def setUp(self):
oc_settings = OpenClinicaSettings(
domain=DOMAIN,
study=StudySettings(
is_ws_enabled=False,
metadata=TEST_METADATA
)
)
oc_settings.save()
def setUp(self):
oc_settings = OpenClinicaSettings(
domain=DOMAIN,
study=StudySettings(
is_ws_enabled=False,
metadata=TEST_METADATA
)
)
oc_settings.save()
def _close(self):
from custom.openclinica.models import OpenClinicaAPI, OpenClinicaSettings
# Create the subjects and events that are in the ODM export using the API
oc_settings = OpenClinicaSettings.for_domain(self.context['domain'])
if oc_settings.study.is_ws_enabled:
password = bz2.decompress(b64decode(oc_settings.study.password))
api = OpenClinicaAPI(
oc_settings.study.url,
oc_settings.study.username,
password,
oc_settings.study.protocol_id
)
subject_keys = api.get_subject_keys()
for subject in self.context['subjects']:
if subject['subject_key'][3:] not in subject_keys:
# Skip 'SS_' prefix ^^ that OpenClinica wants in ODM, but isn't in API's subject keys
api.create_subject(subject)
# NOTE: In the interests of keeping data in OpenClinica tidy, we are only scheduling events for
# subjects who don't yet exist in OpenClinica. New events of existing subjects must be added
# manually, or subjects must be deleted from OpenClinica before a re-import.
for event in subject['events']:
api.schedule_event(subject, event)
self.file.write(render_to_string('couchexport/odm_export.xml', self.context))
def _close(self):
from custom.openclinica.models import OpenClinicaAPI, OpenClinicaSettings
# Create the subjects and events that are in the ODM export using the API
oc_settings = OpenClinicaSettings.for_domain(self.context['domain'])
if oc_settings.study.is_ws_enabled:
password = bz2.decompress(b64decode(oc_settings.study.password))
api = OpenClinicaAPI(
oc_settings.study.url,
oc_settings.study.username,
password,
oc_settings.study.protocol_id
)
subject_keys = api.get_subject_keys()
for subject in self.context['subjects']:
if subject['subject_key'][3:] not in subject_keys:
# Skip 'SS_' prefix ^^ that OpenClinica wants in ODM, but isn't in API's subject keys
api.create_subject(subject)
# NOTE: In the interests of keeping data in OpenClinica tidy, we are only scheduling events for
# subjects who don't yet exist in OpenClinica. New events of existing subjects must be added
# manually, or subjects must be deleted from OpenClinica before a re-import.
for event in subject['events']:
api.schedule_event(subject, event)
self.file.write(render_to_string('couchexport/odm_export.xml', self.context))
def get_study_metadata_string(domain):
"""
Return the study metadata for the given domain as a string
Metadata is fetched from the OpenClinica web service
"""
from custom.openclinica.models import OpenClinicaAPI, OpenClinicaSettings
oc_settings = OpenClinicaSettings.for_domain(domain)
if oc_settings.study.is_ws_enabled:
password = bz2.decompress(b64decode(oc_settings.study.password))
api = OpenClinicaAPI(
oc_settings.study.url,
oc_settings.study.username,
password,
oc_settings.study.protocol_id
)
string = api.get_study_metadata_string(oc_settings['STUDY'])
else:
string = oc_settings.study.metadata
# If the XML is Unicode but it says that it's UTF-8, then make it UTF-8.
if isinstance(string, unicode):
match = re.match(r'<\?xml .*?encoding="([\w-]+)".*?\?>', string) # Assumes no whitespace up front
if match:
string = string.encode(match.group(1))
return string
def get_study_metadata_string(domain):
"""
Return the study metadata for the given domain as a string
Metadata is fetched from the OpenClinica web service
"""
from custom.openclinica.models import OpenClinicaAPI, OpenClinicaSettings
oc_settings = OpenClinicaSettings.for_domain(domain)
if oc_settings.study.is_ws_enabled:
password = bz2.decompress(b64decode(oc_settings.study.password))
api = OpenClinicaAPI(
oc_settings.study.url,
oc_settings.study.username,
password,
oc_settings.study.protocol_id
)
string = api.get_study_metadata_string(oc_settings['STUDY'])
else:
string = oc_settings.study.metadata
# If the XML is Unicode but it says that it's UTF-8, then make it UTF-8.
if isinstance(string, six.text_type):
match = re.match(r'<\?xml .*?encoding="([\w-]+)".*?\?>', string) # Assumes no whitespace up front
if match:
string = string.encode(match.group(1))
return string
def save(self, domain):
try:
settings = OpenClinicaSettings.for_domain(domain.name)
if settings is None:
settings = OpenClinicaSettings(domain=domain.name)
settings.study.is_ws_enabled = self.cleaned_data['is_ws_enabled']
settings.study.url = self.cleaned_data['url']
settings.study.username = self.cleaned_data['username']
if self.cleaned_data['password']:
# Simple symmetric encryption. We don't need it to be strong, considering we'd have to store the
# algorithm and the key together anyway; it just shouldn't be plaintext.
settings.study.password = b64encode(bz2.compress(self.cleaned_data['password']))
settings.study.protocol_id = self.cleaned_data['protocol_id']
settings.study.metadata = self.cleaned_data['metadata']
settings.save()
return True
except Exception as err:
logging.error('Unable to save OpenClinica settings: %s' % err)
return False
def save(self, domain):
try:
settings = OpenClinicaSettings.for_domain(domain.name)
if settings is None:
settings = OpenClinicaSettings(domain=domain.name)
settings.study.is_ws_enabled = self.cleaned_data['is_ws_enabled']
settings.study.url = self.cleaned_data['url']
settings.study.username = self.cleaned_data['username']
if self.cleaned_data['password']:
# Simple symmetric encryption. We don't need it to be strong, considering we'd have to store the
# algorithm and the key together anyway; it just shouldn't be plaintext.
settings.study.password = b64encode(bz2.compress(self.cleaned_data['password']))
settings.study.protocol_id = self.cleaned_data['protocol_id']
settings.study.metadata = self.cleaned_data['metadata']
settings.save()
return True
except Exception as err:
logging.error('Unable to save OpenClinica settings: %s' % err)
return False
def get_study_metadata_string(domain):
"""
Return the study metadata for the given domain as an XML string
"""
from custom.openclinica.models import OpenClinicaSettings
oc_settings = OpenClinicaSettings.for_domain(domain)
if oc_settings.study.is_ws_enabled:
raise NotImplementedError('Fetching study metadata using web services is not yet available')
else:
string = oc_settings.study.metadata
# If the XML is Unicode but it says that it's UTF-8, then make it UTF-8.
if isinstance(string, unicode):
match = re.match(r'<\?xml .*?encoding="([\w-]+)".*?\?>', string) # Assumes no whitespace up front
if match:
string = string.encode(match.group(1))
return string
def openclinica_settings_form(self):
oc_settings = OpenClinicaSettings.for_domain(self.domain_object.name)
initial = dict(oc_settings.study) if oc_settings else {}
if self.request.method == 'POST':
return OpenClinicaSettingsForm(self.request.POST, initial=initial)
return OpenClinicaSettingsForm(initial=initial)
def openclinica_settings_form(self):
oc_settings = OpenClinicaSettings.for_domain(self.domain_object.name)
initial = dict(oc_settings.study) if oc_settings else {}
if self.request.method == 'POST':
return OpenClinicaSettingsForm(self.request.POST, initial=initial)
return OpenClinicaSettingsForm(initial=initial)
