from cwltool.process import shortname, UnsupportedRequirement
from cwltool.pathmapper import adjustFileObjs
+from cwltool.draft2tool import compute_checksums
from arvados.api import OrderedJsonModel
logger = logging.getLogger('arvados.cwl-runner')
useruuid = self.api.users().current().execute()["uuid"]
self.project_uuid = kwargs.get("project_uuid") if kwargs.get("project_uuid") else useruuid
self.pipeline = None
+ make_fs_access = kwargs.get("make_fs_access") or partial(CollectionFsAccess, api_client=self.api)
+ self.fs_access = make_fs_access(kwargs["basedir"])
if kwargs.get("create_template"):
tmpl = RunnerTemplate(self, tool, job_order, kwargs.get("enable_reuse"))
self.debug = kwargs.get("debug")
self.ignore_docker_for_reuse = kwargs.get("ignore_docker_for_reuse")
- make_fs_access = kwargs.get("make_fs_access") or partial(CollectionFsAccess, api_client=self.api)
- self.fs_access = make_fs_access(kwargs["basedir"])
kwargs["make_fs_access"] = make_fs_access
kwargs["enable_reuse"] = kwargs.get("enable_reuse")
kwargs["use_container"] = True
raise WorkflowException("Workflow did not return a result.")
if kwargs.get("compute_checksum"):
- def compute_checksums(fileobj):
- if "checksum" not in fileobj:
- checksum = hashlib.sha1()
- with self.fs_access.open(fileobj["location"], "rb") as f:
- contents = f.read(1024*1024)
- while contents != "":
- checksum.update(contents)
- contents = f.read(1024*1024)
- fileobj["checksum"] = "sha1$%s" % checksum.hexdigest()
-
- adjustFileObjs(self.final_output, compute_checksums)
+ adjustFileObjs(self.final_output, partial(compute_checksums, self.fs_access))
return self.final_output