def upgrade(tool):
# Hack prevent out-of-date upgrading
# Related: PR #1484
# https://github.com/bikalabs/Bika-LIMS/pull/1484
from lims.upgrade import skip_pre315
if skip_pre315(aq_parent(aq_inner(tool))):
return True
portal = aq_parent(aq_inner(tool))
# Fix Analysis Services IMM incoherences
for service in portal.bika_setup.bika_analysisservices.objectValues('AnalysisService'):
if (service.getInstrumentEntryOfResults() == False):
# Remove any assigned instrument
service.setInstruments([])
service.setInstrument(None)
if (service.getManualEntryOfResults() == False):
# Remove any assigned manual method
service.setMethods([])
service.set_Method(None)
service.reindexObject()
return True
def upgrade(tool):
""" Sort by Type in instruments
"""
# Hack prevent out-of-date upgrading
# Related: PR #1484
# https://github.com/bikalabs/Bika-LIMS/pull/1484
from lims.upgrade import skip_pre315
if skip_pre315(aq_parent(aq_inner(tool))):
return True
portal = aq_parent(aq_inner(tool))
bsc = getToolByName(portal, 'bika_setup_catalog', None)
if 'getInstrumentType' not in bsc.indexes():
bsc.addIndex('getInstrumentType', 'FieldIndex')
bsc.addColumn('getInstrumentType')
bsc.addIndex('getInstrumentTypeName','FieldIndex')
bsc.addColumn('getInstrumentTypeName')
#Del old "getType" Index, it's not used now.
if 'getType' in bsc.indexes():
bsc.delIndex('getType')
if 'getType' in bsc.indexes():
bsc.delColumn('getType')
setup = portal.portal_setup
logger.info("Reindex added indexes in bika_setup_catalog")
bsc.manage_reindexIndex(
ids=['getInstrumentType', 'getInstrumentTypeName', ])
return True
def upgrade(tool):
# Hack prevent out-of-date upgrading
# Related: PR #1484
# https://github.com/bikalabs/Bika-LIMS/pull/1484
from lims.upgrade import skip_pre315
if skip_pre315(aq_parent(aq_inner(tool))):
return True
portal = aq_parent(aq_inner(tool))
setup = portal.portal_setup
setup.runImportStepFromProfile('profile-bika.lims:default', 'typeinfo')
stub('bika.lims.content.invoicelineitem', 'InvoiceLineItem',
BaseContent)
for inv in portal['invoices'].objectValues():
inv.invoice_lineitems = []
for invl in inv.objectValues():
item = dict(
ItemDate=invl.ItemDate,
ItemDescription=invl.ItemDescription,
ClientOrderNumber=invl.ClientOrderNumber,
Subtotal=invl.Subtotal,
VATAmount=invl.VATAmount,
Total=invl.Total,
)
inv.invoice_lineitems.append(item)
return True
def upgrade(tool):
""" Adding getRawSamplePoint/Type idx to obtain Sample's uid easly
"""
# Hack prevent out-of-date upgrading
# Related: PR #1484
# https://github.com/bikalabs/Bika-LIMS/pull/1484
from lims.upgrade import skip_pre315
if skip_pre315(aq_parent(aq_inner(tool))):
return True
portal = aq_parent(aq_inner(tool))
bsc = getToolByName(portal, 'bika_setup_catalog', None)
if 'getRawSamplePoints' not in bsc.indexes():
bsc.addIndex('getRawSamplePoints', 'KeywordIndex')
if 'getRawSampleTypes' not in bsc.indexes():
bsc.addIndex('getRawSampleTypes', 'KeywordIndex')
logger.info("Reindex added indexes in bika_setup_catalog")
bsc.manage_reindexIndex(ids=[
'getRawSamplePoints',
])
bsc.manage_reindexIndex(ids=[
'getRawSampleTypes',
])
return True
def upgrade(tool):
# Hack prevent out-of-date upgrading
# Related: PR #1484
# https://github.com/bikalabs/Bika-LIMS/pull/1484
from lims.upgrade import skip_pre315
if skip_pre315(aq_parent(aq_inner(tool))):
return True
portal = aq_parent(aq_inner(tool))
setup = portal.portal_setup
mp = portal.bika_setup.manage_permission
mp('Access contents information', ['Authenticated', 'Analyst', 'LabClerk'],
1)
mp(permissions.View, ['Authenticated', 'Analyst', 'LabClerk'], 1)
portal.bika_setup.reindexObject()
for obj in portal.bika_setup.bika_analysisservices.objectValues():
mp = obj.manage_permission
mp(permissions.View, ['Manager', 'LabManager', 'Analyst', 'LabClerk'],
0)
mp('Access contents information', [
'Manager', 'LabManager', 'Member', 'LabClerk', 'Analyst',
'Sampler', 'Preserver', 'Owner'
], 0)
obj.reindexObject()
def upgrade(tool):
# Hack prevent out-of-date upgrading
# Related: PR #1484
# https://github.com/bikalabs/Bika-LIMS/pull/1484
from lims.upgrade import skip_pre315
if skip_pre315(aq_parent(aq_inner(tool))):
return True
portal = aq_parent(aq_inner(tool))
setup = portal.portal_setup
mp = portal.bika_setup.manage_permission
mp('Access contents information', ['Authenticated', 'Analyst'], 1)
mp(permissions.View, ['Authenticated', 'Analyst'], 1)
portal.bika_setup.reindexObject()
for obj in portal.bika_setup.bika_analysisservices.objectValues():
mp = obj.manage_permission
mp(permissions.View, ['Manager', 'LabManager', 'Analyst'], 0)
mp('Access contents information', [
'Manager', 'LabManager', 'Member', 'LabClerk', 'Analyst',
'Sampler', 'Preserver', 'Owner'
], 0)
obj.reindexObject()
wf = getToolByName(portal, 'portal_workflow')
# update affected tools
setup.runImportStepFromProfile('profile-bika.lims:default', 'typeinfo')
setup.runImportStepFromProfile('profile-bika.lims:default', 'workflow-csv')
wf.updateRoleMappings()
return True
def upgrade(tool):
""" Fix workflow variable review_history permission guard.
"""
# Hack prevent out-of-date upgrading
# Related: PR #1484
# https://github.com/bikalabs/Bika-LIMS/pull/1484
from lims.upgrade import skip_pre315
if skip_pre315(aq_parent(aq_inner(tool))):
return True
wf_ids = [
'bika_analysis_workflow',
'bika_batch_workflow',
'bika_cancellation_workflow',
'bika_duplicateanalysis_workflow',
'bika_inactive_workflow',
'bika_publication_workflow',
'bika_referenceanalysis_workflow',
'bika_referencesample_workflow',
'bika_reject_analysis_workflow',
'bika_sample_workflow',
'bika_worksheet_workflow',
'bika_worksheetanalysis_workflow',
]
portal = aq_parent(aq_inner(tool))
workflow = getToolByName(portal, 'portal_workflow')
for wf_id in wf_ids:
wf = workflow.getWorkflowById(wf_id)
if wf:
rhdef = wf.variables['review_history']
rhdef.info_guard = None
return True
def upgrade(tool):
# Hack prevent out-of-date upgrading
# Related: PR #1484
# https://github.com/bikalabs/Bika-LIMS/pull/1484
from lims.upgrade import skip_pre315
if skip_pre315(aq_parent(aq_inner(tool))):
return True
portal = aq_parent(aq_inner(tool))
setup = portal.portal_setup
workflow = getToolByName(portal, "portal_workflow")
# /arimports folder permissions
mp = portal.arimports.manage_permission
mp(ManageARImport, ['Manager', ], 1)
mp(permissions.ListFolderContents, ['Manager','Member',], 1)
mp(permissions.AddPortalContent, ['Manager', ], 0)
mp(permissions.DeleteObjects, ['Manager'], 0)
mp(permissions.View, ['Manager','Member'], 0)
portal.arimports.reindexObject()
try:
workflow.doActionFor(portal.arimports, "hide")
except:
pass
portal.arimports.setLayout('@@arimports')
return True
def upgrade(tool):
# Hack prevent out-of-date upgrading
# Related: PR #1484
# https://github.com/bikalabs/Bika-LIMS/pull/1484
from lims.upgrade import skip_pre315
if skip_pre315(aq_parent(aq_inner(tool))):
return True
portal = aq_parent(aq_inner(tool))
setup = portal.portal_setup
setup.runImportStepFromProfile('profile-bika.lims:default', 'typeinfo')
stub('bika.lims.content.invoicelineitem', 'InvoiceLineItem', BaseContent)
for inv in portal['invoices'].objectValues():
inv.invoice_lineitems = []
for invl in inv.objectValues():
item = dict(
ItemDate=invl.ItemDate,
ItemDescription=invl.ItemDescription,
ClientOrderNumber=invl.ClientOrderNumber,
Subtotal=invl.Subtotal,
VATAmount=invl.VATAmount,
Total=invl.Total,
)
inv.invoice_lineitems.append(item)
return True
def upgrade(tool):
# Hack prevent out-of-date upgrading
# Related: PR #1484
# https://github.com/bikalabs/Bika-LIMS/pull/1484
from 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')
at.setCatalogsByType('SubGroup', ['bika_setup_catalog', ])
setup = portal.portal_setup
setup.runImportStepFromProfile('profile-bika.lims:default', 'controlpanel')
try:
_createObjectByType("SubGroups", portal.bika_setup, "bika_subgroups",
title="Sub-groups")
obj = portal.bika_setup.bika_subgroups
obj.unmarkCreationFlag()
obj.reindexObject()
except BadRequest:
# folder already exists
pass
return True
def upgrade(tool):
# Hack prevent out-of-date upgrading
# Related: PR #1484
# https://github.com/bikalabs/Bika-LIMS/pull/1484
from 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')
at.setCatalogsByType('SubGroup', [
'bika_setup_catalog',
])
setup = portal.portal_setup
setup.runImportStepFromProfile('profile-bika.lims:default', 'controlpanel')
try:
_createObjectByType("SubGroups",
portal.bika_setup,
"bika_subgroups",
title="Sub-groups")
obj = portal.bika_setup.bika_subgroups
obj.unmarkCreationFlag()
obj.reindexObject()
except BadRequest:
# folder already exists
pass
return True
def upgrade(tool):
# Hack prevent out-of-date upgrading
# Related: PR #1484
# https://github.com/bikalabs/Bika-LIMS/pull/1484
from lims.upgrade import skip_pre315
if skip_pre315(aq_parent(aq_inner(tool))):
return True
portal = aq_parent(aq_inner(tool))
setup = portal.portal_setup
# update affected tools
setup.runImportStepFromProfile('profile-bika.lims:default', 'workflow-csv')
# /supplyorders folder permissions
mp = portal.supplyorders.manage_permission
mp(CancelAndReinstate, ['Manager', 'LabManager', 'LabClerk'], 0)
mp(ManagePricelists, ['Manager', 'LabManager', 'Owner'], 1)
mp(permissions.ListFolderContents, ['Member'], 1)
mp(permissions.AddPortalContent, ['Manager', 'LabManager', 'Owner'], 0)
mp(permissions.DeleteObjects, ['Manager', 'LabManager', 'Owner'], 0)
mp(permissions.View, ['Manager', 'LabManager'], 0)
portal.supplyorders.reindexObject()
wf = getToolByName(portal, 'portal_workflow')
wf.updateRoleMappings()
return True
def upgrade(tool):
# Hack prevent out-of-date upgrading
# Related: PR #1484
# https://github.com/bikalabs/Bika-LIMS/pull/1484
from lims.upgrade import skip_pre315
if skip_pre315(aq_parent(aq_inner(tool))):
return True
portal = aq_parent(aq_inner(tool))
setup = portal.portal_setup
typestool = getToolByName(portal, 'portal_types')
# Add the object to bika_setup
try:
portal.bika_setup.manage_delObjects('bika_arpriorities')
except BadRequest:
logger.info("Folder doesn't exist")
try:
typestool.constructContent(type_name="ARPriorities",
container=portal.bika_setup,
id='bika_arpriorities',
title='AR Priorities')
obj = portal.bika_setup.bika_arpriorities
obj.unmarkCreationFlag()
obj.reindexObject()
except BadRequest:
# folder already exists
pass
return True
def upgrade(tool):
# Hack prevent out-of-date upgrading
# Related: PR #1484
# https://github.com/bikalabs/Bika-LIMS/pull/1484
from lims.upgrade import skip_pre315
if skip_pre315(aq_parent(aq_inner(tool))):
return True
portal = aq_parent(aq_inner(tool))
setup = portal.portal_setup
# update affected tools
setup.runImportStepFromProfile('profile-bika.lims:default', 'workflow-csv')
# /supplyorders folder permissions
mp = portal.supplyorders.manage_permission
mp(CancelAndReinstate, ['Manager', 'LabManager', 'LabClerk'], 0)
mp(ManagePricelists, ['Manager', 'LabManager', 'Owner'], 1)
mp(permissions.ListFolderContents, ['Member'], 1)
mp(permissions.AddPortalContent, ['Manager', 'LabManager', 'Owner'], 0)
mp(permissions.DeleteObjects, ['Manager', 'LabManager', 'Owner'], 0)
mp(permissions.View, ['Manager', 'LabManager'], 0)
portal.supplyorders.reindexObject()
wf = getToolByName(portal, 'portal_workflow')
wf.updateRoleMappings()
return True
def upgrade(tool):
"""Added bika.lims.loader.js and bika.lims.artemplate.edit.js
Also fix LIMS-1352 (would have been 3042, but metadata.xml is not up to date!).
"""
# Hack prevent out-of-date upgrading
# Related: PR #1484
# https://github.com/bikalabs/Bika-LIMS/pull/1484
from lims.upgrade import skip_pre315
if skip_pre315(aq_parent(aq_inner(tool))):
return True
portal = aq_parent(aq_inner(tool))
setup = portal.portal_setup
# update affected tools
setup.runImportStepFromProfile('profile-bika.lims:default', 'jsregistry')
# LIMS-1352
proxies = portal.bika_catalog(portal_type='Sample')
for brain in proxies:
sample = brain.getObject()
sample.setSamplingWorkflowEnabled(
sample.getSamplingWorkflowEnabledDefault())
return True
def upgrade(tool):
# Hack prevent out-of-date upgrading
# Related: PR #1484
# https://github.com/bikalabs/Bika-LIMS/pull/1484
from lims.upgrade import skip_pre315
if skip_pre315(aq_parent(aq_inner(tool))):
return True
portal = aq_parent(aq_inner(tool))
setup = portal.portal_setup
# re-import js registry
setup.runImportStepFromProfile('profile-bika.lims:default', 'jsregistry')
setup.runImportStepFromProfile('profile-bika.lims:default', 'typeinfo')
# Update permissions according to Bika Setup
# By default, restrict user access and management to WS
bs = portal.bika_setup
bs.setRestrictWorksheetUsersAccess(True)
bs.setRestrictWorksheetManagement(True)
bs.reindexObject()
# Only LabManagers are able to create worksheets.
mp = portal.manage_permission
mp(ManageWorksheets, ['Manager', 'LabManager'],1)
return True
def upgrade(tool):
""" Sort by Type in instruments
"""
# Hack prevent out-of-date upgrading
# Related: PR #1484
# https://github.com/bikalabs/Bika-LIMS/pull/1484
from lims.upgrade import skip_pre315
if skip_pre315(aq_parent(aq_inner(tool))):
return True
portal = aq_parent(aq_inner(tool))
bsc = getToolByName(portal, 'bika_setup_catalog', None)
if 'getInstrumentType' not in bsc.indexes():
bsc.addIndex('getInstrumentType', 'FieldIndex')
bsc.addColumn('getInstrumentType')
bsc.addIndex('getInstrumentTypeName', 'FieldIndex')
bsc.addColumn('getInstrumentTypeName')
#Del old "getType" Index, it's not used now.
if 'getType' in bsc.indexes():
bsc.delIndex('getType')
if 'getType' in bsc.indexes():
bsc.delColumn('getType')
setup = portal.portal_setup
logger.info("Reindex added indexes in bika_setup_catalog")
bsc.manage_reindexIndex(ids=[
'getInstrumentType',
'getInstrumentTypeName',
])
return True
def upgrade(tool):
# Hack prevent out-of-date upgrading
# Related: PR #1484
# https://github.com/bikalabs/Bika-LIMS/pull/1484
from lims.upgrade import skip_pre315
if skip_pre315(aq_parent(aq_inner(tool))):
return True
portal = aq_parent(aq_inner(tool))
setup = portal.portal_setup
setup.runImportStepFromProfile('profile-bika.lims:default', 'typeinfo')
stub('bika.lims.content.pricelistlineitem', 'PricelistLineItem',
BaseContent)
for pl in portal['pricelists'].objectValues():
pl.pricelist_lineitems = []
for pli in pl.objectValues():
item = dict(
title=pli.title,
ItemDescription=pli.ItemDescription,
Accredited=pli.Accredited,
Subtotal="%d.%d" % (pli.Subtotal[0], pli.Subtotal[1]),
VATAmount="%d.%d" % (pli.VATAmount[0], pli.VATAmount[1]),
Total="%d.%d" % (pli.Total[0], pli.Total[1]),
CategoryTitle=pli.CategoryTitle,
)
pl.pricelist_lineitems.append(item)
return True
def upgrade(tool):
""" Refactor ARs listing to allow sorting by priority
"""
# Hack prevent out-of-date upgrading
# Related: PR #1484
# https://github.com/bikalabs/Bika-LIMS/pull/1484
from lims.upgrade import skip_pre315
if skip_pre315(aq_parent(aq_inner(tool))):
return True
def addIndex(cat, *args):
try:
cat.addIndex(*args)
except:
pass
portal = aq_parent(aq_inner(tool))
# Create new indexes
bc = getToolByName(portal, 'bika_catalog')
addIndex(bc, 'Priority', 'FieldIndex')
addIndex(bc, 'BatchUID', 'FieldIndex')
bc.manage_reindexIndex(ids=[
'Priority',
'BatchUID',
])
bac = getToolByName(portal, 'bika_analysis_catalog')
addIndex(bac, 'Priority', 'FieldIndex')
bac.manage_reindexIndex(ids=[
'Priority',
])
return True
def upgrade(tool):
# Hack prevent out-of-date upgrading
# Related: PR #1484
# https://github.com/bikalabs/Bika-LIMS/pull/1484
from lims.upgrade import skip_pre315
if skip_pre315(aq_parent(aq_inner(tool))):
return True
portal = aq_parent(aq_inner(tool))
setup = portal.portal_setup
# re-import js registry
setup.runImportStepFromProfile('profile-bika.lims:default', 'jsregistry')
setup.runImportStepFromProfile('profile-bika.lims:default', 'typeinfo')
# Update permissions according to Bika Setup
# By default, restrict user access and management to WS
bs = portal.bika_setup
bs.setRestrictWorksheetUsersAccess(True)
bs.setRestrictWorksheetManagement(True)
bs.reindexObject()
# Only LabManagers are able to create worksheets.
mp = portal.manage_permission
mp(ManageWorksheets, ['Manager', 'LabManager'], 1)
return True
def upgrade(tool):
# Hack prevent out-of-date upgrading
# Related: PR #1484
# https://github.com/bikalabs/Bika-LIMS/pull/1484
from lims.upgrade import skip_pre315
if skip_pre315(aq_parent(aq_inner(tool))):
return True
portal = aq_parent(aq_inner(tool))
setup = portal.portal_setup
mp = portal.bika_setup.manage_permission
mp('Access contents information', ['Authenticated', 'Analyst'], 1)
mp(permissions.View, ['Authenticated', 'Analyst'], 1)
portal.bika_setup.reindexObject()
for obj in portal.bika_setup.bika_analysisservices.objectValues():
mp = obj.manage_permission
mp(permissions.View, ['Manager', 'LabManager', 'Analyst'], 0)
mp('Access contents information', ['Manager', 'LabManager', 'Member', 'LabClerk', 'Analyst', 'Sampler', 'Preserver', 'Owner'], 0)
obj.reindexObject()
wf = getToolByName(portal, 'portal_workflow')
# update affected tools
setup.runImportStepFromProfile('profile-bika.lims:default', 'typeinfo')
setup.runImportStepFromProfile('profile-bika.lims:default', 'workflow-csv')
wf.updateRoleMappings()
return True
def upgrade(tool):
# Hack prevent out-of-date upgrading
# Related: PR #1484
# https://github.com/bikalabs/Bika-LIMS/pull/1484
from lims.upgrade import skip_pre315
if skip_pre315(aq_parent(aq_inner(tool))):
return True
portal = aq_parent(aq_inner(tool))
setup = portal.portal_setup
workflow = getToolByName(portal, "portal_workflow")
# /arimports folder permissions
mp = portal.arimports.manage_permission
mp(ManageARImport, [
'Manager',
], 1)
mp(permissions.ListFolderContents, [
'Manager',
'Member',
], 1)
mp(permissions.AddPortalContent, [
'Manager',
], 0)
mp(permissions.DeleteObjects, ['Manager'], 0)
mp(permissions.View, ['Manager', 'Member'], 0)
portal.arimports.reindexObject()
try:
workflow.doActionFor(portal.arimports, "hide")
except:
pass
portal.arimports.setLayout('@@arimports')
return True
def upgrade(tool):
# Hack prevent out-of-date upgrading
# Related: PR #1484
# https://github.com/bikalabs/Bika-LIMS/pull/1484
from lims.upgrade import skip_pre315
if skip_pre315(aq_parent(aq_inner(tool))):
return True
portal = aq_parent(aq_inner(tool))
setup = portal.portal_setup
# Add new Client role
role = "Client"
if role not in portal.acl_users.portal_role_manager.listRoleIds():
portal.acl_users.portal_role_manager.addRole(role)
portal._addRole(role)
# Add the role Client role to Clients group
portal.portal_groups.editGroup('Clients', roles=['Member',
'Authenticated',
'Client'])
# Add all Client contacts to Clients group
for client in portal.clients.values():
for contact in client.getContacts():
user = portal.portal_membership.getMemberById(contact.getUsername())
if user is not None:
portal.portal_groups.addPrincipalToGroup(user.getUserName(),
"Clients")
# Add AddAttachment permission to Clients
mp = portal.manage_permission
mp(AddAttachment, ['Manager', 'LabManager', 'Owner' 'Analyst', 'LabClerk', 'Client', 'Sampler'], 0)
# Add Analysis Services View permission to Clients
mp = portal.bika_setup.bika_analysisservices.manage_permission
mp('Access contents information', ['Authenticated', 'Analyst', 'Client'], 1)
mp(permissions.View, ['Authenticated', 'Analyst', 'Client'], 1)
portal.bika_setup.bika_analysisservices.reindexObject()
for obj in portal.bika_setup.bika_analysisservices.objectValues():
mp = obj.manage_permission
mp(permissions.View, ['Manager', 'LabManager', 'Analyst', 'Client'], 0)
mp('Access contents information', ['Manager', 'LabManager', 'Member', 'LabClerk', 'Analyst', 'Client', 'Sampler', 'Preserver', 'Owner'], 0)
obj.reindexObject()
# Grant AttachmentType view access to Clients
mp = portal.bika_setup.bika_attachmenttypes.manage_permission
mp('Access contents information', ['Authenticated', 'Analyst', 'Client'], 1)
mp(permissions.View, ['Authenticated', 'Analyst', 'Client'], 1)
portal.bika_setup.bika_attachmenttypes.reindexObject()
wf = getToolByName(portal, 'portal_workflow')
setup.runImportStepFromProfile('profile-bika.lims:default', 'workflow-csv')
wf.updateRoleMappings()
return True
def upgrade(tool):
"""Added bika.lims.analysisservice.edit.js
"""
# Hack prevent out-of-date upgrading
# Related: PR #1484
# https://github.com/bikalabs/Bika-LIMS/pull/1484
from lims.upgrade import skip_pre315
if skip_pre315(aq_parent(aq_inner(tool))):
return True
portal = aq_parent(aq_inner(tool))
setup = portal.portal_setup
# update affected tools
setup.runImportStepFromProfile('profile-bika.lims:default', 'jsregistry')
# apply new method/calculation data to old Analysis Services
portal = aq_parent(aq_inner(tool))
pc = getToolByName(portal, 'portal_catalog')
bsc = getToolByName(portal, 'bika_setup_catalog')
rc = getToolByName(portal, REFERENCE_CATALOG)
proxies = pc(portal_type="AnalysisService")
for proxy in proxies:
an = proxy.getObject()
rels = an.at_references.objectValues()
oldmethod = None
oldinstrument = None
oldcalc = None
for rel in rels:
if rel.relationship == 'AnalysisServiceCalculation':
oldcalc = rc.lookupObject(rel.targetUID)
elif rel.relationship == 'AnalysisServiceInstrument':
oldinstrument = rc.lookupObject(rel.targetUID)
elif rel.relationship == 'AnalysisServiceMethod':
oldmethod = rc.lookupObject(rel.targetUID)
if oldmethod and oldcalc and oldinstrument:
break
# Reset the method, instrument and calculations
if oldmethod:
an.Schema().getField('Methods').set(an, [
oldmethod.UID(),
])
an.Schema().getField('_Method').set(an, oldmethod.UID())
if oldinstrument:
an.Schema().getField('Instruments').set(an, [
oldinstrument.UID(),
])
an.Schema().getField('Instrument').set(an, oldinstrument.UID())
if oldcalc:
an.setUseDefaultCalculation(False)
an.Schema().getField('DeferredCalculation').set(an, oldcalc.UID())
return True
def upgrade(tool):
# Hack prevent out-of-date upgrading
# Related: PR #1484
# https://github.com/bikalabs/Bika-LIMS/pull/1484
from lims.upgrade import skip_pre315
if skip_pre315(aq_parent(aq_inner(tool))):
return True
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')
setup.runImportStepFromProfile('profile-bika.lims:default', 'workflow')
# Add the SupplyOrderFolder /supplyorders
try:
typestool.constructContent(type_name="SupplyOrderFolder",
container=portal,
id='supplyorders',
title='Supply Orders')
obj = portal['supplyorders']
obj.unmarkCreationFlag()
obj.reindexObject()
except BadRequest:
# folder already exists
pass
# /supplyorders folder permissions
mp = portal.supplyorders.manage_permission
mp(permissions.ListFolderContents, [
'Manager',
'LabManager',
'LabClerk',
], 0)
mp(permissions.View, ['Manager', 'LabManager', 'LabClerk'], 0)
mp('Access contents information', ['Manager', 'LabManager', 'LabClerk'], 0)
mp(AddSupplyOrder, ['Manager', 'LabManager', 'Owner'], 0)
portal.supplyorders.reindexObject()
# /pricelists folder permissions
mp = portal.pricelists.manage_permission
mp(permissions.ListFolderContents, [
'Manager',
'LabManager',
'LabClerk',
], 0)
mp(permissions.View, ['Manager', 'LabManager', 'LabClerk'], 0)
mp('Access contents information', ['Manager', 'LabManager', 'LabClerk'], 0)
mp(AddPricelist, ['Manager', 'LabManager', 'LabClerk'], 0)
portal.pricelists.reindexObject()
return True
def upgrade(tool):
# Hack prevent out-of-date upgrading
# Related: PR #1484
# https://github.com/bikalabs/Bika-LIMS/pull/1484
from 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')
at.setCatalogsByType('ARPriority', ['bika_setup_catalog', ])
return True
def upgrade(tool):
# Hack prevent out-of-date upgrading
# Related: PR #1484
# https://github.com/bikalabs/Bika-LIMS/pull/1484
from lims.upgrade import skip_pre315
if skip_pre315(aq_parent(aq_inner(tool))):
return True
portal = aq_parent(aq_inner(tool))
portal.portal_actions.portal_tabs.queries.visible = False
return True
def upgrade(tool):
""" Re-import types tool to add condition for sample/partitions view
"""
# Hack prevent out-of-date upgrading
# Related: PR #1484
# https://github.com/bikalabs/Bika-LIMS/pull/1484
from lims.upgrade import skip_pre315
if skip_pre315(aq_parent(aq_inner(tool))):
return True
portal = aq_parent(aq_inner(tool))
setup = portal.portal_setup
setup.runImportStepFromProfile('profile-bika.lims:default', 'typeinfo')
def upgrade(tool):
"""Added bika.lims.analysisservice.edit.js
"""
# Hack prevent out-of-date upgrading
# Related: PR #1484
# https://github.com/bikalabs/Bika-LIMS/pull/1484
from lims.upgrade import skip_pre315
if skip_pre315(aq_parent(aq_inner(tool))):
return True
portal = aq_parent(aq_inner(tool))
setup = portal.portal_setup
# update affected tools
setup.runImportStepFromProfile('profile-bika.lims:default', 'jsregistry')
# apply new method/calculation data to old Analysis Services
portal = aq_parent(aq_inner(tool))
pc = getToolByName(portal, 'portal_catalog')
bsc = getToolByName(portal, 'bika_setup_catalog')
rc=getToolByName(portal, REFERENCE_CATALOG)
proxies = pc(portal_type="AnalysisService")
for proxy in proxies:
an = proxy.getObject()
rels = an.at_references.objectValues()
oldmethod = None
oldinstrument = None
oldcalc = None
for rel in rels:
if rel.relationship == 'AnalysisServiceCalculation':
oldcalc=rc.lookupObject(rel.targetUID)
elif rel.relationship == 'AnalysisServiceInstrument':
oldinstrument=rc.lookupObject(rel.targetUID)
elif rel.relationship == 'AnalysisServiceMethod':
oldmethod=rc.lookupObject(rel.targetUID)
if oldmethod and oldcalc and oldinstrument:
break
# Reset the method, instrument and calculations
if oldmethod:
an.Schema().getField('Methods').set(an, [oldmethod.UID(),])
an.Schema().getField('_Method').set(an, oldmethod.UID())
if oldinstrument:
an.Schema().getField('Instruments').set(an, [oldinstrument.UID(),])
an.Schema().getField('Instrument').set(an, oldinstrument.UID())
if oldcalc:
an.setUseDefaultCalculation(False);
an.Schema().getField('DeferredCalculation').set(an, oldcalc.UID())
return True
def upgrade(tool):
# Hack prevent out-of-date upgrading
# Related: PR #1484
# https://github.com/bikalabs/Bika-LIMS/pull/1484
from lims.upgrade import skip_pre315
if skip_pre315(aq_parent(aq_inner(tool))):
return True
portal = aq_parent(aq_inner(tool))
setup = portal.portal_setup
# update affected tools
setup.runImportStepFromProfile('profile-bika.lims:default', 'typeinfo')
return True
def upgrade(tool):
# Hack prevent out-of-date upgrading
# Related: PR #1484
# https://github.com/bikalabs/Bika-LIMS/pull/1484
from lims.upgrade import skip_pre315
if skip_pre315(aq_parent(aq_inner(tool))):
return True
portal = aq_parent(aq_inner(tool))
setup = portal.portal_setup
setup.runImportStepFromProfile(
'profile-bika.lims:default', 'propertiestool')
return True
def upgrade(tool):
"""Upgrade step required for Bika LIMS 3.1.9
"""
portal = aq_parent(aq_inner(tool))
# Adding new feature multiple profiles per Analysis Request
multipleAnalysisProfiles(portal)
setup = portal.portal_setup
# Updated profile steps
setup.runImportStepFromProfile('profile-bika.lims:default', 'typeinfo')
setup.runImportStepFromProfile('profile-bika.lims:default', 'jsregistry')
setup.runImportStepFromProfile('profile-bika.lims:default', 'workflow-csv')
# important info about upgrade steps in
# http://stackoverflow.com/questions/7821498/is-there-a-good-reference-list-for-the-names-of-the-genericsetup-import-steps
setup.runImportStepFromProfile('profile-bika.lims:default', 'skins')
# Update workflow permissions
wf = getToolByName(portal, 'portal_workflow')
wf.updateRoleMappings()
qi = portal.portal_quickinstaller
ufrom = qi.upgradeInfo('bika.lims')['installedVersion']
logger.info("Upgrading Bika LIMS: %s -> %s" % (ufrom, '319'))
# Migrations
return True
def upgrade(tool):
# Hack prevent out-of-date upgrading
# Related: PR #1484
# https://github.com/bikalabs/Bika-LIMS/pull/1484
from lims.upgrade import skip_pre315
if skip_pre315(aq_parent(aq_inner(tool))):
return True
portal = aq_parent(aq_inner(tool))
setup = portal.portal_setup
typestool = getToolByName(portal, 'portal_types')
# update affected tools
setup.runImportStepFromProfile('profile-bika.lims:default', 'workflow')
return True
def upgrade(tool):
""" JS structure refactoring
"""
# Hack prevent out-of-date upgrading
# Related: PR #1484
# https://github.com/bikalabs/Bika-LIMS/pull/1484
from lims.upgrade import skip_pre315
if skip_pre315(aq_parent(aq_inner(tool))):
return True
portal = aq_parent(aq_inner(tool))
setup = portal.portal_setup
setup.runImportStepFromProfile('profile-bika.lims:default', 'jsregistry')
return True
def upgrade(tool):
"""Upgrade step required for Bika LIMS 3.1.9
"""
portal = aq_parent(aq_inner(tool))
# Adding new feature multiple profiles per Analysis Request
multipleAnalysisProfiles(portal)
setup = portal.portal_setup
# Updated profile steps
setup.runImportStepFromProfile('profile-bika.lims:default', 'typeinfo')
setup.runImportStepFromProfile('profile-bika.lims:default', 'jsregistry')
setup.runImportStepFromProfile('profile-bika.lims:default', 'workflow-csv')
# important info about upgrade steps in
# http://stackoverflow.com/questions/7821498/is-there-a-good-reference-list-for-the-names-of-the-genericsetup-import-steps
setup.runImportStepFromProfile('profile-bika.lims:default', 'skins')
# Update workflow permissions
wf = getToolByName(portal, 'portal_workflow')
wf.updateRoleMappings()
qi = portal.portal_quickinstaller
ufrom = qi.upgradeInfo('bika.lims')['installedVersion']
logger.info("Upgrading Bika LIMS: %s -> %s" % (ufrom, '319'))
# Migrations
return True
def upgrade(tool):
# Hack prevent out-of-date upgrading
# Related: PR #1484
# https://github.com/bikalabs/Bika-LIMS/pull/1484
from lims.upgrade import skip_pre315
if skip_pre315(aq_parent(aq_inner(tool))):
return True
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')
setup.runImportStepFromProfile('profile-bika.lims:default', 'workflow')
# Add the SupplyOrderFolder /supplyorders
try:
typestool.constructContent(type_name="SupplyOrderFolder",
container=portal,
id='supplyorders',
title='Supply Orders')
obj = portal['supplyorders']
obj.unmarkCreationFlag()
obj.reindexObject()
except BadRequest:
# folder already exists
pass
# /supplyorders folder permissions
mp = portal.supplyorders.manage_permission
mp(permissions.ListFolderContents, ['Manager', 'LabManager', 'LabClerk', ], 0)
mp(permissions.View, ['Manager', 'LabManager', 'LabClerk'], 0)
mp('Access contents information', ['Manager', 'LabManager', 'LabClerk'], 0)
mp(AddSupplyOrder, ['Manager', 'LabManager', 'Owner'], 0)
portal.supplyorders.reindexObject()
# /pricelists folder permissions
mp = portal.pricelists.manage_permission
mp(permissions.ListFolderContents, ['Manager', 'LabManager', 'LabClerk', ], 0)
mp(permissions.View, ['Manager', 'LabManager', 'LabClerk'], 0)
mp('Access contents information', ['Manager', 'LabManager', 'LabClerk'], 0)
mp(AddPricelist, ['Manager', 'LabManager', 'LabClerk'], 0)
portal.pricelists.reindexObject()
return True
def upgrade(tool):
"""Added bika.lims.client.view.js
"""
# Hack prevent out-of-date upgrading
# Related: PR #1484
# https://github.com/bikalabs/Bika-LIMS/pull/1484
from lims.upgrade import skip_pre315
if skip_pre315(aq_parent(aq_inner(tool))):
return True
portal = aq_parent(aq_inner(tool))
setup = portal.portal_setup
# reread jsregistry with the new data
setup.runImportStepFromProfile('profile-bika.lims:default', 'jsregistry')
return True
def upgrade(tool):
""" Remove Maintenance, Validations, Calibrations ans Schedule
https://github.com/bikalabs/Bika-LIMS/issues/1134
"""
# Hack prevent out-of-date upgrading
# Related: PR #1484
# https://github.com/bikalabs/Bika-LIMS/pull/1484
from lims.upgrade import skip_pre315
if skip_pre315(aq_parent(aq_inner(tool))):
return True
portal = aq_parent(aq_inner(tool))
setup = portal.portal_setup
# update affected tools
setup.runImportStepFromProfile('profile-bika.lims:default', 'typeinfo')
return True
def upgrade(tool):
"""Added bika.lims.loader.js and bika.lims.method.edit.js
"""
# Hack prevent out-of-date upgrading
# Related: PR #1484
# https://github.com/bikalabs/Bika-LIMS/pull/1484
from lims.upgrade import skip_pre315
if skip_pre315(aq_parent(aq_inner(tool))):
return True
portal = aq_parent(aq_inner(tool))
setup = portal.portal_setup
# update affected tools
setup.runImportStepFromProfile('profile-bika.lims:default', 'jsregistry')
return True
def upgrade(tool):
""" Remove Maintenance, Validations, Calibrations ans Schedule
https://github.com/bikalabs/Bika-LIMS/issues/1134
"""
# Hack prevent out-of-date upgrading
# Related: PR #1484
# https://github.com/bikalabs/Bika-LIMS/pull/1484
from lims.upgrade import skip_pre315
if skip_pre315(aq_parent(aq_inner(tool))):
return True
portal = aq_parent(aq_inner(tool))
setup = portal.portal_setup
# update affected tools
setup.runImportStepFromProfile('profile-bika.lims:default', 'typeinfo')
return True
def upgrade(tool):
"""Added D3.js library and D3 Control-chart for Instrument QC
"""
# Hack prevent out-of-date upgrading
# Related: PR #1484
# https://github.com/bikalabs/Bika-LIMS/pull/1484
from lims.upgrade import skip_pre315
if skip_pre315(aq_parent(aq_inner(tool))):
return True
portal = aq_parent(aq_inner(tool))
setup = portal.portal_setup
# update affected tools
setup.runImportStepFromProfile('profile-bika.lims:default', 'jsregistry')
return True
def upgrade(tool):
"""Add the bika-frontpage view to the selectable views. This will not
set the default, but all new sites will have the 'properties.xml' loaded,
which does set the default.
"""
# Hack prevent out-of-date upgrading
# Related: PR #1484
# https://github.com/bikalabs/Bika-LIMS/pull/1484
from lims.upgrade import skip_pre315
if skip_pre315(aq_parent(aq_inner(tool))):
return True
portal = aq_parent(aq_inner(tool))
setup = portal.portal_setup
setup.runImportStepFromProfile('profile-bika.lims:default', 'typeinfo')
return True
def upgrade(tool):
""" Convert analysis specs to AR specs in AR.ResultsRange.
"""
# Hack prevent out-of-date upgrading
# Related: PR #1484
# https://github.com/bikalabs/Bika-LIMS/pull/1484
from lims.upgrade import skip_pre315
if skip_pre315(aq_parent(aq_inner(tool))):
return True
portal = aq_parent(aq_inner(tool))
bc = getToolByName(portal, 'bika_catalog', None)
bsc = getToolByName(portal, 'bika_setup_catalog', None)
# for each AR
proxies = bc(portal_type="AnalysisRequest")
for proxy in proxies:
ar = proxy.getObject()
# get the AR.Specification
arspec = ar.getSpecification()
rr = arspec.getResultsRange() if arspec else []
# Get analysis specifications
specs = []
for analysis in ar.getAnalyses(full_objects=True):
spec = getattr(analysis, 'specification', False)
if spec:
spec['keyword'] = analysis.getService().getKeyword()
spec['uid'] = analysis.UID()
specs.append(spec)
# mix in the analysis spec values
for s in specs:
s_in_rr = False
for i, r in enumerate(rr):
if s['keyword'] == r['keyword']:
rr[i].update(s)
s_in_rr = True
if not s_in_rr:
rr.append(s)
# set AR.ResultsRange
ar.setResultsRange(rr)
return True
def upgrade(tool):
"""Add the bika-frontpage view to the selectable views. This will not
set the default, but all new sites will have the 'properties.xml' loaded,
which does set the default.
"""
# Hack prevent out-of-date upgrading
# Related: PR #1484
# https://github.com/bikalabs/Bika-LIMS/pull/1484
from lims.upgrade import skip_pre315
if skip_pre315(aq_parent(aq_inner(tool))):
return True
portal = aq_parent(aq_inner(tool))
setup = portal.portal_setup
setup.runImportStepFromProfile('profile-bika.lims:default', 'typeinfo')
return True
def upgrade(tool):
"""
"""
# Hack prevent out-of-date upgrading
# Related: PR #1484
# https://github.com/bikalabs/Bika-LIMS/pull/1484
from lims.upgrade import skip_pre315
if skip_pre315(aq_parent(aq_inner(tool))):
return True
portal = aq_parent(aq_inner(tool))
portal_catalog = getToolByName(portal, "portal_catalog")
typestool = getToolByName(portal, "portal_types")
workflowtool = getToolByName(portal, "portal_workflow")
setup = portal.portal_setup
# Changes to the catalogs
at = getToolByName(portal, "archetype_tool")
at.setCatalogsByType("Batch", ["bika_catalog", "portal_catalog"])
at.setCatalogsByType("AnalysisRequest", ["bika_catalog", "portal_catalog"])
at.setCatalogsByType("Sample", ["bika_catalog", "portal_catalog"])
at.setCatalogsByType("SamplePartition", ["bika_catalog", "portal_catalog"])
at.setCatalogsByType("ReferenceSample", ["bika_catalog", "portal_catalog"])
at.setCatalogsByType("Report", ["bika_catalog", "portal_catalog"])
at.setCatalogsByType("Worksheet", ["bika_catalog", "portal_catalog"])
at.setCatalogsByType("AnalysisService", ["bika_setup_catalog", "portal_catalog"])
at.setCatalogsByType("SampleType", ["bika_setup_catalog", "portal_catalog"])
at.setCatalogsByType("SamplePoint", ["bika_setup_catalog", "portal_catalog"])
at.setCatalogsByType("Instrument", ["bika_setup_catalog", "portal_catalog"])
at.setCatalogsByType("Method", ["bika_setup_catalog", "portal_catalog"])
at.setCatalogsByType("Calculation", ["bika_setup_catalog", "portal_catalog"])
at.setCatalogsByType("AnalysisProfile", ["bika_setup_catalog", "portal_catalog"])
at.setCatalogsByType("ARTemplate", ["bika_setup_catalog", "portal_catalog"])
at.setCatalogsByType("LabProduct", ["bika_setup_catalog", "portal_catalog"])
at.setCatalogsByType("LabContact", ["bika_setup_catalog", "portal_catalog"])
at.setCatalogsByType("ReferenceManufacturer", ["bika_setup_catalog", "portal_catalog"])
at.setCatalogsByType("ReferenceSupplier", ["bika_setup_catalog", "portal_catalog"])
at.setCatalogsByType("ReferenceDefinition", ["bika_setup_catalog", "portal_catalog"])
at.setCatalogsByType("WorksheetTemplate", ["bika_setup_catalog", "portal_catalog"])
portal_catalog.clearFindAndRebuild()
return True
def upgrade(tool):
# Hack prevent out-of-date upgrading
# Related: PR #1484
# https://github.com/bikalabs/Bika-LIMS/pull/1484
from lims.upgrade import skip_pre315
if skip_pre315(aq_parent(aq_inner(tool))):
return True
portal = aq_parent(aq_inner(tool))
# missing /supplyorders folder permission
clients = portal.clients.objectValues()
for client in clients:
mp = client.manage_permission
mp(AddSupplyOrder, ['Manager', 'LabManager', 'Owner'], 0)
client.reindexObject()
return True
def upgrade(tool):
"""LIMS-1275 - Remove acquisition for "Modify portal content" permission
"""
# Hack prevent out-of-date upgrading
# Related: PR #1484
# https://github.com/bikalabs/Bika-LIMS/pull/1484
from lims.upgrade import skip_pre315
if skip_pre315(aq_parent(aq_inner(tool))):
return True
portal = aq_parent(aq_inner(tool))
# /bika_setup -
mp = portal.bika_setup.manage_permission
mp(permissions.ModifyPortalContent, ['Manager', 'LabManager'], 0)
portal.batches.reindexObject()
return True
def upgrade(tool):
# Hack prevent out-of-date upgrading
# Related: PR #1484
# https://github.com/bikalabs/Bika-LIMS/pull/1484
from lims.upgrade import skip_pre315
if skip_pre315(aq_parent(aq_inner(tool))):
return True
portal = aq_parent(aq_inner(tool))
for pricelist in portal.pricelists.objectValues('Pricelist'):
for broken in pricelist.objectValues('PriceListLineItem'):
pricelist.manage_delObjects([broken.id])
pc = getToolByName(portal, 'portal_catalog')
pc.refreshCatalog(clear=1)
return True
def upgrade(tool):
""" Add Storage locacations to ARs and Samples.
"""
# Hack prevent out-of-date upgrading
# Related: PR #1484
# https://github.com/bikalabs/Bika-LIMS/pull/1484
from lims.upgrade import skip_pre315
if skip_pre315(aq_parent(aq_inner(tool))):
return True
portal = aq_parent(aq_inner(tool))
setup = portal.portal_setup
bc = getToolByName(portal, 'bika_catalog')
for brain in bc(portal_type='AnalysisRequest'):
obj = brain.getObject()
if not obj.getPriority():
obj.setDefaultPriority()