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The start of an AskOmics query ("start" button) remains in active waiting and displays an error message "Query time is too long, Use Run & Save to get your results" #489

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The start of an AskOmics query ("start" button) remains in active waiting and displays an error message "Query time is too long, Use Run & Save to get your results"#489
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mboudet
@ofilangi

Description

@ofilangi
ofilangi
opened on Feb 18, 2025

Description

Unable to start an AskOmics query. The query on the abstraction apparently blocks and does not allow any query to be performed

the service is available at : https://askomics-forum-plants-192-168-100-118.vm.openstack.genouest.org/

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Logs

askomics-1              | Traceback (most recent call last):
redis-1                 | 1:M 17 Feb 21:50:57.010 * 1 changes in 3600 seconds. Saving...
redis-1                 | 1:M 17 Feb 21:50:57.011 * Background saving started by pid 24
redis-1                 | 24:C 17 Feb 21:50:57.014 * DB saved on disk
redis-1                 | 24:C 17 Feb 21:50:57.014 * RDB: 0 MB of memory used by copy-on-write
redis-1                 | 1:M 17 Feb 21:50:57.111 * Background saving terminated with success
redis-1                 | 1:M 17 Feb 22:50:58.085 * 1 changes in 3600 seconds. Saving...
redis-1                 | 1:M 17 Feb 22:50:58.086 * Background saving started by pid 25
redis-1                 | 25:C 17 Feb 22:50:58.089 * DB saved on disk
redis-1                 | 25:C 17 Feb 22:50:58.089 * RDB: 0 MB of memory used by copy-on-write
redis-1                 | 1:M 17 Feb 22:50:58.186 * Background saving terminated with success
redis-1                 | 1:M 17 Feb 23:50:59.085 * 1 changes in 3600 seconds. Saving...
redis-1                 | 1:M 17 Feb 23:50:59.086 * Background saving started by pid 26
redis-1                 | 26:C 17 Feb 23:50:59.088 * DB saved on disk
redis-1                 | 26:C 17 Feb 23:50:59.089 * RDB: 0 MB of memory used by copy-on-write
redis-1                 | 1:M 17 Feb 23:50:59.186 * Background saving terminated with success
redis-1                 | 1:M 18 Feb 00:51:00.039 * 1 changes in 3600 seconds. Saving...
redis-1                 | 1:M 18 Feb 00:51:00.039 * Background saving started by pid 27
redis-1                 | 27:C 18 Feb 00:51:00.041 * DB saved on disk
redis-1                 | 27:C 18 Feb 00:51:00.042 * RDB: 0 MB of memory used by copy-on-write
redis-1                 | 1:M 18 Feb 00:51:00.140 * Background saving terminated with success
redis-1                 | 1:M 18 Feb 01:51:01.073 * 1 changes in 3600 seconds. Saving...
redis-1                 | 1:M 18 Feb 01:51:01.074 * Background saving started by pid 28
redis-1                 | 28:C 18 Feb 01:51:01.077 * DB saved on disk
redis-1                 | 28:C 18 Feb 01:51:01.078 * RDB: 0 MB of memory used by copy-on-write
redis-1                 | 1:M 18 Feb 01:51:01.175 * Background saving terminated with success
redis-1                 | 1:M 18 Feb 02:51:02.050 * 1 changes in 3600 seconds. Saving...
redis-1                 | 1:M 18 Feb 02:51:02.051 * Background saving started by pid 29
redis-1                 | 29:C 18 Feb 02:51:02.053 * DB saved on disk
redis-1                 | 29:C 18 Feb 02:51:02.054 * RDB: 0 MB of memory used by copy-on-write
redis-1                 | 1:M 18 Feb 02:51:02.151 * Background saving terminated with success
redis-1                 | 1:M 18 Feb 03:51:03.093 * 1 changes in 3600 seconds. Saving...
redis-1                 | 1:M 18 Feb 03:51:03.093 * Background saving started by pid 30
redis-1                 | 30:C 18 Feb 03:51:03.095 * DB saved on disk
redis-1                 | 30:C 18 Feb 03:51:03.096 * RDB: 0 MB of memory used by copy-on-write
redis-1                 | 1:M 18 Feb 03:51:03.194 * Background saving terminated with success
redis-1                 | 1:M 18 Feb 04:51:04.010 * 1 changes in 3600 seconds. Saving...
redis-1                 | 1:M 18 Feb 04:51:04.011 * Background saving started by pid 31
redis-1                 | 31:C 18 Feb 04:51:04.013 * DB saved on disk
redis-1                 | 31:C 18 Feb 04:51:04.014 * RDB: 0 MB of memory used by copy-on-write
redis-1                 | 1:M 18 Feb 04:51:04.111 * Background saving terminated with success
redis-1                 | 1:M 18 Feb 05:51:05.038 * 1 changes in 3600 seconds. Saving...
redis-1                 | 1:M 18 Feb 05:51:05.039 * Background saving started by pid 32
redis-1                 | 32:C 18 Feb 05:51:05.042 * DB saved on disk
redis-1                 | 32:C 18 Feb 05:51:05.042 * RDB: 0 MB of memory used by copy-on-write
redis-1                 | 1:M 18 Feb 05:51:05.140 * Background saving terminated with success
redis-1                 | 1:M 18 Feb 06:51:06.013 * 1 changes in 3600 seconds. Saving...
redis-1                 | 1:M 18 Feb 06:51:06.013 * Background saving started by pid 33
redis-1                 | 33:C 18 Feb 06:51:06.016 * DB saved on disk
redis-1                 | 33:C 18 Feb 06:51:06.016 * RDB: 0 MB of memory used by copy-on-write
redis-1                 | 1:M 18 Feb 06:51:06.114 * Background saving terminated with success
redis-1                 | 1:M 18 Feb 07:51:07.008 * 1 changes in 3600 seconds. Saving...
redis-1                 | 1:M 18 Feb 07:51:07.009 * Background saving started by pid 34
redis-1                 | 34:C 18 Feb 07:51:07.012 * DB saved on disk
redis-1                 | 34:C 18 Feb 07:51:07.013 * RDB: 0 MB of memory used by copy-on-write
redis-1                 | 1:M 18 Feb 07:51:07.110 * Background saving terminated with success
askomics-1              |   File "/askomics/askomics/libaskomics/SparqlQueryLauncher.py", line 321, in execute_query
askomics-1              |     results = self.endpoint.query().convert()
askomics-1              |   File "/askomics/venv/lib/python3.8/site-packages/SPARQLWrapper/Wrapper.py", line 960, in query
askomics-1              |     return QueryResult(self._query())
askomics-1              |   File "/askomics/venv/lib/python3.8/site-packages/SPARQLWrapper/Wrapper.py", line 926, in _query
askomics-1              |     response = urlopener(request)
askomics-1              |   File "/usr/lib/python3.8/urllib/request.py", line 222, in urlopen
askomics-1              |     return opener.open(url, data, timeout)
askomics-1              |   File "/usr/lib/python3.8/urllib/request.py", line 525, in open
askomics-1              |     response = self._open(req, data)
askomics-1              |   File "/usr/lib/python3.8/urllib/request.py", line 542, in _open
askomics-1              |     result = self._call_chain(self.handle_open, protocol, protocol +
askomics-1              |   File "/usr/lib/python3.8/urllib/request.py", line 502, in _call_chain
askomics-1              |     result = func(*args)
askomics-1              |   File "/usr/lib/python3.8/urllib/request.py", line 1383, in http_open
askomics-1              |     return self.do_open(http.client.HTTPConnection, req)
askomics-1              |   File "/usr/lib/python3.8/urllib/request.py", line 1357, in do_open
askomics-1              |     raise URLError(err)
askomics-1              | urllib.error.URLError: <urlopen error [Errno 111] Connection refused>
askomics-1              | 
askomics-1              | During handling of the above exception, another exception occurred:
askomics-1              | 
askomics-1              | Traceback (most recent call last):
askomics-1              |   File "/askomics/askomics/api/query.py", line 39, in query
askomics-1              |     startpoints = tse.get_startpoints()
askomics-1              |   File "/askomics/askomics/libaskomics/TriplestoreExplorer.py", line 153, in get_startpoints
askomics-1              |     header, data = query_launcher.process_query(query_builder.prefix_query(query))
askomics-1              |   File "/askomics/askomics/libaskomics/SparqlQueryLauncher.py", line 266, in process_query
askomics-1              |     return self.parse_results(self.execute_query(query, isql_api=isql_api, is_update=is_update))
askomics-1              |   File "/askomics/askomics/libaskomics/SparqlQueryLauncher.py", line 329, in execute_query
askomics-1              |     raise type(e)("Triplestore error: {}".format(str(e))).with_traceback(sys.exc_info()[2])
askomics-1              |   File "/askomics/askomics/libaskomics/SparqlQueryLauncher.py", line 321, in execute_query
askomics-1              |     results = self.endpoint.query().convert()
askomics-1              |   File "/askomics/venv/lib/python3.8/site-packages/SPARQLWrapper/Wrapper.py", line 960, in query
askomics-1              |     return QueryResult(self._query())
askomics-1              |   File "/askomics/venv/lib/python3.8/site-packages/SPARQLWrapper/Wrapper.py", line 926, in _query
askomics-1              |     response = urlopener(request)
askomics-1              |   File "/usr/lib/python3.8/urllib/request.py", line 222, in urlopen
askomics-1              |     return opener.open(url, data, timeout)
askomics-1              |   File "/usr/lib/python3.8/urllib/request.py", line 525, in open
askomics-1              |     response = self._open(req, data)
askomics-1              |   File "/usr/lib/python3.8/urllib/request.py", line 542, in _open
askomics-1              |     result = self._call_chain(self.handle_open, protocol, protocol +
askomics-1              |   File "/usr/lib/python3.8/urllib/request.py", line 502, in _call_chain
askomics-1              |     result = func(*args)
askomics-1              |   File "/usr/lib/python3.8/urllib/request.py", line 1383, in http_open
askomics-1              |     return self.do_open(http.client.HTTPConnection, req)
askomics-1              |   File "/usr/lib/python3.8/urllib/request.py", line 1357, in do_open
askomics-1              |     raise URLError(err)
askomics-1              | urllib.error.URLError: <urlopen error Triplestore error: <urlopen error [Errno 111] Connection refused>>
askomics-1              | [2025-02-17 15:51:42 +0000] [891] [ERROR] Worker (pid:893) exited with code 1
askomics-1              | [2025-02-17 15:51:42 +0000] [891] [ERROR] Worker (pid:893) exited with code 1.
askomics-1              | [2025-02-17 15:51:42 +0000] [1031] [INFO] Booting worker with pid: 1031
askomics-1              | [2025-02-17 15:57:21 +0000] [891] [CRITICAL] WORKER TIMEOUT (pid:1031)
askomics-1              | [2025-02-17 15:57:21 +0000] [1031] [INFO] Worker exiting (pid: 1031)
askomics-1              | [2025-02-17 15:57:21 +0000] [891] [ERROR] Worker (pid:1031) exited with code 1
askomics-1              | [2025-02-17 15:57:21 +0000] [891] [ERROR] Worker (pid:1031) exited with code 1.
askomics-1              | [2025-02-17 15:57:21 +0000] [1077] [INFO] Booting worker with pid: 1077
askomics-1              | [2025-02-18 07:02:36 +0000] [891] [CRITICAL] WORKER TIMEOUT (pid:1077)
askomics-1              | [2025-02-18 07:02:36 +0000] [1077] [INFO] Worker exiting (pid: 1077)
askomics-1              | [2025-02-18 07:02:36 +0000] [891] [ERROR] Worker (pid:1077) exited with code 1
askomics-1              | [2025-02-18 07:02:36 +0000] [891] [ERROR] Worker (pid:1077) exited with code 1.
askomics-1              | [2025-02-18 07:02:36 +0000] [1123] [INFO] Booting worker with pid: 1123
askomics-1              | [2025-02-18 07:02:51 +0000] [891] [CRITICAL] WORKER TIMEOUT (pid:985)
askomics-1              | [2025-02-18 07:02:51 +0000] [985] [INFO] Worker exiting (pid: 985)
askomics-1              | [2025-02-18 07:02:51 +0000] [891] [ERROR] Worker (pid:985) exited with code 1
askomics-1              | [2025-02-18 07:02:51 +0000] [891] [ERROR] Worker (pid:985) exited with code 1.
askomics-1              | [2025-02-18 07:02:51 +0000] [1169] [INFO] Booting worker with pid: 1169
askomics-1              | [2025-02-18 08:25:42 +0000] [891] [CRITICAL] WORKER TIMEOUT (pid:1123)
askomics-1              | [2025-02-18 08:25:42 +0000] [1123] [INFO] Worker exiting (pid: 1123)
askomics-1              | [2025-02-18 08:25:42 +0000] [891] [ERROR] Worker (pid:1123) exited with code 1
askomics-1              | [2025-02-18 08:25:42 +0000] [891] [ERROR] Worker (pid:1123) exited with code 1.
askomics-1              | [2025-02-18 08:25:42 +0000] [1215] [INFO] Booting worker with pid: 1215
services:
    askomics:
        image: askomics/flaskomics:4.5.0
        env_file:
            - askomics.env
        volumes:
            - ./output/askomics:/tmp/askomics

    celery_askomics:
        image: askomics/celery-flaskomics:4.5.0
        env_file:
            - askomics.env
        volumes:
            - ./output/askomics:/tmp/askomics

    celerybeat_askomics:
        image: askomics/celery-flaskomics:4.5.0
        env_file:
            - askomics.env
        volumes:
            - ./output/askomics:/tmp/askomics
        command: make serve-celery-beat

    virtuoso:
        image: askomics/virtuoso:latest
        env_file:
            - virtuoso_16GB.env
        volumes:
            - ./output/virtuoso:/data
    isqlapi:
        image: xgaia/isql-api:2.1.1
        environment:
            WORKER_NUMBER: 20
            ISQL_API_VIRTUOSO_DSN: virtuoso
            VIRTUOSO_HOST: virtuoso
            VIRTUOSO_ISQL_PORT: 1111
            ISQL_API_VIRTUOSO_USERNAME: XXXXXXXXXXXXXX
            ISQL_API_VIRTUOSO_PASSWORD: XXXXXXXXXXXXX
    
    formulaires_askomics:
        build:
            context: ./formulaires_askomics
            dockerfile: Dockerfile
        volumes:
            - ./formulaires_askomics:/app
        environment:
            - SPARQL_ENDPOINT=http://virtuoso:8890/sparql
        depends_on:
            - virtuoso
    redis:
        image: redis:4.0

    nginx:
        image: nginx:1.17
        volumes:
            - ./nginx.conf:/tmp/nginx.conf
            - ./output/nginx/log:/var/log/nginx
        ports:
            - "80:80"
        env_file:
            - nginx.env
        command: /bin/bash -c "envsubst < /tmp/nginx.conf > /etc/nginx/conf.d/default.conf && nginx -g 'daemon off;'"

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