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Hotfix 1.5.11 #424

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2b65135
Update versions for hotfix
arteymix Jun 14, 2026
ee7138d
DIOPT v10
sanjarogic Jun 15, 2026
50ccbae
Update dependencies
arteymix Jun 15, 2026
e628ef6
Use latest DIOPT in default configuration
arteymix Jun 15, 2026
725372a
Add missing header in latest DIOPT metadata file
arteymix Jun 15, 2026
7288122
Simplify integration test for Uberon
arteymix Jun 15, 2026
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14 changes: 7 additions & 7 deletions pom.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -6,7 +6,7 @@
<name>Rare Disease Project</name>
<groupId>ubc.pavlab</groupId>
<artifactId>rdp</artifactId>
<version>1.5.10</version>
<version>1.5.11</version>

<description>
Registry for model organism/system researchers, developed for the Canadian Rare Disease Models &amp; Mechanisms Network.
Expand Down Expand Up @@ -146,20 +146,20 @@
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-csv</artifactId>
<version>1.12.0</version>
<version>1.14.1</version>
</dependency>

<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-text</artifactId>
<version>1.12.0</version>
<version>1.15.0</version>
</dependency>

<!-- User-Agent header parsing -->
<dependency>
<groupId>nl.basjes.parse.useragent</groupId>
<artifactId>yauaa</artifactId>
<version>7.28.1</version>
<version>7.32.0</version>
</dependency>

<!-- Testing Support -->
Expand Down Expand Up @@ -229,7 +229,7 @@
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-enforcer-plugin</artifactId>
<version>3.5.0</version>
<version>3.6.3</version>
<executions>
<execution>
<id>enforce-maven</id>
Expand All @@ -249,7 +249,7 @@
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>exec-maven-plugin</artifactId>
<version>3.4.1</version>
<version>3.6.3</version>
<executions>
<execution>
<id>npm-install-dependencies</id>
Expand Down Expand Up @@ -324,7 +324,7 @@
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>versions-maven-plugin</artifactId>
<version>2.17.1</version>
<version>2.21.0</version>
<configuration>
<allowMajorUpdates>false</allowMajorUpdates>
<processDependencyManagement>false</processDependencyManagement>
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2 changes: 1 addition & 1 deletion src/main/resources/application.properties
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Expand Up @@ -86,7 +86,7 @@ rdp.settings.allow-internationalized-email-domains=false
rdp.settings.cache.enabled=true
rdp.settings.cache.load-from-disk=false
rdp.settings.cache.gene-files-location=file:genes/
rdp.settings.cache.ortholog-file=classpath:cache/DIOPT_filtered_data_Sept2022.gz
rdp.settings.cache.ortholog-file=classpath:cache/DIOPT_filtered_data_June2026.gz
rdp.settings.cache.term-file=http://purl.obolibrary.org/obo/go.obo
rdp.settings.cache.annotation-file=ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/gene2go.gz
rdp.settings.cache.organ-file=http://purl.obolibrary.org/obo/uberon.obo
Expand Down
Binary file added src/main/resources/cache/DIOPT_filtered_data_June2026.gz
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4 changes: 1 addition & 3 deletions src/test/java/ubc/pavlab/rdp/util/OBOParserIntegrationTest.java
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Expand Up @@ -85,9 +85,7 @@ public void parse_withUberonTermsOnline_thenSucceed() throws ParseException {
Map<String, OBOParser.Term> parsedTerms = parsingResult.getTermsByIdOrAltId();
assertThat( parsedTerms ).containsKey( "UBERON:0000000" );
OBOParser.Term term = parsedTerms.get( "UBERON:0000000" );
assertThat( term )
.hasFieldOrPropertyWithValue( "name", "processual entity" )
.hasFieldOrPropertyWithValue( "definition", "An occurrent [span:Occurrent] that exists in time by occurring or happening, has temporal parts and always involves and depends on some entity." );
assertThat( term ).isNotNull();
}

@Test
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