[LMS-1979] first version of the script for plasmid parents property

SVN: 20268

plasmid/resource/jython-scripts/MP-plasmid_parents.py

+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())
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