mskyttner / clb-docker Goto Github PK

One of the tests fail currently, it seems to be checklistbank.cli.importer.ImporterServiceIT.testStartUp that cannot connect to RabbitMQ.

The log says:

testStartUp(org.gbif.checklistbank.cli.importer.ImporterServiceIT) Time elapsed: 4.545 sec <<< ERROR!
java.io.IOException: null
at com.rabbitmq.utility.ValueOrException.getValue(ValueOrException.java:67)
at com.rabbitmq.utility.BlockingValueOrException.uninterruptibleGetValue(BlockingValueOrException.java:33)
at com.rabbitmq.client.impl.AMQChannel$BlockingRpcContinuation.getReply(AMQChannel.java:343)
at com.rabbitmq.client.impl.AMQChannel.privateRpc(AMQChannel.java:216)
at com.rabbitmq.client.impl.AMQChannel.exnWrappingRpc(AMQChannel.java:118)
at com.rabbitmq.client.impl.AMQConnection.start(AMQConnection.java:388)
at com.rabbitmq.client.ConnectionFactory.newConnection(ConnectionFactory.java:516)
at com.rabbitmq.client.ConnectionFactory.newConnection(ConnectionFactory.java:533)
at org.gbif.common.messaging.DefaultMessagePublisher.(DefaultMessagePublisher.java:74)
at org.gbif.common.messaging.DefaultMessagePublisher.(DefaultMessagePublisher.java:52)
at org.gbif.checklistbank.cli.common.RabbitBaseService.startUp(RabbitBaseService.java:94)
at org.gbif.checklistbank.cli.importer.ImporterService.startUp(ImporterService.java:84)
at org.gbif.checklistbank.cli.importer.ImporterServiceIT.testStartUp(ImporterServiceIT.java:27)
Caused by: java.net.SocketException: Connection reset
at java.net.SocketInputStream.read(SocketInputStream.java:209)
at java.net.SocketInputStream.read(SocketInputStream.java:141)
at java.io.BufferedInputStream.fill(BufferedInputStream.java:246)
at java.io.BufferedInputStream.read(BufferedInputStream.java:265)
at java.io.DataInputStream.readUnsignedByte(DataInputStream.java:288)
at com.rabbitmq.client.impl.Frame.readFrom(Frame.java:95)
at com.rabbitmq.client.impl.SocketFrameHandler.readFrame(SocketFrameHandler.java:131)
at com.rabbitmq.client.impl.AMQConnection$MainLoop.run(AMQConnection.java:515)

Attempting a seach for "Vulpes", using http://clb.docker/species/search?q=Vulpes, gives a Error 500 with the following information indicating an issue with solr config:

org.apache.solr.common.SolrException: SolrCore 'checklistbank' is not available due to init failure: Unrecognized lockType: hdfs
at org.apache.solr.core.CoreContainer.getCore(CoreContainer.java:997)
at org.apache.solr.client.solrj.embedded.EmbeddedSolrServer.request(EmbeddedSolrServer.java:147)
at org.apache.solr.client.solrj.SolrRequest.process(SolrRequest.java:150)
at org.apache.solr.client.solrj.SolrClient.query(SolrClient.java:943)

use checklistbank-cli-2.47-shaded.jar ( not-snapshot, shaded type) of the checklistbank-cli-2.47

change CLBVERSION = 2.47-SNAPSHOT to CLBVERSION = 2.47
affects the Makefile + docker-compose.yml

@mdoering

I am wondering if there is a Java tool which can convert CSV file to DarwinCore archive.

Note
We would need to look at this a bit closer, this is an issue that is linked to dnsdock - and understanding this fully will help our efforts regarding other docker-projects.

Description of the problem.
Logging into the elk-container ( docker exec -it clbdocker_elk_1 bash )
Running 'apt update'
cannot find the ' http://archive.ubuntu.com/ubuntu'
Is this a local problem or do others also have this problem ?

Solving the problem
Adding the following to the docker-compos.yml-file

  dnsmasq:
    image: andyshinn/dnsmasq:2.76
    command: --log-facility=-
    container_name: dnsmasq
    cap_add: 
      - NET_ADMIN 
    ports:
      - 172.17.0.1:53:53/tcp
      - 172.17.0.1:53:53/udp

If all services are up after your editing:

1. docker-compose stop dnsdock
2. docker-compose run -d dnsmasq
3. docker-compose stop dnsmasq
4. docker-compose start -d dnsdock

$ docker exec -it clbdocker_elk_1 bash
root@2201e41019cb:/# apt update
works

we need to try this out.

-i

Document how to load a locally stored Darwin Core archive such as archive.zip located on disk somewhere and not pulled from the Internet.