From 81f9e0417c18728e63e626644e62019d3146a47a Mon Sep 17 00:00:00 2001
From: heisner-tillman <theisner@posteo.de>
Date: Thu, 8 Feb 2024 11:18:01 +0100
Subject: [PATCH] Refactor execute operation to receive files in payload and
 adjust the corresponding service methods

---
 lib/galaxy/webapps/galaxy/api/tools.py      | 28 ++------------
 lib/galaxy/webapps/galaxy/services/tools.py | 43 +++++++--------------
 2 files changed, 17 insertions(+), 54 deletions(-)

diff --git a/lib/galaxy/webapps/galaxy/api/tools.py b/lib/galaxy/webapps/galaxy/api/tools.py
index 455a68809f31..32372be3631f 100644
--- a/lib/galaxy/webapps/galaxy/api/tools.py
+++ b/lib/galaxy/webapps/galaxy/api/tools.py
@@ -51,6 +51,7 @@
     APIContentTypeRoute,
     as_form,
     BaseGalaxyAPIController,
+    depend_on_either_json_or_form_data,
     depends,
     DependsOnTrans,
     Router,
@@ -121,37 +122,14 @@ async def fetch_form(
     @router.post(
         "/api/tools",
         summary="Execute tool with a given parameter payload",
-        route_class_override=JsonApiRoute,
     )
-    async def execute_json(
+    def execute(
         self,
-        payload: CreateToolBody,
+        payload: ExecuteToolPayload = depend_on_either_json_or_form_data(ExecuteToolPayload),
         trans: ProvidesHistoryContext = DependsOnTrans,
     ) -> ToolResponse:
         return self.service.execute(trans, payload)
 
-    @router.post(
-        "/api/tools",
-        summary="Execute tool with a given parameter payload",
-        route_class_override=FormDataApiRoute,
-    )
-    async def execute_form(
-        self,
-        request: Request,
-        payload: ExecuteToolPayload = Depends(CreateDataForm.as_form),
-        files: Optional[List[UploadFile]] = None,
-        trans: ProvidesHistoryContext = DependsOnTrans,
-    ) -> ToolResponse:
-        files2: List[StarletteUploadFile] = cast(List[StarletteUploadFile], files or [])
-
-        # FastAPI's UploadFile is a very light wrapper around starlette's UploadFile
-        if not files2:
-            data = await request.form()
-            for value in data.values():
-                if isinstance(value, StarletteUploadFile):
-                    files2.append(value)
-        return self.service.execute(trans, payload, files2)
-
 
 class ToolsController(BaseGalaxyAPIController, UsesVisualizationMixin):
     """
diff --git a/lib/galaxy/webapps/galaxy/services/tools.py b/lib/galaxy/webapps/galaxy/services/tools.py
index 595dbc09da05..9053cccce56a 100644
--- a/lib/galaxy/webapps/galaxy/services/tools.py
+++ b/lib/galaxy/webapps/galaxy/services/tools.py
@@ -1,5 +1,4 @@
 import logging
-import re
 import shutil
 import tempfile
 from json import dumps
@@ -78,30 +77,13 @@ def create_temp_file(self, trans, files) -> Dict[str, FilesPayload]:
             )
         return files_payload
 
-    def create_temp_file_execute(self, trans, files) -> Dict[str, FilesPayload]:
-        # TODO - could access headers from request maybe better to do that
-        # header_content = request.headers["content-type"]
-        files_payload = {}
-        for i, upload_file in enumerate(files):
-            with tempfile.NamedTemporaryFile(
-                dir=trans.app.config.new_file_path, prefix="upload_file_data_", delete=False
-            ) as dest:
-                shutil.copyfileobj(upload_file.file, dest)  # type: ignore[misc]  # https://github.com/python/mypy/issues/15031
-            upload_file.file.close()
-
-            # try to grab the name from the header
-            try:
-                header_items = upload_file.headers.items()[0]
-                name_search = re.search(r'name="([^"]+)"', header_items[1])
-                if name_search:
-                    name = name_search.group(1)
-                else:
-                    raise Exception("No name found in header")
-            # if we can't find the name in the header use the index
-            except Exception:
-                name = f"files_{i}|file_data"
-            files_payload[name] = FilesPayload(filename=upload_file.filename, local_filename=dest.name)
-        return files_payload
+    def create_temp_file_execute(self, trans, upload_file) -> FilesPayload:
+        with tempfile.NamedTemporaryFile(
+            dir=trans.app.config.new_file_path, prefix="upload_file_data_", delete=False
+        ) as dest:
+            shutil.copyfileobj(upload_file.file, dest)  # type: ignore[misc]  # https://github.com/python/mypy/issues/15031
+        upload_file.file.close()
+        return FilesPayload(filename=upload_file.filename, local_filename=dest.name)
 
     def create_fetch(
         self,
@@ -142,7 +124,6 @@ def execute(
         self,
         trans: ProvidesHistoryContext,
         payload: ExecuteToolPayload,
-        files: Optional[List[UploadFile]] = None,
     ) -> ToolResponse:
         tool_id = payload.tool_id
         tool_uuid = payload.tool_uuid
@@ -152,10 +133,14 @@ def execute(
             )
         if tool_id is None and tool_uuid is None:
             raise HTTPException(status_code=400, detail="Must specify a valid tool_id to use this endpoint.")
-
         create_payload = payload.model_dump(exclude_unset=True)
-        if files:
-            create_payload.update(self.create_temp_file_execute(trans, files))
+
+        # create temporary files from the uploaded files
+        files = {}
+        for key in list(create_payload.keys()):
+            if key.startswith("files_") or key.startswith("__files_"):
+                files[key] = self.create_temp_file_execute(trans, create_payload.pop(key))
+        create_payload.update(files)
         return self._create(trans, create_payload)
 
     def _create(self, trans: ProvidesHistoryContext, payload) -> ToolResponse: