Implement group tag testing in tools.

galaxyproject · Aug 6, 2024 · 7185a12 · 7185a12
1 parent e0b6532
commit 7185a12
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Showing 4 changed files with 40 additions and 1 deletion.
diff --git a/lib/galaxy/tool_util/verify/interactor.py b/lib/galaxy/tool_util/verify/interactor.py
@@ -505,10 +505,14 @@ def stage_data_async(
         tool_version: Optional[str] = None,
     ) -> Callable[[], None]:
         fname = test_data["fname"]
+        tags = test_data.get("tags")
         tool_input = {
             "file_type": test_data["ftype"],
             "dbkey": test_data["dbkey"],
         }
+        if tags:
+            tool_input["tags"] = tags
+
         metadata = test_data.get("metadata", {})
         if not hasattr(metadata, "items"):
             raise Exception(f"Invalid metadata description found for input [{fname}] - [{metadata}]")
@@ -1865,6 +1869,7 @@ def test_data_iter(required_files):
             ftype=extra.get("ftype", DEFAULT_FTYPE),
             dbkey=extra.get("dbkey", DEFAULT_DBKEY),
             location=extra.get("location", None),
+            tags=extra.get("tags", []),
         )
         edit_attributes = extra.get("edit_attributes", [])
 

diff --git a/lib/galaxy/tools/actions/upload_common.py b/lib/galaxy/tools/actions/upload_common.py
@@ -276,7 +276,13 @@ def new_upload(
                 )
     else:
         upload_target_dataset_instance = __new_history_upload(trans, uploaded_dataset, history=history, state=state)
-
+        if uploaded_dataset.tags:
+            new_tags = tag_handler.parse_tags_list(uploaded_dataset.tags.split(","))
+            for tag in new_tags:
+                log.info(f"applying item tag.... {tag}")
+                tag_handler.apply_item_tag(
+                    user=trans.user, item=upload_target_dataset_instance, name=tag[0], value=tag[1], flush=True
+                )
     if tag_list:
         tag_handler.add_tags_from_list(trans.user, upload_target_dataset_instance, tag_list, flush=False)
 

diff --git a/test/functional/tools/parameters/gx_group_tag.xml b/test/functional/tools/parameters/gx_group_tag.xml
@@ -0,0 +1,27 @@
+<tool id="gx_group_tag" name="gx_group_tag" version="1.0.0">
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <command><![CDATA[
+echo "parameter: $parameter" > '$output'
+    ]]></command>
+    <inputs>
+        <param name="ref_parameter" type="data_collection" format="tabular" />
+        <param name="parameter" type="group_tag" data_ref="ref_parameter" />
+    </inputs>
+    <expand macro="simple_text_output" />
+    <tests>
+        <test>
+            <param name="ref_parameter">
+                <collection type="paired">
+                    <element name="forward" value="simple_line.txt" tags="group:type:single" />
+                    <element name="reverse" value="simple_line_alternative.txt" tags="group:type:split" />
+                </collection>
+            </param>
+            <param name="parameter" value="type:single" />
+            <expand macro="assert_output">
+                <has_line line="parameter: type:single"/>
+            </expand>
+        </test>
+    </tests>
+</tool>
diff --git a/tools/data_source/upload.xml b/tools/data_source/upload.xml
@@ -59,6 +59,7 @@
     </upload_dataset>
     <param name="force_composite" type="hidden" value="false" />
     <param name="dbkey" type="genomebuild" label="Genome" />
+    <param name="tags" type="hidden" value="" />
     <conditional name="files_metadata" value_from="self:app.datatypes_registry.get_upload_metadata_params" value_ref="file_type" value_ref_in_group="False" />
     <!-- <param name="other_dbkey" type="text" label="Or user-defined Genome" /> -->
   </inputs>