def setupTools(context, logger=None):
if logger is None:
logger = LOG
logger.info('BCCVL site tools handler')
# only run for this product
if context.readDataFile('org.bccvl.site.marker.txt') is None:
return
portal = context.getSite()
# setup job catalog
from org.bccvl.site.job.catalog import setup_job_catalog
setup_job_catalog(portal)
# setup userannotation storage
from org.bccvl.site.userannotation.utility import init_user_annotation
init_user_annotation()
def upgrade_200_210_1(context, logger=None):
if logger is None:
logger = LOG
# Run GS steps
portal = api.portal.get()
# Do some registry cleanup:
registry = getUtility(IRegistry)
for key in list(registry.records.keys()):
if (key.startswith('plone.app.folderui')
or key.startswith('dexterity.membrane')
or key.startswith('collective.embedly')):
del registry.records[key]
setup = api.portal.get_tool('portal_setup')
setup.runImportStepFromProfile(PROFILE_ID, 'propertiestool')
setup.runImportStepFromProfile(PROFILE_ID, 'typeinfo')
setup.runImportStepFromProfile(PROFILE_ID, 'toolset')
setup.runImportStepFromProfile(PROFILE_ID, 'controlpanel')
setup.runImportStepFromProfile(PROFILE_ID, 'org.bccvl.site.content')
setup.runImportStepFromProfile(PROFILE_ID, 'plone.app.registry')
setup.runImportStepFromProfile(PROFILE_ID, 'workflow')
# make error logs visible
ignored_exceptions = portal.error_log._ignored_exceptions
portal.error_log._ignored_exceptions = ()
from org.bccvl.site.job.catalog import setup_job_catalog
setup_job_catalog(portal)
pc = api.portal.get_tool('portal_catalog')
# Update job_params with algorithm used for Climate Change Experiments
LOG.info('Updating job params of old projection experiments')
for brain in pc.searchResults(portal_type='org.bccvl.content.projectionexperiment'):
# go through all results
for result in brain.getObject().values():
if 'function' in result.job_params:
continue
# Add algorithm to job_params if missing algorithm
try:
sdmds = uuidToObject(
result.job_params['species_distribution_models'])
algorithm = sdmds.__parent__.job_params['function']
if algorithm:
result.job_params['function'] = algorithm
except Exception as e:
LOG.warning("Can't add algorithm id to %s: %s", result, e)
from org.bccvl.site.job.interfaces import IJobUtility
jobtool = getUtility(IJobUtility)
# search all datasets and create job object with infos from dataset
# -> delete job info on dataset
LOG.info('Migrating job data for datasets')
DS_TYPES = ['org.bccvl.content.dataset',
'org.bccvl.content.remotedataset']
for brain in pc.searchResults(portal_type=DS_TYPES):
job = jobtool.find_job_by_uuid(brain.UID)
if job:
# already processed ... skip
continue
try:
ds = brain.getObject()
except Exception as e:
LOG.warning('Could not resolve %s: %s', brain.getPath(), e)
continue
annots = IAnnotations(ds)
old_job = annots.get('org.bccvl.state', None)
if not old_job:
# no job state here ... skip it
continue
job = jobtool.new_job()
job.created = ds.created()
job.message = old_job['progress']['message']
job.progress = old_job['progress']['state']
job.state = old_job['state']
job.title = old_job['name']
job.taskid = old_job['taskid']
job.userid = ds.getOwner().getId()
job.content = IUUID(ds)
job.type = brain.portal_type
jobtool.reindex_job(job)
del annots['org.bccvl.state']
# search all experiments and create job object with infos from experiment
# -> delete job info on experiment
LOG.info('Migrating job data for experiments')
EXP_TYPES = ['org.bccvl.content.sdmexperiment',
'org.bccvl.content.projectionexperiment',
'org.bccvl.content.biodiverseexperiment',
'org.bccvl.content.ensemble',
'org.bccvl.content.speciestraitsexperiment'
]
for brain in pc.searchResults(portal_type=EXP_TYPES):
# go through all results
for result in brain.getObject().values():
job = None
try:
job = jobtool.find_job_by_uuid(IUUID(result))
except Exception as e:
LOG.info('Could not resolve %s: %s', result, e)
continue
if job:
# already processed ... skip
continue
annots = IAnnotations(result)
old_job = annots.get('org.bccvl.state', None)
if not old_job:
# no job state here ... skip it
continue
job = jobtool.new_job()
job.created = result.created()
job.message = old_job['progress']['message']
job.progress = old_job['progress']['state']
job.state = old_job['state']
job.title = old_job['name']
job.taskid = old_job['taskid']
job.userid = result.getOwner().getId()
job.content = IUUID(result)
job.type = brain.portal_type
job.function = result.job_paramsi.get('function')
if job.function:
job.toolkit = IUUID(
portal[defaults.TOOLKITS_FOLDER_ID][job.function])
jobtool.reindex_job(job)
del annots['org.bccvl.state']
LOG.info('Updating layer metadata for projection outputs')
from org.bccvl.site.interfaces import IBCCVLMetadata
for brain in pc.searchResults(BCCDataGenre=('DataGenreCP', 'DataGenreCP_ENVLOP', 'DataGenreFP', 'DataGenreClampingMask')):
ds = brain.getObject()
md = IBCCVLMetadata(ds)
# md['layers'][ds.file.filename] ... there should be only one key
keys = md['layers'].keys()
if len(keys) != 1:
LOG.warning(
'Found multiple layer keys; do not know what to do: %s', ds.absolute_url())
continue
layermd = md['layers'][keys[0]]
if 'layer' in layermd:
# already converted
continue
if md['genre'] == 'DataGenreClampingMask':
layerid = 'clamping_mask'
else: # DataGenreCP and DataGenreFP
algorithm = ds.__parent__.job_params['function']
if algorithm in ('circles', 'convhull', 'voronoiHull'):
layerid = 'projection_binary'
elif algorithm in ('maxent',):
layerid = 'projection_suitability'
else:
layerid = 'projection_probability'
layermd['layer'] = layerid
md['layers'] = {layerid: layermd}
# restore error_log filter
portal.error_log._ignored_exceptions = ignored_exceptions
LOG.info('Upgrade step finished')
