Re: [GUSDEV] [ApiDB] issue: ExternalNaSequence, VirtualSequence and NaSequence

[Chris S. <sto...@pc...>]

As I mentioned in another gusdev mail thread, I would like (Frank) to  
generate a list of proposed changes to incorporate into a GUS 3.6  
release hopefully sometime this month. If those on the gusdev list  
agree then sometime next month we will start assigning changes for  
supported plug ins.

Chris

On Mar 2, 2007, at 4:19 PM, Steve Fischer wrote:

> ok, great.
>
> no, source_id is string1 in one view and string2.  we'd have to  
> adjust that.
>
> in Api we plan on correcting this with a schema/data patch.
>
> steve
>
> pi...@pc... wrote:
>
>> I agree with this. In fact, the current database being used by our  
>> mammalian
>> DoTS build has incorporated a source_id into the assembly view of
>> NASequence. I
>> believe (could be wrong on this) that this is the only view without a
>> source_id.   So this would clear the way to having source_id in the
>> super class
>> for the "official" GUS schema. Are all the nasequenceimp views  
>> using the same
>> field for source_id? Are there other views missing a source_id?
>>
>>
>>
>>
>> Quoting Steve Fischer <sfi...@pc...>:
>>
>>
>>
>>> folks-
>>>
>>> we've been again reminded of the issue that toxo stores its  
>>> chromosome
>>> sequence in VirtualSequence while the other two use  
>>> ExternalNaSequence.
>>>
>>> this means that we cannot re-use sql code, which is a headache.
>>>
>>> our proposed solution is to upgrade NaSequence view (the  
>>> superclass) to
>>> have a source_id column.   We feel that this is correct  
>>> semantically,
>>> and also solves our problem.
>>>
>>> the semantics are that:
>>> (1) NaSequence already has an external_database_release_id, which
>>> makes no sense w/o source_id
>>> (2) the pair (external_database_release_id, source_id) has  
>>> "universal"
>>> semantics (ie, not just limited to "external" sequences).  that
>>> semantics is "dataset and stable_id"
>>>
>>> steve
>>> _______________________________________________
>>> ApiDB mailing list
>>> Ap...@pc...
>>> https://mail.pcbi.upenn.edu/mailman/listinfo/apidb
>>>
>>>
>>>
>>
>>
>>
>>
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