def setup_handler(context):
"""Generic setup handler
"""
if context.readDataFile("{}.txt".format(PRODUCT_NAME)) is None:
return
logger.info("{} setup handler [BEGIN]".format(PRODUCT_NAME.upper()))
portal = context.getSite()
# Setup patient content type
add_patient_folder(portal)
# Configure visible navigation items
setup_navigation_types(portal)
# Setup catalogs
setup_catalogs(portal)
# Apply ID format to content types
setup_id_formatting(portal)
# Setup workflow (for field permissions mostly)
setup_workflow(portal)
logger.info("{} setup handler [DONE]".format(PRODUCT_NAME.upper()))
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("{} install handler [BEGIN]".format(PRODUCT_NAME.upper()))
context = portal_setup._getImportContext(PROFILE_ID) # noqa
portal = context.getSite() # noqa
logger.info("{} install handler [DONE]".format(PRODUCT_NAME.upper()))
def afterUpgradeStepHandler(event):
"""Event handler that is executed after running an upgrade step of senaite.core
"""
if not is_installed():
return
logger.info("Run senaite.patient.afterUpgradeStepHandler ...")
portal = get_portal()
setup_navigation_types(portal)
setup_id_formatting(portal)
setup_workflow(portal)
logger.info("Run senaite.patient.afterUpgradeStepHandler [DONE]")
def post_uninstall(portal_setup):
"""Runs after the last import step of the *uninstall* profile
This handler is registered as a *post_handler* in the generic setup profile
:param portal_setup: SetupTool
"""
logger.info("{} uninstall handler [BEGIN]".format(PRODUCT_NAME.upper()))
# https://docs.plone.org/develop/addons/components/genericsetup.html#custom-installer-code-setuphandlers-py
profile_id = "profile-{}:uninstall".format(PRODUCT_NAME)
context = portal_setup._getImportContext(profile_id) # noqa
portal = context.getSite() # noqa
logger.info("{} uninstall handler [DONE]".format(PRODUCT_NAME.upper()))
def setup_id_formatting(portal, format_definition=None):
"""Setup default ID formatting
"""
if not format_definition:
logger.info("Setting up ID formatting ...")
for formatting in ID_FORMATTING:
setup_id_formatting(portal, format_definition=formatting)
logger.info("Setting up ID formatting [DONE]")
return
bs = portal.bika_setup
p_type = format_definition.get("portal_type", None)
if not p_type:
return
form = format_definition.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 bs.getIDFormatting():
if record.get('portal_type', '') == p_type:
continue
ids.append(record)
ids.append(format_definition)
bs.setIDFormatting(ids)
def migrate_to_patient_catalog(portal):
"""Migrate portal_catalog -> patient_catalog
"""
logger.info("Migrate patient catalog...")
# 1. Setup catalogs
setup_catalogs(portal)
# 2. Clean up indexes
for catalog_id, idx_id in DELETE_INDEXES:
catalog = api.get_tool(catalog_id)
indexes = get_indexes(catalog)
if idx_id in indexes:
del_index(catalog, idx_id)
logger.info("Deleted index '%s' from catalog '%s'" %
(idx_id, catalog_id))
# 3. Clean up columns
for catalog_id, column in DELETE_COLUMNS:
catalog = api.get_tool(catalog_id)
columns = get_columns(catalog)
if column in columns:
del_column(catalog, column)
logger.info("Deleted column '%s' from catalog '%s'" %
(column, catalog_id))
# 4. Reindex patient catalog
patient_catalog = api.get_tool(PATIENT_CATALOG)
patient_catalog.clearFindAndRebuild()
logger.info("Migrate patient catalog [DONE]")
def update_patient(instance):
if instance.isMedicalRecordTemporary():
return
mrn = instance.getMedicalRecordNumberValue()
# Allow empty value when patients are not required for samples
if mrn is None:
return
patient = patient_api.get_patient_by_mrn(mrn, include_inactive=True)
if patient is None:
logger.info("Creating new Patient with MRN #: {}".format(mrn))
patient = patient_api.create_empty_patient()
# XXX: Sync the values back from Sample -> Patient?
values = get_patient_fields(instance)
patient_api.update_patient(patient, **values)
def update_workflow(portal, workflow_id, settings):
"""Updates the workflow with workflow_id with the settings passed-in
"""
logger.info("Updating workflow '{}' ...".format(workflow_id))
wf_tool = api.get_tool("portal_workflow")
workflow = wf_tool.getWorkflowById(workflow_id)
if not workflow:
logger.warn("Workflow '{}' not found [SKIP]".format(workflow_id))
states = settings.get("states", {})
for state_id, values in states.items():
update_workflow_state(workflow, state_id, values)
transitions = settings.get("transitions", {})
for transition_id, values in transitions.items():
update_workflow_transition(workflow, transition_id, values)
def fix_patients_fullname(portal):
"""Update the value of attribute 'firstname' with the value of 'fullname'
"""
logger.info("Fixing patients full names ...")
for patient in portal.patients.objectValues():
if patient.get_firstname():
# This one has the value set already
continue
raw = patient.__dict__
firstname = raw.get("fullname", None)
if firstname:
patient.set_firstname(firstname)
del (patient.__dict__["fullname"])
patient.reindexObject()
logger.info("Fixing patients full names ... [DONE]")
def migrate_birthdates(portal):
"""Migrate all birthdates from patients to be timezone aware
"""
logger.info("Migrate patient birthdate timezones ...")
catalog = api.get_tool(PATIENT_CATALOG)
results = catalog({"portal_type": "Patient"})
timezone = dtime.get_os_timezone()
for brain in results:
patient = api.get_object(brain)
birthdate = patient.birthdate
if birthdate:
# clean existing time and timezone
date = birthdate.strftime("%Y-%m-%d")
# append current OS timezone if possible
if timezone:
date = date + " %s" % timezone
patient.set_birthdate(date)
patient.reindexObject()
logger.info("Migrate patient birthdate timezones [DONE]")
def migrate_patient_item_to_container(portal):
"""Migrate patient objects to be folderish
Base class changed from Item -> Container
https://community.plone.org/t/changing-dx-content-type-base-class-from-item-to-container
http://blog.redturtle.it/2013/02/25/migrating-dexterity-items-to-dexterity-containers
"""
logger.info("Migrate patients to be folderish ...")
patients = portal.patients
for patient in patients.objectValues():
pid = patient.getId()
patients._delOb(pid)
patient.__class__ = Patient
patients._setOb(pid, patient)
BTreeFolder2Base._initBTrees(patients[pid])
patients[pid].reindexObject()
transaction.commit()
logger.info("Migrate patients to be folderish [DONE]")
def update_workflow_transition(workflow, transition_id, settings):
logger.info("Updating workflow '{}', transition: '{}'".format(
workflow.id, transition_id))
if transition_id not in workflow.transitions:
workflow.transitions.addTransition(transition_id)
transition = workflow.transitions.get(transition_id)
transition.setProperties(title=settings.get("title"),
new_state_id=settings.get("new_state"),
after_script_name=settings.get(
"after_script", ""),
actbox_name=settings.get("action",
settings.get("title")))
guard = transition.guard or Guard()
guard_props = {
"guard_permissions": "",
"guard_roles": "",
"guard_expr": ""
}
guard_props = settings.get("guard", guard_props)
guard.changeFromProperties(guard_props)
transition.guard = guard
def upgrade(tool):
portal = tool.aq_inner.aq_parent
setup = portal.portal_setup
ut = UpgradeUtils(portal)
ver_from = ut.getInstalledVersion(PRODUCT_NAME)
if ut.isOlderVersion(PRODUCT_NAME, version):
logger.info("Skipping upgrade of {0}: {1} > {2}".format(
PRODUCT_NAME, ver_from, version))
return True
logger.info("Upgrading {0}: {1} -> {2}".format(PRODUCT_NAME, ver_from,
version))
# -------- ADD YOUR STUFF BELOW --------
# Allow/Disallow to verify/publish samples with temporary MRN
setup.runImportStepFromProfile(PROFILE_ID, "plone.app.registry")
# Update schema interface
setup.runImportStepFromProfile(PROFILE_ID, "typeinfo")
setup.runImportStepFromProfile(PROFILE_ID, "workflow")
# https://github.com/senaite/senaite.patient/pull/24
migrate_patient_item_to_container(portal)
# https://github.com/senaite/senaite.patient/pull/14
migrate_to_patient_catalog(portal)
# Firstname + lastname instead of fullname
fix_patients_fullname(portal)
logger.info("{0} upgraded to version {1}".format(PRODUCT_NAME, version))
return True
def update_workflow_state(workflow, status_id, settings):
logger.info("Updating workflow '{}', status: '{}' ...".format(
workflow.id, status_id))
# Create the status (if does not exist yet)
new_status = workflow.states.get(status_id)
if not new_status:
workflow.states.addState(status_id)
new_status = workflow.states.get(status_id)
# Set basic info (title, description, etc.)
new_status.title = settings.get("title", new_status.title)
new_status.description = settings.get("description",
new_status.description)
# Set transitions
trans = settings.get("transitions", ())
if settings.get("preserve_transitions", False):
trans = tuple(set(new_status.transitions + trans))
new_status.transitions = trans
# Set permissions
update_workflow_state_permissions(workflow, new_status, settings)
def upgrade(tool):
portal = tool.aq_inner.aq_parent
setup = portal.portal_setup # noqa
ut = UpgradeUtils(portal)
ver_from = ut.getInstalledVersion(PRODUCT_NAME)
if ut.isOlderVersion(PRODUCT_NAME, version):
logger.info("Skipping upgrade of {0}: {1} > {2}".format(
PRODUCT_NAME, ver_from, version))
return True
logger.info("Upgrading {0}: {1} -> {2}".format(PRODUCT_NAME, ver_from,
version))
# -------- ADD YOUR STUFF BELOW --------
# add dateindex for birthdates
setup_catalogs(portal)
# migrate birthdates w/o time but with valid timezone
migrate_birthdates(portal)
logger.info("{0} upgraded to version {1}".format(PRODUCT_NAME, version))
return True
def add_patient_folder(portal):
"""Adds the initial Patient folder
"""
if portal.get("patients") is None:
logger.info("Adding Patient Folder")
portal.invokeFactory("PatientFolder", "patients", title="Patients")
def update_workflow_state_permissions(workflow, status, settings):
# Copy permissions from another state?
permissions_copy_from = settings.get("permissions_copy_from", None)
if permissions_copy_from:
logger.info("Copying permissions from '{}' to '{}' ...".format(
permissions_copy_from, status.id))
copy_from_state = workflow.states.get(permissions_copy_from)
if not copy_from_state:
logger.info("State '{}' not found [SKIP]".format(copy_from_state))
else:
for perm_id in copy_from_state.permissions:
perm_info = copy_from_state.getPermissionInfo(perm_id)
acquired = perm_info.get("acquired", 1)
roles = perm_info.get("roles", acquired and [] or ())
logger.info(
"Setting permission '{}' (acquired={}): '{}'".format(
perm_id, repr(acquired), ', '.join(roles)))
status.setPermission(perm_id, acquired, roles)
# Override permissions
logger.info("Overriding permissions for '{}' ...".format(status.id))
state_permissions = settings.get('permissions', {})
if not state_permissions:
logger.info("No permissions set for '{}' [SKIP]".format(status.id))
return
for permission_id, roles in state_permissions.items():
state_roles = roles and roles or ()
if isinstance(state_roles, tuple):
acq = 0
else:
acq = 1
logger.info("Setting permission '{}' (acquired={}): '{}'".format(
permission_id, repr(acq), ', '.join(state_roles)))
# Check if this permission is defined globally for this workflow
if permission_id not in workflow.permissions:
workflow.permissions = workflow.permissions + (permission_id, )
status.setPermission(permission_id, acq, state_roles)