Deleteriousness CADD Score REST API Query Fails in IVA

[nicholsn]

I am setting up iva-0.7.0 to work with opencga-1.2.0-rc and seeing an error.

When I set a filter on the cadd_raw and cad_scaled deleteriousness scores, the web console throws an error when accessing the following REST endpoint:

http://localhost:8080/opencga-1.2.0-rc/webservices/rest/v1/analysis/variant/query?sid=eyJhbGciOiJIUzI1NiJ9.eyJzdWIiOiJvcGVuY2dhIiwiYXVkIjoiT3BlbkNHQSB1c2VycyIsImlhdCI6MTUwNjExNDU2MSwiZXhwIjoxNTA2MTE2MzYxfQ.V1bBllHHXMKQhdfZ2h0DiDO72vklkViWFWpV8HDWRRM&timeout=60000&summary=true&annot-functional-score=cadd_raw%3C%3C.3%2Ccadd_scaled%3E%3E%3D5&studies=opencga%40hgi%3ABOBCAT&exclude=studies&limit=10&skip=0

The JSON response is the following:

{
"apiVersion": "v1",
"warning": "",
"error": "Malformed \"annot-functional-score\" query : \"cadd_raw<<=5,cadd_scaled>>.3\". Expected: Functional score: {functional_score}[<|>|<=|>=]{number}, e.g. cadd_scaled>5.2,cadd_raw<=0.3",
"queryOptions": {
"metadata": true,
"skipCount": true,
"exclude": [
"studies"
],
"skip": 0,
"timeout": 60000,
"limit": 10
},
"response": [
{
"id": "",
"dbTime": -1,
"numResults": -1,
"numTotalResults": -1,
"warningMsg": "Future errors will ONLY be shown in the QueryResponse body",
"errorMsg": "DEPRECATED: org.opencb.opencga.storage.core.variant.adaptors.VariantQueryException: Malformed \"annot-functional-score\" query : \"cadd_raw<<=5,cadd_scaled>>.3\". Expected: Functional score: {functional_score}[<|>|<=|>=]{number}, e.g. cadd_scaled>5.2,cadd_raw<=0.3",
"resultType": "",
"result": []
}
]
}

If I update my query to use the suggested example of functional_score=cadd_scaled%3E5.2,cadd_raw%3C=0.3 I get a response, but the filters do not appear to be respected (i.e., the cadd scores are not within the expected range)

http://localhost:8080/opencga-1.2.0-rc/webservices/rest/v1/analysis/variant/query?sid=eyJhbGciOiJIUzI1NiJ9.eyJzdWIiOiJvcGVuY2dhIiwiYXVkIjoiT3BlbkNHQSB1c2VycyIsImlhdCI6MTUwNjE3OTAyMiwiZXhwIjoxNTA2MTgwODIyfQ.x73ZDJEKT08R0PA9pFnsS1e2uyzZQS-4AK1_2Y8Fme8&timeout=60000&summary=true&functional_score=cadd_scaled%3E5.2,cadd_raw%3C=0.3&studies=opencga%40hgi%3ABOBCAT&exclude=studies&limit=10&skip=0

Any idea what I am doing wrong here?

[nicholsn]

@imedina, any thoughts on this?