peterk87 / fast5watch Goto Github PK
View Code? Open in Web Editor NEWNanopore run watcher
Nanopore run watcher
Use libpython-clj to import Python modules and functions and use them within the app.
Required Python libraries
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.
/run
and /run/<id>/fast5
endpoints?Requires #3
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.
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