How to use the biothings.ConfigurationDefault function in biothings

To help you get started, we’ve selected a few biothings examples, based on popular ways it is used in public projects.

Secure your code as it's written. Use Snyk Code to scan source code in minutes - no build needed - and fix issues immediately.

biothings / myvariant.info / src / config_hub.py View on Github

DATA_PLUGIN_FOLDER = ConfigurationDefault(
        default="./plugins",
        desc="Define path to folder which will contain all 3rd party parsers, dumpers, etc...")

# Path to folder containing diff files
DIFF_PATH = ConfigurationDefault(
        default=ConfigurationValue("""os.path.join(DATA_ARCHIVE_ROOT,"diff")"""),
        desc="Define path to folder which will contain output files from diff")

# Path to folder containing release note files
RELEASE_PATH = ConfigurationDefault(
        default=ConfigurationValue("""os.path.join(DATA_ARCHIVE_ROOT,"release")"""),
        desc="Define path to folder which will contain release files")

# this dir must be created manually
LOG_FOLDER = ConfigurationDefault(
        default=ConfigurationValue("""os.path.join(DATA_ARCHIVE_ROOT,"logs")"""),
        desc="Define path to folder which will contain log files")

IDS_S3_BUCKET =  ConfigurationDefault(
        default="myvariant-ids",
        desc="Define a bucket name to upload myvariant _ids to")

# default hub logger
logger = ConfigurationDefault(
        default=logging,
        desc="Provide a default hub logger instance (use setup_default_log(name,log_folder)")

ACTIVE_DATASOURCES = [
    # auto-updated
    'hub.dataload.sources.clinvar',
    'hub.dataload.sources.dbsnp',

biothings / mygene.info / src / config_hub.py View on Github

DATA_ARCHIVE_ROOT = ConfigurationError("Define path to folder which will contain all downloaded data, cache files, etc...")

# Path to a folder to store all 3rd party parsers, dumpers, etc...
DATA_PLUGIN_FOLDER = ConfigurationDefault(
        default="./plugins",
        desc="Define path to folder which will contain all 3rd party parsers, dumpers, etc...")

# Path to folder containing diff files
DIFF_PATH = ConfigurationDefault(
        default=ConfigurationValue("""os.path.join(DATA_ARCHIVE_ROOT,"diff")"""),
        desc="Define path to folder which will contain output files from diff")
# Usually inside DATA_ARCHIVE_ROOT
#DIFF_PATH = os.path.join(DATA_ARCHIVE_ROOT,"diff")

# Path to folder containing release note files
RELEASE_PATH = ConfigurationDefault(
        default=ConfigurationValue("""os.path.join(DATA_ARCHIVE_ROOT,"release")"""),
        desc="Define path to folder which will contain release files")

# Usually inside DATA_ARCHIVE_ROOT
#RELEASE_PATH = os.path.join(DATA_ARCHIVE_ROOT,"release")

# this dir must be created manually
LOG_FOLDER = ConfigurationDefault(
        default=ConfigurationValue("""os.path.join(DATA_ARCHIVE_ROOT,"logs")"""),
        desc="Define path to folder which will contain log files")
# Usually inside DATA_ARCHIVE_ROOT
#LOG_FOLDER = os.path.join(DATA_ARCHIVE_ROOT,'logs')

# default hub logger
from biothings.utils.loggers import setup_default_log
logger = ConfigurationDefault(

biothings / myvariant.info / src / config_hub.py View on Github

# Path to folder containing release note files
RELEASE_PATH = ConfigurationDefault(
        default=ConfigurationValue("""os.path.join(DATA_ARCHIVE_ROOT,"release")"""),
        desc="Define path to folder which will contain release files")

# this dir must be created manually
LOG_FOLDER = ConfigurationDefault(
        default=ConfigurationValue("""os.path.join(DATA_ARCHIVE_ROOT,"logs")"""),
        desc="Define path to folder which will contain log files")

IDS_S3_BUCKET =  ConfigurationDefault(
        default="myvariant-ids",
        desc="Define a bucket name to upload myvariant _ids to")

# default hub logger
logger = ConfigurationDefault(
        default=logging,
        desc="Provide a default hub logger instance (use setup_default_log(name,log_folder)")

ACTIVE_DATASOURCES = [
    # auto-updated
    'hub.dataload.sources.clinvar',
    'hub.dataload.sources.dbsnp',
    'hub.dataload.sources.dbnsfp',
    'hub.dataload.sources.exac',
    'hub.dataload.sources.clingen',

    # manually-updated
    'hub.dataload.sources.cadd',
    'hub.dataload.sources.grasp',
    'hub.dataload.sources.emv',
    'hub.dataload.sources.evs',

biothings / myvariant.info / src / config_hub.py View on Github

#        "module" : "biothings.utils.mongo",
#        "uri" : "mongodb://localhost:27017",
#        #"uri" : "mongodb://user:passwd@localhost:27017", # mongodb std URI
#        }
#HUB_DB_BACKEND = {
#        "module" : "biothings.utils.es",
#        "host" : "localhost:9200",
#        }

#ES_HOST = ConfigurationError("Define ElasticSearch host used for index creation (eg localhost:9200)")

# Path to a folder to store all downloaded files, logs, caches, etc...
DATA_ARCHIVE_ROOT = ConfigurationError("Define path to folder which will contain all downloaded data, cache files, etc...")

# Path to a folder to store all 3rd party parsers, dumpers, etc...
DATA_PLUGIN_FOLDER = ConfigurationDefault(
        default="./plugins",
        desc="Define path to folder which will contain all 3rd party parsers, dumpers, etc...")

# Path to folder containing diff files
DIFF_PATH = ConfigurationDefault(
        default=ConfigurationValue("""os.path.join(DATA_ARCHIVE_ROOT,"diff")"""),
        desc="Define path to folder which will contain output files from diff")

# Path to folder containing release note files
RELEASE_PATH = ConfigurationDefault(
        default=ConfigurationValue("""os.path.join(DATA_ARCHIVE_ROOT,"release")"""),
        desc="Define path to folder which will contain release files")

# this dir must be created manually
LOG_FOLDER = ConfigurationDefault(
        default=ConfigurationValue("""os.path.join(DATA_ARCHIVE_ROOT,"logs")"""),

biothings / mygene.info / src / config_hub.py View on Github

#        }
#HUB_DB_BACKEND = {
#        "module" : "biothings.utils.es",
#        "host" : "localhost:9200",
#        }

# List of package paths for active datasources (expect data-plugin based sources)
ACTIVE_DATASOURCES = ConfigurationDefault(
        default=[],
        desc="List of package paths for active datasources")

# Path to a folder to store all downloaded files, logs, caches, etc...
DATA_ARCHIVE_ROOT = ConfigurationError("Define path to folder which will contain all downloaded data, cache files, etc...")

# Path to a folder to store all 3rd party parsers, dumpers, etc...
DATA_PLUGIN_FOLDER = ConfigurationDefault(
        default="./plugins",
        desc="Define path to folder which will contain all 3rd party parsers, dumpers, etc...")

# Path to folder containing diff files
DIFF_PATH = ConfigurationDefault(
        default=ConfigurationValue("""os.path.join(DATA_ARCHIVE_ROOT,"diff")"""),
        desc="Define path to folder which will contain output files from diff")
# Usually inside DATA_ARCHIVE_ROOT
#DIFF_PATH = os.path.join(DATA_ARCHIVE_ROOT,"diff")

# Path to folder containing release note files
RELEASE_PATH = ConfigurationDefault(
        default=ConfigurationValue("""os.path.join(DATA_ARCHIVE_ROOT,"release")"""),
        desc="Define path to folder which will contain release files")

# Usually inside DATA_ARCHIVE_ROOT

biothings / mygene.info / src / config_hub.py View on Github

#HUB_DB_BACKEND = {
#        "module" : "biothings.utils.sqlite3",
#        "sqlite_db_foder" : "./db",
#        }
#HUB_DB_BACKEND = {
#        "module" : "biothings.utils.mongo",
#        "uri" : "mongodb://localhost:27017",
#        #"uri" : "mongodb://user:passwd@localhost:27017", # mongodb std URI
#        }
#HUB_DB_BACKEND = {
#        "module" : "biothings.utils.es",
#        "host" : "localhost:9200",
#        }

# List of package paths for active datasources (expect data-plugin based sources)
ACTIVE_DATASOURCES = ConfigurationDefault(
        default=[],
        desc="List of package paths for active datasources")

# Path to a folder to store all downloaded files, logs, caches, etc...
DATA_ARCHIVE_ROOT = ConfigurationError("Define path to folder which will contain all downloaded data, cache files, etc...")

# Path to a folder to store all 3rd party parsers, dumpers, etc...
DATA_PLUGIN_FOLDER = ConfigurationDefault(
        default="./plugins",
        desc="Define path to folder which will contain all 3rd party parsers, dumpers, etc...")

# Path to folder containing diff files
DIFF_PATH = ConfigurationDefault(
        default=ConfigurationValue("""os.path.join(DATA_ARCHIVE_ROOT,"diff")"""),
        desc="Define path to folder which will contain output files from diff")
# Usually inside DATA_ARCHIVE_ROOT

biothings / mygene.info / src / config_hub.py View on Github

default=ConfigurationValue("""os.path.join(DATA_ARCHIVE_ROOT,"release")"""),
        desc="Define path to folder which will contain release files")

# Usually inside DATA_ARCHIVE_ROOT
#RELEASE_PATH = os.path.join(DATA_ARCHIVE_ROOT,"release")

# this dir must be created manually
LOG_FOLDER = ConfigurationDefault(
        default=ConfigurationValue("""os.path.join(DATA_ARCHIVE_ROOT,"logs")"""),
        desc="Define path to folder which will contain log files")
# Usually inside DATA_ARCHIVE_ROOT
#LOG_FOLDER = os.path.join(DATA_ARCHIVE_ROOT,'logs')

# default hub logger
from biothings.utils.loggers import setup_default_log
logger = ConfigurationDefault(
        default=logging,
        desc="Provide a default hub logger instance (use setup_default_log(name,log_folder)")
# Usually use default setup
#logger = setup_default_log("hub", LOG_FOLDER)

# Set whether configuration parameters can be edited
# and superseded by user through ConfigurationManger
# Note: once config manager has been configured with this
# field, it's deleted to make sure we can't change it at runtime
CONFIG_READONLY = True

biothings / mygene.info / src / config_hub.py View on Github

DIFF_PATH = ConfigurationDefault(
        default=ConfigurationValue("""os.path.join(DATA_ARCHIVE_ROOT,"diff")"""),
        desc="Define path to folder which will contain output files from diff")
# Usually inside DATA_ARCHIVE_ROOT
#DIFF_PATH = os.path.join(DATA_ARCHIVE_ROOT,"diff")

# Path to folder containing release note files
RELEASE_PATH = ConfigurationDefault(
        default=ConfigurationValue("""os.path.join(DATA_ARCHIVE_ROOT,"release")"""),
        desc="Define path to folder which will contain release files")

# Usually inside DATA_ARCHIVE_ROOT
#RELEASE_PATH = os.path.join(DATA_ARCHIVE_ROOT,"release")

# this dir must be created manually
LOG_FOLDER = ConfigurationDefault(
        default=ConfigurationValue("""os.path.join(DATA_ARCHIVE_ROOT,"logs")"""),
        desc="Define path to folder which will contain log files")
# Usually inside DATA_ARCHIVE_ROOT
#LOG_FOLDER = os.path.join(DATA_ARCHIVE_ROOT,'logs')

# default hub logger
from biothings.utils.loggers import setup_default_log
logger = ConfigurationDefault(
        default=logging,
        desc="Provide a default hub logger instance (use setup_default_log(name,log_folder)")
# Usually use default setup
#logger = setup_default_log("hub", LOG_FOLDER)

# Set whether configuration parameters can be edited
# and superseded by user through ConfigurationManger
# Note: once config manager has been configured with this

biothings / mychem.info / src / config_hub.py View on Github

#LOG_FOLDER = os.path.join(DATA_ARCHIVE_ROOT,'logs')

# Path to folder containing diff files
DIFF_PATH = ConfigurationError("Define path to folder which will contain output files from diff")                                                                                                                                       
# Usually inside DATA_ARCHIVE_ROOT
#DIFF_PATH = os.path.join(DATA_ARCHIVE_ROOT,"diff")

# Path to folder containing release note files
RELEASE_PATH = ConfigurationError("Define path to folder which will contain output files from diff")
# Usually inside DATA_ARCHIVE_ROOT
#RELEASE_PATH = os.path.join(DATA_ARCHIVE_ROOT,"release")

# default hub logger
from biothings.utils.loggers import setup_default_log
import logging
logger = ConfigurationDefault(
        default=logging,
        desc="Provide a default hub logger instance (use setup_default_log(name,log_folder)")

biothings / mygene.info / src / config_hub.py View on Github

# List of package paths for active datasources (expect data-plugin based sources)
ACTIVE_DATASOURCES = ConfigurationDefault(
        default=[],
        desc="List of package paths for active datasources")

# Path to a folder to store all downloaded files, logs, caches, etc...
DATA_ARCHIVE_ROOT = ConfigurationError("Define path to folder which will contain all downloaded data, cache files, etc...")

# Path to a folder to store all 3rd party parsers, dumpers, etc...
DATA_PLUGIN_FOLDER = ConfigurationDefault(
        default="./plugins",
        desc="Define path to folder which will contain all 3rd party parsers, dumpers, etc...")

# Path to folder containing diff files
DIFF_PATH = ConfigurationDefault(
        default=ConfigurationValue("""os.path.join(DATA_ARCHIVE_ROOT,"diff")"""),
        desc="Define path to folder which will contain output files from diff")
# Usually inside DATA_ARCHIVE_ROOT
#DIFF_PATH = os.path.join(DATA_ARCHIVE_ROOT,"diff")

# Path to folder containing release note files
RELEASE_PATH = ConfigurationDefault(
        default=ConfigurationValue("""os.path.join(DATA_ARCHIVE_ROOT,"release")"""),
        desc="Define path to folder which will contain release files")

# Usually inside DATA_ARCHIVE_ROOT
#RELEASE_PATH = os.path.join(DATA_ARCHIVE_ROOT,"release")

# this dir must be created manually
LOG_FOLDER = ConfigurationDefault(
        default=ConfigurationValue("""os.path.join(DATA_ARCHIVE_ROOT,"logs")"""),

How to use the biothings.ConfigurationDefault function in biothings

To help you get started, we’ve selected a few biothings examples, based on popular ways it is used in public projects.

biothings

Package Health Score

Popular biothings functions

Similar packages