From 6e2ad6d1dce53926657a4a638327a421cb33b688 Mon Sep 17 00:00:00 2001
From: juanf <juanf>
Date: Fri, 14 Nov 2014 10:47:36 +0000
Subject: [PATCH] SSDM-983 : PAPER - Annotations on Batch Import
SVN: 32824
---
.../newbrowser/1/compatibility/managed.py | 41 ++++++++-----------
1 file changed, 18 insertions(+), 23 deletions(-)
diff --git a/plasmid/source/core-plugins/newbrowser/1/compatibility/managed.py b/plasmid/source/core-plugins/newbrowser/1/compatibility/managed.py
index 0126a00311f..e97ae2c28a7 100644
--- a/plasmid/source/core-plugins/newbrowser/1/compatibility/managed.py
+++ b/plasmid/source/core-plugins/newbrowser/1/compatibility/managed.py
@@ -111,24 +111,22 @@ def getPropertyType(propertyTypeCode):
return propertyType
return None;
-def createAnnotationsFor(permId, annotations):
+def createAnnotationsFor(identifier, annotations):
+ permId = entityInformationProvider().getSamplePermId(identifier);
newAnnotation = elementFactory().createSampleLink(permId)
+
+ newAnnotation.addAttribute("identifier", identifier)
for annotation in annotations:
newAnnotation.addAttribute(annotation, annotations[annotation])
return newAnnotation
def getWidgetForAdd(sampleTypeCode, annotableType):
widgets = []
- widgetPermId = inputWidgetFactory().createTextInputField("permId")\
- .setMandatory(True)\
- .setValue("")\
- .setDescription("")
- widgets.append(widgetPermId)
- widgetCode = inputWidgetFactory().createTextInputField("code")\
+ widgetIdentifier = inputWidgetFactory().createTextInputField("identifier")\
.setMandatory(True)\
.setValue("")\
.setDescription("")
- widgets.append(widgetCode)
+ widgets.append(widgetIdentifier)
for propertyTypeCode in getPropertyTypesForSampleTypeFromAnnotableType(sampleTypeCode, annotableType):
propertyType = getPropertyType(propertyTypeCode)
widget = inputWidgetFactory().createTextInputField(propertyType.label)\
@@ -139,7 +137,6 @@ def getWidgetForAdd(sampleTypeCode, annotableType):
return widgets;
def isValid(dataType, value):
- print "isValid"
return True
##
## Main Methods
@@ -148,9 +145,8 @@ def configureUI():
annotableType = None
# Add Headers
tableBuilder = createTableBuilder()
- tableBuilder.addHeader("permId")
- tableBuilder.addHeader("code")
- usedTableHeaders = {"permId" : True, "code" : True}
+ tableBuilder.addHeader("identifier")
+ usedTableHeaders = {"identifier" : True }
for sampleTypeCode in getAllAnnotableSampleTypesForType(annotableType):
for propertyTypeCode in getPropertyTypesForSampleTypeFromAnnotableType(sampleTypeCode, annotableType):
if propertyTypeCode not in usedTableHeaders:
@@ -166,7 +162,8 @@ def configureUI():
for sample in samples:
row = tableBuilder.addRow()
for annotation in sample.getAttributes():
- row.setCell(annotation, sample.getAttribute(annotation))
+ if annotation != "permId":
+ row.setCell(annotation, sample.getAttribute(annotation))
# Add Create buttons
for sampleTypeCode in getAllAnnotableSampleTypesForType(annotableType):
@@ -187,7 +184,7 @@ def updateFromUI(action):
if action.name.startswith("Add"):
sampleTypeCode = action.name[4:]
- permId = action.getInputValue("permId")
+ identifier = action.getInputValue("identifier")
annotations = {}
for propertyTypeCode in getPropertyTypesForSampleTypeFromAnnotableType(sampleTypeCode, annotableType):
propertyType = getPropertyType(propertyTypeCode)
@@ -195,7 +192,7 @@ def updateFromUI(action):
if not isValid(propertyType.dataType, propertyTypeValue):
raise ValidationException("Property " + str(propertyType.label) + " with invalid value " + str(propertyTypeValue))
annotations[propertyTypeCode] = propertyTypeValue
- newAnnotation = createAnnotationsFor(permId, annotations)
+ newAnnotation = createAnnotationsFor(identifier, annotations)
elements.append(newAnnotation)
if action.name.startswith("Delete"):
@@ -223,23 +220,21 @@ def updateFromBatchInput(bindings):
annotatedSamples = bindings.get(annotableSampleType)
if annotatedSamples != None and annotatedSamples != "":
for sampleLine in annotatedSamples.splitlines():
- foundCode = False
- foundPermId = False
+ foundIdentifier = False
propertyTypes = getPropertyTypesForSampleTypeFromAnnotableType(annotableSampleType, annotableType)
sampleLink = None
for sampleProperty in sampleLine.split(";"):
propertyName = sampleProperty.split(":")[0]
propertyValue = sampleProperty.split(":")[1]
- if propertyName == "permId":
- foundPermId = True
- sampleLink = elementFactory().createSampleLink(propertyValue)
- elif propertyName == "code":
- foundCode = True
+ if propertyName == "identifier":
+ foundIdentifier = True
+ permId = entityInformationProvider().getSamplePermId(propertyValue)
+ sampleLink = elementFactory().createSampleLink(permId)
sampleLink.addAttribute(propertyName, propertyValue)
elif propertyTypes[propertyName] != None:
sampleLink.addAttribute(propertyName, propertyValue)
else:
raise NameError('Found invalid property: ' + propertyName + " on type " + annotableSampleType)
- if foundPermId and foundCode:
+ if foundIdentifier:
elements.append(sampleLink)
property.value = propertyConverter().convertToString(elements)
\ No newline at end of file
--
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