Minor fixes - env variables

EBI-Metagenomics · Feb 4, 2024 · a2756d2 · a2756d2
1 parent ff723f3
commit a2756d2
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Showing 2 changed files with 10 additions and 14 deletions.
diff --git a/.gitignore b/.gitignore
@@ -1,5 +1,3 @@
-cluster_uploader_wrapper.py
-
 #IntelliJ project structure files
 *.iml
 *.xml
@@ -71,6 +69,7 @@ venv/
 ENV/
 env.bak/
 venv.bak/
+.genome_uploader.config.env
 
 # Rope project settings
 .ropeproject
@@ -80,3 +79,6 @@ venv.bak/
 
 # Ruff
 .ruff_cache/
+
+#personal
+cluster_uploader_wrapper.py
diff --git a/genomeuploader/genome_upload.py b/genomeuploader/genome_upload.py
@@ -494,8 +494,6 @@ def combine_ENA_info(genomeInfo, ENADict):
 
         genomeInfo[g]["accessions"] = ','.join(genomeInfo[g]["accessions"])
 
-
-
 def getAccessions(accessionsFile):
     accessionDict = {}
     with open(accessionsFile, 'r') as f:
@@ -826,15 +824,15 @@ def __init__(self, argv=sys.argv[1:]):
             self.username = self.args.webin
             self.password = self.args.password
         else:
-            # Config file #
-            user_config = Path.home() / ".genome_uploader.config"
+            # Config file
+            user_config = Path.home() / ".genome_uploader.config.env"
             if user_config.exists():
-                logger.debug(f"Loading the env variables from {user_config}")
+                logger.debug("Loading the env variables from ".format(user_config))
                 load_dotenv(str(user_config))
             else:
-                cwd_config = Path.cwd() / ".genome_uploader.config"
+                cwd_config = Path.cwd() / ".genome_uploader.config.env"
                 if cwd_config.exists():
-                    logger.debug(f"Loading the variables from the current directory {Path.cwd()}.genome_uploader.config")
+                    logger.debug("Loading the variables from the current directory.")
                     load_dotenv(str(cwd_config))
                 else:
                     logger.debug("Trying to load env variables from the .env file")
@@ -857,11 +855,7 @@ def __init__(self, argv=sys.argv[1:]):
 
     def parse_args(self, argv):
         parser = argparse.ArgumentParser(formatter_class = argparse.ArgumentDefaultsHelpFormatter,
-            description="Allows to create xmls and manifest files for genome upload to ENA. " +
-            "--xmls and --manifests are needed to determine the action the script " +
-            "should perform. The use of more than one option is encouraged. To spare time, " +
-            "-xmls and -manifests should be called only if respective xml or manifest files " +
-            "do not already exist.")
+            description="Create xmls and manifest files for genome upload to ENA. ")
 
         parser.add_argument('-u', '--upload_study', type=str, help="Study accession for genomes upload")
         parser.add_argument('--genome_info', type=str, required=True, help="Genomes metadata file")