Implementing latest changes in the API spec

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

@@ -176,12 +176,22 @@ function checkResultAndGetResponse(params, samples, countTotal) {
 
     if (samples && samples.length > 0) { // a value was found by mongodb
 
-        responseResource.observed = samples.length;
+        // SD, May 2016: according to the specs, observed parameter was removed from BeaconDatasetAlleleResponse.
+        // We could divide the sample.length by the total number of samples in order to fill the frequency parameters
+        // for instance (and if of interest for arrayMap).
+        // responseResource.observed = samples.length;
+        responseResource.NOT_BEACON_numberMatchedSamples = samples.length;
+
         var matchedSegments = samples.map(function (s) { return checkResult(params, s)});
 
         if (!matchedSegments || !matchedSegments[0] || !matchedSegments[0].matchedSegment) {
             responseResource.exists = null;
-            responseResource.error = "Internal error, DB returned a value but post check is not valid."
+            // BeaconError instead of simple string
+            // (error is not null if and only of exists is null)
+            responseResource.error = {
+                errorCode: 500,
+                message: "Internal error, DB returned a value but post check is not valid."
+            };
         } else {
             responseResource.exists = true;
             responseResource.NOT_BEACON_ARRAYMAP_DEBUG_INFO = {"matchedSegments" : matchedSegments};

app/node-app/routes/index.js

@@ -54,8 +54,7 @@ router.get('/v0.2/query/', function (req, res) {
     console.log("Building MongoDB query params: " + JSON.stringify(mongoQuery));
 
     req.db.samples.count({'ICDMORPHOLOGYCODE': req.query.dataset}, function(err, count){
-
-        req.db.samples.find(mongoQuery, {}, function (err, docs){
+            req.db.samples.find(mongoQuery, {}, function (err, docs){
             var response = beacon.checkResultAndGetResponse(req.query, docs, count);
             response.NOT_BEACON_totalInDataSet = count;
             res.json(response);
@@ -77,8 +76,14 @@ router.get('/v0.3/query/', function (req, res) {
     var mongoQuery = beacon.buildMongoQuery(req.query);
     console.log("Building MongoDB query params: " + JSON.stringify(mongoQuery));
 
-    req.db.samples.count({'ICDMORPHOLOGYCODE': req.query.dataset}, function(err, count){
+    // Count: list of datasets (and not 1 dataset)
+    var orConditions = [];
+    var identifiers = req.query.datasetIds.split(','); // comma separated list of datasets
+    identifiers.forEach(function (id) {
+        orConditions.push({ICDMORPHOLOGYCODE: id});
+    });
 
+    req.db.samples.count({$or: orConditions}, function(err, count){
             req.db.samples.find(mongoQuery, {}, function (err, docs){
                 var response = beacon.checkResultAndGetResponse(req.query, docs, count);
                 response.NOT_BEACON_totalInDataSet = count;