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To add an attribute to a table in SBEAMS:
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The examples used throughout the file are for changes to table in
PeptideAtlas module, but can be applied to other modules.  Please feel
free to edit or send me email if directions aren't clear (email is nking).

(1) First make sure your dev area is up to date so that any changes
you check in will not conflict with current version.

    cd to dev area 

    cvs update -dPR

(2) Edit the load script for the SBEAMS table [in dev area]:

    cd /net/dblocal/www/html/devUser/sbeams/lib/scripts/PeptideAtlas 

    edit load_atlas_build.pl 

    to include 
    - read-in or calculate new attribute
    - add the new attribute in relevant %rowdata for updateOrInsertRow
      operation


(3) Edit the SBEAMS table column file [in dev area]:

    cd /net/dblocal/www/html/devUser/sbeams/lib/conf/PeptideAtlas

    edit PeptideAtlas_table_column.txt 

    add the new attribute to the relevant table section

    (NOTE: if you want tkdiff and cvs diff to show changes between
    revisions most clearly, stick to using either Excel for editing
    the file, or a linux tool such as OpenOffice.  OpenOffice encloses
    strings in quotes, so you'll see that tkdiff and cvs diff will
    unfortunately flag everthing as different if the previous file 
    didn't have enlcosing quotes.)


(4) If the new attribute is to be a searchable constraint in an
    SBEAMS cgi:
    
    If this is the case, you'll need to edit the table columns
    for the cgi in the table column file:

    cd /net/dblocal/www/html/devUser/sbeams/lib/conf/PeptideAtlas

    edit PeptideAtlas_table_column.txt
    (see AT_GetPeptides section and follow existing constraints)


(5) Populate the SQL transaction scripts in SBEAMS [in dev area]:

    cd /net/dblocal/www/html/devNK/sbeams/lib/scripts/PeptideAtlas

    ./create_peptideatlas_sql.csh


(6) Update the driver tables in SBEAMS:  

    Note that updating the drivers updates the live production SBEAMS,
    so even though you'll be testing in your dev area, the table structure
    changes will be changed globally.
 
    cd /net/dblocal/www/html/devNK/sbeams/lib/scripts/Core

    set CONFDIR = "../../conf"

    ./update_driver_tables.pl $CONFDIR/PeptideAtlas/PeptideAtlas_table_column.txt 

    ./update_driver_tables.pl $CONFDIR/PeptideAtlas/PeptideAtlas_table_property.txt 

(7)  Alter the database tables with SQL calls:

     Use assql, or AquaDataStudio or other tool to alter table add column ...

     Paste the CREATE or ALTER statement, etc, directly out of the relevant
     sql file:

     For example, relevant file for this example:
     /net/dblocal/www/html/devNK/sbeams/lib/sql/PeptideAtlas/PeptideAtlas_CREATETABLES.mssql

     Example sql statements:

       ALTER TABLE peptideatlas.dbo.peptide_instance ADD search_batch_ids varchar(255)

       ALTER TABLE peptideatlas.dbo.peptide_instance ADD n_genome_locations int
       ALTER TABLE peptideatlas.dbo.peptide_instance DROP COLUMN n_mapped_locations 


(8)  If you want to include the new attribute on the web page:

     Edit the cgi page:

     cd /net/dblocal/www/html/devNK/sbeams/cgi/PeptideAtlas

     edit GetPeptides 


(9) Test your changes in your dev area

    If receive errors listing table columns, etc. that you changed,
    but it appears that the cgi hasn't received them, it may be
    a known problem with update_drivers.pl.
    see http://db.systemsbiology.net/mantis/bug_view_page.php?bug_id=0000013

    In this case, please contact Eric Deutsch for advice.


(10) Commit [dev area] changes to SBEAMS cvs 

    use tkdiff or cvs diff to check that differences to files are only
    what you modified (someone may have checked in changes in between
    your update and now, especially if you've taken awhile to get
    to this stage.)

    cd /net/dblocal/www/html/devNK/sbeams/lib/scripts/PeptideAtlas 
    cvs commit load_atlas_build.pl

    cd /net/dblocal/www/html/devNK/sbeams/lib/conf/PeptideAtlas
    cvs commit

    cd /net/dblocal/www/html/devNK/sbeams/cgi/PeptideAtlas
    cvs commit GetPeptides

    cd /net/dblocal/www/html/devNK/sbeams/lib/perl/SBEAMS/PeptideAtlas
    cvs commit Tables.pm


(11) Commit the dev changes to production:

    Log in to db as user sbeams and run:  

    cd /net/dblocal/www/html/sbeams/dirPath  
    cvs update -dP  yourFile

    cd /net/db/lib/sbeams/dirPath
    cvs update -dP yourFile
 
    cd /net/dblocal/wwwSSL/html/sbeams/dirPath
    cvs update -dP yourFile

    cd /net/dblocal/www/html/macrogenics/sbeams/dirPath
    cvs update -dP yourFile

(12) Load module tables:

    cd /net/dblocal/www/html/devNK/sbeams/lib/scripts/PeptideAtlas

    use ./load_atlas_build.pl

    (Note that for PeptideAtlas, you'll need to use the SBEAMS web
    interface, ManageTable, to add a record before running the load
    script.)