+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: Apache-2.0
+
+from future.utils import viewvalues
+
import re
from cwltool.errors import WorkflowException
from collections import deque
def done(self, record, tmpdir, outdir, keepdir):
- colname = "Output %s of %s" % (record["output"][0:7], self.name)
-
- # 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=["manifest_text"]
+ cols = [
+ ("output", "Output %s of %s" % (record["output"][0:7], self.name), record["output"]),
+ ("log", "Log of %s" % (record["uuid"]), record["log"])
+ ]
+
+ for coltype, colname, colpdh in cols:
+ # 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', '=', colpdh],
+ ["name", "=", colname]]
).execute(num_retries=self.arvrunner.num_retries)
- if not collections["items"]:
- raise WorkflowException(
- "[job %s] output '%s' cannot be found on API server" % (
- self.name, 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)
+ if not collection_exists["items"]:
+ # Create a collection located in the same project as the
+ # pipeline with the contents of the output/log.
+ # First, get output/log record.
+ collections = self.arvrunner.api.collections().list(
+ limit=1,
+ filters=[['portable_data_hash', '=', colpdh]],
+ select=["manifest_text"]
+ ).execute(num_retries=self.arvrunner.num_retries)
+
+ if not collections["items"]:
+ raise WorkflowException(
+ "[job %s] %s '%s' cannot be found on API server" % (
+ self.name, coltype, colpdh))
+
+ # Create new collection in the parent project
+ # with the output/log contents.
+ self.arvrunner.api.collections().create(body={
+ "owner_uuid": self.arvrunner.project_uuid,
+ "name": colname,
+ "portable_data_hash": colpdh,
+ "manifest_text": collections["items"][0]["manifest_text"]
+ }, ensure_unique_name=True).execute(
+ num_retries=self.arvrunner.num_retries)
return done_outputs(self, record, tmpdir, outdir, keepdir)
def done_outputs(self, record, tmpdir, outdir, keepdir):
self.builder.outdir = outdir
self.builder.pathmapper.keepdir = keepdir
- return self.collect_outputs("keep:" + record["output"])
+ return self.collect_outputs("keep:" + record["output"], record["exit_code"])
crunchstat_re = re.compile(r"^\d{4}-\d\d-\d\d_\d\d:\d\d:\d\d [a-z0-9]{5}-8i9sb-[a-z0-9]{15} \d+ \d+ stderr crunchstat:")
timestamp_re = re.compile(r"^(\d{4}-\d\d-\d\dT\d\d:\d\d:\d\d\.\d+Z) (.*)")
-def logtail(logcollection, logger, header, maxlen=25):
+def logtail(logcollection, logfunc, header, maxlen=25, include_crunchrun=True):
if len(logcollection) == 0:
- logger.info(header)
- logger.info(" ** log is empty **")
+ logfunc("%s\n%s", header, " ** log is empty **")
return
- containersapi = ("crunch-run.txt" in logcollection)
mergelogs = {}
+ logfiles = ["stdout.txt", "stderr.txt"]
+
+ if include_crunchrun:
+ logfiles.append("crunch-run.txt")
+
+ for log in logfiles:
+ if log not in logcollection:
+ continue
+ logname = log[:-4] # trim off the .txt
+ logt = deque([], maxlen)
+ mergelogs[logname] = logt
+ with logcollection.open(log, encoding="utf-8") as f:
+ for l in f:
+ g = timestamp_re.match(l)
+ logt.append((g.group(1), g.group(2)))
+
+ keys = list(mergelogs)
+ loglines = []
- for log in logcollection.keys():
- if not containersapi or log in ("crunch-run.txt", "stdout.txt", "stderr.txt"):
- logname = log[:-4]
- logt = deque([], maxlen)
- mergelogs[logname] = logt
- with logcollection.open(log) as f:
- for l in f:
- if containersapi:
- g = timestamp_re.match(l)
- logt.append((g.group(1), g.group(2)))
- elif not crunchstat_re.match(l):
- logt.append(l)
-
- if len(mergelogs) > 1:
- keys = mergelogs.keys()
- loglines = []
- while True:
- earliest = None
- for k in keys:
- if mergelogs[k]:
- if earliest is None or mergelogs[k][0][0] < mergelogs[earliest][0][0]:
- earliest = k
- if earliest is None:
- break
- ts, msg = mergelogs[earliest].popleft()
- loglines.append("%s %s %s" % (ts, earliest, msg))
- loglines = loglines[-maxlen:]
- else:
- loglines = mergelogs.values()[0]
+ # we assume the log lines are all in order so this this is a
+ # straight linear merge where we look at the next timestamp of
+ # each log and take whichever one is earliest.
+ while True:
+ earliest = None
+ for k in keys:
+ if mergelogs[k]:
+ if earliest is None or mergelogs[k][0][0] < mergelogs[earliest][0][0]:
+ earliest = k
+ if earliest is None:
+ break
+ ts, msg = mergelogs[earliest].popleft()
+ loglines.append("%s %s %s" % (ts, earliest, msg))
+ loglines = loglines[-maxlen:]
logtxt = "\n ".join(l.strip() for l in loglines)
- logger.info(header)
- logger.info("\n %s", logtxt)
+ logfunc("%s\n\n %s\n", header, logtxt)
projects / arvados.git / blobdiff