def loadStudy(self):
"""Extract Study domain object according to ODM from metadata XML
"""
study = None
# Check if file path is setup
if (self.isFileLoaded):
documentTree = ET.ElementTree(file=self.filename)
# Locate Study data in XML file via XPath
for element in documentTree.iterfind('.//odm:Study',
namespaces=nsmaps):
study = Study()
study.setOid(element.attrib['OID'])
for studyName in documentTree.iterfind(
'.//odm:Study[@OID="' + study.oid() +
'"]/odm:GlobalVariables/odm:StudyName',
namespaces=nsmaps):
study.setName(studyName.text)
for studyDescription in documentTree.iterfind(
'.//odm:Study[@OID="' + study.oid() +
'"]/odm:GlobalVariables/odm:StudyDescription',
namespaces=nsmaps):
study.setDescription(studyDescription.text)
# # In case I need this information later
# for studyProtocolName in documentTree.iterfind('.//odm:Study[@OID="' + study.oid() + '"]/odm:GlobalVariables/odm:ProtocolName', namespaces=nsmaps):
# print studyProtocolName.text
# The resulting study element
return study
def listAll(self):
"""Get hierarchical list of studies together with their study sites
"""
result = ""
studies = []
params = SimpleXMLElement("""<?xml version="1.0" encoding="UTF-8"?>
<listAllRequest />""")
response = self.client.call('listAllRequest', params)
documentTree = ET.ElementTree((ET.fromstring(str(response.as_xml()))))
# Locate Study data in XML file via XPath
for study in documentTree.iterfind('.//study:study',
namespaces=nsmaps):
identifier = ""
oid = ""
name = ""
sites = []
for element in study:
print element.tag
if (str(element.tag)).strip(
) == "{http://openclinica.org/ws/study/v1}identifier":
identifier = element.text
elif (str(element.tag)
).strip() == "{http://openclinica.org/ws/study/v1}oid":
oid = element.text
elif (str(element.tag)
).strip() == "{http://openclinica.org/ws/study/v1}name":
name = element.text
if (str(element.tag)
).strip() == "{http://openclinica.org/ws/study/v1}sites":
for site in element:
siteid = ""
siteoid = ""
sitename = ""
for siteelement in site:
if (str(siteelement.tag)).strip(
) == "{http://openclinica.org/ws/study/v1}identifier":
siteid = siteelement.text
elif (str(siteelement.tag)).strip(
) == "{http://openclinica.org/ws/study/v1}oid":
siteoid = siteelement.text
elif (str(siteelement.tag)).strip(
) == "{http://openclinica.org/ws/study/v1}name":
sitename = siteelement.text
obtainedSite = StudySite(siteid, siteoid, sitename)
sites.append(obtainedSite)
obtainedStudy = Study(identifier, oid, name)
obtainedStudy.sites = sites
studies.append(obtainedStudy)
# Result of WS call
result = str(response.result)
return result, studies
def listAll(self):
"""Get hierarchical list of studies together with their study sites
"""
result = ""
studies = []
params = SimpleXMLElement("""<?xml version="1.0" encoding="UTF-8"?>
<listAllRequest />""")
response = self.client.call('listAllRequest', params)
documentTree = ET.ElementTree((ET.fromstring(str(response.as_xml()))))
# Locate Study data in XML file via XPath
for study in documentTree.iterfind('.//study:study', namespaces=nsmaps):
identifier = ""
oid = ""
name = ""
sites = []
for element in study:
print element.tag
if (str(element.tag)).strip() == "{http://openclinica.org/ws/study/v1}identifier":
identifier = element.text
elif (str(element.tag)).strip() == "{http://openclinica.org/ws/study/v1}oid":
oid = element.text
elif (str(element.tag)).strip() == "{http://openclinica.org/ws/study/v1}name":
name = element.text
if (str(element.tag)).strip() == "{http://openclinica.org/ws/study/v1}sites":
for site in element:
siteid = ""
siteoid = ""
sitename = ""
for siteelement in site:
if (str(siteelement.tag)).strip() == "{http://openclinica.org/ws/study/v1}identifier":
siteid = siteelement.text
elif (str(siteelement.tag)).strip() == "{http://openclinica.org/ws/study/v1}oid":
siteoid = siteelement.text
elif (str(siteelement.tag)).strip() == "{http://openclinica.org/ws/study/v1}name":
sitename = siteelement.text
obtainedSite = StudySite(siteid, siteoid, sitename)
sites.append(obtainedSite)
obtainedStudy = Study(identifier, oid, name)
obtainedStudy.sites = sites
studies.append(obtainedStudy)
# Result of WS call
result = str(response.result)
return result, studies
def loadStudy(self):
"""Extract Study domain object according to ODM from metadata XML
"""
study = None
# Check if file path is setup
if (self.isFileLoaded) :
documentTree = ET.ElementTree(file=self.filename)
# Locate Study data in XML file via XPath
for element in documentTree.iterfind('.//odm:Study', namespaces=nsmaps):
study = Study()
study.setOid(element.attrib['OID'])
for studyName in documentTree.iterfind('.//odm:Study[@OID="' + study.oid() + '"]/odm:GlobalVariables/odm:StudyName', namespaces=nsmaps):
study.setName(studyName.text)
for studyDescription in documentTree.iterfind('.//odm:Study[@OID="' + study.oid() + '"]/odm:GlobalVariables/odm:StudyDescription', namespaces=nsmaps):
study.setDescription(studyDescription.text)
# # In case I need this information later
# for studyProtocolName in documentTree.iterfind('.//odm:Study[@OID="' + study.oid() + '"]/odm:GlobalVariables/odm:ProtocolName', namespaces=nsmaps):
# print studyProtocolName.text
# The resulting study element
return study