Merge pull request #3129 from Clinical-Genomics/avoid_file_system_crash

Attempt at fixing file system not mounted IGV crash

CHANGELOG.md

@@ -35,6 +35,7 @@ About changelog [here](https://keepachangelog.com/en/1.0.0/)
 - Fix code typos
 - Disable codefactor raised by ESLint for javascript functions located on another file
 - Loading spinner stuck after downloading a PDF gene panel report
+- IGV browser crashing when file system with alignment files is not mounted
 
 ## [4.47]
 ### Added

scout/server/blueprints/alignviewers/partial.py

@@ -28,7 +28,10 @@ def parse_byte_range(byte_range):
 def send_file_partial(path):
     range_header = request.headers.get("Range", None)
     if not range_header:
-        return send_file(path)
+        try:
+            return send_file(path)
+        except IOError:
+            return abort(404, "File not found")
 
     try:
         byte_range = parse_byte_range(request.headers["Range"])

scout/server/blueprints/alignviewers/views.py

@@ -3,16 +3,7 @@
 import os.path
 
 import requests
-from flask import (
-    Blueprint,
-    Response,
-    abort,
-    current_app,
-    flash,
-    render_template,
-    request,
-    send_file,
-)
+from flask import Blueprint, Response, abort, render_template, request, send_file
 
 from . import controllers
 from .partial import send_file_partial
@@ -67,7 +58,7 @@ def remote_cors(remote_url):
 @alignviewers_bp.route("/remote/static", methods=["OPTIONS", "GET"])
 def remote_static():
     """Stream *large* static files with special requirements."""
-    file_path = request.args.get("file")
+    file_path = request.args.get("file") or ""
     range_header = request.headers.get("Range", None)
     if not range_header and (file_path.endswith(".bam") or file_path.endswith(".cram")):
         return abort(500)