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JATS writer: support author affiliations (#6867)

Closes: #6687

commit797db8d30631cbd704575ee11d3bdda5bf57270f authorAlbert Krewinkel <albert@zeitkraut.de> dateFri 20 Nov 2020, 18:57 (6 years ago) parentc647948
4 files changed+127−6
data/templates/affiliations.jats+35 data/templates/article.jats_publishing+4−3 data/templates/default.jats_articleauthoring+4−3 doc/jats.md+84
data/templates/affiliations.jatsnew file+35
@@ -0,0 +1,35 @@
1+$--
2+$-- Affiliations
3+$--
4+$for(affiliation)$
5+<aff id="aff-$affiliation.id$">
6+$-- wrap affiliation if it has a known institution identifier
7+$if(affiliation.group)$
8+<institution content-type="group">$affiliation.group$</institution>
9+$endif$
10+$if(affiliation.department)$
11+<institution content-type="dept">$affiliation.department$</institution>
12+$endif$
13+<institution-wrap>
14+$if(affiliation.organization)$
15+<institution>$affiliation.organization$</institution>
16+$else$
17+<institution>$affiliation.name$</institution>
18+$endif$
19+$if(affiliation.isni)$
20+<institution-id institution-id-type="ISNI">$affiliation.isni$</institution-id>
21+$endif$
22+$if(affiliation.ringgold)$
23+<institution-id institution-id-type="Ringgold">$affiliation.ringgold$</institution-id>
24+$endif$
25+$if(affiliation.ror)$
26+<institution-id institution-id-type="ROR">$affiliation.ror$</institution-id>
27+$endif$
28+</institution-wrap>$if(affiliation.street-address)$,
29+$for(affiliation.street-address)$
30+<addr-line>$affiliation.street-address$</addr-line>$sep$,
31+$endfor$
32+$else$$if(affiliation.city)$, <city>$affiliation.city$</city>$endif$$endif$$if(affiliation.country)$,
33+<country$if(affiliation.country-code)$ country="$affiliation.country-code$"$endif$>$affiliation.country$</country>$endif$
34+</aff>
35+$endfor$
data/templates/article.jats_publishing+4−3
@@ -101,14 +101,15 @@ $endif$
101101$if(author.email)$
102102<email>$author.email$</email>
103103$endif$
104−$if(author.aff-id)$
105−<xref ref-type="aff" rid="aff-$contrib.aff-id$"/>
106−$endif$
104+$for(author.affiliation)$
105+<xref ref-type="aff" rid="aff-$author.affiliation$"/>
106+$endfor$
107107$if(author.cor-id)$
108108<xref ref-type="corresp" rid="cor-$author.cor-id$"><sup>*</sup></xref>
109109$endif$
110110</contrib>
111111$endfor$
112+${ affiliations.jats() }
112113</contrib-group>
113114$endif$
114115$if(article.author-notes)$
data/templates/default.jats_articleauthoring+4−3
@@ -34,14 +34,15 @@ $endif$
3434$if(author.email)$
3535<email>$author.email$</email>
3636$endif$
37−$if(author.aff-id)$
38−<xref ref-type="aff" rid="aff-$contrib.aff-id$"/>
39−$endif$
37+$for(author.affiliation)$
38+<xref ref-type="aff" rid="aff-$author.affiliation$"/>
39+$endfor$
4040$if(author.cor-id)$
4141<xref ref-type="corresp" rid="cor-$author.cor-id$"><sup>*</sup></xref>
4242$endif$
4343</contrib>
4444$endfor$
45+${ affiliations.jats() }
4546</contrib-group>
4647$endif$
4748$if(copyright)$
doc/jats.md+84
@@ -39,6 +39,12 @@ Metadata Values
3939 Used as the contents of the [`<email>`][elem:given-names]
4040 element.
4141
42+ `affiliation`
43+ : list of affiliation identifiers; marks the organizations
44+ with which an author is affiliated. Each identifier in this
45+ list must also occur as the `id` of an affiliation listed in
46+ the top-level `affiliation` list.
47+
4248 `cor-id`
4349 : identifier linking to the contributor's correspondence
4450 information. The info itself must be stored in as an item in
@@ -48,6 +54,73 @@ Metadata Values
4854 [`rid`][attr:rid] attribute is set to `cor-<ID>`, where
4955 `<ID>` is the stringified value of this attribute.
5056
57+`affiliation`
58+: the list of organizations with which contributors are
59+ affiliated. Each institution is added as an [`<aff>`] element to
60+ the author's contrib-group.
61+
62+ The fields are given in the order in which they are included in
63+ the output.
64+
65+ `id`
66+ : internal identifier; used as the [`<aff>`] element's `id`
67+ value, prefixed with `aff-`.
68+
69+ `group`
70+ : name of the research group or other low-level organizational
71+ structure; used as value of an [`<institution>`] element with
72+ [`content-type`][attr:content-type] set to `group`.
73+
74+ `department`
75+ : name of the department or other mid-level organizational
76+ structure; used as value of an [`<institution>`] element with
77+ [`content-type`][attr:content-type] set to `dept`.
78+
79+ `organization`
80+ : name of the company, university, or other top-level
81+ organizational structure; used as value of an
82+ [`<institution>`] element. The institution element is wrapped
83+ in an [`<institution-wrap>`] element; any identifiers, like
84+ `ringgold` or `ror`, are added to the wrapper and must hence
85+ belong to this organization (not the department or group).
86+
87+ `isni`
88+ : International Standard Name Identifier of the organization.
89+ Added via an [`<institution-id>`] element with
90+ [`institution-id-type`](attr:institution-id-type) set to
91+ `ISNI`.
92+
93+ `ringgold`
94+ : [Ringgold] identifier of the organization. Added via an
95+ [`<institution-id>`] element with
96+ [`institution-id-type`](attr:institution-id-type) set to
97+ `Ringgold`.
98+
99+ `ror`
100+ : Research Organization Registry identifier of the
101+ organization. Added via an [`<institution-id>`] element with
102+ [`institution-id-type`](attr:institution-id-type) set to
103+ `ROR`.
104+
105+ `street-address`
106+ : The organization's street address; each list item is wrapped
107+ in an [`<addr-line>`] element, separated by a comma and
108+ space (`, `).
109+
110+ `city`
111+ : City in which the organization is located; used only if
112+ `street-address` is not given, in which case the value is
113+ wrapped in a [`<city>`] element.
114+
115+ `country`
116+ : Country in which the organization is located; used as the
117+ value of a [`<country>`] element.
118+
119+ `country-code`
120+ : Two letter ISO-3166-1 country identifier; used as the
121+ [`country`][attr:country] attribute in element [`<country>`]
122+ (if the latter is present).
123+
51124`copyright`
52125: Licensing and copyright information. This information is
53126 rendered via the [`<permissions>`][elem:permissions] element.
@@ -258,7 +331,10 @@ Required metadata values:
258331 `journal.pmc`.
259332- One or more of `journal.pissn`, `journal.eissn`.
260333
334+[Ringgold]: https://ringgold.com/
335+[attr:content-type]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/attribute/content-type.html
261336[attr:fn-type]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/attribute/fn-type.html
337+[attr:institution-id-type]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/attribute/institution-id-type.html
262338[attr:iso-8601-date]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/attribute/iso-8601-date.html
263339[attr:journal-id-type]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/attribute/journal-id-type.html
264340[attr:kwd-group-type]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/attribute/kwd-group-type.html
@@ -297,3 +373,11 @@ Required metadata values:
297373[elem:subject]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/element/subject.html
298374[elem:surname]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/element/surname.html
299375[elem:xref]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/element/xref.html
376+
377+[`<addr-line>`]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/element/addr-line.html
378+[`<aff>`]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/element/aff.html
379+[`<city>`]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/element/city.html
380+[`<country>`]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/element/country.html
381+[`<institution-id>`]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/element/institution-id.html
382+[`<institution-wrap>`]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/element/institution-wrap.html
383+[`<institution>`]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/element/institution.html