def ready(self):
from varapp.common import manage_dbs, utils, db_utils
from varapp.common.versioning import add_versions
from varapp.stats.stats_service import stats_service
from varapp.variants.genotypes_service import genotypes_service
# Check that there are tables in the users_db,
# because this code is also run when manage.py is used,
# for instance to generate the tables.
# It needs more that 1 table, which could be only django_migrations.
user_db_ready = db_utils.connection_has_tables('default', 5)
# Manage.py must work without the following to execute.
#print(user_db_ready)
#print(''.join(sys.argv))
if user_db_ready and "migrate" not in sys.argv:
# At startup, fill settings.DATABASES with what is in VariantsDb.
# Do not add any new db here, as unlike deactivation, inserts
# are not idempotent and this code could be executed several times.
# Return the valid databases added to connections,
# since they need to be in there to be read for vcf_header, stats etc.
added_connections = manage_dbs.copy_VariantsDb_to_settings()
# Check that the Redis service is running.
# It is necessary for stats and genotypes cache.
redis_ready = utils.check_redis_connection()
if redis_ready:
# Fill the stats cache
if settings.WARMUP_STATS_CACHE:
for dbname in added_connections:
stats_service(dbname)
# Fill the genotypes cache
if settings.WARMUP_GENOTYPES_CACHE:
for dbname in added_connections:
genotypes_service(dbname)
# Update the *annotation* table with versions of all programs used,
# i.e. Gemini, VEP, their dbs, etc.
for dbname in added_connections:
add_versions(dbname)
else:
logger.warning(
"(!) Could not connect to Redis. Make sure Redis is installed, "
"is up and running (try `redis-cli ping`) "
"and serves at 127.0.0.1:6379 (or whatever is defined in settings)."
)
return 2
return 0
else:
logger.warning("(!) Users db is not ready or it is migration.")
return 1
def __init__(self, request, db):
"""Extract filters etc. information from http request."""
self.db = db
self.sort = sort_from_request(request)
self.pg = pagination_from_request(request)
self.ss = samples_selection_from_request(request, db)
self.fc = variant_filters_from_request(request, db, self.ss)
self.stats = stats_service(db)
def __init__(self, request, db):
"""Extract filters etc. information from http request."""
self.db = db
self.sort = sort_from_request(request)
self.pg = pagination_from_request(request)
self.ss = samples_selection_from_request(request, db)
self.fc = variant_filters_from_request(request, db, self.ss)
self.stats = stats_service(db)
def stats(request, db, user=None):
"""Return a JSON with stats over the whole db (to query only once at startup)."""
stat = stats_service(db).get_global_stats()
return JsonResponse(stat.expose(), safe=False)
def stats(request, db, user=None):
"""Return a JSON with stats over the whole db (to query only once at startup)."""
stat = stats_service(db).get_global_stats()
return JsonResponse(stat.expose(), safe=False)
def ready(self):
from varapp.common import manage_dbs, utils, db_utils
from varapp.common.versioning import add_versions
from varapp.stats.stats_service import stats_service
from varapp.variants.genotypes_service import genotypes_service
# Check that there are tables in the users_db,
# because this code is also run when manage.py is used,
# for instance to generate the tables.
# It needs more that 1 table, which could be only django_migrations.
mysql_connection_attempts = 0
connected_to_mysql = False
user_db_ready = False
error = None
while mysql_connection_attempts < 50 and not connected_to_mysql:
try:
mysql_connection_attempts += 1
user_db_ready = db_utils.connection_has_tables('default', 5)
connected_to_mysql = True
logger.info("Connected to MySQL")
except django.db.utils.OperationalError as err:
error = str(err)
if mysql_connection_attempts == 1:
logger.error(error)
logger.warning(
"(!) Could not connect to users db. Retrying in 1 second... ({})"
.format(mysql_connection_attempts))
time.sleep(0.5)
if not connected_to_mysql:
raise ConnectionError(
"Could not connect to users db. Check your MySQL connection and settings. Error message: {}"
.format(error))
# Manage.py must work without the following to execute.
if user_db_ready and "migrat" not in ''.join(sys.argv):
# At startup, fill settings.DATABASES with what is in VariantsDb.
# Do not add any new db here, as unlike deactivation, inserts
# are not idempotent and this code could be executed several times.
# Return the valid databases added to connections,
# since they need to be in there to be read for vcf_header, stats etc.
added_connections = manage_dbs.copy_VariantsDb_to_settings()
# Check that the Redis service is running.
# It is necessary for stats and genotypes cache.
redis_ready = utils.check_redis_connection()
if redis_ready:
# Fill the stats cache
if settings.WARMUP_STATS_CACHE:
for dbname in added_connections:
stats_service(dbname)
# Fill the genotypes cache
if settings.WARMUP_GENOTYPES_CACHE:
for dbname in added_connections:
genotypes_service(dbname)
# Update the *annotation* table with versions of all programs used,
# i.e. Gemini, VEP, their dbs, etc.
for dbname in added_connections:
add_versions(dbname)
else:
logger.warning(
"(!) Could not connect to Redis. Make sure Redis is installed, "
"is up and running (try `redis-cli ping`) "
"and serves at '{}').".format(
settings.CACHES['redis']['LOCATION']))
return 2
return 0
else:
logger.warning("(!) Users db has no tables.")
return 1
def test_stats_service(self):
"""stats_service(db) creates a GlobalStatsService"""
sts = stats_service(db='test')
self.assertIsInstance(sts, GlobalStatsService)
def test_stats_service(self):
"""stats_service(db) creates a GlobalStatsService"""
sts = stats_service(db='test')
self.assertIsInstance(sts, GlobalStatsService)
def ready(self):
from varapp.common import manage_dbs, utils, db_utils
from varapp.common.versioning import add_versions
from varapp.stats.stats_service import stats_service
from varapp.variants.genotypes_service import genotypes_service
# Check that there are tables in the users_db,
# because this code is also run when manage.py is used,
# for instance to generate the tables.
# It needs more that 1 table, which could be only django_migrations.
mysql_connection_attempts = 0
connected_to_mysql = False
user_db_ready = False
error = None
while mysql_connection_attempts < 50 and not connected_to_mysql:
try:
mysql_connection_attempts += 1
user_db_ready = db_utils.connection_has_tables('default', 5)
connected_to_mysql = True
logger.info("Connected to MySQL")
except django.db.utils.OperationalError as err:
error = str(err)
if mysql_connection_attempts == 1:
logger.error(error)
logger.warning("(!) Could not connect to users db. Retrying in 1 second... ({})".format(mysql_connection_attempts))
time.sleep(0.5)
if not connected_to_mysql:
raise ConnectionError("Could not connect to users db. Check your MySQL connection and settings. Error message: {}".format(error))
# Manage.py must work without the following to execute.
if user_db_ready and "migrat" not in ''.join(sys.argv):
# At startup, fill settings.DATABASES with what is in VariantsDb.
# Do not add any new db here, as unlike deactivation, inserts
# are not idempotent and this code could be executed several times.
# Return the valid databases added to connections,
# since they need to be in there to be read for vcf_header, stats etc.
added_connections = manage_dbs.copy_VariantsDb_to_settings()
# Check that the Redis service is running.
# It is necessary for stats and genotypes cache.
redis_ready = utils.check_redis_connection()
if redis_ready:
# Fill the stats cache
if settings.WARMUP_STATS_CACHE:
for dbname in added_connections:
stats_service(dbname)
# Fill the genotypes cache
if settings.WARMUP_GENOTYPES_CACHE:
for dbname in added_connections:
genotypes_service(dbname)
# Update the *annotation* table with versions of all programs used,
# i.e. Gemini, VEP, their dbs, etc.
for dbname in added_connections:
add_versions(dbname)
else:
logger.warning("(!) Could not connect to Redis. Make sure Redis is installed, "
"is up and running (try `redis-cli ping`) "
"and serves at '{}').".format(settings.CACHES['redis']['LOCATION']))
return 2
return 0
else:
logger.warning("(!) Users db has no tables.")
return 1