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"

[ofilangi]

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/

Screenshot

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;'"