def loadStudyEvents(self):
"""Extract a list of Study Event domain objects according to ODM from metadata XML
"""
studyEvents = []
# Check if file path is setup
if (self.isFileLoaded):
documentTree = ET.ElementTree(file=self.filename)
# First obtain list of references (OIDs) to study events defined in ODM -> Study -> MetaDataVersion -> Protocol
studyEventRefs = []
for studyEventRef in documentTree.iterfind('.//odm:StudyEventRef', namespaces=nsmaps):
studyEventRefs.append(studyEventRef.attrib['StudyEventOID'])
# # In case I need this information later
# print studyEventRef.attrib['Mandatory']
# print studyEventRef.attrib['OrderNumber']
# Now for each study event reference find study event definition
for eventRef in studyEventRefs:
for element in documentTree.iterfind('.//odm:StudyEventDef[@OID="' + eventRef + '"]', namespaces=nsmaps):
studyEvent = StudyEventDefinition()
studyEvent.setOid(element.attrib['OID'])
studyEvent.setName(element.attrib['Name'])
studyEvent.setRepeating(element.attrib['Repeating'])
studyEvent.setType(element.attrib['Type'])
studyEvents.append(studyEvent)
# Return resulting study event defintion elements
return studyEvents
def listAllByStudy(self, study):
"""
"""
params = SimpleXMLElement("""<?xml version="1.0" encoding="UTF-8"?>
<listAllRequest>
<v1:studyEventDefinitionListAll xmlns:v1="http://openclinica.org/ws/studyEventDefinition/v1">
<bean:studyRef xmlns:bean="http://openclinica.org/ws/beans">
<bean:identifier>""" + study.identifier + """</bean:identifier>
</bean:studyRef>
</v1:studyEventDefinitionListAll>
</listAllRequest>""")
response = self.client.call('listAllRequest', params)
studyEventDefinitions = []
for studyEventDefinition in response.studyEventDefinitions.children():
oid = str(studyEventDefinition.oid)
name = str(studyEventDefinition.name)
eventDefinitionCrfs = []
for eventDefinitionCrf in studyEventDefinition.eventDefinitionCrfs.children(
):
required = str(eventDefinitionCrf.required)
doubleDataEntry = str(eventDefinitionCrf.doubleDataEntry)
passwordRequired = str(eventDefinitionCrf.passwordRequired)
hideCrf = str(eventDefinitionCrf.hideCrf)
sourceDataVerificaiton = str(
eventDefinitionCrf.sourceDataVerificaiton)
# Ugly but it works
index = 0
defaultCrfVersionOid = None
obtainedDefaultCrfVersion = None
for ch in eventDefinitionCrf.children():
if ch.children():
if index == 0:
crfOid = str(ch.oid)
crfName = str(ch.name)
obtainedCrf = Crf(crfOid, crfName)
elif index == 1:
defaultCrfVersionOid = str(ch.oid)
defaultCrfVersionName = str(ch.name)
obtainedDefaultCrfVersion = CrfVersion(
defaultCrfVersionOid, defaultCrfVersionName)
index = index + 1
obtainedEventDefinitionCrf = EventDefinitionCrf(
required, doubleDataEntry, passwordRequired, hideCrf,
sourceDataVerificaiton, obtainedCrf,
obtainedDefaultCrfVersion)
eventDefinitionCrfs.append(obtainedEventDefinitionCrf)
obtainedStudyEventDefintion = StudyEventDefinition(
oid, name, eventDefinitionCrfs)
studyEventDefinitions.append(obtainedStudyEventDefintion)
return studyEventDefinitions
def loadEventsFromMetadata(self, metadata):
"""Extract a list of Study Event domain objects according to ODM from metadata XML
"""
studyEvents = []
# Check if file path is setup
if metadata:
documentTree = ET.ElementTree((ET.fromstring(str(metadata))))
# First obtain list of references (OIDs) to study events defined in ODM -> Study -> MetaDataVersion -> Protocol
studyEventRefs = []
for studyEventRef in documentTree.iterfind(".//odm:StudyEventRef", namespaces=nsmaps):
studyEventRefs.append(studyEventRef.attrib["StudyEventOID"])
# In case I need this information later
eventIsMandatory = studyEventRef.attrib["Mandatory"] == "Yes"
eventOrderInProtocol = int(studyEventRef.attrib["OrderNumber"])
# Now for each study event reference find study event definition
for eventRef in studyEventRefs:
for element in documentTree.iterfind(
'.//odm:StudyEventDef[@OID="' + eventRef + '"]', namespaces=nsmaps
):
studyEvent = StudyEventDefinition()
studyEvent.oid = element.attrib["OID"]
studyEvent.name = element.attrib["Name"]
studyEvent.repeating = element.attrib["Repeating"] == "Yes"
studyEvent.type = element.attrib["Type"]
studyEvent.mandatory = eventIsMandatory
studyEvent.orderNumber = eventOrderInProtocol
for eventElement in element:
if (
str(eventElement.tag)
).strip() == "{http://www.openclinica.org/ns/odm_ext_v130/v3.1}EventDefinitionDetails":
for detailsElement in eventElement:
if (
str(detailsElement.tag)
).strip() == "{http://www.openclinica.org/ns/odm_ext_v130/v3.1}Description":
studyEvent.description = detailsElement.text
elif (
str(detailsElement.tag)
).strip() == "{http://www.openclinica.org/ns/odm_ext_v130/v3.1}Category":
studyEvent.category = detailsElement.text
studyEvents.append(studyEvent)
# Return resulting study event defintion elements
return studyEvents
def loadStudyEvents(self):
"""Extract a list of Study Event domain objects according to ODM from metadata XML
"""
studyEvents = []
# Check if file path is setup
if (self.isFileLoaded):
documentTree = ET.ElementTree(file=self.filename)
# First obtain list of references (OIDs) to study events defined in ODM -> Study -> MetaDataVersion -> Protocol
studyEventRefs = []
for studyEventRef in documentTree.iterfind('.//odm:StudyEventRef',
namespaces=nsmaps):
studyEventRefs.append(studyEventRef.attrib['StudyEventOID'])
# # In case I need this information later
# print studyEventRef.attrib['Mandatory']
# print studyEventRef.attrib['OrderNumber']
# Now for each study event reference find study event definition
for eventRef in studyEventRefs:
for element in documentTree.iterfind(
'.//odm:StudyEventDef[@OID="' + eventRef + '"]',
namespaces=nsmaps):
studyEvent = StudyEventDefinition()
studyEvent.setOid(element.attrib['OID'])
studyEvent.setName(element.attrib['Name'])
studyEvent.setRepeating(element.attrib['Repeating'])
studyEvent.setType(element.attrib['Type'])
studyEvents.append(studyEvent)
# Return resulting study event defintion elements
return studyEvents
def loadEventsFromMetadata(self, metadata):
"""Extract a list of Study Event domain objects according to ODM from metadata XML
"""
studyEvents = []
# Check if file path is setup
if (metadata):
documentTree = ET.ElementTree((ET.fromstring(str(metadata))))
# First obtain list of references (OIDs) to study events defined in ODM -> Study -> MetaDataVersion -> Protocol
studyEventRefs = []
for studyEventRef in documentTree.iterfind('.//odm:StudyEventRef', namespaces=nsmaps):
studyEventRefs.append(studyEventRef.attrib['StudyEventOID'])
# # In case I need this information later
# print studyEventRef.attrib['Mandatory']
# print studyEventRef.attrib['OrderNumber']
# Now for each study event reference find study event definition
for eventRef in studyEventRefs:
for element in documentTree.iterfind('.//odm:StudyEventDef[@OID="' + eventRef + '"]', namespaces=nsmaps):
studyEvent = StudyEventDefinition()
studyEvent.setOid(element.attrib['OID'])
studyEvent.setName(element.attrib['Name'])
studyEvent.setRepeating(element.attrib['Repeating'] == "Yes")
studyEvent.setType(element.attrib['Type'])
for eventElement in element:
if (str(eventElement.tag)).strip() == "{http://www.openclinica.org/ns/odm_ext_v130/v3.1}EventDefinitionDetails":
for detailsElement in eventElement:
if (str(detailsElement.tag)).strip() == "{http://www.openclinica.org/ns/odm_ext_v130/v3.1}Description":
studyEvent.description = detailsElement.text
elif (str(detailsElement.tag)).strip() == "{http://www.openclinica.org/ns/odm_ext_v130/v3.1}Category":
studyEvent.category = detailsElement.text
studyEvents.append(studyEvent)
# Return resulting study event defintion elements
return studyEvents
