def generateOdmXmlForStudyFromMetadata(self, studyOid, subject,
studyEventDefinition, studyEventCrf,
itemValues, metadata):
"""Obsolate: DO NOT USE!
"""
odm = ET.Element('ODM')
clinicalData = ET.SubElement(odm, 'ClinicalData')
clinicalData.set('StudyOID', studyOid)
clinicalData.set('MetaDataVersionOID', 'v1.0.0')
fileSubjectCounter = 0
subjectData = ET.SubElement(clinicalData, 'SubjectData')
subjectData.set('SubjectKey', subject.oid)
studyEventData = ET.SubElement(subjectData, 'StudyEventData')
studyEventData.set('StudyEventOID', studyEventDefinition.oid())
formData = ET.SubElement(studyEventData, 'FormData')
formData.set('FormOID', studyEventCrf.defaultCrfVersion().oid())
items = []
for ivalue in itemValues:
item = Item()
item.value = ivalue
items.append(item)
patientIdItemOid = self.getItemOidFromMetadata(
metadata,
studyEventCrf.defaultCrfVersion().oid(), self.ocPatientIdItemName)
studyUidItemOid = self.getItemOidFromMetadata(
metadata,
studyEventCrf.defaultCrfVersion().oid(), self.ocStudyUidItemName)
items[0].oid = patientIdItemOid
items[1].oid = studyUidItemOid
itemGroupPatientOid = self.getItemGroupOidFromMetadata(
metadata, patientIdItemOid)
itemGroupStudyOid = self.getItemGroupOidFromMetadata(
metadata, studyUidItemOid)
# Both should be in the same group
if (itemGroupPatientOid == itemGroupStudyOid):
itemGroupData = ET.SubElement(formData, 'ItemGroupData')
itemGroupData.set('ItemGroupOID', itemGroupStudyOid)
itemGroupData.set('TransactionType', 'Insert')
for item in items:
itemData = ET.SubElement(itemGroupData, 'ItemData')
itemData.set('ItemOID', item.oid)
itemData.set('Value', item.value)
xmlstring = ET.tostring(odm, encoding="UTF-8")
xmlstring = xmlstring.replace("<?xml version='1.0' encoding='UTF-8'?>",
"")
return xmlstring
def generateOdmXmlForStudyFromMetadata(self, studyOid, subject, studyEventDefinition, studyEventCrf, itemValues, metadata):
"""Obsolate: DO NOT USE!
"""
odm = ET.Element('ODM')
clinicalData = ET.SubElement(odm, 'ClinicalData')
clinicalData.set('StudyOID', studyOid)
clinicalData.set('MetaDataVersionOID', 'v1.0.0')
fileSubjectCounter = 0
subjectData = ET.SubElement(clinicalData, 'SubjectData')
subjectData.set('SubjectKey', subject.oid)
studyEventData = ET.SubElement(subjectData, 'StudyEventData')
studyEventData.set('StudyEventOID', studyEventDefinition.oid())
formData = ET.SubElement(studyEventData, 'FormData')
formData.set('FormOID', studyEventCrf.defaultCrfVersion().oid())
items = []
for ivalue in itemValues:
item = Item()
item.value = ivalue
items.append(item)
patientIdItemOid = self.getItemOidFromMetadata(metadata, studyEventCrf.defaultCrfVersion().oid(), self.ocPatientIdItemName)
studyUidItemOid = self.getItemOidFromMetadata(metadata, studyEventCrf.defaultCrfVersion().oid(), self.ocStudyUidItemName)
items[0].oid = patientIdItemOid
items[1].oid = studyUidItemOid
itemGroupPatientOid = self.getItemGroupOidFromMetadata(metadata, patientIdItemOid)
itemGroupStudyOid = self.getItemGroupOidFromMetadata(metadata, studyUidItemOid)
# Both should be in the same group
if (itemGroupPatientOid == itemGroupStudyOid):
itemGroupData = ET.SubElement(formData, 'ItemGroupData')
itemGroupData.set('ItemGroupOID', itemGroupStudyOid)
itemGroupData.set('TransactionType', 'Insert')
for item in items:
itemData = ET.SubElement(itemGroupData, 'ItemData')
itemData.set('ItemOID', item.oid)
itemData.set('Value', item.value)
xmlstring = ET.tostring(odm, encoding="UTF-8")
xmlstring = xmlstring.replace("<?xml version='1.0' encoding='UTF-8'?>", "")
return xmlstring
def loadCrfItem(self, formOid, itemOid, metadata):
"""Load CRF item details from ODM metadata
"""
item = None
self.logger.info("CRF form OID: " + formOid)
self.logger.info("CRF item OID: " + itemOid)
# Check if file path is setup
if metadata:
documentTree = ET.ElementTree((ET.fromstring(str(metadata))))
# Locate ItemDefs data in XML file via XPath
for itemElement in documentTree.iterfind('.//odm:ItemDef[@OID="' + itemOid + '"]', namespaces=nsmaps):
# Check FormOID, normally I would do it in XPath but python does not support contaions wildcard
if itemElement.attrib["{http://www.openclinica.org/ns/odm_ext_v130/v3.1}FormOIDs"].find(formOid) != -1:
item = Item()
item.oid = itemElement.attrib['OID']
item.name = itemElement.attrib['Name']
item.description = itemElement.attrib['Comment']
item.dataType = itemElement.attrib['DataType']
for itemDetails in itemElement:
if (str(itemDetails.tag)).strip() == "{http://www.openclinica.org/ns/odm_ext_v130/v3.1}ItemDetails":
for detailsElement in itemDetails:
if (str(detailsElement.tag)).strip() == "{http://www.openclinica.org/ns/odm_ext_v130/v3.1}ItemPresentInForm":
for presentForm in detailsElement:
if (str(presentForm.tag)).strip() == "{http://www.openclinica.org/ns/odm_ext_v130/v3.1}LeftItemText":
item.label = presentForm.text
# Return resulting CRT item
return item
def loadCrfItem(self, formOid, itemOid, metadata):
"""Load CRF item details from ODM metadata
"""
item = None
self.logger.info("CRF form OID: " + formOid)
self.logger.info("CRF item OID: " + itemOid)
# Check if file path is setup
if (metadata):
documentTree = ET.ElementTree((ET.fromstring(str(metadata))))
# Locate ItemDefs data in XML file via XPath
for itemElement in documentTree.iterfind('.//odm:ItemDef[@OID="' + itemOid + '"]', namespaces=nsmaps):
# Check FormOID, normally I would do it in XPath but python does not support contaions wildcard
if itemElement.attrib["{http://www.openclinica.org/ns/odm_ext_v130/v3.1}FormOIDs"].find(formOid) != -1:
item = Item()
item.oid = itemElement.attrib['OID']
item.name = itemElement.attrib['Name']
item.description = itemElement.attrib['Comment']
item.dataType = itemElement.attrib['DataType']
for itemDetails in itemElement:
if (str(itemDetails.tag)).strip() == "{http://www.openclinica.org/ns/odm_ext_v130/v3.1}ItemDetails":
for detailsElement in itemDetails:
if (str(detailsElement.tag)).strip() == "{http://www.openclinica.org/ns/odm_ext_v130/v3.1}ItemPresentInForm":
for presentForm in detailsElement:
if (str(presentForm.tag)).strip() == "{http://www.openclinica.org/ns/odm_ext_v130/v3.1}LeftItemText":
item.label = presentForm.text
# Return resulting CRT item
return item
def getStudyCasebookEvents(self, data, thread=None):
"""Get study casebook subject events
"""
if data:
ocBaseUrl = data[0]
studyOid = data[1]
subjectOid = data[2]
method = studyOid + "/" + subjectOid + "/*/*"
results = []
r = self._ocRequest(ocBaseUrl, method)
if r.status_code == 200:
if "ClinicalData" in r.json():
if "SubjectData" in r.json()["ClinicalData"]:
if "StudyEventData" in r.json(
)["ClinicalData"]["SubjectData"]:
eventData = r.json(
)["ClinicalData"]["SubjectData"]["StudyEventData"]
# Multiple events
if type(eventData) is list:
for ed in eventData:
event = Event()
event.eventDefinitionOID = ed["@StudyEventOID"]
event.status = ed["@OpenClinica:Status"]
dateString = ed["@OpenClinica:StartDate"]
format = ""
# Is it only date or datetime
if len(dateString) == 11:
format = "%d-%b-%Y"
elif len(dateString) == 20:
format = "%d-%b-%Y %H:%M:%S"
event.startDate = datetime.strptime(
dateString, format)
event.studyEventRepeatKey = ed[
"@StudyEventRepeatKey"]
# Subject Age At Event is optional (because collect birth date is optional)
if "OpenClinica:SubjectAgeAtEvent" in ed:
event.subjectAgeAtEvent = ed[
"OpenClinica:SubjectAgeAtEvent"]
# Resulting eCRFs
if "FormData" in ed:
formData = ed["FormData"]
# Multiple forms
if type(formData) is list:
for frm in formData:
crf = Crf()
crf.oid = frm["@FormOID"]
crf.version = frm[
"@OpenClinica:Version"]
crf.status = frm[
"@OpenClinica:Status"]
event.addCrf(crf)
# Only one form in event
elif type(formData) is dict:
frm = formData
crf = Crf()
crf.oid = frm["@FormOID"]
crf.version = frm[
"@OpenClinica:Version"]
crf.status = frm["@OpenClinica:Status"]
event.addCrf(crf)
# + automatically schedule default version only (if it is not)
eventFormOids = []
eventDefinition = r.json(
)["Study"]["MetaDataVersion"]["StudyEventDef"]
if type(eventDefinition) is list:
for ed in eventDefinition:
formRef = ed["FormRef"]
if type(formRef) is list:
for fr in formRef:
eventFormOids.append(
fr["@FormOID"])
elif type(formRef) is dict:
eventFormOids.append(
formRef["@FormOID"])
elif type(eventDefinition) is dict:
ed = eventDefinition
formRef = ed["FormRef"]
if type(formRef) is list:
for fr in formRef:
eventFormOids.append(
fr["@FormOID"])
elif type(formRef) is dict:
eventFormOids.append(
formRef["@FormOID"])
formDefinition = r.json(
)["Study"]["MetaDataVersion"]["FormDef"]
if type(formDefinition) is list:
for fd in formDefinition:
if fd["@OID"] in eventFormOids:
if not event.hasScheduledCrf(
fd["@OID"]):
if fd["OpenClinica:FormDetails"][
"OpenClinica:PresentInEventDefinition"][
"@IsDefaultVersion"] == "Yes":
event.addCrf(
Crf(
fd["@OID"],
fd["@Name"]))
else:
if fd["OpenClinica:FormDetails"][
"OpenClinica:PresentInEventDefinition"][
"@IsDefaultVersion"] == "Yes":
crf = event.getCrf(
fd["@OID"])
crf.name = fd["@Name"]
# Collect references to ItemGroups in any case
igRef = fd["ItemGroupRef"]
if type(igRef) is list:
for igr in igRef:
itemGroupOids.append(
igr["@ItemGroupOID"])
elif type(igRef) is dict:
igr = igRef
itemGroupOids.append(
igr["@ItemGroupOID"])
elif type(formDefinition) is dict:
fd = formDefinition
if fd["@OID"] in eventFormOids:
if not event.hasScheduledCrf(
fd["@OID"]):
if fd["OpenClinica:FormDetails"][
"OpenClinica:PresentInEventDefinition"][
"@IsDefaultVersion"] == "Yes":
event.addCrf(
Crf(
fd["@OID"],
fd["@Name"]))
else:
if fd["OpenClinica:FormDetails"][
"OpenClinica:PresentInEventDefinition"][
"@IsDefaultVersion"] == "Yes":
crf = event.getCrf(fd["@OID"])
crf.name = fd["@Name"]
# Collect references to ItemGroups in any case
igRef = fd["ItemGroupRef"]
if type(igRef) is list:
for igr in igRef:
itemGroupOids.append(
igr["@ItemGroupOID"])
elif type(igRef) is dict:
igr = igRef
itemGroupOids.append(
igr["@ItemGroupOID"])
# Discover items base on theri refOIDs
itemOids = []
itemGroupDefinition = r.json(
)["Study"]["MetaDataVersion"]["ItemGroupDef"]
if type(itemGroupDefinition) is list:
for igd in itemGroupDefinition:
if igd["@OID"] in itemGroupOids:
crf = event.getCrf(igd[
"OpenClinica:ItemGroupDetails"][
"OpenClinica:PresentInForm"]
["@FormOID"])
group = ItemGroup()
group.oid = igd["@OID"]
group.name = igd["@Name"]
iRef = igd["ItemRef"]
if type(iRef) is list:
for ir in iRef:
item = Item()
item.oid = ir["@ItemOID"]
group.addItem(item)
itemOids.append(
ir["@ItemOID"])
elif type(iRef) is dict:
ir = iRef
item = Item()
item.oid = ir["@ItemOID"]
group.addItem(item)
itemOids.append(ir["@ItemOID"])
crf.addItemGroup(group)
elif type(itemGroupDefinition) is dict:
igd = itemGroupDefinition
if igd["@OID"] in itemGroupOids:
crf = event.getCrf(
igd["OpenClinica:ItemGroupDetails"]
["OpenClinica:PresentInForm"]
["@FormOID"])
group = ItemGroup()
group.oid = igd["@OID"]
group.name = igd["@Name"]
iRef = igd["ItemRef"]
if type(iRef) is list:
for ir in iRef:
item = Item()
item.oid = ir["@ItemOID"]
group.addItem(item)
itemOids.append(ir["@ItemOID"])
elif type(iRef) is dict:
ir = iRef
item = Item()
item.oid = ir["@ItemOID"]
group.addItem(item)
itemOids.append(ir["@ItemOID"])
crf.addItemGroup(group)
# Setup items for CRF in event
itemDefinition = r.json(
)["Study"]["MetaDataVersion"]["ItemDef"]
if type(itemDefinition) is list:
for itemDef in itemDefinition:
if itemDef["@OID"] in itemOids:
crf = event.getCrf(itemDef[
"@OpenClinica:FormOIDs"])
item = Item()
item.oid = itemDef["@OID"]
item.name = itemDef["@Name"]
item.dataType = itemDef[
"@DataType"]
item.description = itemDef[
"@Comment"]
gr = crf.findGroupForItem(item.oid)
item.itemGroupOid = gr.oid
crf.items.append(item)
elif type(itemDefinition) is dict:
itemDef = itemDefinition
if itemDef["@OID"] in itemOids:
crf = event.getCrf(
itemDef["@OpenClinica:FormOIDs"])
item = Item()
item.oid = itemDef["@OID"]
item.name = itemDef["@Name"]
item.dataType = itemDef["@DataType"]
item.description = itemDef["@Comment"]
gr = crf.findGroupForItem(item.oid)
item.itemGroupOid = gr.oid
crf.items.append(item)
results.append(event)
# Only one event reported
elif type(eventData) is dict:
ed = eventData
event = Event()
event.eventDefinitionOID = ed["@StudyEventOID"]
event.status = ed["@OpenClinica:Status"]
dateString = ed["@OpenClinica:StartDate"]
format = ""
# Is it only date or datetime
if len(dateString) == 11:
format = "%d-%b-%Y"
elif len(dateString) == 20:
format = "%d-%b-%Y %H:%M:%S"
event.startDate = datetime.strptime(
dateString, format)
event.studyEventRepeatKey = ed[
"@StudyEventRepeatKey"]
# Subject Age At Event is optional (because collect birth date is optional)
if "OpenClinica:SubjectAgeAtEvent" in ed:
event.subjectAgeAtEvent = ed[
"OpenClinica:SubjectAgeAtEvent"]
# Resulting eCRFs
if "FormData" in ed:
formData = ed["FormData"]
# Multiple forms
if type(formData) is list:
for frm in formData:
crf = Crf()
crf.oid = frm["@FormOID"]
crf.version = frm[
"@OpenClinica:Version"]
crf.status = frm["@OpenClinica:Status"]
event.addCrf(crf)
# Only one form in event
elif type(formData) is dict:
frm = formData
crf = Crf()
crf.oid = frm["@FormOID"]
crf.version = frm["@OpenClinica:Version"]
crf.status = frm["@OpenClinica:Status"]
event.addCrf(crf)
# + automatically default version (if it is not)
eventFormOids = []
eventDefinition = r.json(
)["Study"]["MetaDataVersion"]["StudyEventDef"]
if type(eventDefinition) is list:
for ed in eventDefinition:
formRef = ed["FormRef"]
if type(formRef) is list:
for fr in formRef:
eventFormOids.append(
fr["@FormOID"])
elif type(formRef) is dict:
eventFormOids.append(
formRef["@FormOID"])
elif type(eventDefinition) is dict:
ed = eventDefinition
formRef = ed["FormRef"]
if type(formRef) is list:
for fr in formRef:
eventFormOids.append(fr["@FormOID"])
elif type(formRef) is dict:
eventFormOids.append(formRef["@FormOID"])
itemGroupOids = []
formDefinition = r.json(
)["Study"]["MetaDataVersion"]["FormDef"]
if type(formDefinition) is list:
for fd in formDefinition:
if fd["@OID"] in eventFormOids:
if not event.hasScheduledCrf(
fd["@OID"]):
if fd["OpenClinica:FormDetails"][
"OpenClinica:PresentInEventDefinition"][
"@IsDefaultVersion"] == "Yes":
event.addCrf(
Crf(
fd["@OID"],
fd["@Name"]))
else:
if fd["OpenClinica:FormDetails"][
"OpenClinica:PresentInEventDefinition"][
"@IsDefaultVersion"] == "Yes":
crf = event.getCrf(fd["@OID"])
crf.name = fd["@Name"]
# Collect references to ItemGroups in any case
igRef = fd["ItemGroupRef"]
if type(igRef) is list:
for igr in igRef:
itemGroupOids.append(
igr["@ItemGroupOID"])
elif type(igRef) is dict:
igr = igRef
itemGroupOids.append(
igr["@ItemGroupOID"])
elif type(formDefinition) is dict:
fd = formDefinition
if fd["@OID"] in eventFormOids:
if not event.hasScheduledCrf(fd["@OID"]):
if fd["OpenClinica:FormDetails"][
"OpenClinica:PresentInEventDefinition"][
"@IsDefaultVersion"] == "Yes":
event.addCrf(
Crf(fd["@OID"], fd["@Name"]))
else:
if fd["OpenClinica:FormDetails"][
"OpenClinica:PresentInEventDefinition"][
"@IsDefaultVersion"] == "Yes":
crf = event.getCrf(fd["@OID"])
crf.name = fd["@Name"]
# Collect references to ItemGroups in any case
igRef = fd["ItemGroupRef"]
if type(igRef) is list:
for igr in igRef:
itemGroupOids.append(
igr["@ItemGroupOID"])
elif type(igRef) is dict:
igr = igRef
itemGroupOids.append(
igr["@ItemGroupOID"])
# Discover items base on theri refOIDs
itemOids = []
itemGroupDefinition = r.json(
)["Study"]["MetaDataVersion"]["ItemGroupDef"]
if type(itemGroupDefinition) is list:
for igd in itemGroupDefinition:
if igd["@OID"] in itemGroupOids:
crf = event.getCrf(
igd["OpenClinica:ItemGroupDetails"]
["OpenClinica:PresentInForm"]
["@FormOID"])
group = ItemGroup()
group.oid = igd["@OID"]
group.name = igd["@Name"]
iRef = igd["ItemRef"]
if type(iRef) is list:
for ir in iRef:
item = Item()
item.oid = ir["@ItemOID"]
group.addItem(item)
itemOids.append(ir["@ItemOID"])
elif type(iRef) is dict:
ir = iRef
item = Item()
item.oid = ir["@ItemOID"]
group.addItem(item)
itemOids.append(ir["@ItemOID"])
crf.addItemGroup(group)
elif type(itemGroupDefinition) is dict:
igd = itemGroupDefinition
if igd["@OID"] in itemGroupOids:
crf = event.getCrf(
igd["OpenClinica:ItemGroupDetails"]
["OpenClinica:PresentInForm"]
["@FormOID"])
group = ItemGroup()
group.oid = igd["@OID"]
group.name = igd["@Name"]
iRef = igd["ItemRef"]
if type(iRef) is list:
for ir in iRef:
item = Item()
item.oid = ir["@ItemOID"]
group.addItem(item)
itemOids.append(ir["@ItemOID"])
elif type(iRef) is dict:
ir = iRef
item = Item()
item.oid = ir["@ItemOID"]
group.addItem(item)
itemOids.append(ir["@ItemOID"])
crf.addItemGroup(group)
# Setup items for CRF in event
itemDefinition = r.json(
)["Study"]["MetaDataVersion"]["ItemDef"]
if type(itemDefinition) is list:
for itemDef in itemDefinition:
if itemDef["@OID"] in itemOids:
crf = event.getCrf(
itemDef["@OpenClinica:FormOIDs"])
item = Item()
item.oid = itemDef["@OID"]
item.name = itemDef["@Name"]
item.dataType = itemDef["@DataType"]
item.description = itemDef["@Comment"]
gr = crf.findGroupForItem(item.oid)
item.itemGroupOid = gr.oid
crf.items.append(item)
elif type(itemDefinition) is dict:
itemDef = itemDefinition
if itemDef["@OID"] in itemOids:
crf = event.getCrf(
itemDef["@OpenClinica:FormOIDs"])
item = Item()
item.oid = itemDef["@OID"]
item.name = itemDef["@Name"]
item.dataType = itemDef["@DataType"]
item.description = itemDef["@Comment"]
gr = crf.findGroupForItem(item.oid)
item.itemGroupOid = gr.oid
crf.items.append(item)
results.append(event)
if thread:
thread.emit(QtCore.SIGNAL("finished(QVariant)"), results)
return None
else:
return results
def getStudyCasebookEvents(self, data, thread=None):
"""Get study casebook subject events
"""
if data:
ocBaseUrl = data[0]
studyOid = data[1]
subjectOid = data[2]
method = studyOid + "/" + subjectOid + "/*/*"
results = []
r = self._ocRequest(ocBaseUrl, method)
if r.status_code == 200:
if "ClinicalData" in r.json():
if "SubjectData" in r.json()["ClinicalData"]:
if "StudyEventData" in r.json()["ClinicalData"]["SubjectData"]:
eventData = r.json()["ClinicalData"]["SubjectData"]["StudyEventData"]
# Multiple events
if type(eventData) is list:
for ed in eventData:
event = Event()
event.eventDefinitionOID = ed["@StudyEventOID"]
event.status = ed["@OpenClinica:Status"]
dateString = ed["@OpenClinica:StartDate"]
format = ""
# Is it only date or datetime
if len(dateString) == 11:
format = "%d-%b-%Y"
elif len(dateString) == 20:
format = "%d-%b-%Y %H:%M:%S"
event.startDate = datetime.strptime(dateString, format)
event.studyEventRepeatKey = ed["@StudyEventRepeatKey"]
# Subject Age At Event is optional (because collect birth date is optional)
if "OpenClinica:SubjectAgeAtEvent" in ed:
event.subjectAgeAtEvent = ed["OpenClinica:SubjectAgeAtEvent"]
# Resulting eCRFs
if "FormData" in ed:
formData = ed["FormData"]
# Multiple forms
if type(formData) is list:
for frm in formData:
crf = Crf()
crf.oid = frm["@FormOID"]
crf.version = frm["@OpenClinica:Version"]
crf.status = frm["@OpenClinica:Status"]
event.addCrf(crf)
# Only one form in event
elif type(formData) is dict:
frm = formData
crf = Crf()
crf.oid = frm["@FormOID"]
crf.version = frm["@OpenClinica:Version"]
crf.status = frm["@OpenClinica:Status"]
event.addCrf(crf)
# + automatically schedule default version only (if it is not)
eventFormOids = []
eventDefinition = r.json()["Study"]["MetaDataVersion"]["StudyEventDef"]
if type(eventDefinition) is list:
for ed in eventDefinition:
formRef = ed["FormRef"]
if type(formRef) is list:
for fr in formRef:
eventFormOids.append(fr["@FormOID"])
elif type(formRef) is dict:
eventFormOids.append(formRef["@FormOID"])
elif type(eventDefinition) is dict:
ed = eventDefinition
formRef = ed["FormRef"]
if type(formRef) is list:
for fr in formRef:
eventFormOids.append(fr["@FormOID"])
elif type(formRef) is dict:
eventFormOids.append(formRef["@FormOID"])
formDefinition = r.json()["Study"]["MetaDataVersion"]["FormDef"]
if type(formDefinition) is list:
for fd in formDefinition:
if fd["@OID"] in eventFormOids:
if not event.hasScheduledCrf(fd["@OID"]):
if fd["OpenClinica:FormDetails"]["OpenClinica:PresentInEventDefinition"]["@IsDefaultVersion"] == "Yes":
event.addCrf(
Crf(fd["@OID"], fd["@Name"])
)
else:
if fd["OpenClinica:FormDetails"]["OpenClinica:PresentInEventDefinition"]["@IsDefaultVersion"] == "Yes":
crf = event.getCrf(fd["@OID"])
crf.name = fd["@Name"]
# Collect references to ItemGroups in any case
igRef = fd["ItemGroupRef"]
if type(igRef) is list:
for igr in igRef:
itemGroupOids.append(igr["@ItemGroupOID"])
elif type (igRef) is dict:
igr = igRef
itemGroupOids.append(igr["@ItemGroupOID"])
elif type(formDefinition) is dict:
fd = formDefinition
if fd["@OID"] in eventFormOids:
if not event.hasScheduledCrf(fd["@OID"]):
if fd["OpenClinica:FormDetails"]["OpenClinica:PresentInEventDefinition"]["@IsDefaultVersion"] == "Yes":
event.addCrf(
Crf(fd["@OID"], fd["@Name"])
)
else:
if fd["OpenClinica:FormDetails"]["OpenClinica:PresentInEventDefinition"]["@IsDefaultVersion"] == "Yes":
crf = event.getCrf(fd["@OID"])
crf.name = fd["@Name"]
# Collect references to ItemGroups in any case
igRef = fd["ItemGroupRef"]
if type(igRef) is list:
for igr in igRef:
itemGroupOids.append(igr["@ItemGroupOID"])
elif type (igRef) is dict:
igr = igRef
itemGroupOids.append(igr["@ItemGroupOID"])
# Discover items base on theri refOIDs
itemOids = []
itemGroupDefinition = r.json()["Study"]["MetaDataVersion"]["ItemGroupDef"]
if type(itemGroupDefinition) is list:
for igd in itemGroupDefinition:
if igd["@OID"] in itemGroupOids:
crf = event.getCrf(
igd["OpenClinica:ItemGroupDetails"]["OpenClinica:PresentInForm"]["@FormOID"]
)
group = ItemGroup()
group.oid = igd["@OID"]
group.name = igd["@Name"]
iRef = igd["ItemRef"]
if type(iRef) is list:
for ir in iRef:
item = Item()
item.oid = ir["@ItemOID"]
group.addItem(item)
itemOids.append(ir["@ItemOID"])
elif type(iRef) is dict:
ir = iRef
item = Item()
item.oid = ir["@ItemOID"]
group.addItem(item)
itemOids.append(ir["@ItemOID"])
crf.addItemGroup(group)
elif type(itemGroupDefinition) is dict:
igd = itemGroupDefinition
if igd["@OID"] in itemGroupOids:
crf = event.getCrf(
igd["OpenClinica:ItemGroupDetails"]["OpenClinica:PresentInForm"]["@FormOID"]
)
group = ItemGroup()
group.oid = igd["@OID"]
group.name = igd["@Name"]
iRef = igd["ItemRef"]
if type(iRef) is list:
for ir in iRef:
item = Item()
item.oid = ir["@ItemOID"]
group.addItem(item)
itemOids.append(ir["@ItemOID"])
elif type(iRef) is dict:
ir = iRef
item = Item()
item.oid = ir["@ItemOID"]
group.addItem(item)
itemOids.append(ir["@ItemOID"])
crf.addItemGroup(group)
# Setup items for CRF in event
itemDefinition = r.json()["Study"]["MetaDataVersion"]["ItemDef"]
if type(itemDefinition) is list:
for itemDef in itemDefinition:
if itemDef["@OID"] in itemOids:
crf = event.getCrf(itemDef["@OpenClinica:FormOIDs"])
item = Item()
item.oid = itemDef["@OID"]
item.name = itemDef["@Name"]
item.dataType = itemDef["@DataType"]
item.description = itemDef["@Comment"]
gr = crf.findGroupForItem(item.oid)
item.itemGroupOid = gr.oid
crf.items.append(item)
elif type(itemDefinition) is dict:
itemDef = itemDefinition
if itemDef["@OID"] in itemOids:
crf = event.getCrf(itemDef["@OpenClinica:FormOIDs"])
item = Item()
item.oid = itemDef["@OID"]
item.name = itemDef["@Name"]
item.dataType = itemDef["@DataType"]
item.description = itemDef["@Comment"]
gr = crf.findGroupForItem(item.oid)
item.itemGroupOid = gr.oid
crf.items.append(item)
results.append(event)
# Only one event reported
elif type(eventData) is dict:
ed = eventData
event = Event()
event.eventDefinitionOID = ed["@StudyEventOID"]
event.status = ed["@OpenClinica:Status"]
dateString = ed["@OpenClinica:StartDate"]
format = ""
# Is it only date or datetime
if len(dateString) == 11:
format = "%d-%b-%Y"
elif len(dateString) == 20:
format = "%d-%b-%Y %H:%M:%S"
event.startDate = datetime.strptime(dateString, format)
event.studyEventRepeatKey = ed["@StudyEventRepeatKey"]
# Subject Age At Event is optional (because collect birth date is optional)
if "OpenClinica:SubjectAgeAtEvent" in ed:
event.subjectAgeAtEvent = ed["OpenClinica:SubjectAgeAtEvent"]
# Resulting eCRFs
if "FormData" in ed:
formData = ed["FormData"]
# Multiple forms
if type(formData) is list:
for frm in formData:
crf = Crf()
crf.oid = frm["@FormOID"]
crf.version = frm["@OpenClinica:Version"]
crf.status = frm["@OpenClinica:Status"]
event.addCrf(crf)
# Only one form in event
elif type(formData) is dict:
frm = formData
crf = Crf()
crf.oid = frm["@FormOID"]
crf.version = frm["@OpenClinica:Version"]
crf.status = frm["@OpenClinica:Status"]
event.addCrf(crf)
# + automatically default version (if it is not)
eventFormOids = []
eventDefinition = r.json()["Study"]["MetaDataVersion"]["StudyEventDef"]
if type(eventDefinition) is list:
for ed in eventDefinition:
formRef = ed["FormRef"]
if type(formRef) is list:
for fr in formRef:
eventFormOids.append(fr["@FormOID"])
elif type(formRef) is dict:
eventFormOids.append(formRef["@FormOID"])
elif type(eventDefinition) is dict:
ed = eventDefinition
formRef = ed["FormRef"]
if type(formRef) is list:
for fr in formRef:
eventFormOids.append(fr["@FormOID"])
elif type(formRef) is dict:
eventFormOids.append(formRef["@FormOID"])
itemGroupOids = []
formDefinition = r.json()["Study"]["MetaDataVersion"]["FormDef"]
if type(formDefinition) is list:
for fd in formDefinition:
if fd["@OID"] in eventFormOids:
if not event.hasScheduledCrf(fd["@OID"]):
if fd["OpenClinica:FormDetails"]["OpenClinica:PresentInEventDefinition"]["@IsDefaultVersion"] == "Yes":
event.addCrf(
Crf(fd["@OID"], fd["@Name"])
)
else:
if fd["OpenClinica:FormDetails"]["OpenClinica:PresentInEventDefinition"]["@IsDefaultVersion"] == "Yes":
crf = event.getCrf(fd["@OID"])
crf.name = fd["@Name"]
# Collect references to ItemGroups in any case
igRef = fd["ItemGroupRef"]
if type(igRef) is list:
for igr in igRef:
itemGroupOids.append(igr["@ItemGroupOID"])
elif type (igRef) is dict:
igr = igRef
itemGroupOids.append(igr["@ItemGroupOID"])
elif type(formDefinition) is dict:
fd = formDefinition
if fd["@OID"] in eventFormOids:
if not event.hasScheduledCrf(fd["@OID"]):
if fd["OpenClinica:FormDetails"]["OpenClinica:PresentInEventDefinition"]["@IsDefaultVersion"] == "Yes":
event.addCrf(
Crf(fd["@OID"], fd["@Name"])
)
else:
if fd["OpenClinica:FormDetails"]["OpenClinica:PresentInEventDefinition"]["@IsDefaultVersion"] == "Yes":
crf = event.getCrf(fd["@OID"])
crf.name = fd["@Name"]
# Collect references to ItemGroups in any case
igRef = fd["ItemGroupRef"]
if type(igRef) is list:
for igr in igRef:
itemGroupOids.append(igr["@ItemGroupOID"])
elif type (igRef) is dict:
igr = igRef
itemGroupOids.append(igr["@ItemGroupOID"])
# Discover items base on theri refOIDs
itemOids = []
itemGroupDefinition = r.json()["Study"]["MetaDataVersion"]["ItemGroupDef"]
if type(itemGroupDefinition) is list:
for igd in itemGroupDefinition:
if igd["@OID"] in itemGroupOids:
crf = event.getCrf(
igd["OpenClinica:ItemGroupDetails"]["OpenClinica:PresentInForm"]["@FormOID"]
)
group = ItemGroup()
group.oid = igd["@OID"]
group.name = igd["@Name"]
iRef = igd["ItemRef"]
if type(iRef) is list:
for ir in iRef:
item = Item()
item.oid = ir["@ItemOID"]
group.addItem(item)
itemOids.append(ir["@ItemOID"])
elif type(iRef) is dict:
ir = iRef
item = Item()
item.oid = ir["@ItemOID"]
group.addItem(item)
itemOids.append(ir["@ItemOID"])
crf.addItemGroup(group)
elif type(itemGroupDefinition) is dict:
igd = itemGroupDefinition
if igd["@OID"] in itemGroupOids:
crf = event.getCrf(
igd["OpenClinica:ItemGroupDetails"]["OpenClinica:PresentInForm"]["@FormOID"]
)
group = ItemGroup()
group.oid = igd["@OID"]
group.name = igd["@Name"]
iRef = igd["ItemRef"]
if type(iRef) is list:
for ir in iRef:
item = Item()
item.oid = ir["@ItemOID"]
group.addItem(item)
itemOids.append(ir["@ItemOID"])
elif type(iRef) is dict:
ir = iRef
item = Item()
item.oid = ir["@ItemOID"]
group.addItem(item)
itemOids.append(ir["@ItemOID"])
crf.addItemGroup(group)
# Setup items for CRF in event
itemDefinition = r.json()["Study"]["MetaDataVersion"]["ItemDef"]
if type(itemDefinition) is list:
for itemDef in itemDefinition:
if itemDef["@OID"] in itemOids:
crf = event.getCrf(itemDef["@OpenClinica:FormOIDs"])
item = Item()
item.oid = itemDef["@OID"]
item.name = itemDef["@Name"]
item.dataType = itemDef["@DataType"]
item.description = itemDef["@Comment"]
gr = crf.findGroupForItem(item.oid)
item.itemGroupOid = gr.oid
crf.items.append(item)
elif type(itemDefinition) is dict:
itemDef = itemDefinition
if itemDef["@OID"] in itemOids:
crf = event.getCrf(itemDef["@OpenClinica:FormOIDs"])
item = Item()
item.oid = itemDef["@OID"]
item.name = itemDef["@Name"]
item.dataType = itemDef["@DataType"]
item.description = itemDef["@Comment"]
gr = crf.findGroupForItem(item.oid)
item.itemGroupOid = gr.oid
crf.items.append(item)
results.append(event)
if thread:
thread.emit(QtCore.SIGNAL("finished(QVariant)"), results)
return None
else:
return results
