Merge pull request #53 from iDigBio/update-docs

Resume testing on MacOS and specify HTTP/2

.Rbuildignore

@@ -5,3 +5,5 @@
 ^docs$
 ^pkgdown$
 ^\.github$
+^doc$
+^Meta$

.github/workflows/R-Git-Check.yml

@@ -26,6 +26,7 @@ jobs:
       fail-fast: false
       matrix:
         config:
+          - {os: macos-latest,   r: 'release'}
           - {os: windows-latest, r: 'release'}
           - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
           - {os: ubuntu-latest,   r: 'release'}
@@ -35,6 +36,12 @@ jobs:
       R_KEEP_PKG_SOURCE: yes
 
     steps:
+      - name: Install specific version of curl (macOS)
+        if: runner.os == 'macOS'
+        run: |
+          brew reinstall curl  # Adjust version as needed
+          brew link --force curl
+
       - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
@@ -44,11 +51,24 @@ jobs:
           r-version: ${{ matrix.config.r }}
           http-user-agent: ${{ matrix.config.http-user-agent }}
           use-public-rspm: true
-
+      
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
           extra-packages: any::rcmdcheck
           needs: check
+          cache-version: "no-cache"
+
+      # Install remotes package to handle versioned installations
+      - name: Install remotes package
+        if: runner.os == 'macOS'
+        run: |
+          R -e "install.packages('remotes')"
+
+      # Install r-curl 5.2.2 from CRAN Archive using remotes
+      - name: Install r-curl 5.2.2 from CRAN Archive
+        if: runner.os == 'macOS'
+        run: |
+          R -e "remotes::install_version('curl', '5.2.2')"
 
       - uses: r-lib/actions/check-r-package@v2
         with:

.gitignore

@@ -5,4 +5,6 @@
 ridigbio.Rproj
 .DS_Store
 inst/doc
-docs
+docs
+/doc/
+/Meta/

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: ridigbio
 Title: Interface to the iDigBio Data API
-Version: 0.3.9
-Date: 2024-8-19
+Version: 0.4.0
+Date: 2024-9-3
 Encoding: UTF-8
 Authors@R: c(person("Francois", "Michonneau", comment="Original Author", role=c("aut", "cph"),
   email="[email protected]"),

NEWS.md

@@ -1,3 +1,8 @@
+ridigbio 0.4.0
+===========
+### Enhancements
+* Offline build capability added
+
 ridigbio 0.3.9
 ===========
 

R/base.R

@@ -47,14 +47,27 @@ idig_parse <- function(req) {
 ##' @return nothing. Stops if HTTP code is >= 400
 ##' @author Francois Michonneau
 idig_check <- function(req) {
-  if (req$status_code >= 400) {
-    msg <- substr(req, 1, 200)
-    stop("HTTP failure: ", req$status_code, "\n",
-      "Error message from API server: ", msg,
-      call. = FALSE
-    )
-  }
-  idig_check_error(req)
+  tryCatch(
+    {
+      if (req$status_code >= 400) {
+        msg <- substr(req, 1, 200)
+        stop("HTTP failure: ", req$status_code, "\n",
+          "Error message from API server: ", msg,
+          call. = FALSE
+        )
+      }
+      idig_check_error(req)
+    },
+    error = function(e) {
+      warning("Error during API request: ", e$message)
+      msg <- substr(req, 1, 200)
+      stop("HTTP failure: ", req$status_code, "\n",
+        "Error message from API server: ", msg,
+        call. = FALSE
+      )
+      idig_check_error(req)
+    }
+  )
 }
 
 ##' Checks for error messages that can be returned by the API in JSON.
@@ -110,7 +123,6 @@ idig_POST <- function(path, body, ...) {
     httr::content_type_json(), ...
   )
   idig_check(req)
-
   req
 }
 

README.md

@@ -57,7 +57,6 @@ library("ridigbio")
 idig_search_records(rq=list(genus="galax"))
 idig_search_records(rq=list(family="diapensiaceae"), limit=1000)
 ```
-
 # Meta
 
 * [Please report any bugs or issues.](https://github.com/iDigBio/ridigbio/issues)

tests/testthat/test-base.R

@@ -3,6 +3,7 @@ context("test GET")
 
 test_that("list of all top-level fields returned in JSON", {
   testthat::skip_on_cran()
+  testthat::skip_if_offline()
   getReq <- list(rq = jsonlite::toJSON(list(family = "holothuriidae")))
   r <- idig_GET("search/records", query = getReq)
 
@@ -16,6 +17,7 @@ context("test POST")
 
 test_that("list of all top-level fields returned in JSON", {
   testthat::skip_on_cran()
+  testthat::skip_if_offline()
   fm <- list(rq = list(family = "holothuriidae"))
   r <- idig_POST("search/records", body = fm)
 
@@ -25,6 +27,7 @@ test_that("list of all top-level fields returned in JSON", {
 
 test_that("400 errors print messages", {
   testthat::skip_on_cran()
+  testthat::skip_if_offline()
 
   expect_error(
     idig_search_records(rq = list("asdf" = "asdf")),

tests/testthat/test-idig_build_attrib.R

@@ -2,6 +2,7 @@ context("test idig_build_attrib")
 
 test_that("attribution dataframe built from results dataframe and item counts match", {
   testthat::skip_on_cran()
+  testthat::skip_if_offline()
 
   testQuery <- idig_search_records(rq = list(family = "holothuriidae"))
   df <- idig_build_attrib(testQuery)
@@ -11,6 +12,7 @@ test_that("attribution dataframe built from results dataframe and item counts ma
 
 test_that("limited results, attribution counts match limit and result counts", {
   testthat::skip_on_cran()
+  testthat::skip_if_offline()
 
   df <- idig_search_records(rq = list(genus = "acer"), limit = 10)
   tt <- idig_build_attrib(df)

tests/testthat/test-idig_count_media.R

@@ -5,6 +5,8 @@ dqs <- 0
 
 test_that("all media records is a large number", {
   testthat::skip_on_cran()
+  testthat::skip_if_offline()
+
   num <- idig_count_media()
 
   expect_that(num, is_a("integer"))
@@ -14,6 +16,8 @@ test_that("all media records is a large number", {
 
 test_that("rq searches on the endpoint is a small number", {
   testthat::skip_on_cran()
+  testthat::skip_if_offline()
+
   num <- idig_count_media(rq = list("recordset" = recordset))
 
   expect_that(num, is_a("integer"))
@@ -22,6 +26,8 @@ test_that("rq searches on the endpoint is a small number", {
 
 test_that("mq searches on the endpoint is a small number", {
   testthat::skip_on_cran()
+  testthat::skip_if_offline()
+
   num <- idig_count_media(mq = list("dqs" = dqs))
 
   expect_that(num, is_a("integer"))

tests/testthat/test-idig_count_records.R

@@ -4,6 +4,8 @@ recordset <- "7450a9e3-ef95-4f9e-8260-09b498d2c5e6"
 
 test_that("all records is a large number", {
   testthat::skip_on_cran()
+  testthat::skip_if_offline()
+
   num <- idig_count_records()
 
   expect_that(num, is_a("integer"))
@@ -13,6 +15,8 @@ test_that("all records is a large number", {
 
 test_that("rq searches on the endpoint is a small number", {
   testthat::skip_on_cran()
+  testthat::skip_if_offline()
+
   num <- idig_count_records(rq = list("recordset" = recordset))
 
   expect_that(num, is_a("integer"))

tests/testthat/test-idig_meta_fields.R

@@ -2,6 +2,8 @@ context("test idig_meta_fields")
 
 test_that("records field list returns", {
   testthat::skip_on_cran()
+  testthat::skip_if_offline()
+
   f <- idig_meta_fields()
 
   expect_that(f, is_a("list"))
@@ -12,6 +14,8 @@ test_that("records field list returns", {
 
 test_that("records indexed subset returns", {
   testthat::skip_on_cran()
+  testthat::skip_if_offline()
+
   f <- idig_meta_fields(subset = "indexed")
 
   expect_null(f[["data"]])
@@ -21,6 +25,8 @@ test_that("records indexed subset returns", {
 
 test_that("records raw subset returns", {
   testthat::skip_on_cran()
+  testthat::skip_if_offline()
+
   f <- idig_meta_fields(subset = "raw")
 
   expect_null(f[["uuid"]])
@@ -29,6 +35,8 @@ test_that("records raw subset returns", {
 
 test_that("media list returns", {
   testthat::skip_on_cran()
+  testthat::skip_if_offline()
+
   f <- idig_meta_fields(type = "media")
 
   expect_that(f, is_a("list"))
@@ -39,6 +47,8 @@ test_that("media list returns", {
 
 test_that("media indexed subset returns", {
   testthat::skip_on_cran()
+  testthat::skip_if_offline()
+
   f <- idig_meta_fields(type = "media", subset = "indexed")
 
   expect_null(f[["data"]])
@@ -48,6 +58,8 @@ test_that("media indexed subset returns", {
 
 test_that("media raw subset returns", {
   testthat::skip_on_cran()
+  testthat::skip_if_offline()
+
   f <- idig_meta_fields(type = "media", subset = "raw")
 
   expect_null(f[["uuid"]])

tests/testthat/test-idig_search_media.R

@@ -11,6 +11,8 @@ u <- "00d96710-77dd-492c-9d5c-095a8cf9ee5a"
 
 test_that("full results for rq searches return", {
   testthat::skip_on_cran()
+  testthat::skip_if_offline()
+
   df <- idig_search_media(rq = rq, limit = 6000)
 
   expect_that(df, is_a("data.frame"))
@@ -20,6 +22,8 @@ test_that("full results for rq searches return", {
 
 test_that("full results for rq & mq queries together return", {
   testthat::skip_on_cran()
+  testthat::skip_if_offline()
+
   df <- idig_search_media(rq = rq, mq = mq, limit = 6000)
 
   expect_that(df, is_a("data.frame"))
@@ -29,6 +33,8 @@ test_that("full results for rq & mq queries together return", {
 
 test_that("full results for mq queries return", {
   testthat::skip_on_cran()
+  testthat::skip_if_offline()
+
   df <- idig_search_media(mq = mq, limit = 6000)
   u <- "00003b7d-07fb-4c36-a81a-18f7cde49203"
 
@@ -41,6 +47,8 @@ test_that("full results for mq queries return", {
 
 test_that("limits and custom fields return", {
   testthat::skip_on_cran()
+  testthat::skip_if_offline()
+
   df <- idig_search_media(mq = mq, fields = fields, limit = 10)
 
   expect_true(nrow(df) == 10)

tests/testthat/test-idig_search_records.R

@@ -6,6 +6,8 @@ fields <- c("uuid", "genus", "specificepithet", "data.dwc:occurrenceID")
 
 test_that("basic search, full results works", {
   testthat::skip_on_cran()
+  testthat::skip_if_offline()
+
   df <- idig_search_records(rq = rq, limit = 6000)
 
   expect_that(df, is_a("data.frame"))
@@ -18,6 +20,8 @@ test_that("basic search, full results works", {
 
 test_that("limited results, custom fields works", {
   testthat::skip_on_cran()
+  testthat::skip_if_offline()
+
   df <- idig_search_records(rq = rq, fields = fields, limit = 10)
 
   expect_true(nrow(df) == 10)
@@ -29,6 +33,7 @@ test_that("limited results, custom fields works", {
 
 test_that("offset works", {
   testthat::skip_on_cran()
+  testthat::skip_if_offline()
 
   df <- idig_search_records(rq = rq, fields = fields, limit = 2, offset = 0)
   second_uuid <- df[["uuid"]][[2]]
@@ -40,6 +45,8 @@ test_that("offset works", {
 
 test_that("sorting works", {
   testthat::skip_on_cran()
+  testthat::skip_if_offline()
+
   df <- idig_search_records(rq = rq, fields = fields, limit = 1)
 
   expect_true(substr(df[["uuid"]], 1, 2) == "00")
@@ -56,6 +63,7 @@ test_that("sorting works", {
 
 test_that("max items disabled is thrown for large queries", {
   testthat::skip_on_cran()
+  testthat::skip_if_offline()
 
   expect_that(
     df <- idig_search_records(rq = list("country" = "united states")),
@@ -65,6 +73,7 @@ test_that("max items disabled is thrown for large queries", {
 
 test_that("max items disabled is thrown for windows past 100k", {
   testthat::skip_on_cran()
+  testthat::skip_if_offline()
 
   expect_that(
     df <- idig_search_records(
@@ -77,6 +86,7 @@ test_that("max items disabled is thrown for windows past 100k", {
 
 test_that("can get the 100000th result", {
   testthat::skip_on_cran()
+  testthat::skip_if_offline()
 
   df <- idig_search_records(
     rq = list("country" = "united states"),
@@ -87,13 +97,17 @@ test_that("can get the 100000th result", {
 
 test_that("all fields returns a lot of fields", {
   testthat::skip_on_cran()
+  testthat::skip_if_offline()
+
   df <- idig_search_records(rq = rq, fields = "all", limit = 10)
 
   expect_true(ncol(df) > 50)
 })
 
 test_that("empty results return empty df with correct columns", {
   testthat::skip_on_cran()
+  testthat::skip_if_offline()
+
   df <- idig_search_records(rq = list("uuid" = "nobodyhome"), fields = fields)
 
   expect_true(nrow(df) == 0)
@@ -102,6 +116,8 @@ test_that("empty results return empty df with correct columns", {
 
 test_that("geopoint and special fields are expanded or excluded as appropriate", {
   testthat::skip_on_cran()
+  testthat::skip_if_offline()
+
   fields_special <- c("uuid", "geopoint", "mediarecords", "flags", "recordids")
   df <- idig_search_records(
     rq = list("uuid" = "f84faea8-82ac-4f71-b256-6b2be5d1b59d"),