Squashed 'cwltool/schemas/' changes from d6780795..f9d95cbd

f9d95cbd Refactor loadContents to be available on InputParameter, WorkflowStepInput, CommandOutputBinding.  Note that InputBinding on WorkflowInputParameter is deprecated.  Add conformance tests.

git-subtree-dir: cwltool/schemas
git-subtree-split: f9d95cbdc7b4f3c26d544d76067e6032f31c8e43

Author: Peter Amstutz

v1.1.0-dev1/CommandLineTool.yml

@@ -198,6 +198,7 @@ $graph:
 
 - type: record
   name: CommandOutputBinding
+  extends: LoadContents
   doc: |
     Describes how to generate an output parameter based on the files produced
     by a CommandLineTool.
@@ -224,15 +225,6 @@ $graph:
         return a string or an array of strings, which will then be evaluated as
         one or more glob patterns.  Must only match and return files which
         actually exist.
-    - name: loadContents
-      type:
-        - "null"
-        - boolean
-      jsonldPredicate: "cwl:loadContents"
-      doc: |
-        For each file matched in `glob`, read up to
-        the first 64 KiB of text from the file and place it in the `contents`
-        field of the file object for manipulation by `outputEval`.
     - name: outputEval
       type:
         - "null"
@@ -346,9 +338,6 @@ $graph:
   name: CommandInputParameter
   extends: InputParameter
   doc: An input parameter for a CommandLineTool.
-  specialize:
-    - specializeFrom: InputBinding
-      specializeTo: CommandLineBinding
   fields:
     - name: type
       type:
@@ -373,6 +362,9 @@ $graph:
         typeDSL: True
       doc: |
         Specify valid types of data that may be assigned to this parameter.
+    - name: inputBinding
+      type: CommandLineBinding?
+      jsonldPredicate: "cwl:inputBinding"
 
 - type: record
   name: CommandOutputParameter

v1.1.0-dev1/Process.yml

@@ -433,6 +433,23 @@ $graph:
       jsonldPredicate: "@id"
       doc: "The unique identifier for this object."
 
+
+- name: LoadContents
+  type: record
+  abstract: true
+  fields:
+    - name: loadContents
+      type:
+        - "null"
+        - boolean
+      jsonldPredicate: "cwl:loadContents"
+      doc: |
+        Only valid when `type: File` or is an array of `items: File`.
+
+        Read up to the first 64 KiB of text from the file and place it in the
+        "contents" field of the file object for use by expressions.
+
+
 - name: FieldBase
   type: record
   extends: Labeled
@@ -562,14 +579,18 @@ $graph:
         - boolean
       jsonldPredicate: "cwl:loadContents"
       doc: |
+        Use of `loadContents` in `InputBinding` is deprecated.
+        Preserved for v1.0 backwards compatability.  May be removed in
+        a future spec.  Use `InputParameter.loadContents` instead.
+
         Only valid when `type: File` or is an array of `items: File`.
 
         Read up to the first 64 KiB of text from the file and place it in the
         "contents" field of the file object for use by expressions.
 
 
 - name: InputSchema
-  extends: [Labeled, sld:Documented, BindsInput]
+  extends: [Labeled, sld:Documented]
   type: record
   abstract: true
   fields:
@@ -584,18 +605,10 @@ $graph:
   type: record
   abstract: true
 
-- name: BindsInput
-  type: record
-  abstract: true
-  fields:
-    - name: inputBinding
-      type: InputBinding?
-      jsonldPredicate: "cwl:inputBinding"
-
 
 - name: InputRecordField
   type: record
-  extends: [sld:RecordField, FieldBase, BindsInput, InputFormat]
+  extends: [sld:RecordField, FieldBase, InputFormat, LoadContents]
   specialize:
     - specializeFrom: "sld:RecordSchema"
       specializeTo: InputRecordSchema
@@ -681,9 +694,8 @@ $graph:
 - name: InputParameter
   type: record
   abstract: true
-  extends: [Parameter, BindsInput, InputFormat]
+  extends: [Parameter, InputFormat, LoadContents]
   fields:
-
     - name: default
       type: Any?
       jsonldPredicate:

v1.1.0-dev1/Workflow.yml

@@ -118,6 +118,11 @@ $graph:
         typeDSL: True
       doc: |
         Specify valid types of data that may be assigned to this parameter.
+    - name: inputBinding
+      type: InputBinding?
+      doc: Deprecated.  Preserved for v1.0 backwards compatability.  Use `InputParameter.loadContents` instead.
+      jsonldPredicate: "cwl:inputBinding"
+
 
 - type: record
   name: ExpressionTool
@@ -228,7 +233,7 @@ $graph:
 
 - type: record
   name: WorkflowStepInput
-  extends: [Identified, Sink]
+  extends: [Identified, Sink, LoadContents]
   docParent: "#WorkflowStep"
   doc: |
     The input of a workflow step connects an upstream parameter (from the

v1.1.0-dev1/conformance_test_v1.1.0-dev1.yaml

@@ -1686,3 +1686,35 @@
   tool: v1.1.0-dev1/record-out-format.cwl
   doc: Test format on output record fields
   tags: [ required ]
+
+- job: v1.1.0-dev1/wf-loadContents-job.yml
+  output: {
+    "my_int": 42
+  }
+  tool: v1.1.0-dev1/wf-loadContents.cwl
+  doc: Test WorkflowInputParameter.inputBinding.loadContents
+  tags: [ required ]
+
+- job: v1.1.0-dev1/wf-loadContents-job.yml
+  output: {
+    "my_int": 42
+  }
+  tool: v1.1.0-dev1/wf-loadContents2.cwl
+  doc: Test WorkflowInputParameter.loadContents
+  tags: [ required ]
+
+- job: v1.1.0-dev1/wf-loadContents-job.yml
+  output: {
+    "my_int": 42
+  }
+  tool: v1.1.0-dev1/wf-loadContents3.cwl
+  doc: Test loadContents on InputParameter.loadContents (expression)
+  tags: [ required ]
+
+- job: v1.1.0-dev1/wf-loadContents-job.yml
+  output: {
+    "my_int": 42
+  }
+  tool: v1.1.0-dev1/wf-loadContents4.cwl
+  doc: Test WorkflowStepInput.loadContents
+  tags: [ required ]

v1.1.0-dev1/v1.1.0-dev1/wf-loadContents-job.yml

@@ -0,0 +1,3 @@
+my_file:
+  class: File
+  location: answer

v1.1.0-dev1/v1.1.0-dev1/wf-loadContents.cwl

@@ -0,0 +1,30 @@
+cwlVersion: v1.1.0-dev1
+class: Workflow
+requirements:
+  StepInputExpressionRequirement: {}
+  InlineJavascriptRequirement: {}
+inputs:
+  my_file:
+    type: File
+    inputBinding:
+      loadContents: true
+
+steps:
+  one:
+    run:
+      class: ExpressionTool
+      requirements: { InlineJavascriptRequirement: {} }
+      inputs: { my_number: int }
+      outputs: { my_int: int }
+      expression: |
+        ${ return { "my_int": inputs.my_number }; }
+    in:
+      my_number:
+        source: my_file
+        valueFrom: $(parseInt(self.contents))
+    out: [ my_int ]
+
+outputs:
+  my_int:
+    type: int
+    outputSource: one/my_int

v1.1.0-dev1/v1.1.0-dev1/wf-loadContents2.cwl

@@ -0,0 +1,29 @@
+cwlVersion: v1.1.0-dev1
+class: Workflow
+requirements:
+  StepInputExpressionRequirement: {}
+  InlineJavascriptRequirement: {}
+inputs:
+  my_file:
+    type: File
+    loadContents: true
+
+steps:
+  one:
+    run:
+      class: ExpressionTool
+      requirements: { InlineJavascriptRequirement: {} }
+      inputs: { my_number: int }
+      outputs: { my_int: int }
+      expression: |
+        ${ return { "my_int": inputs.my_number }; }
+    in:
+      my_number:
+        source: my_file
+        valueFrom: $(parseInt(self.contents))
+    out: [ my_int ]
+
+outputs:
+  my_int:
+    type: int
+    outputSource: one/my_int

v1.1.0-dev1/v1.1.0-dev1/wf-loadContents3.cwl

@@ -0,0 +1,28 @@
+cwlVersion: v1.1.0-dev1
+class: Workflow
+requirements:
+  StepInputExpressionRequirement: {}
+  InlineJavascriptRequirement: {}
+inputs:
+  my_file: File
+
+steps:
+  one:
+    run:
+      class: ExpressionTool
+      requirements: { InlineJavascriptRequirement: {} }
+      inputs:
+        my_number:
+          type: File
+          loadContents: true
+      outputs: { my_int: int }
+      expression: |
+        ${ return { "my_int": parseInt(inputs.my_number.contents) }; }
+    in:
+      my_number: my_file
+    out: [ my_int ]
+
+outputs:
+  my_int:
+    type: int
+    outputSource: one/my_int

v1.1.0-dev1/v1.1.0-dev1/wf-loadContents4.cwl

@@ -0,0 +1,28 @@
+cwlVersion: v1.1.0-dev1
+class: Workflow
+requirements:
+  StepInputExpressionRequirement: {}
+  InlineJavascriptRequirement: {}
+inputs:
+  my_file: File
+
+steps:
+  one:
+    run:
+      class: ExpressionTool
+      requirements: { InlineJavascriptRequirement: {} }
+      inputs: { my_number: int }
+      outputs: { my_int: int }
+      expression: |
+        ${ return { "my_int": inputs.my_number }; }
+    in:
+      my_number:
+        source: my_file
+        loadContents: true
+        valueFrom: $(parseInt(self.contents))
+    out: [ my_int ]
+
+outputs:
+  my_int:
+    type: int
+    outputSource: one/my_int