Fix arg parser and move exception to ena.py

EBI-Metagenomics · Jan 25, 2024 · 56fa1be · 56fa1be
1 parent 5fcf179
commit 56fa1be
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Showing 2 changed files with 4 additions and 5 deletions.
diff --git a/genomeuploader/ena.py b/genomeuploader/ena.py
@@ -28,6 +28,9 @@
 logger = logging.getLogger(__name__)
 
 
+class NoDataException(ValueError):
+    pass
+
 
 RUN_DEFAULT_FIELDS = ','.join([
     'study_accession',

diff --git a/genomeuploader/genome_upload.py b/genomeuploader/genome_upload.py
@@ -25,7 +25,6 @@
 
 import xml.etree.ElementTree as ET
 import xml.dom.minidom as minidom
-import requests
 
 from .ena import ENA
 
@@ -37,9 +36,6 @@
 
 ena = ENA()
 
-class NoDataException(ValueError):
-    pass
-
 
 
 '''
@@ -838,7 +834,7 @@ def __init__(self, argv=sys.argv[1:]):
         workDir = self.args.out if self.args.out else os.getcwd()
         self.upload_dir = self.generate_genomes_upload_dir(workDir, self.genomeType)
 
-    def parse_args(argv):
+    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 " +