chemicalchecker.util.config

Chemical Checker config.

The config is defined in a JSON file (i.e. cc_config.json) and it holds information that are necessary throughout the Chemical Checker.

The path to this file can be passed to the Config constructor or it can be set in the environment variable CC_CONFIG. In this case the specified config will be used by default.

When instantiated the variables will be attributes of the config instance:

from chemicalchecker.util import Config
cfg = Config()
cfg.PATH.CC_TMP
>>> /tmp/

An example of this file will contain:

{
    "PATH": {
        "CC_ROOT": "'/aloy/web_checker/current'",
        "CC_DATA": "'/aloy/scratch/oguitart/download/'",
        "CC_TMP": "'/tmp/'",
        "CC_REPO": "'/opt/chemical_checker'",
        "SINGULARITY_IMAGE": "'/aloy/web_checker/images/cc.simg'",
        "validation_path": "'/aloy/web_checker/package_cc/validation_sets/'"
    },
    "DB": {
        "dialect": "'postgresql'",
        "port":  "'5432'",
        "host": "'10.5.4.240'",
        "user": "'cc_user'",
        "password": "'checker'",
        "database": "'cc_package'",
        "calcdata_dbname": "'cc_calcdata'",
        "uniprot_db_version" : "'2019_01'"
    },
    "HPC": {
        "system" : "'sge'",
        "host": "'pac-one-head'",
        "queue": "'all.q'",
        "username": "'cc_user'"
    }
}

As you can see json fields are organized sections. The most important is the PATH which contains the following information:

• PATH.CC_ROOT default root directory of a CC instance (see

  chemcheck).

• PATH.CC_DATA directory for data download (see

  download).

• PATH.CC_TMP directory for temporary data.

• PATH.CC_REPO directory of the default CC package.

• PATH.SINGULARITY_IMAGE path to the singularity image used to submit HPC jobs (see hpc)

• PATH.validation_path directory holding validation set for ROC AUC calculation.

The section DB holds parameters needed to connect to local DBS (used in chemicalchecker.database). The HPC section contain parameters used in HPC job submission (used in chemicalchecker.util.HPC).

chemicalchecker.util.config.config

Chemical Checker config.