FTA-130

[ianlongden]

Start Cassettes.

[gm119]

There are some issues with the code that exports the (has_reg_region, tagged_with, carries_tool) cassette component information - I added a comment to the relevant JIRA ticket (FTA-134)

[gm119]

I've made some comments and code commits for issues I found. Hope they are useful.

[gm119]

you could remove the find_in_vitro_alleles method (lines 226-248) as the function is no longer needed (there is now a new add_in_vitro_allele_entries method in cassette_handler.py that replaces this data is now used in cassettes and not here. Might be good to remove to prevent potential confusion in future !

[gm119]

lines 274-276:

            # NOTE: pub 383755 | FlyBase Experimental Tool information Is the only one used
            # for cassettes. But not in lookup pub curies!
            # So pub_curies will be empty.

this comment is not correct so will need to be removed, and the cassette code in various places will need changing so that pub_curies are reported where appropriate.

I think that this comment (or at least the first line) got inherited from transgenic tool code, but its only true that pub 383755 is the only one used for most information attached directly to FBto (and for FBto-to-FBto associations).
For cassettes (and associations between cassettes and FBto) we use 'regular' attribution of data, like for other data classes - i.e. the attribution is to whichever published paper contained the data that we curated, and we want those pubs to get into the Alliance submission