From: Peter Amstutz Date: Fri, 9 Aug 2019 15:34:02 +0000 (-0400) Subject: 15133: Remove more referencesto arv-run and arv-run-pipeline-instance X-Git-Tag: 2.0.0~225^2~8 X-Git-Url: https://git.arvados.org/arvados.git/commitdiff_plain/14626b1a574924a23f18073b8bb6eff829d66e5a 15133: Remove more referencesto arv-run and arv-run-pipeline-instance Arvados-DCO-1.1-Signed-off-by: Peter Amstutz --- diff --git a/doc/_includes/_arv_run_redirection.liquid b/doc/_includes/_arv_run_redirection.liquid deleted file mode 100644 index 663de0b796..0000000000 --- a/doc/_includes/_arv_run_redirection.liquid +++ /dev/null @@ -1,27 +0,0 @@ -{% comment %} -Copyright (C) The Arvados Authors. All rights reserved. - -SPDX-License-Identifier: CC-BY-SA-3.0 -{% endcomment %} - - -
-$ cd ~/keep/by_id/3229739b505d2b878b62aed09895a55a+142
-$ ls *.fastq
-$ arv-run grep -H -n ATTGGAGGAAAGATGAGTGAC \< *.fastq \> output.txt
-[...]
- 1 stderr run-command: grep -H -n ATTGGAGGAAAGATGAGTGAC < /keep/3229739b505d2b878b62aed09895a55a+142/HWI-ST1027_129_D0THKACXX.1_1.fastq > output.txt
- 2 stderr run-command: grep -H -n ATTGGAGGAAAGATGAGTGAC < /keep/3229739b505d2b878b62aed09895a55a+142/HWI-ST1027_129_D0THKACXX.1_2.fastq > output.txt
- 2 stderr run-command: completed with exit code 0 (success)
- 2 stderr run-command: the following output files will be saved to keep:
- 2 stderr run-command: 121 ./output.txt
- 2 stderr run-command: start writing output to keep
- 1 stderr run-command: completed with exit code 0 (success)
- 1 stderr run-command: the following output files will be saved to keep:
- 1 stderr run-command: 363 ./output.txt
- 1 stderr run-command: start writing output to keep
- 2 stderr upload wrote 121 total 121
- 1 stderr upload wrote 363 total 363
-[..]
-
- diff --git a/doc/api/execution.html.textile.liquid b/doc/api/execution.html.textile.liquid index cada9ab1b8..74942ba55f 100644 --- a/doc/api/execution.html.textile.liquid +++ b/doc/api/execution.html.textile.liquid @@ -49,10 +49,3 @@ For example, for a 3.75 GiB node, default Keep cache, and no extra RAM reserved: (3840 * 0.95) - 256 = 3392 MiB To run on this instance type, the container can request at most 3392 MiB of working RAM. - -h2. Job API (deprecated) - -# To submit work, create a "job":{{site.baseurl}}/api/methods/jobs.html . If the same job has been submitted in the past, it will return an existing job in @Completed@ state. -# The dispatcher process will notice a new job in @Queued@ state and attempt to allocate nodes to run the job. -# The job executes. -# Retrieve the @output@ field with the portable data hash of the collection with the output files of the job. diff --git a/doc/sdk/cli/subcommands.html.textile.liquid b/doc/sdk/cli/subcommands.html.textile.liquid index b23ec46fa7..50d5d89871 100644 --- a/doc/sdk/cli/subcommands.html.textile.liquid +++ b/doc/sdk/cli/subcommands.html.textile.liquid @@ -339,98 +339,3 @@ optional arguments: Default 3. - - -h3(#arv-pipeline-run). arv pipeline run - -WARNING: this uses the obsolete "job" API. Don't use this. You should use @arvados-cwl-runner@ instead. - -@arv pipeline run@ can be used to start a pipeline run from the command line. - -The User Guide has a page with a bit more information on "using arv pipeline run":{{site.baseurl}}/user/topics/running-pipeline-command-line.html. - - -
-$ arv pipeline run --help
-Options:
-        --dry-run, -n:   Do not start any new jobs or wait for existing jobs to
-                         finish. Just find out whether jobs are finished,
-                         queued, or running for each component.
-    --status-text <s>:   Store plain text status in given file. (Default:
-                         /dev/stdout)
-    --status-json <s>:   Store json-formatted pipeline in given file. (Default:
-                         /dev/null)
-            --no-wait:   Do not wait for jobs to finish. Just look up status,
-                         submit new jobs if needed, and exit.
-           --no-reuse:   Do not reuse existing jobs to satisfy pipeline
-                         components. Submit a new job for every component.
-          --debug, -d:   Print extra debugging information on stderr.
-    --debug-level <i>:   Set debug verbosity level.
-       --template <s>:   UUID of pipeline template, or path to local pipeline
-                         template file.
-       --instance <s>:   UUID of pipeline instance.
-             --submit:   Submit the pipeline instance to the server, and exit.
-                         Let the Crunch dispatch service satisfy the components
-                         by finding/running jobs.
-  --run-pipeline-here:   Manage the pipeline instance in-process. Submit jobs
-                         to Crunch as needed. Do not exit until the pipeline
-                         finishes (or fails).
-      --run-jobs-here:   Run jobs in the local terminal session instead of
-                         submitting them to Crunch. Implies
-                         --run-pipeline-here. Note: this results in a
-                         significantly different job execution environment, and
-                         some Crunch features are not supported. It can be
-                         necessary to modify a pipeline in order to make it run
-                         this way.
-           --run-here:   Synonym for --run-jobs-here.
-    --description <s>:   Description for the pipeline instance.
-        --version, -v:   Print version and exit
-           --help, -h:   Show this message
-
- - -h3(#arv-run). arv run - -WARNING: this uses the obsolete "job" API. Don't use this. You should use @arvados-cwl-runner@ instead. - -The @arv-run@ command creates Arvados pipelines at the command line that fan out to multiple concurrent tasks across Arvados compute nodes. - -The User Guide has a page on "using arv-run":{{site.baseurl}}/user/topics/arv-run.html. - - -
-$ arv run --help
-usage: arv-run [-h] [--retries RETRIES] [--dry-run] [--local]
-               [--docker-image DOCKER_IMAGE] [--ignore-rcode] [--no-reuse]
-               [--no-wait] [--project-uuid PROJECT_UUID] [--git-dir GIT_DIR]
-               [--repository REPOSITORY] [--script-version SCRIPT_VERSION]
-               ...
-
-positional arguments:
-  args
-
-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.
-  --dry-run             Print out the pipeline that would be submitted and
-                        exit
-  --local               Run locally using arv-run-pipeline-instance
-  --docker-image DOCKER_IMAGE
-                        Docker image to use, otherwise use instance default.
-  --ignore-rcode        Commands that return non-zero return codes should not
-                        be considered failed.
-  --no-reuse            Do not reuse past jobs.
-  --no-wait             Do not wait and display logs after submitting command,
-                        just exit.
-  --project-uuid PROJECT_UUID
-                        Parent project of the pipeline
-  --git-dir GIT_DIR     Git repository passed to arv-crunch-job when using
-                        --local
-  --repository REPOSITORY
-                        repository field of component, default 'arvados'
-  --script-version SCRIPT_VERSION
-                        script_version field of component, default 'master'
-
- diff --git a/lib/cli/external.go b/lib/cli/external.go index 35933f99fc..eddb563f7a 100644 --- a/lib/cli/external.go +++ b/lib/cli/external.go @@ -31,9 +31,6 @@ var ( "normalize": externalCmd{"arv-normalize"}, "docker": externalCmd{"arv-keepdocker"}, }) - Pipeline = cmd.Multi(map[string]cmd.Handler{ - "run": externalCmd{"arv-run-pipeline-instance"}, - }) // user, group, container, specimen, etc. APICall = apiCallCmd{} ) @@ -94,7 +91,7 @@ func (ec externalCmd) RunCommand(prog string, args []string, stdin io.Reader, st return 1 case *exec.Error: fmt.Fprintln(stderr, err) - if ec.prog == "arv" || ec.prog == "arv-run-pipeline-instance" { + if ec.prog == "arv" { fmt.Fprint(stderr, rubyInstallHints) } else if strings.HasPrefix(ec.prog, "arv-") { fmt.Fprint(stderr, pythonInstallHints) diff --git a/lib/config/export.go b/lib/config/export.go index b125d7dc91..b6d0236bb0 100644 --- a/lib/config/export.go +++ b/lib/config/export.go @@ -96,13 +96,8 @@ var whitelist = map[string]bool{ "Containers.DefaultKeepCacheRAM": true, "Containers.DispatchPrivateKey": false, "Containers.JobsAPI": true, - "Containers.JobsAPI.CrunchJobUser": false, - "Containers.JobsAPI.CrunchJobWrapper": false, - "Containers.JobsAPI.CrunchRefreshTrigger": false, - "Containers.JobsAPI.DefaultDockerImage": false, "Containers.JobsAPI.Enable": true, "Containers.JobsAPI.GitInternalDir": false, - "Containers.JobsAPI.ReuseJobIfOutputsDiffer": false, "Containers.Logging": false, "Containers.LogReuseDecisions": false, "Containers.MaxComputeVMs": false, diff --git a/sdk/cli/bin/arv b/sdk/cli/bin/arv index 7110b4b991..25c28bea23 100755 --- a/sdk/cli/bin/arv +++ b/sdk/cli/bin/arv @@ -131,16 +131,6 @@ def check_subcommands client, arvados, subcommand, global_opts, remaining_opts puts "Available methods: ls, get, put, docker" end abort - when 'pipeline' - sub = remaining_opts.shift - if sub == 'run' - exec_bin "arv-run-pipeline-instance", remaining_opts - else - puts "Usage: arv pipeline [method] [--parameters]\n" - puts "Use 'arv pipeline [method] --help' to get more information about specific methods.\n\n" - puts "Available methods: run" - end - abort end end diff --git a/services/api/app/models/pipeline_instance.rb b/services/api/app/models/pipeline_instance.rb index c0781ef228..23579ff132 100644 --- a/services/api/app/models/pipeline_instance.rb +++ b/services/api/app/models/pipeline_instance.rb @@ -109,30 +109,7 @@ class PipelineInstance < ArvadosModel end def cancel(cascade: false, need_transaction: true) - if need_transaction - ActiveRecord::Base.transaction do - cancel(cascade: cascade, need_transaction: false) - end - return - end - - if self.state.in?([RunningOnServer, RunningOnClient]) - self.state = Paused - self.save! - elsif self.state != Paused - raise InvalidStateTransitionError - end - - return if !cascade - - # cancel all child jobs - children = self.components.andand.collect{|_, c| c['job']}.compact.collect{|j| j['uuid']}.compact - - return if children.empty? - - Job.where(uuid: children, state: [Job::Queued, Job::Running]).each do |job| - job.cancel(cascade: cascade, need_transaction: false) - end + raise "No longer supported" end protected