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Merged
rpoet-jh merged 3 commits into from
Mar 16, 2026
Merged

Upgrade dependencies #175

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b1e812d
Upgrade pom dependencies
rpoet-jh Mar 12, 2026
ec7637f
Upgrade Dockerfiles
rpoet-jh Mar 12, 2026
d243c1a
Disable spring cloud aws paramstore for tests
rpoet-jh Mar 12, 2026
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19 changes: 8 additions & 11 deletions pass-data-client/pom.xml
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Expand Up @@ -14,16 +14,14 @@

<properties>
<!-- Properties for dependency versions -->
<okhttp.version>4.12.0</okhttp.version>
<moshi.version>4.12.0</moshi.version>
<jsonapi-adapters.version>1.1.0</jsonapi-adapters.version>
<slf4j.version>2.0.16</slf4j.version>
<logback.version>1.5.16</logback.version>
<commons-lang3.version>3.18.0</commons-lang3.version>
<junit.jupiter.version>5.10.5</junit.jupiter.version>
<mockito.version>5.11.0</mockito.version>
<testcontainers.version>1.19.8</testcontainers.version>
<maven-model.version>3.9.9</maven-model.version>
<slf4j.version>2.0.17</slf4j.version>
<logback.version>1.5.32</logback.version>
<commons-lang3.version>3.20.0</commons-lang3.version>
<junit.jupiter.version>5.14.3</junit.jupiter.version>
<mockito.version>5.22.0</mockito.version>
<testcontainers.version>1.21.4</testcontainers.version>
<maven-model.version>3.9.13</maven-model.version>
</properties>

<dependencyManagement>
Expand Down Expand Up @@ -53,8 +51,7 @@

<dependency>
<groupId>com.squareup.okhttp3</groupId>
<artifactId>okhttp</artifactId>
<version>${okhttp.version}</version>
<artifactId>okhttp-jvm</artifactId>
</dependency>

<dependency>
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2 changes: 1 addition & 1 deletion pass-deposit-services/deposit-core/Dockerfile
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FROM eclipse-temurin:17.0.8_7-jre-jammy
FROM eclipse-temurin:17.0.18_8-jre-noble

WORKDIR /app

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20 changes: 9 additions & 11 deletions pass-deposit-services/deposit-core/pom.xml
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Expand Up @@ -29,17 +29,16 @@
<description>PASS Deposit Services Core</description>

<properties>
<amazon.sqs.version>2.1.3</amazon.sqs.version>
<handlebars.version>4.4.0</handlebars.version>
<amazon.sqs.version>2.1.4</amazon.sqs.version>
<handlebars.version>4.5.0</handlebars.version>
<sshd.version>2.14.0</sshd.version>
<jsoup.version>1.18.1</jsoup.version>
<okhttp.version>4.12.0</okhttp.version>
<greenmail-junit5.version>2.1.0</greenmail-junit5.version>
<jsoup.version>1.22.1</jsoup.version>
<greenmail-junit5.version>2.1.8</greenmail-junit5.version>
<jakarta-json.version>2.0.1</jakarta-json.version>
<maven-model.version>3.9.9</maven-model.version>
<msal4j.version>1.17.2</msal4j.version>
<json-path.version>2.9.0</json-path.version>
<wiremock.version>3.9.1</wiremock.version>
<maven-model.version>3.9.13</maven-model.version>
<msal4j.version>1.24.0</msal4j.version>
<json-path.version>2.10.0</json-path.version>
<wiremock.version>3.13.2</wiremock.version>
</properties>

<dependencies>
Expand Down Expand Up @@ -92,8 +91,7 @@

<dependency>
<groupId>com.squareup.okhttp3</groupId>
<artifactId>okhttp</artifactId>
<version>${okhttp.version}</version>
<artifactId>okhttp-jvm</artifactId>
</dependency>

<dependency>
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1 change: 1 addition & 0 deletions pass-deposit-services/deposit-core/src/test/resources/test-application.properties
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Expand Up @@ -16,6 +16,7 @@
spring.jms.listener.auto-startup=false
pass.deposit.jobs.disabled=true
spring.cloud.aws.s3.enabled=false
spring.cloud.aws.parameterstore.enabled=false

pass.client.url=http://localhost:8080/
pass.client.user=test
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58 changes: 15 additions & 43 deletions pass-deposit-services/pom.xml
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Expand Up @@ -38,21 +38,19 @@
</modules>

<properties>
<spring-boot-maven-plugin.version>3.4.2</spring-boot-maven-plugin.version>
<awsspring.version>3.2.1</awsspring.version>
<commons-compress.version>1.27.1</commons-compress.version>
<commons-io.version>2.17.0</commons-io.version>
<commons-lang3.version>3.18.0</commons-lang3.version>
<okhttp.version>4.12.0</okhttp.version>
<xmlunit.version>2.10.0</xmlunit.version>
<commons-codec.version>1.17.1</commons-codec.version>
<mets-api.version>1.3</mets-api.version>
<tika.version>3.2.2</tika.version>
<gson.version>2.11.0</gson.version>
<joda-time.version>2.13.0</joda-time.version>
<spring-boot-maven-plugin.version>3.5.11</spring-boot-maven-plugin.version>
<awsspring.version>3.4.2</awsspring.version>
<commons-compress.version>1.28.0</commons-compress.version>
<commons-io.version>2.21.0</commons-io.version>
<commons-lang3.version>3.20.0</commons-lang3.version>
<xmlunit.version>2.11.0</xmlunit.version>
<commons-codec.version>1.21.0</commons-codec.version>
<tika.version>3.2.3</tika.version>
<gson.version>2.13.2</gson.version>
<joda-time.version>2.14.1</joda-time.version>
<xom.version>1.3.9</xom.version>
<servlet-api.version>2.4</servlet-api.version>
<json-smart.version>2.5.2</json-smart.version>
<servlet-api.version>2.5</servlet-api.version>
<json-smart.version>2.6.0</json-smart.version>
</properties>

<dependencyManagement>
Expand Down Expand Up @@ -148,18 +146,6 @@
<version>${tika.version}</version>
</dependency>

<dependency>
<groupId>com.squareup.okhttp3</groupId>
<artifactId>okhttp</artifactId>
<version>${okhttp.version}</version>
</dependency>

<dependency>
<groupId>com.squareup.okhttp3</groupId>
<artifactId>logging-interceptor</artifactId>
<version>${okhttp.version}</version>
</dependency>

<dependency>
<groupId>javax.servlet</groupId>
<artifactId>servlet-api</artifactId>
Expand All @@ -183,33 +169,19 @@
<artifactId>json-smart</artifactId>
<version>${json-smart.version}</version>
</dependency>

<!-- The following are transitive deps with convergence issues. -->
<!-- These should all be checked whenever deps are upgraded. -->
<dependency>
<groupId>org.ow2.asm</groupId>
<artifactId>asm</artifactId>
<version>9.6</version>
</dependency>
<dependency>
<groupId>org.jsoup</groupId>
<artifactId>jsoup</artifactId>
<version>1.18.1</version>
<version>9.7.1</version>
</dependency>
<!-- End of transitive deps with convergence issues. -->

<!-- The following deps were declared to resolve CVEs from transitive deps. -->
<!-- These should all be checked whenever deps are upgraded. Should be removed if possible once parent -->
<!-- dep updates with fixed version. -->
<dependency>
<groupId>io.netty</groupId>
<artifactId>netty-handler</artifactId>
<version>4.1.118.Final</version>
</dependency>
<dependency>
<groupId>io.netty</groupId>
<artifactId>netty-common</artifactId>
<version>4.1.118.Final</version>
</dependency>
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-lang3</artifactId>
Expand Down Expand Up @@ -394,7 +366,7 @@
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-help-plugin</artifactId>
<version>3.4.0</version>
<version>3.5.1</version>
</plugin>
</plugins>
</build>
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2 changes: 1 addition & 1 deletion pass-grant-loader/Dockerfile
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FROM eclipse-temurin:17.0.13_11-jre-jammy
FROM eclipse-temurin:17.0.18_8-jre-noble

WORKDIR /app

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22 changes: 6 additions & 16 deletions pass-grant-loader/pom.xml
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Expand Up @@ -30,13 +30,13 @@
<description>PASS Grant Data Loader</description>

<properties>
<spring-boot-maven-plugin.version>3.4.2</spring-boot-maven-plugin.version>
<awsspring.version>3.2.1</awsspring.version>
<spring-boot-maven-plugin.version>3.5.11</spring-boot-maven-plugin.version>
<awsspring.version>3.4.2</awsspring.version>
<args4j.version>2.37</args4j.version>
<commons.csv.version>1.12.0</commons.csv.version>
<mysql.jdbc.version>9.4.0</mysql.jdbc.version>
<maven-model.version>3.9.9</maven-model.version>
<commons-lang3.version>3.18.0</commons-lang3.version>
<commons.csv.version>1.14.1</commons.csv.version>
<mysql.jdbc.version>9.6.0</mysql.jdbc.version>
<maven-model.version>3.9.13</maven-model.version>
<commons-lang3.version>3.20.0</commons-lang3.version>
</properties>

<dependencyManagement>
Expand All @@ -59,16 +59,6 @@
<!-- The following deps were declared to resolve CVEs from transitive deps. -->
<!-- These should all be checked whenever deps are upgraded. Should be removed if possible once parent -->
<!-- dep updates with fixed version. -->
<dependency>
<groupId>io.netty</groupId>
<artifactId>netty-handler</artifactId>
<version>4.1.118.Final</version>
</dependency>
<dependency>
<groupId>io.netty</groupId>
<artifactId>netty-common</artifactId>
<version>4.1.118.Final</version>
</dependency>
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-lang3</artifactId>
Expand Down
4 changes: 3 additions & 1 deletion pass-grant-loader/src/test/resources/test-application.properties
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Expand Up @@ -12,4 +12,6 @@ spring.datasource.password=sa

grant.db.url=${spring.datasource.url}
grant.db.username=sa
grant.db.password=sa
grant.db.password=sa

spring.cloud.aws.parameterstore.enabled=false
2 changes: 1 addition & 1 deletion pass-journal-loader/pass-journal-loader-nih/Dockerfile
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FROM eclipse-temurin:17.0.13_11-jre-jammy
FROM eclipse-temurin:17.0.18_8-jre-noble

WORKDIR /app

Expand Down
6 changes: 3 additions & 3 deletions pass-journal-loader/pass-journal-loader-nih/pom.xml
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Expand Up @@ -15,9 +15,9 @@

<properties>
<!-- Properties for dependency versions -->
<wiremock.version>3.9.2</wiremock.version>
<testcontainers.version>1.19.8</testcontainers.version>
<maven-model.version>3.9.9</maven-model.version>
<wiremock.version>3.13.2</wiremock.version>
<testcontainers.version>1.21.4</testcontainers.version>
<maven-model.version>3.9.13</maven-model.version>
</properties>

<dependencies>
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12 changes: 6 additions & 6 deletions pass-journal-loader/pom.xml
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Expand Up @@ -19,13 +19,13 @@
</modules>

<properties>
<spring-boot-maven-plugin.version>3.3.5</spring-boot-maven-plugin.version>
<spring-boot-maven-plugin.version>3.5.11</spring-boot-maven-plugin.version>
<commons.csv.version>1.12.0</commons.csv.version>
<commons-lang3.version>3.18.0</commons-lang3.version>
<slf4j.version>2.0.16</slf4j.version>
<logback.version>1.5.16</logback.version>
<junit.jupiter.version>5.10.5</junit.jupiter.version>
<mockito.version>5.11.0</mockito.version>
<slf4j.version>2.0.17</slf4j.version>
<logback.version>1.5.32</logback.version>
<junit.jupiter.version>5.14.3</junit.jupiter.version>
<mockito.version>5.22.0</mockito.version>
</properties>

<dependencyManagement>
Expand Down Expand Up @@ -137,7 +137,7 @@
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-help-plugin</artifactId>
<version>3.4.0</version>
<version>3.5.1</version>
</plugin>
</plugins>
</build>
Expand Down
3 changes: 1 addition & 2 deletions pass-nihms-loader/nihms-data-harvest/pom.xml
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Expand Up @@ -35,12 +35,11 @@
<dependency>
<groupId>commons-io</groupId>
<artifactId>commons-io</artifactId>
<version>${commons-io.version}</version>
</dependency>

<dependency>
<groupId>com.squareup.okhttp3</groupId>
<artifactId>okhttp</artifactId>
<artifactId>okhttp-jvm</artifactId>
</dependency>

<dependency>
Expand Down
4 changes: 3 additions & 1 deletion pass-nihms-loader/nihms-data-harvest/src/test/resources/test-application.properties
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Expand Up @@ -10,4 +10,6 @@ nihmsetl.api.url.param.api-token=test-token
# By default this date will be set to the current month, one year ago
nihmsetl.api.url.param.pdf=07/2018
# Date in MM/YYYY format that the PACM data should end at (leave blank to default to the current month)
nihmsetl.api.url.param.pdt=07/2019
nihmsetl.api.url.param.pdt=07/2019

spring.cloud.aws.parameterstore.enabled=false
7 changes: 3 additions & 4 deletions pass-nihms-loader/nihms-data-transform-load/pom.xml
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Expand Up @@ -14,8 +14,8 @@
<description>PASS NIHMS Transform/Load Data Loader</description>

<properties>
<wiremock-version>3.9.2</wiremock-version>
<maven-model.version>3.9.9</maven-model.version>
<wiremock-version>3.13.2</wiremock-version>
<maven-model.version>3.9.13</maven-model.version>
</properties>

<dependencies>
Expand All @@ -38,7 +38,6 @@
<dependency>
<groupId>commons-io</groupId>
<artifactId>commons-io</artifactId>
<version>${commons-io.version}</version>
</dependency>

<dependency>
Expand Down Expand Up @@ -97,7 +96,7 @@

<dependency>
<groupId>com.squareup.okhttp3</groupId>
<artifactId>okhttp</artifactId>
<artifactId>okhttp-jvm</artifactId>
</dependency>

<!-- Test dependencies -->
Expand Down
4 changes: 3 additions & 1 deletion pass-nihms-loader/nihms-data-transform-load/src/test/resources/test-application.properties
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Expand Up @@ -6,4 +6,6 @@ pmc.entrez.service.url=http://localhost:9911/entrez/eutils/esummary.fcgi?db=pubm
# pass-core properties
pass.client.url=http://localhost:8080/
pass.client.user=backend
pass.client.password=moo
pass.client.password=moo

spring.cloud.aws.parameterstore.enabled=false
2 changes: 1 addition & 1 deletion pass-nihms-loader/nihms-docker/Dockerfile
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FROM eclipse-temurin:17.0.13_11-jre-jammy
FROM eclipse-temurin:17.0.18_8-jre-noble

WORKDIR /app

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2 changes: 1 addition & 1 deletion pass-nihms-loader/nihms-docker/pom.xml
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Expand Up @@ -17,7 +17,7 @@
<plugins>
<plugin>
<artifactId>maven-resources-plugin</artifactId>
<version>3.1.0</version>
<version>3.5.0</version>
<executions>
<execution>
<id>copy-jar-files-for-dockerfile</id>
Expand Down
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