Ensure that rewrite_out option of pack returns all identifier rewrites. (#738)

* Ensure that rewrite_out option of pack returns all identifier rewrites.

* Add test that rewrite_out includes all identifiers.

Author: tetron

cwltool/pack.py

@@ -58,6 +58,7 @@ def replace_refs(d, rewrite, stem, newstem):
                     d[s] = rewrite[v]
                 elif v.startswith(stem):
                     d[s] = newstem + v[len(stem):]
+                    rewrite[v] = d[s]
             else:
                 replace_refs(v, rewrite, stem, newstem)
     elif isinstance(d, dict):
@@ -72,6 +73,7 @@ def replace_refs(d, rewrite, stem, newstem):
                         d[s] = "#" + id_
                     else:
                         d[s] = newstem + id_
+                    rewrite[v] = d[s]
             replace_refs(v, rewrite, stem, newstem)
 
 def import_embed(d, seen):
@@ -182,7 +184,7 @@ def rewrite_id(r, mainuri):
     if schemas:
         packed["$schemas"] = list(schemas)
 
-    for r in rewrite:
+    for r in list(rewrite.keys()):
         v = rewrite[r]
         replace_refs(packed, rewrite, r + "/" if "#" in r else r + "#", v + "/")
 

tests/test_pack.py

@@ -43,6 +43,17 @@ def test_pack(self):
 
         self.assertEqual(expect_packed, packed)
 
+
+    def test_pack_rewrites(self):
+        load_tool.loaders = {}
+
+        document_loader, workflowobj, uri = fetch_document(get_data("tests/wf/default-wf5.cwl"))
+        document_loader, avsc_names, processobj, metadata, uri = validate_document(
+            document_loader, workflowobj, uri)
+        rewrites = {}
+        packed = cwltool.pack.pack(document_loader, processobj, uri, metadata, rewrite_out=rewrites)
+        self.assertEqual(6, len(rewrites))
+
     def test_pack_missing_cwlVersion(self):
         """Test to ensure the generated pack output is not missing
         the `cwlVersion` in case of single tool workflow and single step workflow"""

tests/wf/default-dir5.cwl

@@ -0,0 +1,21 @@
+cwlVersion: v1.0
+class: Workflow
+inputs: []
+outputs: []
+$namespaces:
+  arv: "http://arvados.org/cwl#"
+steps:
+  step1:
+    in: []
+    out: []
+    run:
+      id: stepid
+      class: CommandLineTool
+      inputs:
+        inp2:
+          type: Directory
+          default:
+            class: Directory
+            location: inp1
+      outputs: []
+      arguments: [echo, $(inputs.inp2)]

tests/wf/default-wf5.cwl

@@ -0,0 +1,13 @@
+cwlVersion: v1.0
+class: Workflow
+inputs: []
+outputs: []
+$namespaces:
+  arv: "http://arvados.org/cwl#"
+requirements:
+  SubworkflowFeatureRequirement: {}
+steps:
+  step1:
+    in: []
+    out: []
+    run: default-dir5.cwl