Changes between Version 34 and Version 35 of SopUpdateBbmriApp

Timestamp:

2013-05-29T14:25:36+02:00 (11 years ago)

Author:

antonak

Comment:

--

SopUpdateBbmriApp

@@ -98 +98 @@
    '''How to update bbmri app'''
 }}}
-       '''Quick tutorial'''
+  ''' Quick tutorial'''
 
 1) Copy the mysqldump from the live server to the test server [[BR]] 2) Deploy the new war file on the testserver[[BR]] 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[[BR]] 
+2.2) If there are changes, make the migration script[[BR]]
 
 '''Detailed tutorial'''
@@ -113 +112 @@
 
 '''1.1 Run the app on your molgenis-legacy workspace (using tomcat, not standalone)'''
-
 
  1. Export the war file
@@ -120 +118 @@
 
 '''2. Deploy to test server'''
-
 
  1. 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/) .
@@ -128 +125 @@
 
 '''2.1 Create migration script according to data in live server'''
-
 
  1. If you know the exact changes of the database, compared to the old version in live server, then the migration script is consisted of the commands that synchornize the two versions.
@@ -141 +137 @@
 '''2.2 Copy war file & migration script from your computer to test server'''
 
-
  1. Copy the war file and the mysql migration script from your computer to the server as follows:
    1. scp <filename>.war molgenis@molgenis35.target.rug.nl:./
@@ -148 +143 @@
 '''2.3 Copy live data from your computer to test server'''
 
-
  1. scp ./mysql<date>LIVEdata.mysql molgenis@molgenis35.target.rug.nl:./databaseDumps/mysql<date>LIVEdata.mysql
 
 '''2.4 Deploy at test server'''
-
 
  1. Ssh to the server:
@@ -160 +153 @@
 '''2.5 Backup Database'''
 
-
  1. mysqldump bbmri -u molgenis –pmolgenis > ~/databaseDumps/<date>bbmriDB.mysql
  1. Check the dumbed file if it is not just an error file …
@@ -166 +158 @@
 '''2.6 Insert the data from live server to test server'''
 
-
  * '''Insert live data (copied from your computer previously)'''
    * mysql -u molgenis -pmolgenis bbmri < ./databaseDumps/mysql<date>LIVEdata.mysql
 
 '''2.7 Apply migration steps:'''
-
 
  * mysql -u molgenis –pmolgenis
@@ -178 +168 @@
 
 '''2.8 Backup & replace the war file on server:'''
-
 
  * The war file is in /usr/share/tomcat6/webapps/biobanks.war
@@ -192 +181 @@
 '''3. Check your deployment'''
 
-
  * Check your deployment at: https://molgenis35.target.rug.nl/biobanks/
 
 '''4. Inform bbmri office'''
 
-
  * Email David [mailto:david.van.enckevort@nbic.nl david.van.enckevort AT nbic.nl]. and wait till they test the server. When that step is done you can deploy to live server.
 
@@ -203 +190 @@
 
 '''Copy war & db from test to live'''
-
 
  * From your computer:
@@ -220 +206 @@
 '''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;
+ 
+{{{
+ 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;
+}}}