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Springboot upgrade 2.5 to 2.7 #205

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merged 10 commits into from
Jan 10, 2024
Merged

Springboot upgrade 2.5 to 2.7 #205

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e168ff0
update to java 17
ahmadshadab Nov 10, 2023
1969a33
update objectmapper
ahmadshadab Nov 13, 2023
e39ea93
use hibernate validtor 6.2
ahmadshadab Nov 14, 2023
00b8fe1
change junit version to same as store
ahmadshadab Nov 14, 2023
b95a62e
make mockito version consistent with store and rest
ahmadshadab Nov 23, 2023
6824a90
update build docker image
ahmadshadab Nov 30, 2023
a2e7e64
replace wget with curl due to unavailability of util in docker image
ahmadshadab Nov 30, 2023
2535a31
fix curl
ahmadshadab Nov 30, 2023
73c0b03
address review comment
ahmadshadab Dec 6, 2023
a7db375
Merge branch 'main' into springboot_upgrade
ahmadshadab Jan 9, 2024
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4 changes: 2 additions & 2 deletions .gitlab-ci.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -10,7 +10,7 @@ variables:
SONAR_USER_HOME: "${CI_PROJECT_DIR}/.sonar"
JACOCO_AGGREGATE_REPORT: "jacoco-aggregate-report/target/site/jacoco-aggregate/jacoco.xml"

image: maven:3.6.3-jdk-11
image: maven:3.8.5-openjdk-17
cache:
key: "$CI_COMMIT_REF_SLUG"
paths:
Expand All @@ -27,7 +27,7 @@ stages:
core:settings:
stage: build
before_script:
- 'wget --no-cache --no-cookies -O ${MAVEN_SETTINGS} "${URL_MAVEN_SETTINGS}"'
- 'curl --location "${URL_MAVEN_SETTINGS}" --output ${MAVEN_SETTINGS}'
script:
- if [ ! -f ${MAVEN_SETTINGS} ];
then echo "CI settings file missing";
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2 changes: 1 addition & 1 deletion ff-parser/pom.xml
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Expand Up @@ -15,7 +15,7 @@
<properties>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<antlr4.version>4.5.3</antlr4.version>
<hibernate-validator.version>6.1.5.Final</hibernate-validator.version>
<hibernate-validator.version>6.2.5.Final</hibernate-validator.version>
</properties>

<dependencies>
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6 changes: 5 additions & 1 deletion json-parser/pom.xml
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Expand Up @@ -13,7 +13,6 @@
<artifactId>json-parser</artifactId>

<properties>
<jackson.version>2.11.4</jackson.version>
<mbknor-jackson-jsonschema.version>1.0.31</mbknor-jackson-jsonschema.version>
</properties>

Expand All @@ -38,6 +37,11 @@
<artifactId>jackson-datatype-jdk8</artifactId>
<version>${jackson.version}</version>
</dependency>
<dependency>
<groupId>com.fasterxml.jackson.datatype</groupId>
<artifactId>jackson-datatype-jsr310</artifactId>
<version>${jackson.version}</version>
</dependency>
<dependency>
<groupId>com.kjetland</groupId>
<artifactId>mbknor-jackson-jsonschema_2.12</artifactId>
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2 changes: 2 additions & 0 deletions json-parser/src/main/java/org/uniprot/core/json/parser/JsonConfig.java
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Expand Up @@ -7,9 +7,11 @@
import com.fasterxml.jackson.annotation.PropertyAccessor;
import com.fasterxml.jackson.databind.DeserializationFeature;
import com.fasterxml.jackson.databind.ObjectMapper;
import com.fasterxml.jackson.databind.SerializationFeature;
import com.fasterxml.jackson.databind.ser.PropertyFilter;
import com.fasterxml.jackson.databind.ser.impl.SimpleBeanPropertyFilter;
import com.fasterxml.jackson.databind.ser.impl.SimpleFilterProvider;
import com.fasterxml.jackson.datatype.jsr310.JavaTimeModule;
import com.github.bohnman.squiggly.filter.SquigglyPropertyFilter;
import com.github.bohnman.squiggly.filter.SquigglyPropertyFilterMixin;

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5 changes: 4 additions & 1 deletion ...-parser/src/main/java/org/uniprot/core/json/parser/uniparc/UniParcCrossRefJsonConfig.java
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Expand Up @@ -2,6 +2,7 @@

import java.time.LocalDate;

import com.fasterxml.jackson.datatype.jsr310.JavaTimeModule;
import org.uniprot.core.CrossReference;
import org.uniprot.core.Database;
import org.uniprot.core.impl.CrossReferenceImpl;
Expand Down Expand Up @@ -67,6 +68,8 @@ private ObjectMapper initObjectMapper() {
}

private ObjectMapper initPrettyObjectMapper() {
return getDefaultSimpleObjectMapper();
ObjectMapper simpleObjectMapper = getDefaultSimpleObjectMapper();
simpleObjectMapper.registerModule(new JavaTimeModule());
return simpleObjectMapper;
}
}
1 change: 1 addition & 0 deletions ...ser/src/test/java/org/uniprot/core/json/parser/uniparc/UniParcCrossRefJsonConfigTest.java
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Expand Up @@ -3,6 +3,7 @@
import static org.junit.jupiter.api.Assertions.fail;
import static org.uniprot.core.json.parser.uniparc.UniParcEntryTest.getCompleteUniParcEntry;

import com.fasterxml.jackson.datatype.jsr310.JavaTimeModule;
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Can you please remove this import (I do not think this is being used)

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This is being used by Java time module.

import org.junit.jupiter.api.Test;
import org.uniprot.core.json.parser.ValidateJson;
import org.uniprot.core.uniparc.UniParcCrossReference;
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11 changes: 7 additions & 4 deletions pom.xml
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Expand Up @@ -11,18 +11,20 @@
<name>UniProt Core Aggregator</name>

<properties>
<jackson-bom.version>2.13.4</jackson-bom.version>
<jackson.version>2.13.4</jackson.version>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<surefire-version>2.22.2</surefire-version>
<failsafe-version>2.22.2</failsafe-version>
<mockito-version>3.0.0</mockito-version>
<mockito-version>4.5.1</mockito-version>
<slf4j.version>1.7.28</slf4j.version>
<logback.version>1.2.3</logback.version>
<junit-jupiter.version>5.5.2</junit-jupiter.version>
<junit-jupiter.version>5.8.2</junit-jupiter.version>
<hamcrest.version>1.3</hamcrest.version>
<maven-compiler-plugin.version>3.8.1</maven-compiler-plugin.version>
<jacoco-maven-plugin.version>0.8.4</jacoco-maven-plugin.version>
<http-uniprot-private-url>https://wwwdev.ebi.ac.uk/uniprot/artifactory</http-uniprot-private-url>
<java.version>11</java.version>
<java.version>17</java.version>
<skipITs>false</skipITs>
<skipUTs>false</skipUTs>
<guava.version>30.0-jre</guava.version>
Expand All @@ -40,7 +42,7 @@
<!-- Integration test report path -->
<jacoco.out.it.file>jacoco-it.exec</jacoco.out.it.file>
<jacoco.itReportPath>${jacoco.outputDir}/${jacoco.out.it.file}</jacoco.itReportPath>
<jacoco.version>0.8.5</jacoco.version>
<jacoco.version>0.8.8</jacoco.version>
</properties>

<dependencyManagement>
Expand Down Expand Up @@ -184,6 +186,7 @@
<includes>
<include>*</include>
</includes>
<argLine>--add-opens java.base/java.time=ALL-UNNAMED</argLine>
</configuration>
</plugin>
<plugin>
Expand Down
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