Strucutural variant endpoint to power plotting position.

  Eschew additional info for initial implementation.

bravo_api/blueprints/structvar/structvar.py

@@ -0,0 +1,74 @@
+import logging
+import pymongo
+from flask import current_app, Blueprint, jsonify, make_response, Response
+from flask_cors import CORS
+from webargs import fields
+from webargs.flaskparser import FlaskParser
+from marshmallow import RAISE
+
+logger = logging.getLogger(__name__)
+bp = Blueprint('structvar', __name__)
+CORS(bp)
+
+
+class Parser(FlaskParser):
+    # Override in order to raise validation error for unknown args
+    DEFAULT_UNKNOWN_BY_LOCATION = {"query": RAISE}
+
+
+parser = Parser()
+
+sv_region_argmap = {
+    'chrom': fields.Str(required=False, validate=lambda x: len(x) > 0,
+                        error_messages={'validator_failed': 'Value must be a non-empty string.'}),
+    'start': fields.Int(required=False, validate=lambda x: x >= 0,
+                        error_messages={
+                            'validator_failed': 'Value must be greater than or equal to 0.'
+                        }),
+    'stop': fields.Int(required=False, validate=lambda x: x > 0,
+                       error_messages={'validator_failed': 'Value must be greater than 0.'}),
+}
+
+
+@bp.route('/sv/region', methods=['GET'])
+@parser.use_args(sv_region_argmap, location='query')
+def get_sv_region(args: dict) -> Response:
+    result = sv_region(current_app.mmongo.db.structvar, args['chrom'], args['start'], args['stop'])
+    return make_response(jsonify(result))
+
+
+def sv_region(structvars: pymongo.collection.Collection,
+              chrom: str, roi_start: int, roi_stop: int) -> list:
+    """ Lookup structual variant data by region. Include all structural variants where the pos OR
+    end is within the given range of interest.
+
+    @param structvars: Structural variants collection
+    @param chrom: Chromosome containing regoin of interest.
+    @param roi_start: Start position of region of interest.
+    @param roi_stop: Stop position of region of interest.
+    """
+
+    pipeline = [
+        {'$match': {
+            '$and': [
+                {'chrom': {'$eq': chrom}},
+                {'$or': [
+                    {'$and': [
+                        {'pos': {'$gte': roi_start}},
+                        {'pos': {'$lte': roi_stop}}
+                    ]},
+                    {'$and': [
+                        {'end': {'$gte': roi_start}},
+                        {'end': {'$lte': roi_stop}}
+                    ]},
+                    {'$and': [
+                        {'pos': {'$lte': roi_start}},
+                        {'end': {'$gte': roi_stop}}
+                    ]}
+                ]}
+            ]}
+         }
+    ]
+
+    cursor = structvars.aggregate(pipeline)
+    return [item for item in cursor]

tests/mongo_fixtures/structvar.json

@@ -0,0 +1,57 @@
+[
+  {
+    "_id": {
+      "$oid": "deadbeefdeadbeef22000001"
+    },
+    "chrom": "1",
+    "pos": 718601,
+    "ref": "A",
+    "sv_type": "DUP",
+    "sv_len": 105000,
+    "end": 823600
+  },
+  {
+    "_id": {
+      "$oid": "deadbeefdeadbeef22000002"
+    },
+    "chrom": "1",
+    "pos": 968168,
+    "ref": "G",
+    "sv_type": "DEL",
+    "sv_len": 20516,
+    "end": 988683
+  },
+  {
+    "_id": {
+      "$oid": "deadbeefdeadbeef22000003"
+    },
+    "chrom": "3",
+    "pos": 957868,
+    "ref": "A",
+    "sv_type": "INV",
+    "sv_len": 343440,
+    "end": 1301307
+  },
+  {
+    "_id": {
+      "$oid": "deadbeefdeadbeef22000004"
+    },
+    "chrom": "3",
+    "pos": 966074,
+    "ref": "A",
+    "sv_type": "DUP",
+    "sv_len": 174,
+    "end": 966247
+  },
+  {
+    "_id": {
+      "$oid": "deadbeefdeadbeef22000005"
+    },
+    "chrom": "3",
+    "pos": 968537,
+    "ref": "C",
+    "sv_type": "DUP",
+    "sv_len": 51788,
+    "end": 1020324
+  }
+]

tests/structvar/test_structvar.py

@@ -0,0 +1,40 @@
+from bravo_api.blueprints.structvar import structvar
+from flask import Flask
+
+app = Flask('dummy')
+app.register_blueprint(structvar.bp)
+
+# See mongo_fixtures/strucvar.json for structvar collection fixture values
+
+
+def test_structvar_fully_within_roi(mongodb):
+    result = structvar.sv_region(mongodb.structvar, "1", roi_start=718600, roi_stop=823600)
+    assert isinstance(result, list)
+    assert len(result) == 1
+    assert result[0]['pos'] == 718601
+
+
+def test_structvar_only_start_in_roi(mongodb):
+    result = structvar.sv_region(mongodb.structvar, "1", roi_start=718600, roi_stop=718700)
+    assert isinstance(result, list)
+    assert len(result) == 1
+    assert result[0]['pos'] == 718601
+
+
+def test_structvar_not_in_roi(mongodb):
+    result = structvar.sv_region(mongodb.structvar, "1", roi_start=600600, roi_stop=718600)
+    assert isinstance(result, list)
+    assert len(result) == 0
+
+
+def test_structvar_spans_roi(mongodb):
+    result = structvar.sv_region(mongodb.structvar, "1", roi_start=720000, roi_stop=820000)
+    assert isinstance(result, list)
+    assert len(result) == 1
+    assert result[0]['pos'] == 718601
+
+
+def test_structvar_multiple_results(mocker, mongodb):
+    result = structvar.sv_region(mongodb.structvar, "3", roi_start=950000, roi_stop=1400000)
+    assert isinstance(result, list)
+    assert len(result) == 3