Unverified Commit 13f9977d authored by mvdbeek's avatar mvdbeek
Browse files

Merge branch 'release_24.0' into release_24.1

parents e1599f3d 31c0eba7

lib/galaxy/managers/jobs.py

+1 −1
Original line number Diff line number Diff line
@@ -286,7 +286,7 @@ class JobManager: 


    def stop(self, job, message=None):

        if not job.finished:

            job.mark_deleted(self.app.config.track_jobs_in_database)

            job.mark_deleted(self.app.config.track_jobs_in_database, message)

            session = self.app.model.session

            with transaction(session):

                session.commit()

lib/galaxy/model/__init__.py

+15 −8
Original line number Diff line number Diff line
@@ -1880,7 +1880,7 @@ class Job(Base, JobLike, UsesCreateAndUpdateTime, Dictifiable, Serializable): 
        else:

            self.state = Job.states.STOPPED



    def mark_deleted(self, track_jobs_in_database=False):

    def mark_deleted(self, track_jobs_in_database=False, message=None):

        """

        Mark this job as deleted, and mark any output datasets as discarded.

        """
@@ -1891,7 +1891,8 @@ class Job(Base, JobLike, UsesCreateAndUpdateTime, Dictifiable, Serializable): 
            self.state = Job.states.DELETING

        else:

            self.state = Job.states.DELETED

        self.info = "Job output deleted by user before job completed."

        info = message or "Job output deleted by user before job completed."

        self.info = info

        for jtoda in self.output_datasets:

            output_hda = jtoda.dataset

            output_hda.deleted = True
@@ -1901,7 +1902,7 @@ class Job(Base, JobLike, UsesCreateAndUpdateTime, Dictifiable, Serializable): 
                shared_hda.deleted = True

                shared_hda.blurb = "deleted"

                shared_hda.peek = "Job deleted"

                shared_hda.info = "Job output deleted by user before job completed"

                shared_hda.info = info



    def mark_failed(self, info="Job execution failed", blurb=None, peek=None):

        """
@@ -4905,11 +4906,16 @@ class DatasetInstance(RepresentById, UsesCreateAndUpdateTime, _HasTable): 
    def display_info(self):

        return self.datatype.display_info(self)



    def get_converted_files_by_type(self, file_type):

    def get_converted_files_by_type(self, file_type, include_errored=False):

        for assoc in self.implicitly_converted_datasets:

            if not assoc.deleted and assoc.type == file_type:

                item = assoc.dataset or assoc.dataset_ldda

                if not item.deleted and item.state in Dataset.valid_input_states:

                valid_states = (

                    (Dataset.states.ERROR, *Dataset.valid_input_states)

                    if include_errored

                    else Dataset.valid_input_states

                )

                if not item.deleted and item.state in valid_states:

                    return item

        return None
@@ -4924,7 +4930,7 @@ class DatasetInstance(RepresentById, UsesCreateAndUpdateTime, _HasTable): 
            depends_list = []

        return {dep: self.get_converted_dataset(trans, dep) for dep in depends_list}



    def get_converted_dataset(self, trans, target_ext, target_context=None, history=None):

    def get_converted_dataset(self, trans, target_ext, target_context=None, history=None, include_errored=False):

        """

        Return converted dataset(s) if they exist, along with a dict of dependencies.

        If not converted yet, do so and return None (the first time). If unconvertible, raise exception.
@@ -4936,7 +4942,7 @@ class DatasetInstance(RepresentById, UsesCreateAndUpdateTime, _HasTable): 
        converted_dataset = self.get_metadata_dataset(target_ext)

        if converted_dataset:

            return converted_dataset

        converted_dataset = self.get_converted_files_by_type(target_ext)

        converted_dataset = self.get_converted_files_by_type(target_ext, include_errored=include_errored)

        if converted_dataset:

            return converted_dataset

        deps = {}
@@ -5160,7 +5166,8 @@ class DatasetInstance(RepresentById, UsesCreateAndUpdateTime, _HasTable): 


        # Get converted dataset; this will start the conversion if necessary.

        try:

            converted_dataset = self.get_converted_dataset(trans, target_type)

            # Include errored datasets here, we let user chose to retry or view error

            converted_dataset = self.get_converted_dataset(trans, target_type, include_errored=True)

        except NoConverterException:

            return self.conversion_messages.NO_CONVERTER

        except ConverterDependencyException as dep_error:

lib/galaxy_test/api/test_jobs.py

+18 −0
Original line number Diff line number Diff line
@@ -1062,6 +1062,24 @@ steps: 
        self._assert_status_code_is(empty_search_response, 200)

        assert len(empty_search_response.json()) == 0



    @pytest.mark.require_new_history

    def test_delete_job_with_message(self, history_id):

        input_dataset_id = self.__history_with_ok_dataset(history_id)

        inputs = json.dumps({"input1": {"src": "hda", "id": input_dataset_id}})

        search_payload = self._search_payload(history_id=history_id, tool_id="cat1", inputs=inputs)

        # create a job

        tool_response = self._post("tools", data=search_payload).json()

        job_id = tool_response["jobs"][0]["id"]

        output_dataset_id = tool_response["outputs"][0]["id"]

        # delete the job with message

        expected_message = "test message"

        delete_job_response = self._delete(f"jobs/{job_id}", data={"message": expected_message}, json=True)

        self._assert_status_code_is(delete_job_response, 200)

        # Check the output dataset is deleted and the info field contains the message

        dataset_details = self._get(f"histories/{history_id}/contents/{output_dataset_id}").json()

        assert dataset_details["deleted"] is True

        assert dataset_details["misc_info"] == expected_message



    @pytest.mark.require_new_history

    def test_destination_params(self, history_id):

        dataset_id = self.__history_with_ok_dataset(history_id)