_and_name ON groups USING btree (owner_uuid, name) WHERE (is_trashed = false);
+CREATE UNIQUE INDEX index_groups_on_owner_uuid_and_name ON public.groups USING btree (owner_uuid, name) WHERE (is_trashed = false);
--
-- Name: index_groups_on_trash_at; Type: INDEX; Schema: public; Owner: -
--
-CREATE INDEX index_groups_on_trash_at ON groups USING btree (trash_at);
+CREATE INDEX index_groups_on_trash_at ON public.groups USING btree (trash_at);
--
-- Name: index_groups_on_uuid; Type: INDEX; Schema: public; Owner: -
--
-CREATE UNIQUE INDEX index_groups_on_uuid ON groups USING btree (uuid);
+CREATE UNIQUE INDEX index_groups_on_uuid ON public.groups USING btree (uuid);
--
-- Name: index_humans_on_owner_uuid; Type: INDEX; Schema: public; Owner: -
--
-CREATE INDEX index_humans_on_owner_uuid ON humans USING btree (owner_uuid);
+CREATE INDEX index_humans_on_owner_uuid ON public.humans USING btree (owner_uuid);
--
-- Name: index_humans_on_uuid; Type: INDEX; Schema: public; Owner: -
--
-CREATE UNIQUE INDEX index_humans_on_uuid ON humans USING btree (uuid);
+CREATE UNIQUE INDEX index_humans_on_uuid ON public.humans USING btree (uuid);
--
-- Name: index_job_tasks_on_created_at; Type: INDEX; Schema: public; Owner: -
--
-CREATE INDEX index_job_tasks_on_created_at ON job_tasks USING btree (created_at);
+CREATE INDEX index_job_tasks_on_created_at ON public.job_tasks USING btree (created_at);
--
-- Name: index_job_tasks_on_created_by_job_task_uuid; Type: INDEX; Schema: public; Owner: -
--
-CREATE INDEX index_job_tasks_on_created_by_job_task_uuid ON job_tasks USING btree (created_by_job_task_uuid);
+CREATE INDEX index_job_tasks_on_created_by_job_task_uuid ON public.job_tasks USING btree (created_by_job_task_uuid);
--
-- Name: index_job_tasks_on_job_uuid; Type: INDEX; Schema: public; Owner: -
--
-CREATE INDEX index_job_tasks_on_job_uuid ON job_tasks USING btree (job_uuid);
+CREATE INDEX index_job_tasks_on_job_uuid ON public.job_tasks USING btree (job_uuid);
--
-- Name: index_job_tasks_on_modified_at; Type: INDEX; Schema: public; Owner: -
--
-CREATE INDEX index_job_tasks_on_modified_at ON job_tasks USING btree (modified_at);
+CREATE INDEX index_job_tasks_on_modified_at ON public.job_tasks USING btree (modified_at);
--
-- Name: index_job_tasks_on_owner_uuid; Type: INDEX; Schema: public; Owner: -
--
-CREATE INDEX index_job_tasks_on_owner_uuid ON job_tasks USING btree (owner_uuid);
+CREATE INDEX index_job_tasks_on_owner_uuid ON public.job_tasks USING btree (owner_uuid);
--
-- Name: index_job_tasks_on_sequence; Type: INDEX; Schema: public; Owner: -
--
-CREATE INDEX index_job_tasks_on_sequence ON job_tasks USING btree (sequence);
+CREATE INDEX index_job_tasks_on_sequence ON public.job_tasks USING btree (sequence);
--
-- Name: index_job_tasks_on_success; Type: INDEX; Schema: public; Owner: -
--
-CREATE INDEX index_job_tasks_on_success ON job_tasks USING btree (success);
+CREATE INDEX index_job_tasks_on_success ON public.job_tasks USING btree (success);
--
-- Name: index_job_tasks_on_uuid; Type: INDEX; Schema: public; Owner: -
--
-CREATE UNIQUE INDEX index_job_tasks_on_uuid ON job_tasks USING btree (uuid);
+CREATE UNIQUE INDEX index_job_tasks_on_uuid ON public.job_tasks USING btree (uuid);
--
-- Name: index_jobs_on_created_at; Type: INDEX; Schema: public; Owner: -
--
-CREATE INDEX index_jobs_on_created_at ON jobs USING btree (created_at);
+CREATE INDEX index_jobs_on_created_at ON public.jobs USING btree (created_at);
--
-- Name: index_jobs_on_finished_at; Type: INDEX; Schema: public; Owner: -
--
-CREATE INDEX index_jobs_on_finished_at ON jobs USING btree (finished_at);
+CREATE INDEX index_jobs_on_finished_at ON public.jobs USING btree (finished_at);
--
-- Name: index_jobs_on_modified_at; Type: INDEX; Schema: public; Owner: -
--
-CREATE INDEX index_jobs_on_modified_at ON jobs USING btree (modified_at);
+CREATE INDEX index_jobs_on_modified_at ON public.jobs USING btree (modified_at);
--
-- Name: index_jobs_on_modified_at_uuid; Type: INDEX; Schema: public; Owner: -
--
-CREATE INDEX index_jobs_on_modified_at_uuid ON jobs USING btree (modified_at DESC, uuid);
+CREATE INDEX index_jobs_on_modified_at_uuid ON public.jobs USING btree (modified_at DESC, uuid);
--
-- Name: index_jobs_on_output; Type: INDEX; Schema: public; Owner: -
--
-CREATE INDEX index_jobs_on_output ON jobs USING btree (output);
+CREATE INDEX index_jobs_on_output ON public.jobs USING btree (output);
--
-- Name: index_jobs_on_owner_uuid; Type: INDEX; Schema: public; Owner: -
--
-CREATE INDEX index_jobs_on_owner_uuid ON jobs USING btree (owner_uuid);
+CREATE INDEX index_jobs_on_owner_uuid ON public.jobs USING btree (owner_uuid);
--
-- Name: index_jobs_on_script; Type: INDEX; Schema: public; Owner: -
--
-CREATE INDEX index_jobs_on_script ON jobs USING btree (script);
+CREATE INDEX index_jobs_on_script ON public.jobs USING btree (script);
--
-- Name: index_jobs_on_script_parameters_digest; Type: INDEX; Schema: public; Owner: -
--
-CREATE INDEX index_jobs_on_script_parameters_digest ON jobs USING btree (script_parameters_digest);
+CREATE INDEX index_jobs_on_script_parameters_digest ON public.jobs USING btree (script_parameters_digest);
--
-- Name: index_jobs_on_started_at; Type: INDEX; Schema: public; Owner: -
--
-CREATE INDEX index_jobs_on_started_at ON jobs USING btree (started_at);
+CREATE INDEX index_jobs_on_started_at ON public.jobs USING btree (started_at);
--
-- Name: index_jobs_on_submit_id; Type: INDEX; Schema: public; Owner: -
--
-CREATE UNIQUE INDEX index_jobs_on_submit_id ON jobs USING btree (submit_id);
+CREATE UNIQUE INDEX index_jobs_on_submit_id ON public.jobs USING btree (submit_id);
--
-- Name: index_jobs_on_uuid; Type: INDEX; Schema: public; Owner: -
--
-CREATE UNIQUE INDEX index_jobs_on_uuid ON jobs USING btree (uuid);
+CREATE UNIQUE INDEX index_jobs_on_uuid ON public.jobs USING btree (uuid);
--
-- Name: index_keep_disks_on_filesystem_uuid; Type: INDEX; Schema: public; Owner: -
--
-CREATE INDEX index_keep_disks_on_filesystem_uuid ON keep_disks USING btree (filesystem_uuid);
+CREATE INDEX index_keep_disks_on_filesystem_uuid ON public.keep_disks USING btree (filesystem_uuid);
--
-- Name: index_keep_disks_on_last_ping_at; Type: INDEX; Schema: public; Owner: -
--
-CREATE INDEX index_keep_disks_on_last_ping_at ON keep_disks USING btree (last_ping_at);
+CREATE INDEX index_keep_disks_on_last_ping_at ON public.keep_disks USING btree (last_ping_at);
--
-- Name: index_keep_disks_on_node_uuid; Type: INDEX; Schema: public; Owner: -
--
-CREATE INDEX index_keep_disks_on_node_uuid ON keep_disks USING btree (node_uuid);
+CREATE INDEX index_keep_disks_on_node_uuid ON public.keep_disks USING btree (node_uuid);
--
-- Name: index_keep_disks_on_owner_uuid; Type: INDEX; Schema: public; Owner: -
--
-CREATE INDEX index_keep_disks_on_owner_uuid ON keep_disks USING btree (owner_uuid);
+CREATE INDEX index_keep_disks_on_owner_uuid ON public.keep_disks USING btree (owner_uuid);
--
-- Name: index_keep_disks_on_uuid; Type: INDEX; Schema: public; Owner: -
--
-CREATE UNIQUE INDEX index_keep_disks_on_uuid ON keep_disks USING btree (uuid);
+CREATE UNIQUE INDEX index_keep_disks_on_uuid ON public.keep_disks USING btree (uuid);
--
-- Name: index_keep_services_on_owner_uuid; Type: INDEX; Schema: public; Owner: -
--
-CREATE INDEX index_keep_services_on_owner_uuid ON keep_services USING btree (owner_uuid);
+CREATE INDEX index_keep_services_on_owner_uuid ON public.keep_services USING btree (owner_uuid);
--
-- Name: index_keep_services_on_uuid; Type: INDEX; Schema: public; Owner: -
--
-CREATE UNIQUE INDEX index_keep_services_on_uuid ON keep_services USING btree (uuid);
+CREATE UNIQUE INDEX index_keep_services_on_uuid ON public.keep_services USING btree (uuid);
--
-- Name: index_links_on_created_at; Type: INDEX; Schema: public; Owner: -
--
-CREATE INDEX index_links_on_created_at ON links USING btree (created_at);
+CREATE INDEX index_links_on_created_at ON public.links USING btree (created_at);
--
-- Name: index_links_on_head_uuid; Type: INDEX; Schema: public; Owner: -
--
-CREATE INDEX index_links_on_head_uuid ON links USING btree (head_uuid);
+CREATE INDEX index_links_on_head_uuid ON public.links USING btree (head_uuid);
--
-- Name: index_links_on_modified_at; Type: INDEX; Schema: public; Owner: -
--
-CREATE INDEX index_links_on_modified_at ON links USING btree (modified_at);
+CREATE INDEX index_links_on_modified_at ON public.links USING btree (modified_at);
--
-- Name: index_links_on_modified_at_uuid; Type: INDEX; Schema: public; Owner: -
--
-CREATE INDEX index_links_on_modified_at_uuid ON links USING btree (modified_at DESC, uuid);
+CREATE INDEX index_links_on_modified_at_uuid ON public.links USING btree (modified_at DESC, uuid);
--
-- Name: index_links_on_owner_uuid; Type: INDEX; Schema: public; Owner: -
--
-CREATE INDEX index_links_on_owner_uuid ON links USING btree (owner_uuid);
+CREATE INDEX index_links_on_owner_uuid ON public.links USING btree (owner_uuid);
--
-- Name: index_links_on_tail_uuid; Type: INDEX; Schema: public; Owner: -
--
-CREATE INDEX index_links_on_tail_uuid ON links USING btree (tail_uuid);
+CREATE INDEX index_links_on_tail_uuid ON public.links USING btree (tail_uuid);
--
-- Name: index_links_on_uuid; Type: INDEX; Schema: public; Owner: -
--
-CREATE UNIQUE INDEX index_links_on_uuid ON links USING btree (uuid);
+CREATE UNIQUE INDEX index_links_on_uuid ON public.links USING btree (uuid);
--
-- Name: index_logs_on_created_at; Type: INDEX; Schema: public; Owner: -
--
-CREATE INDEX index_logs_on_created_at ON logs USING btree (created_at);
+CREATE INDEX index_logs_on_created_at ON public.logs USING btree (created_at);
--
-- Name: index_logs_on_event_at; Type: INDEX; Schema: public; Owner: -
--
-CREATE INDEX index_logs_on_event_at ON logs USING btree (event_at);
+CREATE INDEX index_logs_on_event_at ON public.logs USING btree (event_at);
--
-- Name: index_logs_on_event_type; Type: INDEX; Schema: public; Owner: -
--
-CREATE INDEX index_logs_on_event_type ON logs USING btree (event_type);
+CREATE INDEX index_logs_on_event_type ON public.logs USING btree (event_type);
--
-- Name: index_logs_on_modified_at; Type: INDEX; Schema: public; Owner: -
--
-CREATE INDEX index_logs_on_modified_at ON logs USING btree (modified_at);
+CREATE INDEX index_logs_on_modified_at ON public.logs USING btree (modified_at);
--
-- Name: index_logs_on_modified_at_uuid; Type: INDEX; Schema: public; Owner: -
--
-CREATE INDEX index_logs_on_modified_at_uuid ON logs USING btree (modified_at DESC, uuid);
+CREATE INDEX index_logs_on_modified_at_uuid ON public.logs USING btree (modified_at DESC, uuid);
--
-- Name: index_logs_on_object_owner_uuid; Type: INDEX; Schema: public; Owner: -
--
-CREATE INDEX index_logs_on_object_owner_uuid ON logs USING btree (object_owner_uuid);
+CREATE INDEX index_logs_on_object_owner_uuid ON public.logs USING btree (object_owner_uuid);
--
-- Name: index_logs_on_object_uuid; Type: INDEX; Schema: public; Owner: -
--
-CREATE INDEX index_logs_on_object_uuid ON logs USING btree (object_uuid);
+CREATE INDEX index_logs_on_object_uuid ON public.logs USING btree (object_uuid);
--
-- Name: index_logs_on_owner_uuid; Type: INDEX; Schema: public; Owner: -
--
-CREATE INDEX index_logs_on_owner_uuid ON logs USING btree (owner_uuid);
+CREATE INDEX index_logs_on_owner_uuid ON public.logs USING btree (owner_uuid);
--
-- Name: index_logs_on_summary; Type: INDEX; Schema: public; Owner: -
--
-CREATE INDEX index_logs_on_summary ON logs USING btree (summary);
+CREATE INDEX index_logs_on_summary ON public.logs USING btree (summary);
--
-- Name: index_logs_on_uuid; Type: INDEX; Schema: public; Owner: -
--
-CREATE UNIQUE INDEX index_logs_on_uuid ON logs USING btree (uuid);
+CREATE UNIQUE INDEX index_logs_on_uuid ON public.logs USING btree (uuid);
--
-- Name: index_nodes_on_created_at; Type: INDEX; Schema: public; Owner: -
--
-CREATE INDEX index_nodes_on_created_at ON nodes USING btree (created_at);
+CREATE INDEX index_nodes_on_created_at ON public.nodes USING btree (created_at);
--
-- Name: index_nodes_on_hostname; Type: INDEX; Schema: public; Owner: -
--
-CREATE INDEX index_nodes_on_hostname ON nodes USING btree (hostname);
+CREATE INDEX index_nodes_on_hostname ON public.nodes USING btree (hostname);
--
-- Name: index_nodes_on_modified_at; Type: INDEX; Schema: public; Owner: -
--
-CREATE INDEX index_nodes_on_modified_at ON nodes USING btree (modified_at);
+CREATE INDEX index_nodes_on_modified_at ON public.nodes USING btree (modified_at);
--
-- Name: index_nodes_on_owner_uuid; Type: INDEX; Schema: public; Owner: -
--
-CREATE INDEX index_nodes_on_owner_uuid ON nodes USING btree (owner_uuid);
+CREATE INDEX index_nodes_on_owner_uuid ON public.nodes USING btree (owner_uuid);
--
-- Name: index_nodes_on_slot_number; Type: INDEX; Schema: public; Owner: -
--
-CREATE UNIQUE INDEX index_nodes_on_slot_number ON nodes USING btree (slot_number);
+CREATE UNIQUE INDEX index_nodes_on_slot_number ON public.nodes USING btree (slot_number);
--
-- Name: index_nodes_on_uuid; Type: INDEX; Schema: public; Owner: -
--
-CREATE UNIQUE INDEX index_nodes_on_uuid ON nodes USING btree (uuid);
+CREATE UNIQUE INDEX index_nodes_on_uuid ON public.nodes USING btree (uuid);
--
-- Name: index_pipeline_instances_on_created_at; Type: INDEX; Schema: public; Owner: -
--
-CREATE INDEX index_pipeline_instances_on_created_at ON pipeline_instances USING btree (created_at);
+CREATE INDEX index_pipeline_instances_on_created_at ON public.pipeline_instances USING btree (created_at);
--
-- Name: index_pipeline_instances_on_modified_at; Type: INDEX; Schema: public; Owner: -
--
-CREATE INDEX index_pipeline_instances_on_modified_at ON pipeline_instances USING btree (modified_at);
+CREATE INDEX index_pipeline_instances_on_modified_at ON public.pipeline_instances USING btree (modified_at);
--
-- Name: index_pipeline_instances_on_modified_at_uuid; Type: INDEX; Schema: public; Owner: -
--
-CREATE INDEX index_pipeline_instances_on_modified_at_uuid ON pipeline_instances USING btree (modified_at DESC, uuid);
+CREATE INDEX index_pipeline_instances_on_modified_at_uuid ON public.pipeline_instances USING btree (modified_at DESC, uuid);
--
-- Name: index_pipeline_instances_on_owner_uuid; Type: INDEX; Schema: public; Owner: -
--
-CREATE INDEX index_pipeline_instances_on_owner_uuid ON pipeline_instances USING btree (owner_uuid);
+CREATE INDEX index_pipeline_instances_on_owner_uuid ON public.pipeline_instances USING btree (owner_uuid);
--
-- Name: index_pipeline_instances_on_uuid; Type: INDEX; Schema: public; Owner: -
--
-CREATE UNIQUE INDEX index_pipeline_instances_on_uuid ON pipeline_instances USING btree (uuid);
+CREATE UNIQUE INDEX index_pipeline_instances_on_uuid ON public.pipeline_instances USING btree (uuid);
--
-- Name: index_pipeline_templates_on_created_at; Type: INDEX; Schema: public; Owner: -
--
-CREATE INDEX index_pipeline_templates_on_created_at ON pipeline_templates USING btree (created_at);
+CREATE INDEX index_pipeline_templates_on_created_at ON public.pipeline_templates USING btree (created_at);
--
-- Name: index_pipeline_templates_on_modified_at; Type: INDEX; Schema: public; Owner: -
--
-CREATE INDEX index_pipeline_templates_on_modified_at ON pipeline_templates USING btree (modified_at);
+CREATE INDEX index_pipeline_templates_on_modified_at ON public.pipeline_templates USING btree (modified_at);
--
-- Name: index_pipeline_templates_on_modified_at_uuid; Type: INDEX; Schema: public; Owner: -
--
-CREATE INDEX index_pipeline_templates_on_modified_at_uuid ON pipeline_templates USING btree (modified_at DESC, uuid);
+CREATE INDEX index_pipeline_templates_on_modified_at_uuid ON public.pipeline_templates USING btree (modified_at DESC, uuid);
--
-- Name: index_pipeline_templates_on_owner_uuid; Type: INDEX; Schema: public; Owner: -
--
-CREATE INDEX index_pipeline_templates_on_owner_uuid ON pipeline_templates USING btree (owner_uuid);
+CREATE INDEX index_pipeline_templates_on_owner_uuid ON public.pipeline_templates USING btree (owner_uuid);
--
-- Name: index_pipeline_templates_on_uuid; Type: INDEX; Schema: public; Owner: -
--
-CREATE UNIQUE INDEX index_pipeline_templates_on_uuid ON pipeline_templates USING btree (uuid);
+CREATE UNIQUE INDEX index_pipeline_templates_on_uuid ON public.pipeline_templates USING btree (uuid);
--
-- Name: index_repositories_on_modified_at_uuid; Type: INDEX; Schema: public; Owner: -
--
-CREATE INDEX index_repositories_on_modified_at_uuid ON repositories USING btree (modified_at DESC, uuid);
+CREATE INDEX index_repositories_on_modified_at_uuid ON public.repositories USING btree (modified_at DESC, uuid);
--
-- Name: index_repositories_on_name; Type: INDEX; Schema: public; Owner: -
--
-CREATE UNIQUE INDEX index_repositories_on_name ON repositories USING btree (name);
+CREATE UNIQUE INDEX index_repositories_on_name ON public.repositories USING btree (name);
--
-- Name: index_repositories_on_owner_uuid; Type: INDEX; Schema: public; Owner: -
--
-CREATE INDEX index_repositories_on_owner_uuid ON repositories USING btree (owner_uuid);
+CREATE INDEX index_repositories_on_owner_uuid ON public.repositories USING btree (owner_uuid);
--
-- Name: index_repositories_on_uuid; Type: INDEX; Schema: public; Owner: -
--
-CREATE UNIQUE INDEX index_repositories_on_uuid ON repositories USING btree (uuid);
+CREATE UNIQUE INDEX index_repositories_on_uuid ON public.repositories USING btree (uuid);
--
-- Name: index_specimens_on_created_at; Type: INDEX; Schema: public; Owner: -
--
-CREATE INDEX index_specimens_on_created_at ON specimens USING btree (created_at);
+CREATE INDEX index_specimens_on_created_at ON public.specimens USING btree (created_at);
--
-- Name: index_specimens_on_modified_at; Type: INDEX; Schema: public; Owner: -
--
-CREATE INDEX index_specimens_on_modified_at ON specimens USING btree (modified_at);
+CREATE INDEX index_specimens_on_modified_at ON public.specimens USING btree (modified_at);
--
-- Name: index_specimens_on_owner_uuid; Type: INDEX; Schema: public; Owner: -
--
-CREATE INDEX index_specimens_on_owner_uuid ON specimens USING btree (owner_uuid);
+CREATE INDEX index_specimens_on_owner_uuid ON public.specimens USING btree (owner_uuid);
--
-- Name: index_specimens_on_uuid; Type: INDEX; Schema: public; Owner: -
--
-CREATE UNIQUE INDEX index_specimens_on_uuid ON specimens USING btree (uuid);
+CREATE UNIQUE INDEX index_specimens_on_uuid ON public.specimens USING btree (uuid);
--
-- Name: index_traits_on_name; Type: INDEX; Schema: public; Owner: -
--
-CREATE INDEX index_traits_on_name ON traits USING btree (name);
+CREATE INDEX index_traits_on_name ON public.traits USING btree (name);
--
-- Name: index_traits_on_owner_uuid; Type: INDEX; Schema: public; Owner: -
--
-CREATE INDEX index_traits_on_owner_uuid ON traits USING btree (owner_uuid);
+CREATE INDEX index_traits_on_owner_uuid ON public.traits USING btree (owner_uuid);
--
-- Name: index_traits_on_uuid; Type: INDEX; Schema: public; Owner: -
--
-CREATE UNIQUE INDEX index_traits_on_uuid ON traits USING btree (uuid);
+CREATE UNIQUE INDEX index_traits_on_uuid ON public.traits USING btree (uuid);
--
-- Name: index_users_on_created_at; Type: INDEX; Schema: public; Owner: -
--
-CREATE INDEX index_users_on_created_at ON users USING btree (created_at);
+CREATE INDEX index_users_on_created_at ON public.users USING btree (created_at);
--
-- Name: index_users_on_modified_at; Type: INDEX; Schema: public; Owner: -
--
-CREATE INDEX index_users_on_modified_at ON users USING btree (modified_at);
+CREATE INDEX index_users_on_modified_at ON public.users USING btree (modified_at);
--
-- Name: index_users_on_modified_at_uuid; Type: INDEX; Schema: public; Owner: -
--
-CREATE INDEX index_users_on_modified_at_uuid ON users USING btree (modified_at DESC, uuid);
+CREATE INDEX index_users_on_modified_at_uuid ON public.users USING btree (modified_at DESC, uuid);
--
-- Name: index_users_on_owner_uuid; Type: INDEX; Schema: public; Owner: -
--
-CREATE INDEX index_users_on_owner_uuid ON users USING btree (owner_uuid);
+CREATE INDEX index_users_on_owner_uuid ON public.users USING btree (owner_uuid);
--
-- Name: index_users_on_username; Type: INDEX; Schema: public; Owner: -
--
-CREATE UNIQUE INDEX index_users_on_username ON users USING btree (username);
+CREATE UNIQUE INDEX index_users_on_username ON public.users USING btree (username);
--
-- Name: index_users_on_uuid; Type: INDEX; Schema: public; Owner: -
--
-CREATE UNIQUE INDEX index_users_on_uuid ON users USING btree (uuid);
+CREATE UNIQUE INDEX index_users_on_uuid ON public.users USING btree (uuid);
--
-- Name: index_virtual_machines_on_hostname; Type: INDEX; Schema: public; Owner: -
--
-CREATE INDEX index_virtual_machines_on_hostname ON virtual_machines USING btree (hostname);
+CREATE INDEX index_virtual_machines_on_hostname ON public.virtual_machines USING btree (hostname);
--
-- Name: index_virtual_machines_on_modified_at_uuid; Type: INDEX; Schema: public; Owner: -
--
-CREATE INDEX index_virtual_machines_on_modified_at_uuid ON virtual_machines USING btree (modified_at DESC, uuid);
+CREATE INDEX index_virtual_machines_on_modified_at_uuid ON public.virtual_machines USING btree (modified_at DESC, uuid);
--
-- Name: index_virtual_machines_on_owner_uuid; Type: INDEX; Schema: public; Owner: -
--
-CREATE INDEX index_virtual_machines_on_owner_uuid ON virtual_machines USING btree (owner_uuid);
+CREATE INDEX index_virtual_machines_on_owner_uuid ON public.virtual_machines USING btree (owner_uuid);
--
-- Name: index_virtual_machines_on_uuid; Type: INDEX; Schema: public; Owner: -
--
-CREATE UNIQUE INDEX index_virtual_machines_on_uuid ON virtual_machines USING btree (uuid);
+CREATE UNIQUE INDEX index_virtual_machines_on_uuid ON public.virtual_machines USING btree (uuid);
--
-- Name: index_workflows_on_modified_at_uuid; Type: INDEX; Schema: public; Owner: -
--
-CREATE INDEX index_workflows_on_modified_at_uuid ON workflows USING btree (modified_at DESC, uuid);
+CREATE INDEX index_workflows_on_modified_at_uuid ON public.workflows USING btree (modified_at DESC, uuid);
--
-- Name: index_workflows_on_owner_uuid; Type: INDEX; Schema: public; Owner: -
--
-CREATE INDEX index_workflows_on_owner_uuid ON workflows USING btree (owner_uuid);
+CREATE INDEX index_workflows_on_owner_uuid ON public.workflows USING btree (owner_uuid);
--
-- Name: index_workflows_on_uuid; Type: INDEX; Schema: public; Owner: -
--
-CREATE UNIQUE INDEX index_workflows_on_uuid ON workflows USING btree (uuid);
+CREATE UNIQUE INDEX index_workflows_on_uuid ON public.workflows USING btree (uuid);
--
-- Name: job_tasks_search_index; Type: INDEX; Schema: public; Owner: -
--
-CREATE INDEX job_tasks_search_index ON job_tasks USING btree (uuid, owner_uuid, modified_by_client_uuid, modified_by_user_uuid, job_uuid, created_by_job_task_uuid);
+CREATE INDEX job_tasks_search_index ON public.job_tasks USING btree (uuid, owner_uuid, modified_by_client_uuid, modified_by_user_uuid, job_uuid, created_by_job_task_uuid);
--
-- Name: jobs_full_text_search_idx; Type: INDEX; Schema: public; Owner: -
--
-CREATE INDEX jobs_full_text_search_idx ON jobs USING gin (to_tsvector('english'::regconfig, (((((((((((((((((((((((((((((((((((((((((((COALESCE(uuid, ''::character varying))::text || ' '::text) || (COALESCE(owner_uuid, ''::character varying))::text) || ' '::text) || (COALESCE(modified_by_client_uuid, ''::character varying))::text) || ' '::text) || (COALESCE(modified_by_user_uuid, ''::character varying))::text) || ' '::text) || (COALESCE(submit_id, ''::character varying))::text) || ' '::text) || (COALESCE(script, ''::character varying))::text) || ' '::text) || (COALESCE(script_version, ''::character varying))::text) || ' '::text) || COALESCE(script_parameters, ''::text)) || ' '::text) || (COALESCE(cancelled_by_client_uuid, ''::character varying))::text) || ' '::text) || (COALESCE(cancelled_by_user_uuid, ''::character varying))::text) || ' '::text) || (COALESCE(output, ''::character varying))::text) || ' '::text) || (COALESCE(is_locked_by_uuid, ''::character varying))::text) || ' '::text) || (COALESCE(log, ''::character varying))::text) || ' '::text) || COALESCE(tasks_summary, ''::text)) || ' '::text) || COALESCE(runtime_constraints, ''::text)) || ' '::text) || (COALESCE(repository, ''::character varying))::text) || ' '::text) || (COALESCE(supplied_script_version, ''::character varying))::text) || ' '::text) || (COALESCE(docker_image_locator, ''::character varying))::text) || ' '::text) || (COALESCE(description, ''::character varying))::text) || ' '::text) || (COALESCE(state, ''::character varying))::text) || ' '::text) || (COALESCE(arvados_sdk_version, ''::character varying))::text) || ' '::text) || COALESCE(components, ''::text))));
+CREATE INDEX jobs_full_text_search_idx ON public.jobs USING gin (to_tsvector('english'::regconfig, (((((((((((((((((((((((((((((((((((((((((((COALESCE(uuid, ''::character varying))::text || ' '::text) || (COALESCE(owner_uuid, ''::character varying))::text) || ' '::text) || (COALESCE(modified_by_client_uuid, ''::character varying))::text) || ' '::text) || (COALESCE(modified_by_user_uuid, ''::character varying))::text) || ' '::text) || (COALESCE(submit_id, ''::character varying))::text) || ' '::text) || (COALESCE(script, ''::character varying))::text) || ' '::text) || (COALESCE(script_version, ''::character varying))::text) || ' '::text) || COALESCE(script_parameters, ''::text)) || ' '::text) || (COALESCE(cancelled_by_client_uuid, ''::character varying))::text) || ' '::text) || (COALESCE(cancelled_by_user_uuid, ''::character varying))::text) || ' '::text) || (COALESCE(output, ''::character varying))::text) || ' '::text) || (COALESCE(is_locked_by_uuid, ''::character varying))::text) || ' '::text) || (COALESCE(log, ''::character varying))::text) || ' '::text) || COALESCE(tasks_summary, ''::text)) || ' '::text) || COALESCE(runtime_constraints, ''::text)) || ' '::text) || (COALESCE(repository, ''::character varying))::text) || ' '::text) || (COALESCE(supplied_script_version, ''::character varying))::text) || ' '::text) || (COALESCE(docker_image_locator, ''::character varying))::text) || ' '::text) || (COALESCE(description, ''::character varying))::text) || ' '::text) || (COALESCE(state, ''::character varying))::text) || ' '::text) || (COALESCE(arvados_sdk_version, ''::character varying))::text) || ' '::text) || COALESCE(components, ''::text))));
--
-- Name: jobs_search_index; Type: INDEX; Schema: public; Owner: -
--
-CREATE INDEX jobs_search_index ON jobs USING btree (uuid, owner_uuid, modified_by_client_uuid, modified_by_user_uuid, submit_id, script, script_version, cancelled_by_client_uuid, cancelled_by_user_uuid, output, is_locked_by_uuid, log, repository, supplied_script_version, docker_image_locator, state, arvados_sdk_version);
+CREATE INDEX jobs_search_index ON public.jobs USING btree (uuid, owner_uuid, modified_by_client_uuid, modified_by_user_uuid, submit_id, script, script_version, cancelled_by_client_uuid, cancelled_by_user_uuid, output, is_locked_by_uuid, log, repository, supplied_script_version, docker_image_locator, state, arvados_sdk_version);
--
-- Name: keep_disks_search_index; Type: INDEX; Schema: public; Owner: -
--
-CREATE INDEX keep_disks_search_index ON keep_disks USING btree (uuid, owner_uuid, modified_by_client_uuid, modified_by_user_uuid, ping_secret, node_uuid, filesystem_uuid, keep_service_uuid);
+CREATE INDEX keep_disks_search_index ON public.keep_disks USING btree (uuid, owner_uuid, modified_by_client_uuid, modified_by_user_uuid, ping_secret, node_uuid, filesystem_uuid, keep_service_uuid);
--
-- Name: keep_services_search_index; Type: INDEX; Schema: public; Owner: -
--
-CREATE INDEX keep_services_search_index ON keep_services USING btree (uuid, owner_uuid, modified_by_client_uuid, modified_by_user_uuid, service_host, service_type);
+CREATE INDEX keep_services_search_index ON public.keep_services USING btree (uuid, owner_uuid, modified_by_client_uuid, modified_by_user_uuid, service_host, service_type);
--
-- Name: links_index_on_properties; Type: INDEX; Schema: public; Owner: -
--
-CREATE INDEX links_index_on_properties ON links USING gin (properties);
+CREATE INDEX links_index_on_properties ON public.links USING gin (properties);
--
-- Name: links_search_index; Type: INDEX; Schema: public; Owner: -
--
-CREATE INDEX links_search_index ON links USING btree (uuid, owner_uuid, modified_by_client_uuid, modified_by_user_uuid, tail_uuid, link_class, name, head_uuid);
+CREATE INDEX links_search_index ON public.links USING btree (uuid, owner_uuid, modified_by_client_uuid, modified_by_user_uuid, tail_uuid, link_class, name, head_uuid);
--
-- Name: links_tail_name_unique_if_link_class_name; Type: INDEX; Schema: public; Owner: -
--
-CREATE UNIQUE INDEX links_tail_name_unique_if_link_class_name ON links USING btree (tail_uuid, name) WHERE ((link_class)::text = 'name'::text);
+CREATE UNIQUE INDEX links_tail_name_unique_if_link_class_name ON public.links USING btree (tail_uuid, name) WHERE ((link_class)::text = 'name'::text);
--
-- Name: logs_search_index; Type: INDEX; Schema: public; Owner: -
--
-CREATE INDEX logs_search_index ON logs USING btree (uuid, owner_uuid, modified_by_client_uuid, modified_by_user_uuid, object_uuid, event_type, object_owner_uuid);
+CREATE INDEX logs_search_index ON public.logs USING btree (uuid, owner_uuid, modified_by_client_uuid, modified_by_user_uuid, object_uuid, event_type, object_owner_uuid);
--
-- Name: nodes_index_on_info; Type: INDEX; Schema: public; Owner: -
--
-CREATE INDEX nodes_index_on_info ON nodes USING gin (info);
+CREATE INDEX nodes_index_on_info ON public.nodes USING gin (info);
--
-- Name: nodes_index_on_properties; Type: INDEX; Schema: public; Owner: -
--
-CREATE INDEX nodes_index_on_properties ON nodes USING gin (properties);
+CREATE INDEX nodes_index_on_properties ON public.nodes USING gin (properties);
--
-- Name: nodes_search_index; Type: INDEX; Schema: public; Owner: -
--
-CREATE INDEX nodes_search_index ON nodes USING btree (uuid, owner_uuid, modified_by_client_uuid, modified_by_user_uuid, hostname, domain, ip_address, job_uuid);
+CREATE INDEX nodes_search_index ON public.nodes USING btree (uuid, owner_uuid, modified_by_client_uuid, modified_by_user_uuid, hostname, domain, ip_address, job_uuid);
--
-- Name: permission_target_trashed; Type: INDEX; Schema: public; Owner: -
--
-CREATE INDEX permission_target_trashed ON materialized_permission_view USING btree (trashed, target_uuid);
+CREATE INDEX permission_target_trashed ON public.materialized_permission_view USING btree (trashed, target_uuid);
--
-- Name: permission_target_user_trashed_level; Type: INDEX; Schema: public; Owner: -
--
-CREATE INDEX permission_target_user_trashed_level ON materialized_permission_view USING btree (user_uuid, trashed, perm_level);
+CREATE INDEX permission_target_user_trashed_level ON public.materialized_permission_view USING btree (user_uuid, trashed, perm_level);
--
-- Name: pipeline_instances_full_text_search_idx; Type: INDEX; Schema: public; Owner: -
--
-CREATE INDEX pipeline_instances_full_text_search_idx ON pipeline_instances USING gin (to_tsvector('english'::regconfig, (((((((((((((((((((((COALESCE(uuid, ''::character varying))::text || ' '::text) || (COALESCE(owner_uuid, ''::character varying))::text) || ' '::text) || (COALESCE(modified_by_client_uuid, ''::character varying))::text) || ' '::text) || (COALESCE(modified_by_user_uuid, ''::character varying))::text) || ' '::text) || (COALESCE(pipeline_template_uuid, ''::character varying))::text) || ' '::text) || (COALESCE(name, ''::character varying))::text) || ' '::text) || COALESCE(components, ''::text)) || ' '::text) || COALESCE(properties, ''::text)) || ' '::text) || (COALESCE(state, ''::character varying))::text) || ' '::text) || COALESCE(components_summary, ''::text)) || ' '::text) || (COALESCE(description, ''::character varying))::text)));
+CREATE INDEX pipeline_instances_full_text_search_idx ON public.pipeline_instances USING gin (to_tsvector('english'::regconfig, (((((((((((((((((((((COALESCE(uuid, ''::character varying))::text || ' '::text) || (COALESCE(owner_uuid, ''::character varying))::text) || ' '::text) || (COALESCE(modified_by_client_uuid, ''::character varying))::text) || ' '::text) || (COALESCE(modified_by_user_uuid, ''::character varying))::text) || ' '::text) || (COALESCE(pipeline_template_uuid, ''::character varying))::text) || ' '::text) || (COALESCE(name, ''::character varying))::text) || ' '::text) || COALESCE(components, ''::text)) || ' '::text) || COALESCE(properties, ''::text)) || ' '::text) || (COALESCE(state, ''::character varying))::text) || ' '::text) || COALESCE(components_summary, ''::text)) || ' '::text) || (COALESCE(description, ''::character varying))::text)));
--
-- Name: pipeline_instances_search_index; Type: INDEX; Schema: public; Owner: -
--
-CREATE INDEX pipeline_instances_search_index ON pipeline_instances USING btree (uuid, owner_uuid, modified_by_client_uuid, modified_by_user_uuid, pipeline_template_uuid, name, state);
+CREATE INDEX pipeline_instances_search_index ON public.pipeline_instances USING btree (uuid, owner_uuid, modified_by_client_uuid, modified_by_user_uuid, pipeline_template_uuid, name, state);
--
-- Name: pipeline_template_owner_uuid_name_unique; Type: INDEX; Schema: public; Owner: -
--
-CREATE UNIQUE INDEX pipeline_template_owner_uuid_name_unique ON pipeline_templates USING btree (owner_uuid, name);
+CREATE UNIQUE INDEX pipeline_template_owner_uuid_name_unique ON public.pipeline_templates USING btree (owner_uuid, name);
--
-- Name: pipeline_templates_full_text_search_idx; Type: INDEX; Schema: public; Owner: -
--
-CREATE INDEX pipeline_templates_full_text_search_idx ON pipeline_templates USING gin (to_tsvector('english'::regconfig, (((((((((((((COALESCE(uuid, ''::character varying))::text || ' '::text) || (COALESCE(owner_uuid, ''::character varying))::text) || ' '::text) || (COALESCE(modified_by_client_uuid, ''::character varying))::text) || ' '::text) || (COALESCE(modified_by_user_uuid, ''::character varying))::text) || ' '::text) || (COALESCE(name, ''::character varying))::text) || ' '::text) || COALESCE(components, ''::text)) || ' '::text) || (COALESCE(description, ''::character varying))::text)));
+CREATE INDEX pipeline_templates_full_text_search_idx ON public.pipeline_templates USING gin (to_tsvector('english'::regconfig, (((((((((((((COALESCE(uuid, ''::character varying))::text || ' '::text) || (COALESCE(owner_uuid, ''::character varying))::text) || ' '::text) || (COALESCE(modified_by_client_uuid, ''::character varying))::text) || ' '::text) || (COALESCE(modified_by_user_uuid, ''::character varying))::text) || ' '::text) || (COALESCE(name, ''::character varying))::text) || ' '::text) || COALESCE(components, ''::text)) || ' '::text) || (COALESCE(description, ''::character varying))::text)));
--
-- Name: pipeline_templates_search_index; Type: INDEX; Schema: public; Owner: -
--
-CREATE INDEX pipeline_templates_search_index ON pipeline_templates USING btree (uuid, owner_uuid, modified_by_client_uuid, modified_by_user_uuid, name);
+CREATE INDEX pipeline_templates_search_index ON public.pipeline_templates USING btree (uuid, owner_uuid, modified_by_client_uuid, modified_by_user_uuid, name);
--
-- Name: repositories_search_index; Type: INDEX; Schema: public; Owner: -
--
-CREATE INDEX repositories_search_index ON repositories USING btree (uuid, owner_uuid, modified_by_client_uuid, modified_by_user_uuid, name);
+CREATE INDEX repositories_search_index ON public.repositories USING btree (uuid, owner_uuid, modified_by_client_uuid, modified_by_user_uuid, name);
--
-- Name: specimens_search_index; Type: INDEX; Schema: public; Owner: -
--
-CREATE INDEX specimens_search_index ON specimens USING btree (uuid, owner_uuid, modified_by_client_uuid, modified_by_user_uuid, material);
+CREATE INDEX specimens_search_index ON public.specimens USING btree (uuid, owner_uuid, modified_by_client_uuid, modified_by_user_uuid, material);
--
-- Name: traits_search_index; Type: INDEX; Schema: public; Owner: -
--
-CREATE INDEX traits_search_index ON traits USING btree (uuid, owner_uuid, modified_by_client_uuid, modified_by_user_uuid, name);
+CREATE INDEX traits_search_index ON public.traits USING btree (uuid, owner_uuid, modified_by_client_uuid, modified_by_user_uuid, name);
--
-- Name: unique_schema_migrations; Type: INDEX; Schema: public; Owner: -
--
-CREATE UNIQUE INDEX unique_schema_migrations ON schema_migrations USING btree (version);
+CREATE UNIQUE INDEX unique_schema_migrations ON public.schema_migrations USING btree (version);
--
-- Name: users_search_index; Type: INDEX; Schema: public; Owner: -
--
-CREATE INDEX users_search_index ON users USING btree (uuid, owner_uuid, modified_by_client_uuid, modified_by_user_uuid, email, first_name, last_name, identity_url, default_owner_uuid, username, redirect_to_user_uuid);
+CREATE INDEX users_search_index ON public.users USING btree (uuid, owner_uuid, modified_by_client_uuid, modified_by_user_uuid, email, first_name, last_name, identity_url, default_owner_uuid, username, redirect_to_user_uuid);
--
-- Name: virtual_machines_search_index; Type: INDEX; Schema: public; Owner: -
--
-CREATE INDEX virtual_machines_search_index ON virtual_machines USING btree (uuid, owner_uuid, modified_by_client_uuid, modified_by_user_uuid, hostname);
+CREATE INDEX virtual_machines_search_index ON public.virtual_machines USING btree (uuid, owner_uuid, modified_by_client_uuid, modified_by_user_uuid, hostname);
--
-- Name: workflows_full_text_search_idx; Type: INDEX; Schema: public; Owner: -
--
-CREATE INDEX workflows_full_text_search_idx ON workflows USING gin (to_tsvector('english'::regconfig, (((((((((((COALESCE(uuid, ''::character varying))::text || ' '::text) || (COALESCE(owner_uuid, ''::character varying))::text) || ' '::text) || (COALESCE(modified_by_client_uuid, ''::character varying))::text) || ' '::text) || (COALESCE(modified_by_user_uuid, ''::character varying))::text) || ' '::text) || (COALESCE(name, ''::character varying))::text) || ' '::text) || COALESCE(description, ''::text))));
+CREATE INDEX workflows_full_text_search_idx ON public.workflows USING gin (to_tsvector('english'::regconfig, (((((((((((COALESCE(uuid, ''::character varying))::text || ' '::text) || (COALESCE(owner_uuid, ''::character varying))::text) || ' '::text) || (COALESCE(modified_by_client_uuid, ''::character varying))::text) || ' '::text) || (COALESCE(modified_by_user_uuid, ''::character varying))::text) || ' '::text) || (COALESCE(name, ''::character varying))::text) || ' '::text) || COALESCE(description, ''::text))));
--
-- Name: workflows_search_idx; Type: INDEX; Schema: public; Owner: -
--
-CREATE INDEX workflows_search_idx ON workflows USING btree (uuid, owner_uuid, modified_by_client_uuid, modified_by_user_uuid, name);
+CREATE INDEX workflows_search_idx ON public.workflows USING btree (uuid, owner_uuid, modified_by_client_uuid, modified_by_user_uuid, name);
--
INSERT INTO schema_migrations (version) VALUES ('20180514135529');
+INSERT INTO schema_migrations (version) VALUES ('20180607175050');
+
INSERT INTO schema_migrations (version) VALUES ('20180608123145');
-INSERT INTO schema_migrations (version) VALUES ('20180607175050');
+INSERT INTO schema_migrations (version) VALUES ('20180806133039');
+
@docker_bin = ENV['CRUNCH_JOB_DOCKER_BIN']
@docker_run_args = ENV['CRUNCH_JOB_DOCKER_RUN_ARGS']
@cgroup_root = ENV['CRUNCH_CGROUP_ROOT']
+ @srun_sync_timeout = ENV['CRUNCH_SRUN_SYNC_TIMEOUT']
@arvados_internal = Rails.configuration.git_internal_dir
if not File.exist? @arvados_internal
cmd_args += ['--docker-run-args', @docker_run_args]
end
+ if @srun_sync_timeout
+ cmd_args += ['--srun-sync-timeout', @srun_sync_timeout]
+ end
+
if have_job_lock?(job)
cmd_args << "--force-unlock"
end
# Load params[:limit], params[:offset] and params[:order]
# into @limit, @offset, @orders
- def load_limit_offset_order_params
+ def load_limit_offset_order_params(fill_table_names: true)
if params[:limit]
unless params[:limit].to_s.match(/^\d+$/)
raise ArgumentError.new("Invalid value for limit parameter")
# has used set_table_name to use an alternate table name from the Rails standard.
# I could not find a perfect way to handle this well, but ActiveRecord::Base.send(:descendants)
# would be a place to start if this ever becomes necessary.
- if attr.match(/^[a-z][_a-z0-9]+$/) and
- model_class.columns.collect(&:name).index(attr) and
- ['asc','desc'].index direction.downcase
- @orders << "#{table_name}.#{attr} #{direction.downcase}"
+ if (attr.match(/^[a-z][_a-z0-9]+$/) &&
+ model_class.columns.collect(&:name).index(attr) &&
+ ['asc','desc'].index(direction.downcase))
+ if fill_table_names
+ @orders << "#{table_name}.#{attr} #{direction.downcase}"
+ else
+ @orders << "#{attr} #{direction.downcase}"
+ end
elsif attr.match(/^([a-z][_a-z0-9]+)\.([a-z][_a-z0-9]+)$/) and
['asc','desc'].index(direction.downcase) and
ActiveRecord::Base.connection.tables.include?($1) and
assert_includes ids, collections(:baz_file_in_asubproject).uuid
end
- [['asc', :<=],
- ['desc', :>=]].each do |order, operator|
- test "user with project read permission can sort project collections #{order}" do
+ [
+ ['collections.name', 'asc', :<=, "name"],
+ ['collections.name', 'desc', :>=, "name"],
+ ['name', 'asc', :<=, "name"],
+ ['name', 'desc', :>=, "name"],
+ ['collections.created_at', 'asc', :<=, "created_at"],
+ ['collections.created_at', 'desc', :>=, "created_at"],
+ ['created_at', 'asc', :<=, "created_at"],
+ ['created_at', 'desc', :>=, "created_at"],
+ ].each do |column, order, operator, field|
+ test "user with project read permission can sort projects on #{column} #{order}" do
authorize_with :project_viewer
get :contents, {
id: groups(:asubproject).uuid,
format: :json,
filters: [['uuid', 'is_a', "arvados#collection"]],
- order: "collections.name #{order}"
+ order: "#{column} #{order}"
}
- sorted_names = json_response['items'].collect { |item| item["name"] }
- # Here we avoid assuming too much about the database
- # collation. Both "alice"<"Bob" and "alice">"Bob" can be
- # correct. Hopefully it _is_ safe to assume that if "a" comes
- # before "b" in the ascii alphabet, "aX">"bY" is never true for
- # any strings X and Y.
- reliably_sortable_names = sorted_names.select do |name|
- name[0] >= 'a' and name[0] <= 'z'
- end.uniq do |name|
- name[0]
- end
- # Preserve order of sorted_names. But do not use &=. If
- # sorted_names has out-of-order duplicates, we want to preserve
- # them here, so we can detect them and fail the test below.
- sorted_names.select! do |name|
- reliably_sortable_names.include? name
- end
- actually_checked_anything = false
- previous = nil
- sorted_names.each do |entry|
- if previous
- assert_operator(previous, operator, entry,
- "Entries sorted incorrectly.")
- actually_checked_anything = true
+ sorted_values = json_response['items'].collect { |item| item[field] }
+ if field == "name"
+ # Here we avoid assuming too much about the database
+ # collation. Both "alice"<"Bob" and "alice">"Bob" can be
+ # correct. Hopefully it _is_ safe to assume that if "a" comes
+ # before "b" in the ascii alphabet, "aX">"bY" is never true for
+ # any strings X and Y.
+ reliably_sortable_names = sorted_values.select do |name|
+ name[0] >= 'a' && name[0] <= 'z'
+ end.uniq do |name|
+ name[0]
+ end
+ # Preserve order of sorted_values. But do not use &=. If
+ # sorted_values has out-of-order duplicates, we want to preserve
+ # them here, so we can detect them and fail the test below.
+ sorted_values.select! do |name|
+ reliably_sortable_names.include? name
end
- previous = entry
end
- assert actually_checked_anything, "Didn't even find two names to compare."
+ assert_sorted(operator, sorted_values)
+ end
+ end
+
+ def assert_sorted(operator, sorted_items)
+ actually_checked_anything = false
+ previous = nil
+ sorted_items.each do |entry|
+ if !previous.nil?
+ assert_operator(previous, operator, entry,
+ "Entries sorted incorrectly.")
+ actually_checked_anything = true
+ end
+ previous = entry
end
+ assert actually_checked_anything, "Didn't even find two items to compare."
end
test 'list objects across multiple projects' do
crArgs = append(crArgs, container.UUID)
crScript := strings.NewReader(execScript(crArgs))
- disp.sqCheck.L.Lock()
- defer disp.sqCheck.L.Unlock()
-
sbArgs, err := disp.sbatchArgs(container)
if err != nil {
return err
}
}
func (disp *Dispatcher) scancel(ctr arvados.Container) {
- disp.sqCheck.L.Lock()
err := disp.slurm.Cancel(ctr.UUID)
- disp.sqCheck.L.Unlock()
-
if err != nil {
log.Printf("scancel: %s", err)
time.Sleep(time.Second)
var containers arvados.ContainerList
err = arv.List("containers", params, &containers)
c.Check(err, IsNil)
- c.Check(len(containers.Items), Equals, 1)
+ c.Assert(len(containers.Items), Equals, 1)
s.disp.CrunchRunCommand = []string{"echo"}
queue map[string]*slurmJob
startOnce sync.Once
done chan struct{}
- sync.Cond
+ lock sync.RWMutex
+ notify sync.Cond
}
// HasUUID checks if a given container UUID is in the slurm queue.
func (sqc *SqueueChecker) HasUUID(uuid string) bool {
sqc.startOnce.Do(sqc.start)
- sqc.L.Lock()
- defer sqc.L.Unlock()
+ sqc.lock.RLock()
+ defer sqc.lock.RUnlock()
// block until next squeue broadcast signaling an update.
- sqc.Wait()
+ sqc.notify.Wait()
_, exists := sqc.queue[uuid]
return exists
}
// container.
func (sqc *SqueueChecker) SetPriority(uuid string, want int64) {
sqc.startOnce.Do(sqc.start)
- sqc.L.Lock()
- defer sqc.L.Unlock()
- job, ok := sqc.queue[uuid]
- if !ok {
+
+ sqc.lock.RLock()
+ job := sqc.queue[uuid]
+ if job == nil {
// Wait in case the slurm job was just submitted and
// will appear in the next squeue update.
- sqc.Wait()
- if job, ok = sqc.queue[uuid]; !ok {
- return
- }
+ sqc.notify.Wait()
+ job = sqc.queue[uuid]
+ }
+ needUpdate := job != nil && job.wantPriority != want
+ sqc.lock.RUnlock()
+
+ if needUpdate {
+ sqc.lock.Lock()
+ job.wantPriority = want
+ sqc.lock.Unlock()
}
- job.wantPriority = want
}
// adjust slurm job nice values as needed to ensure slurm priority
// order matches Arvados priority order.
func (sqc *SqueueChecker) reniceAll() {
- sqc.L.Lock()
- defer sqc.L.Unlock()
-
+ // This is slow (it shells out to scontrol many times) and no
+ // other goroutines update sqc.queue or any of the job fields
+ // we use here, so we don't acquire a lock.
jobs := make([]*slurmJob, 0, len(sqc.queue))
for _, j := range sqc.queue {
if j.wantPriority == 0 {
// (perhaps it's not an Arvados job)
continue
}
- if j.priority == 0 {
+ if j.priority <= 2*slurm15NiceLimit {
// SLURM <= 15.x implements "hold" by setting
// priority to 0. If we include held jobs
// here, we'll end up trying to push other
// queued). If it succeeds, it updates sqc.queue and wakes up any
// goroutines that are waiting in HasUUID() or All().
func (sqc *SqueueChecker) check() {
- // Mutex between squeue sync and running sbatch or scancel. This
- // establishes a sequence so that squeue doesn't run concurrently with
- // sbatch or scancel; the next update of squeue will occur only after
- // sbatch or scancel has completed.
- sqc.L.Lock()
- defer sqc.L.Unlock()
-
cmd := sqc.Slurm.QueueCommand([]string{"--all", "--noheader", "--format=%j %y %Q %T %r"})
stdout, stderr := &bytes.Buffer{}, &bytes.Buffer{}
cmd.Stdout, cmd.Stderr = stdout, stderr
log.Printf("warning: ignoring unparsed line in squeue output: %q", line)
continue
}
+
+ // No other goroutines write to jobs' priority or nice
+ // fields, so we can read and write them without
+ // locks.
replacing, ok := sqc.queue[uuid]
if !ok {
replacing = &slurmJob{uuid: uuid}
// resolved the same way.
log.Printf("releasing held job %q (priority=%d, state=%q, reason=%q)", uuid, p, state, reason)
sqc.Slurm.Release(uuid)
- } else if p < 1<<20 && replacing.wantPriority > 0 {
+ } else if state != "RUNNING" && p <= 2*slurm15NiceLimit && replacing.wantPriority > 0 {
log.Printf("warning: job %q has low priority %d, nice %d, state %q, reason %q", uuid, p, n, state, reason)
}
}
+ sqc.lock.Lock()
sqc.queue = newq
- sqc.Broadcast()
+ sqc.lock.Unlock()
+ sqc.notify.Broadcast()
}
// Initialize, and start a goroutine to call check() once per
// squeue.Period until terminated by calling Stop().
func (sqc *SqueueChecker) start() {
- sqc.L = &sync.Mutex{}
+ sqc.notify.L = sqc.lock.RLocker()
sqc.done = make(chan struct{})
go func() {
ticker := time.NewTicker(sqc.Period)
case <-ticker.C:
sqc.check()
sqc.reniceAll()
+ select {
+ case <-ticker.C:
+ // If this iteration took
+ // longer than sqc.Period,
+ // consume the next tick and
+ // wait. Otherwise we would
+ // starve other goroutines.
+ default:
+ }
}
}
}()
// names reported by squeue.
func (sqc *SqueueChecker) All() []string {
sqc.startOnce.Do(sqc.start)
- sqc.L.Lock()
- defer sqc.L.Unlock()
- sqc.Wait()
+ sqc.lock.RLock()
+ defer sqc.lock.RUnlock()
+ sqc.notify.Wait()
var uuids []string
for u := range sqc.queue {
uuids = append(uuids, u)
CgroupParent: runner.expectCgroupParent,
CgroupRoot: runner.cgroupRoot,
PollPeriod: runner.statInterval,
+ TempDir: runner.parentTemp,
}
runner.statReporter.Start()
return nil
}
// Funnel stderr through our channel
- stderr_pipe, err := cmd.StderrPipe()
+ stderrPipe, err := cmd.StderrPipe()
if err != nil {
logger.Fatalln("error in StderrPipe:", err)
}
os.Stdin.Close()
os.Stdout.Close()
- copyPipeToChildLog(stderr_pipe, log.New(os.Stderr, "", 0))
+ copyPipeToChildLog(stderrPipe, log.New(os.Stderr, "", 0))
return cmd.Wait()
}
import (
"sync"
- "sync/atomic"
"time"
"git.curoverse.com/arvados.git/sdk/go/arvados"
"git.curoverse.com/arvados.git/sdk/go/arvadosclient"
"github.com/hashicorp/golang-lru"
+ "github.com/prometheus/client_golang/prometheus"
)
+const metricsUpdateInterval = time.Second / 10
+
type cache struct {
TTL arvados.Duration
UUIDTTL arvados.Duration
MaxPermissionEntries int
MaxUUIDEntries int
- stats cacheStats
+ registry *prometheus.Registry
+ metrics cacheMetrics
pdhs *lru.TwoQueueCache
collections *lru.TwoQueueCache
permissions *lru.TwoQueueCache
setupOnce sync.Once
}
-type cacheStats struct {
- Requests uint64 `json:"Cache.Requests"`
- CollectionBytes uint64 `json:"Cache.CollectionBytes"`
- CollectionEntries int `json:"Cache.CollectionEntries"`
- CollectionHits uint64 `json:"Cache.CollectionHits"`
- PDHHits uint64 `json:"Cache.UUIDHits"`
- PermissionHits uint64 `json:"Cache.PermissionHits"`
- APICalls uint64 `json:"Cache.APICalls"`
+type cacheMetrics struct {
+ requests prometheus.Counter
+ collectionBytes prometheus.Gauge
+ collectionEntries prometheus.Gauge
+ collectionHits prometheus.Counter
+ pdhHits prometheus.Counter
+ permissionHits prometheus.Counter
+ apiCalls prometheus.Counter
+}
+
+func (m *cacheMetrics) setup(reg *prometheus.Registry) {
+ m.requests = prometheus.NewCounter(prometheus.CounterOpts{
+ Namespace: "arvados",
+ Subsystem: "keepweb_collectioncache",
+ Name: "requests",
+ Help: "Number of targetID-to-manifest lookups handled.",
+ })
+ reg.MustRegister(m.requests)
+ m.collectionHits = prometheus.NewCounter(prometheus.CounterOpts{
+ Namespace: "arvados",
+ Subsystem: "keepweb_collectioncache",
+ Name: "hits",
+ Help: "Number of pdh-to-manifest cache hits.",
+ })
+ reg.MustRegister(m.collectionHits)
+ m.pdhHits = prometheus.NewCounter(prometheus.CounterOpts{
+ Namespace: "arvados",
+ Subsystem: "keepweb_collectioncache",
+ Name: "pdh_hits",
+ Help: "Number of uuid-to-pdh cache hits.",
+ })
+ reg.MustRegister(m.pdhHits)
+ m.permissionHits = prometheus.NewCounter(prometheus.CounterOpts{
+ Namespace: "arvados",
+ Subsystem: "keepweb_collectioncache",
+ Name: "permission_hits",
+ Help: "Number of targetID-to-permission cache hits.",
+ })
+ reg.MustRegister(m.permissionHits)
+ m.apiCalls = prometheus.NewCounter(prometheus.CounterOpts{
+ Namespace: "arvados",
+ Subsystem: "keepweb_collectioncache",
+ Name: "api_calls",
+ Help: "Number of outgoing API calls made by cache.",
+ })
+ reg.MustRegister(m.apiCalls)
+ m.collectionBytes = prometheus.NewGauge(prometheus.GaugeOpts{
+ Namespace: "arvados",
+ Subsystem: "keepweb_collectioncache",
+ Name: "cached_manifest_bytes",
+ Help: "Total size of all manifests in cache.",
+ })
+ reg.MustRegister(m.collectionBytes)
+ m.collectionEntries = prometheus.NewGauge(prometheus.GaugeOpts{
+ Namespace: "arvados",
+ Subsystem: "keepweb_collectioncache",
+ Name: "cached_manifests",
+ Help: "Number of manifests in cache.",
+ })
+ reg.MustRegister(m.collectionEntries)
}
type cachedPDH struct {
if err != nil {
panic(err)
}
+
+ reg := c.registry
+ if reg == nil {
+ reg = prometheus.NewRegistry()
+ }
+ c.metrics.setup(reg)
+ go func() {
+ for range time.Tick(metricsUpdateInterval) {
+ c.updateGauges()
+ }
+ }()
}
-var selectPDH = map[string]interface{}{
- "select": []string{"portable_data_hash"},
+func (c *cache) updateGauges() {
+ c.metrics.collectionBytes.Set(float64(c.collectionBytes()))
+ c.metrics.collectionEntries.Set(float64(c.collections.Len()))
}
-func (c *cache) Stats() cacheStats {
- c.setupOnce.Do(c.setup)
- return cacheStats{
- Requests: atomic.LoadUint64(&c.stats.Requests),
- CollectionBytes: c.collectionBytes(),
- CollectionEntries: c.collections.Len(),
- CollectionHits: atomic.LoadUint64(&c.stats.CollectionHits),
- PDHHits: atomic.LoadUint64(&c.stats.PDHHits),
- PermissionHits: atomic.LoadUint64(&c.stats.PermissionHits),
- APICalls: atomic.LoadUint64(&c.stats.APICalls),
- }
+var selectPDH = map[string]interface{}{
+ "select": []string{"portable_data_hash"},
}
// Update saves a modified version (fs) to an existing collection
func (c *cache) Get(arv *arvadosclient.ArvadosClient, targetID string, forceReload bool) (*arvados.Collection, error) {
c.setupOnce.Do(c.setup)
-
- atomic.AddUint64(&c.stats.Requests, 1)
+ c.metrics.requests.Inc()
permOK := false
permKey := arv.ApiToken + "\000" + targetID
c.permissions.Remove(permKey)
} else {
permOK = true
- atomic.AddUint64(&c.stats.PermissionHits, 1)
+ c.metrics.permissionHits.Inc()
}
}
c.pdhs.Remove(targetID)
} else {
pdh = ent.pdh
- atomic.AddUint64(&c.stats.PDHHits, 1)
+ c.metrics.pdhHits.Inc()
}
}
// likely, the cached PDH is still correct; if so,
// _and_ the current token has permission, we can
// use our cached manifest.
- atomic.AddUint64(&c.stats.APICalls, 1)
+ c.metrics.apiCalls.Inc()
var current arvados.Collection
err := arv.Get("collections", targetID, selectPDH, ¤t)
if err != nil {
}
// Collection manifest is not cached.
- atomic.AddUint64(&c.stats.APICalls, 1)
+ c.metrics.apiCalls.Inc()
err := arv.Get("collections", targetID, nil, &collection)
if err != nil {
return nil, err
}
func (c *cache) lookupCollection(key string) *arvados.Collection {
- if ent, cached := c.collections.Get(key); !cached {
+ e, cached := c.collections.Get(key)
+ if !cached {
+ return nil
+ }
+ ent := e.(*cachedCollection)
+ if ent.expire.Before(time.Now()) {
+ c.collections.Remove(key)
return nil
- } else {
- ent := ent.(*cachedCollection)
- if ent.expire.Before(time.Now()) {
- c.collections.Remove(key)
- return nil
- } else {
- atomic.AddUint64(&c.stats.CollectionHits, 1)
- return ent.collection
- }
}
+ c.metrics.collectionHits.Inc()
+ return ent.collection
}
package main
import (
+ "bytes"
+
"git.curoverse.com/arvados.git/sdk/go/arvados"
"git.curoverse.com/arvados.git/sdk/go/arvadosclient"
"git.curoverse.com/arvados.git/sdk/go/arvadostest"
+ "github.com/prometheus/client_golang/prometheus"
+ "github.com/prometheus/common/expfmt"
"gopkg.in/check.v1"
)
+func (s *UnitSuite) checkCacheMetrics(c *check.C, reg *prometheus.Registry, regs ...string) {
+ mfs, err := reg.Gather()
+ c.Check(err, check.IsNil)
+ buf := &bytes.Buffer{}
+ enc := expfmt.NewEncoder(buf, expfmt.FmtText)
+ for _, mf := range mfs {
+ c.Check(enc.Encode(mf), check.IsNil)
+ }
+ mm := buf.String()
+ for _, reg := range regs {
+ c.Check(mm, check.Matches, `(?ms).*collectioncache_`+reg+`\n.*`)
+ }
+}
+
func (s *UnitSuite) TestCache(c *check.C) {
arv, err := arvadosclient.MakeArvadosClient()
c.Assert(err, check.Equals, nil)
cache := DefaultConfig().Cache
+ cache.registry = prometheus.NewRegistry()
// Hit the same collection 5 times using the same token. Only
// the first req should cause an API call; the next 4 should
c.Check(coll.PortableDataHash, check.Equals, arvadostest.FooPdh)
c.Check(coll.ManifestText[:2], check.Equals, ". ")
}
- c.Check(cache.Stats().Requests, check.Equals, uint64(5))
- c.Check(cache.Stats().CollectionHits, check.Equals, uint64(4))
- c.Check(cache.Stats().PermissionHits, check.Equals, uint64(4))
- c.Check(cache.Stats().PDHHits, check.Equals, uint64(4))
- c.Check(cache.Stats().APICalls, check.Equals, uint64(1))
+ s.checkCacheMetrics(c, cache.registry,
+ "requests 5",
+ "hits 4",
+ "permission_hits 4",
+ "pdh_hits 4",
+ "api_calls 1")
// Hit the same collection 2 more times, this time requesting
// it by PDH and using a different token. The first req should
c.Check(coll2.ManifestText[:2], check.Equals, ". ")
c.Check(coll2.ManifestText, check.Not(check.Equals), coll.ManifestText)
- c.Check(cache.Stats().Requests, check.Equals, uint64(5+1))
- c.Check(cache.Stats().CollectionHits, check.Equals, uint64(4+0))
- c.Check(cache.Stats().PermissionHits, check.Equals, uint64(4+0))
- c.Check(cache.Stats().PDHHits, check.Equals, uint64(4+0))
- c.Check(cache.Stats().APICalls, check.Equals, uint64(1+1))
+ s.checkCacheMetrics(c, cache.registry,
+ "requests 6",
+ "hits 4",
+ "permission_hits 4",
+ "pdh_hits 4",
+ "api_calls 2")
coll2, err = cache.Get(arv, arvadostest.FooPdh, false)
c.Check(err, check.Equals, nil)
c.Check(coll2.PortableDataHash, check.Equals, arvadostest.FooPdh)
c.Check(coll2.ManifestText[:2], check.Equals, ". ")
- c.Check(cache.Stats().Requests, check.Equals, uint64(5+2))
- c.Check(cache.Stats().CollectionHits, check.Equals, uint64(4+1))
- c.Check(cache.Stats().PermissionHits, check.Equals, uint64(4+1))
- c.Check(cache.Stats().PDHHits, check.Equals, uint64(4+0))
- c.Check(cache.Stats().APICalls, check.Equals, uint64(1+1))
+ s.checkCacheMetrics(c, cache.registry,
+ "requests 7",
+ "hits 5",
+ "permission_hits 5",
+ "pdh_hits 4",
+ "api_calls 2")
// Alternating between two collections N times should produce
// only 2 more API calls.
_, err := cache.Get(arv, target, false)
c.Check(err, check.Equals, nil)
}
- c.Check(cache.Stats().Requests, check.Equals, uint64(5+2+20))
- c.Check(cache.Stats().CollectionHits, check.Equals, uint64(4+1+18))
- c.Check(cache.Stats().PermissionHits, check.Equals, uint64(4+1+18))
- c.Check(cache.Stats().PDHHits, check.Equals, uint64(4+0+18))
- c.Check(cache.Stats().APICalls, check.Equals, uint64(1+1+2))
+ s.checkCacheMetrics(c, cache.registry,
+ "requests 27",
+ "hits 23",
+ "permission_hits 23",
+ "pdh_hits 22",
+ "api_calls 4")
}
func (s *UnitSuite) TestCacheForceReloadByPDH(c *check.C) {
c.Assert(err, check.Equals, nil)
cache := DefaultConfig().Cache
+ cache.registry = prometheus.NewRegistry()
for _, forceReload := range []bool{false, true, false, true} {
_, err := cache.Get(arv, arvadostest.FooPdh, forceReload)
c.Check(err, check.Equals, nil)
}
- c.Check(cache.Stats().Requests, check.Equals, uint64(4))
- c.Check(cache.Stats().CollectionHits, check.Equals, uint64(3))
- c.Check(cache.Stats().PermissionHits, check.Equals, uint64(1))
- c.Check(cache.Stats().PDHHits, check.Equals, uint64(0))
- c.Check(cache.Stats().APICalls, check.Equals, uint64(3))
+ s.checkCacheMetrics(c, cache.registry,
+ "requests 4",
+ "hits 3",
+ "permission_hits 1",
+ "pdh_hits 0",
+ "api_calls 3")
}
func (s *UnitSuite) TestCacheForceReloadByUUID(c *check.C) {
c.Assert(err, check.Equals, nil)
cache := DefaultConfig().Cache
+ cache.registry = prometheus.NewRegistry()
for _, forceReload := range []bool{false, true, false, true} {
_, err := cache.Get(arv, arvadostest.FooCollection, forceReload)
c.Check(err, check.Equals, nil)
}
- c.Check(cache.Stats().Requests, check.Equals, uint64(4))
- c.Check(cache.Stats().CollectionHits, check.Equals, uint64(3))
- c.Check(cache.Stats().PermissionHits, check.Equals, uint64(1))
- c.Check(cache.Stats().PDHHits, check.Equals, uint64(3))
- c.Check(cache.Stats().APICalls, check.Equals, uint64(3))
+ s.checkCacheMetrics(c, cache.registry,
+ "requests 4",
+ "hits 3",
+ "permission_hits 1",
+ "pdh_hits 3",
+ "api_calls 3")
}
}
func (h *handler) serveStatus(w http.ResponseWriter, r *http.Request) {
- status := struct {
- cacheStats
- Version string
- }{
- cacheStats: h.Config.Cache.Stats(),
- Version: version,
- }
- json.NewEncoder(w).Encode(status)
+ json.NewEncoder(w).Encode(struct{ Version string }{version})
}
// updateOnSuccess wraps httpserver.ResponseWriter. If the handler
"net/http"
"git.curoverse.com/arvados.git/sdk/go/httpserver"
+ "github.com/prometheus/client_golang/prometheus"
)
type server struct {
func (srv *server) Start() error {
h := &handler{Config: srv.Config}
- mh := httpserver.Instrument(nil, httpserver.AddRequestIDs(httpserver.LogRequests(nil, h)))
+ reg := prometheus.NewRegistry()
+ h.Config.Cache.registry = reg
+ mh := httpserver.Instrument(reg, nil, httpserver.AddRequestIDs(httpserver.LogRequests(nil, h)))
h.MetricsAPI = mh.ServeAPI(http.NotFoundHandler())
srv.Handler = mh
srv.Addr = srv.Config.Listen
resp, err := http.DefaultClient.Do(req)
c.Assert(err, check.IsNil)
c.Check(resp.StatusCode, check.Equals, http.StatusOK)
- req, _ = http.NewRequest("GET", origin+"/foo", nil)
- req.Host = arvadostest.FooCollection + ".example.com"
- req.Header.Set("Authorization", "Bearer "+arvadostest.ActiveToken)
- resp, err = http.DefaultClient.Do(req)
- c.Assert(err, check.IsNil)
- c.Check(resp.StatusCode, check.Equals, http.StatusOK)
- buf, _ := ioutil.ReadAll(resp.Body)
- c.Check(buf, check.DeepEquals, []byte("foo"))
+ for i := 0; i < 2; i++ {
+ req, _ = http.NewRequest("GET", origin+"/foo", nil)
+ req.Host = arvadostest.FooCollection + ".example.com"
+ req.Header.Set("Authorization", "Bearer "+arvadostest.ActiveToken)
+ resp, err = http.DefaultClient.Do(req)
+ c.Assert(err, check.IsNil)
+ c.Check(resp.StatusCode, check.Equals, http.StatusOK)
+ buf, _ := ioutil.ReadAll(resp.Body)
+ c.Check(buf, check.DeepEquals, []byte("foo"))
+ resp.Body.Close()
+ }
+
+ s.testServer.Config.Cache.updateGauges()
req, _ = http.NewRequest("GET", origin+"/metrics.json", nil)
resp, err = http.DefaultClient.Do(req)
Value float64
}
}
+ type counter struct {
+ Value int64
+ }
+ type gauge struct {
+ Value float64
+ }
var ents []struct {
Name string
Help string
Name string
Value string
}
+ Counter counter
+ Gauge gauge
Summary summary
}
}
json.NewDecoder(resp.Body).Decode(&ents)
- flat := map[string]summary{}
+ summaries := map[string]summary{}
+ gauges := map[string]gauge{}
+ counters := map[string]counter{}
for _, e := range ents {
for _, m := range e.Metric {
labels := map[string]string{}
for _, lbl := range m.Label {
labels[lbl.Name] = lbl.Value
}
- flat[e.Name+"/"+labels["method"]+"/"+labels["code"]] = m.Summary
+ summaries[e.Name+"/"+labels["method"]+"/"+labels["code"]] = m.Summary
+ counters[e.Name+"/"+labels["method"]+"/"+labels["code"]] = m.Counter
+ gauges[e.Name+"/"+labels["method"]+"/"+labels["code"]] = m.Gauge
}
}
- c.Check(flat["request_duration_seconds/get/200"].SampleSum, check.Not(check.Equals), 0)
- c.Check(flat["request_duration_seconds/get/200"].SampleCount, check.Equals, "2")
- c.Check(flat["request_duration_seconds/get/404"].SampleCount, check.Equals, "1")
- c.Check(flat["time_to_status_seconds/get/404"].SampleCount, check.Equals, "1")
+ c.Check(summaries["request_duration_seconds/get/200"].SampleSum, check.Not(check.Equals), 0)
+ c.Check(summaries["request_duration_seconds/get/200"].SampleCount, check.Equals, "3")
+ c.Check(summaries["request_duration_seconds/get/404"].SampleCount, check.Equals, "1")
+ c.Check(summaries["time_to_status_seconds/get/404"].SampleCount, check.Equals, "1")
+ c.Check(counters["arvados_keepweb_collectioncache_requests//"].Value, check.Equals, int64(2))
+ c.Check(counters["arvados_keepweb_collectioncache_api_calls//"].Value, check.Equals, int64(1))
+ c.Check(counters["arvados_keepweb_collectioncache_hits//"].Value, check.Equals, int64(1))
+ c.Check(counters["arvados_keepweb_collectioncache_pdh_hits//"].Value, check.Equals, int64(1))
+ c.Check(counters["arvados_keepweb_collectioncache_permission_hits//"].Value, check.Equals, int64(1))
+ c.Check(gauges["arvados_keepweb_collectioncache_cached_manifests//"].Value, check.Equals, float64(1))
+ // FooCollection's cached manifest size is 45 ("1f4b0....+45") plus one 51-byte blob signature
+ c.Check(gauges["arvados_keepweb_collectioncache_cached_manifest_bytes//"].Value, check.Equals, float64(45+51))
// If the Host header indicates a collection, /metrics.json
// refers to a file in the collection -- the metrics handler
var status map[string]interface{}
err := json.NewDecoder(resp.Body).Decode(&status)
c.Check(err, check.IsNil)
- c.Check(status["Cache.Requests"], check.Equals, float64(0))
c.Check(status["Version"], check.Not(check.Equals), "")
}
rtr.limiter = httpserver.NewRequestLimiter(theConfig.MaxRequests, rtr)
- stack := httpserver.Instrument(nil,
+ stack := httpserver.Instrument(nil, nil,
httpserver.AddRequestIDs(httpserver.LogRequests(nil, rtr.limiter)))
return stack.ServeAPI(stack)
}
s.files = ["bin/arvados-login-sync", "agpl-3.0.txt"]
s.executables << "arvados-login-sync"
s.required_ruby_version = '>= 2.1.0'
- s.add_runtime_dependency 'arvados', '~> 0.1', '>= 0.1.20150615153458'
+ s.add_runtime_dependency 'arvados', '~> 1.1.0', '>= 1.1.4'
s.homepage =
'https://arvados.org'
end
'Daemon': {'min_nodes': '0',
'max_nodes': '1',
'poll_time': '60',
+ 'cloudlist_poll_time': '0',
+ 'nodelist_poll_time': '0',
+ 'wishlist_poll_time': '0',
'max_poll_time': '300',
'poll_stale_after': '600',
'max_total_price': '0',
poll_time = config.getfloat('Daemon', 'poll_time')
max_poll_time = config.getint('Daemon', 'max_poll_time')
+ cloudlist_poll_time = config.getfloat('Daemon', 'cloudlist_poll_time') or poll_time
+ nodelist_poll_time = config.getfloat('Daemon', 'nodelist_poll_time') or poll_time
+ wishlist_poll_time = config.getfloat('Daemon', 'wishlist_poll_time') or poll_time
+
timer = TimedCallBackActor.start(poll_time / 10.0).tell_proxy()
cloud_node_poller = CloudNodeListMonitorActor.start(
- config.new_cloud_client(), timer, server_calculator, poll_time, max_poll_time).tell_proxy()
+ config.new_cloud_client(), timer, server_calculator, cloudlist_poll_time, max_poll_time).tell_proxy()
arvados_node_poller = ArvadosNodeListMonitorActor.start(
- config.new_arvados_client(), timer, poll_time, max_poll_time).tell_proxy()
+ config.new_arvados_client(), timer, nodelist_poll_time, max_poll_time).tell_proxy()
job_queue_poller = JobQueueMonitorActor.start(
config.new_arvados_client(), timer, server_calculator,
config.getboolean('Arvados', 'jobs_queue'),
config.getboolean('Arvados', 'slurm_queue'),
- poll_time, max_poll_time
+ wishlist_poll_time, max_poll_time
).tell_proxy()
return timer, cloud_node_poller, arvados_node_poller, job_queue_poller
# a snapshot of internal state.
# Management server listening address (default 127.0.0.1)
-#address = 0.0.0.0
+address = 0.0.0.0
# Management server port number (default -1, server is disabled)
-#port = 8989
+port = 8989
+
+MangementToken = xxx
[Daemon]
# The dispatcher can customize the start and stop procedure for
ADD crunch-setup.sh gitolite.rc \
keep-setup.sh common.sh createusers.sh \
logger runsu.sh waitforpostgres.sh \
- application_yml_override.py api-setup.sh \
+ yml_override.py api-setup.sh \
go-setup.sh \
/usr/local/lib/arvbox/
fi
blob_signing_key=$(cat /var/lib/arvados/blob_signing_key)
+if ! test -s /var/lib/arvados/management_token ; then
+ ruby -e 'puts rand(2**400).to_s(36)' > /var/lib/arvados/management_token
+fi
+management_token=$(cat /var/lib/arvados/management_token)
+
# self signed key will be created by SSO server script.
test -s /var/lib/arvados/self-signed.key
default_collection_replication: 1
docker_image_formats: ["v2"]
keep_web_service_url: http://$localip:${services[keep-web]}/
+ ManagementToken: $management_token
EOF
-(cd config && /usr/local/lib/arvbox/application_yml_override.py)
+(cd config && /usr/local/lib/arvbox/yml_override.py application.yml)
if ! test -f /var/lib/arvados/api_database_pw ; then
ruby -e 'puts rand(2**128).to_s(36)' > /var/lib/arvados/api_database_pw
declare -A services
services=(
[workbench]=80
- [api]=8000
+ [api]=8004
+ [controller]=8003
+ [controller-ssl]=8000
[sso]=8900
[composer]=4200
[arv-git-httpd]=9001
RAILS_ENV=development
fi
-export ARVADOS_API_HOST=$localip:${services[api]}
+export ARVADOS_API_HOST=$localip:${services[controller-ssl]}
export ARVADOS_API_HOST_INSECURE=1
export ARVADOS_API_TOKEN=$(cat /usr/src/arvados/services/api/superuser_token)
export CRUNCH_JOB_BIN=/usr/src/arvados/sdk/cli/bin/crunch-job
mkdir -p /var/lib/arvados/$1
-export ARVADOS_API_HOST=$localip:${services[api]}
+export ARVADOS_API_HOST=$localip:${services[controller-ssl]}
export ARVADOS_API_HOST_INSECURE=1
export ARVADOS_API_TOKEN=$(cat /var/lib/arvados/superuser_token)
echo $UUID > /var/lib/arvados/$1-uuid
fi
+management_token=$(cat /var/lib/arvados/management_token)
+
set +e
killall -HUP keepproxy
-exec /usr/local/bin/keepstore \
- -listen=:$2 \
- -enforce-permissions=true \
- -blob-signing-key-file=/var/lib/arvados/blob_signing_key \
- -data-manager-token-file=/var/lib/arvados/superuser_token \
- -max-buffers=20 \
- -volume=/var/lib/arvados/$1
+cat >/var/lib/arvados/$1.yml <<EOF
+Listen: ":$2"
+BlobSigningKeyFile: /var/lib/arvados/blob_signing_key
+SystemAuthTokenFile: /var/lib/arvados/superuser_token
+ManagementToken: $management_token
+MaxBuffers: 20
+Volumes:
+ - Type: Directory
+ Root: /var/lib/arvados/$1
+EOF
+
+exec /usr/local/bin/keepstore -config=/var/lib/arvados/$1.yml
exit
fi
-exec bundle exec passenger start --port=${services[api]} \
- --ssl --ssl-certificate=/var/lib/arvados/self-signed.pem \
- --ssl-certificate-key=/var/lib/arvados/self-signed.key
+exec bundle exec passenger start --port=${services[api]}
exit
fi
-export ARVADOS_API_HOST=$localip:${services[api]}
+export ARVADOS_API_HOST=$localip:${services[controller-ssl]}
export ARVADOS_API_HOST_INSECURE=1
export PATH="$PATH:/var/lib/arvados/git/bin"
cd ~git
exit
fi
-echo "apiEndPoint: https://${localip}:${services[api]}" > /usr/src/composer/src/composer.yml
+echo "apiEndPoint: https://${localip}:${services[controller-ssl]}" > /usr/src/composer/src/composer.yml
exec node_modules/.bin/ng serve --host 0.0.0.0 --port 4200 --env=webdev
--- /dev/null
+/usr/local/lib/arvbox/logger
\ No newline at end of file
--- /dev/null
+#!/bin/bash
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: AGPL-3.0
+
+exec 2>&1
+set -ex -o pipefail
+
+. /usr/local/lib/arvbox/common.sh
+. /usr/local/lib/arvbox/go-setup.sh
+
+flock /var/lib/gopath/gopath.lock go get -t "git.curoverse.com/arvados.git/cmd/arvados-server"
+install $GOPATH/bin/arvados-server /usr/local/bin
+(cd /usr/local/bin && ln -sf arvados-server arvados-controller)
+
+if test "$1" = "--only-deps" ; then
+ exit
+fi
+
+uuid_prefix=$(cat /var/lib/arvados/api_uuid_prefix)
+database_pw=$(cat /var/lib/arvados/api_database_pw)
+
+mkdir -p /etc/arvados
+
+cat >/var/lib/arvados/cluster_config.yml <<EOF
+Clusters:
+ ${uuid_prefix}:
+ NodeProfiles:
+ "*":
+ arvados-controller:
+ Listen: ":${services[controller]}" # choose a port
+ arvados-api-server:
+ Listen: ":${services[api]}" # must match Rails server port in your Nginx config
+ PostgreSQL:
+ ConnectionPool: 32 # max concurrent connections per arvados server daemon
+ Connection:
+ # All parameters here are passed to the PG client library in a connection string;
+ # see https://www.postgresql.org/docs/current/static/libpq-connect.html#LIBPQ-PARAMKEYWORDS
+ Host: localhost
+ User: arvados
+ Password: ${database_pw}
+ DBName: arvados_development
+ client_encoding: utf8
+EOF
+
+/usr/local/lib/arvbox/yml_override.py /var/lib/arvados/cluster_config.yml
+
+cp /var/lib/arvados/cluster_config.yml /etc/arvados/config.yml
+
+exec /usr/local/lib/arvbox/runsu.sh /usr/local/bin/arvados-controller
EOF
chmod +x /usr/local/bin/crunch-run.sh
-export ARVADOS_API_HOST=$localip:${services[api]}
+export ARVADOS_API_HOST=$localip:${services[controller-ssl]}
export ARVADOS_API_HOST_INSECURE=1
export ARVADOS_API_TOKEN=$(cat /var/lib/arvados/superuser_token)
+++ /dev/null
-/usr/local/lib/arvbox/runsu.sh
\ No newline at end of file
--- /dev/null
+#!/bin/sh
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: AGPL-3.0
+
+set -e
+
+/usr/local/lib/arvbox/runsu.sh $0-service
+sv stop doc
exit
fi
-set -u
-
-cat <<EOF >/var/lib/arvados/doc-nginx.conf
-worker_processes auto;
-pid /var/lib/arvados/doc-nginx.pid;
-
-error_log stderr;
-daemon off;
-
-events {
- worker_connections 64;
-}
-
-http {
- access_log off;
- include /etc/nginx/mime.types;
- default_type application/octet-stream;
- server {
- listen ${services[doc]} default_server;
- listen [::]:${services[doc]} default_server;
- root /usr/src/arvados/doc/.site;
- index index.html;
- server_name _;
- }
-}
-EOF
-
cd /usr/src/arvados/doc
-bundle exec rake generate baseurl=http://$localip:${services[doc]} arvados_api_host=$localip:${services[api]} arvados_workbench_host=http://$localip
-
-exec nginx -c /var/lib/arvados/doc-nginx.conf
+bundle exec rake generate baseurl=http://$localip:${services[doc]} arvados_api_host=$localip:${services[controller-ssl]} arvados_workbench_host=http://$localip
mkdir -p /var/lib/arvados/git
-export ARVADOS_API_HOST=$localip:${services[api]}
+export ARVADOS_API_HOST=$localip:${services[controller-ssl]}
export ARVADOS_API_HOST_INSECURE=1
export ARVADOS_API_TOKEN=$(cat /var/lib/arvados/superuser_token)
$RAILS_ENV:
gitolite_url: /var/lib/arvados/git/repositories/gitolite-admin.git
gitolite_tmp: /var/lib/arvados/git
- arvados_api_host: $localip:${services[api]}
+ arvados_api_host: $localip:${services[controller-ssl]}
arvados_api_token: "$ARVADOS_API_TOKEN"
arvados_api_host_insecure: true
gitolite_arvados_git_user_key: "$git_user_key"
exit
fi
-export ARVADOS_API_HOST=$localip:${services[api]}
+export ARVADOS_API_HOST=$localip:${services[controller-ssl]}
export ARVADOS_API_HOST_INSECURE=1
export ARVADOS_API_TOKEN=$(cat /var/lib/arvados/superuser_token)
exit
fi
-export ARVADOS_API_HOST=$localip:${services[api]}
+export ARVADOS_API_HOST=$localip:${services[controller-ssl]}
export ARVADOS_API_HOST_INSECURE=1
export ARVADOS_API_TOKEN=$(cat /var/lib/arvados/superuser_token)
--- /dev/null
+/usr/local/lib/arvbox/logger
\ No newline at end of file
--- /dev/null
+/usr/local/lib/arvbox/runsu.sh
\ No newline at end of file
--- /dev/null
+#!/bin/bash
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: AGPL-3.0
+
+exec 2>&1
+set -ex -o pipefail
+
+. /usr/local/lib/arvbox/common.sh
+
+cat <<EOF >/var/lib/arvados/nginx.conf
+worker_processes auto;
+pid /var/lib/arvados/nginx.pid;
+
+error_log stderr;
+daemon off;
+
+events {
+ worker_connections 64;
+}
+
+http {
+ access_log off;
+ include /etc/nginx/mime.types;
+ default_type application/octet-stream;
+ server {
+ listen ${services[doc]} default_server;
+ listen [::]:${services[doc]} default_server;
+ root /usr/src/arvados/doc/.site;
+ index index.html;
+ server_name _;
+ }
+
+ upstream controller {
+ server localhost:${services[controller]};
+ }
+ server {
+ listen *:${services[controller-ssl]} ssl default_server;
+ server_name controller;
+ ssl_certificate "/var/lib/arvados/self-signed.pem";
+ ssl_certificate_key "/var/lib/arvados/self-signed.key";
+ location / {
+ proxy_pass http://controller;
+ proxy_set_header Host \$http_host;
+ proxy_set_header X-Forwarded-For \$proxy_add_x_forwarded_for;
+ proxy_set_header X-Forwarded-Proto https;
+ proxy_redirect off;
+ }
+ }
+}
+
+EOF
+
+exec nginx -c /var/lib/arvados/nginx.conf
+++ /dev/null
-/usr/local/lib/arvbox/runsu.sh
\ No newline at end of file
--- /dev/null
+#!/bin/sh
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: AGPL-3.0
+
+set -e
+
+/usr/local/lib/arvbox/runsu.sh $0-service
+sv stop ready
waiting="$waiting crunch-dispatch"
fi
-export ARVADOS_API_HOST=$localip:${services[api]}
+export ARVADOS_API_HOST=$localip:${services[controller-ssl]}
export ARVADOS_API_HOST_INSECURE=1
vm_ok=0
echo "Workbench is running at http://$localip"
rm -r /tmp/arvbox-ready
-
-sv stop ready >/dev/null
allow_account_registration: true
EOF
-(cd config && /usr/local/lib/arvbox/application_yml_override.py)
+(cd config && /usr/local/lib/arvbox/yml_override.py application.yml)
if ! test -f /var/lib/arvados/sso_database_pw ; then
ruby -e 'puts rand(2**128).to_s(36)' > /var/lib/arvados/sso_database_pw
cd /usr/src/arvados/services/login-sync
-export ARVADOS_API_HOST=$localip:${services[api]}
+export ARVADOS_API_HOST=$localip:${services[controller-ssl]}
export ARVADOS_API_HOST_INSECURE=1
export ARVADOS_API_TOKEN=$(cat /var/lib/arvados/superuser_token)
export ARVADOS_VIRTUAL_MACHINE_UUID=$(cat /var/lib/arvados/vm-uuid)
set -u
-export ARVADOS_API_HOST=$localip:${services[api]}
+export ARVADOS_API_HOST=$localip:${services[controller-ssl]}
export ARVADOS_API_HOST_INSECURE=1
export ARVADOS_API_TOKEN=$(cat /var/lib/arvados/superuser_token)
export ARVADOS_VIRTUAL_MACHINE_UUID=$(cat /var/lib/arvados/vm-uuid)
cat >/var/lib/arvados/arvados-ws.yml <<EOF
Client:
- APIHost: $localip:${services[api]}
+ APIHost: $localip:${services[controller-ssl]}
Insecure: true
Postgres:
dbname: arvados_$RAILS_ENV
cat >config/application.yml <<EOF
$RAILS_ENV:
secret_token: $secret_token
- arvados_login_base: https://$localip:${services[api]}/login
- arvados_v1_base: https://$localip:${services[api]}/arvados/v1
+ arvados_login_base: https://$localip:${services[controller-ssl]}/login
+ arvados_v1_base: https://$localip:${services[controller-ssl]}/arvados/v1
arvados_insecure_https: true
keep_web_download_url: http://$localip:${services[keep-web]}/c=%{uuid_or_pdh}
keep_web_url: http://$localip:${services[keep-web]}/c=%{uuid_or_pdh}
bundle exec rake assets:precompile
-(cd config && /usr/local/lib/arvbox/application_yml_override.py)
+(cd config && /usr/local/lib/arvbox/yml_override.py application.yml)
# SPDX-License-Identifier: AGPL-3.0
import yaml
+import sys
+
+fn = sys.argv[1]
try:
- with open("application.yml.override") as f:
+ with open(fn+".override") as f:
b = yaml.load(f)
except IOError:
exit()
-with open("application.yml") as f:
+with open(fn) as f:
a = yaml.load(f)
def recursiveMerge(a, b):
else:
return b
-with open("application.yml", "w") as f:
+with open(fn, "w") as f:
yaml.dump(recursiveMerge(a, b), f)
projects / arvados.git / commitdiff
