Merge pull request #56 from agduncan94/develop

release 0.1.6

.travis.yml

@@ -33,7 +33,33 @@ install:
   - 'if [ "$TRAVIS_PULL_REQUEST" = "false" ]; then docker-compose build --build-arg plugin_version=${TRAVIS_BRANCH}; fi'
   - docker-compose up -d
   - cd ../
+  - cpanm --notest Text::Markdown DateTime JSON
+  - cd ../
+  - git clone https://github.com/GMOD/jbrowse.git
+  - cp -R $TRAVIS_BUILD_DIR jbrowse/plugins/
+  - cd $TRAVIS_BUILD_DIR
 
 script:
-  # - $(npm bin)/cypress run --record
-  - $(npm bin)/cypress run
+  - $(npm bin)/cypress run
+  # Only build below if on a tag
+  - |
+    if [[ "x$TRAVIS_TAG" != "x" ]]; then
+      cd ../jbrowse/
+      RELEASE_VERSION=`node -e 'require("fs").readFile("src/JBrowse/package.json", (e,d)=>console.log(JSON.parse(d).version))'`
+      make -f build/Makefile release-min
+      rm -rf JBrowse-*/
+      unzip -q JBrowse-$RELEASE_VERSION.zip
+      cd $TRAVIS_BUILD_DIR
+    fi
+
+deploy:
+  provider: s3
+  skip_cleanup: true
+  access_key_id: $AWS_ACCESS_KEY
+  secret_access_key: $AWS_SECRET
+  bucket: "gdc-jbrowse"
+  local-dir: ../jbrowse/JBrowse-$RELEASE_VERSION
+  upload-dir: code/gdc-viewer/$TRAVIS_BRANCH
+  on:
+    repo: agduncan94/gdc-viewer
+    tags: true

cypress/integration/ExploreGDC.js

@@ -120,7 +120,7 @@ describe('Explore GDC', function() {
         })
 
         checkAllResultsTab(
-            ['Showing 1 to 20 of 3,107', 'TCGA-A5-A1OF', 'TCGA-AJ-A3EK'],
+            ['Showing 1 to 20 of 3,110', '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']
         )

cypress/integration/ExportCNVTrack.js

@@ -54,9 +54,9 @@ describe('CNV track', function() {
     // Assumption: loc=1%3A1..248956422
     it('Should be able to export CNV in various export formats', function() {
         testExport(2, 'GFF3', ['##gff-version 3', '##sequence-region'])
-        testExport(3, 'bedGraph', ['track type=bedGraph name="GDC_CNV"', '1	51354263	51519328	-1'])
-        testExport(4, 'CSV', ['start,end,score', '51354263,51519328,-1'])
-        testExport(5, 'Wiggle', ['track type=wiggle_0 name="GDC_CNV"', 'variableStep chrom=1 span=165065'])
+        testExport(3, 'bedGraph', ['track type=bedGraph name="GDC_CNV"', '1	51354262	51519328	-1'])
+        testExport(4, 'CSV', ['start,end,score', '51354262,51519328,-1'])
+        testExport(5, 'Wiggle', ['track type=wiggle_0 name="GDC_CNV"', 'variableStep chrom=1 span=165066'])
         cy.fixture('ExportCNVs/track-conf-export.conf').then((json) => {
             testExport(6, 'Track Config', [json])
         })

cypress/integration/ExportGeneTrack.js

@@ -73,9 +73,9 @@ describe('Gene track', function() {
     // Assumption: loc=1%3A1..248956422
     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', ['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'])
+        testExport(3, 'BED', ['track name="GDC_Genes" useScore=0', '1	152302174	152325203	ENSG00000143631		-'])
+        testExport(4, 'CSV', ['id,type,start,end,chromosome,strand,gene name,biotype,symbol,synonyms', 'ENSG00000143631,Gene,152302174,152325203,1,-1,filaggrin,protein_coding,FLG'])
+        testExport(5, 'Sequin Table', ['>Feature 1', '152325203	152302175	Gene'])
         cy.fixture('ExportGenes/track-conf-export.conf').then((json) => {
             testExport(6, 'Track Config', [json])
         })

cypress/integration/ExportSSMTrack.js

@@ -73,9 +73,9 @@ describe('SSM track', function() {
     // Assumption: loc=1%3A1..248956422
     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', ['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'])
+        testExport(3, 'BED', ['track name="GDC_SSM" useScore=0', '1	56496416	56496417	ec690998-d555-5ed3-ab18-55e8685b2bfd'])
+        testExport(4, 'CSV', ['id,type,start,end,chromosome,reference allele,dna change,subtype', 'ec690998-d555-5ed3-ab18-55e8685b2bfd,Simple Somatic Mutation,56496416,56496417,,T,chr1:g.56496417delT,Small deletion'])
+        testExport(5, 'Sequin Table', ['>Feature 1', '56496417	56496417	Simple Somatic Mutation'])
         cy.fixture('ExportSSMs/track-conf-export.conf').then((json) => {
             testExport(6, 'Track Config', [json])
         })

data/tracks.conf

@@ -14,4 +14,18 @@ metadata.datatype=Gene
 storeClass=gdc-viewer/Store/SeqFeature/CNVs
 type=gdc-viewer/View/Track/CNVTrack
 key=GDC CNV
-metadata.datatype=CNV
+metadata.datatype=CNV
+
+[tracks.GDC_SSM-Cancer_Gene_Census]
+storeClass=gdc-viewer/Store/SeqFeature/SimpleSomaticMutations
+type=gdc-viewer/View/Track/SSMTrack
+key=GDC SSM - Cancer Gene Census
+metadata.datatype=SSM
+filters={"op":"and","content":[{"op":"in","content":{"field":"genes.is_cancer_gene_census","value":["1"]}}]}
+
+[tracks.GDC_Genes-Cancer_Gene_Census]
+storeClass=gdc-viewer/Store/SeqFeature/Genes
+type=gdc-viewer/View/Track/GeneTrack
+key=GDC Genes - Cancer Gene Census
+metadata.datatype=Gene
+filters={"op":"and","content":[{"op":"in","content":{"field":"genes.is_cancer_gene_census","value":["1"]}}]}

docs/Gemfile

@@ -8,18 +8,18 @@ source "https://rubygems.org"
 #
 # This will help ensure the proper Jekyll version is running.
 # Happy Jekylling!
-gem "jekyll", "~> 3.7.3"
+gem "jekyll", "~> 3.8.7"
 
 # This is the default theme for new Jekyll sites. You may change this to anything you like.
-gem "minima", "~> 2.0"
+gem "minima", "~> 2.5.1"
 
 # 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"
+  gem "jekyll-feed", "~> 0.13.0"
 end
 
 # Windows does not include zoneinfo files, so bundle the tzinfo-data gem

docs/Gemfile.lock

@@ -9,12 +9,12 @@ GEM
       eventmachine (>= 0.12.9)
       http_parser.rb (~> 0.6.0)
     eventmachine (1.2.7)
-    ffi (1.12.2)
+    ffi (1.13.0)
     forwardable-extended (2.6.0)
     http_parser.rb (0.6.0)
     i18n (0.9.5)
       concurrent-ruby (~> 1.0)
-    jekyll (3.7.4)
+    jekyll (3.8.7)
       addressable (~> 2.4)
       colorator (~> 1.0)
       em-websocket (~> 0.5)
@@ -35,9 +35,11 @@ GEM
       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)
+    just-the-docs (0.2.8)
+      bundler (~> 2.1.4)
+      jekyll (>= 3.8.5, < 4.1.0)
+      jekyll-seo-tag (~> 2.0)
+      rake (>= 12.3.1, < 13.1.0)
     kramdown (1.17.0)
     liquid (4.0.3)
     listen (3.2.1)
@@ -50,12 +52,12 @@ GEM
       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)
+    public_suffix (4.0.5)
+    rake (13.0.1)
+    rb-fsevent (0.10.4)
     rb-inotify (0.10.1)
       ffi (~> 1.0)
-    rouge (3.17.0)
+    rouge (3.19.0)
     safe_yaml (1.0.5)
     sass (3.7.4)
       sass-listen (~> 4.0.0)
@@ -67,10 +69,10 @@ PLATFORMS
   ruby
 
 DEPENDENCIES
-  jekyll (~> 3.7.3)
-  jekyll-feed (~> 0.6)
+  jekyll (~> 3.8.7)
+  jekyll-feed (~> 0.13.0)
   just-the-docs
-  minima (~> 2.0)
+  minima (~> 2.5.1)
   tzinfo-data
 
 BUNDLED WITH

docs/tracks.md

@@ -143,7 +143,7 @@ storeClass=gdc-viewer/Store/SeqFeature/CNVs
 type=gdc-viewer/View/Track/CNVTrack
 key=GDC CNV
 metadata.datatype=CNV
-
+filters={"op":"=","content":{"field":"cnv_change","value":["Gain"]}}
 ```
 
 ![GDC CNVs]({{ site.url }}/assets/images/GDC-cnv-gain.png)

gdc-viewer/js/Store/SeqFeature/CNVs.js

@@ -110,7 +110,7 @@ function(
             cnvFeature = {
                 id: cnv.id,
                 data: {
-                    'start': cnv.start_position,
+                    'start': cnv.start_position - 1,
                     'end': cnv.end_position,
                     'score': thisB.convertCNVChangeToScore(cnv.cnv_change)
                 }

gdc-viewer/js/Store/SeqFeature/Genes.js

@@ -70,7 +70,7 @@ function(
                 id: gene.gene_id,
                 data: {
                     'entity_name': gene.gene_id,
-                    'start': thisB.prettyText(gene.gene_start),
+                    'start': thisB.prettyText(gene.gene_start - 1),
                     'end': thisB.prettyText(gene.gene_end),
                     'strand': thisB.prettyText(gene.gene_strand),
                     'type': 'Gene',

gdc-viewer/js/Store/SeqFeature/SimpleSomaticMutations.js

@@ -143,7 +143,7 @@ function(
                 id: mutation.ssm_id,
                 data: {
                     'entity_name': mutation.ssm_id,
-                    'start': thisB.prettyText(mutation.start_position),
+                    'start': thisB.prettyText(mutation.start_position - 1),
                     'end': thisB.prettyText(mutation.end_position),
                     'type': 'Simple Somatic Mutation',
                     'projects': mutation.ssm_id,