class Core(object):
def __init__(self, host=None, user=None, passwd=None, group=None,
keep_tokens=1, study_label=None, logger=None):
self.kb = KB(driver='omero')(host, user, passwd, group, keep_tokens)
self.logger = logger if logger else logging.getLogger()
self.record_counter = 0
self.default_study = None
if study_label:
s = self.kb.get_study(study_label)
if not s:
raise ValueError('No known study with label %s' % study_label)
self.logger.info('Selecting %s[%d,%s] as default study' %
(s.label, s.omero_id, s.id))
self.default_study = s
@classmethod
def find_action_setup_conf(klass, args):
action_setup_conf = {}
for x in dir(args):
if not (x.startswith('_') or x.startswith('func')):
action_setup_conf[x] = getattr(args, x)
# HACKS
action_setup_conf['ifile'] = action_setup_conf['ifile'].name
action_setup_conf['ofile'] = action_setup_conf['ofile'].name
action_setup_conf['report_file'] = action_setup_conf['report_file'].name
return action_setup_conf
@classmethod
def get_action_setup_options(klass, record, action_setup_conf = None,
object_history = None):
options = {}
if 'options' in record and record['options']:
kvs = record['options'].split(',')
for kv in kvs:
k, v = kv.split('=')
options[k] = v
if action_setup_conf:
options['importer_setup'] = action_setup_conf
if object_history:
options['object_history'] = object_history
return json.dumps(options)
def get_device(self, label, maker, model, release):
device = self.kb.get_device(label)
if not device:
self.logger.debug('creating a device')
device = self.kb.create_device(label, maker, model, release)
return device
def get_action_setup(self, label, conf):
"""
Return the ActionSetup corresponding to label if there is one,
else create a new one using conf.
"""
asetup = self.kb.get_action_setup(label)
if not asetup:
kb_conf = {
'label': label,
'conf': json.dumps(conf),
}
asetup = self.kb.factory.create(self.kb.ActionSetup, kb_conf).save()
return asetup
def get_study(self, label):
if self.default_study:
return self.default_study
study = self.kb.get_study(label)
if not study:
study = self.kb.factory.create(self.kb.Study, {'label': label}).save()
return study
def find_study(self, records):
study_label = records[0]['study']
for r in records:
if r['study'] != study_label:
m = 'all records should have the same study label'
self.logger.critical(m)
raise ValueError(m)
return self.get_study(study_label)
def find_klass(self, col_name, records):
o_type = records[0][col_name]
for r in records:
if r[col_name] != o_type:
m = 'all records should have the same %s' % col_name
self.logger.critical(m)
raise ValueError(m)
return getattr(self.kb, o_type)
def __preload_items__(self, key_field, klass, preloaded):
objs = self.kb.get_objects(klass)
for o in objs:
assert not getattr(o, key_field) in preloaded
preloaded[getattr(o, key_field)] = o
def preload_by_type(self, name, klass, preloaded):
self.logger.info('start preloading %s' % name)
self.__preload_items__('id', klass, preloaded)
self.logger.info('done preloading %s' % name)
def preload_studies(self, preloaded):
self.logger.info('start preloading studies')
self.__preload_items__('label', self.kb.Study, preloaded)
self.logger.info('done preloading studies')
def missing_fields(self, fields, r):
for f in fields:
if f not in r:
return f
return False
class Core(object):
def __init__(self,
host=None,
user=None,
passwd=None,
group=None,
keep_tokens=1,
study_label=None,
logger=None):
self.kb = KB(driver='omero')(host, user, passwd, group, keep_tokens)
self.logger = logger if logger else logging.getLogger()
self.record_counter = 0
self.default_study = None
if study_label:
s = self.kb.get_study(study_label)
if not s:
raise ValueError('No known study with label %s' % study_label)
self.logger.info('Selecting %s[%d,%s] as default study' %
(s.label, s.omero_id, s.id))
self.default_study = s
@classmethod
def find_action_setup_conf(klass, args):
action_setup_conf = {}
for x in dir(args):
if not (x.startswith('_') or x.startswith('func')):
action_setup_conf[x] = getattr(args, x)
# HACKS
action_setup_conf['ifile'] = action_setup_conf['ifile'].name
action_setup_conf['ofile'] = action_setup_conf['ofile'].name
action_setup_conf['report_file'] = action_setup_conf[
'report_file'].name
return action_setup_conf
@classmethod
def get_action_setup_options(klass,
record,
action_setup_conf=None,
object_history=None):
options = {}
if 'options' in record and record['options']:
kvs = record['options'].split(',')
for kv in kvs:
k, v = kv.split('=')
options[k] = v
if action_setup_conf:
options['importer_setup'] = action_setup_conf
if object_history:
options['object_history'] = object_history
return json.dumps(options)
def get_device(self, label, maker, model, release):
device = self.kb.get_device(label)
if not device:
self.logger.debug('creating a device')
device = self.kb.create_device(label, maker, model, release)
return device
def get_action_setup(self, label, conf):
"""
Return the ActionSetup corresponding to label if there is one,
else create a new one using conf.
"""
asetup = self.kb.get_action_setup(label)
if not asetup:
kb_conf = {
'label': label,
'conf': json.dumps(conf),
}
asetup = self.kb.factory.create(self.kb.ActionSetup,
kb_conf).save()
return asetup
def get_study(self, label):
if self.default_study:
return self.default_study
study = self.kb.get_study(label)
if not study:
study = self.kb.factory.create(self.kb.Study, {
'label': label
}).save()
return study
def find_study(self, records):
study_label = records[0]['study']
for r in records:
if r['study'] != study_label:
m = 'all records should have the same study label'
self.logger.critical(m)
raise ValueError(m)
return self.get_study(study_label)
def find_klass(self, col_name, records):
o_type = records[0][col_name]
for r in records:
if r[col_name] != o_type:
m = 'all records should have the same %s' % col_name
self.logger.critical(m)
raise ValueError(m)
return getattr(self.kb, o_type)
def __preload_items__(self, key_field, klass, preloaded):
objs = self.kb.get_objects(klass)
for o in objs:
assert not getattr(o, key_field) in preloaded
preloaded[getattr(o, key_field)] = o
def preload_by_type(self, name, klass, preloaded):
self.logger.info('start preloading %s' % name)
self.__preload_items__('id', klass, preloaded)
self.logger.info('done preloading %s' % name)
def preload_studies(self, preloaded):
self.logger.info('start preloading studies')
self.__preload_items__('label', self.kb.Study, preloaded)
self.logger.info('done preloading studies')
def missing_fields(self, fields, r):
for f in fields:
if f not in r:
return f
return False
