[26.0] Hide hidden tools in the tool form

client/src/components/Tool/ToolCard.vue

@@ -116,8 +116,16 @@ const { isOnlyPreference } = useStorageLocationConfiguration();
 const { currentUser, isAnonymous } = storeToRefs(useUserStore());
 const { isLoaded: isConfigLoaded, config } = storeToRefs(useConfigStore());
 const hasUser = computed(() => !isAnonymous.value);
-const versions = computed(() => props.options.versions);
-const showVersions = computed(() => props.options.versions?.length > 1);
+const versions = computed(() => props.options.versions ?? []);
+const hiddenVersions = computed(() => props.options.hidden_versions ?? []);
+const visibleVersions = computed(() => {
+    const filtered = versions.value.filter((v) => !hiddenVersions.value.includes(v));
+    if (props.version && !filtered.includes(props.version) && versions.value.includes(props.version)) {
+        filtered.push(props.version);
+    }
+    return filtered;
+});
+const showVersions = computed(() => visibleVersions.value.length > 1);
 
 const storageLocationModalTitle = computed(() => {
     if (isOnlyPreference.value) {
@@ -164,7 +172,7 @@ onBeforeMount(() => {
                 <ToolVersionsButton
                     v-if="showVersions"
                     :version="props.version"
-                    :versions="versions"
+                    :versions="visibleVersions"
                     @onChangeVersion="onChangeVersion" />
                 <ToolOptionsButton
                     :id="props.id"

lib/galaxy/tools/__init__.py

@@ -189,7 +189,6 @@
 from galaxy.tools.parameters.wrapped_json import json_wrap
 from galaxy.util import (
     in_directory,
-    listify,
     Params,
     parse_xml_string,
     rst_to_html,
@@ -202,7 +201,6 @@
 from galaxy.util.compression_utils import get_fileobj_raw
 from galaxy.util.dictifiable import UsesDictVisibleKeys
 from galaxy.util.expressions import ExpressionContext
-from galaxy.util.form_builder import SelectField
 from galaxy.util.json import (
     safe_loads,
     swap_inf_nan,
@@ -687,33 +685,6 @@ def create_dynamic_tool(self, dynamic_tool: "DynamicTool") -> "Tool":
             tool.name = tool.id
         return tool
 
-    def get_tool_components(self, tool_id, tool_version=None, get_loaded_tools_by_lineage=False, set_selected=False):
-        """
-        Retrieve all loaded versions of a tool from the toolbox and return a select list enabling
-        selection of a different version, the list of the tool's loaded versions, and the specified tool.
-        """
-        tool_version_select_field = None
-        tools = []
-        tool = None
-        # Backwards compatibility for datasource tools that have default tool_id configured, but which
-        # are now using only GALAXY_URL.
-        tool_ids = listify(tool_id)
-        for tool_id in tool_ids:
-            if tool_id.endswith("/"):
-                # Some data sources send back redirects ending with `/`, this takes care of that case
-                tool_id = tool_id[:-1]
-            if get_loaded_tools_by_lineage:
-                tools = self.get_loaded_tools_by_lineage(tool_id)
-            else:
-                tools = self.get_tool(tool_id, tool_version=tool_version, get_all_versions=True)
-            if tools:
-                tool = self.get_tool(tool_id, tool_version=tool_version, get_all_versions=False)
-                assert tool
-                if len(tools) > 1:
-                    tool_version_select_field = self.__build_tool_version_select_field(tools, tool.id, set_selected)
-                break
-        return tool_version_select_field, tools, tool
-
     def _path_template_kwds(self):
         return {
             "model_tools_path": MODEL_TOOLS_PATH,
@@ -763,20 +734,6 @@ def _load_workflow(self, workflow_id: str) -> "Workflow":
         stored = session.get_one(StoredWorkflow, id)
         return stored.latest_workflow
 
-    def __build_tool_version_select_field(self, tools, tool_id, set_selected):
-        """Build a SelectField whose options are the ids for the received list of tools."""
-        options: list[tuple[str, str]] = []
-        for tool in tools:
-            options.insert(0, (tool.version, tool.id))
-        select_field = SelectField(name="tool_id")
-        for option_tup in options:
-            selected = set_selected and option_tup[1] == tool_id
-            if selected:
-                select_field.add_option(f"version {option_tup[0]}", option_tup[1], selected=True)
-            else:
-                select_field.add_option(f"version {option_tup[0]}", option_tup[1])
-        return select_field
-
 
 class DefaultToolState:
     """
@@ -1166,6 +1123,18 @@ def tool_versions(self):
         else:
             return []
 
+    @property
+    def hidden_tool_versions(self):
+        if not self.lineage or not self.id:
+            return []
+        versions_by_id = self.app.toolbox._tool_versions_by_id.get(self.id, {})
+        hidden_versions = []
+        for version in self.lineage.tool_versions:
+            tool = versions_by_id.get(version)
+            if tool and tool.hidden:
+                hidden_versions.append(version)
+        return hidden_versions
+
     @property
     def is_latest_version(self):
         tool_versions = self.tool_versions
@@ -2967,6 +2936,8 @@ def to_dict(self, trans, link_details=False, io_details=False, tool_help=False):
         tool_dict["hidden"] = self.hidden
         tool_dict["is_workflow_compatible"] = self.is_workflow_compatible
         tool_dict["xrefs"] = self.xrefs
+        tool_dict["versions"] = self.tool_versions
+        tool_dict["hidden_versions"] = self.hidden_tool_versions
 
         if self.dynamic_tool:
             tool_dict["uuid"] = str(self.dynamic_tool.uuid)
@@ -3120,6 +3091,7 @@ def to_json(
                 "message": tool_message,
                 "warnings": tool_warnings,
                 "versions": self.tool_versions,
+                "hidden_versions": self.hidden_tool_versions,
                 "requirements": [{"name": r.name, "version": r.version} for r in self.requirements],
                 "credentials": [credential.to_dict() for credential in self.credentials] if self.credentials else [],
                 "errors": state_errors,
@@ -3220,9 +3192,8 @@ def _compare_tool_version(self, job: Job):
             return None
         message = ""
         try:
-            select_field, tools, tool = self.app.toolbox.get_tool_components(
-                tool_id, tool_version=tool_version, get_loaded_tools_by_lineage=False, set_selected=True
-            )
+            tools = self.app.toolbox.get_tool(tool_id, tool_version=tool_version, get_all_versions=True) or []
+            tool = self.app.toolbox.get_tool(tool_id, tool_version=tool_version) if tools else None
             if tool is None:
                 raise exceptions.MessageException(
                     f"This dataset was created by an obsolete tool ({tool_id}). Can't re-run."

lib/galaxy/webapps/galaxy/controllers/tool_runner.py

@@ -37,11 +37,10 @@ def default(self, trans, tool_id=None, **kwd):
         """Catches the tool id and redirects as needed"""
         return self.index(trans, tool_id=tool_id, **kwd)
 
-    def __get_tool(self, tool_id, tool_version=None, get_loaded_tools_by_lineage=False, set_selected=False):
-        tool_version_select_field, tools, tool = self.get_toolbox().get_tool_components(
-            tool_id, tool_version, get_loaded_tools_by_lineage, set_selected
-        )
-        return tool
+    def __get_tool(self, tool_id, tool_version=None):
+        # Some data sources send back redirects ending with `/`, this takes care of that case
+        tool_id = tool_id.rstrip("/")
+        return self.get_toolbox().get_tool(tool_id, tool_version=tool_version)
 
     @web.expose
     def index(self, trans, tool_id=None, from_noframe=None, **kwd):

lib/galaxy_test/api/test_tools.py

@@ -1653,6 +1653,28 @@ def test_show_with_wrong_tool_version_in_tool_id(self):
         # Return last version
         assert tool_info["version"] == "0.2"
 
+    @skip_without_tool("multiple_versions_hidden")
+    def test_show_lists_hidden_versions_separately(self):
+        tool_info = self._show_valid_tool("multiple_versions_hidden", tool_version="0.1")
+        assert tool_info["version"] == "0.1"
+        assert tool_info["versions"] == ["0.1", "0.2"]
+        assert tool_info["hidden_versions"] == ["0.1"]
+
+    @skip_without_tool("multiple_versions_hidden")
+    def test_run_hidden_version(self):
+        with self.dataset_populator.test_history_for(self.test_run_hidden_version) as history_id:
+            outputs = self._run(
+                tool_id="multiple_versions_hidden",
+                history_id=history_id,
+                tool_version="0.1",
+                assert_ok=True,
+                wait_for_job=True,
+            )
+            assert len(outputs["outputs"]) == 1
+            output = outputs["outputs"][0]
+            output_content = self.dataset_populator.get_history_dataset_content(history_id, dataset=output)
+            assert output_content.strip() == "Hidden Version 0.1"
+
     @skip_without_tool("cat1")
     def test_run_cat1_single_meta_wrapper(self):
         with self.dataset_populator.test_history_for(self.test_run_cat1_single_meta_wrapper) as history_id:

test/functional/tools/multiple_versions_hidden_v01.xml

@@ -0,0 +1,11 @@
+<tool id="multiple_versions_hidden" name="multiple_versions_hidden" version="0.1">
+    <command><![CDATA[
+        echo "Hidden Version 0.1" > '$out_file1'
+    ]]></command>
+    <inputs>
+        <param name="inttest" value="1" type="integer" />
+    </inputs>
+    <outputs>
+        <data name="out_file1" format="txt" />
+    </outputs>
+</tool>

test/functional/tools/multiple_versions_hidden_v02.xml

@@ -0,0 +1,11 @@
+<tool id="multiple_versions_hidden" name="multiple_versions_hidden" version="0.2">
+    <command><![CDATA[
+        echo "Hidden Version 0.2" > '$out_file1'
+    ]]></command>
+    <inputs>
+        <param name="inttest" value="1" type="integer" />
+    </inputs>
+    <outputs>
+        <data name="out_file1" format="txt" />
+    </outputs>
+</tool>

test/functional/tools/sample_tool_conf.xml

@@ -247,6 +247,8 @@
   <tool file="multiple_versions_v01.xml" />
   <tool file="multiple_versions_v01galaxy6.xml" />
   <tool file="multiple_versions_v02.xml" />
+  <tool file="multiple_versions_hidden_v01.xml" hidden="true" />
+  <tool file="multiple_versions_hidden_v02.xml" />
   <section id="test_section_multi" name="Test Section with Multiple Versions">
     <tool file="multiple_versions_v01.xml" />
     <tool file="multiple_versions_v01galaxy6.xml" />