diff --git a/plasmid/resource/jython-scripts/generic_annotations.py b/plasmid/resource/jython-scripts/generic_annotations.py
index 854d6c426dc13dd8df216cadf453cf2683f9e697..3625b9e3dcb618d93be558ff7b13ec62cfa41440 100644
--- a/plasmid/resource/jython-scripts/generic_annotations.py
+++ b/plasmid/resource/jython-scripts/generic_annotations.py
@@ -1,5 +1,5 @@
"""
-Managed Property Script for links to samples with concentration, quantity, comments
+Managed Property Script for links to samples with concentration, quantity, details
@@ -13,17 +13,15 @@ SPACE = "YEAST_LAB"
"""code attribute name"""
ATR_CODE = "code"
ATR_QUANTITY = "quantity"
-ATR_CONC = "concentration"
-ATR_COMMENT = "comment"
+ATR_DETAIL = "detail"
ATR_NAME="name"
"""labels of table columns"""
LINK_LABEL = "link"
CODE_LABEL = "code"
QUANTITY_LABEL = "quantity"
-CONC_LABEL = "concentration"
NAME_LABEL="name"
-COMMENT_LABEL = "comment"
+DETAIL_LABEL = "details"
"""action labels"""
@@ -34,7 +32,7 @@ DELETE_ACTION_LABEL = "Delete"
"""helper functions"""
-def _createSampleLink(entities_list, quantity_list, concentration_list, comment_list):
+def _createSampleLink(entities_list, quantity_list, detail_list):
"""
Creates sample link XML element for sample with specified 'code'. The element will contain
given code as 'code' attribute apart from standard 'permId' attribute.
@@ -56,13 +54,10 @@ def _createSampleLink(entities_list, quantity_list, concentration_list, comment_
sampleLink.addAttribute(ATR_NAME, name)
if not quantity_list:
quantity_list = ' '
- if not concentration_list:
- concentration_list =' '
- if not comment_list:
- comment_list=' '
+ if not detail_list:
+ detail_list=' '
sampleLink.addAttribute(ATR_QUANTITY, quantity_list)
- sampleLink.addAttribute(ATR_CONC, concentration_list)
- sampleLink.addAttribute(ATR_COMMENT, comment_list)
+ sampleLink.addAttribute(ATR_DETAIL, detail_list)
return sampleLink
@@ -77,17 +72,16 @@ def showRawValueInForms():
return False
def batchColumnNames():
- return [CODE_LABEL, QUANTITY_LABEL, CONC_LABEL, COMMENT_LABEL]
+ return [CODE_LABEL, QUANTITY_LABEL, DETAIL_LABEL]
def updateFromRegistrationForm(bindings):
elements = []
for item in bindings:
entities_list = item.get('CODE')
quantity_list = item.get('QUANTITY')
- concentration_list = item.get('CONCENTRATION')
- comment_list = item.get('COMMENT')
+ detail_list = item.get('DETAIL')
if entities_list:
- sampleLink = _createSampleLink(entities_list, quantity_list, concentration_list, comment_list)
+ sampleLink = _createSampleLink(entities_list, quantity_list, detail_list)
elements.append(sampleLink)
@@ -100,8 +94,7 @@ def configureUI():
tableBuilder.addHeader(CODE_LABEL)
tableBuilder.addHeader(NAME_LABEL)
tableBuilder.addHeader(QUANTITY_LABEL)
- tableBuilder.addHeader(CONC_LABEL)
- tableBuilder.addHeader(COMMENT_LABEL)
+ tableBuilder.addHeader(DETAIL_LABEL)
"""The property value should contain XML with list of samples. Add a new row for every sample."""
@@ -110,16 +103,14 @@ def configureUI():
entities_list = entity.getAttribute(ATR_CODE, "")
name = entity.getAttribute(ATR_NAME,"")
quantity_list=entity.getAttribute(ATR_QUANTITY, "")
- concentration_list=entity.getAttribute(ATR_CONC, "")
- comment_list=entity.getAttribute(ATR_COMMENT, "")
+ detail_list=entity.getAttribute(ATR_DETAIL, "")
row = tableBuilder.addRow()
row.setCell(LINK_LABEL, entity, entities_list)
row.setCell(CODE_LABEL, entities_list)
row.setCell(NAME_LABEL, name)
row.setCell(QUANTITY_LABEL, quantity_list)
- row.setCell(CONC_LABEL, concentration_list)
- row.setCell(COMMENT_LABEL, comment_list)
+ row.setCell(DETAIL_LABEL, detail_list)
"""Specify that the property should be shown in a tab and set the table output."""
property.setOwnTab(True)
@@ -140,10 +131,7 @@ def configureUI():
inputWidgetFactory().createTextInputField(QUANTITY_LABEL)\
.setMandatory(False)\
.setDescription('Quantity'),
- inputWidgetFactory().createTextInputField(CONC_LABEL)\
- .setMandatory(False)\
- .setDescription('Concentration'),
- inputWidgetFactory().createMultilineTextInputField(COMMENT_LABEL)\
+ inputWidgetFactory().createMultilineTextInputField(DETAIL_LABEL)\
.setMandatory(False)\
.setDescription('Comment')
]
@@ -163,10 +151,7 @@ def configureUI():
inputWidgetFactory().createTextInputField(QUANTITY_LABEL)\
.setMandatory(False)\
.setDescription('Quantity of the entity sample, e.g. "1M"'),
- inputWidgetFactory().createTextInputField(CONC_LABEL)\
- .setMandatory(False)\
- .setDescription('Concentration'),
- inputWidgetFactory().createMultilineTextInputField(COMMENT_LABEL)\
+ inputWidgetFactory().createMultilineTextInputField(DETAIL_LABEL)\
.setMandatory(False)\
.setDescription('Comment')
]
@@ -174,8 +159,7 @@ def configureUI():
# Bind field name with column name.
editAction.addBinding(CODE_LABEL, CODE_LABEL)
editAction.addBinding(QUANTITY_LABEL, QUANTITY_LABEL)
- editAction.addBinding(CONC_LABEL, CONC_LABEL)
- editAction.addBinding(COMMENT_LABEL, COMMENT_LABEL)
+ editAction.addBinding(DETAIL_LABEL, DETAIL_LABEL)
"""
@@ -200,9 +184,8 @@ def updateFromUI(action):
"""
entities_list = action.getInputValue(CODE_LABEL)
quantity_list = action.getInputValue(QUANTITY_LABEL)
- concentration_list = action.getInputValue(CONC_LABEL)
- comment_list = action.getInputValue(COMMENT_LABEL)
- sampleLink = _createSampleLink(entities_list, quantity_list, concentration_list, comment_list)
+ detail_list = action.getInputValue(DETAIL_LABEL)
+ sampleLink = _createSampleLink(entities_list, quantity_list, detail_list)
elements.append(sampleLink)
elif action.name == EDIT_ACTION_LABEL:
@@ -212,11 +195,10 @@ def updateFromUI(action):
"""
entities_list = action.getInputValue(CODE_LABEL)
quantity_list = action.getInputValue(QUANTITY_LABEL)
- concentration_list = action.getInputValue(CONC_LABEL)
- comment_list = action.getInputValue(COMMENT_LABEL)
+ detail_list = action.getInputValue(DETAIL_LABEL)
- sampleLink = _createSampleLink(entities_list, quantity_list, concentration_list, comment_list)
+ sampleLink = _createSampleLink(entities_list, quantity_list, detail_list)
@@ -243,16 +225,16 @@ def updateFromBatchInput(bindings):
if input is not None:
entities = input.split(',')
for entity in entities:
- (code, quantity, concentration, comment) = _extractCodeAndQuantity(entity)
+ (code, quantity, detail) = _extractCodeAndQuantity(entity)
# sampleLink = _createSampleLink(code, quantity, concentration)
- sampleLink = _createSampleLink(entities_list, quantity_list, concentration_list, comment_list)
+ sampleLink = _createSampleLink(entities_list, quantity_list, detail_list)
elements.append(sampleLink)
property.value = propertyConverter().convertToString(elements)
def _extractCodeAndQuantity(entity):
codeAndQuantity = entity.split(':')
- if (len(codeAndQuantity) == 4):
- return (codeAndQuantity[0].strip(), codeAndQuantity[1].strip(), codeAndQuantity[2].strip(), codeAndQuantity[3].strip())
+ if (len(codeAndQuantity) == 3):
+ return (codeAndQuantity[0].strip(), codeAndQuantity[1].strip(), codeAndQuantity[2].strip())
else:
return (codeAndQuantity[0].strip(), "n.a.")