Site generation works again

Author: Peter Amstutz

site/cwlsite.cwl

@@ -31,9 +31,8 @@ inputs:
 
 outputs:
   doc_out:
-    type: File[]
-    outputSource: [docs/out, brandimg]
-    linkMerge: merge_flattened
+    type: File
+    outputSource: merge/dir
   report:
     type: File
     outputSource: report/out
@@ -50,8 +49,6 @@ requirements:
   - class: SubworkflowFeatureRequirement
   - class: MultipleInputFeatureRequirement
   - class: InlineJavascriptRequirement
-    expressionLib:
-      - $include: cwlpath.js
 
 hints:
   - class: DockerRequirement
@@ -90,10 +87,25 @@ steps:
     out: [out, targetdir]
     run:  makedoc.cwl
 
+  merge:
+    in:
+      primary:
+        source: docs/out
+        valueFrom: $(self[0])
+      secondary:
+        source: [docs/out, brandimg]
+        linkMerge: merge_flattened
+        valueFrom: $(self.slice(1))
+      dirs:
+        source: [docs/targetdir, empty]
+        linkMerge: merge_flattened
+        valueFrom: $(self.slice(1))
+    out: [dir]
+    run: mergesecondary.cwl
+
   report:
     in:
-      inp: { source: [docs/out, brandimg], linkMerge: merge_flattened }
-      dirs: { source: [docs/targetdir, empty], linkMerge: merge_flattened }
+      inp: merge/dir
       target: { default: "linkchecker-report.txt"}
     out: [out]
     run: linkchecker.cwl

site/linkchecker.cwl

@@ -1,68 +1,29 @@
 class: CommandLineTool
 cwlVersion: draft-4.dev3
-requirements:
-  - class: ShellCommandRequirement
-  - class: InlineJavascriptRequirement
-    expressionLib:
-      - $include: cwlpath.js
 hints:
   DockerRequirement:
     dockerFile: |
       FROM debian:8
       RUN apt-get update && \
           DEBIAN_FRONTEND=noninteractive apt-get -yq install w3c-linkchecker \
     dockerImageId: commonworkflowlanguage/checklink
-  InitialWorkDirRequirement:
-    listing: |
-      ${
-        var r = [];
-        for (var i=0; i < inputs.dirs.length; i++) {
-          if (inputs.dirs[i] != "") {
-            r.push({
-              "entryname": inputs.dirs[i],
-              "entry": {
-                "class": "Directory",
-                "listing": [inputs.inp[i]]
-              }
-            });
-          } else {
-            r.push(inputs.inp[i]);
-          }
-        }
-        return r;
-      }
-
 inputs:
   inp:
-    type:
-      type: array
-      items: Directory
-  target:
-    type: string
+    type: File
+    inputBinding: {position: 1}
+  target: string
 outputs:
   out:
     type: File
     outputBinding:
       glob: $(inputs.target)
-
-baseCommand: []
-arguments:
-  - "checklink"
-  - "-X(http.*|mailto:.*)"
-  - "-q"
-  - valueFrom: |
-      ${
-        var r = [];
-        for (var i=0; i < inputs.inp.length; i++) {
-          if (inputs.dirs[i] != "") {
-            r.push(inputs.dirs[i] + "/" + inputs.inp[i].basename);
-          } else {
-            r.push(inputs.inp[i].basename);
-          }
-        }
-        return r;
-      }
-  - {valueFrom: " > ", shellQuote: false}
-  - valueFrom: $(inputs.target)
-  - {valueFrom: " && ! test -s", shellQuote: false}
-  - valueFrom: $(inputs.target)
+      loadContents: true
+      #outputEval: |
+      #  ${
+      #    return if (self.contents.length > 0) {
+      #
+      #    }
+      #  }
+baseCommand: checklink
+arguments: ["-X(http.*|mailto:.*)", "-q"]
+stdout: $(inputs.target)

site/makedoc.cwl

@@ -35,8 +35,19 @@ inputs:
     inputBinding: {prefix: "--primtype"}
 outputs:
   out:
-    type: Directory
+    type: File
+    outputBinding:
+      glob: $(inputs.target)
+  targetdir:
+    type: string
     outputBinding:
-      glob: .
+      outputEval: |
+        ${
+          var m = inputs.target.match(/^([^/]+)\/[^/]/);
+          if (m)
+            return m[1];
+          else
+            return "";
+        }
 baseCommand: [python, "-mschema_salad.makedoc"]
 stdout: $(inputs.target)