change labels in revtool wf (#972)

Makes for better debugging experience

Author: psafont

tests/test_provenance.py

@@ -176,7 +176,7 @@ def check_output_object(base_path):
     compare_location = "../data/b9/b9214658cc453331b62c2282b772a5c063dbd284"
     with open(output_obj) as fp:
         out_json = json.load(fp)
-    f1 = out_json["output"]
+    f1 = out_json["sorted_output"]
     assert f1["checksum"] == compare_checksum
     assert f1["location"] == compare_location
 

tests/wf/expect_packed.cwl

@@ -10,6 +10,12 @@
                 }
             ],
             "inputs": [
+                {
+                    "type": "boolean",
+                    "default": true,
+                    "doc": "If true, reverse (decending) sort",
+                    "id": "#main/reverse_sort"
+                },
                 {
                     "type": "File",
                     "doc": "The input file to be processed.",
@@ -18,50 +24,44 @@
                         "class": "File",
                         "location": "hello.txt"
                     },
-                    "id": "#main/input"
-                },
-                {
-                    "type": "boolean",
-                    "default": true,
-                    "doc": "If true, reverse (decending) sort",
-                    "id": "#main/reverse_sort"
+                    "id": "#main/workflow_input"
                 }
             ],
             "outputs": [
                 {
                     "type": "File",
-                    "outputSource": "#main/sorted/output",
+                    "outputSource": "#main/sorted/sorted_output",
                     "doc": "The output with the lines reversed and sorted.",
-                    "id": "#main/output"
+                    "id": "#main/sorted_output"
                 }
             ],
             "steps": [
                 {
                     "in": [
                         {
-                            "source": "#main/input",
-                            "id": "#main/rev/input"
+                            "source": "#main/workflow_input",
+                            "id": "#main/rev/revtool_input"
                         }
                     ],
                     "out": [
-                        "#main/rev/output"
+                        "#main/rev/revtool_output"
                     ],
                     "run": "#revtool.cwl",
                     "id": "#main/rev"
                 },
                 {
                     "in": [
-                        {
-                            "source": "#main/rev/output",
-                            "id": "#main/sorted/input"
-                        },
                         {
                             "source": "#main/reverse_sort",
                             "id": "#main/sorted/reverse"
+                        },
+                        {
+                            "source": "#main/rev/revtool_output",
+                            "id": "#main/sorted/sorted_input"
                         }
                     ],
                     "out": [
-                        "#main/sorted/output"
+                        "#main/sorted/sorted_output"
                     ],
                     "run": "#sorttool.cwl",
                     "id": "#main/sorted"
@@ -79,7 +79,7 @@
                 {
                     "type": "File",
                     "inputBinding": {},
-                    "id": "#revtool.cwl/input"
+                    "id": "#revtool.cwl/revtool_input"
                 }
             ],
             "outputs": [
@@ -88,7 +88,7 @@
                     "outputBinding": {
                         "glob": "output.txt"
                     },
-                    "id": "#revtool.cwl/output"
+                    "id": "#revtool.cwl/revtool_output"
                 }
             ],
             "baseCommand": "rev",
@@ -108,7 +108,7 @@
                     }
                 },
                 {
-                    "id": "#sorttool.cwl/input",
+                    "id": "#sorttool.cwl/sorted_input",
                     "type": "File",
                     "inputBinding": {
                         "position": 2
@@ -117,7 +117,7 @@
             ],
             "outputs": [
                 {
-                    "id": "#sorttool.cwl/output",
+                    "id": "#sorttool.cwl/sorted_output",
                     "type": "File",
                     "outputBinding": {
                         "glob": "output.txt"
@@ -131,7 +131,7 @@
     ],
     "cwlVersion": "v1.0",
     "$schemas": [
-        "file:///home/mcrusoe/cwltool/tests/wf/empty2.ttl",
-        "file:///home/mcrusoe/cwltool/tests/wf/empty.ttl"
+        "empty.ttl",
+        "empty2.ttl"
     ]
 }

tests/wf/revsort-job.json

@@ -1,5 +1,5 @@
 {
-  "input": {
+  "workflow_input": {
     "class": "File",
     "location": "whale.txt",
     "format": "https://www.iana.org/assignments/media-types/text/plain"

tests/wf/revsort.cwl

@@ -21,7 +21,7 @@ hints:
 # field "reverse_sort" is not provided in the input object, the default value will
 # be used.
 inputs:
-  input:
+  workflow_input:
     type: File
     doc: "The input file to be processed."
     format: iana:text/plain
@@ -37,36 +37,36 @@ inputs:
 # the outputs of the workflow.
 #
 # Each output field must be connected to the output of one of the workflow
-# steps using the "connect" field.  Here, the parameter "#output" of the
-# workflow comes from the "#sorted" output of the "sort" step.
+# steps using the "outputSource" field.  Here, the parameter "sorted_output" of the
+# workflow comes from the "sorted_output" output of the "sorted" step.
 outputs:
-  output:
+  sorted_output:
     type: File
-    outputSource: sorted/output
+    outputSource: sorted/sorted_output
     doc: "The output with the lines reversed and sorted."
 
 # The "steps" array lists the executable steps that make up the workflow.
 # The tool to execute each step is listed in the "run" field.
 #
-# In the first step, the "inputs" field of the step connects the upstream
-# parameter "#input" of the workflow to the input parameter of the tool
-# "revtool.cwl#input"
+# In the first step, the "in" field of the step connects the upstream
+# parameter "workflow_input" of the workflow to the input parameter of the tool
+# "revtool_input"
 #
-# In the second step, the "inputs" field of the step connects the output
-# parameter "#reversed" from the first step to the input parameter of the
-# tool "sorttool.cwl#input".
+# In the second step, the "in" field of the step connects the output
+# parameter "revtool_output" from the first step to the input parameter of the
+# tool "sorted_input".
 steps:
   rev:
     in:
-      input: input
-    out: [output]
+      revtool_input: workflow_input
+    out: [revtool_output]
     run: revtool.cwl
 
   sorted:
     in:
-      input: rev/output
+      sorted_input: rev/revtool_output
       reverse: reverse_sort
-    out: [output]
+    out: [sorted_output]
     run: sorttool.cwl
 
 $namespaces:

tests/wf/revtool.cwl

@@ -17,7 +17,7 @@ $schemas:
 # which indicates that the file name should be added to the command line at
 # a default location.
 inputs:
-  input:
+  revtool_input:
     type: File
     inputBinding: {}
 
@@ -27,7 +27,7 @@ inputs:
 # and after the program executes, the output value will be the file
 # output.txt in the designated output directory.
 outputs:
-  output:
+  revtool_output:
     type: File
     outputBinding:
       glob: output.txt

tests/wf/sorttool.cwl

@@ -21,13 +21,13 @@ inputs:
     inputBinding:
       position: 1
       prefix: "--reverse"
-  - id: input
+  - id: sorted_input
     type: File
     inputBinding:
       position: 2
 
 outputs:
-  - id: output
+  - id: sorted_output
     type: File
     outputBinding:
       glob: output.txt