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Fix RNA notebook error #13

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david4096 opened this issue Dec 6, 2016 · 4 comments
Closed

Fix RNA notebook error #13

david4096 opened this issue Dec 6, 2016 · 4 comments

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@david4096
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There is currently a 400 bad request error in the RNA quantification notebook. We need to figure out the reason and fix it in the notebook.

@saupchurch
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There are also still some hard cded IDs that were missed in #12

@saupchurch
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saupchurch commented Dec 7, 2016

It looks like the 1kg server is having a problem parsing the JSON that the notebook is sending.

The server is reporting this error:
ERROR:ga4gh.client.client:400 {"errorCode": 1918634080, "message": "Cannot parse JSON: '{\"bioSampleId\": \"\", \"pageToken\": \"\", \"pageSize\": 0, \"rnaQuantificationSetId\": \"WyIxa2dlbm9tZXMiLCJFLUdFVVYtMSAxMDAwIEdlbm9tZXMgUk5BIFF1YW50aWZpY2F0aW9uIl0\"}'"}

which looks like it is coming from runSearchRequest in backend.py:
request = protocol.fromJson(requestStr, requestClass) is throwing a protocol.json_format.ParseError

Could this have been introduced when biosampleID was added to the RNA API?

@david4096
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^ confirmed the version on 1kgenomes needs to be updated.

@david4096
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#16

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