annotate data/models.R @ 19:2937e72e5891 draft

" master branch Updating"

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

list(
    adduct = DBModelR::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 = DBModelR::ModelDefinition(
        table = "cluster",
        fields = list(
            clusterID = "INTEGER",
            formula = "TEXT",
            annotation = "TEXT",
            coeff = "FLOAT",
            r_squared = "FLOAT",
            charge = "INTEGER",
            mean_rt = "FLOAT",
            score = "FLOAT",
            deviation = "FLOAT",
            status = "TEXT",
            # adduct = "TEXT",
            curent_group = "INTEGER",
            pc_group = "INTEGER",
            align_group = "INTEGER",
            xcms_group = "INTEGER"
        ),
        one = list("compound", "adduct"),
        many = list("sample")
    ),
    compound = DBModelR::ModelDefinition(
        table = "compound",
        fields = list(
            name = "TEXT",
            common_name = "TEXT",
            formula = "TEXT",
            charge = "INTEGER",
            date = "TEXT",
            mz = "FLOAT"
        )
    ),
    feature = DBModelR::ModelDefinition(
        table = "feature",
        fields = list(
            featureID = "INTEGER",
            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"
        ),
        one = list("cluster"),
        many = list("sample")
    ),
    instrument = DBModelR::ModelDefinition(
        table = "instrument",
        fields = list(
            model = "TEXT",
            manufacturer = "TEXT",
            analyzer = "TEXT",
            detector_type = "TEXT",
            ion_source = "TEXT"
        )
    ),
    instrument_config = DBModelR::ModelDefinition(
        table = "instrument_config",
        fields = list(
            resolution = "TEXT",
            agc_target = "TEXT",
            maximum_IT = "TEXT",
            number_of_scan_range = "TEXT",
            scan_range = "TEXT",
            version = "TEXT"
        )
    ),
    project = DBModelR::ModelDefinition(
        table = "project",
        fields = list(
            name = "TEXT",
            comment = "TEXT"
        ),
        one = list("sample")
    ),
    sample = DBModelR::ModelDefinition(
        table = "sample",
        fields = list(
            name = "TEXT",
            path = "TEXT",
            polarity = "TEXT",
            kind = "TEXT", ## rdata or mxml or enriched_rdata
            raw = "BLOB"
        ),
        one = list(
            "peak_picking_parameters",
            "pairing_parameters",
            "alignmenmt_parameters",
            "camera_parameters",
            "instrument",
            "instrument_config",
            "software",
            "smol_xcms_set"
        )
    ),
    smol_xcms_set = DBModelR::ModelDefinition(
        table = "smol_xcms_set",
        fields = list(
            raw = "BLOB"
        )
    ),
    software = DBModelR::ModelDefinition(
        table = "software",
        fields = list(
            name = "TEXT",
            version = "TEXT"
        )
    ),
    peak_picking_parameters = DBModelR::ModelDefinition(
        table = "peak_picking_parameters",
        fields = list(
            ppm = "FLOAT",
            peakwidth = "TEXT",
            snthresh = "TEXT",
            prefilterStep = "TEXT",
            prefilterLevel = "TEXT",
            mzdiff = "TEXT",
            fitgauss = "TEXT",
            noise = "TEXT",
            mzCenterFun = "TEXT",
            integrate = "INTEGER",
            firstBaselineCheck = "TEXT",
            snthreshIsoROIs = "TEXT",
            maxCharge = "INTEGER",
            maxIso = "INTEGER",
            mzIntervalExtension = "TEXT"
        )
    ),
    alignmenmt_parameters = DBModelR::ModelDefinition(
        table = "alignmenmt_parameters",
        fields = list(
            binSize = "TEXT",
            centerSample = "TEXT",
            response = "TEXT",
            distFun = "TEXT",
            gapInit = "TEXT",
            gapExtend = "TEXT",
            factorDiag = "TEXT",
            factorGap = "TEXT",
            localAlignment = "INTEGER",
            initPenalty = "TEXT",
            bw = "TEXT",
            minFraction = "TEXT",
            minSamples = "TEXT",
            maxFeatures = "TEXT"
        )
    )
)