[ARVADOS] created: 67e6092c464fcce21eecf79b93366231820e7705

[git at public.curoverse.com]

        at  67e6092c464fcce21eecf79b93366231820e7705 (commit)


commit 67e6092c464fcce21eecf79b93366231820e7705
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date:   Thu Nov 13 17:12:05 2014 -0500

    4035: Looks for "tooldescription" in the component, if found, processes common-workflow-language and submits a run-command from that.

diff --git a/sdk/cli/bin/arv-run-pipeline-instance b/sdk/cli/bin/arv-run-pipeline-instance
index 63313fc..51f82d6 100755
--- a/sdk/cli/bin/arv-run-pipeline-instance
+++ b/sdk/cli/bin/arv-run-pipeline-instance
@@ -521,28 +521,89 @@ class WhRunPipelineInstance
           # are fully specified (any output_of script_parameters are resolved
           # to real value)
           my_submit_id = "instance #{@instance[:uuid]} rand #{rand(2**64).to_s(36)}"
-          job = JobCache.create(@instance, cname, {
-            :script => c[:script],
-            :script_parameters => Hash[c[:script_parameters].map do |key, spec|
-                                         [key, spec[:value]]
-                                       end],
-            :script_version => c[:script_version],
-            :repository => c[:repository],
-            :nondeterministic => c[:nondeterministic],
-            :runtime_constraints => c[:runtime_constraints],
-            :owner_uuid => owner_uuid,
-            :is_locked_by_uuid => (@options[:run_jobs_here] ? owner_uuid : nil),
-            :submit_id => my_submit_id,
-            :state => (if @options[:run_jobs_here] then "Running" else "Queued" end)
-          }, {
-            # This is the right place to put these attributes when
-            # dealing with new API servers.
-            :minimum_script_version => c[:minimum_script_version],
-            :exclude_script_versions => c[:exclude_minimum_script_versions],
-            :find_or_create => (@instance[:properties][:run_options].andand[:enable_job_reuse] &&
-                                !c[:nondeterministic]),
-            :filters => c[:filters]
-          })
+
+          if c[:tooldescription]
+            require 'shellwords'
+            # command workflow language tool description
+            tooldesc = JSON.load(`arv-get #{c[:tooldescription].shellescape}`)
+            if $?.exitstatus == 0
+              require 'tempfile'
+              tooldesc_file = Tempfile.new('tooldesc')
+              jobdesc_file = Tempfile.new('jobdesc')
+              begin
+                tooldesc_file.write(tooldesc.to_json)
+                tooldesc_file.close
+
+                jobdesc_file.write({"inputs" => Hash[c[:script_parameters].map do |key, spec|
+                                           [key, spec[:value]]
+                                         end]}.to_json)
+                jobdesc_file.close
+
+                args = JSON.load(`cwltool --conformance-test --no-container --basedir=/keep #{tooldesc_file.path} #{jobdesc_file.path}`)
+                script_parameters = {}
+                script_parameters["command"] = args["args"]
+                script_parameters["task.stdout"] = args["stdout"]
+                script_parameters["task.stdin"] = args["stdin"]
+
+                runtime_constraints = {}
+                container = tooldesc["requirements"].andand["environment"].andand["container"]
+                if container and container["type"] == "docker"
+                  runtime_constraints["docker_image"] = container["imageId"]
+                end
+
+                job = JobCache.create(@instance, cname, {
+                                        :script => "run-command",
+                                        :script_parameters => script_parameters,
+                                        :script_version => "master",
+                                        :repository => "arvados",
+                                        :nondeterministic => c[:nondeterministic],
+                                        :runtime_constraints => runtime_constraints,
+                                        :owner_uuid => owner_uuid,
+                                        :is_locked_by_uuid => (@options[:run_jobs_here] ? owner_uuid : nil),
+                                        :submit_id => my_submit_id,
+                                        :state => (if @options[:run_jobs_here] then "Running" else "Queued" end)
+                                      }, {
+                                        # This is the right place to put these attributes when
+                                        # dealing with new API servers.
+                                        :minimum_script_version => c[:minimum_script_version],
+                                        :exclude_script_versions => c[:exclude_minimum_script_versions],
+                                        :find_or_create => (@instance[:properties][:run_options].andand[:enable_job_reuse] &&
+                                                            !c[:nondeterministic]),
+                                        :filters => c[:filters]
+                                      })
+
+              ensure
+                tooldesc_file.unlink
+                jobdesc_file.unlink
+              end
+            else
+              debuglog "component #{cname} new job failed with output #{tooldesc}", 0
+              job_creation_failed += 1
+            end
+          else
+            job = JobCache.create(@instance, cname, {
+                                    :script => c[:script],
+                                    :script_parameters => Hash[c[:script_parameters].map do |key, spec|
+                                                                 [key, spec[:value]]
+                                                               end],
+                                    :script_version => c[:script_version],
+                                    :repository => c[:repository],
+                                    :nondeterministic => c[:nondeterministic],
+                                    :runtime_constraints => c[:runtime_constraints],
+                                    :owner_uuid => owner_uuid,
+                                    :is_locked_by_uuid => (@options[:run_jobs_here] ? owner_uuid : nil),
+                                    :submit_id => my_submit_id,
+                                    :state => (if @options[:run_jobs_here] then "Running" else "Queued" end)
+                                  }, {
+                                    # This is the right place to put these attributes when
+                                    # dealing with new API servers.
+                                    :minimum_script_version => c[:minimum_script_version],
+                                    :exclude_script_versions => c[:exclude_minimum_script_versions],
+                                    :find_or_create => (@instance[:properties][:run_options].andand[:enable_job_reuse] &&
+                                                        !c[:nondeterministic]),
+                                    :filters => c[:filters]
+                                  })
+          end
           if job
             debuglog "component #{cname} new job #{job[:uuid]}"
             c[:job] = job

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hooks/post-receive
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