Unverified Commit 77f79169 authored by Marius van den Beek's avatar Marius van den Beek Committed by GitHub
Browse files

Merge pull request #15038 from mvdbeek/fix_metadata_import_for_discovered_metadata_files 

[22.05] Fix metadata setting for discovered datasets with extended metadata
parents 988f4e58 b6117ee3

lib/galaxy/model/store/__init__.py

+9 −5
Original line number Diff line number Diff line
@@ -430,12 +430,14 @@ class ModelImportStore(metaclass=abc.ABCMeta): 
                    )

                else:

                    raise Exception("Unknown dataset instance type encountered")

                metadata = replace_metadata_file(metadata, dataset_instance, self.sa_session)

                if self.sessionless:

                    dataset_instance._metadata_collection = MetadataCollection(

                        dataset_instance, session=self.sa_session

                    )

                    metadata = replace_metadata_file(metadata, dataset_instance, self.sa_session)

                    dataset_instance._metadata = metadata

                else:

                    dataset_instance.metadata = metadata

                self._attach_raw_id_if_editing(dataset_instance, dataset_attrs)



                # Older style...
@@ -578,6 +580,8 @@ class ModelImportStore(metaclass=abc.ABCMeta): 
                        else:

                            # Need a user to run library jobs to generate metadata...

                            pass

                        if not self.import_options.allow_edit:

                            # external import, metadata files need to be regenerated (as opposed to extended metadata dataset import)

                            self.app.datatypes_registry.set_external_metadata_tool.regenerate_imported_metadata_if_needed(

                                dataset_instance, history, **regenerate_kwds

                            )

test/functional/tools/discover_metadata_files.xml

0 → 100644
+23 −0
Original line number Diff line number Diff line 
<tool id="discover_metadata_files" name="discover metadata files" version="1.0.0" profile="16.04">

  <command>

    <![CDATA[

mkdir outputs && cp '$input_bam' outputs/output.bam

  ]]>

  </command>

  <inputs>

    <param name="input_bam" type="data" format="bam" label="BAM File" />

  </inputs>

  <outputs>

    <data format="txt" name="bam_output" label="discovered bam" hidden="true">

      <discover_datasets pattern="__name__" directory="outputs" ext="bam" visible="true" />

    </data>

  </outputs>

  <tests>

    <test>

      <param name="input_bam" value="3.bam" ftype="bam" />

      <output name="bam_output">

        <discovered_dataset designation="output.bam" file="3.bam" ftype="bam" />

      </output>

    </test>

  </tests>

</tool>

test/functional/tools/samples_tool_conf.xml

+1 −0
Original line number Diff line number Diff line
@@ -66,6 +66,7 @@ 
  <tool file="vcf_bgzip.xml" />

  <tool file="metadata.xml" />

  <tool file="metadata_bam.xml" />

  <tool file="discover_metadata_files.xml" />

  <tool file="metadata_bcf.xml" />

  <tool file="metadata_bed.xml" />

  <tool file="metadata_biom1.xml" />

test/integration/test_extended_metadata.py

+1 −1
Original line number Diff line number Diff line
@@ -28,6 +28,7 @@ TEST_TOOL_IDS = [ 
    "composite_output_tests",

    "metadata",

    "metadata_bam",

    "discover_metadata_files",

    "output_format",

    "output_auto_format",

    "collection_paired_test",
@@ -123,7 +124,6 @@ class ExtendedMetadataDeferredIntegrationTestCase(integration_util.IntegrationTe 




class ExtendedMetadataIntegrationInstance(integration_util.IntegrationInstance):

    """Describe a Galaxy test instance with embedded pulsar configured."""



    framework_tool_and_types = True