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Warning
titleNote

SHRINE 1.25.4 is not backwards-compatible with any previous version!

PLEASE MAKE SURE THAT YOU HAVE SHRINE 1.22.8 INSTALLED BEFORE YOU FOLLOW THESE UPGRADE INSTRUCTIONS!

 


This guide makes the following assumptions of a current 1.22.8 system. Make sure all of these conditions are satisfied before proceeding:

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$ /opt/shrine/tomcat/bin/shutdown.sh

 


Create Backups

Now that SHRINE is stopped, it is a good idea to back up the current versions of the components we will be upgrading. The exact method for making this backups may vary, but these instructions will place the backups in a folder called /opt/shrine/upgrade-backups.

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$ rm /opt/shrine/tomcat/webapps/*.war

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Deploy New .war Files
Deploy New SHRINE core
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You will need to remove a primary key constraint within the pm_user_login table in the i2b2pm schema. An unneeded compound primary key limits the PM cell to only processing one authentication attempt per second. In Postgres, remove it with:

 
 Code Block
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bash-4.1$ psql
postgres=# \c i2b2pm
i2b2pm=# \d+ pm_user_login
                           Table "public.pm_user_login"
    Column     |            Type             | Modifiers | Storage  | Description
---------------+-----------------------------+-----------+----------+-------------
 user_id       | character varying(50)       | not null  | extended |
 attempt_cd    | character varying(50)       | not null  | extended |
 entry_date    | timestamp without time zone | not null  | plain    |
 changeby_char | character varying(50)       |           | extended |
 status_cd     | character varying(50)       |           | extended |
Indexes:
    "pm_user_login_pkey" PRIMARY KEY, btree (entry_date, user_id)
Has OIDs: no
 
i2b2pm=# ALTER TABLE "pm_user_login" DROP CONSTRAINT "pm_user_login_pkey" ;
ALTER TABLE
 
i2b2pm=# \d+ pm_user_login
                           Table "public.pm_user_login"
    Column     |            Type             | Modifiers | Storage  | Description
---------------+-----------------------------+-----------+----------+-------------
 user_id       | character varying(50)       | not null  | extended |
 attempt_cd    | character varying(50)       | not null  | extended |
 entry_date    | timestamp without time zone | not null  | plain    |
 changeby_char | character varying(50)       |           | extended |
 status_cd     | character varying(50)       |           | extended |
Has OIDs: no
 

Allow for More Types of Status from the i2b2 CRC
Change the shrine_query_history's QUERY_RESULT's status column's type from an enum to a text field to accommodate more types from the i2b2 CRC. This will allow some results previously interpreted as errors to be interpreted as 'QUEUED'. 

For Mysql:

 
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mysql> use shrine_query_history;
mysql> alter table QUERY_RESULT change status status varchar(30) not null;
 
 


For Oracle:
 

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-- To find the constraint name on the status column:
SELECT COLUMN_NAME,CONSTRAINT_NAME,TABLE_NAME FROM user_cons_columns WHERE TABLE_NAME = 'QUERY_RESULT';
-- To drop that constraint:
ALTER TABLE QUERY_RESULT DROP CONSTRAINT <constraint_name_for_status>;
 
 


For MS SQL Server:
 

 Code Block
languagesql
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USE shrine_query_history;
  
-- To find the constraint name on the status column:
 
SELECT * FROM INFORMATION_SCHEMA.TABLE_CONSTRAINTS WHERE TABLE_NAME= 'QUERY_RESULT';
 
-- To drop that constraint:
 
ALTER TABLE QUERY_RESULT DROP CONSTRAINT <constraint_name_for_status>;
 
 


Changes to the context.xml file
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 Info
titleNote
Please note that qepAuditDB is set to 512 connections, which will help in scaling issues for a larger network.
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Changes to the i2b2_config_data.js file
  • You will need to make a change in the i2b2_config_data.js file, by adding this line of code:

     Code Block
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    themerdark
    shrineUrl: 'https://your_shrine_url:6443/shrine-metadata/',
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 Code Block
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 files: [
     “dist/shrine.bundle.js”
//   “shrine.controller.js”,
//   “i2b2_msgs.js”,
//   “shrine.plugin.js”
  ],
You'll need to add "dist/shrine.bundle.js" under the files section as well as "wrapperHtmlFile: "./js-shrine/shrine.plugin.html"" under the readApprovedURL parameter.
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Set Java system properties to use a client-side https proxy. In /opt/shrine/tomcat/bin/setenv.sh , add values for https.proxyHost and https.proxyPort to the export CATALINA_OPTS=""  

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export CATALINA_OPTS="-Dhttps.proxyHost=yourProxyHost -Dhttps.proxyPort=yourProxyHostPort"
 Info
titleNote
Please note, if you are not running a client-side proxy, you can skip this section!
 

Start SHRINE
The only thing left to do at this point is start SHRINE back up. Simply do the following:
 Code Block
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$ /opt/shrine/tomcat/bin/startup.sh
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Verify SHRINE Upgrade
After starting SHRINE up, verify that the upgrade was properly deployed by checking the SHRINE Dashboard. The exact address you will need to go to depends on your configuration, but the general format looks like the following:
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