Add a few annotations to test out schema info rendering

galaxyproject · Jan 31, 2025 · a0c1e15 · a0c1e15
1 parent 7d53fba
commit a0c1e15
Show file tree

Hide file tree

Showing 3 changed files with 47 additions and 7 deletions.
diff --git a/lib/galaxy/tool_util/models.py b/lib/galaxy/tool_util/models.py
@@ -93,7 +93,14 @@ class UserToolSource(BaseModel):
     description: Optional[str] = None
     container: str
     requirements: Optional[List[Union[JavascriptRequirement, ResourceRequirement, ContainerRequirement]]] = []
-    shell_command: str
+    shell_command: Annotated[
+        str,
+        Field(
+            title="shell_command",
+            description="A string that contains the command to be executed. Parameters can be referenced inside $().",
+            examples=["head -n '$(inputs.n_lines)' '$(inputs.data_input.path)'"],
+        ),
+    ]
     inputs: List[GalaxyToolParameterModel] = []
     outputs: List[IncomingToolOutput] = []
     citations: Optional[List[Citation]] = None

diff --git a/lib/galaxy/tool_util/parser/interface.py b/lib/galaxy/tool_util/parser/interface.py
@@ -8,6 +8,7 @@
 from enum import Enum
 from os.path import join
 from typing import (
+    Annotated,
     Any,
     cast,
     Dict,
@@ -19,7 +20,10 @@
 )
 
 import packaging.version
-from pydantic import BaseModel
+from pydantic import (
+    BaseModel,
+    Field,
+)
 from typing_extensions import (
     Literal,
     NotRequired,
@@ -90,7 +94,26 @@ class ResourceRequirement(BaseModel):
 
 class JavascriptRequirement(BaseModel):
     type: Literal["javascript"]
-    expression_lib: Optional[List[str]]
+    expression_lib: Optional[
+        List[
+            Annotated[
+                str,
+                Field(
+                    title="expression_lib",
+                    description="Provide Javascript/ECMAScript 5.1 code here that will be available for expressions inside the `shell_command` field.",
+                    examples=[
+                        r"""function pickValue() {
+    if (inputs.conditional_parameter.test_parameter == "a") {
+        return inputs.conditional_parameter.integer_parameter
+    } else {
+        return inputs.conditional_parameter.boolean_parameter
+    }
+}"""
+                    ],
+                ),
+            ]
+        ]
+    ]
 
 
 class AssertionDict(TypedDict):

diff --git a/lib/galaxy/tool_util/parser/output_models.py b/lib/galaxy/tool_util/parser/output_models.py
@@ -36,8 +36,10 @@
 
 
 class ToolOutputBaseModelG(BaseModel, Generic[IncomingNotRequiredBoolT, IncomingNotRequiredStringT]):
-    name: IncomingNotRequiredStringT
-    label: Optional[str] = None
+    name: Annotated[
+        IncomingNotRequiredStringT, Field(description="Parameter name. Used when referencing parameter in workflows.")
+    ]
+    label: Optional[Annotated[str, Field(description="Output label. Will be used as dataset name in history.")]] = None
     hidden: IncomingNotRequiredBoolT
 
 
@@ -49,11 +51,19 @@ class ToolOutputDatasetG(
     Generic[IncomingNotRequiredBoolT, IncomingNotRequiredStringT],
 ):
     type: Literal["data"]
-    format: IncomingNotRequiredStringT
+    format: Annotated[IncomingNotRequiredStringT, Field(description="The short name for the output datatype.")]
     format_source: Optional[str] = None
     metadata_source: Optional[str] = None
     discover_datasets: Optional[List["DatasetCollectionDescriptionT"]] = None
-    from_work_dir: Optional[str] = None
+    from_work_dir: Optional[
+        Annotated[
+            str,
+            Field(
+                title="from_work_dir",
+                description="Relative path to a file produced by the tool in its working directory. Output’s contents are set to this file’s contents.",
+            ),
+        ]
+    ] = None
 
 
 ToolOutputDataset = ToolOutputDatasetG[bool, str]