From ee7c04dd2f7e3a2c26f1dd81b85d72aedc3bd7bf Mon Sep 17 00:00:00 2001
From: juanf <juanf>
Date: Mon, 10 Nov 2014 12:51:41 +0000
Subject: [PATCH] SSDM-983 : PAPER - Annotations on Batch Import
SVN: 32766
---
.../newbrowser/1/as/initialize-master-data.py | 2 +
.../newbrowser/1/compatibility/managed.py | 117 ++++++++++++++++--
2 files changed, 108 insertions(+), 11 deletions(-)
diff --git a/plasmid/source/core-plugins/newbrowser/1/as/initialize-master-data.py b/plasmid/source/core-plugins/newbrowser/1/as/initialize-master-data.py
index 8655da1e465..40b43b8e41c 100644
--- a/plasmid/source/core-plugins/newbrowser/1/as/initialize-master-data.py
+++ b/plasmid/source/core-plugins/newbrowser/1/as/initialize-master-data.py
@@ -52,6 +52,7 @@ def addTermWithLabel(vocabulary, termCode, termLabel):
def createSampleTypeWithProperties(sampleTypeCode, description, properties):
newSampleType = tr.getOrCreateNewSampleType(sampleTypeCode);
newSampleType.setDescription(description);
+ newSampleType.setShowParents(True);
newSampleType.setAutoGeneratedCode(True);
newSampleType.setGeneratedCodePrefix(sampleTypeCode[:3]);
addProperties(newSampleType, properties);
@@ -89,6 +90,7 @@ def addProperty(entity, propertyCode, section, propertyLabel, dataType, vocabula
propertyAssignment.setSection(section);
if managedScript != None:
propertyAssignment.setManaged(True);
+ propertyAssignment.setShownEdit(True);
propertyAssignment.setScriptName(managedScript);
def createProperty(propertyCode, dataType, propertyLabel, propertyDescription, vocabularyCode):
diff --git a/plasmid/source/core-plugins/newbrowser/1/compatibility/managed.py b/plasmid/source/core-plugins/newbrowser/1/compatibility/managed.py
index eb26c1d5b52..de68800ec1b 100644
--- a/plasmid/source/core-plugins/newbrowser/1/compatibility/managed.py
+++ b/plasmid/source/core-plugins/newbrowser/1/compatibility/managed.py
@@ -3,7 +3,80 @@ 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["CHEMICAL"] = { "QUANTITY" : False, "COMMENTS" : False }
+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 }
+ };
+
+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 }
+ };
#Global Variables
server = CommonServiceProvider.getCommonServer()
@@ -13,6 +86,20 @@ propertyTypes = server.listPropertyTypes(contextOrNull.getSessionToken(), False)
##
## Help Methods
##
+def getAllAnnotableSampleTypes():
+ allTypes = {};
+ for sampleTypeWithAnnotations in configuration:
+ for sampleTypeWithAnnotationsForType in configuration[sampleTypeWithAnnotations]:
+ allTypes[sampleTypeWithAnnotationsForType] = True;
+ return allTypes;
+
+def getPropertyTypesForSampleTypeIgnoringCurrentType(sampleTypeCodeToFind):
+ for sampleTypeWithAnnotations in configuration:
+ for sampleTypeWithAnnotationsForType in configuration[sampleTypeWithAnnotations]:
+ if sampleTypeWithAnnotationsForType == sampleTypeCodeToFind:
+ return configuration[sampleTypeWithAnnotations][sampleTypeWithAnnotationsForType];
+ return None;
+
def getPropertyType(propertyTypeCode):
print "Searching property type: " + propertyTypeCode
for propertyType in propertyTypes:
@@ -28,15 +115,20 @@ def createAnnotationsFor(permId, annotations):
def getWidgetForAdd(sampleTypeCode):
widgets = []
- widget = inputWidgetFactory().createTextInputField("permId")\
+ widgetPermId = inputWidgetFactory().createTextInputField("permId")\
+ .setMandatory(True)\
+ .setValue("")\
+ .setDescription("")
+ widgets.append(widgetPermId)
+ widgetCode = inputWidgetFactory().createTextInputField("code")\
.setMandatory(True)\
.setValue("")\
.setDescription("")
- widgets.append(widget)
- for propertyTypeCode in configuration[sampleTypeCode].keys():
+ widgets.append(widgetCode)
+ for propertyTypeCode in getPropertyTypesForSampleTypeIgnoringCurrentType(sampleTypeCode):
propertyType = getPropertyType(propertyTypeCode)
widget = inputWidgetFactory().createTextInputField(propertyType.label)\
- .setMandatory(configuration[sampleTypeCode][propertyTypeCode])\
+ .setMandatory(getPropertyTypesForSampleTypeIgnoringCurrentType(sampleTypeCode)[propertyTypeCode])\
.setValue("")\
.setDescription(propertyType.description)
widgets.append(widget)
@@ -49,13 +141,16 @@ def isValid(dataType, value):
## Help Methods
##
def configureUI():
- print "All property types: " + str(propertyTypes)
# Add Headers
tableBuilder = createTableBuilder()
tableBuilder.addHeader("permId")
- for sampleTypeCode in configuration.keys():
- for propertyTypeCode in configuration[sampleTypeCode].keys():
- tableBuilder.addHeader(propertyTypeCode)
+ tableBuilder.addHeader("code")
+ usedTableHeaders = {"permId" : True, "code" : True}
+ for sampleTypeCode in getAllAnnotableSampleTypes():
+ for propertyTypeCode in getPropertyTypesForSampleTypeIgnoringCurrentType(sampleTypeCode):
+ if propertyTypeCode not in usedTableHeaders:
+ tableBuilder.addHeader(propertyTypeCode)
+ usedTableHeaders[propertyTypeCode] = True
property.setOwnTab(True)
uiDescription = property.getUiDescription()
@@ -69,7 +164,7 @@ def configureUI():
row.setCell(annotation, sample.getAttribute(annotation))
# Add Create buttons
- for sampleTypeCode in configuration.keys():
+ for sampleTypeCode in getAllAnnotableSampleTypes():
title = "Add " + sampleTypeCode;
addAction = uiDescription.addTableAction(title).setDescription(title)
widgets = getWidgetForAdd(sampleTypeCode)
@@ -88,7 +183,7 @@ def updateFromUI(action):
sampleTypeCode = action.name[4:]
permId = action.getInputValue("permId")
annotations = {}
- for propertyTypeCode in configuration[sampleTypeCode]:
+ for propertyTypeCode in getPropertyTypesForSampleTypeIgnoringCurrentType(sampleTypeCode):
propertyType = getPropertyType(propertyTypeCode)
propertyTypeValue = action.getInputValue(propertyType.label)
if not isValid(propertyType.dataType, propertyTypeValue):
--
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