From 505a7ea161eff734eb6160c9ea3dd8f42e7061b2 Mon Sep 17 00:00:00 2001
From: barillac <barillac>
Date: Fri, 9 May 2014 09:29:52 +0000
Subject: [PATCH] Quantity replaced with Concentration
SVN: 31475
---
.../resource/jython-scripts/enzymes_script.py | 83 +++++++------------
1 file changed, 30 insertions(+), 53 deletions(-)
diff --git a/plasmid/resource/jython-scripts/enzymes_script.py b/plasmid/resource/jython-scripts/enzymes_script.py
index aa6fc078412..a437958c0bf 100644
--- a/plasmid/resource/jython-scripts/enzymes_script.py
+++ b/plasmid/resource/jython-scripts/enzymes_script.py
@@ -1,5 +1,5 @@
"""
-Managed Property Script for handling General Enzymes.
+Managed Property Script for handling ENZYMES.
"""
@@ -7,18 +7,18 @@ Managed Property Script for handling General Enzymes.
import re
""""space that all parents come from (fixed)"""
-SPACE = "YEAST_LAB"
+SPACE = "YEAST_LAB"F
"""code attribute name"""
ATR_CODE = "code"
-ATR_NAME = "name"
-ATR_CONC = "concentration"
+ATR_CONCENTRATION = "concentration"
+ATR_NAME="name"
"""labels of table columns"""
LINK_LABEL = "link"
CODE_LABEL = "code"
-NAME_LABEL = "name"
-CONC_LABEL = "concentration"
+CONCENTRATION_LABEL = "concentration"
+NAME_LABEL="name"
"""action labels"""
@@ -43,29 +43,27 @@ def _createSampleLink(enzymes_list, concentration_list):
permId =entityInformationProvider().getSamplePermId(SPACE, enzymes_list)
if not permId:
permId = enzymes_list
- name = entityInformationProvider().getSamplePropertyValue(permId, 'NAME')
- print "the name is", name
+ name = entityInformationProvider().getSamplePropertyValue(permId, 'NAME')
sampleLink = elementFactory().createSampleLink(permId)
sampleLink.addAttribute(ATR_CODE, enzymes_list)
sampleLink.addAttribute(ATR_NAME, name)
- sampleLink.addAttribute(ATR_CONC, concentration_list)
-
+ sampleLink.addAttribute(ATR_CONCENTRATION, concentration_list)
+
return sampleLink
"""
Example input:
-FRC1, FRC2, FRC3, FRC4
+FRC1:2nM, FRC2, FRC3:3 nM
"""
-
def showRawValueInForms():
return False
def batchColumnNames():
- return [CODE_LABEL, CONC_LABEL]
+ return [CODE_LABEL, CONCENTRATION_LABEL]
def updateFromRegistrationForm(bindings):
elements = []
@@ -78,33 +76,27 @@ def updateFromRegistrationForm(bindings):
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(CONC_LABEL)
- tableBuilder.addHeader(NAME_LABEL)
-
+ tableBuilder.addHeader(CONCENTRATION_LABEL)
+ tableBuilder.addHeader(NAME_LABEL)
"""The property value should contain XML with list of samples. Add a new row for every sample."""
elements = list(propertyConverter().convertToElements(property))
for enzyme in elements:
enzymes_list = enzyme.getAttribute(ATR_CODE, "")
- name = enzyme.getAttribute(ATR_NAME,"")
- concentration_list=enzyme.getAttribute(ATR_CONC, "")
-
+ name = enzyme.getAttribute(ATR_NAME,"")
+ concentration_list=enzyme.getAttribute(ATR_CONCENTRATION, "")
+
row = tableBuilder.addRow()
row.setCell(LINK_LABEL, enzyme, enzymes_list)
row.setCell(CODE_LABEL, enzymes_list)
row.setCell(NAME_LABEL, name)
- row.setCell(CONC_LABEL, concentration_list)
-
-
+ row.setCell(CONCENTRATION_LABEL, concentration_list)
"""Specify that the property should be shown in a tab and set the table output."""
property.setOwnTab(True)
@@ -120,12 +112,11 @@ def configureUI():
widgets = [
inputWidgetFactory().createTextInputField(CODE_LABEL)\
.setMandatory(True)\
- .setValue('FRE')\
- .setDescription('Code of enzyme, e.g. "FRE1"'),
- inputWidgetFactory().createTextInputField(CONC_LABEL)\
+ .setValue('FRC')\
+ .setDescription('Code of enzyme, e.g. "FRC1"'),
+ inputWidgetFactory().createTextInputField(CONCENTRATION_LABEL)\
.setMandatory(True)\
.setDescription('Concentration')
-
]
addAction.addInputWidgets(widgets)
@@ -139,15 +130,15 @@ def configureUI():
widgets = [
inputWidgetFactory().createTextInputField(CODE_LABEL)\
.setMandatory(True)\
- .setDescription('Code of enzyme sample, e.g. "FRE1"'),
- inputWidgetFactory().createTextInputField(CONC_LABEL)\
+ .setDescription('Code of enzyme sample, e.g. "FRC1"'),
+ inputWidgetFactory().createTextInputField(CONCENTRATION_LABEL)\
.setMandatory(True)\
- .setDescription('Concentration')
+ .setDescription('Concentration of the enzyme 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)
+ editAction.addBinding(CONCENTRATION_LABEL, CONCENTRATION_LABEL)
@@ -172,7 +163,7 @@ def updateFromUI(action):
and add it to existing elements.
"""
enzymes_list = action.getInputValue(CODE_LABEL)
- concentration_list = action.getInputValue(CONC_LABEL)
+ concentration_list = action.getInputValue(CONCENTRATION_LABEL)
sampleLink = _createSampleLink(enzymes_list, concentration_list)
elements.append(sampleLink)
@@ -182,7 +173,8 @@ def updateFromUI(action):
and replace it with an element with values from input fields.
"""
enzymes_list = action.getInputValue(CODE_LABEL)
- concentration_list = action.getInputValue(CONC_LABEL)
+ concentration_list = action.getInputValue(CONCENTRATION_LABEL)
+
sampleLink = _createSampleLink(enzymes_list, concentration_list)
@@ -204,17 +196,8 @@ def updateFromUI(action):
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:
-# commentEntry = _createCommentEntry(input)
-# elements.append(commentEntry)
-# property.value = propertyConverter().convertToString(elements)
-
-
+ property.value = converter.convertToString(elements)
+
def updateFromBatchInput(bindings):
elements = []
input = bindings.get('')
@@ -222,10 +205,8 @@ def updateFromBatchInput(bindings):
enzymes = input.split(',')
for enzyme in enzymes:
(code, concentration) = _extractCodeAndConcentration(enzyme)
- commentEntry = _createCommentEntry(input)
sampleLink = _createSampleLink(code, concentration)
- elements.append(sampleLink, commentEntry)
- property.value = propertyConverter().convertToString(elements)
+ elements.append(sampleLink)
property.value = propertyConverter().convertToString(elements)
@@ -235,7 +216,3 @@ def _extractCodeAndConcentration(enzyme):
return (codeAndConcentration[0].strip(), codeAndConcentration[1].strip())
else:
return (codeAndConcentration[0].strip(), "n.a.")
-
-
-
-
\ No newline at end of file
--
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