Allow to broker to private projects

bin/add_ext_reference.py

@@ -25,7 +25,8 @@
 from ebi_eva_internal_pyutils.pg_utils import get_all_results_for_query, execute_query
 from retry import retry
 
-from eva_submission.eload_utils import check_project_exists_in_evapro, check_existing_project_in_ena
+from eva_submission.eload_utils import check_project_exists_in_evapro, \
+    check_existing_public_project_in_ena
 from eva_submission.submission_config import load_config
 
 logger = log_cfg.get_logger(__name__)
@@ -110,7 +111,7 @@ def main():
     if not check_project_exists_in_evapro(args.project_accession):
         logger.error(f'{args.project_accession} does not exist in EVAPRO')
         return 1
-    if not check_existing_project_in_ena(args.project_accession):
+    if not check_existing_public_project_in_ena(args.project_accession):
         logger.error(f'{args.project_accession} does not exist or is not public in ENA')
         return 1
     if _curie_exist(args.source_database + ":" + args.identifier):

bin/broker_submission.py

@@ -35,6 +35,8 @@ def ENA_Project(project):
 
 
 def main():
+    # Load the config_file from default location
+    load_config()
     argparse = ArgumentParser(description='Broker validated ELOAD to BioSamples and ENA')
     argparse.add_argument('--eload', required=True, type=int, help='The ELOAD number for this submission')
     argparse.add_argument('--debug', action='store_true', default=False,
@@ -61,8 +63,6 @@ def main():
     if args.debug:
         log_cfg.set_log_level(logging.DEBUG)
 
-    # Load the config_file from default location
-    load_config()
     # Optionally Set the valid VCF and metadata file
     with EloadBrokering(args.eload, args.vcf_files, args.metadata_file) as brokering:
         brokering.upgrade_config_if_needed()

eva_submission/eload_utils.py

@@ -162,8 +162,12 @@ def check_project_format(project_accession):
     return re.match(r'^PRJ(EB|NA)', project_accession)
 
 
-@retry(tries=4, delay=2, backoff=1.2, jitter=(1, 3))
 def check_existing_project_in_ena(project_accession):
+    return check_existing_public_project_in_ena(project_accession) or \
+        check_existing_private_project_in_ena(project_accession)
+
+
+def check_existing_public_project_in_ena(project_accession):
     """
     Check if a project accession exists and is public in ENA
     :param project_accession:
@@ -176,6 +180,21 @@ def check_existing_project_in_ena(project_accession):
     return True
 
 
+def check_existing_private_project_in_ena(project_accession):
+    """
+    Check if a project accession exists and is private in ENA
+    :param project_accession:
+    :return:
+    """
+    try:
+        response = requests.get(f'https://www.ebi.ac.uk/ena/submit/drop-box/cli/reference/project/{project_accession}',
+                     auth=HTTPBasicAuth(cfg.query('ena', 'username'), cfg.query('ena', 'password')))
+        response.raise_for_status()
+    except requests.exceptions.HTTPError:
+        return False
+    return True
+
+
 # Create the databases if they do not exists. Then shard them.
 collections_shard_key_map = {
     "variants_2_0": (["chr", "start"], False),