def __init__(self, parser, context, idsearchcriteria, override,
allowed_ar_states=None, allowed_analysis_states=None,
instrument_uid=''):
AnalysisResultsImporter.__init__(self, parser, context, idsearchcriteria,
override, allowed_ar_states,
allowed_analysis_states,
instrument_uid)
def __init__(self, parser, context, override,
allowed_ar_states=None, allowed_analysis_states=None,
instrument_uid=''):
AnalysisResultsImporter.__init__(self, parser, context,
override, allowed_ar_states,
allowed_analysis_states,
instrument_uid)
def GenericImport(context, request, parser, importer=None):
infile = getResultsInputFile(request)
fileformat = getFileFormat(request)
artoapply = request.form['artoapply']
override = request.form['results_override']
instrument = request.form.get('instrument', None)
errors = []
logs = []
warns = []
# Load the most suitable parser according to file extension/options/etc...
if not hasattr(infile, 'filename'):
errors.append(_("No file selected"))
if parser:
# Load the importer
status = ['sample_received', 'attachment_due', 'to_be_verified']
if artoapply == 'received':
status = ['sample_received']
elif artoapply == 'received_tobeverified':
status = ['sample_received', 'attachment_due', 'to_be_verified']
over = [False, False]
if override == 'nooverride':
over = [False, False]
elif override == 'override':
over = [True, False]
elif override == 'overrideempty':
over = [True, True]
imp = importer
if not imp:
imp = AnalysisResultsImporter(parser=parser,
context=context,
allowed_ar_states=status,
allowed_analysis_states=None,
override=over,
instrument_uid=instrument)
tbex = ''
try:
imp.process()
except:
tbex = traceback.format_exc()
errors = imp.errors
logs = imp.logs
warns = imp.warns
if tbex:
errors.append(tbex)
results = {'errors': errors, 'log': logs, 'warns': warns}
return json.dumps(results)
def __init__(self, parser, context, idsearchcriteria, override,
allowed_ar_states=None, allowed_analysis_states=None,
instrument_uid=None):
AnalysisResultsImporter.__init__(self,
parser,
context,
idsearchcriteria=['getSampleID', 'getId', 'getClientSampleID'],
override=override,
allowed_ar_states=allowed_ar_states,
allowed_analysis_states=allowed_analysis_states,
instrument_uid=instrument_uid)
def __init__(self,
parser,
context,
idsearchcriteria,
override,
allowed_ar_states=None,
allowed_analysis_states=None,
instrument_uid='',
form=None):
AnalysisResultsImporter.__init__(self, parser, context,
idsearchcriteria, override,
allowed_ar_states,
allowed_analysis_states,
instrument_uid)
def _process_analysis(self, objid, analysis, values):
ret = AnalysisResultsImporter._process_analysis(
self, objid, analysis, values)
# HEALTH-567
if values.get('Value') and str(values['Value'])[0] in "<>":
analysis.setDetectionLimitOperand('<')
return ret
def __call__(self):
request = self.request
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)
parser = get_automatic_parser(interface, result_file)
if not parser:
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)
importer = AnalysisResultsImporter(
parser=parser,
context=self.portal,
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 GenericImport(context, request, parser, importer=None):
infile = getResultsInputFile(request)
fileformat = getFileFormat(request)
artoapply = request.form['artoapply']
override = request.form['results_override']
sample = request.form.get('sample', 'requestid')
instrument = request.form.get('qcinstrument', None)
errors = []
logs = []
warns = []
# Load the most suitable parser according to file extension/options/etc...
if not hasattr(infile, 'filename'):
errors.append(_("No file selected"))
if parser:
# Load the importer
status = ['sample_received', 'attachment_due', 'to_be_verified']
if artoapply == 'received':
status = ['sample_received']
elif artoapply == 'received_tobeverified':
status = ['sample_received', 'attachment_due', 'to_be_verified']
over = [False, False]
if override == 'nooverride':
over = [False, False]
elif override == 'override':
over = [True, False]
elif override == 'overrideempty':
over = [True, True]
sam = ['getRequestID', 'getSampleID', 'getClientSampleID']
if sample == 'requestid':
sam = ['getRequestID']
if sample == 'sampleid':
sam = ['getSampleID']
elif sample == 'clientsid':
sam = ['getClientSampleID']
elif sample == 'sample_clientsid':
sam = ['getSampleID', 'getClientSampleID']
imp = importer
if not imp:
imp = AnalysisResultsImporter(parser=parser,
context=context,
idsearchcriteria=sam,
allowed_ar_states=status,
allowed_analysis_states=None,
override=over,
instrument_uid=instrument)
tbex = ''
try:
imp.process()
except:
tbex = traceback.format_exc()
errors = imp.errors
logs = imp.logs
warns = imp.warns
if tbex:
errors.append(tbex)
results = {'errors': errors, 'log': logs, 'warns': warns}
return json.dumps(results)
def Import(self, context, request):
""" Import Form
"""
infile = request.form['instrument_results_file']
fileformat = request.form.get('instrument_results_file_format', 'xls')
artoapply = request.form['artoapply']
override = request.form['results_override']
instrument = request.form.get('instrument', None)
errors = []
logs = []
warns = []
# Load the most suitable parser according to file extension/options/etc...
parser = None
if not hasattr(infile, 'filename'):
errors.append(_("No file selected"))
if fileformat in ('xls', 'xlsx'):
parser = AORCParser(infile, encoding=fileformat)
else:
errors.append(
t(
_("Unrecognized file format ${fileformat}",
mapping={"fileformat": fileformat})))
if parser:
# Load the importer
status = ['sample_received', 'attachment_due', 'to_be_verified']
if artoapply == 'received':
status = ['sample_received']
elif artoapply == 'received_tobeverified':
status = [
'sample_received', 'attachment_due', 'to_be_verified'
]
over = [False, False]
if override == 'nooverride':
over = [False, False]
elif override == 'override':
over = [True, False]
elif override == 'overrideempty':
over = [True, True]
importer = AnalysisResultsImporter(parser=parser,
context=context,
allowed_ar_states=status,
allowed_analysis_states=None,
override=over,
instrument_uid=instrument)
tbex = ''
try:
importer.process()
errors = importer.errors
logs = importer.logs
warns = importer.warns
except Exception as e:
tbex = traceback.format_exc()
errors.append(tbex)
results = {'errors': errors, 'log': logs, 'warns': warns}
return json.dumps(results)
