612 taxon id

[ejacox]

Replace NCBI taxon ID integer with ontology term in References and ReferenceSets. Propagates issue ga4gh/ga4gh-schemas#612 and pull request ga4gh/ga4gh-schemas#699.

[codecov-io]

Codecov Report

Merging #1513 into master will increase coverage by -0.17%.

@@            Coverage Diff             @@
##           master    #1513      +/-   ##
==========================================
- Coverage   84.95%   84.79%   -0.17%     
==========================================
  Files          32       32              
  Lines        7087     7110      +23     
  Branches      897      902       +5     
==========================================
+ Hits         6021     6029       +8     
- Misses        907      919      +12     
- Partials      159      162       +3

Impacted Files	Coverage Δ
ga4gh/server/datarepo.py	93.97% <ø> (ø)	✅
ga4gh/server/cli/repomanager.py	84.8% <ø> (-0.32%)	❌
ga4gh/server/datamodel/references.py	93.49% <63.15%> (-5.17%)	❌

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[david4096]

Great!

http post localhost:8000/references/search referenceSetId=WyJoZzM3Il0

Gives:

HTTP/1.0 200 OK
Content-Length: 367
Content-Type: application/json
Date: Thu, 22 Dec 2016 01:59:13 GMT
Server: Werkzeug/0.11.5 Python/2.7.12+

{
    "nextPageToken": "", 
    "references": [
        {
            "id": "WyJoZzM3IiwicmVmX2JyY2ExIl0", 
            "isDerived": false, 
            "length": "81188", 
            "md5checksum": "90977a37195d3fd247e4916b5b4cbae8", 
            "name": "ref_brca1", 
            "sourceAccessions": [
                "GA4GH_CTS_01_BRCA1"
            ], 
            "sourceDivergence": 0.0, 
            "sourceUri": "", 
            "species": {
                "id": "9606", 
                "sourceName": "NCBI", 
                "sourceVersion": "", 
                "term": "Homo sapiens"
            }
        }
    ]
}

Looks good!

Set my own species ID from the repo command line using:

python repo_dev.py add-referenceset ga4gh-example-data/registry.db ga4gh-example-data/ref_brca1.fa.gz --species '{"id": "1234"}'

And inspected the database, which nicely had my entry.

WyJyZWZfYnJjYTEiXQ|ref_brca1|||0|12827085103f42e97428dc05a7f26fec|{"sourceName": "", "sourceVersion": "", "term": "", "id": "1234"}|[]||/home/david/git/server-1/ga4gh-example-data/ref_brca1.fa.gz

Ran this branch of compliance against it reporting one already known failure.

In the future we might provide an improved interface for setting species ontology terms via the repo manager.

+1

[david4096]

You provide the class as a second argument (protocol.OntologyTerm) when inserting a reference set. Any reason for the discrepancy? Does it produce a nice exception?

[david4096]

Closes #1490