#
# SPDX-License-Identifier: Apache-2.0
+from future import standard_library
+standard_library.install_aliases()
+from builtins import str
+
import logging
import json
import os
-import urllib
+import urllib.request, urllib.parse, urllib.error
import time
import datetime
import ciso8601
import uuid
import math
-from arvados_cwl.util import get_current_container, get_intermediate_collection_info
+import arvados_cwl.util
import ruamel.yaml as yaml
from cwltool.errors import WorkflowException
class ArvadosContainer(JobBase):
"""Submit and manage a Crunch container request for executing a CWL CommandLineTool."""
- def __init__(self, runner,
+ def __init__(self, runner, job_runtime,
builder, # type: Builder
joborder, # type: Dict[Text, Union[Dict[Text, Any], List, Text]]
make_path_mapper, # type: Callable[..., PathMapper]
):
super(ArvadosContainer, self).__init__(builder, joborder, make_path_mapper, requirements, hints, name)
self.arvrunner = runner
+ self.job_runtime = job_runtime
self.running = False
self.uuid = None
# ArvadosContainer object by CommandLineTool.job() before
# run() is called.
+ runtimeContext = self.job_runtime
+
container_request = {
"command": self.command_line,
"name": self.name,
}
runtime_constraints = {}
- if self.arvrunner.project_uuid:
- container_request["owner_uuid"] = self.arvrunner.project_uuid
+ if runtimeContext.project_uuid:
+ container_request["owner_uuid"] = runtimeContext.project_uuid
if self.arvrunner.secret_store.has_secret(self.command_line):
raise WorkflowException("Secret material leaked on command line, only file literals may contain secrets")
"kind": "collection",
"portable_data_hash": pdh
}
+ if pdh in self.pathmapper.pdh_to_uuid:
+ mounts[targetdir]["uuid"] = self.pathmapper.pdh_to_uuid[pdh]
if len(sp) == 2:
if tp == "Directory":
path = sp[1]
vwd = arvados.collection.Collection(api_client=self.arvrunner.api,
keep_client=self.arvrunner.keep_client,
num_retries=self.arvrunner.num_retries)
- generatemapper = NoFollowPathMapper([self.generatefiles], "", "",
+ generatemapper = NoFollowPathMapper(self.generatefiles["listing"], "", "",
separateDirs=False)
- sorteditems = sorted(generatemapper.items(), None, key=lambda n: n[1].target)
+ sorteditems = sorted(generatemapper.items(), key=lambda n: n[1].target)
logger.debug("generatemapper is %s", sorteditems)
}
else:
with vwd.open(p.target, "w") as n:
- n.write(p.resolved.encode("utf-8"))
+ n.write(p.resolved)
def keepemptydirs(p):
if isinstance(p, arvados.collection.RichCollectionBase):
keepemptydirs(vwd)
if not runtimeContext.current_container:
- runtimeContext.current_container = get_current_container(self.arvrunner.api, self.arvrunner.num_retries, logger)
- info = get_intermediate_collection_info(self.name, runtimeContext.current_container, runtimeContext.intermediate_output_ttl)
+ runtimeContext.current_container = arvados_cwl.util.get_current_container(self.arvrunner.api, self.arvrunner.num_retries, logger)
+ info = arvados_cwl.util.get_intermediate_collection_info(self.name, runtimeContext.current_container, runtimeContext.intermediate_output_ttl)
vwd.save_new(name=info["name"],
- owner_uuid=self.arvrunner.project_uuid,
+ owner_uuid=runtimeContext.project_uuid,
ensure_unique_name=True,
trash_at=info["trash_at"],
properties=info["properties"])
container_request["container_image"] = arv_docker_get_image(self.arvrunner.api,
docker_req,
runtimeContext.pull_image,
- self.arvrunner.project_uuid,
- runtimeContext.submit_runner_cluster)
+ runtimeContext.project_uuid)
+
+ network_req, _ = self.get_requirement("NetworkAccess")
+ if network_req:
+ runtime_constraints["API"] = network_req["networkAccess"]
api_req, _ = self.get_requirement("http://arvados.org/cwl#APIRequirement")
if api_req:
scheduling_parameters["max_run_time"] = self.timelimit
extra_submit_params = {}
- cluster_target_req, _ = self.get_requirement("http://arvados.org/cwl#ClusterTarget")
- if cluster_target_req:
- cluster_id = cluster_target_req.get("clusterID")
- if cluster_id:
- extra_submit_params["cluster_id"] = cluster_id
- if cluster_target_req.get("ownerUUID"):
- container_request["owner_uuid"] = cluster_target_req.get("ownerUUID")
+ if runtimeContext.submit_runner_cluster:
+ extra_submit_params["cluster_id"] = runtimeContext.submit_runner_cluster
container_request["output_name"] = "Output for step %s" % (self.name)
container_request["output_ttl"] = self.output_ttl
logger.info("%s reused container %s", self.arvrunner.label(self), response["container_uuid"])
else:
logger.info("%s %s state is %s", self.arvrunner.label(self), response["uuid"], response["state"])
- except Exception as e:
- logger.error("%s got error %s" % (self.arvrunner.label(self), str(e)))
+ except Exception:
+ logger.exception("%s got an error", self.arvrunner.label(self))
self.output_callback({}, "permanentFail")
def done(self, record):
else:
processStatus = "permanentFail"
- if processStatus == "permanentFail":
- logc = arvados.collection.CollectionReader(container["log"],
+ if processStatus == "permanentFail" and record["log_uuid"]:
+ logc = arvados.collection.CollectionReader(record["log_uuid"],
api_client=self.arvrunner.api,
keep_client=self.arvrunner.keep_client,
num_retries=self.arvrunner.num_retries)
if record["output_uuid"]:
if self.arvrunner.trash_intermediate or self.arvrunner.intermediate_output_ttl:
# Compute the trash time to avoid requesting the collection record.
- trash_at = ciso8601.parse_datetime_unaware(record["modified_at"]) + datetime.timedelta(0, self.arvrunner.intermediate_output_ttl)
+ trash_at = ciso8601.parse_datetime_as_naive(record["modified_at"]) + datetime.timedelta(0, self.arvrunner.intermediate_output_ttl)
aftertime = " at %s" % trash_at.strftime("%Y-%m-%d %H:%M:%S UTC") if self.arvrunner.intermediate_output_ttl else ""
orpart = ", or" if self.arvrunner.trash_intermediate and self.arvrunner.intermediate_output_ttl else ""
oncomplete = " upon successful completion of the workflow" if self.arvrunner.trash_intermediate else ""
if container["output"]:
outputs = done.done_outputs(self, container, "/tmp", self.outdir, "/keep")
except WorkflowException as e:
+ # Only include a stack trace if in debug mode.
+ # A stack trace may obfuscate more useful output about the workflow.
logger.error("%s unable to collect output from %s:\n%s",
self.arvrunner.label(self), container["output"], e, exc_info=(e if self.arvrunner.debug else False))
processStatus = "permanentFail"
- except Exception as e:
- logger.exception("%s while getting output object: %s", self.arvrunner.label(self), e)
+ except Exception:
+ logger.exception("%s while getting output object:", self.arvrunner.label(self))
processStatus = "permanentFail"
finally:
self.output_callback(outputs, processStatus)
"secret_mounts": secret_mounts,
"runtime_constraints": {
"vcpus": math.ceil(self.submit_runner_cores),
- "ram": math.ceil(1024*1024 * self.submit_runner_ram),
+ "ram": 1024*1024 * (math.ceil(self.submit_runner_ram) + math.ceil(self.collection_cache_size)),
"API": True
},
"use_existing": self.enable_reuse,
"properties": {}
}
- if self.tool.tool.get("id", "").startswith("keep:"):
- sp = self.tool.tool["id"].split('/')
+ if self.embedded_tool.tool.get("id", "").startswith("keep:"):
+ sp = self.embedded_tool.tool["id"].split('/')
workflowcollection = sp[0][5:]
workflowname = "/".join(sp[1:])
workflowpath = "/var/lib/cwl/workflow/%s" % workflowname
"portable_data_hash": "%s" % workflowcollection
}
else:
- packed = packed_workflow(self.arvrunner, self.tool, self.merged_map)
+ packed = packed_workflow(self.arvrunner, self.embedded_tool, self.merged_map)
workflowpath = "/var/lib/cwl/workflow.json#main"
container_req["mounts"]["/var/lib/cwl/workflow.json"] = {
"kind": "json",
"content": packed
}
- if self.tool.tool.get("id", "").startswith("arvwf:"):
- container_req["properties"]["template_uuid"] = self.tool.tool["id"][6:33]
+ if self.embedded_tool.tool.get("id", "").startswith("arvwf:"):
+ container_req["properties"]["template_uuid"] = self.embedded_tool.tool["id"][6:33]
# --local means execute the workflow instead of submitting a container request
# --eval-timeout is the timeout for javascript invocation
# --parallel-task-count is the number of threads to use for job submission
# --enable/disable-reuse sets desired job reuse
+ # --collection-cache-size sets aside memory to store collections
command = ["arvados-cwl-runner",
"--local",
"--api=containers",
"--disable-validate",
"--eval-timeout=%s" % self.arvrunner.eval_timeout,
"--thread-count=%s" % self.arvrunner.thread_count,
- "--enable-reuse" if self.enable_reuse else "--disable-reuse"]
+ "--enable-reuse" if self.enable_reuse else "--disable-reuse",
+ "--collection-cache-size=%s" % self.collection_cache_size]
if self.output_name:
command.append("--output-name=" + self.output_name)
if self.arvrunner.project_uuid:
command.append("--project-uuid="+self.arvrunner.project_uuid)
+ if self.enable_dev:
+ command.append("--enable-dev")
+
command.extend([workflowpath, "/var/lib/cwl/cwl.input.json"])
container_req["command"] = command
extra_submit_params["cluster_id"] = runtimeContext.submit_runner_cluster
if runtimeContext.submit_request_uuid:
+ if "cluster_id" in extra_submit_params:
+ # Doesn't make sense for "update" and actually fails
+ del extra_submit_params["cluster_id"]
response = self.arvrunner.api.container_requests().update(
uuid=runtimeContext.submit_request_uuid,
body=job_spec,
container = self.arvrunner.api.containers().get(
uuid=record["container_uuid"]
).execute(num_retries=self.arvrunner.num_retries)
- except Exception as e:
- logger.exception("%s while getting runner container: %s", self.arvrunner.label(self), e)
+ container["log"] = record["log_uuid"]
+ except Exception:
+ logger.exception("%s while getting runner container", self.arvrunner.label(self))
self.arvrunner.output_callback({}, "permanentFail")
else:
super(RunnerContainer, self).done(container)
projects / arvados.git / blobdiff