def __call__(self, value, *args, **kwargs):
instance = kwargs['instance']
ts = getToolByName(instance, 'translation_service').translate
if instance.REQUEST.get('validated', '') == self.name:
return True
else:
instance.REQUEST['validated'] = self.name
pmins = instance.REQUEST.get('minpanic', {})[0]
pmaxs = instance.REQUEST.get('maxpanic', {})[0]
uids = pmins.keys()
for uid in uids:
pmin = pmins.get(uid, '') == '' and '0' or pmins[uid]
pmax = pmaxs.get(uid, '') == '' and '0' or pmaxs[uid]
# Values must be numbers
try:
pmin = float(pmin)
except:
return ts(_("Validation failed: Panic min value must be "
"numeric"))
try:
pmax = float(pmax)
except:
return ts(_("Validation failed: Panic min value must be "
"numeric"))
if pmin > pmax:
return ts(_("Validation failed: Panic max value must be "
"greater than panic min value"))
return True
def __call__(self):
mtool = getToolByName(self.context, 'portal_membership')
addPortalMessage = self.context.plone_utils.addPortalMessage
if mtool.checkPermission(AddPatient, self.context):
clients = self.context.clients.objectIds()
if clients:
self.context_actions[_('Add')] = {
'url': 'createObject?type_name=Patient',
'icon': '++resource++bika.lims.images/add.png'
}
else:
msg = _("Cannot create patients without any system clients configured.")
addPortalMessage(self.context.translate(msg))
if mtool.checkPermission(ViewPatients, self.context):
self.review_states[0]['transitions'].append({'id':'deactivate'})
self.review_states.append(
{'id': 'inactive',
'title': _('Dormant'),
'contentFilter': {'inactive_state': 'inactive'},
'transitions': [{'id':'activate'}, ],
'columns': ['getPatientID', 'getClientPatientID',
'Title', 'getGender', 'getAgeSplittedStr',
'getBirthDate', 'getCitizenship', 'getPrimaryReferrer']})
self.review_states.append(
{'id': 'all',
'title': _('All'),
'contentFilter':{},
'transitions':[{'id':'empty'}, ],
'columns': ['Title', 'getPatientID', 'getClientPatientID',
'getGender', 'getAgeSplittedStr',
'getBirthDate', 'getCitizenship',
'getPrimaryReferrer']})
stat = self.request.get("%s_review_state" % self.form_id, 'default')
self.show_select_column = stat != 'all'
return super(PatientsView, self).__call__()
def __call__(self):
self.context_actions = {}
wf = getToolByName(self.context, 'portal_workflow')
mtool = getToolByName(self.context, 'portal_membership')
addPortalMessage = self.context.plone_utils.addPortalMessage
PR = self.context.getPrimaryReferrer()
if isActive(self.context):
if mtool.checkPermission(AddAnalysisRequest, PR):
#client contact required
contacts = [
c for c in PR.objectValues('Contact')
if wf.getInfoFor(c, 'inactive_state', '') == 'active'
]
if contacts:
self.context_actions[self.context.translate(_('Add'))] = {
'url': PR.absolute_url() + "/portal_factory/"
"AnalysisRequest/Request new analyses/ar_add",
'icon': '++resource++bika.lims.images/add.png'
}
else:
msg = _(
"Client contact required before request may be submitted"
)
addPortalMessage(self.context.translate(msg))
return super(AnalysisRequestsView, self).__call__()
def update(self):
"""Before template render hook
"""
super(DoctorsView, self).update()
if IDoctors.providedBy(self.context):
# Top-level doctors listing
self.request.set("disable_border", 1)
elif "disable_border" in self.request:
del (self.request["disable_border"])
# By default, only users with AddDoctor permissions for the current
# context can add doctors.
self.context_actions = {
_("Add"): {
"url": "createObject?type_name=Doctor",
"permission": AddDoctor,
"icon": "++resource++bika.lims.images/add.png"
}
}
# If current user is a client contact and current context is not a
# Client, then modify the url for Add action so the Doctor gets created
# inside the Client object the current user belongs to
client = self.get_user_client()
if client and check_permission(AddDoctor, client):
add_url = self.context_actions[_("Add")]["url"]
add_url = "{}/{}".format(api.get_url(client), add_url)
self.context_actions[_("Add")]["url"] = add_url
del (self.context_actions[_("Add")]["permission"])
if self.get_client():
# The current context is a Client, remove the client column
self.remove_column('getPrimaryReferrer')
def before_render(self):
# Rename columns BatchID and ClientBatchID
self.listing.columns["BatchID"]["title"] = _("Case ID")
self.listing.columns["ClientBatchID"]["title"] = _("Client Case ID")
# Change the contentFilter and transitions from review_states
self.update_review_states()
# Additional review_satuses
self.add_review_states()
# Additional columns
self.add_columns()
# Remove unnecessary columns
column_ids = [
"Title",
"BatchDate",
"Description",
]
if self.is_client_user or self.is_in_client:
# Hide client-specific columns
column_ids.extend(["Client", "ClientID"])
self.hide_columns(column_ids)
def __call__(self):
mtool = getToolByName(self.context, 'portal_membership')
if mtool.checkPermission(AddDoctor, self.context):
self.context_actions[_('Add')] = {
'url': 'createObject?type_name=Doctor',
'icon': '++resource++bika.lims.images/add.png'
}
if mtool.checkPermission(ManageDoctors, self.context):
self.review_states[0]['transitions'].append({'id':'deactivate'})
self.review_states.append(
{'id':'inactive',
'title': _('Dormant'),
'contentFilter': {'inactive_state': 'inactive'},
'transitions': [{'id':'activate'}, ],
'columns': ['getDoctorID',
'getFullname',
'getEmailAddress',
'getBusinessPhone',
'getMobilePhone']})
self.review_states.append(
{'id':'all',
'title': _('All'),
'contentFilter':{},
'transitions':[{'id':'empty'}],
'columns': ['getDoctorID',
'getFullname',
'getEmailAddress',
'getBusinessPhone',
'getMobilePhone']})
stat = self.request.get("%s_review_state"%self.form_id, 'default')
self.show_select_column = stat != 'all'
return super(DoctorsView, self).__call__()
def add_review_states(self):
if self.is_external_user:
# If the logged in user is external, there is no need to display
# shared/private filters, it might cause confusion
return
# Do not display the filters unless current context is not inside an
# external client
if not is_from_external_client(self.context):
self.listing.review_states.insert(
1, {
"id": "shared",
"title": _("Open (shared)"),
"contentFilter": {
"review_state": "shared"
},
"transitions": [],
"columns": self.listing.columns.keys(),
})
self.listing.review_states.insert(
2, {
"id": "private",
"title": _("Open (private)"),
"contentFilter": {
"review_state": "private"
},
"transitions": [],
"columns": self.listing.columns.keys(),
})
def __init__(self, context, request):
super(SamplesView, self).__init__(context, request)
# Add Patient fields
self.columns['getPatientID'] = {
'title': _('Patient ID'),
'sortable': False,
'toggle': True
}
self.columns['getClientPatientID'] = {
'title': _("Client PID"),
'sortable': False,
'toggle': True
}
self.columns['getPatient'] = {
'title': _('Patient'),
'sortable': False,
'toggle': True
}
self.columns['getDoctor'] = {
'title': _('Doctor'),
'sortable': False,
'toggle': True
}
for rs in self.review_states:
i = rs['columns'].index('getSampleID') + 1
rs['columns'].insert(i, 'getClientPatientID')
rs['columns'].insert(i, 'getPatientID')
rs['columns'].insert(i, 'getPatient')
rs['columns'].insert(i, 'getDoctor')
def __call__(self, context):
items = [
(_('Email'),'email'),
(_('PDF'), 'pdf')
]
for name, item in getAdapters((context, ), ICustomPubPref):
items.append(item)
return SimpleVocabulary.fromItems(items)
def __init__(self, context, request):
super(PatientsView, self).__init__(context, request)
self.catalog = 'bika_patient_catalog'
self.contentFilter = {'portal_type': 'Patient',
'sort_on': 'sortable_title'}
self.context_actions = {}
self.title = _("Patients")
self.icon = self.portal_url + "/++resource++bika.health.images/patient_big.png"
self.description = ""
self.show_sort_column = False
self.show_select_row = False
self.show_select_column = False
self.pagesize = 25
self.columns = {
'Title': {'title': _('Patient'),
'index': 'sortable_title'},
'getPatientID': {'title': _('Patient ID'),
'index': 'getPatientID'},
'getClientPatientID': {'title': _('Client PID'),
'index': 'getClientPatientID'},
'getGender': {'title': _('Gender'),
'index': 'getGender',
'toggle': True},
'getAgeSplittedStr': {'title': _('Age'),
'index': 'getAgeSplittedStr',
'toggle': True},
'getBirthDate': {'title': _('BirthDate'),
'index': 'getBirthDate',
'toggle': True},
'getCitizenship': {'title': _('Citizenship'),
'index': 'getCitizenship',
'toggle': True},
'getPrimaryReferrer': {'title': _('Primary Referrer'),
'index': 'getPrimaryReferrerTitle',
'toggle': True},
}
self.review_states = [
{'id': 'default',
'title': _('Active'),
'contentFilter': {'inactive_state': 'active'},
'transitions': [],
'columns': ['getPatientID', 'getClientPatientID',
'Title', 'getGender', 'getAgeSplittedStr',
'getBirthDate', 'getCitizenship', 'getPrimaryReferrer']},
]
def __init__(self, context, request):
super(InsuranceCompaniesView, self).__init__(context, request)
self.catalog = 'bika_setup_catalog'
self.contentFilter = {'portal_type': 'InsuranceCompany',
'sort_on': 'sortable_title'}
self.context_actions = {_('Add'):
{'url': 'createObject?type_name=InsuranceCompany',
'icon': '++resource++bika.lims.images/add.png'}}
self.title = self.context.translate(_("Insurance Companies"))
self.icon = self.portal_url + "/++resource++bika.lims.images/laboratory_big.png"
self.description = ""
self.show_sort_column = False
self.show_select_row = False
self.show_select_column = True
self.pagesize = 25
self.columns = {
'Name': {'title': _('Company Name'),
'index':'sortable_title'},
'EmailAddress': {'title': _('Email'),
'toggle': True},
'Phone': {'title': _('Phone'),
'toggle': True},
'Fax': {'title': _('Fax'),
'toggle': False},
'Description': {'title': _('Description'),
'index': 'description',
'toggle': False},
}
self.review_states = [
{'id':'default',
'title': _('Active'),
'contentFilter': {'is_active': True},
'transitions': [{'id':'deactivate'}, ],
'columns': ['Name',
'EmailAddress',
'Phone',
'Fax',
'Description']},
{'id':'inactive',
'title': _('Dormant'),
'contentFilter': {'is_active': False},
'transitions': [{'id':'activate'}, ],
'columns': ['Name',
'EmailAddress',
'Phone',
'Fax',
'Description']},
{'id':'all',
'title': _('All'),
'contentFilter':{},
'columns': ['Name',
'EmailAddress',
'Phone',
'Fax',
'Description']},
]
def __call__(self):
workflow = getToolByName(self.context, 'portal_workflow')
translate = self.context.translate
plone.protect.CheckAuthenticator(self.request)
bc = getToolByName(self.context, 'bika_catalog')
ar = bc(UID=self.request.get('uid', None))
if ar:
ar = ar[0].getObject()
self.ccs = []
self.recipients = []
contact = ar.getContact()
if contact:
email = contact.getEmailAddress()
if email:
self.recipients = [{'uid': contact.UID(),
'name': contact.Title(),
'email': email}]
for cc in ar.getCCContact():
ccemail = cc.getEmailAddress()
if ccemail:
self.ccs.append({'uid': cc.UID(),
'name': cc.Title(),
'email': ccemail})
analyses = ar.getAnalyses()
strans = []
for analysis in analyses:
analysis = analysis.getObject()
astate = workflow.getInfoFor(analysis, 'review_state')
if astate == 'retracted':
continue
panic_alerts = ResultOutOfRange(analysis)()
if panic_alerts:
serviceTitle = analysis.getServiceTitle()
result = analysis.getResult()
strans.append("- {0}, {1}: {2}".format(
serviceTitle, translate(_("Result")), result))
stran = "\n".join(strans)
laboratory = self.context.bika_setup.laboratory
lab_address = "\n".join(laboratory.getPrintAddress())
self.body = translate(
_("Some results from the Analysis Request ${ar} "
"exceeded the panic levels that may indicate an "
"imminent life-threatening condition: \n\n${arlist}\n"
"\n\n${lab_address}",
mapping={'ar': ar.getRequestID(),
'arlist': stran,
'lab_address': lab_address})
)
self.subject = translate(
_("Some results from ${ar} exceeded panic range",
mapping={'ar': ar.getRequestID()})
)
return self.template()
def __init__(self, context, request):
super(ContactsView, self).__init__(context, request)
self.catalog = "portal_catalog"
self.contentFilter = {
'portal_type': 'VaccinationCenterContact',
'sort_on':'sortable_title',
'path': {
"query": "/".join(context.getPhysicalPath()),
"level" : 0
}
}
self.context_actions = {_('Add'):
{'url': 'createObject?type_name=VaccinationCenterContact',
'icon': '++resource++bika.lims.images/add.png'}
}
self.show_table_only = False
self.show_sort_column = False
self.show_select_row = False
self.show_select_column = True
self.pagesize = 50
self.icon = self.portal_url + "/++resource++bika.health.images/vaccinationcenter_contact_big.png"
self.title = _b("Contacts")
self.columns = {
'getFullname': {'title': _('Full Name')},
'getEmailAddress': {'title': _('Email Address')},
'getBusinessPhone': {'title': _('Business Phone')},
'getMobilePhone': {'title': _('Mobile Phone')},
'getFax': {'title': _('Fax')},
}
self.review_states = [
{'id':'default',
'title': _('Active'),
'contentFilter': {'inactive_state': 'active'},
'transitions': [{'id':'deactivate'}, ],
'columns': ['getFullname',
'getEmailAddress',
'getBusinessPhone',
'getMobilePhone',
'getFax']},
{'id':'inactive',
'title': _('Dormant'),
'contentFilter': {'inactive_state': 'inactive'},
'transitions': [{'id':'activate'}, ],
'columns': ['getFullname',
'getEmailAddress',
'getBusinessPhone',
'getMobilePhone',
'getFax']},
{'id':'all',
'title': _('All'),
'contentFilter':{},
'columns': ['getFullname',
'getEmailAddress',
'getBusinessPhone',
'getMobilePhone',
'getFax']},
]
def __init__(self, context, request):
super(SamplesView, self).__init__(context, request)
# Add Patient fields
self.columns['getPatientID'] = {'title': _('Patient ID'), 'toggle': True}
self.columns['getClientPatientID'] = {'title': _("Client PID"), 'toggle': True}
self.columns['getPatient'] = {'title': _('Patient'), 'toggle': True}
for rs in self.review_states:
i = rs['columns'].index('getClientSampleID') + 1
rs['columns'].insert(i, 'getClientPatientID')
rs['columns'].insert(i, 'getPatientID')
rs['columns'].insert(i, 'getPatient')
def __init__(self, context, request):
super(PatientsView, self).__init__(context, request)
self.catalog = 'bika_patient_catalog'
self.contentFilter = {'portal_type': 'Patient',
'sort_on': 'sortable_title'}
self.context_actions = {}
self.title = self.context.translate(_("Patients"))
self.icon = self.portal_url + "/++resource++bika.health.images/patient_big.png"
self.description = ""
self.show_sort_column = False
self.show_select_row = False
self.show_select_column = False
self.pagesize = 25
self.columns = {
'Title': {'title': _('Patient'),
'index': 'sortable_title'},
'getPatientID': {'title': _('Patient ID'),
'index': 'getPatientID'},
'getClientPatientID': {'title': _('Client PID'),
'index': 'getClientPatientID'},
'getGender': {'title': _('Gender'),
'index': 'getGender',
'toggle': True},
'getAgeSplittedStr': {'title': _('Age'),
'index': 'getAgeSplittedStr',
'toggle': True},
'getBirthDate': {'title': _('BirthDate'),
'index': 'getBirthDate',
'toggle': True},
'getCitizenship': {'title': _('Citizenship'),
'index': 'getCitizenship',
'toggle': True},
'getPrimaryReferrer': {'title': _('Primary Referrer'),
'index': 'getPrimaryReferrerTitle',
'toggle': True},
}
self.review_states = [
{'id': 'default',
'title': _b('Active'),
'contentFilter': {'inactive_state': 'active'},
'transitions': [],
'columns': ['getPatientID', 'getClientPatientID',
'Title', 'getGender', 'getAgeSplittedStr',
'getBirthDate', 'getCitizenship', 'getPrimaryReferrer']},
]
def __init__(self, context, request):
super(AnalysisRequestsView, self).__init__(context, request)
self.columns["BatchID"]["title"] = _("Case ID")
# Add Client Patient fields
self.columns["getPatientID"] = {"title": _("Patient ID"), "toggle": True}
self.columns["getClientPatientID"] = {"title": _("Client PID"), "toggle": True}
self.columns["getPatient"] = {"title": _("Patient"), "toggle": True}
for rs in self.review_states:
i = rs["columns"].index("BatchID") + 1
rs["columns"].insert(i, "getClientPatientID")
rs["columns"].insert(i, "getPatientID")
rs["columns"].insert(i, "getPatient")
def __init__(self, context, request):
super(SamplesView, self).__init__(context, request)
# Add Patient fields
self.columns["getPatientID"] = {"title": _("Patient ID"), "toggle": True}
self.columns["getClientPatientID"] = {"title": _("Client PID"), "toggle": True}
self.columns["getPatient"] = {"title": _("Patient"), "toggle": True}
self.columns["getDoctor"] = {"title": _("Doctor"), "toggle": True}
for rs in self.review_states:
i = rs["columns"].index("getSampleID") + 1
rs["columns"].insert(i, "getClientPatientID")
rs["columns"].insert(i, "getPatientID")
rs["columns"].insert(i, "getPatient")
rs["columns"].insert(i, "getDoctor")
def getImmunizationForms(context):
""" Return the current list of immunization forms
"""
# Active immunization entails the introduction of a foreign molecule into the body,
# which causes the body itself to generate immunity against the target. Vaccination
# is an active form of immunization.
# Passive immunization is where pre-synthesized elements of the immune system are
# transferred to a person so that the body does not need to produce these elements
# itself. Currently, antibodies can be used for passive immunization.
types = [
('active', context.translate(_('Active immunization'))),
('passive', context.translate(_('Passive immunization'))),
]
return DisplayList(types)
def getImmunizationForms(context):
""" Return the current list of immunization forms
"""
# Active immunization entails the introduction of a foreign molecule into the body,
# which causes the body itself to generate immunity against the target. Vaccination
# is an active form of immunization.
# Passive immunization is where pre-synthesized elements of the immune system are
# transferred to a person so that the body does not need to produce these elements
# itself. Currently, antibodies can be used for passive immunization.
types = [
('active', context.translate(_('Active immunization'))),
('passive', context.translate(_('Passive immunization'))),
]
return DisplayList(types)
def __init__(self, context, request):
super(DoctorsView, self).__init__(context, request)
# Add new column definitions
self.columns.extend({
'AFerret': {'title': _('A Ferret')},
'AField': {'title': _('A Field')},
})
# all dicts in self.review_states have a list of columns,
# which we must update. We will choose to show the new
# fields in all filter states:
for i in len(self.review_states):
self.review_states[i]['columns'].append('AFerret', 'AField')
def fiddle(self, schema):
# Add panic alert range columns
validator = AnalysisSpecificationPanicValidator()
schema["ResultsRange"].subfields += ("minpanic", "maxpanic")
schema["ResultsRange"].subfield_validators["minpanic"] = validator
schema["ResultsRange"].subfield_validators["maxpanic"] = validator
schema["ResultsRange"].subfield_labels["minpanic"] = _("Min panic")
schema["ResultsRange"].subfield_labels["maxpanic"] = _("Max panic")
srcwidget = schema["ResultsRange"].widget
schema["ResultsRange"].widget = AnalysisSpecificationWidget(
checkbox_bound=srcwidget.checkbox_bound, label=srcwidget.label, description=srcwidget.description
)
return schema
def __init__(self, context, request):
super(AnalysisRequestsView, self).__init__(context, request)
self.patient_catalog = None
self.columns['BatchID']['title'] = _('Case ID')
# Add Client Patient fields
self.columns['getPatientID'] = {
'title': _('Patient ID'),
}
self.columns['getClientPatientID'] = {
'title': _("Client PID"),
'sortable': False,
}
self.columns['getPatient'] = {
'title': _('Patient'),
}
def sendAlertEmail(self):
# Send an alert email
laboratory = self.context.bika_setup.laboratory
subject = self.request.get('subject')
to = self.request.get('to')
body = self.request.get('body')
body = "<br/>".join(body.split("\r\n"))
mime_msg = MIMEMultipart('related')
mime_msg['Subject'] = subject
mime_msg['From'] = formataddr(
(encode_header(laboratory.getName()),
laboratory.getEmailAddress()))
mime_msg['To'] = to
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)
succeed = False
try:
host = getToolByName(self.context, 'MailHost')
host.send(mime_msg.as_string(), immediate=True)
except Exception, msg:
ar = self.context.id
logger.error("Panic level email %s: %s" % (ar, str(msg)))
message = _('Unable to send an email to alert client '
'that some results exceeded the panic levels') \
+ (": %s" % str(msg))
self.addMessage(message, 'warning')
def __call__(self):
url = self.portal.absolute_url()
self.context_actions[_('Add')] = dict(
url="{}{}".format(url, "/batches/createObject?type_name=Batch"),
icon="{}{}".format(url, "/++resource++bika.lims.images/add.png"))
return HealthBatchesView.__call__(self)
def _initFormParams(self):
mtool = getToolByName(self.context, 'portal_membership')
addPortalMessage = self.context.plone_utils.addPortalMessage
if mtool.checkPermission(AddPatient, self.context):
clients = self.context.clients.objectIds()
if clients:
self.context_actions[_b('Add')] = {
'url': 'createObject?type_name=Patient',
'icon': '++resource++bika.lims.images/add.png'
}
else:
msg = _("Cannot create patients without any system clients configured.")
addPortalMessage(self.context.translate(msg))
if mtool.checkPermission(ViewPatients, self.context):
self.review_states[0]['transitions'].append({'id':'deactivate'})
self.review_states.append(
{'id': 'inactive',
'title': _b('Dormant'),
'contentFilter': {'inactive_state': 'inactive'},
'transitions': [{'id':'activate'}, ],
'columns': ['getPatientID', 'getClientPatientID',
'Title', 'getGender', 'getAgeSplittedStr',
'getBirthDate', 'getCitizenship', 'getPrimaryReferrer']})
self.review_states.append(
{'id': 'all',
'title': _b('All'),
'contentFilter':{},
'transitions':[{'id':'empty'}, ],
'columns': ['Title', 'getPatientID', 'getClientPatientID',
'getGender', 'getAgeSplittedStr',
'getBirthDate', 'getCitizenship',
'getPrimaryReferrer']})
stat = self.request.get("%s_review_state" % self.form_id, 'default')
self.show_select_column = stat != 'all'
def before_render(self):
"""Called before the listing renders
"""
super(DoctorBatchListingViewAdapter, self).before_render()
# Remove unnecessary columns
hide = [
"Doctor",
]
self.hide_columns(hide)
# Filter by doctor
query = dict(getDoctorUID=api.get_uid(self.context))
self.listing.contentFilter.update(query)
for rv in self.listing.review_states:
if "contentFilter" not in rv:
rv["contentFilter"] = {}
rv["contentFilter"].update(query)
url = api.get_url(self.context)
self.listing.context_actions = {
_("Add"): {
"url": "{}/createObject?type_name=Batch".format(url),
"permission": AddBatch,
"icon": "++resource++bika.lims.images/add.png"
}
}
def update(self):
"""Called before the listings renders
"""
super(PatientsView, self).update()
# Render the Add button. We need to do this here because patients live
# inside site.patients folder
self.context_actions = {}
patients = api.get_portal().patients
if security.check_permission(AddPatient, patients):
self.context_actions = {
_("Add"): {
"url": "createObject?type_name=Patient",
"icon": "++resource++bika.lims.images/add.png"}
}
# If the current user is a client contact, display those patients that
# belong to same client or that do not belong to any client
client = api.get_current_client()
if client:
query = dict(client_uid=[api.get_uid(client), "-1"])
# We add UID "-1" to also include Patients w/o Client assigned
self.contentFilter.update(query)
for rv in self.review_states:
rv["contentFilter"].update(query)
# If the current context is a Client, remove the title column
if IClient.providedBy(self.context):
self.remove_column('getPrimaryReferrerTitle')
def before_render(self):
# Additional columns
self.add_columns()
# Remove unnecessary columns
self.hide_columns()
# Apply client filter, if necessary
client = api.get_current_client()
if client:
query = dict(getClientUID=api.get_uid(client))
self.listing.contentFilter.update(query)
for rv in self.listing.review_states:
if "contentFilter" not in rv:
rv["contentFilter"] = {}
rv["contentFilter"].update(query)
# Render the Add button
self.listing.context_actions = {}
batches = api.get_portal().batches
if security.check_permission(AddBatch, batches):
url = api.get_url(batches)
self.listing.context_actions = {
_("Add"): {
"url": "{}/createObject?type_name=Batch".format(url),
"icon": "++resource++bika.lims.images/add.png"
}
}
def __call__(self):
self.context_actions[_('Add')] = \
{'url': self.portal.absolute_url() \
+ '/batches/createObject?type_name=Batch',
'icon': self.portal.absolute_url() \
+ '/++resource++bika.lims.images/add.png'}
return BatchFolderContentsView.__call__(self)
def before_render(self):
# Additional columns
self.add_columns()
# Remove unnecessary columns
self.hide_columns()
# Apply client filter, if necessary
client = api.get_current_client()
if client:
query = dict(getClientUID=api.get_uid(client))
self.listing.contentFilter.update(query)
for rv in self.listing.review_states:
if "contentFilter" not in rv:
rv["contentFilter"] = {}
rv["contentFilter"].update(query)
# Render the Add button
self.listing.context_actions = {}
batches = api.get_portal().batches
if security.check_permission(AddBatch, batches):
url = api.get_url(batches)
self.listing.context_actions = {
_("Add"): {
"url": "{}/createObject?type_name=Batch".format(url),
"icon": "++resource++bika.lims.images/add.png"}
}
def sendAlertEmail(self):
# Send an alert email
laboratory = self.context.bika_setup.laboratory
subject = self.request.get('subject')
to = self.request.get('to')
body = self.request.get('body')
body = "<br/>".join(body.split("\r\n"))
mime_msg = MIMEMultipart('related')
mime_msg['Subject'] = subject
mime_msg['From'] = formataddr((encode_header(laboratory.getName()),
laboratory.getEmailAddress()))
mime_msg['To'] = to
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)
succeed = False
try:
host = getToolByName(self.context, 'MailHost')
host.send(mime_msg.as_string(), immediate=True)
except Exception, msg:
ar = self.context.id
logger.error("Panic level email %s: %s" % (ar, str(msg)))
message = _('Unable to send an email to alert client '
'that some results exceeded the panic levels') \
+ (": %s" % str(msg))
self.addMessage(message, 'warning')
def fiddle(self, schema):
# Add panic alert range columns
validator = AnalysisSpecificationPanicValidator()
schema['ResultsRange'].subfields += ('minpanic', 'maxpanic')
schema['ResultsRange'].subfield_validators['minpanic'] = validator
schema['ResultsRange'].subfield_validators['maxpanic'] = validator
schema['ResultsRange'].subfield_labels['minpanic'] = _('Min panic')
schema['ResultsRange'].subfield_labels['maxpanic'] = _('Max panic')
srcwidget = schema['ResultsRange'].widget
schema['ResultsRange'].widget = AnalysisSpecificationWidget(
checkbox_bound=srcwidget.checkbox_bound,
label=srcwidget.label,
description=srcwidget.description,
)
return schema
def update(self):
"""Called before the listings renders
"""
super(PatientsView, self).update()
# Render the Add button. We need to do this here because patients live
# inside site.patients folder
self.context_actions = {}
patients = api.get_portal().patients
if security.check_permission(AddPatient, patients):
self.context_actions = {
_("Add"): {
"url": "createObject?type_name=Patient",
"icon": "++resource++bika.lims.images/add.png"
}
}
# If the current user is a client contact, display those patients that
# belong to same client or that do not belong to any client
client = api.get_current_client()
if client:
query = dict(client_uid=[api.get_uid(client), "-1"])
# We add UID "-1" to also include Patients w/o Client assigned
self.contentFilter.update(query)
for rv in self.review_states:
rv["contentFilter"].update(query)
# If the current context is a Client, remove the title column
if IClient.providedBy(self.context):
self.remove_column('getPrimaryReferrerTitle')
def folderitem(self, obj, item, index):
# Date of Birth
dob = obj.getBirthDate
item['getBirthDate'] = dob and self.ulocalized_time(dob) or ""
try:
item["age"] = dob and get_age_ymd(dob) or ""
except:
# Wrong date??
msg = _("Date of Birth might be wrong")
img = get_image("exclamation.png", title=msg)
item["replace"]["age"] = img
# make the columns patient title, patient ID and client patient ID
# redirect to the Analysis Requests of the patient
ars_url = "{}/{}".format(api.get_url(obj), "analysisrequests")
for column in ['Title', 'getPatientID', 'getClientPatientID']:
value = getattr(obj, column, None)
if value:
item["replace"][column] = get_link(ars_url, value)
# Display the internal/external icons, but only if the logged-in user
# does not belong to an external client
if not self.is_external_user():
# Renders an icon (shared/private/warn) next to the title of the
# item based on the client
item["before"]["Title"] = get_client_aware_html_image(obj)
return item
def process_form(self):
num_analyses = 0
uids_arr = [
ar.get('Analyses', []) for ar in self.valid_states.values()
]
for arr in uids_arr:
num_analyses += len(arr)
if num_analyses < 50:
# Do not process Asynchronously
return AnalysisRequestSubmit.process_form(self)
# Only load asynchronously if queue ar-create is available
task_queue = queryUtility(ITaskQueue, name='ar-create')
if task_queue is None:
# ar-create queue not registered, create synchronously
return AnalysisRequestSubmit.process_form(self)
else:
# ar-create queue registered, create asynchronously
path = self.request.PATH_INFO
path = path.replace('_submit_async', '_submit')
task_queue.add(path, method='POST')
msg = _('One job added to the Analysis Request creation queue')
self.context.plone_utils.addPortalMessage(msg, 'info')
return json.dumps({'success': 'With taskqueue'})
def _initFormParams(self):
mtool = getToolByName(self.context, 'portal_membership')
addPortalMessage = self.context.plone_utils.addPortalMessage
can_add_patients = mtool.checkPermission(AddPatient, self.context)
if not can_add_patients and IClient.providedBy(self.context):
# The user logged in is a Contact from this Client?
# Tip: when a client contact is created, bika.lims assigns that
# contact as the owner of the client, so he/she can access to the
# Client he/she is owner of but not to the rest of Clients.
# See bika.lims.browser.contact._link_user(userid)
client = self.context
owners = client.users_with_local_role('Owner')
member = mtool.getAuthenticatedMember()
can_add_patients = member.id in owners
if can_add_patients:
# TODO Performance tweak. Is this really needed?
clients = self.context.clients.objectIds()
if clients:
add_patient_url = '{}/patients/createObject?type_name=Patient'\
.format(self.portal_url)
self.context_actions[_b('Add')] = {
'url': add_patient_url,
'icon': '++resource++bika.lims.images/add.png'
}
else:
msg = _("Cannot create patients without any system clients "
"configured.")
addPortalMessage(self.context.translate(msg))
if mtool.checkPermission(ViewPatients, self.context):
self.review_states[0]['transitions'].append({'id': 'deactivate'})
self.review_states.append({
'id': 'inactive',
'title': _b('Dormant'),
'contentFilter': {
'inactive_state': 'inactive'
},
'transitions': [
{
'id': 'activate'
},
],
'columns': self.get_columns()
})
self.review_states.append({
'id': 'all',
'title': _b('All'),
'contentFilter': {},
'transitions': [
{
'id': 'empty'
},
],
'columns': self.get_columns()
})
stat = self.request.get("%s_review_state" % self.form_id,
'default')
self.show_select_column = stat != 'all'
def fiddle(self, schema):
# Add panic alert range columns
validator = AnalysisSpecificationPanicValidator()
schema['ResultsRange'].subfields += ('minpanic', 'maxpanic')
schema['ResultsRange'].subfield_validators['minpanic'] = validator
schema['ResultsRange'].subfield_validators['maxpanic'] = validator
schema['ResultsRange'].subfield_labels['minpanic'] = _('Min panic')
schema['ResultsRange'].subfield_labels['maxpanic'] = _('Max panic')
srcwidget = schema['ResultsRange'].widget
schema['ResultsRange'].widget = AnalysisSpecificationWidget(
checkbox_bound=srcwidget.checkbox_bound,
label=srcwidget.label,
description=srcwidget.description,
)
return schema
def __call__(self):
self.context_actions[_('Add')] = \
{'url': self.portal.absolute_url() \
+ '/batches/createObject?type_name=Batch',
'icon': self.portal.absolute_url() \
+ '/++resource++bika.lims.images/add.png'}
return BatchFolderContentsView.__call__(self)
def validate_form(self):
# Create new Anonymous Patients as needed
uc = getToolByName(self.context, 'uid_catalog')
cpt = getToolByName(self.context, CATALOG_PATIENT_LISTING)
form = self.request.form
formc = self.request.form.copy()
state = json.loads(formc.get('state'))
if not state:
# BaseClass deals with state
BaseClass.validate_form(self)
return
for key in state.keys():
values = state[key].copy()
patuid = values.get('Patient', '')
if patuid == '' and values.get('Analyses') != []:
msg = t(_('Required fields have no values: Patient'))
ajax_form_error(self.errors, arnum=key, message=msg)
continue
elif patuid == 'anonymous':
clientpatientid = values.get('ClientPatientID', '')
# Check if has already been created
proxies = cpt(getClientPatientID=clientpatientid)
if proxies and len(proxies) > 0:
patient = proxies[0].getObject()
else:
# Create an anonymous patient
client = uc(UID=values['Client'])[0].getObject()
_id = client.patients.invokeFactory('Patient', id=tmpID())
patient = client.patients[_id]
patient.edit(Anonymous=1,
Gender="dk",
PrimaryReferrer=client.UID(),
Firstname=_("AP"),
Surname=clientpatientid,
ClientPatientID=clientpatientid)
patient.unmarkCreationFlag()
patient.reindexObject()
client.reindexObject()
renameAfterCreation(patient)
values['Patient'] = patient.UID()
state[key] = values
formc['state'] = json.JSONEncoder().encode(state)
self.request.form = formc
BaseClass.validate_form(self)
def get_client_aware_html_image(obj):
"""Renders an icon based on the client the object belongs to
"""
if is_from_external_client(obj):
icon_info = ("lock.png", _("Private, from an external client"))
elif is_from_internal_client(obj):
if api.get_review_status(obj) == "shared":
icon_info = ("share.png", _("Shared, from an internal client"))
else:
icon_info = ("share_lock.png",
_("From an internal client, but not shared"))
else:
logger.warn("No client assigned for {}".format(repr(obj)))
icon_info = ("exclamation_red.png", _("No client assigned"))
return get_html_image(icon_info[0], title=icon_info[1])
def __init__(self, context, request):
super(HistoricResultsView, self).__init__(context, request)
self._rows = None
self._dates = None
path = "/++resource++bika.health.images"
self.icon = self.portal_url + path + "/historicresults_big.png"
self.title = self.context.translate(_("Historic Results"))
self.description = ""
def fiddle(self, schema):
schema['title'].required = False
schema['title'].widget.visible = False
schema['description'].required = False
schema['description'].widget.visible = False
schema['BatchLabels'].widget.visible = False
schema['ClientBatchID'].widget.label = _("Client Case ID")
return schema
def __init__(self, context, request):
super(AnalysisRequestsView, self).__init__(context, request)
self.columns['BatchID']['title'] = _('Case ID')
# Add Client Patient fields
self.columns['getPatientID'] = {
'title': _('Patient ID'),
}
self.columns['getClientPatientID'] = {
'title': _("Client PID"),
'sortable': False,
}
self.columns['getPatientTitle'] = {
'title': _('Patient'),
}
self.columns['getDoctorTitle'] = {
'title': _('Doctor'),
}
def __init__(self, context, request):
super(VaccinationCentersView, self).__init__(context, request)
self.catalog = 'bika_setup_catalog'
self.contentFilter = {'portal_type': 'VaccinationCenter',
'sort_on': 'getName'}
self.context_actions = {_('Add'):
{'url': 'createObject?type_name=VaccinationCenter',
'icon': '++resource++bika.lims.images/add.png'}}
self.title = self.context.translate(_("Vaccination Centers"))
self.icon = self.portal_url + "/++resource++bika.health.images/vaccinationcenter_big.png"
self.description = ""
self.show_sort_column = False
self.show_select_row = False
self.show_select_column = True
self.pagesize = 50
self.columns = {
'Name': {'title': _('Name'),
'index': 'getName'},
'Email': {'title': _('Email'),
'toggle': True},
'Phone': {'title': _('Phone'),
'toggle': True},
'Fax': {'title': _('Fax'),
'toggle': True},
}
self.review_states = [
{'id':'default',
'title': _('Active'),
'contentFilter': {'is_active': True},
'transitions': [{'id':'deactivate'}, ],
'columns': ['Name',
'Email',
'Phone',
'Fax']},
{'id':'inactive',
'title': _('Dormant'),
'contentFilter': {'is_active': False},
'transitions': [{'id':'activate'}, ],
'columns': ['Name',
'Email',
'Phone',
'Fax']},
{'id':'all',
'title': _('All'),
'contentFilter':{},
'columns': ['Name',
'Email',
'Phone',
'Fax']},
]
def setup_panic_alerts(portal):
"""Setups the template texts for panic alert email's subject and body
"""
email_body = _(
"Some results from the Sample ${sample_id} exceeded the panic levels "
"that may indicate an imminent life-threatening condition:\n\n"
"${analyses}\n\n--\n${lab_address}")
ploneapi.portal.set_registry_record("senaite.panic.email_body", email_body)
def __init__(self, context, request):
super(DoctorsView, self).__init__(context, request)
self.contentFilter = {'portal_type': 'Doctor',
'sort_on': 'sortable_title'}
self.context_actions = {}
self.title = self.context.translate(_("Doctors"))
self.icon = self.portal_url + "/++resource++bika.health.images/doctor_big.png"
self.description = ""
self.show_sort_column = False
self.show_select_row = False
self.show_select_column = False
self.pagesize = 50
self.columns = {
'getDoctorID': {'title': _('Doctor ID'),
'index': 'getDoctorID'},
'getFullname': {'title': _('Full Name'),
'index': 'getFullname'},
'getEmailAddress': {'title': _('Email Address')},
'getBusinessPhone': {'title': _('Business Phone')},
'getMobilePhone': {'title': _('Mobile Phone')},
}
self.review_states = [
{'id':'default',
'title': _('Active'),
'contentFilter': {'inactive_state': 'active'},
'transitions': [],
'columns': ['getDoctorID',
'getFullname',
'getEmailAddress',
'getBusinessPhone',
'getMobilePhone']},
]
def __call__(self):
mtool = getToolByName(self.context, 'portal_membership')
if mtool.checkPermission(AddDoctor, self.context):
self.context_actions[_('Add')] = {
'url': 'createObject?type_name=Doctor',
'icon': '++resource++bika.lims.images/add.png'
}
if mtool.checkPermission(ManageDoctors, self.context):
self.review_states[0]['transitions'].append({'id': 'deactivate'})
self.review_states.append({
'id':
'inactive',
'title':
_('Dormant'),
'contentFilter': {
'inactive_state': 'inactive'
},
'transitions': [
{
'id': 'activate'
},
],
'columns': [
'getDoctorID', 'getFullname', 'getEmailAddress',
'getBusinessPhone', 'getMobilePhone'
]
})
self.review_states.append({
'id':
'all',
'title':
_('All'),
'contentFilter': {},
'transitions': [{
'id': 'empty'
}],
'columns': [
'getDoctorID', 'getFullname', 'getEmailAddress',
'getBusinessPhone', 'getMobilePhone'
]
})
stat = self.request.get("%s_review_state" % self.form_id,
'default')
self.show_select_column = stat != 'all'
return super(DoctorsView, self).__call__()
def getEthnicitiesVocabulary(self, instance=None):
"""
Obtain all the ethnicities registered in the system and returns them as a list
"""
bsc = getToolByName(self, "bika_setup_catalog")
items = [(c.UID, c.Title) for c in bsc(portal_type="Ethnicity", inactive_state="active")]
items.sort(lambda x, y: cmp(x[1], y[1]))
items.insert(0, ("", t(_(""))))
return DisplayList(items)
def __init__(self, context, request):
super(DoctorsView, self).__init__(context, request)
# Add new column definitions
self.columns.extend({
'AFerret': {
'title': _('A Ferret')
},
'AField': {
'title': _('A Field')
},
})
# all dicts in self.review_states have a list of columns,
# which we must update. We will choose to show the new
# fields in all filter states:
for i in len(self.review_states):
self.review_states[i]['columns'].append('AFerret', 'AField')
def __init__(self,context,request):
super(SymptomsView,self).__init__(context,request)
self.catalog='bika_setup_catalog'
self.contentFilter={'portal_type': 'Symptom',
'sort_on': 'sortable_title'}
self.context_actions={_('Add'):
{'url': 'createObject?type_name=Symptom',
'icon': '++resource++bika.lims.images/add.png'}}
self.title=_("Symptoms")
self.icon = self.portal_url + "/++resource++bika.health.images/symptom_big.png"
self.description=_("Additional Symptoms not covered by ICD codes, can be entered here.")
self.show_sort_column=False
self.show_select_row=False
self.show_select_column=True
self.pagesize=25
self.columns={
'Title': {'title': _('Symptom'),
'index':'sortable_title'},
'Description': {'title': _('Description'),
'index': 'description',
'toggle': True},
'Gender': {'title': _('Gender'),
'index': 'gender',
'toggle': True},
}
self.review_states=[
{'id':'default',
'title': _('Active'),
'contentFilter': {'inactive_state': 'active'},
'transitions': [{'id':'deactivate'},],
'columns': ['Title',
'Description',
'Gender']},
{'id':'inactive',
'title': _('Dormant'),
'contentFilter': {'inactive_state': 'inactive'},
'transitions': [{'id':'activate'},],
'columns': ['Title',
'Description',
'Gender']},
{'id':'all',
'title': _('All'),
'contentFilter':{},
'columns': ['Title',
'Description',
'Gender']},
]
def __init__(self,context,request):
super(SymptomsView,self).__init__(context,request)
self.catalog='bika_setup_catalog'
self.contentFilter={'portal_type': 'Symptom',
'sort_on': 'sortable_title'}
self.context_actions={_('Add'):
{'url': 'createObject?type_name=Symptom',
'icon': '++resource++bika.lims.images/add.png'}}
self.title=self.context.translate(_("Symptoms"))
self.icon = self.portal_url + "/++resource++bika.health.images/symptom_big.png"
self.description=_("Additional Symptoms not covered by ICD codes, can be entered here.")
self.show_sort_column=False
self.show_select_row=False
self.show_select_column=True
self.pagesize=25
self.columns={
'Title': {'title': _('Symptom'),
'index':'sortable_title'},
'Description': {'title': _('Description'),
'index': 'description',
'toggle': True},
'Gender': {'title': _('Gender'),
'index': 'getGender',
'toggle': True},
}
self.review_states=[
{'id':'default',
'title': _('Active'),
'contentFilter': {'is_active': True},
'transitions': [{'id':'deactivate'},],
'columns': ['Title',
'Description',
'Gender']},
{'id':'inactive',
'title': _('Dormant'),
'contentFilter': {'is_active': False},
'transitions': [{'id':'activate'},],
'columns': ['Title',
'Description',
'Gender']},
{'id':'all',
'title': _('All'),
'contentFilter':{},
'columns': ['Title',
'Description',
'Gender']},
]
def __init__(self, context, request):
super(EpidemiologicalYearsView, self).__init__(context, request)
self.catalog = 'bika_setup_catalog'
self.contentFilter = {'portal_type': 'EpidemiologicalYear',
'sort_on': 'sortable_title'}
self.context_actions = {_('Add'):
{'url': 'createObject?type_name=EpidemiologicalYear',
'icon': '++resource++bika.lims.images/add.png'}}
self.title = self.context.translate(_("Epidemiological Years"))
self.icon = self.portal_url + "/++resource++bika.health.images/epidemiologicalyear_big.png"
self.description = _("Epidemiological year calendars")
self.show_sort_column = False
self.show_select_row = False
self.show_select_column = True
self.pagesize = 25
self.columns = {
'Title': {'title': _('Title'),
'index':'sortable_title'},
'getStartDate': {'title':_('Start Date'),
'index':'getStartDate'},
'getEndDate': {'title':_('End Date'),
'index': 'getEndDate'},
}
self.review_states = [
{'id':'default',
'title': _('Active'),
'contentFilter': {'inactive_state': 'active'},
'transitions': [{'id':'deactivate'}, ],
'columns': ['Title',
'getStartDate',
'getEndDate']},
{'id':'inactive',
'title': _('Dormant'),
'contentFilter': {'inactive_state': 'inactive'},
'transitions': [{'id':'activate'}, ],
'columns': ['Title',
'getStartDate',
'getEndDate']},
{'id':'all',
'title': _('All'),
'contentFilter':{},
'columns': ['Title',
'getStartDate',
'getEndDate']},
]
def __init__(self, context, request):
BrowserView.__init__(self, context, request)
self.context = context
self.request = request
self._rows = None
self._dates = None
path = "/++resource++bika.health.images"
self.icon = self.portal_url + path + "/historicresults_big.png"
self.title = self.context.translate(_("Historic Results"))
self.description = ""
def fiddle(self, schema):
schema['title'].required = False
schema['title'].widget.visible = False
schema['description'].required = False
schema['description'].widget.visible = False
schema['BatchLabels'].widget.visible = False
schema['ClientBatchID'].widget.label = _("Client Case ID")
schema['BatchDate'].widget.visible = False
schema['InheritedObjectsUI'].widget.visible = False
return schema
def getEthnicitiesVocabulary(self, instance=None):
"""
Obtain all the ethnicities registered in the system and returns them as a list
"""
bsc = getToolByName(self, 'bika_setup_catalog')
items = [(c.UID, c.Title)
for c in bsc(portal_type='Ethnicity', is_active=True)]
items.sort(lambda x, y: cmp(x[1], y[1]))
items.insert(0, ('', t(_(''))))
return DisplayList(items)
def __call__(self):
# Create new Anonymous Patients as needed
uc = getToolByName(self.context, 'uid_catalog')
bpc = getToolByName(self.context, 'bika_patient_catalog')
form = self.request.form
formc = self.request.form.copy()
state = json.loads(formc['state'])
for key in state.keys():
values = state[key].copy()
patuid = values.get('Patient', '')
if patuid == '' and values.get('Analyses') != []:
msg = t(_('Required fields have no values: Patient'))
ajax_form_error(self.errors, arnum=key, message=msg)
continue
elif patuid == 'anonymous':
clientpatientid = values.get('ClientPatientID', '')
# Check if has already been created
proxies = bpc(getClientPatientID=clientpatientid)
if proxies and len(proxies) > 0:
patient = proxies[0].getObject()
else:
# Create an anonymous patient
client = uc(UID=values['Client'])[0].getObject()
_id = client.patients.invokeFactory('Patient', id=tmpID())
patient = client.patients[_id]
patient.edit(Anonymous = 1,
Gender = "dk",
PrimaryReferrer = client.UID(),
Firstname = _("AP"),
Surname = clientpatientid,
ClientPatientID = clientpatientid)
patient.unmarkCreationFlag()
patient.reindexObject()
client.reindexObject()
renameAfterCreation(patient)
values['Patient']=patient.UID()
state[key] = values
formc['state'] = json.JSONEncoder().encode(state)
self.request.form = formc
return BaseClass.__call__(self)
def getEthnicitiesVocabulary(self, instance=None):
"""
Obtain all the ethnicities registered in the system and returns them as a list
"""
bsc = getToolByName(self, 'bika_setup_catalog')
items = [(c.UID, c.Title)
for c in bsc(portal_type='Ethnicity',
is_active=True)]
items.sort(lambda x, y: cmp(x[1], y[1]))
items.insert(0, ('', t(_(''))))
return DisplayList(items)
def fiddle(self, schema):
schema['title'].required = False
schema['title'].widget.visible = False
schema['description'].required = False
schema['description'].widget.visible = False
schema['BatchLabels'].widget.visible = False
schema['ClientBatchID'].widget.label = _("Client Case ID")
schema['BatchDate'].widget.visible = False
schema['InheritedObjectsUI'].widget.visible = False
schema['Doctor'].required = isCaseDoctorIsMandatory()
return schema