current implementation

.gitignore

@@ -20,6 +20,7 @@ dist
 .sass-cache
 app/components
 app/data
+db/sh
 python
 app/bower_components
 npm-debug.log

app/configurations/atlas.json

@@ -1,6 +1,7 @@
 {
     "default_genelist": ["BRCA1", "RAD51", "TP53", "KRAS", "CC2D1A"],
     "all_tags_url": "svc/datastores/FFN/LOOKUPS/all_tags",
+    "all_clinical_url": "svc/datastores/FFN/LOOKUPS/all_clinical",
     "maps": [
         {
             "id": "mutations_combo",
@@ -23,14 +24,6 @@
                             "url_suffix": "/mutation_summary"
                         },
                         "mutsig": "datamodel/mutations/mutsig_rankings",
-                        "features": {
-                            "uri": "datamodel/tcga_datawarehouse",
-                            "url_suffix": "/feature_matrix",
-                            "base_query": {
-                                "source": "GNAB",
-                                "label": "y_n_somatic"
-                            }
-                        },
                         "mutated_samples": {
                             "uri": "datamodel/tcga_datawarehouse",
                             "url_suffix": "/mutated_samples"
@@ -75,6 +68,9 @@
                             "url_suffix": "/feature_matrix",
                             "query_clinical_variables": true
                         }
+                    },
+                    "feature_sources_order": {
+                        "GEXP": 1
                     }
                 }
             ]
@@ -91,7 +87,10 @@
                     "view": "views/stacksvis/view",
                     "label": "Distributions",
                     "datamodels": {
-                        "copy_number": "datamodel/copy_number/copy_number_gistic2",
+                        "copy_number": {
+                            "uri": "datamodel/tcga_datawarehouse",
+                            "url_suffix": "/copy_number_gistic"
+                        },
                         "q_value": "datamodel/copy_number/copy_number_qvalue",
                         "mutated_samples": {
                             "uri": "datamodel/tcga_datawarehouse",

app/configurations/datamodel.json

@@ -141,19 +141,14 @@
                 "STAD-20140123": {
                     "tumor_type": "STAD",
                     "service": "datastores/dev_ffn_20140520/STAD",
-                    "description": "This dataset was prepared from TCGA feature matrices aggregated at ISB",
+                    "description": "This dataset was prepared from TCGA feature matrices aggregated at ISB.<br/><br/>STAD gene expression levels were available from RNAseq data as RPKM only, whereas levels for other tumor types were available in terms of RSEM (June 2014).  To approximate RSEM values, STAD values were linearly transformed using the equation 4.550681+ STAD *1.271340. The coefficient were obtained from regressing median gene expression levels for COAD against those for STAD. COAD was selected over other tumor types due to anatomical proximity and the relative concordance of the distributions of the COAD and STAD medians.",
                     "label": "STAD dataset for January 2014"
                 }
             }
         },
         "copy_number": {
             "label": "Copy Number Datasets",
             "catalog": {
-                "copy_number_gistic2": {
-                    "label": "Copy Number Gistic (13sep)",
-                    "service": "datastores/copy_number/qed_lookups/copyNumber_Gistic2_13sep",
-                    "model": "models/gs/by_tumor_type"
-                },
                 "copy_number_qvalue": {
                     "label": "Copy Number Q-Values",
                     "service": "datastores/copy_number/qed_lookups/copy_number_qvalue"

app/configurations/lookups.json

@@ -8,9 +8,6 @@
                 "NA": "Other"
             }
         },
-        "clinical_variables": {
-            "url": "svc/datastores/FFN/LOOKUPS/clinical_variables"
-        },
         "chromosomes": {
             "url": "svc/data/lookups/chromosomes",
             "model": "models/annotations"

app/index.html

@@ -65,7 +65,10 @@ <h5>Browser Display Dimensions</h5>
                 var increment = function () {
                     progress += 10;
                     try {
-                        document.getElementById("progressbar").style.width = progress + "%";
+                        var progressbarEl = document.getElementById("progressbar");
+                        if (!progressbarEl) return;
+
+                        progressbarEl.style.width = progress + "%";
                         if (progress < 100) setTimeout(increment, 300);
                     } catch (e) {
                         console.error(e);

app/scripts/models/gs/by_tumor_type.js

@@ -1,43 +1,32 @@
 define(["jquery", "underscore", "backbone"],
     function ($, _, Backbone) {
         return Backbone.Model.extend({
-
-            initialize: function (options) {
-                _.extend(this, options);
+            initialize: function(attributes, options) {
+                this.set(this.parse(attributes));
             },
 
             parse: function (data) {
-                this.set("items", data.items);
+                var items = data["items"];
+                this.set("items", items);
 
-                if (_.isEmpty(data.items)) {
-                    return { "ROWS": [], "COLUMNS": [], "DATA": [] };
-                }
+                if (_.isEmpty(items)) return { "ROWS": [], "COLUMNS": [], "DATA": [] };
 
-                var itemsByTumorType = _.groupBy(data.items, "cancer");
-                var dataByTumorType = {};
-                _.each(itemsByTumorType, function (items, tumor_type) {
-                    if (_.isEmpty(data.items)) {
-                        dataByTumorType[tumor_type] = { "ROWS": [], "COLUMNS": [], "DATA": [] };
-                    } else {
-                        var ROWS = _.pluck(items, "gene");
-                        var COLUMNS = _.pluck(items[0].values, "id");
-                        var coldict = {};
-                        _.each(COLUMNS, function (col, idx) {
-                            coldict[col] = idx;
-                        });
+                var ROWS = _.pluck(items, "gene");
+                var COLUMNS = _.keys(_.first(items)["values"]);
+                var coldict = {};
+                _.each(COLUMNS, function (col, idx) {
+                    coldict[col] = idx;
+                });
 
-                        var DATA = _.map(items, function (data_item) {
-                            var row_array = [];
-                            _.each(data_item.values, function (value_obj) {
-                                row_array[coldict[value_obj.id]] = value_obj.v;
-                            });
-                            return row_array;
-                        });
-                        dataByTumorType[tumor_type] = { "ROWS": ROWS, "COLUMNS": COLUMNS, "DATA": DATA };
-                    }
+                var DATA = _.map(items, function (data_item) {
+                    var row_array = [];
+                    _.each(data_item["values"], function (value, id) {
+                        row_array[coldict[id]] = value;
+                    });
+                    return row_array;
                 });
 
-                return { "BY_TUMOR_TYPE": dataByTumorType };
+                return { "ROWS": ROWS, "COLUMNS": COLUMNS, "DATA": DATA  };
             }
         });
     });

app/scripts/models/gs/item_set.js

@@ -0,0 +1,82 @@
+define([
+    "jquery",
+    "underscore",
+    "backbone"
+],
+function ($, _, Backbone
+) {
+    var URL = "svc/collections/samplelists";
+
+    return Backbone.Collection.extend({
+        "url": URL,
+
+        "model": Backbone.Model.extend({
+            idAttribute: "_id"
+        }),
+
+        initialize: function() {
+            this.on("add", this.__add_handler, this);
+            this.on("remove", this.__remove_handler, this);
+            this.on("change", this.__change_handler, this);
+        },
+
+        __add_handler: function() {
+
+        },
+
+        __remove_handler: function(model, collection, index) {
+            Backbone.sync("delete", new Backbone.Model({}), {
+                "url": URL + "/" + model["id"], "success": this.__refresh
+            });
+        },
+
+        __change_handler: function() {
+
+        },
+
+        __createModelForSync: function(model) {
+            var data = _.omit(model.toJSON(), "uri", "id", "_id");
+            return new Backbone.Model(data);
+        },
+
+        updateSampleList: function(model_id, sample_list) {
+            var model = this.get(model_id);
+            var successFn = _.bind(function() {
+                model.trigger("change");
+            }, this);
+
+            model.set({
+                samples: sample_list
+            });
+
+            this.sync("update", this.__createModelForSync(model), {
+                url: URL + "/" + model["id"],
+                success: successFn,
+                context: this
+            });
+        },
+
+        updateSampleListByUnion: function(model_id, sample_list) {
+            var sample_id_set = this.get(model_id).get("samples");
+            Array.prototype.push.apply(sample_id_set, sample_list);
+            this.updateSampleList(model_id, _.unique(sample_id_set));
+        },
+
+        addSampleList: function(label, sample_id_array) {
+            var sample_list_model = new this.model({
+                "label": label,
+                "samples": sample_id_array
+            });
+
+            var successFn = _.bind(function(response, status) {
+                this.add(_.extend(sample_list_model, {"id": response["id"]}));
+            }, this);
+
+            this.sync("create", sample_list_model, {
+                url: URL,
+                success: successFn,
+                context: this
+            });
+        }
+    });
+});

app/scripts/templates/datamodel_collector/container.hbs

@@ -21,7 +21,7 @@
                                             <a class="btn btn-mini" href="{{url}}" target="_blank">Web Service API</a>
                                         </div>
                                         <h6>{{label}}</h6>
-                                        <small>{{description}}</small>
+                                        <small>{{{description}}}</small>
                                         {{#if publications}}
                                             <h6>Related Publications</h6>
                                             <ul class="nav nav-list">
@@ -49,7 +49,7 @@
                                                 <a class="btn btn-mini" href="{{url}}" target="_blank">Web Service API</a>
                                             </div>
                                             <h6>{{label}}</h6>
-                                            <small>{{description}}</small>
+                                            <small>{{{description}}}</small>
                                             {{#if publications}}
                                                 <h6>Related Publications</h6>
                                                 <ul class="nav nav-list">

app/scripts/templates/fmx_distributions/container.hbs

@@ -68,7 +68,7 @@
                 <a href="#" onclick="return false;" class="dropdown-toggle" data-toggle="dropdown">
                     <i class="icon-tint"></i> Color By <b class="caret"></b>
                 </a>
-                <ul class="dropdown-menu color_by_selector" role="menu">
+                <ul class="dropdown-menu color_by_selector pre-scrollable" role="menu">
                     <li class="active"><a href="#" onclick="return false;" data-id="tumor_type">Tumor Type</a></li>
                     {{#if sample_types}}
                         <li><a href="#" onclick="return false;" data-id="sample_type">Sample Type</a></li>

app/scripts/templates/gs/atlas.hbs

@@ -31,6 +31,9 @@
     <li>
         <a href="#" onclick="return false;" data-toggle="collapse" data-target="#clinvarlist-collapser">Clinical and Sample Variables <i class="pull-right icon-chevron-right"></i></a>
     </li>
+    <li>
+        <a href="#" onclick="return false;" data-toggle="collapse" data-target="#samplelist-collapser">Sample Lists <i class="pull-right icon-chevron-right"></i></a>
+    </li>
     <li class="divider"/>
     <!--<li>-->
         <!--<a href="#" onclick="return false;" data-toggle="collapse" data-target="#collected-maps-collapser">Collected Maps <i class="pull-right icon-chevron-right"></i></a>-->
@@ -60,6 +63,9 @@
     <div id="clinvarlist-collapser" class="list-container collapse">
         <div class="clinvarlist-container"></div>
     </div>
+    <div id="samplelist-collapser" class="list-container collapse">
+        <div class="samplelist-container"></div>
+    </div>
     <!--<div id="collected-maps-collapser" class="list-container collapse">-->
         <!--<div class="collected-maps-container"></div>-->
     <!--</div>-->

app/scripts/templates/gs/maps_list_container.hbs

@@ -3,14 +3,14 @@
     {{#unless disabled}}
         <div class="alert {{#if isPrimary}}alert-success{{/if}}{{#unless isPrimary}}alert-info{{/unless}}">
             <h5>{{label}}</h5>
-            <p>{{description}}</p>
+            <p>{{{description}}}</p>
             <p><button type="button" data-id="{{id}}" class="btn btn-info btn-small open-map">{{#if buttonLabel}}{{buttonLabel}}{{/if}}{{#unless buttonLabel}}open{{/unless}}</button></p>
         </div>
     {{/unless}}
     {{#if disabled}}
         <div class="alert alert-danger">
             <h5>{{label}}</h5>
-            <p>{{description}}</p>
+            <p>{{{description}}}</p>
             <p>This map is not currently available</p>
             <p><button type="button" class="btn btn-small btn-danger disabled" title="not available">{{#if buttonLabel}}{{buttonLabel}}{{/if}}{{#unless buttonLabel}}disabled{{/unless}}</button></p>
         </div>

app/scripts/templates/samplelist/container.hbs

@@ -0,0 +1,38 @@
+<h4>Sample Lists</h4>
+<div class="input-append">
+    <input type="text" class="new-list-name" placeholder="New list name...">
+    <button class="btn add-new-list" type="button" title="Add a list"><i class="icon-plus"></i></button>
+</div>
+{{#if samplelists.length}}
+    <div class="row">
+        <div class="span7">
+            <div class="tabs-left">
+                <ul class="nav nav-tabs sample-lists">
+                    {{#each samplelists}}
+                        <li{{#unless @index}} class="active"{{/unless}} data-id="{{id}}"><a
+                                href="#tab-slists-slist-{{id}}" data-toggle="tab">{{label}}</a></li>
+                    {{/each}}
+                </ul>
+            </div>
+
+            <div class="tab-content">
+                {{#each samplelists}}
+                    <div class="tab-pane{{#unless @index}} active{{/unless}}" id="tab-slists-slist-{{id}}">
+                        <h5>{{number_samples}} Samples</h5>
+                        <textarea rows="10" id="samplelist-contents-{{id}}">{{text}}</textarea>
+                        <div>
+                            <button class="btn btn-small list-update" data-id="{{id}}" type="button">Update list contents</button>
+                        </div>
+                        <hr/>
+                        <div class="btn-group">
+                            <button class="btn btn-small list-remover" data-id="{{id}}" type="button"><i class="icon-trash"></i></button>
+                            <button class="btn btn-small list-remover" data-id="{{id}}" type="button">Delete list '{{label}}'</button>
+                        </div>
+                    </div>
+                {{/each}}
+            </div>
+        </div>
+    </div>
+{{else}}
+    <h5 style="color: red;">No sample lists stored</h5>
+{{/if}}

app/scripts/templates/seqpeek/mutations_map.hbs

@@ -27,9 +27,32 @@
             {{/each}}
         </ul>
     </li>
-    <button class="btn btn-default seqpeek-zoom-enable">Zoom</button>
-    <button class="btn btn-default seqpeek-selection-enable">Select</button>
-    <button class="btn btn-default seqpeek-print-ids">Print selection</button>
-    <button class="btn btn-default seqpeek-toggle-bars">Bars / Lollipops</button>
+    <li class="dropdown sample-list-dialog">
+        <a href="#" onclick="return false;" class="sample-list-dropdown">
+            <!-- sample_list_dropdown_caption.hbs -->
+        </a>
+
+        <div class="dropdown-menu span5">
+            <div class="input-append">
+                <input type="text" class="new-list-name" placeholder="New list name...">
+                <button class="btn add-new-list" type="button" title="Add a list"><i class="icon-plus"></i></button>
+            </div>
+            <div class="sample-list-operations">
+
+            </div>
+        </div>
+   </li>
+    <li>
+        <button class="btn btn-default seqpeek-zoom-enable">Zoom</button>
+    </li>
+    <li>
+        <button class="btn btn-default seqpeek-selection-enable">Select</button>
+    </li>
+    <li>
+        <button class="btn btn-default seqpeek-toggle-bars">Bars / Lollipops</button>
+    </li>
+    <li>
+        <button class="btn btn-default seqpeek-toggle-genomic">Protein / Genomic</button>
+    </li>
 </ul>
 <div class="mutations_map_table"></div>

app/scripts/templates/seqpeek/mutations_map_table.hbs

@@ -4,7 +4,7 @@
         <th>Tumor Type</th>
         <th>MutSig Rank</th>
         <th>Samples (#)</th>
-        <th></th>
+        <th style="text-align: center;"><canvas class="seqpeek-mini-locator" width="400" height="24"></canvas></th>
     </tr>
     </thead>
     <tbody>
@@ -17,7 +17,7 @@
         </tr>
     {{/each}}
     <tr>
-        <td style="color: blue;">ALL</td>
+        <td style="color: blue;">COMBINED</td>
         <td></td>
         <td>{{total.samples}}</td>
         <td id="seqpeek-all-row"></td>