From ec2cf1dcff971967dd02f249d682070220904741 Mon Sep 17 00:00:00 2001 From: Patrick Jentsch Date: Mon, 3 Feb 2020 15:26:04 +0100 Subject: [PATCH] Fix zip switch integration --- nlp | 37 ++++++++++++++++++------------------- wrapper/nlp | 2 +- 2 files changed, 19 insertions(+), 20 deletions(-) diff --git a/nlp b/nlp index a8078a8..e4156d4 100755 --- a/nlp +++ b/nlp @@ -35,14 +35,12 @@ def parse_arguments(): help='total number of cores available', required=False, type=int) - parser.add_argument( - '--zip', - action='store_true', - default=False, - dest='zip', - help='package result files in zip bundles', - required=False - ) + parser.add_argument('--zip', + action='store_true', + default=False, + dest='zip', + help='package result files in zip bundles', + required=False) return parser.parse_args() @@ -100,18 +98,19 @@ class NLPWorkflow(WorkflowRunner): ) ) - vrt_zip_jobs = [] - vrt_zip_job_dependencies = nlp_jobs - cmd = 'cd "%s" && zip -m vrt.zip */*.vrt -x "pyflow.data*" && cd -' % ( - self.output_dir - ) - vrt_zip_jobs.append( - self.addTask( - command=cmd, - dependencies=vrt_zip_job_dependencies, - label='vrt_zip_job' + if zip: + vrt_zip_jobs = [] + vrt_zip_job_dependencies = nlp_jobs + cmd = 'cd "%s" && zip -m vrt.zip */*.vrt -x "pyflow.data*" && cd -' % ( + self.output_dir + ) + vrt_zip_jobs.append( + self.addTask( + command=cmd, + dependencies=vrt_zip_job_dependencies, + label='vrt_zip_job' + ) ) - ) def analyze_jobs(input_dir, output_dir): diff --git a/wrapper/nlp b/wrapper/nlp index 07332c8..36d0e08 100755 --- a/wrapper/nlp +++ b/wrapper/nlp @@ -5,7 +5,7 @@ import argparse import os import subprocess -container_image = 'gitlab.ub.uni-bielefeld.de:4567/sfb1288inf/nlp:2.1.0' +container_image = 'gitlab.ub.uni-bielefeld.de:4567/sfb1288inf/nlp:latest' container_input_dir = '/input' container_output_dir = '/output' uid = str(os.getuid())