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  1. Pegasus
  2. PM-1531

pegasus-db-admin fails on macosx on a clean db

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    Details

    • Type: Bug
    • Status: Resolved
    • Priority: Major
    • Resolution: Fixed
    • Affects Version/s: master
    • Fix Version/s: master, 5.0.0
    • Component/s: CLI: pegasus-db-admin
    • Labels:
      None

      Description

      (environment) shivalik:015-shell-hierarchic-workflow vahi$ rm -rf ~/.pegasus/workflow.db
      (environment) shivalik:015-shell-hierarchic-workflow vahi$ /Users/vahi/Pegasus/software/pegasus/pegasus-5.0.0dev/bin/pegasus-db-admin update -t master -c /Users/vahi/Pegasus/work/015-shell-hierarchic-workflow/work/submit/20200427_125525N/pegasus.5808622231803098829.properties -vvvv
      Warning: Using a non-system Python (/Users/vahi/Pegasus/work/virtualevn/python3/environment/bin/python3)
      2020-04-27 12:57:30,867:DEBUG:Pegasus.tools.properties(245): processing properties file /Users/vahi/Pegasus/work/015-shell-hierarchic-workflow/work/submit/20200427_125525N/pegasus.5808622231803098829.properties...
      2020-04-27 12:57:30,867:DEBUG:Pegasus.tools.properties(145): # parsing properties in <_io.TextIOWrapper name='/Users/vahi/Pegasus/work/015-shell-hierarchic-workflow/work/submit/20200427_125525N/pegasus.5808622231803098829.properties' mode='r' encoding='UTF-8'>...
      2020-04-27 12:57:30,867:DEBUG:Pegasus.tools.properties(176): #Property being parsed is # pegasus.dir.storage.deep=false
      2020-04-27 12:57:30,867:DEBUG:Pegasus.tools.properties(184): #Property being stored is # pegasus.dir.storage.deep ==> false
      2020-04-27 12:57:30,867:DEBUG:Pegasus.tools.properties(176): #Property being parsed is # pegasus.home.sharedstatedir=/Users/vahi/Pegasus/software/pegasus/pegasus-5.0.0dev/share/pegasus
      2020-04-27 12:57:30,867:DEBUG:Pegasus.tools.properties(184): #Property being stored is # pegasus.home.sharedstatedir ==> /Users/vahi/Pegasus/software/pegasus/pegasus-5.0.0dev/share/pegasus
      2020-04-27 12:57:30,867:DEBUG:Pegasus.tools.properties(176): #Property being parsed is # pegasus.data.configuration=sharedfs
      2020-04-27 12:57:30,868:DEBUG:Pegasus.tools.properties(184): #Property being stored is # pegasus.data.configuration ==> sharedfs
      2020-04-27 12:57:30,868:DEBUG:Pegasus.tools.properties(176): #Property being parsed is # pegasus.code.generator=Shell
      2020-04-27 12:57:30,868:DEBUG:Pegasus.tools.properties(184): #Property being stored is # pegasus.code.generator ==> Shell
      2020-04-27 12:57:30,868:DEBUG:Pegasus.tools.properties(176): #Property being parsed is # pegasus.home.bindir=/Users/vahi/Pegasus/software/pegasus/pegasus-5.0.0dev/bin
      2020-04-27 12:57:30,868:DEBUG:Pegasus.tools.properties(184): #Property being stored is # pegasus.home.bindir ==> /Users/vahi/Pegasus/software/pegasus/pegasus-5.0.0dev/bin
      2020-04-27 12:57:30,868:DEBUG:Pegasus.tools.properties(176): #Property being parsed is # dagman.maxpre=1
      2020-04-27 12:57:30,868:DEBUG:Pegasus.tools.properties(184): #Property being stored is # dagman.maxpre ==> 1
      2020-04-27 12:57:30,868:DEBUG:Pegasus.tools.properties(176): #Property being parsed is # pegasus.condor.logs.symlink=false
      2020-04-27 12:57:30,868:DEBUG:Pegasus.tools.properties(184): #Property being stored is # pegasus.condor.logs.symlink ==> false
      2020-04-27 12:57:30,868:DEBUG:Pegasus.tools.properties(176): #Property being parsed is # pegasus.home.sysconfdir=/Users/vahi/Pegasus/software/pegasus/pegasus-5.0.0dev/etc
      2020-04-27 12:57:30,868:DEBUG:Pegasus.tools.properties(184): #Property being stored is # pegasus.home.sysconfdir ==> /Users/vahi/Pegasus/software/pegasus/pegasus-5.0.0dev/etc
      2020-04-27 12:57:30,868:DEBUG:Pegasus.tools.properties(176): #Property being parsed is # pegasus.dir.useTimestamp=true
      2020-04-27 12:57:30,868:DEBUG:Pegasus.tools.properties(184): #Property being stored is # pegasus.dir.useTimestamp ==> true
      2020-04-27 12:57:30,868:DEBUG:Pegasus.tools.properties(176): #Property being parsed is # pegasus.home.schemadir=/Users/vahi/Pegasus/software/pegasus/pegasus-5.0.0dev/share/pegasus/schema
      2020-04-27 12:57:30,868:DEBUG:Pegasus.tools.properties(184): #Property being stored is # pegasus.home.schemadir ==> /Users/vahi/Pegasus/software/pegasus/pegasus-5.0.0dev/share/pegasus/schema
      2020-04-27 12:57:30,868:DEBUG:Pegasus.db.connection(355): Using database: sqlite:////Users/vahi/.pegasus/workflow.db
      2020-04-27 12:57:30,868:DEBUG:Pegasus.db.connection(126): Connecting to: sqlite:////Users/vahi/.pegasus/workflow.db with connection params as None
      2020-04-27 12:57:30,870:DEBUG:Pegasus.db.connection(401): Turning on foreign keys
      2020-04-27 12:57:30,871:DEBUG:Pegasus.db.connection(401): Turning on foreign keys
      2020-04-27 12:57:30,871:DEBUG:Pegasus.db.connection(401): Turning on foreign keys
      2020-04-27 12:57:30,874:DEBUG:Pegasus.db.connection(401): Turning on foreign keys
      Created Pegasus database in: sqlite:////Users/vahi/.pegasus/workflow.db
      2020-04-27 12:57:30,875:DEBUG:Pegasus.db.connection(401): Turning on foreign keys
      2020-04-27 12:57:31,125:ERROR:Pegasus.db.admin.commands(120): Unable to find a $JAVA_HOME at "/usr", continuing with system-provided Java...

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            • Assignee:
              rafsilva Rafael Ferreira Da Silva
              Reporter:
              vahi Karan Vahi
            • Watchers:
              1 Start watching this issue

              Dates

              • Created:
                Updated:
                Resolved: