MATLAB DATABASE Configuration

1st time use: Matlab ODBC Database A data source is a combination of: Data we want to access How to find the data Data sources are accessed by ODBC drivers Matlab ODBC Database An ODBC driver is a standard Windows interface that enables communication between database management systems and SQL-based applications

Configuration: Open Matlab Click Start Toolboxes Database Visual Query Builder

Query  Define ODBC Data Source..

Click the Add button Choose SQL Server and click Finish

Type in the data source name “gene_arch”, choose LIRANSRV for the server and click finish Click OK

Now “gene_arch” is showing in the data sources list Back in Matlab – a conn object of type database was added Please notice that you receive a valid handle

2nd time use and up: Any other time after the first configuration just type conn = database('gene_arch','','password')

Observing database structure DB’s tables: dbmeta = dmd(conn); databasetables = tables(dbmeta, 'Gene-Architecture','dbo') Table’s columns: dbmeta = dmd(conn); tabcolumns = columns(dbmeta, 'Gene- Architecture','dbo',’TableName’)

MATLAB Data manipulation

Fetch data results= fetch(connection,select) connection = the connection we established before select = SQL select statement: 'select ColumnName1,…, ColumnNameN, from TableName‘ Example: results= fetch(conn,'select Name, Details from Species');

fastinsert(conn,’TableName’,columnNames,data) Insert data fastinsert(conn,’TableName’,columnNames,data) columnNames = {‘ColumnName1';’ColumnName2’; … ; ColumnNameN'}; data = either cell array (i.e. {'A';'B'}) cell array in a structure (i.e. st.Names={'A';'B'},st.Details={'Apple';'Banana'}) Example: fastinsert(conn,'Species`, {'Name';'Details'}, data);

Update data Example: where = SQL where clause: update(conn,’TableName’,columnNames,data,where) where = SQL where clause: {‘where ColumnName1 operator value1’; … ; ‘where ColumnName2 operator value2’} operators: =, >, <, like, in,… Example: update(conn,‘Species‘,{‘Details’},data,{‘where Name like ‘’Anopheles gambiae’’’});

Execute general query query = Any SQL query. i.e.: curs = exec(conn,query) query = Any SQL query. i.e.: 'delete from Orthologous_db where idOrthologous_db=12’ curs = A cursor, an object which holds information about the transaction with the database Why not to use exec?

Commit & Rollback commit(conn)makes permanent changes made to the database connection since the last commit or rollback function was run rollback(conn)reverses changes made to a database using fastinsert, insert, or update (and not to exec!) via the database connection To use rollback, the AutoCommit flag for conn must be off set(conn,'AutoCommit','off')

DB Preferences: setdbprefs ErrorHandling: store/report/… Sets preferences for retrieval format, errors, NULLs, and more ErrorHandling: store/report/… DataReturnFormat: cellarray /numeric/structure NullStringRead: NULL/’’/… Example: s = setdbprefs; s.ErrorHandling = 'report‘; setdbprefs(s);

A good demo Can be found here Combines tools from both bioinformatics and database matlab toolboxes Note it uses insert instead of fastinsert (slower and older) A “shlif” of functions can be found in the same folder (shlif.m) Also, an example connection script (connecting.m)