From f20ea50fcaf11280fe5b6dd3f6f5db8d4870a9ee Mon Sep 17 00:00:00 2001
From: buczekp <buczekp>
Date: Wed, 9 Mar 2011 20:30:32 +0000
Subject: [PATCH] [LMS-1979] display sample's code in links; minor: code
cleanup & documentation
SVN: 20276
---
.../jython-scripts/MP-plasmid_parents.py | 99 ++++++++++++++++---
.../jython-scripts/MP-yeast_parents.py | 33 +++++--
2 files changed, 110 insertions(+), 22 deletions(-)
diff --git a/plasmid/resource/jython-scripts/MP-plasmid_parents.py b/plasmid/resource/jython-scripts/MP-plasmid_parents.py
index 7b00fe2d2d4..e11952c8022 100644
--- a/plasmid/resource/jython-scripts/MP-plasmid_parents.py
+++ b/plasmid/resource/jython-scripts/MP-plasmid_parents.py
@@ -1,9 +1,20 @@
+"""
+Managed Property Script for handling plasmid parents of yeast samples.
+
+@author: Piotr Buczek
+"""
+
import re
-""""space that all parents come from (fixed)"""
+"""space that all parents come from (fixed)"""
SPACE = "YEAST_LAB"
-"""examples of input: FRP1 (DEL:URA3), FRP2 (INT), FRP3 (MOD:URA3), FRP4"""
+"""input pattern matching one plasmid, e.g.:
+- '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')
@@ -16,46 +27,82 @@ INPUT_PATTERN = """
# no '$': allow whitespace at the end
"""
+"""tuple of supported relationship types as shortcuts"""
REL_TYPES = ('DEL', 'INT', 'MOD')
+"""dictionary from relationship type shortcut to its 'character' representation"""
REL_TYPE_CHARS = {
- 'DEL': 'd',
+ 'DEL': '^',
'INT': '::',
'MOD': '_'
}
+"""dictionary from relationship type shortcut to its full name/label"""
REL_TYPE_LABELS = {
'DEL': 'deletion',
'INT': 'integration',
'MOD': 'modification'
}
+"""names of additional sample XML element attributes"""
+
ATR_CODE = "code"
ATR_RELATIONSHIP = "rel"
ATR_ANNOTATION = "annotation"
+"""labels of table columns"""
+
CONNECTION_LABEL = "connection"
LINK_LABEL = "link"
CODE_LABEL = "code"
RELATIONSHIP_LABEL = "relationship"
ANNOTATION_LABEL = "annotation"
+
"""helper functions"""
def _group(pattern, input):
+ """@return: groups returned by performing pattern search with given @pattern on given @input"""
return pattern.search(input).groups()
+
def _translateToChar(relationship):
- if relationship in REL_TYPE_CHARS:
- return REL_TYPE_CHARS[relationship]
+ """
+ @param relationship: relationship type as a shortcut (@see REL_TYPES), may be null
+ @return: character representation of given @relationship,
+ empty string for null
+ '[<relationship>]' for unknown relationship
+ """
+ if relationship:
+ if relationship in REL_TYPE_CHARS:
+ return REL_TYPE_CHARS[relationship]
+ else:
+ return "[" + relationship + "]"
else:
- return "[" + relationship + "]"
+ return ""
+
def _translateToLabel(relationship):
- if relationship in REL_TYPE_LABELS:
- return REL_TYPE_LABELS[relationship]
+ """
+ @param relationship: relationship type as a shortcut (@see REL_TYPES), may be null
+ @return: full name of given @relationship,
+ empty string for null,
+ '[<relationship>]' for unknown relationship
+ """
+ if relationship:
+ if relationship in REL_TYPE_LABELS:
+ return REL_TYPE_LABELS[relationship]
+ else:
+ return "[" + relationship + "]"
else:
- return "[" + relationship + "]"
+ return ""
+
def _createConnectionString(code, relationship, annotation):
+ """
+ @param code: code of a sample
+ @param relationship: relationship type as a shortcut (@see REL_TYPES), may be null
+ @param annotation: annotation of the relationship, may be null
+ @return: string representation of a connection with @relationship translated to a 'character'
+ """
result = code
if relationship:
result += _translateToChar(relationship)
@@ -63,7 +110,25 @@ def _createConnectionString(code, relationship, annotation):
result += annotation
return result
+
def _createSampleLink(code, relationship, annotation):
+ """
+ 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 specified
+ @relationship or @annotation are not null they will also be contained as attributes.
+
+ If the sample doesn't exist in DB a fake link will be created with @code as permId.
+
+ @param code: code of a sample
+ @param relationship: relationship type as a shortcut (@see REL_TYPES), may be null
+ @param annotation: annotation of the relationship, may be null
+ @return: sample link XML element as string, e.g.:
+ - '<Sample code="FRP1" permId="20110309154532868-4219"/>'
+ - '<Sample code="FRP2" permId="20110309154532868-4219" relationship="DEL" annotation="URA3"/>'
+ - '<Sample code="FAKE_SAMPLE_CODE" permId="FAKE_SAMPLE_CODE"/>
+ - '<Sample code="FRP4" permId="20110309154532868-4219" relationship="INT"/>'
+ @raise ValidationException: if the specified relationship type is unknown
+ """
permId = entityInformationProvider().getSamplePermId(SPACE, code)
if not permId:
permId = code
@@ -80,8 +145,9 @@ def _createSampleLink(code, relationship, annotation):
sampleLink.addAttribute(ATR_ANNOTATION, annotation)
return sampleLink
-"""
-Example input:
+""" MAIN FUNCTIONS """
+
+"""Example input:
FRP1 (DEL:URA3), FRP2 (INT), FRP3 (MOD:URA3), FRP4
@@ -91,6 +157,7 @@ Relationship types:
- MOD: modification
"""
def updateFromBatchInput(bindings):
+
inputPattern = re.compile(INPUT_PATTERN, re.VERBOSE)
input = bindings.get('')
plasmids = input.split(',')
@@ -101,8 +168,10 @@ def updateFromBatchInput(bindings):
elements.append(sampleLink)
property.value = propertyConverter().convertToString(elements)
+
def configureUI():
- """create table builder and add columns"""
+
+ """Create table builder and add columns."""
tableBuilder = createTableBuilder()
tableBuilder.addHeader(LINK_LABEL)
tableBuilder.addHeader(CONNECTION_LABEL)
@@ -119,12 +188,12 @@ def configureUI():
row = tableBuilder.addRow()
row.setCell(CONNECTION_LABEL, _createConnectionString(code, relationship, annotation))
- row.setCell(LINK_LABEL, plasmid)
+ row.setCell(LINK_LABEL, plasmid, code)
row.setCell(CODE_LABEL, code)
- row.setCell(RELATIONSHIP_LABEL, relationship)
+ row.setCell(RELATIONSHIP_LABEL, _translateToLabel(relationship))
row.setCell(ANNOTATION_LABEL, annotation)
- """specify that the property should be shown in a tab and set the table output"""
+ """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
diff --git a/plasmid/resource/jython-scripts/MP-yeast_parents.py b/plasmid/resource/jython-scripts/MP-yeast_parents.py
index 703b742757e..876aca43439 100644
--- a/plasmid/resource/jython-scripts/MP-yeast_parents.py
+++ b/plasmid/resource/jython-scripts/MP-yeast_parents.py
@@ -1,17 +1,33 @@
+"""
+Managed Property Script for handling yeast parents of yeast samples.
+
+@author: Piotr Buczek
+"""
+
import re
""""space that all parents come from (fixed)"""
SPACE = "YEAST_LAB"
+"""code attribute name"""
ATR_CODE = "code"
-CONNECTION_LABEL = "connection"
+"""labels of table columns"""
LINK_LABEL = "link"
CODE_LABEL = "code"
-RELATIONSHIP_LABEL = "relationship"
-ANNOTATION_LABEL = "annotation"
+
def _createSampleLink(code):
+ """
+ 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.:
+ - '<Sample code="FRP1" permId="20110309154532868-4219"/>'
+ - '<Sample code="FAKE_SAMPLE_CODE" permId="FAKE_SAMPLE_CODE"/>
+ """
permId = entityInformationProvider().getSamplePermId(SPACE, code)
if not permId:
permId = code
@@ -19,6 +35,7 @@ def _createSampleLink(code):
sampleLink.addAttribute(ATR_CODE, code)
return sampleLink
+
"""
Example input:
@@ -33,11 +50,13 @@ def updateFromBatchInput(bindings):
elements.append(sampleLink)
property.value = propertyConverter().convertToString(elements)
+
def configureUI():
- """create table builder and add columns"""
+
+ """Create table builder and add columns."""
tableBuilder = createTableBuilder()
tableBuilder.addHeader(LINK_LABEL)
- tableBuilder.addHeader(CODE_LABEL)
+ tableBuilder.addHeader(CODE_LABEL, true)
"""The property value should contain XML with list of samples. Add a new row for every sample."""
elements = list(propertyConverter().convertToElements(property))
@@ -45,10 +64,10 @@ def configureUI():
code = plasmid.getAttribute(ATR_CODE, "")
row = tableBuilder.addRow()
- row.setCell(LINK_LABEL, plasmid)
+ row.setCell(LINK_LABEL, plasmid, code)
row.setCell(CODE_LABEL, code)
- """specify that the property should be shown in a tab and set the table output"""
+ """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
--
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