import os
from cwltool.errors import WorkflowException
-from cwltool.process import get_feature, adjustFiles, UnsupportedRequirement, shortname
+from cwltool.process import get_feature, UnsupportedRequirement, shortname
+from cwltool.pathmapper import adjustFiles
import arvados.collection
"command": self.command_line,
"owner_uuid": self.arvrunner.project_uuid,
"name": self.name,
- "output_path": "/var/spool/cwl",
- "cwd": "/var/spool/cwl",
+ "output_path": self.outdir,
+ "cwd": self.outdir,
"priority": 1,
"state": "Committed"
}
runtime_constraints = {}
mounts = {
- "/var/spool/cwl": {
+ self.outdir: {
"kind": "tmp"
}
}
+ dirs = set()
for f in self.pathmapper.files():
- _, p = self.pathmapper.mapper(f)
- mounts[p] = {
- "kind": "collection",
- "portable_data_hash": p[6:]
- }
+ _, p, tp = self.pathmapper.mapper(f)
+ if tp == "Directory" and '/' not in p[6:]:
+ mounts[p] = {
+ "kind": "collection",
+ "portable_data_hash": p[6:]
+ }
+ dirs.add(p[6:])
+ for f in self.pathmapper.files():
+ _, p, tp = self.pathmapper.mapper(f)
+ if p[6:].split("/")[0] not in dirs:
+ mounts[p] = {
+ "kind": "collection",
+ "portable_data_hash": p[6:]
+ }
- if self.generatefiles:
+ if self.generatefiles["listing"]:
raise UnsupportedRequirement("Generate files not supported")
- container_request["environment"] = {"TMPDIR": "/tmp"}
+ container_request["environment"] = {"TMPDIR": self.tmpdir, "HOME": self.outdir}
if self.environment:
container_request["environment"].update(self.environment)
if self.stdin:
raise UnsupportedRequirement("Stdin redirection currently not suppported")
+ if self.stderr:
+ raise UnsupportedRequirement("Stderr redirection currently not suppported")
+
if self.stdout:
mounts["stdout"] = {"kind": "file",
- "path": "/var/spool/cwl/%s" % (self.stdout)}
+ "path": "%s/%s" % (self.outdir, self.stdout)}
(docker_req, docker_is_req) = get_feature(self, "DockerRequirement")
if not docker_req:
self.arvrunner.processes[response["container_uuid"]] = self
- logger.info("Container %s (%s) request state is %s", self.name, response["container_uuid"], response["state"])
+ logger.info("Container %s (%s) request state is %s", self.name, response["uuid"], response["state"])
if response["state"] == "Final":
self.done(response)
try:
outputs = {}
if record["output"]:
- outputs = done.done(self, record, "/tmp", "/var/spool/cwl", "/keep")
+ outputs = done.done(self, record, "/tmp", self.outdir, "/keep")
except WorkflowException as e:
logger.error("Error while collecting container outputs:\n%s", e, exc_info=(e if self.arvrunner.debug else False))
processStatus = "permanentFail"