import arvados.events
import arvados.commands.keepdocker
import arvados.commands.run
+import arvados.collection
+import arvados.util
import cwltool.draft2tool
import cwltool.workflow
import cwltool.main
import logging
import re
import os
+import sys
from cwltool.process import get_feature
+from arvados.api import OrderedJsonModel
logger = logging.getLogger('arvados.cwl-runner')
logger.setLevel(logging.INFO)
+crunchrunner_pdh = "83db29f08544e1c319572a6bd971088a+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: \$\(task\.keep\)=(.*)")
+
+
def arv_docker_get_image(api_client, dockerRequirement, pull_image):
if "dockerImageId" not in dockerRequirement and "dockerPull" in dockerRequirement:
dockerRequirement["dockerImageId"] = dockerRequirement["dockerPull"]
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)
+ resources = self.builder.resources
+ if resources is not None:
+ if "coresMin" in resources.keys():
+ try:
+ runtime_constraints["min_cores_per_node"] = int(resources["coresMin"])
+ except:
+ runtime_constraints["min_cores_per_node"] = None
+ if "ramMin" in resources.keys():
+ try:
+ runtime_constraints["min_ram_mb_per_node"] = int(resources["ramMin"])
+ except:
+ runtime_constraints["min_ram_mb_per_node"] = None
+
try:
response = self.arvrunner.api.jobs().create(body={
"script": "crunchrunner",
- "repository": kwargs["repository"],
- "script_version": "master",
- "script_parameters": {"tasks": [script_parameters]},
+ "repository": "arvados",
+ "script_version": "8488-cwl-crunchrunner-collection",
+ "script_parameters": {"tasks": [script_parameters], "crunchrunner": crunchrunner_pdh+"/crunchrunner"},
"runtime_constraints": runtime_constraints
}, find_or_create=kwargs.get("enable_reuse", True)).execute(num_retries=self.arvrunner.num_retries)
try:
outputs = {}
if record["output"]:
+ logc = arvados.collection.Collection(record["log"])
+ log = logc.open(logc.keys()[0])
+ tmpdir = None
+ outdir = None
+ keepdir = None
+ for l in log.readlines():
+ g = tmpdirre.match(l)
+ if g:
+ tmpdir = g.group(1)
+ g = outdirre.match(l)
+ if g:
+ outdir = g.group(1)
+ g = keepre.match(l)
+ if g:
+ keepdir = g.group(1)
+ if tmpdir and outdir and keepdir:
+ break
+
+ self.builder.outdir = outdir
+ self.builder.pathmapper.keepdir = keepdir
outputs = self.collect_outputs("keep:" + record["output"])
except Exception as e:
logger.exception("Got exception while collecting job outputs:")
arvrunner.add_uploaded(src, (ab, st.fn))
self._pathmap[src] = (ab, st.fn)
+ self.keepdir = None
+
+ def reversemap(self, target):
+ if target.startswith("keep:"):
+ return target
+ elif self.keepdir and target.startswith(self.keepdir):
+ return "keep:" + target[len(self.keepdir)+1:]
+ else:
+ return super(ArvPathMapper, self).reversemap(target)
class ArvadosCommandTool(cwltool.draft2tool.CommandLineTool):
def __init__(self, arvrunner, toolpath_object, **kwargs):
- super(ArvadosCommandTool, self).__init__(toolpath_object, outdir="$(task.outdir)", tmpdir="$(task.tmpdir)", **kwargs)
+ super(ArvadosCommandTool, self).__init__(toolpath_object, **kwargs)
self.arvrunner = arvrunner
def makeJobRunner(self):
def arvExecutor(self, tool, job_order, input_basedir, args, **kwargs):
events = arvados.events.subscribe(arvados.api('v1'), [["object_uuid", "is_a", "arvados#job"]], self.on_message)
- self.pipeline = self.api.pipeline_instances().create(body={"name": shortname(tool.tool["id"]),
- "components": {},
- "state": "RunningOnClient"}).execute(num_retries=self.num_retries)
+ 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
kwargs["enable_reuse"] = args.enable_reuse
- kwargs["repository"] = args.repository
+
+ kwargs["outdir"] = "$(task.outdir)"
+ kwargs["tmpdir"] = "$(task.tmpdir)"
if kwargs.get("conformance_test"):
return cwltool.main.single_job_executor(tool, job_order, input_basedir, args, **kwargs)
else:
- jobiter = tool.job(job_order,
- input_basedir,
- self.output_callback,
- **kwargs)
-
- for runnable in jobiter:
- if runnable:
- with self.lock:
- runnable.run(**kwargs)
- else:
- if self.jobs:
- try:
- self.cond.acquire()
- self.cond.wait()
- finally:
- self.cond.release()
- else:
- logger.error("Workflow cannot make any more progress.")
- break
-
- while self.jobs:
- try:
- self.cond.acquire()
- self.cond.wait()
- finally:
- self.cond.release()
+ self.pipeline = self.api.pipeline_instances().create(body={"name": shortname(tool.tool["id"]),
+ "components": {},
+ "state": "RunningOnClient"}).execute(num_retries=self.num_retries)
- events.close()
+ jobiter = tool.job(job_order,
+ input_basedir,
+ self.output_callback,
+ docker_outdir="$(task.outdir)",
+ **kwargs)
- if self.final_output is None:
- raise cwltool.workflow.WorkflowException("Workflow did not return a result.")
+ try:
+ for runnable in jobiter:
+ if runnable:
+ with self.lock:
+ runnable.run(**kwargs)
+ else:
+ if self.jobs:
+ try:
+ self.cond.acquire()
+ self.cond.wait(1)
+ except RuntimeError:
+ pass
+ finally:
+ self.cond.release()
+ else:
+ logger.error("Workflow cannot make any more progress.")
+ break
+
+ while self.jobs:
+ try:
+ self.cond.acquire()
+ self.cond.wait(1)
+ except RuntimeError:
+ pass
+ finally:
+ self.cond.release()
+
+ events.close()
+
+ if self.final_output is None:
+ raise cwltool.workflow.WorkflowException("Workflow did not return a result.")
+
+ except:
+ if sys.exc_info()[0] is not KeyboardInterrupt:
+ logger.exception("Caught unhandled exception, marking pipeline as failed")
+ self.api.pipeline_instances().update(uuid=self.pipeline["uuid"],
+ body={"state": "Failed"}).execute(num_retries=self.num_retries)
return self.final_output
def main(args, stdout, stderr, api_client=None):
- runner = ArvCwlRunner(api_client=arvados.api('v1'))
args.insert(0, "--leave-outputs")
parser = cwltool.main.arg_parser()
exgroup = parser.add_mutually_exclusive_group()
default=False, dest="enable_reuse",
help="")
- parser.add_argument('--repository', type=str, default="peter/crunchrunner", help="Repository containing the 'crunchrunner' program.")
+ try:
+ runner = ArvCwlRunner(api_client=arvados.api('v1', model=OrderedJsonModel()))
+ except Exception as e:
+ logger.error(e)
+ return 1
return cwltool.main.main(args, executor=runner.arvExecutor, makeTool=runner.arvMakeTool, parser=parser)
projects / arvados.git / blobdiff