arvados-cli 0.1.20140813140640 → 0.1.20140813163950

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 22110a572737a88fb8e942d35638ec83ea8b7a2f
-  data.tar.gz: b622e9fb6b2819979b86ae00061fb43e101568e0
+  metadata.gz: b37b987ad9590136675ca8f33824071d47695fb7
+  data.tar.gz: af38929fb8566e70449a85eeb6a897a4ae0f9b74
 SHA512:
-  metadata.gz: 78f1cd06ff3890a5ec0ae688a6ce2eeb2110dca97e2d36762398b1c738929154fa6cf0c2fe8cc88ae83cf3ff8b96630b5ca3411f5577798c039d01b1fd264e05
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+  metadata.gz: fbae3de1461375f0efbdf8cbf38de5170c4e33e408cd883d9f6ae524de567b39c05bd3993a37b93ac090d942212f909d11bbe7cc342547ea872205638e4a38ba
+  data.tar.gz: dcaafc1451a75704bc13835aa131419a7741f14e9e41d07c52e6467d99645ee8cfaf20ea74f9868acb0d96514a82fc53e9a1b955c26b6c2e869a3c31f6937afc

data/bin/arv-run-pipeline-instance

@@ -285,6 +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 = {}
@@ -345,19 +355,7 @@ class JobCache
       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']
-                      })
+      pipeline.log_stderr(msg)
       nil
     end
   end
@@ -380,10 +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 => {
@@ -422,8 +416,25 @@ class WhRunPipelineInstance
       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|
@@ -711,6 +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)

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: arvados-cli
 version: !ruby/object:Gem::Version
-  version: 0.1.20140813140640
+  version: 0.1.20140813163950
 platform: ruby
 authors:
 - Arvados Authors
@@ -166,7 +166,7 @@ dependencies:
     - - "<"
       - !ruby/object:Gem::Version
         version: 1.0.0
-description: This is the Arvados SDK CLI gem, git revision 3cc80b447efcaf416ea4d6857d6d40583e462ff8
+description: This is the Arvados SDK CLI gem, git revision 7482410350df49dbddab05448b167bf61f14d71e
 email: gem-dev@curoverse.com
 executables:
 - arv