Merge branch 'release_24.1' into dev

lib/galaxy/datatypes/display_applications/configs/biom/biom_simple.xml

@@ -2,6 +2,6 @@
 <display id="biom_simple" version="1.0.0" name="view biom at">
     <dynamic_links from_data_table="biom_simple_display" skip_startswith="#" id="value" name="name">
         <url>${ url % { 'biom_file_url_qp': $biom_file.qp } }</url>
-        <param type="data" name="biom_file" url="galaxy_${DATASET_HASH}.biom" />
+        <param type="data" name="biom_file" url="galaxy_${DATASET_HASH}.biom" allow_cors="true" />
     </dynamic_links>
 </display>

lib/galaxy/datatypes/display_applications/configs/qiime/qiime2/q2view.xml

@@ -2,6 +2,6 @@
 <display id="q2view" version="1.0.0" name="view at">
     <dynamic_links from_data_table="q2view_display" skip_startswith="#" id="value" name="name">
         <url>${ url % { 'q2view_file_url_qp': $q2view_file.qp } }</url>
-        <param type="data" name="q2view_file" url="galaxy_${DATASET_HASH}.${dataset.ext}" />
+        <param type="data" name="q2view_file" url="galaxy_${DATASET_HASH}.${dataset.ext}" allow_cors="true"/>
     </dynamic_links>
 </display>

lib/galaxy/managers/context.py

@@ -39,10 +39,13 @@ import abc
 import string
 from json import dumps
 from typing import (
+    Any,
     Callable,
     cast,
+    Dict,
     List,
     Optional,
+    Tuple,
 )
 
 from sqlalchemy import select
@@ -206,6 +209,13 @@ class ProvidesUserContext(ProvidesAppContext):
 
     galaxy_session: Optional[GalaxySession] = None
     _tag_handler: Optional[GalaxyTagHandlerSession] = None
+    _short_term_cache: Dict[Tuple[str, ...], Any]
+
+    def set_cache_value(self, args: Tuple[str, ...], value: Any):
+        self._short_term_cache[args] = value
+
+    def get_cache_value(self, args: Tuple[str, ...], default: Any = None) -> Any:
+        return self._short_term_cache.get(args, default)
 
     @property
     def tag_handler(self):

lib/galaxy/tools/__init__.py

@@ -3790,6 +3790,17 @@ class FilterEmptyDatasetsTool(FilterDatasetsTool):
         return False
 
 
+class FilterNullTool(FilterDatasetsTool):
+    tool_type = "filter_null"
+    require_dataset_ok = True
+
+    @staticmethod
+    def element_is_valid(element: model.DatasetCollectionElement):
+        element_object = element.element_object
+        assert isinstance(element_object, model.DatasetInstance)
+        return element_object.extension == "expression.json" and element_object.blurb == "skipped"
+
+
 class FlattenTool(DatabaseOperationTool):
     tool_type = "flatten_collection"
     require_terminal_states = False

lib/galaxy/tools/parameters/dynamic_options.py

@@ -286,14 +286,12 @@ class ParamValueFilter(Filter):
         return self.ref_name
 
     def filter_options(self, options, trans, other_values):
-        if trans is not None and trans.workflow_building_mode:
-            return []
         ref = other_values.get(self.ref_name, None)
-        if ref is None:
+        if ref is None or is_runtime_value(ref):
             ref = []
 
         # - for HDCAs the list of contained HDAs is extracted
-        # - single values are transformed in a single eleent list
+        # - single values are transformed in a single element list
         # - remaining cases are already lists (select and data parameters with multiple=true)
         if isinstance(ref, HistoryDatasetCollectionAssociation):
             ref = ref.to_hda_representative(multiple=True)
@@ -835,6 +833,9 @@ class DynamicOptions:
         return rval
 
     def get_options(self, trans, other_values):
+
+        rval = []
+
         def to_triple(values):
             if len(values) == 2:
                 return [str(values[0]), str(values[1]), False]
@@ -877,8 +878,7 @@ class DynamicOptions:
                     data = []
 
             # We only support the very specific ["name", "value", "selected"] format for now.
-            return [to_triple(d) for d in data]
-        rval = []
+            rval = [to_triple(d) for d in data]
         if (
             self.file_fields is not None
             or self.tool_data_table is not None

lib/galaxy/webapps/base/webapp.py

@@ -14,6 +14,7 @@ from typing import (
     Any,
     Dict,
     Optional,
+    Tuple,
 )
 from urllib.parse import urlparse
 
@@ -325,6 +326,7 @@ class GalaxyWebTransaction(base.DefaultWebTransaction, context.ProvidesHistoryCo
         self.galaxy_session = None
         self.error_message = None
         self.host = self.request.host
+        self._short_term_cache: Dict[Tuple[str, ...], Any] = {}
 
         # set any cross origin resource sharing headers if configured to do so
         self.set_cors_headers()

lib/galaxy/work/context.py

@@ -49,12 +49,6 @@ class WorkRequestContext(ProvidesHistoryContext):
         self.workflow_building_mode = workflow_building_mode
         self.galaxy_session = galaxy_session
 
-    def set_cache_value(self, args: Tuple[str, ...], value: Any):
-        self._short_term_cache[args] = value
-
-    def get_cache_value(self, args: Tuple[str, ...], default: Any = None) -> Any:
-        return self._short_term_cache.get(args, default)
-
     @property
     def app(self):
         return self._app

lib/galaxy/workflow/modules.py

@@ -1423,7 +1423,7 @@ class InputParameterModule(WorkflowModule):
 
                     def callback(input, prefixed_name, context, **kwargs):
                         if prefixed_name == connection.input_name and hasattr(input, "get_options"):  # noqa: B023
-                            static_options.append(input.get_options(self.trans, {}))
+                            static_options.append(input.get_options(self.trans, context))
 
                     visit_input_values(tool_inputs, module.state.inputs, callback)
                 elif isinstance(module, SubWorkflowModule):

lib/galaxy_test/api/test_workflow_build_module.py

@@ -0,0 +1,19 @@
+from galaxy_test.base.populators import (
+    skip_without_tool,
+    WorkflowPopulator,
+)
+from ._framework import ApiTestCase
+
+
+class TestBuildWorkflowModule(ApiTestCase):
+
+    def setUp(self):
+        super().setUp()
+        self.workflow_populator = WorkflowPopulator(self.galaxy_interactor)
+
+    @skip_without_tool("select_from_url")
+    def test_build_module_filter_dynamic_select(self):
+        # Verify that filtering on parameters that depend on parameter and validators works
+        # fine in workflow building mode.
+        module = self.workflow_populator.build_module(step_type="tool", content_id="select_from_url")
+        assert not module["errors"], module["errors"]

lib/galaxy_test/base/populators.py

@@ -2298,6 +2298,12 @@ class WorkflowPopulator(GalaxyInteractorHttpMixin, BaseWorkflowPopulator, Import
         assert upload_response.status_code == 200, upload_response
         return upload_response.json()
 
+    def build_module(self, step_type: str, content_id: Optional[str] = None, inputs: Optional[Dict[str, Any]] = None):
+        payload = {"inputs": inputs or {}, "type": step_type, "content_id": content_id}
+        response = self._post("workflows/build_module", data=payload, json=True)
+        assert response.status_code == 200, response
+        return response.json()
+
     def _import_tool_response(self, tool) -> Response:
         using_requirement("admin")
         tool_str = json.dumps(tool, indent=4)

test/functional/tools/select_from_url.xml

@@ -10,6 +10,13 @@ echo '$url_param_value_header_and_body' > '$param_value_header_and_body'
             <options from_url="https://usegalaxy.org/api/genomes">
             </options>
         </param>
+        <param name="dynamic_param_filtered_with_validator" type="select">
+            <!-- tested in test_build_module_filter_dynamic_select -->
+            <options from_url="https://usegalaxy.org/api/genomes">
+                <filter type="param_value" ref="url_param_value" column="1" />
+            </options>
+            <validator type="no_options" message="Need at least one option here" />
+        </param>
         <!--
         <param name="url_param_value_templated" type="select">
             <options from_url="http://localhost:8000/data?user=$__user_id__">