Fix PBSPRO queue status fetch

[HDash]

Closes #5528

A simple conditional if statement to check if the output is empty fixes the issue.

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[bentsherman]

I have a sneaking suspicion that this worked on whatever PBSPro cluster it was tested on, and maybe the status text changed across different versions. It would be good to have some clear documentation on how the status text is supposed to look, so that we can test against it, like here:

nextflow/modules/nextflow/src/test/groovy/nextflow/executor/PbsProExecutorTest.groovy

Lines 219 to 238 in fa0e8e0

	def 'should parse queue status'() {
	setup:
	def executor = [:] as PbsProExecutor
	def text =
	"""
	Job Id: 12.localhost
	job_state = F
	Job Id: 13.localhost
	job_state = R
	Job Id: 14.localhost
	job_state = Q
	Job Id: 15.localhost
	job_state = S
	Job Id: 16.localhost
	job_state = E
	Job Id: 17.localhost
	job_state = H
	""".stripIndent().trim()

At the same time, I'm pretty sure the PBSPro executor was added at my request, to support my university cluster 😅 And I do remember seeing these "failed to fetch queue status" warnings but I never figured out why they were happening

[HDash]

Hello @bentsherman,

You are correct—I’ve been encountering this issue on Imperial’s cluster. It seems that qstat -B returns a phantom empty server string, which causes an error when passed to qstat -f. I have detailed the output in the mentioned issue.

The job state parsing portion of the code, however, appears to work perfectly and functions as intended. The failure lies in fetching the job state strings.

With my fork, qstat -f $( qstat -B | grep -E -v '(^Server|^---)' | awk -v ORS=' ' '{if ($1 != "") print "@"$1}' ) | { grep -E '(Job Id:|job_state =)' || true; } outputs:

Job Id: 297959.pbs
    job_state = Q

Which is exactly what we want. My queued job is labelled appropriately.

For current version, qstat -f $( qstat -B | grep -E -v '(^Server|^---)' | awk -v ORS=' ' '{print "@"$1}' ) | { grep -E '(Job Id:|job_state =)' || true; } outputs:

qstat: illegally formed destination: @