doc/install/*.xlsx
sdk/cwl/tests/wf/hello.txt
sdk/cwl/tests/wf/indir1/hello2.txt
-sdk/cwl/tests/chipseq/data/Genomes/*
\ No newline at end of file
+sdk/cwl/tests/chipseq/data/Genomes/*
+CITATION.cff
Thomas Mooney <tmooney@genome.wustl.edu>
Chen Chen <aflyhorse@gmail.com>
Veritas Genetics, Inc. <*@veritasgenetics.com>
-Curii Corporation, Inc. <*@curii.com>
+Curii Corporation <*@curii.com>
Dante Tsang <dante@dantetsang.com>
Codex Genetics Ltd <info@codexgenetics.com>
Bruno P. Kinoshita <brunodepaulak@yahoo.com.br>
--- /dev/null
+cff-version: 1.2.0
+message: "If you use this software, please cite it as below."
+authors:
+- name: "The Arvados Authors"
+- family-names: "Amstutz"
+ given-names: "Peter"
+ orcid: "https://orcid.org/0000-0003-3566-7705"
+- family-names: "Bértoli"
+ given-names: "Javier"
+ family-names: "César"
+ given-names: "Nico"
+- family-names: "Clegg"
+ given-names: "Tom"
+ orcid: "https://orcid.org/0000-0001-6751-2930"
+- family-names: "Di Pentima"
+ given-names: "Lucas"
+ orcid: "https://orcid.org/0000-0002-2807-6854"
+- family-names: "Kutyła"
+ given-names: "Daniel"
+- family-names: "Li"
+ given-names: "Jiayong"
+- family-names: "Smith"
+ given-names: "Stephen"
+- family-names: "Vandewege"
+ given-names: "Ward"
+ orcid: "https://orcid.org/0000-0002-2527-6949"
+- family-names: "Wait Zaranek"
+ given-names: "Alexander"
+ orcid: "https://orcid.org/0000-0002-0415-9655"
+- family-names: "Wait Zaranek"
+ given-names: "Sarah"
+ orcid: "https://orcid.org/0000-0003-4716-9121"
+title: "Arvados"
+abstract: "Arvados is an open source platform for managing, processing, and sharing genomic and other large scientific and biomedical data."
+type: software
+url: "https://github.com/arvados/arvados/"
+doi: 10.5281/zenodo.6382942
def find_objects_for_index
@objects ||= model_class
- @objects = @objects.filter(@filters).limit(@limit).offset(@offset)
+ @objects = @objects.filter(@filters).limit(@limit).offset(@offset).order(@order)
@objects.fetch_multiple_pages(false)
end
ConfigValidators.validate_wb2_url_config()
ConfigValidators.validate_download_config()
end
+ if Rails.configuration.Users.AnonymousUserToken and
+ !Rails.configuration.Users.AnonymousUserToken.starts_with?("v2/")
+ Rails.configuration.Users.AnonymousUserToken = "v2/#{clusterID}-gj3su-anonymouspublic/#{Rails.configuration.Users.AnonymousUserToken}"
+ end
end
"Check health of all Arvados cluster services"
package_go_binary services/keep-balance keep-balance "$FORMAT" "$ARCH" \
"Rebalance and garbage-collect data blocks stored in Arvados Keep"
-package_go_binary services/keepproxy keepproxy "$FORMAT" "$ARCH" \
+package_go_binary cmd/arvados-server keepproxy "$FORMAT" "$ARCH" \
"Make a Keep cluster accessible to clients that are not on the LAN"
package_go_binary cmd/arvados-server keepstore "$FORMAT" "$ARCH" \
"Keep storage daemon, accessible to clients on the LAN"
# Usage: handle_libarvados_perl
handle_libarvados_perl () {
- if [[ -n "$ONLY_BUILD" ]] || [[ "$ONLY_BUILD" != "libarvados-perl" ]] ; then
+ if [[ -n "$ONLY_BUILD" ]] && [[ "$ONLY_BUILD" != "libarvados-perl" ]] ; then
debug_echo -e "Skipping build of libarvados-perl package."
return 0
fi
- cd "$WORKSPACE/sdk/perl"
+ # The perl sdk subdirectory is so old that it has no tag in its history,
+ # which causes version_at_commit.sh to fail. Just rebuild it every time.
+ cd "$WORKSPACE"
libarvados_perl_version="$(version_from_git)"
+ cd "$WORKSPACE/sdk/perl"
cd $WORKSPACE/packages/$TARGET
test_package_presence libarvados-perl "$libarvados_perl_version"
perl Makefile.PL INSTALL_BASE=install >"$STDOUT_IF_DEBUG" && \
make install INSTALLDIRS=perl >"$STDOUT_IF_DEBUG" && \
fpm_build "$WORKSPACE/sdk/perl" install/lib/=/usr/share libarvados-perl \
- dir "$(version_from_git)" install/man/=/usr/share/man \
+ dir "$libarvados_perl_version" install/man/=/usr/share/man \
"$WORKSPACE/apache-2.0.txt=/usr/share/doc/libarvados-perl/apache-2.0.txt" && \
mv --no-clobber libarvados-perl*.$FORMAT "$WORKSPACE/packages/$TARGET/"
fi
done
"$bundle" version | tee /dev/stderr | grep -q 'version 2'
) || fatal 'install bundler'
+ if test -d /var/lib/arvados-arvbox/ ; then
+ # Inside arvbox, use bundler-installed binstubs. The
+ # system bundler and rail's own bin/bundle refuse to work.
+ # I don't know why.
+ bundle=binstubs/bundle
+ fi
fi
}
"git.arvados.org/arvados.git/lib/install"
"git.arvados.org/arvados.git/lib/lsf"
"git.arvados.org/arvados.git/lib/recovercollection"
+ "git.arvados.org/arvados.git/services/keepproxy"
"git.arvados.org/arvados.git/services/keepstore"
"git.arvados.org/arvados.git/services/ws"
)
"dispatch-lsf": lsf.DispatchCommand,
"install": install.Command,
"init": install.InitCommand,
+ "keepproxy": keepproxy.Command,
"keepstore": keepstore.Command,
"recover-collection": recovercollection.Command,
"workbench2": wb2command{},
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
-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:
+First, configure some @InstanceTypes@ that have @Preemptible: true@. For a preemptible instance, @Price@ determines the maximum bid price; the actual price paid is dynamic and will likely be lower.
+
+Typically you want to add both preemptible and non-preemptible entries for each cloud provider VM type. To do this automatically, use @PreemptiblePriceFactor@ to enable a preemptible version of each listed type, using the given factor to set the maximum bid price relative to the non-preemptible price. Alternatively, you can configure preemptible instance types explicitly. For example, the following two configurations are equivalent:
<pre>
Clusters:
ClusterID:
+ Containers:
+ PreemptiblePriceFactor: 0.8
InstanceTypes:
m4.large:
- Preemptible: false
ProviderType: m4.large
VCPUs: 2
RAM: 8GiB
AddedScratch: 32GB
Price: 0.1
- m4.large.spot:
- Preemptible: true
+</pre>
+
+<pre>
+Clusters:
+ ClusterID:
+ InstanceTypes:
+ m4.large:
ProviderType: m4.large
VCPUs: 2
RAM: 8GiB
AddedScratch: 32GB
Price: 0.1
+ m4.large.preemptible:
+ Preemptible: true
+ ProviderType: m4.large
+ VCPUs: 2
+ RAM: 8GiB
+ AddedScratch: 32GB
+ Price: 0.08
</pre>
Next, you can choose to enable automatic use of preemptible instances:
<pre>
+Clusters:
+ ClusterID:
Containers:
AlwaysUsePreemptibleInstances: true
</pre>
<div class="releasenotes">
</notextile>
-h2(#main). development main (as of 2022-03-08)
+h2(#main). development main (as of 2022-04-08)
-"previous: Upgrading to 2.3.0":#v2_3_0
+"previous: Upgrading to 2.4.0":#v2_4_0
+
+h2(#v2_4_0). v2.4.0 (2022-04-08)
+
+"previous: Upgrading to 2.3.1":#v2_3_1
+
+h3. Default result order changed
+
+When requesting a list of objects without an explicit @order@ parameter, the default order has changed from @modified_at desc, uuid asc@ to @modified_at desc, uuid desc@. This means that if two objects have identical @modified_at@ timestamps, the tiebreaker will now be based on @uuid@ in decending order where previously it would be ascending order. The practical effect of this should be minor; with microsecond precision it is unusual to have two records with exactly the same timestamp, and order-sensitive queries should already provide an explicit @order@ parameter.
h3. Ubuntu 18.04 Arvados Python packages now depend on python-3.8
h3. Anonymous token changes
-The anonymous token configured in @Users.AnonymousUserToken@ must now be 32 characters or longer. This was already the suggestion in the documentation, now it is enforced. The @script/get_anonymous_user_token.rb@ script that was needed to register the anonymous user token in the database has been removed. Registration of the anonymous token is no longer necessary. If the anonymous token in @config.yml@ is specified as a full V2 token, that will now generate a warning - it should be updated to list just the secret (i.e. the part after the last forward slash).
-
-h3. Preemptible instance types are used automatically, if any are configured
+The anonymous token configured in @Users.AnonymousUserToken@ must now be 32 characters or longer. This was already the suggestion in the documentation, now it is enforced. The @script/get_anonymous_user_token.rb@ script that was needed to register the anonymous user token in the database has been removed. Registration of the anonymous token is no longer necessary.
-The default behavior for selecting "preemptible instances":{{site.baseurl}}/admin/spot-instances.html has changed. If your configuration lists any instance types with @Preemptible: true@, all child (non-top-level) containers will automatically be scheduled on preemptible instances. To avoid using preemptible instances except when explicitly requested by clients, add @AlwaysUsePreemptibleInstances: false@ in the @Containers@ config section. (Previously, preemptible instance types were never used unless the configuration specified @UsePreemptibleInstances: true@. That flag has been removed.)
+h3. Preemptible instance support changes
-h3. Role groups are visible to all users by default
+The @Containers.UsePreemptibleInstances@ option has been renamed to @Containers.AlwaysUsePreemptibleInstances@ and has the same behavior when @true@ and one or more preemptible instances are configured. However, a value of @false@ no longer disables support for preemptible instances, instead users can now enable use of preemptible instances at the level of an individual workflow or workflow step.
-The permission model has changed such that all role groups are visible to all active users. This enables users to share objects with groups they don't belong to. To preserve the previous behavior, where role groups are only visible to members and admins, add @RoleGroupsVisibleToAll: false@ to the @Users@ section of your configuration file.
+In addition, there is a new configuration option @Containers.PreemptiblePriceFactor@ will automatically add a preemptible instance type corresponding to each regular instance type. See "Using Preemptible instances":spot-instances.html for details.
h3. Default LSF arguments have changed
If you use LSF and your configuration specifies @Containers.LSF.BsubArgumentsList@, you should update it to include the new arguments (@"-R", "select[mem>=%MMB]", ...@, see "configuration reference":{{site.baseurl}}/admin/config.html). Otherwise, containers that are too big to run on any LSF host will remain in the LSF queue instead of being cancelled.
-h3. Previously trashed role groups will be deleted
+h3. Support for NVIDIA CUDA GPUs
-Due to a bug in previous versions, the @DELETE@ operation on a role group caused the group to be flagged as trash in the database, but continue to grant permissions regardless. After upgrading, any role groups that had been trashed this way will be deleted. This might surprise some users if they were relying on permissions that were still in effect due to this bug. Future @DELETE@ operations on a role group will immediately delete the group and revoke the associated permissions.
+Arvados now supports requesting NVIDIA CUDA GPUs for cloud and LSF (Slurm is currently not supported). To be able to request GPU nodes, some additional configuration is needed:
-h3. Users are visible to other users by default
+"Including GPU support in cloud compute node image":{{site.baseurl}}/install/crunch2-cloud/install-compute-node.html#nvidia
-When a new user is set up (either via @AutoSetupNewUsers@ config or via Workbench admin interface) the user immediately becomes visible to other users. To revert to the previous behavior, where the administrator must add two users to the same group using the Workbench admin interface in order for the users to see each other, change the new @Users.ActivatedUsersAreVisibleToOthers@ config to @false@.
+"Configure cloud dispatcher for GPU support":{{site.baseurl}}/install/crunch2-cloud/install-dispatch-cloud.html#GPUsupport
+
+"LSF GPU configuration":{{site.baseurl}}/install/crunch2-lsf/install-dispatch.html
+
+h3. Role groups are visible to all users by default
+
+The permission model has changed such that all role groups are visible to all active users. This enables users to share objects with groups they don't belong to. To preserve the previous behavior, where role groups are only visible to members and admins, add @RoleGroupsVisibleToAll: false@ to the @Users@ section of your configuration file.
+
+h3. Previously trashed role groups will be deleted
+
+Due to a bug in previous versions, the @DELETE@ operation on a role group caused the group to be flagged as trash in the database, but continue to grant permissions regardless. After upgrading, any role groups that had been trashed this way will be deleted. This might surprise some users if they were relying on permissions that were still in effect due to this bug. Future @DELETE@ operations on a role group will immediately delete the group and revoke the associated permissions.
h3. Dedicated keepstore process for each container
* If you already have a robust permanent keepstore infrastructure, you can set @Containers.LocalKeepBlobBuffersPerVCPU@ to 0 to disable this feature and preserve the previous behavior of sending container I/O traffic to your separately provisioned keepstore servers.
* This feature is enabled only if no volumes use @AccessViaHosts@, and no volumes have underlying @Replication@ less than @Collections.DefaultReplication@. If the feature is configured but cannot be enabled due to an incompatible volume configuration, this will be noted in the @crunch-run.txt@ file in the container log.
+h2(#v2_3_1). v2.3.1 (2021-11-24)
+
+"previous: Upgrading to 2.3.0":#v2_3_0
+
+h3. Users are visible to other users by default
+
+When a new user is set up (either via @AutoSetupNewUsers@ config or via Workbench admin interface) the user immediately becomes visible to other users. To revert to the previous behavior, where the administrator must add two users to the same group using the Workbench admin interface in order for the users to see each other, change the new @Users.ActivatedUsersAreVisibleToOthers@ config to @false@.
+
h3. Backend support for vocabulary checking
If your installation uses the vocabulary feature on Workbench2, you will need to update the cluster configuration by moving the vocabulary definition file to the node where @controller@ runs, and set the @API.VocabularyPath@ configuration parameter to the local path where the file was placed.
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.
</code></pre>
</notextile>
-h4. NVIDIA GPU support
+h4(#GPUsupport). NVIDIA GPU support
To specify instance types with NVIDIA GPUs, you must include an additional @CUDA@ section:
<notextile>
<pre>
$ <code class="userinput">arv keep get --help</code>
-usage: arv-get [-h] [--retries RETRIES]
+usage: arv-get [-h] [--retries RETRIES] [--version]
[--progress | --no-progress | --batch-progress]
- [--hash HASH | --md5sum] [-n] [-r] [-f | --skip-existing]
+ [--hash HASH | --md5sum] [-n] [-r]
+ [-f | -v | --skip-existing | --strip-manifest] [--threads N]
locator [destination]
Copy data from Keep to a local file or pipe.
locator Collection locator, optionally with a file path or
prefix.
destination Local file or directory where the data is to be written.
- Default: /dev/stdout.
+ Default: stdout.
optional arguments:
-h, --help show this help message and exit
--retries RETRIES Maximum number of times to retry server requests that
- encounter temporary failures (e.g., server down). Default
- 3.
+ encounter temporary failures (e.g., server down).
+ Default 3.
+ --version Print version and exit.
--progress Display human-readable progress on stderr (bytes and, if
possible, percentage of total data size). This is the
default behavior when it is not expected to interfere
with the output: specifically, stderr is a tty _and_
- either stdout is not a tty, or output is being written to
- named files rather than stdout.
+ either stdout is not a tty, or output is being written
+ to named files rather than stdout.
--no-progress Do not display human-readable progress on stderr.
--batch-progress Display machine-readable progress on stderr (bytes and,
if known, total data size).
-f Overwrite existing files while writing. The default
behavior is to refuse to write *anything* if any of the
output files already exist. As a special case, -f is not
- needed to write to /dev/stdout.
- --skip-existing Skip files that already exist. The default behavior is to
- refuse to write *anything* if any files exist that would
- have to be overwritten. This option causes even devices,
- sockets, and fifos to be skipped.
+ needed to write to stdout.
+ -v Once for verbose mode, twice for debug mode.
+ --skip-existing Skip files that already exist. The default behavior is
+ to refuse to write *anything* if any files exist that
+ would have to be overwritten. This option causes even
+ devices, sockets, and fifos to be skipped.
+ --strip-manifest When getting a collection manifest, strip its access
+ tokens before writing it.
+ --threads N Set the number of download threads to be used. Take into
+ account that using lots of threads will increase the RAM
+ requirements. Default is to use 4 threads. On high
+ latency installations, using a greater number will
+ improve overall throughput.
</pre>
</notextile>
cwltool:CUDARequirement:
cudaVersionMin: "11.0"
- cudaComputeCapabilityMin: "9.0"
- deviceCountMin: 1
- deviceCountMax: 1
+ cudaComputeCapability: "9.0"
+ cudaDeviceCountMin: 1
+ cudaDeviceCountMax: 1
arv:UsePreemptible:
usePreemptible: true
table(table table-bordered table-condensed).
|_. Field |_. Type |_. Description |
|cudaVersionMin|string|Required. The CUDA SDK version corresponding to the minimum driver version supported by the container (generally, the SDK version 'X.Y' the application was compiled against).|
-|cudaComputeCapabilityMin|string|Required. The minimum CUDA hardware capability (in 'X.Y' format) required by the application's PTX or C++ GPU code (will be JIT compiled for the available hardware).|
-|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@.|
+|cudaComputeCapability|string|Required. The minimum CUDA hardware capability (in 'X.Y' format) required by the application's PTX or C++ GPU code (will be JIT compiled for the available hardware).|
+|cudaDeviceCountMin|integer|Minimum number of GPU devices to allocate on a single node. Required.|
+|cudaDeviceCountMax|integer|Maximum number of GPU devices to allocate on a single node. Optional. If not specified, same as @cudaDeviceCountMin@.|
h2(#UsePreemptible). arv:UsePreemptible
runServiceCommand{name: "controller", svc: super.cluster.Services.Controller, depends: []supervisedTask{seedDatabase{}}},
runGoProgram{src: "services/arv-git-httpd", svc: super.cluster.Services.GitHTTP},
runGoProgram{src: "services/health", svc: super.cluster.Services.Health},
- runGoProgram{src: "services/keepproxy", svc: super.cluster.Services.Keepproxy, depends: []supervisedTask{runPassenger{src: "services/api"}}},
+ runServiceCommand{name: "keepproxy", svc: super.cluster.Services.Keepproxy, depends: []supervisedTask{runPassenger{src: "services/api"}}},
runServiceCommand{name: "keepstore", svc: super.cluster.Services.Keepstore},
runGoProgram{src: "services/keep-web", svc: super.cluster.Services.WebDAV},
runServiceCommand{name: "ws", svc: super.cluster.Services.Websocket, depends: []supervisedTask{seedDatabase{}}},
#
# This flag is ignored if no preemptible instance types are
# configured, and has no effect on top-level containers.
- AlwaysUsePreemptibleInstances: true
+ AlwaysUsePreemptibleInstances: false
+
+ # Automatically add a preemptible variant for every
+ # non-preemptible entry in InstanceTypes below. The maximum bid
+ # price for the preemptible variant will be the non-preemptible
+ # price multiplied by PreemptiblePriceFactor. If 0, preemptible
+ # variants are not added automatically.
+ #
+ # A price factor of 1.0 is a reasonable starting point.
+ PreemptiblePriceFactor: 0
# PEM encoded SSH key (RSA, DSA, or ECDSA) used by the
# cloud dispatcher for executing containers on worker VMs.
"Containers.MaxDispatchAttempts": false,
"Containers.MaxRetryAttempts": true,
"Containers.MinRetryPeriod": true,
+ "Containers.PreemptiblePriceFactor": false,
"Containers.ReserveExtraRAM": true,
"Containers.RuntimeEngine": true,
"Containers.ShellAccess": true,
}
}
+ // Preprocess/automate some configs
+ for id, cc := range cfg.Clusters {
+ ldr.autofillPreemptible("Clusters."+id, &cc)
+
+ if strings.Count(cc.Users.AnonymousUserToken, "/") == 3 {
+ // V2 token, strip it to just a secret
+ tmp := strings.Split(cc.Users.AnonymousUserToken, "/")
+ cc.Users.AnonymousUserToken = tmp[2]
+ }
+
+ cfg.Clusters[id] = cc
+ }
+
// Check for known mistakes
for id, cc := range cfg.Clusters {
for remote := range cc.RemoteClusters {
return nil, err
}
}
- if strings.Count(cc.Users.AnonymousUserToken, "/") == 3 {
- // V2 token, strip it to just a secret
- tmp := strings.Split(cc.Users.AnonymousUserToken, "/")
- cc.Users.AnonymousUserToken = tmp[2]
- }
}
return &cfg, nil
}
if !strings.HasPrefix(token, "v2/") {
return fmt.Errorf("%s: unacceptable characters in token (only a-z, A-Z, 0-9 are acceptable)", label)
}
- ldr.Logger.Warnf("%s: token is a full V2 token, should just be a secret (remove everything up to and including the last forward slash)", label)
if !acceptableTokenRe.MatchString(tmp[2]) {
return fmt.Errorf("%s: unacceptable characters in V2 token secret (only a-z, A-Z, 0-9 are acceptable)", label)
}
+ if len(tmp[2]) < acceptableTokenLength {
+ ldr.Logger.Warnf("%s: secret is too short (should be at least %d characters)", label, acceptableTokenLength)
+ }
} else if len(token) < acceptableTokenLength {
if ldr.Logger != nil {
ldr.Logger.Warnf("%s: token is too short (should be at least %d characters)", label, acceptableTokenLength)
}
}
}
+
+func (ldr *Loader) autofillPreemptible(label string, cc *arvados.Cluster) {
+ if factor := cc.Containers.PreemptiblePriceFactor; factor > 0 {
+ for name, it := range cc.InstanceTypes {
+ if !it.Preemptible {
+ it.Preemptible = true
+ it.Price = it.Price * factor
+ it.Name = name + ".preemptible"
+ if it2, exists := cc.InstanceTypes[it.Name]; exists && it2 != it {
+ ldr.Logger.Warnf("%s.InstanceTypes[%s]: already exists, so not automatically adding a preemptible variant of %s", label, it.Name, name)
+ continue
+ }
+ cc.InstanceTypes[it.Name] = it
+ }
+ }
+ }
+
+}
func (s *LoadSuite) TestNoWarningsForDumpedConfig(c *check.C) {
var logbuf bytes.Buffer
- logger := logrus.New()
- logger.Out = &logbuf
cfg, err := testLoader(c, `
Clusters:
zzzzz:
_, err = ldr.Load()
c.Assert(err, check.ErrorMatches, `there is no default storage class.*`)
}
+
+func (s *LoadSuite) TestPreemptiblePriceFactor(c *check.C) {
+ yaml := `
+Clusters:
+ z1111:
+ InstanceTypes:
+ Type1:
+ RAM: 12345M
+ VCPUs: 8
+ Price: 1.23
+ z2222:
+ Containers:
+ PreemptiblePriceFactor: 0.5
+ InstanceTypes:
+ Type1:
+ RAM: 12345M
+ VCPUs: 8
+ Price: 1.23
+ z3333:
+ Containers:
+ PreemptiblePriceFactor: 0.5
+ InstanceTypes:
+ Type1:
+ RAM: 12345M
+ VCPUs: 8
+ Price: 1.23
+ Type1.preemptible: # higher price than the auto-added variant would use -- should generate warning
+ ProviderType: Type1
+ RAM: 12345M
+ VCPUs: 8
+ Price: 1.23
+ Preemptible: true
+ Type2:
+ RAM: 23456M
+ VCPUs: 16
+ Price: 2.46
+ Type2.preemptible: # identical to the auto-added variant -- so no warning
+ ProviderType: Type2
+ RAM: 23456M
+ VCPUs: 16
+ Price: 1.23
+ Preemptible: true
+`
+ var logbuf bytes.Buffer
+ cfg, err := testLoader(c, yaml, &logbuf).Load()
+ c.Assert(err, check.IsNil)
+ cc, err := cfg.GetCluster("z1111")
+ c.Assert(err, check.IsNil)
+ c.Check(cc.InstanceTypes["Type1"].Price, check.Equals, 1.23)
+ c.Check(cc.InstanceTypes, check.HasLen, 1)
+
+ cc, err = cfg.GetCluster("z2222")
+ c.Assert(err, check.IsNil)
+ c.Check(cc.InstanceTypes["Type1"].Preemptible, check.Equals, false)
+ c.Check(cc.InstanceTypes["Type1"].Price, check.Equals, 1.23)
+ c.Check(cc.InstanceTypes["Type1.preemptible"].Preemptible, check.Equals, true)
+ c.Check(cc.InstanceTypes["Type1.preemptible"].Price, check.Equals, 1.23/2)
+ c.Check(cc.InstanceTypes["Type1.preemptible"].ProviderType, check.Equals, "Type1")
+ c.Check(cc.InstanceTypes, check.HasLen, 2)
+
+ cc, err = cfg.GetCluster("z3333")
+ c.Assert(err, check.IsNil)
+ // Don't overwrite the explicitly configured preemptible variant
+ c.Check(cc.InstanceTypes["Type1.preemptible"].Price, check.Equals, 1.23)
+ c.Check(cc.InstanceTypes, check.HasLen, 4)
+ c.Check(logbuf.String(), check.Matches, `(?ms).*Clusters\.z3333\.InstanceTypes\[Type1\.preemptible\]: already exists, so not automatically adding a preemptible variant of Type1.*`)
+ c.Check(logbuf.String(), check.Not(check.Matches), `(?ms).*Type2\.preemptible.*`)
+ c.Check(logbuf.String(), check.Not(check.Matches), `(?ms).*(z1111|z2222)[^\n]*InstanceTypes.*`)
+}
return nil, errors.New("no token provided")
}
for _, token := range incoming.Tokens {
- if strings.HasPrefix(token, "v2/"+cluster.ClusterID+"-") && remoteID == cluster.Login.LoginCluster {
- // If we did this, the login cluster
- // would call back to us and then
- // reject our response because the
- // user UUID prefix (i.e., the
- // LoginCluster prefix) won't match
- // the token UUID prefix (i.e., our
- // prefix).
+ if strings.HasPrefix(token, "v2/"+cluster.ClusterID+"-") &&
+ !strings.HasPrefix(token, "v2/"+cluster.ClusterID+"-gj3su-anonymouspublic/") &&
+ remoteID == cluster.Login.LoginCluster {
+ // If we did this, the login cluster would call back to us and then
+ // reject our response because the user UUID prefix (i.e., the
+ // LoginCluster prefix) won't match the token UUID prefix (i.e., our
+ // prefix). The anonymous token is OK to forward, because (unlike other
+ // local tokens for real users) the validation callback will return the
+ // locally issued anonymous user ID instead of a login-cluster user ID.
+ // That anonymous user ID gets mapped to the local anonymous user
+ // automatically on the login cluster.
return nil, httpErrorf(http.StatusUnauthorized, "cannot use a locally issued token to forward a request to our login cluster (%s)", remoteID)
}
salted, err := auth.SaltToken(token, remoteID)
package controller
import (
+ "bytes"
"context"
"crypto/tls"
"encoding/json"
+ "io"
"io/ioutil"
"net/http"
"net/http/httptest"
type HandlerSuite struct {
cluster *arvados.Cluster
handler *Handler
+ logbuf *bytes.Buffer
ctx context.Context
cancel context.CancelFunc
}
func (s *HandlerSuite) SetUpTest(c *check.C) {
+ s.logbuf = &bytes.Buffer{}
s.ctx, s.cancel = context.WithCancel(context.Background())
- s.ctx = ctxlog.Context(s.ctx, ctxlog.New(os.Stderr, "json", "debug"))
+ s.ctx = ctxlog.Context(s.ctx, ctxlog.New(io.MultiWriter(os.Stderr, s.logbuf), "json", "debug"))
s.cluster = &arvados.Cluster{
ClusterID: "zzzzz",
PostgreSQL: integrationTestCluster().PostgreSQL,
}
}
+func (s *HandlerSuite) TestLogTokenUUID(c *check.C) {
+ req := httptest.NewRequest("GET", "https://0.0.0.0/arvados/v1/users/current", nil)
+ req.Header.Set("Authorization", "Bearer "+arvadostest.ActiveTokenV2)
+ req = req.WithContext(s.ctx)
+ resp := httptest.NewRecorder()
+ httpserver.LogRequests(s.handler).ServeHTTP(resp, req)
+ c.Check(resp.Code, check.Equals, http.StatusOK)
+ c.Check(s.logbuf.String(), check.Matches, `(?ms).*"tokenUUIDs":\["`+strings.Split(arvadostest.ActiveTokenV2, "/")[1]+`"\].*`)
+}
+
func (s *HandlerSuite) TestCreateAPIToken(c *check.C) {
req := httptest.NewRequest("GET", "/arvados/v1/users/current", nil)
auth, err := s.handler.createAPItoken(req, arvadostest.ActiveUserUUID, nil)
c.Check(coll.PortableDataHash, check.Equals, pdh)
}
+// z3333 should forward the locally-issued anonymous user token to its login
+// cluster z1111. That is no problem because the login cluster controller will
+// map any anonymous user token to its local anonymous user.
+//
+// This needs to work because wb1 has a tendency to slap the local anonymous
+// user token on every request as a reader_token, which gets folded into the
+// request token list controller.
+//
+// Use a z1111 user token and the anonymous token from z3333 passed in as a
+// reader_token to do a request on z3333, asking for the z1111 anonymous user
+// object. The request will be forwarded to the z1111 cluster. The presence of
+// the z3333 anonymous user token should not prohibit the request from being
+// forwarded.
+func (s *IntegrationSuite) TestForwardAnonymousTokenToLoginCluster(c *check.C) {
+ conn1 := s.testClusters["z1111"].Conn()
+ s.testClusters["z3333"].Conn()
+
+ rootctx1, _, _ := s.testClusters["z1111"].RootClients()
+ _, anonac3, _ := s.testClusters["z3333"].AnonymousClients()
+
+ // Make a user connection to z3333 (using a z1111 user, because that's the login cluster)
+ _, userac1, _, _ := s.testClusters["z3333"].UserClients(rootctx1, c, conn1, "user@example.com", true)
+
+ // Get the anonymous user token for z3333
+ var anon3Auth arvados.APIClientAuthorization
+ err := anonac3.RequestAndDecode(&anon3Auth, "GET", "/arvados/v1/api_client_authorizations/current", nil, nil)
+ c.Check(err, check.IsNil)
+
+ var userList arvados.UserList
+ where := make(map[string]string)
+ where["uuid"] = "z1111-tpzed-anonymouspublic"
+ err = userac1.RequestAndDecode(&userList, "GET", "/arvados/v1/users", nil,
+ map[string]interface{}{
+ "reader_tokens": []string{anon3Auth.TokenV2()},
+ "where": where,
+ },
+ )
+ // The local z3333 anonymous token must be allowed to be forwarded to the login cluster
+ c.Check(err, check.IsNil)
+
+ userac1.AuthToken = "v2/z1111-gj3su-asdfasdfasdfasd/this-token-does-not-validate-so-anonymous-token-will-be-used-instead"
+ err = userac1.RequestAndDecode(&userList, "GET", "/arvados/v1/users", nil,
+ map[string]interface{}{
+ "reader_tokens": []string{anon3Auth.TokenV2()},
+ "where": where,
+ },
+ )
+ c.Check(err, check.IsNil)
+}
+
// Get a token from the login cluster (z1111), use it to submit a
// container request on z2222.
func (s *IntegrationSuite) TestCreateContainerRequestWithFedToken(c *check.C) {
"apiOptsType": fmt.Sprintf("%T", opts),
"apiOpts": opts,
}).Debug("exec")
+ // Extract the token UUIDs (or a placeholder for v1 tokens)
+ var tokenUUIDs []string
+ for _, t := range creds.Tokens {
+ if strings.HasPrefix(t, "v2/") {
+ tokenParts := strings.Split(t, "/")
+ if len(tokenParts) >= 3 {
+ tokenUUIDs = append(tokenUUIDs, tokenParts[1])
+ }
+ } else {
+ end := t
+ if len(t) > 5 {
+ end = t[len(t)-5:]
+ }
+ tokenUUIDs = append(tokenUUIDs, "v1 token ending in "+end)
+ }
+ }
+ httpserver.SetResponseLogFields(req.Context(), logrus.Fields{"tokenUUIDs": tokenUUIDs})
resp, err := exec(ctx, opts)
if err != nil {
logger.WithError(err).Debugf("returning error type %T", err)
"URL": listenURL,
"Listen": srv.Addr,
"Service": c.svcName,
+ "Version": cmd.Version.String(),
}).Info("listening")
if _, err := daemon.SdNotify(false, "READY=1"); err != nil {
logger.WithError(err).Errorf("error notifying init daemon")
Package: ArvadosR
Type: Package
Title: Arvados R SDK
-Version: 0.0.6
+Version: 2.4.0
Authors@R: c(person("Fuad", "Muhic", role = c("aut", "ctr"), email = "fmuhic@capeannenterprises.com"),
person("Peter", "Amstutz", role = c("cre"), email = "peter.amstutz@curii.com"))
Description: This is the Arvados R SDK
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
"errors"
"fmt"
"io"
+ "io/fs"
"io/ioutil"
"log"
"net/http"
}
// NewClientFromEnv creates a new Client that uses the default HTTP
-// client with the API endpoint and credentials given by the
-// ARVADOS_API_* environment variables.
+// client, and loads API endpoint and credentials from ARVADOS_*
+// environment variables (if set) and
+// $HOME/.config/arvados/settings.conf (if readable).
+//
+// If a config exists in both locations, the environment variable is
+// used.
+//
+// If there is an error (other than ENOENT) reading settings.conf,
+// NewClientFromEnv logs the error to log.Default(), then proceeds as
+// if settings.conf did not exist.
+//
+// Space characters are trimmed when reading the settings file, so
+// these are equivalent:
+//
+// ARVADOS_API_HOST=localhost\n
+// ARVADOS_API_HOST=localhost\r\n
+// ARVADOS_API_HOST = localhost \n
+// \tARVADOS_API_HOST = localhost\n
func NewClientFromEnv() *Client {
+ vars := map[string]string{}
+ home := os.Getenv("HOME")
+ conffile := home + "/.config/arvados/settings.conf"
+ if home == "" {
+ // no $HOME => just use env vars
+ } else if settings, err := os.ReadFile(conffile); errors.Is(err, fs.ErrNotExist) {
+ // no config file => just use env vars
+ } else if err != nil {
+ // config file unreadable => log message, then use env vars
+ log.Printf("continuing without loading %s: %s", conffile, err)
+ } else {
+ for _, line := range bytes.Split(settings, []byte{'\n'}) {
+ kv := bytes.SplitN(line, []byte{'='}, 2)
+ k := string(bytes.TrimSpace(kv[0]))
+ if len(kv) != 2 || !strings.HasPrefix(k, "ARVADOS_") {
+ // Same behavior as python sdk:
+ // silently skip leading # (comments),
+ // blank lines, typos, and non-Arvados
+ // vars.
+ continue
+ }
+ vars[k] = string(bytes.TrimSpace(kv[1]))
+ }
+ }
+ for _, env := range os.Environ() {
+ if !strings.HasPrefix(env, "ARVADOS_") {
+ continue
+ }
+ kv := strings.SplitN(env, "=", 2)
+ if len(kv) == 2 {
+ vars[kv[0]] = kv[1]
+ }
+ }
var svcs []string
- for _, s := range strings.Split(os.Getenv("ARVADOS_KEEP_SERVICES"), " ") {
+ for _, s := range strings.Split(vars["ARVADOS_KEEP_SERVICES"], " ") {
if s == "" {
continue
} else if u, err := url.Parse(s); err != nil {
}
}
var insecure bool
- if s := strings.ToLower(os.Getenv("ARVADOS_API_HOST_INSECURE")); s == "1" || s == "yes" || s == "true" {
+ if s := strings.ToLower(vars["ARVADOS_API_HOST_INSECURE"]); s == "1" || s == "yes" || s == "true" {
insecure = true
}
return &Client{
Scheme: "https",
- APIHost: os.Getenv("ARVADOS_API_HOST"),
- AuthToken: os.Getenv("ARVADOS_API_TOKEN"),
+ APIHost: vars["ARVADOS_API_HOST"],
+ AuthToken: vars["ARVADOS_API_TOKEN"],
Insecure: insecure,
KeepServiceURIs: svcs,
Timeout: 5 * time.Minute,
"io/ioutil"
"net/http"
"net/url"
+ "os"
+ "strings"
"sync"
- "testing"
"testing/iotest"
+
+ check "gopkg.in/check.v1"
)
type stubTransport struct {
}, nil
}
-func TestCurrentUser(t *testing.T) {
- t.Parallel()
+var _ = check.Suite(&clientSuite{})
+
+type clientSuite struct{}
+
+func (*clientSuite) TestCurrentUser(c *check.C) {
stub := &stubTransport{
Responses: map[string]string{
"/arvados/v1/users/current": `{"uuid":"zzzzz-abcde-012340123401234"}`,
},
}
- c := &Client{
+ client := &Client{
Client: &http.Client{
Transport: stub,
},
APIHost: "zzzzz.arvadosapi.com",
AuthToken: "xyzzy",
}
- u, err := c.CurrentUser()
- if err != nil {
- t.Fatal(err)
- }
- if x := "zzzzz-abcde-012340123401234"; u.UUID != x {
- t.Errorf("got uuid %q, expected %q", u.UUID, x)
- }
- if len(stub.Requests) < 1 {
- t.Fatal("empty stub.Requests")
- }
+ u, err := client.CurrentUser()
+ c.Check(err, check.IsNil)
+ c.Check(u.UUID, check.Equals, "zzzzz-abcde-012340123401234")
+ c.Check(stub.Requests, check.Not(check.HasLen), 0)
hdr := stub.Requests[len(stub.Requests)-1].Header
- if hdr.Get("Authorization") != "OAuth2 xyzzy" {
- t.Errorf("got headers %+q, expected Authorization header", hdr)
- }
+ c.Check(hdr.Get("Authorization"), check.Equals, "OAuth2 xyzzy")
- c.Client.Transport = &errorTransport{}
- u, err = c.CurrentUser()
- if err == nil {
- t.Errorf("got nil error, expected something awful")
- }
+ client.Client.Transport = &errorTransport{}
+ u, err = client.CurrentUser()
+ c.Check(err, check.NotNil)
}
-func TestAnythingToValues(t *testing.T) {
+func (*clientSuite) TestAnythingToValues(c *check.C) {
type testCase struct {
in interface{}
// ok==nil means anythingToValues should return an
ok: nil,
},
} {
- t.Logf("%#v", tc.in)
+ c.Logf("%#v", tc.in)
out, err := anythingToValues(tc.in)
- switch {
- case tc.ok == nil:
- if err == nil {
- t.Errorf("got %#v, expected error", out)
- }
- case err != nil:
- t.Errorf("got err %#v, expected nil", err)
- case !tc.ok(out):
- t.Errorf("got %#v but tc.ok() says that is wrong", out)
+ if tc.ok == nil {
+ c.Check(err, check.NotNil)
+ continue
}
+ c.Check(err, check.IsNil)
+ c.Check(tc.ok(out), check.Equals, true)
}
}
+
+func (*clientSuite) TestLoadConfig(c *check.C) {
+ oldenv := os.Environ()
+ defer func() {
+ os.Clearenv()
+ for _, s := range oldenv {
+ i := strings.IndexRune(s, '=')
+ os.Setenv(s[:i], s[i+1:])
+ }
+ }()
+
+ tmp := c.MkDir()
+ os.Setenv("HOME", tmp)
+ for _, s := range os.Environ() {
+ if strings.HasPrefix(s, "ARVADOS_") {
+ i := strings.IndexRune(s, '=')
+ os.Unsetenv(s[:i])
+ }
+ }
+ os.Mkdir(tmp+"/.config", 0777)
+ os.Mkdir(tmp+"/.config/arvados", 0777)
+
+ // Use $HOME/.config/arvados/settings.conf if no env vars are
+ // set
+ os.WriteFile(tmp+"/.config/arvados/settings.conf", []byte(`
+ ARVADOS_API_HOST = localhost:1
+ ARVADOS_API_TOKEN = token_from_settings_file1
+ `), 0777)
+ client := NewClientFromEnv()
+ c.Check(client.AuthToken, check.Equals, "token_from_settings_file1")
+ c.Check(client.APIHost, check.Equals, "localhost:1")
+ c.Check(client.Insecure, check.Equals, false)
+
+ // ..._INSECURE=true, comments, ignored lines in settings.conf
+ os.WriteFile(tmp+"/.config/arvados/settings.conf", []byte(`
+ (ignored) = (ignored)
+ #ARVADOS_API_HOST = localhost:2
+ ARVADOS_API_TOKEN = token_from_settings_file2
+ ARVADOS_API_HOST_INSECURE = true
+ `), 0777)
+ client = NewClientFromEnv()
+ c.Check(client.AuthToken, check.Equals, "token_from_settings_file2")
+ c.Check(client.APIHost, check.Equals, "")
+ c.Check(client.Insecure, check.Equals, true)
+
+ // Environment variables override settings.conf
+ os.Setenv("ARVADOS_API_HOST", "[::]:3")
+ os.Setenv("ARVADOS_API_HOST_INSECURE", "0")
+ client = NewClientFromEnv()
+ c.Check(client.AuthToken, check.Equals, "token_from_settings_file2")
+ c.Check(client.APIHost, check.Equals, "[::]:3")
+ c.Check(client.Insecure, check.Equals, false)
+}
StaleLockTimeout Duration
SupportedDockerImageFormats StringSet
AlwaysUsePreemptibleInstances bool
+ PreemptiblePriceFactor float64
RuntimeEngine string
LocalKeepBlobBuffersPerVCPU int
LocalKeepLogsToContainerLog string
"context"
"net"
"net/http"
+ "sync"
"time"
"git.arvados.org/arvados.git/sdk/go/ctxlog"
}
var (
- requestTimeContextKey = contextKey{"requestTime"}
+ requestTimeContextKey = contextKey{"requestTime"}
+ responseLogFieldsContextKey = contextKey{"responseLogFields"}
+ mutexContextKey = contextKey{"mutex"}
)
type hijacker interface {
})
}
+func SetResponseLogFields(ctx context.Context, fields logrus.Fields) {
+ m, _ := ctx.Value(&mutexContextKey).(*sync.Mutex)
+ c, _ := ctx.Value(&responseLogFieldsContextKey).(logrus.Fields)
+ if m == nil || c == nil {
+ return
+ }
+ m.Lock()
+ defer m.Unlock()
+ for k, v := range fields {
+ c[k] = v
+ }
+}
+
// LogRequests wraps an http.Handler, logging each request and
// response.
func LogRequests(h http.Handler) http.Handler {
})
ctx := req.Context()
ctx = context.WithValue(ctx, &requestTimeContextKey, time.Now())
+ ctx = context.WithValue(ctx, &responseLogFieldsContextKey, logrus.Fields{})
+ ctx = context.WithValue(ctx, &mutexContextKey, &sync.Mutex{})
ctx = ctxlog.Context(ctx, lgr)
req = req.WithContext(ctx)
"timeWriteBody": stats.Duration(tDone.Sub(writeTime)),
})
}
+ if responseLogFields, ok := req.Context().Value(&responseLogFieldsContextKey).(logrus.Fields); ok {
+ lgr = lgr.WithFields(responseLogFields)
+ }
respCode := w.WroteStatus()
if respCode == 0 {
respCode = http.StatusOK
DEFAULT_PUT_THREADS = 2
DEFAULT_GET_THREADS = 2
- def __init__(self, keep, copies=None, put_threads=None, num_retries=None, storage_classes_func=None):
+ def __init__(self, keep, copies=None, put_threads=None, num_retries=None, storage_classes_func=None, get_threads=None):
"""keep: KeepClient object to use"""
self._keep = keep
self._bufferblocks = collections.OrderedDict()
self.lock = threading.Lock()
self.prefetch_enabled = True
self.num_put_threads = put_threads or _BlockManager.DEFAULT_PUT_THREADS
- self.num_get_threads = _BlockManager.DEFAULT_GET_THREADS
+ self.num_get_threads = get_threads or _BlockManager.DEFAULT_GET_THREADS
self.copies = copies
self.storage_classes = storage_classes_func or (lambda: [])
self._pending_write_size = 0
b = self._prefetch_queue.get()
if b is None:
return
- self._keep.get(b)
+ self._keep.get(b, prefetch=True)
except Exception:
_logger.exception("Exception doing block prefetch")
if not self.prefetch_enabled:
return
- if self._keep.get_from_cache(locator) is not None:
- return
-
with self.lock:
if locator in self._bufferblocks:
return
if size == 0 or offset >= self.size():
return b''
readsegs = locators_and_ranges(self._segments, offset, size)
- prefetch = locators_and_ranges(self._segments, offset + size, config.KEEP_BLOCK_SIZE, limit=32)
+ prefetch = locators_and_ranges(self._segments, offset + size, config.KEEP_BLOCK_SIZE * self.parent._my_block_manager().num_get_threads, limit=32)
locs = set()
data = []
block_manager=None,
replication_desired=None,
storage_classes_desired=None,
- put_threads=None):
+ put_threads=None,
+ get_threads=None):
"""Collection constructor.
:manifest_locator_or_text:
self.replication_desired = replication_desired
self._storage_classes_desired = storage_classes_desired
self.put_threads = put_threads
+ self.get_threads = get_threads
if apiconfig:
self._config = apiconfig
copies = (self.replication_desired or
self._my_api()._rootDesc.get('defaultCollectionReplication',
2))
- self._block_manager = _BlockManager(self._my_keep(), copies=copies, put_threads=self.put_threads, num_retries=self.num_retries, storage_classes_func=self.storage_classes_desired)
+ self._block_manager = _BlockManager(self._my_keep(),
+ copies=copies,
+ put_threads=self.put_threads,
+ num_retries=self.num_retries,
+ storage_classes_func=self.storage_classes_desired,
+ get_threads=self.get_threads,)
return self._block_manager
def _remember_api_response(self, response):
it.
""")
+parser.add_argument('--threads', type=int, metavar='N', default=4,
+ help="""
+Set the number of download threads to be used. Take into account that
+using lots of threads will increase the RAM requirements. Default is
+to use 4 threads.
+On high latency installations, using a greater number will improve
+overall throughput.
+""")
+
def parse_arguments(arguments, stdout, stderr):
args = parser.parse_args(arguments)
try:
reader = arvados.CollectionReader(
- col_loc, api_client=api_client, num_retries=args.retries)
+ col_loc, api_client=api_client, num_retries=args.retries,
+ keep_client=arvados.keep.KeepClient(block_cache=arvados.keep.KeepBlockCache((args.threads+1)*64 * 1024 * 1024)),
+ get_threads=args.threads)
except Exception as error:
logger.error("failed to read collection: {}".format(error))
return 1
else:
return None
- def get_from_cache(self, loc):
+ def get_from_cache(self, loc_s):
"""Fetch a block only if is in the cache, otherwise return None."""
- slot = self.block_cache.get(loc)
+ locator = KeepLocator(loc_s)
+ slot = self.block_cache.get(locator.md5sum)
if slot is not None and slot.ready.is_set():
return slot.get()
else:
def get(self, loc_s, **kwargs):
return self._get_or_head(loc_s, method="GET", **kwargs)
- def _get_or_head(self, loc_s, method="GET", num_retries=None, request_id=None, headers=None):
+ def _get_or_head(self, loc_s, method="GET", num_retries=None, request_id=None, headers=None, prefetch=False):
"""Get data from Keep.
This method fetches one or more blocks of data from Keep. It
if method == "GET":
slot, first = self.block_cache.reserve_cache(locator.md5sum)
if not first:
+ if prefetch:
+ # this is request for a prefetch, if it is
+ # already in flight, return immediately.
+ # clear 'slot' to prevent finally block from
+ # calling slot.set()
+ slot = None
+ return None
self.hits_counter.add(1)
blob = slot.get()
if blob is None:
return True
if os.path.exists(os.path.join(self.local_store, locator.md5sum)):
return True
-
- def is_cached(self, locator):
- return self.block_cache.reserve_cache(expect_hash)
pagesize = 1000
kwargs["limit"] = pagesize
kwargs["count"] = 'none'
- kwargs["order"] = ["%s %s" % (order_key, "asc" if ascending else "desc"), "uuid asc"]
+ asc = "asc" if ascending else "desc"
+ kwargs["order"] = ["%s %s" % (order_key, asc), "uuid %s" % asc]
other_filters = kwargs.get("filters", [])
if "select" in kwargs and "uuid" not in kwargs["select"]:
if firstitem[order_key] == lastitem[order_key]:
# Got a page where every item has the same order key.
# Switch to using uuid for paging.
- nextpage = [[order_key, "=", lastitem[order_key]], ["uuid", ">", lastitem["uuid"]]]
+ nextpage = [[order_key, "=", lastitem[order_key]], ["uuid", ">" if ascending else "<", lastitem["uuid"]]]
prev_page_all_same_order_key = True
else:
# Start from the last order key seen, but skip the last
def __init__(self, blocks):
self.blocks = blocks
self.requests = []
- def get(self, locator, num_retries=0):
+ def get(self, locator, num_retries=0, prefetch=False):
self.requests.append(locator)
return self.blocks.get(locator)
def get_from_cache(self, locator):
def __init__(self, blocks, nocache):
self.blocks = blocks
self.nocache = nocache
+ self.num_get_threads = 1
def block_prefetch(self, loc):
pass
def __init__(self, content, num_retries=0):
self.content = content
- def get(self, locator, num_retries=0):
+ def get(self, locator, num_retries=0, prefetch=False):
return self.content[locator]
def test_stream_reader(self):
def test_onepage_desc(self):
ks = KeysetTestHelper([[
- {"limit": 1000, "count": "none", "order": ["created_at desc", "uuid asc"], "filters": []},
+ {"limit": 1000, "count": "none", "order": ["created_at desc", "uuid desc"], "filters": []},
{"items": [{"created_at": "2", "uuid": "2"}, {"created_at": "1", "uuid": "1"}]}
], [
- {"limit": 1000, "count": "none", "order": ["created_at desc", "uuid asc"], "filters": [["created_at", "<=", "1"], ["uuid", "!=", "1"]]},
+ {"limit": 1000, "count": "none", "order": ["created_at desc", "uuid desc"], "filters": [["created_at", "<=", "1"], ["uuid", "!=", "1"]]},
{"items": []}
]])
def get_permissions
if current_user.andand.can?(manage: @object)
# find all links and return them
- @objects = Link.where(link_class: "permission",
- head_uuid: params[:uuid])
+ @objects = Link.unscoped.where(link_class: "permission",
+ head_uuid: params[:uuid])
@offset = 0
@limit = @objects.count
render_list
protected
def find_object_by_uuid
+ if params[:id] && params[:id].match(/\D/)
+ params[:uuid] = params.delete :id
+ end
if action_name == 'get_permissions'
# get_permissions accepts a UUID for any kind of object.
@object = ArvadosModel::resource_class_for_uuid(params[:uuid])
.readable_by(*@read_users)
.where(uuid: params[:uuid])
.first
- else
+ elsif !current_user
super
+ else
+ # The usual permission-filtering index query is unnecessarily
+ # inefficient, and doesn't match all permission links that
+ # should be visible (see #18865). Instead, we look up the link
+ # by UUID, then check whether (a) its tail_uuid is the current
+ # user or (b) its head_uuid is an object the current_user
+ # can_manage.
+ link = Link.unscoped.where(uuid: params[:uuid]).first
+ if link && link.link_class != 'permission'
+ # Not a permission link. Re-fetch using generic
+ # permission-filtering query.
+ super
+ elsif link && (current_user.uuid == link.tail_uuid ||
+ current_user.can?(manage: link.head_uuid))
+ # Permission granted.
+ @object = link
+ else
+ # Permission denied, i.e., link is invisible => 404.
+ @object = nil
+ end
end
end
k
end
end
+
+ # If the provided filters are enough to limit the results to
+ # permission links with specific head_uuids or
+ # tail_uuid=current_user, bypass the normal readable_by query
+ # (which doesn't match all can_manage-able items, see #18865) --
+ # just ensure the current user actually has can_manage permission
+ # for the provided head_uuids, removing any that don't. At that
+ # point the caller's filters are an effective permission filter.
+ if @filters.include?(['link_class', '=', 'permission'])
+ @filters.map do |k|
+ if k[0] == 'tail_uuid' && k[1] == '=' && k[2] == current_user.uuid
+ @objects = Link.unscoped
+ elsif k[0] == 'head_uuid'
+ if k[1] == '=' && current_user.can?(manage: k[2])
+ @objects = Link.unscoped
+ elsif k[1] == 'in'
+ # Modify the filter operand element (k[2]) in place,
+ # removing any non-permitted UUIDs.
+ k[2].select! do |head_uuid|
+ current_user.can?(manage: head_uuid)
+ end
+ @objects = Link.unscoped
+ end
+ end
+ end
+ end
end
end
clnt
end
- def self.check_anonymous_user_token token
+ def self.check_anonymous_user_token(token:, remote:)
case token[0..2]
when 'v2/'
_, token_uuid, secret, optional = token.split('/')
secret = token
end
+ # Usually, the secret is salted
+ salted_secret = OpenSSL::HMAC.hexdigest('sha1', Rails.configuration.Users.AnonymousUserToken, remote)
+
+ # The anonymous token could be specified as a full v2 token in the config,
+ # but the config loader strips it down to the secret part.
# The anonymous token content and minimum length is verified in lib/config
- if secret.length >= 0 && secret == Rails.configuration.Users.AnonymousUserToken
+ if secret.length >= 0 && (secret == Rails.configuration.Users.AnonymousUserToken || secret == salted_secret)
return ApiClientAuthorization.new(user: User.find_by_uuid(anonymous_user_uuid),
uuid: Rails.configuration.ClusterID+"-gj3su-anonymouspublic",
- api_token: token,
+ api_token: secret,
api_client: anonymous_user_token_api_client,
scopes: ['GET /'])
else
return nil if token.nil? or token.empty?
remote ||= Rails.configuration.ClusterID
- auth = self.check_anonymous_user_token(token)
+ auth = self.check_anonymous_user_token(token: token, remote: remote)
if !auth.nil?
return auth
end
end
def self.default_orders
- ["#{table_name}.modified_at desc", "#{table_name}.uuid"]
+ ["#{table_name}.modified_at desc", "#{table_name}.uuid desc"]
end
def self.unique_columns
--- /dev/null
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: AGPL-3.0
+
+class FixCreatedAtIndexes < ActiveRecord::Migration[5.2]
+ @@idxtables = [:collections, :container_requests, :groups, :links, :repositories, :users, :virtual_machines, :workflows, :logs]
+
+ def up
+ @@idxtables.each do |table|
+ ActiveRecord::Base.connection.execute("DROP INDEX IF EXISTS index_#{table.to_s}_on_created_at")
+ ActiveRecord::Base.connection.execute("DROP INDEX IF EXISTS index_#{table.to_s}_on_created_at_uuid")
+ ActiveRecord::Base.connection.execute("DROP INDEX IF EXISTS index_#{table.to_s}_on_created_at_and_uuid")
+ ActiveRecord::Base.connection.execute("DROP INDEX IF EXISTS index_#{table.to_s}_on_modified_at")
+ ActiveRecord::Base.connection.execute("DROP INDEX IF EXISTS index_#{table.to_s}_on_modified_at_uuid")
+ ActiveRecord::Base.connection.execute("DROP INDEX IF EXISTS index_#{table.to_s}_on_modified_at_and_uuid")
+
+ ActiveRecord::Base.connection.execute("CREATE INDEX IF NOT EXISTS index_#{table.to_s}_on_created_at_and_uuid ON #{table.to_s} USING btree (created_at, uuid)")
+ ActiveRecord::Base.connection.execute("CREATE INDEX IF NOT EXISTS index_#{table.to_s}_on_modified_at_and_uuid ON #{table.to_s} USING btree (modified_at, uuid)")
+ end
+ end
+
+ def down
+ @@idxtables.each do |table|
+ ActiveRecord::Base.connection.execute("DROP INDEX IF EXISTS index_#{table.to_s}_on_modified_at_and_uuid")
+ ActiveRecord::Base.connection.execute("CREATE INDEX IF NOT EXISTS index_#{table.to_s}_on_modified_at_uuid ON #{table.to_s} USING btree (modified_at desc, uuid asc)")
+ end
+ end
+end
--
--- Name: index_collections_on_created_at; Type: INDEX; Schema: public; Owner: -
+-- Name: index_collections_on_created_at_and_uuid; Type: INDEX; Schema: public; Owner: -
--
-CREATE INDEX index_collections_on_created_at ON public.collections USING btree (created_at);
+CREATE INDEX index_collections_on_created_at_and_uuid ON public.collections USING btree (created_at, uuid);
--
--
--- Name: index_collections_on_modified_at; Type: INDEX; Schema: public; Owner: -
+-- Name: index_collections_on_modified_at_and_uuid; Type: INDEX; Schema: public; Owner: -
--
-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 public.collections USING btree (modified_at DESC, uuid);
+CREATE INDEX index_collections_on_modified_at_and_uuid ON public.collections USING btree (modified_at, uuid);
--
--
--- Name: index_container_requests_on_modified_at_uuid; Type: INDEX; Schema: public; Owner: -
+-- Name: index_container_requests_on_created_at_and_uuid; Type: INDEX; Schema: public; Owner: -
+--
+
+CREATE INDEX index_container_requests_on_created_at_and_uuid ON public.container_requests USING btree (created_at, uuid);
+
+
+--
+-- Name: index_container_requests_on_modified_at_and_uuid; Type: INDEX; Schema: public; Owner: -
--
-CREATE INDEX index_container_requests_on_modified_at_uuid ON public.container_requests USING btree (modified_at DESC, uuid);
+CREATE INDEX index_container_requests_on_modified_at_and_uuid ON public.container_requests USING btree (modified_at, uuid);
--
--
--- Name: index_groups_on_created_at; Type: INDEX; Schema: public; Owner: -
+-- Name: index_groups_on_created_at_and_uuid; Type: INDEX; Schema: public; Owner: -
--
-CREATE INDEX index_groups_on_created_at ON public.groups USING btree (created_at);
+CREATE INDEX index_groups_on_created_at_and_uuid ON public.groups USING btree (created_at, uuid);
--
--
--- Name: index_groups_on_modified_at; Type: INDEX; Schema: public; Owner: -
+-- Name: index_groups_on_modified_at_and_uuid; Type: INDEX; Schema: public; Owner: -
--
-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 public.groups USING btree (modified_at DESC, uuid);
+CREATE INDEX index_groups_on_modified_at_and_uuid ON public.groups USING btree (modified_at, uuid);
--
--
--- Name: index_links_on_created_at; Type: INDEX; Schema: public; Owner: -
+-- Name: index_links_on_created_at_and_uuid; Type: INDEX; Schema: public; Owner: -
--
-CREATE INDEX index_links_on_created_at ON public.links USING btree (created_at);
+CREATE INDEX index_links_on_created_at_and_uuid ON public.links USING btree (created_at, uuid);
--
--
--- Name: index_links_on_modified_at; Type: INDEX; Schema: public; Owner: -
+-- Name: index_links_on_modified_at_and_uuid; Type: INDEX; Schema: public; Owner: -
--
-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 public.links USING btree (modified_at DESC, uuid);
+CREATE INDEX index_links_on_modified_at_and_uuid ON public.links USING btree (modified_at, uuid);
--
--
--- Name: index_logs_on_created_at; Type: INDEX; Schema: public; Owner: -
+-- Name: index_logs_on_created_at_and_uuid; Type: INDEX; Schema: public; Owner: -
--
-CREATE INDEX index_logs_on_created_at ON public.logs USING btree (created_at);
+CREATE INDEX index_logs_on_created_at_and_uuid ON public.logs USING btree (created_at, uuid);
--
--
--- Name: index_logs_on_modified_at; Type: INDEX; Schema: public; Owner: -
+-- Name: index_logs_on_modified_at_and_uuid; Type: INDEX; Schema: public; Owner: -
--
-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 public.logs USING btree (modified_at DESC, uuid);
+CREATE INDEX index_logs_on_modified_at_and_uuid ON public.logs USING btree (modified_at, uuid);
--
--
--- Name: index_repositories_on_modified_at_uuid; Type: INDEX; Schema: public; Owner: -
+-- Name: index_repositories_on_created_at_and_uuid; Type: INDEX; Schema: public; Owner: -
--
-CREATE INDEX index_repositories_on_modified_at_uuid ON public.repositories USING btree (modified_at DESC, uuid);
+CREATE INDEX index_repositories_on_created_at_and_uuid ON public.repositories USING btree (created_at, uuid);
+
+
+--
+-- Name: index_repositories_on_modified_at_and_uuid; Type: INDEX; Schema: public; Owner: -
+--
+
+CREATE INDEX index_repositories_on_modified_at_and_uuid ON public.repositories USING btree (modified_at, uuid);
--
--
--- Name: index_users_on_created_at; Type: INDEX; Schema: public; Owner: -
+-- Name: index_users_on_created_at_and_uuid; Type: INDEX; Schema: public; Owner: -
--
-CREATE INDEX index_users_on_created_at ON public.users USING btree (created_at);
+CREATE INDEX index_users_on_created_at_and_uuid ON public.users USING btree (created_at, uuid);
--
--
--- Name: index_users_on_modified_at; Type: INDEX; Schema: public; Owner: -
---
-
-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: -
+-- Name: index_users_on_modified_at_and_uuid; Type: INDEX; Schema: public; Owner: -
--
-CREATE INDEX index_users_on_modified_at_uuid ON public.users USING btree (modified_at DESC, uuid);
+CREATE INDEX index_users_on_modified_at_and_uuid ON public.users USING btree (modified_at, uuid);
--
CREATE UNIQUE INDEX index_users_on_uuid ON public.users USING btree (uuid);
+--
+-- Name: index_virtual_machines_on_created_at_and_uuid; Type: INDEX; Schema: public; Owner: -
+--
+
+CREATE INDEX index_virtual_machines_on_created_at_and_uuid ON public.virtual_machines USING btree (created_at, uuid);
+
+
--
-- Name: index_virtual_machines_on_hostname; Type: INDEX; Schema: public; Owner: -
--
--
--- Name: index_virtual_machines_on_modified_at_uuid; Type: INDEX; Schema: public; Owner: -
+-- Name: index_virtual_machines_on_modified_at_and_uuid; Type: INDEX; Schema: public; Owner: -
--
-CREATE INDEX index_virtual_machines_on_modified_at_uuid ON public.virtual_machines USING btree (modified_at DESC, uuid);
+CREATE INDEX index_virtual_machines_on_modified_at_and_uuid ON public.virtual_machines USING btree (modified_at, uuid);
--
--
--- Name: index_workflows_on_modified_at_uuid; Type: INDEX; Schema: public; Owner: -
+-- Name: index_workflows_on_created_at_and_uuid; Type: INDEX; Schema: public; Owner: -
+--
+
+CREATE INDEX index_workflows_on_created_at_and_uuid ON public.workflows USING btree (created_at, uuid);
+
+
+--
+-- Name: index_workflows_on_modified_at_and_uuid; Type: INDEX; Schema: public; Owner: -
--
-CREATE INDEX index_workflows_on_modified_at_uuid ON public.workflows USING btree (modified_at DESC, uuid);
+CREATE INDEX index_workflows_on_modified_at_and_uuid ON public.workflows USING btree (modified_at, uuid);
--
('20211027154300'),
('20220224203102'),
('20220301155729'),
-('20220303204419');
+('20220303204419'),
+('20220401153101');
cancelled_at: ~
cancelled_by_user_uuid: ~
cancelled_by_client_uuid: ~
- created_at: <%= 3.minute.ago.to_s(:db) %>
- started_at: <%= 3.minute.ago.to_s(:db) %>
+ created_at: <%= 2.7.minute.ago.to_s(:db) %>
+ started_at: <%= 2.7.minute.ago.to_s(:db) %>
finished_at: ~
script: hash
repository: active/foo
state: Ready
uuid: zzzzz-d1hrv-1yfj6xkidf2muk3
owner_uuid: zzzzz-tpzed-xurymjxw79nv3jz
- created_at: <%= 3.1.minute.ago.to_s(:db) %>
+ created_at: <%= 2.9.minute.ago.to_s(:db) %>
components:
foo:
script: foo
# Helps test that clients cope with funny-shaped components.
# For an example, see #3321.
uuid: zzzzz-d1hrv-1yfj61234abcdk4
- created_at: <%= 2.minute.ago.to_s(:db) %>
+ created_at: <%= 4.minute.ago.to_s(:db) %>
owner_uuid: zzzzz-tpzed-xurymjxw79nv3jz
modified_by_client_uuid: zzzzz-ozdt8-brczlopd8u8d0jr
modified_by_user_uuid: zzzzz-tpzed-xurymjxw79nv3jz
state: Ready
uuid: zzzzz-d1hrv-1yfj61234abcdk3
owner_uuid: zzzzz-tpzed-xurymjxw79nv3jz
- created_at: <%= 3.1.minute.ago.to_s(:db) %>
+ created_at: <%= 3.2.minute.ago.to_s(:db) %>
components:
part-one:
script_parameters:
uuid: zzzzz-d1hrv-1yfj6dcba4321k3
pipeline_template_uuid: zzzzz-p5p6p-aox0k0ofxrystgw
owner_uuid: zzzzz-tpzed-xurymjxw79nv3jz
- created_at: <%= 3.1.minute.ago.to_s(:db) %>
+ created_at: <%= 3.3.minute.ago.to_s(:db) %>
components:
part-one:
script_parameters:
uuid: zzzzz-d1hrv-ri9dvgkgqs9y09j
owner_uuid: zzzzz-tpzed-0fusedrivertest
pipeline_template_uuid: zzzzz-p5p6p-vq4wuvy84xvaq2r
- created_at: 2014-09-15 12:00:00
+ created_at: 2014-09-16 12:00:00
name: "pipeline instance owned by FUSE"
components:
foo:
uuid: zzzzz-d1hrv-scarxiyajtshq3l
owner_uuid: zzzzz-j7d0g-0000ownedbyfuse
pipeline_template_uuid: zzzzz-p5p6p-vq4wuvy84xvaq2r
- created_at: 2014-09-15 12:00:00
+ created_at: 2014-09-17 12:00:00
name: "pipeline instance in FUSE project"
components:
foo:
state: Complete
uuid: zzzzz-d1hrv-ju5ghi0i9z2kqc6
owner_uuid: zzzzz-j7d0g-v955i6s2oi1cbso
- created_at: 2014-09-15 12:00:00
+ created_at: 2014-09-18 12:00:00
components:
foo:
script: foo
state: Complete
uuid: zzzzz-d1hrv-lihrbd0i9z2kqc6
owner_uuid: zzzzz-tpzed-xurymjxw79nv3jz
- created_at: 2014-09-15 12:00:00
+ created_at: 2014-09-19 12:00:00
components:
foo:
script: foo
name: Pipeline in public project with other objects elsewhere
pipeline_template_uuid: zzzzz-p5p6p-aox0k0ofxrystgw
state: Complete
- created_at: 2014-09-15 12:00:00
+ created_at: 2014-09-20 12:00:00
components:
foo:
script: foo
name: Pipeline in New state in publicly accessible project
pipeline_template_uuid: zzzzz-p5p6p-tmpltpublicproj
state: New
- created_at: 2014-09-15 12:00:00
+ created_at: 2014-09-21 12:00:00
components:
foo:
script: foo
name: Pipeline in New state in public project with objects elsewhere
pipeline_template_uuid: zzzzz-p5p6p-aox0k0ofxrystgw
state: New
- created_at: 2014-09-15 12:00:00
+ created_at: 2014-09-22 12:00:00
components:
foo:
script: foo
name: Pipeline in public project in New state with file type data class with objects elsewhere
pipeline_template_uuid: zzzzz-p5p6p-aox0k0ofxrystgw
state: New
- created_at: 2014-09-15 12:00:00
+ created_at: 2014-09-23 12:00:00
components:
foo:
script: foo
name: running_with_job
uuid: zzzzz-d1hrv-runningpipeline
owner_uuid: zzzzz-tpzed-xurymjxw79nv3jz
- created_at: <%= 3.1.minute.ago.to_s(:db) %>
- started_at: <%= 3.1.minute.ago.to_s(:db) %>
+ created_at: <%= 2.8.minute.ago.to_s(:db) %>
+ started_at: <%= 2.8.minute.ago.to_s(:db) %>
state: RunningOnServer
components:
foo:
uuid: zzzzz-d1hrv-twodonepipeline
owner_uuid: zzzzz-tpzed-xurymjxw79nv3jz
state: Complete
- created_at: <%= 3.minute.ago.to_s(:db) %>
+ created_at: <%= 2.5.minute.ago.to_s(:db) %>
started_at: <%= 2.minute.ago.to_s(:db) %>
finished_at: <%= 1.minute.ago.to_s(:db) %>
components:
controller: 'logs',
}
assert_response :success
- assert_equal('logs.event_type asc, logs.modified_at desc, logs.uuid',
+ assert_equal('logs.event_type asc, logs.modified_at desc, logs.uuid desc',
assigns(:objects).order_values.join(', '))
end
controller: 'logs',
}
assert_response :success
- assert_equal('logs.modified_at asc, logs.uuid',
+ assert_equal('logs.modified_at asc, logs.uuid desc',
assigns(:objects).order_values.join(', '))
end
controller: 'logs',
}
assert_response :success
- assert_equal('logs.modified_at asc, logs.event_type desc, logs.uuid',
+ assert_equal('logs.modified_at asc, logs.event_type desc, logs.uuid desc',
assigns(:objects).order_values.join(', '))
end
# Should be able to read links directly too
get "/arvados/v1/links/#{can_read_uuid}",
- params: {},
headers: auth(:active)
assert_response :success
+ ### Create some objects of different types (other than projects)
+ ### inside a subproject inside the shared project, and share those
+ ### individual objects with a 3rd user ("spectator").
+ post '/arvados/v1/groups',
+ params: {
+ group: {
+ owner_uuid: groups(:public).uuid,
+ name: 'permission test subproject',
+ group_class: 'project',
+ },
+ },
+ headers: auth(:admin)
+ assert_response :success
+ subproject_uuid = json_response['uuid']
+
+ test_types = ['collection', 'workflow', 'container_request']
+ test_type_create_attrs = {
+ 'container_request' => {
+ 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},
+ },
+ }
+
+ test_object = {}
+ test_object_perm_link = {}
+ test_types.each do |test_type|
+ post "/arvados/v1/#{test_type}s",
+ params: {
+ test_type.to_sym => {
+ owner_uuid: subproject_uuid,
+ name: "permission test #{test_type} in subproject",
+ }.merge(test_type_create_attrs[test_type] || {}).to_json,
+ },
+ headers: auth(:admin)
+ assert_response :success
+ test_object[test_type] = json_response
+
+ post '/arvados/v1/links',
+ params: {
+ link: {
+ tail_uuid: users(:spectator).uuid,
+ link_class: 'permission',
+ name: 'can_read',
+ head_uuid: test_object[test_type]['uuid'],
+ }
+ },
+ headers: auth(:admin)
+ assert_response :success
+ test_object_perm_link[test_type] = json_response
+ end
+
+ # The "active-can_manage-project" permission should cause the
+ # "spectator-can_read-object" links to be visible to the "active"
+ # user.
+ test_types.each do |test_type|
+ get "/arvados/v1/permissions/#{test_object[test_type]['uuid']}",
+ headers: auth(:active)
+ assert_response :success
+ perm_uuids = json_response['items'].map { |item| item['uuid'] }
+ assert_includes perm_uuids, test_object_perm_link[test_type]['uuid'], "can_read_uuid not found"
+
+ get "/arvados/v1/links/#{test_object_perm_link[test_type]['uuid']}",
+ headers: auth(:active)
+ assert_response :success
+
+ [
+ ['head_uuid', '=', test_object[test_type]['uuid']],
+ ['head_uuid', 'in', [test_object[test_type]['uuid']]],
+ ['head_uuid', 'in', [users(:admin).uuid, test_object[test_type]['uuid']]],
+ ].each do |filter|
+ get "/arvados/v1/links",
+ params: {
+ filters: ([['link_class', '=', 'permission'], filter]).to_json,
+ },
+ headers: auth(:active)
+ assert_response :success
+ assert_not_empty json_response['items'], "could not find can_read link using index with filter #{filter}"
+ assert_equal test_object_perm_link[test_type]['uuid'], json_response['items'][0]['uuid']
+ end
+
+ # The "spectator-can_read-object" link should be visible to the
+ # subject user ("spectator") in a filter query, even without
+ # can_manage permission on the target object.
+ [
+ ['tail_uuid', '=', users(:spectator).uuid],
+ ].each do |filter|
+ get "/arvados/v1/links",
+ params: {
+ filters: ([['link_class', '=', 'permission'], filter]).to_json,
+ },
+ headers: auth(:spectator)
+ assert_response :success
+ perm_uuids = json_response['items'].map { |item| item['uuid'] }
+ assert_includes perm_uuids, test_object_perm_link[test_type]['uuid'], "could not find can_read link using index with filter #{filter}"
+ end
+ end
+
### Now delete the can_manage link
delete "/arvados/v1/links/#{can_manage_uuid}",
- params: nil,
headers: auth(:active)
assert_response :success
# Should not be able read these permission links again
- get "/arvados/v1/permissions/#{groups(:public).uuid}",
- params: nil,
+ test_types.each do |test_type|
+ get "/arvados/v1/permissions/#{groups(:public).uuid}",
+ headers: auth(:active)
+ assert_response 404
+
+ get "/arvados/v1/permissions/#{test_object[test_type]['uuid']}",
+ headers: auth(:active)
+ assert_response 404
+
+ get "/arvados/v1/links",
+ params: {
+ filters: [["link_class", "=", "permission"], ["head_uuid", "=", groups(:public).uuid]].to_json
+ },
+ headers: auth(:active)
+ assert_response :success
+ assert_equal [], json_response['items']
+
+ [
+ ['head_uuid', '=', test_object[test_type]['uuid']],
+ ['head_uuid', 'in', [users(:admin).uuid, test_object[test_type]['uuid']]],
+ ['head_uuid', 'in', []],
+ ].each do |filter|
+ get "/arvados/v1/links",
+ params: {
+ :filters => [["link_class", "=", "permission"], filter].to_json
+ },
+ headers: auth(:active)
+ assert_response :success
+ assert_equal [], json_response['items']
+ end
+
+ # Should not be able to read links directly either
+ get "/arvados/v1/links/#{can_read_uuid}",
+ headers: auth(:active)
+ assert_response 404
+
+ test_types.each do |test_type|
+ get "/arvados/v1/links/#{test_object_perm_link[test_type]['uuid']}",
+ headers: auth(:active)
+ assert_response 404
+ end
+ end
+
+ ### Create a collection, and share it with a direct permission
+ ### link (as opposed to sharing its parent project)
+ post "/arvados/v1/collections",
+ params: {
+ collection: {
+ name: 'permission test',
+ }
+ },
+ headers: auth(:admin)
+ assert_response :success
+ collection_uuid = json_response['uuid']
+ post "/arvados/v1/links",
+ params: {
+ link: {
+ tail_uuid: users(:spectator).uuid,
+ link_class: 'permission',
+ name: 'can_read',
+ head_uuid: collection_uuid,
+ properties: {}
+ }
+ },
+ headers: auth(:admin)
+ assert_response :success
+ can_read_collection_uuid = json_response['uuid']
+
+ # Should not be able read the permission link via permissions API,
+ # because permission is only can_read, not can_manage
+ get "/arvados/v1/permissions/#{collection_uuid}",
headers: auth(:active)
assert_response 404
- get "/arvados/v1/links",
- params: {
- :filters => [["link_class", "=", "permission"], ["head_uuid", "=", groups(:public).uuid]].to_json
- },
+ # Should not be able to read the permission link directly, for
+ # same reason
+ get "/arvados/v1/links/#{can_read_collection_uuid}",
headers: auth(:active)
+ assert_response 404
+
+ ### Now add a can_manage link
+ post "/arvados/v1/links",
+ params: {
+ link: {
+ tail_uuid: users(:active).uuid,
+ link_class: 'permission',
+ name: 'can_manage',
+ head_uuid: collection_uuid,
+ properties: {}
+ }
+ },
+ headers: auth(:admin)
assert_response :success
- assert_equal [], json_response['items']
+ can_manage_collection_uuid = json_response['uuid']
- # Should not be able to read links directly either
- get "/arvados/v1/links/#{can_read_uuid}",
- params: {},
+ # Should be able read both permission links via permissions API
+ get "/arvados/v1/permissions/#{collection_uuid}",
headers: auth(:active)
- assert_response 404
+ assert_response :success
+ perm_uuids = json_response['items'].map { |item| item['uuid'] }
+ assert_includes perm_uuids, can_read_collection_uuid, "can_read_uuid not found"
+ assert_includes perm_uuids, can_manage_collection_uuid, "can_manage_uuid not found"
+
+ # Should be able to read both permission links directly
+ [can_read_collection_uuid, can_manage_collection_uuid].each do |uuid|
+ get "/arvados/v1/links/#{uuid}",
+ headers: auth(:active)
+ assert_response :success
+ end
end
test "get_permissions returns 404 for nonexistent uuid" do
headers: auth(:admin)
assert_response :success
uuids = json_response['items'].collect { |i| i['uuid'] }
- assert_equal uuids, uuids.sort
+ assert_equal uuids, uuids.sort.reverse
end
def assert_link_classes_ascend(current_class, prev_class)
end
end
- test "Having preemptible_instances=true create a committed child container request and verify the scheduling parameter of its container" do
+ test "AlwaysUsePreemptibleInstances makes child containers preemptible" do
+ Rails.configuration.Containers.AlwaysUsePreemptibleInstances = true
common_attrs = {cwd: "test",
priority: 1,
command: ["echo", "hello"],
self.collection.update()
new_collection_record = self.collection.api_response()
else:
+ # If there's too many prefetch threads and you
+ # max out the CPU, delivering data to the FUSE
+ # layer actually ends up being slower.
+ # Experimentally, capping 7 threads seems to
+ # be a sweet spot.
+ get_threads = min(max((self.api.keep.block_cache.cache_max // (64 * 1024 * 1024)) - 1, 1), 7)
# Create a new collection object
if uuid_pattern.match(self.collection_locator):
coll_reader = arvados.collection.Collection(
self.collection_locator, self.api, self.api.keep,
- num_retries=self.num_retries)
+ num_retries=self.num_retries,
+ get_threads=get_threads)
else:
coll_reader = arvados.collection.CollectionReader(
self.collection_locator, self.api, self.api.keep,
- num_retries=self.num_retries)
+ num_retries=self.num_retries,
+ get_threads=get_threads)
new_collection_record = coll_reader.api_response() or {}
# If the Collection only exists in Keep, there will be no API
# response. Fill in the fields we need.
class MagicDirApiError(FuseMagicTest):
def setUp(self):
api = mock.MagicMock()
+ api.keep.block_cache = mock.MagicMock(cache_max=1)
super(MagicDirApiError, self).setUp(api=api)
api.collections().get().execute.side_effect = iter([
Exception('API fail'),
WithField("collection_file_path", filepath)
props["collection_uuid"] = collection.UUID
props["collection_file_path"] = filepath
+ // h.determineCollection populates the collection_uuid prop with the PDH, if
+ // this collection is being accessed via PDH. In that case, blank the
+ // collection_uuid field so that consumers of the log entries can rely on it
+ // being a UUID, or blank. The PDH remains available via the
+ // portable_data_hash property.
+ if props["collection_uuid"] == collection.PortableDataHash {
+ props["collection_uuid"] = ""
+ }
}
if r.Method == "PUT" || r.Method == "POST" {
log.Info("File upload")
//
// SPDX-License-Identifier: AGPL-3.0
-package main
+package keepproxy
import (
"context"
"errors"
- "flag"
"fmt"
"io"
"io/ioutil"
"net"
"net/http"
- "os"
- "os/signal"
"regexp"
"strings"
- "syscall"
"time"
- "git.arvados.org/arvados.git/lib/cmd"
- "git.arvados.org/arvados.git/lib/config"
+ "git.arvados.org/arvados.git/lib/service"
"git.arvados.org/arvados.git/sdk/go/arvados"
"git.arvados.org/arvados.git/sdk/go/arvadosclient"
"git.arvados.org/arvados.git/sdk/go/ctxlog"
"git.arvados.org/arvados.git/sdk/go/health"
"git.arvados.org/arvados.git/sdk/go/httpserver"
"git.arvados.org/arvados.git/sdk/go/keepclient"
- "github.com/coreos/go-systemd/daemon"
- "github.com/ghodss/yaml"
"github.com/gorilla/mux"
lru "github.com/hashicorp/golang-lru"
+ "github.com/prometheus/client_golang/prometheus"
"github.com/sirupsen/logrus"
)
-var version = "dev"
-
-var (
- listener net.Listener
- router http.Handler
-)
-
const rfc3339NanoFixed = "2006-01-02T15:04:05.000000000Z07:00"
-func configure(args []string) (*arvados.Cluster, logrus.FieldLogger, error) {
- prog := args[0]
- flags := flag.NewFlagSet(prog, flag.ContinueOnError)
-
- dumpConfig := flags.Bool("dump-config", false, "write current configuration to stdout and exit")
- getVersion := flags.Bool("version", false, "Print version information and exit.")
-
- initLogger := logrus.New()
- initLogger.Formatter = &logrus.JSONFormatter{
- TimestampFormat: rfc3339NanoFixed,
- }
- var logger logrus.FieldLogger = initLogger
-
- loader := config.NewLoader(os.Stdin, logger)
- loader.SetupFlags(flags)
- args = loader.MungeLegacyConfigArgs(logger, args[1:], "-legacy-keepproxy-config")
-
- if ok, code := cmd.ParseFlags(flags, prog, args, "", os.Stderr); !ok {
- os.Exit(code)
- } else if *getVersion {
- fmt.Printf("keepproxy %s\n", version)
- return nil, logger, nil
- }
-
- cfg, err := loader.Load()
- if err != nil {
- return nil, logger, err
- }
- cluster, err := cfg.GetCluster("")
- if err != nil {
- return nil, logger, err
- }
-
- logger = ctxlog.New(os.Stderr, cluster.SystemLogs.Format, cluster.SystemLogs.LogLevel).WithFields(logrus.Fields{
- "ClusterID": cluster.ClusterID,
- "PID": os.Getpid(),
- })
-
- if *dumpConfig {
- out, err := yaml.Marshal(cfg)
- if err != nil {
- return nil, logger, err
- }
- if _, err := os.Stdout.Write(out); err != nil {
- return nil, logger, err
- }
- return nil, logger, nil
- }
+var Command = service.Command(arvados.ServiceNameKeepproxy, newHandlerOrErrorHandler)
- return cluster, logger, nil
-}
-
-func main() {
- cluster, logger, err := configure(os.Args)
- if err != nil {
- logger.Fatal(err)
- }
- if cluster == nil {
- return
- }
-
- logger.Printf("keepproxy %s started", version)
-
- if err := run(logger, cluster); err != nil {
- logger.Fatal(err)
- }
-
- logger.Println("shutting down")
-}
-
-func run(logger logrus.FieldLogger, cluster *arvados.Cluster) error {
+func newHandlerOrErrorHandler(ctx context.Context, cluster *arvados.Cluster, token string, reg *prometheus.Registry) service.Handler {
client, err := arvados.NewClientFromConfig(cluster)
if err != nil {
- return err
+ return service.ErrorHandler(ctx, cluster, fmt.Errorf("Error setting up arvados client: %w", err))
}
- client.AuthToken = cluster.SystemRootToken
-
arv, err := arvadosclient.New(client)
if err != nil {
- return fmt.Errorf("Error setting up arvados client %v", err)
- }
-
- // If a config file is available, use the keepstores defined there
- // instead of the legacy autodiscover mechanism via the API server
- for k := range cluster.Services.Keepstore.InternalURLs {
- arv.KeepServiceURIs = append(arv.KeepServiceURIs, strings.TrimRight(k.String(), "/"))
- }
-
- if cluster.SystemLogs.LogLevel == "debug" {
- keepclient.DebugPrintf = logger.Printf
+ return service.ErrorHandler(ctx, cluster, fmt.Errorf("Error setting up arvados client: %w", err))
}
kc, err := keepclient.MakeKeepClient(arv)
if err != nil {
- return fmt.Errorf("Error setting up keep client %v", err)
+ return service.ErrorHandler(ctx, cluster, fmt.Errorf("Error setting up keep client: %w", err))
}
keepclient.RefreshServiceDiscoveryOnSIGHUP()
-
- if cluster.Collections.DefaultReplication > 0 {
- kc.Want_replicas = cluster.Collections.DefaultReplication
- }
-
- var listen arvados.URL
- for listen = range cluster.Services.Keepproxy.InternalURLs {
- break
- }
-
- var lErr error
- listener, lErr = net.Listen("tcp", listen.Host)
- if lErr != nil {
- return fmt.Errorf("listen(%s): %v", listen.Host, lErr)
- }
-
- if _, err := daemon.SdNotify(false, "READY=1"); err != nil {
- logger.Printf("Error notifying init daemon: %v", err)
- }
- logger.Println("listening at", listener.Addr())
-
- // Shut down the server gracefully (by closing the listener)
- // if SIGTERM is received.
- term := make(chan os.Signal, 1)
- go func(sig <-chan os.Signal) {
- s := <-sig
- logger.Println("caught signal:", s)
- listener.Close()
- }(term)
- signal.Notify(term, syscall.SIGTERM)
- signal.Notify(term, syscall.SIGINT)
-
- // Start serving requests.
- router, err = MakeRESTRouter(kc, time.Duration(keepclient.DefaultProxyRequestTimeout), cluster, logger)
+ router, err := newHandler(ctx, kc, time.Duration(keepclient.DefaultProxyRequestTimeout), cluster)
if err != nil {
- return err
- }
- server := http.Server{
- Handler: httpserver.AddRequestIDs(httpserver.LogRequests(router)),
- BaseContext: func(net.Listener) context.Context {
- return ctxlog.Context(context.Background(), logger)
- },
+ return service.ErrorHandler(ctx, cluster, err)
}
- return server.Serve(listener)
+ return router
}
-type TokenCacheEntry struct {
+type tokenCacheEntry struct {
expire int64
user *arvados.User
}
-type APITokenCache struct {
+type apiTokenCache struct {
tokens *lru.TwoQueueCache
expireTime int64
}
// RememberToken caches the token and set an expire time. If the
// token is already in the cache, it is not updated.
-func (cache *APITokenCache) RememberToken(token string, user *arvados.User) {
+func (cache *apiTokenCache) RememberToken(token string, user *arvados.User) {
now := time.Now().Unix()
_, ok := cache.tokens.Get(token)
if !ok {
- cache.tokens.Add(token, TokenCacheEntry{
+ cache.tokens.Add(token, tokenCacheEntry{
expire: now + cache.expireTime,
user: user,
})
// RecallToken checks if the cached token is known and still believed to be
// valid.
-func (cache *APITokenCache) RecallToken(token string) (bool, *arvados.User) {
+func (cache *apiTokenCache) RecallToken(token string) (bool, *arvados.User) {
val, ok := cache.tokens.Get(token)
if !ok {
return false, nil
}
- cacheEntry := val.(TokenCacheEntry)
+ cacheEntry := val.(tokenCacheEntry)
now := time.Now().Unix()
if now < cacheEntry.expire {
// Token is known and still valid
}
}
-// GetRemoteAddress returns a string with the remote address for the request.
-// If the X-Forwarded-For header is set and has a non-zero length, it returns a
-// string made from a comma separated list of all the remote addresses,
-// starting with the one(s) from the X-Forwarded-For header.
-func GetRemoteAddress(req *http.Request) string {
- if xff := req.Header.Get("X-Forwarded-For"); xff != "" {
- return xff + "," + req.RemoteAddr
- }
- return req.RemoteAddr
+func (h *proxyHandler) Done() <-chan struct{} {
+ return nil
+}
+
+func (h *proxyHandler) CheckHealth() error {
+ return nil
}
-func (h *proxyHandler) CheckAuthorizationHeader(req *http.Request) (pass bool, tok string, user *arvados.User) {
+func (h *proxyHandler) checkAuthorizationHeader(req *http.Request) (pass bool, tok string, user *arvados.User) {
parts := strings.SplitN(req.Header.Get("Authorization"), " ", 2)
if len(parts) < 2 || !(parts[0] == "OAuth2" || parts[0] == "Bearer") || len(parts[1]) == 0 {
return false, "", nil
op = "write"
}
- if ok, user := h.APITokenCache.RecallToken(op + ":" + tok); ok {
+ if ok, user := h.apiTokenCache.RecallToken(op + ":" + tok); ok {
// Valid in the cache, short circuit
return true, tok, user
}
}
}
if err != nil {
- ctxlog.FromContext(req.Context()).Printf("%s: CheckAuthorizationHeader error: %v", GetRemoteAddress(req), err)
+ ctxlog.FromContext(req.Context()).WithError(err).Info("checkAuthorizationHeader error")
return false, "", nil
}
}
// Success! Update cache
- h.APITokenCache.RememberToken(op+":"+tok, user)
+ h.apiTokenCache.RememberToken(op+":"+tok, user)
return true, tok, user
}
type proxyHandler struct {
http.Handler
*keepclient.KeepClient
- *APITokenCache
+ *apiTokenCache
timeout time.Duration
transport *http.Transport
- logger logrus.FieldLogger
cluster *arvados.Cluster
}
-// MakeRESTRouter returns an http.Handler that passes GET and PUT
-// requests to the appropriate handlers.
-func MakeRESTRouter(kc *keepclient.KeepClient, timeout time.Duration, cluster *arvados.Cluster, logger logrus.FieldLogger) (http.Handler, error) {
+func newHandler(ctx context.Context, kc *keepclient.KeepClient, timeout time.Duration, cluster *arvados.Cluster) (service.Handler, error) {
rest := mux.NewRouter()
transport := defaultTransport
KeepClient: kc,
timeout: timeout,
transport: &transport,
- APITokenCache: &APITokenCache{
+ apiTokenCache: &apiTokenCache{
tokens: cacheQ,
expireTime: 300,
},
- logger: logger,
cluster: cluster,
}
Prefix: "/_health/",
}).Methods("GET")
- rest.NotFoundHandler = InvalidPathHandler{}
+ rest.NotFoundHandler = invalidPathHandler{}
return h, nil
}
func (h *proxyHandler) checkLoop(resp http.ResponseWriter, req *http.Request) error {
if via := req.Header.Get("Via"); strings.Index(via, " "+viaAlias) >= 0 {
- h.logger.Printf("proxy loop detected (request has Via: %q): perhaps keepproxy is misidentified by gateway config as an external client, or its keep_services record does not have service_type=proxy?", via)
+ ctxlog.FromContext(req.Context()).Printf("proxy loop detected (request has Via: %q): perhaps keepproxy is misidentified by gateway config as an external client, or its keep_services record does not have service_type=proxy?", via)
http.Error(resp, errLoopDetected.Error(), http.StatusInternalServerError)
return errLoopDetected
}
return nil
}
-func SetCorsHeaders(resp http.ResponseWriter) {
+func setCORSHeaders(resp http.ResponseWriter) {
resp.Header().Set("Access-Control-Allow-Methods", "GET, HEAD, POST, PUT, OPTIONS")
resp.Header().Set("Access-Control-Allow-Origin", "*")
resp.Header().Set("Access-Control-Allow-Headers", "Authorization, Content-Length, Content-Type, X-Keep-Desired-Replicas")
resp.Header().Set("Access-Control-Max-Age", "86486400")
}
-type InvalidPathHandler struct{}
+type invalidPathHandler struct{}
-func (InvalidPathHandler) ServeHTTP(resp http.ResponseWriter, req *http.Request) {
- ctxlog.FromContext(req.Context()).Printf("%s: %s %s unroutable", GetRemoteAddress(req), req.Method, req.URL.Path)
+func (invalidPathHandler) ServeHTTP(resp http.ResponseWriter, req *http.Request) {
http.Error(resp, "Bad request", http.StatusBadRequest)
}
func (h *proxyHandler) Options(resp http.ResponseWriter, req *http.Request) {
- ctxlog.FromContext(req.Context()).Printf("%s: %s %s", GetRemoteAddress(req), req.Method, req.URL.Path)
- SetCorsHeaders(resp)
+ setCORSHeaders(resp)
}
var errBadAuthorizationHeader = errors.New("Missing or invalid Authorization header, or method not allowed")
if err := h.checkLoop(resp, req); err != nil {
return
}
- SetCorsHeaders(resp)
+ setCORSHeaders(resp)
resp.Header().Set("Via", req.Proto+" "+viaAlias)
locator := mux.Vars(req)["locator"]
var expectLength, responseLength int64
var proxiedURI = "-"
+ logger := ctxlog.FromContext(req.Context())
defer func() {
- h.logger.Println(GetRemoteAddress(req), req.Method, req.URL.Path, status, expectLength, responseLength, proxiedURI, err)
+ httpserver.SetResponseLogFields(req.Context(), logrus.Fields{
+ "locator": locator,
+ "expectLength": expectLength,
+ "responseLength": responseLength,
+ "proxiedURI": proxiedURI,
+ "err": err,
+ })
if status != http.StatusOK {
http.Error(resp, err.Error(), status)
}
var pass bool
var tok string
var user *arvados.User
- if pass, tok, user = h.CheckAuthorizationHeader(req); !pass {
+ if pass, tok, user = h.checkAuthorizationHeader(req); !pass {
status, err = http.StatusForbidden, errBadAuthorizationHeader
return
}
+ httpserver.SetResponseLogFields(req.Context(), logrus.Fields{
+ "userUUID": user.UUID,
+ "userFullName": user.FullName,
+ })
// Copy ArvadosClient struct and use the client's API token
arvclient := *kc.Arvados
locator = removeHint.ReplaceAllString(locator, "$1")
- if locator != "" {
- parts := strings.SplitN(locator, "+", 3)
- if len(parts) >= 2 {
- logger := h.logger
- if user != nil {
- logger = logger.WithField("user_uuid", user.UUID).
- WithField("user_full_name", user.FullName)
- }
- logger.WithField("locator", fmt.Sprintf("%s+%s", parts[0], parts[1])).Infof("Block download")
- }
- }
-
switch req.Method {
case "HEAD":
expectLength, proxiedURI, err = kc.Ask(locator)
}
if expectLength == -1 {
- h.logger.Println("Warning:", GetRemoteAddress(req), req.Method, proxiedURI, "Content-Length not provided")
+ logger.Warn("Content-Length not provided")
}
switch respErr := err.(type) {
if err := h.checkLoop(resp, req); err != nil {
return
}
- SetCorsHeaders(resp)
+ setCORSHeaders(resp)
resp.Header().Set("Via", "HTTP/1.1 "+viaAlias)
kc := h.makeKeepClient(req)
var locatorOut string = "-"
defer func() {
- h.logger.Println(GetRemoteAddress(req), req.Method, req.URL.Path, status, expectLength, kc.Want_replicas, wroteReplicas, locatorOut, err)
+ httpserver.SetResponseLogFields(req.Context(), logrus.Fields{
+ "expectLength": expectLength,
+ "wantReplicas": kc.Want_replicas,
+ "wroteReplicas": wroteReplicas,
+ "locator": strings.SplitN(locatorOut, "+A", 2)[0],
+ "err": err,
+ })
if status != http.StatusOK {
http.Error(resp, err.Error(), status)
}
var pass bool
var tok string
var user *arvados.User
- if pass, tok, user = h.CheckAuthorizationHeader(req); !pass {
+ if pass, tok, user = h.checkAuthorizationHeader(req); !pass {
err = errBadAuthorizationHeader
status = http.StatusForbidden
return
}
+ httpserver.SetResponseLogFields(req.Context(), logrus.Fields{
+ "userUUID": user.UUID,
+ "userFullName": user.FullName,
+ })
// Copy ArvadosClient struct and use the client's API token
arvclient := *kc.Arvados
locatorOut, wroteReplicas, err = kc.PutHR(locatorIn, req.Body, expectLength)
}
- if locatorOut != "" {
- parts := strings.SplitN(locatorOut, "+", 3)
- if len(parts) >= 2 {
- logger := h.logger
- if user != nil {
- logger = logger.WithField("user_uuid", user.UUID).
- WithField("user_full_name", user.FullName)
- }
- logger.WithField("locator", fmt.Sprintf("%s+%s", parts[0], parts[1])).Infof("Block upload")
- }
- }
-
// Tell the client how many successful PUTs we accomplished
resp.Header().Set(keepclient.XKeepReplicasStored, fmt.Sprintf("%d", wroteReplicas))
// Aborts on any errors
// Concatenates responses from all those keep servers and returns
func (h *proxyHandler) Index(resp http.ResponseWriter, req *http.Request) {
- SetCorsHeaders(resp)
+ setCORSHeaders(resp)
prefix := mux.Vars(req)["prefix"]
var err error
}()
kc := h.makeKeepClient(req)
- ok, token, _ := h.CheckAuthorizationHeader(req)
+ ok, token, _ := h.checkAuthorizationHeader(req)
if !ok {
status, err = http.StatusForbidden, errBadAuthorizationHeader
return
+++ /dev/null
-# Copyright (C) The Arvados Authors. All rights reserved.
-#
-# SPDX-License-Identifier: AGPL-3.0
-
-[Unit]
-Description=Arvados Keep Proxy
-Documentation=https://doc.arvados.org/
-After=network.target
-
-# systemd>=230 (debian:9) obeys StartLimitIntervalSec in the [Unit] section
-StartLimitIntervalSec=0
-
-[Service]
-Type=notify
-ExecStart=/usr/bin/keepproxy
-# Set a reasonable default for the open file limit
-LimitNOFILE=65536
-Restart=always
-RestartSec=1
-
-# systemd<=219 (centos:7, debian:8, ubuntu:trusty) obeys StartLimitInterval in the [Service] section
-StartLimitInterval=0
-
-[Install]
-WantedBy=multi-user.target
//
// SPDX-License-Identifier: AGPL-3.0
-package main
+package keepproxy
import (
"bytes"
+ "context"
"crypto/md5"
"fmt"
"io/ioutil"
"math/rand"
+ "net"
"net/http"
"net/http/httptest"
"strings"
"git.arvados.org/arvados.git/sdk/go/arvadosclient"
"git.arvados.org/arvados.git/sdk/go/arvadostest"
"git.arvados.org/arvados.git/sdk/go/ctxlog"
+ "git.arvados.org/arvados.git/sdk/go/httpserver"
"git.arvados.org/arvados.git/sdk/go/keepclient"
log "github.com/sirupsen/logrus"
var TestProxyUUID = "zzzzz-bi6l4-lrixqc4fxofbmzz"
-// Wait (up to 1 second) for keepproxy to listen on a port. This
-// avoids a race condition where we hit a "connection refused" error
-// because we start testing the proxy too soon.
-func waitForListener() {
- const (
- ms = 5
- )
- for i := 0; listener == nil && i < 10000; i += ms {
- time.Sleep(ms * time.Millisecond)
- }
- if listener == nil {
- panic("Timed out waiting for listener to start")
- }
-}
-
-func closeListener() {
- if listener != nil {
- listener.Close()
- }
-}
-
func (s *ServerRequiredSuite) SetUpSuite(c *C) {
arvadostest.StartKeep(2, false)
}
arvadostest.ResetEnv()
}
-func runProxy(c *C, bogusClientToken bool, loadKeepstoresFromConfig bool, kp *arvados.UploadDownloadRolePermissions) (*keepclient.KeepClient, *bytes.Buffer) {
+type testServer struct {
+ *httpserver.Server
+ proxyHandler *proxyHandler
+}
+
+func runProxy(c *C, bogusClientToken bool, loadKeepstoresFromConfig bool, kp *arvados.UploadDownloadRolePermissions) (*testServer, *keepclient.KeepClient, *bytes.Buffer) {
cfg, err := config.NewLoader(nil, ctxlog.TestLogger(c)).Load()
c.Assert(err, Equals, nil)
cluster, err := cfg.GetCluster("")
cluster.Collections.KeepproxyPermission = *kp
}
- listener = nil
logbuf := &bytes.Buffer{}
logger := log.New()
logger.Out = logbuf
- go func() {
- run(logger, cluster)
- defer closeListener()
- }()
- waitForListener()
+ ctx := ctxlog.Context(context.Background(), logger)
+
+ handler := newHandlerOrErrorHandler(ctx, cluster, cluster.SystemRootToken, nil).(*proxyHandler)
+ srv := &testServer{
+ Server: &httpserver.Server{
+ Server: http.Server{
+ BaseContext: func(net.Listener) context.Context { return ctx },
+ Handler: httpserver.AddRequestIDs(
+ httpserver.LogRequests(handler)),
+ },
+ Addr: ":",
+ },
+ proxyHandler: handler,
+ }
+ err = srv.Start()
+ c.Assert(err, IsNil)
client := arvados.NewClientFromEnv()
arv, err := arvadosclient.New(client)
- c.Assert(err, Equals, nil)
+ c.Assert(err, IsNil)
if bogusClientToken {
arv.ApiToken = "bogus-token"
}
kc := keepclient.New(arv)
sr := map[string]string{
- TestProxyUUID: "http://" + listener.Addr().String(),
+ TestProxyUUID: "http://" + srv.Addr,
}
kc.SetServiceRoots(sr, sr, sr)
kc.Arvados.External = true
-
- return kc, logbuf
+ return srv, kc, logbuf
}
func (s *ServerRequiredSuite) TestResponseViaHeader(c *C) {
- runProxy(c, false, false, nil)
- defer closeListener()
+ srv, _, _ := runProxy(c, false, false, nil)
+ defer srv.Close()
req, err := http.NewRequest("POST",
- "http://"+listener.Addr().String()+"/",
+ "http://"+srv.Addr+"/",
strings.NewReader("TestViaHeader"))
c.Assert(err, Equals, nil)
req.Header.Add("Authorization", "OAuth2 "+arvadostest.ActiveToken)
resp.Body.Close()
req, err = http.NewRequest("GET",
- "http://"+listener.Addr().String()+"/"+string(locator),
+ "http://"+srv.Addr+"/"+string(locator),
nil)
c.Assert(err, Equals, nil)
resp, err = (&http.Client{}).Do(req)
}
func (s *ServerRequiredSuite) TestLoopDetection(c *C) {
- kc, _ := runProxy(c, false, false, nil)
- defer closeListener()
+ srv, kc, _ := runProxy(c, false, false, nil)
+ defer srv.Close()
sr := map[string]string{
- TestProxyUUID: "http://" + listener.Addr().String(),
+ TestProxyUUID: "http://" + srv.Addr,
}
- router.(*proxyHandler).KeepClient.SetServiceRoots(sr, sr, sr)
+ srv.proxyHandler.KeepClient.SetServiceRoots(sr, sr, sr)
content := []byte("TestLoopDetection")
_, _, err := kc.PutB(content)
}
func (s *ServerRequiredSuite) TestStorageClassesHeader(c *C) {
- kc, _ := runProxy(c, false, false, nil)
- defer closeListener()
+ srv, kc, _ := runProxy(c, false, false, nil)
+ defer srv.Close()
// Set up fake keepstore to record request headers
var hdr http.Header
sr := map[string]string{
TestProxyUUID: ts.URL,
}
- router.(*proxyHandler).KeepClient.SetServiceRoots(sr, sr, sr)
+ srv.proxyHandler.KeepClient.SetServiceRoots(sr, sr, sr)
// Set up client to ask for storage classes to keepproxy
kc.StorageClasses = []string{"secure"}
}
func (s *ServerRequiredSuite) TestStorageClassesConfirmedHeader(c *C) {
- runProxy(c, false, false, nil)
- defer closeListener()
+ srv, _, _ := runProxy(c, false, false, nil)
+ defer srv.Close()
content := []byte("foo")
hash := fmt.Sprintf("%x", md5.Sum(content))
client := &http.Client{}
req, err := http.NewRequest("PUT",
- fmt.Sprintf("http://%s/%s", listener.Addr().String(), hash),
+ fmt.Sprintf("http://%s/%s", srv.Addr, hash),
bytes.NewReader(content))
c.Assert(err, IsNil)
req.Header.Set("X-Keep-Storage-Classes", "default")
}
func (s *ServerRequiredSuite) TestDesiredReplicas(c *C) {
- kc, _ := runProxy(c, false, false, nil)
- defer closeListener()
+ srv, kc, _ := runProxy(c, false, false, nil)
+ defer srv.Close()
content := []byte("TestDesiredReplicas")
hash := fmt.Sprintf("%x", md5.Sum(content))
}
func (s *ServerRequiredSuite) TestPutWrongContentLength(c *C) {
- kc, _ := runProxy(c, false, false, nil)
- defer closeListener()
+ srv, kc, _ := runProxy(c, false, false, nil)
+ defer srv.Close()
content := []byte("TestPutWrongContentLength")
hash := fmt.Sprintf("%x", md5.Sum(content))
// fixes the invalid Content-Length header. In order to test
// our server behavior, we have to call the handler directly
// using an httptest.ResponseRecorder.
- rtr, err := MakeRESTRouter(kc, 10*time.Second, &arvados.Cluster{}, log.New())
+ rtr, err := newHandler(context.Background(), kc, 10*time.Second, &arvados.Cluster{})
c.Assert(err, check.IsNil)
type testcase struct {
{"abcdef", http.StatusLengthRequired},
} {
req, err := http.NewRequest("PUT",
- fmt.Sprintf("http://%s/%s+%d", listener.Addr().String(), hash, len(content)),
+ fmt.Sprintf("http://%s/%s+%d", srv.Addr, hash, len(content)),
bytes.NewReader(content))
c.Assert(err, IsNil)
req.Header.Set("Content-Length", t.sendLength)
}
func (s *ServerRequiredSuite) TestManyFailedPuts(c *C) {
- kc, _ := runProxy(c, false, false, nil)
- defer closeListener()
- router.(*proxyHandler).timeout = time.Nanosecond
+ srv, kc, _ := runProxy(c, false, false, nil)
+ defer srv.Close()
+ srv.proxyHandler.timeout = time.Nanosecond
buf := make([]byte, 1<<20)
rand.Read(buf)
}
func (s *ServerRequiredSuite) TestPutAskGet(c *C) {
- kc, logbuf := runProxy(c, false, false, nil)
- defer closeListener()
+ srv, kc, logbuf := runProxy(c, false, false, nil)
+ defer srv.Close()
hash := fmt.Sprintf("%x", md5.Sum([]byte("foo")))
var hash2 string
c.Check(err, Equals, nil)
c.Log("Finished PutB (expected success)")
- c.Check(logbuf.String(), Matches, `(?ms).*msg="Block upload" locator=acbd18db4cc2f85cedef654fccc4a4d8\+3 user_full_name="TestCase Administrator" user_uuid=zzzzz-tpzed-d9tiejq69daie8f.*`)
+ c.Check(logbuf.String(), Matches, `(?ms).* locator=acbd18db4cc2f85cedef654fccc4a4d8\+3.* userFullName="TestCase Administrator".* userUUID=zzzzz-tpzed-d9tiejq69daie8f.*`)
logbuf.Reset()
}
c.Assert(err, Equals, nil)
c.Check(blocklen, Equals, int64(3))
c.Log("Finished Ask (expected success)")
- c.Check(logbuf.String(), Matches, `(?ms).*msg="Block download" locator=acbd18db4cc2f85cedef654fccc4a4d8\+3 user_full_name="TestCase Administrator" user_uuid=zzzzz-tpzed-d9tiejq69daie8f.*`)
+ c.Check(logbuf.String(), Matches, `(?ms).* locator=acbd18db4cc2f85cedef654fccc4a4d8\+3.* userFullName="TestCase Administrator".* userUUID=zzzzz-tpzed-d9tiejq69daie8f.*`)
logbuf.Reset()
}
c.Check(all, DeepEquals, []byte("foo"))
c.Check(blocklen, Equals, int64(3))
c.Log("Finished Get (expected success)")
- c.Check(logbuf.String(), Matches, `(?ms).*msg="Block download" locator=acbd18db4cc2f85cedef654fccc4a4d8\+3 user_full_name="TestCase Administrator" user_uuid=zzzzz-tpzed-d9tiejq69daie8f.*`)
+ c.Check(logbuf.String(), Matches, `(?ms).* locator=acbd18db4cc2f85cedef654fccc4a4d8\+3.* userFullName="TestCase Administrator".* userUUID=zzzzz-tpzed-d9tiejq69daie8f.*`)
logbuf.Reset()
}
}
func (s *ServerRequiredSuite) TestPutAskGetForbidden(c *C) {
- kc, _ := runProxy(c, true, false, nil)
- defer closeListener()
+ srv, kc, _ := runProxy(c, true, false, nil)
+ defer srv.Close()
hash := fmt.Sprintf("%x+3", md5.Sum([]byte("bar")))
kp.User = perm
}
- kc, logbuf := runProxy(c, false, false, &kp)
- defer closeListener()
+ srv, kc, logbuf := runProxy(c, false, false, &kp)
+ defer srv.Close()
if admin {
kc.Arvados.ApiToken = arvadostest.AdminToken
} else {
c.Check(err, Equals, nil)
c.Log("Finished PutB (expected success)")
if admin {
- c.Check(logbuf.String(), Matches, `(?ms).*msg="Block upload" locator=acbd18db4cc2f85cedef654fccc4a4d8\+3 user_full_name="TestCase Administrator" user_uuid=zzzzz-tpzed-d9tiejq69daie8f.*`)
+ c.Check(logbuf.String(), Matches, `(?ms).* locator=acbd18db4cc2f85cedef654fccc4a4d8\+3.* userFullName="TestCase Administrator".* userUUID=zzzzz-tpzed-d9tiejq69daie8f.*`)
} else {
- c.Check(logbuf.String(), Matches, `(?ms).*msg="Block upload" locator=acbd18db4cc2f85cedef654fccc4a4d8\+3 user_full_name="Active User" user_uuid=zzzzz-tpzed-xurymjxw79nv3jz.*`)
+ c.Check(logbuf.String(), Matches, `(?ms).* locator=acbd18db4cc2f85cedef654fccc4a4d8\+3.* userFullName="Active User".* userUUID=zzzzz-tpzed-xurymjxw79nv3jz.*`)
}
} else {
c.Check(hash2, Equals, "")
c.Check(blocklen, Equals, int64(3))
c.Log("Finished Get (expected success)")
if admin {
- c.Check(logbuf.String(), Matches, `(?ms).*msg="Block download" locator=acbd18db4cc2f85cedef654fccc4a4d8\+3 user_full_name="TestCase Administrator" user_uuid=zzzzz-tpzed-d9tiejq69daie8f.*`)
+ c.Check(logbuf.String(), Matches, `(?ms).* locator=acbd18db4cc2f85cedef654fccc4a4d8\+3.* userFullName="TestCase Administrator".* userUUID=zzzzz-tpzed-d9tiejq69daie8f.*`)
} else {
- c.Check(logbuf.String(), Matches, `(?ms).*msg="Block download" locator=acbd18db4cc2f85cedef654fccc4a4d8\+3 user_full_name="Active User" user_uuid=zzzzz-tpzed-xurymjxw79nv3jz.*`)
+ c.Check(logbuf.String(), Matches, `(?ms).* locator=acbd18db4cc2f85cedef654fccc4a4d8\+3.* userFullName="Active User".* userUUID=zzzzz-tpzed-xurymjxw79nv3jz.*`)
}
} else {
c.Check(err, FitsTypeOf, &keepclient.ErrNotFound{})
}
func (s *ServerRequiredSuite) TestCorsHeaders(c *C) {
- runProxy(c, false, false, nil)
- defer closeListener()
+ srv, _, _ := runProxy(c, false, false, nil)
+ defer srv.Close()
{
client := http.Client{}
req, err := http.NewRequest("OPTIONS",
- fmt.Sprintf("http://%s/%x+3", listener.Addr().String(), md5.Sum([]byte("foo"))),
+ fmt.Sprintf("http://%s/%x+3", srv.Addr, md5.Sum([]byte("foo"))),
nil)
c.Assert(err, IsNil)
req.Header.Add("Access-Control-Request-Method", "PUT")
}
{
- resp, err := http.Get(
- fmt.Sprintf("http://%s/%x+3", listener.Addr().String(), md5.Sum([]byte("foo"))))
+ resp, err := http.Get(fmt.Sprintf("http://%s/%x+3", srv.Addr, md5.Sum([]byte("foo"))))
c.Check(err, Equals, nil)
c.Check(resp.Header.Get("Access-Control-Allow-Headers"), Equals, "Authorization, Content-Length, Content-Type, X-Keep-Desired-Replicas")
c.Check(resp.Header.Get("Access-Control-Allow-Origin"), Equals, "*")
}
func (s *ServerRequiredSuite) TestPostWithoutHash(c *C) {
- runProxy(c, false, false, nil)
- defer closeListener()
+ srv, _, _ := runProxy(c, false, false, nil)
+ defer srv.Close()
{
client := http.Client{}
req, err := http.NewRequest("POST",
- "http://"+listener.Addr().String()+"/",
+ "http://"+srv.Addr+"/",
strings.NewReader("qux"))
c.Check(err, IsNil)
req.Header.Add("Authorization", "OAuth2 "+arvadostest.ActiveToken)
}
func getIndexWorker(c *C, useConfig bool) {
- kc, _ := runProxy(c, false, useConfig, nil)
- defer closeListener()
+ srv, kc, _ := runProxy(c, false, useConfig, nil)
+ defer srv.Close()
// Put "index-data" blocks
data := []byte("index-data")
}
func (s *ServerRequiredSuite) TestCollectionSharingToken(c *C) {
- kc, _ := runProxy(c, false, false, nil)
- defer closeListener()
+ srv, kc, _ := runProxy(c, false, false, nil)
+ defer srv.Close()
hash, _, err := kc.PutB([]byte("shareddata"))
c.Check(err, IsNil)
kc.Arvados.ApiToken = arvadostest.FooCollectionSharingToken
}
func (s *ServerRequiredSuite) TestPutAskGetInvalidToken(c *C) {
- kc, _ := runProxy(c, false, false, nil)
- defer closeListener()
+ srv, kc, _ := runProxy(c, false, false, nil)
+ defer srv.Close()
// Put a test block
hash, rep, err := kc.PutB([]byte("foo"))
}
func (s *ServerRequiredSuite) TestAskGetKeepProxyConnectionError(c *C) {
- kc, _ := runProxy(c, false, false, nil)
- defer closeListener()
+ srv, kc, _ := runProxy(c, false, false, nil)
+ defer srv.Close()
// Point keepproxy at a non-existent keepstore
locals := map[string]string{
TestProxyUUID: "http://localhost:12345",
}
- router.(*proxyHandler).KeepClient.SetServiceRoots(locals, nil, nil)
+ srv.proxyHandler.KeepClient.SetServiceRoots(locals, nil, nil)
// Ask should result in temporary bad gateway error
hash := fmt.Sprintf("%x", md5.Sum([]byte("foo")))
}
func (s *NoKeepServerSuite) TestAskGetNoKeepServerError(c *C) {
- kc, _ := runProxy(c, false, false, nil)
- defer closeListener()
+ srv, kc, _ := runProxy(c, false, false, nil)
+ defer srv.Close()
hash := fmt.Sprintf("%x", md5.Sum([]byte("foo")))
for _, f := range []func() error{
}
func (s *ServerRequiredSuite) TestPing(c *C) {
- kc, _ := runProxy(c, false, false, nil)
- defer closeListener()
+ srv, kc, _ := runProxy(c, false, false, nil)
+ defer srv.Close()
- rtr, err := MakeRESTRouter(kc, 10*time.Second, &arvados.Cluster{ManagementToken: arvadostest.ManagementToken}, log.New())
+ rtr, err := newHandler(context.Background(), kc, 10*time.Second, &arvados.Cluster{ManagementToken: arvadostest.ManagementToken})
c.Assert(err, check.IsNil)
req, err := http.NewRequest("GET",
- "http://"+listener.Addr().String()+"/_health/ping",
+ "http://"+srv.Addr+"/_health/ping",
nil)
c.Assert(err, IsNil)
req.Header.Set("Authorization", "Bearer "+arvadostest.ManagementToken)
//
// SPDX-License-Identifier: AGPL-3.0
-package main
+package keepproxy
import (
"net/http"
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 \
# SPDX-License-Identifier: AGPL-3.0
exec 2>&1
-sleep 2
set -ex -o pipefail
. /usr/local/lib/arvbox/common.sh
. /usr/local/lib/arvbox/go-setup.sh
-flock /var/lib/gopath/gopath.lock go install "git.arvados.org/arvados.git/services/keepproxy"
-install $GOPATH/bin/keepproxy /usr/local/bin
+(cd /usr/local/bin && ln -sf arvados-server keepproxy)
if test "$1" = "--only-deps" ; then
exit
fi
-exec /usr/local/bin/keepproxy
+/usr/local/lib/arvbox/runsu.sh flock $ARVADOS_CONTAINER_PATH/cluster_config.yml.lock /usr/local/lib/arvbox/cluster-config.sh
+
+exec /usr/local/lib/arvbox/runsu.sh /usr/local/bin/keepproxy
# Networking
# WEBUI PORT
- arv.vm.network "forwarded_port", guest: 9443, host: 9443
+ arv.vm.network "forwarded_port", guest: 443, host: 9443
# WORKBENCH1
- arv.vm.network "forwarded_port", guest: 9444, host: 9444
+ arv.vm.network "forwarded_port", guest: 8805, host: 9444
# WORKBENCH2
- arv.vm.network "forwarded_port", guest: 9445, host: 9445
+ arv.vm.network "forwarded_port", guest: 443, host: 9445
# KEEPPROXY
- arv.vm.network "forwarded_port", guest: 35101, host: 35101
+ arv.vm.network "forwarded_port", guest: 8801, host: 35101
# KEEPWEB
- arv.vm.network "forwarded_port", guest: 11002, host: 11002
+ arv.vm.network "forwarded_port", guest: 8802, host: 11002
# WEBSHELL
- arv.vm.network "forwarded_port", guest: 14202, host: 14202
+ arv.vm.network "forwarded_port", guest: 8803, host: 14202
# WEBSOCKET
- arv.vm.network "forwarded_port", guest: 18002, host: 18002
+ arv.vm.network "forwarded_port", guest: 8804, host: 18002
arv.vm.provision "shell",
inline: "cp -vr /vagrant/config_examples/single_host/single_hostname /home/vagrant/local_config_dir;
cp -vr /vagrant/tests /home/vagrant/tests;
+# -*- coding: utf-8 -*-
+# vim: ft=yaml
---
# Copyright (C) The Arvados Authors. All rights reserved.
#
host: __DATABASE_INT_IP__
password: "__DATABASE_PASSWORD__"
user: __CLUSTER___arvados
- encoding: en_US.utf8
- client_encoding: UTF8
+ extra_conn_params:
+ client_encoding: UTF8
+ # Centos7 does not enable SSL by default, so we disable
+ # it here just for testing of the formula purposes only.
+ # You should not do this in production, and should
+ # configure Postgres certificates correctly
+ {%- if grains.os_family in ('RedHat',) %}
+ sslmode: disable
+ {%- endif %}
tls:
# certificate: ''
# key: ''
- # required to test with arvados-snakeoil certs
+ # When using arvados-snakeoil certs set insecure: true
insecure: false
+ resources:
+ virtual_machines:
+ shell:
+ name: shell
+ backend: __SHELL_INT_IP__
+ port: 4200
+
### TOKENS
tokens:
system_root: __SYSTEM_ROOT_TOKEN__
--- /dev/null
+# -*- coding: utf-8 -*-
+# vim: ft=yaml
+---
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: AGPL-3.0
+
+# This config file is used to test a multi-node deployment using a local
+# dispatcher. This setup is not recommended for production use.
+
+# The variables commented out are the default values that the formula uses.
+# The uncommented values are REQUIRED values. If you don't set them, running
+# this formula will fail.
+arvados:
+ ### GENERAL CONFIG
+ version: '__VERSION__'
+ ## It makes little sense to disable this flag, but you can, if you want :)
+ # use_upstream_repo: true
+
+ ## Repo URL is built with grains values. If desired, it can be completely
+ ## overwritten with the pillar parameter 'repo_url'
+ # repo:
+ # humanname: Arvados Official Repository
+
+ release: __RELEASE__
+
+ ## IMPORTANT!!!!!
+ ## api, workbench and shell require some gems, so you need to make sure ruby
+ ## and deps are installed in order to install and compile the gems.
+ ## We default to `false` in these two variables as it's expected you already
+ ## manage OS packages with some other tool and you don't want us messing up
+ ## with your setup.
+ ruby:
+ ## We set these to `true` here for testing purposes.
+ ## They both default to `false`.
+ manage_ruby: true
+ manage_gems_deps: true
+ # pkg: ruby
+ # gems_deps:
+ # - curl
+ # - g++
+ # - gcc
+ # - git
+ # - libcurl4
+ # - libcurl4-gnutls-dev
+ # - libpq-dev
+ # - libxml2
+ # - libxml2-dev
+ # - make
+ # - python3-dev
+ # - ruby-dev
+ # - zlib1g-dev
+
+ # config:
+ # file: /etc/arvados/config.yml
+ # user: root
+ ## IMPORTANT!!!!!
+ ## If you're intalling any of the rails apps (api, workbench), the group
+ ## should be set to that of the web server, usually `www-data`
+ # group: root
+ # mode: 640
+
+ ### ARVADOS CLUSTER CONFIG
+ cluster:
+ name: __CLUSTER__
+ domain: __DOMAIN__
+
+ database:
+ # max concurrent connections per arvados server daemon
+ # connection_pool_max: 32
+ name: __CLUSTER___arvados
+ host: 127.0.0.1
+ password: "__DATABASE_PASSWORD__"
+ user: __CLUSTER___arvados
+ extra_conn_params:
+ client_encoding: UTF8
+ # Centos7 does not enable SSL by default, so we disable
+ # it here just for testing of the formula purposes only.
+ # You should not do this in production, and should
+ # configure Postgres certificates correctly
+ {%- if grains.os_family in ('RedHat',) %}
+ sslmode: disable
+ {%- endif %}
+
+ tls:
+ # certificate: ''
+ # key: ''
+ # When using arvados-snakeoil certs set insecure: true
+ insecure: true
+
+ resources:
+ virtual_machines:
+ shell:
+ name: shell
+ backend: __SHELL_INT_IP__
+ port: 4200
+
+ ### TOKENS
+ tokens:
+ system_root: __SYSTEM_ROOT_TOKEN__
+ management: __MANAGEMENT_TOKEN__
+ anonymous_user: __ANONYMOUS_USER_TOKEN__
+
+ ### KEYS
+ secrets:
+ blob_signing_key: __BLOB_SIGNING_KEY__
+ workbench_secret_key: __WORKBENCH_SECRET_KEY__
+
+ Login:
+ Test:
+ Enable: true
+ Users:
+ __INITIAL_USER__:
+ Email: __INITIAL_USER_EMAIL__
+ Password: __INITIAL_USER_PASSWORD__
+
+ ### VOLUMES
+ ## This should usually match all your `keepstore` instances
+ Volumes:
+ # the volume name will be composed with
+ # <cluster>-nyw5e-<volume>
+ __CLUSTER__-nyw5e-000000000000000:
+ AccessViaHosts:
+ 'http://__KEEPSTORE0_INT_IP__:25107':
+ ReadOnly: false
+ Replication: 2
+ Driver: Directory
+ DriverParameters:
+ Root: /tmp
+ __CLUSTER__-nyw5e-000000000000001:
+ AccessViaHosts:
+ 'http://__KEEPSTORE1_INT_IP__:25107':
+ ReadOnly: false
+ Replication: 2
+ Driver: Directory
+ DriverParameters:
+ Root: /tmp
+
+ Users:
+ NewUsersAreActive: true
+ AutoAdminFirstUser: true
+ AutoSetupNewUsers: true
+ AutoSetupNewUsersWithRepository: true
+
+ Services:
+ Controller:
+ ExternalURL: 'https://__CLUSTER__.__DOMAIN__:__CONTROLLER_EXT_SSL_PORT__'
+ InternalURLs:
+ 'http://localhost:8003': {}
+ Keepbalance:
+ InternalURLs:
+ 'http://__CONTROLLER_INT_IP__:9005': {}
+ Keepproxy:
+ ExternalURL: 'https://__CLUSTER__.__DOMAIN__:__KEEP_EXT_SSL_PORT__'
+ InternalURLs:
+ 'http://__KEEP_INT_IP__:25100': {}
+ Keepstore:
+ InternalURLs:
+ 'http://__KEEPSTORE0_INT_IP__:25107': {}
+ 'http://__KEEPSTORE1_INT_IP__:25107': {}
+ RailsAPI:
+ InternalURLs:
+ 'http://localhost:8004': {}
+ WebDAV:
+ ExternalURL: 'https://__CLUSTER__.__DOMAIN__:__KEEPWEB_EXT_SSL_PORT__'
+ InternalURLs:
+ 'http://localhost:9002': {}
+ WebDAVDownload:
+ ExternalURL: 'https://__CLUSTER__.__DOMAIN__:__KEEPWEB_EXT_SSL_PORT__'
+ WebShell:
+ ExternalURL: 'https://__CLUSTER__.__DOMAIN__:__WEBSHELL_EXT_SSL_PORT__'
+ Websocket:
+ ExternalURL: 'wss://__CLUSTER__.__DOMAIN__:__WEBSOCKET_EXT_SSL_PORT__/websocket'
+ InternalURLs:
+ 'http://__WEBSOCKET_INT_IP__:8005': {}
+ Workbench1:
+ ExternalURL: 'https://__CLUSTER__.__DOMAIN__:__WORKBENCH1_EXT_SSL_PORT__'
+ Workbench2:
+ ExternalURL: 'https://__CLUSTER__.__DOMAIN__:__WORKBENCH2_EXT_SSL_PORT__'
--- /dev/null
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: Apache-2.0
+
+# This state tries to query the controller using the parameters set in
+# the `arvados.cluster.resources.virtual_machines` pillar, to get the
+# ARVADOS_VIRTUAL_MACHINE_UUID for the host and configure the arvados login-sync cron
+# as described in https://doc.arvados.org/main/install/install-shell-server.html
+
+{%- set curr_tpldir = tpldir %}
+{%- set tpldir = 'arvados' %}
+{%- from "arvados/map.jinja" import arvados with context %}
+{%- from "arvados/libtofs.jinja" import files_switch with context %}
+{%- set tpldir = curr_tpldir %}
+
+{%- set virtual_machines = arvados.cluster.resources.virtual_machines | default({}) %}
+{%- set api_token = arvados.cluster.tokens.system_root | yaml_encode %}
+{%- set api_host = arvados.cluster.Services.Controller.ExternalURL | regex_replace('^http(s?)://', '', ignorecase=true) %}
+
+extra_shell_cron_add_login_sync_add_jq_pkg_installed:
+ pkg.installed:
+ - name: jq
+
+{%- for vm, vm_params in virtual_machines.items() %}
+ {%- set vm_name = vm_params.name | default(vm) %}
+
+ # Check if any of the specified virtual_machines parameters corresponds to this instance
+ # It should be an error if we get more than one occurrence
+ {%- if vm_name in [grains['id'], grains['host'], grains['fqdn'], grains['nodename']] or
+ vm_params.backend in [grains['id'], grains['host'], grains['fqdn'], grains['nodename']] +
+ grains['ipv4'] + grains['ipv6'] %}
+
+ # We need to query the VM UUID
+ {%- set cmd_query_vm_uuid = 'arv --short virtual_machine list' ~
+ ' --filters \'[["hostname", "=", "' ~ vm_name ~ '"]]\''
+ %}
+
+extra_shell_cron_add_login_sync_add_{{ vm }}_get_vm_uuid_cmd_run:
+ cmd.run:
+ - env:
+ - ARVADOS_API_TOKEN: {{ api_token }}
+ - ARVADOS_API_HOST: {{ api_host }}
+ - ARVADOS_API_HOST_INSECURE: {{ arvados.cluster.tls.insecure | default(false) }}
+ - name: {{ cmd_query_vm_uuid }} | head -1 | tee /tmp/vm_uuid_{{ vm }}
+ - unless:
+ - /bin/grep -qE "[a-z0-9]{5}-2x53u-[a-z0-9]{15}" /tmp/vm_uuid_{{ vm }}
+ - require:
+ - gem: arvados-shell-package-install-gem-arvados-cli-installed
+
+extra_shell_cron_add_login_sync_add_{{ vm }}_arvados_api_host_cron_env_present:
+ cron.env_present:
+ - name: ARVADOS_API_HOST
+ - value: {{ api_host }}
+ - onlyif:
+ - /bin/grep -qE "[a-z0-9]{5}-2x53u-[a-z0-9]{15}" /tmp/vm_uuid_{{ vm }}
+
+extra_shell_cron_add_login_sync_add_{{ vm }}_arvados_api_token_cron_env_present:
+ cron.env_present:
+ - name: ARVADOS_API_TOKEN
+ - value: {{ api_token }}
+ - onlyif:
+ - /bin/grep -qE "[a-z0-9]{5}-2x53u-[a-z0-9]{15}" /tmp/vm_uuid_{{ vm }}
+
+extra_shell_cron_add_login_sync_add_{{ vm }}_arvados_api_host_insecure_cron_env_present:
+ cron.env_present:
+ - name: ARVADOS_API_HOST_INSECURE
+ - value: {{ arvados.cluster.tls.insecure | default(false) }}
+ - onlyif:
+ - /bin/grep -qE "[a-z0-9]{5}-2x53u-[a-z0-9]{15}" /tmp/vm_uuid_{{ vm }}
+
+extra_shell_cron_add_login_sync_add_{{ vm }}_arvados_virtual_machine_uuid_cron_env_present:
+ cron.env_present:
+ - name: ARVADOS_VIRTUAL_MACHINE_UUID
+ - value: __slot__:salt:cmd.run("cat /tmp/vm_uuid_{{ vm }}")
+ - onlyif:
+ - /bin/grep -qE "[a-z0-9]{5}-2x53u-[a-z0-9]{15}" /tmp/vm_uuid_{{ vm }}
+
+extra_shell_cron_add_login_sync_add_{{ vm }}_arvados_login_sync_cron_present:
+ cron.present:
+ - name: /usr/local/bin/arvados-login-sync
+ - minute: '*/2'
+ - onlyif:
+ - /bin/grep -qE "[a-z0-9]{5}-2x53u-[a-z0-9]{15}" /tmp/vm_uuid_{{ vm }}
+
+ {%- endif %}
+{%- endfor %}
--- /dev/null
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: Apache-2.0
+
+{%- set curr_tpldir = tpldir %}
+{%- set tpldir = 'arvados' %}
+{%- from "arvados/map.jinja" import arvados with context %}
+{%- set tpldir = curr_tpldir %}
+
+extra_shell_sudo_passwordless_sudo_pkg_installed:
+ pkg.installed:
+ - name: sudo
+
+extra_shell_sudo_passwordless_config_file_managed:
+ file.managed:
+ - name: /etc/sudoers.d/arvados_passwordless
+ - makedirs: true
+ - user: root
+ - group: root
+ - mode: '0440'
+ - replace: false
+ - contents: |
+ # This file managed by Salt, do not edit by hand!!
+ # Allow members of group sudo to execute any command without password
+ %sudo ALL=(ALL:ALL) NOPASSWD:ALL
+ - require:
+ - pkg: extra_shell_sudo_passwordless_sudo_pkg_installed
## manage OS packages with some other tool and you don't want us messing up
## with your setup.
ruby:
-
## We set these to `true` here for testing purposes.
## They both default to `false`.
manage_ruby: true
virtual_machines:
shell:
name: webshell
- backend: 127.0.1.1
+ backend: 127.0.0.1
port: 4200
### TOKENS
resources:
virtual_machines:
shell:
- name: webshell
- backend: 127.0.1.1
+ name: __HOSTNAME_EXT__
+ backend: 127.0.0.1
port: 4200
### TOKENS
--- /dev/null
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: Apache-2.0
+
+# This state tries to query the controller using the parameters set in
+# the `arvados.cluster.resources.virtual_machines` pillar, to get the
+# ARVADOS_VIRTUAL_MACHINE_UUID for the host and configure the arvados login-sync cron
+# as described in https://doc.arvados.org/main/install/install-shell-server.html
+
+{%- set curr_tpldir = tpldir %}
+{%- set tpldir = 'arvados' %}
+{%- from "arvados/map.jinja" import arvados with context %}
+{%- from "arvados/libtofs.jinja" import files_switch with context %}
+{%- set tpldir = curr_tpldir %}
+
+{%- set virtual_machines = arvados.cluster.resources.virtual_machines | default({}) %}
+{%- set api_token = arvados.cluster.tokens.system_root | yaml_encode %}
+{%- set api_host = arvados.cluster.Services.Controller.ExternalURL | regex_replace('^http(s?)://', '', ignorecase=true) %}
+
+extra_shell_cron_add_login_sync_add_jq_pkg_installed:
+ pkg.installed:
+ - name: jq
+
+{%- for vm, vm_params in virtual_machines.items() %}
+ {%- set vm_name = vm_params.name | default(vm) %}
+
+ # Check if any of the specified virtual_machines parameters corresponds to this instance
+ # It should be an error if we get more than one occurrence
+ {%- if vm_name in [grains['id'], grains['host'], grains['fqdn'], grains['nodename']] or
+ vm_params.backend in [grains['id'], grains['host'], grains['fqdn'], grains['nodename']] +
+ grains['ipv4'] + grains['ipv6'] %}
+
+ # We need to query the VM UUID
+ {%- set cmd_query_vm_uuid = 'arv --short virtual_machine list' ~
+ ' --filters \'[["hostname", "=", "' ~ vm_name ~ '"]]\''
+ %}
+
+extra_shell_cron_add_login_sync_add_{{ vm }}_get_vm_uuid_cmd_run:
+ cmd.run:
+ - env:
+ - ARVADOS_API_TOKEN: {{ api_token }}
+ - ARVADOS_API_HOST: {{ api_host }}
+ - ARVADOS_API_HOST_INSECURE: {{ arvados.cluster.tls.insecure | default(false) }}
+ - name: {{ cmd_query_vm_uuid }} | head -1 | tee /tmp/vm_uuid_{{ vm }}
+ - unless:
+ - /bin/grep -qE "[a-z0-9]{5}-2x53u-[a-z0-9]{15}" /tmp/vm_uuid_{{ vm }}
+ - require:
+ - gem: arvados-shell-package-install-gem-arvados-cli-installed
+
+extra_shell_cron_add_login_sync_add_{{ vm }}_arvados_api_host_cron_env_present:
+ cron.env_present:
+ - name: ARVADOS_API_HOST
+ - value: {{ api_host }}
+ - onlyif:
+ - /bin/grep -qE "[a-z0-9]{5}-2x53u-[a-z0-9]{15}" /tmp/vm_uuid_{{ vm }}
+
+extra_shell_cron_add_login_sync_add_{{ vm }}_arvados_api_token_cron_env_present:
+ cron.env_present:
+ - name: ARVADOS_API_TOKEN
+ - value: {{ api_token }}
+ - onlyif:
+ - /bin/grep -qE "[a-z0-9]{5}-2x53u-[a-z0-9]{15}" /tmp/vm_uuid_{{ vm }}
+
+extra_shell_cron_add_login_sync_add_{{ vm }}_arvados_api_host_insecure_cron_env_present:
+ cron.env_present:
+ - name: ARVADOS_API_HOST_INSECURE
+ - value: {{ arvados.cluster.tls.insecure | default(false) }}
+ - onlyif:
+ - /bin/grep -qE "[a-z0-9]{5}-2x53u-[a-z0-9]{15}" /tmp/vm_uuid_{{ vm }}
+
+extra_shell_cron_add_login_sync_add_{{ vm }}_arvados_virtual_machine_uuid_cron_env_present:
+ cron.env_present:
+ - name: ARVADOS_VIRTUAL_MACHINE_UUID
+ - value: __slot__:salt:cmd.run("cat /tmp/vm_uuid_{{ vm }}")
+ - onlyif:
+ - /bin/grep -qE "[a-z0-9]{5}-2x53u-[a-z0-9]{15}" /tmp/vm_uuid_{{ vm }}
+
+extra_shell_cron_add_login_sync_add_{{ vm }}_arvados_login_sync_cron_present:
+ cron.present:
+ - name: /usr/local/bin/arvados-login-sync
+ - minute: '*/2'
+ - onlyif:
+ - /bin/grep -qE "[a-z0-9]{5}-2x53u-[a-z0-9]{15}" /tmp/vm_uuid_{{ vm }}
+
+ {%- endif %}
+{%- endfor %}
--- /dev/null
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: Apache-2.0
+
+{%- set curr_tpldir = tpldir %}
+{%- set tpldir = 'arvados' %}
+{%- from "arvados/map.jinja" import arvados with context %}
+{%- set tpldir = curr_tpldir %}
+
+extra_shell_sudo_passwordless_sudo_pkg_installed:
+ pkg.installed:
+ - name: sudo
+
+extra_shell_sudo_passwordless_config_file_managed:
+ file.managed:
+ - name: /etc/sudoers.d/arvados_passwordless
+ - makedirs: true
+ - user: root
+ - group: root
+ - mode: '0440'
+ - replace: false
+ - contents: |
+ # This file managed by Salt, do not edit by hand!!
+ # Allow members of group sudo to execute any command without password
+ %sudo ALL=(ALL:ALL) NOPASSWD:ALL
+ - require:
+ - pkg: extra_shell_sudo_passwordless_sudo_pkg_installed
set -o pipefail
+_exit_handler() {
+ local rc="$?"
+ trap - EXIT
+ if [ "$rc" -ne 0 ]; then
+ echo "Error occurred ($rc) while running $0 at line $1 : $BASH_COMMAND"
+ fi
+ exit "$rc"
+}
+
+trap '_exit_handler $LINENO' EXIT ERR
+
# capture the directory that the script is running from
SCRIPT_DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )"
git clone --quiet https://git.arvados.org/arvados-formula.git ${F_DIR}/arvados
# If we want to try a specific branch of the formula
-if [ "x${BRANCH}" != "x" ]; then
+if [ "x${BRANCH}" != "x" -a $(git rev-parse --abbrev-ref HEAD) != "${BRANCH}" ]; then
( cd ${F_DIR}/arvados && git checkout --quiet -t origin/"${BRANCH}" -b "${BRANCH}" )
-elif [ "x${ARVADOS_TAG}" != "x" ]; then
+elif [ "x${ARVADOS_TAG}" != "x" -a $(git rev-parse --abbrev-ref HEAD) != "${ARVADOS_TAG}" ]; then
( cd ${F_DIR}/arvados && git checkout --quiet tags/"${ARVADOS_TAG}" -b "${ARVADOS_TAG}" )
fi
"${f}" > "${P_DIR}"/$(basename "${f}")
done
-if [ "x${TEST}" = "xyes" ] && [ ! -d "${SOURCE_TESTS_DIR}" ]; then
- echo "You requested to run tests, but ${SOURCE_TESTS_DIR} does not exist or is not a directory. Exiting."
- exit 1
-fi
-mkdir -p ${T_DIR}
-# Replace cluster and domain name in the test files
-for f in $(ls "${SOURCE_TESTS_DIR}"/*); do
- FILTERS="s#__CLUSTER__#${CLUSTER}#g;
- s#__CONTROLLER_EXT_SSL_PORT__#${CONTROLLER_EXT_SSL_PORT}#g;
- s#__DOMAIN__#${DOMAIN}#g;
- s#__IP_INT__#${IP_INT}#g;
- s#__INITIAL_USER_EMAIL__#${INITIAL_USER_EMAIL}#g;
- s#__INITIAL_USER_PASSWORD__#${INITIAL_USER_PASSWORD}#g
- s#__INITIAL_USER__#${INITIAL_USER}#g;
- s#__DATABASE_PASSWORD__#${DATABASE_PASSWORD}#g;
- s#__SYSTEM_ROOT_TOKEN__#${SYSTEM_ROOT_TOKEN}#g"
- if [ "$USE_SINGLE_HOSTNAME" = "yes" ]; then
- FILTERS="s#__CLUSTER__.__DOMAIN__#${HOSTNAME_EXT}#g;
- $FILTERS"
+if [ ! -d "${SOURCE_TESTS_DIR}" ]; then
+ echo "WARNING: The tests directory was not copied to \"${SOURCE_TESTS_DIR}\"."
+ if [ "x${TEST}" = "xyes" ]; then
+ echo "WARNING: Disabling tests for this installation."
fi
- sed "$FILTERS" \
- "${f}" > ${T_DIR}/$(basename "${f}")
-done
-chmod 755 ${T_DIR}/run-test.sh
+ TEST="no"
+else
+ mkdir -p ${T_DIR}
+ # Replace cluster and domain name in the test files
+ for f in $(ls "${SOURCE_TESTS_DIR}"/*); do
+ FILTERS="s#__CLUSTER__#${CLUSTER}#g;
+ s#__CONTROLLER_EXT_SSL_PORT__#${CONTROLLER_EXT_SSL_PORT}#g;
+ s#__DOMAIN__#${DOMAIN}#g;
+ s#__IP_INT__#${IP_INT}#g;
+ s#__INITIAL_USER_EMAIL__#${INITIAL_USER_EMAIL}#g;
+ s#__INITIAL_USER_PASSWORD__#${INITIAL_USER_PASSWORD}#g
+ s#__INITIAL_USER__#${INITIAL_USER}#g;
+ s#__DATABASE_PASSWORD__#${DATABASE_PASSWORD}#g;
+ s#__SYSTEM_ROOT_TOKEN__#${SYSTEM_ROOT_TOKEN}#g"
+ if [ "$USE_SINGLE_HOSTNAME" = "yes" ]; then
+ FILTERS="s#__CLUSTER__.__DOMAIN__#${HOSTNAME_EXT}#g;
+ $FILTERS"
+ fi
+ sed "$FILTERS" \
+ "${f}" > ${T_DIR}/$(basename "${f}")
+ done
+ chmod 755 ${T_DIR}/run-test.sh
+fi
# Replace helper state files that differ from the formula's examples
if [ -d "${SOURCE_STATES_DIR}" ]; then
# Same when using self-signed certificates.
SKIP_SNAKE_OIL="dont_add_snakeoil_certs"
fi
- for f in $(ls "${F_DIR}"/extra/extra/*.sls | grep -v ${SKIP_SNAKE_OIL}); do
+ for f in $(ls "${F_DIR}"/extra/extra/*.sls | egrep -v "${SKIP_SNAKE_OIL}|shell_"); do
echo " - extra.$(basename ${f} | sed 's/.sls$//g')" >> ${S_DIR}/top.sls
done
# Use byo or self-signed certificates
echo " - postgres" >> ${S_DIR}/top.sls
echo " - docker.software" >> ${S_DIR}/top.sls
echo " - arvados" >> ${S_DIR}/top.sls
+ echo " - extra.shell_sudo_passwordless" >> ${S_DIR}/top.sls
+ echo " - extra.shell_cron_add_login_sync" >> ${S_DIR}/top.sls
# Pillars
echo " - docker" >> ${P_DIR}/top.sls
sed -i "s/__NGINX_INSTALL_SOURCE__/${NGINX_INSTALL_SOURCE}/g" ${P_DIR}/nginx_passenger.sls
;;
"controller" | "websocket" | "workbench" | "workbench2" | "webshell" | "keepweb" | "keepproxy")
+ NGINX_INSTALL_SOURCE="install_from_repo"
# States
if [ "${R}" = "workbench" ]; then
NGINX_INSTALL_SOURCE="install_from_phusionpassenger"
s#__CERT_PEM__#/etc/nginx/ssl/arvados-${R}.pem#g;
s#__CERT_KEY__#/etc/nginx/ssl/arvados-${R}.key#g" \
${P_DIR}/nginx_${R}_configuration.sls
- grep -q ${R} ${P_DIR}/extra_custom_certs.sls || echo " - ${R}" >> ${P_DIR}/extra_custom_certs.sls
+ grep -q ${R}$ ${P_DIR}/extra_custom_certs.sls || echo " - ${R}" >> ${P_DIR}/extra_custom_certs.sls
fi
fi
# We need to tweak the Nginx's pillar depending whether we want plain nginx or nginx+passenger
;;
"shell")
# States
+ echo " - extra.shell_sudo_passwordless" >> ${S_DIR}/top.sls
+ echo " - extra.shell_cron_add_login_sync" >> ${S_DIR}/top.sls
grep -q "docker" ${S_DIR}/top.sls || echo " - docker.software" >> ${S_DIR}/top.sls
grep -q "arvados.${R}" ${S_DIR}/top.sls || echo " - arvados.${R}" >> ${S_DIR}/top.sls
# Pillars
# Leave a copy of the Arvados CA so the user can copy it where it's required
if [ "$DEV_MODE" = "yes" ]; then
- echo "Copying the Arvados CA certificate to the installer dir, so you can import it"
+ ARVADOS_SNAKEOIL_CA_DEST_FILE="${SCRIPT_DIR}/${CLUSTER}.${DOMAIN}-arvados-snakeoil-ca.pem"
+
# If running in a vagrant VM, also add default user to docker group
if [ "x${VAGRANT}" = "xyes" ]; then
- cp /etc/ssl/certs/arvados-snakeoil-ca.pem /vagrant/${CLUSTER}.${DOMAIN}-arvados-snakeoil-ca.pem
-
echo "Adding the vagrant user to the docker group"
usermod -a -G docker vagrant
- else
- cp /etc/ssl/certs/arvados-snakeoil-ca.pem ${SCRIPT_DIR}/${CLUSTER}.${DOMAIN}-arvados-snakeoil-ca.pem
+ ARVADOS_SNAKEOIL_CA_DEST_FILE="/vagrant/${CLUSTER}.${DOMAIN}-arvados-snakeoil-ca.pem"
+ fi
+ if [ -f /etc/ssl/certs/arvados-snakeoil-ca.pem ]; then
+ echo "Copying the Arvados CA certificate to the installer dir, so you can import it"
+ cp /etc/ssl/certs/arvados-snakeoil-ca.pem ${ARVADOS_SNAKEOIL_CA_DEST_FILE}
fi
fi
set -o pipefail
-# First, validate that the CA is installed and that we can query it with no errors.
-if ! curl -s -o /dev/null https://${ARVADOS_API_HOST}/users/welcome?return_to=%2F; then
- echo "The Arvados CA was not correctly installed. Although some components will work,"
- echo "others won't. Please verify that the CA cert file was installed correctly and"
- echo "retry running these tests."
- exit 1
-fi
-
# https://doc.arvados.org/v2.0/install/install-jobs-image.html
echo "Creating Arvados Standard Docker Images project"
uuid_prefix=$(arv --format=uuid user current | cut -d- -f1)
import arvados.util
import datetime
import ciso8601
+import csv
def parse_arguments(arguments):
arg_parser = argparse.ArgumentParser()
- arg_parser.add_argument('--days', type=int, required=True)
+ arg_parser.add_argument('--start', help='Start date for the report in YYYY-MM-DD format (UTC)')
+ arg_parser.add_argument('--end', help='End date for the report in YYYY-MM-DD format (UTC)')
+ arg_parser.add_argument('--days', type=int, help='Number of days before now() to start the report')
+ arg_parser.add_argument('--csv', action='store_true', help='Output in csv format (default: false)')
args = arg_parser.parse_args(arguments)
- return args
+
+ if args.days and (args.start or args.end):
+ arg_parser.print_help()
+ print("Error: either specify --days or both --start and --end")
+ exit(1)
+
+ if not args.days and (not args.start or not args.end):
+ arg_parser.print_help()
+ print("\nError: either specify --days or both --start and --end")
+ exit(1)
+
+ if (args.start and not args.end) or (args.end and not args.start):
+ arg_parser.print_help()
+ print("\nError: no start or end date found, either specify --days or both --start and --end")
+ exit(1)
+
+ if args.days:
+ to = datetime.datetime.utcnow()
+ since = to - datetime.timedelta(days=args.days)
+
+ if args.start:
+ try:
+ since = datetime.datetime.strptime(args.start,"%Y-%m-%d")
+ except:
+ arg_parser.print_help()
+ print("\nError: start date must be in YYYY-MM-DD format")
+ exit(1)
+
+ if args.end:
+ try:
+ to = datetime.datetime.strptime(args.end,"%Y-%m-%d")
+ except:
+ arg_parser.print_help()
+ print("\nError: end date must be in YYYY-MM-DD format")
+ exit(1)
+
+ return args, since, to
def getowner(arv, uuid, owners):
if uuid is None:
return getowner(arv, owners[uuid], owners)
def getuserinfo(arv, uuid):
- u = arv.users().get(uuid=uuid).execute()
+ try:
+ u = arv.users().get(uuid=uuid).execute()
+ except:
+ return "deleted user (%susers/%s)" % (arv.config()["Services"]["Workbench1"]["ExternalURL"],
+ uuid)
prof = "\n".join(" %s: \"%s\"" % (k, v) for k, v in u["prefs"].get("profile", {}).items() if v)
if prof:
prof = "\n"+prof+"\n"
return "%s %s <%s> (%susers/%s)%s" % (u["first_name"], u["last_name"], u["email"],
arv.config()["Services"]["Workbench1"]["ExternalURL"],
uuid, prof)
+def getuserinfocsv(arv, uuid):
+ try:
+ u = arv.users().get(uuid=uuid).execute()
+ except:
+ return [uuid,"deleted","user",""]
+ return [uuid, u["first_name"], u["last_name"], u["email"]]
+
collectionNameCache = {}
-def getCollectionName(arv, uuid):
- if uuid not in collectionNameCache:
- u = arv.collections().get(uuid=uuid).execute()
- collectionNameCache[uuid] = u["name"]
- return collectionNameCache[uuid]
+def getCollectionName(arv, uuid, pdh):
+ lookupField = uuid
+ filters = [["uuid","=",uuid]]
+ cached = uuid in collectionNameCache
+ # look up by uuid if it is available, fall back to look up by pdh
+ if len(uuid) != 27:
+ # Look up by pdh. Note that this can be misleading; the download could
+ # have happened from a collection with the same pdh but different name.
+ # We arbitrarily pick the oldest collection with the pdh to lookup the
+ # name, if the uuid for the request is not known.
+ lookupField = pdh
+ filters = [["portable_data_hash","=",pdh]]
+ cached = pdh in collectionNameCache
+
+ if not cached:
+ u = arv.collections().list(filters=filters,order="created_at",limit=1).execute().get("items")
+ if len(u) < 1:
+ return "(deleted)"
+ collectionNameCache[lookupField] = u[0]["name"]
+ return collectionNameCache[lookupField]
def getname(u):
return "\"%s\" (%s)" % (u["name"], u["uuid"])
if arguments is None:
arguments = sys.argv[1:]
- args = parse_arguments(arguments)
+ args, since, to = parse_arguments(arguments)
arv = arvados.api()
- since = datetime.datetime.utcnow() - datetime.timedelta(days=args.days)
+ prefix = ''
+ suffix = "\n"
+ if args.csv:
+ prefix = '# '
+ suffix = ''
+ print("%sUser activity on %s between %s and %s%s" % (prefix, arv.config()["ClusterID"],
+ since.isoformat(sep=" ", timespec="minutes"),
+ to.isoformat(sep=" ", timespec="minutes"), suffix))
- print("User activity on %s between %s and %s\n" % (arv.config()["ClusterID"],
- (datetime.datetime.now() - datetime.timedelta(days=args.days)).isoformat(sep=" ", timespec="minutes"),
- datetime.datetime.now().isoformat(sep=" ", timespec="minutes")))
-
- events = arvados.util.keyset_list_all(arv.logs().list, filters=[["created_at", ">=", since.isoformat()]])
+ events = arvados.util.keyset_list_all(arv.logs().list, filters=[["created_at", ">=", since.isoformat()],["created_at", "<", to.isoformat()]])
users = {}
owners = {}
owner = getowner(arv, e["object_owner_uuid"], owners)
users.setdefault(owner, [])
event_at = ciso8601.parse_datetime(e["event_at"]).astimezone().isoformat(sep=" ", timespec="minutes")
- # loguuid = e["uuid"]
- loguuid = ""
+ loguuid = e["uuid"]
if e["event_type"] == "create" and e["object_uuid"][6:11] == "tpzed":
users.setdefault(e["object_uuid"], [])
- users[e["object_uuid"]].append("%s User account created" % event_at)
+ users[e["object_uuid"]].append([loguuid, event_at, "User account created"])
elif e["event_type"] == "update" and e["object_uuid"][6:11] == "tpzed":
pass
elif e["event_type"] == "create" and e["object_uuid"][6:11] == "xvhdp":
if e["properties"]["new_attributes"]["requesting_container_uuid"] is None:
- users[owner].append("%s Ran container %s %s" % (event_at, getname(e["properties"]["new_attributes"]), loguuid))
+ users[owner].append([loguuid, event_at, "Ran container %s" % (getname(e["properties"]["new_attributes"]))])
elif e["event_type"] == "update" and e["object_uuid"][6:11] == "xvhdp":
pass
elif e["event_type"] == "create" and e["object_uuid"][6:11] == "j7d0g":
- users[owner].append("%s Created project %s" % (event_at, getname(e["properties"]["new_attributes"])))
+ users[owner].append([loguuid, event_at,"Created project %s" % (getname(e["properties"]["new_attributes"]))])
elif e["event_type"] == "delete" and e["object_uuid"][6:11] == "j7d0g":
- users[owner].append("%s Deleted project %s" % (event_at, getname(e["properties"]["old_attributes"])))
+ users[owner].append([loguuid, event_at,"Deleted project %s" % (getname(e["properties"]["old_attributes"]))])
elif e["event_type"] == "update" and e["object_uuid"][6:11] == "j7d0g":
- users[owner].append("%s Updated project %s" % (event_at, getname(e["properties"]["new_attributes"])))
+ users[owner].append([loguuid, event_at,"Updated project %s" % (getname(e["properties"]["new_attributes"]))])
elif e["event_type"] in ("create", "update") and e["object_uuid"][6:11] == "gj3su":
since_last = None
- if len(users[owner]) > 0 and users[owner][-1].endswith("activity"):
- sp = users[owner][-1].split(" ")
- start = sp[0]+" "+sp[1]
- since_last = ciso8601.parse_datetime(event_at) - ciso8601.parse_datetime(sp[3]+" "+sp[4])
+ if len(users[owner]) > 0 and users[owner][-1][-1].endswith("activity"):
+ sp = users[owner][-1][-1].split(" ")
+ start = users[owner][-1][1]
+ since_last = ciso8601.parse_datetime(event_at) - ciso8601.parse_datetime(sp[1]+" "+sp[2])
span = ciso8601.parse_datetime(event_at) - ciso8601.parse_datetime(start)
if since_last is not None and since_last < datetime.timedelta(minutes=61):
- users[owner][-1] = "%s to %s (%02d:%02d) Account activity" % (start, event_at, span.days*24 + int(span.seconds/3600), int((span.seconds % 3600)/60))
+ users[owner][-1] = [loguuid, start,"to %s (%02d:%02d) Account activity" % (event_at, span.days*24 + int(span.seconds/3600), int((span.seconds % 3600)/60))]
else:
- users[owner].append("%s to %s (0:00) Account activity" % (event_at, event_at))
+ users[owner].append([loguuid, event_at,"to %s (0:00) Account activity" % (event_at)])
elif e["event_type"] == "create" and e["object_uuid"][6:11] == "o0j2j":
if e["properties"]["new_attributes"]["link_class"] == "tag":
- users[owner].append("%s Tagged %s" % (event_at, e["properties"]["new_attributes"]["head_uuid"]))
+ users[owner].append([event_at,"Tagged %s" % (e["properties"]["new_attributes"]["head_uuid"])])
elif e["properties"]["new_attributes"]["link_class"] == "permission":
- users[owner].append("%s Shared %s with %s" % (event_at, e["properties"]["new_attributes"]["tail_uuid"], e["properties"]["new_attributes"]["head_uuid"]))
+ users[owner].append([loguuid, event_at,"Shared %s with %s" % (e["properties"]["new_attributes"]["tail_uuid"], e["properties"]["new_attributes"]["head_uuid"])])
else:
- users[owner].append("%s %s %s %s" % (e["event_type"], e["object_kind"], e["object_uuid"], loguuid))
+ users[owner].append([loguuid, event_at,"%s %s %s" % (e["event_type"], e["object_kind"], e["object_uuid"])])
elif e["event_type"] == "delete" and e["object_uuid"][6:11] == "o0j2j":
if e["properties"]["old_attributes"]["link_class"] == "tag":
- users[owner].append("%s Untagged %s" % (event_at, e["properties"]["old_attributes"]["head_uuid"]))
+ users[owner].append([loguuid, event_at,"Untagged %s" % (e["properties"]["old_attributes"]["head_uuid"])])
elif e["properties"]["old_attributes"]["link_class"] == "permission":
- users[owner].append("%s Unshared %s with %s" % (event_at, e["properties"]["old_attributes"]["tail_uuid"], e["properties"]["old_attributes"]["head_uuid"]))
+ users[owner].append([loguuid, event_at,"Unshared %s with %s" % (e["properties"]["old_attributes"]["tail_uuid"], e["properties"]["old_attributes"]["head_uuid"])])
else:
- users[owner].append("%s %s %s %s" % (e["event_type"], e["object_kind"], e["object_uuid"], loguuid))
+ users[owner].append([loguuid, event_at,"%s %s %s" % (e["event_type"], e["object_kind"], e["object_uuid"])])
elif e["event_type"] == "create" and e["object_uuid"][6:11] == "4zz18":
if e["properties"]["new_attributes"]["properties"].get("type") in ("log", "output", "intermediate"):
pass
else:
- users[owner].append("%s Created collection %s %s" % (event_at, getname(e["properties"]["new_attributes"]), loguuid))
+ users[owner].append([loguuid, event_at,"Created collection %s" % (getname(e["properties"]["new_attributes"]))])
elif e["event_type"] == "update" and e["object_uuid"][6:11] == "4zz18":
- users[owner].append("%s Updated collection %s %s" % (event_at, getname(e["properties"]["new_attributes"]), loguuid))
+ users[owner].append([loguuid, event_at,"Updated collection %s" % (getname(e["properties"]["new_attributes"]))])
elif e["event_type"] == "delete" and e["object_uuid"][6:11] == "4zz18":
if e["properties"]["old_attributes"]["properties"].get("type") in ("log", "output", "intermediate"):
pass
else:
- users[owner].append("%s Deleted collection %s %s" % (event_at, getname(e["properties"]["old_attributes"]), loguuid))
+ users[owner].append([loguuid, event_at, "Deleted collection %s" % (getname(e["properties"]["old_attributes"]))])
elif e["event_type"] == "file_download":
- users[e["object_uuid"]].append("%s Downloaded file \"%s\" from \"%s\" (%s) (%s)" % (event_at,
+ users.setdefault(e["object_uuid"], [])
+ users[e["object_uuid"]].append([loguuid, event_at, "Downloaded file \"%s\" from \"%s\" (%s) (%s)" % (
e["properties"].get("collection_file_path") or e["properties"].get("reqPath"),
- getCollectionName(arv, e["properties"].get("collection_uuid")),
+ getCollectionName(arv, e["properties"].get("collection_uuid"), e["properties"].get("portable_data_hash")),
e["properties"].get("collection_uuid"),
- e["properties"].get("portable_data_hash")))
+ e["properties"].get("portable_data_hash"))])
+
elif e["event_type"] == "file_upload":
- users[e["object_uuid"]].append("%s Uploaded file \"%s\" to \"%s\" (%s)" % (event_at,
+ users.setdefault(e["object_uuid"], [])
+ users[e["object_uuid"]].append([loguuid, event_at, "Uploaded file \"%s\" to \"%s\" (%s)" % (
e["properties"].get("collection_file_path") or e["properties"].get("reqPath"),
- getCollectionName(arv, e["properties"].get("collection_uuid")),
- e["properties"].get("collection_uuid")))
+ getCollectionName(arv, e["properties"].get("collection_uuid"), e["properties"].get("portable_data_hash")),
+ e["properties"].get("collection_uuid"))])
else:
- users[owner].append("%s %s %s %s" % (e["event_type"], e["object_kind"], e["object_uuid"], loguuid))
+ users[owner].append([loguuid, event_at, "%s %s %s" % (e["event_type"], e["object_kind"], e["object_uuid"])])
+
+ if args.csv:
+ csvwriter = csv.writer(sys.stdout, dialect='unix')
for k,v in users.items():
if k is None or k.endswith("-tpzed-000000000000000"):
continue
- print(getuserinfo(arv, k))
- for ev in v:
- print(" %s" % ev)
- print("")
+ if not args.csv:
+ print(getuserinfo(arv, k))
+ for ev in v:
+ # Remove the log entry uuid, this report is intended for human consumption
+ ev.pop(0)
+ print(" %s" % ' '.join(ev))
+ print("")
+ else:
+ user = getuserinfocsv(arv, k)
+ for ev in v:
+ ev = user + ev
+ csvwriter.writerow(ev)
if __name__ == "__main__":
main()
projects / arvados.git / commitdiff