Source code for toil.test.batchSystems.test_lsf_helper

"""lsfHelper.py shouldn't need a batch system and so the unit tests here should aim to run on any system."""

from toil.batchSystems.lsfHelper import parse_mem_and_cmd_from_output
from toil.test import ToilTest




class LSFHelperTest(ToilTest):


    def test_parse_mem_and_cmd_from_output(self):
        # https://github.com/DataBiosphere/toil/pull/3475
        output = (
            "\nJob <2924748>, Job Name <toil_job_64>, User <thiagogenez>, Project <default>, S"
            "\n                     tatus <RUN>, Queue <research-rh74>, Job Priority <50>, Com"
            "\n                     mand <_toil_worker CactusBarRecursion file:/hps/nobackup/p"
            "\n                     roduction/ensembl/thiagogenez/pairwises/arabidopsis/run/jo"
            "\n                     bstore/3 kind-CactusBarRecursion/instance-iu6wo56x --conte"
            "\n                     xt gAShortenedh32xqlE51Yi4=>, Share group charged </thiago"
            "\n                     genez>, Esub <esub>"
            "\nThu Mar 18 02:06:32: Submitted from host <noah-login-01>, CWD </hps/nobackup/pr"
            "\n                     oduction/ensembl/thiagogenez/pairwises/arabidopsis/run>, S"
            "\n                     pecified CWD </hps/nobackup/production/ensembl/thiagogenez"
            "\n                     /pairwises/arabidopsis/run/.>, Output File </tmp/toil_work"
            "\n                     flow_10e83102-2e4b-4093-9128-2a52f4bbc65a_job_64_batch_lsf"
            "\n                     _2924748_std_output.log>, Error File </tmp/toil_workflow_1"
            "\n                     0e83102-2e4b-4093-9128-2a52f4bbc65a_job_64_batch_lsf_29247"
            "\n                     48_std_error.log>, Requested Resources <select[(mem>4000)]"
            "\n                      rusage[mem=4000:duration=480, numcpus=1:duration=480]>;"
            "\nThu Mar 18 02:06:33: Started on <hx-noah-31-02>, Execution Home </homes/thiagog"
            "\n                     enez>, Execution CWD </hps/nobackup/production/ensembl/thi"
            "\n                     agogenez/pairwises/arabidopsis/run/.>;"
            "\nThu Mar 18 17:07:47: Resource usage collected."
            "\n                     The CPU time used is 53936 seconds."
            "\n                     MEM: 344 Mbytes;  SWAP: 1.3 Gbytes;  NTHREAD: 5"
            "\n                     PGID: 433168;  PIDs: 433168 433177 433179 444026 "
            "\n"
            "\n RUNLIMIT                "
            "\n 10085.0 min"
            "\n"
            "\n CORELIMIT MEMLIMIT"
            "\n      0 M     3.9 G "
            "\n"
            "\n MEMORY USAGE:"
            "\n MAX MEM: 2.5 Gbytes;  AVG MEM: 343 Mbytes"
            "\n"
            "\n SCHEDULING PARAMETERS:"
            "\n           r15s   r1m  r15m   ut      pg    io   ls    it    tmp    swp    mem"
            "\n loadSched   -     -     -     -    10.0     -    -     -   500M     -   1000M "
            "\n loadStop    -     -     -     -       -     -    -     -     -      -      -  "
            "\n"
            "\n          availcpus "
            "\n loadSched      1.0 "
            "\n loadStop        -  "
            "\n"
            "\n RESOURCE REQUIREMENT DETAILS:"
            "\n Combined: select[((mem>4000)) && (type == local)] order[r15s:pg] rusage[mem=40"
            "\n                     00.00:duration=8h:decay=0,numcpus=1.00:duration=8h:decay=0"
            "\n                     ] span[hosts=1]"
            "\n Effective: select[(((mem>4000))) && (type == local)] order[r15s:pg] rusage[mem"
            "\n                     =4000.00:duration=8h:decay=0,numcpus=1.00:duration=8h:deca"
            "\n                     y=0] span[hosts=1] "
            "\n"
            "\n"
        )
        max_mem, command = parse_mem_and_cmd_from_output(output=output)
        assert len(max_mem.groups()) == 1
        expected_mem = "2.5 Gbytes"
        assert (
            max_mem.group(1) == expected_mem
        ), f'Actual: {max_mem.group(1)}, Expected: "{expected_mem}"'

        assert len(command.groups()) == 1
        expected_command = (
            "_toil_worker CactusBarRecursion file:/hps/nobackup/production/ensembl/thiagogenez/"
            "pairwises/arabidopsis/run/jobstore/3 kind-CactusBarRecursion/instance-iu6wo56x "
            "--context gAShortenedh32xqlE51Yi4="
        )
        assert (
            command.group(1) == expected_command
        ), f'Actual: {command.group(1)}, Expected: "{expected_command}"'
        print(command)

        max_mem, command = parse_mem_and_cmd_from_output(output="")
        assert max_mem == None
        assert command == None