def get_datastore(project_id=None):
global _datastore
global x_custom_populations_map
#sys.stderr.write("get_datastore(%s) called\n" % project_id)
# xBrowse instances can optionally use a secondary datastore
# whether a secondary datastore should be used is determined by whether settings.SECONDARY_DATASTORE_PROJECTS is set
if hasattr(settings, 'SECONDARY_DATASTORE_PROJECTS'):
if project_id is None:
raise Exception(
"project_id is required if secondary datastore is used, else we don't know which database to use"
)
if project_id in settings.SECONDARY_DATASTORE_PROJECTS:
#sys.stderr.write("get secondary datastore for %s\n" % project_id)
return _get_secondary_datastore()
#else:
#sys.stderr.write("get new 3.0 datastore for %s\n" % project_id)
if _datastore is None:
if x_custom_populations_map is None:
raise Exception('x_custom_populations_map has not been set yet')
#sys.stderr.write("create new 3.0 datastore for %s\n" % project_id)
_datastore = MongoDatastore(
settings.DATASTORE_DB,
get_annotator(),
get_custom_population_store(),
x_custom_populations_map,
)
return _datastore
def get_project_datastore(project_id=None):
global _project_datastore
global x_custom_populations_map
# see note on get_datastore()
if hasattr(settings, 'SECONDARY_DATASTORE_PROJECTS'):
if project_id is None:
raise Exception(
"project_id is required if secondary datastore is used, else we don't know which database to use"
)
if project_id in settings.SECONDARY_DATASTORE_PROJECTS:
#sys.stderr.write("Using secondary project datastore: %s\n" % project_id)
return _get_secondary_project_datastore()
#else:
#sys.stderr.write("Using new project datastore: %s\n" % project_id)
if _project_datastore is None:
if x_custom_populations_map is None:
raise Exception('x_custom_populations_map has not been set yet')
_project_datastore = MongoDatastore(
settings.PROJECT_DATASTORE_DB,
get_annotator(),
get_custom_population_store(),
x_custom_populations_map,
)
return _project_datastore
def _get_secondary_project_datastore():
global _secondary_project_datastore
global x_custom_populations_map
if _secondary_project_datastore is None:
_secondary_project_datastore = MongoDatastore(
settings.SECONDARY_PROJECT_DATASTORE_DB,
get_annotator(),
get_custom_population_store(),
x_custom_populations_map,
)
return _secondary_project_datastore
def get_mongo_project_datastore():
global _project_mongo_datastore
if _project_mongo_datastore is None:
if x_custom_populations_map is None:
raise Exception('x_custom_populations_map has not been set yet')
_project_mongo_datastore = MongoDatastore(
settings.PROJECT_DATASTORE_DB,
get_annotator(),
get_custom_population_store(),
x_custom_populations_map,
)
return _project_mongo_datastore
def get_datastore(project=None):
global _mongo_datastore
global _elasticsearch_datastore
global x_custom_populations_map
if project.get_elasticsearch_index() is None:
if _mongo_datastore is None:
if x_custom_populations_map is None:
raise Exception(
'x_custom_populations_map has not been set yet')
_mongo_datastore = MongoDatastore(
settings.DATASTORE_DB,
get_annotator(),
get_custom_population_store(),
x_custom_populations_map,
)
return _mongo_datastore
else:
if _elasticsearch_datastore is None:
_elasticsearch_datastore = ElasticsearchDatastore(get_annotator())
return _elasticsearch_datastore
django.setup()
import pymongo
from xbrowse.reference import Reference
from xbrowse.annotation import VariantAnnotator
from xbrowse.coverage import CoverageDatastore
from xbrowse.datastore import MongoDatastore
import reference_settings
import annotator_settings
from xbrowse_server.base.models import Project, Family, Individual
reference_db = pymongo.MongoClient('xbrowse_reference')
reference = Reference(reference_settings)
annotator_db = pymongo.MongoClient('xbrowse_annotator')
annotator = VariantAnnotator(annotator_settings, reference)
annotator._ensure_indices()
datastore_db = pymongo.MongoClient('xbrowse_datastore')
datastore = MongoDatastore(datastore_db, annotator)
user_ns = {
'annotator': annotator,
'datastore': datastore,
'Project': Project,
'Family': Family,
'Individual': Individual,
}
import IPython
IPython.embed(user_ns=user_ns)
population_frequency_store_settings)
vep_settings = imp.load_source('vep_settings',
SETTINGS_DIR + 'vep_settings.py')
VEP_ANNOTATOR = HackedVEPAnnotator(vep_settings)
annotator_settings = imp.load_source('annotator_settings',
SETTINGS_DIR + 'annotator_settings.py')
ANNOTATOR = VariantAnnotator(
settings_module=annotator_settings,
reference=REFERENCE,
population_frequency_store=POPULATION_FREQUENCY_STORE,
vep_annotator=VEP_ANNOTATOR,
)
_conn = pymongo.Connection()
datastore_db = _conn['xbrowse_datastore']
population_datastore_db = _conn['xbrowse_pop_datastore']
DATASTORE = MongoDatastore(datastore_db, ANNOTATOR)
POPULATION_DATASTORE = PopulationDatastore(population_datastore_db, ANNOTATOR)
coverage_db = _conn['xbrowse_coverage']
COVERAGE_STORE = CoverageDatastore(coverage_db, REFERENCE)
project_datastore_db = _conn['xbrowse_proj_store']
PROJECT_DATASTORE = ProjectDatastore(project_datastore_db, ANNOTATOR)
cnv_store_settings = imp.load_source('cnv_store_settings',
SETTINGS_DIR + 'cnv_store_settings.py')
CNV_STORE = CNVStore(cnv_store_settings, REFERENCE)