Merge branch 'prov_secondary_files' of https://github.com/common-workflow-language/cwltool into prov_secondary_files

Author: FarahZKhan

cwltool/provenance.py

@@ -539,9 +539,9 @@ def declare_file(self, value):
                     value["checksum"] = "%s$%s" % (SHA1, checksum)
 
 
-        if not entity and 'content' in value:
+        if not entity and 'contents' in value:
             # Anonymous file, add content as string
-            entity,checksum = self.declare_string(value["content"])
+            entity,checksum = self.declare_string(value["contents"])
 
         # By here one of them should have worked!
         if not entity:

tests/test_provenance.py

@@ -135,6 +135,13 @@ def test_secondary_files_explicit(self):
         self.check_provenance(secondary_files=True)
         self.check_secondary_files()
 
+    def test_secondary_files_output(self):
+        # secondary will be picked up by .idx
+        self.cwltool(get_data('tests/wf/sec-wf-out.cwl'))
+        self.check_provenance(secondary_files=True)
+        # Skipped, not the same secondary files as above
+        #self.check_secondary_files()
+
     def test_directory_workflow(self):
         dir2 = os.path.join(tempfile.mkdtemp("test_directory_workflow"),
             "dir2")
@@ -503,7 +510,6 @@ def check_prov(self, nested=False, single_tool=False, directory=False,
                 prim_basename = set(g.objects(prim, CWLPROV.basename)).pop()
                 prim_nameroot = set(g.objects(prim, CWLPROV.nameroot)).pop()
                 prim_nameext = set(g.objects(prim, CWLPROV.nameext)).pop()
-                self.assertEquals(sec_nameroot, prim_basename)
                 self.assertEquals(str(prim_basename), "%s%s" % (prim_nameroot, prim_nameext))
 
 

tests/wf/sec-wf-out.cwl

@@ -0,0 +1,44 @@
+class: Workflow
+cwlVersion: v1.0
+inputs: []
+outputs:
+  file1:
+    type: File
+    outputSource: step1/file1
+
+
+steps:
+  step1:
+    in: []
+    out:
+      - file1
+      - file1csv
+    run:
+      class: CommandLineTool
+      requirements:
+      - class: ShellCommandRequirement
+      arguments:
+      - shellQuote: false
+        valueFrom: >
+          echo "abc" > f.txt;
+          echo "3" > f.txt.size;
+          echo "a" > f.txt.firstletter;
+          echo "a,b,c" > f.csv;
+          echo "1,2,3" > f.csv.columns;
+          echo "ignored" > f.txt.ignoreme;
+      inputs: []
+      outputs:
+        file1:
+          type: File
+          outputBinding:
+            glob: "f.txt"
+          secondaryFiles:
+            - ".size"
+            - ".firstletter"
+            - "^.csv"
+        file1csv:
+            type: File
+            outputBinding:
+              glob: "f.csv"
+            secondaryFiles:
+            - ".columns"