def migrate(context, annotations, oldnotes):
# construct a set of old notes to verify whether or not to use
# the CellML profile.
oldnote_set = set(oldnotes)
session_file = None
if 'opencellsession' in oldnote_set:
# It can die here because something wrong with getting the
# vocabulary from the manifest.
session_file = annotations['opencellsession'].filename
# discard this.
oldnote_set.remove('opencellsession')
groups = {}
groups['opencellsession'] = [('filename', session_file),]
if cellml_force or (cellml_type_notes and oldnote_set == cellml_notes):
context.file_type = cellml_type
# update views
context.views = cellml_type_notes
context.setSubject(cellml_type_tags)
groups['license_citation'] = [('format', u'cellml_rdf_metadata')]
groups['source_text'] = [('langtype', u'xml')]
else:
# reuse the existing views, and unknown profile.
pass
# annotate using the form.
form = ExposureFileTypeAnnotatorForm(context, None)
# It can die here too because of various reasons (workspace
# missing, malformed input data, incompatibilities of existing
# data with new formatting scheme, stray electrons, etc.).
form._annotate(groups)
def filetype_bulk_update(context):
import traceback
import transaction
from pmr2.app.annotation.interfaces import IExposureFileNote
from pmr2.app.exposure.browser.util import viewinfo
try:
from pmr2.app.exposure.browser.browser import \
ExposureFileTypeAnnotatorForm
except ImportError:
from pmr2.app.browser.exposure import ExposureFileTypeAnnotatorForm
logger = getLogger('pmr2.app')
catalog = getToolByName(context, 'portal_catalog')
brains = catalog(portal_type='ExposureFileType')
filetypes = dict([(b.getPath(), b.pmr2_eftype_views) for b in brains])
if not filetypes:
logger.error('Please reindex or create some Exposure File Types '
'before running this.')
return
errors = []
commit_interval = 100
files = catalog(portal_type='ExposureFile')
t = len(files)
for c, b in enumerate(files, 1):
file_sp = transaction.savepoint()
file = b.getObject()
logger.info('Rebuilding notes for `%s` (%d/%d).',
file.absolute_url_path(), c, t)
ftpath = file.file_type
if not ftpath:
continue
if not ftpath in filetypes:
# XXX only log this information for now, we may need to give
# adminstrators some way to automatically migrate to a new
# existing type since the old one was removed.
logger.warning('`%s` has `%s` as its filetype but it no longer '
'exists ' % (file.absolute_url_path(), ftpath))
continue
cftviews = filetypes[ftpath] # file type views for current file
try:
# assign the new set of views
# annotate using the form.
file.views = cftviews
# XXX does not set the new subjects, i.e. not applying tags
# via setSubject method of this file object
groups = {}
for k, v in viewinfo(file):
groups[k] = v and v.items() or None
form = ExposureFileTypeAnnotatorForm(file, None)
form._annotate(groups)
file.reindexObject()
except:
file_sp.rollback()
errors.append(file.absolute_url_path())
logger.error('Failed to rebuild `%s`' % file.absolute_url_path())
logger.warning(traceback.format_exc())
continue
if c % commit_interval == 0:
transaction.get().commit()
logger.info('Committed transaction, interval %d reached' %
commit_interval)
if errors:
logger.error('The following file(s) have failed to rebuild:\n%s' %
'\n'.join(errors))
