Download all the manual correction/curation history records from Apollo

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Xiaomei Li

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Nov 4, 2022, 12:08:11 AM11/4/22
to apollo
Hi all,

Do you know how to download all the manual correction/curation history records from Apollo? I used the History Sevices API, but it did not work. My script is:

curl --header 'Content-Type:application/json' --data '{"username":"de...@demo.com","password":"demo"}' http://demo.genomearchitect.io/Apollo2/featureEvent/findChanges

Do you have any idea how to achieve my purpose? Thank you for your help!

Regards,

Xiaomei.

Nathan Dunn

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Nov 5, 2022, 4:06:44 PM11/5/22
to Xiaomei Li, apollo, Robert Buels, Garrett Stevens

I think what you want is “getHistoryForFeatures”. 


Its a little confusing because its under “Annotation Services”.

In theory you can pass in multiple features as an array.  

You will need to pass in the uniquename associated with the feature (sometimes we call the ID), which is a UUID, though, not the given name.  You should be able to get that from other API methods. 

Nathan


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Xiaomei Li

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Nov 14, 2022, 3:03:36 AM11/14/22
to Nathan Dunn, apollo, Robert Buels, Garrett Stevens
Thank you Nathan.

I tried curl --header 'Content-Type:application/json' --data '{"username":"de...@demo.com","password":"demo", organism: 'Yeast', sequence: 'chrI', features: '9702518f-25fb-419f-a231-eb1776f6e186'}' http://demo.genomearchitect.io/Apollo2/annotationEditor/getHistoryForFeatures

However, it does not work. Do you have any idea about the reason? I found out there are also other API does not work when I follow the instructions. I used http://demo.genomearchitect.io/Apollo2/annotationEditor/getFeatures to get all features for a sequence and it works fine. For example the results could be: {"sequence":"chrI","features":[{"owner":"de...@demo.com","parent_name":"YAL051Wa","uniquename":"2822da45-00a8-4e14-80de-a55b8af962a4","type":{"cv":{"name":"sequence"},"name":"mRNA"},"parent_type":{"cv":{"name":"sequence"},"name":"gene"},"date_creation":1608105184523,"sequence":"chrI","children":[{"owner":"None", ..}

But I am not sure how to pass the result from getFeatures to getHistoryForFeatures API.

Thank you for your help!

Regards,
Xiaomei.

Nathan Dunn

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Nov 14, 2022, 11:22:40 AM11/14/22
to Xiaomei Li, apollo, Robert Buels, Garrett Stevens

So there are 2 issues:

1 - you have to pass in unique name as a JSON object within a JSON array (example below).

2 - you can’t get history on a gene, just a transcript. 


curl --header 'Content-Type:application/json' --data '{"username":"de...@demo.com","password":"demo", organism: 'Yeast', sequence: 'chrI', features: [{uniquename:'2822da45-00a8-4e14-80de-a55b8af962a4'}]}' http://demo.genomearchitect.io/Apollo2/annotationEditor/getHistoryForFeatures




Documentation kind of infers this, but isn’t very explicit. 

This emulates the right-click on the transcript to get history, so you can see what the network tab sends. 

Nathan
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