import logging
import re
-from . import done
-from .arvdocker import arv_docker_get_image
-from cwltool.process import get_feature
+import copy
+
+from cwltool.process import get_feature, shortname
from cwltool.errors import WorkflowException
+from cwltool.draft2tool import revmap_file, CommandLineTool
+from cwltool.load_tool import fetch_document
+from cwltool.builder import Builder
+
import arvados.collection
+from .arvdocker import arv_docker_get_image
+from .runner import Runner
+from .pathmapper import InitialWorkDirPathMapper
+from . import done
+
logger = logging.getLogger('arvados.cwl-runner')
tmpdirre = re.compile(r"^\S+ \S+ \d+ \d+ stderr \S+ \S+ crunchrunner: \$\(task\.tmpdir\)=(.*)")
def __init__(self, runner):
self.arvrunner = runner
self.running = False
+ self.uuid = None
def run(self, dry_run=False, pull_image=True, **kwargs):
script_parameters = {
}
runtime_constraints = {}
- if self.generatefiles:
+ if self.generatefiles["listing"]:
vwd = arvados.collection.Collection()
script_parameters["task.vwd"] = {}
- for t in self.generatefiles:
- if isinstance(self.generatefiles[t], dict):
- src, rest = self.arvrunner.fs_access.get_collection(self.generatefiles[t]["path"].replace("$(task.keep)/", "keep:"))
- vwd.copy(rest, t, source_collection=src)
- else:
- with vwd.open(t, "w") as f:
- f.write(self.generatefiles[t])
+ generatemapper = InitialWorkDirPathMapper([self.generatefiles], "", "",
+ separateDirs=False)
+ for f, p in generatemapper.items():
+ if p.type == "CreateFile":
+ with vwd.open(p.target, "w") as n:
+ n.write(p.resolved.encode("utf-8"))
vwd.save_new()
- for t in self.generatefiles:
- script_parameters["task.vwd"][t] = "$(task.keep)/%s/%s" % (vwd.portable_data_hash(), t)
+ for f, p in generatemapper.items():
+ if p.type == "File":
+ script_parameters["task.vwd"][p.target] = p.resolved
+ if p.type == "CreateFile":
+ script_parameters["task.vwd"][p.target] = "$(task.keep)/%s/%s" % (vwd.portable_data_hash(), p.target)
script_parameters["task.env"] = {"TMPDIR": "$(task.tmpdir)"}
if self.environment:
script_parameters["task.env"].update(self.environment)
if self.stdin:
- script_parameters["task.stdin"] = self.pathmapper.mapper(self.stdin)[1]
+ script_parameters["task.stdin"] = self.stdin
if self.stdout:
script_parameters["task.stdout"] = self.stdout
+ if self.stderr:
+ script_parameters["task.stderr"] = self.stderr
+
+ if self.successCodes:
+ script_parameters["task.successCodes"] = self.successCodes
+ if self.temporaryFailCodes:
+ script_parameters["task.temporaryFailCodes"] = self.temporaryFailCodes
+ if self.permanentFailCodes:
+ script_parameters["task.permanentFailCodes"] = self.permanentFailCodes
+
(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)
find_or_create=kwargs.get("enable_reuse", True)
).execute(num_retries=self.arvrunner.num_retries)
- self.arvrunner.jobs[response["uuid"]] = self
+ self.arvrunner.processes[response["uuid"]] = self
self.update_pipeline_component(response)
self.output_callback(outputs, processStatus)
finally:
- del self.arvrunner.jobs[record["uuid"]]
+ del self.arvrunner.processes[record["uuid"]]
+
+
+class RunnerJob(Runner):
+ """Submit and manage a Crunch job that runs crunch_scripts/cwl-runner."""
+
+ def arvados_job_spec(self, dry_run=False, pull_image=True, **kwargs):
+ """Create an Arvados job specification for this workflow.
+
+ The returned dict can be used to create a job (i.e., passed as
+ the +body+ argument to jobs().create()), or as a component in
+ a pipeline template or pipeline instance.
+ """
+
+ workflowmapper = super(RunnerJob, self).arvados_job_spec(dry_run=dry_run, pull_image=pull_image, **kwargs)
+
+ self.job_order["cwl:tool"] = workflowmapper.mapper(self.tool.tool["id"])[1]
+ return {
+ "script": "cwl-runner",
+ "script_version": "master",
+ "repository": "arvados",
+ "script_parameters": self.job_order,
+ "runtime_constraints": {
+ "docker_image": "arvados/jobs"
+ }
+ }
+
+ def run(self, *args, **kwargs):
+ job_spec = self.arvados_job_spec(*args, **kwargs)
+ job_spec.setdefault("owner_uuid", self.arvrunner.project_uuid)
+
+ response = self.arvrunner.api.jobs().create(
+ body=job_spec,
+ find_or_create=self.enable_reuse
+ ).execute(num_retries=self.arvrunner.num_retries)
+
+ self.uuid = response["uuid"]
+ self.arvrunner.processes[self.uuid] = self
+
+ logger.info("Submitted job %s", response["uuid"])
+
+ if kwargs.get("submit"):
+ self.pipeline = self.arvrunner.api.pipeline_instances().create(
+ body={
+ "owner_uuid": self.arvrunner.project_uuid,
+ "name": shortname(self.tool.tool["id"]),
+ "components": {"cwl-runner": {"job": {"uuid": self.uuid, "state": response["state"]} } },
+ "state": "RunningOnClient"}).execute(num_retries=self.arvrunner.num_retries)
+
+ if response["state"] in ("Complete", "Failed", "Cancelled"):
+ self.done(response)
+
+
+class RunnerTemplate(object):
+ """An Arvados pipeline template that invokes a CWL workflow."""
+
+ type_to_dataclass = {
+ 'boolean': 'boolean',
+ 'File': 'File',
+ 'float': 'number',
+ 'int': 'number',
+ 'string': 'text',
+ }
+
+ def __init__(self, runner, tool, job_order, enable_reuse):
+ self.runner = runner
+ self.tool = tool
+ self.job = RunnerJob(
+ runner=runner,
+ tool=tool,
+ job_order=job_order,
+ enable_reuse=enable_reuse)
+
+ def pipeline_component_spec(self):
+ """Return a component that Workbench and a-r-p-i will understand.
+
+ Specifically, translate CWL input specs to Arvados pipeline
+ format, like {"dataclass":"File","value":"xyz"}.
+ """
+ spec = self.job.arvados_job_spec()
+
+ # Most of the component spec is exactly the same as the job
+ # spec (script, script_version, etc.).
+ # spec['script_parameters'] isn't right, though. A component
+ # spec's script_parameters hash is a translation of
+ # self.tool.tool['inputs'] with defaults/overrides taken from
+ # the job order. So we move the job parameters out of the way
+ # and build a new spec['script_parameters'].
+ job_params = spec['script_parameters']
+ spec['script_parameters'] = {}
+
+ for param in self.tool.tool['inputs']:
+ param = copy.deepcopy(param)
+
+ # Data type and "required" flag...
+ types = param['type']
+ if not isinstance(types, list):
+ types = [types]
+ param['required'] = 'null' not in types
+ non_null_types = set(types) - set(['null'])
+ if len(non_null_types) == 1:
+ the_type = [c for c in non_null_types][0]
+ dataclass = self.type_to_dataclass.get(the_type)
+ if dataclass:
+ param['dataclass'] = dataclass
+ # Note: If we didn't figure out a single appropriate
+ # dataclass, we just left that attribute out. We leave
+ # the "type" attribute there in any case, which might help
+ # downstream.
+
+ # Title and description...
+ title = param.pop('label', '')
+ descr = param.pop('doc', '').rstrip('\n')
+ if title:
+ param['title'] = title
+ if descr:
+ param['description'] = descr
+
+ # Fill in the value from the current job order, if any.
+ param_id = shortname(param.pop('id'))
+ value = job_params.get(param_id)
+ if value is None:
+ pass
+ elif not isinstance(value, dict):
+ param['value'] = value
+ elif param.get('dataclass') == 'File' and value.get('location'):
+ param['value'] = value['location']
+
+ spec['script_parameters'][param_id] = param
+ spec['script_parameters']['cwl:tool'] = job_params['cwl:tool']
+ return spec
+
+ def save(self):
+ job_spec = self.pipeline_component_spec()
+ response = self.runner.api.pipeline_templates().create(body={
+ "components": {
+ self.job.name: job_spec,
+ },
+ "name": self.job.name,
+ "owner_uuid": self.runner.project_uuid,
+ }, ensure_unique_name=True).execute(num_retries=self.runner.num_retries)
+ self.uuid = response["uuid"]
+ logger.info("Created template %s", self.uuid)
projects / arvados.git / blobdiff