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Rc/5.8.4 #360

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merged 16 commits into from
Apr 19, 2023
Merged

Rc/5.8.4 #360

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d9b775f
add test branch deployability
justincorrigible Mar 3, 2023
1f4664f
Score no such key issue #324 (#345)
UmmulkiramR Mar 6, 2023
beedc4a
Merge branch 'master' into develop
justincorrigible Mar 6, 2023
67240ce
Mergeback/5.8.3 snapshot versioning from prod (#348)
justincorrigible Mar 6, 2023
ad05150
correct slack notifications container in jenkins
justincorrigible Mar 7, 2023
fe7e80b
Changes for score-client JDK update from 11 to 17, changing analysisI…
dahiyaAD Mar 31, 2023
09cb8e4
Merge pull request #353 from overture-stack/score-client-jdk-upgrade
dahiyaAD Apr 3, 2023
e9ec637
Increasing the timeout for jenkins build to 60 minutes from 30 minute…
dahiyaAD Apr 4, 2023
49b692c
Merge pull request #354 from overture-stack/score-client-jdk-upgrade
dahiyaAD Apr 4, 2023
07a5588
add Maven repositories (#355)
leoraba Apr 4, 2023
2af57b7
Revert "Jenkins timeout change"
dahiyaAD Apr 4, 2023
e5b6938
Merge pull request #356 from overture-stack/revert-354-score-client-j…
dahiyaAD Apr 4, 2023
88aa2db
View showing header only - #229
dahiyaAD Apr 18, 2023
8a0fd2c
Merge pull request #358 from overture-stack/Header-Only-Issue
dahiyaAD Apr 18, 2023
0ecf5e0
RC for view showing header only #229
dahiyaAD Apr 19, 2023
a8130bb
RC for view showing header only #229 POM update
dahiyaAD Apr 19, 2023
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26 changes: 13 additions & 13 deletions Dockerfile
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Original file line number Diff line number Diff line change
Expand Up @@ -36,7 +36,7 @@ RUN cd score-client/target \
FROM ubuntu:18.04 as client

ENV CLIENT_DIST_DIR /score-client-dist
ENV JDK_DOWNLOAD_URL https://download.java.net/openjdk/jdk11/ri/openjdk-11+28_linux-x64_bin.tar.gz
ENV JDK_DOWNLOAD_URL https://download.java.net/openjdk/jdk17/ri/openjdk-17+35_linux-x64_bin.tar.gz
ENV SCORE_CLIENT_HOME /score-client
ENV PATH /usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:$SCORE_CLIENT_HOME/bin
ENV SCORE_USER score
Expand All @@ -51,20 +51,20 @@ RUN useradd $SCORE_USER \
# Copy client dist from previous docker build staget
COPY --from=builder $CLIENT_DIST_DIR/ $SCORE_CLIENT_HOME

# Install Open JDK 11, and remove unused things at runtime
# Install Open JDK 17, and remove unused things at runtime
RUN mkdir /usr/lib/jvm \
&& cd /usr/lib/jvm \
&& wget $JDK_DOWNLOAD_URL -O openjdk11.tar.gz \
&& tar zxvf openjdk11.tar.gz \
&& rm -rf openjdk11.tar.gz \
&& echo 'PATH=$PATH:/usr/lib/jvm/jdk-11/bin' >> /etc/environment \
&& echo 'JAVA_HOME=/usr/lib/jvm/jdk-11' >> /etc/environment \
&& rm -rf /usr/lib/jvm/jdk-11/jmods \
&& rm -rf /usr/lib/jvm/jdk-11/lib/src.zip \
&& update-alternatives --install "/usr/bin/java" "java" "/usr/lib/jvm/jdk-11/bin/java" 0 \
&& update-alternatives --install "/usr/bin/javac" "javac" "/usr/lib/jvm/jdk-11/bin/javac" 0 \
&& update-alternatives --set java /usr/lib/jvm/jdk-11/bin/java \
&& update-alternatives --set javac /usr/lib/jvm/jdk-11/bin/javac \
&& wget $JDK_DOWNLOAD_URL -O openjdk17.tar.gz \
&& tar zxvf openjdk17.tar.gz \
&& rm -rf openjdk17.tar.gz \
&& echo 'PATH=$PATH:/usr/lib/jvm/jdk-17/bin' >> /etc/environment \
&& echo 'JAVA_HOME=/usr/lib/jvm/jdk-17' >> /etc/environment \
&& rm -rf /usr/lib/jvm/jdk-17/jmods \
&& rm -rf /usr/lib/jvm/jdk-17/lib/src.zip \
&& update-alternatives --install "/usr/bin/java" "java" "/usr/lib/jvm/jdk-17/bin/java" 0 \
&& update-alternatives --install "/usr/bin/javac" "javac" "/usr/lib/jvm/jdk-17/bin/javac" 0 \
&& update-alternatives --set java /usr/lib/jvm/jdk-17/bin/java \
&& update-alternatives --set javac /usr/lib/jvm/jdk-17/bin/javac \
&& update-alternatives --list java \
&& update-alternatives --list javac \
&& java -version \
Expand Down
26 changes: 13 additions & 13 deletions Dockerfile.dev
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Expand Up @@ -4,7 +4,7 @@
FROM ubuntu:18.04 as client

ENV CLIENT_DIST_DIR /score-client-dist
ENV JDK_DOWNLOAD_URL https://download.java.net/openjdk/jdk11/ri/openjdk-11+28_linux-x64_bin.tar.gz
ENV JDK_DOWNLOAD_URL https://download.java.net/openjdk/jdk17/ri/openjdk-17+35_linux-x64_bin.tar.gz
ENV SCORE_CLIENT_HOME /score-client
ENV PATH /usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:$SCORE_CLIENT_HOME/bin
ENV SCORE_USER score
Expand All @@ -19,20 +19,20 @@ RUN useradd $SCORE_USER \

COPY score-client/target/score-client-*-dist.tar.gz /score-client.tar.gz

# Install Open JDK 11, and remove unused things at runtime
# Install Open JDK 17, and remove unused things at runtime
RUN mkdir /usr/lib/jvm \
&& cd /usr/lib/jvm \
&& wget $JDK_DOWNLOAD_URL -O openjdk11.tar.gz \
&& tar zxvf openjdk11.tar.gz \
&& rm -rf openjdk11.tar.gz \
&& echo 'PATH=$PATH:/usr/lib/jvm/jdk-11/bin' >> /etc/environment \
&& echo 'JAVA_HOME=/usr/lib/jvm/jdk-11' >> /etc/environment \
&& rm -rf /usr/lib/jvm/jdk-11/jmods \
&& rm -rf /usr/lib/jvm/jdk-11/lib/src.zip \
&& update-alternatives --install "/usr/bin/java" "java" "/usr/lib/jvm/jdk-11/bin/java" 0 \
&& update-alternatives --install "/usr/bin/javac" "javac" "/usr/lib/jvm/jdk-11/bin/javac" 0 \
&& update-alternatives --set java /usr/lib/jvm/jdk-11/bin/java \
&& update-alternatives --set javac /usr/lib/jvm/jdk-11/bin/javac \
&& wget $JDK_DOWNLOAD_URL -O openjdk17.tar.gz \
&& tar zxvf openjdk17.tar.gz \
&& rm -rf openjdk17.tar.gz \
&& echo 'PATH=$PATH:/usr/lib/jvm/jdk-17/bin' >> /etc/environment \
&& echo 'JAVA_HOME=/usr/lib/jvm/jdk-17' >> /etc/environment \
&& rm -rf /usr/lib/jvm/jdk-17/jmods \
&& rm -rf /usr/lib/jvm/jdk-17/lib/src.zip \
&& update-alternatives --install "/usr/bin/java" "java" "/usr/lib/jvm/jdk-17/bin/java" 0 \
&& update-alternatives --install "/usr/bin/javac" "javac" "/usr/lib/jvm/jdk-17/bin/javac" 0 \
&& update-alternatives --set java /usr/lib/jvm/jdk-17/bin/java \
&& update-alternatives --set javac /usr/lib/jvm/jdk-17/bin/javac \
&& update-alternatives --list java \
&& update-alternatives --list javac \
&& java -version
Expand Down
11 changes: 8 additions & 3 deletions Jenkinsfile
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Expand Up @@ -56,6 +56,11 @@ spec:
value: tcp://localhost:2375
- name: HOME
value: /home/jenkins/agent
- name: curl
image: curlimages/curl
command:
- cat
tty: true
securityContext:
runAsUser: 1000
volumes:
Expand Down Expand Up @@ -352,7 +357,7 @@ pipeline {
credentialsId: 'OvertureSlackJenkinsWebhookURL',
variable: 'fixed_slackChannelURL'
)]) {
container('node') {
container('curl') {
script {
if (env.BRANCH_NAME ==~ /(develop|master|test\S*)/) {
sh "curl \
Expand All @@ -374,7 +379,7 @@ pipeline {
credentialsId: 'OvertureSlackJenkinsWebhookURL',
variable: 'success_slackChannelURL'
)]) {
container('node') {
container('curl') {
script {
if (env.BRANCH_NAME ==~ /(test\S*)/) {
sh "curl \
Expand All @@ -396,7 +401,7 @@ pipeline {
credentialsId: 'OvertureSlackJenkinsWebhookURL',
variable: 'failed_slackChannelURL'
)]) {
container('node') {
container('curl') {
script {
if (env.BRANCH_NAME ==~ /(develop|master|test\S*)/) {
sh "curl \
Expand Down
55 changes: 49 additions & 6 deletions pom.xml
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Expand Up @@ -20,7 +20,7 @@ ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF S

<groupId>bio.overture</groupId>
<artifactId>score</artifactId>
<version>5.8.2</version>
<version>5.8.4</version>
<packaging>pom</packaging>
<name>${project.artifactId}</name>
<description>${project.name}</description>
Expand All @@ -34,11 +34,54 @@ ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF S
</modules>

<repositories>
<!-- DCC -->
<repository>
<id>dcc-release</id>
<url>https://artifacts.oicr.on.ca/artifactory/dcc-release</url>
</repository>
<repository>
<id>spring-releases</id>
<name>Spring Releases</name>
<url>https://repo.spring.io/release</url>
<snapshots>
<enabled>false</enabled>
</snapshots>
</repository>
<repository>
<id>spring-snapshots</id>
<name>Spring Snapshots</name>
<url>https://repo.spring.io/snapshot</url>
<releases>
<enabled>false</enabled>
</releases>
<snapshots>
<enabled>true</enabled>
</snapshots>
</repository>
<!-- DCC -->
<repository>
<id>dcc-release</id>
<url>https://artifacts.oicr.on.ca/artifactory/dcc-release</url>
<snapshots>
<enabled>false</enabled>
</snapshots>
</repository>
<repository>
<id>dcc-snapshot</id>
<url>https://artifacts.oicr.on.ca/artifactory/dcc-snapshot</url>
<releases>
<enabled>false</enabled>
</releases>
<snapshots>
<enabled>true</enabled>
</snapshots>
</repository>
<repository>
<id>conjars.org</id>
<url>https://conjars.wensel.net/repo/</url>
<releases>
<enabled>false</enabled>
</releases>
<snapshots>
<enabled>false</enabled>
</snapshots>
</repository>

</repositories>

<dependencies>
Expand Down
2 changes: 1 addition & 1 deletion score-client/pom.xml
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Expand Up @@ -21,7 +21,7 @@ ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF S
<parent>
<groupId>bio.overture</groupId>
<artifactId>score</artifactId>
<version>5.8.2</version>
<version>5.8.4</version>
<relativePath>../pom.xml</relativePath>
</parent>

Expand Down
4 changes: 2 additions & 2 deletions score-client/src/main/java/bio/overture/score/client/command/DownloadCommand.java
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Expand Up @@ -364,8 +364,8 @@ private void validateParms() {
checkParameter(
Stream.of(!objectId.isEmpty(), manifestResource != null,analysisId != null && programId != null).
filter(i -> i == Boolean.TRUE).count() == 1,
"Only one of --object-id, --manifest, or --analysisId may be specified. "
+ "--studyId may only be used together with --analysisId, and is required if analysisId is specified.");
"Only one of --object-id, --manifest, or --analysis-id may be specified. "
+ "--study-id may only be used together with --analysis-id, and is required if analysis-id is specified.");
}
}

7 changes: 6 additions & 1 deletion ...client/src/main/java/bio/overture/score/client/metadata/legacy/LegacyMetadataService.java
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Expand Up @@ -56,13 +56,18 @@ public Optional<Entity> getIndexEntity(Entity entity) {
}

private static boolean isIndexFile(Entity e, String fileName) {
return isBaiFile(e, fileName) || isTbiFile(e, fileName) || isIdxFile(e, fileName);
return isCraiFile(e, fileName) || isBaiFile(e, fileName) || isTbiFile(e, fileName) || isIdxFile(e, fileName);
}

private static boolean isTbiFile(Entity e, String fileName) {
return isMatch(e, fileName + ".tbi");
}

private static boolean isCraiFile(Entity e, String fileName) {
return isMatch(e, fileName + ".crai");
}


private static boolean isIdxFile(Entity e, String fileName) {
return isMatch(e, fileName + ".idx");
}
Expand Down
2 changes: 1 addition & 1 deletion score-core/pom.xml
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Expand Up @@ -21,7 +21,7 @@ ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF S
<parent>
<groupId>bio.overture</groupId>
<artifactId>score</artifactId>
<version>5.8.2</version>
<version>5.8.4</version>
<relativePath>../pom.xml</relativePath>
</parent>

Expand Down
2 changes: 1 addition & 1 deletion score-fs/pom.xml
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Expand Up @@ -21,7 +21,7 @@ ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF S
<parent>
<groupId>bio.overture</groupId>
<artifactId>score</artifactId>
<version>5.8.2</version>
<version>5.8.4</version>
<relativePath>../pom.xml</relativePath>
</parent>

Expand Down
2 changes: 1 addition & 1 deletion score-server/pom.xml
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Expand Up @@ -21,7 +21,7 @@ ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF S
<parent>
<groupId>bio.overture</groupId>
<artifactId>score</artifactId>
<version>5.8.2</version>
<version>5.8.4</version>
<relativePath>../pom.xml</relativePath>
</parent>

Expand Down
2 changes: 1 addition & 1 deletion score-test/pom.xml
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Expand Up @@ -21,7 +21,7 @@ ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF S
<parent>
<groupId>bio.overture</groupId>
<artifactId>score</artifactId>
<version>5.8.2</version>
<version>5.8.4</version>
<relativePath>../pom.xml</relativePath>
</parent>

Expand Down