This is a log of changes to the database schema.  Unfortunately I should have started this a long time ago
but didn't, so I tried to reconstruct the stuff prior to 4/2014.

At some point in the future we may start using flyway or liquibase to better manage database schema changes.
In the meantime, if you are a CIPRES developer and you make schema changes, please add an entry to this
file to describe the change, and commit an sql script or a java program, that will migrate a database to
your new format.  Provide instructions here on how to run the migration code, and how to tell whether
a database is both ready for the migration and needs the migration.

Before migrating a database: 
	1. shutdown cipres and its daemons and disable cron jobs that restart them, to make sure nothing is using the db.
	2. backup the db. See example script for doing this, dump_cipres_data.
	3. Run the migration.
	4. If the migration fails and you want to restore from backup, see example script, copy, except
	you already have the mysqldump, so run mysql with stdin redirected from the dump you created in step 2.

11/3/2014:
	Add DATE_CREATED column that's automatically set on insert to users and applications tables.
	Existing rows have the field set to the current date at the time the col is added.
	Run  11_03_2014.sql to make the changes to the db.


8/19/2014:
	Changes to "user" table to support email activation registration.  Added 
		`ACTIVATION_CODE` varchar(50) DEFAULT NULL,
		`ACTIVATION_SENT` datetime  DEFAULT NULL,
		KEY `ACTIVATION` (`ACTIVATION_SENT`)
	If activation code is set, user is not activated and shouldn't be allowed to login.  If you
	don't want to require email activation, then registration just doesn't set activation_code.  If you do
	want to require activation, as the rest service does, then registration will set activation_code and
	activation_sent.  When user activates (by clicking on an emailed link) we clear activation_code and activation_sent.
	Can delete unactivated user records where activation_sent is older than a certain time (Mark and I discussed 
	somewhere between 1 hr and 24 hrs). 

	Run script aug_19_2014.sql to add these fields and index. Ran this script on all our databases, cipresprod, 
	cipres_copy (test), resttest and restprod on 8/28.  It's ok to have extra fields in a table that the code
	doesn't yet reference.

	I also changed the User.find methods so that some find all users and some only find activated users.

5/29/2014:
	- realized the current email/role unique index doesn't let two umbrella apps register
	users with the same email address and we need to allow that.  So
		- add umbrella_appname to user record.  Will be empty string unless role=REST_END_USER_UMBRELLA
		- change unique email index to be email, role, umbrella_appname
	Since we don't have REST in production yet, I'll manually fill in the umbrella_appname for the cipres_copy,
	ngbwalpha and resttest dbs

	Script to make these changes is may_29_2014.sql.  (Read and edit before running as diffent sets of
	changes are needed for dbs where we applied may_2014.sql: ngbwalpha and cipres_copy, vs dbs where
	we haven't yet: resttest and cipres production).

5/27/2014:
	- add table application_preferences (like user_preferences), to server as optional
	properties for applications.  Planned use is to override global usage limit
	settings on a per app basis, same as they can be overriden on a per user basis via
	user_preferences

	Put these changes in a script may_2014.sql and ran it on ngbwalpha and cipres_copy.

5/1/2014: Don't want users to have to create separate account for each CRA enabled app they use
so we need to keep track of which app submitted the job in tasks and job_stats.  
	- removed users.appname, removed EMAIL index and recreated it as unique index email (email,role)
	- added appname to job_stats and tasks
	- added job_stats.su_override column (can use when time is creditted back to us)


???:  new way of storing source docs, hashing content, not storing multiple copies of same content
	- Paul modified source_documents, adding signature field and index.  Use sdkrun org.ngbw.sdk.utils.MigrageDbFiles
	to handle the conversion.  It modifies the schema, then starts converting the data.  Let it finish 
	modifying the schema before starting cipres, but it can convert the data while cipres is running.

??? :  
	- alter table job_stats add  SU_PREDICTED bigint(20) ;
    - alter table job_stats add  SU_COMPUTED bigint(20) ;
    - alter table job_stats add  SU_CHARGED bigint(20) ;

Jan/2014 : I made the changes indicated in the convert*.sql scripts by running them.