Merge branch 'release_24.1' into dev

client/src/components/Workflow/Editor/Actions/stepActions.ts

@@ -423,34 +423,46 @@ export function useStepActions(
         }
     }
 
+    interface ChangeValueOrCreateActionOptions<K extends keyof Step> {
+        step: Step;
+        key: K;
+        value: Step[K];
+        name?: string;
+        actionConstructor?: () => LazyMutateStepAction<K>;
+        keepActionAlive?: boolean;
+        timeout?: number;
+    }
+
     /**
      * Mutates a queued lazy action, if a matching one exists,
      * otherwise creates a new lazy action ans queues it.
      */
     function changeValueOrCreateAction<K extends keyof Step>(
-        step: Step,
-        key: K,
-        value: Step[K],
-        name?: string,
-        actionConstructor?: () => LazyMutateStepAction<K>
+        options: ChangeValueOrCreateActionOptions<K>
     ): InstanceType<typeof LazyMutateStepAction<K>> {
+        const { step, key, value, name, keepActionAlive, timeout } = options;
         const actionForKey = actionForIdAndKey(step.id, key);
 
         if (actionForKey) {
             actionForKey.changeValue(value);
 
+            if (keepActionAlive) {
+                undoRedoStore.setLazyActionTimeout(timeout);
+            }
+
             return actionForKey;
         } else {
-            actionConstructor =
-                actionConstructor ?? (() => new LazyMutateStepAction(stepStore, step.id, key, step[key], value));
+            const actionConstructor =
+                options.actionConstructor ??
+                (() => new LazyMutateStepAction(stepStore, step.id, key, step[key], value));
 
             const action = actionConstructor();
 
             if (name) {
                 action.name = name;
             }
 
-            undoRedoStore.applyLazyAction(action);
+            undoRedoStore.applyLazyAction(action, timeout);
 
             action.onUndoRedo = () => {
                 stateStore.activeNodeId = step.id;
@@ -462,11 +474,11 @@ export function useStepActions(
     }
 
     function setPosition(step: Step, position: NonNullable<Step["position"]>) {
-        changeValueOrCreateAction(step, "position", position, "change step position");
+        changeValueOrCreateAction({ step, key: "position", value: position, name: "change step position" });
     }
 
     function setAnnotation(step: Step, annotation: Step["annotation"]) {
-        changeValueOrCreateAction(step, "annotation", annotation, "modify step annotation");
+        changeValueOrCreateAction({ step, key: "annotation", value: annotation, name: "modify step annotation" });
     }
 
     function setOutputLabel(
@@ -478,18 +490,28 @@ export function useStepActions(
         const actionConstructor = () =>
             new LazySetOutputLabelAction(stepStore, stateStore, step.id, fromLabel, toLabel, workflowOutputs);
 
-        changeValueOrCreateAction(
+        changeValueOrCreateAction({
             step,
-            "workflow_outputs",
-            workflowOutputs,
-            "modify step output label",
-            actionConstructor
-        );
+            key: "workflow_outputs",
+            value: workflowOutputs,
+            name: "modify step output label",
+            actionConstructor,
+            keepActionAlive: true,
+            timeout: 2000,
+        });
     }
 
     function setLabel(step: Step, label: Step["label"]) {
         const actionConstructor = () => new LazySetLabelAction(stepStore, stateStore, step.id, step.label, label);
-        changeValueOrCreateAction(step, "label", label, "modify step label", actionConstructor);
+        changeValueOrCreateAction({
+            step,
+            key: "label",
+            value: label,
+            name: "modify step label",
+            actionConstructor,
+            keepActionAlive: true,
+            timeout: 2000,
+        });
     }
 
     const { refresh } = useRefreshFromStore();

client/src/stores/undoRedoStore/index.ts

@@ -108,7 +108,7 @@ export const useUndoRedoStore = defineScopedStore("undoRedoStore", () => {
         }
     }
 
-    function setLazyActionTimeout(timeout: number) {
+    function setLazyActionTimeout(timeout = 1000) {
         clearTimeout(lazyActionTimeout);
         lazyActionTimeout = setTimeout(() => flushLazyAction(), timeout);
     }

client/src/utils/mountVueComponent.js

@@ -4,8 +4,12 @@
 
 import BootstrapVue from "bootstrap-vue";
 import { iconPlugin, localizationPlugin, vueRxShortcutPlugin } from "components/plugins";
+import { createPinia, PiniaVuePlugin } from "pinia";
 import Vue from "vue";
 
+// Load Pinia
+Vue.use(PiniaVuePlugin);
+
 // Bootstrap components
 Vue.use(BootstrapVue);
 
@@ -18,15 +22,18 @@ Vue.use(vueRxShortcutPlugin);
 // font-awesome svg icon registration/loading
 Vue.use(iconPlugin);
 
+// Create Pinia
+const pinia = createPinia();
+
 export const mountVueComponent = (ComponentDefinition) => {
     const component = Vue.extend(ComponentDefinition);
-    return (propsData, el) => new component({ propsData, el });
+    return (propsData, el) => new component({ propsData, el, pinia });
 };
 
 export const replaceChildrenWithComponent = (el, ComponentDefinition, propsData = {}) => {
     const container = document.createElement("div");
     el.replaceChildren(container);
     const component = Vue.extend(ComponentDefinition);
-    const mountFn = (propsData, el) => new component({ propsData, el });
+    const mountFn = (propsData, el) => new component({ propsData, el, pinia });
     return mountFn(propsData, container);
 };

lib/galaxy/app.py

@@ -28,6 +28,7 @@
     jobs,
     tools,
 )
+from galaxy.carbon_emissions import get_carbon_intensity_entry
 from galaxy.celery.base_task import (
     GalaxyTaskBeforeStart,
     GalaxyTaskBeforeStartUserRateLimitPostgres,
@@ -556,6 +557,10 @@ def __init__(self, configure_logging=True, use_converters=True, use_display_appl
         self.application_stack = self._register_singleton(ApplicationStack, application_stack_instance(app=self))
         if configure_logging:
             config.configure_logging(self.config, self.application_stack.facts)
+        # Carbon emissions configuration
+        carbon_intensity_entry = get_carbon_intensity_entry(self.config.geographical_server_location_code)
+        self.carbon_intensity = carbon_intensity_entry["carbon_intensity"]
+        self.geographical_server_location_name = carbon_intensity_entry["location_name"]
         # Initialize job metrics manager, needs to be in place before
         # config so per-destination modifications can be made.
         self.job_metrics = self._register_singleton(

lib/galaxy/config/__init__.py

@@ -34,7 +34,6 @@
 
 import yaml
 
-from galaxy.carbon_emissions import get_carbon_intensity_entry
 from galaxy.config.schema import AppSchema
 from galaxy.exceptions import ConfigurationError
 from galaxy.util import (
@@ -700,15 +699,13 @@ class GalaxyAppConfiguration(BaseAppConfiguration, CommonConfigurationMixin):
 
     allowed_origin_hostnames: List[str]
     builds_file_path: str
-    carbon_intensity: float
     container_resolvers_config_file: str
     database_connection: str
     drmaa_external_runjob_script: str
     email_from: Optional[str]
     enable_tool_shed_check: bool
     galaxy_data_manager_data_path: str
     galaxy_infrastructure_url: str
-    geographical_server_location_name: str
     hours_between_check: int
     integrated_tool_panel_config: str
     involucro_path: str
@@ -814,11 +811,6 @@ def _process_config(self, kwargs: Dict[str, Any]) -> None:
         else:
             self.version_extra = extra_info
 
-        # Carbon emissions configuration
-        carbon_intensity_entry = get_carbon_intensity_entry(kwargs.get("geographical_server_location_code", ""))
-        self.carbon_intensity = carbon_intensity_entry["carbon_intensity"]
-        self.geographical_server_location_name = carbon_intensity_entry["location_name"]
-
         # Database related configuration
         self.check_migrate_databases = string_as_bool(kwargs.get("check_migrate_databases", True))
         if not self.database_connection:  # Provide default if not supplied by user

lib/galaxy/managers/configuration.py

@@ -183,8 +183,8 @@ def _config_is_truthy(item, key, **context):
             "interactivetools_enable": _use_config,
             "aws_estimate": _use_config,
             "carbon_emission_estimates": _defaults_to(True),
-            "carbon_intensity": _use_config,
-            "geographical_server_location_name": _use_config,
+            "carbon_intensity": lambda item, key, **context: self.app.carbon_intensity,
+            "geographical_server_location_name": lambda item, key, **context: self.app.geographical_server_location_name,
             "geographical_server_location_code": _use_config,
             "power_usage_effectiveness": _use_config,
             "message_box_content": _use_config,

lib/galaxy/structured_app.py

@@ -101,8 +101,10 @@ class MinimalApp(BasicSharedApp):
 
 class MinimalManagerApp(MinimalApp):
     # Minimal App that is sufficient to run Celery tasks
+    carbon_intensity: float
     file_sources: ConfiguredFileSources
     genome_builds: GenomeBuilds
+    geographical_server_location_name: str
     dataset_collection_manager: "DatasetCollectionManager"
     tool_data_tables: "ToolDataTableManager"
     history_manager: "HistoryManager"

packages/app/pytest.ini

@@ -0,0 +1 @@
+../package-pytest.ini

packages/auth/pytest.ini

@@ -0,0 +1 @@
+../package-pytest.ini

packages/config/pytest.ini

@@ -0,0 +1 @@
+../package-pytest.ini

packages/data/pytest.ini

@@ -0,0 +1 @@
+../package-pytest.ini

packages/files/pytest.ini

@@ -0,0 +1 @@
+../package-pytest.ini

packages/job_execution/pytest.ini

@@ -0,0 +1 @@
+../package-pytest.ini

packages/job_metrics/pytest.ini

@@ -0,0 +1 @@
+../package-pytest.ini

packages/meta/pytest.ini

@@ -0,0 +1 @@
+../package-pytest.ini

packages/navigation/pytest.ini

@@ -0,0 +1 @@
+../package-pytest.ini

packages/objectstore/pytest.ini

@@ -0,0 +1 @@
+../package-pytest.ini

packages/package-pytest.ini

@@ -0,0 +1,6 @@
+[pytest]
+# Prevent execution of alembic/env.py at test collection stage (alembic.context not set).
+# Also ignore functional tests (galaxy_test/ and tool_shed/test/).
+addopts = --doctest-modules --ignore=galaxy/model/migrations/alembic/ --ignore=galaxy/tools/bundled/ --ignore=galaxy_test/ --ignore=tool_shed/test/ --ignore=tool_shed/webapp/model/migrations/alembic/ --doctest-continue-on-failure --verbosity=1
+asyncio_mode = auto
+log_level = DEBUG

packages/schema/pytest.ini

@@ -0,0 +1 @@
+../package-pytest.ini

packages/selenium/pytest.ini

@@ -0,0 +1 @@
+../package-pytest.ini

packages/test.sh

@@ -63,11 +63,8 @@ while read -r package_dir || [ -n "$package_dir" ]; do  # https://stackoverflow.
     else
         marker_args=()
     fi
-    # Prevent execution of alembic/env.py at test collection stage (alembic.context not set)
-    # Also ignore functional tests (galaxy_test/ and tool_shed/test/).
-    unit_extra=(--doctest-modules --ignore=galaxy/model/migrations/alembic/ --ignore=galaxy_test/ --ignore=tool_shed/test/ --ignore=tool_shed/webapp/model/migrations/alembic/ "${marker_args[@]}")
     # Ignore exit code 5 (no tests ran)
-    pytest "${unit_extra[@]}" . || test $? -eq 5
+    pytest "${marker_args[@]}" . || test $? -eq 5
     if [ $FOR_PULSAR -eq 0 ]; then
         make mypy
     fi

packages/test_api/pytest.ini

@@ -0,0 +1 @@
+../package-pytest.ini

packages/test_base/pytest.ini

@@ -0,0 +1 @@
+../package-pytest.ini

packages/test_driver/pytest.ini

@@ -0,0 +1 @@
+../package-pytest.ini

packages/test_driver/setup.cfg

@@ -40,8 +40,6 @@ install_requires =
     galaxy-util
     galaxy-web-apps
     pytest
-    graphene-sqlalchemy==3.0.0rc1  # these are only needed by tool shed - which we've split out but the test driver loads
-    starlette-graphene3
 packages = find:
 python_requires = >=3.8
 

packages/test_selenium/pytest.ini

@@ -0,0 +1 @@
+../package-pytest.ini

packages/tool_shed/MANIFEST.in

@@ -1 +1,2 @@
 include *.rst *.txt LICENSE */py.typed
+graft tool_shed/webapp/templates/

packages/tool_shed/pytest.ini

@@ -0,0 +1 @@
+../package-pytest.ini

packages/tool_shed/setup.cfg

@@ -32,8 +32,33 @@ version = 23.2.dev0
 [options]
 include_package_data = True
 install_requires =
+    galaxy-app
+    galaxy-auth
+    galaxy-config
+    galaxy-data
+    galaxy-util
+    galaxy-web-framework
     galaxy-web-stack
     galaxy-web-apps
+    a2wsgi
+    alembic
+    fastapi>=0.101.0
+    graphene
+    graphene-sqlalchemy>=3.0.0rc1
+    graphql-core
+    Mako
+    MarkupSafe
+    mercurial
+    Paste
+    pydantic>=2,!=2.6.0,!=2.6.1
+    Routes
+    SQLAlchemy>=2.0,<2.1
+    starlette
+    starlette-context
+    starlette-graphene3
+    typing-extensions
+    WebOb
+    Whoosh
 packages = find:
 python_requires = >=3.8
 

packages/tool_util/pytest.ini

@@ -0,0 +1 @@
+../package-pytest.ini

packages/tours/pytest.ini

@@ -0,0 +1 @@
+../package-pytest.ini

packages/util/pytest.ini

@@ -0,0 +1 @@
+../package-pytest.ini

packages/web_apps/MANIFEST.in

@@ -7,5 +7,3 @@ prune galaxy/webapps/base/static/plugins/
 exclude galaxy/webapps/base/static/style/base.css
 exclude galaxy/webapps/base/static/welcome.html
 graft galaxy/webapps/base/templates/
-include tool_shed/webapp/model/migrate/migrate.cfg
-graft tool_shed/webapp/templates/

packages/web_apps/pytest.ini

@@ -0,0 +1 @@
+../package-pytest.ini

packages/web_apps/setup.cfg

@@ -49,7 +49,6 @@ install_requires =
     importlib-resources;python_version<'3.9'
     Mako
     MarkupSafe
-    mercurial
     Paste
     pydantic>=2,!=2.6.0,!=2.6.1
     PyJWT
@@ -67,7 +66,6 @@ install_requires =
     uvicorn
     uvloop
     WebOb
-    Whoosh
 packages = find:
 python_requires = >=3.8
 

packages/web_framework/pytest.ini

@@ -0,0 +1 @@
+../package-pytest.ini

packages/web_stack/pytest.ini

@@ -0,0 +1 @@
+../package-pytest.ini

pyproject.toml

@@ -61,7 +61,9 @@ fastapi-slim = ">=0.111.0"
 fs = "*"
 future = ">=1.0.0"  # Python 3.12 support
 galaxy_sequence_utils = "*"
-graphene-sqlalchemy = "3.0.0rc1"  # need a beta release to be compat. with starlette plugin
+graphene = "*"
+graphene-sqlalchemy = ">=3.0.0rc1"  # need a beta release to be compat. with starlette plugin
+graphql-core = "*"
 gravity = ">=1.0.4"
 gunicorn = "*"
 gxformat2 = "*"