예제 #1
0
def register_builtin_processes(container):
    # type: (AnyRegistryContainer) -> None
    """
    Registers every ``builtin`` CWL package to the processes database.

    CWL definitions must be located within the :mod:`weaver.processes.builtin` module.
    """
    restapi_url = get_wps_restapi_base_url(container)
    builtin_apps_mapping = _get_builtin_reference_mapping(
        os.path.abspath(os.path.dirname(__file__)))
    builtin_processes = []
    for process_id, process_path in builtin_apps_mapping.items():
        process_info = get_process_definition({},
                                              package=None,
                                              reference=process_path)
        process_url = "/".join([restapi_url, "processes", process_id])
        process_package = _get_builtin_package(process_id,
                                               process_info["package"])
        process_abstract = _get_builtin_metadata(process_id,
                                                 process_path,
                                                 "__doc__",
                                                 clean=True)
        process_version = _get_builtin_metadata(process_id, process_path,
                                                "__version__")
        process_title = _get_builtin_metadata(process_id, process_path,
                                              "__title__")
        process_payload = {
            "processDescription": {
                "process": {
                    "id": process_id,
                    "type": ProcessType.BUILTIN,
                    "title": process_title,
                    "version": process_version,
                    "abstract": process_abstract,
                }
            },
            "deploymentProfileName":
            "http://www.opengis.net/profiles/eoc/builtinApplication",
            "executionUnit": [{
                "unit": process_package
            }],
        }
        process_payload["processDescription"]["process"].update(
            ows_context_href(process_url))
        builtin_processes.append(
            Process(
                id=process_id,
                type=ProcessType.BUILTIN,
                title=process_title,
                version=process_version,
                abstract=process_abstract,
                payload=process_payload,
                package=process_package,
                inputs=process_info["inputs"],
                outputs=process_info["outputs"],
                processDescriptionURL=process_url,
                processEndpointWPS1=get_wps_url(container),
                executeEndpoint="/".join([process_url, "jobs"]),
                jobControlOptions=ExecuteControlOption.values(),
                visibility=Visibility.PUBLIC,
            ))

    # registration of missing/updated apps automatically applied with 'default_processes'
    get_db(container).get_store(StoreProcesses,
                                default_processes=builtin_processes)
예제 #2
0
def deploy_process_from_payload(payload, container, overwrite=False):
    # type: (JSON, AnyContainer, bool) -> HTTPException
    """
    Deploy the process after resolution of all references and validation of the parameters from payload definition.

    Adds a :class:`weaver.datatype.Process` instance to storage using the provided JSON ``payload``
    matching :class:`weaver.wps_restapi.swagger_definitions.ProcessDescription`.

    :param payload: JSON payload that was specified during the process deployment request.
    :param container: container to retrieve application settings.
    :param overwrite: whether to allow override of an existing process definition if conflict occurs.
    :returns: HTTPOk if the process registration was successful.
    :raises HTTPException: for any invalid process deployment step.
    """
    # use deepcopy of to remove any circular dependencies before writing to mongodb or any updates to the payload
    payload_copy = deepcopy(payload)
    payload = _check_deploy(payload)

    # validate identifier naming for unsupported characters
    process_description = payload.get("processDescription")
    process_info = process_description.get("process", {})
    process_href = process_description.pop("href", None)

    # retrieve CWL package definition, either via "href" (WPS-1/2), "owsContext" or "executionUnit" (package/reference)
    deployment_profile_name = payload.get("deploymentProfileName", "").lower()
    ows_context = process_info.pop("owsContext", None)
    reference = None
    package = None
    if process_href:
        reference = process_href  # reference type handled downstream
    elif isinstance(ows_context, dict):
        offering = ows_context.get("offering")
        if not isinstance(offering, dict):
            raise HTTPUnprocessableEntity(
                "Invalid parameter 'processDescription.process.owsContext.offering'."
            )
        content = offering.get("content")
        if not isinstance(content, dict):
            raise HTTPUnprocessableEntity(
                "Invalid parameter 'processDescription.process.owsContext.offering.content'."
            )
        package = None
        reference = content.get("href")
    elif deployment_profile_name:
        if not any(
                deployment_profile_name.endswith(typ)
                for typ in [PROCESS_APPLICATION, PROCESS_WORKFLOW]):
            raise HTTPBadRequest(
                "Invalid value for parameter 'deploymentProfileName'.")
        execution_units = payload.get("executionUnit")
        if not isinstance(execution_units, list):
            raise HTTPUnprocessableEntity("Invalid parameter 'executionUnit'.")
        for execution_unit in execution_units:
            if not isinstance(execution_unit, dict):
                raise HTTPUnprocessableEntity(
                    "Invalid parameter 'executionUnit'.")
            package = execution_unit.get("unit")
            reference = execution_unit.get("href")
            # stop on first package/reference found, simultaneous usage will raise during package retrieval
            if package or reference:
                break
    else:
        raise HTTPBadRequest(
            "Missing one of required parameters [href, owsContext, deploymentProfileName]."
        )

    if process_info.get("type", "") == PROCESS_BUILTIN:
        raise HTTPBadRequest(
            "Invalid process type resolved from package: [{0}]. Deployment of {0} process is not allowed."
            .format(PROCESS_BUILTIN))

    # update and validate process information using WPS process offering, CWL/WPS reference or CWL package definition
    settings = get_settings(container)
    headers = getattr(
        container, "headers", {}
    )  # container is any request (as when called from API Deploy request)
    process_info = _validate_deploy_process_info(process_info, reference,
                                                 package, settings, headers)

    restapi_url = get_wps_restapi_base_url(settings)
    description_url = "/".join(
        [restapi_url, "processes", process_info["identifier"]])
    execute_endpoint = "/".join([description_url, "jobs"])

    # ensure that required "processEndpointWPS1" in db is added,
    # will be auto-fixed to localhost if not specified in body
    process_info["processEndpointWPS1"] = process_description.get(
        "processEndpointWPS1")
    process_info["executeEndpoint"] = execute_endpoint
    process_info["payload"] = payload_copy
    process_info["jobControlOptions"] = process_description.get(
        "jobControlOptions", [])
    process_info["outputTransmission"] = process_description.get(
        "outputTransmission", [])
    process_info["processDescriptionURL"] = description_url
    # insert the "resolved" context using details retrieved from "executionUnit"/"href" or directly with "owsContext"
    if "owsContext" not in process_info and reference:
        process_info["owsContext"] = {
            "offering": {
                "content": {
                    "href": str(reference)
                }
            }
        }
    elif isinstance(ows_context, dict):
        process_info["owsContext"] = ows_context
    # bw-compat abstract/description (see: ProcessDeployment schema)
    if "description" not in process_info or not process_info["description"]:
        process_info["description"] = process_info.get("abstract", "")

    # FIXME: handle colander invalid directly in tween (https://github.com/crim-ca/weaver/issues/112)
    try:
        store = get_db(container).get_store(StoreProcesses)
        process = Process(process_info)
        sd.ProcessSummary().deserialize(
            process)  # make if fail before save if invalid
        store.save_process(process, overwrite=overwrite)
        process_summary = process.summary()
    except ProcessRegistrationError as ex:
        raise HTTPConflict(detail=str(ex))
    except (ValueError, colander.Invalid) as ex:
        # raised on invalid process name
        raise HTTPBadRequest(detail=str(ex))

    return HTTPCreated(
        json={
            "description": sd.OkPostProcessesResponse.description,
            "processSummary": process_summary,
            "deploymentDone": True
        })
예제 #3
0
def deploy_process_from_payload(payload, container):
    # type: (JSON, AnyContainer) -> HTTPException
    """
    Adds a :class:`weaver.datatype.Process` instance to storage using the provided JSON ``payload`` matching
    :class:`weaver.wps_restapi.swagger_definitions.ProcessDescription`.

    :returns: HTTPOk if the process registration was successful
    :raises HTTPException: otherwise
    """
    _check_deploy(payload)

    # use deepcopy of to remove any circular dependencies before writing to mongodb or any updates to the payload
    payload_copy = deepcopy(payload)

    # validate identifier naming for unsupported characters
    process_description = payload.get("processDescription")
    process_info = process_description.get("process", {})
    process_href = process_description.pop("href", None)

    # retrieve CWL package definition, either via "href" (WPS-1/2), "owsContext" or "executionUnit" (package/reference)
    deployment_profile_name = payload.get("deploymentProfileName", "").lower()
    ows_context = process_info.pop("owsContext", None)
    reference = None
    package = None
    if process_href:
        reference = process_href  # reference type handled downstream
    elif isinstance(ows_context, dict):
        offering = ows_context.get("offering")
        if not isinstance(offering, dict):
            raise HTTPUnprocessableEntity(
                "Invalid parameter 'processDescription.process.owsContext.offering'."
            )
        content = offering.get("content")
        if not isinstance(content, dict):
            raise HTTPUnprocessableEntity(
                "Invalid parameter 'processDescription.process.owsContext.offering.content'."
            )
        package = None
        reference = content.get("href")
    elif deployment_profile_name:
        if not any(
                deployment_profile_name.endswith(typ)
                for typ in [PROCESS_APPLICATION, PROCESS_WORKFLOW]):
            raise HTTPBadRequest(
                "Invalid value for parameter 'deploymentProfileName'.")
        execution_units = payload.get("executionUnit")
        if not isinstance(execution_units, list):
            raise HTTPUnprocessableEntity("Invalid parameter 'executionUnit'.")
        for execution_unit in execution_units:
            if not isinstance(execution_unit, dict):
                raise HTTPUnprocessableEntity(
                    "Invalid parameter 'executionUnit'.")
            package = execution_unit.get("unit")
            reference = execution_unit.get("href")
            # stop on first package/reference found, simultaneous usage will raise during package retrieval
            if package or reference:
                break
    else:
        raise HTTPBadRequest(
            "Missing one of required parameters [href, owsContext, deploymentProfileName]."
        )

    # obtain updated process information using WPS process offering, CWL/WPS reference or CWL package definition
    process_info = _get_deploy_process_info(process_info, reference, package)

    # validate process type against weaver configuration
    settings = get_settings(container)
    process_type = process_info["type"]
    if process_type == PROCESS_WORKFLOW:
        weaver_config = get_weaver_configuration(settings)
        if weaver_config != WEAVER_CONFIGURATION_EMS:
            raise HTTPBadRequest(
                "Invalid [{0}] package deployment on [{1}].".format(
                    process_type, weaver_config))

    restapi_url = get_wps_restapi_base_url(settings)
    description_url = "/".join(
        [restapi_url, "processes", process_info["identifier"]])
    execute_endpoint = "/".join([description_url, "jobs"])

    # ensure that required "processEndpointWPS1" in db is added,
    # will be auto-fixed to localhost if not specified in body
    process_info["processEndpointWPS1"] = process_description.get(
        "processEndpointWPS1")
    process_info["executeEndpoint"] = execute_endpoint
    process_info["payload"] = payload_copy
    process_info["jobControlOptions"] = process_description.get(
        "jobControlOptions", [])
    process_info["outputTransmission"] = process_description.get(
        "outputTransmission", [])
    process_info["processDescriptionURL"] = description_url
    # insert the "resolved" context using details retrieved from "executionUnit"/"href" or directly with "owsContext"
    if "owsContext" not in process_info and reference:
        process_info["owsContext"] = {
            "offering": {
                "content": {
                    "href": str(reference)
                }
            }
        }
    elif isinstance(ows_context, dict):
        process_info["owsContext"] = ows_context

    try:
        store = get_db(container).get_store(StoreProcesses)
        saved_process = store.save_process(Process(process_info),
                                           overwrite=False)
    except ProcessRegistrationError as ex:
        raise HTTPConflict(detail=str(ex))
    except ValueError as ex:
        # raised on invalid process name
        raise HTTPBadRequest(detail=str(ex))

    json_response = {
        "processSummary": saved_process.process_summary(),
        "deploymentDone": True
    }
    return HTTPOk(
        json=json_response
    )  # FIXME: should be 201 (created), update swagger accordingly
예제 #4
0
def test_process_split_version(process_id, result):
    assert Process.split_version(process_id) == result
예제 #5
0
def execute_process(task, job_id, wps_url, headers=None):
    # type: (Task, UUID, str, Optional[HeadersType]) -> StatusType
    """
    Celery task that executes the WPS process job monitoring as status updates (local and remote).
    """
    from weaver.wps.service import get_pywps_service

    LOGGER.debug("Job execute process called.")

    task_process = get_celery_process()
    rss_start = task_process.memory_info().rss
    registry = get_registry(
        None)  # local thread, whether locally or dispatched celery
    settings = get_settings(registry)
    db = get_db(
        registry, reset_connection=True
    )  # reset the connection because we are in a forked celery process
    store = db.get_store(StoreJobs)
    job = store.fetch_by_id(job_id)
    job.started = now()
    job.status = Status.STARTED  # will be mapped to 'RUNNING'
    job.status_message = f"Job {Status.STARTED}."  # will preserve detail of STARTED vs RUNNING
    job.save_log(message=job.status_message)

    task_logger = get_task_logger(__name__)
    job.save_log(logger=task_logger, message="Job task setup initiated.")
    load_pywps_config(settings)
    job.progress = JobProgress.SETUP
    job.task_id = task.request.id
    job.save_log(logger=task_logger, message="Job task setup completed.")
    job = store.update_job(job)

    # Flag to keep track if job is running in background (remote-WPS, CWL app, etc.).
    # If terminate signal is sent to worker task via API dismiss request while still running in background,
    # the raised exception within the task will switch the job to Status.FAILED, but this will not raise an
    # exception here. Since the task execution 'succeeds' without raising, it skips directly to the last 'finally'.
    # Patch it back to Status.DISMISSED in this case.
    task_terminated = True

    try:
        job.progress = JobProgress.DESCRIBE
        job.save_log(logger=task_logger,
                     message=f"Employed WPS URL: [{wps_url!s}]",
                     level=logging.DEBUG)
        job.save_log(
            logger=task_logger,
            message=f"Execute WPS request for process [{job.process!s}]")
        wps_process = fetch_wps_process(job, wps_url, headers, settings)

        # prepare inputs
        job.progress = JobProgress.GET_INPUTS
        job.save_log(logger=task_logger,
                     message="Fetching job input definitions.")
        wps_inputs = parse_wps_inputs(wps_process, job)

        # prepare outputs
        job.progress = JobProgress.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=wps_url)
            process = Process.from_ows(wps_process, service, settings)

        job.progress = JobProgress.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..."
        )

        wps_worker = get_pywps_service(environ=settings, is_worker=True)
        execution = wps_worker.execute_job(job,
                                           wps_inputs=wps_inputs,
                                           wps_outputs=wps_outputs,
                                           remote_process=process,
                                           headers=headers)
        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 = JobProgress.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=f"Updated job status location: [{wps_status_path}].")

        job.status = Status.RUNNING
        job.status_message = execution.statusMessage or f"{job!s} initiation done."
        job.status_location = wps_status_path
        job.request = execution.request
        job.response = execution.response
        job.progress = JobProgress.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:
                job.save_log(errors=execution.errors, logger=task_logger)
                job = store.update_job(job)
                raise Exception(
                    f"Could not read status document after {max_retries} retries. Giving up."
                )
            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 = JobProgress.EXECUTE_MONITOR_LOOP
                progress_max = JobProgress.EXECUTE_MONITOR_DONE
                job.progress = progress_min
                run_delay = wait_secs(run_step)
                execution = check_wps_status(location=wps_status_path,
                                             settings=settings,
                                             sleep_secs=run_delay)
                job_msg = (execution.statusMessage or "").strip()
                job.response = execution.response
                job.status = map_status(execution.getStatus())
                job_status_msg = job_msg or "n/a"
                job_percent = execution.percentCompleted
                job.status_message = f"Job execution monitoring (progress: {job_percent}%, status: {job_status_msg})."

                if execution.isComplete():
                    msg_progress = f" (status: {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 = f"Job succeeded{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 = f"Job failed{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)
                    job = store.update_job(job)

            except Exception as exc:
                num_retries += 1
                task_logger.debug("Exception raised: %s", repr(exc))
                job.status_message = f"Could not read status XML document for {job!s}. Trying again..."
                job.save_log(errors=execution.errors, logger=task_logger)
                job = store.update_job(job)
                sleep(1)
            else:
                num_retries = 0
                run_step += 1
            finally:
                task_terminated = False  # reached only if WPS execution completed (worker not terminated beforehand)
                job = store.update_job(job)

    except Exception as exc:
        # if 'execute_job' finishes quickly before even reaching the 'monitoring loop'
        # consider WPS execution produced an error (therefore Celery worker not terminated)
        task_terminated = False
        LOGGER.exception("Failed running [%s]", job)
        LOGGER.debug("Failed job [%s] raised an exception.", job, exc_info=exc)
        # note: don't update the progress here to preserve last one that was set
        job.status = map_status(Status.FAILED)
        job.status_message = f"Failed to run {job!s}."
        errors = f"{fully_qualified_name(exc)}: {exc!s}"
        job.save_log(errors=errors, logger=task_logger)
        job = store.update_job(job)
    finally:
        # if task worker terminated, local 'job' is out of date compared to remote/background runner last update
        job = store.fetch_by_id(job.id)
        if task_terminated and map_status(job.status) == Status.FAILED:
            job.status = Status.DISMISSED
        task_success = map_status(
            job.status) not in JOB_STATUS_CATEGORIES[StatusCategory.FAILED]
        collect_statistics(task_process, settings, job, rss_start)
        if task_success:
            job.progress = JobProgress.EXECUTE_MONITOR_END
        job.status_message = f"Job {job.status}."
        job.save_log(logger=task_logger)

        if task_success:
            job.progress = JobProgress.NOTIFY
        send_job_complete_notification_email(job, task_logger, settings)

        if job.status not in JOB_STATUS_CATEGORIES[StatusCategory.FINISHED]:
            job.status = Status.SUCCEEDED
        job.status_message = f"Job {job.status}."
        job.mark_finished()
        if task_success:
            job.progress = JobProgress.DONE
        job.save_log(logger=task_logger, message="Job task complete.")
        job = store.update_job(job)

    return job.status
예제 #6
0
    def list_processes(
        self,
        visibility=None,  # type: Optional[str]
        page=None,  # type: Optional[int]
        limit=None,  # type: Optional[int]
        sort=None,  # type: Optional[str]
        total=False,  # type: bool
    ):  # type: (...) -> Union[List[Process], Tuple[List[Process], int]]
        """
        Lists all processes in database, optionally filtered by `visibility`.

        :param visibility: One value amongst `weaver.visibility`.
        :param page: page number to return when using result paging.
        :param limit: number of processes per page when using result paging.
        :param sort: field which is used for sorting results (default: process ID, descending).
        :param total: request the total number of processes to be calculated (ignoring paging).
        :returns:
            List of sorted, and possibly page-filtered, processes matching queries.
            If ``total`` was requested, return a tuple of this list and the number of processes.
        """
        search_filters = {}
        if visibility is None:
            visibility = VISIBILITY_VALUES
        if isinstance(visibility, str):
            visibility = [visibility]
        for v in visibility:
            if v not in VISIBILITY_VALUES:
                raise ValueError(
                    "Invalid visibility value '{0!s}' is not one of {1!s}".
                    format(v, list(VISIBILITY_VALUES)))
        search_filters["visibility"] = {"$in": list(visibility)}

        # processes do not have 'created', but ObjectID in '_id' has the particularity of embedding creation time
        if sort == SORT_CREATED:
            sort = "_id"
        # replace equivalent aliases to corresponding fields in db
        if sort in [SORT_ID, SORT_PROCESS]:
            sort = SORT_ID_LONG
        sort_allowed = list(PROCESS_SORT_VALUES) + ["_id"]
        sort_method = {
            "$sort": self._apply_sort_method(sort, SORT_ID_LONG, sort_allowed)
        }

        search_pipeline = [{"$match": search_filters}, sort_method]
        paging_pipeline = []
        if page is not None and limit is not None:
            paging_pipeline = self._apply_paging_pipeline(page, limit)
        if total:
            pipeline = self._apply_total_result(search_pipeline,
                                                paging_pipeline)
        else:
            pipeline = search_pipeline + paging_pipeline
        LOGGER.debug("Process listing pipeline:\n%s",
                     repr_json(pipeline, indent=2))

        found = list(
            self.collection.aggregate(pipeline,
                                      collation=Collation(locale="en")))
        if total:
            items = [Process(item) for item in found[0]["items"]]
            total = found[0]["total"]
            return items, total
        return [Process(item) for item in found]
예제 #7
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def test_stdout_stderr_logging_for_commandline_tool_failure():
    """
    Execute a process and assert that stderr is correctly logged to log file.
    """
    process = Process({
        "title": "test-stdout-stderr",
        "id": "test-stdout-stderr",
        "package": {
            "cwlVersion": "v1.0",
            "class": "CommandLineTool",
            "baseCommand": "not_existing_command",
            "inputs": {
                "message": {
                    "type": "string",
                    "inputBinding": {
                        "position": 1
                    }
                }
            },
            "outputs": {}
        }
    })

    payload = process
    package = process["package"]
    title = process["title"]
    identifier = process["id"]

    # WPSPackage._handle()
    log_file = tempfile.NamedTemporaryFile()
    status_location = log_file.name
    workdir = tempfile.TemporaryDirectory()

    class TestWpsPackage(WpsPackage):
        @property
        def status_location(self):
            return status_location

    wps_package_instance = TestWpsPackage(identifier=identifier,
                                          title=title,
                                          payload=payload,
                                          package=package)
    wps_package_instance.set_workdir(workdir.name)

    # WPSRequest mock
    wps_request = WPSRequest()
    wps_request.json = {
        "identifier": "test-stdout-stderr",
        "operation": "execute",
        "version": "1.0.0",
        "language": "null",
        "identifiers": "null",
        "store_execute": "true",
        "status": "true",
        "lineage": "true",
        "raw": "false",
        "inputs": {
            "message": [{
                "identifier": "message",
                "title": "A dummy message",
                "type": "literal",
                "data_type": "string",
                "data": "Dummy message",
                "allowed_values": [],
            }]
        },
        "outputs": {}
    }

    # ExecuteResponse mock
    wps_response = type("", (object, ), {
        "_update_status": lambda *_, **__: 1
    })()

    from weaver.exceptions import PackageExecutionError

    try:
        wps_package_instance._handler(wps_request, wps_response)
    except PackageExecutionError as exception:
        assert "Completed permanentFail" in exception.args[0]
    else:
        fail(
            "\"wps_package._handler()\" was expected to throw \"PackageExecutionError\" exception"
        )
예제 #8
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def test_stdout_stderr_logging_for_commandline_tool_success():
    """
    Execute a process and assert that stdout is correctly logged to log file.
    """
    process = Process({
        "title": "test-stdout-stderr",
        "id": "test-stdout-stderr",
        "package": {
            "cwlVersion": "v1.0",
            "class": "CommandLineTool",
            "baseCommand": "echo",
            "inputs": {
                "message": {
                    "type": "string",
                    "inputBinding": {
                        "position": 1
                    }
                }
            },
            "outputs": {}
        }
    })

    payload = process
    package = process["package"]
    title = process["title"]
    identifier = process["id"]

    # WPSPackage._handle()
    log_file = tempfile.NamedTemporaryFile()
    status_location = log_file.name
    workdir = tempfile.TemporaryDirectory()

    class TestWpsPackage(WpsPackage):
        @property
        def status_location(self):
            return status_location

    wps_package_instance = TestWpsPackage(identifier=identifier,
                                          title=title,
                                          payload=payload,
                                          package=package)
    wps_package_instance.set_workdir(workdir.name)

    # WPSRequest mock
    wps_request = WPSRequest()
    wps_request.json = {
        "identifier": "test-stdout-stderr",
        "operation": "execute",
        "version": "1.0.0",
        "language": "null",
        "identifiers": "null",
        "store_execute": "true",
        "status": "true",
        "lineage": "true",
        "raw": "false",
        "inputs": {
            "message": [{
                "identifier": "message",
                "title": "A dummy message",
                "type": "literal",
                "data_type": "string",
                "data": "Dummy message",
                "allowed_values": [],
            }]
        },
        "outputs": {}
    }

    # ExecuteResponse mock
    wps_response = type("", (object, ), {
        "_update_status": lambda *_, **__: 1
    })()

    wps_package_instance._handler(wps_request, wps_response)

    # log assertions
    with open(status_location + ".log", "r") as file:
        log_data = file.read()
        assert "Dummy message" in log_data
예제 #9
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파일: utils.py 프로젝트: crim-ca/weaver
def get_job(request):
    # type: (PyramidRequest) -> Job
    """
    Obtain a :term:`Job` from request parameters.

    .. versionchanged:: 4.20
        When looking for :term:`Job` that refers to a local :term:`Process`, allow implicit resolution of the
        unspecified ``version`` portion to automatically resolve the identifier. Consider that validation of
        the expected :term:`Process` for this :term:`Job` is "good enough", since the specific ID is not actually
        required to obtain the :term:`Job` (could be queried by ID only on the ``/jobs/{jobId}`` endpoint.
        If the ``version`` is provided though (either query parameter or tagged representation), the validation
        will ensure that it matches explicitly.

    :param request: Request with path and query parameters to retrieve the desired job.
    :returns: Job information if found.
    :raise HTTPNotFound: with JSON body details on missing/non-matching job, process, provider IDs.
    """
    job_id = request.matchdict.get("job_id")
    try:
        if not is_uuid(job_id):
            raise JobInvalidParameter
        store = get_db(request).get_store(StoreJobs)
        job = store.fetch_by_id(job_id)
    except (JobInvalidParameter, JobNotFound) as exc:
        exception = type(exc)
        if exception is JobInvalidParameter:
            desc = "Invalid job reference is not a valid UUID."
        else:
            desc = "Could not find job with specified reference."
        title = "NoSuchJob"
        raise exception(
            # new format: https://docs.ogc.org/is/18-062r2/18-062r2.html#req_core_job-exception-no-such-job
            json={
                "title": title,
                "type":
                "http://www.opengis.net/def/exceptions/ogcapi-processes-1/1.0/no-such-job",
                "detail": desc,
                "status": exception.code,
                "cause": str(job_id)
            },
            code=title,
            locator="JobID",
            description=desc  # old format
        )

    provider_id = request.matchdict.get("provider_id", job.service)
    process_tag = request.matchdict.get("process_id")
    if process_tag:
        process_tag = resolve_process_tag(
            request)  # find version if available as well
    else:
        process_tag = job.process
    if provider_id:
        forbid_local_only(request)

    if job.service != provider_id:
        title = "NoSuchProvider"
        desc = "Could not find job reference corresponding to specified provider reference."
        raise OWSNotFound(
            # new format: https://docs.ogc.org/is/18-062r2/18-062r2.html#req_core_job-exception-no-such-job
            json={
                "title": title,
                "type":
                "http://www.opengis.net/def/exceptions/ogcapi-processes-1/1.0/no-such-job",
                "detail": desc,
                "status": OWSNotFound.code,
                "cause": str(provider_id)
            },
            code=title,
            locator="provider",
            description=desc  # old format
        )

    process_id = Process.split_version(process_tag)[0]
    if job.process not in [process_id, process_tag]:
        title = "NoSuchProcess"
        desc = "Could not find job reference corresponding to specified process reference."
        raise OWSNotFound(
            # new format: https://docs.ogc.org/is/18-062r2/18-062r2.html#req_core_job-exception-no-such-job
            # note: although 'no-such-process' error, return 'no-such-job' because process could exist, only mismatches
            json={
                "title": title,
                "type":
                "http://www.opengis.net/def/exceptions/ogcapi-processes-1/1.0/no-such-job",
                "detail": desc,
                "status": OWSNotFound.code,
                "cause": str(process_tag)
            },
            code=title,
            locator="process",
            description=desc  # old format
        )
    return job
예제 #10
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def get_opensearch_process():
    return Process(load_json_test_file("opensearch_process.json"))