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nctreport.py
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nctreport.py
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#!/usr/bin/env python
"""
Maintain data for an clinical trials report
"""
__author__ = 'Rodney L. Summerscales'
import xmlutil
class ReportEntry:
""" A text block for an entry in a trial registry """
sentences = None
name = None
def __init__(self, node):
""" create a list of sentences given an XML node containing a list of sentence
elements """
self.name = xmlutil.getNodeTagName(node)
self.sentences = parseSentences(node)
def getXML(self, doc):
""" return an xml node with information for this entity """
return createSentenceListNode(self.name, self.sentences, doc)
class Intervention:
name = None
description = None
""" Intervention information from a trial registry """
def __init__(self, node):
self.name = []
self.description = []
nodes = node.getElementsByTagName('name')
if len(nodes) > 0:
self.name = parseSentences(nodes[0])
nodes = node.getElementsByTagName('description')
if len(nodes) > 0:
self.description = parseSentences(nodes[0])
def getXML(self, doc):
node = doc.createElement('intervention')
if len(self.name) > 0:
node.appendChild(createSentenceListNode('name', self.name, doc))
if len(self.description) > 0:
node.appendChild(createSentenceListNode('description', self.description, doc))
return node
class Outcome:
""" Outcome information from a trial registry """
primary = False
name = None
times = None
description = None
def __init__(self, node):
self.name = []
self.times = []
self.description = []
primaryStr = node.getAttribute('primary')
if primaryStr != None and primaryStr.lower() == 'true':
self.primary = True
else:
self.primary = False
nodes = node.getElementsByTagName('name')
if len(nodes) > 0:
self.name = parseSentences(nodes[0])
nodes = node.getElementsByTagName('description')
if len(nodes) > 0:
self.description = parseSentences(nodes[0])
nodes = node.getElementsByTagName('times')
if len(nodes) > 0:
self.times = parseSentences(nodes[0])
def getXML(self, doc):
node = doc.createElement('outcome')
if self.primary:
node.setAttribute('primary', 'true')
else:
node.setAttribute('primary', 'false')
if len(self.name) > 0:
node.appendChild(createSentenceListNode('name', self.name, doc))
if len(self.description) > 0:
node.appendChild(createSentenceListNode('description', self.description, doc))
if len(self.times) > 0:
node.appendChild(createSentenceListNode('times', self.times, doc))
return node
class Report:
""" Data from a NCT report. """
id = ''
gender = ''
minAge = ''
maxAge = ''
locations = None
conditions = None
eligibilityCriteria = None
inclusionCriteria = None
exclusionCriteria = None
interventions = None
outcomes = None
def __init__(self, node):
self.id = xmlutil.getTextFromNodeCalled('id', node)
self.gender = xmlutil.getTextFromNodeCalled('gender', node)
self.minAge = xmlutil.getTextFromNodeCalled('minAge', node)
self.maxAge = xmlutil.getTextFromNodeCalled('maxAge', node)
self.locations = []
lcNodes = node.getElementsByTagName('location_countries')
if len(lcNodes) > 0:
cNodes = lcNodes[0].getElementsByTagName('country')
for countryNode in cNodes:
self.locations.append(xmlutil.getText(countryNode))
self.conditions = []
cNodes = node.getElementsByTagName('condition')
for cNode in cNodes:
self.conditions.append(ReportEntry(cNode))
self.eligibilityCriteria = []
ecNodes = node.getElementsByTagName('eligibility')
if len(ecNodes) > 0:
cNodes = ecNodes[0].getElementsByTagName('criteria')
for cNode in cNodes:
self.eligibilityCriteria.append(ReportEntry(cNode))
self.inclusionCriteria = []
icNodes = node.getElementsByTagName('inclusion')
if len(icNodes) > 0:
cNodes = icNodes[0].getElementsByTagName('criteria')
for cNode in cNodes:
self.inclusionCriteria.append(ReportEntry(cNode))
self.exclusionCriteria = []
ecNodes = node.getElementsByTagName('exclusion')
if len(ecNodes) > 0:
cNodes = ecNodes[0].getElementsByTagName('criteria')
for cNode in cNodes:
self.exclusionCriteria.append(ReportEntry(cNode))
self.interventions = []
iNodes = node.getElementsByTagName('intervention')
for iNode in iNodes:
self.interventions.append(Intervention(iNode))
self.outcomes = []
oNodes = node.getElementsByTagName('outcome')
for oNode in oNodes:
self.outcomes.append(Outcome(oNode))
def getXML(self, doc):
""" return an xml element containing information for a clinical report element"""
node = doc.createElement('report')
node.appendChild(xmlutil.createNodeWithTextChild(doc, 'id', self.id))
node.appendChild(xmlutil.createNodeWithTextChild(doc, 'gender', self.gender))
node.appendChild(xmlutil.createNodeWithTextChild(doc, 'minAge', self.minAge))
node.appendChild(xmlutil.createNodeWithTextChild(doc, 'maxAge', self.maxAge))
if len(self.locations) > 0:
lcNode = doc.createElement('location_countries')
node.appendChild(lcNode)
for country in self.locations:
lcNode.appendChild(xmlutil.createNodeWithTextChild(doc, 'country', country))
for condition in self.conditions:
node.appendChild(condition.getXML(doc))
if len(self.eligibilityCriteria) > 0:
ecNode = doc.createElement('eligibility')
node.appendChild(ecNode)
for ec in self.eligibilityCriteria:
ecNode.appendChild(ec.getXML(doc))
if len(self.inclusionCriteria) > 0:
icNode = doc.createElement('inclusion')
node.appendChild(icNode)
for ic in self.inclusionCriteria:
icNode.appendChild(ic.getXML(doc))
if len(self.exclusionCriteria) > 0:
ecNode = doc.createElement('exclusion')
node.appendChild(ecNode)
for ec in self.exclusionCriteria:
ecNode.appendChild(ec.getXML(doc))
for intervention in self.interventions:
node.appendChild(intervention.getXML(doc))
for outcome in self.outcomes:
node.appendChild(outcome.getXML(doc))
return node