Not all annotations show up in view

Description

A user need a way to query for entities filter by annotations: https://github.com/Sage-Bionetworks/synapser/issues/195
In his use case, the entity annotation is a list of items. In view, only the first item shows up.

I repro this with entity: https://www.synapse.org/#!Synapse:syn11472588
and view: https://www.synapse.org/#!Synapse:syn15672495/tables/

Environment

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Kara Woo
January 9, 2020, 11:10 PM

Unless I am missing something, the new feature is not documented on that page. What I am trying to figure out how to do is filter a file view based on one of the values in the list of annotations, e.g.

which works if ‘a' is the only value for the annotation mykey, but (understandably) not if ‘a’ is one of several. I don’t see the syntax for how to do this query when mykey is a list column.

 

To your question about whether this addresses my comment from Nov. 2018, I think the answer is also no, but I think that is intentional? The use case of tracking specimen IDs in annotations would require support for many more values than we are supporting with this feature (possibly tens of thousands, as we discussed in June). This feature will certainly be useful for other situations, but probably not the one from my comment above.

Bruce Hoff
January 9, 2020, 11:42 PM

thanks for your reply.

do you agree that the new feature should be documented in the [query examples|ttps://rest-docs.synapse.org/rest/org/sagebionetworks/repo/web/controller/TableExamples.html] page? (I believe the syntax is 'HAS', e.g. 'SELECT * from <synID> WHERE mykey HAS 'a' .)

> The use case of tracking specimen IDs in annotations would require support for many more values than we are supporting with this feature

Yes, in that case the use case you mentioned on 16/Nov would not be used to validate this issue.

Kara Woo
January 15, 2020, 10:43 PM
Edited

It looks like it's SELECT * FROM <synID> WHERE mykey HAS ('a') (parentheses are necessary). This works in the web but not in synapser, I'm guessing that's known and that programmatic client support is a separate issue. So from my perspective this is done once it makes it into the documentation.

Bruce Hoff
January 17, 2020, 2:06 AM

> This works in the web but not in synapser, I'm guessing that's known and that programmatic client support is a separate issue

Yes: We are tracking that here:

Bruce Hoff
January 24, 2020, 10:53 PM

Closing based on Kara's last comment. (The related outstanding issues are tracked elsewhere.)

Fixed

Assignee

Ziming Dong

Reporter

Kimyen Truong

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Validator

Kara Woo

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Priority

Minor
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