table(table table-bordered table-condensed).
|_. Key|_. Type|_. Description|_. Notes|
|partitions|array of strings|The names of one or more compute partitions that may run this container. If not provided, the system will choose where to run the container.|Optional.|
-|preemptible|boolean|If true, the dispatcher will ask for a preemptible cloud node instance (eg: AWS Spot Instance) to run this container.|Optional. Default is false.|
+|preemptible|boolean|If true, the dispatcher should use a preemptible cloud node instance (eg: AWS Spot Instance) to run this container. Whether a preemptible instance is actually used "depends on cluster configuration.":{{site.baseurl}}/admin/spot-instances.html|Optional. Default is false.|
|max_run_time|integer|Maximum running time (in seconds) that this container will be allowed to run before being cancelled.|Optional. Default is 0 (no limit).|
h2. Configuration
-First, ensure automatic selection of preemptible instances is not disabled in your configuration file (this is enabled by default, but can be disabled with @AlwaysUsePreemptibleInstances: false@), and add entries to @InstanceTypes@ that have @Preemptible: true@. Typically you want to add both preemptible and non-preemptible entries for each cloud provider VM type. The @Price@ for preemptible instances is the maximum bid price, the actual price paid is dynamic and will likely be lower. For example:
+Add entries to @InstanceTypes@ that have @Preemptible: true@. Typically you want to add both preemptible and non-preemptible entries for each cloud provider VM type. The @Price@ for preemptible instances is the maximum bid price, the actual price paid is dynamic and will likely be lower. For example:
<pre>
Clusters:
- ClusterID:
- Containers:
- AlwaysUsePreemptibleInstances: true
+ ClusterID:
InstanceTypes:
m4.large:
Preemptible: false
Price: 0.1
</pre>
-When @AlwaysUsePreemptibleInstances@ is enabled, child containers (workflow steps) will automatically be made preemptible. Note that because preempting the workflow runner would cancel the entire workflow, the workflow runner runs in a reserved (non-preemptible) instance.
+Next, you can choose to enable automatic use of preemptible instances:
+
+<pre>
+ Containers:
+ AlwaysUsePreemptibleInstances: true
+</pre>
+
+If @AlwaysUsePreemptibleInstances@ is "true", child containers (workflow steps) will always select preemptible instances, regardless of user option.
+
+If @AlwaysUsePreemptibleInstances@ is "false" (the default) or unspecified, preemptible instance are "used when requested by the user.":{{site.baseurl}}/user/cwl/cwl-run-options.html#preemptible
+
+Note that regardless of the value of @AlwaysUsePreemptibleInstances@, the top level workflow runner container always runs in a reserved (non-preemptible) instance, to avoid situations where the workflow runner is killed requiring the entire to be restarted.
No additional configuration is required, "arvados-dispatch-cloud":{{site.baseurl}}/install/crunch2-cloud/install-dispatch-cloud.html will now start preemptible instances where appropriate.
Note: Because adding access tokens to manifests can be computationally expensive, the @manifest_text@ field is not included in results by default. If you need it, pass a @select@ parameter that includes @manifest_text@.
+h4. Searching Collections for names of file or directories
+
+You can search collections for specific file or directory names (whole or part) using the following filter in a @list@ query.
+
+<pre>
+filters: [["file_names", "ilike", "%sample1234.fastq%"]]
+</pre>
+
+Note: @file_names@ is a hidden field used for indexing. It is not returned by any API call. On the client, you can programmatically enumerate all the files in a collection using @arv-ls@, the Python SDK @Collection@ class, Go SDK @FileSystem@ struct, the WebDAV API, or the S3-compatible API.
+
+As of this writing (Arvados 2.4), you can also search for directory paths, but _not_ complete file paths.
+
+In other words, this will work (when @dir3@ is a directory):
+
+<pre>
+filters: [["file_names", "ilike", "%dir1/dir2/dir3%"]]
+</pre>
+
+However, this will _not_ return the desired results (where @sample1234.fastq@ is a file):
+
+<pre>
+filters: [["file_names", "ilike", "%dir1/dir2/dir3/sample1234.fastq%"]]
+</pre>
+
+As a workaround, you can search for both the directory path and file name separately, and then filter on the client side.
+
+<pre>
+filters: [["file_names", "ilike", "%dir1/dir2/dir3%"], ["file_names", "ilike", "%sample1234.fastq%"]]
+</pre>
+
h3. update
Update attributes of an existing Collection.
|trash_at|datetime|If @trash_at@ is non-null and in the past, this group and all objects directly or indirectly owned by the group will be hidden from API calls. May be untrashed.||
|delete_at|datetime|If @delete_at@ is non-null and in the past, the group and all objects directly or indirectly owned by the group may be permanently deleted.||
|is_trashed|datetime|True if @trash_at@ is in the past, false if not.||
+|frozen_by_uuid|string|For a frozen project, indicates the user who froze the project; null in all other cases. When a project is frozen, no further changes can be made to the project or its contents, even by admins. Attempting to add new items or modify, rename, move, trash, or delete the project or its contents, including any subprojects, will return an error.||
+
+h3. Frozen projects
+
+A user with @manage@ permission can set the @frozen_by_uuid@ attribute of a @project@ group to their own user UUID. Once this is done, no further changes can be made to the project or its contents, including subprojects.
+
+The @frozen_by_uuid@ attribute can be cleared by an admin user. It can also be cleared by a user with @manage@ permission, unless the @API.UnfreezeProjectRequiresAdmin@ configuration setting is active.
+
+The optional @API.FreezeProjectRequiresDescription@ and @API.FreezeProjectRequiresProperties@ configuration settings can be used to prevent users from freezing projects that have empty @description@ and/or specified @properties@ entries.
+
+h3. Filter groups
@filter@ groups are virtual groups; they can not own other objects. Filter groups have a special @properties@ field named @filters@, which must be an array of filter conditions. See "list method filters":{{site.baseurl}}/api/methods.html#filters for details on the syntax of valid filters, but keep in mind that the attributes must include the object type (@collections@, @container_requests@, @groups@, @workflows@), separated with a dot from the field to be filtered on.
SPDX-License-Identifier: CC-BY-SA-3.0
{% endcomment %}
-Arvados requires at least version *9.4* of PostgreSQL.
+Arvados requires at least version *9.4* of PostgreSQL. We recommend using version 10 or newer.
* "AWS":#aws
* "CentOS 7":#centos7
cudaComputeCapabilityMin: "9.0"
deviceCountMin: 1
deviceCountMax: 1
+
+ arv:UsePreemptible:
+ usePreemptible: true
{% endcodeblock %}
h2(#RunInSingleContainer). arv:RunInSingleContainer
|deviceCountMin|integer|Minimum number of GPU devices to allocate on a single node. Required.|
|deviceCountMax|integer|Maximum number of GPU devices to allocate on a single node. Optional. If not specified, same as @minDeviceCount@.|
+h2(#UsePreemptible). arv:UsePreemptible
+
+Specify whether a workflow step should request preemptible (e.g. AWS Spot market) instances. Such instances are generally cheaper, but can be taken back by the cloud provider at any time (preempted) causing the step to fail. When this happens, Arvados will automatically re-try the step, up to the configuration value of @Containers.MaxRetryAttempts@ (default 3) times.
+
+table(table table-bordered table-condensed).
+|_. Field |_. Type |_. Description |
+|usePreemptible|boolean|Required, true to opt-in to using preemptible instances, false to opt-out.|
+
h2. arv:dockerCollectionPDH
This is an optional extension field appearing on the standard @DockerRequirement@. It specifies the portable data hash of the Arvados collection containing the Docker image. If present, it takes precedence over @dockerPull@ or @dockerImageId@.
|==--priority== PRIORITY|Workflow priority (range 1..1000, higher has precedence over lower)|
|==--thread-count== THREAD_COUNT|Number of threads to use for container submit and output collection.|
|==--http-timeout== HTTP_TIMEOUT|API request timeout in seconds. Default is 300 seconds (5 minutes).|
+|==--enable-preemptible==|Use preemptible instances. Control individual steps with "arv:UsePreemptible":cwl-extensions.html#UsePreemptible hint.|
+|==--disable-preemptible==|Don't use preemptible instances.|
+|==--skip-schemas==|Skip loading of extension schemas (the $schemas section).|
|==--trash-intermediate==|Immediately trash intermediate outputs on workflow success.|
|==--no-trash-intermediate==|Do not trash intermediate outputs (default).|
h3(#federation). Run workflow on a remote federated cluster
By default, the workflow runner will run on the local (home) cluster. Using @--submit-runner-cluster@ you can specify that the runner should be submitted to a remote federated cluster. When doing this, @--project-uuid@ should specify a project on that cluster. Steps making up the workflow will be submitted to the remote federated cluster by default, but the behavior of @arv:ClusterTarget@ is unchanged. Note: when using this option, any resources that need to be uploaded in order to run the workflow (such as files or Docker images) will be uploaded to the local (home) cluster, and streamed to the federated cluster on demand.
+
+h3(#preemptible). Using preemptible (spot) instances
+
+Preemptible instances typically offer lower cost computation with a tradeoff of lower service guarantees. If a compute node is preempted, Arvados will restart the computation on a new instance.
+
+If the sitewide configuration @Containers.AlwaysUsePreemptibleInstances@ is true, workflow steps will always select preemptible instances, regardless of user option.
+
+If @Containers.AlwaysUsePreemptibleInstances@ is false, you can request preemptible instances for a specific run with the @arvados-cwl-runner --enable-preemptible@ option.
+
+Within the workflow, you can control whether individual steps should be preemptible with the "arv:UsePreemptible":cwl-extensions.html#UsePreemptible hint.
+
+If a workflow requests preemptible instances with "arv:UsePreemptible":cwl-extensions.html#UsePreemptible , but you _do not_ want to use preemptible instances, you can override it for a specific run with the @arvados-cwl-runner --disable-preemptible@ option.
+
+h3(#gpu). Use CUDA GPU instances
+
+See "cwltool:CUDARequirement":cwl-extensions.html#CUDARequirement .
To get the best perfomance from your workflows, be aware of the following Arvados features, behaviors, and best practices.
-Does your application support NVIDIA GPU acceleration? Use "cwltool:CUDARequirement":cwl-extensions.html#CUDARequirement to request nodes with GPUs.
+h3. Does your application support NVIDIA GPU acceleration?
+
+Use "cwltool:CUDARequirement":cwl-extensions.html#CUDARequirement to request nodes with GPUs.
+
+h3. Trying to reduce costs?
+
+Try "using preemptible (spot) instances":cwl-run-options.html#preemptible .
+
+h3. You have a sequence of short-running steps
If you have a sequence of short-running steps (less than 1-2 minutes each), use the Arvados extension "arv:RunInSingleContainer":cwl-extensions.html#RunInSingleContainer to avoid scheduling and data transfer overhead by running all the steps together in the same container on the same node. To use this feature, @cwltool@ must be installed in the container image. Example:
run: subworkflow-with-short-steps.cwl
{% endcodeblock %}
+h3. Avoid declaring @InlineJavascriptRequirement@ or @ShellCommandRequirement@
+
Avoid declaring @InlineJavascriptRequirement@ or @ShellCommandRequirement@ unless you specifically need them. Don't include them "just in case" because they change the default behavior and may add extra overhead.
+h3. Prefer text substitution to Javascript
+
When combining a parameter value with a string, such as adding a filename extension, write @$(inputs.file.basename).ext@ instead of @$(inputs.file.basename + 'ext')@. The first form is evaluated as a simple text substitution, the second form (using the @+@ operator) is evaluated as an arbitrary Javascript expression and requires that you declare @InlineJavascriptRequirement@.
+h3. Use @ExpressionTool@ to efficiently rearrange input files
+
Use @ExpressionTool@ to efficiently rearrange input files between steps of a Workflow. For example, the following expression accepts a directory containing files paired by @_R1_@ and @_R2_@ and produces an array of Directories containing each pair.
{% codeblock as yaml %}
}
{% endcodeblock %}
-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
+h3. Limit RAM requests to what you really need
+
+Available compute nodes types vary over time and across different cloud providers, so it is important 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.
+h3. Avoid scattering by step by step
+
+Instead of a scatter step that feeds into another scatter step, 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:
To write workflows that are easy to modify and portable across CWL runners (in the event you need to share your workflow with others), there are several best practices to follow:
+h3. Always provide @DockerRequirement@
+
Workflows should always provide @DockerRequirement@ in the @hints@ or @requirements@ section.
+h3. Build a reusable library of components
+
Build a reusable library of components. Share tool wrappers and subworkflows between projects. Make use of and contribute to "community maintained workflows and tools":https://github.com/common-workflow-library and tool registries such as "Dockstore":http://dockstore.org .
+h3. Supply scripts as input parameters
+
CommandLineTools wrapping custom scripts should represent the script as an input parameter with the script file as a default value. Use @secondaryFiles@ for scripts that consist of multiple files. For example:
{% codeblock as yaml %}
glob: "*.fastq"
{% endcodeblock %}
+h3. Getting the temporary and output directories
+
You can get the designated temporary directory using @$(runtime.tmpdir)@ in your CWL file, or from the @$TMPDIR@ environment variable in your script.
Similarly, you can get the designated output directory using $(runtime.outdir), or from the @HOME@ environment variable in your script.
-Avoid specifying resource requirements in CommandLineTool. Prefer to specify them in the workflow. You can provide a default resource requirement in the top level @hints@ section, and individual steps can override it with their own resource requirement.
+h3. Specifying @ResourceRequirement@
+
+Avoid specifying resources in the @requirements@ section of a @CommandLineTool@, put it in the @hints@ section instead. This enables you to override the tool resource hint with a workflow step level requirement:
{% codeblock as yaml %}
cwlVersion: v1.0
class: Workflow
inputs:
inp: File
-hints:
- ResourceRequirement:
- ramMin: 1000
- coresMin: 1
- tmpdirMin: 45000
steps:
step1:
in: {inp: inp}
in: {inp: step1/inp}
out: [out]
run: tool2.cwl
- hints:
+ requirements:
ResourceRequirement:
ramMin: 2000
coresMin: 2
# https://doc.arvados.org/admin/metadata-vocabulary.html
VocabularyPath: ""
+ # If true, a project must have a non-empty description field in
+ # order to be frozen.
+ FreezeProjectRequiresDescription: false
+
+ # Project properties that must have non-empty values in order to
+ # freeze a project. Example: {"property_name": true}
+ FreezeProjectRequiresProperties: {}
+
+ # If true, only an admin user can un-freeze a project. If false,
+ # any user with "manage" permission can un-freeze.
+ UnfreezeProjectRequiresAdmin: false
+
Users:
# Config parameters to automatically setup new users. If enabled,
# this users will be able to self-activate. Enable this if you want
# If false, containers are scheduled on preemptible instances
# only when requested by the submitter.
#
- # Note that arvados-cwl-runner does not currently offer a
- # feature to request preemptible instances, so this value
- # effectively acts as a cluster-wide decision about whether to
- # use preemptible instances.
- #
# This flag is ignored if no preemptible instance types are
# configured, and has no effect on top-level containers.
- AlwaysUsePreemptibleInstances: true
+ AlwaysUsePreemptibleInstances: false
# PEM encoded SSH key (RSA, DSA, or ECDSA) used by the
# cloud dispatcher for executing containers on worker VMs.
"API": true,
"API.AsyncPermissionsUpdateInterval": false,
"API.DisabledAPIs": false,
+ "API.FreezeProjectRequiresDescription": true,
+ "API.FreezeProjectRequiresProperties": true,
"API.KeepServiceRequestTimeout": false,
"API.MaxConcurrentRequests": false,
"API.MaxIndexDatabaseRead": false,
"API.MaxTokenLifetime": false,
"API.RequestTimeout": true,
"API.SendTimeout": true,
+ "API.UnfreezeProjectRequiresAdmin": true,
"API.VocabularyPath": false,
"API.WebsocketClientEventQueue": false,
"API.WebsocketServerEventQueue": false,
for k := range direct {
if _, ok := skippedFields[k]; ok {
continue
- } else if val, ok := proxied[k]; ok {
- if direct["kind"] == "arvados#collection" && k == "manifest_text" {
- // Tokens differ from request to request
- c.Check(strings.Split(val.(string), "+A")[0], check.Equals, strings.Split(direct[k].(string), "+A")[0])
- } else {
- c.Check(val, check.DeepEquals, direct[k],
- check.Commentf("RailsAPI %s key %q's value %q differs from controller's %q.", direct["kind"], k, direct[k], val))
- }
- } else {
+ } else if val, ok := proxied[k]; !ok {
c.Errorf("%s's key %q missing on controller's response.", direct["kind"], k)
+ } else if direct["kind"] == "arvados#collection" && k == "manifest_text" {
+ // Tokens differ from request to request
+ c.Check(strings.Split(val.(string), "+A")[0], check.Equals, strings.Split(direct[k].(string), "+A")[0])
+ } else {
+ c.Check(val, check.DeepEquals, direct[k],
+ check.Commentf("RailsAPI %s key %q's value %q differs from controller's %q.", direct["kind"], k, direct[k], val))
}
}
}
// they appear in responses as null, rather than a
// zero value.
switch k {
- case "output_uuid", "output_name", "log_uuid", "description", "requesting_container_uuid", "container_uuid":
+ case "output_uuid", "output_name", "log_uuid", "description", "requesting_container_uuid", "container_uuid", "modified_by_client_uuid", "frozen_by_uuid":
if v == "" {
tmp[k] = nil
}
"os"
"os/exec"
"os/signal"
+ "os/user"
"path"
"path/filepath"
"regexp"
// Run the full container lifecycle.
func (runner *ContainerRunner) Run() (err error) {
runner.CrunchLog.Printf("crunch-run %s started", cmd.Version.String())
+ runner.CrunchLog.Printf("%s", currentUserAndGroups())
runner.CrunchLog.Printf("Executing container '%s' using %s runtime", runner.Container.UUID, runner.executor.Runtime())
hostname, hosterr := os.Hostname()
os.Setenv("ARVADOS_KEEP_SERVICES", url)
return cmd, nil
}
+
+// return current uid, gid, groups in a format suitable for logging:
+// "crunch-run process has uid=1234(arvados) gid=1234(arvados)
+// groups=1234(arvados),114(fuse)"
+func currentUserAndGroups() string {
+ u, err := user.Current()
+ if err != nil {
+ return fmt.Sprintf("error getting current user ID: %s", err)
+ }
+ s := fmt.Sprintf("crunch-run process has uid=%s(%s) gid=%s", u.Uid, u.Username, u.Gid)
+ if g, err := user.LookupGroupId(u.Gid); err == nil {
+ s += fmt.Sprintf("(%s)", g.Name)
+ }
+ s += " groups="
+ if gids, err := u.GroupIds(); err == nil {
+ for i, gid := range gids {
+ if i > 0 {
+ s += ","
+ }
+ s += gid
+ if g, err := user.LookupGroupId(gid); err == nil {
+ s += fmt.Sprintf("(%s)", g.Name)
+ }
+ }
+ }
+ return s
+}
c.Assert(s.api.Logs["crunch-run"], NotNil)
c.Check(s.api.Logs["crunch-run"].String(), Matches, `(?ms).*crunch-run \S+ \(go\S+\) start.*`)
+ c.Check(s.api.Logs["crunch-run"].String(), Matches, `(?ms).*crunch-run process has uid=\d+\(.+\) gid=\d+\(.+\) groups=\d+\(.+\)(,\d+\(.+\))*\n.*`)
c.Check(s.api.Logs["crunch-run"].String(), Matches, `(?ms).*Executing container 'zzzzz-zzzzz-zzzzzzzzzzzzzzz' using stub runtime.*`)
}
parser.add_argument("--http-timeout", type=int,
default=5*60, dest="http_timeout", help="API request timeout in seconds. Default is 300 seconds (5 minutes).")
+ exgroup = parser.add_mutually_exclusive_group()
+ exgroup.add_argument("--enable-preemptible", dest="enable_preemptible", default=None, action="store_true", help="Use preemptible instances. Control individual steps with arv:UsePreemptible hint.")
+ exgroup.add_argument("--disable-preemptible", dest="enable_preemptible", default=None, action="store_false", help="Don't use preemptible instances.")
+
parser.add_argument(
"--skip-schemas",
action="store_true",
"http://arvados.org/cwl#ClusterTarget",
"http://arvados.org/cwl#OutputStorageClass",
"http://arvados.org/cwl#ProcessProperties",
- "http://commonwl.org/cwltool#CUDARequirement"
+ "http://commonwl.org/cwltool#CUDARequirement",
+ "http://arvados.org/cwl#UsePreemptible",
])
def exit_signal_handler(sigcode, frame):
doc: |
Maximum number of GPU devices to request. If not specified,
same as `cudaDeviceCountMin`.
+
+- name: UsePreemptible
+ type: record
+ extends: cwl:ProcessRequirement
+ inVocab: false
+ doc: |
+ Specify a workflow step should opt-in or opt-out of using preemptible (spot) instances.
+ fields:
+ class:
+ type: string
+ doc: "Always 'arv:UsePreemptible"
+ jsonldPredicate:
+ _id: "@type"
+ _type: "@vocab"
+ usePreemptible: boolean
doc: |
Maximum number of GPU devices to request. If not specified,
same as `cudaDeviceCountMin`.
+
+- name: UsePreemptible
+ type: record
+ extends: cwl:ProcessRequirement
+ inVocab: false
+ doc: |
+ Specify a workflow step should opt-in or opt-out of using preemptible (spot) instances.
+ fields:
+ class:
+ type: string
+ doc: "Always 'arv:UsePreemptible"
+ jsonldPredicate:
+ _id: "@type"
+ _type: "@vocab"
+ usePreemptible: boolean
doc: |
Maximum number of GPU devices to request. If not specified,
same as `cudaDeviceCountMin`.
+
+- name: UsePreemptible
+ type: record
+ extends: cwl:ProcessRequirement
+ inVocab: false
+ doc: |
+ Specify a workflow step should opt-in or opt-out of using preemptible (spot) instances.
+ fields:
+ class:
+ type: string
+ doc: "Always 'arv:UsePreemptible"
+ jsonldPredicate:
+ _id: "@type"
+ _type: "@vocab"
+ usePreemptible: boolean
"hardware_capability": aslist(cuda_req["cudaComputeCapability"])[0]
}
+ if runtimeContext.enable_preemptible is False:
+ scheduling_parameters["preemptible"] = False
+ else:
+ preemptible_req, _ = self.get_requirement("http://arvados.org/cwl#UsePreemptible")
+ if preemptible_req:
+ scheduling_parameters["preemptible"] = preemptible_req["usePreemptible"]
+ elif runtimeContext.enable_preemptible is True:
+ scheduling_parameters["preemptible"] = True
+ elif runtimeContext.enable_preemptible is None:
+ pass
+
if self.timelimit is not None and self.timelimit > 0:
scheduling_parameters["max_run_time"] = self.timelimit
if self.enable_dev:
command.append("--enable-dev")
+ if runtimeContext.enable_preemptible is True:
+ command.append("--enable-preemptible")
+
+ if runtimeContext.enable_preemptible is False:
+ command.append("--disable-preemptible")
+
command.extend([workflowpath, "/var/lib/cwl/cwl.input.json"])
container_req["command"] = command
self.always_submit_runner = False
self.collection_cache_size = 256
self.match_local_docker = False
+ self.enable_preemptible = None
super(ArvRuntimeContext, self).__init__(kwargs)
import arvados.collection
from .util import collectionUUID
-import ruamel.yaml as yaml
+from ruamel.yaml import YAML
from ruamel.yaml.comments import CommentedMap, CommentedSeq
import arvados_cwl.arvdocker
textIO = StringIO(text.decode('utf-8'))
else:
textIO = StringIO(text)
- return yaml.safe_load(textIO)
+ yamlloader = YAML(typ='safe', pure=True)
+ return yamlloader.load(textIO)
else:
return {}
git clone https://github.com/common-workflow-language/cwl-\${version}.git
fi
cd cwl-\${version}
+ git checkout \${version}.0
elif [[ "$suite" != "integration" ]] ; then
echo "ERROR: unknown suite '$suite'"
exit 1
fi
-if [[ "$suite" != "integration" ]] ; then
- git pull
-fi
+#if [[ "$suite" != "integration" ]] ; then
+# git pull
+#fi
export ARVADOS_API_HOST=localhost:8000
export ARVADOS_API_HOST_INSECURE=1
arv-keepdocker arvados/jobs latest
fi
-cat >/tmp/cwltest/arv-cwl-jobs <<EOF2
-#!/bin/sh
-exec arvados-cwl-runner --api=jobs \\\$@
-EOF2
-chmod +x /tmp/cwltest/arv-cwl-jobs
-
-cat >/tmp/cwltest/arv-cwl-containers <<EOF2
-#!/bin/sh
-exec arvados-cwl-runner --api=containers \\\$@
-EOF2
-chmod +x /tmp/cwltest/arv-cwl-containers
-
EXTRA=--compute-checksum
if [[ $devcwl -eq 1 ]] ; then
if [[ "$suite" = "integration" ]] ; then
cd /usr/src/arvados/sdk/cwl/tests
exec ./arvados-tests.sh $@
+elif [[ "$suite" = "conformance-v1.2" ]] ; then
+ exec cwltest --tool arvados-cwl-runner --test conformance_tests.yaml -N307 $@ -- \$EXTRA
else
- exec ./run_test.sh RUNNER=/tmp/cwltest/arv-cwl-${runapi} EXTRA="\$EXTRA" $@
+ exec ./run_test.sh RUNNER=arvados-cwl-runner EXTRA="\$EXTRA" $@
fi
EOF
body=JsonDiffMatcher(container_request))
+ # The test passes no builder.resources
+ # Hence the default resources will apply: {'cores': 1, 'ram': 1024, 'outdirSize': 1024, 'tmpdirSize': 1024}
+ @mock.patch("arvados.commands.keepdocker.list_images_in_arv")
+ def test_run_preemptible_hint(self, keepdocker):
+ arvados_cwl.add_arv_hints()
+ for enable_preemptible in (None, True, False):
+ for preemptible_hint in (None, True, False):
+ arv_docker_clear_cache()
+
+ runner = mock.MagicMock()
+ runner.ignore_docker_for_reuse = False
+ runner.intermediate_output_ttl = 0
+ runner.secret_store = cwltool.secrets.SecretStore()
+ runner.api._rootDesc = {"revision": "20210628"}
+
+ keepdocker.return_value = [("zzzzz-4zz18-zzzzzzzzzzzzzz3", "")]
+ runner.api.collections().get().execute.return_value = {
+ "portable_data_hash": "99999999999999999999999999999993+99"}
+
+ if preemptible_hint is not None:
+ hints = [{
+ "class": "http://arvados.org/cwl#UsePreemptible",
+ "usePreemptible": preemptible_hint
+ }]
+ else:
+ hints = []
+
+ tool = cmap({
+ "inputs": [],
+ "outputs": [],
+ "baseCommand": "ls",
+ "arguments": [{"valueFrom": "$(runtime.outdir)"}],
+ "id": "",
+ "class": "CommandLineTool",
+ "cwlVersion": "v1.2",
+ "hints": hints
+ })
+
+ loadingContext, runtimeContext = self.helper(runner)
+
+ runtimeContext.name = 'test_run_enable_preemptible_'+str(enable_preemptible)+str(preemptible_hint)
+ runtimeContext.enable_preemptible = enable_preemptible
+
+ arvtool = cwltool.load_tool.load_tool(tool, loadingContext)
+ arvtool.formatgraph = None
+
+ # Test the interactions between --enable/disable-preemptible
+ # and UsePreemptible hint
+
+ if enable_preemptible is None:
+ if preemptible_hint is None:
+ sched = {}
+ else:
+ sched = {'preemptible': preemptible_hint}
+ else:
+ if preemptible_hint is None:
+ sched = {'preemptible': enable_preemptible}
+ else:
+ sched = {'preemptible': enable_preemptible and preemptible_hint}
+
+ for j in arvtool.job({}, mock.MagicMock(), runtimeContext):
+ j.run(runtimeContext)
+ runner.api.container_requests().create.assert_called_with(
+ body=JsonDiffMatcher({
+ 'environment': {
+ 'HOME': '/var/spool/cwl',
+ 'TMPDIR': '/tmp'
+ },
+ 'name': runtimeContext.name,
+ 'runtime_constraints': {
+ 'vcpus': 1,
+ 'ram': 268435456
+ },
+ 'use_existing': True,
+ 'priority': 500,
+ 'mounts': {
+ '/tmp': {'kind': 'tmp',
+ "capacity": 1073741824
+ },
+ '/var/spool/cwl': {'kind': 'tmp',
+ "capacity": 1073741824 }
+ },
+ 'state': 'Committed',
+ 'output_name': 'Output for step '+runtimeContext.name,
+ 'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz',
+ 'output_path': '/var/spool/cwl',
+ 'output_ttl': 0,
+ 'container_image': '99999999999999999999999999999993+99',
+ 'command': ['ls', '/var/spool/cwl'],
+ 'cwd': '/var/spool/cwl',
+ 'scheduling_parameters': sched,
+ 'properties': {},
+ 'secret_mounts': {},
+ 'output_storage_classes': ["default"]
+ }))
+
+
class TestWorkflow(unittest.TestCase):
def setUp(self):
self.assertEqual(exited, 0)
+ @stubs
+ def test_submit_enable_preemptible(self, stubs):
+ exited = arvados_cwl.main(
+ ["--submit", "--no-wait", "--api=containers", "--debug", "--enable-preemptible",
+ "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
+ stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
+
+ expect_container = copy.deepcopy(stubs.expect_container_spec)
+ expect_container['command'] = ['arvados-cwl-runner', '--local', '--api=containers',
+ '--no-log-timestamps', '--disable-validate', '--disable-color',
+ '--eval-timeout=20', '--thread-count=0',
+ '--enable-reuse', "--collection-cache-size=256", '--debug', '--on-error=continue',
+ '--enable-preemptible',
+ '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
+
+ stubs.api.container_requests().create.assert_called_with(
+ body=JsonDiffMatcher(expect_container))
+ self.assertEqual(stubs.capture_stdout.getvalue(),
+ stubs.expect_container_request_uuid + '\n')
+ self.assertEqual(exited, 0)
+
+ @stubs
+ def test_submit_disable_preemptible(self, stubs):
+ exited = arvados_cwl.main(
+ ["--submit", "--no-wait", "--api=containers", "--debug", "--disable-preemptible",
+ "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
+ stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
+
+ expect_container = copy.deepcopy(stubs.expect_container_spec)
+ expect_container['command'] = ['arvados-cwl-runner', '--local', '--api=containers',
+ '--no-log-timestamps', '--disable-validate', '--disable-color',
+ '--eval-timeout=20', '--thread-count=0',
+ '--enable-reuse', "--collection-cache-size=256", '--debug', '--on-error=continue',
+ '--disable-preemptible',
+ '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
+
+ stubs.api.container_requests().create.assert_called_with(
+ body=JsonDiffMatcher(expect_container))
+ self.assertEqual(stubs.capture_stdout.getvalue(),
+ stubs.expect_container_request_uuid + '\n')
+ self.assertEqual(exited, 0)
+
+
class TestCreateWorkflow(unittest.TestCase):
existing_workflow_uuid = "zzzzz-7fd4e-validworkfloyml"
expect_workflow = StripYAMLComments(
PostgreSQL PostgreSQL
API struct {
- AsyncPermissionsUpdateInterval Duration
- DisabledAPIs StringSet
- MaxIndexDatabaseRead int
- MaxItemsPerResponse int
- MaxConcurrentRequests int
- MaxKeepBlobBuffers int
- MaxRequestAmplification int
- MaxRequestSize int
- MaxTokenLifetime Duration
- RequestTimeout Duration
- SendTimeout Duration
- WebsocketClientEventQueue int
- WebsocketServerEventQueue int
- KeepServiceRequestTimeout Duration
- VocabularyPath string
+ AsyncPermissionsUpdateInterval Duration
+ DisabledAPIs StringSet
+ MaxIndexDatabaseRead int
+ MaxItemsPerResponse int
+ MaxConcurrentRequests int
+ MaxKeepBlobBuffers int
+ MaxRequestAmplification int
+ MaxRequestSize int
+ MaxTokenLifetime Duration
+ RequestTimeout Duration
+ SendTimeout Duration
+ WebsocketClientEventQueue int
+ WebsocketServerEventQueue int
+ KeepServiceRequestTimeout Duration
+ VocabularyPath string
+ FreezeProjectRequiresDescription bool
+ FreezeProjectRequiresProperties StringSet
+ UnfreezeProjectRequiresAdmin bool
}
AuditLogs struct {
MaxAge Duration
Properties map[string]interface{} `json:"properties"`
WritableBy []string `json:"writable_by,omitempty"`
Description string `json:"description"`
+ FrozenByUUID string `json:"frozen_by_uuid"`
}
// GroupList is an arvados#groupList resource.
# If current user cannot write this object, just return
# [self.owner_uuid].
def writable_by
+ # Return [] if this is a frozen project and the current user can't
+ # unfreeze
+ return [] if respond_to?(:frozen_by_uuid) && frozen_by_uuid &&
+ (Rails.configuration.API.UnfreezeProjectRequiresAdmin ?
+ !current_user.andand.is_admin :
+ !current_user.can?(manage: uuid))
+ # Return [] if nobody can write because this object is inside a
+ # frozen project
+ return [] if FrozenGroup.where(uuid: owner_uuid).any?
return [owner_uuid] if not current_user
unless (owner_uuid == current_user.uuid or
current_user.is_admin or
user_uuids = users_list.map { |u| u.uuid }
all_user_uuids = []
+ admin = users_list.select { |u| u.is_admin }.any?
+
# For details on how the trashed_groups table is constructed, see
# see db/migrate/20200501150153_permission_table.rb
- exclude_trashed_records = ""
- if !include_trash and (sql_table == "groups" or sql_table == "collections") then
- # Only include records that are not trashed
- exclude_trashed_records = "AND (#{sql_table}.trash_at is NULL or #{sql_table}.trash_at > statement_timestamp())"
- end
+ # excluded_trash is a SQL expression that determines whether a row
+ # should be excluded from the results due to being trashed.
+ # Trashed items inside frozen projects are invisible to regular
+ # (non-admin) users even when using include_trash, so we have:
+ #
+ # (item_trashed || item_inside_trashed_project)
+ # &&
+ # (!caller_requests_include_trash ||
+ # (item_inside_frozen_project && caller_is_not_admin))
+ if (admin && include_trash) || sql_table == "api_client_authorizations"
+ excluded_trash = "false"
+ else
+ excluded_trash = "(#{sql_table}.owner_uuid IN (SELECT group_uuid FROM #{TRASHED_GROUPS} " +
+ "WHERE trash_at <= statement_timestamp()))"
+ if sql_table == "groups" || sql_table == "collections"
+ excluded_trash = "(#{excluded_trash} OR #{sql_table}.trash_at <= statement_timestamp() IS TRUE)"
+ end
- trashed_check = ""
- if !include_trash && sql_table != "api_client_authorizations"
- trashed_check = "#{sql_table}.owner_uuid NOT IN (SELECT group_uuid FROM #{TRASHED_GROUPS} " +
- "where trash_at <= statement_timestamp()) #{exclude_trashed_records}"
+ if include_trash
+ # Exclude trash inside frozen projects
+ excluded_trash = "(#{excluded_trash} AND #{sql_table}.owner_uuid IN (SELECT uuid FROM #{FROZEN_GROUPS}))"
+ end
end
- if users_list.select { |u| u.is_admin }.any?
- # Admin skips most permission checks, but still want to filter on trashed items.
+ if admin
+ # Admin skips most permission checks, but still want to filter
+ # on trashed items.
if !include_trash && sql_table != "api_client_authorizations"
# Only include records where the owner is not trashed
- sql_conds = trashed_check
+ sql_conds = "NOT (#{excluded_trash})"
end
else
# The core of the permission check is a join against the
" WHERE user_uuid IN (#{user_uuids_subquery}) AND perm_level >= 3))) "
end
- sql_conds = "(#{owner_check} #{direct_check} #{links_cond}) #{trashed_check.empty? ? "" : "AND"} #{trashed_check}"
+ sql_conds = "(#{owner_check} #{direct_check} #{links_cond}) AND NOT (#{excluded_trash})"
end
if check_uuid.nil?
# old_owner_uuid is nil? New record, no need to check.
elsif !current_user.can?(write: check_uuid)
- logger.warn "User #{current_user.uuid} tried to set ownership of #{self.class.to_s} #{self.uuid} but does not have permission to write #{which} owner_uuid #{check_uuid}"
- errors.add :owner_uuid, "cannot be set or changed without write permission on #{which} owner"
+ if FrozenGroup.where(uuid: check_uuid).any?
+ errors.add :owner_uuid, "cannot be set or changed because #{which} owner is frozen"
+ else
+ logger.warn "User #{current_user.uuid} tried to set ownership of #{self.class.to_s} #{self.uuid} but does not have permission to write #{which} owner_uuid #{check_uuid}"
+ errors.add :owner_uuid, "cannot be set or changed without write permission on #{which} owner"
+ end
raise PermissionDeniedError
elsif rsc_class == Group && Group.find_by_uuid(owner_uuid).group_class != "project"
errors.add :owner_uuid, "must be a project"
else
# If the object already existed and we're not changing
# owner_uuid, we only need write permission on the object
- # itself.
- if !current_user.can?(write: self.uuid)
+ # itself. (If we're in the act of unfreezing, we only need
+ # :unfreeze permission, which means "what write permission would
+ # be if target weren't frozen")
+ unless ((respond_to?(:frozen_by_uuid) && frozen_by_uuid_was && !frozen_by_uuid) ?
+ current_user.can?(unfreeze: uuid) :
+ current_user.can?(write: uuid))
logger.warn "User #{current_user.uuid} tried to modify #{self.class.to_s} #{self.uuid} without write permission"
errors.add :uuid, " #{uuid} is not writable by #{current_user.uuid}"
raise PermissionDeniedError
end
def permission_to_create
- current_user.andand.is_active
+ return current_user.andand.is_active
end
def permission_to_update
--- /dev/null
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: AGPL-3.0
+
+class FrozenGroup < ApplicationRecord
+end
validate :ensure_filesystem_compatible_name
validate :check_group_class
validate :check_filter_group_filters
+ validate :check_frozen_state_change_allowed
before_create :assign_name
after_create :after_ownership_change
after_create :update_trash
+ after_create :update_frozen
before_update :before_ownership_change
after_update :after_ownership_change
after_create :add_role_manage_link
after_update :update_trash
- before_destroy :clear_permissions_and_trash
+ after_update :update_frozen
+ before_destroy :clear_permissions_trash_frozen
api_accessible :user, extend: :common do |t|
t.add :name
t.add :trash_at
t.add :is_trashed
t.add :properties
+ t.add :frozen_by_uuid
end
def ensure_filesystem_compatible_name
end
end
+ def check_frozen_state_change_allowed
+ if frozen_by_uuid == ""
+ self.frozen_by_uuid = nil
+ end
+ if frozen_by_uuid_changed? || (new_record? && frozen_by_uuid)
+ if group_class != "project"
+ errors.add(:frozen_by_uuid, "cannot be modified on a non-project group")
+ return
+ end
+ if frozen_by_uuid_was && Rails.configuration.API.UnfreezeProjectRequiresAdmin && !current_user.is_admin
+ errors.add(:frozen_by_uuid, "can only be changed by an admin user, once set")
+ return
+ end
+ if frozen_by_uuid && frozen_by_uuid != current_user.uuid
+ errors.add(:frozen_by_uuid, "can only be set to the current user's UUID")
+ return
+ end
+ if !new_record? && !current_user.can?(manage: uuid)
+ raise PermissionDeniedError
+ end
+ if trash_at || delete_at || (!new_record? && TrashedGroup.where(group_uuid: uuid).any?)
+ errors.add(:frozen_by_uuid, "cannot be set on a trashed project")
+ end
+ if frozen_by_uuid_was.nil?
+ if Rails.configuration.API.FreezeProjectRequiresDescription && !attribute_present?(:description)
+ errors.add(:frozen_by_uuid, "can only be set if description is non-empty")
+ end
+ Rails.configuration.API.FreezeProjectRequiresProperties.andand.each do |key, _|
+ key = key.to_s
+ if !properties[key] || properties[key] == ""
+ errors.add(:frozen_by_uuid, "can only be set if properties[#{key}] value is non-empty")
+ end
+ end
+ end
+ end
+ end
+
def update_trash
- if saved_change_to_trash_at? or saved_change_to_owner_uuid?
- # The group was added or removed from the trash.
- #
- # Strategy:
- # Compute project subtree, propagating trash_at to subprojects
- # Remove groups that don't belong from trash
- # Add/update groups that do belong in the trash
-
- temptable = "group_subtree_#{rand(2**64).to_s(10)}"
- ActiveRecord::Base.connection.exec_query %{
-create temporary table #{temptable} on commit drop
-as select * from project_subtree_with_trash_at($1, LEAST($2, $3)::timestamp)
-},
- 'Group.update_trash.select',
- [[nil, self.uuid],
- [nil, TrashedGroup.find_by_group_uuid(self.owner_uuid).andand.trash_at],
- [nil, self.trash_at]]
-
- ActiveRecord::Base.connection.exec_delete %{
-delete from trashed_groups where group_uuid in (select target_uuid from #{temptable} where trash_at is NULL);
-},
- "Group.update_trash.delete"
-
- ActiveRecord::Base.connection.exec_query %{
-insert into trashed_groups (group_uuid, trash_at)
- select target_uuid as group_uuid, trash_at from #{temptable} where trash_at is not NULL
-on conflict (group_uuid) do update set trash_at=EXCLUDED.trash_at;
-},
- "Group.update_trash.insert"
+ return unless saved_change_to_trash_at? || saved_change_to_owner_uuid?
+
+ # The group was added or removed from the trash.
+ #
+ # Strategy:
+ # Compute project subtree, propagating trash_at to subprojects
+ # Ensure none of the newly trashed descendants were frozen (if so, bail out)
+ # Remove groups that don't belong from trash
+ # Add/update groups that do belong in the trash
+
+ temptable = "group_subtree_#{rand(2**64).to_s(10)}"
+ ActiveRecord::Base.connection.exec_query(
+ "create temporary table #{temptable} on commit drop " +
+ "as select * from project_subtree_with_trash_at($1, LEAST($2, $3)::timestamp)",
+ "Group.update_trash.select",
+ [[nil, self.uuid],
+ [nil, TrashedGroup.find_by_group_uuid(self.owner_uuid).andand.trash_at],
+ [nil, self.trash_at]])
+ frozen_descendants = ActiveRecord::Base.connection.exec_query(
+ "select uuid from frozen_groups, #{temptable} where uuid = target_uuid",
+ "Group.update_trash.check_frozen")
+ if frozen_descendants.any?
+ raise ArgumentError.new("cannot trash project containing frozen project #{frozen_descendants[0]["uuid"]}")
+ end
+ ActiveRecord::Base.connection.exec_delete(
+ "delete from trashed_groups where group_uuid in (select target_uuid from #{temptable} where trash_at is NULL)",
+ "Group.update_trash.delete")
+ ActiveRecord::Base.connection.exec_query(
+ "insert into trashed_groups (group_uuid, trash_at) "+
+ "select target_uuid as group_uuid, trash_at from #{temptable} where trash_at is not NULL " +
+ "on conflict (group_uuid) do update set trash_at=EXCLUDED.trash_at",
+ "Group.update_trash.insert")
+ end
+
+ def update_frozen
+ return unless saved_change_to_frozen_by_uuid? || saved_change_to_owner_uuid?
+ temptable = "group_subtree_#{rand(2**64).to_s(10)}"
+ ActiveRecord::Base.connection.exec_query(
+ "create temporary table #{temptable} on commit drop as select * from project_subtree_with_is_frozen($1,$2)",
+ "Group.update_frozen.select",
+ [[nil, self.uuid],
+ [nil, !self.frozen_by_uuid.nil?]])
+ if frozen_by_uuid
+ rows = ActiveRecord::Base.connection.exec_query(
+ "select cr.uuid, cr.state from container_requests cr, #{temptable} frozen " +
+ "where cr.owner_uuid = frozen.uuid and frozen.is_frozen " +
+ "and cr.state not in ($1, $2) limit 1",
+ "Group.update_frozen.check_container_requests",
+ [[nil, ContainerRequest::Uncommitted],
+ [nil, ContainerRequest::Final]])
+ if rows.any?
+ raise ArgumentError.new("cannot freeze project containing container request #{rows.first['uuid']} with state = #{rows.first['state']}")
+ end
end
+ ActiveRecord::Base.connection.exec_delete(
+ "delete from frozen_groups where uuid in (select uuid from #{temptable} where not is_frozen)",
+ "Group.update_frozen.delete")
+ ActiveRecord::Base.connection.exec_query(
+ "insert into frozen_groups (uuid) select uuid from #{temptable} where is_frozen on conflict do nothing",
+ "Group.update_frozen.insert")
end
def before_ownership_change
end
end
- def clear_permissions_and_trash
+ def clear_permissions_trash_frozen
MaterializedPermission.where(target_uuid: uuid).delete_all
- ActiveRecord::Base.connection.exec_delete %{
-delete from trashed_groups where group_uuid=$1
-}, "Group.clear_permissions_and_trash", [[nil, self.uuid]]
-
+ ActiveRecord::Base.connection.exec_delete(
+ "delete from trashed_groups where group_uuid=$1",
+ "Group.clear_permissions_trash_frozen",
+ [[nil, self.uuid]])
+ ActiveRecord::Base.connection.exec_delete(
+ "delete from frozen_groups where uuid=$1",
+ "Group.clear_permissions_trash_frozen",
+ [[nil, self.uuid]])
end
def assign_name
end
end
end
+
+ def permission_to_update
+ if !super
+ return false
+ elsif frozen_by_uuid && frozen_by_uuid_was
+ errors.add :uuid, "#{uuid} is frozen and cannot be modified"
+ return false
+ else
+ return true
+ end
+ end
+
+ def self.full_text_searchable_columns
+ super - ["frozen_by_uuid"]
+ end
end
VAL_FOR_PERM =
{:read => 1,
:write => 2,
+ :unfreeze => 3,
:manage => 3}
).any?
return false
end
+
+ if action == :write
+ if FrozenGroup.where(uuid: [target_uuid, target_owner_uuid]).any?
+ # self or parent is frozen
+ return false
+ end
+ elsif action == :unfreeze
+ # "unfreeze" permission means "can write, but only if
+ # explicitly un-freezing at the same time" (see
+ # ArvadosModel#ensure_owner_uuid_is_permitted). If the
+ # permission query above passed the permission level of
+ # :unfreeze (which is the same as :manage), and the parent
+ # isn't also frozen, then un-freeze is allowed.
+ if FrozenGroup.where(uuid: target_owner_uuid).any?
+ return false
+ end
+ end
end
true
end
--- /dev/null
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: AGPL-3.0
+
+class AddFrozenByUuidToGroups < ActiveRecord::Migration[5.2]
+ def change
+ add_column :groups, :frozen_by_uuid, :string
+ end
+end
--- /dev/null
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: AGPL-3.0
+
+require '20200501150153_permission_table_constants'
+
+class FrozenGroups < ActiveRecord::Migration[5.0]
+ def up
+ create_table :frozen_groups, :id => false do |t|
+ t.string :uuid
+ end
+ add_index :frozen_groups, :uuid, :unique => true
+
+ ActiveRecord::Base.connection.execute %{
+create or replace function project_subtree_with_is_frozen (starting_uuid varchar(27), starting_is_frozen boolean)
+returns table (uuid varchar(27), is_frozen boolean)
+STABLE
+language SQL
+as $$
+WITH RECURSIVE
+ project_subtree(uuid, is_frozen) as (
+ values (starting_uuid, starting_is_frozen)
+ union
+ select groups.uuid, project_subtree.is_frozen or groups.frozen_by_uuid is not null
+ from groups join project_subtree on project_subtree.uuid = groups.owner_uuid
+ )
+ select uuid, is_frozen from project_subtree;
+$$;
+}
+
+ # Initialize the table. After this, it is updated incrementally.
+ # See app/models/group.rb#update_frozen_groups
+ refresh_frozen
+ end
+
+ def down
+ drop_table :frozen_groups
+ end
+end
--- /dev/null
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: AGPL-3.0
+
+class AddFrozenByUuidToGroupSearchIndex < ActiveRecord::Migration[5.0]
+ disable_ddl_transaction!
+
+ def up
+ remove_index :groups, :name => 'groups_search_index'
+ add_index :groups, ["uuid", "owner_uuid", "modified_by_client_uuid", "modified_by_user_uuid", "name", "group_class", "frozen_by_uuid"], name: 'groups_search_index', algorithm: :concurrently
+ end
+
+ def down
+ remove_index :groups, :name => 'groups_search_index'
+ add_index :groups, ["uuid", "owner_uuid", "modified_by_client_uuid", "modified_by_user_uuid", "name", "group_class"], name: 'groups_search_index', algorithm: :concurrently
+ end
+end
$$;
+--
+-- Name: project_subtree_with_is_frozen(character varying, boolean); Type: FUNCTION; Schema: public; Owner: -
+--
+
+CREATE FUNCTION public.project_subtree_with_is_frozen(starting_uuid character varying, starting_is_frozen boolean) RETURNS TABLE(uuid character varying, is_frozen boolean)
+ LANGUAGE sql STABLE
+ AS $$
+WITH RECURSIVE
+ project_subtree(uuid, is_frozen) as (
+ values (starting_uuid, starting_is_frozen)
+ union
+ select groups.uuid, project_subtree.is_frozen or groups.frozen_by_uuid is not null
+ from groups join project_subtree on (groups.owner_uuid = project_subtree.uuid)
+ )
+ select uuid, is_frozen from project_subtree;
+$$;
+
+
--
-- Name: project_subtree_with_trash_at(character varying, timestamp without time zone); Type: FUNCTION; Schema: public; Owner: -
--
ALTER SEQUENCE public.containers_id_seq OWNED BY public.containers.id;
+--
+-- Name: frozen_groups; Type: TABLE; Schema: public; Owner: -
+--
+
+CREATE TABLE public.frozen_groups (
+ uuid character varying
+);
+
+
--
-- Name: groups; Type: TABLE; Schema: public; Owner: -
--
trash_at timestamp without time zone,
is_trashed boolean DEFAULT false NOT NULL,
delete_at timestamp without time zone,
- properties jsonb DEFAULT '{}'::jsonb
+ properties jsonb DEFAULT '{}'::jsonb,
+ frozen_by_uuid character varying
);
-- Name: groups_search_index; Type: INDEX; Schema: public; Owner: -
--
-CREATE INDEX groups_search_index ON public.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, frozen_by_uuid);
--
CREATE UNIQUE INDEX index_containers_on_uuid ON public.containers USING btree (uuid);
+--
+-- Name: index_frozen_groups_on_uuid; Type: INDEX; Schema: public; Owner: -
+--
+
+CREATE UNIQUE INDEX index_frozen_groups_on_uuid ON public.frozen_groups USING btree (uuid);
+
+
--
-- Name: index_groups_on_created_at; Type: INDEX; Schema: public; Owner: -
--
('20210126183521'),
('20210621204455'),
('20210816191509'),
-('20211027154300');
+('20211027154300'),
+('20220224203102'),
+('20220301155729'),
+('20220303204419');
# update_permissions reference that file instead.
PERMISSION_VIEW = "materialized_permissions"
-
TRASHED_GROUPS = "trashed_groups"
+FROZEN_GROUPS = "frozen_groups"
# We need to use this parameterized query in a few different places,
# including as a subquery in a larger query.
}, "refresh_permission_view.do"
end
end
+
+def refresh_frozen
+ ActiveRecord::Base.transaction do
+ ActiveRecord::Base.connection.execute("LOCK TABLE #{FROZEN_GROUPS}")
+ ActiveRecord::Base.connection.execute("DELETE FROM #{FROZEN_GROUPS}")
+
+ # Compute entire frozen_groups table, starting with top-level
+ # projects (i.e., project groups owned by a user).
+ ActiveRecord::Base.connection.execute(%{
+INSERT INTO #{FROZEN_GROUPS}
+select ps.uuid from groups,
+ lateral project_subtree_with_is_frozen(groups.uuid, groups.frozen_by_uuid is not null) ps
+ where groups.owner_uuid like '_____-tpzed-_______________'
+ and group_class = 'project'
+ and ps.is_frozen
+})
+ end
+end
assert_response 422
end
+
+ test "include_trash does not return trash inside frozen project" do
+ authorize_with :active
+ trashtime = Time.now - 1.second
+ outerproj = Group.create!(group_class: 'project')
+ innerproj = Group.create!(group_class: 'project', owner_uuid: outerproj.uuid)
+ innercoll = Collection.create!(name: 'inner-not-trashed', owner_uuid: innerproj.uuid)
+ innertrash = Collection.create!(name: 'inner-trashed', owner_uuid: innerproj.uuid, trash_at: trashtime)
+ innertrashproj = Group.create!(group_class: 'project', name: 'inner-trashed-proj', owner_uuid: innerproj.uuid, trash_at: trashtime)
+ outertrash = Collection.create!(name: 'outer-trashed', owner_uuid: outerproj.uuid, trash_at: trashtime)
+ innerproj.update_attributes!(frozen_by_uuid: users(:active).uuid)
+ get :contents, params: {id: outerproj.uuid, include_trash: true, recursive: true}
+ assert_response :success
+ uuids = json_response['items'].collect { |item| item['uuid'] }
+ assert_includes uuids, outertrash.uuid
+ assert_includes uuids, innerproj.uuid
+ assert_includes uuids, innercoll.uuid
+ refute_includes uuids, innertrash.uuid
+ refute_includes uuids, innertrashproj.uuid
+ end
end
assert Link.where(tail_uuid: g3, head_uuid: g4, link_class: "permission", name: "can_manage").any?
assert !Link.where(link_class: 'permission', name: 'can_manage', tail_uuid: g5, head_uuid: g4).any?
end
+
+ test "freeze project" do
+ act_as_user users(:active) do
+ Rails.configuration.API.UnfreezeProjectRequiresAdmin = false
+
+ test_cr_attrs = {
+ command: ["echo", "foo"],
+ container_image: links(:docker_image_collection_tag).name,
+ cwd: "/tmp",
+ environment: {},
+ mounts: {"/out" => {"kind" => "tmp", "capacity" => 1000000}},
+ output_path: "/out",
+ runtime_constraints: {"vcpus" => 1, "ram" => 2},
+ name: "foo",
+ description: "bar",
+ }
+ parent = Group.create!(group_class: 'project', name: 'freeze-test-parent', owner_uuid: users(:active).uuid)
+ proj = Group.create!(group_class: 'project', name: 'freeze-test', owner_uuid: parent.uuid)
+ proj_inner = Group.create!(group_class: 'project', name: 'freeze-test-inner', owner_uuid: proj.uuid)
+ coll = Collection.create!(name: 'freeze-test-collection', manifest_text: '', owner_uuid: proj_inner.uuid)
+
+ # Cannot set frozen_by_uuid to a different user
+ assert_raises do
+ proj.update_attributes!(frozen_by_uuid: users(:spectator).uuid)
+ end
+ proj.reload
+
+ # Cannot set frozen_by_uuid without can_manage permission
+ act_as_system_user do
+ Link.create!(link_class: 'permission', name: 'can_write', tail_uuid: users(:spectator).uuid, head_uuid: proj.uuid)
+ end
+ act_as_user users(:spectator) do
+ # First confirm we have write permission
+ assert Collection.create(name: 'bar', owner_uuid: proj.uuid)
+ assert_raises(ArvadosModel::PermissionDeniedError) do
+ proj.update_attributes!(frozen_by_uuid: users(:spectator).uuid)
+ end
+ end
+ proj.reload
+
+ # Cannot set frozen_by_uuid without description (if so configured)
+ Rails.configuration.API.FreezeProjectRequiresDescription = true
+ err = assert_raises do
+ proj.update_attributes!(frozen_by_uuid: users(:active).uuid)
+ end
+ assert_match /can only be set if description is non-empty/, err.inspect
+ proj.reload
+ err = assert_raises do
+ proj.update_attributes!(frozen_by_uuid: users(:active).uuid, description: '')
+ end
+ assert_match /can only be set if description is non-empty/, err.inspect
+ proj.reload
+
+ # Cannot set frozen_by_uuid without properties (if so configured)
+ Rails.configuration.API.FreezeProjectRequiresProperties['frobity'] = true
+ err = assert_raises do
+ proj.update_attributes!(
+ frozen_by_uuid: users(:active).uuid,
+ description: 'ready to freeze')
+ end
+ assert_match /can only be set if properties\[frobity\] value is non-empty/, err.inspect
+ proj.reload
+
+ # Cannot set frozen_by_uuid while project or its parent is
+ # trashed
+ [parent, proj].each do |trashed|
+ trashed.update_attributes!(trash_at: db_current_time)
+ err = assert_raises do
+ proj.update_attributes!(
+ frozen_by_uuid: users(:active).uuid,
+ description: 'ready to freeze',
+ properties: {'frobity' => 'bar baz'})
+ end
+ assert_match /cannot be set on a trashed project/, err.inspect
+ proj.reload
+ trashed.update_attributes!(trash_at: nil)
+ end
+
+ # Can set frozen_by_uuid if all conditions are met
+ ok = proj.update_attributes(
+ frozen_by_uuid: users(:active).uuid,
+ description: 'ready to freeze',
+ properties: {'frobity' => 'bar baz'})
+ assert ok, proj.errors.messages.inspect
+
+ # Once project is frozen, cannot create new items inside it or
+ # its descendants
+ [proj, proj_inner].each do |frozen|
+ assert_raises do
+ collections(:collection_owned_by_active).update_attributes!(owner_uuid: frozen.uuid)
+ end
+ assert_raises do
+ Collection.create!(owner_uuid: frozen.uuid, name: 'inside-frozen-project')
+ end
+ assert_raises do
+ Group.create!(owner_uuid: frozen.uuid, group_class: 'project', name: 'inside-frozen-project')
+ end
+ cr = ContainerRequest.new(test_cr_attrs.merge(owner_uuid: frozen.uuid))
+ assert_raises ArvadosModel::PermissionDeniedError do
+ cr.save
+ end
+ assert_match /frozen/, cr.errors.inspect
+ # Check the frozen-parent condition is the only reason save failed.
+ cr.owner_uuid = users(:active).uuid
+ assert cr.save
+ cr.destroy
+ end
+
+ # Once project is frozen, cannot change name/contents, move,
+ # trash, or delete the project or anything beneath it
+ [proj, proj_inner, coll].each do |frozen|
+ assert_raises(StandardError, "should reject rename of #{frozen.uuid} (#{frozen.name}) with parent #{frozen.owner_uuid}") do
+ frozen.update_attributes!(name: 'foo2')
+ end
+ frozen.reload
+
+ if frozen.is_a?(Collection)
+ assert_raises(StandardError, "should reject manifest change of #{frozen.uuid}") do
+ frozen.update_attributes!(manifest_text: ". d41d8cd98f00b204e9800998ecf8427e+0 0:0:foo\n")
+ end
+ else
+ assert_raises(StandardError, "should reject moving a project into #{frozen.uuid}") do
+ groups(:private).update_attributes!(owner_uuid: frozen.uuid)
+ end
+ end
+ frozen.reload
+
+ assert_raises(StandardError, "should reject moving #{frozen.uuid} to a different parent project") do
+ frozen.update_attributes!(owner_uuid: groups(:private).uuid)
+ end
+ frozen.reload
+ assert_raises(StandardError, "should reject setting trash_at of #{frozen.uuid}") do
+ frozen.update_attributes!(trash_at: db_current_time)
+ end
+ frozen.reload
+ assert_raises(StandardError, "should reject setting delete_at of #{frozen.uuid}") do
+ frozen.update_attributes!(delete_at: db_current_time)
+ end
+ frozen.reload
+ assert_raises(StandardError, "should reject delete of #{frozen.uuid}") do
+ frozen.destroy
+ end
+ frozen.reload
+ if frozen != proj
+ assert_equal [], frozen.writable_by
+ end
+ end
+
+ # User with write permission (but not manage) cannot unfreeze
+ act_as_user users(:spectator) do
+ # First confirm we have write permission on the parent project
+ assert Collection.create(name: 'bar', owner_uuid: parent.uuid)
+ assert_raises(ArvadosModel::PermissionDeniedError) do
+ proj.update_attributes!(frozen_by_uuid: nil)
+ end
+ end
+ proj.reload
+
+ # User with manage permission can unfreeze, then create items
+ # inside it and its children
+ assert proj.update_attributes(frozen_by_uuid: nil)
+ assert Collection.create!(owner_uuid: proj.uuid, name: 'inside-unfrozen-project')
+ assert Collection.create!(owner_uuid: proj_inner.uuid, name: 'inside-inner-unfrozen-project')
+
+ # Re-freeze, and reconfigure so only admins can unfreeze.
+ assert proj.update_attributes(frozen_by_uuid: users(:active).uuid)
+ Rails.configuration.API.UnfreezeProjectRequiresAdmin = true
+
+ # Owner cannot unfreeze, because not admin.
+ err = assert_raises do
+ proj.update_attributes!(frozen_by_uuid: nil)
+ end
+ assert_match /can only be changed by an admin user, once set/, err.inspect
+ proj.reload
+
+ # Cannot trash or delete a frozen project's ancestor
+ assert_raises(StandardError, "should not be able to set trash_at on parent of frozen project") do
+ parent.update_attributes!(trash_at: db_current_time)
+ end
+ parent.reload
+ assert_raises(StandardError, "should not be able to set delete_at on parent of frozen project") do
+ parent.update_attributes!(delete_at: db_current_time)
+ end
+ parent.reload
+ assert_nil parent.frozen_by_uuid
+
+ act_as_user users(:admin) do
+ # Even admin cannot change frozen_by_uuid to someone else's UUID.
+ err = assert_raises do
+ proj.update_attributes!(frozen_by_uuid: users(:project_viewer).uuid)
+ end
+ assert_match /can only be set to the current user's UUID/, err.inspect
+ proj.reload
+
+ # Admin can unfreeze.
+ assert proj.update_attributes(frozen_by_uuid: nil), proj.errors.messages
+ end
+
+ # Cannot freeze a project if it contains container requests in
+ # Committed state (this would cause operations on the relevant
+ # Containers to fail when syncing container request state)
+ creq_uncommitted = ContainerRequest.create!(test_cr_attrs.merge(owner_uuid: proj_inner.uuid))
+ creq_committed = ContainerRequest.create!(test_cr_attrs.merge(owner_uuid: proj_inner.uuid, state: 'Committed'))
+ err = assert_raises do
+ proj.update_attributes!(frozen_by_uuid: users(:active).uuid)
+ end
+ assert_match /container request zzzzz-xvhdp-.* with state = Committed/, err.inspect
+ proj.reload
+
+ # Can freeze once all container requests are in Uncommitted or
+ # Final state
+ creq_committed.update_attributes!(state: ContainerRequest::Final)
+ assert proj.update_attributes(frozen_by_uuid: users(:active).uuid)
+ end
+ end
end
end
end
end
+
+ # Show query plan for readable_by query. The plan for a test db
+ # might not resemble the plan for a production db, but it doesn't
+ # hurt to show the test db plan in test logs, and the .
+ [false, true].each do |include_trash|
+ test "query plan, include_trash=#{include_trash}" do
+ sql = Collection.readable_by(users(:active), include_trash: include_trash).to_sql
+ sql = "explain analyze #{sql}"
+ STDERR.puts sql
+ q = ActiveRecord::Base.connection.exec_query(sql)
+ q.rows.each do |row| STDERR.puts(row) end
+ end
+ end
end
arvswitch <name>
Set ARVADOS_API_HOST and ARVADOS_API_TOKEN in the current environment based on
$HOME/.config/arvados/<name>.conf
- With no arguments, list available Arvados configurations.
+ With no arguments, print current API host and available Arvados configurations.
arvsave <name>
- Save values of ARVADOS_API_HOST and ARVADOS_API_TOKEN in the current environment to
+ Save current values of ARVADOS_API_HOST and ARVADOS_API_TOKEN in the current environment to
$HOME/.config/arvados/<name>.conf
arvrm <name>
arvboxswitch <name>
Set ARVBOX_CONTAINER to <name>
- With no arguments, list available arvboxes.
+ With no arguments, print current arvbox and available arvboxes.
-arvopen:
+arvopen <uuid>
Open an Arvados uuid in web browser (http://arvadosapi.com)
-arvissue
+arvissue <issue number>
Open an Arvados ticket in web browser (http://dev.arvados.org)
EOF
fi
else
echo "Switch Arvados environment conf"
- echo "Usage: arvswitch name"
+ echo "Current host: ${ARVADOS_API_HOST}"
+ echo "Usage: arvswitch <name>"
echo "Available confs:" $((cd $HOME/.config/arvados && ls --indicator-style=none *.conf) | rev | cut -c6- | rev)
fi
}
env | grep ARVADOS_ > $HOME/.config/arvados/$1.conf
else
echo "Save current Arvados environment variables to conf file"
- echo "Usage: arvsave name"
+ echo "Usage: arvsave <name>"
fi
}
fi
else
echo "Delete Arvados environment conf"
- echo "Usage: arvrm name"
+ echo "Usage: arvrm <name>"
fi
}
arvboxswitch() {
if [[ -n "$1" ]] ; then
+ export ARVBOX_CONTAINER=$1
if [[ -d $HOME/.arvbox/$1 ]] ; then
- export ARVBOX_CONTAINER=$1
echo "Arvbox switched to $1"
else
- echo "$1 unknown"
+ echo "Warning: $1 doesn't exist, will be created."
fi
else
if test -z "$ARVBOX_CONTAINER" ; then
ARVBOX_CONTAINER=arvbox
fi
echo "Switch Arvbox environment conf"
- echo "Usage: arvboxswitch name"
echo "Your current container is: $ARVBOX_CONTAINER"
+ echo "Usage: arvboxswitch <name>"
echo "Available confs:" $(cd $HOME/.arvbox && ls --indicator-style=none)
fi
}
xdg-open https://arvadosapi.com/$1
else
echo "Open Arvados uuid in browser"
- echo "Usage: arvopen uuid"
+ echo "Usage: arvopen <uuid>"
fi
}
xdg-open https://dev.arvados.org/issues/$1
else
echo "Open Arvados issue in browser"
- echo "Usage: arvissue uuid"
+ echo "Usage: arvissue <issue number>"
fi
}
fi
if ! (docker ps -a | grep -E "$ARVBOX_CONTAINER-data$" -q) ; then
- docker create -v /var/lib/postgresql -v $ARVADOS_CONTAINER_PATH --name $ARVBOX_CONTAINER-data arvados/arvbox-demo /bin/true
+ docker create -v /var/lib/postgresql -v $ARVADOS_CONTAINER_PATH --name $ARVBOX_CONTAINER-data arvados/arvbox-demo$TAG /bin/true
fi
docker run \
chown arvbox:arvbox -R /usr/local $ARVADOS_CONTAINER_PATH \
/var/lib/passenger /var/lib/postgresql \
/var/lib/nginx /var/log/nginx /etc/ssl/private \
- /var/lib/gopath /var/lib/pip /var/lib/npm \
- /var/lib/arvados
+ /var/lib/gopath /var/lib/pip /var/lib/npm
fi
mkdir -p /tmp/crunch0 /tmp/crunch1
chown crunch:crunch -R /tmp/crunch0 /tmp/crunch1
- # singularity needs to be owned by root and suid
- chown root /var/lib/arvados/bin/singularity \
- /var/lib/arvados/etc/singularity/singularity.conf \
- /var/lib/arvados/etc/singularity/capability.json \
- /var/lib/arvados/etc/singularity/ecl.toml
- chmod u+s /var/lib/arvados/bin/singularity
-
echo "arvbox ALL=(crunch) NOPASSWD: ALL" >> /etc/sudoers
cat <<EOF > /etc/profile.d/paths.sh
projects / arvados.git / commitdiff