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
new file mode 100644
index 0000000000000000000000000000000000000000..b915eedfbc305a9f4c43a2a787f4fe9a6d3c566a
--- /dev/null
+++ b/plasmid/source/core-plugins/stellingmigration/1/dss/drop-boxes/stellingmigration/managed.py
@@ -0,0 +1,167 @@
+from ch.systemsx.cisd.openbis.generic.server import CommonServiceProvider
+
+##
+## Configuration
+##
+
+# This needs to be edited for each sample type to match the Profile.js ANNOTATION_PROPERTIES map.
+configuration = {}
+
+configuration["GENERAL_PROTOCOL"] = {
+ "CHEMICALS" : {"QUANTITY" : False, "CHEMICAL_NAME" : False },
+ };
+
+#Global Variables
+annotableType = "<REPLACE_WITH_ANNOTABLE_TYPE>"
+server = CommonServiceProvider.getCommonServer()
+contextOrNull = server.tryToAuthenticateAsSystem()
+propertyTypes = server.listPropertyTypes(contextOrNull.getSessionToken(), False)
+
+##
+## Help Methods
+##
+def getAllAnnotableSampleTypesForType(fromAnnotableType):
+ allTypes = {};
+ for sampleTypeWithAnnotations in configuration:
+ if (fromAnnotableType == None) or (fromAnnotableType == sampleTypeWithAnnotations):
+ for sampleTypeWithAnnotationsForType in configuration[sampleTypeWithAnnotations]:
+ allTypes[sampleTypeWithAnnotationsForType] = True;
+ return allTypes;
+
+def getPropertyTypesForSampleTypeFromAnnotableType(sampleTypeCodeToFind, fromAnnotableType):
+ for sampleTypeWithAnnotations in configuration:
+ if (fromAnnotableType == None) or (fromAnnotableType == sampleTypeWithAnnotations):
+ for sampleTypeWithAnnotationsForType in configuration[sampleTypeWithAnnotations]:
+ if sampleTypeWithAnnotationsForType == sampleTypeCodeToFind:
+ return configuration[sampleTypeWithAnnotations][sampleTypeWithAnnotationsForType];
+ return None;
+
+def getPropertyType(propertyTypeCode):
+ for propertyType in propertyTypes:
+ if propertyType.code == propertyTypeCode:
+ return propertyType
+ return None;
+
+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 = []
+ widgetIdentifier = inputWidgetFactory().createTextInputField("identifier")\
+ .setMandatory(True)\
+ .setValue("")\
+ .setDescription("")
+ widgets.append(widgetIdentifier)
+ for propertyTypeCode in getPropertyTypesForSampleTypeFromAnnotableType(sampleTypeCode, annotableType):
+ propertyType = getPropertyType(propertyTypeCode)
+ widget = inputWidgetFactory().createTextInputField(propertyType.label)\
+ .setMandatory(getPropertyTypesForSampleTypeFromAnnotableType(sampleTypeCode, annotableType)[propertyTypeCode])\
+ .setValue("")\
+ .setDescription(propertyType.description)
+ widgets.append(widget)
+ return widgets;
+
+def isValid(dataType, value):
+ return True
+##
+## Main Methods
+##
+def configureUI():
+ # Add Headers
+ tableBuilder = createTableBuilder()
+ tableBuilder.addHeader("identifier")
+ usedTableHeaders = {"identifier" : True }
+ for sampleTypeCode in getAllAnnotableSampleTypesForType(annotableType):
+ for propertyTypeCode in getPropertyTypesForSampleTypeFromAnnotableType(sampleTypeCode, annotableType):
+ if propertyTypeCode not in usedTableHeaders:
+ tableBuilder.addHeader(propertyTypeCode)
+ usedTableHeaders[propertyTypeCode] = True
+
+ property.setOwnTab(True)
+ uiDescription = property.getUiDescription()
+ uiDescription.useTableOutput(tableBuilder.getTableModel())
+
+ # Add Rows
+ samples = list(propertyConverter().convertToElements(property))
+ for sample in samples:
+ row = tableBuilder.addRow()
+ for annotation in sample.getAttributes():
+ if annotation != "permId":
+ row.setCell(annotation, sample.getAttribute(annotation))
+
+ # Add Create buttons
+ for sampleTypeCode in getAllAnnotableSampleTypesForType(annotableType):
+ title = "Add " + sampleTypeCode;
+ addAction = uiDescription.addTableAction(title).setDescription(title)
+ widgets = getWidgetForAdd(sampleTypeCode, annotableType)
+ addAction.addInputWidgets(widgets)
+
+ # Add Delete button
+ deleteAction = uiDescription.addTableAction("Delete")\
+ .setDescription('Are you sure you want to delete selected annotation?')
+ deleteAction.setRowSelectionRequired() # Delete is enabled when at least 1 row is selected.
+
+def updateFromUI(action):
+ converter = propertyConverter()
+ elements = list(converter.convertToElements(property))
+
+ if action.name.startswith("Add"):
+ sampleTypeCode = action.name[4:]
+ identifier = action.getInputValue("identifier")
+ annotations = {}
+ for propertyTypeCode in getPropertyTypesForSampleTypeFromAnnotableType(sampleTypeCode, annotableType):
+ propertyType = getPropertyType(propertyTypeCode)
+ propertyTypeValue = action.getInputValue(propertyType.label)
+ if not isValid(propertyType.dataType, propertyTypeValue):
+ raise ValidationException("Property " + str(propertyType.label) + " with invalid value " + str(propertyTypeValue))
+ annotations[propertyTypeCode] = propertyTypeValue
+ newAnnotation = createAnnotationsFor(identifier, annotations)
+ elements.append(newAnnotation)
+
+ if action.name.startswith("Delete"):
+ rowIds = list(action.getSelectedRows())
+ rowIds.reverse()
+ for rowId in rowIds:
+ elements.pop(rowId)
+
+ property.value = converter.convertToString(elements)
+
+##
+## Batch Import Methods
+##
+def batchColumnNames():
+ allTypes = []
+ for sampleTypeCode in getAllAnnotableSampleTypesForType(annotableType):
+ allTypes.append(sampleTypeCode)
+ return allTypes
+
+def updateFromBatchInput(bindings):
+ elements = []
+ for annotableSampleType in getAllAnnotableSampleTypesForType(annotableType):
+ annotatedSamples = bindings.get(annotableSampleType)
+ if annotatedSamples != None and annotatedSamples != "":
+ for sampleLine in annotatedSamples.split("\\"):
+ foundIdentifier = False
+ propertyTypes = getPropertyTypesForSampleTypeFromAnnotableType(annotableSampleType, annotableType)
+ sampleLink = None
+ for sampleProperty in sampleLine.split(";"):
+ propertyName = sampleProperty.split(":")[0]
+ propertyValue = sampleProperty.split(":")[1]
+ 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 foundIdentifier:
+ elements.append(sampleLink)
+ property.value = propertyConverter().convertToString(elements)
\ No newline at end of file
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 b69fde97a07a698fb80faff75cf2b3c27ca372fb..be137f8d901c281b0d4821a819354818673ef936 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
@@ -3,6 +3,7 @@ from datetime import datetime
from ch.systemsx.cisd.openbis.generic.shared.api.v1.dto import SearchCriteria, SearchSubCriteria
import ch.systemsx.cisd.openbis.generic.server.jython.api.v1.DataType as DataType
import xml.etree.ElementTree as ET
+
##
## Generic Process Method
##
@@ -60,39 +61,34 @@ def translate(tr, sample, properties):
# Create new annotations from scratch
newAnnotations = sample.getPropertyValue("ANNOTATIONS_STATE")
newAnnotationsRoot = None
-# if (newAnnotations is not None) and (newAnnotations is not ""):
-# newAnnotationsRoot = ET.fromstring(newAnnotations)
-# if (newAnnotations is None) or (newAnnotations is ""):
newAnnotationsRoot = ET.Element("root")
# Read old annotations
for property in properties:
- if property == "CHEMICALS":
- oldAnnotationsRoot = None
- try:
- propertyValue = unicode(sample.getPropertyValue(property), "utf-8")
- oldAnnotationsRoot = ET.fromstring(propertyValue)
- except Exception:
- print "Exception on " + 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()
-
- concentration = getValueOrNull(child.attrib, "concentration")
- if(concentration is not None):
- newAnnotationsNode.attrib["concentration"] = concentration
- chemicalName = getValueOrNull(child.attrib, "name")
- if(chemicalName is not None):
- newAnnotationsNode.attrib["chemicalName"] = chemicalName
-
- if sampleType == "GENERAL_PROTOCOL":
- save(tr, sample, "ANNOTATIONS_STATE", ET.tostring(newAnnotationsRoot, encoding='utf-8'))
+ oldAnnotationsRoot = None
+ try:
+ propertyValue = unicode(sample.getPropertyValue(property), "utf-8")
+ if '<root>' in propertyValue:
+ oldAnnotationsRoot = ET.fromstring(propertyValue)
+ except Exception:
+ print "Exception on " + sample.code + " " + property
+ if oldAnnotationsRoot is not None:
+ for child in oldAnnotationsRoot:
+ if property == "CHEMICALS":
+ 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()
+
+ concentration = getValueOrNull(child.attrib, "concentration")
+ if(concentration is not None):
+ newAnnotationsNode.attrib["QUANTITY"] = concentration
+ chemicalName = getValueOrNull(child.attrib, "name")
+ if(chemicalName is not None):
+ newAnnotationsNode.attrib["CHEMICAL_NAME"] = chemicalName
+ save(tr, sample, "ANNOTATIONS_STATE", ET.tostring(newAnnotationsRoot, encoding='utf-8'))
def save(tr, sample, property, propertyValue):
mutableSample = tr.makeSampleMutable(sample)
diff --git a/plasmid/source/core-plugins/stellingmigration/1/dss/drop-boxes/stellingmigration/notes.txt b/plasmid/source/core-plugins/stellingmigration/1/dss/drop-boxes/stellingmigration/notes.txt
new file mode 100644
index 0000000000000000000000000000000000000000..314349113314973d49a4e40439ca004f53ba2ee3
--- /dev/null
+++ b/plasmid/source/core-plugins/stellingmigration/1/dss/drop-boxes/stellingmigration/notes.txt
@@ -0,0 +1,10 @@
+##
+## Property Types Created in openBIS for the annotations
+##
+
+#
+# CHEMICALS
+#
+
+QUANTITY
+CHEMICAL_NAME
\ No newline at end of file