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Merge a012d6e into 8172f2e
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@talavis
talavis committed Aug 26, 2019
2 parents 8172f2e + a012d6e commit 5a53fce
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Showing 5 changed files with 84 additions and 83 deletions.
72 changes: 36 additions & 36 deletions frontend/src/js/controller.browserController.js
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Original file line number Diff line number Diff line change
Expand Up @@ -55,95 +55,95 @@
localThis.itemType = "transcript";
localThis.item = $routeParams.transcript;
Browser.getTranscript($routeParams.dataset, $routeParams.version, $routeParams.transcript)
.then( function(data) {
.then( function(data) {
localThis.transcript = data.transcript;
localThis.gene = data.gene;
localThis.coverage.region.exons = data.exons;
})
.catch((err) => {
.catch((err) => {
localThis.transcript = {"statusCode": err.status,
"statusText": err.statusText};
});
;
});

}
if ($routeParams.region) {
localThis.itemType = "region";
localThis.item = $routeParams.region;
Browser.getRegion($routeParams.dataset, $routeParams.version, $routeParams.region)
.then( function(data) {
.then( function(data) {
localThis.region = data.region;
})
.catch((err) => {
.catch((err) => {
localThis.region = {"statusCode": err.status,
"statusText": err.statusText,
"variantId": $routeParams.region};
});
"statusText": err.statusText,
"variantId": $routeParams.region};
});
}
if ($routeParams.gene) {
localThis.itemType = "gene";
localThis.item = $routeParams.gene;
Browser.getGene($routeParams.dataset, $routeParams.version, $routeParams.gene)
.then( function(data) {
.then( function(data) {
localThis.gene = data.gene;
localThis.transcripts = data.transcripts;
localThis.coverage.region.exons = data.exons;
})
.catch((err) => {
.catch((err) => {
localThis.gene = {"statusCode": err.status,
"statusText": err.statusText};
});
"statusText": err.statusText};
});
}
if (localThis.itemType) {
Browser.getVariants($routeParams.dataset, $routeParams.version, localThis.itemType, localThis.item)
.then( function(data) {
.then( function(data) {
localThis.variants = data.variants;
localThis.headers = data.headers;

// TODO Move to function later
let mapFunction = function(variant) {
variant.isPass = variant.filter == "PASS";
if (variant.flags.indexOf("LoF") === -1)
variant.isLof = false;
else
variant.isLof = true;
if (variant.flags.indexOf("LoF") === -1)
variant.isLof = false;
else
variant.isLof = true;
variant.isMissense = variant.majorConsequence == "missense";
};
localThis.variants.map(mapFunction);

localThis.filterVariants();
localThis.variants.loaded = true;
localThis.variants.loaded = true;
})
.catch((err) => {
localThis.variants = {"statusCode": err.status,
"statusText": err.statusText,
"loaded": true,};
});
.catch((err) => {
localThis.variants = {"statusCode": err.status,
"statusText": err.statusText,
"loaded": true,};
});
Browser.getCoveragePos($routeParams.dataset, $routeParams.version, localThis.itemType, localThis.item)
.then( function(data) {
.then( function(data) {
localThis.coverage.region.start = data.start;
localThis.coverage.region.stop = data.stop;
localThis.coverage.region.chrom = data.chrom;
});
Browser.getCoverage($routeParams.dataset, $routeParams.version, localThis.itemType, localThis.item)
.then(function(data) {
.then(function(data) {
localThis.coverage.data = data.coverage;
localThis.coverage.loaded = true;
})
.catch((err) => {
localThis.coverage = {"statusCode": err.status,
"statusText": err.statusText,
"loaded": true,};
});
.catch((err) => {
localThis.coverage = {"statusCode": err.status,
"statusText": err.statusText,
"loaded": true,};
});
}
if ($routeParams.variant) {
Browser.getVariant($routeParams.dataset, $routeParams.version, $routeParams.variant)
.then( function(data) {
.then( function(data) {
localThis.variant = data.variant;
})
.catch((err) => {
localThis.variant = {"statusCode": err.status,
"statusText": err.statusText};
});
.catch((err) => {
localThis.variant = {"statusCode": err.status,
"statusText": err.statusText};
});

}
Dataset.getDataset($routeParams.dataset, $routeParams.version, $routeParams.version)
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26 changes: 13 additions & 13 deletions frontend/src/js/controller.datasetBeaconController.js
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Original file line number Diff line number Diff line change
Expand Up @@ -12,9 +12,9 @@
function activate() {
Beacon.getBeaconReferences($routeParams.dataset, $routeParams.version)
.then(function(data) {
if (data) {
if (data) {
localThis.beaconInfo = data;
}
}
});

User.getUser().then(function(data) {
Expand All @@ -34,7 +34,7 @@
function search() {
Beacon.queryBeacon(localThis)
.then(function(response) {
if (response.data.exists===false) { // value may be null -> error
if (response.data.exists===false) { // value may be null -> error
localThis.queryResponses.push({
"response": { "state": "Absent" },
"query": {
Expand All @@ -44,19 +44,19 @@
"referenceAllele": localThis.referenceAllele,
}
});
}
else if (response.data.exists===true) {
}
else if (response.data.exists===true) {
localThis.queryResponses.push({
"response": { "state": "Present" },
"query": {
"response": { "state": "Present" },
"query": {
"chromosome": localThis.chromosome,
"position": localThis.position,
"allele": localThis.allele,
"referenceAllele": localThis.referenceAllele,
}
});
}
else {
}
else {
localThis.queryResponses.push({
"response": { "state": "Error" },
"query": {
Expand All @@ -82,10 +82,10 @@
);
}
function fillExample() {
localThis.chromosome = "22";
localThis.position = 46615880;
localThis.referenceAllele = "T";
localThis.allele = "C";
localThis.chromosome = "22";
localThis.position = 46615880;
localThis.referenceAllele = "T";
localThis.allele = "C";
}
}]);
})();
6 changes: 3 additions & 3 deletions frontend/src/js/controller.datasetDownloadController.js
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Original file line number Diff line number Diff line change
Expand Up @@ -44,10 +44,10 @@
}

function updateAuthorizationLevel() {
if (!localThis.hasOwnProperty("user") || localThis.user.user == null) {
if (!Object.prototype.hasOwnProperty.call(localThis, "user") || localThis.user.user == null) {
localThis.authorizationLevel = "logged_out";
}
else if (localThis.hasOwnProperty("dataset")) {
else if (Object.prototype.hasOwnProperty.call(localThis, "dataset")) {
localThis.authorizationLevel = localThis.dataset.authorizationLevel;
}
}
Expand Down Expand Up @@ -89,7 +89,7 @@
}

function dataContactIsEmail() {
return localThis.hasOwnProperty("dataset") &&
return Object.prototype.hasOwnProperty.call(localThis, "dataset") &&
localThis.dataset.version.dataContactLink.indexOf("@") > -1;
}
}]);
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45 changes: 23 additions & 22 deletions frontend/src/js/factory.beacon.js
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Original file line number Diff line number Diff line change
Expand Up @@ -8,41 +8,42 @@

function getBeaconReferences(name, version) {
return $http.get("/api/beacon-elixir/").then(function(data) {
var d = data.data.datasets;
let d = data.data.datasets;

if (version) {
for (var i = 0; i < d.length; i++) {
var dataset = d[i].id;
for (let i = 0; i < d.length; i++) {
let dataset = d[i].id;
if (dataset.indexOf(name) != -1 && dataset.indexOf(version) != -1) {
return {
"reference": dataset.split(":")[0].substring(0, 6),
"datasetId": dataset,
}
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;
let references = [];
for (let i = 0; i < d.length; i++) {
let dataset = d[i].id;
if (dataset.indexOf(name) !== -1) {
references.push(dataset);
references.push(dataset);
}
}
var highest_ver = 0;
var reference = "";
for (var i = 0; i < references.length; i++) {
var ver = parseInt(references[i].split(":")[2]);
if (ver > highest_ver) {
highest_ver = ver;
reference = references[i].split(":")[0].substring(0, 6);
beaconId = references[i];
let beaconId = "";
let highestVer = 0;
let reference = "";
for (let i = 0; i < references.length; i++) {
let ver = parseInt(references[i].split(":")[2]);
if (ver > highestVer) {
highestVer = ver;
reference = references[i].split(":")[0].substring(0, 6);
beaconId = references[i];
}
}
return {
}
return {
"reference": reference,
"datasetId": beaconId,
}
};
}
});
}
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18 changes: 9 additions & 9 deletions frontend/src/js/factory.browser.js
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Expand Up @@ -14,16 +14,16 @@
};

function baseUrl(dataset, version) {
var url = "/api/dataset/" + dataset + "/";
if ( version ) {
url += "version/" + version + "/"
}
url += 'browser/';
return url;
var url = "/api/dataset/" + dataset + "/";
if ( version ) {
url += "version/" + version + "/";
}
url += "browser/";
return url;
}

function getGene(dataset, version, gene) {
return $http.get(baseUrl(dataset, version) + "gene/" + gene).then(function(data) {
return $http.get(baseUrl(dataset, version) + "gene/" + gene).then(function(data) {
return data.data;
});
}
Expand All @@ -41,9 +41,9 @@
}

function getVariant(dataset, version, variant) {
return $http.get(baseUrl(dataset, version) + "variant/" + variant).then(function(data) {
return $http.get(baseUrl(dataset, version) + "variant/" + variant).then(function(data) {
return data.data;
});
});
}

function search(dataset, version, query) {
Expand Down

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