CRAN Version 1.1.0

tabledap now retrus values as same type as in the dds

Author: rmendels

.github/workflows/R-check.yml

@@ -0,0 +1,101 @@
+on: [push, pull_request]
+
+name: R-check
+
+jobs:
+  R-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+        - { os: windows-latest, r: 'release'}
+        - { os: macOS-latest, r: 'release'}
+        # - { os: macOS-latest, r: 'devel'}
+        - { os: ubuntu-18.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/bionic/latest"}
+
+    env:
+      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
+      RSPM: ${{ matrix.config.rspm }}
+      VCR_VERBOSE_ERRORS: true
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: r-lib/actions/setup-r@v1
+        with:
+          r-version: ${{ matrix.config.r }}
+
+      - uses: r-lib/actions/setup-pandoc@v1
+
+      - name: Query dependencies
+        run: |
+          install.packages('remotes')
+          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
+          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
+        shell: Rscript {0}
+
+      - name: Cache R packages
+        if: runner.os != 'Windows'
+        uses: actions/cache@v2
+        with:
+          path: ${{ env.R_LIBS_USER }}
+          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
+          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
+
+      - name: install macOS system dependencies
+        if: runner.os == 'macOS'
+        continue-on-error: true
+        run: |
+          brew install pkg-config gdal udunits proj netcdf
+
+      - name: Install system dependencies
+        if: runner.os == 'Linux'
+        env:
+          RHUB_PLATFORM: linux-x86_64-ubuntu-gcc
+        run: |
+          sudo apt update
+          sudo apt install -y --no-install-recommends \
+            gdal-bin \
+            libgdal-dev \
+            libproj-dev \
+            netcdf-bin
+      
+      - name: Install dependencies
+        run: |
+          remotes::install_deps(dependencies = TRUE)
+          remotes::install_cran(c("rcmdcheck", "taxize"))
+        shell: Rscript {0}
+
+      - name: Session info
+        run: |
+          options(width = 100)
+          pkgs <- installed.packages()[, "Package"]
+          sessioninfo::session_info(pkgs, include_base = TRUE)
+        shell: Rscript {0}
+
+      - name: Check
+        env:
+          _R_CHECK_CRAN_INCOMING_: false
+        run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
+        shell: Rscript {0}
+
+      - name: Show testthat output
+        if: always()
+        run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true
+        shell: bash
+
+      - name: Upload check results
+        if: failure()
+        uses: actions/upload-artifact@v2
+        with:
+          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
+          path: check
+
+      - name: Test coverage
+        if: matrix.config.os == 'ubuntu-18.04' && matrix.config.r == 'release'
+        run: |
+          Rscript -e 'remotes::install_cran("covr")' -e 'covr::codecov(token = "${{secrets.CODECOV_TOKEN}}")'

CRAN-SUBMISSION

@@ -1,3 +1,3 @@
-Version: 1.0.4
-Date: 2023-08-23 01:37:27 UTC
-SHA: 5c8c7179d4e63b927a08e707d8bb1c8b6bd0c693
+Version: 1.1.0
+Date: 2024-01-12 17:22:06 UTC
+SHA: 9662d98df70233be405dedcd27534c721b9136f5

DESCRIPTION

@@ -5,8 +5,8 @@ Description: General purpose R client for 'ERDDAP' servers. Includes
     'datasets', and fetch 'datasets', in either 'csv' or 'netCDF' format.
     'ERDDAP' information: 
     <https://upwell.pfeg.noaa.gov/erddap/information.html>.
-Version: 1.0.4
-Date: 2023-08-23
+Version: 1.1.0
+Date: 2024-1-12
 License: MIT + file LICENSE
 Authors@R: c(
     person("Scott", "Chamberlain", role = "aut"),
@@ -23,16 +23,18 @@ Roxygen: list(markdown = TRUE)
 Encoding: UTF-8
 Language: en-US
 Imports:
-    utils,
     crul (>= 0.7.4),
     dplyr (>= 0.5.0),
     data.table (>= 1.12.0),
-    jsonlite (>= 1.6),
-    xml2 (>= 1.2.0),
     digest,
+    hoardr (>= 0.5.2),
+    jsonlite (>= 1.6),
+    lubridate,
+    methods,
     ncdf4 (>= 1.16),
     tibble,
-    hoardr (>= 0.5.2)
+    utils,
+    xml2 (>= 1.2.0)
 Suggests:
     knitr,
     rmarkdown

NEWS.md

@@ -1,3 +1,7 @@
+rerddap 1.1.0
+=============
+* 'tabledap()' responses now have the datatype given in the file .dds
+
 rerddap 1.0.4
 =============
 * fixes problem with time bounds check and "last"

R/ncdf_helpers.R

@@ -12,7 +12,10 @@ ncdf4_get <- function(file){
   for (i in seq_along(dims)) {
     out[[dims[i]]] <- ncdf4::ncvar_get(nc, nc$dim[[dims[i]]])
   }
-  out$time <- sapply(out$time, convert_time)
+  if ('time' %in% names(out)){
+    out$time <- sapply(out$time, convert_time)
+    
+  }
   vars <- names(nc$var)
   outvars <- list()
   for (i in seq_along(vars)) {

R/table.R

@@ -208,8 +208,27 @@ tabledap <- function(x, ..., fields=NULL, distinct=FALSE, orderby=NULL,
   }
   resp <- erd_tab_GET(url, dset = attr(x, "datasetid"), store, callopts)
   loc <- if (store$store == "disk") resp else "memory"
+  temp_table <- read_table(resp)
+  # change response type
+  dds_url <- sub('csv', 'dds', url)
+  # strip off constraints
+  amp_location <- regexpr("&", dds_url)
+  if (amp_location[1] > 0) {
+    dds_url <- substr(dds_url, 1, amp_location[1] - 1)
+  }
+  dds <- try(suppressWarnings(utils::read.table(dds_url)), silent = TRUE)
+  # if (class(dds) == 'try-error') {
+  if (methods::is(dds, 'try-error')) {
+    print('failed to get variable datatype information')
+    print('will leave units unchanged')
+  } else{
+    temp_table <- set_units(temp_table, dds)
+  }
+ 
+    
   structure(
-    read_table(resp),
+    #read_table(resp),
+    temp_table,
     class = c("tabledap", "data.frame"),
     datasetid = attr(x, "datasetid"),
     path = loc,
@@ -262,3 +281,25 @@ makevar <- function(x, y){
     NULL
   }
 }
+
+set_units <- function(temp_t, dds) {
+    for (i in seq(3, (nrow(dds) - 2))) {
+        var_type <- dds[i, 1]
+        var_name <- dds[i, 2]
+        var_name <- substr(var_name, 1, nchar(var_name)-1)
+        if (var_name == 'time') {
+            # make certain lubridate can convert time
+            temp_time <- suppressWarnings(lubridate::as_datetime(temp_t$time))
+           if (!any(is.na(temp_time))) {
+               temp_t$time <- temp_time
+           }
+       } else {
+           if (grepl('Float', var_type)) {
+               temp_t[[var_name]] <- as.numeric(temp_t[[var_name]])
+           } else if(grepl('Int', var_type)) {
+              temp_t[[var_name]] <- as.integer(temp_t[[var_name]])
+           }
+       }
+    } 
+  return(temp_t)
+}

cran-comments.md

@@ -1,6 +1,6 @@
 ## Test environments
 
-* local macOS install, R 4.3.1
+* local macOS install, R 4.3.2
 * rhub (devtools::check_rhub())
 * macOS Builder (devtools::check_mac_release())
 * win-builder (devel and release - devtools::check_win_*())
@@ -15,7 +15,7 @@ OK from all checks
 
 ---
 
-This version fixes problems with the time bounds checks and "last"
+'tabledap()' responses now have the datatype given in the file .dds
 
 Thanks! 
 Roy Mendelssohn