From 8d2c31bc571cfb18cf657bf011ec28d399389d99 Mon Sep 17 00:00:00 2001 From: Luca Foppiano Date: Mon, 3 Jun 2024 16:36:49 +1200 Subject: [PATCH 1/6] Fix stylesheet to support the data availability statements --- Stylesheets/NLM2TEI-article.xsl | 19 ++++++++++++++++--- 1 file changed, 16 insertions(+), 3 deletions(-) diff --git a/Stylesheets/NLM2TEI-article.xsl b/Stylesheets/NLM2TEI-article.xsl index 4448e85..691595c 100644 --- a/Stylesheets/NLM2TEI-article.xsl +++ b/Stylesheets/NLM2TEI-article.xsl @@ -24,7 +24,7 @@ - + @@ -1195,11 +1195,12 @@ - + + @@ -1354,7 +1355,7 @@ + not explicitly addressed by means of an XPath in another template--> @@ -2256,6 +2257,18 @@ + +
+ + + +

+ +

+ +
+ + From 46c28e2654ce81b3f676fa99f508a02eb3bb491c Mon Sep 17 00:00:00 2001 From: Luca Foppiano Date: Tue, 4 Jun 2024 14:31:32 +1200 Subject: [PATCH 2/6] transform URLs that are tagged as

- +

From 9fc42d49e72f775fa10151d559717d2136c32f97 Mon Sep 17 00:00:00 2001 From: Luca Foppiano Date: Wed, 19 Jun 2024 17:34:58 +0900 Subject: [PATCH 3/6] more dirty thanks to the JATS jungle --- Stylesheets/NLM2TEI-article.xsl | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/Stylesheets/NLM2TEI-article.xsl b/Stylesheets/NLM2TEI-article.xsl index c9a988a..cda3d4c 100644 --- a/Stylesheets/NLM2TEI-article.xsl +++ b/Stylesheets/NLM2TEI-article.xsl @@ -2533,6 +2533,16 @@ + +
+ +
+ + +
+ +
+ From d620225ab9742acf89539fb036d2a7aa36f3fa25 Mon Sep 17 00:00:00 2001 From: Luca Foppiano Date: Wed, 19 Jun 2024 19:41:50 +0900 Subject: [PATCH 4/6] capture some funding statements --- Stylesheets/NLM2TEI-article.xsl | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/Stylesheets/NLM2TEI-article.xsl b/Stylesheets/NLM2TEI-article.xsl index cda3d4c..a2d3f58 100644 --- a/Stylesheets/NLM2TEI-article.xsl +++ b/Stylesheets/NLM2TEI-article.xsl @@ -2538,11 +2538,21 @@ + +
+ +
+
+ +
+ +
+ From a216fc8d2e874688afc37413aaf0fcb9c6b93fba Mon Sep 17 00:00:00 2001 From: Luca Foppiano Date: Thu, 4 Jul 2024 15:33:55 +0900 Subject: [PATCH 5/6] add missing divs --- Stylesheets/NLM2TEI-article.xsl | 34 ++++++++++++++++++++++----------- 1 file changed, 23 insertions(+), 11 deletions(-) diff --git a/Stylesheets/NLM2TEI-article.xsl b/Stylesheets/NLM2TEI-article.xsl index a2d3f58..a52c60f 100644 --- a/Stylesheets/NLM2TEI-article.xsl +++ b/Stylesheets/NLM2TEI-article.xsl @@ -2253,18 +2253,22 @@
- +
+ +
- - - -

- -

+
+ + + +

+ +

+
@@ -2535,22 +2539,30 @@
- +
+ +
- +
+ +
- +
+ +
- +
+ +
From 66e8f6e3b8db9b617507dca981afac6d2e71fdec Mon Sep 17 00:00:00 2001 From: Luca Foppiano Date: Thu, 5 Dec 2024 20:39:36 +0000 Subject: [PATCH 6/6] build and github actions --- .github/workflows/ci-build-manual.yml | 34 ++++++++++++++++----------- build.gradle | 2 +- 2 files changed, 21 insertions(+), 15 deletions(-) diff --git a/.github/workflows/ci-build-manual.yml b/.github/workflows/ci-build-manual.yml index 606b0ce..319b005 100644 --- a/.github/workflows/ci-build-manual.yml +++ b/.github/workflows/ci-build-manual.yml @@ -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 ] @@ -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 }} diff --git a/build.gradle b/build.gradle index a088f55..148e616 100644 --- a/build.gradle +++ b/build.gradle @@ -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'