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Make beacon searches specific to dataset.
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Also remove reference selection from the frontend as the current frontend only supports the reference used with the dataset.
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@talavis
talavis committed Apr 30, 2019
1 parent 7ef2c91 commit 5be11e0
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Showing 3 changed files with 39 additions and 34 deletions.
29 changes: 18 additions & 11 deletions frontend/src/js/controller.datasetBeaconController.js
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Original file line number Diff line number Diff line change
Expand Up @@ -12,7 +12,7 @@
Beacon.getBeaconReferences($routeParams.dataset, $routeParams.version)
.then(function(data) {
if (data) {
localThis.references = data;
localThis.beaconInfo = data;
}
});

Expand All @@ -33,30 +33,38 @@
function search() {
Beacon.queryBeacon(localThis)
.then(function(response) {
if (!response.data.datasetAlleleResponses[0]) {
if (response.data.exists===false) { // value may be null -> error
localThis.queryResponses.push({
"response": { "state": "Absent" },
"query": {
"chromosome": localThis.chromosome,
"position": localThis.position,
"allele": localThis.allele,
"referenceAllele": localThis.referenceAllele,
"reference": localThis.reference
}
});
}
else {
else if (response.data.exists===true) {
localThis.queryResponses.push({
"response": { "state": "Present" },
"query": {
"chromosome": response.data.datasetAlleleResponses[0].referenceName,
"position": response.data.datasetAlleleResponses[0].start + 1, // Beacon is 0-based
"allele": response.data.datasetAlleleResponses[0].alternateBases,
"referenceAllele": response.data.datasetAlleleResponses[0].referenceBases,
"reference": response.data.datasetAlleleResponses[0].datasetId.substring(0, 6),
}
"chromosome": localThis.chromosome,
"position": localThis.position,
"allele": localThis.allele,
"referenceAllele": localThis.referenceAllele,
}
});
}
else {
localThis.queryResponses.push({
"response": { "state": "Error" },
"query": {
"chromosome": localThis.chromosome,
"position": localThis.position,
"allele": localThis.allele,
"referenceAllele": localThis.referenceAllele,
}
});
},
function() {
localThis.queryResponses.push({
Expand All @@ -66,7 +74,6 @@
"position": localThis.position,
"allele": localThis.allele,
"referenceAllele": localThis.referenceAllele,
"reference": localThis.reference
}
});
}
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22 changes: 14 additions & 8 deletions frontend/src/js/factory.beacon.js
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Original file line number Diff line number Diff line change
Expand Up @@ -14,28 +14,35 @@
for (var i = 0; i < d.length; i++) {
var dataset = d[i].id;
if (dataset.indexOf(name) != -1 && dataset.indexOf(version) != -1) {
return [dataset.split(":")[0].substring(0, 6)];
return {
"reference": dataset.split(":")[0].substring(0, 6),
"datasetId": dataset,
}
}
}
}
else {
var references = [];
for (var i = 0; i < d.length; i++) {
var dataset = d[i].id;
if (dataset.indexOf(name) != -1) {
if (dataset.indexOf(name) !== -1) {
references.push(dataset);
}
}
var highest_ver = 0;
var reference = "";
for (var i = 0; i < references.length; i++) {
var ver = parseInt(dataset.split(":")[2]);
var ver = parseInt(references[i].split(":")[2]);
if (ver > highest_ver) {
highest_ver = ver;
reference = dataset.split(":")[0].substring(0, 6);
reference = references[i].split(":")[0].substring(0, 6);
beaconId = references[i];
}
}
return [reference]
return {
"reference": reference,
"datasetId": beaconId,
}
}
});
}
Expand All @@ -47,9 +54,8 @@
"start": query.position - 1, // Beacon is 0-based
"alternateBases": query.allele,
"referenceBases": query.referenceAllele,
"datasetIds": query.dataset.shortName,
"assemblyId": query.reference,
"includeDatasetResponses": "HIT"
"datasetIds": query.beaconInfo.datasetId,
"assemblyId": query.beaconInfo.reference,
}
}
);
Expand Down
22 changes: 7 additions & 15 deletions frontend/templates/ng-templates/dataset-beacon.html
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Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,7 @@
[% block controller %]datasetBeaconController[% endblock %]
[% block contents %]
<h2>Search</h2>
<div class="alert alert-danger" ng-if="!ctrl.references[0]">
<div class="alert alert-danger" ng-if="!ctrl.beaconInfo.reference">
<h3>Beacon error</h3>
<p>Unable to retrieve the reference set from the Beacon.</p>
<p>Either the dataset version is not available or the service is down.</p>
Expand All @@ -13,37 +13,31 @@ <h3>Beacon error</h3>
<div class="form-group">
<label for="chromosome" class="col-sm-3 control-label">Chromosome</label>
<div class="col-sm-3">
<input type="text" required ng-pattern='/^([1-9]|1[0-9]|2[0-2]|X|Y|x|y)$/' class="form-control" id="chromosome" name="chromosome" ng-model="ctrl.chromosome" placeholder="Chromosome" ng-disabled="!ctrl.references[0]">
<input type="text" required ng-pattern='/^([1-9]|1[0-9]|2[0-2]|X|Y|x|y)$/' class="form-control" id="chromosome" name="chromosome" ng-model="ctrl.chromosome" placeholder="Chromosome" ng-disabled="!ctrl.beaconInfo.reference">
</div>

<label for="position" class="col-sm-3 control-label">Position</label>
<div class="col-sm-3">
<input type="number" required class="form-control" id="position" ng-model="ctrl.position" placeholder="Position" ng-disabled="!ctrl.references[0]">
<input type="number" required class="form-control" id="position" ng-model="ctrl.position" placeholder="Position" ng-disabled="!ctrl.beaconInfo.reference">
</div>
</div>

<div class="form-group">
<label for="referenceAllele" class="col-sm-3 control-label">Reference Allele</label>
<div class="col-sm-3">
<input type="text" required ng-pattern='/^([ATCGatcg]+)$/' class="form-control" id="referenceAllele" ng-model="ctrl.referenceAllele" name='referenceAllele' placeholder="Reference Allele" ng-disabled="!ctrl.references[0]">
<input type="text" required ng-pattern='/^([ATCGatcg]+)$/' class="form-control" id="referenceAllele" ng-model="ctrl.referenceAllele" name='referenceAllele' placeholder="Reference Allele" ng-disabled="!ctrl.beaconInfo.reference">
</div>

<label for="allele" class="col-sm-3 control-label">Alternate Allele</label>
<div class="col-sm-3">
<input type="text" required ng-pattern='/^([ATCGatcg]+)$/' class="form-control" id="allele" ng-model="ctrl.allele" name='allele' placeholder="Alternate Allele" ng-disabled="!ctrl.references[0]">
</div>
</div>

<div class="form-group">
<label for="reference" class="col-sm-3 control-label">Reference</label>
<div class="col-sm-3">
<select required class="form-control" ng-disabled="!ctrl.references[0]" ng-model="ctrl.reference" ng-options="r as r for r in ctrl.references"></select>
<input type="text" required ng-pattern='/^([ATCGatcg]+)$/' class="form-control" id="allele" ng-model="ctrl.allele" name='allele' placeholder="Alternate Allele" ng-disabled="!ctrl.beaconInfo.reference">
</div>
</div>

<div class="form-group">
<div class="col-sm-offset-3 col-sm-7">
<button ng-click="ctrl.search()" class="btn btn-primary" ng-disabled="!(ctrl.chromosome && ctrl.position && ctrl.referenceAllele && ctrl.allele && ctrl.reference)">Search</button><span class="left-margin alert-text" ng-if="!(ctrl.chromosome && ctrl.position && ctrl.referenceAllele && ctrl.allele && ctrl.reference)">Need to fill in all values before searching</span>
<button ng-click="ctrl.search()" class="btn btn-primary" ng-disabled="!(ctrl.chromosome && ctrl.position && ctrl.referenceAllele && ctrl.allele && ctrl.beaconInfo.reference)">Search</button>
<span class="left-margin alert-text" ng-if="!(ctrl.chromosome && ctrl.position && ctrl.referenceAllele && ctrl.allele) && ctrl.beaconInfo.reference">Need to fill in all values before searching</span>
</div>
<div class="col-sm-2">
<a style='cursor: pointer' ng-click="showDetails = ! showDetails" class="pull-right">
Expand Down Expand Up @@ -75,15 +69,13 @@ <h2>Results</h2>
<th>Position</th>
<th>Reference Allele</th>
<th>Alternate Allele</th>
<th>Reference</th>
</tr>
<tr ng-repeat="row in ctrl.queryResponses">
<td>{{row.response.state}}</td>
<td>{{row.query.chromosome}}</td>
<td>{{row.query.position}}</td>
<td>{{row.query.referenceAllele}}</td>
<td>{{row.query.allele}}</td>
<td>{{row.query.reference}}</td>
</tr>
</table>
</div>
Expand Down

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