You will learn

How to upgrade from 2.8.5 or 2.8.5.1 to 2.8.6.1

Prerequisites

Audience: IT Professional and/or End User
Difficulty: Advanced
Time needed: Approximately 60 minutes
Tools required: Tomcat, MySQL or MS SQL Server

ALWAYS PERFORM A FULL BACKUP OF YOUR DATABASE BEFORE ATTEMPTING ANY UPGRADE!

MySQL Server: You can run the mysqldump command from the MySQL server, e.g., mysqldump -u mydbuser -p mydatabase > path/to/backup.sql (we do not recommend using MySQL Workbench to perform the backup).

MS SQL Server: Using SSMS, right-click on the database, select Tasks → Back Up…, then choose the location & name of the backup file and click OK.

The National Vulnerability Database has identified a high risk exploit, Spring4Shell, which affects applications running Tomcat as a WAR deployment. To mitigate risk of exposure ThreadFix recommends users update their Tomcat to the latest (8.5.78 at a minimum) in addition to upgrading to ThreadFix 2.8.6.1.

If you have any questions or concerns or if you wish to upgrade from an older version of ThreadFix, please reach out to our support team here: support@threadfix.it

ThreadFix Deployment Update

Follow these steps to deploy the updated version of ThreadFix:

Stop the Tomcat instance on which ThreadFix is running.
Move your current ThreadFix deployment directory from your Tomcat webapps folder into a backup directory.
1. webapps directory location: //TOMCAT_HOME/webapps
Copy the updated ThreadFix folder from your new artifact into your webapps directory.
1. webapps directory location: //TOMCAT_HOME/webapps
Copy the following files from your backed up ThreadFix directory to the newly updated ThreadFix directory:
(FROM: <previous-threadfix-deploy>/WEB-INF/classes/, TO: <new-threadfix-deploy>/WEB-INF/classes/, except as noted below)
1. custom.properties
2. ESAPI.properties
  If upgrading from 2.8.5, see REQUIRED update below:
  1. Be sure that Log4jfactory is no longer referenced as the ESAPI.Logger in your ESAPI.properties.
  2. Replace with ESAPI.Logger=com.denimgroup.threadfix.logging.esapi.slf4j.CustomESAPISlf4jLogFactory
3. jdbc.properties
4. jms.properties
5. threadfix.license
6. If you've updated any of these in your previous deployment, copy them as well:
  1. <threadfix-deploy>/WEB-INF/security.xml
    If upgrading from 2.8.5, see REQUIRED update below:
    - Replace bean definition in security.xml file:
      <bean id="velocityEngine" class="org.springframework.security.saml.util.VelocityFactory" factory-method="getEngine"/>
    - With:
      <bean id="velocityEngine" class="com.denimgroup.threadfix.service.saml.CustomSamlVelocityFactory" factory-method="getEngine"/>
  2. <threadfix-deploy>/WEB-INF/classes/security/samlKeystore.jks (and/or any other Java keystore that you've saved in this directory)
  3. Note: If upgrading from 2.8.5, do not copy log4j.xml. As of version 2.8.5.1, log4j.xml was replaced with logback.xml, so there’s no need to copy log4j.xml from your previous artifact.
    - Any changes that you had made in log4j.xml will need to be made in logback.xml if you want them to persist.
Copy the velocityTemplates directory from your backed up ThreadFix directory to the newly-updated ThreadFix directory.
(FROM: <previous-threadfix-deploy> TO:<new-threadfix-deploy>)
In Linux environments, you may need to grant your tomcat user/group ownership and permissions to the newly-deployed artifact.
Examples:
sudo chown -R tomcat:tomcat /opt/tomcat sudo chmod -R 775 /opt/tomcat
Cleanup - Delete the following:
1. The contents of the <tomcat-deploy>/work directory
2. Your web browser's cache/history

Before-Restart Database Updates

Database Updates

Do Not Restart Tomcat If Scripts Do Not Complete

If you receive an error when running before-restart database update scripts, please report the issue to ThreadFix Support (create a ticket in Service Desk), including a screenshot of the script & error message.

You should NOT proceed to start Tomcat until the issue is resolved. If you do, Hibernate may make unrecoverable changes that will require you to restore your database from backup.

Caution/warning messages are OK; just not errors.

Expand the MySQL or MS SQL Server code block to reveal the scripts:

INSERT INTO RemoteProviderAuthenticationField (filterable, name, placeholder, required, secret, type, applicationId)
VALUES (0, 'Application Type', null, 1, 0, 'select', (SELECT id FROM RemoteProviderType WHERE name = 'Contrast'));
  
INSERT INTO SelectOption(tip, value)
VALUES (null, 'Environments'),
       (null, 'Modules');
  
INSERT INTO RemoteProviderAuthenticationField_SelectOption_Join(remoteProviderAuthenticationField_id, selectOptions_id)
VALUES ((SELECT id FROM RemoteProviderAuthenticationField WHERE name = 'Application Type'),
        (SELECT id FROM SelectOption WHERE value = 'Environments')),
       ((SELECT id FROM RemoteProviderAuthenticationField WHERE name = 'Application Type'),
        (SELECT id FROM SelectOption WHERE value = 'Modules'));
  
create table RemoteProviderNativeMetadataKey
(
    id                   int auto_increment
        primary key,
    name                 varchar(60) not null,
    remoteProviderTypeId int         null,
    constraint RemoteProviderNativeMetadata_RemoteProviderType_id_fk
        foreign key (remoteProviderTypeId) references RemoteProviderType (id)
);
  
create table RemoteProviderNativeMetadataValue
(
    id                                int auto_increment
        primary key,
    value                             varchar(512) not null,
    remoteProviderApplicationId       int          not null,
    remoteProviderNativeMetadataKeyId int          not null,
    constraint RPNativeMetadataValue_RPApplication_id_fk
        foreign key (remoteProviderApplicationId) references RemoteProviderApplication (id),
    constraint RPNativeMetadataValue_RPNativeMetadataKey_id_fk
        foreign key (remoteProviderNativeMetadataKeyId) references RemoteProviderNativeMetadataKey (id)
);
  
INSERT INTO RemoteProviderNativeMetadataKey(name, remoteProviderTypeId)
VALUES ('Environment', (SELECT id FROM RemoteProviderType WHERE name = 'Contrast'));
 
INSERT INTO ChannelType (name,url,version,exportInfo,customChannel,isDenyListMode,isPenTestChannel)
SELECT 'GitHub',
        'https://github.com/',
        '1.0.0',
        'Use as a Remote Provider',
        FALSE,TRUE,FALSE
       WHERE NOT EXISTS (
       SELECT name FROM ChannelType WHERE name = 'GitHub');
 
SET @channelId = (SELECT id FROM ChannelType WHERE name = 'GitHub');
 
 
INSERT INTO RemoteProviderType (encrypted,hasApiKey,hasUserNamePassword,findingSyncEnabled,name,channelTypeId)
SELECT FALSE, FALSE, FALSE, FALSE,
        'GitHub Beta',
        @channelId
        WHERE NOT EXISTS (
        SELECT name FROM RemoteProviderType WHERE name = 'GitHub Beta' AND channelTypeId = @channelId
      );
 
SET @remoteProChannelId = (SELECT id FROM RemoteProviderType WHERE name = 'GitHub Beta');
 
INSERT INTO RemoteProviderAuthenticationField (filterable,name,placeholder,required,secret,type,applicationId)
SELECT FALSE,
    'Owner',
    'GitHub Repositories Owner',
    TRUE,
    FALSE,
    NULL,
    @remoteProChannelId
    WHERE NOT EXISTS (
    SELECT name FROM RemoteProviderAuthenticationField WHERE applicationId = @remoteProChannelId and name = 'Owner'
  );
 
INSERT INTO RemoteProviderAuthenticationField (filterable,name,placeholder,required,secret,type,applicationId)
SELECT FALSE,
    'OAuth Token',
    NULL,
    TRUE,
    TRUE,
    NULL,
    @remoteProChannelId
    WHERE NOT EXISTS (
    SELECT name FROM RemoteProviderAuthenticationField WHERE applicationId = @remoteProChannelId and name = 'OAuth Token'
  );
 
INSERT INTO RemoteProviderAuthenticationEntity(encryptedValue, value, remoteProviderAuthenticationFieldId, remoteProviderEntityId)
(SELECT NULL, 'Modules', rpafId, rpeId FROM
((SELECT rpe.id AS rpeId
FROM RemoteProviderEntity rpe
INNER JOIN RemoteProviderType rpt ON rpt.id = rpe.remoteProviderTypeId
WHERE rpt.name = 'Contrast') AS a,
(SELECT id as rpafId
FROM RemoteProviderAuthenticationField WHERE name = 'Application Type'
AND applicationId = (SELECT id FROM RemoteProviderType WHERE name = 'Contrast'))
AS b));
 
UPDATE ChannelVulnerability cv
JOIN ChannelType ct ON cv.channelTypeId = ct.id
SET channelTypeId = (
    SELECT ChannelType.id
    FROM ChannelType
    WHERE ChannelType.name = 'AppScan Source')
WHERE ct.name = 'AppScan Source Edition';

INSERT INTO RemoteProviderAuthenticationField (filterable, name, placeholder, required, secret, type, applicationId)
VALUES (0, 'Application Type', null, 1, 0, 'select', (SELECT id FROM RemoteProviderType WHERE name = 'Contrast'));
 
INSERT INTO SelectOption(tip, value)
VALUES (null, 'Environments'),
       (null, 'Modules');
 
INSERT INTO RemoteProviderAuthenticationField_SelectOption_Join(remoteProviderAuthenticationField_id, selectOptions_id)
VALUES ((SELECT id FROM RemoteProviderAuthenticationField WHERE name = 'Application Type'),
        (SELECT id FROM SelectOption WHERE value = 'Environments')),
       ((SELECT id FROM RemoteProviderAuthenticationField WHERE name = 'Application Type'),
        (SELECT id FROM SelectOption WHERE value = 'Modules'));
 
CREATE TABLE RemoteProviderNativeMetadataKey
(
    id                     int IDENTITY(1,1) NOT NULL,
    name                   varchar(60) NOT NULL,
    remoteProviderTypeId   int
) ON [PRIMARY]
GO
 
ALTER TABLE RemoteProviderNativeMetadataKey
    ADD CONSTRAINT PK_RemoteProviderNativeMetadataKey PRIMARY KEY CLUSTERED (id)
GO
 
ALTER TABLE RemoteProviderNativeMetadataKey
    ADD CONSTRAINT RemoteProviderNativeMetadata_RemoteProviderType_id_fk FOREIGN KEY (remoteProviderTypeId) REFERENCES RemoteProviderType (id);
GO
 
 
CREATE TABLE RemoteProviderNativeMetadataValue
(
    id                                 int IDENTITY(1,1) NOT NULL,
    value                              varchar(512) NOT NULL,
    remoteProviderApplicationId        int NOT NULL,
    remoteProviderNativeMetadataKeyId  int NOT NULL
) ON [PRIMARY]
GO
 
ALTER TABLE RemoteProviderNativeMetadataValue
    ADD CONSTRAINT PK_RemoteProviderNativeMetadataValue PRIMARY KEY CLUSTERED (id)
GO
 
ALTER TABLE RemoteProviderNativeMetadataValue
    ADD CONSTRAINT RPNativeMetadataValue_RPApplication_id_fk FOREIGN KEY (remoteProviderApplicationId) REFERENCES RemoteProviderApplication (id);
GO
 
ALTER TABLE RemoteProviderNativeMetadataValue
    ADD CONSTRAINT RPNativeMetadataValue_RPNativeMetadataKey_id_fk FOREIGN KEY (remoteProviderNativeMetadataKeyId) REFERENCES RemoteProviderNativeMetadataKey (id);
GO
 
INSERT INTO RemoteProviderNativeMetadataKey(name, remoteProviderTypeId)
VALUES ('Environment', (SELECT id FROM RemoteProviderType WHERE name = 'Contrast'));
GO
 
INSERT INTO ChannelType (name,url,version,exportInfo,customChannel,isDenyListMode,isPenTestChannel)
SELECT 'GitHub',
       'https://github.com/',
       '1.0.0',
       'Use as a Remote Provider',
       0,
       1,
       0
       WHERE NOT EXISTS (
       SELECT name FROM ChannelType WHERE name = 'GitHub');
 
DECLARE @channelId INT = (SELECT id FROM ChannelType WHERE name = 'GitHub');
 
 
INSERT INTO RemoteProviderType (encrypted,hasApiKey,hasUserNamePassword,findingSyncEnabled,name,channelTypeId)
SELECT 0, 0, 0, 0,
        'GitHub Beta',
        @channelId
        WHERE NOT EXISTS (
        SELECT name FROM RemoteProviderType WHERE name = 'GitHub Beta' AND channelTypeId = @channelId
      );
 
DECLARE @remoteProChannelId INT = (SELECT id FROM RemoteProviderType WHERE name = 'GitHub Beta');
 
INSERT INTO RemoteProviderAuthenticationField (filterable,name,placeholder,required,secret,type,applicationId)
SELECT 0,
       'Owner',
       'GitHub Repositories Owner',
    1,
    0,
    NULL,
    @remoteProChannelId
    WHERE NOT EXISTS (
    SELECT name FROM RemoteProviderAuthenticationField WHERE applicationId = @remoteProChannelId and name = 'Owner'
  );
 
INSERT INTO RemoteProviderAuthenticationField (filterable,name,placeholder,required,secret,type,applicationId)
SELECT 0,
   'OAuth Token',
    NULL,
    1,
    1,
    NULL,
    @remoteProChannelId
    WHERE NOT EXISTS (
    SELECT name FROM RemoteProviderAuthenticationField WHERE applicationId = @remoteProChannelId and name = 'OAuth Token'
  );
 GO
 
INSERT INTO RemoteProviderAuthenticationEntity(encryptedValue, value, remoteProviderAuthenticationFieldId, remoteProviderEntityId)  
 (SELECT NULL, 'Modules', rpafId, rpeId FROM
(SELECT rpe.id AS rpeId
 FROM RemoteProviderEntity rpe
INNER JOIN RemoteProviderType rpt ON rpt.id = rpe.remoteProviderTypeId
WHERE rpt.name = 'Contrast') AS a,
(SELECT id as rpafId
FROM RemoteProviderAuthenticationField WHERE name = 'Application Type'
AND applicationId = (SELECT id FROM RemoteProviderType WHERE name = 'Contrast')) AS c);
GO
 
UPDATE cv
SET channelTypeId = (
    SELECT ChannelType.id
    FROM ChannelType
    WHERE ChannelType.name = 'AppScan Source')
FROM ChannelVulnerability cv
JOIN ChannelType ct ON cv.channelTypeId = ct.id
WHERE ct.name = 'AppScan Source Edition';
GO

Start Tomcat/ThreadFix

Restart Tomcat/ThreadFix.
Navigate to the login page to ensure that it loads as expected. If so, you may now log in and verify that the new version is installed; the version is included in the page footer after logging in.

ThreadFix Documentation

Upgrade from 2.8.5/2.8.5.1 to 2.8.6.1