Merge pull request #1 from OxfordIHTM/dev

create minimum releasable package

.Rbuildignore

@@ -4,3 +4,6 @@
 ^README\.Rmd$
 ^\.github$
 ^codecov\.yml$
+^_pkgdown\.yml$
+^docs$
+^pkgdown$

.github/CODE_OF_CONDUCT.md

@@ -0,0 +1,126 @@
+# Contributor Covenant Code of Conduct
+
+## Our Pledge
+
+We as members, contributors, and leaders pledge to make participation in our
+community a harassment-free experience for everyone, regardless of age, body
+size, visible or invisible disability, ethnicity, sex characteristics, gender
+identity and expression, level of experience, education, socio-economic status,
+nationality, personal appearance, race, caste, color, religion, or sexual
+identity and orientation.
+
+We pledge to act and interact in ways that contribute to an open, welcoming,
+diverse, inclusive, and healthy community.
+
+## Our Standards
+
+Examples of behavior that contributes to a positive environment for our
+community include:
+
+* Demonstrating empathy and kindness toward other people
+* Being respectful of differing opinions, viewpoints, and experiences
+* Giving and gracefully accepting constructive feedback
+* Accepting responsibility and apologizing to those affected by our mistakes,
+  and learning from the experience
+* Focusing on what is best not just for us as individuals, but for the overall
+  community
+
+Examples of unacceptable behavior include:
+
+* The use of sexualized language or imagery, and sexual attention or advances of
+  any kind
+* Trolling, insulting or derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or email address,
+  without their explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+  professional setting
+
+## Enforcement Responsibilities
+
+Community leaders are responsible for clarifying and enforcing our standards of
+acceptable behavior and will take appropriate and fair corrective action in
+response to any behavior that they deem inappropriate, threatening, offensive,
+or harmful.
+
+Community leaders have the right and responsibility to remove, edit, or reject
+comments, commits, code, wiki edits, issues, and other contributions that are
+not aligned to this Code of Conduct, and will communicate reasons for moderation
+decisions when appropriate.
+
+## Scope
+
+This Code of Conduct applies within all community spaces, and also applies when
+an individual is officially representing the community in public spaces.
+Examples of representing our community include using an official e-mail address,
+posting via an official social media account, or acting as an appointed
+representative at an online or offline event.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported to the community leaders responsible for enforcement at [email protected]. 
+All complaints will be reviewed and investigated promptly and fairly.
+
+All community leaders are obligated to respect the privacy and security of the
+reporter of any incident.
+
+## Enforcement Guidelines
+
+Community leaders will follow these Community Impact Guidelines in determining
+the consequences for any action they deem in violation of this Code of Conduct:
+
+### 1. Correction
+
+**Community Impact**: Use of inappropriate language or other behavior deemed
+unprofessional or unwelcome in the community.
+
+**Consequence**: A private, written warning from community leaders, providing
+clarity around the nature of the violation and an explanation of why the
+behavior was inappropriate. A public apology may be requested.
+
+### 2. Warning
+
+**Community Impact**: A violation through a single incident or series of
+actions.
+
+**Consequence**: A warning with consequences for continued behavior. No
+interaction with the people involved, including unsolicited interaction with
+those enforcing the Code of Conduct, for a specified period of time. This
+includes avoiding interactions in community spaces as well as external channels
+like social media. Violating these terms may lead to a temporary or permanent
+ban.
+
+### 3. Temporary Ban
+
+**Community Impact**: A serious violation of community standards, including
+sustained inappropriate behavior.
+
+**Consequence**: A temporary ban from any sort of interaction or public
+communication with the community for a specified period of time. No public or
+private interaction with the people involved, including unsolicited interaction
+with those enforcing the Code of Conduct, is allowed during this period.
+Violating these terms may lead to a permanent ban.
+
+### 4. Permanent Ban
+
+**Community Impact**: Demonstrating a pattern of violation of community
+standards, including sustained inappropriate behavior, harassment of an
+individual, or aggression toward or disparagement of classes of individuals.
+
+**Consequence**: A permanent ban from any sort of public interaction within the
+community.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage],
+version 2.1, available at
+<https://www.contributor-covenant.org/version/2/1/code_of_conduct.html>.
+
+Community Impact Guidelines were inspired by
+[Mozilla's code of conduct enforcement ladder][https://github.com/mozilla/inclusion].
+
+For answers to common questions about this code of conduct, see the FAQ at
+<https://www.contributor-covenant.org/faq>. Translations are available at <https://www.contributor-covenant.org/translations>.
+
+[homepage]: https://www.contributor-covenant.org

.github/CONTRIBUTING.md

@@ -0,0 +1,35 @@
+# Contributing
+
+## Bugs
+
+* Submit an issue on the [issues page](https://github.com/OxfordIHTM/aurora/issues)
+
+## Code contributions
+
+* Fork this repository to your Github account
+
+* Clone your version on your account down to your machine from your account
+
+```
+git clone https://github.com/<yourgithubusername>/aurora.git
+```
+
+* Make sure to track progress upstream i.e., on our version of `aurora`
+at `OxfordIHTM/aurora`, by doing
+
+```
+git remote add upstream https://github.com/OxfordIHTM/aurora.git
+```
+
+* Before making changes make sure to pull changes in from `upstream` by doing
+either `git fetch upstream` then merge later or `git pull upstream` to fetch
+and merge in one step
+
+* Make your changes on a new feature branch
+
+* Please write a test or tests for your changes if they affect code and not just
+documentation
+
+* Push up changes to your account
+
+* Submit a pull request at `OxfordIHTM/aurora`

.github/workflows/pkgdown.yaml

@@ -0,0 +1,48 @@
+# 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@v4
+
+      - 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/[email protected]
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs

.gitignore

@@ -2,3 +2,4 @@
 .Rhistory
 .RData
 .Ruserdata
+docs

DESCRIPTION

@@ -25,6 +25,5 @@ Language: en-GB
 LazyData: true
 RoxygenNote: 7.3.1
 Roxygen: list(markdown = TRUE)
-URL: https://oxford-ihtm.io/aurora/, https://github.com/OxfordIHTM/aurora
+URL: https://oxford-ihtm.io/aurora/, https://github.com/OxfordIHTM/aurora, http://oxford-ihtm.io/aurora/
 BugReports: https://github.com/OxfordIHTM/aurora/issues
-

NAMESPACE

@@ -1,8 +1,11 @@
 # Generated by roxygen2: do not edit by hand
 
 export(ora_identify)
-export(ora_identify_structure)
+export(ora_list_meta_formats)
 export(ora_list_records)
+export(ora_list_records_id)
+export(ora_list_sets)
+export(ora_structure_identify)
 importFrom(httr2,req_perform)
 importFrom(httr2,req_url_query)
 importFrom(httr2,request)

R/aurora.R

@@ -1,5 +1,5 @@
 #'
-#' Interface to the Oxford University Research Archive
+#' Interface to the Oxford University Research Archive (ORA) API
 #'
 #' The [Oxford University Research Archive (ORA)](https://ora.ox.ac.uk/) is an
 #' Open Access platform and is the institutional repository for the

R/ora_list_metadata_formats.R

@@ -0,0 +1,30 @@
+#'
+#' List metadata formats
+#'
+#' @param base_url The OAI-PMH endpoint base URL. Set to
+#'   https://ora.ox.ac.uk/oai2
+#'
+#' @returns XML OAI response
+#'
+#' @examples
+#' ora_list_meta_formats()
+#'
+#' @export
+#'
+
+ora_list_meta_formats <- function(base_url = "https://ora.ox.ac.uk/oai2") {
+  ## Make base request ----
+  req <- httr2::request(base_url)
+
+  ## Add query ----
+  req <- req |>
+    httr2::req_url_query(verb = "ListMetadataFormats")
+
+  ## Perform request ----
+  resp <- req |>
+    httr2::req_perform() |>
+    httr2::resp_body_xml()
+
+  ## Return resp ----
+  resp
+}

R/ora_list_records.R

@@ -15,7 +15,9 @@
 #'
 #' @examples
 #' ora_list_records()
+#' ora_list_records_id()
 #'
+#' @rdname ora_list_records
 #' @export
 #'
 
@@ -50,3 +52,41 @@ ora_list_records <- function(base_url = "https://ora.ox.ac.uk/oai2",
   ## Return resp ----
   resp
 }
+
+
+#'
+#' @rdname ora_list_records
+#' @export
+#'
+
+ora_list_records_id <- function(base_url = "https://ora.ox.ac.uk/oai2",
+                                metadata_prefix = c("oai_dc",
+                                                    "datacite_dc",
+                                                    "dart_dc",
+                                                    "solo_dc",
+                                                    "base_dc",
+                                                    "oai_openaire",
+                                                    "uketd_dc",
+                                                    "rioxx_terms",
+                                                    "rioxx_terms_cc0")) {
+  ## Determine prefix ----
+  metadata_prefix <- match.arg(metadata_prefix)
+
+  ## Make base request ----
+  req <- httr2::request(base_url)
+
+  ## Add query ----
+  req <- req |>
+    httr2::req_url_query(
+      verb = "ListIdentifiers",
+      metadataPrefix = metadata_prefix
+    )
+
+  ## Perform request ----
+  resp <- req |>
+    httr2::req_perform() |>
+    httr2::resp_body_xml()
+
+  ## Return resp ----
+  resp
+}

R/ora_list_sets.R

@@ -0,0 +1,34 @@
+#'
+#' List sets of work
+#'
+#' @param base_url The OAI-PMH endpoint base URL. Set to
+#'   https://ora.ox.ac.uk/oai2
+#'
+#' @returns XML OAI response
+#'
+#' @section List Sets: ORA records are available for selective harvesting as a
+#'   separate set based on their **Type of work** within the ORA system, e.g.
+#'   *"thesis"*, *"dataset"*, *"journal article"*.
+#'
+#' @examples
+#' ora_list_sets()
+#'
+#' @export
+#'
+
+ora_list_sets <- function(base_url = "https://ora.ox.ac.uk/oai2") {
+  ## Make base request ----
+  req <- httr2::request(base_url)
+
+  ## Add query ----
+  req <- req |>
+    httr2::req_url_query(verb = "ListSets")
+
+  ## Perform request ----
+  resp <- req |>
+    httr2::req_perform() |>
+    httr2::resp_body_xml()
+
+  ## Return resp ----
+  resp
+}

R/ora_structure.R

@@ -12,7 +12,7 @@
 #' @export
 #'
 
-ora_identify_structure <- function(ora_xml) {
+ora_structure_identify <- function(ora_xml) {
   field_names <- ora_xml |>
     xml2::xml_children() |>
     xml2::xml_children() |>