Add CRediT roles to JATS

AUTHORS.md

@@ -69,6 +69,7 @@
 - Cezary Drożak
 - Chandrahas77
 - Charanjit Singh
+- Charles Tapley Hoyt
 - Charlotte Koch
 - Chris Black
 - Christian Conkle
@@ -197,6 +198,7 @@
 - Jeroen de Haas
 - Jerry Sky
 - Jesse Rosenthal
+- Jez Cope
 - Joe Hermaszewski
 - Joe Hillenbrand
 - John KetzerX

data/templates/article.jats_publishing

@@ -109,6 +109,17 @@ $elseif(author.name)$
 $else$
 <string-name>$author$</string-name>
 $endif$
+$for(author.roles)$
+$if(it.credit)$
+<role vocab="credit"$if(it.degree)$ degree-contribution="$it.degree$"$endif$
+      vocab-identifier="https://credit.niso.org/"
+      vocab-term-identifier="https://credit.niso.org/contributor-roles/$it.credit$/"
+      vocab-term="$it.credit-name$"
+>$if(it.name)$$it.name$$else$$it.credit-name$$endif$</role>
+$elseif(it.name)$
+<role>$it.name$</role>
+$endif$
+$endfor$
 $if(author.email)$
 <email>$author.email$</email>
 $endif$

doc/jats.md

@@ -61,6 +61,85 @@ Metadata Values
         set it used, as affiliation links are not allowed in that
         schema.
 
+    `roles`
+    :   a list of dictionaries describing the author's role(s).
+        Each role is added as an [`<role>`] element to
+        the author's [`<contrib>`] element. The following examples
+        illustrate:
+
+        An ad-hoc role:
+
+        ```yaml
+        roles:
+          - name: Dolphin Catcher
+        ```
+
+        A role specified with CRediT.
+
+        ```yaml
+        roles:
+          - credit: writing-review-editing
+        ```
+
+        The `credit-name` is automatically looked up from
+        the CRediT taxonomy, but you can also specify it
+        yourself:
+
+        ```yaml
+        roles:
+          - credit: writing-review-editing
+            credit-name: Writing – review & editing
+        ```
+
+        A role specified with CRediT, including an
+        optional degree of contribution. Note that
+        specifying the degree only is allowed when
+        using CRediT roles and not ad-hoc roles.
+
+        ```yaml
+        roles:
+          - credit: writing-review-editing
+            degree: Lead
+        ```
+
+        A role specified with CRediT with a label override,
+        useful for internationalization:
+
+        ```yaml
+        roles:
+          - credit: writing-review-editing
+            name: Escrita – revisão e edição
+        ```
+
+        The value for `credit` and `credit-name`
+        must be from one of the 14 terms from the
+        Contribution Role Taxonomy (CRediT):
+
+        | `credit`                 | `credit-name`              |
+        |--------------------------|----------------------------|
+        | `conceptualization`      | Conceptualization          |
+        | `data-curation`          | Data curation              |
+        | `formal-analysis`        | Formal analysis            |
+        | `funding-acquisition`    | Funding acquisition        |
+        | `investigation`          | Investigation              |
+        | `methodology`            | Methodology                |
+        | `project-administration` | Project administration     |
+        | `resources`              | Resources                  |
+        | `software`               | Software                   |
+        | `supervision`            | Supervision                |
+        | `validation`             | Validation                 |
+        | `visualization`          | Visualization              |
+        | `writing-original-draft` | Writing – original draft   |
+        | `writing-review-editing` | Writing – review & editing |
+
+        JATS suggests in [`<degree-contribution>`] to use one of
+        the following three values when specifying the degree of
+        contribution:
+
+        1. `Lead`
+        2. `Equal`
+        3. `Supporting`
+
     `equal-contrib`
     :   boolean attribute used to mark authors who contributed
         equally to the work. The
@@ -483,3 +562,5 @@ Required metadata values:
 [`<institution-wrap>`]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/element/institution-wrap.html
 [`<institution>`]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/element/institution.html
 [`<pub-date>`]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/element/pub-date.html
+[`<role>`]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/element/role.html
+[`<degree-contribution>`]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/attribute/degree-contribution.html

src/Text/Pandoc/Writers/JATS.hs

@@ -27,7 +27,7 @@ import Control.Monad.Reader
 import Control.Monad.State
 import Data.Generics (everywhere, mkT)
 import qualified Data.Map as M
-import Data.Maybe (fromMaybe, listToMaybe)
+import Data.Maybe (fromMaybe, listToMaybe, isNothing)
 import Data.Time (toGregorian, Day, parseTimeM, defaultTimeLocale, formatTime)
 import qualified Data.Text as T
 import Data.Text (Text)
@@ -43,7 +43,7 @@ import Text.DocLayout
 import Text.Pandoc.Shared
 import Text.Pandoc.URI
 import Text.Pandoc.Templates (renderTemplate)
-import Text.DocTemplates (Context(..), Val(..))
+import Text.DocTemplates (Context(..), Val(..), toVal)
 import Text.Pandoc.Writers.JATS.References (referencesToJATS)
 import Text.Pandoc.Writers.JATS.Table (tableToJATS)
 import Text.Pandoc.Writers.JATS.Types
@@ -54,6 +54,54 @@ import Text.TeXMath
 import qualified Text.Pandoc.Writers.AnnotatedTable as Ann
 import qualified Text.XML.Light as Xml
 
+-- | Default human-readable names for roles in the Contributor Role
+-- Taxonomy (CRediT). This is useful for generating JATS that annotate
+-- contributor roles
+creditNames :: M.Map Text Text
+creditNames = M.fromList [
+    ("conceptualization", "Conceptualization"),
+    ("data-curation", "Data curation"),
+    ("formal-analysis", "Formal analysis"),
+    ("funding-acquisition", "Funding acquisition"),
+    ("investigation", "Investigation"),
+    ("methodology", "Methodology"),
+    ("project-administration", "Project administration"),
+    ("resources", "Resources"),
+    ("software", "Software"),
+    ("supervision", "Supervision"),
+    ("validation", "Validation"),
+    ("visualization", "Visualization"),
+    ("writing-original-draft", "Writing – original draft"),
+    ("writing-review-editing", "Writing – review & editing")]
+
+-- | Ensure every role with a `credit` key also has a `credit-name`,
+-- using a default value if necessary
+addCreditNames :: Context Text -> Context Text
+addCreditNames context =
+  case getField "author" context of
+    -- If there is an "authors" key, then we replace the existing value
+    -- with one we mutate by running the addCreditNamesToAuthor helper
+    -- function on each
+    Just (ListVal authors) ->
+      resetField "author" (map addCreditNamesToAuthor authors) context
+    -- If there is no "authors" key in the context, then we don't have to do
+    -- anything, and just return the context as is
+    _ -> context
+  where
+    addCreditNamesToAuthor :: Val Text -> Val Text
+    addCreditNamesToAuthor val = fromMaybe val $ do
+      MapVal authorCtx <- pure val
+      ListVal roles <- getField "roles" authorCtx
+      return $ toVal $ resetField "roles" (map addCreditNameToRole roles) authorCtx
+
+    addCreditNameToRole :: Val Text -> Val Text
+    addCreditNameToRole val = fromMaybe val $ do
+      MapVal roleCtx <- pure val
+      guard $ isNothing (getField "credit-name" roleCtx :: Maybe (Val Text))
+      creditId <- getField "credit" roleCtx
+      creditName <- M.lookup creditId creditNames
+      return $ toVal $ resetField "credit-name" creditName roleCtx
+
 -- | Convert a @'Pandoc'@ document to JATS (Archiving and Interchange
 -- Tag Set.)
 writeJatsArchiving :: PandocMonad m => WriterOptions -> Pandoc -> m Text
@@ -159,6 +207,7 @@ docToJATS opts (Pandoc meta blocks') = do
                (lookupMetaInlines "title" meta)
   let context = defField "body" main
               $ defField "back" back
+              $ addCreditNames
               $ resetField "title" title'
               $ resetField "date" date
               $ defField "mathml" (case writerHTMLMathMethod opts of