def __call__(self):
ar = self.context
workflow = getToolByName(ar, 'portal_workflow')
# If is a retracted AR, show the link to child AR and show a warn msg
if workflow.getInfoFor(ar, 'review_state') == 'invalid':
childar = hasattr(ar, 'getChildAnalysisRequest') \
and ar.getChildAnalysisRequest() or None
childid = childar and childar.getRequestID() or None
message = _('This Analysis Request has been withdrawn and is shown '
'for trace-ability purposes only. Retest: '
'${retest_child_id}.',
mapping={'retest_child_id': safe_unicode(childid) or ''})
self.context.plone_utils.addPortalMessage(message, 'warning')
# If is an AR automatically generated due to a Retraction, show it's
# parent AR information
if hasattr(ar, 'getParentAnalysisRequest') \
and ar.getParentAnalysisRequest():
par = ar.getParentAnalysisRequest()
message = _('This Analysis Request has been '
'generated automatically due to '
'the retraction of the Analysis '
'Request ${retracted_request_id}.',
mapping={'retracted_request_id': safe_unicode(par.getRequestID())})
self.context.plone_utils.addPortalMessage(
t(message), 'info')
template = LogView.__call__(self)
return template
def Title(self):
""" Return the Batch ID if title is not defined """
titlefield = self.Schema().getField('title')
if titlefield.widget.visible:
return safe_unicode(self.title).encode('utf-8')
else:
return safe_unicode(self.id).encode('utf-8')
def getMaintenanceTypes(self):
""" Return the current list of maintenance types
"""
types = [('Preventive',safe_unicode(_('Preventive')).encode('utf-8')),
('Repair', safe_unicode(_('Repair')).encode('utf-8')),
('Enhancement', safe_unicode(_('Enhancement')).encode('utf-8'))]
return DisplayList(types)
def workflow_action_preserve(self):
form = self.request.form
workflow = getToolByName(self.context, 'portal_workflow')
action, came_from = WorkflowAction._get_form_workflow_action(self)
checkPermission = self.context.portal_membership.checkPermission
# Partition Preservation
# the partition table shown in AR and Sample views sends it's
# action button submits here.
objects = WorkflowAction._get_selected_items(self)
transitioned = []
incomplete = []
for obj_uid, obj in objects.items():
part = obj
# can't transition inactive items
if workflow.getInfoFor(part, 'inactive_state', '') == 'inactive':
continue
if not checkPermission(PreserveSample, part):
continue
# grab this object's Preserver and DatePreserved from the form
Preserver = form['getPreserver'][0][obj_uid].strip()
Preserver = Preserver and Preserver or ''
DatePreserved = form['getDatePreserved'][0][obj_uid].strip()
DatePreserved = DatePreserved and DateTime(DatePreserved) or ''
# write them to the sample
part.setPreserver(Preserver)
part.setDatePreserved(DatePreserved)
# transition the object if both values are present
if Preserver and DatePreserved:
workflow.doActionFor(part, action)
transitioned.append(part.id)
else:
incomplete.append(part.id)
part.reindexObject()
part.aq_parent.reindexObject()
message = None
if len(transitioned) > 1:
message = _('${items} are waiting to be received.',
mapping={'items': safe_unicode(', '.join(transitioned))})
self.context.plone_utils.addPortalMessage(message, 'info')
elif len(transitioned) == 1:
message = _('${item} is waiting to be received.',
mapping={'item': safe_unicode(', '.join(transitioned))})
self.context.plone_utils.addPortalMessage(message, 'info')
if not message:
message = _('No changes made.')
self.context.plone_utils.addPortalMessage(message, 'info')
if len(incomplete) > 1:
message = _('${items} are missing Preserver or Date Preserved',
mapping={'items': safe_unicode(', '.join(incomplete))})
self.context.plone_utils.addPortalMessage(message, 'error')
elif len(incomplete) == 1:
message = _('${item} is missing Preserver or Preservation Date',
mapping={'item': safe_unicode(', '.join(incomplete))})
self.context.plone_utils.addPortalMessage(message, 'error')
self.destination_url = self.request.get_header("referer",
self.context.absolute_url())
self.request.response.redirect(self.destination_url)
def getTaskTypes(self):
""" Return the current list of task types
"""
types = [('Calibration', safe_unicode(_('Calibration')).encode('utf-8')),
('Enhancement', safe_unicode(_('Enhancement')).encode('utf-8')),
('Preventive',safe_unicode(_('Preventive')).encode('utf-8')),
('Repair', safe_unicode(_('Repair')).encode('utf-8')),
('Validation', safe_unicode(_('Validation')).encode('utf-8'))]
return DisplayList(types)
def __call__(self):
CheckAuthenticator(self.request)
bsc = getToolByName(self.context, 'bika_setup_catalog')
term = safe_unicode(self.request.get('term', '')).lower()
items = []
if not term:
return json.dumps(items)
# Strip "Lab: " from sample point title
term = term.replace("%s: " % _("Lab"), '')
sampletype = safe_unicode(self.request.get('sampletype', ''))
if sampletype and len(sampletype) > 1:
st = bsc(portal_type = "SampleType",
title = sampletype,
inactive_state = 'active')
if not st:
return json.dumps([])
st = st[0].getObject()
items = [o.Title() for o in st.getSamplePoints()]
if not items:
client_items = lab_items = []
# User (client) sample points
if self.context.portal_type in ('Client', 'AnalysisRequest'):
if self.context.portal_type == 'Client':
client_path = self.context.getPhysicalPath()
else:
client_path = self.context.aq_parent.getPhysicalPath()
client_items = list(
bsc(portal_type = "SamplePoint",
path = {"query": "/".join(client_path), "level" : 0 },
inactive_state = 'active',
sort_on='sortable_title'))
# Global (lab) sample points
lab_path = self.context.bika_setup.bika_samplepoints.getPhysicalPath()
lab_items = list(
bsc(portal_type = "SamplePoint",
path = {"query": "/".join(lab_path), "level" : 0 },
inactive_state = 'active',
sort_on='sortable_title'))
client_items = [callable(s.Title) and s.Title() or s.title
for s in self.filter_list(client_items, term)]
lab_items = [callable(s.Title) and s.Title() or s.title
for s in self.filter_list(lab_items, term)]
lab_items = ["%s: %s" % (_("Lab"), safe_unicode(i))
for i in lab_items]
items = client_items + lab_items
return json.dumps(items)
def __call__(self, value, *args, **kwargs):
instance = kwargs['instance']
fieldname = kwargs['field'].getName()
# request = kwargs.get('REQUEST', {})
# form = request.get('form', {})
translate = getToolByName(instance, 'translation_service').translate
if value == instance.get(fieldname):
return True
for item in aq_parent(instance).objectValues():
if hasattr(item, 'UID') and item.UID() != instance.UID() and \
fieldname in item.Schema() and \
str(item.Schema()[fieldname].get(item)) == str(value): # We have to compare them as strings because
# even if a number (as an id) is saved inside
# a string widget and string field, it will be
# returned as an int. I don't know if it is
# caused because is called with
# <item.Schema()[fieldname].get(item)>,
# but it happens...
msg = _("Validation failed: '${value}' is not unique",
mapping={'value': safe_unicode(value)})
return to_utf8(translate(msg))
return True
def __call__(self, value, *args, **kwargs):
instance = kwargs['instance']
# fieldname = kwargs['field'].getName()
# request = kwargs.get('REQUEST', {})
# form = request.get('form', {})
translate = getToolByName(instance, 'translation_service').translate
bsc = getToolByName(instance, 'bika_setup_catalog')
# uc = getToolByName(instance, 'uid_catalog')
failures = []
for category in value:
if not category:
continue
services = bsc(portal_type="AnalysisService",
getCategoryUID=category)
for service in services:
service = service.getObject()
calc = service.getCalculation()
deps = calc and calc.getDependentServices() or []
for dep in deps:
if dep.getCategoryUID() not in value:
title = dep.getCategoryTitle()
if title not in failures:
failures.append(title)
if failures:
msg = _("Validation failed: The selection requires the following "
"categories to be selected: ${categories}",
mapping={'categories': safe_unicode(','.join(failures))})
return to_utf8(translate(msg))
return True
def __call__(self, value, *args, **kwargs):
if not value:
return True
instance = kwargs['instance']
# fieldname = kwargs['field'].getName()
request = kwargs.get('REQUEST', {})
form = request.form
interim_fields = form.get('InterimFields')
translate = getToolByName(instance, 'translation_service').translate
bsc = getToolByName(instance, 'bika_setup_catalog')
interim_keywords = interim_fields and \
[f['keyword'] for f in interim_fields] or []
keywords = re.compile(r"\[([^\.^\]]+)\]").findall(value)
for keyword in keywords:
# Check if the service keyword exists and is active.
dep_service = bsc(getKeyword=keyword, inactive_state="active")
if not dep_service and \
not keyword in interim_keywords:
msg = _("Validation failed: Keyword '${keyword}' is invalid",
mapping={'keyword': safe_unicode(keyword)})
return to_utf8(translate(msg))
# Wildcards
# LIMS-1769 Allow to use LDL and UDL in calculations
# https://jira.bikalabs.com/browse/LIMS-1769
allowedwds = ['LDL', 'UDL', 'BELOWLDL', 'ABOVEUDL']
keysandwildcards = re.compile(r"\[([^\]]+)\]").findall(value)
keysandwildcards = [k for k in keysandwildcards if '.' in k]
keysandwildcards = [k.split('.',1) for k in keysandwildcards]
errwilds = [k[1] for k in keysandwildcards if k[0] not in keywords]
if len(errwilds) > 0:
msg = _("Wildcards for interims are not allowed: ${wildcards}",
mapping={'wildcards': safe_unicode(', '.join(errwilds))})
return to_utf8(translate(msg))
wildcards = [k[1] for k in keysandwildcards if k[0] in keywords]
wildcards = [wd for wd in wildcards if wd not in allowedwds]
if len(wildcards) > 0:
msg = _("Invalid wildcards found: ${wildcards}",
mapping={'wildcards': safe_unicode(', '.join(wildcards))})
return to_utf8(translate(msg))
return True
def __call__(self):
uc = getToolByName(self.context, 'uid_catalog')
if 'copy_form_submitted' not in self.request:
uids = self.request.form.get('uids', [])
self.services = []
for uid in uids:
proxies = uc(UID=uid)
if proxies:
self.services.append(proxies[0].getObject())
return self.template()
else:
self.savepoint = savepoint()
sources = self.request.form.get('uids', [])
titles = self.request.form.get('dst_title', [])
keywords = self.request.form.get('dst_keyword', [])
self.created = []
for i, s in enumerate(sources):
if not titles[i]:
message = _('Validation failed: title is required')
self.context.plone_utils.addPortalMessage(message, 'info')
self.savepoint.rollback()
self.created = []
break
if not keywords[i]:
message = _('Validation failed: keyword is required')
self.context.plone_utils.addPortalMessage(message, 'info')
self.savepoint.rollback()
self.created = []
break
title = self.copy_service(s, titles[i], keywords[i])
if title:
self.created.append(title)
if len(self.created) > 1:
message = t(_(
'${items} were successfully created.',
mapping={'items': safe_unicode(', '.join(self.created))}))
elif len(self.created) == 1:
message = t(_(
'${item} was successfully created.',
mapping={'item': safe_unicode(self.created[0])}))
else:
message = _('No new items were created.')
self.context.plone_utils.addPortalMessage(message, 'info')
self.request.response.redirect(self.context.absolute_url())
def __call__(self, value, *args, **kwargs):
instance = kwargs['instance']
# fieldname = kwargs['field'].getName()
# request = kwargs.get('REQUEST', {})
# form = request.get('form', {})
translate = getToolByName(instance, 'translation_service').translate
if re.findall(r"[^A-Za-z\w\d\-\_]", value):
return _("Validation failed: keyword contains invalid characters")
# check the value against all AnalysisService keywords
# this has to be done from catalog so we don't
# clash with ourself
bsc = getToolByName(instance, 'bika_setup_catalog')
services = bsc(portal_type='AnalysisService', getKeyword=value)
for service in services:
if service.UID != instance.UID():
msg = _("Validation failed: '${title}': This keyword "
"is already in use by service '${used_by}'",
mapping={'title': safe_unicode(value),
'used_by': safe_unicode(service.Title)})
return to_utf8(translate(msg))
calc = hasattr(instance, 'getCalculation') and \
instance.getCalculation() or None
our_calc_uid = calc and calc.UID() or ''
# check the value against all Calculation Interim Field ids
calcs = [c for c in bsc(portal_type='Calculation')]
for calc in calcs:
calc = calc.getObject()
interim_fields = calc.getInterimFields()
if not interim_fields:
continue
for field in interim_fields:
if field['keyword'] == value and our_calc_uid != calc.UID():
msg = _("Validation failed: '${title}': This keyword "
"is already in use by calculation '${used_by}'",
mapping={'title': safe_unicode(value),
'used_by': safe_unicode(calc.Title())})
return to_utf8(translate(msg))
return True
def checkInstrumentsValidity(self):
""" Checks the validity of the instruments used in the Analyses
If an analysis with an invalid instrument (out-of-date or
with calibration tests failed) is found, a warn message
will be displayed.
"""
invalid = []
ans = [a.getObject() for a in self.context.getAnalyses()]
for an in ans:
valid = an.isInstrumentValid()
if not valid:
inv = '%s (%s)' % (safe_unicode(an.Title()), safe_unicode(an.getInstrument().Title()))
if inv not in invalid:
invalid.append(inv)
if len(invalid) > 0:
message = _("Some analyses use out-of-date or uncalibrated "
"instruments. Results edition not allowed")
message = "%s: %s" % (message, (', '.join(invalid)))
self.context.plone_utils.addPortalMessage(message, 'warn')
def __call__(self):
CheckAuthenticator(self.request)
bsc = getToolByName(self.context, 'bika_setup_catalog')
term = safe_unicode(self.request.get('term', '')).lower()
items = []
if not term:
return json.dumps(items)
samplepoint = safe_unicode(self.request.get('samplepoint', ''))
# Strip "Lab: " from sample point titles
samplepoint = samplepoint.replace("%s: " % _("Lab"), '')
if samplepoint and len(samplepoint) > 1:
sp = bsc(portal_type = "SamplePoint",
inactive_state = 'active',
title=samplepoint)
if not sp:
return json.dumps([])
sp = sp[0].getObject()
items = sp.getSampleTypes()
if not items:
items = bsc(portal_type = "SampleType",
inactive_state = 'active',
sort_on='sortable_title')
if term and len(term) < 3:
# Items that start with A or AA
items = [s.getObject()
for s in items
if s.title.lower().startswith(term)]
if not items:
# or, items that contain A or AA
items = [s.getObject()
for s in items
if s.title.lower().find(term) > -1]
else:
# or, items that contain term.
items = [s.getObject()
for s in items
if s.title.lower().find(term) > -1]
items = [callable(s.Title) and s.Title() or s.title
for s in items]
return json.dumps(items)
def sendEmail(self):
added = []
to = ''
for analysis in self.analyses:
department = analysis.getService().getDepartment()
if department is None:
continue
department_id = department.UID()
if department_id in added:
continue
added.append(department_id)
manager = department.getManager()
if manager is None:
continue
manager_id = manager.UID()
if manager_id not in added and manager.getEmailAddress():
added.append(manager_id)
name = safe_unicode(manager.getFullname()).encode('utf-8')
email = safe_unicode(manager.getEmailAddress()).encode('utf-8')
to = '%s, %s' % (to, formataddr((encode_header(name), email)))
html = safe_unicode(self.template()).encode('utf-8')
lab = self.context.bika_setup.laboratory
mime_msg = MIMEMultipart('related')
mime_msg['Subject'] = self.title
mime_msg['From'] = formataddr(
(encode_header(lab.getName()),
lab.getEmailAddress()))
mime_msg['To'] = to
mime_msg.preamble = 'This is a multi-part MIME message.'
msg_txt = MIMEText(html, _subtype='html')
mime_msg.attach(msg_txt)
# Send the email
try:
host = getToolByName(self.context, 'MailHost')
host.send(mime_msg.as_string(), immediate=True)
except SMTPServerDisconnected as msg:
raise SMTPServerDisconnected(msg)
except SMTPRecipientsRefused as msg:
raise WorkflowException(str(msg))
def __call__(self):
CheckAuthenticator(self.request)
bsc = getToolByName(self.context, 'bika_setup_catalog')
term = safe_unicode(self.request.get('term', '')).lower()
if not term:
return json.dumps([])
client_items = lab_items = []
# User (client) storage locations
if self.context.portal_type == 'Client':
client_path = self.context.getPhysicalPath()
client_items = list(
bsc(portal_type = "StorageLocation",
path = {"query": "/".join(client_path), "level" : 0 },
inactive_state = 'active',
sort_on='sortable_title'))
# Global (lab) storage locations
lab_path = \
self.context.bika_setup.bika_storagelocations.getPhysicalPath()
lab_items = list(
bsc(portal_type = "StorageLocation",
path = {"query": "/".join(lab_path), "level" : 0 },
inactive_state = 'active',
sort_on='sortable_title'))
client_items = [callable(s.Title) and s.Title() or s.title
for s in self.filter_list(client_items, term)]
lab_items = [callable(s.Title) and s.Title() or s.title
for s in self.filter_list(lab_items, term)]
lab_items = ["%s: %s" % (_("Lab"), safe_unicode(i))
for i in lab_items]
items = client_items + lab_items
return json.dumps(items)
def workflow_script_activate(self):
wf = getToolByName(self, 'portal_workflow')
pu = getToolByName(self, 'plone_utils')
# A calculation cannot be re-activated if services it depends on
# are deactivated.
services = self.getDependentServices()
inactive_services = []
for service in services:
if wf.getInfoFor(service, "inactive_state") == "inactive":
inactive_services.append(service.Title())
if inactive_services:
msg = _("Cannot activate calculation, because the following "
"service dependencies are inactive: ${inactive_services}",
mapping={'inactive_services': safe_unicode(", ".join(inactive_services))})
pu.addPortalMessage(msg, 'error')
transaction.get().abort()
raise WorkflowException
def workflow_script_deactivate(self):
bsc = getToolByName(self, 'bika_setup_catalog')
pu = getToolByName(self, 'plone_utils')
# A calculation cannot be deactivated if active services are using it.
services = bsc(portal_type="AnalysisService", inactive_state="active")
calc_services = []
for service in services:
service = service.getObject()
calc = service.getCalculation()
if calc and calc.UID() == self.UID():
calc_services.append(service.Title())
if calc_services:
msg = _('Cannot deactivate calculation, because it is in use by the '
'following services: ${calc_services}',
mapping={'calc_services': safe_unicode(", ".join(calc_services))})
pu.addPortalMessage(msg, 'error')
transaction.get().abort()
raise WorkflowException
def publish(self):
""" Publish the AR report/s. Generates a results pdf file
associated to each AR, sends an email with the report to
the lab manager and sends a notification (usually an email
with the PDF attached) to the AR's contact and CCs.
Transitions each published AR to statuses 'published',
'prepublished' or 'republished'.
Returns a list with the AR identifiers that have been
published/prepublished/republished (only those 'verified',
'published' or at least have one 'verified' result).
"""
if len(self._ars) > 1:
published_ars = []
for ar in self._ars:
arpub = AnalysisRequestPublishView(ar, self.request, publish=True)
ar = arpub.publish()
published_ars.extend(ar)
published_ars = [par.id for par in published_ars]
return published_ars
results_html = safe_unicode(self.template()).encode('utf-8')
return self.publishFromHTML(results_html)
def sortable_title(portal, title):
"""Convert title to sortable title
"""
if not title:
return ''
def_charset = portal.plone_utils.getSiteEncoding()
sortabletitle = title.lower().strip()
# Replace numbers with zero filled numbers
sortabletitle = num_sort_regex.sub(zero_fill, sortabletitle)
# Truncate to prevent bloat
for charset in [def_charset, 'latin-1', 'utf-8']:
try:
sortabletitle = safe_unicode(sortabletitle, charset)[:30]
sortabletitle = sortabletitle.encode(def_charset or 'utf-8')
break
except UnicodeError:
pass
except TypeError:
# If we get a TypeError if we already have a unicode string
sortabletitle = sortabletitle[:30]
break
return sortabletitle
def __init__(self, context, request):
super(AccreditationView, self).__init__(context, request)
self.contentFilter = {
'portal_type': 'AnalysisService',
'sort_on': 'sortable_title',
'getAccredited': True,
'inactive_state': 'active'
}
self.context_actions = {}
self.icon = self.portal_url + "/++resource++bika.lims.images/accredited_big.png"
self.title = self.context.translate(_("Accreditation"))
lab = context.bika_setup.laboratory
accredited = lab.getLaboratoryAccredited()
self.mapping = {
'lab_is_accredited':
accredited,
'lab_name':
safe_unicode(lab.getName()),
'lab_country':
safe_unicode(lab.getPhysicalAddress().get('country', '')),
'confidence':
safe_unicode(lab.getConfidence()),
'accreditation_body_abbr':
safe_unicode(lab.getAccreditationBody()),
'accreditation_body_name':
safe_unicode(lab.getAccreditationBodyURL()),
'accreditation_standard':
safe_unicode(lab.getAccreditation()),
'accreditation_reference':
safe_unicode(lab.getAccreditationReference())
}
if accredited:
self.description = t(
_(safe_unicode(lab.getAccreditationPageHeader()),
mapping=self.mapping))
else:
self.description = t(
_("The lab is not accredited, or accreditation has "
"not been configured. "))
msg = t(_("All Accredited analysis services are listed here."))
self.description = "%s<p><br/>%s</p>" % (self.description, msg)
self.show_select_column = False
request.set('disable_border', 1)
self.columns = {
'Title': {
'title': _('Service'),
'sortable': False
},
'Keyword': {
'title': _('Keyword'),
'sortable': False
},
'Category': {
'title': _('Category'),
'sortable': False
},
'Department': {
'title': _('Department'),
'sortable': False
},
'Instrument': {
'title': _('Instrument'),
'sortable': False
},
'Unit': {
'title': _('Unit'),
'sortable': False
},
'Price': {
'title': _('Price'),
'sortable': False
},
'MaxTimeAllowed': {
'title': _('Max Time'),
'sortable': False
},
'DuplicateVariation': {
'title': _('Dup Var'),
'sortable': False
},
'Calculation': {
'title': _('Calculation'),
'sortable': False
},
}
self.review_states = [
{
'id':
'default',
'title':
_('All'),
'contentFilter': {},
'transitions': [
{
'id': 'empty'
},
], # none
'columns': [
'Title',
'Keyword',
'Category',
'Price',
'MaxTimeAllowed',
'DuplicateVariation',
],
},
]
def getOrderNumber(self):
return safe_unicode(self.getId()).encode('utf-8')
def getCurrentStateI18n(self):
return safe_unicode(_(self.getCurrentState()).encode('utf-8'))
def Title(self):
return to_utf8(safe_unicode(self.title))
def read(context, request):
tag = AuthenticatorView(context, request).authenticator()
pattern = '<input .*name="(\w+)".*value="(\w+)"'
_authenticator = re.match(pattern, tag).groups()[1]
ret = {
"url": router.url_for("read", force_external=True),
"success": True,
"error": False,
"objects": [],
"_authenticator": _authenticator,
}
debug_mode = True #App.config.getConfiguration().debug_mode "Commented by Yasir"
catalog_name = request.get("catalog_name", "portal_catalog")
if not catalog_name:
raise ValueError("bad or missing catalog_name: " + catalog_name)
catalog = getToolByName(context, catalog_name)
indexes = catalog.indexes()
contentFilter = {}
for index in indexes:
if index in request:
if index == 'review_state' and "{" in request[index]:
continue
contentFilter[index] = safe_unicode(request[index])
if "%s[]"%index in request:
value = request["%s[]"%index]
contentFilter[index] = [safe_unicode(v) for v in value]
if 'limit' in request:
try:
contentFilter['sort_limit'] = int(request["limit"])
except ValueError:
pass
sort_on = request.get('sort_on', 'id')
contentFilter['sort_on'] = sort_on
# sort order
sort_order = request.get('sort_order', '')
if sort_order:
contentFilter['sort_order'] = sort_order
else:
sort_order = 'ascending'
contentFilter['sort_order'] = 'ascending'
include_fields = get_include_fields(request)
if debug_mode:
logger.info("contentFilter: " + str(contentFilter))
# Get matching objects from catalog
proxies = catalog(**contentFilter)
# batching items
page_nr = int(request.get("page_nr", 0))
try:
page_size = int(request.get("page_size", 10))
except ValueError:
page_size = 10
# page_size == 0: show all
if page_size == 0:
page_size = len(proxies)
first_item_nr = page_size * page_nr
if first_item_nr > len(proxies):
first_item_nr = 0
page_proxies = proxies[first_item_nr:first_item_nr + page_size]
for proxy in page_proxies:
obj_data = {}
# Place all proxy attributes into the result.
obj_data.update(load_brain_metadata(proxy, include_fields))
# Place all schema fields ino the result.
obj = proxy.getObject()
obj_data.update(load_field_values(obj, include_fields))
obj_data['path'] = "/".join(obj.getPhysicalPath())
# call any adapters that care to modify this data.
adapters = getAdapters((obj, ), IJSONReadExtender)
for name, adapter in adapters:
adapter(request, obj_data)
ret['objects'].append(obj_data)
ret['total_objects'] = len(proxies)
ret['first_object_nr'] = first_item_nr
last_object_nr = first_item_nr + len(page_proxies)
if last_object_nr > ret['total_objects']:
last_object_nr = ret['total_objects']
ret['last_object_nr'] = last_object_nr
if debug_mode:
logger.info("{0} objects returned".format(len(ret['objects'])))
return ret
def Title(self):
return to_utf8(safe_unicode(self.title))
def to_utf8(text):
if text is None:
text = ''
return safe_unicode(text).encode('utf-8')
def Title(self):
return safe_unicode(self.getField('title').get(self)).encode('utf-8')
def Title(self):
""" Return the Organisation's Name as its title """
field = self.getField('Name')
field = field and field.get(self) or ''
return safe_unicode(field).encode('utf-8')
def Title(self):
""" Return the Service ID as title """
s = self.getService()
s = s and s.Title() or ''
return safe_unicode(s).encode('utf-8')
def Title(self):
title = self.getName() and self.getName() or _("Laboratory")
return safe_unicode(title).encode('utf-8')
def Title(self):
return safe_unicode(self.getField('title').get(self)).encode('utf-8')
def Title(self):
""" Return the Id """
return safe_unicode(self.getId()).encode('utf-8')
def workflow_action_retract_ar(self):
workflow = getToolByName(self.context, 'portal_workflow')
# AR should be retracted
# Can't transition inactive ARs
if not isActive(self.context):
message = _('Item is inactive.')
self.context.plone_utils.addPortalMessage(message, 'info')
self.request.response.redirect(self.context.absolute_url())
return
# 1. Copies the AR linking the original one and viceversa
ar = self.context
newar = self.cloneAR(ar)
# 2. The old AR gets a status of 'invalid'
workflow.doActionFor(ar, 'retract_ar')
# 3. The new AR copy opens in status 'to be verified'
changeWorkflowState(newar, 'bika_ar_workflow', 'to_be_verified')
# 4. The system immediately alerts the client contacts who ordered
# the results, per email and SMS, that a possible mistake has been
# picked up and is under investigation.
# A much possible information is provided in the email, linking
# to the AR online.
laboratory = self.context.bika_setup.laboratory
lab_address = "<br/>".join(laboratory.getPrintAddress())
mime_msg = MIMEMultipart('related')
mime_msg['Subject'] = t(
_("Erroneus result publication from ${request_id}",
mapping={"request_id": ar.getRequestID()}))
mime_msg['From'] = formataddr((encode_header(laboratory.getName()),
laboratory.getEmailAddress()))
to = []
contact = ar.getContact()
if contact:
to.append(
formataddr((encode_header(contact.Title()),
contact.getEmailAddress())))
for cc in ar.getCCContact():
formatted = formataddr(
(encode_header(cc.Title()), cc.getEmailAddress()))
if formatted not in to:
to.append(formatted)
managers = self.context.portal_groups.getGroupMembers('LabManagers')
for bcc in managers:
user = self.portal.acl_users.getUser(bcc)
if user:
uemail = user.getProperty('email')
ufull = user.getProperty('fullname')
formatted = formataddr((encode_header(ufull), uemail))
if formatted not in to:
to.append(formatted)
mime_msg['To'] = ','.join(to)
aranchor = "<a href='%s'>%s</a>" % (ar.absolute_url(),
ar.getRequestID())
naranchor = "<a href='%s'>%s</a>" % (newar.absolute_url(),
newar.getRequestID())
addremarks = ('addremarks' in self.request
and ar.getRemarks()) \
and ("<br/><br/>"
+ _("Additional remarks:")
+ "<br/>"
+ ar.getRemarks().split("===")[1].strip()
+ "<br/><br/>") \
or ''
sub_d = dict(request_link=aranchor,
new_request_link=naranchor,
remarks=addremarks,
lab_address=lab_address)
body = Template(
"Some errors have been detected in the results report "
"published from the Analysis Request $request_link. The Analysis "
"Request $new_request_link has been created automatically and the "
"previous has been invalidated.<br/>The possible mistake "
"has been picked up and is under investigation.<br/><br/>"
"$remarks $lab_address").safe_substitute(sub_d)
msg_txt = MIMEText(safe_unicode(body).encode('utf-8'), _subtype='html')
mime_msg.preamble = 'This is a multi-part MIME message.'
mime_msg.attach(msg_txt)
try:
host = getToolByName(self.context, 'MailHost')
host.send(mime_msg.as_string(), immediate=True)
except Exception as msg:
message = _(
'Unable to send an email to alert lab '
'client contacts that the Analysis Request has been '
'retracted: ${error}',
mapping={'error': safe_unicode(msg)})
self.context.plone_utils.addPortalMessage(message, 'warning')
message = _('${items} invalidated.',
mapping={'items': ar.getRequestID()})
self.context.plone_utils.addPortalMessage(message, 'warning')
self.request.response.redirect(newar.absolute_url())
def workflow_action_preserve(self):
form = self.request.form
workflow = getToolByName(self.context, 'portal_workflow')
action, came_from = WorkflowAction._get_form_workflow_action(self)
checkPermission = self.context.portal_membership.checkPermission
# Partition Preservation
# the partition table shown in AR and Sample views sends it's
# action button submits here.
objects = WorkflowAction._get_selected_items(self)
transitioned = []
incomplete = []
for obj_uid, obj in objects.items():
part = obj
# can't transition inactive items
if workflow.getInfoFor(part, 'inactive_state', '') == 'inactive':
continue
if not checkPermission(PreserveSample, part):
continue
# grab this object's Preserver and DatePreserved from the form
Preserver = form['getPreserver'][0][obj_uid].strip()
Preserver = Preserver and Preserver or ''
DatePreserved = form['getDatePreserved'][0][obj_uid].strip()
DatePreserved = DatePreserved and DateTime(DatePreserved) or ''
# write them to the sample
part.setPreserver(Preserver)
part.setDatePreserved(DatePreserved)
# transition the object if both values are present
if Preserver and DatePreserved:
workflow.doActionFor(part, action)
transitioned.append(part.id)
else:
incomplete.append(part.id)
part.reindexObject()
part.aq_parent.reindexObject()
message = None
if len(transitioned) > 1:
message = _(
'${items} are waiting to be received.',
mapping={'items': safe_unicode(', '.join(transitioned))})
self.context.plone_utils.addPortalMessage(message, 'info')
elif len(transitioned) == 1:
message = _(
'${item} is waiting to be received.',
mapping={'item': safe_unicode(', '.join(transitioned))})
self.context.plone_utils.addPortalMessage(message, 'info')
if not message:
message = _('No changes made.')
self.context.plone_utils.addPortalMessage(message, 'info')
if len(incomplete) > 1:
message = _('${items} are missing Preserver or Date Preserved',
mapping={'items': safe_unicode(', '.join(incomplete))})
self.context.plone_utils.addPortalMessage(message, 'error')
elif len(incomplete) == 1:
message = _('${item} is missing Preserver or Preservation Date',
mapping={'item': safe_unicode(', '.join(incomplete))})
self.context.plone_utils.addPortalMessage(message, 'error')
self.destination_url = self.request.get_header(
"referer", self.context.absolute_url())
self.request.response.redirect(self.destination_url)
def to_unicode(text):
if text is None:
text = ''
return safe_unicode(text)
def folderitems(self):
rc = getToolByName(self.context, REFERENCE_CATALOG)
bsc = getToolByName(self.context, 'bika_setup_catalog')
workflow = getToolByName(self.context, 'portal_workflow')
mtool = getToolByName(self.context, 'portal_membership')
checkPermission = mtool.checkPermission
if not self.allow_edit:
can_edit_analyses = False
else:
if self.contentFilter.get('getPointOfCapture', '') == 'field':
can_edit_analyses = checkPermission(EditFieldResults,
self.context)
else:
can_edit_analyses = checkPermission(EditResults, self.context)
self.allow_edit = can_edit_analyses
self.show_select_column = self.allow_edit
context_active = isActive(self.context)
self.categories = []
items = super(AnalysesView, self).folderitems(full_objects=True)
# manually skim retracted analyses from the list
new_items = []
for i, item in enumerate(items):
# self.contentsMethod may return brains or objects.
if not ('obj' in items[i]):
continue
obj = hasattr(items[i]['obj'], 'getObject') and \
items[i]['obj'].getObject() or \
items[i]['obj']
if workflow.getInfoFor(obj, 'review_state') == 'retracted' \
and not checkPermission(ViewRetractedAnalyses, self.context):
continue
new_items.append(item)
items = new_items
methods = self.get_methods_vocabulary()
self.interim_fields = {}
self.interim_columns = {}
self.specs = {}
show_methodinstr_columns = False
for i, item in enumerate(items):
# self.contentsMethod may return brains or objects.
obj = hasattr(items[i]['obj'], 'getObject') and \
items[i]['obj'].getObject() or \
items[i]['obj']
if workflow.getInfoFor(obj, 'review_state') == 'retracted' \
and not checkPermission(ViewRetractedAnalyses, self.context):
continue
result = obj.getResult()
service = obj.getService()
calculation = service.getCalculation()
unit = service.getUnit()
keyword = service.getKeyword()
if self.show_categories:
cat = obj.getService().getCategoryTitle()
items[i]['category'] = cat
if cat not in self.categories:
self.categories.append(cat)
# Check for InterimFields attribute on our object,
interim_fields = hasattr(obj, 'getInterimFields') \
and obj.getInterimFields() or []
# kick some pretty display values in.
for x in range(len(interim_fields)):
interim_fields[x]['formatted_value'] = \
format_numeric_result(obj, interim_fields[x]['value'])
self.interim_fields[obj.UID()] = interim_fields
items[i]['service_uid'] = service.UID()
items[i]['Service'] = service.Title()
items[i]['Keyword'] = keyword
items[i]['Unit'] = format_supsub(unit) if unit else ''
items[i]['Result'] = ''
items[i]['formatted_result'] = ''
items[i]['interim_fields'] = interim_fields
items[i]['Remarks'] = obj.getRemarks()
items[i]['Uncertainty'] = ''
items[i]['DetectionLimit'] = ''
items[i]['retested'] = obj.getRetested()
items[i]['class']['retested'] = 'center'
items[i]['result_captured'] = self.ulocalized_time(
obj.getResultCaptureDate(), long_format=0)
items[i]['calculation'] = calculation and True or False
try:
items[i]['Partition'] = obj.getSamplePartition().getId()
except AttributeError:
items[i]['Partition'] = ''
if obj.portal_type == "ReferenceAnalysis":
items[i]['DueDate'] = self.ulocalized_time(
obj.aq_parent.getExpiryDate(), long_format=0)
else:
items[i]['DueDate'] = self.ulocalized_time(obj.getDueDate(),
long_format=1)
cd = obj.getResultCaptureDate()
items[i]['CaptureDate'] = cd and self.ulocalized_time(
cd, long_format=1) or ''
items[i]['Attachments'] = ''
item['allow_edit'] = []
client_or_lab = ""
tblrowclass = items[i].get('table_row_class')
if obj.portal_type == 'ReferenceAnalysis':
items[i]['st_uid'] = obj.aq_parent.UID()
items[i]['table_row_class'] = ' '.join(
[tblrowclass, 'qc-analysis'])
elif obj.portal_type == 'DuplicateAnalysis' and \
obj.getAnalysis().portal_type == 'ReferenceAnalysis':
items[i]['st_uid'] = obj.aq_parent.UID()
items[i]['table_row_class'] = ' '.join(
[tblrowclass, 'qc-analysis'])
else:
sample = None
if self.context.portal_type == 'AnalysisRequest':
sample = self.context.getSample()
elif self.context.portal_type == 'Worksheet':
if obj.portal_type in ('DuplicateAnalysis',
'RejectAnalysis'):
sample = obj.getAnalysis().getSample()
else:
sample = obj.aq_parent.getSample()
elif self.context.portal_type == 'Sample':
sample = self.context
st_uid = sample.getSampleType().UID() if sample else ''
items[i]['st_uid'] = st_uid
if checkPermission(ManageBika, self.context):
service_uid = service.UID()
latest = rc.lookupObject(service_uid).version_id
items[i]['Service'] = service.Title()
items[i]['class']['Service'] = "service_title"
# Show version number of out-of-date objects
# No: This should be done in another column, if at all.
# The (vX) value confuses some more fragile forms.
# if hasattr(obj, 'reference_versions') and \
# service_uid in obj.reference_versions and \
# latest != obj.reference_versions[service_uid]:
# items[i]['after']['Service'] = "(v%s)" % \
# (obj.reference_versions[service_uid])
# choices defined on Service apply to result fields.
choices = service.getResultOptions()
if choices:
item['choices']['Result'] = choices
# permission to view this item's results
can_view_result = \
getSecurityManager().checkPermission(ViewResults, obj)
# permission to edit this item's results
# Editing Field Results is possible while in Sample Due.
poc = self.contentFilter.get("getPointOfCapture", 'lab')
can_edit_analysis = self.allow_edit and context_active and \
( (poc == 'field' and getSecurityManager().checkPermission(EditFieldResults, obj))
or
(poc != 'field' and getSecurityManager().checkPermission(EditResults, obj)) )
allowed_method_states = [
'to_be_sampled', 'to_be_preserved', 'sample_received',
'sample_registered', 'sampled', 'assigned'
]
# Prevent from being edited if the instrument assigned
# is not valid (out-of-date or uncalibrated), except if
# the analysis is a QC with assigned status
can_edit_analysis = can_edit_analysis \
and (obj.isInstrumentValid() \
or (obj.portal_type == 'ReferenceAnalysis' \
and item['review_state'] in allowed_method_states))
if can_edit_analysis:
items[i]['allow_edit'].extend(['Analyst', 'Result', 'Remarks'])
# if the Result field is editable, our interim fields are too
for f in self.interim_fields[obj.UID()]:
items[i]['allow_edit'].append(f['keyword'])
# if there isn't a calculation then result must be re-testable,
# and if there are interim fields, they too must be re-testable.
if not items[i]['calculation'] or \
(items[i]['calculation'] and self.interim_fields[obj.UID()]):
items[i]['allow_edit'].append('retested')
# TODO: Only the labmanager must be able to change the method
# can_set_method = getSecurityManager().checkPermission(SetAnalysisMethod, obj)
can_set_method = can_edit_analysis \
and item['review_state'] in allowed_method_states
method = obj.getMethod() \
if hasattr(obj, 'getMethod') and obj.getMethod() \
else service.getMethod()
# Display the methods selector if the AS has at least one
# method assigned
item['Method'] = ''
item['replace']['Method'] = ''
if can_set_method:
voc = self.get_methods_vocabulary(obj)
if voc:
# The service has at least one method available
item['Method'] = method.UID() if method else ''
item['choices']['Method'] = voc
item['allow_edit'].append('Method')
show_methodinstr_columns = True
elif method:
# This should never happen
# The analysis has set a method, but its parent
# service hasn't any method available O_o
item['Method'] = method.Title()
item['replace']['Method'] = "<a href='%s'>%s</a>" % \
(method.absolute_url(), method.Title())
show_methodinstr_columns = True
elif method:
# Edition not allowed, but method set
item['Method'] = method.Title()
item['replace']['Method'] = "<a href='%s'>%s</a>" % \
(method.absolute_url(), method.Title())
show_methodinstr_columns = True
# TODO: Instrument selector dynamic behavior in worksheet Results
# Only the labmanager must be able to change the instrument to be used. Also,
# the instrument selection should be done in accordance with the method selected
# can_set_instrument = service.getInstrumentEntryOfResults() and getSecurityManager().checkPermission(SetAnalysisInstrument, obj)
can_set_instrument = service.getInstrumentEntryOfResults() \
and can_edit_analysis \
and item['review_state'] in allowed_method_states
item['Instrument'] = ''
item['replace']['Instrument'] = ''
if service.getInstrumentEntryOfResults():
instrument = None
# If the analysis has an instrument already assigned, use it
if service.getInstrumentEntryOfResults() \
and hasattr(obj, 'getInstrument') \
and obj.getInstrument():
instrument = obj.getInstrument()
# Otherwise, use the Service's default instrument
elif service.getInstrumentEntryOfResults():
instrument = service.getInstrument()
if can_set_instrument:
# Edition allowed
voc = self.get_instruments_vocabulary(obj)
if voc:
# The service has at least one instrument available
item['Instrument'] = instrument.UID(
) if instrument else ''
item['choices']['Instrument'] = voc
item['allow_edit'].append('Instrument')
show_methodinstr_columns = True
elif instrument:
# This should never happen
# The analysis has an instrument set, but the
# service hasn't any available instrument
item['Instrument'] = instrument.Title()
item['replace']['Instrument'] = "<a href='%s'>%s</a>" % \
(instrument.absolute_url(), instrument.Title())
show_methodinstr_columns = True
elif instrument:
# Edition not allowed, but instrument set
item['Instrument'] = instrument.Title()
item['replace']['Instrument'] = "<a href='%s'>%s</a>" % \
(instrument.absolute_url(), instrument.Title())
show_methodinstr_columns = True
else:
# Manual entry of results, instrument not allowed
item['Instrument'] = _('Manual')
msgtitle = t(
_(
"Instrument entry of results not allowed for ${service}",
mapping={"service": safe_unicode(service.Title())},
))
item['replace']['Instrument'] = \
'<a href="#" title="%s">%s</a>' % (msgtitle, t(_('Manual')))
# Sets the analyst assigned to this analysis
if can_edit_analysis:
analyst = obj.getAnalyst()
# widget default: current user
if not analyst:
analyst = mtool.getAuthenticatedMember().getUserName()
items[i]['Analyst'] = analyst
item['choices']['Analyst'] = self.getAnalysts()
else:
items[i]['Analyst'] = obj.getAnalystName()
# If the user can attach files to analyses, show the attachment col
can_add_attachment = \
getSecurityManager().checkPermission(AddAttachment, obj)
if can_add_attachment or can_view_result:
attachments = ""
if hasattr(obj, 'getAttachment'):
for attachment in obj.getAttachment():
af = attachment.getAttachmentFile()
icon = af.getBestIcon()
attachments += "<span class='attachment' attachment_uid='%s'>" % (
attachment.UID())
if icon:
attachments += "<img src='%s/%s'/>" % (
self.portal_url, icon)
attachments += '<a href="%s/at_download/AttachmentFile"/>%s</a>' % (
attachment.absolute_url(), af.filename)
if can_edit_analysis:
attachments += "<img class='deleteAttachmentButton' attachment_uid='%s' src='%s'/>" % (
attachment.UID(),
"++resource++bika.lims.images/delete.png")
attachments += "</br></span>"
items[i]['replace'][
'Attachments'] = attachments[:-12] + "</span>"
# Only display data bearing fields if we have ViewResults
# permission, otherwise just put an icon in Result column.
if can_view_result:
items[i]['Result'] = result
scinot = self.context.bika_setup.getScientificNotationResults()
dmk = self.context.bika_setup.getResultsDecimalMark()
items[i]['formatted_result'] = obj.getFormattedResult(
sciformat=int(scinot), decimalmark=dmk)
# LIMS-1379 Allow manual uncertainty value input
# https://jira.bikalabs.com/browse/LIMS-1379
fu = format_uncertainty(obj,
result,
decimalmark=dmk,
sciformat=int(scinot))
fu = fu if fu else ''
if can_edit_analysis and service.getAllowManualUncertainty(
) == True:
unc = obj.getUncertainty(result)
item['allow_edit'].append('Uncertainty')
items[i]['Uncertainty'] = unc if unc else ''
items[i]['before']['Uncertainty'] = '± '
items[i]['after'][
'Uncertainty'] = '<em class="discreet" style="white-space:nowrap;"> %s</em>' % items[
i]['Unit']
elif fu:
items[i]['Uncertainty'] = fu
items[i]['before']['Uncertainty'] = '± '
items[i]['after'][
'Uncertainty'] = '<em class="discreet" style="white-space:nowrap;"> %s</em>' % items[
i]['Unit']
# LIMS-1700. Allow manual input of Detection Limits
# LIMS-1775. Allow to select LDL or UDL defaults in results with readonly mode
# https://jira.bikalabs.com/browse/LIMS-1700
# https://jira.bikalabs.com/browse/LIMS-1775
if can_edit_analysis and \
hasattr(obj, 'getDetectionLimitOperand') and \
hasattr(service, 'getDetectionLimitSelector') and \
service.getDetectionLimitSelector() == True:
isldl = obj.isBelowLowerDetectionLimit()
isudl = obj.isAboveUpperDetectionLimit()
dlval = ''
if isldl or isudl:
dlval = '<' if isldl else '>'
item['allow_edit'].append('DetectionLimit')
item['DetectionLimit'] = dlval
choices = [{
'ResultValue': '<',
'ResultText': '<'
}, {
'ResultValue': '>',
'ResultText': '>'
}]
item['choices']['DetectionLimit'] = choices
self.columns['DetectionLimit']['toggle'] = True
srv = obj.getService()
defdls = {
'min': srv.getLowerDetectionLimit(),
'max': srv.getUpperDetectionLimit(),
'manual': srv.getAllowManualDetectionLimit()
}
defin = '<input type="hidden" id="DefaultDLS.%s" value=\'%s\'/>'
defin = defin % (obj.UID(), json.dumps(defdls))
item['after']['DetectionLimit'] = defin
# LIMS-1769. Allow to use LDL and UDL in calculations.
# https://jira.bikalabs.com/browse/LIMS-1769
# Since LDL, UDL, etc. are wildcards that can be used
# in calculations, these fields must be loaded always
# for 'live' calculations.
if can_edit_analysis:
dls = {
'default_ldl': 'none',
'default_udl': 'none',
'below_ldl': False,
'above_udl': False,
'is_ldl': False,
'is_udl': False,
'manual_allowed': False,
'dlselect_allowed': False
}
if hasattr(obj, 'getDetectionLimits'):
dls['below_ldl'] = obj.isBelowLowerDetectionLimit()
dls['above_udl'] = obj.isBelowLowerDetectionLimit()
dls['is_ldl'] = obj.isLowerDetectionLimit()
dls['is_udl'] = obj.isUpperDetectionLimit()
dls['default_ldl'] = service.getLowerDetectionLimit()
dls['default_udl'] = service.getUpperDetectionLimit()
dls['manual_allowed'] = service.getAllowManualDetectionLimit(
)
dls['dlselect_allowed'] = service.getDetectionLimitSelector(
)
dlsin = '<input type="hidden" id="AnalysisDLS.%s" value=\'%s\'/>'
dlsin = dlsin % (obj.UID(), json.dumps(dls))
item['after']['Result'] = dlsin
else:
items[i]['Specification'] = ""
if 'Result' in items[i]['allow_edit']:
items[i]['allow_edit'].remove('Result')
items[i]['before']['Result'] = \
'<img width="16" height="16" ' + \
'src="%s/++resource++bika.lims.images/to_follow.png"/>' % \
(self.portal_url)
# Everyone can see valid-ranges
spec = self.get_analysis_spec(obj)
if spec:
min_val = spec.get('min', '')
min_str = ">{0}".format(min_val) if min_val else ''
max_val = spec.get('max', '')
max_str = "<{0}".format(max_val) if max_val else ''
error_val = spec.get('error', '')
error_str = "{0}%".format(error_val) if error_val else ''
rngstr = ",".join(
[x for x in [min_str, max_str, error_str] if x])
else:
rngstr = ""
items[i]['Specification'] = rngstr
# Add this analysis' interim fields to the interim_columns list
for f in self.interim_fields[obj.UID()]:
if f['keyword'] not in self.interim_columns and not f.get(
'hidden', False):
self.interim_columns[f['keyword']] = f['title']
# and to the item itself
items[i][f['keyword']] = f
items[i]['class'][f['keyword']] = 'interim'
# check if this analysis is late/overdue
resultdate = obj.aq_parent.getDateSampled() \
if obj.portal_type == 'ReferenceAnalysis' \
else obj.getResultCaptureDate()
duedate = obj.aq_parent.getExpiryDate() \
if obj.portal_type == 'ReferenceAnalysis' \
else obj.getDueDate()
items[i]['replace']['DueDate'] = \
self.ulocalized_time(duedate, long_format=1)
if items[i]['review_state'] not in [
'to_be_sampled', 'to_be_preserved', 'sample_due',
'published'
]:
if (resultdate and resultdate > duedate) \
or (not resultdate and DateTime() > duedate):
items[i]['replace']['DueDate'] = '%s <img width="16" height="16" src="%s/++resource++bika.lims.images/late.png" title="%s"/>' % \
(self.ulocalized_time(duedate, long_format=1),
self.portal_url,
t(_("Late Analysis")))
# Submitting user may not verify results (admin can though)
if items[i]['review_state'] == 'to_be_verified' and \
not checkPermission(VerifyOwnResults, obj):
user_id = getSecurityManager().getUser().getId()
self_submitted = False
try:
review_history = list(
workflow.getInfoFor(obj, 'review_history'))
review_history.reverse()
for event in review_history:
if event.get('action') == 'submit':
if event.get('actor') == user_id:
self_submitted = True
break
if self_submitted:
items[i]['after']['state_title'] = \
"<img src='++resource++bika.lims.images/submitted-by-current-user.png' title='%s'/>" % \
(t(_("Cannot verify: Submitted by current user")))
except WorkflowException:
pass
# add icon for assigned analyses in AR views
if self.context.portal_type == 'AnalysisRequest':
obj = items[i]['obj']
if obj.portal_type in ['ReferenceAnalysis',
'DuplicateAnalysis'] or \
workflow.getInfoFor(obj, 'worksheetanalysis_review_state') == 'assigned':
br = obj.getBackReferences('WorksheetAnalysis')
if len(br) > 0:
ws = br[0]
items[i]['after']['state_title'] = \
"<a href='%s'><img src='++resource++bika.lims.images/worksheet.png' title='%s'/></a>" % \
(ws.absolute_url(),
t(_("Assigned to: ${worksheet_id}",
mapping={'worksheet_id': safe_unicode(ws.id)})))
# the TAL requires values for all interim fields on all
# items, so we set blank values in unused cells
for item in items:
for field in self.interim_columns:
if field not in item:
item[field] = ''
# XXX order the list of interim columns
interim_keys = self.interim_columns.keys()
interim_keys.reverse()
# add InterimFields keys to columns
for col_id in interim_keys:
if col_id not in self.columns:
self.columns[col_id] = {
'title': self.interim_columns[col_id],
'input_width': '6',
'input_class': 'ajax_calculate numeric',
'sortable': False
}
if can_edit_analyses:
new_states = []
for state in self.review_states:
# InterimFields are displayed in review_state
# They are anyway available through View.columns though.
# In case of hidden fields, the calcs.py should check calcs/services
# for additional InterimFields!!
pos = 'Result' in state['columns'] and \
state['columns'].index('Result') or len(state['columns'])
for col_id in interim_keys:
if col_id not in state['columns']:
state['columns'].insert(pos, col_id)
# retested column is added after Result.
pos = 'Result' in state['columns'] and \
state['columns'].index('Uncertainty') + 1 or len(state['columns'])
state['columns'].insert(pos, 'retested')
new_states.append(state)
self.review_states = new_states
# Allow selecting individual analyses
self.show_select_column = True
# Dry Matter.
# The Dry Matter column is never enabled for reference sample contexts
# and refers to getReportDryMatter in ARs.
if items and \
(hasattr(self.context, 'getReportDryMatter') and \
self.context.getReportDryMatter()):
# look through all items
# if the item's Service supports ReportDryMatter, add getResultDM().
for item in items:
if item['obj'].getService().getReportDryMatter():
item['ResultDM'] = item['obj'].getResultDM()
else:
item['ResultDM'] = ''
if item['ResultDM']:
item['after']['ResultDM'] = "<em class='discreet'>%</em>"
# modify the review_states list to include the ResultDM column
new_states = []
for state in self.review_states:
pos = 'Result' in state['columns'] and \
state['columns'].index('Uncertainty') + 1 or len(state['columns'])
state['columns'].insert(pos, 'ResultDM')
new_states.append(state)
self.review_states = new_states
self.categories.sort()
# self.json_specs = json.dumps(self.specs)
self.json_interim_fields = json.dumps(self.interim_fields)
self.items = items
# Method and Instrument columns must be shown or hidden at the
# same time, because the value assigned to one causes
# a value reassignment to the other (one method can be performed
# by different instruments)
self.columns['Method']['toggle'] = show_methodinstr_columns
self.columns['Instrument']['toggle'] = show_methodinstr_columns
return items
def Title(self):
""" Return the Organisation's Name as its title """
return safe_unicode(self.getField('Name').get(self)).encode('utf-8')
def workflow_action_retract_ar(self):
workflow = getToolByName(self.context, 'portal_workflow')
# AR should be retracted
# Can't transition inactive ARs
if not isActive(self.context):
message = _('Item is inactive.')
self.context.plone_utils.addPortalMessage(message, 'info')
self.request.response.redirect(self.context.absolute_url())
return
# 1. Copies the AR linking the original one and viceversa
ar = self.context
newar = self.cloneAR(ar)
# 2. The old AR gets a status of 'invalid'
workflow.doActionFor(ar, 'retract_ar')
# 3. The new AR copy opens in status 'to be verified'
changeWorkflowState(newar, 'bika_ar_workflow', 'to_be_verified')
# 4. The system immediately alerts the client contacts who ordered
# the results, per email and SMS, that a possible mistake has been
# picked up and is under investigation.
# A much possible information is provided in the email, linking
# to the AR online.
laboratory = self.context.bika_setup.laboratory
lab_address = "<br/>".join(laboratory.getPrintAddress())
mime_msg = MIMEMultipart('related')
mime_msg['Subject'] = t(_("Erroneus result publication from ${request_id}",
mapping={"request_id": ar.getRequestID()}))
mime_msg['From'] = formataddr(
(encode_header(laboratory.getName()),
laboratory.getEmailAddress()))
to = []
contact = ar.getContact()
if contact:
to.append(formataddr((encode_header(contact.Title()),
contact.getEmailAddress())))
for cc in ar.getCCContact():
formatted = formataddr((encode_header(cc.Title()),
cc.getEmailAddress()))
if formatted not in to:
to.append(formatted)
managers = self.context.portal_groups.getGroupMembers('LabManagers')
for bcc in managers:
user = self.portal.acl_users.getUser(bcc)
if user:
uemail = user.getProperty('email')
ufull = user.getProperty('fullname')
formatted = formataddr((encode_header(ufull), uemail))
if formatted not in to:
to.append(formatted)
mime_msg['To'] = ','.join(to)
aranchor = "<a href='%s'>%s</a>" % (ar.absolute_url(),
ar.getRequestID())
naranchor = "<a href='%s'>%s</a>" % (newar.absolute_url(),
newar.getRequestID())
addremarks = ('addremarks' in self.request
and ar.getRemarks()) \
and ("<br/><br/>"
+ _("Additional remarks:")
+ "<br/>"
+ ar.getRemarks().split("===")[1].strip()
+ "<br/><br/>") \
or ''
sub_d = dict(request_link=aranchor,
new_request_link=naranchor,
remarks=addremarks,
lab_address=lab_address)
body = Template("Some errors have been detected in the results report "
"published from the Analysis Request $request_link. The Analysis "
"Request $new_request_link has been created automatically and the "
"previous has been invalidated.<br/>The possible mistake "
"has been picked up and is under investigation.<br/><br/>"
"$remarks $lab_address").safe_substitute(sub_d)
msg_txt = MIMEText(safe_unicode(body).encode('utf-8'),
_subtype='html')
mime_msg.preamble = 'This is a multi-part MIME message.'
mime_msg.attach(msg_txt)
try:
host = getToolByName(self.context, 'MailHost')
host.send(mime_msg.as_string(), immediate=True)
except Exception as msg:
message = _('Unable to send an email to alert lab '
'client contacts that the Analysis Request has been '
'retracted: ${error}',
mapping={'error': safe_unicode(msg)})
self.context.plone_utils.addPortalMessage(message, 'warning')
message = _('${items} invalidated.',
mapping={'items': ar.getRequestID()})
self.context.plone_utils.addPortalMessage(message, 'warning')
self.request.response.redirect(newar.absolute_url())
def __call__(self):
form = self.request.form
CheckAuthenticator(self.request.form)
PostOnly(self.request.form)
uc = getToolByName(self.context, 'uid_catalog')
bsc = getToolByName(self.context, 'bika_setup_catalog')
portal_catalog = getToolByName(self.context, 'portal_catalog')
# Load the form data from request.state. If anything goes wrong here,
# put a bullet through the whole process.
try:
states = json.loads(form['state'])
except Exception as e:
message = t(_('Badly formed state: ${errmsg}',
mapping={'errmsg': e.message}))
ajax_form_error(self.errors, message=message)
return json.dumps({'errors': self.errors})
# Validate incoming form data
required = [field.getName() for field
in AnalysisRequestSchema.fields()
if field.required] + ["Analyses"]
# First remove all states which are completely empty; if all
# required fields are not present, we assume that the current
# AR had no data entered, and can be ignored
nonblank_states = {}
for arnum, state in states.items():
for key, val in state.items():
if val \
and "%s_hidden" % key not in state \
and not key.endswith('hidden'):
nonblank_states[arnum] = state
break
# in valid_states, all ars that pass validation will be stored
valid_states = {}
for arnum, state in nonblank_states.items():
# Secondary ARs are a special case, these fields are not required
if state.get('Sample', ''):
if 'SamplingDate' in required:
required.remove('SamplingDate')
if 'SampleType' in required:
required.remove('SampleType')
# fields flagged as 'hidden' are not considered required because
# they will already have default values inserted in them
for fieldname in required:
if fieldname + '_hidden' in state:
required.remove(fieldname)
missing = [f for f in required if not state.get(f, '')]
# If there are required fields missing, flag an error
if missing:
msg = t(_('Required fields have no values: '
'${field_names}',
mapping={'field_names': ', '.join(missing)}))
ajax_form_error(self.errors, arnum=arnum, message=msg)
continue
# This ar is valid!
valid_states[arnum] = state
# - Expand lists of UIDs returned by multiValued reference widgets
# - Transfer _uid values into their respective fields
for arnum in valid_states.keys():
for field, value in valid_states[arnum].items():
if field.endswith('_uid') and ',' in value:
valid_states[arnum][field] = value.split(',')
elif field.endswith('_uid'):
valid_states[arnum][field] = value
if self.errors:
return json.dumps({'errors': self.errors})
# Now, we will create the specified ARs.
ARs = []
for arnum, state in valid_states.items():
# Create the Analysis Request
ar = create_analysisrequest(
portal_catalog(UID=state['Client'])[0].getObject(),
self.request,
state
)
ARs.append(ar.Title())
# Display the appropriate message after creation
if len(ARs) > 1:
message = _('Analysis requests ${ARs} were successfully created.',
mapping={'ARs': safe_unicode(', '.join(ARs))})
else:
message = _('Analysis request ${AR} was successfully created.',
mapping={'AR': safe_unicode(ARs[0])})
self.context.plone_utils.addPortalMessage(message, 'info')
# Automatic label printing won't print "register" labels for Secondary. ARs
new_ars = [ar for ar in ARs if ar[-2:] == '01']
if 'register' in self.context.bika_setup.getAutoPrintStickers() \
and new_ars:
return json.dumps({
'success': message,
'stickers': new_ars,
'stickertemplate': self.context.bika_setup.getAutoStickerTemplate()
})
else:
return json.dumps({'success': message})
def Title(self):
""" Return the Organisation's Name as its title """
return safe_unicode(self.getField('Name').get(self)).encode('utf-8')
def __call__(self, value, *args, **kwargs):
instance = kwargs['instance']
fieldname = kwargs['field'].getName()
request = kwargs.get('REQUEST', {})
form = request.form
interim_fields = form.get(fieldname, [])
translate = getToolByName(instance, 'translation_service').translate
bsc = getToolByName(instance, 'bika_setup_catalog')
# We run through the validator once per form submit, and check all values
# this value in request prevents running once per subfield value.
key = instance.id + fieldname
if instance.REQUEST.get(key, False):
return True
for x in range(len(interim_fields)):
row = interim_fields[x]
keys = row.keys()
if 'title' not in keys:
instance.REQUEST[key] = to_utf8(translate(_("Validation failed: title is required")))
return instance.REQUEST[key]
if 'keyword' not in keys:
instance.REQUEST[key] = to_utf8(translate(_("Validation failed: keyword is required")))
return instance.REQUEST[key]
if not re.match(r"^[A-Za-z\w\d\-\_]+$", row['keyword']):
instance.REQUEST[key] = _("Validation failed: keyword contains invalid characters")
return instance.REQUEST[key]
# keywords and titles used once only in the submitted form
keywords = {}
titles = {}
for field in interim_fields:
if 'keyword' in field:
if field['keyword'] in keywords:
keywords[field['keyword']] += 1
else:
keywords[field['keyword']] = 1
if 'title' in field:
if field['title'] in titles:
titles[field['title']] += 1
else:
titles[field['title']] = 1
for k in [k for k in keywords.keys() if keywords[k] > 1]:
msg = _("Validation failed: '${keyword}': duplicate keyword",
mapping={'keyword': safe_unicode(k)})
instance.REQUEST[key] = to_utf8(translate(msg))
return instance.REQUEST[key]
for t in [t for t in titles.keys() if titles[t] > 1]:
msg = _("Validation failed: '${title}': duplicate title",
mapping={'title': safe_unicode(t)})
instance.REQUEST[key] = to_utf8(translate(msg))
return instance.REQUEST[key]
# check all keywords against all AnalysisService keywords for dups
services = bsc(portal_type='AnalysisService', getKeyword=value)
if services:
msg = _("Validation failed: '${title}': "
"This keyword is already in use by service '${used_by}'",
mapping={'title': safe_unicode(value),
'used_by': safe_unicode(services[0].Title)})
instance.REQUEST[key] = to_utf8(translate(msg))
return instance.REQUEST[key]
# any duplicated interimfield titles must share the same keyword
# any duplicated interimfield keywords must share the same title
calcs = bsc(portal_type='Calculation')
keyword_titles = {}
title_keywords = {}
for calc in calcs:
if calc.UID == instance.UID():
continue
calc = calc.getObject()
for field in calc.getInterimFields():
keyword_titles[field['keyword']] = field['title']
title_keywords[field['title']] = field['keyword']
for field in interim_fields:
if field['keyword'] != value:
continue
if 'title' in field and \
field['title'] in title_keywords.keys() and \
title_keywords[field['title']] != field['keyword']:
msg = _("Validation failed: column title '${title}' "
"must have keyword '${keyword}'",
mapping={'title': safe_unicode(field['title']),
'keyword': safe_unicode(title_keywords[field['title']])})
instance.REQUEST[key] = to_utf8(translate(msg))
return instance.REQUEST[key]
if 'keyword' in field and \
field['keyword'] in keyword_titles.keys() and \
keyword_titles[field['keyword']] != field['title']:
msg = _("Validation failed: keyword '${keyword}' "
"must have column title '${title}'",
mapping={'keyword': safe_unicode(field['keyword']),
'title': safe_unicode(keyword_titles[field['keyword']])})
instance.REQUEST[key] = to_utf8(translate(msg))
return instance.REQUEST[key]
instance.REQUEST[key] = True
return True
def Title(self):
""" Return the Sample ID as title """
return safe_unicode(self.getId()).encode('utf-8')
def toPdf(self):
html = safe_unicode(self.template()).encode('utf-8')
pdf_data = createPdf(html)
return pdf_data
def read(context, request):
tag = AuthenticatorView(context, request).authenticator()
pattern = '<input .*name="(\w+)".*value="(\w+)"'
_authenticator = re.match(pattern, tag).groups()[1]
ret = {
"url": router.url_for("read", force_external=True),
"success": True,
"error": False,
"objects": [],
"_authenticator": _authenticator,
}
debug_mode = True #App.config.getConfiguration().debug_mode "Commented by Yasir"
catalog_name = request.get("catalog_name", "portal_catalog")
if not catalog_name:
raise ValueError("bad or missing catalog_name: " + catalog_name)
catalog = getToolByName(context, catalog_name)
indexes = catalog.indexes()
contentFilter = {}
for index in indexes:
if index in request:
if index == 'review_state' and "{" in request[index]:
continue
contentFilter[index] = safe_unicode(request[index])
if "%s[]" % index in request:
value = request["%s[]" % index]
contentFilter[index] = [safe_unicode(v) for v in value]
if 'limit' in request:
try:
contentFilter['sort_limit'] = int(request["limit"])
except ValueError:
pass
sort_on = request.get('sort_on', 'id')
contentFilter['sort_on'] = sort_on
# sort order
sort_order = request.get('sort_order', '')
if sort_order:
contentFilter['sort_order'] = sort_order
else:
sort_order = 'ascending'
contentFilter['sort_order'] = 'ascending'
include_fields = get_include_fields(request)
if debug_mode:
logger.info("contentFilter: " + str(contentFilter))
# Get matching objects from catalog
proxies = catalog(**contentFilter)
# batching items
page_nr = int(request.get("page_nr", 0))
try:
page_size = int(request.get("page_size", 10))
except ValueError:
page_size = 10
# page_size == 0: show all
if page_size == 0:
page_size = len(proxies)
first_item_nr = page_size * page_nr
if first_item_nr > len(proxies):
first_item_nr = 0
page_proxies = proxies[first_item_nr:first_item_nr + page_size]
for proxy in page_proxies:
obj_data = {}
# Place all proxy attributes into the result.
obj_data.update(load_brain_metadata(proxy, include_fields))
# Place all schema fields ino the result.
obj = proxy.getObject()
obj_data.update(load_field_values(obj, include_fields))
obj_data['path'] = "/".join(obj.getPhysicalPath())
# call any adapters that care to modify this data.
adapters = getAdapters((obj, ), IJSONReadExtender)
for name, adapter in adapters:
adapter(request, obj_data)
ret['objects'].append(obj_data)
ret['total_objects'] = len(proxies)
ret['first_object_nr'] = first_item_nr
last_object_nr = first_item_nr + len(page_proxies)
if last_object_nr > ret['total_objects']:
last_object_nr = ret['total_objects']
ret['last_object_nr'] = last_object_nr
if debug_mode:
logger.info("{0} objects returned".format(len(ret['objects'])))
return ret
def Title(self):
""" Return the OrderNumber as title """
return safe_unicode(self.getOrderNumber()).encode('utf-8')
def Title(self):
""" Return the contact's Fullname as title """
return safe_unicode(self.getFullname()).encode('utf-8')
def Title(self):
""" Return the contact's Fullname as title """
return safe_unicode(self.getFullname()).encode('utf-8')
def __call__(self):
if self.request.form.has_key("submitted"):
def error(field, message):
if field:
message = "%s: %s" % (field, message)
self.context.plone_utils.addPortalMessage(message, 'error')
return self.template()
form = self.request.form
contact = self.context
password = safe_unicode(form.get('password', '')).encode('utf-8')
username = safe_unicode(form.get('username', '')).encode('utf-8')
confirm = form.get('confirm', '')
email = safe_unicode(form.get('email', '')).encode('utf-8')
if not username:
return error('username',
PMF("Input is required but not given."))
if not email:
return error('email', PMF("Input is required but not given."))
reg_tool = self.context.portal_registration
properties = self.context.portal_properties.site_properties
## if properties.validate_email:
## password = reg_tool.generatePassword()
## else:
if password != confirm:
return error('password', PMF("Passwords do not match."))
if not password:
return error('password',
PMF("Input is required but not given."))
if not confirm:
return error('password', PMF("Passwords do not match."))
if len(password) < 5:
return error('password',
PMF("Passwords must contain at least 5 letters."))
try:
reg_tool.addMember(username,
password,
properties={
'username': username,
'email': email,
'fullname': username
})
except ValueError, msg:
return error(None, msg)
contact.setUsername(username)
contact.setEmailAddress(email)
# If we're being created in a Client context, then give
# the contact an Owner local role on client.
if contact.aq_parent.portal_type == 'Client':
contact.aq_parent.manage_setLocalRoles(username, [
'Owner',
])
if hasattr(aq_base(contact.aq_parent),
'reindexObjectSecurity'):
contact.aq_parent.reindexObjectSecurity()
# add user to Clients group
group = self.context.portal_groups.getGroupById('Clients')
group.addMember(username)
# Additional groups for LabContact users.
# not required (not available for client Contact)
if 'groups' in self.request and self.request['groups']:
groups = self.request['groups']
if not type(groups) in (list, tuple):
groups = [
groups,
]
for group in groups:
group = self.portal_groups.getGroupById(group)
group.addMember(username)
contact.reindexObject()
if properties.validate_email or self.request.get('mail_me', 0):
try:
reg_tool.registeredNotify(username)
except:
import transaction
transaction.abort()
return error(None, PMF("SMTP server disconnected."))
message = PMF("Member registered.")
self.context.plone_utils.addPortalMessage(message, 'info')
return self.template()
def Title(self):
""" Return the Organisation's Name as its title """
field = self.getField('Name')
field = field and field.get(self) or ''
return safe_unicode(field).encode('utf-8')
def Title(self):
""" Return the Product as title """
return safe_unicode(self.getSampleName()).encode('utf-8')