Merge pull request chop-dbhi#349 from cbmi/variant-sets

Add support for result/variant sets

.travis.yml

@@ -25,13 +25,15 @@ install:
     - "if [[ $TRAVIS_PYTHON_VERSION == '2.6' ]]; then pip install --use-mirrors cython && pip install --use-mirrors pysam argparse counter ordereddict importlib; fi"
     - pip install flake8
     - pip install httpretty
+    - npm install jshint
 
 services:
     - memcached
     - redis-server
 
 before_script:
     - flake8
+    - jshint varify/static/js/src/
     - psql -c 'create database varifydb;' -U postgres
 
 script:

test_suite.py

@@ -12,7 +12,8 @@
         'assessments',
         'south_tests',
         'geneset_form',
-        'resources'
+        'resources',
+        'samples'
     ]
 
 management.call_command('test', *apps)

tests/cases/samples/tests.py

@@ -0,0 +1,67 @@
+import json
+import os
+from openpyxl import Workbook, cell
+from restlib2.http import codes
+from vdw.samples.models import Project
+from guardian.shortcuts import assign
+from ..base import AuthenticatedBaseTestCase
+
+
+class VariantUploadResourceTestCase(AuthenticatedBaseTestCase):
+    fixtures = ['initial_variants.json']
+
+    def setUp(self):
+        super(VariantUploadResourceTestCase, self).setUp()
+
+    def test_post(self):
+        book = Workbook()
+        sheet1 = book.get_active_sheet()
+        sheet1.title = 'Variants List'
+        fields = ['Chromosome', 'Start', 'Reference', 'Allele 1', 'Allele 2',
+                  'dbSNP']
+
+        # Create variants to cover all edge cases, including the case
+        # where there is a variation at the same genomic position.
+        # Also consider the case where the dbSNP id is incorrect.
+        variants = [['1', '20000', '.', 'AC', 'AC', ''],
+                    ['1', '20000', 'A', 'A', '.', ''],
+                    ['3', '20002', 'GAT', '.', '.', 'rs9160301'],
+                    ['1', '20003', '.', '.', 'TTTCTT', ''],
+                    ['3', '20004', 'A', 'C', 'C', 'rs916000'],
+                    ['1', '20007', 'GTCATTGGAACAGTC', '.',
+                     'GTCATTGGAACAGTC', '']]
+
+        # Write our fields in first.
+        for i in range(0, 6):
+            sheet1.cell(row=0, column=i).set_value_explicit(
+                value=fields[i], data_type=cell.Cell.TYPE_STRING)
+
+        # Write the variants to the excel sheet.
+        row = 1
+        for v in variants:
+            for col in range(0, 6):
+                sheet1.cell(row=row, column=col).set_value_explicit(
+                    value=v[col], data_type=cell.Cell.TYPE_STRING)
+            row += 1
+
+        book.save('variantList.xlsx')
+
+        with open('variantList.xlsx') as fp:
+            # Assign permissions for test user to access the project.
+            p = Project.objects.get(pk=1)
+            assign('samples.view_project', self.user, p)
+
+            response = self.client.post('/api/samples/9/variants/sets/',
+                                        {'name': 'variants',
+                                         'source': fp})
+            response_obj = json.loads(response.content)
+
+            # An array of matching variants are returned. Make sure
+            # that exactly 5 were found and 1 was added to the
+            # list of unmatched variants.
+            self.assertEqual(response.status_code, codes.created)
+            self.assertEqual(response_obj['num_total_records'], 6)
+            self.assertEqual(response_obj['count'], 5)
+            self.assertEqual(len(response_obj['invalid_records']), 1)
+
+        os.remove('variantList.xlsx')