Merge branch '18248-fix-ubuntu-18.04-testing'

[arvados.git] / sdk / cwl / arvados_cwl / runner.py

diff --git a/sdk/cwl/arvados_cwl/runner.py b/sdk/cwl/arvados_cwl/runner.py
index 42d4b552acc92bc8d76a3ffbbf32edc539682aad..ada64ae69aa62f0c1e4487bd28160c071fb3d0a1 100644 (file)
--- a/sdk/cwl/arvados_cwl/runner.py
+++ b/sdk/cwl/arvados_cwl/runner.py
@@ -105,7 +105,8 @@ def make_builder(joborder, hints, requirements, runtimeContext, metadata):
                  outdir="",              # type: Text
                  tmpdir="",              # type: Text
                  stagedir="",            # type: Text
-                 cwlVersion=metadata.get("http://commonwl.org/cwltool#original_cwlVersion") or metadata.get("cwlVersion")
+                 cwlVersion=metadata.get("http://commonwl.org/cwltool#original_cwlVersion") or metadata.get("cwlVersion"),
+                 container_engine="docker"
                 )
 
 def search_schemadef(name, reqs):
@@ -183,7 +184,7 @@ def set_secondary(fsaccess, builder, inputschema, secondaryspec, primary, discov
             elif isinstance(pattern, dict):
                 specs.append(pattern)
             elif isinstance(pattern, str):
-                specs.append({"pattern": pattern})
+                specs.append({"pattern": pattern, "required": sf.get("required")})
             else:
                 raise SourceLine(primary["secondaryFiles"], i, validate.ValidationException).makeError(
                     "Expression must return list, object, string or null")
@@ -192,7 +193,9 @@ def set_secondary(fsaccess, builder, inputschema, secondaryspec, primary, discov
         for i, sf in enumerate(specs):
             if isinstance(sf, dict):
                 if sf.get("class") == "File":
-                    pattern = sf["basename"]
+                    pattern = None
+                    sfpath = sf["location"]
+                    required = True
                 else:
                     pattern = sf["pattern"]
                     required = sf.get("required")
@@ -203,11 +206,16 @@ def set_secondary(fsaccess, builder, inputschema, secondaryspec, primary, discov
                 raise SourceLine(primary["secondaryFiles"], i, validate.ValidationException).makeError(
                     "Expression must return list, object, string or null")
 
-            sfpath = substitute(primary["location"], pattern)
+            if pattern is not None:
+                sfpath = substitute(primary["location"], pattern)
+
             required = builder.do_eval(required, context=primary)
 
             if fsaccess.exists(sfpath):
-                found.append({"location": sfpath, "class": "File"})
+                if pattern is not None:
+                    found.append({"location": sfpath, "class": "File"})
+                else:
+                    found.append(sf)
             elif required:
                 raise SourceLine(primary["secondaryFiles"], i, validate.ValidationException).makeError(
                     "Required secondary file '%s' does not exist" % sfpath)
@@ -427,7 +435,8 @@ def upload_dependencies(arvrunner, name, document_loader,
     if "$schemas" in workflowobj:
         sch = CommentedSeq()
         for s in workflowobj["$schemas"]:
-            sch.append(mapper.mapper(s).resolved)
+            if s in mapper:
+                sch.append(mapper.mapper(s).resolved)
         workflowobj["$schemas"] = sch
 
     return mapper
@@ -470,7 +479,7 @@ def packed_workflow(arvrunner, tool, merged_map):
 
     def visit(v, cur_id):
         if isinstance(v, dict):
-            if v.get("class") in ("CommandLineTool", "Workflow"):
+            if v.get("class") in ("CommandLineTool", "Workflow", "ExpressionTool"):
                 if tool.metadata["cwlVersion"] == "v1.0" and "id" not in v:
                     raise SourceLine(v, None, Exception).makeError("Embedded process object is missing required 'id' field, add an 'id' or use to cwlVersion: v1.1")
                 if "id" in v:
@@ -478,10 +487,11 @@ def packed_workflow(arvrunner, tool, merged_map):
             if "path" in v and "location" not in v:
                 v["location"] = v["path"]
                 del v["path"]
-            if "location" in v and not v["location"].startswith("keep:"):
-                v["location"] = merged_map[cur_id].resolved[v["location"]]
-            if "location" in v and v["location"] in merged_map[cur_id].secondaryFiles:
-                v["secondaryFiles"] = merged_map[cur_id].secondaryFiles[v["location"]]
+            if "location" in v and cur_id in merged_map:
+                if v["location"] in merged_map[cur_id].resolved:
+                    v["location"] = merged_map[cur_id].resolved[v["location"]]
+                if v["location"] in merged_map[cur_id].secondaryFiles:
+                    v["secondaryFiles"] = merged_map[cur_id].secondaryFiles[v["location"]]
             if v.get("class") == "DockerRequirement":
                 v["http://arvados.org/cwl#dockerCollectionPDH"] = arvados_cwl.arvdocker.arv_docker_get_image(arvrunner.api, v, True,
                                                                                                              arvrunner.project_uuid,