Unverified Commit e5ab06ff authored by Marius van den Beek's avatar Marius van den Beek Committed by GitHub
Browse files

Merge pull request #20929 from bernt-matthias/extract-common-prefix-dir 

Extract: do not use common prefix dir
parents 3e349928 8a31f0ad

lib/galaxy/datatypes/converters/archive_to_directory.xml

+39 −2
Original line number Diff line number Diff line 
<tool id="CONVERTER_archive_to_directory" name="Unpack archive to directory" version="1.0.0" profile="21.09">

    <!-- Use compression_utils instead of shell commands (tar/unzip) so we can verify safety of results -->

    <requirements>

        <requirement type="package" version="25.0">galaxy-util</requirement>

        <requirement type="package" version="25.1">galaxy-util</requirement>

    </requirements>

    <command><![CDATA[

        mkdir '$output1.files_path' &&
@@ -31,7 +31,44 @@ 
        <test>

            <param name="input1" ftype="tar" value="testdir1.tar"/>

            <param name="__target_datatype__" value="directory"/>

            <output name="output1" ftype="directory" value="testdir1.tar.directory"/>

            <output name="output1" ftype="directory" value="testdir1.tar.directory">

                <extra_files name="testdir1/file1">

                    <assert_contents>

                        <has_text text="hello"/>

                    </assert_contents>

                </extra_files>

                <extra_files name="testdir1/file2">

                    <assert_contents>

                        <has_text text="world"/>

                    </assert_contents>

                </extra_files>

                <extra_files name="testdir1/dir1/file3">

                    <assert_contents>

                        <has_text text="subdirfile"/>

                    </assert_contents>

                </extra_files>

            </output>

        </test>

        <test>

            <param name="input1" ftype="tar" value="testdir1_flat.zip"/>

            <param name="__target_datatype__" value="directory"/>

            <output name="output1" ftype="directory" value="testdir1.tar.directory">

                <extra_files name="file1">

                    <assert_contents>

                        <has_text text="hello"/>

                    </assert_contents>

                </extra_files>

                <extra_files name="file2">

                    <assert_contents>

                        <has_text text="world"/>

                    </assert_contents>

                </extra_files>

                <extra_files name="dir1/file3">

                    <assert_contents>

                        <has_text text="subdirfile"/>

                    </assert_contents>

                </extra_files>

            </output>

        </test>

    </tests>

    <help>

lib/galaxy/util/compression_utils.py

+0 −4
Original line number Diff line number Diff line
@@ -253,10 +253,6 @@ class CompressedFile: 
                    members_z = cast(Iterable[str], self.safemembers())

                    self.archive.extractall(extraction_path, members=members_z)

        else:

            if not common_prefix_dir:

                extraction_path = os.path.join(path, self.file_name)

                if not os.path.exists(extraction_path):

                    os.makedirs(extraction_path)

            if isinstance(self.archive, tarfile.TarFile):

                members_t = cast(Iterable[tarfile.TarInfo], self.safemembers())

                self.archive.extractall(extraction_path, members=members_t)

test/unit/data/model/test_model_store.py

+2 −2
Original line number Diff line number Diff line
@@ -740,12 +740,12 @@ def test_export_invocation_to_ro_crate_archive(tmp_path): 
    workflow_invocation = _setup_invocation(app)



    crate_zip = tmp_path / "crate.zip"

    crate_directory = tmp_path / "crate"

    with store.ROCrateArchiveModelExportStore(crate_zip, app=app, export_files="symlink") as export_store:

        export_store.export_workflow_invocation(workflow_invocation)

    with CompressedFile(crate_zip) as compressed_file:

        assert compressed_file.file_type == "zip"

        compressed_file.extract(tmp_path)

    crate_directory = tmp_path / "crate"

        compressed_file.extract(crate_directory)

    validate_invocation_crate_directory(crate_directory)