def _enableUpgradeFlag(self):
"""Setup upgrade flag to application config
"""
AppConfigurationService().add("Temp")
AppConfigurationService().set("Temp", "isUpgrading", str(True))
AppConfigurationService().set("Temp", "upgradeFinished", str(False))
AppConfigurationService().saveConfiguration()
def startup():
"""Start the updater
"""
logger = logging.getLogger(__name__)
logging.config.fileConfig("logging.ini", disable_existing_loggers=False)
logger.info("Updater folder contains: ")
logger.info(os.listdir("./"))
appConfig = None
# Running from source or packed executable
if (os.path.isfile("mainClient.py")
or os.path.isfile("RadPlanBio-client.exe")):
appConfig = AppConfigurationService("radplanbio-client.cfg")
else:
appConfig = AppConfigurationService("../radplanbio-client.cfg")
section = "Temp"
if appConfig.hasSection(section):
isUpgrading = appConfig.get(section)["isupgrading"]
upgradeFinished = appConfig.get(section)["upgradefinished"]
app = QtGui.QApplication(sys.argv)
# Startup
if isUpgrading == "False":
# Exit updater
app.quit()
else:
# Start upgrade procedure
svcUpgrade = UpgradeService()
svcUpgrade.upgrade()
# Start client (RadPlanBio-client.exe)
if platform.system() == "Windows":
if os.path.isfile("../RadPlanBio-client.exe"):
QtCore.QProcess.startDetached("../RadPlanBio-client.exe")
elif os.path.isfile("RadPlanBio-client.exe"):
QtCore.QProcess.startDetached("RadPlanBio-client.exe")
else:
QtCore.QProcess.startDetached("python mainClient.py")
elif platform.system() == "Linux":
if os.path.isfile("../RadPlanBio-client"):
QtCore.QProcess.startDetached("../RadPlanBio-client")
else:
QtCore.QProcess.startDetached("python mainClient.py")
else:
QtCore.QProcess.startDetached("python mainClient.py")
# Exit updater
app.quit()
def configure():
"""Read configuration settings from config file
"""
appConfig = AppConfigurationService(ConfigDetails().configFileName)
section = "OpenClinica"
if appConfig.hasSection(section):
option = "host"
if appConfig.hasOption(section, option):
ConfigDetails().ocHost = appConfig.get(section)[option]
option = "port"
if appConfig.hasOption(section, option):
ConfigDetails().ocPort = appConfig.get(section)[option]
section = "OpenClinica-ws"
if appConfig.hasSection(section):
option = "host"
if appConfig.hasOption(section, option):
ConfigDetails().ocWsHost = appConfig.get(section)[option]
option = "port"
if appConfig.hasOption(section, option):
ConfigDetails().ocWsPort = appConfig.get(section)[option]
section = "Proxy"
if appConfig.hasSection(section):
option = "enabled"
if appConfig.hasOption(section, option):
ConfigDetails().proxyEnabled = appConfig.getboolean(section, option)
option = "host"
if appConfig.hasOption(section, option):
ConfigDetails().proxyHost = appConfig.get(section)[option]
option = "port"
if appConfig.hasOption(section, option):
ConfigDetails().proxyPort = appConfig.get(section)[option]
option = "noproxy"
if appConfig.hasOption(section, option):
ConfigDetails().noProxy = appConfig.get(section)[option]
section = "Proxy-auth"
if appConfig.hasSection(section):
option = "enabled"
if appConfig.hasOption(section, option):
ConfigDetails().proxyAuthEnabled = appConfig.getboolean(section, option)
option = "login"
if appConfig.hasOption(section, option):
ConfigDetails().proxyAuthLogin = appConfig.get(section)[option]
option = "password"
if appConfig.hasOption(section, option):
ConfigDetails().proxyAuthPassword = appConfig.get(section)[option]
section = "GUI"
if appConfig.hasSection(section):
option = "main.width"
if appConfig.hasOption(section, option):
ConfigDetails().width = int(appConfig.get(section)[option])
option = "main.height"
if appConfig.hasOption(section, option):
ConfigDetails().height = int(appConfig.get(section)[option])
def __init__(self, parent=None):
"""Constructor of ExportModule View
"""
QWidget.__init__(self, parent)
self.parent = parent
#-----------------------------------------------------------------------
#----------------------- Logger ----------------------------------------
self.logger = logging.getLogger(__name__)
logging.config.fileConfig('logging.ini',
disable_existing_loggers=False)
#-----------------------------------------------------------------------
#---------------------- App config --------------------------------------
self.appConfig = AppConfigurationService()
#-----------------------------------------------------------------------
#--------------------- Create Module UI --------------------------------
self.setupUi(self)
#-----------------------------------------------------------------------
#----------------------- Services --------------------------------------
# There are two http services, one for communicating with my own
# site server/database
section = "RadPlanBioServer"
hostname = self.appConfig.get(section)["host"]
port = self.appConfig.get(section)["port"]
self.svcHttp = HttpConnectionService(hostname, port, UserDetails())
#TODO: SiteName according to user account
self.mySite = self.svcHttp.getPartnerSiteByName("DKTK-DRESDEN")
baseUrl = self.mySite.edc.soapbaseurl
# Create connection artefact to OC
self.ocConnectInfo = OCConnectInfo(baseUrl, OCUserDetails().username)
self.ocConnectInfo.setPassword(OCUserDetails().password)
self.ocWebServices = OCWebServices(self.ocConnectInfo)
# Create REST mainzellieste
userName = self.mySite.pidg.adminusername
password = self.mySite.pidg.adminpassword
baseUrl = self.mySite.pidg.generatorbaseurl
apiKey = self.mySite.pidg.apikey
connectInfo = MainzellisteConnectInfo(baseUrl, userName, password,
apiKey)
self.svcPseudonymisation = PseudonymisationService(connectInfo)
#-----------------------------------------------------------------------
#----------------------- On Create -------------------------------------
self.reloadSites()
#-----------------------------------------------------------------------
#---------- Load modules buttons - events definitions ------------------
self.btnNew.clicked.connect(self.btnNewClicked)
self.btnReload.clicked.connect(self.btnReloadClicked)
self.tvStudies.selectionModel().currentChanged.connect(
self.tvStudyChanged)
def _disableUpgradeFlag(self):
"""Remove upgrade flag from application config
"""
AppConfigurationService().remove("Temp")
AppConfigurationService().saveConfiguration()
def _enableUpgradeFinishedFlag(self):
"""
"""
AppConfigurationService().set("Temp", "isUpgrading", str(False))
AppConfigurationService().set("Temp", "upgradeFinished", str(True))
AppConfigurationService().saveConfiguration()
def __init__(self, parent=None):
"""Constructor of ExportModule View
"""
QWidget.__init__(self, parent)
self.parent = parent
#-----------------------------------------------------------------------
#----------------------- Logger ----------------------------------------
self.logger = logging.getLogger(__name__)
logging.config.fileConfig('logging.ini',
disable_existing_loggers=False)
#-----------------------------------------------------------------------
#---------------------- App config --------------------------------------
self.appConfig = AppConfigurationService()
#-----------------------------------------------------------------------
#--------------------- Create Module UI --------------------------------
self.setupUi(self)
#-----------------------------------------------------------------------
#---------- Load modules buttons - events definitions ------------------
self.btnReload.clicked.connect(self.btnReloadClicked)
self.btnMapExportField.clicked.connect(self.btnMapExportFieldClicked)
self.btnLocateDataFilename.clicked.connect(
self.btnLocateDataFilenameClicked)
self.btnLocateMetaDataFilename.clicked.connect(
self.btnLocateMetaDataFilenameClicked)
self.btnValidateMapping.clicked.connect(
self.btnValidateDataTransformationClicked)
self.btnLoadMapping.clicked.connect(self.btnLoadMappingClicked)
self.cmbStudyEvent.currentIndexChanged['QString'].connect(
self.cmbStudyEventChanged)
self.cmbEventForm.currentIndexChanged['QString'].connect(
self.cmbEventFormChanged)
#-----------------------------------------------------------------------
# Domain model
self.__study = None
self.__studyEvents = []
self.__selectedStudyEvent = None
self.__studyEventCrfs = []
self.__selectedEventCrf = None
#-----------------------------------------------------------------------
#----------------------- Services --------------------------------------
# There are two http services, one for communicating with my own
# site server/database
section = "MySiteServer"
hostname = self.appConfig.get(section)["host"]
port = self.appConfig.get(section)["port"]
self.svcHttp = HttpConnectionService(hostname, port, UserDetails())
self.reload()
#-----------------------------------------------------------------------
# TODO: make it a Stragety desing pattern later
self.fileDataService = CsvFileDataService()
self.fileMetaDataService = OdmFileDataService()
self.exportMapping = []
# Just for testing to have guick access to files
self.dataFilename = "/mnt/edv/skripcakt/ulice/branches/radplanbio/data/radiochemotherapy.csv"
self.metaDataFilename = "/mnt/edv/skripcakt/ulice/branches/radplanbio/data/HNSCCStudyMetadata.xml"
#-----------------------------------------------------------------------
# Create REST mainzellieste
userName = "******"
password = "******"
baseUrl = "http://g89rtpsrv.med.tu-dresden.de:8080/mainzelliste-1.1-SNAPSHOT/"
apiKey = "mdatdd"
connectInfo = MainzellisteConnectInfo(baseUrl, userName, password,
apiKey)
self.svcPseudonymisation = PseudonymisationService(connectInfo)
def configure():
"""Read configuration settings from config file
"""
appConfig = AppConfigurationService(ConfigDetails().configFileName)
section = "RadPlanBioServer"
if appConfig.hasSection(section):
if appConfig.hasOption(section, "host"):
ConfigDetails().rpbHost = appConfig.get(section)["host"]
if appConfig.hasOption(section, "port"):
ConfigDetails().rpbHostPort = appConfig.get(section)["port"]
if appConfig.hasOption(section, "application"):
ConfigDetails().rpbApplication = appConfig.get(
section)["application"]
section = "Proxy"
if appConfig.hasSection(section):
if appConfig.hasOption(section, "enabled"):
ConfigDetails().proxyEnabled = appConfig.getboolean(
section, "enabled")
if appConfig.hasOption(section, "host"):
ConfigDetails().proxyHost = appConfig.get(section)["host"]
if appConfig.hasOption(section, "port"):
ConfigDetails().proxyPort = appConfig.get(section)["port"]
if appConfig.hasOption(section, "noproxy"):
ConfigDetails().noProxy = appConfig.get(section)["noproxy"]
section = "Proxy-auth"
if appConfig.hasSection(section):
if appConfig.hasOption(section, "enabled"):
ConfigDetails().proxyAuthEnabled = appConfig.getboolean(
section, "enabled")
if appConfig.hasOption(section, "login"):
ConfigDetails().proxyAuthLogin = appConfig.get(section)["login"]
if appConfig.hasOption(section, "password"):
ConfigDetails().proxyAuthPassword = appConfig.get(
section)["password"]
section = "GUI"
if appConfig.hasSection(section):
if appConfig.hasOption(section, "main.width"):
ConfigDetails().width = int(appConfig.get(section)["main.width"])
if appConfig.hasOption(section, "main.height"):
ConfigDetails().height = int(appConfig.get(section)["main.height"])
section = "DICOM"
if appConfig.hasSection(section):
if appConfig.hasOption(section, "replacepatientnamewith"):
ConfigDetails().replacePatientNameWith = appConfig.get(
section)["replacepatientnamewith"]
if appConfig.hasOption(section, "constpatientname"):
ConfigDetails().constPatientName = appConfig.get(
section)["constpatientname"]
if appConfig.hasOption(section, "allowmultiplepatientids"):
ConfigDetails().allowMultiplePatientIDs = appConfig.getboolean(
section, "allowmultiplepatientids")
if appConfig.hasOption(section, "retainpatientcharacteristicsoption"):
ConfigDetails(
).retainPatientCharacteristicsOption = appConfig.getboolean(
section, "retainpatientcharacteristicsoption")
if appConfig.hasOption(section, "retainstudydate"):
ConfigDetails().retainStudyDate = appConfig.getboolean(
section, "retainstudydate")
if appConfig.hasOption(section, "retainstudytime"):
ConfigDetails().retainStudyTime = appConfig.getboolean(
section, "retainstudytime")
if appConfig.hasOption(section, "retainseriesdate"):
ConfigDetails().retainSeriesDate = appConfig.getboolean(
section, "retainseriesdate")
if appConfig.hasOption(section, "retainseriestime"):
ConfigDetails().retainSeriesTime = appConfig.getboolean(
section, "retainseriestime")
if appConfig.hasOption(section, "retainstudyseriesdescriptions"):
ConfigDetails(
).retainStudySeriesDescriptions = appConfig.getboolean(
section, "retainstudyseriesdescriptions")
if appConfig.hasOption(section, "autortstructmatch"):
ConfigDetails().autoRTStructMatch = appConfig.getboolean(
section, "autortstructmatch")
if appConfig.hasOption(section, "autortstructref"):
ConfigDetails().autoRTStructRef = appConfig.getboolean(
section, "autortstructref")
if appConfig.hasOption(section, "downloaddicompatientfoldername"):
ConfigDetails().downloadDicomPatientFolderName = appConfig.get(
section)["downloaddicompatientfoldername"]
if appConfig.hasOption(section, "downloaddicomstudyfoldername"):
ConfigDetails().downloadDicomStudyFolderName = appConfig.get(
section)["downloaddicomstudyfoldername"]
section = "AE"
if appConfig.hasSection(section):
if appConfig.hasOption(section, "name"):
ConfigDetails().rpbAE = appConfig.get(section)["name"]
if appConfig.hasOption(section, "port"):
ConfigDetails().rpbAEport = int(appConfig.get(section)["port"])
if appConfig.hasOption(section, "aetsuffix"):
ConfigDetails().rpbAETsuffix = appConfig.get(section)["aetsuffix"]
if not ApplicationEntityService().isReady:
if ConfigDetails(
).rpbAE is not None and ConfigDetails().rpbAE != "":
# Consider AET suffix option when creating AE for client
AET = ConfigDetails().rpbAE
if ConfigDetails().rpbAETsuffix == "host":
AET += str(QtNetwork.QHostInfo.localHostName())
elif ConfigDetails().rpbAETsuffix == "fqdn":
AET += str(
QtNetwork.QHostInfo.localHostName()) + "." + str(
QtNetwork.QHostInfo.localDomainName())
ApplicationEntityService().init(AET, ConfigDetails().rpbAEport)
aeCount = 0
section = "RemoteAEs"
if appConfig.hasSection(section):
if appConfig.hasOption(section, "count"):
aeCount = int(appConfig.get(section)["count"])
for i in range(0, aeCount):
section = "RemoteAE" + str(i)
if appConfig.hasSection(section):
address = ""
if appConfig.hasOption(section, "address"):
address = appConfig.get(section)["address"]
port = -1
if appConfig.hasOption(section, "port"):
port = int(appConfig.get(section)["port"])
aet = ""
if appConfig.hasOption(section, "aet"):
aet = appConfig.get(section)["aet"]
ConfigDetails().remoteAEs.append(
dict(Address=address, Port=port, AET=aet))
section = "SanityTests"
if appConfig.hasSection(section):
if appConfig.hasOption(section, "patientgendermatch"):
ConfigDetails().patientGenderMatch = appConfig.getboolean(
section, "patientGenderMatch")
if appConfig.hasOption(section, "patientdobmatch"):
ConfigDetails().patientDobMatch = appConfig.getboolean(
section, "patientDobMatch")
section = "General"
if appConfig.hasSection(section):
if appConfig.hasOption(section, "startupupdatecheck"):
ConfigDetails().startupUpdateCheck = appConfig.getboolean(
section, "startupupdatecheck")
section = "Temp"
if appConfig.hasSection(section):
if appConfig.hasOption(section, "isupgrading"):
ConfigDetails().isUpgrading = appConfig.get(section)["isupgrading"]
if appConfig.hasOption(section, "upgradefinished"):
ConfigDetails().upgradeFinished = appConfig.get(
section)["upgradefinished"]