Make test robust against unavailable services

Test logs are without internet.

5 files changed, 40 insertions, 19 deletions

diff --git a/R/chent.R b/R/chent.R
index 05066b8..038fe7b 100644
--- a/R/chent.R
+++ b/R/chent.R
@@ -219,10 +219,10 @@ chent <- R6Class("chent",
     #' @description
     #' Get chemical information from RDKit if available
     get_rdkit = function(template = NULL) {
-      
+
       if (!rdkit_available) stop("RDKit is not available")
       if (is.null(self$smiles)) stop("RDKit would need a SMILES code")
-      
+
       available_smiles <- names(self$smiles)
       smiles_preference <- c("user", "PubChem", "PubChem_Connectivity")
       smiles_preferred_i <- min(match(available_smiles, smiles_preference))
@@ -492,7 +492,7 @@ chent <- R6Class("chent",
     #' @param N The Freundlich exponent
     #' @param perc_clay The percentage of clay in the soil
     #' @param CEC The cation exchange capacity
-    add_soil_sorption = function(soils, 
+    add_soil_sorption = function(soils,
       Kf, Kfoc, N,
       type = NA, pH_orig = NA, pH_medium = NA,
       pH_H2O = NA,
diff --git a/log/test.log b/log/test.log
index 0e8fc46..daa7c22 100644
--- a/log/test.log
+++ b/log/test.log
@@ -7,18 +7,29 @@ The following object is masked from ‘package:devtools’:
 
     test_file
 
+Error in curl::curl_fetch_memory(url, handle = handle): Could not resolve hostname [pesticidecompendium.bcpc.org]:
+Could not resolve host: pesticidecompendium.bcpc.org
+Request failed [ERROR]. Retrying in 1.5 seconds...
+Error in curl::curl_fetch_memory(url, handle = handle): Could not resolve hostname [pesticidecompendium.bcpc.org]:
+Could not resolve host: pesticidecompendium.bcpc.org
+Request failed [ERROR]. Retrying in 1.5 seconds...
+Error in curl::curl_fetch_memory(url, handle = handle) : 
+  Could not resolve hostname [pesticidecompendium.bcpc.org]:
+Could not resolve host: pesticidecompendium.bcpc.org
 ✔ | F W  S  OK | Context
 
 ⠏ |          0 | chent                                                          
 ⠸ |          4 | chent                                                          
-⠧ |          8 | chent                                                          
-✔ |         10 | chent [4.4s]
+✔ |      1   4 | chent [9.8s]
 
 ⠏ |          0 | pai                                                            
-⠋ |          1 | pai                                                            
-✔ |          9 | pai [6.1s]
+✔ |      1   0 | pai
 
 ══ Results ═════════════════════════════════════════════════════════════════════
-Duration: 10.6 s
+Duration: 9.8 s
 
-[ FAIL 0 | WARN 0 | SKIP 0 | PASS 19 ]
+── Skipped tests (2) ───────────────────────────────────────────────────────────
+• bcpc_up & pc_up is not TRUE (1): 'test_pai.R:3:3'
+• pc_up is not TRUE (1): 'test_chent.R:20:3'
+
+[ FAIL 0 | WARN 0 | SKIP 2 | PASS 4 ]
diff --git a/tests/testthat/setup.R b/tests/testthat/setup.R
index fb55272..4232120 100644
--- a/tests/testthat/setup.R
+++ b/tests/testthat/setup.R
@@ -2,3 +2,7 @@
 skip_if_no_rdkit <- function() {
   if (!chents:::rdkit_available) skip("RDKit is not available via reticulate")
 }
+
+# Check availability of BCPC and PubChem
+bcpc_up <- webchem::ping_service("bcpc")
+pc_up <- webchem::ping_service("pc")
diff --git a/tests/testthat/test_chent.R b/tests/testthat/test_chent.R
index 76af7aa..4017042 100644
--- a/tests/testthat/test_chent.R
+++ b/tests/testthat/test_chent.R
@@ -3,15 +3,20 @@ test_that("We can initialise an object and add information", {
   expect_equal(oct$identifier, c(X1.octanol = "1-octanol")) # The name of the identifier is generated using make.names()
   expect_equal(oct$inchikey, structure(NA, source = "user"))
   expect_equal(oct$smiles, c(user = "CCCCCCCCO"))
-  oct$try_pubchem() |> 
-    expect_message("Querying PubChem for name 1-octanol") |> 
-    expect_warning("Overwriting uninitialized InChIKey")
-  expect_equal(oct$inchikey, structure("KBPLFHHGFOOTCA-UHFFFAOYSA-N", source = "pubchem"))
-  expect_equal(oct$smiles[["PubChem"]], "CCCCCCCCO")
+
+  if (webchem::ping_service("pc")) {
+    oct$try_pubchem() |> 
+      expect_message("Querying PubChem for name 1-octanol") |> 
+      expect_warning("Overwriting uninitialized InChIKey")
+    expect_equal(oct$inchikey, structure("KBPLFHHGFOOTCA-UHFFFAOYSA-N", source = "pubchem"))
+    expect_equal(oct$smiles[["PubChem"]], "CCCCCCCCO")
+    expect_equal(round(oct$mw, 2), structure(130.23, source = "pubchem"))
+  }
 
   skip_if_no_rdkit()
   oct$get_rdkit() |> 
     expect_message("Get chemical information from RDKit using user SMILES")
-  expect_equal(round(oct$mw, 2), structure(130.23, source = "pubchem"))
+
+  skip_if_not(pc_up)
   expect_snapshot(print(oct))
 })
diff --git a/tests/testthat/test_pai.R b/tests/testthat/test_pai.R
index 9d73b58..7d9c566 100644
--- a/tests/testthat/test_pai.R
+++ b/tests/testthat/test_pai.R
@@ -1,14 +1,15 @@
 test_that("a pai object is correctly generated", {
 
-  {glyphosate <- pai$new("glyphosate", rdkit = FALSE)} |> 
-    expect_message("Querying BCPC for glyphosate") |> 
+  skip_if_not(bcpc_up & pc_up)
+  {glyphosate <- pai$new("glyphosate", rdkit = FALSE)} |>
+    expect_message("Querying BCPC for glyphosate") |>
     expect_message("Querying PubChem for inchikey ")
-  
+
   # Check BCPC results
   expect_equal(glyphosate$bcpc$cas, "1071-83-6")
   expect_equal(glyphosate$bcpc$formula, "C3H8NO5P")
   expect_equal(glyphosate$bcpc$iupac_name, "N-(phosphonomethyl)glycine")
-  
+
   expect_equal(names(glyphosate$identifier), "glyphosate")
 
   # Check PubChem results