mediadive transform requires mediadive API

[realmarcin]

This means that there is something missing in the download step, likely specific API calls.

Processing mediadive: medium:137: 4%|█████▊ | 142/3325 [07:01<2:37:29, 2.97s/it] Traceback (most recent call last): File "/Users/marcin/Documents/VIMSS/ontology/KG-Hub/KG-Microbe/kg-microbe/venv/lib/python3.10/site-packages/urllib3/connectionpool.py", line 467, in _make_request self._validate_conn(conn) File "/Users/marcin/Documents/VIMSS/ontology/KG-Hub/KG-Microbe/kg-microbe/venv/lib/python3.10/site-packages/urllib3/connectionpool.py", line 1099, in _validate_conn conn.connect() File "/Users/marcin/Documents/VIMSS/ontology/KG-Hub/KG-Microbe/kg-microbe/venv/lib/python3.10/site-packages/urllib3/connection.py", line 653, in connect sock_and_verified = _ssl_wrap_socket_and_match_hostname( File "/Users/marcin/Documents/VIMSS/ontology/KG-Hub/KG-Microbe/kg-microbe/venv/lib/python3.10/site-packages/urllib3/connection.py", line 806, in ssl_wrap_socket_and_match_hostname ssl_sock = ssl_wrap_socket( File "/Users/marcin/Documents/VIMSS/ontology/KG-Hub/KG-Microbe/kg-microbe/venv/lib/python3.10/site-packages/urllib3/util/ssl.py", line 465, in ssl_wrap_socket ssl_sock = ssl_wrap_socket_impl(sock, context, tls_in_tls, server_hostname) File "/Users/marcin/Documents/VIMSS/ontology/KG-Hub/KG-Microbe/kg-microbe/venv/lib/python3.10/site-packages/urllib3/util/ssl.py", line 509, in _ssl_wrap_socket_impl return ssl_context.wrap_socket(sock, server_hostname=server_hostname) File "/Users/marcin/.pyenv/versions/3.10.11/lib/python3.10/ssl.py", line 513, in wrap_socket return self.sslsocket_class._create( File "/Users/marcin/.pyenv/versions/3.10.11/lib/python3.10/ssl.py", line 1071, in _create self.do_handshake() File "/Users/marcin/.pyenv/versions/3.10.11/lib/python3.10/ssl.py", line 1342, in do_handshake self._sslobj.do_handshake() TimeoutError: _ssl.c:990: The handshake operation timed out

The above exception was the direct cause of the following exception:

Traceback (most recent call last): File "/Users/marcin/Documents/VIMSS/ontology/KG-Hub/KG-Microbe/kg-microbe/venv/lib/python3.10/site-packages/requests/adapters.py", line 486, in send resp = conn.urlopen( File "/Users/marcin/Documents/VIMSS/ontology/KG-Hub/KG-Microbe/kg-microbe/venv/lib/python3.10/site-packages/urllib3/connectionpool.py", line 847, in urlopen retries = retries.increment( File "/Users/marcin/Documents/VIMSS/ontology/KG-Hub/KG-Microbe/kg-microbe/venv/lib/python3.10/site-packages/urllib3/util/retry.py", line 470, in increment raise reraise(type(error), error, _stacktrace) File "/Users/marcin/Documents/VIMSS/ontology/KG-Hub/KG-Microbe/kg-microbe/venv/lib/python3.10/site-packages/urllib3/util/util.py", line 39, in reraise raise value File "/Users/marcin/Documents/VIMSS/ontology/KG-Hub/KG-Microbe/kg-microbe/venv/lib/python3.10/site-packages/urllib3/connectionpool.py", line 793, in urlopen response = self._make_request( File "/Users/marcin/Documents/VIMSS/ontology/KG-Hub/KG-Microbe/kg-microbe/venv/lib/python3.10/site-packages/urllib3/connectionpool.py", line 491, in _make_request raise new_e File "/Users/marcin/Documents/VIMSS/ontology/KG-Hub/KG-Microbe/kg-microbe/venv/lib/python3.10/site-packages/urllib3/connectionpool.py", line 469, in _make_request self._raise_timeout(err=e, url=url, timeout_value=conn.timeout) File "/Users/marcin/Documents/VIMSS/ontology/KG-Hub/KG-Microbe/kg-microbe/venv/lib/python3.10/site-packages/urllib3/connectionpool.py", line 370, in _raise_timeout raise ReadTimeoutError( urllib3.exceptions.ReadTimeoutError: HTTPSConnectionPool(host='mediadive.dsmz.de', port=443): Read timed out. (read timeout=30)

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "", line 1, in File "/Users/marcin/Documents/VIMSS/ontology/KG-Hub/KG-Microbe/kg-microbe/venv/lib/python3.10/site-packages/click/core.py", line 1157, in call return self.main(*args, **kwargs) File "/Users/marcin/Documents/VIMSS/ontology/KG-Hub/KG-Microbe/kg-microbe/venv/lib/python3.10/site-packages/click/core.py", line 1078, in main rv = self.invoke(ctx) File "/Users/marcin/Documents/VIMSS/ontology/KG-Hub/KG-Microbe/kg-microbe/venv/lib/python3.10/site-packages/click/core.py", line 1688, in invoke return _process_result(sub_ctx.command.invoke(sub_ctx)) File "/Users/marcin/Documents/VIMSS/ontology/KG-Hub/KG-Microbe/kg-microbe/venv/lib/python3.10/site-packages/click/core.py", line 1434, in invoke return ctx.invoke(self.callback, **ctx.params) File "/Users/marcin/Documents/VIMSS/ontology/KG-Hub/KG-Microbe/kg-microbe/venv/lib/python3.10/site-packages/click/core.py", line 783, in invoke return __callback(*args, **kwargs) File "/Users/marcin/Documents/VIMSS/ontology/KG-Hub/KG-Microbe/kg-microbe/kg_microbe/run.py", line 72, in transform kg_transform(*args, **kwargs) File "/Users/marcin/Documents/VIMSS/ontology/KG-Hub/KG-Microbe/kg-microbe/kg_microbe/transform.py", line 89, in transform t.run(show_status=show_status) File "/Users/marcin/Documents/VIMSS/ontology/KG-Hub/KG-Microbe/kg-microbe/kg_microbe/transform_utils/mediadive/mediadive.py", line 413, in run ingredients_dict.update(self.get_compounds_of_solution(str(solution_id))) File "/Users/marcin/Documents/VIMSS/ontology/KG-Hub/KG-Microbe/kg-microbe/kg_microbe/transform_utils/mediadive/mediadive.py", line 150, in get_compounds_of_solution data = self._get_mediadive_json(url) File "/Users/marcin/Documents/VIMSS/ontology/KG-Hub/KG-Microbe/kg-microbe/kg_microbe/transform_utils/mediadive/mediadive.py", line 132, in _get_mediadive_json r = requests.get(url, timeout=30) File "/Users/marcin/Documents/VIMSS/ontology/KG-Hub/KG-Microbe/kg-microbe/venv/lib/python3.10/site-packages/requests/api.py", line 73, in get return request("get", url, params=params, **kwargs) File "/Users/marcin/Documents/VIMSS/ontology/KG-Hub/KG-Microbe/kg-microbe/venv/lib/python3.10/site-packages/requests/api.py", line 59, in request return session.request(method=method, url=url, **kwargs) File "/Users/marcin/Documents/VIMSS/ontology/KG-Hub/KG-Microbe/kg-microbe/venv/lib/python3.10/site-packages/requests_cache/session.py", line 182, in request return super().request(method, url, *args, headers=headers, **kwargs) # type: ignore File "/Users/marcin/Documents/VIMSS/ontology/KG-Hub/KG-Microbe/kg-microbe/venv/lib/python3.10/site-packages/requests/sessions.py", line 589, in request resp = self.send(prep, **send_kwargs) File "/Users/marcin/Documents/VIMSS/ontology/KG-Hub/KG-Microbe/kg-microbe/venv/lib/python3.10/site-packages/requests_cache/session.py", line 229, in send response = self._send_and_cache(request, actions, cached_response, **kwargs) File "/Users/marcin/Documents/VIMSS/ontology/KG-Hub/KG-Microbe/kg-microbe/venv/lib/python3.10/site-packages/requests_cache/session.py", line 253, in _send_and_cache response = super().send(request, **kwargs) File "/Users/marcin/Documents/VIMSS/ontology/KG-Hub/KG-Microbe/kg-microbe/venv/lib/python3.10/site-packages/requests/sessions.py", line 703, in send r = adapter.send(request, **kwargs) File "/Users/marcin/Documents/VIMSS/ontology/KG-Hub/KG-Microbe/kg-microbe/venv/lib/python3.10/site-packages/requests/adapters.py", line 532, in send raise ReadTimeout(e, request=request) requests.exceptions.ReadTimeout: HTTPSConnectionPool(host='mediadive.dsmz.de', port=443): Read timed out. (read timeout=30)