Merge pull request galaxyproject#18673 from jmchilton/parameter_models_2

Another round of parameter model improvements.

lib/galaxy/tool_util/parameters/factory.py

@@ -16,6 +16,7 @@
 )
 from galaxy.util import string_as_bool
 from .models import (
+    BaseUrlParameterModel,
     BooleanParameterModel,
     ColorParameterModel,
     ConditionalParameterModel,
@@ -31,8 +32,11 @@
     DataCollectionParameterModel,
     DataColumnParameterModel,
     DataParameterModel,
+    DirectoryUriParameterModel,
     DrillDownParameterModel,
     FloatParameterModel,
+    GenomeBuildParameterModel,
+    GroupTagParameterModel,
     HiddenParameterModel,
     IntegerParameterModel,
     LabelValue,
@@ -67,6 +71,9 @@ def _from_input_source_galaxy(input_source: InputSource) -> ToolParameterT:
                 int_value = int(value)
             elif optional:
                 int_value = None
+            elif value == "" or value is None:
+                # A truly required parameter: https://github.com/galaxyproject/galaxy/pull/16966/files
+                int_value = None
             else:
                 raise ParameterDefinitionError()
             return IntegerParameterModel(name=input_source.parse_name(), optional=optional, value=int_value)
@@ -101,9 +108,11 @@ def _from_input_source_galaxy(input_source: InputSource) -> ToolParameterT:
             )
         elif param_type == "hidden":
             optional = input_source.parse_optional()
+            value = input_source.get("value")
             return HiddenParameterModel(
                 name=input_source.parse_name(),
                 optional=optional,
+                value=value,
             )
         elif param_type == "color":
             optional = input_source.parse_optional()
@@ -164,6 +173,26 @@ def _from_input_source_galaxy(input_source: InputSource) -> ToolParameterT:
             return DataColumnParameterModel(
                 name=input_source.parse_name(),
             )
+        elif param_type == "group_tag":
+            return GroupTagParameterModel(
+                name=input_source.parse_name(),
+            )
+        elif param_type == "baseurl":
+            return BaseUrlParameterModel(
+                name=input_source.parse_name(),
+            )
+        elif param_type == "genomebuild":
+            optional = input_source.parse_optional()
+            multiple = input_source.get_bool("multiple", False)
+            return GenomeBuildParameterModel(
+                name=input_source.parse_name(),
+                optional=optional,
+                multiple=multiple,
+            )
+        elif param_type == "directory_uri":
+            return DirectoryUriParameterModel(
+                name=input_source.parse_name(),
+            )
         else:
             raise Exception(f"Unknown Galaxy parameter type {param_type}")
     elif input_type == "conditional":
@@ -308,6 +337,10 @@ def input_models_for_pages(pages: PagesSource) -> List[ToolParameterT]:
 def input_models_for_page(page_source: PageSource) -> List[ToolParameterT]:
     input_models = []
     for input_source in page_source.parse_input_sources():
+        input_type = input_source.parse_input_type()
+        if input_type == "display":
+            # not a real input... just skip this. Should this be handled in the parser layer better?
+            continue
         tool_parameter_model = from_input_source(input_source)
         input_models.append(tool_parameter_model)
     return input_models

lib/galaxy/tool_util/parameters/models.py

@@ -16,12 +16,14 @@
 )
 
 from pydantic import (
+    AnyUrl,
     BaseModel,
     ConfigDict,
     create_model,
     Discriminator,
     Field,
     field_validator,
+    HttpUrl,
     RootModel,
     StrictBool,
     StrictFloat,
@@ -48,10 +50,7 @@
 
 # TODO:
 # - implement job vs request...
-# - drill down
 # - implement data_ref on rules and implement some cross model validation
-# - Optional conditionals... work through that?
-# - Sections - fight that battle again...
 
 # + request: Return info needed to build request pydantic model at runtime.
 # + request_internal: This is a pydantic model to validate what Galaxy expects to find in the database,
@@ -185,7 +184,7 @@ def pydantic_template(self, state_representation: StateRepresentationT) -> Dynam
 
     @property
     def request_requires_value(self) -> bool:
-        return False
+        return not self.optional and self.value is None
 
 
 class FloatParameterModel(BaseGalaxyToolParameterModelDefinition):
@@ -347,6 +346,7 @@ def request_requires_value(self) -> bool:
 
 class HiddenParameterModel(BaseGalaxyToolParameterModelDefinition):
     parameter_type: Literal["gx_hidden"] = "gx_hidden"
+    value: Optional[str]
 
     @property
     def py_type(self) -> Type:
@@ -357,7 +357,7 @@ def pydantic_template(self, state_representation: StateRepresentationT) -> Dynam
 
     @property
     def request_requires_value(self) -> bool:
-        return not self.optional
+        return not self.optional and self.value is None
 
 
 def ensure_color_valid(value: Optional[Any]):
@@ -423,8 +423,14 @@ def request_requires_value(self) -> bool:
 
 
 class DirectoryUriParameterModel(BaseGalaxyToolParameterModelDefinition):
-    parameter_type: Literal["gx_directory_uri"]
-    value: Optional[str]
+    parameter_type: Literal["gx_directory_uri"] = "gx_directory_uri"
+
+    @property
+    def py_type(self) -> Type:
+        return AnyUrl
+
+    def pydantic_template(self, state_representation: StateRepresentationT) -> DynamicModelInformation:
+        return dynamic_model_information_from_py_type(self, self.py_type)
 
     @property
     def request_requires_value(self) -> bool:
@@ -464,8 +470,11 @@ class SelectParameterModel(BaseGalaxyToolParameterModelDefinition):
     @property
     def py_type(self) -> Type:
         if self.options is not None:
-            literal_options: List[Type] = [cast_as_type(Literal[o.value]) for o in self.options]
-            py_type = union_type(literal_options)
+            if len(self.options) > 0:
+                literal_options: List[Type] = [cast_as_type(Literal[o.value]) for o in self.options]
+                py_type = union_type(literal_options)
+            else:
+                py_type = type(None)
         else:
             py_type = StrictStr
         if self.multiple:
@@ -499,6 +508,26 @@ def request_requires_value(self) -> bool:
         return self.multiple and not self.optional
 
 
+class GenomeBuildParameterModel(BaseGalaxyToolParameterModelDefinition):
+    parameter_type: Literal["gx_genomebuild"] = "gx_genomebuild"
+    multiple: bool
+
+    @property
+    def py_type(self) -> Type:
+        py_type: Type = StrictStr
+        if self.multiple:
+            py_type = list_type(py_type)
+        return optional_if_needed(py_type, self.optional)
+
+    def pydantic_template(self, state_representation: StateRepresentationT) -> DynamicModelInformation:
+        return dynamic_model_information_from_py_type(self, self.py_type)
+
+    @property
+    def request_requires_value(self) -> bool:
+        # assumes it uses behavior of select parameters - an API test to reference for this would be nice
+        return self.multiple and not self.optional
+
+
 DrillDownHierarchyT = Literal["recurse", "exact"]
 
 
@@ -587,6 +616,36 @@ def request_requires_value(self) -> bool:
         return False
 
 
+class GroupTagParameterModel(BaseGalaxyToolParameterModelDefinition):
+    parameter_type: Literal["gx_group_tag"] = "gx_group_tag"
+
+    @property
+    def py_type(self) -> Type:
+        return StrictStr
+
+    def pydantic_template(self, state_representation: StateRepresentationT) -> DynamicModelInformation:
+        return dynamic_model_information_from_py_type(self, self.py_type)
+
+    @property
+    def request_requires_value(self) -> bool:
+        return True
+
+
+class BaseUrlParameterModel(BaseGalaxyToolParameterModelDefinition):
+    parameter_type: Literal["gx_baseurl"] = "gx_baseurl"
+
+    @property
+    def py_type(self) -> Type:
+        return HttpUrl
+
+    def pydantic_template(self, state_representation: StateRepresentationT) -> DynamicModelInformation:
+        return dynamic_model_information_from_py_type(self, self.py_type)
+
+    @property
+    def request_requires_value(self) -> bool:
+        return True
+
+
 DiscriminatorType = Union[bool, str]
 
 
@@ -920,6 +979,9 @@ def request_requires_value(self) -> bool:
     DirectoryUriParameterModel,
     RulesParameterModel,
     DrillDownParameterModel,
+    GroupTagParameterModel,
+    BaseUrlParameterModel,
+    GenomeBuildParameterModel,
     ColorParameterModel,
     ConditionalParameterModel,
     RepeatParameterModel,

lib/galaxy/tool_util/unittest_utils/parameters.py

@@ -11,6 +11,7 @@
     ToolSource,
 )
 from galaxy.util import galaxy_directory
+from . import functional_test_tool_path
 
 
 class ParameterBundle(ToolParameterBundle):
@@ -23,6 +24,12 @@ def parameter_bundle(parameter: ToolParameterT) -> ParameterBundle:
     return ParameterBundle(parameter)
 
 
+def parameter_bundle_for_framework_tool(filename: str) -> ToolParameterBundleModel:
+    path = functional_test_tool_path(filename)
+    tool_source = get_tool_source(path, macro_paths=[])
+    return input_models_for_tool_source(tool_source)
+
+
 def parameter_bundle_for_file(filename: str) -> ToolParameterBundleModel:
     tool_source = parameter_tool_source(filename)
     return input_models_for_tool_source(tool_source)

lib/galaxy/tool_util/verify/interactor.py

@@ -505,10 +505,14 @@ def stage_data_async(
         tool_version: Optional[str] = None,
     ) -> Callable[[], None]:
         fname = test_data["fname"]
+        tags = test_data.get("tags")
         tool_input = {
             "file_type": test_data["ftype"],
             "dbkey": test_data["dbkey"],
         }
+        if tags:
+            tool_input["tags"] = tags
+
         metadata = test_data.get("metadata", {})
         if not hasattr(metadata, "items"):
             raise Exception(f"Invalid metadata description found for input [{fname}] - [{metadata}]")
@@ -1865,6 +1869,7 @@ def test_data_iter(required_files):
             ftype=extra.get("ftype", DEFAULT_FTYPE),
             dbkey=extra.get("dbkey", DEFAULT_DBKEY),
             location=extra.get("location", None),
+            tags=extra.get("tags", []),
         )
         edit_attributes = extra.get("edit_attributes", [])
 

lib/galaxy/tools/actions/upload_common.py

@@ -276,7 +276,13 @@ def new_upload(
                 )
     else:
         upload_target_dataset_instance = __new_history_upload(trans, uploaded_dataset, history=history, state=state)
-
+        tags_raw = getattr(uploaded_dataset, "tags", None)
+        if tags_raw:
+            new_tags = tag_handler.parse_tags_list(tags_raw.split(","))
+            for tag in new_tags:
+                tag_handler.apply_item_tag(
+                    user=trans.user, item=upload_target_dataset_instance, name=tag[0], value=tag[1], flush=True
+                )
     if tag_list:
         tag_handler.add_tags_from_list(trans.user, upload_target_dataset_instance, tag_list, flush=False)
 

lib/galaxy_test/api/test_tools.py

@@ -898,6 +898,38 @@ def test_select_first_by_default(self):
             self._assert_status_code_is(response, 400)
             assert "an invalid option" in response.text
 
+    @skip_without_tool("gx_select_multiple")
+    @skip_without_tool("gx_select_multiple_optional")
+    def test_select_multiple_null_handling(self):
+        with self.dataset_populator.test_history(require_new=False) as history_id:
+            inputs: Dict[str, Any] = {}
+            response = self._run("gx_select_multiple", history_id, inputs, assert_ok=True)
+            output = response["outputs"][0]
+            output1_content = self.dataset_populator.get_history_dataset_content(history_id, dataset=output)
+            assert output1_content.strip() == "None"
+
+            inputs = {}
+            response = self._run("gx_select_multiple_optional", history_id, inputs, assert_ok=True)
+            output = response["outputs"][0]
+            output1_content = self.dataset_populator.get_history_dataset_content(history_id, dataset=output)
+            assert output1_content.strip() == "None"
+
+            inputs = {
+                "parameter": None,
+            }
+            response = self._run("gx_select_multiple", history_id, inputs, assert_ok=True)
+            output = response["outputs"][0]
+            output1_content = self.dataset_populator.get_history_dataset_content(history_id, dataset=output)
+            assert output1_content.strip() == "None"
+
+            inputs = {
+                "parameter": None,
+            }
+            response = self._run("gx_select_multiple_optional", history_id, inputs, assert_ok=True)
+            output = response["outputs"][0]
+            output1_content = self.dataset_populator.get_history_dataset_content(history_id, dataset=output)
+            assert output1_content.strip() == "None"
+
     @skip_without_tool("gx_drill_down_exact")
     @skip_without_tool("gx_drill_down_exact_multiple")
     @skip_without_tool("gx_drill_down_recurse")