3826: Merge branch 'master' into 3826-crunchstat-netstats

[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 ded7ab152049308b8dfd685a2190672f72ad89ab..63313fc8082a18b7c637a222d92cabafc76e4ab3 100755 (executable)
--- a/sdk/cli/bin/arv-run-pipeline-instance
+++ b/sdk/cli/bin/arv-run-pipeline-instance
@@ -445,12 +445,17 @@ class WhRunPipelineInstance
         if value.nil? and
             ![false,'false',0,'0'].index parameter[:required]
           if parameter[:output_of]
+            if not @components[parameter[:output_of].intern]
+              errors << [componentname, parametername, "output_of refers to nonexistent component '#{parameter[:output_of]}'"]
+            end
             next
           end
           errors << [componentname, parametername, "required parameter is missing"]
         end
         debuglog "parameter #{componentname}::#{parametername} == #{value}"
-        component[:script_parameters][parametername] = value
+
+        component[:script_parameters][parametername] =
+          parameter.dup.merge(value: value)
       end
     end
     if !errors.empty?
@@ -518,7 +523,9 @@ class WhRunPipelineInstance
           my_submit_id = "instance #{@instance[:uuid]} rand #{rand(2**64).to_s(36)}"
           job = JobCache.create(@instance, cname, {
             :script => c[:script],
-            :script_parameters => c[:script_parameters],
+            :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],
@@ -594,7 +601,7 @@ class WhRunPipelineInstance
               c2[:script_parameters].each do |pname, p|
                 if p.is_a? Hash and p[:output_of] == cname.to_s
                   debuglog "parameter #{c2name}::#{pname} == #{c[:job][:output]}"
-                  c2[:script_parameters][pname] = c[:job][:output]
+                  c2[:script_parameters][pname] = {value: c[:job][:output]}
                   moretodo = true
                 end
               end
@@ -652,8 +659,9 @@ class WhRunPipelineInstance
                 end
               end
             end
-          elsif c[:job][:state] == "Running"
-            # Job is still running
+          elsif ["Queued", "Running"].include? c[:job][:state]
+            # Job is running or queued to run, so indicate that pipeline
+            # should continue to run
             moretodo = true
           elsif c[:job][:state] == "Cancelled"
             debuglog "component #{cname} job #{c[:job][:uuid]} cancelled."
@@ -686,11 +694,11 @@ class WhRunPipelineInstance
       end
     end
 
-    c_in_state = @components.values.group_by { |c| 
+    c_in_state = @components.values.group_by { |c|
       c[:job] and c[:job][:state]
     }
-    succeeded = c_in_state["Complete"].count
-    failed = c_in_state["Failed"].count + c_in_state["Cancelled"].count
+    succeeded = c_in_state["Complete"].andand.count || 0
+    failed = (c_in_state["Failed"].andand.count || 0) + (c_in_state["Cancelled"].andand.count || 0)
     ended = succeeded + failed
 
     success = (succeeded == @components.length)