"""
Managed Property Script for handling SOLUTIONS BUFFERS.
"""
import re
""""space that all parents come from (fixed)"""
SPACE = "YEAST_LAB"
"""code attribute name"""
ATR_CODE = "code"
ATR_CONC = "concentration"
ATR_NAME = "name"
"""labels of table columns"""
LINK_LABEL = "link"
CODE_LABEL = "code"
CONC_LABEL = "concentration"
NAME_LABEL = "name"
"""action labels"""
ADD_ACTION_LABEL = "Add"
EDIT_ACTION_LABEL = "Edit"
DELETE_ACTION_LABEL = "Delete"
"""helper functions"""
def _createSampleLink(buffers_list, buffer_concentration_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.:
- ''
- '
"""
bufferPath= "/YEAST_LAB/" + buffers_list
permId =entityInformationProvider().getSamplePermId(SPACE, buffers_list)
if not permId:
permId = buffers_list
name = entityInformationProvider().getSamplePropertyValue(permId, 'NAME')
sampleLink = elementFactory().createSampleLink(permId)
sampleLink.addAttribute(ATR_CODE, buffers_list)
sampleLink.addAttribute(ATR_NAME, name)
sampleLink.addAttribute(ATR_CONC, buffer_concentration_list)
return sampleLink
"""
Example input:
FRC1, FRC2, FRC3, FRC4
"""
def inputWidgets():
factory = inputWidgetFactory()
link = factory.createTextInputField('link').setMandatory(True)
code = factory.createTextInputField('code').setMandatory(True)
name = factory.createTextInputField('name').setMandatory(True)
concentration = factory.createTextInputField('concentration').setMandatory(True)
return [link, code, name, concentration]
def updateBufferFromBatchInput(buffers_list, buffer_concentration_list):
elements = []
input = buffers_list
input2 = buffer_concentration_list
if input is not None:
for i, j in zip(buffers_list,buffer_concentration_list): #zip is used to iterate over two lists in parallel
sampleLink = _createSampleLink(i.strip(), j.strip())
elements.append(sampleLink)
return 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(CONC_LABEL)
"""The property value should contain XML with list of samples. Add a new row for every sample."""
elements = list(propertyConverter().convertToElements(property))
for buffer in elements:
buffers_list = buffer.getAttribute(ATR_CODE, "")
name = buffer.getAttribute(ATR_NAME,"")
buffer_concentration_list=buffer.getAttribute(ATR_CONC, "")
row = tableBuilder.addRow()
row.setCell(LINK_LABEL, buffer, buffers_list)
row.setCell(CODE_LABEL, buffers_list)
row.setCell(NAME_LABEL,name)
row.setCell(CONC_LABEL, buffer_concentration_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 buffer,
"""
addAction = uiDescription.addTableAction(ADD_ACTION_LABEL)\
.setDescription('Add new buffer relationship:')
widgets = [
inputWidgetFactory().createTextInputField(CODE_LABEL)\
.setMandatory(True)\
.setValue('FRC')\
.setDescription('Code of buffer, e.g. "FRC1"'),
inputWidgetFactory().createTextInputField(CONC_LABEL)\
.setMandatory(True)\
.setDescription('Concentration')
]
addAction.addInputWidgets(widgets)
"""
2. modify attributes of a selected yeast parent,
"""
editAction = uiDescription.addTableAction(EDIT_ACTION_LABEL)\
.setDescription('Edit selected buffer relationship:')
# Exactly 1 row needs to be selected to enable action.
editAction.setRowSelectionRequiredSingle()
widgets = [
inputWidgetFactory().createTextInputField(CODE_LABEL)\
.setMandatory(True)\
.setDescription('Code of buffer sample, e.g. "FRC1"'),
inputWidgetFactory().createTextInputField(CONC_LABEL)\
.setMandatory(True)\
.setDescription('Concentration of the buffer sample, e.g. "1M"'),
]
editAction.addInputWidgets(widgets)
# Bind field name with column name.
editAction.addBinding(CODE_LABEL, CODE_LABEL)
editAction.addBinding(CONC_LABEL, CONC_LABEL)
"""
3. delete selected yeast parents.
"""
deleteAction = uiDescription.addTableAction(DELETE_ACTION_LABEL)\
.setDescription('Are you sure you want to delete the selected buffer 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 buffer element with values from input fields
and add it to existing elements.
"""
buffers_list = action.getInputValue(CODE_LABEL)
buffer_concentration_list = action.getInputValue(CONC_LABEL)
sampleLink = _createSampleLink(buffers_list, buffer_concentration_list)
elements.append(sampleLink)
elif action.name == EDIT_ACTION_LABEL:
"""
For 'edit' action find the buffer element corresponding to selected row
and replace it with an element with values from input fields.
"""
buffers_list = action.getInputValue(CODE_LABEL)
buffer_concentration_list = action.getInputValue(CONC_LABEL)
sampleLink = _createSampleLink(buffers_list, buffer_concentration_list)
selectedRowId = action.getSelectedRows()[0]
elements[selectedRowId] = sampleLink
elif action.name == DELETE_ACTION_LABEL:
"""
For 'delete' action delete buffers 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:
buffers = input.split(',')
for buffer in buffers:
(code, concentration) = _extractCodeAndConcentration(buffer)
sampleLink = _createSampleLink(code, concentration)
elements.append(sampleLink)
property.value = propertyConverter().convertToString(elements)
def _extractCodeAndConcentration(buffer):
codeAndConcentration = buffer.split(':')
if (len(codeAndConcentration) == 2):
return (codeAndConcentration[0].strip(), codeAndConcentration[1].strip())
else:
return (codeAndConcentration[0].strip(), "n.a.")