From 28486e02064b6eeac4aa0a25f498e8849fb55b19 Mon Sep 17 00:00:00 2001
From: buczekp <buczekp>
Date: Wed, 9 Mar 2011 14:34:47 +0000
Subject: [PATCH] [LMS-1979] cleanup and new script for yeast parents
SVN: 20270
---
.../jython-scripts/MP-plasmid_parents.py | 83 ++++++++-----------
.../jython-scripts/MP-yeast_parents.py | 55 ++++++++++++
2 files changed, 89 insertions(+), 49 deletions(-)
create mode 100644 plasmid/resource/jython-scripts/MP-yeast_parents.py
diff --git a/plasmid/resource/jython-scripts/MP-plasmid_parents.py b/plasmid/resource/jython-scripts/MP-plasmid_parents.py
index c100ebe57e2..0aa98dd95d4 100644
--- a/plasmid/resource/jython-scripts/MP-plasmid_parents.py
+++ b/plasmid/resource/jython-scripts/MP-plasmid_parents.py
@@ -1,22 +1,9 @@
-import sys
import re
-"""debug sys path"""
-#print(sys.path)
-
-'''
-FRP1 (DEL:URA3), FRP2 (INT), FRP3 (MOD:URA3), FRP4
-
-Relationship types:
-
- * DEL: deletion
- * INT: integration
- * MOD: modification
-'''
-
""""space that all parents come from (fixed)"""
SPACE = "YEAST_LAB"
+"""examples of input: FRP1 (DEL:URA3), FRP2 (INT), FRP3 (MOD:URA3), FRP4"""
INPUT_PATTERN = """
# no '^': allow whitespace at the beginning
([^ (]*) # 1st group: match code of a sample, everything before a space or '(' (e.g. 'FRP')
@@ -29,17 +16,6 @@ INPUT_PATTERN = """
# no '$': allow whitespace at the end
"""
-def group(pattern, input):
- return pattern.search(input).groups()
-
-EXAMPLES = [
- 'FRP1 (DEL:URA3)',
- 'FRP2 (INT)',
- 'FRP3 (MOD:URA3)',
- 'FRP4',
- 'FRPS5'
-]
-
REL_TYPES = ('DEL', 'INT', 'MOD')
REL_TYPE_CHARS = {
'DEL': 'd',
@@ -56,23 +32,38 @@ ATR_CODE = "code"
ATR_RELATIONSHIP = "rel"
ATR_ANNOTATION = "annotation"
+CONNECTION_LABEL = "connection"
+LINK_LABEL = "link"
+CODE_LABEL = "code"
+RELATIONSHIP_LABEL = "relationship"
+ANNOTATION_LABEL = "annotation"
+
"""helper functions"""
-def translateToChar(relationship):
+def _group(pattern, input):
+ return pattern.search(input).groups()
+
+def _translateToChar(relationship):
if relationship in REL_TYPE_CHARS:
return REL_TYPE_CHARS[relationship]
else:
return "[" + relationship + "]"
+
+def _translateToLabel(relationship):
+ if relationship in REL_TYPE_LABELS:
+ return REL_TYPE_LABELS[relationship]
+ else:
+ return "[" + relationship + "]"
-def createConnectionString(code, relationship, annotation):
+def _createConnectionString(code, relationship, annotation):
result = code
if relationship:
- result += translateToChar(relationship)
+ result += _translateToChar(relationship)
if annotation:
result += annotation
return result
-def createSampleLink(code, relationship, annotation):
+def _createSampleLink(code, relationship, annotation):
permId = entityInformationProvider().getSamplePermId(SPACE, code)
if not permId:
permId = code
@@ -81,40 +72,36 @@ def createSampleLink(code, relationship, annotation):
if relationship:
sampleLink.addAttribute(ATR_RELATIONSHIP, relationship)
if relationship in REL_TYPES:
- connectionString = createConnectionString(code, relationship, annotation)
+ connectionString = _createConnectionString(code, relationship, annotation)
else:
raise ValidationException("Unknown relationship: '" + relationship +
- "'. Expected one of: " + REL_TYPES)
+ "'. Expected one of: " + REL_TYPES)
if annotation:
sampleLink.addAttribute(ATR_ANNOTATION, annotation)
return sampleLink
-"""main functions"""
+"""
+Example input:
-""" updateFromBatchInput """
+FRP1 (DEL:URA3), FRP2 (INT), FRP3 (MOD:URA3), FRP4
+Relationship types:
+- DEL: deletion
+- INT: integration
+- MOD: modification
+"""
def updateFromBatchInput(bindings):
inputPattern = re.compile(INPUT_PATTERN, re.VERBOSE)
input = bindings.get('')
plasmids = input.split(',')
elements = []
for p in plasmids:
- (code, g, relationship, annotation) = group(inputPattern, p.strip())
- sampleLink = createSampleLink(code, relationship, annotation)
+ (code, g, relationship, annotation) = _group(inputPattern, p.strip())
+ sampleLink = _createSampleLink(code, relationship, annotation)
elements.append(sampleLink)
property.value = propertyConverter().convertToString(elements)
-""" configureUI """
-
-CONNECTION_LABEL = "connection"
-LINK_LABEL = "link"
-CODE_LABEL = "code"
-RELATIONSHIP_LABEL = "relationship"
-ANNOTATION_LABEL = "annotation"
-
def configureUI():
- inputPattern = re.compile(INPUT_PATTERN, re.VERBOSE)
-
"""create table builder and add columns"""
tableBuilder = createTableBuilder()
tableBuilder.addHeader(CONNECTION_LABEL)
@@ -123,17 +110,15 @@ def configureUI():
tableBuilder.addHeader(RELATIONSHIP_LABEL)
tableBuilder.addHeader(ANNOTATION_LABEL)
- """The property value should contain XML with list of sample. Add a new row for every sample."""
+ """The property value should contain XML with list of samples. Add a new row for every sample."""
elements = list(propertyConverter().convertToElements(property))
for plasmid in elements:
- permId = plasmid.getPermId()
code = plasmid.getAttribute(ATR_CODE, "")
relationship = plasmid.getAttribute(ATR_RELATIONSHIP, "")
- code = plasmid.getAttribute(ATR_CODE, "")
annotation = plasmid.getAttribute(ATR_ANNOTATION, "")
row = tableBuilder.addRow()
- row.setCell(CONNECTION_LABEL, createConnectionString(code, relationship, annotation))
+ row.setCell(CONNECTION_LABEL, _createConnectionString(code, relationship, annotation))
row.setCell(LINK_LABEL, plasmid)
row.setCell(CODE_LABEL, code)
row.setCell(RELATIONSHIP_LABEL, relationship)
diff --git a/plasmid/resource/jython-scripts/MP-yeast_parents.py b/plasmid/resource/jython-scripts/MP-yeast_parents.py
new file mode 100644
index 00000000000..3ce90e5fdf5
--- /dev/null
+++ b/plasmid/resource/jython-scripts/MP-yeast_parents.py
@@ -0,0 +1,55 @@
+import re
+
+""""space that all parents come from (fixed)"""
+SPACE = "YEAST_LAB"
+
+ATR_CODE = "code"
+
+CONNECTION_LABEL = "connection"
+LINK_LABEL = "link"
+CODE_LABEL = "code"
+RELATIONSHIP_LABEL = "relationship"
+ANNOTATION_LABEL = "annotation"
+
+def _createSampleLink(code):
+ permId = entityInformationProvider().getSamplePermId(SPACE, code)
+ if not permId:
+ permId = code
+ sampleLink = elementFactory().createSampleLink(permId)
+ sampleLink.addAttribute(ATR_CODE, code)
+ return sampleLink
+
+
+"""
+Example input:
+
+FRY1, FRY2, FRY3, FRY4
+"""
+def updateFromBatchInput(bindings):
+ input = bindings.get('')
+ samples = input.split(',')
+ elements = []
+ for p in samples:
+ sampleLink = createSampleLink(code)
+ 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)
+
+ """The property value should contain XML with list of samples. Add a new row for every sample."""
+ elements = list(propertyConverter().convertToElements(property))
+ for plasmid in elements:
+ code = plasmid.getAttribute(ATR_CODE, "")
+
+ row = tableBuilder.addRow()
+ row.setCell(LINK_LABEL, plasmid)
+ row.setCell(CODE_LABEL, code)
+
+ """specify that the property should be shown in a tab and set the table output"""
+ property.setOwnTab(True)
+ uiDesc = property.getUiDescription()
+ uiDesc.useTableOutput(tableBuilder.getTableModel())
\ No newline at end of file
--
GitLab