Merge branch 'bcbio-nextgen' refs #2991

[arvados.git] / sdk / cli / bin / arv-run-pipeline-instance

diff --git a/sdk/cli/bin/arv-run-pipeline-instance b/sdk/cli/bin/arv-run-pipeline-instance
index bf493cfeba8f5791abaf09967af7ac02d564a441..8b18d377ed9e17dc96234d4e9fcddd141eb64531 100755 (executable)
--- a/sdk/cli/bin/arv-run-pipeline-instance
+++ b/sdk/cli/bin/arv-run-pipeline-instance
@@ -187,7 +187,9 @@ if $options[:instance]
     abort "#{$0}: syntax error: --instance cannot be combined with --template or --submit."
   end
 elsif not $options[:template]
-  abort "#{$0}: syntax error: you must supply a --template or --instance."
+  puts "error: you must supply a --template or --instance."
+  p.educate
+  abort
 end
 
 if $options[:run_here] == $options[:submit]
@@ -322,10 +324,16 @@ class JobCache
   end
   def self.create(job, create_params)
     @cache ||= {}
+
+    jsonified_create_params = {}
+    create_params.each do |k, v|
+      jsonified_create_params[k] = v.to_json unless v.nil?
+    end
+
     result = $client.execute(:api_method => $arvados.jobs.create,
                              :body => {
                                :job => job.to_json
-                             }.merge(create_params),
+                             }.merge(jsonified_create_params),
                              :authenticated => false,
                              :headers => {
                                authorization: 'OAuth2 '+ENV['ARVADOS_API_TOKEN']
@@ -443,25 +451,12 @@ class WhRunPipelineInstance
     moretodo = true
     interrupted = false
 
-    # check if the pipeline os owned by a group
-    owner_uuid = nil
-    group_result = $client.execute(:api_method => $arvados.groups.get,
-                               :parameters => {
-                                 :uuid => @instance[:owner_uuid]
-                               },
-                               :authenticated => false,
-                               :headers => {
-                                 authorization: 'OAuth2 '+ENV['ARVADOS_API_TOKEN']
-                               })
-    group = JSON.parse group_result.body, :symbolize_names => true
-    if group[:uuid]
-      owner_uuid = group[:uuid]
-    end
-
+    job_creation_failed = 0
     while moretodo
       moretodo = false
       @components.each do |cname, c|
         job = nil
+        owner_uuid = @instance[:owner_uuid]
         # Is the job satisfying this component already known to be
         # finished? (Already meaning "before we query API server about
         # the job's current state")
@@ -480,26 +475,22 @@ class WhRunPipelineInstance
             :repository => c[:repository],
             :nondeterministic => c[:nondeterministic],
             :output_is_persistent => c[:output_is_persistent] || false,
+            :runtime_constraints => c[:runtime_constraints],
             :owner_uuid => owner_uuid,
-            # TODO: Delete the following three attributes when
-            # supporting pre-20140418 API servers is no longer
-            # important. New API servers take these as flags that
-            # control behavior of create, rather than job attributes.
-            :minimum_script_version => c[:minimum_script_version],
-            :exclude_script_versions => c[:exclude_minimum_script_versions],
-            :no_reuse => @options[:no_reuse] || c[:nondeterministic],
           }, {
             # 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 => !(@options[:no_reuse] || c[:nondeterministic]),
+            :filters => c[:filters]
           })
           if job
             debuglog "component #{cname} new job #{job[:uuid]}"
             c[:job] = job
           else
-            debuglog "component #{cname} new job failed"
+            debuglog "component #{cname} new job failed", 0
+            job_creation_failed += 1
           end
         end
 
@@ -576,6 +567,11 @@ class WhRunPipelineInstance
         moretodo = false
       end
 
+      # If job creation fails, just give up on this pipeline instance.
+      if job_creation_failed > 0
+        moretodo = false
+      end
+
       if moretodo
         begin
           sleep 10
@@ -592,11 +588,11 @@ class WhRunPipelineInstance
     failed = 0
     @components.each do |cname, c|
       if c[:job]
-        if c[:job][:finished_at]
+        if c[:job][:finished_at] or c[:job][:cancelled_at] or (c[:job][:running] == false and c[:job][:success] == false)
           ended += 1
           if c[:job][:success] == true
             succeeded += 1
-          elsif c[:job][:success] == false
+          elsif c[:job][:success] == false or c[:job][:cancelled_at]
             failed += 1
           end
         end
@@ -605,6 +601,13 @@ class WhRunPipelineInstance
 
     success = (succeeded == @components.length)
 
+    # A job create call failed. Just give up.
+    if job_creation_failed > 0
+      debuglog "job creation failed - giving up on this pipeline instance", 0
+      success = false
+      failed += 1
+    end
+
     if interrupted
      if success
         @instance[:state] = 'Complete'
@@ -617,6 +620,8 @@ class WhRunPipelineInstance
       end
     end
 
+    debuglog "pipeline instance state is #{@instance[:state]}"
+
     # set components_summary
     components_summary = {"todo" => @components.length - ended, "done" => succeeded, "failed" => failed}
     @instance[:components_summary] = components_summary