Merge pull request #2257 from cBioPortal/release-1.5.0

Release 1.5.0

.travis.yml

@@ -76,7 +76,7 @@ script:
                 -Ddb.password=somepassword \
                 -Ddb.host=127.0.0.1 \
                 -Ddb.connection_string=jdbc:mysql://127.0.0.1:3306/ \
-                clean test
+                clean integration-test
         fi
     # end-to-end tests
     # compile war to use amazon db

CONTRIBUTING.md

@@ -45,7 +45,7 @@ A few tips:
 * Make commits in logical/cohesive units.
 * Make sure your commit messages end with a Signed-off-by string (this line can be automatically added by git if you run the git-commit command with the -s option).
 * Make sure you have added the necessary tests for your changes.
-* Run _all_ tests to assure nothing else was accidentally broken.  This is done by running:  ```mvn test```.
+* Run _all_ tests to assure nothing else was accidentally broken in the java part (data loading and front-end parts are tested by other scripts in travis). This is done by running:  ```mvn integration-test```.
 
 When you are ready to submit your pull-request:
 

Dockerfile

@@ -0,0 +1,32 @@
+FROM tomcat:8-jre8
+MAINTAINER Alexandros Sigaras <[email protected]>, Fedde Schaeffer <[email protected]>
+LABEL Description="cBioPortal for Cancer Genomics"
+ENV APP_NAME="cbioportal" \
+    PORTAL_HOME="/cbioportal"
+#======== Install Prerequisites ===============#
+RUN apt-get update && apt-get install -y --no-install-recommends \
+        git \
+        libmysql-java \
+        patch \
+        python \
+        python-jinja2 \
+        python-mysqldb \
+        python-requests \
+    # install new versions of these packages backported to Debian stable;
+    # Debian does not add new features or break backwards compatibility within
+    # a stable release, but for these dependencies we need versions that do.
+    && apt-get install -y --no-install-recommends -t jessie-backports \
+        maven \
+        openjdk-8-jdk \
+    && ln -s /usr/share/java/mysql-connector-java.jar "$CATALINA_HOME"/lib/ \
+    && rm -rf $CATALINA_HOME/webapps/examples \
+    && rm -rf /var/lib/apt/lists/*
+#======== Configure cBioPortal ===========================#
+COPY . $PORTAL_HOME
+WORKDIR $PORTAL_HOME
+EXPOSE 8080
+#======== Build cBioPortal on Startup ===============#
+CMD mvn -DskipTests clean install \
+     && cp $PORTAL_HOME/portal/target/cbioportal*.war $CATALINA_HOME/webapps/cbioportal.war \
+     && find $PWD/core/src/main/scripts/ -type f -executable \! -name '*.pl'  -print0 | xargs -0 -- ln -st /usr/local/bin \
+     && sh $CATALINA_HOME/bin/catalina.sh run

README.md

@@ -1,3 +1,4 @@
+# cBioPortal
 The cBioPortal for Cancer Genomics provides visualization, analysis, and download of large-scale cancer genomics data sets.  The cBioPortal is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License, version 3, as published by the Free Software Foundation.
 
 This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of
@@ -9,10 +10,16 @@ If you would like to know how to setup a private instance of the portal and/or g
 
 If you are interested in coordinating the development of new features, please contact [email protected].
 
-[![Deploy](https://www.herokucdn.com/deploy/button.svg)](https://heroku.com/deploy)
-
-[![ZenHub] (https://raw.githubusercontent.com/ZenHubIO/support/master/zenhub-badge.png)] (https://zenhub.io)
-
+## Test status
 [![Build Status](https://travis-ci.org/cBioPortal/cbioportal.svg?branch=master)](https://travis-ci.org/cBioPortal/cbioportal)
 
+## Code Quality
 [![codebeat badge](https://codebeat.co/badges/0738d3c9-5ffe-4b61-80c4-abb5698d8d44)](https://codebeat.co/projects/github-com-cbioportal-cbioportal)
+
+## Documentation
+[![Documentation Status](https://readthedocs.org/projects/cbioportal/badge/?version=latest)](http://cbioportal.readthedocs.io/en/latest/?badge=latest)
+
+## Deployment
+[![Deploy](https://www.herokucdn.com/deploy/button.svg)](https://heroku.com/deploy)
+
+[![Docker Automated build](https://img.shields.io/docker/automated/jrottenberg/ffmpeg.svg)](https://hub.docker.com/r/cbioportal/cbioportal/) [![Docker Pulls](https://img.shields.io/docker/pulls/cbioportal/cbioportal.svg)](https://hub.docker.com/r/cbioportal/cbioportal/) [![Docker Stars](https://img.shields.io/docker/stars/cbioportal/cbioportal.svg)](https://hub.docker.com/r/cbioportal/cbioportal/)

business/pom.xml

@@ -4,7 +4,7 @@
   <parent>
     <artifactId>master</artifactId>
     <groupId>org.mskcc.cbio</groupId>
-    <version>1.4.3</version>
+    <version>1.5.0</version>
   </parent>
   <modelVersion>4.0.0</modelVersion>
   <artifactId>business</artifactId>
@@ -19,7 +19,7 @@
     </dependency>
     <dependency>
       <groupId>org.mskcc.cbio</groupId>
-      <artifactId>service</artifactId>
+      <artifactId>model</artifactId>
       <version>${project.version}</version>
     </dependency>
   </dependencies>

business/src/main/java/org/cbioportal/model/MutationWithSampleListId.java

@@ -2,6 +2,7 @@
 
 import java.io.Serializable;
 import com.fasterxml.jackson.annotation.JsonUnwrapped;
+import org.mskcc.cbio.portal.model.Mutation;
 
 public class MutationWithSampleListId implements Serializable {
 

persistence/persistence-api/src/main/java/org/cbioportal/persistence/dto/AltCount.java → business/src/main/java/org/mskcc/cbio/portal/model/AltCount.java

@@ -1,4 +1,4 @@
-package org.cbioportal.persistence.dto;
+package org.mskcc.cbio.portal.model;
 
 import java.io.Serializable;
 

model/src/main/java/org/cbioportal/model/CNSegmentData.java → business/src/main/java/org/mskcc/cbio/portal/model/CNSegmentData.java

@@ -3,7 +3,7 @@
  * To change this template file, choose Tools | Templates
  * and open the template in the editor.
  */
-package org.cbioportal.model;
+package org.mskcc.cbio.portal.model;
 
 import java.io.Serializable;
 

business/src/main/java/org/mskcc/cbio/portal/model/CosmicCount.java

@@ -0,0 +1,43 @@
+package org.mskcc.cbio.portal.model;
+
+import java.io.Serializable;
+
+public class CosmicCount implements Serializable {
+
+    private String cosmicMutationId;
+    private String proteinChange;
+    private String keyword;
+    private Integer count;
+
+    public String getCosmicMutationId() {
+        return cosmicMutationId;
+    }
+
+    public void setCosmicMutationId(String cosmicMutationId) {
+        this.cosmicMutationId = cosmicMutationId;
+    }
+
+    public String getProteinChange() {
+        return proteinChange;
+    }
+
+    public void setProteinChange(String proteinChange) {
+        this.proteinChange = proteinChange;
+    }
+
+    public String getKeyword() {
+        return keyword;
+    }
+
+    public void setKeyword(String keyword) {
+        this.keyword = keyword;
+    }
+
+    public Integer getCount() {
+        return count;
+    }
+
+    public void setCount(Integer count) {
+        this.count = count;
+    }
+}

model/src/main/java/org/cbioportal/model/GenePanel.java → business/src/main/java/org/mskcc/cbio/portal/model/GenePanel.java

@@ -29,13 +29,15 @@
  * You should have received a copy of the GNU Affero General Public License
  * along with this program.  If not, see <http://www.gnu.org/licenses/>.
 */
-package org.cbioportal.model;
+package org.mskcc.cbio.portal.model;
 
 /**
  *
  * @author heinsz
  */
 
+import org.cbioportal.model.Gene;
+
 import java.io.Serializable;
 import java.util.List;
 

model/src/main/java/org/cbioportal/model/GenePanelWithSamples.java → business/src/main/java/org/mskcc/cbio/portal/model/GenePanelWithSamples.java

@@ -29,7 +29,7 @@
  * You should have received a copy of the GNU Affero General Public License
  * along with this program.  If not, see <http://www.gnu.org/licenses/>.
 */
-package org.cbioportal.model;
+package org.mskcc.cbio.portal.model;
 import java.util.List;
 
 /**

persistence/persistence-api/src/main/java/org/cbioportal/persistence/dto/KeywordSampleCount.java → business/src/main/java/org/mskcc/cbio/portal/model/KeywordSampleCount.java

@@ -1,4 +1,4 @@
-package org.cbioportal.persistence.dto;
+package org.mskcc.cbio.portal.model;
 
 import java.io.Serializable;
 

persistence/persistence-api/src/main/java/org/cbioportal/persistence/dto/MutatedGeneSampleCount.java → business/src/main/java/org/mskcc/cbio/portal/model/MutatedGeneSampleCount.java

@@ -1,4 +1,4 @@
-package org.cbioportal.persistence.dto;
+package org.mskcc.cbio.portal.model;
 
 import java.io.Serializable;