def __init__(self, context, request):
super(ASTPanelView, self).__init__(context, request)
self.title = _("AST Panel")
self.catalog = SETUP_CATALOG
self.contentFilter = {
"portal_type": "Microorganism",
"is_active": True,
"sort_on": "sortable_title",
"sort_order": "ascending",
}
self.omit_form = True
self.show_search = True
self.show_select_column = False
self.show_categories = False
self.show_column_toggles = False
self.fetch_transitions_on_select = False
self.show_workflow_action_buttons = False
# Only the first column is defined here, the rest of columns, that are
# the antibiotics abbreviations are added dynamically
self.columns = collections.OrderedDict((("Microorganism", {
"title": _("Microorganism"),
}), ))
self.review_states = [{
"id": "default",
"title": _("All microorganisms"),
"contentFilter": {},
"columns": self.columns.keys(),
}]
def __init__(self, context, request):
super(ASTPanelFolderView, self).__init__(context, request)
self.catalog = SETUP_CATALOG
self.contentFilter = {
"portal_type": "ASTPanel",
"sort_on": "sortable_title",
"sort_order": "ascending",
}
self.context_actions = {
_c("Add"): {
"url": "++add++ASTPanel",
"icon": "add.png"}
}
self.show_select_column = True
self.columns = collections.OrderedDict((
("Title", {
"title": _c("Title"),
"index": "sortable_title"
}),
("Description", {
"title": _c("Description"),
"index": "Description"
}),
("Microorganisms", {
"title": _("Microorganisms"),
}),
("Antibiotics", {
"title": _("Antibiotics"),
})
))
self.review_states = [
{
"id": "default",
"title": _c("Active"),
"contentFilter": {"is_active": True},
"transitions": [],
"columns": self.columns.keys(),
}, {
"id": "inactive",
"title": _c("Inactive"),
"contentFilter": {'is_active': False},
"transitions": [],
"columns": self.columns.keys(),
}, {
"id": "all",
"title": _c("All"),
"contentFilter": {},
"columns": self.columns.keys(),
},
]
def handle_save(self):
"""Handles the save action
"""
form = self.request.form
# Key uids are antibiotics (columns)
uids = filter(api.is_uid, form.keys())
antibiotics = map(api.get_object_by_uid, uids)
# Generate a transposed dict microorganism->antibiotics
# Add all microorganisms, so analyses without any antibiotic selected
# can also be removed
microorganisms = self.get_microorganisms()
mapping = dict(map(lambda m: (api.get_uid(m), []), microorganisms))
for antibiotic in antibiotics:
abx_uid = api.get_uid(antibiotic)
for uid in form[abx_uid].keys():
mapping.setdefault(uid, []).append(antibiotic)
# Update existing analyses and create new ones
for uid, abx in mapping.items():
microorganism = self.get_object(uid)
self.update_analyses(microorganism, abx)
return self.redirect(_("AST analyses updated"))
class ASTAnalysesViewlet(LabAnalysesViewlet):
"""AST Analyses section viewlet for Sample view
"""
title = _("Antibiotic Sensitivities")
icon_name = "ast_panel"
capture = "ast"
def available(self):
"""Returns true if senaite.ast is installed
"""
return is_installed()
class IMicroorganismBehavior(model.Schema):
gram_stain = schema.Choice(
title=_(u"Gram stain"),
vocabulary="senaite.microorganism.vocabularies.gram_stains",
)
glass = schema.Bool(
title=_(u"GLASS organism"),
description=_(
"Whether this is an infectious organism included in the Global "
"Antimicrobial Resistance Surveillance System (GLASS) for the "
"the collection, analysis and sharing of Antimicrobial Resistance "
"(AMR) data at a global level"),
required=False,
)
multi_resistant = schema.Bool(
title=_(u"MRO Organism"),
description=_(
"Whether this organism is considered multi resistant (MRO)", ),
required=False,
)
mro_phenotype = schema.TextLine(
title=_(u"MRO phenotype"),
required=False,
)
def __init__(self, context, request):
super(ManageResultsView, self).__init__(context, request)
self.contentFilter.update({
"getPointOfCapture": "ast",
"getAncestorsUIDs": [api.get_uid(context)],
"sort_on": "title",
"sort_order": "ascending",
})
self.form_id = "ast_analyses"
self.allow_edit = True
self.show_workflow_action_buttons = True
self.show_search = False
# Add the Microorganism column
new_columns = (("Microorganism", {
"title": _("Microorganism"),
"sortable": False
}), )
old_columns = self.columns.items()
self.columns = OrderedDict(list(new_columns) + list(old_columns))
self.columns["Service"].update({
"title": _("Result"),
})
# Remove the columns we are not interested in from review_states
hide = [
"Method", "Instrument", "Analyst", "DetectionLimitOperand",
"Specification", "Uncertainty", "retested", "Attachments",
"DueDate", "Result", "Hidden"
]
all_columns = self.columns.keys()
all_columns = filter(lambda c: c not in hide, all_columns)
for review_state in self.review_states:
review_state.update({"columns": all_columns})
def get_microorganism_info(self, uid_brain_object):
uid = api.get_uid(uid_brain_object)
obj = api.get_object(uid_brain_object)
title = api.get_title(obj)
params = {
"href": api.get_url(obj),
"value": title,
}
if obj.multi_resistant:
params.update({
"value": "{}*".format(title),
"title": _("Multi-resistant (MRO)")
})
return {
"uid": uid,
"link": get_link(**params),
"title": title,
}
def after_initialize(analysis):
"""Event fired when an analysis is initialized
"""
if analysis.getKeyword() != IDENTIFICATION_KEY:
return
# Get the names list of active microorganisms
query = {"portal_type": "Microorganism", "is_active": True}
names = sorted(map(api.get_title, api.search(query, SETUP_CATALOG)))
# Maybe no microorganisms where identified
names.insert(0, _("No culture growth obtained"))
# Generate the analysis result options
options = zip(range(len(names)), names)
options = map(lambda m: {"ResultValue": m[0], "ResultText": m[1]}, options)
analysis.setResultOptions(options)
analysis.setResultOptionsType("multiselect")
analysis.reindexObject()
class IASTPanelBehavior(model.Schema):
microorganisms = schema.List(
title=_(u"Microorganisms"),
description=_(
"The names of selected microorganisms are displayed as row headers "
"in the sensitivity results entry view. From all microorganisms "
"selected here, only those identified in the Sample are added in "
"results entry view"),
required=True,
value_type=schema.Choice(
source="senaite.ast.vocabularies.microorganisms"))
antibiotics = schema.List(
title=_(u"Antibiotics"),
description=_(
"The abbreviations of selected antibiotics are displayed as "
"column headers in the sensitivity results entry view"),
required=True,
value_type=schema.Choice(
source="senaite.ast.vocabularies.antibiotics"))
zone_size = schema.Bool(
title=_(u"Include zone size in mm"),
description=_(
"When enabled, an additional row for the introduction of the zone "
"size (in mm) is displayed in the results entry view, below "
"resistance call options"),
default=True,
)
selective_reporting = schema.Bool(
title=_(u"Selective reporting"),
description=_(
"When enabled, an additional row to indicate whether the "
"resistance result for each microorganism-antibiotic tuple has to "
"be reported in results report or not"),
default=True,
)
def before_render(self):
# If there are microorganisms identified for the current sample,
# display a new filter "Identified microorganisms" and make it the
# default, so only identified microorganisms are listed
microorganisms = utils.get_identified_microorganisms(self.context)
if microorganisms:
# Get the microorganisms uids
uids = map(api.get_uid, microorganisms)
# Make the original review state not default's
self.listing.review_states[0].update({
"id": "all"
})
# Insert the new "default" review state
self.listing.review_states.insert(0, {
"id": "default",
"title": _("Identified microorganisms"),
"contentFilter": {"UID": uids},
"columns": self.listing.columns.keys()
})
# This program is distributed in the hope that it will be useful, but WITHOUT
# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
# FOR A PARTICULAR PURPOSE. See the GNU General Public License for more
# details.
#
# You should have received a copy of the GNU General Public License along with
# this program; if not, write to the Free Software Foundation, Inc., 51
# Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
#
# Copyright 2020 by it's authors.
# Some rights reserved, see README and LICENSE.
from senaite.ast import messageFactory as _
# Analysis Category name AST Services will be added into
SERVICE_CATEGORY = _("Antibiotic Sensitivity Testing (AST)")
# Keyword of the Analysis Service to be used as the template for the creation
# of zone size (mm) results. This service is automatically created on install
# and is not editable
ZONE_SIZE_KEY = "senaite_ast_zone"
# Keyword of the Analysis Service to be used as the template for the creation
# of AST analyses. This Service is automatically created on install and is not
# editable
RESISTANCE_KEY = "senaite_ast_resistance"
# Keyword of the Analysis Service to be used as the template for the creation
# of analyses that will be used to tell whether the AST result has to be
# reported in results report or not
REPORT_KEY = "senaite_ast_report"
def __init__(self, context, request):
super(ASTPanelReportingView, self).__init__(context, request)
self.title = _("AST Panel Selective Reporting")
self.show_search = False
