import re
from cStringIO import StringIO
+from schema_salad.sourceline import SourceLine
+
import cwltool.draft2tool
from cwltool.draft2tool import CommandLineTool
import cwltool.workflow
-from cwltool.process import get_feature, scandeps, UnsupportedRequirement, normalizeFilesDirs
+from cwltool.process import get_feature, scandeps, UnsupportedRequirement, normalizeFilesDirs, shortname
from cwltool.load_tool import fetch_document
from cwltool.pathmapper import adjustFileObjs, adjustDirObjs
+from cwltool.utils import aslist
+from cwltool.builder import substitute
import arvados.collection
import ruamel.yaml as yaml
from .arvdocker import arv_docker_get_image
from .pathmapper import ArvPathMapper
from ._version import __version__
+from . import done
logger = logging.getLogger('arvados.cwl-runner')
loaded = set()
def loadref(b, u):
- joined = urlparse.urljoin(b, u)
+ joined = document_loader.fetcher.urljoin(b, u)
defrg, _ = urlparse.urldefrag(joined)
if defrg not in loaded:
loaded.add(defrg)
sc = scandeps(uri, scanobj,
loadref_fields,
set(("$include", "$schemas", "location")),
- loadref)
+ loadref, urljoin=document_loader.fetcher.urljoin)
normalizeFilesDirs(sc)
if isinstance(tool, CommandLineTool):
(docker_req, docker_is_req) = get_feature(tool, "DockerRequirement")
if docker_req:
+ if docker_req.get("dockerOutputDirectory"):
+ # TODO: can be supported by containers API, but not jobs API.
+ raise SourceLine(docker_req, "dockerOutputDirectory", UnsupportedRequirement).makeError(
+ "Option 'dockerOutputDirectory' of DockerRequirement not supported.")
arv_docker_get_image(arvrunner.api, docker_req, True, arvrunner.project_uuid)
elif isinstance(tool, cwltool.workflow.Workflow):
for s in tool.steps:
def upload_instance(arvrunner, name, tool, job_order):
upload_docker(arvrunner, tool)
+ for t in tool.tool["inputs"]:
+ def setSecondary(fileobj):
+ if isinstance(fileobj, dict) and fileobj.get("class") == "File":
+ if "secondaryFiles" not in fileobj:
+ fileobj["secondaryFiles"] = [{"location": substitute(fileobj["location"], sf), "class": "File"} for sf in t["secondaryFiles"]]
+
+ if isinstance(fileobj, list):
+ for e in fileobj:
+ setSecondary(e)
+
+ if shortname(t["id"]) in job_order and t.get("secondaryFiles"):
+ setSecondary(job_order[shortname(t["id"])])
+
workflowmapper = upload_dependencies(arvrunner,
name,
tool.doc_loader,
tool.tool,
tool.tool["id"],
True)
-
jobmapper = upload_dependencies(arvrunner,
os.path.basename(job_order.get("id", "#")),
tool.doc_loader,
return img
class Runner(object):
- def __init__(self, runner, tool, job_order, enable_reuse, output_name):
+ def __init__(self, runner, tool, job_order, enable_reuse,
+ output_name, output_tags, submit_runner_ram=0,
+ name=None, on_error=None):
self.arvrunner = runner
self.tool = tool
self.job_order = job_order
self.uuid = None
self.final_output = None
self.output_name = output_name
+ self.output_tags = output_tags
+ self.name = name
+ self.on_error = on_error
+
+ if submit_runner_ram:
+ self.submit_runner_ram = submit_runner_ram
+ else:
+ self.submit_runner_ram = 1024
+
+ if self.submit_runner_ram <= 0:
+ raise Exception("Value of --submit-runner-ram must be greater than zero")
def update_pipeline_component(self, record):
pass
def arvados_job_spec(self, *args, **kwargs):
- self.name = os.path.basename(self.tool.tool["id"])
+ if self.name is None:
+ self.name = self.tool.tool.get("label") or os.path.basename(self.tool.tool["id"])
+
+ # Need to filter this out, gets added by cwltool when providing
+ # parameters on the command line.
+ if "job_order" in self.job_order:
+ del self.job_order["job_order"]
+
workflowmapper = upload_instance(self.arvrunner, self.name, self.tool, self.job_order)
adjustDirObjs(self.job_order, trim_listing)
return workflowmapper
def done(self, record):
- if record["state"] == "Complete":
- if record.get("exit_code") is not None:
- if record["exit_code"] == 33:
- processStatus = "UnsupportedRequirement"
- elif record["exit_code"] == 0:
- processStatus = "success"
+ try:
+ if record["state"] == "Complete":
+ if record.get("exit_code") is not None:
+ if record["exit_code"] == 33:
+ processStatus = "UnsupportedRequirement"
+ elif record["exit_code"] == 0:
+ processStatus = "success"
+ else:
+ processStatus = "permanentFail"
else:
- processStatus = "permanentFail"
+ processStatus = "success"
else:
- processStatus = "success"
- else:
- processStatus = "permanentFail"
+ processStatus = "permanentFail"
- outputs = None
- try:
- try:
- self.final_output = record["output"]
- outc = arvados.collection.CollectionReader(self.final_output,
+ outputs = {}
+
+ if processStatus == "permanentFail":
+ logc = arvados.collection.CollectionReader(record["log"],
api_client=self.arvrunner.api,
keep_client=self.arvrunner.keep_client,
num_retries=self.arvrunner.num_retries)
+ done.logtail(logc, logger, "%s error log:" % self.arvrunner.label(self), maxlen=40)
+
+ self.final_output = record["output"]
+ outc = arvados.collection.CollectionReader(self.final_output,
+ api_client=self.arvrunner.api,
+ keep_client=self.arvrunner.keep_client,
+ num_retries=self.arvrunner.num_retries)
+ if "cwl.output.json" in outc:
with outc.open("cwl.output.json") as f:
- outputs = json.load(f)
- def keepify(fileobj):
- path = fileobj["location"]
- if not path.startswith("keep:"):
- fileobj["location"] = "keep:%s/%s" % (record["output"], path)
- adjustFileObjs(outputs, keepify)
- adjustDirObjs(outputs, keepify)
- except Exception as e:
- logger.error("While getting final output object: %s", e)
+ if f.size() > 0:
+ outputs = json.load(f)
+ def keepify(fileobj):
+ path = fileobj["location"]
+ if not path.startswith("keep:"):
+ fileobj["location"] = "keep:%s/%s" % (record["output"], path)
+ adjustFileObjs(outputs, keepify)
+ adjustDirObjs(outputs, keepify)
+ except Exception as e:
+ logger.exception("[%s] While getting final output object: %s", self.name, e)
+ self.arvrunner.output_callback({}, "permanentFail")
+ else:
self.arvrunner.output_callback(outputs, processStatus)
finally:
- del self.arvrunner.processes[record["uuid"]]
+ if record["uuid"] in self.arvrunner.processes:
+ del self.arvrunner.processes[record["uuid"]]
projects / arvados.git / blobdiff