Fix ttl and context generation

Author: Peter Amstutz

site/cwlsite.cwl

@@ -36,12 +36,6 @@ outputs:
   report:
     type: File
     outputSource: report/out
-  context:
-    type: File[]
-    outputSource: context/out
-  rdfs:
-    type: File[]
-    outputSource: rdfs/out
 
 requirements:
   - class: ScatterFeatureRequirement
@@ -61,16 +55,16 @@ steps:
       schemas: schemas
       schema: { valueFrom: $(inputs.schemas.schema_in) }
       target: { valueFrom: $(inputs.schemas.rdfs_target) }
-    out: [out]
+    out: [out, targetdir]
     run: makerdfs.cwl
 
   context:
     scatter: schemas
     in:
       schemas: schemas
       schema: { valueFrom: $(inputs.schemas.schema_in) }
-      target: { valueFrom: $(inputs.schemas.rdfs_target) }
-    out: [out]
+      target: { valueFrom: $(inputs.schemas.context_target) }
+    out: [out, targetdir]
     run: makecontext.cwl
 
   docs:
@@ -93,11 +87,11 @@ steps:
         source: docs/out
         valueFrom: $(self[0])
       secondary:
-        source: [docs/out, brandimg]
+        source: [docs/out, rdfs/out, context/out, brandimg]
         linkMerge: merge_flattened
         valueFrom: $(self.slice(1))
       dirs:
-        source: [docs/targetdir, empty]
+        source: [docs/targetdir, rdfs/targetdir, context/targetdir, empty]
         linkMerge: merge_flattened
         valueFrom: $(self.slice(1))
     out: [dir]

site/makecontext.cwl

@@ -1,15 +1,15 @@
-cwlVersion: "cwl:draft-3"
+cwlVersion: draft-4.dev3
 class: CommandLineTool
 inputs:
-  - id: schema
+  schema:
     type: File
     inputBinding: {position: 1}
-  - id: target
-    type: string
+  target: string
 outputs:
-  - id: out
-    type: File
+  out: stdout
+  targetdir:
+    type: string
     outputBinding:
-      glob: $(inputs.target)
+      outputEval: $(inputs.target.match(/^([^/]+)\/[^/]/)[1])
 baseCommand: [python, "-mschema_salad", "--print-jsonld-context"]
 stdout: $(inputs.target)

site/makedoc.cwl

@@ -34,10 +34,7 @@ inputs:
     type: ["null", string]
     inputBinding: {prefix: "--primtype"}
 outputs:
-  out:
-    type: File
-    outputBinding:
-      glob: $(inputs.target)
+  out: stdout
   targetdir:
     type: string
     outputBinding:

site/makerdfs.cwl

@@ -6,9 +6,10 @@ inputs:
     inputBinding: {position: 1}
   target: string
 outputs:
-  out:
-    type: File
+  out: stdout
+  targetdir:
+    type: string
     outputBinding:
-      glob: $(inputs.target)
+      outputEval: $(inputs.target.match(/^([^/]+)\/[^/]/)[1])
 baseCommand: [python, "-mschema_salad", "--print-rdfs"]
 stdout: $(inputs.target)