0.1.1

.github/.gitignore

@@ -0,0 +1 @@
+*.html

.github/workflows/pkgdown.yaml

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+# 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: [main, master]
+  pull_request:
+    branches: [main, master]
+  release:
+    types: [published]
+  workflow_dispatch:
+
+name: pkgdown
+
+jobs:
+  pkgdown:
+    runs-on: ubuntu-latest
+    # Only restrict concurrency for non-PR jobs
+    concurrency:
+      group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    permissions:
+      contents: write
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::pkgdown, local::.
+          needs: website
+
+      - name: Build site
+        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
+        shell: Rscript {0}
+
+      - name: Deploy to GitHub pages 🚀
+        if: github.event_name != 'pull_request'
+        uses: JamesIves/github-pages-deploy-action@v4.4.1
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs

.github/workflows/test-coverage.yaml

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+# 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: [main, master]
+  pull_request:
+    branches: [main, master]
+
+name: test-coverage
+
+permissions: read-all
+
+jobs:
+  test-coverage:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::covr, any::xml2
+          needs: coverage
+
+      - name: Test coverage
+        run: |
+          cov <- covr::package_coverage(
+            quiet = FALSE,
+            clean = FALSE,
+            install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
+          )
+          covr::to_cobertura(cov)
+        shell: Rscript {0}
+
+      - uses: codecov/codecov-action@v4
+        with:
+          fail_ci_if_error: ${{ github.event_name != 'pull_request' && true || false }}
+          file: ./cobertura.xml
+          plugin: noop
+          disable_search: true
+          token: ${{ secrets.CODECOV_TOKEN }}
+
+      - name: Show testthat output
+        if: always()
+        run: |
+          ## --------------------------------------------------------------------
+          find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true
+        shell: bash
+
+      - name: Upload test results
+        if: failure()
+        uses: actions/upload-artifact@v4
+        with:
+          name: coverage-test-failures
+          path: ${{ runner.temp }}/package

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: tuRtle
 Title: Parse and Export R Data with the Turtle Syntax for the Resource Description Framework. 
-Date: 2024-01-28
-Version: 0.1.0
+Date: 2024-06-11
+Version: 0.1.1
 Authors@R: 
     c(person(given = "Daniel", family = "Antal", 
            email = "daniel.antal@dataobservatory.eu", 
@@ -17,11 +17,14 @@ BugReports: https://github.com/dataobservatory-eu/tuRtle/issues
 License: GPL (>= 3)
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.0
+RoxygenNote: 7.3.1
 Imports: 
-    dataset
+    dataset,
+    utils
 Suggests: 
     knitr,
     remotes,
+    spelling,
     testthat (>= 3.0.0)
 Config/testthat/edition: 3
+Language: en-GB

NAMESPACE

@@ -1,3 +1,7 @@
 # Generated by roxygen2: do not edit by hand
 
+export(dataset_ttl_write)
+export(ttl_prefix_write)
+export(ttl_statements_write)
 export(ttl_write)
+importFrom(utils,data)

NEWS.md

@@ -1,3 +1,4 @@
-# tuRtle 0.1.0
+# tuRtle 0.1.1
 
-* Initial development version on Zenodo and GitHub.
+* 2024-01-28. Initial development version 0.1.0 on Zenodo and GitHub.
+* 2024-06-11. Version 0.1.11 has separate functions for writing a namespace prefix and statements, and has extensive unit tests.

R/ttl_dataset_write.R

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+#' @title Write a dataset into Turtle serialisation
+#' @description
+#' Write a dataset into a Turtle serialisation.
+#'
+#' @param tdf A dataset in exactly three columns.
+#' @param ttl_namespace The namespace definitions of the dataset.
+#' @param file_path The path to the file that should be written or appended.
+#' @param overwrite If the file exists, overwrite it? Defaults to \code{TRUE}.
+#' @return A text file with the prefix and the observation serialisations.
+#' @examples
+#' testtdf <- data.frame (s = c("eg:o1", "eg:01", "eg:02"),
+#'                        p = c("a", "eg-var:", "eg-var"),
+#'                        o = c("qb:Observation",
+#'                              "\"1\"^^<xs:decimal>",
+#'                              "\"2\"^^<xs:decimal>"))
+#'
+#' examplefile <- file.path(tempdir(), "ttl_dataset_write.ttl")
+#'
+#' dataset_ttl_write(tdf=testtdf, file_path = examplefile)
+#'
+#' readLines(examplefile)
+#' @export
+
+dataset_ttl_write <- function(tdf,
+                              ttl_namespace = NULL,
+                              file_path = NULL,
+                              overwrite = TRUE) {
+
+  ## load dataset_namespace
+  default_namespace <- getdata("dataset_namespace", "dataset")
+  default_namespace <- default_namespace[
+    which(default_namespace$prefix %in% c("rdf:", "rdfs:", "owl:",
+                                          "qb:", "dcat:", "xsd:")),]
+
+  ## validate dataset
+  validate_tdf(tdf)
+
+  ## use subject predicate, object names
+  names(tdf) <- c("s", "p", "o")
+
+  if (is.null(file_path)) file_path <- file.path(tempdir(), "tmp.ttl")
+
+  if (is.null(ttl_namespace)) {
+    ttl_namespace <- default_namespace
+  }
+
+  ttl_prefix_write(ttl_namespace = ttl_namespace,
+                   file_path=file_path,
+                   overwrite=overwrite)
+
+  invisible(ttl_observations_write(tdf, file_path))
+}
+

R/ttl_prefix_write.R

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+#' @title Write TTL prefix
+#' @description Write the namespace prefixes into the header of a Turtle serialisation
+#' @param ttl_namespace A namespace definition as a two-column dataset.
+#' @param file_path A file_path to write the TTL prefix namespace definitions.
+#' @param overwrite Boolean, if the file should be overwritten (if it exists at all.) 
+#' Defaults to \code{TRUE}.
+#' @export
+#' @examples
+#' ttl_namespace <- data.frame(
+#'   prefix = c("dbo:", "dcterms:"), 
+#'   uri = c("<http://dbpedia.org/ontology/>", 
+#'           "<http://purl.org/dc/terms/>")
+#' )
+#' file_path <- tempfile()
+#' ttl_prefix_write(ttl_namespace, file_path)
+#' readLines(file_path)
+#' 
+
+ttl_prefix_write <- function(ttl_namespace, file_path, overwrite=TRUE) {
+  if ( file.exists(file_path) & overwrite ) file.remove(file_path)
+
+  create_string <- paste(
+    apply ( ttl_namespace, 1, function(x) {
+      prefix <- x[[1]]
+      n <- max(12-nchar(x[[1]]), 1)
+      separator <- paste(rep (" ", n), collapse="")
+      paste0("@prefix  ", prefix, separator, x[[2]], " .")
+    }), sep = "", collapse = "\n"
+  )
+
+  if (overwrite) {
+    write(create_string, file=file_path, append = F )
+  } else {
+    write(create_string, file=file_path, append = T )
+  }
+}

R/ttl_statements_write.R

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+#' @title Write statements into a TTL file
+#' @param tdf A dataset in exactly three columns.
+#' @param file_path The path to the file that should be written or appended.
+#' @param overwrite If the file exists, overwrite it? Defaults to \code{TRUE}.
+#' @examples
+#' tdf <- data.frame (s = c("eg:01","eg:02",  "eg:01", "eg:02", "eg:01" ),
+#'                    p = c("a", "a", "eg-var:", "eg-var:", "rdfs:label"),
+#'                    o = c("qb:Observation",
+#'                          "qb:Observation",
+#'                          "\"1\"^^<xs:decimal>",
+#'                          "\"2\"^^<xs:decimal>", 
+#'                          '"Example observation"'))
+#'
+#' examplefile <- file.path(tempdir(), "ttl_dataset_write.ttl")
+#'
+#' dataset_ttl_write(tdf=tdf, file_path = examplefile)
+#'
+#' readLines(examplefile)
+#' @export
+
+ttl_statements_write <- function(tdf, file_path, overwrite=TRUE) {
+  ## tdf must be s, o, p
+  validate_tdf(tdf)
+
+  if (overwrite) {
+    reset_text_file(file_path=file_path)
+  } else {
+    write("\n", file=file_path, append = TRUE)
+  }
+
+  unique_subjects <- unique(tdf$s)
+
+  lapply ( unique_subjects, function(x) write_statements(x, tdf, file_path))
+
+  invisible(TRUE)
+}
+
+#' @keywords internal
+get_class_definition <- function(instance) {
+  return_value <- which(instance$p == "a")[1]
+  if (length(return_value)==0) stop(instance$s, " has no class definition.")
+  return_value
+}
+
+#' @keywords internal
+write_statements <- function(x, tdf, file_path) {
+  instance <- tdf[which(tdf$s == x), ]
+  instance_definition <- get_class_definition(instance)
+  instance_rows <- 1:nrow(instance)
+  instance_rows <- instance_rows[!instance_rows %in% instance_definition]
+
+  definition_statement <- paste0(instance$s[instance_definition], 
+                                 "    a    ",  
+                                 instance$o[instance_definition], ";")
+
+  if (length(instance_rows)>0) {
+    write(x = paste0(definition_statement),
+          file = file_path, append = T
+    )
+    statements <- c(
+      #further statements 
+      unique(paste0("   ", instance$p[instance_rows], "   ", instance$o[instance_rows], " ;"))
+    )
+
+    # last statement must end with a .
+    last_statement <- statements[length(statements)]
+    statements[length(statements)] <- paste0(substr(last_statement,1, nchar(last_statement)-1), ".")
+    write( statements,
+           file = file_path, append = T
+    ) 
+    write( "\n",
+           file = file_path, append = T
+    ) 
+
+    } else {
+      ## there is only a class definition
+      write(x = paste0(definition_statement, " ."),
+            file = file_path, append = T
+      )
+
+      write( "\n",
+             file = file_path, append = T
+      ) 
+      ## what if no class definition?
+    }
+}