opening genomics on submap fixed

frontend-js/src/main/js/map/data/DataOverlay.js

@@ -210,7 +210,7 @@ DataOverlay.prototype.getFullAliasById = function (id) {
   var self = this;
   var alias = self.getAliasById(id);
   if (alias !== undefined) {
-    if (alias.getType() === LayoutAlias.LIGTH) {
+    if (alias.getType() === LayoutAlias.LIGHT) {
       return ServerConnector.getFullOverlayElement({
         element: new IdentifiedElement(alias),
         overlay: self

frontend-js/src/main/js/map/data/LayoutAlias.js

@@ -15,7 +15,7 @@ function LayoutAlias(javaObject) {
   this.setModelId(javaObject.modelId);
   this.setDescription(javaObject.description);
   if (javaObject.type === undefined) {
-    this.setType(LayoutAlias.LIGTH);
+    this.setType(LayoutAlias.LIGHT);
   } else if (javaObject.type === LayoutAlias.GENETIC_VARIANT) {
     this.setType(LayoutAlias.GENETIC_VARIANT);
   } else if (javaObject.type === LayoutAlias.GENERIC) {

frontend-js/src/main/js/map/window/AliasInfoWindow.js

@@ -291,7 +291,7 @@ AliasInfoWindow.prototype.createGenomicDiv = function () {
       if (data !== null && data !== undefined && data.getType() === LayoutAlias.GENETIC_VARIANT) {
         geneticInformation = true;
         return Promise.each(data.getGeneVariants(), function (variant) {
-          return self.getCustomMap().getReferenceGenome(variant.getReferenceGenomeType(),
+          return self.getCustomMap().getTopMap().getReferenceGenome(variant.getReferenceGenomeType(),
             variant.getReferenceGenomeVersion()).then(
             function (genome) {
               if (genome.getUrl() !== null && genome.getUrl() !== undefined) {

frontend-js/src/test/js/helper.js

@@ -220,6 +220,11 @@ Helper.prototype.createAlias = function (map) {
   return result;
 };
 
+/**
+ *
+ * @param {Alias} [alias]
+ * @returns {LayoutAlias}
+ */
 Helper.prototype.createLayoutAlias = function (alias) {
   var id;
   var modelId;
@@ -237,7 +242,7 @@ Helper.prototype.createLayoutAlias = function (alias) {
       a: 23
     },
     modelId: modelId,
-    geneVariations: [{}]
+    geneVariations: []
   });
 };
 

frontend-js/src/test/js/map/window/AliasInfoWindow-test.js

@@ -7,6 +7,7 @@ var Promise = require("bluebird");
 var functions = require('../../../../main/js/Functions');
 
 var Alias = require('../../../../main/js/map/data/Alias');
+var LayoutAlias = require('../../../../main/js/map/data/LayoutAlias');
 var Drug = require('../../../../main/js/map/data/Drug');
 var GeneVariant = require('../../../../main/js/map/data/GeneVariant');
 var AliasInfoWindow = require('../../../../main/js/map/window/AliasInfoWindow');
@@ -220,107 +221,144 @@ describe('AliasInfoWindow', function () {
     });
   });
 
-  xit("createGeneticsDiv", function () {
-    var map;
-    var overlay;
-
-    var layoutAlias;
-    var win;
-
-    return ServerConnector.getProject().then(function (project) {
-      map = helper.createCustomMap(project);
-      overlay = new DataOverlay(18077, "xxx");
-      return overlay.init();
-    }).then(function () {
-      return overlay.getFullAliasById(overlay.getAliases()[0].getId());
-    }).then(function (data) {
-      layoutAlias = data;
-      return map.getModel().getAliasById(layoutAlias.getId());
-    }).then(function (alias) {
-      win = new AliasInfoWindow({
-        alias: alias,
-        map: map,
-        marker: helper.createMarker({element: alias, map: map})
+  describe("createGeneticsDiv", function () {
+    it("on top map", function () {
+      var map;
+      var overlay;
+
+      var layoutAlias;
+      var win;
+
+      return ServerConnector.getProject().then(function (project) {
+        map = helper.createCustomMap(project);
+        overlay = new DataOverlay(18077, "xxx");
+        return overlay.init();
+      }).then(function () {
+        return overlay.getFullAliasById(overlay.getAliases()[0].getId());
+      }).then(function (data) {
+        layoutAlias = data;
+        return map.getModel().getAliasById(layoutAlias.getId());
+      }).then(function (alias) {
+        win = new AliasInfoWindow({
+          alias: alias,
+          map: map,
+          marker: helper.createMarker({element: alias, map: map})
+        });
+        return win.init();
+      }).then(function () {
+        win.layoutAliases = [layoutAlias];
+        win.layoutNames = ["xxx"];
+        return win.createGenomicDiv();
+      }).then(function (div) {
+        assert.ok(div);
+        assert.ok(div.innerHTML.indexOf("No reference genome data available on minerva platform") === -1);
+        win.destroy();
       });
-      return win.init();
-    }).then(function () {
-      win.layoutAliases = [layoutAlias];
-      win.layoutNames = ["xxx"];
-      return win.createGenomicDiv();
-    }).then(function (div) {
-      assert.ok(div);
-      assert.ok(div.innerHTML.indexOf("No reference genome data available on minerva platform") === -1);
-      win.destroy();
-    });
-
-  });
-
-  it("createGeneticsDiv with no genetic data", function () {
-    var map;
 
-    var win;
-    var aliasId = 329173;
+    });
 
-    return ServerConnector.getProject().then(function (project) {
-      map = helper.createCustomMap(project);
-      var overlay = new DataOverlay(18077, "xxx");
-      return overlay.init();
-    }).then(function () {
-      return map.getModel().getAliasById(aliasId);
-    }).then(function (alias) {
-      win = new AliasInfoWindow({
-        alias: alias,
-        map: map,
-        marker: helper.createMarker({element: alias, map: map})
+    it("on submap map", function () {
+      helper.setUrl("http://test/?id=complex_model_with_submaps");
+
+      var map, submap, overlay, win, alias;
+
+      return ServerConnector.getProject().then(function (project) {
+        map = helper.createCustomMap(project);
+        submap = map.getSubmapById(16731);
+        overlay = new DataOverlay(18077, "xxx");
+        overlay.setInitialized(true);
+        return map.openSubmap(submap.getId());
+      }).then(function () {
+        return submap.getModel().getAliasById(345337);
+      }).then(function (data) {
+        alias = data;
+        win = new AliasInfoWindow({
+          alias: alias,
+          map: submap,
+          marker: helper.createMarker({element: alias, map: submap})
+        });
+        return win.init();
+      }).then(function () {
+        var layoutAlias = helper.createLayoutAlias(alias);
+        layoutAlias.setType(LayoutAlias.GENETIC_VARIANT);
+        win.layoutAliases = [layoutAlias];
+        win.layoutNames = ["xxx"];
+        return win.createGenomicDiv();
+      }).then(function (div) {
+        assert.ok(div);
+        win.destroy();
+        return map.destroy();
       });
-      return win.init();
-    }).then(function () {
-      win.layoutAliases = [undefined];
-      return win.createGenomicDiv();
-    }).then(function (div) {
-      assert.ok(div);
-      assert.ok(div.innerHTML.indexOf("No reference genome data available on minerva platform") === -1);
-      win.destroy();
-    });
 
-  });
+    });
 
-  it("createGeneticsDivForUnknownOrganism", function () {
-    var map;
-    var overlay;
+    it("with no genetic data", function () {
+      var map;
+
+      var win;
+      var aliasId = 329173;
+
+      return ServerConnector.getProject().then(function (project) {
+        map = helper.createCustomMap(project);
+        var overlay = new DataOverlay(18077, "xxx");
+        return overlay.init();
+      }).then(function () {
+        return map.getModel().getAliasById(aliasId);
+      }).then(function (alias) {
+        win = new AliasInfoWindow({
+          alias: alias,
+          map: map,
+          marker: helper.createMarker({element: alias, map: map})
+        });
+        return win.init();
+      }).then(function () {
+        win.layoutAliases = [undefined];
+        return win.createGenomicDiv();
+      }).then(function (div) {
+        assert.ok(div);
+        assert.ok(div.innerHTML.indexOf("No reference genome data available on minerva platform") === -1);
+        win.destroy();
+      });
 
-    var layoutAlias;
-    var win;
+    });
 
-    return ServerConnector.getProject().then(function (project) {
-      project.setOrganism({
-        type: "TAXONOMY",
-        resource: "123456"
+    it("for unknown organism", function () {
+      var map;
+      var overlay;
+
+      var layoutAlias;
+      var win;
+
+      return ServerConnector.getProject().then(function (project) {
+        project.setOrganism({
+          type: "TAXONOMY",
+          resource: "123456"
+        });
+        map = helper.createCustomMap(project);
+        overlay = new DataOverlay(18077, "xxx");
+        return overlay.init();
+      }).then(function () {
+        return overlay.getFullAliasById(overlay.getAliases()[0].getId());
+      }).then(function (data) {
+        layoutAlias = data;
+        return map.getModel().getAliasById(layoutAlias.getId());
+      }).then(function (alias) {
+        win = new AliasInfoWindow({
+          alias: alias,
+          map: map,
+          marker: helper.createMarker({element: alias, map: map})
+        });
+        return win.init();
+      }).then(function () {
+        win.layoutAliases = [layoutAlias];
+        return win.createGenomicDiv();
+      }).then(function (div) {
+        assert.ok(div);
+        assert.ok(div.innerHTML.indexOf("No reference genome data available on minerva platform") >= -1);
+        win.destroy();
       });
-      map = helper.createCustomMap(project);
-      overlay = new DataOverlay(18077, "xxx");
-      return overlay.init();
-    }).then(function () {
-      return overlay.getFullAliasById(overlay.getAliases()[0].getId());
-    }).then(function (data) {
-      layoutAlias = data;
-      return map.getModel().getAliasById(layoutAlias.getId());
-    }).then(function (alias) {
-      win = new AliasInfoWindow({
-        alias: alias,
-        map: map,
-        marker: helper.createMarker({element: alias, map: map})
-      });
-      return win.init();
-    }).then(function () {
-      win.layoutAliases = [layoutAlias];
-      return win.createGenomicDiv();
-    }).then(function (div) {
-      assert.ok(div);
-      assert.ok(div.innerHTML.indexOf("No reference genome data available on minerva platform") >= -1);
-      win.destroy();
-    });
 
+    });
   });
 
   it("createWaitingContentDiv", function () {
@@ -392,7 +430,7 @@ describe('AliasInfoWindow', function () {
       referenceGenomeVersion: "hg19"
     });
     var str = aliasWindow.createVcfString([variant, variant2]);
-    assert.ok(str.indexOf("null") === -1,"null shouldn't appear in vcf format");
+    assert.ok(str.indexOf("null") === -1, "null shouldn't appear in vcf format");
   });
 
 });

frontend-js/testFiles/apiCalls/genomics/taxonomies/1570291/genomeTypes/UCSC/versions/eboVir3/token=MOCK_TOKEN_ID&

+{"downloadProgress":100.0,"geneMapping":[],"idObject":1830,"localUrl":"../minerva-big//9395/eboVir3.2bit","organism":{"annotatorClassName":"","descriptionByType":"","descriptionByTypeRelation":"","id":1150730,"link":"http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=1570291","resource":"1570291","type":"TAXONOMY"},"sourceUrl":"ftp://hgdownload.cse.ucsc.edu/goldenPath/eboVir3/bigZips/eboVir3.2bit","type":"UCSC","version":"eboVir3"}
\ No newline at end of file

frontend-js/testFiles/apiCalls/projects/sample/token=ADMIN_TOKEN_ID&

-{"version":"0","disease":{"annotatorClassName":"","descriptionByType":"","descriptionByTypeRelation":"","id":1104479,"link":"http://bioportal.bioontology.org/ontologies/1351?p=terms&conceptid=D010300","resource":"D010300","type":"MESH_2012"},"organism":{"annotatorClassName":"","descriptionByType":"","descriptionByTypeRelation":"","id":1104480,"link":"http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=9606","resource":"9606","type":"TAXONOMY"},"idObject":14898,"status":"Ok","directory":"5e8ff9bf55ba3508199d22e984129be6","progress":100.0,"notifyEmail":"","warnings":true,"errors":false,"name":"UNKNOWN DISEASE MAP","projectId":"sample","mapCanvasType":"OPEN_LAYERS","overviewImageViews":[],"topOverviewImage":null}
\ No newline at end of file
+{"version":"0","disease":{"annotatorClassName":"","descriptionByType":"","descriptionByTypeRelation":"","id":1104479,"link":"http://bioportal.bioontology.org/ontologies/1351?p=terms&conceptid=D010300","resource":"D010300","type":"MESH_2012"},"organism":{"annotatorClassName":"","descriptionByType":"","descriptionByTypeRelation":"","id":1104480,"link":"http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=1570291","resource":"1570291","type":"TAXONOMY"},"idObject":14898,"status":"Ok","directory":"5e8ff9bf55ba3508199d22e984129be6","progress":100.0,"notifyEmail":"","warnings":true,"errors":false,"name":"UNKNOWN DISEASE MAP","projectId":"sample","mapCanvasType":"OPEN_LAYERS","overviewImageViews":[],"topOverviewImage":null}
\ No newline at end of file

frontend-js/testFiles/apiCalls/projects/sample/token=MOCK_TOKEN_ID&

-{"version":"0","disease":{"annotatorClassName":"","descriptionByType":"","descriptionByTypeRelation":"","id":1104479,"link":"http://bioportal.bioontology.org/ontologies/1351?p=terms&conceptid=D010300","resource":"D010300","type":"MESH_2012"},"organism":{"annotatorClassName":"","descriptionByType":"","descriptionByTypeRelation":"","id":1104480,"link":"http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=9606","resource":"9606","type":"TAXONOMY"},"idObject":14898,"status":"Ok","directory":"5e8ff9bf55ba3508199d22e984129be6","progress":100.0,"notifyEmail":"","warnings":true,"errors":false,"name":"UNKNOWN DISEASE MAP","projectId":"sample","mapCanvasType":"OPEN_LAYERS","overviewImageViews":[],"topOverviewImage":null}
\ No newline at end of file
+{"version":"0","disease":{"annotatorClassName":"","descriptionByType":"","descriptionByTypeRelation":"","id":1104479,"link":"http://bioportal.bioontology.org/ontologies/1351?p=terms&conceptid=D010300","resource":"D010300","type":"MESH_2012"},"organism":{"annotatorClassName":"","descriptionByType":"","descriptionByTypeRelation":"","id":1104480,"link":"http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=1570291","resource":"1570291","type":"TAXONOMY"},"idObject":14898,"status":"Ok","directory":"5e8ff9bf55ba3508199d22e984129be6","progress":100.0,"notifyEmail":"","warnings":true,"errors":false,"name":"UNKNOWN DISEASE MAP","projectId":"sample","mapCanvasType":"OPEN_LAYERS","overviewImageViews":[],"topOverviewImage":null}
\ No newline at end of file