from bioflow.neo4j_db.GraphDeclarator import DatabaseGraph
from bioflow.utils.log_behavior import get_logger
from bioflow.neo4j_db.db_io_routines import stable_get_all
log = get_logger(__name__)
def print_node_look_up_by_id(domain, search_legacy_id):
"""
Looks up a node by legacy ID and prints it's access url. The lookup is a case-sensitive strict
match.
:param domain: Node type of the form of DatabaseGraph.Object
:param search_legacy_id: requested legacy ID
:return: list of the items found
"""
accumulator = []
lookup_generator = domain.index.lookup(ID=search_legacy_id)
if not lookup_generator:
print "nothing found"
if lookup_generator:
for item in lookup_generator:
print item
accumulator.append(item)
return accumulator
def count_nodes(domain):
"""
Stupid counter that gets the number of items in a given domain
import numpy as np
from scipy.stats import gaussian_kde
from matplotlib import pyplot as plt
from scipy import histogram2d
from csv import reader as csv_reader
from bioflow.main_configs import interactome_rand_samp_db
from bioflow.utils.log_behavior import get_logger
from bioflow.molecular_network.InteractomeInterface import InteractomeInterface
from bioflow.algorithms_bank.conduction_routines import perform_clustering
from bioflow.main_configs import Dumps
# from bioflow.algorithms_bank.conduction_routines import get_current_through_nodes
from matplotlib.cm import get_cmap
log = get_logger(__name__)
interactome_interface_instance = InteractomeInterface(True, True)
interactome_interface_instance.fast_load()
md5_hash = interactome_interface_instance.md5_hash()
print "samples found to test against:\t %s" % interactome_rand_samp_db.find({'size': 2,
'sys_hash': md5_hash,
'sparse_rounds': False}).count()
essential_genes_bulbs_ids = []
with open(Dumps.analysis_set_bulbs_ids, 'r') as source:
reader = csv_reader(source)
from mock import Mock as MagicMock
from bioflow.utils.log_behavior import get_logger
log = get_logger('DB_IO_Mocks @ unittests')
log.debug('Mocking DB_IO module')
def look_up_annotation_set(supplied_list):
return supplied_list, [(elt, '') for elt in supplied_list], ['' for _ in supplied_list]
"""
Tests the logger behavior
"""
import unittest
import os
from bioflow.main_configs import log_location
from bioflow.utils.general_utils.high_level_os_io import wipe_dir
from bioflow.utils.log_behavior import get_logger
log = get_logger('LoggerTester @ unittests')
class TestLogs(unittest.TestCase):
@classmethod
def setUpClass(cls):
log.debug('This is a debug test')
log.info('This is an info logging test')
log.warning('This is a warning test')
log.error('This is an error test')
log.critical('This is a critical test')
@classmethod
def tearDownClass(cls):
wipe_dir(log_location)
def test_file_creation(self):
self.assertTrue(os.path.isdir(log_location))
def test_low_level_logs(self):
with open(os.path.join(log_location, 'debug.log'), 'r') as source_file:
contents = ''.join(source_file.read())
from mock import Mock as MagicMock
from bioflow.utils.log_behavior import get_logger
log = get_logger('DB_IO_Mocks @ unittests')
log.debug('Mocking DB_IO module')
def look_up_annotation_set(supplied_list):
return supplied_list, [(elt, '') for elt in supplied_list
], ['' for _ in supplied_list]
