3373: arv-run-pipeline-instance: removed .to_json where objects are supplied to ...

[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 8b18d377ed9e17dc96234d4e9fcddd141eb64531..0fdf27d96ff5ea9a3d56e462d9f6e9a5f6f646fd 100755 (executable)
--- a/sdk/cli/bin/arv-run-pipeline-instance
+++ b/sdk/cli/bin/arv-run-pipeline-instance
@@ -243,7 +243,7 @@ class PipelineInstance
   end
   def self.create(attributes)
     result = $client.execute(:api_method => $arvados.pipeline_instances.create,
-                             :body => {
+                             :body_object => {
                                :pipeline_instance => attributes
                              },
                              :authenticated => false,
@@ -252,7 +252,7 @@ class PipelineInstance
                              })
     j = JSON.parse result.body, :symbolize_names => true
     unless j.is_a? Hash and j[:uuid]
-      abort "Failed to create pipeline_instance: #{j[:errors] rescue nil} #{j.inspect}"
+      abort "\n#{Time.now} -- pipeline_template #{@template[:uuid]}\nFailed to create pipeline_instance: #{j[:errors] rescue nil} #{j.inspect}"
     end
     debuglog "Created pipeline instance: #{j[:uuid]}"
     self.new(j)
@@ -262,8 +262,8 @@ class PipelineInstance
                              :parameters => {
                                :uuid => @pi[:uuid]
                              },
-                             :body => {
-                               :pipeline_instance => @attributes_to_update.to_json
+                             :body_object => {
+                               :pipeline_instance => @attributes_to_update
                              },
                              :authenticated => false,
                              :headers => {
@@ -322,18 +322,13 @@ class JobCache
       []
     end
   end
-  def self.create(job, create_params)
+  def self.create(pipeline, component, job, create_params)
     @cache ||= {}
 
-    jsonified_create_params = {}
-    create_params.each do |k, v|
-      jsonified_create_params[k] = v.to_json unless v.nil?
-    end
+    body = {job: no_nil_values(job)}.merge(no_nil_values(create_params))
 
     result = $client.execute(:api_method => $arvados.jobs.create,
-                             :body => {
-                               :job => job.to_json
-                             }.merge(jsonified_create_params),
+                             :body_object => body,
                              :authenticated => false,
                              :headers => {
                                authorization: 'OAuth2 '+ENV['ARVADOS_API_TOKEN']
@@ -342,10 +337,36 @@ class JobCache
     if j.is_a? Hash and j[:uuid]
       @cache[j[:uuid]] = j
     else
-      debuglog "create job: #{j[:errors] rescue nil} with attributes #{job}", 0
+      debuglog "create job: #{j[:errors] rescue nil} with attributes #{body}", 0
+
+      msg = ""
+      j[:errors].each do |err|
+        msg += "Error creating job for component #{component}: #{err}\n"
+      end
+      msg += "Job submission was: #{body.to_json}"
+
+      $client.execute(:api_method => $arvados.logs.create,
+                      :body_object => {
+                        :log => {
+                          :object_uuid => pipeline[:uuid],
+                          :event_type => 'stderr',
+                          :owner_uuid => pipeline[:owner_uuid],
+                          :properties => {"text" => msg}
+                        }
+                      },
+                      :authenticated => false,
+                      :headers => {
+                        authorization: 'OAuth2 '+ENV['ARVADOS_API_TOKEN']
+                      })
       nil
     end
   end
+
+  protected
+
+  def self.no_nil_values(hash)
+    hash.reject { |key, value| value.nil? }
+  end
 end
 
 class WhRunPipelineInstance
@@ -397,7 +418,7 @@ class WhRunPipelineInstance
         param = params_args.shift.sub /^--/, ''
         params[param] = params_args.shift
       else
-        abort "Syntax error: I do not know what to do with arg \"#{params_args[0]}\""
+        abort "\n#{Time.now} -- pipeline_template #{@template[:uuid]}\nSyntax error: I do not know what to do with arg \"#{params_args[0]}\""
       end
     end
 
@@ -426,7 +447,7 @@ class WhRunPipelineInstance
       end
     end
     if !errors.empty?
-      abort "Errors:\n#{errors.collect { |c,p,e| "#{c}::#{p} - #{e}\n" }.join ""}"
+      abort "\n#{Time.now} -- pipeline_template #{@template[:uuid]}\nErrors:\n#{errors.collect { |c,p,e| "#{c}::#{p} - #{e}\n" }.join ""}"
     end
     debuglog "options=" + @options.pretty_inspect
     self
@@ -468,7 +489,7 @@ class WhRunPipelineInstance
           # No job yet associated with this component and is component inputs
           # are fully specified (any output_of script_parameters are resolved
           # to real value)
-          job = JobCache.create({
+          job = JobCache.create(@instance, cname, {
             :script => c[:script],
             :script_parameters => c[:script_parameters],
             :script_version => c[:script_version],