Unverified Commit 33f27d54 authored by mvdbeek's avatar mvdbeek
Browse files

Merge branch 'release_24.0' into release_24.1

parents 9d601f8c 58c55d4a

lib/galaxy/job_execution/setup.py

+12 −8
Original line number Diff line number Diff line
@@ -213,22 +213,26 @@ class JobIO(Dictifiable): 
        for value in ds.metadata.values():

            if isinstance(value, MetadataFile):

                filenames.append(value.get_file_name())

        if ds.dataset and ds.dataset.extra_files_path_exists():

            filenames.append(ds.dataset.extra_files_path)

        return filenames



    def get_input_fnames(self) -> List[str]:

    def get_input_datasets(self) -> List[DatasetInstance]:

        job = self.job

        return [

            da.dataset for da in job.input_datasets + job.input_library_datasets if da.dataset

        ]  # da is JobToInputDatasetAssociation object



    def get_input_fnames(self) -> List[str]:

        filenames = []

        for da in job.input_datasets + job.input_library_datasets:  # da is JobToInputDatasetAssociation object

            if da.dataset:

                filenames.extend(self.get_input_dataset_fnames(da.dataset))

        for ds in self.get_input_datasets():

            filenames.extend(self.get_input_dataset_fnames(ds))

        return filenames



    def get_input_paths(self) -> List[DatasetPath]:

        job = self.job

        paths = []

        for da in job.input_datasets + job.input_library_datasets:  # da is JobToInputDatasetAssociation object

            if da.dataset:

                paths.append(self.get_input_path(da.dataset))

        for ds in self.get_input_datasets():

            paths.append(self.get_input_path(ds))

        return paths



    def get_input_path(self, dataset: DatasetInstance) -> DatasetPath:

lib/galaxy/jobs/splitters/basic.py

+1 −1
Original line number Diff line number Diff line
@@ -13,7 +13,7 @@ def set_basic_defaults(job_wrapper): 




def do_split(job_wrapper):

    if len(job_wrapper.job_io.get_input_fnames()) > 1 or len(job_wrapper.job_io.get_output_fnames()) > 1:

    if len(job_wrapper.job_io.get_input_datasets()) > 1 or len(job_wrapper.job_io.get_output_fnames()) > 1:

        log.error("The basic splitter is not capable of handling jobs with multiple inputs or outputs.")

        raise Exception("Job Splitting Failed, the basic splitter only handles tools with one input and one output")

    # add in the missing information for splitting the one input and merging the one output

lib/galaxy/managers/users.py

+1 −1
Original line number Diff line number Diff line
@@ -616,7 +616,7 @@ class UserManager(base.ModelManager, deletable.PurgableManagerMixin): 
        reset_user = get_user_by_email(trans.sa_session, email, self.app.model.User)

        if not reset_user and email != email.lower():

            reset_user = self._get_user_by_email_case_insensitive(trans.sa_session, email)

        if reset_user:

        if reset_user and not reset_user.deleted:

            prt = self.app.model.PasswordResetToken(reset_user)

            trans.sa_session.add(prt)

            with transaction(trans.sa_session):

lib/galaxy/managers/workflows.py

+3 −3
Original line number Diff line number Diff line
@@ -1416,7 +1416,7 @@ class WorkflowContentsManager(UsesAnnotations): 
        If `allow_upgrade`, the workflow and sub-workflows might use updated tool versions when refactoring.

        """

        annotation_str = ""

        tag_str = ""

        tags_list = []

        annotation_owner = None

        if stored is not None:

            if stored.id:
@@ -1427,7 +1427,7 @@ class WorkflowContentsManager(UsesAnnotations): 
                    or self.get_item_annotation_str(trans.sa_session, annotation_owner, stored)

                    or ""

                )

                tag_str = stored.make_tag_string_list()

                tags_list = stored.make_tag_string_list()

            else:

                # dry run with flushed workflow objects, just use the annotation

                annotations = stored.annotations
@@ -1440,7 +1440,7 @@ class WorkflowContentsManager(UsesAnnotations): 
        data["format-version"] = "0.1"

        data["name"] = workflow.name

        data["annotation"] = annotation_str

        data["tags"] = tag_str

        data["tags"] = tags_list

        if workflow.uuid is not None:

            data["uuid"] = str(workflow.uuid)

        steps: Dict[int, Dict[str, Any]] = {}

lib/galaxy/workflow/refactor/execute.py

+3 −0
Original line number Diff line number Diff line
@@ -531,6 +531,9 @@ class WorkflowRefactorExecutor: 
                if upgrade_input["name"] == input_name:

                    matching_input = upgrade_input

                    break

                elif step.when_expression and f"inputs.{input_name}" in step.when_expression:

                    # TODO: eventually track step inputs more formally

                    matching_input = upgrade_input



            # In the future check parameter type, format, mapping status...

            if matching_input is None: