Added dataverse upload endpoint

pyenzyme/enzymeml/core/enzymemldocument.py

@@ -311,7 +311,9 @@ def toXMLString(self):
     @validate_arguments
     def uploadToDataverse(
         self,
-        dataverse_name: str
+        dataverse_name: str,
+        base_url: Optional[str] = None,
+        api_token: Optional[str] = None
     ):
         """Uploads an EnzymeML document to a Dataverse installation of choice.
 
@@ -324,7 +326,9 @@ def uploadToDataverse(
         """
         uploadToDataverse(
             enzmldoc=self,
-            dataverse_name=dataverse_name
+            dataverse_name=dataverse_name,
+            base_url=base_url,
+            api_token=api_token
         )
 
     # ! Utility methods

pyenzyme/enzymeml/databases/dataverse.py

@@ -14,13 +14,13 @@
 import os
 import pydantic
 
-from typing import Any
+from typing import Any, Optional
 from pyDaRUS import EnzymeMl, Citation, Dataset
 from pyDaRUS.metadatablocks.enzymeML import Constant
 from pyDaRUS.metadatablocks.citation import SubjectEnum
 
 
-def uploadToDataverse(enzmldoc, dataverse_name: str) -> None:
+def uploadToDataverse(enzmldoc, dataverse_name: str, base_url: Optional[str] = None, api_token: Optional[str] = None) -> None:
     """Uploads a givene EnzymeMLDocument object to a dataverse installation.
 
     It should be noted, that the environment variables 'DATAVERSE_URL' and 'DATAVERSE_API_TOKEN'
@@ -29,6 +29,8 @@ def uploadToDataverse(enzmldoc, dataverse_name: str) -> None:
     Args:
         enzmldoc (EnzymeMLDocument): The EnzymeMLDocument to be uploaded.
         dataverse_name (str): Name of the dataverse to be uploaded to.
+        base_url (str): Base URL of the dataverse to upload. Defaults to None. If None the URL will be drawn from env vars.
+        api_token (str): API Token of the dataverse to upload. Defaults to None. If None the API Token will be drawn from env vars.
     """
 
     # Fill in all the metadatablocks
@@ -48,7 +50,9 @@ def uploadToDataverse(enzmldoc, dataverse_name: str) -> None:
     try:
         dataset.upload(
             dataverse_name=dataverse_name,
-            filenames=[f"{enzmldoc.name.replace(' ', '_')}.omex"]
+            filenames=[f"{enzmldoc.name.replace(' ', '_')}.omex"],
+            base_url=base_url,
+            api_token=api_token
         )
     except Exception as e:
         os.remove(f"{enzmldoc.name.replace(' ', '_')}.omex")
@@ -202,7 +206,6 @@ def add_object(json_data, mapping, add_fun):
         # TODO find a better way to handle this error
         for error in e.errors():
             if error["loc"][0] == "unit":
-                print(params["name"], params["unit"])
                 params.pop("unit")
                 add_fun(**params)
 

pyenzyme_server.py

@@ -1,6 +1,7 @@
 import os
 
 from fastapi import FastAPI, UploadFile, File, Request
+from pydantic import BaseSettings
 from starlette.responses import FileResponse, JSONResponse
 from starlette.background import BackgroundTasks
 
@@ -16,6 +17,17 @@
     ParticipantIdentifierError
 )
 
+
+# * Settings
+
+
+class Settings(BaseSettings):
+    # Used for Dataverse upload
+    DATAVERSE_URL: str
+    DATAVERSE_API_TOKEN: str
+
+
+settings = Settings()
 app = FastAPI(title="PyEnzyme REST-API", version="1.2", docs_url="/")
 
 # * Functions
@@ -74,6 +86,34 @@ def parse_measurement_data(measurement, key, nu_measurement, enzmldoc):
         )
 
 
+@app.post(
+    "/upload/dataverse",
+    summary="Uploads an OMEX archive to a dataverse installation.",
+    description="Use this endpoint as form-data and specify the document to be uploaded via the key 'omex_archive' for a succesfull upload.",
+    tags=["Databases"]
+)
+async def upload_to_dataverse(background_tasks: BackgroundTasks, dataverse_name: str, omex_archive: UploadFile = File(...)):
+
+    # Write to file
+    file_name = omex_archive.filename
+    content = await omex_archive.read()
+    with open(file_name, "wb") as file_handle:
+        file_handle.write(content)
+
+    # Read EnzymeML document
+    try:
+        enzmldoc = EnzymeMLDocument.fromFile(file_name)
+        enzmldoc.uploadToDataverse(
+            dataverse_name=dataverse_name,
+            base_url=settings.DATAVERSE_URL,
+            api_token=settings.DATAVERSE_API_TOKEN
+        )
+    except Exception as e:
+        return f"{e.__class__.__name__}: {str(e)}"
+    finally:
+        background_tasks.add_task(remove_file, path=file_name)
+
+
 @app.post(
     "/read",
     summary="Reads an EnzymeML document served in an OMEX archive to a JSON representation",