logger = logging.getLogger('arvados.cwl-runner')
logger.setLevel(logging.INFO)
-crunchrunner_pdh = "ff6fc71e593081ef9733afacaeee15ea+140"
-crunchrunner_download = "https://cloud.curoverse.com/collections/download/qr1hi-4zz18-n3m1yxd0vx78jic/1i1u2qtq66k1atziv4ocfgsg5nu5tj11n4r6e0bhvjg03rix4m/crunchrunner"
-certs_download = "https://cloud.curoverse.com/collections/download/qr1hi-4zz18-n3m1yxd0vx78jic/1i1u2qtq66k1atziv4ocfgsg5nu5tj11n4r6e0bhvjg03rix4m/ca-certificates.crt"
-
tmpdirre = re.compile(r"^\S+ \S+ \d+ \d+ stderr \S+ \S+ crunchrunner: \$\(task\.tmpdir\)=(.*)")
outdirre = re.compile(r"^\S+ \S+ \d+ \d+ stderr \S+ \S+ crunchrunner: \$\(task\.outdir\)=(.*)")
keepre = re.compile(r"^\S+ \S+ \d+ \d+ stderr \S+ \S+ crunchrunner: \$\(task\.keep\)=(.*)")
(docker_req, docker_is_req) = get_feature(self, "DockerRequirement")
if docker_req and kwargs.get("use_container") is not False:
runtime_constraints["docker_image"] = arv_docker_get_image(self.arvrunner.api, docker_req, pull_image, self.arvrunner.project_uuid)
+ else:
+ runtime_constraints["docker_image"] = "arvados/jobs"
resources = self.builder.resources
if resources is not None:
"repository": "arvados",
"script_version": "master",
"minimum_script_version": "9e5b98e8f5f4727856b53447191f9c06e3da2ba6",
- "script_parameters": {"tasks": [script_parameters], "crunchrunner": crunchrunner_pdh+"/crunchrunner"},
+ "script_parameters": {"tasks": [script_parameters]},
"runtime_constraints": runtime_constraints
}, find_or_create=kwargs.get("enable_reuse", True)).execute(num_retries=self.arvrunner.num_retries)
tmpdir = None
outdir = None
keepdir = None
- for l in log.readlines():
+ for l in log:
+ # Determine the tmpdir, outdir and keepdir paths from
+ # the job run. Unfortunately, we can't take the first
+ # values we find (which are expected to be near the
+ # top) and stop scanning because if the node fails and
+ # the job restarts on a different node these values
+ # will different runs, and we need to know about the
+ # final run that actually produced output.
+
g = tmpdirre.match(l)
if g:
tmpdir = g.group(1)
if g:
keepdir = g.group(1)
- # It turns out if the job fails and restarts it can
- # come up on a different compute node, so we have to
- # read the log to the end to be sure instead of taking the
- # easy way out.
- #
- #if tmpdir and outdir and keepdir:
- # break
+ colname = "Output %s of %s" % (record["output"][0:7], self.name)
- # Create a collection located in the same project as the pipeline with the contents of the output.
+ # check if collection already exists with same owner, name and content
+ collection_exists = self.arvrunner.api.collections().list(
+ filters=[["owner_uuid", "=", self.arvrunner.project_uuid],
+ ['portable_data_hash', '=', record["output"]],
+ ["name", "=", colname]]
+ ).execute(num_retries=self.arvrunner.num_retries)
+
+ if not collection_exists["items"]:
+ # Create a collection located in the same project as the
+ # pipeline with the contents of the output.
# First, get output record.
- collections = self.arvrunner.api.collections().list(limit=1,
- filters=[['portable_data_hash', '=', record["output"]]],
- select=["portable_data_hash", "manifest_text"]
+ collections = self.arvrunner.api.collections().list(
+ limit=1,
+ filters=[['portable_data_hash', '=', record["output"]]],
+ select=["manifest_text"]
).execute(num_retries=self.arvrunner.num_retries)
- if collections["items"]:
- colname = "Output %s of %s" % (record["output"][0:7], self.name)
-
- # check if there is a name collision.
- name_collision = self.arvrunner.api.collections().list(filters=[["owner_uuid", "=", self.arvrunner.project_uuid],
- ["name", "=", name]]
- ).execute(num_retries=self.arvrunner.num_retries)
-
- if not name_collision["items"]:
- # Create new collection in the parent project
- # with the output contents.
- self.arvrunner.api.collections().create(body={
- "owner_uuid": self.arvrunner.project_uuid,
- "name": colname,
- "portable_data_hash": collections[0]["portable_data_hash"],
- "manifest_text": collections[0]["manifest_text"]
- }, ensure_unique_name=True).execute(num_retries=self.arvrunner.num_retries)
-
- # else: there is already a collection with the same name and the
- # same contents, so nothing to do.
+ if not collections["items"]:
+ raise WorkflowException(
+ "Job output '%s' cannot be found on API server" % (
+ record["output"]))
+
+ # Create new collection in the parent project
+ # with the output contents.
+ self.arvrunner.api.collections().create(body={
+ "owner_uuid": self.arvrunner.project_uuid,
+ "name": colname,
+ "portable_data_hash": record["output"],
+ "manifest_text": collections["items"][0]["manifest_text"]
+ }, ensure_unique_name=True).execute(
+ num_retries=self.arvrunner.num_retries)
self.builder.outdir = outdir
self.builder.pathmapper.keepdir = keepdir
events = arvados.events.subscribe(arvados.api('v1'), [["object_uuid", "is_a", "arvados#job"]], self.on_message)
self.debug = args.debug
-
- try:
- self.api.collections().get(uuid=crunchrunner_pdh).execute()
- except arvados.errors.ApiError as e:
- import httplib2
- h = httplib2.Http(ca_certs=arvados.util.ca_certs_path())
- resp, content = h.request(crunchrunner_download, "GET")
- resp2, content2 = h.request(certs_download, "GET")
- with arvados.collection.Collection() as col:
- with col.open("crunchrunner", "w") as f:
- f.write(content)
- with col.open("ca-certificates.crt", "w") as f:
- f.write(content2)
-
- col.save_new("crunchrunner binary", ensure_unique_name=True)
-
self.fs_access = CollectionFsAccess(input_basedir)
kwargs["fs_access"] = self.fs_access
projects / arvados.git / blobdiff