self.collection_cache = CollectionCache(self.api, self.keep_client, self.num_retries)
self.work_api = None
- expected_api = ["containers", "jobs"]
+ expected_api = ["jobs", "containers"]
for api in expected_api:
try:
methods = self.api._rootDesc.get('resources')[api]['methods']
fs_access=CollectionFsAccess("", collection_cache=self.collection_cache),
num_retries=self.num_retries,
overrides=kwargs.get("override_tools"))
+ kwargs["resolver"] = partial(collectionResolver, self.api, num_retries=self.num_retries)
if "class" in toolpath_object and toolpath_object["class"] == "CommandLineTool":
return ArvadosCommandTool(self, toolpath_object, **kwargs)
elif "class" in toolpath_object and toolpath_object["class"] == "Workflow":
self.check_features(v)
elif isinstance(obj, list):
for i,v in enumerate(obj):
- with SourceLine(obj, i, UnsupportedRequirement):
+ with SourceLine(obj, i, UnsupportedRequirement, logger.isEnabledFor(logging.DEBUG)):
self.check_features(v)
def make_output_collection(self, name, tagsString, outputObj):
def rewrite(fileobj):
fileobj["location"] = generatemapper.mapper(fileobj["location"]).target
- for k in ("basename", "listing", "contents"):
+ for k in ("basename", "listing", "contents", "nameext", "nameroot", "dirname"):
if k in fileobj:
del fileobj[k]
if self.work_api == "containers":
if tool.tool["class"] == "CommandLineTool" and kwargs.get("wait"):
kwargs["runnerjob"] = tool.tool["id"]
- upload_dependencies(self,
- kwargs["name"],
- tool.doc_loader,
- tool.tool,
- tool.tool["id"],
- False)
runnerjob = tool.job(job_order,
self.output_callback,
**kwargs).next()
parser.add_argument("--api", type=str,
default=None, dest="work_api",
choices=("jobs", "containers"),
- help="Select work submission API. Default is 'containers' if that API is available, otherwise 'jobs'.")
+ help="Select work submission API. Default is 'jobs' if that API is available, otherwise 'containers'.")
parser.add_argument("--compute-checksum", action="store_true", default=False,
help="Compute checksum of contents while collecting outputs",
arvargs.conformance_test = None
arvargs.use_container = True
arvargs.relax_path_checks = True
- arvargs.validate = None
+ arvargs.print_supported_versions = False
make_fs_access = partial(CollectionFsAccess,
collection_cache=runner.collection_cache)