Merge branch '18947-githttpd'

[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 ada64ae69aa62f0c1e4487bd28160c071fb3d0a1..7d4310b0e0ce94b9430ded7f60ca04416e2964b9 100644 (file)
--- 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, "required": sf.get("required")})
+                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")
@@ -194,6 +197,9 @@ def set_secondary(fsaccess, builder, inputschema, secondaryspec, primary, discov
             if isinstance(sf, dict):
                 if sf.get("class") == "File":
                     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:
@@ -259,7 +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 {}
 
@@ -277,9 +284,18 @@ 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(("$include", "location")),
+                         loadref, urljoin=document_loader.fetcher.urljoin,
+                         nestdirs=False)
+
+    optional_deps = scandeps(uri, scanobj,
+                                  loadref_fields,
+                                  set(("$schemas",)),
+                                  loadref, urljoin=document_loader.fetcher.urljoin,
+                                  nestdirs=False)
+
+    sc_result.extend(optional_deps)
 
     sc = []
     uuids = {}
@@ -337,24 +353,14 @@ def upload_dependencies(arvrunner, name, document_loader,
     if include_primary and "id" in workflowobj:
         sc.append({"class": "File", "location": workflowobj["id"]})
 
-    if "$schemas" in workflowobj:
-        for s in workflowobj["$schemas"]:
-            sc.append({"class": "File", "location": s})
-
     def visit_default(obj):
-        remove = [False]
-        def ensure_default_location(f):
+        def defaults_are_optional(f):
             if "location" not in f and "path" in f:
                 f["location"] = f["path"]
                 del f["path"]
-            if "location" in f and not arvrunner.fs_access.exists(f["location"]):
-                # Doesn't exist, remove from list of dependencies to upload
-                sc[:] = [x for x in sc if x["location"] != f["location"]]
-                # Delete "default" from workflowobj
-                remove[0] = True
-        visit_class(obj["default"], ("File", "Directory"), ensure_default_location)
-        if remove[0]:
-            del obj["default"]
+            normalizeFilesDirs(f)
+            optional_deps.append(f)
+        visit_class(obj["default"], ("File", "Directory"), defaults_are_optional)
 
     find_defaults(workflowobj, visit_default)
 
@@ -390,7 +396,8 @@ def upload_dependencies(arvrunner, name, document_loader,
                            "keep:%s",
                            "keep:%s/%s",
                            name=name,
-                           single_collection=True)
+                           single_collection=True,
+                           optional_deps=optional_deps)
 
     def setloc(p):
         loc = p.get("location")
@@ -454,12 +461,14 @@ 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)
@@ -496,7 +505,8 @@ 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):
@@ -603,7 +613,8 @@ 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) )