search

SynBioHub / synbiohub

Web application enabling users and software to browse, upload, and share synthetic biology designs
https://wiki.synbiohub.org
BSD 2-Clause "Simplified" License
73 stars 23 forks source link

Download single toplevel without dependencies #663

Closed jakebeal closed 5 years ago

jakebeal commented 6 years ago

Is it possible to download a single toplevel without getting all of its dependencies?

For example, if I download a yeast strain, I'd like to be able to get just the lightweight ModuleDefinition and outward pointers to the chromosomes, rather than all the chromosomes and the entire genomic sequence.

ccing: @nroehner, @bbartley

cjmyers commented 6 years ago

Sorry but this is not currently possible.

Sent from my iPad

On Aug 7, 2018, at 4:36 PM, Jacob Beal notifications@github.com wrote:

Is it possible to download a single toplevel without getting all of its dependencies?

For example, if I download a yeast strain, I'd like to be able to get just the lightweight ModuleDefinition and outward pointers to the chromosomes, rather than all the chromosomes and the entire genomic sequence.

ccing: @nroehner, @bbartley

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub, or mute the thread.

jakebeal commented 6 years ago

OK, we would like to make this a feature request.

jakebeal commented 6 years ago

I would like to bump the priority of this feature request, as this is greatly slowing down the operation of the SD2 Dictionary Maintainer. Every time that the dictionary-maintainer pulls information about a strain, it gets sent the entire genome sequence as well, which is forcing it to take 1 minute per entry or more.

cjmyers commented 6 years ago

Ok will have a look when Zach and I return next week.

cjmyers commented 6 years ago

This is now implemented as a new endpoint "/sbolnr" and there is a new option to getSBOL in the SBH Frontend in libSBOLj that indicates if you want the recursive document or not. This is deployed on SBH Utah and ready for testing.

nroehner commented 6 years ago

This looks like it's working for me, I'm able to use /sbolnr to download the SBOL for just a Collection and its two member properties, excluding the promoter ComponentDefinitions to which these member properties refer.

One thing I am noticing, however, is that if I fail to log in and call /sbolnr for a private object, rather than receiving a response that the object was not found like with /sbol, I get a 200 code response with an empty SBOL document as its content.

cjmyers commented 6 years ago

@nroehner this should be sorted on SBH Utah now. It should fail on a private object or a non-existent one as not found.