Source code for weaver.processes.execution

import logging
import os
from time import sleep
from typing import TYPE_CHECKING

import colander
from celery.utils.log import get_task_logger
from owslib.util import clean_ows_url
from owslib.wps import ComplexDataInput
from pyramid.httpexceptions import HTTPBadRequest, HTTPNotAcceptable, HTTPNotImplemented
from pyramid_celery import celery_app as app

from weaver.database import get_db
from weaver.datatype import Process, Service
from weaver.execute import (
from weaver.formats import ACCEPT_LANGUAGES, CONTENT_TYPE_APP_JSON
from weaver.notify import encrypt_email, notify_job_complete
from weaver.owsexceptions import OWSNoApplicableCode
from weaver.processes import wps_package
from weaver.processes.constants import WPS_COMPLEX_DATA
from weaver.processes.convert import ows2json_output_data
from weaver.processes.types import PROCESS_WORKFLOW
from import StoreJobs
from weaver.utils import get_any_id, get_any_value, get_settings, now, raise_on_xml_exception, wait_secs
from weaver.visibility import VISIBILITY_PUBLIC
from weaver.wps.utils import (
from weaver.wps_restapi import swagger_definitions as sd
from weaver.wps_restapi.utils import get_wps_restapi_base_url

[docs]LOGGER = logging.getLogger(__name__)
if TYPE_CHECKING: from typing import List, Optional, Union from pyramid.request import Request from weaver.datatype import Job from weaver.typedefs import HeaderCookiesType, JSON, SettingsType # job process execution progress
[docs]def execute_process(self, job_id, url, headers=None): # pylint: disable=R1260,too-complex # FIXME: simplify operations from weaver.wps.service import get_pywps_service LOGGER.debug("Job execute process called.") settings = get_settings(app) task_logger = get_task_logger(__name__) load_pywps_config(settings) task_logger.debug("Job task setup.") # reset the connection because we are in a forked celery process db = get_db(app, reset_connection=True) store = db.get_store(StoreJobs) job = store.fetch_by_id(job_id) job.started = now() job.task_id = job.progress = JOB_PROGRESS_SETUP job.save_log(logger=task_logger, message="Job task setup completed.") job = store.update_job(job) try: try: job.progress = JOB_PROGRESS_DESCRIBE job.save_log(logger=task_logger, message="Employed WPS URL: [{!s}]".format(url), level=logging.DEBUG) job.save_log(logger=task_logger, message="Execute WPS request for process [{!s}]".format(job.process)) wps = get_wps_client(url, settings, headers=headers, language=job.accept_language) raise_on_xml_exception(wps._capabilities) # noqa except Exception as ex: job.save_log(errors=ex, message="Failed WPS client creation for process [{!s}]".format(job.process)) raise OWSNoApplicableCode("Failed to retrieve WPS capabilities. Error: [{}].".format(str(ex))) try: wps_process = wps.describeprocess(job.process) except Exception as ex: raise OWSNoApplicableCode("Failed to retrieve WPS process description. Error: [{}].".format(str(ex))) # prepare inputs job.progress = JOB_PROGRESS_GET_INPUTS job.save_log(logger=task_logger, message="Fetching job input definitions.") complex_inputs = [] for process_input in wps_process.dataInputs: if WPS_COMPLEX_DATA in process_input.dataType: complex_inputs.append(process_input.identifier) try: wps_inputs = list() # parse both dict and list type inputs job_inputs = job.inputs.items() if isinstance(job.inputs, dict) else job.get("inputs", []) for process_input in job_inputs: if isinstance(process_input, tuple): input_id = process_input[0] process_value = process_input[1] else: input_id = get_any_id(process_input) process_value = get_any_value(process_input) # in case of array inputs, must repeat (id,value) input_values = process_value if isinstance(process_value, list) else [process_value] # we need to support file:// scheme but PyWPS doesn't like them so remove the scheme file:// input_values = [ # when value is an array of dict that each contain a file reference (get_any_value(val)[7:] if str(get_any_value(val)).startswith("file://") else get_any_value(val)) if isinstance(val, dict) else # when value is directly a single dict with file reference (val[7:] if str(val).startswith("file://") else val) for val in input_values ] # need to use ComplexDataInput structure for complex input # need to use literal String for anything else than complex # TODO: BoundingBox not supported wps_inputs.extend([ (input_id, ComplexDataInput(input_value) if input_id in complex_inputs else str(input_value)) for input_value in input_values]) except KeyError: wps_inputs = [] # prepare outputs job.progress = JOB_PROGRESS_GET_OUTPUTS job.save_log(logger=task_logger, message="Fetching job output definitions.") wps_outputs = [(o.identifier, o.dataType == WPS_COMPLEX_DATA) for o in wps_process.processOutputs] # if process refers to a remote WPS provider, pass it down to avoid unnecessary re-fetch request if job.is_local: process = None # already got all the information needed pre-loaded in PyWPS service else: service = Service(name=job.service, url=url) process = Process.from_ows(wps_process, service, settings) job.progress = JOB_PROGRESS_EXECUTE_REQUEST job.save_log(logger=task_logger, message="Starting job process execution.") job.save_log(logger=task_logger, message="Following updates could take a while until the Application Package answers...") mode = EXECUTE_MODE_ASYNC if job.execute_async else EXECUTE_MODE_SYNC lang = job.accept_language wps_worker = get_pywps_service(environ=settings, is_worker=True) execution = wps_worker.execute_job(job.process, wps_inputs=wps_inputs, wps_outputs=wps_outputs, mode=mode,, remote_process=process, language=lang) if not execution.process and execution.errors: raise execution.errors[0] # adjust status location wps_status_path = get_wps_local_status_location(execution.statusLocation, settings) job.progress = JOB_PROGRESS_EXECUTE_STATUS_LOCATION LOGGER.debug("WPS status location that will be queried: [%s]", wps_status_path) if not wps_status_path.startswith("http") and not os.path.isfile(wps_status_path): LOGGER.warning("WPS status location not resolved to local path: [%s]", wps_status_path) job.save_log(logger=task_logger, level=logging.DEBUG, message="Updated job status location: [{}].".format(wps_status_path)) job.status = map_status(STATUS_STARTED) job.status_message = execution.statusMessage or "{} initiation done.".format(str(job)) job.status_location = wps_status_path job.request = execution.request job.response = execution.response job.progress = JOB_PROGRESS_EXECUTE_MONITOR_START job.save_log(logger=task_logger, message="Starting monitoring of job execution.") job = store.update_job(job) max_retries = 5 num_retries = 0 run_step = 0 while execution.isNotComplete() or run_step == 0: if num_retries >= max_retries: raise Exception("Could not read status document after {} retries. Giving up.".format(max_retries)) try: # NOTE: # Don't actually log anything here until process is completed (success or fail) so that underlying # WPS execution logs can be inserted within the current job log and appear continuously. # Only update internal job fields in case they get referenced elsewhere. progress_min = JOB_PROGRESS_EXECUTE_MONITOR_LOOP progress_max = JOB_PROGRESS_EXECUTE_MONITOR_DONE job.progress = progress_min execution = check_wps_status(location=wps_status_path, settings=settings, sleep_secs=wait_secs(run_step)) job_msg = (execution.statusMessage or "").strip() job.response = execution.response job.status = map_status(execution.getStatus()) job.status_message = ( "Job execution monitoring (progress: {}%, status: {})." .format(execution.percentCompleted, job_msg or "n/a") ) # job.save_log(logger=task_logger) # job = store.update_job(job) if execution.isComplete(): msg_progress = " (status: {})".format(job_msg) if job_msg else "" if execution.isSucceded(): wps_package.retrieve_package_job_log(execution, job, progress_min, progress_max) job.status = map_status(STATUS_SUCCEEDED) job.status_message = "Job succeeded{}.".format(msg_progress) job.progress = progress_max job.save_log(logger=task_logger) job_results = [ows2json_output_data(output, process, settings) for output in execution.processOutputs] job.results = make_results_relative(job_results, settings) else: task_logger.debug("Job failed.") wps_package.retrieve_package_job_log(execution, job, progress_min, progress_max) job.status_message = "Job failed{}.".format(msg_progress) job.progress = progress_max job.save_log(errors=execution.errors, logger=task_logger) task_logger.debug("Mapping Job references with generated WPS locations.") map_locations(job, settings) except Exception as exc: num_retries += 1 task_logger.debug("Exception raised: %s", repr(exc)) job.status_message = "Could not read status XML document for {!s}. Trying again...".format(job) job.save_log(errors=execution.errors, logger=task_logger) sleep(1) else: # job.status_message = "Update {}...".format(str(job)) # job.save_log(logger=task_logger) num_retries = 0 run_step += 1 finally: job = store.update_job(job) except Exception as exc: LOGGER.exception("Failed running [%s]", job) LOGGER.debug("Failed job [%s] raised an exception.", job, exc_info=exc) job.status = map_status(STATUS_FAILED) job.status_message = "Failed to run {!s}.".format(job) job.progress = JOB_PROGRESS_EXECUTE_MONITOR_ERROR exception_class = "{}.{}".format(type(exc).__module__, type(exc).__name__) errors = "{0}: {1!s}".format(exception_class, exc) job.save_log(errors=errors, logger=task_logger) finally: job.progress = JOB_PROGRESS_EXECUTE_MONITOR_END job.status_message = "Job {}.".format(job.status) job.save_log(logger=task_logger) # Send email if requested if job.notification_email is not None: job.progress = JOB_PROGRESS_NOTIFY try: notify_job_complete(job, job.notification_email, settings) message = "Notification email sent successfully." job.save_log(logger=task_logger, message=message) except Exception as exc: exception_class = "{}.{}".format(type(exc).__module__, type(exc).__name__) exception = "{0}: {1!s}".format(exception_class, exc) message = "Couldn't send notification email ({})".format(exception) job.save_log(errors=message, logger=task_logger, message=message) job.mark_finished() job.progress = JOB_PROGRESS_DONE job.save_log(logger=task_logger, message="Job task complete.") job = store.update_job(job) return job.status
[docs]def make_results_relative(results, settings): # type: (List[JSON], SettingsType) -> List[JSON] """ Converts file references to a pseudo-relative location to allow the application to dynamically generate paths. Redefines job results to be saved in database as pseudo-relative paths to configured WPS output directory. This allows the application to easily adjust the exposed result HTTP path according to the service configuration (i.e.: relative to ``weaver.wps_output_dir`` and/or ``weaver.wps_output_url``) and it also avoids rewriting the database job results entry if those settings are changed later on following reboot of the web application. Only references prefixed with ``weaver.wps_output_dir``, ``weaver.wps_output_url`` or a corresponding resolution from ``weaver.wps_output_path`` with ``weaver.url`` will be modified to pseudo-relative paths. Other references (file/URL endpoints that do not correspond to `Weaver`) will be left untouched for literal remote reference. Results that do not correspond to a reference are also unmodified. .. note:: The references are not *real* relative paths (i.e.: starting with ``./``), as those could also be specified as input, and there would be no way to guarantee proper differentiation from paths already handled and stored in the database. Instead, *pseudo-relative* paths employ an explicit *absolute*-like path (i.e.: starting with ``/``) and are assumed to always require to be prefixed by the configured WPS locations (i.e.: ``weaver.wps_output_dir`` or ``weaver.wps_output_url`` based on local or HTTP response context). With this approach, data persistence with mapped volumes into the dockerized `Weaver` service can be placed anywhere at convenience. This is important because sibling docker execution require exact mappings such that volume mount ``/data/path:/data/path`` resolve correctly on both sides (host and image path must be identical). If volumes get remapped differently, ensuring that ``weaver.wps_output_dir`` setting follows the same remapping update will automatically resolve to the proper location for both local references and exposed URL endpoints. :param results: JSON mapping of data results as ``{"<id>": <definition>}`` entries where a reference can be found. :param settings: container to retrieve current application settings. """ wps_url = get_wps_output_url(settings) wps_path = get_wps_output_path(settings) for res in results: ref = res.get("reference") if isinstance(ref, str) and ref: if ref.startswith(wps_url): ref = ref.replace(wps_url, "", 1) if ref.startswith(wps_path): ref = ref.replace(wps_path, "", 1) res["reference"] = ref return results
[docs]def map_locations(job, settings): # type: (Job, SettingsType) -> None """ Maps directory locations between :mod:`pywps` process execution and produced jobs storage. Generates symlink references from the Job UUID to PyWPS UUID results (outputs directory, status and log locations). Update the Job's WPS ID if applicable (job executed locally). Assumes that all results are located under the same reference UUID. """ local_path = get_wps_local_status_location(job.status_location, settings) if not local_path: LOGGER.debug("Not possible to map Job to WPS locations.") return base_dir, status_xml = os.path.split(local_path) job.wps_id = os.path.splitext(status_xml)[0] wps_loc = os.path.join(base_dir, job.wps_id) job_loc = os.path.join(base_dir, if wps_loc == job_loc: LOGGER.debug("Job already refers to WPS locations.") return for loc_ext in ["", ".log", ".xml"]: wps_ref = wps_loc + loc_ext job_ref = job_loc + loc_ext if os.path.exists(wps_ref): # possible that there are no results (e.g.: failed job) os.symlink(wps_ref, job_ref)
[docs]def submit_job(request, reference, tags=None): # type: (Request, Union[Service, Process], Optional[List[str]]) -> JSON """ Generates the job submission from details retrieved in the request. .. seealso:: :func:`submit_job_handler` to provide elements pre-extracted from requests or from other parsing. """ # validate body with expected JSON content and schema if CONTENT_TYPE_APP_JSON not in request.content_type: raise HTTPBadRequest("Request 'Content-Type' header other than '{}' not supported." .format(CONTENT_TYPE_APP_JSON)) try: json_body = request.json_body except Exception as ex: raise HTTPBadRequest("Invalid JSON body cannot be decoded for job submission. [{}]".format(ex)) provider_id = None # None OK if local process_id = None # None OK if remote, but can be found as well if available from WPS-REST path tags = tags or [] lang = request.accept_language.header_value # can only preemptively check if local process if isinstance(reference, Process): service_url = reference.processEndpointWPS1 process_id = visibility = reference.visibility is_workflow = reference.type == PROCESS_WORKFLOW is_local = True tags += "local" if lang and request.accept_language.best_match(ACCEPT_LANGUAGES) is None: raise HTTPNotAcceptable("Requested language [{}] is not in supported languages [{}].".format( lang, ", ".join(ACCEPT_LANGUAGES) )) elif isinstance(reference, Service): service_url = reference.url provider_id = process_id = request.matchdict.get("process_id") visibility = VISIBILITY_PUBLIC is_workflow = False is_local = False tags += "remote" else: LOGGER.error("Expected process/service, got: %s", type(reference)) raise TypeError("Invalid process or service reference to execute job.") tags = request.params.get("tags", "").split(",") + tags user = request.authenticated_userid headers = dict(request.headers) settings = get_settings(request) return submit_job_handler(json_body, settings, service_url, provider_id, process_id, is_workflow, is_local, visibility, language=lang, auth=headers, tags=tags, user=user)
# FIXME: this should not be necessary if schema validators correctly implement OneOf(values)
[docs]def _validate_job_parameters(json_body): """ Tests supported parameters not automatically validated by colander deserialize. """ if json_body["mode"] not in [EXECUTE_MODE_ASYNC, EXECUTE_MODE_AUTO]: raise HTTPNotImplemented(detail="Execution mode '{}' not supported.".format(json_body["mode"])) if json_body["response"] != EXECUTE_RESPONSE_DOCUMENT: raise HTTPNotImplemented(detail="Execution response type '{}' not supported.".format(json_body["response"])) for job_output in json_body["outputs"]: mode = job_output["transmissionMode"] if mode not in EXECUTE_TRANSMISSION_MODE_OPTIONS: raise HTTPNotImplemented(detail="Execute transmissionMode '{}' not supported.".format(mode))
[docs]def submit_job_handler(payload, # type: JSON settings, # type: SettingsType service_url, # type: str provider_id=None, # type: Optional[str] process_id=None, # type: str is_workflow=False, # type: bool is_local=True, # type: bool visibility=None, # type: Optional[str] language=None, # type: Optional[str] auth=None, # type: Optional[HeaderCookiesType] tags=None, # type: Optional[List[str]] user=None, # type: Optional[int] ): # type: (...) -> JSON """ Submits the job to the Celery worker with provided parameters. Assumes that parameters have been pre-fetched and validated, except for the input payload. """ try: json_body = sd.Execute().deserialize(payload) except colander.Invalid as ex: raise HTTPBadRequest("Invalid schema: [{}]".format(str(ex))) # TODO: remove when all parameter variations are supported _validate_job_parameters(json_body) is_execute_async = json_body["mode"] != EXECUTE_MODE_SYNC # convert auto to async notification_email = json_body.get("notification_email") encrypted_email = encrypt_email(notification_email, settings) if notification_email else None store = get_db(settings).get_store(StoreJobs) job = store.save_job(task_id=STATUS_ACCEPTED, process=process_id, service=provider_id, inputs=json_body.get("inputs"), is_local=is_local, is_workflow=is_workflow, access=visibility, user_id=user, execute_async=is_execute_async, custom_tags=tags, notification_email=encrypted_email, accept_language=language) result = execute_process.delay(, url=clean_ows_url(service_url), headers=auth) LOGGER.debug("Celery pending task [%s] for job [%s].",, # local/provider process location location_base = "/providers/{provider_id}".format(provider_id=provider_id) if provider_id else "" location = "{base_url}{location_base}/processes/{process_id}/jobs/{job_id}".format( base_url=get_wps_restapi_base_url(settings), location_base=location_base, process_id=process_id, body_data = { "jobID":, "processID": job.process, "providerID": provider_id, # dropped by validator if not applicable "status": map_status(STATUS_ACCEPTED), "location": location } return body_data