tests/testthat/tests_configuration.R

In LainPavot/DBModelR: A Model-Database Interface to Make the Database Layer Abstract

DB_PATH <- "./testdb.sqlite"

tryCatch({
    ModelDefinition(table="yui", fields=list(yui="INTEGER"))
}, error=function(e) {
    stop("Please, load the ORM before you source this file.")
})

MODELS <- list(
    adduct=ModelDefinition(
        table="adduct",
        fields=list(
            name="TEXT",
            mass="FLOAT",
            charge="INTEGER",
            multi="INTEGER",
            formula_add="TEXT",
            formula_ded="TEXT",
            sign="TEXT",
            oidscore="INTEGER",
            quasi="INTEGER",
            ips="FLOAT"
        )
    ),
    cluster=ModelDefinition(
        table="cluster",
        fields=list(
            formula="TEXT",
            annotation="TEXT",
            coeff="REAL",
            r_squared="REAL",
            charge="INTEGER",
            mean_rt="REAL",
            score="REAL",
            deviation="REAL",
            status="TEXT",
            adduct="TEXT",
            curent_group="INTEGER",
            pc_group="INTEGER",
            align_group="INTEGER",
            xcms_group="INTEGER"
        ),
        one=list("sample", "compound"),
        many=list("feature")
    ),
    compound=ModelDefinition(
        table="compound",
        fields=list(
            name="TEXT",
            common_name="TEXT",
            formula="TEXT",
            charge="INTEGER",
            date="TEXT",
            mz="REAL"
        )
    ),
    feature=ModelDefinition(
        table="feature",
        fields=list(
            mz="FLOAT",
            mz_min="FLOAT",
            mz_max="FLOAT",
            rt="FLOAT",
            rt_min="FLOAT",
            rt_max="FLOAT",
            int_o="FLOAT",
            int_b="FLOAT",
            max_o="FLOAT",
            iso="TEXT",
            abundance="FLOAT"
        ),
        many=list("cluster")
    ),
    instrument=ModelDefinition(
        table="instrument",
        fields=list(
            model="TEXT",
            manufacturer="TEXT",
            analyzer="TEXT",
            dector_type="TEXT"
        )
    ),
    instrument_config=ModelDefinition(
        table="instrument_config",
        fields=list(
            resolution="TEXT",
            agc_target="TEXT",
            maximum_IT="TEXT",
            number_of_scan_range="TEXT",
            scan_range="TEXT",
            version="TEXT"
        )
    ),
    software=ModelDefinition(
        table="software",
        fields=list(
            name="TEXT",
            version="TEXT"
        )
    ),
    sample=ModelDefinition(
        table="sample",
        fields=list(
            name="TEXT",
            path="TEXT",
            raw_path="TEXT",
            polarity="TEXT",
            raw="BLOB"
        ),
        one=list("instrument", "instrument_config", "software")
    )
)