Beacon version 0.3: Handling of datasetIds

app/node-app/arraymap-beacon/v0.3/beacon-query.js

@@ -56,6 +56,13 @@ function checkPreconditions(params) {
         };
     }
 
+    if (!params.datasetIds) {
+        return {
+            hasError: true,
+            msg: "No dataset provided"
+        };
+    }
+
     console.log(Boolean(variantClassMap[params.variantClass]));
 
     if (!params.variantClass) {
@@ -78,20 +85,21 @@ function checkPreconditions(params) {
 
 }
 
-
-
 function buildMongoQuery(params) {
 
     var position = parseInt(params.start);
-
-    var conditions = [];
-    //add constraint on dataset if it exsits
-    if (params.dataset) conditions.push({
-        ICDMORPHOLOGYCODE: params.dataset
+    var andConditions = [];
+    var orConditions  = [];
+
+    //add constraint on datasets if required
+    if (params.datasetIds){
+        var identifiers = params.datasetIds.split(','); // comma separated list of datasets
+        identifiers.forEach(function(id) {
+            orConditions.push({ICDMORPHOLOGYCODE: id});
         });
+    }
 
     var segType = variantClassMap[params.variantClass]
-
     var convertedReference = referenceMap[params.assemblyId || defaultReference];
 
     var cond = {};
@@ -107,10 +115,11 @@ function buildMongoQuery(params) {
             }
         }
     }
+    andConditions.push(cond);
+    andConditions.push({$or: orConditions});
 
-    conditions.push(cond);
     return {
-        $and: conditions
+        $and: andConditions
     };
 }
 
@@ -142,7 +151,7 @@ function checkResultAndGetResponse(params, samples, countTotal) {
         "referenceName": params.referenceName,
         "start": params.start,
         "assemblyId": params.assemblyId,
-        "datasetid": params.dataset
+        "datasetIds": params.datasetIds
     };
 
 
@@ -156,15 +165,13 @@ function checkResultAndGetResponse(params, samples, countTotal) {
 
 function checkResult(params, sample) {
 
-    var convertedReference = referenceMap[params.reference || defaultReference];
+    var convertedReference = referenceMap[params.assemblyId || defaultReference];
     var expectedSegType = variantClassMap[params.variantClass]
     var position = parseInt(params.start);
 
-    //TODO should check for dataset and genomre reference as well
-
+    //TODO should check for datasets and genome reference as well
     var foundSegment;
 
-
     sample[convertedReference].forEach(function (segment) {
         if (segment.CHRO === params.referenceName) {
 
@@ -179,7 +186,6 @@ function checkResult(params, sample) {
         }
     })
 
-
     var result = {
         matchedSampleUID: sample.UID,
         matchedDataSet: sample.ICDMORPHOLOGYCODE,
@@ -188,7 +194,6 @@ function checkResult(params, sample) {
     return result;
 }
 
-
 module.exports.checkPreconditions = checkPreconditions;
 module.exports.buildMongoQuery = buildMongoQuery;
 module.exports.checkResultAndGetResponse = checkResultAndGetResponse;
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