def workflow_script_import(self):
"""Create objects from valid ARImport
"""
bsc = getToolByName(self, 'bika_setup_catalog')
client = self.aq_parent
title = _('Submitting Sample Import')
description = _('Creating and initialising objects')
bar = ProgressBar(self, self.REQUEST, title, description)
notify(InitialiseProgressBar(bar))
profiles = [x.getObject() for x in bsc(portal_type='AnalysisProfile')]
gridrows = self.schema['SampleData'].get(self)
row_cnt = 0
for therow in gridrows:
row = deepcopy(therow)
row_cnt += 1
# Profiles are titles, profile keys, or UIDS: convert them to UIDs.
newprofiles = []
for title in row['Profiles']:
objects = [x for x in profiles
if title in (x.getProfileKey(), x.UID(), x.Title())]
for obj in objects:
newprofiles.append(obj.UID())
row['Profiles'] = newprofiles
# Same for analyses
newanalyses = set(self.get_row_services(row) +
self.get_row_profile_services(row))
# get batch
batch = self.schema['Batch'].get(self)
if batch:
row['Batch'] = batch.UID()
# Add AR fields from schema into this row's data
row['ClientReference'] = self.getClientReference()
row['ClientOrderNumber'] = self.getClientOrderNumber()
contact_uid =\
self.getContact().UID() if self.getContact() else None
row['Contact'] = contact_uid
# Creating analysis request from gathered data
ar = create_analysisrequest(
client,
self.REQUEST,
row,
analyses=list(newanalyses),)
# progress marker update
progress_index = float(row_cnt) / len(gridrows) * 100
progress = ProgressState(self.REQUEST, progress_index)
notify(UpdateProgressEvent(progress))
# document has been written to, and redirect() fails here
self.REQUEST.response.write(
'<script>document.location.href="%s"</script>' % (
self.absolute_url()))
def workflow_script_import(self):
"""Create objects from valid ARImport
"""
bsc = getToolByName(self, 'bika_setup_catalog')
workflow = getToolByName(self, 'portal_workflow')
client = self.aq_parent
title = _('Submitting AR Import')
description = _('Creating and initialising objects')
bar = ProgressBar(self, self.REQUEST, title, description)
notify(InitialiseProgressBar(bar))
gridrows = self.schema['SampleData'].get(self)
row_cnt = 0
for therow in gridrows:
row = therow.copy()
row_cnt += 1
# Create Sample
sample = _createObjectByType('Sample', client, tmpID())
sample.unmarkCreationFlag()
# First convert all row values into something the field can take
sample.edit(**row)
sample._renameAfterCreation()
event.notify(ObjectInitializedEvent(sample))
sample.at_post_create_script()
swe = self.bika_setup.getSamplingWorkflowEnabled()
if swe:
workflow.doActionFor(sample, 'sampling_workflow')
else:
workflow.doActionFor(sample, 'no_sampling_workflow')
part = _createObjectByType('SamplePartition', sample, 'part-1')
part.unmarkCreationFlag()
if swe:
workflow.doActionFor(part, 'sampling_workflow')
else:
workflow.doActionFor(part, 'no_sampling_workflow')
# Container is special... it could be a containertype.
container = self.get_row_container(row)
if container:
if container.portal_type == 'ContainerType':
containers = container.getContainers()
# XXX And so we must calculate the best container for this partition
part.edit(Container=containers[0])
# Profiles are titles, convert them to UIDs.
newprofiles = []
for title in row['Profiles']:
brains = bsc(portal_type='AnalysisProfile', title=title)
for brain in brains:
newprofiles.append(brain.UID)
row['Profiles'] = newprofiles
# BBB in bika.lims < 3.1.9, only one profile is permitted
# on an AR. The services are all added, but only first selected
# profile name is stored.
row['Profile'] = newprofiles[0] if newprofiles else None
# Same for analyses
newanalyses = set(self.get_row_services(row) +
self.get_row_profile_services(row))
row['Analyses'] = []
# get batch
batch = self.schema['Batch'].get(self)
if batch:
row['Batch'] = batch
# Create AR
ar = _createObjectByType("AnalysisRequest", client, tmpID())
ar.setSample(sample)
ar.unmarkCreationFlag()
ar.edit(**row)
ar._renameAfterCreation()
for analysis in ar.getAnalyses(full_objects=True):
analysis.setSamplePartition(part)
ar.at_post_create_script()
if swe:
workflow.doActionFor(ar, 'sampling_workflow')
else:
workflow.doActionFor(ar, 'no_sampling_workflow')
ar.setAnalyses(list(newanalyses))
progress_index = float(row_cnt) / len(gridrows) * 100
progress = ProgressState(self.REQUEST, progress_index)
notify(UpdateProgressEvent(progress))
# document has been written to, and redirect() fails here
self.REQUEST.response.write(
'<script>document.location.href="%s"</script>' % (
self.absolute_url()))
def _import_file(self, importoption, csvfile, client_id):
fullfilename = csvfile.filename
fullfilename = fullfilename.split('/')[-1]
filename = fullfilename.split('.')[0]
log = []
r = self.portal_catalog(portal_type='Client', id=client_id)
if len(r) == 0:
#This is not a user input issue - client_id is added to template
log.append(' Could not find Client %s' % client_id)
return None, '\n'.join(log)
client = r[0].getObject()
updateable_states = ['sample_received', 'assigned']
reader = csv.reader(csvfile.readlines())
samples = []
sample_headers = None
batch_headers = None
batch_remarks = []
row_count = 0
for row in reader:
row_count = row_count + 1
if not row:
continue
# a new batch starts
if row_count == 1:
if row[0] == 'Header':
continue
else:
msg = '%s invalid batch header' % row
transaction_note(msg)
return None, msg
elif row_count == 2:
msg = None
if row[1] != 'Import':
msg = 'Invalid batch header - Import required in cell B2'
transaction_note(msg)
return None, msg
entered_name = fullfilename.split('.')[0]
if not row[2] or entered_name.lower() != row[2].lower():
msg = 'Filename, %s, does not match entered filename, %s' \
% (filename, row[2])
transaction_note(msg)
return None, msg
batch_headers = row[0:]
arimport_id = tmpID()
title = filename
idx = 1
while title in [i.Title() for i in client.objectValues()]:
title = '%s-%s' % (filename, idx)
idx += 1
arimport = _createObjectByType("ARImport",
client,
arimport_id,
title=title)
arimport.unmarkCreationFlag()
continue
elif row_count == 3:
sample_headers = row[10:]
continue
elif row_count in [4, 5, 6]:
continue
#otherwise add to list of sample
samples.append(row)
if not row_count:
msg = 'Invalid batch header'
transaction_note(msg)
return None, msg
pad = 8192 * ' '
request = self.request
title = 'Importing file'
bar = ProgressBar(self.context, self.request, title, description='')
notify(InitialiseProgressBar(bar))
sample_count = len(samples)
row_count = 0
for sample in samples:
next_num = tmpID()
row_count = row_count + 1
item_remarks = []
progress_index = float(row_count) / float(sample_count) * 100.0
progress = ProgressState(self.request, progress_index)
notify(UpdateProgressEvent(progress))
#TODO REmove for production - just to look pretty
#time.sleep(1)
analyses = []
for i in range(10, len(sample)):
if sample[i] != '1':
continue
analyses.append(sample_headers[(i - 10)])
if len(analyses) > 0:
aritem_id = '%s_%s' % ('aritem', (str(next_num)))
aritem = _createObjectByType("ARImportItem", arimport,
aritem_id)
aritem.edit(
SampleName=sample[0],
ClientRef=sample[1],
SampleDate=sample[2],
SampleType=sample[3],
PickingSlip=sample[4],
ContainerType=sample[5],
ReportDryMatter=sample[6],
Priority=sample[7],
)
aritem.setRemarks(item_remarks)
if importoption == 'c':
aritem.setAnalyses(analyses)
elif importoption == 'p':
aritem.setAnalysisProfile(analyses)
cc_names_report = ','.join(
[i.strip() for i in batch_headers[6].split(';')]) \
if (batch_headers and len(batch_headers) > 7) else ""
cc_emails_report = ','.join(
[i.strip() for i in batch_headers[7].split(';')]) \
if batch_headers and len(batch_headers) > 8 else ""
cc_emails_invoice = ','.join(
[i.strip() for i in batch_headers[8].split(';')]) \
if batch_headers and len(batch_headers) > 9 else ""
try:
numOfSamples = int(batch_headers[12])
except:
numOfSamples = 0
arimport.edit(
ImportOption=importoption,
FileName=batch_headers[2],
OriginalFile=csvfile,
ClientTitle=batch_headers[3],
ClientID=batch_headers[4],
ContactID=batch_headers[5],
CCNamesReport=cc_names_report,
CCEmailsReport=cc_emails_report,
CCEmailsInvoice=cc_emails_invoice,
OrderID=batch_headers[9],
QuoteID=batch_headers[10],
SamplePoint=batch_headers[11],
NumberSamples=numOfSamples,
Remarks=batch_remarks,
Analyses=sample_headers,
DateImported=DateTime(),
)
arimport._renameAfterCreation()
valid = arimport.validateIt()
return arimport, msg
def _submit_arimport_p(self):
""" load the profiles import layout """
ars = []
samples = []
valid_batch = False
client = self.aq_parent
contact_obj = None
cc_contact_obj = None
# validate contact
for contact in client.objectValues('Contact'):
if contact.getUsername() == self.getContactID():
contact_obj = contact
if self.getCCContactID() == None:
if contact_obj != None:
break
else:
if contact.getUsername() == self.getCCContactID():
cc_contact_obj = contact
if contact_obj != None:
break
if contact_obj == None:
valid_batch = False
# get Keyword to ServiceId Map
services = {}
service_uids = {}
for service in self.bika_setup_catalog(
portal_type = 'AnalysisService'):
obj = service.getObject()
keyword = obj.getKeyword()
if keyword:
services[keyword] = '%s:%s' % (obj.UID(), obj.getPrice())
service_uids[obj.UID()] = '%s:%s' % (obj.UID(), obj.getPrice())
samplepoints = self.bika_setup_catalog(
portal_type = 'SamplePoint',
Title = self.getSamplePoint())
if not samplepoints:
valid_batch = False
profiles = {}
aritems = self.objectValues('ARImportItem')
request = self.REQUEST
title = 'Submitting AR Import'
bar = ProgressBar(
self, request, title, description='')
event.notify(InitialiseProgressBar(bar))
row_count = 0
item_count = len(aritems)
prefix = 'Sample'
for aritem in aritems:
# set up analyses
ar_profile = None
analyses = []
row_count += 1
for profilekey in aritem.getAnalysisProfile():
this_profile = None
if not profiles.has_key(profilekey):
profiles[profilekey] = []
# there is no profilekey index
l_prox = self._findProfileKey(profilekey)
if l_prox:
profiles[profilekey] = \
[s.UID() for s in l_prox.getService()]
this_profile = l_prox
else:
#TODO This will not find it!!
# there is no profilekey index
c_prox = self.bika_setup_catalog(
portal_type = 'AnalysisProfile',
getClientUID = client.UID(),
getProfileKey = profilekey)
if c_prox:
obj = c_prox[0].getObject()
profiles[profilekey] = \
[s.UID() for s in obj.getService()]
this_profile = obj
if ar_profile is None:
ar_profile = obj
else:
ar_profile = None
profile = profiles[profilekey]
for analysis in profile:
if not service_uids.has_key(analysis):
service = tool.lookupObject(analysis)
keyword = service.getKeyword()
service_uids[obj.UID()] = '%s:%s' % (obj.UID(), obj.getPrice())
if keyword:
services[keyword] = '%s:%s' % (obj.UID(), obj.getPrice())
if service_uids.has_key(analysis):
if not service_uids[analysis] in analyses:
analyses.append(service_uids[analysis])
else:
valid_batch = False
for analysis in aritem.getAnalyses(full_objects=True):
if not services.has_key(analysis):
for service in self.bika_setup_catalog(
portal_type = 'AnalysisService',
getKeyword = analysis):
obj = service.getObject()
services[analysis] = '%s:%s' % (obj.UID(), obj.getPrice())
service_uids[obj.UID()] = '%s:%s' % (obj.UID(), obj.getPrice())
if services.has_key(analysis):
analyses.append(services[analysis])
else:
valid_batch = False
sampletypes = self.portal_catalog(
portal_type = 'SampleType',
sortable_title = aritem.getSampleType().lower(),
)
if not sampletypes:
valid_batch = False
return
sampletypeuid = sampletypes[0].getObject().UID()
if aritem.getSampleDate():
date_items = aritem.getSampleDate().split('/')
sample_date = DateTime(
int(date_items[2]), int(date_items[0]), int(date_items[1]))
else:
sample_date = None
sample_id = '%s-%s' % (prefix, tmpID())
sample = _createObjectByType("Sample", client, sample_id)
sample.unmarkCreationFlag()
sample.edit(
SampleID = sample_id,
ClientReference = aritem.getClientRef(),
ClientSampleID = aritem.getClientSid(),
SampleType = aritem.getSampleType(),
DateSampled = sample_date,
SamplingDate = sample_date,
DateReceived = DateTime(),
Remarks = aritem.getClientRemarks(),
)
sample._renameAfterCreation()
sample.setSamplePoint(self.getSamplePoint())
sample.setSampleID(sample.getId())
event.notify(ObjectInitializedEvent(sample))
sample.at_post_create_script()
sample_uid = sample.UID()
samples.append(sample_id)
aritem.setSample(sample_uid)
priorities = self.bika_setup_catalog(
portal_type = 'ARPriority',
sortable_title = aritem.Priority.lower(),
)
if len(priorities) < 1:
logger.warning(
'Invalid Priority: validation should have prevented this')
priority = ''
else:
priority = priorities[0].getObject()
ar_id = tmpID()
ar = _createObjectByType("AnalysisRequest", client, ar_id)
report_dry_matter = False
ar.unmarkCreationFlag()
ar.edit(
RequestID = ar_id,
Contact = self.getContact(),
CCContact = self.getCCContact(),
CCEmails = self.getCCEmailsInvoice(),
ClientOrderNumber = self.getOrderID(),
ReportDryMatter = report_dry_matter,
Profile = ar_profile,
Analyses = analyses,
Remarks = aritem.getClientRemarks(),
Priority = priority,
)
ar.setSample(sample_uid)
sample = ar.getSample()
ar.setSampleType(sampletypeuid)
ar_uid = ar.UID()
aritem.setAnalysisRequest(ar_uid)
ars.append(ar_id)
ar._renameAfterCreation()
progress_index = float(row_count)/float(item_count)*100.0
progress = ProgressState(request, progress_index)
event.notify(UpdateProgressEvent(progress))
self._add_services_to_ar(ar, analyses)
self.setDateApplied(DateTime())
self.reindexObject()
def _submit_arimport_c(self):
""" load the classic import layout """
ars = []
samples = []
valid_batch = True
client = self.aq_parent
contact_obj = None
cc_contact_obj = None
# validate contact
for contact in client.objectValues('Contact'):
if contact.getUsername() == self.getContactID():
contact_obj = contact
if self.getCCContactID() == None:
if contact_obj != None:
break
else:
if contact.getUsername() == self.getCCContactID():
cc_contact_obj = contact
if contact_obj != None:
break
if contact_obj == None:
valid_batch = False
# get Keyword to ServiceId Map
services = {}
for service in self.bika_setup_catalog(
portal_type = 'AnalysisService'):
obj = service.getObject()
keyword = obj.getKeyword()
if keyword:
services[keyword] = '%s:%s' % (obj.UID(), obj.getPrice())
samplepoints = self.bika_setup_catalog(
portal_type = 'SamplePoint',
Title = self.getSamplePoint())
if not samplepoints:
valid_batch = False
aritems = self.objectValues('ARImportItem')
request = self.REQUEST
title = 'Submitting AR Import'
bar = ProgressBar(
self, request, title, description='')
event.notify(InitialiseProgressBar(bar))
SamplingWorkflowEnabled = \
self.bika_setup.getSamplingWorkflowEnabled()
row_count = 0
item_count =len(aritems)
prefix = 'Sample'
for aritem in aritems:
row_count += 1
# set up analyses
analyses = []
for analysis in aritem.getAnalyses(full_objects=True):
if services.has_key(analysis):
analyses.append(services[analysis])
else:
valid_batch = False
sampletypes = self.portal_catalog(
portal_type = 'SampleType',
sortable_title = aritem.getSampleType().lower(),
)
if not sampletypes:
valid_batch = False
return
sampletypeuid = sampletypes[0].getObject().UID()
if aritem.getSampleDate():
date_items = aritem.getSampleDate().split('/')
sample_date = DateTime(
int(date_items[2]), int(date_items[1]), int(date_items[0]))
else:
sample_date = None
sample_id = '%s-%s' % (prefix, tmpID())
sample = _createObjectByType("Sample", client, sample_id)
sample.unmarkCreationFlag()
sample.edit(
SampleID = sample_id,
ClientReference = aritem.getClientRef(),
ClientSampleID = aritem.getClientSid(),
SampleType = aritem.getSampleType(),
DateSampled = sample_date,
SamplingDate = sample_date,
DateReceived = DateTime(),
)
sample._renameAfterCreation()
#sp_id = client.invokeFactory('SamplePoint', id=tmpID())
#sp = client[sp_id]
#sp.edit(title=self.getSamplePoint())
sample.setSamplePoint(self.getSamplePoint())
sample.setSampleID(sample.getId())
event.notify(ObjectInitializedEvent(sample))
sample.at_post_create_script()
sample_uid = sample.UID()
samples.append(sample_id)
aritem.setSample(sample_uid)
priorities = self.bika_setup_catalog(
portal_type = 'ARPriority',
sortable_title = aritem.Priority.lower(),
)
if len(priorities) < 1:
logger.warning(
'Invalid Priority: validation should have prevented this')
#Create AR
ar_id = tmpID()
ar = _createObjectByType("AnalysisRequest", client, ar_id)
if aritem.getReportDryMatter().lower() == 'y':
report_dry_matter = True
else:
report_dry_matter = False
ar.unmarkCreationFlag()
ar.edit(
RequestID = ar_id,
Contact = self.getContact(),
CCContact = self.getCCContact(),
CCEmails = self.getCCEmailsInvoice(),
ClientOrderNumber = self.getOrderID(),
ReportDryMatter = report_dry_matter,
Analyses = analyses,
Priority = priorities[0].getObject(),
)
ar.setSample(sample_uid)
sample = ar.getSample()
ar.setSampleType(sampletypeuid)
ar_uid = ar.UID()
aritem.setAnalysisRequest(ar_uid)
ars.append(ar_id)
ar._renameAfterCreation()
self._add_services_to_ar(ar, analyses)
progress_index = float(row_count)/float(item_count)*100.0
progress = ProgressState(request, progress_index)
event.notify(UpdateProgressEvent(progress))
#TODO REmove for production - just to look pretty
#time.sleep(1)
self.setDateApplied(DateTime())
self.reindexObject()
def workflow_script_import(self):
"""Create objects from valid ARImport
"""
def convert_date_string(datestr):
return datestr.replace('-', '/')
def lookup_sampler_uid(import_user):
#Lookup sampler's uid
found = False
userid = None
user_ids = []
users = getUsers(self, ['LabManager', 'Sampler']).items()
for (samplerid, samplername) in users:
if import_user == samplerid:
found = True
userid = samplerid
break
if import_user == samplername:
user_ids.append(samplerid)
if found:
return userid
if len(user_ids) == 1:
return user_ids[0]
if len(user_ids) > 1:
#raise ValueError('Sampler %s is ambiguous' % import_user)
return ''
#Otherwise
#raise ValueError('Sampler %s not found' % import_user)
return ''
bsc = getToolByName(self, 'bika_setup_catalog')
workflow = getToolByName(self, 'portal_workflow')
client = self.aq_parent
title = _('Submitting AR Import')
description = _('Creating and initialising objects')
bar = ProgressBar(self, self.REQUEST, title, description)
notify(InitialiseProgressBar(bar))
profiles = [x.getObject() for x in bsc(portal_type='AnalysisProfile')]
gridrows = self.schema['SampleData'].get(self)
row_cnt = 0
for therow in gridrows:
row = therow.copy()
row_cnt += 1
# Create Sample
sample = _createObjectByType('Sample', client, tmpID())
sample.unmarkCreationFlag()
# First convert all row values into something the field can take
sample.edit(**row)
sample._renameAfterCreation()
event.notify(ObjectInitializedEvent(sample))
sample.at_post_create_script()
swe = self.bika_setup.getSamplingWorkflowEnabled()
if swe:
workflow.doActionFor(sample, 'sampling_workflow')
else:
workflow.doActionFor(sample, 'no_sampling_workflow')
part = _createObjectByType('SamplePartition', sample, 'part-1')
part.unmarkCreationFlag()
renameAfterCreation(part)
if swe:
workflow.doActionFor(part, 'sampling_workflow')
else:
workflow.doActionFor(part, 'no_sampling_workflow')
# Container is special... it could be a containertype.
container = self.get_row_container(row)
if container:
if container.portal_type == 'ContainerType':
containers = container.getContainers()
# XXX And so we must calculate the best container for this partition
part.edit(Container=containers[0])
# Profiles are titles, profile keys, or UIDS: convert them to UIDs.
newprofiles = []
for title in row['Profiles']:
objects = [
x for x in profiles
if title in (x.getProfileKey(), x.UID(), x.Title())
]
for obj in objects:
newprofiles.append(obj.UID())
row['Profiles'] = newprofiles
# BBB in bika.lims < 3.1.9, only one profile is permitted
# on an AR. The services are all added, but only first selected
# profile name is stored.
row['Profile'] = newprofiles[0] if newprofiles else None
# Same for analyses
newanalyses = set(
self.get_row_services(row) +
self.get_row_profile_services(row))
row['Analyses'] = []
# get batch
batch = self.schema['Batch'].get(self)
if batch:
row['Batch'] = batch
# Add AR fields from schema into this row's data
row['ClientReference'] = self.getClientReference()
row['ClientOrderNumber'] = self.getClientOrderNumber()
row['Contact'] = self.getContact()
row['DateSampled'] = convert_date_string(row['DateSampled'])
if row['Sampler']:
row['Sampler'] = lookup_sampler_uid(row['Sampler'])
# Create AR
ar = _createObjectByType("AnalysisRequest", client, tmpID())
ar.setSample(sample)
ar.unmarkCreationFlag()
ar.edit(**row)
ar._renameAfterCreation()
ar.setAnalyses(list(newanalyses))
for analysis in ar.getAnalyses(full_objects=True):
analysis.setSamplePartition(part)
ar.at_post_create_script()
if swe:
workflow.doActionFor(ar, 'sampling_workflow')
else:
workflow.doActionFor(ar, 'no_sampling_workflow')
progress_index = float(row_cnt) / len(gridrows) * 100
progress = ProgressState(self.REQUEST, progress_index)
notify(UpdateProgressEvent(progress))
# document has been written to, and redirect() fails here
self.REQUEST.response.write(
'<script>document.location.href="%s"</script>' %
(self.aq_parent.absolute_url()))