Squashed 'cwltool/schemas/' changes from 36b3da1..1550753

1550753 Merge pull request common-workflow-language#302 from common-workflow-language/build-v1.1.0-dev1-pages
09d3412 build v1.1.0-dev1 webpages
1318a55 rename draft-4 to v1.0.0 in site/
f188887 Merge pull request common-workflow-language#301 from common-workflow-language/fix-stdin-tests
d71528d fix stdin shortcut tests
6fc30e1 Merge pull request common-workflow-language#300 from common-workflow-language/stdin-shortcut
REVERT: 36b3da1 put stdin type in correct place

git-subtree-dir: cwltool/schemas
git-subtree-split: 1550753

site/cwlsite-job.yaml

@@ -0,0 +1,20 @@
+#!/usr/bin/env cwl-runner
+brand: CWL
+brandimg: {class: File, path: CWL-Logo-Header.png}
+cwl:tool: cwlsite.cwl
+render:
+- brandimg: '<img src=''CWL-Logo-Header.png'' style=''height: 61px; margin-top: -20px;
+    margin-left: -20px''></img>'
+  brandlink: index.html
+  primtype: null
+  redirect: []
+  renderlist: []
+  source: {class: File, path: ../README.md}
+  target: index.html
+- {$import: cwlsite-draft3-job.json}
+- {$import: cwlsite-v1.0.0-job.json}
+- {$import: cwlsite-v1.1.0-dev1-job.yaml}
+schemas:
+- {$import: cwlsite-draft3-schemas.json}
+- {$import: cwlsite-v1.0.0-schemas.json}
+- {$import: cwlsite-v1.1.0-dev1-schemas.yaml}

site/cwlsite-draft4-job.json → site/cwlsite-v1.0.0-job.json

@@ -14,7 +14,7 @@
             "source": {
                 "class": "File",
                 "path": "../v1.0/CommandLineTool-standalone.yml",
-                "secondaryFiles": {"$import": "draft4-deps.json"}
+                "secondaryFiles": {"$import": "v1.0.0-deps.json"}
             },
             "target": "v1.0/CommandLineTool.html",
             "renderlist": [
@@ -30,7 +30,7 @@
             "source": {
                 "class": "File",
                 "path": "../v1.0/CommonWorkflowLanguage.yml",
-                "secondaryFiles": {"$import": "draft4-deps.json"}
+                "secondaryFiles": {"$import": "v1.0.0-deps.json"}
             },
             "target": "v1.0/Workflow.html",
             "renderlist": [
@@ -50,7 +50,7 @@
             "primtype": "#CWLType"
         },
         {
-            "source": {$import: draft4-metaschema.json},
+            "source": {$import: v1.0.0-metaschema.json},
             "target": "v1.0/SchemaSalad.html",
             "renderlist": [
                 "https://w3id.org/cwl/salad#Semantic_Annotations_for_Linked_Avro_Data",

site/cwlsite-draft4-schemas.json → site/cwlsite-v1.0.0-schemas.json

@@ -2,12 +2,12 @@
         "schema_in": {
             "class": "File",
             "path": "../v1.0/CommonWorkflowLanguage.yml",
-            "secondaryFiles": {"$import": "draft4-deps.json"}
+            "secondaryFiles": {"$import": "v1.0.0-deps.json"}
         },
         "context_target": "v1.0/cwl-context.json",
         "rdfs_target": "v1.0/cwl.ttl"
     }, {
-        "schema_in": {$import: draft4-metaschema.json},
+        "schema_in": {$import: v1.0.0-metaschema.json},
         "context_target": "v1.0/salad-context.json",
         "rdfs_target": "v1.0/salad.ttl"
     }

site/cwlsite-v1.1.0-dev1-job.yaml

@@ -0,0 +1,53 @@
+- brandimg: '<img src=''../CWL-Logo-Header.png'' style=''height: 61px; margin-top:
+    -20px; margin-left: -20px''></img>'
+  brandlink: ../index.html
+  primtype: null
+  redirect: []
+  renderlist: []
+  source: {class: File, path: ../v1.1.0-dev1/README.md}
+  target: v1.1.0-dev1/index.html
+- brandimg: '<img src=''../CWL-Logo-Header.png'' style=''height: 61px; margin-top:
+    -20px; margin-left: -20px''></img>'
+  brandlink: index.html
+  primtype: '#CWLType'
+  redirect: []
+  renderlist: ['https://w3id.org/cwl/cwl#CommandLineToolDoc', 'https://w3id.org/cwl/cwl#CommandLineTool']
+  source:
+    class: File
+    path: ../v1.1.0-dev1/CommandLineTool-standalone.yml
+    secondaryFiles: {$import: v1.1.0-dev1-deps.yaml}
+  target: v1.1.0-dev1/CommandLineTool.html
+- brandimg: '<img src=''../CWL-Logo-Header.png'' style=''height: 61px; margin-top:
+    -20px; margin-left: -20px''></img>'
+  brandlink: index.html
+  primtype: '#CWLType'
+  redirect: ['https://w3id.org/cwl/cwl#CommandLineTool=CommandLineTool.html#CommandLineTool',
+    'https://w3id.org/cwl/cwl#DockerRequirement=CommandLineTool.html#DockerRequirement',
+    'https://w3id.org/cwl/cwl#CreateFileRequirement=CommandLineTool.html#CreateFileRequirement',
+    'https://w3id.org/cwl/cwl#EnvVarRequirement=CommandLineTool.html#EnvVarRequirement',
+    'https://w3id.org/cwl/cwl#ShellCommandRequirement=CommandLineTool.html#ShellCommandRequirement',
+    'https://w3id.org/cwl/cwl#ResourceRequirement=CommandLineTool.html#ResourceRequirement']
+  renderlist: ['https://w3id.org/cwl/cwl#WorkflowDoc', 'https://w3id.org/cwl/cwl#Workflow']
+  source:
+    class: File
+    path: ../v1.1.0-dev1/CommonWorkflowLanguage.yml
+    secondaryFiles: {$import: v1.1.0-dev1-deps.yaml}
+  target: v1.1.0-dev1/Workflow.html
+- brandimg: '<img src=''../CWL-Logo-Header.png'' style=''height: 61px; margin-top:
+    -20px; margin-left: -20px''></img>'
+  brandlink: index.html
+  primtype: null
+  redirect: []
+  renderlist: ['https://w3id.org/cwl/salad#Semantic_Annotations_for_Linked_Avro_Data',
+    'https://w3id.org/cwl/salad#SaladRecordSchema', 'https://w3id.org/cwl/salad#SaladEnumSchema',
+    'https://w3id.org/cwl/salad#Documentation']
+  source: {$import: v1.1.0-dev1-metaschema.yaml}
+  target: v1.1.0-dev1/SchemaSalad.html
+- brandimg: '<img src=''../CWL-Logo-Header.png'' style=''height: 61px; margin-top:
+    -20px; margin-left: -20px''></img>'
+  brandlink: index.html
+  primtype: null
+  redirect: []
+  renderlist: []
+  source: {$import: userguide-v1.1.0-dev1-input.yaml}
+  target: v1.1.0-dev1/UserGuide.html

site/cwlsite-v1.1.0-dev1-schemas.yaml

@@ -0,0 +1,9 @@
+- context_target: v1.1.0-dev1/cwl-context.json
+  rdfs_target: v1.1.0-dev1/cwl.ttl
+  schema_in:
+    class: File
+    path: ../v1.1.0-dev1/CommonWorkflowLanguage.yml
+    secondaryFiles: {$import: v1.1.0-dev1-deps.yaml}
+- context_target: v1.1.0-dev1/salad-context.json
+  rdfs_target: v1.1.0-dev1/salad.ttl
+  schema_in: {$import: v1.1.0-dev1-metaschema.yaml}

site/userguide-v1.1.0-dev1-input.yaml

@@ -0,0 +1,35 @@
+class: File
+location: ../v1.1.0-dev1/UserGuide.yml
+secondaryFiles:
+- {basename: userguide-intro.md, class: File, location: ../v1.1.0-dev1/userguide-intro.md}
+- basename: examples
+  class: Directory
+  listing:
+  - {basename: record-job1.yml, class: File, location: ../v1.1.0-dev1/examples/record-job1.yml}
+  - {basename: expression.cwl, class: File, location: ../v1.1.0-dev1/examples/expression.cwl}
+  - {basename: array-outputs-job.yml, class: File, location: ../v1.1.0-dev1/examples/array-outputs-job.yml}
+  - {basename: tar-param.cwl, class: File, location: ../v1.1.0-dev1/examples/tar-param.cwl}
+  - {basename: inp-job.yml, class: File, location: ../v1.1.0-dev1/examples/inp-job.yml}
+  - {basename: 1st-workflow-job.yml, class: File, location: ../v1.1.0-dev1/examples/1st-workflow-job.yml}
+  - {basename: record-job2.yml, class: File, location: ../v1.1.0-dev1/examples/record-job2.yml}
+  - {basename: record-job3.yml, class: File, location: ../v1.1.0-dev1/examples/record-job3.yml}
+  - {basename: echo-job.yml, class: File, location: ../v1.1.0-dev1/examples/echo-job.yml}
+  - {basename: array-outputs.cwl, class: File, location: ../v1.1.0-dev1/examples/array-outputs.cwl}
+  - {basename: array-inputs-job.yml, class: File, location: ../v1.1.0-dev1/examples/array-inputs-job.yml}
+  - {basename: 1st-workflow.cwl, class: File, location: ../v1.1.0-dev1/examples/1st-workflow.cwl}
+  - {basename: docker.cwl, class: File, location: ../v1.1.0-dev1/examples/docker.cwl}
+  - {basename: stdout.cwl, class: File, location: ../v1.1.0-dev1/examples/stdout.cwl}
+  - {basename: docker-job.yml, class: File, location: ../v1.1.0-dev1/examples/docker-job.yml}
+  - {basename: tar.cwl, class: File, location: ../v1.1.0-dev1/examples/tar.cwl}
+  - {basename: createfile.cwl, class: File, location: ../v1.1.0-dev1/examples/createfile.cwl}
+  - {basename: 1st-tool.cwl, class: File, location: ../v1.1.0-dev1/examples/1st-tool.cwl}
+  - {basename: env.cwl, class: File, location: ../v1.1.0-dev1/examples/env.cwl}
+  - {basename: arguments-job.yml, class: File, location: ../v1.1.0-dev1/examples/arguments-job.yml}
+  - {basename: tar-param-job.yml, class: File, location: ../v1.1.0-dev1/examples/tar-param-job.yml}
+  - {basename: array-inputs.cwl, class: File, location: ../v1.1.0-dev1/examples/array-inputs.cwl}
+  - {basename: inp.cwl, class: File, location: ../v1.1.0-dev1/examples/inp.cwl}
+  - {basename: arguments.cwl, class: File, location: ../v1.1.0-dev1/examples/arguments.cwl}
+  - {basename: linkfile.cwl, class: File, location: ../v1.1.0-dev1/examples/linkfile.cwl}
+  - {basename: record.cwl, class: File, location: ../v1.1.0-dev1/examples/record.cwl}
+  - {basename: tar-job.yml, class: File, location: ../v1.1.0-dev1/examples/tar-job.yml}
+  location: _:4f9d886b-443f-49bd-8e0e-f3517a8a5c34

site/v1.1.0-dev1-deps.yaml

@@ -0,0 +1,33 @@
+- basename: Process.yml
+  class: File
+  location: ../v1.1.0-dev1/Process.yml
+  secondaryFiles:
+  - {basename: concepts.md, class: File, location: ../v1.1.0-dev1/concepts.md}
+  - basename: salad
+    class: Directory
+    listing:
+    - basename: schema_salad
+      class: Directory
+      listing:
+      - basename: metaschema
+        class: Directory
+        listing:
+        - {basename: metaschema_base.yml, class: File, location: ../v1.1.0-dev1/salad/schema_salad/metaschema/metaschema_base.yml}
+        location: _:8d932277-54ee-49f7-b7b3-007108151ed4
+      location: _:31c5c0f1-dfcb-4a68-a5e1-063d03e85d3a
+    location: _:4a097285-861e-42ac-9322-20244d69dc96
+- basename: CommandLineTool.yml
+  class: File
+  location: ../v1.1.0-dev1/CommandLineTool.yml
+  secondaryFiles:
+  - {basename: contrib.md, class: File, location: ../v1.1.0-dev1/contrib.md}
+  - {basename: concepts.md, class: File, location: ../v1.1.0-dev1/concepts.md}
+  - {basename: invocation.md, class: File, location: ../v1.1.0-dev1/invocation.md}
+  - {basename: intro.md, class: File, location: ../v1.1.0-dev1/intro.md}
+- basename: Workflow.yml
+  class: File
+  location: ../v1.1.0-dev1/Workflow.yml
+  secondaryFiles:
+  - {basename: contrib.md, class: File, location: ../v1.1.0-dev1/contrib.md}
+  - {basename: concepts.md, class: File, location: ../v1.1.0-dev1/concepts.md}
+  - {basename: intro.md, class: File, location: ../v1.1.0-dev1/intro.md}

site/v1.1.0-dev1-metaschema.yaml

@@ -0,0 +1,34 @@
+class: File
+location: ../v1.1.0-dev1/salad/schema_salad/metaschema/metaschema.yml
+secondaryFiles:
+- basename: link_res.yml
+  class: File
+  location: ../v1.1.0-dev1/salad/schema_salad/metaschema/link_res.yml
+  secondaryFiles:
+  - {basename: link_res_schema.yml, class: File, location: ../v1.1.0-dev1/salad/schema_salad/metaschema/link_res_schema.yml}
+  - {basename: link_res_src.yml, class: File, location: ../v1.1.0-dev1/salad/schema_salad/metaschema/link_res_src.yml}
+  - {basename: link_res_proc.yml, class: File, location: ../v1.1.0-dev1/salad/schema_salad/metaschema/link_res_proc.yml}
+- {basename: salad.md, class: File, location: ../v1.1.0-dev1/salad/schema_salad/metaschema/salad.md}
+- {basename: metaschema_base.yml, class: File, location: ../v1.1.0-dev1/salad/schema_salad/metaschema/metaschema_base.yml}
+- {basename: import_include.md, class: File, location: ../v1.1.0-dev1/salad/schema_salad/metaschema/import_include.md}
+- basename: field_name.yml
+  class: File
+  location: ../v1.1.0-dev1/salad/schema_salad/metaschema/field_name.yml
+  secondaryFiles:
+  - {basename: field_name_src.yml, class: File, location: ../v1.1.0-dev1/salad/schema_salad/metaschema/field_name_src.yml}
+  - {basename: field_name_schema.yml, class: File, location: ../v1.1.0-dev1/salad/schema_salad/metaschema/field_name_schema.yml}
+  - {basename: field_name_proc.yml, class: File, location: ../v1.1.0-dev1/salad/schema_salad/metaschema/field_name_proc.yml}
+- basename: ident_res.yml
+  class: File
+  location: ../v1.1.0-dev1/salad/schema_salad/metaschema/ident_res.yml
+  secondaryFiles:
+  - {basename: ident_res_proc.yml, class: File, location: ../v1.1.0-dev1/salad/schema_salad/metaschema/ident_res_proc.yml}
+  - {basename: ident_res_schema.yml, class: File, location: ../v1.1.0-dev1/salad/schema_salad/metaschema/ident_res_schema.yml}
+  - {basename: ident_res_src.yml, class: File, location: ../v1.1.0-dev1/salad/schema_salad/metaschema/ident_res_src.yml}
+- basename: vocab_res.yml
+  class: File
+  location: ../v1.1.0-dev1/salad/schema_salad/metaschema/vocab_res.yml
+  secondaryFiles:
+  - {basename: vocab_res_schema.yml, class: File, location: ../v1.1.0-dev1/salad/schema_salad/metaschema/vocab_res_schema.yml}
+  - {basename: vocab_res_proc.yml, class: File, location: ../v1.1.0-dev1/salad/schema_salad/metaschema/vocab_res_proc.yml}
+  - {basename: vocab_res_src.yml, class: File, location: ../v1.1.0-dev1/salad/schema_salad/metaschema/vocab_res_src.yml}

v1.1.0-dev1/CommandLineTool.yml

@@ -367,32 +367,14 @@ $graph:
   extends: InputParameter
   doc: An input parameter for a CommandLineTool.
   specialize:
+    - specializeFrom: InputRecordSchema
+      specializeTo: CommandInputRecordSchema
+    - specializeFrom: InputEnumSchema
+      specializeTo: CommandInputEnumSchema
+    - specializeFrom: InputArraySchema
+      specializeTo: CommandInputArraySchema
     - specializeFrom: InputBinding
       specializeTo: CommandLineBinding
-  fields:
-    - name: type
-      type:
-        - "null"
-        - CWLType
-        - stdin
-        - CommandInputRecordSchema
-        - CommandInputEnumSchema
-        - CommandInputArraySchema
-        - string
-        - type: array
-          items:
-            - CWLType
-            - CommandInputRecordSchema
-            - CommandInputEnumSchema
-            - CommandInputArraySchema
-            - string
-      jsonldPredicate:
-        "_id": "sld:type"
-        "_type": "@vocab"
-        refScope: 2
-        typeDSL: True
-      doc: |
-        Specify valid types of data that may be assigned to this parameter.
 
 - type: record
   name: CommandOutputParameter
@@ -406,6 +388,7 @@ $graph:
       type:
         - "null"
         - CWLType
+        - stdin
         - stdout
         - stderr
         - CommandOutputRecordSchema
@@ -430,7 +413,7 @@ $graph:
 - name: stdin
   type: enum
   symbols: [ "cwl:stdin" ]
-  docParent: "#CommandInputParameter"
+  docParent: "#CommandOutputParameter"
   doc: |
     Only valid as a `type` for a `CommandLineTool` input with no
     `inputBinding` set. `stdin` must not be specified at the `CommandLineTool`

v1.1.0-dev1/Process.yml

@@ -568,6 +568,28 @@ $graph:
         The default value for this parameter if not provided in the input
         object.
 
+    - name: type
+      type:
+        - "null"
+        - CWLType
+        - InputRecordSchema
+        - InputEnumSchema
+        - InputArraySchema
+        - string
+        - type: array
+          items:
+            - CWLType
+            - InputRecordSchema
+            - InputEnumSchema
+            - InputArraySchema
+            - string
+      jsonldPredicate:
+        "_id": "sld:type"
+        "_type": "@vocab"
+        refScope: 2
+        typeDSL: True
+      doc: |
+        Specify valid types of data that may be assigned to this parameter.
 
 - name: OutputParameter
   type: record

v1.1.0-dev1/Workflow.yml

@@ -107,39 +107,10 @@ $graph:
       doc: |
         Specify valid types of data that may be assigned to this parameter.
 
-- name: RegularInputParameter
-  type: record
-  extends: InputParameter
-  fields:
-    - name: type
-      type:
-        - "null"
-        - CWLType
-        - InputRecordSchema
-        - InputEnumSchema
-        - InputArraySchema
-        - string
-        - type: array
-          items:
-            - CWLType
-            - InputRecordSchema
-            - InputEnumSchema
-            - InputArraySchema
-            - string
-      jsonldPredicate:
-        "_id": "sld:type"
-        "_type": "@vocab"
-        refScope: 2
-        typeDSL: True
-      doc: |
-        Specify valid types of data that may be assigned to this parameter.
-
 - type: record
   name: ExpressionTool
   extends: Process
   specialize:
-    - specializeFrom: "#InputParameter"
-      specializeTo: "#RegularInputParameter"
     - specializeFrom: "#OutputParameter"
       specializeTo: "#ExpressionToolOutputParameter"
   documentRoot: true
@@ -491,8 +462,6 @@ $graph:
   extends: "#Process"
   documentRoot: true
   specialize:
-    - specializeFrom: "#InputParameter"
-      specializeTo: "#RegularInputParameter"
     - specializeFrom: "#OutputParameter"
       specializeTo: "#WorkflowOutputParameter"
   doc: |