Address CR, add test for order, restyle

common/helpers.py

@@ -46,6 +46,8 @@ def order(lst, ordering, key=None):
         lookup = lambda x: x
     elif isinstance(key, basestring):
         lookup = lambda x: x[key]
+    else: # the key is a function
+        lookup = key
     ordering = {name: idx for idx, name in enumerate(ordering)}
     lst.sort(key=lambda x: ordering[lookup(x)])
     return lst

common/relational_vcf.py

@@ -186,8 +186,8 @@ def vcf_format(val):
     if len(vals) <= 1:
         return val
     else: # It's a list.
-        assert v[0] == '['
-        assert v[-1] == ']'
+        assert val[0] == '['
+        assert val[-1] == ']'
         return ','.join(v.strip() for v in vals)[1:-1]
 
 

cycledash/genotypes.py

@@ -28,9 +28,8 @@ def spec(vcf_id):
     ANNOTATIONS: {attrA: ...}}
     """
     with tables(db, 'vcfs') as (con, vcfs):
-        q = select(
-            [vcfs.c.vcf_header, vcfs.c.extant_columns]
-        ).where(vcfs.c.id == vcf_id)
+        q = (select([vcfs.c.vcf_header, vcfs.c.extant_columns])
+                    .where(vcfs.c.id == vcf_id))
         res = con.execute(q).fetchone()
     return _header_spec(res['vcf_header'], res['extant_columns'])
 
@@ -50,13 +49,10 @@ def samples(vcf_id):
 def contigs(vcf_id):
     """Return a sorted list of contig names found in the given vcf."""
     with tables(db, 'genotypes') as (con, genotypes):
-        q = select(
-            [genotypes.c.contig]
-        ).where(
-            genotypes.c.vcf_id == vcf_id
-        ).group_by(
-            genotypes.c.contig
-        ).order_by(func.length(genotypes.c.contig), genotypes.c.contig)
+        q = (select([genotypes.c.contig])
+             .where(genotypes.c.vcf_id == vcf_id)
+             .group_by(genotypes.c.contig)
+             .order_by(func.length(genotypes.c.contig), genotypes.c.contig))
         results = con.execute(q).fetchall()
     return [contig for (contig,) in results]
 
@@ -287,11 +283,9 @@ def vcf_type_to_sqla_type(column_type='integer'):
 
 def derive_truth_vcf_id(dataset_name):
     with tables(db, 'vcfs') as (con, vcfs):
-        truth_vcf_q = select(
-            [vcfs.c.id]
-        ).where(
-            vcfs.c.validation_vcf == True
-        ).where(vcfs.c.dataset_name == dataset_name)
+        truth_vcf_q = (select([vcfs.c.id])
+                       .where(vcfs.c.validation_vcf == True)
+                       .where(vcfs.c.dataset_name == dataset_name))
         truth_vcf_rel = con.execute(truth_vcf_q).fetchone()
         if truth_vcf_rel:
             return truth_vcf_rel.id

cycledash/static/css/examine.css

@@ -335,8 +335,8 @@ a.download-vcf {
   color: #6d6d6d;
   font-size: 0.92em;
   text-decoration: none;
-  padding-left: 23px;
-  background: url(/static/img/noun_4501.svg) no-repeat 3px 2px;
+  padding-left: 38px;
+  background: url(/static/img/noun_4501.svg) no-repeat 11px 2px;
   background-size: 15px 15px;
   opacity: 0.55;
 }

cycledash/static/js/examine/components/Downloads.js

@@ -10,7 +10,7 @@ var Downloads = React.createClass({
     query: React.PropTypes.object
   },
   render: function() {
-    var jsonQuery = JSON.stringify(this.props.query),
+    var jsonQuery = encodeURIComponent(JSON.stringify(this.props.query)),
         link = `/runs/${this.props.run_id}/download?query=${jsonQuery}`;
     return <a className='download-vcf' href={link}>Download VCF</a>;
   }

tests/python/test.py

@@ -1,5 +1,6 @@
 import nose
 
+from common.helpers import order
 from cycledash.helpers import underscorize
 from common.relational_vcf import vcf_to_csv
 
@@ -29,3 +30,15 @@ def test_vcf_to_csv():
     assert rows[0] == ['44', '', '81', 'True']
     assert rows[-1] == ['40', '', '74', 'True']
     assert len(rows) == 20
+
+
+def test_order():
+    o1 = order([132, 99, 22], ordering=[99, 22, 44, 132])
+    o2 = order([{'thing': 'bathrobe'}, {'thing': 'toga'}],
+               ['toga', 'bathrobe'], key='thing')
+    o3 = order([2,4,1,4],
+               [1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16], key=lambda x: x * x)
+
+    assert o1 == [99, 22, 132]
+    assert o2 == [{'thing': 'toga'}, {'thing': 'bathrobe'}]
+    assert o3 == [1, 2, 4, 4]