""" Summary for a given abstract. All mentions, quantities should be found

and associated. """

abstract = None # abstract for which this is a summary

subjectList = None # list of groups w/descriptions

outcomeList = None # list of outcomes measured in abstract

locationList = None # list of locations where study is performed

summaryStatsList = None # list of summary statistics in abstract

randomized = False # is the abstract describing an RCT?

randomizedTerms = {'randomized', 'randomised', 'randomly', 'randomization',

'randomisation'}

useTrialReports = False

def __init__(self, abstract, useAnnotated=False, useTrialReports=False):

""" build EBM related summary for a given abstract object """

self.abstract = abstract

self.useTrialReports = useTrialReports

self.subjectList = subjectlist.SubjectList(abstract, useAnnotated, self.useTrialReports)

self.outcomeList = outcomelist.OutcomeList(abstract, useAnnotated, self.useTrialReports)

self.locationList = demographicelements.LocationList(abstract, self.useTrialReports)

self.summaryStatList = None

self.randomized = False

for s in abstract.titleSentences:

if self.containsRandomized(s):

self.randomized = True

break

if self.randomized is False:

for s in abstract.allSentences():

if self.containsRandomized(s):

self.randomized = True

break

def getEvaluationStrings(self, version):

""" Return list of SQL strings containing summary element evaluations.

These strings are part of SQL insert command into the answer table in EBM db.

"""

eStrings = []

tString = time.strftime("%a, %d %b %Y %H:%M:%S")

for av in self.subjectList.ageInfo.ageValues.values():

eStrings.append(self.sqlEvaluationString('Age', av.evaluation.id, av.evaluation.rating,

version, tString))

for cTemplate in self.subjectList.conditionTemplates:

eStrings.append(self.sqlEvaluationString('Condition', cTemplate.evaluation.id,

cTemplate.evaluation.rating, version, tString))

for gTemplate in self.subjectList.groupTemplates:

eStrings.append(self.sqlEvaluationString('Group', gTemplate.evaluation.id,

gTemplate.evaluation.rating, version, tString))

if gTemplate.groupSizeEvaluation.isComplete():

eStrings.append(self.sqlEvaluationString('Group_Size', gTemplate.groupSizeEvaluation.id,

gTemplate.groupSizeEvaluation.rating, version, tString))

for oTemplate in self.outcomeList.outcomeTemplates:

eStrings.append(self.sqlEvaluationString('Outcome', oTemplate.evaluation.id,

oTemplate.evaluation.rating, version, tString))

if oTemplate.primaryOutcomeEvaluation.isComplete():

eStrings.append(self.sqlEvaluationString('Primary_Outcome',

oTemplate.primaryOutcomeEvaluation.id,

oTemplate.primaryOutcomeEvaluation.rating, version, tString))

for ssTemplate in oTemplate.summaryStats:

eStrings.append(self.sqlEvaluationString('Endpoint', ssTemplate.evaluation.id,

ssTemplate.evaluation.rating, version, tString))

eStrings.append(self.sqlEvaluationString('actual_Age', 'Actual_Ages_no.s',

self.subjectList.ageInfo.nTrueAgeValues, version, tString))

eStrings.append(self.sqlEvaluationString('actual_Condition', 'Actual_Condition_no.s',

self.subjectList.nTrueConditions, version, tString))

eStrings.append(self.sqlEvaluationString('actual_Group', 'Actual_Group_no.s',

self.subjectList.nTrueGroups, version, tString))

eStrings.append(self.sqlEvaluationString('actual_Outcome', 'Actual_Outcomes_no.s',

self.outcomeList.nTrueOutcomes, version, tString))

eStrings.append(self.sqlEvaluationString('actual_Endpoint', 'Actual_ARR_no.s',

len(self.abstract.trueSummaryStats.stats), version, tString))

return eStrings

def sqlEvaluationString(self, elementType, elementId, answerDesc, version, timeString):

""" return SQL element evaluation string """

eString = '(%s, \'%s\', \'%s\', \'%s\', \'%s\',\'%s\', \'%s\')' \

% (self.abstract.id, version, elementType, elementId, answerDesc, 'auto', timeString)

return eString

def getElementStrings(self):

""" Return list of SQL strings containing evaluated summary element values.

These strings are part of SQL insert command into the element table in EBM db.

"""

eStrings = []

for av in self.subjectList.ageInfo.ageValues.values():

eStrings.append(self.sqlElementString(av.evaluation.id, av.toString(), None, False))

for cTemplate in self.subjectList.conditionTemplates:

eStrings.append(self.sqlElementString(cTemplate.evaluation.id,

cTemplate.toString(), cTemplate.matchedTemplate,

cTemplate.exactMatch))

for gTemplate in self.subjectList.groupTemplates:

eStrings.append(self.sqlElementString(gTemplate.evaluation.id,

gTemplate.toString(), gTemplate.matchedTemplate,

gTemplate.exactMatch))

if gTemplate.groupSizeEvaluation.isComplete():

eStrings.append(self.sqlElementString(gTemplate.groupSizeEvaluation.id,

gTemplate.getSize(maxSize=True), None, False))

for oTemplate in self.outcomeList.outcomeTemplates:

eStrings.append(self.sqlElementString(oTemplate.evaluation.id,

oTemplate.toString(), oTemplate.matchedTemplate,

oTemplate.exactMatch))

if oTemplate.primaryOutcomeEvaluation.isComplete():

eStrings.append(self.sqlElementString(oTemplate.primaryOutcomeEvaluation.id,

oTemplate.toString(), None, False))

for ssTemplate in oTemplate.summaryStats:

eStrings.append(self.sqlElementString(ssTemplate.evaluation.id,

ssTemplate.toString(), ssTemplate.matchingStat,

ssTemplate.correctlyMatched))

return eStrings

@staticmethod

def sqlElementString(elementId, elementDescription, matchingElement, exactMatch):

""" return SQL element description string """

if matchingElement is None:

eString = '(\'%s\', \'%s\', NULL, %s)' % (elementId, elementDescription, exactMatch)

else:

eString = '(\'%s\', \'%s\', \'%s\', %s)' \

% (elementId, elementDescription, matchingElement.toString(), exactMatch)

return eString

def containsRandomized(self, sentence):

""" return True if given sentence contains language that implies that the study

was randomized """

for token in sentence:

if token.text.lower() in self.randomizedTerms:

return True

return False

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 writeHTML(self, out, includeReport=False, showError=True):

""" write summary in html format to given output stream. """

htmlutil.HTMLBeginTable(out, classStyle='publicationinfotable')

htmlutil.HTMLBeginRow(out)

link = 'http://www.ncbi.nlm.nih.gov/pubmed/' + self.abstract.id

out.write('<h2><a href="%s">%s:</a></h2>\n' % (link, self.abstract.id))

htmlutil.HTMLColumnBreak(out)

titleString = ''

for s in self.abstract.titleSentences:

titleString += s.toPrettyString()

out.write('<h2>' + titleString + '</h2>')

htmlutil.HTMLEndRow(out)

htmlutil.HTMLBeginRow(out)

htmlutil.HTMLBeginRow(out)

htmlutil.HTMLWriteText(out,'Authors:', bold=True)

htmlutil.HTMLColumnBreak(out)

authorList = self.abstract.publicationInformation.getAuthors()

authorString = ', '.join(authorList)

out.write(authorString)

htmlutil.HTMLEndRow(out)

htmlutil.HTMLBeginRow(out)

htmlutil.HTMLWriteText(out,'Affiliation:', bold=True)

htmlutil.HTMLColumnBreak(out)

for affiliationSentence in self.abstract.affiliationSentences:

out.write(affiliationSentence.toPrettyString()+' ')

htmlutil.HTMLEndRow(out)

htmlutil.HTMLBeginRow(out)

htmlutil.HTMLWriteText(out,'Journal:', bold=True)

htmlutil.HTMLColumnBreak(out)

out.write(self.abstract.publicationInformation.getJournal())

htmlutil.HTMLEndRow(out)

htmlutil.HTMLBeginRow(out)

htmlutil.HTMLWriteText(out,'J. Country:', bold=True)

htmlutil.HTMLColumnBreak(out)

country = self.abstract.publicationInformation.getCountry()

out.write(country)

htmlutil.HTMLEndRow(out)

htmlutil.HTMLBeginRow(out)

htmlutil.HTMLWriteText(out,'Year pub:', bold=True)

htmlutil.HTMLColumnBreak(out)

out.write(self.abstract.publicationInformation.getPublicationDate())

htmlutil.HTMLEndRow(out)

htmlutil.HTMLBeginRow(out)

htmlutil.HTMLWriteText(out,'Pub. types:', bold=True)

htmlutil.HTMLColumnBreak(out)

pTypeList = self.abstract.publicationInformation.getPublicationTypes()

for pType in pTypeList:

htmlutil.HTMLWriteText(out, pType+'<br>')

htmlutil.HTMLEndRow(out)

htmlutil.HTMLEndTable(out)

# output abstract

htmlutil.HTMLBeginTable(out, classStyle='abstractsummarytable')

htmlutil.HTMLBeginRow(out, firstColumnWidth='60%', firstColumnBordersOn=False)

self.abstract.writeHTML(out, ['group', 'outcome', 'condition',

'eventrate', 'on', 'gs', 'cost_value'], showError)

# self.abstract.writeHTML(out)

htmlutil.HTMLColumnBreak(out, width='40%', nextColumnBordersOn=True)

# output summary

self.subjectList.writeHTML(out)

self.outcomeList.writeHTML(out, showError)

htmlutil.HTMLEndRow(out)

htmlutil.HTMLEndTable(out)