def test_get_client_wrong_uri():
## GIVEN a mongomock MongoClient
## WHEN checking if the connection works
## THEN assert that the connection is valid since it is a mock
with pytest.raises(InvalidURI):
get_client(uri="wierd uri")
def database_group(context, username, password, host, port, uri, database):
db_config = {}
db_config['host'] = host or context.obj.get('host') or 'localhost'
db_config['port'] = port or context.obj.get('port') or 27017
db_config['uri'] = uri or context.obj.get('uri')
db_config['username'] = username or context.obj.get('username')
db_config['password'] = password or context.obj.get('password')
if uri:
LOG.info("Establishing connection with uri {}".format(
db_config['uri']))
else:
LOG.info("Establishing connection with host {}, on port {}".format(
db_config['host'], db_config['port']))
mutacc_client = mongo_adapter.get_client(**db_config)
if not mongo_adapter.check_connection(mutacc_client):
LOG.warning("Connection could not be established")
context.abort()
context.obj['client'] = mutacc_client
context.obj['adapter'] = MutaccAdapter(client=mutacc_client,
db_name=context.obj['db_name'])
def database(uri: str = None, db_name: str = None) -> MongoAdapter:
uri = uri or settings.uri
db_name = db_name or settings.db_name
try:
client = get_client(uri=uri, )
except DB_Error:
raise HTTPException(status_code=status.HTTP_503_SERVICE_UNAVAILABLE,
detail="Could not connect to database")
return MongoAdapter(client, db_name=db_name)
def cli(ctx, database, username, password, authdb, port, host, uri, verbose,
config, test, genome_build):
"""loqusdb: manage a local variant count database."""
loglevel = "INFO"
if verbose:
loglevel = "DEBUG"
coloredlogs.install(level=loglevel)
LOG.info("Running loqusdb version %s", __version__)
configs = {}
if config:
try:
configs = yaml.safe_load(config)
except yaml.YAMLError as err:
LOG.warning(err)
ctx.abort()
uri = configs.get("uri") or uri
if test:
uri = "mongomock://"
try:
client = get_client(
host=configs.get("host") or host,
port=configs.get("port") or port,
username=configs.get("username") or username,
password=configs.get("password") or password,
authdb=authdb or database or "loqusdb",
uri=uri,
)
except DB_Error as err:
LOG.warning(err)
ctx.abort()
database = configs.get("db_name") or database
if not database:
database = "loqusdb"
if uri:
uri_info = uri_parser.parse_uri(uri)
database = uri_info.get("database")
adapter = MongoAdapter(client, db_name=database)
genome_build = genome_build or configs.get("genome_build") or GRCH37
ctx.obj = {}
ctx.obj["db"] = database
if uri:
ctx.obj["uri"] = uri
else:
ctx.obj["port"] = port
ctx.obj["host"] = host
ctx.obj["adapter"] = adapter
ctx.obj["version"] = __version__
ctx.obj["genome_build"] = genome_build
def cli(ctx, database, username, password, authdb, port, host, uri, verbose,
config, test, genome_build):
"""loqusdb: manage a local variant count database."""
loglevel = "INFO"
if verbose:
loglevel = "DEBUG"
coloredlogs.install(level=loglevel)
LOG.info("Running loqusdb version %s", __version__)
configs = {}
if config:
try:
configs = yaml.safe_load(config)
except yaml.YAMLError as err:
LOG.warning(err)
ctx.abort()
uri = configs.get('uri') or uri
if test:
uri = "mongomock://"
try:
client = get_client(
host=configs.get('host') or host,
port=configs.get('port') or port,
username=configs.get('username') or username,
password=configs.get('password') or password,
authdb=authdb or database or 'loqusdb',
uri=uri,
)
except DB_Error as err:
LOG.warning(err)
ctx.abort()
database = configs.get('db_name') or database
if not database:
database = 'loqusdb'
if uri:
uri_info = uri_parser.parse_uri(uri)
database = uri_info.get('database')
adapter = MongoAdapter(client, db_name=database)
genome_build = genome_build or configs.get('genome_build') or GRCH37
ctx.obj = {}
ctx.obj['db'] = database
ctx.obj['user'] = username
ctx.obj['password'] = password
ctx.obj['port'] = port
ctx.obj['host'] = host
ctx.obj['adapter'] = adapter
ctx.obj['version'] = __version__
ctx.obj['genome_build'] = genome_build
def test_get_connection():
## GIVEN a mongomock URI
uri = "mongomock://"
## WHEN getting a client
mock_client = get_client(uri=uri)
## THEN assert that the client is a mock client
assert isinstance(mock_client, mongomock.MongoClient)
## THEN assert that the connection is valid since it is a mock
assert check_connection(mock_client)
# -*- coding: utf-8 -*-
import os
import logging
from flask import Flask
from mongo_adapter import (get_client, check_connection)
from paneldb.adapter.mongo import PanelAdapter
logging.basicConfig(level=logging.INFO)
LOG = logging.getLogger(__name__)
#configuration files are relative to the instance folder
app = Flask(__name__,
template_folder='server/templates',
instance_relative_config=True)
app.config.from_pyfile('paneldb_config.cfg')
client = get_client(mongodb=app.config['MONGODB_DATABASE_NAME'], timeout=20)
app.adapter = PanelAdapter(client=client,
db_name=app.config['MONGODB_DATABASE_NAME'])
import paneldb.server.views