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Make the frontend beacon use the elixir beacon #550

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merged 4 commits into from
Apr 29, 2019
Merged

Make the frontend beacon use the elixir beacon #550

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cc485c7
Change beacon to use the elixir beacon instead of the simple internal…
talavis Apr 25, 2019
0d2c571
remove beacon
talavis Apr 26, 2019
2518ccb
do not import beacon
talavis Apr 26, 2019
3b898de
remove debugging message
talavis Apr 29, 2019
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135 changes: 0 additions & 135 deletions backend/beacon.py
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13 changes: 2 additions & 11 deletions backend/route.py
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Original file line number Diff line number Diff line change
Expand Up @@ -9,8 +9,6 @@
import handlers
import auth
import settings as swefreq_settings
import beacon
#import template

from modules.browser.route import routes as browser_routes

Expand Down Expand Up @@ -43,7 +41,7 @@ def __init__(self, settings):
{"path": "static/"}),
(r'/(favicon.ico)', tornado.web.StaticFileHandler,
{"path": "static/img/"}),
(r"/release/(?P<dataset>[^\/]+)/(?P<hash_value>[^\/]+)/(?P<file>[^\/]+)",handlers.TemporaryStaticNginxFileHandler,
(r"/release/(?P<dataset>[^\/]+)/(?P<hash_value>[^\/]+)/(?P<file>[^\/]+)", handlers.TemporaryStaticNginxFileHandler,
{"path": "/release-files/"}),
(r"/release/(?P<dataset>[^\/]+)/versions/(?P<ds_version>[^/]+)/(?P<file>[^\/]+)", handlers.AuthorizedStaticNginxFileHandler,
{"path": "/release-files/"}),
Expand All @@ -66,7 +64,7 @@ def __init__(self, settings):
(r"/api/dataset/(?P<dataset>[^\/]+)/log/(?P<event>[^\/]+)/(?P<target>[^\/]+)", application.LogEvent),
(r"/api/dataset/(?P<dataset>[^\/]+)/logo", application.ServeLogo),
(r"/api/dataset/(?P<dataset>[^\/]+)/(?:versions/(?P<ds_version>[^/]+)/)?files", application.DatasetFiles),
(r"/api/dataset/(?P<dataset>[^\/]+)/(?:versions/(?P<ds_version>[^/]+)/)?collection", application.Collection),
(r"/api/dataset/(?P<dataset>[^\/]+)/(?:versions/(?P<ds_version>[^/]+)/)?collection", application.Collection),
(r"/api/dataset/(?P<dataset>[^\/]+)/users_current", application.DatasetUsersCurrent),
(r"/api/dataset/(?P<dataset>[^\/]+)/users_pending", application.DatasetUsersPending),
(r"/api/dataset/(?P<dataset>[^\/]+)/(?:versions/(?P<ds_version>[^/]+)/)?temporary_link", application.GenerateTemporaryLink),
Expand All @@ -77,13 +75,6 @@ def __init__(self, settings):
(r"/api/dataset/(?P<dataset>[^\/]+)/versions/(?P<version>[^\/]+)", application.GetDataset),
(r"/api/dataset/(?P<dataset>[^\/]+)/versions/(?P<version>[^\/]+)/files", application.DatasetFiles),
(r"/api/dataset/(?P<dataset>[^\/]+)/versions/(?P<version>[^\/]+)/temporary_link", application.GenerateTemporaryLink),
### Beacon API
(r"/api/beacon/query", beacon.Query),
(r"/api/beacon/info", beacon.Info),
# # # # # Legacy beacon URIs # # # # #
(r"/query", beacon.Query),
(r"/info", tornado.web.RedirectHandler,
{"url": "/api/beacon/info"}),
]

## Adding module handlers
Expand Down
8 changes: 8 additions & 0 deletions frontend/src/css/main.scss
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Original file line number Diff line number Diff line change
Expand Up @@ -295,6 +295,14 @@ table.variant-table {
}
}

/* text for search button */
.alert-text {
color: #900;
}
.left-margin {
margin-left: 5px;
}

#annotationPanel {
position: absolute;
visibility: hidden;
Expand Down
40 changes: 30 additions & 10 deletions frontend/src/js/controller.datasetBeaconController.js
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Original file line number Diff line number Diff line change
Expand Up @@ -8,13 +8,13 @@

activate();


function activate() {
Beacon.getBeaconReferences($routeParams.dataset).then(
function(data) {
localThis.references = data;
}
);
Beacon.getBeaconReferences($routeParams.dataset, $routeParams.version)
.then(function(data) {
if (data) {
localThis.references = data;
}
});

User.getUser().then(function(data) {
localThis.user = data;
Expand All @@ -33,10 +33,30 @@
function search() {
Beacon.queryBeacon(localThis)
.then(function(response) {
var d = response.data;
d.query.position += 1; // Beacon is 0-based
d.response.state = d.response.exists ? "Present" : "Absent";
localThis.queryResponses.push(d);
if (!response.data.datasetAlleleResponses[0]) {
localThis.queryResponses.push({
"response": { "state": "Absent" },
"query": {
"chromosome": localThis.chromosome,
"position": localThis.position,
"allele": localThis.allele,
"referenceAllele": localThis.referenceAllele,
"reference": localThis.reference
}
});
}
else {
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),
}
});
}
},
function() {
localThis.queryResponses.push({
Expand Down
52 changes: 36 additions & 16 deletions frontend/src/js/factory.beacon.js
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Original file line number Diff line number Diff line change
Expand Up @@ -6,30 +6,50 @@
queryBeacon: queryBeacon
};

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

for (var i = 0; i < d.length; i++) {
var dataset = d[i];
if (dataset.id === name) {
references.push(dataset.reference);
if (version) {
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 references;
}
else {
var references = [];
for (var i = 0; i < d.length; i++) {
var dataset = d[i].id;
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]);
if (ver > highest_ver) {
highest_ver = ver;
reference = dataset.split(":")[0].substring(0, 6);
}
}
return [reference]
}
});
}

function queryBeacon(query) {
return $http.get("/api/beacon/query", {
return $http.get("/api/beacon-elixir/query", {
"params": {
"chrom": query.chromosome,
"pos": query.position - 1, // Beacon is 0-based
"allele": query.allele,
"referenceAllele": query.referenceAllele,
"dataset": query.dataset.shortName,
"ref": query.reference
"referenceName": query.chromosome,
"start": query.position - 1, // Beacon is 0-based
"alternateBases": query.allele,
"referenceBases": query.referenceAllele,
"datasetIds": query.dataset.shortName,
"assemblyId": query.reference,
"includeDatasetResponses": "HIT"
}
}
);
Expand Down
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