def create_analysisservices(self, as_data):
"""
Creates a set of analaysis services to be used in the tests
:as_data: [{
'title':'xxx',
'ShortTitle':'xxx',
'Keyword': 'xxx',
'PointOfCapture': 'Lab',
'Category':category object,
'Methods': [methods object,],
},
...]
"""
folder = self.portal.bika_setup.bika_analysisservices
ans_list = []
for as_d in as_data:
_id = folder.invokeFactory('AnalysisService', id=tmpID())
ans = folder[_id]
ans.edit(
title=as_d['title'],
ShortTitle=as_d.get('ShortTitle', ''),
Keyword=as_d.get('Keyword', ''),
PointOfCapture=as_d.get('PointOfCapture', 'Lab'),
Category=as_d.get('Category', ''),
Methods=as_d.get('Methods', []),
)
ans.unmarkCreationFlag()
renameAfterCreation(ans)
ans_list.append(ans)
return ans_list
def create_methods(self, methods_data):
"""
Creates a set of methods to be used in the tests
:methods_data: [{
'title':'xxx',
'description':'xxx',
'Instructions':'xxx',
'MethodID':'xxx',
'Accredited':'False/True'},
...]
"""
folder = self.portal.bika_setup.methods
methods_list = []
for meth_d in methods_data:
_id = folder.invokeFactory('Method', id=tmpID())
meth = folder[_id]
meth.edit(
title=meth_d['title'],
description=meth_d.get('description', ''),
Instructions=meth_d.get('Instructions', ''),
MethodID=meth_d.get('MethodID', ''),
Accredited=meth_d.get('Accredited', True),
)
meth.unmarkCreationFlag()
renameAfterCreation(meth)
methods_list.append(meth)
return methods_list
def load_analysis_profiles(self, sheet):
nr_rows = sheet.get_highest_row()
nr_cols = sheet.get_highest_column()
## self.request.response.write("<input type='hidden' id='load_section' value='Analysis Profiles' max='%s'/>"%(nr_rows-3))
## self.request.response.flush()
rows = [[sheet.cell(row=row_nr, column=col_nr).value for col_nr in range(nr_cols)] for row_nr in range(nr_rows)]
fields = rows[1]
folder = self.context.bika_setup.bika_arprofiles
for row in rows[3:]:
row = dict(zip(fields, row))
_id = folder.invokeFactory("ARProfile", id="tmp")
obj = folder[_id]
services = [d.strip() for d in unicode(row["Service"]).split(",")]
proxies = self.bsc(portal_type="AnalysisService", getKeyword=services)
if len(proxies) != len(services):
raise Exception(
"Analysis Profile services invalid. Got %s, found %s" % (services, [p.getKeyword for p in proxies])
)
obj.edit(
title=unicode(row["title"]),
description=unicode(row["description"]),
Service=[s.UID for s in proxies],
ProfileKey=unicode(row["ProfileKey"]),
)
obj.unmarkCreationFlag()
renameAfterCreation(obj)
def load_analysis_specifications(self, sheet):
nr_rows = sheet.get_highest_row()
nr_cols = sheet.get_highest_column()
## self.request.response.write("<input type='hidden' id='load_section' value='Analysis Specifications' max='%s'/>"%(nr_rows-3))
## self.request.response.flush()
rows = [[sheet.cell(row=row_nr, column=col_nr).value for col_nr in range(nr_cols)] for row_nr in range(nr_rows)]
fields = rows[1]
folder = self.context.bika_setup.bika_analysisspecs
ResultsRange = []
for row in rows[3:]:
row = dict(zip(fields, row))
if row["SampleType"]:
if ResultsRange:
obj.setResultsRange(ResultsRange)
ResultsRange = []
_id = folder.invokeFactory("AnalysisSpec", id="tmp")
obj = folder[_id]
SampleType = self.sampletypes[row["SampleType"]]
obj.edit(SampleType=SampleType.UID(), title=row["SampleType"])
obj.unmarkCreationFlag()
renameAfterCreation(obj)
else:
ResultsRange.append(
{
"keyword": row["keyword"],
"min": str(row["min"]),
"max": str(row["max"]),
"error": str(row["error"]),
}
)
def load_methods(self, sheet):
nr_rows = sheet.get_highest_row()
nr_cols = sheet.get_highest_column()
## self.request.response.write("<input type='hidden' id='load_section' value='Methods' max='%s'/>"%(nr_rows-3))
## self.request.response.flush()
rows = [[sheet.cell(row=row_nr, column=col_nr).value for col_nr in range(nr_cols)] for row_nr in range(nr_rows)]
fields = rows[1]
folder = self.context.bika_methods
self.methods = {}
for row in rows[3:]:
row = dict(zip(fields, row))
_id = folder.invokeFactory("Method", id="tmp")
obj = folder[_id]
obj.edit(
title=unicode(row["title"]),
description=unicode(row["description"]),
Instructions=unicode(row["Instructions"]),
)
if row["MethodDocument"]:
file_title = sortable_title(obj, row["MethodDocument"])
path = resource_filename(
"bika.lims", "setupdata/%s/methods/%s" % (self.file_name, row["MethodDocument"])
)
# file_id = obj.invokeFactory("File", id=row['MethodDocument'])
# thisfile = obj[file_id]
file_data = open(path, "rb").read()
obj.setMethodDocument(file_data)
obj.unmarkCreationFlag()
renameAfterCreation(obj)
self.methods[unicode(row["title"])] = obj
def __call__(self):
if "viewlet_submitted" in self.request.form:
data = {}
try:
data = self.validate_form_inputs()
except ValidationError as e:
self.form_error(e.message)
return
from Products.CMFPlone.utils import _createObjectByType
from bika.lims.utils import tmpID
instance = _createObjectByType('InvoiceBatch', self.context, tmpID(), title=data['title'])
instance.unmarkCreationFlag()
instance.edit(
Project=data['project_uid'],
Services=data['services'],
BatchStartDate=data['start_date'],
BatchEndDate=data['end_date']
)
renameAfterCreation(instance)
instance.processForm()
msg = u'Invoice for period "%s" to "%s" created.' % (data['start_date'], data['end_date'])
self.context.plone_utils.addPortalMessage(msg)
self.request.response.redirect(self.context.absolute_url())
def load_lab_departments(self, sheet):
self.departments = {}
lab_contacts = self.bsc(portal_type="LabContact")
nr_rows = sheet.get_highest_row()
nr_cols = sheet.get_highest_column()
## self.request.response.write("<input type='hidden' id='load_section' value='Lab Departments' max='%s'/>"%(nr_rows-3))
## self.request.response.flush()
rows = [[sheet.cell(row=row_nr, column=col_nr).value for col_nr in range(nr_cols)] for row_nr in range(nr_rows)]
fields = rows[1]
folder = self.context.bika_setup.bika_departments
for row in rows[3:]:
row = dict(zip(fields, row))
_id = folder.invokeFactory("Department", id="tmp")
obj = folder[_id]
manager = None
for contact in lab_contacts:
contact = contact.getObject()
if contact.getFullname() == unicode(row["_LabContact_Fullname"]):
manager = contact
break
if not manager:
message = "Error: lookup of '%s' in LabContacts/Fullname failed." % unicode(row["_LabContact_Fullname"])
self.plone_utils.addPortalMessage(message)
raise Exception(message)
obj.edit(title=unicode(row["title"]), description=unicode(row["description"]), Manager=manager.UID())
self.departments[unicode(row["title"])] = obj
obj.unmarkCreationFlag()
renameAfterCreation(obj)
# set importedlab contact's department references
if hasattr(self, "lab_contacts"):
for contact in self.lab_contacts:
if contact["Department"] == unicode(row["title"]):
contact["obj"].setDepartment(obj.UID())
def load_instruments(self, sheet):
nr_rows = sheet.get_highest_row()
nr_cols = sheet.get_highest_column()
## self.request.response.write("<input type='hidden' id='load_section' value='Instruments' max='%s'/>"%(nr_rows-3))
## self.request.response.flush()
rows = [[sheet.cell(row=row_nr, column=col_nr).value for col_nr in range(nr_cols)] for row_nr in range(nr_rows)]
fields = rows[1]
folder = self.context.bika_setup.bika_instruments
for row in rows[3:]:
row = dict(zip(fields, row))
_id = folder.invokeFactory("Instrument", id="tmp")
obj = folder[_id]
obj.edit(
title=unicode(row["title"]),
description=unicode(row["description"]),
Type=unicode(row["Type"]),
Brand=unicode(row["Brand"]),
Model=unicode(row["Model"]),
SerialNo=unicode(row["SerialNo"]),
CalibrationCertificate=unicode(row["CalibrationCertificate"]),
CalibrationExpiryDate=unicode(row["CalibrationExpiryDate"]),
DataInterface=row["DataInterface"],
)
self.instruments[unicode(row["title"])] = obj
obj.unmarkCreationFlag()
renameAfterCreation(obj)
def load_lab_contacts(self, sheet):
self.lab_contacts = []
nr_rows = sheet.get_highest_row()
nr_cols = sheet.get_highest_column()
## self.request.response.write("<input type='hidden' id='load_section' value='Lab Contacts' max='%s'/>"%(nr_rows-3))
## self.request.response.flush()
rows = [[sheet.cell(row=row_nr, column=col_nr).value for col_nr in range(nr_cols)] for row_nr in range(nr_rows)]
fields = rows[1]
folder = self.context.bika_setup.bika_labcontacts
for row in rows[3:]:
row = dict(zip(fields, row))
_id = folder.invokeFactory("LabContact", id="tmp")
obj = folder[_id]
obj.unmarkCreationFlag()
renameAfterCreation(obj)
Fullname = unicode(row["Firstname"]) + " " + unicode(row["Surname"])
obj.edit(
title=Fullname,
description=Fullname,
Firstname=unicode(row["Firstname"]),
Surname=unicode(row["Surname"]),
EmailAddress=unicode(row["EmailAddress"]),
BusinessPhone=unicode(row["BusinessPhone"]),
BusinessFax=unicode(row["BusinessFax"]),
MobilePhone=unicode(row["MobilePhone"]),
JobTitle=unicode(row["JobTitle"]),
)
# Department = row['Department'],
# Signature = row['Signature'],
row["obj"] = obj
self.lab_contacts.append(row)
def load_containers(self, sheet):
nr_rows = sheet.get_highest_row()
nr_cols = sheet.get_highest_column()
## self.request.response.write("<input type='hidden' id='load_section' value='Containers' max='%s'/>"%(nr_rows-3))
## self.request.response.flush()
rows = [[sheet.cell(row=row_nr, column=col_nr).value for col_nr in range(nr_cols)] for row_nr in range(nr_rows)]
fields = rows[1]
folder = self.context.bika_setup.bika_containers
self.containers = {}
for row in rows[3:]:
row = dict(zip(fields, row))
_id = folder.invokeFactory("Container", id="tmp")
obj = folder[_id]
P = row["Preservation"]
obj.edit(
title=unicode(row["title"]),
description=unicode(row["description"]),
Capacity=unicode(row["Capacity"]),
ContainerType=row["ContainerType"] and self.containertypes[row["ContainerType"]] or None,
PrePreserved=row["PrePreserved"] and row["PrePreserved"] or False,
Preservation=P and self.preservations[P] or None,
)
obj.unmarkCreationFlag()
renameAfterCreation(obj)
self.containers[unicode(row["title"])] = obj
def load_preservations(self, sheet):
nr_rows = sheet.get_highest_row()
nr_cols = sheet.get_highest_column()
## self.request.response.write("<input type='hidden' id='load_section' value='Preservations' max='%s'/>"%(nr_rows-3))
## self.request.response.flush()
rows = [[sheet.cell(row=row_nr, column=col_nr).value for col_nr in range(nr_cols)] for row_nr in range(nr_rows)]
fields = rows[1]
folder = self.context.bika_setup.bika_preservations
self.preservations = {}
for row in rows[3:]:
row = dict(zip(fields, row))
_id = folder.invokeFactory("Preservation", id="tmp")
obj = folder[_id]
containertypes = []
if row["ContainerType"]:
for ct in row["ContainerType"].split(","):
containertypes.append(self.containertypes[ct.strip()])
obj.edit(
title=unicode(row["title"]),
description=unicode(row["description"]),
RetentionPeriod=row["RetentionPeriod"] and eval(row["RetentionPeriod"]) or {},
ContainerType=containertypes,
)
obj.unmarkCreationFlag()
renameAfterCreation(obj)
self.preservations[unicode(row["title"])] = obj
def workflow_script_receive(self):
""" receive order """
products = self.aq_parent.objectValues('Product')
items = self.order_lineitems
for item in items:
quantity = int(item['Quantity'])
if quantity < 1:
continue
product = [p for p in products if p.getId() == item['Product']][0]
folder = self.bika_setup.bika_stockitems
for i in range(quantity):
pi = _createObjectByType('StockItem', folder, tmpID())
pi.setProduct(product)
pi.setOrderId(self.getId())
pi.setDateReceived(DateTime())
pi.unmarkCreationFlag()
renameAfterCreation(pi)
# Manually reindex stock item in catalog
self.bika_setup_catalog.reindexObject(pi)
product.setQuantity(product.getQuantity() + quantity)
self.setDateReceived(DateTime())
self.reindexObject()
# Print stock item stickers if opted for
if self.bika_setup.getAutoPrintInventoryStickers():
# TODO: Use better method to redirect after transition
self.REQUEST.response.write(
"<script>window.location.href='%s'</script>" % (
self.absolute_url() + '/stickers/?items=' + self.getId()))
def addReferenceAnalysis(self, service_uid, reference_type):
""" add an analysis to the sample """
rc = getToolByName(self, REFERENCE_CATALOG)
service = rc.lookupObject(service_uid)
analysis = _createObjectByType("ReferenceAnalysis", self, tmpID())
analysis.unmarkCreationFlag()
calculation = service.getCalculation()
interim_fields = calculation and calculation.getInterimFields() or []
renameAfterCreation(analysis)
# maxtime = service.getMaxTimeAllowed() and service.getMaxTimeAllowed() \
# or {'days':0, 'hours':0, 'minutes':0}
# starttime = DateTime()
# max_days = float(maxtime.get('days', 0)) + \
# (
# (float(maxtime.get('hours', 0)) * 3600 + \
# float(maxtime.get('minutes', 0)) * 60)
# / 86400
# )
# duetime = starttime + max_days
analysis.setReferenceType(reference_type)
analysis.setService(service_uid)
analysis.setInterimFields(interim_fields)
return analysis.UID()
def create_reflex_rule(self, title, method, rules_data):
"""
Given a dict with reflex rules data, it creates a reflex rules object
:title: a string with the title
:method: a method object
:rules_data: there is an example
[{'actions': [{'act_row_idx': 0,
'action': 'repeat',
'an_result_id': 'rep-1',
'analyst': '',
'otherWS': 'current',
'setresultdiscrete': '',
'setresulton': 'original',
'setresultvalue': '',
'worksheettemplate': ''}],
'conditions': [{'analysisservice': '52853cf7d5114b5aa8c159afad2f3da1',
'and_or': 'no',
'cond_row_idx': 0,
'discreteresult': '',
'range0': '11',
'range1': '12'}],
'mother_service_uid': '52853cf7d5114b5aa8c159afad2f3da1',
'rulenumber': '0',
'trigger': 'submit'},
{'actions': [{'act_row_idx': 0,
'action': 'repeat',
'an_result_id': 'rep-2',
'analyst': '',
'otherWS': 'current',
'setresultdiscrete': '',
'setresulton': 'original',
'setresultvalue': '',
'worksheettemplate': ''}],
'conditions': [{'analysisservice': 'rep-1',
'and_or': 'no',
'cond_row_idx': 0,
'discreteresult': '',
'range0': '12',
'range1': '12'},],
'mother_service_uid': '52853cf7d5114b5aa8c159afad2f3da1',
'rulenumber': '2',
'trigger': 'submit'}]
"""
# Creating a rule
rules_list = []
folder = self.portal.bika_setup.bika_reflexrulefolder
_id = folder.invokeFactory('ReflexRule', id=tmpID())
rule = folder[_id]
rule.edit(
title=title,
)
rule.setMethod(method.UID())
if rules_data:
rule.setReflexRules(rules_data)
rule.unmarkCreationFlag()
renameAfterCreation(rule)
return rule
def Import(self):
folder = self.context.patients
rows = self.get_rows(3)
for row in rows:
if not row['Firstname'] or not row['PrimaryReferrer']:
continue
pc = getToolByName(self.context, 'portal_catalog')
client = pc(portal_type='Client', Title=row['PrimaryReferrer'])
if len(client) == 0:
raise IndexError("Primary referrer invalid: '%s'" % row['PrimaryReferrer'])
client = client[0].getObject()
_id = folder.invokeFactory('Patient', id=tmpID())
obj = folder[_id]
obj.unmarkCreationFlag()
renameAfterCreation(obj)
Fullname = (row['Firstname'] + " " + row.get('Surname', '')).strip()
obj.edit(title=Fullname,
ClientPatientID = row.get('ClientPatientID', ''),
Salutation = row.get('Salutation', ''),
Firstname = row.get('Firstname', ''),
Surname = row.get('Surname', ''),
PrimaryReferrer = client.UID(),
Gender = row.get('Gender', 'dk'),
Age = row.get('Age', ''),
BirthDate = row.get('BirthDate', ''),
BirthDateEstimated =self.to_bool(row.get('BirthDateEstimated','False')),
BirthPlace = row.get('BirthPlace', ''),
Ethnicity = row.get('Ethnicity', ''),
Citizenship =row.get('Citizenship', ''),
MothersName = row.get('MothersName', ''),
CivilStatus =row.get('CivilStatus', ''),
Anonymous = self.to_bool(row.get('Anonymous','False'))
)
self.fill_contactfields(row, obj)
self.fill_addressfields(row, obj)
if 'Photo' in row and row['Photo']:
try:
path = resource_filename("bika.lims",
"setupdata/%s/%s" \
% (self.dataset_name, row['Photo']))
file_data = open(path, "rb").read()
obj.setPhoto(file_data)
except:
logger.error("Unable to load Photo %s"%row['Photo'])
if 'Feature' in row and row['Feature']:
try:
path = resource_filename("bika.lims",
"setupdata/%s/%s" \
% (self.dataset_name, row['Feature']))
file_data = open(path, "rb").read()
obj.setFeature(file_data)
except:
logger.error("Unable to load Feature %s"%row['Feature'])
obj.unmarkCreationFlag()
renameAfterCreation(obj)
def Import(self):
folder = self.context.bika_setup.bika_casesyndromicclassifications
for row in self.get_rows(3):
obj = _createObjectByType('CaseSyndromicClassification', folder, tmpID())
if row['title']:
obj.edit(title=row['title'],
description=row.get('description', ''),)
obj.unmarkCreationFlag()
renameAfterCreation(obj)
def Import(self):
folder = self.context.bika_setup.bika_identifiertypes
for row in self.get_rows(3):
obj = _createObjectByType('IdentifierType', folder, tmpID())
if row['title']:
obj.edit(title=row['title'],
description=row.get('description', ''),)
obj.unmarkCreationFlag()
renameAfterCreation(obj)
def Import(self):
folder = self.context.bika_setup.bika_cultivars
for row in self.get_rows(3):
if 'title' in row and row['title']:
_id = folder.invokeFactory('Cultivar', id=tmpID())
obj = folder[_id]
obj.edit(title=row['title'],
description=row['description'])
obj.unmarkCreationFlag()
renameAfterCreation(obj)
def Import(self):
folder = self.context.bika_setup.bika_ethnicities
rows = self.get_rows(3)
for row in rows:
_id = folder.invokeFactory('Ethnicity', id=tmpID())
obj = folder[_id]
if row.get('Title', None):
obj.edit(title=row['Title'],
description=row.get('Description', ''))
obj.unmarkCreationFlag()
renameAfterCreation(obj)
def Import(self):
folder = self.context.bika_setup.bika_casestatuses
rows = self.get_rows(3)
for row in rows:
if row['title']:
_id = folder.invokeFactory('CaseStatus', id=tmpID())
obj = folder[_id]
obj.edit(title=row['title'],
description=row.get('description', ''))
obj.unmarkCreationFlag()
renameAfterCreation(obj)
def Import(self):
folder = self.context.bika_setup.bika_diseases
rows = self.get_rows(3)
for row in rows:
_id = folder.invokeFactory('Disease', id=tmpID())
obj = folder[_id]
if row['Title']:
obj.edit(ICDCode=row.get('ICDCode', ''),
title=row['Title'],
description=row.get('Description', ''))
obj.unmarkCreationFlag()
renameAfterCreation(obj)
def Import(self):
print "EOOO"
s_t = ''
c_t = 'lab'
bucket = {}
pc = getToolByName(self.context, 'portal_catalog')
bsc = getToolByName(self.context, 'bika_setup_catalog')
# collect up all values into the bucket
for row in self.get_rows(3):
c_t = row['Client_title'] if row['Client_title'] else 'lab'
if c_t not in bucket:
bucket[c_t] = {}
s_t = row['SampleType_title'] if row['SampleType_title'] else s_t
if s_t not in bucket[c_t]:
bucket[c_t][s_t] = []
service = bsc(portal_type='AnalysisService', title=row['service'])
if not service:
service = bsc(portal_type='AnalysisService',
getKeyword=row['service'])
try:
service = service[0].getObject()
bucket[c_t][s_t].append({
'keyword': service.getKeyword(),
'min': row.get('min','0'),
'max': row.get('max','0'),
'minpanic': row.get('minpanic','0'),
'maxpanic': row.get('maxpanic','0'),
'error': row.get('error','0'),
})
except IndexError:
warning = "Error with service name %s on sheet %s. Service not uploaded."
logger.warning(warning, row.get('service', ''), self.sheetname)
# write objects.
for c_t in bucket:
if c_t == 'lab':
folder = self.context.bika_setup.bika_analysisspecs
else:
folder = pc(portal_type='Client', title=c_t)
if (not folder or len(folder) != 1):
logger.warn("Client %s not found. Omiting client specifications." % c_t)
continue
folder = folder[0].getObject()
for s_t in bucket[c_t]:
resultsrange = bucket[c_t][s_t]
sampletype = bsc(portal_type='SampleType', title=s_t)[0]
_id = folder.invokeFactory('AnalysisSpec', id=tmpID())
obj = folder[_id]
obj.edit(
title=sampletype.Title,
ResultsRange=resultsrange)
obj.setSampleType(sampletype.UID)
obj.unmarkCreationFlag()
renameAfterCreation(obj)
def Import(self):
folder = self.context.bika_setup.bika_storagetypes
rows = self.get_rows(3)
for row in rows:
title = row.get('title')
description = row.get('description', '')
obj = _createObjectByType('StorageType', folder, tmpID())
obj.edit(
title=title,
description=description
)
obj.unmarkCreationFlag()
renameAfterCreation(obj)
def add_to_logs(self, instrument, interface, log, filename):
if not log:
return
log = ''.join(log)
log = log[:80]+'...' if len(log) > 80 else log
_id = instrument.invokeFactory("AutoImportLog", id=tmpID(),
Instrument=instrument,
Interface=interface,
Results=log,
ImportedFile=filename)
item = instrument[_id]
item.unmarkCreationFlag()
renameAfterCreation(item)
def Import(self):
subtypes = self.get_subtypes()
folder = self.context.bika_setup.bika_aetiologicagents
for row in self.get_rows(3):
obj = _createObjectByType('AetiologicAgent', folder, tmpID())
if not row['title']:
continue
ae_title = row['title']
ae_subtypes = subtypes.get(ae_title, [])
obj.edit(title=row['title'],
description=row.get('description', ''),
AetiologicAgentSubtypes=ae_subtypes)
obj.unmarkCreationFlag()
renameAfterCreation(obj)
def Import(self):
folder = self.context.bika_setup.bika_treatments
for row in self.get_rows(3):
obj = _createObjectByType('Treatment', folder, tmpID())
if row['title']:
obj.edit(title=row['title'],
description=row.get('description', ''),
Type=row.get('Type', 'active'),
Procedure=row.get('Procedure', ''),
Care=row.get('Care', ''),
SubjectiveClinicalFindings=row.get('SubjectiveClinicalFindings', ''),
ObjectiveClinicalFindings=row.get('ObjectiveClinicalFindings', ''),)
obj.unmarkCreationFlag()
renameAfterCreation(obj)
def Import(self):
folder = self.context.bika_setup.bika_drugs
for row in self.get_rows(3):
obj = _createObjectByType('Drug', folder, tmpID())
if row['title']:
obj.edit(title=row['title'],
description=row.get('description', ''),
Category=row.get('Category', ''),
Indications=row.get('Indications', ''),
Posology=row.get('Posology', ''),
SideEffects=row.get('SideEffects', ''),
Preservation=row.get('Preservation', ''),)
obj.unmarkCreationFlag()
renameAfterCreation(obj)
def Import(self):
folder = self.context.bika_setup.bika_symptoms
rows = self.get_rows(3)
for row in rows:
_id = folder.invokeFactory('Symptom', id=tmpID())
obj = folder[_id]
if row['Title']:
obj.edit(Code=row.get('Code', ''),
title=row['Title'],
description=row.get('Description', ''),
Gender=row.get('Gender', 'dk'),
SeverityAllowed=self.to_bool(row.get('SeverityAllowed', 1)))
obj.unmarkCreationFlag()
renameAfterCreation(obj)
def load_worksheet_templates(self, sheet):
nr_rows = sheet.get_highest_row()
nr_cols = sheet.get_highest_column()
## self.request.response.write("<input type='hidden' id='load_section' value='Worksheet Templates' max='%s'/>"%(nr_rows-3))
## self.request.response.flush()
rows = [[sheet.cell(row=row_nr, column=col_nr).value for col_nr in range(nr_cols)] for row_nr in range(nr_rows)]
fields = rows[1]
folder = self.context.bika_setup.bika_worksheettemplates
for row in rows[3:]:
row = dict(zip(fields, row))
if not row["title"]:
if row["pos"]:
control_ref = self.definitions.get(unicode(row["control_ref"]), "")
blank_ref = self.definitions.get(unicode(row["blank_ref"]), "")
l = [
{
"pos": unicode(row["pos"]),
"type": unicode(row["type"]),
"control_ref": control_ref,
"blank_ref": blank_ref,
"dup": unicode(row["dup"]),
}
]
wst_obj.setLayout(wst_obj.getLayout() + l)
continue
_id = folder.invokeFactory("WorksheetTemplate", id="tmp")
obj = folder[_id]
services = row["Service"] and [d.strip() for d in unicode(row["Service"]).split(",")] or []
proxies = services and self.bsc(portal_type="AnalysisService", getKeyword=services) or []
services = [p.UID for p in proxies]
control_ref = self.definitions.get(unicode(row["control_ref"]), "")
blank_ref = self.definitions.get(unicode(row["blank_ref"]), "")
obj.edit(
title=unicode(row["title"]),
description=unicode(row["description"]),
Service=services,
Layout=[
{
"pos": unicode(row["pos"]),
"type": unicode(row["type"]),
"control_ref": control_ref,
"blank_ref": blank_ref,
"dup": unicode(row["dup"]),
}
],
)
wst_obj = obj
obj.unmarkCreationFlag()
renameAfterCreation(obj)
def CreateServiceObjects(self, services):
deferred = 0
if not hasattr(self, "service_objs"):
self.service_objs = {}
if not self.deferred.has_key("Analysis Services"):
self.deferred["Analysis Services"] = []
folder = self.context.bika_setup.bika_analysisservices
for row in services:
if row["Calculation"] and not row["Calculation"] in [c.Title() for c in self.calcs.values()]:
self.deferred["Analysis Services"].append(row)
deferred = 1
continue
deferred = 0
_id = folder.invokeFactory("AnalysisService", id="tmp")
obj = folder[_id]
obj.edit(
title=unicode(row["title"]),
description=row["description"] and unicode(row["description"]) or "",
Method=row["Method"] and self.methods[unicode(row["Method"])] or None,
Container=row["Container"] and [self.containers[c] for c in row["Container"].split(",")] or [],
Preservation=row["Preservation"]
and [self.preservations[c] for c in row["Preservation"].split(",")]
or [],
PointOfCapture=unicode(row["PointOfCapture"]),
Unit=row["Unit"] and unicode(row["Unit"]) or None,
Category=self.cats[unicode(row["Category"])].UID(),
Price="%02f" % float(row["Price"]),
CorporatePrice="%02f" % float(row["BulkPrice"]),
VAT="%02f" % float(row["VAT"]),
Precision=unicode(row["Precision"]),
Accredited=row["Accredited"] and True or False,
Keyword=unicode(row["Keyword"]),
MaxTimeAllowed=row["MaxTimeAllowed"] and eval(row["MaxTimeAllowed"]) or {},
DuplicateVariation="%02f" % float(row["DuplicateVariation"]),
Uncertanties=row["Uncertainties"] and eval(row["Uncertainties"]) or [],
ResultOptions=row["ResultOptions"] and eval(row["ResultOptions"]) or [],
ReportDryMatter=row["ReportDryMatter"] and True or False,
)
if row["Instrument"]:
obj.setInstrument(row["Instrument"] in self.instruments and self.instruments[row["Instrument"]].UID()),
if row["Calculation"]:
obj.setCalculation(self.calcs[row["Calculation"]])
service_obj = obj
self.services[row["Keyword"]] = obj
obj.unmarkCreationFlag()
renameAfterCreation(obj)
def publishFromHTML(self, aruid, results_html):
# The AR can be published only and only if allowed
uc = getToolByName(self.context, 'uid_catalog')
#ars = uc(UID=aruid)
ars = [p.getObject() for p in uc(UID=aruid)]
if not ars or len(ars) != 1:
return []
ar = ars[0]
wf = getToolByName(ar, 'portal_workflow')
allowed_states = ['verified', 'published']
# Publish/Republish allowed?
if wf.getInfoFor(ar, 'review_state') not in allowed_states:
# Pre-publish allowed?
if not ar.getAnalyses(review_state=allowed_states):
return []
# HTML written to debug file
debug_mode = App.config.getConfiguration().debug_mode
if debug_mode:
tmp_fn = tempfile.mktemp(suffix=".html")
logger.debug("Writing HTML for %s to %s" % (ar.Title(), tmp_fn))
open(tmp_fn, "wb").write(results_html)
# Create the pdf report (will always be attached to the AR)
# we must supply the file ourself so that createPdf leaves it alone.
pdf_fn = tempfile.mktemp(suffix=".pdf")
pdf_report = createPdf(htmlreport=results_html, outfile=pdf_fn)
# PDF written to debug file
if debug_mode:
logger.debug("Writing PDF for %s to %s" % (ar.Title(), pdf_fn))
else:
os.remove(pdf_fn)
recipients = []
contact = ar.getContact()
lab = ar.bika_setup.laboratory
# BIKA Cannabis hack. Create the CSV they desire here now
#csvdata = self.create_cannabis_csv(ars)
csvdata = self.create_metrc_csv(ars)
pdf_fn = to_utf8(ar.getRequestID())
if pdf_report:
if contact:
recipients = [{
'UID':
contact.UID(),
'Username':
to_utf8(contact.getUsername()),
'Fullname':
to_utf8(contact.getFullname()),
'EmailAddress':
to_utf8(contact.getEmailAddress()),
'PublicationModes':
contact.getPublicationPreference()
}]
reportid = ar.generateUniqueId('ARReport')
report = _createObjectByType("ARReport", ar, reportid)
report.edit(AnalysisRequest=ar.UID(),
Pdf=pdf_report,
CSV=csvdata,
Html=results_html,
Recipients=recipients)
report.unmarkCreationFlag()
renameAfterCreation(report)
# Set blob properties for fields containing file data
fld = report.getField('Pdf')
fld.get(report).setFilename(pdf_fn + ".pdf")
fld.get(report).setContentType('application/pdf')
fld = report.getField('CSV')
fld.get(report).setFilename(pdf_fn + ".csv")
fld.get(report).setContentType('text/csv')
# Set status to prepublished/published/republished
status = wf.getInfoFor(ar, 'review_state')
transitions = {'verified': 'publish', 'published': 'republish'}
transition = transitions.get(status, 'prepublish')
try:
wf.doActionFor(ar, transition)
except WorkflowException:
pass
# compose and send email.
# The managers of the departments for which the current AR has
# at least one AS must receive always the pdf report by email.
# https://github.com/bikalabs/Bika-LIMS/issues/1028
mime_msg = MIMEMultipart('related')
mime_msg['Subject'] = self.get_mail_subject(ar)[0]
mime_msg['From'] = formataddr(
(encode_header(lab.getName()), lab.getEmailAddress()))
mime_msg.preamble = 'This is a multi-part MIME message.'
msg_txt = MIMEText(results_html, _subtype='html')
mime_msg.attach(msg_txt)
to = []
#mngrs = ar.getResponsible()
#for mngrid in mngrs['ids']:
# name = mngrs['dict'][mngrid].get('name', '')
# email = mngrs['dict'][mngrid].get('email', '')
# if (email != ''):
# to.append(formataddr((encode_header(name), email)))
#if len(to) > 0:
# # Send the email to the managers
# mime_msg['To'] = ','.join(to)
# attachPdf(mime_msg, pdf_report, pdf_fn)
# # BIKA Cannabis hack. Create the CSV they desire here now
# fn = pdf_fn
# attachCSV(mime_msg,csvdata,fn)
# try:
# host = getToolByName(ar, 'MailHost')
# host.send(mime_msg.as_string(), immediate=True)
# except SMTPServerDisconnected as msg:
# logger.warn("SMTPServerDisconnected: %s." % msg)
# except SMTPRecipientsRefused as msg:
# raise WorkflowException(str(msg))
# Send report to recipients
recips = self.get_recipients(ar)
for recip in recips:
if 'email' not in recip.get('pubpref', []) \
or not recip.get('email', ''):
continue
title = encode_header(recip.get('title', ''))
email = recip.get('email')
formatted = formataddr((title, email))
# Create the new mime_msg object, cause the previous one
# has the pdf already attached
mime_msg = MIMEMultipart('related')
mime_msg['Subject'] = self.get_mail_subject(ar)[0]
mime_msg['From'] = formataddr(
(encode_header(lab.getName()), lab.getEmailAddress()))
mime_msg.preamble = 'This is a multi-part MIME message.'
msg_txt = MIMEText(results_html, _subtype='html')
mime_msg.attach(msg_txt)
mime_msg['To'] = formatted
# Attach the pdf to the email if requested
if pdf_report and 'pdf' in recip.get('pubpref'):
attachPdf(mime_msg, pdf_report, pdf_fn)
# BIKA Cannabis hack. Create the CSV they desire here now
fn = pdf_fn
attachCSV(mime_msg, csvdata, fn)
# For now, I will simply ignore mail send under test.
if hasattr(self.portal, 'robotframework'):
continue
msg_string = mime_msg.as_string()
# content of outgoing email written to debug file
if debug_mode:
tmp_fn = tempfile.mktemp(suffix=".email")
logger.debug("Writing MIME message for %s to %s" %
(ar.Title(), tmp_fn))
open(tmp_fn, "wb").write(msg_string)
try:
host = getToolByName(ar, 'MailHost')
host.send(msg_string, immediate=True)
except SMTPServerDisconnected as msg:
logger.warn("SMTPServerDisconnected: %s." % msg)
except SMTPRecipientsRefused as msg:
raise WorkflowException(str(msg))
# Save file on the filesystem
folder = os.environ.get('COAs_FOLDER', '')
if len(folder) != 0:
client_path = '{}/{}/'.format(folder, ar.getClientID())
if not os.path.exists(client_path):
os.makedirs(client_path)
today = self.ulocalized_time(DateTime(), long_format=0)
today_path = '{}{}/'.format(client_path, today)
if not os.path.exists(today_path):
os.makedirs(today_path)
fname = '{}{}.pdf'.format(today_path, pdf_fn)
f = open(fname, 'w')
f.write(pdf_report)
f.close()
csvname = '{}{}.csv'.format(today_path, pdf_fn)
fcsv = open(csvname, 'w')
fcsv.write(csvdata)
fcsv.close()
return [ar]
def _renameAfterCreation(self, check_auto_id=False):
"""Rename with the IDServer
"""
from bika.lims.idserver import renameAfterCreation
renameAfterCreation(self)
def Import(self):
folder = self.context.patients
rows = self.get_rows(3)
for row in rows:
if not row['Firstname'] or not row['PrimaryReferrer']:
continue
pc = getToolByName(self.context, 'portal_catalog')
client = pc(portal_type='Client', Title=row['PrimaryReferrer'])
if len(client) == 0:
error = "Primary referrer invalid: '%s'. Patient '%s %s' will not be uploaded"
logger.error(error, row['PrimaryReferrer'], row['Firstname'],
row.get('Surname', ''))
continue
client = client[0].getObject()
# Getting an existing ethnicity
bsc = getToolByName(self.context, 'bika_setup_catalog')
ethnicity = bsc(portal_type='Ethnicity',
Title=row.get('Ethnicity', ''))
if len(ethnicity) == 0:
raise IndexError("Invalid ethnicity: '%s'" % row['Ethnicity'])
ethnicity = ethnicity[0].getObject()
_id = folder.invokeFactory('Patient', id=tmpID())
obj = folder[_id]
obj.unmarkCreationFlag()
renameAfterCreation(obj)
Fullname = (row['Firstname'] + " " +
row.get('Surname', '')).strip()
obj.edit(
PatientID=row.get('PatientID'),
title=Fullname,
ClientPatientID=row.get('ClientPatientID', ''),
Salutation=row.get('Salutation', ''),
Firstname=row.get('Firstname', ''),
Surname=row.get('Surname', ''),
PrimaryReferrer=client.UID(),
Gender=row.get('Gender', 'dk'),
Age=row.get('Age', ''),
BirthDate=row.get('BirthDate', ''),
BirthDateEstimated=self.to_bool(
row.get('BirthDateEstimated', 'False')),
BirthPlace=row.get('BirthPlace', ''),
# TODO Ethnicity_Obj -> Ethnicity on health v319
Ethnicity_Obj=ethnicity.UID(),
Citizenship=row.get('Citizenship', ''),
MothersName=row.get('MothersName', ''),
CivilStatus=row.get('CivilStatus', ''),
Anonymous=self.to_bool(row.get('Anonymous', 'False')))
self.fill_contactfields(row, obj)
self.fill_addressfields(row, obj)
if 'Photo' in row and row['Photo']:
try:
path = resource_filename(self.dataset_project,
"setupdata/%s/%s" \
% (self.dataset_name, row['Photo']))
file_data = open(path, "rb").read() if os.path.isfile(path) \
else open(path+'.jpg', "rb").read()
obj.setPhoto(file_data)
except:
logger.error("Unable to load Photo %s" % row['Photo'])
if 'Feature' in row and row['Feature']:
try:
path = resource_filename(self.dataset_project,
"setupdata/%s/%s" \
% (self.dataset_name, row['Feature']))
file_data = open(path, "rb").read() if os.path.isfile(path) \
else open(path+'.pdf', "rb").read()
obj.setFeature(file_data)
except:
logger.error("Unable to load Feature %s" % row['Feature'])
obj.unmarkCreationFlag()
transaction.savepoint(optimistic=True)
if row.get('PatientID'):
# To maintain the patient spreadsheet's IDs, we cannot do a 'renameaftercreation()'
if obj.getPatientID() != row.get('PatientID'):
transaction.savepoint(optimistic=True)
obj.aq_inner.aq_parent.manage_renameObject(
obj.id, row.get('PatientID'))
else:
renameAfterCreation(obj)
def Import(self):
logger.info("*** Custom import of Analysis Specifications ***")
for row in self.get_rows(3):
keyword = row.get('utestid')
if not keyword:
logger.warn("No keyword found")
continue
query = dict(portal_type="AnalysisService", getKeyword=keyword)
analysis = api.search(query, 'bika_setup_catalog')
if not analysis:
logger.warn("No analysis service found for {}".format(keyword))
continue
if len(analysis) > 1:
logger.warn(
"More than one service found for {}".format(keyword))
continue
analysis = api.get_object(analysis[0])
# TODO No Sample Type defined in the file, just use Whole Blood
st_title = row.get('sample_type', 'Whole Blood')
query = dict(portal_type="SampleType", title=st_title)
sample_type = api.search(query, 'bika_setup_catalog')
if not sample_type:
logger.warn("No sample type found for {}".format(st_title))
continue
if len(sample_type) > 1:
logger.warn(
"More than one sample type found for {}".format(st_title))
continue
sample_type = api.get_object(sample_type[0])
unit = row.get('utestid_units')
min_spec = row.get('lln', '')
max_spec = row.get('uln', '')
gender = row.get('gender', 'a')
gender = gender == 'mf' and 'a' or gender
age_low = row.get('age_low', '')
if age_low:
age_low = '{}{}'.format(age_low, row.get('age_low_unit', 'd'))
age_high = row.get('age_high', '')
if age_high:
age_high = '{}{}'.format(age_high,
row.get('age_high_unit', 'd'))
if not age_low and not age_high:
logger.warn(
"Cannot create Spec, Age low and high not defined.")
continue
max_panic = row.get('panic_high_value', '')
min_panic = row.get('panic_low_value', '')
# TODO No Specs title defined in the file, just use sample type's
specs_title = row.get('title', st_title)
specs_key = []
specs_key.append(specs_title)
if gender:
str_gender = gender.upper()
if gender == 'a':
str_gender = 'MF'
specs_key.append(str_gender)
if age_low and age_high:
specs_key.append('{} - {}'.format(age_low, age_high))
elif age_low:
specs_key.append('({}+)'.format(age_low))
elif age_high:
specs_key.append('(-{})'.format(age_high))
specs_title = ' '.join(specs_key)
specs_dict = {
'keyword': analysis.getKeyword(),
'min': min_spec,
'max': max_spec,
'minpanic': min_panic,
'maxpanic': max_panic,
'warn_min': '',
'warn_max': '',
'hidemin': '',
'hidemax': '',
'rangecomments': '',
}
query = dict(portal_type='AnalysisSpec', title=specs_title)
aspec = api.search(query, 'bika_setup_catalog')
if not aspec:
# Create a new one
folder = self.context.bika_setup.bika_analysisspecs
_id = folder.invokeFactory('AnalysisSpec', id=tmpID())
aspec = folder[_id]
aspec.edit(title=specs_title)
aspec.Schema().getField("Gender").set(aspec, gender)
aspec.Schema().getField("Agefrom").set(aspec, age_low)
aspec.Schema().getField("Ageto").set(aspec, age_high)
aspec.unmarkCreationFlag()
renameAfterCreation(aspec)
elif len(aspec) > 1:
logger.warn(
"More than one Analysis Specification found for {}".format(
specs_title))
continue
else:
aspec = api.get_object(aspec[0])
result_range = aspec.Schema().getField('ResultsRange').get(aspec)
result_range.append(specs_dict)
aspec.Schema().getField('ResultsRange').set(aspec, result_range)
aspec.setSampleType(sample_type.UID())
aspec.reindexObject()
def create_analysisrequest(client,
request,
values,
analyses=None,
partitions=None,
specifications=None,
prices=None):
"""This is meant for general use and should do everything necessary to
create and initialise an AR and any other required auxilliary objects
(Sample, SamplePartition, Analysis...)
:param client:
The container (Client) in which the ARs will be created.
:param request:
The current Request object.
:param values:
a dict, where keys are AR|Sample schema field names.
:param analyses:
Analysis services list. If specified, augments the values in
values['Analyses']. May consist of service objects, UIDs, or Keywords.
:param partitions:
A list of dictionaries, if specific partitions are required. If not
specified, AR's sample is created with a single partition.
:param specifications:
These values augment those found in values['Specifications']
:param prices:
Allow different prices to be set for analyses. If not set, prices
are read from the associated analysis service.
"""
# Don't pollute the dict param passed in
values = dict(values.items())
# Create the Analysis Request
ar = _createObjectByType('AnalysisRequest', client, tmpID())
# Resolve the services uids and set the analyses for this Analysis Request
service_uids = get_services_uids(context=client,
values=values,
analyses_serv=analyses)
ar.setAnalyses(service_uids, prices=prices, specs=specifications)
values.update({"Analyses": service_uids})
ar.processForm(REQUEST=request, values=values)
# Handle rejection reasons
rejection_reasons = resolve_rejection_reasons(values)
ar.setRejectionReasons(rejection_reasons)
# Handle secondary Analysis Request
primary = ar.getPrimaryAnalysisRequest()
if primary:
# Mark the secondary with the `IAnalysisRequestSecondary` interface
alsoProvides(ar, IAnalysisRequestSecondary)
# Rename the secondary according to the ID server setup
renameAfterCreation(ar)
# Set dates to match with those from the primary
ar.setDateSampled(primary.getDateSampled())
ar.setSamplingDate(primary.getSamplingDate())
ar.setDateReceived(primary.getDateReceived())
# Force the transition of the secondary to received and set the
# description/comment in the transition accordingly.
if primary.getDateReceived():
primary_id = primary.getId()
comment = "Auto-received. Secondary Sample of {}".format(
primary_id)
changeWorkflowState(ar,
AR_WORKFLOW_ID,
"sample_received",
action="receive",
comments=comment)
# Mark the secondary as received
alsoProvides(ar, IReceived)
# Initialize analyses
do_action_to_analyses(ar, "initialize")
# Notify the ar has ben modified
modified(ar)
# Reindex the AR
ar.reindexObject()
# If rejection reasons have been set, reject automatically
if rejection_reasons:
doActionFor(ar, "reject")
# In "received" state already
return ar
# Try first with no sampling transition, cause it is the most common config
success, message = doActionFor(ar, "no_sampling_workflow")
if not success:
doActionFor(ar, "to_be_sampled")
# If rejection reasons have been set, reject the sample automatically
if rejection_reasons:
doActionFor(ar, "reject")
return ar
def create_analysisrequest(client,
request,
values,
analyses=None,
results_ranges=None,
prices=None):
"""Creates a new AnalysisRequest (a Sample) object
:param client: The container where the Sample will be created
:param request: The current Http Request object
:param values: A dict, with keys as AnalaysisRequest's schema field names
:param analyses: List of Services or Analyses (brains, objects, UIDs,
keywords). Extends the list from values["Analyses"]
:param results_ranges: List of Results Ranges. Extends the results ranges
from the Specification object defined in values["Specification"]
:param prices: Mapping of AnalysisService UID -> price. If not set, prices
are read from the associated analysis service.
"""
# Don't pollute the dict param passed in
values = dict(values.items())
# Resolve the Service uids of analyses to be added in the Sample. Values
# passed-in might contain Profiles and also values that are not uids. Also,
# additional analyses can be passed-in through either values or services
service_uids = to_services_uids(values=values, services=analyses)
# Remove the Analyses from values. We will add them manually
values.update({"Analyses": []})
# Create the Analysis Request and submit the form
ar = _createObjectByType('AnalysisRequest', client, tmpID())
ar.processForm(REQUEST=request, values=values)
# Set the analyses manually
ar.setAnalyses(service_uids, prices=prices, specs=results_ranges)
# Handle hidden analyses from template and profiles
# https://github.com/senaite/senaite.core/issues/1437
# https://github.com/senaite/senaite.core/issues/1326
apply_hidden_services(ar)
# Handle rejection reasons
rejection_reasons = resolve_rejection_reasons(values)
ar.setRejectionReasons(rejection_reasons)
# Handle secondary Analysis Request
primary = ar.getPrimaryAnalysisRequest()
if primary:
# Mark the secondary with the `IAnalysisRequestSecondary` interface
alsoProvides(ar, IAnalysisRequestSecondary)
# Rename the secondary according to the ID server setup
renameAfterCreation(ar)
# Set dates to match with those from the primary
ar.setDateSampled(primary.getDateSampled())
ar.setSamplingDate(primary.getSamplingDate())
ar.setDateReceived(primary.getDateReceived())
# Force the transition of the secondary to received and set the
# description/comment in the transition accordingly.
if primary.getDateReceived():
primary_id = primary.getId()
comment = "Auto-received. Secondary Sample of {}".format(
primary_id)
changeWorkflowState(ar,
AR_WORKFLOW_ID,
"sample_received",
action="receive",
comments=comment)
# Mark the secondary as received
alsoProvides(ar, IReceived)
# Initialize analyses
do_action_to_analyses(ar, "initialize")
# Notify the ar has ben modified
modified(ar)
# Reindex the AR
ar.reindexObject()
# If rejection reasons have been set, reject automatically
if rejection_reasons:
doActionFor(ar, "reject")
# In "received" state already
return ar
# Try first with no sampling transition, cause it is the most common config
success, message = doActionFor(ar, "no_sampling_workflow")
if not success:
doActionFor(ar, "to_be_sampled")
# If rejection reasons have been set, reject the sample automatically
if rejection_reasons:
doActionFor(ar, "reject")
return ar
def _renameAfterCreation(self, check_auto_id=False):
"""Autogenerate the ID of the object based on core's ID formatting
settings for this type
"""
idserver.renameAfterCreation(self)
def cloneAR(self, ar):
newar = _createObjectByType("AnalysisRequest", ar.aq_parent, tmpID())
newar.title = ar.title
newar.description = ar.description
newar.setContact(ar.getContact())
newar.setCCContact(ar.getCCContact())
newar.setCCEmails(ar.getCCEmails())
newar.setBatch(ar.getBatch())
newar.setTemplate(ar.getTemplate())
newar.setProfile(ar.getProfile())
newar.setSamplingDate(ar.getSamplingDate())
newar.setSampleType(ar.getSampleType())
newar.setSamplePoint(ar.getSamplePoint())
newar.setStorageLocation(ar.getStorageLocation())
newar.setSamplingDeviation(ar.getSamplingDeviation())
newar.setPriority(ar.getPriority())
newar.setSampleCondition(ar.getSampleCondition())
newar.setSample(ar.getSample())
newar.setClientOrderNumber(ar.getClientOrderNumber())
newar.setClientReference(ar.getClientReference())
newar.setClientSampleID(ar.getClientSampleID())
newar.setDefaultContainerType(ar.getDefaultContainerType())
newar.setAdHoc(ar.getAdHoc())
newar.setComposite(ar.getComposite())
newar.setReportDryMatter(ar.getReportDryMatter())
newar.setInvoiceExclude(ar.getInvoiceExclude())
newar.setAttachment(ar.getAttachment())
newar.setInvoice(ar.getInvoice())
newar.setDateReceived(ar.getDateReceived())
newar.setMemberDiscount(ar.getMemberDiscount())
# Set the results for each AR analysis
ans = ar.getAnalyses(full_objects=True)
for an in ans:
nan = _createObjectByType("Analysis", newar, an.getKeyword())
nan.setService(an.getService())
nan.setCalculation(an.getCalculation())
nan.setInterimFields(an.getInterimFields())
nan.setResult(an.getResult())
nan.setResultDM(an.getResultDM())
nan.setRetested = False,
nan.setMaxTimeAllowed(an.getMaxTimeAllowed())
nan.setDueDate(an.getDueDate())
nan.setDuration(an.getDuration())
nan.setReportDryMatter(an.getReportDryMatter())
nan.setAnalyst(an.getAnalyst())
nan.setInstrument(an.getInstrument())
nan.setSamplePartition(an.getSamplePartition())
nan.unmarkCreationFlag()
zope.event.notify(ObjectInitializedEvent(nan))
changeWorkflowState(nan, 'bika_analysis_workflow',
'to_be_verified')
nan.reindexObject()
newar.reindexObject()
newar.aq_parent.reindexObject()
renameAfterCreation(newar)
newar.setRequestID(newar.getId())
if hasattr(ar, 'setChildAnalysisRequest'):
ar.setChildAnalysisRequest(newar)
newar.setParentAnalysisRequest(ar)
return newar
def publishFromHTML(self, ar_uids, results_html):
"""ar_uids can be a single UID or a list of AR uids. The resulting
ARs will be published together (ie, sent as a single outbound email)
and the entire report will be saved in each AR's published-results
tab.
"""
debug_mode = App.config.getConfiguration().debug_mode
wf = getToolByName(self.context, 'portal_workflow')
# The AR can be published only and only if allowed
uc = getToolByName(self.context, 'uid_catalog')
ars = [p.getObject() for p in uc(UID=ar_uids)]
if not ars:
return []
results_html = self.localize_images(results_html)
# Create the pdf report for the supplied HTML.
open('/tmp/2499.html', 'w').write(results_html)
pdf_report = createPdf(results_html, False)
# PDF written to debug file?
if debug_mode:
pdf_fn = tempfile.mktemp(suffix=".pdf")
logger.info("Writing PDF for {} to {}".format(
', '.join([ar.Title() for ar in ars]), pdf_fn))
open(pdf_fn, 'wb').write(pdf_report)
for ar in ars:
# Generate in each relevant AR, a new ARReport
reportid = ar.generateUniqueId('ARReport')
report = _createObjectByType("ARReport", ar, reportid)
report.edit(
AnalysisRequest=ar.UID(),
Pdf=pdf_report,
Html=results_html,
)
report.unmarkCreationFlag()
renameAfterCreation(report)
# Modify the workflow state of each AR that's been published
status = wf.getInfoFor(ar, 'review_state')
transitions = {'verified': 'publish', 'published': 'republish'}
transition = transitions.get(status, 'prepublish')
try:
wf.doActionFor(ar, transition)
except WorkflowException:
pass
# compose and send email.
# The managers of the departments for which the current AR has
# at least one AS must receive always the pdf report by email.
# https://github.com/bikalabs/Bika-LIMS/issues/1028
lab = ars[0].bika_setup.laboratory
mime_msg = MIMEMultipart('related')
mime_msg['Subject'] = "Published results for %s" % \
",".join([ar.Title() for ar in ars])
mime_msg['From'] = formataddr(
(encode_header(lab.getName()), lab.getEmailAddress()))
mime_msg.preamble = 'This is a multi-part MIME message.'
msg_txt = MIMEText(results_html, _subtype='html')
mime_msg.attach(msg_txt)
to = []
to_emails = []
mngrs = []
for ar in ars:
resp = ar.getResponsible()
if 'dict' in resp and resp['dict']:
for mngrid, mngr in resp['dict'].items():
if mngr['email'] not in [m['email'] for m in mngrs]:
mngrs.append(mngr)
for mngr in mngrs:
name = mngr['name']
email = mngr['email']
to.append(formataddr((encode_header(name), email)))
# Send report to recipients
for ar in ars:
recips = self.get_recipients(ar)
for recip in recips:
if 'email' not in recip.get('pubpref', []) \
or not recip.get('email', ''):
continue
title = encode_header(recip.get('title', ''))
email = recip.get('email')
if email not in to_emails:
to.append(formataddr((title, email)))
to_emails.append(email)
# Create the new mime_msg object, cause the previous one
# has the pdf already attached
mime_msg = MIMEMultipart('related')
mime_msg['Subject'] = "Published results for %s" % \
",".join([ar.Title() for ar in ars])
mime_msg['From'] = formataddr(
(encode_header(lab.getName()), lab.getEmailAddress()))
mime_msg.preamble = 'This is a multi-part MIME message.'
msg_txt = MIMEText(results_html, _subtype='html')
mime_msg.attach(msg_txt)
mime_msg['To'] = ",".join(to)
# Attach the pdf to the email
fn = "_".join([ar.Title() for ar in ars])
attachPdf(mime_msg, pdf_report, fn)
# ALS hack. Create the CSV they desire here now
csvdata = self.create_als_csv(ars)
# Attach to email
part = MIMEBase('text', "csv")
fn = self.current_certificate_number()
part.add_header('Content-Disposition',
'attachment; filename="{}.csv"'.format(fn))
part.set_payload(csvdata)
mime_msg.attach(part)
msg_string = mime_msg.as_string()
try:
host = getToolByName(ars[0], 'MailHost')
host.send(msg_string, immediate=True)
except SMTPServerDisconnected as msg:
logger.warn("SMTPServerDisconnected: %s." % msg)
except SMTPRecipientsRefused as msg:
raise WorkflowException(str(msg))
return ars
def notify_rejection(analysisrequest):
"""
Notifies via email that a given Analysis Request has been rejected. The
notification is sent to the Client contacts assigned to the Analysis
Request.
:param analysisrequest: Analysis Request to which the notification refers
:returns: true if success
"""
# We do this imports here to avoid circular dependencies until we deal
# better with this notify_rejection thing.
from bika.lims.browser.analysisrequest.reject import \
AnalysisRequestRejectPdfView, AnalysisRequestRejectEmailView
arid = analysisrequest.getId()
# This is the template to render for the pdf that will be either attached
# to the email and attached the the Analysis Request for further access
tpl = AnalysisRequestRejectPdfView(analysisrequest,
analysisrequest.REQUEST)
html = tpl.template()
html = safe_unicode(html).encode('utf-8')
filename = '%s-rejected' % arid
pdf_fn = tempfile.mktemp(suffix=".pdf")
pdf = createPdf(htmlreport=html, outfile=pdf_fn)
if pdf:
# Attach the pdf to the Analysis Request
attid = analysisrequest.aq_parent.generateUniqueId('Attachment')
att = _createObjectByType("Attachment", analysisrequest.aq_parent,
attid)
att.setAttachmentFile(open(pdf_fn))
# Awkward workaround to rename the file
attf = att.getAttachmentFile()
attf.filename = '%s.pdf' % filename
att.setAttachmentFile(attf)
att.unmarkCreationFlag()
renameAfterCreation(att)
analysisrequest.addAttachment(att)
os.remove(pdf_fn)
# This is the message for the email's body
tpl = AnalysisRequestRejectEmailView(analysisrequest,
analysisrequest.REQUEST)
html = tpl.template()
html = safe_unicode(html).encode('utf-8')
# compose and send email.
mailto = []
lab = analysisrequest.bika_setup.laboratory
mailfrom = formataddr(
(encode_header(lab.getName()), lab.getEmailAddress()))
mailsubject = _('%s has been rejected') % arid
contacts = [analysisrequest.getContact()] + analysisrequest.getCCContact()
for contact in contacts:
name = to_utf8(contact.getFullname())
email = to_utf8(contact.getEmailAddress())
if email:
mailto.append(formataddr((encode_header(name), email)))
if not mailto:
return False
mime_msg = MIMEMultipart('related')
mime_msg['Subject'] = mailsubject
mime_msg['From'] = mailfrom
mime_msg['To'] = ','.join(mailto)
mime_msg.preamble = 'This is a multi-part MIME message.'
msg_txt = MIMEText(html, _subtype='html')
mime_msg.attach(msg_txt)
if pdf:
attachPdf(mime_msg, pdf, filename)
try:
host = getToolByName(analysisrequest, 'MailHost')
host.send(mime_msg.as_string(), immediate=True)
except:
logger.warning(
"Email with subject %s was not sent (SMTP connection error)" %
mailsubject)
return True
def _renameAfterCreation(self, check_auto_id=False):
renameAfterCreation(self)
def __call__(self):
form = self.request.form
plone.protect.CheckAuthenticator(form)
workflow = getToolByName(self.context, 'portal_workflow')
rc = getToolByName(self.context, REFERENCE_CATALOG)
uc = getToolByName(self.context, 'uid_catalog')
action, came_from = WorkflowAction._get_form_workflow_action(self)
if action == 'duplicate':
selected_services = WorkflowAction._get_selected_items(self)
## Create a copy of the selected services
folder = self.context.bika_setup.bika_analysisservices
created = []
for service in selected_services.values():
_id = folder.invokeFactory('AnalysisService', id = 'tmp')
folder[_id].setTitle('%s (copy)' % service.Title())
_id = renameAfterCreation(folder[_id])
folder[_id].unmarkCreationFlag()
folder[_id].edit(
description = service.Description(),
PointOfCapture = service.getPointOfCapture(),
ReportDryMatter = service.getReportDryMatter(),
Unit = service.getUnit(),
Precision = service.getPrecision(),
Price = service.getPrice(),
BulkDiscount = service.getBulkPrice(),
VAT = service.getVAT(),
Calculation = service.getCalculation(),
Instrument = service.getInstrument(),
MaxTimeAllowed = service.getMaxTimeAllowed(),
DuplicateVariation = service.getDuplicateVariation(),
Category = service.getCategory(),
Department = service.getDepartment(),
Accredited = service.getAccredited(),
Uncertainties = service.getUncertainties(),
ResultOptions = service.getResultOptions()
)
folder[_id].reindexObject()
created.append(_id)
if len(created) > 1:
message = self.context.translate(
_('Services ${services} were successfully created.',
mapping = {'services': ', '.join(created)}))
self.destination_url = \
self.request.get_header("referer",
self.context.absolute_url())
else:
message = self.context.translate(
_('Analysis request ${service} was successfully created.',
mapping = {'service': ', '.join(created)}))
self.destination_url = folder[_id].absolute_url() + "/base_edit"
self.context.plone_utils.addPortalMessage(message, 'info')
self.request.response.redirect(self.destination_url)
else:
# default bika_listing.py/WorkflowAction for other transitions
WorkflowAction.__call__(self)
def _renameAfterCreation(self, check_auto_id=False):
from bika.lims.idserver import renameAfterCreation
# ResourceLockedError: Object "multifile..." is locked via WebDAV
self.wl_clearLocks()
renameAfterCreation(self)
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 = self.get_row_container(row)
if container:
part.edit(Container=container)
# 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')
# If the Sampling Workflow field values are valid,
# and the SamplingWorkflow is enabled, we will
# automatically kick off the "sample" transition now
tids = [t['id'] for t in get_transitions_for(ar)]
if 'sample' in tids and ar.getSampler() and ar.getDateSampled():
do_transition_for(ar, 'sample')
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()))
def create_retest(ar):
"""Creates a retest (Analysis Request) from an invalidated Analysis Request
:param ar: The invalidated Analysis Request
:type ar: IAnalysisRequest
:rtype: IAnalysisRequest
"""
if not ar:
raise ValueError("Source Analysis Request cannot be None")
if not IAnalysisRequest.providedBy(ar):
raise ValueError("Type not supported: {}".format(repr(type(ar))))
if ar.getRetest():
# Do not allow the creation of another retest!
raise ValueError("Retest already set")
if not ar.isInvalid():
# Analysis Request must be in 'invalid' state
raise ValueError(
"Cannot do a retest from an invalid Analysis Request".format(
repr(ar)))
# Open the actions pool
actions_pool = ActionHandlerPool.get_instance()
actions_pool.queue_pool()
# Create the Retest (Analysis Request)
ignore = ['Analyses', 'DatePublished', 'Invalidated', 'Sample']
retest = _createObjectByType("AnalysisRequest", ar.aq_parent, tmpID())
copy_field_values(ar, retest, ignore_fieldnames=ignore)
# Mark the retest with the `IAnalysisRequestRetest` interface
alsoProvides(retest, IAnalysisRequestRetest)
# Assign the source to retest
retest.setInvalidated(ar)
# Rename the retest according to the ID server setup
renameAfterCreation(retest)
# Copy the analyses from the source
intermediate_states = ['retracted', 'reflexed']
for an in ar.getAnalyses(full_objects=True):
if (api.get_workflow_status_of(an) in intermediate_states):
# Exclude intermediate analyses
continue
nan = _createObjectByType("Analysis", retest, an.getKeyword())
# Make a copy
ignore_fieldnames = ['DataAnalysisPublished']
copy_field_values(an, nan, ignore_fieldnames=ignore_fieldnames)
nan.unmarkCreationFlag()
push_reindex_to_actions_pool(nan)
# Transition the retest to "sample_received"!
changeWorkflowState(retest, 'bika_ar_workflow', 'sample_received')
alsoProvides(retest, IReceived)
# Initialize analyses
for analysis in retest.getAnalyses(full_objects=True):
if not IRoutineAnalysis.providedBy(analysis):
continue
changeWorkflowState(analysis, "bika_analysis_workflow", "unassigned")
# Reindex and other stuff
push_reindex_to_actions_pool(retest)
push_reindex_to_actions_pool(retest.aq_parent)
# Resume the actions pool
actions_pool.resume()
return retest
def auto_generate_id(obj, event):
"""Generate ID with the IDServer from senaite.core
"""
logger.info("Auto-Generate ID for {}".format(repr(obj)))
renameAfterCreation(obj)
def import_specifications(portal):
"""Creates (or updates) dynamic specifications from
resources/results_ranges.xlsx
"""
logger.info("*** Importing specifications ***")
def get_bs_object(xlsx_row, xlsx_keyword, portal_type, criteria):
text_value = xlsx_row.get(xlsx_keyword, None)
if not text_value:
logger.warn("Value not set for keyword {}".format(xlsx_keyword))
return None
query = {"portal_type": portal_type, criteria: text_value}
brain = api.search(query, 'bika_setup_catalog')
if not brain:
logger.warn("No objects found for type {} and {} '{}'".format(
portal_type, criteria, text_value))
return None
if len(brain) > 1:
logger.warn(
"More than one object found for type {} and {} '{}'".format(
portal_type, criteria, text_value))
return None
return api.get_object(brain[0])
raw_specifications = get_xls_specifications()
for spec in raw_specifications:
# Valid Sample Type?
sample_type = get_bs_object(spec, "sample_type", "SampleType", "title")
if not sample_type:
continue
# Valid Analysis Service?
service = get_bs_object(spec, "keyword", "AnalysisService",
"getKeyword")
if not service:
continue
# The calculation exists?
calc_title = "Ranges calculation"
query = dict(calculation=calc_title)
calc = get_bs_object(query, "calculation", "Calculation", "title")
if not calc:
# Create a new one
folder = portal.bika_setup.bika_calculations
_id = folder.invokeFactory("Calculation", id=tmpID())
calc = folder[_id]
calc.edit(title=calc_title,
PythonImports=[{
"module": "bhp.lims.specscalculations",
"function": "get_specification_for"
}],
Formula="get_specification_for($spec)")
calc.unmarkCreationFlag()
renameAfterCreation(calc)
# Existing AnalysisSpec?
specs_title = "{} - calculated".format(sample_type.Title())
query = dict(portal_type='AnalysisSpec', title=specs_title)
aspec = api.search(query, 'bika_setup_catalog')
if not aspec:
# Create the new AnalysisSpecs object!
folder = portal.bika_setup.bika_analysisspecs
_id = folder.invokeFactory('AnalysisSpec', id=tmpID())
aspec = folder[_id]
aspec.edit(title=specs_title)
aspec.unmarkCreationFlag()
renameAfterCreation(aspec)
elif len(aspec) > 1:
logger.warn(
"More than one Analysis Specification found for {}".format(
specs_title))
continue
else:
aspec = api.get_object(aspec[0])
aspec.setSampleType(sample_type)
# Set the analysis keyword and bind it to the calculation to use
keyword = service.getKeyword()
specs_dict = {
'keyword': keyword,
'min_operator': 'geq',
'min': '0',
'max_operator': 'lt',
'max': '0',
'minpanic': '',
'maxpanic': '',
'warn_min': '',
'warn_max': '',
'hidemin': '',
'hidemax': '',
'rangecomments': '',
'calculation': api.get_uid(calc),
}
ranges = _api.get_field_value(aspec, 'ResultsRange', [{}])
ranges = filter(lambda val: val.get('keyword') != keyword, ranges)
ranges.append(specs_dict)
aspec.setResultsRange(ranges)