bika.health.setuphandlers.setup_id_formatting() - Code Metrics - senaite/senaite.health - Measure and Improve Code Quality continuously with Scrutinizer

bika.health.setuphandlers.setup_id_formatting() C
last analyzed 2020-02-18 09:40 UTC

↳ Parent: bika.health.setuphandlers

Complexity

Conditions

Size

Total Lines	34
Code Lines	29

Duplication

Lines	0
Ratio	0 %

Importance

Changes

Metric	Value
eloc	29
dl	0
loc	34
rs	6.6666
c	0
b	0
f	0
cc	9
nop	2

# -*- coding: utf-8 -*-
#
# This file is part of SENAITE.HEALTH.
#
# SENAITE.HEALTH is free software: you can redistribute it and/or modify it
# under the terms of the GNU General Public License as published by the Free
# Software Foundation, version 2.
#
# 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 2018-2019 by it's authors.
# Some rights reserved, see README and LICENSE.

import itertools

from Acquisition import aq_base
from Products.CMFCore import permissions
from Products.CMFCore.permissions import AccessContentsInformation
from Products.CMFCore.permissions import ListFolderContents
from Products.CMFCore.permissions import View
from Products.CMFCore.utils import getToolByName
from plone import api as ploneapi

from bika.health import bikaMessageFactory as _
from bika.health import logger
from bika.health.catalog import \
    getCatalogDefinitions as getCatalogDefinitionsHealth
from bika.health.catalog import getCatalogExtensions
from bika.health.config import DEFAULT_PROFILE_ID
from bika.health.permissions import ViewPatients
from bika.lims import api
from bika.lims.catalog import \
    getCatalogDefinitions as getCatalogDefinitionsLIMS
from bika.lims.catalog import setup_catalogs
from bika.lims.idserver import renameAfterCreation
from bika.lims.permissions import AddAnalysisRequest
from bika.lims.permissions import AddBatch
from bika.lims.utils import tmpID


class Empty(object):
    pass


ROLES = [
    # Tuple of (role, permissions)
    # NOTE: here we only expect permissions that belong to other products and
    #       plone, cause health-specific permissions for this role are
    #       explicitly set in profile/rolemap.xml
    ("Doctor", [View, AccessContentsInformation, ListFolderContents]),
    ("Client", [AddBatch])
]

GROUPS = [
    # Tuple of (group_name, roles_group
    ("Doctors", ["Member", "Doctor"], ),
]

ID_FORMATTING = [
    {
        # P000001, P000002
        "portal_type": "Patient",
        "form": "P{seq:06d}",
        "prefix": "patient",
        "sequence_type": "generated",
        "counter_type": "",
        "split_length": 1,
    }, {
        # D0001, D0002, D0003
        "portal_type": "Doctor",
        "form": "D{seq:04d}",
        "prefix": "doctor",
        "sequence_type": "generated",
        "counter_type": "",
        "split_length": 1,
    }
]


def post_install(portal_setup):
    """Runs after the last import step of the *default* profile
    This handler is registered as a *post_handler* in the generic setup profile
    :param portal_setup: SetupTool
    """
    logger.info("SENAITE Health post-install handler [BEGIN]")
    context = portal_setup._getImportContext(DEFAULT_PROFILE_ID)
    portal = context.getSite()
    # Setup catalogs
    # TODO use upgrade.utils.setup_catalogs instead!
    setup_health_catalogs(portal)

    # Setup portal permissions
    setup_roles_permissions(portal)

    # Setup user groups (e.g. Doctors)
    setup_user_groups(portal)

    # Setup site structure
    setup_site_structure(context)

    # Setup javascripts
    setup_javascripts(portal)

    # Setup content actions
    setup_content_actions(portal)

    # Setup ID formatting for Health types
    setup_id_formatting(portal)

    # Setup default ethnicities
    setup_ethnicities(portal)

    # Allow patients inside clients
    # Note: this should always be run if core's typestool is reimported
    allow_patients_inside_clients(portal)

    # Reindex the top level folder in the portal and setup to fix missing icons
    reindex_content_structure(portal)

    # When installing senaite health together with core, health's skins are not
    # set before core's, even if after-before is set in profiles/skins.xml
    # Ensure health's skin layer(s) always gets priority over core's
    portal_setup.runImportStepFromProfile(DEFAULT_PROFILE_ID, "skins")

    # Setup default email body and subject for panic alerts
    setup_panic_alerts(portal)

    logger.info("SENAITE Health post-install handler [DONE]")


def setup_user_groups(portal):
    logger.info("Setup User Groups ...")
    portal_groups = portal.portal_groups
    for group_name, roles in GROUPS:
        if group_name not in portal_groups.listGroupIds():
            portal_groups.addGroup(group_name, title=group_name, roles=roles)
            logger.info("Group '{}' with roles '{}' added"
                        .format(group_name, ", ".join(roles)))
        else:
            logger.info("Group '{}' already exist [SKIP]".format(group_name))
    logger.info("Setup User Groups [DONE]")


def setup_roles_permissions(portal):
    """Setup the top-level permissions for new roles. The new role is added to
    the roles that already have the permission granted (acquire=1)
    """
    logger.info("Setup roles permissions ...")
    for role_name, permissions in ROLES:
        for permission in permissions:
            add_permission_for_role(portal, permission, role_name)

    # Add "Add AnalysisRequest" permission for Clients in base analysisrequests
    # This makes the "Add" button to appear in AnalysisRequestsFolder view
    analysis_requests = portal.analysisrequests
    add_permission_for_role(analysis_requests, AddAnalysisRequest, "Client")
    logger.info("Setup roles permissions [DONE]")


def add_permission_for_role(folder, permission, role):
    """Grants a permission to the given role and given folder
    :param folder: the folder to which the permission for the role must apply
    :param permission: the permission to be assigned
    :param role: role to which the permission must be granted
    :return True if succeed, otherwise, False
    """
    roles = filter(lambda perm: perm.get('selected') == 'SELECTED',
                   folder.rolesOfPermission(permission))
    roles = map(lambda perm_role: perm_role['name'], roles)
    if role in roles:
        # Nothing to do, the role has the permission granted already
        logger.info(
            "Role '{}' has permission {} for {} already".format(role,
                                                                repr(permission),
                                                                repr(folder)))
        return False
    roles.append(role)
    acquire = folder.acquiredRolesAreUsedBy(permission) == 'CHECKED' and 1 or 0
    folder.manage_permission(permission, roles=roles, acquire=acquire)
    folder.reindexObject()
    logger.info(
        "Added permission {} to role '{}' for {}".format(repr(permission), role,
                                                         repr(folder)))
    return True


def setup_ethnicities(portal):
    """
    Creates standard ethnicities
    """
    logger.info("Setup default ethnicities ...")
    ethnicities = ['Native American', 'Asian', 'Black',
                   'Native Hawaiian or Other Pacific Islander', 'White',
                   'Hispanic or Latino']
    folder = portal.bika_setup.bika_ethnicities
    for ethnicityName in ethnicities:
        _id = folder.invokeFactory('Ethnicity', id=tmpID())
        obj = folder[_id]
        obj.edit(title=ethnicityName,
                 description='')
        obj.unmarkCreationFlag()
        renameAfterCreation(obj)
    logger.info("Setup default ethnicities [DONE]")


def setup_site_structure(context):
    """ Setup contents structure for health
    """
    if context.readDataFile('bika.health.txt') is None:
        return
    portal = context.getSite()
    logger.info("Setup site structure ...")

    # index objects - importing through GenericSetup doesn't
    for obj_id in ('doctors',
                   'patients', ):
        obj = portal._getOb(obj_id)
        obj.unmarkCreationFlag()
        obj.reindexObject()

    # same for objects in bika_setup
    bika_setup = portal.bika_setup
    for obj_id in ('bika_aetiologicagents',
                   'bika_analysiscategories',
                   'bika_drugs',
                   'bika_drugprohibitions',
                   'bika_diseases',
                   'bika_treatments',
                   'bika_immunizations',
                   'bika_vaccinationcenters',
                   'bika_casestatuses',
                   'bika_caseoutcomes',
                   'bika_identifiertypes',
                   'bika_casesyndromicclassifications',
                   'bika_insurancecompanies',
                   'bika_ethnicities',):
        obj = bika_setup._getOb(obj_id)
        obj.unmarkCreationFlag()
        obj.reindexObject()

    logger.info("Setup site structure [DONE]")


def setup_javascripts(portal):
    # Plone's jQuery gets clobbered when jsregistry is loaded.
    setup = portal.portal_setup
    setup.runImportStepFromProfile('profile-plone.app.jquery:default',
                                   'jsregistry')
    setup.runImportStepFromProfile('profile-plone.app.jquerytools:default',
                                   'jsregistry')

    # Load bika.lims js always before bika.health ones.
    setup.runImportStepFromProfile('profile-bika.lims:default', 'jsregistry')


def setup_content_actions(portal):
    """Add "patients" and "doctors" action views inside Client view
    """
    logger.info("Setup content actions ...")
    client_type = portal.portal_types.getTypeInfo("Client")

    remove_action(client_type, "patients")
    client_type.addAction(
        id="patients",
        name="Patients",
        action="string:${object_url}/patients",
        permission=ViewPatients,
        category="object",
        visible=True,
        icon_expr="string:${portal_url}/images/patient.png",
        link_target="",
        description="",
        condition="")

    remove_action(client_type, "doctors")
    client_type.addAction(
        id="doctors",
        name="Doctors",
        action="string:${object_url}/doctors",
        permission=permissions.View,
        category="object",
        visible=True,
        icon_expr="string:${portal_url}/images/doctor.png",
        link_target="",
        description="",
        condition="")
    logger.info("Setup content actions [DONE]")


def remove_action(type_info, action_id):
    """Removes the action id from the type passed in
    """
    actions = map(lambda action: action.id, type_info._actions)
    if action_id not in actions:
        return True
    index = actions.index(action_id)
    type_info.deleteActions([index])
    return remove_action(type_info, action_id)


def setup_health_catalogs(portal):
    # an item should belong to only one catalog.
    # that way looking it up means first looking up *the* catalog
    # in which it is indexed, as well as making it cheaper to index.
    def addIndex(cat, *args):
        try:
            cat.addIndex(*args)
        except:
            pass

    def addColumn(cat, col):
        try:
            cat.addColumn(col)
        except:
            pass

    logger.info("Setup catalogs ...")

    # bika_catalog
    bc = getToolByName(portal, 'bika_catalog', None)
    if not bc:
        logger.warning('Could not find the bika_catalog tool.')
        return
    addIndex(bc, 'getClientTitle', 'FieldIndex')
    addIndex(bc, 'getPatientID', 'FieldIndex')
    addIndex(bc, 'getPatientUID', 'FieldIndex')
    addIndex(bc, 'getPatientTitle', 'FieldIndex')
    addIndex(bc, 'getDoctorID', 'FieldIndex')
    addIndex(bc, 'getDoctorUID', 'FieldIndex')
    addIndex(bc, 'getDoctorTitle', 'FieldIndex')
    addIndex(bc, 'getClientPatientID', 'FieldIndex')
    addColumn(bc, 'getClientTitle')
    addColumn(bc, 'getPatientID')
    addColumn(bc, 'getPatientUID')
    addColumn(bc, 'getPatientTitle')
    addColumn(bc, 'getDoctorID')
    addColumn(bc, 'getDoctorUID')
    addColumn(bc, 'getDoctorTitle')
    addColumn(bc, 'getClientPatientID')

    # portal_catalog
    pc = getToolByName(portal, 'portal_catalog', None)
    if not pc:
        logger.warning('Could not find the portal_catalog tool.')
        return
    addIndex(pc, 'getDoctorID', 'FieldIndex')
    addIndex(pc, 'getDoctorUID', 'FieldIndex')
    addIndex(pc, 'getPrimaryReferrerUID', 'FieldIndex')
    addColumn(pc, 'getDoctorID')
    addColumn(pc, 'getDoctorUID')

    # bika_setup_catalog
    bsc = getToolByName(portal, 'bika_setup_catalog', None)
    if not bsc:
        logger.warning('Could not find the bika_setup_catalog tool.')
        return
    at = getToolByName(portal, 'archetype_tool')
    at.setCatalogsByType('Disease', ['bika_setup_catalog', ])
    at.setCatalogsByType('AetiologicAgent', ['bika_setup_catalog', ])
    at.setCatalogsByType('Treatment', ['bika_setup_catalog'])
    at.setCatalogsByType('Symptom', ['bika_setup_catalog'])
    at.setCatalogsByType('Drug', ['bika_setup_catalog'])
    at.setCatalogsByType('DrugProhibition', ['bika_setup_catalog'])
    at.setCatalogsByType('VaccinationCenter', ['bika_setup_catalog', ])
    at.setCatalogsByType('InsuranceCompany', ['bika_setup_catalog', ])
    at.setCatalogsByType('Immunization', ['bika_setup_catalog', ])
    at.setCatalogsByType('CaseStatus', ['bika_setup_catalog', ])
    at.setCatalogsByType('CaseOutcome', ['bika_setup_catalog', ])
    at.setCatalogsByType('IdentifierType', ['bika_setup_catalog', ])
    at.setCatalogsByType('CaseSyndromicClassification', ['bika_setup_catalog'])
    at.setCatalogsByType('Ethnicity', ['bika_setup_catalog', ])

    addIndex(bsc, 'getGender', 'FieldIndex')
    addColumn(bsc, 'getGender')

    catalog_definitions_lims_health = getCatalogDefinitionsLIMS()
    catalog_definitions_lims_health.update(getCatalogDefinitionsHealth())
    # Updating health catalogs if there is any change in them
    setup_catalogs(
        portal, catalog_definitions_lims_health,
        catalogs_extension=getCatalogExtensions())

    logger.info("Setup catalogs [DONE]")


def setup_id_formatting(portal, format=None):
    """Setup default ID Formatting for health content types
    """
    if not format:
        logger.info("Setup ID formatting ...")
        for formatting in ID_FORMATTING:
            setup_id_formatting(portal, format=formatting)
        logger.info("Setup ID formatting [DONE]")
        return

    bs = portal.bika_setup
    p_type = format.get("portal_type", None)
    if not p_type:
        return
    id_map = bs.getIDFormatting()
    id_format = filter(lambda idf: idf.get("portal_type", "") == p_type, id_map)

    if id_format:
        logger.info("ID Format for {} already set: '{}' [SKIP]"
                    .format(p_type, id_format[0]["form"]))
        return

    form = format.get("form", "")
    if not form:
        logger.info("Param 'form' for portal type {} not set [SKIP")
        return

    logger.info("Applying format '{}' for {}".format(form, p_type))
    ids = list()
    for record in id_map:
        if record.get('portal_type', '') == p_type:
            continue
        ids.append(record)
    ids.append(format)
    bs.setIDFormatting(ids)


def reindex_content_structure(portal):
    """Reindex contents generated by Generic Setup
    """
    logger.info("*** Reindex content structure ***")

    def reindex(obj, recurse=False):
        # skip catalog tools etc.
        if api.is_object(obj):
            obj.reindexObject()
        if recurse and hasattr(aq_base(obj), "objectValues"):
            map(reindex, obj.objectValues())

    setup = api.get_setup()
    setupitems = setup.objectValues()
    rootitems = portal.objectValues()

    for obj in itertools.chain(setupitems, rootitems):
        if not api.is_object(obj):
            continue
        logger.info("Reindexing {}".format(repr(obj)))
        reindex(obj)


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 allow_patients_inside_clients(portal):
    """Allows Patient content type to be created inside Client
    """
    portal_types = api.get_tool('portal_types')
    client = getattr(portal_types, 'Client')
    allowed_types = client.allowed_content_types
    if 'Patient' not in allowed_types:
        client.allowed_content_types = allowed_types + ('Patient', )


1			# -- coding: utf-8 --
2			#
3			# This file is part of SENAITE.HEALTH.
4			#
5			# SENAITE.HEALTH is free software: you can redistribute it and/or modify it
6			# under the terms of the GNU General Public License as published by the Free
7			# Software Foundation, version 2.
8			#
9			# This program is distributed in the hope that it will be useful, but WITHOUT
10			# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
11			# FOR A PARTICULAR PURPOSE. See the GNU General Public License for more
12			# details.
13			#
14			# You should have received a copy of the GNU General Public License along with
15			# this program; if not, write to the Free Software Foundation, Inc., 51
16			# Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
17			#
18			# Copyright 2018-2019 by it's authors.
19			# Some rights reserved, see README and LICENSE.
20
21			import itertools
22
23			from Acquisition import aq_base
24			from Products.CMFCore import permissions
25			from Products.CMFCore.permissions import AccessContentsInformation
26			from Products.CMFCore.permissions import ListFolderContents
27			from Products.CMFCore.permissions import View
28			from Products.CMFCore.utils import getToolByName
29			from plone import api as ploneapi
30
31			from bika.health import bikaMessageFactory as _
32			from bika.health import logger
33			from bika.health.catalog import \
34			getCatalogDefinitions as getCatalogDefinitionsHealth
35			from bika.health.catalog import getCatalogExtensions
36			from bika.health.config import DEFAULT_PROFILE_ID
37			from bika.health.permissions import ViewPatients
38			from bika.lims import api
39			from bika.lims.catalog import \
40			getCatalogDefinitions as getCatalogDefinitionsLIMS
41			from bika.lims.catalog import setup_catalogs
42			from bika.lims.idserver import renameAfterCreation
43			from bika.lims.permissions import AddAnalysisRequest
44			from bika.lims.permissions import AddBatch
45			from bika.lims.utils import tmpID
46
47
48			class Empty(object):
49			pass
50
51
52			ROLES = [
53			# Tuple of (role, permissions)
54			# NOTE: here we only expect permissions that belong to other products and
55			# plone, cause health-specific permissions for this role are
56			# explicitly set in profile/rolemap.xml
57			("Doctor", [View, AccessContentsInformation, ListFolderContents]),
58			("Client", [AddBatch])
59			]
60
61			GROUPS = [
62			# Tuple of (group_name, roles_group
63			("Doctors", ["Member", "Doctor"], ),
64			]
65
66			ID_FORMATTING = [
67			{
68			# P000001, P000002
69			"portal_type": "Patient",
70			"form": "P{seq:06d}",
71			"prefix": "patient",
72			"sequence_type": "generated",
73			"counter_type": "",
74			"split_length": 1,
75			}, {
76			# D0001, D0002, D0003
77			"portal_type": "Doctor",
78			"form": "D{seq:04d}",
79			"prefix": "doctor",
80			"sequence_type": "generated",
81			"counter_type": "",
82			"split_length": 1,
83			}
84			]
85
86
87			def post_install(portal_setup):
88			"""Runs after the last import step of the default profile
89			This handler is registered as a post_handler in the generic setup profile
90			:param portal_setup: SetupTool
91			"""
92			logger.info("SENAITE Health post-install handler [BEGIN]")
93			context = portal_setup._getImportContext(DEFAULT_PROFILE_ID)
94			portal = context.getSite()
95			# Setup catalogs
96			# TODO use upgrade.utils.setup_catalogs instead!
97			setup_health_catalogs(portal)
98
99			# Setup portal permissions
100			setup_roles_permissions(portal)
101
102			# Setup user groups (e.g. Doctors)
103			setup_user_groups(portal)
104
105			# Setup site structure
106			setup_site_structure(context)
107
108			# Setup javascripts
109			setup_javascripts(portal)
110
111			# Setup content actions
112			setup_content_actions(portal)
113
114			# Setup ID formatting for Health types
115			setup_id_formatting(portal)
116
117			# Setup default ethnicities
118			setup_ethnicities(portal)
119
120			# Allow patients inside clients
121			# Note: this should always be run if core's typestool is reimported
122			allow_patients_inside_clients(portal)
123
124			# Reindex the top level folder in the portal and setup to fix missing icons
125			reindex_content_structure(portal)
126
127			# When installing senaite health together with core, health's skins are not
128			# set before core's, even if after-before is set in profiles/skins.xml
129			# Ensure health's skin layer(s) always gets priority over core's
130			portal_setup.runImportStepFromProfile(DEFAULT_PROFILE_ID, "skins")
131
132			# Setup default email body and subject for panic alerts
133			setup_panic_alerts(portal)
134
135			logger.info("SENAITE Health post-install handler [DONE]")
136
137
138			def setup_user_groups(portal):
139			logger.info("Setup User Groups ...")
140			portal_groups = portal.portal_groups
141			for group_name, roles in GROUPS:
142			if group_name not in portal_groups.listGroupIds():
143			portal_groups.addGroup(group_name, title=group_name, roles=roles)
144			logger.info("Group '{}' with roles '{}' added"
145			.format(group_name, ", ".join(roles)))
146			else:
147			logger.info("Group '{}' already exist [SKIP]".format(group_name))
148			logger.info("Setup User Groups [DONE]")
149
150
151			def setup_roles_permissions(portal):
152			"""Setup the top-level permissions for new roles. The new role is added to
153			the roles that already have the permission granted (acquire=1)
154			"""
155			logger.info("Setup roles permissions ...")
156			for role_name, permissions in ROLES:
157			for permission in permissions:
158			add_permission_for_role(portal, permission, role_name)
159
160			# Add "Add AnalysisRequest" permission for Clients in base analysisrequests
161			# This makes the "Add" button to appear in AnalysisRequestsFolder view
162			analysis_requests = portal.analysisrequests
163			add_permission_for_role(analysis_requests, AddAnalysisRequest, "Client")
164			logger.info("Setup roles permissions [DONE]")
165
166
167			def add_permission_for_role(folder, permission, role):
168			"""Grants a permission to the given role and given folder
169			:param folder: the folder to which the permission for the role must apply
170			:param permission: the permission to be assigned
171			:param role: role to which the permission must be granted
172			:return True if succeed, otherwise, False
173			"""
174			roles = filter(lambda perm: perm.get('selected') == 'SELECTED',
175			folder.rolesOfPermission(permission))
176			roles = map(lambda perm_role: perm_role['name'], roles)
177			if role in roles:
178			# Nothing to do, the role has the permission granted already
179			logger.info(
180			"Role '{}' has permission {} for {} already".format(role,
181			repr(permission),
182			repr(folder)))
183			return False
184			roles.append(role)
185			acquire = folder.acquiredRolesAreUsedBy(permission) == 'CHECKED' and 1 or 0
186			folder.manage_permission(permission, roles=roles, acquire=acquire)
187			folder.reindexObject()
188			logger.info(
189			"Added permission {} to role '{}' for {}".format(repr(permission), role,
190			repr(folder)))
191			return True
192
193
194			def setup_ethnicities(portal):
195			"""
196			Creates standard ethnicities
197			"""
198			logger.info("Setup default ethnicities ...")
199			ethnicities = ['Native American', 'Asian', 'Black',
200			'Native Hawaiian or Other Pacific Islander', 'White',
201			'Hispanic or Latino']
202			folder = portal.bika_setup.bika_ethnicities
203			for ethnicityName in ethnicities:
204			_id = folder.invokeFactory('Ethnicity', id=tmpID())
205			obj = folder[_id]
206			obj.edit(title=ethnicityName,
207			description='')
208			obj.unmarkCreationFlag()
209			renameAfterCreation(obj)
210			logger.info("Setup default ethnicities [DONE]")
211
212
213			def setup_site_structure(context):
214			""" Setup contents structure for health
215			"""
216			if context.readDataFile('bika.health.txt') is None:
217			return
218			portal = context.getSite()
219			logger.info("Setup site structure ...")
220
221			# index objects - importing through GenericSetup doesn't
222			for obj_id in ('doctors',
223			'patients', ):
224			obj = portal._getOb(obj_id)
225			obj.unmarkCreationFlag()
226			obj.reindexObject()
227
228			# same for objects in bika_setup
229			bika_setup = portal.bika_setup
230			for obj_id in ('bika_aetiologicagents',
231			'bika_analysiscategories',
232			'bika_drugs',
233			'bika_drugprohibitions',
234			'bika_diseases',
235			'bika_treatments',
236			'bika_immunizations',
237			'bika_vaccinationcenters',
238			'bika_casestatuses',
239			'bika_caseoutcomes',
240			'bika_identifiertypes',
241			'bika_casesyndromicclassifications',
242			'bika_insurancecompanies',
243			'bika_ethnicities',):
244			obj = bika_setup._getOb(obj_id)
245			obj.unmarkCreationFlag()
246			obj.reindexObject()
247
248			logger.info("Setup site structure [DONE]")
249
250
251			def setup_javascripts(portal):
252			# Plone's jQuery gets clobbered when jsregistry is loaded.
253			setup = portal.portal_setup
254			setup.runImportStepFromProfile('profile-plone.app.jquery:default',
255			'jsregistry')
256			setup.runImportStepFromProfile('profile-plone.app.jquerytools:default',
257			'jsregistry')
258
259			# Load bika.lims js always before bika.health ones.
260			setup.runImportStepFromProfile('profile-bika.lims:default', 'jsregistry')
261
262
263			def setup_content_actions(portal):
264			"""Add "patients" and "doctors" action views inside Client view
265			"""
266			logger.info("Setup content actions ...")
267			client_type = portal.portal_types.getTypeInfo("Client")
268
269			remove_action(client_type, "patients")
270			client_type.addAction(
271			id="patients",
272			name="Patients",
273			action="string:${object_url}/patients",
274			permission=ViewPatients,
275			category="object",
276			visible=True,
277			icon_expr="string:${portal_url}/images/patient.png",
278			link_target="",
279			description="",
280			condition="")
281
282			remove_action(client_type, "doctors")
283			client_type.addAction(
284			id="doctors",
285			name="Doctors",
286			action="string:${object_url}/doctors",
287			permission=permissions.View,
288			category="object",
289			visible=True,
290			icon_expr="string:${portal_url}/images/doctor.png",
291			link_target="",
292			description="",
293			condition="")
294			logger.info("Setup content actions [DONE]")
295
296
297			def remove_action(type_info, action_id):
298			"""Removes the action id from the type passed in
299			"""
300			actions = map(lambda action: action.id, type_info._actions)
301			if action_id not in actions:
302			return True
303			index = actions.index(action_id)
304			type_info.deleteActions([index])
305			return remove_action(type_info, action_id)
306
307
308			def setup_health_catalogs(portal):
309			# an item should belong to only one catalog.
310			# that way looking it up means first looking up the catalog
311			# in which it is indexed, as well as making it cheaper to index.
312			def addIndex(cat, *args):
313			try:
314			cat.addIndex(*args)
315			except:
316			pass
317
318			def addColumn(cat, col):
319			try:
320			cat.addColumn(col)
321			except:
322			pass
323
324			logger.info("Setup catalogs ...")
325
326			# bika_catalog
327			bc = getToolByName(portal, 'bika_catalog', None)
328			if not bc:
329			logger.warning('Could not find the bika_catalog tool.')
330			return
331			addIndex(bc, 'getClientTitle', 'FieldIndex')
332			addIndex(bc, 'getPatientID', 'FieldIndex')
333			addIndex(bc, 'getPatientUID', 'FieldIndex')
334			addIndex(bc, 'getPatientTitle', 'FieldIndex')
335			addIndex(bc, 'getDoctorID', 'FieldIndex')
336			addIndex(bc, 'getDoctorUID', 'FieldIndex')
337			addIndex(bc, 'getDoctorTitle', 'FieldIndex')
338			addIndex(bc, 'getClientPatientID', 'FieldIndex')
339			addColumn(bc, 'getClientTitle')
340			addColumn(bc, 'getPatientID')
341			addColumn(bc, 'getPatientUID')
342			addColumn(bc, 'getPatientTitle')
343			addColumn(bc, 'getDoctorID')
344			addColumn(bc, 'getDoctorUID')
345			addColumn(bc, 'getDoctorTitle')
346			addColumn(bc, 'getClientPatientID')
347
348			# portal_catalog
349			pc = getToolByName(portal, 'portal_catalog', None)
350			if not pc:
351			logger.warning('Could not find the portal_catalog tool.')
352			return
353			addIndex(pc, 'getDoctorID', 'FieldIndex')
354			addIndex(pc, 'getDoctorUID', 'FieldIndex')
355			addIndex(pc, 'getPrimaryReferrerUID', 'FieldIndex')
356			addColumn(pc, 'getDoctorID')
357			addColumn(pc, 'getDoctorUID')
358
359			# bika_setup_catalog
360			bsc = getToolByName(portal, 'bika_setup_catalog', None)
361			if not bsc:
362			logger.warning('Could not find the bika_setup_catalog tool.')
363			return
364			at = getToolByName(portal, 'archetype_tool')
365			at.setCatalogsByType('Disease', ['bika_setup_catalog', ])
366			at.setCatalogsByType('AetiologicAgent', ['bika_setup_catalog', ])
367			at.setCatalogsByType('Treatment', ['bika_setup_catalog'])
368			at.setCatalogsByType('Symptom', ['bika_setup_catalog'])
369			at.setCatalogsByType('Drug', ['bika_setup_catalog'])
370			at.setCatalogsByType('DrugProhibition', ['bika_setup_catalog'])
371			at.setCatalogsByType('VaccinationCenter', ['bika_setup_catalog', ])
372			at.setCatalogsByType('InsuranceCompany', ['bika_setup_catalog', ])
373			at.setCatalogsByType('Immunization', ['bika_setup_catalog', ])
374			at.setCatalogsByType('CaseStatus', ['bika_setup_catalog', ])
375			at.setCatalogsByType('CaseOutcome', ['bika_setup_catalog', ])
376			at.setCatalogsByType('IdentifierType', ['bika_setup_catalog', ])
377			at.setCatalogsByType('CaseSyndromicClassification', ['bika_setup_catalog'])
378			at.setCatalogsByType('Ethnicity', ['bika_setup_catalog', ])
379
380			addIndex(bsc, 'getGender', 'FieldIndex')
381			addColumn(bsc, 'getGender')
382
383			catalog_definitions_lims_health = getCatalogDefinitionsLIMS()
384			catalog_definitions_lims_health.update(getCatalogDefinitionsHealth())
385			# Updating health catalogs if there is any change in them
386			setup_catalogs(
387			portal, catalog_definitions_lims_health,
388			catalogs_extension=getCatalogExtensions())
389
390			logger.info("Setup catalogs [DONE]")
391
392
393			def setup_id_formatting(portal, format=None):
394			"""Setup default ID Formatting for health content types
395			"""
396			if not format:
397			logger.info("Setup ID formatting ...")
398			for formatting in ID_FORMATTING:
399			setup_id_formatting(portal, format=formatting)
400			logger.info("Setup ID formatting [DONE]")
401			return
402
403			bs = portal.bika_setup
404			p_type = format.get("portal_type", None)
405			if not p_type:
406			return
407			id_map = bs.getIDFormatting()
408			id_format = filter(lambda idf: idf.get("portal_type", "") == p_type, id_map)
			0 ignored issues – show introduced 2019-04-08 21:29 UTC by Report Bug Copy Issue Report The variable `p_type` does not seem to be defined for all execution paths. Loading history...
409			if id_format:
410			logger.info("ID Format for {} already set: '{}' [SKIP]"
411			.format(p_type, id_format[0]["form"]))
412			return
413
414			form = format.get("form", "")
415			if not form:
416			logger.info("Param 'form' for portal type {} not set [SKIP")
417			return
418
419			logger.info("Applying format '{}' for {}".format(form, p_type))
420			ids = list()
421			for record in id_map:
422			if record.get('portal_type', '') == p_type:
423			continue
424			ids.append(record)
425			ids.append(format)
426			bs.setIDFormatting(ids)
427
428
429			def reindex_content_structure(portal):
430			"""Reindex contents generated by Generic Setup
431			"""
432			logger.info("* Reindex content structure *")
433
434			def reindex(obj, recurse=False):
435			# skip catalog tools etc.
436			if api.is_object(obj):
437			obj.reindexObject()
438			if recurse and hasattr(aq_base(obj), "objectValues"):
439			map(reindex, obj.objectValues())
440
441			setup = api.get_setup()
442			setupitems = setup.objectValues()
443			rootitems = portal.objectValues()
444
445			for obj in itertools.chain(setupitems, rootitems):
446			if not api.is_object(obj):
447			continue
448			logger.info("Reindexing {}".format(repr(obj)))
449			reindex(obj)
450
451
452			def setup_panic_alerts(portal):
453			"""Setups the template texts for panic alert email's subject and body
454			"""
455			email_body = _(
456			"Some results from the Sample ${sample_id} exceeded the panic levels "
457			"that may indicate an imminent life-threatening condition:\n\n"
458			"${analyses}\n\n--\n${lab_address}")
459			ploneapi.portal.set_registry_record("senaite.panic.email_body", email_body)
460
461
462			def allow_patients_inside_clients(portal):
463			"""Allows Patient content type to be created inside Client
464			"""
465			portal_types = api.get_tool('portal_types')
466			client = getattr(portal_types, 'Client')
467			allowed_types = client.allowed_content_types
468			if 'Patient' not in allowed_types:
469			client.allowed_content_types = allowed_types + ('Patient', )
470

senaite / senaite.health

bika.health.setuphandlers.setup_id_formatting() C last analyzed 2020-02-18 09:40 UTC

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bika.health.setuphandlers.setup_id_formatting() C
last analyzed 2020-02-18 09:40 UTC