Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

[Chore] Upgrade to Java17 #202

Draft
wants to merge 3 commits into
base: develop
Choose a base branch
from
+16 −16
Draft

[Chore] Upgrade to Java17 #202

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
3 commits
Select commit Hold shift + click to select a range
56b5a44
Add latest submodule changes
ke4 Jun 3, 2024
34c6116
Change java version to 17
ke4 Jun 3, 2024
b894dc7
Improve SitemapWriterIT
ke4 Jun 11, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
8 changes: 4 additions & 4 deletions app/build.gradle
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -27,10 +27,10 @@ def cache2kVersion = '1.2.4.Final'
dependencies {
implementation project(':atlas-web-core')

implementation 'org.springframework:spring-context:5.1.5.RELEASE'
implementation 'org.springframework:spring-web:5.1.5.RELEASE'
implementation 'org.springframework:spring-jdbc:5.1.5.RELEASE'
implementation 'org.springframework:spring-webmvc:5.1.5.RELEASE'
implementation 'org.springframework:spring-context:5.3.26'
implementation 'org.springframework:spring-web:5.3.26'
implementation 'org.springframework:spring-jdbc:5.3.26'
implementation 'org.springframework:spring-webmvc:5.3.26'

implementation 'javax.validation:validation-api:2.0.1.Final'
implementation 'commons-net:commons-net:3.8.0'
Expand Down
2 changes: 1 addition & 1 deletion app/src/main/javascript/modules/experiments-summary-panel
Open in desktop
Submodule experiments-summary-panel updated 1 files
+6 −1 README.md
2 changes: 1 addition & 1 deletion app/src/main/javascript/modules/species-summary-panel
Open in desktop
Submodule species-summary-panel updated 1 files
+4 −0 README.md
6 changes: 3 additions & 3 deletions app/src/test/java/uk/ac/ebi/atlas/sitemaps/SitemapWriterIT.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -51,15 +51,15 @@ void producesValidXmlForMainSitemapOfSitemaps() throws Exception {
var baos = new ByteArrayOutputStream();
SitemapWriter.writeSitemapIndex(baos, randomSubsetOfSpecies);

assertThat(parseXml(baos).getDocumentElement()).hasFieldOrPropertyWithValue("tagName", "sitemapindex");
assertThat(parseXml(baos).getDocumentElement().getTagName()).isEqualTo("sitemapindex");
}

@Test
void producesValidXmlForExperiments() throws Exception {
var baos = new ByteArrayOutputStream();
SitemapWriter.writeExperimentsSitemap(baos);

assertThat(parseXml(baos).getDocumentElement()).hasFieldOrPropertyWithValue("tagName", "urlset");
assertThat(parseXml(baos).getDocumentElement().getTagName()).isEqualTo("urlset");
}

@Test
Expand All @@ -83,7 +83,7 @@ void producesValidXmlForBioentityIdentifiers() throws Exception {
var baos = new ByteArrayOutputStream();
SitemapWriter.writeBioentityIdentifiersSitemap(baos, ImmutableList.of(), true);

assertThat(parseXml(baos).getDocumentElement()).hasFieldOrPropertyWithValue("tagName", "urlset");
assertThat(parseXml(baos).getDocumentElement().getTagName()).isEqualTo( "urlset");
}

private Document parseXml(final ByteArrayOutputStream outputStream) throws Exception {
Expand Down
6 changes: 3 additions & 3 deletions buildSrc/src/main/groovy/atlas-web-app.java-conventions.gradle
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -6,8 +6,8 @@ plugins {
group = 'uk.ac.ebi.ge'
version = '1.0.0'

sourceCompatibility = 11
targetCompatibility = 11
sourceCompatibility = 17
targetCompatibility = 17

repositories {
mavenCentral()
Expand Down Expand Up @@ -61,7 +61,7 @@ dependencies {
exclude group: 'org.apache.logging.log4j', module: 'log4j-slf4j-impl'
}

testImplementation 'org.springframework:spring-test:5.1.5.RELEASE'
testImplementation 'org.springframework:spring-test:5.3.26'
testImplementation 'com.h2database:h2:1.4.199'
testImplementation 'org.junit.jupiter:junit-jupiter-params:5.4.1'
testImplementation 'org.mockito:mockito-core:5.2.0'
Expand Down
2 changes: 1 addition & 1 deletion docker/docker-compose-gradle-test.yml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@ version: "3.6"

services:
gxa-gradle:
image: gradle:7.0-jdk11
image: gradle:7.6.4-jdk17
networks:
- atlas-test-net
ports:
Expand Down
2 changes: 1 addition & 1 deletion docker/docker-compose-gradle.yml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@ version: "3.6"

services:
gxa-gradle:
image: gradle:7.0-jdk11
image: gradle:7.6.4-jdk17
networks:
- atlas-test-net
volumes:
Expand Down
2 changes: 1 addition & 1 deletion docker/docker-compose-tomcat.yml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@ version: "3.6"

services:
gxa-tomcat:
image: tomcat:9-jdk11
image: tomcat:9-jdk17
container_name: gxa-tomcat
networks:
- atlas-test-net
Expand Down
2 changes: 1 addition & 1 deletion schemas
Open in desktop
Submodule schemas updated 12 files
+10 −0 .github/workflows/run_ci_tests.yml
+0 −12 .travis.yml
+0 −14 Dockerfile
+90 −65 README.md
+21 −0 flyway/gxa/migrations/V8__gxa-create-exp-design.sql
+5 −0 flyway/scxa/migrations/V16__coords_query_indices.sql
+1 −0 flyway/scxa/migrations/V17__remove_tsne_table.sql
+4 −0 flyway/scxa/migrations/V18__remove_clusters_markers_tables.sql
+59 −0 flyway/scxa/migrations/V19__anndata_import_changes.sql
+20 −0 flyway/scxa/migrations/V20__scxa-create-exp-design.sql
+7 −2 run_tests_with_containers.sh
+1 −1 tests/run_tests.sh
Loading