Improve handling of json parsing errors

luomus · Jan 21, 2025 · 1159243 · 1159243
1 parent 392059d
commit 1159243
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diff --git a/CITATION.cff b/CITATION.cff
@@ -1,7 +1,7 @@
 # YAML 1.2
 ---
 version: "0.9.9.9000"
-date-released: 2024-11-05
+date-released: 2025-01-21
 title: finbif
 abstract: |
     "The `finbif` R package is a programmatic interface to the [Finnish
@@ -49,7 +49,7 @@ preferred-citation:
       orcid: "https://orcid.org/0000-0002-8686-4154"
   title: Introduction to the finbif package
   type: manual
-  year: 2024
+  year: 2025
   doi: "10.5281/zenodo.3612814"
   notes: "R package version 0.9.9.9000"
   url: "https://finbif-docs-dev.netlify.app/articles/finbif.html"

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -33,6 +33,7 @@ Depends: R (>= 3.5.0)
 Imports:
     digest,
     httr,
+    jsonlite,
     lutz,
     utils
 Roxygen: list(markdown = TRUE)

diff --git a/LICENSE b/LICENSE
@@ -1,2 +1,2 @@
-YEAR: 2019-2024
+YEAR: 2019-2025
 COPYRIGHT HOLDER: LUOMUS - Finnish Museum of Natural History
diff --git a/LICENSE.md b/LICENSE.md
@@ -1,6 +1,6 @@
 # MIT License
 
-Copyright (c) 2019-2024 LUOMUS - Finnish Museum of Natural History
+Copyright (c) 2019-2025 LUOMUS - Finnish Museum of Natural History
 
 Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
 

diff --git a/NAMESPACE b/NAMESPACE
@@ -29,6 +29,7 @@ importFrom(httr,RETRY)
 importFrom(httr,content)
 importFrom(httr,progress)
 importFrom(httr,write_disk)
+importFrom(jsonlite,validate)
 importFrom(lutz,tz_lookup_coords)
 importFrom(utils,packageVersion)
 importFrom(utils,read.delim)

diff --git a/NEWS.md b/NEWS.md
@@ -2,7 +2,7 @@
 
 # finbif 0.9.9.9000
 
-   - This is the current development version.
+   - Improvements have been made to the way errors in parsing json are handled. 
 
 # finbif 0.9.9
 

diff --git a/R/api_get.R b/R/api_get.R
@@ -1,6 +1,7 @@
 #' @noRd
 #' @importFrom digest digest
 #' @importFrom httr content RETRY
+#' @importFrom jsonlite validate
 #' @importFrom utils packageVersion
 
 api_get <- function(obj) {
@@ -244,21 +245,30 @@ api_get <- function(obj) {
 
   resp[[c("request", "url")]] <- notoken
 
-  parsed <- httr::content(resp)
+  txt <- httr::content(resp, type = "text", encoding = "UTF-8")
 
-  if (!identical(resp[["status_code"]], 200L)) {
+  valid <- jsonlite::validate(txt)
+
+  if (!identical(resp[["status_code"]], 200L) || !valid) {
+
+    parsed <- httr::content(resp)
 
     obj <- NULL
 
     err_msg <- paste0(
-      "API request failed [", resp[["status_code"]], "]\n", parsed[["message"]]
+      "API request failed [",
+      resp[["status_code"]],
+      "]\n",
+      parsed[["message"]],
+      "\n",
+      txt
     )
 
     stop(err_msg, call. = FALSE)
 
   }
 
-  obj[["content"]] <- parsed
+  obj[["content"]] <- httr::content(resp)
 
   obj[["response"]] <- resp
 

diff --git a/README.md b/README.md
@@ -87,8 +87,8 @@ FinBIF itself and the contributed datasets please visit this link:
 
 To cite the finbif R package in publications please use:
 
-  Morris, William K. (2024). Introduction to the finbif package. R
-  package version 0.9.9, https://doi.org/10.5281/zenodo.3612814
+  Morris, William K. (2025). Introduction to the finbif package. R
+  package version 0.9.9.9000, https://doi.org/10.5281/zenodo.3612814
 
 ----
 

diff --git a/codemeta.json b/codemeta.json
@@ -201,6 +201,18 @@
       "sameAs": "https://CRAN.R-project.org/package=httr"
     },
     "4": {
+      "@type": "SoftwareApplication",
+      "identifier": "jsonlite",
+      "name": "jsonlite",
+      "provider": {
+        "@id": "https://cran.r-project.org",
+        "@type": "Organization",
+        "name": "Comprehensive R Archive Network (CRAN)",
+        "url": "https://cran.r-project.org"
+      },
+      "sameAs": "https://CRAN.R-project.org/package=jsonlite"
+    },
+    "5": {
       "@type": "SoftwareApplication",
       "identifier": "lutz",
       "name": "lutz",
@@ -212,7 +224,7 @@
       },
       "sameAs": "https://CRAN.R-project.org/package=lutz"
     },
-    "5": {
+    "6": {
       "@type": "SoftwareApplication",
       "identifier": "utils",
       "name": "utils"
@@ -222,11 +234,11 @@
   "applicationCategory": "Biodiversity",
   "isPartOf": "https://species.fi",
   "keywords": ["api", "biodiversity", "biodiversity-informatics", "biodiversity-information", "finbif", "finbif-access", "occurrences", "r-package", "r-programming", "rstats", "species", "specimens", "taxon", "taxonomy", "web-services"],
-  "fileSize": "12098.553KB",
+  "fileSize": "12101.633KB",
   "citation": [
     {
       "@type": "SoftwareSourceCode",
-      "datePublished": "2024",
+      "datePublished": "2025",
       "author": [
         {
           "@type": "Person",

diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html
diff --git a/docs/LICENSE.html b/docs/LICENSE.html
diff --git a/docs/index.html b/docs/index.html
diff --git a/docs/news/index.html b/docs/news/index.html
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
@@ -7,7 +7,7 @@ articles:
   v03_selecting_variables: v03_selecting_variables.html
   v04_metadata: v04_metadata.html
   v05_filtering: v05_filtering.html
-last_built: 2025-01-09T12:46Z
+last_built: 2025-01-21T09:30Z
 urls:
   reference: https://finbif-docs-dev.netlify.app/reference
   article: https://finbif-docs-dev.netlify.app/articles
diff --git a/docs/search.json b/docs/search.json
-Original file line number
+Diff line change
@@ Expand Up / @@ -33,6 +33,7 @@ Depends: R (>= 3.5.0) @@
     Imports:
         digest,
         httr,
+        jsonlite,
         lutz,
         utils
     Roxygen: list(markdown = TRUE)
@@ Expand Down @@