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

Jump to bottom

Get project version from git #5403

Merged
merged 7 commits into from
Dec 12, 2018
Merged

Get project version from git #5403

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
7 commits
Select commit Hold shift + click to select a range
9564d21
Get project version from git
inodb Dec 6, 2018
4b178bd
Heroku fixes
inodb Dec 6, 2018
d7a98ac
Use com.github.cbioportal.maven-external-version
inodb Dec 7, 2018
8adb776
maven-external-version - fetch all tags
inodb Dec 7, 2018
d07f8cc
update maven-external-version
inodb Dec 7, 2018
45456d4
Travis Updates
inodb Dec 8, 2018
f0fb5c6
scripts shade plugin dont create dep reduced pom
inodb Dec 11, 2018
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
19 changes: 10 additions & 9 deletions .travis.yml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -9,10 +9,10 @@ cache:
- $HOME/maven
env:
matrix:
- MAVEN_VERSION=3.3.9 TEST=core
- MAVEN_VERSION=3.3.9 TEST=python-validator
- MAVEN_VERSION=3.3.9 TEST=sanity-checks
- MAVEN_VERSION=3.3.9 TEST=end-to-end
- MAVEN_VERSION=3.5.4 TEST=core
- MAVEN_VERSION=3.5.4 TEST=python-validator
- MAVEN_VERSION=3.5.4 TEST=sanity-checks
- MAVEN_VERSION=3.5.4 TEST=end-to-end
install:
- |
if [[ "${TEST}" == core || "${TEST}" == end-to-end ]]
Expand Down Expand Up @@ -71,18 +71,19 @@ script:
then
~/maven/$MAVEN_VERSION/bin/mvn \
-e \
-Ppublic \
-Dfinal.war.name=cbioportal \
-U \
-Ddb.user=cbio_user \
-Ddb.password=somepassword \
clean integration-test
clean \
install \
integration-test
fi
- |
if [[ "${TEST}" == end-to-end ]]
then
~/maven/$MAVEN_VERSION/bin/mvn \
-Ppublic -DskipTests \
-Dfinal.war.name=cbioportal \
-U \
-DskipTests \
clean install
fi
- |
Expand Down
2 changes: 1 addition & 1 deletion app.json
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -21,7 +21,7 @@
},
"SPRING_OPTS": {
"description":"set spring properties with e.g. -Dshow.civic=true (TODO: not all props work atm)",
"value":"-Dauthenticate=false -Dtomcat.catalina.scope=runtime -Ddb.user=cbio_user -Ddb.password=cbio_pass -Ddb.portal_db_name=public_test_small -Ddb.connection_string=jdbc:mysql://devdb.cbioportal.org:3306/ -Ddb.host=devdb.cbioportal.org -Dshow.civic=true -Ddbconnector=dbcp -Dsuppress_schema_version_mismatch_errors=true"
"value":"-Dauthenticate=false -Dtomcat.catalina.scope=runtime -Ddb.user=cbio_user -Ddb.password=cbio_pass -Ddb.portal_db_name=public_test -Ddb.connection_string=jdbc:mysql://devdb.cbioportal.org:3306/ -Ddb.host=devdb.cbioportal.org -Dshow.civic=true -Ddbconnector=dbcp -Dsuppress_schema_version_mismatch_errors=true"
}
},
"buildpacks": [
Expand Down
4 changes: 3 additions & 1 deletion business/pom.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,9 @@
<parent>
<artifactId>master</artifactId>
<groupId>org.mskcc.cbio</groupId>
<version>1.18.2-SNAPSHOT</version>
<!-- project version is generated through git or can be passed as
PROJECT_VERSION env variable (see version.sh) -->
<version>0-unknown-version-SNAPSHOT</version>
</parent>
<modelVersion>4.0.0</modelVersion>
<artifactId>business</artifactId>
Expand Down
36 changes: 3 additions & 33 deletions core/pom.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,9 @@
<parent>
<artifactId>master</artifactId>
<groupId>org.mskcc.cbio</groupId>
<version>1.18.2-SNAPSHOT</version>
<!-- project version is generated through git or can be passed as
PROJECT_VERSION env variable (see version.sh) -->
<version>0-unknown-version-SNAPSHOT</version>
</parent>
<modelVersion>4.0.0</modelVersion>
<artifactId>core</artifactId>
Expand Down Expand Up @@ -290,38 +292,6 @@
</dependency>
</dependencies>

<profiles>
<profile>
<id>heroku</id>
<build>
<plugins>
<!-- remove core temp build files -->
<plugin>
<artifactId>maven-clean-plugin</artifactId>
<version>2.5</version>
<executions>
<execution>
<id>clean-artifacts</id>
<phase>install</phase>
<goals>
<goal>clean</goal>
</goals>
<configuration>
<excludeDefaultDirectories>true</excludeDefaultDirectories>
<filesets>
<fileset>
<directory>target</directory>
</fileset>
</filesets>
</configuration>
</execution>
</executions>
</plugin>
</plugins>
</build>
</profile>
</profiles>

<build>
<plugins>
<!-- surefire (test) config -->
Expand Down
4 changes: 3 additions & 1 deletion db-scripts/pom.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,9 @@
<parent>
<artifactId>master</artifactId>
<groupId>org.mskcc.cbio</groupId>
<version>1.18.2-SNAPSHOT</version>
<!-- project version is generated through git or can be passed as
PROJECT_VERSION env variable (see version.sh) -->
<version>0-unknown-version-SNAPSHOT</version>
</parent>
<modelVersion>4.0.0</modelVersion>

Expand Down
2 changes: 1 addition & 1 deletion docs/System-Requirements.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -27,7 +27,7 @@ On Ubuntu: [See Recommended Installation Instructions](https://www.digitalocean

## Apache Maven

The cBioPortal source code is an [Apache Maven](https://maven.apache.org/) driven project. The software needs to be downloaded and installed prior to building the application from source code. It can be found on the [Apache Maven](https://maven.apache.org/download.cgi) website.
The cBioPortal source code is an [Apache Maven](https://maven.apache.org/) driven project. The software needs to be downloaded and installed prior to building the application from source code. It can be found on the [Apache Maven](https://maven.apache.org/download.cgi) website. We are currently using version 3.5.4.

On Ubuntu: ```sudo apt-get install maven```

Expand Down
4 changes: 3 additions & 1 deletion model/pom.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,9 @@
<parent>
<artifactId>master</artifactId>
<groupId>org.mskcc.cbio</groupId>
<version>1.18.2-SNAPSHOT</version>
<!-- project version is generated through git or can be passed as
PROJECT_VERSION env variable (see version.sh) -->
<version>0-unknown-version-SNAPSHOT</version>
</parent>
<modelVersion>4.0.0</modelVersion>

Expand Down
4 changes: 3 additions & 1 deletion persistence/persistence-api/pom.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,9 @@
<parent>
<artifactId>persistence</artifactId>
<groupId>org.mskcc.cbio</groupId>
<version>1.18.2-SNAPSHOT</version>
<!-- project version is generated through git or can be passed as
PROJECT_VERSION env variable (see version.sh) -->
<version>0-unknown-version-SNAPSHOT</version>
</parent>
<modelVersion>4.0.0</modelVersion>

Expand Down
4 changes: 3 additions & 1 deletion persistence/persistence-mybatis/pom.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,9 @@
<parent>
<artifactId>persistence</artifactId>
<groupId>org.mskcc.cbio</groupId>
<version>1.18.2-SNAPSHOT</version>
<!-- project version is generated through git or can be passed as
PROJECT_VERSION env variable (see version.sh) -->
<version>0-unknown-version-SNAPSHOT</version>
</parent>
<modelVersion>4.0.0</modelVersion>

Expand Down
4 changes: 3 additions & 1 deletion persistence/pom.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,9 @@
<parent>
<artifactId>master</artifactId>
<groupId>org.mskcc.cbio</groupId>
<version>1.18.2-SNAPSHOT</version>
<!-- project version is generated through git or can be passed as
PROJECT_VERSION env variable (see version.sh) -->
<version>0-unknown-version-SNAPSHOT</version>
</parent>
<modelVersion>4.0.0</modelVersion>

Expand Down
23 changes: 21 additions & 2 deletions pom.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -6,7 +6,9 @@
<artifactId>master</artifactId>
<packaging>pom</packaging>
<name>Portal Master</name>
<version>1.18.2-SNAPSHOT</version>
<!-- project version is generated through git or can be passed as
PROJECT_VERSION env variable (see version.sh) -->
<version>0-unknown-version-SNAPSHOT</version>
<description>master maven module</description>

<scm>
Expand All @@ -23,6 +25,12 @@
</snapshots>
</repository>
</repositories>
<pluginRepositories>
<pluginRepository>
<id>jitpack.io</id>
<url>https://jitpack.io</url>
</pluginRepository>
</pluginRepositories>

<profiles>
<profile>
Expand All @@ -35,6 +43,17 @@
</properties>
<build>
<plugins>
<plugin>
<groupId>com.github.cbioportal.maven-external-version</groupId>
<artifactId>maven-external-version-plugin</artifactId>
<version>f09c2b9608744881111f24e55d55a91e54e6cb5f</version>
<extensions>true</extensions>
<configuration>
<strategy hint="script">
<script>./version.sh</script>
inodb marked this conversation as resolved.
Show resolved Hide resolved
</strategy>
</configuration>
</plugin>
<plugin>
<groupId>org.jacoco</groupId>
<artifactId>jacoco-maven-plugin</artifactId>
Expand Down Expand Up @@ -250,7 +269,7 @@
<jacoco-maven-plugin.version>0.7.6.201602180812</jacoco-maven-plugin.version>
<mockito.version>1.10.19</mockito.version>

<final.war.name>cbioportal-${project.version}</final.war.name>
<final.war.name>cbioportal</final.war.name>

<db.test.driver>com.mysql.jdbc.Driver</db.test.driver>
<!-- For MySQL < 5.5 change 'default_storage_engine' to 'storage_engine' -->
Expand Down
4 changes: 3 additions & 1 deletion portal/pom.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,9 @@
<parent>
<artifactId>master</artifactId>
<groupId>org.mskcc.cbio</groupId>
<version>1.18.2-SNAPSHOT</version>
<!-- project version is generated through git or can be passed as
PROJECT_VERSION env variable (see version.sh) -->
<version>0-unknown-version-SNAPSHOT</version>
</parent>
<modelVersion>4.0.0</modelVersion>
<artifactId>cbioportal</artifactId>
Expand Down
5 changes: 4 additions & 1 deletion scripts/pom.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,9 @@
<parent>
<artifactId>master</artifactId>
<groupId>org.mskcc.cbio</groupId>
<version>1.18.2-SNAPSHOT</version>
<!-- project version is generated through git or can be passed as
PROJECT_VERSION env variable (see version.sh) -->
<version>0-unknown-version-SNAPSHOT</version>
</parent>
<modelVersion>4.0.0</modelVersion>
<artifactId>scripts</artifactId>
Expand Down Expand Up @@ -65,6 +67,7 @@
<goal>shade</goal>
</goals>
<configuration>
<createDependencyReducedPom>false</createDependencyReducedPom>
<artifactSet>
<excludes>
<exclude>org.bouncycastle:bcprov-jdk15</exclude>
Expand Down
4 changes: 3 additions & 1 deletion security/pom.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,9 @@
<parent>
<artifactId>master</artifactId>
<groupId>org.mskcc.cbio</groupId>
<version>1.18.2-SNAPSHOT</version>
<!-- project version is generated through git or can be passed as
PROJECT_VERSION env variable (see version.sh) -->
<version>0-unknown-version-SNAPSHOT</version>
</parent>
<modelVersion>4.0.0</modelVersion>

Expand Down
4 changes: 3 additions & 1 deletion security/security-spring/pom.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,9 @@
<parent>
<artifactId>security</artifactId>
<groupId>org.mskcc.cbio</groupId>
<version>1.18.2-SNAPSHOT</version>
<!-- project version is generated through git or can be passed as
PROJECT_VERSION env variable (see version.sh) -->
<version>0-unknown-version-SNAPSHOT</version>
</parent>
<modelVersion>4.0.0</modelVersion>

Expand Down
4 changes: 3 additions & 1 deletion service/pom.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,9 @@
<parent>
<artifactId>master</artifactId>
<groupId>org.mskcc.cbio</groupId>
<version>1.18.2-SNAPSHOT</version>
<!-- project version is generated through git or can be passed as
PROJECT_VERSION env variable (see version.sh) -->
<version>0-unknown-version-SNAPSHOT</version>
</parent>
<modelVersion>4.0.0</modelVersion>

Expand Down
13 changes: 13 additions & 0 deletions version.sh
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,13 @@
#!/usr/bin/env bash
if [ -n "$PROJECT_VERSION" ]; then
# use env variable PROJECT_VERSION if defined
echo $PROJECT_VERSION
inodb marked this conversation as resolved.
Show resolved Hide resolved
elif ! [ -x "$(command -v git)" ] || ! [ -d .git ]; then
# git is not installed, or not in a git repo
echo '0-unknown-version'
else
# fetch all tags silently
git fetch --tags --quiet > /dev/null 2> /dev/null
# get human readable commit id from git
git describe --tags --always --dirty | sed 's/^v//'
Copy link
Contributor

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

If git describe always goes back to a tag, does it mean that portal dependencies can only be brought in from a tagged commit that is pushed to the cbioportal github repo? If a single PR makes changes in both the service and web layer (like changing the service interface), will the "new" web layer be able to bring in the "new" service layer even if a tag has not been created (in a pr to rc, for instance)? Maybe the extra info after the tag is enough to provide the additional path since the tag (the "dirty" part I guess?)

% git describe --tags --always --dirty

v1.18.0-120-g05c7ad6-dirty

Copy link
Member Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

@sheridancbio Portal dependencies can be brought in locally or remotely. It doesn't need to be tagged/committed in the github repo. Maven continues to function in the same way, so if u compile something locally the artifacts will end up in your ~/.m2 folder and you can include them in another project as a dependency.

Copy link
Contributor

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

sounds good. I was mainly thinking about dependencies between the modules within cbioportal, but packaging the cbioportal code into other codebases is also needed.

fi
4 changes: 3 additions & 1 deletion web/pom.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,9 @@
<parent>
<artifactId>master</artifactId>
<groupId>org.mskcc.cbio</groupId>
<version>1.18.2-SNAPSHOT</version>
<!-- project version is generated through git or can be passed as
PROJECT_VERSION env variable (see version.sh) -->
<version>0-unknown-version-SNAPSHOT</version>
</parent>
<modelVersion>4.0.0</modelVersion>
<artifactId>web</artifactId>
Expand Down