0.3.0 Release

.github/workflows/R-CMD-check.yaml

@@ -1,5 +1,5 @@
-# For help debugging build failures open an issue on the RStudio community with the 'github-actions' tag.
-# https://community.rstudio.com/new-topic?category=Package%20development&tags=github-actions
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
     branches:
@@ -12,7 +12,9 @@ on:
       - master
       - dev
 
-name: R-CMD-check
+name: R-CMD-check.yaml
+
+permissions: read-all
 
 jobs:
   R-CMD-check:
@@ -26,60 +28,32 @@ jobs:
         config:
           - {os: windows-latest, r: 'release'}
           - {os: macOS-latest, r: 'release'}
-          - {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
-          - {os: ubuntu-20.04, r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+          - {os: ubuntu-22.04, r: 'release', rspm: "https://packagemanager.posit.co/cran/__linux__/jammy/latest"}
+          - {os: ubuntu-22.04, r: 'devel', rspm: "https://packagemanager.posit.co/cran/__linux__/jammy/latest"}
+          - {os: ubuntu-latest,  r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,  r: 'release'}
 
     env:
-      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
-      RSPM: ${{ matrix.config.rspm }}
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-pandoc@v2
 
       - uses: r-lib/actions/setup-r@v2
         with:
           r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
 
-      - uses: r-lib/actions/setup-pandoc@v2
-
-      - 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
+      - uses: r-lib/actions/setup-r-dependencies@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 system dependencies
-        if: runner.os == 'Linux'
-        run: |
-          while read -r cmd
-          do
-            eval sudo $cmd
-          done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))')
-
-      - name: Install dependencies
-        run: |
-          remotes::install_deps(dependencies = TRUE)
-          remotes::install_cran("rcmdcheck")
-        shell: Rscript {0}
-
-      - name: Check
-        env:
-          _R_CHECK_CRAN_INCOMING_REMOTE_: false
-        run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
-        shell: Rscript {0}
+          extra-packages: any::rcmdcheck
+          needs: check
 
-      - name: Upload check results
-        if: failure()
-        uses: actions/upload-artifact@main
+      - uses: r-lib/actions/check-r-package@v2
         with:
-          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
-          path: check
+          upload-snapshots: true
+          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'

.github/workflows/rhub.yaml

@@ -0,0 +1,95 @@
+# R-hub's generic GitHub Actions workflow file. It's canonical location is at
+# https://github.com/r-hub/actions/blob/v1/workflows/rhub.yaml
+# You can update this file to a newer version using the rhub2 package:
+#
+# rhub::rhub_setup()
+#
+# It is unlikely that you need to modify this file manually.
+
+name: R-hub
+run-name: "${{ github.event.inputs.id }}: ${{ github.event.inputs.name || format('Manually run by {0}', github.triggering_actor) }}"
+
+on:
+  workflow_dispatch:
+    inputs:
+      config:
+        description: 'A comma separated list of R-hub platforms to use.'
+        type: string
+        default: 'linux,windows,macos'
+      name:
+        description: 'Run name. You can leave this empty now.'
+        type: string
+      id:
+        description: 'Unique ID. You can leave this empty now.'
+        type: string
+
+jobs:
+
+  setup:
+    runs-on: ubuntu-latest
+    outputs:
+      containers: ${{ steps.rhub-setup.outputs.containers }}
+      platforms: ${{ steps.rhub-setup.outputs.platforms }}
+
+    steps:
+    # NO NEED TO CHECKOUT HERE
+    - uses: r-hub/actions/setup@v1
+      with:
+        config: ${{ github.event.inputs.config }}
+      id: rhub-setup
+
+  linux-containers:
+    needs: setup
+    if: ${{ needs.setup.outputs.containers != '[]' }}
+    runs-on: ubuntu-latest
+    name: ${{ matrix.config.label }}
+    strategy:
+      fail-fast: false
+      matrix:
+        config: ${{ fromJson(needs.setup.outputs.containers) }}
+    container:
+      image: ${{ matrix.config.container }}
+
+    steps:
+      - uses: r-hub/actions/checkout@v1
+      - uses: r-hub/actions/platform-info@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+      - uses: r-hub/actions/setup-deps@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+      - uses: r-hub/actions/run-check@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+
+  other-platforms:
+    needs: setup
+    if: ${{ needs.setup.outputs.platforms != '[]' }}
+    runs-on: ${{ matrix.config.os }}
+    name: ${{ matrix.config.label }}
+    strategy:
+      fail-fast: false
+      matrix:
+        config: ${{ fromJson(needs.setup.outputs.platforms) }}
+
+    steps:
+      - uses: r-hub/actions/checkout@v1
+      - uses: r-hub/actions/setup-r@v1
+        with:
+          job-config: ${{ matrix.config.job-config }}
+          token: ${{ secrets.RHUB_TOKEN }}
+      - uses: r-hub/actions/platform-info@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+      - uses: r-hub/actions/setup-deps@v1
+        with:
+          job-config: ${{ matrix.config.job-config }}
+          token: ${{ secrets.RHUB_TOKEN }}
+      - uses: r-hub/actions/run-check@v1
+        with:
+          job-config: ${{ matrix.config.job-config }}
+          token: ${{ secrets.RHUB_TOKEN }}

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: datasetjson
 Type: Package
 Title: Read and Write CDISC Dataset JSON Files
-Version: 0.2.0
+Version: 0.3.0
 Authors@R: c(
     person(given = "Mike",
            family = "Stackhouse",
@@ -13,24 +13,31 @@ Authors@R: c(
            email = "[email protected]",
            role = "aut")
     )
-Description: Read, construct and write CDISC (Clinical Data Interchange Standards Consortium) Dataset JSON (JavaScript Object Notation) files, while validating per the Dataset JSON schema file, as described in CDISC (2023) <https://www.cdisc.org/dataset-json>.
-URL: https://github.com/atorus-research/datasetjson
-BugReports: https://github.com/atorus-research/datasetjson/issues
+Description: Read, construct and write CDISC (Clinical Data Interchange Standards Consortium) Dataset JSON (JavaScript Object Notation) files, while validating per the Dataset JSON schema file, as described in CDISC (2023) <https://www.cdisc.org/standards/data-exchange/dataset-json>.
+URL: https://atorus-research.github.io/datasetjson/
+BugReports: https://github.com/atorus-research/datasetjson/issues/
 Encoding: UTF-8
 Language: en-US
 License: Apache License (>= 2)
 LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.3
-Depends: R (>= 3.5)
+RoxygenNote: 7.3.2
+Depends: R (>= 4.0)
 Imports:
-    jsonlite (>= 1.8.0),
-    jsonvalidate (>= 1.3.1)
+    yyjsonr (>= 0.1.18),
+    jsonvalidate (>= 1.3.1),
+    hms
 Suggests:
     testthat (>= 2.1.0),
+    jsonlite (>= 1.8.0),
     knitr,
     haven,
     rmarkdown,
-    withr
+    withr,
+    purrr,
+    tibble,
+    dplyr,
+    lubridate,
+    data.table
 VignetteBuilder: knitr
 Config/testthat/edition: 3

NAMESPACE

@@ -1,30 +1,28 @@
 # Generated by roxygen2: do not edit by hand
 
-S3method(set_metadata_ref,data_metadata)
-S3method(set_metadata_ref,datasetjson)
-S3method(set_metadata_ref,default)
-S3method(set_metadata_version,data_metadata)
-S3method(set_metadata_version,datasetjson)
-S3method(set_metadata_version,default)
-S3method(set_study_oid,data_metadata)
-S3method(set_study_oid,datasetjson)
-S3method(set_study_oid,default)
-export(data_metadata)
 export(dataset_json)
-export(dataset_metadata)
-export(file_metadata)
+export(get_column_metadata)
 export(read_dataset_json)
-export(set_data_type)
+export(set_dataset_label)
+export(set_dataset_name)
 export(set_file_oid)
+export(set_item_oid)
+export(set_last_modified)
 export(set_metadata_ref)
 export(set_metadata_version)
 export(set_originator)
 export(set_source_system)
 export(set_study_oid)
+export(set_variable_attributes)
 export(validate_dataset_json)
 export(write_dataset_json)
-importFrom(jsonlite,fromJSON)
-importFrom(jsonlite,toJSON)
+importFrom(hms,as_hms)
 importFrom(jsonvalidate,json_validate)
 importFrom(tools,file_path_sans_ext)
 importFrom(utils,tail)
+importFrom(yyjsonr,opts_read_json)
+importFrom(yyjsonr,opts_write_json)
+importFrom(yyjsonr,read_json_file)
+importFrom(yyjsonr,read_json_str)
+importFrom(yyjsonr,write_json_file)
+importFrom(yyjsonr,write_json_str)

NEWS.md

@@ -1,3 +1,14 @@
+# datasetjson 0.3.0
+
+This release provides a significant overhaul of the package due to the updates 
+for Dataset JSON 1.1.0. Performance has also been significantly improved, as well
+as the main object interface.
+
+-  Initial support for Dataset JSON v1.1.0 schema
+-  Flip JSON backend to {yyjsonr} (#32)
+-  Redesign of core objects
+-  New vignettes and helper functions
+
 # datasetjson 0.2.0
 
 - Remove schema validation on read and write (#26)

R/archive/data_metadata.R

@@ -0,0 +1,56 @@
+#' Create the data metadata container for a Dataset JSON object
+#'
+#' @param study Study OID value
+#' @param metadata_version Metadata version OID value
+#' @param metadata_ref Metadata reference (i.e. path to Define.xml)
+#'
+#' @return data_metadata object
+#' @export
+#'
+#' @examples
+#' # Create object directly
+#' data_meta <- data_metadata(
+#'   study = "SOMESTUDY",
+#'   metadata_version = "MDV.MSGv2.0.SDTMIG.3.3.SDTM.1.7",
+#'   metadata_ref = "some/define.xml"
+#' )
+#'
+#' # Use setter functions
+#' data_meta <- data_metadata()
+#' data_meta_updated <- set_metadata_ref(data_meta, "some/define.xml")
+#' data_meta_updated <- set_metadata_version(data_meta_updated, "MDV.MSGv2.0.SDTMIG.3.3.SDTM.1.7")
+#' data_meta_updated <- set_study_oid(data_meta_updated, "SOMESTUDY")
+#'
+data_metadata <- function(study = NULL, metadata_version = NULL, metadata_ref = NULL) {
+
+  x <- list(
+    studyOID = study,
+    metaDataVersionOID = metadata_version,
+    metaDataRef = metadata_ref,
+    itemGroupData = NULL
+  )
+
+  structure(
+    x,
+    class = c("data_metadata", "list")
+  )
+}
+
+#' Set data metadata parameters
+#'
+#' This set of functions
+#' @param x data metadata or datasetjson object
+#' @param study Study OID value
+#' @param ... Additional parameters
+#'
+#' @return A datasetjson or data_metadata object
+#' @export
+#'
+#' @family Data metadata setters
+#' @rdname data_metadata_setters
+#'
+#' @examples
+#' data_meta <- data_metadata()
+#' data_meta_updated <- set_metadata_ref(data_meta, "some/define.xml")
+#' data_meta_updated <- set_metadata_version(data_meta_updated, "MDV.MSGv2.0.SDTMIG.3.3.SDTM.1.7")
+#' data_meta_updated <- set_study_oid(data_meta_updated, "SOMESTUDY")

R/dataset_metadata.R → R/archive/dataset_metadata.R

@@ -95,7 +95,7 @@ set_item_data <- function(x, .data, ...) {
 
   # Insert into object in proper spots
   x[[1]][['records']] <- records
-  x[[1]][['itemData']] <- item_data
+  x[[1]][['itemData']] <- unname(item_data)
   x
 }