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())