cbioportal / cbioportal

cBioPortal for Cancer Genomics

cBioPortal

The cBioPortal for Cancer Genomics provides visualization, analysis, and download of large-scale cancer genomics data sets. For a short intro on cBioPortal, see these introductory slides.

If you would like to know how to setup a private instance of the portal and/or get set up for developing, see the documentation. For details on contributing code changes via pull requests, see our Contributing document.

If you are interested in coordinating the development of new features, please contact [email protected] or reach out on https://slack.cbioportal.org.

📘 Documentation

See https://docs.cbioportal.org

🤝 License

See LICENSE

💻 Run Backend

cBioPortal consists of several components, please read the Architecture docs to figure out what repo would be relevant to edit. If you e.g. only want to make frontend changes, one can directly edit the frontend repo instead. Read the instructions in that repo for more info on how to do frontend development. This repo only contains the backend part. Before editing the backend, it's good to read the backend code organization.

Local Development

What MySQL database to use

We recommend to set up a MySQL database using Docker Compose. It's useful to know how to do this as it allows you to import any dataset of your choice. For debugging production issues, we also have a database available with all the data on https://cbioportal.org that one can connect to directly. Please reach out on slack to get the credentials.

Command Line

If you want to run the cBioPortal web app from the command line please follow these instructions. First, we want to make sure that all ports are open for the services set up through docker compose (i.e. not just accessible to other containers within the same Docker Compose file). To do so, in the docker compose repo run:

docker compose -f docker-compose.yml -f open-ports.yml up

This should open the ports. Now we are ready to run the cBioPortal web app locally. You can compile the backend code with:

java -Xms2g -Xmx4g \
     -Dauthenticate=noauthsessionservice \
     -Dsession.service.url=http://localhost:5000/api/sessions/my_portal/ \
     -Dsession.service.origin='*' \
     -Dspring.datasource.username=cbio_user \
     -Dspring.datasource.password=somepassword \
     -Dspring.datasource.driver-class-name=com.mysql.cj.jdbc.Driver \
     -Dspring.jpa.database-platform=org.hibernate.dialect.MySQL5InnoDBDialect \
     -Dspring.datasource.url='jdbc:mysql://cbio_user:somepassword@localhost:3306/cbioportal?useSSL=false&allowPublicKeyRetrieval=true' \
     -Dshow.civic=true \
     -Dskin.footer='' \
     -Dapp.name='my-portal' \
     -Ddbconnector=dbcp \
     -cp "$PWD:$PWD/BOOT-INF/lib/*" \
     org.cbioportal.PortalApplication

The app should now show up at http://localhost:8080.

Deploy your development image inside Docker Compose

Another option is to deploy your development image directly into the docker-compose file. First build the image like this

docker build -t cbioportal/cbioportal:my-dev-cbioportal-image -f docker/web-and-data/Dockerfile .

Then change the env file to use cbioportal/cbioportal:my-dev-cbioportal-image.

Local Development

Note: internally we have a dev database available with the public data set that one can connect to directly. Please reach out on slack to get the credentials. It is usually best to use a small test dataset, but if a copy of the production database is necessary for e.g. fixing a bug specific to production data that can be useful.

🕵️‍♀️ Debugging

If you want to attach a debugger you can change the docker-compose.yml file to include the paramaters: -Xdebug -Xrunjdwp:transport=dt_socket,server=y,suspend=n,address=5005 (make sure to expose the debug port by adding 5005:5005 in the ports section of the cbioportal container). If you are running the java app outside of docker you can add the same parameters to the java command line arguments instead.

You can then use a JAVA IDE to connect to that port. E.g. in VSCode, one would add the following configuration to launch.json to connect:

{
    "version": "0.2.0",
    "configurations": [
        {
            "type": "java",
            "name": "Debug (Attach)",
            "request": "attach",
            "hostName": "localhost",
            "port": 5005,
            "projectName": "cbioportal"
        }
    ]
}

🌳 Branch Information

	main branch	upcoming release branch	later release candidate branch
Branch name	master	--	rc
Description	All bug fixes and features not requiring database migrations go here. This code is either already in production or will be released this week	Next release that requires database migrations. Thorough manual product review often takes place for this branch before release	Later releases with features that require database migrations. This is useful to allow merging in new features without affecting the upcoming release. Could be seen as a development branch, but note that only high quality pull requests are merged. That is the feature should be pretty much ready for release after merge.
Live instance	https://www.cbioportal.org / https://master.cbioportal.org	--	https://rc.cbioportal.org
Live instance version	https://www.cbioportal.org/api/info / https://master.cbioportal.org/api/info	--	https://rc.cbioportal.org/api/info
Docker Image	cbioportal/cbioportal:master	--	cbioportal/cbioportal:rc
Kubernetes Config	production / master	--	rc
Status		--	--

🚀 Releases

Release Notes on GitHub:

https://github.com/cBioPortal/cbioportal/releases

See also the cBioPortal News section for user focused release information:

https://www.cbioportal.org/news

Docker Images are available for each tag and branch:

https://hub.docker.com/repository/docker/cbioportal/cbioportal/tags

👉 Other Repos

Read the Architecture docs to see how these relate:

• https://github.com/cBioPortal/cbioportal-frontend
• https://github.com/cbioportal/session-service
• https://github.com/cBioPortal/datahub/

cbioportal's Issues

mRNA up/down not displaying in oncoprint

http://bit.ly/1GKCddL

Selecting genes from MutSig and GISTIC no longer works

Since rolling out the new tree-based way of selecting cancer studies, the buttons for "Select from MutSig" and "Select from GISTIC" no longer work.

To recreate the error:

1. Go to: http://www.cbioportal.org/
2. Select Breast --> Breast Invasive Carcinoma (TCGA Provisional)
3. User Gene Set, select either MutSig or GISTIC.

You then get an empty modal dialog box (see below).

I believe this a Javascript error related to: #select_cancer_type. This is how we previously identified which cancer type was chosen. But, with the tree, my guess is that this value is now empty. Just a guess though.

Make mvn tomcat:run work

For debugging purposes when things go pear-shaped, it would be nice to make mvn tomcat:run and mvnDebug tomcat:run work such that the one setting things up can connect to the server with a remote debugger, e.g., from Eclipse.

With the current master branch, I get the following error message:

org.springframework.beans.factory.BeanDefinitionStoreException: Unexpected exception parsing XML document from class path resource [applicationContext-security.xml]; nested exception is java.lang.IllegalArgumentException: Could not resolve placeholder 'authenticate' in string value "jndi,${authenticate}"
    at org.springframework.beans.factory.xml.XmlBeanDefinitionReader.doLoadBeanDefinitions(XmlBeanDefinitionReader.java:413)

Local Install -- Networks are sometimes super small

On my local installation, I have noticed that the network tab appears, but (sometimes, but not always) appears to be empty. Example attached. It looks as if there is no network, but it's actually there, just super tiny. If you zoom in, you can see the network. Has anyone else experienced / seen this?

Loading of some data sets hangs

I am trying to load mutation data and a bunch of case sets. For example:

$PORTAL_HOME/core/src/main/scripts/cbioportalImporter.py --jvm-args "-cp $CONNECTOR_JAR:$PORTAL_HOME/core/target/core-1.0-SNAPSHOT.jar" --command import-study-data --meta-filename profile_out/meta_mutations_extended.txt --data-filename profile_out/data_mutations_extended.txt

$PORTAL_HOME/core/src/main/scripts/cbioportalImporter.py --jvm-args "-cp $CONNECTOR_JAR:$PORTAL_HOME/core/target/core-1.0-SNAPSHOT.jar" --command import-patient-list --meta-filename profile_out/case_lists

Both of these commands just seem to hang, and I get no output. But, when I check the database, all (or most) of the data is there.

Very strange. I will try to fix. But, just curious if any one else has seen this?

Table in "Copy Number Alterations" would be gone after second click

Hello, when I go to "Copy Number Alterations" tab for the first time, it is fine, but when I click the "Mutated Genes" tab and then go back to "Copy Number Alterations". The table is gone.

Wiki Page for Google OAuth2

We need to add a wiki page on setting up portal with Google OAuth2. Assigning to self.

Missing allele frequencies

• https://cbioportal.mskcc.org/case.do?cancer_study_id=coadread_cmo_rosenn_5212_g&case_id=p_NR_labraf_009
• https://cbioportal.mskcc.org/case.do?cancer_study_id=coadread_cmo_rosenn_5212_g&sample_id=s_NR_labraf_009_X1

If reference allele count == 0, no data is displayed in the variant allele frequency columns in the patient and sample views

Wiki Page Describing Clinical Data File Format needs Clarifications

I am trying to load a simple clinical data file.

But, nothing is going in.

I think this is because I am misunderstanding the clinical file format described here: https://github.com/cBioPortal/cbioportal/wiki/File-Formats#clinical-data

I am happy to fix the docs, but need some help from others with a few questions:

1. Is it possible to load a clinical data file with only a PATIENT_ID column (e.g. no SAMPLE_ID)?
2. If the above is true, I think it is correct to say that one must specify:

one of (PATIENT_ID or SAMPLE_ID) or (PATIENT_ID followed by SAMPLE_ID)

These lines are also a little confusing: "A clinical data file is a two dimensional matrix with a sample id per row and a clinical attribute per column. For each sample-attribute, an atomic value represents the clinical attribute for that sample."

Should it be: "A clinical data file is a two dimensional matrix with multiple clinical attributes which can be attached to either a patient or a sample."?

Display patient clinical attribute first.

Resurrecting Build a Case Set Feature

I know that you can (partially) do this via the study view now, but I'd like to resurrect / reimagine the "Build a Case Set" feature. My group can also volunteer to do the implementation. Not sure on what time-scale, but starting this issue, so that we can gather initial requirements / mockups, etc.

Mutation file format docs do not mention correct column for Amino_Acid_Change

In this wiki document:

https://github.com/cBioPortal/cbioportal/wiki/File-Formats#mutation-data

we do not specify the column name for "Amino_Acid_Change". Assigning to self.

NullPointerException in PortalMetaDataJSON

Hi,

I'm getting a NullPointerException in PortalMetaDataJSON while accessing the home page:

SEVERE: Servlet.service() for servlet [portal_meta_data_json] in context with path [/cbio] threw exception
java.lang.NullPointerException
        at org.mskcc.cbio.portal.servlet.PortalMetaDataJSON.doGet(PortalMetaDataJSON.java:246)
        at javax.servlet.http.HttpServlet.service(HttpServlet.java:624)
        at javax.servlet.http.HttpServlet.service(HttpServlet.java:731)
        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:303)
        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
        at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52)
...

The offending line is
visibleTypeOfCancerMap.put(typeOfCancerId, typeOfCancerMap.get(typeOfCancerId).getName());
so I'm guessing typeOfCancerMap.get(typeOfCancerId) is returning null there.
We loaded the sample study following the steps on the Wiki, and the database tables look fine.

Any ideas?

Thanks,

Istvan

Wiki Pages are missing information and navigation issue

Two steps are missing from the wiki. Here are the two steps I copy from Hongxin's cBioPortal Development Environment Setup document:

Step 6. If no settings.xml exists under your maven folder, you need to create it under ~/.m2 folder. The content is

settingsKey [your mysql username] [your mysql password] localhost [your tomcat username] [your tomcat password]

Step 7. Create database schema cgds_test

Wiki pages plus these two steps are sufficient to help a user setup cBioPortal at local machine.

However, the wiki is not very easy to navigate. Here is an example of a user following the wiki to setup local environment:

1. Click the link "Setting up a cBioPortal (start here)" from home page, jump to "Setting up a cBioPortal" page.
2. Open "System Requirements" page, and follow the instruction to install tools like Tomcat and Maven.
3. Open "Database Setup" page, and follow the instruction to setup local database.
4. The user is asked to refer to "System Requirements" page again to setup tomcat. And from "System Requirements" page the user is asked to refer to "Software Configuration" page.
5. Go to "Building cBioPortal from Source" page to get the instruction to build the project. First two part of this page has the links to "System Requirements" and "Software Configuration" page.

...

To make the wiki more user-friendly, two issues can be avoided:

1. The same or similar content appears on multiple pages.
2. User is asked to refer to one part of a certain page, and after a few steps following other pages, is asked to refer to another part of the same page again.

Basically, I think we can improve the wiki by rearrange pages and reorder the content.

cBio Skins -- Enhanced

Another high priority item for us, which I can volunteer us for... We need a way to fully customize a local installation -- from turning on/off all tabs, creating news pages, setting logos, about pages, footers, etc. Ideally, the whole thing can be configured and documented via portal.properties.

I have hacked my way to a solution, but this is a complete hack in modifying JSP pages, and not easy to maintain. Also, doesn't help others who want to cusotmize their install. Starting this now to gather requirements.

MutSig and Gistic gene selection box not working

Debugging / IDE

Hi,

Quick question: what do you guys use to debug cBio?
Do you run it in an IDE (Spring Tool Suite / Eclipse)?

Thanks,

Istvan

Disable user authorization

Hi cBioPortal team,

Thank you for making the source code public! It has been very useful. I went through the instructions and installed a local copy of cbioportal. The issue that I have right now is I can't bypass the login page. Probably there are some settings that I need to set in portal.properties to disable it but I have no idea how since I'm not that familiar with the whole framework. Would you please tell me how to disable google authorization and skip the login page? Thank you so much!

By the way, I also followed your instructions to add users in mysql but it complained about "missing client_id".

Best,
Jia

Numeric entries can be added to the Search Query

There is no check for the numeric entries and if we search some number the user interface is crashing.

Timeline shows gray dots on specimen track

Timeline should show numbers of the samples

• https://cbioportal.mskcc.org/case.do?cancer_study_id=mskimpact&case_id=P-0001104

Also for single sample

• https://cbioportal.mskcc.org/case.do?cancer_study_id=mskimpact&sample_id=P-0001104-T01-IM3

Using cbioportal.war

When using cbioportal.war from bitbucket.

i followed all needed step as i know.

there's error about type_of_cancers is null.

but i insert sample brca_study data successfully.
and i can select it with jndi.

below is snapshot of firefox & firebug.

give me any tiny hint whatever you can suppose.

thanks.

3D Protein not displaying

Trailing tab when downloading mutation data

This is very low priority but just wanted to mention it. When downloading mutation data from a study

the resulting tsv has a trailing tab

This could cause problems when reading the tsv. For instance when using pandas read_csv in python an extra column is created.

Not sure if this applies to other tsvs one can download from the cBioPortal as well.

mutation assessor link not working on patient view

getma.org not working any more -- replace it with mutationassessor.org

Fraction Genome Altered Row Breaks OncoPrint

To Reproduce:

1. Go to British Columbia Dataset and input a predefined query
2. Move over OncoPrint and click the "+" on the tool menu to add data.
3. Select Fraction Genome Altered.

You should observe that this breaks the OncoPrint. A d3js error appears in the console but without a stack trace.

Predefined study selection does not work on Firefox

If you click on one of the predefined study selections, such as "tcga" on http://www.cbioportal.org/
you get a popup with [object Object] in firefox 37.0.2. No problems in in chrome, neither in safari.

Bitly Links are Not Working within Local Install

I pasted my Bitly username and token into portal.properties, and redeployed WAR file. But, I still get an error when creating bitly links within my local install. Assigning to self, to look into further.

change log4j.properties location

Currently in web.xml, the log4j config file points to file://${PORTAL_HOME}/log4j.properties. We should change this to internal file in war. May need to modify WIKI page accordingly.

Improve styling prev/next case in patient view

Change prev and next case buttons to be more in line with the rest of the patient view styling

JSmol

Hi cBioPortal team,

I have successfully installed a local portal. But the JSmol is not working properly somehow. It complains that the file downloaded from pdb doesn't have supported format. I think the error is associated with the binary file format (*.gz) since manually loading the ".pdb" file locally works just fine. Because you guys made it work, would you please share some experience with me about tackling this error? Am I missing some settings? Thank you!

Best,
Seqseek

Do not display "undefined" is certain attribute is not available in the patient header

Patient view show sample info for single sample

Currently for a single sample location and whether it is met/primary is not displayed on the single sample view.

Source Build contains hardcoded NEWS section

Hello,

The source build currently contains a lot of hardcoded information like the NEWS and FAQ pages.

Especially the NEWS page is confusing to users as you mention all the imports that are available on the cbioportal.org site but are not available for local installations.

thanks,
Martin

Database Host not picked up from portal.properties

Hello,

It seems that neither the db.host, db.connection_string.

When I build on a host that is remote to the MySQL database then the build fails with the error below. As soon as I build on a host that has MySQL available on localhost things work.

~/.m2/settings.xml

<settings>
    <proxies>
        <proxy>
          <id>px</id>
          <active>true</active>
          <protocol>http</protocol>
          <host>px</host>
          <port>80</port>
          <username>user</username>
          <password>pass</password>
          <nonProxyHosts>*.example.invalid|localhost|bio-mysql|172.20.96.0/22</nonProxyHosts>
          <!-- this has no effect either
          <nonProxyHosts>*.example.invalid|localhost|bio-mysql.example.invalid|172.20.96.0/22</nonProxyHosts>         
          -->
        </proxy>
    </proxies>
    <servers>
        <server>
            <id>settingsKey</id>
            <username>cbio_user</username>
            <password>supersecure</password>
        </server>
    </servers>
</settings>

portal.properties

# app name
app.name=cbioportal
app.version=1.0

# database
db.user=cbio_user
db.password=supersecure
# FQDN's also don't get picked up
db.host=bio-mysql
db.portal_db_name=cbioportal
db.driver=com.mysql.jdbc.Driver
# FQDN's also don't get picked up
db.connection_string=jdbc:mysql://bio-mysql/
db.tomcat_resource_name=jdbc/cbioportal
# .... cut for brevity...

mvn -DskipTests install

...
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary:
[INFO]
[INFO] Portal Master ...................................... SUCCESS [  0.495 s]
[INFO] Portal Business Layer .............................. SUCCESS [ 11.675 s]
[INFO] Portal Core ........................................ FAILURE [  4.647 s]
[INFO] Portal Web Layer ................................... SKIPPED
[INFO] cBio Cancer Genomics Portal ........................ SKIPPED
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 17.070 s
[INFO] Finished at: 2015-05-11T14:06:40+02:00
[INFO] Final Memory: 52M/1860M
[INFO] ------------------------------------------------------------------------
[ERROR] Failed to execute goal org.codehaus.mojo:sql-maven-plugin:1.5:execute (default) on project core: Communications link failure due to underlying exception:
[ERROR]
[ERROR] ** BEGIN NESTED EXCEPTION **
[ERROR]
[ERROR] java.net.SocketException
[ERROR] MESSAGE: java.net.ConnectException: Connection refused
[ERROR]
[ERROR] STACKTRACE:
[ERROR]
[ERROR] java.net.SocketException: java.net.ConnectException: Connection refused
[ERROR] at com.mysql.jdbc.StandardSocketFactory.connect(StandardSocketFactory.java:156)
[ERROR] at com.mysql.jdbc.MysqlIO.<init>(MysqlIO.java:276)
[ERROR] at com.mysql.jdbc.Connection.createNewIO(Connection.java:2641)
[ERROR] at com.mysql.jdbc.Connection.<init>(Connection.java:1531)
[ERROR] at com.mysql.jdbc.NonRegisteringDriver.connect(NonRegisteringDriver.java:266)
[ERROR] at org.codehaus.mojo.sql.SqlExecMojo.getConnection(SqlExecMojo.java:899)
[ERROR] at org.codehaus.mojo.sql.SqlExecMojo.execute(SqlExecMojo.java:612)
[ERROR] at org.apache.maven.plugin.DefaultBuildPluginManager.executeMojo(DefaultBuildPluginManager.java:134)
[ERROR] at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:208)
[ERROR] at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:153)
[ERROR] at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:145)
[ERROR] at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject(LifecycleModuleBuilder.java:116)
[ERROR] at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject(LifecycleModuleBuilder.java:80)
[ERROR] at org.apache.maven.lifecycle.internal.builder.singlethreaded.SingleThreadedBuilder.build(SingleThreadedBuilder.java:51)
[ERROR] at org.apache.maven.lifecycle.internal.LifecycleStarter.execute(LifecycleStarter.java:128)
[ERROR] at org.apache.maven.DefaultMaven.doExecute(DefaultMaven.java:307)
[ERROR] at org.apache.maven.DefaultMaven.doExecute(DefaultMaven.java:193)
[ERROR] at org.apache.maven.DefaultMaven.execute(DefaultMaven.java:106)
[ERROR] at org.apache.maven.cli.MavenCli.execute(MavenCli.java:862)
[ERROR] at org.apache.maven.cli.MavenCli.doMain(MavenCli.java:286)
[ERROR] at org.apache.maven.cli.MavenCli.main(MavenCli.java:197)
[ERROR] at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
[ERROR] at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
[ERROR] at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
[ERROR] at java.lang.reflect.Method.invoke(Method.java:497)
[ERROR] at org.codehaus.plexus.classworlds.launcher.Launcher.launchEnhanced(Launcher.java:289)
[ERROR] at org.codehaus.plexus.classworlds.launcher.Launcher.launch(Launcher.java:229)
[ERROR] at org.codehaus.plexus.classworlds.launcher.Launcher.mainWithExitCode(Launcher.java:415)
[ERROR] at org.codehaus.plexus.classworlds.launcher.Launcher.main(Launcher.java:356)
[ERROR]
[ERROR]
[ERROR] ** END NESTED EXCEPTION **
[ERROR]
[ERROR]
[ERROR]
[ERROR] Last packet sent to the server was 9 ms ago.
[ERROR] -> [Help 1]
[ERROR]
[ERROR] To see the full stack trace of the errors, re-run Maven with the -e switch.
[ERROR] Re-run Maven using the -X switch to enable full debug logging.
[ERROR]
[ERROR] For more information about the errors and possible solutions, please read the following articles:
[ERROR] [Help 1] http://cwiki.apache.org/confluence/display/MAVEN/MojoExecutionException
[ERROR]
[ERROR] After correcting the problems, you can resume the build with the command
[ERROR]   mvn <goals> -rf :core

Why don't +/-1s (gains and losses) show up in copy number data?

I have a dataset with copy number data which happens not to have any 2s nor -2s (amplifications and homozygous deletions). cBioPortal shows no alterations at all. I've checked the code and it seems to happen (among other places) here CrossCancerJSON:

                    boolean isAnyCnaChanged = isAnyCnaUp || isAnyCnaDown;
                    if(isAnyMutated && !isAnyCnaChanged)
                        noOfMutated++;
                    else if(isAnyMutated && isAnyCnaChanged)
                        noOfOther++;
                    else if(isAnyCnaUp)
                        noOfCnaUp++;
                    else if(isAnyCnaDown)
                        noOfCnaDown++;
                    else if(isAnyCnaGain)
                        noOfCnaGain++;
                    else if(isAnyCnaLoss)
                        noOfCnaLoss++;

Why does it ignore isCnaLoss and isCnaGain?

Wiki : Broken links - Drug target and clinical-trial data

Not a big deal here but the link at to the PDQ cancer page at wiki page is broken.

plots tab not working in Firefox

http://bit.ly/1Pa0D0K

In FireBugs:

remove-study does not remove all data from database

According to the documentation, I am trying to remove a formerly imported study from the mysql database (in addition to import study, I added also some data with import-patient-list, and import-study-data)

after running the following script:

$PORTAL_HOME/core/src/main/scripts/cbioportalImporter.py --jvm-args "-cp $CONNECTOR_JAR:$PORTAL_HOME/core/target/core-1.0-SNAPSHOT.jar" --command remove-study --meta-filename meta_study.txt

I compare my database backup with the current database (using mysqldbcompare).

Even though the db and the backup db should be identical, I see a number of additional rows in table genetic_alteration.

Are there any convenient ways to import data, apart from the python script/java program?
How can I get rid of the additional data?

Wiki Page for Authenticated Users via SAML

With much help from Ben, I think I now understand how to get SAML working within a new instance of cBioPortal.

I have distilled all my notes from Ben into a new wiki doc: https://github.com/cBioPortal/cbioportal/wiki/Authenticating-Users-via-SAML

I also made a few tweaks to this page:

https://github.com/cBioPortal/cbioportal/wiki/User-Authorization

Please take a look, and let me know if you would like me to make any revisions. Once I get feedback, I will close this issue. Thanks.

mvn compile fails with error about `${PORTAL_HOME}`

Hi,

I'm trying to evaluate cbioportal for an on premise installation. I cloned the repository and tried a simple mvn compile. It fails with some error about ${PORTAL_HOME}.

Unfortunately there aren't any installation instructions or I am unable to find them. Let me know if you need any details about this.

$ lsb_release -a
LSB Version:    :base-4.0-amd64:base-4.0-noarch:core-4.0-amd64:core-4.0-noarch:graphics-4.0-amd64:graphics-4.0-noarch:printing-4.0-amd64:printing-4.0-noarch
Distributor ID: Scientific
Description:    Scientific Linux release 6.6 (Carbon)
Release:        6.6
Codename:       Carbon

$ java -version
java version "1.8.0_45"
Java(TM) SE Runtime Environment (build 1.8.0_45-b14)
Java HotSpot(TM) 64-Bit Server VM (build 25.45-b02, mixed mode)

$ mvn --version
Apache Maven 3.3.3 (7994120775791599e205a5524ec3e0dfe41d4a06; 2015-04-22T13:57:37+02:00)
Maven home: /net/home/marcherm/easybuildinstall/software/Maven/3.3.3
Java version: 1.8.0_45, vendor: Oracle Corporation
Java home: /apps/prod/easybuild/software/Java/1.8.0_45/jre
Default locale: en_US, platform encoding: UTF-8
OS name: "linux", version: "2.6.32-431.11.2.el6.x86_64", arch: "amd64", family: "unix"

$ mvn -X compile
Apache Maven 3.3.3 (7994120775791599e205a5524ec3e0dfe41d4a06; 2015-04-22T13:57:37+02:00)
Maven home: /net/home/marcherm/easybuildinstall/software/Maven/3.3.3
Java version: 1.8.0_45, vendor: Oracle Corporation
Java home: /apps/prod/easybuild/software/Java/1.8.0_45/jre
Default locale: en_US, platform encoding: UTF-8
OS name: "linux", version: "2.6.32-431.11.2.el6.x86_64", arch: "amd64", family: "unix"
[DEBUG] Created new class realm maven.api
[DEBUG] Importing foreign packages into class realm maven.api
[DEBUG]   Imported: javax.enterprise.inject.* < plexus.core
[DEBUG]   Imported: javax.enterprise.util.* < plexus.core
[DEBUG]   Imported: javax.inject.* < plexus.core
[DEBUG]   Imported: org.apache.maven.* < plexus.core
[DEBUG]   Imported: org.apache.maven.artifact < plexus.core
[DEBUG]   Imported: org.apache.maven.classrealm < plexus.core
[DEBUG]   Imported: org.apache.maven.cli < plexus.core
[DEBUG]   Imported: org.apache.maven.configuration < plexus.core
[DEBUG]   Imported: org.apache.maven.exception < plexus.core
[DEBUG]   Imported: org.apache.maven.execution < plexus.core
[DEBUG]   Imported: org.apache.maven.execution.scope < plexus.core
[DEBUG]   Imported: org.apache.maven.lifecycle < plexus.core
[DEBUG]   Imported: org.apache.maven.model < plexus.core
[DEBUG]   Imported: org.apache.maven.monitor < plexus.core
[DEBUG]   Imported: org.apache.maven.plugin < plexus.core
[DEBUG]   Imported: org.apache.maven.profiles < plexus.core
[DEBUG]   Imported: org.apache.maven.project < plexus.core
[DEBUG]   Imported: org.apache.maven.reporting < plexus.core
[DEBUG]   Imported: org.apache.maven.repository < plexus.core
[DEBUG]   Imported: org.apache.maven.rtinfo < plexus.core
[DEBUG]   Imported: org.apache.maven.settings < plexus.core
[DEBUG]   Imported: org.apache.maven.toolchain < plexus.core
[DEBUG]   Imported: org.apache.maven.usability < plexus.core
[DEBUG]   Imported: org.apache.maven.wagon.* < plexus.core
[DEBUG]   Imported: org.apache.maven.wagon.authentication < plexus.core
[DEBUG]   Imported: org.apache.maven.wagon.authorization < plexus.core
[DEBUG]   Imported: org.apache.maven.wagon.events < plexus.core
[DEBUG]   Imported: org.apache.maven.wagon.observers < plexus.core
[DEBUG]   Imported: org.apache.maven.wagon.proxy < plexus.core
[DEBUG]   Imported: org.apache.maven.wagon.repository < plexus.core
[DEBUG]   Imported: org.apache.maven.wagon.resource < plexus.core
[DEBUG]   Imported: org.codehaus.classworlds < plexus.core
[DEBUG]   Imported: org.codehaus.plexus.* < plexus.core
[DEBUG]   Imported: org.codehaus.plexus.classworlds < plexus.core
[DEBUG]   Imported: org.codehaus.plexus.component < plexus.core
[DEBUG]   Imported: org.codehaus.plexus.configuration < plexus.core
[DEBUG]   Imported: org.codehaus.plexus.container < plexus.core
[DEBUG]   Imported: org.codehaus.plexus.context < plexus.core
[DEBUG]   Imported: org.codehaus.plexus.lifecycle < plexus.core
[DEBUG]   Imported: org.codehaus.plexus.logging < plexus.core
[DEBUG]   Imported: org.codehaus.plexus.personality < plexus.core
[DEBUG]   Imported: org.codehaus.plexus.util.xml.Xpp3Dom < plexus.core
[DEBUG]   Imported: org.codehaus.plexus.util.xml.pull.XmlPullParser < plexus.core
[DEBUG]   Imported: org.codehaus.plexus.util.xml.pull.XmlPullParserException < plexus.core
[DEBUG]   Imported: org.codehaus.plexus.util.xml.pull.XmlSerializer < plexus.core
[DEBUG]   Imported: org.eclipse.aether.* < plexus.core
[DEBUG]   Imported: org.eclipse.aether.artifact < plexus.core
[DEBUG]   Imported: org.eclipse.aether.collection < plexus.core
[DEBUG]   Imported: org.eclipse.aether.deployment < plexus.core
[DEBUG]   Imported: org.eclipse.aether.graph < plexus.core
[DEBUG]   Imported: org.eclipse.aether.impl < plexus.core
[DEBUG]   Imported: org.eclipse.aether.installation < plexus.core
[DEBUG]   Imported: org.eclipse.aether.internal.impl < plexus.core
[DEBUG]   Imported: org.eclipse.aether.metadata < plexus.core
[DEBUG]   Imported: org.eclipse.aether.repository < plexus.core
[DEBUG]   Imported: org.eclipse.aether.resolution < plexus.core
[DEBUG]   Imported: org.eclipse.aether.spi < plexus.core
[DEBUG]   Imported: org.eclipse.aether.transfer < plexus.core
[DEBUG]   Imported: org.eclipse.aether.version < plexus.core
[DEBUG]   Imported: org.slf4j.* < plexus.core
[DEBUG]   Imported: org.slf4j.spi.* < plexus.core
[DEBUG] Populating class realm maven.api
[INFO] Error stacktraces are turned on.
[DEBUG] Reading global settings from /net/home/marcherm/easybuildinstall/software/Maven/3.3.3/conf/settings.xml
[DEBUG] Reading user settings from /net/home/marcherm/.m2/settings.xml
[DEBUG] Reading global toolchains from /net/home/marcherm/easybuildinstall/software/Maven/3.3.3/conf/toolchains.xml
[DEBUG] Reading user toolchains from /net/home/marcherm/.m2/toolchains.xml
[DEBUG] Using local repository at /net/home/marcherm/.m2/repository
[DEBUG] Using manager EnhancedLocalRepositoryManager with priority 10.0 for /net/home/marcherm/.m2/repository
[INFO] Scanning for projects...
[DEBUG] Extension realms for project org.mskcc.cbio:master:pom:1.0-SNAPSHOT: (none)
[DEBUG] Looking up lifecyle mappings for packaging pom from ClassRealm[plexus.core, parent: null]
[DEBUG] Extension realms for project org.mskcc.cbio:cbioportal:war:1.0-SNAPSHOT: (none)
[DEBUG] Looking up lifecyle mappings for packaging war from ClassRealm[plexus.core, parent: null]
[DEBUG] Extension realms for project org.mskcc.cbio:core:jar:1.0-SNAPSHOT: (none)
[DEBUG] Looking up lifecyle mappings for packaging jar from ClassRealm[plexus.core, parent: null]
[DEBUG] Extension realms for project org.mskcc.cbio:business:jar:1.0-SNAPSHOT: (none)
[DEBUG] Looking up lifecyle mappings for packaging jar from ClassRealm[plexus.core, parent: null]
[DEBUG] Extension realms for project org.mskcc.cbio:web:jar:1.0-SNAPSHOT: (none)
[DEBUG] Looking up lifecyle mappings for packaging jar from ClassRealm[plexus.core, parent: null]
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Build Order:
[INFO]
[INFO] Portal Master
[INFO] Portal Business Layer
[INFO] Portal Core
[INFO] Portal Web Layer
[INFO] cBio Cancer Genomics Portal
[DEBUG] === REACTOR BUILD PLAN ================================================
[DEBUG] Project: org.mskcc.cbio:master:pom:1.0-SNAPSHOT
[DEBUG] Tasks:   [compile]
[DEBUG] Style:   Regular
[DEBUG] -----------------------------------------------------------------------
[DEBUG] Project: org.mskcc.cbio:business:jar:1.0-SNAPSHOT
[DEBUG] Tasks:   [compile]
[DEBUG] Style:   Regular
[DEBUG] -----------------------------------------------------------------------
[DEBUG] Project: org.mskcc.cbio:core:jar:1.0-SNAPSHOT
[DEBUG] Tasks:   [compile]
[DEBUG] Style:   Regular
[DEBUG] -----------------------------------------------------------------------
[DEBUG] Project: org.mskcc.cbio:web:jar:1.0-SNAPSHOT
[DEBUG] Tasks:   [compile]
[DEBUG] Style:   Regular
[DEBUG] -----------------------------------------------------------------------
[DEBUG] Project: org.mskcc.cbio:cbioportal:war:1.0-SNAPSHOT
[DEBUG] Tasks:   [compile]
[DEBUG] Style:   Regular
[DEBUG] =======================================================================
[INFO]
[INFO] ------------------------------------------------------------------------
[INFO] Building Portal Master 1.0-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[DEBUG] Lifecycle default -> [validate, initialize, generate-sources, process-sources, generate-resources, process-resources, compile, process-classes, generate-test-sources, process-test-sources, generate-test-resources, process-test-resources, test-compile, process-test-classes, test, prepare-package, package, pre-integration-test, integration-test, post-integration-test, verify, install, deploy]
[DEBUG] Lifecycle clean -> [pre-clean, clean, post-clean]
[DEBUG] Lifecycle site -> [pre-site, site, post-site, site-deploy]
[DEBUG] === PROJECT BUILD PLAN ================================================
[DEBUG] Project:       org.mskcc.cbio:master:1.0-SNAPSHOT
[DEBUG] Dependencies (collect): []
[DEBUG] Dependencies (resolve): []
[DEBUG] Repositories (dependencies): [spring-milestones (http://repo.spring.io/milestone, default, releases), central (https://repo.maven.apache.org/maven2, default, releases)]
[DEBUG] Repositories (plugins)     : [central (https://repo.maven.apache.org/maven2, default, releases)]
[DEBUG] =======================================================================
[INFO]
[INFO] ------------------------------------------------------------------------
[INFO] Building Portal Business Layer 1.0-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[DEBUG] Lifecycle default -> [validate, initialize, generate-sources, process-sources, generate-resources, process-resources, compile, process-classes, generate-test-sources, process-test-sources, generate-test-resources, process-test-resources, test-compile, process-test-classes, test, prepare-package, package, pre-integration-test, integration-test, post-integration-test, verify, install, deploy]
[DEBUG] Lifecycle clean -> [pre-clean, clean, post-clean]
[DEBUG] Lifecycle site -> [pre-site, site, post-site, site-deploy]
[DEBUG] Lifecycle default -> [validate, initialize, generate-sources, process-sources, generate-resources, process-resources, compile, process-classes, generate-test-sources, process-test-sources, generate-test-resources, process-test-resources, test-compile, process-test-classes, test, prepare-package, package, pre-integration-test, integration-test, post-integration-test, verify, install, deploy]
[DEBUG] Lifecycle clean -> [pre-clean, clean, post-clean]
[DEBUG] Lifecycle site -> [pre-site, site, post-site, site-deploy]
[DEBUG] Lifecycle default -> [validate, initialize, generate-sources, process-sources, generate-resources, process-resources, compile, process-classes, generate-test-sources, process-test-sources, generate-test-resources, process-test-resources, test-compile, process-test-classes, test, prepare-package, package, pre-integration-test, integration-test, post-integration-test, verify, install, deploy]
[DEBUG] Lifecycle clean -> [pre-clean, clean, post-clean]
[DEBUG] Lifecycle site -> [pre-site, site, post-site, site-deploy]
[DEBUG] Lifecycle default -> [validate, initialize, generate-sources, process-sources, generate-resources, process-resources, compile, process-classes, generate-test-sources, process-test-sources, generate-test-resources, process-test-resources, test-compile, process-test-classes, test, prepare-package, package, pre-integration-test, integration-test, post-integration-test, verify, install, deploy]
[DEBUG] Lifecycle clean -> [pre-clean, clean, post-clean]
[DEBUG] Lifecycle site -> [pre-site, site, post-site, site-deploy]
[DEBUG] === PROJECT BUILD PLAN ================================================
[DEBUG] Project:       org.mskcc.cbio:business:1.0-SNAPSHOT
[DEBUG] Dependencies (collect): []
[DEBUG] Dependencies (resolve): [compile]
[DEBUG] Repositories (dependencies): [spring-milestones (http://repo.spring.io/milestone, default, releases), central (https://repo.maven.apache.org/maven2, default, releases)]
[DEBUG] Repositories (plugins)     : [central (https://repo.maven.apache.org/maven2, default, releases)]
[DEBUG] -----------------------------------------------------------------------
[DEBUG] Goal:          org.apache.maven.plugins:maven-resources-plugin:2.6:copy-resources (copy-parent-resources)
[DEBUG] Style:         Regular
[DEBUG] Configuration: <?xml version="1.0" encoding="UTF-8"?>
<configuration>
  <buildFilters default-value="${project.build.filters}"/>
  <encoding default-value="${project.build.sourceEncoding}">${encoding}</encoding>
  <escapeString>${maven.resources.escapeString}</escapeString>
  <escapeWindowsPaths default-value="true">${maven.resources.escapeWindowsPaths}</escapeWindowsPaths>
  <includeEmptyDirs default-value="false">${maven.resources.includeEmptyDirs}</includeEmptyDirs>
  <outputDirectory>/net/home/marcherm/git/cbioportal/business/target/classes</outputDirectory>
  <overwrite default-value="false">${maven.resources.overwrite}</overwrite>
  <project default-value="${project}"/>
  <resources>
    <resource>
      <directory>${PORTAL_HOME}/src/main/resources</directory>
      <includes>
        <include>**/*.properties</include>
      </includes>
      <excludes>
        <exclude>**/portal.properties.*</exclude>
        <exclude>**/log4j.properties.*</exclude>
        <exclude>**/*.EXAMPLE</exclude>
      </excludes>
    </resource>
  </resources>
  <session default-value="${session}"/>
  <supportMultiLineFiltering default-value="false">${maven.resources.supportMultiLineFiltering}</supportMultiLineFiltering>
  <useBuildFilters default-value="true"/>
  <useDefaultDelimiters default-value="true"/>
</configuration>
[DEBUG] -----------------------------------------------------------------------
[DEBUG] Goal:          org.apache.maven.plugins:maven-resources-plugin:2.6:resources (default-resources)
[DEBUG] Style:         Regular
[DEBUG] Configuration: <?xml version="1.0" encoding="UTF-8"?>
<configuration>
  <buildFilters default-value="${project.build.filters}"/>
  <encoding default-value="${project.build.sourceEncoding}">${encoding}</encoding>
  <escapeString>${maven.resources.escapeString}</escapeString>
  <escapeWindowsPaths default-value="true">${maven.resources.escapeWindowsPaths}</escapeWindowsPaths>
  <includeEmptyDirs default-value="false">${maven.resources.includeEmptyDirs}</includeEmptyDirs>
  <outputDirectory default-value="${project.build.outputDirectory}"/>
  <overwrite default-value="false">${maven.resources.overwrite}</overwrite>
  <project default-value="${project}"/>
  <resources default-value="${project.resources}"/>
  <session default-value="${session}"/>
  <supportMultiLineFiltering default-value="false">${maven.resources.supportMultiLineFiltering}</supportMultiLineFiltering>
  <useBuildFilters default-value="true"/>
  <useDefaultDelimiters default-value="true"/>
</configuration>
[DEBUG] -----------------------------------------------------------------------
[DEBUG] Goal:          org.apache.maven.plugins:maven-compiler-plugin:2.0.2:compile (default-compile)
[DEBUG] Style:         Regular
[DEBUG] Configuration: <?xml version="1.0" encoding="UTF-8"?>
<configuration>
  <basedir>${basedir}</basedir>
  <buildDirectory>${project.build.directory}</buildDirectory>
  <classpathElements>${project.compileClasspathElements}</classpathElements>
  <compileSourceRoots>${project.compileSourceRoots}</compileSourceRoots>
  <compilerId default-value="javac">${maven.compiler.compilerId}</compilerId>
  <compilerVersion>${maven.compiler.compilerVersion}</compilerVersion>
  <debug default-value="true">${maven.compiler.debug}</debug>
  <encoding>${maven.compiler.encoding}</encoding>
  <executable>${maven.compiler.executable}</executable>
  <failOnError default-value="true">${maven.compiler.failOnError}</failOnError>
  <fork default-value="false"/>
  <maxmem>${maven.compiler.maxmem}</maxmem>
  <meminitial>${maven.compiler.meminitial}</meminitial>
  <optimize default-value="false">${maven.compiler.optimize}</optimize>
  <outputDirectory>${project.build.outputDirectory}</outputDirectory>
  <outputFileName>${project.build.finalName}</outputFileName>
  <projectArtifact>${project.artifact}</projectArtifact>
  <showDeprecation default-value="false">${maven.compiler.showDeprecation}</showDeprecation>
  <showWarnings default-value="false">${maven.compiler.showWarnings}</showWarnings>
  <source>1.7</source>
  <staleMillis default-value="0">${lastModGranularityMs}</staleMillis>
  <target>1.7</target>
  <verbose default-value="false">${maven.compiler.verbose}</verbose>
</configuration>
[DEBUG] =======================================================================
[DEBUG] Dependency collection stats: {ConflictMarker.analyzeTime=4, ConflictMarker.markTime=2, ConflictMarker.nodeCount=349, ConflictIdSorter.graphTime=2, ConflictIdSorter.topsortTime=1, ConflictIdSorter.conflictIdCount=80, ConflictIdSorter.conflictIdCycleCount=0, ConflictResolver.totalTime=19, ConflictResolver.conflictItemCount=219, DefaultDependencyCollector.collectTime=1515, DefaultDependencyCollector.transformTime=38}
[DEBUG] org.mskcc.cbio:business:jar:1.0-SNAPSHOT
[DEBUG]    commons-collections:commons-collections:jar:3.2.1:compile
[DEBUG]    log4j:apache-log4j-extras:jar:1.1:compile
[DEBUG]    commons-dbcp:commons-dbcp:jar:1.4:compile
[DEBUG]       commons-pool:commons-pool:jar:1.5.4:compile
[DEBUG]    commons-beanutils:commons-beanutils:jar:1.9.1:compile
[DEBUG]       commons-logging:commons-logging:jar:1.1.1:compile
[DEBUG]    org.apache.httpcomponents:httpclient:jar:4.3.4:compile
[DEBUG]       commons-codec:commons-codec:jar:1.6:compile
[DEBUG]    org.apache.httpcomponents:httpcore:jar:4.3.2:compile
[DEBUG]    junit:junit:jar:4.8.2:compile
[DEBUG]    log4j:log4j:jar:1.2.16:compile
[DEBUG]    mysql:mysql-connector-java:jar:5.1.16:provided
[DEBUG]    org.slf4j:slf4j-log4j12:jar:1.6.6:compile
[DEBUG]    org.slf4j:slf4j-api:jar:1.6.6:compile
[DEBUG]    org.springframework:spring-core:jar:4.0.4.RELEASE:compile
[DEBUG]    org.springframework:spring-expression:jar:4.0.4.RELEASE:compile
[DEBUG]    org.springframework:spring-beans:jar:4.0.4.RELEASE:compile
[DEBUG]    org.springframework:spring-aop:jar:4.0.4.RELEASE:compile
[DEBUG]       aopalliance:aopalliance:jar:1.0:compile
[DEBUG]    org.springframework:spring-context:jar:4.0.4.RELEASE:compile
[DEBUG]    org.springframework:spring-context-support:jar:4.1.2.RELEASE:compile
[DEBUG]    org.springframework.integration:spring-integration-core:jar:4.1.0.RELEASE:compile
[DEBUG]       org.projectreactor:reactor-core:jar:1.1.4.RELEASE:compile
[DEBUG]          com.goldmansachs:gs-collections:jar:5.1.0:compile
[DEBUG]             com.goldmansachs:gs-collections-api:jar:5.1.0:compile
[DEBUG]          com.lmax:disruptor:jar:3.2.1:compile
[DEBUG]          io.gatling:jsr166e:jar:1.0:compile
[DEBUG]       org.springframework:spring-messaging:jar:4.1.2.RELEASE:compile
[DEBUG]       org.springframework.retry:spring-retry:jar:1.1.1.RELEASE:compile
[DEBUG]    org.springframework.integration:spring-integration-sftp:jar:4.1.0.RELEASE:compile
[DEBUG]       org.springframework.integration:spring-integration-stream:jar:4.1.0.RELEASE:compile
[DEBUG]       com.jcraft:jsch:jar:0.1.51:compile
[DEBUG]       org.springframework.integration:spring-integration-file:jar:4.1.0.RELEASE:compile
[DEBUG]          commons-io:commons-io:jar:2.4:compile
[DEBUG]    org.springframework:spring-tx:jar:4.0.4.RELEASE:compile
[DEBUG]    org.springframework:spring-orm:jar:4.0.4.RELEASE:compile
[DEBUG]    org.springframework:spring-jdbc:jar:4.0.4.RELEASE:compile
[DEBUG]    org.springframework:spring-webmvc:jar:4.0.4.RELEASE:compile
[DEBUG]    org.springframework:spring-web:jar:4.0.4.RELEASE:compile
[DEBUG]    org.springframework.security:spring-security-acl:jar:3.2.5.RELEASE:compile
[DEBUG]    org.springframework.security:spring-security-config:jar:3.2.5.RELEASE:compile
[DEBUG]    org.springframework.security:spring-security-core:jar:3.2.5.RELEASE:compile
[DEBUG]    org.springframework.security:spring-security-ldap:jar:3.2.5.RELEASE:compile
[DEBUG]       org.springframework.ldap:spring-ldap-core:jar:1.3.2.RELEASE:compile
[DEBUG]          commons-lang:commons-lang:jar:2.4:compile
[DEBUG]    org.springframework.security:spring-security-openid:jar:3.2.5.RELEASE:compile
[DEBUG]       com.google.inject:guice:jar:2.0:compile
[DEBUG]       org.openid4java:openid4java-nodeps:jar:0.9.6:compile
[DEBUG]          net.jcip:jcip-annotations:jar:1.0:compile
[DEBUG]       net.sourceforge.nekohtml:nekohtml:jar:1.9.20:runtime
[DEBUG]          xerces:xercesImpl:jar:2.10.0:runtime
[DEBUG]    org.springframework.security.extensions:spring-security-saml2-core:jar:1.0.0.RELEASE:compile
[DEBUG]       org.opensaml:opensaml:jar:2.6.1:compile
[DEBUG]          org.opensaml:openws:jar:1.5.1:compile
[DEBUG]             org.opensaml:xmltooling:jar:1.4.1:compile
[DEBUG]                org.bouncycastle:bcprov-jdk15:jar:1.46:compile
[DEBUG]                ca.juliusdavies:not-yet-commons-ssl:jar:0.3.9:compile
[DEBUG]             commons-httpclient:commons-httpclient:jar:3.1:compile
[DEBUG]             org.apache.santuario:xmlsec:jar:1.5.6:compile
[DEBUG]          org.apache.velocity:velocity:jar:1.7:compile
[DEBUG]          org.owasp.esapi:esapi:jar:2.0.1:compile
[DEBUG]          joda-time:joda-time:jar:2.2:compile
[DEBUG]          xalan:serializer:jar:2.7.1:runtime
[DEBUG]          xml-resolver:xml-resolver:jar:1.2:runtime
[DEBUG]          xalan:xalan:jar:2.7.1:runtime
[DEBUG]       xml-apis:xml-apis:jar:1.4.01:runtime
[DEBUG]    org.springframework.security:spring-security-taglibs:jar:3.2.5.RELEASE:compile
[DEBUG]    org.springframework.security:spring-security-web:jar:3.2.5.RELEASE:compile
[DEBUG]    org.mybatis:mybatis-spring:jar:1.2.2:compile
[DEBUG]    org.mybatis:mybatis:jar:3.2.7:compile
[DEBUG]    org.springframework.social:spring-social-config:jar:1.1.0.RELEASE:compile
[DEBUG]    org.springframework.social:spring-social-core:jar:1.1.0.RELEASE:compile
[DEBUG]    org.springframework.social:spring-social-security:jar:1.1.0.RELEASE:compile
[DEBUG]    org.springframework.social:spring-social-web:jar:1.1.0.RELEASE:compile
[DEBUG]       javax.inject:javax.inject:jar:1:compile
[DEBUG]    org.springframework.social:spring-social-google:jar:1.0.0.RELEASE:compile
[DEBUG]       com.fasterxml.jackson.core:jackson-annotations:jar:2.3.3:compile
[DEBUG]       com.fasterxml.jackson.core:jackson-core:jar:2.3.3:compile
[DEBUG]       com.fasterxml.jackson.core:jackson-databind:jar:2.3.3:compile
[INFO]
[INFO] --- maven-resources-plugin:2.6:copy-resources (copy-parent-resources) @ business ---
[DEBUG] Dependency collection stats: {ConflictMarker.analyzeTime=1, ConflictMarker.markTime=1, ConflictMarker.nodeCount=77, ConflictIdSorter.graphTime=0, ConflictIdSorter.topsortTime=0, ConflictIdSorter.conflictIdCount=26, ConflictIdSorter.conflictIdCycleCount=0, ConflictResolver.totalTime=5, ConflictResolver.conflictItemCount=74, DefaultDependencyCollector.collectTime=760, DefaultDependencyCollector.transformTime=7}
[DEBUG] org.apache.maven.plugins:maven-resources-plugin:jar:2.6:
[DEBUG]    org.apache.maven:maven-plugin-api:jar:2.0.6:compile
[DEBUG]    org.apache.maven:maven-project:jar:2.0.6:compile
[DEBUG]       org.apache.maven:maven-profile:jar:2.0.6:compile
[DEBUG]       org.apache.maven:maven-artifact-manager:jar:2.0.6:compile
[DEBUG]       org.apache.maven:maven-plugin-registry:jar:2.0.6:compile
[DEBUG]    org.apache.maven:maven-core:jar:2.0.6:compile
[DEBUG]       org.apache.maven:maven-plugin-parameter-documenter:jar:2.0.6:compile
[DEBUG]       org.apache.maven.reporting:maven-reporting-api:jar:2.0.6:compile
[DEBUG]          org.apache.maven.doxia:doxia-sink-api:jar:1.0-alpha-7:compile
[DEBUG]       org.apache.maven:maven-repository-metadata:jar:2.0.6:compile
[DEBUG]       org.apache.maven:maven-error-diagnostics:jar:2.0.6:compile
[DEBUG]       commons-cli:commons-cli:jar:1.0:compile
[DEBUG]       org.apache.maven:maven-plugin-descriptor:jar:2.0.6:compile
[DEBUG]       org.codehaus.plexus:plexus-interactivity-api:jar:1.0-alpha-4:compile
[DEBUG]       classworlds:classworlds:jar:1.1:compile
[DEBUG]    org.apache.maven:maven-artifact:jar:2.0.6:compile
[DEBUG]    org.apache.maven:maven-settings:jar:2.0.6:compile
[DEBUG]    org.apache.maven:maven-model:jar:2.0.6:compile
[DEBUG]    org.apache.maven:maven-monitor:jar:2.0.6:compile
[DEBUG]    org.codehaus.plexus:plexus-container-default:jar:1.0-alpha-9-stable-1:compile
[DEBUG]       junit:junit:jar:3.8.1:compile
[DEBUG]    org.codehaus.plexus:plexus-utils:jar:2.0.5:compile
[DEBUG]    org.apache.maven.shared:maven-filtering:jar:1.1:compile
[DEBUG]       org.sonatype.plexus:plexus-build-api:jar:0.0.4:compile
[DEBUG]    org.codehaus.plexus:plexus-interpolation:jar:1.13:compile
[DEBUG] Created new class realm plugin>org.apache.maven.plugins:maven-resources-plugin:2.6
[DEBUG] Importing foreign packages into class realm plugin>org.apache.maven.plugins:maven-resources-plugin:2.6
[DEBUG]   Imported:  < maven.api
[DEBUG] Populating class realm plugin>org.apache.maven.plugins:maven-resources-plugin:2.6
[DEBUG]   Included: org.apache.maven.plugins:maven-resources-plugin:jar:2.6
[DEBUG]   Included: org.apache.maven.reporting:maven-reporting-api:jar:2.0.6
[DEBUG]   Included: org.apache.maven.doxia:doxia-sink-api:jar:1.0-alpha-7
[DEBUG]   Included: commons-cli:commons-cli:jar:1.0
[DEBUG]   Included: org.codehaus.plexus:plexus-interactivity-api:jar:1.0-alpha-4
[DEBUG]   Included: junit:junit:jar:3.8.1
[DEBUG]   Included: org.codehaus.plexus:plexus-utils:jar:2.0.5
[DEBUG]   Included: org.apache.maven.shared:maven-filtering:jar:1.1
[DEBUG]   Included: org.sonatype.plexus:plexus-build-api:jar:0.0.4
[DEBUG]   Included: org.codehaus.plexus:plexus-interpolation:jar:1.13
[DEBUG] Configuring mojo org.apache.maven.plugins:maven-resources-plugin:2.6:copy-resources from plugin realm ClassRealm[plugin>org.apache.maven.plugins:maven-resources-plugin:2.6, parent: sun.misc.Launcher$AppClassLoader@4e25154f]
[DEBUG] Configuring mojo 'org.apache.maven.plugins:maven-resources-plugin:2.6:copy-resources' with basic configurator -->
[DEBUG]   (f) buildFilters = [/net/home/marcherm/git/cbioportal/business/${PORTAL_HOME}/src/main/resources/portal.properties]
[DEBUG]   (f) encoding = UTF-8
[DEBUG]   (f) escapeWindowsPaths = true
[DEBUG]   (s) includeEmptyDirs = false
[DEBUG]   (s) outputDirectory = /net/home/marcherm/git/cbioportal/business/target/classes
[DEBUG]   (s) overwrite = false
[DEBUG]   (f) project = MavenProject: org.mskcc.cbio:business:1.0-SNAPSHOT @ /net/home/marcherm/git/cbioportal/business/pom.xml
[DEBUG]   (s) directory = ${PORTAL_HOME}/src/main/resources
[DEBUG]   (s) includes = [**/*.properties]
[DEBUG]   (s) excludes = [**/portal.properties.*, **/log4j.properties.*, **/*.EXAMPLE]
[DEBUG]   (s) resources = [Resource {targetPath: null, filtering: false, FileSet {directory: ${PORTAL_HOME}/src/main/resources, PatternSet [includes: {**/*.properties}, excludes: {**/portal.properties.*, **/log4j.properties.*, **/*.EXAMPLE}]}}]
[DEBUG]   (f) session = org.apache.maven.execution.MavenSession@26b894bd
[DEBUG]   (f) supportMultiLineFiltering = false
[DEBUG]   (f) useBuildFilters = true
[DEBUG]   (s) useDefaultDelimiters = true
[DEBUG] -- end configuration --
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary:
[INFO]
[INFO] Portal Master ...................................... SUCCESS [  0.004 s]
[INFO] Portal Business Layer .............................. FAILURE [  3.481 s]
[INFO] Portal Core ........................................ SKIPPED
[INFO] Portal Web Layer ................................... SKIPPED
[INFO] cBio Cancer Genomics Portal ........................ SKIPPED
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 3.738 s
[INFO] Finished at: 2015-05-06T14:04:05+02:00
[INFO] Final Memory: 26M/1963M
[INFO] ------------------------------------------------------------------------
[ERROR] Failed to execute goal org.apache.maven.plugins:maven-resources-plugin:2.6:copy-resources (copy-parent-resources) on project business: Error loading property file '/net/home/marcherm/git/cbioportal/business/${PORTAL_HOME}/src/main/resources/portal.properties' -> [Help 1]
org.apache.maven.lifecycle.LifecycleExecutionException: Failed to execute goal org.apache.maven.plugins:maven-resources-plugin:2.6:copy-resources (copy-parent-resources) on project business: Error loading property file '/net/home/marcherm/git/cbioportal/business/${PORTAL_HOME}/src/main/resources/portal.properties'
        at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:216)
        at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:153)
        at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:145)
        at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject(LifecycleModuleBuilder.java:116)
        at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject(LifecycleModuleBuilder.java:80)
        at org.apache.maven.lifecycle.internal.builder.singlethreaded.SingleThreadedBuilder.build(SingleThreadedBuilder.java:51)
        at org.apache.maven.lifecycle.internal.LifecycleStarter.execute(LifecycleStarter.java:128)
        at org.apache.maven.DefaultMaven.doExecute(DefaultMaven.java:307)
        at org.apache.maven.DefaultMaven.doExecute(DefaultMaven.java:193)
        at org.apache.maven.DefaultMaven.execute(DefaultMaven.java:106)
        at org.apache.maven.cli.MavenCli.execute(MavenCli.java:862)
        at org.apache.maven.cli.MavenCli.doMain(MavenCli.java:286)
        at org.apache.maven.cli.MavenCli.main(MavenCli.java:197)
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.lang.reflect.Method.invoke(Method.java:497)
        at org.codehaus.plexus.classworlds.launcher.Launcher.launchEnhanced(Launcher.java:289)
        at org.codehaus.plexus.classworlds.launcher.Launcher.launch(Launcher.java:229)
        at org.codehaus.plexus.classworlds.launcher.Launcher.mainWithExitCode(Launcher.java:415)
        at org.codehaus.plexus.classworlds.launcher.Launcher.main(Launcher.java:356)
Caused by: org.apache.maven.plugin.MojoExecutionException: Error loading property file '/net/home/marcherm/git/cbioportal/business/${PORTAL_HOME}/src/main/resources/portal.properties'
        at org.apache.maven.plugin.resources.ResourcesMojo.execute(ResourcesMojo.java:307)
        at org.apache.maven.plugin.DefaultBuildPluginManager.executeMojo(DefaultBuildPluginManager.java:134)
        at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:208)
        ... 20 more
Caused by: org.apache.maven.shared.filtering.MavenFilteringException: Error loading property file '/net/home/marcherm/git/cbioportal/business/${PORTAL_HOME}/src/main/resources/portal.properties'
        at org.apache.maven.shared.filtering.DefaultMavenFileFilter.loadProperties(DefaultMavenFileFilter.java:290)
        at org.apache.maven.shared.filtering.DefaultMavenFileFilter.getDefaultFilterWrappers(DefaultMavenFileFilter.java:205)
        at org.apache.maven.shared.filtering.DefaultMavenResourcesFiltering.filterResources(DefaultMavenResourcesFiltering.java:161)
        at org.apache.maven.plugin.resources.ResourcesMojo.execute(ResourcesMojo.java:301)
        ... 22 more
Caused by: java.io.FileNotFoundException: /net/home/marcherm/git/cbioportal/business/${PORTAL_HOME}/src/main/resources/portal.properties
        at org.apache.maven.shared.filtering.PropertyUtils.loadPropertyFile(PropertyUtils.java:65)
        at org.apache.maven.shared.filtering.DefaultMavenFileFilter.loadProperties(DefaultMavenFileFilter.java:284)
        ... 25 more
[ERROR]
[ERROR]
[ERROR] For more information about the errors and possible solutions, please read the following articles:
[ERROR] [Help 1] http://cwiki.apache.org/confluence/display/MAVEN/MojoExecutionException
[ERROR]
[ERROR] After correcting the problems, you can resume the build with the command
[ERROR]   mvn <goals> -rf :business

Add CANCER_TYPE, CANCER_TYPE_DETAILED to patient view

Should be:

DMP0041 M, 56 years old, Esophagogastric Carcinoma (Adenocarcinoma of the Gastroesophageal Junction), LIVING (13 months)

Change patient details formatting on patient view

• Remove "(Stomach)” behind age

• Put detailed cancer type in parentheses i.e.

  Esophagogastric Carcinoma (Stomach Adenocarcinoma)

Loading of mutation lollipops can be very slow (local install only)

(Note: this only appears to happen w/i my local installation, following the wiki docs, and not on the production site).

But, in a nutshell, I have noticed that loading of mutation lollipops can be quite slow.

So far, I have traced it to this request: http://localhost:8080/cbioportal/getPfamSequence.json?geneSymbol=EGFR

this one request can take 1-2 seconds on my local machine, and seems to account for most of the delay.

looking into this further, and also looping in @onursumer, as I think he may have worked on this a while back...

update cancer genes with new impact list

Pan-Sample Summary Stats

As discussed with @schultzn, I / we would like a way to visualize / summarize genomic alterations across multiple cancer types within one study. For example, if you have a large study (such as MSK-IMPACT or DFCI Profile), there should be a way to enter a gene or gene set, and see the frequency of alterations across all cancer types within that study. I have gotten this request about 5 times since starting at DFCI, and therefore think it is high priority for us. Again, not sure of timeline, but my group can volunteer for implementation. Starting this issue to gather initial feedback.

One thought also is that if one queries across some very large set of samples, e.g. >2K, we replace the OncoPrint tab (which is too slow for this many samples), and replace with a summary stats tab.

Cancer Genes List Documentation

Is the Cancer Genes List functionality already supported, e.g. providing a list of genes within a targeted panel?

If so, can someone please add a wiki page with documentation?

Add log rank p value for survival plots on study view

At least add p values for two group comparison.

Using Docker to streamline Setup

Docker is a tool for helping developers create images to be deployed anywhere: in the cloud, on your in house server, or on your personal machine. There are already docker base images for MySQL and Apache Tomcat and I think that we may be able to build on those images to create a cBioPortal database image, a cBioPortal server image, etc.

I think that Docker might allow people to avoid installing MySQL and importing data. This might reduce the number of problems that people have as well as lower the bar of entry for new users.

Some links from my little bit of research:

• https://www.docker.com/
• on managing data within containers (e.g. for MySQL): http://docs.docker.com/userguide/dockervolumes/
• MySQL image: https://registry.hub.docker.com/_/mysql/
• Tomcat image: https://registry.hub.docker.com/_/tomcat/

Patient View Page tries to go to OncoKB

When I open up a patient view page on my local installation, I see spinning circles next to each gene.

Trying to debug this, I see an error message in the console about not being able to connect to oncokb:

Single sample view include patient info

On a single sample view, we want to include the patient info and show the tree

• https://cbioportal.mskcc.org/case.do?cancer_study_id=mskimpact&sample_id=P-0001104-T03-IM3

The more about this tumor button should disappear:

• https://cbioportal.mskcc.org/case.do?sample_id=TCGA-AP-A0LF-01&cancer_study_id=ucec_tcga_pub