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 __call__(self, result=None, specification=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"]
if spec:
rngstr = " ({0} {1}, {2}, {3})".format(t(_("min")),
str(spec['min']),
t(_("max")),
str(spec['max']))
else:
rngstr = ""
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 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 __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['min']),
t(_("max")), str(spec['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 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 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 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 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 __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 ${retracted_request_id}.',
mapping={
'retracted_request_id': safe_unicode(par.getRequestID())
})
self.context.plone_utils.addPortalMessage(t(message), 'info')
template = LogView.__call__(self)
return template
def __init__(self, context, request):
BikaListingView.__init__(self, context, request)
self.show_sort_column = False
self.show_select_row = False
self.show_select_column = False
self.show_workflow_action_buttons = False
self.pagesize = 999999
self.icon = self.portal_url + "/++resource++bika.lims.images/%s_big.png" % \
context.portal_type.lower()
self.title = to_utf8(self.context.Title()) + " " + t(_("Log"))
self.description = ""
self.columns = {
'Version': {'title': _('Version'), 'sortable': False},
'Date': {'title': _('Date'), 'sortable': False},
'User': {'title': _('User'), 'sortable': False},
'Action': {'title': _('Action'), 'sortable': False},
'Description': {'title': _('Description'), 'sortable': False},
}
self.review_states = [
{'id': 'default',
'title': 'All',
'contentFilter': {},
'columns': ['Version',
'Date',
'User',
'Action',
'Description']},
]
def __call__(self):
ar = self.context
workflow = getToolByName(ar, 'portal_workflow')
# If is a retracted AR, show the link to child AR and show a warn msg
if workflow.getInfoFor(ar, 'review_state') == 'invalid':
childar = hasattr(ar, 'getChildAnalysisRequest') \
and ar.getChildAnalysisRequest() or None
childid = childar and childar.getRequestID() or None
message = _('This Analysis Request has been withdrawn and is shown '
'for trace-ability purposes only. Retest: '
'${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 __call__(self, result=None, specification=None, **kwargs):
workflow = getToolByName(self.context, 'portal_workflow')
astate = workflow.getInfoFor(self.context, 'review_state')
if astate == 'retracted':
return {}
result = self.context.getResult() if result is None else result
alerts = {}
path = '++resource++bika.lims.images'
uid = self.context.UID()
try:
indet = result.startswith("<") or result.startswith(">")
except AttributeError:
indet = False
if indet:
alert = {
'field': 'Result',
'icon': path + '/exclamation.png',
'msg': t(_("Indeterminate result"))
}
if uid in alerts:
alerts[uid].append(alert)
else:
alerts[uid] = [
alert,
]
return alerts
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 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')
# 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 self.review_state:
for transition_dict in self.review_state['transitions']:
if transition_dict['id'] in transitions:
actions.append(transitions[transition_dict['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 custom_actions: %s. (complete list: %s)."%(action,actions))
# and these are removed
if 'hide_transitions' in self.review_state:
actions = [a for a in actions
if a['id'] not in self.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 self.review_state['some_state']['custom_actions'] attribute
# on the BikaListingView, add these actions to the list.
if 'custom_actions' in self.review_state:
for action in self.review_state['custom_actions']:
if isinstance(action, dict) \
and 'id' in action:
actions.append(action)
for a,action in enumerate(actions):
actions[a]['title'] = t(PMF(actions[a]['id'] + "_transition_title"))
return actions
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)
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 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 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 dependencies.dependency import DT2dt
from dependencies.dependency 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.getReferenceManufacturer() and \
obj.getReferenceManufacturer().Title() or ''
items[x]['Definition'] = obj.getReferenceDefinition() and \
obj.getReferenceDefinition().Title() or ''
items[x]['DateSampled'] = self.ulocalized_time(
obj.getDateSampled())
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 __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 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 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 dependencies.dependency import DT2dt
from dependencies.dependency 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.getReferenceManufacturer() and \
obj.getReferenceManufacturer().Title() or ''
items[x]['Definition'] = obj.getReferenceDefinition() and \
obj.getReferenceDefinition().Title() or ''
items[x]['DateSampled'] = self.ulocalized_time(obj.getDateSampled())
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 getDataInterfaces(context):
""" Return the current list of data interfaces
"""
from 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 _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 _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 _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 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 "By Yasir"
# 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 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 "By Yasir"
# 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 __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 = 999999
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, 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 __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 __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 __call__(self, **kwargs):
site = getSite()
request = aq_get(site, 'REQUEST', None)
catalog = getToolByName(site, self.catalog)
if 'inactive_state' in catalog.indexes():
self.contentFilter['inactive_state'] = 'active'
if 'cancellation_state' in catalog.indexes():
self.contentFilter['cancellation_state'] = 'active'
self.contentFilter.update(**kwargs)
objects = (b.getObject() for b in catalog(self.contentFilter))
items = []
for obj in objects:
key = obj[self.key]
key = callable(key) and key() or key
value = obj[self.value]
value = callable(value) and value() or value
items.append((key, t(value)))
return DisplayList(items)
def __call__(self, **kwargs):
site = getSite()
request = aq_get(site, 'REQUEST', None)
catalog = getToolByName(site, self.catalog)
if 'inactive_state' in catalog.indexes():
self.contentFilter['inactive_state'] = 'active'
if 'cancellation_state' in catalog.indexes():
self.contentFilter['cancellation_state'] = 'active'
self.contentFilter.update(**kwargs)
objects = (b.getObject() for b in catalog(self.contentFilter))
items = []
for obj in objects:
key = obj[self.key]
key = callable(key) and key() or key
value = obj[self.value]
value = callable(value) and value() or value
items.append((key, t(value)))
return DisplayList(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 artemplates(self):
""" Return applicable client and Lab ARTemplate records
"""
res = []
templates = []
client = self.context.portal_type == 'AnalysisRequest' \
and self.context.aq_parent or self.context
for template in client.objectValues("ARTemplate"):
if isActive(template):
templates.append((template.Title(), template))
templates.sort(lambda x, y: cmp(x[0], y[0]))
res += templates
templates = []
for template in self.context.bika_setup.bika_artemplates.objectValues("ARTemplate"):
if isActive(template):
lab = t(_('Lab'))
title = to_utf8(template.Title())
templates.append(("%s: %s" % (lab, title), template))
templates.sort(lambda x, y: cmp(x[0], y[0]))
res += templates
return res
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'}
return super(ClientAnalysisRequestsView, self).__call__()
def analysisprofiles(self):
""" Return applicable client and Lab AnalysisProfile records
"""
res = []
profiles = []
client = self.context.portal_type == 'AnalysisRequest' \
and self.context.aq_parent or self.context
for profile in client.objectValues("AnalysisProfile"):
if isActive(profile):
profiles.append((profile.Title(), profile))
profiles.sort(lambda x, y: cmp(x[0], y[0]))
res += profiles
profiles = []
for profile in self.context.bika_setup.bika_analysisprofiles.objectValues("AnalysisProfile"):
if isActive(profile):
lab = t(_('Lab'))
title = to_utf8(profile.Title())
profiles.append(("%s: %s" % (lab, title), profile))
profiles.sort(lambda x, y: cmp(x[0], y[0]))
res += profiles
return res
def __call__(self, result=None, **kwargs):
translate = self.context.translate
path = "++resource++bika.lims.images"
alerts = {}
for name, adapter in getAdapters((self.context,), IResultOutOfRange):
ret = adapter(result, **kwargs)
if not ret:
continue
out_of_range = ret["out_of_range"]
spec = ret["spec_values"]
if out_of_range:
message = t(
_(
"Relative percentage difference, ${variation_here} %, is out of valid range (${variation} %))",
mapping={"variation_here": ret["variation_here"], "variation": ret["variation"]},
)
)
alerts[self.context.UID()] = [{"msg": message, "field": "Result", "icon": path + "/exclamation.png"}]
break
return alerts
def __call__(self, result=None, specification=None, **kwargs):
workflow = getToolByName(self.context, 'portal_workflow')
astate = workflow.getInfoFor(self.context, 'review_state')
if astate == 'retracted':
return {}
result = self.context.getResult() if result is None else result
alerts = {}
path = '++resource++bika.lims.images'
uid = self.context.UID()
try:
indet = result.startswith("<") or result.startswith(">")
except AttributeError:
indet = False
if indet:
alert = {'field': 'Result',
'icon': path + '/exclamation.png',
'msg': t(_("Indeterminate result"))}
if uid in alerts:
alerts[uid].append(alert)
else:
alerts[uid] = [alert, ]
return alerts
def artemplates(self):
""" Return applicable client and Lab ARTemplate records
"""
res = []
templates = []
client = self.context.portal_type == 'AnalysisRequest' \
and self.context.aq_parent or self.context
for template in client.objectValues("ARTemplate"):
if isActive(template):
templates.append((template.Title(), template))
templates.sort(lambda x, y: cmp(x[0], y[0]))
res += templates
templates = []
for template in self.context.bika_setup.bika_artemplates.objectValues(
"ARTemplate"):
if isActive(template):
lab = t(_('Lab'))
title = to_utf8(template.Title())
templates.append(("%s: %s" % (lab, title), template))
templates.sort(lambda x, y: cmp(x[0], y[0]))
res += templates
return res
def analysisprofiles(self):
""" Return applicable client and Lab AnalysisProfile records
"""
res = []
profiles = []
client = self.context.portal_type == 'AnalysisRequest' \
and self.context.aq_parent or self.context
for profile in client.objectValues("AnalysisProfile"):
if isActive(profile):
profiles.append((profile.Title(), profile))
profiles.sort(lambda x, y: cmp(x[0], y[0]))
res += profiles
profiles = []
for profile in self.context.bika_setup.bika_analysisprofiles.objectValues(
"AnalysisProfile"):
if isActive(profile):
lab = t(_('Lab'))
title = to_utf8(profile.Title())
profiles.append(("%s: %s" % (lab, title), profile))
profiles.sort(lambda x, y: cmp(x[0], y[0]))
res += profiles
return res
def __call__(self, result=None, **kwargs):
translate = self.context.translate
path = "++resource++bika.lims.images"
alerts = {}
for name, adapter in getAdapters((self.context, ), IResultOutOfRange):
ret = adapter(result, **kwargs)
if not ret:
continue
out_of_range = ret["out_of_range"]
spec = ret["spec_values"]
if out_of_range:
message = t(_("Relative percentage difference, ${variation_here} %, is out of valid range (${variation} %))",
mapping={'variation_here': ret['variation_here'], 'variation': ret['variation'], } ))
alerts[self.context.UID()] = [
{
'msg': message,
'field': 'Result',
'icon': path + '/exclamation.png',
},
]
break
return alerts
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 __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'
})
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'
})
# 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 __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
}
}
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': {
'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_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':
('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 __call__(self):
bsc = getToolByName(self.context, 'bika_setup_catalog')
bac = getToolByName(self.context, 'bika_analysis_catalog')
self.report_content = {}
parms = []
headings = {}
headings['header'] = _("Analyses out of range")
headings['subheader'] = _("Analyses results out of specified range")
count_all = 0
query = {"portal_type": "Analysis",
"sort_order": "reverse"}
spec_uid = self.request.form.get("spec", False)
spec_obj = None
spec_title = ""
if spec_uid:
brains = bsc(UID=spec_uid)
if brains:
spec_obj = brains[0].getObject()
spec_title = spec_obj.Title()
parms.append(
{"title": _("Range spec"),
"value": spec_title,
"type": "text"})
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
col_heads = [_('Client'),
_('Request'),
_('Sample type'),
_('Sample point'),
_('Category'),
_('Analysis'),
_('Result'),
_('Min'),
_('Max'),
_('Status'),
]
if isAttributeHidden('Sample', 'SamplePoint'):
col_heads.remove(_('Sample point'))
formats = {'columns': 10,
'col_heads': col_heads,
'class': '',
}
datalines = []
for a_proxy in bac(query):
analysis = a_proxy.getObject()
if analysis.getResult():
try:
result = float(analysis.getResult())
except:
continue
else:
continue
keyword = analysis.getKeyword()
# determine which specs to use for this particular analysis
# 1) if a spec is given in the query form, use it.
# 2) if a spec is entered directly on the analysis, use it.
# otherwise just continue to the next object.
spec_dict = False
if spec_obj:
rr = spec_obj.getResultsRangeDict()
if keyword in rr:
spec_dict = rr[keyword]
else:
ar = analysis.aq_parent
rr = dicts_to_dict(ar.getResultsRange(), 'keyword')
if keyword in rr:
spec_dict = rr[keyword]
else:
continue
if not spec_dict:
continue
try:
spec_min = float(spec_dict['min'])
spec_max = float(spec_dict['max'])
except ValueError:
continue
if spec_min <= result <= spec_max:
continue
# check if in shoulder: out of range, but in acceptable
# error percentage
shoulder = False
error = 0
try:
error = float(spec_dict.get('error', '0'))
except:
error = 0
pass
error_amount = (result / 100) * error
error_min = result - error_amount
error_max = result + error_amount
if ((result < spec_min) and (error_max >= spec_min)) or \
((result > spec_max) and (error_min <= spec_max)):
shoulder = True
dataline = []
dataitem = {'value': analysis.getClientTitle()}
dataline.append(dataitem)
dataitem = {'value': analysis.getRequestID()}
dataline.append(dataitem)
dataitem = {'value': analysis.aq_parent.getSampleTypeTitle()}
dataline.append(dataitem)
if isAttributeHidden('Sample', 'SamplePoint'):
dataitem = {'value': analysis.aq_parent.getSamplePointTitle()}
dataline.append(dataitem)
dataitem = {'value': analysis.getCategoryTitle()}
dataline.append(dataitem)
dataitem = {'value': analysis.getServiceTitle()}
dataline.append(dataitem)
if shoulder:
dataitem = {'value': analysis.getResult(),
'img_after': '++resource++bika.lims.images/exclamation.png'}
else:
dataitem = {'value': analysis.getResult()}
dataline.append(dataitem)
dataitem = {'value': spec_dict['min']}
dataline.append(dataitem)
dataitem = {'value': spec_dict['max']}
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 out of range for period'),
'colspan': 9,
'class': 'total_label'}
footline.append(footitem)
footitem = {'value': count_all}
footline.append(footitem)
footlines.append(footline)
# report footer data
footnotes = []
footline = []
footitem = {'value': _('Analysis result within error range'),
'img_before': '++resource++bika.lims.images/exclamation.png'
}
footline.append(footitem)
footnotes.append(footline)
self.report_content = {
'headings': headings,
'parms': parms,
'formats': formats,
'datalines': datalines,
'footings': footlines,
'footnotes': footnotes}
title = t(headings['header'])
return {'report_title': title,
'report_data': self.template()}
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'] = formatDuration(
self.context, 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'] = formatDuration(
self.context, 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': formatDuration(self.context, 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': formatDuration(self.context, 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 Import(context, request):
""" Read biodrop analysis results
"""
infile = request.form['filename']
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 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]
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 = BioDropImporter(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, full_objects = False):
"""
>>> portal = layer['portal']
>>> portal_url = portal.absolute_url()
>>> from plone.app.testing import SITE_OWNER_NAME
>>> from plone.app.testing import SITE_OWNER_PASSWORD
Test page batching https://github.com/bikalabs/Bika-LIMS/issues/1276
When visiting the second page, the Water sampletype should be displayed:
>>> browser = layer['getBrowser'](portal, loggedIn=True, username=SITE_OWNER_NAME, password=SITE_OWNER_PASSWORD)
>>> browser.open(portal_url+"/bika_setup/bika_sampletypes/folder_view?",
... "list_pagesize=10&list_review_state=default&list_pagenumber=2")
>>> browser.contents
'...Water...'
"""
#self.contentsMethod = self.context.getFolderContents
if not hasattr(self, 'contentsMethod'):
self.contentsMethod = getToolByName(self.context, self.catalog)
context = aq_inner(self.context)
plone_layout = getMultiAdapter((context, self.request), name = u'plone_layout')
plone_utils = getToolByName(context, 'plone_utils')
plone_view = getMultiAdapter((context, self.request), name = u'plone')
portal_properties = getToolByName(context, 'portal_properties')
portal_types = getToolByName(context, 'portal_types')
workflow = getToolByName(context, 'portal_workflow')
site_properties = portal_properties.site_properties
norm = getUtility(IIDNormalizer).normalize
if self.request.get('show_all', '').lower() == 'true' \
or self.show_all == True \
or self.pagesize == 0:
show_all = True
else:
show_all = False
pagenumber = int(self.request.get('pagenumber', 1) or 1)
pagesize = self.pagesize
start = (pagenumber - 1) * pagesize
end = start + pagesize - 1
if (hasattr(self, 'And') and self.And) \
or (hasattr(self, 'Or') and self.Or):
# if contentsMethod is capable, we do an AdvancedQuery.
if hasattr(self.contentsMethod, 'makeAdvancedQuery'):
aq = self.contentsMethod.makeAdvancedQuery(self.contentFilter)
if hasattr(self, 'And') and self.And:
tmpAnd = And()
for q in self.And:
tmpAnd.addSubquery(q)
aq &= tmpAnd
if hasattr(self, 'Or') and self.Or:
tmpOr = Or()
for q in self.Or:
tmpOr.addSubquery(q)
aq &= tmpOr
brains = self.contentsMethod.evalAdvancedQuery(aq)
else:
# otherwise, self.contentsMethod must handle contentFilter
brains = self.contentsMethod(self.contentFilter)
else:
brains = self.contentsMethod(self.contentFilter)
results = []
self.page_start_index = 0
current_index = -1
for i, obj in enumerate(brains):
# we don't know yet if it's a brain or an object
path = hasattr(obj, 'getPath') and obj.getPath() or \
"/".join(obj.getPhysicalPath())
if hasattr(obj, 'getObject'):
obj = obj.getObject()
# check if the item must be rendered or not (prevents from
# doing it later in folderitems) and dealing with paging
if not self.isItemAllowed(obj):
continue
# 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
current_index += 1
if not show_all and not (start <= current_index <= end):
results.append(dict(path = path, uid = obj.UID()))
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 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 = [],
# "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 = {},
)
try:
rs = workflow.getInfoFor(obj, 'review_state')
st_title = workflow.getTitleForStateOnType(rs, obj.portal_type)
st_title = t(PMF(st_title))
except:
rs = 'active'
st_title = None
if rs:
results_dict['review_state'] = rs
for state_var, state in states.items():
if not st_title:
st_title = workflow.getTitleForStateOnType(
state, obj.portal_type)
results_dict[state_var] = state
results_dict['state_title'] = st_title
# extra classes for individual fields on this item { field_id : "css classes" }
results_dict['class'] = {}
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 hasattr(obj, key):
# if the key is already in the results dict
# then we don't replace it's value
if results_dict.has_key(key):
continue
value = getattr(obj, key)
if callable(value):
value = value()
results_dict[key] = value
results.append(results_dict)
return results
def folderitems(self, full_objects=False):
workflow = getToolByName(self.context, "portal_workflow")
items = BikaListingView.folderitems(self)
mtool = getToolByName(self.context, 'portal_membership')
member = mtool.getAuthenticatedMember()
roles = member.getRoles()
hideclientlink = 'RegulatoryInspector' in roles \
and 'Manager' not in roles \
and 'LabManager' not in roles \
and 'LabClerk' not in roles
for x in range(len(items)):
if 'obj' not in items[x]:
continue
obj = items[x]['obj']
sample = obj.getSample()
if getSecurityManager().checkPermission(EditResults, obj):
url = obj.absolute_url() + "/manage_results"
else:
url = obj.absolute_url()
items[x]['Client'] = obj.aq_parent.Title()
if (hideclientlink is False):
items[x]['replace']['Client'] = "<a href='%s'>%s</a>" % \
(obj.aq_parent.absolute_url(), obj.aq_parent.Title())
items[x]['Creator'] = self.user_fullname(obj.Creator())
items[x]['getRequestID'] = obj.getRequestID()
items[x]['replace']['getRequestID'] = "<a href='%s'>%s</a>" % \
(url, items[x]['getRequestID'])
items[x]['getSample'] = sample
items[x]['replace']['getSample'] = \
"<a href='%s'>%s</a>" % (sample.absolute_url(), sample.Title())
if obj.getAnalysesNum():
items[x]['getAnalysesNum'] = str(
obj.getAnalysesNum()[0]) + '/' + str(
obj.getAnalysesNum()[1])
else:
items[x]['getAnalysesNum'] = ''
batch = obj.getBatch()
if batch:
items[x]['BatchID'] = batch.getBatchID()
items[x]['replace']['BatchID'] = "<a href='%s'>%s</a>" % \
(batch.absolute_url(), items[x]['BatchID'])
else:
items[x]['BatchID'] = ''
val = obj.Schema().getField('SubGroup').get(obj)
items[x]['SubGroup'] = val.Title() if val else ''
samplingdate = obj.getSample().getSamplingDate()
items[x]['SamplingDate'] = self.ulocalized_time(samplingdate,
long_format=1)
items[x]['getDateReceived'] = self.ulocalized_time(
obj.getDateReceived())
items[x]['getDatePublished'] = self.ulocalized_time(
obj.getDatePublished())
deviation = sample.getSamplingDeviation()
items[x]['SamplingDeviation'] = deviation and deviation.Title(
) or ''
priority = obj.getPriority()
items[x]['Priority'] = '' # priority.Title()
items[x]['getStorageLocation'] = sample.getStorageLocation(
) and sample.getStorageLocation().Title() or ''
items[x]['AdHoc'] = sample.getAdHoc() and True or ''
after_icons = ""
state = 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 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:
items[x]['after']['getRequestID'] = after_icons
items[x]['Created'] = self.ulocalized_time(obj.created())
contact = obj.getContact()
if contact:
items[x]['ClientContact'] = contact.Title()
items[x]['replace']['ClientContact'] = "<a href='%s'>%s</a>" % \
(contact.absolute_url(), contact.Title())
else:
items[x]['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)
items[x]['class']['getDateSampled'] = 'provisional'
sampler = sample.getSampler().strip()
if sampler:
items[x]['replace']['getSampler'] = self.user_fullname(
sampler)
if 'Sampler' in member.getRoles() and not sampler:
sampler = member.id
items[x]['class']['getSampler'] = 'provisional'
else:
datesampled = ''
sampler = ''
items[x]['getDateSampled'] = datesampled
items[x]['getSampler'] = sampler
# sampling workflow - inline edits for Sampler and Date Sampled
checkPermission = self.context.portal_membership.checkPermission
state = workflow.getInfoFor(obj, 'review_state')
if state == 'to_be_sampled' \
and checkPermission(SampleSample, obj) \
and not samplingdate > DateTime():
items[x]['required'] = ['getSampler', 'getDateSampled']
items[x]['allow_edit'] = ['getSampler', 'getDateSampled']
samplers = getUsers(sample,
['Sampler', 'LabManager', 'Manager'])
username = member.getUserName()
users = [({
'ResultValue': u,
'ResultText': samplers.getValue(u)
}) for u in samplers]
items[x]['choices'] = {'getSampler': users}
Sampler = sampler and sampler or \
(username in samplers.keys() and username) or ''
items[x]['getSampler'] = Sampler
# These don't exist on ARs
# XXX This should be a list of preservers...
items[x]['getPreserver'] = ''
items[x]['getDatePreserved'] = ''
# inline edits for Preserver and Date Preserved
checkPermission = self.context.portal_membership.checkPermission
if checkPermission(PreserveSample, obj):
items[x]['required'] = ['getPreserver', 'getDatePreserved']
items[x]['allow_edit'] = ['getPreserver', 'getDatePreserved']
preservers = getUsers(obj,
['Preserver', 'LabManager', 'Manager'])
username = member.getUserName()
users = [({
'ResultValue': u,
'ResultText': preservers.getValue(u)
}) for u in preservers]
items[x]['choices'] = {'getPreserver': users}
preserver = username in preservers.keys() and username or ''
items[x]['getPreserver'] = preserver
items[x]['getDatePreserved'] = self.ulocalized_time(
DateTime(), long_format=1)
items[x]['class']['getPreserver'] = 'provisional'
items[x]['class']['getDatePreserved'] = 'provisional'
# Submitting user may not verify results
if items[x]['review_state'] == 'to_be_verified' and \
not checkPermission(VerifyOwnResults, obj):
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') == member.getId():
self_submitted = True
break
if self_submitted:
items[x]['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
# Hide Preservation/Sampling workflow actions if the edit columns
# are not displayed.
toggle_cols = self.get_toggle_cols()
new_states = []
for i, state in enumerate(self.review_states):
if state['id'] == self.review_state:
if 'getSampler' not in toggle_cols \
or 'getDateSampled' not in toggle_cols:
if 'hide_transitions' in state:
state['hide_transitions'].append('sample')
else:
state['hide_transitions'] = [
'sample',
]
if 'getPreserver' not in toggle_cols \
or 'getDatePreserved' not in toggle_cols:
if 'hide_transitions' in state:
state['hide_transitions'].append('preserve')
else:
state['hide_transitions'] = [
'preserve',
]
new_states.append(state)
self.review_states = new_states
return items
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']
sample = formitems['sample']
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]
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 = SysmexXS500iImporter(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 Import(context, request):
""" Abaxix VetScan VS2 analysis 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 = AbaxisVetScanCSVVS2Parser(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 = AbaxisVetScanVS2Importer(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 __call__(self):
form = self.request.form
CheckAuthenticator(self.request.form)
PostOnly(self.request.form)
uc = getToolByName(self.context, 'uid_catalog')
bsc = getToolByName(self.context, 'bika_setup_catalog')
portal_catalog = getToolByName(self.context, 'portal_catalog')
# Load the form data from request.state. If anything goes wrong here,
# put a bullet through the whole process.
try:
states = json.loads(form['state'])
except Exception as e:
message = t(
_('Badly formed state: ${errmsg}',
mapping={'errmsg': e.message}))
ajax_form_error(self.errors, message=message)
return json.dumps({'errors': self.errors})
# Validate incoming form data
required = [
field.getName()
for field in AnalysisRequestSchema.fields() if field.required
] + ["Analyses"]
# First remove all states which are completely empty; if all
# required fields are not present, we assume that the current
# AR had no data entered, and can be ignored
nonblank_states = {}
for arnum, state in states.items():
for key, val in state.items():
if val \
and "%s_hidden" % key not in state \
and not key.endswith('hidden'):
nonblank_states[arnum] = state
break
# in valid_states, all ars that pass validation will be stored
valid_states = {}
for arnum, state in nonblank_states.items():
# Secondary ARs are a special case, these fields are not required
if state.get('Sample', ''):
if 'SamplingDate' in required:
required.remove('SamplingDate')
if 'SampleType' in required:
required.remove('SampleType')
# fields flagged as 'hidden' are not considered required because
# they will already have default values inserted in them
for fieldname in required:
if fieldname + '_hidden' in state:
required.remove(fieldname)
missing = [f for f in required if not state.get(f, '')]
# If there are required fields missing, flag an error
if missing:
msg = t(
_('Required fields have no values: '
'${field_names}',
mapping={'field_names': ', '.join(missing)}))
ajax_form_error(self.errors, arnum=arnum, message=msg)
continue
# This ar is valid!
valid_states[arnum] = state
# - Expand lists of UIDs returned by multiValued reference widgets
# - Transfer _uid values into their respective fields
for arnum in valid_states.keys():
for field, value in valid_states[arnum].items():
if field.endswith('_uid') and ',' in value:
valid_states[arnum][field] = value.split(',')
elif field.endswith('_uid'):
valid_states[arnum][field] = value
if self.errors:
return json.dumps({'errors': self.errors})
# Now, we will create the specified ARs.
ARs = []
for arnum, state in valid_states.items():
# Create the Analysis Request
ar = create_analysisrequest(
portal_catalog(UID=state['Client'])[0].getObject(),
self.request, state)
ARs.append(ar.Title())
# Display the appropriate message after creation
if len(ARs) > 1:
message = _('Analysis requests ${ARs} were successfully created.',
mapping={'ARs': safe_unicode(', '.join(ARs))})
else:
message = _('Analysis request ${AR} was successfully created.',
mapping={'AR': safe_unicode(ARs[0])})
self.context.plone_utils.addPortalMessage(message, 'info')
# Automatic label printing won't print "register" labels for Secondary. ARs
new_ars = [ar for ar in ARs if ar[-2:] == '01']
if 'register' in self.context.bika_setup.getAutoPrintStickers() \
and new_ars:
return json.dumps({
'success':
message,
'stickers':
new_ars,
'stickertemplate':
self.context.bika_setup.getAutoStickerTemplate()
})
else:
return json.dumps({'success': message})
def __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"] = _("Analyses per analysis service")
headings["subheader"] = _("Number of analyses requested per analysis service")
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"})
date_query = formatDateQuery(self.context, "Published")
if date_query:
query["getDatePublished"] = date_query
published = formatDateParms(self.context, "Published")
parms.append({"title": _("Published"), "value": published, "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"})
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"})
# and now lets do the actual report lines
formats = {"columns": 2, "col_heads": [_("Analysis service"), _("Number of analyses")], "class": ""}
datalines = []
count_all = 0
for cat in sc(portal_type="AnalysisCategory", sort_on="sortable_title"):
dataline = [{"value": cat.Title, "class": "category_heading", "colspan": 2}]
datalines.append(dataline)
for service in sc(portal_type="AnalysisService", getCategoryUID=cat.UID, sort_on="sortable_title"):
query["getServiceUID"] = service.UID
analyses = bc(query)
count_analyses = len(analyses)
dataline = []
dataitem = {"value": service.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,
}
title = t(headings["header"])
if self.request.get("output_format", "") == "CSV":
import csv
import StringIO
import datetime
fieldnames = ["Analysis Service", "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:
if len(row) == 1:
# category heading thingy
continue
dw.writerow({"Analysis Service": 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="analysesperservice_%s.csv"' % date)
self.request.RESPONSE.write(report_data)
else:
return {"report_title": title, "report_data": self.template()}
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"] = formatDuration(self.context, 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"] = formatDuration(self.context, 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": formatDuration(self.context, 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": formatDuration(self.context, 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 workflow_action_retract_ar(self):
workflow = getToolByName(self.context, 'portal_workflow')
# AR should be retracted
# Can't transition inactive ARs
if not isActive(self.context):
message = _('Item is inactive.')
self.context.plone_utils.addPortalMessage(message, 'info')
self.request.response.redirect(self.context.absolute_url())
return
# 1. Copies the AR linking the original one and viceversa
ar = self.context
newar = self.cloneAR(ar)
# 2. The old AR gets a status of 'invalid'
workflow.doActionFor(ar, 'retract_ar')
# 3. The new AR copy opens in status 'to be verified'
changeWorkflowState(newar, 'bika_ar_workflow', 'to_be_verified')
# 4. The system immediately alerts the client contacts who ordered
# the results, per email and SMS, that a possible mistake has been
# picked up and is under investigation.
# A much possible information is provided in the email, linking
# to the AR online.
laboratory = self.context.bika_setup.laboratory
lab_address = "<br/>".join(laboratory.getPrintAddress())
mime_msg = MIMEMultipart('related')
mime_msg['Subject'] = t(_("Erroneus result publication from ${request_id}",
mapping={"request_id": ar.getRequestID()}))
mime_msg['From'] = formataddr(
(encode_header(laboratory.getName()),
laboratory.getEmailAddress()))
to = []
contact = ar.getContact()
if contact:
to.append(formataddr((encode_header(contact.Title()),
contact.getEmailAddress())))
for cc in ar.getCCContact():
formatted = formataddr((encode_header(cc.Title()),
cc.getEmailAddress()))
if formatted not in to:
to.append(formatted)
managers = self.context.portal_groups.getGroupMembers('LabManagers')
for bcc in managers:
user = self.portal.acl_users.getUser(bcc)
if user:
uemail = user.getProperty('email')
ufull = user.getProperty('fullname')
formatted = formataddr((encode_header(ufull), uemail))
if formatted not in to:
to.append(formatted)
mime_msg['To'] = ','.join(to)
aranchor = "<a href='%s'>%s</a>" % (ar.absolute_url(),
ar.getRequestID())
naranchor = "<a href='%s'>%s</a>" % (newar.absolute_url(),
newar.getRequestID())
addremarks = ('addremarks' in self.request
and ar.getRemarks()) \
and ("<br/><br/>"
+ _("Additional remarks:")
+ "<br/>"
+ ar.getRemarks().split("===")[1].strip()
+ "<br/><br/>") \
or ''
sub_d = dict(request_link=aranchor,
new_request_link=naranchor,
remarks=addremarks,
lab_address=lab_address)
body = Template("Some errors have been detected in the results report "
"published from the Analysis Request $request_link. The Analysis "
"Request $new_request_link has been created automatically and the "
"previous has been invalidated.<br/>The possible mistake "
"has been picked up and is under investigation.<br/><br/>"
"$remarks $lab_address").safe_substitute(sub_d)
msg_txt = MIMEText(safe_unicode(body).encode('utf-8'),
_subtype='html')
mime_msg.preamble = 'This is a multi-part MIME message.'
mime_msg.attach(msg_txt)
try:
host = getToolByName(self.context, 'MailHost')
host.send(mime_msg.as_string(), immediate=True)
except Exception as msg:
message = _('Unable to send an email to alert lab '
'client contacts that the Analysis Request has been '
'retracted: ${error}',
mapping={'error': safe_unicode(msg)})
self.context.plone_utils.addPortalMessage(message, 'warning')
message = _('${items} invalidated.',
mapping={'items': ar.getRequestID()})
self.context.plone_utils.addPortalMessage(message, 'warning')
self.request.response.redirect(newar.absolute_url())
def __call__(self):
form = self.request.form
CheckAuthenticator(self.request.form)
PostOnly(self.request.form)
uc = getToolByName(self.context, 'uid_catalog')
bsc = getToolByName(self.context, 'bika_setup_catalog')
portal_catalog = getToolByName(self.context, 'portal_catalog')
# Load the form data from request.state. If anything goes wrong here,
# put a bullet through the whole process.
try:
states = json.loads(form['state'])
except Exception as e:
message = t(_('Badly formed state: ${errmsg}',
mapping={'errmsg': e.message}))
ajax_form_error(self.errors, message=message)
return json.dumps({'errors': self.errors})
# Validate incoming form data
required = [field.getName() for field
in AnalysisRequestSchema.fields()
if field.required] + ["Analyses"]
# First remove all states which are completely empty; if all
# required fields are not present, we assume that the current
# AR had no data entered, and can be ignored
nonblank_states = {}
for arnum, state in states.items():
for key, val in state.items():
if val \
and "%s_hidden" % key not in state \
and not key.endswith('hidden'):
nonblank_states[arnum] = state
break
# in valid_states, all ars that pass validation will be stored
valid_states = {}
for arnum, state in nonblank_states.items():
# Secondary ARs are a special case, these fields are not required
if state.get('Sample', ''):
if 'SamplingDate' in required:
required.remove('SamplingDate')
if 'SampleType' in required:
required.remove('SampleType')
# fields flagged as 'hidden' are not considered required because
# they will already have default values inserted in them
for fieldname in required:
if fieldname + '_hidden' in state:
required.remove(fieldname)
missing = [f for f in required if not state.get(f, '')]
# If there are required fields missing, flag an error
if missing:
msg = t(_('Required fields have no values: '
'${field_names}',
mapping={'field_names': ', '.join(missing)}))
ajax_form_error(self.errors, arnum=arnum, message=msg)
continue
# This ar is valid!
valid_states[arnum] = state
# - Expand lists of UIDs returned by multiValued reference widgets
# - Transfer _uid values into their respective fields
for arnum in valid_states.keys():
for field, value in valid_states[arnum].items():
if field.endswith('_uid') and ',' in value:
valid_states[arnum][field] = value.split(',')
elif field.endswith('_uid'):
valid_states[arnum][field] = value
if self.errors:
return json.dumps({'errors': self.errors})
# Now, we will create the specified ARs.
ARs = []
for arnum, state in valid_states.items():
# Create the Analysis Request
ar = create_analysisrequest(
portal_catalog(UID=state['Client'])[0].getObject(),
self.request,
state
)
ARs.append(ar.Title())
# Display the appropriate message after creation
if len(ARs) > 1:
message = _('Analysis requests ${ARs} were successfully created.',
mapping={'ARs': safe_unicode(', '.join(ARs))})
else:
message = _('Analysis request ${AR} was successfully created.',
mapping={'AR': safe_unicode(ARs[0])})
self.context.plone_utils.addPortalMessage(message, 'info')
# Automatic label printing won't print "register" labels for Secondary. ARs
new_ars = [ar for ar in ARs if ar[-2:] == '01']
if 'register' in self.context.bika_setup.getAutoPrintStickers() \
and new_ars:
return json.dumps({
'success': message,
'stickers': new_ars,
'stickertemplate': self.context.bika_setup.getAutoStickerTemplate()
})
else:
return json.dumps({'success': message})
