Versions Compared

Old Version 14

changes.mady.by.user Sam Tsoi

Saved on

compared with

New Version Current

changes.mady.by.user Sam Tsoi

Saved on

Key

  • This line was added.
  • This line was removed.
  • Formatting was changed.

...

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:

...

Code Block
languagebash
themeRDark
$ /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.
...
 Code Block
languagebash
themeRDark
$ rm /opt/shrine/tomcat/webapps/*.war
...

Deploy New .war Files
Deploy New SHRINE core
...
  1. You will need to add a new code block within the main shrine {} block:
     Code Block
    languagebash
    themeRDark
    messagequeue {
	blockingq {
		serverUrl = “https://shrine_hub_url:6443/shrine-metadata/mom”
	}
}
  2. Please take note that the database profile class names have changed: 
    1. slick.driver.MySQLDriver$ to slick.jdbc.MySQLProfile$ 
    2. slick.driver.H2Profile$ to slick.jdbc.H2Profile$ 
    3. slick.driver.PostgresProfile$ to slick.jdbc.PostgresProfile$ 
    4. slick.driver.SQLServerProfile$ to slick.jdbc.SQLServerProfile$ 
    5. slick.driver.JdbcProfile$ to slick.jdbc.JdbcProfile$
    6. slick.driver.OracleProfile$ to slick.jdbc.OracleProfile$

  3. Add externalStewardBaseUrl to the 'emailDataSteward' section under the steward {} block:
    1. externalStewardBaseUrl = "https://your_shrine_url:port/steward"

  4. If you are not using port 6443 to serve SHRINE:
    You will need to override a URL in shrine.conf to see progress and results from QUEUED queries. 
     Code Block
    languagebash
    themerdark
    shrine {
  queryEntryPoint {
    queuedQueryPollUrl = "https://localhost:6443/shrine/rest/i2b2/request" //Change to your url and port number
  }
}
     
Sample SHRINE configuration file (for a downstream node)
...
  1. You will need to add in a database block within the problems section:
     Code Block
    languagebash
    theme
...
  1. rdark
    problem {
  
...
  1.  
...
  1.    
...
  1. problemHandler = "
...
  1. net.shrine.problem.LogAndDatabaseProblemHandler$"
      database {
    
...
  1. 	dataSourceFrom = 
...
  1. "JNDI"
    	jndiDataSourceName = "java:comp/env/jdbc/problemDB"
    	slickProfileClassName = "slick.jdbc.MySQLProfile$"
            
...
  1.  
...
  1.  
...
  1.     
...
  1.  
...
  1.  
...
  1.     
...
  1.  
...
  1.  
...
  1.     
...
  1.  
...
  1.  //slick.jdbc.H2Profile$
     
...
  1.  
...
  1.  
...
  1.   
...
  1.   
...
  1.  
...
  1.     
...
  1.  
...
  1.         
...
  1.  
...
  1.       //slick.jdbc.PostgresProfile$
      
...
  1.   
...
  1.   
...
  1.   
...
  1.  
...
  1.     
...
  1.  
...
  1.       
...
  1.  
...
  1.  
...
  1.  
...
  1.  
...
  1.     
...
  1. //slick.jdbc.SQLServerProfile$
    
...
  1.  
...
  1.       
...
  1.  
...
  1.  
...
  1.  
...
  1.  
...
  1.     
...
  1.     
...
  1.  
...
  1.       
...
  1.  
...
  1.  //slick.jdbc.JdbcProfile$
       
...
  1.  
...
  1.     
...
  1.  
...
  1.       
...
  1.  
...
  1.  
...
  1.  
...
  1.  
...
  1.     
...
  1.   
...
  1.   
...
  1.  //slick.jdbc.OracleProfile$
    
...
  1.  
...
  1.  
...
  1. }
    }
Sample SHRINE configuration file (for a downstream node)
 
 Code Block
languagebash
themeRDark
titleshrine.conf
collapsetrue
shrineaudit {
  pmEndpoint {
   collectQepAudit url = false"http://i2b2_node_url:9090/i2b2/services/PMService/getServices"
  }
    databaseontEndpoint {
    url = "http://i2b2_node_url:9090/i2b2/services/OntologyService"
  dataSourceFrom}
 = "JNDI"
  hiveCredentials {
    domain jndiDataSourceName = "java:comp/env/jdbc/qepAuditDBi2b2demo"
    username = "demo"
  slickProfileClassName  password = "slick.jdbc.MySQLProfile$demouser"
    crcProjectId = }"Demo"
    }
ontProjectId = "SHRINE"
    
    trustModelIsHub = true}

    attachSigningCert = truemessagequeue {
    authenticationType = "pm"blockingq {
    authorizationType = "shrine-steward"
 
    queuedQueryPollUrlserverUrl = "https://your_shrine_urlshrine-act-test.hms.harvard.edu:6443/shrine/rest/i2b2/request" //Change to your url and port number

    shrineSteward-metadata/mom"
    }
  }
  
  breakdownResultOutputTypes {
    PATIENT_AGE_COUNT_XML {
      qepUserNamedescription = "qepAge patient breakdown"
    }
   qepPassword = "trustme" PATIENT_RACE_COUNT_XML {
      stewardBaseUrldescription = "https://localhost:6443Race patient breakdown"
    }
    PATIENT_VITALSTATUS_COUNT_XML {
      includeAggregateResultsdescription = false
"Vital Status patient breakdown"
   
 } 
    maxQueryWaitTimePATIENT_GENDER_COUNT_XML {
      description  minutes = 5
"Gender      }

    broadcasterServiceEndpoint {
        url = "https://shrine-act-test.hms.harvard.edu:6443/shrine/rest/broadcaster/broadcast"patient breakdown"
    }
  } //end queryEntryPoint

  adapterqueryEntryPoint {
    create = true
    audit {
      collectAdapterAuditcollectQepAudit = false
      database {
        dataSourceFrom = "JNDI"
        jndiDataSourceName = "java:comp/env/jdbc/adapterAuditDBqepAuditDB"
        slickProfileClassName = "slick.jdbc.MySQLProfile$"
      
      }
    }

    crcEndpoint {
      url = "http://i2b2_node_url:9090/i2b2/services/QueryToolService"
    }

    //slick.jdbc.H2Profile$
                  adapterLockoutAttemptsThreshold = 0
    setSizeObfuscation = true
    adapterMappingsFileName = "AdapterMappings.csv"

 //slick.jdbc.PostgresProfile$
          maxSignatureAge {
      minutes = 5
    }

    immediatelyRunIncomingQueries = true

  } // end adapter

slick.jdbc.SQLServerProfile$
         networkStatusQuery = "\\\\SHRINE\\SHRINE\\Demographics\\Gender\\Male\\"
    humanReadableNodeName = "Harvard Test Node"
    shrineDatabaseType = "mysql"

    keystore {
      file = "/opt/shrine/shrine.keystore"/slick.jdbc.JdbcProfile$
      password = "password"
      privateKeyAlias = "privateKeyAlias"
      keyStoreType = "JKS"
      caCertAliases = ["shrine-hub-ca"] //slick.jdbc.OracleProfile$
      }

    problem {}
      problemHandler = "net.shrine.problem.LogAndDatabaseProblemHandler$"
    trustModelIsHub = database {true
    	dataSourceFromattachSigningCert = "JNDI"true
    	jndiDataSourceNameauthenticationType = "java:comp/env/jdbc/problemDBpm"
    	slickProfileClassNameauthorizationType = "slick.jdbc.MySQLProfile$"
      }shrine-steward"
 
    }

  dashboard {
    happyBaseUrlqueuedQueryPollUrl = "https://localhostyour_shrine_url:6443/shrine/rest/happyi2b2/request"
    statusBaseUrl = "https://localhost:6443/shrine/rest/internalstatus" //Change to your url and port number

    databaseshrineSteward {
      dataSourceFromqepUserName = "JNDIqep"
      jndiDataSourceNameqepPassword = "java:comp/env/jdbc/problemDBtrustme"
      slickProfileClassNamestewardBaseUrl = "slick.jdbc.MySQLProfile$https://localhost:6443"
    }

  } //end dashboard

  includeAggregateResults = status {false
      permittedHostOfOrigin = "localhost"
    }

    squerylDataSourcemaxQueryWaitTime {
      database {
 minutes = 5
      }

   dataSourceFrom =broadcasterServiceEndpoint "JNDI"{
        jndiDataSourceNameurl = "java:comp/env/jdbc/shrineDBhttps://shrine-act-test.hms.harvard.edu:6443/shrine/rest/broadcaster/broadcast"
      }
  } //end }queryEntryPoint

    authenticateadapter {
    create = usersource {true
    audit {
   domain = "i2b2demo"
 collectAdapterAudit = false
   }
   database }{

   steward {
    createTopicsModedataSourceFrom = Approved"JNDI"

     emailDataSteward {
   jndiDataSourceName = "java:comp/env/jdbc/adapterAuditDB"
       sendAuditEmails slickProfileClassName = false"slick.jdbc.MySQLProfile$" 
   //false to turn off the whole works of emailing the data steward      //interval = "1 day" //Audit researchers daily
      //timeAfterMidnight = "6 hours" //Audit researchers at 6 am. If the interval is less than 1 day then this delay is ignored.
slick.jdbc.H2Profile$
                             //maxQueryCountBetweenAudits = 30 //If a researcher runs more than this many queries since the last audit audit her
slick.jdbc.PostgresProfile$
                    //minTimeBetweenAudits = "30 days" //If a researcher runs at least one query, audit those queries if this much time has passed
 
 //slick.jdbc.SQLServerProfile$
               //You must provide the email address of the shrine node system admin, to handle bounces and invalid addresses
 //slick.jdbc.JdbcProfile$
        //from  = "shrine-admin@example.com"
      //You must provide the email address of the data steward
      //to = "shrine-steward@example.com"slick.jdbc.OracleProfile$
 
     }
 //subject = "Audit SHRINE researchers" }

      //The baseUrl for the data steward to be substituted in to email text. Must be supplied if it is used in the email text.crcEndpoint {
      url = "http://i2b2_node_url:9090/i2b2/services/QueryToolService"
    }

    adapterLockoutAttemptsThreshold = 0
    setSizeObfuscation  //stewardBaseUrl = "https://example.com:6443/steward/"= true
     adapterMappingsFileName //externalStewardBaseUrl = "https://example.com:6443/steward/AdapterMappings.csv"

 
   maxSignatureAge {
  //Text to use for theminutes email= audit.5
    }

  //AUDIT_LINES will beimmediatelyRunIncomingQueries replaced= bytrue

 a researcherLine} for// each researcher to audit.end adapter

    networkStatusQuery  //STEWARD_BASE_URL will be replaced by the value in stewardBaseUrl if available.= "\\\\SHRINE\\SHRINE\\Demographics\\Gender\\Male\\"
    humanReadableNodeName = "Harvard Test Node"
     shrineDatabaseType //emailBody = """Please audit the following users at STEWARD_BASE_URL at your earliest convinience: AUDIT_LINES"""mysql"

    keystore {
      file = "/opt/shrine/shrine.keystore"
      //note that this can be a multiline message
 
password = "password"
      privateKeyAlias = "privateKeyAlias"
      keyStoreType //Text to use per researcher to audit.
      //FULLNAME, USERNAME, COUNT and LAST_AUDIT_DATE will be replaced with appropriate text.= "JKS"
      caCertAliases = ["shrine-hub-ca"]
    }

    problem {
      //researcherLineproblemHandler = "FULLNAME (USERNAME) has run COUNT queries since LAST_AUDIT_DATE.net.shrine.problem.LogAndDatabaseProblemHandler$"
    }

    database {
      	dataSourceFrom = "JNDI"
      	jndiDataSourceName = "java:comp/env/jdbc/stewardDBproblemDB"
      	slickProfileClassName = "slick.jdbc.MySQLProfile$"
      }
  } // end steward}

  emaildashboard {
  }
} // endhappyBaseUrl shrine section
Changes to i2b2 PM cell database
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:
 
...
languagesql
themerdark
...
= "https://localhost:6443/shrine/rest/happy"
    statusBaseUrl = "https://localhost:6443/shrine/rest/internalstatus"

    database {
      dataSourceFrom = "JNDI"
      jndiDataSourceName = "java:comp/env/jdbc/problemDB"
      slickProfileClassName 
...
= "
...
slick.jdbc.MySQLProfile$"
      
...
     
...
            
...
         //slick.jdbc.H2Profile$
    
...
   
...
 
...
 
...
  
...
 
...
 
...
       
...
 
...
 
...
       
...
 
...
 
...
 //slick.jdbc.PostgresProfile$
        
...
 
...
 
...
       
...
 
...
 
...
  
...
 
...
 
...
 
...
    
...
 
...
 
...
 
...
 //slick.jdbc.SQLServerProfile$
          
...
 
...
 
...
 
...
 
...
       
...
           
...
//slick.jdbc.JdbcProfile$
 
...
     
...
 
...
 
...
       
...
           
...
 
...
 
...
    
...
//slick.jdbc.OracleProfile$
    }
  } //end dashboard

    status {
      permittedHostOfOrigin = "localhost"
    }

    squerylDataSource {
      database {
        dataSourceFrom = "JNDI"
        jndiDataSourceName 
...
= "java:comp/env/jdbc/shrineDB"
    
...
  }
   
...
 }

    authenticate {
      
...
usersource {
        domain = "i2b2demo"
      
...
}
  
...
 
...
 
...
}

  
...
steward 
...
 
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:
 
 Code Block
languagesql
themerdark
mysql> use shrine_query_history;
mysql> alter table QUERY_RESULT change status status varchar(30) not null;
 
 
For Oracle:
 
 Code Block
languagesql
themerdark
-- 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
themerdark
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
In SHRINE 1.25.4, we will need to change context.xml to utilize new parameters as the old ones are going to be deprecated. The old parameters were:
  • maxActive
  • maxWait
You will now use the new parameters:
  • maxTotal
  • maxWaitMillis
As part of the changes, here's a sample context.xml file, with the values that you should have:
 Code Block
langaugexml
languagexml
themeRDark
titlecontext.xml
collapsetrue
<?xml version='1.0' encoding='utf-8'?>
<!-- The contents of this file will be loaded for each web application -->

<Context>
    <WatchedResource>WEB-INF/web.xml</WatchedResource>
    <Resource name="jdbc/problemDB" auth="Container" type="javax.sql.DataSource"
              maxTotal="128" maxIdle="32" maxWaitMillis="10000"
              username="shrine" password="demouser" driverClassName="com.mysql.jdbc.Driver"
              url="jdbc:mysql://localhost:3306/shrine_query_history"
              testOnBorrow="true" validationQuery="SELECT 1" />

    <Resource name="jdbc/shrineDB" auth="Container" type="javax.sql.DataSource{
    createTopicsMode = Approved

    emailDataSteward {
      sendAuditEmails = false  //false to turn off the whole works of emailing the data steward      //interval = "1 day" //Audit researchers daily
      //timeAfterMidnight = "6 hours" //Audit researchers at 6 am. If the interval is less than 1 day then this delay is ignored.
      //maxQueryCountBetweenAudits = 30 //If a researcher runs more than this many queries since the last audit audit her
      //minTimeBetweenAudits = "30 days" //If a researcher runs at least one query, audit those queries if this much time has passed
 
      //You must provide the email address of the shrine node system admin, to handle bounces and invalid addresses
      //from = "shrine-admin@example.com"
      //You must provide the email address of the data steward
      //to = "shrine-steward@example.com"
 
      //subject = "Audit SHRINE researchers"
      //The baseUrl for the data steward to be substituted in to email text. Must be supplied if it is used in the email text.
      //stewardBaseUrl = "https://example.com:6443/steward/"
      //externalStewardBaseUrl = "https://example.com:6443/steward/"
 
      //Text to use for the email audit.
      //AUDIT_LINES will be replaced by a researcherLine for each researcher to audit.
      //STEWARD_BASE_URL will be replaced by the value in stewardBaseUrl if available.
      //emailBody = """Please audit the following users at STEWARD_BASE_URL at your earliest convenience: AUDIT_LINES"""
      //note that this can be a multiline message
 
      //Text to use per researcher to audit.
      //FULLNAME, USERNAME, COUNT and LAST_AUDIT_DATE will be replaced with appropriate text.
      //researcherLine = "FULLNAME (USERNAME) has run COUNT queries since LAST_AUDIT_DATE."
    }

    database {
      dataSourceFrom = "JNDI"
      jndiDataSourceName = "java:comp/env/jdbc/stewardDB"
      slickProfileClassName = "slick.jdbc.MySQLProfile$"
              maxTotal="128" maxIdle="32" maxWaitMillis="10000"
              username="shrine" password="demouser" driverClassName="com.mysql.jdbc.Driver"
 //slick.jdbc.H2Profile$
               url="jdbc:mysql://localhost:3306/shrine_query_history"
              testOnBorrow="true" validationQuery="SELECT 1" />

/slick.jdbc.PostgresProfile$
      <Resource name="jdbc/adapterAuditDB" auth="Container" type="javax.sql.DataSource"
              maxTotal="128" maxIdle="32" maxWaitMillis="10000"
       //slick.jdbc.SQLServerProfile$
       username="shrine" password="demouser" driverClassName="com.mysql.jdbc.Driver"
                 url="jdbc:mysql://localhost:3306/adapterAuditDB"
        //slick.jdbc.JdbcProfile$
      testOnBorrow="true" validationQuery="SELECT 1" />

    <Resource name="jdbc/qepAuditDB" auth="Container" type="javax.sql.DataSource"
              maxTotal="512" maxIdle="32" maxWaitMillis="10000"
              username="shrine" password="demouser" driverClassName="com.mysql.jdbc.Driver" //slick.jdbc.OracleProfile$
    }
          url="jdbc:mysql://localhost:3306/qepAuditDB"
              testOnBorrow="true" validationQuery="SELECT 1" />

    <Resource name="jdbc/stewardDB" auth="Container" type="javax.sql.DataSource"} // end steward

  email {
  }
} // end shrine section

Changes to i2b2 PM cell database
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
languagesql
themerdark
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:

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


For Oracle:

 Code Block
languagesql
themerdark
-- 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
themerdark
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
In SHRINE 1.25.4, we will need to change context.xml to utilize new parameters as the old ones are going to be deprecated. The old parameters were:
  • maxActive
  • maxWait
You will now use the new parameters:
  • maxTotal
  • maxWaitMillis

 Warning
titleOracle Users
If you are using Oracle, please change the driverClassName to "oracle.jdbc.driver.OracleDriver".

As part of the changes, here's a sample context.xml file, with the values that you should have (assuming MySQL used):
 Code Block
langaugexml
languagexml
themeRDark
titlecontext.xml
collapsetrue
<?xml version='1.0' encoding='utf-8'?>
<!-- The contents of this file will be loaded for each web application -->

<Context>
    <WatchedResource>WEB-INF/web.xml</WatchedResource>
    <Resource name="jdbc/problemDB" auth="Container" type="javax.sql.DataSource"
              maxTotal="128" maxIdle="32" maxWaitMillis="10000"
              username="shrine" password="demouser" driverClassName="com.mysql.jdbc.Driver"
              url="jdbc:mysql://localhost:3306/shrine_query_history"
              testOnBorrow="true" validationQuery="SELECT 1" />

    <Resource name="jdbc/shrineDB" auth="Container" type="javax.sql.DataSource"
              maxTotal="128" maxIdle="32" maxWaitMillis="10000"
              username="shrine" password="demouser" driverClassName="com.mysql.jdbc.Driver"
              url="jdbc:mysql://localhost:3306/shrine_query_history"
              testOnBorrow="true" validationQuery="SELECT 1" />

    <Resource name="jdbc/adapterAuditDB" auth="Container" type="javax.sql.DataSource"
              maxTotal="128" maxIdle="32" maxWaitMillis="10000"
              username="shrine" password="demouser" driverClassName="com.mysql.jdbc.Driver"
              url="jdbc:mysql://localhost:3306/adapterAuditDB"
              testOnBorrow="true" validationQuery="SELECT 1" />

    <Resource name="jdbc/qepAuditDB" auth="Container" type="javax.sql.DataSource"
              maxTotal="512" maxIdle="32" maxWaitMillis="10000"
              username="shrine" password="demouser" driverClassName="com.mysql.jdbc.Driver"
              url="jdbc:mysql://localhost:3306/qepAuditDB"
              testOnBorrow="true" validationQuery="SELECT 1" />

    <Resource name="jdbc/stewardDB" auth="Container" type="javax.sql.DataSource"
              maxTotal="128" maxIdle="32" maxWaitMillis="10000"
              username="shrine" password="demouser" driverClassName="com.mysql.jdbc.Driver"
              url="jdbc:mysql://localhost:3306/stewardDB"
              testOnBorrow="true" validationQuery="SELECT 1" />
</Context>
 Info
titleNote
Please note that qepAuditDB is set to 512 connections, which will help in scaling issues for a larger network.


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
    languagebash
    themerdark
    shrineUrl: 'https://your_shrine_url:6443/shrine-metadata/',
  • Here's the whole i2b2_config_data.js file for reference:
     Code Block
    languagebash
    themerdark
    {
  urlProxy: "/shrine-proxy/request",
  urlFramework: "js-i2b2/",
  loginTimeout: 15, // in seconds
  username_label:"SHRINE ACT Hub username:", //Username Label
  password_label:"SHRINE ACT Hub password:", //Password Label
  clientHelpUrl:'help/pdf/shrine-client-guide.pdf',
  networkHelpUrl:'help/pdf/shrine-network-guide.pdf',
  wikiBaseUrl:'https://open.med.harvard.edu/wiki/display/SHRINE',
  obfuscation: 10,
  resultName: "patients",
  shrineUrl: 'https://your_shrine_url:6443/shrine-metadata/',
  // -------------------------------------------------------------------------------------------
  // THESE ARE ALL THE DOMAINS A USER CAN LOGIN TO
  lstDomains: [
    {
      domain: "your domain name",
      name: "your node name",
      debug: true,
      urlCellPM: "http://your_i2b2_url:9090/i2b2/services/PMService/",
      allowAnalysis: true,
      isSHRINE: true      
    }
  ]
  // -------------------------------------------------------------------------------------------
}
 Info
titleNote
Please note that qepAuditDB is set to 512 connections, which will help in scaling issues for a larger network.
 
 
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
    languagebash
    themerdark
    shrineUrl: 'https://your_shrine_url:6443/shrine-metadata',

Changes to the cell_config_data.js file
...
 Code Block
languagebash
themerdark
 files: [
     “dist"dist/shrine.bundle.js”js"
//   “shrine"shrine.controller.js”js",
//   “i2b2"i2b2_msgs.js”js",
//   “shrine"shrine.plugin.js”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.
...
 Code Block
languagebash
themeRDark
{
  files: [
    "dist/shrine.bundle.js"
  ],

  css: [],
  config: {
    // additional configuration variables that are set by the system
    name: "SHRINE Cell",
    description: "The SHRINE cell...",
    category: ["core","cell","shrine"],
    newTopicURL: "https://your_shrine_url:6443/steward/client/index.html",
    readApprovedURL:"https://your_shrine_url:6443/shrine/rest/i2b2/request",
    wrapperHtmlFile: "./js-shrine/shrine.plugin.html"
  }
}


Configure support for client-side https Proxies
...
Set Java system properties to use a client-side https proxy. In /opt/shrine/tomcat/bin/setenv.sh , add values for httphttps.proxyHost and httphttps.proxyPort to the export CATALINA_OPTS=""  

 Code Block
languagebash
themerdark
export CATALINA_OPTS="-DhttpDhttps.proxyHost=yourProxyHost -DhttpDhttps.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
languagebash
themerdark
$ /opt/shrine/tomcat/bin/startup.sh
...

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:
...