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1 change: 1 addition & 0 deletions .env
Original file line number Diff line number Diff line change
Expand Up @@ -4,6 +4,7 @@ DB_PORT=8293
DB_USER=pguser
DB_PASSWORD=password
DB_DATA=./docker/postgres-data/
DB_CONNECTION_POOL=30

APP_CONTEXT=ubo
APP_HTTP=8291
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3 changes: 2 additions & 1 deletion .github/workflows/maven-publish-snapshot.yml
Original file line number Diff line number Diff line change
Expand Up @@ -9,7 +9,8 @@ on:
- 'main'
- '2025.06.x'
- '2024.06.x'

workflow_dispatch:

jobs:
build:

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1 change: 1 addition & 0 deletions docker-compose.prod.yml
Original file line number Diff line number Diff line change
Expand Up @@ -31,6 +31,7 @@ services:
- JDBC_PASSWORD=${DB_PASSWORD}
- JDBC_DRIVER=org.postgresql.Driver
- JDBC_URL=jdbc:postgresql://db:5432/ubo
- JDBC_CONNECTION_POOL_SIZE=${DB_CONNECTION_POOL}
- SOLR_URL=http://solr:8983
- SOLR_CORE=ubo
- SOLR_CLASSIFICATION_CORE=ubo-classifications
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1 change: 1 addition & 0 deletions docker-compose.yml
Original file line number Diff line number Diff line change
Expand Up @@ -39,6 +39,7 @@ services:
- JDBC_DRIVER=org.postgresql.Driver
- JDBC_URL=jdbc:postgresql://db:5432/ubo
- JDBC_SCHEMA=${DB_SCHEMA}
- JDBC_CONNECTION_POOL_SIZE=${DB_CONNECTION_POOL}
- SOLR_URL=http://solr:8983
- SOLR_CORE=ubo
- SOLR_CLASSIFICATION_CORE=ubo-classifications
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2 changes: 1 addition & 1 deletion docker-entrypoint.sh
Original file line number Diff line number Diff line change
Expand Up @@ -158,7 +158,7 @@ function setDockerValues() {

# s/(<\/properties>)/<property name=\"hibernate.hikari.maximumPoolSize\" value=\"30\" \/>\n<property name=\"hibernate.hikari.minimumIdle\" value=\"2\" \/>\n<property name=\"hibernate.hikari.idleTimeout\" value=\"30000\" \/>\n<property name=\"hibernate.hikari.maxLifetime\" value=\"1800000\" \/>\n<property name=\"hibernate.hikari.leakDetectionThreshold\" value=\"9000\" \/>\n<property name=\"\" value=\"true\" \/>
setOrAddProperty "MCR.JPA.Connection.ProviderClass" "org.hibernate.hikaricp.internal.HikariCPConnectionProvider"
setOrAddProperty "MCR.JPA.Connection.MaximumPoolSize" "30"
setOrAddProperty "MCR.JPA.Connection.MaximumPoolSize" "${JDBC_CONNECTION_POOL_SIZE:-30}"
setOrAddProperty "MCR.JPA.Connection.MinimumIdle" "2"
setOrAddProperty "MCR.JPA.Connection.IdleTimeout" "30000"
setOrAddProperty "MCR.JPA.Connection.MaxLifetime" "180000"
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Original file line number Diff line number Diff line change
Expand Up @@ -695,7 +695,7 @@ MCR.MODS.EnrichmentResolver.DataSource.EVALuna.evaluna.URI=xslStyle:import/evalu
######################################################################

UBO.PubMed.Link=https://www.ncbi.nlm.nih.gov/pubmed/
UBO.PubMed.REST.URL=https://www.ebi.ac.uk/europepmc/webservices/rest/search/resulttype=core&query=
UBO.PubMed.REST.URL=https://www.ebi.ac.uk/europepmc/webservices/rest/search?resulttype=core&query=

# Configuration for importing PubMed RSS feed
MCR.MODS.RSSFeedImporter.PubMed.FeedURL=https://eutils.ncbi.nlm.nih.gov/entrez/eutils/erss.cgi?rss_guid=1LgINZmdEb7dTjgV40Ro8AN9MSFRAFarM7cb16kssgU3LD2Afd
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2 changes: 1 addition & 1 deletion ubo-common/src/main/resources/xsl/import/pubmed2mods.xsl
Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
<?xml version="1.0" encoding="UTF-8"?>

<!-- Converts PubMed core format to MODS -->
<!-- http://www.ebi.ac.uk/europepmc/webservices/rest/search/resulttype=core&query=ext_id:26063869 -->
<!-- http://www.ebi.ac.uk/europepmc/webservices/rest/search?resulttype=core&query=ext_id:26063869 -->

<xsl:stylesheet version="1.0"
xmlns:xsl="http://www.w3.org/1999/XSL/Transform"
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2 changes: 1 addition & 1 deletion ubo-common/src/main/resources/xsl/response.xsl
Original file line number Diff line number Diff line change
Expand Up @@ -305,7 +305,7 @@
<div class="result mt-2 mb-2">
<div class="hit card">
<xsl:variable name="id" select="str[@name='id']" />
<xsl:variable name="mycoreobject" select="document(concat('mcrobject:',$id))/mycoreobject" />
<xsl:variable name="mycoreobject" select="document(concat('notnull:mcrobject:',$id))/mycoreobject" />
<xsl:for-each select="$mycoreobject/metadata/def.modsContainer/modsContainer/mods:mods">
<div class="labels card-header ">
<xsl:apply-templates select="." mode="badges"/>
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