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Give necessary rights to APPS user, so it can select on any other schema objects. For example, SELECT ANY TABLE privilege can be given to APPS and similarly other ANY type Grants can be given to APPS user.
Use custom schema user in FlexDeploy to create objects and grant to APPS.
Create custom user and password properties on Deploy workflow to be at Target Scope. For example,
Defined values for these user and password in various Target pages in Topology.
Use custom properties on Project Files tab for specific Files.
If you want the file to populate with the correct schema user and password property attached, create the filename like "SCHEMASCHEMANAME_FILENAME.sql"
e.g. SCHEMAPOS_registertrans.tbl
This will automatically try to use the properties FDEBS_DB_SCHEMAPOS_USER and and FDEBS_DB_SCHEMAPOS_PASSWORD, so if using the filenames to link the schema users, follow this naming standard of the property codes.