ENV loading prototype

.env.example

@@ -0,0 +1,2 @@
+ENA_WEBIN=""
+ENA_WEBIN_PASSWORD=""

genomeuploader/genome_upload.py

@@ -20,9 +20,12 @@
 import argparse
 import re
 import json
-import pandas as pd
+from pathlib import Path
 from datetime import date, datetime as dt
 
+import pandas as pd
+from dotenv import load_dotenv
+
 import xml.etree.ElementTree as ET
 import xml.dom.minidom as minidom
 
@@ -825,8 +828,33 @@ def __init__(self, argv=sys.argv[1:]):
         self.genomeMetadata = self.args.genome_info
         self.genomeType = "bins" if self.args.bins else "MAGs"
         self.live = True if self.args.live else False
-        self.username = self.args.webin
-        self.password = self.args.password
+
+        if self.args.webin and self.args.password:
+            self.username = self.args.webin
+            self.password = self.args.password
+        else:
+            # Config file #
+            user_config = Path.home() / ".genome_uploader.config"
+            if user_config.exists():
+                logger.debug("Loading the env variables from {user_config}")
+                load_dotenv(str(user_config))
+            else:
+                cwd_config = Path.cwd() / ".genome_uploader.config"
+                if not cwd_config.exists():
+                    logger.debug(f"Loading the variables from the current directory {Path.cwd()}.genome_uploader.config")
+                    load_dotenv(str(cwd_config))
+                else:
+                    logger.debug("Trying to load env variables from the .env file")
+                    # from a local .env file
+                    load_dotenv()
+
+            self.username = os.getenv("ENA_WEBIN")
+            self.password = os.getenv("ENA_WEBIN_PASSWORD")
+
+        if not self.username or not self.password:
+            logger.error("ENA Webin username or password are empty")
+            sys.exit(1)
+
         self.tpa = True if self.args.tpa else False
         self.centre_name = self.args.centre_name
         self.force = True if self.args.force else False
@@ -855,9 +883,10 @@ def parse_args(self, argv):
             "option allows to validate samples beforehand")
         parser.add_argument('--tpa', action='store_true', help="Select if uploading TPA-generated genomes")
 
-        parser.add_argument('--webin', required=True, help="Webin id")
-        parser.add_argument('--password', required=True, help="Webin password")
-        parser.add_argument('--centre_name', required=True, help="Name of the centre uploading genomes")
+        # Users can provide their credentials and centre name manually or using a config file
+        parser.add_argument('--webin', required=False, help="Webin id")
+        parser.add_argument('--password', required=False, help="Webin password")
+        parser.add_argument('--centre_name', required=False, help="Name of the centre uploading genomes")
 
         args = parser.parse_args(argv)
 

pyproject.toml

@@ -22,7 +22,8 @@ classifiers = [
 
 dependencies = [
     "requests==2.26.0",
-    "pandas==1.4.1"
+    "pandas==1.4.1",
+    "python-dotenv==1.0.1"
 ]
 
 [project.optional-dependencies]