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Data availability jungle #27

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Data availability jungle #27

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8d2c31b
Fix stylesheet to support the data availability statements
lfoppiano Jun 3, 2024
46c28e2
transform URLs that are tagged as <ext:link
lfoppiano Jun 4, 2024
9fc42d4
more dirty thanks to the JATS jungle
lfoppiano Jun 19, 2024
d620225
capture some funding statements
lfoppiano Jun 19, 2024
a216fc8
add missing divs
lfoppiano Jul 4, 2024
66e8f6e
build and github actions
lfoppiano Dec 5, 2024
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34 changes: 20 additions & 14 deletions .github/workflows/ci-build-manual.yml
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Original file line number Diff line number Diff line change
@@ -1,23 +1,28 @@
name: Build and push a development version on docker
name: Build and push a development version on docker

on:
workflow_dispatch:

on:
workflow_dispatch:
inputs:
custom_tag:
type: string
description: Docker image tag
required: true
default: "latest-develop"

jobs:
build:
runs-on: ubuntu-latest

steps:
- uses: actions/checkout@v4
- name: Set up JDK 11
uses: actions/setup-java@v4
with:
java-version: '11'
distribution: 'temurin'
cache: 'gradle'
- name: Build with Gradle
run: ./gradlew build -x test
- uses: actions/checkout@v4
- name: Set up JDK 11
uses: actions/setup-java@v4
with:
java-version: '11'
distribution: 'temurin'
cache: 'gradle'
- name: Build with Gradle
run: ./gradlew build -x test

docker-build:
needs: [ build ]
Expand All @@ -42,6 +47,7 @@ jobs:
image: lfoppiano/pub2tei
registry: docker.io
pushImage: true
tags: latest-develop
tags: |
latest-develop, ${{ github.event.inputs.custom_tag}}
- name: Image digest
run: echo ${{ steps.docker_build.outputs.digest }}
51 changes: 48 additions & 3 deletions Stylesheets/NLM2TEI-article.xsl
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Expand Up @@ -24,7 +24,7 @@
<xsl:when test="//pubfm/categ/@id[string-length() &gt; 0]">
<xsl:value-of select="$codeGenreNature"/>
</xsl:when>
<!-- if no article-type in the orignial metadata -->
<!-- if no article-type in the original metadata -->
<xsl:otherwise>
<xsl:choose>
<xsl:when test="//article/front/article-meta/abstract[string-length()&gt; 0]">
Expand Down Expand Up @@ -1195,11 +1195,12 @@
</group>
</xsl:if>

<xsl:if test="back | bm |front/article-meta/product">
<xsl:if test="back | bm | front/article-meta/product | front/article-meta/custom-meta-group/custom-meta[@id='data-availability']">
<back>
<!-- SG - source des book-reviews, données qualifiés de production chez Cambridge -->
<xsl:apply-templates select="front/article-meta/product"/>
<xsl:apply-templates select="back/* | bm/ack | bm/bibl"/>
<xsl:apply-templates select="front/article-meta/custom-meta-group/custom-meta[@id='data-availability']"/>
</back>
</xsl:if>
</text>
Expand Down Expand Up @@ -1354,7 +1355,7 @@
</xsl:template>

<!-- We do not care about components from <article-meta> which are
not explicitely addressed by means of an XPath in another template-->
not explicitly addressed by means of an XPath in another template-->
<xsl:template match="article-meta"/>

<!-- Building the sourceDesc bibliographical representation -->
Expand Down Expand Up @@ -2252,6 +2253,22 @@

<xsl:template match="ack">
<div type="acknowledgements">
<div>
<xsl:apply-templates/>
</div>
</div>
</xsl:template>

<xsl:template match="front/article-meta/custom-meta-group/custom-meta[@id='data-availability']">
<div type="availability">
<div>
<head>
<xsl:value-of select="meta-name"/>
</head>
<p>
<xsl:apply-templates select="meta-value/node()"/>
</p>
</div>
<xsl:apply-templates/>
</div>
</xsl:template>
Expand Down Expand Up @@ -2520,6 +2537,34 @@
<xsl:apply-templates/>
</div>
</xsl:template>
<xsl:template match="back/notes[@notes-type='data-availability']">
<div type="availability">
<div>
<xsl:apply-templates/>
</div>
</div>
</xsl:template>
<xsl:template match="back/notes[@notes-type='funding-information']">
<div type="funding">
<div>
<xsl:apply-templates/>
</div>
</div>
</xsl:template>
<xsl:template match="back/*/sec[@sec-type='data-availability']">
<div type="availability">
<div>
<xsl:apply-templates/>
</div>
</div>
</xsl:template>
<xsl:template match="back/*/sec[@sec-type='funding-information']">
<div type="funding">
<div>
<xsl:apply-templates/>
</div>
</div>
</xsl:template>
<xsl:template match="fn-group/fn">
<xsl:choose>
<xsl:when test="ancestor::title-group/fn-group/fn">
Expand Down
2 changes: 1 addition & 1 deletion build.gradle
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Expand Up @@ -119,7 +119,7 @@ dependencies {
implementation 'javax.xml.bind:jaxb-api:2.3.0'
implementation 'org.apache.opennlp:opennlp-tools:1.9.1'
implementation 'black.ninia:jep:4.0.2'
implementation "org.apache.httpcomponents:httpclient:4.5.3"
implementation "org.apache.httpcomponents:httpclient:4.5.13"
implementation "org.apache.lucene:lucene-analyzers-common:4.5.1"
implementation group: 'org.jruby', name: 'jruby-complete', version: '9.2.13.0'

Expand Down