Merge pull request #15786 from ahmedhamidawan/related_filter_refactor

Add API test and refactor code for related:hid history filter

lib/galaxy/managers/history_contents.py

@@ -531,34 +531,23 @@ class HistoryContentsFilters(
 
     def parse_query_filters_with_relations(self, query_filters: ValueFilterQueryParams, history_id):
         """Parse query filters but consider case where related filter is included."""
-        if query_filters.q and query_filters.qv and "related-eq" in query_filters.q:
-            qv_index = query_filters.q.index("related-eq")
+        has_related_q = [q for q in ("related-eq", "related") if query_filters.q and q in query_filters.q]
+        if query_filters.q and query_filters.qv and has_related_q:
+            qv_index = query_filters.q.index(has_related_q[0])
             qv_hid = query_filters.qv[qv_index]
 
             # Type check whether hid is int
             if not qv_hid.isdigit():
                 raise glx_exceptions.RequestParameterInvalidException(
-                    "unparsable value for filter",
+                    "unparsable value for related filter",
                     column="related",
                     operation="eq",
                     value=qv_hid,
                     ValueError="invalid type in filter",
                 )
 
-            # Make new q and qv excluding related filter
-            new_q = [x for i, x in enumerate(query_filters.q) if i != qv_index]
-            new_qv = [x for i, x in enumerate(query_filters.qv) if i != qv_index]
-
-            # Get list of related item hids from job_connections manager
-            job_connections_manager = JobConnectionsManager(self.app.model.session)
-            related = job_connections_manager.get_related_hids(history_id, qv_hid)
-
-            # Make new query_filters with updated list of related hids for given hid
-            new_q.append("related-eq")
-            new_qv.append(json.dumps(related))
-            query_filters_with_relations = ValueFilterQueryParams(
-                q=new_q,
-                qv=new_qv,
+            query_filters_with_relations = self.get_query_filters_with_relations(
+                query_filters=query_filters, related_q=has_related_q[0], history_id=history_id
             )
             return super().parse_query_filters(query_filters_with_relations)
         return super().parse_query_filters(query_filters)
@@ -617,6 +606,30 @@ class HistoryContentsFilters(
             return self.parsed_filter(filter_type="orm", filter=column_filter)
         return super()._parse_orm_filter(attr, op, val)
 
+    def get_query_filters_with_relations(self, query_filters: ValueFilterQueryParams, related_q: str, history_id):
+        """Return `query_filters_with_relations` changing `related:hid` to `related:[hid1, hid2, ...]`."""
+        if query_filters.q and query_filters.qv:
+            qv_index = query_filters.q.index(related_q)
+            qv_hid = query_filters.qv[qv_index]
+
+            # Make new q and qv excluding related filter
+            new_q = [x for i, x in enumerate(query_filters.q) if i != qv_index]
+            new_qv = [x for i, x in enumerate(query_filters.qv) if i != qv_index]
+
+            # Get list of related item hids from job_connections manager
+            job_connections_manager = JobConnectionsManager(self.app.model.session)
+            related = job_connections_manager.get_related_hids(history_id, int(qv_hid))
+
+            # Make new query_filters with updated list of related hids for given hid
+            new_q.append("related-eq")
+            new_qv.append(json.dumps(related))
+            query_filters_with_relations = ValueFilterQueryParams(
+                q=new_q,
+                qv=new_qv,
+            )
+            return query_filters_with_relations
+        return query_filters
+
     def decode_type_id(self, type_id):
         TYPE_ID_SEP = "-"
         split = type_id.split(TYPE_ID_SEP, 1)
@@ -638,8 +651,6 @@ class HistoryContentsFilters(
         self.orm_filter_parsers.update(
             {
                 "history_content_type": {"op": ("eq")},
-                # maybe remove related from here, as there's no corresponding field?
-                "related": {"op": ("eq")},
                 "type_id": {"op": ("eq", "in"), "val": self.parse_type_id_list},
                 "hid": {"op": ("eq", "ge", "le", "gt", "lt"), "val": int},
                 # TODO: needs a different val parser - but no way to add to the above

lib/galaxy/managers/job_connections.py

@@ -18,7 +18,7 @@ class JobConnectionsManager:
     def __init__(self, sa_session: galaxy_scoped_session):
         self.sa_session = sa_session
 
-    def get_connections_graph(self, id, src):
+    def get_connections_graph(self, id: int, src: str):
         """Get connections graph of inputs and outputs for given item id"""
         if src == "HistoryDatasetAssociation":
             output_selects = self.outputs_derived_from_input_hda(id)
@@ -34,7 +34,7 @@ class JobConnectionsManager:
         result["inputs"] = self._get_union_results(*input_selects)
         return result
 
-    def get_related_hids(self, history_id, hid):
+    def get_related_hids(self, history_id, hid: int):
         """Get connections graph of inputs and outputs for given item hid from the given history_id"""
         # Get id(s) and src(s) for the given hid
         items_by_hid = self.sa_session.execute(
@@ -63,7 +63,7 @@ class JobConnectionsManager:
             result.append({"src": row.src, "id": row.id})
         return result
 
-    def outputs_derived_from_input_hda(self, input_hda_id):
+    def outputs_derived_from_input_hda(self, input_hda_id: int):
         hda_select = (
             select(
                 [
@@ -94,7 +94,7 @@ class JobConnectionsManager:
         )
         return hda_select, hdca_select
 
-    def outputs_derived_from_input_hdca(self, input_hdca_id):
+    def outputs_derived_from_input_hdca(self, input_hdca_id: int):
         hda_select = (
             select(
                 [
@@ -126,7 +126,7 @@ class JobConnectionsManager:
         )
         return hda_select, hdca_select
 
-    def inputs_for_hda(self, input_hda_id):
+    def inputs_for_hda(self, input_hda_id: int):
         input_hdas = (
             select(
                 [
@@ -157,7 +157,7 @@ class JobConnectionsManager:
         )
         return input_hdas, input_hdcas
 
-    def inputs_for_hdca(self, input_hdca_id):
+    def inputs_for_hdca(self, input_hdca_id: int):
         input_hdas = (
             select(
                 [

lib/galaxy_test/api/test_history_contents.py

@@ -737,6 +737,38 @@ class TestHistoryContentsApi(ApiTestCase):
         ).json()
         assert len(contents_response) == 0
 
+    @skip_without_tool("cat_data_and_sleep")
+    def test_index_filter_by_related_items(self, history_id):
+        # initialise history with 2 datasets
+        input_hda_id = self.dataset_populator.new_dataset(history_id)["id"]
+        unrelated_hid = self.dataset_populator.new_dataset(history_id)["hid"]
+
+        # Run tool on first dataset to get 3rd, related dataset
+        inputs = {
+            "input1": {"src": "hda", "id": input_hda_id},
+            "sleep_time": 0,
+        }
+        run_response = self.dataset_populator.run_tool_raw(
+            "cat_data_and_sleep",
+            inputs,
+            history_id,
+        )
+        related_hid = run_response.json()["outputs"][0]["hid"]
+
+        # Test q = related-eq, for related items
+        contents_response = self._get(f"histories/{history_id}/contents?v=dev&q=related-eq&qv={related_hid}").json()
+        assert len(contents_response) == 2
+
+        # Test q = related, for unrelated item
+        contents_response = self._get(f"histories/{history_id}/contents?v=dev&q=related&qv={unrelated_hid}").json()
+        assert len(contents_response) == 1
+
+        # Test error case: qv is string
+        related_qv = "one"
+        contents_response = self._get(f"histories/{history_id}/contents?v=dev&q=related-eq&qv={related_qv}")
+        assert contents_response.status_code == 400
+        assert contents_response.json()["err_msg"] == "unparsable value for related filter"
+
     def test_elements_datatypes_field(self, history_id):
         collection_name = "homogeneous"
         expected_datatypes = ["txt"]