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OpenSILEX / opensilex-docker-compose

This project aims to create a opensilex instance running on docker-compose stack
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Unable to open opensilex web application #4

Open harryle95 opened 4 months ago

harryle95 commented 4 months ago

Hi everyone,

I followed the steps in README but was not able to open the application at http://localhost:28081/sandbox/app

The commands used were: 

git clone --branch 1.2.1 https://github.com/OpenSILEX/opensilex-docker-compose
cd opensilex-docker-compose
docker compose --env-file opensilex.env build --build-arg UID=$(id -u) --build-arg GID=$(id -g)
docker compose --env-file opensilex.env up start_opensilex_stack -d

After this step, I tried creating the admin account:

docker exec -it opensilex-docker-opensilexapp ./bin/opensilex.sh user add --admin --email=admin@opensilex.org --lang=fr --firstName=firstName --lastName=lastName --password=admin

This is the output of docker ps: image

And this is the logs of the opensilex container: image

Trying to open the app on browser gives me a connection reset error: image

System information: Ubuntu: 22.04 Docker version: 25.0.3

harryle95 commented 4 months ago

Just to follow up, after rebooting my computer and change rd4j port to 8080, this is the output of docker logs opensilex-docker-opensilexapp:

Running ./bin/opensilex.sh server start --host=localhost --port=8081 --adminPort=4081 --CONFIG_FILE=/home/opensilex/config/opensilex.yml 
12 Feb 2024;02:31:24.804 [main] INFO  org.opensilex.server.extensions.APIExtension     - CLI input parameters : server
12 Feb 2024;02:31:24.807 [main] INFO  org.opensilex.server.extensions.APIExtension     - CLI input parameters : start
12 Feb 2024;02:31:24.807 [main] INFO  org.opensilex.server.extensions.APIExtension     - CLI input parameters : --host=localhost
12 Feb 2024;02:31:24.807 [main] INFO  org.opensilex.server.extensions.APIExtension     - CLI input parameters : --port=8081
12 Feb 2024;02:31:24.808 [main] INFO  org.opensilex.server.extensions.APIExtension     - CLI input parameters : --adminPort=4081
12 Feb 2024;02:31:24.808 [main] INFO  org.opensilex.server.extensions.APIExtension     - Using config file : /home/opensilex/config/opensilex.yml
12 Feb 2024;02:44:11.799 [main] INFO  org.reflections.Reflections - Reflections took 220 ms to scan 10 urls, producing 239 keys and 1528 values 
12 Feb 2024;02:44:12.213 [main] INFO  org.mongodb.driver.client - MongoClient with metadata {"driver": {"name": "mongo-java-driver|sync", "version": "4.11.0"}, "os": {"type": "Linux", "name": "Linux", "architecture": "amd64", "version": "6.1.0-1029-oem"}, "platform": "Java/Oracle Corporation/11.0.16+8"} created with settings MongoClientSettings{readPreference=primary, writeConcern=WriteConcern{w=null, wTimeout=null ms, journal=null}, retryWrites=true, retryReads=true, readConcern=ReadConcern{level=null}, credential=null, transportSettings=null, streamFactoryFactory=null, commandListeners=[], codecRegistry=ProvidersCodecRegistry{codecProviders=[ProvidersCodecRegistry{codecProviders=[ValueCodecProvider{}, BsonValueCodecProvider{}, DBRefCodecProvider{}, DBObjectCodecProvider{}, DocumentCodecProvider{}, CollectionCodecProvider{}, IterableCodecProvider{}, MapCodecProvider{}, GeoJsonCodecProvider{}, GridFSFileCodecProvider{}, Jsr310CodecProvider{}, JsonObjectCodecProvider{}, BsonCodecProvider{}, EnumCodecProvider{}, com.mongodb.client.model.mql.ExpressionCodecProvider@351c6341, com.mongodb.Jep395RecordCodecProvider@32069394, com.mongodb.KotlinCodecProvider@70421a08]}, ProvidersCodecRegistry{codecProviders=[MapOfCodecsProvider{codecsMap={class java.lang.Object=org.opensilex.nosql.mongodb.codec.ObjectCodec@5dba3fdc, class java.net.URI=org.opensilex.nosql.mongodb.codec.URICodec@bea5941, class java.time.ZonedDateTime=org.opensilex.nosql.mongodb.codec.ZonedDateTimeCodec@df6f19b}}]}, ProvidersCodecRegistry{codecProviders=[GeoJsonCodecProvider{}, org.bson.codecs.pojo.PojoCodecProvider@6d842877]}]}, loggerSettings=LoggerSettings{maxDocumentLength=1000}, clusterSettings={hosts=[opensilex-docker-mongodb:27017], srvServiceName=mongodb, mode=SINGLE, requiredClusterType=UNKNOWN, requiredReplicaSetName='null', serverSelector='null', clusterListeners='[]', serverSelectionTimeout='10000 ms', localThreshold='15 ms'}, socketSettings=SocketSettings{connectTimeoutMS=10000, readTimeoutMS=30000, receiveBufferSize=0, proxySettings=ProxySettings{host=null, port=null, username=null, password=null}}, heartbeatSocketSettings=SocketSettings{connectTimeoutMS=10000, readTimeoutMS=10000, receiveBufferSize=0, proxySettings=ProxySettings{host=null, port=null, username=null, password=null}}, connectionPoolSettings=ConnectionPoolSettings{maxSize=100, minSize=0, maxWaitTimeMS=120000, maxConnectionLifeTimeMS=0, maxConnectionIdleTimeMS=0, maintenanceInitialDelayMS=0, maintenanceFrequencyMS=60000, connectionPoolListeners=[], maxConnecting=2}, serverSettings=ServerSettings{heartbeatFrequencyMS=10000, minHeartbeatFrequencyMS=500, serverListeners='[]', serverMonitorListeners='[]'}, sslSettings=SslSettings{enabled=false, invalidHostNameAllowed=false, context=null}, applicationName='null', compressorList=[], uuidRepresentation=UNSPECIFIED, serverApi=null, autoEncryptionSettings=null, dnsClient=null, inetAddressResolver=null, contextProvider=null}
12 Feb 2024;02:44:12.240 [cluster-ClusterId{value='65c985fc56318a664d8f32e2', description='null'}-opensilex-docker-mongodb:27017] INFO  org.mongodb.driver.cluster - Monitor thread successfully connected to server with description ServerDescription{address=opensilex-docker-mongodb:27017, type=REPLICA_SET_PRIMARY, state=CONNECTED, ok=true, minWireVersion=0, maxWireVersion=13, maxDocumentSize=16777216, logicalSessionTimeoutMinutes=30, roundTripTimeNanos=22470312, setName='opensilex', canonicalAddress=opensilex-docker-mongodb:27017, hosts=[opensilex-docker-mongodb:27017], passives=[], arbiters=[], primary='opensilex-docker-mongodb:27017', tagSet=TagSet{[]}, electionId=7fffffff000000000000001a, setVersion=1, topologyVersion=TopologyVersion{processId=65c94bac23092b2cfa7958fc, counter=6}, lastWriteDate=Mon Feb 12 02:44:05 UTC 2024, lastUpdateTimeNanos=14101774328057}
12 Feb 2024;02:44:12.245 [main] INFO  org.mongodb.driver.cluster - No server chosen by WritableServerSelector from cluster description ClusterDescription{type=UNKNOWN, connectionMode=SINGLE, serverDescriptions=[ServerDescription{address=opensilex-docker-mongodb:27017, type=UNKNOWN, state=CONNECTING}]}. Waiting for 10000 ms before timing out
12 Feb 2024;02:44:12.284 [main] INFO  org.mongodb.driver.client - MongoClient with metadata {"driver": {"name": "mongo-java-driver|sync", "version": "4.11.0"}, "os": {"type": "Linux", "name": "Linux", "architecture": "amd64", "version": "6.1.0-1029-oem"}, "platform": "Java/Oracle Corporation/11.0.16+8"} created with settings MongoClientSettings{readPreference=primary, writeConcern=WriteConcern{w=null, wTimeout=null ms, journal=null}, retryWrites=true, retryReads=true, readConcern=ReadConcern{level=null}, credential=null, transportSettings=null, streamFactoryFactory=null, commandListeners=[], codecRegistry=ProvidersCodecRegistry{codecProviders=[ProvidersCodecRegistry{codecProviders=[ValueCodecProvider{}, BsonValueCodecProvider{}, DBRefCodecProvider{}, DBObjectCodecProvider{}, DocumentCodecProvider{}, CollectionCodecProvider{}, IterableCodecProvider{}, MapCodecProvider{}, GeoJsonCodecProvider{}, GridFSFileCodecProvider{}, Jsr310CodecProvider{}, JsonObjectCodecProvider{}, BsonCodecProvider{}, EnumCodecProvider{}, com.mongodb.client.model.mql.ExpressionCodecProvider@351c6341, com.mongodb.Jep395RecordCodecProvider@32069394, com.mongodb.KotlinCodecProvider@70421a08]}, ProvidersCodecRegistry{codecProviders=[MapOfCodecsProvider{codecsMap={class java.lang.Object=org.opensilex.nosql.mongodb.codec.ObjectCodec@6651efa4, class java.net.URI=org.opensilex.nosql.mongodb.codec.URICodec@1ac25dbb, class java.time.ZonedDateTime=org.opensilex.nosql.mongodb.codec.ZonedDateTimeCodec@4db568e1}}]}, ProvidersCodecRegistry{codecProviders=[GeoJsonCodecProvider{}, org.bson.codecs.pojo.PojoCodecProvider@7bc8ffbc]}]}, loggerSettings=LoggerSettings{maxDocumentLength=1000}, clusterSettings={hosts=[opensilex-docker-mongodb:27017], srvServiceName=mongodb, mode=SINGLE, requiredClusterType=UNKNOWN, requiredReplicaSetName='null', serverSelector='null', clusterListeners='[]', serverSelectionTimeout='10000 ms', localThreshold='15 ms'}, socketSettings=SocketSettings{connectTimeoutMS=10000, readTimeoutMS=30000, receiveBufferSize=0, proxySettings=ProxySettings{host=null, port=null, username=null, password=null}}, heartbeatSocketSettings=SocketSettings{connectTimeoutMS=10000, readTimeoutMS=10000, receiveBufferSize=0, proxySettings=ProxySettings{host=null, port=null, username=null, password=null}}, connectionPoolSettings=ConnectionPoolSettings{maxSize=100, minSize=0, maxWaitTimeMS=120000, maxConnectionLifeTimeMS=0, maxConnectionIdleTimeMS=0, maintenanceInitialDelayMS=0, maintenanceFrequencyMS=60000, connectionPoolListeners=[], maxConnecting=2}, serverSettings=ServerSettings{heartbeatFrequencyMS=10000, minHeartbeatFrequencyMS=500, serverListeners='[]', serverMonitorListeners='[]'}, sslSettings=SslSettings{enabled=false, invalidHostNameAllowed=false, context=null}, applicationName='null', compressorList=[], uuidRepresentation=UNSPECIFIED, serverApi=null, autoEncryptionSettings=null, dnsClient=null, inetAddressResolver=null, contextProvider=null}
12 Feb 2024;02:44:12.285 [main] INFO  org.mongodb.driver.cluster - No server chosen by WritableServerSelector from cluster description ClusterDescription{type=UNKNOWN, connectionMode=SINGLE, serverDescriptions=[ServerDescription{address=opensilex-docker-mongodb:27017, type=UNKNOWN, state=CONNECTING}]}. Waiting for 10000 ms before timing out
12 Feb 2024;02:44:12.285 [cluster-ClusterId{value='65c985fc56318a664d8f32e3', description='null'}-opensilex-docker-mongodb:27017] INFO  org.mongodb.driver.cluster - Monitor thread successfully connected to server with description ServerDescription{address=opensilex-docker-mongodb:27017, type=REPLICA_SET_PRIMARY, state=CONNECTED, ok=true, minWireVersion=0, maxWireVersion=13, maxDocumentSize=16777216, logicalSessionTimeoutMinutes=30, roundTripTimeNanos=1328952, setName='opensilex', canonicalAddress=opensilex-docker-mongodb:27017, hosts=[opensilex-docker-mongodb:27017], passives=[], arbiters=[], primary='opensilex-docker-mongodb:27017', tagSet=TagSet{[]}, electionId=7fffffff000000000000001a, setVersion=1, topologyVersion=TopologyVersion{processId=65c94bac23092b2cfa7958fc, counter=6}, lastWriteDate=Mon Feb 12 02:44:05 UTC 2024, lastUpdateTimeNanos=14101820845361}
12 Feb 2024;02:44:12.297 [main] INFO  org.mongodb.driver.client - MongoClient with metadata {"driver": {"name": "mongo-java-driver|sync", "version": "4.11.0"}, "os": {"type": "Linux", "name": "Linux", "architecture": "amd64", "version": "6.1.0-1029-oem"}, "platform": "Java/Oracle Corporation/11.0.16+8"} created with settings MongoClientSettings{readPreference=primary, writeConcern=WriteConcern{w=null, wTimeout=null ms, journal=null}, retryWrites=true, retryReads=true, readConcern=ReadConcern{level=null}, credential=null, transportSettings=null, streamFactoryFactory=null, commandListeners=[], codecRegistry=ProvidersCodecRegistry{codecProviders=[ProvidersCodecRegistry{codecProviders=[ValueCodecProvider{}, BsonValueCodecProvider{}, DBRefCodecProvider{}, DBObjectCodecProvider{}, DocumentCodecProvider{}, CollectionCodecProvider{}, IterableCodecProvider{}, MapCodecProvider{}, GeoJsonCodecProvider{}, GridFSFileCodecProvider{}, Jsr310CodecProvider{}, JsonObjectCodecProvider{}, BsonCodecProvider{}, EnumCodecProvider{}, com.mongodb.client.model.mql.ExpressionCodecProvider@351c6341, com.mongodb.Jep395RecordCodecProvider@32069394, com.mongodb.KotlinCodecProvider@70421a08]}, ProvidersCodecRegistry{codecProviders=[MapOfCodecsProvider{codecsMap={class java.lang.Object=org.opensilex.nosql.mongodb.codec.ObjectCodec@7cbe3a05, class java.net.URI=org.opensilex.nosql.mongodb.codec.URICodec@40b70f31, class java.time.ZonedDateTime=org.opensilex.nosql.mongodb.codec.ZonedDateTimeCodec@3adde4ea}}]}, ProvidersCodecRegistry{codecProviders=[GeoJsonCodecProvider{}, org.bson.codecs.pojo.PojoCodecProvider@75663443]}]}, loggerSettings=LoggerSettings{maxDocumentLength=1000}, clusterSettings={hosts=[opensilex-docker-mongodb:27017], srvServiceName=mongodb, mode=SINGLE, requiredClusterType=UNKNOWN, requiredReplicaSetName='null', serverSelector='null', clusterListeners='[]', serverSelectionTimeout='10000 ms', localThreshold='15 ms'}, socketSettings=SocketSettings{connectTimeoutMS=10000, readTimeoutMS=30000, receiveBufferSize=0, proxySettings=ProxySettings{host=null, port=null, username=null, password=null}}, heartbeatSocketSettings=SocketSettings{connectTimeoutMS=10000, readTimeoutMS=10000, receiveBufferSize=0, proxySettings=ProxySettings{host=null, port=null, username=null, password=null}}, connectionPoolSettings=ConnectionPoolSettings{maxSize=100, minSize=0, maxWaitTimeMS=120000, maxConnectionLifeTimeMS=0, maxConnectionIdleTimeMS=0, maintenanceInitialDelayMS=0, maintenanceFrequencyMS=60000, connectionPoolListeners=[], maxConnecting=2}, serverSettings=ServerSettings{heartbeatFrequencyMS=10000, minHeartbeatFrequencyMS=500, serverListeners='[]', serverMonitorListeners='[]'}, sslSettings=SslSettings{enabled=false, invalidHostNameAllowed=false, context=null}, applicationName='null', compressorList=[], uuidRepresentation=UNSPECIFIED, serverApi=null, autoEncryptionSettings=null, dnsClient=null, inetAddressResolver=null, contextProvider=null}
12 Feb 2024;02:44:12.298 [main] INFO  org.opensilex.nosql.mongodb.MongoDBService - [CHECK_MONGO_SERVER_CONNECTION] timeout: 10000ms [START]
12 Feb 2024;02:44:12.298 [cluster-ClusterId{value='65c985fc56318a664d8f32e4', description='null'}-opensilex-docker-mongodb:27017] INFO  org.mongodb.driver.cluster - Monitor thread successfully connected to server with description ServerDescription{address=opensilex-docker-mongodb:27017, type=REPLICA_SET_PRIMARY, state=CONNECTED, ok=true, minWireVersion=0, maxWireVersion=13, maxDocumentSize=16777216, logicalSessionTimeoutMinutes=30, roundTripTimeNanos=1238815, setName='opensilex', canonicalAddress=opensilex-docker-mongodb:27017, hosts=[opensilex-docker-mongodb:27017], passives=[], arbiters=[], primary='opensilex-docker-mongodb:27017', tagSet=TagSet{[]}, electionId=7fffffff000000000000001a, setVersion=1, topologyVersion=TopologyVersion{processId=65c94bac23092b2cfa7958fc, counter=6}, lastWriteDate=Mon Feb 12 02:44:05 UTC 2024, lastUpdateTimeNanos=14101834503577}
12 Feb 2024;02:44:12.321 [main] INFO  org.opensilex.nosql.mongodb.MongoDBService - [CHECK_MONGO_SERVER_CONNECTION Document{{ok=1.0, $clusterTime=Document{{clusterTime=Timestamp{value=7334540755463045121, seconds=1707705845, inc=1}, signature=Document{{hash=org.bson.types.Binary@c98f581, keyId=0}}}}, operationTime=Timestamp{value=7334540755463045121, seconds=1707705845, inc=1}}} [OK]
Exception in thread "main" org.opensilex.sparql.exceptions.SPARQLException: org.eclipse.rdf4j.repository.http.HTTPQueryEvaluationException: Request failed with status 404: http://opensilex-docker-rdf4j:8080/rdf4j-server/repositories/opensilex-docker-db
    at org.opensilex.sparql.ontology.store.AbstractOntologyStore.load(AbstractOntologyStore.java:157)
    at org.opensilex.sparql.SPARQLModule.initOntologyStore(SPARQLModule.java:200)
    at org.opensilex.sparql.SPARQLModule.startup(SPARQLModule.java:219)
    at org.opensilex.OpenSilex.startup(OpenSilex.java:537)
    at org.opensilex.cli.MainCommand.main(MainCommand.java:95)
Caused by: org.eclipse.rdf4j.repository.http.HTTPQueryEvaluationException: Request failed with status 404: http://opensilex-docker-rdf4j:8080/rdf4j-server/repositories/opensilex-docker-db
    at org.eclipse.rdf4j.repository.http.HTTPTupleQuery.evaluate(HTTPTupleQuery.java:50)
    at org.opensilex.sparql.rdf4j.RDF4JConnection.executeSelectQueryAsStream(RDF4JConnection.java:162)
    at org.opensilex.sparql.service.SPARQLService.executeSelectQueryAsStream(SPARQLService.java:237)
    at org.opensilex.sparql.ontology.store.OntologyStoreLoader.getModels(OntologyStoreLoader.java:218)
    at org.opensilex.sparql.ontology.store.OntologyStoreLoader.getClasses(OntologyStoreLoader.java:256)
    at org.opensilex.sparql.ontology.store.AbstractOntologyStore.load(AbstractOntologyStore.java:133)
    ... 4 more
Caused by: org.eclipse.rdf4j.repository.RepositoryException: Request failed with status 404: http://opensilex-docker-rdf4j:8080/rdf4j-server/repositories/opensilex-docker-db
    at org.eclipse.rdf4j.http.client.SPARQLProtocolSession.executeOK(SPARQLProtocolSession.java:1008)
    at org.eclipse.rdf4j.http.client.SPARQLProtocolSession.sendTupleQueryViaHttp(SPARQLProtocolSession.java:755)
    at org.eclipse.rdf4j.http.client.SPARQLProtocolSession.getBackgroundTupleQueryResult(SPARQLProtocolSession.java:650)
    at org.eclipse.rdf4j.http.client.SPARQLProtocolSession.sendTupleQuery(SPARQLProtocolSession.java:363)
    at org.eclipse.rdf4j.repository.http.HTTPTupleQuery.evaluate(HTTPTupleQuery.java:47)
    ... 9 more
Running ./bin/opensilex.sh server start --host=localhost --port=8081 --adminPort=4081 --CONFIG_FILE=/home/opensilex/config/opensilex.yml 
14 Feb 2024;01:02:31.975 [main] INFO  org.opensilex.server.extensions.APIExtension     - CLI input parameters : server
14 Feb 2024;01:02:31.978 [main] INFO  org.opensilex.server.extensions.APIExtension     - CLI input parameters : start
14 Feb 2024;01:02:31.978 [main] INFO  org.opensilex.server.extensions.APIExtension     - CLI input parameters : --host=localhost
14 Feb 2024;01:02:31.978 [main] INFO  org.opensilex.server.extensions.APIExtension     - CLI input parameters : --port=8081
14 Feb 2024;01:02:31.978 [main] INFO  org.opensilex.server.extensions.APIExtension     - CLI input parameters : --adminPort=4081
14 Feb 2024;01:02:31.978 [main] INFO  org.opensilex.server.extensions.APIExtension     - Using config file : /home/opensilex/config/opensilex.yml
14 Feb 2024;01:02:44.290 [main] INFO  org.reflections.Reflections - Reflections took 322 ms to scan 10 urls, producing 239 keys and 1528 values 
14 Feb 2024;01:02:44.792 [main] INFO  org.mongodb.driver.client - MongoClient with metadata {"driver": {"name": "mongo-java-driver|sync", "version": "4.11.0"}, "os": {"type": "Linux", "name": "Linux", "architecture": "amd64", "version": "6.1.0-1033-oem"}, "platform": "Java/Oracle Corporation/11.0.16+8"} created with settings MongoClientSettings{readPreference=primary, writeConcern=WriteConcern{w=null, wTimeout=null ms, journal=null}, retryWrites=true, retryReads=true, readConcern=ReadConcern{level=null}, credential=null, transportSettings=null, streamFactoryFactory=null, commandListeners=[], codecRegistry=ProvidersCodecRegistry{codecProviders=[ProvidersCodecRegistry{codecProviders=[ValueCodecProvider{}, BsonValueCodecProvider{}, DBRefCodecProvider{}, DBObjectCodecProvider{}, DocumentCodecProvider{}, CollectionCodecProvider{}, IterableCodecProvider{}, MapCodecProvider{}, GeoJsonCodecProvider{}, GridFSFileCodecProvider{}, Jsr310CodecProvider{}, JsonObjectCodecProvider{}, BsonCodecProvider{}, EnumCodecProvider{}, com.mongodb.client.model.mql.ExpressionCodecProvider@5ad57e90, com.mongodb.Jep395RecordCodecProvider@1a345298, com.mongodb.KotlinCodecProvider@4ad896f7]}, ProvidersCodecRegistry{codecProviders=[MapOfCodecsProvider{codecsMap={class java.lang.Object=org.opensilex.nosql.mongodb.codec.ObjectCodec@c318864, class java.net.URI=org.opensilex.nosql.mongodb.codec.URICodec@7d61468c, class java.time.ZonedDateTime=org.opensilex.nosql.mongodb.codec.ZonedDateTimeCodec@45796b2a}}]}, ProvidersCodecRegistry{codecProviders=[GeoJsonCodecProvider{}, org.bson.codecs.pojo.PojoCodecProvider@4b98225c]}]}, loggerSettings=LoggerSettings{maxDocumentLength=1000}, clusterSettings={hosts=[opensilex-docker-mongodb:27017], srvServiceName=mongodb, mode=SINGLE, requiredClusterType=UNKNOWN, requiredReplicaSetName='null', serverSelector='null', clusterListeners='[]', serverSelectionTimeout='10000 ms', localThreshold='15 ms'}, socketSettings=SocketSettings{connectTimeoutMS=10000, readTimeoutMS=30000, receiveBufferSize=0, proxySettings=ProxySettings{host=null, port=null, username=null, password=null}}, heartbeatSocketSettings=SocketSettings{connectTimeoutMS=10000, readTimeoutMS=10000, receiveBufferSize=0, proxySettings=ProxySettings{host=null, port=null, username=null, password=null}}, connectionPoolSettings=ConnectionPoolSettings{maxSize=100, minSize=0, maxWaitTimeMS=120000, maxConnectionLifeTimeMS=0, maxConnectionIdleTimeMS=0, maintenanceInitialDelayMS=0, maintenanceFrequencyMS=60000, connectionPoolListeners=[], maxConnecting=2}, serverSettings=ServerSettings{heartbeatFrequencyMS=10000, minHeartbeatFrequencyMS=500, serverListeners='[]', serverMonitorListeners='[]'}, sslSettings=SslSettings{enabled=false, invalidHostNameAllowed=false, context=null}, applicationName='null', compressorList=[], uuidRepresentation=UNSPECIFIED, serverApi=null, autoEncryptionSettings=null, dnsClient=null, inetAddressResolver=null, contextProvider=null}
14 Feb 2024;01:02:44.818 [cluster-ClusterId{value='65cc1134a4846851cd740f0a', description='null'}-opensilex-docker-mongodb:27017] INFO  org.mongodb.driver.cluster - Monitor thread successfully connected to server with description ServerDescription{address=opensilex-docker-mongodb:27017, type=REPLICA_SET_PRIMARY, state=CONNECTED, ok=true, minWireVersion=0, maxWireVersion=13, maxDocumentSize=16777216, logicalSessionTimeoutMinutes=30, roundTripTimeNanos=21831706, setName='opensilex', canonicalAddress=opensilex-docker-mongodb:27017, hosts=[opensilex-docker-mongodb:27017], passives=[], arbiters=[], primary='opensilex-docker-mongodb:27017', tagSet=TagSet{[]}, electionId=7fffffff000000000000001c, setVersion=1, topologyVersion=TopologyVersion{processId=65cc1086e0d00467be6e4d9a, counter=6}, lastWriteDate=Wed Feb 14 01:02:40 UTC 2024, lastUpdateTimeNanos=186769420689}
14 Feb 2024;01:02:44.870 [main] INFO  org.mongodb.driver.client - MongoClient with metadata {"driver": {"name": "mongo-java-driver|sync", "version": "4.11.0"}, "os": {"type": "Linux", "name": "Linux", "architecture": "amd64", "version": "6.1.0-1033-oem"}, "platform": "Java/Oracle Corporation/11.0.16+8"} created with settings MongoClientSettings{readPreference=primary, writeConcern=WriteConcern{w=null, wTimeout=null ms, journal=null}, retryWrites=true, retryReads=true, readConcern=ReadConcern{level=null}, credential=null, transportSettings=null, streamFactoryFactory=null, commandListeners=[], codecRegistry=ProvidersCodecRegistry{codecProviders=[ProvidersCodecRegistry{codecProviders=[ValueCodecProvider{}, BsonValueCodecProvider{}, DBRefCodecProvider{}, DBObjectCodecProvider{}, DocumentCodecProvider{}, CollectionCodecProvider{}, IterableCodecProvider{}, MapCodecProvider{}, GeoJsonCodecProvider{}, GridFSFileCodecProvider{}, Jsr310CodecProvider{}, JsonObjectCodecProvider{}, BsonCodecProvider{}, EnumCodecProvider{}, com.mongodb.client.model.mql.ExpressionCodecProvider@5ad57e90, com.mongodb.Jep395RecordCodecProvider@1a345298, com.mongodb.KotlinCodecProvider@4ad896f7]}, ProvidersCodecRegistry{codecProviders=[MapOfCodecsProvider{codecsMap={class java.lang.Object=org.opensilex.nosql.mongodb.codec.ObjectCodec@2913ca3e, class java.net.URI=org.opensilex.nosql.mongodb.codec.URICodec@636dbfe7, class java.time.ZonedDateTime=org.opensilex.nosql.mongodb.codec.ZonedDateTimeCodec@42ecc554}}]}, ProvidersCodecRegistry{codecProviders=[GeoJsonCodecProvider{}, org.bson.codecs.pojo.PojoCodecProvider@443af394]}]}, loggerSettings=LoggerSettings{maxDocumentLength=1000}, clusterSettings={hosts=[opensilex-docker-mongodb:27017], srvServiceName=mongodb, mode=SINGLE, requiredClusterType=UNKNOWN, requiredReplicaSetName='null', serverSelector='null', clusterListeners='[]', serverSelectionTimeout='10000 ms', localThreshold='15 ms'}, socketSettings=SocketSettings{connectTimeoutMS=10000, readTimeoutMS=30000, receiveBufferSize=0, proxySettings=ProxySettings{host=null, port=null, username=null, password=null}}, heartbeatSocketSettings=SocketSettings{connectTimeoutMS=10000, readTimeoutMS=10000, receiveBufferSize=0, proxySettings=ProxySettings{host=null, port=null, username=null, password=null}}, connectionPoolSettings=ConnectionPoolSettings{maxSize=100, minSize=0, maxWaitTimeMS=120000, maxConnectionLifeTimeMS=0, maxConnectionIdleTimeMS=0, maintenanceInitialDelayMS=0, maintenanceFrequencyMS=60000, connectionPoolListeners=[], maxConnecting=2}, serverSettings=ServerSettings{heartbeatFrequencyMS=10000, minHeartbeatFrequencyMS=500, serverListeners='[]', serverMonitorListeners='[]'}, sslSettings=SslSettings{enabled=false, invalidHostNameAllowed=false, context=null}, applicationName='null', compressorList=[], uuidRepresentation=UNSPECIFIED, serverApi=null, autoEncryptionSettings=null, dnsClient=null, inetAddressResolver=null, contextProvider=null}
14 Feb 2024;01:02:44.871 [main] INFO  org.mongodb.driver.cluster - No server chosen by WritableServerSelector from cluster description ClusterDescription{type=UNKNOWN, connectionMode=SINGLE, serverDescriptions=[ServerDescription{address=opensilex-docker-mongodb:27017, type=UNKNOWN, state=CONNECTING}]}. Waiting for 10000 ms before timing out
14 Feb 2024;01:02:44.871 [cluster-ClusterId{value='65cc1134a4846851cd740f0b', description='null'}-opensilex-docker-mongodb:27017] INFO  org.mongodb.driver.cluster - Monitor thread successfully connected to server with description ServerDescription{address=opensilex-docker-mongodb:27017, type=REPLICA_SET_PRIMARY, state=CONNECTED, ok=true, minWireVersion=0, maxWireVersion=13, maxDocumentSize=16777216, logicalSessionTimeoutMinutes=30, roundTripTimeNanos=2456415, setName='opensilex', canonicalAddress=opensilex-docker-mongodb:27017, hosts=[opensilex-docker-mongodb:27017], passives=[], arbiters=[], primary='opensilex-docker-mongodb:27017', tagSet=TagSet{[]}, electionId=7fffffff000000000000001c, setVersion=1, topologyVersion=TopologyVersion{processId=65cc1086e0d00467be6e4d9a, counter=6}, lastWriteDate=Wed Feb 14 01:02:40 UTC 2024, lastUpdateTimeNanos=186825908891}
14 Feb 2024;01:02:44.893 [main] INFO  org.mongodb.driver.client - MongoClient with metadata {"driver": {"name": "mongo-java-driver|sync", "version": "4.11.0"}, "os": {"type": "Linux", "name": "Linux", "architecture": "amd64", "version": "6.1.0-1033-oem"}, "platform": "Java/Oracle Corporation/11.0.16+8"} created with settings MongoClientSettings{readPreference=primary, writeConcern=WriteConcern{w=null, wTimeout=null ms, journal=null}, retryWrites=true, retryReads=true, readConcern=ReadConcern{level=null}, credential=null, transportSettings=null, streamFactoryFactory=null, commandListeners=[], codecRegistry=ProvidersCodecRegistry{codecProviders=[ProvidersCodecRegistry{codecProviders=[ValueCodecProvider{}, BsonValueCodecProvider{}, DBRefCodecProvider{}, DBObjectCodecProvider{}, DocumentCodecProvider{}, CollectionCodecProvider{}, IterableCodecProvider{}, MapCodecProvider{}, GeoJsonCodecProvider{}, GridFSFileCodecProvider{}, Jsr310CodecProvider{}, JsonObjectCodecProvider{}, BsonCodecProvider{}, EnumCodecProvider{}, com.mongodb.client.model.mql.ExpressionCodecProvider@5ad57e90, com.mongodb.Jep395RecordCodecProvider@1a345298, com.mongodb.KotlinCodecProvider@4ad896f7]}, ProvidersCodecRegistry{codecProviders=[MapOfCodecsProvider{codecsMap={class java.lang.Object=org.opensilex.nosql.mongodb.codec.ObjectCodec@24aedcc5, class java.net.URI=org.opensilex.nosql.mongodb.codec.URICodec@74ebd159, class java.time.ZonedDateTime=org.opensilex.nosql.mongodb.codec.ZonedDateTimeCodec@1850f2da}}]}, ProvidersCodecRegistry{codecProviders=[GeoJsonCodecProvider{}, org.bson.codecs.pojo.PojoCodecProvider@38d42ab7]}]}, loggerSettings=LoggerSettings{maxDocumentLength=1000}, clusterSettings={hosts=[opensilex-docker-mongodb:27017], srvServiceName=mongodb, mode=SINGLE, requiredClusterType=UNKNOWN, requiredReplicaSetName='null', serverSelector='null', clusterListeners='[]', serverSelectionTimeout='10000 ms', localThreshold='15 ms'}, socketSettings=SocketSettings{connectTimeoutMS=10000, readTimeoutMS=30000, receiveBufferSize=0, proxySettings=ProxySettings{host=null, port=null, username=null, password=null}}, heartbeatSocketSettings=SocketSettings{connectTimeoutMS=10000, readTimeoutMS=10000, receiveBufferSize=0, proxySettings=ProxySettings{host=null, port=null, username=null, password=null}}, connectionPoolSettings=ConnectionPoolSettings{maxSize=100, minSize=0, maxWaitTimeMS=120000, maxConnectionLifeTimeMS=0, maxConnectionIdleTimeMS=0, maintenanceInitialDelayMS=0, maintenanceFrequencyMS=60000, connectionPoolListeners=[], maxConnecting=2}, serverSettings=ServerSettings{heartbeatFrequencyMS=10000, minHeartbeatFrequencyMS=500, serverListeners='[]', serverMonitorListeners='[]'}, sslSettings=SslSettings{enabled=false, invalidHostNameAllowed=false, context=null}, applicationName='null', compressorList=[], uuidRepresentation=UNSPECIFIED, serverApi=null, autoEncryptionSettings=null, dnsClient=null, inetAddressResolver=null, contextProvider=null}
14 Feb 2024;01:02:44.893 [cluster-ClusterId{value='65cc1134a4846851cd740f0c', description='null'}-opensilex-docker-mongodb:27017] INFO  org.mongodb.driver.cluster - Monitor thread successfully connected to server with description ServerDescription{address=opensilex-docker-mongodb:27017, type=REPLICA_SET_PRIMARY, state=CONNECTED, ok=true, minWireVersion=0, maxWireVersion=13, maxDocumentSize=16777216, logicalSessionTimeoutMinutes=30, roundTripTimeNanos=2429473, setName='opensilex', canonicalAddress=opensilex-docker-mongodb:27017, hosts=[opensilex-docker-mongodb:27017], passives=[], arbiters=[], primary='opensilex-docker-mongodb:27017', tagSet=TagSet{[]}, electionId=7fffffff000000000000001c, setVersion=1, topologyVersion=TopologyVersion{processId=65cc1086e0d00467be6e4d9a, counter=6}, lastWriteDate=Wed Feb 14 01:02:40 UTC 2024, lastUpdateTimeNanos=186847683605}
14 Feb 2024;01:02:44.894 [main] INFO  org.opensilex.nosql.mongodb.MongoDBService - [CHECK_MONGO_SERVER_CONNECTION] timeout: 10000ms [START]
14 Feb 2024;01:02:44.913 [main] INFO  org.opensilex.nosql.mongodb.MongoDBService - [CHECK_MONGO_SERVER_CONNECTION Document{{ok=1.0, $clusterTime=Document{{clusterTime=Timestamp{value=7335256790935797761, seconds=1707872560, inc=1}, signature=Document{{hash=org.bson.types.Binary@c98f581, keyId=0}}}}, operationTime=Timestamp{value=7335256790935797761, seconds=1707872560, inc=1}}} [OK]
Exception in thread "main" org.opensilex.sparql.exceptions.SPARQLException: org.eclipse.rdf4j.repository.http.HTTPQueryEvaluationException: Request failed with status 404: http://opensilex-docker-rdf4j:8080/rdf4j-server/repositories/opensilex-docker-db
    at org.opensilex.sparql.ontology.store.AbstractOntologyStore.load(AbstractOntologyStore.java:157)
    at org.opensilex.sparql.SPARQLModule.initOntologyStore(SPARQLModule.java:200)
    at org.opensilex.sparql.SPARQLModule.startup(SPARQLModule.java:219)
    at org.opensilex.OpenSilex.startup(OpenSilex.java:537)
    at org.opensilex.cli.MainCommand.main(MainCommand.java:95)
Caused by: org.eclipse.rdf4j.repository.http.HTTPQueryEvaluationException: Request failed with status 404: http://opensilex-docker-rdf4j:8080/rdf4j-server/repositories/opensilex-docker-db
    at org.eclipse.rdf4j.repository.http.HTTPTupleQuery.evaluate(HTTPTupleQuery.java:50)
    at org.opensilex.sparql.rdf4j.RDF4JConnection.executeSelectQueryAsStream(RDF4JConnection.java:162)
    at org.opensilex.sparql.service.SPARQLService.executeSelectQueryAsStream(SPARQLService.java:237)
    at org.opensilex.sparql.ontology.store.OntologyStoreLoader.getModels(OntologyStoreLoader.java:218)
    at org.opensilex.sparql.ontology.store.OntologyStoreLoader.getClasses(OntologyStoreLoader.java:256)
    at org.opensilex.sparql.ontology.store.AbstractOntologyStore.load(AbstractOntologyStore.java:133)
    ... 4 more
Caused by: org.eclipse.rdf4j.repository.RepositoryException: Request failed with status 404: http://opensilex-docker-rdf4j:8080/rdf4j-server/repositories/opensilex-docker-db
    at org.eclipse.rdf4j.http.client.SPARQLProtocolSession.executeOK(SPARQLProtocolSession.java:1008)
    at org.eclipse.rdf4j.http.client.SPARQLProtocolSession.sendTupleQueryViaHttp(SPARQLProtocolSession.java:755)
    at org.eclipse.rdf4j.http.client.SPARQLProtocolSession.getBackgroundTupleQueryResult(SPARQLProtocolSession.java:650)
    at org.eclipse.rdf4j.http.client.SPARQLProtocolSession.sendTupleQuery(SPARQLProtocolSession.java:363)
    at org.eclipse.rdf4j.repository.http.HTTPTupleQuery.evaluate(HTTPTupleQuery.java:47)
    ... 9 more
niio972 commented 4 months ago

Hi @haryle, sorry for the delay. Thanks you for using opensilex docker compose project. It seems that you can't access to opensilex docker config. What are the permissions given to the config directory ?