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Support contributor roles via CRediT
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‎CHANGELOG.md‎

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`Inara` uses [SemVer][] (semantic versioning).
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## UNRELEASED
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- Support for annotating contributor roles with the Contribution Role Taxonomy (CRediT).
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A text table is generated at the bottom of the PDF and preprint template containing
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this information. As of https://github.com/jgm/pandoc/pull/10153, Pandoc will generate
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conformant JATS containing contibutor roles. (https://github.com/openjournals/inara/pull/87)
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## Inara v1.1.4
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Released 2024-11-06.

‎Dockerfile‎

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FROM pandoc/latex:3.2.0-alpine
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# WARNING: this PR contains changes to pandoc from https://github.com/jgm/pandoc/pull/10153
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# that aren't yet released. They should land in the 3.6.3 future version
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FROM pandoc/latex:3.6.3-alpine
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RUN apk add --no-cache ttf-hack
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‎data/defaults/jats.yaml‎

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# do it here for that reason.
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type: lua
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path: orcid-uri.lua
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- type: lua
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path: prepare-credit.lua

‎data/defaults/pdf.yaml‎

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path: self-citation.lua
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- type: lua
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path: fix-bibentry-spacing.lua
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- type: lua
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path: prepare-credit.lua
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variables:
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# styling options
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colorlinks: true

‎data/defaults/preprint.yaml‎

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to: latex
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output-file: paper.preprint.tex
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template: preprint.latex
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filters:
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- type: lua
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path: prepare-credit.lua
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variables:
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# styling options
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colorlinks: true

‎data/defaults/tex.yaml‎

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path: self-citation.lua
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- type: lua
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path: fix-bibentry-spacing.lua
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- type: lua
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path: prepare-credit.lua
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variables:
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# styling options
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colorlinks: true

‎data/filters/prepare-credit.lua‎

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-- Checks if any contributor information is available
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local roles = {
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["conceptualization"] = {
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name = "Conceptualization",
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id = "8b73531f-db56-4914-9502-4cc4d4d8ed73",
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uri = "https://credit.niso.org/contributor-roles/conceptualization/"
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},
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["data-curation"] = {
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name = "Data curation",
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id = "f93e0f44-f2a4-4ea1-824a-4e0853b05c9d",
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uri = "https://credit.niso.org/contributor-roles/data-curation/"
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},
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["formal-analysis"] = {
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name = "Formal analysis",
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id = "95394cbd-4dc8-4735-b589-7e5f9e622b3f",
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uri = "https://credit.niso.org/contributor-roles/formal-analysis/"
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},
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["funding-acquisition"] = {
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name = "Funding acquisition",
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id = "34ff6d68-132f-4438-a1f4-fba61ccf364a",
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uri = "https://credit.niso.org/contributor-roles/funding-acquisition/"
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},
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["investigation"] = {
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name = "Investigation",
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id = "2451924d-425e-4778-9f4c-36c848ca70c2",
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uri = "https://credit.niso.org/contributor-roles/investigation/"
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},
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["methodology"] = {
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name = "Methodology",
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id = "f21e2be9-4e38-4ab7-8691-d6f72d5d5843",
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uri = "https://credit.niso.org/contributor-roles/methodology/"
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},
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["project-administration"] = {
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name = "Project administration",
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id = "a693fe76-ea33-49ad-9dcc-5e4f3ac5f938",
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uri = "https://credit.niso.org/contributor-roles/project-administration/"
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},
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["resources"] = {
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name = "Resources",
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id = "ebd781f0-bf79-492c-ac21-b31b9c3c990c",
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uri = "https://credit.niso.org/contributor-roles/resources/"
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},
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["software"] = {
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name = "Software",
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id = "f89c5233-01b0-4778-93e9-cc7d107aa2c8",
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uri = "https://credit.niso.org/contributor-roles/software/"
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},
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["supervision"] = {
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name = "Supervision",
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id = "0c8ca7d4-06ad-4527-9cea-a8801fcb8746",
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uri = "https://credit.niso.org/contributor-roles/supervision/"
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},
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["validation"] = {
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name = "Validation",
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id = "4b1bf348-faf2-4fc4-bd66-4cd3a84b9d44",
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uri = "https://credit.niso.org/contributor-roles/validation/"
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},
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["visualization"] = {
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name = "Visualization",
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id = "76b9d56a-e430-4e0a-84c9-59c11be343ae",
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uri = "https://credit.niso.org/contributor-roles/visualization/"
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},
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["writing-original-draft"] = {
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name = "Writing – original draft",
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id = "43ebbd94-98b4-42f1-866b-c930cef228ca",
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uri = "https://credit.niso.org/contributor-roles/writing-original-draft/"
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},
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["writing-review-editing"] = {
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name = "Writing – review & editing",
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id = "d3aead86-f2a2-47f7-bb99-79de6421164d",
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uri = "https://credit.niso.org/contributor-roles/writing-review-editing/"
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}
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}
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-- An enumeration of the JATS-recommended degrees of contribution
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degrees = pandoc.List {
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"Lead",
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"Supporting",
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"Equal"
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}
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-- Check if the given string is one of the 14 valid
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-- CRediT identifiers by looking at the `roles` dict
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-- defined above
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function invalidCreditID(str)
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return roles[str] == nil
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end
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-- Check if the degree contribution is valid based on the JATS recommendation,
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-- see https://jats.taylorandfrancis.com/jats-guide/topics/author-contributions-credit/#degree-of-contribution
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function invalidDegree(str)
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return not degrees:includes(str)
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end
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function join_with_commas_and(list)
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local len = #list
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if len == 0 then
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return ""
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elseif len == 1 then
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return list[1]
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elseif len == 2 then
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return list[1] .. " & " .. list[2]
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else
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local result = table.concat(list, ", ", 1, len - 1)
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return result .. ", & " .. list[len]
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end
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end
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function capitalize_first_letter(str)
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return str:sub(1, 1):upper() .. str:sub(2)
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end
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-- If the data is just a string corresponding to a
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-- CRediT identifier, upgrade it to a dictionary,
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-- otherwise return it as is
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function clean_role_dict(d)
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if d.credit then
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return d
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else
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return { ["credit"] = pandoc.utils.stringify(d) }
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end
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end
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local function prepare_credit (meta)
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meta.hasRoles = false
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for _, author in ipairs(meta.authors or {}) do
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if author.roles then
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roleList = {}
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for _, roleDict in ipairs(author.roles) do
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roleDict = clean_role_dict(roleDict)
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credit_id = pandoc.utils.stringify(roleDict.credit)
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if invalidCreditID(credit_id) then
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print("invalid credit ID for author " .. author.name .. ": " .. credit_id)
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elseif roleDict.degree then
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degree = capitalize_first_letter(pandoc.utils.stringify(roleDict.degree))
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if invalidDegree(degree) then
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print("invalid degree for author " .. author.name .. ": " .. degree)
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-- even though the degree is invalid, add the role anyway
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table.insert(roleList, roles[credit_id].name)
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else
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table.insert(roleList, roles[credit_id].name .. " (" .. degree .. ")")
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end
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else
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table.insert(roleList, roles[credit_id].name)
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end
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end
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if #roleList > 0 then
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meta.hasRoles = true
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author.rolesString = join_with_commas_and(roleList)
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end
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end
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end
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return meta
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end
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function Meta (meta)
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local ok, result = pcall(prepare_credit, meta)
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if ok then
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return result
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end
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end
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function assertEqual(expected, actual)
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assert(expected == actual, "got \"" .. actual .. "\", expected \"" .. expected .. "\"")
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end
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function tests()
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assert("" == join_with_commas_and({ }))
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assert("foo" == join_with_commas_and({ "foo" }))
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assert("foo & bar" == join_with_commas_and({ "foo", "bar" }))
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assert("foo, bar, & baz" == join_with_commas_and({ "foo", "bar", "baz" }))
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local m1 = {
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["authors"] = {
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{
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["name"] = "Author 1",
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["roles"] = {
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"methodology"
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}
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},
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{
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["name"] = "Author 2",
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['roles'] = {
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{ ["credit"] = "methodology" }
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}
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},
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{
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["name"] = "Author 3",
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['roles'] = {
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{ ["credit"] = "methodology" },
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{ ["credit"] = "data-curation" },
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{ ["credit"] = "conceptualization" },
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}
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},
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{
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["name"] = "Author 4",
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['roles'] = {
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{ ["credit"] = "methodology", ["degree"] = "lead" },
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{ ["credit"] = "data-curation", ["degree"] = "supporting" },
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{ ["credit"] = "conceptualization" },
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}
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},
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}
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}
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local m1t = prepare_credit(m1)
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assert(m1t.hasRoles, "hasRoles should be set to true")
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assertEqual("Methodology", m1t['authors'][1].rolesString)
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assertEqual("Methodology", m1t['authors'][2].rolesString)
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assertEqual("Methodology, Data curation, & Conceptualization", m1t['authors'][3].rolesString)
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assertEqual("Methodology (Lead), Data curation (Supporting), & Conceptualization", m1t['authors'][4].rolesString)
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local m2 = {
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["authors"] = {
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{
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["name"] = "Author 1"
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},
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{
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["name"] = "Author 2"
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}
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}
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}
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local m2t = prepare_credit(m2)
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assert(not m2t.hasRoles, "hasRoles should be set to false")
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end
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tests()

‎data/templates/default.latex‎

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$endif$
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$body$
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$if(hasRoles)$
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\section{Author Contributions}\label{author-contributions}
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\begin{enumerate}
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$for(authors)$
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$if(it.rolesString)$
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\item $it.name$ - $it.rolesString$
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$endif$
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$endfor$
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\end{enumerate}
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$endif$
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$if(natbib)$
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$if(bibliography)$
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$if(biblio-title)$

‎data/templates/preprint.latex‎

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$endif$
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$body$
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$if(hasRoles)$
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\section{Author Contributions}\label{author-contributions}
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\begin{enumerate}
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$for(authors)$
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$if(it.rolesString)$
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\item $it.name$ - $it.rolesString$
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$endif$
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$endfor$
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\end{enumerate}
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$endif$
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$if(has-frontmatter)$
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\backmatter
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$endif$

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