Nothing
tests/testthat/test-00-stacomir.R
In stacomiR: Fish Migration Monitoring
context("stacomi base connection")
# while crashing in some test for reportFonctionnement DF or report_dc,
#the program will set time to GMT, this will cause some errors hard to understand in some of
# the classes (report_mig, report_mig_mult), with the following you can check this problem
# test_that("Test that the program is running under the right locale",{
# skip_on_cran()
# if(Sys.info()["sysname"] == "Linux")
# expect_equal(Sys.getlocale(category = "LC_TIME"),"fr_FR.UTF-8")
# else
# expect_equal(Sys.getlocale(category = "LC_TIME"),"French_France.1252")
#
# }
# )
test_that("Test that user host and password are set for test",{
skip_on_cran()
env_set_test_stacomi()
expect_true(exists("user"))
expect_true(exists("password"))
})
context("Database connection")
test_that("Test that stacomirtools connects",{
skip_on_cran()
env_set_test_stacomi()
envir_stacomi <- new.env(parent = asNamespace("stacomiR"))
con <- new("ConnectionDB")
con@user <- user
con@password <- password
con <- connect(con)
expect_is(connect(con),'ConnectionDB')
expect_equal(con@status,"Connection OK")
pool::poolClose(con@connection)
rm("envir_stacomi")
})
test_that("Test that positive count for nrow(ref.tr_taxon_tax)",{
skip_on_cran()
envir_stacomi <- new.env(parent = asNamespace("stacomiR"))
env_set_test_stacomi()
base <- c("bd_contmig_nat","localhost","5432",user,password)
requete=new("RequeteDB")
requete <- connect(requete,base)
requete@sql="select count(*) from ref.tr_taxon_tax"
requete <- stacomirtools::query(requete)
expect_true(as.numeric(requete@query)>0)
rm("envir_stacomi")
})
test_that("Tests positive count for sch.t_operation_ope",{
skip_on_cran()
envir_stacomi <- new.env(parent = asNamespace("stacomiR"))
env_set_test_stacomi()
base <- c("bd_contmig_nat","localhost","5432",user,password)
requete=new("RequeteDB")
requete <- connect(requete,base)
sch <- paste("iav",".",sep="")
requete@sql=paste("select count(*) from ",sch,"t_operation_ope",sep="")
requete <- stacomirtools::query(requete)
expect_true(as.numeric(requete@query)>0)
rm("envir_stacomi")
})
context("Loading program")
test_that("Test that working environment is created",{
skip_on_cran()
env_set_test_stacomi()
stacomi(database_expected=TRUE)
expect_true(exists("envir_stacomi"))
})
test_that("Test get_schema",{
skip_on_cran()
env_set_test_stacomi()
stacomi(database_expected=TRUE)
sch <- get_schema()
expect_equal(sch,"iav.")
rm("sch", envir=envir_stacomi)
sch <- get_schema(default="volga.")
expect_equal(sch,"volga.")
stacomi(database_expected = TRUE, sch = "logrami")
sch <- get_schema()
expect_equal(sch,"logrami.")
org <- get_org()
expect_equal(org,"LOGRAMI")
})
# pour schema rlang::env_get(envir_stacomi, "sch")
context(stringr::str_c("Database integrity"))
test_that("Test that tickets have been launched",
{
skip_on_cran()
envir_stacomi <- new.env(parent = asNamespace("stacomiR"))
env_set_test_stacomi()
req=new("RequeteDB")
sch <- "iav."
req@sql <- paste("select * from ",sch," ts_maintenance_main")
req <- stacomirtools::query(req)
result <- req@query
# using dput(ticket)
tickets <- structure(list(
main_ticket = c(59L,
40L,
42L,
67L,
72L,
121L,
122L,
81L,
61L,
152L,
147L), main_description = c("creation de la table de maintenance",
"ajout des clé étrangères manquantes",
"modification des propriétaires sur les tables à séquence et grant select sur ref.tr_typedf_tdf oublié",
"org code rajouté dans les tables t_operationmarquage_omq, tj_coefficientconversion_coe,tj_prelevementlot_prl",
"creation d'une tableref.ts_messager_msr pour l'internationalisation",
"ajout de la notion de cohorte pour les saumons passant très précocément",
"Mise à jour des localisations anatomiques",
"Mise à jour vers la version 0.4 alpha, mise à jour des référentiels du SANDRE, script ticjet81_mise_en_conformite_sandre, révision 98",
"Mise à jour vers la version 0.4 alpha, mise à jour des constraintes stationmesure modification limites coordonnées géographiques",
"Mise à jour vers la version 0.4 alpha, problèmes de clé étrangères, script total",
"Mise à jour vers la version 0.4 alpha, creation des masques"
)),
.Names = c("main_ticket", "main_description"),
class = "data.frame",
row.names = c(NA,
11L))
check_exist_tickets=tickets$main_ticket%in%result$main_ticket
for (i in 1:nrow(tickets)){
expect_true(check_exist_tickets[i],label=paste('Missing ticket :',tickets$main_ticket[i]))
}
})
# test on current schema
# attention your may need superuser rights for that test
test_that("All foreign keys are present",
{
skip_on_cran()
env_set_test_stacomi()
skip_if_not(test_foreign_keys,"skipping foreign key test, set options in test/helper to change this")
req=new("RequeteDB")
env_set_test_stacomi()
req@sql=paste(stringr::str_c("SELECT
distinct on (tc.constraint_name) tc.constraint_name, tc.table_name
FROM
information_schema.table_constraints AS tc
JOIN information_schema.key_column_usage AS kcu
ON tc.constraint_name = kcu.constraint_name
JOIN information_schema.constraint_column_usage AS ccu
ON ccu.constraint_name = tc.constraint_name
WHERE constraint_type = 'FOREIGN KEY' and tc.constraint_schema='",paste(schema),"';"))
req <- query(req)
result <- req@query
fk <- structure(list(constraint_name = c("c_fk_act_lot_identifiant",
"c_fk_act_mqe_reference", "c_fk_act_org_code", "c_fk_bjo_org_code",
"c_fk_bjo_std_code", "c_fk_bjo_tax_code", "c_fk_bme_std_code",
"c_fk_bme_tax_code", "c_fk_car_lot_identifiant", "c_fk_car_org_code",
"c_fk_car_par_code", "c_fk_car_val_par_identifiant", "c_fk_coe_org_code",
"c_fk_coe_qte_code", "c_fk_coe_std_code", "c_fk_coe_tax_code",
"c_fk_dft_df_identifiant", "c_fk_dft_org_code", "c_fk_dft_tdf_code",
"c_fk_dic_dif_identifiant", "c_fk_dic_dis_identifiant", "c_fk_dic_org_code",
"c_fk_dic_tdc_code", "c_fk_dif_dis_identifiant", "c_fk_dif_org_code",
"c_fk_dif_ouv_identifiant", "c_fk_dtx_dif_identifiant", "c_fk_dtx_org_code",
"c_fk_dtx_tax_code", "c_fk_env_org_code", "c_fk_env_stm_identifiant",
"c_fk_env_val_identifiant", "c_fk_lot_dev_code", "c_fk_lot_lot_identifiant",
"c_fk_lot_ope_identifiant", "c_fk_lot_org_code", "c_fk_lot_qte_code",
"c_fk_lot_std_code", "c_fk_lot_tax_code", "c_fk_maa_mal_id",
"c_fk_mac_valeurqualitatifdefaut", "c_fk_mae_mao_id", "c_fk_mae_stm_identifiant",
"c_fk_mal_mas_id", "c_fk_mao_mas_id", "c_fk_mqe_loc_code", "c_fk_mqe_nmq_code",
"c_fk_mqe_omq_reference", "c_fk_mqe_org_code", "c_fk_omq_org_code",
"c_fk_ope_dic_identifiant", "c_fk_ope_org_code", "c_fk_ouv_nov_code",
"c_fk_ouv_org_code", "c_fk_ouv_sta_code", "c_fk_pco_imp_code",
"c_fk_pco_loc_code", "c_fk_pco_lot_identifiant", "c_fk_pco_org_code",
"c_fk_pco_pat_code", "c_fk_per_dis_identifiant", "c_fk_per_org_code",
"c_fk_per_tar_code", "c_fk_prl_loc_code", "c_fk_prl_lot_identifiant",
"c_fk_prl_org_code", "c_fk_prl_pre_nom", "c_fk_prl_typeprelevement",
"c_fk_sta_org_code", "c_fk_std_code", "c_fk_stm_org_code", "c_fk_stm_par_code",
"c_fk_stm_sta_code", "c_fk_tav_dic_identifiant", "c_fk_tav_org_code",
"c_fk_txe_ech_code", "c_fk_txe_org_code", "c_fk_txe_sta_code",
"c_fk_txe_std_code", "c_fk_txe_tax_code", "c_fk_txv_org_code",
"c_fk_txv_std_code", "c_fk_txv_tax_code"), table_name = c("tj_actionmarquage_act",
"tj_actionmarquage_act", "tj_actionmarquage_act", "t_bilanmigrationjournalier_bjo",
"t_bilanmigrationjournalier_bjo", "t_bilanmigrationjournalier_bjo",
"t_reportmigrationmensuel_bme", "t_reportmigrationmensuel_bme",
"tj_caracteristiquelot_car", "tj_caracteristiquelot_car", "tj_caracteristiquelot_car",
"tj_caracteristiquelot_car", "tj_coefficientconversion_coe",
"tj_coefficientconversion_coe", "tj_coefficientconversion_coe",
"tj_coefficientconversion_coe", "tj_dfesttype_dft", "tj_dfesttype_dft",
"tj_dfesttype_dft", "t_dispositifcomptage_dic", "t_dispositifcomptage_dic",
"t_dispositifcomptage_dic", "t_dispositifcomptage_dic", "t_dispositiffranchissement_dif",
"t_dispositiffranchissement_dif", "t_dispositiffranchissement_dif",
"tj_dfestdestinea_dtx", "tj_dfestdestinea_dtx", "tj_dfestdestinea_dtx",
"tj_conditionenvironnementale_env", "tj_conditionenvironnementale_env",
"tj_conditionenvironnementale_env", "t_lot_lot", "t_lot_lot",
"t_lot_lot", "t_lot_lot", "t_lot_lot", "t_lot_lot", "t_lot_lot",
"ts_masqueordreaffichage_maa", "ts_masquecaracteristiquelot_mac",
"ts_masqueconditionsenvironnementales_mae", "ts_masqueconditionsenvironnementales_mae",
"ts_masquelot_mal", "ts_masqueope_mao", "t_marque_mqe", "t_marque_mqe",
"t_marque_mqe", "t_marque_mqe", "t_operationmarquage_omq", "t_operation_ope",
"t_operation_ope", "t_ouvrage_ouv", "t_ouvrage_ouv", "t_ouvrage_ouv",
"tj_pathologieconstatee_pco", "tj_pathologieconstatee_pco", "tj_pathologieconstatee_pco",
"tj_pathologieconstatee_pco", "tj_pathologieconstatee_pco", "t_periodefonctdispositif_per",
"t_periodefonctdispositif_per", "t_periodefonctdispositif_per",
"tj_prelevementlot_prl", "tj_prelevementlot_prl", "tj_prelevementlot_prl",
"tj_prelevementlot_prl", "tj_prelevementlot_prl", "t_station_sta",
"ts_taxavideo_txv", "tj_stationmesure_stm", "tj_stationmesure_stm",
"tj_stationmesure_stm", "ts_taillevideo_tav", "ts_taillevideo_tav",
"tj_tauxechappement_txe", "tj_tauxechappement_txe", "tj_tauxechappement_txe",
"tj_tauxechappement_txe", "tj_tauxechappement_txe", "ts_taxavideo_txv",
"ts_taxavideo_txv", "ts_taxavideo_txv")), .Names = c("constraint_name",
"table_name"), row.names = c(NA, 83L), class = "data.frame")
check_exist_fk=fk$constraint_name%in%result$constraint_name
for (i in 1:nrow(fk)){
expect_true(check_exist_fk[i],label=paste("Missing foreign key :",fk$constraint_name[i],"table :",fk$table_name[i]))
}
rm(list=ls(all=TRUE))
})
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context("stacomi base connection")
# while crashing in some test for reportFonctionnement DF or report_dc,
#the program will set time to GMT, this will cause some errors hard to understand in some of
# the classes (report_mig, report_mig_mult), with the following you can check this problem
# test_that("Test that the program is running under the right locale",{
# skip_on_cran()
# if(Sys.info()["sysname"] == "Linux")
# expect_equal(Sys.getlocale(category = "LC_TIME"),"fr_FR.UTF-8")
# else
# expect_equal(Sys.getlocale(category = "LC_TIME"),"French_France.1252")
#
# }
# )
test_that("Test that user host and password are set for test",{
skip_on_cran()
env_set_test_stacomi()
expect_true(exists("user"))
expect_true(exists("password"))
})
context("Database connection")
test_that("Test that stacomirtools connects",{
skip_on_cran()
env_set_test_stacomi()
envir_stacomi <- new.env(parent = asNamespace("stacomiR"))
con <- new("ConnectionDB")
con@user <- user
con@password <- password
con <- connect(con)
expect_is(connect(con),'ConnectionDB')
expect_equal(con@status,"Connection OK")
pool::poolClose(con@connection)
rm("envir_stacomi")
})
test_that("Test that positive count for nrow(ref.tr_taxon_tax)",{
skip_on_cran()
envir_stacomi <- new.env(parent = asNamespace("stacomiR"))
env_set_test_stacomi()
base <- c("bd_contmig_nat","localhost","5432",user,password)
requete=new("RequeteDB")
requete <- connect(requete,base)
requete@sql="select count(*) from ref.tr_taxon_tax"
requete <- stacomirtools::query(requete)
expect_true(as.numeric(requete@query)>0)
rm("envir_stacomi")
})
test_that("Tests positive count for sch.t_operation_ope",{
skip_on_cran()
envir_stacomi <- new.env(parent = asNamespace("stacomiR"))
env_set_test_stacomi()
base <- c("bd_contmig_nat","localhost","5432",user,password)
requete=new("RequeteDB")
requete <- connect(requete,base)
sch <- paste("iav",".",sep="")
requete@sql=paste("select count(*) from ",sch,"t_operation_ope",sep="")
requete <- stacomirtools::query(requete)
expect_true(as.numeric(requete@query)>0)
rm("envir_stacomi")
})
context("Loading program")
test_that("Test that working environment is created",{
skip_on_cran()
env_set_test_stacomi()
stacomi(database_expected=TRUE)
expect_true(exists("envir_stacomi"))
})
test_that("Test get_schema",{
skip_on_cran()
env_set_test_stacomi()
stacomi(database_expected=TRUE)
sch <- get_schema()
expect_equal(sch,"iav.")
rm("sch", envir=envir_stacomi)
sch <- get_schema(default="volga.")
expect_equal(sch,"volga.")
stacomi(database_expected = TRUE, sch = "logrami")
sch <- get_schema()
expect_equal(sch,"logrami.")
org <- get_org()
expect_equal(org,"LOGRAMI")
})
# pour schema rlang::env_get(envir_stacomi, "sch")
context(stringr::str_c("Database integrity"))
test_that("Test that tickets have been launched",
{
skip_on_cran()
envir_stacomi <- new.env(parent = asNamespace("stacomiR"))
env_set_test_stacomi()
req=new("RequeteDB")
sch <- "iav."
req@sql <- paste("select * from ",sch," ts_maintenance_main")
req <- stacomirtools::query(req)
result <- req@query
# using dput(ticket)
tickets <- structure(list(
main_ticket = c(59L,
40L,
42L,
67L,
72L,
121L,
122L,
81L,
61L,
152L,
147L), main_description = c("creation de la table de maintenance",
"ajout des clé étrangères manquantes",
"modification des propriétaires sur les tables à séquence et grant select sur ref.tr_typedf_tdf oublié",
"org code rajouté dans les tables t_operationmarquage_omq, tj_coefficientconversion_coe,tj_prelevementlot_prl",
"creation d'une tableref.ts_messager_msr pour l'internationalisation",
"ajout de la notion de cohorte pour les saumons passant très précocément",
"Mise à jour des localisations anatomiques",
"Mise à jour vers la version 0.4 alpha, mise à jour des référentiels du SANDRE, script ticjet81_mise_en_conformite_sandre, révision 98",
"Mise à jour vers la version 0.4 alpha, mise à jour des constraintes stationmesure modification limites coordonnées géographiques",
"Mise à jour vers la version 0.4 alpha, problèmes de clé étrangères, script total",
"Mise à jour vers la version 0.4 alpha, creation des masques"
)),
.Names = c("main_ticket", "main_description"),
class = "data.frame",
row.names = c(NA,
11L))
check_exist_tickets=tickets$main_ticket%in%result$main_ticket
for (i in 1:nrow(tickets)){
expect_true(check_exist_tickets[i],label=paste('Missing ticket :',tickets$main_ticket[i]))
}
})
# test on current schema
# attention your may need superuser rights for that test
test_that("All foreign keys are present",
{
skip_on_cran()
env_set_test_stacomi()
skip_if_not(test_foreign_keys,"skipping foreign key test, set options in test/helper to change this")
req=new("RequeteDB")
env_set_test_stacomi()
req@sql=paste(stringr::str_c("SELECT
distinct on (tc.constraint_name) tc.constraint_name, tc.table_name
FROM
information_schema.table_constraints AS tc
JOIN information_schema.key_column_usage AS kcu
ON tc.constraint_name = kcu.constraint_name
JOIN information_schema.constraint_column_usage AS ccu
ON ccu.constraint_name = tc.constraint_name
WHERE constraint_type = 'FOREIGN KEY' and tc.constraint_schema='",paste(schema),"';"))
req <- query(req)
result <- req@query
fk <- structure(list(constraint_name = c("c_fk_act_lot_identifiant",
"c_fk_act_mqe_reference", "c_fk_act_org_code", "c_fk_bjo_org_code",
"c_fk_bjo_std_code", "c_fk_bjo_tax_code", "c_fk_bme_std_code",
"c_fk_bme_tax_code", "c_fk_car_lot_identifiant", "c_fk_car_org_code",
"c_fk_car_par_code", "c_fk_car_val_par_identifiant", "c_fk_coe_org_code",
"c_fk_coe_qte_code", "c_fk_coe_std_code", "c_fk_coe_tax_code",
"c_fk_dft_df_identifiant", "c_fk_dft_org_code", "c_fk_dft_tdf_code",
"c_fk_dic_dif_identifiant", "c_fk_dic_dis_identifiant", "c_fk_dic_org_code",
"c_fk_dic_tdc_code", "c_fk_dif_dis_identifiant", "c_fk_dif_org_code",
"c_fk_dif_ouv_identifiant", "c_fk_dtx_dif_identifiant", "c_fk_dtx_org_code",
"c_fk_dtx_tax_code", "c_fk_env_org_code", "c_fk_env_stm_identifiant",
"c_fk_env_val_identifiant", "c_fk_lot_dev_code", "c_fk_lot_lot_identifiant",
"c_fk_lot_ope_identifiant", "c_fk_lot_org_code", "c_fk_lot_qte_code",
"c_fk_lot_std_code", "c_fk_lot_tax_code", "c_fk_maa_mal_id",
"c_fk_mac_valeurqualitatifdefaut", "c_fk_mae_mao_id", "c_fk_mae_stm_identifiant",
"c_fk_mal_mas_id", "c_fk_mao_mas_id", "c_fk_mqe_loc_code", "c_fk_mqe_nmq_code",
"c_fk_mqe_omq_reference", "c_fk_mqe_org_code", "c_fk_omq_org_code",
"c_fk_ope_dic_identifiant", "c_fk_ope_org_code", "c_fk_ouv_nov_code",
"c_fk_ouv_org_code", "c_fk_ouv_sta_code", "c_fk_pco_imp_code",
"c_fk_pco_loc_code", "c_fk_pco_lot_identifiant", "c_fk_pco_org_code",
"c_fk_pco_pat_code", "c_fk_per_dis_identifiant", "c_fk_per_org_code",
"c_fk_per_tar_code", "c_fk_prl_loc_code", "c_fk_prl_lot_identifiant",
"c_fk_prl_org_code", "c_fk_prl_pre_nom", "c_fk_prl_typeprelevement",
"c_fk_sta_org_code", "c_fk_std_code", "c_fk_stm_org_code", "c_fk_stm_par_code",
"c_fk_stm_sta_code", "c_fk_tav_dic_identifiant", "c_fk_tav_org_code",
"c_fk_txe_ech_code", "c_fk_txe_org_code", "c_fk_txe_sta_code",
"c_fk_txe_std_code", "c_fk_txe_tax_code", "c_fk_txv_org_code",
"c_fk_txv_std_code", "c_fk_txv_tax_code"), table_name = c("tj_actionmarquage_act",
"tj_actionmarquage_act", "tj_actionmarquage_act", "t_bilanmigrationjournalier_bjo",
"t_bilanmigrationjournalier_bjo", "t_bilanmigrationjournalier_bjo",
"t_reportmigrationmensuel_bme", "t_reportmigrationmensuel_bme",
"tj_caracteristiquelot_car", "tj_caracteristiquelot_car", "tj_caracteristiquelot_car",
"tj_caracteristiquelot_car", "tj_coefficientconversion_coe",
"tj_coefficientconversion_coe", "tj_coefficientconversion_coe",
"tj_coefficientconversion_coe", "tj_dfesttype_dft", "tj_dfesttype_dft",
"tj_dfesttype_dft", "t_dispositifcomptage_dic", "t_dispositifcomptage_dic",
"t_dispositifcomptage_dic", "t_dispositifcomptage_dic", "t_dispositiffranchissement_dif",
"t_dispositiffranchissement_dif", "t_dispositiffranchissement_dif",
"tj_dfestdestinea_dtx", "tj_dfestdestinea_dtx", "tj_dfestdestinea_dtx",
"tj_conditionenvironnementale_env", "tj_conditionenvironnementale_env",
"tj_conditionenvironnementale_env", "t_lot_lot", "t_lot_lot",
"t_lot_lot", "t_lot_lot", "t_lot_lot", "t_lot_lot", "t_lot_lot",
"ts_masqueordreaffichage_maa", "ts_masquecaracteristiquelot_mac",
"ts_masqueconditionsenvironnementales_mae", "ts_masqueconditionsenvironnementales_mae",
"ts_masquelot_mal", "ts_masqueope_mao", "t_marque_mqe", "t_marque_mqe",
"t_marque_mqe", "t_marque_mqe", "t_operationmarquage_omq", "t_operation_ope",
"t_operation_ope", "t_ouvrage_ouv", "t_ouvrage_ouv", "t_ouvrage_ouv",
"tj_pathologieconstatee_pco", "tj_pathologieconstatee_pco", "tj_pathologieconstatee_pco",
"tj_pathologieconstatee_pco", "tj_pathologieconstatee_pco", "t_periodefonctdispositif_per",
"t_periodefonctdispositif_per", "t_periodefonctdispositif_per",
"tj_prelevementlot_prl", "tj_prelevementlot_prl", "tj_prelevementlot_prl",
"tj_prelevementlot_prl", "tj_prelevementlot_prl", "t_station_sta",
"ts_taxavideo_txv", "tj_stationmesure_stm", "tj_stationmesure_stm",
"tj_stationmesure_stm", "ts_taillevideo_tav", "ts_taillevideo_tav",
"tj_tauxechappement_txe", "tj_tauxechappement_txe", "tj_tauxechappement_txe",
"tj_tauxechappement_txe", "tj_tauxechappement_txe", "ts_taxavideo_txv",
"ts_taxavideo_txv", "ts_taxavideo_txv")), .Names = c("constraint_name",
"table_name"), row.names = c(NA, 83L), class = "data.frame")
check_exist_fk=fk$constraint_name%in%result$constraint_name
for (i in 1:nrow(fk)){
expect_true(check_exist_fk[i],label=paste("Missing foreign key :",fk$constraint_name[i],"table :",fk$table_name[i]))
}
rm(list=ls(all=TRUE))
})
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