def __call__(self, result=None, **kwargs):
translate = self.context.translate
path = '++resource++bika.lims.images'
alerts = {}
# We look for IResultOutOfRange adapters for this object
for name, adapter in getAdapters((self.context, ), IResultOutOfRange):
ret = adapter(result)
if not ret:
continue
spec = ret["spec_values"]
rngstr = "{0} {1}, {2} {3}".format(
t(_("min")), str(spec.get('min','')),
t(_("max")), str(spec.get('max','')))
if ret["out_of_range"]:
if ret["acceptable"]:
message = "{0} ({1})".format(
t(_('Result in shoulder range')),
rngstr
)
icon = path + '/warning.png'
else:
message = "{0} ({1})".format(
t(_('Result out of range')),
rngstr
)
icon = path + '/exclamation.png'
alerts[self.context.UID()] = [
{
'icon': icon,
'msg': message,
'field': 'Result',
},
]
break
return alerts
def render_field_view(self, field):
fieldname = field.getName()
field = self.context.Schema()[fieldname]
ret = {'fieldName': fieldname, 'mode': 'view'}
try:
adapter = getAdapter(self.context,
interface=IHeaderTableFieldRenderer,
name=fieldname)
except ComponentLookupError:
adapter = None
if adapter:
ret = {'fieldName': fieldname,
'mode': 'structure',
'html': adapter(field)}
else:
if field.getType().find("ool") > -1:
value = field.get(self.context)
ret = {
'fieldName': fieldname,
'mode': 'structure',
'html': t(_('Yes')) if value else t(_('No'))
}
elif field.getType().find("Reference") > -1:
# Prioritize method retrieval over schema's field
targets = None
if hasattr(self.context, 'get%s' % fieldname):
fieldaccessor = getattr(self.context, 'get%s' % fieldname)
if callable(fieldaccessor):
targets = fieldaccessor()
if not targets:
targets = field.get(self.context)
if targets:
if not type(targets) == list:
targets = [targets, ]
sm = getSecurityManager()
if all([sm.checkPermission(view, ta) for ta in targets]):
a = ["<a href='%s'>%s</a>" % (target.absolute_url(),
target.Title())
for target in targets]
ret = {'fieldName': fieldname,
'mode': 'structure',
'html': ", ".join(a)}
else:
ret = {'fieldName': fieldname,
'mode': 'structure',
'html': ", ".join([ta.Title() for ta in targets])}
else:
ret = {'fieldName': fieldname,
'mode': 'structure',
'html': ''}
elif field.getType().lower().find('datetime') > -1:
value = field.get(self.context)
ret = {
'fieldName': fieldname,
'mode': 'structure',
'html': self.ulocalized_time(value, long_format=True)
}
return ret
def get_custom_fields(self):
""" Returns a dictionary with custom fields to be rendered after
header_table with this structure:
{<fieldid>:{title:<title>, value:<html>}
"""
custom = {}
ar = self.context
workflow = getToolByName(self.context, '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
anchor = childar and ("<a href='%s'>%s</a>" % (childar.absolute_url(), childar.getRequestID())) or None
if anchor:
custom['ChildAR'] = {
'title': t(_("AR for retested results")),
'value': anchor
}
# 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()
anchor = "<a href='%s'>%s</a>" % (par.absolute_url(), par.getRequestID())
custom['ParentAR'] = {
'title': t(_("Invalid AR retested")),
'value': anchor
}
return custom
def folderitem(self, obj, item, index):
if item.get('review_state', 'current') == 'current':
# Check expiry date
exdate = obj.getExpiryDate()
if exdate:
expirydate = DT2dt(exdate).replace(tzinfo=None)
if (datetime.today() > expirydate):
# Trigger expiration
workflow.doActionFor(obj, 'expire')
item['review_state'] = 'expired'
item['obj'] = obj
if self.contentFilter.get('review_state', '') \
and item.get('review_state', '') == 'expired':
# This item must be omitted from the list
return None
item['ID'] = obj.id
item['DateSampled'] = self.ulocalized_time(obj.getDateSampled(), long_format=True)
item['DateReceived'] = self.ulocalized_time(obj.getDateReceived())
item['DateOpened'] = self.ulocalized_time(obj.getDateOpened())
item['ExpiryDate'] = self.ulocalized_time(obj.getExpiryDate())
after_icons = ''
if obj.getBlank():
after_icons += "<img\
src='%s/++resource++bika.lims.images/blank.png' \
title='%s'>" % (self.portal_url, t(_('Blank')))
if obj.getHazardous():
after_icons += "<img\
src='%s/++resource++bika.lims.images/hazardous.png' \
title='%s'>" % (self.portal_url, t(_('Hazardous')))
item['replace']['ID'] = "<a href='%s/base_view'>%s</a> %s" % \
(item['url'], item['ID'], after_icons)
return item
def extra(self):
workflow = self.tools.workflow()
state = self.context_state.workflow_state()
stateTitle = self._currentStateTitle()
if workflow.getInfoFor(self.context, 'cancellation_state', '') == 'cancelled':
title2 = t(_('Cancelled'))
# cater for bika_one_state_workflow (always Active)
if not stateTitle or \
workflow.getInfoFor(self.context, 'review_state', '') == 'active':
stateTitle = t(_('Cancelled'))
else:
stateTitle = "%s (%s)" % (stateTitle, _(title2))
return {'id': 'plone-contentmenu-workflow',
'class': 'state-cancelled',
'state': state,
'stateTitle': stateTitle, }
elif workflow.getInfoFor(self.context, 'inactive_state', '') == 'inactive':
title2 = t(_('Dormant'))
# cater for bika_one_state_workflow (always Active)
if not stateTitle or \
(workflow.getInfoFor(self.context, 'review_state', '') in
('active', 'current')):
stateTitle = t(_('Dormant'))
else:
stateTitle = "%s (%s)" % (stateTitle, _(title2))
return {'id': 'plone-contentmenu-workflow',
'class': 'state-inactive',
'state': state,
'stateTitle': stateTitle, }
else:
return {'id': 'plone-contentmenu-workflow',
'class': 'state-%s' % state,
'state': state,
'stateTitle': stateTitle, }
def make_title(o):
# the javascript uses these strings to decide if it should
# check the blank or hazardous checkboxes when a reference
# definition is selected (./js/referencesample.js)
if not o:
return ''
title = _u(o.Title())
if o.getBlank():
title += " %s" % t(_('(Blank)'))
if o.getHazardous():
title += " %s" % t(_('(Hazardous)'))
return title
def folderitems(self):
translate = self.context.translate
workflow = getToolByName(self.context, 'portal_workflow')
items = super(ReferenceSamplesView, self).folderitems()
new_items = []
for x in range(len(items)):
if not items[x].has_key('obj'): continue
obj = items[x]['obj']
if self.control_type == 'b' and not obj.getBlank(): continue
if self.control_type == 'c' and obj.getBlank(): continue
ref_services = obj.getServices()
ws_ref_services = [rs for rs in ref_services if
rs.UID() in self.service_uids]
if ws_ref_services:
if workflow.getInfoFor(obj, 'review_state') != 'current':
continue
services = [rs.Title() for rs in ws_ref_services]
items[x]['nr_services'] = len(services)
items[x]['Definition'] = (obj.getReferenceDefinition() and obj.getReferenceDefinition().Title()) or ''
services.sort(lambda x, y: cmp(x.lower(), y.lower()))
items[x]['Services'] = ", ".join(services)
items[x]['replace'] = {}
after_icons = "<a href='%s' target='_blank'><img src='++resource++bika.lims.images/referencesample.png' title='%s: %s'></a>" % \
(obj.absolute_url(), \
t(_("Reference sample")), obj.Title())
items[x]['before']['ID'] = after_icons
new_items.append(items[x])
new_items = sorted(new_items, key = itemgetter('nr_services'))
new_items.reverse()
return new_items
def __call__(self):
self.context_actions = {}
wf = getToolByName(self.context, 'portal_workflow')
mtool = getToolByName(self.context, 'portal_membership')
addPortalMessage = self.context.plone_utils.addPortalMessage
translate = self.context.translate
# client contact required
active_contacts = [c for c in self.context.objectValues('Contact') if
wf.getInfoFor(c, 'inactive_state', '') == 'active']
if isActive(self.context):
if self.context.portal_type == "Client" and not active_contacts:
msg = _("Client contact required before request may be submitted")
addPortalMessage(msg)
else:
if mtool.checkPermission(AddAnalysisRequest, self.context):
self.context_actions[t(_('Add'))] = {
'url': self.context.absolute_url() + "/portal_factory/"
"AnalysisRequest/Request new analyses/ar_add",
'icon': '++resource++bika.lims.images/add.png'}
# in client context we can use a permission check for this transition
# in multi-client listings, we must rather check against user roles.
if mtool.checkPermission(ModifyPortalContent, self.context):
review_states = []
for review_state in self.review_states:
review_state['custom_actions'].extend(
[{'id': 'copy_to_new',
'title': _('Copy to new'),
'url': 'workflow_action?action=copy_to_new'}, ])
review_states.append(review_state)
self.review_states = review_states
return super(ClientAnalysisRequestsView, self).__call__()
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 ${retracted_request_id}.',
mapping={'retracted_request_id': safe_unicode(par.getRequestID())})
self.context.plone_utils.addPortalMessage(
t(message), 'info')
template = LogView.__call__(self)
return template
def __init__(self, context, request):
BikaListingView.__init__(self, context, request)
self.show_sort_column = False
self.show_select_row = False
self.show_select_column = False
self.show_workflow_action_buttons = False
self.pagesize = 0
self.icon = self.portal_url + "/++resource++bika.lims.images/%s_big.png" % \
context.portal_type.lower()
self.title = to_utf8(self.context.Title()) + " " + t(_("Log"))
self.description = ""
self.columns = {
'Version': {'title': _('Version'), 'sortable': False},
'Date': {'title': _('Date'), 'sortable': False},
'User': {'title': _('User'), 'sortable': False},
'Action': {'title': _('Action'), 'sortable': False},
'Description': {'title': _('Description'), 'sortable': False},
}
self.review_states = [
{'id': 'default',
'title': 'All',
'contentFilter': {},
'columns': ['Version',
'Date',
'User',
'Action',
'Description']},
]
def __call__(self):
ar = self.context
workflow = getToolByName(ar, "portal_workflow")
# If is a retracted AR, show the link to child AR and show a warn msg
if workflow.getInfoFor(ar, "review_state") == "invalid":
childar = hasattr(ar, "getChildAnalysisRequest") and ar.getChildAnalysisRequest() or None
childid = childar and childar.getRequestID() or None
message = _(
"This Analysis Request has been withdrawn and is shown "
"for trace-ability purposes only. Retest: "
"${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 get_workflow_actions(self):
""" Compile a list of possible workflow transitions for items
in this Table.
"""
# cbb return empty list if we are unable to select items
if not self.bika_listing.show_select_column:
return []
workflow = getToolByName(self.context, 'portal_workflow')
# get all transitions for all items.
transitions = {}
actions = []
for obj in [i.get('obj', '') for i in self.items]:
obj = get_object(obj)
for it in workflow.getTransitionsFor(obj):
transitions[it['id']] = it
# the list is restricted to and ordered by these transitions.
if 'transitions' in self.bika_listing.review_state:
for tdict in self.bika_listing.review_state['transitions']:
if tdict['id'] in transitions:
actions.append(transitions[tdict['id']])
else:
actions = transitions.values()
new_actions = []
# remove any invalid items with a warning
for a, action in enumerate(actions):
if isinstance(action, dict) \
and 'id' in action:
new_actions.append(action)
else:
logger.warning("bad action in review_state['transitions']: %s. "
"(complete list: %s)." % (action, actions))
actions = new_actions
# and these are removed
if 'hide_transitions' in self.bika_listing.review_state:
hidden_transitions = self.bika_listing.review_state['hide_transitions']
actions = [a for a in actions if a['id'] not in hidden_transitions]
# cheat: until workflow_action is abolished, all URLs defined in
# GS workflow setup will be ignored, and the default will apply.
# (that means, WorkflowAction-bound URL is called).
for i, action in enumerate(actions):
actions[i]['url'] = ''
# if there is a self.review_state['some_state']['custom_transitions']
# attribute on the BikaListingView, add these actions to the list.
if 'custom_transitions' in self.bika_listing.review_state:
for action in self.bika_listing.review_state['custom_transitions']:
if isinstance(action, dict) and 'id' in action:
actions.append(action)
for a, action in enumerate(actions):
actions[a]['title'] = t(PMF(actions[a]['title']))
return actions
def getInstrumentLocations(self):
bsc = getToolByName(self, 'bika_setup_catalog')
items = [(c.UID, c.Title)
for c in bsc(portal_type='InstrumentLocation',
inactive_state='active')]
items.sort(lambda x, y: cmp(x[1], y[1]))
items.insert(0, ('', t(_('None'))))
return DisplayList(items)
def extra(self):
workflow = self.tools.workflow()
state = self.context_state.workflow_state()
stateTitle = self._currentStateTitle()
if workflow.getInfoFor(self.context, 'cancellation_state', '') == 'cancelled':
title2 = t(_('Cancelled'))
# cater for bika_one_state_workflow (always Active)
if not stateTitle or \
workflow.getInfoFor(self.context, 'review_state', '') == 'active':
stateTitle = t(_('Cancelled'))
else:
stateTitle = "%s (%s)" % (stateTitle, _(title2))
return {'id': 'plone-contentmenu-workflow',
'class': 'state-cancelled',
'state': state,
'stateTitle': stateTitle, }
elif workflow.getInfoFor(self.context, 'inactive_state', '') == 'inactive':
title2 = t(_('Dormant'))
# cater for bika_one_state_workflow (always Active)
if not stateTitle or \
(workflow.getInfoFor(self.context, 'review_state', '') in
('active', 'current')):
stateTitle = t(_('Dormant'))
else:
stateTitle = "%s (%s)" % (stateTitle, _(title2))
return {'id': 'plone-contentmenu-workflow',
'class': 'state-inactive',
'state': state,
'stateTitle': stateTitle, }
elif workflow.getInfoFor(self.context, 'sampleprep_review_state', 0):
prep_wf_id = self.context.getPreparationWorkflow()
prep_wf = workflow.getWorkflowById(prep_wf_id)
prep_state = workflow.getInfoFor(
self.context, 'sampleprep_review_state')
prep_title = prep_wf.states[prep_state].title
stateTitle = "%s (%s)" % (stateTitle, _(prep_title))
return {'id': 'plone-contentmenu-workflow',
'class': 'state-sampleprep',
'state': state,
'stateTitle': stateTitle, }
else:
return {'id': 'plone-contentmenu-workflow',
'class': 'state-%s' % state,
'state': state,
'stateTitle': stateTitle, }
def ajax_form_error(errors, field=None, arnum=None, message=None):
if not message:
message = t(PMF('Input is required but no input given.'))
if (arnum or field):
error_key = ' %s.%s' % (int(arnum) + 1, field or '')
else:
error_key = 'Form Error'
errors[error_key] = message
def get_workflow_actions(self):
""" Compile a list of possible workflow transitions for items
in this Table.
"""
# cbb return empty list if we are unable to select items
if not self.show_select_column:
return []
workflow = getToolByName(self.context, 'portal_workflow')
# check POST for a specified review_state selection
selected_state = self.request.get("%s_review_state"%self.form_id,
'default')
# get review_state id=selected_state
states = [r for r in self.review_states
if r['id'] == selected_state]
review_state = states and states[0] \
or self.review_states[0]
# get all transitions for all items.
transitions = {}
actions = []
for obj in [i.get('obj', '') for i in self.items]:
obj = hasattr(obj, 'getObject') and obj.getObject() or obj
for it in workflow.getTransitionsFor(obj):
transitions[it['id']] = it
# the list is restricted to and ordered by these transitions.
if 'transitions' in review_state:
for transition_dict in review_state['transitions']:
if transition_dict['id'] in transitions:
actions.append(transitions[transition_dict['id']])
else:
actions = transitions.values()
# and these are removed
if 'hide_transitions' in review_state:
actions = [a for a in actions
if a['id'] not in review_state['hide_transitions']]
# cheat: until workflow_action is abolished, all URLs defined in
# GS workflow setup will be ignored, and the default will apply.
# (that means, WorkflowAction-bound URL is called).
for i, action in enumerate(actions):
actions[i]['url'] = ''
# if there is a review_state['some_state']['custom_actions'] attribute
# on the BikaListingView, add these actions to the list.
if 'custom_actions' in review_state:
for action in review_state['custom_actions']:
actions.append(action)
for a,action in enumerate(actions):
actions[a]['title'] = \
t(PMF(actions[a]['id'] + "_transition_title"))
return actions
def getDataInterfaces(context):
""" Return the current list of data interfaces
"""
from bika.lims.exportimport import instruments
exims = [('', t(_('None')))]
for exim_id in instruments.__all__:
exim = instruments.getExim(exim_id)
exims.append((exim_id, exim.title))
return DisplayList(exims)
def msg(self, array, msg, numline=None, line=None, mapping={}):
prefix = ''
suffix = ''
msg = t(_(safe_unicode(msg), mapping=mapping))
if numline:
prefix = "[%s] " % numline
if line:
suffix = ": %s" % line
array.append(prefix + msg + suffix)
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 folderitems(self):
items = BikaListingView.folderitems(self)
outitems = []
workflow = getToolByName(self.context, 'portal_workflow')
for x in range(len(items)):
if not items[x].has_key('obj'): continue
obj = items[x]['obj']
if workflow.getInfoFor(obj, 'review_state') == 'current':
# Check expiry date
from Products.ATContentTypes.utils import DT2dt
from datetime import datetime
expirydate = DT2dt(obj.getExpiryDate()).replace(tzinfo=None)
if (datetime.today() > expirydate):
workflow.doActionFor(obj, 'expire')
items[x]['review_state'] = 'expired'
items[x]['obj'] = obj
if 'review_state' in self.contentFilter \
and self.contentFilter['review_state'] == 'current':
continue
items[x]['ID'] = obj.id
items[x]['Manufacturer'] = obj.getManufacturer() and \
obj.getManufacturer().Title() or ''
items[x]['Definition'] = obj.getReferenceDefinition() and \
obj.getReferenceDefinition().Title() or ''
items[x]['DateSampled'] = self.ulocalized_time(
obj.getDateSampled(), long_format=True)
items[x]['DateReceived'] = self.ulocalized_time(obj.getDateReceived())
items[x]['DateOpened'] = self.ulocalized_time(obj.getDateOpened())
items[x]['ExpiryDate'] = self.ulocalized_time(obj.getExpiryDate())
after_icons = ''
if obj.getBlank():
after_icons += "<img\
src='%s/++resource++bika.lims.images/blank.png' \
title='%s'>" % (self.portal_url, t(_('Blank')))
if obj.getHazardous():
after_icons += "<img\
src='%s/++resource++bika.lims.images/hazardous.png' \
title='%s'>" % (self.portal_url, t(_('Hazardous')))
items[x]['replace']['ID'] = "<a href='%s/base_view'>%s</a> %s" % \
(items[x]['url'], items[x]['ID'], after_icons)
outitems.append(items[x])
return outitems
def _getAvailableMethods(self):
""" Returns the available (active) methods.
One method can be done by multiple instruments, but one
instrument can only be used in one method.
"""
bsc = getToolByName(self, "bika_setup_catalog")
items = [(c.UID, c.Title) for c in bsc(portal_type="Method", inactive_state="active")]
items.sort(lambda x, y: cmp(x[1], y[1]))
items.insert(0, ("", t(_("None"))))
return DisplayList(items)
def getDataInterfaces(context):
""" Return the current list of data interfaces
"""
from bika.lims.exportimport import instruments
exims = []
for exim_id in instruments.__all__:
exim = instruments.getExim(exim_id)
exims.append((exim_id, exim.title))
exims.sort(lambda x, y: cmp(x[1].lower(), y[1].lower()))
exims.insert(0, ('', t(_('None'))))
return DisplayList(exims)
def __call__(self, context, request):
""" Horiba Jobin-Yvon ICPanalysis results
"""
self.request = request
self.errors = []
self.logs = []
self.warns = []
infile = self.request.form['data_file']
if not hasattr(infile, 'filename'):
self.errors.append(_("No file selected"))
return self.ret()
parser = HoribaJobinYvonICPCSVParser(infile)
# Load the most suitable parser according to file extension/options/etc...
format = self.request.form['format']
parser = None
if not hasattr(infile, 'filename'):
self.errors.append(_("No file selected"))
elif format == 'csv':
parser = HoribaJobinYvonCSVParser(infile)
else:
self.errors.append(t(_("Unrecognized file format ${format}",
mapping={"format": format})))
if parser:
ar_states = self.get_allowed_ar_states()
over = self.get_overrides()
crit = self.get_id_search_criteria()
instrument = request.form.get('instrument', None)
importer = HoribaJobinYvonICPImporter(parser=parser,
context=context,
idsearchcriteria=crit,
allowed_ar_states=ar_states,
allowed_analysis_states=None,
override=over,
instrument_uid=instrument)
exception_string = ''
try:
importer.process()
except:
exception_string = traceback.format_exc()
self.errors = importer.errors
self.logs = importer.logs
self.warns = importer.warns
if exception_string:
self.errors.append(exception_string)
return self.ret()
def _getCalculations(self):
""" Returns a DisplayList with the available Calculations
registered in Bika-Setup. Used to fill the Calculation
ReferenceWidget.
"""
bsc = getToolByName(self, 'bika_setup_catalog')
items = [(c.UID, c.Title) \
for c in bsc(portal_type='Calculation',
inactive_state = 'active')]
items.sort(lambda x,y: cmp(x[1], y[1]))
items.insert(0, ('', t(_('None'))))
return DisplayList(list(items))
def getImportDataInterfaces(context, import_only=False):
""" Return the current list of import data interfaces
"""
from bika.lims.exportimport import instruments
exims = []
for exim_id in instruments.__all__:
exim = instruments.getExim(exim_id)
if import_only and not hasattr(exim, 'Import'):
pass
else:
exims.append((exim_id, exim.title))
exims.sort(lambda x, y: cmp(x[1].lower(), y[1].lower()))
exims.insert(0, ('', t(_('None'))))
return DisplayList(exims)
def getDataInterfaces(self):
""" Return the current list of data interfaces
"""
from bika.equigerminal.exportimport import instruments
from bika.lims.exportimport import instruments as blinstruments
instrs = deepcopy(instruments.__all__)
instrs.extend(blinstruments.__all__)
exims = []
for exim_id in instrs:
exim = instruments.getExim(exim_id)
exims.append((exim_id, exim.title))
exims.sort(lambda x, y: cmp(x[1].lower(), y[1].lower()))
exims.insert(0, ('', t(_('None'))))
return DisplayList(exims)
def folderitems(self):
items = BikaListingView.folderitems(self)
valid = [c.UID() for c in self.context.getValidCertifications()]
latest = self.context.getLatestValidCertification()
latest = latest.UID() if latest else ''
for x in range (len(items)):
if not items[x].has_key('obj'): continue
obj = items[x]['obj']
# items[x]['getAgency'] = obj.getAgency()
items[x]['getDate'] = self.ulocalized_time(obj.getDate(), long_format=0)
items[x]['getValidFrom'] = self.ulocalized_time(obj.getValidFrom(), long_format=0)
items[x]['getValidTo'] = self.ulocalized_time(obj.getValidTo(), long_format=0)
items[x]['replace']['Title'] = "<a href='%s'>%s</a>" % \
(items[x]['url'], items[x]['Title'])
if obj.getInternal() == True:
items[x]['replace']['getAgency'] = ""
items[x]['state_class'] = '%s %s' % (items[x]['state_class'], 'internalcertificate')
items[x]['getDocument'] = ""
items[x]['replace']['getDocument'] = ""
try:
doc = obj.getDocument()
if doc and doc.get_size() > 0:
anchor = "<a href='%s/at_download/Document'>%s</a>" % \
(obj.absolute_url(), doc.filename)
items[x]['getDocument'] = doc.filename
items[x]['replace']['getDocument'] = anchor
except:
# POSKeyError: 'No blob file'
# Show the record, but not the link
title = _('Not available')
items[x]['getDocument'] = _('Not available')
items[x]['replace']['getDocument'] = _('Not available')
uid = obj.UID()
if uid in valid:
# Valid calibration.
items[x]['state_class'] = '%s %s' % (items[x]['state_class'], 'active')
elif uid == latest:
# Latest valid certificate
img = "<img title='%s' src='%s/++resource++bika.lims.images/exclamation.png'/> " \
% (t(_('Out of date')), self.portal_url)
items[x]['replace']['getValidTo'] = '%s %s' % (items[x]['getValidTo'], img)
items[x]['state_class'] = '%s %s' % (items[x]['state_class'], 'inactive outofdate')
else:
# Old and further calibrations
items[x]['state_class'] = '%s %s' % (items[x]['state_class'], 'inactive')
return items
def __call__(self, context):
site = getSite()
request = aq_get(site, "REQUEST", None)
items = []
wf = site.portal_workflow
for folder in self.folders:
folder = site.restrictedTraverse(folder)
for portal_type in self.portal_types:
objects = list(folder.objectValues(portal_type))
objects = [o for o in objects if wf.getInfoFor(o, "inactive_state") == "active"]
if not objects:
continue
objects.sort(lambda x, y: cmp(x.Title().lower(), y.Title().lower()))
xitems = [(t(item.Title()), item.Title()) for item in objects]
xitems = [SimpleTerm(i[1], i[1], i[0]) for i in xitems]
items += xitems
return SimpleVocabulary(items)
def emailInvoice(self, templateHTML, to=[]):
"""
Send the invoice via email.
:param templateHTML: The invoice template in HTML, ready to be send.
:param to: A list with the addresses to send the invoice.
"""
ar = self.aq_parent
# SMTP errors are silently ignored if server is in debug mode
debug_mode = App.config.getConfiguration().debug_mode
# Useful variables
lab = ar.bika_setup.laboratory
# Compose and send email.
subject = t(_('Invoice')) + ' ' + ar.getInvoice().getId()
mime_msg = MIMEMultipart('related')
mime_msg['Subject'] = subject
mime_msg['From'] = formataddr(
(encode_header(lab.getName()), lab.getEmailAddress()))
mime_msg.preamble = 'This is a multi-part MIME message.'
msg_txt_t = MIMEText(templateHTML.encode('utf-8'), _subtype='html')
mime_msg.attach(msg_txt_t)
# Build the responsible's addresses
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)))
# Build the client's address
caddress = ar.aq_parent.getEmailAddress()
cname = ar.aq_parent.getName()
if (caddress != ''):
to.append(formataddr((encode_header(cname), caddress)))
if len(to) > 0:
# Send the emails
mime_msg['To'] = ','.join(to)
try:
host = getToolByName(ar, 'MailHost')
host.send(mime_msg.as_string(), immediate=True)
except SMTPServerDisconnected as msg:
pass
if not debug_mode:
raise SMTPServerDisconnected(msg)
except SMTPRecipientsRefused as msg:
raise WorkflowException(str(msg))
def __call__(self, context):
portal = getSite()
wftool = getToolByName(portal, 'portal_workflow', None)
if wftool is None:
return SimpleVocabulary([])
# XXX This is evil. A vocabulary shouldn't be request specific.
# The sorting should go into a separate widget.
# we get REQUEST from wftool because context may be an adapter
request = aq_get(wftool, 'REQUEST', None)
wf = wftool.getWorkflowById('bika_ar_workflow')
items = wftool.listWFStatesByTitle(filter_similar=True)
items_dict = dict([(i[1], t(i[0])) for i in items])
items_list = [(k, v) for k, v in items_dict.items()]
items_list.sort(lambda x, y: cmp(x[1], y[1]))
terms = [SimpleTerm(k, title=u'%s' % v) for k, v in items_list]
return SimpleVocabulary(terms)
def _folder_item_verify_icons(self, analysis_brain, item):
"""Set the analysis' verification icons to the item passed in.
:param analysis_brain: Brain that represents an analysis
:param item: analysis' dictionary counterpart that represents a row
"""
submitter = analysis_brain.getSubmittedBy
if not submitter:
# This analysis hasn't yet been submitted, no verification yet
return
if analysis_brain.review_state == 'retracted':
# Don't display icons and additional info about verification
return
verifiers = analysis_brain.getVerificators
in_verifiers = submitter in verifiers
if in_verifiers:
# If analysis has been submitted and verified by the same person,
# display a warning icon
msg = t(_("Submitted and verified by the same user: {}"))
icon = get_image('warning.png', title=msg.format(submitter))
self._append_html_element(item, 'state_title', icon)
num_verifications = analysis_brain.getNumberOfRequiredVerifications
if num_verifications > 1:
# More than one verification required, place an icon and display
# the number of verifications done vs. total required
done = analysis_brain.getNumberOfVerifications
pending = num_verifications - done
ratio = float(done) / float(num_verifications) if done > 0 else 0
ratio = int(ratio * 100)
scale = ratio == 0 and 0 or (ratio / 25) * 25
anchor = "<a href='#' title='{} {} {}' " \
"class='multi-verification scale-{}'>{}/{}</a>"
anchor = anchor.format(t(_("Multi-verification required")),
str(pending),
t(_("verification(s) pending")), str(scale),
str(done), str(num_verifications))
self._append_html_element(item, 'state_title', anchor)
if analysis_brain.review_state != 'to_be_verified':
# The verification of analysis has already been done or first
# verification has not been done yet. Nothing to do
return
# Check if the user has "Bika: Verify" privileges
if not self.has_permission(TransitionVerify):
# User cannot verify, do nothing
return
username = api.get_current_user().id
if username not in verifiers:
# Current user has not verified this analysis
if submitter != username:
# Current user is neither a submitter nor a verifier
return
# Current user is the same who submitted the result
if analysis_brain.isSelfVerificationEnabled:
# Same user who submitted can verify
title = t(_("Can verify, but submitted by current user"))
html = get_image('warning.png', title=title)
self._append_html_element(item, 'state_title', html)
return
# User who submitted cannot verify
title = t(_("Cannot verify, submitted by current user"))
html = get_image('submitted-by-current-user.png', title=title)
self._append_html_element(item, 'state_title', html)
return
# This user verified this analysis before
multi_verif = self.context.bika_setup.getTypeOfmultiVerification()
if multi_verif != 'self_multi_not_cons':
# Multi verification by same user is not allowed
title = t(_("Cannot verify, was verified by current user"))
html = get_image('submitted-by-current-user.png', title=title)
self._append_html_element(item, 'state_title', html)
return
# Multi-verification by same user, but non-consecutively, is allowed
if analysis_brain.getLastVerificator != username:
# Current user was not the last user to verify
title = t(
_("Can verify, but was already verified by current user"))
html = get_image('warning.png', title=title)
self._append_html_element(item, 'state_title', html)
return
# Last user who verified is the same as current user
title = t(_("Cannot verify, last verified by current user"))
html = get_image('submitted-by-current-user.png', title=title)
self._append_html_element(item, 'state_title', html)
return
def translate(id):
return t(PMF(id + "_transition_title"))
def __init__(self, context, request):
super(AnalysisRequestsView, self).__init__(context, request)
request.set('disable_plone.rightcolumn', 1)
self.catalog = "bika_catalog"
self.contentFilter = {
'portal_type': 'AnalysisRequest',
'sort_on': 'created',
'sort_order': 'reverse',
'path': {
"query": "/",
"level": 0
},
'cancellation_state': 'active',
}
self.context_actions = {}
if self.context.portal_type == "AnalysisRequestsFolder":
self.request.set('disable_border', 1)
if self.view_url.find("analysisrequests") == -1:
self.view_url = self.view_url + "/analysisrequests"
self.allow_edit = True
self.show_sort_column = False
self.show_select_row = False
self.show_select_column = True
self.form_id = "analysisrequests"
self.icon = self.portal_url + "/++resource++bika.lims.images/analysisrequest_big.png"
self.title = self.context.translate(_("Analysis Requests"))
self.description = ""
SamplingWorkflowEnabled = self.context.bika_setup.getSamplingWorkflowEnabled(
)
mtool = getToolByName(self.context, 'portal_membership')
member = mtool.getAuthenticatedMember()
user_is_preserver = 'Preserver' in member.getRoles()
self.columns = {
'getRequestID': {
'title': _('Request ID'),
'index': 'getRequestID'
},
'getClientOrderNumber': {
'title': _('Client Order'),
'index': 'getClientOrderNumber',
'toggle': True
},
'Creator': {
'title': PMF('Creator'),
'index': 'Creator',
'toggle': True
},
'Created': {
'title': PMF('Date Created'),
'index': 'created',
'toggle': False
},
'getSample': {
'title': _("Sample"),
'toggle': True,
},
'BatchID': {
'title': _("Batch ID"),
'toggle': True
},
'SubGroup': {
'title': _('Sub-group')
},
'Client': {
'title': _('Client'),
'toggle': True
},
'getClientReference': {
'title': _('Client Ref'),
'index': 'getClientReference',
'toggle': True
},
'getClientSampleID': {
'title': _('Client SID'),
'index': 'getClientSampleID',
'toggle': True
},
'ClientContact': {
'title': _('Contact'),
'toggle': False
},
'getSampleTypeTitle': {
'title': _('Sample Type'),
'index': 'getSampleTypeTitle',
'toggle': True
},
'getSamplePointTitle': {
'title': _('Sample Point'),
'index': 'getSamplePointTitle',
'toggle': False
},
'getStorageLocation': {
'title': _('Storage Location'),
'toggle': False
},
'SamplingDeviation': {
'title': _('Sampling Deviation'),
'toggle': False
},
'Priority': {
'title': _('Priority'),
'toggle': True,
'index': 'Priority',
'sortable': True
},
'AdHoc': {
'title': _('Ad-Hoc'),
'toggle': False
},
'SamplingDate': {
'title': _('Sampling Date'),
'index': 'getSamplingDate',
'toggle': True
},
'getDateSampled': {
'title': _('Date Sampled'),
'index': 'getDateSampled',
'toggle': SamplingWorkflowEnabled,
'input_class': 'datepicker_nofuture',
'input_width': '10'
},
'getSampler': {
'title': _('Sampler'),
'toggle': SamplingWorkflowEnabled
},
'getDatePreserved': {
'title': _('Date Preserved'),
'toggle': user_is_preserver,
'input_class': 'datepicker_nofuture',
'input_width': '10',
'sortable': False
}, # no datesort without index
'getPreserver': {
'title': _('Preserver'),
'toggle': user_is_preserver
},
'getDateReceived': {
'title': _('Date Received'),
'index': 'getDateReceived',
'toggle': False
},
'getDatePublished': {
'title': _('Date Published'),
'index': 'getDatePublished',
'toggle': False
},
'state_title': {
'title': _('State'),
'index': 'review_state'
},
'getProfilesTitle': {
'title': _('Profile'),
'index': 'getProfilesTitle',
'toggle': False
},
'getAnalysesNum': {
'title': _('Number of Analyses'),
'index': 'getAnalysesNum',
'sortable': True,
'toggle': False
},
'getTemplateTitle': {
'title': _('Template'),
'index': 'getTemplateTitle',
'toggle': False
},
}
self.review_states = [
{
'id':
'default',
'title':
_('Active'),
'contentFilter': {
'sort_on': 'created',
'sort_order': 'reverse'
},
'transitions': [{
'id': 'sample'
}, {
'id': 'preserve'
}, {
'id': 'receive'
}, {
'id': 'retract'
}, {
'id': 'verify'
}, {
'id': 'prepublish'
}, {
'id': 'publish'
}, {
'id': 'republish'
}, {
'id': 'cancel'
}, {
'id': 'reinstate'
}],
'custom_actions': [],
'columns': [
'getRequestID', 'getSample', 'BatchID', 'SubGroup',
'Client', 'Creator', 'Created', 'getClientOrderNumber',
'getClientReference', 'ClientContact', 'getClientSampleID',
'getProfilesTitle', 'getTemplateTitle',
'getSampleTypeTitle', 'getSamplePointTitle',
'getStorageLocation', 'SamplingDeviation', 'Priority',
'AdHoc', 'SamplingDate', 'getDateSampled', 'getSampler',
'getDatePreserved', 'getPreserver', 'getDateReceived',
'getAnalysesNum', 'state_title'
]
},
{
'id':
'sample_due',
'title':
_('Due'),
'contentFilter': {
'review_state':
('to_be_sampled', 'to_be_preserved', 'sample_due'),
'sort_on':
'created',
'sort_order':
'reverse'
},
'transitions': [{
'id': 'sample'
}, {
'id': 'preserve'
}, {
'id': 'receive'
}, {
'id': 'cancel'
}, {
'id': 'reinstate'
}],
'custom_actions': [],
'columns': [
'getRequestID', 'getSample', 'BatchID', 'SubGroup',
'Client', 'getProfilesTitle', 'getTemplateTitle',
'Creator', 'Created', 'getClientOrderNumber',
'getClientReference', 'getClientSampleID', 'ClientContact',
'getDateSampled', 'getSampler', 'getDatePreserved',
'getPreserver', 'getSampleTypeTitle',
'getSamplePointTitle', 'getStorageLocation',
'SamplingDeviation', 'Priority', 'AdHoc', 'getAnalysesNum',
'state_title'
]
},
{
'id':
'sample_received',
'title':
_('Received'),
'contentFilter': {
'review_state': 'sample_received',
'sort_on': 'created',
'sort_order': 'reverse'
},
'transitions': [{
'id': 'prepublish'
}, {
'id': 'cancel'
}, {
'id': 'reinstate'
}],
'custom_actions': [],
'columns': [
'getRequestID', 'getSample', 'BatchID', 'SubGroup',
'Client', 'getProfilesTitle', 'getTemplateTitle',
'Creator', 'Created', 'getClientOrderNumber',
'getClientReference', 'getClientSampleID', 'ClientContact',
'getSampleTypeTitle', 'getSamplePointTitle',
'getStorageLocation', 'SamplingDeviation', 'Priority',
'AdHoc', 'getDateSampled', 'getSampler',
'getDatePreserved', 'getPreserver', 'getAnalysesNum',
'getDateReceived'
]
},
{
'id':
'to_be_verified',
'title':
_('To be verified'),
'contentFilter': {
'review_state': 'to_be_verified',
'sort_on': 'created',
'sort_order': 'reverse'
},
'transitions': [{
'id': 'retract'
}, {
'id': 'verify'
}, {
'id': 'prepublish'
}, {
'id': 'cancel'
}, {
'id': 'reinstate'
}],
'custom_actions': [],
'columns': [
'getRequestID', 'getSample', 'BatchID', 'SubGroup',
'Client', 'getProfilesTitle', 'getTemplateTitle',
'Creator', 'Created', 'getClientOrderNumber',
'getClientReference', 'getClientSampleID', 'ClientContact',
'getSampleTypeTitle', 'getSamplePointTitle',
'getStorageLocation', 'SamplingDeviation', 'Priority',
'AdHoc', 'getDateSampled', 'getSampler',
'getDatePreserved', 'getPreserver', 'getAnalysesNum',
'getDateReceived'
]
},
{
'id':
'verified',
'title':
_('Verified'),
'contentFilter': {
'review_state': 'verified',
'sort_on': 'created',
'sort_order': 'reverse'
},
'transitions': [{
'id': 'publish'
}],
'custom_actions': [],
'columns': [
'getRequestID', 'getSample', 'BatchID', 'SubGroup',
'Client', 'getProfilesTitle', 'getTemplateTitle',
'Creator', 'Created', 'getClientOrderNumber',
'getClientReference', 'getClientSampleID', 'ClientContact',
'getSampleTypeTitle', 'getSamplePointTitle',
'getStorageLocation', 'SamplingDeviation', 'Priority',
'AdHoc', 'getDateSampled', 'getSampler',
'getDatePreserved', 'getPreserver', 'getAnalysesNum',
'getDateReceived'
]
},
{
'id':
'published',
'title':
_('Published'),
'contentFilter': {
'review_state': ('published', 'invalid'),
'sort_on': 'created',
'sort_order': 'reverse'
},
'transitions': [{
'id': 'republish'
}],
'custom_actions': [],
'columns': [
'getRequestID', 'getSample', 'BatchID', 'SubGroup',
'Client', 'getProfilesTitle', 'getTemplateTitle',
'Creator', 'Created', 'getClientOrderNumber',
'getClientReference', 'getClientSampleID', 'ClientContact',
'getSampleTypeTitle', 'getSamplePointTitle',
'getStorageLocation', 'SamplingDeviation', 'Priority',
'AdHoc', 'getDateSampled', 'getSampler',
'getDatePreserved', 'getPreserver', 'getDateReceived',
'getAnalysesNum', 'getDatePublished'
]
},
{
'id':
'cancelled',
'title':
_('Cancelled'),
'contentFilter': {
'cancellation_state':
'cancelled',
'review_state':
('sample_registered', 'to_be_sampled', 'to_be_preserved',
'sample_due', 'sample_received', 'to_be_verified',
'attachment_due', 'verified', 'published'),
'sort_on':
'created',
'sort_order':
'reverse'
},
'transitions': [{
'id': 'reinstate'
}],
'custom_actions': [],
'columns': [
'getRequestID', 'getSample', 'BatchID', 'SubGroup',
'Client', 'getProfilesTitle', 'getTemplateTitle',
'Creator', 'Created', 'getClientOrderNumber',
'getClientReference', 'getClientSampleID', 'ClientContact',
'getSampleTypeTitle', 'getSamplePointTitle',
'getStorageLocation', 'SamplingDeviation', 'Priority',
'AdHoc', 'getDateSampled', 'getSampler',
'getDatePreserved', 'getPreserver', 'getDateReceived',
'getDatePublished', 'getAnalysesNum', 'state_title'
]
},
{
'id':
'invalid',
'title':
_('Invalid'),
'contentFilter': {
'review_state': 'invalid',
'sort_on': 'created',
'sort_order': 'reverse'
},
'transitions': [],
'custom_actions': [],
'columns': [
'getRequestID', 'getSample', 'BatchID', 'SubGroup',
'Client', 'getProfilesTitle', 'getTemplateTitle',
'Creator', 'Created', 'getClientOrderNumber',
'getClientReference', 'getClientSampleID', 'ClientContact',
'getSampleTypeTitle', 'getSamplePointTitle',
'getStorageLocation', 'SamplingDeviation', 'Priority',
'AdHoc', 'getDateSampled', 'getSampler',
'getDatePreserved', 'getPreserver', 'getDateReceived',
'getAnalysesNum', 'getDatePublished'
]
},
{
'id':
'assigned',
'title':
"<img title='%s'\
src='%s/++resource++bika.lims.images/assigned.png'/>" %
(t(_("Assigned")), self.portal_url),
'contentFilter': {
'worksheetanalysis_review_state':
'assigned',
'review_state':
('sample_received', 'to_be_verified', 'attachment_due',
'verified', 'published'),
'sort_on':
'created',
'sort_order':
'reverse'
},
'transitions': [{
'id': 'retract'
}, {
'id': 'verify'
}, {
'id': 'prepublish'
}, {
'id': 'publish'
}, {
'id': 'republish'
}, {
'id': 'cancel'
}, {
'id': 'reinstate'
}],
'custom_actions': [],
'columns': [
'getRequestID', 'getSample', 'BatchID', 'SubGroup',
'Client', 'getProfilesTitle', 'getTemplateTitle',
'Creator', 'Created', 'getClientOrderNumber',
'getClientReference', 'getClientSampleID', 'ClientContact',
'getSampleTypeTitle', 'getSamplePointTitle',
'getStorageLocation', 'SamplingDeviation', 'Priority',
'AdHoc', 'getDateSampled', 'getSampler',
'getDatePreserved', 'getPreserver', 'getDateReceived',
'getAnalysesNum', 'state_title'
]
},
{
'id':
'unassigned',
'title':
"<img title='%s'\
src='%s/++resource++bika.lims.images/unassigned.png'/>"
% (t(_("Unassigned")), self.portal_url),
'contentFilter': {
'worksheetanalysis_review_state':
'unassigned',
'review_state':
('sample_received', 'to_be_verified', 'attachment_due',
'verified', 'published'),
'sort_on':
'created',
'sort_order':
'reverse'
},
'transitions': [{
'id': 'receive'
}, {
'id': 'retract'
}, {
'id': 'verify'
}, {
'id': 'prepublish'
}, {
'id': 'publish'
}, {
'id': 'republish'
}, {
'id': 'cancel'
}, {
'id': 'reinstate'
}],
'custom_actions': [],
'columns': [
'getRequestID', 'getSample', 'BatchID', 'SubGroup',
'Client', 'getProfilesTitle', 'getTemplateTitle',
'Creator', 'Created', 'getClientOrderNumber',
'getClientReference', 'getClientSampleID', 'ClientContact',
'getSampleTypeTitle', 'getSamplePointTitle',
'getStorageLocation', 'SamplingDeviation', 'Priority',
'AdHoc', 'SamplingDate', 'getDateSampled', 'getSampler',
'getDatePreserved', 'getPreserver', 'getDateReceived',
'getAnalysesNum', 'state_title'
]
},
]
def Import(context, request):
""" Read biodrop analysis results
"""
infile = request.form['filename']
fileformat = request.form['format']
artoapply = request.form['artoapply']
override = request.form['override']
instrument = request.form.get('instrument', None)
errors = []
logs = []
warns = []
# Load the suitable parser
parser = None
if not hasattr(infile, 'filename'):
errors.append(_("No file selected"))
elif fileformat == 'csv':
analysis = request.form.get('analysis', None)
if analysis:
parser = BioDropCSVParser(infile, analysis)
else:
errors.append(t(_("No analysis selected")))
else:
errors.append(
t(
_("Unrecognized file format ${fileformat}",
mapping={"fileformat": fileformat})))
if parser:
# Load the importer
status = ['sample_received', 'attachment_due', 'to_be_verified']
if artoapply == 'received':
status = ['sample_received']
elif artoapply == 'received_tobeverified':
status = ['sample_received', 'attachment_due', 'to_be_verified']
over = [False, False]
if override == 'nooverride':
over = [False, False]
elif override == 'override':
over = [True, False]
elif override == 'overrideempty':
over = [True, True]
importer = BioDropImporter(parser=parser,
context=context,
allowed_ar_states=status,
allowed_analysis_states=None,
override=over,
instrument_uid=instrument)
tbex = ''
try:
importer.process()
except:
tbex = traceback.format_exc()
errors = importer.errors
logs = importer.logs
warns = importer.warns
if tbex:
errors.append(tbex)
results = {'errors': errors, 'log': logs, 'warns': warns}
return json.dumps(results)
def __init__(self, context, request, **kwargs):
self.catalog = "bika_analysis_catalog"
self.contentFilter = dict(kwargs)
self.contentFilter['portal_type'] = 'Analysis'
self.contentFilter['sort_on'] = 'sortable_title'
self.context_actions = {}
self.show_sort_column = False
self.show_select_row = False
self.show_select_column = False
self.show_column_toggles = False
self.pagesize = 0
self.form_id = 'analyses_form'
self.portal = getToolByName(context, 'portal_url').getPortalObject()
self.portal_url = self.portal.absolute_url()
request.set('disable_plone.rightcolumn', 1);
# each editable item needs it's own allow_edit
# which is a list of field names.
self.allow_edit = False
self.columns = {
'Service': {
'title': _('Analysis'),
'sortable': False},
'Partition': {
'title': _("Partition"),
'sortable':False},
'Method': {
'title': _('Method'),
'sortable': False,
'toggle': True},
'Instrument': {
'title': _('Instrument'),
'sortable': False,
'toggle': True},
'Analyst': {
'title': _('Analyst'),
'sortable': False,
'toggle': True},
'state_title': {
'title': _('Status'),
'sortable': False},
'Result': {
'title': _('Result'),
'input_width': '6',
'input_class': 'ajax_calculate numeric',
'sortable': False},
'Specification': {
'title': _('Specification'),
'sortable': False},
'ResultDM': {
'title': _('Dry'),
'sortable': False},
'Uncertainty': {
'title': _('+-'),
'sortable': False},
'retested': {
'title': "<img title='%s' src='%s/++resource++bika.lims.images/retested.png'/>"%\
(t(_('Retested')), self.portal_url),
'type':'boolean',
'sortable': False},
'Attachments': {
'title': _('Attachments'),
'sortable': False},
'CaptureDate': {
'title': _('Captured'),
'index': 'getResultCaptureDate',
'sortable':False},
'DueDate': {
'title': _('Due Date'),
'index': 'getDueDate',
'sortable':False},
}
self.review_states = [
{'id': 'default',
'title': _('All'),
'contentFilter': {},
'columns': ['Service',
'Partition',
'Result',
'Specification',
'Method',
'Instrument',
'Analyst',
'Uncertainty',
'CaptureDate',
'DueDate',
'state_title']
},
]
if not context.bika_setup.getShowPartitions():
self.review_states[0]['columns'].remove('Partition')
super(AnalysesView, self).__init__(context,
request,
show_categories=context.bika_setup.getCategoriseAnalysisServices(),
expand_all_categories=True)
def render_field_view(self, field):
fieldname = field.getName()
field = self.context.Schema()[fieldname]
ret = {'fieldName': fieldname, 'mode': 'view'}
try:
adapter = getAdapter(self.context,
interface=IHeaderTableFieldRenderer,
name=fieldname)
except ComponentLookupError:
adapter = None
if adapter:
ret = {
'fieldName': fieldname,
'mode': 'structure',
'html': adapter(field)
}
else:
if field.getType().find("ool") > -1:
value = field.get(self.context)
ret = {
'fieldName': fieldname,
'mode': 'structure',
'html': t(_('Yes')) if value else t(_('No'))
}
elif field.getType().find("Reference") > -1:
# Prioritize method retrieval over schema's field
targets = None
if hasattr(self.context, 'get%s' % fieldname):
fieldaccessor = getattr(self.context, 'get%s' % fieldname)
if callable(fieldaccessor):
targets = fieldaccessor()
if not targets:
targets = field.get(self.context)
if targets:
if not type(targets) == list:
targets = [
targets,
]
sm = getSecurityManager()
if all([sm.checkPermission(view, ta) for ta in targets]):
a = [
"<a href='%s'>%s</a>" %
(target.absolute_url(), target.Title())
for target in targets
]
ret = {
'fieldName': fieldname,
'mode': 'structure',
'html': ", ".join(a)
}
else:
ret = {
'fieldName': fieldname,
'mode': 'structure',
'html': ", ".join([ta.Title() for ta in targets])
}
else:
ret = {
'fieldName': fieldname,
'mode': 'structure',
'html': ''
}
elif field.getType().lower().find('datetime') > -1:
value = field.get(self.context)
ret = {
'fieldName': fieldname,
'mode': 'structure',
'html': self.ulocalized_time(value, long_format=True)
}
return ret
def __init__(self, context, request):
super(AnalysisRequestsView, self).__init__(context, request)
self.catalog = "portal_catalog"
SamplingWorkflowEnabled = self.context.bika_setup.getSamplingWorkflowEnabled(
)
self.columns = {
'securitySealIntact': {
'title': _('Security Seal Intact'),
'toggle': True
},
'samplingRoundTemplate': {
'title': _('Sampling Round Template'),
'toggle': True
},
'getId': {
'title': _('Request ID'),
'index': 'getId'
},
'getDateSampled': {
'title': _('Date Sampled'),
'index': 'getDateSampled',
'toggle': True,
'input_class': 'datetimepicker',
'input_width': '10'
},
'state_title': {
'title': _('State'),
'index': 'review_state'
},
'getProfilesTitle': {
'title': _('Profile'),
'toggle': False
},
'getTemplateTitle': {
'title': _('Template'),
'toggle': False
},
}
self.review_states = [
{
'id':
'default',
'title':
_('Active'),
'contentFilter': {
'cancellation_state': 'active',
'sort_on': 'created',
'sort_order': 'reverse'
},
'transitions': [{
'id': 'sample'
}, {
'id': 'preserve'
}, {
'id': 'receive'
}, {
'id': 'retract'
}, {
'id': 'verify'
}, {
'id': 'prepublish'
}, {
'id': 'publish'
}, {
'id': 'republish'
}, {
'id': 'cancel'
}, {
'id': 'reinstate'
}],
'custom_transitions': [],
'columns': [
'securitySealIntact', 'getId', 'samplingRoundTemplate',
'getDateSampled', 'state_title'
]
},
{
'id':
'sample_due',
'title':
_('Due'),
'contentFilter': {
'review_state':
('to_be_sampled', 'to_be_preserved', 'sample_due'),
'sort_on':
'created',
'sort_order':
'reverse'
},
'transitions': [{
'id': 'sample'
}, {
'id': 'preserve'
}, {
'id': 'receive'
}, {
'id': 'cancel'
}, {
'id': 'reinstate'
}],
'custom_transitions': [],
'columns': [
'securitySealIntact', 'getId', 'samplingRoundTemplate',
'getDateSampled', 'state_title'
]
},
{
'id':
'sample_received',
'title':
_('Received'),
'contentFilter': {
'review_state': 'sample_received',
'sort_on': 'created',
'sort_order': 'reverse'
},
'transitions': [{
'id': 'prepublish'
}, {
'id': 'cancel'
}, {
'id': 'reinstate'
}],
'custom_transitions': [],
'columns': [
'securitySealIntact', 'getId', 'samplingRoundTemplate',
'getDateSampled', 'state_title'
]
},
{
'id':
'to_be_verified',
'title':
_('To be verified'),
'contentFilter': {
'review_state': 'to_be_verified',
'sort_on': 'created',
'sort_order': 'reverse'
},
'transitions': [{
'id': 'retract'
}, {
'id': 'verify'
}, {
'id': 'prepublish'
}, {
'id': 'cancel'
}, {
'id': 'reinstate'
}],
'custom_transitions': [],
'columns': [
'securitySealIntact', 'getId', 'samplingRoundTemplate',
'getDateSampled', 'state_title'
]
},
{
'id':
'verified',
'title':
_('Verified'),
'contentFilter': {
'review_state': 'verified',
'sort_on': 'created',
'sort_order': 'reverse'
},
'transitions': [{
'id': 'publish'
}],
'custom_transitions': [],
'columns': [
'securitySealIntact', 'getId', 'samplingRoundTemplate',
'getDateSampled', 'state_title'
]
},
{
'id':
'published',
'title':
_('Published'),
'contentFilter': {
'review_state': ('published', 'invalid'),
'sort_on': 'created',
'sort_order': 'reverse'
},
'transitions': [{
'id': 'republish'
}],
'custom_transitions': [],
'columns': [
'securitySealIntact', 'getId', 'samplingRoundTemplate',
'getDateSampled', 'state_title'
]
},
{
'id':
'cancelled',
'title':
_('Cancelled'),
'contentFilter': {
'cancellation_state':
'cancelled',
'review_state':
('to_be_sampled', 'to_be_preserved', 'sample_due',
'sample_received', 'to_be_verified', 'attachment_due',
'verified', 'published'),
'sort_on':
'created',
'sort_order':
'reverse'
},
'transitions': [{
'id': 'reinstate'
}],
'custom_transitions': [],
'columns': [
'securitySealIntact', 'getId', 'samplingRoundTemplate',
'getDateSampled', 'state_title'
]
},
{
'id':
'invalid',
'title':
_('Invalid'),
'contentFilter': {
'review_state': 'invalid',
'sort_on': 'created',
'sort_order': 'reverse'
},
'transitions': [],
'custom_transitions': [],
'columns': [
'securitySealIntact', 'getId', 'samplingRoundTemplate',
'getDateSampled', 'state_title'
]
},
{
'id':
'assigned',
'title':
"<img title='%s'\
src='%s/++resource++bika.lims.images/assigned.png'/>" %
(t(_("Assigned")), self.portal_url),
'contentFilter': {
'assigned_state':
'assigned',
'review_state':
('sample_received', 'to_be_verified', 'attachment_due',
'verified', 'published'),
'sort_on':
'created',
'sort_order':
'reverse'
},
'transitions': [{
'id': 'retract'
}, {
'id': 'verify'
}, {
'id': 'prepublish'
}, {
'id': 'publish'
}, {
'id': 'republish'
}, {
'id': 'cancel'
}, {
'id': 'reinstate'
}],
'custom_transitions': [],
'columns': [
'securitySealIntact', 'getId', 'samplingRoundTemplate',
'getDateSampled', 'state_title'
]
},
{
'id':
'unassigned',
'title':
"<img title='%s'\
src='%s/++resource++bika.lims.images/unassigned.png'/>"
% (t(_("Unassigned")), self.portal_url),
'contentFilter': {
'assigned_state':
'unassigned',
'review_state':
('sample_received', 'to_be_verified', 'attachment_due',
'verified', 'published'),
'sort_on':
'created',
'sort_order':
'reverse'
},
'transitions': [{
'id': 'receive'
}, {
'id': 'retract'
}, {
'id': 'verify'
}, {
'id': 'prepublish'
}, {
'id': 'publish'
}, {
'id': 'republish'
}, {
'id': 'cancel'
}, {
'id': 'reinstate'
}],
'custom_transitions': [],
'columns': [
'securitySealIntact', 'getId', 'samplingRoundTemplate',
'getDateSampled', 'state_title'
]
},
]
def __call__(self):
form = self.request.form
plone.protect.CheckAuthenticator(self.request.form)
plone.protect.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 = crar(
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 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 Import(context, request):
""" Import Form
"""
infile = request.form['nuclisens_easyq_file']
fileformat = request.form['nuclisens_easyq_format']
artoapply = request.form['nuclisens_easyq_artoapply']
override = request.form['nuclisens_easyq_override']
instrument = request.form.get('instrument', None)
errors = []
logs = []
warns = []
# Load the most suitable parser according to file extension/options/etc...
parser = None
if not hasattr(infile, 'filename'):
errors.append(_("No file selected"))
if fileformat == 'xlsx':
parser = EasyQParser(infile)
elif fileformat == 'xml':
parser = EasyQXMLParser(infile)
else:
errors.append(
t(
_("Unrecognized file format ${fileformat}",
mapping={"fileformat": fileformat})))
if parser:
# Load the importer
status = ['sample_received', 'attachment_due', 'to_be_verified']
if artoapply == 'received':
status = ['sample_received']
elif artoapply == 'received_tobeverified':
status = ['sample_received', 'attachment_due', 'to_be_verified']
over = [False, False]
if override == 'nooverride':
over = [False, False]
elif override == 'override':
over = [True, False]
elif override == 'overrideempty':
over = [True, True]
importer = EasyQImporter(parser=parser,
context=context,
allowed_ar_states=status,
allowed_analysis_states=None,
override=over,
instrument_uid=instrument)
tbex = ''
try:
importer.process()
except:
tbex = traceback.format_exc()
errors = importer.errors
logs = importer.logs
warns = importer.warns
if tbex:
errors.append(tbex)
results = {'errors': errors, 'log': logs, 'warns': warns}
return json.dumps(results)
def __call__(self):
MinimumResults = self.context.bika_setup.getMinimumResults()
warning_icon = "<img " + \
"src='" + self.portal_url + "/++resource++bika.lims.images/warning.png' " + \
"height='9' width='9'/>"
error_icon = "<img " + \
"src='" + self.portal_url + "/++resource++bika.lims.images/exclamation.png' " + \
"height='9' width='9'/>"
header = _("Results per sample point")
subheader = _(
"Analysis results for per sample point and analysis service")
self.contentFilter = {
'portal_type': 'Analysis',
'review_state': ['verified', 'published']
}
parms = []
titles = []
val = self.selection_macros.parse_client(self.request)
if val:
self.contentFilter[val['contentFilter']
[0]] = val['contentFilter'][1]
parms.append(val['parms'])
titles.append(val['titles'])
val = self.selection_macros.parse_samplepoint(self.request)
sp_uid = val
if val:
self.contentFilter[val['contentFilter']
[0]] = val['contentFilter'][1]
parms.append(val['parms'])
titles.append(val['titles'])
val = self.selection_macros.parse_sampletype(self.request)
st_uid = val
if val:
self.contentFilter[val['contentFilter']
[0]] = val['contentFilter'][1]
parms.append(val['parms'])
titles.append(val['titles'])
val = self.selection_macros.parse_analysisservice(self.request)
if val:
self.contentFilter[val['contentFilter']
[0]] = val['contentFilter'][1]
parms.append(val['parms'])
else:
message = _("No analysis services were selected.")
self.context.plone_utils.addPortalMessage(message, 'error')
return self.default_template()
val = self.selection_macros.parse_daterange(self.request,
'getDateSampled',
'DateSampled')
if val:
self.contentFilter[val['contentFilter']
[0]] = val['contentFilter'][1]
parms.append(val['parms'])
titles.append(val['titles'])
val = self.selection_macros.parse_state(
self.request, 'bika_worksheetanalysis_workflow',
'worksheetanalysis_review_state', 'Worksheet state')
if val:
self.contentFilter[val['contentFilter']
[0]] = val['contentFilter'][1]
parms.append(val['parms'])
# Query the catalog and store analysis data in a dict
analyses = {}
out_of_range_count = 0
in_shoulder_range_count = 0
analysis_count = 0
proxies = self.bika_analysis_catalog(self.contentFilter)
if not proxies:
message = _("No analyses matched your query")
self.context.plone_utils.addPortalMessage(message, 'error')
return self.default_template()
# # Compile a list of dictionaries, with all relevant analysis data
for analysis in proxies:
analysis = analysis.getObject()
result = analysis.getResult()
client = analysis.aq_parent.aq_parent
uid = analysis.UID()
service = analysis.getService()
keyword = service.getKeyword()
service_title = "%s (%s)" % (service.Title(), keyword)
result_in_range = self.ResultOutOfRange(analysis)
if service_title not in analyses.keys():
analyses[service_title] = []
try:
result = float(analysis.getResult())
except:
# XXX Unfloatable analysis results should be indicated
continue
analyses[service_title].append({
'service':
service,
'obj':
analysis,
'Request ID':
analysis.aq_parent.getId(),
'Analyst':
analysis.getAnalyst(),
'Result':
result,
'Sampled':
analysis.getDateSampled(),
'Captured':
analysis.getResultCaptureDate(),
'Uncertainty':
analysis.getUncertainty(),
'result_in_range':
result_in_range,
'Unit':
service.getUnit(),
'Keyword':
keyword,
'icons':
'',
})
analysis_count += 1
keys = analyses.keys()
keys.sort()
parms += [
{
"title": _("Total analyses"),
"value": analysis_count
},
]
## This variable is output to the TAL
self.report_data = {
'header': header,
'subheader': subheader,
'parms': parms,
'tables': [],
'footnotes': [],
}
plotscript = """
set terminal png transparent truecolor enhanced size 700,350 font "Verdana, 8"
set title "%(title)s"
set xlabel "%(xlabel)s"
set ylabel "%(ylabel)s"
set key off
#set logscale
set timefmt "%(date_format_long)s"
set xdata time
set format x "%(date_format_short)s\\n%(time_format)s"
set xrange ["%(x_start)s":"%(x_end)s"]
set auto fix
set offsets graph 0, 0, 1, 1
set xtics border nomirror rotate by 90 font "Verdana, 5" offset 0,-3
set ytics nomirror
f(x) = mean_y
fit f(x) 'gpw_DATAFILE_gpw' u 1:3 via mean_y
stddev_y = sqrt(FIT_WSSR / (FIT_NDF + 1))
plot mean_y-stddev_y with filledcurves y1=mean_y lt 1 lc rgb "#efefef",\
mean_y+stddev_y with filledcurves y1=mean_y lt 1 lc rgb "#efefef",\
mean_y with lines lc rgb '#ffffff' lw 3,\
"gpw_DATAFILE_gpw" using 1:3 title 'data' with points pt 7 ps 1 lc rgb '#0000ee' lw 2,\
'' using 1:3 smooth unique lc rgb '#aaaaaa' lw 2,\
'' using 1:4 with lines lc rgb '#000000' lw 1,\
'' using 1:5 with lines lc rgb '#000000' lw 1"""
## Compile plots and format data for display
for service_title in keys:
# used to calculate XY axis ranges
result_values = [int(o['Result']) for o in analyses[service_title]]
result_dates = [o['Sampled'] for o in analyses[service_title]]
parms = []
plotdata = str()
range_min = ''
range_max = ''
for a in analyses[service_title]:
a['Sampled'] = a['Sampled'].strftime(
self.date_format_long) if a['Sampled'] else ''
a['Captured'] = a['Captured'].strftime(self.date_format_long) if \
a['Captured'] else ''
R = a['Result']
U = a['Uncertainty']
a['Result'] = a['obj'].getFormattedResult()
in_range = a['result_in_range']
# result out of range
if str(in_range[0]) == 'False':
out_of_range_count += 1
a['Result'] = "%s %s" % (a['Result'], error_icon)
# result almost out of range
if str(in_range[0]) == '1':
in_shoulder_range_count += 1
a['Result'] = "%s %s" % (a['Result'], warning_icon)
spec = {}
if hasattr(a["obj"],
'specification') and a["obj"].specification:
spec = a["obj"].specification
plotdata += "%s\t%s\t%s\t%s\t%s\n" % (
a['Sampled'],
R,
spec.get("min", ""),
spec.get("max", ""),
U and U or 0,
)
plotdata.encode('utf-8')
unit = analyses[service_title][0]['Unit']
if MinimumResults <= len(dict([(d, d) for d in result_dates])):
_plotscript = str(plotscript) % {
'title':
"",
'xlabel':
t(_("Date Sampled")),
'ylabel':
unit and unit or '',
'x_start':
"%s" % min(result_dates).strftime(self.date_format_long),
'x_end':
"%s" % max(result_dates).strftime(self.date_format_long),
'date_format_long':
self.date_format_long,
'date_format_short':
self.date_format_short,
'time_format':
self.time_format,
}
plot_png = plot(str(plotdata),
plotscript=str(_plotscript),
usefifo=False)
# Temporary PNG data file
fh, data_fn = tempfile.mkstemp(suffix='.png')
os.write(fh, plot_png)
plot_url = data_fn
self.request['to_remove'].append(data_fn)
plot_url = data_fn
else:
plot_url = ""
table = {
'title':
"%s: %s" % (t(_("Analysis Service")), service_title),
'parms':
parms,
'columns':
['Request ID', 'Analyst', 'Result', 'Sampled', 'Captured'],
'data':
analyses[service_title],
'plot_url':
plot_url,
}
self.report_data['tables'].append(table)
translate = self.context.translate
## footnotes
if out_of_range_count:
msgid = _("Analyses out of range")
self.report_data['footnotes'].append("%s %s" %
(error_icon, t(msgid)))
if in_shoulder_range_count:
msgid = _("Analyses in error shoulder range")
self.report_data['footnotes'].append("%s %s" %
(warning_icon, t(msgid)))
self.report_data['parms'].append({
"title": _("Analyses out of range"),
"value": out_of_range_count
})
self.report_data['parms'].append({
"title":
_("Analyses in error shoulder range"),
"value":
in_shoulder_range_count
})
title = t(header)
if titles:
title += " (%s)" % " ".join(titles)
return {
'report_title': title,
'report_data': self.template(),
}
def __call__(self):
# get all the data into datalines
sc = getToolByName(self.context, 'bika_setup_catalog')
bac = getToolByName(self.context, 'bika_analysis_catalog')
rc = getToolByName(self.context, 'reference_catalog')
self.report_content = {}
parm_lines = {}
parms = []
headings = {}
headings['header'] = _("Analyses per sample type")
headings['subheader'] = _("Number of analyses requested per sample type")
count_all = 0
query = {'portal_type': 'Analysis'}
client_title = None
if 'ClientUID' in self.request.form:
client_uid = self.request.form['ClientUID']
query['getClientUID'] = client_uid
client = rc.lookupObject(client_uid)
client_title = client.Title()
else:
client = logged_in_client(self.context)
if client:
client_title = client.Title()
query['getClientUID'] = client.UID()
if client_title:
parms.append(
{'title': _('Client'),
'value': client_title,
'type': 'text'})
date_query = formatDateQuery(self.context, 'Requested')
if date_query:
query['created'] = date_query
requested = formatDateParms(self.context, 'Requested')
parms.append(
{'title': _('Requested'),
'value': requested,
'type': 'text'})
workflow = getToolByName(self.context, 'portal_workflow')
if 'bika_analysis_workflow' in self.request.form:
query['review_state'] = self.request.form['bika_analysis_workflow']
review_state = workflow.getTitleForStateOnType(
self.request.form['bika_analysis_workflow'], 'Analysis')
parms.append(
{'title': _('Status'),
'value': review_state,
'type': 'text'})
if 'bika_cancellation_workflow' in self.request.form:
query['cancellation_state'] = self.request.form[
'bika_cancellation_workflow']
cancellation_state = workflow.getTitleForStateOnType(
self.request.form['bika_cancellation_workflow'], 'Analysis')
parms.append(
{'title': _('Active'),
'value': cancellation_state,
'type': 'text'})
# and now lets do the actual report lines
formats = {'columns': 2,
'col_heads': [_('Sample type'), _('Number of analyses')],
'class': '',
}
datalines = []
for sampletype in sc(portal_type="SampleType",
sort_on='sortable_title'):
query['getSampleTypeUID'] = sampletype.UID
analyses = bac(query)
count_analyses = len(analyses)
dataline = []
dataitem = {'value': sampletype.Title}
dataline.append(dataitem)
dataitem = {'value': count_analyses}
dataline.append(dataitem)
datalines.append(dataline)
count_all += count_analyses
# footer data
footlines = []
footline = []
footitem = {'value': _('Total'),
'class': 'total_label'}
footline.append(footitem)
footitem = {'value': count_all}
footline.append(footitem)
footlines.append(footline)
self.report_content = {
'headings': headings,
'parms': parms,
'formats': formats,
'datalines': datalines,
'footings': footlines}
if self.request.get('output_format', '') == 'CSV':
import csv
import StringIO
import datetime
fieldnames = [
'Sample Type',
'Analyses',
]
output = StringIO.StringIO()
dw = csv.DictWriter(output, extrasaction='ignore',
fieldnames=fieldnames)
dw.writerow(dict((fn, fn) for fn in fieldnames))
for row in datalines:
dw.writerow({
'Sample Type': row[0]['value'],
'Analyses': row[1]['value'],
})
report_data = output.getvalue()
output.close()
date = datetime.datetime.now().strftime("%Y%m%d%H%M")
setheader = self.request.RESPONSE.setHeader
setheader('Content-Type', 'text/csv')
setheader("Content-Disposition",
"attachment;filename=\"analysespersampletype_%s.csv\"" % date)
self.request.RESPONSE.write(report_data)
else:
return {'report_title': t(headings['header']),
'report_data': self.template()}
def __call__(self):
# get all the data into datalines
pc = getToolByName(self.context, 'portal_catalog')
rc = getToolByName(self.context, 'reference_catalog')
self.report_content = {}
parms = []
headings = {}
headings['header'] = _("Attachments")
headings['subheader'] = _(
"The attachments linked to analysis requests and analyses")
count_all = 0
query = {'portal_type': 'Attachment'}
if 'ClientUID' in self.request.form:
client_uid = self.request.form['ClientUID']
query['getClientUID'] = client_uid
client = rc.lookupObject(client_uid)
client_title = client.Title()
else:
client = logged_in_client(self.context)
if client:
client_title = client.Title()
query['getClientUID'] = client.UID()
else:
client_title = 'All'
parms.append({
'title': _('Client'),
'value': client_title,
'type': 'text'
})
date_query = formatDateQuery(self.context, 'Loaded')
if date_query:
query['getDateLoaded'] = date_query
loaded = formatDateParms(self.context, 'Loaded')
parms.append({
'title': _('Loaded'),
'value': loaded,
'type': 'text'
})
# and now lets do the actual report lines
formats = {
'columns':
6,
'col_heads': [
_('Request'),
_('File'),
_('Attachment type'),
_('Content type'),
_('Size'),
_('Loaded'),
],
'class':
'',
}
datalines = []
attachments = pc(query)
for a_proxy in attachments:
attachment = a_proxy.getObject()
attachment_file = attachment.getAttachmentFile()
icon = attachment_file.icon
filename = attachment_file.filename
filesize = attachment_file.get_size()
filesize = filesize / 1024
sizeunit = "Kb"
if filesize > 1024:
filesize = filesize / 1024
sizeunit = "Mb"
dateloaded = attachment.getDateLoaded()
dataline = []
dataitem = {'value': attachment.getTextTitle()}
dataline.append(dataitem)
dataitem = {'value': filename, 'img_before': icon}
dataline.append(dataitem)
dataitem = {
'value':
attachment.getAttachmentType().Title()
if attachment.getAttachmentType() else ''
}
dataline.append(dataitem)
dataitem = {
'value':
self.context.lookupMime(attachment_file.getContentType())
}
dataline.append(dataitem)
dataitem = {'value': '%s%s' % (filesize, sizeunit)}
dataline.append(dataitem)
dataitem = {'value': self.ulocalized_time(dateloaded)}
dataline.append(dataitem)
datalines.append(dataline)
count_all += 1
# footer data
footlines = []
footline = []
footitem = {'value': _('Total'), 'colspan': 5, 'class': 'total_label'}
footline.append(footitem)
footitem = {'value': count_all}
footline.append(footitem)
footlines.append(footline)
self.report_content = {
'headings': headings,
'parms': parms,
'formats': formats,
'datalines': datalines,
'footings': footlines
}
if self.request.get('output_format', '') == 'CSV':
import csv
import StringIO
import datetime
fieldnames = [
_('Request'),
_('File'),
_('Attachment type'),
_('Content type'),
_('Size'),
_('Loaded'),
]
output = StringIO.StringIO()
dw = csv.DictWriter(output, fieldnames=fieldnames)
dw.writerow(dict((fn, fn) for fn in fieldnames))
for row in datalines:
dw.writerow(row)
report_data = output.getvalue()
output.close()
date = datetime.datetime.now().strftime("%Y%m%d%H%M")
setheader = self.request.RESPONSE.setHeader
setheader('Content-Type', 'text/csv')
setheader(
"Content-Disposition",
"attachment;filename=\"analysesattachments_%s.csv\"" % date)
self.request.RESPONSE.write(report_data)
else:
return {
'report_title': t(headings['header']),
'report_data': self.template()
}
def folderitem(self, obj, item, index):
"""Service triggered each time an item is iterated in folderitems.
The use of this service prevents the extra-loops in child objects.
:obj: the instance of the class to be foldered
:item: dict containing the properties of the object to be used by
the template
:index: current index of the item
"""
# ensure we have an object and not a brain
obj = api.get_object(obj)
uid = api.get_uid(obj)
url = api.get_url(obj)
title = api.get_title(obj)
# get the category
category = obj.getCategoryTitle()
item["category"] = category
if category not in self.categories:
self.categories.append(category)
config = self.configuration.get(uid, {})
partition = config.get("partition", "part-1")
hidden = config.get("hidden", False)
item["replace"]["Title"] = get_link(url, value=title)
item["Price"] = self.format_price(obj.Price)
item["allow_edit"] = self.get_editable_columns()
item["required"].append("Partition")
item["choices"]["Partition"] = self.partition_choices
item["Partition"] = partition
item["Hidden"] = hidden
item["selected"] = uid in self.configuration
# Add methods
methods = obj.getMethods()
if methods:
links = map(
lambda m: get_link(
m.absolute_url(), value=m.Title(), css_class="link"),
methods)
item["replace"]["Methods"] = ", ".join(links)
else:
item["methods"] = ""
# Icons
after_icons = ""
if obj.getAccredited():
after_icons += get_image(
"accredited.png", title=t(_("Accredited")))
if obj.getAttachmentOption() == "r":
after_icons += get_image(
"attach_reqd.png", title=t(_("Attachment required")))
if obj.getAttachmentOption() == "n":
after_icons += get_image(
"attach_no.png", title=t(_('Attachment not permitted')))
if after_icons:
item["after"]["Title"] = after_icons
return item
def workflow_action_submit(self):
form = self.request.form
rc = getToolByName(self.context, REFERENCE_CATALOG)
action, came_from = WorkflowAction._get_form_workflow_action(self)
checkPermission = self.context.portal_membership.checkPermission
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
# calcs.js has kept item_data and form input interim values synced,
# so the json strings from item_data will be the same as the form values
item_data = {}
if 'item_data' in form:
if isinstance(form['item_data'], list):
for i_d in form['item_data']:
for i, d in json.loads(i_d).items():
item_data[i] = d
else:
item_data = json.loads(form['item_data'])
selected_analyses = WorkflowAction._get_selected_items(self)
results = {}
hasInterims = {}
# check that the form values match the database
# save them if not.
for uid, result in self.request.form.get('Result', [{}])[0].items():
# Do not save data for analyses that are not selected.
if uid not in selected_analyses:
continue
analysis = selected_analyses[uid]
# never save any part of rows with empty result values.
# https://jira.bikalabs.com/browse/LIMS-1944:
if not result:
continue
# ignore result if analysis object no longer exists
if not analysis:
continue
# Prevent saving data if the analysis is already transitioned
if not (checkPermission(EditResults, analysis)
or checkPermission(EditFieldResults, analysis)):
title = safe_unicode(analysis.getService().Title())
msgid = _(
'Result for ${analysis} could not be saved because '
'it was already submitted by another user.',
mapping={'analysis': title})
message = safe_unicode(t(msgid))
self.context.plone_utils.addPortalMessage(message)
continue
# if the AR has ReportDryMatter set, get dry_result from form.
dry_result = ''
if hasattr(self.context, 'getReportDryMatter') \
and self.context.getReportDryMatter():
for k, v in self.request.form['ResultDM'][0].items():
if uid == k:
dry_result = v
break
results[uid] = result
interimFields = item_data[uid]
if len(interimFields) > 0:
hasInterims[uid] = True
else:
hasInterims[uid] = False
retested = 'retested' in form and uid in form['retested']
remarks = form.get('Remarks', [
{},
])[0].get(uid, '')
# Don't save uneccessary things
# https://github.com/bikalabs/Bika-LIMS/issues/766:
# Somehow, using analysis.edit() fails silently when
# logged in as Analyst.
if analysis.getInterimFields() != interimFields or \
analysis.getRetested() != retested or \
analysis.getRemarks() != remarks:
analysis.setInterimFields(interimFields)
analysis.setRetested(retested)
analysis.setRemarks(remarks)
# save results separately, otherwise capture date is rewritten
if analysis.getResult() != result or \
analysis.getResultDM() != dry_result:
analysis.setResultDM(dry_result)
analysis.setResult(result)
methods = self.request.form.get('Method', [{}])[0]
instruments = self.request.form.get('Instrument', [{}])[0]
analysts = self.request.form.get('Analyst', [{}])[0]
uncertainties = self.request.form.get('Uncertainty', [{}])[0]
dlimits = self.request.form.get('DetectionLimit', [{}])[0]
# discover which items may be submitted
submissable = []
for uid, analysis in selected_analyses.items():
analysis_active = isActive(analysis)
# Need to save the instrument?
if uid in instruments and analysis_active:
# TODO: Add SetAnalysisInstrument permission
# allow_setinstrument = sm.checkPermission(SetAnalysisInstrument)
allow_setinstrument = True
# ---8<-----
if allow_setinstrument == True:
# The current analysis allows the instrument regards
# to its analysis service and method?
if (instruments[uid] == ''):
previnstr = analysis.getInstrument()
if previnstr:
previnstr.removeAnalysis(analysis)
analysis.setInstrument(None)
elif analysis.isInstrumentAllowed(instruments[uid]):
previnstr = analysis.getInstrument()
if previnstr:
previnstr.removeAnalysis(analysis)
analysis.setInstrument(instruments[uid])
instrument = analysis.getInstrument()
instrument.addAnalysis(analysis)
# Need to save the method?
if uid in methods and analysis_active:
# TODO: Add SetAnalysisMethod permission
# allow_setmethod = sm.checkPermission(SetAnalysisMethod)
allow_setmethod = True
# ---8<-----
if allow_setmethod == True and analysis.isMethodAllowed(
methods[uid]):
analysis.setMethod(methods[uid])
# Need to save the analyst?
if uid in analysts and analysis_active:
analysis.setAnalyst(analysts[uid])
# Need to save the uncertainty?
if uid in uncertainties and analysis_active:
analysis.setUncertainty(uncertainties[uid])
# Need to save the detection limit?
if analysis_active:
analysis.setDetectionLimitOperand(dlimits.get(uid, None))
if uid not in results or not results[uid]:
continue
can_submit = True
# guard_submit does a lot of the same stuff, too.
# the code there has also been commented.
# we must find a better way to allow dependencies to control
# this process.
# for dependency in analysis.getDependencies():
# dep_state = workflow.getInfoFor(dependency, 'review_state')
# if hasInterims[uid]:
# if dep_state in ('to_be_sampled', 'to_be_preserved',
# 'sample_due', 'sample_received',
# 'attachment_due', 'to_be_verified',):
# can_submit = False
# break
# else:
# if dep_state in ('to_be_sampled', 'to_be_preserved',
# 'sample_due', 'sample_received',):
# can_submit = False
# break
if can_submit and analysis not in submissable:
submissable.append(analysis)
# and then submit them.
for analysis in submissable:
doActionFor(analysis, 'submit')
# LIMS-2366: Finally, when we are done processing all applicable
# analyses, we must attempt to initiate the submit transition on the
# AR itself. This is for the case where "general retraction" has been
# done, or where the last "received" analysis has been removed, and
# the AR is in state "received" while there are no "received" analyses
# left to trigger the parent transition.
if self.context.portal_type == 'Sample':
ar = self.context.getAnalysisRequests()[0]
elif self.context.portal_type == 'Analysis':
ar = self.context.aq_parent
else:
ar = self.context
doActionFor(ar, 'submit')
message = PMF("Changes saved.")
self.context.plone_utils.addPortalMessage(message, 'info')
if checkPermission(EditResults, self.context):
self.destination_url = self.context.absolute_url(
) + "/manage_results"
else:
self.destination_url = self.context.absolute_url()
self.request.response.redirect(self.destination_url)
def _folderitems(self, full_objects=False):
"""WARNING: :full_objects: could create a big performance hit.
"""
# Setting up some attributes
plone_layout = getMultiAdapter((self.context.aq_inner, self.request),
name=u'plone_layout')
plone_utils = getToolByName(self.context.aq_inner, 'plone_utils')
portal_types = getToolByName(self.context.aq_inner, 'portal_types')
if self.request.form.get('show_all', '').lower() == 'true' \
or self.show_all is True \
or self.pagesize == 0:
show_all = True
else:
show_all = False
# idx increases one unit each time an object is added to the 'items'
# dictionary to be returned. Note that if the item is not rendered,
# the idx will not increase.
idx = 0
results = []
self.show_more = False
brains = self._fetch_brains(self.limit_from)
for obj in brains:
# avoid creating unnecessary info for items outside the current
# batch; only the path is needed for the "select all" case...
# we only take allowed items into account
if not show_all and idx >= self.pagesize:
# Maximum number of items to be shown reached!
self.show_more = True
break
# we don't know yet if it's a brain or an object
path = hasattr(obj, 'getPath') and obj.getPath() or \
"/".join(obj.getPhysicalPath())
# This item must be rendered, we need the object instead of a brain
obj = obj.getObject() if hasattr(obj, 'getObject') else obj
# check if the item must be rendered or not (prevents from
# doing it later in folderitems) and dealing with paging
if not obj or not self.isItemAllowed(obj):
continue
uid = obj.UID()
title = obj.Title()
description = obj.Description()
icon = plone_layout.getIcon(obj)
url = obj.absolute_url()
relative_url = obj.absolute_url(relative=True)
fti = portal_types.get(obj.portal_type)
if fti is not None:
type_title_msgid = fti.Title()
else:
type_title_msgid = obj.portal_type
url_href_title = '%s at %s: %s' % (
t(type_title_msgid),
path,
to_utf8(description))
modified = self.ulocalized_time(obj.modified()),
# element css classes
type_class = 'contenttype-' + \
plone_utils.normalizeString(obj.portal_type)
state_class = ''
states = {}
for w in self.workflow.getWorkflowsFor(obj):
state = w._getWorkflowStateOf(obj).id
states[w.state_var] = state
state_class += "state-%s " % state
results_dict = dict(
obj=obj,
id=obj.getId(),
title=title,
uid=uid,
path=path,
url=url,
fti=fti,
item_data=json.dumps([]),
url_href_title=url_href_title,
obj_type=obj.Type,
size=obj.getObjSize,
modified=modified,
icon=icon.html_tag(),
type_class=type_class,
# a list of lookups for single-value-select fields
choices={},
state_class=state_class,
relative_url=relative_url,
view_url=url,
table_row_class="",
category='None',
# a list of names of fields that may be edited on this item
allow_edit=[],
# a list of names of fields that are compulsory (if editable)
required=[],
# a dict where the column name works as a key and the value is
# the name of the field related with the column. It is used
# when the name given to the column and the content field it
# represents diverges. bika_listing_table_items.pt defines an
# attribute for each item, this attribute is named 'field' and
# the system fills it taking advantage of this dictionary or
# the name of the column if it isn't defined in the dict.
field={},
# "before", "after" and replace: dictionary (key is column ID)
# A snippet of HTML which will be rendered
# before/after/instead of the table cell content.
before={}, # { before : "<a href=..>" }
after={},
replace={},
)
rs = None
wf_state_var = None
workflows = self.workflow.getWorkflowsFor(obj)
for wf in workflows:
if wf.state_var:
wf_state_var = wf.state_var
break
if wf_state_var is not None:
rs = self.workflow.getInfoFor(obj, wf_state_var)
st_title = self.workflow.getTitleForStateOnType(
rs, obj.portal_type)
st_title = t(_(st_title))
if rs:
results_dict['review_state'] = rs
for state_var, state in states.items():
if not st_title:
st_title = self.workflow.getTitleForStateOnType(
state, obj.portal_type)
results_dict[state_var] = state
results_dict['state_title'] = st_title
results_dict['class'] = {}
# As far as I am concerned, adapters for IFieldIcons are only used
# for Analysis content types. Since AnalysesView is not using this
# "classic" folderitems from bikalisting anymore, this logic has
# been added in AnalysesView. Even though, this logic hasn't been
# removed from here, cause this _folderitems function is marked as
# deprecated, so it will be eventually removed alltogether.
for name, adapter in getAdapters((obj,), IFieldIcons):
auid = obj.UID() if hasattr(obj, 'UID') and callable(
obj.UID) else None
if not auid:
continue
alerts = adapter()
# logger.info(str(alerts))
if alerts and auid in alerts:
if auid in self.field_icons:
self.field_icons[auid].extend(alerts[auid])
else:
self.field_icons[auid] = alerts[auid]
# Search for values for all columns in obj
for key in self.columns.keys():
# if the key is already in the results dict
# then we don't replace it's value
value = results_dict.get(key, '')
if key not in results_dict:
attrobj = getFromString(obj, key)
value = attrobj if attrobj else value
# Custom attribute? Inspect to set the value
# for the current column dinamically
vattr = self.columns[key].get('attr', None)
if vattr:
attrobj = getFromString(obj, vattr)
value = attrobj if attrobj else value
results_dict[key] = value
# Replace with an url?
replace_url = self.columns[key].get('replace_url', None)
if replace_url:
attrobj = getFromString(obj, replace_url)
if attrobj:
results_dict['replace'][key] = \
'<a href="%s">%s</a>' % (attrobj, value)
# The item basics filled. Delegate additional actions to folderitem
# service. folderitem service is frequently overriden by child
# objects
item = self.folderitem(obj, results_dict, idx)
# Call folder_item from subscriber adapters
for subscriber in self.get_listing_view_adapters():
subscriber.folder_item(obj, item, idx)
if item:
results.append(item)
idx += 1
return results
def Import(context, request, instrumentname='sysmex_xs_500i'):
""" Sysmex XS - 500i analysis results
"""
# I don't really know how this file works, for this reason I added an 'Analysis Service selector'.
# If non Analysis Service is selected, each 'data' column will be interpreted as a different Analysis Service. In
# the case that an Analysis Service was selected, all the data columns would be interpreted as different data from
# an unique Analysis Service.
formitems = getForm(instrumentname, request)
infile = formitems['infile']
fileformat = formitems['fileformat']
artoapply = formitems['artoapply']
override = formitems['override']
instrument = formitems['instrument']
errors = []
logs = []
warns = []
# Load the most suitable parser according to file extension/options/etc...
parser = None
if not hasattr(infile, 'filename'):
errors.append(_("No file selected"))
if fileformat == 'csv':
# Get the Analysis Service selected, if there is one.
analysis = request.form.get('analysis_service', None)
if analysis:
# Get default result key
defaultresult = request.form.get('default_result', None)
# Rise an error if default result is missing.
parser = SysmexXS500iCSVParser(infile, analysis, defaultresult) if defaultresult \
else errors.append(t(_("You should introduce a default result key.",
mapping={"fileformat": fileformat})))
else:
parser = SysmexXS500iCSVParser(infile)
else:
errors.append(
t(
_("Unrecognized file format ${fileformat}",
mapping={"fileformat": fileformat})))
if parser:
# Load the importer
status = ['sample_received', 'attachment_due', 'to_be_verified']
if artoapply == 'received':
status = ['sample_received']
elif artoapply == 'received_tobeverified':
status = ['sample_received', 'attachment_due', 'to_be_verified']
over = [False, False]
if override == 'nooverride':
over = [False, False]
elif override == 'override':
over = [True, False]
elif override == 'overrideempty':
over = [True, True]
importer = SysmexXS500iImporter(parser=parser,
context=context,
allowed_ar_states=status,
allowed_analysis_states=None,
override=over,
instrument_uid=instrument)
tbex = ''
try:
importer.process()
except:
tbex = traceback.format_exc()
errors = importer.errors
logs = importer.logs
warns = importer.warns
if tbex:
errors.append(tbex)
results = {'errors': errors, 'log': logs, 'warns': warns}
return json.dumps(results)
def folderitem(self, obj, item, index):
"""Service triggered each time an item is iterated in folderitems.
The use of this service prevents the extra-loops in child objects.
:obj: the instance of the class to be foldered
:item: dict containing the properties of the object to be used by
the template
:index: current index of the item
"""
# ensure we have an object and not a brain
obj = api.get_object(obj)
uid = api.get_uid(obj)
# settings for this analysis
service_settings = self.context.getAnalysisServiceSettings(uid)
hidden = service_settings.get("hidden", obj.getHidden())
# get the category
category = obj.getCategoryTitle()
item["category"] = category
if category not in self.categories:
self.categories.append(category)
parts = filter(api.is_active, self.get_partitions())
partitions = map(
lambda part: {
"ResultValue": part.Title(),
"ResultText": part.getId()
}, parts)
keyword = obj.getKeyword()
partition = None
if uid in self.analyses:
analysis = self.analyses[uid]
# Might differ from the service keyword
keyword = analysis.getKeyword()
# Mark the row as disabled if the analysis is not in an open state
item["disabled"] = not analysis.isOpen()
# get the hidden status of the analysis
hidden = analysis.getHidden()
# get the partition of the analysis
partition = self.get_partition(analysis)
else:
partition = self.get_partitions()[0]
# get the specification of this object
rr = self.get_results_range()
spec = rr.get(keyword, ResultsRangeDict())
item["Title"] = obj.Title()
item["Unit"] = obj.getUnit()
item["Price"] = obj.getPrice()
item["before"]["Price"] = self.get_currency_symbol()
item["allow_edit"] = self.get_editable_columns(obj)
item["selected"] = uid in self.selected
item["min"] = str(spec.get("min", ""))
item["max"] = str(spec.get("max", ""))
item["warn_min"] = str(spec.get("warn_min", ""))
item["warn_max"] = str(spec.get("warn_max", ""))
item["Hidden"] = hidden
item["Partition"] = partition.getId()
item["choices"]["Partition"] = partitions
# Icons
after_icons = ""
if obj.getAccredited():
after_icons += get_image("accredited.png",
title=t(_("Accredited")))
if obj.getAttachmentOption() == "r":
after_icons += get_image("attach_reqd.png",
title=t(_("Attachment required")))
if obj.getAttachmentOption() == "n":
after_icons += get_image("attach_no.png",
title=t(_('Attachment not permitted')))
if after_icons:
item["after"]["Title"] = after_icons
return item
def __call__(self):
self.service_uids = self.request.get('service_uids', '').split(",")
self.control_type = self.request.get('control_type', '')
if not self.control_type:
return t(_("No control type specified"))
return super(ReferenceSamplesView, self).contents_table()
def __call__(self):
# get all the data into datalines
sc = getToolByName(self.context, 'bika_setup_catalog')
bc = getToolByName(self.context, 'bika_analysis_catalog')
rc = getToolByName(self.context, 'reference_catalog')
self.report_content = {}
parms = []
headings = {}
headings['header'] = _("Analysis turnaround times")
headings['subheader'] = _("The turnaround time of analyses")
query = {'portal_type': 'Analysis'}
client_title = None
if 'ClientUID' in self.request.form:
client_uid = self.request.form['ClientUID']
query['getClientUID'] = client_uid
client = rc.lookupObject(client_uid)
client_title = client.Title()
else:
client = logged_in_client(self.context)
if client:
client_title = client.Title()
query['getClientUID'] = client.UID()
if client_title:
parms.append(
{'title': _('Client'),
'value': client_title,
'type': 'text'})
date_query = formatDateQuery(self.context, 'Received')
if date_query:
query['created'] = date_query
received = formatDateParms(self.context, 'Received')
parms.append(
{'title': _('Received'),
'value': received,
'type': 'text'})
query['review_state'] = 'published'
workflow = getToolByName(self.context, 'portal_workflow')
if 'bika_worksheetanalysis_workflow' in self.request.form:
query['worksheetanalysis_review_state'] = self.request.form[
'bika_worksheetanalysis_workflow']
ws_review_state = workflow.getTitleForStateOnType(
self.request.form['bika_worksheetanalysis_workflow'], 'Analysis')
parms.append(
{'title': _('Assigned to worksheet'), 'value': ws_review_state,
'type': 'text'})
# query all the analyses and increment the counts
count_early = 0
mins_early = 0
count_late = 0
mins_late = 0
count_undefined = 0
services = {}
analyses = bc(query)
for a in analyses:
analysis = a.getObject()
service_uid = analysis.getServiceUID()
if service_uid not in services:
services[service_uid] = {'count_early': 0,
'count_late': 0,
'mins_early': 0,
'mins_late': 0,
'count_undefined': 0,
}
earliness = analysis.getEarliness()
if earliness < 0:
count_late = services[service_uid]['count_late']
mins_late = services[service_uid]['mins_late']
count_late += 1
mins_late -= earliness
services[service_uid]['count_late'] = count_late
services[service_uid]['mins_late'] = mins_late
if earliness > 0:
count_early = services[service_uid]['count_early']
mins_early = services[service_uid]['mins_early']
count_early += 1
mins_early += earliness
services[service_uid]['count_early'] = count_early
services[service_uid]['mins_early'] = mins_early
if earliness == 0:
count_undefined = services[service_uid]['count_undefined']
count_undefined += 1
services[service_uid]['count_undefined'] = count_undefined
# calculate averages
for service_uid in services.keys():
count_early = services[service_uid]['count_early']
mins_early = services[service_uid]['mins_early']
if count_early == 0:
services[service_uid]['ave_early'] = ''
else:
avemins = (mins_early) / count_early
services[service_uid]['ave_early'] = \
api.to_dhm_format(minutes=avemins)
count_late = services[service_uid]['count_late']
mins_late = services[service_uid]['mins_late']
if count_late == 0:
services[service_uid]['ave_late'] = ''
else:
avemins = mins_late / count_late
services[service_uid]['ave_late'] = api.to_dhm_format(avemins)
# and now lets do the actual report lines
formats = {'columns': 7,
'col_heads': [_('Analysis'),
_('Count'),
_('Undefined'),
_('Late'),
_('Average late'),
_('Early'),
_('Average early'),
],
'class': '',
}
total_count_early = 0
total_count_late = 0
total_mins_early = 0
total_mins_late = 0
total_count_undefined = 0
datalines = []
for cat in sc(portal_type='AnalysisCategory',
sort_on='sortable_title'):
catline = [{'value': cat.Title,
'class': 'category_heading',
'colspan': 7}, ]
first_time = True
cat_count_early = 0
cat_count_late = 0
cat_count_undefined = 0
cat_mins_early = 0
cat_mins_late = 0
for service in sc(portal_type="AnalysisService",
getCategoryUID=cat.UID,
sort_on='sortable_title'):
dataline = [{'value': service.Title,
'class': 'testgreen'}, ]
if service.UID not in services:
continue
if first_time:
datalines.append(catline)
first_time = False
# analyses found
cat_count_early += services[service.UID]['count_early']
cat_count_late += services[service.UID]['count_late']
cat_count_undefined += services[service.UID]['count_undefined']
cat_mins_early += services[service.UID]['mins_early']
cat_mins_late += services[service.UID]['mins_late']
count = services[service.UID]['count_early'] + \
services[service.UID]['count_late'] + \
services[service.UID]['count_undefined']
dataline.append({'value': count,
'class': 'number'})
dataline.append(
{'value': services[service.UID]['count_undefined'],
'class': 'number'})
dataline.append({'value': services[service.UID]['count_late'],
'class': 'number'})
dataline.append({'value': services[service.UID]['ave_late'],
'class': 'number'})
dataline.append({'value': services[service.UID]['count_early'],
'class': 'number'})
dataline.append({'value': services[service.UID]['ave_early'],
'class': 'number'})
datalines.append(dataline)
# category totals
dataline = [{'value': '%s - total' % (cat.Title),
'class': 'subtotal_label'}, ]
dataline.append({'value': cat_count_early +
cat_count_late +
cat_count_undefined,
'class': 'subtotal_number'})
dataline.append({'value': cat_count_undefined,
'class': 'subtotal_number'})
dataline.append({'value': cat_count_late,
'class': 'subtotal_number'})
if cat_count_late:
dataitem = {'value': cat_mins_late / cat_count_late,
'class': 'subtotal_number'}
else:
dataitem = {'value': 0,
'class': 'subtotal_number'}
dataline.append(dataitem)
dataline.append({'value': cat_count_early,
'class': 'subtotal_number'})
if cat_count_early:
dataitem = {'value': cat_mins_early / cat_count_early,
'class': 'subtotal_number'}
else:
dataitem = {'value': 0,
'class': 'subtotal_number'}
dataline.append(dataitem)
total_count_early += cat_count_early
total_count_late += cat_count_late
total_count_undefined += cat_count_undefined
total_mins_early += cat_mins_early
total_mins_late += cat_mins_late
# footer data
footlines = []
footline = []
footline = [{'value': _('Total'),
'class': 'total'}, ]
footline.append({'value': total_count_early +
total_count_late +
total_count_undefined,
'class': 'total number'})
footline.append({'value': total_count_undefined,
'class': 'total number'})
footline.append({'value': total_count_late,
'class': 'total number'})
if total_count_late:
ave_mins = total_mins_late / total_count_late
footline.append({'value': api.to_dhm_format(minutes=ave_mins),
'class': 'total number'})
else:
footline.append({'value': ''})
footline.append({'value': total_count_early,
'class': 'total number'})
if total_count_early:
ave_mins = total_mins_early / total_count_early
footline.append({'value': api.to_dhm_format(minutes=ave_mins),
'class': 'total number'})
else:
footline.append({'value': '',
'class': 'total number'})
footlines.append(footline)
self.report_content = {
'headings': headings,
'parms': parms,
'formats': formats,
'datalines': datalines,
'footings': footlines}
if self.request.get('output_format', '') == 'CSV':
import csv
import StringIO
import datetime
fieldnames = [
'Analysis',
'Count',
'Undefined',
'Late',
'Average late',
'Early',
'Average early',
]
output = StringIO.StringIO()
dw = csv.DictWriter(output, extrasaction='ignore',
fieldnames=fieldnames)
dw.writerow(dict((fn, fn) for fn in fieldnames))
for row in datalines:
if len(row) == 1:
# category heading thingy
continue
dw.writerow({
'Analysis': row[0]['value'],
'Count': row[1]['value'],
'Undefined': row[2]['value'],
'Late': row[3]['value'],
'Average late': row[4]['value'],
'Early': row[5]['value'],
'Average early': row[6]['value'],
})
report_data = output.getvalue()
output.close()
date = datetime.datetime.now().strftime("%Y%m%d%H%M")
setheader = self.request.RESPONSE.setHeader
setheader('Content-Type', 'text/csv')
setheader("Content-Disposition",
"attachment;filename=\"analysestats_%s.csv\"" % date)
self.request.RESPONSE.write(report_data)
else:
return {'report_title': t(headings['header']),
'report_data': self.template()}
def __call__(self):
# get all the data into datalines
catalog = api.get_tool(CATALOG_ANALYSIS_LISTING, self.context)
self.report_content = {}
parms = []
headings = {}
headings['header'] = ""
count_all = 0
query = {}
# Getting the query filters
val = self.selection_macros.parse_client(self.request)
if val:
query[val['contentFilter'][0]] = val['contentFilter'][1]
parms.append(val['parms'])
val = self.selection_macros.parse_sampletype(self.request)
if val:
query[val['contentFilter'][0]] = val['contentFilter'][1]
parms.append(val['parms'])
val = self.selection_macros.parse_analysisservice(self.request)
if val:
query[val['contentFilter'][0]] = val['contentFilter'][1]
parms.append(val['parms'])
val = self.selection_macros.parse_daterange(self.request, 'created',
'Created')
if val:
query[val['contentFilter'][0]] = val['contentFilter'][1]
parms.append(val['parms'])
val = self.selection_macros.parse_daterange(self.request,
'getDatePublished',
'Date Published')
if val:
query[val['contentFilter'][0]] = val['contentFilter'][1]
parms.append(val['parms'])
val = self.selection_macros.parse_daterange(self.request,
'getDateReceived',
'Date Received')
if val:
query[val['contentFilter'][0]] = val['contentFilter'][1]
parms.append(val['parms'])
formats = {
'columns':
25,
'col_heads': [
_('Lab Number'),
_('Testing Lab'),
_('First Name'),
_('Middle Name'),
_('Last Name'),
_('Gender'),
_('Age'),
_('Age Type'),
_('Town'),
_('Reporting County'),
_('Reporting District'),
_('Reporting Facility'),
_('Date Onset'),
_('Date of Reporting'),
_('Was Specimen collected? '),
_('Date specimen collected'),
_('Type of Specimen'),
_('Date Specimen Sent to Lab'),
_('Date Specimen Received in Lab'),
_('Date Published'),
_('Condition of Specimen'),
_('Comment'),
_('Test Result')
],
}
# and now lets do the actual report lines
datalines = []
laboratory = self.context.bika_setup.laboratory
# Get analyses brains
logger.info("Searching Analyses: {}".format(repr(query)))
brains = catalog(query)
# Collect all AR uids and Patient UIDs so only one query to get all
# them will be needed
ar_uids = list(set([brain.getParentUID for brain in brains]))
ar_uids = filter(None, ar_uids)
self.map_uids_to_brains(ar_uids)
logger.info("Filling datalines with {} Analyses".format(len(brains)))
for analysis in brains:
# We get the AR and the patient of the
# analysis here to avoid having to get them
# inside each of the following method calls.
# If they are not found its value will be None
ar_brain = self.get_ar_brain(analysis)
patient_brain = self.get_patient_brain(analysis)
dataline = []
# Lab Number
dataitem = self.get_lab_number(analysis)
dataline.append(dataitem)
# Testing Lab
dataline.append({'value': laboratory.Title()})
#First Name
dataitem = self.get_firstname(patient_brain)
dataline.append(dataitem)
#Middle Name
dataitem = self.get_middlename(patient_brain)
dataline.append(dataitem)
#Last Name
dataitem = self.get_lastname(patient_brain)
dataline.append(dataitem)
#Gender
dataitem = self.get_gender(patient_brain)
dataline.append(dataitem)
#Age
dataitem = self.get_age(patient_brain)
dataline.append(dataitem)
#AgeType
dataitem = self.get_agetype(patient_brain)
dataline.append(dataitem)
# Facility Province
dataitem = self.get_facility_province(ar_brain)
dataline.append(dataitem)
# Facility District
dataitem = self.get_facility_district(ar_brain)
dataline.append(dataitem)
# Facility
dataitem = self.get_client_name(ar_brain)
dataline.append(dataitem)
# Date of Collection - Onset
dataitem = self.get_date_of_collection(ar_brain)
dataline.append(dataitem)
# Date Reporting
dataitem = self.get_date_of_dispatch(ar_brain)
dataline.append(dataitem)
# Specimen Collected
dataitem = self.get_date_of_collection(ar_brain)
dataline.append(dataitem)
# Date of Collection - Onset
dataitem = self.get_date_of_collection(ar_brain)
dataline.append(dataitem)
# Specimen Type
dataitem = self.get_specimentype(ar_brain)
dataline.append(dataitem)
# Date of Dispatch
dataitem = self.get_date_of_dispatch(ar_brain)
dataline.append(dataitem)
# Date of Receiving
dataitem = self.get_date_of_receiving(ar_brain)
dataline.append(dataitem)
# Date of Publication
dataitem = self.get_date_published(analysis)
dataline.append(dataitem)
# Condition of Specimen
#dataitem = self.get_date_published(analysis)
#dataline.append(dataitem)
# Comment
#dataitem = self.get_date_published(analysis)
##dataline.append(dataitem)
# Sex
#dataitem = self.get_patient_sex(patient_brain)
#dataline.append(dataitem)
# Date Of Birth
#dataitem = self.get_patient_dob(patient_brain)
#dataline.append(dataitem)
# Date of Testing
#dataitem = self.get_date_of_testing(analysis)
#dataline.append(dataitem)
#Test Result
dataitem = self.get_result(analysis)
dataline.append(dataitem)
count_all += 1
datalines.append(dataline)
logger.info("Generating output")
# footer data
footlines = []
footline = []
footitem = {'value': _('Total'), 'class': 'total_label'}
footline.append(footitem)
footitem = {'value': count_all}
footline.append(footitem)
footlines.append(footline)
self.report_content = {
'headings': headings,
'parms': parms,
'formats': formats,
'datalines': datalines,
'footings': footlines
}
if self.request.get('output_format', '') == 'CSV':
fieldnames = formats.get('col_heads')
output = StringIO.StringIO()
dw = csv.DictWriter(output,
extrasaction='ignore',
fieldnames=fieldnames)
dw.writerow(dict((fn, fn) for fn in fieldnames))
for row in datalines:
dict_row = {}
row_idx = 0
for column in fieldnames:
dict_row[column] = row[row_idx]['value']
row_idx += 1
dw.writerow(dict_row)
report_data = output.getvalue()
output.close()
date = datetime.datetime.now().strftime("%Y%m%d%H%M")
setheader = self.request.RESPONSE.setHeader
setheader('Content-Type', 'text/csv')
setheader(
"Content-Disposition",
"attachment;filename=\"analysisresultbyclient_%s.csv"
"\"" % date)
self.request.RESPONSE.write(report_data)
else:
return {
'report_title': t(headings['header']),
'report_data': self.template()
}
def __init__(self, context, request):
super(AccreditationView, self).__init__(context, request)
self.contentFilter = {
'portal_type': 'AnalysisService',
'sort_on': 'sortable_title',
'getAccredited': True,
'is_active': True
}
self.context_actions = {}
self.title = self.context.translate(_("Accreditation"))
self.icon = self.portal_url + \
"/++resource++bika.lims.images/accredited_big.png"
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.review_states = [
{
'id':
'default',
'title':
_('All'),
'contentFilter': {},
'transitions': [
{
'id': 'empty'
},
], # none
'columns': [
'Title',
'Keyword',
'Price',
'MaxTimeAllowed',
'DuplicateVariation',
],
},
]
if not self.context.bika_setup.getShowPrices():
self.review_states[0]['columns'].remove('Price')
def process(self):
self._parser.parse()
parsed = self._parser.resume()
self._errors = self._parser.errors
self._warns = self._parser.warns
self._logs = self._parser.logs
self._priorizedsearchcriteria = ''
if parsed is False:
return False
# Allowed analysis states
allowed_ar_states_msg = [t(_(s)) for s in self.getAllowedARStates()]
allowed_an_states_msg = [
t(_(s)) for s in self.getAllowedAnalysisStates()]
self.log("Allowed Analysis Request states: ${allowed_states}",
mapping={'allowed_states': ', '.join(allowed_ar_states_msg)})
self.log("Allowed analysis states: ${allowed_states}",
mapping={'allowed_states': ', '.join(allowed_an_states_msg)})
# Exclude non existing ACODEs
acodes = []
ancount = 0
instprocessed = []
importedars = {}
importedinsts = {}
rawacodes = self._parser.getAnalysisKeywords()
exclude = self.getKeywordsToBeExcluded()
for acode in rawacodes:
if acode in exclude or not acode:
continue
service = self.bsc(getKeyword=acode)
if not service:
self.warn('Service keyword ${analysis_keyword} not found',
mapping={"analysis_keyword": acode})
else:
acodes.append(acode)
if len(acodes) == 0:
self.warn("Service keywords: no matches found")
# Attachments will be created in any worksheet that contains
# analyses that are updated by this import
attachments = {}
infile = self._parser.getInputFile()
# searchcriteria = self.getIdSearchCriteria()
# self.log(_("Search criterias: %s") % (', '.join(searchcriteria)))
for objid, results in self._parser.getRawResults().iteritems():
# Allowed more than one result for the same sample and analysis.
# Needed for calibration tests
for result in results:
analyses = self._getZODBAnalyses(objid)
inst = None
if len(analyses) == 0 and self.instrument_uid:
# No registered analyses found, but maybe we need to
# create them first if an instruemnt id has been set in
insts = self.bsc(portal_type='Instrument',
UID=self.instrument_uid)
if len(insts) == 0:
# No instrument found
self.warn("No Analysis Request with "
"'${allowed_ar_states}' "
"states found, And no QC"
"analyses found for ${object_id}",
mapping={"allowed_ar_states": ', '.join(
allowed_ar_states_msg),
"object_id": objid})
self.warn("Instrument not found")
continue
inst = insts[0].getObject()
# Create a new ReferenceAnalysis and link it to
# the Instrument
# Here we have an objid (i.e. R01200012) and
# a dict with results (the key is the AS keyword).
# How can we create a ReferenceAnalysis if we don't know
# which ReferenceSample we might use?
# Ok. The objid HAS to be the ReferenceSample code.
refsample = self.bc(portal_type='ReferenceSample',
id=objid)
if refsample and len(refsample) == 1:
refsample = refsample[0].getObject()
elif refsample and len(refsample) > 1:
# More than one reference sample found!
self.warn(
"More than one reference sample found for"
"'${object_id}'",
mapping={"object_id": objid})
continue
else:
# No reference sample found!
self.warn("No Reference Sample found for ${object_id}",
mapping={"object_id": objid})
continue
# For each acode, create a ReferenceAnalysis and attach it
# to the Reference Sample
services = self.bsc(portal_type='AnalysisService')
service_uids = [service.UID for service in services
if service.getObject().getKeyword()
in result.keys()]
analyses = inst.addReferences(refsample, service_uids)
elif len(analyses) == 0:
# No analyses found
self.warn("No Analysis Request with "
"'${allowed_ar_states}' "
"states neither QC analyses found "
"for ${object_id}",
mapping={
"allowed_ar_states": ', '.join(
allowed_ar_states_msg),
"object_id": objid})
continue
# Look for timestamp
capturedate = result.get('DateTime', {}).get('DateTime', None)
if capturedate:
del result['DateTime']
for acode, values in result.iteritems():
if acode not in acodes:
# Analysis keyword doesn't exist
continue
ans = [analysis for analysis in analyses
if analysis.getKeyword() == acode]
if len(ans) > 1:
self.warn("More than one analysis found for "
"${object_id} and ${analysis_keyword}",
mapping={"object_id": objid,
"analysis_keyword": acode})
continue
elif len(ans) == 0:
self.warn("No analyses found for ${object_id} "
"and ${analysis_keyword}",
mapping={"object_id": objid,
"analysis_keyword": acode})
continue
analysis = ans[0]
# Create attachment in worksheet linked to this analysis.
# Only if this import has not already created the
# attachment
# And only if the filename of the attachment is unique in
# this worksheet. Otherwise we will attempt to use
# existing attachment.
wss = analysis.getBackReferences('WorksheetAnalysis')
ws = wss[0] if wss else None
if ws:
if ws.getId() not in attachments:
fn = infile.filename
fn_attachments = self.get_attachment_filenames(ws)
if fn in fn_attachments.keys():
attachments[ws.getId()] = fn_attachments[fn]
else:
attachments[ws.getId()] = \
self.create_attachment(ws, infile)
if capturedate:
values['DateTime'] = capturedate
processed = self._process_analysis(objid, analysis, values)
if processed:
ancount += 1
if inst:
# Calibration Test (import to Instrument)
instprocessed.append(inst.UID())
importedinst = inst.title in importedinsts.keys() \
and importedinsts[inst.title] or []
if acode not in importedinst:
importedinst.append(acode)
importedinsts[inst.title] = importedinst
else:
ar = analysis.portal_type == 'Analysis' \
and analysis.aq_parent or None
if ar and ar.UID:
importedar = ar.getId() in importedars.keys() \
and importedars[ar.getId()] or []
if acode not in importedar:
importedar.append(acode)
importedars[ar.getId()] = importedar
if ws:
self.attach_attachment(
analysis, attachments[ws.getId()])
else:
self.warn(
"Attachment cannot be linked to analysis as "
"it is not assigned to a worksheet (%s)" %
analysis)
for arid, acodes in importedars.iteritems():
acodesmsg = ["Analysis %s" % acod for acod in acodes]
self.log(
"${request_id}: ${analysis_keywords} imported sucessfully",
mapping={"request_id": arid,
"analysis_keywords": acodesmsg})
for instid, acodes in importedinsts.iteritems():
acodesmsg = ["Analysis %s" % acod for acod in acodes]
msg = "%s: %s %s" % (instid,
", ".join(acodesmsg),
"imported sucessfully")
self.log(msg)
if self.instrument_uid:
self.log(
"Import finished successfully: ${nr_updated_ars} ARs, "
"${nr_updated_instruments} Instruments and "
"${nr_updated_results} "
"results updated",
mapping={"nr_updated_ars": str(len(importedars)),
"nr_updated_instruments": str(len(importedinsts)),
"nr_updated_results": str(ancount)})
else:
self.log(
"Import finished successfully: ${nr_updated_ars} ARs and "
"${nr_updated_results} results updated",
mapping={"nr_updated_ars": str(len(importedars)),
"nr_updated_results": str(ancount)})
def Import(context, request):
""" Horiba Jobin-Yvon ICPanalysis results
"""
infile = request.form['data_file']
fileformat = request.form['format']
artoapply = request.form['artoapply']
override = request.form['override']
sample = request.form.get('sample', 'requestid')
instrument = request.form.get('instrument', None)
errors = []
logs = []
warns = []
# Load the most suitable parser according to file extension/options/etc...
parser = None
if not hasattr(infile, 'filename'):
errors.append(_("No file selected"))
if fileformat == 'csv':
parser = HoribaJobinYvonICPCSVParser(infile)
else:
errors.append(
t(
_("Unrecognized file format ${fileformat}",
mapping={"fileformat": fileformat})))
if parser:
# Load the importer
status = ['sample_received', 'attachment_due', 'to_be_verified']
if artoapply == 'received':
status = ['sample_received']
elif artoapply == 'received_tobeverified':
status = ['sample_received', 'attachment_due', 'to_be_verified']
over = [False, False]
if override == 'nooverride':
over = [False, False]
elif override == 'override':
over = [True, False]
elif override == 'overrideempty':
over = [True, True]
sam = ['getRequestID', 'getSampleID', 'getClientSampleID']
if sample == 'requestid':
sam = ['getRequestID']
if sample == 'sampleid':
sam = ['getSampleID']
elif sample == 'clientsid':
sam = ['getClientSampleID']
elif sample == 'sample_clientsid':
sam = ['getSampleID', 'getClientSampleID']
importer = HoribaJobinYvonICPImporter(parser=parser,
context=context,
idsearchcriteria=sam,
allowed_ar_states=status,
allowed_analysis_states=None,
override=over,
instrument_uid=instrument)
tbex = ''
try:
importer.process()
except:
tbex = traceback.format_exc()
errors = importer.errors
logs = importer.logs
warns = importer.warns
if tbex:
errors.append(tbex)
results = {'errors': errors, 'log': logs, 'warns': warns}
return json.dumps(results)
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]['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:
if self.context.portal_type == 'AnalysisRequest':
sample = self.context.getSample()
st_uid = sample.getSampleType().UID()
items[i]['st_uid'] = st_uid
if st_uid not in self.specs:
proxies = bsc(portal_type = 'AnalysisSpec',
getSampleTypeUID = st_uid)
elif self.context.portal_type == "Worksheet":
if obj.portal_type == "DuplicateAnalysis":
sample = obj.getAnalysis().getSample()
elif obj.portal_type == "RejectAnalysis":
sample = obj.getAnalysis().getSample()
else:
sample = obj.aq_parent.getSample()
st_uid = sample.getSampleType().UID()
items[i]['st_uid'] = st_uid
if st_uid not in self.specs:
proxies = bsc(portal_type = 'AnalysisSpec',
getSampleTypeUID = st_uid)
elif self.context.portal_type == 'Sample':
st_uid = self.context.getSampleType().UID()
items[i]['st_uid'] = st_uid
if st_uid not in self.specs:
proxies = bsc(portal_type = 'AnalysisSpec',
getSampleTypeUID = st_uid)
else:
proxies = []
if st_uid not in self.specs:
for spec in (p.getObject() for p in proxies):
if spec.getClientUID() == obj.getClientUID():
client_or_lab = 'client'
elif spec.getClientUID() == self.context.bika_setup.bika_analysisspecs.UID():
client_or_lab = 'lab'
else:
continue
for keyword, results_range in \
spec.getResultsRangeDict().items():
# hidden form field 'specs' keyed by sampletype uid:
# {st_uid: {'lab/client':{keyword:{min,max,error}}}}
if st_uid in self.specs:
if client_or_lab in self.specs[st_uid]:
self.specs[st_uid][client_or_lab][keyword] = results_range
else:
self.specs[st_uid][client_or_lab] = {keyword: results_range}
else:
self.specs[st_uid] = {client_or_lab: {keyword: results_range}}
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)
items[i]['Uncertainty'] = format_uncertainty(obj, result, decimalmark=dmk, sciformat=int(scinot))
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 __call__(self):
bac = getToolByName(self.context, 'bika_analysis_catalog')
self.report_content = {}
parm_lines = {}
parms = []
headings = {}
headings['header'] = _("Analyses retested")
headings['subheader'] = _("Analyses which have been retested")
count_all = 0
query = {'portal_type': 'Analysis',
'getRetested': True,
'sort_order': 'reverse'}
date_query = formatDateQuery(self.context, 'Received')
if date_query:
query['getDateReceived'] = date_query
received = formatDateParms(self.context, 'Received')
else:
received = 'Undefined'
parms.append(
{'title': _('Received'),
'value': received,
'type': 'text'})
wf_tool = getToolByName(self.context, 'portal_workflow')
if self.request.form.has_key('bika_analysis_workflow'):
query['review_state'] = self.request.form['bika_analysis_workflow']
review_state = wf_tool.getTitleForStateOnType(
self.request.form['bika_analysis_workflow'], 'Analysis')
else:
review_state = 'Undefined'
parms.append(
{'title': _('Status'),
'value': review_state,
'type': 'text'})
if self.request.form.has_key('bika_cancellation_workflow'):
query['cancellation_state'] = self.request.form[
'bika_cancellation_workflow']
cancellation_state = wf_tool.getTitleForStateOnType(
self.request.form['bika_cancellation_workflow'], 'Analysis')
else:
cancellation_state = 'Undefined'
parms.append(
{'title': _('Active'),
'value': cancellation_state,
'type': 'text'})
if self.request.form.has_key('bika_worksheetanalysis_workflow'):
query['worksheetanalysis_review_state'] = self.request.form[
'bika_worksheetanalysis_workflow']
ws_review_state = wf_tool.getTitleForStateOnType(
self.request.form['bika_worksheetanalysis_workflow'], 'Analysis')
else:
ws_review_state = 'Undefined'
parms.append(
{'title': _('Assigned to worksheet'),
'value': ws_review_state,
'type': 'text'})
# and now lets do the actual report lines
formats = {'columns': 8,
'col_heads': [_('Client'),
_('Request'),
_('Sample type'),
_('Sample point'),
_('Category'),
_('Analysis'),
_('Received'),
_('Status'),
],
'class': '',
}
datalines = []
clients = {}
sampletypes = {}
samplepoints = {}
categories = {}
services = {}
for a_proxy in bac(query):
analysis = a_proxy.getObject()
dataline = []
dataitem = {'value': analysis.getClientTitle()}
dataline.append(dataitem)
dataitem = {'value': analysis.getRequestID()}
dataline.append(dataitem)
dataitem = {'value': analysis.aq_parent.getSampleTypeTitle()}
dataline.append(dataitem)
dataitem = {'value': analysis.aq_parent.getSamplePointTitle()}
dataline.append(dataitem)
dataitem = {'value': analysis.getCategoryTitle()}
dataline.append(dataitem)
dataitem = {'value': analysis.getServiceTitle()}
dataline.append(dataitem)
dataitem = {'value': self.ulocalized_time(analysis.getDateReceived())}
dataline.append(dataitem)
state = wf_tool.getInfoFor(analysis, 'review_state', '')
review_state = wf_tool.getTitleForStateOnType(
state, 'Analysis')
dataitem = {'value': review_state}
dataline.append(dataitem)
datalines.append(dataline)
count_all += 1
# table footer data
footlines = []
footline = []
footitem = {'value': _('Number of analyses retested for period'),
'colspan': 7,
'class': 'total_label'}
footline.append(footitem)
footitem = {'value': count_all}
footline.append(footitem)
footlines.append(footline)
self.report_content = {
'headings': headings,
'parms': parms,
'formats': formats,
'datalines': datalines,
'footings': footlines}
title = t(headings['header'])
return {'report_title': title,
'report_data': self.template()}
def __call__(self):
header = _("Reference analysis QC")
subheader = _("Reference analysis quality control graphs ")
MinimumResults = self.context.bika_setup.getMinimumResults()
warning_icon = "<img src='" + self.portal_url + "/++resource++bika.lims.images/warning.png' height='9' width='9'/>"
error_icon = "<img src='" + self.portal_url + "/++resource++bika.lims.images/exclamation.png' height='9' width='9'/>"
self.parms = []
titles = []
sample_uid = self.request.form.get('ReferenceSampleUID', '')
sample = self.reference_catalog.lookupObject(sample_uid)
if not sample:
message = _("No reference sample was selected.")
self.context.plone_utils.addPortalMessage(message, 'error')
return self.default_template()
self.parms.append({
'title': _("Reference Sample"),
'value': sample.Title()
})
titles.append(sample.Title())
service_uid = self.request.form.get('ReferenceServiceUID', '')
service = self.reference_catalog.lookupObject(service_uid)
if not service:
message = _("No analysis services were selected.")
self.context.plone_utils.addPortalMessage(message, 'error')
return self.default_template()
self.contentFilter = {
'portal_type': 'ReferenceAnalysis',
'review_state': ['verified', 'published'],
'path': {
"query": "/".join(sample.getPhysicalPath()),
"level": 0
}
}
self.parms.append({
'title': _("Analysis Service"),
'value': service.Title()
})
titles.append(service.Title())
val = self.selection_macros.parse_daterange(self.request,
'getDateVerified',
'DateVerified')
if val:
self.contentFilter[val['contentFilter']
[0]] = val['contentFilter'][1]
self.parms.append(val['parms'])
titles.append(val['titles'])
proxies = self.bika_analysis_catalog(self.contentFilter)
if not proxies:
message = _("No analyses matched your query")
self.context.plone_utils.addPortalMessage(message, 'error')
return self.default_template()
# Compile a list with all relevant analysis data
analyses = []
out_of_range_count = 0
results = []
capture_dates = []
plotdata = ""
tabledata = []
for analysis in proxies:
analysis = analysis.getObject()
service = analysis.getService()
resultsrange = \
[x for x in sample.getReferenceResults() if x['uid'] == service_uid][
0]
try:
result = float(analysis.getResult())
results.append(result)
except:
result = analysis.getResult()
capture_dates.append(analysis.getResultCaptureDate())
if result < float(resultsrange['min']) or result > float(
resultsrange['max']):
out_of_range_count += 1
try:
precision = str(service.getPrecision())
except:
precision = "2"
try:
formatted_result = str("%." + precision + "f") % result
except:
formatted_result = result
tabledata.append({
_("Analysis"):
analysis.getId(),
_("Result"):
formatted_result,
_("Analyst"):
analysis.getAnalyst(),
_("Captured"):
analysis.getResultCaptureDate().strftime(self.date_format_long)
})
plotdata += "%s\t%s\t%s\t%s\n" % (
analysis.getResultCaptureDate().strftime(
self.date_format_long), result, resultsrange['min'],
resultsrange['max'])
plotdata.encode('utf-8')
result_values = [int(r) for r in results]
result_dates = [c for c in capture_dates]
self.parms += [
{
"title": _("Total analyses"),
"value": len(proxies)
},
]
# # This variable is output to the TAL
self.report_data = {
'header': header,
'subheader': subheader,
'parms': self.parms,
'tables': [],
'footnotes': [],
}
if MinimumResults <= len(proxies):
plotscript = """
set terminal png transparent truecolor enhanced size 700,350 font "Verdana, 8"
set title "%(title)s"
set xlabel "%(xlabel)s"
set ylabel "%(ylabel)s"
set key off
#set logscale
set timefmt "%(timefmt)s"
set xdata time
set format x "%(xformat)s"
set xrange ["%(x_start)s":"%(x_end)s"]
set auto fix
set offsets graph 0, 0, 1, 1
set xtics border nomirror rotate by 90 font "Verdana, 5" offset 0,-3
set ytics nomirror
f(x) = mean_y
fit f(x) 'gpw_DATAFILE_gpw' u 1:3 via mean_y
stddev_y = sqrt(FIT_WSSR / (FIT_NDF + 1))
plot mean_y-stddev_y with filledcurves y1=mean_y lt 1 lc rgb "#efefef",\
mean_y+stddev_y with filledcurves y1=mean_y lt 1 lc rgb "#efefef",\
mean_y with lines lc rgb '#ffffff' lw 3,\
"gpw_DATAFILE_gpw" using 1:3 title 'data' with points pt 7 ps 1 lc rgb '#0000ee' lw 2,\
'' using 1:3 smooth unique lc rgb '#aaaaaa' lw 2,\
'' using 1:4 with lines lc rgb '#000000' lw 1,\
'' using 1:5 with lines lc rgb '#000000' lw 1""" % \
{
'title': "",
'xlabel': "",
'ylabel': service.getUnit(),
'x_start': "%s" % min(result_dates).strftime(
self.date_format_short),
'x_end': "%s" % max(result_dates).strftime(
self.date_format_short),
'timefmt': r'%Y-%m-%d %H:%M',
'xformat': '%%Y-%%m-%%d\n%%H:%%M',
}
plot_png = plot(str(plotdata),
plotscript=str(plotscript),
usefifo=False)
# Temporary PNG data file
fh, data_fn = tempfile.mkstemp(suffix='.png')
os.write(fh, plot_png)
plot_url = data_fn
self.request['to_remove'].append(data_fn)
plot_url = data_fn
else:
plot_url = ""
table = {
'title':
"%s: %s (%s)" %
(t(_("Analysis Service")), service.Title(), service.getKeyword()),
'columns':
[_('Analysis'),
_('Result'),
_('Analyst'),
_('Captured')],
'parms': [],
'data':
tabledata,
'plot_url':
plot_url,
}
self.report_data['tables'].append(table)
translate = self.context.translate
## footnotes
if out_of_range_count:
msgid = _("Analyses out of range")
self.report_data['footnotes'].append("%s %s" %
(error_icon, t(msgid)))
self.report_data['parms'].append({
"title": _("Analyses out of range"),
"value": out_of_range_count
})
title = t(header)
if titles:
title += " (%s)" % " ".join(titles)
return {
'report_title': title,
'report_data': self.template(),
}
def pretty_title_or_id(context, obj, empty_value=_marker, domain='plone'):
_ = MessageFactory(domain)
title = _pretty_title_or_id(context, obj, empty_value=_marker)
return t(context.translate(_(safe_unicode(title))))
def folderitem(self, obj, item, index):
# Additional info from AnalysisRequest to be added in the item generated
# by default by bikalisting.
# Call the folderitem method from the base class
item = BikaListingView.folderitem(self, obj, item, index)
if not item:
return None
member = self.mtool.getAuthenticatedMember()
roles = member.getRoles()
hideclientlink = 'RegulatoryInspector' in roles \
and 'Manager' not in roles \
and 'LabManager' not in roles \
and 'LabClerk' not in roles
sample = obj.getSample()
url = obj.absolute_url()
if getSecurityManager().checkPermission(EditResults, obj):
url += "/manage_results"
item['Client'] = obj.aq_parent.Title()
if (hideclientlink == False):
item['replace']['Client'] = "<a href='%s'>%s</a>" % \
(obj.aq_parent.absolute_url(), obj.aq_parent.Title())
item['Creator'] = self.user_fullname(obj.Creator())
item['getRequestID'] = obj.getRequestID()
item['replace']['getRequestID'] = "<a href='%s'>%s</a>" % \
(url, item['getRequestID'])
item['getSample'] = sample
item['replace']['getSample'] = \
"<a href='%s'>%s</a>" % (sample.absolute_url(), sample.Title())
item['replace']['getProfilesTitle'] = ", ".join(
[p.Title() for p in obj.getProfiles()])
analysesnum = obj.getAnalysesNum()
if analysesnum:
item['getAnalysesNum'] = str(analysesnum[0]) + '/' + str(
analysesnum[1])
else:
item['getAnalysesNum'] = ''
batch = obj.getBatch()
if batch:
item['BatchID'] = batch.getBatchID()
item['replace']['BatchID'] = "<a href='%s'>%s</a>" % \
(batch.absolute_url(), item['BatchID'])
else:
item['BatchID'] = ''
val = obj.Schema().getField('SubGroup').get(obj)
item['SubGroup'] = val.Title() if val else ''
samplingdate = obj.getSample().getSamplingDate()
item['SamplingDate'] = self.ulocalized_time(samplingdate,
long_format=1)
item['getDateReceived'] = self.ulocalized_time(obj.getDateReceived())
item['getDatePublished'] = self.ulocalized_time(obj.getDatePublished())
deviation = sample.getSamplingDeviation()
item['SamplingDeviation'] = deviation and deviation.Title() or ''
priority = obj.getPriority()
item['Priority'] = '' # priority.Title()
item['getStorageLocation'] = sample.getStorageLocation(
) and sample.getStorageLocation().Title() or ''
item['AdHoc'] = sample.getAdHoc() and True or ''
after_icons = ""
state = self.workflow.getInfoFor(obj, 'worksheetanalysis_review_state')
if state == 'assigned':
after_icons += "<img src='%s/++resource++bika.lims.images/worksheet.png' title='%s'/>" % \
(self.portal_url, t(_("All analyses assigned")))
if self.workflow.getInfoFor(obj, 'review_state') == 'invalid':
after_icons += "<img src='%s/++resource++bika.lims.images/delete.png' title='%s'/>" % \
(self.portal_url, t(_("Results have been withdrawn")))
if obj.getLate():
after_icons += "<img src='%s/++resource++bika.lims.images/late.png' title='%s'>" % \
(self.portal_url, t(_("Late Analyses")))
if samplingdate > DateTime():
after_icons += "<img src='%s/++resource++bika.lims.images/calendar.png' title='%s'>" % \
(self.portal_url, t(_("Future dated sample")))
if obj.getInvoiceExclude():
after_icons += "<img src='%s/++resource++bika.lims.images/invoice_exclude.png' title='%s'>" % \
(self.portal_url, t(_("Exclude from invoice")))
if sample.getSampleType().getHazardous():
after_icons += "<img src='%s/++resource++bika.lims.images/hazardous.png' title='%s'>" % \
(self.portal_url, t(_("Hazardous")))
if after_icons:
item['after']['getRequestID'] = after_icons
item['Created'] = self.ulocalized_time(obj.created())
contact = obj.getContact()
if contact:
item['ClientContact'] = contact.Title()
item['replace']['ClientContact'] = "<a href='%s'>%s</a>" % \
(contact.absolute_url(), contact.Title())
else:
item['ClientContact'] = ""
SamplingWorkflowEnabled = sample.getSamplingWorkflowEnabled()
if SamplingWorkflowEnabled and not samplingdate > DateTime():
datesampled = self.ulocalized_time(sample.getDateSampled())
if not datesampled:
datesampled = self.ulocalized_time(DateTime(), long_format=1)
item['class']['getDateSampled'] = 'provisional'
sampler = sample.getSampler().strip()
if sampler:
item['replace']['getSampler'] = self.user_fullname(sampler)
if 'Sampler' in member.getRoles() and not sampler:
sampler = member.id
item['class']['getSampler'] = 'provisional'
else:
datesampled = ''
sampler = ''
item['getDateSampled'] = datesampled
item['getSampler'] = sampler
# sampling workflow - inline edits for Sampler and Date Sampled
checkPermission = self.context.portal_membership.checkPermission
state = self.workflow.getInfoFor(obj, 'review_state')
if state == 'to_be_sampled' \
and checkPermission(SampleSample, obj) \
and not samplingdate > DateTime():
item['required'] = ['getSampler', 'getDateSampled']
item['allow_edit'] = ['getSampler', 'getDateSampled']
samplers = getUsers(sample, ['Sampler', 'LabManager', 'Manager'])
username = member.getUserName()
users = [({
'ResultValue': u,
'ResultText': samplers.getValue(u)
}) for u in samplers]
item['choices'] = {'getSampler': users}
Sampler = sampler and sampler or \
(username in samplers.keys() and username) or ''
item['getSampler'] = Sampler
# These don't exist on ARs
# XXX This should be a list of preservers...
item['getPreserver'] = ''
item['getDatePreserved'] = ''
# inline edits for Preserver and Date Preserved
checkPermission = self.context.portal_membership.checkPermission
if checkPermission(PreserveSample, obj):
item['required'] = ['getPreserver', 'getDatePreserved']
item['allow_edit'] = ['getPreserver', 'getDatePreserved']
preservers = getUsers(obj, ['Preserver', 'LabManager', 'Manager'])
username = member.getUserName()
users = [({
'ResultValue': u,
'ResultText': preservers.getValue(u)
}) for u in preservers]
item['choices'] = {'getPreserver': users}
preserver = username in preservers.keys() and username or ''
item['getPreserver'] = preserver
item['getDatePreserved'] = self.ulocalized_time(DateTime(),
long_format=1)
item['class']['getPreserver'] = 'provisional'
item['class']['getDatePreserved'] = 'provisional'
# Submitting user may not verify results
if item['review_state'] == 'to_be_verified' and \
not checkPermission(VerifyOwnResults, obj):
self_submitted = False
try:
review_history = list(
self.workflow.getInfoFor(obj, 'review_history'))
review_history.reverse()
for event in review_history:
if event.get('action') == 'submit':
if event.get('actor') == member.getId():
self_submitted = True
break
if self_submitted:
item['after']['state_title'] = \
"<img src='++resource++bika.lims.images/submitted-by-current-user.png' title='%s'/>" % \
t(_("Cannot verify: Submitted by current user"))
except Exception:
pass
return item
def process(self):
self._parser.parse()
parsed = self._parser.resume()
self._errors = self._parser.errors
self._warns = self._parser.warns
self._logs = self._parser.logs
self._priorizedsearchcriteria = ''
if parsed == False:
return False
# Allowed analysis states
allowed_ar_states_msg = [t(_(s)) for s in self.getAllowedARStates()]
allowed_an_states_msg = [
t(_(s)) for s in self.getAllowedAnalysisStates()
]
self.log("Allowed Analysis Request states: ${allowed_states}",
mapping={'allowed_states': ', '.join(allowed_ar_states_msg)})
self.log("Allowed analysis states: ${allowed_states}",
mapping={'allowed_states': ', '.join(allowed_an_states_msg)})
# Exclude non existing ACODEs
acodes = []
ancount = 0
arprocessed = []
instprocessed = []
importedars = {}
importedinsts = {}
rawacodes = self._parser.getAnalysisKeywords()
exclude = self.getKeywordsToBeExcluded()
for acode in rawacodes:
if acode in exclude:
continue
service = self.bsc(getKeyword=acode)
if not service:
self.warn('Service keyword ${analysis_keyword} not found',
mapping={"analysis_keyword": acode})
else:
acodes.append(acode)
if len(acodes) == 0:
self.err("Service keywords: no matches found")
searchcriteria = self.getIdSearchCriteria()
#self.log(_("Search criterias: %s") % (', '.join(searchcriteria)))
for objid, results in self._parser.getRawResults().iteritems():
# Allowed more than one result for the same sample and analysis.
# Needed for calibration tests
for result in results:
analyses = self._getZODBAnalyses(objid)
inst = None
if len(analyses) == 0 and self.instrument_uid:
# No registered analyses found, but maybe we need to
# create them first if an instruemnt id has been set in
insts = self.bsc(portal_type='Instrument',
UID=self.instrument_uid)
if len(insts) == 0:
# No instrument found
self.err(
"No Analysis Request with '${allowed_ar_states}' "
"states found, And no QC analyses found for ${object_id}",
mapping={
"allowed_ar_states":
', '.join(allowed_ar_states_msg),
"object_id":
objid
})
self.err("Instrument not found")
continue
inst = insts[0].getObject()
# Create a new ReferenceAnalysis and link it to the Instrument
# Here we have an objid (i.e. R01200012) and
# a dict with results (the key is the AS keyword).
# How can we create a ReferenceAnalysis if we don't know
# which ReferenceSample we might use?
# Ok. The objid HAS to be the ReferenceSample code.
refsample = self.bc(portal_type='ReferenceSample',
id=objid)
if refsample and len(refsample) == 1:
refsample = refsample[0].getObject()
elif refsample and len(refsample) > 1:
# More than one reference sample found!
self.err(
"More than one reference sample found for '${object_id}'",
mapping={"object_id": objid})
continue
else:
# No reference sample found!
self.err("No Reference Sample found for ${object_id}",
mapping={"object_id": objid})
continue
# For each acode, create a ReferenceAnalysis and attach it
# to the Reference Sample
service_uids = []
reference_type = 'b' if refsample.getBlank(
) == True else 'c'
services = self.bsc(portal_type='AnalysisService')
service_uids = [service.UID for service in services \
if service.getObject().getKeyword() in result.keys()]
analyses = inst.addReferences(refsample, service_uids)
elif len(analyses) == 0:
# No analyses found
self.err(
"No Analysis Request with '${allowed_ar_states}' "
"states neither QC analyses found for ${object_id}",
mapping={
"allowed_ar_states":
', '.join(allowed_ar_states_msg),
"object_id": objid
})
continue
# Look for timestamp
capturedate = result.get('DateTime', {}).get('DateTime', None)
if capturedate:
del result['DateTime']
for acode, values in result.iteritems():
if acode not in acodes:
# Analysis keyword doesn't exist
continue
ans = [analysis for analysis in analyses \
if analysis.getKeyword() == acode]
if len(ans) > 1:
self.err(
"More than one analyses found for ${object_id} and ${analysis_keyword}",
mapping={
"object_id": objid,
"analysis_keyword": acode
})
continue
elif len(ans) == 0:
self.err(
"No analyses found for ${object_id} and ${analysis_keyword}",
mapping={
"object_id": objid,
"analysis_keyword": acode
})
continue
analysis = ans[0]
if capturedate:
values['DateTime'] = capturedate
processed = self._process_analysis(objid, analysis, values)
if processed:
ancount += 1
if inst:
# Calibration Test (import to Instrument)
instprocessed.append(inst.UID())
importedinst = inst.title in importedinsts.keys() \
and importedinsts[inst.title] or []
if acode not in importedinst:
importedinst.append(acode)
importedinsts[inst.title] = importedinst
else:
ar = analysis.portal_type == 'Analysis' and analysis.aq_parent or None
if ar and ar.UID:
# Set AR imported info
arprocessed.append(ar.UID())
importedar = ar.getRequestID() in importedars.keys() \
and importedars[ar.getRequestID()] or []
if acode not in importedar:
importedar.append(acode)
importedars[ar.getRequestID()] = importedar
# Create the AttachmentType for mime type if not exists
attuid = None
attachmentType = self.bsc(
portal_type="AttachmentType",
title=self._parser.getAttachmentFileType())
if len(attachmentType) == 0:
try:
folder = self.context.bika_setup.bika_attachmenttypes
obj = _createObjectByType(
"AttachmentType", folder, tmpID())
obj.edit(
title=self._parser.getAttachmentFileType(),
description="Autogenerated file type")
obj.unmarkCreationFlag()
renameAfterCreation(obj)
attuid = obj.UID()
except:
attuid = None
self.err(
"Unable to create the Attachment Type ${mime_type}",
mapping={
"mime_type":
self._parser.getFileMimeType()
})
else:
attuid = attachmentType[0].UID
if attuid is not None:
try:
# Attach the file to the Analysis
wss = analysis.getBackReferences(
'WorksheetAnalysis')
if wss and len(wss) > 0:
#TODO: Mirar si es pot evitar utilitzar el WS i utilitzar directament l'Anàlisi (útil en cas de CalibrationTest)
ws = wss[0]
attachment = _createObjectByType(
"Attachment", ws, tmpID())
attachment.edit(
AttachmentFile=self._parser.
getInputFile(),
AttachmentType=attuid,
AttachmentKeys=
'Results, Automatic import')
attachment.reindexObject()
others = analysis.getAttachment()
attachments = []
for other in others:
if other.getAttachmentFile(
).filename != attachment.getAttachmentFile(
).filename:
attachments.append(other.UID())
attachments.append(attachment.UID())
analysis.setAttachment(attachments)
except:
# self.err(_("Unable to attach results file '${file_name}' to AR ${request_id}",
# mapping={"file_name": self._parser.getInputFile().filename,
# "request_id": ar.getRequestID()}))
pass
# Calculate analysis dependencies
for aruid in arprocessed:
ar = self.bc(portal_type='AnalysisRequest', UID=aruid)
ar = ar[0].getObject()
analyses = ar.getAnalyses()
for analysis in analyses:
analysis = analysis.getObject()
if analysis.calculateResult(True, True):
self.log(
"${request_id} calculated result for '${analysis_keyword}': '${analysis_result}'",
mapping={
"request_id": ar.getRequestID(),
"analysis_keyword": analysis.getKeyword(),
"analysis_result": str(analysis.getResult())
})
# Not sure if there's any reason why ReferenceAnalyses have not
# defined the method calculateResult...
# Needs investigation.
#for instuid in instprocessed:
# inst = self.bsc(portal_type='Instrument',UID=instuid)[0].getObject()
# analyses = inst.getAnalyses()
# for analysis in analyses:
# if (analysis.calculateResult(True, True)):
# self.log(_("%s calculated result for '%s': '%s'") %
# (inst.title, analysis.getKeyword(), str(analysis.getResult())))
for arid, acodes in importedars.iteritems():
acodesmsg = ["Analysis %s" % acod for acod in acodes]
self.log(
"${request_id}: ${analysis_keywords} imported sucessfully",
mapping={
"request_id": arid,
"analysis_keywords": acodesmsg
})
for instid, acodes in importedinsts.iteritems():
acodesmsg = ["Analysis %s" % acod for acod in acodes]
msg = "%s: %s %s" % (instid, ", ".join(acodesmsg),
"imported sucessfully")
self.log(msg)
if self.instrument_uid:
self.log(
"Import finished successfully: ${nr_updated_ars} ARs, "
"${nr_updated_instruments} Instruments and ${nr_updated_results} "
"results updated",
mapping={
"nr_updated_ars": str(len(importedars)),
"nr_updated_instruments": str(len(importedinsts)),
"nr_updated_results": str(ancount)
})
else:
self.log(
"Import finished successfully: ${nr_updated_ars} ARs and "
"${nr_updated_results} results updated",
mapping={
"nr_updated_ars": str(len(importedars)),
"nr_updated_results": str(ancount)
})
