Beacon v0.4

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

@@ -83,27 +83,33 @@ function checkPreconditions(params) {
     if (!params.alternateBases) {
         return {
             hasError: true,
-            msg: "Alternate bases not defined, arrayMap supports DUP or DEL followed by optional length"
+            msg: "Alternate bases not defined, arrayMap supports DUP or DEL"
         };
     }
 
-    // Beacon 0.4
-    // alternate bases: DEL[0-9]* AND DUP[0-9]*
-    var alternate = params.alternateBases.replace(/\d+/, "");
-    if (!alternateBasesMap[alternate]) {
+    if (!alternateBasesMap[params.alternateBases]) {
         return {
             hasError: true,
-            msg: "Alternate bases not supported, arrayMap supports DUP or DEL followed by optional length"
+            msg: "Alternate bases not supported, arrayMap supports DUP or DEL"
         };
     }
 
-    if (params.length && !Number(params.length)) {
+    // Do not allow minLength and maxLength to be compliant with 0.3
+    /*
+    if (params.minlength && !Number(params.minlength)) {
         return {
             hasError: true,
-            msg: "Length not a number"
+            msg: "min. length not a number"
         };
     }
 
+    if (params.maxlength && !Number(params.maxlength)) {
+        return {
+            hasError: true,
+            msg: "max length not a number"
+        };
+    }*/
+
     //TODO add additional checks
 
     return {
@@ -137,7 +143,19 @@ function checkPreconditions(params) {
 function buildMongoQuery(params) {
 
     var position = parseInt(params.start);
-    var length = params.alternateBases.replace(/(DUP|DEL)/, "") ? parseInt(params.alternateBases.replace(/(DUP|DEL)/, "")) : 0;
+
+    // Do not allow minLength and maxLength to be compliant with 0.3
+    /*
+    if(params.alternateBases == 'DEL') {
+
+        var minLength = params.minlength ? parseInt(params.minlength) : 0;
+        var maxLength = params.maxlength ? parseInt(params.maxlength) : 0;
+
+        if(!minLength && (maxLength > 0)){
+            minLength = 1;
+        }
+
+    }*/
 
     var andConditions = [];
     var orConditions  = [];
@@ -152,9 +170,7 @@ function buildMongoQuery(params) {
         }
     }
 
-    // Beacon 0.4
-    // alternate bases: DEL[0-9]* AND DUP[0-9]*
-    var segType = alternateBasesMap[params.alternateBases.replace(/\d+/, "")]
+    var segType = alternateBasesMap[params.alternateBases]
     var convertedReference = referenceMap[params.assemblyId || defaultReference];
 
     var condition = {};
@@ -167,14 +183,22 @@ function buildMongoQuery(params) {
 
     //elem match element
     var condElemMatch = condition[convertedReference]['$elemMatch'];
-    if (length > 0) {
-        condElemMatch.SEGSIZE  = length;
-        condElemMatch.SEGSTART = position;
-    }
-    else {
-        condElemMatch.SEGSTOP  = {$gte: position};
-        condElemMatch.SEGSTART = {$lte: position};
-    }
+
+    // Do not allow minLength and maxLength to be compliant with 0.3
+    /*
+    if (minLength > 0) { //There is a minLength
+        if (maxLength > 0) { //There is always a minLenght, if there is a max length specified (see code above)
+            condElemMatch.SEGSIZE = { $gte: minLength,$lte: maxLength } // min. and max lengths
+            condElemMatch.SEGSTART = position // exact position
+        }else { //If there is no max length specified
+            condElemMatch.SEGSIZE = { $gte: minLength }; // min. length
+            condElemMatch.SEGSTART = position; // exact position
+        }
+    }else { //If there is a position specific
+    */
+        condElemMatch.SEGSTOP = { $gte: position };
+        condElemMatch.SEGSTART = { $lte: position };
+    //}
 
     andConditions.push(condition);
     if (orConditions.length > 0) {
@@ -202,6 +226,23 @@ function buildMongoQuery(params) {
 
 function checkResultAndGetResponse(params, datasets) {
 
+    // Do not allow minLength and maxLength to be compliant with 0.3
+    // var length = 0;
+    /*
+    if (typeof params.minlength != undefined && params.minlength != null && params.minlength != '')
+    {
+        length = parseInt(params.minlength);
+        if (params.alternateBases == 'DUP') {
+            responseResource.note = "Length provided but not considered when querying DUP";
+        }
+    }
+
+    var maxLength = 0;
+    if (typeof params.maxlength != undefined && params.maxlength != null && params.maxlength != '')
+    {
+        maxLength = parseInt(params.maxlength);
+    }
+    */
     var responses = [];
 
     // The query returns only datasets for which there is at least one sample with at least one matching SEGMENT...
@@ -258,9 +299,7 @@ function checkResultAndGetResponse(params, datasets) {
             "error": null,
         };
 
-        // Beacon 0.4
-        // alternate bases: DEL[0-9]* AND DUP[0-9]*
-        if (!alternateBasesMap[params.alternateBases.replace(/\d+/,"")]) {
+        if (!alternateBasesMap[params.alternateBases]) {
             response.note = "Type of variant not supported by arrayMap.";
         }
         else {
@@ -275,9 +314,12 @@ function checkResultAndGetResponse(params, datasets) {
         "start": params.start,
         "assemblyId": params.assemblyId,
         "datasetIds": params.datasetIds,
-        // Beacon 0.4
-        // alternate bases: DEL[0-9]* AND DUP[0-9]*
         "alternateBases": params.alternateBases
+        // Do not allow minLength and maxLength to be compliant with 0.3
+        /*
+        "length": length,
+        "maxlength": maxLength
+        */
     };
 
     // BeaconAlleleResponse

app/node-app/arraymap-beacon/v0.4/arraymap-beacon.js

+var beacon = {};
+
+beacon.info = require('./beacon-info.js').info
+
+beacon.checkResultAndGetResponse = require('./beacon-query.js').checkResultAndGetResponse
+beacon.checkPreconditions = require('./beacon-query.js').checkPreconditions
+beacon.buildMongoQuery = require('./beacon-query.js').buildMongoQuery
+
+beacon.checkDatasetIdentifier = require('./beacon-dataset.js').checkDatasetIdentifier
+beacon.buildMongoDatasetQuery = require('./beacon-dataset.js').buildMongoDatasetQuery
+beacon.checkDatasetResultAndGetResponse = require('./beacon-dataset.js').checkDatasetResultAndGetResponse
+
+module.exports = beacon;
\ No newline at end of file

app/node-app/arraymap-beacon/v0.4/beacon-dataset.js

+/**
+ * Created by sduvaud on 26/05/16.
+ */
+
+var info = require('./beacon-info.js').info;
+
+// store all the dataset identifiers
+var allDatasetIds = [];
+info['info']['info']['datasets'].forEach(function(dataset){
+    allDatasetIds.push(dataset.id);
+});
+
+function checkDatasetIdentifier(params) {
+
+    if (!params.id) {
+        return {
+            hasError: true,
+            msg: "No identifier specified"
+        };
+    }
+    return {
+        hasError: false
+    };
+}
+
+function buildMongoDatasetQuery(params)
+{
+    console.log("ID=" + params.id);
+
+    var groupCondition = {
+        $group: {
+            _id: "$ICDMORPHOLOGYCODE",
+            sampleCount: {$sum: 1},
+            name: { $first: "$ICDMORPHOLOGY"}
+        }
+    };
+
+    if (params.id == 'all') {
+        return [
+            groupCondition
+        ];
+    }
+    else {
+
+        var orConditions = [];
+        var identifiers = params.id.split(','); // comma separated list of datasets
+        identifiers.forEach(function (id) {
+            orConditions.push({ICDMORPHOLOGYCODE: id});
+        });
+
+        return [
+            {
+                $match: {
+                    $or: orConditions
+                }
+            },
+            groupCondition
+        ];
+    }
+}
+
+function checkDatasetResultAndGetResponse(params, datasets) {
+
+    var matchedIdentifiers = [];
+    datasets.forEach(function(dataset){
+        matchedIdentifiers.push(dataset._id);
+    });
+
+    var submittedIdentifiers = allDatasetIds;
+    if (params.id != 'all') {
+        submittedIdentifiers = params.id.split(',');
+    }
+
+    if (submittedIdentifiers.length != matchedIdentifiers.length) {
+        var missingIdentifiers = [];
+        submittedIdentifiers.forEach(function(submitted) {
+                var found = false;
+                matchedIdentifiers.forEach(function(matched) {
+                        if (matched == submitted) {
+                            found = true;
+                        }
+                    }
+                );
+                if (!found) {
+                    missingIdentifiers.push(submitted);
+                }
+            }
+        );
+        missingIdentifiers.forEach(function (missing) {
+                var json =  {
+                    "_id": missing,
+                    "sampleCount": 0,
+                    "name": "Dataset not found"
+                };
+                datasets.push(json);
+            }
+        );
+    }
+    return datasets;
+}
+
+module.exports.checkDatasetIdentifier = checkDatasetIdentifier;
+module.exports.buildMongoDatasetQuery = buildMongoDatasetQuery;
+module.exports.checkDatasetResultAndGetResponse = checkDatasetResultAndGetResponse;
\ No newline at end of file

app/node-app/arraymap-beacon/v0.4/beacon-query.js

+var info = require('./beacon-info.js').info;
+
+// store all the dataset identifiers
+// not used when a list of datasets is entered
+// find a better place for this?
+var allDatasetIds = [];
+info['info']['info']['datasets'].forEach(function(dataset){
+    allDatasetIds.push(dataset.id);
+});
+
+var referenceMap = {
+    'GRCh38': 'SEGMENTS_HG38',
+    'GRCh37': 'SEGMENTS_HG19',
+    'GRCh36': 'SEGMENTS_HG18'
+};
+
+//correspondence to arraymap class
+var alternateBasesMap = {
+    "DEL": -1,
+    "DUP": 1
+};
+
+// By default doe Maximilien takes Reference 37. https://github.com/maximilianh/ucscBeacon/blob/master/help.txt
+//TODO Should it be the same as Maximilen? Is it specified by beacon documentaiton?    
+var defaultReference = 'GRCh38';
+
+function checkPreconditions(params) {
+
+    if (!params.referenceName) {
+        return {
+            hasError: true,
+            msg: "reference name is not present"
+        };
+    }
+
+    var referenceNameInvalid = {
+        hasError: true,
+        msg: params.referenceName + " reference name not valid"
+    };
+
+    if (Number(params.referenceName)) {
+        if (params.referenceName < 1 || params.referenceName > 23) {
+            return referenceNameInvalid;
+        }
+    }
+    else {
+        if (params.referenceName.match(/^(X|Y)$/i) == null) {
+            return referenceNameInvalid;
+        }
+    }
+
+    if (!params.start) {
+        return {
+            hasError: true,
+            msg: "position not present"
+        };
+    }
+
+    if (!Number(params.start)) {
+        return {
+            hasError: true,
+            msg: "position not a number"
+        };
+    }
+
+    if (!params.datasetIds) {
+        return {
+            hasError: true,
+            msg: "No dataset provided"
+        };
+    }
+
+    if (params.datasetIds != 'all') {
+        var error = checkDatasetIdentifiers(params.datasetIds, allDatasetIds);
+        if (error.length > 0) {
+            return {
+                hasError: true,
+                msg: "Incorrect dataset(s): " + error.toString()
+            };
+        }
+    }
+
+    if (!params.alternateBases) {
+        return {
+            hasError: true,
+            msg: "Alternate bases not defined, arrayMap supports DUP or DEL followed by optional length"
+        };
+    }
+
+    // Beacon 0.4
+    // alternate bases: DEL[0-9]* AND DUP[0-9]*
+    var alternate = params.alternateBases.replace(/\d+/, "");
+    if (!alternateBasesMap[alternate]) {
+        return {
+            hasError: true,
+            msg: "Alternate bases not supported, arrayMap supports DUP or DEL followed by optional length"
+        };
+    }
+
+    if (params.length && !Number(params.length)) {
+        return {
+            hasError: true,
+            msg: "Length not a number"
+        };
+    }
+
+    //TODO add additional checks
+
+    return {
+        hasError: false
+    };
+}
+
+/*
+* Latest version of API v-0.3
+*
+* BeaconAlleleRequest:
+* referenceName
+* start
+* alternateBases
+* assemblyId
+* datasetIds
+*
+* BeaconAlleleResponse
+* beaconId
+* beaconAlleleRequest
+* beacondatasetAlleleResponse[]
+* beaconError
+*
+* BeaconDatasetAlleleResponse
+* datasetId
+* exists
+* beaconError
+* note
+*
+* */
+function buildMongoQuery(params) {
+
+    var position = parseInt(params.start);
+    var length = params.alternateBases.replace(/(DUP|DEL)/, "") ? parseInt(params.alternateBases.replace(/(DUP|DEL)/, "")) : 0;
+
+    var andConditions = [];
+    var orConditions  = [];
+
+    //add constraint on datasets if required
+    if (params.datasetIds) {
+        if (params.datasetIds != 'all') {
+            var identifiers = params.datasetIds.split(','); // comma separated list of datasets
+            identifiers.forEach(function (id) {
+                orConditions.push({ICDMORPHOLOGYCODE: id});
+            });
+        }
+    }
+
+    // Beacon 0.4
+    // alternate bases: DEL[0-9]* AND DUP[0-9]*
+    var segType = alternateBasesMap[params.alternateBases.replace(/\d+/, "")]
+    var convertedReference = referenceMap[params.assemblyId || defaultReference];
+
+    var condition = {};
+    condition[convertedReference] = {
+        '$elemMatch': {
+            'CHRO': params.referenceName,
+            'SEGTYPE': segType
+        }
+    };
+
+    //elem match element
+    var condElemMatch = condition[convertedReference]['$elemMatch'];
+    if (length > 0) {
+        condElemMatch.SEGSIZE  = length;
+        condElemMatch.SEGSTART = position;
+    }
+    else {
+        condElemMatch.SEGSTOP  = {$gte: position};
+        condElemMatch.SEGSTART = {$lte: position};
+    }
+
+    andConditions.push(condition);
+    if (orConditions.length > 0) {
+        andConditions.push({$or: orConditions});
+    }
+
+    return [
+        {
+            "$match": {
+                "$and": andConditions
+            }
+        },
+        {
+            "$group": {
+                _id: "$ICDMORPHOLOGYCODE",
+                // Number of samples with at least one segment
+                // Datasets with no sample are not shown
+                // This is of an issue when the user asks for
+                // all datasets.
+                observed : { $sum : 1 }
+            }
+        }
+    ];
+}
+
+function checkResultAndGetResponse(params, datasets) {
+
+    var responses = [];
+
+    // The query returns only datasets for which there is at least one sample with at least one matching SEGMENT...
+    // What should we do with "unmatched" datasets?
+    // Should we show them, as well with an exists: false?
+    // what about cases where all the datasets are requested?
+
+    if (datasets && datasets.length > 0)
+    {
+        // var matchedDatasets = datasets.map(function (s) { return checkResult(params, s)}); // checks to be added!
+        var matchedDatasets = checkResult(params, datasets);
+        var response;
+
+        if (typeof matchedDatasets == undefined && matchedDatasets == null) {
+            response = {
+                "exists": null,
+                "datasetId": null,
+                "sampleCount": 0,
+                "error": {
+                    errorCode: 500,
+                    message: "Internal error, DB returned a value but post check is not valid."
+                },
+                "note": null
+            };
+            responses.push(response);
+        }else {
+            matchedDatasets.forEach(function (dataset) {
+                if (dataset.observed == 0) {
+                    response = {
+                        "exists": false,
+                        "error": null,
+                        "note": null,
+                        "datasetId": dataset._id,
+                        "sampleCount": 0
+                    };
+                }else {
+                    response = {
+                        "exists": true,
+                        "error": null,
+                        "note": null,
+                        "datasetId": dataset._id,
+                        "sampleCount": dataset.observed
+                    };
+                }
+                responses.push(response);
+            })
+        }
+    }else {
+
+        response = {
+            "exists": false,
+            "datasetId": null,
+            "sampleCount": 0,
+            "error": null,
+        };
+
+        // Beacon 0.4
+        // alternate bases: DEL[0-9]* AND DUP[0-9]*
+        if (!alternateBasesMap[params.alternateBases.replace(/\d+/,"")]) {
+            response.note = "Type of variant not supported by arrayMap.";
+        }
+        else {
+            response.note = "No result from arrayMap.";
+        }
+
+        responses.push(response);
+    }
+
+    var queryResource = {
+        "referenceName": params.referenceName,
+        "start": params.start,
+        "assemblyId": params.assemblyId,
+        "datasetIds": params.datasetIds,
+        // Beacon 0.4
+        // alternate bases: DEL[0-9]* AND DUP[0-9]*
+        "alternateBases": params.alternateBases
+    };
+
+    // BeaconAlleleResponse
+    return {
+        "beaconId": info['info']['info']['id'],
+        "datasetAlleleResponses": responses,
+        "alleleRequest": queryResource,
+        "error": null
+    };
+}
+
+// checks to be added!
+// Pending for now!
+function checkResult(params, datasets) {
+
+    var allDatasets = datasets;
+
+    var matchedIdentifiers = [];
+    datasets.forEach(function(dataset){
+        matchedIdentifiers.push(dataset._id);
+    });
+
+    var submittedIdentifiers = allDatasetIds;
+    if (params.datasetIds != 'all') {
+        submittedIdentifiers = params.datasetIds.split(',');
+    }
+
+    var missedIdentifiers = checkDatasetIdentifiers(submittedIdentifiers.toString(), matchedIdentifiers);
+    if (missedIdentifiers != null) {
+        missedIdentifiers.forEach(function (missed) {
+            var missedObj = {
+                "_id": missed,
+                "observed": 0
+            }
+            allDatasets.push(missedObj);
+        });
+    }
+    return allDatasets;
+}
+
+function checkDatasetIdentifiers(userDatasetIdentifiers, allDatasetIdentifiers) {
+    var identifiers = userDatasetIdentifiers.split(','); // comma separated list of datasets
+    var found;
+    var error = [];
+    identifiers.forEach(function (id) {
+        found = false;
+        allDatasetIdentifiers.forEach(function (all) {
+            if (all == id) {