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fast5watch's Issues

Restart run watcher fast5watch.watchers.core/run-watcher on exception

The run-watcher component should be robust to errors.

For example, if encountering java.nio.file.AccessDeniedException

Exception in thread "Thread-26" java.nio.file.AccessDeniedException: /tmp/fast5watch-dev-test/some/path/to/fast5/
        at sun.nio.fs.UnixException.translateToIOException(UnixException.java:84)
        at sun.nio.fs.UnixException.asIOException(UnixException.java:111)
        at sun.nio.fs.LinuxWatchService$Poller.implRegister(LinuxWatchService.java:266)
        at sun.nio.fs.AbstractPoller.processRequests(AbstractPoller.java:260)
        at sun.nio.fs.LinuxWatchService$Poller.run(LinuxWatchService.java:364)
        at java.lang.Thread.run(Thread.java:748)

the watcher thread dies and currently need to go into the REPL and restart it.

Add call to an HTTP endpoint if specified in the config

e.g. in the (dev|prod)-config.edn

{:port                   3000
 :external-http-endpoint "http://123.45.67.89:9000/api/fast5watch"
}

New run and fast5 info would be HTTP POSTed to the endpoint.

  • base endpoint? expect /run and /run/<id>/fast5 endpoints?
  • just enough info to download fast5 files and know how to organize them?

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