X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/879e1f31b0165c6abaa35a023ff66400757bb44b..b17d7233f5ccb8ec3d857ae3e506d53377207376:/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 e9b3f00b61..980ce83ae3 100755
--- 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]
@@ -241,7 +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,
@@ -250,7 +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)
@@ -260,8 +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 => {
@@ -283,6 +285,16 @@ class PipelineInstance
   def [](x)
     @pi[x]
   end
+
+  def log_stderr(msg)
+    $arv.log.create log: {
+      event_type: 'stderr',
+      object_uuid: self[:uuid],
+      owner_uuid: self[:owner_uuid],
+      properties: {"text" => msg},
+    }
+  end
+
   protected
   def initialize(j)
     @attributes_to_update = {}
@@ -320,12 +332,13 @@ class JobCache
       []
     end
   end
-  def self.create(job, create_params)
+  def self.create(pipeline, component, job, create_params)
     @cache ||= {}
+
+    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(create_params),
+                             :body_object => body,
                              :authenticated => false,
                              :headers => {
                                authorization: 'OAuth2 '+ENV['ARVADOS_API_TOKEN']
@@ -334,10 +347,24 @@ 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}"
+
+      pipeline.log_stderr(msg)
       nil
     end
   end
+
+  protected
+
+  def self.no_nil_values(hash)
+    hash.reject { |key, value| value.nil? }
+  end
 end
 
 class WhRunPipelineInstance
@@ -351,10 +378,6 @@ class WhRunPipelineInstance
     if template.match /[^-0-9a-z]/
       # Doesn't look like a uuid -- use it as a filename.
       @template = JSON.parse File.read(template), :symbolize_names => true
-      if !@template[:components]
-        abort ("#{$0}: Template loaded from #{template} " +
-               "does not have a \"components\" key")
-      end
     else
       result = $client.execute(:api_method => $arvados.pipeline_templates.get,
                                :parameters => {
@@ -389,12 +412,29 @@ 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
 
+    if not @template[:components].is_a?(Hash)
+      abort "\n#{Time.now} -- pipeline_template #{@template[:uuid]}\nSyntax error: Template missing \"components\" hash"
+    end
     @components = @template[:components].dup
 
+    bad_components = @components.each_pair.select do |cname, cspec|
+      not cspec.is_a?(Hash)
+    end
+    if bad_components.any?
+      abort "\n#{Time.now} -- pipeline_template #{@template[:uuid]}\nSyntax error: Components not specified with hashes: #{bad_components.map(&:first).join(', ')}"
+    end
+
+    bad_components = @components.each_pair.select do |cname, cspec|
+      not cspec[:script_parameters].is_a?(Hash)
+    end
+    if bad_components.any?
+      abort "\n#{Time.now} -- pipeline_template #{@template[:uuid]}\nSyntax error: Components missing \"script_parameters\" hashes: #{bad_components.map(&:first).join(', ')}"
+    end
+
     errors = []
     @components.each do |componentname, component|
       component[:script_parameters].each do |parametername, parameter|
@@ -418,23 +458,35 @@ 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
   end
 
   def setup_instance
-    if $options[:submit]
-      @instance ||= PipelineInstance.
-        create(:components => @components,
-              :pipeline_template_uuid => @template[:uuid],
-              :state => 'New')
+    if @instance
+      @instance[:properties][:run_options] ||= {}
+      if @options[:no_reuse]
+        # override properties of existing instance
+        @instance[:properties][:run_options][:enable_job_reuse] = false
+      else
+        # Default to "enable reuse" if not specified. (This code path
+        # can go away when old clients go away.)
+        if @instance[:properties][:run_options][:enable_job_reuse].nil?
+          @instance[:properties][:run_options][:enable_job_reuse] = true
+        end
+      end
     else
-      @instance ||= PipelineInstance.
-        create(:components => @components,
-             :pipeline_template_uuid => @template[:uuid],
-             :state => 'RunningOnClient')
+      @instance = PipelineInstance.
+        create(components: @components,
+               properties: {
+                 run_options: {
+                   enable_job_reuse: !@options[:no_reuse]
+                 }
+               },
+               pipeline_template_uuid: @template[:uuid],
+               state: ($options[:submit] ? 'RunningOnServer' : 'RunningOnClient'))
     end
     self
   end
@@ -443,6 +495,7 @@ class WhRunPipelineInstance
     moretodo = true
     interrupted = false
 
+    job_creation_failed = 0
     while moretodo
       moretodo = false
       @components.each do |cname, c|
@@ -459,33 +512,30 @@ 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],
             :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]),
+            :find_or_create => (@instance[:properties][:run_options].andand[:enable_job_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
 
@@ -562,6 +612,11 @@ 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
@@ -582,7 +637,7 @@ class WhRunPipelineInstance
           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
@@ -591,6 +646,13 @@ 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'
@@ -603,6 +665,8 @@ 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
@@ -658,6 +722,18 @@ class WhRunPipelineInstance
       end
     end
   end
+
+  def abort(msg)
+    if @instance
+      if ["New", "Ready", "RunningOnClient",
+          "RunningOnServer"].include?(@instance[:state])
+        @instance[:state] = "Failed"
+        @instance.save
+      end
+      @instance.log_stderr(msg)
+    end
+    Kernel::abort(msg)
+  end
 end
 
 runner = WhRunPipelineInstance.new($options)