Refactor RuntimeValue utils for re-use

Moving this to tools.parameters.workflow_utils avoids a circular
dependency when importing is_runtime_value in
tools.parameters.dynamic_options.

lib/galaxy/managers/workflows.py

@@ -90,12 +90,14 @@
     visit_input_values,
 )
 from galaxy.tools.parameters.basic import (
-    ConnectedValue,
     DataCollectionToolParameter,
     DataToolParameter,
+)
+from galaxy.tools.parameters.workflow_utils import (
+    ConnectedValue,
     RuntimeValue,
+    workflow_building_modes,
 )
-from galaxy.tools.parameters.workflow_building_modes import workflow_building_modes
 from galaxy.util.hash_util import md5_hash_str
 from galaxy.util.json import (
     safe_dumps,

lib/galaxy/tools/__init__.py

@@ -142,7 +142,7 @@
 )
 from galaxy.tools.parameters.input_translation import ToolInputTranslator
 from galaxy.tools.parameters.meta import expand_meta_parameters
-from galaxy.tools.parameters.workflow_building_modes import workflow_building_modes
+from galaxy.tools.parameters.workflow_utils import workflow_building_modes
 from galaxy.tools.parameters.wrapped_json import json_wrap
 from galaxy.tools.test import parse_tests
 from galaxy.util import (

lib/galaxy/tools/actions/__init__.py

@@ -33,9 +33,9 @@
 from galaxy.tools.parameters.basic import (
     DataCollectionToolParameter,
     DataToolParameter,
-    RuntimeValue,
     SelectToolParameter,
 )
+from galaxy.tools.parameters.workflow_utils import RuntimeValue
 from galaxy.tools.parameters.wrapped import (
     LegacyUnprefixedDict,
     WrappedParameters,

lib/galaxy/tools/execute.py

@@ -34,7 +34,7 @@
     on_text_for_names,
     ToolExecutionCache,
 )
-from galaxy.tools.parameters.basic import is_runtime_value
+from galaxy.tools.parameters.workflow_utils import is_runtime_value
 
 if typing.TYPE_CHECKING:
     from galaxy.tools import Tool

lib/galaxy/tools/parameters/__init__.py

@@ -16,9 +16,7 @@
 from .basic import (
     DataCollectionToolParameter,
     DataToolParameter,
-    is_runtime_value,
     ParameterValueError,
-    runtime_to_json,
     SelectToolParameter,
     ToolParameter,
 )
@@ -29,6 +27,10 @@
     Section,
     UploadDataset,
 )
+from .workflow_utils import (
+    is_runtime_value,
+    runtime_to_json,
+)
 from .wrapped import flat_to_nested_state
 
 REPLACE_ON_TRUTHY = object()

lib/galaxy/tools/parameters/basic.py

@@ -42,7 +42,7 @@
 from galaxy.model.dataset_collections import builder
 from galaxy.schema.fetch_data import FilesPayload
 from galaxy.tool_util.parser import get_input_source as ensure_input_source
-from galaxy.tools.parameters.workflow_building_modes import workflow_building_modes
+from galaxy.tools.parameters.workflow_utils import workflow_building_modes
 from galaxy.util import (
     sanitize_param,
     string_as_bool,
@@ -61,6 +61,12 @@
 )
 from .dataset_matcher import get_dataset_matcher_factory
 from .sanitize import ToolParameterSanitizer
+from .workflow_utils import (
+    is_runtime_value,
+    runtime_to_json,
+    runtime_to_object,
+    RuntimeValue,
+)
 
 if TYPE_CHECKING:
     from sqlalchemy.orm import Session
@@ -87,12 +93,6 @@ def contains_workflow_parameter(value, search=False):
     return False
 
 
-def is_runtime_value(value):
-    return isinstance(value, RuntimeValue) or (
-        isinstance(value, MutableMapping) and value.get("__class__") in ["RuntimeValue", "ConnectedValue"]
-    )
-
-
 def is_runtime_context(trans, other_values):
     if trans.workflow_building_mode:
         return True
@@ -2777,36 +2777,6 @@ def write_elements_to_collection(has_elements, collection_builder):
 )
 
 
-def runtime_to_json(runtime_value):
-    if isinstance(runtime_value, ConnectedValue) or (
-        isinstance(runtime_value, MutableMapping) and runtime_value["__class__"] == "ConnectedValue"
-    ):
-        return {"__class__": "ConnectedValue"}
-    else:
-        return {"__class__": "RuntimeValue"}
-
-
-def runtime_to_object(runtime_value):
-    if isinstance(runtime_value, ConnectedValue) or (
-        isinstance(runtime_value, MutableMapping) and runtime_value["__class__"] == "ConnectedValue"
-    ):
-        return ConnectedValue()
-    else:
-        return RuntimeValue()
-
-
-class RuntimeValue:
-    """
-    Wrapper to note a value that is not yet set, but will be required at runtime.
-    """
-
-
-class ConnectedValue(RuntimeValue):
-    """
-    Wrapper to note a value that is not yet set, but will be inferred from a connection.
-    """
-
-
 def history_item_dict_to_python(value, app, name):
     if isinstance(value, MutableMapping) and "src" in value:
         if value["src"] not in ("hda", "dce", "ldda", "hdca"):

lib/galaxy/tools/parameters/dynamic_options.py

@@ -28,7 +28,10 @@
     User,
 )
 from galaxy.tools.expressions import do_eval
-from galaxy.tools.parameters.workflow_building_modes import workflow_building_modes
+from galaxy.tools.parameters.workflow_utils import (
+    is_runtime_value,
+    workflow_building_modes,
+)
 from galaxy.util import (
     Element,
     string_as_bool,
@@ -969,6 +972,8 @@ def _get_ref_data(other_values, ref_name):
             list,
         ),
     ):
+        if is_runtime_value(ref):
+            return []
         raise ValueError
     if isinstance(ref, DatasetCollectionElement) and ref.hda:
         ref = ref.hda

lib/galaxy/tools/parameters/workflow_utils.py

@@ -0,0 +1,43 @@
+from collections.abc import MutableMapping
+
+
+class workflow_building_modes:
+    DISABLED = False
+    ENABLED = True
+    USE_HISTORY = 1
+
+
+def runtime_to_json(runtime_value):
+    if isinstance(runtime_value, ConnectedValue) or (
+        isinstance(runtime_value, MutableMapping) and runtime_value["__class__"] == "ConnectedValue"
+    ):
+        return {"__class__": "ConnectedValue"}
+    else:
+        return {"__class__": "RuntimeValue"}
+
+
+def runtime_to_object(runtime_value):
+    if isinstance(runtime_value, ConnectedValue) or (
+        isinstance(runtime_value, MutableMapping) and runtime_value["__class__"] == "ConnectedValue"
+    ):
+        return ConnectedValue()
+    else:
+        return RuntimeValue()
+
+
+class RuntimeValue:
+    """
+    Wrapper to note a value that is not yet set, but will be required at runtime.
+    """
+
+
+class ConnectedValue(RuntimeValue):
+    """
+    Wrapper to note a value that is not yet set, but will be inferred from a connection.
+    """
+
+
+def is_runtime_value(value):
+    return isinstance(value, RuntimeValue) or (
+        isinstance(value, MutableMapping) and value.get("__class__") in ["RuntimeValue", "ConnectedValue"]
+    )

lib/galaxy/tools/recommendations.py

@@ -10,7 +10,7 @@
 import yaml
 
 from galaxy.tools.parameters import populate_state
-from galaxy.tools.parameters.workflow_building_modes import workflow_building_modes
+from galaxy.tools.parameters.workflow_utils import workflow_building_modes
 from galaxy.util import DEFAULT_SOCKET_TIMEOUT
 from galaxy.workflow.modules import module_factory
 

lib/galaxy/webapps/galaxy/api/workflows.py

@@ -86,7 +86,7 @@
 from galaxy.tool_shed.galaxy_install.install_manager import InstallRepositoryManager
 from galaxy.tools import recommendations
 from galaxy.tools.parameters import populate_state
-from galaxy.tools.parameters.workflow_building_modes import workflow_building_modes
+from galaxy.tools.parameters.workflow_utils import workflow_building_modes
 from galaxy.util.sanitize_html import sanitize_html
 from galaxy.version import VERSION
 from galaxy.web import (

lib/galaxy/webapps/galaxy/controllers/workflow.py

@@ -17,7 +17,7 @@
 )
 from galaxy.model.base import transaction
 from galaxy.model.item_attrs import UsesItemRatings
-from galaxy.tools.parameters.workflow_building_modes import workflow_building_modes
+from galaxy.tools.parameters.workflow_utils import workflow_building_modes
 from galaxy.util import FILENAME_VALID_CHARS
 from galaxy.util.sanitize_html import sanitize_html
 from galaxy.web import url_for

lib/galaxy/workflow/modules.py

@@ -68,16 +68,13 @@
     BaseDataToolParameter,
     BooleanToolParameter,
     ColorToolParameter,
-    ConnectedValue,
     DataCollectionToolParameter,
     DataToolParameter,
     FloatToolParameter,
     HiddenToolParameter,
     IntegerToolParameter,
-    is_runtime_value,
     parameter_types,
     raw_to_galaxy,
-    runtime_to_json,
     SelectToolParameter,
     TextToolParameter,
 )
@@ -86,7 +83,12 @@
     ConditionalWhen,
 )
 from galaxy.tools.parameters.history_query import HistoryQuery
-from galaxy.tools.parameters.workflow_building_modes import workflow_building_modes
+from galaxy.tools.parameters.workflow_utils import (
+    ConnectedValue,
+    is_runtime_value,
+    runtime_to_json,
+    workflow_building_modes,
+)
 from galaxy.tools.parameters.wrapped import make_dict_copy
 from galaxy.util import (
     listify,

lib/galaxy/workflow/refactor/execute.py

@@ -6,9 +6,9 @@
 
 from galaxy.exceptions import RequestParameterInvalidException
 from galaxy.tools.parameters import visit_input_values
-from galaxy.tools.parameters.basic import (
+from galaxy.tools.parameters.basic import contains_workflow_parameter
+from galaxy.tools.parameters.workflow_utils import (
     ConnectedValue,
-    contains_workflow_parameter,
     runtime_to_json,
 )
 from .schema import (

test/integration/test_workflow_refactoring.py

@@ -21,7 +21,7 @@
     WorkflowStepConnection,
 )
 from galaxy.model.base import transaction
-from galaxy.tools.parameters.workflow_building_modes import workflow_building_modes
+from galaxy.tools.parameters.workflow_utils import workflow_building_modes
 from galaxy.workflow.refactor.schema import RefactorActionExecutionMessageTypeEnum
 from galaxy_test.base.populators import WorkflowPopulator
 from galaxy_test.base.uses_shed_api import UsesShedApi

test/unit/app/tools/test_select_parameters.py

@@ -4,7 +4,7 @@
 
 from galaxy import model
 from galaxy.model.base import transaction
-from galaxy.tools.parameters import basic
+from galaxy.tools.parameters.workflow_utils import RuntimeValue
 from .util import BaseParameterTestCase
 
 
@@ -36,7 +36,7 @@ def test_unvalidated_datasets(self):
         self.options_xml = """<options><filter type="data_meta" ref="input_bam" key="dbkey"/></options>"""
         self.trans.workflow_building_mode = True
         assert isinstance(
-            self.param.from_json(model.HistoryDatasetAssociation(), self.trans, {"input_bam": basic.RuntimeValue()}),
+            self.param.from_json(model.HistoryDatasetAssociation(), self.trans, {"input_bam": RuntimeValue()}),
             model.HistoryDatasetAssociation,
         )