Add missing metadata to the JATS template plugin

[kaitlinnewson]

Description:
The JATS template plugin generates a mostly complete JATS record, but some metadata elements are handled in the OAI JATS plugin instead, but can be moved to the JATS template plugin. This will mean a more complete JATS record is created in the JATS template plugin, and this can be used for export plugins that support JATS (e.g. Pubmed, Portico) so we can offload most JATS creation to this plugin.

A preliminary comparison of the output from the JATS template plugin and the Portico plugin shows that abstract, DOI, issue, and volume are missing in the JATS template plugin.

Related discussion thread: #7974

What application are you using?
OJS 3.5/main

Additional Information
previous PRs targeted for #11540 (closed now)
pkp/oaiJats#81
pkp/jatsTemplate#88

PRs

main

oaiJats --> pkp/oaiJats#84
jatsTemplate --> pkp/jatsTemplate#92
ojs --> pkp/ojs#5136 [TEST ONLY]

[touhidurabir]

As part of ongoing work of #11540 , following is the comparison of jats xml generated by jatsTemplate and oaiJats :

XML generated by jatsTemplate plugin (few missing metadata already added as part of #11540)

<?xml version="1.0" encoding="UTF-8"?>
<article
	xmlns:xlink="http://www.w3.org/1999/xlink" xml:lang="en"
	xmlns:mml="http://www.w3.org/1998/Math/MathML"
	xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
	<front>
		<journal-meta>
			<journal-id journal-id-type="ojs">publicknowledge</journal-id>
			<journal-title-group>
				<journal-title xml:lang="en">Journal of Public Knowledge</journal-title>
				<trans-title-group xml:lang="fr-CA">
					<trans-title>Journal de la connaissance du public</trans-title>
				</trans-title-group>
				<abbrev-journal-title xml:lang="en">publicknowledgeJ Pub Know</abbrev-journal-title>
			</journal-title-group>
			<publisher>
				<publisher-name>Public Knowledge Project</publisher-name>
				<publisher-loc>
					<country>IS</country>
				</publisher-loc>
			</publisher>
			<issn pub-type="epub">0378-5955</issn>
			<issn pub-type="ppub">0378-5955</issn>
			<self-uri xlink:href="http://ojs-main.test/index.php/publicknowledge"/>
		</journal-meta>
		<article-meta>
			<article-id pub-id-type="publisher-id">15</article-id>
			<article-id pub-id-type="doi">10.1234/4qwz8z90</article-id>
			<volume seq="1">1</volume>
			<issue>2</issue>
			<issue-id>1</issue-id>
			<article-categories>
				<subj-group xml:lang="en" subj-group-type="heading">
					<subject>Articles</subject>
				</subj-group>
			</article-categories>
			<title-group>
				<article-title xml:lang="en">Yam diseases and its management in Nigeria</article-title>
			</title-group>
			<contrib-group content-type="author">
				<contrib corresp="yes">
					<name-alternatives>
						<name name-style="western" specific-use="primary">
							<surname>Baiyewu</surname>
							<given-names>Rana</given-names>
						</name>
					</name-alternatives>
					<email>rbaiyewu@mailinator.com</email>
					<xref ref-type="aff" rid="aff-1"/>
				</contrib>
			</contrib-group>
			<aff id="aff-1">
				<institution-wrap>
					<institution content-type="orgname">University of Nairobi</institution>
					<institution-id institution-id-type="ROR">https://ror.org/02y9nww90</institution-id>
				</institution-wrap>
			</aff>
			<abstract xml:lang="en">
				<p>This review presents different diseases associated with yam and the management strategies employed in combating its menace in Nigeria. The field and storage diseases are presented, anthracnose is regarded as the most widely spread of all the field diseases, while yam mosaic virus disease is considered to cause the most severe losses in yams. Dry rot is considered as the most devastating of all the storage diseases of yam. Dry rot of yams alone causes a marked reduction in the quantity, marketable value and edible portions of tubers and those reductions are more severe in stored yams. The management strategies adopted and advocated for combating the field diseases includes the use of crop rotation, fallowing, planting of healthy material, the destruction of infected crop cultivars and the use of resistant cultivars. With regards to the storage diseases, the use of Tecto (Thiabendazole), locally made dry gins or wood ash before storage has been found to protect yam tubers against fungal infection in storage. Finally, processing of yam tubers into chips or cubes increases its shelf live for a period of between 6 months and one year.</p>
			</abstract>
			<trans-abstract xml:lang="fr-CA">
				<p>Cette revue présente différentes maladies associées à l'igname et les stratégies de gestion employées pour lutter contre cette menace au Nigéria. Les maladies de plein champ et de stockage sont présentées. L'anthracnose est considérée comme la plus répandue de toutes les maladies de plein champ, tandis que la maladie virale de la mosaïque de l'igname est considérée comme causant les pertes les plus importantes chez les ignames. La pourriture sèche est considérée comme la plus dévastatrice de toutes les maladies de stockage de l'igname. La pourriture sèche de l'igname à elle seule entraîne une réduction marquée de la quantité, de la valeur marchande et des parties comestibles des tubercules, et ces réductions sont plus importantes pour les ignames stockées. Les stratégies de gestion adoptées et préconisées pour lutter contre les maladies de plein champ comprennent la rotation des cultures, la jachère, la plantation de matériel sain, la destruction des cultivars infectés et l'utilisation de cultivars résistants. Concernant les maladies de stockage, l'utilisation de Tecto (thiabendazole), d'égreneuses à sec fabriquées localement ou de cendres de bois avant le stockage s'est avérée efficace pour protéger les tubercules d'igname contre les infections fongiques. Enfin, la transformation des tubercules d’igname en chips ou en cubes augmente leur durée de conservation d’une durée comprise entre 6 mois et un an.</p>
			</trans-abstract>
			<abstract abstract-type="plain-language-summary" xml:lang="en">
				<p>This review discusses diseases that affect yams in Nigeria and how they are managed. In the field, anthracnose is the most common disease, while yam mosaic virus causes the heaviest losses. In storage, dry rot is the most damaging, reducing the quantity, market value, and edible parts of yams, especially in stored tubers. To manage field diseases, farmers use crop rotation, fallowing, healthy planting material, destroy infected crops, and plant resistant yam varieties. For storage diseases, applying Tecto (Thiabendazole), local dry gins, or wood ash before storage helps protect yams from fungal infections. Processing yams into chips or cubes also extends their shelf life for 6 months to a year.</p>
			</abstract>
			<trans-abstract abstract-type="plain-language-summary" xml:lang="fr-CA">
				<p>Cette revue examine les maladies qui affectent les ignames au Nigéria et leur gestion. Sur le terrain, l'anthracnose est la maladie la plus courante, tandis que le virus de la mosaïque de l'igname cause les pertes les plus lourdes. En stockage, la pourriture sèche est la plus dommageable, réduisant la quantité, la valeur marchande et les parties comestibles des ignames, en particulier les tubercules stockés. Pour lutter contre les maladies sur le terrain, les agriculteurs ont recours à la rotation des cultures, à la jachère, à un matériel végétal sain, à la destruction des cultures infectées et à la plantation de variétés d'ignames résistantes. Pour les maladies liées au stockage, l'application de Tecto (thiabendazole), d'égreneuses sèches locales ou de cendres de bois avant le stockage permet de protéger les ignames des infections fongiques. La transformation des ignames en chips ou en cubes prolonge également leur durée de conservation de 6 mois à un an.</p>
			</trans-abstract>
			<pub-date date-type="pub" publication-format="epub">
				<day>21</day>
				<month>07</month>
				<year>2025</year>
			</pub-date>
			<pub-history>
				<event event-type="received">
					<event-desc>Received: 
						<date date-type="received" iso-8601-date="2025-07-20T06:13:29+00:00">
							<day>20</day>
							<month>7</month>
							<year>2025</year>
						</date>
					</event-desc>
				</event>
			</pub-history>
			<permissions>
				<copyright-statement>Copyright (c) 2025 Journal of Public Knowledge</copyright-statement>
				<copyright-year>2025</copyright-year>
				<copyright-holder>Journal of Public Knowledge</copyright-holder>
			</permissions>
			<self-uri xlink:href="http://ojs-main.test/index.php/publicknowledge/article/view/15"/>
			<kwd-group xml:lang="en">
				<kwd>test</kwd>
				<kwd>test01</kwd>
				<kwd>test02</kwd>
			</kwd-group>
			<custom-meta-group/>
		</article-meta>
	</front>
	<body/>
	<back/>
</article>

xml generated by oaiJats

<article xml:lang="en" dtd-version="1.1" specific-use="eps-0.1" >
	<front>
		<journal-meta>
			<journal-id journal-id-type="publisher" >publicknowledge</journal-id>
			<journal-id journal-id-type="ojs" >publicknowledge</journal-id>
			<journal-title-group>
				<journal-title xml:lang="en" >Journal of Public Knowledge</journal-title>
				<trans-title-group xml:lang="fr-CA" >
					<trans-title>Journal de la connaissance du public</trans-title>
				</trans-title-group>
				<abbrev-journal-title xml:lang="en" >publicknowledgeJ Pub Know</abbrev-journal-title>
			</journal-title-group>
			<contrib-group>
				<contrib contrib-type="jmanager" >
					<name>
						<surname>admin</surname>
						<given-names>admin</given-names>
					</name>
				</contrib>
				<contrib contrib-type="jmanager" >
					<name>
						<surname>Vaca</surname>
						<given-names>Ramiro</given-names>
					</name>
				</contrib>
				<contrib contrib-type="editor" >
					<name>
						<surname>Barnes</surname>
						<given-names>Daniel</given-names>
					</name>
				</contrib>
				<contrib contrib-type="secteditor" >
					<name>
						<surname>Buskins</surname>
						<given-names>David</given-names>
					</name>
				</contrib>
				<contrib contrib-type="secteditor" >
					<name>
						<surname>Berardo</surname>
						<given-names>Stephanie</given-names>
					</name>
				</contrib>
				<contrib contrib-type="secteditor" >
					<name>
						<surname>Inoue</surname>
						<given-names>Minoti</given-names>
					</name>
				</contrib>
			</contrib-group>
			<publisher>
				<publisher-name>Public Knowledge Project</publisher-name>
				<publisher-loc>
					<country>IS</country>
				</publisher-loc>
			</publisher>
			<issn pub-type="epub" >0378-5955</issn>
			<issn pub-type="ppub" >0378-5955</issn>
			<self-uri xlink:href="http://ojs-main.test/index.php/publicknowledge" ></self-uri>
		</journal-meta>
		<article-meta>
			<article-id pub-id-type="publisher-id" >15</article-id>
			<article-id pub-id-type="doi" >10.1234/4qwz8z90</article-id>
			<pub-date date-type="collection" >
				<year>2014</year>
			</pub-date>
			<volume seq="1" >11</volume>
			<issue>2</issue>
			<issue-id>21</issue-id>
			<article-categories>
				<subj-group subj-group-type="heading" xml:lang="en" >
					<subject>Articles</subject>
				</subj-group>
			</article-categories>
			<title-group>
				<article-title xml:lang="en" >Yam diseases and its management in Nigeria</article-title>
			</title-group>
			<contrib-group content-type="author" >
				<contrib corresp="yes" >
					<name-alternatives>
						<name name-style="western" specific-use="primary" >
							<surname>Baiyewu</surname>
							<given-names>Rana</given-names>
						</name>
					</name-alternatives>
					<email>rbaiyewu@mailinator.com</email>
					<xref ref-type="aff" rid="aff-1" ></xref>
				</contrib>
			</contrib-group>
			<aff id="aff-1" >
				<institution-wrap>
					<institution content-type="orgname" >University of Nairobi</institution>
					<institution-id institution-id-type="ROR" >https://ror.org/02y9nww90</institution-id>
				</institution-wrap>
			</aff>
			<self-uri xlink:href="http://ojs-main.test/index.php/publicknowledge/article/view/15" ></self-uri>
			<pub-date date-type="pub" publication-format="epub" >
				<day>21</day>
				<month>07</month>
				<year>2025</year>
			</pub-date>
			<pub-history>
				<event event-type="received" >
					<event-desc>Received:

						<date date-type="received" iso-8601-date="2025-07-20T06:13:29+00:00" >
							<day>20</day>
							<month>7</month>
							<year>2025</year>
						</date>
					</event-desc>
				</event>
			</pub-history>
			<permissions>
				<copyright-statement>Copyright (c) 2025 Journal of Public Knowledge</copyright-statement>
				<copyright-year>2025</copyright-year>
				<copyright-holder>Journal of Public Knowledge</copyright-holder>
			</permissions>
			<abstract>This review presents different diseases associated with yam and the management strategies employed in combating its menace in Nigeria. The field and storage diseases are presented, anthracnose is regarded as the most widely spread of all the field diseases, while yam mosaic virus disease is considered to cause the most severe losses in yams. Dry rot is considered as the most devastating of all the storage diseases of yam. Dry rot of yams alone causes a marked reduction in the quantity, marketable value and edible portions of tubers and those reductions are more severe in stored yams. The management strategies adopted and advocated for combating the field diseases includes the use of crop rotation, fallowing, planting of healthy material, the destruction of infected crop cultivars and the use of resistant cultivars. With regards to the storage diseases, the use of Tecto (Thiabendazole), locally made dry gins or wood ash before storage has been found to protect yam tubers against fungal infection in storage. Finally, processing of yam tubers into chips or cubes increases its shelf live for a period of between 6 months and one year.</abstract>
			<abstract abstract-type="plain-language-summary" >
				<p>This review discusses diseases that affect yams in Nigeria and how they are managed. In the field, anthracnose is the most common disease, while yam mosaic virus causes the heaviest losses. In storage, dry rot is the most damaging, reducing the quantity, market value, and edible parts of yams, especially in stored tubers. To manage field diseases, farmers use crop rotation, fallowing, healthy planting material, destroy infected crops, and plant resistant yam varieties. For storage diseases, applying Tecto (Thiabendazole), local dry gins, or wood ash before storage helps protect yams from fungal infections. Processing yams into chips or cubes also extends their shelf life for 6 months to a year.</p>
			</abstract>
			<trans-abstract xml:lang="fr-CA" >
				<p>Cette revue présente différentes maladies associées à l'igname et les stratégies de gestion employées pour lutter contre cette menace au Nigéria. Les maladies de plein champ et de stockage sont présentées. L'anthracnose est considérée comme la plus répandue de toutes les maladies de plein champ, tandis que la maladie virale de la mosaïque de l'igname est considérée comme causant les pertes les plus importantes chez les ignames. La pourriture sèche est considérée comme la plus dévastatrice de toutes les maladies de stockage de l'igname. La pourriture sèche de l'igname à elle seule entraîne une réduction marquée de la quantité, de la valeur marchande et des parties comestibles des tubercules, et ces réductions sont plus importantes pour les ignames stockées. Les stratégies de gestion adoptées et préconisées pour lutter contre les maladies de plein champ comprennent la rotation des cultures, la jachère, la plantation de matériel sain, la destruction des cultivars infectés et l'utilisation de cultivars résistants. Concernant les maladies de stockage, l'utilisation de Tecto (thiabendazole), d'égreneuses à sec fabriquées localement ou de cendres de bois avant le stockage s'est avérée efficace pour protéger les tubercules d'igname contre les infections fongiques. Enfin, la transformation des tubercules d’igname en chips ou en cubes augmente leur durée de conservation d’une durée comprise entre 6 mois et un an.</p>
			</trans-abstract>
			<trans-abstract abstract-type="plain-language-summary" xml:lang="fr-CA" >
				<p>Cette revue examine les maladies qui affectent les ignames au Nigéria et leur gestion. Sur le terrain, l'anthracnose est la maladie la plus courante, tandis que le virus de la mosaïque de l'igname cause les pertes les plus lourdes. En stockage, la pourriture sèche est la plus dommageable, réduisant la quantité, la valeur marchande et les parties comestibles des ignames, en particulier les tubercules stockés. Pour lutter contre les maladies sur le terrain, les agriculteurs ont recours à la rotation des cultures, à la jachère, à un matériel végétal sain, à la destruction des cultures infectées et à la plantation de variétés d'ignames résistantes. Pour les maladies liées au stockage, l'application de Tecto (thiabendazole), d'égreneuses sèches locales ou de cendres de bois avant le stockage permet de protéger les ignames des infections fongiques. La transformation des ignames en chips ou en cubes prolonge également leur durée de conservation de 6 mois à un an.</p>
			</trans-abstract>
			<kwd-group xml:lang="en" >
				<title>Keywords</title>
				<kwd>test</kwd>
				<kwd>test01</kwd>
				<kwd>test02</kwd>
			</kwd-group>
			<custom-meta-group>
				<custom-meta>
					<meta-name>issue-cover</meta-name>
					<meta-value>
						<inline-graphic xlink:href="http://ojs-main.test/public/journals/1/cover_issue_1_en.png" ></inline-graphic>
					</meta-value>
				</custom-meta>
			</custom-meta-group>
			<custom-meta-group></custom-meta-group>
		</article-meta>
	</front>
	<body></body>
	<back></back>
</article> 

Comparison Table

Section/Element	oaiJats XML	JatsTemplate XML	What's Missing/Incorrect in JatsTemplate
<article> Root Element	<article xml:lang="en" dtd-version="1.1" specific-use="eps-0.1">	<article xmlns:xlink="http://www.w3.org/1999/xlink" xml:lang="en" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">	- Missing dtd-version="1.1" attribute. - Missing specific-use="eps-0.1" attribute. - Includes unused namespaces xmlns:mml and xmlns:xsi, which are not present in oaiJats.
<journal-meta>: <journal-id>	<journal-id journal-id-type="publisher">publicknowledge</journal-id> <journal-id journal-id-type="ojs">publicknowledge</journal-id>	<journal-id journal-id-type="ojs">publicknowledge</journal-id>	- Missing <journal-id journal-id-type="publisher">publicknowledge</journal-id>.
<journal-meta>: <contrib-group>	<contrib-group> with 6 contributors (2 jmanager, 1 editor, 3 secteditor) containing <name> with <surname> and <given-names>.	Absent	- Missing entire <contrib-group> with journal managers and editors.
<journal-meta>: Other Elements	<journal-title-group>, <publisher>, <issn>, <self-uri> are identical.	Same as oaiJats.	- No differences; <journal-title-group>, <publisher>, <issn pub-type="epub">, <issn pub-type="ppub">, and <self-uri> match exactly.
<article-meta>: <pub-date>	<pub-date date-type="collection"><year>2014</year></pub-date> <pub-date date-type="pub" publication-format="epub">...</pub-date>	<pub-date date-type="pub" publication-format="epub">...</pub-date>	- Missing <pub-date date-type="collection"><year>2014</year></pub-date>.
<article-meta>: <volume>	<volume seq="1">11</volume>	<volume seq="1">1</volume>	- Incorrect volume number (1 instead of 11). Likely a data retrieval issue (e.g., $issue->getVolume()).
<article-meta>: <issue>	<issue>2</issue>	<issue>2</issue>	- No difference; matches exactly.
<article-meta>: <issue-id>	<issue-id>21</issue-id>	<issue-id>1</issue-id>	- Incorrect issue ID (1 instead of 21). Likely a data retrieval issue (e.g., $issue->getId() vs. $issue->getNumber()).
<article-meta>: <abstract>	<abstract>...</abstract> (no xml:lang for primary locale en)	<abstract xml:lang="en">...</abstract>	- Incorrectly includes xml:lang="en" for the primary locale. Should omit xml:lang for en.
<article-meta>: <abstract abstract-type="plain-language-summary">	<abstract abstract-type="plain-language-summary">...</abstract> (no xml:lang for primary locale en)	<abstract abstract-type="plain-language-summary" xml:lang="en">...</abstract>	- Incorrectly includes xml:lang="en" for the primary locale. Should omit xml:lang for en.
<article-meta>: <trans-abstract>	<trans-abstract xml:lang="fr-CA">...</trans-abstract>	<trans-abstract xml:lang="fr-CA">...</trans-abstract>	- No difference; matches exactly.
<article-meta>: <trans-abstract abstract-type="plain-language-summary">	<trans-abstract abstract-type="plain-language-summary" xml:lang="fr-CA">...</trans-abstract>	<trans-abstract abstract-type="plain-language-summary" xml:lang="fr-CA">...</trans-abstract>	- No difference; matches exactly.
<article-meta>: <kwd-group>	<kwd-group xml:lang="en"><title>Keywords</title><kwd>...</kwd>...</kwd-group>	<kwd-group xml:lang="en"><kwd>...</kwd>...</kwd-group>	- Missing <title>Keywords</title> element within <kwd-group>.
<article-meta>: <custom-meta-group>	Two <custom-meta-group> elements, one with <custom-meta> containing <meta-name>issue-cover</meta-name> and <meta-value><inline-graphic xlink:href="..."></inline-graphic></meta-value>, and one empty.	Single empty <custom-meta-group/>	- Missing <custom-meta-group> with <custom-meta> containing the issue cover image (<inline-graphic>).
Other Elements	<article-categories>, <title-group>, <contrib-group content-type="author">, <aff>, <self-uri>, <pub-date date-type="pub">, <pub-history>, <permissions> are identical.	Same as oaiJats.	- No differences in these sections.
<body> and <back>	<body></body><back></back>	<body/><back/>	- No functional difference; empty elements are equivalent (self-closing vs. explicit closing tags).

Summary of Differences

The JatsTemplate XML is missing or incorrect in the following areas compared to the oaiJats XML:

1. Root <article> Attributes:

   • Missing dtd-version="1.1" and specific-use="eps-0.1".
   • Includes unused xmlns:mml and xmlns:xsi namespaces, which are absent in oaiJats.

2. <journal-meta>:

   • Missing <journal-id journal-id-type="publisher">publicknowledge</journal-id>.
   • Missing <contrib-group> with journal managers and editors (6 contributors: 2 jmanager, 1 editor, 3 secteditor).

3. <article-meta>:

   • Missing <pub-date date-type="collection"><year>2014</year></pub-date>.
   • Incorrect <volume> value (1 instead of 11), likely due to incorrect data retrieval (e.g., $issue->getVolume()).
   • Incorrect <issue-id> value (1 instead of 21), likely due to using $issue->getNumber() instead of $issue->getId().
   • Incorrectly includes xml:lang="en" on <abstract> and <abstract abstract-type="plain-language-summary"> for the primary locale (en), which should be omitted.
   • Missing <title>Keywords</title> in <kwd-group>.
   • Missing <custom-meta-group> with <custom-meta> containing issue cover image metadata (<inline-graphic>).

4. Data Issues:

   • The incorrect <volume> (1 vs. 11) and <issue-id> (1 vs. 21) suggest issues with data retrieval in JatsTemplate, possibly due to incorrect method calls or database configuration.

The final Comparison Table and the Summary of Differences above are optimised by grok ai .

@kaitlinnewson can you please take a look and point out if anything I am missing here .

[kaitlinnewson]

Hi @touhidurabir, I think this mostly captures it. A few notes:

• The <article> attributes in oaiJats look to be added specifically for coalition publica harvesting, so we may not need to carry them over to Jats Template as long as they are in OAIJats, but @asmecher can probably confirm (see https://eruditps.docs.erudit.org/tagset/element-article.html)

• I'm not seeing this issue with incorrect volume and issue numbers in my local install from main with the oai Jats export, but I am using a different publication so maybe that's the difference

• References metadata is missing in the samples, but the references metadata are present in both so no need to address it

• In my local main install, there in an extra self-uri for galleys in oaiJats which is not present in JatsTemplate:

  <self-uri xlink:href="http://localhost:8000/index.php/publicknowledge/article/download/mwandenga/2/12"
            content-type="application/pdf"/>

[asmecher]

@touhidurabir, yes, please leave the dtd-version and specific-use attributes in OAIJats per @kaitlinnewson's suggestion above.