Clarity in this case, definitely needs the 1.

On Feb 19, 2013, at 3:38 PM, Peter Cock <p.j.a.c...@googlemail.com> wrote:

> On Tue, Feb 19, 2013 at 6:45 PM, Nicola Soranzo <sora...@crs4.it> wrote:
>> Il giorno mar, 19/02/2013 alle 14.15 +0000, Peter Cock ha scritto:
>>> On Tue, Feb 19, 2013 at 2:00 PM, James Taylor <ja...@jamestaylor.org> wrote:
>>>> On Tue, Feb 19, 2013 at 6:32 AM, Peter Cock wrote:
>>>>> I think it could make sense to define generic 'asn1' and
>>>>> 'asn1-binary' formats in the Galaxy core (name suggestions
>>>>> welcome)
>> 
>> What about
>> 
>> extension="asn" type="galaxy.datatypes.data:GenericAsn1"
>> 
>> and
>> 
>> extension="asnb" type="galaxy.datatypes.binary:GenericAsn1Binary"
>> 
>> like GenericXml class?
> 
> Those seem sensible to me as the class names, although I'm
> not so sure about the format names (aka 'extensions' in Galaxy
> terms). I'd prefer to see the '1' in the name for clarity. My
> suggestions of 'asn1' and 'asn1-binary' were based on NCBI usage.
> 
> Perhaps the Galaxy team could comment on their views here
> for conciseness versus clarity in file format names for Galaxy?
> 
>>>>> Would a pull request implementing this be acceptable?
>>>> 
>>>> Yes. My understanding is that ASN is a completely flexible metaformat,
>>>> like XML, and so should be under either Text or Data, with appropriate
>>>> subtypes defined for blast, et cetera.
>>> 
>>> Thank James,
>>> 
>>> Yes - very like XML, but with the subtlety that ASN.1 comes in text and
>>> binary favours (which I presume applies to all the variants, although
>>> the binary versions may not be as commonly used for the smaller files).
>>> 
>>> Nicola - do you want to make a pull request to galaxy-central defining
>>> ASN.1 text and binary formats (which we can then subclass for the
>>> NCBI BLAST+ wrappers)? Or should I?
>> 
>> If you mean a minimal implementation, I can surely do that. If something
>> more elaborated is needed, then probably you are more qualified than me!
> 
> The current minimal implementation you sent me for BLAST+
> would be an excellent start. Things like data type sniffers etc
> would be a nice to have feature, but can be added later I think.
> And the sooner this gets into the Galaxy core, the sooner we
> can use it in the BLAST+ wrappers :)
> 
>>> I think the mime-type for the base ASN.1 text format should probably
>>> be text/plain based on the NCBI usage patterns.
>> 
>> Ok.
>> 
>>> I'm not sure what the mime-type for the base ASN.1 binary format
>>> should be (but I don't think it should be chemical/ncbi-asn1-binary).
>> 
>> application/octet-stream ?
> 
> Probably OK - we can/should test this by uploading a test
> binary ASN.1 file into Galaxy and downloading it out again.
> 
> Thanks,
> 
> Peter

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