wiki:SopUpdateBbmriApp

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Version 22 (modified by Roan Kanninga, 11 years ago) (diff)
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How to update bbmri app

Export war & mysql file

Run the app on your molgenis-legacy workspace (using tomcat, not standalone)
Export the war file
1. In eclipse: File--> export --> Web --> war file
The database is updated as follows: apply the mysql changes that you have made locally to the database on the server, so that you have the latest version of data for the server and the changes you want applied there. About the database changes you need to track them in a migration a file like one in the end of this document.

Quick tutorial

1) Copy the mysqldump from the live server to the test server
2) Deploy the new war file on the testserver
2.1) Check if there are errors according to changes in the model. There are 2 ways:

compare the mysql from the live and the testserver
check in the application if there are errors

2.2) If there are changes, make the migration script

Deploy to server

As also listed here: http://www.molgenis.org/wiki/MolgenisServers the test server is at molgenis35(https://molgenis35.target.rug.nl/biobanks/) and the production server at molgenis14(https://catalogue.bbmri.nl/biobanks/) .
First deploy at test server, notify david.van.enckevort AT nbic.nl. He will notify BBMRI office, they will review the changes and if everything is ok proceed to updating bbmri production server.
Deploy at test server: molgenis35 (Take a look here also http://www.molgenis.org/wiki/SopCreateMolgenisVM#SopDeploymentForDevs ) :
1. Ask credentials for molgenis35/molgenis14 from Pieter or Morris.

copy war file & migration script from your computer to test server

Copy the war file and the mysql migration script from your computer to the server as follows:
1. scp <filename>.war molgenis@…:./
2. scp <migrationScriptFilename> molgenis@…:./

Export data from LIVE server

Ssh to the server:
- ssh molgenis@molgenis14.target.rug.nl
Get data:
- mysqldump bbmri -u molgenis –pmolgenis > ~/databaseDumps/<date>bbmriDB.mysql

Copy data from LIVE server to your computer

scp molgenis@…:./databaseDumps/<date>bbmriDB.mysql ./mysql<date>LIVEdata.mysql

Copy data from your computer to test server

scp ./mysql<date>LIVEdata.mysql molgenis@…:./databaseDumps/mysql<date>LIVEdata.mysql

Deploy at test server

Ssh to the server:
- ssh molgenis@molgenis35.target.rug.nl
- You are now at /srv/molgenis/ where your files where copied.

Backup

BACKUP your DATABASE FIRST:
- mysqldump bbmri -u molgenis –pmolgenis > ~/databaseDumps/<date>bbmriDB.mysql
- Check the dumbed file if it is not just an error file …

Insert the data from live server to test server

compare the sql file from test server with the live server. then make a migrationscript and insert this tables into testserver

* mysql -u molgenis -pmolgenis bbmri < 29Maydump.mysql

===

Apply migration steps:

mysql -u molgenis –pmolgenis
use bbmri
<apply mysql commands>
Backup & replace the war file on server:
- The war file is in /usr/share/tomcat6/webapps/biobanks.war
- cp /usr/share/tomcat6/webapps/biobanks.war ~/warFiles/<date_bbmri.war>
Delete the old *.war (Do NOT stop tomcat; leave it running): rm /usr/share/tomcat6/webapps/biobanks.war
Wait a few seconds; Tomcat will notice the *.war is gone and then it will remove the unzipped folder.
Copy the the new *.war to the webapps dir; Tomcat will detect the new *.war and unzip it.
- cp <filename>.war /usr/share/tomcat6/webapps/biobanks.war
You can check the tomcat & mysql service with:
- sudo service tomcat6 status
- sudo service mysqld status

Check your deployment at: https://molgenis35.target.rug.nl/biobanks/

The same steps apply to the production server molgenis14 .

Appendix

Find miscellaneous issues here: http://www.molgenis.org/wiki/DespoinaLog
An old example migration file:

   CREATE TABLE !`BiobankSubCategory` (
    !`id` int(11) NOT NULL,
    PRIMARY KEY (!`id`),
    CONSTRAINT !`biobanksubcategory_ibfk_1` FOREIGN KEY (!`id`) REFERENCES !`OntologyTerm` (!`id`) ON DELETE CASCADE
  ) ENGINE=InnoDB DEFAULT CHARSET=utf8 COLLATE=utf8_unicode_ci;
   
   
  INSERT INTO !BiobankSubCategory (id)
  SELECT id
  FROM !BiobankCategory
  WHERE id  NOT IN ("281", "284", "285") ;
   
  CREATE TABLE !BiobankPersonRole (
              id INTEGER NOT NULL
              , PRIMARY KEY(id)
  );
   
  alter table !OntologyTerm modify   column !__Type enum('!OntologyTerm','!PersonRole','Species','!AlternateId','!BiobankCategory','!BiobankTopic','!BiobankDataType', '!BiobankSubCategory','!BiobankPersonRole');
   
   
  ALTER TABLE Biobank DROP FOREIGN KEY biobank_ibfk_5;
   
  ALTER TABLE !BiobankSubCategory ADD FOREIGN KEY (id) REFERENCES !OntologyTerm (id) ON DELETE CASCADE;
   
  ALTER TABLE !`BiobankSubCategory` 
  ADD CONSTRAINT !`biobank_ibfk_5`
      FOREIGN KEY (!`id`) REFERENCES !OntologyTerm (id) ON DELETE CASCADE; this exists already from his creation)
   
  ALTER TABLE Biobank ADD FOREIGN KEY (!SubCategory) REFERENCES !BiobankSubCategory (id) ON DELETE RESTRICT;
   
  ALTER TABLE !`Biobank` 
  ADD CONSTRAINT !`biobank_ibfk_885`
      FOREIGN KEY (!`SubCategory`) REFERENCES !BiobankSubCategory (id)  ON DELETE CASCADE;
   
   
   
  DELETE FROM !BiobankCategory
  WHERE id  NOT IN ("281", "284", "285") ;  
   
   
   
  ALTER TABLE !BiobankPersonRole ADD FOREIGN KEY (id) REFERENCES !PersonRole (id) ON DELETE CASCADE;
   
   
  ALTER TABLE !`BiobankPersonRole` 
  ADD CONSTRAINT !`BiobankPersonRole_ibfk_33`
      FOREIGN KEY (!`id`) REFERENCES !PersonRole (id)  ON DELETE CASCADE;
   
  UPDATE !OntologyTerm  SET !__Type="!BiobankSubCategory" WHERE id='282';
  UPDATE !OntologyTerm  SET !__Type="!BiobankSubCategory" WHERE id='283';
  UPDATE !OntologyTerm  SET !__Type="!BiobankSubCategory" WHERE id='286';
  UPDATE !OntologyTerm  SET !__Type="!BiobankSubCategory" WHERE id='287';
  UPDATE !OntologyTerm  SET !__Type="!BiobankSubCategory" WHERE id='288';
  UPDATE !OntologyTerm  SET !__Type="!BiobankSubCategory" WHERE id='289';
  UPDATE !OntologyTerm  SET !__Type="!BiobankSubCategory" WHERE id='290';
  UPDATE !OntologyTerm  SET !__Type="!BiobankSubCategory" WHERE id='291';
  UPDATE !OntologyTerm  SET !__Type="!BiobankSubCategory" WHERE id='292';
  UPDATE !OntologyTerm  SET !__Type="!BiobankSubCategory" WHERE id='293';
  UPDATE !OntologyTerm  SET !__Type="!BiobankSubCategory" WHERE id='295';
  UPDATE !OntologyTerm  SET !__Type="!BiobankSubCategory" WHERE id='296';
  UPDATE !OntologyTerm  SET !__Type="!BiobankSubCategory" WHERE id='297';
  UPDATE !OntologyTerm  SET !__Type="!BiobankSubCategory" WHERE id='298';
  UPDATE !OntologyTerm  SET !__Type="!BiobankSubCategory" WHERE id='564';
  UPDATE !OntologyTerm  SET !__Type="!BiobankSubCategory" WHERE id='299';
  UPDATE !OntologyTerm  SET !__Type="!BiobankSubCategory" WHERE id='294';
   
   
   
  select * from !OntologyTerm where name="Software Engineer";
  delete from !OntologyTerm where id=561;
  select * from !BiobankPersonRole;
  insert into !BiobankPersonRole values(561);
   
  select * from !OntologyTerm where name="coordinator";
  delete from !OntologyTerm where id=593;
  select * from !BiobankPersonRole;
  insert into !BiobankPersonRole values(277);
   
  select * from !OntologyTerm where name="postdoc";
  delete from !OntologyTerm where id=594;
   select * from !BiobankPersonRole;
  insert into !BiobankPersonRole values(278);
   
  select * from !OntologyTerm where name="administrator";
  delete from !OntologyTerm where id=595;
  select * from !BiobankPersonRole;
  insert into !BiobankPersonRole values(279);
   
   
  select * from !OntologyTerm where name="IT responsible";
  delete from !OntologyTerm where id=596;
  select * from !BiobankPersonRole;
  insert into !BiobankPersonRole values(280);
   
  //how to make values of Person Role appear in ui , you have to delete some old from DB :
   
  create a new Coordinator Role in the ui and remember the id 591 (select * from !PersonRole; --> the latest one, or check from ui )
  correct the Person table with t he new entry(that is not show in the ui) :
   
  update Person set Roles=591 where Roles=277
   
  delete the old one : 
   
  delete from !PersonRole where id=277;
  delete from  !BiobankPersonRole  where id=277;
  delete from !OntologyTerm  where id=277;
   
  repeat the same step for all of them
   
   
  COMMIT;
   
  ===========================================================
  !SubCategory
  biobank_ibfk_1
    CONSTRAINT !`biobank_ibfk_5` FOREIGN KEY (!`SubCategory`) REFERENCES !`BiobankSubCategory` (!`id`)
    CONSTRAINT !`biobank_ibfk_5` FOREIGN KEY (!`SubCategory`) REFERENCES !`BiobankSubCategory` (!`id`),
   
   
  CREATE TABLE !BiobankPersonRole (
              id INTEGER NOT NULL
              , PRIMARY KEY(id)
  );
   
  ALTER TABLE !BiobankPersonRole ADD FOREIGN KEY (id) REFERENCES !PersonRole (id) ON DELETE CASCADE;
   
  alter table !OntologyTerm modify   column !__Type enum('!OntologyTerm','!PersonRole','Species','!AlternateId','!BiobankCategory','!BiobankTopic','!BiobankDataType', '!BiobankSubCategory','!BiobankPersonRole');
   
  UPDATE !OntologyTerm  SET !__Type="!BiobankSubCategory" WHERE id='282';
  UPDATE !OntologyTerm  SET !__Type="!BiobankSubCategory" WHERE id='283';
  UPDATE !OntologyTerm  SET !__Type="!BiobankSubCategory" WHERE id='286';
  UPDATE !OntologyTerm  SET !__Type="!BiobankSubCategory" WHERE id='287';
  UPDATE !OntologyTerm  SET !__Type="!BiobankSubCategory" WHERE id='288';
  UPDATE !OntologyTerm  SET !__Type="!BiobankSubCategory" WHERE id='289';
  UPDATE !OntologyTerm  SET !__Type="!BiobankSubCategory" WHERE id='290';
  UPDATE !OntologyTerm  SET !__Type="!BiobankSubCategory" WHERE id='291';
  UPDATE !OntologyTerm  SET !__Type="!BiobankSubCategory" WHERE id='292';
  UPDATE !OntologyTerm  SET !__Type="!BiobankSubCategory" WHERE id='293';
  UPDATE !OntologyTerm  SET !__Type="!BiobankSubCategory" WHERE id='295';
  UPDATE !OntologyTerm  SET !__Type="!BiobankSubCategory" WHERE id='296';
  UPDATE !OntologyTerm  SET !__Type="!BiobankSubCategory" WHERE id='297';
  UPDATE !OntologyTerm  SET !__Type="!BiobankSubCategory" WHERE id='298';
  UPDATE !OntologyTerm  SET !__Type="!BiobankSubCategory" WHERE id='564';
   
  /*below we resolve the problem of duplicate entries in ontology term for !PersonRole*/
   
  select * from !OntologyTerm where name="Software Engineer";
  delete from !OntologyTerm where id=561;
  select * from !BiobankPersonRole;
  insert into !BiobankPersonRole values(561);
   
  select * from !OntologyTerm where name="coordinator";
  delete from !OntologyTerm where id=593;
  select * from !BiobankPersonRole;
  insert into !BiobankPersonRole values(277);
   
  select * from !OntologyTerm where name="postdoc";
  delete from !OntologyTerm where id=594;
   select * from !BiobankPersonRole;
  insert into !BiobankPersonRole values(278);
   
  select * from !OntologyTerm where name="administrator";
  delete from !OntologyTerm where id=595;
  select * from !BiobankPersonRole;
  insert into !BiobankPersonRole values(279);
   
   
  select * from !OntologyTerm where name="IT responsible";
  delete from !OntologyTerm where id=596;
  select * from !BiobankPersonRole;
  insert into !BiobankPersonRole values(280);
   
   
  COMMIT;

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