From efceb4b82217977893c46cdcd60be85878ee9ac2 Mon Sep 17 00:00:00 2001
From: juanf <juanf>
Date: Wed, 4 Feb 2015 15:52:05 +0000
Subject: [PATCH] SSDM-1070 : PAPER - OPENBIS - Migrate Manage Properties
YeastLab (Configurable)
SVN: 33392
---
.../drop-boxes/stellingmigration/managed.py | 4 +++
.../drop-boxes/stellingmigration/migration.py | 36 ++++++++++++-------
2 files changed, 27 insertions(+), 13 deletions(-)
diff --git a/plasmid/source/core-plugins/stellingmigration/1/dss/drop-boxes/stellingmigration/managed.py b/plasmid/source/core-plugins/stellingmigration/1/dss/drop-boxes/stellingmigration/managed.py
index 0fc50a64e4d..1a993a1bc76 100644
--- a/plasmid/source/core-plugins/stellingmigration/1/dss/drop-boxes/stellingmigration/managed.py
+++ b/plasmid/source/core-plugins/stellingmigration/1/dss/drop-boxes/stellingmigration/managed.py
@@ -26,6 +26,10 @@ configuration["PCR"] = {
"ENZYMES" : {"NAME" : False }
};
+configuration["POMBE"] = {
+ "PLASMIDS" : {"RELATIONSHIP" : False, "ANNOTATION" : False }
+ };
+
#Global Variables
annotableType = "<REPLACE_WITH_ANNOTABLE_TYPE>"
server = CommonServiceProvider.getCommonServer()
diff --git a/plasmid/source/core-plugins/stellingmigration/1/dss/drop-boxes/stellingmigration/migration.py b/plasmid/source/core-plugins/stellingmigration/1/dss/drop-boxes/stellingmigration/migration.py
index aeff2ca7997..7b12048b2e6 100644
--- a/plasmid/source/core-plugins/stellingmigration/1/dss/drop-boxes/stellingmigration/migration.py
+++ b/plasmid/source/core-plugins/stellingmigration/1/dss/drop-boxes/stellingmigration/migration.py
@@ -55,6 +55,13 @@ definitions = {
"ENZYMES" : {
"name" : "NAME"
}
+ },
+ "POMBE" :
+ {
+ "PLASMIDS" : {
+ "rel" : "RELATIONSHIP",
+ "annotation" : "ANNOTATION"
+ }
}
};
@@ -101,22 +108,25 @@ def translate(tr, sample, properties):
if '<root>' in propertyValue:
oldAnnotationsRoot = ET.fromstring(propertyValue)
except Exception:
- print "Exception on " + sample.code + " " + property
+ print "[ERROR - PROCESSING PROPERTY_CODE] " + sample.code + " " + property
if oldAnnotationsRoot is not None:
for child in oldAnnotationsRoot:
- newAnnotationsNode = ET.SubElement(newAnnotationsRoot, "Sample")
- permId = child.attrib["permId"]
- print sample.code + " " + permId
- newAnnotationsNode.attrib["permId"] = permId
- linkedSample = getSampleByPermId(tr, permId)
- newAnnotationsNode.attrib["identifier"] = linkedSample.getSampleIdentifier()
-
- for oldName in propertyDefinitions:
- newName = propertyDefinitions[oldName]
- value = getValueOrNull(child.attrib, oldName)
- if(value is not None):
- newAnnotationsNode.attrib[newName] = value
+ try:
+ newAnnotationsNode = ET.SubElement(newAnnotationsRoot, "Sample")
+ permId = child.attrib["permId"]
+ print "[INFO - PROCESSING PERM_ID] " + sample.code + " " + permId
+ newAnnotationsNode.attrib["permId"] = permId
+ linkedSample = getSampleByPermId(tr, permId)
+ newAnnotationsNode.attrib["identifier"] = linkedSample.getSampleIdentifier()
+
+ for oldName in propertyDefinitions:
+ newName = propertyDefinitions[oldName]
+ value = getValueOrNull(child.attrib, oldName)
+ if(value is not None):
+ newAnnotationsNode.attrib[newName] = value
+ except Exception:
+ print "[ERROR - PROCESSING PERM_ID] " + sample.code + " " + permId
save(tr, sample, "ANNOTATIONS_STATE", ET.tostring(newAnnotationsRoot, encoding='utf-8'))
def save(tr, sample, property, propertyValue):
--
GitLab