Fix insert/update doi, add --skip-registration option and refactor do…

…i commands

isimip_publisher/commands.py

@@ -471,6 +471,11 @@ def insert_doi():
     session.commit()
     session.close()
 
+    if not settings.SKIP_REGISTRATION and dois.confirm_upload():
+        dois.upload_doi(resource, settings.ISIMIP_DATA_URL,
+                        settings.DATACITE_USERNAME, settings.DATACITE_PASSWORD,
+                        settings.DATACITE_PREFIX, settings.DATACITE_TEST_MODE)
+
 
 def update_doi():
     session = database.init_database_session(settings.DATABASE)
@@ -483,12 +488,14 @@ def update_doi():
     session.commit()
     session.close()
 
+    if not settings.SKIP_REGISTRATION and dois.confirm_upload():
+        dois.upload_doi(resource, settings.ISIMIP_DATA_URL,
+                        settings.DATACITE_USERNAME, settings.DATACITE_PASSWORD,
+                        settings.DATACITE_PREFIX, settings.DATACITE_TEST_MODE)
 
-def register_doi():
-    print('Registering a DOI with DataCite is permanent. Please type "yes" to confirm.')
-    string = input()
 
-    if string.lower() == 'yes':
+def register_doi():
+    if dois.confirm_upload():
         session = database.init_database_session(settings.DATABASE)
         resource = database.fetch_resource(session, settings.DOI)
         dois.upload_doi(resource, settings.ISIMIP_DATA_URL,

isimip_publisher/main.py

@@ -93,6 +93,8 @@ def get_parser(add_path=False, add_subparsers=False):
                         help='Rights/license for the files [default: None]')
     parser.add_argument('--archived', dest='archived', action='store_true', default=False,
                         help='Check also archived files')
+    parser.add_argument('--skip-registration', dest='skip_registration', action='store_true', default=False,
+                         help='Skip the registration of the DOI when inserting/updating a resource')
     parser.add_argument('--skip-checksum', dest='skip_checksum', action='store_true', default=False,
                          help='Skip the computation of the checksum when checking')
     parser.add_argument('--log-level', dest='log_level', default='WARN',

isimip_publisher/utils/database.py

@@ -562,10 +562,10 @@ def insert_resource(session, datacite, paths, datacite_prefix):
     if not paths:
         raise RuntimeError(f'No paths were provided for {doi}.')
 
-    # gather datasets
-    datasets = []
+    # gather datasets, use a set to remove duplicate datasets (for links)
+    datasets = set()
     for path in paths:
-        datasets += retrieve_datasets(session, path, public=True, follow=True)
+        datasets.update(retrieve_datasets(session, path, public=True, follow=True))
 
     if not datasets:
         message = f'No datasets found for {doi}.'

isimip_publisher/utils/dois.py

@@ -36,3 +36,8 @@ def upload_doi(resource, isimip_data_url,
     # register the doi
     mds_doi_response = mds_client.doi_post(doi, url)
     print(mds_doi_response)
+
+
+def confirm_upload():
+    print('Registering a DOI with DataCite is permanent. Please type "yes" to confirm.')
+    return input().lower() == 'yes'