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')