def writeXML(self, filename):
""" write abstract out to xml file with given filename """
print 'Writing:', filename
doc = xml.dom.minidom.Document()
node = self.getXML(doc)
out = open(filename, 'w')
out.write('<?xml version="1.0" encoding="utf-8"?>\n')
out.write('<?xml-stylesheet href="http://www.andrews.edu/~summersc/abstract.xsl" type="text/xsl"?>\n')
xmlutil.writexml(node, out)
out.close()
def writeXML(self, filename):
""" write abstract out to xml file with given filename """
print 'Writing:', filename
doc = xml.dom.minidom.Document()
node = self.getXML(doc)
out = open(filename, 'w')
out.write('<?xml version="1.0" encoding="utf-8"?>\n')
out.write(
'<?xml-stylesheet href="http://www.andrews.edu/~summersc/abstract.xsl" type="text/xsl"?>\n'
)
xmlutil.writexml(node, out)
out.close()
def writeXML(self, path, version):
""" Write summary to XML file in the destination directory specified
by path. """
idPrefix = self.abstract.id + 'v' + version
# build XML summary
doc = xml.dom.minidom.Document()
articleNode = doc.createElement('Study')
if self.randomized:
articleNode.setAttribute('RandomizationPresent', 'true')
else:
articleNode.setAttribute('RandomizationPresent', 'false')
articleNode.setAttribute('Version', version)
gmTime = time.gmtime()
cNode = doc.createElement('Created')
articleNode.appendChild(cNode)
cNode.appendChild(xmlutil.createNodeWithTextChild(doc, 'Month', str(gmTime.tm_mon)))
cNode.appendChild(xmlutil.createNodeWithTextChild(doc, 'Day', str(gmTime.tm_mday)))
cNode.appendChild(xmlutil.createNodeWithTextChild(doc, 'Year', str(gmTime.tm_year)))
nameNode = xmlutil.createNodeWithTextChild(doc, 'Name', self.abstract.id)
articleNode.appendChild(nameNode)
titleString = ''
for s in self.abstract.titleSentences:
titleString += s.toString()
titleNode = xmlutil.createNodeWithTextChild(doc, 'Title', titleString)
articleNode.appendChild(titleNode)
link = 'http://www.ncbi.nlm.nih.gov/pubmed/' + self.abstract.id
linkNode = xmlutil.createNodeWithTextChild(doc, 'AbstractLink', link)
articleNode.appendChild(linkNode)
if self.abstract.report is not None and self.abstract.report.id[0:3] == 'NCT':
link = 'http://clinicaltrials.gov/ct2/show/study/' + self.abstract.report.id
linkNode = xmlutil.createNodeWithTextChild(doc, 'TrialRegistryLink', link)
articleNode.appendChild(linkNode)
node = self.locationList.getXML(doc, idPrefix)
if node is not None:
articleNode.appendChild(node)
if self.useTrialReports and self.abstract.report is not None \
and len(self.abstract.report.conditions) > 0:
cListNode = doc.createElement('ConditionsOfInterest')
articleNode.appendChild(cListNode)
for condition in self.abstract.report.conditions:
cNode = doc.createElement('Condition')
cNode.appendChild(xmlutil.createNodeWithTextChild(doc, 'Name',
condition.sentences[0].toString()))
cNode.setAttribute('source', 'trial_registry')
cListNode.appendChild(cNode)
node = self.subjectList.getXML(doc, idPrefix)
if node is not None:
articleNode.appendChild(node)
node = self.outcomeList.getXML(doc, idPrefix)
if node is not None:
articleNode.appendChild(node)
if self.abstract.meshHeadingList is not None:
articleNode.appendChild(self.abstract.meshHeadingList.getXML(doc))
htmlString = StringIO.StringIO()
self.writeHTML(htmlString, showError=False)
htmlNode = xmlutil.createNodeWithTextChild(doc, 'HTMLData', htmlString.getvalue())
articleNode.appendChild(htmlNode)
htmlString.close()
# write summary to XML file
filename = path + self.abstract.id + '.summary.xml'
out = open(filename, 'w')
out.write('<?xml version="1.0" encoding="utf-8"?>\n')
# out.write('<?xml-stylesheet href="abstract.xsl" type="text/xsl"?>\n')
xmlutil.writexml(articleNode, out)
out.close()
def writeXML(self, path, version):
""" Write summary to XML file in the destination directory specified
by path. """
idPrefix = self.abstract.id + 'v' + version
# build XML summary
doc = xml.dom.minidom.Document()
articleNode = doc.createElement('Study')
if self.randomized:
articleNode.setAttribute('RandomizationPresent', 'true')
else:
articleNode.setAttribute('RandomizationPresent', 'false')
articleNode.setAttribute('Version', version)
gmTime = time.gmtime()
cNode = doc.createElement('Created')
articleNode.appendChild(cNode)
cNode.appendChild(
xmlutil.createNodeWithTextChild(doc, 'Month', str(gmTime.tm_mon)))
cNode.appendChild(
xmlutil.createNodeWithTextChild(doc, 'Day', str(gmTime.tm_mday)))
cNode.appendChild(
xmlutil.createNodeWithTextChild(doc, 'Year', str(gmTime.tm_year)))
nameNode = xmlutil.createNodeWithTextChild(doc, 'Name',
self.abstract.id)
articleNode.appendChild(nameNode)
titleString = ''
for s in self.abstract.titleSentences:
titleString += s.toString()
titleNode = xmlutil.createNodeWithTextChild(doc, 'Title', titleString)
articleNode.appendChild(titleNode)
link = 'http://www.ncbi.nlm.nih.gov/pubmed/' + self.abstract.id
linkNode = xmlutil.createNodeWithTextChild(doc, 'AbstractLink', link)
articleNode.appendChild(linkNode)
if self.abstract.report is not None and self.abstract.report.id[
0:3] == 'NCT':
link = 'http://clinicaltrials.gov/ct2/show/study/' + self.abstract.report.id
linkNode = xmlutil.createNodeWithTextChild(doc,
'TrialRegistryLink',
link)
articleNode.appendChild(linkNode)
node = self.locationList.getXML(doc, idPrefix)
if node is not None:
articleNode.appendChild(node)
if self.useTrialReports and self.abstract.report is not None \
and len(self.abstract.report.conditions) > 0:
cListNode = doc.createElement('ConditionsOfInterest')
articleNode.appendChild(cListNode)
for condition in self.abstract.report.conditions:
cNode = doc.createElement('Condition')
cNode.appendChild(
xmlutil.createNodeWithTextChild(
doc, 'Name', condition.sentences[0].toString()))
cNode.setAttribute('source', 'trial_registry')
cListNode.appendChild(cNode)
node = self.subjectList.getXML(doc, idPrefix)
if node is not None:
articleNode.appendChild(node)
node = self.outcomeList.getXML(doc, idPrefix)
if node is not None:
articleNode.appendChild(node)
if self.abstract.meshHeadingList is not None:
articleNode.appendChild(self.abstract.meshHeadingList.getXML(doc))
htmlString = StringIO.StringIO()
self.writeHTML(htmlString, showError=False)
htmlNode = xmlutil.createNodeWithTextChild(doc, 'HTMLData',
htmlString.getvalue())
articleNode.appendChild(htmlNode)
htmlString.close()
# write summary to XML file
filename = path + self.abstract.id + '.summary.xml'
out = open(filename, 'w')
out.write('<?xml version="1.0" encoding="utf-8"?>\n')
# out.write('<?xml-stylesheet href="abstract.xsl" type="text/xsl"?>\n')
xmlutil.writexml(articleNode, out)
out.close()