Attaching .ab1 files

[beyerh]

Hello,

Is there a way to attach .ab1 traces (or any attachments other than .gb) using icebreaker?
Thank you very much.

[veghp]

Hi,
I'm not sure, but would the IceClient.requests files parameter work?

https://edinburgh-genome-foundry.github.io/icebreaker/#icebreaker.IceClient.request

I plan to review the codebase in the near future to make sure it works with the latest ICE, then can have a look into it.

[beyerh]

Thank you for your feedback. I manage to do it with JSON data using IceClients.requests and PUT but not with BLOB data such as ab1 files (Object type bytes is not JSON serializable).

[veghp]

I see. Did you manage to add this ab1 file via the web interface? There is an attachment upload box, but when ICEbreaker was developed it was not yet available: JBEI/ice#83

This is the API docs entry I found regarding attachments: https://ice.jbei.org/apidocs/org/jbei/ice/lib/entry/attachment/Attachments.html

[beyerh]

Yes, I can upload using the web interface.
My understanding is that IceClinets.requests only works with REST API, which attachments are not, right?

However, the ICEbreaker states that one can upload files using the parameter files as a dict of the form {fileId: (filename, content, mimetype)}.

I am not very sure how to do that. I have been unsuccessful so far and my naive attempts likely have several issues if it is possible at all that way:

ice.request("PUT","entry/286", files={'100': ('test.ab1', theblob[0][0], 'multipart/form-data')})

I am very unsure about the endpoint, fileId, and mimetype to use.