Restore deprecated ToolsApi and create new api route for new panel st…

…ructure

- restore `api/tools` that had the older (list of tool sections
  with `.elems`) structure
- but use the new `api/tool_panel` structure in the client

client/src/components/Panels/ToolBox.test.js

@@ -26,9 +26,9 @@ describe("ToolBox", () => {
 
     it("test filter functions correctly matching: (1) Tools store array-of-objects with (2) Results array", async () => {
         axiosMock
-            .onGet(`/api/tools`)
+            .onGet(`/api/tool_panel`)
             .replyOnce(200, toolsListInPanel)
-            .onGet(`/api/tools?in_panel=False`)
+            .onGet(`/api/tool_panel?in_panel=False`)
             .replyOnce(200, toolsMock)
             .onGet(/api\/tools?.*/)
             .replyOnce(200, resultsMock);

client/src/components/ToolsView/ToolsSchemaJson/ToolsJson.test.js

@@ -18,8 +18,8 @@ describe("ToolSchemaJson/ToolsView.vue", () => {
 
     beforeEach(async () => {
         axiosMock = new MockAdapter(axios);
-        axiosMock.onGet("/api/tools?in_panel=False&tool_help=True").reply(200, testToolsListResponse);
-        axiosMock.onGet("/api/tools").reply(200, testToolsListInPanelResponse);
+        axiosMock.onGet("/api/tool_panel?in_panel=False&tool_help=True").reply(200, testToolsListResponse);
+        axiosMock.onGet("/api/tool_panel").reply(200, testToolsListInPanelResponse);
         wrapper = shallowMount(ToolsJson, { localVue });
         await flushPromises();
     });

client/src/components/ToolsView/ToolsSchemaJson/ToolsJson.vue

@@ -13,7 +13,7 @@ export default {
     async created() {
         let tools = {};
         await axios
-            .get(`${getAppRoot()}api/tools?in_panel=False&tool_help=True`)
+            .get(`${getAppRoot()}api/tool_panel?in_panel=False&tool_help=True`)
             .then(({ data }) => {
                 tools = data.tools;
             })
@@ -22,7 +22,7 @@ export default {
             });
         if (Object.keys(tools).length > 0) {
             await axios
-                .get(`${getAppRoot()}api/tools`)
+                .get(`${getAppRoot()}api/tool_panel`)
                 .then(({ data }) => {
                     this.schemaTagObj = this.createToolsJson(tools, data.default);
                     const el = document.createElement("script");

client/src/components/Toolshed/RepositoryDetails/Index.test.js

@@ -34,7 +34,7 @@ Services.mockImplementation(() => {
 describe("RepositoryDetails", () => {
     it("test repository details index", async () => {
         const axiosMock = new MockAdapter(axios);
-        axiosMock.onGet("api/tools?in_panel=true&view=default").reply(200, {});
+        axiosMock.onGet("api/tool_panel?in_panel=true&view=default").reply(200, {});
         mockFetcher.path("/api/configuration").method("get").mock({ data: {} });
         const localVue = getLocalVue();
         const pinia = createPinia();

client/src/store/index.js

@@ -14,7 +14,6 @@ import { datasetPathDestinationStore } from "./datasetPathDestinationStore";
 import { gridSearchStore } from "./gridSearchStore";
 import { invocationStore } from "./invocationStore";
 import { jobDestinationParametersStore } from "./jobDestinationParametersStore";
-import { panelStore } from "./panelStore";
 import { syncVuextoGalaxy } from "./syncVuextoGalaxy";
 import { tagStore } from "./tagStore";
 
@@ -48,7 +47,6 @@ export function createStore() {
             datasetPathDestination: datasetPathDestinationStore,
             invocations: invocationStore,
             gridSearch: gridSearchStore,
-            panels: panelStore,
             tags: tagStore,
         },
     };

client/src/stores/toolStore.ts

@@ -156,7 +156,7 @@ export const useToolStore = defineStore("toolStore", () => {
         if (!loading.value && !allToolsByIdFetched.value) {
             loading.value = true;
             await axios
-                .get(`${getAppRoot()}api/tools?in_panel=False`)
+                .get(`${getAppRoot()}api/tool_panel?in_panel=False`)
                 .then(({ data }) => {
                     saveAllTools(data.tools);
                     loading.value = false;
@@ -177,7 +177,7 @@ export const useToolStore = defineStore("toolStore", () => {
                 currentPanelView.value = panelView;
             }
             await axios
-                .get(`${getAppRoot()}api/tools?in_panel=true&view=${panelView}`)
+                .get(`${getAppRoot()}api/tool_panel?in_panel=true&view=${panelView}`)
                 .then(({ data }) => {
                     loading.value = false;
                     savePanelView(panelView, data[panelView]);
@@ -199,14 +199,14 @@ export const useToolStore = defineStore("toolStore", () => {
                 return;
             }
             loading.value = true;
-            const { data } = await axios.get(`${getAppRoot()}api/tools?in_panel=true&view=${panelView}`);
+            const { data } = await axios.get(`${getAppRoot()}api/tool_panel?in_panel=true&view=${panelView}`);
             savePanelView(panelView, data[panelView]);
             loading.value = false;
         }
     }
 
     async function fetchPanel(panelView: string) {
-        const { data } = await axios.get(`${getAppRoot()}api/tools?in_panel=true&view=${panelView}`);
+        const { data } = await axios.get(`${getAppRoot()}api/tool_panel?in_panel=true&view=${panelView}`);
         savePanelView(panelView, data[panelView]);
     }
 

lib/galaxy/webapps/galaxy/api/tools.py

@@ -167,6 +167,62 @@ def index(self, trans: GalaxyWebTransaction, **kwds):
             detected_versions = self.service._detect(trans, tool_id)
             return detected_versions
 
+        # Return everything.
+        try:
+            return self.app.toolbox.to_dict(
+                trans, in_panel=in_panel, trackster=trackster, tool_help=tool_help, view=view
+            )
+        except exceptions.MessageException:
+            raise
+        except Exception:
+            raise exceptions.InternalServerError("Error: Could not convert toolbox to dictionary")
+
+    @expose_api_anonymous_and_sessionless
+    def panel_view(self, trans: GalaxyWebTransaction, **kwds):
+        """
+        GET /api/tool_panel
+
+        returns a dictionary of all tools or panels defined by parameters
+
+        :param in_panel: if true, tool sections are returned in panel
+                         structure, with tool ids and labels
+        :param view: ToolBox view to apply (default is 'default')
+        :param trackster: if true, only tools that are compatible with
+                          Trackster are returned
+        :param q: if present search on the given query will be performed
+        :param tool_id: if present the given tool_id will be searched for
+                        all installed versions
+        """
+
+        # Read params.
+        in_panel = util.string_as_bool(kwds.get("in_panel", "True"))
+        trackster = util.string_as_bool(kwds.get("trackster", "False"))
+        q = kwds.get("q", "")
+        tool_id = kwds.get("tool_id", "")
+        tool_help = util.string_as_bool(kwds.get("tool_help", "False"))
+        view = kwds.get("view", None)
+
+        # Find whether to search.
+        if q:
+            hits = self.service._search(q, view)
+            results = []
+            if hits:
+                for hit in hits:
+                    try:
+                        tool = self.service._get_tool(trans, hit, user=trans.user)
+                        if tool:
+                            results.append(tool.id)
+                    except exceptions.AuthenticationFailed:
+                        pass
+                    except exceptions.ObjectNotFound:
+                        pass
+            return results
+
+        # Find whether to detect.
+        if tool_id:
+            detected_versions = self.service._detect(trans, tool_id)
+            return detected_versions
+
         # Return everything.
         try:
             return self.app.toolbox.to_panel_view(

lib/galaxy/webapps/galaxy/buildapp.py

@@ -367,6 +367,7 @@ def populate_api_routes(webapp, app):
     # ====== TOOLS API ======
     # =======================
 
+    webapp.mapper.connect("/api/tool_panel", action="panel_view", controller="tools")
     webapp.mapper.connect("/api/tools/all_requirements", action="all_requirements", controller="tools")
     webapp.mapper.connect("/api/tools/error_stack", action="error_stack", controller="tools")
     webapp.mapper.connect("/api/tools/{id:.+?}/build", action="build", controller="tools")

lib/galaxy_test/api/test_tools.py

@@ -164,7 +164,7 @@ def test_search_grep(self):
         assert "Grep1" in get_response
 
     def test_no_panel_index(self):
-        index = self._get("tools", data=dict(in_panel=False))
+        index = self._get("tool_panel", data=dict(in_panel=False))
         tools_index = index.json().get("tools", {})
         # No need to flatten out sections, with in_panel=False, only tools by
         # ids are returned.
@@ -2640,7 +2640,7 @@ def _run_cat1(self, history_id, inputs, assert_ok=False, **kwargs):
         return self._run("cat1", history_id, inputs, assert_ok=assert_ok, **kwargs)
 
     def __tool_ids(self):
-        index = self._get("tools")
+        index = self._get("tool_panel")
         tools_index = index.json().get("default", {})
         # In panels by default, so flatten out sections...
         tool_ids = []

lib/galaxy_test/base/populators.py

@@ -154,7 +154,7 @@ def skip_without_tool(tool_id: str):
     def method_wrapper(method):
         def get_tool_ids(api_test_case: HasAnonymousGalaxyInteractor):
             interactor = api_test_case.anonymous_galaxy_interactor
-            index = interactor.get("tools", data=dict(in_panel=False))
+            index = interactor.get("tool_panel", data=dict(in_panel=False))
             api_asserts.assert_status_code_is_ok(index, "Failed to fetch toolbox for target Galaxy.")
             tools = index.json().get("tools", {})
             # `in_panel=False`, so we have a toolsById dict...
@@ -2287,7 +2287,7 @@ def _run_cwl_tool_job(
 
         if os.path.exists(tool_id):
             raw_tool_id = os.path.basename(tool_id)
-            index = self.dataset_populator._get("tools", data=dict(in_panel=False))
+            index = self.dataset_populator._get("tool_panel", data=dict(in_panel=False))
             index.raise_for_status()
             tools = index.json().get("tools", {})
             tool_ids = list(tools.keys())

lib/tool_shed/test/functional/test_galaxy_install.py

@@ -10,7 +10,7 @@ def test_install_simple_tool(self):
         installable_revisions = populator.get_ordered_installable_revisions(owner, name)
         latest_install_revision = installable_revisions.__root__[-1]
         self.install_repository(owner, name, latest_install_revision, tool_shed_url=self.url)
-        response = self.galaxy_interactor._get("tools?in_panel=False")
+        response = self.galaxy_interactor._get("tool_panel?in_panel=False")
         response.raise_for_status()
         expected_tool = populator.tool_guid(self, repository, "Add_a_column1", "1.1.0")
         tool_ids = list((response.json().get("tools", {})).keys())
@@ -26,7 +26,7 @@ def test_install_simple_after_repository_metadata_reset(self):
         metadata_response = populator.reset_metadata(repository)
         assert metadata_response.status == "ok"
         self.install_repository(owner, name, latest_install_revision, tool_shed_url=self.url)
-        response = self.galaxy_interactor._get("tools?in_panel=False")
+        response = self.galaxy_interactor._get("tool_panel?in_panel=False")
         response.raise_for_status()
         expected_tool = f"{self.host}:{self.port}/repos/{owner}/{name}/Add_a_column1/1.1.0"
         tool_ids = list((response.json().get("tools", {})).keys())

test/integration/test_edam_toolbox.py

@@ -10,7 +10,7 @@ def handle_galaxy_config_kwds(cls, config):
         config["edam_panel_views"] = "merged"
 
     def test_edam_toolbox(self):
-        index = self.galaxy_interactor.get("tools", data=dict(in_panel=True, view="ontology:edam_merged"))
+        index = self.galaxy_interactor.get("tool_panel", data=dict(in_panel=True, view="ontology:edam_merged"))
         index.raise_for_status()
         index_panel = index.json().get("ontology:edam_merged", {})
         sections = [x for _, x in index_panel.items() if x["model_class"] == "ToolSection"]
@@ -40,7 +40,7 @@ def handle_galaxy_config_kwds(cls, config):
         config["default_panel_view"] = "ontology:edam_topics"
 
     def test_edam_toolbox(self):
-        index = self.galaxy_interactor.get("tools", data=dict(in_panel=True))
+        index = self.galaxy_interactor.get("tool_panel", data=dict(in_panel=True))
         index.raise_for_status()
         index_panel = index.json().get("ontology:edam_topics", {})
         sections = [x for _, x in index_panel.items() if x["model_class"] == "ToolSection"]