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Commit bcc8bcb5 authored by Severine Duvaud's avatar Severine Duvaud
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Added the length to DEL or DUP as agreed for Beacon v0.4

parent 6853e4a2
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app/node-app/arraymap-beacon/v0.3/beacon-query.js
View file @ bcc8bcb5
......@@ -83,33 +83,27 @@ function checkPreconditions(params) {
if (!params.alternateBases) {
return {
hasError: true,
msg: "Alternate bases not defined, arrayMap supports DUP or DEL"
msg: "Alternate bases not defined, arrayMap supports DUP or DEL followed by optional length"
};
}
if (!alternateBasesMap[params.alternateBases]) {
// 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"
msg: "Alternate bases not supported, arrayMap supports DUP or DEL followed by optional length"
};
}
// Do not allow minLength and maxLength to be compliant with 0.3
/*
if (params.minlength && !Number(params.minlength)) {
if (params.length && !Number(params.length)) {
return {
hasError: true,
msg: "min. length not a number"
msg: "Length not a number"
};
}
if (params.maxlength && !Number(params.maxlength)) {
return {
hasError: true,
msg: "max length not a number"
};
}*/
//TODO add additional checks
return {
......@@ -143,19 +137,7 @@ function checkPreconditions(params) {
function buildMongoQuery(params) {
var position = parseInt(params.start);
// 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 length = params.alternateBases.replace(/(DUP|DEL)/, "") ? parseInt(params.alternateBases.replace(/(DUP|DEL)/, "")) : 0;
var andConditions = [];
var orConditions = [];
......@@ -170,7 +152,9 @@ function buildMongoQuery(params) {
}
}
var segType = alternateBasesMap[params.alternateBases]
// 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 = {};
......@@ -183,22 +167,14 @@ function buildMongoQuery(params) {
//elem match element
var condElemMatch = condition[convertedReference]['$elemMatch'];
// 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 = { $lte: position };
//}
if (length > 0) {
condElemMatch.SEGSIZE = length;
condElemMatch.SEGSTART = position;
}
else {
condElemMatch.SEGSTOP = {$gte: position};
condElemMatch.SEGSTART = {$lte: position};
}
andConditions.push(condition);
if (orConditions.length > 0) {
......@@ -226,23 +202,6 @@ function buildMongoQuery(params) {
function checkResultAndGetResponse(params, datasets) {
// Do not allow minLength and maxLength to be compliant with 0.3
// var length = 0;
/*
if (typeof params.minlength != undefined && params.minlength != null && params.minlength != '')
{
length = parseInt(params.minlength);
if (params.alternateBases == 'DUP') {
responseResource.note = "Length provided but not considered when querying DUP";
}
}
var maxLength = 0;
if (typeof params.maxlength != undefined && params.maxlength != null && params.maxlength != '')
{
maxLength = parseInt(params.maxlength);
}
*/
var responses = [];
// The query returns only datasets for which there is at least one sample with at least one matching SEGMENT...
......@@ -299,7 +258,9 @@ function checkResultAndGetResponse(params, datasets) {
"error": null,
};
if (!alternateBasesMap[params.alternateBases]) {
// Beacon 0.4
// alternate bases: DEL[0-9]* AND DUP[0-9]*
if (!alternateBasesMap[params.alternateBases.replace(/\d+/,"")]) {
response.note = "Type of variant not supported by arrayMap.";
}
else {
......@@ -314,12 +275,9 @@ function checkResultAndGetResponse(params, datasets) {
"start": params.start,
"assemblyId": params.assemblyId,
"datasetIds": params.datasetIds,
// Beacon 0.4
// alternate bases: DEL[0-9]* AND DUP[0-9]*
"alternateBases": params.alternateBases
// Do not allow minLength and maxLength to be compliant with 0.3
/*
"length": length,
"maxlength": maxLength
*/
};
// BeaconAlleleResponse
......
app/node-app/public/js/index.js
View file @ bcc8bcb5
......@@ -22,7 +22,8 @@ arrayMap.controller('BeaconController', ['$scope', '$location', function ($scope
"start": 34439881,
"assemblyId": "GRCh38",
"datasetIds": "8070/3",
"alternateBases": "DEL"
"alternateBases": "DEL",
"length": ''
// Do not allow minLength and maxLength to be compliant with 0.3
/*
"minlength": '',
......@@ -44,7 +45,8 @@ arrayMap.controller('BeaconController', ['$scope', '$location', function ($scope
"&start=" + conf.start +
"&assemblyId=" + conf.assemblyId +
"&datasetIds=" + conf.datasetIds +
((conf.alternateBases === "") ? "all" : "&alternateBases=" + conf.alternateBases);
((conf.alternateBases === "") ? "all" : "&alternateBases=" + conf.alternateBases) +
((conf.length === '') ? "" : conf.length);
// Do not allow minLength and maxLength to be compliant with 0.3
/*
((conf.minlength === '') ? "" : "&minlength=" + conf.minlength) +
......
app/node-app/public/partials/beacon-home.html
View file @ bcc8bcb5
<div ng-controller="BeaconController" ng-cloak class="container">
<div class="jumbotron">
<h1>Beacon ArrayMap</h1>
<p>First Prototype of a <a target="_blank" href="https://genomicsandhealth.org/work-products-demonstration-projects/beacon-project-0">Beacon</a>
<p><a target="_blank" href="https://genomicsandhealth.org/work-products-demonstration-projects/beacon-project-0">Beacon</a>
<a target="_blank" href="https://docs.google.com/document/d/1n7qtCBFwsExP_k2GPfWS_PN53Xeh8YxeCBOgyZ5itOw/edit#"> v0.3</a> implementation for <a target="_blank" href="http://arraymap.org/">ArrayMap</a>.</p>
</div>
<form class="form-horizontal">
......@@ -37,17 +37,19 @@
<label style="color:green" for="alternateBases" class="col-sm-2 control-label">Alternate bases</label>
<div class="col-sm-4">
<select id="alternateBases" ng-model="config.alternateBases" class="form-control">
<!--<option value="">Substitution (For precise variants)</option>-->
<option value="DEL">DEL (Deletion)</option>
<!--<option value="INS">INS (Insertion)</option>-->
<option value="DUP">DUP (Duplication)</option>
<!--<option value="INV">INV (Inversion)</option>
<option value="CNV">CNV (Copy Number Variation)</option>
<option value="BND">BND (Breakend???)</option>-->
</select>
</div>
</div>
<div class="form-group">
<label for="length" class="col-sm-2 control-label">Length</label>
<div class="col-sm-4">
<input type="text" class="form-control" id="length" ng-model="config.length" placeholder="">
</div>
</div>
<!-- Do not allow minLength and maxLength to be compliant with 0.3
<div class="form-group">
<label for="minlength" class="col-sm-2 control-label">Minimal length</label>
......
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