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Add a log message when gnb is really running and ready #61

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abretaud opened this issue Feb 2, 2024 · 0 comments
Closed

Add a log message when gnb is really running and ready #61

abretaud opened this issue Feb 2, 2024 · 0 comments

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@abretaud
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abretaud commented Feb 2, 2024

Currently the galaxy tool is watching the logs for GeneNoteBook server started, serving during the startup of gnb. Apparently this message is printed before gnb is really serving. I had this kind of logs:

## LOG: 2024-02-01T21:09:54.752Z Jobqueue started
## LOG: 2024-02-01T21:10:35.273Z GeneNoteBook server started, serving at http://localhost:7000/
## LOG: 2024-02-01T21:10:35.273Z Running GeneNoteBook version 0.4.12
## LOG: 2024-02-01T21:10:35.274Z Migrating user roles schema v1 --> v2
## WARNING: 2024-02-01T21:10:35.278Z MongoServerError: index not found with name [name_1]
    at MessageStream.messageHandler (/_conda/envs/__genoboo@0.4.12/share/genoboo-0.4.12-0/programs/server/npm/node_modules/meteor/npm-mongo/node_modules/mongodb/lib/cmap/connection.js:462:30)
    at MessageStream.emit (node:events:369:20)
    at MessageStream.emit (node:domain:470:12)
    at processIncomingData (/_conda/envs/__genoboo@0.4.12/share/genoboo-0.4.12-0/programs/server/npm/node_modules/meteor/npm-mongo/node_modules/mongodb/lib/cmap/message_stream.js:108:16)
    at MessageStream._write (/_conda/envs/__genoboo@0.4.12/share/genoboo-0.4.12-0/programs/server/npm/node_modules/meteor/npm-mongo/node_modules/mongodb/lib/cmap/message_stream.js:28:9)
    at writeOrBuffer (node:internal/streams/writable:395:12)
    at MessageStream.Writable.write (node:internal/streams/writable:340:10)
    at Socket.ondata (node:internal/streams/readable:750:22)
    at Socket.emit (node:events:369:20)
    at Socket.emit (node:domain:470:12)
    at addChunk (node:internal/streams/readable:313:12)
    at readableAddChunk (node:internal/streams/readable:288:9)
    at Socket.Readable.push (node:internal/streams/readable:227:10)
    at Pipe.onStreamRead (node:internal/stream_base_commons:190:23) {
  ok: 0,
  code: 27,
  codeName: 'IndexNotFound'
}
## LOG: 2024-02-01T21:10:35.283Z Creating new role "registered"
## LOG: 2024-02-01T21:10:35.285Z Creating new role "user"
## LOG: 2024-02-01T21:10:35.286Z Linking registered --> user
## LOG: 2024-02-01T21:10:35.295Z Creating new role "curator"
## LOG: 2024-02-01T21:10:35.296Z Linking user --> curator
## LOG: 2024-02-01T21:10:35.305Z Creating new role "admin"
## LOG: 2024-02-01T21:10:35.307Z Linking curator --> admin
## LOG: 2024-02-01T21:10:35.318Z Adding default admin user
## LOG: 2024-02-01T21:10:35.422Z Adding default filter option: Note
## LOG: 2024-02-01T21:10:41.002Z Adding default filter option: Dbxref
## LOG: 2024-02-01T21:10:41.008Z Adding default filter option: Ontology Term
## LOG: 2024-02-01T21:10:41.014Z Adding default filter option: Orthogroup
## LOG: 2024-02-01T21:10:41.020Z Adding default filter option: Gene ID
## LOG: 2024-02-01T21:10:41.024Z Adding default filter option: Has changes
## LOG: 2024-02-01T21:10:41.029Z Adding default filter option: Genome
## LOG: 2024-02-01T21:10:41.035Z Adding default filter option: Annotation
node:events:346
      throw er; // Unhandled 'error' event
      ^

Error: listen EADDRINUSE: address already in use 0.0.0.0:7000
    at Server.setupListenHandle [as _listen2] (node:net:1311:16)
    at listenInCluster (node:net:1359:12)
    at doListen (node:net:1497:7)
    at processTicksAndRejections (node:internal/process/task_queues:82:21)
Emitted 'error' event on Server instance at:
    at emitErrorNT (node:net:1338:8)
    at processTicksAndRejections (node:internal/process/task_queues:81:21) {
  code: 'EADDRINUSE',
  errno: -98,
  syscall: 'listen',
  address: '0.0.0.0',
  port: 7000
}

Galaxy is not able to detect the error because of the previous GeneNoteBook server started, serving

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