diff options
| author | Johannes Ranke <jranke@uni-bremen.de> | 2024-08-05 19:03:21 +0200 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2024-08-05 19:03:21 +0200 |
| commit | 77189d666eb39d2660245c2f008175dc4560f647 (patch) | |
| tree | fbd07f059b5da70c813526047f16464f7e4d745f | |
| parent | 1b58327278038a1111a88c521e6992c15e0b17ea (diff) | |
| -rw-r--r-- | R/chent.R | 24 | ||||
| -rw-r--r-- | test.log | 27 | ||||
| -rw-r--r-- | tests/testthat/test_chent.R | 2 |
3 files changed, 37 insertions, 16 deletions
@@ -195,19 +195,25 @@ chent <- R6Class("chent", self$inchikey <- self$pubchem$InChIKey attr(self$inchikey, "source") <- "pubchem" } else { - if (length(self$inchikey) > 1) { - message("InChIKey ", self$inchikey, " retreived from ", - attr(self$inchikey, "source"), - " has length > 1, using PubChem InChIKey") + if (is.na(self$inchikey)) { + warning("Overwriting uninitialized InChIKey") self$inchikey <- self$pubchem$InChIKey attr(self$inchikey, "source") <- "pubchem" } else { - if (self$pubchem$InChIKey != self$inchikey) { - message("InChiKey ", self$pubchem$InChIKey, " from PubChem record does not match\n", - "InChiKey ", self$inchikey, " retreived from ", - attr(self$inchikey, "source")) + if (length(self$inchikey) > 1) { + message("InChIKey ", self$inchikey, " retreived from ", + attr(self$inchikey, "source"), + " has length > 1, using PubChem InChIKey") + self$inchikey <- self$pubchem$InChIKey + attr(self$inchikey, "source") <- "pubchem" } else { - attr(self$inchikey, "source") <- c(attr(self$inchikey, "source"), "pubchem") + if (self$pubchem$InChIKey != self$inchikey) { + message("InChiKey ", self$pubchem$InChIKey, " from PubChem record does not match\n", + "InChiKey ", self$inchikey, " retreived from ", + attr(self$inchikey, "source")) + } else { + attr(self$inchikey, "source") <- c(attr(self$inchikey, "source"), "pubchem") + } } } } @@ -1,11 +1,26 @@ Loading required package: usethis -ℹ Loading chents ℹ Testing chents -✔ | F W S OK | Context -✔ | 6 | Generation of chent objects [3.3s] -✔ | 8 | Generation of pai objects [8.1s] + +Attaching package: ‘testthat’ + +The following object is masked from ‘package:devtools’: + + test_file + +✔ | F W S OK | Context + +⠏ | 0 | chent +⠏ | 0 | Generation of chent objects +⠋ | 1 | Generation of chent objects +⠸ | 4 | Generation of chent objects +✔ | 7 | Generation of chent objects [4.9s] + +⠏ | 0 | pai +⠏ | 0 | Generation of pai objects +⠋ | 1 | Generation of pai objects +✔ | 8 | Generation of pai objects [6.8s] ══ Results ═════════════════════════════════════════════════════════════════════ -Duration: 11.4 s +Duration: 11.7 s -[ FAIL 0 | WARN 0 | SKIP 0 | PASS 14 ] +[ FAIL 0 | WARN 0 | SKIP 0 | PASS 15 ] diff --git a/tests/testthat/test_chent.R b/tests/testthat/test_chent.R index 4551cf7..7594640 100644 --- a/tests/testthat/test_chent.R +++ b/tests/testthat/test_chent.R @@ -15,7 +15,7 @@ test_that("We can generate a chent object from SMILES using RDKit", { }) test_that("We can add information retrieved from PubChem via webchem", { - oct$try_pubchem() + expect_warning(oct$try_pubchem(), "Overwriting uninitialized InChIKey") expect_equivalent(round(oct$mw, 2), 130.23) ik = "KBPLFHHGFOOTCA-UHFFFAOYSA-N" attr(ik, "source") <- "pubchem" |