From c1eb1ddcddef36a79f068f15bb19bbe9db7c0766 Mon Sep 17 00:00:00 2001
From: juanf <juanf>
Date: Fri, 22 May 2015 13:57:55 +0000
Subject: [PATCH] SSDM-1922: CORE - YEASTLAB: Delete repeated annotations
SVN: 34025
---
.../stellingconsistency/consistency.py | 23 ++++++++++++++-----
1 file changed, 17 insertions(+), 6 deletions(-)
diff --git a/plasmid/source/core-plugins/stellingmigration/1/dss/drop-boxes/stellingconsistency/consistency.py b/plasmid/source/core-plugins/stellingmigration/1/dss/drop-boxes/stellingconsistency/consistency.py
index 35ead1ad3f2..54f7eab8754 100644
--- a/plasmid/source/core-plugins/stellingmigration/1/dss/drop-boxes/stellingconsistency/consistency.py
+++ b/plasmid/source/core-plugins/stellingmigration/1/dss/drop-boxes/stellingconsistency/consistency.py
@@ -7,9 +7,10 @@ import xml.etree.ElementTree as ET
##
## Definitions
##
+UPDATES_ENABLED = False
sampleTypesToVerify = ["YEAST","POMBE"]
-logLevelsToPrint = ["ERROR", "REPORT", "MANUAL-FIX"] #INFO not included, use it for debug only
+logLevelsToPrint = ["ERROR", "REPORT", "MANUAL-FIX", "UPDATED"] #INFO not included, use it for debug only
##
## Logging
@@ -152,13 +153,22 @@ def verify(tr, sample):
if areAnnotationDuplicated(sample):
logManualFix("Case 6 - Same annotation coming from different parents: ", sample.getSample().getRegistrator().getUserId(), sample.getSampleIdentifier(), "?", "?", "?")
newAnnotationsReady = False
- if newAnnotationsReady:
+ global UPDATES_ENABLED;
+ if newAnnotationsReady and UPDATES_ENABLED:
global numberOfCanBeUpdated;
numberOfCanBeUpdated = numberOfCanBeUpdated + 1;
+ log("UPDATED", str(newAnnotations))
+ sample = tr.makeSampleMutable(sample);
#1. Create new annotations XML
-
- #2. Add LOST parents
-
+ newAnnotationsRoot = ET.Element("root");
+ for newAnnotation in newAnnotations:
+ newAnnotationsNode = ET.SubElement(newAnnotationsRoot, "Sample")
+ for newAttribute in newAnnotation:
+ newAnnotationsNode.attrib[newAttribute] = newAnnotation[newAttribute];
+ if getValueOrNull(newAnnotation, "PLASMID_RELATIONSHIP") == "LOT": #2. Add LOST parents
+ sample.getParentSampleIdentifiers().add(newAnnotation["identifier"]);
+ sample.setPropertyValue("ANNOTATIONS_STATE", ET.tostring(newAnnotationsRoot, encoding='utf-8'));
+
def areAnnotationDuplicated(sample):
annotated = {}; #They should be parents of the sample and not been missing
annotationsRoot = getAnnotationsRootNodeFromSample(sample);
@@ -226,7 +236,8 @@ def getAnnotationMap(annotation):
map = {};
for key in annotation.attrib:
value = getValueOrNull(annotation.attrib, key)
- map[key] = value;
+ if value is not None:
+ map[key] = value;
return map
def areAnnotationsEqual(annotationA, annotationB):
--
GitLab