Using SBEAMS

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Revision as of 19:06, 15 June 2009 Tfarrah (Talk | contribs) (→Miscellaneous useful SQL queries) ← Previous diff		Revision as of 19:08, 15 June 2009 Tfarrah (Talk | contribs) (→To query SBEAMS directly) Next diff →
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	Will need administrator privileges on your account if you want to do more than just view the data.		Will need administrator privileges on your account if you want to do more than just view the data.
-		+	===Random notes from Terry's log===
-		+	<pre>
-		+
-	6/9/09: Eric D. gave me permission to alter DB via Aqua Data Studio	+
-		+
	load PA build: $SBEAMS/lib/scripts		load PA build: $SBEAMS/lib/scripts
	lib/conf/* describe schema		lib/conf/* describe schema
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	Mysql slightly diff from our sql server. Latter is preferred. but		Mysql slightly diff from our sql server. Latter is preferred. but
	PeptideAtlas is by and large mysql compliant		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		I can monkey around in PeptideAtlas_Test with impunity
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	I should set my devTF (in SBEAMS.conf) to send my log info to my own		I should set my devTF (in SBEAMS.conf) to send my log info to my own
	log files		log files
-		+	</pre>
	===Miscellaneous useful SQL queries===		===Miscellaneous useful SQL queries===

---

Revision as of 19:08, 15 June 2009

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.

Random notes from Terry's log

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 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