From eb3823418cf816b2517a5eb924b68baeeff06383 Mon Sep 17 00:00:00 2001
From: Etienne Boileau <boileau@uni-heidelberg.de>
Date: Wed, 22 May 2024 10:05:55 +0200
Subject: [PATCH] WIP #47 FIX upload path

---
 server/src/scimodom/api/dataset.py         | 7 +++++--
 server/src/scimodom/services/comparison.py | 7 +++----
 server/src/scimodom/services/file.py       | 5 +----
 3 files changed, 9 insertions(+), 10 deletions(-)

diff --git a/server/src/scimodom/api/dataset.py b/server/src/scimodom/api/dataset.py
index ce23b2ca..38312216 100644
--- a/server/src/scimodom/api/dataset.py
+++ b/server/src/scimodom/api/dataset.py
@@ -1,9 +1,11 @@
 import logging
+from pathlib import Path
 
 from flask import Blueprint, request
 from flask_cors import cross_origin
 from flask_jwt_extended import jwt_required, get_jwt_identity
 
+from scimodom.config import Config
 from scimodom.services.comparison import (
     get_comparison_service,
     FailedUploadError,
@@ -43,14 +45,15 @@ def is_true(value):
 
     reference_ids = request.args.getlist("reference", type=str)
     comparison_ids = request.args.getlist("comparison", type=str)
-    upload_path = request.args.get("upload", type=str)
+    upload_id = request.args.get("upload", type=str)
     operation = request.args.get("operation", type=str)
     is_strand = request.args.get("strand", type=is_true)
     is_euf = request.args.get("euf", type=is_true)
 
     comparison_service = get_comparison_service(operation, is_strand)
-    if upload_path:
+    if upload_id:
         try:
+            upload_path = Path(Config.UPLOAD_PATH, upload_id)
             comparison_service.upload_records(upload_path, is_euf)
         except FileNotFoundError as exc:
             return (
diff --git a/server/src/scimodom/services/comparison.py b/server/src/scimodom/services/comparison.py
index 2ea4e1e1..8f5e4c86 100644
--- a/server/src/scimodom/services/comparison.py
+++ b/server/src/scimodom/services/comparison.py
@@ -155,15 +155,14 @@ def _construct_query(idx: str):
                 raise NoRecordsFoundError
             self._comparison_records.append(records)
 
-    def upload_records(self, upload: str, is_euf: bool):
+    def upload_records(self, upload_path: Path, is_euf: bool):
         """Upload records.
 
-        :param upload: Uploaded dataset to compare
-        :type upload: str | Path
+        :param upload_path: Uploaded dataset to compare
+        :type upload_path: Path
         :param is_euf: BED6 or bedRMod (EUF)
         :type is_euf: bool
         """
-        upload_path = Path(upload)
         if not upload_path.is_file():
             msg = f"No such file or directory: {upload_path.as_posix()}"
             raise FileNotFoundError(msg)
diff --git a/server/src/scimodom/services/file.py b/server/src/scimodom/services/file.py
index c7c9acd9..8ddba358 100644
--- a/server/src/scimodom/services/file.py
+++ b/server/src/scimodom/services/file.py
@@ -30,10 +30,7 @@ def __init__(self, session: Session):
     # general
 
     def upload_tmp_file(self, stream, max_file_size):
-        parent = join(Config.DATA_PATH, "tmp")
-        if not exists(parent):
-            makedirs(parent)
-        fp, path = mkstemp(dir=parent)
+        fp, path = mkstemp(dir=Config.UPLOAD_PATH)
         close(fp)
         file_id = basename(path)
         self._stream_to_file(stream, path, max_file_size, overwrite_is_ok=True)