sequenceserver 2.0.0.beta1 → 2.0.0.beta3

checksums.yaml

@@ -1,7 +1,7 @@
 ---
-SHA1:
-  metadata.gz: 9e93a0ff5ecf5f80747e270285cf563557ecfb46
-  data.tar.gz: 17d972e191f301ffb704bb3838b5f7de0b8f0f4c
+SHA256:
+  metadata.gz: c896a2ea19a91dbb08a321031f4ef62489ea85191821d9f67bfed2e88dd918ad
+  data.tar.gz: 9d4e09e3097a6fa5ec1bf691e7d1ca216cbcb062b63df4dfbdd4d0daee9e1906
 SHA512:
-  metadata.gz: 15ef2d18c14fc2cfaec9a422ee1b569cfa380ea23df1258045c4085ccb2fbfef8f0b26a5eccde5a58ceb68eace7c67669cef6bade15dc11ec0e85fbfb07bb4dd
-  data.tar.gz: 9ecd465890cb316446748d181b9c4a2a29a53b203d943142d76f23e2a53cd8bbabbaf5f798f8478317aef09ed0b3d23dfbbe4487f97eee013167de4b2dee410c
+  metadata.gz: 8eb71af6ecddeef7bab23be7b6208f2309406a8ebd68079e0c231fcceed7991e82113f671f815fd2c817e7126521bd9d7ab2be944268f0a867b869c77c283364
+  data.tar.gz: b5e2acc07ccdcd254f769e772c1d46579ae3009b81ff8e327b221ccac7b39c28885ffa0f108c5fdd8ba66d57db310ed7673977a2b1f80798a23979784a963b9f

data/.travis.yml

@@ -2,43 +2,34 @@ language: ruby
 
 rvm:
   - 2.3
-  - 2.4
   - 2.5
 
-addons:
-  sauce_connect: true
-
 branches:
   only:
     - 1.0.x  # stable
     - master
 
 install:
-  - wget -c "ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.6.0/ncbi-blast-2.6.0+-x64-linux.tar.gz"
+  - wget -c "https://github.com/mozilla/geckodriver/releases/download/v0.24.0/geckodriver-v0.24.0-linux64.tar.gz"
+  - mkdir geckodriver && tar xvf geckodriver-*.tar.gz -C geckodriver
+  - export PATH="geckodriver:$PATH"
+  - wget -c "ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.9.0/ncbi-blast-2.9.0+-x64-linux.tar.gz"
   - tar xvf ncbi-blast-*.tar.gz
   - gem install bundler && bundle
-  - bundle exec bin/sequenceserver -s -b ncbi-blast-2.6.0+/bin -d spec/database/sample
+  - bundle exec bin/sequenceserver -s -b ncbi-blast-2.9.0+/bin -d spec/database/sample
 
 before_script:
   - curl -L https://codeclimate.com/downloads/test-reporter/test-reporter-latest-linux-amd64 > ./cc-test-reporter && chmod +x ./cc-test-reporter
   - ./cc-test-reporter before-build
 script:
-  - bundle exec rspec --exclude-pattern 'capybara*' # unit tests
-  - platform='macOS 10.14' browserName=safari browserVersion=12 bundle exec rspec spec/capybara_spec.rb
-  - platform='macOS 10.14' browserName=chrome browserVersion=71 bundle exec rspec spec/capybara_spec.rb
-  - platform='macOS 10.14' browserName=firefox browserVersion=64 bundle exec rspec spec/capybara_spec.rb
-  - platform='Windows 10' browserName=microsoftedge browserVersion='16.16299' bundle exec rspec spec/capybara_spec.rb
-  - platform='Windows 10' browserName=chrome browserVersion=71 bundle exec rspec spec/capybara_spec.rb
-  - platform='Windows 10' browserName=firefox browserVersion=64 bundle exec rspec spec/capybara_spec.rb
-  - platform='Linux' browserName=chrome browserVersion=48 bundle exec rspec spec/capybara_spec.rb
-  - platform='Linux' browserName=firefox browserVersion=45 bundle exec rspec spec/capybara_spec.rb
+  - bundle exec rspec
 after_script:
   - ./cc-test-reporter after-build # --exit-code $TRAVIS_TEST_RESULT
 
 cache:
   directories:
     - vendor/bundle
-    - ncbi-blast-2.6.0+
+    - ncbi-blast-2.9.0+
 
 sudo: false
 

data/Dockerfile

@@ -11,18 +11,13 @@ RUN apt-get update  && apt-get install -y --no-install-recommends \
         curl wget \
         gnupg \
         git \
-        ncbi-blast+ \
         zlib1g-dev
 
-RUN curl -sL https://deb.nodesource.com/setup_8.x | bash - && \
-        apt-get update  && apt-get install -y --no-install-recommends \
-        nodejs npm && \
-        rm -rf /var/lib/apt/lists/*
-
 VOLUME ["/db"]
 EXPOSE 4567
 
 COPY . /sequenceserver
 WORKDIR /sequenceserver
-RUN gem install bundler && bundle && npm install
+RUN gem install bundler && bundle install --without=development
+RUN yes '' | bundle exec bin/sequenceserver -s
 ENTRYPOINT ["bundle", "exec", "bin/sequenceserver", "-d", "/db"]

data/README.md

@@ -4,7 +4,7 @@
 [![gitter chat](https://badges.gitter.im/gitterHQ/gitter.png)](https://gitter.im/wurmlab/sequenceserver)
 
 **Beta version:** 
-[![new gem version](https://img.shields.io/badge/version-1.1.0%20(new%20beta)-yellowgreen.svg)](http://rubygems.org/gems/sequenceserver) **GitHub Master:** [![build status](https://secure.travis-ci.org/wurmlab/sequenceserver.png)](https://travis-ci.org/wurmlab/sequenceserver)
+[![new gem version](https://img.shields.io/badge/version-2.0%20(beta)-yellowgreen.svg)](http://rubygems.org/gems/sequenceserver) **GitHub Master:** [![build status](https://secure.travis-ci.org/wurmlab/sequenceserver.png)](https://travis-ci.org/wurmlab/sequenceserver)
 
 
 
@@ -39,13 +39,15 @@ use of 'bundler' Ruby gem to install dependencies and to run SequenceServer:
     # Use bundler command to run SequenceServer
     bundle exec bin/sequenceserver
 
-If you use SequenceServer, please cite our preprint:
+If you use SequenceServer, please cite:
 
-> [Priyam A, Woodcroft BJ, Rai V, Munagala A, Moghul I, Ter F, Gibbins MA, Moon H, Leonard G, Rumpf W & Wurm Y. 2015. Sequenceserver: A modern graphical user interface for custom BLAST databases. biorxiv doi: 10.1101/033142](http://www.biorxiv.org/content/early/2015/11/27/033142).
+> [Sequenceserver: A modern graphical user interface for custom BLAST
+  databases. Molecular Biology and Evolution
+  (2019).](https://doi.org/10.1093/molbev/msz185)
 
-## Version 1.1.0-beta12
+## Version 2.0 (beta)
 
-This is a beta release of SequenceServer 2.0
+Beta release of SequenceServer version 2.0.
 
 Here, we have changed the underlying architecture to persist jobs so that
 the results can be bookmarked or shared, and to support integration with
@@ -58,15 +60,15 @@ The new beta releases are announced on [Google Group](https://groups.google.com/
 
 ### Install and configure
 
-To get the latest 1.1.0-beta release, run:
+To get the latest 2.0 (beta) release, run:
 
     gem install --pre sequenceserver
 
 If you are new to the above command, please consult the 'Install or update'
 section on our website http://sequenceserver.com.
 
-If you want to install and use the beta versions from source, the process is
-the same as for the old stable release (instructions above).
+If you want to install and use the beta versions from source, the process
+is the same as for the old stable release (instructions above).
 
 ### Develop and contribute
 
@@ -124,7 +126,3 @@ docker run --rm -ti -p 4567:4567 -v $(pwd)/db:/db wurmlab/sequenceserver:1.0.11
 * Anurag Priyam (architect) - [email](mailto:anurag08priyam@gmail.com) | [@yeban](//twitter.com/yeban)
 * Yannick Wurm  (PI) - [email](mailto:yannickwurm@gmail.com) | [@yannick\_\_](//twitter.com/yannick__)
 * [Mailing list / forum](https://groups.google.com/forum/#!forum/sequenceserver)
-
-## Big Thanks
-
-Cross-browser Testing Platform and Open Source <3 Provided by [Sauce Labs](https://saucelabs.com)

data/lib/sequenceserver/version.rb

@@ -1,4 +1,4 @@
 # Define version number.
 module SequenceServer
-  VERSION = '2.0.0.beta1'.freeze
+  VERSION = '2.0.0.beta3'.freeze
 end

data/package.json

@@ -1,7 +1,7 @@
 {
   "name": "SequenceServer",
   "description": "BLAST searching made easy!",
-  "version": "1.1.0-beta",
+  "version": "2.0.0-beta",
   "homepage": "http://www.sequenceserver.com",
   "repository": "https://github.com/yannickwurm/sequenceserver",
   "author": {

data/public/js/report.js

@@ -112,22 +112,14 @@ var Report = React.createClass({
     },
 
     /**
-     * Incrementally update state so that the rendering process is
-     * not overwhelemed when there are too many queries.
+     * Incrementally update state (50 queries at a time) so that the rendering
+     * process is not overwhelemed when there are too many queries.
      */
     updateState: function(responseJSON) {
         var queries = responseJSON.queries;
-
-        // Render results for first 50 queries and set flag if total queries is
-        // more than 250.
-        var numHits = 0;
+        responseJSON.num_queries = queries.length;
         responseJSON.veryBig = queries.length > 250;
-        //responseJSON.veryBig = !_.every(queries, (query) => {
-            //numHits += query.hits.length;
-            //return (numHits <= 500);
-        //});
         responseJSON.queries = queries.splice(0, 50);
-        responseJSON.num_queries = queries.length;
         this.setState(responseJSON);
 
         // Render results for remaining queries.
@@ -306,10 +298,6 @@ var Report = React.createClass({
         if (this.updateCycle === 1 ) this.affixSidebar();
     },
 
-    /**
-     * Prevents folding of hits during text-selection, etc.
-     */
-
     /**
      * Called after all results have been rendered.
      */
@@ -926,6 +914,7 @@ var SideBar = React.createClass({
         }).get();
         var database_ids = _.map(this.props.data.querydb, _.iteratee('id'));
         downloadFASTA(sequence_ids, database_ids);
+        return false;
     },
 
     /**
@@ -937,6 +926,7 @@ var SideBar = React.createClass({
         }).get();
         var database_ids = _.map(this.props.data.querydb, _.iteratee('id'));
         downloadFASTA(sequence_ids, database_ids);
+        return false;
     },
 
     downloadAlignmentOfAll: function() {
@@ -956,6 +946,7 @@ var SideBar = React.createClass({
         }, this));
         console.log('len '+hsps_arr.length);
         aln_exporter.export_alignments(hsps_arr, "alignment-"+sequence_ids.length+"_hits");
+        return false;
     },
 
     downloadAlignmentOfSelected: function () {
@@ -977,6 +968,7 @@ var SideBar = React.createClass({
             });
         }, this));
         aln_exporter.export_alignments(hsps_arr, "alignment-"+sequence_ids.length+"_hits");
+        return false;
     },
 
 
@@ -1043,29 +1035,28 @@ var SideBar = React.createClass({
                 <ul className="nav">
                     {
                         !this.props.data.imported_xml && <li>
-                            <a className="download-fasta-of-all"
+                            <a href="#" className="btn-link download-fasta-of-all"
                                 onClick={this.downloadFastaOfAll}>
                                 FASTA of all hits
                             </a>
                         </li>
                     }
                     {
-                       !this.props.data.imported_xml && <li>
-                        <a
-                            className="download-fasta-of-selected disabled"
-                            onClick={this.downloadFastaOfSelected}>
-                            FASTA of <span className="text-bold"></span> selected hit(s)
-                        </a>
-                    </li>
+                        !this.props.data.imported_xml && <li>
+                            <a href="#" className="btn-link download-fasta-of-selected disabled"
+                                onClick={this.downloadFastaOfSelected}>
+                                FASTA of <span className="text-bold"></span> selected hit(s)
+                            </a>
+                        </li>
                     }
                     <li>
-                        <a className="download-alignment-of-all"
+                        <a href="#" className="btn-link download-alignment-of-all"
                             onClick={this.downloadAlignmentOfAll}>
                             Alignment of all hits
                         </a>
                     </li>
                     <li>
-                        <a className="download-alignment-of-selected disabled"
+                        <a href="#" className="btn-link download-alignment-of-selected disabled"
                             onClick={this.downloadAlignmentOfSelected}>
                             Alignment of <span className="text-bold"></span> selected hit(s)
                         </a>

data/public/sequenceserver-report.min.js

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The page will update automatically when BLAST is done.",e.createElement("br",null),e.createElement("br",null),"You can bookmark the page and come back to it later or share the link with someone.")))},resultsJSX:function(){return e.createElement("div",{className:"row"},this.shouldShowSidebar()&&e.createElement("div",{className:"col-md-3 hidden-sm hidden-xs"},e.createElement(t,{data:this.state,shouldShowIndex:this.shouldShowIndex()})),e.createElement("div",{className:this.shouldShowSidebar()?"col-md-9":"col-md-12"},this.overviewJSX(),this.isHitsAvailable()?e.createElement(h,{queries:this.state.queries,program:this.state.program,collapsed:"true"}):e.createElement("span",null),g.map(this.state.queries,g.bind(function(a){return e.createElement(p,{key:"Query_"+a.id,program:this.state.program,querydb:this.state.querydb,query:a,num_queries:this.state.num_queries,veryBig:this.state.veryBig,selectHit:this.selectHit,imported_xml:this.state.imported_xml})},this))))},overviewJSX:function(){return 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this.state.queries.length<=8},componentDidMount:function(){this.preventCollapseOnSelection()},componentDidUpdate:function(){this.updateCycle+=1,1===this.updateCycle&&this.affixSidebar()},componentFinishedUpdating:function(){this.shouldShowIndex()&&this.setupScrollSpy()},preventCollapseOnSelection:function(){$("body").on("mousedown",".hit > .section-header > h4",function(a){var b=$(this);b.on("mouseup mousemove",function a(c){if("mouseup"===c.type){b.attr("data-toggle","collapse");var d=$("#"+b.attr("data-target"));d.toggleClass("in"),b.find(".fa-chevron-down").toggleClass("fa-rotate-270")}else b.attr("data-toggle","");b.off("mouseup mousemove",a)})})},affixSidebar:function(){var a=$(".sidebar");a.affix({offset:{top:a.offset().top}})},setupScrollSpy:function(){$("body").scrollspy({target:".sidebar"})},selectHit:function(a){var b=$("#"+a),c=$(".hit-links :checkbox:checked").length;if(b&&b.val()){var 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"),e.createElement("button",{className:"btn btn-link download-fa",onClick:this.downloadFASTA},e.createElement("i",{className:"fa fa-download"})," FASTA")],e.createElement("span",null," | "),e.createElement("button",{className:"btn btn-link download-aln",onClick:this.downloadAlignment},e.createElement("i",{className:"fa fa-download"})," Alignment"),g.map(this.props.hit.links,g.bind(function(a){return[e.createElement("span",null," | "),this.a(a)]},this)))},hspListJSX:function(){var a=this;return e.createElement("div",{className:"hsps"},this.props.hit.hsps.map(function(b){return e.createElement(k,{key:b.number,algorithm:a.props.algorithm,queryNumber:a.props.query.number,hitNumber:a.props.hit.number,hsp:b})},this))}}),s=function(){var a=e.createClass({displayName:"Viewer",widgetClass:"biojs-vis-sequence",render:function(){return this.widgetID=this.widgetClass+"-"+(new Date).getUTCMilliseconds(),e.createElement("div",{className:"fastan"},e.createElement("div",{className:"section-header"},e.createElement("h4",null,this.props.sequence.id,e.createElement("small",null,"  ",this.props.sequence.title))),e.createElement("div",{className:"section-content"},e.createElement("div",{className:this.widgetClass,id:this.widgetID})))},componentDidMount:function(){var a=new Sequence({sequence:this.props.sequence.value,target:this.widgetID,format:"PRIDE",columns:{size:40,spacedEach:0},formatOptions:{title:!1,footer:!1}});a.hideFormatSelector()}});return e.createClass({show:function(){this.modal().modal("show")},modal:function(){return $(e.findDOMNode(this.refs.modal))},resultsJSX:function(){return e.createElement("div",{className:"modal-body"},g.map(this.state.error_msgs,g.bind(function(a){return e.createElement("div",{className:"fastan"},e.createElement("div",{className:"section-header"},e.createElement("h4",null,a[0])),e.createElement("div",{className:"section-content"},e.createElement("pre",{className:"pre-reset"},a[1])))},this)),g.map(this.state.sequences,g.bind(function(b){return e.createElement(a,{sequence:b})},this)))},loadingJSX:function(){return e.createElement("div",{className:"modal-body text-center"},e.createElement("i",{className:"fa fa-spinner fa-3x fa-spin"}))},getInitialState:function(){return{error_msgs:[],sequences:[],requestCompleted:!1}},render:function(){return e.createElement("div",{className:"modal sequence-viewer",ref:"modal",tabIndex:"-1"},e.createElement("div",{className:"modal-dialog"},e.createElement("div",{className:"modal-content"},e.createElement("div",{className:"modal-header"},e.createElement("h3",null,"View sequence")),this.state.requestCompleted&&this.resultsJSX()||this.loadingJSX())))},componentDidMount:function(){this.show(),$.getJSON(this.props.url).done(g.bind(function(a){this.setState({sequences:a.sequences,error_msgs:a.error_msgs,requestCompleted:!0})},this)).fail(function(a,b,c){l(a,function(){this.hide()})}),this.modal().on("hidden.bs.modal",this.props.onHide)}})}(),t=e.createClass({displayName:"SideBar",downloadFastaOfAll:function(){var a=$(".hit-links :checkbox").map(function(){return this.value}).get(),b=g.map(this.props.data.querydb,g.iteratee("id"));m(a,b)},downloadFastaOfSelected:function(){var a=$(".hit-links :checkbox:checked").map(function(){return this.value}).get(),b=g.map(this.props.data.querydb,g.iteratee("id"));m(a,b)},downloadAlignmentOfAll:function(){var a=$(".hit-links :checkbox").map(function(){return this.value}).get(),b=[],c=new j;g.each(this.props.data.queries,g.bind(function(a){g.each(a.hits,function(c){g.each(c.hsps,function(d){d.hit_id=c.id,d.query_id=a.id,b.push(d)})})},this)),console.log("len "+b.length),c.export_alignments(b,"alignment-"+a.length+"_hits")},downloadAlignmentOfSelected:function(){var a=$(".hit-links :checkbox:checked").map(function(){return this.value}).get(),b=[],c=new j;console.log("check "+a.toString()),g.each(this.props.data.queries,g.bind(function(c){g.each(c.hits,function(d){g.indexOf(a,d.accession)!=-1&&g.each(d.hsps,function(a){a.hit_id=d.id,a.query_id=c.id,b.push(a)})})},this)),c.export_alignments(b,"alignment-"+a.length+"_hits")},render:function(){return e.createElement("div",{className:"sidebar"},this.props.shouldShowIndex&&this.index(),this.downloads())},index:function(){return e.createElement("div",{className:"index"},e.createElement("div",{className:"section-header"},e.createElement("h4",null,this.summary())),e.createElement("ul",{className:"nav hover-reset 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b,c,d,e,f,g,h,i,j,k,l,m,n,o,p,q,r,s,t;return{setters:[function(a){b=a},function(a){c=a.default},function(a){d=a.default},function(a){e=a.default},function(a){f=a.default},function(a){},function(a){g=a.default},function(a){h=a.default},function(a){i=a.default},function(a){j=a.default},function(a){k=a.default},function(a){},function(a){l=a.default}],execute:function(){m=function(a,b){function c(a,b){d.append($("<input>").attr("type","hidden").attr("name",a).val(b))}var d=$("<form/>").attr("method","post").attr("action","get_sequence");c("sequence_ids",a),c("database_ids",b),d.appendTo("body").submit().remove()},n=e.createClass({displayName:"Page",render:function(){return e.createElement("div",null,e.createElement("div",{className:"container"},e.createElement(o,{ref:"report"})),e.createElement("canvas",{id:"png-exporter",hidden:!0}))}}),o=e.createClass({displayName:"Report",getInitialState:function(){return this.fetchResults(),this.updateCycle=0,{search_id:"",program:"",program_version:"",submitted_at:"",num_queries:0,queries:[],querydb:[],params:[],stats:[]}},fetchResults:function(){function a(){$.getJSON(location.pathname+".json").complete(function(d){switch(d.status){case 202:var e;e=1===b.length?b[0]:b.shift(),setTimeout(a,e);break;case 200:c.updateState(d.responseJSON);break;case 404:case 400:case 500:l(d.responseJSON)}})}var b=[200,400,800,1200,2e3,3e3,5e3],c=this;a()},updateState:function(a){var b=a.queries;a.num_queries=b.length,a.veryBig=b.length>250,a.queries=b.splice(0,50),this.setState(a);var c=function a(){b.length>0?(this.setState({queries:this.state.queries.concat(b.splice(0,50))}),setTimeout(a.bind(this),500)):this.componentFinishedUpdating()};setTimeout(c.bind(this),500)},render:function(){return this.isResultAvailable()?this.resultsJSX():this.loadingJSX()},loadingJSX:function(){return e.createElement("div",{className:"row"},e.createElement("div",{className:"col-md-6 col-md-offset-3 text-center"},e.createElement("h1",null,e.createElement("i",{className:"fa fa-cog fa-spin"}),"  BLAST-ing"),e.createElement("p",null,e.createElement("br",null),"This can take some time depending on the size of your query and database(s). The page will update automatically when BLAST is done.",e.createElement("br",null),e.createElement("br",null),"You can bookmark the page and come back to it later or share the link with someone.")))},resultsJSX:function(){return e.createElement("div",{className:"row"},this.shouldShowSidebar()&&e.createElement("div",{className:"col-md-3 hidden-sm hidden-xs"},e.createElement(t,{data:this.state,shouldShowIndex:this.shouldShowIndex()})),e.createElement("div",{className:this.shouldShowSidebar()?"col-md-9":"col-md-12"},this.overviewJSX(),this.isHitsAvailable()?e.createElement(h,{queries:this.state.queries,program:this.state.program,collapsed:"true"}):e.createElement("span",null),g.map(this.state.queries,g.bind(function(a){return e.createElement(p,{key:"Query_"+a.id,program:this.state.program,querydb:this.state.querydb,query:a,num_queries:this.state.num_queries,veryBig:this.state.veryBig,selectHit:this.selectHit,imported_xml:this.state.imported_xml})},this))))},overviewJSX:function(){return e.createElement("div",{className:"overview"},e.createElement("pre",{className:"pre-reset"},this.state.program_version,this.state.submitted_at&&"; query submitted on "+this.state.submitted_at,e.createElement("br",null),"Databases (",this.state.stats.nsequences," sequences, ",this.state.stats.ncharacters," characters): ",this.state.querydb.map(function(a){return a.title}).join(", "),e.createElement("br",null),"Parameters: ",g.map(this.state.params,function(a,b){return b+" "+a}).join(", ")))},isResultAvailable:function(){return this.state.queries.length>=1},isHitsAvailable:function(){var a=0;return g.each(this.state.queries,function(b){0==b.hits.length&&a++}),!(a==this.state.queries.length)},shouldShowSidebar:function(){return!(1==this.state.queries.length&&0==this.state.queries[0].hits.length)},shouldShowIndex:function(){return this.state.queries.length<=8},componentDidMount:function(){this.preventCollapseOnSelection()},componentDidUpdate:function(){this.updateCycle+=1,1===this.updateCycle&&this.affixSidebar()},componentFinishedUpdating:function(){this.shouldShowIndex()&&this.setupScrollSpy()},preventCollapseOnSelection:function(){$("body").on("mousedown",".hit > .section-header > h4",function(a){var b=$(this);b.on("mouseup mousemove",function a(c){if("mouseup"===c.type){b.attr("data-toggle","collapse");var d=$("#"+b.attr("data-target"));d.toggleClass("in"),b.find(".fa-chevron-down").toggleClass("fa-rotate-270")}else b.attr("data-toggle","");b.off("mouseup mousemove",a)})})},affixSidebar:function(){var a=$(".sidebar");a.affix({offset:{top:a.offset().top}})},setupScrollSpy:function(){$("body").scrollspy({target:".sidebar"})},selectHit:function(a){var b=$("#"+a),c=$(".hit-links :checkbox:checked").length;if(b&&b.val()){var d=$(b.data("target"));if(b.is(":checked")?(d.find(".section-content").addClass("glow"),$(".download-alignment-of-selected").enable(),$(".download-fasta-of-selected").enable()):d.find(".section-content").removeClass("glow"),c>=1){var e=$(".download-fasta-of-selected"),f=$(".download-alignment-of-selected");e.find(".text-bold").html(c),f.find(".text-bold").html(c)}if(0==c){var e=$(".download-fasta-of-selected"),f=$(".download-alignment-of-selected");e.addClass("disabled").find(".text-bold").html(""),f.addClass("disabled").find(".text-bold").html("")}}}}),p=e.createClass({displayName:"Query",domID:function(){return"Query_"+this.props.query.number},numhits:function(){return this.props.query.hits.length},render:function(){return e.createElement("div",{className:"resultn",id:this.domID(),"data-query-len":this.props.query.length,"data-algorithm":this.props.program},e.createElement("div",{className:"section-header"},e.createElement("h3",null,"Query= ",this.props.query.id," ",e.createElement("small",null,this.props.query.title)),e.createElement("span",{className:"label label-reset pos-label",title:"Query"+this.props.query.number+".","data-toggle":"tooltip"},this.props.query.number+"/"+this.props.num_queries)),this.numhits()&&e.createElement("div",{className:"section-content"},e.createElement(c,{key:"GO_"+this.props.query.number,query:this.props.query,program:this.props.program,collapsed:this.props.veryBig}),e.createElement(d,{key:"LD_"+this.props.query.id,query:this.props.query,algorithm:this.props.program,collapsed:"true"}),e.createElement(q,{key:"HT_"+this.props.query.number,query:this.props.query,imported_xml:this.props.imported_xml}),e.createElement("div",{id:"hits"},g.map(this.props.query.hits,g.bind(function(a){return e.createElement(r,{hit:a,key:"HIT_"+a.number,algorithm:this.props.program,querydb:this.props.querydb,query:this.props.query,imported_xml:this.props.imported_xml,selectHit:this.props.selectHit})},this))))||e.createElement("div",{className:"section-content"},e.createElement("p",null,"Query length: ",this.props.query.length),e.createElement("br",null),e.createElement("br",null),e.createElement("p",null,e.createElement("strong",null," ****** No hits found ****** "))))},shouldComponentUpdate:function(a,b){if(!this.props.query)return!0}}),q=e.createClass({displayName:"HitsTable",mixins:[f],render:function(){var a=g.every(this.props.query.hits,function(a){return""!==a.sciname});return e.createElement("table",{className:"table table-hover table-condensed tabular-view"},e.createElement("thead",null,e.createElement("th",{className:"text-left"},"#"),e.createElement("th",null,"Similar sequences"),a&&e.createElement("th",{className:"text-left"},"Species"),!this.props.imported_xml&&e.createElement("th",{className:"text-right"},"Query coverage (%)"),e.createElement("th",{className:"text-right"},"Total score"),e.createElement("th",{className:"text-right"},"E value"),e.createElement("th",{className:"text-right","data-toggle":"tooltip","data-placement":"left",title:"Total identity of all hsps / total length of all hsps"},"Identity (%)")),e.createElement("tbody",null,g.map(this.props.query.hits,g.bind(function(b){return e.createElement("tr",{key:b.number},e.createElement("td",{className:"text-left"},b.number+"."),e.createElement("td",null,e.createElement("a",{href:"#Query_"+this.props.query.number+"_hit_"+b.number},b.id)),a&&e.createElement("td",{className:"text-left"},b.sciname),!this.props.imported_xml&&e.createElement("td",{className:"text-right"},b.qcovs),e.createElement("td",{className:"text-right"},b.score),e.createElement("td",{className:"text-right"},this.inExponential(b.hsps[0].evalue)),e.createElement("td",{className:"text-right"},b.identity))},this))))}}),r=e.createClass({displayName:"Hit",mixins:[f],accession:function(){return this.props.hit.accession},length:function(){return this.props.hit.length},domID:function(){return"Query_"+this.props.query.number+"_hit_"+this.props.hit.number},databaseIDs:function(){return g.map(this.props.querydb,g.iteratee("id"))},showSequenceViewer:function(a){this.setState({showSequenceViewer:!0}),a&&a.preventDefault()},hideSequenceViewer:function(){this.setState({showSequenceViewer:!1})},viewSequenceLink:function(){return encodeURI("get_sequence/?sequence_ids="+this.accession()+"&database_ids="+this.databaseIDs())},downloadFASTA:function(a){var b=[this.accession()];m(b,this.databaseIDs())},downloadAlignment:function(a){var b=g.map(this.props.hit.hsps,g.bind(function(a){return a.query_id=this.props.query.id,a.hit_id=this.props.hit.id,a},this)),c=new j;c.export_alignments(b,this.props.query.id+"_"+this.props.hit.id)},getInitialState:function(){return{showSequenceViewer:!1}},viewSequenceButton:function(){return this.length()>1e4?e.createElement("button",{className:"btn btn-link view-sequence disabled",title:"Sequence too long",disabled:"true"},e.createElement("i",{className:"fa fa-eye"})," Sequence"):e.createElement("button",{
+className:"btn btn-link view-sequence",onClick:this.showSequenceViewer},e.createElement("i",{className:"fa fa-eye"})," Sequence")},render:function(){return e.createElement("div",{className:"hit",id:this.domID(),"data-hit-def":this.props.hit.id,"data-hit-evalue":this.props.hit.evalue,"data-hit-len":this.props.hit.length},e.createElement("div",{className:"section-header"},e.createElement("h4",{"data-toggle":"collapse","data-target":this.domID()+"_content"},e.createElement("i",{className:"fa fa-chevron-down"})," ",e.createElement("span",null,this.props.hit.id," ",e.createElement("small",null,this.props.hit.title))),e.createElement("span",{className:"label label-reset pos-label",title:"Query "+this.props.query.number+". Hit "+this.props.hit.number+" of "+this.props.query.hits.length+".","data-toggle":"tooltip"},this.props.hit.number+"/"+this.props.query.hits.length)),e.createElement("div",{id:this.domID()+"_content",className:"section-content collapse in"},this.hitLinks(),e.createElement(i,{key:"kablammo"+this.props.query.id,query:this.props.query,hit:this.props.hit,algorithm:this.props.algorithm}),this.hspListJSX()))},hitLinks:function(){return e.createElement("div",{className:"hit-links"},e.createElement("label",null,e.createElement("input",{type:"checkbox",id:this.domID()+"_checkbox",value:this.accession(),onChange:function(){this.props.selectHit(this.domID()+"_checkbox")}.bind(this),"data-target":"#"+this.domID()})," Select"),!this.props.imported_xml&&[e.createElement("span",null," | "),this.viewSequenceButton(),this.state.showSequenceViewer&&e.createElement(s,{url:this.viewSequenceLink(),onHide:this.hideSequenceViewer})],!this.props.imported_xml&&[e.createElement("span",null," | "),e.createElement("button",{className:"btn btn-link download-fa",onClick:this.downloadFASTA},e.createElement("i",{className:"fa fa-download"})," FASTA")],e.createElement("span",null," | "),e.createElement("button",{className:"btn btn-link download-aln",onClick:this.downloadAlignment},e.createElement("i",{className:"fa fa-download"})," Alignment"),g.map(this.props.hit.links,g.bind(function(a){return[e.createElement("span",null," | "),this.a(a)]},this)))},hspListJSX:function(){var a=this;return e.createElement("div",{className:"hsps"},this.props.hit.hsps.map(function(b){return e.createElement(k,{key:b.number,algorithm:a.props.algorithm,queryNumber:a.props.query.number,hitNumber:a.props.hit.number,hsp:b})},this))}}),s=function(){var a=e.createClass({displayName:"Viewer",widgetClass:"biojs-vis-sequence",render:function(){return this.widgetID=this.widgetClass+"-"+(new Date).getUTCMilliseconds(),e.createElement("div",{className:"fastan"},e.createElement("div",{className:"section-header"},e.createElement("h4",null,this.props.sequence.id,e.createElement("small",null,"  ",this.props.sequence.title))),e.createElement("div",{className:"section-content"},e.createElement("div",{className:this.widgetClass,id:this.widgetID})))},componentDidMount:function(){var a=new Sequence({sequence:this.props.sequence.value,target:this.widgetID,format:"PRIDE",columns:{size:40,spacedEach:0},formatOptions:{title:!1,footer:!1}});a.hideFormatSelector()}});return e.createClass({show:function(){this.modal().modal("show")},modal:function(){return $(e.findDOMNode(this.refs.modal))},resultsJSX:function(){return e.createElement("div",{className:"modal-body"},g.map(this.state.error_msgs,g.bind(function(a){return e.createElement("div",{className:"fastan"},e.createElement("div",{className:"section-header"},e.createElement("h4",null,a[0])),e.createElement("div",{className:"section-content"},e.createElement("pre",{className:"pre-reset"},a[1])))},this)),g.map(this.state.sequences,g.bind(function(b){return e.createElement(a,{sequence:b})},this)))},loadingJSX:function(){return e.createElement("div",{className:"modal-body text-center"},e.createElement("i",{className:"fa fa-spinner fa-3x fa-spin"}))},getInitialState:function(){return{error_msgs:[],sequences:[],requestCompleted:!1}},render:function(){return e.createElement("div",{className:"modal sequence-viewer",ref:"modal",tabIndex:"-1"},e.createElement("div",{className:"modal-dialog"},e.createElement("div",{className:"modal-content"},e.createElement("div",{className:"modal-header"},e.createElement("h3",null,"View sequence")),this.state.requestCompleted&&this.resultsJSX()||this.loadingJSX())))},componentDidMount:function(){this.show(),$.getJSON(this.props.url).done(g.bind(function(a){this.setState({sequences:a.sequences,error_msgs:a.error_msgs,requestCompleted:!0})},this)).fail(function(a,b,c){l(a,function(){this.hide()})}),this.modal().on("hidden.bs.modal",this.props.onHide)}})}(),t=e.createClass({displayName:"SideBar",downloadFastaOfAll:function(){var a=$(".hit-links :checkbox").map(function(){return this.value}).get(),b=g.map(this.props.data.querydb,g.iteratee("id"));return m(a,b),!1},downloadFastaOfSelected:function(){var a=$(".hit-links :checkbox:checked").map(function(){return this.value}).get(),b=g.map(this.props.data.querydb,g.iteratee("id"));return m(a,b),!1},downloadAlignmentOfAll:function(){var a=$(".hit-links :checkbox").map(function(){return this.value}).get(),b=[],c=new j;return g.each(this.props.data.queries,g.bind(function(a){g.each(a.hits,function(c){g.each(c.hsps,function(d){d.hit_id=c.id,d.query_id=a.id,b.push(d)})})},this)),console.log("len "+b.length),c.export_alignments(b,"alignment-"+a.length+"_hits"),!1},downloadAlignmentOfSelected:function(){var a=$(".hit-links :checkbox:checked").map(function(){return this.value}).get(),b=[],c=new j;return console.log("check "+a.toString()),g.each(this.props.data.queries,g.bind(function(c){g.each(c.hits,function(d){g.indexOf(a,d.accession)!=-1&&g.each(d.hsps,function(a){a.hit_id=d.id,a.query_id=c.id,b.push(a)})})},this)),c.export_alignments(b,"alignment-"+a.length+"_hits"),!1},render:function(){return e.createElement("div",{className:"sidebar"},this.props.shouldShowIndex&&this.index(),this.downloads())},index:function(){return e.createElement("div",{className:"index"},e.createElement("div",{className:"section-header"},e.createElement("h4",null,this.summary())),e.createElement("ul",{className:"nav hover-reset active-bold"},g.map(this.props.data.queries,g.bind(function(a){return e.createElement("li",{key:"Side_bar_"+a.id},e.createElement("a",{className:"nowrap-ellipsis hover-bold",href:"#Query_"+a.number,title:"Query= "+a.id+" "+a.title},"Query= "+a.id))},this))))},summary:function(){var a=this.props.data.program,b=this.props.data.queries.length,c=this.props.data.querydb.length;return a.toUpperCase()+": "+b+" "+(b>1?"queries":"query")+", "+c+" "+(c>1?"databases":"database")},downloads:function(){return e.createElement("div",{className:"downloads"},e.createElement("div",{className:"section-header"},e.createElement("h4",null,"Download FASTA, XML, TSV")),e.createElement("ul",{className:"nav"},!this.props.data.imported_xml&&e.createElement("li",null,e.createElement("a",{href:"#",className:"btn-link download-fasta-of-all",onClick:this.downloadFastaOfAll},"FASTA of all hits")),!this.props.data.imported_xml&&e.createElement("li",null,e.createElement("a",{href:"#",className:"btn-link download-fasta-of-selected disabled",onClick:this.downloadFastaOfSelected},"FASTA of ",e.createElement("span",{className:"text-bold"})," selected hit(s)")),e.createElement("li",null,e.createElement("a",{href:"#",className:"btn-link download-alignment-of-all",onClick:this.downloadAlignmentOfAll},"Alignment of all hits")),e.createElement("li",null,e.createElement("a",{href:"#",className:"btn-link download-alignment-of-selected disabled",onClick:this.downloadAlignmentOfSelected},"Alignment of ",e.createElement("span",{className:"text-bold"})," selected hit(s)")),!this.props.data.imported_xml&&e.createElement("li",null,e.createElement("a",{className:"download","data-toggle":"tooltip",title:"15 columns: query and subject ID; scientific name, alignment length, mismatches, gaps, identity, start and end coordinates, e value, bitscore, query coverage per subject and per HSP.",href:"download/"+this.props.data.search_id+".std_tsv"},"Standard tabular report")),!this.props.data.imported_xml&&e.createElement("li",null,e.createElement("a",{className:"download","data-toggle":"tooltip",title:"44 columns: query and subject ID, GI, accessions, and length; alignment details; taxonomy details of subject sequence(s) and query coverage per subject and per HSP.",href:"download/"+this.props.data.search_id+".full_tsv"},"Full tabular report")),!this.props.data.imported_xml&&e.createElement("li",null,e.createElement("a",{className:"download","data-toggle":"tooltip",title:"Results in XML format.",href:"download/"+this.props.data.search_id+".xml"},"Full XML report"))))}}),e.render(e.createElement(n,null),document.getElementById("view"))}}})})(function(a){a()});

data/sequenceserver.gemspec

@@ -24,15 +24,14 @@ Gem::Specification.new do |s|
   s.add_dependency('sinatra',   '~> 2.0',  '>= 2.0.0')
   s.add_dependency('slop',      '~> 3.6',  '>= 3.6.0')
 
-  s.add_development_dependency('capybara', '~> 3.12', '>= 3.12.0')
+  s.add_development_dependency('capybara', '~> 3.15', '>= 3.15.1')
   s.add_development_dependency('capybara-screenshot', '~> 1.0', '>= 1.0.23')
-  s.add_development_dependency('codeclimate-test-reporter',
-                               '~> 1.0', '>= 1.0.8')
   s.add_development_dependency('rack-test', '~> 1.0', '>= 1.0.0')
   s.add_development_dependency('rake', '~> 10.3', '>= 10.3.2')
   s.add_development_dependency('rspec', '~> 3.7', '>= 3.7.0')
   s.add_development_dependency('sauce_whisk', '~> 0.0', '>= 0.0.19')
-  s.add_development_dependency('selenium-webdriver', '~> 3.141', '>= 3.141.0')
+  s.add_development_dependency('selenium-webdriver', '~> 3.142', '>= 3.142.3')
+  s.add_development_dependency('simplecov', '~> 0.17.0', '>= 0.17.0')
 
   # gem
   s.files         = `git ls-files`.split("\n") - ['Gemfile', 'Gemfile.lock']

data/spec/capybara_spec.rb

@@ -1,49 +1,4 @@
-require 'spec_helper'
-require 'sauce_whisk'
-require 'capybara/rspec'
-require 'selenium-webdriver'
-
-RSpec.configure do |config|
-  config.include Capybara::DSL
-end
-
-describe 'a browser', :js => true do
-  before do |scenario|
-    Capybara.app = SequenceServer.init
-    Capybara.server = :webrick
-    Capybara.javascript_driver = :selenium
-    Capybara.default_max_wait_time = 30
-
-    Capybara.register_driver :selenium do |app|
-      capabilities = {
-        name: scenario.full_description,
-        platform: ENV['platform'],
-        browserName: ENV['browserName'],
-        browserVersion: ENV['browserVersion'],
-        build: ENV['TRAVIS_BUILD_NUMBER'],
-        'tunnel-identifier': ENV['TRAVIS_JOB_NUMBER']
-      }
-      url = "https://#{ENV['SAUCE_USERNAME']}:#{ENV['SAUCE_ACCESS_KEY']}" \
-            "@ondemand.saucelabs.com:443/wd/hub".strip
-
-      Capybara::Selenium::Driver.new(app, browser: :remote, url: url,
-                                     desired_capabilities: capabilities)
-    end
-  end
-
-  before :each do |scenario|
-    jobname = scenario.full_description
-    Capybara.session_name = "#{jobname} - #{ENV['platform']} - " \
-                            "#{ENV['browserName']} - #{ENV['browserVersion']}"
-
-    @driver = Capybara.current_session.driver
-
-    # Output sessionId and jobname to std out for Sauce OnDemand Plugin to
-    # display embeded results
-    @session_id = @driver.browser.session_id
-    puts "SauceOnDemandSessionID=#{@session_id} job-name=#{jobname}"
-  end
-
+describe 'a browser', type: :feature, js: true do
   it 'properly controls blast button' do
     visit '/'
 
@@ -73,39 +28,268 @@ describe 'a browser', :js => true do
   it 'can run a simple blastn search' do
     perform_search query: nucleotide_query,
       databases: nucleotide_databases
+    page.should have_content('BLASTN')
   end
 
   it 'can run a simple blastp search' do
     perform_search query: protein_query,
       databases: protein_databases
+    page.should have_content('BLASTP')
   end
 
   it 'can run a simple blastx search' do
     perform_search query: nucleotide_query,
       databases: protein_databases
+    page.should have_content('BLASTX')
   end
 
   it 'can run a simple tblastx search' do
     perform_search query: nucleotide_query,
       databases: nucleotide_databases,
       method: 'tblastx'
+    page.should have_content('TBLASTX')
   end
 
   it 'can run a simple tblastn search' do
     perform_search query: protein_query,
       databases: nucleotide_databases
+    page.should have_content('TBLASTN')
+  end
+
+  ### Test aspects of the generated report.
+
+  it "can download FASTA of each hit" do
+    # Do a BLASTP search. protein_query refers to the first two sequence in
+    # protein_databases[0], so the top hits are the query sequences themselves.
+    perform_search(query: protein_query,
+                   databases: protein_databases.values_at(0))
+
+    # Click on the first FASTA download button on the page and wait for the
+    # download to finish.
+    page.execute_script("$('.download-fa:eq(0)').click()")
+    wait_for_download
+
+    # Test name and content of the downloaded file.
+    expect(File.basename(downloaded_file)).
+      to eq('sequenceserver-SI2.2.0_06267.fa')
+    expect(File.read(downloaded_file)).
+      to eq(File.read("#{__dir__}/sequences/sequenceserver-SI2.2.0_06267.fa"))
   end
 
-  after :each do |scenario|
-    @driver.quit
-    Capybara.use_default_driver
-    if scenario.exception
-      SauceWhisk::Jobs.fail_job @session_id
-    else
-      SauceWhisk::Jobs.pass_job @session_id
+  it "can download FASTA of selected hits" do
+    # Do a BLASTP search. protein_query refers to the first two sequence in
+    # protein_databases[0], so the top hits are the query sequences themselves.
+    perform_search(query: protein_query,
+                   databases: protein_databases.values_at(0))
+
+    # Select first hit for each query and click 'FASTA of 2 selected hits'.
+    page.check('Query_1_hit_1_checkbox')
+    page.check('Query_2_hit_1_checkbox')
+    page.click_link('FASTA of 2 selected hit(s)')
+    wait_for_download
+
+    expect(File.basename(downloaded_file)).to eq('sequenceserver-2_hits.fa')
+    expect(File.read(downloaded_file)).to eq(File.read("spec/sequences/sequenceserver-2_hits.fa"))
+  end
+
+  it "can download FASTA of all hits" do
+    # Do a BLASTP search. protein_query refers to the first two sequence in
+    # protein_databases[0], so the top hits are the query sequences themselves.
+    perform_search(query: protein_query,
+                   databases: protein_databases.values_at(0))
+
+    # Click 'FASTA of all hits'.
+    page.click_link('FASTA of all hits')
+    wait_for_download
+
+    expect(File.basename(downloaded_file)).to eq('sequenceserver-2_hits.fa')
+    expect(File.read(downloaded_file)).to eq(File.read("spec/sequences/sequenceserver-2_hits.fa"))
+  end
+
+  it "can download alignment for each hit" do
+    # Do a BLASTP search. protein_query refers to the first two sequence in
+    # protein_databases[0], so the top hits are the query sequences themselves.
+    perform_search(query: protein_query,
+                   databases: protein_databases.values_at(0))
+
+    # Click on the first Alignment download button on the page and wait for the
+    # download to finish.
+    page.execute_script("$('.download-aln:eq(0)').click()")
+    wait_for_download
+
+    # Test name and content of the downloaded file.
+    expect(File.basename(downloaded_file)).to eq('Query_1_SI2_2_0_06267.txt')
+    expect(File.read(downloaded_file)).
+      to eq(File.read("#{__dir__}/sequences/Query_1_SI2_2_0_06267.txt"))
+  end
+
+  it "can download Alignment of selected hits" do
+    # Do a BLASTP search. protein_query refers to the first two sequence in
+    # protein_databases[0], so the top hits are the query sequences themselves.
+    perform_search(query: protein_query,
+                   databases: protein_databases.values_at(0))
+
+    # Select first hit for each query and click 'Alignment of 2 selected hits'.
+    page.check('Query_1_hit_1_checkbox')
+    page.check('Query_2_hit_1_checkbox')
+    page.click_link('Alignment of 2 selected hit(s)')
+    wait_for_download
+
+    expect(File.basename(downloaded_file)).to eq('alignment-2_hits.txt')
+    expect(File.read(downloaded_file)).to eq(File.read("spec/sequences/alignment-2_hits.txt"))
+  end
+
+  it "can download Alignment of all hits" do
+    # Do a BLASTP search. protein_query refers to the first two sequence in
+    # protein_databases[0], so the top hits are the query sequences themselves.
+    perform_search(query: protein_query,
+                   databases: protein_databases.values_at(0))
+
+    # Click 'Alignment of all hits'.
+    page.click_link('Alignment of all hits')
+    wait_for_download
+
+    expect(File.basename(downloaded_file)).to eq('alignment-2_hits.txt')
+    expect(File.read(downloaded_file)).to eq(File.read("spec/sequences/alignment-2_hits.txt"))
+  end
+
+  it 'can download BLAST results in XML and tabular formats' do
+    # Do a BLASTP search. protein_query refers to the first two sequence in
+    # protein_databases[0], so the top hits are the query sequences themselves.
+    perform_search(query: protein_query,
+                   databases: protein_databases.values_at(0))
+
+    page.click_link('Standard tabular report')
+    wait_for_download
+    expect(File.basename(downloaded_file)).to eq('sequenceserver-std_tsv_report.tsv')
+    clear_downloads
+
+    page.click_link('Full tabular report')
+    wait_for_download
+    expect(File.basename(downloaded_file)).to eq('sequenceserver-full_tsv_report.tsv')
+    clear_downloads
+
+    page.click_link('Full XML report')
+    wait_for_download
+    expect(File.basename(downloaded_file)).to eq('sequenceserver-xml_report.xml')
+    clear_downloads
+  end
+
+  it 'can show hit sequences in a modal' do
+    # Do a BLASTP search. protein_query refers to the first two sequence in
+    # protein_databases[0], so the top hits are the query sequences themselves.
+    perform_search(query: protein_query,
+                   databases: protein_databases.values_at(0))
+
+    # Click on the first sequence viewer link in the report.
+    page.execute_script("$('.view-sequence:eq(0)').click()")
+
+    within('.sequence-viewer') do
+      page.should have_content('SI2.2.0_06267')
+      page.should have_content(<<~SEQ.chomp)
+        MNTLWLSLWDYPGKLPLNFMVFDTKDDLQAAYWRDPYSIP
+        LAVIFEDPQPISQRLIYEIRTNPSYTLPPPPTKLYSAPIS
+        CRKNKTGHWMDDILSIKTGESCPVNNYLHSGFLALQMITD
+        ITKIKLENSDVTIPDIKLIMFPKEPYTADWMLAFRVVIPL
+        YMVLALSQFITYLLILIVGEKENKIKEGMKMMGLNDSVF
+      SEQ
+    end
+
+    # Dismiss the first modal.
+    page.execute_script("$('.sequence-viewer').modal('hide')")
+
+    # Click on the second sequence viewer link in the report.
+    page.execute_script("$('.view-sequence:eq(1)').click()")
+
+    within('.sequence-viewer') do
+      page.should have_content('SI2.2.0_13722')
+      page.should have_content(<<~SEQ.chomp)
+        MSANRLNVLVTLMLAVALLVTESGNAQVDGYLQFNPKRSA
+        VSSPQKYCGKKLSNALQIICDGVYNSMFKKSGQDFPPQNK
+        RHIAHRINGNEEESFTTLKSNFLNWCVEVYHRHYRFVFVS
+        EMEMADYPLAYDISPYLPPFLSRARARGMLDGRFAGRRYR
+        RESRGIHEECCINGCTINELTSYCGP
+      SEQ
     end
   end
 
+  it 'disables sequence viewer links if hits are longer than 10kb' do
+    # BLASTN transcripts against genome. nucleotide_query refers to two fire
+    # ant transcripts and nucleotide_databases[0] is subset of the fire ant
+    # genome (few longest scaffolds). We expect sequence viewer links to be
+    # disabled for all hits of this search.
+    perform_search(query: nucleotide_query,
+                   databases: nucleotide_databases.values_at(0))
+
+    # Check that the sequence viewer links are disabled.
+    page.evaluate_script("$('.view-sequence').is(':disabled')").should eq(true)
+  end
+
+  it 'can download visualisations in svg and png format' do
+    # Do a BLASTP search. protein_query refers to the first two sequence in
+    # protein_databases[0], so the top hits are the query sequences themselves.
+    perform_search(query: protein_query,
+                   databases: protein_databases.values_at(0))
+
+    ## Check that there is a circos vis and unfold it.
+    page.should have_content('Circos')
+    page.execute_script("$('.circos > .grapher-header > h5').click()")
+    sleep 1
+
+    page.execute_script("$('.export-to-svg:eq(0)').click()")
+    wait_for_download
+    expect(File.basename(downloaded_file)).to eq('Circos-visualisation.svg')
+    clear_downloads
+
+    page.execute_script("$('.export-to-png:eq(0)').click()")
+    wait_for_download
+    expect(File.basename(downloaded_file)).to eq('Circos-visualisation.png')
+    clear_downloads
+
+
+    ## Check that there is a graphical overview of hits.
+    page.should have_content('Graphical overview of hits')
+
+    page.execute_script("$('.export-to-svg:eq(1)').click()")
+    wait_for_download
+    expect(File.basename(downloaded_file)).to eq('Alignment-Overview-Query_1.svg')
+    clear_downloads
+
+    page.execute_script("$('.export-to-png:eq(1)').click()")
+    wait_for_download
+    expect(File.basename(downloaded_file)).to eq('Alignment-Overview-Query_1.png')
+    clear_downloads
+
+
+    ## Check that there is a length distribution of hits.
+    page.should have_content('Length distribution of hits')
+    page.execute_script("$('.length-distribution > .grapher-header > h5').click()")
+    sleep 1
+
+    page.execute_script("$('.export-to-svg:eq(2)').click()")
+    wait_for_download
+    expect(File.basename(downloaded_file)).to eq('length-distribution-Query_1.svg')
+    clear_downloads
+
+    page.execute_script("$('.export-to-png:eq(2)').click()")
+    wait_for_download
+    expect(File.basename(downloaded_file)).to eq('length-distribution-Query_1.png')
+    clear_downloads
+
+    ## Check that there is a kablammo vis of query vs hit.
+    page.should have_content('Graphical overview of aligning region(s)')
+
+    page.execute_script("$('.export-to-svg:eq(3)').click()")
+    wait_for_download
+    expect(File.basename(downloaded_file)).to eq('Kablammo-Query_1-SI2_2_0_06267.svg')
+    clear_downloads
+
+    page.execute_script("$('.export-to-png:eq(3)').click()")
+    wait_for_download
+    expect(File.basename(downloaded_file)).to eq('Kablammo-Query_1-SI2_2_0_06267.png')
+    clear_downloads
+  end
+
   ## Helpers ##
 
   def perform_search(query: , databases: , method: nil)
@@ -121,19 +305,20 @@ describe 'a browser', :js => true do
     end
     click_button('method')
 
-    # switch to new window because link opens in new window
+    # Switch to new window because link opens in new window
     page.driver.browser.switch_to.window(page.driver.browser.window_handles.last)
 
-    # Check that results loaded.
+    # It is important to have this line or the examples end prematurely with a
+    # failure.
     page.should have_content('Query')
   end
 
   def nucleotide_query
-    File.read File.join __dir__, 'nucleotide_query.fa'
+    File.read File.join(__dir__, 'sequences', 'nucleotide_query.fa')
   end
 
   def protein_query
-    File.read File.join __dir__, 'protein_query.fa'
+    File.read File.join(__dir__, 'sequences', 'protein_query.fa')
   end
 
   def nucleotide_databases