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Merge pull request #282 from USEPA/198-update-github-actions-to-inclu…
…de-dev-branch Large update to unit test suite including mocking invitrodb and CTX API data
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| Original file line number | Diff line number | Diff line change |
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@@ -74,9 +74,9 @@ tcplConf <- function (drvr = NULL, user = NULL, pass = NULL, host = NULL, | |
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| if (drvr == "API") { | ||
| options("TCPL_DRVR" = "API") | ||
| if (is.null(pass)) stop("'API' driver requires an API-key, supply it to | ||
| the 'pass' parameter. To request a key, send an | ||
| email to [email protected].") | ||
| if (is.null(pass)) stop("'API' driver requires an API-key, supply it to ", | ||
| "the 'pass' parameter. To request a key, send an ", | ||
| "email to [email protected].") | ||
| if (is.null(host)) options("TCPL_HOST" = "https://api-ccte.epa.gov/bioactivity") | ||
| register_ctx_api_key(key = pass) | ||
| } | ||
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,161 @@ | ||
| #==============================================================================# | ||
| # NOTE: This script is written such that it is run from 'top' to 'bottom' | ||
| # or programmatically via the Terminal. | ||
| # ('R CMD BATCH --vanilla <script.R>'.) | ||
| # Please do not jump around when running this script. | ||
| #==============================================================================# | ||
| # NOTE: You MUST temporarily update tcplQuery() by adding a line at the top of the | ||
| # function: print(query). | ||
| # This is because the queries will be captured from output and saved as | ||
| # part of the mocking data. | ||
| #==============================================================================# | ||
| ## r packages | ||
| devtools::load_all() | ||
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| library(here) | ||
| library(dplyr) | ||
| library(stringr) | ||
| #---------------------------# | ||
| ## code to prepare `mc_test` dataset goes here | ||
| # source the user ID, password, host, and database information for connection | ||
| # - NOTE: To replicate one will need to save their own 'db_cred.R', including | ||
| # the 'userid', 'userpwd', 'host', and DB collection via 'ivtdb'. | ||
| source(file = here::here("data-raw/db_cred.R"),verbose = FALSE) | ||
| # connect to the DB | ||
| tcplConf(user = userid, | ||
| pass = userpwd, | ||
| host = host, | ||
| db = ivtdb, | ||
| drvr = "MySQL") | ||
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| # pick endpoints and ids | ||
| # load the number of rows and max hitc per aeid | ||
| mc5_counts <- tcplQuery("SELECT DISTINCT aeid, | ||
| COUNT( aeid ) as n, | ||
| max(hitc) as max_hitc | ||
| FROM invitrodb.mc5 GROUP BY aeid") | ||
| # filter to only include where at least one sample is active and n < 10 | ||
| mc5_counts <- mc5_counts %>% filter(max_hitc > 0.9 & n == 2) | ||
| # pick one aeid | ||
| aeid <- selected <- mc5_counts[sample(1:nrow(mc5_counts),size = 1,replace = FALSE),aeid] | ||
| # obtain the acid for the example dataset | ||
| acid <- tcplLoadAcid(fld = 'aeid',val = aeid)$acid | ||
| # pick one sample/row from each level (lvl 3 contains ids back to lvl 0 and lvl 6 does back to lvl 4) | ||
| l3 <- tcplLoadData(lvl = 3, fld = "acid", val = acid) | ||
| l3_sample1 <- l3[sample(1:nrow(l3),size = 1,replace = FALSE)] | ||
| l3_sample2 <- l3[sample(1:nrow(l3),size = 2,replace = FALSE)] | ||
| l5 <- tcplLoadData(lvl = 5, fld = "aeid", val = aeid, add.fld = FALSE) | ||
| l5_sample1 <- l5[sample(1:nrow(l5),size = 1,replace = FALSE)] | ||
| l5_sample2 <- l5[sample(1:nrow(l5),size = 2,replace = FALSE)] | ||
| l6 <- tcplLoadData(lvl = 6, fld = "aeid", val = aeid, add.fld = FALSE) | ||
| l6_sample1 <- l6[sample(1:nrow(l6),size = 1,replace = FALSE)] | ||
| l6_sample2 <- l6[sample(1:nrow(l6),size = 2,replace = FALSE)] | ||
| l7 <- tcplLoadData(lvl = 7, fld = "aeid", val = aeid, add.fld = FALSE) | ||
| l7_sample1 <- l7[sample(1:nrow(l7),size = 1,replace = FALSE)] | ||
| l7_sample2 <- l7[sample(1:nrow(l7),size = 2,replace = FALSE)] | ||
| # pick compare.val endpoints and ids | ||
| # be sure to only allow to choose from endpoints with the same number of samples | ||
| mc5_counts <- filter(mc5_counts, n == mc5_counts[aeid == selected]$n & aeid != selected) | ||
| compare.aeid <- mc5_counts[sample(1:nrow(mc5_counts),size = 1,replace = FALSE),aeid] | ||
| compare.l5 <- tcplLoadData(lvl = 5, fld = "aeid", val = compare.aeid) | ||
| compare.l5_sample1 <- compare.l5[sample(1:nrow(compare.l5),size = 1,replace = FALSE)] | ||
| compare.l5_sample2 <- compare.l5[sample(1:nrow(compare.l5),size = 2,replace = FALSE)] | ||
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| get_query_data <- function(lvl, fld, val, compare.val = NULL, add.fld = TRUE, func = "tcplLoadData") { | ||
| message(compare.val) | ||
| if (func == "tcplLoadData") { | ||
| # IMPORTANT || MUST ADD TEMPORARY LINE TO TCPLQUERY -------------------------- | ||
| # add temporary line to top of tcplQuery to get the query string: print(query) | ||
| query_strings <- capture.output(result<-tcplLoadData(lvl = lvl, fld = fld, val = val, add.fld = add.fld)) | ||
| } else if (func == "tcplPlot") { | ||
| query_strings <- capture.output(result<-tcplPlot(type = "mc", fld = fld, | ||
| val = val, compare.val = compare.val, | ||
| output = "pdf", multi = TRUE, flags = TRUE, | ||
| fileprefix = "temp_tcplPlot")) | ||
| file.remove(stringr::str_subset(list.files(), "^temp_tcplPlot")) # clean up | ||
| } | ||
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| query_strings <- unique(gsub("\\\\", "\\\"", gsub("\"", "", gsub("\\\\n", "\\\n", gsub("\\[1\\] ", "", query_strings))))) | ||
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| # use queries to save data | ||
| dat <- lapply(query_strings, function(query_string) { | ||
| return(tcplQuery(query_string)) | ||
| }) | ||
| names(dat) <- query_strings | ||
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| # also store fld and val in list object for use in test case | ||
| dat[fld] <- val | ||
| if (!is.null(compare.val)) dat[sprintf("compare.%s", fld)] <- compare.val | ||
| return(dat) | ||
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| } | ||
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| # to add more tests with new/different data to test-tcplLoadData.R, add lines below and run script | ||
| mc_test <- list( | ||
| tcplConfQuery = tcplQuery("SHOW VARIABLES LIKE 'max_allowed_packet'"), | ||
| mc0_by_m0id = get_query_data(lvl = 0, fld = "m0id", val = l3_sample1$m0id), | ||
| mc0_by_acid = get_query_data(lvl = 0, fld = "acid", val = acid), | ||
| mc1_by_m1id = get_query_data(lvl = 1, fld = "m1id", val = l3_sample1$m1id), | ||
| mc1_by_acid = get_query_data(lvl = 1, fld = "acid", val = acid), | ||
| mc2_by_m2id = get_query_data(lvl = 2, fld = "m2id", val = l3_sample1$m2id), | ||
| mc2_by_acid = get_query_data(lvl = 2, fld = "acid", val = acid), | ||
| mc3_by_m3id = get_query_data(lvl = 3, fld = "m3id", val = l3_sample1$m3id), | ||
| mc3_by_aeid = get_query_data(lvl = 3, fld = "aeid", val = aeid), | ||
| mc4_by_m4id = get_query_data(lvl = 4, fld = "m4id", val = l5_sample1$m4id), | ||
| mc4_by_aeid = get_query_data(lvl = 4, fld = "aeid", val = aeid, add.fld = FALSE), | ||
| mc5_by_m5id = get_query_data(lvl = 5, fld = "m5id", val = l5_sample1$m5id), | ||
| mc5_by_aeid = get_query_data(lvl = 5, fld = "aeid", val = aeid, add.fld = FALSE), | ||
| mc6_by_m6id = get_query_data(lvl = 6, fld = "m6id", val = l6_sample1$m6id), | ||
| mc6_by_aeid = get_query_data(lvl = 6, fld = "aeid", val = aeid), | ||
| mc7_by_m7id = get_query_data(lvl = 7, fld = "m7id", val = l7_sample1$m7id), | ||
| mc7_by_aeid = get_query_data(lvl = 7, fld = "aeid", val = aeid), | ||
| mcagg_by_aeid = get_query_data(lvl = "agg", fld = "aeid", val = aeid), | ||
| plot_single_m4id = get_query_data(fld = "m4id", | ||
| val = l5_sample1$m4id, | ||
| func = "tcplPlot"), | ||
| plot_multiple_m4id = get_query_data(fld = "m4id", | ||
| val = list(l5_sample2$m4id), | ||
| func = "tcplPlot"), | ||
| plot_single_aeid = get_query_data(fld = "aeid", | ||
| val = aeid, | ||
| func = "tcplPlot"), | ||
| plot_multiple_aeid = get_query_data(fld = "aeid", | ||
| val = list(c(aeid, compare.aeid)), | ||
| func = "tcplPlot"), | ||
| plot_single_spid = get_query_data(fld = c("spid", "aeid"), | ||
| val = list(l5_sample1$spid, aeid), | ||
| func = "tcplPlot"), | ||
| plot_multiple_spid = get_query_data(fld = c("spid", "aeid"), | ||
| val = list(l5_sample2$spid, aeid), | ||
| func = "tcplPlot"), | ||
| plot_single_m4id_compare = get_query_data(fld = "m4id", | ||
| val = l5_sample1$m4id, | ||
| compare.val = compare.l5_sample1$m4id, | ||
| func = "tcplPlot"), | ||
| plot_multiple_m4id_compare = get_query_data(fld = "m4id", | ||
| val = list(l5_sample2$m4id), | ||
| compare.val = list(compare.l5_sample2$m4id), | ||
| func = "tcplPlot"), | ||
| plot_single_aeid_compare = get_query_data(fld = "aeid", | ||
| val = aeid, | ||
| compare.val = compare.aeid, | ||
| func = "tcplPlot"), | ||
| plot_multiple_aeid_compare = get_query_data(fld = "aeid", | ||
| val = list(c(aeid, compare.aeid)), | ||
| compare.val = list(c(compare.aeid, aeid)), | ||
| func = "tcplPlot"), | ||
| plot_single_spid_compare = get_query_data(fld = c("spid", "aeid"), | ||
| val = list(l5_sample1$spid, aeid), | ||
| compare.val = list(compare.l5_sample1$spid, compare.aeid), | ||
| func = "tcplPlot"), | ||
| plot_multiple_spid_compare = get_query_data(fld = c("spid", "aeid"), | ||
| val = list(l5_sample2$spid, aeid), | ||
| compare.val = list(compare.l5_sample2$spid, compare.aeid), | ||
| func = "tcplPlot") | ||
| ) | ||
| #---------------------------# | ||
| ## save the data | ||
| usethis::use_data(mc_test, overwrite = TRUE) | ||
| #---------------------------# |
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