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I had doctrine and ORM working very well together.

Then I removed three rows from my MySQL db and removed those values from my model. Now doctrine returns absolutely nothing. Not even a NULL value from the function or an error.

I'm wondering if doctrine caches my schema somewhere or if I'm missing something

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Well if you removed the rows (ie data from the table) then you wouldnt get anything returned as ther eis no data to return. If you mean you removed/modfied the table(s) structure then you need to rebuild your model.

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Yes I did modified the table structure (removed three rows). How do I rebuild the model other then edit and save?
those arent rows they are columns :-) a row is a set of data for each column - ie. a record. Anyhow you need to use doctrine build-model assumign youre using the command line task set up. doctrine-project.org/documentation/manual/1_1/en/…
I dont know much about CI, much prefer Symfony and Agavi :-) At any rate you need to remove the stuff specific to those columns from your models (and corresponding table classes if youre using concrete tables). The easiest way to do this is to use the cli tasks to rebuild schmea/db/models but if youve done everythign manually then you need to undo everything manually that relates to what you changed.

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