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Installing nrseq-fasta-importer

1. Install MySQL, Java, and Apache Tomcat (if necessary)

This documentation assumes that Java (JDK version, 1.7 or later) and the Apache Tomcat (7 or later) servlet container are installed on the same computer on which you are installing ProXL. (Note: Apache Tomcat requires the JDK version of Java be installed.)

This documentation also assumes that MySQL (5.6 or later) has been installed and is accessible by the installation of Apache Tomcat. This does not need to be on the same machine as Apache Tomcat.

These software (and nrseq-fasta-importer) should work equally well on any operating system for which MySQL and Java are available (MS Windows, Apple OS X, or Linux). Other servlet containers and database server software may work as well, though this documentation assumes that the above are installed. Please refer to the respective websites for more information about MySQL, Java, or Apache Tomcat installation.

You may need to download and install the MySQL JDBC driver. This is available from the MySQL Connector/J website. To install, copy the downloaded jar file into $CATALINA_HOME/lib directory on the server on which Apache Tomcat is installed (e.g. /usr/local/apache-tomcat-7.0.65/lib).

2. Set up the YRC_NRSEQ database

To set up this database, first download :download:`YRC_NRSEQ_create.sql <../Database/YRC_NRSEQ_create.sql>`. To run this SQL script, you may log into your MySQL server and either paste in the contents of this file to MySQL or use source /location/to/YRC_NRSEQ_create.sql. To use the latter, the .sql file must be in a directory to which MySQL has read access.

3. Set up the nrseq_fasta_importer database

To set up this database, first download :download:`database_schema_create.sql <../Database/database_schema_create.sql>`. To run this SQL script, you may log into your MySQL server and either paste in the contents of this file to MySQL or (preferably) use source /location/to/database_schema_create.sql. To use the latter, the .sql file must be in a directory to which MySQL has read access.

Update configuration table

Download and open :download:`config_inserts.sql <../Database/config_inserts.sql>` in a text editor. Edit the SQL statements to reflect your configuration options--see the comments in the file for information about the options. Once finished either:

  1. Paste the file into MySQL
    1. Copy the contents of the file
    2. Type USE nrseq_fasta_importer; in MySQL
    3. Paste contents of the file.
  2. Save the file and source /location/to/config_inserts.sql.

4. Configure Apache Tomcat database connection

This section describes how to connect Tomcat to the YRC_NRSEQ and nrseq_fasta_importer databases.

On the MySQL side:

Log in to MySQL as root:
shell> mysql --user=root mysql

Create the MySQL user:
mysql> CREATE USER 'nrseq_user'@'localhost' IDENTIFIED BY 'password';

Replace nrseq_user with the username you would prefer, localhost with the
relative hostname of the machine connecting to the MySQL database (usually localhost),
and password with your preferred password.

Grant the necessary privileges in MySQL:
GRANT ALL ON YRC_NRSEQ.* TO 'nrseq_user'@'localhost'
GRANT ALL ON nrseq_fasta_importer.* TO 'nrseq_user'@'localhost'

Replace nrseq_user and localhost with the username and hostname you used
when creating the user.

On the Tomcat side:

Add the following to $CATALINA_HOME/conf/context.xml, inside the <Context></Context> root element. Be sure to change nrseq_user and password to the username and password you set up above. If necessary, change localhost and 3306 to the hostname and port of your MySQL server.

<Resource     name="jdbc/nrseq_fasta_importer"
              auth="Container"
              type="javax.sql.DataSource"
              factory="org.apache.commons.dbcp.BasicDataSourceFactory"
              maxActive="50"
              maxIdle="1"
              maxWait="10000"

                                      minIdle="0"
                                      minEvictableIdleTimeMillis="21600000"
                                      timeBetweenEvictionRunsMillis="30000"
                                      validationQuery="select 1 from dual"
                                      testOnBorrow="true"






              username="nrseq_user"
              password="password"
              driverClassName="com.mysql.jdbc.Driver"
              url="jdbc:mysql://localhost:3306/nrseq_fasta_importer?autoReconnect=true&amp;tcpKeepAlive=true&amp;useUnicode=true&amp;characterEncoding=ISO8859_1&amp;characterSetResults=ISO8859_1"/>

<Resource     name="jdbc/nrseq"
              auth="Container"
              type="javax.sql.DataSource"
              factory="org.apache.tomcat.dbcp.dbcp.BasicDataSourceFactory"
              maxActive="10"
              maxIdle="1"
              maxWait="10000"

                                      minIdle="0"
                                      minEvictableIdleTimeMillis="21600000"
                                      timeBetweenEvictionRunsMillis="30000"

                                      validationQuery="select 1 from dual"
                                      testOnBorrow="true"



              username="nrseq_user"
              password="password"
              driverClassName="com.mysql.jdbc.Driver"
              url="jdbc:mysql://localhost:3306/YRC_NRSEQ?autoReconnect=true"/>

5. Install WAR file into Apache Tomcat

Download the latest release of nrseq-fasta-importer from github at https://github.com/yeastrc/nrseq-fasta-importer/releases

Unzip the downloaded file and copy nrseq-fasta-importer.war into $CATALINA_HOME/webapps/. The WAR file should automatically deploy. If not, restart Tomcat to force the file to deploy.

Your web application should now be available at http://your.host:8080/nrseq-fasta-importer/ (Depending on how you have configured your web server, the :8080 may not be different or not required.) If you have a firewall running, will need to allow access through this port.

6. Configure security for Apache Tomcat (optional but recommended)

To prevent unauthorized access to your nrseq-fasta-importer web application, it is recommended that you set up user authentication. These instructions describe how to set up basic authentication for Tomcat. For more detailed instructions, see https://tomcat.apache.org/tomcat-7.0-doc/realm-howto.html

First, add the following lines within the <tomcat-users></tomcat-users> element in $CATALINA_HOME/conf/tomcat-users.xml. Substitute USERNAME and PASSWORD with the username and password you wish to use to secure access to your web application.

<role rolename="nrseq-fasta-upload-group"/>
<user username="USERNAME" password="PASSWORD" roles="nrseq-fasta-upload-group"/>

Second, add the following lines within the <web-app></web-app> root element in $CATALINA_HOME/webapps/nrseq-fasta-importer/WEB-INF/web.xml (the web.xml for your deployed nrseq-fasta-importer web app).

<security-constraint>
        <web-resource-collection>
                <web-resource-name>NRSEQ FASTA Upload Server</web-resource-name>
                <url-pattern>/*</url-pattern>
        </web-resource-collection>
        <auth-constraint>
                <description>Authorized NRSEQ FASTA Upload User</description>
                <role-name>nrseq-fasta-upload-group</role-name>
        </auth-constraint>
</security-constraint>
<security-role>
        <role-name>nrseq-fasta-upload-group</role-name>
</security-role>
<login-config>
        <auth-method>BASIC</auth-method>
        <realm-name>nrseq-fasta-upload-server</realm-name>
</login-config>

You will need to restart Tomcat for these changes to take effect.