something went wonky - sys?

[enuggetry]

I can't understand why this starts to happen sometimes and I can't figure out what I did to get it to stop...

I had added a little debug coding in there (since it started happening) and it indicated the sys() function seemed to stop working.

    def assert_blast_installed_and_compatible

      begin

        aa = sys('blastdbcmd -version', path: config[:bin])

        puts ["output: version ",aa.count]

        aa.each { |item| puts item }

        out, = sys('blastdbcmd -version', path: config[:bin])

...

ericiam@graingenes:/data/seqserv2rc8$ bundle exec bin/sequenceserver -c /data/seqserv2rc8/gg-sequenceserver/sequenceserver.conf

[2022-02-01 07:00:15] INFO  Reading configuration file: /data/seqserv2rc8/gg-sequenceserver/sequenceserver.conf.
output: version
2
   <----  nothing from sys()

Something went wonky

Looks like you have encountered a bug in SequenceServer. Please could you
report this incident to our Google Group -
https://groups.google.com/forum/?fromgroups#!forum/sequenceserver

Error:
  undefined method `empty?' for nil:NilClass
/data/seqserv2rc8/lib/sequenceserver.rb:251:in `assert_blast_installed_and_compatible'
/data/seqserv2rc8/lib/sequenceserver.rb:192:in `init_binaries'
/data/seqserv2rc8/lib/sequenceserver.rb:81:in `init'
bin/sequenceserver:180:in `block (2 levels) in <top (required)>'
/var/lib/gems/2.7.0/gems/slop-3.6.0/lib/slop.rb:260:in `parse!'
/var/lib/gems/2.7.0/gems/slop-3.6.0/lib/slop.rb:65:in `parse!'
bin/sequenceserver:48:in `<top (required)>'
/var/lib/gems/2.7.0/gems/bundler-2.2.30/lib/bundler/cli/exec.rb:58:in `load'
/var/lib/gems/2.7.0/gems/bundler-2.2.30/lib/bundler/cli/exec.rb:58:in `kernel_load'

...

???????????????

In the past, I had never seen this problem, then all of a sudden, today, it started happening.

Later, it just magically started working after changing the debug code a little (seemingly inconsequential change).

[2022-02-01 07:23:54] INFO  Reading configuration file: /data/seqserv2rc8/sequenceserver.conf.
output: version
2
blastdbcmd: 2.12.0+  <---- surprise!!!  started working!  why???
 Package: blast 2.12.0, build Jun  4 2021 03:22:54

...

Running sequenceserver 2 rc8

[Anurag Priyam]

Hmm, the error message suggests that sys is returning an empty array on the second invocation. That should technically only happen if stdout, and stderr options were given to sys:

sys(command, path: …, stdout: ‘/path/to/redirect/stdout/to’, stderr: ‘/path/to/redirect/stderr/to’)

Not sure what else could cause that.

What version of Ruby?

Priyam

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