from builtins import next
from builtins import object
from builtins import str
-from future.utils import viewvalues
+from future.utils import viewvalues, viewitems
import argparse
import logging
import arvados_cwl.util
from .arvcontainer import RunnerContainer
-from .arvjob import RunnerJob, RunnerTemplate
from .runner import Runner, upload_docker, upload_job_order, upload_workflow_deps
from .arvtool import ArvadosCommandTool, validate_cluster_target, ArvadosExpressionTool
from .arvworkflow import ArvadosWorkflow, upload_workflow
from cwltool.process import shortname, UnsupportedRequirement, use_custom_schema
from cwltool.pathmapper import adjustFileObjs, adjustDirObjs, get_listing, visit_class
from cwltool.command_line_tool import compute_checksums
+from cwltool.load_tool import load_tool
logger = logging.getLogger('arvados.cwl-runner')
metrics = logging.getLogger('arvados.cwl-runner.metrics')
def __init__(self, runtime_status_update_func):
super(RuntimeStatusLoggingHandler, self).__init__()
self.runtime_status_update = runtime_status_update_func
+ self.updatingRuntimeStatus = False
def emit(self, record):
kind = None
kind = 'error'
elif record.levelno >= logging.WARNING:
kind = 'warning'
- if kind is not None:
- log_msg = record.getMessage()
- if '\n' in log_msg:
- # If the logged message is multi-line, use its first line as status
- # and the rest as detail.
- status, detail = log_msg.split('\n', 1)
- self.runtime_status_update(
- kind,
- "%s: %s" % (record.name, status),
- detail
- )
- else:
- self.runtime_status_update(
- kind,
- "%s: %s" % (record.name, record.getMessage())
- )
+ if kind is not None and self.updatingRuntimeStatus is not True:
+ self.updatingRuntimeStatus = True
+ try:
+ log_msg = record.getMessage()
+ if '\n' in log_msg:
+ # If the logged message is multi-line, use its first line as status
+ # and the rest as detail.
+ status, detail = log_msg.split('\n', 1)
+ self.runtime_status_update(
+ kind,
+ "%s: %s" % (record.name, status),
+ detail
+ )
+ else:
+ self.runtime_status_update(
+ kind,
+ "%s: %s" % (record.name, record.getMessage())
+ )
+ finally:
+ self.updatingRuntimeStatus = False
+
class ArvCwlExecutor(object):
- """Execute a CWL tool or workflow, submit work (using either jobs or
- containers API), wait for them to complete, and report output.
+ """Execute a CWL tool or workflow, submit work (using containers API),
+ wait for them to complete, and report output.
"""
self.poll_interval = 12
self.loadingContext = None
self.should_estimate_cache_size = True
+ self.fs_access = None
+ self.secret_store = None
if keep_client is not None:
self.keep_client = keep_client
num_retries=self.num_retries)
self.work_api = None
- expected_api = ["jobs", "containers"]
+ expected_api = ["containers"]
for api in expected_api:
try:
methods = self.api._rootDesc.get('resources')[api]['methods']
raise Exception("Unsupported API '%s', expected one of %s" % (arvargs.work_api, expected_api))
if self.work_api == "jobs":
- logger.warning("""
+ logger.error("""
*******************************
-Using the deprecated 'jobs' API.
-
-To get rid of this warning:
-
-Users: read about migrating at
-http://doc.arvados.org/user/cwl/cwl-style.html#migrate
-and use the option --api=containers
-
-Admins: configure the cluster to disable the 'jobs' API as described at:
-http://doc.arvados.org/install/install-api-server.html#disable_api_methods
+The 'jobs' API is no longer supported.
*******************************""")
+ exit(1)
self.loadingContext = ArvLoadingContext(vars(arvargs))
self.loadingContext.fetcher_constructor = self.fetcher_constructor
activity statuses, for example in the RuntimeStatusLoggingHandler.
"""
with self.workflow_eval_lock:
- current = arvados_cwl.util.get_current_container(self.api, self.num_retries, logger)
+ current = None
+ try:
+ current = arvados_cwl.util.get_current_container(self.api, self.num_retries, logger)
+ except Exception as e:
+ logger.info("Couldn't get current container: %s", e)
if current is None:
return
runtime_status = current.get('runtime_status', {})
return "[%s %s]" % (self.work_api[0:-1], obj.name)
def poll_states(self):
- """Poll status of jobs or containers listed in the processes dict.
+ """Poll status of containers listed in the processes dict.
Runs in a separate thread.
"""
begin_poll = time.time()
if self.work_api == "containers":
table = self.poll_api.container_requests()
- elif self.work_api == "jobs":
- table = self.poll_api.jobs()
pageSize = self.poll_api._rootDesc.get('maxItemsPerResponse', 1000)
while keys:
page = keys[:pageSize]
- keys = keys[pageSize:]
try:
proc_states = table.list(filters=[["uuid", "in", page]]).execute(num_retries=self.num_retries)
except Exception:
"new_attributes": p
}
})
+ keys = keys[pageSize:]
+
finish_poll = time.time()
remain_wait = self.poll_interval - (finish_poll - begin_poll)
except:
except (KeyboardInterrupt, SystemExit):
break
- def check_features(self, obj):
+ def check_features(self, obj, parentfield=""):
if isinstance(obj, dict):
- if obj.get("writable") and self.work_api != "containers":
- raise SourceLine(obj, "writable", UnsupportedRequirement).makeError("InitialWorkDir feature 'writable: true' not supported with --api=jobs")
if obj.get("class") == "DockerRequirement":
if obj.get("dockerOutputDirectory"):
- if self.work_api != "containers":
- raise SourceLine(obj, "dockerOutputDirectory", UnsupportedRequirement).makeError(
- "Option 'dockerOutputDirectory' of DockerRequirement not supported with --api=jobs.")
if not obj.get("dockerOutputDirectory").startswith('/'):
raise SourceLine(obj, "dockerOutputDirectory", validate.ValidationException).makeError(
"Option 'dockerOutputDirectory' must be an absolute path.")
- if obj.get("class") == "http://commonwl.org/cwltool#Secrets" and self.work_api != "containers":
- raise SourceLine(obj, "class", UnsupportedRequirement).makeError("Secrets not supported with --api=jobs")
- for v in viewvalues(obj):
- self.check_features(v)
+ if obj.get("class") == "InplaceUpdateRequirement":
+ if obj["inplaceUpdate"] and parentfield == "requirements":
+ raise SourceLine(obj, "class", UnsupportedRequirement).makeError("InplaceUpdateRequirement not supported for keep collections.")
+ for k,v in viewitems(obj):
+ self.check_features(v, parentfield=k)
elif isinstance(obj, list):
for i,v in enumerate(obj):
with SourceLine(obj, i, UnsupportedRequirement, logger.isEnabledFor(logging.DEBUG)):
- self.check_features(v)
+ self.check_features(v, parentfield=parentfield)
def make_output_collection(self, name, storage_classes, tagsString, outputObj):
outputObj = copy.deepcopy(outputObj)
num_retries=self.num_retries)
for k,v in generatemapper.items():
- if k.startswith("_:"):
- if v.type == "Directory":
+ if v.type == "Directory" and v.resolved.startswith("_:"):
continue
- if v.type == "CreateFile":
- with final.open(v.target, "wb") as f:
- f.write(v.resolved.encode("utf-8"))
+ if v.type == "CreateFile" and (k.startswith("_:") or v.resolved.startswith("_:")):
+ with final.open(v.target, "wb") as f:
+ f.write(v.resolved.encode("utf-8"))
continue
- if not k.startswith("keep:"):
+ if not v.resolved.startswith("keep:"):
raise Exception("Output source is not in keep or a literal")
- sp = k.split("/")
+ sp = v.resolved.split("/")
srccollection = sp[0][5:]
try:
reader = self.collection_cache.get(srccollection)
logger.error("Creating CollectionReader for '%s' '%s': %s", k, v, e)
raise
except IOError as e:
- logger.warning("While preparing output collection: %s", e)
+ logger.error("While preparing output collection: %s", e)
+ raise
def rewrite(fileobj):
fileobj["location"] = generatemapper.mapper(fileobj["location"]).target
with final.open("cwl.output.json", "w") as f:
res = str(json.dumps(outputObj, sort_keys=True, indent=4, separators=(',',': '), ensure_ascii=False))
- f.write(res)
+ f.write(res)
final.save_new(name=name, owner_uuid=self.project_uuid, storage_classes=storage_classes, ensure_unique_name=True)
except Exception:
logger.exception("Setting container output")
return
- elif self.work_api == "jobs" and "TASK_UUID" in os.environ:
- self.api.job_tasks().update(uuid=os.environ["TASK_UUID"],
- body={
- 'output': self.final_output_collection.portable_data_hash(),
- 'success': self.final_status == "success",
- 'progress':1.0
- }).execute(num_retries=self.num_retries)
-
- def arv_executor(self, tool, job_order, runtimeContext, logger=None):
+
+ def apply_reqs(self, job_order_object, tool):
+ if "https://w3id.org/cwl/cwl#requirements" in job_order_object:
+ if tool.metadata.get("http://commonwl.org/cwltool#original_cwlVersion") == 'v1.0':
+ raise WorkflowException(
+ "`cwl:requirements` in the input object is not part of CWL "
+ "v1.0. You can adjust to use `cwltool:overrides` instead; or you "
+ "can set the cwlVersion to v1.1 or greater and re-run with "
+ "--enable-dev.")
+ job_reqs = job_order_object["https://w3id.org/cwl/cwl#requirements"]
+ for req in job_reqs:
+ tool.requirements.append(req)
+
+ def arv_executor(self, updated_tool, job_order, runtimeContext, logger=None):
self.debug = runtimeContext.debug
- tool.visit(self.check_features)
+ updated_tool.visit(self.check_features)
self.project_uuid = runtimeContext.project_uuid
self.pipeline = None
raise Exception("--submit-request-uuid requires containers API, but using '{}' api".format(self.work_api))
if not runtimeContext.name:
- runtimeContext.name = self.name = tool.tool.get("label") or tool.metadata.get("label") or os.path.basename(tool.tool["id"])
+ runtimeContext.name = self.name = updated_tool.tool.get("label") or updated_tool.metadata.get("label") or os.path.basename(updated_tool.tool["id"])
+
+ # Upload local file references in the job order.
+ job_order = upload_job_order(self, "%s input" % runtimeContext.name,
+ updated_tool, job_order)
+
+ # the last clause means: if it is a command line tool, and we
+ # are going to wait for the result, and always_submit_runner
+ # is false, then we don't submit a runner process.
+
+ submitting = (runtimeContext.update_workflow or
+ runtimeContext.create_workflow or
+ (runtimeContext.submit and not
+ (updated_tool.tool["class"] == "CommandLineTool" and
+ runtimeContext.wait and
+ not runtimeContext.always_submit_runner)))
+
+ loadingContext = self.loadingContext.copy()
+ loadingContext.do_validate = False
+ loadingContext.do_update = False
+ if submitting:
+ # Document may have been auto-updated. Reload the original
+ # document with updating disabled because we want to
+ # submit the document with its original CWL version, not
+ # the auto-updated one.
+ tool = load_tool(updated_tool.tool["id"], loadingContext)
+ else:
+ tool = updated_tool
# Upload direct dependencies of workflow steps, get back mapping of files to keep references.
# Also uploads docker images.
merged_map = upload_workflow_deps(self, tool)
- # Reload tool object which may have been updated by
- # upload_workflow_deps
- # Don't validate this time because it will just print redundant errors.
- loadingContext = self.loadingContext.copy()
+ # Recreate process object (ArvadosWorkflow or
+ # ArvadosCommandTool) because tool document may have been
+ # updated by upload_workflow_deps in ways that modify
+ # inheritance of hints or requirements.
loadingContext.loader = tool.doc_loader
loadingContext.avsc_names = tool.doc_schema
loadingContext.metadata = tool.metadata
- loadingContext.do_validate = False
-
- tool = self.arv_make_tool(tool.doc_loader.idx[tool.tool["id"]],
- loadingContext)
-
- # Upload local file references in the job order.
- job_order = upload_job_order(self, "%s input" % runtimeContext.name,
- tool, job_order)
+ tool = load_tool(tool.tool, loadingContext)
existing_uuid = runtimeContext.update_workflow
if existing_uuid or runtimeContext.create_workflow:
# Create a pipeline template or workflow record and exit.
- if self.work_api == "jobs":
- tmpl = RunnerTemplate(self, tool, job_order,
- runtimeContext.enable_reuse,
- uuid=existing_uuid,
- submit_runner_ram=runtimeContext.submit_runner_ram,
- name=runtimeContext.name,
- merged_map=merged_map,
- loadingContext=loadingContext)
- tmpl.save()
- # cwltool.main will write our return value to stdout.
- return (tmpl.uuid, "success")
- elif self.work_api == "containers":
+ if self.work_api == "containers":
return (upload_workflow(self, tool, job_order,
self.project_uuid,
uuid=existing_uuid,
merged_map=merged_map),
"success")
+ self.apply_reqs(job_order, tool)
+
self.ignore_docker_for_reuse = runtimeContext.ignore_docker_for_reuse
self.eval_timeout = runtimeContext.eval_timeout
runtimeContext.docker_outdir = "/var/spool/cwl"
runtimeContext.tmpdir = "/tmp"
runtimeContext.docker_tmpdir = "/tmp"
- elif self.work_api == "jobs":
- if runtimeContext.priority != DEFAULT_PRIORITY:
- raise Exception("--priority not implemented for jobs API.")
- runtimeContext.outdir = "$(task.outdir)"
- runtimeContext.docker_outdir = "$(task.outdir)"
- runtimeContext.tmpdir = "$(task.tmpdir)"
if runtimeContext.priority < 1 or runtimeContext.priority > 1000:
raise Exception("--priority must be in the range 1..1000.")
if runtimeContext.submit:
# Submit a runner job to run the workflow for us.
if self.work_api == "containers":
- if tool.tool["class"] == "CommandLineTool" and runtimeContext.wait and (not runtimeContext.always_submit_runner):
- runtimeContext.runnerjob = tool.tool["id"]
+ if submitting:
+ tool = RunnerContainer(self, updated_tool,
+ tool, loadingContext, runtimeContext.enable_reuse,
+ self.output_name,
+ self.output_tags,
+ submit_runner_ram=runtimeContext.submit_runner_ram,
+ name=runtimeContext.name,
+ on_error=runtimeContext.on_error,
+ submit_runner_image=runtimeContext.submit_runner_image,
+ intermediate_output_ttl=runtimeContext.intermediate_output_ttl,
+ merged_map=merged_map,
+ priority=runtimeContext.priority,
+ secret_store=self.secret_store,
+ collection_cache_size=runtimeContext.collection_cache_size,
+ collection_cache_is_default=self.should_estimate_cache_size)
else:
- tool = RunnerContainer(self, tool, loadingContext, runtimeContext.enable_reuse,
- self.output_name,
- self.output_tags,
- submit_runner_ram=runtimeContext.submit_runner_ram,
- name=runtimeContext.name,
- on_error=runtimeContext.on_error,
- submit_runner_image=runtimeContext.submit_runner_image,
- intermediate_output_ttl=runtimeContext.intermediate_output_ttl,
- merged_map=merged_map,
- priority=runtimeContext.priority,
- secret_store=self.secret_store,
- collection_cache_size=runtimeContext.collection_cache_size,
- collection_cache_is_default=self.should_estimate_cache_size)
- elif self.work_api == "jobs":
- tool = RunnerJob(self, tool, loadingContext, runtimeContext.enable_reuse,
- self.output_name,
- self.output_tags,
- submit_runner_ram=runtimeContext.submit_runner_ram,
- name=runtimeContext.name,
- on_error=runtimeContext.on_error,
- submit_runner_image=runtimeContext.submit_runner_image,
- merged_map=merged_map)
- elif runtimeContext.cwl_runner_job is None and self.work_api == "jobs":
- # Create pipeline for local run
- self.pipeline = self.api.pipeline_instances().create(
- body={
- "owner_uuid": self.project_uuid,
- "name": runtimeContext.name if runtimeContext.name else shortname(tool.tool["id"]),
- "components": {},
- "state": "RunningOnClient"}).execute(num_retries=self.num_retries)
- logger.info("Pipeline instance %s", self.pipeline["uuid"])
+ runtimeContext.runnerjob = tool.tool["id"]
if runtimeContext.cwl_runner_job is not None:
self.uuid = runtimeContext.cwl_runner_job.get('uuid')
if self.pipeline:
self.api.pipeline_instances().update(uuid=self.pipeline["uuid"],
body={"state": "Failed"}).execute(num_retries=self.num_retries)
- if runtimeContext.submit and isinstance(tool, Runner):
- runnerjob = tool
- if runnerjob.uuid and self.work_api == "containers":
- self.api.container_requests().update(uuid=runnerjob.uuid,
- body={"priority": "0"}).execute(num_retries=self.num_retries)
+
+ if self.work_api == "containers" and not current_container:
+ # Not running in a crunch container, so cancel any outstanding processes.
+ for p in self.processes:
+ try:
+ self.api.container_requests().update(uuid=p,
+ body={"priority": "0"}
+ ).execute(num_retries=self.num_retries)
+ except Exception:
+ pass
finally:
self.workflow_eval_lock.release()
self.task_queue.drain()
projects / arvados.git / blobdiff