diff --git a/plasmid/source/core-plugins/weismigration/1/as/definitions.py b/plasmid/source/core-plugins/weismigration/1/as/definitions.py
index 5674e9f144c28d8832b2a0cc5ab2e635bdecf1b1..c3491ef0f6af08d7a289dfed6471a65369e65016 100644
--- a/plasmid/source/core-plugins/weismigration/1/as/definitions.py
+++ b/plasmid/source/core-plugins/weismigration/1/as/definitions.py
@@ -19,7 +19,7 @@ commentsScriptName = "COMMENTS";
gcScriptName= "GC"
atScriptName= "AT"
lengthScriptName= "SEQUENCE_LENGTH"
-
+annotationsScriptName="ANNOTATIONS"
#
# Storage
diff --git a/plasmid/source/core-plugins/weismigration/1/as/initialize-master-data.py b/plasmid/source/core-plugins/weismigration/1/as/initialize-master-data.py
index a9763c5223dc618b2173af3b1c1610dfc5124093..c4f6eb17b1ae3bff3715027a5a4b3826fec84132 100644
--- a/plasmid/source/core-plugins/weismigration/1/as/initialize-master-data.py
+++ b/plasmid/source/core-plugins/weismigration/1/as/initialize-master-data.py
@@ -130,7 +130,21 @@ def createScript(path, name, description, scriptType, entityType):
script.setScriptType(scriptType);
script.setEntityForScript(entityType);
return script;
-
+
+
+def createAnnotationsScriptForType(sampleTypeCode):
+ annotationsScriptName = None;
+ if PATH_TO_MANAGE_PROPERTIES_SCRIPTS != None:
+ annotationsScriptName = "ANNOTATIONS_" + sampleTypeCode;
+ annotationsScriptAsString = open(PATH_TO_MANAGE_PROPERTIES_SCRIPTS + "managed.py", 'r').read();
+ annotationsScriptAsString = annotationsScriptAsString.replace("<REPLACE_WITH_ANNOTABLE_TYPE>", sampleTypeCode);
+ annotationsScript = tr.getOrCreateNewScript(annotationsScriptName);
+ annotationsScript.setName(annotationsScriptName);
+ annotationsScript.setDescription("Annotations Handler for " + sampleTypeCode);
+ annotationsScript.setScript(annotationsScriptAsString);
+ annotationsScript.setScriptType("MANAGED_PROPERTY");
+ annotationsScript.setEntityForScript("SAMPLE");
+ return annotationsScriptName;
##
## Managed properties scripts
##
@@ -166,6 +180,9 @@ lengthScriptName = createScript(PATH_TO_MANAGE_PROPERTIES_SCRIPTS + "length.py",
"Count length sequence",
"DYNAMIC_PROPERTY",
"SAMPLE");
+
+
+
##
## Vocabulary Types
##
diff --git a/plasmid/source/core-plugins/weismigration/1/compatibility/managed.py b/plasmid/source/core-plugins/weismigration/1/compatibility/managed.py
new file mode 100644
index 0000000000000000000000000000000000000000..6d6312c0f92b6c8bcc7e59032b5bbad4d7005858
--- /dev/null
+++ b/plasmid/source/core-plugins/weismigration/1/compatibility/managed.py
@@ -0,0 +1,331 @@
+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["MEDIA"] = {
+ "CHEMICAL" : {"QUANTITY" : False, "COMMENTS" : False },
+ "SOLUTION_BUFFER" : {"QUANTITY" : False, "COMMENTS" : False },
+ "MEDIA" : {"QUANTITY" : False, "COMMENTS" : False }
+ };
+
+configuration["SOLUTION_BUFFER"] = {
+ "CHEMICAL" : {"QUANTITY" : False, "COMMENTS" : False },
+ "SOLUTION_BUFFER" : {"QUANTITY" : False, "COMMENTS" : False },
+ "MEDIA" : {"QUANTITY" : False, "COMMENTS" : False }
+ };
+
+configuration["GENERAL_PROTOCOL"] = {
+ "CHEMICAL" : {"QUANTITY" : False, "COMMENTS" : False },
+ "SOLUTION_BUFFER" : {"QUANTITY" : False, "COMMENTS" : False },
+ "MEDIA" : {"QUANTITY" : False, "COMMENTS" : False },
+ "ENZYME" : {"QUANTITY" : False, "COMMENTS" : False },
+ "GENERAL_PROTOCOL" : {"COMMENTS" : False }
+ };
+
+configuration["PCR_PROTOCOL"] = {
+ "CHEMICAL" : {"QUANTITY" : False, "COMMENTS" : False },
+ "SOLUTION_BUFFER" : {"QUANTITY" : False, "COMMENTS" : False },
+ "ENZYME" : {"QUANTITY" : False, "COMMENTS" : False }
+ };
+
+configuration["WESTERN_BLOTTING_PROTOCOL"] = {
+ "CHEMICAL" : {"QUANTITY" : False, "COMMENTS" : False },
+ "SOLUTION_BUFFER" : {"QUANTITY" : False, "COMMENTS" : False },
+ "ANTIBODY" : {"QUANTITY" : False, "COMMENTS" : False }
+ };
+
+configuration["PLASMID"] = {
+ "PLASMID" : {"COMMENTS" : False }
+ };
+
+configuration["BACTERIA"] = {
+ "BACTERIA" : {"COMMENTS" : False },
+ "PLASMID" : {"PLASMID_RELATIONSHIP" : False, "PLASMID_ANNOTATION" : False, "COMMENTS" : False }
+ };
+
+configuration["YEAST"] = {
+ "YEAST" : {"COMMENTS" : False },
+ "PLASMID" : {"PLASMID_RELATIONSHIP" : False, "PLASMID_ANNOTATION" : False, "COMMENTS" : False, "CONTAINED" : False }
+ };
+
+configuration["CELL_LINE"] = {
+ "CELL_LINE" : {"COMMENTS" : False },
+ "PLASMID" : {"PLASMID_RELATIONSHIP" : False, "PLASMID_ANNOTATION" : False, "COMMENTS" : False },
+ "FLY" : {"COMMENTS" : False }
+ };
+
+configuration["FLY"] = {
+ "FLY" : {"COMMENTS" : False },
+ "PLASMID" : {"PLASMID_RELATIONSHIP" : False, "PLASMID_ANNOTATION" : False, "COMMENTS" : False }
+ };
+
+configuration["EXPERIMENTAL_STEP"] = {
+ "ANTIBODY" : {"QUANTITY" : False, "COMMENTS" : False },
+ "BACTERIA" : {"COMMENTS" : False },
+ "CELL_LINE" : {"COMMENTS" : False },
+ "CHEMICAL" : {"QUANTITY" : False, "COMMENTS" : False },
+ "ENZYME" : {"QUANTITY" : False, "COMMENTS" : False },
+ "FLY" : {"COMMENTS" : False },
+ "MEDIA" : {"QUANTITY" : False, "COMMENTS" : False },
+ "OLIGO" : {"COMMENTS" : False },
+ "PLASMID" : {"COMMENTS" : False },
+ "RNA" : {"COMMENTS" : False },
+ "SOLUTION_BUFFER" : {"QUANTITY" : False, "COMMENTS" : False },
+ "YEAST" : {"COMMENTS" : False },
+ "GENERAL_PROTOCOL" : {"COMMENTS" : False },
+ "PCR_PROTOCOL" : {"COMMENTS" : False },
+ "WESTERN_BLOTTING_PROTOCOL" : {"COMMENTS" : False }
+ };
+
+configurationCopyParents = {}
+configurationCopyParents["YEAST"] = { "YEAST" : "PLASMID" };
+
+#Global Variables
+annotableType = "<REPLACE_WITH_ANNOTABLE_TYPE>"
+propertyTypes = None
+def getPropertyTypes():
+ global propertyTypes
+ if propertyTypes is None:
+ server = CommonServiceProvider.getCommonServer()
+ contextOrNull = server.tryToAuthenticateAsSystem()
+ propertyTypes = server.listPropertyTypes(contextOrNull.getSessionToken(), False)
+ return propertyTypes;
+
+##
+## 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 getPropertyTypes():
+ if propertyType.code == propertyTypeCode:
+ return propertyType
+ return None;
+
+def createAnnotationsFor(identifier, annotations, sampleType):
+ permId = entityInformationProvider().getSamplePermId(identifier);
+ newAnnotation = elementFactory().createSampleLink(permId)
+
+ newAnnotation.addAttribute("identifier", identifier)
+ newAnnotation.addAttribute("sampleType", sampleType)
+ for annotation in annotations:
+ newAnnotation.addAttribute(annotation, annotations[annotation])
+ return newAnnotation
+
+def getWidgetForAdd(sampleTypeCode, annotableType):
+ #print "sampleTypeCode:" + sampleTypeCode + " - " + annotableType #Deleting this comment causes the thing to break
+ 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
+
+##
+## Registration form (EXPERIMENTAL)
+##
+
+# def inputWidgets():
+# print "EXECUTING inputWidgets START"
+# widgetsToCopyFrom = []
+# if annotableType in configurationCopyParents:
+# toCopyFrom = configurationCopyParents[annotableType]
+# if(toCopyFrom is not None):
+# for key in toCopyFrom:
+# widgetLabel = key + " to copy " + toCopyFrom[key]
+# print "EXECUTING inputWidgets key: " + widgetLabel
+# widgetToCopyFrom = inputWidgetFactory().createTextInputField(widgetLabel).setMandatory(False)
+# widgetsToCopyFrom.append(widgetToCopyFrom)
+# print "EXECUTING inputWidgets " + str(len(widgetsToCopyFrom))
+# return widgetsToCopyFrom
+#
+# def updateFromRegistrationForm(bindings):
+# print "EXECUTING updateFromaRegistrationForm"
+# for key in bindings:
+# print "MANAGED WITH KEY: " + str(key)
+
+##
+## Main Methods
+##
+def configureUI():
+ # Add Headers
+ tableBuilder = createTableBuilder()
+ tableBuilder.addHeader("identifier")
+ tableBuilder.addHeader("sampleType")
+ tableBuilder.addHeader("name")
+
+ usedTableHeaders = {"identifier" : True, "sampleType" : True, "name" : 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()
+ permId = sample.getAttribute("permId")
+
+ nameValue = entityInformationProvider().getSamplePropertyValue(permId, "NAME")
+ if nameValue is not None:
+ row.setCell("name", nameValue)
+
+ for annotation in sample.getAttributes():
+ if annotation != "permId":
+ if annotation == "identifier":
+ row.setCell(annotation, sample, sample.getAttribute(annotation))
+ else:
+ 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)
+
+ # TO-DO Edit button for each type with different hooks to the columns depending on the type
+ # Add Edit Button (EXPERIMENTAL)
+# editAction = uiDescription.addTableAction('Edit').setDescription('Edit selected table row')
+# editAction.setRowSelectionRequiredSingle()
+# editWidgets = []
+# for headerKey in usedTableHeaders:
+# editWidgets.append(inputWidgetFactory().createTextInputField(headerKey))
+# editAction.addBinding(headerKey, headerKey)
+# editAction.addInputWidgets(editWidgets)
+
+ # 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))
+ if propertyTypeValue is None:
+ propertyTypeValue = ""
+ annotations[propertyTypeCode] = propertyTypeValue
+ newAnnotation = createAnnotationsFor(identifier, annotations, sampleTypeCode)
+ 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):
+ #print "--------> UPDATE FROM BATCH INPUT: "
+ elements = []
+
+ #Links Configuration
+ typesToCopyFrom = []
+ if annotableType in configurationCopyParents:
+ typesToCopyFrom = configurationCopyParents[annotableType]
+
+ for annotableSampleType in getAllAnnotableSampleTypesForType(annotableType):
+ annotatedSamples = bindings.get(annotableSampleType)
+ #print "-----> TYPE: " + str(annotableSampleType) + " BINDINGS: " + str(annotatedSamples)
+ if (annotatedSamples != None and annotatedSamples != ""):
+ #Annotations
+ #print "-----> Annotations"
+ if annotableSampleType not in typesToCopyFrom:
+ for sampleLine in annotatedSamples.split("\\"):
+ propertyTypes = getPropertyTypesForSampleTypeFromAnnotableType(annotableSampleType, annotableType)
+ identifier = None
+ permId = None
+ sampleLink = None
+ for sampleProperty in sampleLine.split(";"):
+ propertyName = sampleProperty.split(":")[0]
+ propertyValue = sampleProperty.split(":")[1]
+ if propertyName == "identifier":
+ 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)
+ #print "-----> COPYING: " + str(parentAnnotation.getAttribute('identifier'))
+ elements.append(parentAnnotation)
+ property.value = propertyConverter().convertToString(elements)
\ No newline at end of file