def __init__(self, portal, migrator, src_portal_type=None, dst_portal_type=None,
**kwargs):
self.portal = portal
self.catalog = getToolByName(portal, 'portal_catalog')
self.migrator = migrator
if src_portal_type is None:
self.src_portal_type = self.migrator.src_portal_type
else:
self.src_portal_type = src_portal_type
if dst_portal_type is None:
self.dst_portal_type = self.migrator.dst_portal_type
else:
self.dst_portal_type = dst_portal_type
self.src_meta_type = self.migrator.src_meta_type
self.dst_meta_type = self.migrator.dst_meta_type
self.transaction_size = int(kwargs.get('transaction_size', 20))
self.full_transaction = kwargs.get('full_transaction', False)
self.use_savepoint = kwargs.get('use_savepoint', False)
if self.full_transaction and self.use_savepoint:
raise ValueError
self.out = StringIO()
self.counter = 0
self.errors = []
# Disable schema cache
request = getattr(portal, 'REQUEST', None)
if request is not None:
disableCache(request)
def markNewContentObject(obj, event):
"""Mark newly created content as Pigeonhole-aware if its
portal type is in our list of Aware types"""
# get our local utility
# this is incidentally also our lame check
# to see if PH is installed here
try:
utility = getUtility(IPigeonholizer)
except ComponentLookupError:
# ignore problems when we can't find the utility -- PH might not
# be installed
utility = None
if utility is not None:
if obj.portal_type in utility.ph_aware_types:
alsoProvides(obj, IPigeonholeAware)
elif blobsAvailable:
# in Plone 3, the meta_type for blob-based Images and Files
# is just ATBlob, but thanks to a custom factory, they DO have
# marker interfaces set. Check them!
if "Image" in utility.ph_aware_types and \
IATBlobImage.providedBy(obj):
alsoProvides(obj, IPigeonholeAware)
elif "File" in utility.ph_aware_types and \
IATBlobFile.providedBy(obj):
alsoProvides(obj, IPigeonholeAware)
if disableCache is not None:
disableCache(getSite().REQUEST)
def upgrade12to13(setupTool):
_logger.info('Upgrading EDRN Public Portal from profile version 12 to profile version 13')
portal = _getPortal(setupTool)
request = portal.REQUEST
catalog, setup = getToolByName(portal, 'portal_catalog'), getToolByName(portal, 'portal_setup')
_logger.info("Disabling schema extender's cache")
from archetypes.schemaextender.extender import disableCache
disableCache(request)
propTool = getToolByName(portal, 'portal_properties')
propTool.site_properties.getProperty('enable_link_integrity_checks', True)
contentRuleStorage = getUtility(IRuleStorage)
_logger.info('Disabling link integrity checks')
propTool.site_properties.manage_changeProperties(enable_link_integrity_checks=False)
_logger.info('Disabling content rules')
contentRuleStorage.active = False
qi = getToolByName(portal, 'portal_quickinstaller')
qi.upgradeProduct('eke.ecas')
_logger.info('Ingesting everything fully')
setAutoIngestProperties(portal)
portal.unrestrictedTraverse('@@ingestEverythingFully')()
_logger.info('Clearing ingest paths to prevent automatic ingest')
if portal.hasProperty('edrnIngestPaths'):
portal.manage_delProperties(['edrnIngestPaths'])
_logger.info('Resetting portal "from" email address')
portal.manage_changeProperties(email_from_address='*****@*****.**')
_logger.info('Clearing, finding, and re-building the catalog')
catalog.clearFindAndRebuild()
uidCatalog = getToolByName(portal, 'uid_catalog')
_logger.info('Rebuilding the UID catalog')
uidCatalog.manage_rebuildCatalog()
transaction.commit()
_logger.info('Upgrade 12-to-13 complete')
def upgrade10to11(setupTool):
_logger.info('Upgrading EDRN Public Portal from profile version 10 to profile version 11 with nifty visualizations')
portal = _getPortal(setupTool)
request = portal.REQUEST
catalog, setup = getToolByName(portal, 'portal_catalog'), getToolByName(portal, 'portal_setup')
_logger.info("Disabling schema extender's cache")
from archetypes.schemaextender.extender import disableCache
disableCache(request)
qi = getToolByName(portal, 'portal_quickinstaller')
propTool = getToolByName(portal, 'portal_properties')
propTool.site_properties.getProperty('enable_link_integrity_checks', True)
contentRuleStorage = getUtility(IRuleStorage)
_logger.info('Disabling link integrity checks')
propTool.site_properties.manage_changeProperties(enable_link_integrity_checks=False)
_logger.info('Disabling content rules')
contentRuleStorage.active = False
# Set new summarizer data sources
_logger.info('Setting up new summary data sources')
import socket
if not socket.gethostname().startswith('tumor'):
biomarkerSummary = 'https://edrn.jpl.nasa.gov/cancerdataexpo/summarizer-data/biomarker/@@summary'
siteSummary = 'https://edrn.jpl.nasa.gov/cancerdataexpo/summarizer-data/collaboration/@@summary'
pubSummary = 'https://edrn.jpl.nasa.gov/cancerdataexpo/summarizer-data/publication/@@summary'
else:
biomarkerSummary = 'https://edrn-dev.jpl.nasa.gov/cancerdataexpo/summarizer-data/biomarker/@@summary'
siteSummary = 'https://edrn-dev.jpl.nasa.gov/cancerdataexpo/summarizer-data/collaboration/@@summary'
pubSummary = 'https://edrn-dev.jpl.nasa.gov/cancerdataexpo/summarizer-data/publication/@@summary'
if 'biomarkers' in portal.keys():
_logger.info('Setting biomarkers summary data source to %s', biomarkerSummary)
o = portal['biomarkers']
o.bmSumDataSource = biomarkerSummary
if 'committees' in portal.keys():
_logger.info('Setting committees summary data source to %s', siteSummary)
o = portal['committees']
o.siteSumDataSource = siteSummary
if 'publications' in portal.keys():
_logger.info('Setting publications summary data source to %s', pubSummary)
o = portal['publications']
o.pubSumDataSource = pubSummary
_logger.info('Ingesting everything fully')
setAutoIngestProperties(portal)
portal.unrestrictedTraverse('@@ingestEverythingFully')()
_logger.info('Clearing ingest paths to prevent automatic ingest')
if portal.hasProperty('edrnIngestPaths'):
portal.manage_delProperties(['edrnIngestPaths'])
_logger.info('Resetting portal "from" email address')
portal.manage_changeProperties(email_from_address='*****@*****.**')
_logger.info('Clearing, finding, and re-building the catalog')
catalog.clearFindAndRebuild()
uidCatalog = getToolByName(portal, 'uid_catalog')
_logger.info('Rebuilding the UID catalog')
uidCatalog.manage_rebuildCatalog()
transaction.commit()
_logger.info('Upgrade 10-to-11 complete')
def upgrade9to10(setupTool):
_logger.info('Upgrading EDRN Public Portal from profile version 9 to profile version 10')
portal = _getPortal(setupTool)
request = portal.REQUEST
catalog, setup = getToolByName(portal, 'portal_catalog'), getToolByName(portal, 'portal_setup')
_logger.info("Disabling schema extender's cache")
from archetypes.schemaextender.extender import disableCache
disableCache(request)
qi = getToolByName(portal, 'portal_quickinstaller')
propTool = getToolByName(portal, 'portal_properties')
propTool.site_properties.getProperty('enable_link_integrity_checks', True)
contentRuleStorage = getUtility(IRuleStorage)
_logger.info('Disabling link integrity checks')
propTool.site_properties.manage_changeProperties(enable_link_integrity_checks=False)
_logger.info('Disabling content rules')
contentRuleStorage.active = False
# No, decided not to write secretome with Plone:
# qi.installProduct('eke.secretome')
# setup.runAllImportStepsFromProfile('profile-eke.secretome:default')
disablePublicationsPortlets(portal)
# Set the new bmuDataSource on biomarkers, but not on testing (this is ugly)
if 'biomarkers' in portal.keys():
import socket
if not socket.gethostname().startswith('tumor'):
b = portal['biomarkers']
b.bmuDataSource = 'http://edrn.jpl.nasa.gov/cancerdataexpo/rdf-data/biomuta/@@rdf'
_logger.info('Ingesting everything fully')
portal.unrestrictedTraverse('@@ingestEverythingFully')()
_logger.info('Clearing ingest paths to prevent automatic ingest')
if portal.hasProperty('edrnIngestPaths'):
portal.manage_delProperties(['edrnIngestPaths'])
_logger.info('Resetting portal "from" email address')
portal.manage_changeProperties(email_from_address='*****@*****.**')
_logger.info('Clearing, finding, and re-building the catalog')
catalog.clearFindAndRebuild()
uidCatalog = getToolByName(portal, 'uid_catalog')
_logger.info('Rebuilding the UID catalog')
uidCatalog.manage_rebuildCatalog()
transaction.commit()
_logger.info('Upgrade 9-to-10 complete')
def __init__(self,
portal,
migrator,
src_portal_type=None,
dst_portal_type=None,
**kwargs):
self.portal = portal
self.catalog = getToolByName(portal, 'portal_catalog')
self.migrator = migrator
if src_portal_type is None:
self.src_portal_type = self.migrator.src_portal_type
else:
self.src_portal_type = src_portal_type
if dst_portal_type is None:
self.dst_portal_type = self.migrator.dst_portal_type
else:
self.dst_portal_type = dst_portal_type
self.src_meta_type = self.migrator.src_meta_type
self.dst_meta_type = self.migrator.dst_meta_type
self.transaction_size = int(kwargs.get('transaction_size', 20))
self.full_transaction = kwargs.get('full_transaction', False)
self.use_savepoint = kwargs.get('use_savepoint', False)
self.limit = kwargs.get('limit', False)
if self.full_transaction and self.use_savepoint:
raise ValueError
self.out = StringIO()
self.counter = 0
self.errors = []
# Disable schema cache
request = getattr(portal, 'REQUEST', None)
if request is not None:
disableCache(request)
def addSubmission(self, REQUEST, folder, portal_type):
"""
Perform content operations as the appropriate user.
"""
form = aq_parent(aq_inner(self))
if folder is None:
folder = self
order = folder.getOrdering()
if not hasattr(order, '__contains__'):
order = folder.contentIds()
title_field_name = self.getTitleField() or 'title'
changed = {}
if title_field_name in form:
# Get the title from a form field in the submission
title_field = form[title_field_name]
title, kwargs = title_field.fgField.widget.process_form(
title_field, title_field.fgField, REQUEST.form)
changed[title_field_name] = title
else:
# Generate a title from the form title
title = '{0} Submission'.format(form.Title())
# Generate an id from the title, adding a suffix if existing
id_ = str(norm_ifaces.IUserPreferredURLNormalizer(
REQUEST).normalize(title))
if id_ in order:
# Exising objects have the id, find the next index suffix
order_idx = len(folder) - 1
base_id = id_
idx = 0
while id_ in order:
while order_idx >= 0:
# Start at the end to try and find the highest index
order_id = order[order_idx]
if order_id.startswith(base_id + '-'):
idx = int(order_id[len(base_id + '-'):])
break
order_idx -= 1
id_ = '{0}-{1}'.format(base_id, (idx + 1))
new_id = folder.invokeFactory(portal_type, id_, title=title)
submission = folder[new_id]
submission.addReference(self, relationship='submissionFolderAdapter')
# Mark the item as a form submission so the schema is extended with the
# form schema
interface.alsoProvides(submission, IFormSubmission)
# Set the submission field values now that the extender applies
extender.disableCache(REQUEST)
schema = submission.Schema()
for field in schema.fields():
if field.__name__ in ('id', 'title'):
# skip factory arguments
continue
result = field.widget.process_form(
submission, field, REQUEST.form,
empty_marker=BaseObject._marker,
validating=False)
if result is BaseObject._marker or result is None:
continue
changed[field.__name__] = result[0]
if field.__name__ in ('id', 'title'):
# already set in the factory
continue
field.set(submission, result[0], **result[1])
# Apply workflow transitions
workflow = getToolByName(submission, 'portal_workflow')
for transition in self.getSubmissionTransitions():
try:
workflow.doActionFor(submission, transition)
except WorkflowCore.WorkflowException:
logger.exception(
'Workflow transition {0!r} failed on form submission: {1}'
.format(transition, self.absolute_url))
submission.setLayout('base_view')
return submission, changed
def upgrade6to7(setupTool):
_logger.info('Upgrading EDRN Public Portal from profile version 6 to profile version 7')
portal = _getPortal(setupTool)
request = portal.REQUEST
# _logger.info('Fixing login lockout plugin')
# fixLoginLockoutPlugin(portal)
_logger.info("Disabling schema extender's cache")
from archetypes.schemaextender.extender import disableCache
disableCache(request)
qi = getToolByName(portal, 'portal_quickinstaller')
propTool = getToolByName(portal, 'portal_properties')
propTool.site_properties.getProperty('enable_link_integrity_checks', True)
contentRuleStorage = getUtility(IRuleStorage)
_logger.info('Disabling link integrity checks')
propTool.site_properties.manage_changeProperties(enable_link_integrity_checks=False)
_logger.info('Disabling content rules')
contentRuleStorage.active = False
# _logger.info('Reloading Javascript Registry')
# setupTool.runImportStepFromProfile(PROFILE_ID, 'jsregistry')
# Clear the catalog
catalog = getToolByName(portal, 'portal_catalog')
_logger.info('Clearing the catalog')
catalog.manage_catalogClear()
_logger.info('Disabling Google Analytics')
removeGoogleAnalytics(portal)
_logger.info('Clearing the login-lockout table')
clearLoginLockoutTable(portal) # CA-873
_logger.info('Installing new packages')
installNewPackages(portal, _newPackages7)
_logger.info('Reinstalling products %r', _dependencies7)
qi.reinstallProducts(_dependencies7)
for product in _dependencies7:
_logger.info('Upgrading product "%s"', product)
qi.upgradeProduct(product)
transaction.commit()
for thing in _reinstall7:
_logger.info('Uninstalling then reinstalling "%s"' % thing)
qi.uninstallProducts([thing])
qi.installProduct(thing)
# edrnThemeUpgrade4to5(setupTool)
# ekeCommitteesReloadTypes4to5(setupTool)
# ekeSpecimensSetupCatalog(setupTool)
# 2013-10-08: no longer needed, ops BMDB is fine:
# _logger.info('Setting biomarkers to ingest from TEST BMDB')
#setBiomarkerIngestPaths(portal, 'http://tumor.jpl.nasa.gov/bmdb/rdf/biomarkers',
# 'http://tumor.jpl.nasa.gov/bmdb/rdf/biomarkerorgans')
# 2013-10-08: we will have to re-do this after Portal 4.2 is finally deployed at NCI:
removeCustomQuickLinksPortlet(portal)
loadPortalTypes(setupTool)
upgradeBiomarkerFolders(setupTool)
# /2013-10-08
_logger.info('Ingesting everything fully')
portal.unrestrictedTraverse('@@ingestEverythingFully')()
_logger.info('Clearing ingest paths to prevent automatic ingest')
if portal.hasProperty('edrnIngestPaths'):
portal.manage_delProperties(['edrnIngestPaths'])
_logger.info('Resetting portal "from" email address')
portal.manage_changeProperties(email_from_address='*****@*****.**')
_logger.info('Clearing, finding, and re-building the catalog')
catalog.clearFindAndRebuild()
uidCatalog = getToolByName(portal, 'uid_catalog')
_logger.info('Rebuilding the UID catalog')
uidCatalog.manage_rebuildCatalog()
transaction.commit()
def upgrade4to5(setupTool):
_logger.info('Upgrading EDRN Public Portal from profile version 4 to profile version 5')
portal = _getPortal(setupTool)
request = portal.REQUEST
# Whew. Thanks to @davisagli (freakin' brilliant dude) for figuring this out:
_logger.info("Disabling schema extender's cache")
from archetypes.schemaextender.extender import disableCache
disableCache(request)
# Without the above two lines, we eventually construct an Active ERNE Set during the full ingest below
# and it mistakenly picks up a Person's schema instead of its own. When getting its title, a person's
# is computed, so it looks for a _computeTitle function, but an ActiveERNESet has no such function.
# Ingest then fails.
#
# Whew!
#
# Now, onward:
# Disable annoying link integrity checking
qi = getToolByName(portal, 'portal_quickinstaller')
propTool = getToolByName(portal, 'portal_properties')
propTool.site_properties.getProperty('enable_link_integrity_checks', True)
contentRuleStorage = getUtility(IRuleStorage)
_logger.info('Disabling link integrity checks')
propTool.site_properties.manage_changeProperties(enable_link_integrity_checks=False)
_logger.info('Disabling content rules')
contentRuleStorage.active = False
# Clear the catalog
catalog = getToolByName(portal, 'portal_catalog')
_logger.info('Clearing the catalog')
catalog.manage_catalogClear()
_logger.info('Terminating existing committees with extreme prejudice')
if 'committees' in portal.keys():
committees = portal['committees']
committees.manage_delObjects(committees.keys())
_logger.info('Enabling JQuery')
enableJQuery(portal) # Enable jquery.js. Fixes CA-872.
_logger.info('Disabling Google Analytics')
removeGoogleAnalytics(portal)
_logger.info('Clearing the login-lockout table')
clearLoginLockoutTable(portal) # CA-873
_logger.info('Installing new packages')
installNewPackages(portal, _newPackages5)
_logger.info('Reinstalling products %r', _dependencies5)
qi.reinstallProducts(_dependencies5)
for product in _dependencies5:
_logger.info('Upgrading product "%s"', product)
qi.upgradeProduct(product)
transaction.commit()
if 'specimens' in portal.keys():
_logger.info('Nuking the specimens tab')
portal.manage_delObjects('specimens')
from eke.specimens.upgrades import addSampleSpecimenSets
# Recreate the members list page to fix the problem with upgrading eea.facetednavigation 4.0rc1→4.5
_logger.info('Re-creating the members list search page')
createMembersListSearchPage(portal)
# Likewise, but for the publications folder: disable and then re-enable faceted view
if 'publications' in portal.keys():
publications = portal['publications']
subtyper = getMultiAdapter((publications, request), name=u'faceted_subtyper')
_logger.info('Disabling, then re-enabling the faceted subtyper on the publications tab')
subtyper.disable()
subtyper.enable()
_logger.info('Adding sample specimen sets')
addSampleSpecimenSets(setupTool)
_logger.info('Disabling portlets on the specimens tab')
disableSpecimenPortlets(portal)
_logger.info('Re-setting the auto-ingest paths')
portal.manage_delProperties(['edrnIngestPaths'])
setAutoIngestProperties(portal)
_logger.info('Ingesting everything fully')
portal.unrestrictedTraverse('@@ingestEverythingFully')()
_logger.info('Clearing ingest paths to prevent automatic ingest')
if portal.hasProperty('edrnIngestPaths'):
portal.manage_delProperties(['edrnIngestPaths'])
_logger.info('Resetting portal "from" email address')
portal.manage_changeProperties(email_from_address='*****@*****.**')
_logger.info('Clearing, finding, and re-building the catalog')
catalog.clearFindAndRebuild()
uidCatalog = getToolByName(portal, 'uid_catalog')
_logger.info('Rebuilding the UID catalog')
uidCatalog.manage_rebuildCatalog()
transaction.commit()