fix: set correct permissions for uploaded file

Fixes issue #1215
Looks like wasn't about http vs https, nginx was handling this
correctly, just different set of permissions for different targets,
probably an artefact of the way they were processed.

media_serve/urls.py

@@ -4,15 +4,11 @@
 from . import views
 
 urlpatterns = [
-    # path("pdbs/<file_path>/", views.prot_download, name="get_protein"),
-    # path("pdbs/", views.prot_download, name="get_protein"),
-    # re_path(r"^pdbs/(?P<file_path>.+)", views.prot_download, name="get_protein"),
+    re_path(r"^pdbs/(?P<file_path>.+)", views.prot_download, name="get_protein"),
     path("bound/<file_path>/", views.bound_download, name="get_bound"),
     path("metadata/<file_path>/", views.metadata_download, name="get_metadata"),
     path("targets/<file_path>/", views.archive_download, name="get_archive"),
     path("maps/<file_path>/", views.map_download, name='get_map'),
-    # path("target_loader_data/<file_path>", views.file_download, name='get_file'),
-    # re_path(r"^target_loader_data/48225dbf-204a-48e1-8ae7-f1632f4dba89/Mpro-v2/Mpro/upload_2/aligned_files/Mpro_Nterm-x0029/(?P<file_path>.+)", views.file_download, name='get_file'),
     re_path(r"^target_loader_data/(?P<file_path>.+)", views.tld_download, name="get_tld"),
     re_path(r"^pdbs/(?P<file_path>.+)", views.file_download, name="get_file"),
 ]

viewer/target_loader.py

@@ -1,3 +1,4 @@
+import os
 from dataclasses import dataclass
 from typing import Any
 import logging
@@ -1336,6 +1337,8 @@ def load_target(
             target_loader.abs_final_path.parent.joinpath(target_loader.data_bundle)
         )
 
+        set_directory_permissions(target_loader.abs_final_path, 0o755)
+
         update_task(task, "SUCCESS", upload_report)
         target_loader.experiment_upload.message = upload_report
 
@@ -1355,3 +1358,16 @@ def update_task(task, state, message):
     except AttributeError:
         # no task passed to method, nothing to do
         pass
+
+
+def set_directory_permissions(path, permissions):
+    for root, dirs, files in os.walk(path):
+        # Set permissions for directories
+        for directory in dirs:
+            dir_path = os.path.join(root, directory)
+            os.chmod(dir_path, permissions)
+
+        # Set permissions for files
+        for file in files:
+            file_path = os.path.join(root, file)
+            os.chmod(file_path, permissions)