ndb

Web application and database providing a harmonized and comprehensive collection of genetic variants published in peer-reviewed literature.

For the latest application code, see the development branch.

Prerequisites

• Java 8
• Tomcat 8.5
• MySQL 5.7+
• Maven 3.0.5+

Local installation

1. Clone the git repository.

2. Create these two files (content is an example only) in your home directory:

   ndb.properties

   ndb.db=ndb_staging
   ndb.email[email protected]
   ndb.admin.email[email protected]

   db.properties

   ndb_staging.url=java:comp/env/jdbc/ndb_staging
   ndb_staging.username=[USER]
   ndb_staging.password=[PASSWORD]

3. Add the <Resource/> tag to your Tomcat configuration under conf/context.xml:

   <?xml version="1.0" encoding="UTF-8"?>
   <Context>
       <Resource
           name="jdbc/ndb_staging"
           type="javax.sql.DataSource"
           factory="org.apache.tomcat.jdbc.pool.DataSourceFactory"
           maxActive="100"
           maxIdle="30"
           maxWait="10000"
           testWhileIdle="true"
           timeBetweenEvictionRunsMillis="300000"
           url="jdbc:mysql://localhost/ndb_staging"
           driverClassName="com.mysql.cj.jdbc.Driver"
           initialSize="0"
           alternateUsernameAllowed="true"/>
   </Context>

Now, all you need to do is to deploy the ndb.war file.

Build from sources

mvn package

To run integration tests, you will need to configure a test database and specify some options in your Maven configuration.

In your ~/.m2/ directory, add or edit your settings.xml file.

<?xml version="1.0"?>
<settings>
    <!-- see quimby /local/bamboo/.m2/settings.xml -->
    <localRepository>/home/[LINUXUSER]/.m2/repository</localRepository>
    <profiles>
        <profile>
            <id>dev</id>
            <properties>
                <!-- ndb production configuration (only required for dumping data & updating the heatmap) -->
                <ndb.db.host>[HOST]</ndb.db.host>
                <ndb.db.port>[PORT]</ndb.db.port>
                <ndb.db.database>[DATABASE]</ndb.db.database>
                <ndb.db.user>[USER]</ndb.db.user>
                <ndb.db.password>[PASSWORD]</ndb.db.password>
                <!-- ndb testing configuration -->
                <ndb.testdb.name>ndbtest</ndb.testdb.name>
                <ndb.testdb.build.user>[USER]</ndb.testdb.build.user>
                <ndb.testdb.build.password>[PASSWORD]</ndb.testdb.build.password>
                <ndb.testdb.build.url>jdbc:mysql://127.0.0.1:3306/ndbtest</ndb.testdb.build.url>
            </properties>
        </profile>
    </profiles>
    <activeProfiles>
        <activeProfile>dev</activeProfile>
        <activeProfile>local-deploy</activeProfile>
        <!--activeProfile>eclipse build</activeProfile-->
    </activeProfiles>
</settings>

Update the heatmap and data dumps

To update the heatmap and data dumps, you must provide -Pexport-data-and-visualization flag to Maven. Generating the heatmap and VCF output require Python 3, Bokeh and Pandas. (optional)

mvn package -Pexport-data-and-visualization

The heatmap will be updated under src/main/webapp/resources/static/variant_heatmap_latest.html and the data export under target/etc/data/export_latest.tsv and target/etc/data/export_latest.vcf.

Live deployment

Contact [email protected] for further information.

Troubleshooting

com.mysql.jdbc.driver problem

If you get errors with com.mysql.jdbc.driver during deployment, download mysql-connector-java, unpack it and put the JAR to your Tomcat lib/ directory.

sql_mode=only_full_group_by problem

If the project is deployed but instead of homepage you see an error like this:

Expression #1 of SELECT list is not in GROUP BY clause and contains nonaggregated column 'gene_id' which is not functionally dependent on columns in GROUP BY clause; this is incompatible with sql_mode=only_full_group_by This can be fixed by configuration via the instructions here for creating a local.cnf file: Developer Workstation Setup#MySQL

Alternatively, the manual instructions:

• Then run a mysql terminal and remove the 'ONLY_FULL_GROUP_BY' flag from global.sql_mode variable.
• Useful commands for that:

#returns current content of the sql_mode variable
mysql> select @@global.sql_mode;

#Copy-pasted the output of the first command and removed the ONLY_FULL_GROUP_BY part
mysql> set GLOBAL sql_mode = 'STRICT_TRANS_TABLES,NO_ZERO_IN_DATE,NO_ZERO_DATE,ERROR_FOR_DIVISION_BY_ZERO,NO_AUTO_CREATE_USER,NO_ENGINE_SUBSTITUTION'

Authors

• Pavlidis Lab - Developers and maintainers - GitHub

See also the list of contributors who participated in this project.

License

The source code for this project is licensed under the Apache 2.0 - see the LICENSE file for details