bug: do not return complex R object (ex glmDS2) #465
Description
It should not be necessary to return complex R objects to the R client: (1) it is a potential vulnerability (potential code execution on R client), (2) data volume transferred is too big and (3) it over complexifies the serialization in JSON format making non-R clients too difficult to implement.
Example of glmDS2 call:
- The returned
familyvalue is a family R object: see assignment at glmDS2.R#L126 - The usage of it in dsBaseClient is simply to get the family name: see assignment ds.glm.R#L568 and usage ds.glm.R#L643
- The JSON serialization falls back to the raw serialization strategy because of the embedded values with complex type. See "family" object:
{
"server1": {
"type": "list",
"attributes": {
"names": {
"type": "character",
"attributes": {},
"value": [
"family",
"info.matrix",
"score.vect",
"numsubs",
"dev",
"Nvalid",
"Nmissing",
"Ntotal",
"disclosure.risk",
"errorMessage2"
]
}
},
"value": [
{
"type": "list",
"attributes": {
"names": {
"type": "character",
"attributes": {},
"value": [
"family",
"link",
"linkfun",
"linkinv",
"variance",
"dev.resids",
"aic",
"mu.eta",
"initialize",
"validmu",
"valideta",
"simulate",
"dispersion"
]
},
"class": {
"type": "character",
"attributes": {},
"value": [
"family"
]
}
},
"value": [
{
"type": "character",
"attributes": {},
"value": [
"binomial"
]
},
{
"type": "character",
"attributes": {},
"value": [
"logit"
]
},
{
"type": "closure",
"attributes": {
"names": {
"type": "character",
"attributes": {},
"value": [
"mu",
""
]
}
},
"value": [
{
"type": "symbol",
"attributes": {},
"value": [
""
]
},
{
"type": "language",
"attributes": {},
"value": [
".Call(C_logit_link, mu)"
]
}
]
},
{
"type": "closure",
"attributes": {
"names": {
"type": "character",
"attributes": {},
"value": [
"eta",
""
]
}
},
"value": [
{
"type": "symbol",
"attributes": {},
"value": [
""
]
},
{
"type": "language",
"attributes": {},
"value": [
".Call(C_logit_linkinv, eta)"
]
}
]
},
{
"type": "closure",
"attributes": {
"names": {
"type": "character",
"attributes": {},
"value": [
"mu",
""
]
}
},
"value": [
{
"type": "symbol",
"attributes": {},
"value": [
""
]
},
{
"type": "language",
"attributes": {},
"value": [
"mu * (1 - mu)"
]
}
]
},
{
"type": "closure",
"attributes": {
"names": {
"type": "character",
"attributes": {},
"value": [
"y",
"mu",
"wt",
""
]
}
},
"value": [
{
"type": "symbol",
"attributes": {},
"value": [
""
]
},
{
"type": "symbol",
"attributes": {},
"value": [
""
]
},
{
"type": "symbol",
"attributes": {},
"value": [
""
]
},
{
"type": "language",
"attributes": {},
"value": [
".Call(C_binomial_dev_resids, y, mu, wt)"
]
}
]
},
{
"type": "closure",
"attributes": {
"names": {
"type": "character",
"attributes": {},
"value": [
"y",
"n",
"mu",
"wt",
"dev",
""
]
}
},
"value": [
{
"type": "symbol",
"attributes": {},
"value": [
""
]
},
{
"type": "symbol",
"attributes": {},
"value": [
""
]
},
{
"type": "symbol",
"attributes": {},
"value": [
""
]
},
{
"type": "symbol",
"attributes": {},
"value": [
""
]
},
{
"type": "symbol",
"attributes": {},
"value": [
""
]
},
{
"type": "language",
"attributes": {},
"value": [
"{",
" m <- if (any(n > 1)) ",
" n",
" else wt",
" -2 * sum(ifelse(m > 0, (wt/m), 0) * dbinom(round(m * y), ",
" round(m), mu, log = TRUE))",
"}"
]
}
]
},
{
"type": "closure",
"attributes": {
"names": {
"type": "character",
"attributes": {},
"value": [
"eta",
""
]
}
},
"value": [
{
"type": "symbol",
"attributes": {},
"value": [
""
]
},
{
"type": "language",
"attributes": {},
"value": [
".Call(C_logit_mu_eta, eta)"
]
}
]
},
{
"type": "language",
"attributes": {},
"value": [
"{",
" if (NCOL(y) == 1) {",
" if (is.factor(y)) ",
" y <- y != levels(y)[1L]",
" n <- rep.int(1, nobs)",
" y[weights == 0] <- 0",
" if (any(y < 0 | y > 1)) ",
" stop(\"y values must be 0 <= y <= 1\")",
" mustart <- (weights * y + 0.5)/(weights + 1)",
" m <- weights * y",
" if (\"binomial\" == \"binomial\" && any(abs(m - round(m)) > ",
" 0.001)) ",
" warning(gettextf(\"non-integer #successes in a %s glm!\", ",
" \"binomial\"), domain = NA)",
" }",
" else if (NCOL(y) == 2) {",
" if (\"binomial\" == \"binomial\" && any(abs(y - round(y)) > ",
" 0.001)) ",
" warning(gettextf(\"non-integer counts in a %s glm!\", ",
" \"binomial\"), domain = NA)",
" n <- (y1 <- y[, 1L]) + y[, 2L]",
" y <- y1/n",
" if (any(n0 <- n == 0)) ",
" y[n0] <- 0",
" weights <- weights * n",
" mustart <- (n * y + 0.5)/(n + 1)",
" }",
" else stop(gettextf(\"for the '%s' family, y must be a vector of 0 and 1's\\nor a 2 column matrix where col 1 is no. successes and col 2 is no. failures\", ",
" \"binomial\"), domain = NA)",
"}"
]
},
{
"type": "closure",
"attributes": {
"names": {
"type": "character",
"attributes": {},
"value": [
"mu",
""
]
}
},
"value": [
{
"type": "symbol",
"attributes": {},
"value": [
""
]
},
{
"type": "language",
"attributes": {},
"value": [
"all(is.finite(mu)) && all(mu > 0 & mu < 1)"
]
}
]
},
{
"type": "closure",
"attributes": {
"names": {
"type": "character",
"attributes": {},
"value": [
"eta",
""
]
}
},
"value": [
{
"type": "symbol",
"attributes": {},
"value": [
""
]
},
{
"type": "logical",
"attributes": {},
"value": [
true
]
}
]
},
{
"type": "closure",
"attributes": {
"names": {
"type": "character",
"attributes": {},
"value": [
"object",
"nsim",
""
]
}
},
"value": [
{
"type": "symbol",
"attributes": {},
"value": [
""
]
},
{
"type": "symbol",
"attributes": {},
"value": [
""
]
},
{
"type": "language",
"attributes": {},
"value": [
"{",
" ftd <- fitted(object)",
" n <- length(ftd)",
" ntot <- n * nsim",
" wts <- object$prior.weights",
" if (any(wts%%1 != 0)) ",
" stop(\"cannot simulate from non-integer prior.weights\")",
" if (!is.null(m <- object$model)) {",
" y <- model.response(m)",
" if (is.factor(y)) {",
" yy <- factor(1 + rbinom(ntot, size = 1, prob = ftd), ",
" labels = levels(y))",
" split(yy, rep(seq_len(nsim), each = n))",
" }",
" else if (is.matrix(y) && ncol(y) == 2) {",
" yy <- vector(\"list\", nsim)",
" for (i in seq_len(nsim)) {",
" Y <- rbinom(n, size = wts, prob = ftd)",
" YY <- cbind(Y, wts - Y)",
" colnames(YY) <- colnames(y)",
" yy[[i]] <- YY",
" }",
" yy",
" }",
" else rbinom(ntot, size = wts, prob = ftd)/wts",
" }",
" else rbinom(ntot, size = wts, prob = ftd)/wts",
"}"
]
}
]
},
{
"type": "double",
"attributes": {},
"value": [
1
]
}
]
},
{
"type": "double",
"attributes": {
"dim": {
"type": "integer",
"attributes": {},
"value": [
4,
4
]
},
"dimnames": {
"type": "list",
"attributes": {},
"value": [
{
"type": "character",
"attributes": {},
"value": [
"(Intercept)",
"GENDER1",
"PM_BMI_CONTINUOUS",
"LAB_HDL"
]
},
{
"type": "character",
"attributes": {},
"value": [
"(Intercept)",
"GENDER1",
"PM_BMI_CONTINUOUS",
"LAB_HDL"
]
}
]
}
},
"value": [
433,
216.5,
11854.745,
680.87462925,
216.5,
216.5,
5813.9525,
351.703075,
11854.745,
5813.9525,
334837.6683,
18532.82128799,
680.87462925,
351.703075,
18532.82128799,
1144.17968051
]
},
{
"type": "double",
"attributes": {
"dim": {
"type": "integer",
"attributes": {},
"value": [
4,
1
]
},
"dimnames": {
"type": "list",
"attributes": {},
"value": [
{
"type": "character",
"attributes": {},
"value": [
"(Intercept)",
"GENDER1",
"PM_BMI_CONTINUOUS",
"LAB_HDL"
]
},
{
"type": "NULL"
}
]
}
},
"value": [
-842,
-424,
-22985.76,
-1327.9215585
]
},
{
"type": "integer",
"attributes": {},
"value": [
1732
]
},
{
"type": "double",
"attributes": {},
"value": [
2401.06183346
]
},
{
"type": "integer",
"attributes": {},
"value": [
1732
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},
{
"type": "integer",
"attributes": {},
"value": [
431
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},
{
"type": "integer",
"attributes": {},
"value": [
2163
]
},
{
"type": "double",
"attributes": {},
"value": [
0
]
},
{
"type": "character",
"attributes": {},
"value": [
"No errors"
]
}
]
}
}