Squashed 'cwltool/schemas/' changes from 50bd76a..3e1b02c

3e1b02c Merge commit '6ac559ed62780091eb0cfff914018ed101ef46ef' into scoped-ref-and-typedsl
6ac559e version bump
2cfde6b Merge pull request #32 from common-workflow-language/type_dsl
b8edddc re-enable test_avro_regression
bedb736 Merge branch 'type_dsl' of github.com:common-workflow-language/schema_salad into type_dsl
e93b038 Add missing file
9ca6cc9 remove more str types, possible fix for edam failed test
d65fb83 more unicode
4350b30 type clarification
96f08e8 Merge remote-tracking branch 'origin/master' into type_dsl
57f7e83 borrow the updated re.pyi from typeshed
c03eb1e type fixes
6e71f35 Merge remote-tracking branch 'origin/master' into type_dsl
68a5c6c More updating to draft-4.dev2
97e8f75 More updating to draft-4.dev2
e554b2b Merge pull request #33 from common-workflow-language/fix-resolve_all_refactor
ad34521 fix bug introduced by refactor
5393edc fixes types, removes a few more Anys
e298bdc Detect when an abstract class is used but doesn't have a concrete subtype.

git-subtree-dir: cwltool/schemas
git-subtree-split: 3e1b02c

Author: mr-c

draft-4/draft-4/count-lines1-wf.cwl

@@ -9,17 +9,17 @@ inputs:
 outputs:
   count_output:
     type: int
-    source: step2/output
+    outputSource: step2/output
 
 steps:
   step1:
     run: wc-tool.cwl
     in:
-      file1: "#file1"
+      file1: file1
     out: [output]
 
   step2:
     run: parseInt-tool.cwl
     in:
-      file1: "#step1/output"
+      file1: step1/output
     out: [output]

draft-4/draft-4/count-lines2-wf.cwl

@@ -11,13 +11,12 @@ inputs:
 outputs:
     count_output:
       type: int
-      source: "#step2/parseInt_output"
+      outputSource: step2/parseInt_output
 
 steps:
   step1:
     in:
-      wc_file1:
-        source: "#file1"
+      wc_file1: file1
     out: [wc_output]
     run:
       id: wc
@@ -36,7 +35,7 @@ steps:
 
   step2:
     in:
-      parseInt_file1: "#step1/wc_output"
+      parseInt_file1: step1/wc_output
     out: [parseInt_output]
     run:
       class: ExpressionTool

draft-4/draft-4/count-lines3-wf.cwl

@@ -4,20 +4,20 @@ cwlVersion: cwl:draft-4.dev2
 
 inputs:
     file1:
-      type: { type: array, items: File }
+      type: File[]
 
 outputs:
     count_output:
-      type: { type: array, items: int }
-      source: "#step1/output"
+      type: int[]
+      outputSource: step1/output
 
 requirements:
   ScatterFeatureRequirement: {}
 
 steps:
   step1:
     run: wc2-tool.cwl
-    scatter: "#step1/file1"
+    scatter: file1
     in:
-      file1: "#file1"
+      file1: file1
     out: [output]

draft-4/draft-4/count-lines4-wf.cwl

@@ -10,8 +10,8 @@ inputs:
 
 outputs:
     count_output:
-      type: {type: array, items: int}
-      source: "#step1/output"
+      type: int[]
+      outputSource: step1/output
 
 requirements:
   - class: ScatterFeatureRequirement
@@ -20,7 +20,7 @@ requirements:
 steps:
   step1:
     run: wc2-tool.cwl
-    scatter: "#step1/file1"
+    scatter: file1
     in:
-      file1: ["#file1", "#file2"]
+      file1: [file1, file2]
     out: [output]

draft-4/draft-4/count-lines5-wf.cwl

@@ -9,11 +9,10 @@ inputs:
 outputs:
     count_output:
       type: int
-      source: "#step1/output"
+      outputSource: step1/output
 steps:
   step1:
     run: wc2-tool.cwl
     in:
-      file1:
-        source: "#file1"
+      file1: file1
     out: [output]

draft-4/draft-4/count-lines6-wf.cwl

@@ -3,15 +3,13 @@ class: Workflow
 cwlVersion: cwl:draft-4.dev2
 
 inputs:
-    file1:
-      type: {type: array, items: File}
-    file2:
-      type: {type: array, items: File}
+    file1: File[]
+    file2: File[]
 
 outputs:
     count_output:
-      type: {type: array, items: int}
-      source: "#step1/output"
+      type: int[]
+      outputSource: step1/output
 
 requirements:
   - class: ScatterFeatureRequirement
@@ -20,9 +18,9 @@ requirements:
 steps:
   step1:
     run: wc3-tool.cwl
-    scatter: "#step1/file1"
+    scatter: file1
     in:
       file1:
-        source: ["#file1", "#file2"]
+        source: [file1, file2]
         linkMerge: merge_nested
     out: [output]

draft-4/draft-4/count-lines7-wf.cwl

@@ -7,20 +7,20 @@ requirements:
 
 inputs:
     file1:
-      type: {type: array, items: File}
+      type: File[]
     file2:
-      type: {type: array, items: File}
+      type: File[]
 
 outputs:
     count_output:
       type: int
-      source: "#step1/output"
+      outputSource: step1/output
 
 steps:
   step1:
     run: wc3-tool.cwl
     in:
       file1:
-        source: ["#file1", "#file2"]
+        source: [file1, file2]
         linkMerge: merge_flattened
     out: [output]

draft-4/draft-4/count-lines8-wf.cwl

@@ -3,13 +3,12 @@ class: Workflow
 cwlVersion: cwl:draft-4.dev2
 
 inputs:
-    file1:
-      type: File
+    file1: File
 
 outputs:
     count_output:
       type: int
-      source: "#step1/count_output"
+      outputSource: step1/count_output
 
 requirements:
   - class: SubworkflowFeatureRequirement
@@ -18,5 +17,5 @@ steps:
   step1:
     run: count-lines1-wf.cwl
     in:
-      file1: "#file1"
+      file1: file1
     out: [count_output]

draft-4/draft-4/count-lines9-wf.cwl

@@ -7,7 +7,7 @@ inputs: []
 outputs:
   count_output:
     type: int
-    source: "#step2/output"
+    outputSource: step2/output
 
 steps:
   step1:
@@ -22,5 +22,5 @@ steps:
   step2:
     run: parseInt-tool.cwl
     in:
-      file1: "#step1/output"
+      file1: step1/output
     out: [output]

draft-4/draft-4/env-tool1.cwl

@@ -1,8 +1,7 @@
 class: CommandLineTool
 cwlVersion: cwl:draft-4.dev2
 inputs:
-  in:
-    type: string
+  in: string
 outputs:
   out:
     type: File

draft-4/draft-4/env-wf1.cwl

@@ -8,7 +8,7 @@ inputs:
 outputs:
     out:
       type: File
-      source: "#step1/out"
+      outputSource: step1/out
 
 requirements:
   - class: SubworkflowFeatureRequirement
@@ -20,5 +20,5 @@ steps:
   step1:
     run: env-tool1.cwl
     in:
-      in: "#in"
+      in: in
     out: [out]

draft-4/draft-4/env-wf2.cwl

@@ -8,7 +8,7 @@ inputs:
 outputs:
     out:
       type: File
-      source: "#step1/out"
+      outputSource: step1/out
 
 requirements:
   - class: SubworkflowFeatureRequirement
@@ -20,5 +20,5 @@ steps:
   step1:
     run: env-tool2.cwl
     in:
-      in: "#in"
+      in: in
     out: [out]

draft-4/draft-4/glob-expr-list.cwl

@@ -3,17 +3,13 @@ cwlVersion: cwl:draft-4.dev2
 
 inputs:
   ids:
-    type:
-      type: array
-      items: string
+    type: string[]
     inputBinding:
       position: 1
 
 outputs:
   files:
-    type:
-      type: array
-      items: File
+    type: File[]
     outputBinding:
       glob: $(inputs.ids)
 

draft-4/draft-4/metadata.cwl

@@ -24,7 +24,7 @@ inputs:
     type: File
     inputBinding: {position: 1}
   numbering:
-    type: ["null", boolean]
+    type: boolean?
     inputBinding:
       position: 0
       prefix: -n

draft-4/draft-4/null-expression1-tool.cwl

@@ -11,7 +11,6 @@ inputs:
     default: "the-default"
 
 outputs:
-  output:
-    type: int
+  output: int
 
 expression: "$({'output': (inputs.i1 == 'the-default' ? 1 : 2)})"

draft-4/draft-4/null-expression2-tool.cwl

@@ -6,11 +6,9 @@ requirements:
 cwlVersion: cwl:draft-4.dev2
 
 inputs:
-  i1:
-    type: Any
+  i1: Any
 
 outputs:
-  output:
-    type: int
+  output: int
 
 expression: "$({'output': (inputs.i1 == 'the-default' ? 1 : 2)})"

draft-4/draft-4/optional-output.cwl

@@ -19,7 +19,7 @@ outputs:
     secondaryFiles:
       - .idx
   optional_file:
-    type: ["null", File]
+    type: File?
     outputBinding:
       glob: bumble.txt
 baseCommand: cat

draft-4/draft-4/parseInt-tool.cwl

@@ -11,7 +11,6 @@ inputs:
     inputBinding: { loadContents: true }
 
 outputs:
-  output:
-    type: int
+  output: int
 
 expression: "$({'output': parseInt(inputs.file1.contents)})"

draft-4/draft-4/rename.cwl

@@ -7,10 +7,8 @@ requirements:
       - filename: $(inputs.newname)
         fileContent: $(inputs.srcfile)
 inputs:
-  srcfile:
-    type: File
-  newname:
-    type: string
+  srcfile: File
+  newname: string
 outputs:
   outfile:
     type: File

draft-4/draft-4/revsort.cwl

@@ -37,7 +37,7 @@ inputs:
 outputs:
   output:
     type: File
-    source: "#sorted/output"
+    outputSource: sorted/output
     description: "The output with the lines reversed and sorted."
 
 # The "steps" array lists the executable steps that make up the workflow.
@@ -53,13 +53,13 @@ outputs:
 steps:
   rev:
     in:
-      input: "#input"
+      input: input
     out: [output]
     run: revtool.cwl
 
   sorted:
     in:
-      input: "#rev/output"
-      reverse: "#reverse_sort"
+      input: rev/output
+      reverse: reverse_sort
     out: [output]
     run: sorttool.cwl

draft-4/draft-4/scatter-valuefrom-wf1.cwl

@@ -16,7 +16,7 @@ outputs:
     type:
       type: array
       items: string
-    source: "#step1/echo_out"
+    outputSource: step1/echo_out
 
 requirements:
   - class: ScatterFeatureRequirement
@@ -26,13 +26,13 @@ steps:
   step1:
     in:
       echo_in:
-        source: "#inp"
+        source: inp
         valueFrom: $(self.instr)
       first:
-        source: "#inp"
+        source: inp
         valueFrom: "$(self[0].instr)"
     out: [echo_out]
-    scatter: "#step1/echo_in"
+    scatter: echo_in
     run:
       class: CommandLineTool
       inputs: