Just get the whole directory archive for now

We could get fancier and get individual files one by one ... but not sure there's any point in making it so complicated ?
galaxyproject · Oct 30, 2023 · b8c9968 · b8c9968
1 parent b61c354
commit b8c9968
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Showing 2 changed files with 22 additions and 2 deletions.
diff --git a/lib/galaxy/tool_util/cwl/util.py b/lib/galaxy/tool_util/cwl/util.py
@@ -625,7 +625,11 @@ def dir_listing(dir_path):
                     "basename": basename,
                     "listing": listing,
                 }
-                _handle_pseudo_location(properties, pseudo_location=pseudo_location, download_url=output_metadata["download_url"] + "?to_ext=directory")
+                _handle_pseudo_location(
+                    properties,
+                    pseudo_location=pseudo_location,
+                    download_url=output_metadata["download_url"] + "?to_ext=directory",
+                )
 
                 extra_files = get_extra_files(output_metadata)
                 for extra_file in extra_files:

diff --git a/lib/galaxy_test/base/populators.py b/lib/galaxy_test/base/populators.py
@@ -266,6 +266,14 @@ def conformance_tests_gen(directory, filename="conformance_tests.yaml"):
             yield conformance_test
 
 
+def to_local_location(listing, location):
+    for item in listing:
+        if "basename" in item:
+            item["location"] = f"file://{os.path.join(location[len('file://'):], item['basename'])}"
+            if "listing" in item:
+                to_local_location(item["listing"], location=item["location"])
+
+
 def output_to_disk(output, download_folder):
     if isinstance(output, dict):
         if "secondaryFiles" in output:
@@ -274,9 +282,17 @@ def output_to_disk(output, download_folder):
             ]
         if "basename" in output:
             download_path = os.path.join(download_folder, output["basename"])
-            download_to_file(output["location"], download_path)
+            if output["class"] == "Directory":
+                zip_path = f"{download_path}.zip"
+                download_to_file(output["location"], zip_path)
+                CompressedFile(zip_path).extract(download_folder)
+                os.remove(zip_path)
+            else:
+                download_to_file(output["location"], download_path)
             output["path"] = download_path
             output["location"] = f"file://{download_path}"
+            if "listing" in output:
+                to_local_location(output["listing"], output["location"])
             return output
         else:
             new_output = {}