add requirement for JWT token to create database

backend/metagenedb/settings/django.py

@@ -116,7 +116,7 @@ REST_FRAMEWORK = {
 # JWT Authorization settings
 
 JWT_AUTH = {
-    'JWT_EXPIRATION_DELTA': datetime.timedelta(seconds=3600)
+    'JWT_EXPIRATION_DELTA': datetime.timedelta(days=7)
 }
 
 

backend/scripts/populate_db/import_igc_data.py

@@ -24,12 +24,12 @@ class ImportIGCGenes(object):
     GENUS_COL = 'taxo_genus'
     SELECTED_KEYS = ['gene_id', 'length', 'kegg_ko', PHYLUM_COL, GENUS_COL]
 
-    def __init__(self, annotation_file, url, skip_tax=False, skip_functions=False):
+    def __init__(self, annotation_file, url, jwt_token, skip_tax=False, skip_functions=False):
         self.annotation_file = annotation_file
         self.url = url
-        self.metagenedb_gene_api = self.METAGENEDB_GENE_API(base_url=self.url)
-        self.metagenedb_taxonomy_api = self.METAGENEDB_TAXONOMY_API(base_url=self.url)
-        self.metagenedb_function_api = self.METAGENEDB_FUNCTION_API(base_url=self.url)
+        self.metagenedb_gene_api = self.METAGENEDB_GENE_API(base_url=self.url, jwt_token=jwt_token)
+        self.metagenedb_taxonomy_api = self.METAGENEDB_TAXONOMY_API(base_url=self.url, jwt_token=jwt_token)
+        self.metagenedb_function_api = self.METAGENEDB_FUNCTION_API(base_url=self.url, jwt_token=jwt_token)
         self.total_genes = self._get_number_genes()
         self._reset_counters()
         # Skip some insertion if specified in script options
@@ -177,6 +177,7 @@ def parse_arguments():
     # Common arguments for analysis and annotations
     parser.add_argument('annotation', help='IGC annotation file')
     parser.add_argument('--url', help='base URL of the instance.', default='http://localhost/')
+    parser.add_argument('-t', '--jwt_token', help='your JWT token obtain from web app', required=True)
     parser.add_argument('--chunk_size', type=int, default=1000,
                         help='How many genes to handle and create in the same time.')
     parser.add_argument('--skip_taxonomy', action='store_true', help='Skip taxonomy information from genes.')
@@ -194,7 +195,7 @@ def run():
     args = parse_arguments()
     if args.verbose:
         logger.setLevel(logging.INFO)
-    import_igc_genes = ImportIGCGenes(args.annotation, args.url,
+    import_igc_genes = ImportIGCGenes(args.annotation, args.url, args.jwt_token,
                                       skip_tax=args.skip_taxonomy, skip_functions=args.skip_functions)
     import_igc_genes.load_annotation_file_to_db_in_chunks(chunk_size=args.chunk_size, test=args.test)
 

backend/scripts/populate_db/import_ncbi_taxonomy.py

@@ -18,8 +18,8 @@ class ImportNCBITaxonomy(object):
     METAGENEDB_TAX_API = MetageneDBCatalogTaxonomyAPI
     FOREIGN_KEY_FIELDS = ['parent_tax_id']
 
-    def __init__(self, url, tax_names_file, tax_nodes_file):
-        self.metagenedb_tax_api = self.METAGENEDB_TAX_API(base_url=url)
+    def __init__(self, url, jwt_token, tax_names_file, tax_nodes_file):
+        self.metagenedb_tax_api = self.METAGENEDB_TAX_API(base_url=url, jwt_token=jwt_token)
         self.tax_names_file = tax_names_file
         self.tax_nodes_file = tax_nodes_file
         self.total_tax = self._get_number_nodes()
@@ -104,6 +104,7 @@ def parse_arguments():
     parser.add_argument('--names', help='names.dmp file from ncbi_taxonomy', required=True)
     parser.add_argument('--skip_creation', action='store_true', help='Skip taxonomy creation.')
     parser.add_argument('--url', help='base URL of the instance.', default='http://localhost/')
+    parser.add_argument('-t', '--jwt_token', help='your JWT token obtain from web app', required=True)
     parser.add_argument('-v', '--verbose', action='store_true')
 
     try:
@@ -116,7 +117,7 @@ def run():
     args = parse_arguments()
     if args.verbose:
         logger.setLevel(logging.INFO)
-    import_ncbi_tax = ImportNCBITaxonomy(args.url, args.names, args.nodes)
+    import_ncbi_tax = ImportNCBITaxonomy(args.url, args.jwt_token, args.names, args.nodes)
     taxonomy_names = import_ncbi_tax.import_names()
     if not args.skip_creation:
         import_ncbi_tax.create_taxo_nodes(taxonomy_names)

backend/scripts/populate_db/load_kegg_ko.py

@@ -21,9 +21,9 @@ class ImportKEGGKO(object):
     ORM_SOURCE_KEY = 'source'
     KEGG_SOURCE = 'kegg'
 
-    def __init__(self, url, kegg_ko_list_api=KEGG_KO_LIST_API):
+    def __init__(self, url, jwt_token, kegg_ko_list_api=KEGG_KO_LIST_API):
         self.kegg_ko_list_api = kegg_ko_list_api
-        self.metagenedb_function_api = self.METAGENEDB_FUNCTION_API(base_url=url)
+        self.metagenedb_function_api = self.METAGENEDB_FUNCTION_API(base_url=url, jwt_token=jwt_token)
         self.processed_kegg = 0
         self.created_kegg = 0
         self.updated_kegg = 0
@@ -55,6 +55,7 @@ def parse_arguments():
     """
     parser = argparse.ArgumentParser(description=f'Populate KEGG KO database from {KEGG_KO_LIST_API}.')
     parser.add_argument('--url', help='base URL of the instance.', default='http://localhost/')
+    parser.add_argument('-t', '--jwt_token', help='your JWT token obtain from web app', required=True)
     parser.add_argument('-v', '--verbose', action='store_true')
     try:
         return parser.parse_args()
@@ -66,7 +67,7 @@ def run():
     args = parse_arguments()
     if args.verbose:
         logger.setLevel(logging.INFO)
-    import_kegg_ko = ImportKEGGKO(args.url)
+    import_kegg_ko = ImportKEGGKO(args.url, args.jwt_token)
     import_kegg_ko.load_all_kegg_ko()