sequenceserver 2.0.0.beta4 → 2.0.0.rc1

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: a8617ffb07710b984f84dfc0dfb7d43c66cac4c3
-  data.tar.gz: 14ddad09e8dcb15793d8e06227138ee4c862b280
+  metadata.gz: a05949fcff69da464c286499cb974ea9c2cbe2c2
+  data.tar.gz: 5b697c08198c4424561fa226136719d2fb49c3cd
 SHA512:
-  metadata.gz: c130d6e3828eae5dae108786e08433d5641112305962884dc2dada918a6a92c17632f7c46400c58ea0adabf106cb02e348bf6adc35dc8cbf296300081221fc99
-  data.tar.gz: 17a41dcb923c2e64337b960de1e3717b458077a9658a9e7785ab5815c43860aff09033aacd7812146e0f1fe368878f649794b1aa5bd8bbaf13c8a4a34fe7b0ac
+  metadata.gz: 9bdb8c9a31a2323d587c1f1e3a79357c22b0c4f6b0612e5872b1c0f6a6e1f7c720718ae7ef9e0f168dc0d420957cfa98d72ae6335c888c2360c609a8d98c21b8
+  data.tar.gz: d58521faa39150d36ac2df81b21ad68e80d8c465e792049ff10ca46e7ca8a60fb84a9f43404eb01c4efa8c799796e645108e0a46cb53b8494c30a9657a50a8b1

data/.travis.yml

@@ -24,14 +24,17 @@ before_install:
   - wget -c "https://github.com/mozilla/geckodriver/releases/download/v0.24.0/geckodriver-v0.24.0-linux64.tar.gz" && tar xvf geckodriver-*.tar.gz -C bin
   # Download codeclimate test reporter to bin and make it executable
   - wget -c "https://codeclimate.com/downloads/test-reporter/test-reporter-latest-linux-amd64" -O bin/cc-test-reporter && chmod +x bin/cc-test-reporter
-  # Download and extract NCBI BLAST+ 2.9.0
-  - 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
+  # Download and extract NCBI BLAST+ 2.10.0
+  - wget -c "ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.10.0/ncbi-blast-2.10.0+-x64-linux.tar.gz" && tar xvf ncbi-blast-*.tar.gz
   # Conclude installation by adding opt/bin/ containing codeclimate test reporter
-  # and geckodriver, and opt/ncbi-blast-2.9.0+/bin containing BLAST+ binaries to
+  # and geckodriver, and opt/ncbi-blast-2.10.0+/bin containing BLAST+ binaries to
   # PATH.
-  - export PATH="$PWD/bin:$PWD/ncbi-blast-2.9.0+/bin:$PATH"
+  - export PATH="$PWD/bin:$PWD/ncbi-blast-2.10.0+/bin:$PATH"
   # Reset working directory or subsequent steps may fail.
   - cd ..
+  # Update bundler. Travis was using bundler 1.16.2 at the time of this writing
+  # and the builds were failing because Gemfile.lock requires bundler > 2.0
+  - gem install bundler -v 2.1.4
 
 env:
   global:

data/AppImage/sequenceserver.sh

@@ -1,3 +1,8 @@
+# cd back to the directory where the AppImage was launched from. AppRun changes
+# the working directory so as to work with binaries that have /usr hard-coded;
+# we don't.
+cd $OWD
+
 # Set GEM_PATH to where we installed gems in the AppImage.
 export GEM_PATH=$APPDIR/var/lib/gems/2.3.0
 

data/lib/sequenceserver.rb

@@ -5,7 +5,7 @@ require 'resolv'
 # Top level module / namespace.
 module SequenceServer
   # Use a fixed minimum version of BLAST+
-  BLAST_VERSION = '2.9.0+'.freeze
+  BLAST_VERSION = '2.10.0+'.freeze
 
   # Default location of configuration file.
   DEFAULT_CONFIG_FILE = '~/.sequenceserver.conf'.freeze
@@ -138,10 +138,14 @@ module SequenceServer
       puts
       puts '** Thank you for using SequenceServer :).'
       puts '   Please cite: '
-      puts '       Priyam A, Woodcroft BJ, Rai V, Munagala A, Moghul I, Ter F,'
-      puts '       Gibbins MA, Moon H, Leonard G, Rumpf W & Wurm Y. 2015.'
-      puts '       Sequenceserver: a modern graphical user interface for'
-      puts '       custom BLAST databases. biorxiv doi: 10.1101/033142.'
+      puts '       Priyam A, Woodcroft BJ, Rai V, Moghul I, Munagala A, Ter F,'
+      puts '       Chowdhary H, Pieniak I, Maynard LJ, Gibbins MA, Moon H,'
+      puts '       Davis-Richardson A, Uludag M, Watson-Haigh N, Challis R,'
+      puts '       Nakamura H, Favreau E, Gómez EA, Pluskal T, Leonard G,'
+      puts '       Rumpf W & Wurm Y.'
+      puts '       Sequenceserver: A modern graphical user interface for'
+      puts '       custom BLAST databases.'
+      puts '       Molecular Biology and Evolution (2019)'
     end
 
     # This method is invoked by the -i switch to start an IRB shell with

data/lib/sequenceserver/blast/job.rb

@@ -13,7 +13,6 @@ module SequenceServer
             # itself is self-contained. This will help with tests among
             # other things.
             FileUtils.cp(params[:xml], dir)
-            @advanced_params = {}
             @databases = []
             done!
           end
@@ -23,17 +22,19 @@ module SequenceServer
             @method    = params[:method]
             @qfile     = store('query.fa', params[:sequence])
             @databases = Database[params[:databases]]
-            @options   = params[:advanced].to_s.strip + defaults
-            @advanced_params = parse_advanced params[:advanced]
+            @advanced  = params[:advanced].to_s.strip
+            @options   = @advanced + defaults
           end
         end
       end
 
-      attr_reader :advanced_params
-
       # :nodoc:
       # Attributes used by us - should be considered private.
-      attr_reader :method, :qfile, :databases, :options
+      attr_reader :method, :qfile, :databases, :advanced, :options
+
+      # :nodoc:
+      # Deprecated; see Report#extract_params
+      attr_reader :advanced_params
 
       # :nodoc:
       # Returns path to the imported xml file if the job was created using the
@@ -94,24 +95,6 @@ module SequenceServer
 
       private
 
-      def parse_advanced(param_line)
-        param_list = (param_line || '').split(' ')
-        res = {}
-
-        param_list.each_with_index do |word, i|
-          nxt = param_list[i + 1]
-          if word.start_with? '-'
-            word.sub!('-', '')
-            unless nxt.nil? || nxt.start_with?('-')
-              res[word] = nxt
-            else
-              res[word] = 'True'
-            end
-          end
-        end
-        res
-      end
-
       def validate(params)
         validate_method params[:method]
         validate_sequences params[:sequence]

data/lib/sequenceserver/blast/report.rb

@@ -24,34 +24,15 @@ module SequenceServer
     class Report < Report
       def initialize(job)
         super do
-          @querydb = job.databases
           @queries = []
         end
       end
 
-      # Attributes parsed out from XML output.
-      attr_reader :program, :program_version, :params, :stats, :queries
-
-      # This is obtained from the job object.
-      attr_reader :querydb
+      # Attributes parsed out from BLAST output.
+      attr_reader :program, :program_version, :stats, :queries
 
-      # Returns database type (nucleotide or protein) used for running BLAST
-      # search. If we ran the BLAST search, this information is available
-      # from Job#databases. For imported XML, this is inferred from
-      # Report#program (i.e., the BLAST algorithm)
-      def dbtype
-        return @dbtype if @dbtype
-        @dbtype = if @querydb.empty?
-                    case program
-                    when /blastn|tblastn|tblastx/
-                      'nucleotide'
-                    when /blastp|blastx/
-                      'protein'
-                    end
-                  else
-                    @querydb.first.type
-                  end
-      end
+      # Attributes parsed from job metadata and BLAST output.
+      attr_reader :querydb, :dbtype, :params
 
       def to_json
         [:querydb, :program, :program_version, :params, :stats,
@@ -68,6 +49,8 @@ module SequenceServer
       # Generate report.
       def generate
         job.raise!
+        xml_ir = nil
+        tsv_ir = nil
         if job.imported_xml_file
           xml_ir = parse_xml File.read(job.imported_xml_file)
           tsv_ir = Hash.new do |h1,k1|
@@ -75,18 +58,15 @@ module SequenceServer
               h2[k2]=['','',[]]
             end
           end
-          extract_program_info xml_ir
-          extract_params xml_ir
-          extract_stats xml_ir
-          extract_queries xml_ir, tsv_ir
         else
           xml_ir = parse_xml File.read(Formatter.run(job, 'xml').file)
-          tsv_ir = parse_tsv File.read(Formatter.run(job, 'custom_tsv').file )
-          extract_program_info xml_ir
-          extract_params xml_ir
-          extract_stats xml_ir
-          extract_queries xml_ir, tsv_ir
+          tsv_ir = parse_tsv File.read(Formatter.run(job, 'custom_tsv').file)
         end
+        extract_program_info xml_ir
+        extract_db_info xml_ir
+        extract_params xml_ir
+        extract_stats xml_ir
+        extract_queries xml_ir, tsv_ir
       end
 
       # Make program name and program name + version available via `program`
@@ -96,6 +76,20 @@ module SequenceServer
         @program_version = ir[1]
       end
 
+      # Get database information (title and type) from job yaml or from XML.
+      # Sets `querydb` and `dbtype` attributes.
+      def extract_db_info(ir)
+        if job.databases.empty?
+          @querydb = ir[3].split.map do |path|
+            { title: File.basename(path) }
+          end
+          @dbtype = dbtype_from_program
+        else
+          @querydb = job.databases
+          @dbtype = @querydb.first.type
+        end
+      end
+
       # Make search params available via `params` attribute.
       #
       # Search params tweak the results. Like evalue cutoff or penalty to open
@@ -103,11 +97,20 @@ module SequenceServer
       # matrix, evalue, gapopen, gapextend, and filters are available from XML
       # output.
       def extract_params(ir)
+        # Parse/get params from the job first.
+        job_params = parse_advanced(job.advanced)
+        # Old jobs from beta releases may not have the advanced key but they
+        # will have the deprecated advanced_params key.
+        job_params.update(job.advanced_params) if job.advanced_params
+
+        # Parse params from BLAST XML.
         @params = Hash[
           *ir[7].first.map { |k, v| [k.gsub('Parameters_', ''), v] }.flatten
         ]
         @params['evalue'] = @params.delete('expect')
-        @params = job.advanced_params.merge(@params)
+
+        # Merge into job_params.
+        @params = job_params.merge(@params)
       end
 
       # Make search stats available via `stats` attribute.
@@ -232,6 +235,36 @@ module SequenceServer
         end
         ir
       end
+
+      # Parse BLAST CLI string from job.advanced.
+      def parse_advanced(param_line)
+        param_list = (param_line || '').split(' ')
+        res = {}
+
+        param_list.each_with_index do |word, i|
+          nxt = param_list[i + 1]
+          if word.start_with? '-'
+            word.sub!('-', '')
+            unless nxt.nil? || nxt.start_with?('-')
+              res[word] = nxt
+            else
+              res[word] = 'True'
+            end
+          end
+        end
+        res
+      end
+
+      # Returns database type (nucleotide or protein) inferred from
+      # Report#program (i.e., the BLAST algorithm)
+      def dbtype_from_program
+        case program
+        when /blastn|tblastn|tblastx/
+          'nucleotide'
+        when /blastp|blastx/
+          'protein'
+        end
+      end
     end
   end
 end

data/lib/sequenceserver/routes.rb

@@ -69,10 +69,16 @@ module SequenceServer
     # include available databases and user-defined search options.
     get '/searchdata.json' do
       searchdata = {
+        query: Database.retrieve(params[:query]),
         database: Database.all,
-        options: SequenceServer.config[:options],
-        query: Database.retrieve(params[:query])
+        options: SequenceServer.config[:options]
       }
+
+      # If a job_id is specified, update searchdata from job meta data (i.e.,
+      # query, pre-selected databases, advanced options used). Query is only
+      # updated if params[:query] is not specified.
+      update_searchdata_from_job(searchdata) if params[:job_id]
+
       searchdata.to_json
     end
 
@@ -180,5 +186,25 @@ module SequenceServer
 
       error_data.to_json
     end
+
+    # Get the query sequences, selected databases, and advanced params used.
+    def update_searchdata_from_job(searchdata)
+      job = Job.fetch(params[:job_id])
+      return if job.imported_xml_file
+
+      # Only read job.qfile if we are not going to use Database.retrieve.
+      searchdata[:query] = File.read(job.qfile) if !params[:query]
+
+      # Which databases to pre-select.
+      searchdata[:preSelectedDbs] = job.databases
+
+      # job.advanced may be nil in case of old jobs. In this case, we do not
+      # override searchdata so that default advanced parameters can be applied.
+      # Note that, job.advanced will be an empty string if a user deletes the
+      # default advanced parameters from the advanced params input field. In
+      # this case, we do want the advanced params input field to be empty when
+      # the user hits the back button. Thus we do not test for empty string.
+      searchdata[:options][job.method] = [job.advanced] if job.advanced
+    end
   end
 end

data/lib/sequenceserver/version.rb

@@ -1,4 +1,4 @@
 # Define version number.
 module SequenceServer
-  VERSION = '2.0.0.beta4'.freeze
+  VERSION = '2.0.0.rc1'.freeze
 end

data/public/css/grapher.css

@@ -1,18 +1,20 @@
 /** Common styles for container element of all graphs. **/
 .grapher {
-  margin: 20px 0;
+  margin: 0;
+}
+.grapher-header {
+  padding-right: 1px;
 }
 .caption {
   display: inline-block;
-  letter-spacing: 1px;
-  padding: 0 0 0 5px;
+  padding: 0 0 0 1px;
   margin: 0 0;
   cursor: pointer;
 }
 .graph-links {
   float: right;
-  padding: 0 7px 0 0;
   text-align: right;
+  color: #174465;
 }
 
 /** Common SVG styles for all graphs. **/
@@ -35,22 +37,16 @@ svg .axis path,
 
 .grapher.circos .caption {
   padding: 0;
+  font-size: 16px;
+  font-weight: bold;
 }
 
 /* Graphical overview of hits */
-.grapher.alignment-overview {
-  margin-top: 10px;
-  margin-bottom: 0;
-}
 .alignment-overview.svg-container {
   text-align: center;
 }
 
 /* Length distribution of hits */
-.grapher.length-distribution {
-  margin-top: 0;
-  margin-bottom: 0;
-}
 .length-distribution.svg-container {
   height: 150px;
 }
@@ -59,9 +55,6 @@ svg .bar:hover {
 }
 
 /* Graphical overview of HSP */
-.kablammo.grapher {
-  margin: 10px 0 10px 0;
-}
 .kablammo.svg-container {
   height: 150px;
 }

data/public/css/sequenceserver.css

@@ -22,6 +22,15 @@ body {
  */
 a:hover, .btn-link:hover {
   text-decoration: none;
+  color: #c74f14;
+}
+
+a {
+  color: #1b557a;
+}
+
+label:hover {
+  color: #c74f14;
 }
 
 /**
@@ -32,6 +41,10 @@ textarea {
   min-height: 214px;
 }
 
+hr {
+  border-top: transparent;
+}
+
 /**
  * Use normal font weight for labels and indicate they are clickable by setting
  * `cursor: pointer`.
@@ -40,17 +53,27 @@ label {
   cursor: pointer;
   margin-bottom: 0;
   font-weight: normal;
+  color: #1b557a;
 }
 
 small {
   color: inherit !important;
 }
 
+h3 {
+  font-size: 16px;
+}
+h4 {
+  font-size: 14px;
+}
+h3 > .fa, h4 > .fa {
+  vertical-align: bottom;
+}
 /**
  * Without this .disabled elements hardly look disabled.
  */
 .disabled {
-  color: #ccc;
+  color: #ccc !important;
 }
 a.disabled:hover,
 .btn-link[disabled]:hover {
@@ -64,34 +87,49 @@ a.disabled:hover,
 .navbar {
   margin-bottom: 0;
   border-radius: 0;
-  border-bottom: 1px solid #eee;
+  border-bottom: 1px solid #c74f14;
 }
 .navbar-brand {
   height: auto;
-  padding: 20px 15px;
+  padding: 10px 7.5px;
   font-size: 32px;
   color: rgb(51, 51, 51);
 }
 .navbar-brand > small {
   font-size: 50%;
+  vertical-align: text-bottom;
 }
 
 .navbar-nav > li > a {
-  padding: 24px 15px;
+  padding: 10px 7.5px;
   font-size: 14px;
-  color: rgb(51, 51, 51);
+  color: #174465;
+}
+/* logo */
+.navbar-brand > img {
+  display: inline-block;
 }
 
 /**
  * Like BS' .page-header but without extra margin and the ability to display a
  * sub-text on right.
  */
+/* Hit header styling */
 .section-header {
-  border-bottom: 1px solid #ddd;
-  padding-bottom: 5px;
+  border-bottom: 1px solid  #c74f14;
+  padding-left: 1px;
+  display: table;
+  width: 100%;
+}
+.section-header-sidebar {
+  padding-left: 1px;
   display: table;
   width: 100%;
 }
+.section-header-sidebar > h4 {
+  font-weight: bold;
+  margin-bottom: 0px;
+}
 .section-header > * {
   display: table-cell;
 }
@@ -99,7 +137,7 @@ a.disabled:hover,
   width: 100%;
 }
 .section-content {
-  padding: 5px 0 0 0px;
+  padding: 0 0 0 1px;
 }
 /**
  * Take out border, cut down margin and padding, and remove background color
@@ -112,11 +150,14 @@ a.disabled:hover,
   box-shadow: none;
 }
 .panel .panel-heading {
-  padding: 4px 0 5px 0;
+  padding: 0;
   background-color: inherit;
+  border-bottom: 1px solid #c74f14;
 }
 .panel .panel-heading h4 {
   margin: 0;
+  font-size: 16px;
+  font-weight: bold;
 }
 
 /**
@@ -140,11 +181,12 @@ a.disabled:hover,
 .table>thead>tr>th, .table>tbody>tr>th, .table>tfoot>tr>th, .table>thead>tr>td,
 .table>tbody>tr>td, .table>tfoot>tr>td {
   border-top: none;
-  padding-left: 0;
   font-weight: normal;
+  padding: 0 0 0 4px;
 }
 .table>thead>tr>th {
-  border-bottom: 1px solid #ddd;
+  border-bottom: none;
+  color: #5f5f5f;
 }
 
 /**
@@ -216,12 +258,15 @@ a.disabled:hover,
  */
 .nav.hover-reset>li>a:hover {
   background-color: inherit;
+  color: #c74f14;
 }
 .nav.focus-reset>li>a:focus {
   background-color: inherit;
+  color: #c74f14;
 }
 .nav.active-bold>.active>a {
   font-weight: bold;
+  color: #c74f14;
 }
 
 /**
@@ -231,8 +276,11 @@ a.disabled:hover,
   color: inherit;
   line-height: inherit;
   font-weight: normal;
+  font-size: inherit;
+}
+.pos-label {
+  padding: 0 0 0 0.6em;
 }
-
 /**
  * Reset Bootstrap's CSS for pre tags.
  */
@@ -297,7 +345,7 @@ a.disabled:hover,
 
 .databases .list-group-item {
   border: none;
-  padding: 3px 0 0;
+  padding: 1px 0 0;
 }
 
 #help pre:hover {
@@ -346,13 +394,11 @@ input[type=checkbox] {
  **********************/
 .sidebar > div {
   /* To line up with the results on the right */
-  margin-top: 20px;
-}
-.sidebar h4 {
-  font-size: 14px;
+  margin-top: 0px;
 }
+
 .sidebar li a {
-  padding: 7px 10px;
+  padding: 3px 10px;
 }
 
 .sidebar.affix {
@@ -375,10 +421,13 @@ input[type=checkbox] {
 /* Result per query. */
 .overview {
   /* To line up with the sidebar on the left */
-  margin: 20px 0;
+  margin: 10px 0 6px 0;
+}
+.overview p {
+  margin: 0;
 }
 .resultn {
-  margin-bottom: 25px;
+  margin-top: 6px;
 }
 
 .graphical-overview {
@@ -390,61 +439,41 @@ input[type=checkbox] {
   padding-bottom: 0;
 }
 
-.tabular-view {
-  margin-top: 14px;
-  margin-left: 6px;
-  margin-bottom: 14px;
-}
-
 .hit {
-  padding-top: 14px;
   margin-top: 4px;
 }
-.hit:first-child {
-  padding-top: 0;
-}
-.hit h4 {
+.hit .section-header h4 {
   cursor: pointer;
+  padding-left: 1px;
 }
-.hit h4 span {
+.hit .section-header h4 span,
+.hit .section-header h4 strong {
   cursor: text;
 }
-.hit > p {
-  margin-top: 0;
-  margin-bottom: 0;
+.hit-links {
+  height: 16px;
 }
 
-.hsps {
-  padding: 0 0 10px 10px;
-}
 .hsp {
-  padding-bottom: 14px;
-}
-.hsp:last-child {
-  padding-bottom: 0;
+  padding: 1px 0 1px 2px;
 }
-
 .hsp-stats {
   font-size: 12px;
+  color:#5f5f5f;
 }
-.hsp .hsp-lines {
+.hsp-lines {
   margin-top: 5px;
-  font-size: 10px;
+  font-size: 11px;
   letter-spacing: 1.2px;
 }
-.hsp .hsp-coords {
-  color: rgb(110, 110, 110);
+.hsp-coords {
+  color: #5f5f5f;
 }
 
-.hit-links * {
-  padding-left: 3px;
-  letter-spacing: 1px;
-  vertical-align: baseline;
-}
 .btn-link {
   border: none;
   padding: 0px;
-  letter-spacing: 1px;
+  color: #1b557a;
 }
 
 .fastan > .section-header {
@@ -480,11 +509,42 @@ input[type=checkbox] {
 .dnd-overlay-container p {
   font-size: 48px;
 }
-
+/* higlight when hit is selected */
 .glow {
-  border-left: 2px solid #f0ad4e;
+  border-left: 2px solid #c74f14;
 }
 
 .downloads a {
   cursor: pointer;
 }
+/* CSS class for logo */
+.logo {
+  width: 205.05px;
+  max-height: 35px;
+}
+/* CSS class for vertical line separating the hit links */
+.line {
+  color: #c74f14;
+  margin: 0 5px 0 5px;
+}
+/* override bootstrap focus color in the text field of the search page */
+.form-control:focus {
+  border-color: #1b557a;
+}
+/* override bootstrap btn-color for the search "BlAST" button on the search page.*/
+.btn-primary {
+  background-color: #1b557a;
+  border-color: #174465;
+}
+.btn-primary:hover {
+  background-color: #174465;
+  border-color: #174465;
+}
+.btn-primary:disabled, .btn-primary[disabled]:hover {
+  background-color: #881C14;
+  border-color: #881C14;
+}
+/* CSS class to facilitate the hit header wrapping */
+.hit-header {
+  display: table-cell;
+}