Add detection network tests env var

This is to allow the env var to control skipping the tests which call OpenGWAS.

Author: remlapmot

tests/testthat/test_add_metadata.r

@@ -1,5 +1,6 @@
 context("add metadata")
 
+skip_if(Sys.getenv('TWOSAMPLEMR_ENABLE_OPENGWAS_TESTS') != TRUE, "Tests requiring OpenGWAS")
 skip_if_offline()
 skip_if_offline(host = "api.opengwas.io")
 skip_on_cran()

tests/testthat/test_create_test_data.r

@@ -1,4 +1,5 @@
 test_that("Create local data", {
+  skip_if(Sys.getenv('TWOSAMPLEMR_ENABLE_OPENGWAS_TESTS') != TRUE, "Tests requiring OpenGWAS")
 skip("Skip local data creation unless you have good access to the API.")
 
 exp_dat <- extract_instruments("ieu-a-2")

tests/testthat/test_instruments.R

@@ -1,5 +1,6 @@
 context("Instruments")
 
+skip_if(Sys.getenv('TWOSAMPLEMR_ENABLE_OPENGWAS_TESTS') != TRUE, "Tests requiring OpenGWAS")
 skip_if_offline()
 skip_if_offline(host = "api.opengwas.io")
 skip_on_cran()

tests/testthat/test_ld.R

@@ -1,5 +1,6 @@
 context("ld")
 
+skip_if(Sys.getenv('TWOSAMPLEMR_ENABLE_OPENGWAS_TESTS') != TRUE, "Tests requiring OpenGWAS")
 skip_if_offline()
 skip_if_offline(host = "api.opengwas.io")
 skip_on_cran()

tests/testthat/test_ldsc.R

@@ -1,7 +1,7 @@
 context("LDSC")
 
-
 test_that("get afl2", {
+  skip_if(Sys.getenv('TWOSAMPLEMR_ENABLE_OPENGWAS_TESTS') != TRUE, "Tests requiring OpenGWAS")
 	skip("Very slow")
 	hm3info <- ieugwasr::afl2_list("hapmap3")
 	if(inherits(hm3info, "response")) skip("Server issues")

tests/testthat/test_mvmr.R

@@ -1,5 +1,6 @@
 context("mvmr")
 
+skip_if(Sys.getenv('TWOSAMPLEMR_ENABLE_OPENGWAS_TESTS') != TRUE, "Tests requiring OpenGWAS")
 skip_on_cran()
 skip_if_offline()
 skip_if_offline(host = "api.opengwas.io")

tests/testthat/test_mvmr_local.R

@@ -10,6 +10,7 @@ context("mvmr local")
 load(system.file("extdata", "test_add_mvmr_local.RData", package="TwoSampleMR"))
 
 test_that("mv exposure local", {
+  skip_if(Sys.getenv('TWOSAMPLEMR_ENABLE_OPENGWAS_TESTS') != TRUE, "Tests requiring OpenGWAS")
   skip_if_offline()
   skip_if_offline(host = "api.opengwas.io")
 	skip_on_cran()

tests/testthat/test_otherformats.R

@@ -13,6 +13,7 @@ test_that("MRInput", {
 })
 
 test_that("MRInput with cor", {
+  skip_if(Sys.getenv('TWOSAMPLEMR_ENABLE_OPENGWAS_TESTS') != TRUE, "Tests requiring OpenGWAS")
   skip_on_cran()
   skip_if_offline()
   skip_if_offline(host = "api.opengwas.io")

tests/testthat/test_outcomes.R

@@ -1,5 +1,6 @@
 context("outcome")
 
+skip_if(Sys.getenv('TWOSAMPLEMR_ENABLE_OPENGWAS_TESTS') != TRUE, "Tests requiring OpenGWAS")
 skip_if_offline()
 skip_if_offline(host = "api.opengwas.io")
 skip_on_cran()

tests/testthat/test_rsq.r

@@ -10,6 +10,7 @@ test_that("exposure data 1", {
 })
 
 test_that("exposure data 2", {
+  skip_if(Sys.getenv('TWOSAMPLEMR_ENABLE_OPENGWAS_TESTS') != TRUE, "Tests requiring OpenGWAS")
   skip_if_offline()
   skip_if_offline(host = "api.opengwas.io")
   skip_on_cran()
@@ -23,6 +24,7 @@ test_that("exposure data 2", {
 exposure <- exp_dat[1:5,]
 
 test_that("outcome data 1", {
+  skip_if(Sys.getenv('TWOSAMPLEMR_ENABLE_OPENGWAS_TESTS') != TRUE, "Tests requiring OpenGWAS")
   skip_if_offline()
   skip_if_offline(host = "api.opengwas.io")
   skip_on_cran()
@@ -36,6 +38,7 @@ test_that("outcome data 1", {
 })
 
 test_that("outcome data 2", {
+  skip_if(Sys.getenv('TWOSAMPLEMR_ENABLE_OPENGWAS_TESTS') != TRUE, "Tests requiring OpenGWAS")
   skip_if_offline()
   skip_if_offline(host = "api.opengwas.io")
   skip_on_cran()
@@ -49,6 +52,7 @@ test_that("outcome data 2", {
 })
 
 test_that("dat 2", {
+  skip_if(Sys.getenv('TWOSAMPLEMR_ENABLE_OPENGWAS_TESTS') != TRUE, "Tests requiring OpenGWAS")
   skip_if_offline()
   skip_if_offline(host = "api.opengwas.io")
   skip_on_cran()
@@ -60,6 +64,7 @@ test_that("dat 2", {
 })
 
 test_that("dat ukb-d", {
+  skip_if(Sys.getenv('TWOSAMPLEMR_ENABLE_OPENGWAS_TESTS') != TRUE, "Tests requiring OpenGWAS")
   skip_if_offline()
   skip_if_offline(host = "api.opengwas.io")
   skip_on_cran()
@@ -77,6 +82,7 @@ test_that("effective n", {
 })
 
 test_that("get_population_allele_frequency", {
+  skip_if(Sys.getenv('TWOSAMPLEMR_ENABLE_OPENGWAS_TESTS') != TRUE, "Tests requiring OpenGWAS")
   skip_if_offline()
   skip_if_offline(host = "api.opengwas.io")
   skip_on_cran()
@@ -94,6 +100,7 @@ test_that("get_population_allele_frequency", {
 })
 
 test_that("bbj-a-1", {
+  skip_if(Sys.getenv('TWOSAMPLEMR_ENABLE_OPENGWAS_TESTS') != TRUE, "Tests requiring OpenGWAS")
   skip_on_cran()
   skip_if_offline()
   skip_if_offline(host = "api.opengwas.io")
@@ -105,6 +112,7 @@ test_that("bbj-a-1", {
 })
 
 test_that("bsen vs pn", {
+  skip_if(Sys.getenv('TWOSAMPLEMR_ENABLE_OPENGWAS_TESTS') != TRUE, "Tests requiring OpenGWAS")
   skip_if_offline()
   skip_if_offline(host = "api.opengwas.io")
   skip_on_cran()