def __init__(self, ocConnectInfo, proxyHost="", proxyPort="", noProxy="", proxyUsr="", proxyPass="", trace=logging.INFO):
"""Constructor
Param ocConnectInfo holds the basic OpenClinica connection information
"""
self._logger = logging.getLogger(__name__)
logging.config.fileConfig("logging.ini", disable_existing_loggers=False)
self.ocConnectInfo = ocConnectInfo
proxyStr = None
if noProxy != "" and noProxy is not whitespace and noProxy in self.ocConnectInfo.baseUrl:
proxyStr = None
else:
if proxyHost != "" and proxyHost is not whitespace and proxyPort != "" and proxyPort is not whitespace:
proxyStr = proxyHost + ":" + proxyPort
if proxyStr:
self._logger.info("OC SOAP web services are going to use: " + proxyStr)
else:
self._logger.info("OC SOAP web services are going to be used with enviromental proxy (including no proxy).")
self._logger.info("OC SOAP web services are going to be used with authentication: " + str(proxyUsr))
# Define OC WS bindings
self.studyBinding = OCStudyWsService(self.ocConnectInfo.baseUrl + STUDYURL, proxyStr, proxyUsr, proxyPass, trace)
self.dataBinding = OCDataWsService(self.ocConnectInfo.baseUrl + DATAURL, proxyStr, proxyUsr, proxyPass, trace)
self.studySubjectBinding = OCStudySubjectWsService(self.ocConnectInfo.baseUrl + STUDYSUBJECTURL, proxyStr, proxyUsr, proxyPass, trace)
self.studyEventDefinitionBinding = OCStudyEventDefinitionWsService(self.ocConnectInfo.baseUrl + STUDYEVENTDEFURL, proxyStr, proxyUsr, proxyPass, trace)
self.eventBinding = OCEventWsService(self.ocConnectInfo.baseUrl + DATAURL, proxyStr, proxyUsr, proxyPass, trace)
# Define WSSE security
self.studyBinding.wsse(self.ocConnectInfo.userName, self.ocConnectInfo.passwordHash)
self.dataBinding.wsse(self.ocConnectInfo.userName, self.ocConnectInfo.passwordHash)
self.studySubjectBinding.wsse(self.ocConnectInfo.userName, self.ocConnectInfo.passwordHash)
self.studyEventDefinitionBinding.wsse(self.ocConnectInfo.userName, self.ocConnectInfo.passwordHash)
self.eventBinding.wsse(self.ocConnectInfo.userName, self.ocConnectInfo.passwordHash)
def __init__(self,
ocConnectInfo,
proxyHost="",
proxyPort="",
noProxy="",
proxyUsr="",
proxyPass="",
trace=logging.INFO):
"""Constructor
Param ocConnectInfo holds the basic OpenClinica connection information
"""
self._logger = logging.getLogger(__name__)
logging.config.fileConfig("logging.ini",
disable_existing_loggers=False)
self.ocConnectInfo = ocConnectInfo
proxyStr = None
if noProxy != "" and noProxy is not whitespace and noProxy in self.ocConnectInfo.baseUrl:
proxyStr = None
else:
if proxyHost != "" and proxyHost is not whitespace and proxyPort != "" and proxyPort is not whitespace:
proxyStr = proxyHost + ":" + proxyPort
if proxyStr:
self._logger.info("OC SOAP web services are going to use: " +
proxyStr)
else:
self._logger.info(
"OC SOAP web services are going to be used with enviromental proxy (including no proxy)."
)
self._logger.info(
"OC SOAP web services are going to be used with authentication: " +
str(proxyUsr))
# Define OC WS bindings
self.studyBinding = OCStudyWsService(
self.ocConnectInfo.baseUrl + STUDYURL, proxyStr, proxyUsr,
proxyPass, trace)
self.dataBinding = OCDataWsService(
self.ocConnectInfo.baseUrl + DATAURL, proxyStr, proxyUsr,
proxyPass, trace)
self.studySubjectBinding = OCStudySubjectWsService(
self.ocConnectInfo.baseUrl + STUDYSUBJECTURL, proxyStr, proxyUsr,
proxyPass, trace)
self.studyEventDefinitionBinding = OCStudyEventDefinitionWsService(
self.ocConnectInfo.baseUrl + STUDYEVENTDEFURL, proxyStr, proxyUsr,
proxyPass, trace)
self.eventBinding = OCEventWsService(
self.ocConnectInfo.baseUrl + DATAURL, proxyStr, proxyUsr,
proxyPass, trace)
# Define WSSE security
self.studyBinding.wsse(self.ocConnectInfo.userName,
self.ocConnectInfo.passwordHash)
self.dataBinding.wsse(self.ocConnectInfo.userName,
self.ocConnectInfo.passwordHash)
self.studySubjectBinding.wsse(self.ocConnectInfo.userName,
self.ocConnectInfo.passwordHash)
self.studyEventDefinitionBinding.wsse(self.ocConnectInfo.userName,
self.ocConnectInfo.passwordHash)
self.eventBinding.wsse(self.ocConnectInfo.userName,
self.ocConnectInfo.passwordHash)
class OCWebServices():
"""SOAP web services to OpenClinica
Unify and simplify the access to OC web services methods
"""
#----------------------------------------------------------------------
#--------------------------- Constructors -----------------------------
def __init__(self, ocConnectInfo, proxyHost="", proxyPort="", noProxy="", proxyUsr="", proxyPass="", trace=logging.INFO):
"""Constructor
Param ocConnectInfo holds the basic OpenClinica connection information
"""
self._logger = logging.getLogger(__name__)
logging.config.fileConfig("logging.ini", disable_existing_loggers=False)
self.ocConnectInfo = ocConnectInfo
proxyStr = None
if noProxy != "" and noProxy is not whitespace and noProxy in self.ocConnectInfo.baseUrl:
proxyStr = None
else:
if proxyHost != "" and proxyHost is not whitespace and proxyPort != "" and proxyPort is not whitespace:
proxyStr = proxyHost + ":" + proxyPort
if proxyStr:
self._logger.info("OC SOAP web services are going to use: " + proxyStr)
else:
self._logger.info("OC SOAP web services are going to be used with enviromental proxy (including no proxy).")
self._logger.info("OC SOAP web services are going to be used with authentication: " + str(proxyUsr))
# Define OC WS bindings
self.studyBinding = OCStudyWsService(self.ocConnectInfo.baseUrl + STUDYURL, proxyStr, proxyUsr, proxyPass, trace)
self.dataBinding = OCDataWsService(self.ocConnectInfo.baseUrl + DATAURL, proxyStr, proxyUsr, proxyPass, trace)
self.studySubjectBinding = OCStudySubjectWsService(self.ocConnectInfo.baseUrl + STUDYSUBJECTURL, proxyStr, proxyUsr, proxyPass, trace)
self.studyEventDefinitionBinding = OCStudyEventDefinitionWsService(self.ocConnectInfo.baseUrl + STUDYEVENTDEFURL, proxyStr, proxyUsr, proxyPass, trace)
self.eventBinding = OCEventWsService(self.ocConnectInfo.baseUrl + DATAURL, proxyStr, proxyUsr, proxyPass, trace)
# Define WSSE security
self.studyBinding.wsse(self.ocConnectInfo.userName, self.ocConnectInfo.passwordHash)
self.dataBinding.wsse(self.ocConnectInfo.userName, self.ocConnectInfo.passwordHash)
self.studySubjectBinding.wsse(self.ocConnectInfo.userName, self.ocConnectInfo.passwordHash)
self.studyEventDefinitionBinding.wsse(self.ocConnectInfo.userName, self.ocConnectInfo.passwordHash)
self.eventBinding.wsse(self.ocConnectInfo.userName, self.ocConnectInfo.passwordHash)
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#----------------------------------------------------------------------
#----------------------------- Studies --------------------------------
def getStudyMetadata(self, study, thread=None):
"""Get ODM metadata for study
Param study specifies the study
Returns XML ODM metadata of the study
"""
sucessfull = False
result = ""
data = None
result, data = self.studyBinding.getMetadata(study)
if result == STATUSSUCCCESS:
sucessfull = True
elif result == STATUSFAIL:
sucessfull = False
if thread:
thread.emit(QtCore.SIGNAL("finished(QVariant)"), str(data))
return None
else:
return sucessfull, data
def listAllStudies(self, data=None, thread=None):
"""Query studies available for the user
Returns collection of study domain objects
"""
self._logger.debug("listAllStudies")
successful = False
result = ""
data = None
result, data = self.studyBinding.listAll()
if result == STATUSSUCCCESS:
successful = True
elif result == STATUSFAIL:
successful = False
if thread:
thread.emit(QtCore.SIGNAL("finished(QVariant)"), data)
return None
else:
return successful, data
#----------------------------------------------------------------------
#----------------------------- Subjects -------------------------------
def listAllStudySubjectsByStudy(self, data=None, thread=None):
"""Query all study subject by study
Returns collection of studySubject domain objects
"""
if data:
study = data[0]
metadata = data[1]
result = self.studySubjectBinding.listAllByStudy(study, metadata)
if thread:
thread.emit(QtCore.SIGNAL("finished(QVariant)"), result)
return None
else:
return result
def listAllStudySubjectsByStudySite(self, data=None, thread=None):
"""Query all study subject by study site
Returns collection of studySubject domain objects
"""
if data:
study = data[0]
site = data[1]
metadata = data[2]
result = self.studySubjectBinding.listAllByStudySite(study, site, metadata)
if thread:
thread.emit(QtCore.SIGNAL("finished(QVariant)"), result)
return None
else:
return result
def createStudySubject(self, studySubject, study, studySite=None, metedata=None):
"""Create new StudySubject entity in OC
"""
return self.studySubjectBinding.create(studySubject, study)
def isStudySbuject(self, studySubject, study, studySite= None):
"""Checks if the specified subject belgons to OC studySbujects
"""
return self.studySubjectBinding.isStudySubject(studySubject, study)
#----------------------------------------------------------------------
#----------------------------- Study Event ----------------------------
def scheduleStudyEvent(self, study, studySubject, event):
"""Schedule study event for studySbuject
"""
successful = False
result = ""
result = self.eventBinding.schedule(study, studySubject, event)
if result == STATUSSUCCCESS:
successful = True
elif result == STATUSFAIL:
successful = False
return successful
def listAllStydyEventDefinitionsByStudy(self, study):
"""Query all study events by study
Returns collection of studyEventDefinition domain objects
"""
return self.studyEventDefinitionBinding.listAllByStudy(study)
#----------------------------------------------------------------------
#--------------------------------- Data -------------------------------
def importODM(self, odm):
"""Import ODM structured data into OC
Param odm is XML formated data according to ODM and study metadata
Returns result of the import
"""
successful = False
result = ""
result = self.dataBinding.importData(odm)
if result == STATUSSUCCCESS:
successful = True
elif result == STATUSFAIL:
successful = False
return successful
class OCWebServices():
"""SOAP web services to OpenClinica
Unify and simplify the access to OC web services methods
"""
#----------------------------------------------------------------------
#--------------------------- Constructors -----------------------------
def __init__(self,
ocConnectInfo,
proxyHost="",
proxyPort="",
noProxy="",
proxyUsr="",
proxyPass="",
trace=logging.INFO):
"""Constructor
Param ocConnectInfo holds the basic OpenClinica connection information
"""
self._logger = logging.getLogger(__name__)
logging.config.fileConfig("logging.ini",
disable_existing_loggers=False)
self.ocConnectInfo = ocConnectInfo
proxyStr = None
if noProxy != "" and noProxy is not whitespace and noProxy in self.ocConnectInfo.baseUrl:
proxyStr = None
else:
if proxyHost != "" and proxyHost is not whitespace and proxyPort != "" and proxyPort is not whitespace:
proxyStr = proxyHost + ":" + proxyPort
if proxyStr:
self._logger.info("OC SOAP web services are going to use: " +
proxyStr)
else:
self._logger.info(
"OC SOAP web services are going to be used with enviromental proxy (including no proxy)."
)
self._logger.info(
"OC SOAP web services are going to be used with authentication: " +
str(proxyUsr))
# Define OC WS bindings
self.studyBinding = OCStudyWsService(
self.ocConnectInfo.baseUrl + STUDYURL, proxyStr, proxyUsr,
proxyPass, trace)
self.dataBinding = OCDataWsService(
self.ocConnectInfo.baseUrl + DATAURL, proxyStr, proxyUsr,
proxyPass, trace)
self.studySubjectBinding = OCStudySubjectWsService(
self.ocConnectInfo.baseUrl + STUDYSUBJECTURL, proxyStr, proxyUsr,
proxyPass, trace)
self.studyEventDefinitionBinding = OCStudyEventDefinitionWsService(
self.ocConnectInfo.baseUrl + STUDYEVENTDEFURL, proxyStr, proxyUsr,
proxyPass, trace)
self.eventBinding = OCEventWsService(
self.ocConnectInfo.baseUrl + DATAURL, proxyStr, proxyUsr,
proxyPass, trace)
# Define WSSE security
self.studyBinding.wsse(self.ocConnectInfo.userName,
self.ocConnectInfo.passwordHash)
self.dataBinding.wsse(self.ocConnectInfo.userName,
self.ocConnectInfo.passwordHash)
self.studySubjectBinding.wsse(self.ocConnectInfo.userName,
self.ocConnectInfo.passwordHash)
self.studyEventDefinitionBinding.wsse(self.ocConnectInfo.userName,
self.ocConnectInfo.passwordHash)
self.eventBinding.wsse(self.ocConnectInfo.userName,
self.ocConnectInfo.passwordHash)
## ## ######## ######## ## ## ####### ######## ######
### ### ## ## ## ## ## ## ## ## ## ##
#### #### ## ## ## ## ## ## ## ## ##
## ### ## ###### ## ######### ## ## ## ## ######
## ## ## ## ## ## ## ## ## ## ##
## ## ## ## ## ## ## ## ## ## ## ##
## ## ######## ## ## ## ####### ######## ######
#----------------------------------------------------------------------
#----------------------------- Studies --------------------------------
def getStudyMetadata(self, study, thread=None):
"""Get ODM metadata for study
Param study specifies the study
Returns XML ODM metadata of the study
"""
sucessfull = False
result = ""
data = None
result, data = self.studyBinding.getMetadata(study)
if result == STATUSSUCCCESS:
sucessfull = True
elif result == STATUSFAIL:
sucessfull = False
if thread:
thread.emit(QtCore.SIGNAL("finished(QVariant)"), str(data))
return None
else:
return sucessfull, data
def listAllStudies(self, data=None, thread=None):
"""Query studies available for the user
Returns collection of study domain objects
"""
self._logger.debug("listAllStudies")
successful = False
result = ""
data = None
result, data = self.studyBinding.listAll()
if result == STATUSSUCCCESS:
successful = True
elif result == STATUSFAIL:
successful = False
if thread:
thread.emit(QtCore.SIGNAL("finished(QVariant)"), data)
return None
else:
return successful, data
#----------------------------------------------------------------------
#----------------------------- Subjects -------------------------------
def listAllStudySubjectsByStudy(self, data=None, thread=None):
"""Query all study subject by study
Returns collection of studySubject domain objects
"""
if data:
study = data[0]
metadata = data[1]
result = self.studySubjectBinding.listAllByStudy(study, metadata)
if thread:
thread.emit(QtCore.SIGNAL("finished(QVariant)"), result)
return None
else:
return result
def listAllStudySubjectsByStudySite(self, data=None, thread=None):
"""Query all study subject by study site
Returns collection of studySubject domain objects
"""
if data:
study = data[0]
site = data[1]
metadata = data[2]
result = self.studySubjectBinding.listAllByStudySite(
study, site, metadata)
if thread:
thread.emit(QtCore.SIGNAL("finished(QVariant)"), result)
return None
else:
return result
def createStudySubject(self,
studySubject,
study,
studySite=None,
metedata=None):
"""Create new StudySubject entity in OC
"""
return self.studySubjectBinding.create(studySubject, study)
def isStudySbuject(self, studySubject, study, studySite=None):
"""Checks if the specified subject belgons to OC studySbujects
"""
return self.studySubjectBinding.isStudySubject(studySubject, study)
#----------------------------------------------------------------------
#----------------------------- Study Event ----------------------------
def scheduleStudyEvent(self, study, studySubject, event):
"""Schedule study event for studySbuject
"""
successful = False
result = ""
result = self.eventBinding.schedule(study, studySubject, event)
if result == STATUSSUCCCESS:
successful = True
elif result == STATUSFAIL:
successful = False
return successful
def listAllStydyEventDefinitionsByStudy(self, study):
"""Query all study events by study
Returns collection of studyEventDefinition domain objects
"""
return self.studyEventDefinitionBinding.listAllByStudy(study)
#----------------------------------------------------------------------
#--------------------------------- Data -------------------------------
def importODM(self, odm):
"""Import ODM structured data into OC
Param odm is XML formated data according to ODM and study metadata
Returns result of the import
"""
successful = False
result = ""
result = self.dataBinding.importData(odm)
if result == STATUSSUCCCESS:
successful = True
elif result == STATUSFAIL:
successful = False
return successful