"""
Managed Property Script for links to samples with concentration, quantity, details
"""
import re
""""space that all parents come from (fixed)"""
SPACE = "YEAST_LAB"
"""code attribute name"""
ATR_CODE = "code"
ATR_QUANTITY = "quantity"
ATR_DETAIL = "detail"
ATR_NAME="name"
"""labels of table columns"""
LINK_LABEL = "link"
CODE_LABEL = "code"
QUANTITY_LABEL = "quantity"
NAME_LABEL="name"
DETAIL_LABEL = "details"
"""action labels"""
ADD_ACTION_LABEL = "Add"
EDIT_ACTION_LABEL = "Edit"
DELETE_ACTION_LABEL = "Delete"
"""helper functions"""
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.
If the sample doesn't exist in DB a fake link will be created with the 'code' as permId.
@return: sample link XML element as string, e.g.:
- ''
- '
"""
entityPath= "/YEAST_LAB/" + entities_list
permId =entityInformationProvider().getSamplePermId(SPACE, entities_list)
if not permId:
permId = entities_list
name = entityInformationProvider().getSamplePropertyValue(permId, 'NAME')
sampleLink = elementFactory().createSampleLink(permId)
sampleLink.addAttribute(ATR_CODE, entities_list)
sampleLink.addAttribute(ATR_NAME, name)
if not quantity_list:
quantity_list = ' '
if not detail_list:
detail_list=' '
sampleLink.addAttribute(ATR_QUANTITY, quantity_list)
sampleLink.addAttribute(ATR_DETAIL, detail_list)
return sampleLink
"""
Example input:
FRC1:2nM, FRC2, FRC3:3 nM
"""
def showRawValueInForms():
return False
def batchColumnNames():
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')
detail_list = item.get('DETAIL')
if entities_list:
sampleLink = _createSampleLink(entities_list, quantity_list, detail_list)
elements.append(sampleLink)
property.value = propertyConverter().convertToString(elements)
def configureUI():
"""Create table builder and add columns."""
tableBuilder = createTableBuilder()
tableBuilder.addHeader(LINK_LABEL)
tableBuilder.addHeader(CODE_LABEL)
tableBuilder.addHeader(NAME_LABEL)
tableBuilder.addHeader(QUANTITY_LABEL)
tableBuilder.addHeader(DETAIL_LABEL)
"""The property value should contain XML with list of samples. Add a new row for every sample."""
elements = list(propertyConverter().convertToElements(property))
for entity in elements:
entities_list = entity.getAttribute(ATR_CODE, "")
name = entity.getAttribute(ATR_NAME,"")
quantity_list=entity.getAttribute(ATR_QUANTITY, "")
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(DETAIL_LABEL, detail_list)
"""Specify that the property should be shown in a tab and set the table output."""
property.setOwnTab(True)
uiDescription = property.getUiDescription()
uiDescription.useTableOutput(tableBuilder.getTableModel())
"""
Define and add actions with input fields used to:
1. specify attributes of new entity,
"""
addAction = uiDescription.addTableAction(ADD_ACTION_LABEL)\
.setDescription('Add new entity relationship:')
widgets = [
inputWidgetFactory().createTextInputField(CODE_LABEL)\
.setMandatory(True)\
.setValue('FR')\
.setDescription('Code of entity, e.g. "FRC1"'),
inputWidgetFactory().createTextInputField(QUANTITY_LABEL)\
.setMandatory(False)\
.setDescription('Quantity'),
inputWidgetFactory().createMultilineTextInputField(DETAIL_LABEL)\
.setMandatory(False)\
.setDescription('Comment')
]
addAction.addInputWidgets(widgets)
"""
2. modify attributes of a selected yeast parent,
"""
editAction = uiDescription.addTableAction(EDIT_ACTION_LABEL)\
.setDescription('Edit selected entity relationship:')
# Exactly 1 row needs to be selected to enable action.
editAction.setRowSelectionRequiredSingle()
widgets = [
inputWidgetFactory().createTextInputField(CODE_LABEL)\
.setMandatory(True)\
.setDescription('Code of entity sample, e.g. "FRC1"'),
inputWidgetFactory().createTextInputField(QUANTITY_LABEL)\
.setMandatory(False)\
.setDescription('Quantity of the entity sample, e.g. "1M"'),
inputWidgetFactory().createMultilineTextInputField(DETAIL_LABEL)\
.setMandatory(False)\
.setDescription('Comment')
]
editAction.addInputWidgets(widgets)
# Bind field name with column name.
editAction.addBinding(CODE_LABEL, CODE_LABEL)
editAction.addBinding(QUANTITY_LABEL, QUANTITY_LABEL)
editAction.addBinding(DETAIL_LABEL, DETAIL_LABEL)
"""
3. delete selected yeast parents.
"""
deleteAction = uiDescription.addTableAction(DELETE_ACTION_LABEL)\
.setDescription('Are you sure you want to delete the selected entity relationships?')
# Delete is enabled when at least 1 row is selected.
deleteAction.setRowSelectionRequired()
def updateFromUI(action):
"""Extract list of elements from old value of the property."""
converter = propertyConverter()
elements = list(converter.convertToElements(property))
"""Implement behaviour of user actions."""
if action.name == ADD_ACTION_LABEL:
"""
For 'add' action create new entity element with values from input fields
and add it to existing elements.
"""
entities_list = action.getInputValue(CODE_LABEL)
quantity_list = action.getInputValue(QUANTITY_LABEL)
detail_list = action.getInputValue(DETAIL_LABEL)
sampleLink = _createSampleLink(entities_list, quantity_list, detail_list)
elements.append(sampleLink)
elif action.name == EDIT_ACTION_LABEL:
"""
For 'edit' action find the entity element corresponding to selected row
and replace it with an element with values from input fields.
"""
entities_list = action.getInputValue(CODE_LABEL)
quantity_list = action.getInputValue(QUANTITY_LABEL)
detail_list = action.getInputValue(DETAIL_LABEL)
sampleLink = _createSampleLink(entities_list, quantity_list, detail_list)
selectedRowId = action.getSelectedRows()[0]
elements[selectedRowId] = sampleLink
elif action.name == DELETE_ACTION_LABEL:
"""
For 'delete' action delete entities that correspond to selected rows.
NOTE: As many rows can be deleted at once it is easier to delete them in reversed order.
"""
rowIds = list(action.getSelectedRows())
rowIds.reverse()
for rowId in rowIds:
elements.pop(rowId)
else:
raise ValidationException('action not supported')
"""Update value of the managed property to XML string created from modified list of elements."""
property.value = converter.convertToString(elements)
def updateFromBatchInput(bindings):
elements = []
input = bindings.get('')
if input is not None:
entities = input.split(',')
for entity in entities:
(code, quantity, detail) = _extractCodeAndQuantity(entity)
# sampleLink = _createSampleLink(code, quantity, concentration)
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) == 3):
return (codeAndQuantity[0].strip(), codeAndQuantity[1].strip(), codeAndQuantity[2].strip())
else:
return (codeAndQuantity[0].strip(), "n.a.")