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Merge pull request #770 from EBIBioSamples/dev
Preparing for release 5.3.13
2 parents b7d2c05 + afe83b3 commit 4592f4d

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‎.gitlab-ci.yml‎

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@@ -4,40 +4,85 @@ services:
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variables:
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DEPLOY_PATH: ~/gitlab
7+
DOCKER_DRIVER: overlay2
8+
DOCKER_TLS_CERTDIR: ""
9+
DOCKER_TAG: $CI_COMMIT_REF_SLUG-$CI_COMMIT_SHORT_SHA
10+
DOCKER_IMAGE_NAME: $CI_REGISTRY_IMAGE:$DOCKER_TAG
11+
DOCKER_PULL_SECRET: docker-registry-secret
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APP_NAME: $CI_PROJECT_NAME
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before_script:
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- echo $CI_BUILD_REF
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- echo $CI_PROJECT_DIR
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- apk update && apk add git
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1320
stages:
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- build
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- package
1523
- config
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- deploy
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18-
maven-package:
26+
maven-package-webapps-core:
1927
image: ${CI_REGISTRY_IMAGE}/eclipse-temurin:17-jdk
20-
stage: package
28+
stage: build
2129
script:
22-
- './mvnw -q deploy -P embl-ebi -s ci_settings.xml -DskipTests -Dmaven.source.skip=true'
23-
- mkdir deployment
24-
- cp webapps/core/target/webapps-core-*.war deployment/webapps-core.war
25-
- cp webapps/core-v2/target/webapps-core-v2*.jar deployment/webapps-core-v2.jar
26-
- cp agents/solr/target/agents-solr-*.jar deployment/agents-solr.jar
27-
- cp agents/uploadworkers/target/agents-uploadworkers-*.jar deployment/agents-uploadworkers.jar
28-
- cp pipelines/curation/target/pipelines-curation-*.jar deployment/pipelines-curation.jar
29-
# - cp pipelines/ena/target/pipelines-ena-*.jar deployment/pipelines-ena.jar
30-
# - cp pipelines/ncbi-ena-link/target/pipelines-ncbi-ena-link-*.jar deployment/pipelines-ncbi-ena-link.jar
31-
- cp pipelines/sample-release/target/pipelines-sample-release-*.jar deployment/pipelines-sample-release.jar
32-
- cp pipelines/sample-post-release-action/target/pipelines-sample-post-release-action*.jar deployment/pipelines-sample-post-release-action.jar
33-
- cp pipelines/ncbi/target/pipelines-ncbi-*.jar deployment/pipelines-ncbi.jar
34-
- cp pipelines/reindex/target/pipelines-reindex-*.jar deployment/pipelines-reindex.jar
35-
- cp pipelines/sample-transformation-dtol/target/pipelines-sample-transformation-dtol-*.jar deployment/pipelines-sample-transformation-dtol.jar
30+
- './mvnw -q deploy -pl webapps/core -am -P embl-ebi -s ci_settings.xml -DskipTests -Dmaven.source.skip=true'
3631
artifacts:
3732
paths:
38-
- deployment
33+
- webapps/core/target/webapps-core-*.war
34+
35+
# maven-package:
36+
# image: ${CI_REGISTRY_IMAGE}/eclipse-temurin:17-jdk
37+
# stage: build
38+
# script:
39+
# - './mvnw -q deploy -P embl-ebi -s ci_settings.xml -DskipTests -Dmaven.source.skip=true'
40+
# - mkdir deployment
41+
# - cp webapps/core/target/webapps-core-*.war deployment/webapps-core.war
42+
# - cp webapps/core-v2/target/webapps-core-v2*.jar deployment/webapps-core-v2.jar
43+
# - cp agents/solr/target/agents-solr-*.jar deployment/agents-solr.jar
44+
# - cp agents/uploadworkers/target/agents-uploadworkers-*.jar deployment/agents-uploadworkers.jar
45+
# - cp pipelines/curation/target/pipelines-curation-*.jar deployment/pipelines-curation.jar
46+
# - cp pipelines/ena/target/pipelines-ena-*.jar deployment/pipelines-ena.jar
47+
# - cp pipelines/ncbi-ena-link/target/pipelines-ncbi-ena-link-*.jar deployment/pipelines-ncbi-ena-link.jar
48+
# - cp pipelines/sample-release/target/pipelines-sample-release-*.jar deployment/pipelines-sample-release.jar
49+
# - cp pipelines/sample-post-release-action/target/pipelines-sample-post-release-action*.jar deployment/pipelines-sample-post-release-action.jar
50+
# - cp pipelines/ncbi/target/pipelines-ncbi-*.jar deployment/pipelines-ncbi.jar
51+
# - cp pipelines/reindex/target/pipelines-reindex-*.jar deployment/pipelines-reindex.jar
52+
# - cp pipelines/sample-transformation-dtol/target/pipelines-sample-transformation-dtol-*.jar deployment/pipelines-sample-transformation-dtol.jar
53+
# artifacts:
54+
# paths:
55+
# - deployment
3956
# when: manual
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58+
build_docker_image:
59+
stage: package
60+
image: docker:stable
61+
services:
62+
- docker:stable-dind
63+
before_script:
64+
- echo "$CI_REGISTRY_PASSWORD" | docker login --username "$CI_REGISTRY_USER" --password-stdin "$CI_REGISTRY"
65+
script:
66+
- docker build --build-arg DOCKER_REGISTRY=${CI_REGISTRY_IMAGE} -t $DOCKER_IMAGE_NAME -f webapps/core/Dockerfile .
67+
- docker push $DOCKER_IMAGE_NAME
68+
after_script:
69+
- docker logout ${CI_REGISTRY_IMAGE}
70+
71+
deploy-dev-bsd-v1:
72+
image: dtzar/helm-kubectl:3.11.0
73+
stage: deploy
74+
script:
75+
- cd webapps/core
76+
- sed -i "s|%DOCKER_IMAGE%|$DOCKER_IMAGE_NAME|g" core-deployment.yaml
77+
- kubectl config set-cluster bsd-cluster --server="${K8_HL_SERVER}"
78+
- kubectl config set clusters.bsd-cluster.certificate-authority-data ${K8_HL_CERTIFICATE_AUTHORITY_DATA}
79+
- kubectl config set-credentials bsd-user --token="${K8_HL_CREDENTIALS}"
80+
- kubectl config set-context bsd-context --cluster=bsd-cluster --user=bsd-user
81+
- kubectl config use-context bsd-context
82+
- kubectl apply -f core-deployment.yaml --namespace=biosamples-dev
83+
- kubectl apply -f core-service.yaml --namespace=biosamples-dev
84+
when: manual
85+
4186
clone-config-dev:
4287
stage: config
4388
script:
@@ -127,7 +172,7 @@ deploy-production:
127172
parallel:
128173
matrix:
129174
- BSD_NODE_NAME: bsd_prod
130-
BSD_HOST_NAME: [wp-p2m-40, wp-p2m-41, wp-p1m-40, wp-p1m-41]
175+
BSD_HOST_NAME: [ wp-p2m-40, wp-p2m-41, wp-p1m-40, wp-p1m-41 ]
131176
environment:
132177
name: prod-${BSD_HOST_NAME}
133178
url: http://${BSD_HOST_NAME}:8081/biosamples/
@@ -144,7 +189,7 @@ deploy-production-solr:
144189
parallel:
145190
matrix:
146191
- BSD_NODE_NAME: bsd_prod
147-
BSD_SOLR_HOST_NAME: [wp-p1m-42, wp-p2m-42]
192+
BSD_SOLR_HOST_NAME: [ wp-p1m-42, wp-p2m-42 ]
148193
environment:
149194
name: prod-solr-${BSD_HOST_NAME}
150195
url: http://${BSD_SOLR_HOST_NAME}.ebi.ac.uk:8983/solr

‎RELEASE.adoc‎

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This pages contains links to release notes for BioSamples for version 4.0.0 and higher. This release represents a comprehensive overhaul and therefore previous release notes are no longer applicable.
55

6+
[[v5.3.13]]
7+
== v5.3.13 Release notes
8+
* Zenodo archive for the publication
9+
610
[[v5.3.12]]
711
== v5.3.12 Release notes
812
* EBI Survey banner

‎agents/pom.xml‎

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<parent>
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<groupId>uk.ac.ebi.biosamples</groupId>
1111
<artifactId>biosamples</artifactId>
12-
<version>5.3.12</version>
12+
<version>5.3.13-SNAPSHOT</version>
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</parent>
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1515
<modules>

‎agents/solr/pom.xml‎

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<parent>
88
<groupId>uk.ac.ebi.biosamples</groupId>
99
<artifactId>biosamples</artifactId>
10-
<version>5.3.12</version>
10+
<version>5.3.13-SNAPSHOT</version>
1111
<relativePath>../../</relativePath>
1212
</parent>
1313

1414
<dependencies>
1515
<dependency>
1616
<groupId>uk.ac.ebi.biosamples</groupId>
1717
<artifactId>properties</artifactId>
18-
<version>5.3.12</version>
18+
<version>5.3.13-SNAPSHOT</version>
1919
</dependency>
2020
<dependency>
2121
<groupId>uk.ac.ebi.biosamples</groupId>
22-
<artifactId>models-solr</artifactId>
23-
<version>5.3.12</version>
24-
</dependency>
25-
<dependency>
26-
<groupId>uk.ac.ebi.biosamples</groupId>
27-
<artifactId>messaging</artifactId>
28-
<version>5.3.12</version>
29-
</dependency>
30-
<dependency>
31-
<groupId>uk.ac.ebi.biosamples</groupId>
32-
<artifactId>utils-ols</artifactId>
33-
<version>5.3.12</version>
22+
<artifactId>core</artifactId>
23+
<version>5.3.13-SNAPSHOT</version>
3424
</dependency>
3525

3626
<dependency>
3727
<groupId>org.springframework.hateoas</groupId>
3828
<artifactId>spring-hateoas</artifactId>
3929
<version>1.3.4</version>
4030
</dependency>
31+
<dependency>
32+
<groupId>org.springframework.boot</groupId>
33+
<artifactId>spring-boot-starter-web</artifactId>
34+
</dependency>
4135
<dependency>
4236
<groupId>com.github.ben-manes.caffeine</groupId>
4337
<artifactId>caffeine</artifactId>

‎agents/solr/src/main/java/uk/ac/ebi/biosamples/solr/MessageHandlerSolr.java‎

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Original file line numberDiff line numberDiff line change
@@ -19,10 +19,10 @@
1919
import org.slf4j.LoggerFactory;
2020
import org.springframework.amqp.rabbit.annotation.RabbitListener;
2121
import org.springframework.stereotype.Service;
22-
import uk.ac.ebi.biosamples.MessageContent;
23-
import uk.ac.ebi.biosamples.Messaging;
24-
import uk.ac.ebi.biosamples.model.Attribute;
25-
import uk.ac.ebi.biosamples.model.Sample;
22+
import uk.ac.ebi.biosamples.core.model.Attribute;
23+
import uk.ac.ebi.biosamples.core.model.Sample;
24+
import uk.ac.ebi.biosamples.messaging.MessagingConstants;
25+
import uk.ac.ebi.biosamples.messaging.model.MessageContent;
2626
import uk.ac.ebi.biosamples.solr.model.SolrSample;
2727
import uk.ac.ebi.biosamples.solr.repo.SolrSampleRepository;
2828
import uk.ac.ebi.biosamples.solr.service.SampleToSolrSampleConverter;
@@ -51,14 +51,14 @@ public MessageHandlerSolr(
5151
}
5252

5353
@RabbitListener(
54-
queues = Messaging.INDEXING_QUEUE,
54+
queues = MessagingConstants.INDEXING_QUEUE,
5555
containerFactory = "biosamplesAgentSolrContainerFactory")
5656
public void handleIndexing(final MessageContent messageContent) {
5757
handle(messageContent);
5858
}
5959

6060
@RabbitListener(
61-
queues = Messaging.REINDEXING_QUEUE,
61+
queues = MessagingConstants.REINDEXING_QUEUE,
6262
containerFactory = "biosamplesAgentSolrContainerFactory")
6363
public void handleReindexing(final MessageContent messageContent) {
6464
handle(messageContent);

‎agents/solr/src/main/java/uk/ac/ebi/biosamples/solr/SolrRunner.java‎

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@@ -17,8 +17,8 @@
1717
import org.springframework.boot.ApplicationRunner;
1818
import org.springframework.stereotype.Component;
1919
import uk.ac.ebi.biosamples.BioSamplesProperties;
20-
import uk.ac.ebi.biosamples.MessageUtils;
21-
import uk.ac.ebi.biosamples.Messaging;
20+
import uk.ac.ebi.biosamples.messaging.MessagingConstants;
21+
import uk.ac.ebi.biosamples.messaging.service.MessageUtils;
2222

2323
@Component
2424
public class SolrRunner implements ApplicationRunner {
@@ -36,9 +36,9 @@ public void run(final ApplicationArguments args) throws Exception {
3636
|| messageCount == null
3737
|| messageCount > 0) {
3838
Thread.sleep(1000);
39-
messageCount = messageUtils.getQueueCount(Messaging.INDEXING_QUEUE);
39+
messageCount = messageUtils.getQueueCount(MessagingConstants.INDEXING_QUEUE);
4040

41-
log.trace("Messages remaining in " + Messaging.INDEXING_QUEUE + " " + messageCount);
41+
log.trace("Messages remaining in " + MessagingConstants.INDEXING_QUEUE + " " + messageCount);
4242
}
4343
}
4444
}

‎agents/solr/src/test/java/uk/ac/ebi/biosamples/solr/MessageHandlerSolrTest.java‎

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Original file line numberDiff line numberDiff line change
@@ -25,9 +25,9 @@
2525
import org.springframework.http.converter.HttpMessageConverter;
2626
import org.springframework.http.converter.json.MappingJackson2HttpMessageConverter;
2727
import org.springframework.web.client.RestTemplate;
28-
import uk.ac.ebi.biosamples.model.Attribute;
29-
import uk.ac.ebi.biosamples.model.Sample;
30-
import uk.ac.ebi.biosamples.model.SampleStatus;
28+
import uk.ac.ebi.biosamples.core.model.Attribute;
29+
import uk.ac.ebi.biosamples.core.model.Sample;
30+
import uk.ac.ebi.biosamples.core.model.SampleStatus;
3131

3232
public class MessageHandlerSolrTest {
3333

‎agents/uploadworkers/pom.xml‎

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1-
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
2-
<modelVersion>4.0.0</modelVersion>
1+
<project xmlns="http://maven.apache.org/POM/4.0.0"
2+
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
3+
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
34

5+
<modelVersion>4.0.0</modelVersion>
46
<artifactId>agents-uploadworkers</artifactId>
57
<packaging>jar</packaging>
68

79
<parent>
810
<groupId>uk.ac.ebi.biosamples</groupId>
911
<artifactId>biosamples</artifactId>
10-
<version>5.3.12</version>
12+
<version>5.3.13-SNAPSHOT</version>
1113
<relativePath>../../</relativePath>
1214
</parent>
1315

1416
<dependencies>
17+
18+
<!-- Internal BioSamples Modules -->
1519
<dependency>
1620
<groupId>uk.ac.ebi.biosamples</groupId>
1721
<artifactId>biosamples-spring-boot-starter</artifactId>
18-
<version>5.3.12</version>
22+
<version>5.3.13-SNAPSHOT</version>
1923
</dependency>
24+
<dependency>
25+
<groupId>uk.ac.ebi.biosamples</groupId>
26+
<artifactId>properties</artifactId>
27+
<version>5.3.13-SNAPSHOT</version>
28+
</dependency>
29+
<dependency>
30+
<groupId>uk.ac.ebi.biosamples</groupId>
31+
<artifactId>core</artifactId>
32+
<version>5.3.13-SNAPSHOT</version>
33+
</dependency>
34+
35+
<!-- Spring Boot -->
2036
<dependency>
2137
<groupId>org.springframework.boot</groupId>
2238
<artifactId>spring-boot-starter-web</artifactId>
@@ -30,31 +46,14 @@
3046
<artifactId>spring-hateoas</artifactId>
3147
<version>1.3.4</version>
3248
</dependency>
33-
<dependency>
34-
<groupId>uk.ac.ebi.biosamples</groupId>
35-
<artifactId>properties</artifactId>
36-
<version>5.3.12</version>
37-
</dependency>
38-
<dependency>
39-
<groupId>uk.ac.ebi.biosamples</groupId>
40-
<artifactId>utils-webapp</artifactId>
41-
<version>5.3.12</version>
42-
</dependency>
43-
<dependency>
44-
<groupId>uk.ac.ebi.biosamples</groupId>
45-
<artifactId>messaging</artifactId>
46-
<version>5.3.12</version>
47-
</dependency>
48-
<dependency>
49-
<groupId>uk.ac.ebi.biosamples</groupId>
50-
<artifactId>models-mongo</artifactId>
51-
<version>5.3.12</version>
52-
</dependency>
49+
50+
<!-- CSV Utility -->
5351
<dependency>
5452
<groupId>org.apache.commons</groupId>
5553
<artifactId>commons-csv</artifactId>
5654
<version>1.8</version>
5755
</dependency>
56+
5857
</dependencies>
5958

6059
<build>
@@ -72,4 +71,5 @@
7271
</plugin>
7372
</plugins>
7473
</build>
74+
7575
</project>

‎agents/uploadworkers/src/main/java/uk/ac/ebi/biosamples/runner/FileUploadMessageQueueRunner.java‎

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@@ -16,8 +16,8 @@
1616
import org.springframework.boot.ApplicationArguments;
1717
import org.springframework.boot.ApplicationRunner;
1818
import org.springframework.stereotype.Component;
19-
import uk.ac.ebi.biosamples.MessageUtils;
20-
import uk.ac.ebi.biosamples.Messaging;
19+
import uk.ac.ebi.biosamples.messaging.MessagingConstants;
20+
import uk.ac.ebi.biosamples.messaging.service.MessageUtils;
2121

2222
@Component
2323
public class FileUploadMessageQueueRunner implements ApplicationRunner {
@@ -30,9 +30,9 @@ public void run(final ApplicationArguments args) {
3030
while (true) {
3131
log.trace(
3232
"Messages remaining in "
33-
+ Messaging.UPLOAD_QUEUE
33+
+ MessagingConstants.UPLOAD_QUEUE
3434
+ " "
35-
+ messageUtils.getQueueCount(Messaging.UPLOAD_QUEUE));
35+
+ messageUtils.getQueueCount(MessagingConstants.UPLOAD_QUEUE));
3636
}
3737
}
3838
}

‎agents/uploadworkers/src/main/java/uk/ac/ebi/biosamples/submission/FileUploadSubmissionService.java‎

Lines changed: 5 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -27,11 +27,11 @@
2727
import org.springframework.beans.factory.annotation.Autowired;
2828
import org.springframework.beans.factory.annotation.Qualifier;
2929
import org.springframework.stereotype.Service;
30-
import uk.ac.ebi.biosamples.Messaging;
3130
import uk.ac.ebi.biosamples.client.BioSamplesClient;
32-
import uk.ac.ebi.biosamples.exceptions.GlobalExceptions;
33-
import uk.ac.ebi.biosamples.model.Relationship;
34-
import uk.ac.ebi.biosamples.model.Sample;
31+
import uk.ac.ebi.biosamples.core.model.Relationship;
32+
import uk.ac.ebi.biosamples.core.model.Sample;
33+
import uk.ac.ebi.biosamples.exception.GlobalExceptions;
34+
import uk.ac.ebi.biosamples.messaging.MessagingConstants;
3535
import uk.ac.ebi.biosamples.model.SubmissionFile;
3636
import uk.ac.ebi.biosamples.mongo.model.MongoFileUpload;
3737
import uk.ac.ebi.biosamples.mongo.repository.MongoFileUploadRepository;
@@ -56,7 +56,7 @@ public class FileUploadSubmissionService {
5656
@Autowired MongoSampleRepository mongoSampleRepository;
5757

5858
@RabbitListener(
59-
queues = Messaging.UPLOAD_QUEUE,
59+
queues = MessagingConstants.UPLOAD_QUEUE,
6060
containerFactory = "biosamplesFileUploadSubmissionContainerFactory")
6161
public void receiveMessageFromBioSamplesFileUploaderQueue(final String mongoFileId) {
6262
handleMessage(mongoFileId);

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