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ClickHouse-Only cBioPortal Demo based on standard schema #10839

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ClickHouse-Only cBioPortal Demo based on standard schema #10839

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5e80c6d
Change mybatis mapper to use uppercase table and column names
pvannierop Apr 18, 2024
35b86ff
fixes/changes to the point of home page rendering
sheridancbio Jun 7, 2024
827227b
whitespace standardization and clickhouse driver
sheridancbio Jun 11, 2024
fd18424
lower case standardize field names
sheridancbio Jun 17, 2024
075c9b5
progress to rendering of study view page
sheridancbio Jun 18, 2024
6304607
beginning of effort to get unit tests working
sheridancbio Aug 15, 2024
6272157
Dockerfile fixes for docker v2 updates
sheridancbio Aug 20, 2024
eab18ce
restore password in CustomRedisCachingProvider
sheridancbio Aug 21, 2024
91d2f69
correct missed uppcase fieldname in DiscreteCopyNumberMapper.xml
sheridancbio Sep 3, 2024
8636e62
drop undefined sub expressions from sample list sub query
sheridancbio Sep 3, 2024
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4 changes: 2 additions & 2 deletions docker/web-and-data/Dockerfile
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Original file line number Diff line number Diff line change
Expand Up @@ -11,7 +11,7 @@
# NOTE: the .git folder is included in the build stage, but excluded
# from the final image. No confidential information is exposed.
# (see: stackoverflow.com/questions/56278325)
FROM maven:3-eclipse-temurin-21 as build
FROM maven:3-eclipse-temurin-21 AS build

# download maven dependencies first to take advantage of docker caching
COPY pom.xml /cbioportal/
Expand All @@ -22,7 +22,7 @@ WORKDIR /cbioportal

RUN mvn dependency:go-offline --fail-never

COPY $PWD /cbioportal
COPY . /cbioportal
RUN mvn install package -DskipTests -q
RUN mkdir -p target/dependency && (cd target/dependency; jar -xf ../*-exec.jar)

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4 changes: 2 additions & 2 deletions docker/web/Dockerfile
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Expand Up @@ -13,8 +13,8 @@
#
# WARNING: the shendoah image is a nightly, untested, experimental build. If
# you want to use an official openjdk image instead use the web-and-data image.
FROM maven:3-eclipse-temurin-21 as build
COPY $PWD /cbioportal
FROM maven:3-eclipse-temurin-21 AS build
COPY . /cbioportal
WORKDIR /cbioportal
ARG MAVEN_OPTS=-DskipTests
# Use quite output so we can see the build steps easily
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46 changes: 43 additions & 3 deletions pom.xml
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Expand Up @@ -24,13 +24,12 @@
<maven.compiler.target>21</maven.compiler.target>
<maven.build.timestamp.format>yyyyMMdd-HHmm</maven.build.timestamp.format>
<timestamp>${maven.build.timestamp}</timestamp>
<!-- TODO replace with version of cbioportal frontend with compatible
login url-->
<!-- TODO replace with version of cbioportal frontend with compatible login url-->
<frontend.groupId>com.github.cbioportal</frontend.groupId>
<frontend.version>v6.0.5</frontend.version>

<!-- THIS SHOULD BE KEPT IN SYNC TO VERSION IN CGDS.SQL -->
<db.version>2.13.1</db.version>
<db.version>3.0.0</db.version>

<!-- Version properties for dependencies that should have same version. -->
<!-- The rest can be set in the dependencyManagement section -->
Expand Down Expand Up @@ -98,6 +97,8 @@
<selenium_chrome_driver.version>3.14.0</selenium_chrome_driver.version>
<selenium.version>4.17.0</selenium.version>
<sentry.version>7.1.0</sentry.version>
<clickhouse_testcontainer.version>1.19.7</clickhouse_testcontainer.version>
<clickhouse-java.version>0.6.0</clickhouse-java.version>


<!-- No sure what these are for -->
Expand Down Expand Up @@ -266,6 +267,12 @@
<artifactId>mysql-connector-java</artifactId>
<version>${mysql_driver.version}</version>
</dependency>
<dependency>
<groupId>com.clickhouse</groupId>
<artifactId>clickhouse-jdbc</artifactId>
<version>${clickhouse-java.version}</version>
<classifier>all</classifier>
</dependency>
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-thymeleaf</artifactId>
Expand Down Expand Up @@ -357,6 +364,23 @@
<artifactId>sentry-spring-boot-starter-jakarta</artifactId>
<version>${sentry.version}</version>
</dependency>
<dependency>
<groupId>org.testcontainers</groupId>
<artifactId>clickhouse</artifactId>
<version>${clickhouse_testcontainer.version}</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.mybatis.spring.boot</groupId>
<artifactId>mybatis-spring-boot-test-autoconfigure</artifactId>
<version>3.0.3</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-testcontainers</artifactId>
<scope>test</scope>
</dependency>
</dependencies>

<dependencyManagement>
Expand Down Expand Up @@ -421,9 +445,25 @@
<includes>
<include>cgds.sql</include>
<include>migration.sql</include>
<include>clickhouse/clickhouse.sql</include>
<include>clickhouse/materialized_views.sql</include>
</includes>
</resource>
</resources>
<testResources>
<testResource>
<directory>src/main/resources/db-scripts</directory>
<filtering>false</filtering>
<includes>
<include>clickhouse/clickhouse.sql</include>
<include>clickhouse/materialized_views.sql</include>
</includes>
</testResource>
<testResource>
<directory>src/test/resources</directory>
<filtering>false</filtering>
</testResource>
</testResources>

<plugins>
<plugin>
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