From efeb25d8c117baee72cdece8d9ddd1e22b47952d Mon Sep 17 00:00:00 2001
From: gpawel <gpawel>
Date: Thu, 3 May 2012 09:52:02 +0000
Subject: [PATCH] bugfix: weird problem related to jython threading forces us
to compile the re pattern on the script top level (it fails in function's
body)
SVN: 25151
---
plasmid/resource/jython-scripts/MP-plasmid_parents.py | 8 ++++++--
1 file changed, 6 insertions(+), 2 deletions(-)
diff --git a/plasmid/resource/jython-scripts/MP-plasmid_parents.py b/plasmid/resource/jython-scripts/MP-plasmid_parents.py
index c539c5286e9..935b0eaf9e7 100644
--- a/plasmid/resource/jython-scripts/MP-plasmid_parents.py
+++ b/plasmid/resource/jython-scripts/MP-plasmid_parents.py
@@ -27,6 +27,9 @@ INPUT_PATTERN = """
# no '$': allow whitespace at the end
"""
+""" due to some weird jython threading issue, we need to compile the pattern outside the function body """
+inputPattern = re.compile(INPUT_PATTERN, re.VERBOSE)
+
"""relationship types shortcuts"""
DEL_REL_TYPE = 'DEL'
@@ -187,7 +190,6 @@ def updateFromBatchInput(bindings):
elements = []
input = bindings.get('')
if input is not None:
- inputPattern = re.compile(INPUT_PATTERN, re.VERBOSE)
plasmids = input.split(',')
for p in plasmids:
(code, g, relationship, annotation) = _group(inputPattern, p.strip())
@@ -198,8 +200,10 @@ def updateFromBatchInput(bindings):
if parentsInput is not None:
parents = parentsInput.split(',')
for parent in parents:
- permId = entityInformationProvider().getSamplePermId(SPACE, parent)
+ permId = entityInformationProvider().getSamplePermId(SPACE, parent.strip())
parentPlasmids = entityInformationProvider().getSamplePropertyValue(permId, 'PLASMIDS')
+ if parentPlasmids is None:
+ continue
parentElements = list(propertyConverter().convertStringToElements(parentPlasmids))
for parentLink in parentElements:
elements.append(parentLink)
--
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