def prepareServices(self):
"""Prepare services for this module
"""
# HTTP connection to RadPlanBio server (Database)
self.svcHttp = HttpConnectionService(ConfigDetails().ocHost, ConfigDetails().ocPort, UserDetails())
if ConfigDetails().proxyEnabled:
self.svcHttp.setupProxy(ConfigDetails().proxyHost, ConfigDetails().proxyPort, ConfigDetails().noProxy)
if ConfigDetails().proxyAuthEnabled:
self.svcHttp.setupProxyAuth(ConfigDetails().proxyAuthLogin, ConfigDetails().proxyAuthPassword)
# Create connection artefact to users main OpenClinica SOAP
self.ocConnectInfo = OCConnectInfo(ConfigDetails().ocWsHost, OCUserDetails().username)
self.ocConnectInfo.setPasswordHash(OCUserDetails().passwordHash)
if ConfigDetails().proxyEnabled:
self.ocWebServices = OCWebServices(
self.ocConnectInfo,
ConfigDetails().proxyHost,
ConfigDetails().proxyPort,
ConfigDetails().noProxy,
ConfigDetails().proxyAuthLogin,
ConfigDetails().proxyAuthPassword,
)
else:
self.ocWebServices = OCWebServices(self.ocConnectInfo)
# ODM XML metadata processing
self.svcOdm = OdmFileDataService()
def handleLogin(self):
"""Send authenticate user message to site server
"""
username = str(self.txtUsername.text())
password = str(self.txtPassword.text())
passwordHash = hashlib.sha1(password).hexdigest()
# Create connection artefact to users main OpenClinica SOAP
ocConnectInfo = OCConnectInfo(ConfigDetails().ocWsHost, username)
ocConnectInfo.setPasswordHash(passwordHash)
if ConfigDetails().proxyEnabled:
ocWebServices = OCWebServices(ocConnectInfo,
ConfigDetails().proxyHost,
ConfigDetails().proxyPort,
ConfigDetails().noProxy,
ConfigDetails().proxyAuthLogin,
ConfigDetails().proxyAuthPassword)
else:
ocWebServices = OCWebServices(ocConnectInfo)
successfull = False
try:
successfull, studies = ocWebServices.listAllStudies()
except:
QtGui.QMessageBox.warning(
self, "Error",
"Cannot communicate with the server, no network connection or the server is not running."
)
if (successfull):
OCUserDetails().username = username
OCUserDetails().passwordHash = passwordHash
OCUserDetails().connected = True
UserDetails().username = username
UserDetails().clearpass = password
UserDetails().password = passwordHash
self.accept()
else:
QtGui.QMessageBox.warning(self, 'Error',
'Wrong username or password.')
def handleLogin(self):
"""Send authenticate user message to site server
"""
username = str(self.txtUsername.text())
password = str(self.txtPassword.text())
passwordHash = hashlib.sha1(password).hexdigest()
# Create connection artefact to users main OpenClinica SOAP
ocConnectInfo = OCConnectInfo(ConfigDetails().ocWsHost, username)
ocConnectInfo.setPasswordHash(passwordHash)
if ConfigDetails().proxyEnabled:
ocWebServices = OCWebServices(
ocConnectInfo,
ConfigDetails().proxyHost,
ConfigDetails().proxyPort,
ConfigDetails().noProxy,
ConfigDetails().proxyAuthLogin,
ConfigDetails().proxyAuthPassword
)
else:
ocWebServices = OCWebServices(ocConnectInfo)
successfull = False
try:
successfull, studies = ocWebServices.listAllStudies()
except:
QtGui.QMessageBox.warning(self, "Error", "Cannot communicate with the server, no network connection or the server is not running.")
if (successfull):
OCUserDetails().username = username
OCUserDetails().passwordHash = passwordHash
OCUserDetails().connected = True
UserDetails().username = username
UserDetails().clearpass = password
UserDetails().password = passwordHash
self.accept()
else:
QtGui.QMessageBox.warning(self, 'Error', 'Wrong username or password.')
def prepareServices(self):
"""Prepare services for this module
"""
# HTTP connection to RadPlanBio server (Database)
self.svcHttp = HttpConnectionService(ConfigDetails().ocHost, ConfigDetails().ocPort, UserDetails())
if ConfigDetails().proxyEnabled:
self.svcHttp.setupProxy(ConfigDetails().proxyHost, ConfigDetails().proxyPort, ConfigDetails().noProxy)
if ConfigDetails().proxyAuthEnabled:
self.svcHttp.setupProxyAuth(ConfigDetails().proxyAuthLogin, ConfigDetails().proxyAuthPassword)
# Create connection artefact to users main OpenClinica SOAP
self.ocConnectInfo = OCConnectInfo(ConfigDetails().ocWsHost, OCUserDetails().username)
self.ocConnectInfo.setPasswordHash(OCUserDetails().passwordHash)
if ConfigDetails().proxyEnabled:
self.ocWebServices = OCWebServices(self.ocConnectInfo, ConfigDetails().proxyHost, ConfigDetails().proxyPort, ConfigDetails().noProxy, ConfigDetails().proxyAuthLogin, ConfigDetails().proxyAuthPassword)
else:
self.ocWebServices = OCWebServices(self.ocConnectInfo)
# ODM XML metadata processing
self.svcOdm = OdmFileDataService()
# Domain
from domain.StudySubject import StudySubject
from domain.Subject import Subject
ocWsHost = "http://skripcak.net:8080/OpenClinica-ws"
password = "******"
OCUserDetails().username = "******"
OCUserDetails().connected = False
# Create connection artefact to users main OpenClinica SOAP
ocConnectInfo = OCConnectInfo(ocWsHost, OCUserDetails().username)
ocConnectInfo.setPassword(password)
# Initialise SOAP services
ocWebServices = OCWebServices(ocConnectInfo)
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()
ocWsHost = "http://skripcak.net:8080/OpenClinica-ws"
password = "******"
OCUserDetails().username = "******"
OCUserDetails().connected = False
# Create connection artefact to users main OpenClinica SOAP
ocConnectInfo = OCConnectInfo(
ocWsHost,
OCUserDetails().username
)
ocConnectInfo.setPassword(password)
# Initialise SOAP services
# Debug lvls ... trace=logging.INFO, trace=logging.DEBUG in OCWebServices constructor
ocWebServices = OCWebServices(ocConnectInfo)
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
break
ConfigDetails().ocHost = "http://skripcak.net:8080/OpenClinica"
ConfigDetails().ocPort = "80"
ocWsHost = "http://skripcak.net:8080/OpenClinica-ws"
password = "******"
OCUserDetails().username = "******"
OCUserDetails().connected = False
# Create connection artefact to users main OpenClinica SOAP
ocConnectInfo = OCConnectInfo(
ocWsHost,
OCUserDetails().username
)
ocConnectInfo.setPassword(password)
# Initialise SOAP services
ocWebServices = OCWebServices(ocConnectInfo)
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
# Load subject for whole study or only site if it is multicentre study
if selectedStudy and selectedStudy.isMulticentre:
# Services
from soap.OCConnectInfo import OCConnectInfo
from soap.OCWebServices import OCWebServices
ocWsHost = "http://skripcak.net:8080/OpenClinica-ws"
password = "******"
OCUserDetails().username = "******"
OCUserDetails().connected = False
# Create connection artefact to users main OpenClinica SOAP
ocConnectInfo = OCConnectInfo(ocWsHost, OCUserDetails().username)
ocConnectInfo.setPassword(password)
# Initialise SOAP services
ocWebServices = OCWebServices(ocConnectInfo)
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
# Load subject for whole study or only site if it is multicentre study
class OcModule(QWidget, OcModuleUI):
"""OC data module
"""
def __init__(self, parent=None):
"""Default Constructor
"""
# Setup GUI
QWidget.__init__(self, parent)
self.parent = parent
self.setupUi(self)
# Hide summary of XML for importing data to OC (for user not necessary)
self.lblSummary.hide()
# Setup logger - use config file
self._logger = logging.getLogger(__name__)
logging.config.fileConfig("logging.ini", disable_existing_loggers=False)
# List of worker threads
self._threadPool = []
# Prepares services and main data for this ViewModel
self.prepareServices()
# Initialize data structures for UI
self._studies = []
self._studySubjects = []
self.reloadData()
# Finish UI setup
self.lblOcConnection.setText("[" + OCUserDetails().username + "] " + ConfigDetails().ocHost)
# Register handlers
self.btnReloadStudySubjects.clicked.connect(self.btnReloadStudySubjectsClicked)
self.btnNewStudySubject.clicked.connect(self.btnNewStudySubjectClicked)
self.btnNewEvent.clicked.connect(self.btnNewEventClicked)
self.btnUpload.clicked.connect(self.btnImportClicked)
self.cmbStudy.currentIndexChanged["QString"].connect(self.cmbStudyChanged)
self.destroyed.connect(self.handleDestroyed)
## ## ### ## ## ######## ## ######## ######## ######
## ## ## ## ### ## ## ## ## ## ## ## ## ##
## ## ## ## #### ## ## ## ## ## ## ## ##
######### ## ## ## ## ## ## ## ## ###### ######## ######
## ## ######### ## #### ## ## ## ## ## ## ##
## ## ## ## ## ### ## ## ## ## ## ## ## ##
## ## ## ## ## ## ######## ######## ######## ## ## ######
def cmbStudyChanged(self, text):
"""Executed when the concrete study is selected from studies combobox
"""
# Reset table views
self.tvStudies.setModel(None)
self.tvStudySubjects.setModel(None)
self.tvStudyEvents.setModel(None)
self.tvCrfs.setModel(None)
self.tvItems.setModel(None)
self.textBrowserProgress.clear()
# Set selected study and reload sites
self._selectedStudy = first.first(
study for study in self._studies if study.name.encode("utf-8") == text.toUtf8()
)
# Reload study sites
if self._selectedStudy:
self._logger.debug("Selected study: %s" % (self._selectedStudy.name))
self.reloadStudySites()
def tblStudyItemChanged(self, current, previous):
"""Event handler which is triggered when selectedStudy change
When the study is selected I have to clean all the other data elements
Which depends on study. It means: StudySubjects, StudyEventDefinitions, StudyEventCRFs
"""
# Clean the model before loading the new one
self.tvStudySubjects.setModel(None)
self.tvStudyEvents.setModel(None)
self.tvCrfs.setModel(None)
self.tvItems.setModel(None)
self.textBrowserProgress.clear()
# Take the first column of selected row from table view
index = self.studyProxyModel.index(current.row(), 0)
# Multicentric
if len(self._selectedStudy.sites) > 0:
self._selectedStudySite = first.first(
studySite
for studySite in self._selectedStudy.sites
if studySite.identifier.encode("utf-8") == index.data().toPyObject().toUtf8()
)
# Get the study metadata
self.reloadStudyMetadata()
def btnReloadStudySubjectsClicked(self):
"""Reload study subjects button clicked
"""
# Reload
self.reloadSubjects()
def btnNewStudySubjectClicked(self):
"""New study subject button clicked
"""
if self._selectedStudy:
# Initialize dialog and bind data to UI
dialog = NewSubjectDialog(self)
dialog.setData(self._selectedStudy, self._selectedStudySite)
# When ok commit session transaction
if dialog.exec_() == QtGui.QDialog.Accepted:
try:
newStudySubject = dialog.newStudySubject
self.ocWebServices.createStudySubject(newStudySubject, self._selectedStudy)
except:
QtGui.QMessageBox.warning(self, "Error", "OC study subject not created.")
# Reload
self.reloadSubjects()
def tblStudySubjectItemChanged(self, current, previous):
"""Event handler which is triggered when selectedStudySubject change
"""
self.tvStudyEvents.setModel(None)
self.tvCrfs.setModel(None)
self.tvItems.setModel(None)
self.textBrowserProgress.clear()
# Take the second column (StudySubjectID) of selected row from table view
column = 1
index = self.studySubjectProxyModel.index(current.row(), column)
print index.data().toPyObject()
if index.data().toPyObject():
self._selectedStudySubject = first.first(
subject
for subject in self._studySubjects
if subject.label.encode("utf-8") == index.data().toPyObject().toUtf8()
)
if self._selectedStudySubject:
# Load scheduled events for selected subject
self.reloadEvents()
def btnNewEventClicked(self):
"""Schedule new study event button clicked
"""
events = self.ocWebServices.listAllStydyEventDefinitionsByStudy(self._selectedStudy)
# Initialize dialog and bind data to UI
dialog = NewEventDialog(self)
dialog.setData(self._selectedStudy, self._selectedStudySite, self._selectedStudySubject, events)
# When ok commit session transaction
if dialog.exec_() == QtGui.QDialog.Accepted:
newEvent = dialog.selectedEvent
self.ocWebServices.scheduleStudyEvent(self._selectedStudy, self._selectedStudySubject, newEvent)
# Reload
temp = self._selectedStudySubject
self.reloadSubjects()
self._selectedStudySubject = temp
# self.reloadEvents()
def tblStudyEventItemChanged(self, current, previous):
"""Event handler which is triggered when selectedStudyEventDefintion change
When the studyEvent is selected. Create a model for the event CRFs view.
"""
self.textBrowserProgress.clear()
# Selected studyEventDefinitions
# Take the first column of selected row from table view
# index = self.studyEventProxyModel.index(current.row(), 0);
# self._selectedStudyEvent = first.first(e for e in self._selectedStudySubject.events if e.name.encode("utf-8") == index.data().toPyObject().toUtf8())
self._selectedStudyEvent = self._selectedStudySubject.events[current.row()]
self.reloadCrfs()
def tblEventCrfItemChanged(self, current, previous):
"""
"""
self.tvItems.setModel(None)
self.textBrowserProgress.clear()
# Take the second column (OID) of selected row from table view
column = 1
index = self.crfProxyModel.index(current.row(), column)
if index.data().toPyObject():
self._selectedCrf = first.first(
crf
for crf in self._selectedStudyEvent.forms
if crf.oid.encode("utf-8") == index.data().toPyObject().toUtf8()
)
self.reloadItems()
def tblCrfFieldItemChanged(self, current, previous):
"""
"""
self.textBrowserProgress.clear()
# Take the second column (OID) of selected row from table view
column = 1
index = self.itemProxyModel.index(current.row(), column)
if index.data().toPyObject():
self._selectedItem = first.first(
i for i in self._selectedCrf.items if i.oid.encode("utf-8") == index.data().toPyObject().toUtf8()
)
# Show the selected import target
msg = "Selected import target: "
msg += self._selectedStudy.name + "/"
if len(self._selectedStudy.sites) > 0:
msg += self._selectedStudySite.name + "/"
msg += "StudySubjectID: " + self._selectedStudySubject.label + "/"
if self._selectedStudyEvent.isRepeating:
msg += self._selectedStudyEvent.name + " [" + self._selectedStudyEvent.studyEventRepeatKey + "]/"
else:
msg += self._selectedStudyEvent.name + "/"
msg += self._selectedCrf.name + "/"
msg += self._selectedItem.name
self._logger.debug(msg)
self.textBrowserProgress.append(msg)
def btnImportClicked(self):
"""Upload button pressed (DICOM upload workflow started)
"""
QtGui.qApp.processEvents(QtCore.QEventLoop.AllEvents, 1000)
self.progressBar.setRange(0, 100)
self.progressBar.setValue(0)
# Make textBrowser visible
self.textBrowserProgress.setVisible(True)
self.textBrowserProgress.append("Wait please:")
# Disable upload button for now but better is to desable whole UI
self.btnUpload.setEnabled(False)
self.performDataImport()
def handleTaskUpdated(self, data):
"""Move progress bar precento by precento
"""
if type(data) is list:
if data[0]:
processed = data[0]
if data[1]:
size = data[1]
progress = processed * 100 / size
self.window().statusBar.showMessage("Processed files: [" + str(processed) + "/" + str(size) + "]")
self.progressBar.setValue(progress)
def handleDestroyed(self):
"""Kill runnign threads
"""
self._logger.debug("Destroying module")
for thread in self._threadPool:
thread.terminate()
thread.wait()
self._logger.debug("Thread killed.")
def getStudyOid(self):
"""Return study or site OID depending on mono/multi centre configuration
"""
# Multicentre
if len(self._selectedStudy.sites) > 0:
return self._selectedStudySite.oid
# Monocentre
else:
return self._selectedStudy.oid
###### ####### ## ## ## ## ### ## ## ######## ######
## ## ## ## ### ### ### ### ## ## ### ## ## ## ## ##
## ## ## #### #### #### #### ## ## #### ## ## ## ##
## ## ## ## ### ## ## ### ## ## ## ## ## ## ## ## ######
## ## ## ## ## ## ## ######### ## #### ## ## ##
## ## ## ## ## ## ## ## ## ## ## ### ## ## ## ##
###### ####### ## ## ## ## ## ## ## ## ######## ######
def prepareServices(self):
"""Prepare services for this module
"""
# HTTP connection to RadPlanBio server (Database)
self.svcHttp = HttpConnectionService(ConfigDetails().ocHost, ConfigDetails().ocPort, UserDetails())
if ConfigDetails().proxyEnabled:
self.svcHttp.setupProxy(ConfigDetails().proxyHost, ConfigDetails().proxyPort, ConfigDetails().noProxy)
if ConfigDetails().proxyAuthEnabled:
self.svcHttp.setupProxyAuth(ConfigDetails().proxyAuthLogin, ConfigDetails().proxyAuthPassword)
# Create connection artefact to users main OpenClinica SOAP
self.ocConnectInfo = OCConnectInfo(ConfigDetails().ocWsHost, OCUserDetails().username)
self.ocConnectInfo.setPasswordHash(OCUserDetails().passwordHash)
if ConfigDetails().proxyEnabled:
self.ocWebServices = OCWebServices(
self.ocConnectInfo,
ConfigDetails().proxyHost,
ConfigDetails().proxyPort,
ConfigDetails().noProxy,
ConfigDetails().proxyAuthLogin,
ConfigDetails().proxyAuthPassword,
)
else:
self.ocWebServices = OCWebServices(self.ocConnectInfo)
# ODM XML metadata processing
self.svcOdm = OdmFileDataService()
def reloadData(self):
"""Initialization of data for UI
"""
# OpenClinica study
del self._studies[:]
self._studies = []
self._selectedStudy = None
self._studyMetadata = None
# OpenClinica study site
self._selectedStudySite = None
# OpenClinica study subjects
del self._studySubjects[:]
self._studySubjects = []
self._selectedStudySubject = None
# Selected sheduled study event for subject
self._selectedStudyEvent = None
# Selected event CRF
self._selectedCrf = None
# Selected item
self._selectedItem = None
# Load studies
self.reloadStudies()
def reloadStudies(self):
"""Reload OpenClinica studies (in working thread)
"""
# Setup loading UI
self.window().statusBar.showMessage("Loading list of clinical studies...")
self.window().enableIndefiniteProgess()
self.tabWidget.setEnabled(False)
# Create data loading thread
self._threadPool.append(WorkerThread(self.ocWebServices.listAllStudies))
# Connect slots
self.connect(
self._threadPool[len(self._threadPool) - 1], QtCore.SIGNAL("finished(QVariant)"), self.loadStudiesFinished
)
# Start thread
self._threadPool[len(self._threadPool) - 1].start()
def reloadStudyMetadata(self):
"""Reload study metadata for selected study
"""
# Setup loading UI
self.window().statusBar.showMessage("Loading study metadata...")
self.window().enableIndefiniteProgess()
self.tabWidget.setEnabled(False)
# Create data loading thread
self._threadPool.append(WorkerThread(self.ocWebServices.getStudyMetadata, self._selectedStudy))
# Connect slots
self.connect(
self._threadPool[len(self._threadPool) - 1],
QtCore.SIGNAL("finished(QVariant)"),
self.loadStudyMetadataFinished,
)
# Start thread
self._threadPool[len(self._threadPool) - 1].start()
def reloadStudySites(self):
"""Reload sites for selected OpenClinica sutdy (in memory processing)
(If it is monocentric study show one default site)
"""
# Quick way of crating simple viewModel
self.studySitesModel = QtGui.QStandardItemModel()
self.studySitesModel.setHorizontalHeaderLabels(["Identifier", "Partner Site", "Study"])
row = 0
if len(self._selectedStudy.sites) > 0:
for site in self._selectedStudy.sites:
siteIdentifierValue = QtGui.QStandardItem(site.identifier)
siteNameValue = QtGui.QStandardItem(site.name)
studyNameValue = QtGui.QStandardItem(self._selectedStudy.name)
self.studySitesModel.setItem(row, 0, siteIdentifierValue)
self.studySitesModel.setItem(row, 1, siteNameValue)
self.studySitesModel.setItem(row, 2, studyNameValue)
row = row + 1
else:
studyIdentifierValue = QtGui.QStandardItem(self._selectedStudy.identifier)
studyNameValue = QtGui.QStandardItem(self._selectedStudy.name)
self.studySitesModel.setItem(row, 0, studyIdentifierValue)
self.studySitesModel.setItem(row, 2, studyNameValue)
row = row + 1
# Create a proxy model to enable Sorting and filtering
self.studyProxyModel = QtGui.QSortFilterProxyModel()
self.studyProxyModel.setSourceModel(self.studySitesModel)
self.studyProxyModel.setDynamicSortFilter(True)
self.studyProxyModel.setFilterCaseSensitivity(QtCore.Qt.CaseInsensitive)
# Connect to filtering UI element
QtCore.QObject.connect(
self.txtStudyFilter, QtCore.SIGNAL("textChanged(QString)"), self.studyProxyModel.setFilterRegExp
)
self.tvStudies.setModel(self.studyProxyModel)
self.tvStudies.resizeColumnsToContents()
# After the view has model, set currentChanged behaviour
self.tvStudies.selectionModel().currentChanged.connect(self.tblStudyItemChanged)
def reloadSubjects(self):
"""Reload OpenClinica study subects enrolled into selected study/site in working thread
"""
# Clear study subjects
del self._studySubjects[:]
self._studySubjects = []
self._selectedStudySubject = None
self._studySubjects = None
self._subjectsREST = None
# Setup loading UI
self.window().statusBar.showMessage("Loading list of study subjects...")
self.window().enableIndefiniteProgess()
self.tabWidget.setEnabled(False)
# Load subject for whole study or only site if it is multicentre study
if self._selectedStudy and self._selectedStudy.isMulticentre:
self._threadPool.append(
WorkerThread(
self.ocWebServices.listAllStudySubjectsByStudySite,
[self._selectedStudy, self._selectedStudySite, self._studyMetadata],
)
)
else:
self._threadPool.append(
WorkerThread(self.ocWebServices.listAllStudySubjectsByStudy, [self._selectedStudy, self._studyMetadata])
)
# Connect slots
self.connect(
self._threadPool[len(self._threadPool) - 1], QtCore.SIGNAL("finished(QVariant)"), self.loadSubjectsFinished
)
# Start thread
self._threadPool[len(self._threadPool) - 1].start()
# TODO: it would be much faster if I request REST subject only for the selected one
# TODO: however we have to migrate to a new version of OC first
# Need to get OIDs of subjects
self._threadPool.append(
WorkerThread(self.svcHttp.getStudyCasebookSubjects, [ConfigDetails().ocHost, self.getStudyOid()])
)
# Connect slots
self.connect(
self._threadPool[len(self._threadPool) - 1],
QtCore.SIGNAL("finished(QVariant)"),
self.loadSubjectsRESTFinished,
)
# Start thread
self._threadPool[len(self._threadPool) - 1].start()
def reloadEvents(self):
"""Reload OpenClinica events scheduled for selected study subject
"""
# Setup loading UI
self.window().statusBar.showMessage("Loading subject scheduled events...")
self.window().enableIndefiniteProgess()
self.tabWidget.setEnabled(False)
# Define a job
# Need to get EventRepeatKeys
self._threadPool.append(
WorkerThread(
self.svcHttp.getStudyCasebookEvents,
[ConfigDetails().ocHost, self.getStudyOid(), self._selectedStudySubject.oid],
)
)
# Connect slots
self.connect(
self._threadPool[len(self._threadPool) - 1], QtCore.SIGNAL("finished(QVariant)"), self.loadEventsFinished
)
# Start thread
self._threadPool[len(self._threadPool) - 1].start()
def reloadCrfs(self):
"""
"""
self._selectedCrf = None
# Setup loading UI
self.window().statusBar.showMessage("Loading list of eCRFs...")
self.window().enableIndefiniteProgess()
self.tabWidget.setEnabled(False)
# Quick way of crating simple viewModel
self.crfsModel = QtGui.QStandardItemModel()
self.crfsModel.setHorizontalHeaderLabels(["Name", "OID"])
row = 0
for crf in self._selectedStudyEvent.forms:
nameItem = QtGui.QStandardItem(crf.name)
oidItem = QtGui.QStandardItem(crf.oid)
self.crfsModel.setItem(row, 0, nameItem)
self.crfsModel.setItem(row, 1, oidItem)
row = row + 1
self.crfProxyModel = QtGui.QSortFilterProxyModel()
self.crfProxyModel.setSourceModel(self.crfsModel)
self.crfProxyModel.setDynamicSortFilter(True)
self.crfProxyModel.setFilterCaseSensitivity(QtCore.Qt.CaseInsensitive)
QtCore.QObject.connect(
self.txtCrfsFilter, QtCore.SIGNAL("textChanged(QString)"), self.crfProxyModel.setFilterRegExp
)
self.tvCrfs.setModel(self.crfProxyModel)
self.tvCrfs.resizeColumnsToContents()
self.tvCrfs.selectionModel().currentChanged.connect(self.tblEventCrfItemChanged)
# Update status bar
self.tabWidget.setEnabled(True)
self.window().statusBar.showMessage("Ready")
self.window().disableIndefiniteProgess()
def reloadItems(self):
"""
"""
self._selectedItem = None
# Setup loading UI
self.window().statusBar.showMessage("Loading list of CRF items...")
self.window().enableIndefiniteProgess()
self.tabWidget.setEnabled(False)
# Quick way of crating simple viewModel
self.itemModel = QtGui.QStandardItemModel()
self.itemModel.setHorizontalHeaderLabels(["Name", "OID", "DataType", "Description", "ItemGroupOID"])
row = 0
for item in self._selectedCrf.items:
nameItem = QtGui.QStandardItem(item.name)
oidItem = QtGui.QStandardItem(item.oid)
dataTypeItem = QtGui.QStandardItem(item.dataType)
descriptionItem = QtGui.QStandardItem(item.description)
itemGroupOidItem = QtGui.QStandardItem(item.itemGroupOid)
self.itemModel.setItem(row, 0, nameItem)
self.itemModel.setItem(row, 1, oidItem)
self.itemModel.setItem(row, 2, dataTypeItem)
self.itemModel.setItem(row, 3, descriptionItem)
self.itemModel.setItem(row, 4, itemGroupOidItem)
row = row + 1
self.itemProxyModel = QtGui.QSortFilterProxyModel()
self.itemProxyModel.setSourceModel(self.itemModel)
self.itemProxyModel.setDynamicSortFilter(True)
self.itemProxyModel.setFilterCaseSensitivity(QtCore.Qt.CaseInsensitive)
QtCore.QObject.connect(
self.txtItemsFilter, QtCore.SIGNAL("textChanged(QString)"), self.itemProxyModel.setFilterRegExp
)
self.tvItems.setModel(self.itemProxyModel)
self.tvItems.resizeColumnsToContents()
self.tvItems.selectionModel().currentChanged.connect(self.tblCrfFieldItemChanged)
# Update status bar
self.tabWidget.setEnabled(True)
self.window().statusBar.showMessage("Ready")
self.window().disableIndefiniteProgess()
def performDataImport(self):
"""Perform upload of anonymised DICOM data and import of DICOM Patient ID, and Study Intance UID into OpenClinica
Called after agter annonymise is finished
"""
self.textBrowserProgress.append("Importing data into eCRF...")
# Dialog asking for value (depending on data type)
itemImportDialog = ItemImportDialog()
itemImportDialog.setModel(self._selectedItem)
# Show dialog
if itemImportDialog.exec_():
# Mapping will be passed to DICOM service via worker parameters
# Generate ODM XML for selection
self._selectedItem.value = itemImportDialog.item.value
odm = self.svcOdm.generateOdmXmlForStudyItem(
self.getStudyOid(),
self._selectedStudySubject,
self._selectedStudyEvent,
self._selectedCrf,
self._selectedItem,
)
self._logger.debug(odm)
importSucessfull = self.ocWebServices.importODM(odm)
if importSucessfull:
self.textBrowserProgress.append("Import to OpenClinica sucessfull...")
else:
self.textBrowserProgress.append("Import Error. Cannot continue.")
self.tabWidget.setEnabled(True)
self.window().statusBar.showMessage("Ready")
self.window().disableIndefiniteProgess()
self.Message("Import finished.")
else:
self.tabWidget.setEnabled(True)
self.window().statusBar.showMessage("Ready")
self.window().disableIndefiniteProgess()
self.btnUpload.setDisabled(False)
return
def loadStudiesFinished(self, studies):
"""Finished loading studies from server
"""
self._studies = studies.toPyObject()
self._studies.sort(cmp=lambda x, y: cmp(x.name(), y.name()))
# And prepare ViewModel for the GUI
studiesModel = QtGui.QStandardItemModel()
for study in self._studies:
text = QtGui.QStandardItem(study.name)
studiesModel.appendRow([text])
self.cmbStudy.setModel(studiesModel)
# Select the first study
self._selectedStudy = self._studies[0]
# Update status bar
self.tabWidget.setEnabled(True)
self.window().statusBar.showMessage("Ready")
self.window().disableIndefiniteProgess()
def loadStudyMetadataFinished(self, metadata):
"""Finished loading metadata from server
"""
self._studyMetadata = metadata.toPyObject()
# Update status bar
self.tabWidget.setEnabled(False)
self.window().statusBar.showMessage("Ready")
self.window().disableIndefiniteProgess()
# Reload study subjects with scheduled events (extedn them with metadata)
self.reloadSubjects()
def loadSubjectsFinished(self, subjects):
"""Finished loading of SOAP subject data
"""
self._studySubjects = subjects.toPyObject()
self.syncSubjectAndRESTSubjects()
def loadSubjectsRESTFinished(self, subjects):
"""Finished loading of REST subject data
"""
self._subjectsREST = subjects.toPyObject()
self.syncSubjectAndRESTSubjects()
def syncSubjectAndRESTSubjects(self):
"""Syncrhonize results from SOAP and REST subject loading
"""
# In case the REST worker finished sooner than the SOAP worker
if self._studySubjects != None and self._subjectsREST != None:
# Create the ViewModels for Views
self.subjectsModel = QtGui.QStandardItemModel()
self.subjectsModel.setHorizontalHeaderLabels(
["PersonID", "StudySubjectID", "SecondaryID", "Gender", "Enrollment date", "OID"]
)
row = 0
for studySubject in self._studySubjects:
# Always mandatory
labelItem = QtGui.QStandardItem(studySubject.label)
enrollmentDateItem = QtGui.QStandardItem(studySubject.enrollmentDate)
# Optional
secondaryLabelItem = QtGui.QStandardItem("")
if studySubject.secondaryLabel != None:
secondaryLabelItem = QtGui.QStandardItem(studySubject.secondaryLabel)
# Not everything has to be collected (depend on study setup)
pidItem = QtGui.QStandardItem("")
genderItem = QtGui.QStandardItem("")
if studySubject.subject != None:
if studySubject.subject.uniqueIdentifier != None:
pidItem = QtGui.QStandardItem(studySubject.subject.uniqueIdentifier)
if studySubject.subject.gender != None:
genderItem = QtGui.QStandardItem(studySubject.subject.gender)
oidItem = QtGui.QStandardItem("")
for sREST in self._subjectsREST:
if sREST.studySubjectId == studySubject.label:
oidItem = QtGui.QStandardItem(sREST.oid)
studySubject.oid = sREST.oid
self.subjectsModel.setItem(row, 0, pidItem)
self.subjectsModel.setItem(row, 1, labelItem)
self.subjectsModel.setItem(row, 2, secondaryLabelItem)
self.subjectsModel.setItem(row, 3, genderItem)
self.subjectsModel.setItem(row, 4, enrollmentDateItem)
self.subjectsModel.setItem(row, 5, oidItem)
row = row + 1
# Create a proxy model to enable Sorting and filtering
self.studySubjectProxyModel = QtGui.QSortFilterProxyModel()
self.studySubjectProxyModel.setSourceModel(self.subjectsModel)
self.studySubjectProxyModel.setDynamicSortFilter(True)
self.studySubjectProxyModel.setFilterCaseSensitivity(QtCore.Qt.CaseInsensitive)
# Connect to filtering UI element
QtCore.QObject.connect(
self.txtStudySubjectFilter,
QtCore.SIGNAL("textChanged(QString)"),
self.studySubjectProxyModel.setFilterRegExp,
)
# Set the models Views
self.tvStudySubjects.setModel(self.studySubjectProxyModel)
# Resize the width of columns to fit the content
self.tvStudySubjects.resizeColumnsToContents()
# After the view has model, set currentChanged behaviour
self.tvStudySubjects.selectionModel().currentChanged.connect(self.tblStudySubjectItemChanged)
self.tabWidget.setEnabled(True)
self.window().statusBar.showMessage("Ready")
self.window().disableIndefiniteProgess()
def loadEventsFinished(self, events):
"""Finished loading events data
"""
eventsREST = events.toPyObject()
# Quick way of crating simple viewModel
self.eventsModel = QtGui.QStandardItemModel()
self.eventsModel.setHorizontalHeaderLabels(
["Name", "Description", "Category", "Type", "Repeating", "Start date", "Status"]
)
row = 0
for event in self._selectedStudySubject.events:
nameItem = QtGui.QStandardItem(event.name)
descriptionItem = QtGui.QStandardItem(event.description)
categoryItem = QtGui.QStandardItem(event.category)
typeItem = QtGui.QStandardItem(event.eventType)
isRepeatingItem = QtGui.QStandardItem(str(event.isRepeating))
startDateItem = QtGui.QStandardItem("{:%d-%m-%Y}".format(event.startDate))
# Enhance with information from REST
statusItem = QtGui.QStandardItem()
for e in eventsREST:
if (
e.eventDefinitionOID == event.eventDefinitionOID
and e.startDate.isoformat() == event.startDate.isoformat()
):
event.status = e.status
event.studyEventRepeatKey = e.studyEventRepeatKey
if event.isRepeating:
nameItem = QtGui.QStandardItem(event.name + " [" + event.studyEventRepeatKey + "]")
statusItem = QtGui.QStandardItem(event.status)
event.forms = e.forms
self.eventsModel.setItem(row, 0, nameItem)
self.eventsModel.setItem(row, 1, descriptionItem)
self.eventsModel.setItem(row, 2, categoryItem)
self.eventsModel.setItem(row, 3, typeItem)
self.eventsModel.setItem(row, 4, isRepeatingItem)
self.eventsModel.setItem(row, 5, startDateItem)
self.eventsModel.setItem(row, 6, statusItem)
row = row + 1
self.studyEventProxyModel = QtGui.QSortFilterProxyModel()
self.studyEventProxyModel.setSourceModel(self.eventsModel)
self.studyEventProxyModel.setDynamicSortFilter(True)
self.studyEventProxyModel.setFilterCaseSensitivity(QtCore.Qt.CaseInsensitive)
QtCore.QObject.connect(
self.txtStudyEventFilter, QtCore.SIGNAL("textChanged(QString)"), self.studyEventProxyModel.setFilterRegExp
)
self.tvStudyEvents.setModel(self.studyEventProxyModel)
self.tvStudyEvents.resizeColumnsToContents()
self.tvStudyEvents.selectionModel().currentChanged.connect(self.tblStudyEventItemChanged)
# Update status bar
self.tabWidget.setEnabled(True)
self.window().statusBar.showMessage("Ready")
self.window().disableIndefiniteProgess()
## ## ######## ###### ###### ### ###### ######## ######
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def Question(self, string):
"""Question message box
"""
reply = QtGui.QMessageBox.question(self, "Question", string, QtGui.QMessageBox.Yes, QtGui.QMessageBox.No)
if reply == QtGui.QMessageBox.Yes:
self.btnUpload.setEnabled(False)
else:
self.btnUpload.setEnabled(True)
def Error(self, string):
"""Error message box
"""
QtGui.QMessageBox.critical(self, "Error", string)
self.btnUpload.setEnabled(True)
def Warning(self, string):
"""Warning message box
"""
QtGui.QMessageBox.warning(self, "Warning", string)
self.btnUpload.setEnabled(True)
def Message(self, string):
"""Called from message event, opens a small window with the message
"""
QtGui.QMessageBox.about(self, "Info", string)
self.btnUpload.setEnabled(True)
def LogMessage(self, string):
"""Called from log event in thread and adds log into textbrowser UI
"""
self.textBrowserProgress.append(string)
ocWsHost = "http://skripcak.net:8080/OpenClinica-ws"
password = "******"
OCUserDetails().username = "******"
OCUserDetails().connected = False
# Create connection artefact to users main OpenClinica SOAP
ocConnectInfo = OCConnectInfo(
ocWsHost,
OCUserDetails().username
)
ocConnectInfo.setPassword(password)
# Initialise SOAP services
ocWebServices = OCWebServices(ocConnectInfo)
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()
# Services
from soap.OCConnectInfo import OCConnectInfo
from soap.OCWebServices import OCWebServices
ocWsHost = "http://skripcak.net:8080/OpenClinica-ws"
password = "******"
OCUserDetails().username = "******"
OCUserDetails().connected = False
# Create connection artefact to users main OpenClinica SOAP
ocConnectInfo = OCConnectInfo(
ocWsHost,
OCUserDetails().username
)
ocConnectInfo.setPassword(password)
# Initialise SOAP services
# Debug lvls ... trace=logging.INFO, trace=logging.DEBUG in OCWebServices constructor
ocWebServices = OCWebServices(ocConnectInfo)
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:
print study
from soap.OCConnectInfo import OCConnectInfo
from soap.OCWebServices import OCWebServices
ocWsHost = "http://skripcak.net:8080/OpenClinica-ws"
password = "******"
OCUserDetails().username = "******"
OCUserDetails().connected = False
# Create connection artefact to users main OpenClinica SOAP
ocConnectInfo = OCConnectInfo(
ocWsHost,
OCUserDetails().username
)
ocConnectInfo.setPassword(password)
# Initialise SOAP services
ocWebServices = OCWebServices(ocConnectInfo)
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:
studyMetadata = ocWebServices.getStudyMetadata(study)
break
print studyMetadata
from contexts.OCUserDetails import OCUserDetails
# Services
from soap.OCConnectInfo import OCConnectInfo
from soap.OCWebServices import OCWebServices
ocWsHost = "http://skripcak.net:8080/OpenClinica-ws"
password = "******"
OCUserDetails().username = "******"
OCUserDetails().connected = False
# Create connection artefact to users main OpenClinica SOAP
ocConnectInfo = OCConnectInfo(ocWsHost, OCUserDetails().username)
ocConnectInfo.setPassword(password)
# Initialise SOAP services
ocWebServices = OCWebServices(ocConnectInfo)
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:
studyMetadata = ocWebServices.getStudyMetadata(study)
break
print studyMetadata
class OcModule(QWidget, OcModuleUI):
"""OC data module
"""
def __init__(self, parent = None):
"""Default Constructor
"""
# Setup GUI
QWidget.__init__(self, parent)
self.parent = parent
self.setupUi(self)
# Hide summary of XML for importing data to OC (for user not necessary)
self.lblSummary.hide()
# Setup logger - use config file
self._logger = logging.getLogger(__name__)
logging.config.fileConfig("logging.ini", disable_existing_loggers=False)
# List of worker threads
self._threadPool = []
# Prepares services and main data for this ViewModel
self.prepareServices()
# Initialize data structures for UI
self._studies = []
self._studySubjects = []
self.reloadData()
# Finish UI setup
self.lblOcConnection.setText("[" + OCUserDetails().username + "] " + ConfigDetails().ocHost)
# Register handlers
self.btnReloadStudySubjects.clicked.connect(self.btnReloadStudySubjectsClicked)
self.btnNewStudySubject.clicked.connect(self.btnNewStudySubjectClicked)
self.btnNewEvent.clicked.connect(self.btnNewEventClicked)
self.btnUpload.clicked.connect(self.btnImportClicked)
self.cmbStudy.currentIndexChanged["QString"].connect(self.cmbStudyChanged)
self.destroyed.connect(self.handleDestroyed)
## ## ### ## ## ######## ## ######## ######## ######
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## ## ## ## ## ## ######## ######## ######## ## ## ######
def cmbStudyChanged(self, text):
"""Executed when the concrete study is selected from studies combobox
"""
# Reset table views
self.tvStudies.setModel(None)
self.tvStudySubjects.setModel(None)
self.tvStudyEvents.setModel(None)
self.tvCrfs.setModel(None)
self.tvItems.setModel(None)
self.textBrowserProgress.clear()
# Set selected study and reload sites
self._selectedStudy = first.first(
study for study in self._studies if study.name.encode("utf-8") == text.toUtf8()
)
# Reload study sites
if self._selectedStudy:
self._logger.debug("Selected study: %s" % (self._selectedStudy.name))
self.reloadStudySites()
def tblStudyItemChanged(self, current, previous):
"""Event handler which is triggered when selectedStudy change
When the study is selected I have to clean all the other data elements
Which depends on study. It means: StudySubjects, StudyEventDefinitions, StudyEventCRFs
"""
# Clean the model before loading the new one
self.tvStudySubjects.setModel(None)
self.tvStudyEvents.setModel(None)
self.tvCrfs.setModel(None)
self.tvItems.setModel(None)
self.textBrowserProgress.clear()
# Take the first column of selected row from table view
index = self.studyProxyModel.index(current.row(), 0);
# Multicentric
if len(self._selectedStudy.sites) > 0:
self._selectedStudySite = first.first(
studySite for studySite in self._selectedStudy.sites if studySite.identifier.encode("utf-8") == index.data().toPyObject().toUtf8()
)
# Get the study metadata
self.reloadStudyMetadata()
def btnReloadStudySubjectsClicked(self):
"""Reload study subjects button clicked
"""
# Reload
self.reloadSubjects()
def btnNewStudySubjectClicked(self):
"""New study subject button clicked
"""
if (self._selectedStudy):
# Initialize dialog and bind data to UI
dialog = NewSubjectDialog(self)
dialog.setData(self._selectedStudy, self._selectedStudySite)
# When ok commit session transaction
if dialog.exec_() == QtGui.QDialog.Accepted:
try:
newStudySubject = dialog.newStudySubject
self.ocWebServices.createStudySubject(
newStudySubject,
self._selectedStudy
)
except:
QtGui.QMessageBox.warning(self, "Error", "OC study subject not created.")
# Reload
self.reloadSubjects()
def tblStudySubjectItemChanged(self, current, previous):
"""Event handler which is triggered when selectedStudySubject change
"""
self.tvStudyEvents.setModel(None)
self.tvCrfs.setModel(None)
self.tvItems.setModel(None)
self.textBrowserProgress.clear()
# Take the second column (StudySubjectID) of selected row from table view
column = 1
index = self.studySubjectProxyModel.index(current.row(), column);
print index.data().toPyObject()
if index.data().toPyObject():
self._selectedStudySubject = (
first.first(
subject for subject in self._studySubjects if subject.label.encode("utf-8") == index.data().toPyObject().toUtf8()
)
)
if self._selectedStudySubject:
# Load scheduled events for selected subject
self.reloadEvents()
def btnNewEventClicked(self):
"""Schedule new study event button clicked
"""
events = self.ocWebServices.listAllStydyEventDefinitionsByStudy(
self._selectedStudy
)
# Initialize dialog and bind data to UI
dialog = NewEventDialog(self)
dialog.setData(
self._selectedStudy,
self._selectedStudySite,
self._selectedStudySubject,
events
)
# When ok commit session transaction
if dialog.exec_() == QtGui.QDialog.Accepted:
newEvent = dialog.selectedEvent
self.ocWebServices.scheduleStudyEvent(
self._selectedStudy,
self._selectedStudySubject,
newEvent
)
# Reload
temp = self._selectedStudySubject
self.reloadSubjects()
self._selectedStudySubject = temp
#self.reloadEvents()
def tblStudyEventItemChanged(self, current, previous):
"""Event handler which is triggered when selectedStudyEventDefintion change
When the studyEvent is selected. Create a model for the event CRFs view.
"""
self.textBrowserProgress.clear()
# Selected studyEventDefinitions
# Take the first column of selected row from table view
#index = self.studyEventProxyModel.index(current.row(), 0);
#self._selectedStudyEvent = first.first(e for e in self._selectedStudySubject.events if e.name.encode("utf-8") == index.data().toPyObject().toUtf8())
self._selectedStudyEvent = self._selectedStudySubject.events[current.row()]
self.reloadCrfs()
def tblEventCrfItemChanged(self, current, previous):
"""
"""
self.tvItems.setModel(None)
self.textBrowserProgress.clear()
# Take the second column (OID) of selected row from table view
column = 1
index = self.crfProxyModel.index(current.row(), column);
if index.data().toPyObject():
self._selectedCrf = (
first.first(
crf for crf in self._selectedStudyEvent.forms if crf.oid.encode("utf-8") == index.data().toPyObject().toUtf8()
)
)
self.reloadItems()
def tblCrfFieldItemChanged(self, current, previous):
"""
"""
self.textBrowserProgress.clear()
# Take the second column (OID) of selected row from table view
column = 1
index = self.itemProxyModel.index(current.row(), column);
if index.data().toPyObject():
self._selectedItem = (
first.first(
i for i in self._selectedCrf.items if i.oid.encode("utf-8") == index.data().toPyObject().toUtf8()
)
)
# Show the selected import target
msg = "Selected import target: "
msg += self._selectedStudy.name + "/"
if len(self._selectedStudy.sites) > 0:
msg += self._selectedStudySite.name + "/"
msg += "StudySubjectID: " + self._selectedStudySubject.label + "/"
if self._selectedStudyEvent.isRepeating:
msg += self._selectedStudyEvent.name + " [" + self._selectedStudyEvent.studyEventRepeatKey + "]/"
else:
msg += self._selectedStudyEvent.name + "/"
msg += self._selectedCrf.name + "/"
msg += self._selectedItem.name
self._logger.debug(msg)
self.textBrowserProgress.append(msg)
def btnImportClicked(self):
"""Upload button pressed (DICOM upload workflow started)
"""
QtGui.qApp.processEvents(QtCore.QEventLoop.AllEvents, 1000)
self.progressBar.setRange(0, 100)
self.progressBar.setValue(0)
# Make textBrowser visible
self.textBrowserProgress.setVisible(True)
self.textBrowserProgress.append('Wait please:')
# Disable upload button for now but better is to desable whole UI
self.btnUpload.setEnabled(False)
self.performDataImport()
def handleTaskUpdated(self, data):
"""Move progress bar precento by precento
"""
if type(data) is list:
if data[0]:
processed = data[0]
if data[1]:
size = data[1]
progress = processed * 100 / size
self.window().statusBar.showMessage("Processed files: [" + str(processed) + "/" + str(size) + "]")
self.progressBar.setValue(progress)
def handleDestroyed(self):
"""Kill runnign threads
"""
self._logger.debug("Destroying module")
for thread in self._threadPool:
thread.terminate()
thread.wait()
self._logger.debug("Thread killed.")
def getStudyOid(self):
"""Return study or site OID depending on mono/multi centre configuration
"""
# Multicentre
if len(self._selectedStudy.sites) > 0:
return self._selectedStudySite.oid
# Monocentre
else:
return self._selectedStudy.oid
###### ####### ## ## ## ## ### ## ## ######## ######
## ## ## ## ### ### ### ### ## ## ### ## ## ## ## ##
## ## ## #### #### #### #### ## ## #### ## ## ## ##
## ## ## ## ### ## ## ### ## ## ## ## ## ## ## ## ######
## ## ## ## ## ## ## ######### ## #### ## ## ##
## ## ## ## ## ## ## ## ## ## ## ### ## ## ## ##
###### ####### ## ## ## ## ## ## ## ## ######## ######
def prepareServices(self):
"""Prepare services for this module
"""
# HTTP connection to RadPlanBio server (Database)
self.svcHttp = HttpConnectionService(ConfigDetails().ocHost, ConfigDetails().ocPort, UserDetails())
if ConfigDetails().proxyEnabled:
self.svcHttp.setupProxy(ConfigDetails().proxyHost, ConfigDetails().proxyPort, ConfigDetails().noProxy)
if ConfigDetails().proxyAuthEnabled:
self.svcHttp.setupProxyAuth(ConfigDetails().proxyAuthLogin, ConfigDetails().proxyAuthPassword)
# Create connection artefact to users main OpenClinica SOAP
self.ocConnectInfo = OCConnectInfo(ConfigDetails().ocWsHost, OCUserDetails().username)
self.ocConnectInfo.setPasswordHash(OCUserDetails().passwordHash)
if ConfigDetails().proxyEnabled:
self.ocWebServices = OCWebServices(self.ocConnectInfo, ConfigDetails().proxyHost, ConfigDetails().proxyPort, ConfigDetails().noProxy, ConfigDetails().proxyAuthLogin, ConfigDetails().proxyAuthPassword)
else:
self.ocWebServices = OCWebServices(self.ocConnectInfo)
# ODM XML metadata processing
self.svcOdm = OdmFileDataService()
def reloadData(self):
"""Initialization of data for UI
"""
# OpenClinica study
del self._studies[:]
self._studies = []
self._selectedStudy = None
self._studyMetadata = None
# OpenClinica study site
self._selectedStudySite = None
# OpenClinica study subjects
del self._studySubjects[:]
self._studySubjects = []
self._selectedStudySubject = None
# Selected sheduled study event for subject
self._selectedStudyEvent = None
# Selected event CRF
self._selectedCrf = None
# Selected item
self._selectedItem = None
# Load studies
self.reloadStudies()
def reloadStudies(self):
"""Reload OpenClinica studies (in working thread)
"""
# Setup loading UI
self.window().statusBar.showMessage("Loading list of clinical studies...")
self.window().enableIndefiniteProgess()
self.tabWidget.setEnabled(False)
# Create data loading thread
self._threadPool.append(
WorkerThread(self.ocWebServices.listAllStudies)
)
# Connect slots
self.connect(
self._threadPool[len(self._threadPool) - 1],
QtCore.SIGNAL("finished(QVariant)"),
self.loadStudiesFinished
)
# Start thread
self._threadPool[len(self._threadPool) - 1].start()
def reloadStudyMetadata(self):
"""Reload study metadata for selected study
"""
# Setup loading UI
self.window().statusBar.showMessage("Loading study metadata...")
self.window().enableIndefiniteProgess()
self.tabWidget.setEnabled(False)
# Create data loading thread
self._threadPool.append(
WorkerThread(
self.ocWebServices.getStudyMetadata, self._selectedStudy
)
)
# Connect slots
self.connect(
self._threadPool[len(self._threadPool) - 1],
QtCore.SIGNAL("finished(QVariant)"),
self.loadStudyMetadataFinished
)
# Start thread
self._threadPool[len(self._threadPool) - 1].start()
def reloadStudySites(self):
"""Reload sites for selected OpenClinica sutdy (in memory processing)
(If it is monocentric study show one default site)
"""
# Quick way of crating simple viewModel
self.studySitesModel = QtGui.QStandardItemModel()
self.studySitesModel.setHorizontalHeaderLabels(["Identifier", "Partner Site", "Study"])
row = 0
if len(self._selectedStudy.sites) > 0:
for site in self._selectedStudy.sites:
siteIdentifierValue = QtGui.QStandardItem(site.identifier)
siteNameValue = QtGui.QStandardItem(site.name)
studyNameValue = QtGui.QStandardItem(self._selectedStudy.name)
self.studySitesModel.setItem(row, 0, siteIdentifierValue)
self.studySitesModel.setItem(row, 1, siteNameValue)
self.studySitesModel.setItem(row, 2, studyNameValue)
row = row + 1
else:
studyIdentifierValue = QtGui.QStandardItem(self._selectedStudy.identifier)
studyNameValue = QtGui.QStandardItem(self._selectedStudy.name)
self.studySitesModel.setItem(row, 0, studyIdentifierValue)
self.studySitesModel.setItem(row, 2, studyNameValue)
row = row + 1
# Create a proxy model to enable Sorting and filtering
self.studyProxyModel = QtGui.QSortFilterProxyModel()
self.studyProxyModel.setSourceModel(self.studySitesModel)
self.studyProxyModel.setDynamicSortFilter(True)
self.studyProxyModel.setFilterCaseSensitivity(QtCore.Qt.CaseInsensitive)
# Connect to filtering UI element
QtCore.QObject.connect(self.txtStudyFilter, QtCore.SIGNAL("textChanged(QString)"), self.studyProxyModel.setFilterRegExp)
self.tvStudies.setModel(self.studyProxyModel)
self.tvStudies.resizeColumnsToContents()
# After the view has model, set currentChanged behaviour
self.tvStudies.selectionModel().currentChanged.connect(self.tblStudyItemChanged)
def reloadSubjects(self):
"""Reload OpenClinica study subects enrolled into selected study/site in working thread
"""
# Clear study subjects
del self._studySubjects[:]
self._studySubjects = []
self._selectedStudySubject = None
self._studySubjects = None
self._subjectsREST = None
# Setup loading UI
self.window().statusBar.showMessage("Loading list of study subjects...")
self.window().enableIndefiniteProgess()
self.tabWidget.setEnabled(False)
# Load subject for whole study or only site if it is multicentre study
if self._selectedStudy and self._selectedStudy.isMulticentre:
self._threadPool.append(
WorkerThread(
self.ocWebServices.listAllStudySubjectsByStudySite,
[self._selectedStudy, self._selectedStudySite, self._studyMetadata]
)
)
else:
self._threadPool.append(
WorkerThread(
self.ocWebServices.listAllStudySubjectsByStudy,
[self._selectedStudy, self._studyMetadata]
)
)
# Connect slots
self.connect(
self._threadPool[len(self._threadPool) - 1],
QtCore.SIGNAL("finished(QVariant)"),
self.loadSubjectsFinished
)
# Start thread
self._threadPool[len(self._threadPool) - 1].start()
# TODO: it would be much faster if I request REST subject only for the selected one
# TODO: however we have to migrate to a new version of OC first
# Need to get OIDs of subjects
self._threadPool.append(
WorkerThread(
self.svcHttp.getStudyCasebookSubjects, [ConfigDetails().ocHost, self.getStudyOid()]
)
)
# Connect slots
self.connect(
self._threadPool[len(self._threadPool) - 1],
QtCore.SIGNAL("finished(QVariant)"),
self.loadSubjectsRESTFinished
)
# Start thread
self._threadPool[len(self._threadPool) - 1].start()
def reloadEvents(self):
"""Reload OpenClinica events scheduled for selected study subject
"""
# Setup loading UI
self.window().statusBar.showMessage("Loading subject scheduled events...")
self.window().enableIndefiniteProgess()
self.tabWidget.setEnabled(False)
# Define a job
# Need to get EventRepeatKeys
self._threadPool.append(
WorkerThread(
self.svcHttp.getStudyCasebookEvents,
[ConfigDetails().ocHost, self.getStudyOid(), self._selectedStudySubject.oid]
)
)
# Connect slots
self.connect(
self._threadPool[len(self._threadPool) - 1],
QtCore.SIGNAL("finished(QVariant)"),
self.loadEventsFinished
)
# Start thread
self._threadPool[len(self._threadPool) - 1].start()
def reloadCrfs(self):
"""
"""
self._selectedCrf = None
# Setup loading UI
self.window().statusBar.showMessage("Loading list of eCRFs...")
self.window().enableIndefiniteProgess()
self.tabWidget.setEnabled(False)
# Quick way of crating simple viewModel
self.crfsModel = QtGui.QStandardItemModel()
self.crfsModel.setHorizontalHeaderLabels(["Name", "OID"])
row = 0
for crf in self._selectedStudyEvent.forms:
nameItem = QtGui.QStandardItem(crf.name)
oidItem = QtGui.QStandardItem(crf.oid)
self.crfsModel.setItem(row, 0, nameItem)
self.crfsModel.setItem(row, 1, oidItem)
row = row + 1
self.crfProxyModel = QtGui.QSortFilterProxyModel()
self.crfProxyModel.setSourceModel(self.crfsModel)
self.crfProxyModel.setDynamicSortFilter(True)
self.crfProxyModel.setFilterCaseSensitivity(QtCore.Qt.CaseInsensitive)
QtCore.QObject.connect(
self.txtCrfsFilter,
QtCore.SIGNAL("textChanged(QString)"),
self.crfProxyModel.setFilterRegExp
)
self.tvCrfs.setModel(self.crfProxyModel)
self.tvCrfs.resizeColumnsToContents()
self.tvCrfs.selectionModel().currentChanged.connect(
self.tblEventCrfItemChanged
)
# Update status bar
self.tabWidget.setEnabled(True)
self.window().statusBar.showMessage("Ready")
self.window().disableIndefiniteProgess()
def reloadItems(self):
"""
"""
self._selectedItem = None
# Setup loading UI
self.window().statusBar.showMessage("Loading list of CRF items...")
self.window().enableIndefiniteProgess()
self.tabWidget.setEnabled(False)
# Quick way of crating simple viewModel
self.itemModel = QtGui.QStandardItemModel()
self.itemModel.setHorizontalHeaderLabels(["Name", "OID", "DataType", "Description", "ItemGroupOID"])
row = 0
for item in self._selectedCrf.items:
nameItem = QtGui.QStandardItem(item.name)
oidItem = QtGui.QStandardItem(item.oid)
dataTypeItem = QtGui.QStandardItem(item.dataType)
descriptionItem = QtGui.QStandardItem(item.description)
itemGroupOidItem = QtGui.QStandardItem(item.itemGroupOid)
self.itemModel.setItem(row, 0, nameItem)
self.itemModel.setItem(row, 1, oidItem)
self.itemModel.setItem(row, 2, dataTypeItem)
self.itemModel.setItem(row, 3, descriptionItem)
self.itemModel.setItem(row, 4, itemGroupOidItem)
row = row + 1
self.itemProxyModel = QtGui.QSortFilterProxyModel()
self.itemProxyModel.setSourceModel(self.itemModel)
self.itemProxyModel.setDynamicSortFilter(True)
self.itemProxyModel.setFilterCaseSensitivity(QtCore.Qt.CaseInsensitive)
QtCore.QObject.connect(
self.txtItemsFilter,
QtCore.SIGNAL("textChanged(QString)"),
self.itemProxyModel.setFilterRegExp
)
self.tvItems.setModel(self.itemProxyModel)
self.tvItems.resizeColumnsToContents()
self.tvItems.selectionModel().currentChanged.connect(
self.tblCrfFieldItemChanged
)
# Update status bar
self.tabWidget.setEnabled(True)
self.window().statusBar.showMessage("Ready")
self.window().disableIndefiniteProgess()
def performDataImport(self):
"""Perform upload of anonymised DICOM data and import of DICOM Patient ID, and Study Intance UID into OpenClinica
Called after agter annonymise is finished
"""
self.textBrowserProgress.append("Importing data into eCRF...")
# Dialog asking for value (depending on data type)
itemImportDialog = ItemImportDialog()
itemImportDialog.setModel(self._selectedItem)
# Show dialog
if itemImportDialog.exec_():
# Mapping will be passed to DICOM service via worker parameters
# Generate ODM XML for selection
self._selectedItem.value = itemImportDialog.item.value
odm = self.svcOdm.generateOdmXmlForStudyItem(
self.getStudyOid(),
self._selectedStudySubject,
self._selectedStudyEvent,
self._selectedCrf,
self._selectedItem
)
self._logger.debug(odm)
importSucessfull = self.ocWebServices.importODM(odm)
if importSucessfull:
self.textBrowserProgress.append("Import to OpenClinica sucessfull...")
else:
self.textBrowserProgress.append("Import Error. Cannot continue.")
self.tabWidget.setEnabled(True)
self.window().statusBar.showMessage("Ready")
self.window().disableIndefiniteProgess()
self.Message("Import finished.")
else:
self.tabWidget.setEnabled(True)
self.window().statusBar.showMessage("Ready")
self.window().disableIndefiniteProgess()
self.btnUpload.setDisabled(False)
return
def loadStudiesFinished(self, studies):
"""Finished loading studies from server
"""
self._studies = studies.toPyObject()
self._studies .sort(cmp = lambda x, y: cmp(x.name(), y.name()))
# And prepare ViewModel for the GUI
studiesModel = QtGui.QStandardItemModel()
for study in self._studies:
text = QtGui.QStandardItem(study.name)
studiesModel.appendRow([text])
self.cmbStudy.setModel(studiesModel)
# Select the first study
self._selectedStudy = self._studies[0]
# Update status bar
self.tabWidget.setEnabled(True)
self.window().statusBar.showMessage("Ready")
self.window().disableIndefiniteProgess()
def loadStudyMetadataFinished(self, metadata):
"""Finished loading metadata from server
"""
self._studyMetadata = metadata.toPyObject()
# Update status bar
self.tabWidget.setEnabled(False)
self.window().statusBar.showMessage("Ready")
self.window().disableIndefiniteProgess()
# Reload study subjects with scheduled events (extedn them with metadata)
self.reloadSubjects()
def loadSubjectsFinished(self, subjects):
"""Finished loading of SOAP subject data
"""
self._studySubjects = subjects.toPyObject()
self.syncSubjectAndRESTSubjects()
def loadSubjectsRESTFinished(self, subjects):
"""Finished loading of REST subject data
"""
self._subjectsREST = subjects.toPyObject()
self.syncSubjectAndRESTSubjects()
def syncSubjectAndRESTSubjects(self):
"""Syncrhonize results from SOAP and REST subject loading
"""
# In case the REST worker finished sooner than the SOAP worker
if self._studySubjects != None and self._subjectsREST != None:
# Create the ViewModels for Views
self.subjectsModel = QtGui.QStandardItemModel()
self.subjectsModel.setHorizontalHeaderLabels(["PersonID", "StudySubjectID", "SecondaryID", "Gender", "Enrollment date", "OID"])
row = 0
for studySubject in self._studySubjects:
# Always mandatory
labelItem = QtGui.QStandardItem(studySubject.label)
enrollmentDateItem = QtGui.QStandardItem(studySubject.enrollmentDate)
# Optional
secondaryLabelItem = QtGui.QStandardItem("")
if studySubject.secondaryLabel != None:
secondaryLabelItem = QtGui.QStandardItem(studySubject.secondaryLabel)
# Not everything has to be collected (depend on study setup)
pidItem = QtGui.QStandardItem("")
genderItem = QtGui.QStandardItem("")
if studySubject.subject != None:
if studySubject.subject.uniqueIdentifier != None:
pidItem = QtGui.QStandardItem(studySubject.subject.uniqueIdentifier)
if studySubject.subject.gender != None:
genderItem = QtGui.QStandardItem(studySubject.subject.gender)
oidItem = QtGui.QStandardItem("")
for sREST in self._subjectsREST:
if sREST.studySubjectId == studySubject.label:
oidItem = QtGui.QStandardItem(sREST.oid)
studySubject.oid = sREST.oid
self.subjectsModel.setItem(row, 0, pidItem)
self.subjectsModel.setItem(row, 1, labelItem)
self.subjectsModel.setItem(row, 2, secondaryLabelItem)
self.subjectsModel.setItem(row, 3, genderItem)
self.subjectsModel.setItem(row, 4, enrollmentDateItem)
self.subjectsModel.setItem(row, 5, oidItem)
row = row + 1
# Create a proxy model to enable Sorting and filtering
self.studySubjectProxyModel = QtGui.QSortFilterProxyModel()
self.studySubjectProxyModel.setSourceModel(self.subjectsModel)
self.studySubjectProxyModel.setDynamicSortFilter(True)
self.studySubjectProxyModel.setFilterCaseSensitivity(QtCore.Qt.CaseInsensitive)
# Connect to filtering UI element
QtCore.QObject.connect(self.txtStudySubjectFilter, QtCore.SIGNAL("textChanged(QString)"), self.studySubjectProxyModel.setFilterRegExp)
# Set the models Views
self.tvStudySubjects.setModel(self.studySubjectProxyModel)
# Resize the width of columns to fit the content
self.tvStudySubjects.resizeColumnsToContents()
# After the view has model, set currentChanged behaviour
self.tvStudySubjects.selectionModel().currentChanged.connect(self.tblStudySubjectItemChanged)
self.tabWidget.setEnabled(True)
self.window().statusBar.showMessage("Ready")
self.window().disableIndefiniteProgess()
def loadEventsFinished(self, events):
"""Finished loading events data
"""
eventsREST = events.toPyObject()
# Quick way of crating simple viewModel
self.eventsModel = QtGui.QStandardItemModel()
self.eventsModel.setHorizontalHeaderLabels(["Name", "Description", "Category", "Type", "Repeating", "Start date", "Status"])
row = 0
for event in self._selectedStudySubject.events:
nameItem = QtGui.QStandardItem(event.name)
descriptionItem = QtGui.QStandardItem(event.description)
categoryItem = QtGui.QStandardItem(event.category)
typeItem = QtGui.QStandardItem(event.eventType)
isRepeatingItem = QtGui.QStandardItem(str(event.isRepeating))
startDateItem = QtGui.QStandardItem("{:%d-%m-%Y}".format(event.startDate))
# Enhance with information from REST
statusItem = QtGui.QStandardItem()
for e in eventsREST:
if e.eventDefinitionOID == event.eventDefinitionOID and e.startDate.isoformat() == event.startDate.isoformat():
event.status = e.status
event.studyEventRepeatKey = e.studyEventRepeatKey
if event.isRepeating:
nameItem = QtGui.QStandardItem(event.name + " [" + event.studyEventRepeatKey + "]")
statusItem = QtGui.QStandardItem(event.status)
event.forms = e.forms
self.eventsModel.setItem(row, 0, nameItem)
self.eventsModel.setItem(row, 1, descriptionItem)
self.eventsModel.setItem(row, 2, categoryItem)
self.eventsModel.setItem(row, 3, typeItem)
self.eventsModel.setItem(row, 4, isRepeatingItem)
self.eventsModel.setItem(row, 5, startDateItem)
self.eventsModel.setItem(row, 6, statusItem)
row = row + 1
self.studyEventProxyModel = QtGui.QSortFilterProxyModel()
self.studyEventProxyModel.setSourceModel(self.eventsModel)
self.studyEventProxyModel.setDynamicSortFilter(True)
self.studyEventProxyModel.setFilterCaseSensitivity(QtCore.Qt.CaseInsensitive)
QtCore.QObject.connect(self.txtStudyEventFilter, QtCore.SIGNAL("textChanged(QString)"), self.studyEventProxyModel.setFilterRegExp)
self.tvStudyEvents.setModel(self.studyEventProxyModel)
self.tvStudyEvents.resizeColumnsToContents()
self.tvStudyEvents.selectionModel().currentChanged.connect(self.tblStudyEventItemChanged)
# Update status bar
self.tabWidget.setEnabled(True)
self.window().statusBar.showMessage("Ready")
self.window().disableIndefiniteProgess()
## ## ######## ###### ###### ### ###### ######## ######
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#### #### ## ## ## ## ## ## ## ##
## ### ## ###### ###### ###### ## ## ## #### ###### ######
## ## ## ## ## ######### ## ## ## ##
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def Question(self, string):
"""Question message box
"""
reply = QtGui.QMessageBox.question(self, "Question", string, QtGui.QMessageBox.Yes, QtGui.QMessageBox.No)
if reply == QtGui.QMessageBox.Yes:
self.btnUpload.setEnabled(False)
else:
self.btnUpload.setEnabled(True)
def Error(self, string):
"""Error message box
"""
QtGui.QMessageBox.critical(self, "Error", string)
self.btnUpload.setEnabled(True)
def Warning(self, string):
"""Warning message box
"""
QtGui.QMessageBox.warning(self, "Warning", string)
self.btnUpload.setEnabled(True)
def Message(self, string):
"""Called from message event, opens a small window with the message
"""
QtGui.QMessageBox.about(self, "Info", string)
self.btnUpload.setEnabled(True)
def LogMessage(self, string):
"""Called from log event in thread and adds log into textbrowser UI
"""
self.textBrowserProgress.append(string)
ocWsHost = "http://skripcak.net:8080/OpenClinica-ws"
password = "******"
OCUserDetails().username = "******"
OCUserDetails().connected = False
# Create connection artefact to users main OpenClinica SOAP
ocConnectInfo = OCConnectInfo(
ocWsHost,
OCUserDetails().username
)
ocConnectInfo.setPassword(password)
# Initialise SOAP services
ocWebServices = OCWebServices(ocConnectInfo)
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
# Load subject for whole study or only site if it is multicentre study
if selectedStudy and selectedStudy.isMulticentre:
from rest.HttpConnectionService import HttpConnectionService
from soap.OCConnectInfo import OCConnectInfo
from soap.OCWebServices import OCWebServices
ocWsHost = "http://skripcak.net:8080/OpenClinica-ws"
password = "******"
OCUserDetails().username = "******"
OCUserDetails().connected = False
# Create connection artefact to users main OpenClinica SOAP
ocConnectInfo = OCConnectInfo(ocWsHost, OCUserDetails().username)
ocConnectInfo.setPassword(password)
# Initialise SOAP services
ocWebServices = OCWebServices(ocConnectInfo)
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
# Load subject for whole study or only site if it is multicentre study
ocWsHost = "http://skripcak.net:8080/OpenClinica-ws"
password = "******"
OCUserDetails().username = "******"
OCUserDetails().connected = False
# Create connection artefact to users main OpenClinica SOAP
ocConnectInfo = OCConnectInfo(
ocWsHost,
OCUserDetails().username
)
ocConnectInfo.setPassword(password)
# Initialise SOAP services
ocWebServices = OCWebServices(ocConnectInfo)
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
eventDefinitions = ocWebServices.listAllStydyEventDefinitionsByStudy(selectedStudy)