Rework ParsedTool for reuse outside of the tool shed.

lib/galaxy/tool_util/models.py

@@ -0,0 +1,74 @@
+"""Define the ParsedTool model representing metadata extracted from a tool's source.
+
+This is abstraction exported by newer tool shed APIS (circa 2024) and should be sufficient
+for reasoning about tool state externally from Galaxy.
+"""
+
+from typing import (
+    List,
+    Optional,
+)
+
+from pydantic import BaseModel
+
+from .parameters import (
+    input_models_for_tool_source,
+    ToolParameterT,
+)
+from .parser.interface import (
+    Citation,
+    ToolSource,
+    XrefDict,
+)
+from .parser.output_models import (
+    from_tool_source,
+    ToolOutput,
+)
+
+
+class ParsedTool(BaseModel):
+    id: str
+    version: Optional[str]
+    name: str
+    description: Optional[str]
+    inputs: List[ToolParameterT]
+    outputs: List[ToolOutput]
+    citations: List[Citation]
+    license: Optional[str]
+    profile: Optional[str]
+    edam_operations: List[str]
+    edam_topics: List[str]
+    xrefs: List[XrefDict]
+    help: Optional[str]
+
+
+def parse_tool(tool_source: ToolSource) -> ParsedTool:
+    id = tool_source.parse_id()
+    version = tool_source.parse_version()
+    name = tool_source.parse_name()
+    description = tool_source.parse_description()
+    inputs = input_models_for_tool_source(tool_source).input_models
+    outputs = from_tool_source(tool_source)
+    citations = tool_source.parse_citations()
+    license = tool_source.parse_license()
+    profile = tool_source.parse_profile()
+    edam_operations = tool_source.parse_edam_operations()
+    edam_topics = tool_source.parse_edam_topics()
+    xrefs = tool_source.parse_xrefs()
+    help = tool_source.parse_help()
+
+    return ParsedTool(
+        id=id,
+        version=version,
+        name=name,
+        description=description,
+        profile=profile,
+        inputs=inputs,
+        outputs=outputs,
+        license=license,
+        citations=citations,
+        edam_operations=edam_operations,
+        edam_topics=edam_topics,
+        xrefs=xrefs,
+        help=help,
+    )

lib/tool_shed/managers/tools.py

@@ -8,8 +8,6 @@
     Tuple,
 )
 
-from pydantic import BaseModel
-
 from galaxy import exceptions
 from galaxy.exceptions import (
     InternalServerError,
@@ -21,18 +19,14 @@
     clone_repository,
     get_changectx_for_changeset,
 )
-from galaxy.tool_util.parameters import (
-    input_models_for_tool_source,
-    ToolParameterT,
+from galaxy.tool_util.models import (
+    parse_tool,
+    ParsedTool,
 )
 from galaxy.tool_util.parser import (
     get_tool_source,
     ToolSource,
 )
-from galaxy.tool_util.parser.interface import (
-    Citation,
-    XrefDict,
-)
 from galaxy.tools.stock import stock_tool_sources
 from tool_shed.context import (
     ProvidesRepositoriesContext,
@@ -46,53 +40,6 @@
 STOCK_TOOL_SOURCES: Optional[Dict[str, Dict[str, ToolSource]]] = None
 
 
-# parse the tool source with galaxy.util abstractions to provide a bit richer
-# information about the tool than older tool shed abstractions.
-class ParsedTool(BaseModel):
-    id: str
-    version: Optional[str]
-    name: str
-    description: Optional[str]
-    inputs: List[ToolParameterT]
-    citations: List[Citation]
-    license: Optional[str]
-    profile: Optional[str]
-    edam_operations: List[str]
-    edam_topics: List[str]
-    xrefs: List[XrefDict]
-    help: Optional[str]
-
-
-def _parse_tool(tool_source: ToolSource) -> ParsedTool:
-    id = tool_source.parse_id()
-    version = tool_source.parse_version()
-    name = tool_source.parse_name()
-    description = tool_source.parse_description()
-    inputs = input_models_for_tool_source(tool_source).input_models
-    citations = tool_source.parse_citations()
-    license = tool_source.parse_license()
-    profile = tool_source.parse_profile()
-    edam_operations = tool_source.parse_edam_operations()
-    edam_topics = tool_source.parse_edam_topics()
-    xrefs = tool_source.parse_xrefs()
-    help = tool_source.parse_help()
-
-    return ParsedTool(
-        id=id,
-        version=version,
-        name=name,
-        description=description,
-        profile=profile,
-        inputs=inputs,
-        license=license,
-        citations=citations,
-        edam_operations=edam_operations,
-        edam_topics=edam_topics,
-        xrefs=xrefs,
-        help=help,
-    )
-
-
 def search(trans: SessionRequestContext, q: str, page: int = 1, page_size: int = 10) -> dict:
     """
     Perform the search over TS tools index.
@@ -165,7 +112,7 @@ def parsed_tool_model_for(
     trans: ProvidesRepositoriesContext, trs_tool_id: str, tool_version: str, repository_clone_url: Optional[str] = None
 ) -> ParsedTool:
     tool_source = tool_source_for(trans, trs_tool_id, tool_version, repository_clone_url=repository_clone_url)
-    return _parse_tool(tool_source)
+    return parse_tool(tool_source)
 
 
 def tool_source_for(

lib/tool_shed/webapp/api2/tools.py

@@ -7,14 +7,14 @@
     Response,
 )
 
+from galaxy.tool_util.models import ParsedTool
 from galaxy.tool_util.parameters import (
     RequestToolState,
     to_json_schema_string,
 )
 from tool_shed.context import SessionRequestContext
 from tool_shed.managers.tools import (
     parsed_tool_model_cached_for,
-    ParsedTool,
     search,
 )
 from tool_shed.managers.trs import (