Updated services prior to merge

opentargets-archive · Aug 29, 2017 · 51761e9 · 51761e9
1 parent 2a25d26
commit 51761e9
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Showing 39 changed files with 174 additions and 703 deletions.
diff --git a/app/facets/data-distribution/data-distribution-facet-parser.js b/app/facets/data-distribution/data-distribution-facet-parser.js
@@ -1,6 +1,6 @@
 angular.module('facets')
 
-    .factory('dataDistributionFacetParser', ['otConsts', 'otFiltersService', function (otConsts, otFiltersService) {
+    .factory('dataDistributionFacetParser', ['otConsts', 'otFacetsFilters', function (otConsts, otFacetsFilters) {
         'use strict';
 
 
@@ -27,7 +27,7 @@ angular.module('facets')
             // TODO:
             // this is not gonna work now!
             // NEED TO CHANGE all facets to return a config object rathen than just the list of filters...
-            var search = otFiltersService.parseURL();
+            var search = otFacetsFilters.parseURL();
             search.score_min = search.score_min || [otConsts.defaults.SCORE_MIN.toFixed(2)];
             search.score_max = search.score_max || [otConsts.defaults.SCORE_MAX.toFixed(2)];
             search.score_str = search.score_str || [otConsts.defaults.STRINGENCY];

diff --git a/app/plugins/disease-classification-directive.js b/app/plugins/disease-classification-directive.js
@@ -1,5 +1,5 @@
 angular.module('plugins')
-    .directive('diseaseClassification', ['otAPIservice', '$timeout', 'otUtils', function (otAPIservice, $timeout, otUtils) {
+    .directive('diseaseClassification', ['otApi', '$timeout', 'otUtils', function (otApi, $timeout, otUtils) {
         'use strict';
 
         return {
@@ -18,7 +18,7 @@ angular.module('plugins')
                         .width(scope.width - 40) // 40 for margins
                         .height(700)
                         .data(scope.disease)
-                        .cttvApi(otAPIservice.getSelf());
+                        .cttvApi(otApi.getSelf());
 
                     efoGraph(container);
 

diff --git a/app/plugins/genome-browser-directive.js b/app/plugins/genome-browser-directive.js
@@ -1,5 +1,5 @@
 angular.module('plugins')
-    .directive('genomeBrowser', ['otAPIservice', 'otUtils', function (otAPIservice, otUtils) {
+    .directive('genomeBrowser', ['otApi', 'otUtils', function (otApi, otUtils) {
         'use strict';
 
         // Decorate the svg for exporting
@@ -108,7 +108,7 @@ angular.module('plugins')
                 gB.rest().prefix('/proxy/rest.ensembl.org').protocol('').domain('');
                 var theme = targetGenomeBrowser()
                     .efo(efo)
-                    .cttvRestApi(otAPIservice.getSelf());
+                    .cttvRestApi(otApi.getSelf());
                 theme(gB, newDiv);
 
                 if (otUtils.browser.name !== 'IE') {

diff --git a/app/plugins/interactions-viewer.js b/app/plugins/interactions-viewer.js
@@ -1,5 +1,5 @@
 angular.module('plugins')
-    .directive('interactionsViewer', ['$log', '$timeout', '$http', '$q', 'otAPIservice', 'otOmnipathdbSources', function ($log, $timeout, $http, $q, otAPIservice, otOmnipathdbSources) {
+    .directive('interactionsViewer', ['$log', '$timeout', '$http', '$q', 'otApi', 'otOmnipathdbSources', function ($log, $timeout, $http, $q, otApi, otOmnipathdbSources) {
         function getNames (bestHits) {
             var mapNames = {};
             for (var i = 0; i < bestHits.length; i++) {
@@ -75,7 +75,7 @@ angular.module('plugins')
                             trackCall: false
                         };
 
-                        promises.push(otAPIservice.getBestHitSearch(queryObject));
+                        promises.push(otApi.getBestHitSearch(queryObject));
 
                         // Both promises run in parallel
                         $q.all(promises)

diff --git a/app/plugins/related-diseases-directive.js b/app/plugins/related-diseases-directive.js
@@ -1,5 +1,5 @@
 angular.module('plugins')
-    .directive('relatedDiseases', ['otUtils', 'otConsts', 'otDictionary', 'otAPIservice', '$timeout', function (otUtils, otConsts, otDictionary, otAPIservice, $timeout) {
+    .directive('relatedDiseases', ['otUtils', 'otConsts', 'otDictionary', 'otApi', '$timeout', function (otUtils, otConsts, otDictionary, otApi, $timeout) {
         'use strict';
 
         // Details table --
@@ -148,8 +148,8 @@ angular.module('plugins')
             paramsObj.size = 200;
             paramsObj.direct = true;
             paramsObj.facets = false;
-            // TODO: Include POST in otAPIservice
-            var cttvApi = otAPIservice.getSelf(); // No POST in the service yet
+            // TODO: Include POST in otApi
+            var cttvApi = otApi.getSelf(); // No POST in the service yet
             var url = cttvApi.url.associations();
 
             cttvApi.call(url, paramsObj)
@@ -244,7 +244,7 @@ angular.module('plugins')
                         .skip(1)
                         .size(600)
                         .score('jackard_weighted')
-                        .cttvApi(otAPIservice.getSelf());
+                        .cttvApi(otApi.getSelf());
 
                     // v.on("load", function (d) {
                     //     $log.log("LOADED------------------------------------");

diff --git a/app/plugins/related-targets-directive.js b/app/plugins/related-targets-directive.js
@@ -1,5 +1,5 @@
 angular.module('plugins')
-    .directive('relatedTargets', ['$log', 'otAPIservice', function ($log, otAPIservice) {
+    .directive('relatedTargets', ['$log', 'otApi', function ($log, otApi) {
         'use strict';
 
         return {
@@ -9,7 +9,7 @@ angular.module('plugins')
                 target: '='
             },
             link: function (scope, element, attrs) {
-                otAPIservice.getTargetRelation({
+                otApi.getTargetRelation({
                     id: scope.target.id
                 })
                     .then(
@@ -21,7 +21,7 @@ angular.module('plugins')
                         },
 
                         // error handler
-                        otAPIservice.defaultErrorHandler
+                        otApi.defaultErrorHandler
                     );
             }
         };

diff --git a/app/src/components/batch-search/target-list-mapping-directive.js b/app/src/components/batch-search/target-list-mapping-directive.js
@@ -1,7 +1,7 @@
 angular.module('otDirectives')
 
 
-    .directive('otTargetListMapping', ['otAPIservice', 'otUtils', 'otLoadedLists', 'otConfig', function (otAPIservice, otUtils, otLoadedLists, otConfig) {
+    .directive('otTargetListMapping', ['otApi', 'otUtils', 'otLoadedLists', 'otConfig', function (otApi, otUtils, otLoadedLists, otConfig) {
         'use strict';
 
         return {
@@ -27,7 +27,7 @@ angular.module('otDirectives')
                         }
                     };
 
-                    return otAPIservice.getSearch(queryObject);
+                    return otApi.getSearch(queryObject);
                 }
 
                 // scope.setNewItem = function (oldQuery, res) {

diff --git a/app/src/components/batch-search/target-list-upload-directive.js b/app/src/components/batch-search/target-list-upload-directive.js
@@ -1,5 +1,5 @@
 angular.module('otDirectives')
-    .directive('otTargetListUpload', ['otAPIservice', 'otLoadedLists', 'otConfig', function (otAPIservice, otLoadedLists, otConfig) {
+    .directive('otTargetListUpload', ['otApi', 'otLoadedLists', 'otConfig', function (otApi, otLoadedLists, otConfig) {
         'use strict';
 
         return {
@@ -76,7 +76,7 @@ angular.module('otDirectives')
                         params: opts
                     };
 
-                    return otAPIservice.getBestHitSearch(queryObject)
+                    return otApi.getBestHitSearch(queryObject)
                         .then(function (resp) {
                             var listName = otLoadedLists.parseBestHitSearch(name, resp.body);
 

diff --git a/app/src/components/disease-associations/disease-associations-table-directive.js b/app/src/components/disease-associations/disease-associations-table-directive.js
@@ -14,7 +14,7 @@ angular.module('otDirectives')
 *   In this example, "loading" is the name of the var in the parent scope, pointing to $scope.loading.
 *   This is useful in conjunction with a spinner where you can have ng-show="loading"
 */
-    .directive('otDiseaseAssociations', ['otUtils', 'otDictionary', 'otConsts', 'otAPIservice', '$q', function (otUtils, otDictionary, otConsts, otAPIservice, $q) {
+    .directive('otDiseaseAssociations', ['otUtils', 'otDictionary', 'otConsts', 'otApi', '$q', function (otUtils, otDictionary, otConsts, otApi, $q) {
         'use strict';
 
         var draw = 1;
@@ -196,13 +196,13 @@ angular.module('otDirectives')
                         opts.target = target;
                     }
 
-                    opts = otAPIservice.addFacetsOptions(filters, opts);
+                    opts = otApi.addFacetsOptions(filters, opts);
                     var queryObject = {
                         method: 'POST',
                         params: opts
                     };
 
-                    otAPIservice.getAssociations(queryObject)
+                    otApi.getAssociations(queryObject)
                         .then(function (resp) {
                             var dtData = parseServerResponse(resp.body.data);
                             var o = {
@@ -376,13 +376,13 @@ angular.module('otDirectives')
                     if (scope.targets && scope.targets.length) {
                         optsPreFlight.target = scope.targets;
                     }
-                    optsPreFlight = otAPIservice.addFacetsOptions(scope.filters, optsPreFlight);
+                    optsPreFlight = otApi.addFacetsOptions(scope.filters, optsPreFlight);
 
                     var queryObject = {
                         method: 'POST',
                         params: optsPreFlight
                     };
-                    otAPIservice.getAssociations(queryObject)
+                    otApi.getAssociations(queryObject)
                         .then(function (resp) {
                             var total = resp.body.total;
 
@@ -416,14 +416,14 @@ angular.module('otDirectives')
                                     opts.target = scope.targets;
                                 }
 
-                                opts = otAPIservice.addFacetsOptions(scope.filters, opts);
+                                opts = otApi.addFacetsOptions(scope.filters, opts);
 
                                 var queryObject = {
                                     method: 'POST',
                                     params: opts
                                 };
 
-                                return otAPIservice.getAssociations(queryObject)
+                                return otApi.getAssociations(queryObject)
                                     .then(function (resp) {
                                         var moreText = resp.body;
 
@@ -466,7 +466,7 @@ angular.module('otDirectives')
                                 // hiddenElement.download = scope.filename + ".csv";
                                 // hiddenElement.click();
                             });
-                        }, otAPIservice.defaultErrorHandler);
+                        }, otApi.defaultErrorHandler);
                 };
 
 

diff --git a/app/src/components/efo-graph/efo-graph-directive.js b/app/src/components/efo-graph/efo-graph-directive.js
@@ -1,5 +1,5 @@
 angular.module('otDirectives')
-    .directive('otEfoGraph', ['otAPIservice', function (otAPIservice) {
+    .directive('otEfoGraph', ['otApi', function (otApi) {
         'use strict';
         return {
             restrict: 'E',
@@ -11,7 +11,7 @@ angular.module('otDirectives')
                 var efoGraph = diseaseGraph()
                     .width(w)
                     .height(700)
-                    .cttvApi(otAPIservice.getSelf());
+                    .cttvApi(otApi.getSelf());
 
                 scope.$watch(function () { return attrs.efo; }, function (efo_str) {
                     if (!efo_str) {

diff --git a/app/src/components/facets/facets.js b/app/src/components/facets/facets.js
@@ -36,7 +36,7 @@ angular.module('facets', [])
     * Top level container for all the facets.
     * This contains accordion etc
     */
-    .directive('cttvFacets', ['otFiltersService', function (otFiltersService) {
+    .directive('cttvFacets', ['otFacetsFilters', function (otFacetsFilters) {
         'use strict';
 
         return {
@@ -49,13 +49,13 @@ angular.module('facets', [])
 
             link: function (scope) {
                 // scope.dataDistribution =
-                scope.filters = otFiltersService.getFilters();
-                scope.selectedFilters = otFiltersService.getSelectedFilters();
-                scope.deselectAll = otFiltersService.deselectAll;
+                scope.filters = otFacetsFilters.getFilters();
+                scope.selectedFilters = otFacetsFilters.getSelectedFilters();
+                scope.deselectAll = otFacetsFilters.deselectAll;
 
-                // scope.respStatus = 1; //otFiltersService.status(); // TODO: handle response status
+                // scope.respStatus = 1; //otFacetsFilters.status(); // TODO: handle response status
                 // scope.updateFilter = function(id){
-                //    otFiltersService.getFilter(id).toggle();
+                //    otFacetsFilters.getFilter(id).toggle();
                 // }
             }
 

diff --git a/app/src/components/filter-by-file-targets/filter-by-file-targets-directive.js b/app/src/components/filter-by-file-targets/filter-by-file-targets-directive.js
@@ -7,7 +7,7 @@ angular.module('otDirectives')
  *   <ot-filter-by-file-targets> </ot-filter-by-file-targets>
  *
  */
-    .directive('otFilterByFileTargets', ['$log', 'otAPIservice', '$q', '$analytics', 'otLoadedLists', '$location', 'otUtils', function ($log, otAPIservice, $q, $analytics, otLoadedLists, $location, otUtils) {
+    .directive('otFilterByFileTargets', ['$log', 'otApi', '$q', '$analytics', 'otLoadedLists', '$location', 'otUtils', function ($log, otApi, $q, $analytics, otLoadedLists, $location, otUtils) {
         'use strict';
 
         return {
@@ -177,7 +177,7 @@ angular.module('otDirectives')
                         params: opts
                     };
 
-                    return otAPIservice.getBestHitSearch(queryObject)
+                    return otApi.getBestHitSearch(queryObject)
                         .then(function (resp) {
                             if (resp.body.data.length) {
                                 var listName = otLoadedLists.parseBestHitSearch(scope.fileName, resp.body);

diff --git a/app/src/components/hpa-tissue-expression/hpa-tissue-expression-directive.js b/app/src/components/hpa-tissue-expression/hpa-tissue-expression-directive.js
@@ -11,7 +11,7 @@ angular.module('otDirectives')
     *   In this example, "loading" is the name of the var in the parent scope, pointing to $scope.loading.
     *   This is useful in conjunction with a spinner where you can have ng-show="loading"
     */
-    .directive('cttvHpaTissueExpression', ['otAPIservice', 'otUtils', function (otAPIservice, otUtils) {
+    .directive('cttvHpaTissueExpression', ['otApi', 'otUtils', function (otApi, otUtils) {
         'use strict';
 
         var colorScale = otUtils.colorScales.BLUE_1_3; // blue orig
@@ -77,11 +77,11 @@ angular.module('otDirectives')
                 scope.$watch(
                     'target',
                     function () {
-                        // move otAPIservice.getExpression ({ in here
+                        // move otApi.getExpression ({ in here
                         // ......
 
                         if (scope.target) {
-                            otAPIservice.getExpression({
+                            otApi.getExpression({
                                 'method': 'GET',
                                 'params': {
                                     gene: scope.target  // TODO: should be TARGET in API!!!
@@ -146,7 +146,7 @@ angular.module('otDirectives')
                                     },
 
                                     // error
-                                    otAPIservice.defaultErrorHandler
+                                    otApi.defaultErrorHandler
                                 );
                         }
                     }

diff --git a/app/src/components/known-drug-table/known-drug-table-directive.js b/app/src/components/known-drug-table/known-drug-table-directive.js
@@ -3,7 +3,7 @@
 angular.module('otDirectives')
 
 /* Directive to display the known drug evidence table */
-    .directive('otKnownDrugTable', ['otAPIservice', 'otConsts', 'otUtils', 'otConfig', '$location', 'otDictionary', function (otAPIservice, otConsts, otUtils, otConfig, $location, otDictionary) {
+    .directive('otKnownDrugTable', ['otApi', 'otConsts', 'otUtils', 'otConfig', '$location', 'otDictionary', function (otApi, otConsts, otUtils, otConfig, $location, otDictionary) {
         'use strict';
         // var dbs = otConsts.dbs;
         var searchObj = otUtils.search.translateKeys($location.search());
@@ -92,7 +92,7 @@ angular.module('otDirectives')
                             method: 'GET',
                             params: opts
                         };
-                        return otAPIservice.getFilterBy(queryObject)
+                        return otApi.getFilterBy(queryObject)
                             .then(
                                 function (resp) {
                                     if (resp.body.data) {
@@ -102,7 +102,7 @@ angular.module('otDirectives')
                                         // $log.warn("Empty response : drug data");
                                     }
                                 },
-                                otAPIservice.defaultErrorHandler
+                                otApi.defaultErrorHandler
                             )
                             .finally(function () {
                                 scope.loadFlag = false;

diff --git a/app/src/components/log-session/log-session-directive.js b/app/src/components/log-session/log-session-directive.js
@@ -1,13 +1,13 @@
 angular.module('otDirectives')
 
 
-    .directive('logSession', ['otAPIservice', function (otAPIservice) {
+    .directive('logSession', ['otApi', function (otApi) {
         'use strict';
 
         return {
             restrict: 'E',
             link: function () {
-                otAPIservice.logSession();
+                otApi.logSession();
             }
         };
     }]);
diff --git a/app/src/components/multiple-targets/multiple-targets-drugs-summary-directives.js b/app/src/components/multiple-targets/multiple-targets-drugs-summary-directives.js
@@ -1,6 +1,6 @@
 angular.module('otDirectives')
 
-    .directive('multipleTargetsDrugsSummary', ['otAPIservice', 'otConfig', 'otUtils', function (otAPIservice, otConfig, otUtils) {
+    .directive('multipleTargetsDrugsSummary', ['otApi', 'otConfig', 'otUtils', function (otApi, otConfig, otUtils) {
         'use strict';
 
         function formatDrugDataToArray (drugs) {
@@ -57,7 +57,7 @@ angular.module('otDirectives')
                             ]
                         }
                     };
-                    otAPIservice.getFilterBy(queryObject)
+                    otApi.getFilterBy(queryObject)
                         .then(function (resp) {
                             var drugs = {};
                             for (var i = 0; i < resp.body.data.length; i++) {

diff --git a/app/src/components/multiple-targets/multiple-targets-tissues-summary-directive.js b/app/src/components/multiple-targets/multiple-targets-tissues-summary-directive.js
@@ -1,6 +1,6 @@
 angular.module('otDirectives')
 
-    .directive('multipleTargetsTissuesSummary', ['$log', '$http', '$q', 'otUtils', 'otAPIservice', function ($log, $http, $q, otUtils, otAPIservice) {
+    .directive('multipleTargetsTissuesSummary', ['$log', '$http', '$q', 'otUtils', 'otApi', function ($log, $http, $q, otUtils, otApi) {
         'use strict';
 
         var tissuesOrdered = [
@@ -147,7 +147,7 @@ angular.module('otDirectives')
                     var baseGtexUrlSufix = '?boxplot=true';
                     for (var i = 0; i < scope.targets.length; i++) {
                         var target = scope.targets[i];
-                        var targetPromise = otAPIservice.getTarget({
+                        var targetPromise = otApi.getTarget({
                             method: 'GET',
                             trackCall: true,
                             params: {