Merge pull request #2 from OxfordIHTM/dev

refresh repository

DESCRIPTION

@@ -18,7 +18,11 @@ Description: The Oxford University Research Archive (ORA) <https://ora.ox.ac.uk/
     functions to interface with the ORA API <https://ora.ox.ac.uk/api>.
 License: GPL (>= 3)
 Imports: 
+    dplyr,
     httr2,
+    rlang,
+    tibble,
+    tidyr,
     xml2
 Encoding: UTF-8
 Language: en-GB

NAMESPACE

@@ -6,10 +6,14 @@ export(ora_list_records)
 export(ora_list_records_id)
 export(ora_list_sets)
 export(ora_structure_identify)
+export(ora_structure_meta_formats)
+importFrom(dplyr,bind_cols)
+importFrom(dplyr,bind_rows)
 importFrom(httr2,req_perform)
 importFrom(httr2,req_url_query)
 importFrom(httr2,request)
 importFrom(httr2,resp_body_xml)
-importFrom(xml2,xml_attrs)
-importFrom(xml2,xml_children)
-importFrom(xml2,xml_contents)
+importFrom(rlang,.data)
+importFrom(tibble,tibble)
+importFrom(tidyr,unnest)
+importFrom(xml2,as_list)

R/aurora.R

@@ -15,6 +15,10 @@
 #' @name aurora
 #' @keywords internal
 #' @importFrom httr2 request req_url_query req_perform resp_body_xml
-#' @importFrom xml2 xml_children xml_contents xml_attrs
+#' @importFrom xml2 as_list
+#' @importFrom dplyr bind_rows bind_cols
+#' @importFrom tidyr unnest
+#' @importFrom rlang .data
+#' @importFrom tibble tibble
 #'
 "_PACKAGE"

R/ora_identify.R

@@ -1,18 +1,22 @@
 #'
-#' Identify
+#' Retrieve information about Oxford University OAI repository
 #'
 #' @param base_url The OAI-PMH endpoint base URL. Set to
-#'   https://ora.ox.ac.uk/oai2
+#'   https://ora.ox.ac.uk/oai2.
+#' @param tabular Logical. Should response be structured into a table?
+#'   Default is TRUE.
 #'
-#' @returns XML OAI response
+#' @returns A data.frame (default) or an XML document (if `tabular = FALSE`)
+#'   with identifying information on the OAI repository.
 #'
 #' @examples
 #' ora_identify()
 #'
 #' @export
 #'
 
-ora_identify <- function(base_url = "https://ora.ox.ac.uk/oai2") {
+ora_identify <- function(base_url = "https://ora.ox.ac.uk/oai2",
+                         tabular = TRUE) {
   ## Make base request ----
   req <- httr2::request(base_url)
 
@@ -25,6 +29,10 @@ ora_identify <- function(base_url = "https://ora.ox.ac.uk/oai2") {
     httr2::req_perform() |>
     httr2::resp_body_xml()
 
+  ## Structure resp? ----
+  if (tabular)
+    resp <- ora_structure_identify(resp)
+
   ## Return resp ----
   resp
 }

R/ora_list_metadata_formats.R

@@ -2,17 +2,21 @@
 #' List metadata formats
 #'
 #' @param base_url The OAI-PMH endpoint base URL. Set to
-#'   https://ora.ox.ac.uk/oai2
+#'   https://ora.ox.ac.uk/oai2.
+#' @param tabular Logical. Should response be structured into a table?
+#'   Default is TRUE.
 #'
-#' @returns XML OAI response
+#' @returns A data.frame (default) or an XML document (if `tabular = FALSE`)
+#'   with identifying information on the OAI metadata formats.
 #'
 #' @examples
 #' ora_list_meta_formats()
 #'
 #' @export
 #'
 
-ora_list_meta_formats <- function(base_url = "https://ora.ox.ac.uk/oai2") {
+ora_list_meta_formats <- function(base_url = "https://ora.ox.ac.uk/oai2",
+                                  tabular = TRUE) {
   ## Make base request ----
   req <- httr2::request(base_url)
 
@@ -25,6 +29,10 @@ ora_list_meta_formats <- function(base_url = "https://ora.ox.ac.uk/oai2") {
     httr2::req_perform() |>
     httr2::resp_body_xml()
 
+  ## Structure resp ----
+  if (tabular)
+    resp <- ora_structure_meta_formats(resp)
+
   ## Return resp ----
   resp
 }

R/ora_structure.R

@@ -1,28 +1,78 @@
 #'
 #' Structure ORA XML outputs
 #'
-#' @param ora_xml XML outputs
+#' @param ora_xml XML outputs.
 #'
-#' @return A structured output
+#' @return A tibble outputs.
 #'
 #' @examples
-#' #ora_identify() |> ora_identify_structure()
+#' ora_identify()
+#' ora_list_meta_formats()
 #'
 #' @rdname ora_structure
 #' @export
 #'
 
 ora_structure_identify <- function(ora_xml) {
-  field_names <- ora_xml |>
-    xml2::xml_children() |>
-    xml2::xml_children() |>
-    xml2::xml_name()
-
-  values <- ora_xml |>
-    xml2::xml_children() |>
-    xml2::xml_attrs(".//verb")
-    xml2::xml_children() |>
-    xml2::xml_contents() |>
-    xml2::xml_children() |>
-    xml2::xml_contents()
+  xml_list <- xml2::as_list(ora_xml)
+
+  responseDate <- xml_list |>
+    unlist(recursive = FALSE) |>
+    (\(x) x[[1]][[1]])()
+
+  request <- xml_list[[1]][2] |>
+    (\(x) paste0(x$request, "?verb=", attributes(x$request)))()
+
+  description <- xml_list |>
+    unlist(recursive = FALSE) |>
+    (\(x) x[[3]][8])() |>
+    unlist() |>
+    dplyr::bind_rows()
+
+  names(description) <- names(description) |>
+    tools::file_ext()
+
+  tibble::tibble(
+    responseDate,
+    request,
+    xml_list |>
+      unlist(recursive = FALSE) |>
+    (\(x) x[[3]][1:7] |> unlist() |> dplyr::bind_rows())(),
+    description
+  )
+}
+
+#'
+#' @rdname ora_structure
+#' @export
+#'
+
+ora_structure_meta_formats <- function(ora_xml) {
+  xml_list <- ora_xml |>
+    xml2::as_list() |>
+    unlist(recursive = FALSE)
+
+  xml_list[1:2] <- xml_list[1:2] |>
+    unlist(recursive = FALSE)
+
+  xml_list[2] <- paste0(
+    xml_list[2],
+    "?verb=",
+    ora_xml |>
+      xml2::as_list() |>
+      (\(x) attributes(x[[1]][2][[1]]))()
+  )
+
+  names(xml_list) <- names(xml_list) |>
+    tools::file_ext()
+
+  xml_list[[3]] <- xml_list[[3]] |>
+    dplyr::bind_rows() |>
+    tidyr::unnest(
+      cols = c(
+        .data$metadataPrefix, .data$schema, .data$metadataNamespace
+      )
+    )
+
+  dplyr::bind_cols(xml_list)
 }

README.Rmd

@@ -23,25 +23,25 @@ knitr::opts_chunk$set(
 [![CodeFactor](https://www.codefactor.io/repository/github/oxfordihtm/aurora/badge)](https://www.codefactor.io/repository/github/oxfordihtm/aurora)
 <!-- badges: end -->
 
-The [Oxford University Research Archive (ORA)](https://ora.ox.ac.uk/) is an Open Access platform and is the institutional repository for the University of Oxford. ORA serves as a permanent and secure online archive of research materials produced by members of the University of Oxford. ORA supports and participates in the Open Archives Initiative (OAI). ORA is a registered OAI-PMH data-provider and provides metadata for all public records which is updated as soon as each record is published or updated. ORA also provides API access to its resources. This package provides low level functions to interface with the [ORA API](https://ora.ox.ac.uk/api).
+The [Oxford University Research Archive (ORA)](https://ora.ox.ac.uk/) is an Open Access platform and is the institutional repository for the [University of Oxford](https://ox.ac.uk). ORA serves as a permanent and secure online archive of research materials produced by members of the University of Oxford. ORA supports and participates in the Open Archives Initiative (OAI). ORA is a registered OAI-PMH data-provider and provides metadata for all public records which is updated as soon as each record is published or updated. ORA also provides API access to its resources. This package provides low level functions to interface with the [ORA API](https://ora.ox.ac.uk/api).
 
 ## What does `aurora` do?
 
 Please note that `aurora` is still highly experimental and is undergoing a lot of development. Hence, any functionalities described below and in the rest of the package documentation have a high likelihood of changing interface or approach as we aim for a stable working version.
 
-Currently, the package provides functions that wrap each of the verb endpoints provided by OAI 2.0:
+Currently, the package provides functions that wrap each of the verb request endpoints provided by [OAI 2.0](https://www.openarchives.org/OAI/openarchivesprotocol.html):
 
 * `Identify`
 * `ListRecords`
 * `ListSets`
 * `ListMetadataFormats`
 * `ListIdentifiers`
 
-From here, the plan is to develope functions that structure these XML OAI responses into useful tabular formats useful for analysis.
+From here, the plan is to develope functions that structure these XML OAI responses into tabular formats useful for analysis.
 
 ## Installation
 
-`aurora` is not yet on CRAN but can be installed from the [Oxford IHTM R universe](https://oxfordihtm.r-universe.dev) as follows:
+`aurora` is not yet on CRAN but can be installed from the [Oxford IHTM R-universe](https://oxfordihtm.r-universe.dev) as follows:
 
 ```{r install-r-universe, eval = FALSE}
 install.packages(

README.md

@@ -18,12 +18,12 @@ coverage](https://codecov.io/gh/OxfordIHTM/ourora/branch/main/graph/badge.svg)](
 
 The [Oxford University Research Archive (ORA)](https://ora.ox.ac.uk/) is
 an Open Access platform and is the institutional repository for the
-University of Oxford. ORA serves as a permanent and secure online
-archive of research materials produced by members of the University of
-Oxford. ORA supports and participates in the Open Archives Initiative
-(OAI). ORA is a registered OAI-PMH data-provider and provides metadata
-for all public records which is updated as soon as each record is
-published or updated. ORA also provides API access to its resources.
+[University of Oxford](https://ox.ac.uk). ORA serves as a permanent and
+secure online archive of research materials produced by members of the
+University of Oxford. ORA supports and participates in the Open Archives
+Initiative (OAI). ORA is a registered OAI-PMH data-provider and provides
+metadata for all public records which is updated as soon as each record
+is published or updated. ORA also provides API access to its resources.
 This package provides low level functions to interface with the [ORA
 API](https://ora.ox.ac.uk/api).
 
@@ -35,7 +35,8 @@ the rest of the package documentation have a high likelihood of changing
 interface or approach as we aim for a stable working version.
 
 Currently, the package provides functions that wrap each of the verb
-endpoints provided by OAI 2.0:
+request endpoints provided by [OAI
+2.0](https://www.openarchives.org/OAI/openarchivesprotocol.html):
 
 - `Identify`
 - `ListRecords`
@@ -44,12 +45,12 @@ endpoints provided by OAI 2.0:
 - `ListIdentifiers`
 
 From here, the plan is to develope functions that structure these XML
-OAI responses into useful tabular formats useful for analysis.
+OAI responses into tabular formats useful for analysis.
 
 ## Installation
 
-`aurora` is not yet on CRAN but can be installed from the [Oxford IHTM R
-universe](https://oxfordihtm.r-universe.dev) as follows:
+`aurora` is not yet on CRAN but can be installed from the [Oxford IHTM
+R-universe](https://oxfordihtm.r-universe.dev) as follows:
 
 ``` r
 install.packages(
@@ -67,20 +68,20 @@ citation provided by a call to the `citation()` function as follows:
 
 ``` r
 citation("aurora")
-#> To cite codigo in publications use:
+#> To cite aurora in publications use:
 #> 
-#>   Anita Makori and Ernest Guevarra (2024). codigo: Interface to the
-#>   International Classification of Diseases (ICD) API. R package version
-#>   0.0.9000. URL https://oxford-ihtm.io/codigo/
+#>   Ernest Guevarra (2024). _aurora: Interface to the Oxord University
+#>   Research Archive (ORA) API_. R package version 0.0.9000,
+#>   <https://oxford-ihtm.io/aurora/>.
 #> 
 #> A BibTeX entry for LaTeX users is
 #> 
 #>   @Manual{,
-#>     title = {codigo: Interface to the International Classification of Diseases (ICD) API},
-#>     author = {{Anita Makori} and {Ernest Guevarra}},
+#>     title = {aurora: Interface to the Oxord University Research Archive (ORA) API},
+#>     author = {{Ernest Guevarra}},
 #>     year = {2024},
 #>     note = {R package version 0.0.9000},
-#>     url = {https://oxford-ihtm.io/codigo/},
+#>     url = {https://oxford-ihtm.io/aurora/},
 #>   }
 ```
 

inst/CITATION

@@ -1,16 +1,9 @@
-citHeader("To cite codigo in publications use:")
-
-citEntry(
-  entry    = "Manual",
-  title    = "codigo: Interface to the International Classification of Diseases (ICD) API",
-  author   = c(person("Anita Makori"),  person("Ernest Guevarra")),
-  year     = "2024",
-  note     = "R package version 0.0.9000",
-  url      = "https://oxford-ihtm.io/codigo/",
-  textVersion = paste(
-    paste("Anita Makori and Ernest Guevarra (2024).",
-          "codigo: Interface to the International Classification of Diseases (ICD) API.",
-          "R package version 0.0.9000.",
-          "URL https://oxford-ihtm.io/codigo/")
-  )
+bibentry(
+  bibtype = "Manual",
+  header  = "To cite aurora in publications use:",
+  title   = "aurora: Interface to the Oxord University Research Archive (ORA) API",
+  author  = person("Ernest Guevarra"),
+  year    = "2024",
+  note    = "R package version 0.0.9000",
+  url     = "https://oxford-ihtm.io/aurora/"
 )