Rename subcollection_type to map_over_type to avoid the need for an api depreciation

client/src/components/Form/Elements/FormData/FormData.test.js

@@ -29,7 +29,7 @@ const defaultOptions = {
     dce: [
         { id: "dce1", name: "dceName1", src: "dce", is_dataset: true },
         { id: "dce2", name: "dceName2", src: "dce" },
-        { id: "dce3", name: "dceName3", src: "dce", subcollection_type: "subcollectionType" },
+        { id: "dce3", name: "dceName3", src: "dce", map_over_type: "mapOverType" },
         { id: "dce4", name: "dceName4", src: "dce", is_dataset: true },
     ],
     hda: [
@@ -55,12 +55,12 @@ describe("FormData", () => {
         const value_0 = {
             batch: false,
             product: false,
-            values: [{ id: "hda3", src: "hda", subcollection_type: null }],
+            values: [{ id: "hda3", src: "hda", map_over_type: null }],
         };
         const value_1 = {
             batch: false,
             product: false,
-            values: [{ id: "hda1", src: "hda", subcollection_type: null }],
+            values: [{ id: "hda1", src: "hda", map_over_type: null }],
         };
         const options = wrapper.find(".btn-group").findAll("button");
         expect(options.length).toBe(4);
@@ -114,8 +114,8 @@ describe("FormData", () => {
             batch: false,
             product: false,
             values: [
-                { id: "hda2", subcollection_type: null, src: "hda" },
-                { id: "hda3", subcollection_type: null, src: "hda" },
+                { id: "hda2", map_over_type: null, src: "hda" },
+                { id: "hda3", map_over_type: null, src: "hda" },
             ],
         });
         expect(wrapper.emitted().input.length).toEqual(1);
@@ -127,8 +127,8 @@ describe("FormData", () => {
             batch: false,
             product: false,
             values: [
-                { id: "hda2", subcollection_type: null, src: "hda" },
-                { id: "hda3", subcollection_type: null, src: "hda" },
+                { id: "hda2", map_over_type: null, src: "hda" },
+                { id: "hda3", map_over_type: null, src: "hda" },
             ],
         };
         expect(wrapper.emitted().input[0][0]).toEqual(value_0);
@@ -136,7 +136,7 @@ describe("FormData", () => {
         const value_1 = {
             batch: false,
             product: false,
-            values: [{ id: "hda2", subcollection_type: null, src: "hda" }],
+            values: [{ id: "hda2", map_over_type: null, src: "hda" }],
         };
         expect(wrapper.emitted().input[1][0]).toEqual(value_1);
         await wrapper.setProps({ value: value_1 });
@@ -144,7 +144,7 @@ describe("FormData", () => {
         const value_2 = {
             batch: false,
             product: false,
-            values: [{ id: "hda2", subcollection_type: null, src: "hda" }],
+            values: [{ id: "hda2", map_over_type: null, src: "hda" }],
         };
         expect(wrapper.emitted().input[1][0]).toEqual(value_2);
         await wrapper.setProps({ value: value_2 });
@@ -160,7 +160,7 @@ describe("FormData", () => {
         const value_0 = {
             batch: false,
             product: false,
-            values: [{ id: "dce1", subcollection_type: null, src: "dce" }],
+            values: [{ id: "dce1", map_over_type: null, src: "dce" }],
         };
         expect(wrapper.emitted().input[0][0]).toEqual(value_0);
         expect(wrapper.emitted().input.length).toEqual(1);
@@ -180,12 +180,12 @@ describe("FormData", () => {
         expect(wrapper.emitted().input.length).toEqual(2);
     });
 
-    it("dataset collection element as hdca without subcollection_type", async () => {
+    it("dataset collection element as hdca without map_over_type", async () => {
         const wrapper = createTarget({
             value: { values: [{ id: "dce2", src: "dce" }] },
             options: defaultOptions,
         });
-        const value_0 = { batch: true, product: false, values: [{ id: "dce2", subcollection_type: null, src: "dce" }] };
+        const value_0 = { batch: true, product: false, values: [{ id: "dce2", map_over_type: null, src: "dce" }] };
         expect(wrapper.emitted().input[0][0]).toEqual(value_0);
         const messageBatch = wrapper.find("[data-description='form data batch label']");
         expect(messageBatch.text()).toBe("This data input will be submitted in batch mode.");
@@ -199,7 +199,7 @@ describe("FormData", () => {
         const value_0 = {
             batch: true,
             product: false,
-            values: [{ id: "dce3", subcollection_type: "subcollectionType", src: "dce" }],
+            values: [{ id: "dce3", map_over_type: "mapOverType", src: "dce" }],
         };
         expect(wrapper.emitted().input[0][0]).toEqual(value_0);
         const message = wrapper.findAll("[data-description='form data label']");
@@ -207,7 +207,7 @@ describe("FormData", () => {
         expect(message.at(0).text()).toBe("1. dceName3 (as dataset collection)");
         const messageSubcollection = wrapper.findAll("[data-description='form data collection type']");
         expect(messageSubcollection.length).toBe(1);
-        expect(messageSubcollection.at(0).text()).toBe("Batch mode input with collection type: subcollectionType.");
+        expect(messageSubcollection.at(0).text()).toBe("Batch mode input with collection type: mapOverType.");
     });
 
     it("dataset collection element as hdca mapped to non-batch field", async () => {
@@ -219,7 +219,7 @@ describe("FormData", () => {
         const value_0 = {
             batch: true,
             product: false,
-            values: [{ id: "dce3", subcollection_type: "subcollectionType", src: "dce" }],
+            values: [{ id: "dce3", map_over_type: "mapOverType", src: "dce" }],
         };
         expect(wrapper.emitted().input[0][0]).toEqual(value_0);
     });
@@ -233,7 +233,7 @@ describe("FormData", () => {
         const value_0 = {
             batch: false,
             product: false,
-            values: [{ id: "hdca4", subcollection_type: null, src: "hdca" }],
+            values: [{ id: "hdca4", map_over_type: null, src: "hdca" }],
         };
         expect(wrapper.emitted().input[0][0]).toEqual(value_0);
     });
@@ -252,8 +252,8 @@ describe("FormData", () => {
             batch: true,
             product: false,
             values: [
-                { id: "dce1", subcollection_type: null, src: "dce" },
-                { id: "dce4", subcollection_type: null, src: "dce" },
+                { id: "dce1", map_over_type: null, src: "dce" },
+                { id: "dce4", map_over_type: null, src: "dce" },
             ],
         };
         expect(wrapper.emitted().input[0][0]).toEqual(value_0);
@@ -270,7 +270,7 @@ describe("FormData", () => {
         expect(wrapper.emitted().input[1][0]).toEqual({
             batch: true,
             product: false,
-            values: [{ id: "hdca4", subcollection_type: null, src: "hdca" }],
+            values: [{ id: "hdca4", map_over_type: null, src: "hdca" }],
         });
         eventStore.setDragData({ id: "hda2", history_content_type: "dataset" });
         dispatchEvent(wrapper, "dragenter");
@@ -278,7 +278,7 @@ describe("FormData", () => {
         expect(wrapper.emitted().input[2][0]).toEqual({
             batch: false,
             product: false,
-            values: [{ id: "hda2", subcollection_type: null, src: "hda" }],
+            values: [{ id: "hda2", map_over_type: null, src: "hda" }],
         });
     });
 
@@ -291,7 +291,7 @@ describe("FormData", () => {
         expect(wrapper.emitted().input[0][0]).toEqual({
             batch: false,
             product: false,
-            values: [{ id: "hda3", subcollection_type: null, src: "hda" }],
+            values: [{ id: "hda3", map_over_type: null, src: "hda" }],
         });
         const noCheckLinked = wrapper.find("input[type='checkbox']");
         expect(noCheckLinked.exists()).toBeFalsy();
@@ -299,7 +299,7 @@ describe("FormData", () => {
         expect(wrapper.emitted().input[1][0]).toEqual({
             batch: true,
             product: false,
-            values: [{ id: "hda3", subcollection_type: null, src: "hda" }],
+            values: [{ id: "hda3", map_over_type: null, src: "hda" }],
         });
         const checkLinked = wrapper.find("input[type='checkbox']");
         expect(wrapper.find(".custom-switch span").text()).toBe(
@@ -313,7 +313,7 @@ describe("FormData", () => {
         expect(wrapper.emitted().input[2][0]).toEqual({
             batch: true,
             product: true,
-            values: [{ id: "hda3", subcollection_type: null, src: "hda" }],
+            values: [{ id: "hda3", map_over_type: null, src: "hda" }],
         });
     });
 
@@ -334,7 +334,7 @@ describe("FormData", () => {
             expect(wrapper.emitted().input[i][0]).toEqual({
                 batch: false,
                 product: false,
-                values: [{ id: "hdca4", subcollection_type: null, src: "hdca" }],
+                values: [{ id: "hdca4", map_over_type: null, src: "hdca" }],
             });
         }
         expect(wrapper.emitted().input.length).toEqual(2);
@@ -346,7 +346,7 @@ describe("FormData", () => {
         expect(wrapper.emitted().input[2][0]).toEqual({
             batch: false,
             product: false,
-            values: [{ id: "hda3", subcollection_type: null, src: "hda" }],
+            values: [{ id: "hda3", map_over_type: null, src: "hda" }],
         });
         const newSelectedValues = wrapper.findAll(SELECTED_VALUE);
         expect(newSelectedValues.at(0).text()).toBe("3: hdaName3");

client/src/components/Form/Elements/FormData/FormData.vue

@@ -181,8 +181,8 @@ const isLDDA = computed(() => {
 const matchedBatchMode = computed(() => {
     const values = matchedValues.value;
     if (variant.value && values.length > 0 && values[0]) {
-        const hasSubcollectionType = values.find((v) => !!v.subcollection_type);
-        if (hasSubcollectionType) {
+        const hasMapOverType = values.find((v) => !!v.map_over_type);
+        if (hasMapOverType) {
             return true;
         }
         const isMultiple = values.length > 1;
@@ -247,7 +247,7 @@ function createValue(val: Array<DataOption> | DataOption | null) {
     if (val) {
         const values = Array.isArray(val) ? val : [val];
         if (variant.value && values.length > 0 && values[0]) {
-            const hasSubcollectionType = values.find((v) => !!v.subcollection_type);
+            const hasMapOverType = values.find((v) => !!v.map_over_type);
             const isMultiple = values.length > 1;
 
             // Determine source representation (uses only the initial value)
@@ -277,12 +277,12 @@ function createValue(val: Array<DataOption> | DataOption | null) {
 
             // Emit new value
             return {
-                batch: batch !== BATCH.DISABLED || !!hasSubcollectionType,
+                batch: batch !== BATCH.DISABLED || !!hasMapOverType,
                 product: batch === BATCH.ENABLED && !currentLinked.value,
                 values: values.map((entry) => ({
                     id: entry.id,
                     src: entry.src,
-                    subcollection_type: entry.subcollection_type || null,
+                    map_over_type: entry.map_over_type || null,
                 })),
             };
         }
@@ -491,8 +491,8 @@ watch(
                     <span>{{ v.name }}</span>
                     <span>(as {{ getSourceLabel(getSourceType(v)) }})</span>
                 </div>
-                <small v-if="v.subcollection_type" class="ml-2" data-description="form data collection type">
-                    Batch mode input with collection type: {{ v.subcollection_type }}.
+                <small v-if="v.map_over_type" class="ml-2" data-description="form data collection type">
+                    Batch mode input with collection type: {{ v.map_over_type }}.
                 </small>
             </div>
         </b-alert>

client/src/components/Form/Elements/FormData/types.ts

@@ -3,8 +3,8 @@ export interface DataOption {
     hid: number;
     is_dataset?: boolean;
     keep: boolean;
+    map_over_type?: string;
     name: string;
     src: string;
-    subcollection_type?: string;
     tags: Array<string>;
 }

lib/galaxy/tools/parameters/basic.py

@@ -2299,7 +2299,7 @@ class DataToolParameter(BaseDataToolParameter):
                 "keep": keep,
             }
             if subcollection_type:
-                value["subcollection_type"] = subcollection_type
+                value["map_over_type"] = subcollection_type
             return list.append(value)
 
         def append_dce(dce):
@@ -2553,8 +2553,8 @@ class DataCollectionToolParameter(BaseDataToolParameter):
             d["options"]["hdca"].append(
                 {
                     "id": trans.security.encode_id(hdca.id),
-                    "subcollection_type": subcollection_type,
                     "hid": hdca.hid,
+                    "map_over_type": subcollection_type,
                     "name": name,
                     "src": "hdca",
                     "tags": [t.user_tname if not t.value else f"{t.user_tname}:{t.value}" for t in hdca.tags],

lib/galaxy/tools/parameters/meta.py

@@ -260,7 +260,7 @@ def __expand_collection_parameter(trans, input_key, incoming_val, collections_to
             if src != "hdca":
                 raise exceptions.ToolMetaParameterException(f"Invalid dataset collection source type {src}")
             encoded_hdc_id = incoming_val["id"]
-            subcollection_type = incoming_val.get("subcollection_type", None)
+            subcollection_type = incoming_val.get("map_over_type", None)
         except TypeError:
             encoded_hdc_id = incoming_val
             subcollection_type = None

lib/galaxy_test/api/test_jobs.py

@@ -841,14 +841,14 @@ steps:
         list_id_a = self.__history_with_ok_collection(collection_type="list:pair", history_id=history_id)
         inputs = json.dumps(
             {
-                "f1": {"batch": True, "values": [{"src": "hdca", "id": list_id_a, "subcollection_type": "paired"}]},
+                "f1": {"batch": True, "values": [{"src": "hdca", "id": list_id_a, "map_over_type": "paired"}]},
             }
         )
         self._job_search(tool_id="collection_paired_test", history_id=history_id, inputs=inputs)
 
     def _get_simple_rerun_params(self, history_id, private=False):
         list_id_a = self.__history_with_ok_collection(collection_type="list:pair", history_id=history_id)
-        inputs = {"f1": {"batch": True, "values": [{"src": "hdca", "id": list_id_a, "subcollection_type": "paired"}]}}
+        inputs = {"f1": {"batch": True, "values": [{"src": "hdca", "id": list_id_a, "map_over_type": "paired"}]}}
         run_response = self._run(
             history_id=history_id,
             tool_id="collection_paired_test",
@@ -907,9 +907,7 @@ steps:
         assert first_element["element_type"] == "dataset_collection"
         assert first_element["element_identifier"] == "test0"
         assert first_element["model_class"] == "DatasetCollectionElement"
-        inputs = {
-            "input1": {"batch": True, "values": [{"src": "hdca", "id": list_list_id, "subcollection_type": "list"}]}
-        }
+        inputs = {"input1": {"batch": True, "values": [{"src": "hdca", "id": list_list_id, "map_over_type": "list"}]}}
         run_response = self._run(
             history_id=history_id,
             tool_id="identifier_collection",

lib/galaxy_test/api/test_tools.py

@@ -609,7 +609,7 @@ class TestToolsApi(ApiTestCase, TestsTools):
             inputs = {
                 "input": {
                     "batch": True,
-                    "values": [{"src": "hdca", "subcollection_type": "paired", "id": hdca_id}],
+                    "values": [{"src": "hdca", "map_over_type": "paired", "id": hdca_id}],
                 }
             }
             response = self._run("__UNZIP_COLLECTION__", history_id, inputs, assert_ok=True)
@@ -795,7 +795,7 @@ class TestToolsApi(ApiTestCase, TestsTools):
             inputs = {
                 "input": {
                     "batch": batch,
-                    "values": [{"subcollection_type": "list:paired", "src": "hdca", "id": failed_hdca_id}],
+                    "values": [{"map_over_type": "list:paired", "src": "hdca", "id": failed_hdca_id}],
                 },
             }
         else:
@@ -1691,7 +1691,7 @@ class TestToolsApi(ApiTestCase, TestsTools):
     @skip_without_tool("output_action_change_format_paired")
     def test_map_over_with_nested_paired_output_format_actions(self, history_id):
         hdca_id = self.__build_nested_list(history_id)
-        inputs = {"input": {"batch": True, "values": [dict(subcollection_type="paired", src="hdca", id=hdca_id)]}}
+        inputs = {"input": {"batch": True, "values": [dict(map_over_type="paired", src="hdca", id=hdca_id)]}}
         create = self._run("output_action_change_format_paired", history_id, inputs).json()
         outputs = create["outputs"]
         jobs = create["jobs"]
@@ -2109,7 +2109,7 @@ class TestToolsApi(ApiTestCase, TestsTools):
     def test_paired_input_map_over_nested_collections(self, history_id):
         hdca_id = self.__build_nested_list(history_id)
         inputs = {
-            "input1": {"batch": True, "values": [dict(subcollection_type="paired", src="hdca", id=hdca_id)]},
+            "input1": {"batch": True, "values": [dict(map_over_type="paired", src="hdca", id=hdca_id)]},
         }
         self.dataset_populator.wait_for_history(history_id, assert_ok=True)
         create = self._run("collection_paired_structured_like", history_id, inputs, assert_ok=True)
@@ -2127,7 +2127,7 @@ class TestToolsApi(ApiTestCase, TestsTools):
         hdca_id = self.__build_nested_list(history_id)
         inputs = {
             "cond|cond_param": "paired",
-            "cond|input1": {"batch": True, "values": [dict(subcollection_type="paired", src="hdca", id=hdca_id)]},
+            "cond|input1": {"batch": True, "values": [dict(map_over_type="paired", src="hdca", id=hdca_id)]},
         }
         self.dataset_populator.wait_for_history(history_id, assert_ok=True)
         create = self._run("collection_paired_conditional_structured_like", history_id, inputs, assert_ok=True)
@@ -2440,7 +2440,7 @@ class TestToolsApi(ApiTestCase, TestsTools):
                 "f1": {"src": "hdca", "id": hdca1_id},
                 "f2": {
                     "batch": True,
-                    "values": [{"src": "hdca", "subcollection_type": "list", "id": hdca2_id}],
+                    "values": [{"src": "hdca", "map_over_type": "list", "id": hdca2_id}],
                 },
             }
             create = self._run("multi_data_param", history_id, inputs, assert_ok=True)
@@ -2569,7 +2569,7 @@ class TestToolsApi(ApiTestCase, TestsTools):
             inputs = {
                 "f1": {
                     "batch": True,
-                    "values": [{"src": "hdca", "subcollection_type": "paired", "id": hdca_list_id}],
+                    "values": [{"src": "hdca", "map_over_type": "paired", "id": hdca_list_id}],
                 }
             }
             self._check_simple_subcollection_mapping(history_id, inputs)
@@ -2598,7 +2598,7 @@ class TestToolsApi(ApiTestCase, TestsTools):
             inputs = {
                 "f1": {
                     "batch": True,
-                    "values": [{"src": "hdca", "subcollection_type": "paired", "id": nested_list_id}],
+                    "values": [{"src": "hdca", "map_over_type": "paired", "id": nested_list_id}],
                 },
                 "f2": {
                     "batch": True,
@@ -2975,7 +2975,7 @@ class TestToolsApi(ApiTestCase, TestsTools):
         dataset_collection = self.dataset_collection_populator.wait_for_fetched_collection(fetch_response)
         hdca_id = dataset_collection["id"]
         inputs = {
-            "input1": {"batch": True, "values": [dict(subcollection_type="paired", src="hdca", id=hdca_id)]},
+            "input1": {"batch": True, "values": [dict(map_over_type="paired", src="hdca", id=hdca_id)]},
         }
         self.dataset_populator.wait_for_history(history_id, assert_ok=True)
         create = self._run("collection_paired_structured_like", history_id, inputs, assert_ok=True)