Issue #77: Top exomiser hits now uses the variant display table from …

…variant store application Conflicts: similarity-data-impl/src/main/java/org/phenotips/data/similarity/script/ExomiserViewScriptService.java
phenotips · Nov 22, 2016 · b86b12b · b86b12b
1 parent 55c1f91
commit b86b12b
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Showing 2 changed files with 45 additions and 316 deletions.
diff --git a/...ta-impl/src/main/java/org/phenotips/data/similarity/script/ExomiserViewScriptService.java b/...ta-impl/src/main/java/org/phenotips/data/similarity/script/ExomiserViewScriptService.java
@@ -89,35 +89,56 @@ public boolean hasGenotype(Patient patient)
      */
     public JSONArray getTopGenesAsJSON(Patient patient, int g, int v)
     {
-        JSONArray result = new JSONArray();
-        if (patient == null || g <= 0) {
-            return result;
+        JSONArray variantsJSON = new JSONArray();
+
+        if (patient == null || g < 0) {
+            return variantsJSON;
         }
 
         boolean restrictGenes =
             (!this.pm.getPatientAccess(patient).hasAccessLevel(this.editAccess) && g > MAXIMUM_UNPRIVILEGED_GENES);
         int maxGenes = restrictGenes ? MAXIMUM_UNPRIVILEGED_GENES : g;
 
         Exome patientExome = this.exomeManager.getExome(patient);
+
         for (String geneName : patientExome.getTopGenes(maxGenes)) {
-            JSONObject geneJSON = new JSONObject();
-            geneJSON.put("name", geneName);
-            geneJSON.put("score", patientExome.getGeneScore(geneName));
 
-            JSONArray variantsJSON = new JSONArray();
+            Double geneScore = patientExome.getGeneScore(geneName);
+
             boolean restrictVariants = (!this.pm.getPatientAccess(patient).hasAccessLevel(this.editAccess)
                 && v > MAXIMUM_UNPRIVILEGED_VARIANTS);
+
             int maxVars = restrictVariants ? MAXIMUM_UNPRIVILEGED_VARIANTS : v;
+
             List<Variant> topVariants = patientExome.getTopVariants(geneName, v);
-            for (int i = 0; i < topVariants.size(); i++) {
+            maxVars = Math.min(maxVars, topVariants.size());
+
+            for (int i = 0; i < maxVars; i++) {
                 Variant variant = topVariants.get(i);
                 if (variant != null) {
-                    variantsJSON.put(variant.toJSON());
+                    variantsJSON.put(this.mapToGAVariantJSON(variant, geneName, geneScore));
                 }
             }
-            geneJSON.put("variants", variantsJSON);
-            result.put(geneJSON);
         }
-        return result;
+        return variantsJSON;
+    }
+
+    private JSONObject mapToGAVariantJSON(Variant variant, String geneName, Double geneScore)
+    {
+        JSONObject resultJson = new JSONObject();
+        resultJson.put("start", variant.getPosition());
+        resultJson.put("referenceBases", variant.getRef());
+        resultJson.put("alternateBases", variant.getAlt());
+        resultJson.put("referenceName", variant.getChrom());
+        resultJson.put("end", variant.getPosition() + variant.getAlt().length());
+
+        JSONObject infoJson = new JSONObject();
+        infoJson.put("EXOMISER_VARIANT_SCORE", variant.getScore());
+        infoJson.put("EXOMISER_GENE_VARIANT_SCORE", geneScore);
+        infoJson.put("GENE_EFFECT", variant.getAnnotation("FUNCTIONAL_CLASS"));
+        infoJson.put("GENE", geneName);
+
+        resultJson.put("info", infoJson);
+        return resultJson;
     }
 }