microbiomedata / sample-annotator

NMDC Sample Annotator
https://microbiomedata.github.io/sample-annotator/static/intro.html
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Integrate ORNL DAAC Identify calls #10

Closed cmungall closed 2 years ago

cmungall commented 3 years ago

The goal is to implement methods within the NMDC sample-annotator framework to access DAAC APIs, and transform the results into json objects conforming to the JSON schema. Broadly there are two types of calls, those that produce (1) QUantityValues, e.g. elevation (2) qualitative, e.g. soil types.

@StantonMartin started on code here: https://github.com/StantonMartin/Identify/

However, this functionality will not be implemented as a standalone script, but in sample-annotator framework. Before attempting to implement this ticket, the implementor must familiarize themselves with the code in this repo, see the README and the unit tests.

As a stub example, the existing codebase uses the google maps API to query for elevation.

See code:

https://github.com/microbiomedata/sample-annotator/blob/bc17c1267b1331e92c33685a9e6cdda47e7ac8e0/sample_annotator/geolocation/geotools.py#L34-L36

and the unit test:

https://github.com/microbiomedata/sample-annotator/blob/bc17c1267b1331e92c33685a9e6cdda47e7ac8e0/tests/test_elevation.py#L16-L26

You can see how this is implemented within the main sample annotator here:

https://github.com/microbiomedata/sample-annotator/blob/bc17c1267b1331e92c33685a9e6cdda47e7ac8e0/sample_annotator/sample_annotator.py#L213-L251

[ADDING MORE LATER...]

For qualitative data we will curate mapping tables, see my PR here: https://github.com/StantonMartin/Identify/pull/1

ssarrafan commented 3 years ago

@cmungall @dehays let me know if this should be re-assigned to Stan or if I should create a new issue for Stan related to this and the meeting you had with him last week.

ssarrafan commented 2 years ago

@cmungall @StantonMartin should this issue be closed, moved to the backlog or moved to the October sprint?

ssarrafan commented 2 years ago

No updates on this since August so I've added the backlog label and removed from the project board.
FYI @cmungall @emileyfadrosh

StantonMartin commented 2 years ago

Integration complete. Closing