Add test for gx_allow_uri_if_protocol with deferred collections

galaxyproject · Nov 3, 2024 · 2bdcec0 · 2bdcec0
1 parent 53e8a23
commit 2bdcec0
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Showing 2 changed files with 61 additions and 11 deletions.
diff --git a/lib/galaxy_test/api/test_tools.py b/lib/galaxy_test/api/test_tools.py
@@ -2591,6 +2591,53 @@ def test_allow_uri_if_protocol_on_deferred_input(self, history_id):
         output_content = self.dataset_populator.get_history_dataset_content(history_id, dataset=output)
         assert output_content.strip() == source_uri.strip()
 
+    @skip_without_tool("gx_allow_uri_if_protocol")
+    def test_allow_uri_if_protocol_on_collection_with_deferred(self, history_id):
+        source_uris = [
+            "https://raw.githubusercontent.com/galaxyproject/galaxy/dev/test-data/simple_line.txt",
+            "https://raw.githubusercontent.com/galaxyproject/galaxy/dev/test-data/simple_line_alternative.txt",
+        ]
+        elements = [
+            {
+                "src": "url",
+                "url": source_uri,
+                "deferred": True,
+                "ext": "txt",
+            }
+            for source_uri in source_uris
+        ]
+        targets = [
+            {
+                "destination": {"type": "hdca"},
+                "elements": elements,
+                "collection_type": "list",
+                "name": "deferred list",
+            }
+        ]
+        payload = {
+            "history_id": history_id,
+            "targets": json.dumps(targets),
+        }
+        fetch_response = self.dataset_populator.fetch(payload, wait=True)
+        dataset_collection = self.dataset_collection_populator.wait_for_fetched_collection(fetch_response)
+        hdca_id = dataset_collection["id"]
+        inputs = {
+            "input1": {"batch": True, "values": [{"src": "hdca", "id": hdca_id}]},
+        }
+        run_response = self.dataset_populator.run_tool(
+            tool_id="gx_allow_uri_if_protocol", inputs=inputs, history_id=history_id
+        )
+        hdca_id = run_response["implicit_collections"][0]["id"]
+        dataset_collection = self.dataset_populator.get_history_collection_details(history_id, id=hdca_id)
+        elements = dataset_collection["elements"]
+        assert len(elements) == 2
+        for element in elements:
+            object = element["object"]
+            assert isinstance(object, dict)
+            assert object["state"] == "ok"
+            output_content = self.dataset_populator.get_history_dataset_content(history_id, dataset=object)
+            assert output_content.strip() in source_uris
+
     @skip_without_tool("cat1")
     def test_run_deferred_mapping(self, history_id: str):
         elements = [

diff --git a/test/functional/tools/parameters/gx_allow_uri_if_protocol.xml b/test/functional/tools/parameters/gx_allow_uri_if_protocol.xml
@@ -1,18 +1,21 @@
 <tool id="gx_allow_uri_if_protocol" name="gx_allow_uri_if_protocol" version="1.0.0">
     <command><![CDATA[
-        ## We should handle the case where the input must be treated as a URI with a specific protocol.
-        #if $input.is_deferred:
-            ## Here, the input is a deferred dataset which source URI has the protocol 'https'.
-            ## The ouput will be the source URI of the input.
-            echo '$input' > '$output'
-        #else:
-            ## Here, the input is a regular dataset or a materialized dataset in case of a 
-            ## deferred dataset which source URI has a protocol different than 'https'.
-            ## The output will be a copy of the input content.
-            cp '$input' '$output'
+        #for $input in $input1:
+            ## We should handle the case where the input must be treated as a URI with a specific protocol.
+            #if $input.is_deferred:
+                ## Here, the input is a deferred dataset which source URI has the protocol 'https'.
+                ## We append the URI to the output file.
+                echo '$input' >> '$output'
+            #else:
+                ## Here, the input is a regular dataset or a materialized dataset in case of a 
+                ## deferred dataset which source URI has a protocol different than 'https'.
+                ## We append the content of the dataset to the output file.
+                cat '$input' >> '$output'
+            #end if
+        #end for
     ]]></command>
     <inputs>
-        <param name="input" type="data" allow_uri_if_protocol="https"/>
+        <param name="input1" type="data" allow_uri_if_protocol="https" multiple="true"/>
     </inputs>
     <outputs>
         <data name="output" format="txt"/>