fabianegli
commented
2 years ago Dumping this here:
https://www.ebi.ac.uk/spot/zooma/docs/api
This is the code in the test that runs throuhgh:
In [1]: from sdrf_pipelines.zooma.zooma import Zooma, SlimOlsClient
In [2]: keyword = 'human'
In [3]: client = Zooma()
In [4]: results = client.recommender(keyword, filters="ontologies:[nbcitaxon]")
In [5]: results
Out[5]:
[{'uri': None,
'annotatedProperty': {'uri': 'http://rdf.ebi.ac.uk/resource/zooma/69A7F59A19C8525E4C7B04C798596A69',
'propertyType': 'factor',
'propertyValue': 'Human'},
'_links': {'olslinks': [{'href': 'https://ves-oy-be:8080/ols/api/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FNCBITaxon_9606',
'semanticTag': 'http://purl.obolibrary.org/obo/NCBITaxon_9606'}]},
'semanticTags': ['http://purl.obolibrary.org/obo/NCBITaxon_9606'],
'replacedBy': [],
'replaces': [],
'derivedFrom': {'uri': 'http://rdf.ebi.ac.uk/resource/zooma/metabolights/8F94CFC1124A59BCEB894A9917CA77C2',
'annotatedProperty': {'uri': 'http://rdf.ebi.ac.uk/resource/zooma/69A7F59A19C8525E4C7B04C798596A69',
'propertyType': 'factor',
'propertyValue': 'Human'},
'_links': {'olslinks': [{'href': 'http://purl.obolibrary.org/obo/NCBITaxon_9606',
'semanticTag': 'http://purl.obolibrary.org/obo/NCBITaxon_9606'}]},
'semanticTags': ['http://purl.obolibrary.org/obo/NCBITaxon_9606'],
'replacedBy': [],
'replaces': [],
'provenance': {'source': {'type': 'DATABASE',
'name': 'metabolights',
'uri': 'https://www.ebi.ac.uk/metabolights'},
'evidence': 'MANUAL_CURATED',
'accuracy': 'NOT_SPECIFIED',
'generator': 'https://www.ebi.ac.uk/metabolights',
'generatedDate': 1649104721000,
'annotator': 'Zoe May Pendlington',
'annotationDate': 1538852400000},
'annotatedBiologicalEntities': [{'uri': 'http://rdf.ebi.ac.uk/resource/zooma/metabolights/1846EDBCECE5A0D6E04AC107EF21F950',
'name': 'metabo_219',
'types': ['http://www.w3.org/2002/07/owl#NamedIndividual',
'http://rdf.ebi.ac.uk/terms/zooma/Target'],
'studies': [{'uri': 'http://rdf.ebi.ac.uk/resource/zooma/metabolights/A6AA403F9EF597D6BCFAAAFB79571724',
'accession': 'MTBLS176',
'types': ['http://www.w3.org/2002/07/owl#NamedIndividual',
'http://rdf.ebi.ac.uk/terms/zooma/DatabaseEntrySource']}]}]},
'confidence': 'HIGH',
'provenance': {'source': {'type': 'DATABASE',
'name': 'zooma',
'uri': 'www.ebi.ac.uk/spot/zooma'},
'evidence': 'ZOOMA_INFERRED_FROM_CURATED',
'accuracy': None,
'generator': 'ZOOMA',
'generatedDate': 1654622176809,
'annotator': 'ZOOMA',
'annotationDate': 1654622176809},
'annotatedBiologicalEntities': []}]
In [6]: ols_terms = client.process_zooma_results(results)
In [7]: ols_terms
Out[7]:
[{'queryValue': 'Human',
'confidence': 'HIGH',
'ols_url': 'https://ves-oy-be:8080/ols/api/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FNCBITaxon_9606'}]
In [8]: ols_client = SlimOlsClient()this then fails (simplified for interative debugging)
In [9]: ols_client.get_term_from_url(ols_terms[0]['ols_url'], ontology="ncbitaxon")
---------------------------------------------------------------------------
gaierror Traceback (most recent call last)
File ~/github/fabianegli/sdrf-pipelines/venv/lib/python3.8/site-packages/urllib3/connection.py:174, in HTTPConnection._new_conn(self)
173 try:
--> 174 conn = connection.create_connection(
175 (self._dns_host, self.port), self.timeout, **extra_kw
176 )
178 except SocketTimeout:
File ~/github/fabianegli/sdrf-pipelines/venv/lib/python3.8/site-packages/urllib3/util/connection.py:72, in create_connection(address, timeout, source_address, socket_options)
68 return six.raise_from(
69 LocationParseError(u"'%s', label empty or too long" % host), None
70 )
---> 72 for res in socket.getaddrinfo(host, port, family, socket.SOCK_STREAM):
73 af, socktype, proto, canonname, sa = res
File /Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/socket.py:918, in getaddrinfo(host, port, family, type, proto, flags)
917 addrlist = []
--> 918 for res in _socket.getaddrinfo(host, port, family, type, proto, flags):
919 af, socktype, proto, canonname, sa = res
gaierror: [Errno 8] nodename nor servname provided, or not known
During handling of the above exception, another exception occurred:
NewConnectionError Traceback (most recent call last)
File ~/github/fabianegli/sdrf-pipelines/venv/lib/python3.8/site-packages/urllib3/connectionpool.py:703, in HTTPConnectionPool.urlopen(self, method, url, body, headers, retries, redirect, assert_same_host, timeout, pool_timeout, release_conn, chunked, body_pos, **response_kw)
702 # Make the request on the httplib connection object.
--> 703 httplib_response = self._make_request(
704 conn,
705 method,
706 url,
707 timeout=timeout_obj,
708 body=body,
709 headers=headers,
710 chunked=chunked,
711 )
713 # If we're going to release the connection in ``finally:``, then
714 # the response doesn't need to know about the connection. Otherwise
715 # it will also try to release it and we'll have a double-release
716 # mess.
File ~/github/fabianegli/sdrf-pipelines/venv/lib/python3.8/site-packages/urllib3/connectionpool.py:386, in HTTPConnectionPool._make_request(self, conn, method, url, timeout, chunked, **httplib_request_kw)
385 try:
--> 386 self._validate_conn(conn)
387 except (SocketTimeout, BaseSSLError) as e:
388 # Py2 raises this as a BaseSSLError, Py3 raises it as socket timeout.
File ~/github/fabianegli/sdrf-pipelines/venv/lib/python3.8/site-packages/urllib3/connectionpool.py:1040, in HTTPSConnectionPool._validate_conn(self, conn)
1039 if not getattr(conn, "sock", None): # AppEngine might not have `.sock`
-> 1040 conn.connect()
1042 if not conn.is_verified:
File ~/github/fabianegli/sdrf-pipelines/venv/lib/python3.8/site-packages/urllib3/connection.py:358, in HTTPSConnection.connect(self)
356 def connect(self):
357 # Add certificate verification
--> 358 self.sock = conn = self._new_conn()
359 hostname = self.host
File ~/github/fabianegli/sdrf-pipelines/venv/lib/python3.8/site-packages/urllib3/connection.py:186, in HTTPConnection._new_conn(self)
185 except SocketError as e:
--> 186 raise NewConnectionError(
187 self, "Failed to establish a new connection: %s" % e
188 )
190 return conn
NewConnectionError: <urllib3.connection.HTTPSConnection object at 0x10c74d6a0>: Failed to establish a new connection: [Errno 8] nodename nor servname provided, or not known
During handling of the above exception, another exception occurred:
MaxRetryError Traceback (most recent call last)
File ~/github/fabianegli/sdrf-pipelines/venv/lib/python3.8/site-packages/requests/adapters.py:440, in HTTPAdapter.send(self, request, stream, timeout, verify, cert, proxies)
439 if not chunked:
--> 440 resp = conn.urlopen(
441 method=request.method,
442 url=url,
443 body=request.body,
444 headers=request.headers,
445 redirect=False,
446 assert_same_host=False,
447 preload_content=False,
448 decode_content=False,
449 retries=self.max_retries,
450 timeout=timeout
451 )
453 # Send the request.
454 else:
File ~/github/fabianegli/sdrf-pipelines/venv/lib/python3.8/site-packages/urllib3/connectionpool.py:785, in HTTPConnectionPool.urlopen(self, method, url, body, headers, retries, redirect, assert_same_host, timeout, pool_timeout, release_conn, chunked, body_pos, **response_kw)
783 e = ProtocolError("Connection aborted.", e)
--> 785 retries = retries.increment(
786 method, url, error=e, _pool=self, _stacktrace=sys.exc_info()[2]
787 )
788 retries.sleep()
File ~/github/fabianegli/sdrf-pipelines/venv/lib/python3.8/site-packages/urllib3/util/retry.py:592, in Retry.increment(self, method, url, response, error, _pool, _stacktrace)
591 if new_retry.is_exhausted():
--> 592 raise MaxRetryError(_pool, url, error or ResponseError(cause))
594 log.debug("Incremented Retry for (url='%s'): %r", url, new_retry)
MaxRetryError: HTTPSConnectionPool(host='ves-oy-be', port=8080): Max retries exceeded with url: /ols/api/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FNCBITaxon_9606&size=100 (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x10c74d6a0>: Failed to establish a new connection: [Errno 8] nodename nor servname provided, or not known'))
During handling of the above exception, another exception occurred:
ConnectionError Traceback (most recent call last)
Input In [9], in <cell line: 1>()
----> 1 ols_client.get_term_from_url(ols_terms[0]['ols_url'], ontology="ncbitaxon")
File ~/github/fabianegli/sdrf-pipelines/sdrf_pipelines/zooma/zooma.py:33, in SlimOlsClient.get_term_from_url(url, page_size, ontology)
25 """
26 Return a list of terms by ontology
27 :param url:
(...)
30 :return:
31 """
32 url += "&" + "size=" + str(page_size)
---> 33 r = requests.get(url)
34 if r.status_code == 414:
35 raise HTTPError('URL do not exist in OLS')
File ~/github/fabianegli/sdrf-pipelines/venv/lib/python3.8/site-packages/requests/api.py:75, in get(url, params, **kwargs)
64 def get(url, params=None, **kwargs):
65 r"""Sends a GET request.
66
67 :param url: URL for the new :class:`Request` object.
(...)
72 :rtype: requests.Response
73 """
---> 75 return request('get', url, params=params, **kwargs)
File ~/github/fabianegli/sdrf-pipelines/venv/lib/python3.8/site-packages/requests/api.py:61, in request(method, url, **kwargs)
57 # By using the 'with' statement we are sure the session is closed, thus we
58 # avoid leaving sockets open which can trigger a ResourceWarning in some
59 # cases, and look like a memory leak in others.
60 with sessions.Session() as session:
---> 61 return session.request(method=method, url=url, **kwargs)
File ~/github/fabianegli/sdrf-pipelines/venv/lib/python3.8/site-packages/requests/sessions.py:529, in Session.request(self, method, url, params, data, headers, cookies, files, auth, timeout, allow_redirects, proxies, hooks, stream, verify, cert, json)
524 send_kwargs = {
525 'timeout': timeout,
526 'allow_redirects': allow_redirects,
527 }
528 send_kwargs.update(settings)
--> 529 resp = self.send(prep, **send_kwargs)
531 return resp
File ~/github/fabianegli/sdrf-pipelines/venv/lib/python3.8/site-packages/requests/sessions.py:645, in Session.send(self, request, **kwargs)
642 start = preferred_clock()
644 # Send the request
--> 645 r = adapter.send(request, **kwargs)
647 # Total elapsed time of the request (approximately)
648 elapsed = preferred_clock() - start
File ~/github/fabianegli/sdrf-pipelines/venv/lib/python3.8/site-packages/requests/adapters.py:519, in HTTPAdapter.send(self, request, stream, timeout, verify, cert, proxies)
515 if isinstance(e.reason, _SSLError):
516 # This branch is for urllib3 v1.22 and later.
517 raise SSLError(e, request=request)
--> 519 raise ConnectionError(e, request=request)
521 except ClosedPoolError as e:
522 raise ConnectionError(e, request=request)
ConnectionError: HTTPSConnectionPool(host='ves-oy-be', port=8080): Max retries exceeded with url: /ols/api/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FNCBITaxon_9606&size=100 (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x10c74d6a0>: Failed to establish a new connection: [Errno 8] nodename nor servname provided, or not known'))from zooma.py
def process_zumma_results(results):
class SlimOlsClient(:
The CI currently fails because some test tries to retrieve
http://purl.obolibrary.org/obo/NCBITaxon_9606&size=100
which fails.
When this URL is entered in a browser the browser is redirected to http://ontologies.berkeleybop.org/