def upgrade(tool):
portal = aq_parent(aq_inner(tool))
bc = getToolByName(portal, 'bika_catalog')
bac = getToolByName(portal, 'bika_analysis_catalog')
pc = getToolByName(portal, 'portal_catalog')
portal = aq_parent(aq_inner(tool))
setup = portal.portal_setup
wf = getToolByName(portal, 'portal_workflow')
# Update all tools in which changes have been made
setup.runImportStepFromProfile('profile-bika.lims:default', 'propertiestool')
setup.runImportStepFromProfile('profile-bika.lims:default', 'typeinfo')
setup.runImportStepFromProfile('profile-bika.lims:default', 'repositorytool')
setup.runImportStepFromProfile('profile-bika.lims:default', 'workflow')
setup.runImportStepFromProfile('profile-bika.lims:default', 'factorytool')
setup.runImportStepFromProfile('profile-bika.lims:default', 'jsregistry')
setup.runImportStepFromProfile('profile-bika.lims:default', 'portlets', run_dependencies=False)
setup.runImportStepFromProfile('profile-bika.lims:default', 'viewlets')
setup.runImportStepFromProfile('profile-plone.app.jquery:default', 'jsregistry')
# Re-import the default permission maps
gen = BikaGenerator()
gen.setupPermissions(portal)
logger.info("Updating workflow role/permission mappings")
wf.updateRoleMappings()
logger.info("Rebuilding portal_catalog")
pc.clearFindAndRebuild()
logger.info("Rebuilding bika_analysis_catalog")
bac.clearFindAndRebuild()
logger.info("Rebuilding bika_catalog")
bc.clearFindAndRebuild()
return True
def upgrade(tool):
"""
issue #948 requires permission updates
"""
portal = aq_parent(aq_inner(tool))
setup = portal.portal_setup
typestool = getToolByName(portal, 'portal_types')
# update affected tools
setup.runImportStepFromProfile('profile-bika.lims:default', 'typeinfo')
# re-import default permissions
from bika.lims.setuphandlers import BikaGenerator
gen = BikaGenerator()
gen.setupPermissions(portal)
return True
def upgrade(tool):
portal = aq_parent(aq_inner(tool))
bc = getToolByName(portal, 'bika_catalog')
bac = getToolByName(portal, 'bika_analysis_catalog')
pc = getToolByName(portal, 'portal_catalog')
portal = aq_parent(aq_inner(tool))
setup = portal.portal_setup
wf = getToolByName(portal, 'portal_workflow')
# Update all tools in which changes have been made
setup.runImportStepFromProfile('profile-bika.lims:default',
'propertiestool')
setup.runImportStepFromProfile('profile-bika.lims:default', 'typeinfo')
setup.runImportStepFromProfile('profile-bika.lims:default',
'repositorytool')
setup.runImportStepFromProfile('profile-bika.lims:default', 'workflow')
setup.runImportStepFromProfile('profile-bika.lims:default', 'factorytool')
setup.runImportStepFromProfile('profile-bika.lims:default', 'jsregistry')
setup.runImportStepFromProfile('profile-bika.lims:default',
'portlets',
run_dependencies=False)
setup.runImportStepFromProfile('profile-bika.lims:default', 'viewlets')
setup.runImportStepFromProfile('profile-plone.app.jquery:default',
'jsregistry')
# Re-import the default permission maps
gen = BikaGenerator()
gen.setupPermissions(portal)
logger.info("Updating workflow role/permission mappings")
wf.updateRoleMappings()
logger.info("Rebuilding portal_catalog")
pc.clearFindAndRebuild()
logger.info("Rebuilding bika_analysis_catalog")
bac.clearFindAndRebuild()
logger.info("Rebuilding bika_catalog")
bc.clearFindAndRebuild()
return True
def upgrade(tool):
portal = aq_parent(aq_inner(tool))
at = getToolByName(portal, 'archetype_tool')
bc = getToolByName(portal, 'bika_catalog')
bac = getToolByName(portal, 'bika_analysis_catalog')
bsc = getToolByName(portal, 'bika_setup_catalog')
pc = getToolByName(portal, 'portal_catalog')
portal = aq_parent(aq_inner(tool))
portal_catalog = getToolByName(portal, 'portal_catalog')
portal_groups = portal.portal_groups
setup = portal.portal_setup
typestool = getToolByName(portal, 'portal_types')
wf = getToolByName(portal, 'portal_workflow')
# Update all tools in which changes have been made
setup.runImportStepFromProfile('profile-bika.lims:default', 'propertiestool')
setup.runImportStepFromProfile('profile-bika.lims:default', 'typeinfo')
setup.runImportStepFromProfile('profile-bika.lims:default', 'repositorytool')
setup.runImportStepFromProfile('profile-bika.lims:default', 'workflow')
setup.runImportStepFromProfile('profile-bika.lims:default', 'workflow-csv')
setup.runImportStepFromProfile('profile-bika.lims:default', 'factorytool')
setup.runImportStepFromProfile('profile-bika.lims:default', 'jsregistry')
setup.runImportStepFromProfile('profile-bika.lims:default', 'portlets', run_dependencies=False)
setup.runImportStepFromProfile('profile-bika.lims:default', 'viewlets')
setup.runImportStepFromProfile('profile-plone.app.jquery:default', 'jsregistry')
# Add RegulatoryInspectors group and RegulatoryInspector role.
# Fix permissions: LabClerks don't see analysis results
role = 'RegulatoryInspector'
group = 'RegulatoryInspectors'
if role not in portal.acl_users.portal_role_manager.listRoleIds():
portal.acl_users.portal_role_manager.addRole(role)
portal._addRole(role)
if group not in portal_groups.listGroupIds():
portal_groups.addGroup('RegulatoryInspectors',
title="Regulatory Inspectors",
roles=['Member', 'RegulatoryInspector', ])
else:
portal_groups.setRolesForGroup('RegulatoryInspectors',
['Member', 'RegulatoryInspector', ])
# Add SampleConditions
at.setCatalogsByType('SampleCondition', ['bika_setup_catalog'])
if not portal['bika_setup'].get('bika_sampleconditions'):
typestool.constructContent(type_name="SampleConditions",
container=portal['bika_setup'],
id='bika_sampleconditions',
title='Sample Conditions')
obj = portal['bika_setup']['bika_sampleconditions']
obj.unmarkCreationFlag()
obj.reindexObject()
# Add SampleCondition to all Sample objects
proxies = portal_catalog(portal_type="Sample")
samples = (proxy.getObject() for proxy in proxies)
for sample in samples:
sample.setSampleCondition(None)
# Some catalog indexes were added or modified
if 'getSampleTypeTitle' in bc.indexes():
bc.delIndex('getSampleTypeTitle')
if 'getSamplePointTitle' in bc.indexes():
bc.delIndex('getSamplePointTitle')
bc.addIndex('getSampleTypeTitle', 'KeywordIndex')
bc.addIndex('getSamplePointTitle', 'KeywordIndex')
if 'getClientSampleID' in pc.indexes():
pc.addIndex('getClientSampleID', 'FieldIndex')
pc.addColumn('getClientSampleID')
if 'getParentUID' not in pc.indexes():
pc.addIndex('getParentUID', 'FieldIndex')
pc.addColumn('getParentUID')
if 'getReferenceAnalysesGroupID' not in bac.indexes():
bac.addIndex('getReferenceAnalysesGroupID', 'FieldIndex')
bac.addColumn('getReferenceAnalysesGroupID')
# Fix broken template partition containers
for p in bsc(portal_type='ARTemplate'):
o = p.getObject()
parts = o.getPartitions()
for i, part in enumerate(parts):
if 'container_uid' in part:
container = bsc(portal_type='Container',
UID=part['container_uid'])
if container:
container = container[0].getObject()
parts[i]['Container'] = container.Title()
if 'preservation_uid' in p:
preservation = bsc(portal_type='Preservation',
UID=part['preservation_uid'])
if preservation:
preservation = preservation[0].getObject()
parts[i]['Preservation'] = preservation.Title()
# Populate ReferenceAnalysesGroupIDs for ReferenceAnalyses
# https://github.com/bikalabs/Bika-LIMS/issues/931
wss = bc(portal_type='Worksheet')
for ws in wss:
ws = ws.getObject()
wsangroups = {}
codes = {}
# Reference Analyses (not duplicates)
refanalyses = [an for an in ws.getAnalyses()
if an.portal_type == 'ReferenceAnalysis'
or an.portal_type == 'DuplicateAnalysis']
layout = ws.getLayout()
for lay in layout:
for an in refanalyses:
if lay['analysis_uid'] == an.UID():
position = lay['position']
if position not in wsangroups.keys():
wsangroups[position] = []
wsangroups[position].append(an)
for position, wsgroup in wsangroups.iteritems():
analysis = wsgroup[0]
if analysis.portal_type == 'ReferenceAnalysis':
refsampleid = wsgroup[0].aq_parent.id
else:
# Duplicate
refsampleid = wsgroup[0].getSamplePartition().id
codre = refsampleid
codws = '%s_%s' % (refsampleid, ws.UID())
codgr = '%s_%s_%s' % (refsampleid, ws.UID(), position)
if codgr in codes.keys():
postfix = codes[codgr]
elif codws in codes.keys():
postfix = codes[codws]
codes[codgr] = postfix
codes[codws] = postfix + 1
elif codre in codes.keys():
postfix = codes[codre]
codes[codgr] = postfix
codes[codws] = postfix + 1
codes[codre] = postfix + 1
else:
postfix = 1
codes[codre] = postfix + 1
for an in wsgroup:
if an.portal_type == 'DuplicateAnalysis':
postfix = str(postfix).zfill(int(2))
refgid = '%s-D%s' % (refsampleid, postfix)
else:
postfix = str(postfix).zfill(int(3))
refgid = '%s-%s' % (refsampleid, postfix)
an.setReferenceAnalysesGroupID(refgid)
# Re-import the default permission maps
gen = BikaGenerator()
gen.setupPermissions(portal)
logger.info("Updating workflow role/permission mappings")
wf.updateRoleMappings()
logger.info("Rebuilding portal_catalog")
pc.clearFindAndRebuild()
logger.info("Rebuilding bika_analysis_catalog")
bac.clearFindAndRebuild()
logger.info("Rebuilding bika_catalog")
bc.clearFindAndRebuild()
return True
def upgrade(tool):
# Hack prevent out-of-date upgrading
# Related: PR #1484
# https://github.com/bikalabs/Bika-LIMS/pull/1484
from bika.lims.upgrade import skip_pre315
if skip_pre315(aq_parent(aq_inner(tool))):
return True
portal = aq_parent(aq_inner(tool))
at = getToolByName(portal, 'archetype_tool')
bc = getToolByName(portal, 'bika_catalog')
bac = getToolByName(portal, 'bika_analysis_catalog')
bsc = getToolByName(portal, 'bika_setup_catalog')
pc = getToolByName(portal, 'portal_catalog')
portal = aq_parent(aq_inner(tool))
portal_catalog = getToolByName(portal, 'portal_catalog')
portal_groups = portal.portal_groups
setup = portal.portal_setup
typestool = getToolByName(portal, 'portal_types')
wf = getToolByName(portal, 'portal_workflow')
# Update all tools in which changes have been made
setup.runImportStepFromProfile('profile-bika.lims:default',
'propertiestool')
setup.runImportStepFromProfile('profile-bika.lims:default', 'typeinfo')
setup.runImportStepFromProfile('profile-bika.lims:default',
'repositorytool')
setup.runImportStepFromProfile('profile-bika.lims:default', 'workflow')
setup.runImportStepFromProfile('profile-bika.lims:default', 'workflow-csv')
setup.runImportStepFromProfile('profile-bika.lims:default', 'factorytool')
setup.runImportStepFromProfile('profile-bika.lims:default', 'jsregistry')
setup.runImportStepFromProfile('profile-bika.lims:default',
'portlets',
run_dependencies=False)
setup.runImportStepFromProfile('profile-bika.lims:default', 'viewlets')
setup.runImportStepFromProfile('profile-plone.app.jquery:default',
'jsregistry')
# Add RegulatoryInspectors group and RegulatoryInspector role.
# Fix permissions: LabClerks don't see analysis results
role = 'RegulatoryInspector'
group = 'RegulatoryInspectors'
if role not in portal.acl_users.portal_role_manager.listRoleIds():
portal.acl_users.portal_role_manager.addRole(role)
portal._addRole(role)
if group not in portal_groups.listGroupIds():
portal_groups.addGroup('RegulatoryInspectors',
title="Regulatory Inspectors",
roles=[
'Member',
'RegulatoryInspector',
])
else:
portal_groups.setRolesForGroup('RegulatoryInspectors', [
'Member',
'RegulatoryInspector',
])
# Add SampleConditions
at.setCatalogsByType('SampleCondition', ['bika_setup_catalog'])
if not portal['bika_setup'].get('bika_sampleconditions'):
typestool.constructContent(type_name="SampleConditions",
container=portal['bika_setup'],
id='bika_sampleconditions',
title='Sample Conditions')
obj = portal['bika_setup']['bika_sampleconditions']
obj.unmarkCreationFlag()
obj.reindexObject()
# Add SampleCondition to all Sample objects
proxies = portal_catalog(portal_type="Sample")
samples = (proxy.getObject() for proxy in proxies)
for sample in samples:
sample.setSampleCondition(None)
# Some catalog indexes were added or modified
if 'getSampleTypeTitle' in bc.indexes():
bc.delIndex('getSampleTypeTitle')
if 'getSamplePointTitle' in bc.indexes():
bc.delIndex('getSamplePointTitle')
bc.addIndex('getSampleTypeTitle', 'KeywordIndex')
bc.addIndex('getSamplePointTitle', 'KeywordIndex')
if 'getClientSampleID' not in pc.indexes():
pc.addIndex('getClientSampleID', 'FieldIndex')
pc.addColumn('getClientSampleID')
if 'getParentUID' not in pc.indexes():
pc.addIndex('getParentUID', 'FieldIndex')
pc.addColumn('getParentUID')
if 'getReferenceAnalysesGroupID' not in bac.indexes():
bac.addIndex('getReferenceAnalysesGroupID', 'FieldIndex')
bac.addColumn('getReferenceAnalysesGroupID')
# Fix broken template partition containers
for p in bsc(portal_type='ARTemplate'):
o = p.getObject()
parts = o.getPartitions()
for i, part in enumerate(parts):
if 'container_uid' in part:
container = bsc(portal_type='Container',
UID=part['container_uid'])
if container:
container = container[0].getObject()
parts[i]['Container'] = container.Title()
if 'preservation_uid' in p:
preservation = bsc(portal_type='Preservation',
UID=part['preservation_uid'])
if preservation:
preservation = preservation[0].getObject()
parts[i]['Preservation'] = preservation.Title()
# Populate ReferenceAnalysesGroupIDs for ReferenceAnalyses
# https://github.com/bikalabs/Bika-LIMS/issues/931
wss = bc(portal_type='Worksheet')
for ws in wss:
ws = ws.getObject()
wsangroups = {}
codes = {}
# Reference Analyses (not duplicates)
refanalyses = [
an for an in ws.getAnalyses()
if an.portal_type == 'ReferenceAnalysis'
or an.portal_type == 'DuplicateAnalysis'
]
layout = ws.getLayout()
for lay in layout:
for an in refanalyses:
if lay['analysis_uid'] == an.UID():
position = lay['position']
if position not in wsangroups.keys():
wsangroups[position] = []
wsangroups[position].append(an)
for position, wsgroup in wsangroups.iteritems():
analysis = wsgroup[0]
if analysis.portal_type == 'ReferenceAnalysis':
refsampleid = wsgroup[0].aq_parent.id
else:
# Duplicate
_analysis = wsgroup[0].getAnalysis()
if _analysis.portal_type == 'ReferenceAnalysis':
refsampleid = _analysis.aq_parent.id
else:
refsampleid = wsgroup[0].getSamplePartition().id
codre = refsampleid
codws = '%s_%s' % (refsampleid, ws.UID())
codgr = '%s_%s_%s' % (refsampleid, ws.UID(), position)
if codgr in codes.keys():
postfix = codes[codgr]
elif codws in codes.keys():
postfix = codes[codws]
codes[codgr] = postfix
codes[codws] = postfix + 1
elif codre in codes.keys():
postfix = codes[codre]
codes[codgr] = postfix
codes[codws] = postfix + 1
codes[codre] = postfix + 1
else:
postfix = 1
codes[codre] = postfix + 1
for an in wsgroup:
if an.portal_type == 'DuplicateAnalysis':
postfix = str(postfix).zfill(int(2))
refgid = '%s-D%s' % (refsampleid, postfix)
else:
postfix = str(postfix).zfill(int(3))
refgid = '%s-%s' % (refsampleid, postfix)
an.setReferenceAnalysesGroupID(refgid)
# Re-import the default permission maps
gen = BikaGenerator()
gen.setupPermissions(portal)
logger.info("Updating workflow role/permission mappings")
wf.updateRoleMappings()
logger.info("Reindex added indexes in portal_catalog")
pc.manage_reindexIndex(ids=[
'getClientSampleID',
'getParentUID',
])
logger.info("Reindex added indexes in bika_analysis_catalog")
bac.manage_reindexIndex(ids=[
'getReferenceAnalysesGroupID',
])
logger.info("Reindex added indexes in bika_catalog")
bc.manage_reindexIndex(ids=[
'getSampleTypeTitle',
'getSamplePointTitle',
])
return True
def upgrade(tool):
# Hack prevent out-of-date upgrading
# Related: PR #1484
# https://github.com/bikalabs/Bika-LIMS/pull/1484
from bika.lims.upgrade import skip_pre315
if skip_pre315(aq_parent(aq_inner(tool))):
return True
portal = aq_parent(aq_inner(tool))
at = getToolByName(portal, "archetype_tool")
bc = getToolByName(portal, "bika_catalog")
bac = getToolByName(portal, "bika_analysis_catalog")
bsc = getToolByName(portal, "bika_setup_catalog")
pc = getToolByName(portal, "portal_catalog")
portal = aq_parent(aq_inner(tool))
portal_catalog = getToolByName(portal, "portal_catalog")
portal_groups = portal.portal_groups
setup = portal.portal_setup
typestool = getToolByName(portal, "portal_types")
wf = getToolByName(portal, "portal_workflow")
# Update all tools in which changes have been made
setup.runImportStepFromProfile("profile-bika.lims:default", "propertiestool")
setup.runImportStepFromProfile("profile-bika.lims:default", "typeinfo")
setup.runImportStepFromProfile("profile-bika.lims:default", "repositorytool")
setup.runImportStepFromProfile("profile-bika.lims:default", "workflow")
setup.runImportStepFromProfile("profile-bika.lims:default", "workflow-csv")
setup.runImportStepFromProfile("profile-bika.lims:default", "factorytool")
setup.runImportStepFromProfile("profile-bika.lims:default", "jsregistry")
setup.runImportStepFromProfile("profile-bika.lims:default", "portlets", run_dependencies=False)
setup.runImportStepFromProfile("profile-bika.lims:default", "viewlets")
setup.runImportStepFromProfile("profile-plone.app.jquery:default", "jsregistry")
# Add RegulatoryInspectors group and RegulatoryInspector role.
# Fix permissions: LabClerks don't see analysis results
role = "RegulatoryInspector"
group = "RegulatoryInspectors"
if role not in portal.acl_users.portal_role_manager.listRoleIds():
portal.acl_users.portal_role_manager.addRole(role)
portal._addRole(role)
if group not in portal_groups.listGroupIds():
portal_groups.addGroup(
"RegulatoryInspectors", title="Regulatory Inspectors", roles=["Member", "RegulatoryInspector"]
)
else:
portal_groups.setRolesForGroup("RegulatoryInspectors", ["Member", "RegulatoryInspector"])
# Add SampleConditions
at.setCatalogsByType("SampleCondition", ["bika_setup_catalog"])
if not portal["bika_setup"].get("bika_sampleconditions"):
typestool.constructContent(
type_name="SampleConditions",
container=portal["bika_setup"],
id="bika_sampleconditions",
title="Sample Conditions",
)
obj = portal["bika_setup"]["bika_sampleconditions"]
obj.unmarkCreationFlag()
obj.reindexObject()
# Add SampleCondition to all Sample objects
proxies = portal_catalog(portal_type="Sample")
samples = (proxy.getObject() for proxy in proxies)
for sample in samples:
sample.setSampleCondition(None)
# Some catalog indexes were added or modified
if "getSampleTypeTitle" in bc.indexes():
bc.delIndex("getSampleTypeTitle")
if "getSamplePointTitle" in bc.indexes():
bc.delIndex("getSamplePointTitle")
bc.addIndex("getSampleTypeTitle", "KeywordIndex")
bc.addIndex("getSamplePointTitle", "KeywordIndex")
if "getClientSampleID" not in pc.indexes():
pc.addIndex("getClientSampleID", "FieldIndex")
pc.addColumn("getClientSampleID")
if "getParentUID" not in pc.indexes():
pc.addIndex("getParentUID", "FieldIndex")
pc.addColumn("getParentUID")
if "getReferenceAnalysesGroupID" not in bac.indexes():
bac.addIndex("getReferenceAnalysesGroupID", "FieldIndex")
bac.addColumn("getReferenceAnalysesGroupID")
# Fix broken template partition containers
for p in bsc(portal_type="ARTemplate"):
o = p.getObject()
parts = o.getPartitions()
for i, part in enumerate(parts):
if "container_uid" in part:
container = bsc(portal_type="Container", UID=part["container_uid"])
if container:
container = container[0].getObject()
parts[i]["Container"] = container.Title()
if "preservation_uid" in p:
preservation = bsc(portal_type="Preservation", UID=part["preservation_uid"])
if preservation:
preservation = preservation[0].getObject()
parts[i]["Preservation"] = preservation.Title()
# Populate ReferenceAnalysesGroupIDs for ReferenceAnalyses
# https://github.com/bikalabs/Bika-LIMS/issues/931
wss = bc(portal_type="Worksheet")
for ws in wss:
ws = ws.getObject()
wsangroups = {}
codes = {}
# Reference Analyses (not duplicates)
refanalyses = [
an
for an in ws.getAnalyses()
if an.portal_type == "ReferenceAnalysis" or an.portal_type == "DuplicateAnalysis"
]
layout = ws.getLayout()
for lay in layout:
for an in refanalyses:
if lay["analysis_uid"] == an.UID():
position = lay["position"]
if position not in wsangroups.keys():
wsangroups[position] = []
wsangroups[position].append(an)
for position, wsgroup in wsangroups.iteritems():
analysis = wsgroup[0]
if analysis.portal_type == "ReferenceAnalysis":
refsampleid = wsgroup[0].aq_parent.id
else:
# Duplicate
_analysis = wsgroup[0].getAnalysis()
if _analysis.portal_type == "ReferenceAnalysis":
refsampleid = _analysis.aq_parent.id
else:
refsampleid = wsgroup[0].getSamplePartition().id
codre = refsampleid
codws = "%s_%s" % (refsampleid, ws.UID())
codgr = "%s_%s_%s" % (refsampleid, ws.UID(), position)
if codgr in codes.keys():
postfix = codes[codgr]
elif codws in codes.keys():
postfix = codes[codws]
codes[codgr] = postfix
codes[codws] = postfix + 1
elif codre in codes.keys():
postfix = codes[codre]
codes[codgr] = postfix
codes[codws] = postfix + 1
codes[codre] = postfix + 1
else:
postfix = 1
codes[codre] = postfix + 1
for an in wsgroup:
if an.portal_type == "DuplicateAnalysis":
postfix = str(postfix).zfill(int(2))
refgid = "%s-D%s" % (refsampleid, postfix)
else:
postfix = str(postfix).zfill(int(3))
refgid = "%s-%s" % (refsampleid, postfix)
an.setReferenceAnalysesGroupID(refgid)
# Re-import the default permission maps
gen = BikaGenerator()
gen.setupPermissions(portal)
logger.info("Updating workflow role/permission mappings")
wf.updateRoleMappings()
logger.info("Reindex added indexes in portal_catalog")
pc.manage_reindexIndex(ids=["getClientSampleID", "getParentUID"])
logger.info("Reindex added indexes in bika_analysis_catalog")
bac.manage_reindexIndex(ids=["getReferenceAnalysesGroupID"])
logger.info("Reindex added indexes in bika_catalog")
bc.manage_reindexIndex(ids=["getSampleTypeTitle", "getSamplePointTitle"])
return True
