feat: adds uploader module

Upload your data:
python -m xchemalign.uploader -i <tarball file> -u <fragalysis url> -p <proposal number> -t <auth token>

Author: kaliif

src/xchemalign/uploader.py

@@ -28,8 +28,7 @@
 )
 
 
-# from xchemalign import utils
-import utils
+from xchemalign import utils
 
 
 LOGIN_URL = "/accounts/login/"
@@ -138,6 +137,9 @@ def upload(input_file, url, proposal, auth_token=None):
             upload_url,
             data=validation_data,
         )
+        if validation_result.url.find("keycloak") > 0:
+            logger.error("You are not logged in to Fragalysis")
+            return
 
         result_json = validation_result.json()
         if not result_json["success"]:
@@ -265,9 +267,6 @@ def main():
 
     upload(args.input, args.url, args.proposal, auth_token=args.token)
 
-    # normal upload
-    # python src/xchemalign/uploader.py -i ../test_data/A71EV2A_xca_staging_20241104_fake_aliases.tar.gz -u http://localhost:8080/ -p lb18145-1
-
 
 if __name__ == "__main__":
     main()

src/xchemalign/utils.py

@@ -264,10 +264,9 @@ def log(self, *args, level=0, **kwargs):
             if self.logfile:
                 print(key, *args, file=self.logfile, **kwargs)
 
-        # this is a hack to display messages coming from the server to
-        # display messages that are already prefixed with error
-        # level. not sure atm how to best integrate this with xca
-        # logging system
+        # this is a hack to display messages coming from the server
+        # that are already prefixed with error level. not sure atm how
+        # to best integrate this with xca logging system
         if level == -1:
             if self.console:
                 print(*args, file=self.console, **kwargs)