diff --git a/drugstone/management/commands/populate_db.py b/drugstone/management/commands/populate_db.py index 94f64ce26a18c2afff81b2c5ef2e754a40f8aa25..5d5e8591fc92a43c6de10b9f6dde178f731b2142 100755 --- a/drugstone/management/commands/populate_db.py +++ b/drugstone/management/commands/populate_db.py @@ -86,8 +86,8 @@ class Command(BaseCommand): def populate(kwargs): - nedrex_api_url_unlicenced= "https://nedrex-api-open.zbh.uni-hamburg.de/" - nedrex_api_url_licenced = "https://nedrex-api-licenced.zbh.uni-hamburg.de/" + nedrex_api_url_open= "https://api.nedrex.net/open" + nedrex_api_url_licenced = "https://nedrex-api-licenced.zbh.uni-hamburg.de/licensed" data_dir = kwargs['data_dir'] @@ -102,7 +102,7 @@ def populate(kwargs): cache = NodeCache() update = True if kwargs['update'] else False - importer = NedrexImporter(nedrex_api_url_licenced, nedrex_api_url_unlicenced, cache) + importer = NedrexImporter(nedrex_api_url_licenced, nedrex_api_url_open, cache) populator = DataPopulator(cache) total_n = 0 @@ -152,7 +152,7 @@ def populate(kwargs): if kwargs['protein_drug']: print('Importing PDIs from unlicenced NeDRexDB...') n = NedrexImporter.import_drug_target_interactions(importer, - DatasetLoader.get_drug_target_nedrex(nedrex_api_url_unlicenced, False), + DatasetLoader.get_drug_target_nedrex(nedrex_api_url_open, False), update) total_n += n print(f'Imported {n} PDIs from unlicenced NeDRexDB') @@ -179,7 +179,7 @@ def populate(kwargs): print('Importing PDis from unlicenced NeDRexDB...') n = NedrexImporter.import_protein_disorder_associations(importer, DatasetLoader.get_protein_disorder_nedrex( - nedrex_api_url_unlicenced, False), + nedrex_api_url_open, False), update) total_n += n print(f'Imported {n} PDis from unlicenced NeDRexDB') @@ -196,7 +196,7 @@ def populate(kwargs): if kwargs['drug_disorder']: print('Importing DrDis from unlicenced NeDRexDB...') n = NedrexImporter.import_drug_disorder_indications(importer, - DatasetLoader.get_drug_disorder_nedrex(nedrex_api_url_unlicenced, False), + DatasetLoader.get_drug_disorder_nedrex(nedrex_api_url_open, False), update) total_n += n print(f'Imported {n} DrDis from unlicenced NeDRexDB') @@ -217,7 +217,7 @@ def populate(kwargs): if kwargs['protein_protein']: print('Importing PPIs from unlicenced NeDRexDB...') n = NedrexImporter.import_protein_protein_interactions(importer, - DatasetLoader.get_ppi_nedrex(nedrex_api_url_unlicenced, False), + DatasetLoader.get_ppi_nedrex(nedrex_api_url_open, False), update) total_n += n print(f'Imported {n} PPIs from unlicended NeDRexDB') diff --git a/drugstone/management/includes/DatasetLoader.py b/drugstone/management/includes/DatasetLoader.py index 804a3df0136edeaca6ce41444f0b1a12c48f4fb2..4ec25387ff4cfe5c4e6902b1f025f9dae39a793a 100644 --- a/drugstone/management/includes/DatasetLoader.py +++ b/drugstone/management/includes/DatasetLoader.py @@ -39,7 +39,9 @@ def get_ppi_biogrid(): def get_nedrex_version(): version = get_today_version() try: - version = get_metadata()['version'] + real_version = get_metadata()['version'] + if real_version != "0.0.0": + version = real_version except RetryError: pass return version @@ -50,7 +52,7 @@ def get_nedrex_source_version(source): # TODO remove once fixed in nedrex db if 'drug_central' in metadata: metadata['drugcentral'] = metadata['drug_central'] - + return metadata[source]['date']