def __call__(self):
translate = self.context.translate
instrument = self.context.getInstrument()
if not instrument:
self.context.plone_utils.addPortalMessage(
_("You must select an instrument"), 'info')
self.request.RESPONSE.redirect(self.context.absolute_url())
return
exim = instrument.getDataInterface()
if not exim:
self.context.plone_utils.addPortalMessage(
_("Instrument has no data interface selected"), 'info')
self.request.RESPONSE.redirect(self.context.absolute_url())
return
# exim refers to filename in instruments/
if type(exim) == list:
exim = exim[0]
exim = exim.lower()
# search instruments module for 'exim' module
if not instruments.getExim(exim):
self.context.plone_utils.addPortalMessage(
_("Instrument exporter not found"), 'error')
self.request.RESPONSE.redirect(self.context.absolute_url())
return
exim = instruments.getExim(exim)
exporter = exim.Export(self.context, self.request)
data = exporter(self.context.getAnalyses())
pass
def __call__(self):
translate = self.context.translate
instrument = self.context.getInstrument()
if not instrument:
self.context.plone_utils.addPortalMessage(
_("You must select an instrument"), 'info')
self.request.RESPONSE.redirect(self.context.absolute_url())
return
exim = instrument.getDataInterface()
if not exim:
self.context.plone_utils.addPortalMessage(
_("Instrument has no data interface selected"), 'info')
self.request.RESPONSE.redirect(self.context.absolute_url())
return
# exim refers to filename in instruments/
if type(exim) == list:
exim = exim[0]
exim = exim.lower()
# search instruments module for 'exim' module
if not instruments.getExim(exim):
self.context.plone_utils.addPortalMessage(
_("Instrument exporter not found"), 'error')
self.request.RESPONSE.redirect(self.context.absolute_url())
return
exim = instruments.getExim(exim)
exporter = exim.Export(self.context, self.request)
data = exporter(self.context.getAnalyses())
pass
def getDataInterfaces(context):
""" Return the current list of data interfaces
"""
from bika.lims.exportimport import instruments
exims = [('', t(_('None')))]
for exim_id in instruments.__all__:
exim = instruments.getExim(exim_id)
exims.append((exim_id, exim.title))
return DisplayList(exims)
def getExim(exim_id):
if exim_id == 'biorad.tc20.tc20':
currmodule = sys.modules[__name__]
members = [obj for name, obj in inspect.getmembers(currmodule) \
if hasattr(obj, '__name__') \
and obj.__name__.endswith(exim_id)]
return members[0] if len(members) > 0 else None
else:
return instruments.getExim(exim_id)
def getDataInterfaces(context):
""" Return the current list of data interfaces
"""
from bika.lims.exportimport import instruments
exims = [('', t(_('None')))]
for exim_id in instruments.__all__:
exim = instruments.getExim(exim_id)
exims.append((exim_id, exim.title))
return DisplayList(exims)
def __call__(self):
if 'submitted' in self.request:
if 'setupfile' in self.request.form or \
'setupexisting' in self.request.form:
lsd = LoadSetupData(self.context, self.request)
return lsd()
else:
exim = instruments.getExim(self.request['exim'])
return exim.Import(self.context, self.request)
else:
return self.template()
def getDataInterfaces(context):
""" Return the current list of data interfaces
"""
from bika.lims.exportimport import instruments
exims = []
for exim_id in instruments.__all__:
exim = instruments.getExim(exim_id)
exims.append((exim_id, exim.title))
exims.sort(lambda x, y: cmp(x[1].lower(), y[1].lower()))
exims.insert(0, ('', t(_('None'))))
return DisplayList(exims)
def __call__(self):
if 'submitted' in self.request:
if 'setupfile' in self.request.form or \
'setupexisting' in self.request.form:
lsd = LoadSetupData(self.context, self.request)
return lsd()
else:
exim = instruments.getExim(self.request['exim'])
return exim.Import(self.context, self.request)
else:
return self.template()
def getDataInterfaces(context):
""" Return the current list of data interfaces
"""
from bika.lims.exportimport import instruments
exims = []
for exim_id in instruments.__all__:
exim = instruments.getExim(exim_id)
exims.append((exim_id, exim.title))
exims.sort(lambda x, y: cmp(x[1].lower(), y[1].lower()))
exims.insert(0, ('', t(_('None'))))
return DisplayList(exims)
def getImportDataInterfaces(context, import_only=False):
""" Return the current list of import data interfaces
"""
from bika.lims.exportimport import instruments
exims = []
for exim_id in instruments.__all__:
exim = instruments.getExim(exim_id)
if import_only and not hasattr(exim, 'Import'):
pass
else:
exims.append((exim_id, exim.title))
exims.sort(lambda x, y: cmp(x[1].lower(), y[1].lower()))
exims.insert(0, ('', t(_('None'))))
return DisplayList(exims)
def getImportDataInterfaces(context, import_only=False):
""" Return the current list of import data interfaces
"""
from bika.lims.exportimport import instruments
exims = []
for exim_id in instruments.__all__:
exim = instruments.getExim(exim_id)
if import_only and not hasattr(exim, 'Import'):
pass
else:
exims.append((exim_id, exim.title))
exims.sort(lambda x, y: cmp(x[1].lower(), y[1].lower()))
exims.insert(0, ('', t(_('None'))))
return DisplayList(exims)
def __call__(self):
if 'submitted' in self.request:
if 'setupfile' in self.request.form or \
'setupexisting' in self.request.form:
lsd = LoadSetupData(self.context, self.request)
return lsd()
else:
exim = instruments.getExim(self.request['exim'])
if not exim:
er_mes = "Importer not found for: %s" % self.request['exim']
results = {'errors': [er_mes], 'log': '', 'warns': ''}
return json.dumps(results)
else:
return exim.Import(self.context, self.request)
else:
return self.template()
def __call__(self):
if 'submitted' in self.request:
if 'setupfile' in self.request.form or \
'setupexisting' in self.request.form:
lsd = LoadSetupData(self.context, self.request)
return lsd()
else:
exim = instruments.getExim(self.request['exim'])
if not exim:
er_mes = "Importer not found for: %s" % self.request['exim']
results = {'errors': [er_mes], 'log': '', 'warns': ''}
return json.dumps(results)
else:
return exim.Import(self.context, self.request)
else:
return self.template()
def __call__(self):
interfaces = []
try:
plone.protect.CheckAuthenticator(self.request)
except Forbidden:
return json.dumps(interfaces)
from bika.lims.exportimport import instruments
bsc = getToolByName(self, 'bika_setup_catalog')
instrument=bsc(portal_type='Instrument',
UID=self.request.get('instrument_uid', ''),
inactive_state='active',)
if instrument and len(instrument) == 1:
instrument = instrument[0].getObject()
for i in instrument.getImportDataInterface():
if i:
exim = instruments.getExim(i)
interface = {'id': i, 'title': exim.title}
interfaces.append(interface)
return json.dumps(interfaces)
def __call__(self):
interfaces = []
try:
plone.protect.CheckAuthenticator(self.request)
except Forbidden:
return json.dumps(interfaces)
from bika.lims.exportimport import instruments
bsc = getToolByName(self, 'bika_setup_catalog')
instrument=bsc(portal_type='Instrument',
UID=self.request.get('instrument_uid', ''),
inactive_state='active',)
if instrument and len(instrument) == 1:
instrument = instrument[0].getObject()
for i in instrument.getImportDataInterface():
if i:
exim = instruments.getExim(i)
interface = {'id': i, 'title': exim.title}
interfaces.append(interface)
return json.dumps(interfaces)
def __call__(self):
request = self.request
if not self.is_import_allowed():
return 'Auto-import skipped due to interval...'
bsc = getToolByName(self, 'bika_setup_catalog')
# Getting instrumnets to run auto-import
query = {'portal_type': 'Instrument', 'inactive_state': 'active'}
if request.get('i_uid', ''):
query['UID'] = request.get('i_uid')
brains = bsc(query)
interfaces = []
for brain in brains:
i = brain.getObject()
logger.info('Auto import for ' + i.Title())
# If Import Interface ID is specified in request, then auto-import
# will run only that interface. Otherwise all available interfaces
# of this instruments
if request.get('interface', ''):
interfaces.append(request.get('interface'))
else:
interfaces = [
pairs.get('InterfaceName', '')
for pairs in i.getResultFilesFolder()
]
folder = ''
for interface in interfaces:
# Each interface must have its folder where result files are
# saved. If not, then we will skip
for pairs in i.getResultFilesFolder():
if pairs['InterfaceName'] == interface:
folder = pairs.get('Folder', '')
if not folder:
continue
logger.info('Auto import for ' + interface)
all_files = [
f for f in listdir(folder) if isfile(join(folder, f))
]
imported_list = self.getAlreadyImportedFiles(folder)
if not imported_list:
logger.warn('imported.csv file not found ' + interface)
self.add_to_logs(i, interface,
'imported.csv File not found...', '')
continue
for file_name in all_files:
if file_name in imported_list:
continue
temp_file = open(folder + '/' + file_name)
# Parsers work with UploadFile object from
# zope.HTTPRequest which has filename attribute.
# To add this attribute we convert the file.
# CHECK should we add headers too?
result_file = ConvertToUploadFile(temp_file)
exim = instruments.getExim(interface)
parser_name = instruments.getParserName(interface)
parser_function = getattr(exim, parser_name) \
if hasattr(exim, parser_name) else ''
if not parser_function:
self.add_to_logs(i, interface, 'Parser not found...',
file_name)
continue
# We will run import with some default parameters
# Expected to be modified in the future.
logger.info('Parsing ' + file_name)
parser = parser_function(result_file)
importer = GeneralImporter(
parser=parser,
context=self.portal,
idsearchcriteria=[
'getId', 'getSampleID', 'getClientSampleID'
],
allowed_ar_states=['sample_received'],
allowed_analysis_states=None,
override=[False, False],
instrument_uid=i.UID())
tbex = ''
try:
importer.process()
except:
tbex = traceback.format_exc()
errors = importer.errors
logs = importer.logs
if tbex:
errors.append(tbex)
final_log = ''
success_log = self.getInfoFromLog(logs, 'Import finished')
if success_log:
final_log = success_log
else:
final_log = errors
self.insert_file_name(folder, file_name)
self.add_to_logs(i, interface, final_log, file_name)
self.add_to_log_file(i.Title(), interface, final_log,
file_name, folder)
logger.info('End of auto import...')
return 'Auto-Import finished...'
def __call__(self):
request = self.request
if not self.is_import_allowed():
return 'Auto-import skipped due to interval...'
bsc = getToolByName(self, 'bika_setup_catalog')
# Getting instrumnets to run auto-import
query = {'portal_type': 'Instrument',
'inactive_state': 'active'}
if request.get('i_uid', ''):
query['UID'] = request.get('i_uid')
brains = bsc(query)
interfaces = []
for brain in brains:
i = brain.getObject()
logger.info('Auto import for ' + i.Title())
# If Import Interface ID is specified in request, then auto-import
# will run only that interface. Otherwise all available interfaces
# of this instruments
if request.get('interface', ''):
interfaces.append(request.get('interface'))
else:
interfaces = [pairs.get('InterfaceName', '') for pairs
in i.getResultFilesFolder()]
folder = ''
for interface in interfaces:
# Each interface must have its folder where result files are
# saved. If not, then we will skip
for pairs in i.getResultFilesFolder():
if pairs['InterfaceName'] == interface:
folder = pairs.get('Folder', '')
if not folder:
continue
logger.info('Auto import for ' + interface)
all_files = [f for f in listdir(folder)
if isfile(join(folder, f))]
imported_list = self.getAlreadyImportedFiles(folder)
if not imported_list:
logger.warn('imported.csv file not found ' + interface)
self.add_to_logs(i, interface,
'imported.csv File not found...', '')
continue
for file_name in all_files:
if file_name in imported_list:
continue
temp_file = open(folder+'/'+file_name)
# Parsers work with UploadFile object from
# zope.HTTPRequest which has filename attribute.
# To add this attribute we convert the file.
# CHECK should we add headers too?
result_file = ConvertToUploadFile(temp_file)
exim = instruments.getExim(interface)
parser_name = instruments.getParserName(interface)
parser_function = getattr(exim, parser_name) \
if hasattr(exim, parser_name) else ''
if not parser_function:
self.add_to_logs(i, interface,
'Parser not found...', file_name)
continue
# We will run import with some default parameters
# Expected to be modified in the future.
logger.info('Parsing ' + file_name)
parser = parser_function(result_file)
importer = GeneralImporter(
parser=parser,
context=self.portal,
idsearchcriteria=['getId',
'getSampleID',
'getClientSampleID'],
allowed_ar_states=['sample_received'],
allowed_analysis_states=None,
override=[False, False],
instrument_uid=i.UID())
tbex = ''
try:
importer.process()
except:
tbex = traceback.format_exc()
errors = importer.errors
logs = importer.logs
if tbex:
errors.append(tbex)
final_log = ''
success_log = self.getInfoFromLog(logs, 'Import finished')
if success_log:
final_log = success_log
else:
final_log = errors
self.insert_file_name(folder, file_name)
self.add_to_logs(i, interface, final_log, file_name)
self.add_to_log_file(i.Title(), interface, final_log,
file_name, folder)
logger.info('End of auto import...')
return 'Auto-Import finished...'
