Using SBEAMS

From SPCTools

To query SBEAMS directly

Use Aqua Data Studio on mimas by copying ~tfarrah/bin/datastudio.sh to your own ~/bin and executing. Or, can install on desktop. Ask Eric D. for an account.

hostname: mssql
port: default is fine
(Terry's account username: usual, password: TFmssql205)
click mssql in left sidebar, then server->properties to adjust username/pwd.
click button with mag. glass over table for query analyzer
Select a database to connect to.
Type in queries and press green triangle to submit.

Will need administrator privileges on your account if you want to do more than just view the data.

6/9/09: Eric D. gave me permission to alter DB via Aqua Data Studio

load PA build: $SBEAMS/lib/scripts

lib/conf/*   describe schema

Add column:

-- edit table in table_columns file (or whatever)
     audit columns e.g. created_by
     can delete a record by setting record status to D
         still appears, but queries can't see it.
-- execute generate_schema.pl  -- to help create SQL statement

generate_schema.pl -table_c PeptideAtlas_table_column.txt --table_p PeptideAtlas_table_property.txt --schema ../../sql/PeptideAtlas/PeptideAtlas --module PeptideAtlas --dest mssql

  == will generate files in ../../sql. these scripts never in svn
-- write out SQL statement and ask Eric to execute
-- document changes in $SBEAMS/doc/upgrade/0.24
      (browse through this)
-- run:
       cd $SBEAMS/lib/script/Core
      ./update_driver_tables.pl \
        ../../conf/PeptideAtlas/PeptideAtlas_table_column.txt
      (example gleaned from $SBEAMS/doc/upgrade/0.24)

Mysql slightly diff from our sql server. Latter is preferred. but

 PeptideAtlas is by and large mysql compliant

I don't need to change schema bec. ProtProphet data is already there. (?) Just need to change view.

PeptideMapping table == mapping of peptide in particular build.

No analagous thing for protein. Could add ProtProph to all peptides
mapping to that prot, or could create a new table.

1) need to find place in schema to hold value 2) need to change view

I can monkey around in PeptideAtlas_Test with impunity

 Dave has changed this for me.

I should set my devTF (in SBEAMS.conf) to send my log info to my own

 log files

Miscellaneous useful SQL queries

If you need to change schema constraints after defining your schema:

1. Change the constraint in $SBEAMS/conf/PeptideAtlas/PeptideAtlas_table_column.txt
2. Actually make the schema change:

ALTER TABLE employee  ADD CONSTRAINT pk_employee PRIMARY KEY (EmployeeId)
ALTER TABLE employee DROP CONSTRAINT pk_employee