From 07ca8d63876b1c95080a7ccf7edfa6b3032814f2 Mon Sep 17 00:00:00 2001
From: Daisie Huang <daisieh@gmail.com>
Date: Mon, 17 Apr 2023 23:22:01 -0700
Subject: [PATCH] don't deal with non-absolute local file paths

---
 htsget_server/drs_operations.py    | 7 ++++++-
 htsget_server/htsget_operations.py | 2 +-
 tests/test_htsget_server.py        | 2 +-
 3 files changed, 8 insertions(+), 3 deletions(-)

diff --git a/htsget_server/drs_operations.py b/htsget_server/drs_operations.py
index 7f556939..985c1970 100644
--- a/htsget_server/drs_operations.py
+++ b/htsget_server/drs_operations.py
@@ -2,6 +2,7 @@
 import database
 from flask import request, Flask
 import os
+import os.path
 import re
 import authz
 from markupsafe import escape
@@ -231,9 +232,13 @@ def _get_file_path(drs_file_obj_id):
             url_pieces = urlparse(method["access_url"]["url"])
             if url_pieces.scheme == "file":
                 if url_pieces.netloc == "" or url_pieces.netloc == "localhost":
-                    result["path"] = url_pieces.path.lstrip("/")
+                    result["path"] = os.path.abspath(url_pieces.path)
+                    if not os.path.exists(result["path"]):
+                        result['message'] = f"No file exists at {result['path']} on the server."
+                        result['status_code'] = 404
     if result['path'] is None:
         result['message'] = f"No file was found for drs_obj {drs_file_obj_id}: {url}"
+        result['status_code'] = 404
         result.pop('path')
     return result
 
diff --git a/htsget_server/htsget_operations.py b/htsget_server/htsget_operations.py
index c3317b62..6772d0ce 100644
--- a/htsget_server/htsget_operations.py
+++ b/htsget_server/htsget_operations.py
@@ -338,7 +338,7 @@ def _get_data(id_, reference_name=None, start=None, end=None, class_=None, forma
     gen_obj = drs_operations._get_genomic_obj(id_)
     if gen_obj is not None:
         if "message" in gen_obj:
-            return gen_obj['message'], gen_obj['status_code']
+            return {"message": gen_obj['message']}, gen_obj['status_code']
         file_in = gen_obj["file"]
         ntf = tempfile.NamedTemporaryFile(prefix='htsget', suffix=format_,
                                  mode='wb', delete=False)
diff --git a/tests/test_htsget_server.py b/tests/test_htsget_server.py
index 43afb651..fdd9c094 100644
--- a/tests/test_htsget_server.py
+++ b/tests/test_htsget_server.py
@@ -126,7 +126,7 @@ def test_post_update():
     obj = response.json()
 
     url = f"{HOST}/ga4gh/drs/v1/objects"
-    access_url = f"file:///./data/files/NA18537.vcf.gz" # this is local within the htsget server container, not from where we're running pytest
+    access_url = f"file:////app/htsget_server/data/files/NA18537.vcf.gz" # this is local within the htsget server container, not from where we're running pytest
     obj["access_methods"] = [
         {
             "type": "file",