Rebase into paired/unpaired...

galaxyproject · Dec 31, 2024 · 2ea7e5b · 2ea7e5b
1 parent 6a1af79
commit 2ea7e5b
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Showing 3 changed files with 46 additions and 14 deletions.
diff --git a/lib/galaxy/model/dataset_collections/types/collection_semantics.yml b/lib/galaxy/model/dataset_collections/types/collection_semantics.yml
@@ -24,6 +24,30 @@
     tests:
     - tool_runtime: "test_tool_execute.py::test_map_over_collection"
 
+- example:
+    label: BASIC_MAPPING_PAIRED_OR_UNPAIRED_PAIRED
+    assumptions:
+    - "f, r are datasets"
+    - "tool = (i: dataset) => {o: dataset}"
+    - "C = CollectionInstance<paired_or_unpaired,[{forward=f, reverse=r}]>"
+    then:
+    - "tool(i=map_over(C)) ~> {o: collection<paired_or_unpaired,[forward=tool(i=f)[o], reverse=tool(i=r)[o]]}"
+    tests:
+    - tool_runtime: test_map_over_data_with_paired_or_unpaired_unpaired
+    - wf_editor: "accepts paired_or_unpaired data -> data connection"
+
+- example:
+    label: BASIC_MAPPING_PAIRED_OR_UNPAIRED_UNPAIRED
+    assumptions:
+    - "u is a dataset"
+    - "tool = (i: dataset) => {o: dataset}"
+    - "C = CollectionInstance<paired_or_unpaired,[{unpaired=u}]>"
+    then:
+    - "tool(i=map_over(C)) ~> {o: collection<paired_or_unpaired,[unpaired=tool(i=u)[o]]}"
+    tests:
+    - tool_runtime: test_map_over_data_with_paired_or_unpaired_paired
+    - wf_editor: "accepts paired_or_unpaired data -> data connection"
+
 - example:
     label: BASIC_MAPPING_LIST
     assumptions:
@@ -144,19 +168,6 @@
     tests:
     - wf_editor: "rejects paired input on multi-data input"
 
-PAIRED_OR_UNPAIRED_1:
-
-If tool(i: data) => {o: data}
-
-tool(i: collection<paired_or_unpaired>) => {o: collection<paired_or_unpaired>}
-
-Mapping a collection of type `paired_or_unpaired` over tool
-input i, yields an implicit collection of type `paired_or_unpaired`
-composed of the outputs o.
-
-- toolruntime: test_map_over_data_with_paired_or_unpaired
-- wfeditor: it("accepts paired_or_unpaired data -> data connection")
-
 PAIRED_OR_UNPAIRED_2:
 
 tool(i: collection<list:paired_or_unpaired>) => {o: collection<list:paired_or_unpaired>}

diff --git a/lib/galaxy_test/api/test_tool_execute.py b/lib/galaxy_test/api/test_tool_execute.py
@@ -381,7 +381,7 @@ def test_map_over_collection(
 
 
 @requires_tool_id("cat|cat1")
-def test_map_over_data_with_paired_or_unpaired(target_history: TargetHistory, required_tool: RequiredTool):
+def test_map_over_data_with_paired_or_unpaired_unpaired(target_history: TargetHistory, required_tool: RequiredTool):
     hdca = target_history.with_unpaired()
     execute = required_tool.execute.with_inputs({"input1": {"batch": True, "values": [hdca.src_dict]}})
     execute.assert_has_n_jobs(1).assert_creates_n_implicit_collections(1)
@@ -390,6 +390,17 @@ def test_map_over_data_with_paired_or_unpaired(target_history: TargetHistory, re
     output_collection.assert_has_dataset_element("unpaired").with_contents_stripped("123")
 
 
+@requires_tool_id("cat|cat1")
+def test_map_over_data_with_paired_or_unpaired_paired(target_history: TargetHistory, required_tool: RequiredTool):
+    hdca = target_history.with_paired_or_unpaired_pair()
+    execute = required_tool.execute.with_inputs({"input1": {"batch": True, "values": [hdca.src_dict]}})
+    execute.assert_creates_n_implicit_collections(1)
+    output_collection = execute.assert_creates_implicit_collection(0)
+    output_collection.assert_collection_type_is("paired_or_unpaired")
+    output_collection.assert_has_dataset_element("forward").with_contents_stripped("123")
+    output_collection.assert_has_dataset_element("reverse").with_contents_stripped("123")
+
+
 @requires_tool_id("cat|cat1")
 def test_map_over_data_with_list_paired_or_unpaired(target_history: TargetHistory, required_tool: RequiredTool):
     hdca = target_history.with_list_of_paired_and_unpaired()

diff --git a/lib/galaxy_test/base/populators.py b/lib/galaxy_test/base/populators.py
@@ -3097,6 +3097,11 @@ def create_unpaired_in_history(self, history_id: str, wait: bool = False, **kwds
         payload = self.__create_payload(history_id, contents=contents, collection_type="paired_or_unpaired", **kwds)
         return self.__create(payload, wait=wait)
 
+    def create_paired_or_unpaired_pair_in_history(self, history_id: str, wait: bool = False, **kwds):
+        contents = [("forward", "123"), ("reverse", "456")]
+        payload = self.__create_payload(history_id, contents=contents, collection_type="paired_or_unpaired", **kwds)
+        return self.__create(payload, wait=wait)
+
     def create_list_of_paired_and_unpaired_in_history(self, history_id: str, wait: bool = False, **kwds):
         contents = [
             {
@@ -3983,6 +3988,11 @@ def with_unpaired(self) -> "HasSrcDict":
             self._dataset_collection_populator.create_unpaired_in_history(self._history_id, wait=True)
         )
 
+    def with_paired_or_unpaired_pair(self) -> "HasSrcDict":
+        return self._fetch_response(
+            self._dataset_collection_populator.create_paired_or_unpaired_pair_in_history(self._history_id, wait=True)
+        )
+
     def with_list_of_paired_and_unpaired(self) -> "HasSrcDict":
         return self._fetch_response(
             self._dataset_collection_populator.create_list_of_paired_and_unpaired_in_history(