def from_connection(connection=None):
connection = get_connection(MODULE_NAME, connection)
engine = create_engine(connection)
session_maker = sessionmaker(bind=engine,
autoflush=False,
expire_on_commit=False)
session = scoped_session(session_maker)
return Manager(engine, session)
def __init__(self, connection=None):
"""
:param Optional[str] connection: The connection string
"""
self.connection = get_connection(MODULE_NAME, connection=connection)
log.info('connected to %s', self.connection)
self.engine = create_engine(self.connection)
self.session_maker = sessionmaker(bind=self.engine,
autoflush=False,
expire_on_commit=False)
self.session = self.session_maker()
self.create_all()
#: a cache from group id to its model
self.group_cache = {}
#: a cache from (tax id, gene id) to its model
self.gene_cache = {}
#: a cache from NCBI tax id to its model
self.species_cache = {}
# -*- coding: utf-8 -*- import os from bio2bel.utils import get_connection, get_data_dir MODULE_NAME = 'phosphosite' DATA_DIR = get_data_dir(MODULE_NAME) DEFAULT_CACHE_CONNECTION = get_connection(MODULE_NAME) PROTEIN_NAMESPACE = 'UNIPROT' PHOSPHORYLATION_URL = 'https://www.phosphosite.org/downloads/Phosphorylation_site_dataset.gz' PHOSPHORYLATION_PATH = os.path.join(DATA_DIR, 'Phosphorylation_site_dataset.gz') ACETYLATION_URL = 'https://www.phosphosite.org/downloads/Acetylation_site_dataset.gz' ACETYLATION_PATH = os.path.join(DATA_DIR, 'Acetylation_site_dataset.gz') O_GALNAC_URL = 'https://www.phosphosite.org/downloads/O-GalNAc_site_dataset.gz' O_GALNAC_PATH = os.path.join(DATA_DIR, 'O-GalNAc_site_dataset.gz') O_GLCNAC_URL = 'https://www.phosphosite.org/downloads/O-GlcNAc_site_dataset.gz' O_GLCNAC_PATH = os.path.join(DATA_DIR, 'O-GlcNAc_site_dataset.gz') SUMOYLATION_URL = 'https://www.phosphosite.org/downloads/Sumoylation_site_dataset.gz' SUMOYLATION_PATH = os.path.join(DATA_DIR, 'Sumoylation_site_dataset.gz') UBIQUITINATION_URL = 'https://www.phosphosite.org/downloads/Ubiquitination_site_dataset.gz' UBIQUITINATION_PATH = os.path.join(DATA_DIR, 'Ubiquitination_site_dataset.gz') REGULATORY_SITES_URL = 'https://www.phosphosite.org/downloads/Regulatory_sites.gz'
MODULE_NAME = 'pathme'
DEFAULT_PATHME_DIR = os.path.join(os.path.expanduser('~'), '.pathme')
PATHME_DIR = os.environ.get('PATHME_DIRECTORY', DEFAULT_PATHME_DIR)
KEGG_PATHWAYS_URL = 'http://rest.kegg.jp/link/pathway/'
def get_data_dir() -> str:
"""Ensure the appropriate PathMe data directory exists for the given module, then returns the file path."""
os.makedirs(PATHME_DIR, exist_ok=True)
return PATHME_DIR
DATA_DIR = get_data_dir()
DEFAULT_CACHE_CONNECTION = get_connection()
# Databases contained in PathMe
#: KEGG
KEGG = 'kegg'
KEGG_DIR = os.path.join(DATA_DIR, KEGG)
KEGG_BEL = os.path.join(KEGG_DIR, 'bel')
KEGG_FILES = os.path.join(KEGG_DIR, 'xml')
KEGG_CACHE = os.path.join(KEGG_DIR, 'cache')
#: Reactome
REACTOME = 'reactome'
REACTOME_DIR = os.path.join(DATA_DIR, REACTOME)
REACTOME_BEL = os.path.join(REACTOME_DIR, 'bel')
REACTOME_FILES = os.path.join(REACTOME_DIR, 'rdf')
