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Add CRediT roles to JATS
Enable annotating author roles using the Contribution Role Taxonomy (CRediT) and export this information in conformant JATS Closes #10152. Co-Authored-By: Jez Cope <457628+jezcope@users.noreply.github.com>
This commit is contained in:
Charles Tapley Hoyt
committed by
John MacFarlane
John MacFarlane
parent
3291605c91
commit
1eed55f391
@@ -69,6 +69,7 @@
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- Cezary Drożak
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- Chandrahas77
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- Charanjit Singh
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- Charles Tapley Hoyt
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- Charlotte Koch
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- Chris Black
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- Christian Conkle
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@@ -197,6 +198,7 @@
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- Jeroen de Haas
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- Jerry Sky
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- Jesse Rosenthal
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- Jez Cope
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- Joe Hermaszewski
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- Joe Hillenbrand
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- John KetzerX
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@@ -109,6 +109,17 @@ $elseif(author.name)$
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$else$
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<string-name>$author$</string-name>
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$endif$
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$for(author.roles)$
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$if(it.credit)$
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<role vocab="credit"$if(it.degree)$ degree-contribution="$it.degree$"$endif$
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vocab-identifier="https://credit.niso.org/"
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vocab-term-identifier="https://credit.niso.org/contributor-roles/$it.credit$/"
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vocab-term="$it.credit-name$"
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>$if(it.name)$$it.name$$else$$it.credit-name$$endif$</role>
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$elseif(it.name)$
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<role>$it.name$</role>
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$endif$
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$endfor$
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$if(author.email)$
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<email>$author.email$</email>
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$endif$
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+81
@@ -61,6 +61,85 @@ Metadata Values
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set it used, as affiliation links are not allowed in that
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schema.
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`roles`
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: a list of dictionaries describing the author's role(s).
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Each role is added as an [`<role>`] element to
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the author's [`<contrib>`] element. The following examples
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illustrate:
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An ad-hoc role:
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```yaml
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roles:
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- name: Dolphin Catcher
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```
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A role specified with CRediT.
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```yaml
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roles:
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- credit: writing-review-editing
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```
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The `credit-name` is automatically looked up from
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the CRediT taxonomy, but you can also specify it
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yourself:
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```yaml
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roles:
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- credit: writing-review-editing
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credit-name: Writing – review & editing
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```
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A role specified with CRediT, including an
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optional degree of contribution. Note that
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specifying the degree only is allowed when
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using CRediT roles and not ad-hoc roles.
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```yaml
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roles:
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- credit: writing-review-editing
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degree: Lead
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```
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A role specified with CRediT with a label override,
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useful for internationalization:
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```yaml
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roles:
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- credit: writing-review-editing
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name: Escrita – revisão e edição
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```
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The value for `credit` and `credit-name`
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must be from one of the 14 terms from the
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Contribution Role Taxonomy (CRediT):
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| `credit` | `credit-name` |
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|--------------------------|----------------------------|
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| `conceptualization` | Conceptualization |
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| `data-curation` | Data curation |
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| `formal-analysis` | Formal analysis |
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| `funding-acquisition` | Funding acquisition |
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| `investigation` | Investigation |
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| `methodology` | Methodology |
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| `project-administration` | Project administration |
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| `resources` | Resources |
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| `software` | Software |
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| `supervision` | Supervision |
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| `validation` | Validation |
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| `visualization` | Visualization |
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| `writing-original-draft` | Writing – original draft |
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| `writing-review-editing` | Writing – review & editing |
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JATS suggests in [`<degree-contribution>`] to use one of
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the following three values when specifying the degree of
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contribution:
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1. `Lead`
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2. `Equal`
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3. `Supporting`
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`equal-contrib`
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: boolean attribute used to mark authors who contributed
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equally to the work. The
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@@ -483,3 +562,5 @@ Required metadata values:
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[`<institution-wrap>`]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/element/institution-wrap.html
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[`<institution>`]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/element/institution.html
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[`<pub-date>`]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/element/pub-date.html
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[`<role>`]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/element/role.html
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[`<degree-contribution>`]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/attribute/degree-contribution.html
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@@ -27,7 +27,7 @@ import Control.Monad.Reader
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import Control.Monad.State
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import Data.Generics (everywhere, mkT)
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import qualified Data.Map as M
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import Data.Maybe (fromMaybe, listToMaybe)
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import Data.Maybe (fromMaybe, listToMaybe, isNothing)
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import Data.Time (toGregorian, Day, parseTimeM, defaultTimeLocale, formatTime)
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import qualified Data.Text as T
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import Data.Text (Text)
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@@ -43,7 +43,7 @@ import Text.DocLayout
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import Text.Pandoc.Shared
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import Text.Pandoc.URI
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import Text.Pandoc.Templates (renderTemplate)
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import Text.DocTemplates (Context(..), Val(..))
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import Text.DocTemplates (Context(..), Val(..), toVal)
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import Text.Pandoc.Writers.JATS.References (referencesToJATS)
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import Text.Pandoc.Writers.JATS.Table (tableToJATS)
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import Text.Pandoc.Writers.JATS.Types
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@@ -54,6 +54,54 @@ import Text.TeXMath
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import qualified Text.Pandoc.Writers.AnnotatedTable as Ann
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import qualified Text.XML.Light as Xml
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-- | Default human-readable names for roles in the Contributor Role
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-- Taxonomy (CRediT). This is useful for generating JATS that annotate
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-- contributor roles
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creditNames :: M.Map Text Text
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creditNames = M.fromList [
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("conceptualization", "Conceptualization"),
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("data-curation", "Data curation"),
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("formal-analysis", "Formal analysis"),
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("funding-acquisition", "Funding acquisition"),
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("investigation", "Investigation"),
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("methodology", "Methodology"),
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("project-administration", "Project administration"),
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("resources", "Resources"),
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("software", "Software"),
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("supervision", "Supervision"),
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("validation", "Validation"),
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("visualization", "Visualization"),
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("writing-original-draft", "Writing – original draft"),
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("writing-review-editing", "Writing – review & editing")]
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-- | Ensure every role with a `credit` key also has a `credit-name`,
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-- using a default value if necessary
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addCreditNames :: Context Text -> Context Text
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addCreditNames context =
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case getField "author" context of
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-- If there is an "authors" key, then we replace the existing value
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-- with one we mutate by running the addCreditNamesToAuthor helper
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-- function on each
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Just (ListVal authors) ->
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resetField "author" (map addCreditNamesToAuthor authors) context
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-- If there is no "authors" key in the context, then we don't have to do
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-- anything, and just return the context as is
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_ -> context
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where
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addCreditNamesToAuthor :: Val Text -> Val Text
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addCreditNamesToAuthor val = fromMaybe val $ do
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MapVal authorCtx <- pure val
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ListVal roles <- getField "roles" authorCtx
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return $ toVal $ resetField "roles" (map addCreditNameToRole roles) authorCtx
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addCreditNameToRole :: Val Text -> Val Text
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addCreditNameToRole val = fromMaybe val $ do
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MapVal roleCtx <- pure val
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guard $ isNothing (getField "credit-name" roleCtx :: Maybe (Val Text))
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creditId <- getField "credit" roleCtx
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creditName <- M.lookup creditId creditNames
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return $ toVal $ resetField "credit-name" creditName roleCtx
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-- | Convert a @'Pandoc'@ document to JATS (Archiving and Interchange
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-- Tag Set.)
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writeJatsArchiving :: PandocMonad m => WriterOptions -> Pandoc -> m Text
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@@ -159,6 +207,7 @@ docToJATS opts (Pandoc meta blocks') = do
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(lookupMetaInlines "title" meta)
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let context = defField "body" main
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$ defField "back" back
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$ addCreditNames
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$ resetField "title" title'
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$ resetField "date" date
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$ defField "mathml" (case writerHTMLMathMethod opts of
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@@ -0,0 +1,446 @@
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# CRediT Roles
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This document contains tests and examples for enabling
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export of roles to JATS. It was added for
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[Issue #10152](https://github.com/jgm/pandoc/issues/10152)
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and corresponding [Pull Request #10153](https://github.com/jgm/pandoc/pull/10153).
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In the first example, we show a fully qualified CRediT role.
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An explicit name isn't given, so the CRediT name is used.
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```
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% pandoc -s -t jats
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---
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title: CRediT Test
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author:
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- name: Max Mustermann
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affiliation: [ 1 ]
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roles:
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- credit: software
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credit-name: Software
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degree: Lead
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affiliation:
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- id: 1
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name: Silverlight University
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---
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^D
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<?xml version="1.0" encoding="utf-8" ?>
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<!DOCTYPE article PUBLIC "-//NLM//DTD JATS (Z39.96) Journal Archiving and Interchange DTD v1.2 20190208//EN"
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"JATS-archivearticle1.dtd">
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<article xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink" dtd-version="1.2" article-type="other">
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<front>
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<journal-meta>
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<journal-id></journal-id>
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<journal-title-group>
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</journal-title-group>
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<issn></issn>
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<publisher>
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<publisher-name></publisher-name>
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</publisher>
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</journal-meta>
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<article-meta>
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<title-group>
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<article-title>CRediT Test</article-title>
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</title-group>
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<contrib-group>
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<contrib contrib-type="author">
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<string-name>Max Mustermann</string-name>
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<role vocab="credit" degree-contribution="Lead"
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vocab-identifier="https://credit.niso.org/"
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vocab-term-identifier="https://credit.niso.org/contributor-roles/software/"
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vocab-term="Software"
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>Software</role>
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<xref ref-type="aff" rid="aff-1"/>
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</contrib>
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<aff id="aff-1">
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<institution-wrap>
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<institution>Silverlight University</institution>
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</institution-wrap>
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</aff>
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</contrib-group>
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<permissions>
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</permissions>
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</article-meta>
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</front>
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<body>
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</body>
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<back>
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</back>
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</article>
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```
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In the second example, we show a fully qualified CRediT role.
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An explicit name is given in a different language.
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```
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% pandoc -s -t jats
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---
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title: CRediT Test
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author:
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- name: Max Mustermann
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affiliation: [ 1 ]
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roles:
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- credit: software
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credit-name: Software
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degree: Lead
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name: Programas
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affiliation:
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- id: 1
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name: Silverlight University
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---
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^D
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<?xml version="1.0" encoding="utf-8" ?>
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<!DOCTYPE article PUBLIC "-//NLM//DTD JATS (Z39.96) Journal Archiving and Interchange DTD v1.2 20190208//EN"
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"JATS-archivearticle1.dtd">
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<article xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink" dtd-version="1.2" article-type="other">
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<front>
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<journal-meta>
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<journal-id></journal-id>
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<journal-title-group>
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</journal-title-group>
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<issn></issn>
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<publisher>
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<publisher-name></publisher-name>
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</publisher>
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</journal-meta>
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<article-meta>
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<title-group>
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<article-title>CRediT Test</article-title>
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</title-group>
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<contrib-group>
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<contrib contrib-type="author">
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<string-name>Max Mustermann</string-name>
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<role vocab="credit" degree-contribution="Lead"
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vocab-identifier="https://credit.niso.org/"
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vocab-term-identifier="https://credit.niso.org/contributor-roles/software/"
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vocab-term="Software"
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>Programas</role>
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<xref ref-type="aff" rid="aff-1"/>
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</contrib>
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<aff id="aff-1">
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<institution-wrap>
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<institution>Silverlight University</institution>
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</institution-wrap>
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</aff>
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</contrib-group>
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<permissions>
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</permissions>
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</article-meta>
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</front>
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<body>
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</body>
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<back>
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</back>
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</article>
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```
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In this example, we show a partially qualified CRediT role
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that does not have a `degree`:
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```
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% pandoc -s -t jats
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---
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title: CRediT Test
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author:
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- name: Max Mustermann
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affiliation: [ 1 ]
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roles:
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- credit: software
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credit-name: Software
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affiliation:
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- id: 1
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name: Silverlight University
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---
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^D
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<?xml version="1.0" encoding="utf-8" ?>
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<!DOCTYPE article PUBLIC "-//NLM//DTD JATS (Z39.96) Journal Archiving and Interchange DTD v1.2 20190208//EN"
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"JATS-archivearticle1.dtd">
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<article xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink" dtd-version="1.2" article-type="other">
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<front>
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<journal-meta>
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<journal-id></journal-id>
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<journal-title-group>
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</journal-title-group>
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<issn></issn>
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<publisher>
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<publisher-name></publisher-name>
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</publisher>
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</journal-meta>
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<article-meta>
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<title-group>
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<article-title>CRediT Test</article-title>
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</title-group>
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<contrib-group>
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<contrib contrib-type="author">
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<string-name>Max Mustermann</string-name>
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<role vocab="credit"
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vocab-identifier="https://credit.niso.org/"
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vocab-term-identifier="https://credit.niso.org/contributor-roles/software/"
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vocab-term="Software"
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>Software</role>
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<xref ref-type="aff" rid="aff-1"/>
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</contrib>
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<aff id="aff-1">
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<institution-wrap>
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<institution>Silverlight University</institution>
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</institution-wrap>
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</aff>
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</contrib-group>
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<permissions>
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</permissions>
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</article-meta>
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</front>
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<body>
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</body>
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<back>
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</back>
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</article>
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```
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In this example, we show a more stripped-down data that requires automatic lookup of the
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`credit-name`.
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```
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% pandoc -s -t jats
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---
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title: CRediT Test
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author:
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- name: Max Mustermann
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affiliation: [ 1 ]
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roles:
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- credit: software
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affiliation:
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- id: 1
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name: Silverlight University
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---
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^D
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<?xml version="1.0" encoding="utf-8" ?>
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<!DOCTYPE article PUBLIC "-//NLM//DTD JATS (Z39.96) Journal Archiving and Interchange DTD v1.2 20190208//EN"
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"JATS-archivearticle1.dtd">
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<article xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink" dtd-version="1.2" article-type="other">
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<front>
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<journal-meta>
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<journal-id></journal-id>
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<journal-title-group>
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</journal-title-group>
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<issn></issn>
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<publisher>
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<publisher-name></publisher-name>
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</publisher>
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</journal-meta>
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<article-meta>
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<title-group>
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<article-title>CRediT Test</article-title>
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</title-group>
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<contrib-group>
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<contrib contrib-type="author">
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<string-name>Max Mustermann</string-name>
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<role vocab="credit"
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vocab-identifier="https://credit.niso.org/"
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vocab-term-identifier="https://credit.niso.org/contributor-roles/software/"
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vocab-term="Software"
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>Software</role>
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<xref ref-type="aff" rid="aff-1"/>
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</contrib>
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<aff id="aff-1">
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<institution-wrap>
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<institution>Silverlight University</institution>
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</institution-wrap>
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</aff>
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</contrib-group>
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<permissions>
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</permissions>
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</article-meta>
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</front>
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<body>
|
||||
|
||||
</body>
|
||||
<back>
|
||||
</back>
|
||||
</article>
|
||||
```
|
||||
|
||||
In this example, we test the correct XML encoding of
|
||||
the CRediT role [Writing – review & editing](https://credit.niso.org/contributor-roles/writing-review-editing/),
|
||||
which annoyingly contains an ampersand in its label.
|
||||
|
||||
```
|
||||
% pandoc -s -t jats
|
||||
---
|
||||
title: CRediT Test
|
||||
author:
|
||||
- name: Max Mustermann
|
||||
affiliation: [ 1 ]
|
||||
roles:
|
||||
- credit: writing-review-editing
|
||||
credit-name: Writing – review & editing
|
||||
degree: Lead
|
||||
affiliation:
|
||||
- id: 1
|
||||
name: Silverlight University
|
||||
---
|
||||
^D
|
||||
<?xml version="1.0" encoding="utf-8" ?>
|
||||
<!DOCTYPE article PUBLIC "-//NLM//DTD JATS (Z39.96) Journal Archiving and Interchange DTD v1.2 20190208//EN"
|
||||
"JATS-archivearticle1.dtd">
|
||||
<article xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink" dtd-version="1.2" article-type="other">
|
||||
<front>
|
||||
<journal-meta>
|
||||
<journal-id></journal-id>
|
||||
<journal-title-group>
|
||||
</journal-title-group>
|
||||
<issn></issn>
|
||||
<publisher>
|
||||
<publisher-name></publisher-name>
|
||||
</publisher>
|
||||
</journal-meta>
|
||||
<article-meta>
|
||||
<title-group>
|
||||
<article-title>CRediT Test</article-title>
|
||||
</title-group>
|
||||
<contrib-group>
|
||||
<contrib contrib-type="author">
|
||||
<string-name>Max Mustermann</string-name>
|
||||
<role vocab="credit" degree-contribution="Lead"
|
||||
vocab-identifier="https://credit.niso.org/"
|
||||
vocab-term-identifier="https://credit.niso.org/contributor-roles/writing-review-editing/"
|
||||
vocab-term="Writing – review & editing"
|
||||
>Writing – review & editing</role>
|
||||
<xref ref-type="aff" rid="aff-1"/>
|
||||
</contrib>
|
||||
<aff id="aff-1">
|
||||
<institution-wrap>
|
||||
<institution>Silverlight University</institution>
|
||||
</institution-wrap>
|
||||
</aff>
|
||||
</contrib-group>
|
||||
<permissions>
|
||||
</permissions>
|
||||
</article-meta>
|
||||
</front>
|
||||
<body>
|
||||
|
||||
</body>
|
||||
<back>
|
||||
</back>
|
||||
</article>
|
||||
```
|
||||
|
||||
In this example, we show a role that isn't qualified with CRediT.
|
||||
|
||||
```
|
||||
% pandoc -s -t jats
|
||||
---
|
||||
title: CRediT Test
|
||||
author:
|
||||
- name: Max Mustermann
|
||||
affiliation: [ 1 ]
|
||||
roles:
|
||||
- name: Dolphin Catcher
|
||||
affiliation:
|
||||
- id: 1
|
||||
name: Silverlight University
|
||||
---
|
||||
^D
|
||||
<?xml version="1.0" encoding="utf-8" ?>
|
||||
<!DOCTYPE article PUBLIC "-//NLM//DTD JATS (Z39.96) Journal Archiving and Interchange DTD v1.2 20190208//EN"
|
||||
"JATS-archivearticle1.dtd">
|
||||
<article xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink" dtd-version="1.2" article-type="other">
|
||||
<front>
|
||||
<journal-meta>
|
||||
<journal-id></journal-id>
|
||||
<journal-title-group>
|
||||
</journal-title-group>
|
||||
<issn></issn>
|
||||
<publisher>
|
||||
<publisher-name></publisher-name>
|
||||
</publisher>
|
||||
</journal-meta>
|
||||
<article-meta>
|
||||
<title-group>
|
||||
<article-title>CRediT Test</article-title>
|
||||
</title-group>
|
||||
<contrib-group>
|
||||
<contrib contrib-type="author">
|
||||
<string-name>Max Mustermann</string-name>
|
||||
<role>Dolphin Catcher</role>
|
||||
<xref ref-type="aff" rid="aff-1"/>
|
||||
</contrib>
|
||||
<aff id="aff-1">
|
||||
<institution-wrap>
|
||||
<institution>Silverlight University</institution>
|
||||
</institution-wrap>
|
||||
</aff>
|
||||
</contrib-group>
|
||||
<permissions>
|
||||
</permissions>
|
||||
</article-meta>
|
||||
</front>
|
||||
<body>
|
||||
|
||||
</body>
|
||||
<back>
|
||||
</back>
|
||||
</article>
|
||||
```
|
||||
|
||||
In this example, we show a role that neither has a CRediT identifer,
|
||||
nor a name, so it's ignored.
|
||||
|
||||
```
|
||||
% pandoc -s -t jats
|
||||
---
|
||||
title: CRediT Test
|
||||
author:
|
||||
- name: Max Mustermann
|
||||
affiliation: [ 1 ]
|
||||
roles:
|
||||
- irrelevant-key: Dolphin Catcher
|
||||
affiliation:
|
||||
- id: 1
|
||||
name: Silverlight University
|
||||
---
|
||||
^D
|
||||
<?xml version="1.0" encoding="utf-8" ?>
|
||||
<!DOCTYPE article PUBLIC "-//NLM//DTD JATS (Z39.96) Journal Archiving and Interchange DTD v1.2 20190208//EN"
|
||||
"JATS-archivearticle1.dtd">
|
||||
<article xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink" dtd-version="1.2" article-type="other">
|
||||
<front>
|
||||
<journal-meta>
|
||||
<journal-id></journal-id>
|
||||
<journal-title-group>
|
||||
</journal-title-group>
|
||||
<issn></issn>
|
||||
<publisher>
|
||||
<publisher-name></publisher-name>
|
||||
</publisher>
|
||||
</journal-meta>
|
||||
<article-meta>
|
||||
<title-group>
|
||||
<article-title>CRediT Test</article-title>
|
||||
</title-group>
|
||||
<contrib-group>
|
||||
<contrib contrib-type="author">
|
||||
<string-name>Max Mustermann</string-name>
|
||||
<xref ref-type="aff" rid="aff-1"/>
|
||||
</contrib>
|
||||
<aff id="aff-1">
|
||||
<institution-wrap>
|
||||
<institution>Silverlight University</institution>
|
||||
</institution-wrap>
|
||||
</aff>
|
||||
</contrib-group>
|
||||
<permissions>
|
||||
</permissions>
|
||||
</article-meta>
|
||||
</front>
|
||||
<body>
|
||||
|
||||
</body>
|
||||
<back>
|
||||
</back>
|
||||
</article>
|
||||
```
|
||||
Reference in New Issue
Block a user