def upgrade(tool):
portal = aq_parent(aq_inner(tool))
setup = portal.portal_setup
ut = UpgradeUtils(portal)
ver_from = ut.getInstalledVersion(product)
if ut.isOlderVersion(product, version):
logger.info("Skipping upgrade of {0}: {1} > {2}".format(
product, ver_from, version))
# The currently installed version is more recent than the target
# version of this upgradestep
return True
logger.info("Upgrading {0}: {1} -> {2}".format(product, ver_from, version))
# The assignment of the whole Calculation object in a metadata column
# was causing a "TypeError: Can't pickle objects in acquisition wrappers".
# getCalculation was only used in analyses listing and can be safely
# replaced by getCalculationUID, cause is only used to determine if a
# calculation is required to compute the result value
# https://github.com/senaite/bika.lims/issues/322
ut.delColumn(CATALOG_ANALYSIS_LISTING, 'getCalculation')
ut.addColumn(CATALOG_ANALYSIS_LISTING, 'getCalculationUID')
ut.refreshCatalogs()
logger.info("{0} upgraded to version {1}".format(product, version))
return True
def upgrade(tool):
portal = tool.aq_inner.aq_parent
setup = portal.portal_setup
ut = UpgradeUtils(portal)
ver_from = ut.getInstalledVersion(product)
if ut.isOlderVersion(product, version):
logger.info("Skipping upgrade of {0}: {1} > {2}".format(
product, ver_from, version))
return True
logger.info("Upgrading {0}: {1} -> {2}".format(product, ver_from, version))
# -------- ADD YOUR STUFF BELOW --------
# Remove QC reports and gpw dependency
# https://github.com/senaite/senaite.core/pull/1058
remove_qc_reports(portal)
# Remove updates notification viewlet
# https://github.com/senaite/senaite.core/pull/1059
setup.runImportStepFromProfile(profile, 'viewlets')
# Remove old portlets except the navigation portlet
# https://github.com/senaite/senaite.core/pull/1060
purge_portlets(portal)
logger.info("{0} upgraded to version {1}".format(product, version))
return True
def upgrade(tool):
portal = tool.aq_inner.aq_parent
ut = UpgradeUtils(portal)
ver_from = ut.getInstalledVersion(product)
if ut.isOlderVersion(product, version):
logger.info("Skipping upgrade of {0}: {1} > {2}".format(
product, ver_from, version))
return True
logger.info("Upgrading {0}: {1} -> {2}".format(product, ver_from, version))
# -------- ADD YOUR STUFF HERE --------
fix_workflow_transitions(portal)
# Migration to senaite.core
setup = portal.portal_setup
setup.runImportStepFromProfile('profile-bika.lims:default', 'typeinfo')
setup.runImportStepFromProfile('profile-bika.lims:default',
'propertiestool')
rename_bika_setup()
logger.info("{0} upgraded to version {1}".format(product, version))
return True
def upgrade(tool):
portal = tool.aq_inner.aq_parent
ut = UpgradeUtils(portal)
ver_from = ut.getInstalledVersion(product)
if ut.isOlderVersion(product, version):
logger.info("Skipping upgrade of {0}: {1} > {2}".format(
product, ver_from, version))
return True
logger.info("Upgrading {0}: {1} -> {2}".format(product, ver_from, version))
# -------- ADD YOUR STUFF HERE --------
# Issue #574: Client batch listings are dumb. This requires Batches to
# be reindexed, as thy now provide an accessor for getClientUID.
reindex_batch_getClientUID(portal)
# The catalog where worksheets are stored (bika_catalog_worksheet_listing)
# had a FieldIndex "WorksheetTemplate" which was causing a TypeError (can't
# pickle acquisition wrappers) when reindexing worksheets with an associated
# Worksheet Template.
fix_worksheet_template_index(portal, ut)
# Adds an entry to the registry to store the roles that can see Samples
# section from Dashboard
add_sample_section_in_dashboard(portal)
# Ability to choose the sticker templates based on sample types (#607)
set_sample_type_default_stickers(portal)
logger.info("{0} upgraded to version {1}".format(product, version))
return True
def upgrade(tool):
portal = tool.aq_inner.aq_parent
ut = UpgradeUtils(portal)
ver_from = ut.getInstalledVersion(product)
if ut.isOlderVersion(product, version):
logger.info("Skipping upgrade of {0}: {1} > {2}".format(
product, ver_from, version))
return True
logger.info("Upgrading {0}: {1} -> {2}".format(product, ver_from, version))
# -------- ADD YOUR STUFF HERE --------
# Issue #574: Client batch listings are dumb. This requires Batches to
# be reindexed, as thy now provide an accessor for getClientUID.
reindex_batch_getClientUID(portal)
# The catalog where worksheets are stored (bika_catalog_worksheet_listing)
# had a FieldIndex "WorksheetTemplate" which was causing a TypeError (can't
# pickle acquisition wrappers) when reindexing worksheets with an associated
# Worksheet Template.
fix_worksheet_template_index(portal, ut)
# Adds an entry to the registry to store the roles that can see Samples
# section from Dashboard
add_sample_section_in_dashboard(portal)
logger.info("{0} upgraded to version {1}".format(product, version))
return True
def upgrade(tool):
portal = tool.aq_inner.aq_parent
setup = portal.portal_setup
ut = UpgradeUtils(portal)
ver_from = ut.getInstalledVersion(product)
if ut.isOlderVersion(product, version):
logger.info("Skipping upgrade of {0}: {1} > {2}".format(
product, ver_from, version))
return True
logger.info("Upgrading {0}: {1} -> {2}".format(product, ver_from, version))
# -------- ADD YOUR STUFF BELOW --------
# Do not display clients folder to Clients. There is no need to do an
# update-role-mappings of clients, cause the permissions at client level
# have not changed, except that now they are acquire=1 for "active" status
setup.runImportStepFromProfile(profile, "workflow")
wf_tool = api.get_tool("portal_workflow")
workflow = wf_tool.getWorkflowById("senaite_clients_workflow")
workflow.updateRoleMappingsFor(portal.clients)
portal.clients.reindexObject()
# New link to My Organization
setup.runImportStepFromProfile(profile, "actions")
logger.info("{0} upgraded to version {1}".format(product, version))
return True
def upgrade(tool):
portal = aq_parent(aq_inner(tool))
setup = portal.portal_setup
ut = UpgradeUtils(portal)
ver_from = ut.getInstalledVersion(product)
if ut.isOlderVersion(product, version):
logger.info("Skipping upgrade of {0}: {1} > {2}".format(
product, ver_from, version))
# The currently installed version is more recent than the target
# version of this upgradestep
return True
logger.info("Upgrading {0}: {1} -> {2}".format(product, ver_from, version))
# The assignment of the whole Calculation object in a metadata column
# was causing a "TypeError: Can't pickle objects in acquisition wrappers".
# getCalculation was only used in analyses listing and can be safely
# replaced by getCalculationUID, cause is only used to determine if a
# calculation is required to compute the result value
# https://github.com/senaite/bika.lims/issues/322
ut.delColumn(CATALOG_ANALYSIS_LISTING, 'getCalculation')
ut.addColumn(CATALOG_ANALYSIS_LISTING, 'getCalculationUID')
ut.refreshCatalogs()
logger.info("{0} upgraded to version {1}".format(product, version))
return True
def upgrade(tool):
portal = tool.aq_inner.aq_parent
ut = UpgradeUtils(portal)
ver_from = ut.getInstalledVersion(product)
if ut.isOlderVersion(product, version):
logger.info("Skipping upgrade of {0}: {1} > {2}".format(
product, ver_from, version))
return True
logger.info("Upgrading {0}: {1} -> {2}".format(product, ver_from, version))
# -------- ADD YOUR STUFF HERE --------
# Ensure health's skins have always priority over core's
setup = portal.portal_setup
setup.runImportStepFromProfile(profile, "skins")
setup.runImportStepFromProfile(profile, 'workflow')
setup.runImportStepFromProfile(profile, "typeinfo")
# Allow clients to list, add and edit doctors
apply_doctor_permissions_for_clients(portal, ut)
logger.info("{0} upgraded to version {1}".format(product, version))
return True
def upgrade(tool):
portal = tool.aq_inner.aq_parent
ut = UpgradeUtils(portal)
ver_from = ut.getInstalledVersion(product)
if ut.isOlderVersion(product, version):
logger.info("Skipping upgrade of {0}: {1} > {2}".format(
product, ver_from, version))
return True
logger.info("Upgrading {0}: {1} -> {2}".format(product, ver_from, version))
# -------- ADD YOUR STUFF HERE --------
ut.delIndexAndColumn(CATALOG_ANALYSIS_REQUEST_LISTING, 'getPatient')
ut.delIndexAndColumn(CATALOG_ANALYSIS_REQUEST_LISTING, 'getDoctor')
ut.addColumn(CATALOG_ANALYSIS_REQUEST_LISTING, 'getPatientID')
ut.addIndexAndColumn(CATALOG_ANALYSIS_REQUEST_LISTING, 'getPatientTitle',
'FieldIndex')
# In case if upgrade was already run after PR #72 got accepted
ut.delColumn(CATALOG_ANALYSIS_REQUEST_LISTING, 'getPatientURL')
ut.addColumn(CATALOG_ANALYSIS_REQUEST_LISTING, 'getPatientURL')
ut.addColumn(CATALOG_ANALYSIS_REQUEST_LISTING, 'getClientPatientID')
ut.addIndexAndColumn(CATALOG_ANALYSIS_REQUEST_LISTING, 'getDoctorTitle',
'FieldIndex')
# In case if upgrade was already run after PR #72 got accepted
ut.delColumn(CATALOG_ANALYSIS_REQUEST_LISTING, 'getDoctorURL')
ut.addColumn(CATALOG_ANALYSIS_REQUEST_LISTING, 'getDoctorURL')
ut.addIndex(CATALOG_PATIENTS, 'listing_searchable_text', 'TextIndexNG3')
ut.refreshCatalogs()
logger.info("{0} upgraded to version {1}".format(product, version))
return True
def upgrade(tool):
portal = tool.aq_inner.aq_parent
setup = portal.portal_setup
ut = UpgradeUtils(portal)
ver_from = ut.getInstalledVersion(product)
if ut.isOlderVersion(product, version):
logger.info("Skipping upgrade of {0}: {1} > {2}".format(
product, ver_from, version))
return True
logger.info("Upgrading {0}: {1} -> {2}".format(product, ver_from, version))
# -------- ADD YOUR STUFF BELOW --------
# Allow to detach a partition from its primary sample (#1420)
setup.runImportStepFromProfile(profile, "rolemap")
# Mixed permissions for transitions in client workflow (#1419)
# Allow to detach a partition from its primary sample (#1420)
setup.runImportStepFromProfile(profile, "workflow")
# Allow to detach a partition from its primary sample (#1420)
update_partitions_role_mappings(portal)
logger.info("{0} upgraded to version {1}".format(product, version))
return True
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 --------
# Compatibility with "Fix error when creating a partition as analyst user",
# that reimports the worklflow tool and do an updateRoleMappings for Samples
# that are in "received" status. Since senaite.storage "overrides" the
# definition the sample_workflow, there is the need to setup workflow again
# https://github.com/senaite/senaite.core/pull/1525
setup_workflows(portal)
update_wf_received_samples(portal)
logger.info("{0} upgraded to version {1}".format(PRODUCT_NAME, version))
return True
def upgrade(tool):
portal = aq_parent(aq_inner(tool))
setup = portal.portal_setup
ut = UpgradeUtils(portal)
ver_from = ut.getInstalledVersion(product)
if ut.isOlderVersion(product, version):
logger.info("Skipping upgrade of {0}: {1} > {2}".format(
product, ver_from, version))
# The currently installed version is more recent than the target
# version of this upgradestep
return True
logger.info("Upgrading {0}: {1} -> {2}".format(product, ver_from, version))
# Required because of a mismatch between the view and workflow states
# selector in Analysis Services view. See @93109be
setup.runImportStepFromProfile('profile-bika.lims:default', 'typeinfo')
# Remove indexes no longer used as per @daf57e3 and PR#307
ut.delIndexAndColumn('bika_setup_catalog', 'getSortKey')
ut.delIndexAndColumn('bika_setup_catalog', 'sortKey')
# Add sortable_title index in analyses catalog, so analyses get sorted
# automatically based on the same rules as Analysis Services do (PR#307):
# sortkey + title ascending
ut.addIndex(CATALOG_ANALYSIS_LISTING, 'sortable_title', 'FieldIndex')
ut.refreshCatalogs()
# Do nothing, we just only want the profile version to be 1.0.0
logger.info("{0} upgraded to version {1}".format(product, version))
return True
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 --------
# https://github.com/senaite/senaite.queue/pull/3
setup.runImportStepFromProfile(PROFILE_ID, "plone.app.registry")
setup.runImportStepFromProfile(PROFILE_ID, "actions")
# Remove queue dispatcher utility, that is no longer used
setup.runImportStepFromProfile(PROFILE_ID, "componentregistry")
remove_queue_dispatcher_utility(portal)
logger.info("{0} upgraded to version {1}".format(PRODUCT_NAME, version))
return True
def upgrade(tool):
portal = tool.aq_inner.aq_parent
ut = UpgradeUtils(portal)
ver_from = ut.getInstalledVersion(product)
if ut.isOlderVersion(product, version):
logger.info("Skipping upgrade of {0}: {1} > {2}".format(
product, ver_from, version))
return True
logger.info("Upgrading {0}: {1} -> {2}".format(product, ver_from, version))
# -------- ADD YOUR STUFF HERE --------
# Unbound the worksheetanalysis_workflow from Analysis Requests and add a
# FieldIndex 'assigned_state' in AR's catalog (for its use on searches)
fix_assign_analysis_requests(portal, ut)
# The number of QC Analyses is not refreshed when a Duplicate or Reference
# Sample in a Worksheet. See #673. Thus, worksheets that are not yet in
# to_be_verified state needs to be reindexed
fix_worksheet_qc_number_analyses_inconsistences(portal, ut)
logger.info("{0} upgraded to version {1}".format(product, version))
return True
def upgrade(tool):
portal = aq_parent(aq_inner(tool))
setup = portal.portal_setup
ut = UpgradeUtils(portal)
ver_from = ut.getInstalledVersion(product)
if ut.isOlderVersion(product, version):
logger.info("Skipping upgrade of {0}: {1} > {2}".format(
product, ver_from, version))
# The currently installed version is more recent than the target
# version of this upgradestep
return True
logger.info("Upgrading {0}: {1} -> {2}".format(product, ver_from, version))
# Required because of a mismatch between the view and workflow states
# selector in Analysis Services view. See @93109be
setup.runImportStepFromProfile('profile-bika.lims:default', 'typeinfo')
# Remove indexes no longer used as per @daf57e3 and PR#307
ut.delIndexAndColumn('bika_setup_catalog', 'getSortKey')
ut.delIndexAndColumn('bika_setup_catalog', 'sortKey')
# Add sortable_title index in analyses catalog, so analyses get sorted
# automatically based on the same rules as Analysis Services do (PR#307):
# sortkey + title ascending
ut.addIndex(CATALOG_ANALYSIS_LISTING, 'sortable_title', 'FieldIndex')
ut.refreshCatalogs()
# Do nothing, we just only want the profile version to be 1.0.0
logger.info("{0} upgraded to version {1}".format(product, version))
return True
def upgrade(tool):
portal = tool.aq_inner.aq_parent
ut = UpgradeUtils(portal)
ver_from = ut.getInstalledVersion(product)
setup = portal.portal_setup
if ut.isOlderVersion(product, version):
logger.info("Skipping upgrade of {0}: {1} > {2}".format(
product, ver_from, version))
return True
logger.info("Upgrading {0}: {1} -> {2}".format(product, ver_from, version))
# -------- ADD YOUR STUFF HERE --------
setup.runImportStepFromProfile(profile, 'catalog')
setup.runImportStepFromProfile(profile, 'workflow')
# Revert upgrade actions performed due to #893 (reverted)
revert_client_permissions_for_batches(portal)
# re-apply the permission for the view tabs on clients
setup.runImportStepFromProfile(profile, 'typeinfo')
# re-apply the permissions from the client workflow + reindex
fix_client_permissions(portal)
fix_items_stuck_in_sample_prep_states(portal, ut)
logger.info("{0} upgraded to version {1}".format(product, version))
return True
def upgrade(tool):
portal = tool.aq_inner.aq_parent
setup = portal.portal_setup
ut = UpgradeUtils(portal)
ver_from = ut.getInstalledVersion(product)
if ut.isOlderVersion(product, version):
logger.info("Skipping upgrade of {0}: {1} > {2}".format(
product, ver_from, version))
return True
logger.info("Upgrading {0}: {1} -> {2}".format(product, ver_from, version))
# -------- ADD YOUR STUFF BELOW --------
# Allow to detach a partition from its primary sample (#1420)
setup.runImportStepFromProfile(profile, "rolemap")
# Mixed permissions for transitions in client workflow (#1419)
# Allow to detach a partition from its primary sample (#1420)
setup.runImportStepFromProfile(profile, "workflow")
# Allow to detach a partition from its primary sample (#1420)
update_partitions_role_mappings(portal)
# Unindex stale catalog brains from the auditlog_catalog
# https://github.com/senaite/senaite.core/issues/1438
unindex_orphaned_brains_in_auditlog_catalog(portal)
logger.info("{0} upgraded to version {1}".format(product, version))
return True
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))
# Re-import the registry profile to add new settings in control panel
setup.runImportStepFromProfile(PROFILE_ID, "plone.app.registry")
# Reset control panel settings to defaults
reset_settings(portal)
# Port old storage mechanism
remove_legacy_storage(portal)
# Install the PAS Plugin to allow authenticating tasks as their creators
setup_pas_plugin(portal)
# Create and store the key to use for auth
reset_auth_key(portal)
logger.info("{0} upgraded to version {1}".format(PRODUCT_NAME, version))
return True
def upgrade(tool):
portal = tool.aq_inner.aq_parent
ut = UpgradeUtils(portal)
ver_from = ut.getInstalledVersion(product)
if ut.isOlderVersion(product, version):
logger.info("Skipping upgrade of {0}: {1} > {2}".format(
product, ver_from, version))
return True
logger.info("Upgrading {0}: {1} -> {2}".format(product, ver_from, version))
# -------- ADD YOUR STUFF HERE --------
# Ensure health's skins have always priority over core's
setup = portal.portal_setup
setup.runImportStepFromProfile(profile, "skins")
setup.runImportStepFromProfile(profile, 'workflow')
setup.runImportStepFromProfile(profile, "typeinfo")
# Allow clients to list, add and edit doctors
apply_doctor_permissions_for_clients(portal, ut)
logger.info("{0} upgraded to version {1}".format(product, version))
return True
def upgrade(tool):
portal = tool.aq_inner.aq_parent
setup = portal.portal_setup
ut = UpgradeUtils(portal)
ver_from = ut.getInstalledVersion(product)
if ut.isOlderVersion(product, version):
logger.info("Skipping upgrade of {0}: {1} > {2}".format(
product, ver_from, version))
return True
logger.info("Upgrading {0}: {1} -> {2}".format(product, ver_from, version))
# -------- ADD YOUR STUFF BELOW --------
setup.runImportStepFromProfile(profile, "actions")
setup.runImportStepFromProfile(profile, "rolemap")
setup.runImportStepFromProfile(profile, "workflow")
setup.runImportStepFromProfile(profile, "typeinfo")
setup.runImportStepFromProfile(profile, "toolset")
setup.runImportStepFromProfile(profile, "content")
setup.runImportStepFromProfile(profile, "controlpanel")
# Remove alls Samples and Partition
# https://github.com/senaite/senaite.core/pull/1359
remove_samples_and_partitions(portal)
# Convert inline images
# https://github.com/senaite/senaite.core/issues/1333
convert_inline_images_to_attachments(portal)
# https://github.com/senaite/senaite.core/pull/1324
# initialize auditlogging
setup_auditlog_catalog(portal)
init_auditlog(portal)
remove_log_action(portal)
# Mark objects based on the transitions performed to them
# https://github.com/senaite/senaite.core/pull/1330
mark_transitions_performed(portal)
# Reindex sortable_title to make sorting case-insenstive
# https://github.com/senaite/senaite.core/pull/1337
reindex_sortable_title(portal)
# Remove unnecessary indexes/metadata from worksheet catalog
# https://github.com/senaite/senaite.core/pull/1362
cleanup_worksheet_catalog(portal)
# Apply permissions for Manage Worksheets
# https://github.com/senaite/senaite.core/issues/1387
update_worksheet_manage_permissions(api.get_setup())
# Add getInternalUse metadata
# https://github.com/senaite/senaite.core/pull/1391
catalog = api.get_tool(CATALOG_ANALYSIS_REQUEST_LISTING)
catalog.addColumn("getInternalUse")
logger.info("{0} upgraded to version {1}".format(product, version))
return True
def upgrade(tool):
portal = tool.aq_inner.aq_parent
setup = portal.portal_setup
ut = UpgradeUtils(portal)
ver_from = ut.getInstalledVersion(PROJECTNAME)
if ut.isOlderVersion(PROJECTNAME, version):
logger.info("Skipping upgrade of {0}: {1} > {2}".format(
PROJECTNAME, ver_from, version))
return True
logger.info("Upgrading {0}: {1} -> {2}".format(PROJECTNAME, ver_from,
version))
# -------- ADD YOUR STUFF BELOW --------
# Added action "batches" for Doctor type
setup.runImportStepFromProfile(profile, "typeinfo")
# Added InternalClient role
setup.runImportStepFromProfile(DEFAULT_PROFILE_ID, "rolemap")
# Added new state "shared" in patient_workflow, doctor_workflow
setup.runImportStepFromProfile(DEFAULT_PROFILE_ID, "workflow")
# Setup custom workflows (Batch)
setup_workflows(portal)
# Setup internal clients top-level folder
setup_internal_clients(portal)
# Sort navigation bar
sort_nav_bar(portal)
# Reindex the top level folder in the portal and setup to fix missing icons
reindex_content_structure(portal)
# Hide Doctor items from navigation bar
hide_doctors_from_navbar(portal)
# Add batches action in Doctor context
sort_doctor_actions(portal)
# Setup groups (new group "InternalClient")
setup_user_groups(portal)
# Allow Patients and Doctors inside Clients
allow_patients_inside_clients(portal)
allow_doctors_inside_clients(portal)
# Move doctors to clients
move_doctors_to_clients(portal)
# Update workflows for shareable objects (Patient, Doctor, Batch)
update_rolemappings_for_shareable(portal)
logger.info("{0} upgraded to version {1}".format(PROJECTNAME, version))
return True
def upgrade(tool):
portal = tool.aq_inner.aq_parent
setup = portal.portal_setup
ut = UpgradeUtils(portal)
ver_from = ut.getInstalledVersion(product)
if ut.isOlderVersion(product, version):
logger.info("Skipping upgrade of {0}: {1} > {2}".format(
product, ver_from, version))
return True
logger.info("Upgrading {0}: {1} -> {2}".format(product, ver_from, version))
# -------- ADD YOUR STUFF HERE --------
# Display supplier view instead of reference samples per default
# https://github.com/senaite/senaite.core/pull/1037
setup.runImportStepFromProfile(profile, 'typeinfo')
# Delete orphaned Attachments
# https://github.com/senaite/senaite.core/issues/1025
delete_orphaned_attachments(portal)
# Migrate report option from attach (a) -> ignore (i)
# https://github.com/senaite/senaite.core/pull/992
migrate_attachment_report_options(portal)
# Reindex object security for client contents
# https://github.com/senaite/senaite.core/pull/991
reindex_client_local_owner_permissions(portal)
# Rename "retract_ar" transition to "invalidate"
# https://github.com/senaite/senaite.core/pull/1027
rename_retract_ar_transition(portal)
# Rebind ARs that were generated because of the invalidation of other ARs
# https://github.com/senaite/senaite.core/pull/1027
rebind_invalidated_ars(portal)
# Reindex Turnaround time and due date related fields
# https://github.com/senaite/senaite.core/pull/1032
recatalog_analyses_due_date(portal)
# Update workflow states and permissions for AR/Sample rejection
# https://github.com/senaite/senaite.core/pull/1041
update_rejection_permissions(portal)
# Remove getLate and add getDueDate metadata in ar_catalog
# https://github.com/senaite/senaite.core/pull/1051
update_analaysisrequests_due_date(portal)
logger.info("{0} upgraded to version {1}".format(product, version))
return True
def upgrade(tool):
portal = tool.aq_inner.aq_parent
setup = portal.portal_setup
ut = UpgradeUtils(portal)
ver_from = ut.getInstalledVersion(PROJECTNAME)
if ut.isOlderVersion(PROJECTNAME, version):
logger.info("Skipping upgrade of {0}: {1} > {2}".format(
PROJECTNAME, ver_from, version))
return True
logger.info("Upgrading {0}: {1} -> {2}".format(PROJECTNAME, ver_from,
version))
# -------- ADD YOUR STUFF BELOW --------
setup.runImportStepFromProfile(profile, "browserlayer")
setup.runImportStepFromProfile(profile, "typeinfo")
setup.runImportStepFromProfile(profile, "skins")
# Setup catalogs
setup_catalogs(CATALOGS_BY_TYPE, INDEXES, COLUMNS)
# Remove indexes and metadata columns
remove_indexes_and_metadata()
# Setup permissions
setup_roles_permissions(portal)
# Setup ID Formatting
setup_id_formatting(portal)
# Add "Patients" and "Doctors" action views in Client type
setup_content_actions(portal)
# Remove "Samples" action views from Doctors and Patients
remove_sample_actions(portal)
# Setup "Owner" roles for patients to client contacts
setup_patients_ownership(portal)
# Setup "Owner" roles for batches to client contacts
setup_batches_ownership(portal)
# Update workflows
update_workflows(portal)
# remove stale CSS
remove_stale_css(portal)
logger.info("{0} upgraded to version {1}".format(PROJECTNAME, version))
return True
def upgrade(tool):
portal = tool.aq_inner.aq_parent
setup = portal.portal_setup
ut = UpgradeUtils(portal)
ver_from = ut.getInstalledVersion(PROJECTNAME)
if ut.isOlderVersion(PROJECTNAME, version):
logger.info("Skipping upgrade of {0}: {1} > {2}".format(
PROJECTNAME, ver_from, version))
return True
logger.info("Upgrading {0}: {1} -> {2}".format(PROJECTNAME, ver_from,
version))
# -------- ADD YOUR STUFF BELOW --------
setup.runImportStepFromProfile(profile, "browserlayer")
setup.runImportStepFromProfile(profile, "typeinfo")
setup.runImportStepFromProfile(profile, "skins")
# Setup catalogs
setup_catalogs(CATALOGS_BY_TYPE, INDEXES, COLUMNS)
# Remove indexes and metadata columns
remove_indexes_and_metadata()
# Setup permissions
setup_roles_permissions(portal)
# Setup ID Formatting
setup_id_formatting(portal)
# Add "Patients" and "Doctors" action views in Client type
setup_content_actions(portal)
# Remove "Samples" action views from Doctors and Patients
remove_sample_actions(portal)
# Setup "Owner" roles for patients to client contacts
setup_patients_ownership(portal)
# Setup "Owner" roles for batches to client contacts
setup_batches_ownership(portal)
# Update workflows
update_workflows(portal)
# remove stale CSS
remove_stale_css(portal)
logger.info("{0} upgraded to version {1}".format(PROJECTNAME, version))
return True
def upgrade(tool):
portal = tool.aq_inner.aq_parent
setup = portal.portal_setup
ut = UpgradeUtils(portal)
ver_from = ut.getInstalledVersion(product)
if ut.isOlderVersion(product, version):
logger.info("Skipping upgrade of {0}: {1} > {2}".format(
product, ver_from, version))
return True
logger.info("Upgrading {0}: {1} -> {2}".format(product, ver_from, version))
# -------- ADD YOUR STUFF BELOW --------
# Do not display clients folder to Clients. There is no need to do an
# update-role-mappings of clients, cause the permissions at client level
# have not changed, except that now they are acquire=1 for "active" status
setup.runImportStepFromProfile(profile, "workflow")
wf_tool = api.get_tool("portal_workflow")
workflow = wf_tool.getWorkflowById("senaite_clients_workflow")
workflow.updateRoleMappingsFor(portal.clients)
portal.clients.reindexObject()
# New link to My Organization
setup.runImportStepFromProfile(profile, "actions")
# Remove getObjectWorkflowStates metadata
# https://github.com/senaite/senaite.core/pull/1579
remove_object_workflow_states_metadata(portal)
# Added "senaite.core: Transition: Retest" permission for analyses
# Added transition "retest" in analysis workflow
# https://github.com/senaite/senaite.core/pull/1580
setup.runImportStepFromProfile(profile, "rolemap")
setup.runImportStepFromProfile(profile, "workflow")
update_workflow_mappings_for_to_be_verified(portal)
# Unset/set specifications with dynamic results ranges assigned
# https://github.com/senaite/senaite.core/pull/1588
update_dynamic_analysisspecs(portal)
# Users with Publisher role cannot publish samples
update_workflow_mappings_contacts(portal)
update_workflow_mappings_labcontacts(portal)
update_workflow_mappings_samples(portal)
logger.info("{0} upgraded to version {1}".format(product, version))
return True
def upgrade(tool):
portal = tool.aq_inner.aq_parent
ut = UpgradeUtils(portal)
ver_from = ut.getInstalledVersion(product)
if ut.isOlderVersion(product, version):
logger.info("Skipping upgrade of {0}: {1} > {2}".format(
product, ver_from, version))
return True
logger.info("Upgrading {0}: {1} -> {2}".format(product, ver_from, version))
# Required to make filtering by department in worksheets work
ut.addIndex(CATALOG_WORKSHEET_LISTING, 'getDepartmentUIDs', 'KeywordIndex')
# Required by https://github.com/senaite/senaite.core/issues/683
ut.addIndexAndColumn('bika_catalog', 'getBatchUIDs', 'KeywordIndex')
# Required by https://github.com/senaite/senaite.core/pulls/752
ut.delIndex(CATALOG_ANALYSIS_LISTING, 'getDateAnalysisPublished')
ut.refreshCatalogs()
# % Error subfield is meaningless in result ranges. Also, the system was
# calculating the %Error based on the result (not based on the range), so
# the shoulder from the left was always smaller than the shoulder from the
# right. One could argue that this could be fixed easily by using the length
# of the valid range to compute the shoulders by using the %error. Again,
# this is a weak solution, cause in some cases the scale of the range might
# be exponential, logaritmic (e.g. pH). Also, the sensitivity of the test
# may differ when the result falls in one end or another. Thus, is for the
# best interest of the labmanger to be able to set the shoulders (and
# therefore, when the warnings must show up) manually.
# See PR#694
remove_error_subfield_from_analysis_specs(portal, ut)
# Reindex ReferenceAnalysis because of Calculation and Interims fields have
# been added to Controls and Blanks. Until now, only routine analyses allowed
# Calculations and Interim fields
# Required by https://github.com/senaite/senaite.core/issues/735
reindex_reference_analysis(portal, ut)
# reload type profiles so that the fix for
# https://github.com/senaite/senaite.core/issues/590
# becomes effective
setup = portal.portal_setup
setup.runImportStepFromProfile('profile-bika.lims:default', 'typeinfo')
logger.info("{0} upgraded to version {1}".format(product, version))
return True
def upgrade(tool):
portal = tool.aq_inner.aq_parent
setup = portal.portal_setup
ut = UpgradeUtils(portal)
ver_from = ut.getInstalledVersion(PROJECTNAME)
if ut.isOlderVersion(PROJECTNAME, version):
logger.info("Skipping upgrade of {0}: {1} > {2}".format(
PROJECTNAME, ver_from, version))
return True
logger.info("Upgrading {0}: {1} -> {2}".format(PROJECTNAME, ver_from,
version))
# -------- ADD YOUR STUFF BELOW --------
setup.runImportStepFromProfile(DEFAULT_PROFILE_ID, "skins")
setup.runImportStepFromProfile(DEFAULT_PROFILE_ID, "jsregistry")
# Install senaite.panic add-on if not yet installed
install_senaite_panic(portal)
# Setup template text for panic level alert emails
# https://github.com/senaite/senaite.health/pull/161
setup_panic_alerts(portal)
# Update Sample's PanicEmailAlertSent field
# https://github.com/senaite/senaite.health/pull/161
update_sample_panic_alert_field(portal)
# Allow Patient content type inside Client
# Note: this should always be run if core's typestool is reimported
allow_patients_inside_clients(portal)
# Remove stale javascripts
remove_stale_javascripts(portal)
# Remove stale css
remove_stale_css(portal)
# Fix email addresses
# https://github.com/senaite/senaite.health/pulls/172
fix_health_email_addresses(portal)
# Remove stale catalog columns
remove_stale_metadata(portal)
logger.info("{0} upgraded to version {1}".format(PROJECTNAME, version))
return True
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))
logger.info("{0} upgraded to version {1}".format(PRODUCT_NAME, version))
return True
def upgrade(tool):
portal = tool.aq_inner.aq_parent
ut = UpgradeUtils(portal)
ver_from = ut.getInstalledVersion(product)
if ut.isOlderVersion(product, version):
logger.info("Skipping upgrade of {0}: {1} > {2}".format(
product, ver_from, version))
return True
logger.info("Upgrading {0}: {1} -> {2}".format(product, ver_from, version))
# -------- ADD YOUR STUFF HERE --------
logger.info("{0} upgraded to version {1}".format(product, version))
return True
def upgrade(tool):
portal = aq_parent(aq_inner(tool))
ut = UpgradeUtils(portal)
ver_from = ut.getInstalledVersion(product)
if ut.isOlderVersion(product, version):
logger.info("Skipping upgrade of {0}: {1} > {2}".format(
product, ver_from, version))
# The currently installed version is more recent than the target
# version of this upgradestep
return True
logger.info("Upgrading {0}: {1} -> {2}".format(product, ver_from, version))
# Do nothing, we just only want the profile version to be 1.1.0
logger.info("{0} upgraded to version {1}".format(product, version))
return True
def upgrade(tool):
portal = tool.aq_inner.aq_parent
ut = UpgradeUtils(portal)
ver_from = ut.getInstalledVersion(product)
if ut.isOlderVersion(product, version):
logger.info("Skipping upgrade of {0}: {1} > {2}".format(
product, ver_from, version))
return True
logger.info("Upgrading {0}: {1} -> {2}".format(product, ver_from, version))
ut.addIndex(CATALOG_PATIENTS, 'getClientPatientID', 'FieldIndex')
ut.refreshCatalogs()
logger.info("{0} upgraded to version {1}".format(product, version))
return True
def upgrade(tool):
portal = tool.aq_inner.aq_parent
ut = UpgradeUtils(portal)
ver_from = ut.getInstalledVersion(product)
if ut.isOlderVersion(product, version):
logger.info("Skipping upgrade of {0}: {1} > {2}".format(
product, ver_from, version))
return True
logger.info("Upgrading {0}: {1} -> {2}".format(product, ver_from, version))
ut.addIndex(CATALOG_PATIENTS, 'getClientPatientID', 'FieldIndex')
ut.refreshCatalogs()
logger.info("{0} upgraded to version {1}".format(product, version))
return True
def upgrade(tool):
portal = tool.aq_inner.aq_parent
ut = UpgradeUtils(portal)
ver_from = ut.getInstalledVersion(product)
if ut.isOlderVersion(product, version):
logger.info("Skipping upgrade of {0}: {1} > {2}".format(
product, ver_from, version))
return True
logger.info("Upgrading {0}: {1} -> {2}".format(product, ver_from, version))
# -------- ADD YOUR STUFF HERE --------
ut.cleanAndRebuildCatalog(CATALOG_ANALYSIS_REQUEST_LISTING)
logger.info("{0} upgraded to version {1}".format(product, version))
return True
def upgrade(tool):
portal = tool.aq_inner.aq_parent
setup = portal.portal_setup
ut = UpgradeUtils(portal)
ver_from = ut.getInstalledVersion(product)
if ut.isOlderVersion(product, version):
logger.info("Skipping upgrade of {0}: {1} > {2}".format(
product, ver_from, version))
# The currently installed version is more recent than the target
# version of this upgradestep
return True
logger.info("Upgrading {0}: {1} -> {2}".format(product, ver_from, version))
# Convert ReferenceField's values into UIDReferenceFields.
UpgradeReferenceFields()
# Calculations not triggered in manage results view
# https://github.com/senaite/bika.lims/issues/355
# Since we've already migrated the ReferenceField DependentServices from
# Calculation (with relation name 'CalculationAnalysisService' above, this
# wouldn't be strictly necessary, but who knows... maybe we've lost the
# at_references too, so just do it.
fix_broken_calculations()
# Backward compatibility with < 1.0.0
RemoveARPriorities(portal)
RemoveVersionableTypes()
handle_AS_wo_category(portal)
migrateFileFields(portal)
# Indexes and colums were changed as per
# https://github.com/senaite/bika.lims/pull/353
ut.delIndex(CATALOG_ANALYSIS_LISTING, 'getAnalysisRequestUID')
ut.addIndex(CATALOG_ANALYSIS_LISTING, 'getRequestUID', 'FieldIndex')
ut.delColumn(CATALOG_ANALYSIS_LISTING, 'getAnalysisRequestURL')
ut.delColumn(CATALOG_ANALYSIS_LISTING, 'getAnalysisRequestTitle')
ut.addColumn(CATALOG_ANALYSIS_LISTING, 'getRequestURL')
ut.addColumn(CATALOG_ANALYSIS_LISTING, 'getRequestTitle')
ut.reindexIndex(CATALOG_ANALYSIS_LISTING, 'getPrioritySortkey')
ut.refreshCatalogs()
return True
def upgrade(tool):
portal = tool.aq_inner.aq_parent
setup = portal.portal_setup
ut = UpgradeUtils(portal)
ver_from = ut.getInstalledVersion(product)
if ut.isOlderVersion(product, version):
logger.info("Skipping upgrade of {0}: {1} > {2}".format(
product, ver_from, version))
# The currently installed version is more recent than the target
# version of this upgradestep
return True
logger.info("Upgrading {0}: {1} -> {2}".format(product, ver_from, version))
# Convert ReferenceField's values into UIDReferenceFields.
UpgradeReferenceFields()
# Calculations not triggered in manage results view
# https://github.com/senaite/bika.lims/issues/355
# Since we've already migrated the ReferenceField DependentServices from
# Calculation (with relation name 'CalculationAnalysisService' above, this
# wouldn't be strictly necessary, but who knows... maybe we've lost the
# at_references too, so just do it.
fix_broken_calculations()
# Backward compatibility with < 1.0.0
RemoveARPriorities(portal)
RemoveVersionableTypes()
handle_AS_wo_category(portal)
migrateFileFields(portal)
# Indexes and colums were changed as per
# https://github.com/senaite/bika.lims/pull/353
ut.delIndex(CATALOG_ANALYSIS_LISTING, 'getAnalysisRequestUID')
ut.addIndex(CATALOG_ANALYSIS_LISTING, 'getRequestUID', 'FieldIndex')
ut.delColumn(CATALOG_ANALYSIS_LISTING, 'getAnalysisRequestURL')
ut.delColumn(CATALOG_ANALYSIS_LISTING, 'getAnalysisRequestTitle')
ut.addColumn(CATALOG_ANALYSIS_LISTING, 'getRequestURL')
ut.addColumn(CATALOG_ANALYSIS_LISTING, 'getRequestTitle')
ut.reindexIndex(CATALOG_ANALYSIS_LISTING, 'getPrioritySortkey')
ut.refreshCatalogs()
return True
def upgrade(tool):
portal = tool.aq_inner.aq_parent
setup = portal.portal_setup
ut = UpgradeUtils(portal)
ver_from = ut.getInstalledVersion(product)
if ut.isOlderVersion(product, version):
logger.info("Skipping upgrade of {0}: {1} > {2}".format(
product, ver_from, version))
return True
logger.info("Upgrading {0}: {1} -> {2}".format(product, ver_from, version))
# -------- ADD YOUR STUFF BELOW --------
setup.runImportStepFromProfile(profile, 'browserlayer')
logger.info("{0} upgraded to version {1}".format(product, version))
return True
def upgrade(tool):
portal = tool.aq_inner.aq_parent
ut = UpgradeUtils(portal)
ver_from = ut.getInstalledVersion(product)
setup = portal.portal_setup
if ut.isOlderVersion(product, version):
logger.info("Skipping upgrade of {0}: {1} > {2}".format(
product, ver_from, version))
return True
logger.info("Upgrading {0}: {1} -> {2}".format(product, ver_from, version))
# -------- ADD YOUR STUFF HERE --------
setup.runImportStepFromProfile(profile, 'workflow')
update_permissions_rejected_analysis_requests()
logger.info("{0} upgraded to version {1}".format(product, version))
return True
def upgrade(tool):
portal = aq_parent(aq_inner(tool))
ut = UpgradeUtils(portal)
ver_from = ut.getInstalledVersion(product)
# Since this upgrade is precisely meant to establish a version regardless
# of the version numbering at bikalims/bika.health, we don't want this check
# to be performed.
# if ut.isOlderVersion(product, version):
# logger.info("Skipping upgrade of {0}: {1} > {2}".format(
# product, ufrom, version))
# # The currently installed version is more recent than the target
# # version of this upgradestep
# return True
logger.info("Upgrading {0}: {1} -> {2}".format(product, ver_from, version))
# Do nothing, we just only want the profile version to be 1.0.0
logger.info("{0} upgraded to version {1}".format(product, version))
return True
def upgrade(tool):
portal = tool.aq_inner.aq_parent
setup = portal.portal_setup
ut = UpgradeUtils(portal)
ver_from = ut.getInstalledVersion(product)
if ut.isOlderVersion(product, version):
logger.info("Skipping upgrade of {0}: {1} > {2}".format(
product, ver_from, version))
# The currently installed version is more recent than the target
# version of this upgradestep
return True
logger.info("Upgrading {0}: {1} -> {2}".format(product, ver_from, version))
# Sync the empty number generator with existing content
prepare_number_generator(portal)
logger.info("{0} upgraded to version {1}".format(product, version))
return True
def upgrade(tool):
portal = tool.aq_inner.aq_parent
ut = UpgradeUtils(portal)
ver_from = ut.getInstalledVersion(product)
if ut.isOlderVersion(product, version):
logger.info("Skipping upgrade of {0}: {1} > {2}".format(
product, ver_from, version))
return True
logger.info("Upgrading {0}: {1} -> {2}".format(product, ver_from, version))
# -------- ADD YOUR STUFF HERE --------
set_guards_to_inactive_workflow()
fix_service_status_inconsistences()
fix_service_profile_template_inconsistences()
logger.info("{0} upgraded to version {1}".format(product, version))
return True
def upgrade(tool):
portal = tool.aq_inner.aq_parent
ut = UpgradeUtils(portal)
ver_from = ut.getInstalledVersion(product)
if ut.isOlderVersion(product, version):
logger.info("Skipping upgrade of {0}: {1} > {2}".format(
product, ver_from, version))
return True
logger.info("Upgrading {0}: {1} -> {2}".format(product, ver_from, version))
# -------- ADD YOUR STUFF HERE --------
setup = portal.portal_setup
setup.runImportStepFromProfile('profile-bika.lims:default', 'plone.app.registry')
upgrade_indexes()
logger.info("{0} upgraded to version {1}".format(product, version))
return True
def upgrade(tool):
portal = aq_parent(aq_inner(tool))
setup = portal.portal_setup
ut = UpgradeUtils(portal)
ver_from = ut.getInstalledVersion(product)
if ut.isOlderVersion(product, version):
logger.info("Skipping upgrade of {0}: {1} > {2}".format(
product, ver_from, version))
# The currently installed version is more recent than the target
# version of this upgradestep
return True
logger.info("Upgrading {0}: {1} -> {2}".format(product, ver_from, version))
# Add inactive_state workflow for Reflex Rules
setup.runImportStepFromProfile(profile, 'workflow')
update_reflexrules_workflow_state(portal)
logger.info("{0} upgraded to version {1}".format(product, version))
return True
def upgrade(tool):
portal = aq_parent(aq_inner(tool))
setup = portal.portal_setup
ut = UpgradeUtils(portal)
ver_from = ut.getInstalledVersion(product)
if ut.isOlderVersion(product, version):
logger.info("Skipping upgrade of {0}: {1} > {2}".format(
product, ver_from, version))
# The currently installed version is more recent than the target
# version of this upgradestep
return True
logger.info("Upgrading {0}: {1} -> {2}".format(product, ver_from, version))
# Attachments must be present in a catalog, otherwise the idserver
# will fall apart. https://github.com/senaite/bika.lims/issues/323
at = getToolByName(portal, 'archetype_tool')
at.setCatalogsByType('Attachment', ['portal_catalog'])
logger.info("{0} upgraded to version {1}".format(product, version))
return True
def upgrade(tool):
portal = aq_parent(aq_inner(tool))
setup = portal.portal_setup
ut = UpgradeUtils(portal)
ver_from = ut.getInstalledVersion(product)
if ut.isOlderVersion(product, version):
logger.info("Skipping upgrade of {0}: {1} > {2}".format(
product, ver_from, version))
# The currently installed version is more recent than the target
# version of this upgradestep
return True
logger.info("Upgrading {0}: {1} -> {2}".format(product, ver_from, version))
# Reindex getPrioritySortkey index. The priority sort key from analyses
# takes also into account analyses have to be sorted by their sortkey, so
# two analyses with same priority, same AR, but different sort key values
# don't get mixed.
ut.reindexIndex(CATALOG_ANALYSIS_LISTING, 'getPrioritySortkey')
ut.refreshCatalogs()
logger.info("{0} upgraded to version {1}".format(product, version))
return True
def upgrade(tool):
portal = tool.aq_inner.aq_parent
ut = UpgradeUtils(portal)
ver_from = ut.getInstalledVersion(product)
if ut.isOlderVersion(product, version):
logger.info("Skipping upgrade of {0}: {1} > {2}".format(
product, ver_from, version))
return True
logger.info("Upgrading {0}: {1} -> {2}".format(product, ver_from, version))
# -------- ADD YOUR STUFF HERE --------
fix_workflow_transitions(portal)
# Migration to senaite.core
setup = portal.portal_setup
setup.runImportStepFromProfile('profile-bika.lims:default', 'typeinfo')
setup.runImportStepFromProfile('profile-bika.lims:default', 'propertiestool')
rename_bika_setup()
logger.info("{0} upgraded to version {1}".format(product, version))
return True
