candig / candig-schemas Goto Github PK

Implement and compile .proto files for the new search schema.

sample query structure:

"query":{
"logic":{
"AND":[
"A",
"B"
]
} "components":[
{
"component_id":"A",
"table":"diagnosis",
"filter":[
{
"field":"datasetId",
"value":"WyJjb25jb3JkYW5jZV9Nb250cmVhbCJd",
"operator":"="
},
{
"field":"cancerType",
"value":"carcinoma" ,
"operator":"in"
}
]
},
{
"component_id":"B",
"table":"variant",
"filter":[
{
"field":"datasetId",
"value":"WyJjb25jb3JkYW5jZV9Nb250cmVhbCJd",
"operator":"="
},
{
"field":"referenceName",
"value":"chr13",
"operator":"=",

        },
        {
           "field":"start",
           "value":32936732,
           "operator":"="
        },
        {
           "field":"end",
           "value":32936733,
           "operator":"="
        }
     ]
  }

],
"return":[
{
"table":"treatment",
"field":[
"startDate",
"stopDate",
"drugList"
]
},
{
"table":"sample",
"field":[
"tumourContent"
]
}
],
"limit":1000
}

At least in setup.py!

Update GA4GH schema to incorporate some pipeline data

A new proto file will be created

Currently, the way of compiling *.proto files does not make a lot of sense, the directory that is specified in the .proto files do not exist, and the existing setup.py within the repo did not work as expected, it is worth taking a look at how we can improve the process.

rather than recompiling the schema at time of sdist it should just use the compiled code as is, revisit this issue once i have time

• run tests on develop branch

In variants_services.proto, two new types of responses/requests should be added.

This is to make sure that the related functions in backend.py in ga4gh-server consumes proper-formatted requests and responses.

Related Issue: CanDIG/candig-server#9

This issue can be closed when:

• The test suite passed
• The schemas can be correctly compiled with python process_schemas.py _some_protocol_version
• The compiled schemas are identical to the ones compiled under python 2.7.

Compatibility with the candig-server shall be tracked and resolved in another ticket.