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
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 {}
sc_result = scandeps(uri, scanobj,
loadref_fields,
- set(("$include", "$schemas", "location")),
+ 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 = {}
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)
"keep:%s",
"keep:%s/%s",
name=name,
- single_collection=True)
+ single_collection=True,
+ optional_deps=optional_deps)
def setloc(p):
loc = p.get("location")
"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)
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):
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) )