This reverts commit 3e24194c.

It's Dan Barrell's fault.

Replaced hardcoded ensadmin with a user command line parameter. If user is not defined then the script will use ensadmin. The script is not dying anymore if the user connected to the MySQL server is not mysqlens but it will throw a warning. This is to be able to run the script outside the Sanger infrastructure...

Funcgen has renamed its sql file from 'efg.sql' to 'table.sql', therefore schema_patcher.pl has to be modified to reflect this change.

Kieron Taylor authored 9 years ago and Magali Ruffier committed 9 years ago

Super-tidying commit. Eliminate unnamed statement handle, don't pass fruitless object types, add some comments, change some others, collapse some code into neater forms

Kieron Taylor authored 9 years ago and Magali Ruffier committed 9 years ago

Old xref connections should not be typed by the new master xref. Generate type mappings for both sets explicitly.

Kieron Taylor authored 9 years ago and Magali Ruffier committed 9 years ago

Put all object types of ensembl IDs needed for a process_dependents() call into a hash. Query that every time a type is required, instead of trusting the calling code type.

Kieron Taylor authored 9 years ago and Magali Ruffier committed 9 years ago

Introduce ensembl type for new xrefs, such that the new ensembl ids object_xrefs are not required to share object type with the original master xref

Kieron Taylor authored 9 years ago and Magali Ruffier committed 9 years ago

Add lookup for current xref object type for each iteration. Also syntax fixes, cleanup, and commenting.

See https://github.com/Ensembl/ensembl/pull/117