===========================================================================
To add a table to SBEAMS:
===========================================================================

The examples used throughout the file use module PeptideAtlas as an example,
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 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 table 

    (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.)

    For datatypes other than primitive types, such as making a column
    a multilink column for example, best to look for existing structures
    and their related tables in the Module_table_column.txt file
    (where Module here is PeptideAtlas). 


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

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

    ./create_peptideatlas_sql.csh

    where create_peptideatlas_sql.csh contains:

    #!/bin/csh

    setenv SBEAMS /net/dblocal/www/html/devNK/sbeams
    cd $SBEAMS/lib/scripts/Core

    foreach dbtype ( mssql mysql pgsql )

        ./generate_schema.pl --table_prop

        ../../conf/PeptideAtlas/PeptideAtlas_table_property.txt \
            --table_col ../../conf/PeptideAtlas/PeptideAtlas_table_column.txt
            --schema_file \
            ../../sql/PeptideAtlas/PeptideAtlas --destination_type $dbtype

    end


(4) Update the driver tables in SBEAMS:  

    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 

(5)  Add the database table using sql statement:

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

     can paste the CREATE statement, directly out of 
     /net/dblocal/www/html/devNK/sbeams/lib/sql/PeptideAtlas/PeptideAtlas_CREATETABLES.mssql
     into AquaDAtaStudio query analyzer and execute it

     something like:

          CREATE TABLE dbo.sample_publication (
            sample_publication_id      int IDENTITY NOT NULL,
            sample_id                  int NOT NULL,
            publication_id             int NOT NULL,
            date_created               datetime NOT NULL DEFAULT CURRENT_TIMESTAMP,
            created_by_id              int NOT NULL DEFAULT '1',
            date_modified              datetime NOT NULL DEFAULT CURRENT_TIMESTAMP,
            modified_by_id             int NOT NULL DEFAULT '1',
            owner_group_id             int NOT NULL DEFAULT '1',
            record_status              char(1) NOT NULL DEFAULT 'N',
            PRIMARY KEY (sample_publication_id)
          )
          GO

(6) If you've added a new table, need to include that in Tables.pm

    edit
    /net/dblocal/www/html/devNK/sbeams/lib/perl/SBEAMS/PeptideAtlas/Tables.pm
   
    to include $TBAT_SAMPLE_PUBLICATION

(7) Try pages in 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.


(8) 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

(9) 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

(11) 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.)