tests/testthat/test-tcplLoadData.R
In USEPA/CompTox-ToxCast-tcpl: ToxCast Data Analysis Pipeline
tcplConf(drvr = "example")
test_that("sc0 loads sc0 data table", {
sc0 <- tcplLoadData(lvl = 0, type = "sc")
expect_true(
is.data.table(sc0)
)
sc0 <- tcplLoadData(lvl = 0L, type = "sc")
expect_true(
is.data.table(sc0)
)
})
test_that("sc1 loads sc1 data table", {
sc1 <- tcplLoadData(lvl = 1, type = "sc")
expect_true(
is.data.table(sc1)
)
sc1 <- tcplLoadData(lvl = 1L, type = "sc")
expect_true(
is.data.table(sc1)
)
})
test_that("sc2 loads sc2 data table", {
sc2 <- tcplLoadData(lvl = 2, type = "sc")
expect_true(
is.data.table(sc2)
)
sc2 <- tcplLoadData(lvl = 2L, type = "sc")
expect_true(
is.data.table(sc2)
)
})
test_that("lvl = 'agg' loads sc agg data table", {
agg <- tcplLoadData(lvl = "agg", type = "sc")
expect_true(
is.data.table(agg)
)
})
test_that("mc0 loads mc0 data table", {
mc0 <- tcplLoadData(lvl = 0, type = "mc")
expect_true(
is.data.table(mc0)
)
mc0 <- tcplLoadData(lvl = 0L, type = "mc")
expect_true(
is.data.table(mc0)
)
})
test_that("mc1 loads mc1 data table", {
mc1 <- tcplLoadData(lvl = 1, type = "mc")
expect_true(
is.data.table(mc1)
)
mc1 <- tcplLoadData(lvl = 1L, type = "mc")
expect_true(
is.data.table(mc1)
)
})
test_that("mc2 loads mc2 data table", {
mc2 <- tcplLoadData(lvl = 2, type = "mc")
expect_true(
is.data.table(mc2)
)
mc2 <- tcplLoadData(lvl = 2L, type = "mc")
expect_true(
is.data.table(mc2)
)
})
test_that("mc3 loads mc3 data table", {
mc3 <- tcplLoadData(lvl = 3, type = "mc")
expect_true(
is.data.table(mc3)
)
mc3 <- tcplLoadData(lvl = 3L, type = "mc")
expect_true(
is.data.table(mc3)
)
})
test_that("mc4 loads mc4 data table", {
mc4 <- tcplLoadData(lvl = 4, type = "mc")
expect_true(
is.data.table(mc4)
)
mc4 <- tcplLoadData(lvl = 4L, type = "mc")
expect_true(
is.data.table(mc4)
)
})
test_that("mc4 !add.fld loads mc4 data table", {
mc4 <- tcplLoadData(lvl = 4, type = "mc", add.fld=FALSE)
expect_true(
is.data.table(mc4)
)
mc4 <- tcplLoadData(lvl = 4L, type = "mc", add.fld=FALSE)
expect_true(
is.data.table(mc4)
)
})
test_that("mc5 loads mc5 data table", {
mc5 <- tcplLoadData(lvl = 5, type = "mc")
expect_true(
is.data.table(mc5)
)
mc5 <- tcplLoadData(lvl = 5L, type = "mc")
expect_true(
is.data.table(mc5)
)
})
test_that("mc5 !add.fld loads mc5 data table", {
mc5 <- tcplLoadData(lvl = 5, type = "mc", add.fld=FALSE)
expect_true(
is.data.table(mc5)
)
mc5 <- tcplLoadData(lvl = 5L, type = "mc", add.fld=FALSE)
expect_true(
is.data.table(mc5)
)
})
test_that("lvl = 'agg' loads mc agg data table", {
agg <- tcplLoadData(lvl = "agg", type = "mc")
expect_true(
is.data.table(agg)
)
})
test_that("invalid input error message", {
expect_error(
tcplLoadData(lvl = "sc", type = 0),
"Invalid 'lvl' and 'type' combination."
)
})
test_that("sc example error message appears", {
expect_error(
tcplLoadData(lvl = 4, type = "sc"),
"example tables for sc0, sc1, sc2, agg available."
)
})
test_that("mc example error message appears", {
expect_error(
tcplLoadData(lvl = 6, type = "mc"),
"example tables for mc0, mc1, mc2, mc3, mc4, mc5, agg available."
)
})
#-------------------------------------------------------------------------------
# Covers testing tcplLoadData with "MySQL" driver
# new method using mocking for tcplQuery function
#-------------------------------------------------------------------------------
# SC0
test_that("tcplLoadData loads sc0 data for one s0id", {
data("sc_test")
mocked <- sc_test$sc0_by_s0id
local_mocked_bindings(
tcplQuery = function(query, db, tbl) {
if (query == "SHOW VARIABLES LIKE 'max_allowed_packet'") sc_test$tcplConfQuery
else mocked[query][[1]]
}
)
tcplConf(drvr = "MySQL", db = "invitrodb") # must include both
dat <- tcplLoadData(type = "sc", lvl = 0, fld = "s0id", val = mocked$s0id)
#expectations
expect_true(is.data.table(dat))
expect_true(nrow(dat) > 0)
expect_true(all(c("s0id", "acid", "spid", "wllt", "wllq", "conc", "rval") %in% colnames(dat)))
expect_true(mocked$s0id %in% dat$s0id)
})
test_that("tcplLoadData loads sc0 data for one acid", {
data("sc_test")
mocked <- sc_test$sc0_by_acid
local_mocked_bindings(
tcplQuery = function(query, db, tbl) {
if (query == "SHOW VARIABLES LIKE 'max_allowed_packet'") sc_test$tcplConfQuery
else mocked[query][[1]]
}
)
tcplConf(drvr = "MySQL", db = "invitrodb") # must include both
dat <- tcplLoadData(type = "sc", lvl = 0, fld = "acid", val = mocked$acid)
#expectations
expect_true(is.data.table(dat))
expect_true(nrow(dat) > 0)
expect_true(all(c("s0id", "acid", "spid", "wllt", "wllq", "conc", "rval") %in% colnames(dat)))
expect_true(mocked$acid %in% dat$acid)
})
# SC1
test_that("tcplLoadData loads sc1 data for one s1id", {
data("sc_test")
mocked <- sc_test$sc1_by_s1id
local_mocked_bindings(
tcplQuery = function(query, db, tbl) {
if (query == "SHOW VARIABLES LIKE 'max_allowed_packet'") sc_test$tcplConfQuery
else mocked[query][[1]]
}
)
tcplConf(drvr = "MySQL", db = "invitrodb") # must include both
dat <- tcplLoadData(type = "sc", lvl = 1, fld = "s1id", val = mocked$s1id)
#expectations
expect_true(is.data.table(dat))
expect_true(nrow(dat) > 0)
expect_true(all(c("s0id", "s1id", "acid", "aeid", "spid", "wllt", "wllq", "conc", "resp") %in% colnames(dat)))
expect_true(mocked$s1id %in% dat$s1id)
})
test_that("tcplLoadData loads sc1 data for one acid", {
data("sc_test")
mocked <- sc_test$sc1_by_acid
local_mocked_bindings(
tcplQuery = function(query, db, tbl) {
if (query == "SHOW VARIABLES LIKE 'max_allowed_packet'") sc_test$tcplConfQuery
else mocked[query][[1]]
}
)
tcplConf(drvr = "MySQL", db = "invitrodb") # must include both
dat <- tcplLoadData(type = "sc", lvl = 1, fld = "acid", val = mocked$acid)
#expectations
expect_true(is.data.table(dat))
expect_true(nrow(dat) > 0)
expect_true(all(c("s0id", "s1id", "acid", "aeid", "spid", "wllt", "wllq", "conc", "resp") %in% colnames(dat)))
expect_true(mocked$acid %in% dat$acid)
})
# SC2
test_that("tcplLoadData loads sc2 data for one s2id", {
data("sc_test")
mocked <- sc_test$sc2_by_s2id
local_mocked_bindings(
tcplQuery = function(query, db, tbl) {
if (query == "SHOW VARIABLES LIKE 'max_allowed_packet'") sc_test$tcplConfQuery
else mocked[query][[1]]
}
)
tcplConf(drvr = "MySQL", db = "invitrodb") # must include both
dat <- tcplLoadData(type = "sc", lvl = 2, fld = "s2id", val = mocked$s2id)
#expectations
expect_true(is.data.table(dat))
expect_true(nrow(dat) > 0)
expect_true(all(c("s2id", "aeid", "spid", "bmad", "max_med", "coff", "hitc") %in% colnames(dat)))
expect_true(mocked$s2id %in% dat$s2id)
})
test_that("tcplLoadData loads sc2 data for one aeid", {
data("sc_test")
mocked <- sc_test$sc2_by_aeid
local_mocked_bindings(
tcplQuery = function(query, db, tbl) {
if (query == "SHOW VARIABLES LIKE 'max_allowed_packet'") sc_test$tcplConfQuery
else mocked[query][[1]]
}
)
tcplConf(drvr = "MySQL", db = "invitrodb") # must include both
dat <- tcplLoadData(type = "sc", lvl = 2, fld = "aeid", val = mocked$aeid)
#expectations
expect_true(is.data.table(dat))
expect_true(nrow(dat) > 0)
expect_true(all(c("s2id", "aeid", "spid", "bmad", "max_med", "coff", "hitc") %in% colnames(dat)))
expect_true(mocked$aeid %in% dat$aeid)
})
# SCagg
test_that("tcplLoadData loads sc 'agg' data for one aeid", {
data("sc_test")
mocked <- sc_test$scagg_by_aeid
local_mocked_bindings(
tcplQuery = function(query, db, tbl) {
if (query == "SHOW VARIABLES LIKE 'max_allowed_packet'") sc_test$tcplConfQuery
else mocked[query][[1]]
}
)
tcplConf(drvr = "MySQL", db = "invitrodb") # must include both
dat <- tcplLoadData(type = "sc", lvl = "agg", fld = "aeid", val = mocked$aeid)
#expectations
expect_true(is.data.table(dat))
expect_true(nrow(dat) > 0)
expect_true(all(c("s0id", "s1id", "s2id", "acid", "aeid", "conc", "resp") %in% colnames(dat)))
expect_true(mocked$aeid %in% dat$aeid)
})
# MC0
test_that("tcplLoadData loads mc0 data for one m0id", {
data("mc_test")
mocked <- mc_test$mc0_by_m0id
local_mocked_bindings(
tcplQuery = function(query, db, tbl) {
if (query == "SHOW VARIABLES LIKE 'max_allowed_packet'") mc_test$tcplConfQuery
else mocked[query][[1]]
}
)
tcplConf(drvr = "MySQL", db = "invitrodb") # must include both
dat <- tcplLoadData(lvl = 0, fld = "m0id", val = mocked$m0id)
#expectations
expect_true(is.data.table(dat))
expect_true(nrow(dat) > 0)
expect_true(all(c("m0id", "acid", "spid", "wllt", "wllq", "conc", "rval") %in% colnames(dat)))
expect_true(mocked$m0id %in% dat$m0id)
})
test_that("tcplLoadData loads mc0 data for one acid", {
data("mc_test")
mocked <- mc_test$mc0_by_acid
local_mocked_bindings(
tcplQuery = function(query, db, tbl) {
if (query == "SHOW VARIABLES LIKE 'max_allowed_packet'") mc_test$tcplConfQuery
else mocked[query][[1]]
}
)
tcplConf(drvr = "MySQL", db = "invitrodb") # must include both
dat <- tcplLoadData(lvl = 0, fld = "acid", val = mocked$acid)
#expectations
expect_true(is.data.table(dat))
expect_true(nrow(dat) > 0)
expect_true(all(c("m0id", "acid", "spid", "wllt", "wllq", "conc", "rval") %in% colnames(dat)))
expect_true(mocked$acid %in% dat$acid)
})
# MC1
test_that("tcplLoadData loads mc1 data for one m1id", {
data("mc_test")
mocked <- mc_test$mc1_by_m1id
local_mocked_bindings(
tcplQuery = function(query, db, tbl) {
if (query == "SHOW VARIABLES LIKE 'max_allowed_packet'") mc_test$tcplConfQuery
else mocked[query][[1]]
}
)
tcplConf(drvr = "MySQL", db = "invitrodb") # must include both
dat <- tcplLoadData(lvl = 1, fld = "m1id", val = mocked$m1id)
#expectations
expect_true(is.data.table(dat))
expect_true(nrow(dat) > 0)
expect_true(all(c("m0id", "m1id", "acid", "spid", "wllt", "wllq", "conc", "rval") %in% colnames(dat)))
expect_true(mocked$m1id %in% dat$m1id)
})
test_that("tcplLoadData loads mc1 data for one acid", {
data("mc_test")
mocked <- mc_test$mc1_by_acid
local_mocked_bindings(
tcplQuery = function(query, db, tbl) {
if (query == "SHOW VARIABLES LIKE 'max_allowed_packet'") mc_test$tcplConfQuery
else mocked[query][[1]]
}
)
tcplConf(drvr = "MySQL", db = "invitrodb") # must include both
dat <- tcplLoadData(lvl = 1, fld = "acid", val = mocked$acid)
#expectations
expect_true(is.data.table(dat))
expect_true(nrow(dat) > 0)
expect_true(all(c("m0id", "m1id", "acid", "spid", "wllt", "wllq", "conc", "rval") %in% colnames(dat)))
expect_true(mocked$acid %in% dat$acid)
})
# MC2
test_that("tcplLoadData loads mc2 data for one m2id", {
data("mc_test")
mocked <- mc_test$mc2_by_m2id
local_mocked_bindings(
tcplQuery = function(query, db, tbl) {
if (query == "SHOW VARIABLES LIKE 'max_allowed_packet'") mc_test$tcplConfQuery
else mocked[query][[1]]
}
)
tcplConf(drvr = "MySQL", db = "invitrodb") # must include both
dat <- tcplLoadData(lvl = 2, fld = "m2id", val = mocked$m2id)
#expectations
expect_true(is.data.table(dat))
expect_true(nrow(dat) > 0)
expect_true(all(c("m0id", "m1id", "m2id", "acid", "spid", "wllt", "wllq", "conc", "rval", "cval") %in% colnames(dat)))
expect_true(mocked$m2id %in% dat$m2id)
})
test_that("tcplLoadData loads mc2 data for one acid", {
data("mc_test")
mocked <- mc_test$mc2_by_acid
local_mocked_bindings(
tcplQuery = function(query, db, tbl) {
if (query == "SHOW VARIABLES LIKE 'max_allowed_packet'") mc_test$tcplConfQuery
else mocked[query][[1]]
}
)
tcplConf(drvr = "MySQL", db = "invitrodb") # must include both
dat <- tcplLoadData(lvl = 2, fld = "acid", val = mocked$acid)
#expectations
expect_true(is.data.table(dat))
expect_true(nrow(dat) > 0)
expect_true(all(c("m0id", "m1id", "m2id", "acid", "spid", "wllt", "wllq", "conc", "rval", "cval") %in% colnames(dat)))
expect_true(mocked$acid %in% dat$acid)
})
# MC3
test_that("tcplLoadData loads mc3 data for one m3id", {
data("mc_test")
mocked <- mc_test$mc3_by_m3id
local_mocked_bindings(
tcplQuery = function(query, db, tbl) {
if (query == "SHOW VARIABLES LIKE 'max_allowed_packet'") mc_test$tcplConfQuery
else mocked[query][[1]]
}
)
tcplConf(drvr = "MySQL", db = "invitrodb") # must include both
dat <- tcplLoadData(lvl = 3, fld = "m3id", val = mocked$m3id)
#expectations
expect_true(is.data.table(dat))
expect_true(nrow(dat) > 0)
expect_true(all(c("m0id", "m1id", "m2id", "m3id", "acid", "aeid", "spid", "wllt", "wllq", "conc", "rval", "resp") %in% colnames(dat)))
expect_true(mocked$m3id %in% dat$m3id)
})
test_that("tcplLoadData loads mc3 data for one aeid", {
data("mc_test")
mocked <- mc_test$mc3_by_aeid
local_mocked_bindings(
tcplQuery = function(query, db, tbl) {
if (query == "SHOW VARIABLES LIKE 'max_allowed_packet'") mc_test$tcplConfQuery
else mocked[query][[1]]
}
)
tcplConf(drvr = "MySQL", db = "invitrodb") # must include both
dat <- tcplLoadData(lvl = 3, fld = "aeid", val = mocked$aeid)
#expectations
expect_true(is.data.table(dat))
expect_true(nrow(dat) > 0)
expect_true(all(c("m0id", "m1id", "m2id", "m3id", "acid", "aeid", "spid", "wllt", "wllq", "conc", "rval", "resp") %in% colnames(dat)))
expect_true(mocked$aeid %in% dat$aeid)
})
# MC4
test_that("tcplLoadData loads mc4 data for one m4id", {
data("mc_test")
mocked <- mc_test$mc4_by_m4id
local_mocked_bindings(
tcplQuery = function(query, db, tbl) {
if (query == "SHOW VARIABLES LIKE 'max_allowed_packet'") mc_test$tcplConfQuery
else mocked[query][[1]]
}
)
tcplConf(drvr = "MySQL", db = "invitrodb") # must include both
dat <- tcplLoadData(lvl = 4, fld = "m4id", val = mocked$m4id)
#expectations
expect_true(is.data.table(dat))
expect_true(nrow(dat) > 0)
expect_true(all(c("m4id", "aeid", "spid", "bmad", "nconc", "nrep", "cnst_aic") %in% colnames(dat)))
expect_true(mocked$m4id %in% dat$m4id)
})
test_that("tcplLoadData loads mc4 data for one aeid with add.fld = FALSE", {
data("mc_test")
mocked <- mc_test$mc4_by_aeid
local_mocked_bindings(
tcplQuery = function(query, db, tbl) {
if (query == "SHOW VARIABLES LIKE 'max_allowed_packet'") mc_test$tcplConfQuery
else mocked[query][[1]]
}
)
tcplConf(drvr = "MySQL", db = "invitrodb") # must include both
dat <- tcplLoadData(lvl = 4, fld = "aeid", val = mocked$aeid, add.fld = FALSE)
#expectations
expect_true(is.data.table(dat))
expect_true(nrow(dat) > 0)
expect_true(all(c("m4id", "aeid", "spid", "bmad", "nconc", "nrep") %in% colnames(dat)))
expect_true(mocked$aeid %in% dat$aeid)
})
# MC5
test_that("tcplLoadData loads mc5 data for one m5id", {
data("mc_test")
mocked <- mc_test$mc5_by_m5id
local_mocked_bindings(
tcplQuery = function(query, db, tbl) {
if (query == "SHOW VARIABLES LIKE 'max_allowed_packet'") mc_test$tcplConfQuery
else mocked[query][[1]]
}
)
tcplConf(drvr = "MySQL", db = "invitrodb") # must include both
dat <- tcplLoadData(lvl = 5, fld = "m5id", val = mocked$m5id)
#expectations
expect_true(is.data.table(dat))
expect_true(nrow(dat) > 0)
expect_true(all(c("m4id", "m5id", "aeid", "spid", "bmad", "nconc", "nrep", "modl", "hitc", "coff", "top") %in% colnames(dat)))
expect_true(mocked$m5id %in% dat$m5id)
})
test_that("tcplLoadData loads mc5 data for one aeid with add.fld = FALSE", {
data("mc_test")
mocked <- mc_test$mc5_by_aeid
local_mocked_bindings(
tcplQuery = function(query, db, tbl) {
if (query == "SHOW VARIABLES LIKE 'max_allowed_packet'") mc_test$tcplConfQuery
else mocked[query][[1]]
}
)
tcplConf(drvr = "MySQL", db = "invitrodb") # must include both
dat <- tcplLoadData(lvl = 5, fld = "aeid", val = mocked$aeid, add.fld = FALSE)
#expectations
expect_true(is.data.table(dat))
expect_true(nrow(dat) > 0)
expect_true(all(c("m4id", "m5id", "aeid", "spid", "bmad", "nconc", "nrep", "modl", "hitc", "coff") %in% colnames(dat)))
expect_true(mocked$aeid %in% dat$aeid)
})
# MC6
test_that("tcplLoadData loads mc6 data for one m6id", {
data("mc_test")
mocked <- mc_test$mc6_by_m6id
local_mocked_bindings(
tcplQuery = function(query, db, tbl) {
if (query == "SHOW VARIABLES LIKE 'max_allowed_packet'") mc_test$tcplConfQuery
else mocked[query][[1]]
}
)
tcplConf(drvr = "MySQL", db = "invitrodb") # must include both
dat <- tcplLoadData(lvl = 6, fld = "m6id", val = mocked$m6id)
#expectations
expect_true(is.data.table(dat))
expect_true(nrow(dat) > 0)
expect_true(all(c("m4id", "m5id", "m6id", "aeid", "spid", "bmad", "nconc", "nrep", "flag") %in% colnames(dat)))
expect_true(mocked$m6id %in% dat$m6id)
})
test_that("tcplLoadData loads mc6 data for one aeid", {
data("mc_test")
mocked <- mc_test$mc6_by_aeid
local_mocked_bindings(
tcplQuery = function(query, db, tbl) {
if (query == "SHOW VARIABLES LIKE 'max_allowed_packet'") mc_test$tcplConfQuery
else mocked[query][[1]]
}
)
tcplConf(drvr = "MySQL", db = "invitrodb") # must include both
dat <- tcplLoadData(lvl = 6, fld = "aeid", val = mocked$aeid)
#expectations
expect_true(is.data.table(dat))
expect_true(nrow(dat) > 0)
expect_true(all(c("m4id", "m5id", "m6id", "aeid", "spid", "bmad", "nconc", "nrep", "flag") %in% colnames(dat)))
expect_true(mocked$aeid %in% dat$aeid)
})
# MC7
test_that("tcplLoadData loads mc7 data for one m7id", {
data("mc_test")
mocked <- mc_test$mc7_by_m7id
local_mocked_bindings(
tcplQuery = function(query, db, tbl) {
if (query == "SHOW VARIABLES LIKE 'max_allowed_packet'") mc_test$tcplConfQuery
else mocked[query][[1]]
}
)
tcplConf(drvr = "MySQL", db = "invitrodb") # must include both
dat <- tcplLoadData(lvl = 7, fld = "m7id", val = mocked$m7id)
#expectations
expect_true(is.data.table(dat))
expect_true(nrow(dat) > 0)
expect_true(all(c("m4id", "m7id", "aeid", "spid", "bmad", "nconc", "nrep", "aed_val") %in% colnames(dat)))
expect_true(mocked$m7id %in% dat$m7id)
})
test_that("tcplLoadData loads mc7 data for one aeid", {
data("mc_test")
mocked <- mc_test$mc7_by_aeid
local_mocked_bindings(
tcplQuery = function(query, db, tbl) {
if (query == "SHOW VARIABLES LIKE 'max_allowed_packet'") mc_test$tcplConfQuery
else mocked[query][[1]]
}
)
tcplConf(drvr = "MySQL", db = "invitrodb") # must include both
dat <- tcplLoadData(lvl = 7, fld = "aeid", val = mocked$aeid)
#expectations
expect_true(is.data.table(dat))
expect_true(nrow(dat) > 0)
expect_true(all(c("m4id", "m7id", "aeid", "spid", "bmad", "nconc", "nrep", "aed_val") %in% colnames(dat)))
expect_true(mocked$aeid %in% dat$aeid)
})
# MCagg
test_that("tcplLoadData loads mc 'agg' data for one aeid", {
data("mc_test")
mocked <- mc_test$mcagg_by_aeid
local_mocked_bindings(
tcplQuery = function(query, db, tbl) {
if (query == "SHOW VARIABLES LIKE 'max_allowed_packet'") mc_test$tcplConfQuery
else mocked[query][[1]]
}
)
tcplConf(drvr = "MySQL", db = "invitrodb") # must include both
dat <- tcplLoadData(lvl = "agg", fld = "aeid", val = mocked$aeid)
#expectations
expect_true(is.data.table(dat))
expect_true(nrow(dat) > 0)
expect_true(all(c("m0id", "m1id", "m2id", "m3id", "m4id", "acid", "aeid", "spid",
"conc", "resp", "bmad", "nconc", "nrep") %in% colnames(dat)))
expect_true(mocked$aeid %in% dat$aeid)
})
# error cases
test_that("invalid lvl and type error message", {
data("mc_test")
mocked <- mc_test$mcagg_by_aeid
local_mocked_bindings(
tcplQuery = function(query, db, tbl) {
if (query == "SHOW VARIABLES LIKE 'max_allowed_packet'") mc_test$tcplConfQuery
else mocked[query][[1]]
}
)
tcplConf(drvr = "MySQL", db = "invitrodb") # must include both
expect_error(
tcplLoadData(lvl = 5, type = "sc"),
"Invalid 'lvl' and 'type' combination."
)
})
test_that("missing val error message", {
data("mc_test")
mocked <- mc_test$mcagg_by_aeid
local_mocked_bindings(
tcplQuery = function(query, db, tbl) {
if (query == "SHOW VARIABLES LIKE 'max_allowed_packet'") mc_test$tcplConfQuery
else mocked[query][[1]]
}
)
tcplConf(drvr = "MySQL", db = "invitrodb") # must include both
expect_error(
tcplLoadData(lvl = 5, type = "mc", fld = "aeid"),
"'val' cannot be NULL check that a valid value was provided for the specified field"
)
})
#-------------------------------------------------------------------------------
# Covers testing tcplLoadData with "API" driver
# Using httptest mocking to automatically save json responses from http requests
# NOTE -- updates to the CTX API may mean stored json files are out of date. In
# this case, delete the 'ctx' folder and rerun this ENTIRE test file (temporarily
# replacing the 'apikey' string with a valid key) to repopulate the stored
# .jsons. These will likely be huge and will need to be edited by hand to reduce
# their sizes. To do this, open the file(s) and remove all but one element of
# the outer array -- we don't need more than one endpoint-sample. When editing
# down the files, it is recommended to make sure the same aeid is present in each
# selected endpoint-sample, or assay for the saved assay.json response, to make
# sure every test has its necessary data still available.
#-------------------------------------------------------------------------------
httptest::with_mock_dir("ctx", {
apikey <- "apikey"
tcplConf(pass = apikey,
drvr = "API")
data(test_api)
test_that("level 3 API data loads by m4id", {
expect_no_error(dat <- tcplLoadData(lvl = 3, fld = "m4id", val = test_api$m4id, add.fld = FALSE))
expect_true(is.data.table(dat))
expect_true(nrow(dat) > 1)
expect_true(all(c("m4id", "spid", "conc", "aeid") %in% colnames(dat)))
expect_true(test_api$m4id %in% dat$m4id)
})
test_that("level 3 API data loads by aeid", {
expect_no_error(dat <- tcplLoadData(lvl = 3, fld = "aeid", val = test_api$aeid, add.fld = FALSE))
expect_true(is.data.table(dat))
expect_true(nrow(dat) > 1)
expect_true(all(c("aeid", "spid", "conc") %in% colnames(dat)))
expect_true(test_api$aeid %in% dat$aeid)
})
test_that("level 3 API data loads by dtxsid", {
expect_no_error(dat <- tcplLoadData(lvl = 3, fld = "dtxsid", val = test_api$dtxsid, add.fld = FALSE))
expect_true(is.data.table(dat))
expect_true(nrow(dat) > 1)
expect_true(all(c("dtxsid", "spid", "conc", "aeid") %in% colnames(dat)))
expect_true(test_api$dtxsid %in% dat$dtxsid)
})
test_that("level 3 API data loads by spid", {
expect_no_error(dat <- tcplLoadData(lvl = 3, fld = "spid", val = test_api$spid, add.fld = FALSE))
expect_true(is.data.table(dat))
expect_true(nrow(dat) > 1)
expect_true(all(c("aeid", "spid", "conc") %in% colnames(dat)))
expect_true(test_api$spid %in% dat$spid)
})
test_that("level 4 API data loads by m4id", {
expect_no_error(dat <- tcplLoadData(lvl = 4, fld = "m4id", val = test_api$m4id, add.fld = FALSE))
expect_true(is.data.table(dat))
expect_equal(nrow(dat), 1)
expect_true(all(c("m4id", "aeid", "bmad", "spid", "max_med", "nconc", "nrep") %in% colnames(dat)))
expect_true(test_api$m4id %in% dat$m4id)
})
test_that("level 4 API data loads by aeid", {
expect_no_error(dat <- tcplLoadData(lvl = 4, fld = "aeid", val = test_api$aeid, add.fld = FALSE))
expect_true(is.data.table(dat))
expect_true(nrow(dat) > 0)
expect_true(all(c("m4id", "aeid", "spid", "bmad", "max_med", "nconc", "nrep") %in% colnames(dat)))
expect_true(test_api$aeid %in% dat$aeid)
})
test_that("level 4 API data loads by dtxsid", {
expect_no_error(dat <- tcplLoadData(lvl = 4, fld = "dtxsid", val = test_api$dtxsid, add.fld = FALSE))
expect_true(is.data.table(dat))
expect_true(nrow(dat) > 0)
expect_true(all(c("dtxsid", "spid", "m4id", "aeid", "bmad", "max_med", "nconc", "nrep") %in% colnames(dat)))
expect_true(test_api$dtxsid %in% dat$dtxsid)
})
test_that("level 4 API data loads by spid", {
expect_no_error(dat <- tcplLoadData(lvl = 4, fld = "spid", val = test_api$spid, add.fld = FALSE))
expect_true(is.data.table(dat))
expect_true(nrow(dat) > 0)
expect_true(all(c("spid", "m4id", "aeid", "bmad", "max_med", "nconc", "nrep") %in% colnames(dat)))
expect_true(test_api$spid %in% dat$spid)
})
test_that("level 5 API data loads by m4id", {
expect_no_error(dat <- tcplLoadData(lvl = 5, fld = "m4id", val = test_api$m4id, add.fld = FALSE))
expect_true(is.data.table(dat))
expect_equal(nrow(dat), 1)
expect_true(all(c("m4id", "m5id", "aeid", "spid", "bmad", "max_med", "nconc", "nrep", "modl", "hitc", "coff", "model_type") %in% colnames(dat)))
expect_true(test_api$m4id %in% dat$m4id)
})
test_that("level 5 API data loads by aeid", {
expect_no_error(dat <- tcplLoadData(lvl = 5, fld = "aeid", val = test_api$aeid, add.fld = FALSE))
expect_true(is.data.table(dat))
expect_true(nrow(dat) > 0)
expect_true(all(c("m4id", "m5id", "aeid", "spid", "bmad", "max_med", "nconc", "nrep", "modl", "hitc", "coff", "model_type") %in% colnames(dat)))
expect_true(test_api$aeid %in% dat$aeid)
})
test_that("level 5 API data loads by dtxsid", {
expect_no_error(dat <- tcplLoadData(lvl = 5, fld = "dtxsid", val = test_api$dtxsid, add.fld = FALSE))
expect_true(is.data.table(dat))
expect_true(nrow(dat) > 0)
expect_true(all(c("dtxsid", "m4id", "m5id", "aeid", "spid", "bmad", "max_med", "nconc", "nrep", "modl", "hitc", "coff", "model_type") %in% colnames(dat)))
expect_true(test_api$dtxsid %in% dat$dtxsid)
})
test_that("level 5 API data loads by spid", {
expect_no_error(dat <- tcplLoadData(lvl = 5, fld = "spid", val = test_api$spid, add.fld = FALSE))
expect_true(is.data.table(dat))
expect_true(nrow(dat) > 0)
expect_true(all(c("m4id", "m5id", "aeid", "spid", "bmad", "max_med", "nconc", "nrep", "modl", "hitc", "coff", "model_type") %in% colnames(dat)))
expect_true(test_api$spid %in% dat$spid)
})
test_that("level 6 API data loads by m4id", {
expect_no_error(dat <- tcplLoadData(lvl = 6, fld = "m4id", val = test_api$m4id, add.fld = FALSE))
expect_true(is.data.table(dat))
expect_true(nrow(dat) > 0)
expect_true(all(c("m4id", "m5id", "aeid", "spid", "bmad", "max_med", "nconc", "nrep", "flag") %in% colnames(dat)))
expect_true(test_api$m4id %in% dat$m4id)
})
test_that("level 6 API data loads by aeid", {
expect_no_error(dat <- tcplLoadData(lvl = 6, fld = "aeid", val = test_api$aeid, add.fld = FALSE))
expect_true(is.data.table(dat))
expect_true(nrow(dat) > 0)
expect_true(all(c("m4id", "m5id", "aeid", "spid", "bmad", "max_med", "nconc", "nrep", "flag") %in% colnames(dat)))
expect_true(test_api$aeid %in% dat$aeid)
})
test_that("level 6 API data loads by dtxsid", {
expect_no_error(dat <- tcplLoadData(lvl = 6, fld = "dtxsid", val = test_api$dtxsid, add.fld = FALSE))
expect_true(is.data.table(dat))
expect_true(nrow(dat) > 0)
expect_true(all(c("dtxsid", "m4id", "m5id", "aeid", "spid", "bmad", "max_med", "nconc", "nrep", "flag") %in% colnames(dat)))
expect_true(test_api$dtxsid %in% dat$dtxsid)
})
test_that("level 6 API data loads by spid", {
expect_no_error(dat <- tcplLoadData(lvl = 6, fld = "spid", val = test_api$spid, add.fld = FALSE))
expect_true(is.data.table(dat))
expect_true(nrow(dat) > 0)
expect_true(all(c("m4id", "m5id", "aeid", "spid", "bmad", "max_med", "nconc", "nrep", "flag") %in% colnames(dat)))
expect_true(test_api$spid %in% dat$spid)
})
test_that("agg level API data loads by m4id", {
expect_no_error(dat <- tcplLoadData(lvl = "agg", fld = "m4id", val = test_api$m4id, add.fld = FALSE))
expect_true(is.data.table(dat))
expect_true(nrow(dat) > 1)
expect_true(all(c("m4id", "aeid", "spid", "bmad", "logc", "resp", "max_med", "nconc", "nrep") %in% colnames(dat)))
expect_true(test_api$m4id %in% dat$m4id)
})
test_that("agg level API data loads by aeid", {
expect_no_error(dat <- tcplLoadData(lvl = "agg", fld = "aeid", val = test_api$aeid, add.fld = FALSE))
expect_true(is.data.table(dat))
expect_true(nrow(dat) > 1)
expect_true(all(c("m4id", "aeid", "spid", "bmad", "logc", "resp", "max_med", "nconc", "nrep") %in% colnames(dat)))
expect_true(test_api$aeid %in% dat$aeid)
})
test_that("agg level API data loads by dtxsid", {
expect_no_error(dat <- tcplLoadData(lvl = "agg", fld = "dtxsid", val = test_api$dtxsid, add.fld = FALSE))
expect_true(is.data.table(dat))
expect_true(nrow(dat) > 1)
expect_true(all(c("dtxsid", "m4id", "aeid", "spid", "bmad", "logc", "resp", "max_med", "nconc", "nrep") %in% colnames(dat)))
expect_true(test_api$dtxsid %in% dat$dtxsid)
})
test_that("agg level API data loads by spid", {
expect_no_error(dat <- tcplLoadData(lvl = "agg", fld = "spid", val = test_api$spid, add.fld = FALSE))
expect_true(is.data.table(dat))
expect_true(nrow(dat) > 1)
expect_true(all(c("m4id", "aeid", "spid", "bmad", "logc", "resp", "max_med", "nconc", "nrep") %in% colnames(dat)))
expect_true(test_api$spid %in% dat$spid)
})
# error cases
test_that("more than one field results in error", {
expect_error(tcplLoadData(lvl = 5, fld = c("aeid", "spid"), val = list(test_api$aeid, test_api$spid), add.fld = FALSE),
"'fld' must be length 1")
})
test_that("fields outside of dtxsid, aeid, m4id, spid result in error", {
expect_error(tcplLoadData(lvl = 3, fld = "acid", val = test_api$acid, add.fld = FALSE),
"'fld' must be one of 'AEID', 'SPID', 'm4id', or 'DTXSID'")
})
test_that("levels other than 3-6 and 'agg' result in error", {
expect_error(tcplLoadData(lvl = 2, fld = "aeid", val = test_api$aeid, add.fld = FALSE),
"Only lvl = c(3,4,5,6) and 'agg' are supported using API data as source.", fixed = TRUE)
})
test_that("type = 'sc' result in error", {
expect_error(tcplLoadData(type = "sc", lvl = 2, fld = "aeid", val = test_api$aeid, add.fld = FALSE),
"Only type = 'mc' is supported using API data as source.")
})
test_that("data not found results in null data.table", {
expect_warning(dat <- tcplLoadData(lvl = 3, fld = "aeid", val = 0, add.fld = FALSE),
"Data not found for the following 'fld' and 'val' combos:
AEID: 0", fixed = TRUE)
expect_equal(nrow(dat), 0)
expect_warning(dat <- tcplLoadData(lvl = 4, fld = "spid", val = "fakespid", add.fld = FALSE),
"Data not found for the following 'fld' and 'val' combos:
SPID: fakespid", fixed = TRUE)
expect_equal(nrow(dat), 0)
expect_warning(dat <- tcplLoadData(lvl = 5, fld = "dtxsid", val = "fakedtxsid", add.fld = FALSE),
"Data not found for the following 'fld' and 'val' combos:
DTXSID: fakedtxsid", fixed = TRUE)
expect_equal(nrow(dat), 0)
expect_warning(dat <- tcplLoadData(lvl = 6, fld = "m4id", val = 0, add.fld = FALSE),
"Data not found for the following 'fld' and 'val' combos:
m4id: 0", fixed = TRUE)
expect_equal(nrow(dat), 0)
})
test_that("some data not found results in warning", {
expect_warning(dat <- tcplLoadData(lvl = 3, fld = "aeid", val = c(0, test_api$aeid), add.fld = FALSE),
"Data not found for the following 'fld' and 'val' combos:
AEID: 0", fixed = TRUE)
expect_true(nrow(dat) > 0)
expect_warning(dat <- tcplLoadData(lvl = 4, fld = "spid", val = c("fakespid", test_api$spid), add.fld = FALSE),
"Data not found for the following 'fld' and 'val' combos:
SPID: fakespid", fixed = TRUE)
expect_true(nrow(dat) > 0)
expect_warning(dat <- tcplLoadData(lvl = 5, fld = "dtxsid", val = c("fakedtxsid", test_api$dtxsid), add.fld = FALSE),
"Data not found for the following 'fld' and 'val' combos:
DTXSID: fakedtxsid", fixed = TRUE)
expect_true(nrow(dat) > 0)
expect_warning(dat <- tcplLoadData(lvl = 6, fld = "m4id", val = c(0, test_api$m4id), add.fld = FALSE),
"Data not found for the following 'fld' and 'val' combos:
m4id: 0", fixed = TRUE)
expect_true(nrow(dat) > 0)
})
})
USEPA/CompTox-ToxCast-tcpl documentation built on June 2, 2025, 3:13 a.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
tcplConf(drvr = "example")
test_that("sc0 loads sc0 data table", {
sc0 <- tcplLoadData(lvl = 0, type = "sc")
expect_true(
is.data.table(sc0)
)
sc0 <- tcplLoadData(lvl = 0L, type = "sc")
expect_true(
is.data.table(sc0)
)
})
test_that("sc1 loads sc1 data table", {
sc1 <- tcplLoadData(lvl = 1, type = "sc")
expect_true(
is.data.table(sc1)
)
sc1 <- tcplLoadData(lvl = 1L, type = "sc")
expect_true(
is.data.table(sc1)
)
})
test_that("sc2 loads sc2 data table", {
sc2 <- tcplLoadData(lvl = 2, type = "sc")
expect_true(
is.data.table(sc2)
)
sc2 <- tcplLoadData(lvl = 2L, type = "sc")
expect_true(
is.data.table(sc2)
)
})
test_that("lvl = 'agg' loads sc agg data table", {
agg <- tcplLoadData(lvl = "agg", type = "sc")
expect_true(
is.data.table(agg)
)
})
test_that("mc0 loads mc0 data table", {
mc0 <- tcplLoadData(lvl = 0, type = "mc")
expect_true(
is.data.table(mc0)
)
mc0 <- tcplLoadData(lvl = 0L, type = "mc")
expect_true(
is.data.table(mc0)
)
})
test_that("mc1 loads mc1 data table", {
mc1 <- tcplLoadData(lvl = 1, type = "mc")
expect_true(
is.data.table(mc1)
)
mc1 <- tcplLoadData(lvl = 1L, type = "mc")
expect_true(
is.data.table(mc1)
)
})
test_that("mc2 loads mc2 data table", {
mc2 <- tcplLoadData(lvl = 2, type = "mc")
expect_true(
is.data.table(mc2)
)
mc2 <- tcplLoadData(lvl = 2L, type = "mc")
expect_true(
is.data.table(mc2)
)
})
test_that("mc3 loads mc3 data table", {
mc3 <- tcplLoadData(lvl = 3, type = "mc")
expect_true(
is.data.table(mc3)
)
mc3 <- tcplLoadData(lvl = 3L, type = "mc")
expect_true(
is.data.table(mc3)
)
})
test_that("mc4 loads mc4 data table", {
mc4 <- tcplLoadData(lvl = 4, type = "mc")
expect_true(
is.data.table(mc4)
)
mc4 <- tcplLoadData(lvl = 4L, type = "mc")
expect_true(
is.data.table(mc4)
)
})
test_that("mc4 !add.fld loads mc4 data table", {
mc4 <- tcplLoadData(lvl = 4, type = "mc", add.fld=FALSE)
expect_true(
is.data.table(mc4)
)
mc4 <- tcplLoadData(lvl = 4L, type = "mc", add.fld=FALSE)
expect_true(
is.data.table(mc4)
)
})
test_that("mc5 loads mc5 data table", {
mc5 <- tcplLoadData(lvl = 5, type = "mc")
expect_true(
is.data.table(mc5)
)
mc5 <- tcplLoadData(lvl = 5L, type = "mc")
expect_true(
is.data.table(mc5)
)
})
test_that("mc5 !add.fld loads mc5 data table", {
mc5 <- tcplLoadData(lvl = 5, type = "mc", add.fld=FALSE)
expect_true(
is.data.table(mc5)
)
mc5 <- tcplLoadData(lvl = 5L, type = "mc", add.fld=FALSE)
expect_true(
is.data.table(mc5)
)
})
test_that("lvl = 'agg' loads mc agg data table", {
agg <- tcplLoadData(lvl = "agg", type = "mc")
expect_true(
is.data.table(agg)
)
})
test_that("invalid input error message", {
expect_error(
tcplLoadData(lvl = "sc", type = 0),
"Invalid 'lvl' and 'type' combination."
)
})
test_that("sc example error message appears", {
expect_error(
tcplLoadData(lvl = 4, type = "sc"),
"example tables for sc0, sc1, sc2, agg available."
)
})
test_that("mc example error message appears", {
expect_error(
tcplLoadData(lvl = 6, type = "mc"),
"example tables for mc0, mc1, mc2, mc3, mc4, mc5, agg available."
)
})
#-------------------------------------------------------------------------------
# Covers testing tcplLoadData with "MySQL" driver
# new method using mocking for tcplQuery function
#-------------------------------------------------------------------------------
# SC0
test_that("tcplLoadData loads sc0 data for one s0id", {
data("sc_test")
mocked <- sc_test$sc0_by_s0id
local_mocked_bindings(
tcplQuery = function(query, db, tbl) {
if (query == "SHOW VARIABLES LIKE 'max_allowed_packet'") sc_test$tcplConfQuery
else mocked[query][[1]]
}
)
tcplConf(drvr = "MySQL", db = "invitrodb") # must include both
dat <- tcplLoadData(type = "sc", lvl = 0, fld = "s0id", val = mocked$s0id)
#expectations
expect_true(is.data.table(dat))
expect_true(nrow(dat) > 0)
expect_true(all(c("s0id", "acid", "spid", "wllt", "wllq", "conc", "rval") %in% colnames(dat)))
expect_true(mocked$s0id %in% dat$s0id)
})
test_that("tcplLoadData loads sc0 data for one acid", {
data("sc_test")
mocked <- sc_test$sc0_by_acid
local_mocked_bindings(
tcplQuery = function(query, db, tbl) {
if (query == "SHOW VARIABLES LIKE 'max_allowed_packet'") sc_test$tcplConfQuery
else mocked[query][[1]]
}
)
tcplConf(drvr = "MySQL", db = "invitrodb") # must include both
dat <- tcplLoadData(type = "sc", lvl = 0, fld = "acid", val = mocked$acid)
#expectations
expect_true(is.data.table(dat))
expect_true(nrow(dat) > 0)
expect_true(all(c("s0id", "acid", "spid", "wllt", "wllq", "conc", "rval") %in% colnames(dat)))
expect_true(mocked$acid %in% dat$acid)
})
# SC1
test_that("tcplLoadData loads sc1 data for one s1id", {
data("sc_test")
mocked <- sc_test$sc1_by_s1id
local_mocked_bindings(
tcplQuery = function(query, db, tbl) {
if (query == "SHOW VARIABLES LIKE 'max_allowed_packet'") sc_test$tcplConfQuery
else mocked[query][[1]]
}
)
tcplConf(drvr = "MySQL", db = "invitrodb") # must include both
dat <- tcplLoadData(type = "sc", lvl = 1, fld = "s1id", val = mocked$s1id)
#expectations
expect_true(is.data.table(dat))
expect_true(nrow(dat) > 0)
expect_true(all(c("s0id", "s1id", "acid", "aeid", "spid", "wllt", "wllq", "conc", "resp") %in% colnames(dat)))
expect_true(mocked$s1id %in% dat$s1id)
})
test_that("tcplLoadData loads sc1 data for one acid", {
data("sc_test")
mocked <- sc_test$sc1_by_acid
local_mocked_bindings(
tcplQuery = function(query, db, tbl) {
if (query == "SHOW VARIABLES LIKE 'max_allowed_packet'") sc_test$tcplConfQuery
else mocked[query][[1]]
}
)
tcplConf(drvr = "MySQL", db = "invitrodb") # must include both
dat <- tcplLoadData(type = "sc", lvl = 1, fld = "acid", val = mocked$acid)
#expectations
expect_true(is.data.table(dat))
expect_true(nrow(dat) > 0)
expect_true(all(c("s0id", "s1id", "acid", "aeid", "spid", "wllt", "wllq", "conc", "resp") %in% colnames(dat)))
expect_true(mocked$acid %in% dat$acid)
})
# SC2
test_that("tcplLoadData loads sc2 data for one s2id", {
data("sc_test")
mocked <- sc_test$sc2_by_s2id
local_mocked_bindings(
tcplQuery = function(query, db, tbl) {
if (query == "SHOW VARIABLES LIKE 'max_allowed_packet'") sc_test$tcplConfQuery
else mocked[query][[1]]
}
)
tcplConf(drvr = "MySQL", db = "invitrodb") # must include both
dat <- tcplLoadData(type = "sc", lvl = 2, fld = "s2id", val = mocked$s2id)
#expectations
expect_true(is.data.table(dat))
expect_true(nrow(dat) > 0)
expect_true(all(c("s2id", "aeid", "spid", "bmad", "max_med", "coff", "hitc") %in% colnames(dat)))
expect_true(mocked$s2id %in% dat$s2id)
})
test_that("tcplLoadData loads sc2 data for one aeid", {
data("sc_test")
mocked <- sc_test$sc2_by_aeid
local_mocked_bindings(
tcplQuery = function(query, db, tbl) {
if (query == "SHOW VARIABLES LIKE 'max_allowed_packet'") sc_test$tcplConfQuery
else mocked[query][[1]]
}
)
tcplConf(drvr = "MySQL", db = "invitrodb") # must include both
dat <- tcplLoadData(type = "sc", lvl = 2, fld = "aeid", val = mocked$aeid)
#expectations
expect_true(is.data.table(dat))
expect_true(nrow(dat) > 0)
expect_true(all(c("s2id", "aeid", "spid", "bmad", "max_med", "coff", "hitc") %in% colnames(dat)))
expect_true(mocked$aeid %in% dat$aeid)
})
# SCagg
test_that("tcplLoadData loads sc 'agg' data for one aeid", {
data("sc_test")
mocked <- sc_test$scagg_by_aeid
local_mocked_bindings(
tcplQuery = function(query, db, tbl) {
if (query == "SHOW VARIABLES LIKE 'max_allowed_packet'") sc_test$tcplConfQuery
else mocked[query][[1]]
}
)
tcplConf(drvr = "MySQL", db = "invitrodb") # must include both
dat <- tcplLoadData(type = "sc", lvl = "agg", fld = "aeid", val = mocked$aeid)
#expectations
expect_true(is.data.table(dat))
expect_true(nrow(dat) > 0)
expect_true(all(c("s0id", "s1id", "s2id", "acid", "aeid", "conc", "resp") %in% colnames(dat)))
expect_true(mocked$aeid %in% dat$aeid)
})
# MC0
test_that("tcplLoadData loads mc0 data for one m0id", {
data("mc_test")
mocked <- mc_test$mc0_by_m0id
local_mocked_bindings(
tcplQuery = function(query, db, tbl) {
if (query == "SHOW VARIABLES LIKE 'max_allowed_packet'") mc_test$tcplConfQuery
else mocked[query][[1]]
}
)
tcplConf(drvr = "MySQL", db = "invitrodb") # must include both
dat <- tcplLoadData(lvl = 0, fld = "m0id", val = mocked$m0id)
#expectations
expect_true(is.data.table(dat))
expect_true(nrow(dat) > 0)
expect_true(all(c("m0id", "acid", "spid", "wllt", "wllq", "conc", "rval") %in% colnames(dat)))
expect_true(mocked$m0id %in% dat$m0id)
})
test_that("tcplLoadData loads mc0 data for one acid", {
data("mc_test")
mocked <- mc_test$mc0_by_acid
local_mocked_bindings(
tcplQuery = function(query, db, tbl) {
if (query == "SHOW VARIABLES LIKE 'max_allowed_packet'") mc_test$tcplConfQuery
else mocked[query][[1]]
}
)
tcplConf(drvr = "MySQL", db = "invitrodb") # must include both
dat <- tcplLoadData(lvl = 0, fld = "acid", val = mocked$acid)
#expectations
expect_true(is.data.table(dat))
expect_true(nrow(dat) > 0)
expect_true(all(c("m0id", "acid", "spid", "wllt", "wllq", "conc", "rval") %in% colnames(dat)))
expect_true(mocked$acid %in% dat$acid)
})
# MC1
test_that("tcplLoadData loads mc1 data for one m1id", {
data("mc_test")
mocked <- mc_test$mc1_by_m1id
local_mocked_bindings(
tcplQuery = function(query, db, tbl) {
if (query == "SHOW VARIABLES LIKE 'max_allowed_packet'") mc_test$tcplConfQuery
else mocked[query][[1]]
}
)
tcplConf(drvr = "MySQL", db = "invitrodb") # must include both
dat <- tcplLoadData(lvl = 1, fld = "m1id", val = mocked$m1id)
#expectations
expect_true(is.data.table(dat))
expect_true(nrow(dat) > 0)
expect_true(all(c("m0id", "m1id", "acid", "spid", "wllt", "wllq", "conc", "rval") %in% colnames(dat)))
expect_true(mocked$m1id %in% dat$m1id)
})
test_that("tcplLoadData loads mc1 data for one acid", {
data("mc_test")
mocked <- mc_test$mc1_by_acid
local_mocked_bindings(
tcplQuery = function(query, db, tbl) {
if (query == "SHOW VARIABLES LIKE 'max_allowed_packet'") mc_test$tcplConfQuery
else mocked[query][[1]]
}
)
tcplConf(drvr = "MySQL", db = "invitrodb") # must include both
dat <- tcplLoadData(lvl = 1, fld = "acid", val = mocked$acid)
#expectations
expect_true(is.data.table(dat))
expect_true(nrow(dat) > 0)
expect_true(all(c("m0id", "m1id", "acid", "spid", "wllt", "wllq", "conc", "rval") %in% colnames(dat)))
expect_true(mocked$acid %in% dat$acid)
})
# MC2
test_that("tcplLoadData loads mc2 data for one m2id", {
data("mc_test")
mocked <- mc_test$mc2_by_m2id
local_mocked_bindings(
tcplQuery = function(query, db, tbl) {
if (query == "SHOW VARIABLES LIKE 'max_allowed_packet'") mc_test$tcplConfQuery
else mocked[query][[1]]
}
)
tcplConf(drvr = "MySQL", db = "invitrodb") # must include both
dat <- tcplLoadData(lvl = 2, fld = "m2id", val = mocked$m2id)
#expectations
expect_true(is.data.table(dat))
expect_true(nrow(dat) > 0)
expect_true(all(c("m0id", "m1id", "m2id", "acid", "spid", "wllt", "wllq", "conc", "rval", "cval") %in% colnames(dat)))
expect_true(mocked$m2id %in% dat$m2id)
})
test_that("tcplLoadData loads mc2 data for one acid", {
data("mc_test")
mocked <- mc_test$mc2_by_acid
local_mocked_bindings(
tcplQuery = function(query, db, tbl) {
if (query == "SHOW VARIABLES LIKE 'max_allowed_packet'") mc_test$tcplConfQuery
else mocked[query][[1]]
}
)
tcplConf(drvr = "MySQL", db = "invitrodb") # must include both
dat <- tcplLoadData(lvl = 2, fld = "acid", val = mocked$acid)
#expectations
expect_true(is.data.table(dat))
expect_true(nrow(dat) > 0)
expect_true(all(c("m0id", "m1id", "m2id", "acid", "spid", "wllt", "wllq", "conc", "rval", "cval") %in% colnames(dat)))
expect_true(mocked$acid %in% dat$acid)
})
# MC3
test_that("tcplLoadData loads mc3 data for one m3id", {
data("mc_test")
mocked <- mc_test$mc3_by_m3id
local_mocked_bindings(
tcplQuery = function(query, db, tbl) {
if (query == "SHOW VARIABLES LIKE 'max_allowed_packet'") mc_test$tcplConfQuery
else mocked[query][[1]]
}
)
tcplConf(drvr = "MySQL", db = "invitrodb") # must include both
dat <- tcplLoadData(lvl = 3, fld = "m3id", val = mocked$m3id)
#expectations
expect_true(is.data.table(dat))
expect_true(nrow(dat) > 0)
expect_true(all(c("m0id", "m1id", "m2id", "m3id", "acid", "aeid", "spid", "wllt", "wllq", "conc", "rval", "resp") %in% colnames(dat)))
expect_true(mocked$m3id %in% dat$m3id)
})
test_that("tcplLoadData loads mc3 data for one aeid", {
data("mc_test")
mocked <- mc_test$mc3_by_aeid
local_mocked_bindings(
tcplQuery = function(query, db, tbl) {
if (query == "SHOW VARIABLES LIKE 'max_allowed_packet'") mc_test$tcplConfQuery
else mocked[query][[1]]
}
)
tcplConf(drvr = "MySQL", db = "invitrodb") # must include both
dat <- tcplLoadData(lvl = 3, fld = "aeid", val = mocked$aeid)
#expectations
expect_true(is.data.table(dat))
expect_true(nrow(dat) > 0)
expect_true(all(c("m0id", "m1id", "m2id", "m3id", "acid", "aeid", "spid", "wllt", "wllq", "conc", "rval", "resp") %in% colnames(dat)))
expect_true(mocked$aeid %in% dat$aeid)
})
# MC4
test_that("tcplLoadData loads mc4 data for one m4id", {
data("mc_test")
mocked <- mc_test$mc4_by_m4id
local_mocked_bindings(
tcplQuery = function(query, db, tbl) {
if (query == "SHOW VARIABLES LIKE 'max_allowed_packet'") mc_test$tcplConfQuery
else mocked[query][[1]]
}
)
tcplConf(drvr = "MySQL", db = "invitrodb") # must include both
dat <- tcplLoadData(lvl = 4, fld = "m4id", val = mocked$m4id)
#expectations
expect_true(is.data.table(dat))
expect_true(nrow(dat) > 0)
expect_true(all(c("m4id", "aeid", "spid", "bmad", "nconc", "nrep", "cnst_aic") %in% colnames(dat)))
expect_true(mocked$m4id %in% dat$m4id)
})
test_that("tcplLoadData loads mc4 data for one aeid with add.fld = FALSE", {
data("mc_test")
mocked <- mc_test$mc4_by_aeid
local_mocked_bindings(
tcplQuery = function(query, db, tbl) {
if (query == "SHOW VARIABLES LIKE 'max_allowed_packet'") mc_test$tcplConfQuery
else mocked[query][[1]]
}
)
tcplConf(drvr = "MySQL", db = "invitrodb") # must include both
dat <- tcplLoadData(lvl = 4, fld = "aeid", val = mocked$aeid, add.fld = FALSE)
#expectations
expect_true(is.data.table(dat))
expect_true(nrow(dat) > 0)
expect_true(all(c("m4id", "aeid", "spid", "bmad", "nconc", "nrep") %in% colnames(dat)))
expect_true(mocked$aeid %in% dat$aeid)
})
# MC5
test_that("tcplLoadData loads mc5 data for one m5id", {
data("mc_test")
mocked <- mc_test$mc5_by_m5id
local_mocked_bindings(
tcplQuery = function(query, db, tbl) {
if (query == "SHOW VARIABLES LIKE 'max_allowed_packet'") mc_test$tcplConfQuery
else mocked[query][[1]]
}
)
tcplConf(drvr = "MySQL", db = "invitrodb") # must include both
dat <- tcplLoadData(lvl = 5, fld = "m5id", val = mocked$m5id)
#expectations
expect_true(is.data.table(dat))
expect_true(nrow(dat) > 0)
expect_true(all(c("m4id", "m5id", "aeid", "spid", "bmad", "nconc", "nrep", "modl", "hitc", "coff", "top") %in% colnames(dat)))
expect_true(mocked$m5id %in% dat$m5id)
})
test_that("tcplLoadData loads mc5 data for one aeid with add.fld = FALSE", {
data("mc_test")
mocked <- mc_test$mc5_by_aeid
local_mocked_bindings(
tcplQuery = function(query, db, tbl) {
if (query == "SHOW VARIABLES LIKE 'max_allowed_packet'") mc_test$tcplConfQuery
else mocked[query][[1]]
}
)
tcplConf(drvr = "MySQL", db = "invitrodb") # must include both
dat <- tcplLoadData(lvl = 5, fld = "aeid", val = mocked$aeid, add.fld = FALSE)
#expectations
expect_true(is.data.table(dat))
expect_true(nrow(dat) > 0)
expect_true(all(c("m4id", "m5id", "aeid", "spid", "bmad", "nconc", "nrep", "modl", "hitc", "coff") %in% colnames(dat)))
expect_true(mocked$aeid %in% dat$aeid)
})
# MC6
test_that("tcplLoadData loads mc6 data for one m6id", {
data("mc_test")
mocked <- mc_test$mc6_by_m6id
local_mocked_bindings(
tcplQuery = function(query, db, tbl) {
if (query == "SHOW VARIABLES LIKE 'max_allowed_packet'") mc_test$tcplConfQuery
else mocked[query][[1]]
}
)
tcplConf(drvr = "MySQL", db = "invitrodb") # must include both
dat <- tcplLoadData(lvl = 6, fld = "m6id", val = mocked$m6id)
#expectations
expect_true(is.data.table(dat))
expect_true(nrow(dat) > 0)
expect_true(all(c("m4id", "m5id", "m6id", "aeid", "spid", "bmad", "nconc", "nrep", "flag") %in% colnames(dat)))
expect_true(mocked$m6id %in% dat$m6id)
})
test_that("tcplLoadData loads mc6 data for one aeid", {
data("mc_test")
mocked <- mc_test$mc6_by_aeid
local_mocked_bindings(
tcplQuery = function(query, db, tbl) {
if (query == "SHOW VARIABLES LIKE 'max_allowed_packet'") mc_test$tcplConfQuery
else mocked[query][[1]]
}
)
tcplConf(drvr = "MySQL", db = "invitrodb") # must include both
dat <- tcplLoadData(lvl = 6, fld = "aeid", val = mocked$aeid)
#expectations
expect_true(is.data.table(dat))
expect_true(nrow(dat) > 0)
expect_true(all(c("m4id", "m5id", "m6id", "aeid", "spid", "bmad", "nconc", "nrep", "flag") %in% colnames(dat)))
expect_true(mocked$aeid %in% dat$aeid)
})
# MC7
test_that("tcplLoadData loads mc7 data for one m7id", {
data("mc_test")
mocked <- mc_test$mc7_by_m7id
local_mocked_bindings(
tcplQuery = function(query, db, tbl) {
if (query == "SHOW VARIABLES LIKE 'max_allowed_packet'") mc_test$tcplConfQuery
else mocked[query][[1]]
}
)
tcplConf(drvr = "MySQL", db = "invitrodb") # must include both
dat <- tcplLoadData(lvl = 7, fld = "m7id", val = mocked$m7id)
#expectations
expect_true(is.data.table(dat))
expect_true(nrow(dat) > 0)
expect_true(all(c("m4id", "m7id", "aeid", "spid", "bmad", "nconc", "nrep", "aed_val") %in% colnames(dat)))
expect_true(mocked$m7id %in% dat$m7id)
})
test_that("tcplLoadData loads mc7 data for one aeid", {
data("mc_test")
mocked <- mc_test$mc7_by_aeid
local_mocked_bindings(
tcplQuery = function(query, db, tbl) {
if (query == "SHOW VARIABLES LIKE 'max_allowed_packet'") mc_test$tcplConfQuery
else mocked[query][[1]]
}
)
tcplConf(drvr = "MySQL", db = "invitrodb") # must include both
dat <- tcplLoadData(lvl = 7, fld = "aeid", val = mocked$aeid)
#expectations
expect_true(is.data.table(dat))
expect_true(nrow(dat) > 0)
expect_true(all(c("m4id", "m7id", "aeid", "spid", "bmad", "nconc", "nrep", "aed_val") %in% colnames(dat)))
expect_true(mocked$aeid %in% dat$aeid)
})
# MCagg
test_that("tcplLoadData loads mc 'agg' data for one aeid", {
data("mc_test")
mocked <- mc_test$mcagg_by_aeid
local_mocked_bindings(
tcplQuery = function(query, db, tbl) {
if (query == "SHOW VARIABLES LIKE 'max_allowed_packet'") mc_test$tcplConfQuery
else mocked[query][[1]]
}
)
tcplConf(drvr = "MySQL", db = "invitrodb") # must include both
dat <- tcplLoadData(lvl = "agg", fld = "aeid", val = mocked$aeid)
#expectations
expect_true(is.data.table(dat))
expect_true(nrow(dat) > 0)
expect_true(all(c("m0id", "m1id", "m2id", "m3id", "m4id", "acid", "aeid", "spid",
"conc", "resp", "bmad", "nconc", "nrep") %in% colnames(dat)))
expect_true(mocked$aeid %in% dat$aeid)
})
# error cases
test_that("invalid lvl and type error message", {
data("mc_test")
mocked <- mc_test$mcagg_by_aeid
local_mocked_bindings(
tcplQuery = function(query, db, tbl) {
if (query == "SHOW VARIABLES LIKE 'max_allowed_packet'") mc_test$tcplConfQuery
else mocked[query][[1]]
}
)
tcplConf(drvr = "MySQL", db = "invitrodb") # must include both
expect_error(
tcplLoadData(lvl = 5, type = "sc"),
"Invalid 'lvl' and 'type' combination."
)
})
test_that("missing val error message", {
data("mc_test")
mocked <- mc_test$mcagg_by_aeid
local_mocked_bindings(
tcplQuery = function(query, db, tbl) {
if (query == "SHOW VARIABLES LIKE 'max_allowed_packet'") mc_test$tcplConfQuery
else mocked[query][[1]]
}
)
tcplConf(drvr = "MySQL", db = "invitrodb") # must include both
expect_error(
tcplLoadData(lvl = 5, type = "mc", fld = "aeid"),
"'val' cannot be NULL check that a valid value was provided for the specified field"
)
})
#-------------------------------------------------------------------------------
# Covers testing tcplLoadData with "API" driver
# Using httptest mocking to automatically save json responses from http requests
# NOTE -- updates to the CTX API may mean stored json files are out of date. In
# this case, delete the 'ctx' folder and rerun this ENTIRE test file (temporarily
# replacing the 'apikey' string with a valid key) to repopulate the stored
# .jsons. These will likely be huge and will need to be edited by hand to reduce
# their sizes. To do this, open the file(s) and remove all but one element of
# the outer array -- we don't need more than one endpoint-sample. When editing
# down the files, it is recommended to make sure the same aeid is present in each
# selected endpoint-sample, or assay for the saved assay.json response, to make
# sure every test has its necessary data still available.
#-------------------------------------------------------------------------------
httptest::with_mock_dir("ctx", {
apikey <- "apikey"
tcplConf(pass = apikey,
drvr = "API")
data(test_api)
test_that("level 3 API data loads by m4id", {
expect_no_error(dat <- tcplLoadData(lvl = 3, fld = "m4id", val = test_api$m4id, add.fld = FALSE))
expect_true(is.data.table(dat))
expect_true(nrow(dat) > 1)
expect_true(all(c("m4id", "spid", "conc", "aeid") %in% colnames(dat)))
expect_true(test_api$m4id %in% dat$m4id)
})
test_that("level 3 API data loads by aeid", {
expect_no_error(dat <- tcplLoadData(lvl = 3, fld = "aeid", val = test_api$aeid, add.fld = FALSE))
expect_true(is.data.table(dat))
expect_true(nrow(dat) > 1)
expect_true(all(c("aeid", "spid", "conc") %in% colnames(dat)))
expect_true(test_api$aeid %in% dat$aeid)
})
test_that("level 3 API data loads by dtxsid", {
expect_no_error(dat <- tcplLoadData(lvl = 3, fld = "dtxsid", val = test_api$dtxsid, add.fld = FALSE))
expect_true(is.data.table(dat))
expect_true(nrow(dat) > 1)
expect_true(all(c("dtxsid", "spid", "conc", "aeid") %in% colnames(dat)))
expect_true(test_api$dtxsid %in% dat$dtxsid)
})
test_that("level 3 API data loads by spid", {
expect_no_error(dat <- tcplLoadData(lvl = 3, fld = "spid", val = test_api$spid, add.fld = FALSE))
expect_true(is.data.table(dat))
expect_true(nrow(dat) > 1)
expect_true(all(c("aeid", "spid", "conc") %in% colnames(dat)))
expect_true(test_api$spid %in% dat$spid)
})
test_that("level 4 API data loads by m4id", {
expect_no_error(dat <- tcplLoadData(lvl = 4, fld = "m4id", val = test_api$m4id, add.fld = FALSE))
expect_true(is.data.table(dat))
expect_equal(nrow(dat), 1)
expect_true(all(c("m4id", "aeid", "bmad", "spid", "max_med", "nconc", "nrep") %in% colnames(dat)))
expect_true(test_api$m4id %in% dat$m4id)
})
test_that("level 4 API data loads by aeid", {
expect_no_error(dat <- tcplLoadData(lvl = 4, fld = "aeid", val = test_api$aeid, add.fld = FALSE))
expect_true(is.data.table(dat))
expect_true(nrow(dat) > 0)
expect_true(all(c("m4id", "aeid", "spid", "bmad", "max_med", "nconc", "nrep") %in% colnames(dat)))
expect_true(test_api$aeid %in% dat$aeid)
})
test_that("level 4 API data loads by dtxsid", {
expect_no_error(dat <- tcplLoadData(lvl = 4, fld = "dtxsid", val = test_api$dtxsid, add.fld = FALSE))
expect_true(is.data.table(dat))
expect_true(nrow(dat) > 0)
expect_true(all(c("dtxsid", "spid", "m4id", "aeid", "bmad", "max_med", "nconc", "nrep") %in% colnames(dat)))
expect_true(test_api$dtxsid %in% dat$dtxsid)
})
test_that("level 4 API data loads by spid", {
expect_no_error(dat <- tcplLoadData(lvl = 4, fld = "spid", val = test_api$spid, add.fld = FALSE))
expect_true(is.data.table(dat))
expect_true(nrow(dat) > 0)
expect_true(all(c("spid", "m4id", "aeid", "bmad", "max_med", "nconc", "nrep") %in% colnames(dat)))
expect_true(test_api$spid %in% dat$spid)
})
test_that("level 5 API data loads by m4id", {
expect_no_error(dat <- tcplLoadData(lvl = 5, fld = "m4id", val = test_api$m4id, add.fld = FALSE))
expect_true(is.data.table(dat))
expect_equal(nrow(dat), 1)
expect_true(all(c("m4id", "m5id", "aeid", "spid", "bmad", "max_med", "nconc", "nrep", "modl", "hitc", "coff", "model_type") %in% colnames(dat)))
expect_true(test_api$m4id %in% dat$m4id)
})
test_that("level 5 API data loads by aeid", {
expect_no_error(dat <- tcplLoadData(lvl = 5, fld = "aeid", val = test_api$aeid, add.fld = FALSE))
expect_true(is.data.table(dat))
expect_true(nrow(dat) > 0)
expect_true(all(c("m4id", "m5id", "aeid", "spid", "bmad", "max_med", "nconc", "nrep", "modl", "hitc", "coff", "model_type") %in% colnames(dat)))
expect_true(test_api$aeid %in% dat$aeid)
})
test_that("level 5 API data loads by dtxsid", {
expect_no_error(dat <- tcplLoadData(lvl = 5, fld = "dtxsid", val = test_api$dtxsid, add.fld = FALSE))
expect_true(is.data.table(dat))
expect_true(nrow(dat) > 0)
expect_true(all(c("dtxsid", "m4id", "m5id", "aeid", "spid", "bmad", "max_med", "nconc", "nrep", "modl", "hitc", "coff", "model_type") %in% colnames(dat)))
expect_true(test_api$dtxsid %in% dat$dtxsid)
})
test_that("level 5 API data loads by spid", {
expect_no_error(dat <- tcplLoadData(lvl = 5, fld = "spid", val = test_api$spid, add.fld = FALSE))
expect_true(is.data.table(dat))
expect_true(nrow(dat) > 0)
expect_true(all(c("m4id", "m5id", "aeid", "spid", "bmad", "max_med", "nconc", "nrep", "modl", "hitc", "coff", "model_type") %in% colnames(dat)))
expect_true(test_api$spid %in% dat$spid)
})
test_that("level 6 API data loads by m4id", {
expect_no_error(dat <- tcplLoadData(lvl = 6, fld = "m4id", val = test_api$m4id, add.fld = FALSE))
expect_true(is.data.table(dat))
expect_true(nrow(dat) > 0)
expect_true(all(c("m4id", "m5id", "aeid", "spid", "bmad", "max_med", "nconc", "nrep", "flag") %in% colnames(dat)))
expect_true(test_api$m4id %in% dat$m4id)
})
test_that("level 6 API data loads by aeid", {
expect_no_error(dat <- tcplLoadData(lvl = 6, fld = "aeid", val = test_api$aeid, add.fld = FALSE))
expect_true(is.data.table(dat))
expect_true(nrow(dat) > 0)
expect_true(all(c("m4id", "m5id", "aeid", "spid", "bmad", "max_med", "nconc", "nrep", "flag") %in% colnames(dat)))
expect_true(test_api$aeid %in% dat$aeid)
})
test_that("level 6 API data loads by dtxsid", {
expect_no_error(dat <- tcplLoadData(lvl = 6, fld = "dtxsid", val = test_api$dtxsid, add.fld = FALSE))
expect_true(is.data.table(dat))
expect_true(nrow(dat) > 0)
expect_true(all(c("dtxsid", "m4id", "m5id", "aeid", "spid", "bmad", "max_med", "nconc", "nrep", "flag") %in% colnames(dat)))
expect_true(test_api$dtxsid %in% dat$dtxsid)
})
test_that("level 6 API data loads by spid", {
expect_no_error(dat <- tcplLoadData(lvl = 6, fld = "spid", val = test_api$spid, add.fld = FALSE))
expect_true(is.data.table(dat))
expect_true(nrow(dat) > 0)
expect_true(all(c("m4id", "m5id", "aeid", "spid", "bmad", "max_med", "nconc", "nrep", "flag") %in% colnames(dat)))
expect_true(test_api$spid %in% dat$spid)
})
test_that("agg level API data loads by m4id", {
expect_no_error(dat <- tcplLoadData(lvl = "agg", fld = "m4id", val = test_api$m4id, add.fld = FALSE))
expect_true(is.data.table(dat))
expect_true(nrow(dat) > 1)
expect_true(all(c("m4id", "aeid", "spid", "bmad", "logc", "resp", "max_med", "nconc", "nrep") %in% colnames(dat)))
expect_true(test_api$m4id %in% dat$m4id)
})
test_that("agg level API data loads by aeid", {
expect_no_error(dat <- tcplLoadData(lvl = "agg", fld = "aeid", val = test_api$aeid, add.fld = FALSE))
expect_true(is.data.table(dat))
expect_true(nrow(dat) > 1)
expect_true(all(c("m4id", "aeid", "spid", "bmad", "logc", "resp", "max_med", "nconc", "nrep") %in% colnames(dat)))
expect_true(test_api$aeid %in% dat$aeid)
})
test_that("agg level API data loads by dtxsid", {
expect_no_error(dat <- tcplLoadData(lvl = "agg", fld = "dtxsid", val = test_api$dtxsid, add.fld = FALSE))
expect_true(is.data.table(dat))
expect_true(nrow(dat) > 1)
expect_true(all(c("dtxsid", "m4id", "aeid", "spid", "bmad", "logc", "resp", "max_med", "nconc", "nrep") %in% colnames(dat)))
expect_true(test_api$dtxsid %in% dat$dtxsid)
})
test_that("agg level API data loads by spid", {
expect_no_error(dat <- tcplLoadData(lvl = "agg", fld = "spid", val = test_api$spid, add.fld = FALSE))
expect_true(is.data.table(dat))
expect_true(nrow(dat) > 1)
expect_true(all(c("m4id", "aeid", "spid", "bmad", "logc", "resp", "max_med", "nconc", "nrep") %in% colnames(dat)))
expect_true(test_api$spid %in% dat$spid)
})
# error cases
test_that("more than one field results in error", {
expect_error(tcplLoadData(lvl = 5, fld = c("aeid", "spid"), val = list(test_api$aeid, test_api$spid), add.fld = FALSE),
"'fld' must be length 1")
})
test_that("fields outside of dtxsid, aeid, m4id, spid result in error", {
expect_error(tcplLoadData(lvl = 3, fld = "acid", val = test_api$acid, add.fld = FALSE),
"'fld' must be one of 'AEID', 'SPID', 'm4id', or 'DTXSID'")
})
test_that("levels other than 3-6 and 'agg' result in error", {
expect_error(tcplLoadData(lvl = 2, fld = "aeid", val = test_api$aeid, add.fld = FALSE),
"Only lvl = c(3,4,5,6) and 'agg' are supported using API data as source.", fixed = TRUE)
})
test_that("type = 'sc' result in error", {
expect_error(tcplLoadData(type = "sc", lvl = 2, fld = "aeid", val = test_api$aeid, add.fld = FALSE),
"Only type = 'mc' is supported using API data as source.")
})
test_that("data not found results in null data.table", {
expect_warning(dat <- tcplLoadData(lvl = 3, fld = "aeid", val = 0, add.fld = FALSE),
"Data not found for the following 'fld' and 'val' combos:
AEID: 0", fixed = TRUE)
expect_equal(nrow(dat), 0)
expect_warning(dat <- tcplLoadData(lvl = 4, fld = "spid", val = "fakespid", add.fld = FALSE),
"Data not found for the following 'fld' and 'val' combos:
SPID: fakespid", fixed = TRUE)
expect_equal(nrow(dat), 0)
expect_warning(dat <- tcplLoadData(lvl = 5, fld = "dtxsid", val = "fakedtxsid", add.fld = FALSE),
"Data not found for the following 'fld' and 'val' combos:
DTXSID: fakedtxsid", fixed = TRUE)
expect_equal(nrow(dat), 0)
expect_warning(dat <- tcplLoadData(lvl = 6, fld = "m4id", val = 0, add.fld = FALSE),
"Data not found for the following 'fld' and 'val' combos:
m4id: 0", fixed = TRUE)
expect_equal(nrow(dat), 0)
})
test_that("some data not found results in warning", {
expect_warning(dat <- tcplLoadData(lvl = 3, fld = "aeid", val = c(0, test_api$aeid), add.fld = FALSE),
"Data not found for the following 'fld' and 'val' combos:
AEID: 0", fixed = TRUE)
expect_true(nrow(dat) > 0)
expect_warning(dat <- tcplLoadData(lvl = 4, fld = "spid", val = c("fakespid", test_api$spid), add.fld = FALSE),
"Data not found for the following 'fld' and 'val' combos:
SPID: fakespid", fixed = TRUE)
expect_true(nrow(dat) > 0)
expect_warning(dat <- tcplLoadData(lvl = 5, fld = "dtxsid", val = c("fakedtxsid", test_api$dtxsid), add.fld = FALSE),
"Data not found for the following 'fld' and 'val' combos:
DTXSID: fakedtxsid", fixed = TRUE)
expect_true(nrow(dat) > 0)
expect_warning(dat <- tcplLoadData(lvl = 6, fld = "m4id", val = c(0, test_api$m4id), add.fld = FALSE),
"Data not found for the following 'fld' and 'val' combos:
m4id: 0", fixed = TRUE)
expect_true(nrow(dat) > 0)
})
})
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.