X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/c1872f15cdaf416ff9ccfc520085e8af1c5ed582..d7e80d62a0e1c8587c65975c8bb020200cd0d7d6:/sdk/cwl/arvados_cwl/runner.py

diff --git a/sdk/cwl/arvados_cwl/runner.py b/sdk/cwl/arvados_cwl/runner.py
index 126a2b511e..38e2c4d806 100644
--- a/sdk/cwl/arvados_cwl/runner.py
+++ b/sdk/cwl/arvados_cwl/runner.py
@@ -40,7 +40,7 @@ import schema_salad.validate as validate
 
 import arvados.collection
 from .util import collectionUUID
-import ruamel.yaml as yaml
+from ruamel.yaml import YAML
 from ruamel.yaml.comments import CommentedMap, CommentedSeq
 
 import arvados_cwl.arvdocker
@@ -184,7 +184,10 @@ def set_secondary(fsaccess, builder, inputschema, secondaryspec, primary, discov
             elif isinstance(pattern, dict):
                 specs.append(pattern)
             elif isinstance(pattern, str):
-                specs.append({"pattern": pattern})
+                if builder.cwlVersion == "v1.0":
+                    specs.append({"pattern": pattern, "required": True})
+                else:
+                    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")
@@ -193,7 +196,12 @@ 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
+                    if sf.get("location") is None:
+                        raise SourceLine(primary["secondaryFiles"], i, validate.ValidationException).makeError(
+                            "File object is missing 'location': %s" % sf)
+                    sfpath = sf["location"]
+                    required = True
                 else:
                     pattern = sf["pattern"]
                     required = sf.get("required")
@@ -204,11 +212,16 @@ 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)
@@ -252,7 +265,8 @@ def upload_dependencies(arvrunner, name, document_loader,
                 textIO = StringIO(text.decode('utf-8'))
             else:
                 textIO = StringIO(text)
-            return yaml.safe_load(textIO)
+            yamlloader = YAML(typ='safe', pure=True)
+            return yamlloader.load(textIO)
         else:
             return {}
 
@@ -270,9 +284,10 @@ def upload_dependencies(arvrunner, name, document_loader,
     metadata = scanobj
 
     sc_result = scandeps(uri, scanobj,
-                  loadref_fields,
-                  set(("$include", "$schemas", "location")),
-                  loadref, urljoin=document_loader.fetcher.urljoin)
+                         loadref_fields,
+                         set(("$include", "$schemas", "location")),
+                         loadref, urljoin=document_loader.fetcher.urljoin,
+                         nestdirs=False)
 
     sc = []
     uuids = {}
@@ -447,12 +462,14 @@ def upload_docker(arvrunner, tool):
                     "Option 'dockerOutputDirectory' of DockerRequirement not supported.")
             arvados_cwl.arvdocker.arv_docker_get_image(arvrunner.api, docker_req, True, arvrunner.project_uuid,
                                                        arvrunner.runtimeContext.force_docker_pull,
-                                                       arvrunner.runtimeContext.tmp_outdir_prefix)
+                                                       arvrunner.runtimeContext.tmp_outdir_prefix,
+                                                       arvrunner.runtimeContext.match_local_docker)
         else:
             arvados_cwl.arvdocker.arv_docker_get_image(arvrunner.api, {"dockerPull": "arvados/jobs:"+__version__},
                                                        True, arvrunner.project_uuid,
                                                        arvrunner.runtimeContext.force_docker_pull,
-                                                       arvrunner.runtimeContext.tmp_outdir_prefix)
+                                                       arvrunner.runtimeContext.tmp_outdir_prefix,
+                                                       arvrunner.runtimeContext.match_local_docker)
     elif isinstance(tool, cwltool.workflow.Workflow):
         for s in tool.steps:
             upload_docker(arvrunner, s.embedded_tool)
@@ -489,7 +506,8 @@ def packed_workflow(arvrunner, tool, merged_map):
                 v["http://arvados.org/cwl#dockerCollectionPDH"] = arvados_cwl.arvdocker.arv_docker_get_image(arvrunner.api, v, True,
                                                                                                              arvrunner.project_uuid,
                                                                                                              arvrunner.runtimeContext.force_docker_pull,
-                                                                                                             arvrunner.runtimeContext.tmp_outdir_prefix)
+                                                                                                             arvrunner.runtimeContext.tmp_outdir_prefix,
+                                                                                                             arvrunner.runtimeContext.match_local_docker)
             for l in v:
                 visit(v[l], cur_id)
         if isinstance(v, list):
@@ -596,7 +614,8 @@ def arvados_jobs_image(arvrunner, img):
     try:
         return arvados_cwl.arvdocker.arv_docker_get_image(arvrunner.api, {"dockerPull": img}, True, arvrunner.project_uuid,
                                                           arvrunner.runtimeContext.force_docker_pull,
-                                                          arvrunner.runtimeContext.tmp_outdir_prefix)
+                                                          arvrunner.runtimeContext.tmp_outdir_prefix,
+                                                          arvrunner.runtimeContext.match_local_docker)
     except Exception as e:
         raise Exception("Docker image %s is not available\n%s" % (img, e) )