Unverified Commit 7eaa54a0 authored by mvdbeek's avatar mvdbeek
Browse files

Add input extra files to `get_input_fnames` 

This should fix volume mounts in kubernetes,
which calls:

```
volume_mounts.extend(generate_relative_mounts(data_claim, job_wrapper.job_io.get_input_fnames()))
```
The only other consumers are pbs, using an undocument config option
(ahem ...).
parent 8a52443a

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