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What is the difference between the
'Run MetaData Wizard' --> Select Data Source
and
‘Create Query Subject' --> 'Data Source' and then picking the datasource from the wizard
Are they the same thing?
They are identical if you pick the options as suggested above.
In the Run Metadata Wizard you have options to import metadata from other Cognos tools or from 3rd party applications.
In the create query subject, you can create Data Source queries, which done directly against the data source.
Model query, which done against other query subjects in the model
and stored procedure, which maps to DB stored procedure that return result set.