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

Extract: do not use common prefix dir

Author: mvdbeek

lib/galaxy/datatypes/converters/archive_to_directory.xml

@@ -1,7 +1,7 @@
 <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

@@ -253,10 +253,6 @@ def extract(self, path: StrPath) -> str:
                     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

@@ -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)