Merge pull request #529 from PoonLab/dev

Minor: Bug fixes

batch.py

@@ -31,7 +31,7 @@ def parse_args():
     parser.add_argument('--mindate', type=str, default='2019-12-01', 
                         help='option, earliest possible sample collection date (ISO format, default '
                               '2019-12-01')
-    parser.add_argument('--poisson-cutoff', type=float, default=0.001,
+    parser.add_argument('--poisson-cutoff', type=float, default=0,
                         help='option, filtering outlying genomes whose distance exceeds the upper '
                              'quantile of Poisson distribution (molecular clock).  Default 0.001 '
                              'corresponds to 99.9%% cutoff.')

covizu/utils/batch_utils.py

@@ -35,7 +35,11 @@ def unpack_records(records):
         # reconstitute the mutations defining this variant
         diffs = []
         for mutation in key.split(','):
-            typ, pos, alt = mutation.split('|')
+            try:
+                typ, pos, alt = mutation.split('|')
+            except ValueError:
+                # Handle case when there are no diffs
+                continue
             if typ == '-':
                 alt = int(alt)  # number of nucleotides in indel
             diffs.append(tuple([typ, int(pos), alt]))

covizu/utils/gisaid_utils.py

@@ -244,6 +244,10 @@ def filter_problematic(records, origin='2019-12-01', rate=0.0655, cutoff=0.005,
         if not encoded:
             record['diffs'] = filtered
 
+            # Exclude sequences with no mutations. See issue #530
+            if len(record['diffs']) == 0:
+                continue
+
             # exclude genomes with excessive divergence from reference
             coldate = record['covv_collection_date']
             if qp.is_outlier(coldate, ndiffs):
@@ -332,8 +336,9 @@ def convert_json(infile, provision):
                 md = metadata.get(accn, None)
                 if md is None:
                     print("Failed to retrieve metadata for accession {}".format(accn))
-                    sys.exit()
-                revised.append([name, accn, location, coldate, md['gender'], md['age'], md['status']])
+                    revised.append([name, accn, location, coldate, 'N/A', 'N/A', 'N/A'])
+                else:
+                    revised.append([name, accn, location, coldate, md['gender'], md['age'], md['status']])
 
             # replace list of samples
             cluster['nodes'][variant] = revised

covizu/utils/seq_utils.py

@@ -185,6 +185,10 @@ def lookup(self, time, timepoints):
         return bisect.bisect(timepoints, time)
 
     def is_outlier(self, coldate, ndiffs):
+        # Return False if cutoff = 0
+        if self.lowerq == 0:
+            return False
+
         if type(coldate) is str:
             coldate = fromisoformat(coldate)
         dt = (coldate - self.origin).days

js/beadplot.js

@@ -1167,9 +1167,13 @@ function gen_details_table(obj) {
                 .style("opacity", 0.9);
 
             let tooltipText = "";
-            tooltipText = `<b>${i18n_text.sample_orig_lab}:</b> ${gd.covv_orig_lab}<br/>`;
-            tooltipText += `<b>${i18n_text.sample_subm_lab}:</b> ${gd.covv_subm_lab}<br/>`;
-            tooltipText += `<b>${i18n_text.sample_authors}:</b> ${gd.covv_authors}`;
+            if (Object.keys(gd).length === 0) {
+              tooltipText = `GISAID API call did not return data for this accession number`;
+            } else {
+              tooltipText = `<b>${i18n_text.sample_orig_lab}:</b> ${gd.covv_orig_lab}<br/>`;
+              tooltipText += `<b>${i18n_text.sample_subm_lab}:</b> ${gd.covv_subm_lab}<br/>`;
+              tooltipText += `<b>${i18n_text.sample_authors}:</b> ${gd.covv_authors}`;
+            }
 
             // Tooltip appears 10 pixels left of the cursor
             cTooltip.html(tooltipText)

js/gisaid/gisaid.js

@@ -159,7 +159,10 @@ var gisaid = gisaid || (function () {
 				  .then(ackData => {
 					  this.ackCache[ackLink] = ackData ;
 					  cb(ackData);
-				});
+				  })
+				  .catch(e => {
+					  cb({});
+				  });
 			} else {
 				cb(this.ackCache[ackLink]);
 			}

server.js

@@ -86,7 +86,7 @@ app.get('/api/regionmap', (req, res) => {
 })
 
 app.get('/api/cid/:accession', (req, res) => {
-  dbManager.get_accession(req.params.accession).then(result=>{
+  dbManager.get_accession(req.params.accession.toUpperCase()).then(result=>{
     res.send(result);
   })
 });