From 7fbd0e0cd0d17bd2e4058d34f464a1b2664b0f04 Mon Sep 17 00:00:00 2001
From: Andrew Duncan <andrew.duncan@oicr.on.ca>
Date: Thu, 28 Nov 2019 11:03:25 -0500
Subject: [PATCH 01/28] CNV requests now properly use size and offset

---
 gdc-viewer/js/Store/SeqFeature/CNVs.js | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/gdc-viewer/js/Store/SeqFeature/CNVs.js b/gdc-viewer/js/Store/SeqFeature/CNVs.js
index 6b3972a..9f5d074 100644
--- a/gdc-viewer/js/Store/SeqFeature/CNVs.js
+++ b/gdc-viewer/js/Store/SeqFeature/CNVs.js
@@ -43,7 +43,7 @@ function(
          */
         createQuery: function(ref, start, end) {
             var thisB = this;
-            var cnvQuery = `query cnvResults($filters: FiltersArgument) { explore { cnvs { hits(filters: $filters) { total edges { node { id cnv_id start_position end_position chromosome ncbi_build cnv_change } } } } } } `;
+            var cnvQuery = `query cnvResults($filters: FiltersArgument $size: Int $offset: Int) { explore { cnvs { hits(first: $size, offset: $offset, filters: $filters) { total edges { node { id cnv_id start_position end_position chromosome ncbi_build cnv_change } } } } } } `;
             var combinedFilters = thisB.getFilterQuery(ref, start, end);
 
             var bodyVal = {

From d4c16adf26ba375b797ed84eb405effd6c5e60d1 Mon Sep 17 00:00:00 2001
From: Andrew Duncan <andrew.duncan@oicr.on.ca>
Date: Thu, 28 Nov 2019 11:03:36 -0500
Subject: [PATCH 02/28] sorting of facets now ignores case

---
 gdc-viewer/js/View/GDCDialog.js | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gdc-viewer/js/View/GDCDialog.js b/gdc-viewer/js/View/GDCDialog.js
index 1e9a936..f633c80 100644
--- a/gdc-viewer/js/View/GDCDialog.js
+++ b/gdc-viewer/js/View/GDCDialog.js
@@ -386,9 +386,9 @@ function (
          * @return {number}
          */
         compareTermElements: function(a, b) {
-            if (a.key < b.key)
+            if (a.key.toLowerCase() < b.key.toLowerCase())
                 return -1;
-            if (a.key > b.key)
+            if (a.key.toLowerCase() > b.key.toLowerCase())
                 return 1;
             return 0;
         },

From a5ea574c8079e7c6954e0ede30105704a21c5ffc Mon Sep 17 00:00:00 2001
From: Andrew Duncan <andrew.duncan@oicr.on.ca>
Date: Tue, 3 Dec 2019 13:12:15 -0500
Subject: [PATCH 03/28] bump up max size for tracks

---
 gdc-viewer/js/View/Track/CommonTrack.js | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/gdc-viewer/js/View/Track/CommonTrack.js b/gdc-viewer/js/View/Track/CommonTrack.js
index 1ecba25..e25ce34 100644
--- a/gdc-viewer/js/View/Track/CommonTrack.js
+++ b/gdc-viewer/js/View/Track/CommonTrack.js
@@ -100,7 +100,7 @@ define(
             value: track.store.size,
             style: "width: 80%",
             id: "sizeTextBox",
-            constraints: { min: 1, max: 1000, places: 0 },
+            constraints: { min: 1, max: 2000, places: 0 },
             smallDelta: 10
         }).placeAt(details);
 

From 179cd5e3064d89366bf4a227378a28725dbb155c Mon Sep 17 00:00:00 2001
From: Andrew Duncan <andrew.duncan@oicr.on.ca>
Date: Tue, 7 Jan 2020 11:11:36 -0500
Subject: [PATCH 04/28] update to readme

---
 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index e687f6e..b4398b0 100644
--- a/README.md
+++ b/README.md
@@ -4,7 +4,7 @@ A plugin for [JBrowse](https://jbrowse.org/) for viewing [GDC](https://gdc.cance
 
 # Installation and Setup
 ## 1. Install JBrowse
-Quick setup of JBrowse - https://github.com/GMOD/jbrowse/#install-jbrowse-from-github-for-developers
+Follow JBrowse readme for [quick setup.](https://github.com/GMOD/jbrowse/#install-jbrowse-from-github-for-developers)
 
 ## 2. Install Plugin
 See [JBrowse - Installing Plugins](https://jbrowse.org/docs/plugins.html) for a general approach to installing plugins.

From a3afac64a3b83e76eb96e152643c4b1500d47090 Mon Sep 17 00:00:00 2001
From: Andrew Duncan <andrew.duncan@oicr.on.ca>
Date: Tue, 7 Jan 2020 11:12:15 -0500
Subject: [PATCH 05/28] fix csv export for all data types

---
 gdc-viewer/js/Store/SeqFeature/Genes.js       |  4 ++-
 .../SeqFeature/SimpleSomaticMutations.js      |  3 +-
 gdc-viewer/js/View/Export/CSV.js              | 33 +++++++++++--------
 3 files changed, 24 insertions(+), 16 deletions(-)

diff --git a/gdc-viewer/js/Store/SeqFeature/Genes.js b/gdc-viewer/js/Store/SeqFeature/Genes.js
index 146ca01..6a5bec6 100644
--- a/gdc-viewer/js/Store/SeqFeature/Genes.js
+++ b/gdc-viewer/js/Store/SeqFeature/Genes.js
@@ -75,12 +75,14 @@ function(
                     'strand': thisB.prettyText(gene.gene_strand),
                     'type': 'Gene',
                     'gene description': thisB.prettyText(gene.description),
+                    'chromosome': gene.gene_chromosome,
                     'about': {
                         'biotype': thisB.prettyText(gene.biotype),
                         'gene name': thisB.prettyText(gene.name),
                         'id': thisB.prettyText(gene.gene_id),
                         'symbol': thisB.prettyText(gene.symbol),
-                        'synonyms': thisB.prettyText(gene.synonyms)
+                        'synonyms': thisB.prettyText(gene.synonyms),
+                        'strand': thisB.prettyText(gene.gene_strand)
                     },
                     'references': {
                         'ncbi gene': thisB.createLinkWithId(NCBI_LINK, gene.external_db_ids.entrez_gene),
diff --git a/gdc-viewer/js/Store/SeqFeature/SimpleSomaticMutations.js b/gdc-viewer/js/Store/SeqFeature/SimpleSomaticMutations.js
index 7625801..d4fa997 100644
--- a/gdc-viewer/js/Store/SeqFeature/SimpleSomaticMutations.js
+++ b/gdc-viewer/js/Store/SeqFeature/SimpleSomaticMutations.js
@@ -147,6 +147,7 @@ function(
                     'end': thisB.prettyText(mutation.end_position),
                     'type': 'Simple Somatic Mutation',
                     'projects': mutation.ssm_id,
+                    'chromosome': mutation.chromosome,
                     'about': {
                         'subtype': thisB.prettyText(mutation.mutation_subtype),
                         'dna change': thisB.prettyText(mutation.genomic_dna_change),
@@ -171,7 +172,7 @@ function(
          */
         createQuery: function(ref, start, end) {
             var thisB = this;
-            var ssmQuery = `query ssmResultsTableQuery( $ssmsTable_size: Int $ssmsTable_offset: Int $ssmsTable_filters: FiltersArgument $score: String $sort: [Sort] ) { viewer { explore { ssms { hits(first: $ssmsTable_size, offset: $ssmsTable_offset, filters: $ssmsTable_filters, score: $score, sort: $sort) { total edges { node { id start_position end_position mutation_type cosmic_id reference_allele ncbi_build score genomic_dna_change mutation_subtype ssm_id consequence { hits { edges { node { transcript { is_canonical annotation { vep_impact polyphen_impact polyphen_score sift_score sift_impact hgvsc } consequence_type gene { gene_id symbol gene_strand } aa_change transcript_id } id } } } } } } } } } } }`;
+            var ssmQuery = `query ssmResultsTableQuery( $ssmsTable_size: Int $ssmsTable_offset: Int $ssmsTable_filters: FiltersArgument $score: String $sort: [Sort] ) { viewer { explore { ssms { hits(first: $ssmsTable_size, offset: $ssmsTable_offset, filters: $ssmsTable_filters, score: $score, sort: $sort) { total edges { node { id start_position end_position mutation_type cosmic_id reference_allele ncbi_build score genomic_dna_change mutation_subtype ssm_id chromosome consequence { hits { edges { node { transcript { is_canonical annotation { vep_impact polyphen_impact polyphen_score sift_score sift_impact hgvsc } consequence_type gene { gene_id symbol gene_strand } aa_change transcript_id } id } } } } } } } } } } }`;
             var combinedFilters = thisB.getFilterQuery(ref, start, end);
 
             var bodyVal = {
diff --git a/gdc-viewer/js/View/Export/CSV.js b/gdc-viewer/js/View/Export/CSV.js
index 33ae771..52ba1f4 100644
--- a/gdc-viewer/js/View/Export/CSV.js
+++ b/gdc-viewer/js/View/Export/CSV.js
@@ -18,12 +18,12 @@ return declare( ExportBase,
         'type',
         'start',
         'end',
-        'strand',
-        'id'
+        'chromosome'
    ],
 
    // The extended header for genes
    geneHeader: [
+        'strand',
         'gene name',
         'biotype',
         'symbol',
@@ -51,21 +51,24 @@ return declare( ExportBase,
      */
    _printHeader: function() {
         this.fullHeader = []
-        if (this.store.config.storeClass === 'gdc-viewer/Store/SeqFeature/Genes') {
-            this.fullHeader = this.geneHeader
-        } else if (this.store.config.storeClass === 'gdc-viewer/Store/SeqFeature/SimpleSomaticMutations') {
-            this.fullHeader = this.ssmHeader
-        } else if (this.store.config.storeClass === 'gdc-viewer/Store/SeqFeature/CNVs') {
-            this.fullHeader = this.cnvHeader
+        if (this.store.config.type === 'gdc-viewer/Store/SeqFeature/Genes' || this.store.config.storeClass === 'gdc-viewer/Store/SeqFeature/Genes') {
+            this.fullHeader = [...this.geneHeader];
+        } else if (this.store.config.type === 'gdc-viewer/Store/SeqFeature/SimpleSomaticMutations' || this.store.config.storeClass === 'gdc-viewer/Store/SeqFeature/SimpleSomaticMutations') {
+            this.fullHeader = [...this.ssmHeader];
+        } else if (this.store.config.type === 'gdc-viewer/Store/SeqFeature/CNVs' || this.store.config.storeClass === 'gdc-viewer/Store/SeqFeature/CNVs') {
+            this.fullHeader = [...this.cnvHeader];
         }
 
         var headerString
-        if (this.store.config.storeClass !== 'gdc-viewer/Store/SeqFeature/CNVs') {
-            headerString = (this.defaultHeader.concat(this.fullHeader)).join(',') + '\n'
+        if (this.store.config.storeClass !== 'gdc-viewer/Store/SeqFeature/CNVs' && this.store.config.type !== 'gdc-viewer/Store/SeqFeature/CNVs') {
+            headerString = (this.defaultHeader.concat(this.fullHeader)).join(',')
         } else {
-            headerString = this.cnvHeader.join(',') + '\n'
+            headerString = this.cnvHeader.join(',')
         }
-        this.print(headerString)
+        if (this.store.config.storeClass !== 'gdc-viewer/Store/SeqFeature/CNVs' && this.store.config.type !== 'gdc-viewer/Store/SeqFeature/CNVs') {
+            this.print('id,')
+        }
+        this.print(headerString + '\n')
    },
 
    /**
@@ -75,10 +78,12 @@ return declare( ExportBase,
    formatFeature: function( feature ) {
         var featureArray = []
 
+        var about = feature.get('about')
+
         // SSM and Gene features have the extra about section
-        if (this.store.config.storeClass !== 'gdc-viewer/Store/SeqFeature/CNVs') {
+        if (this.store.config.storeClass !== 'gdc-viewer/Store/SeqFeature/CNVs' && this.store.config.type !== 'gdc-viewer/Store/SeqFeature/CNVs') {
+            featureArray.push(about['id'])
             this.defaultHeader.forEach(field => featureArray.push(feature.get(field)))
-            var about = feature.get('about')
             this.fullHeader.forEach(field => {
                 if (field === 'synonyms') {
                     if (about[field]) {

From 0e93419277fd06626f2d4b2f8c1dd24c78e8c1a6 Mon Sep 17 00:00:00 2001
From: Andrew Duncan <andrew.duncan@oicr.on.ca>
Date: Tue, 7 Jan 2020 11:19:05 -0500
Subject: [PATCH 06/28] fix tests

---
 cypress/integration/ExportGeneTrack.js | 2 +-
 cypress/integration/ExportSSMTrack.js  | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/cypress/integration/ExportGeneTrack.js b/cypress/integration/ExportGeneTrack.js
index 363b291..8c67dbd 100644
--- a/cypress/integration/ExportGeneTrack.js
+++ b/cypress/integration/ExportGeneTrack.js
@@ -81,7 +81,7 @@ describe('Gene track', function() {
     it('Should be able to export Genes in various export formats', function() {
         testExport(2, 'GFF3', ['##gff-version 3', '##sequence-region', 'Gene'])
         testExport(3, 'BED', ['track name="GDC_Genes" useScore=0', '1	152302175	152325203	ENSG00000143631		-'])
-        testExport(4, 'CSV', ['type,start,end,strand,id,gene name,biotype,symbol,synonyms', 'Gene,152302175,152325203,-1,,filaggrin,protein_coding,FLG'])
+        testExport(4, 'CSV', ['id,type,start,end,chromosome,strand,gene name,biotype,symbol,synonyms', 'ENSG00000143631,Gene,152302175,152325203,1,-1,filaggrin,protein_coding,FLG'])
         testExport(5, 'Sequin Table', ['>Feature 1', '152325203	152302176	Gene'])
         cy.fixture('ExportGenes/track-conf-export.conf').then((json) => {
             testExport(6, 'Track Config', [json])
diff --git a/cypress/integration/ExportSSMTrack.js b/cypress/integration/ExportSSMTrack.js
index fdc63fc..5eb6dcf 100644
--- a/cypress/integration/ExportSSMTrack.js
+++ b/cypress/integration/ExportSSMTrack.js
@@ -81,7 +81,7 @@ describe('SSM track', function() {
     it('Should be able to export SSMs in various export formats', function() {
         testExport(2, 'GFF3', ['##gff-version 3', '##sequence-region', 'Simple Somatic Mutation'])
         testExport(3, 'BED', ['track name="GDC_SSM" useScore=0', '1	56496417	56496417	ec690998-d555-5ed3-ab18-55e8685b2bfd'])
-        testExport(4, 'CSV', ['type,start,end,strand,id,reference allele,dna change,subtype', 'Simple Somatic Mutation,56496417,56496417,,,T,chr1:g.56496417delT,Small deletion'])
+        testExport(4, 'CSV', ['id,type,start,end,chromosome,reference allele,dna change,subtype', 'ec690998-d555-5ed3-ab18-55e8685b2bfd,Simple Somatic Mutation,56496417,56496417,,T,chr1:g.56496417delT,Small deletion'])
         testExport(5, 'Sequin Table', ['>Feature 1', '56496418	56496417	Simple Somatic Mutation'])
         cy.fixture('ExportSSMs/track-conf-export.conf').then((json) => {
             testExport(6, 'Track Config', [json])

From dbbde86b5783b00e2010d120778f204a3a94d0da Mon Sep 17 00:00:00 2001
From: Andrew Duncan <andrew.duncan@oicr.on.ca>
Date: Tue, 7 Jan 2020 11:40:35 -0500
Subject: [PATCH 07/28] fix another test after API changed

---
 cypress/integration/ExploreGDC.js | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/cypress/integration/ExploreGDC.js b/cypress/integration/ExploreGDC.js
index 6f5c5ce..76d8b55 100644
--- a/cypress/integration/ExploreGDC.js
+++ b/cypress/integration/ExploreGDC.js
@@ -120,7 +120,7 @@ describe('Explore GDC', function() {
         })
 
         checkAllResultsTab(
-            ['Showing 1 to 20 of 1,492', 'TCGA-A5-A1OF', 'TCGA-AJ-A3EK'],
+            ['Showing 1 to 20 of 3,102', 'TCGA-A5-A1OF', 'TCGA-AJ-A3EK'],
             ['Showing 1 to 20 of 21,168', 'TP53', 'TTN'],
             ['Showing 1 to 20 of 120,824', 'chr2:g.208248388C>T', 'chr17:g.7673803G>A']
         )

From 62ebf86f52543f5774dc968fafe3a856fb7c003a Mon Sep 17 00:00:00 2001
From: Andrew Duncan <andrew.duncan@oicr.on.ca>
Date: Wed, 15 Jan 2020 15:17:53 -0500
Subject: [PATCH 08/28] sort facets by count

---
 gdc-viewer/js/View/GDCDialog.js | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/gdc-viewer/js/View/GDCDialog.js b/gdc-viewer/js/View/GDCDialog.js
index f633c80..4d41327 100644
--- a/gdc-viewer/js/View/GDCDialog.js
+++ b/gdc-viewer/js/View/GDCDialog.js
@@ -386,10 +386,10 @@ function (
          * @return {number}
          */
         compareTermElements: function(a, b) {
-            if (a.key.toLowerCase() < b.key.toLowerCase())
-                return -1;
-            if (a.key.toLowerCase() > b.key.toLowerCase())
+            if (a.count < b.count)
                 return 1;
+            if (a.count > b.count)
+                return -1;
             return 0;
         },
 

From c95d62d5ad2815a35e5d52f975b3ec42a2f263d6 Mon Sep 17 00:00:00 2001
From: Andrew Duncan <andrew.duncan@oicr.on.ca>
Date: Wed, 15 Jan 2020 15:19:10 -0500
Subject: [PATCH 09/28] fix test

---
 cypress/integration/ExploreGDC.js | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/cypress/integration/ExploreGDC.js b/cypress/integration/ExploreGDC.js
index 76d8b55..3794d61 100644
--- a/cypress/integration/ExploreGDC.js
+++ b/cypress/integration/ExploreGDC.js
@@ -116,7 +116,7 @@ describe('Explore GDC', function() {
         // Select ethnicity -> hispanic or latino
         cy.get('.dijitDialog').within(() => {
             cy.contains('Explore data available on the GDC Data Portal')
-            selectFacetTab(0, 0, 0)
+            selectFacetTab(0, 0, 2)
         })
 
         checkAllResultsTab(

From 97fabacdce8d06c3b3e521d8aba0c56cf10daeeb Mon Sep 17 00:00:00 2001
From: Andrew Duncan <andrew.duncan@oicr.on.ca>
Date: Wed, 15 Jan 2020 15:46:27 -0500
Subject: [PATCH 10/28] slight change to readme

---
 README.md | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/README.md b/README.md
index b4398b0..edeeab1 100644
--- a/README.md
+++ b/README.md
@@ -55,9 +55,9 @@ displayColumns =
 
 Note that this will only show preloaded tracks as well as tracks you have added using the various dialogs. It does not dynamically create tracks based on what is available from the GDC.
 
-# Available Store SeqFeature
+# Available Track Types
 ## A note on filters
-All SeqFeatures support filters as they are defined in the [GDC API Documentation](https://docs.gdc.cancer.gov/API/Users_Guide/Search_and_Retrieval/#filters-specifying-the-query).
+All tracks support filters as they are defined in the [GDC API Documentation](https://docs.gdc.cancer.gov/API/Users_Guide/Search_and_Retrieval/#filters-specifying-the-query).
 
 Note that filters should have the filter type prepended to the front. Ex. Case filters use `cases.`, SSM filters use `ssms.`, and Gene filters use `genes.`. GraphQL is used to retrieve results, so if the filters work there, they work with these Store classes.
 

From 9a9a955fdcc0e4bb7a344abae05746505aba36c4 Mon Sep 17 00:00:00 2001
From: Andrew Duncan <andrew.duncan@oicr.on.ca>
Date: Wed, 22 Jan 2020 15:35:28 -0500
Subject: [PATCH 11/28] Models for SSM and Gene features now extend
 SimpleFeature instead of using FastDeclare

---
 gdc-viewer/js/Model/GeneFeature.js     | 89 ++------------------------
 gdc-viewer/js/Model/SSMFeature.js      | 89 ++------------------------
 gdc-viewer/js/Store/SeqFeature/CNVs.js |  4 +-
 3 files changed, 10 insertions(+), 172 deletions(-)

diff --git a/gdc-viewer/js/Model/GeneFeature.js b/gdc-viewer/js/Model/GeneFeature.js
index 98edab1..58c0e5b 100644
--- a/gdc-viewer/js/Model/GeneFeature.js
+++ b/gdc-viewer/js/Model/GeneFeature.js
@@ -2,43 +2,12 @@
  * Simple implementation of a Gene feature object.
  */
 define([
-    'JBrowse/Util'
+    'JBrowse/Model/SimpleFeature',
+    'dojo/_base/declare'
    ],
-   function( Util ) {
+   function( SimpleFeature, declare ) {
 
-var counter = 0;
-
-var GeneFeature = Util.fastDeclare({
-
-/**
- * @param args.data {Object} key-value data, must include 'start' and 'end'
- * @param args.parent {Feature} optional parent feature
- * @param args.id {String} optional unique identifier.  can also be in data.uniqueID.
- *
- * Note: args.data.subfeatures can be an array of these same args,
- * which will be inflated to more instances of this class.
- */
-constructor: function( args ) {
-    args = args || {};
-    this.data = args.data || {};
-    this._parent = args.parent;
-    this._uniqueID = args.id || this.data.uniqueID || (
-        this._parent ? this._parent.id()+'_'+(counter++) : 'GeneFeature_'+(counter++)
-    );
-
-    // inflate any subfeatures that are not already feature objects
-    var subfeatures;
-    if(( subfeatures = this.data.subfeatures )) {
-        for( var i = 0; i < subfeatures.length; i++ ) {
-            if( typeof subfeatures[i].get != 'function' ) {
-                subfeatures[i] = new GeneFeature(
-                    { data: subfeatures[i],
-                      parent: this
-                    });
-            }
-        }
-    }
-},
+return declare(SimpleFeature, {
 
 projects: undefined,
 
@@ -178,58 +147,8 @@ getValueWithPercentage: function(numerator, denominator) {
 findProjectByKey: function(projects, key) {
     var project = projects.find(project => project.key === key);
     return project ? project.doc_count : 0;
-},
-
-/**
- * Set an item of data.
- */
-set: function( name, val ) {
-    this.data[ name ] = val;
-},
-
-/**
- * Get an array listing which data keys are present in this feature.
- */
-tags: function() {
-    var t = [];
-    var d = this.data;
-    for( var k in d ) {
-        if( d.hasOwnProperty( k ) )
-            t.push( k );
-    }
-    return t;
-},
-
-/**
- * Get the unique ID of this feature.
- */
-id: function( newid ) {
-    if( newid )
-        this._uniqueID = newid;
-    return this._uniqueID;
-},
-
-/**
- * Get this feature's parent feature, or undefined if none.
- */
-parent: function() {
-    return this._parent;
-},
-
-/**
- * Get an array of child features, or undefined if none.
- */
-children: function() {
-    return this.get('subfeatures');
-},
-
-toJSON: function() {
-    const d = Object.assign({},this)
-    delete d._parent
-    return d
 }
 
 });
 
-return GeneFeature;
 });
\ No newline at end of file
diff --git a/gdc-viewer/js/Model/SSMFeature.js b/gdc-viewer/js/Model/SSMFeature.js
index d9d4700..74d6462 100644
--- a/gdc-viewer/js/Model/SSMFeature.js
+++ b/gdc-viewer/js/Model/SSMFeature.js
@@ -2,43 +2,12 @@
  * Simple implementation of an SSM feature object.
  */
 define([
-    'JBrowse/Util'
+    'JBrowse/Model/SimpleFeature',
+    'dojo/_base/declare'
    ],
-   function( Util ) {
+   function( SimpleFeature, declare ) {
 
-var counter = 0;
-
-var SSMFeature = Util.fastDeclare({
-
-/**
- * @param args.data {Object} key-value data, must include 'start' and 'end'
- * @param args.parent {Feature} optional parent feature
- * @param args.id {String} optional unique identifier.  can also be in data.uniqueID.
- *
- * Note: args.data.subfeatures can be an array of these same args,
- * which will be inflated to more instances of this class.
- */
-constructor: function( args ) {
-    args = args || {};
-    this.data = args.data || {};
-    this._parent = args.parent;
-    this._uniqueID = args.id || this.data.uniqueID || (
-        this._parent ? this._parent.id()+'_'+(counter++) : 'SSMFeature_'+(counter++)
-    );
-
-    // inflate any subfeatures that are not already feature objects
-    var subfeatures;
-    if(( subfeatures = this.data.subfeatures )) {
-        for( var i = 0; i < subfeatures.length; i++ ) {
-            if( typeof subfeatures[i].get != 'function' ) {
-                subfeatures[i] = new SSMFeature(
-                    { data: subfeatures[i],
-                      parent: this
-                    });
-            }
-        }
-    }
-},
+return declare(SimpleFeature, {
 
 projects: undefined,
 
@@ -168,58 +137,8 @@ getValueWithPercentage: function(numerator, denominator) {
 findProjectByKey: function(projects, key) {
     var project = projects.find(project => project.key === key);
     return project ? project.doc_count : 0;
-},
-
-/**
- * Set an item of data.
- */
-set: function( name, val ) {
-    this.data[ name ] = val;
-},
-
-/**
- * Get an array listing which data keys are present in this feature.
- */
-tags: function() {
-    var t = [];
-    var d = this.data;
-    for( var k in d ) {
-        if( d.hasOwnProperty( k ) )
-            t.push( k );
-    }
-    return t;
-},
-
-/**
- * Get the unique ID of this feature.
- */
-id: function( newid ) {
-    if( newid )
-        this._uniqueID = newid;
-    return this._uniqueID;
-},
-
-/**
- * Get this feature's parent feature, or undefined if none.
- */
-parent: function() {
-    return this._parent;
-},
-
-/**
- * Get an array of child features, or undefined if none.
- */
-children: function() {
-    return this.get('subfeatures');
-},
-
-toJSON: function() {
-    const d = Object.assign({},this)
-    delete d._parent
-    return d
 }
 
 });
 
-return SSMFeature;
 });
\ No newline at end of file
diff --git a/gdc-viewer/js/Store/SeqFeature/CNVs.js b/gdc-viewer/js/Store/SeqFeature/CNVs.js
index 9f5d074..95ef628 100644
--- a/gdc-viewer/js/Store/SeqFeature/CNVs.js
+++ b/gdc-viewer/js/Store/SeqFeature/CNVs.js
@@ -60,7 +60,7 @@ function(
 
         /**
          * Get the features to be displayed
-         * @param {object} query 
+         * @param {object} query Query object
          * @param {function} featureCallback 
          * @param {function} finishCallback 
          * @param {function} errorCallback 
@@ -102,7 +102,7 @@ function(
 
         /**
          * Creates a CNV feature with the given gene object
-         * @param {object} cnv 
+         * @param {object} cnv CNV object returned by GDC API
          * @param {function} featureCallback 
          */
         createCNVFeature: function(cnv, featureCallback) {

From 4d7dbde32cdc576fd09b5b43d2aa62911bbfed0b Mon Sep 17 00:00:00 2001
From: Andrew Duncan <andrew.duncan@oicr.on.ca>
Date: Wed, 22 Jan 2020 15:49:50 -0500
Subject: [PATCH 12/28] updated readme with some more information about the
 purpose of different files

---
 README.md | 20 +++++++++++++++++++-
 1 file changed, 19 insertions(+), 1 deletion(-)

diff --git a/README.md b/README.md
index edeeab1..05744d3 100644
--- a/README.md
+++ b/README.md
@@ -216,4 +216,22 @@ Cypress.io is used for testing this plugin. The following steps show how to run
 4. Place `cypress/data/tracks.conf` into your `jbrowse/data/` directory. Make sure no other tracks are present.
 5. Run `npx cypress open` or `npx cypress run` or `npm run e2e`
 
-**Note** while some tests have mocked endpoints, not all endpoints are mocked. This could lead to breakage of tests in the future.
\ No newline at end of file
+**Note** while some tests have mocked endpoints, not all endpoints are mocked. This could lead to breakage of tests in the future.
+
+# Extra Notes for Developers
+This section just goes over some areas of the code to help new developers navigate.
+
+## js/Model
+These files override the function for printing to the feature dialog. It overrides the get function to display content that requires extra API calls (on top of the call to grab the whole track). For example, this is used to generate the projects table shown on SSMs and gene feature dialogs.
+
+## js/Store/SeqFeature
+These files connect the GDC API to JBrowse by creating a set of features based on an API call.
+
+## js/View
+The top level contains files that create the various dialog boxes that appear in the menu bar. These allow for the dynamic generation of tracks.
+
+### Export
+These files define export types for SSM, gene, and CNV tracks.
+
+### Track
+These files extend the track dropdown options to include things like shareable links and view filters. This is also where overrides for the format of the feature dialogs are.
\ No newline at end of file

From 5783692e00d8eb6fa429e61adef6a815fa7ea071 Mon Sep 17 00:00:00 2001
From: Andrew Duncan <andrew.duncan@oicr.on.ca>
Date: Thu, 23 Jan 2020 11:29:36 -0500
Subject: [PATCH 13/28] trying to make things more intuitive

---
 gdc-viewer/js/View/GDCDialog.js         | 5 +++++
 gdc-viewer/js/View/Track/CommonTrack.js | 8 ++++----
 2 files changed, 9 insertions(+), 4 deletions(-)

diff --git a/gdc-viewer/js/View/GDCDialog.js b/gdc-viewer/js/View/GDCDialog.js
index 4d41327..1f02236 100644
--- a/gdc-viewer/js/View/GDCDialog.js
+++ b/gdc-viewer/js/View/GDCDialog.js
@@ -449,6 +449,8 @@ function (
                 }
                 dom.empty(thisB.mutationResultsTab.containerNode);
 
+                var ssmExplanation = dom.create('div', { innerHTML: "Add mutation tracks for all cases across the GDC. Optionally apply the selected filters when adding tracks.", style: "font-size: 14px; margin-bottom: 5px; padding: 5px; background-color: lightgrey;" }, thisB.mutationResultsTab.containerNode);
+
                 // Buttons for SSMs
                 var ssmMenu = new Menu({ style: "display: none;"});
                 var menuItemSSMFiltered = new MenuItem({
@@ -560,6 +562,8 @@ function (
                     combinedFilters = JSON.parse(combinedFilters);
                 }
 
+                var geneExplanation = dom.create('div', { innerHTML: "Add gene and CNV tracks for all cases across the GDC. Optionally apply the selected filters when adding tracks.", style: "font-size: 14px; margin-bottom: 5px; padding: 5px; background-color: lightgrey;" }, thisB.geneResultsTab.containerNode);
+
                 // Buttons for Genes
                 var geneMenu = new Menu({ style: "display: none;"});
                 var menuItemGeneFiltered = new MenuItem({
@@ -685,6 +689,7 @@ function (
                 }
                 var endResultCount = thisB.casePage * thisB.pageSize <= totalCases ? thisB.casePage * thisB.pageSize : totalCases;
 
+                var casesExplanation = dom.create('div', { innerHTML: "Add mutation, gene, and CNV tracks for a given case. Optionally apply the selected filters when adding tracks.", style: "font-size: 14px; margin-bottom: 5px; padding: 5px; background-color: lightgrey;" }, thisB.caseResultsTab.containerNode);
                 var resultsInfo = dom.create('div', { innerHTML: "Showing " + startResultCount.toLocaleString() + " to " + endResultCount.toLocaleString() + " of " + totalCases.toLocaleString() }, thisB.caseResultsTab.containerNode);
                 thisB.createDonorsTable(response, thisB.caseResultsTab.containerNode);
                 thisB.createPaginationButtons(thisB.caseResultsTab.containerNode, totalCases / thisB.pageSize, 'case', thisB.casePage);
diff --git a/gdc-viewer/js/View/Track/CommonTrack.js b/gdc-viewer/js/View/Track/CommonTrack.js
index e25ce34..f18146d 100644
--- a/gdc-viewer/js/View/Track/CommonTrack.js
+++ b/gdc-viewer/js/View/Track/CommonTrack.js
@@ -50,11 +50,11 @@ define(
         domConstruct.place(headerElement, details);
 
         // Create help text
-        var helpString = '<span style="width: 80%">The following filters have been applied to the track. You can update the filters here, though no validation is done on the input.</span>';
+        var helpString = '<span style="width: 80%">The following filters have been applied to the track. You can update the filters here, though only basic validation is done on the input.</span>';
         var helpElement = domConstruct.toDom(helpString);
         domConstruct.place(helpElement, details);
 
-        var filterString = '<div style="width: 80%"><h3>Filters</h3></div>';
+        var filterString = '<div style="width: 80%"><h3>Filters</h3><span>Filters narrow down the features displayed on the track. We use the same format as the GDC API.</span></div>';
         var filterElement = domConstruct.toDom(filterString);
         domConstruct.place(filterElement, details);
 
@@ -79,7 +79,7 @@ define(
               }
         }).placeAt(details);
 
-        var caseString = '<div style="width: 80%"><h3>Case UUID</h3></div>';
+        var caseString = '<div style="width: 80%"><h3>Case UUID</h3><span>This is a unique identifier for the case, expressed as a UUID</span></div>';
         var caseElement = domConstruct.toDom(caseString);
         domConstruct.place(caseElement, details);
 
@@ -92,7 +92,7 @@ define(
             trim: true
         }).placeAt(details);
 
-        var sizeHeader = '<div style="width: 80%"><h3>Size</h3></div>';
+        var sizeHeader = '<div style="width: 80%"><h3>Size</h3><span>This is the maximum number of results to return per panel.</span></div>';
         var sizeElement = domConstruct.toDom(sizeHeader);
         domConstruct.place(sizeElement, details);
 

From beea6e12148ff7ae55dc14a2941c61ed1713711f Mon Sep 17 00:00:00 2001
From: Andrew Duncan <andrew.duncan@oicr.on.ca>
Date: Thu, 23 Jan 2020 13:16:51 -0500
Subject: [PATCH 14/28] better description of pages

---
 gdc-viewer/js/View/GDCDialog.js             |  6 +++---
 gdc-viewer/js/View/GDCPrimarySitesDialog.js |  1 +
 gdc-viewer/js/View/GDCProjectDialog.js      |  1 +
 gdc-viewer/js/View/Track/CommonTrack.js     | 10 +++++-----
 4 files changed, 10 insertions(+), 8 deletions(-)

diff --git a/gdc-viewer/js/View/GDCDialog.js b/gdc-viewer/js/View/GDCDialog.js
index 1f02236..b5bb5ad 100644
--- a/gdc-viewer/js/View/GDCDialog.js
+++ b/gdc-viewer/js/View/GDCDialog.js
@@ -449,7 +449,7 @@ function (
                 }
                 dom.empty(thisB.mutationResultsTab.containerNode);
 
-                var ssmExplanation = dom.create('div', { innerHTML: "Add mutation tracks for all cases across the GDC. Optionally apply the selected filters when adding tracks.", style: "font-size: 14px; margin-bottom: 5px; padding: 5px; background-color: lightgrey;" }, thisB.mutationResultsTab.containerNode);
+                var ssmExplanation = dom.create('div', { innerHTML: "Add mutation tracks for all cases across the GDC. Optionally apply the selected filters when adding tracks.", style: "font-size: 14px; margin-bottom: 5px; padding: 5px;" }, thisB.mutationResultsTab.containerNode);
 
                 // Buttons for SSMs
                 var ssmMenu = new Menu({ style: "display: none;"});
@@ -562,7 +562,7 @@ function (
                     combinedFilters = JSON.parse(combinedFilters);
                 }
 
-                var geneExplanation = dom.create('div', { innerHTML: "Add gene and CNV tracks for all cases across the GDC. Optionally apply the selected filters when adding tracks.", style: "font-size: 14px; margin-bottom: 5px; padding: 5px; background-color: lightgrey;" }, thisB.geneResultsTab.containerNode);
+                var geneExplanation = dom.create('div', { innerHTML: "Add gene and CNV tracks for all cases across the GDC. Optionally apply the selected filters when adding tracks.", style: "font-size: 14px; margin-bottom: 5px; padding: 5px;" }, thisB.geneResultsTab.containerNode);
 
                 // Buttons for Genes
                 var geneMenu = new Menu({ style: "display: none;"});
@@ -689,7 +689,7 @@ function (
                 }
                 var endResultCount = thisB.casePage * thisB.pageSize <= totalCases ? thisB.casePage * thisB.pageSize : totalCases;
 
-                var casesExplanation = dom.create('div', { innerHTML: "Add mutation, gene, and CNV tracks for a given case. Optionally apply the selected filters when adding tracks.", style: "font-size: 14px; margin-bottom: 5px; padding: 5px; background-color: lightgrey;" }, thisB.caseResultsTab.containerNode);
+                var casesExplanation = dom.create('div', { innerHTML: "Add mutation, gene, and CNV tracks for a given case. Optionally apply the selected filters when adding tracks.", style: "font-size: 14px; margin-bottom: 5px; padding: 5px;" }, thisB.caseResultsTab.containerNode);
                 var resultsInfo = dom.create('div', { innerHTML: "Showing " + startResultCount.toLocaleString() + " to " + endResultCount.toLocaleString() + " of " + totalCases.toLocaleString() }, thisB.caseResultsTab.containerNode);
                 thisB.createDonorsTable(response, thisB.caseResultsTab.containerNode);
                 thisB.createPaginationButtons(thisB.caseResultsTab.containerNode, totalCases / thisB.pageSize, 'case', thisB.casePage);
diff --git a/gdc-viewer/js/View/GDCPrimarySitesDialog.js b/gdc-viewer/js/View/GDCPrimarySitesDialog.js
index 3915971..7804ab7 100644
--- a/gdc-viewer/js/View/GDCPrimarySitesDialog.js
+++ b/gdc-viewer/js/View/GDCPrimarySitesDialog.js
@@ -54,6 +54,7 @@ function (
             var thisB = this;
             var headerSection = dom.create('div', { style: "margin-bottom: 5px;" }, thisB.dialogContainer);
             var aboutMessage = dom.create('h1', { innerHTML: "View primary sites available on the GDC Data Portal" }, headerSection);
+            var pageExplanation = dom.create('div', { innerHTML: "Add mutation, gene and CNV tracks for all cases across the GDC, filtered by primary site.", style: "font-size: 14px; margin-bottom: 5px; padding: 5px; margin-top:5px;" }, headerSection);
         },
 
         /**
diff --git a/gdc-viewer/js/View/GDCProjectDialog.js b/gdc-viewer/js/View/GDCProjectDialog.js
index f7efdd2..f4d89cd 100644
--- a/gdc-viewer/js/View/GDCProjectDialog.js
+++ b/gdc-viewer/js/View/GDCProjectDialog.js
@@ -54,6 +54,7 @@ function (
             var thisB = this;
             var headerSection = dom.create('div', { style: "margin-bottom: 5px;" }, thisB.dialogContainer);
             var aboutMessage = dom.create('h1', { innerHTML: "View projects available on the GDC Data Portal" }, headerSection);
+            var pageExplanation = dom.create('div', { innerHTML: "Add mutation, gene and CNV tracks for all cases across the GDC, filtered by project.", style: "font-size: 14px; margin-bottom: 5px; padding: 5px; margin-top:5px;" }, headerSection);
         },
 
         /**
diff --git a/gdc-viewer/js/View/Track/CommonTrack.js b/gdc-viewer/js/View/Track/CommonTrack.js
index f18146d..0315691 100644
--- a/gdc-viewer/js/View/Track/CommonTrack.js
+++ b/gdc-viewer/js/View/Track/CommonTrack.js
@@ -45,12 +45,12 @@ define(
         var track = this;
         var details = domConstruct.create('div', { className: 'detail', style: 'display: flex; flex-direction: column; align-items: center; justify-content: center;' });
         
-        var headerString = '<h1 style="width: 80%">Track Filters</h1>';
+        var headerString = '<h1 style="width: 80%; margin-bottom: 5px;">View and Update Filters Applied To The Current Track</h1>';
         var headerElement = domConstruct.toDom(headerString);
         domConstruct.place(headerElement, details);
 
         // Create help text
-        var helpString = '<span style="width: 80%">The following filters have been applied to the track. You can update the filters here, though only basic validation is done on the input.</span>';
+        var helpString = '<span style="width: 80%; font-size: 14px;">The following filters have been applied to the track. You can update the filters here, though only basic validation is done on the input.</span>';
         var helpElement = domConstruct.toDom(helpString);
         domConstruct.place(helpElement, details);
 
@@ -79,7 +79,7 @@ define(
               }
         }).placeAt(details);
 
-        var caseString = '<div style="width: 80%"><h3>Case UUID</h3><span>This is a unique identifier for the case, expressed as a UUID</span></div>';
+        var caseString = '<div style="width: 80%"><h3>Case UUID</h3><span>This is a unique identifier for the case, expressed as a UUID.</span></div>';
         var caseElement = domConstruct.toDom(caseString);
         domConstruct.place(caseElement, details);
 
@@ -105,7 +105,7 @@ define(
         }).placeAt(details);
 
         var updateTrackButton = new Button({
-            label: 'Apply New Filters',
+            label: 'Apply Filters',
             iconClass: 'dijitIconSave',
             onClick: function() {
                 const trackString = document.getElementById("filterTextArea").value;
@@ -171,7 +171,7 @@ define(
         var shareableLink = window.location.protocol + "//" + window.location.host + window.location.pathname + '?' + params.toString();
 
         // Create help text
-        var helpString = '<span style="width: 80%">Use the following link to share the selected track at the current location.</span>';
+        var helpString = '<span style="width: 80%; font-size: 14px;">Use the following link to share the selected track at the current location.</span>';
         var helpElement = domConstruct.toDom(helpString);
         domConstruct.place(helpElement, details);
 

From 13a6ae6001a25fdc4b44f27793d76e188960cc0d Mon Sep 17 00:00:00 2001
From: Andrew Duncan <andrew.duncan@oicr.on.ca>
Date: Thu, 23 Jan 2020 13:27:41 -0500
Subject: [PATCH 15/28] fix test

---
 cypress/integration/ExploreGDC.js | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/cypress/integration/ExploreGDC.js b/cypress/integration/ExploreGDC.js
index 3794d61..e253e8e 100644
--- a/cypress/integration/ExploreGDC.js
+++ b/cypress/integration/ExploreGDC.js
@@ -120,7 +120,7 @@ describe('Explore GDC', function() {
         })
 
         checkAllResultsTab(
-            ['Showing 1 to 20 of 3,102', 'TCGA-A5-A1OF', 'TCGA-AJ-A3EK'],
+            ['Showing 1 to 20 of 3,107', 'TCGA-A5-A1OF', 'TCGA-AJ-A3EK'],
             ['Showing 1 to 20 of 21,168', 'TP53', 'TTN'],
             ['Showing 1 to 20 of 120,824', 'chr2:g.208248388C>T', 'chr17:g.7673803G>A']
         )

From 87593f8f8bac48ba10b29eb851b51ab147a72cce Mon Sep 17 00:00:00 2001
From: Andrew Duncan <andrew.duncan@oicr.on.ca>
Date: Mon, 10 Feb 2020 13:54:46 -0500
Subject: [PATCH 16/28] change reference of ssm to mutation

---
 cypress/integration/ExploreGDC.js           |  2 +-
 cypress/integration/PrimarySites.js         |  2 +-
 cypress/integration/projects.js             |  2 +-
 gdc-viewer/js/View/GDCDialog.js             | 22 ++++++++++-----------
 gdc-viewer/js/View/GDCPrimarySitesDialog.js |  6 +++---
 gdc-viewer/js/View/GDCProjectDialog.js      |  4 ++--
 gdc-viewer/js/View/Track/CommonTrack.js     |  4 ++--
 7 files changed, 21 insertions(+), 21 deletions(-)

diff --git a/cypress/integration/ExploreGDC.js b/cypress/integration/ExploreGDC.js
index e253e8e..5dfd715 100644
--- a/cypress/integration/ExploreGDC.js
+++ b/cypress/integration/ExploreGDC.js
@@ -141,7 +141,7 @@ describe('Explore GDC', function() {
         // Add tracks and check that they were added
         cy.get('.dijitTabContainer').eq(1).within(() => {
             cy.contains('All Genes for Donor').eq(0).click()
-            cy.contains('All SSMs for Donor').eq(0).click()
+            cy.contains('All Mutations for Donor').eq(0).click()
             cy.contains('All CNVs for Donor').eq(0).click()
         })
 
diff --git a/cypress/integration/PrimarySites.js b/cypress/integration/PrimarySites.js
index 827e968..d9426d3 100644
--- a/cypress/integration/PrimarySites.js
+++ b/cypress/integration/PrimarySites.js
@@ -51,7 +51,7 @@ describe('Primary sites dialog', function() {
 
         // Add SSM, Gene, and CNV tracks for primary site bronchus and lung (assume first in list)
         cy.get('#dijit_form_ComboButton_0_arrow').should('be.visible').type('{enter}')
-        cy.contains('SSMs for Primary Site').click()
+        cy.contains('Mutations for Primary Site').click()
 
         cy.get('#dijit_form_ComboButton_0_arrow').should('be.visible').type('{enter}')
         cy.contains('Genes for Primary Site').click()
diff --git a/cypress/integration/projects.js b/cypress/integration/projects.js
index e3eda06..514a3c3 100644
--- a/cypress/integration/projects.js
+++ b/cypress/integration/projects.js
@@ -53,7 +53,7 @@ describe('Project dialog', function() {
         // Add SSM, Gene, and CNV tracks for project FM-AD (assume first in list)
         // Note that even though we select FM-AD, we are mocking TCGA-BRCA
         cy.get('#dijit_form_ComboButton_0_arrow').should('be.visible').type('{enter}')
-        cy.contains('SSMs for Project').click()
+        cy.contains('Mutations for Project').click()
 
         cy.get('#dijit_form_ComboButton_0_arrow').should('be.visible').type('{enter}')
         cy.contains('Genes for Project').click()
diff --git a/gdc-viewer/js/View/GDCDialog.js b/gdc-viewer/js/View/GDCDialog.js
index b5bb5ad..a0d6b17 100644
--- a/gdc-viewer/js/View/GDCDialog.js
+++ b/gdc-viewer/js/View/GDCDialog.js
@@ -454,29 +454,29 @@ function (
                 // Buttons for SSMs
                 var ssmMenu = new Menu({ style: "display: none;"});
                 var menuItemSSMFiltered = new MenuItem({
-                    label: "Filtered SSMs form GDC",
+                    label: "Filtered Mutations form GDC",
                     iconClass: "dijitIconNewTask",
                     onClick: function() {
                         thisB.addTrack('SimpleSomaticMutations', undefined, undefined, combinedFilters, 'gdc-viewer/View/Track/SSMTrack');
-                        alert("Adding track with all SSMs from the GDC, with current filters applied");
+                        alert("Adding track with all Mutations from the GDC, with current filters applied");
                     }
                 });
                 ssmMenu.addChild(menuItemSSMFiltered);
                 ssmMenu.startup();
 
                 var buttonAllSSMs = new ComboButton({
-                    label: "All SSMs from GDC",
+                    label: "All Mutations from GDC",
                     iconClass: "dijitIconNewTask",
                     dropDown: ssmMenu,
                     onClick: function() {
                         thisB.addTrack('SimpleSomaticMutations', undefined, undefined, undefined, 'gdc-viewer/View/Track/SSMTrack');
-                        alert("Add track with all SSMs from the GDC");
+                        alert("Add track with all Mutations from the GDC");
                     }
                 });
                 buttonAllSSMs.placeAt(thisB.mutationResultsTab.containerNode);
                 buttonAllSSMs.startup();
-                thisB.addTooltipToButton(menuItemSSMFiltered, "Add track with all SSMs from the GDC, with current filters applied");
-                thisB.addTooltipToButton(buttonAllSSMs, "Add track with all SSMs from the GDC");
+                thisB.addTooltipToButton(menuItemSSMFiltered, "Add track with all Mutations from the GDC, with current filters applied");
+                thisB.addTooltipToButton(buttonAllSSMs, "Add track with all Mutations from the GDC");
 
                 var totalSSMs = response.data.viewer.explore.ssms.hits.total;
                 var startResultCount = ((thisB.mutationPage - 1) * thisB.pageSize);
@@ -715,7 +715,7 @@ function (
                     <th>Primary Site</th>
                     <th>Gender</th>
                     <th>Genes</th>
-                    <th>SSMs</th>
+                    <th>Mutations</th>
                     <th>CNVs</th>
                 </tr>
             `;
@@ -786,7 +786,7 @@ function (
                     // SSM Buttons
                     var ssmMenu = new Menu({ style: "display: none;"});
                     var menuItemSsmFiltered = new MenuItem({
-                        label: "Filtered SSMs for Donor",
+                        label: "Filtered Mutations for Donor",
                         iconClass: "dijitIconNewTask",
                         onClick: (function(hit, combinedFilters) {
                             return function() {
@@ -799,7 +799,7 @@ function (
                     ssmMenu.startup();
 
                     var buttonAllSsms = new ComboButton({
-                        label: "All SSMs for Donor",
+                        label: "All Mutations for Donor",
                         iconClass: "dijitIconNewTask",
                         dropDown: ssmMenu,
                         onClick: (function(hit) {
@@ -811,8 +811,8 @@ function (
                     });
                     buttonAllSsms.placeAt(ssmButtonNode);
                     buttonAllSsms.startup();
-                    thisB.addTooltipToButton(menuItemSsmFiltered, "Add track with all SSMs for the given donor, with current filters applied");
-                    thisB.addTooltipToButton(buttonAllSsms, "Add track with all SSMS for the given donor");
+                    thisB.addTooltipToButton(menuItemSsmFiltered, "Add track with all Mutations for the given donor, with current filters applied");
+                    thisB.addTooltipToButton(buttonAllSsms, "Add track with all Mutations for the given donor");
 
                     // Place buttons in table
                     dom.place(ssmButtonNode, caseRowContentNode);
diff --git a/gdc-viewer/js/View/GDCPrimarySitesDialog.js b/gdc-viewer/js/View/GDCPrimarySitesDialog.js
index 7804ab7..0845ce8 100644
--- a/gdc-viewer/js/View/GDCPrimarySitesDialog.js
+++ b/gdc-viewer/js/View/GDCPrimarySitesDialog.js
@@ -144,12 +144,12 @@ function (
                     var geneMenu = new Menu({ style: "display: none;"});
 
                     var menuItemSSM = new MenuItem({
-                        label: "SSMs for Primary Site",
+                        label: "Mutations for Primary Site",
                         iconClass: "dijitIconNewTask",
                         onClick: (function(hit) {
                             return function() {
                                 thisB.addTrack('SimpleSomaticMutations', hit.key, 'gdc-viewer/View/Track/SSMTrack');
-                                alert("Adding SSM track for primary site " + hit.key);
+                                alert("Adding Mutation track for primary site " + hit.key);
                             }
                         })(hit)
                     });
@@ -192,7 +192,7 @@ function (
                     // Add  tooltips
                     thisB.addTooltipToButton(menuItemGene, "Add track with all genes for the given primary site");
                     thisB.addTooltipToButton(menuItemCNV, "Add track with all CNVs for the given primary site");
-                    thisB.addTooltipToButton(menuItemSSM, "Add track with all SSMs for the given primary site");
+                    thisB.addTooltipToButton(menuItemSSM, "Add track with all Mutations for the given primary site");
 
                     // Place buttons in table
                     dom.place(projectButtonNode, projectRowContentNode);
diff --git a/gdc-viewer/js/View/GDCProjectDialog.js b/gdc-viewer/js/View/GDCProjectDialog.js
index f4d89cd..8a3a18b 100644
--- a/gdc-viewer/js/View/GDCProjectDialog.js
+++ b/gdc-viewer/js/View/GDCProjectDialog.js
@@ -166,7 +166,7 @@ function (
                     var geneMenu = new Menu({ style: "display: none;"});
 
                     var menuItemSSM = new MenuItem({
-                        label: "SSMs for Project",
+                        label: "Mutations for Project",
                         iconClass: "dijitIconNewTask",
                         onClick: (function(hit) {
                             return function() {
@@ -214,7 +214,7 @@ function (
                     // Add  tooltips
                     thisB.addTooltipToButton(menuItemGene, "Add track with all genes for the given project");
                     thisB.addTooltipToButton(menuItemCNV, "Add track with all CNVs for the given project");
-                    thisB.addTooltipToButton(menuItemSSM, "Add track with all SSMs for the given project");
+                    thisB.addTooltipToButton(menuItemSSM, "Add track with all Mutations for the given project");
 
                     // Place buttons in table
                     dom.place(projectButtonNode, projectRowContentNode);
diff --git a/gdc-viewer/js/View/Track/CommonTrack.js b/gdc-viewer/js/View/Track/CommonTrack.js
index 0315691..4b9a275 100644
--- a/gdc-viewer/js/View/Track/CommonTrack.js
+++ b/gdc-viewer/js/View/Track/CommonTrack.js
@@ -54,7 +54,7 @@ define(
         var helpElement = domConstruct.toDom(helpString);
         domConstruct.place(helpElement, details);
 
-        var filterString = '<div style="width: 80%"><h3>Filters</h3><span>Filters narrow down the features displayed on the track. We use the same format as the GDC API.</span></div>';
+        var filterString = '<div style="width: 80%"><h3>Filters</h3><span>Filters narrow down the features displayed on the track. We use the same format as the <a href="https://docs.gdc.cancer.gov/API/Users_Guide/GraphQL_Examples/" target="_nblank">GDC GraphQL API</a>.</span></div>';
         var filterElement = domConstruct.toDom(filterString);
         domConstruct.place(filterElement, details);
 
@@ -178,7 +178,7 @@ define(
         // Create text area with shareable link
         var textArea = domConstruct.create(
             'textarea',{
-                rows: 10,
+                rows: 1,
                 value: shareableLink,
                 style: "width: 80%",
                 readOnly: true

From 819b60649fb8c763e19f0c029eacaea26800667a Mon Sep 17 00:00:00 2001
From: Andrew Duncan <andrew.duncan@oicr.on.ca>
Date: Mon, 10 Feb 2020 14:17:24 -0500
Subject: [PATCH 17/28] more changes of ssm to mutation

---
 README.md                          | 8 ++++----
 gdc-viewer/js/Model/GeneFeature.js | 2 +-
 gdc-viewer/js/Model/SSMFeature.js  | 2 +-
 gdc-viewer/js/View/GDCDialog.js    | 4 ++--
 4 files changed, 8 insertions(+), 8 deletions(-)

diff --git a/README.md b/README.md
index 05744d3..b83ccdd 100644
--- a/README.md
+++ b/README.md
@@ -113,12 +113,12 @@ filters={"op":"!=","content":{"field":"cases.biotype","value":"protein_coding"}}
 ### Extra notes
 You can set the max number of genes to return with the `size` field (per panel). It defaults to 100. The smaller the number, the faster the results will appear.
 
-## SSMs
+## Mutations (SSMs)
 A simple view of all of the simple somatic mutations seen across all cases.
 
-You can view case specific SSMs by setting the `case` field.
+You can view case specific mutations by setting the `case` field.
 
-You can apply filters to the track too, in the same format as GDC. The below example only shows SSMs whose reference allele is 'G'.
+You can apply filters to the track too, in the same format as GDC. The below example only shows mutations whose reference allele is 'G'.
 ```
 { 
    "op":"=",
@@ -147,7 +147,7 @@ filters={"op":"=","content":{"field":"ssms.reference_allele","value":"G"}}
 ![GDC SSMs](images/GDC-mutations-base-g.png)
 
 ### Extra notes
-You can set the max number of SSMs to return with the `size` field (per panel). It defaults to 100. The smaller the number, the faster the results will appear.
+You can set the max number of mutations to return with the `size` field (per panel). It defaults to 100. The smaller the number, the faster the results will appear.
 
 ## CNVs
 A simple view of all of the CNVs seen across all cases.
diff --git a/gdc-viewer/js/Model/GeneFeature.js b/gdc-viewer/js/Model/GeneFeature.js
index 58c0e5b..e9d8bd5 100644
--- a/gdc-viewer/js/Model/GeneFeature.js
+++ b/gdc-viewer/js/Model/GeneFeature.js
@@ -75,7 +75,7 @@ createProjectTable: function(response) {
             <th class="popup-table-header">Project</th>
             <th class="popup-table-header">Disease Type</th>
             <th class="popup-table-header">Site</th>
-            <th class="popup-table-header"># SSM Affected Cases</th> 
+            <th class="popup-table-header"># Mutation Affected Cases</th> 
             <th class="popup-table-header"># CNV Gains</th>
             <th class="popup-table-header"># CNV Losses</th>
         </tr>
diff --git a/gdc-viewer/js/Model/SSMFeature.js b/gdc-viewer/js/Model/SSMFeature.js
index 74d6462..9165b06 100644
--- a/gdc-viewer/js/Model/SSMFeature.js
+++ b/gdc-viewer/js/Model/SSMFeature.js
@@ -69,7 +69,7 @@ createProjectTable: function(response) {
             <th class="popup-table-header">Project</th>
             <th class="popup-table-header">Disease Type</th>
             <th class="popup-table-header">Site</th>
-            <th class="popup-table-header"># SSM Affected Cases</th>
+            <th class="popup-table-header"># Mutation Affected Cases</th>
         </tr>
     `;
 
diff --git a/gdc-viewer/js/View/GDCDialog.js b/gdc-viewer/js/View/GDCDialog.js
index a0d6b17..0b6a81c 100644
--- a/gdc-viewer/js/View/GDCDialog.js
+++ b/gdc-viewer/js/View/GDCDialog.js
@@ -893,8 +893,8 @@ function (
                 <tr>
                     <th>Symbol</th>
                     <th>Name</th>
-                    <th># SSM Affected Cases in Cohort</th>
-                    <th># SSM Affected Cases Across the GDC</th>
+                    <th># Mutation Affected Cases in Cohort</th>
+                    <th># Mutation Affected Cases Across the GDC</th>
                     <th># CNV Gain</th>
                     <th># CNV Loss</th>
                     <th>Is Cancer Gene Census</th>

From 953b81a18a44ac1dadc07ceea1c14cbfd8fb735b Mon Sep 17 00:00:00 2001
From: Andrew Duncan <andrew.duncan@oicr.on.ca>
Date: Mon, 10 Feb 2020 14:27:29 -0500
Subject: [PATCH 18/28] more ssm to mutation changes

---
 README.md | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/README.md b/README.md
index b83ccdd..9d23de3 100644
--- a/README.md
+++ b/README.md
@@ -59,7 +59,7 @@ Note that this will only show preloaded tracks as well as tracks you have added
 ## A note on filters
 All tracks support filters as they are defined in the [GDC API Documentation](https://docs.gdc.cancer.gov/API/Users_Guide/Search_and_Retrieval/#filters-specifying-the-query).
 
-Note that filters should have the filter type prepended to the front. Ex. Case filters use `cases.`, SSM filters use `ssms.`, and Gene filters use `genes.`. GraphQL is used to retrieve results, so if the filters work there, they work with these Store classes.
+Note that filters should have the filter type prepended to the front. Ex. Case filters use `cases.`, Mutation filters use `ssms.`, and Gene filters use `genes.`. GraphQL is used to retrieve results, so if the filters work there, they work with these Store classes.
 
 The following shows a filter for cases by ethnicity:
 ```
@@ -189,19 +189,19 @@ You can set the max number of CNVs to return with the `size` field (per panel).
 
 # Dynamic Track Generation
 ## Explore cases, genes and mutations
-This dialog is similar to the Exploration section of the GDC data portal. As you apply facets on the left-hand side, updated results will be shown on the right side. You can create donor specific SSM, Gene, and CNV tracks, along with GDC-wide SSM, Gene and CNV tracks.
+This dialog is similar to the Exploration section of the GDC data portal. As you apply facets on the left-hand side, updated results will be shown on the right side. You can create donor specific Mutation, Gene, and CNV tracks, along with GDC-wide Mutation, Gene and CNV tracks.
 ![GDC Portal](images/GDC-portal-explore.png)
 
 ## Explore Projects
-This dialog shows the projects present on the GDC Data Portal. You can add SSM, Gene, and CNV tracks for each project.
+This dialog shows the projects present on the GDC Data Portal. You can add Mutation, Gene, and CNV tracks for each project.
 ![GDC projects](images/GDC-project-browser.png)
 
 ## Explore Primary Sites
-This dialog shows the primary sites present on the GDC Data Portal. You can add SSM, Gene, and CNV tracks for each primary site.
+This dialog shows the primary sites present on the GDC Data Portal. You can add Mutation, Gene, and CNV tracks for each primary site.
 ![GDC primary sites](images/GDC-primary-sites.png)
 
 # Export Types
-The following export types are supported by both GDC Genes and SSMs. To export, select `Save track data` in the track dropdown. Note that not all track information is carried over to the exported file.
+The following export types are supported by both GDC Genes and Mutations. To export, select `Save track data` in the track dropdown. Note that not all track information is carried over to the exported file.
 * BED
 * GFF3
 * Sequin Table
@@ -222,7 +222,7 @@ Cypress.io is used for testing this plugin. The following steps show how to run
 This section just goes over some areas of the code to help new developers navigate.
 
 ## js/Model
-These files override the function for printing to the feature dialog. It overrides the get function to display content that requires extra API calls (on top of the call to grab the whole track). For example, this is used to generate the projects table shown on SSMs and gene feature dialogs.
+These files override the function for printing to the feature dialog. It overrides the get function to display content that requires extra API calls (on top of the call to grab the whole track). For example, this is used to generate the projects table shown on Mutations and gene feature dialogs.
 
 ## js/Store/SeqFeature
 These files connect the GDC API to JBrowse by creating a set of features based on an API call.
@@ -231,7 +231,7 @@ These files connect the GDC API to JBrowse by creating a set of features based o
 The top level contains files that create the various dialog boxes that appear in the menu bar. These allow for the dynamic generation of tracks.
 
 ### Export
-These files define export types for SSM, gene, and CNV tracks.
+These files define export types for Mutation, gene, and CNV tracks.
 
 ### Track
 These files extend the track dropdown options to include things like shareable links and view filters. This is also where overrides for the format of the feature dialogs are.
\ No newline at end of file

From 539e0fbddb3adc98a52c44bb06f1616b763e4a55 Mon Sep 17 00:00:00 2001
From: Andrew Duncan <andrew.duncan@oicr.on.ca>
Date: Mon, 10 Feb 2020 15:03:37 -0500
Subject: [PATCH 19/28] support for multiple case uuids at once

---
 gdc-viewer/js/Store/SeqFeature/CNVs.js                   | 2 +-
 gdc-viewer/js/Store/SeqFeature/Genes.js                  | 2 +-
 gdc-viewer/js/Store/SeqFeature/SimpleSomaticMutations.js | 2 +-
 gdc-viewer/js/View/Track/CommonTrack.js                  | 4 ++--
 4 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/gdc-viewer/js/Store/SeqFeature/CNVs.js b/gdc-viewer/js/Store/SeqFeature/CNVs.js
index 95ef628..87d3ba9 100644
--- a/gdc-viewer/js/Store/SeqFeature/CNVs.js
+++ b/gdc-viewer/js/Store/SeqFeature/CNVs.js
@@ -128,7 +128,7 @@ function(
             var thisB = this;
             var locationFilter = {"op":"and","content":[{"op":">=","content":{"field":"cnvs.start_position","value":start}},{"op":"<=","content":{"field":"cnvs.end_position","value":end}},{"op":"=","content":{"field":"cnvs.chromosome","value":[chr]}}]};
             if (thisB.case) {
-                var caseFilter = {"op":"in","content":{"field": "cases.case_id","value": thisB.case}};
+                var caseFilter = {"op":"in","content":{"field": "cases.case_id","value": thisB.case.split(',')}};
                 locationFilter.content.push(caseFilter);
             }
             return(locationFilter);
diff --git a/gdc-viewer/js/Store/SeqFeature/Genes.js b/gdc-viewer/js/Store/SeqFeature/Genes.js
index 6a5bec6..1fd21a9 100644
--- a/gdc-viewer/js/Store/SeqFeature/Genes.js
+++ b/gdc-viewer/js/Store/SeqFeature/Genes.js
@@ -153,7 +153,7 @@ function(
             var thisB = this;
             var locationFilter = {"op":"and","content":[{"op":">=","content":{"field":"genes.gene_start","value":start}},{"op":"<=","content":{"field":"genes.gene_end","value":end}},{"op":"=","content":{"field":"genes.gene_chromosome","value":[chr]}}]};
             if (thisB.case) {
-                var caseFilter = {"op":"in","content":{"field": "cases.case_id","value": thisB.case}};
+                var caseFilter = {"op":"in","content":{"field": "cases.case_id","value": thisB.case.split(',')}};
                 locationFilter.content.push(caseFilter);
             }
             return(locationFilter);
diff --git a/gdc-viewer/js/Store/SeqFeature/SimpleSomaticMutations.js b/gdc-viewer/js/Store/SeqFeature/SimpleSomaticMutations.js
index d4fa997..5c3d99f 100644
--- a/gdc-viewer/js/Store/SeqFeature/SimpleSomaticMutations.js
+++ b/gdc-viewer/js/Store/SeqFeature/SimpleSomaticMutations.js
@@ -244,7 +244,7 @@ function(
             var thisB = this;
             var locationFilter = {"op":"and","content":[{"op":">=","content":{"field":"ssms.start_position","value":start}},{"op":"<=","content":{"field":"ssms.end_position","value":end}},{"op":"=","content":{"field":"ssms.chromosome","value":['chr'+chr]}}]};
             if (thisB.case) {
-                var caseFilter = {"op":"in","content":{"field": "cases.case_id","value": thisB.case}};
+                var caseFilter = {"op":"in","content":{"field": "cases.case_id","value": thisB.case.split(',')}};
                 locationFilter.content.push(caseFilter);
             }
             return(locationFilter);
diff --git a/gdc-viewer/js/View/Track/CommonTrack.js b/gdc-viewer/js/View/Track/CommonTrack.js
index 4b9a275..e91c59e 100644
--- a/gdc-viewer/js/View/Track/CommonTrack.js
+++ b/gdc-viewer/js/View/Track/CommonTrack.js
@@ -79,7 +79,7 @@ define(
               }
         }).placeAt(details);
 
-        var caseString = '<div style="width: 80%"><h3>Case UUID</h3><span>This is a unique identifier for the case, expressed as a UUID.</span></div>';
+        var caseString = '<div style="width: 80%"><h3>Case UUIDs</h3><span>Comma separated unique identifiers for the case, expressed as UUIDs.</span></div>';
         var caseElement = domConstruct.toDom(caseString);
         domConstruct.place(caseElement, details);
 
@@ -87,7 +87,7 @@ define(
             value: track.store.config.case,
             style: "width: 80%",
             id: "caseTextBox",
-            regExp: "^[a-f0-9]{8}-[a-f0-9]{4}-[a-f0-9]{4}-[a-f0-9]{4}-[a-f0-9]{12}$",
+            regExp: "^[a-f0-9]{8}-[a-f0-9]{4}-[a-f0-9]{4}-[a-f0-9]{4}-[a-f0-9]{12}(,[a-f0-9]{8}-[a-f0-9]{4}-[a-f0-9]{4}-[a-f0-9]{4}-[a-f0-9]{12})*$",
             invalidMessage: "Invalid Case UUID - Must be version 4 UUID",
             trim: true
         }).placeAt(details);

From 1d7d470905c86e21f5510b88f9ff7eb66f4f3369 Mon Sep 17 00:00:00 2001
From: Andrew Duncan <andrew.duncan@oicr.on.ca>
Date: Mon, 10 Feb 2020 15:34:22 -0500
Subject: [PATCH 20/28] attempt to make add tracks less confusing

---
 README.md                                   |  2 +-
 cypress/fixtures/projects/mutations.json    |  2 +-
 cypress/integration/ExploreGDC.js           | 16 ++++-----
 cypress/integration/PrimarySites.js         |  8 ++---
 cypress/integration/projects.js             |  8 ++---
 gdc-viewer/js/View/GDCDialog.js             | 40 ++++++++++-----------
 gdc-viewer/js/View/GDCPrimarySitesDialog.js |  6 ++--
 gdc-viewer/js/View/GDCProjectDialog.js      |  6 ++--
 gdc-viewer/js/main.js                       |  4 +--
 9 files changed, 46 insertions(+), 46 deletions(-)

diff --git a/README.md b/README.md
index 9d23de3..5d9c159 100644
--- a/README.md
+++ b/README.md
@@ -189,7 +189,7 @@ You can set the max number of CNVs to return with the `size` field (per panel).
 
 # Dynamic Track Generation
 ## Explore cases, genes and mutations
-This dialog is similar to the Exploration section of the GDC data portal. As you apply facets on the left-hand side, updated results will be shown on the right side. You can create donor specific Mutation, Gene, and CNV tracks, along with GDC-wide Mutation, Gene and CNV tracks.
+This dialog is similar to the Exploration section of the GDC data portal. As you apply facets on the left-hand side, updated results will be shown on the right side. You can create case specific Mutation, Gene, and CNV tracks, along with GDC-wide Mutation, Gene and CNV tracks.
 ![GDC Portal](images/GDC-portal-explore.png)
 
 ## Explore Projects
diff --git a/cypress/fixtures/projects/mutations.json b/cypress/fixtures/projects/mutations.json
index aed14ed..53a1b9d 100644
--- a/cypress/fixtures/projects/mutations.json
+++ b/cypress/fixtures/projects/mutations.json
@@ -1 +1 @@
-{"data":{"viewer":{"explore":{"ssms":{"hits":{"edges":[{"node":{"consequence":{"hits":{"edges":[{"node":{"id":"U1NNQ29uc2VxdWVuY2U6MDJhYWEzOWEtYWNmMS01YjY0LWJjMjctYmIzYjk3N2EwY2ZhOjBmMmIzOTk0LWRiNTktNTczNS1iODhkLTIyZjkxZjFhNzI1Zg==","transcript":{"aa_change":null,"annotation":{"hgvsc":"n.287+25192delA","polyphen_impact":"","polyphen_score":null,"sift_impact":"","sift_score":null,"vep_impact":"MODIFIER"},"consequence_type":"intron_variant","gene":{"gene_id":"ENSG00000162600","gene_strand":-1,"symbol":"OMA1"},"is_canonical":false,"transcript_id":"ENST00000467509"}}},{"node":{"id":"U1NNQ29uc2VxdWVuY2U6MDJhYWEzOWEtYWNmMS01YjY0LWJjMjctYmIzYjk3N2EwY2ZhOjZiMGYyZjdiLWU5NmUtNTExNS05ODA3LTNkYzI4NTY5NTNlZQ==","transcript":{"aa_change":null,"annotation":{"hgvsc":"n.141-18074delA","polyphen_impact":"","polyphen_score":null,"sift_impact":"","sift_score":null,"vep_impact":"MODIFIER"},"consequence_type":"intron_variant","gene":{"gene_id":"ENSG00000162600","gene_strand":-1,"symbol":"OMA1"},"is_canonical":false,"transcript_id":"ENST00000460671"}}},{"node":{"id":"U1NNQ29uc2VxdWVuY2U6MDJhYWEzOWEtYWNmMS01YjY0LWJjMjctYmIzYjk3N2EwY2ZhOjAwN2U3ODUxLTE2MzgtNTdlYS1hN2E1LWFhM2E0N2QyNTQwMw==","transcript":{"aa_change":null,"annotation":{"hgvsc":"","polyphen_impact":"","polyphen_score":null,"sift_impact":"","sift_score":null,"vep_impact":"MODIFIER"},"consequence_type":"downstream_gene_variant","gene":{"gene_id":"ENSG00000162600","gene_strand":-1,"symbol":"OMA1"},"is_canonical":false,"transcript_id":"ENST00000476933"}}},{"node":{"id":"U1NNQ29uc2VxdWVuY2U6MDJhYWEzOWEtYWNmMS01YjY0LWJjMjctYmIzYjk3N2EwY2ZhOmY0MmI4MDYwLWE3MmItNTU4Yi05NmI3LTMzNzM2NDliZTc5MA==","transcript":{"aa_change":null,"annotation":{"hgvsc":"c.890-6900delA","polyphen_impact":"","polyphen_score":null,"sift_impact":"","sift_score":null,"vep_impact":"MODIFIER"},"consequence_type":"intron_variant","gene":{"gene_id":"ENSG00000162600","gene_strand":-1,"symbol":"OMA1"},"is_canonical":false,"transcript_id":"ENST00000421528"}}},{"node":{"id":"U1NNQ29uc2VxdWVuY2U6MDJhYWEzOWEtYWNmMS01YjY0LWJjMjctYmIzYjk3N2EwY2ZhOjc4Nzk0ZTFlLTBkNmEtNTJkNC05ZjQwLTk0MDZiNGYwMWM4YQ==","transcript":{"aa_change":null,"annotation":{"hgvsc":"c.*97delA","polyphen_impact":"","polyphen_score":null,"sift_impact":"","sift_score":null,"vep_impact":"MODIFIER"},"consequence_type":"3_prime_UTR_variant","gene":{"gene_id":"ENSG00000162600","gene_strand":-1,"symbol":"OMA1"},"is_canonical":true,"transcript_id":"ENST00000371226"}}}]}},"cosmic_id":["COSN1106466"],"end_position":58480868,"genomic_dna_change":"chr1:g.58480868delT","id":"U3NtOjAyYWFhMzlhLWFjZjEtNWI2NC1iYzI3LWJiM2I5NzdhMGNmYSM4OWZhZDliOTY5NzZhOGQ5MjM1Y2ExZDBhYTcyMGUwZSM=","mutation_subtype":"Small deletion","mutation_type":"Simple Somatic 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\ No newline at end of file
diff --git a/cypress/integration/ExploreGDC.js b/cypress/integration/ExploreGDC.js
index 5dfd715..c280c4e 100644
--- a/cypress/integration/ExploreGDC.js
+++ b/cypress/integration/ExploreGDC.js
@@ -93,15 +93,15 @@ describe('Explore GDC', function() {
 
     /**
      * Checks that each results tab has the expected information
-     * Assumes donor tab is already selected
-     * @param {*} donorArray array of strings to check for on donor tab
+     * Assumes case tab is already selected
+     * @param {*} caseArray array of strings to check for on case tab
      * @param {*} geneArray array of strings to check for on gene tab
      * @param {*} mutationArray array of strings to check for on mutation tab
      */
-    var checkAllResultsTab = function(donorArray, geneArray, mutationArray) {
+    var checkAllResultsTab = function(caseArray, geneArray, mutationArray) {
         cy.wait(3000) // wait a few seconds for results to load
-        // Validate donor results
-        checkResultsTab(donorArray)
+        // Validate case results
+        checkResultsTab(caseArray)
 
         // Validate gene results
         selectResultsTab(1)
@@ -140,9 +140,9 @@ describe('Explore GDC', function() {
 
         // Add tracks and check that they were added
         cy.get('.dijitTabContainer').eq(1).within(() => {
-            cy.contains('All Genes for Donor').eq(0).click()
-            cy.contains('All Mutations for Donor').eq(0).click()
-            cy.contains('All CNVs for Donor').eq(0).click()
+            cy.contains('All Genes').eq(0).click()
+            cy.contains('All Mutations').eq(0).click()
+            cy.contains('All CNVs').eq(0).click()
         })
 
         closePopup()
diff --git a/cypress/integration/PrimarySites.js b/cypress/integration/PrimarySites.js
index d9426d3..091337f 100644
--- a/cypress/integration/PrimarySites.js
+++ b/cypress/integration/PrimarySites.js
@@ -40,7 +40,7 @@ describe('Primary sites dialog', function() {
     it('Should be able to view primary sites', function() {
         // Open track menu
         cy.get('#dropdownbutton_gdc').type('{enter}')
-        cy.contains('Explore Primary Sites').click()
+        cy.contains('Explore primary sites').click()
 
         cy.wait('@getPrimarySites')
 
@@ -51,13 +51,13 @@ describe('Primary sites dialog', function() {
 
         // Add SSM, Gene, and CNV tracks for primary site bronchus and lung (assume first in list)
         cy.get('#dijit_form_ComboButton_0_arrow').should('be.visible').type('{enter}')
-        cy.contains('Mutations for Primary Site').click()
+        cy.contains('Mutations').click()
 
         cy.get('#dijit_form_ComboButton_0_arrow').should('be.visible').type('{enter}')
-        cy.contains('Genes for Primary Site').click()
+        cy.contains('Genes').click()
 
         cy.get('#dijit_form_ComboButton_0_arrow').should('be.visible').type('{enter}')
-        cy.contains('CNVs for Primary Site').click()
+        cy.contains('CNVs').click()
 
         cy.contains('GDC Primary Site Browser').parent().within(() => {
             cy.get('.dijitDialogCloseIcon').click()
diff --git a/cypress/integration/projects.js b/cypress/integration/projects.js
index 514a3c3..9f11920 100644
--- a/cypress/integration/projects.js
+++ b/cypress/integration/projects.js
@@ -41,7 +41,7 @@ describe('Project dialog', function() {
     it('Should be able to view projects', function() {
         // Open track menu
         cy.get('#dropdownbutton_gdc').type('{enter}')
-        cy.contains('Explore Projects').click()
+        cy.contains('Explore projects').click()
 
         cy.wait('@getProjects')
 
@@ -53,13 +53,13 @@ describe('Project dialog', function() {
         // Add SSM, Gene, and CNV tracks for project FM-AD (assume first in list)
         // Note that even though we select FM-AD, we are mocking TCGA-BRCA
         cy.get('#dijit_form_ComboButton_0_arrow').should('be.visible').type('{enter}')
-        cy.contains('Mutations for Project').click()
+        cy.contains('Mutations').click()
 
         cy.get('#dijit_form_ComboButton_0_arrow').should('be.visible').type('{enter}')
-        cy.contains('Genes for Project').click()
+        cy.contains('Genes').click()
 
         cy.get('#dijit_form_ComboButton_0_arrow').should('be.visible').type('{enter}')
-        cy.contains('CNVs for Project').click()
+        cy.contains('CNVs').click()
 
         cy.contains('GDC Project Browser').parent().within(() => {
             cy.get('.dijitDialogCloseIcon').click()
diff --git a/gdc-viewer/js/View/GDCDialog.js b/gdc-viewer/js/View/GDCDialog.js
index 0b6a81c..fb409eb 100644
--- a/gdc-viewer/js/View/GDCDialog.js
+++ b/gdc-viewer/js/View/GDCDialog.js
@@ -454,7 +454,7 @@ function (
                 // Buttons for SSMs
                 var ssmMenu = new Menu({ style: "display: none;"});
                 var menuItemSSMFiltered = new MenuItem({
-                    label: "Filtered Mutations form GDC",
+                    label: "Filtered Mutations",
                     iconClass: "dijitIconNewTask",
                     onClick: function() {
                         thisB.addTrack('SimpleSomaticMutations', undefined, undefined, combinedFilters, 'gdc-viewer/View/Track/SSMTrack');
@@ -465,7 +465,7 @@ function (
                 ssmMenu.startup();
 
                 var buttonAllSSMs = new ComboButton({
-                    label: "All Mutations from GDC",
+                    label: "All Mutations",
                     iconClass: "dijitIconNewTask",
                     dropDown: ssmMenu,
                     onClick: function() {
@@ -567,7 +567,7 @@ function (
                 // Buttons for Genes
                 var geneMenu = new Menu({ style: "display: none;"});
                 var menuItemGeneFiltered = new MenuItem({
-                    label: "Filtered Genes from GDC",
+                    label: "Filtered Genes",
                     iconClass: "dijitIconNewTask",
                     onClick: function() {
                         thisB.addTrack('Genes', undefined, undefined, combinedFilters, 'gdc-viewer/View/Track/GeneTrack');
@@ -578,7 +578,7 @@ function (
                 geneMenu.startup();
 
                 var buttonAllGenes = new ComboButton({
-                    label: "All Genes from GDC",
+                    label: "All Genes",
                     iconClass: "dijitIconNewTask",
                     dropDown: geneMenu,
                     style: "padding-right: 8px;",
@@ -595,7 +595,7 @@ function (
                 // Buttons for CNVs
                 var cnvMenu = new Menu({ style: "display: none;"});
                 var menuItemCnvFiltered = new MenuItem({
-                    label: "Filtered CNVs from GDC",
+                    label: "Filtered CNVs",
                     iconClass: "dijitIconNewTask",
                     onClick: function() {
                         thisB.addTrack('CNVs', undefined, undefined, combinedFilters, 'gdc-viewer/View/Track/CNVTrack');
@@ -606,7 +606,7 @@ function (
                 cnvMenu.startup();
 
                 var buttonAllCnvs = new ComboButton({
-                    label: "All CNVs from GDC",
+                    label: "All CNVs",
                     iconClass: "dijitIconNewTask",
                     dropDown: cnvMenu,
                     onClick: function() {
@@ -691,7 +691,7 @@ function (
 
                 var casesExplanation = dom.create('div', { innerHTML: "Add mutation, gene, and CNV tracks for a given case. Optionally apply the selected filters when adding tracks.", style: "font-size: 14px; margin-bottom: 5px; padding: 5px;" }, thisB.caseResultsTab.containerNode);
                 var resultsInfo = dom.create('div', { innerHTML: "Showing " + startResultCount.toLocaleString() + " to " + endResultCount.toLocaleString() + " of " + totalCases.toLocaleString() }, thisB.caseResultsTab.containerNode);
-                thisB.createDonorsTable(response, thisB.caseResultsTab.containerNode);
+                thisB.createCasesTable(response, thisB.caseResultsTab.containerNode);
                 thisB.createPaginationButtons(thisB.caseResultsTab.containerNode, totalCases / thisB.pageSize, 'case', thisB.casePage);
             }).catch(function(err) {
                 console.log(err);
@@ -704,7 +704,7 @@ function (
          * @param {object} response the response from the GDC graphQL query
          * @param {object} location dom element to place the table
          */
-        createDonorsTable: function(response, location) {
+        createCasesTable: function(response, location) {
             var thisB = this;
             var table = `<table class="results-table"></table>`;
             var tableNode = dom.toDom(table);
@@ -749,7 +749,7 @@ function (
                     // Gene Buttons
                     var geneMenu = new Menu({ style: "display: none;"});
                     var menuItemGeneFiltered = new MenuItem({
-                        label: "Filtered Genes for Donor",
+                        label: "Filtered Genes",
                         iconClass: "dijitIconNewTask",
                         onClick: (function(hit, combinedFilters) {
                             return function() {
@@ -762,7 +762,7 @@ function (
                     geneMenu.startup();
 
                     var buttonAllGenes = new ComboButton({
-                        label: "All Genes for Donor",
+                        label: "All Genes",
                         iconClass: "dijitIconNewTask",
                         dropDown: geneMenu,
                         onClick: (function(hit) {
@@ -774,8 +774,8 @@ function (
                     });
                     buttonAllGenes.placeAt(geneButtonNode);
                     buttonAllGenes.startup();
-                    thisB.addTooltipToButton(menuItemGeneFiltered, "Add track with all genes for the given donor, with current filters applied");
-                    thisB.addTooltipToButton(buttonAllGenes, "Add track with all genes for the given donor");
+                    thisB.addTooltipToButton(menuItemGeneFiltered, "Add track with all genes for the given case, with current filters applied");
+                    thisB.addTooltipToButton(buttonAllGenes, "Add track with all genes for the given case");
 
                     // Place buttons in table
                     dom.place(geneButtonNode, caseRowContentNode);
@@ -786,7 +786,7 @@ function (
                     // SSM Buttons
                     var ssmMenu = new Menu({ style: "display: none;"});
                     var menuItemSsmFiltered = new MenuItem({
-                        label: "Filtered Mutations for Donor",
+                        label: "Filtered Mutations",
                         iconClass: "dijitIconNewTask",
                         onClick: (function(hit, combinedFilters) {
                             return function() {
@@ -799,7 +799,7 @@ function (
                     ssmMenu.startup();
 
                     var buttonAllSsms = new ComboButton({
-                        label: "All Mutations for Donor",
+                        label: "All Mutations",
                         iconClass: "dijitIconNewTask",
                         dropDown: ssmMenu,
                         onClick: (function(hit) {
@@ -811,8 +811,8 @@ function (
                     });
                     buttonAllSsms.placeAt(ssmButtonNode);
                     buttonAllSsms.startup();
-                    thisB.addTooltipToButton(menuItemSsmFiltered, "Add track with all Mutations for the given donor, with current filters applied");
-                    thisB.addTooltipToButton(buttonAllSsms, "Add track with all Mutations for the given donor");
+                    thisB.addTooltipToButton(menuItemSsmFiltered, "Add track with all Mutations for the given case, with current filters applied");
+                    thisB.addTooltipToButton(buttonAllSsms, "Add track with all Mutations for the given case");
 
                     // Place buttons in table
                     dom.place(ssmButtonNode, caseRowContentNode);
@@ -823,7 +823,7 @@ function (
                     // CNV Buttons
                     var cnvMenu = new Menu({ style: "display: none;"});
                     var menuItemCnvFiltered = new MenuItem({
-                        label: "Filtered CNVs for Donor",
+                        label: "Filtered CNVs",
                         iconClass: "dijitIconNewTask",
                         onClick: (function(hit, combinedFilters) {
                             return function() {
@@ -836,7 +836,7 @@ function (
                     cnvMenu.startup();
 
                     var buttonAllCnvs = new ComboButton({
-                        label: "All CNVs for Donor",
+                        label: "All CNVs",
                         iconClass: "dijitIconNewTask",
                         dropDown: cnvMenu,
                         onClick: (function(hit) {
@@ -848,8 +848,8 @@ function (
                     });
                     buttonAllCnvs.placeAt(cnvButtonNode);
                     buttonAllCnvs.startup();
-                    thisB.addTooltipToButton(menuItemCnvFiltered, "Add track with all CNVs for the given donor, with current filters applied");
-                    thisB.addTooltipToButton(buttonAllCnvs, "Add track with all CNVs for the given donor");
+                    thisB.addTooltipToButton(menuItemCnvFiltered, "Add track with all CNVs for the given case, with current filters applied");
+                    thisB.addTooltipToButton(buttonAllCnvs, "Add track with all CNVs for the given case");
 
                     // Place buttons in table
                     dom.place(cnvButtonNode, caseRowContentNode);
diff --git a/gdc-viewer/js/View/GDCPrimarySitesDialog.js b/gdc-viewer/js/View/GDCPrimarySitesDialog.js
index 0845ce8..c52b777 100644
--- a/gdc-viewer/js/View/GDCPrimarySitesDialog.js
+++ b/gdc-viewer/js/View/GDCPrimarySitesDialog.js
@@ -144,7 +144,7 @@ function (
                     var geneMenu = new Menu({ style: "display: none;"});
 
                     var menuItemSSM = new MenuItem({
-                        label: "Mutations for Primary Site",
+                        label: "Mutations",
                         iconClass: "dijitIconNewTask",
                         onClick: (function(hit) {
                             return function() {
@@ -156,7 +156,7 @@ function (
                     geneMenu.addChild(menuItemSSM);
 
                     var menuItemGene = new MenuItem({
-                        label: "Genes for Primary Site",
+                        label: "Genes",
                         iconClass: "dijitIconNewTask",
                         onClick: (function(hit) {
                             return function() {
@@ -168,7 +168,7 @@ function (
                     geneMenu.addChild(menuItemGene);
 
                     var menuItemCNV = new MenuItem({
-                        label: "CNVs for Primary Site",
+                        label: "CNVs",
                         iconClass: "dijitIconNewTask",
                         onClick: (function(hit) {
                             return function() {
diff --git a/gdc-viewer/js/View/GDCProjectDialog.js b/gdc-viewer/js/View/GDCProjectDialog.js
index 8a3a18b..e3df1ef 100644
--- a/gdc-viewer/js/View/GDCProjectDialog.js
+++ b/gdc-viewer/js/View/GDCProjectDialog.js
@@ -166,7 +166,7 @@ function (
                     var geneMenu = new Menu({ style: "display: none;"});
 
                     var menuItemSSM = new MenuItem({
-                        label: "Mutations for Project",
+                        label: "Mutations",
                         iconClass: "dijitIconNewTask",
                         onClick: (function(hit) {
                             return function() {
@@ -178,7 +178,7 @@ function (
                     geneMenu.addChild(menuItemSSM);
 
                     var menuItemGene = new MenuItem({
-                        label: "Genes for Project",
+                        label: "Genes",
                         iconClass: "dijitIconNewTask",
                         onClick: (function(hit) {
                             return function() {
@@ -190,7 +190,7 @@ function (
                     geneMenu.addChild(menuItemGene);
 
                     var menuItemCNV = new MenuItem({
-                        label: "CNVs for Project",
+                        label: "CNVs",
                         iconClass: "dijitIconNewTask",
                         onClick: (function(hit) {
                             return function() {
diff --git a/gdc-viewer/js/main.js b/gdc-viewer/js/main.js
index 01ef9d5..9fe0321 100644
--- a/gdc-viewer/js/main.js
+++ b/gdc-viewer/js/main.js
@@ -28,13 +28,13 @@ return declare( JBrowsePlugin,
                 }));
             this.browser.addGlobalMenuItem('gdc', new MenuItem(
                 {
-                    label: 'Explore Projects',
+                    label: 'Explore projects',
                     iconClass: "dijitIconSearch",
                     onClick: lang.hitch(this, 'createGDCProject')
                 }));
             this.browser.addGlobalMenuItem('gdc', new MenuItem(
                 {
-                    label: 'Explore Primary Sites',
+                    label: 'Explore primary sites',
                     iconClass: "dijitIconSearch",
                     onClick: lang.hitch(this, 'createGDCPrimarySites')
                 }));

From 6fe15290354034e53e079c958e8d23fdf800ae43 Mon Sep 17 00:00:00 2001
From: Andrew Duncan <andrew.duncan@oicr.on.ca>
Date: Tue, 11 Feb 2020 10:51:59 -0500
Subject: [PATCH 21/28] increase subheader font

---
 gdc-viewer/js/View/GDCDialog.js | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gdc-viewer/js/View/GDCDialog.js b/gdc-viewer/js/View/GDCDialog.js
index fb409eb..20bbdf4 100644
--- a/gdc-viewer/js/View/GDCDialog.js
+++ b/gdc-viewer/js/View/GDCDialog.js
@@ -449,7 +449,7 @@ function (
                 }
                 dom.empty(thisB.mutationResultsTab.containerNode);
 
-                var ssmExplanation = dom.create('div', { innerHTML: "Add mutation tracks for all cases across the GDC. Optionally apply the selected filters when adding tracks.", style: "font-size: 14px; margin-bottom: 5px; padding: 5px;" }, thisB.mutationResultsTab.containerNode);
+                var ssmExplanation = dom.create('div', { innerHTML: "Add mutation tracks for all mutations available on the GDC portal. Optionally apply the selected filters when adding tracks.", style: "font-size: 14px; margin-bottom: 5px; padding: 5px;" }, thisB.mutationResultsTab.containerNode);
 
                 // Buttons for SSMs
                 var ssmMenu = new Menu({ style: "display: none;"});
@@ -562,7 +562,7 @@ function (
                     combinedFilters = JSON.parse(combinedFilters);
                 }
 
-                var geneExplanation = dom.create('div', { innerHTML: "Add gene and CNV tracks for all cases across the GDC. Optionally apply the selected filters when adding tracks.", style: "font-size: 14px; margin-bottom: 5px; padding: 5px;" }, thisB.geneResultsTab.containerNode);
+                var geneExplanation = dom.create('div', { innerHTML: "Add gene and CNV tracks for all genes available on the GDC portal. Optionally apply the selected filters when adding tracks.", style: "font-size: 14px; margin-bottom: 5px; padding: 5px;" }, thisB.geneResultsTab.containerNode);
 
                 // Buttons for Genes
                 var geneMenu = new Menu({ style: "display: none;"});

From 4e5a5c365a0267c36ad573d271c0473871e1efef Mon Sep 17 00:00:00 2001
From: Andrew Duncan <andrew.duncan@oicr.on.ca>
Date: Tue, 11 Feb 2020 15:17:09 -0500
Subject: [PATCH 22/28] fix tests

---
 cypress/integration/PrimarySites.js         | 6 +++---
 cypress/integration/projects.js             | 6 +++---
 gdc-viewer/js/View/GDCPrimarySitesDialog.js | 6 +++---
 gdc-viewer/js/View/GDCProjectDialog.js      | 6 +++---
 4 files changed, 12 insertions(+), 12 deletions(-)

diff --git a/cypress/integration/PrimarySites.js b/cypress/integration/PrimarySites.js
index 091337f..3ddbef5 100644
--- a/cypress/integration/PrimarySites.js
+++ b/cypress/integration/PrimarySites.js
@@ -51,13 +51,13 @@ describe('Primary sites dialog', function() {
 
         // Add SSM, Gene, and CNV tracks for primary site bronchus and lung (assume first in list)
         cy.get('#dijit_form_ComboButton_0_arrow').should('be.visible').type('{enter}')
-        cy.contains('Mutations').click()
+        cy.contains('All Mutations').click()
 
         cy.get('#dijit_form_ComboButton_0_arrow').should('be.visible').type('{enter}')
-        cy.contains('Genes').click()
+        cy.contains('All Genes').click()
 
         cy.get('#dijit_form_ComboButton_0_arrow').should('be.visible').type('{enter}')
-        cy.contains('CNVs').click()
+        cy.contains('All CNVs').click()
 
         cy.contains('GDC Primary Site Browser').parent().within(() => {
             cy.get('.dijitDialogCloseIcon').click()
diff --git a/cypress/integration/projects.js b/cypress/integration/projects.js
index 9f11920..23b0455 100644
--- a/cypress/integration/projects.js
+++ b/cypress/integration/projects.js
@@ -53,13 +53,13 @@ describe('Project dialog', function() {
         // Add SSM, Gene, and CNV tracks for project FM-AD (assume first in list)
         // Note that even though we select FM-AD, we are mocking TCGA-BRCA
         cy.get('#dijit_form_ComboButton_0_arrow').should('be.visible').type('{enter}')
-        cy.contains('Mutations').click()
+        cy.contains('All Mutations').click()
 
         cy.get('#dijit_form_ComboButton_0_arrow').should('be.visible').type('{enter}')
-        cy.contains('Genes').click()
+        cy.contains('All Genes').click()
 
         cy.get('#dijit_form_ComboButton_0_arrow').should('be.visible').type('{enter}')
-        cy.contains('CNVs').click()
+        cy.contains('All CNVs').click()
 
         cy.contains('GDC Project Browser').parent().within(() => {
             cy.get('.dijitDialogCloseIcon').click()
diff --git a/gdc-viewer/js/View/GDCPrimarySitesDialog.js b/gdc-viewer/js/View/GDCPrimarySitesDialog.js
index c52b777..55b0581 100644
--- a/gdc-viewer/js/View/GDCPrimarySitesDialog.js
+++ b/gdc-viewer/js/View/GDCPrimarySitesDialog.js
@@ -144,7 +144,7 @@ function (
                     var geneMenu = new Menu({ style: "display: none;"});
 
                     var menuItemSSM = new MenuItem({
-                        label: "Mutations",
+                        label: "All Mutations",
                         iconClass: "dijitIconNewTask",
                         onClick: (function(hit) {
                             return function() {
@@ -156,7 +156,7 @@ function (
                     geneMenu.addChild(menuItemSSM);
 
                     var menuItemGene = new MenuItem({
-                        label: "Genes",
+                        label: "All Genes",
                         iconClass: "dijitIconNewTask",
                         onClick: (function(hit) {
                             return function() {
@@ -168,7 +168,7 @@ function (
                     geneMenu.addChild(menuItemGene);
 
                     var menuItemCNV = new MenuItem({
-                        label: "CNVs",
+                        label: "All CNVs",
                         iconClass: "dijitIconNewTask",
                         onClick: (function(hit) {
                             return function() {
diff --git a/gdc-viewer/js/View/GDCProjectDialog.js b/gdc-viewer/js/View/GDCProjectDialog.js
index e3df1ef..509f874 100644
--- a/gdc-viewer/js/View/GDCProjectDialog.js
+++ b/gdc-viewer/js/View/GDCProjectDialog.js
@@ -166,7 +166,7 @@ function (
                     var geneMenu = new Menu({ style: "display: none;"});
 
                     var menuItemSSM = new MenuItem({
-                        label: "Mutations",
+                        label: "All Mutations",
                         iconClass: "dijitIconNewTask",
                         onClick: (function(hit) {
                             return function() {
@@ -178,7 +178,7 @@ function (
                     geneMenu.addChild(menuItemSSM);
 
                     var menuItemGene = new MenuItem({
-                        label: "Genes",
+                        label: "All Genes",
                         iconClass: "dijitIconNewTask",
                         onClick: (function(hit) {
                             return function() {
@@ -190,7 +190,7 @@ function (
                     geneMenu.addChild(menuItemGene);
 
                     var menuItemCNV = new MenuItem({
-                        label: "CNVs",
+                        label: "All CNVs",
                         iconClass: "dijitIconNewTask",
                         onClick: (function(hit) {
                             return function() {

From 34eeff3d9670aee5259d8a37d949333efdebe4df Mon Sep 17 00:00:00 2001
From: Andrew Duncan <andrew.duncan@oicr.on.ca>
Date: Fri, 14 Feb 2020 14:54:25 -0500
Subject: [PATCH 23/28] projects table for gene and ssm feature use only one
 graphql call

---
 gdc-viewer/js/Model/GeneFeature.js | 42 +++++++++++-------------------
 gdc-viewer/js/Model/SSMFeature.js  | 30 +++++++--------------
 2 files changed, 24 insertions(+), 48 deletions(-)

diff --git a/gdc-viewer/js/Model/GeneFeature.js b/gdc-viewer/js/Model/GeneFeature.js
index e9d8bd5..359f4ff 100644
--- a/gdc-viewer/js/Model/GeneFeature.js
+++ b/gdc-viewer/js/Model/GeneFeature.js
@@ -19,41 +19,29 @@ get: function(name) {
     var thisB = this;
     if (name == 'projects') {
         var geneId = this.data[name.toLowerCase()];
-        var bodyValProjects = {
-            query: `query projectData( $count: Int ) { projectsViewer: viewer { projects { hits(first: $count) { edges { node { primary_site disease_type project_id id } } } } } }`,
+
+        var bodyValProjectsTable = {
+            query: `query ProjectTable( $caseAggsFilters: FiltersArgument $ssmTested: FiltersArgument $cnvGain: FiltersArgument $cnvLoss: FiltersArgument $cnvTested: FiltersArgument $cnvTestedByGene: FiltersArgument $cnvAll: FiltersArgument $ssmFilters: FiltersArgument $projectCount: Int ) { viewer { explore { ssms { hits(first: 0, filters: $ssmFilters) { total } } cases { cnvAll: hits(filters: $cnvAll) { total } cnvTestedByGene: hits(filters: $cnvTestedByGene) { total } gain: aggregations(filters: $cnvGain) { project__project_id { buckets { doc_count key } } } loss: aggregations(filters: $cnvLoss) { project__project_id { buckets { doc_count key } } } cnvTotal: aggregations(filters: $cnvTested) { project__project_id { buckets { doc_count key } } } filtered: aggregations(filters: $caseAggsFilters) { project__project_id { buckets { doc_count key } } } total: aggregations(filters: $ssmTested) { project__project_id { buckets { doc_count key } } } } } } projects { hits(first: $projectCount) { edges { node { primary_site disease_type project_id id } } } } }`,
             variables: {
-                "count": 100
+                "caseAggsFilters": { "op": "and", "content": [ { "op": "in", "content": { "field": "cases.available_variation_data", "value": [ "ssm" ] } }, { "op": "NOT", "content": { "field": "cases.gene.ssm.observation.observation_id", "value": "MISSING" } }, { "op": "in", "content": { "field": "genes.gene_id", "value": [ geneId ] } } ] },
+                "ssmTested": { "op": "and", "content": [ { "op": "in", "content": { "field": "cases.available_variation_data", "value": [ "ssm" ] } } ] },
+                "cnvGain": { "op": "and", "content": [ { "op": "in", "content": { "field": "cases.available_variation_data", "value": [ "cnv" ] } }, { "op": "in", "content": { "field": "cnvs.cnv_change", "value": [ "Gain" ] } }, { "op": "in", "content": { "field": "genes.gene_id", "value": [ geneId ] } } ] },
+                "cnvLoss": { "op": "and", "content": [ { "op": "in", "content": { "field": "cases.available_variation_data", "value": [ "cnv" ] } }, { "op": "in", "content": { "field": "cnvs.cnv_change", "value": [ "Loss" ] } }, { "op": "in", "content": { "field": "genes.gene_id", "value": [ geneId ] } } ] },
+                "cnvTested": { "op": "and", "content": [ { "op": "in", "content": { "field": "cases.available_variation_data", "value": [ "cnv" ] } } ] },
+                "cnvTestedByGene": { "op": "and", "content": [ { "op": "in", "content": { "field": "cases.available_variation_data", "value": [ "cnv" ] } }, { "op": "in", "content": { "field": "genes.gene_id", "value": [ geneId ] } } ] },
+                "cnvAll": { "op": "and", "content": [ { "op": "in", "content": { "field": "cases.available_variation_data", "value": [ "cnv" ] } }, { "op": "in", "content": { "field": "cnvs.cnv_change", "value": [ "Gain", "Loss" ] } }, { "op": "in", "content": { "field": "genes.gene_id", "value": [ geneId ] } } ] },
+                "ssmFilters": { "op": "and", "content": [ { "op": "in", "content": { "field": "cases.available_variation_data", "value": [ "ssm" ] } }, { "op": "in", "content": { "field": "genes.gene_id", "value": [ geneId ] } } ] },
+                "projectCount": 100
             }
         }
-        fetch('https://api.gdc.cancer.gov/v0/graphql/gene-projects', {
+        fetch('https://api.gdc.cancer.gov/v0/graphql/projectsTable', {
             method: 'post',
             headers: { 'X-Requested-With': null },
-            body: JSON.stringify(bodyValProjects)
-        }).then(function(response) {
-            return(response.json());
-        }).then(function(response) {
-            thisB.projects = response.data.projectsViewer.projects.hits.edges;
-            var bodyValProjectsTable = {
-                query: `query ProjectTable( $caseAggsFilters: FiltersArgument $ssmTested: FiltersArgument $cnvGain: FiltersArgument $cnvLoss: FiltersArgument $cnvTested: FiltersArgument $cnvTestedByGene: FiltersArgument $cnvAll: FiltersArgument $ssmFilters: FiltersArgument ) { viewer { explore { ssms { hits(first: 0, filters: $ssmFilters) { total } } cases { cnvAll: hits(filters: $cnvAll) { total } cnvTestedByGene: hits(filters: $cnvTestedByGene) { total } gain: aggregations(filters: $cnvGain) { project__project_id { buckets { doc_count key } } } loss: aggregations(filters: $cnvLoss) { project__project_id { buckets { doc_count key } } } cnvTotal: aggregations(filters: $cnvTested) { project__project_id { buckets { doc_count key } } } filtered: aggregations(filters: $caseAggsFilters) { project__project_id { buckets { doc_count key } } } total: aggregations(filters: $ssmTested) { project__project_id { buckets { doc_count key } } } } } } }`,
-                variables: {
-                    "caseAggsFilters": { "op": "and", "content": [ { "op": "in", "content": { "field": "cases.available_variation_data", "value": [ "ssm" ] } }, { "op": "NOT", "content": { "field": "cases.gene.ssm.observation.observation_id", "value": "MISSING" } }, { "op": "in", "content": { "field": "genes.gene_id", "value": [ geneId ] } } ] },
-                    "ssmTested": { "op": "and", "content": [ { "op": "in", "content": { "field": "cases.available_variation_data", "value": [ "ssm" ] } } ] },
-                    "cnvGain": { "op": "and", "content": [ { "op": "in", "content": { "field": "cases.available_variation_data", "value": [ "cnv" ] } }, { "op": "in", "content": { "field": "cnvs.cnv_change", "value": [ "Gain" ] } }, { "op": "in", "content": { "field": "genes.gene_id", "value": [ geneId ] } } ] },
-                    "cnvLoss": { "op": "and", "content": [ { "op": "in", "content": { "field": "cases.available_variation_data", "value": [ "cnv" ] } }, { "op": "in", "content": { "field": "cnvs.cnv_change", "value": [ "Loss" ] } }, { "op": "in", "content": { "field": "genes.gene_id", "value": [ geneId ] } } ] },
-                    "cnvTested": { "op": "and", "content": [ { "op": "in", "content": { "field": "cases.available_variation_data", "value": [ "cnv" ] } } ] },
-                    "cnvTestedByGene": { "op": "and", "content": [ { "op": "in", "content": { "field": "cases.available_variation_data", "value": [ "cnv" ] } }, { "op": "in", "content": { "field": "genes.gene_id", "value": [ geneId ] } } ] },
-                    "cnvAll": { "op": "and", "content": [ { "op": "in", "content": { "field": "cases.available_variation_data", "value": [ "cnv" ] } }, { "op": "in", "content": { "field": "cnvs.cnv_change", "value": [ "Gain", "Loss" ] } }, { "op": "in", "content": { "field": "genes.gene_id", "value": [ geneId ] } } ] },
-                    "ssmFilters": { "op": "and", "content": [ { "op": "in", "content": { "field": "cases.available_variation_data", "value": [ "ssm" ] } }, { "op": "in", "content": { "field": "genes.gene_id", "value": [ geneId ] } } ] }
-                }
-            }
-            return fetch('https://api.gdc.cancer.gov/v0/graphql/projectsTable', {
-                method: 'post',
-                headers: { 'X-Requested-With': null },
-                body: JSON.stringify(bodyValProjectsTable)
-            })
+            body: JSON.stringify(bodyValProjectsTable)
         }).then(function(response) {
             return(response.json());
         }).then(function(response) {
+            thisB.projects = response.data.projects.hits.edges;
             document.getElementsByClassName('value projects')[0].innerHTML = thisB.createProjectTable(response);
         }).catch(function(err) {
             document.getElementsByClassName('value projects')[0].innerHTML = 'Error creating projects table';
diff --git a/gdc-viewer/js/Model/SSMFeature.js b/gdc-viewer/js/Model/SSMFeature.js
index 9165b06..af04f03 100644
--- a/gdc-viewer/js/Model/SSMFeature.js
+++ b/gdc-viewer/js/Model/SSMFeature.js
@@ -19,35 +19,23 @@ get: function(name) {
     var thisB = this;
     if (name == 'projects') {
         var mutationId = this.data[name.toLowerCase()];
-        var bodyValProjects = {
-            query: `query projectData( $count: Int ) { projectsViewer: viewer { projects { hits(first: $count) { edges { node { primary_site disease_type project_id id } } } } } }`,
+
+        var bodyValProjectsTable = {
+            query: `query projectsTable($ssmTested: FiltersArgument, $caseAggsFilter: FiltersArgument, $projectCount: Int) { viewer { explore { cases { filtered: aggregations(filters: $caseAggsFilter) { project__project_id { buckets { doc_count key } } } total: aggregations(filters: $ssmTested) { project__project_id { buckets { doc_count key } } } } } } projects { hits(first: $projectCount) { edges { node { primary_site disease_type project_id id } } } } }`,
             variables: {
-                "count": 100
+                "ssmTested": { "op":"and", "content":[ { "op":"in", "content":{ "field":"cases.available_variation_data", "value":[ "ssm" ] } } ] } ,
+                "caseAggsFilter": { "op":"and", "content":[ { "op":"in", "content":{ "field":"ssms.ssm_id", "value":[ mutationId ] } }, { "op":"in", "content":{ "field":"cases.available_variation_data", "value":[ "ssm" ] } } ] },
+                "projectCount": 100
             }
         }
-        fetch('https://api.gdc.cancer.gov/v0/graphql/ssm-projects', {
+            fetch('https://api.gdc.cancer.gov/v0/graphql/projectsTable', {
             method: 'post',
             headers: { 'X-Requested-With': null },
-            body: JSON.stringify(bodyValProjects)
-        }).then(function(response) {
-            return(response.json());
-        }).then(function(response) {
-            thisB.projects = response.data.projectsViewer.projects.hits.edges;
-            var bodyValProjectsTable = {
-                query: `query projectsTable($ssmTested: FiltersArgument, $caseAggsFilter: FiltersArgument) { viewer { explore { cases { filtered: aggregations(filters: $caseAggsFilter) { project__project_id { buckets { doc_count key } } } total: aggregations(filters: $ssmTested) { project__project_id { buckets { doc_count key } } } } } } }`,
-                variables: {
-                    "ssmTested": { "op":"and", "content":[ { "op":"in", "content":{ "field":"cases.available_variation_data", "value":[ "ssm" ] } } ] } ,
-                    "caseAggsFilter": { "op":"and", "content":[ { "op":"in", "content":{ "field":"ssms.ssm_id", "value":[ mutationId ] } }, { "op":"in", "content":{ "field":"cases.available_variation_data", "value":[ "ssm" ] } } ] }
-                }
-            }
-            return fetch('https://api.gdc.cancer.gov/v0/graphql/projectsTable', {
-                method: 'post',
-                headers: { 'X-Requested-With': null },
-                body: JSON.stringify(bodyValProjectsTable)
-            })
+            body: JSON.stringify(bodyValProjectsTable)
         }).then(function(response) {
             return(response.json());
         }).then(function(response) {
+            thisB.projects = response.data.projects.hits.edges;
             document.getElementsByClassName('value projects')[0].innerHTML = thisB.createProjectTable(response);
         }).catch(function(err) {
             document.getElementsByClassName('value projects')[0].innerHTML = 'Error creating projects table';

From 371ec8bdee4a81490f2e388446eae7d9e9339778 Mon Sep 17 00:00:00 2001
From: Andrew Duncan <andrew.duncan@oicr.on.ca>
Date: Tue, 18 Feb 2020 11:38:37 -0500
Subject: [PATCH 24/28] simplified graphql call

---
 gdc-viewer/js/Model/GeneFeature.js | 5 +----
 1 file changed, 1 insertion(+), 4 deletions(-)

diff --git a/gdc-viewer/js/Model/GeneFeature.js b/gdc-viewer/js/Model/GeneFeature.js
index 359f4ff..82011d2 100644
--- a/gdc-viewer/js/Model/GeneFeature.js
+++ b/gdc-viewer/js/Model/GeneFeature.js
@@ -21,16 +21,13 @@ get: function(name) {
         var geneId = this.data[name.toLowerCase()];
 
         var bodyValProjectsTable = {
-            query: `query ProjectTable( $caseAggsFilters: FiltersArgument $ssmTested: FiltersArgument $cnvGain: FiltersArgument $cnvLoss: FiltersArgument $cnvTested: FiltersArgument $cnvTestedByGene: FiltersArgument $cnvAll: FiltersArgument $ssmFilters: FiltersArgument $projectCount: Int ) { viewer { explore { ssms { hits(first: 0, filters: $ssmFilters) { total } } cases { cnvAll: hits(filters: $cnvAll) { total } cnvTestedByGene: hits(filters: $cnvTestedByGene) { total } gain: aggregations(filters: $cnvGain) { project__project_id { buckets { doc_count key } } } loss: aggregations(filters: $cnvLoss) { project__project_id { buckets { doc_count key } } } cnvTotal: aggregations(filters: $cnvTested) { project__project_id { buckets { doc_count key } } } filtered: aggregations(filters: $caseAggsFilters) { project__project_id { buckets { doc_count key } } } total: aggregations(filters: $ssmTested) { project__project_id { buckets { doc_count key } } } } } } projects { hits(first: $projectCount) { edges { node { primary_site disease_type project_id id } } } } }`,
+            query: `query ProjectTable( $caseAggsFilters: FiltersArgument $ssmTested: FiltersArgument $cnvGain: FiltersArgument $cnvLoss: FiltersArgument $cnvTested: FiltersArgument $projectCount: Int ) { viewer { explore { cases { gain: aggregations(filters: $cnvGain) { project__project_id { buckets { doc_count key } } } loss: aggregations(filters: $cnvLoss) { project__project_id { buckets { doc_count key } } } cnvTotal: aggregations(filters: $cnvTested) { project__project_id { buckets { doc_count key } } } filtered: aggregations(filters: $caseAggsFilters) { project__project_id { buckets { doc_count key } } } total: aggregations(filters: $ssmTested) { project__project_id { buckets { doc_count key } } } } } } projects { hits(first: $projectCount) { edges { node { primary_site disease_type project_id id } } } } }`,
             variables: {
                 "caseAggsFilters": { "op": "and", "content": [ { "op": "in", "content": { "field": "cases.available_variation_data", "value": [ "ssm" ] } }, { "op": "NOT", "content": { "field": "cases.gene.ssm.observation.observation_id", "value": "MISSING" } }, { "op": "in", "content": { "field": "genes.gene_id", "value": [ geneId ] } } ] },
                 "ssmTested": { "op": "and", "content": [ { "op": "in", "content": { "field": "cases.available_variation_data", "value": [ "ssm" ] } } ] },
                 "cnvGain": { "op": "and", "content": [ { "op": "in", "content": { "field": "cases.available_variation_data", "value": [ "cnv" ] } }, { "op": "in", "content": { "field": "cnvs.cnv_change", "value": [ "Gain" ] } }, { "op": "in", "content": { "field": "genes.gene_id", "value": [ geneId ] } } ] },
                 "cnvLoss": { "op": "and", "content": [ { "op": "in", "content": { "field": "cases.available_variation_data", "value": [ "cnv" ] } }, { "op": "in", "content": { "field": "cnvs.cnv_change", "value": [ "Loss" ] } }, { "op": "in", "content": { "field": "genes.gene_id", "value": [ geneId ] } } ] },
                 "cnvTested": { "op": "and", "content": [ { "op": "in", "content": { "field": "cases.available_variation_data", "value": [ "cnv" ] } } ] },
-                "cnvTestedByGene": { "op": "and", "content": [ { "op": "in", "content": { "field": "cases.available_variation_data", "value": [ "cnv" ] } }, { "op": "in", "content": { "field": "genes.gene_id", "value": [ geneId ] } } ] },
-                "cnvAll": { "op": "and", "content": [ { "op": "in", "content": { "field": "cases.available_variation_data", "value": [ "cnv" ] } }, { "op": "in", "content": { "field": "cnvs.cnv_change", "value": [ "Gain", "Loss" ] } }, { "op": "in", "content": { "field": "genes.gene_id", "value": [ geneId ] } } ] },
-                "ssmFilters": { "op": "and", "content": [ { "op": "in", "content": { "field": "cases.available_variation_data", "value": [ "ssm" ] } }, { "op": "in", "content": { "field": "genes.gene_id", "value": [ geneId ] } } ] },
                 "projectCount": 100
             }
         }

From d54b280ad58f653f27ac2e83ba7e57c9ee061323 Mon Sep 17 00:00:00 2001
From: Andrew Duncan <andrew.duncan@oicr.on.ca>
Date: Tue, 25 Feb 2020 10:48:53 -0500
Subject: [PATCH 25/28] small changes to same track

---
 README.md                               | 6 +++---
 gdc-viewer/js/View/Track/CommonTrack.js | 4 ++--
 2 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/README.md b/README.md
index 5d9c159..9519f29 100644
--- a/README.md
+++ b/README.md
@@ -87,7 +87,7 @@ You can apply filters to the track too, in the same format as GDC. The below exa
 { 
    "op":"!=",
    "content":{ 
-      "field":"cases.biotype",
+      "field":"genes.biotype",
       "value":"protein_coding"
    }
 }
@@ -95,7 +95,7 @@ You can apply filters to the track too, in the same format as GDC. The below exa
 
 To put it in the track config you may want to minimize it as such:
 ```
-filters={"op":"!=","content":{"field":"cases.biotype","value":"protein_coding"}}
+filters={"op":"!=","content":{"field":"genes.biotype","value":"protein_coding"}}
 ```
 
 Example Track:
@@ -105,7 +105,7 @@ storeClass=gdc-viewer/Store/SeqFeature/Genes
 type=JBrowse/View/Track/GeneTrack
 key=GDC Genes
 metadata.datatype=Gene
-filters={"op":"!=","content":{"field":"cases.biotype","value":"protein_coding"}}
+filters={"op":"!=","content":{"field":"genes.biotype","value":"protein_coding"}}
 ```
 
 ![GDC Genes](images/GDC-genes-protein-coding.png)
diff --git a/gdc-viewer/js/View/Track/CommonTrack.js b/gdc-viewer/js/View/Track/CommonTrack.js
index e91c59e..9438a11 100644
--- a/gdc-viewer/js/View/Track/CommonTrack.js
+++ b/gdc-viewer/js/View/Track/CommonTrack.js
@@ -178,7 +178,7 @@ define(
         // Create text area with shareable link
         var textArea = domConstruct.create(
             'textarea',{
-                rows: 1,
+                rows: 3,
                 value: shareableLink,
                 style: "width: 80%",
                 readOnly: true
@@ -192,5 +192,5 @@ define(
         return details;
     }
    }); 
-   }   
+   } 
 );
\ No newline at end of file

From b0ccc11b115d4659d7cff8ff8c74475d11db34f3 Mon Sep 17 00:00:00 2001
From: Andrew Duncan <andrew.duncan@oicr.on.ca>
Date: Tue, 25 Feb 2020 11:19:24 -0500
Subject: [PATCH 26/28] fix tests

---
 cypress/fixtures/ExportGenes/GeneProjects.json    |  1 -
 cypress/fixtures/ExportGenes/ProjectTable.json    |  2 +-
 cypress/fixtures/ExportSSMs/ProjectTable.json     |  2 +-
 cypress/fixtures/ExportSSMs/SSMProjects.json      |  1 -
 cypress/fixtures/projects/gene-projects.json      |  1 -
 cypress/fixtures/projects/mutation-projects.json  |  1 -
 cypress/fixtures/projects/project-table-gene.json |  2 +-
 cypress/fixtures/projects/project-table.json      |  2 +-
 cypress/integration/ExportGeneTrack.js            | 11 ++---------
 cypress/integration/ExportSSMTrack.js             |  9 +--------
 cypress/integration/projects.js                   | 14 --------------
 11 files changed, 7 insertions(+), 39 deletions(-)
 delete mode 100644 cypress/fixtures/ExportGenes/GeneProjects.json
 delete mode 100644 cypress/fixtures/ExportSSMs/SSMProjects.json
 delete mode 100644 cypress/fixtures/projects/gene-projects.json
 delete mode 100644 cypress/fixtures/projects/mutation-projects.json

diff --git a/cypress/fixtures/ExportGenes/GeneProjects.json b/cypress/fixtures/ExportGenes/GeneProjects.json
deleted file mode 100644
index 93b1c29..0000000
--- a/cypress/fixtures/ExportGenes/GeneProjects.json
+++ /dev/null
@@ -1 +0,0 @@
-{"data":{"projectsViewer":{"projects":{"hits":{"edges":[{"node":{"disease_type":["Myeloid Leukemias","Not Applicable"],"id":"UHJvamVjdDpUQVJHRVQtQU1M","primary_site":["Unknown","Hematopoietic and reticuloendothelial systems"],"project_id":"TARGET-AML"}},{"node":{"disease_type":["Neuroepitheliomatous Neoplasms"],"id":"UHJvamVjdDpUQVJHRVQtTkJM","primary_site":["Heart, mediastinum, and pleura","Stomach","Bones, joints and articular cartilage of other and unspecified sites","Lymph nodes","Liver and intrahepatic bile ducts","Unknown","Uterus, NOS","Skin","Meninges","Other endocrine glands and related structures","Adrenal gland","Renal pelvis","Connective, subcutaneous and other soft tissues","Other and ill-defined sites","Bones, joints and articular cartilage of limbs","Spinal cord, cranial nerves, and other parts of central nervous system","Retroperitoneum and peritoneum","Peripheral nerves and autonomic nervous system","Hematopoietic and reticuloendothelial systems","Kidney"],"project_id":"TARGET-NBL"}},{"node":{"disease_type":["Gliomas"],"id":"UHJvamVjdDpUQ0dBLUxHRw==","primary_site":["Brain"],"project_id":"TCGA-LGG"}},{"node":{"disease_type":["Cystic, Mucinous and Serous Neoplasms","Adenomas and Adenocarcinomas"],"id":"UHJvamVjdDpUQ0dBLVJFQUQ=","primary_site":["Rectosigmoid junction","Unknown","Rectum","Colon","Connective, subcutaneous and other soft tissues"],"project_id":"TCGA-READ"}},{"node":{"disease_type":["Epithelial Neoplasms, NOS","Adenomas and Adenocarcinomas"],"id":"UHJvamVjdDpUQ0dBLVRIQ0E=","primary_site":["Thyroid gland"],"project_id":"TCGA-THCA"}},{"node":{"disease_type":["Myeloid Leukemias"],"id":"UHJvamVjdDpCRUFUQU1MMS4wLUNSRU5PTEFOSUI=","primary_site":["Hematopoietic and reticuloendothelial systems"],"project_id":"BEATAML1.0-CRENOLANIB"}},{"node":{"disease_type":["Mesothelial Neoplasms"],"id":"UHJvamVjdDpUQ0dBLU1FU08=","primary_site":["Heart, mediastinum, and pleura","Bronchus and lung"],"project_id":"TCGA-MESO"}},{"node":{"disease_type":["Adenomas and Adenocarcinomas"],"id":"UHJvamVjdDpUQ0dBLUFDQw==","primary_site":["Adrenal gland"],"project_id":"TCGA-ACC"}},{"node":{"disease_type":["Myomatous Neoplasms","Soft Tissue Tumors and Sarcomas, NOS","Fibromatous Neoplasms","Lipomatous Neoplasms","Nerve Sheath Tumors","Synovial-like Neoplasms"],"id":"UHJvamVjdDpUQ0dBLVNBUkM=","primary_site":["Corpus uteri","Stomach","Other and unspecified parts of tongue","Meninges","Other and unspecified male genital organs","Colon","Connective, subcutaneous and other soft tissues","Bones, joints and articular cartilage of limbs","Ovary","Retroperitoneum and peritoneum","Peripheral nerves and autonomic nervous system","Uterus, NOS","Kidney"],"project_id":"TCGA-SARC"}},{"node":{"disease_type":["Complex Mixed and Stromal Neoplasms"],"id":"UHJvamVjdDpUQVJHRVQtQ0NTSw==","primary_site":["Kidney"],"project_id":"TARGET-CCSK"}},{"node":{"disease_type":["Adnexal and Skin Appendage Neoplasms","Cystic, Mucinous and Serous Neoplasms","Adenomas and Adenocarcinomas","Basal Cell Neoplasms","Epithelial Neoplasms, NOS","Squamous Cell Neoplasms","Fibroepithelial Neoplasms","Ductal and Lobular Neoplasms","Complex Epithelial Neoplasms"],"id":"UHJvamVjdDpUQ0dBLUJSQ0E=","primary_site":["Breast"],"project_id":"TCGA-BRCA"}},{"node":{"disease_type":["Not Reported","Cystic, Mucinous and Serous Neoplasms"],"id":"UHJvamVjdDpUQ0dBLU9W","primary_site":["Ovary"],"project_id":"TCGA-OV"}},{"node":{"disease_type":["Adenomas and Adenocarcinomas"],"id":"UHJvamVjdDpUQ0dBLUNIT0w=","primary_site":["Other and unspecified parts of biliary tract","Gallbladder","Liver and intrahepatic bile ducts"],"project_id":"TCGA-CHOL"}},{"node":{"disease_type":["Unknown","Adenomas and Adenocarcinomas"],"id":"UHJvamVjdDpPUkdBTk9JRC1QQU5DUkVBVElD","primary_site":["Pancreas"],"project_id":"ORGANOID-PANCREATIC"}},{"node":{"disease_type":["Epithelial Neoplasms, NOS","Squamous Cell Neoplasms"],"id":"UHJvamVjdDpWQVJFUE9QLUFQT0xMTw==","primary_site":["Bronchus and lung"],"project_id":"VAREPOP-APOLLO"}},{"node":{"disease_type":["Adenomas and Adenocarcinomas","Gliomas"],"id":"UHJvamVjdDpIQ01JLUNNREM=","primary_site":["Brain","Rectum","Colon"],"project_id":"HCMI-CMDC"}},{"node":{"disease_type":["Not Reported","Gliomas"],"id":"UHJvamVjdDpUQ0dBLUdCTQ==","primary_site":["Brain"],"project_id":"TCGA-GBM"}},{"node":{"disease_type":["Adenomas and Adenocarcinomas"],"id":"UHJvamVjdDpUQ0dBLUtJUkM=","primary_site":["Kidney"],"project_id":"TCGA-KIRC"}},{"node":{"disease_type":["Nevi and Melanomas"],"id":"UHJvamVjdDpUQ0dBLVNLQ00=","primary_site":["Skin"],"project_id":"TCGA-SKCM"}},{"node":{"disease_type":["Not Reported","Cystic, Mucinous and Serous Neoplasms","Epithelial Neoplasms, NOS","Adenomas and Adenocarcinomas"],"id":"UHJvamVjdDpUQ0dBLVVDRUM=","primary_site":["Corpus uteri","Uterus, NOS"],"project_id":"TCGA-UCEC"}},{"node":{"disease_type":["Cystic, Mucinous and Serous Neoplasms","Adenomas and Adenocarcinomas"],"id":"UHJvamVjdDpUQ0dBLVNUQUQ=","primary_site":["Stomach"],"project_id":"TCGA-STAD"}},{"node":{"disease_type":["Adenomas and Adenocarcinomas"],"id":"UHJvamVjdDpDUFRBQy0z","primary_site":["Kidney","Uterus, NOS","Bronchus and lung"],"project_id":"CPTAC-3"}},{"node":{"disease_type":["Squamous Cell Neoplasms"],"id":"UHJvamVjdDpUQ0dBLUxVU0M=","primary_site":["Bronchus and lung"],"project_id":"TCGA-LUSC"}},{"node":{"disease_type":["Cystic, Mucinous and Serous Neoplasms","Adenomas and Adenocarcinomas","Ductal and Lobular Neoplasms"],"id":"UHJvamVjdDpUQ0dBLVBSQUQ=","primary_site":["Prostate gland"],"project_id":"TCGA-PRAD"}},{"node":{"disease_type":["Myeloid Leukemias","Other Hematologic Disorders","Unknown","Precursor Cell Lymphoblastic Lymphoma","Myelodysplastic Syndromes","Other Leukemias","Chronic Myeloproliferative Disorders","Plasma Cell Tumors","Leukemias, NOS"],"id":"UHJvamVjdDpCRUFUQU1MMS4wLUNPSE9SVA==","primary_site":["Hematopoietic and reticuloendothelial systems"],"project_id":"BEATAML1.0-COHORT"}},{"node":{"disease_type":["Not Reported","Mature B-Cell Lymphomas"],"id":"UHJvamVjdDpUQ0dBLURMQkM=","primary_site":["Heart, mediastinum, and pleura","Testis","Stomach","Lymph nodes","Bones, joints and articular cartilage of other and unspecified sites","Brain","Thyroid gland","Small intestine","Colon","Connective, subcutaneous and other soft tissues","Other and unspecified major salivary glands","Retroperitoneum and peritoneum","Hematopoietic and reticuloendothelial systems","Breast"],"project_id":"TCGA-DLBC"}},{"node":{"disease_type":["Adenomas and Adenocarcinomas"],"id":"UHJvamVjdDpUQ0dBLUtJQ0g=","primary_site":["Kidney"],"project_id":"TCGA-KICH"}},{"node":{"disease_type":["Germ Cell Neoplasms"],"id":"UHJvamVjdDpUQ0dBLVRHQ1Q=","primary_site":["Testis"],"project_id":"TCGA-TGCT"}},{"node":{"disease_type":["Nevi and Melanomas"],"id":"UHJvamVjdDpUQ0dBLVVWTQ==","primary_site":["Eye and 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diff --git a/cypress/fixtures/ExportGenes/ProjectTable.json b/cypress/fixtures/ExportGenes/ProjectTable.json
index d64aeef..f4b2483 100644
--- a/cypress/fixtures/ExportGenes/ProjectTable.json
+++ b/cypress/fixtures/ExportGenes/ProjectTable.json
@@ -1 +1 @@
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\ No newline at end of file
diff --git a/cypress/fixtures/ExportSSMs/ProjectTable.json b/cypress/fixtures/ExportSSMs/ProjectTable.json
index 4166ea1..a048897 100644
--- a/cypress/fixtures/ExportSSMs/ProjectTable.json
+++ b/cypress/fixtures/ExportSSMs/ProjectTable.json
@@ -1 +1 @@
-{"data":{"viewer":{"explore":{"cases":{"filtered":{"project__project_id":{"buckets":[{"doc_count":1,"key":"TCGA-COAD"}]}},"total":{"project__project_id":{"buckets":[{"doc_count":986,"key":"TCGA-BRCA"},{"doc_count":567,"key":"TCGA-LUAD"},{"doc_count":530,"key":"TCGA-UCEC"},{"doc_count":510,"key":"TCGA-LGG"},{"doc_count":508,"key":"TCGA-HNSC"},{"doc_count":498,"key":"TCGA-PRAD"},{"doc_count":495,"key":"TCGA-LUSC"},{"doc_count":492,"key":"TCGA-THCA"},{"doc_count":469,"key":"TCGA-SKCM"},{"doc_count":440,"key":"TCGA-STAD"},{"doc_count":436,"key":"TCGA-OV"},{"doc_count":412,"key":"TCGA-BLCA"},{"doc_count":400,"key":"TCGA-COAD"},{"doc_count":393,"key":"TCGA-GBM"},{"doc_count":364,"key":"TCGA-LIHC"},{"doc_count":336,"key":"TCGA-KIRC"},{"doc_count":289,"key":"TCGA-CESC"},{"doc_count":281,"key":"TCGA-KIRP"},{"doc_count":237,"key":"TCGA-SARC"},{"doc_count":184,"key":"TCGA-ESCA"},{"doc_count":182,"key":"TCGA-PAAD"},{"doc_count":179,"key":"TCGA-PCPG"},{"doc_count":145,"key":"TCGA-TGCT"},{"doc_count":144,"key":"TCGA-LAML"},{"doc_count":137,"key":"TCGA-READ"},{"doc_count":123,"key":"TCGA-THYM"},{"doc_count":92,"key":"TCGA-ACC"},{"doc_count":82,"key":"TCGA-MESO"},{"doc_count":80,"key":"TCGA-UVM"},{"doc_count":66,"key":"TCGA-KICH"},{"doc_count":57,"key":"TCGA-UCS"},{"doc_count":51,"key":"TCGA-CHOL"},{"doc_count":37,"key":"TCGA-DLBC"}]}}}}}}}
\ No newline at end of file
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\ No newline at end of file
diff --git a/cypress/fixtures/ExportSSMs/SSMProjects.json b/cypress/fixtures/ExportSSMs/SSMProjects.json
deleted file mode 100644
index 93b1c29..0000000
--- a/cypress/fixtures/ExportSSMs/SSMProjects.json
+++ /dev/null
@@ -1 +0,0 @@
-{"data":{"projectsViewer":{"projects":{"hits":{"edges":[{"node":{"disease_type":["Myeloid Leukemias","Not Applicable"],"id":"UHJvamVjdDpUQVJHRVQtQU1M","primary_site":["Unknown","Hematopoietic and reticuloendothelial systems"],"project_id":"TARGET-AML"}},{"node":{"disease_type":["Neuroepitheliomatous Neoplasms"],"id":"UHJvamVjdDpUQVJHRVQtTkJM","primary_site":["Heart, mediastinum, and pleura","Stomach","Bones, joints and articular cartilage of other and unspecified sites","Lymph nodes","Liver and intrahepatic bile ducts","Unknown","Uterus, NOS","Skin","Meninges","Other endocrine glands and related structures","Adrenal gland","Renal pelvis","Connective, subcutaneous and other soft tissues","Other and ill-defined sites","Bones, joints and articular cartilage of limbs","Spinal cord, cranial nerves, and other parts of central nervous system","Retroperitoneum and peritoneum","Peripheral nerves and autonomic nervous system","Hematopoietic and reticuloendothelial 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\ No newline at end of file
diff --git a/cypress/fixtures/projects/gene-projects.json b/cypress/fixtures/projects/gene-projects.json
deleted file mode 100644
index 7d24e01..0000000
--- a/cypress/fixtures/projects/gene-projects.json
+++ /dev/null
@@ -1 +0,0 @@
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\ No newline at end of file
diff --git a/cypress/fixtures/projects/mutation-projects.json b/cypress/fixtures/projects/mutation-projects.json
deleted file mode 100644
index 7d24e01..0000000
--- a/cypress/fixtures/projects/mutation-projects.json
+++ /dev/null
@@ -1 +0,0 @@
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\ No newline at end of file
diff --git a/cypress/fixtures/projects/project-table-gene.json b/cypress/fixtures/projects/project-table-gene.json
index 2d877e9..f526e42 100644
--- a/cypress/fixtures/projects/project-table-gene.json
+++ b/cypress/fixtures/projects/project-table-gene.json
@@ -1 +1 @@
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diff --git a/cypress/fixtures/projects/project-table.json b/cypress/fixtures/projects/project-table.json
index 760828d..1b351c7 100644
--- a/cypress/fixtures/projects/project-table.json
+++ b/cypress/fixtures/projects/project-table.json
@@ -1 +1 @@
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tissues","Other and ill-defined sites","Spinal cord, cranial nerves, and other parts of central nervous system","Retroperitoneum and peritoneum"],"project_id":"TCGA-PCPG"}},{"node":{"disease_type":["Adenomas and Adenocarcinomas"],"id":"UHJvamVjdDpUQ0dBLUtJUlA=","primary_site":["Kidney"],"project_id":"TCGA-KIRP"}},{"node":{"disease_type":["Complex Mixed and Stromal Neoplasms"],"id":"UHJvamVjdDpUQ0dBLVVDUw==","primary_site":["Uterus, NOS"],"project_id":"TCGA-UCS"}},{"node":{"disease_type":["Cystic, Mucinous and Serous Neoplasms","Epithelial Neoplasms, NOS","Adenomas and Adenocarcinomas","Ductal and Lobular Neoplasms"],"id":"UHJvamVjdDpUQ0dBLVBBQUQ=","primary_site":["Pancreas"],"project_id":"TCGA-PAAD"}},{"node":{"disease_type":["Cystic, Mucinous and Serous Neoplasms","Acinar Cell Neoplasms","Adenomas and Adenocarcinomas"],"id":"UHJvamVjdDpUQ0dBLUxVQUQ=","primary_site":["Bronchus and lung"],"project_id":"TCGA-LUAD"}},{"node":{"disease_type":["Complex Mixed and Stromal Neoplasms"],"id":"UHJvamVjdDpUQVJHRVQtV1Q=","primary_site":["Kidney"],"project_id":"TARGET-WT"}},{"node":{"disease_type":["Plasma Cell Tumors"],"id":"UHJvamVjdDpNTVJGLUNPTU1QQVNT","primary_site":["Hematopoietic and reticuloendothelial systems"],"project_id":"MMRF-COMMPASS"}},{"node":{"disease_type":["Transitional Cell Papillomas and Carcinomas","Epithelial Neoplasms, NOS","Adenomas and Adenocarcinomas","Squamous Cell Neoplasms"],"id":"UHJvamVjdDpUQ0dBLUJMQ0E=","primary_site":["Bladder"],"project_id":"TCGA-BLCA"}},{"node":{"disease_type":["Lymphoid Neoplasm Diffuse Large B-cell Lymphoma"],"id":"UHJvamVjdDpOQ0lDQ1ItRExCQ0w=","primary_site":["Lymph Nodes"],"project_id":"NCICCR-DLBCL"}},{"node":{"disease_type":["Lymphoid Leukemias"],"id":"UHJvamVjdDpUQVJHRVQtQUxMLVAx","primary_site":["Hematopoietic and reticuloendothelial systems"],"project_id":"TARGET-ALL-P1"}}]}},"explore":{"cases":{"filtered":{"project__project_id":{"buckets":[{"doc_count":6,"key":"TCGA-COAD"},{"doc_count":4,"key":"TCGA-BRCA"},{"doc_count":4,"key":"TCGA-UCEC"},{"doc_count":3,"key":"TCGA-LIHC"},{"doc_count":2,"key":"TCGA-STAD"},{"doc_count":1,"key":"TCGA-LUAD"},{"doc_count":1,"key":"TCGA-LUSC"}]}},"total":{"project__project_id":{"buckets":[{"doc_count":986,"key":"TCGA-BRCA"},{"doc_count":567,"key":"TCGA-LUAD"},{"doc_count":530,"key":"TCGA-UCEC"},{"doc_count":510,"key":"TCGA-LGG"},{"doc_count":508,"key":"TCGA-HNSC"},{"doc_count":498,"key":"TCGA-PRAD"},{"doc_count":495,"key":"TCGA-LUSC"},{"doc_count":492,"key":"TCGA-THCA"},{"doc_count":469,"key":"TCGA-SKCM"},{"doc_count":440,"key":"TCGA-STAD"},{"doc_count":436,"key":"TCGA-OV"},{"doc_count":412,"key":"TCGA-BLCA"},{"doc_count":400,"key":"TCGA-COAD"},{"doc_count":393,"key":"TCGA-GBM"},{"doc_count":364,"key":"TCGA-LIHC"},{"doc_count":336,"key":"TCGA-KIRC"},{"doc_count":289,"key":"TCGA-CESC"},{"doc_count":281,"key":"TCGA-KIRP"},{"doc_count":237,"key":"TCGA-SARC"},{"doc_count":184,"key":"TCGA-ESCA"},{"doc_count":182,"key":"TCGA-PAAD"},{"doc_count":179,"key":"TCGA-PCPG"},{"doc_count":145,"key":"TCGA-TGCT"},{"doc_count":144,"key":"TCGA-LAML"},{"doc_count":137,"key":"TCGA-READ"},{"doc_count":123,"key":"TCGA-THYM"},{"doc_count":92,"key":"TCGA-ACC"},{"doc_count":82,"key":"TCGA-MESO"},{"doc_count":80,"key":"TCGA-UVM"},{"doc_count":66,"key":"TCGA-KICH"},{"doc_count":57,"key":"TCGA-UCS"},{"doc_count":51,"key":"TCGA-CHOL"},{"doc_count":37,"key":"TCGA-DLBC"}]}}}}}}}
\ No newline at end of file
diff --git a/cypress/integration/ExportGeneTrack.js b/cypress/integration/ExportGeneTrack.js
index 8c67dbd..3f19d6f 100644
--- a/cypress/integration/ExportGeneTrack.js
+++ b/cypress/integration/ExportGeneTrack.js
@@ -13,18 +13,11 @@ describe('Gene track', function() {
                 response: 'fixture:ExportGenes/GenesTable.json'
               }).as('getGeneTable')
 
-        cy
-            .route({
-                method: 'POST',
-                url: 'v0/graphql/gene-projects',
-                response: 'fixture:ExportGenes/GeneProjects.json'
-            }).as('getGeneProjects')
-        
         cy
             .route({
                 method: 'POST',
                 url: 'v0/graphql/projectsTable',
-                response: 'fixture:ExportGenes/ProjectTable.json'
+                response: 'fixture:ExportGenes/GeneProjects.json'
             }).as('getProjectsTable')
 
         // Open track menu
@@ -58,7 +51,7 @@ describe('Gene track', function() {
         if (radioIndex === 2) {
             cy.wait('@getGeneTable').then(() => {
                 cy.wait(3000) // Give time to process results
-                cy.wait(['@getGeneProjects.all', '@getProjectsTable.all']).then(() => {
+                cy.wait(['@getProjectsTable.all']).then(() => {
                     cy.wait(3000) // Give time to process results
                     for (var text of textValues) {
                         cy.get('textarea').should('to.include.value', text)
diff --git a/cypress/integration/ExportSSMTrack.js b/cypress/integration/ExportSSMTrack.js
index 5eb6dcf..322cb24 100644
--- a/cypress/integration/ExportSSMTrack.js
+++ b/cypress/integration/ExportSSMTrack.js
@@ -12,13 +12,6 @@ describe('SSM track', function() {
                 url: 'v0/graphql/SsmsTable',
                 response: 'fixture:ExportSSMs/SsmsTable.json'
               }).as('getSSMTable')
-
-        cy
-            .route({
-                method: 'POST',
-                url: 'v0/graphql/ssm-projects',
-                response: 'fixture:ExportSSMs/SSMProjects.json'
-            }).as('getSSMProjects')
         
         cy
             .route({
@@ -58,7 +51,7 @@ describe('SSM track', function() {
         if (radioIndex === 2) {
             cy.wait('@getSSMTable').then(() => {
                 cy.wait(3000) // Give time to process results
-                cy.wait(['@getSSMProjects.all', '@getProjectsTable.all']).then(() => {
+                cy.wait(['@getProjectsTable.all']).then(() => {
                     cy.wait(3000) // Give time to process results
                     for (var text of textValues) {
                         cy.get('textarea').should('to.include.value', text)
diff --git a/cypress/integration/projects.js b/cypress/integration/projects.js
index 23b0455..d219e1c 100644
--- a/cypress/integration/projects.js
+++ b/cypress/integration/projects.js
@@ -72,12 +72,6 @@ describe('Project dialog', function() {
         cy.contains('GDC_CNVs_FM-AD')
 
         // Stub some responses for viewing a mutation
-        cy
-            .route({
-                method: 'POST',
-                url: 'v0/graphql/ssm-projects',
-                response: 'fixture:projects/mutation-projects.json'
-              }).as('getProjectsForMutation')
 
         cy
             .route({
@@ -93,7 +87,6 @@ describe('Project dialog', function() {
 
         // Ensure mutation has right data
         cy.get('.popup-dialog').within(() => {
-            cy.wait('@getProjectsForMutation')
             cy.contains('Simple Somatic Mutation')
             cy.contains('chr1:g.52055208delT')
             cy.contains('7ffb5e22-05d6-5664-a0b0-908184bacbb9')
@@ -117,12 +110,6 @@ describe('Project dialog', function() {
         })
 
         // Stub some responses for viewing a gene
-        cy
-            .route({
-                method: 'POST',
-                url: 'v0/graphql/gene-projects',
-                response: 'fixture:projects/gene-projects.json'
-              }).as('getProjectsForGene')
 
         cy
             .route({
@@ -138,7 +125,6 @@ describe('Project dialog', function() {
 
         // Ensure gene has right data
         cy.get('.popup-dialog').within(() => {
-            cy.wait('@getProjectsForGene')
             cy.contains('Gene')
             cy.contains('The protein encoded by this gene is expressed in the brain, predominantly in the parietal and frontal cortex as well as in dorsal root ganglia.')
             cy.contains('protein_coding')

From 172fd9502eebd318a01bd437bf7ef929bb59e5bb Mon Sep 17 00:00:00 2001
From: Andrew Duncan <andrew.duncan@oicr.on.ca>
Date: Tue, 24 Mar 2020 13:59:32 -0400
Subject: [PATCH 27/28] added some more useful comments

---
 gdc-viewer/js/View/BaseGDCDialog.js            |  2 +-
 gdc-viewer/js/View/GDCDialog.js                |  3 +++
 gdc-viewer/js/View/Track/BaseTrack.js          |  3 +++
 gdc-viewer/js/View/Track/CNVTrack.js           |  3 +++
 gdc-viewer/js/View/Track/CommonTrack.js        | 12 ++++++++++--
 gdc-viewer/js/View/Track/GeneTrack.js          |  8 +++++++-
 gdc-viewer/js/View/Track/SSMTrack.js           |  8 +++++++-
 gdc-viewer/js/View/Track/ValidationTextArea.js |  3 +++
 8 files changed, 37 insertions(+), 5 deletions(-)

diff --git a/gdc-viewer/js/View/BaseGDCDialog.js b/gdc-viewer/js/View/BaseGDCDialog.js
index 9740878..5138a05 100644
--- a/gdc-viewer/js/View/BaseGDCDialog.js
+++ b/gdc-viewer/js/View/BaseGDCDialog.js
@@ -1,5 +1,5 @@
 /**
- * A base class for GDC dialogs
+ * A base class for GDC dialogs, including common functions and variables
  */
 define([
     'dojo/_base/declare',
diff --git a/gdc-viewer/js/View/GDCDialog.js b/gdc-viewer/js/View/GDCDialog.js
index 20bbdf4..26bd7f9 100644
--- a/gdc-viewer/js/View/GDCDialog.js
+++ b/gdc-viewer/js/View/GDCDialog.js
@@ -478,6 +478,7 @@ function (
                 thisB.addTooltipToButton(menuItemSSMFiltered, "Add track with all Mutations from the GDC, with current filters applied");
                 thisB.addTooltipToButton(buttonAllSSMs, "Add track with all Mutations from the GDC");
 
+                // Determine information for pagination and results
                 var totalSSMs = response.data.viewer.explore.ssms.hits.total;
                 var startResultCount = ((thisB.mutationPage - 1) * thisB.pageSize);
                 if (totalSSMs > 0) {
@@ -619,6 +620,7 @@ function (
                 thisB.addTooltipToButton(menuItemCnvFiltered, "Add track with all CNVs from the GDC, with current filters applied");
                 thisB.addTooltipToButton(buttonAllCnvs, "Add track with all CNVs from the GDC");
 
+                // Determine information for pagination and results
                 var totalGenes = response.data.genesTableViewer.explore.genes.hits.total;
                 var startResultCount = ((thisB.genePage - 1) * thisB.pageSize);
                 if (totalGenes > 0) {
@@ -682,6 +684,7 @@ function (
             }).then(function(response) {
                 dom.empty(thisB.caseResultsTab.containerNode);
 
+                // Determine information for pagination and results
                 var totalCases = response.data.exploreCasesTableViewer.explore.cases.hits.total;
                 var startResultCount = ((thisB.casePage - 1) * thisB.pageSize);
                 if (totalCases > 0) {
diff --git a/gdc-viewer/js/View/Track/BaseTrack.js b/gdc-viewer/js/View/Track/BaseTrack.js
index 3ad73d0..21e18fd 100644
--- a/gdc-viewer/js/View/Track/BaseTrack.js
+++ b/gdc-viewer/js/View/Track/BaseTrack.js
@@ -26,6 +26,9 @@ define(
             );
         },
 
+        /**
+         * Override the available export types
+         */
         _exportFormats: function() {
             return [
                 {name: 'gdc-viewer/View/Export/GFF3', label: 'GFF3', fileExt: 'gff3'},
diff --git a/gdc-viewer/js/View/Track/CNVTrack.js b/gdc-viewer/js/View/Track/CNVTrack.js
index e07b30d..ff9d407 100644
--- a/gdc-viewer/js/View/Track/CNVTrack.js
+++ b/gdc-viewer/js/View/Track/CNVTrack.js
@@ -28,6 +28,9 @@ define(
             );
         },
 
+        /**
+         * Override the available export types
+         */
         _exportFormats: function() {
             return [
                 {name: 'GFF3', label: 'GFF3', fileExt: 'gff3'},
diff --git a/gdc-viewer/js/View/Track/CommonTrack.js b/gdc-viewer/js/View/Track/CommonTrack.js
index 9438a11..3e5e891 100644
--- a/gdc-viewer/js/View/Track/CommonTrack.js
+++ b/gdc-viewer/js/View/Track/CommonTrack.js
@@ -19,6 +19,9 @@ define(
        ValidationTextArea) {
    return declare(null, {
 
+    /**
+     * Adds additional track menu options
+     */
     _trackMenuOptions: function () {
         var options = this.inherited(arguments);
         options.push({ type: 'dijit/MenuSeparator' } );
@@ -45,11 +48,12 @@ define(
         var track = this;
         var details = domConstruct.create('div', { className: 'detail', style: 'display: flex; flex-direction: column; align-items: center; justify-content: center;' });
         
+        // Create header text
         var headerString = '<h1 style="width: 80%; margin-bottom: 5px;">View and Update Filters Applied To The Current Track</h1>';
         var headerElement = domConstruct.toDom(headerString);
         domConstruct.place(headerElement, details);
 
-        // Create help text
+        // Create filter help text
         var helpString = '<span style="width: 80%; font-size: 14px;">The following filters have been applied to the track. You can update the filters here, though only basic validation is done on the input.</span>';
         var helpElement = domConstruct.toDom(helpString);
         domConstruct.place(helpElement, details);
@@ -58,7 +62,7 @@ define(
         var filterElement = domConstruct.toDom(filterString);
         domConstruct.place(filterElement, details);
 
-        // Get filtered text
+        // Display filtered text
         var filteredText = JSON.stringify(track.store.filters, null, 2)
 
         var textArea = new ValidationTextArea({
@@ -79,6 +83,7 @@ define(
               }
         }).placeAt(details);
 
+        // Display cases
         var caseString = '<div style="width: 80%"><h3>Case UUIDs</h3><span>Comma separated unique identifiers for the case, expressed as UUIDs.</span></div>';
         var caseElement = domConstruct.toDom(caseString);
         domConstruct.place(caseElement, details);
@@ -92,6 +97,7 @@ define(
             trim: true
         }).placeAt(details);
 
+        // Display size
         var sizeHeader = '<div style="width: 80%"><h3>Size</h3><span>This is the maximum number of results to return per panel.</span></div>';
         var sizeElement = domConstruct.toDom(sizeHeader);
         domConstruct.place(sizeElement, details);
@@ -104,6 +110,7 @@ define(
             smallDelta: 10
         }).placeAt(details);
 
+        // Add button to update the track with changed content
         var updateTrackButton = new Button({
             label: 'Apply Filters',
             iconClass: 'dijitIconSave',
@@ -125,6 +132,7 @@ define(
             }
         }).placeAt(details);
 
+        // Change listeners for text boxes
         caseIdTextBox.on('change', function(e) {
             updateTrackButton.set('disabled', !caseIdTextBox.validate() || !sizeTextBox.validate() || !textArea.validate())
         });
diff --git a/gdc-viewer/js/View/Track/GeneTrack.js b/gdc-viewer/js/View/Track/GeneTrack.js
index c4ec13e..a33e42e 100644
--- a/gdc-viewer/js/View/Track/GeneTrack.js
+++ b/gdc-viewer/js/View/Track/GeneTrack.js
@@ -12,7 +12,13 @@ define(
        domConstruct,
        BaseTrack) {
    return declare(BaseTrack, {
-
+        /**
+         * Override the additional details shown in the dialogs
+         * @param {*} track
+         * @param {*} f
+         * @param {*} featDiv
+         * @param {*} container
+         */
         _renderAdditionalTagsDetail: function( track, f, featDiv, container ) {
             var atElement = domConstruct.create(
                 'div',
diff --git a/gdc-viewer/js/View/Track/SSMTrack.js b/gdc-viewer/js/View/Track/SSMTrack.js
index 9d777a1..d1b2313 100644
--- a/gdc-viewer/js/View/Track/SSMTrack.js
+++ b/gdc-viewer/js/View/Track/SSMTrack.js
@@ -12,7 +12,13 @@ define(
        domConstruct,
        BaseTrack) {
    return declare(BaseTrack, {
-
+        /**
+         * Override the additional details shown in the dialogs
+         * @param {*} track
+         * @param {*} f
+         * @param {*} featDiv
+         * @param {*} container
+         */
         _renderAdditionalTagsDetail: function( track, f, featDiv, container ) {
             var atElement = domConstruct.create(
                 'div',
diff --git a/gdc-viewer/js/View/Track/ValidationTextArea.js b/gdc-viewer/js/View/Track/ValidationTextArea.js
index 9c3dde3..7127d31 100644
--- a/gdc-viewer/js/View/Track/ValidationTextArea.js
+++ b/gdc-viewer/js/View/Track/ValidationTextArea.js
@@ -1,3 +1,6 @@
+/**
+ * Extends SimpleTextArea to support the validation features of the ValidationTextBox
+ */
 define(
     [
         "dojo/_base/declare",

From 3b9dad5c1817212a679e218ffcccfe083303c2bc Mon Sep 17 00:00:00 2001
From: Andrew Duncan <andrew.duncan@oicr.on.ca>
Date: Wed, 25 Mar 2020 10:39:11 -0400
Subject: [PATCH 28/28] add new webpage for viewer

---
 README.md                                     | 236 +-----------------
 docs/.gitignore                               |   3 +
 docs/404.html                                 |  24 ++
 docs/Gemfile                                  |  31 +++
 docs/Gemfile.lock                             |  77 ++++++
 docs/_config.yml                              |  43 ++++
 docs/developers.md                            |  22 ++
 {images => docs/images}/GDC-cnv-gain.png      | Bin
 .../images}/GDC-genes-protein-coding.png      | Bin
 .../images}/GDC-mutations-base-g.png          | Bin
 .../images}/GDC-portal-explore.png            | Bin
 {images => docs/images}/GDC-primary-sites.png | Bin
 .../images}/GDC-project-browser.png           | Bin
 docs/index.md                                 |  27 ++
 docs/install.md                               |  58 +++++
 docs/testing.md                               |  14 ++
 docs/tracks.md                                | 179 +++++++++++++
 17 files changed, 480 insertions(+), 234 deletions(-)
 create mode 100644 docs/.gitignore
 create mode 100644 docs/404.html
 create mode 100644 docs/Gemfile
 create mode 100644 docs/Gemfile.lock
 create mode 100644 docs/_config.yml
 create mode 100644 docs/developers.md
 rename {images => docs/images}/GDC-cnv-gain.png (100%)
 rename {images => docs/images}/GDC-genes-protein-coding.png (100%)
 rename {images => docs/images}/GDC-mutations-base-g.png (100%)
 rename {images => docs/images}/GDC-portal-explore.png (100%)
 rename {images => docs/images}/GDC-primary-sites.png (100%)
 rename {images => docs/images}/GDC-project-browser.png (100%)
 create mode 100644 docs/index.md
 create mode 100644 docs/install.md
 create mode 100644 docs/testing.md
 create mode 100644 docs/tracks.md

diff --git a/README.md b/README.md
index 9519f29..07453e9 100644
--- a/README.md
+++ b/README.md
@@ -1,237 +1,5 @@
 [![Build Status](https://travis-ci.org/agduncan94/gdc-viewer.svg?branch=develop)](https://travis-ci.org/agduncan94/gdc-viewer)
 # GDC JBrowse Plugin
-A plugin for [JBrowse](https://jbrowse.org/) for viewing [GDC](https://gdc.cancer.gov/) data. For any bugs, issues, or feature recommendations please create an issue through GitHub.
+A plugin for [JBrowse](https://jbrowse.org/) for viewing [GDC](https://gdc.cancer.gov/) data. For any bugs, issues, or feature recommendations please create an issue or PR through GitHub.
 
-# Installation and Setup
-## 1. Install JBrowse
-Follow JBrowse readme for [quick setup.](https://github.com/GMOD/jbrowse/#install-jbrowse-from-github-for-developers)
-
-## 2. Install Plugin
-See [JBrowse - Installing Plugins](https://jbrowse.org/docs/plugins.html) for a general approach to installing plugins.
-
-For installing gdc-viewer plugin:
-1. Copy the gdc-viewer folder into the JBrowse `plugins` directory.
-2. Add 'gdc-viewer' to the array of plugins in the `jbrowse_conf.json`.
-
-## 3. Install Reference Sequence Data
-Now setup the reference sequence used. GDC requires the GRCh38 Human reference files.
-
-Download the GRCh38 `.fa` and `.fa.fai` files online (ex. http://bioinfo.hpc.cam.ac.uk/downloads/datasets/fasta/grch38/). Then put the following in `./data/tracks.conf` (note files may be named something else).
-
-```
-refSeqs=GRCh38.genome.fa.fai
-  
-[tracks.refseqs]
-urlTemplate=GRCh38.genome.fa
-```
-
-## 4. Adding new tracks
-We have some basic example tracks in `data/tracks.conf`. You can also add new tracks by using the GDC dialog accessible within JBrowse. These are present in the menu under `GDC`. See [Dynamic Track Generation](#dynamic-track-generation) for more details.
-
-## 5. Run JBrowse
-You'll have to run the following commands:
-
-```
-./setup.sh
-utils/jb_run.js -p 3000
-```
-
-JBrowse should now be running with the GDC Plugin working!
-
-# JBrowse configuration
-## Faceted Track Selector
-Add the following to your jbrowse.conf to use the faceted track selector.
-```
-[trackSelector]
-type = Faceted
-displayColumns =
-  + label
-  + key
-  + datatype
-  + case
-  + project
-  + primarySite
-```
-
-Note that this will only show preloaded tracks as well as tracks you have added using the various dialogs. It does not dynamically create tracks based on what is available from the GDC.
-
-# Available Track Types
-## A note on filters
-All tracks support filters as they are defined in the [GDC API Documentation](https://docs.gdc.cancer.gov/API/Users_Guide/Search_and_Retrieval/#filters-specifying-the-query).
-
-Note that filters should have the filter type prepended to the front. Ex. Case filters use `cases.`, Mutation filters use `ssms.`, and Gene filters use `genes.`. GraphQL is used to retrieve results, so if the filters work there, they work with these Store classes.
-
-The following shows a filter for cases by ethnicity:
-```
-{
-  "op":"in",
-  "content":{
-    "field":"cases.demographic.ethnicity",
-    "value":[
-      "hispanic or latino"
-    ]
-  }
-}
-```
-
-You can view/edit the filters associated with a track by clicking the down arrow for the track menu and selecting `View Applied Filters`. Be careful, there are currently no checks to see if the filters are valid before applying them.
-
-## Genes
-A simple view of all of the genes seen across all cases.
-
-You can view case specific genes by setting the `case` field.
-
-You can apply filters to the track too, in the same format as GDC. The below example only shows Genes whose biotype is not 'protein_coding'.
-
-```
-{ 
-   "op":"!=",
-   "content":{ 
-      "field":"genes.biotype",
-      "value":"protein_coding"
-   }
-}
-```
-
-To put it in the track config you may want to minimize it as such:
-```
-filters={"op":"!=","content":{"field":"genes.biotype","value":"protein_coding"}}
-```
-
-Example Track:
-```
-[tracks.GDC_Genes]
-storeClass=gdc-viewer/Store/SeqFeature/Genes
-type=JBrowse/View/Track/GeneTrack
-key=GDC Genes
-metadata.datatype=Gene
-filters={"op":"!=","content":{"field":"genes.biotype","value":"protein_coding"}}
-```
-
-![GDC Genes](images/GDC-genes-protein-coding.png)
-
-### Extra notes
-You can set the max number of genes to return with the `size` field (per panel). It defaults to 100. The smaller the number, the faster the results will appear.
-
-## Mutations (SSMs)
-A simple view of all of the simple somatic mutations seen across all cases.
-
-You can view case specific mutations by setting the `case` field.
-
-You can apply filters to the track too, in the same format as GDC. The below example only shows mutations whose reference allele is 'G'.
-```
-{ 
-   "op":"=",
-   "content":{ 
-      "field":"ssms.reference_allele",
-      "value":"G"
-   }
-}
-```
-
-To put it in the track config you may want to minimize it as such:
-```
-filters={"op":"=","content":{"field":"ssms.reference_allele","value":"G"}}
-```
-
-Example Track:
-```
-[tracks.GDC_SSM]
-storeClass=gdc-viewer/Store/SeqFeature/SimpleSomaticMutations
-type=gdc-viewer/View/Track/SSMVariants
-key=GDC SSM
-metadata.datatype=SSM
-filters={"op":"=","content":{"field":"ssms.reference_allele","value":"G"}}
-```
-
-![GDC SSMs](images/GDC-mutations-base-g.png)
-
-### Extra notes
-You can set the max number of mutations to return with the `size` field (per panel). It defaults to 100. The smaller the number, the faster the results will appear.
-
-## CNVs
-A simple view of all of the CNVs seen across all cases.
-
-You can view case specific CNVs by setting the `case` field.
-
-You can apply filters to the track too, in the same format as GDC. The below example only shows CNVs that are 'Gains'.
-```
-{ 
-   "op":"=",
-   "content":{ 
-      "field":"cnv_change",
-      "value":[ 
-         "Gain"
-      ]
-   }
-}
-```
-
-To put it in the track config you may want to minimize it as such:
-```
-filters={"op":"=","content":{"field":"cnv_change","value":["Gain"]}}
-```
-
-Example Track:
-```
-[tracks.GDC_CNV]
-storeClass=gdc-viewer/Store/SeqFeature/CNVs
-type=gdc-viewer/View/Track/CNVTrack
-key=GDC CNV
-metadata.datatype=CNV
-
-```
-
-![GDC CNVs](images/GDC-cnv-gain.png)
-
-### Extra notes
-You can set the max number of CNVs to return with the `size` field (per panel). It defaults to 500. The smaller the number, the faster the results will appear.
-
-# Dynamic Track Generation
-## Explore cases, genes and mutations
-This dialog is similar to the Exploration section of the GDC data portal. As you apply facets on the left-hand side, updated results will be shown on the right side. You can create case specific Mutation, Gene, and CNV tracks, along with GDC-wide Mutation, Gene and CNV tracks.
-![GDC Portal](images/GDC-portal-explore.png)
-
-## Explore Projects
-This dialog shows the projects present on the GDC Data Portal. You can add Mutation, Gene, and CNV tracks for each project.
-![GDC projects](images/GDC-project-browser.png)
-
-## Explore Primary Sites
-This dialog shows the primary sites present on the GDC Data Portal. You can add Mutation, Gene, and CNV tracks for each primary site.
-![GDC primary sites](images/GDC-primary-sites.png)
-
-# Export Types
-The following export types are supported by both GDC Genes and Mutations. To export, select `Save track data` in the track dropdown. Note that not all track information is carried over to the exported file.
-* BED
-* GFF3
-* Sequin Table
-* CSV
-* Track Config
-
-# Automated testing
-Cypress.io is used for testing this plugin. The following steps show how to run the tests locally.
-1. Install JBrowse but don't install chromosome files.
-2. Download Chr 1 fasta from `http://ftp.ensembl.org/pub/release-94/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.chromosome.1.fa.gz`. There should be the fasta index file in `cypress/data/Homo_sapiens.GRCh38.dna.chromosome.1.fa.fai`. Put these files into `jbrowse/data/`.
-3. Install Cypress.io with `npm install`.
-4. Place `cypress/data/tracks.conf` into your `jbrowse/data/` directory. Make sure no other tracks are present.
-5. Run `npx cypress open` or `npx cypress run` or `npm run e2e`
-
-**Note** while some tests have mocked endpoints, not all endpoints are mocked. This could lead to breakage of tests in the future.
-
-# Extra Notes for Developers
-This section just goes over some areas of the code to help new developers navigate.
-
-## js/Model
-These files override the function for printing to the feature dialog. It overrides the get function to display content that requires extra API calls (on top of the call to grab the whole track). For example, this is used to generate the projects table shown on Mutations and gene feature dialogs.
-
-## js/Store/SeqFeature
-These files connect the GDC API to JBrowse by creating a set of features based on an API call.
-
-## js/View
-The top level contains files that create the various dialog boxes that appear in the menu bar. These allow for the dynamic generation of tracks.
-
-### Export
-These files define export types for Mutation, gene, and CNV tracks.
-
-### Track
-These files extend the track dropdown options to include things like shareable links and view filters. This is also where overrides for the format of the feature dialogs are.
\ No newline at end of file
+Check out [our documentation](https://agduncan94.github.io/gdc-viewer/) for information on installation, available features, and more.
\ No newline at end of file
diff --git a/docs/.gitignore b/docs/.gitignore
new file mode 100644
index 0000000..45c1505
--- /dev/null
+++ b/docs/.gitignore
@@ -0,0 +1,3 @@
+_site
+.sass-cache
+.jekyll-metadata
diff --git a/docs/404.html b/docs/404.html
new file mode 100644
index 0000000..c472b4e
--- /dev/null
+++ b/docs/404.html
@@ -0,0 +1,24 @@
+---
+layout: default
+---
+
+<style type="text/css" media="screen">
+  .container {
+    margin: 10px auto;
+    max-width: 600px;
+    text-align: center;
+  }
+  h1 {
+    margin: 30px 0;
+    font-size: 4em;
+    line-height: 1;
+    letter-spacing: -1px;
+  }
+</style>
+
+<div class="container">
+  <h1>404</h1>
+
+  <p><strong>Page not found :(</strong></p>
+  <p>The requested page could not be found.</p>
+</div>
diff --git a/docs/Gemfile b/docs/Gemfile
new file mode 100644
index 0000000..cb1de77
--- /dev/null
+++ b/docs/Gemfile
@@ -0,0 +1,31 @@
+source "https://rubygems.org"
+
+# Hello! This is where you manage which Jekyll version is used to run.
+# When you want to use a different version, change it below, save the
+# file and run `bundle install`. Run Jekyll with `bundle exec`, like so:
+#
+#     bundle exec jekyll serve
+#
+# This will help ensure the proper Jekyll version is running.
+# Happy Jekylling!
+gem "jekyll", "~> 3.7.3"
+
+# This is the default theme for new Jekyll sites. You may change this to anything you like.
+gem "minima", "~> 2.0"
+
+# If you want to use GitHub Pages, remove the "gem "jekyll"" above and
+# uncomment the line below. To upgrade, run `bundle update github-pages`.
+# gem "github-pages", group: :jekyll_plugins
+
+# If you have any plugins, put them here!
+group :jekyll_plugins do
+  gem "jekyll-feed", "~> 0.6"
+end
+
+# Windows does not include zoneinfo files, so bundle the tzinfo-data gem
+gem "tzinfo-data", platforms: [:mingw, :mswin, :x64_mingw, :jruby]
+
+# Performance-booster for watching directories on Windows
+gem "wdm", "~> 0.1.0" if Gem.win_platform?
+
+gem "just-the-docs"
diff --git a/docs/Gemfile.lock b/docs/Gemfile.lock
new file mode 100644
index 0000000..ab849bd
--- /dev/null
+++ b/docs/Gemfile.lock
@@ -0,0 +1,77 @@
+GEM
+  remote: https://rubygems.org/
+  specs:
+    addressable (2.7.0)
+      public_suffix (>= 2.0.2, < 5.0)
+    colorator (1.1.0)
+    concurrent-ruby (1.1.6)
+    em-websocket (0.5.1)
+      eventmachine (>= 0.12.9)
+      http_parser.rb (~> 0.6.0)
+    eventmachine (1.2.7)
+    ffi (1.12.2)
+    forwardable-extended (2.6.0)
+    http_parser.rb (0.6.0)
+    i18n (0.9.5)
+      concurrent-ruby (~> 1.0)
+    jekyll (3.7.4)
+      addressable (~> 2.4)
+      colorator (~> 1.0)
+      em-websocket (~> 0.5)
+      i18n (~> 0.7)
+      jekyll-sass-converter (~> 1.0)
+      jekyll-watch (~> 2.0)
+      kramdown (~> 1.14)
+      liquid (~> 4.0)
+      mercenary (~> 0.3.3)
+      pathutil (~> 0.9)
+      rouge (>= 1.7, < 4)
+      safe_yaml (~> 1.0)
+    jekyll-feed (0.13.0)
+      jekyll (>= 3.7, < 5.0)
+    jekyll-sass-converter (1.5.2)
+      sass (~> 3.4)
+    jekyll-seo-tag (2.6.1)
+      jekyll (>= 3.3, < 5.0)
+    jekyll-watch (2.2.1)
+      listen (~> 3.0)
+    just-the-docs (0.1.6)
+      jekyll (~> 3.3)
+      rake (~> 10.0)
+    kramdown (1.17.0)
+    liquid (4.0.3)
+    listen (3.2.1)
+      rb-fsevent (~> 0.10, >= 0.10.3)
+      rb-inotify (~> 0.9, >= 0.9.10)
+    mercenary (0.3.6)
+    minima (2.5.1)
+      jekyll (>= 3.5, < 5.0)
+      jekyll-feed (~> 0.9)
+      jekyll-seo-tag (~> 2.1)
+    pathutil (0.16.2)
+      forwardable-extended (~> 2.6)
+    public_suffix (4.0.3)
+    rake (10.5.0)
+    rb-fsevent (0.10.3)
+    rb-inotify (0.10.1)
+      ffi (~> 1.0)
+    rouge (3.17.0)
+    safe_yaml (1.0.5)
+    sass (3.7.4)
+      sass-listen (~> 4.0.0)
+    sass-listen (4.0.0)
+      rb-fsevent (~> 0.9, >= 0.9.4)
+      rb-inotify (~> 0.9, >= 0.9.7)
+
+PLATFORMS
+  ruby
+
+DEPENDENCIES
+  jekyll (~> 3.7.3)
+  jekyll-feed (~> 0.6)
+  just-the-docs
+  minima (~> 2.0)
+  tzinfo-data
+
+BUNDLED WITH
+   2.1.4
diff --git a/docs/_config.yml b/docs/_config.yml
new file mode 100644
index 0000000..5aadf08
--- /dev/null
+++ b/docs/_config.yml
@@ -0,0 +1,43 @@
+# Welcome to Jekyll!
+#
+# This config file is meant for settings that affect your whole blog, values
+# which you are expected to set up once and rarely edit after that. If you find
+# yourself editing this file very often, consider using Jekyll's data files
+# feature for the data you need to update frequently.
+#
+# For technical reasons, this file is *NOT* reloaded automatically when you use
+# 'bundle exec jekyll serve'. If you change this file, please restart the server process.
+
+# Site settings
+# These are used to personalize your new site. If you look in the HTML files,
+# you will see them accessed via {{ site.title }}, {{ site.email }}, and so on.
+# You can create any custom variable you would like, and they will be accessible
+# in the templates via {{ site.myvariable }}.
+title: GDC Viewer
+description: >- # this means to ignore newlines until "baseurl:"
+  A JBrowse plugin for interacting with the GDC portal
+baseurl: "" # the subpath of your site, e.g. /blog
+url: "https://agduncan94.github.io/gdc-viewer/" # the base hostname & protocol for your site, e.g. http://example.com
+
+# Build settings
+markdown: kramdown
+theme: just-the-docs
+remote_theme: pmarsceill/just-the-docs
+plugins:
+  - jekyll-feed
+
+aux_links:
+  "GDC Viewer on GitHub":
+    - "//github.com/agduncan94/gdc-viewer"
+
+# Exclude from processing.
+# The following items will not be processed, by default. Create a custom list
+# to override the default setting.
+# exclude:
+#   - Gemfile
+#   - Gemfile.lock
+#   - node_modules
+#   - vendor/bundle/
+#   - vendor/cache/
+#   - vendor/gems/
+#   - vendor/ruby/
diff --git a/docs/developers.md b/docs/developers.md
new file mode 100644
index 0000000..1fcf8ea
--- /dev/null
+++ b/docs/developers.md
@@ -0,0 +1,22 @@
+---
+layout: default
+title: Developers
+nav_order: 4
+---
+# Extra Notes for Developers
+This section just goes over some areas of the code to help new developers navigate.
+
+## js/Model
+These files override the function for printing to the feature dialog. It overrides the get function to display content that requires extra API calls (on top of the call to grab the whole track). For example, this is used to generate the projects table shown on Mutations and gene feature dialogs.
+
+## js/Store/SeqFeature
+These files connect the GDC API to JBrowse by creating a set of features based on an API call.
+
+## js/View
+The top level contains files that create the various dialog boxes that appear in the menu bar. These allow for the dynamic generation of tracks.
+
+### Export
+These files define export types for mutation, gene, and CNV tracks.
+
+### Track
+These files extend the track dropdown options to include things like shareable links and view filters. This is also where overrides for the format of the feature dialogs are.
\ No newline at end of file
diff --git a/images/GDC-cnv-gain.png b/docs/images/GDC-cnv-gain.png
similarity index 100%
rename from images/GDC-cnv-gain.png
rename to docs/images/GDC-cnv-gain.png
diff --git a/images/GDC-genes-protein-coding.png b/docs/images/GDC-genes-protein-coding.png
similarity index 100%
rename from images/GDC-genes-protein-coding.png
rename to docs/images/GDC-genes-protein-coding.png
diff --git a/images/GDC-mutations-base-g.png b/docs/images/GDC-mutations-base-g.png
similarity index 100%
rename from images/GDC-mutations-base-g.png
rename to docs/images/GDC-mutations-base-g.png
diff --git a/images/GDC-portal-explore.png b/docs/images/GDC-portal-explore.png
similarity index 100%
rename from images/GDC-portal-explore.png
rename to docs/images/GDC-portal-explore.png
diff --git a/images/GDC-primary-sites.png b/docs/images/GDC-primary-sites.png
similarity index 100%
rename from images/GDC-primary-sites.png
rename to docs/images/GDC-primary-sites.png
diff --git a/images/GDC-project-browser.png b/docs/images/GDC-project-browser.png
similarity index 100%
rename from images/GDC-project-browser.png
rename to docs/images/GDC-project-browser.png
diff --git a/docs/index.md b/docs/index.md
new file mode 100644
index 0000000..6880afc
--- /dev/null
+++ b/docs/index.md
@@ -0,0 +1,27 @@
+---
+layout: default
+title: Home
+nav_order: 1
+description: "GDC Viewer is a JBrowse plugin for creating tracks using data from the GDC portal."
+permalink: /
+---
+
+# GDC JBrowse Plugin
+{: .fs-9 }
+A plugin for [JBrowse](https://jbrowse.org/) for viewing [GDC](https://gdc.cancer.gov/) data.
+{: .fs-6 .fw-300 }
+---
+
+# Overview
+This plugin provides the ability to create mutation, gene, and CNV tracks on JBrowse based on complex query filters. These filters are the same as those used in the GDC API. For example, you could create a track of all mutations found in gliomas that have a high VEP score.
+
+[See the tracks page]({{ site.baseurl }}{% link tracks.md %}) for some examples of what this plugin is capable of. 
+
+# Features
+* Create Mutation, Gene and CNV tracks with rich metadata
+* Used faceted search similar to that found on the GDC Portal to create complex filters
+* Share your tracks with others
+* Export your tracks to common formats like BED, GFF3 and CSV
+
+# Contributing
+For any bugs, issues, or feature recommendations please create an issue or PR through GitHub.
\ No newline at end of file
diff --git a/docs/install.md b/docs/install.md
new file mode 100644
index 0000000..12c6c2c
--- /dev/null
+++ b/docs/install.md
@@ -0,0 +1,58 @@
+---
+layout: default
+title: Installation
+nav_order: 2
+---
+
+# Installation and Setup
+## 1. Install JBrowse
+Follow JBrowse readme for [quick setup.](https://github.com/GMOD/jbrowse/#install-jbrowse-from-github-for-developers)
+
+## 2. Install Plugin
+See [JBrowse - Installing Plugins](https://jbrowse.org/docs/plugins.html) for a general approach to installing plugins.
+
+For installing gdc-viewer plugin:
+1. Copy the gdc-viewer folder into the JBrowse `plugins` directory.
+2. Add 'gdc-viewer' to the array of plugins in the `jbrowse_conf.json`.
+
+## 3. Install Reference Sequence Data
+Now setup the reference sequence used. GDC requires the GRCh38 Human reference files.
+
+Download the GRCh38 `.fa` and `.fa.fai` files online (ex. http://bioinfo.hpc.cam.ac.uk/downloads/datasets/fasta/grch38/). Then put the following in `./data/tracks.conf` (note files may be named something else).
+
+```
+refSeqs=GRCh38.genome.fa.fai
+  
+[tracks.refseqs]
+urlTemplate=GRCh38.genome.fa
+```
+
+## 4. Adding new tracks
+We have some basic example tracks in `data/tracks.conf`. You can also add new tracks by using the GDC dialog accessible within JBrowse.
+
+## 5. Run JBrowse
+You'll have to run the following commands:
+
+```
+./setup.sh
+utils/jb_run.js -p 3000
+```
+
+JBrowse should now be running with the GDC Plugin working!
+
+# JBrowse configuration
+## Faceted Track Selector
+Add the following to your jbrowse.conf to use the faceted track selector.
+```
+[trackSelector]
+type = Faceted
+displayColumns =
+  + label
+  + key
+  + datatype
+  + case
+  + project
+  + primarySite
+```
+
+Note that this will only show preloaded tracks as well as tracks you have added using the various dialogs. It does not dynamically create tracks based on what is available from the GDC.
\ No newline at end of file
diff --git a/docs/testing.md b/docs/testing.md
new file mode 100644
index 0000000..211ea1e
--- /dev/null
+++ b/docs/testing.md
@@ -0,0 +1,14 @@
+---
+layout: default
+title: Testing
+nav_order: 5
+---
+# Automated testing
+Cypress.io is used for testing this plugin. The following steps show how to run the tests locally.
+1. Install JBrowse but don't install chromosome files.
+2. Download Chr 1 fasta from `http://ftp.ensembl.org/pub/release-94/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.chromosome.1.fa.gz`. There should be the fasta index file in `cypress/data/Homo_sapiens.GRCh38.dna.chromosome.1.fa.fai`. Put these files into `jbrowse/data/`.
+3. Install Cypress.io with `npm install`.
+4. Place `cypress/data/tracks.conf` into your `jbrowse/data/` directory. Make sure no other tracks are present.
+5. Run `npx cypress open` or `npx cypress run` or `npm run e2e`
+
+**Note** while some tests have mocked endpoints, not all endpoints are mocked. This could lead to breakage of tests in the future.
\ No newline at end of file
diff --git a/docs/tracks.md b/docs/tracks.md
new file mode 100644
index 0000000..487a81f
--- /dev/null
+++ b/docs/tracks.md
@@ -0,0 +1,179 @@
+---
+layout: default
+title: Tracks
+nav_order: 3
+---
+
+# Tracks
+{: .no_toc }
+
+Create Mutation (SSM), Gene, and CNV tracks using a dynamic track generator
+{: .fs-6 .fw-300 }
+
+## Table of contents
+{: .no_toc .text-delta }
+
+1. TOC
+{:toc}
+
+# Filters
+All tracks support filters as they are defined in the [GDC API Documentation](https://docs.gdc.cancer.gov/API/Users_Guide/Search_and_Retrieval/#filters-specifying-the-query).
+
+Note that filters should have the filter type prepended to the front. Ex. Case filters use `cases.`, Mutation filters use `ssms.`, and Gene filters use `genes.`. GraphQL is used to retrieve results, so if the filters work there, they work with these Store classes.
+
+The following shows a filter for cases by ethnicity:
+```
+{
+  "op":"in",
+  "content":{
+    "field":"cases.demographic.ethnicity",
+    "value":[
+      "hispanic or latino"
+    ]
+  }
+}
+```
+
+You can view/edit the filters associated with a track by clicking the down arrow for the track menu and selecting `View Applied Filters`. Be careful, there are currently no checks to see if the filters are valid before applying them.
+
+# Available Track Types
+
+## Genes
+A simple view of all of the genes seen across all cases.
+
+You can view case specific genes by setting the `case` field. Multiple cases are supported by using commas.
+
+You can apply filters to the track too, in the same format as GDC. The below example only shows Genes whose biotype is not 'protein_coding'.
+
+```
+{ 
+   "op":"!=",
+   "content":{ 
+      "field":"genes.biotype",
+      "value":"protein_coding"
+   }
+}
+```
+
+To put it in the track config you may want to minimize it as such:
+```
+filters={"op":"!=","content":{"field":"genes.biotype","value":"protein_coding"}}
+```
+
+Example Track:
+```
+[tracks.GDC_Genes]
+storeClass=gdc-viewer/Store/SeqFeature/Genes
+type=JBrowse/View/Track/GeneTrack
+key=GDC Genes
+metadata.datatype=Gene
+filters={"op":"!=","content":{"field":"genes.biotype","value":"protein_coding"}}
+```
+
+![GDC Genes](images/GDC-genes-protein-coding.png)
+
+### Extra notes
+{: .no_toc }
+You can set the max number of genes to return with the `size` field (per panel). It defaults to 100. The smaller the number, the faster the results will appear.
+
+## Mutations (SSMs)
+A simple view of all of the simple somatic mutations seen across all cases.
+
+You can view case specific mutations by setting the `case` field. Multiple cases are supported by using commas.
+
+You can apply filters to the track too, in the same format as GDC. The below example only shows mutations whose reference allele is 'G'.
+```
+{ 
+   "op":"=",
+   "content":{ 
+      "field":"ssms.reference_allele",
+      "value":"G"
+   }
+}
+```
+
+To put it in the track config you may want to minimize it as such:
+```
+filters={"op":"=","content":{"field":"ssms.reference_allele","value":"G"}}
+```
+
+Example Track:
+```
+[tracks.GDC_SSM]
+storeClass=gdc-viewer/Store/SeqFeature/SimpleSomaticMutations
+type=gdc-viewer/View/Track/SSMVariants
+key=GDC SSM
+metadata.datatype=SSM
+filters={"op":"=","content":{"field":"ssms.reference_allele","value":"G"}}
+```
+
+![GDC SSMs](images/GDC-mutations-base-g.png)
+
+### Extra notes
+{: .no_toc }
+You can set the max number of mutations to return with the `size` field (per panel). It defaults to 100. The smaller the number, the faster the results will appear.
+
+## CNVs
+A simple view of all of the CNVs seen across all cases.
+
+You can view case specific CNVs by setting the `case` field. Multiple cases are supported by using commas.
+
+You can apply filters to the track too, in the same format as GDC. The below example only shows CNVs that are 'Gains'.
+```
+{ 
+   "op":"=",
+   "content":{ 
+      "field":"cnv_change",
+      "value":[ 
+         "Gain"
+      ]
+   }
+}
+```
+
+To put it in the track config you may want to minimize it as such:
+```
+filters={"op":"=","content":{"field":"cnv_change","value":["Gain"]}}
+```
+
+Example Track:
+```
+[tracks.GDC_CNV]
+storeClass=gdc-viewer/Store/SeqFeature/CNVs
+type=gdc-viewer/View/Track/CNVTrack
+key=GDC CNV
+metadata.datatype=CNV
+
+```
+
+![GDC CNVs](images/GDC-cnv-gain.png)
+
+### Extra notes
+{: .no_toc }
+You can set the max number of CNVs to return with the `size` field (per panel). It defaults to 500. The smaller the number, the faster the results will appear.
+
+# Dynamic Track Generation
+## Explore cases, genes and mutations
+This dialog is similar to the Exploration section of the GDC data portal. As you apply facets on the left-hand side, updated results will be shown on the right side. You can create case specific Mutation, Gene, and CNV tracks, along with GDC-wide Mutation, Gene and CNV tracks.
+
+You can optionally apply the current facets to the track itself when you add a track. For example, say you have applied the facet VEP impact of high. On the `Mutations` tab there is the option to add all mutations from the GDC or add all filtered mutations from the GDC. The first option will create a track with all mutations present on the GDC portal (no filtering). The second option will create a track with only mutations that have a VEP impact of high. As you can see, this becomes very powerful when you combine multiple facets.
+
+![GDC Portal](images/GDC-portal-explore.png)
+
+## Explore Projects
+This dialog shows the projects present on the GDC Data Portal. You can add Mutation, Gene, and CNV tracks for each project.
+
+![GDC projects](images/GDC-project-browser.png)
+
+## Explore Primary Sites
+This dialog shows the primary sites present on the GDC Data Portal. You can add Mutation, Gene, and CNV tracks for each primary site.
+
+![GDC primary sites](images/GDC-primary-sites.png)
+
+# Export Types
+The following export types are supported by both GDC Genes and Mutations. To export, select `Save track data` in the track dropdown. Note that not all track information is carried over to the exported file.
+* BED
+* GFF3
+* Sequin Table
+* CSV
+* Track Config
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