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)
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 = 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)
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
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
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
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')
ut.refreshCatalogs()
logger.info("{0} upgraded to version {1}".format(product, version))
return True
def upgrade(tool):
portal = aq_parent(aq_inner(tool))
ut = UpgradeUtils(portal)
ufrom = ut.getInstalledVersion(product)
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, ufrom, version))
# Add index for LIMS-2082 to allow analyses to be correctly filtered by
# instrument in worksheet/add_analyses
ut.addIndex('bika_analysis_catalog', 'getAllowedInstrumentUIDs',
'KeywordIndex')
# Refresh affected catalogs
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 --------
# Lab Managers can not remove Analyses in "Manage Analyses" form
fix_permission_on_analysisrequests()
# Traceback when submitting duplicate when Duplicate Variation is not set
# Walkthrough all analyses and analyses services and set 0.00 value for
# DuplicateVariation if returns None
# https://github.com/senaite/senaite.core/issues/768
fix_duplicate_variation_nonfloatable_values()
# Analyses submission in Worksheets is slow
# Remove "_LatestReferenceAnalyses" ReferenceField. Is not used anymore,
# https://github.com/senaite/senaite.core/pull/776
del_at_refs('InstrumentLatestReferenceAnalyses')
# Make searches in Analysis Request listings faster
# https://github.com/senaite/senaite.core/pull/771
ut.addIndex(CATALOG_ANALYSIS_REQUEST_LISTING, "listing_searchable_text",
"TextIndexNG3")
ut.refreshCatalogs()
logger.info("{0} upgraded to version {1}".format(product, version))
return True
