From cf9d73c8ad0fe06c04760f91edaf23270d0e78a4 Mon Sep 17 00:00:00 2001
From: buczekp <buczekp>
Date: Wed, 9 Mar 2011 14:06:57 +0000
Subject: [PATCH] [LMS-1979] first version of the script for plasmid parents
property
SVN: 20268
---
.../jython-scripts/MP-plasmid_parents.py | 145 ++++++++++++++++++
1 file changed, 145 insertions(+)
create mode 100644 plasmid/resource/jython-scripts/MP-plasmid_parents.py
diff --git a/plasmid/resource/jython-scripts/MP-plasmid_parents.py b/plasmid/resource/jython-scripts/MP-plasmid_parents.py
new file mode 100644
index 00000000000..c100ebe57e2
--- /dev/null
+++ b/plasmid/resource/jython-scripts/MP-plasmid_parents.py
@@ -0,0 +1,145 @@
+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"
+
+INPUT_PATTERN = """
+ # no '^': allow whitespace at the beginning
+ ([^ (]*) # 1st group: match code of a sample, everything before a space or '(' (e.g. 'FRP')
+ (\ *\( # start of 2nd group (matches an optional relationship type with annotation)
+ # any spaces followed by a '('
+ ([^:]*) # 3rd group: match relationship type, any character but ':' (e.g. 'DEL', 'INT', 'MOD')
+ :? # optional ':' separator
+ (.*) # 4th group: match annotation, any text (e.g. 'URA3')
+ \))? # end of 2nd (optional) group: closing bracket of relationship details
+ # 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',
+ 'INT': '::',
+ 'MOD': '_'
+}
+REL_TYPE_LABELS = {
+ 'DEL': 'deletion',
+ 'INT': 'integration',
+ 'MOD': 'modification'
+}
+
+ATR_CODE = "code"
+ATR_RELATIONSHIP = "rel"
+ATR_ANNOTATION = "annotation"
+
+"""helper functions"""
+
+def translateToChar(relationship):
+ if relationship in REL_TYPE_CHARS:
+ return REL_TYPE_CHARS[relationship]
+ else:
+ return "[" + relationship + "]"
+
+def createConnectionString(code, relationship, annotation):
+ result = code
+ if relationship:
+ result += translateToChar(relationship)
+ if annotation:
+ result += annotation
+ return result
+
+def createSampleLink(code, relationship, annotation):
+ permId = entityInformationProvider().getSamplePermId(SPACE, code)
+ if not permId:
+ permId = code
+ sampleLink = elementFactory().createSampleLink(permId)
+ sampleLink.addAttribute(ATR_CODE, code)
+ if relationship:
+ sampleLink.addAttribute(ATR_RELATIONSHIP, relationship)
+ if relationship in REL_TYPES:
+ connectionString = createConnectionString(code, relationship, annotation)
+ else:
+ raise ValidationException("Unknown relationship: '" + relationship +
+ "'. Expected one of: " + REL_TYPES)
+ if annotation:
+ sampleLink.addAttribute(ATR_ANNOTATION, annotation)
+ return sampleLink
+
+"""main functions"""
+
+""" updateFromBatchInput """
+
+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)
+ 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)
+ tableBuilder.addHeader(LINK_LABEL)
+ tableBuilder.addHeader(CODE_LABEL)
+ 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."""
+ 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(LINK_LABEL, plasmid)
+ row.setCell(CODE_LABEL, code)
+ row.setCell(RELATIONSHIP_LABEL, relationship)
+ row.setCell(ANNOTATION_LABEL, annotation)
+
+ """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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