@client_mtx = Mutex.new
end
- def api(resources_kind, action, data=nil, tokens={})
+ def api(resources_kind, action, data=nil, tokens={}, include_anon_token=true)
profile_checkpoint
'reader_tokens' => ((tokens[:reader_tokens] ||
Thread.current[:reader_tokens] ||
[]) +
- [Rails.configuration.anonymous_user_token]).to_json,
+ (include_anon_token ? [Rails.configuration.anonymous_user_token] : [])).to_json,
}
if !data.nil?
data.each do |k,v|
end
def self.current
- res = arvados_api_client.api self, '/current'
+ res = arvados_api_client.api self, '/current', nil, {}, false
arvados_api_client.unpack_api_response(res)
end
- user/topics/run-command.html.textile.liquid
- user/reference/job-pipeline-ref.html.textile.liquid
- user/examples/crunch-examples.html.textile.liquid
+ - user/topics/arv-sync-groups.html.textile.liquid
- Query the metadata database:
- user/topics/tutorial-trait-search.html.textile.liquid
- Arvados License:
|==--submit-runner-ram== SUBMIT_RUNNER_RAM|RAM (in MiB) required for the workflow runner job (default 1024)|
|==--submit-runner-image== SUBMIT_RUNNER_IMAGE|Docker image for workflow runner job, default arvados/jobs|
|==--name== NAME| Name to use for workflow execution instance.|
-|==--on-error {stop,continue}|Desired workflow behavior when a step fails. One of 'stop' or 'continue'. Default is 'continue'.|
+|==--on-error {stop,continue}==|Desired workflow behavior when a step fails. One of 'stop' or 'continue'. Default is 'continue'.|
|==--enable-dev==| Enable loading and running development versions of CWL spec.|
|==--intermediate-output-ttl== N|If N > 0, intermediate output collections will be trashed N seconds after creation. Default is 0 (don't trash).|
|==--trash-intermediate==| Immediately trash intermediate outputs on workflow success.|
--- /dev/null
+---
+layout: default
+navsection: userguide
+title: "Using arv-sync-groups"
+...
+{% comment %}
+Copyright (C) The Arvados Authors. All rights reserved.
+
+SPDX-License-Identifier: CC-BY-SA-3.0
+{% endcomment %}
+
+The @arv-sync-groups@ tool allows to synchronize remote groups into Arvados from an external source.
+
+h1. Using arv-sync-groups
+
+This tool reads a CSV (comma-separated values) file having information about external groups and their members. When running it for the first time, it'll create a special group named 'Externally synchronized groups' meant to be the parent of all the remote groups.
+
+Every line on the file should have 2 values: a group name and a local user identifier, meaning that the named user is a member of the group. The tool will create the group if it doesn't exist, and add the user to it. If group member is not present on the input file, the account will be removed from the group.
+
+Users can be identified by their email address or username: the tool will check if every user exist on the system, and report back when not found. Groups on the other hand, are identified by their name.
+
+This tool is designed to be run periodically reading a file created by a remote auth system (ie: LDAP) dump script, applying what's included on the file as the source of truth.
+
+
+bq. NOTE: @arv-sync-groups@ needs to perform several administrative tasks on Arvados, so must be run using a superuser token
+
+h2. Options
+
+The following command line options are supported:
+
+table(table table-bordered table-condensed).
+|_. Option |_. Description |
+|==--help==| This list of options|
+|==--parent-group-uuid==| UUID of group to own all the externally synchronized groups|
+|==--user-id== | Identifier to use in looking up user. One of 'email' or 'username' (Default: 'email')|
+|==--verbose==| Log informational messages (Default: False)|
+|==--version==| Print version and exit|
+
+h2. Examples
+
+To sync groups using the username to identify every account, reading from some @external_groups.csv@ file, the command should be called as follows:
+
+<notextile>
+<pre><code>~$ <span class="userinput">arv-sync-groups --user-id username /path/to/external_groups.csv </span>
+</code></pre>
+</notextile>
+
+If you want to use a specific preexisting group as the parent of all the remote groups, you can do it this way:
+
+<notextile>
+<pre><code>~$ <span class="userinput">arv-sync-groups --parent-group-uuid <preexisting group UUID> --user-id username /path/to/external_groups.csv </span>
+</code></pre>
+</notextile>
}
}
+var errorBlacklist = []string{"Cannot connect to the Docker daemon"}
+var brokenNodeHook *string = flag.String("broken-node-hook", "", "Script to run if node is detected to be broken (for example, Docker daemon is not running)")
+
+func (runner *ContainerRunner) checkBrokenNode(goterr error) bool {
+ for _, d := range errorBlacklist {
+ if strings.Index(goterr.Error(), d) != -1 {
+ runner.CrunchLog.Printf("Error suggests node is unable to run containers: %v", goterr)
+ if *brokenNodeHook == "" {
+ runner.CrunchLog.Printf("No broken node hook provided, cannot mark node as broken.")
+ } else {
+ runner.CrunchLog.Printf("Running broken node hook %q", *brokenNodeHook)
+ // run killme script
+ c := exec.Command(*brokenNodeHook)
+ c.Stdout = runner.CrunchLog
+ c.Stderr = runner.CrunchLog
+ err := c.Run()
+ if err != nil {
+ runner.CrunchLog.Printf("Error running broken node hook: %v", err)
+ }
+ }
+ return true
+ }
+ }
+ return false
+}
+
// LoadImage determines the docker image id from the container record and
// checks if it is available in the local Docker image store. If not, it loads
// the image from Keep.
// check for and/or load image
err = runner.LoadImage()
if err != nil {
- runner.finalState = "Cancelled"
+ if !runner.checkBrokenNode(err) {
+ // Failed to load image but not due to a "broken node"
+ // condition, probably user error.
+ runner.finalState = "Cancelled"
+ }
err = fmt.Errorf("While loading container image: %v", err)
return
}
return
}
- runner.StartCrunchstat()
-
if runner.IsCancelled() {
return
}
}
runner.finalState = "Cancelled"
+ runner.StartCrunchstat()
+
err = runner.StartContainer()
if err != nil {
+ runner.checkBrokenNode(err)
return
}
}
api.Retries = 8
- var kc *keepclient.KeepClient
- kc, err = keepclient.MakeKeepClient(api)
- if err != nil {
- log.Fatalf("%s: %v", containerId, err)
+ kc, kcerr := keepclient.MakeKeepClient(api)
+ if kcerr != nil {
+ log.Fatalf("%s: %v", containerId, kcerr)
}
kc.BlockCache = &keepclient.BlockCache{MaxBlocks: 2}
kc.Retries = 4
- var docker *dockerclient.Client
// API version 1.21 corresponds to Docker 1.9, which is currently the
// minimum version we want to support.
- docker, err = dockerclient.NewClient(dockerclient.DefaultDockerHost, "1.21", nil, nil)
- if err != nil {
- log.Fatalf("%s: %v", containerId, err)
- }
-
+ docker, dockererr := dockerclient.NewClient(dockerclient.DefaultDockerHost, "1.21", nil, nil)
dockerClientProxy := ThinDockerClientProxy{Docker: docker}
cr := NewContainerRunner(api, kc, dockerClientProxy, containerId)
+
+ if dockererr != nil {
+ cr.CrunchLog.Printf("%s: %v", containerId, dockererr)
+ cr.checkBrokenNode(dockererr)
+ cr.CrunchLog.Close()
+ os.Exit(1)
+ }
+
cr.statInterval = *statInterval
cr.cgroupRoot = *cgroupRoot
cr.expectCgroupParent = *cgroupParent
}
func (t *TestDockerClient) ImageInspectWithRaw(ctx context.Context, image string) (dockertypes.ImageInspect, []byte, error) {
+ if t.finish == 2 {
+ return dockertypes.ImageInspect{}, nil, fmt.Errorf("Cannot connect to the Docker daemon at unix:///var/run/docker.sock. Is the docker daemon running?")
+ }
+
if t.imageLoaded == image {
return dockertypes.ImageInspect{}, nil, nil
} else {
}
func (t *TestDockerClient) ImageLoad(ctx context.Context, input io.Reader, quiet bool) (dockertypes.ImageLoadResponse, error) {
+ if t.finish == 2 {
+ return dockertypes.ImageLoadResponse{}, fmt.Errorf("Cannot connect to the Docker daemon at unix:///var/run/docker.sock. Is the docker daemon running?")
+ }
_, err := io.Copy(ioutil.Discard, input)
if err != nil {
return dockertypes.ImageLoadResponse{}, err
if api.CalledWith("container.state", "Complete") != nil {
c.Check(err, IsNil)
}
- c.Check(api.WasSetRunning, Equals, true)
-
- c.Check(api.Content[api.Calls-2]["container"].(arvadosclient.Dict)["log"], NotNil)
+ if exitCode != 2 {
+ c.Check(api.WasSetRunning, Equals, true)
+ c.Check(api.Content[api.Calls-2]["container"].(arvadosclient.Dict)["log"], NotNil)
+ }
if err != nil {
for k, v := range api.Logs {
_, err = cr.UploadOutputFile(realTemp+"/"+v, info, err, []string{}, nil, "", "", 0)
c.Assert(err, NotNil)
}
+
+func (s *TestSuite) TestFullBrokenDocker1(c *C) {
+ tf, err := ioutil.TempFile("", "brokenNodeHook-")
+ c.Assert(err, IsNil)
+ defer os.Remove(tf.Name())
+
+ tf.Write([]byte(`#!/bin/sh
+exec echo killme
+`))
+ tf.Close()
+ os.Chmod(tf.Name(), 0700)
+
+ ech := tf.Name()
+ brokenNodeHook = &ech
+
+ api, _, _ := FullRunHelper(c, `{
+ "command": ["echo", "hello world"],
+ "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
+ "cwd": ".",
+ "environment": {},
+ "mounts": {"/tmp": {"kind": "tmp"} },
+ "output_path": "/tmp",
+ "priority": 1,
+ "runtime_constraints": {}
+}`, nil, 2, func(t *TestDockerClient) {
+ t.logWriter.Write(dockerLog(1, "hello world\n"))
+ t.logWriter.Close()
+ })
+
+ c.Check(api.CalledWith("container.state", "Queued"), NotNil)
+ c.Check(api.Logs["crunch-run"].String(), Matches, "(?ms).*unable to run containers.*")
+ c.Check(api.Logs["crunch-run"].String(), Matches, "(?ms).*Running broken node hook.*")
+ c.Check(api.Logs["crunch-run"].String(), Matches, "(?ms).*killme.*")
+
+}
+
+func (s *TestSuite) TestFullBrokenDocker2(c *C) {
+ ech := ""
+ brokenNodeHook = &ech
+
+ api, _, _ := FullRunHelper(c, `{
+ "command": ["echo", "hello world"],
+ "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
+ "cwd": ".",
+ "environment": {},
+ "mounts": {"/tmp": {"kind": "tmp"} },
+ "output_path": "/tmp",
+ "priority": 1,
+ "runtime_constraints": {}
+}`, nil, 2, func(t *TestDockerClient) {
+ t.logWriter.Write(dockerLog(1, "hello world\n"))
+ t.logWriter.Close()
+ })
+
+ c.Check(api.CalledWith("container.state", "Queued"), NotNil)
+ c.Check(api.Logs["crunch-run"].String(), Matches, "(?ms).*unable to run containers.*")
+ c.Check(api.Logs["crunch-run"].String(), Matches, "(?ms).*No broken node hook.*")
+}
projects / arvados.git / commitdiff