def getStudyCasebookSubject(self, ocBaseUrl, studyOid, subjectId):
"""Get casebook of one subject
SubjectId can be StudySubjectOID (SS_) or StudySubjectID (in new version of OC)
"""
method = studyOid + "/" + subjectId + "/*/*"
results = None
r = self._ocRequest(ocBaseUrl, method)
if r.status_code == 200:
if "ClinicalData" in r.json():
subjectData = r.json()["ClinicalData"]["SubjectData"]
# Exactly one subject should be reported
if type(subjectData) is dict:
subj = subjectData
subject = Subject()
subject.oid = subj["@SubjectKey"]
subject.studySubjectId = subj[
"@OpenClinica:StudySubjectID"]
if "@OpenClinica:UniqueIdentifier" in subj:
subject.uniqueIdentifier = subj[
"@OpenClinica:UniqueIdentifier"]
results.append(subject)
return results
def getStudyCasebookSubjects(self, data, thread=None):
"""Get study casebook of all subjects
"""
if data:
ocBaseUrl = data[0]
studyOid = data[1]
method = studyOid + "/*/*/*"
results = []
r = self._ocRequest(ocBaseUrl, method)
if r.status_code == 200:
if "ClinicalData" in r.json():
subjectData = r.json()["ClinicalData"]["SubjectData"]
# Multiple subjects
if type(subjectData) is list:
for subj in subjectData:
subject = Subject()
subject.oid = subj["@SubjectKey"]
subject.studySubjectId = subj[
"@OpenClinica:StudySubjectID"]
if "@OpenClinica:UniqueIdentifier" in subj:
subject.uniqueIdentifier = subj[
"@OpenClinica:UniqueIdentifier"]
results.append(subject)
# Only one subject reported
elif type(subjectData) is dict:
subj = subjectData
subject = Subject()
subject.oid = subj["@SubjectKey"]
subject.studySubjectId = subj[
"@OpenClinica:StudySubjectID"]
if "@OpenClinica:UniqueIdentifier" in subj:
subject.uniqueIdentifier = subj[
"@OpenClinica:UniqueIdentifier"]
results.append(subject)
if thread:
thread.emit(QtCore.SIGNAL("finished(QVariant)"), results)
return None
else:
return results
def getStudyCasebookSubject(self, ocBaseUrl, studyOid, subjectId):
"""Get casebook of one subject
SubjectId can be StudySubjectOID (SS_) or StudySubjectID (in new version of OC)
"""
method = studyOid + "/" + subjectId + "/*/*"
results = None
r = self._ocRequest(ocBaseUrl, method)
if r.status_code == 200:
if "ClinicalData" in r.json():
subjectData = r.json()["ClinicalData"]["SubjectData"]
# Exactly one subject should be reported
if type(subjectData) is dict:
subj = subjectData
subject = Subject()
subject.oid = subj["@SubjectKey"]
subject.studySubjectId = subj["@OpenClinica:StudySubjectID"]
if "@OpenClinica:UniqueIdentifier" in subj:
subject.uniqueIdentifier = subj["@OpenClinica:UniqueIdentifier"]
results.append(subject)
return results
def __init__(self, parent=None):
"""Default constructor
"""
QtGui.QDialog.__init__(self, parent)
#------------------------------------------------------
#-------------------- GUI -----------------------------
self.width = 300
self.height = 300
self.setFixedSize(self.width, self.height)
self.setWindowTitle("Create a new study subject")
# Dialog layout root
rootLayout = QtGui.QVBoxLayout(self)
# Metadata field for mapping UI
rootLayout.addWidget(self.__setupDialogFieldsUI())
# Dialog buttons
btnLayout = QtGui.QGridLayout()
btnLayout.setSpacing(10)
rootLayout.addLayout(btnLayout)
self.btnOk = QtGui.QPushButton("Create")
self.btnCancel = QtGui.QPushButton("Cancel")
btnLayout.addWidget(self.btnOk, 1, 0)
btnLayout.addWidget(self.btnCancel, 1, 1)
#----------------------------------------------------------
#----------------- Event handlers -------------------------
self.btnOk.clicked.connect(self.handleOk)
self.btnCancel.clicked.connect(self.handleCancel)
#-----------------------------------------------------------
#------------------ View Models ----------------------------
self.newStudySubject = StudySubject()
self.newStudySubject.subject = Subject()
# Based on study subject id generation
# if manual than specify
# even if automatic it has to be empty string
self.newStudySubject.label = ""
# Based on metadata (can be optional)
self.newStudySubject.subject.uniqueIdentifier = ""
def __init__(self, parent=None):
"""
"""
QtGui.QDialog.__init__(self, parent)
#------------------------------------------------------
#-------------------- GUI -----------------------------
self.width = 640
self.height = 500
self.setFixedSize(self.width, self.height)
self.setWindowTitle("Create study subject dialog")
# Dialog layout root
rootLayout = QtGui.QVBoxLayout(self)
# Metadata field for mapping UI
rootLayout.addWidget(self.__setupDialogFieldsUI())
# Dialog buttons
btnLayout = QtGui.QGridLayout()
btnLayout.setSpacing(10)
rootLayout.addLayout(btnLayout)
self.btnOk = QtGui.QPushButton("Create")
self.btnCancel = QtGui.QPushButton("Cancel")
btnLayout.addWidget(self.btnOk, 1, 0)
btnLayout.addWidget(self.btnCancel, 1, 1)
#----------------------------------------------------------
#----------------- Event handlers -------------------------
self.btnOk.clicked.connect(self.handleOk)
self.btnCancel.clicked.connect(self.handleCancel)
#-----------------------------------------------------------
#------------------ View Models ----------------------------
self.newStudySubject = StudySubject()
self.newStudySubject.subject = Subject()
#-----------------------------------------------------------
#------------------ Services ----------------------------
self.svcPseudonymisation = None
def getStudyCasebookSubjects(self, data, thread=None):
"""Get study casebook subjects
"""
if data:
ocBaseUrl = data[0]
studyOid = data[1]
method = studyOid + "/*/*/*"
results = []
r = self._ocRequest(ocBaseUrl, method)
if r.status_code == 200:
if "ClinicalData" in r.json():
subjectData = r.json()["ClinicalData"]["SubjectData"]
# Multiple subjects
if type(subjectData) is list:
for subj in subjectData:
subject = Subject()
subject.oid = subj["@SubjectKey"]
subject.studySubjectId = subj["@OpenClinica:StudySubjectID"]
if "@OpenClinica:UniqueIdentifier" in subj:
subject.uniqueIdentifier = subj["@OpenClinica:UniqueIdentifier"]
results.append(subject)
# Only one subject reported
elif type(subjectData) is dict:
subj = subjectData
subject = Subject()
subject.oid = subj["@SubjectKey"]
subject.studySubjectId = subj["@OpenClinica:StudySubjectID"]
if "@OpenClinica:UniqueIdentifier" in subj:
subject.uniqueIdentifier = subj["@OpenClinica:UniqueIdentifier"]
results.append(subject)
if thread:
thread.emit(QtCore.SIGNAL("finished(QVariant)"), results)
return None
else:
return results
successfull = False
try:
successfull, studies = ocWebServices.listAllStudies()
except:
print "Cannot communicate with the server, no network connection or the server is not running."
if successfull:
for study in studies:
selectedStudy = study
sucessfull, studyMetadata = ocWebServices.getStudyMetadata(
selectedStudy)
break
newStudySubject = StudySubject()
newStudySubject.subject = Subject()
# Based on study subject id generation
# if manual than specify
# even if automatic it has to be empty string
newStudySubject.label = ""
# Based on metadata (can be optional)
newStudySubject.subject.uniqueIdentifier = ""
# SecondaryId, BUG OC ignores secondary ID
#newStudySubject.secondaryId = ""
# Should depend on study configuration, BUG OC always requires gender
newStudySubject.subject.gender = "f"
#newStudySubject.subject.gender = "f"
def listAllByStudySite(self, study, studySite, metadata=None):
"""List all study subject assinged in specific study and site
"""
result = ""
params = SimpleXMLElement("""<?xml version="1.0" encoding="UTF-8"?>
<listAllByStudyRequest>
<bean:studyRef xmlns:bean="http://openclinica.org/ws/beans">
<bean:identifier>""" + studySite.identifier + """</bean:identifier>
</bean:studyRef>
</listAllByStudyRequest>""")
response = self.client.call('listAllByStudyRequest', params)
documentTree = ET.ElementTree((ET.fromstring(str(response.as_xml()))))
studySubjects = []
# Locate Study subject data in XML file via XPath
for studySubject in documentTree.iterfind('.//ns2:studySubject',
namespaces=nsmaps):
label = ""
secondaryLabel = ""
enrollmentDate = ""
uniqueIdentifier = ""
gender = ""
# Optional
#dateOfBirth = str(studySubject.subject.dateOfBirth)
events = []
for element in studySubject:
if (str(element.tag)
).strip() == "{http://openclinica.org/ws/beans}label":
label = element.text
elif (str(element.tag)).strip(
) == "{http://openclinica.org/ws/beans}secondaryLabel":
secondaryLabel = element.text
elif (str(element.tag)).strip(
) == "{http://openclinica.org/ws/beans}enrollmentDate":
enrollmentDate = element.text
if (str(element.tag)
).strip() == "{http://openclinica.org/ws/beans}subject":
for subjectElement in element:
if (str(subjectElement.tag)).strip(
) == "{http://openclinica.org/ws/beans}uniqueIdentifier":
uniqueIdentifier = subjectElement.text
elif (str(subjectElement.tag)).strip(
) == "{http://openclinica.org/ws/beans}gender":
gender = subjectElement.text
if (str(element.tag)
).strip() == "{http://openclinica.org/ws/beans}events":
for event in element:
eventDefinitionOID = ""
location = ""
startDate = ""
startTime = ""
endDate = ""
endTime = ""
dateString = ""
timeString = ""
for eventElement in event:
if (str(eventElement.tag)).strip(
) == "{http://openclinica.org/ws/beans}eventDefinitionOID":
eventDefinitionOID = eventElement.text
elif (str(eventElement.tag)).strip(
) == "{http://openclinica.org/ws/beans}location":
location = eventElement.text
elif (str(eventElement.tag)).strip(
) == "{http://openclinica.org/ws/beans}startDate":
dateString = eventElement.text
elif (str(eventElement.tag)).strip(
) == "{http://openclinica.org/ws/beans}startTime":
timeString = eventElement.text
# Deal with both date an datetimes
if timeString == "":
format = "%Y-%m-%d"
startDate = datetime.strptime(dateString, format)
else:
# Carefull it uses 12/24 hour format
format12 = "%Y-%m-%d %I:%M:%S"
format24 = "%Y-%m-%d %H:%M:%S"
try:
startDate = datetime.strptime(
dateString + " " + timeString, format12)
except ValueError:
startDate = datetime.strptime(
dateString + " " + timeString, format24)
obtainedEvent = Event(eventDefinitionOID, startDate)
events.append(obtainedEvent)
obtainedSubject = Subject(uniqueIdentifier, gender)
obtainedStudySubject = StudySubject(label, secondaryLabel,
enrollmentDate,
obtainedSubject, events)
studySubjects.append(obtainedStudySubject)
# Enhance with information from metadata
metadataEvents = self.loadEventsFromMetadata(metadata)
for ss in studySubjects:
for e in ss.events:
for me in metadataEvents:
if e.eventDefinitionOID == me.oid:
e.name = me.name
e.description = me.description
e.isRepeating = me.repeating
e.eventType = me.type
e.category = me.category
e.mandatory = me.mandatory
e.orderNumber = me.orderNumber
result = str(response.result)
return studySubjects