From ebdb80b56d8569356c189d3cdffcf4e9d62964a3 Mon Sep 17 00:00:00 2001
From: juanf <juanf>
Date: Fri, 27 Feb 2015 15:17:24 +0000
Subject: [PATCH] SSDM-1564: PAPER - OPENBIS - Migration Support
SVN: 33534
---
.../1/compatibility/managed.py | 52 ++++++++++---------
1 file changed, 27 insertions(+), 25 deletions(-)
diff --git a/plasmid/source/core-plugins/stellingmigration/1/compatibility/managed.py b/plasmid/source/core-plugins/stellingmigration/1/compatibility/managed.py
index f283dbee3db..fac8ecdc04c 100644
--- a/plasmid/source/core-plugins/stellingmigration/1/compatibility/managed.py
+++ b/plasmid/source/core-plugins/stellingmigration/1/compatibility/managed.py
@@ -196,7 +196,7 @@ def batchColumnNames():
return allTypes
def updateFromBatchInput(bindings):
- #print "--------> UPDATE FROM BATCH INPUT: "
+ print "--------> UPDATE FROM BATCH INPUT: "
elements = []
#Links Configuration
@@ -206,10 +206,10 @@ def updateFromBatchInput(bindings):
for annotableSampleType in getAllAnnotableSampleTypesForType(annotableType):
annotatedSamples = bindings.get(annotableSampleType)
- #print "-----> TYPE: " + str(annotableSampleType) + " BINDINGS: " + str(annotatedSamples)
+ print "-----> TYPE: " + str(annotableSampleType) + " BINDINGS: " + str(annotatedSamples)
if (annotatedSamples != None and annotatedSamples != ""):
#Annotations
- #print "-----> Annotations"
+ print "-----> Annotations"
if annotableSampleType not in typesToCopyFrom:
for sampleLine in annotatedSamples.split("\\"):
propertyTypes = getPropertyTypesForSampleTypeFromAnnotableType(annotableSampleType, annotableType)
@@ -218,37 +218,39 @@ def updateFromBatchInput(bindings):
sampleLink = None
for sampleProperty in sampleLine.split(";"):
propertyName = sampleProperty.split(":")[0]
+ propertyValue = sampleProperty.split(":")[1]
if propertyName == "identifier":
- propertyValue = sampleProperty.split(":")[1]
identifier = propertyValue
permId = entityInformationProvider().getSamplePermId(propertyValue)
sampleLink = elementFactory().createSampleLink(permId)
sampleLink.addAttribute(propertyName, propertyValue)
+ sampleLink.addAttribute('sampleType', annotableSampleType)
elif propertyName in propertyTypes:
sampleLink.addAttribute(propertyName, propertyValue)
else:
raise NameError('Found invalid property: ' + propertyName + " on type " + annotableSampleType)
if identifier is not None:
elements.append(sampleLink)
- #Links
- #print "-----> links"
- for typeToCopyFrom in typesToCopyFrom:
- typeToCopy = typesToCopyFrom[typeToCopyFrom]
- #print "-----> TYPE TO COPY FROM: " + str(typeToCopyFrom)
- #print "-----> TYPE TO COPY: " + str(typeToCopy)
- identifiersToCopyFrom = bindings.get(typeToCopyFrom)
- if identifiersToCopyFrom is not None:
- #print "-----> IDENTIFIERS TO COPY FROM: " + str(identifiersToCopyFrom)
- identifiersForCopy = identifiersToCopyFrom.split(',')
- for identifierToCopyFrom in identifiersForCopy:
- #print "-----> IDENTIFIER TO COPY FROM: " + str(identifierToCopyFrom)
- permIdFromIdentifier = entityInformationProvider().getSamplePermId(identifierToCopyFrom)
- #print "-----> PERMID TO COPY FROM: " + str(permIdFromIdentifier)
- parentsToCopyFromPermId = entityInformationProvider().getSamplePropertyValue(permIdFromIdentifier, "ANNOTATIONS_STATE")
- #print "-----> ELEMENTS TO COPY: " + str(parentsToCopyFromPermId)
- parentElements = list(propertyConverter().convertStringToElements(parentsToCopyFromPermId))
- for parentAnnotation in parentElements:
- if parentAnnotation.getAttribute("sampleType") == typeToCopy:
- parentAnnotation.addAttribute("CONTAINED", identifierToCopyFrom)
- elements.append(parentAnnotation)
+ #Links
+ print "-----> links"
+ for typeToCopyFrom in typesToCopyFrom:
+ typeToCopy = typesToCopyFrom[typeToCopyFrom]
+ print "-----> TYPE TO COPY FROM: " + str(typeToCopyFrom)
+ print "-----> TYPE TO COPY: " + str(typeToCopy)
+ identifiersToCopyFrom = bindings.get(typeToCopyFrom)
+ if identifiersToCopyFrom is not None:
+ print "-----> IDENTIFIERS TO COPY FROM: " + str(identifiersToCopyFrom)
+ identifiersForCopy = identifiersToCopyFrom.split(',')
+ for identifierToCopyFrom in identifiersForCopy:
+ print "-----> IDENTIFIER TO COPY FROM: " + str(identifierToCopyFrom)
+ permIdFromIdentifier = entityInformationProvider().getSamplePermId(identifierToCopyFrom)
+ #print "-----> PERMID TO COPY FROM: " + str(permIdFromIdentifier)
+ parentsToCopyFromPermId = entityInformationProvider().getSamplePropertyValue(permIdFromIdentifier, "ANNOTATIONS_STATE")
+ print "-----> ELEMENTS TO COPY: " + str(parentsToCopyFromPermId)
+ parentElements = list(propertyConverter().convertStringToElements(parentsToCopyFromPermId))
+ for parentAnnotation in parentElements:
+ if parentAnnotation.getAttribute("sampleType") == typeToCopy:
+ parentAnnotation.addAttribute("CONTAINED", identifierToCopyFrom)
+ print "-----> COPYING: " + str(parentAnnotation.getAttribute('identifier'))
+ elements.append(parentAnnotation)
property.value = propertyConverter().convertToString(elements)
\ No newline at end of file
--
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