Unable to connect to mongo while running from docker-compose.

[cbaakman]

When I run the FDP server from docker-compose. I get the following error:

fdp-production-fdp-1         | 2023-06-01 11:55:26,052 27860 [cluster-ClusterId{value='647887191ed7970008416f13', description='null'}-mongo:27017] INFO  org.mongodb.driver.cluster - Exception in monitor thread while connecting to server mongo:27017
fdp-production-fdp-1         | com.mongodb.MongoSocketOpenException: Exception opening socket
fdp-production-fdp-1         | 	at com.mongodb.internal.connection.SocketStream.open(SocketStream.java:67) ~[mongodb-driver-core-3.8.2.jar!/:?]
fdp-production-fdp-1         | 	at com.mongodb.internal.connection.InternalStreamConnection.open(InternalStreamConnection.java:126) ~[mongodb-driver-core-3.8.2.jar!/:?]
fdp-production-fdp-1         | 	at com.mongodb.internal.connection.DefaultServerMonitor$ServerMonitorRunnable.run(DefaultServerMonitor.java:117) [mongodb-driver-core-3.8.2.jar!/:?]
fdp-production-fdp-1         | 	at java.lang.Thread.run(Thread.java:834) [?:?]
fdp-production-fdp-1         | Caused by: java.net.SocketTimeoutException: connect timed out
fdp-production-fdp-1         | 	at java.net.PlainSocketImpl.socketConnect(Native Method) ~[?:?]
fdp-production-fdp-1         | 	at java.net.AbstractPlainSocketImpl.doConnect(AbstractPlainSocketImpl.java:399) ~[?:?]
fdp-production-fdp-1         | 	at java.net.AbstractPlainSocketImpl.connectToAddress(AbstractPlainSocketImpl.java:242) ~[?:?]
fdp-production-fdp-1         | 	at java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:224) ~[?:?]
fdp-production-fdp-1         | 	at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:403) ~[?:?]
fdp-production-fdp-1         | 	at java.net.Socket.connect(Socket.java:609) ~[?:?]
fdp-production-fdp-1         | 	at com.mongodb.internal.connection.SocketStreamHelper.initialize(SocketStreamHelper.java:64) ~[mongodb-driver-core-3.8.2.jar!/:?]
fdp-production-fdp-1         | 	at com.mongodb.internal.connection.SocketStream.open(SocketStream.java:62) ~[mongodb-driver-core-3.8.2.jar!/:?]
fdp-production-fdp-1         | 	... 3 more
fdp-production-fdp-1         | 2023-06-01 11:55:29,295 31103 [cluster-ClusterId{value='6478871d1ed7970008416f14', description='null'}-mongo:27017] INFO  org.mongodb.driver.cluster - Exception in monitor thread while connecting to server mongo:27017
fdp-production-fdp-1         | com.mongodb.MongoSocketOpenException: Exception opening socket
fdp-production-fdp-1         | 	at com.mongodb.internal.connection.SocketStream.open(SocketStream.java:67) ~[mongodb-driver-core-3.8.2.jar!/:?]
fdp-production-fdp-1         | 	at com.mongodb.internal.connection.InternalStreamConnection.open(InternalStreamConnection.java:126) ~[mongodb-driver-core-3.8.2.jar!/:?]
fdp-production-fdp-1         | 	at com.mongodb.internal.connection.DefaultServerMonitor$ServerMonitorRunnable.run(DefaultServerMonitor.java:117) [mongodb-driver-core-3.8.2.jar!/:?]
fdp-production-fdp-1         | 	at java.lang.Thread.run(Thread.java:834) [?:?]
fdp-production-fdp-1         | Caused by: java.net.SocketTimeoutException: connect timed out
fdp-production-fdp-1         | 	at java.net.PlainSocketImpl.socketConnect(Native Method) ~[?:?]
fdp-production-fdp-1         | 	at java.net.AbstractPlainSocketImpl.doConnect(AbstractPlainSocketImpl.java:399) ~[?:?]
fdp-production-fdp-1         | 	at java.net.AbstractPlainSocketImpl.connectToAddress(AbstractPlainSocketImpl.java:242) ~[?:?]
fdp-production-fdp-1         | 	at java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:224) ~[?:?]
fdp-production-fdp-1         | 	at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:403) ~[?:?]
fdp-production-fdp-1         | 	at java.net.Socket.connect(Socket.java:609) ~[?:?]
fdp-production-fdp-1         | 	at com.mongodb.internal.connection.SocketStreamHelper.initialize(SocketStreamHelper.java:64) ~[mongodb-driver-core-3.8.2.jar!/:?]
fdp-production-fdp-1         | 	at com.mongodb.internal.connection.SocketStream.open(SocketStream.java:62) ~[mongodb-driver-core-3.8.2.jar!/:?]
fdp-production-fdp-1         | 	... 3 more

docker-compose.yml:

version: '3'
services:
    proxy:
        ports:
            - 80:80
            - 443:443
        image: nginx:1.17.3
        volumes:
            # Mount the nginx folder with the configuration
            - ./nginx:/etc/nginx:ro
            # Mount the letsencrypt certificates
            - /etc/ssl:/etc/ssl:ro

    fdp:
        image: fairdata/fairdatapoint:1.0
        volumes:
            - ./application.yml:/fdp/application.yml:ro

    fdp-client:
        image: fairdata/fairdatapoint-client:1.0
        environment:
            - FDP_HOST=fdp

    mongo:
        image: mongo:4.0.12
        volumes:
            - ./mongo/data:/data/db

    blazegraph:
        image: metaphacts/blazegraph-basic:2.2.0-20160908.003514-6
        ports:
            - 8080:8080
        volumes:
            - ./blazegraph:/blazegraph-data

application.yml:

instance:
    clientUrl: https://fdp.cmbi.umcn.nl
    persistentUrl: https://fdp.cmbi.umcn.nl
    #persistentUrl: https://www3.cmbi.umcn.nl/fdp

security:
    jwt:
        token:
            secret-key:  <secret>

# repository settings (can be changed to different repository)
repository:
    type: 5
    blazegraph:
        url: https://fdp.cmbi.umcn.nl/blazegraph

All containers seem to run initially, but fdp shuts down after 30 seconds.

[kburger]

Hi @cbaakman, can you try the following:

1. upgrade the fdp and fdp-client images to 1.16
2. if that did not solve the problem, try upgrading the mongo image to a newer (4.x) version.

Let me know if this solves the problem.

[cbaakman]

I upgraded fdp and fdp client to 1.16.
I upgraded mongo to 4.4.6.

The problem persists.

[MarekSuchanek]

Are you sure that mongo is running properly? (docker compose ps, docker compose logs mongo)

[cbaakman]

Actually, we found that the entire VM (that FDP was running on) was not accessible from the outside network. We rebuilt the entire VM and now FDP runs properly again.

It remains a mystery, but probably FDP itself wasn't the cause.

Thanks for thinking along with us.