def __init__(self):
self.name = None
self._indices = []
self._textIndex = None
self.initialize()
assert type(self.name) == str
db_cfg = getDbConfig()
db_connection = getDbConnection()
if cherrypy.config['server']['mode'] == 'testing':
dbName = '%s_test' % db_cfg['database']
else:
dbName = db_cfg['database'] # pragma: no cover
self.database = db_connection[dbName]
self.collection = self.database[self.name]
assert isinstance(self.collection, pymongo.collection.Collection)
assert type(self._indices) == list
for index in self._indices:
self.collection.ensure_index(index)
if type(self._textIndex) is dict:
textIdx = [(k, 'text') for k in self._textIndex.keys()]
self.collection.ensure_index(
textIdx, weights=self._textIndex,
default_language=self._textLanguage)
def __init__(self):
self.name = None
self._indices = []
self._textIndex = None
self._textLanguage = None
self._filterKeys = {
AccessType.READ: set(),
AccessType.WRITE: set(),
AccessType.ADMIN: set(),
AccessType.SITE_ADMIN: set()
}
self.initialize()
db_connection = getDbConnection()
self.database = db_connection.get_default_database()
self.collection = MongoProxy(self.database[self.name])
for index in self._indices:
if isinstance(index, (list, tuple)):
self.collection.ensure_index(index[0], **index[1])
else:
self.collection.ensure_index(index)
if type(self._textIndex) is dict:
textIdx = [(k, 'text') for k in self._textIndex.keys()]
try:
self.collection.ensure_index(
textIdx,
weights=self._textIndex,
default_language=self._textLanguage)
except pymongo.errors.OperationFailure:
print(
TerminalColor.warning('WARNING: Text search not enabled.'))
def __init__(self, assetstore):
"""
:param assetstore: The assetstore to act on.
"""
self.assetstore = assetstore
try:
self.chunkColl = getDbConnection(
assetstore.get('mongohost', None),
assetstore.get('replicaset', None))[assetstore['db']]['chunk']
except pymongo.errors.ConnectionFailure:
logger.error('Failed to connect to GridFS assetstore %s',
assetstore['db'])
self.chunkColl = 'Failed to connect'
self.unavailable = True
return
except pymongo.errors.ConfigurationError:
logger.exception('Failed to configure GridFS assetstore %s',
assetstore['db'])
self.chunkColl = 'Failed to configure'
self.unavailable = True
return
self.chunkColl.ensure_index([
('uuid', pymongo.ASCENDING),
('n', pymongo.ASCENDING)
], unique=True)
def __init__(self):
self.name = None
self._indices = []
self._textIndex = None
self._textLanguage = None
self.initialize()
db_cfg = getDbConfig()
db_connection = getDbConnection()
dbName = db_cfg['database']
self.database = db_connection[dbName]
self.collection = self.database[self.name]
for index in self._indices:
if isinstance(index, (list, tuple)):
self.collection.ensure_index(index[0], **index[1])
else:
self.collection.ensure_index(index)
if type(self._textIndex) is dict:
textIdx = [(k, 'text') for k in self._textIndex.keys()]
try:
self.collection.ensure_index(
textIdx,
weights=self._textIndex,
default_language=self._textLanguage)
except pymongo.errors.OperationFailure:
print(
TerminalColor.warning('WARNING: Text search not enabled.'))
def dropGridFSDatabase(dbName):
"""
Clear all contents from a gridFS database used as an assetstore.
:param dbName: the name of the database to drop.
"""
db_connection = getDbConnection()
db_connection.drop_database(dbName)
def runImageSimilaritySearch(self, params):
assert hasattr(self, 'search_url')
classifications = json.loads(params['classifications']) if 'classifications' in params else []
params['n'] = params['n'] if 'n' in params else str(DEFAULT_PAGE_SIZE)
smqtk_r = requests.get(self.search_url + '/n=' + params['n'] + '/' + params['url']).json()
neighbors_to_distances = dict(zip(smqtk_r['neighbors'], smqtk_r['distances']))
db = getDbConnection().get_default_database()
mapped_paths = db[os.environ['IMAGE_SPACE_SMQTK_MAP_COLLECTION']].find({
'sha': {
'$in': smqtk_r['neighbors']
}
})
solr_id_to_shas = {os.environ['IMAGE_SPACE_SOLR_PREFIX'] + '/' + x['path']: x['sha'] for x in mapped_paths}
documents = solr_documents_from_paths(solr_id_to_shas.keys(), classifications)
for document in documents:
document['im_distance'] = neighbors_to_distances[solr_id_to_shas[document['id']]]
if 'near_duplicates' in params and int(params['near_duplicates']) == 1:
documents = [x for x in documents if x['im_distance'] <= NEAR_DUPLICATES_THRESHOLD]
return {
'numFound': len(documents),
'docs': documents
}
def validateInfo(doc):
"""
Validate the assetstore -- make sure we can connect to it and that the
necessary indexes are set up.
"""
if not doc.get('db', ''):
raise ValidationException('Database name must not be empty.', 'db')
if '.' in doc['db'] or ' ' in doc['db']:
raise ValidationException('Database name cannot contain spaces'
' or periods.', 'db')
chunkColl = getDbConnection(
doc.get('mongohost', None), doc.get('replicaset', None),
autoRetry=False, serverSelectionTimeoutMS=10000)[doc['db']].chunk
try:
chunkColl.create_index([
('uuid', pymongo.ASCENDING),
('n', pymongo.ASCENDING)
], unique=True)
except pymongo.errors.ServerSelectionTimeoutError as e:
raise ValidationException(
'Could not connect to the database: %s' % str(e))
return doc
def __init__(self, assetstore):
"""
:param assetstore: The assetstore to act on.
"""
self.assetstore = assetstore
try:
self.chunkColl = getDbConnection(
assetstore.get('mongohost', None),
assetstore.get('replicaset', None))[assetstore['db']]['chunk']
except pymongo.errors.ConnectionFailure:
logger.error('Failed to connect to GridFS assetstore %s',
assetstore['db'])
self.chunkColl = 'Failed to connect'
self.unavailable = True
return
except pymongo.errors.ConfigurationError:
logger.exception('Failed to configure GridFS assetstore %s',
assetstore['db'])
self.chunkColl = 'Failed to configure'
self.unavailable = True
return
self.chunkColl.ensure_index([
('uuid', pymongo.ASCENDING),
('n', pymongo.ASCENDING)
], unique=True)
def validateInfo(doc):
"""
Validate the assetstore -- make sure we can connect to it and that the
necessary indexes are set up.
"""
if not doc.get('db', ''):
raise ValidationException('Database name must not be empty.', 'db')
if '.' in doc['db'] or ' ' in doc['db']:
raise ValidationException(
'Database name cannot contain spaces'
' or periods.', 'db')
try:
chunkColl = getDbConnection(
doc.get('mongohost', None),
doc.get('replicaset', None),
autoRetry=False,
serverSelectionTimeoutMS=10000)[doc['db']].chunk
chunkColl.create_index([('uuid', pymongo.ASCENDING),
('n', pymongo.ASCENDING)],
unique=True)
except pymongo.errors.ServerSelectionTimeoutError as e:
raise ValidationException('Could not connect to the database: %s' %
str(e))
return doc
def reconnect(self):
"""
Reconnect to the database and rebuild indices if necessary. Users should
typically not have to call this method.
"""
db_connection = getDbConnection()
self.database = db_connection.get_default_database()
self.collection = MongoProxy(self.database[self.name])
for index in self._indices:
if isinstance(index, (list, tuple)):
self.collection.ensure_index(index[0], **index[1])
else:
self.collection.ensure_index(index)
if type(self._textIndex) is dict:
textIdx = [(k, 'text') for k in self._textIndex.keys()]
try:
self.collection.ensure_index(
textIdx,
weights=self._textIndex,
default_language=self._textLanguage)
except pymongo.errors.OperationFailure:
print(
TerminalColor.warning('WARNING: Text search not enabled.'))
def __init__(self):
self.name = None
self._indices = []
self._textIndex = None
self._textLanguage = None
self.initialize()
db_cfg = getDbConfig()
db_connection = getDbConnection()
dbName = db_cfg['database']
self.database = db_connection[dbName]
self.collection = self.database[self.name]
for index in self._indices:
if isinstance(index, (list, tuple)):
self.collection.ensure_index(index[0], **index[1])
else:
self.collection.ensure_index(index)
if type(self._textIndex) is dict:
textIdx = [(k, 'text') for k in self._textIndex.keys()]
try:
self.collection.ensure_index(
textIdx, weights=self._textIndex,
default_language=self._textLanguage)
except pymongo.errors.OperationFailure:
print(
TerminalColor.warning('WARNING: Text search not enabled.'))
def __init__(self):
self.name = None
self._indices = []
self._textIndex = None
self._textLanguage = None
self._filterKeys = {
AccessType.READ: set(),
AccessType.WRITE: set(),
AccessType.ADMIN: set(),
AccessType.SITE_ADMIN: set()
}
self.initialize()
db_connection = getDbConnection()
self.database = db_connection.get_default_database()
self.collection = MongoProxy(self.database[self.name])
for index in self._indices:
if isinstance(index, (list, tuple)):
self.collection.ensure_index(index[0], **index[1])
else:
self.collection.ensure_index(index)
if type(self._textIndex) is dict:
textIdx = [(k, 'text') for k in self._textIndex.keys()]
try:
self.collection.ensure_index(
textIdx, weights=self._textIndex,
default_language=self._textLanguage)
except pymongo.errors.OperationFailure:
print(
TerminalColor.warning('WARNING: Text search not enabled.'))
def testGridFsAssetstore(self):
"""
Test usage of the GridFS assetstore type.
"""
# Clear the assetstore database
conn = getDbConnection()
conn.drop_database('girder_assetstore_test')
self.model('assetstore').remove(self.model('assetstore').getCurrent())
assetstore = self.model('assetstore').createGridFsAssetstore(
name='Test', db='girder_assetstore_test')
self.assetstore = assetstore
chunkColl = conn['girder_assetstore_test']['chunk']
# Upload the two-chunk file
file = self._testUploadFile('helloWorld1.txt')
hash = sha512(chunk1 + chunk2).hexdigest()
self.assertEqual(hash, file['sha512'])
# We should have two chunks in the database
self.assertEqual(chunkColl.find({'uuid': file['chunkUuid']}).count(), 2)
self._testDownloadFile(file, chunk1 + chunk2)
self._testDownloadFolder()
# Delete the file, make sure chunks are gone from database
self._testDeleteFile(file)
self.assertEqual(chunkColl.find({'uuid': file['chunkUuid']}).count(), 0)
empty = self._testEmptyUpload('empty.txt')
self.assertEqual(sha512().hexdigest(), empty['sha512'])
self._testDownloadFile(empty, '')
self._testDeleteFile(empty)
def dropGridFSDatabase(dbName):
"""
Clear all contents from a gridFS database used as an assetstore.
:param dbName: the name of the database to drop.
"""
db_connection = getDbConnection()
db_connection.drop_database(dbName)
def db(request):
"""
Require a Mongo test database.
Provides a Mongo test database named after the requesting test function. Mongo databases are
created/destroyed based on the URI provided with the --mongo-uri option and tear-down
behavior is modified by the --keep-db option.
"""
from girder.models import _dbClients, getDbConnection, pymongo
from girder.models import model_base
from girder.models.user import User
from girder.external import mongodb_proxy
mockDb = request.config.getoption('--mock-db')
dbUri = request.config.getoption('--mongo-uri')
dbName = 'girder_test_%s' % hashlib.md5(_uid(
request.node).encode('utf8')).hexdigest()
keepDb = request.config.getoption('--keep-db')
executable_methods = mongodb_proxy.EXECUTABLE_MONGO_METHODS
realMongoClient = pymongo.MongoClient
if mockDb:
mongodb_proxy.EXECUTABLE_MONGO_METHODS = set()
pymongo.MongoClient = mongomock.MongoClient
connection = getDbConnection(uri='%s/%s' % (dbUri, dbName), quiet=False)
# Force getDbConnection from models to return our connection
_dbClients[(None, None)] = connection
connection.drop_database(dbName)
# Since models store a local reference to the current database, we need to force them all to
# reconnect
for model in model_base._modelSingletons:
model.reconnect()
# Use faster password hashing to avoid unnecessary testing bottlenecks. Any test case
# that creates a user goes through the password hashing process, so we avoid actual bcrypt.
originalCryptContext = User()._cryptContext
User()._cryptContext = originalCryptContext.copy(schemes=['plaintext'])
yield connection
User()._cryptContext = originalCryptContext
if not keepDb:
connection.drop_database(dbName)
connection.close()
# Clear connection cache and model singletons
_dbClients.clear()
for model in model_base._modelSingletons:
model.__class__._instance = None
if mockDb:
mongodb_proxy.EXECUTABLE_MONGO_METHODS = executable_methods
pymongo.MongoClient = realMongoClient
def dropTestDatabase():
"""
Call this to clear all contents from the test database.
"""
from girder.models import getDbConnection
db_connection = getDbConnection()
db_connection.drop_database('%s_test' %
cherrypy.config['database']['database'])
def testGridFsAssetstore(self):
"""
Test usage of the GridFS assetstore type.
"""
# Must also lower GridFS's internal chunk size to support our small chunks
gridfs_assetstore_adapter.CHUNK_SIZE, old = 6, gridfs_assetstore_adapter.CHUNK_SIZE
# Clear any old DB data
base.dropGridFSDatabase('girder_test_file_assetstore')
# Clear the assetstore database
conn = getDbConnection()
conn.drop_database('girder_test_file_assetstore')
Assetstore().remove(Assetstore().getCurrent())
assetstore = Assetstore().createGridFsAssetstore(
name='Test', db='girder_test_file_assetstore')
self.assetstore = assetstore
chunkColl = conn['girder_test_file_assetstore']['chunk']
# Upload the two-chunk file
file = self._testUploadFile('helloWorld1.txt')
hash = sha512(chunkData).hexdigest()
file = File().load(file['_id'], force=True)
self.assertEqual(hash, file['sha512'])
# The file should have no local path
self.assertRaises(FilePathException, File().getLocalFilePath, file)
# We should have two chunks in the database
self.assertEqual(
chunkColl.find({
'uuid': file['chunkUuid']
}).count(), 2)
self._testDownloadFile(file, chunk1 + chunk2)
# Reset chunk size so the large file testing isn't horribly slow
gridfs_assetstore_adapter.CHUNK_SIZE = old
self._testDownloadFolder()
self._testDownloadCollection()
# Delete the file, make sure chunks are gone from database
self._testDeleteFile(file)
self.assertEqual(
chunkColl.find({
'uuid': file['chunkUuid']
}).count(), 0)
empty = self._testEmptyUpload('empty.txt')
self.assertEqual(sha512().hexdigest(), empty['sha512'])
self._testDownloadFile(empty, '')
self._testDeleteFile(empty)
# Test copying a file
copyTestFile = self._testUploadFile('helloWorld1.txt')
self._testCopyFile(copyTestFile)
def _computeSlowStatus(process, status, db):
status["diskPartitions"] = [_objectToDict(part) for part in psutil.disk_partitions()]
try:
# This fails in travis's environment, so guard it
status["diskIO"] = _objectToDict(psutil.disk_io_counters())
except Exception:
pass
# Report on the disk usage where the script is located
if hasattr(girder, "__file__"):
status["girderPath"] = os.path.abspath(girder.__file__)
status["girderDiskUsage"] = _objectToDict(psutil.disk_usage(status["girderPath"]))
# Report where our logs are and how much space is available for them
status["logs"] = []
for handler in logger.handlers:
try:
logInfo = {"path": handler.baseFilename}
logInfo["diskUsage"] = _objectToDict(psutil.disk_usage(logInfo["path"]))
status["logs"].append(logInfo)
except Exception:
# If we can't read information about the log, don't throw an
# exception
pass
status["mongoDbStats"] = db.command("dbStats")
try:
# I don't know if this will work with a sharded database, so guard
# it and don't throw an exception
status["mongoDbPath"] = getDbConnection().admin.command("getCmdLineOpts")["parsed"]["storage"]["dbPath"]
status["mongoDbDiskUsage"] = _objectToDict(psutil.disk_usage(status["mongoDbPath"]))
except Exception:
pass
status["processDirectChildrenCount"] = len(process.children())
status["processAllChildrenCount"] = len(process.children(True))
status["openFiles"] = [_objectToDict(file) for file in process.open_files()]
# I'd rather see textual names for the family and type of connections,
# so make a lookup table for them
connFamily = {getattr(socket, key): key for key in dir(socket) if key.startswith("AF_")}
connType = {getattr(socket, key): key for key in dir(socket) if key.startswith("SOCK_")}
connections = []
for conn in process.connections():
connDict = _objectToDict(conn)
connDict.pop("raddr", None)
connDict.pop("laddr", None)
connDict["family"] = connFamily.get(connDict["family"], connDict["family"])
connDict["type"] = connType.get(connDict["type"], connDict["type"])
connections.append(connDict)
status["connections"] = connections
if hasattr(process, "io_counters"):
status["ioCounters"] = _objectToDict(process.io_counters())
status["cherrypyThreads"] = {}
for threadId in cherrypy.tools.status.seenThreads:
info = cherrypy.tools.status.seenThreads[threadId].copy()
if "end" in info:
info["duration"] = info["end"] - info["start"]
info["idle"] = time.time() - info["end"]
status["cherrypyThreads"][threadId] = info
def dropAllTestDatabases():
"""
Unless otherwise requested, drop all test databases.
"""
if 'keepdb' not in os.environ.get('EXTRADEBUG', '').split():
db_connection = getDbConnection()
for dbName in usedDBs:
db_connection.drop_database(dbName)
usedDBs.clear()
def mongoCollection(self, connectionUri, collectionName):
# TODO not sure if this is a good idea to do this db stuff here
# maybe this suggests a new model?
from girder.models import getDbConnection
dbConn = getDbConnection(connectionUri)
db = dbConn.get_default_database()
from girder.external.mongodb_proxy import MongoProxy
collection = MongoProxy(db[collectionName])
return collection
def dropAllTestDatabases():
"""
Unless otherwise requested, drop all test databases.
"""
if 'keepdb' not in os.environ.get('EXTRADEBUG', '').split():
db_connection = getDbConnection()
for dbName in usedDBs:
db_connection.drop_database(dbName)
usedDBs.clear()
def mongoCollection(self, connectionUri, collectionName):
# TODO not sure if this is a good idea to do this db stuff here
# maybe this suggests a new model?
from girder.models import getDbConnection
dbConn = getDbConnection(connectionUri)
db = dbConn.get_default_database()
from girder.external.mongodb_proxy import MongoProxy
collection = MongoProxy(db[collectionName])
return collection
def __init__(self, assetstore):
"""
:param assetstore: The assetstore to act on.
"""
self.assetstore = assetstore
self.chunkColl = getDbConnection()[assetstore['db']]['chunk']
self.chunkColl.ensure_index([
('uuid', pymongo.ASCENDING),
('n', pymongo.ASCENDING)
], unique=True)
def __init__(self, assetstore):
"""
:param assetstore: The assetstore to act on.
"""
self.assetstore = assetstore
self.chunkColl = getDbConnection()[assetstore['db']]['chunk']
self.chunkColl.ensure_index([
('uuid', pymongo.ASCENDING),
('n', pymongo.ASCENDING)
], unique=True)
def dropTestDatabase():
"""
Call this to clear all contents from the test database. Also forces models
to reload.
"""
from girder.models import getDbConnection
db_connection = getDbConnection()
model_importer._modelInstances = {'core': {}}
db_connection.drop_database('%s_test' %
cherrypy.config['database']['database'])
def dropGridFSDatabase(dbName):
"""
Clear all contents from a gridFS database used as an assetstore.
:param dbName: the name of the database to drop.
"""
db_connection = getDbConnection()
if dbName in db_connection.list_database_names():
if dbName not in usedDBs and 'newdb' in os.environ.get('EXTRADEBUG', '').split():
raise Exception('Warning: database %s already exists' % dbName)
db_connection.drop_database(dbName)
usedDBs[dbName] = True
def dropGridFSDatabase(dbName):
"""
Clear all contents from a gridFS database used as an assetstore.
:param dbName: the name of the database to drop.
"""
db_connection = getDbConnection()
if dbName in db_connection.database_names():
if dbName not in usedDBs and 'newdb' in os.environ.get('EXTRADEBUG', '').split():
raise Exception('Warning: database %s already exists' % dbName)
db_connection.drop_database(dbName)
usedDBs[dbName] = True
def testGridFsAssetstore(self):
"""
Test usage of the GridFS assetstore type.
"""
# Must also lower GridFS's internal chunk size to support our small chunks
gridfs_assetstore_adapter.CHUNK_SIZE, old = 6, gridfs_assetstore_adapter.CHUNK_SIZE
# Clear any old DB data
base.dropGridFSDatabase('girder_test_file_assetstore')
# Clear the assetstore database
conn = getDbConnection()
conn.drop_database('girder_test_file_assetstore')
Assetstore().remove(Assetstore().getCurrent())
assetstore = Assetstore().createGridFsAssetstore(
name='Test', db='girder_test_file_assetstore')
self.assetstore = assetstore
chunkColl = conn['girder_test_file_assetstore']['chunk']
# Upload the two-chunk file
file = self._testUploadFile('helloWorld1.txt')
hash = sha512(chunkData).hexdigest()
file = File().load(file['_id'], force=True)
self.assertEqual(hash, file['sha512'])
# The file should have no local path
self.assertRaises(FilePathException, File().getLocalFilePath, file)
# We should have two chunks in the database
self.assertEqual(chunkColl.find({'uuid': file['chunkUuid']}).count(), 2)
self._testDownloadFile(file, chunk1 + chunk2)
# Reset chunk size so the large file testing isn't horribly slow
gridfs_assetstore_adapter.CHUNK_SIZE = old
self._testDownloadFolder()
self._testDownloadCollection()
# Delete the file, make sure chunks are gone from database
self._testDeleteFile(file)
self.assertEqual(chunkColl.find({'uuid': file['chunkUuid']}).count(), 0)
empty = self._testEmptyUpload('empty.txt')
self.assertEqual(sha512().hexdigest(), empty['sha512'])
self._testDownloadFile(empty, '')
self._testDeleteFile(empty)
# Test copying a file
copyTestFile = self._testUploadFile('helloWorld1.txt')
self._testCopyFile(copyTestFile)
def dropTestDatabase():
"""
Call this to clear all contents from the test database. Also forces models
to reload.
"""
from girder.models import getDbConnection
db_connection = getDbConnection()
model_importer.clearModels() # Must clear the models so indices are rebuit
dbName = cherrypy.config['database']['uri'].split('/')[-1]
if 'girder_test_' not in dbName:
raise Exception(
'Expected a testing database name, but got {}'.format(dbName))
db_connection.drop_database(dbName)
def dropTestDatabase():
"""
Call this to clear all contents from the test database. Also forces models
to reload.
"""
from girder.models import getDbConnection
db_connection = getDbConnection()
model_importer.clearModels() # Must clear the models so indices are rebuilt
dbName = cherrypy.config['database']['database']
if 'girder_test_' not in dbName:
raise Exception('Expected a testing database name, but got {}'
.format(dbName))
db_connection.drop_database(dbName)
def dropTestDatabase(dropModels=True):
"""
Call this to clear all contents from the test database. Also forces models
to reload.
"""
db_connection = getDbConnection()
dbName = cherrypy.config['database']['uri'].split('/')[-1]
if 'girder_test_' not in dbName:
raise Exception('Expected a testing database name, but got %s' % dbName)
db_connection.drop_database(dbName)
if dropModels:
model_importer.reinitializeAll()
def dropTestDatabase(dropModels=True):
"""
Call this to clear all contents from the test database. Also forces models
to reload.
"""
db_connection = getDbConnection()
dbName = cherrypy.config['database']['uri'].split('/')[-1]
if 'girder_test_' not in dbName:
raise Exception('Expected a testing database name, but got %s' % dbName)
db_connection.drop_database(dbName)
if dropModels:
model_importer.reinitializeAll()
def setUp(self):
"""
Set up the mongo db for the external dataset, with 3 collections:
a) tweetsgeo, which has tweet data that is geolocated (lat/long fields).
b) polyGeoIndexed, w/2 polygons in a 2dsphere-indexed 'geometry' field
c) polyGeoIndeces, same as above but without the 2dsphere index
"""
super(MongoDatasetTestCase, self).setUp()
self._user = self.model('user').createUser(
'minervauser', 'password', 'minerva', 'user',
'*****@*****.**')
from girder.utility import config
dbUri = config.getConfig()['database']['uri']
self.dbName = 'minerva_test_external_mongo_dataset'
dbUriParts = dbUri.split('/')[0:-1]
self.dbUri = '/'.join(dbUriParts + [self.dbName])
from girder.models import getDbConnection
self.externalMongoDbConnection = getDbConnection(self.dbUri)
self.externalMongoDb = self.externalMongoDbConnection.get_default_database()
from girder.external.mongodb_proxy import MongoProxy
self.geojsonIndexedName = 'polyGeoIndexed'
self.geojsonNonIndexedName = 'polyGeoNonIndexed'
self.polyIndexedCollection = MongoProxy(self.externalMongoDb[self.geojsonIndexedName])
self.polyNonIndexedCollection = MongoProxy(self.externalMongoDb[self.geojsonNonIndexedName])
self.pluginTestDir = os.path.dirname(os.path.realpath(__file__))
geojsonPath = os.path.join(self.pluginTestDir, 'data', 'polygons.json')
with open(geojsonPath) as geojsonFile:
polys = json.load(geojsonFile)
for poly in polys:
self.polyIndexedCollection.save(poly)
self.polyNonIndexedCollection.save(poly)
self.polyIndexedCollection.create_index([('geometry', '2dsphere')])
self.collectionName = 'tweetsgeo'
self.tweetsgeoCollection = MongoProxy(self.externalMongoDb[self.collectionName])
# add test data to external dataset
self.pluginTestDir = os.path.dirname(os.path.realpath(__file__))
tweets100Path = os.path.join(self.pluginTestDir, 'data', 'tweets100.json')
z = zipfile.ZipFile('%s.zip' % tweets100Path)
tweets = json.load(z.open('tweets100.json'))
from datetime import datetime
dateformat = '%Y-%m-%dT%H:%M:%S'
for tweet in tweets:
d = datetime.strptime((tweet['created_at']), dateformat)
tweet['created_at'] = int((d - datetime(1970, 1, 1)).total_seconds())
self.tweetsgeoCollection.save(tweet)
def atestGridFsAssetstore(self):
"""
Test usage of the GridFS assetstore type.
"""
# Clear any old DB data
base.dropGridFSDatabase('girder_test_file_assetstore')
# Clear the assetstore database
conn = getDbConnection()
conn.drop_database('girder_test_file_assetstore')
self.model('assetstore').remove(self.model('assetstore').getCurrent())
assetstore = self.model('assetstore').createGridFsAssetstore(
name='Test', db='girder_test_file_assetstore')
self.assetstore = assetstore
chunkColl = conn['girder_test_file_assetstore']['chunk']
# Upload the two-chunk file
file = self._testUploadFile('helloWorld1.txt')
hash = sha512(chunkData).hexdigest()
self.assertEqual(hash, file['sha512'])
# We should have two chunks in the database
self.assertEqual(
chunkColl.find({
'uuid': file['chunkUuid']
}).count(), 2)
self._testDownloadFile(file, chunk1 + chunk2)
self._testDownloadFolder()
self._testDownloadCollection()
# Delete the file, make sure chunks are gone from database
self._testDeleteFile(file)
self.assertEqual(
chunkColl.find({
'uuid': file['chunkUuid']
}).count(), 0)
empty = self._testEmptyUpload('empty.txt')
self.assertEqual(sha512().hexdigest(), empty['sha512'])
self._testDownloadFile(empty, '')
self._testDeleteFile(empty)
# Test copying a file
copyTestFile = self._testUploadFile('helloWorld1.txt')
self._testCopyFile(copyTestFile)
def dropTestDatabase(dropModels=True):
"""
Call this to clear all contents from the test database. Also forces models
to reload.
"""
db_connection = getDbConnection()
if dropModels:
# Must clear the models to rebuild indices
model_importer.clearModels()
dbName = cherrypy.config['database']['uri'].split('/')[-1]
if 'girder_test_' not in dbName:
raise Exception('Expected a testing database name, but got {}'
.format(dbName))
db_connection.drop_database(dbName)
def db(request):
"""
Require a Mongo test database.
Provides a Mongo test database named after the requesting test function. Mongo databases are
created/destroyed based on the URI provided with the --mongo-uri option and tear-down
behavior is modified by the --keep-db option.
"""
from girder.models import _dbClients, getDbConnection, pymongo
from girder.models import model_base
from girder.external import mongodb_proxy
mockDb = request.config.getoption('--mock-db')
dbUri = request.config.getoption('--mongo-uri')
dbName = 'girder_test_%s' % hashlib.md5(_uid(
request.node).encode('utf8')).hexdigest()
keepDb = request.config.getoption('--keep-db')
executable_methods = mongodb_proxy.EXECUTABLE_MONGO_METHODS
realMongoClient = pymongo.MongoClient
if mockDb:
mongodb_proxy.EXECUTABLE_MONGO_METHODS = set()
pymongo.MongoClient = mongomock.MongoClient
connection = getDbConnection(uri='%s/%s' % (dbUri, dbName), quiet=False)
# Force getDbConnection from models to return our connection
_dbClients[(None, None)] = connection
connection.drop_database(dbName)
# Since models store a local reference to the current database, we need to force them all to
# reconnect
for model in model_base._modelSingletons:
model.reconnect()
yield connection
if not keepDb:
connection.drop_database(dbName)
connection.close()
if mockDb:
mongodb_proxy.EXECUTABLE_MONGO_METHODS = executable_methods
pymongo.MongoClient = realMongoClient
def getStatus(mode="basic", user=None):
"""
Get a dictionary of status information regarding the girder server.
:param mode: 'basic' returns values available to any anonymous user.
'quick' returns only values that are cheap to acquire.
'slow' provides all of that information and adds additional
:param user: a user record. Must have admin access to get anything other
than basic mode.
:returns: a status dictionary.
"""
isAdmin = user is not None and user.get("admin", False) is True
status = {}
status["bootTime"] = psutil.boot_time()
status["currentTime"] = time.time()
process = psutil.Process(os.getpid())
status["processStartTime"] = process.create_time()
if mode in ("quick", "slow") and isAdmin:
status["virtualMemory"] = _objectToDict(psutil.virtual_memory())
status["swap"] = _objectToDict(psutil.swap_memory())
status["cpuCount"] = psutil.cpu_count()
status["processMemory"] = _objectToDict(process.get_memory_info())
status["processName"] = process.name()
status["cmdline"] = process.cmdline()
status["exe"] = process.exe()
status["cwd"] = process.cwd()
status["userName"] = process.username()
status["processCpuTimes"] = _objectToDict(process.cpu_times())
db = getDbConnection().get_default_database()
status["mongoBuildInfo"] = db.command("buildInfo")
status["cherrypyThreadsMaxUsed"] = len(cherrypy.tools.status.seenThreads)
status["cherrypyThreadsInUse"] = len(
[
True
for threadId in cherrypy.tools.status.seenThreads
if "end" not in cherrypy.tools.status.seenThreads[threadId]
]
)
status["cherrypyThreadPoolSize"] = cherrypy.server.thread_pool
if mode == "slow" and isAdmin:
_computeSlowStatus(process, status, db)
return status
def db(request):
"""
Require a Mongo test database.
Provides a Mongo test database named after the requesting test function. Mongo databases are
created/destroyed based on the URI provided with the --mongo-uri option and tear-down
behavior is modified by the --keep-db option.
"""
from girder.models import _dbClients, getDbConnection, pymongo
from girder.models import model_base
from girder.external import mongodb_proxy
mockDb = request.config.getoption('--mock-db')
dbUri = request.config.getoption('--mongo-uri')
dbName = 'girder_test_%s' % hashlib.md5(_uid(request.node).encode('utf8')).hexdigest()
keepDb = request.config.getoption('--keep-db')
executable_methods = mongodb_proxy.EXECUTABLE_MONGO_METHODS
realMongoClient = pymongo.MongoClient
if mockDb:
mongodb_proxy.EXECUTABLE_MONGO_METHODS = set()
pymongo.MongoClient = mongomock.MongoClient
connection = getDbConnection(uri='%s/%s' % (dbUri, dbName), quiet=False)
# Force getDbConnection from models to return our connection
_dbClients[(None, None)] = connection
connection.drop_database(dbName)
# Since models store a local reference to the current database, we need to force them all to
# reconnect
for model in model_base._modelSingletons:
model.reconnect()
yield connection
if not keepDb:
connection.drop_database(dbName)
connection.close()
if mockDb:
mongodb_proxy.EXECUTABLE_MONGO_METHODS = executable_methods
pymongo.MongoClient = realMongoClient
def db(request):
"""
Require a Mongo test database.
Provides a Mongo test database named after the requesting test function. Mongo databases are
created/destroyed based on the URI provided with the --mongo-uri option and tear-down
semantics are handled by the --drop-db option.
"""
from girder.models import _dbClients, getDbConnection, pymongo
from girder.models.model_base import _modelSingletons
from girder.external import mongodb_proxy
mockDb = request.config.getoption('--mock-db')
dbUri = request.config.getoption('--mongo-uri')
dbName = 'girder_test_%s' % hashlib.md5(
request.node.name.encode('utf8')).hexdigest()
dropDb = request.config.getoption('--drop-db')
executable_methods = mongodb_proxy.EXECUTABLE_MONGO_METHODS
realMongoClient = pymongo.MongoClient
if mockDb:
mongodb_proxy.EXECUTABLE_MONGO_METHODS = set()
pymongo.MongoClient = mongomock.MongoClient
connection = getDbConnection(uri='%s/%s' % (dbUri, dbName), quiet=False)
# Force getDbConnection from models to return our connection
_dbClients[(None, None)] = connection
if dropDb == 'pre':
connection.drop_database(dbName)
for model in _modelSingletons:
model.reconnect()
yield connection
if dropDb == 'post':
connection.drop_database(dbName)
connection.close()
if mockDb:
mongodb_proxy.EXECUTABLE_MONGO_METHODS = executable_methods
pymongo.MongoClient = realMongoClient
def dropTestDatabase(dropModels=True):
"""
Call this to clear all contents from the test database. Also forces models
to reload.
"""
db_connection = getDbConnection()
dbName = cherrypy.config['database']['uri'].split('/')[-1]
if 'girder_test_' not in dbName:
raise Exception('Expected a testing database name, but got %s' % dbName)
if dbName in db_connection.database_names():
if dbName not in usedDBs and 'newdb' in os.environ.get('EXTRADEBUG', '').split():
raise Exception('Warning: database %s already exists' % dbName)
db_connection.drop_database(dbName)
usedDBs[dbName] = True
if dropModels:
model_importer.reinitializeAll()
def dropTestDatabase(dropModels=True):
"""
Call this to clear all contents from the test database. Also forces models
to reload.
"""
db_connection = getDbConnection()
dbName = cherrypy.config['database']['uri'].split('/')[-1]
if 'girder_test_' not in dbName:
raise Exception('Expected a testing database name, but got %s' % dbName)
if dbName in db_connection.database_names():
if dbName not in usedDBs and 'newdb' in os.environ.get('EXTRADEBUG', '').split():
raise Exception('Warning: database %s already exists' % dbName)
db_connection.drop_database(dbName)
usedDBs[dbName] = True
if dropModels:
model_importer.reinitializeAll()
def __init__(self, assetstore):
"""
:param assetstore: The assetstore to act on.
"""
super(GridFsAssetstoreAdapter, self).__init__(assetstore)
recent = False
try:
# Guard in case the connectionArgs is unhashable
key = (self.assetstore.get('mongohost'),
self.assetstore.get('replicaset'),
self.assetstore.get('shard'))
if key in _recentConnections:
recent = (time.time() - _recentConnections[key]['created'] <
RECENT_CONNECTION_CACHE_TIME)
except TypeError:
key = None
try:
# MongoClient automatically reuses connections from a pool, but we
# want to avoid redoing ensureChunkIndices each time we get such a
# connection.
client = getDbConnection(self.assetstore.get('mongohost'),
self.assetstore.get('replicaset'),
quiet=recent)
self.chunkColl = MongoProxy(client[self.assetstore['db']].chunk)
if not recent:
_ensureChunkIndices(self.chunkColl)
if self.assetstore.get('shard') == 'auto':
_setupSharding(self.chunkColl)
if key is not None:
if len(_recentConnections) >= RECENT_CONNECTION_CACHE_MAX_SIZE:
_recentConnections.clear()
_recentConnections[key] = {
'created': time.time()
}
except pymongo.errors.ConnectionFailure:
logger.error('Failed to connect to GridFS assetstore %s',
self.assetstore['db'])
self.chunkColl = 'Failed to connect'
self.unavailable = True
except pymongo.errors.ConfigurationError:
logger.exception('Failed to configure GridFS assetstore %s',
self.assetstore['db'])
self.chunkColl = 'Failed to configure'
self.unavailable = True
def getStatus(mode='basic', user=None):
"""
Get a dictionary of status information regarding the Girder server.
:param mode: 'basic' returns values available to any anonymous user.
'quick' returns only values that are cheap to acquire.
'slow' provides all of that information and adds additional
:param user: a user record. Must have admin access to get anything other
than basic mode.
:returns: a status dictionary.
"""
isAdmin = (user is not None and user['admin'])
status = {}
status['bootTime'] = psutil.boot_time()
status['currentTime'] = time.time()
process = psutil.Process(os.getpid())
status['processStartTime'] = process.create_time()
if mode in ('quick', 'slow') and isAdmin:
status['virtualMemory'] = _objectToDict(psutil.virtual_memory())
status['swap'] = _objectToDict(psutil.swap_memory())
status['cpuCount'] = psutil.cpu_count()
status['processMemory'] = _objectToDict(process.memory_info())
status['processName'] = process.name()
status['cmdline'] = process.cmdline()
status['exe'] = process.exe()
status['cwd'] = process.cwd()
status['userName'] = process.username()
status['processCpuTimes'] = _objectToDict(process.cpu_times())
db = getDbConnection().get_default_database()
status['mongoBuildInfo'] = db.command('buildInfo')
status['cherrypyThreadsMaxUsed'] = len(
cherrypy.tools.status.seenThreads)
status['cherrypyThreadsInUse'] = len([
True for threadId in cherrypy.tools.status.seenThreads
if 'end' not in cherrypy.tools.status.seenThreads[threadId]
])
status['cherrypyThreadPoolSize'] = cherrypy.server.thread_pool
if mode == 'slow' and isAdmin:
_computeSlowStatus(process, status, db)
return status
def __init__(self, assetstore):
"""
:param assetstore: The assetstore to act on.
"""
super(GridFsAssetstoreAdapter, self).__init__(assetstore)
recent = False
try:
# Guard in case the connectionArgs is unhashable
key = (self.assetstore.get('mongohost'),
self.assetstore.get('replicaset'),
self.assetstore.get('shard'))
if key in _recentConnections:
recent = (time.time() - _recentConnections[key]['created'] <
RECENT_CONNECTION_CACHE_TIME)
except TypeError:
key = None
try:
# MongoClient automatically reuses connections from a pool, but we
# want to avoid redoing ensureChunkIndices each time we get such a
# connection.
client = getDbConnection(self.assetstore.get('mongohost'),
self.assetstore.get('replicaset'),
quiet=recent)
self.chunkColl = MongoProxy(client[self.assetstore['db']].chunk)
if not recent:
_ensureChunkIndices(self.chunkColl)
if self.assetstore.get('shard') == 'auto':
_setupSharding(self.chunkColl)
if key is not None:
if len(_recentConnections) >= RECENT_CONNECTION_CACHE_MAX_SIZE:
_recentConnections.clear()
_recentConnections[key] = {
'created': time.time()
}
except pymongo.errors.ConnectionFailure:
logger.error('Failed to connect to GridFS assetstore %s',
self.assetstore['db'])
self.chunkColl = 'Failed to connect'
self.unavailable = True
except pymongo.errors.ConfigurationError:
logger.exception('Failed to configure GridFS assetstore %s',
self.assetstore['db'])
self.chunkColl = 'Failed to configure'
self.unavailable = True
def getStatus(mode='basic', user=None):
"""
Get a dictionary of status information regarding the Girder server.
:param mode: 'basic' returns values available to any anonymous user.
'quick' returns only values that are cheap to acquire.
'slow' provides all of that information and adds additional
:param user: a user record. Must have admin access to get anything other
than basic mode.
:returns: a status dictionary.
"""
isAdmin = (user is not None and user['admin'])
status = {}
status['bootTime'] = psutil.boot_time()
status['currentTime'] = time.time()
process = psutil.Process(os.getpid())
status['processStartTime'] = process.create_time()
if mode in ('quick', 'slow') and isAdmin:
status['virtualMemory'] = _objectToDict(psutil.virtual_memory())
status['swap'] = _objectToDict(psutil.swap_memory())
status['cpuCount'] = psutil.cpu_count()
status['processMemory'] = _objectToDict(process.memory_info())
status['processName'] = process.name()
status['cmdline'] = process.cmdline()
status['exe'] = process.exe()
status['cwd'] = process.cwd()
status['userName'] = process.username()
status['processCpuTimes'] = _objectToDict(process.cpu_times())
db = getDbConnection().get_database()
status['mongoBuildInfo'] = db.command('buildInfo')
status['cherrypyThreadsMaxUsed'] = len(
cherrypy.tools.status.seenThreads)
status['cherrypyThreadsInUse'] = len([
True for threadId in cherrypy.tools.status.seenThreads
if 'end' not in cherrypy.tools.status.seenThreads[threadId]])
status['cherrypyThreadPoolSize'] = cherrypy.server.thread_pool
if mode == 'slow' and isAdmin:
_computeSlowStatus(process, status, db)
return status
def __init__(self):
self.name = None
self._indices = []
self.initialize()
assert type(self.name) == str
db_cfg = getDbConfig()
db_connection = getDbConnection()
if cherrypy.config['server']['mode'] == 'testing':
dbName = '%s_test' % db_cfg['database']
else:
dbName = db_cfg['database'] # pragma: no cover
self.collection = db_connection[dbName][self.name]
assert isinstance(self.collection, pymongo.collection.Collection)
assert type(self._indices) == list
for index in self._indices:
self.collection.ensure_index(index)
def __init__(self, assetstore):
"""
:param assetstore: The assetstore to act on.
"""
self.assetstore = assetstore
try:
self.chunkColl = getDbConnection(
assetstore.get('mongohost', None),
assetstore.get('replicaset', None))[assetstore['db']].chunk
except pymongo.errors.ConnectionFailure:
logger.error('Failed to connect to GridFS assetstore %s',
assetstore['db'])
self.chunkColl = 'Failed to connect'
self.unavailable = True
return
except pymongo.errors.ConfigurationError:
logger.exception('Failed to configure GridFS assetstore %s',
assetstore['db'])
self.chunkColl = 'Failed to configure'
self.unavailable = True
return
def __init__(self, assetstore):
"""
:param assetstore: The assetstore to act on.
"""
self.assetstore = assetstore
try:
self.chunkColl = getDbConnection(
assetstore.get('mongohost', None),
assetstore.get('replicaset', None))[assetstore['db']].chunk
except pymongo.errors.ConnectionFailure:
logger.error('Failed to connect to GridFS assetstore %s',
assetstore['db'])
self.chunkColl = 'Failed to connect'
self.unavailable = True
return
except pymongo.errors.ConfigurationError:
logger.exception('Failed to configure GridFS assetstore %s',
assetstore['db'])
self.chunkColl = 'Failed to configure'
self.unavailable = True
return
def setUp(self):
"""
Set up the mongo db for the external dataset, with a collection
named tweetsgeo, which have tweet data that is geolocated.
"""
super(ExternalMongoDatasetTestCase, self).setUp()
self._user = self.model('user').createUser(
'minervauser', 'password', 'minerva', 'user',
'*****@*****.**')
from girder.utility import config
dbUri = config.getConfig()['database']['uri']
self.dbName = 'minerva_test_external_mongo_dataset'
dbUriParts = dbUri.split('/')[0:-1]
self.dbUri = '/'.join(dbUriParts + [self.dbName])
from girder.models import getDbConnection
self.externalMongoDbConnection = getDbConnection(self.dbUri)
self.externalMongoDb = self.externalMongoDbConnection.get_default_database()
from girder.external.mongodb_proxy import MongoProxy
self.collectionName = 'tweetsgeo'
self.tweetsgeoCollection = MongoProxy(self.externalMongoDb[self.collectionName])
# add test data to external dataset
self.pluginTestDir = os.path.dirname(os.path.realpath(__file__))
tweets100Path = os.path.join(self.pluginTestDir, 'data', 'tweets100.json')
z = zipfile.ZipFile('%s.zip' % tweets100Path)
tweets = json.load(z.open('tweets100.json'))
from datetime import datetime
dateformat = '%Y-%m-%dT%H:%M:%S'
for tweet in tweets:
d = datetime.strptime((tweet['created_at']), dateformat)
tweet['created_at'] = int((d - datetime(1970, 1, 1)).total_seconds())
self.tweetsgeoCollection.save(tweet)
path = '/minerva_dataset/folder'
params = {
'userId': self._user['_id'],
}
# create a dataset folder
self.request(path=path, method='POST', params=params, user=self._user)
def atestGridFsAssetstore(self):
"""
Test usage of the GridFS assetstore type.
"""
# Clear any old DB data
base.dropGridFSDatabase("girder_test_file_assetstore")
# Clear the assetstore database
conn = getDbConnection()
conn.drop_database("girder_test_file_assetstore")
self.model("assetstore").remove(self.model("assetstore").getCurrent())
assetstore = self.model("assetstore").createGridFsAssetstore(name="Test", db="girder_test_file_assetstore")
self.assetstore = assetstore
chunkColl = conn["girder_test_file_assetstore"]["chunk"]
# Upload the two-chunk file
file = self._testUploadFile("helloWorld1.txt")
hash = sha512(chunkData).hexdigest()
self.assertEqual(hash, file["sha512"])
# We should have two chunks in the database
self.assertEqual(chunkColl.find({"uuid": file["chunkUuid"]}).count(), 2)
self._testDownloadFile(file, chunk1 + chunk2)
self._testDownloadFolder()
self._testDownloadCollection()
# Delete the file, make sure chunks are gone from database
self._testDeleteFile(file)
self.assertEqual(chunkColl.find({"uuid": file["chunkUuid"]}).count(), 0)
empty = self._testEmptyUpload("empty.txt")
self.assertEqual(sha512().hexdigest(), empty["sha512"])
self._testDownloadFile(empty, "")
self._testDeleteFile(empty)
# Test copying a file
copyTestFile = self._testUploadFile("helloWorld1.txt")
self._testCopyFile(copyTestFile)
def validateInfo(doc):
"""
Validate the assetstore -- make sure we can connect to it and that the
necessary indexes are set up.
"""
if not doc.get('db', ''):
raise ValidationException('Database name must not be empty.', 'db')
if '.' in doc['db'] or ' ' in doc['db']:
raise ValidationException(
'Database name cannot contain spaces'
' or periods.', 'db')
try:
chunkColl = getDbConnection(
doc.get('mongohost'),
doc.get('replicaset'),
serverSelectionTimeoutMS=10000)[doc['db']].chunk
_ensureChunkIndices(chunkColl)
except pymongo.errors.ServerSelectionTimeoutError as e:
raise ValidationException('Could not connect to the database: %s' %
str(e))
return doc
def __init__(self, assetstore):
"""
:param assetstore: The assetstore to act on.
"""
super(GridFsAssetstoreAdapter, self).__init__(assetstore)
try:
self.chunkColl = getDbConnection(
self.assetstore.get('mongohost', None),
self.assetstore.get('replicaset',
None))[self.assetstore['db']].chunk
_ensureChunkIndices(self.chunkColl)
except pymongo.errors.ConnectionFailure:
logger.error('Failed to connect to GridFS assetstore %s',
self.assetstore['db'])
self.chunkColl = 'Failed to connect'
self.unavailable = True
return
except pymongo.errors.ConfigurationError:
logger.exception('Failed to configure GridFS assetstore %s',
self.assetstore['db'])
self.chunkColl = 'Failed to configure'
self.unavailable = True
return
def __init__(self, assetstore):
"""
:param assetstore: The assetstore to act on.
"""
super(GridFsAssetstoreAdapter, self).__init__(assetstore)
try:
self.chunkColl = getDbConnection(
self.assetstore.get('mongohost', None),
self.assetstore.get('replicaset', None)
)[self.assetstore['db']].chunk
_ensureChunkIndices(self.chunkColl)
except pymongo.errors.ConnectionFailure:
logger.error('Failed to connect to GridFS assetstore %s',
self.assetstore['db'])
self.chunkColl = 'Failed to connect'
self.unavailable = True
return
except pymongo.errors.ConfigurationError:
logger.exception('Failed to configure GridFS assetstore %s',
self.assetstore['db'])
self.chunkColl = 'Failed to configure'
self.unavailable = True
return
def _computeSlowStatus(process, status, db):
status['diskPartitions'] = [_objectToDict(part) for part in
psutil.disk_partitions()]
try:
# This fails in certain environments, so guard it
status['diskIO'] = _objectToDict(psutil.disk_io_counters())
except Exception:
pass
# Report on the disk usage where the script is located
if hasattr(girder, '__file__'):
status['girderPath'] = os.path.abspath(girder.__file__)
status['girderDiskUsage'] = _objectToDict(
psutil.disk_usage(status['girderPath']))
# Report where our logs are and how much space is available for them
status['logs'] = []
for handler in logger.handlers:
try:
logInfo = {'path': handler.baseFilename}
logInfo['diskUsage'] = _objectToDict(
psutil.disk_usage(logInfo['path']))
status['logs'].append(logInfo)
except Exception:
# If we can't read information about the log, don't throw an
# exception
pass
status['mongoDbStats'] = db.command('dbStats')
status['mongoDbPath'] = getDbConnection().admin.command(
'getCmdLineOpts')['parsed']['storage']['dbPath']
status['mongoDbDiskUsage'] = _objectToDict(
psutil.disk_usage(status['mongoDbPath']))
status['processDirectChildrenCount'] = len(process.children())
status['processAllChildrenCount'] = len(process.children(True))
status['openFiles'] = [_objectToDict(file) for file in
process.open_files()]
# I'd rather see textual names for the family and type of connections,
# so make a lookup table for them
connFamily = {getattr(socket, key): key for key in dir(socket)
if key.startswith('AF_')}
connType = {getattr(socket, key): key for key in dir(socket)
if key.startswith('SOCK_')}
connections = []
for conn in process.connections():
connDict = _objectToDict(conn)
connDict.pop('raddr', None)
connDict.pop('laddr', None)
connDict['family'] = connFamily.get(connDict['family'],
connDict['family'])
connDict['type'] = connType.get(connDict['type'], connDict['type'])
connections.append(connDict)
status['connections'] = connections
if hasattr(process, 'io_counters'):
status['ioCounters'] = _objectToDict(process.io_counters())
status['cherrypyThreads'] = {}
for threadId in cherrypy.tools.status.seenThreads:
info = cherrypy.tools.status.seenThreads[threadId].copy()
if 'end' in info:
info['duration'] = info['end'] - info['start']
info['idle'] = time.time() - info['end']
status['cherrypyThreads'][threadId] = info
'resource path. "resource:admin" uses the default admin, '
'"resourceid:<path" is the string id for the resource path.')
parser.add_argument(
'--yaml',
help='Specify parameters for this script in a yaml file. If no value '
'is specified, this defaults to the environment variable of '
'DSA_PROVISION_YAML. No error is thrown if the file does not exist. '
'The yaml file is a dictionary of keys as would be passed to the '
'command line.')
parser.add_argument(
'--no-mongo-compat', action='store_false', dest='mongo_compat',
default=None, help='Do not automatically set the mongo feature '
'compatibility version to the current server version.')
parser.add_argument(
'--verbose', '-v', action='count', default=0, help='Increase verbosity')
opts = parser.parse_args(args=sys.argv[1:])
logger.addHandler(logging.StreamHandler(sys.stderr))
logger.setLevel(max(1, logging.WARNING - 10 * opts.verbose))
logger.debug('Parsed arguments: %r', opts)
opts = merge_yaml_opts(opts, parser)
# This loads plugins, allowing setting validation
configureServer()
if getattr(opts, 'mongo_compat', None) is not False:
try:
db = getDbConnection()
db.admin.command({'setFeatureCompatibilityVersion': '.'.join(
db.server_info()['version'].split('.')[:2])})
except Exception:
logger.warning('Could not set mongo feature compatibility version.')
provision(opts)