Minor fix to restore admin-style dynamic tools

lib/galaxy/managers/tools.py

@@ -70,7 +70,7 @@ def create_tool(self, trans, tool_payload, allow_load=True):
             is_path = src == "from_path"
 
             if is_path:
-                tool_format, representation, _ = artifact_class(None, tool_payload)
+                tool_format, representation, _ = artifact_class(None, tool_payload.dict())
             else:
                 assert src == "representation"
                 representation = tool_payload.representation.dict(by_alias=True, exclude_unset=True)

lib/galaxy/tool_util/models.py

@@ -18,6 +18,7 @@
     BaseModel,
     ConfigDict,
     Field,
+    model_validator,
     RootModel,
 )
 from typing_extensions import (
@@ -47,13 +48,20 @@
 from .verify.assertion_models import assertions
 
 
-class UserToolSource(BaseModel):
-    class_: Annotated[Literal["GalaxyUserTool"], Field(alias="class")]
+def normalize_dict(values, keys: List[str]):
+    for key in keys:
+        items = values.get(key)
+        if isinstance(items, dict):  # dict-of-dicts format
+            # Transform dict-of-dicts to list-of-dicts
+            values[key] = [{"name": k, **v} for k, v in items.items()]
+
+
+class ToolSourceBase(BaseModel):
+    id: Optional[str] = None
     name: str
-    container: str
-    version: str
+    version: Optional[str] = "1.0"
     description: Optional[str] = None
-    shell_command: str
+    container: Optional[str] = None
     inputs: List[GalaxyParameterT]
     outputs: List[IncomingToolOutput]
     citations: Optional[List[Citation]] = None
@@ -64,6 +72,27 @@ class UserToolSource(BaseModel):
     xrefs: Optional[List[XrefDict]] = None
     help: Optional[HelpContent] = None
 
+    @model_validator(mode="before")
+    @classmethod
+    def normalize_items(cls, values):
+        if isinstance(values, dict):
+            normalize_dict(values, ["inputs", "outputs"])
+        return values
+
+
+class UserToolSource(ToolSourceBase):
+    class_: Annotated[Literal["GalaxyUserTool"], Field(alias="class")]
+    shell_command: str
+    container: str
+
+
+class AdminToolSource(ToolSourceBase):
+    class_: Annotated[Literal["GalaxyTool"], Field(alias="class")]
+    command: str
+
+
+DynamicToolSources = Annotated[Union[UserToolSource, AdminToolSource], Field(discriminator="class_")]
+
 
 class ParsedTool(BaseModel):
     id: str

lib/galaxy/webapps/galaxy/api/dynamic_tools.py

@@ -2,6 +2,7 @@
 from typing import (
     Literal,
     Optional,
+    Union,
 )
 
 from pydantic.main import BaseModel
@@ -10,25 +11,35 @@
 from galaxy.managers.context import ProvidesUserContext
 from galaxy.managers.tools import DynamicToolManager
 from galaxy.schema.fields import DecodedDatabaseIdField
-from galaxy.tool_util.models import UserToolSource
+from galaxy.tool_util.models import DynamicToolSources
 from . import (
     depends,
     DependsOnTrans,
     Router,
 )
 
 
-class DynamicToolCreatePayload(BaseModel):
+class BaseDynamicToolCreatePayload(BaseModel):
     allow_load: bool = True
     uuid: Optional[str] = None
-    src: Literal["representation", "path"] = "representation"
-    representation: UserToolSource
     active: Optional[bool] = None
     hidden: Optional[bool] = None
-    path: Optional[str] = None
     tool_directory: Optional[str] = None
 
 
+class DynamicToolCreatePayload(BaseDynamicToolCreatePayload):
+    src: Literal["representation"] = "representation"
+    representation: DynamicToolSources
+
+
+class PathBasedDynamicToolCreatePayload(BaseDynamicToolCreatePayload):
+    src: Literal["from_path"]
+    path: str
+
+
+DynamicToolPayload = Union[DynamicToolCreatePayload, PathBasedDynamicToolCreatePayload]
+
+
 log = logging.getLogger(__name__)
 
 router = Router(tags=["dynamic_tools"])
@@ -50,7 +61,7 @@ def show(self, dynamic_tool_id: DecodedDatabaseIdField):
         return dynamic_tool.to_dict()
 
     @router.post("/api/dynamic_tools", require_admin=True)
-    def create(self, payload: DynamicToolCreatePayload, trans: ProvidesUserContext = DependsOnTrans):
+    def create(self, payload: DynamicToolPayload, trans: ProvidesUserContext = DependsOnTrans):
         dynamic_tool = self.dynamic_tools_manager.create_tool(trans, payload, allow_load=payload.allow_load)
         return dynamic_tool.to_dict()
 

lib/galaxy_test/api/test_tools.py

@@ -43,40 +43,17 @@
     "version": "1.0.0",
     "command": "echo 'Hello World' > $output1",
     "inputs": [],
-    "outputs": dict(
-        output1=dict(format="txt"),
-    ),
+    "outputs": {"output1": {"format": "txt", "type": "data"}},
 }
 MINIMAL_TOOL_NO_ID = {
     "name": "Minimal Tool",
     "class": "GalaxyTool",
     "version": "1.0.0",
     "command": "echo 'Hello World 2' > $output1",
     "inputs": [],
-    "outputs": dict(
-        output1=dict(format="txt"),
-    ),
-}
-TOOL_WITH_BASE_COMMAND = {
-    "name": "Base command tool",
-    "class": "GalaxyTool",
-    "version": "1.0.0",
-    "base_command": "cat",
-    "arguments": ["$(inputs.input.path)", ">", "output.fastq"],
-    "inputs": [
-        {
-            "type": "data",
-            "name": "input",
-        }
-    ],
-    "outputs": {
-        "output": {
-            "type": "data",
-            "from_work_dir": "output.fastq",
-            "name": "output",
-        }
-    },
+    "outputs": {"output1": {"format": "txt", "type": "data"}},
 }
+
 TOOL_WITH_SHELL_COMMAND = {
     "name": "Base command tool",
     "class": "GalaxyUserTool",
@@ -1422,22 +1399,44 @@ def test_dynamic_tool_no_id(self):
         output_content = self.dataset_populator.get_history_dataset_content(history_id)
         assert output_content == "Hello World 2\n"
 
-    def test_dynamic_tool_base_command(self):
-        tool_response = self.dataset_populator.create_tool(TOOL_WITH_BASE_COMMAND)
-        self._assert_has_keys(tool_response, "uuid")
-
-        # Run tool.
-        history_id = self.dataset_populator.new_history()
-        dataset = self.dataset_populator.new_dataset(history_id=history_id, content="abc")
-        self._run(
-            history_id=history_id,
-            tool_uuid=tool_response["uuid"],
-            inputs={"input": {"src": "hda", "id": dataset["id"]}},
-        )
-
-        self.dataset_populator.wait_for_history(history_id, assert_ok=True)
-        output_content = self.dataset_populator.get_history_dataset_content(history_id)
-        assert output_content == "abc\n"
+    # This works except I don't want to add it to the schema right now,
+    # since I think the shell_command is what we'lll go with (at least initially)
+    # def test_dynamic_tool_base_command(self):
+    #     TOOL_WITH_BASE_COMMAND = {
+    #         "name": "Base command tool",
+    #         "class": "GalaxyTool",
+    #         "version": "1.0.0",
+    #         "base_command": "cat",
+    #         "arguments": ["$(inputs.input.path)", ">", "output.fastq"],
+    #         "inputs": [
+    #             {
+    #                 "type": "data",
+    #                 "name": "input",
+    #             }
+    #         ],
+    #         "outputs": {
+    #             "output": {
+    #                 "type": "data",
+    #                 "from_work_dir": "output.fastq",
+    #                 "name": "output",
+    #             }
+    #         },
+    #     }
+    #     tool_response = self.dataset_populator.create_tool(TOOL_WITH_BASE_COMMAND)
+    #     self._assert_has_keys(tool_response, "uuid")
+
+    #     # Run tool.
+    #     history_id = self.dataset_populator.new_history()
+    #     dataset = self.dataset_populator.new_dataset(history_id=history_id, content="abc")
+    #     self._run(
+    #         history_id=history_id,
+    #         tool_uuid=tool_response["uuid"],
+    #         inputs={"input": {"src": "hda", "id": dataset["id"]}},
+    #     )
+
+    #     self.dataset_populator.wait_for_history(history_id, assert_ok=True)
+    #     output_content = self.dataset_populator.get_history_dataset_content(history_id)
+    #     assert output_content == "abc\n"
 
     def test_dynamic_tool_shell_command(self):
         tool_response = self.dataset_populator.create_tool(TOOL_WITH_SHELL_COMMAND)

lib/galaxy_test/base/data/minimal_tool_no_id.json

@@ -6,7 +6,8 @@
     "inputs": [],
     "outputs": {
         "output1": {
-            "format": "txt"
+            "format": "txt",
+            "type": "data"
         }
     }
 }