sequenceserver 2.1.0 → 2.2.0

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 3cf703fae66ad96d285ed0556c387dabb0d69be120db5bdd3c3f9f8a03d3a814
-  data.tar.gz: 503bb0b69cbf773ab536d99f6782f4fff19f4872c49e6377d49a9f7820861c3b
+  metadata.gz: 61b15f95cdc065739de70f2ba94d3022e6beec789dd9c64199ee1be3a2459c63
+  data.tar.gz: d6c108bd39cb8c6a832787d2cbaa52b2c5a3653c0b08b289cb149b7221a9870c
 SHA512:
-  metadata.gz: 1896b2afddf6033c98747f7eba1dabbe15b270940bd19760ebef4ed75af267760d45d40215663173ccb2f964472b458179a459316b86ef72bc26aa75d62faad0
-  data.tar.gz: 4ac1d9a5a205d299af4b1467521a9bc539e3833d0a571cfa90b490b19df958fc0f7ee2e1341e3d8d5e19fccbe2ee6874884fc7fbcbfbdc6abbe1e60df3c9a76e
+  metadata.gz: d4c2b1785980dd4e46a24a8a5a6d36652fb23f5389f9b7320cd9360f081cbad82b6dc6bfe735b5321738611094052631af0de635b77676587d703d466bd5f604
+  data.tar.gz: 235e35e8ba4331894a7ac9f107d950462d3b3d892ddafc6f58d3ba48fbe6a03cfc016ac64798921472e296a0cb5577245aca49cbb517d897094a501ec4483beb

data/bin/sequenceserver

@@ -119,6 +119,11 @@ begin
        'Port to run SequenceServer on',
        argument: true
 
+    on 'o', 'optimistic=',
+       'Optimistic mode does not perform database compatibility checks, which can be faster. ' \
+       'Only use this if you format FASTAs with "sequenceserver -make-blast-databases"',
+       argument: true
+
     on 's', 'set',
        'Set configuration value in default or given config file'
 
@@ -296,7 +301,7 @@ begin
           unless response =~ /^[n]$/i
             puts
             puts 'Searching ...'
-            if SequenceServer.makeblastdb.any_unformatted?
+            if SequenceServer.makeblastdb.any_to_format?
               formatted = SequenceServer.makeblastdb.format
               exit! if formatted.empty? && !set?
               redo unless set?
@@ -353,7 +358,7 @@ begin
       end
 
       if make_blast_databases?
-        if SequenceServer.makeblastdb.scan
+        if SequenceServer.makeblastdb.any_to_format_or_reformat?
           puts
           puts <<~MSG
           SequenceServer has scanned your databases directory and will now offer

data/lib/sequenceserver/blast/formatter.rb

@@ -25,23 +25,32 @@ module SequenceServer
 
       attr_reader :format, :mime, :specifiers
 
-      def file
-        @file ||= File.join(job.dir, filename)
+      def filepath
+        @filepath ||= File.join(job.dir, filename)
+      end
+
+      def size
+        File.size(filepath)
       end
 
       def filename
         @filename ||= "sequenceserver-#{type}_report.#{mime}"
       end
 
+      def read_file
+        File.read(filepath)
+      end
+
       private
 
       attr_reader :job, :type
 
       def run
-        return if File.exist?(file)
+        return if File.exist?(filepath)
+
         command = "blast_formatter -archive '#{job.stdout}'" \
           " -outfmt '#{format} #{specifiers}'"
-        sys(command, path: config[:bin], dir: DOTDIR, stdout: file)
+        sys(command, path: config[:bin], dir: DOTDIR, stdout: filepath)
       rescue CommandFailed => e
         # Mostly we will never get here: empty archive file,
         # file permissions, broken BLAST binaries, etc. will

data/lib/sequenceserver/blast/report.rb

@@ -36,6 +36,8 @@ module SequenceServer
       attr_reader :querydb, :dbtype, :params
 
       def to_json(*_args)
+        generate
+
         %i[querydb program program_version params stats
            queries].inject({}) do |h, k|
           h[k] = send(k)
@@ -48,10 +50,18 @@ module SequenceServer
                    non_parse_seqids: !!job.databases&.any?(&:non_parse_seqids?)).to_json
       end
 
-      private
+      def xml_file_size
+        return File.size(job.imported_xml_file) if job.imported_xml_file
+
+        generate
+
+        xml_formatter.size
+      end
 
       # Generate report.
       def generate
+        return self if @_generated
+
         job.raise!
         xml_ir = nil
         tsv_ir = nil
@@ -63,14 +73,34 @@ module SequenceServer
             end
           end
         else
-          xml_ir = parse_xml File.read(Formatter.run(job, 'xml').file)
-          tsv_ir = parse_tsv File.read(Formatter.run(job, 'custom_tsv').file)
+          xml_ir = parse_xml(xml_formatter.read_file)
+          tsv_ir = parse_tsv(tsv_formatter.read_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
+
+        @_generated = true
+
+        self
+      end
+
+      def done?
+        return true if job.imported_xml_file
+
+        File.exist?(xml_formatter.filepath) && File.exist?(tsv_formatter.filepath)
+      end
+
+      private
+
+      def xml_formatter
+        @xml_formatter ||= Formatter.run(job, 'xml')
+      end
+
+      def tsv_formatter
+        @tsv_formatter ||= Formatter.run(job, 'custom_tsv')
       end
 
       # Make program name and program name + version available via `program`

data/lib/sequenceserver/config.rb

@@ -131,7 +131,10 @@ module SequenceServer
         num_jobs: 1,
         job_lifetime: 43_200,
         # Set cloud_share_url to 'disabled' to disable the cloud sharing feature
-        cloud_share_url: 'https://share.sequenceserver.com/api/v1/shared-job'
+        cloud_share_url: 'https://share.sequenceserver.com/api/v1/shared-job',
+        # Warn in the UI before rendering results larger than this value
+        large_result_warning_threshold: 250 * 1024 * 1024,
+        optimistic: false # Faster, but does not perform DB compatibility checks
       }
     end
   end

data/lib/sequenceserver/makeblastdb.rb

@@ -8,7 +8,8 @@ module SequenceServer
   # Example usage:
   #
   #   makeblastdb = MAKEBLASTDB.new(database_dir)
-  #   makeblastdb.scan && makeblastdb.run
+  #   makeblastdb.run # formats and re-formats databases in database_dir
+  #   makeblastdb.formatted_fastas # lists formatted databases
   #
   class MAKEBLASTDB
     extend Forwardable
@@ -20,56 +21,17 @@ module SequenceServer
     end
 
     attr_reader :database_dir
-    attr_reader :formatted_fastas
-    attr_reader :fastas_to_format
-    attr_reader :fastas_to_reformat
 
-    # Scans the database directory to determine which FASTA files require
-    # formatting or re-formatting.
-    #
-    # Returns `true` if there are files to (re-)format, `false` otherwise.
-    def scan
-      # We need to know the list of formatted FASTAs as reported by blastdbcmd
-      # first. This is required to determine both unformatted FASTAs and those
-      # that require reformatting.
-      @formatted_fastas = []
-      determine_formatted_fastas
-
-      # Now determine FASTA files that are unformatted or require reformatting.
-      @fastas_to_format = []
-      determine_unformatted_fastas
-      @fastas_to_reformat = []
-      determine_fastas_to_reformat
-
-      # Return true if there are files to be (re-)formatted or false otherwise.
-      !@fastas_to_format.empty? || !@fastas_to_reformat.empty?
-    end
-
-    # Returns true if at least one database in database directory is formatted.
     def any_formatted?
-      !@formatted_fastas.empty?
-    end
-
-    # Returns true if there is at least one unformatted FASTA in the databases
-    # directory.
-    def any_unformatted?
-      !@fastas_to_format.empty?
+      formatted_fastas.any?
     end
 
-    # Returns true if the databases directory contains one or more incompatible
-    # databases.
-    #
-    # Note that it is okay to only use V4 databases or only V5 databases.
-    # Incompatibility arises when they are mixed.
-    def any_incompatible?
-      return false if @formatted_fastas.all? { |ff| ff.v4? || ff.alias? }
-      return false if @formatted_fastas.all? { |ff| ff.v5? || ff.alias? }
-      true
+    def any_to_format_or_reformat?
+      any_to_format? || any_to_reformat?
     end
 
-    # Runs makeblastdb on each file in `@fastas_to_format` and
-    # `@fastas_to_reformat`. Will do nothing unless `#scan`
-    # has been run before.
+    # Runs makeblastdb on each file in `fastas_to_format` and
+    # `fastas_to_reformat`.
     def run
       format
       reformat
@@ -80,8 +42,9 @@ module SequenceServer
     def format
       # Make the intent clear as well as ensure the program won't crash if we
       # accidentally call format before calling scan.
-      return unless @fastas_to_format
-      @fastas_to_format.select do |path, title, type|
+      return unless any_to_format?
+
+      fastas_to_format.select do |path, title, type|
         make_blast_database('format', path, title, type)
       end
     end
@@ -91,50 +54,75 @@ module SequenceServer
     def reformat
       # Make the intent clear as well as ensure the program won't crash if
       # we accidentally call reformat before calling scan.
-      return unless @fastas_to_reformat
-      @fastas_to_reformat.select do |path, title, type, non_parse_seqids|
+      return unless any_to_reformat?
+
+      fastas_to_reformat.select do |path, title, type, non_parse_seqids|
         make_blast_database('reformat', path, title, type, non_parse_seqids)
       end
     end
 
-    private
-
     # Determines which FASTA files in the database directory are already
-    # formatted. Adds to @formatted_fastas.
-    def determine_formatted_fastas
+    # formatted.
+    def formatted_fastas
+      return @formatted_fastas if defined?(@formatted_fastas)
+
+      @formatted_fastas = []
+
       blastdbcmd.each_line do |line|
         path, *rest = line.chomp.split("\t")
         next if multipart_database_name?(path)
+
         rest << get_categories(path)
         @formatted_fastas << Database.new(path, *rest)
       end
+
+      @formatted_fastas
+    end
+
+    private
+
+    def any_to_format?
+      fastas_to_format.any?
+    end
+
+    def any_to_reformat?
+      fastas_to_reformat.any?
     end
 
     # Determines which FASTA files in the database directory require
-    # reformatting. Adds to @fastas_to_format.
-    def determine_fastas_to_reformat
-      @formatted_fastas.each do |ff|
-        if ff.v4? || ff.non_parse_seqids?
-          @fastas_to_reformat << [ff.path, ff.title, ff.type, ff.non_parse_seqids?]
-        end
+    # reformatting.
+    def fastas_to_reformat
+      return @fastas_to_reformat if defined?(@fastas_to_reformat)
+
+      @fastas_to_reformat = []
+      formatted_fastas.each do |ff|
+        @fastas_to_reformat << [ff.path, ff.title, ff.type, ff.non_parse_seqids?] if ff.v4? || ff.non_parse_seqids?
       end
+
+      @fastas_to_reformat
     end
 
     # Determines which FASTA files in the database directory are
-    # unformatted. Adds to @fastas_to_format.
-    def determine_unformatted_fastas
+    # unformatted.
+    def fastas_to_format
+      return @fastas_to_format if defined?(@fastas_to_format)
+
+      @fastas_to_format = []
+
       # Add a trailing slash to database_dir - Find.find doesn't work as
       # expected without the trailing slash if database_dir is a symlink
       # inside a docker container.
       Find.find(database_dir + '/') do |path|
         next if File.directory?(path)
         next unless probably_fasta?(path)
-        next if @formatted_fastas.any? { |f| f[0] == path }
+        next if formatted_fastas.any? { |f| f[0] == path }
 
         @fastas_to_format << [path,
-          make_db_title(path),
-          guess_sequence_type_in_fasta(path)]
+                              make_db_title(path),
+                              guess_sequence_type_in_fasta(path)]
       end
+
+      @fastas_to_format
     end
 
     # Runs `blastdbcmd` to determine formatted FASTA files in the database
@@ -146,14 +134,16 @@ module SequenceServer
       out, err = sys(cmd, path: config[:bin])
       errpat = /BLAST Database error/
       fail BLAST_DATABASE_ERROR.new(cmd, err) if err.match(errpat)
-      return out
+
+      out
     rescue CommandFailed => e
-      fail BLAST_DATABASE_ERROR.new(cmd, e.stderr)
+      raise BLAST_DATABASE_ERROR.new(cmd, e.stderr)
     end
 
     # Create BLAST database, given FASTA file and sequence type in FASTA file.
     def make_blast_database(action, file, title, type, non_parse_seqids = false)
       return unless make_blast_database?(action, file, type)
+
       title = confirm_database_title(title)
       extract_fasta(file) unless File.exist?(file)
       taxonomy = taxid_map(file, non_parse_seqids) || taxid
@@ -188,9 +178,10 @@ module SequenceServer
     # using blastdbcmd.
     def taxid_map(db, non_parse_seqids)
       return if non_parse_seqids
+
       taxid_map = db.sub(/#{File.extname(db)}$/, '.taxid_map.txt')
-      extract_taxid_map(db, taxid_map) if !File.exist?(taxid_map)
-      "-taxid_map #{taxid_map}" if !File.zero?(taxid_map)
+      extract_taxid_map(db, taxid_map) unless File.exist?(taxid_map)
+      "-taxid_map #{taxid_map}" unless File.zero?(taxid_map)
     end
 
     # Get taxid from the user. Returns user input or 0.
@@ -211,10 +202,24 @@ module SequenceServer
       cmd = "makeblastdb -parse_seqids -hash_index -in '#{file}'" \
             " -dbtype #{type.to_s.slice(0, 4)} -title '#{title}'" \
             " #{taxonomy}"
-      out, err = sys(cmd, path: config[:bin])
+
+      output = if File.directory?(file)
+                 File.join(file, 'makeblastdb')
+               else
+                 "#{file}.makeblastdb"
+               end
+
+      out, err = sys(
+        cmd,
+        path: config[:bin],
+        stderr: [output, 'stderr'].join,
+        stdout: [output, 'stdout'].join
+      )
+
       puts out.strip
       puts err.strip
-      return true
+
+      true
     rescue CommandFailed => e
       puts <<~MSG
         Could not create BLAST database for: #{file}
@@ -261,7 +266,7 @@ module SequenceServer
     # /home/ben/pd.ben/sequenceserver/db/nr00 => no
     # /mnt/blast-db/refseq_genomic.100 => yes
     def multipart_database_name?(db_name)
-      !(db_name.match(%r{.+/\S+\.\d{2,3}$}).nil?)
+      !db_name.match(%r{.+/\S+\.\d{2,3}$}).nil?
     end
 
     def get_categories(path)
@@ -273,7 +278,10 @@ module SequenceServer
 
     # Returns true if first character of the file is '>'.
     def probably_fasta?(file)
-      return false unless file.match(/((cds)|(fasta)|(fna)|(pep)|(cdna)|(fa)|(prot)|(fas)|(genome)|(nuc)|(dna)|(nt))$/i)
+      unless file.match(/((cdna)|(cds)|(dna)|(fa)|(faa)|(fas)|(fasta)|(fna)|(genome)|(nt)|(nuc)|(pep)|(prot))$/i)
+        return false
+      end
+
       File.read(file, 1) == '>'
     end
 

data/lib/sequenceserver/pool.rb

@@ -42,7 +42,7 @@ class Pool
 
   def shutdown
     @size.times do
-      schedule { throw :exit }
+      queue { throw :exit }
     end
     @pool.map(&:join)
   end

data/lib/sequenceserver/report.rb

@@ -7,11 +7,8 @@ module SequenceServer
   # own report subclass.
   class Report
     class << self
-      # Generates report for the given job. Returns generated report object.
-      #
-      # TODO: Dynamic dispatch.
       def generate(job)
-        BLAST::Report.new(job)
+        BLAST::Report.new(job).generate
       end
     end
 
@@ -23,7 +20,6 @@ module SequenceServer
     def initialize(job)
       @job = job
       yield if block_given?
-      generate
     end
 
     attr_reader :job

data/lib/sequenceserver/routes.rb

@@ -106,7 +106,28 @@ module SequenceServer
     get '/:jid.json' do |jid|
       job = Job.fetch(jid)
       halt 202 unless job.done?
-      Report.generate(job).to_json
+
+      report = Report.generate(job)
+      halt 202 unless report.done?
+
+      display_large_result_warning =
+        SequenceServer.config[:large_result_warning_threshold].to_i.positive? &&
+        params[:bypass_file_size_warning] != 'true' &&
+        report.xml_file_size > SequenceServer.config[:large_result_warning_threshold]
+
+      if display_large_result_warning
+        halt 200,
+             {
+               user_warning: 'LARGE_RESULT',
+               download_links: [
+                 { name: 'Standard Tabular Report', url: "download/#{jid}.std_tsv" },
+                 { name: 'Full Tabular Report', url: "/download/#{jid}.full_tsv" },
+                 { name: 'Results in XML', url: "/download/#{jid}.xml" }
+               ]
+             }.to_json
+      end
+
+      report.to_json
     end
 
     # Returns base HTML. Rest happens client-side: polling for and rendering
@@ -145,7 +166,7 @@ module SequenceServer
     get '/download/:jid.:type' do |jid, type|
       job = Job.fetch(jid)
       out = BLAST::Formatter.new(job, type)
-      send_file out.file, filename: out.filename, type: out.mime
+      send_file out.filepath, filename: out.filename, type: out.mime
     end
 
     post '/cloud_share' do

data/lib/sequenceserver/sys.rb

@@ -67,7 +67,7 @@ module SequenceServer
 
       # Now move the temporary file to the given path.
       # TODO: don't we need to explicitly close the temp file here?
-      FileUtils.mv(temp_files.delete(channel), filename)
+      FileUtils.cp(temp_files[channel], filename)
     end
 
     # Read the remaining temp files into memory. For large outputs,

data/lib/sequenceserver/version.rb

@@ -1,4 +1,4 @@
 # Define version number.
 module SequenceServer
-  VERSION = '2.1.0'.freeze
+  VERSION = '2.2.0'.freeze
 end

data/lib/sequenceserver.rb

@@ -62,6 +62,9 @@ module SequenceServer
 
     # SequenceServer initialisation routine.
     def init(config = {})
+      # Reset makeblastdb cache, because configuration may have changed.
+      @makeblastdb = nil
+
       # Use default config file if caller didn't specify one.
       config[:config_file] ||= DEFAULT_CONFIG_FILE
 
@@ -201,10 +204,13 @@ module SequenceServer
 
       logger.debug("Will look for BLAST+ databases in: #{config[:database_dir]}")
 
-      makeblastdb.scan
-      fail NO_BLAST_DATABASE_FOUND, config[:database_dir] if !makeblastdb.any_formatted?
+      fail NO_BLAST_DATABASE_FOUND, config[:database_dir] unless makeblastdb.any_formatted?
 
       Database.collection = makeblastdb.formatted_fastas
+      check_database_compatibility unless config[:optimistic].to_s == 'true'
+    end
+
+    def check_database_compatibility
       Database.each do |database|
         logger.debug "Found #{database.type} database '#{database.title}' at '#{database.path}'"
         if database.non_parse_seqids?

data/public/js/report.js

@@ -28,6 +28,8 @@ class Report extends Component {
         this.nextHSP = 0;
         this.maxHSPs = 3; // max HSPs to render in a cycle
         this.state = {
+            user_warning: null,
+            download_links: [],
             search_id: '',
             seqserv_version: '',
             program: '',
@@ -52,9 +54,8 @@ class Report extends Component {
     fetchResults() {
         var intervals = [200, 400, 800, 1200, 2000, 3000, 5000];
         var component = this;
-
         function poll() {
-            $.getJSON(location.pathname + '.json').complete(function (jqXHR) {
+            $.getJSON(location.pathname + '.json' + location.search).complete(function (jqXHR) {
                 switch (jqXHR.status) {
                 case 202:
                     var interval;
@@ -86,7 +87,11 @@ class Report extends Component {
     setStateFromJSON(responseJSON) {
         this.lastTimeStamp = Date.now();
         // the callback prepares the download link for all alignments
-        this.setState(responseJSON, this.prepareAlignmentOfAllHits);
+        if (responseJSON.user_warning == 'LARGE_RESULT') {
+            this.setState({user_warning: responseJSON.user_warning, download_links: responseJSON.download_links});
+        } else {
+            this.setState(responseJSON, this.prepareAlignmentOfAllHits);
+        }
     }
     /**
    * Called as soon as the page has loaded and the user sees the loading spinner.
@@ -108,8 +113,8 @@ class Report extends Component {
    * start iteratively adding 1 HSP to the page every 25 milli-seconds.
    */
     componentDidUpdate() {
-    // Log to console how long the last update take?
-        console.log((Date.now() - this.lastTimeStamp) / 1000);
+        // Log to console how long the last update take?
+        // console.log((Date.now() - this.lastTimeStamp) / 1000);
 
         // Lock sidebar in its position on the first update.
         if (this.nextQuery == 0 && this.nextHit == 0 && this.nextHSP == 0) {
@@ -286,6 +291,40 @@ class Report extends Component {
         );
     }
 
+
+    warningJSX() {
+        return(
+            <div className="container">
+                <div className="row">
+                    <div className="col-md-6 col-md-offset-3 text-center">
+                        <h1>
+                            <i className="fa fa-exclamation-triangle"></i>&nbsp; Warning
+                        </h1>
+                        <p>
+                            <br />
+                            The BLAST result might be too large to load in the browser. If you have a powerful machine you can try loading the results anyway. Otherwise, you can download the results and view them locally.
+                        </p>
+                        <br />
+                        <p>
+                            {this.state.download_links.map((link, index) => {
+                                return (
+                                    <a href={link.url} className="btn btn-secondary" key={'download_link_' + index} >
+                                        {link.name}
+                                    </a>
+                                );
+                            })}
+                        </p>
+                        <br />
+                        <p>
+                            <a href={location.pathname + '?bypass_file_size_warning=true'} className="btn btn-primary">
+                                View results in browser anyway
+                            </a>
+                        </p>
+                    </div>
+                </div>
+            </div>
+        );
+    }
     /**
    * Renders report overview.
    */
@@ -350,6 +389,15 @@ class Report extends Component {
         return this.state.queries.length >= 1;
     }
 
+    /**
+     * Indicates the response contains a warning message for the user
+     * in which case we should not render the results and render the
+     * warning instead.
+     **/
+    isUserWarningPresent() {
+        return this.state.user_warning;
+    }
+
     /**
    * Returns true if we have at least one hit.
    */
@@ -539,7 +587,13 @@ class Report extends Component {
     }
 
     render() {
-        return this.isResultAvailable() ? this.resultsJSX() : this.loadingJSX();
+        if (this.isUserWarningPresent()) {
+            return this.warningJSX();
+        } else if (this.isResultAvailable()) {
+            return this.resultsJSX();
+        } else {
+            return this.loadingJSX();
+        }
     }
 }
 

data/public/js/tests/advanced_parameters.spec.js

@@ -0,0 +1,36 @@
+/* eslint-disable no-unused-vars */
+/* eslint-disable no-undef */
+import { render, screen, fireEvent } from '@testing-library/react';
+import { Form } from '../form';
+import { AMINO_ACID_SEQUENCE } from './mock_data/sequences';
+import data from './mock_data/databases.json';
+import userEvent from '@testing-library/user-event';
+import '@testing-library/jest-dom/extend-expect';
+import '@testing-library/react/dont-cleanup-after-each';
+
+export const setMockJSONResult = (result) => {
+    global.$.getJSON = (_, cb) => cb(result);
+};
+describe('ADVANCED PARAMETERS', () => {
+    const getInputElement = () => screen.getByRole('textbox', { name: '' });
+    test('should not render the link to advanced parameters modal if blast algorithm is unknown', () => {
+        setMockJSONResult(data);
+        const {container } =render(<Form onSequenceTypeChanged={() => { }
+        } />);
+        const modalButton = container.querySelector('[data-target="#help"]');
+        expect(modalButton).toBeNull();
+    });
+    test('should render the link to advanced parameters modal if blast algorithm is known', () => {
+        setMockJSONResult(data);
+        const {container } =render(<Form onSequenceTypeChanged={() => { }
+        } />);
+        
+        const inputEl = getInputElement();
+        // populate search and select dbs to determine blast algorithm
+        fireEvent.change(inputEl, { target: { value: AMINO_ACID_SEQUENCE } });
+        const proteinSelectAllBtn = screen.getByRole('heading', { name: /protein databases/i }).parentElement.querySelector('button');
+        fireEvent.click(proteinSelectAllBtn);
+        const modalButton = container.querySelector('[data-target="#help"]');
+        expect(modalButton).not.toBeNull();
+    });
+});

data/public/js/tests/mock_data/sequences.js

@@ -0,0 +1,32 @@
+export const AMINO_ACID_SEQUENCE = `MNTLWLSLWDYPGKLPLNFMVFDTKDDLQAAYWRDPYSIPLAVIFEDPQPISQRLIYEIR
+TNPSYTLPPPPTKLYSAPISCRKNKTGHWMDDILSIKTGESCPVNNYLHSGFLALQMITD
+ITKIKLENSDVTIPDIKLIMFPKEPYTADWMLAFRVVIPLYMVLALSQFITYLLILIVGE
+KENKIKEGMKMMGLNDSVF
+>SI2.2.0_13722 locus=Si_gnF.scaffold06207[1925625..1928536].pep_1 quality=100.00
+MSANRLNVLVTLMLAVALLVTESGNAQVDGYLQFNPKRSAVSSPQKYCGKKLSNALQIIC
+DGVYNSMFKKSGQDFPPQNKRHIAHRINGNEEESFTTLKSNFLNWCVEVYHRHYRFVFVS
+EMEMADYPLAYDISPYLPPFLSRARARGMLDGRFAGRRYRRESRGIHEECCINGCTINEL
+TSYCGP
+`;
+export const NUCLEOTIDE_SEQUENCE = `ATGAATACCCTCTGGCTCTCTTTATGGGATTATCCCGGTAAGCTTCCCTTAAACTTCATG
+GTGTTTGACACGAAGGATGATCTGCAAGCAGCGTATTGGAGAGATCCTTACAGCATACCT
+CTGGCAGTTATCTTCGAGGACCCCCAACCGATATCACAGCGACTTATATATGAAATTAGG
+ACGAATCCTTCATACACTTTGCCGCCACCGCCAACCAAATTGTATTCTGCTCCGATCAGT
+TGTCGAAAGAATAAAACTGGTCACTGGATGGACGACATTTTATCGATAAAAACCGGTGAA
+TCTTGTCCCGTTAACAATTACTTGCATTCTGGCTTCTTGGCTCTGCAAATGATAACGGAT
+ATCACAAAGATAAAATTGGAAAATTCTGACGTGACAATACCGGATATTAAACTCATAATG
+TTTCCTAAAGAGCCGTATACCGCTGACTGGATGCTGGCCTTCAGAGTTGTTATTCCGCTT
+TACATGGTCTTGGCTCTCTCGCAATTTATCACTTATCTTCTGATCCTAATAGTTGGCGAG
+AAGGAAAATAAGATTAAAGAGGGAATGAAGATGATGGGCTTAAATGATTCTGTGTTT
+>SI2.2.0_13722 Si_gnF.scaffold06207[1925625..1928536].pep_1
+ATGTCCGCGAATCGATTGAACGTGCTGGTGACCCTGATGCTCGCCGTCGCGCTTCTTGTG
+ACGGAATCAGGAAATGCACAGGTGGATGGCTATCTCCAATTCAACCCAAAGCGATCCGCC
+GTGAGCTCGCCGCAGAAGTATTGCGGCAAAAAGCTTTCTAATGCTCTACAGATAATCTGT
+GATGGCGTGTACAATTCCATGTTTAAGAAGAGTGGTCAAGATTTTCCCCCGCAAAATAAG
+AGACACATAGCACACAGAATAAATGGGAATGAGGAAGAGAGCTTTACTACGTTAAAGTCG
+AATTTTTTAAACTGGTGTGTTGAAGTTTATCATCGTCACTACAGATTCGTTTTTGTTTCA
+GAGATGGAAATGGCCGATTACCCGCTCGCCTATGATATTTCCCCGTATCTTCCGCCGTTC
+CTGTCGCGAGCGAGGGCACGGGGAATGTTAGACGGTCGCTTCGCCGGCAGACGCTACCGA
+AGGGAGTCGCGGGGCATTCACGAGGAGTGTTGCATCAACGGATGTACGATAAACGAATTG
+ACCAGCTACTGCGGCCCC
+`;

data/public/js/tests/report.spec.js

@@ -25,7 +25,14 @@ const TestSidebar = ({ long }) => {
     />;
 };
 
+const clickCheckboxes = (checkboxes, count) => {
+    Array.from(checkboxes).slice(0, count).forEach((checkbox) => {
+        fireEvent.click(checkbox);
+    });
+};
 describe('REPORT PAGE', () => {
+    global.URL.createObjectURL = jest.fn();//.mockReturnValue('xyz.test');
+    global.setTimeout = (cb) => cb();
     it('should render the report component with initial loading state', () => {
         render(<Report />);
         expect(screen.getByRole('heading', { name: 'BLAST-ing' })).toBeInTheDocument();
@@ -39,7 +46,7 @@ describe('REPORT PAGE', () => {
     });
     it('it should render the report page correctly if there\'s a response provided', () => {
         setMockJSONResult({ status: 200, responseJSON: shortResponseJSON });
-        const { container } = render(<Report />);
+        const { container } = render(<Report getCharacterWidth={jest.fn()} />);
         expect(container.querySelector('#results')).toBeInTheDocument();
 
     });
@@ -63,18 +70,18 @@ describe('REPORT PAGE', () => {
         });
 
         describe('LONG QUERIES (>12)', () => {
-
+            let container;
+            beforeEach(() => {
+                container = render(<TestSidebar long />).container;
+            });
             it('should not show navigation links for long queries', () => {
-                const { container } = render(<TestSidebar long />);
                 expect(container.querySelectorAll('a[href^="#Query_"]').length).toBe(0);
             });
             it('should show only next button if on first query ', () => {
-                render(<TestSidebar long />);
                 expect(nextQueryButton()).toBeInTheDocument();
                 expect(previousQueryButton()).not.toBeInTheDocument();
             });
             it('should show both previous and next buttons if not on first query', () => {
-                render(<TestSidebar long />);
                 const nextBtn = nextQueryButton();
                 expect(nextBtn).toBeInTheDocument();
                 fireEvent.click(nextBtn);
@@ -84,7 +91,6 @@ describe('REPORT PAGE', () => {
             });
             it('should show only previous button if on last query', () => {
                 const { queries } = longResponseJSON;
-                render(<TestSidebar long />);
                 expect(nextQueryButton()).toBeInTheDocument();
                 expect(previousQueryButton()).not.toBeInTheDocument();
 
@@ -95,5 +101,55 @@ describe('REPORT PAGE', () => {
                 expect(previousQueryButton()).toBeInTheDocument();
             });
         });
+
+        describe('DOWNLOAD LINKS', () => {
+            let container;
+            beforeEach(() => {
+                setMockJSONResult({ status: 200, responseJSON: shortResponseJSON });
+                container = render(<Report getCharacterWidth={jest.fn()}  />).container;
+            });
+            describe('ALIGNMENT DOWNLOAD', () => {
+                it('should generate a blob url and filename for downloading alignment of all hits on render', () => {
+                    const alignment_download_link = container.querySelector('.download-alignment-of-all');
+                    const expected_num_hits = container.querySelectorAll('.hit-links input[type="checkbox"]').length;
+                    const file_name = `alignment-${expected_num_hits}_hits.txt`;
+                    expect(alignment_download_link.download).toEqual(file_name);
+                    expect(alignment_download_link.hred).not.toEqual('#');
+                });
+                it('link for downloading alignment of specific number of selected hits should be disabled on initial load', () => {
+                    const alignment_download_link = container.querySelector('.download-alignment-of-selected');
+                    expect(alignment_download_link.classList.contains('disabled')).toBeTruthy();
+    
+                });
+                it('should generate a blob url and filename for downloading alignment of specific number of selected hits', () => {
+                    const alignment_download_link = container.querySelector('.download-alignment-of-selected');
+                    // QUERY ALL HIT LINKS CHECKBOXES
+                    const checkboxes = container.querySelectorAll('.hit-links input[type="checkbox"]');
+                    // SELECT 4 CHECKBOXES
+                    clickCheckboxes(checkboxes, 4);
+                    const file_name = 'alignment-4_hits.txt';
+                    expect(alignment_download_link.textContent).toEqual('Alignment of 4 selected hit(s)');
+                    expect(alignment_download_link.download).toEqual(file_name);
+                });
+            });
+    
+            describe('FASTA DOWNLOAD', () => {
+                let fasta_download_link;
+                beforeEach(() => {
+                    fasta_download_link = container.querySelector('.download-fasta-of-selected');
+                });
+                it('link for downloading fasta of selected number of hits should be disabled on initial load', () => {
+                    expect(fasta_download_link.classList.contains('disabled')).toBeTruthy();
+                });
+    
+                it('link for downloading fasta of specific number of selected hits should be active after selection', () => {
+                    const checkboxes = container.querySelectorAll('.hit-links input[type="checkbox"]');
+                    // SELECT 5 CHECKBOXES
+                    clickCheckboxes(checkboxes, 5);
+                    expect(fasta_download_link.textContent).toEqual('FASTA of 5 selected hit(s)');
+                });
+            });
+        });
     });
+
 });

data/public/js/tests/search_query.spec.js

@@ -3,39 +3,56 @@
 import { render, screen, fireEvent } from '@testing-library/react';
 import { SearchQueryWidget } from '../query';
 import { Form } from '../form';
-import userEvent from '@testing-library/user-event';
+import { AMINO_ACID_SEQUENCE, NUCLEOTIDE_SEQUENCE } from './mock_data/sequences';
 import '@testing-library/jest-dom/extend-expect';
 import '@testing-library/react/dont-cleanup-after-each';
 
-export const AMINO_ACID_SEQUENCE = `MNTLWLSLWDYPGKLPLNFMVFDTKDDLQAAYWRDPYSIPLAVIFEDPQPISQRLIYEIR
-TNPSYTLPPPPTKLYSAPISCRKNKTGHWMDDILSIKTGESCPVNNYLHSGFLALQMITD
-ITKIKLENSDVTIPDIKLIMFPKEPYTADWMLAFRVVIPLYMVLALSQFITYLLILIVGE
-KENKIKEGMKMMGLNDSVF
->SI2.2.0_13722 locus=Si_gnF.scaffold06207[1925625..1928536].pep_1 quality=100.00
-MSANRLNVLVTLMLAVALLVTESGNAQVDGYLQFNPKRSAVSSPQKYCGKKLSNALQIIC
-DGVYNSMFKKSGQDFPPQNKRHIAHRINGNEEESFTTLKSNFLNWCVEVYHRHYRFVFVS
-EMEMADYPLAYDISPYLPPFLSRARARGMLDGRFAGRRYRRESRGIHEECCINGCTINEL
-TSYCGP
-`;
+let container;
+let inputEl;
+
 describe('SEARCH COMPONENT', () => {
-    const getInputElement = () => screen.getByRole('textbox', { name: '' });
+    beforeEach(() => {
+        container  = render(<Form onSequenceTypeChanged={() => { }
+        } />).container;
+        inputEl = screen.getByRole('textbox', { name: '' });
+    });
+    
     test('should render the search component textarea', () => {
-        render(<SearchQueryWidget onSequenceTypeChanged={() => { }
-        } />);
-        const el = getInputElement();
-        expect(el).toHaveClass('form-control');
+        expect(inputEl).toHaveClass('form-control');
     });
 
     test('clear button should only become visible if textarea is not empty', () => {
-        render(<SearchQueryWidget onSequenceTypeChanged={() => { }
-        } />);
         const getButtonWrapper = () => screen.getByRole('button', { name: /clear query sequence\(s\)\./i }).parentElement;
         expect(getButtonWrapper()).toHaveClass('hidden');
-        const inputEl = getInputElement();
         fireEvent.change(inputEl, { target: { value: AMINO_ACID_SEQUENCE } });
         expect(getButtonWrapper()).not.toHaveClass('hidden');
         fireEvent.change(inputEl, { target: { value: '' } });
         expect(getButtonWrapper()).toHaveClass('hidden');
+    });
 
+    test('should correctly detect the amino-acid sequence type and show notification', () => {
+        // populate search
+        fireEvent.change(inputEl, { target: { value: AMINO_ACID_SEQUENCE } });
+        const activeNotification = container.querySelector('.notification.active');
+        expect(activeNotification.id).toBe('protein-sequence-notification');
+        const alertWrapper = activeNotification.children[0];
+        expect(alertWrapper).toHaveTextContent('Detected: amino-acid sequence(s).');
+    });
+
+    test('should correctly detect the nucleotide sequence type and show notification', () => {
+        // populate search
+        fireEvent.change(inputEl, { target: { value: NUCLEOTIDE_SEQUENCE } });
+        const activeNotification = container.querySelector('.notification.active');
+        const alertWrapper = activeNotification.children[0];
+        expect(activeNotification.id).toBe('nucleotide-sequence-notification');
+        expect(alertWrapper).toHaveTextContent('Detected: nucleotide sequence(s).');
+    });
+    
+    test('should correctly detect the mixed sequences and show error notification', () => {
+        fireEvent.change(inputEl, { target: { value: `${NUCLEOTIDE_SEQUENCE}${AMINO_ACID_SEQUENCE}` } });
+        const activeNotification = container.querySelector('.notification.active');
+        expect(activeNotification.id).toBe('mixed-sequence-notification');
+        const alertWrapper = activeNotification.children[0];
+        expect(alertWrapper).toHaveTextContent('Error: mixed nucleotide and amino-acid sequences detected.');
     });
 });

data/public/js/visualisation_helpers.js

@@ -1,5 +1,5 @@
 import _ from 'underscore';
-
+import d3 from 'd3';
 export function get_colors_for_evalue(evalue, hits) {
     var colors = d3.scale
         .log()

data/public/sequenceserver-report.min.js

@@ -181,7 +181,7 @@ eval("__webpack_require__.r(__webpack_exports__);\n/* harmony export */ __webpac
 /***/ ((__unused_webpack_module, __webpack_exports__, __webpack_require__) => {
 
 "use strict";
-eval("__webpack_require__.r(__webpack_exports__);\n/* harmony export */ __webpack_require__.d(__webpack_exports__, {\n/* harmony export */   \"default\": () => (__WEBPACK_DEFAULT_EXPORT__)\n/* harmony export */ });\n/* harmony import */ var _jquery_world__WEBPACK_IMPORTED_MODULE_0__ = __webpack_require__(/*! ./jquery_world */ \"./public/js/jquery_world.js\");\n/* harmony import */ var react__WEBPACK_IMPORTED_MODULE_1__ = __webpack_require__(/*! react */ \"./node_modules/react/index.js\");\n/* harmony import */ var react__WEBPACK_IMPORTED_MODULE_1___default = /*#__PURE__*/__webpack_require__.n(react__WEBPACK_IMPORTED_MODULE_1__);\n/* harmony import */ var underscore__WEBPACK_IMPORTED_MODULE_2__ = __webpack_require__(/*! underscore */ \"./node_modules/underscore/modules/index-all.js\");\n/* harmony import */ var _sidebar__WEBPACK_IMPORTED_MODULE_3__ = __webpack_require__(/*! ./sidebar */ \"./public/js/sidebar.js\");\n/* harmony import */ var _circos__WEBPACK_IMPORTED_MODULE_4__ = __webpack_require__(/*! ./circos */ \"./public/js/circos.js\");\n/* harmony import */ var _query__WEBPACK_IMPORTED_MODULE_5__ = __webpack_require__(/*! ./query */ \"./public/js/query.js\");\n/* harmony import */ var _hit__WEBPACK_IMPORTED_MODULE_6__ = __webpack_require__(/*! ./hit */ \"./public/js/hit.js\");\n/* harmony import */ var _hsp__WEBPACK_IMPORTED_MODULE_7__ = __webpack_require__(/*! ./hsp */ \"./public/js/hsp.js\");\n/* harmony import */ var _alignment_exporter__WEBPACK_IMPORTED_MODULE_8__ = __webpack_require__(/*! ./alignment_exporter */ \"./public/js/alignment_exporter.js\");\n/* harmony import */ var react_jsx_runtime__WEBPACK_IMPORTED_MODULE_9__ = __webpack_require__(/*! react/jsx-runtime */ \"./node_modules/react/jsx-runtime.js\");\n/* provided dependency */ var $ = __webpack_require__(/*! jquery */ \"./node_modules/jquery/dist/jquery.js\");\nfunction _typeof(obj) { \"@babel/helpers - typeof\"; return _typeof = \"function\" == typeof Symbol && \"symbol\" == typeof Symbol.iterator ? function (obj) { return typeof obj; } : function (obj) { return obj && \"function\" == typeof Symbol && obj.constructor === Symbol && obj !== Symbol.prototype ? \"symbol\" : typeof obj; }, _typeof(obj); }\n\nfunction ownKeys(object, enumerableOnly) { var keys = Object.keys(object); if (Object.getOwnPropertySymbols) { var symbols = Object.getOwnPropertySymbols(object); enumerableOnly && (symbols = symbols.filter(function (sym) { return Object.getOwnPropertyDescriptor(object, sym).enumerable; })), keys.push.apply(keys, symbols); } return keys; }\n\nfunction _objectSpread(target) { for (var i = 1; i < arguments.length; i++) { var source = null != arguments[i] ? arguments[i] : {}; i % 2 ? ownKeys(Object(source), !0).forEach(function (key) { _defineProperty(target, key, source[key]); }) : Object.getOwnPropertyDescriptors ? Object.defineProperties(target, Object.getOwnPropertyDescriptors(source)) : ownKeys(Object(source)).forEach(function (key) { Object.defineProperty(target, key, Object.getOwnPropertyDescriptor(source, key)); }); } return target; }\n\nfunction _defineProperty(obj, key, value) { if (key in obj) { Object.defineProperty(obj, key, { value: value, enumerable: true, configurable: true, writable: true }); } else { obj[key] = value; } return obj; }\n\nfunction _classCallCheck(instance, Constructor) { if (!(instance instanceof Constructor)) { throw new TypeError(\"Cannot call a class as a function\"); } }\n\nfunction _defineProperties(target, props) { for (var i = 0; i < props.length; i++) { var descriptor = props[i]; descriptor.enumerable = descriptor.enumerable || false; descriptor.configurable = true; if (\"value\" in descriptor) descriptor.writable = true; Object.defineProperty(target, descriptor.key, descriptor); } }\n\nfunction _createClass(Constructor, protoProps, staticProps) { if (protoProps) _defineProperties(Constructor.prototype, protoProps); if (staticProps) _defineProperties(Constructor, staticProps); Object.defineProperty(Constructor, \"prototype\", { writable: false }); return Constructor; }\n\nfunction _inherits(subClass, superClass) { if (typeof superClass !== \"function\" && superClass !== null) { throw new TypeError(\"Super expression must either be null or a function\"); } subClass.prototype = Object.create(superClass && superClass.prototype, { constructor: { value: subClass, writable: true, configurable: true } }); Object.defineProperty(subClass, \"prototype\", { writable: false }); if (superClass) _setPrototypeOf(subClass, superClass); }\n\nfunction _setPrototypeOf(o, p) { _setPrototypeOf = Object.setPrototypeOf || function _setPrototypeOf(o, p) { o.__proto__ = p; return o; }; return _setPrototypeOf(o, p); }\n\nfunction _createSuper(Derived) { var hasNativeReflectConstruct = _isNativeReflectConstruct(); return function _createSuperInternal() { var Super = _getPrototypeOf(Derived), result; if (hasNativeReflectConstruct) { var NewTarget = _getPrototypeOf(this).constructor; result = Reflect.construct(Super, arguments, NewTarget); } else { result = Super.apply(this, arguments); } return _possibleConstructorReturn(this, result); }; }\n\nfunction _possibleConstructorReturn(self, call) { if (call && (_typeof(call) === \"object\" || typeof call === \"function\")) { return call; } else if (call !== void 0) { throw new TypeError(\"Derived constructors may only return object or undefined\"); } return _assertThisInitialized(self); }\n\nfunction _assertThisInitialized(self) { if (self === void 0) { throw new ReferenceError(\"this hasn't been initialised - super() hasn't been called\"); } return self; }\n\nfunction _isNativeReflectConstruct() { if (typeof Reflect === \"undefined\" || !Reflect.construct) return false; if (Reflect.construct.sham) return false; if (typeof Proxy === \"function\") return true; try { Boolean.prototype.valueOf.call(Reflect.construct(Boolean, [], function () {})); return true; } catch (e) { return false; } }\n\nfunction _getPrototypeOf(o) { _getPrototypeOf = Object.setPrototypeOf ? Object.getPrototypeOf : function _getPrototypeOf(o) { return o.__proto__ || Object.getPrototypeOf(o); }; return _getPrototypeOf(o); }\n\n // for custom $.tooltip function\n\n\n\n\n\n\n\n\n\n/**\n * Renders entire report.\n *\n * Composed of Query and Sidebar components.\n */\n\n\n\n\nvar Report = /*#__PURE__*/function (_Component) {\n  _inherits(Report, _Component);\n\n  var _super = _createSuper(Report);\n\n  function Report(props) {\n    var _this;\n\n    _classCallCheck(this, Report);\n\n    _this = _super.call(this, props); // Properties below are internal state used to render results in small\n    // slices (see updateState).\n\n    _this.numUpdates = 0;\n    _this.nextQuery = 0;\n    _this.nextHit = 0;\n    _this.nextHSP = 0;\n    _this.maxHSPs = 3; // max HSPs to render in a cycle\n\n    _this.state = {\n      search_id: '',\n      seqserv_version: '',\n      program: '',\n      program_version: '',\n      submitted_at: '',\n      queries: [],\n      results: [],\n      querydb: [],\n      params: [],\n      stats: [],\n      alignment_blob_url: '',\n      allQueriesLoaded: false,\n      cloud_sharing_enabled: false\n    };\n    _this.prepareAlignmentOfSelectedHits = _this.prepareAlignmentOfSelectedHits.bind(_assertThisInitialized(_this));\n    _this.prepareAlignmentOfAllHits = _this.prepareAlignmentOfAllHits.bind(_assertThisInitialized(_this));\n    _this.setStateFromJSON = _this.setStateFromJSON.bind(_assertThisInitialized(_this));\n    return _this;\n  }\n  /**\n  * Fetch results.\n  */\n\n\n  _createClass(Report, [{\n    key: \"fetchResults\",\n    value: function fetchResults() {\n      var intervals = [200, 400, 800, 1200, 2000, 3000, 5000];\n      var component = this;\n\n      function poll() {\n        $.getJSON(location.pathname + '.json').complete(function (jqXHR) {\n          switch (jqXHR.status) {\n            case 202:\n              var interval;\n\n              if (intervals.length === 1) {\n                interval = intervals[0];\n              } else {\n                interval = intervals.shift();\n              }\n\n              setTimeout(poll, interval);\n              break;\n\n            case 200:\n              component.setStateFromJSON(jqXHR.responseJSON);\n              break;\n\n            case 404:\n            case 400:\n            case 500:\n              component.props.showErrorModal(jqXHR.responseJSON);\n              break;\n          }\n        });\n      }\n\n      poll();\n    }\n    /**\n    * Calls setState after any required modification to responseJSON.\n    */\n\n  }, {\n    key: \"setStateFromJSON\",\n    value: function setStateFromJSON(responseJSON) {\n      this.lastTimeStamp = Date.now(); // the callback prepares the download link for all alignments\n\n      this.setState(responseJSON, this.prepareAlignmentOfAllHits);\n    }\n    /**\n    * Called as soon as the page has loaded and the user sees the loading spinner.\n    * We use this opportunity to setup services that make use of delegated events\n    * bound to the window, document, or body.\n    */\n\n  }, {\n    key: \"componentDidMount\",\n    value: function componentDidMount() {\n      this.fetchResults(); // This sets up an event handler which enables users to select text from\n      // hit header without collapsing the hit.\n\n      this.preventCollapseOnSelection();\n      this.toggleTable();\n    }\n    /**\n    * Called for the first time after as BLAST results have been retrieved from\n    * the server and added to this.state by fetchResults. Only summary overview\n    * and circos would have been rendered at this point. At this stage we kick\n    * start iteratively adding 1 HSP to the page every 25 milli-seconds.\n    */\n\n  }, {\n    key: \"componentDidUpdate\",\n    value: function componentDidUpdate() {\n      var _this2 = this;\n\n      // Log to console how long the last update take?\n      console.log((Date.now() - this.lastTimeStamp) / 1000); // Lock sidebar in its position on the first update.\n\n      if (this.nextQuery == 0 && this.nextHit == 0 && this.nextHSP == 0) {\n        this.affixSidebar();\n      } // Queue next update if we have not rendered all results yet.\n\n\n      if (this.nextQuery < this.state.queries.length) {\n        // setTimeout is used to clear call stack and space out\n        // the updates giving the browser a chance to respond\n        // to user interactions.\n        setTimeout(function () {\n          return _this2.updateState();\n        }, 25);\n      } else {\n        this.componentFinishedUpdating();\n      }\n    }\n    /**\n    * Push next slice of results to React for rendering.\n    */\n\n  }, {\n    key: \"updateState\",\n    value: function updateState() {\n      var results = [];\n      var numHSPsProcessed = 0;\n\n      while (this.nextQuery < this.state.queries.length) {\n        var query = this.state.queries[this.nextQuery]; // We may see a query multiple times during rendering because only\n        // 3 hsps or are rendered in each cycle, but we want to create the\n        // corresponding Query component only the first time we see it.\n\n        if (this.nextHit == 0 && this.nextHSP == 0) {\n          results.push( /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_9__.jsx)(_query__WEBPACK_IMPORTED_MODULE_5__.ReportQuery, {\n            query: query,\n            program: this.state.program,\n            querydb: this.state.querydb,\n            showQueryCrumbs: this.state.queries.length > 1,\n            non_parse_seqids: this.state.non_parse_seqids,\n            imported_xml: this.state.imported_xml,\n            veryBig: this.state.veryBig\n          }, 'Query_' + query.number));\n        }\n\n        while (this.nextHit < query.hits.length) {\n          var hit = query.hits[this.nextHit]; // We may see a hit multiple times during rendering because only\n          // 10 hsps are rendered in each cycle, but we want to create the\n          // corresponding Hit component only the first time we see it.\n\n          if (this.nextHSP == 0) {\n            results.push( /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_9__.jsx)(_hit__WEBPACK_IMPORTED_MODULE_6__[\"default\"], _objectSpread({\n              query: query,\n              hit: hit,\n              algorithm: this.state.program,\n              querydb: this.state.querydb,\n              selectHit: this.selectHit,\n              imported_xml: this.state.imported_xml,\n              non_parse_seqids: this.state.non_parse_seqids,\n              showQueryCrumbs: this.state.queries.length > 1,\n              showHitCrumbs: query.hits.length > 1,\n              veryBig: this.state.veryBig,\n              onChange: this.prepareAlignmentOfSelectedHits\n            }, this.props), 'Query_' + query.number + '_Hit_' + hit.number));\n          }\n\n          while (this.nextHSP < hit.hsps.length) {\n            // Get nextHSP and increment the counter.\n            var hsp = hit.hsps[this.nextHSP++];\n            results.push( /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_9__.jsx)(_hsp__WEBPACK_IMPORTED_MODULE_7__[\"default\"], _objectSpread({\n              query: query,\n              hit: hit,\n              hsp: hsp,\n              algorithm: this.state.program,\n              showHSPNumbers: hit.hsps.length > 1\n            }, this.props), 'Query_' + query.number + '_Hit_' + hit.number + '_HSP_' + hsp.number));\n            numHSPsProcessed++;\n            if (numHSPsProcessed == this.maxHSPs) break;\n          } // Are we here because we have iterated over all hsps of a hit,\n          // or because of the break clause in the inner loop?\n\n\n          if (this.nextHSP == hit.hsps.length) {\n            this.nextHit = this.nextHit + 1;\n            this.nextHSP = 0;\n          }\n\n          if (numHSPsProcessed == this.maxHSPs) break;\n        } // Are we here because we have iterated over all hits of a query,\n        // or because of the break clause in the inner loop?\n\n\n        if (this.nextHit == query.hits.length) {\n          this.nextQuery = this.nextQuery + 1;\n          this.nextHit = 0;\n        }\n\n        if (numHSPsProcessed == this.maxHSPs) break;\n      } // Push the components to react for rendering.\n\n\n      this.numUpdates++;\n      this.lastTimeStamp = Date.now();\n      this.setState({\n        results: this.state.results.concat(results),\n        veryBig: this.numUpdates >= 250\n      });\n    }\n    /**\n    * Called after all results have been rendered.\n    */\n\n  }, {\n    key: \"componentFinishedUpdating\",\n    value: function componentFinishedUpdating() {\n      if (this.state.allQueriesLoaded) return;\n      this.shouldShowIndex() && this.setupScrollSpy();\n      this.setState({\n        allQueriesLoaded: true\n      });\n    }\n    /**\n    * Returns loading message\n    */\n\n  }, {\n    key: \"loadingJSX\",\n    value: function loadingJSX() {\n      return /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_9__.jsx)(\"div\", {\n        className: \"row\",\n        children: /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_9__.jsxs)(\"div\", {\n          className: \"col-md-6 col-md-offset-3 text-center\",\n          children: [/*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_9__.jsxs)(\"h1\", {\n            children: [/*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_9__.jsx)(\"i\", {\n              className: \"fa fa-cog fa-spin\"\n            }), \"\\xA0 BLAST-ing\"]\n          }), /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_9__.jsxs)(\"p\", {\n            children: [/*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_9__.jsx)(\"br\", {}), \"This can take some time depending on the size of your query and database(s). The page will update automatically when BLAST is done.\", /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_9__.jsx)(\"br\", {}), /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_9__.jsx)(\"br\", {}), \"You can bookmark the page and come back to it later or share the link with someone.\"]\n          })]\n        })\n      });\n    }\n    /**\n    * Return results JSX.\n    */\n\n  }, {\n    key: \"resultsJSX\",\n    value: function resultsJSX() {\n      return /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_9__.jsxs)(\"div\", {\n        className: \"row\",\n        id: \"results\",\n        children: [/*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_9__.jsx)(\"div\", {\n          className: \"col-md-3 hidden-sm hidden-xs\",\n          children: /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_9__.jsx)(_sidebar__WEBPACK_IMPORTED_MODULE_3__[\"default\"], {\n            data: this.state,\n            atLeastOneHit: this.atLeastOneHit(),\n            shouldShowIndex: this.shouldShowIndex(),\n            allQueriesLoaded: this.state.allQueriesLoaded,\n            cloudSharingEnabled: this.state.cloud_sharing_enabled\n          })\n        }), /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_9__.jsxs)(\"div\", {\n          className: \"col-md-9\",\n          children: [this.overviewJSX(), this.circosJSX(), this.state.results]\n        })]\n      });\n    }\n    /**\n    * Renders report overview.\n    */\n\n  }, {\n    key: \"overviewJSX\",\n    value: function overviewJSX() {\n      return /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_9__.jsxs)(\"div\", {\n        className: \"overview\",\n        children: [/*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_9__.jsxs)(\"p\", {\n          children: [/*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_9__.jsxs)(\"strong\", {\n            children: [\"SequenceServer \", this.state.seqserv_version]\n          }), \" using\", ' ', /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_9__.jsx)(\"strong\", {\n            children: this.state.program_version\n          }), this.state.submitted_at && \", query submitted on \".concat(this.state.submitted_at)]\n        }), /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_9__.jsxs)(\"p\", {\n          children: [/*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_9__.jsx)(\"strong\", {\n            children: \" Databases: \"\n          }), this.state.querydb.map(function (db) {\n            return db.title;\n          }).join(', '), ' ', \"(\", this.state.stats.nsequences, \" sequences,\\xA0\", this.state.stats.ncharacters, \" characters)\"]\n        }), /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_9__.jsxs)(\"p\", {\n          children: [/*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_9__.jsx)(\"strong\", {\n            children: \"Parameters: \"\n          }), ' ', underscore__WEBPACK_IMPORTED_MODULE_2__[\"default\"].map(this.state.params, function (val, key) {\n            return key + ' ' + val;\n          }).join(', ')]\n        }), /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_9__.jsxs)(\"p\", {\n          children: [\"Please cite:\", ' ', /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_9__.jsx)(\"a\", {\n            href: \"https://doi.org/10.1093/molbev/msz185\",\n            children: \"https://doi.org/10.1093/molbev/msz185\"\n          })]\n        })]\n      });\n    }\n    /**\n    * Return JSX for circos if we have at least one hit.\n    */\n\n  }, {\n    key: \"circosJSX\",\n    value: function circosJSX() {\n      return this.atLeastTwoHits() ? /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_9__.jsx)(_circos__WEBPACK_IMPORTED_MODULE_4__[\"default\"], {\n        queries: this.state.queries,\n        program: this.state.program,\n        collapsed: \"true\"\n      }) : /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_9__.jsx)(\"span\", {});\n    } // Controller //\n\n    /**\n    * Returns true if results have been fetched.\n    *\n    * A holding message is shown till results are fetched.\n    */\n\n  }, {\n    key: \"isResultAvailable\",\n    value: function isResultAvailable() {\n      return this.state.queries.length >= 1;\n    }\n    /**\n    * Returns true if we have at least one hit.\n    */\n\n  }, {\n    key: \"atLeastOneHit\",\n    value: function atLeastOneHit() {\n      return this.state.queries.some(function (query) {\n        return query.hits.length > 0;\n      });\n    }\n    /**\n    * Does the report have at least two hits? This is used to determine\n    * whether Circos should be enabled or not.\n    */\n\n  }, {\n    key: \"atLeastTwoHits\",\n    value: function atLeastTwoHits() {\n      var hit_num = 0;\n      return this.state.queries.some(function (query) {\n        hit_num += query.hits.length;\n        return hit_num > 1;\n      });\n    }\n    /**\n    * Returns true if index should be shown in the sidebar. Index is shown\n    * only for 2 and 8 queries.\n    */\n\n  }, {\n    key: \"shouldShowIndex\",\n    value: function shouldShowIndex() {\n      var num_queries = this.state.queries.length;\n      return num_queries >= 2 && num_queries <= 12;\n    }\n    /**\n    * Prevents folding of hits during text-selection.\n    */\n\n  }, {\n    key: \"preventCollapseOnSelection\",\n    value: function preventCollapseOnSelection() {\n      $('body').on('mousedown', '.hit > .section-header > h4', function (event) {\n        var $this = $(this);\n        $this.on('mouseup mousemove', function handler(event) {\n          if (event.type === 'mouseup') {\n            // user wants to toggle\n            var hitID = $this.parents('.hit').attr('id');\n            $(\"div[data-parent-hit=\".concat(hitID, \"]\")).toggle();\n            $this.find('i').toggleClass('fa-minus-square-o fa-plus-square-o');\n          } else {\n            // user wants to select\n            $this.attr('data-toggle', '');\n          }\n\n          $this.off('mouseup mousemove', handler);\n        });\n      });\n    }\n    /* Handling the fa icon when Hit Table is collapsed */\n\n  }, {\n    key: \"toggleTable\",\n    value: function toggleTable() {\n      $('body').on('mousedown', '.resultn > .section-content > .table-hit-overview > .caption', function (event) {\n        var $this = $(this);\n        $this.on('mouseup mousemove', function handler(event) {\n          $this.find('i').toggleClass('fa-minus-square-o fa-plus-square-o');\n          $this.off('mouseup mousemove', handler);\n        });\n      });\n    }\n    /**\n    * Affixes the sidebar.\n    */\n\n  }, {\n    key: \"affixSidebar\",\n    value: function affixSidebar() {\n      var $sidebar = $('.sidebar');\n      var sidebarOffset = $sidebar.offset();\n\n      if (sidebarOffset) {\n        $sidebar.affix({\n          offset: {\n            top: sidebarOffset.top\n          }\n        });\n      }\n    }\n    /**\n    * For the query in viewport, highlights corresponding entry in the index.\n    */\n\n  }, {\n    key: \"setupScrollSpy\",\n    value: function setupScrollSpy() {\n      $('body').scrollspy({\n        target: '.sidebar'\n      });\n    }\n    /**\n    * Event-handler when hit is selected\n    * Adds glow to hit component.\n    * Updates number of Fasta that can be downloaded\n    */\n\n  }, {\n    key: \"selectHit\",\n    value: function selectHit(id) {\n      var checkbox = $('#' + id);\n      var num_checked = $('.hit-links :checkbox:checked').length;\n\n      if (!checkbox || !checkbox.val()) {\n        return;\n      }\n\n      var $hit = $(checkbox.data('target')); // Highlight selected hit and enable 'Download FASTA/Alignment of\n      // selected' links.\n\n      if (checkbox.is(':checked')) {\n        $hit.addClass('glow');\n        $hit.next('.hsp').addClass('glow');\n        $('.download-fasta-of-selected').enable();\n        $('.download-alignment-of-selected').enable();\n      } else {\n        $hit.removeClass('glow');\n        $hit.next('.hsp').removeClass('glow');\n      }\n\n      var $a = $('.download-fasta-of-selected');\n      var $b = $('.download-alignment-of-selected');\n\n      if (num_checked >= 1) {\n        $a.find('.text-bold').html(num_checked);\n        $b.find('.text-bold').html(num_checked);\n      }\n\n      if (num_checked == 0) {\n        $a.addClass('disabled').find('.text-bold').html('');\n        $b.addClass('disabled').find('.text-bold').html('');\n      }\n    }\n  }, {\n    key: \"populate_hsp_array\",\n    value: function populate_hsp_array(hit, query_id) {\n      return hit.hsps.map(function (hsp) {\n        return Object.assign(hsp, {\n          hit_id: hit.id,\n          query_id: query_id\n        });\n      });\n    }\n  }, {\n    key: \"prepareAlignmentOfSelectedHits\",\n    value: function prepareAlignmentOfSelectedHits() {\n      var sequence_ids = $('.hit-links :checkbox:checked').map(function () {\n        return this.value;\n      }).get();\n\n      if (!sequence_ids.length) {\n        // remove attributes from link if sequence_ids array is empty\n        $('.download-alignment-of-selected').attr('href', '#').removeAttr('download');\n        return;\n      }\n\n      if (this.state.alignment_blob_url) {\n        // always revoke existing url if any because this method will always create a new url\n        window.URL.revokeObjectURL(this.state.alignment_blob_url);\n      }\n\n      var hsps_arr = [];\n      var aln_exporter = new _alignment_exporter__WEBPACK_IMPORTED_MODULE_8__[\"default\"]();\n      var self = this;\n\n      underscore__WEBPACK_IMPORTED_MODULE_2__[\"default\"].each(this.state.queries, underscore__WEBPACK_IMPORTED_MODULE_2__[\"default\"].bind(function (query) {\n        underscore__WEBPACK_IMPORTED_MODULE_2__[\"default\"].each(query.hits, function (hit) {\n          if (underscore__WEBPACK_IMPORTED_MODULE_2__[\"default\"].indexOf(sequence_ids, hit.id) != -1) {\n            hsps_arr = hsps_arr.concat(self.populate_hsp_array(hit, query.id));\n          }\n        });\n      }, this));\n\n      var filename = 'alignment-' + sequence_ids.length + '_hits.txt';\n      var blob_url = aln_exporter.prepare_alignments_for_export(hsps_arr, filename); // set required download attributes for link\n\n      $('.download-alignment-of-selected').attr('href', blob_url).attr('download', filename); // track new url for future removal\n\n      this.setState({\n        alignment_blob_url: blob_url\n      });\n    }\n  }, {\n    key: \"prepareAlignmentOfAllHits\",\n    value: function prepareAlignmentOfAllHits() {\n      var _this3 = this;\n\n      // Get number of hits and array of all hsps.\n      var num_hits = 0;\n      var hsps_arr = [];\n\n      if (!this.state.queries.length) {\n        return;\n      }\n\n      this.state.queries.forEach(function (query) {\n        return query.hits.forEach(function (hit) {\n          num_hits++;\n          hsps_arr = hsps_arr.concat(_this3.populate_hsp_array(hit, query.id));\n        });\n      });\n      var aln_exporter = new _alignment_exporter__WEBPACK_IMPORTED_MODULE_8__[\"default\"]();\n      var file_name = \"alignment-\".concat(num_hits, \"_hits.txt\");\n      var blob_url = aln_exporter.prepare_alignments_for_export(hsps_arr, file_name);\n      $('.download-alignment-of-all').attr('href', blob_url).attr('download', file_name);\n      return false;\n    }\n  }, {\n    key: \"render\",\n    value: function render() {\n      return this.isResultAvailable() ? this.resultsJSX() : this.loadingJSX();\n    }\n  }]);\n\n  return Report;\n}(react__WEBPACK_IMPORTED_MODULE_1__.Component);\n\n/* harmony default export */ const __WEBPACK_DEFAULT_EXPORT__ = (Report);\n\n//# sourceURL=webpack://SequenceServer/./public/js/report.js?");
+eval("__webpack_require__.r(__webpack_exports__);\n/* harmony export */ __webpack_require__.d(__webpack_exports__, {\n/* harmony export */   \"default\": () => (__WEBPACK_DEFAULT_EXPORT__)\n/* harmony export */ });\n/* harmony import */ var _jquery_world__WEBPACK_IMPORTED_MODULE_0__ = __webpack_require__(/*! ./jquery_world */ \"./public/js/jquery_world.js\");\n/* harmony import */ var react__WEBPACK_IMPORTED_MODULE_1__ = __webpack_require__(/*! react */ \"./node_modules/react/index.js\");\n/* harmony import */ var react__WEBPACK_IMPORTED_MODULE_1___default = /*#__PURE__*/__webpack_require__.n(react__WEBPACK_IMPORTED_MODULE_1__);\n/* harmony import */ var underscore__WEBPACK_IMPORTED_MODULE_2__ = __webpack_require__(/*! underscore */ \"./node_modules/underscore/modules/index-all.js\");\n/* harmony import */ var _sidebar__WEBPACK_IMPORTED_MODULE_3__ = __webpack_require__(/*! ./sidebar */ \"./public/js/sidebar.js\");\n/* harmony import */ var _circos__WEBPACK_IMPORTED_MODULE_4__ = __webpack_require__(/*! ./circos */ \"./public/js/circos.js\");\n/* harmony import */ var _query__WEBPACK_IMPORTED_MODULE_5__ = __webpack_require__(/*! ./query */ \"./public/js/query.js\");\n/* harmony import */ var _hit__WEBPACK_IMPORTED_MODULE_6__ = __webpack_require__(/*! ./hit */ \"./public/js/hit.js\");\n/* harmony import */ var _hsp__WEBPACK_IMPORTED_MODULE_7__ = __webpack_require__(/*! ./hsp */ \"./public/js/hsp.js\");\n/* harmony import */ var _alignment_exporter__WEBPACK_IMPORTED_MODULE_8__ = __webpack_require__(/*! ./alignment_exporter */ \"./public/js/alignment_exporter.js\");\n/* harmony import */ var react_jsx_runtime__WEBPACK_IMPORTED_MODULE_9__ = __webpack_require__(/*! react/jsx-runtime */ \"./node_modules/react/jsx-runtime.js\");\n/* provided dependency */ var $ = __webpack_require__(/*! jquery */ \"./node_modules/jquery/dist/jquery.js\");\nfunction _typeof(obj) { \"@babel/helpers - typeof\"; return _typeof = \"function\" == typeof Symbol && \"symbol\" == typeof Symbol.iterator ? function (obj) { return typeof obj; } : function (obj) { return obj && \"function\" == typeof Symbol && obj.constructor === Symbol && obj !== Symbol.prototype ? \"symbol\" : typeof obj; }, _typeof(obj); }\n\nfunction ownKeys(object, enumerableOnly) { var keys = Object.keys(object); if (Object.getOwnPropertySymbols) { var symbols = Object.getOwnPropertySymbols(object); enumerableOnly && (symbols = symbols.filter(function (sym) { return Object.getOwnPropertyDescriptor(object, sym).enumerable; })), keys.push.apply(keys, symbols); } return keys; }\n\nfunction _objectSpread(target) { for (var i = 1; i < arguments.length; i++) { var source = null != arguments[i] ? arguments[i] : {}; i % 2 ? ownKeys(Object(source), !0).forEach(function (key) { _defineProperty(target, key, source[key]); }) : Object.getOwnPropertyDescriptors ? Object.defineProperties(target, Object.getOwnPropertyDescriptors(source)) : ownKeys(Object(source)).forEach(function (key) { Object.defineProperty(target, key, Object.getOwnPropertyDescriptor(source, key)); }); } return target; }\n\nfunction _defineProperty(obj, key, value) { if (key in obj) { Object.defineProperty(obj, key, { value: value, enumerable: true, configurable: true, writable: true }); } else { obj[key] = value; } return obj; }\n\nfunction _classCallCheck(instance, Constructor) { if (!(instance instanceof Constructor)) { throw new TypeError(\"Cannot call a class as a function\"); } }\n\nfunction _defineProperties(target, props) { for (var i = 0; i < props.length; i++) { var descriptor = props[i]; descriptor.enumerable = descriptor.enumerable || false; descriptor.configurable = true; if (\"value\" in descriptor) descriptor.writable = true; Object.defineProperty(target, descriptor.key, descriptor); } }\n\nfunction _createClass(Constructor, protoProps, staticProps) { if (protoProps) _defineProperties(Constructor.prototype, protoProps); if (staticProps) _defineProperties(Constructor, staticProps); Object.defineProperty(Constructor, \"prototype\", { writable: false }); return Constructor; }\n\nfunction _inherits(subClass, superClass) { if (typeof superClass !== \"function\" && superClass !== null) { throw new TypeError(\"Super expression must either be null or a function\"); } subClass.prototype = Object.create(superClass && superClass.prototype, { constructor: { value: subClass, writable: true, configurable: true } }); Object.defineProperty(subClass, \"prototype\", { writable: false }); if (superClass) _setPrototypeOf(subClass, superClass); }\n\nfunction _setPrototypeOf(o, p) { _setPrototypeOf = Object.setPrototypeOf || function _setPrototypeOf(o, p) { o.__proto__ = p; return o; }; return _setPrototypeOf(o, p); }\n\nfunction _createSuper(Derived) { var hasNativeReflectConstruct = _isNativeReflectConstruct(); return function _createSuperInternal() { var Super = _getPrototypeOf(Derived), result; if (hasNativeReflectConstruct) { var NewTarget = _getPrototypeOf(this).constructor; result = Reflect.construct(Super, arguments, NewTarget); } else { result = Super.apply(this, arguments); } return _possibleConstructorReturn(this, result); }; }\n\nfunction _possibleConstructorReturn(self, call) { if (call && (_typeof(call) === \"object\" || typeof call === \"function\")) { return call; } else if (call !== void 0) { throw new TypeError(\"Derived constructors may only return object or undefined\"); } return _assertThisInitialized(self); }\n\nfunction _assertThisInitialized(self) { if (self === void 0) { throw new ReferenceError(\"this hasn't been initialised - super() hasn't been called\"); } return self; }\n\nfunction _isNativeReflectConstruct() { if (typeof Reflect === \"undefined\" || !Reflect.construct) return false; if (Reflect.construct.sham) return false; if (typeof Proxy === \"function\") return true; try { Boolean.prototype.valueOf.call(Reflect.construct(Boolean, [], function () {})); return true; } catch (e) { return false; } }\n\nfunction _getPrototypeOf(o) { _getPrototypeOf = Object.setPrototypeOf ? Object.getPrototypeOf : function _getPrototypeOf(o) { return o.__proto__ || Object.getPrototypeOf(o); }; return _getPrototypeOf(o); }\n\n // for custom $.tooltip function\n\n\n\n\n\n\n\n\n\n/**\n * Renders entire report.\n *\n * Composed of Query and Sidebar components.\n */\n\n\n\n\nvar Report = /*#__PURE__*/function (_Component) {\n  _inherits(Report, _Component);\n\n  var _super = _createSuper(Report);\n\n  function Report(props) {\n    var _this;\n\n    _classCallCheck(this, Report);\n\n    _this = _super.call(this, props); // Properties below are internal state used to render results in small\n    // slices (see updateState).\n\n    _this.numUpdates = 0;\n    _this.nextQuery = 0;\n    _this.nextHit = 0;\n    _this.nextHSP = 0;\n    _this.maxHSPs = 3; // max HSPs to render in a cycle\n\n    _this.state = {\n      user_warning: null,\n      download_links: [],\n      search_id: '',\n      seqserv_version: '',\n      program: '',\n      program_version: '',\n      submitted_at: '',\n      queries: [],\n      results: [],\n      querydb: [],\n      params: [],\n      stats: [],\n      alignment_blob_url: '',\n      allQueriesLoaded: false,\n      cloud_sharing_enabled: false\n    };\n    _this.prepareAlignmentOfSelectedHits = _this.prepareAlignmentOfSelectedHits.bind(_assertThisInitialized(_this));\n    _this.prepareAlignmentOfAllHits = _this.prepareAlignmentOfAllHits.bind(_assertThisInitialized(_this));\n    _this.setStateFromJSON = _this.setStateFromJSON.bind(_assertThisInitialized(_this));\n    return _this;\n  }\n  /**\n  * Fetch results.\n  */\n\n\n  _createClass(Report, [{\n    key: \"fetchResults\",\n    value: function fetchResults() {\n      var intervals = [200, 400, 800, 1200, 2000, 3000, 5000];\n      var component = this;\n\n      function poll() {\n        $.getJSON(location.pathname + '.json' + location.search).complete(function (jqXHR) {\n          switch (jqXHR.status) {\n            case 202:\n              var interval;\n\n              if (intervals.length === 1) {\n                interval = intervals[0];\n              } else {\n                interval = intervals.shift();\n              }\n\n              setTimeout(poll, interval);\n              break;\n\n            case 200:\n              component.setStateFromJSON(jqXHR.responseJSON);\n              break;\n\n            case 404:\n            case 400:\n            case 500:\n              component.props.showErrorModal(jqXHR.responseJSON);\n              break;\n          }\n        });\n      }\n\n      poll();\n    }\n    /**\n    * Calls setState after any required modification to responseJSON.\n    */\n\n  }, {\n    key: \"setStateFromJSON\",\n    value: function setStateFromJSON(responseJSON) {\n      this.lastTimeStamp = Date.now(); // the callback prepares the download link for all alignments\n\n      if (responseJSON.user_warning == 'LARGE_RESULT') {\n        this.setState({\n          user_warning: responseJSON.user_warning,\n          download_links: responseJSON.download_links\n        });\n      } else {\n        this.setState(responseJSON, this.prepareAlignmentOfAllHits);\n      }\n    }\n    /**\n    * Called as soon as the page has loaded and the user sees the loading spinner.\n    * We use this opportunity to setup services that make use of delegated events\n    * bound to the window, document, or body.\n    */\n\n  }, {\n    key: \"componentDidMount\",\n    value: function componentDidMount() {\n      this.fetchResults(); // This sets up an event handler which enables users to select text from\n      // hit header without collapsing the hit.\n\n      this.preventCollapseOnSelection();\n      this.toggleTable();\n    }\n    /**\n    * Called for the first time after as BLAST results have been retrieved from\n    * the server and added to this.state by fetchResults. Only summary overview\n    * and circos would have been rendered at this point. At this stage we kick\n    * start iteratively adding 1 HSP to the page every 25 milli-seconds.\n    */\n\n  }, {\n    key: \"componentDidUpdate\",\n    value: function componentDidUpdate() {\n      var _this2 = this;\n\n      // Log to console how long the last update take?\n      // console.log((Date.now() - this.lastTimeStamp) / 1000);\n      // Lock sidebar in its position on the first update.\n      if (this.nextQuery == 0 && this.nextHit == 0 && this.nextHSP == 0) {\n        this.affixSidebar();\n      } // Queue next update if we have not rendered all results yet.\n\n\n      if (this.nextQuery < this.state.queries.length) {\n        // setTimeout is used to clear call stack and space out\n        // the updates giving the browser a chance to respond\n        // to user interactions.\n        setTimeout(function () {\n          return _this2.updateState();\n        }, 25);\n      } else {\n        this.componentFinishedUpdating();\n      }\n    }\n    /**\n    * Push next slice of results to React for rendering.\n    */\n\n  }, {\n    key: \"updateState\",\n    value: function updateState() {\n      var results = [];\n      var numHSPsProcessed = 0;\n\n      while (this.nextQuery < this.state.queries.length) {\n        var query = this.state.queries[this.nextQuery]; // We may see a query multiple times during rendering because only\n        // 3 hsps or are rendered in each cycle, but we want to create the\n        // corresponding Query component only the first time we see it.\n\n        if (this.nextHit == 0 && this.nextHSP == 0) {\n          results.push( /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_9__.jsx)(_query__WEBPACK_IMPORTED_MODULE_5__.ReportQuery, {\n            query: query,\n            program: this.state.program,\n            querydb: this.state.querydb,\n            showQueryCrumbs: this.state.queries.length > 1,\n            non_parse_seqids: this.state.non_parse_seqids,\n            imported_xml: this.state.imported_xml,\n            veryBig: this.state.veryBig\n          }, 'Query_' + query.number));\n        }\n\n        while (this.nextHit < query.hits.length) {\n          var hit = query.hits[this.nextHit]; // We may see a hit multiple times during rendering because only\n          // 10 hsps are rendered in each cycle, but we want to create the\n          // corresponding Hit component only the first time we see it.\n\n          if (this.nextHSP == 0) {\n            results.push( /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_9__.jsx)(_hit__WEBPACK_IMPORTED_MODULE_6__[\"default\"], _objectSpread({\n              query: query,\n              hit: hit,\n              algorithm: this.state.program,\n              querydb: this.state.querydb,\n              selectHit: this.selectHit,\n              imported_xml: this.state.imported_xml,\n              non_parse_seqids: this.state.non_parse_seqids,\n              showQueryCrumbs: this.state.queries.length > 1,\n              showHitCrumbs: query.hits.length > 1,\n              veryBig: this.state.veryBig,\n              onChange: this.prepareAlignmentOfSelectedHits\n            }, this.props), 'Query_' + query.number + '_Hit_' + hit.number));\n          }\n\n          while (this.nextHSP < hit.hsps.length) {\n            // Get nextHSP and increment the counter.\n            var hsp = hit.hsps[this.nextHSP++];\n            results.push( /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_9__.jsx)(_hsp__WEBPACK_IMPORTED_MODULE_7__[\"default\"], _objectSpread({\n              query: query,\n              hit: hit,\n              hsp: hsp,\n              algorithm: this.state.program,\n              showHSPNumbers: hit.hsps.length > 1\n            }, this.props), 'Query_' + query.number + '_Hit_' + hit.number + '_HSP_' + hsp.number));\n            numHSPsProcessed++;\n            if (numHSPsProcessed == this.maxHSPs) break;\n          } // Are we here because we have iterated over all hsps of a hit,\n          // or because of the break clause in the inner loop?\n\n\n          if (this.nextHSP == hit.hsps.length) {\n            this.nextHit = this.nextHit + 1;\n            this.nextHSP = 0;\n          }\n\n          if (numHSPsProcessed == this.maxHSPs) break;\n        } // Are we here because we have iterated over all hits of a query,\n        // or because of the break clause in the inner loop?\n\n\n        if (this.nextHit == query.hits.length) {\n          this.nextQuery = this.nextQuery + 1;\n          this.nextHit = 0;\n        }\n\n        if (numHSPsProcessed == this.maxHSPs) break;\n      } // Push the components to react for rendering.\n\n\n      this.numUpdates++;\n      this.lastTimeStamp = Date.now();\n      this.setState({\n        results: this.state.results.concat(results),\n        veryBig: this.numUpdates >= 250\n      });\n    }\n    /**\n    * Called after all results have been rendered.\n    */\n\n  }, {\n    key: \"componentFinishedUpdating\",\n    value: function componentFinishedUpdating() {\n      if (this.state.allQueriesLoaded) return;\n      this.shouldShowIndex() && this.setupScrollSpy();\n      this.setState({\n        allQueriesLoaded: true\n      });\n    }\n    /**\n    * Returns loading message\n    */\n\n  }, {\n    key: \"loadingJSX\",\n    value: function loadingJSX() {\n      return /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_9__.jsx)(\"div\", {\n        className: \"row\",\n        children: /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_9__.jsxs)(\"div\", {\n          className: \"col-md-6 col-md-offset-3 text-center\",\n          children: [/*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_9__.jsxs)(\"h1\", {\n            children: [/*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_9__.jsx)(\"i\", {\n              className: \"fa fa-cog fa-spin\"\n            }), \"\\xA0 BLAST-ing\"]\n          }), /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_9__.jsxs)(\"p\", {\n            children: [/*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_9__.jsx)(\"br\", {}), \"This can take some time depending on the size of your query and database(s). The page will update automatically when BLAST is done.\", /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_9__.jsx)(\"br\", {}), /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_9__.jsx)(\"br\", {}), \"You can bookmark the page and come back to it later or share the link with someone.\"]\n          })]\n        })\n      });\n    }\n    /**\n    * Return results JSX.\n    */\n\n  }, {\n    key: \"resultsJSX\",\n    value: function resultsJSX() {\n      return /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_9__.jsxs)(\"div\", {\n        className: \"row\",\n        id: \"results\",\n        children: [/*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_9__.jsx)(\"div\", {\n          className: \"col-md-3 hidden-sm hidden-xs\",\n          children: /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_9__.jsx)(_sidebar__WEBPACK_IMPORTED_MODULE_3__[\"default\"], {\n            data: this.state,\n            atLeastOneHit: this.atLeastOneHit(),\n            shouldShowIndex: this.shouldShowIndex(),\n            allQueriesLoaded: this.state.allQueriesLoaded,\n            cloudSharingEnabled: this.state.cloud_sharing_enabled\n          })\n        }), /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_9__.jsxs)(\"div\", {\n          className: \"col-md-9\",\n          children: [this.overviewJSX(), this.circosJSX(), this.state.results]\n        })]\n      });\n    }\n  }, {\n    key: \"warningJSX\",\n    value: function warningJSX() {\n      return /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_9__.jsx)(\"div\", {\n        className: \"container\",\n        children: /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_9__.jsx)(\"div\", {\n          className: \"row\",\n          children: /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_9__.jsxs)(\"div\", {\n            className: \"col-md-6 col-md-offset-3 text-center\",\n            children: [/*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_9__.jsxs)(\"h1\", {\n              children: [/*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_9__.jsx)(\"i\", {\n                className: \"fa fa-exclamation-triangle\"\n              }), \"\\xA0 Warning\"]\n            }), /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_9__.jsxs)(\"p\", {\n              children: [/*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_9__.jsx)(\"br\", {}), \"The BLAST result might be too large to load in the browser. If you have a powerful machine you can try loading the results anyway. Otherwise, you can download the results and view them locally.\"]\n            }), /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_9__.jsx)(\"br\", {}), /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_9__.jsx)(\"p\", {\n              children: this.state.download_links.map(function (link, index) {\n                return /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_9__.jsx)(\"a\", {\n                  href: link.url,\n                  className: \"btn btn-secondary\",\n                  children: link.name\n                }, 'download_link_' + index);\n              })\n            }), /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_9__.jsx)(\"br\", {}), /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_9__.jsx)(\"p\", {\n              children: /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_9__.jsx)(\"a\", {\n                href: location.pathname + '?bypass_file_size_warning=true',\n                className: \"btn btn-primary\",\n                children: \"View results in browser anyway\"\n              })\n            })]\n          })\n        })\n      });\n    }\n    /**\n    * Renders report overview.\n    */\n\n  }, {\n    key: \"overviewJSX\",\n    value: function overviewJSX() {\n      return /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_9__.jsxs)(\"div\", {\n        className: \"overview\",\n        children: [/*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_9__.jsxs)(\"p\", {\n          children: [/*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_9__.jsxs)(\"strong\", {\n            children: [\"SequenceServer \", this.state.seqserv_version]\n          }), \" using\", ' ', /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_9__.jsx)(\"strong\", {\n            children: this.state.program_version\n          }), this.state.submitted_at && \", query submitted on \".concat(this.state.submitted_at)]\n        }), /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_9__.jsxs)(\"p\", {\n          children: [/*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_9__.jsx)(\"strong\", {\n            children: \" Databases: \"\n          }), this.state.querydb.map(function (db) {\n            return db.title;\n          }).join(', '), ' ', \"(\", this.state.stats.nsequences, \" sequences,\\xA0\", this.state.stats.ncharacters, \" characters)\"]\n        }), /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_9__.jsxs)(\"p\", {\n          children: [/*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_9__.jsx)(\"strong\", {\n            children: \"Parameters: \"\n          }), ' ', underscore__WEBPACK_IMPORTED_MODULE_2__[\"default\"].map(this.state.params, function (val, key) {\n            return key + ' ' + val;\n          }).join(', ')]\n        }), /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_9__.jsxs)(\"p\", {\n          children: [\"Please cite:\", ' ', /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_9__.jsx)(\"a\", {\n            href: \"https://doi.org/10.1093/molbev/msz185\",\n            children: \"https://doi.org/10.1093/molbev/msz185\"\n          })]\n        })]\n      });\n    }\n    /**\n    * Return JSX for circos if we have at least one hit.\n    */\n\n  }, {\n    key: \"circosJSX\",\n    value: function circosJSX() {\n      return this.atLeastTwoHits() ? /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_9__.jsx)(_circos__WEBPACK_IMPORTED_MODULE_4__[\"default\"], {\n        queries: this.state.queries,\n        program: this.state.program,\n        collapsed: \"true\"\n      }) : /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_9__.jsx)(\"span\", {});\n    } // Controller //\n\n    /**\n    * Returns true if results have been fetched.\n    *\n    * A holding message is shown till results are fetched.\n    */\n\n  }, {\n    key: \"isResultAvailable\",\n    value: function isResultAvailable() {\n      return this.state.queries.length >= 1;\n    }\n    /**\n     * Indicates the response contains a warning message for the user\n     * in which case we should not render the results and render the\n     * warning instead.\n     **/\n\n  }, {\n    key: \"isUserWarningPresent\",\n    value: function isUserWarningPresent() {\n      return this.state.user_warning;\n    }\n    /**\n    * Returns true if we have at least one hit.\n    */\n\n  }, {\n    key: \"atLeastOneHit\",\n    value: function atLeastOneHit() {\n      return this.state.queries.some(function (query) {\n        return query.hits.length > 0;\n      });\n    }\n    /**\n    * Does the report have at least two hits? This is used to determine\n    * whether Circos should be enabled or not.\n    */\n\n  }, {\n    key: \"atLeastTwoHits\",\n    value: function atLeastTwoHits() {\n      var hit_num = 0;\n      return this.state.queries.some(function (query) {\n        hit_num += query.hits.length;\n        return hit_num > 1;\n      });\n    }\n    /**\n    * Returns true if index should be shown in the sidebar. Index is shown\n    * only for 2 and 8 queries.\n    */\n\n  }, {\n    key: \"shouldShowIndex\",\n    value: function shouldShowIndex() {\n      var num_queries = this.state.queries.length;\n      return num_queries >= 2 && num_queries <= 12;\n    }\n    /**\n    * Prevents folding of hits during text-selection.\n    */\n\n  }, {\n    key: \"preventCollapseOnSelection\",\n    value: function preventCollapseOnSelection() {\n      $('body').on('mousedown', '.hit > .section-header > h4', function (event) {\n        var $this = $(this);\n        $this.on('mouseup mousemove', function handler(event) {\n          if (event.type === 'mouseup') {\n            // user wants to toggle\n            var hitID = $this.parents('.hit').attr('id');\n            $(\"div[data-parent-hit=\".concat(hitID, \"]\")).toggle();\n            $this.find('i').toggleClass('fa-minus-square-o fa-plus-square-o');\n          } else {\n            // user wants to select\n            $this.attr('data-toggle', '');\n          }\n\n          $this.off('mouseup mousemove', handler);\n        });\n      });\n    }\n    /* Handling the fa icon when Hit Table is collapsed */\n\n  }, {\n    key: \"toggleTable\",\n    value: function toggleTable() {\n      $('body').on('mousedown', '.resultn > .section-content > .table-hit-overview > .caption', function (event) {\n        var $this = $(this);\n        $this.on('mouseup mousemove', function handler(event) {\n          $this.find('i').toggleClass('fa-minus-square-o fa-plus-square-o');\n          $this.off('mouseup mousemove', handler);\n        });\n      });\n    }\n    /**\n    * Affixes the sidebar.\n    */\n\n  }, {\n    key: \"affixSidebar\",\n    value: function affixSidebar() {\n      var $sidebar = $('.sidebar');\n      var sidebarOffset = $sidebar.offset();\n\n      if (sidebarOffset) {\n        $sidebar.affix({\n          offset: {\n            top: sidebarOffset.top\n          }\n        });\n      }\n    }\n    /**\n    * For the query in viewport, highlights corresponding entry in the index.\n    */\n\n  }, {\n    key: \"setupScrollSpy\",\n    value: function setupScrollSpy() {\n      $('body').scrollspy({\n        target: '.sidebar'\n      });\n    }\n    /**\n    * Event-handler when hit is selected\n    * Adds glow to hit component.\n    * Updates number of Fasta that can be downloaded\n    */\n\n  }, {\n    key: \"selectHit\",\n    value: function selectHit(id) {\n      var checkbox = $('#' + id);\n      var num_checked = $('.hit-links :checkbox:checked').length;\n\n      if (!checkbox || !checkbox.val()) {\n        return;\n      }\n\n      var $hit = $(checkbox.data('target')); // Highlight selected hit and enable 'Download FASTA/Alignment of\n      // selected' links.\n\n      if (checkbox.is(':checked')) {\n        $hit.addClass('glow');\n        $hit.next('.hsp').addClass('glow');\n        $('.download-fasta-of-selected').enable();\n        $('.download-alignment-of-selected').enable();\n      } else {\n        $hit.removeClass('glow');\n        $hit.next('.hsp').removeClass('glow');\n      }\n\n      var $a = $('.download-fasta-of-selected');\n      var $b = $('.download-alignment-of-selected');\n\n      if (num_checked >= 1) {\n        $a.find('.text-bold').html(num_checked);\n        $b.find('.text-bold').html(num_checked);\n      }\n\n      if (num_checked == 0) {\n        $a.addClass('disabled').find('.text-bold').html('');\n        $b.addClass('disabled').find('.text-bold').html('');\n      }\n    }\n  }, {\n    key: \"populate_hsp_array\",\n    value: function populate_hsp_array(hit, query_id) {\n      return hit.hsps.map(function (hsp) {\n        return Object.assign(hsp, {\n          hit_id: hit.id,\n          query_id: query_id\n        });\n      });\n    }\n  }, {\n    key: \"prepareAlignmentOfSelectedHits\",\n    value: function prepareAlignmentOfSelectedHits() {\n      var sequence_ids = $('.hit-links :checkbox:checked').map(function () {\n        return this.value;\n      }).get();\n\n      if (!sequence_ids.length) {\n        // remove attributes from link if sequence_ids array is empty\n        $('.download-alignment-of-selected').attr('href', '#').removeAttr('download');\n        return;\n      }\n\n      if (this.state.alignment_blob_url) {\n        // always revoke existing url if any because this method will always create a new url\n        window.URL.revokeObjectURL(this.state.alignment_blob_url);\n      }\n\n      var hsps_arr = [];\n      var aln_exporter = new _alignment_exporter__WEBPACK_IMPORTED_MODULE_8__[\"default\"]();\n      var self = this;\n\n      underscore__WEBPACK_IMPORTED_MODULE_2__[\"default\"].each(this.state.queries, underscore__WEBPACK_IMPORTED_MODULE_2__[\"default\"].bind(function (query) {\n        underscore__WEBPACK_IMPORTED_MODULE_2__[\"default\"].each(query.hits, function (hit) {\n          if (underscore__WEBPACK_IMPORTED_MODULE_2__[\"default\"].indexOf(sequence_ids, hit.id) != -1) {\n            hsps_arr = hsps_arr.concat(self.populate_hsp_array(hit, query.id));\n          }\n        });\n      }, this));\n\n      var filename = 'alignment-' + sequence_ids.length + '_hits.txt';\n      var blob_url = aln_exporter.prepare_alignments_for_export(hsps_arr, filename); // set required download attributes for link\n\n      $('.download-alignment-of-selected').attr('href', blob_url).attr('download', filename); // track new url for future removal\n\n      this.setState({\n        alignment_blob_url: blob_url\n      });\n    }\n  }, {\n    key: \"prepareAlignmentOfAllHits\",\n    value: function prepareAlignmentOfAllHits() {\n      var _this3 = this;\n\n      // Get number of hits and array of all hsps.\n      var num_hits = 0;\n      var hsps_arr = [];\n\n      if (!this.state.queries.length) {\n        return;\n      }\n\n      this.state.queries.forEach(function (query) {\n        return query.hits.forEach(function (hit) {\n          num_hits++;\n          hsps_arr = hsps_arr.concat(_this3.populate_hsp_array(hit, query.id));\n        });\n      });\n      var aln_exporter = new _alignment_exporter__WEBPACK_IMPORTED_MODULE_8__[\"default\"]();\n      var file_name = \"alignment-\".concat(num_hits, \"_hits.txt\");\n      var blob_url = aln_exporter.prepare_alignments_for_export(hsps_arr, file_name);\n      $('.download-alignment-of-all').attr('href', blob_url).attr('download', file_name);\n      return false;\n    }\n  }, {\n    key: \"render\",\n    value: function render() {\n      if (this.isUserWarningPresent()) {\n        return this.warningJSX();\n      } else if (this.isResultAvailable()) {\n        return this.resultsJSX();\n      } else {\n        return this.loadingJSX();\n      }\n    }\n  }]);\n\n  return Report;\n}(react__WEBPACK_IMPORTED_MODULE_1__.Component);\n\n/* harmony default export */ const __WEBPACK_DEFAULT_EXPORT__ = (Report);\n\n//# sourceURL=webpack://SequenceServer/./public/js/report.js?");
 
 /***/ }),
 
@@ -269,7 +269,7 @@ eval("__webpack_require__.r(__webpack_exports__);\n/* harmony export */ __webpac
 /***/ ((__unused_webpack_module, __webpack_exports__, __webpack_require__) => {
 
 "use strict";
-eval("__webpack_require__.r(__webpack_exports__);\n/* harmony export */ __webpack_require__.d(__webpack_exports__, {\n/* harmony export */   \"get_colors_for_evalue\": () => (/* binding */ get_colors_for_evalue),\n/* harmony export */   \"get_seq_type\": () => (/* binding */ get_seq_type),\n/* harmony export */   \"prettify_evalue\": () => (/* binding */ prettify_evalue),\n/* harmony export */   \"tick_formatter\": () => (/* binding */ tick_formatter),\n/* harmony export */   \"toLetters\": () => (/* binding */ toLetters)\n/* harmony export */ });\n/* harmony import */ var underscore__WEBPACK_IMPORTED_MODULE_0__ = __webpack_require__(/*! underscore */ \"./node_modules/underscore/modules/index-all.js\");\n\nfunction get_colors_for_evalue(evalue, hits) {\n  var colors = d3.scale.log().domain([d3.min([1e-5, d3.min(hits.map(function (d) {\n    if (parseFloat(d.evalue) === 0.0) return undefined;\n    return d.evalue;\n  }))]), d3.max(hits.map(function (d) {\n    return d.evalue;\n  }))]).range([0, 0.8]);\n  var rgb = colors(evalue);\n  return d3.hsl(20, 0.82, rgb);\n}\nfunction toLetters(num) {\n  var mod = num % 26,\n      pow = num / 26 | 0,\n      out = mod ? String.fromCharCode(96 + mod) : (--pow, 'z');\n  return pow ? toLetters(pow) + out : out;\n}\n/**\n * Defines how ticks will be formatted.\n *\n * Examples: 200 aa, 2.4 kbp, 7.6 Mbp.\n *\n * Borrowed from Kablammo. Modified by Priyam based on https://github.com/mbostock/d3/issues/1722.\n */\n\nfunction tick_formatter(scale, seq_type) {\n  var ticks = scale.ticks();\n  var prefix = d3.formatPrefix(ticks[ticks.length - 1]);\n  var suffixes = {\n    amino_acid: 'aa',\n    nucleic_acid: 'bp'\n  };\n  var digits = 0;\n  var format;\n\n  var _ticks;\n\n  do {\n    format = d3.format('.' + digits + 'f');\n    _ticks = scale.ticks().map(function (d) {\n      return format(prefix.scale(d));\n    });\n    digits++;\n  } while (_ticks.length !== underscore__WEBPACK_IMPORTED_MODULE_0__[\"default\"].uniq(_ticks).length);\n\n  return function (d) {\n    if (!prefix.symbol || d === scale.domain()[0]) {\n      return d + ' ' + suffixes[seq_type];\n    } else {\n      return format(prefix.scale(d)) + ' ' + prefix.symbol + suffixes[seq_type];\n    }\n  };\n}\nfunction get_seq_type(algorithm) {\n  var SEQ_TYPES = {\n    blastn: {\n      query_seq_type: 'nucleic_acid',\n      subject_seq_type: 'nucleic_acid'\n    },\n    blastp: {\n      query_seq_type: 'amino_acid',\n      subject_seq_type: 'amino_acid'\n    },\n    blastx: {\n      query_seq_type: 'nucleic_acid',\n      subject_seq_type: 'amino_acid'\n    },\n    tblastx: {\n      query_seq_type: 'nucleic_acid',\n      subject_seq_type: 'nucleic_acid'\n    },\n    tblastn: {\n      query_seq_type: 'amino_acid',\n      subject_seq_type: 'nucleic_acid'\n    }\n  };\n  return SEQ_TYPES[algorithm];\n}\nfunction prettify_evalue(evalue) {\n  var matches = evalue.toString().split('e');\n  var base = matches[0];\n  var power = matches[1];\n\n  if (power) {\n    var s = parseFloat(base).toFixed(2);\n    var element = '<span>' + s + ' &times; 10<sup>' + power + '</sup></span>';\n    return element;\n  } else {\n    if (!(base % 1 == 0)) return parseFloat(base).toFixed(2);else return base;\n  }\n}\n\n//# sourceURL=webpack://SequenceServer/./public/js/visualisation_helpers.js?");
+eval("__webpack_require__.r(__webpack_exports__);\n/* harmony export */ __webpack_require__.d(__webpack_exports__, {\n/* harmony export */   \"get_colors_for_evalue\": () => (/* binding */ get_colors_for_evalue),\n/* harmony export */   \"get_seq_type\": () => (/* binding */ get_seq_type),\n/* harmony export */   \"prettify_evalue\": () => (/* binding */ prettify_evalue),\n/* harmony export */   \"tick_formatter\": () => (/* binding */ tick_formatter),\n/* harmony export */   \"toLetters\": () => (/* binding */ toLetters)\n/* harmony export */ });\n/* harmony import */ var underscore__WEBPACK_IMPORTED_MODULE_0__ = __webpack_require__(/*! underscore */ \"./node_modules/underscore/modules/index-all.js\");\n/* harmony import */ var d3__WEBPACK_IMPORTED_MODULE_1__ = __webpack_require__(/*! d3 */ \"./node_modules/d3/d3.js\");\n/* harmony import */ var d3__WEBPACK_IMPORTED_MODULE_1___default = /*#__PURE__*/__webpack_require__.n(d3__WEBPACK_IMPORTED_MODULE_1__);\n\n\nfunction get_colors_for_evalue(evalue, hits) {\n  var colors = d3__WEBPACK_IMPORTED_MODULE_1___default().scale.log().domain([d3__WEBPACK_IMPORTED_MODULE_1___default().min([1e-5, d3__WEBPACK_IMPORTED_MODULE_1___default().min(hits.map(function (d) {\n    if (parseFloat(d.evalue) === 0.0) return undefined;\n    return d.evalue;\n  }))]), d3__WEBPACK_IMPORTED_MODULE_1___default().max(hits.map(function (d) {\n    return d.evalue;\n  }))]).range([0, 0.8]);\n  var rgb = colors(evalue);\n  return d3__WEBPACK_IMPORTED_MODULE_1___default().hsl(20, 0.82, rgb);\n}\nfunction toLetters(num) {\n  var mod = num % 26,\n      pow = num / 26 | 0,\n      out = mod ? String.fromCharCode(96 + mod) : (--pow, 'z');\n  return pow ? toLetters(pow) + out : out;\n}\n/**\n * Defines how ticks will be formatted.\n *\n * Examples: 200 aa, 2.4 kbp, 7.6 Mbp.\n *\n * Borrowed from Kablammo. Modified by Priyam based on https://github.com/mbostock/d3/issues/1722.\n */\n\nfunction tick_formatter(scale, seq_type) {\n  var ticks = scale.ticks();\n  var prefix = d3__WEBPACK_IMPORTED_MODULE_1___default().formatPrefix(ticks[ticks.length - 1]);\n  var suffixes = {\n    amino_acid: 'aa',\n    nucleic_acid: 'bp'\n  };\n  var digits = 0;\n  var format;\n\n  var _ticks;\n\n  do {\n    format = d3__WEBPACK_IMPORTED_MODULE_1___default().format('.' + digits + 'f');\n    _ticks = scale.ticks().map(function (d) {\n      return format(prefix.scale(d));\n    });\n    digits++;\n  } while (_ticks.length !== underscore__WEBPACK_IMPORTED_MODULE_0__[\"default\"].uniq(_ticks).length);\n\n  return function (d) {\n    if (!prefix.symbol || d === scale.domain()[0]) {\n      return d + ' ' + suffixes[seq_type];\n    } else {\n      return format(prefix.scale(d)) + ' ' + prefix.symbol + suffixes[seq_type];\n    }\n  };\n}\nfunction get_seq_type(algorithm) {\n  var SEQ_TYPES = {\n    blastn: {\n      query_seq_type: 'nucleic_acid',\n      subject_seq_type: 'nucleic_acid'\n    },\n    blastp: {\n      query_seq_type: 'amino_acid',\n      subject_seq_type: 'amino_acid'\n    },\n    blastx: {\n      query_seq_type: 'nucleic_acid',\n      subject_seq_type: 'amino_acid'\n    },\n    tblastx: {\n      query_seq_type: 'nucleic_acid',\n      subject_seq_type: 'nucleic_acid'\n    },\n    tblastn: {\n      query_seq_type: 'amino_acid',\n      subject_seq_type: 'nucleic_acid'\n    }\n  };\n  return SEQ_TYPES[algorithm];\n}\nfunction prettify_evalue(evalue) {\n  var matches = evalue.toString().split('e');\n  var base = matches[0];\n  var power = matches[1];\n\n  if (power) {\n    var s = parseFloat(base).toFixed(2);\n    var element = '<span>' + s + ' &times; 10<sup>' + power + '</sup></span>';\n    return element;\n  } else {\n    if (!(base % 1 == 0)) return parseFloat(base).toFixed(2);else return base;\n  }\n}\n\n//# sourceURL=webpack://SequenceServer/./public/js/visualisation_helpers.js?");
 
 /***/ }),
 

data/public/sequenceserver-search.min.js

@@ -181,7 +181,7 @@ eval("__webpack_require__.r(__webpack_exports__);\n/* harmony export */ __webpac
 /***/ ((__unused_webpack_module, __webpack_exports__, __webpack_require__) => {
 
 "use strict";
-eval("__webpack_require__.r(__webpack_exports__);\n/* harmony export */ __webpack_require__.d(__webpack_exports__, {\n/* harmony export */   \"get_colors_for_evalue\": () => (/* binding */ get_colors_for_evalue),\n/* harmony export */   \"get_seq_type\": () => (/* binding */ get_seq_type),\n/* harmony export */   \"prettify_evalue\": () => (/* binding */ prettify_evalue),\n/* harmony export */   \"tick_formatter\": () => (/* binding */ tick_formatter),\n/* harmony export */   \"toLetters\": () => (/* binding */ toLetters)\n/* harmony export */ });\n/* harmony import */ var underscore__WEBPACK_IMPORTED_MODULE_0__ = __webpack_require__(/*! underscore */ \"./node_modules/underscore/modules/index-all.js\");\n\nfunction get_colors_for_evalue(evalue, hits) {\n  var colors = d3.scale.log().domain([d3.min([1e-5, d3.min(hits.map(function (d) {\n    if (parseFloat(d.evalue) === 0.0) return undefined;\n    return d.evalue;\n  }))]), d3.max(hits.map(function (d) {\n    return d.evalue;\n  }))]).range([0, 0.8]);\n  var rgb = colors(evalue);\n  return d3.hsl(20, 0.82, rgb);\n}\nfunction toLetters(num) {\n  var mod = num % 26,\n      pow = num / 26 | 0,\n      out = mod ? String.fromCharCode(96 + mod) : (--pow, 'z');\n  return pow ? toLetters(pow) + out : out;\n}\n/**\n * Defines how ticks will be formatted.\n *\n * Examples: 200 aa, 2.4 kbp, 7.6 Mbp.\n *\n * Borrowed from Kablammo. Modified by Priyam based on https://github.com/mbostock/d3/issues/1722.\n */\n\nfunction tick_formatter(scale, seq_type) {\n  var ticks = scale.ticks();\n  var prefix = d3.formatPrefix(ticks[ticks.length - 1]);\n  var suffixes = {\n    amino_acid: 'aa',\n    nucleic_acid: 'bp'\n  };\n  var digits = 0;\n  var format;\n\n  var _ticks;\n\n  do {\n    format = d3.format('.' + digits + 'f');\n    _ticks = scale.ticks().map(function (d) {\n      return format(prefix.scale(d));\n    });\n    digits++;\n  } while (_ticks.length !== underscore__WEBPACK_IMPORTED_MODULE_0__[\"default\"].uniq(_ticks).length);\n\n  return function (d) {\n    if (!prefix.symbol || d === scale.domain()[0]) {\n      return d + ' ' + suffixes[seq_type];\n    } else {\n      return format(prefix.scale(d)) + ' ' + prefix.symbol + suffixes[seq_type];\n    }\n  };\n}\nfunction get_seq_type(algorithm) {\n  var SEQ_TYPES = {\n    blastn: {\n      query_seq_type: 'nucleic_acid',\n      subject_seq_type: 'nucleic_acid'\n    },\n    blastp: {\n      query_seq_type: 'amino_acid',\n      subject_seq_type: 'amino_acid'\n    },\n    blastx: {\n      query_seq_type: 'nucleic_acid',\n      subject_seq_type: 'amino_acid'\n    },\n    tblastx: {\n      query_seq_type: 'nucleic_acid',\n      subject_seq_type: 'nucleic_acid'\n    },\n    tblastn: {\n      query_seq_type: 'amino_acid',\n      subject_seq_type: 'nucleic_acid'\n    }\n  };\n  return SEQ_TYPES[algorithm];\n}\nfunction prettify_evalue(evalue) {\n  var matches = evalue.toString().split('e');\n  var base = matches[0];\n  var power = matches[1];\n\n  if (power) {\n    var s = parseFloat(base).toFixed(2);\n    var element = '<span>' + s + ' &times; 10<sup>' + power + '</sup></span>';\n    return element;\n  } else {\n    if (!(base % 1 == 0)) return parseFloat(base).toFixed(2);else return base;\n  }\n}\n\n//# sourceURL=webpack://SequenceServer/./public/js/visualisation_helpers.js?");
+eval("__webpack_require__.r(__webpack_exports__);\n/* harmony export */ __webpack_require__.d(__webpack_exports__, {\n/* harmony export */   \"get_colors_for_evalue\": () => (/* binding */ get_colors_for_evalue),\n/* harmony export */   \"get_seq_type\": () => (/* binding */ get_seq_type),\n/* harmony export */   \"prettify_evalue\": () => (/* binding */ prettify_evalue),\n/* harmony export */   \"tick_formatter\": () => (/* binding */ tick_formatter),\n/* harmony export */   \"toLetters\": () => (/* binding */ toLetters)\n/* harmony export */ });\n/* harmony import */ var underscore__WEBPACK_IMPORTED_MODULE_0__ = __webpack_require__(/*! underscore */ \"./node_modules/underscore/modules/index-all.js\");\n/* harmony import */ var d3__WEBPACK_IMPORTED_MODULE_1__ = __webpack_require__(/*! d3 */ \"./node_modules/d3/d3.js\");\n/* harmony import */ var d3__WEBPACK_IMPORTED_MODULE_1___default = /*#__PURE__*/__webpack_require__.n(d3__WEBPACK_IMPORTED_MODULE_1__);\n\n\nfunction get_colors_for_evalue(evalue, hits) {\n  var colors = d3__WEBPACK_IMPORTED_MODULE_1___default().scale.log().domain([d3__WEBPACK_IMPORTED_MODULE_1___default().min([1e-5, d3__WEBPACK_IMPORTED_MODULE_1___default().min(hits.map(function (d) {\n    if (parseFloat(d.evalue) === 0.0) return undefined;\n    return d.evalue;\n  }))]), d3__WEBPACK_IMPORTED_MODULE_1___default().max(hits.map(function (d) {\n    return d.evalue;\n  }))]).range([0, 0.8]);\n  var rgb = colors(evalue);\n  return d3__WEBPACK_IMPORTED_MODULE_1___default().hsl(20, 0.82, rgb);\n}\nfunction toLetters(num) {\n  var mod = num % 26,\n      pow = num / 26 | 0,\n      out = mod ? String.fromCharCode(96 + mod) : (--pow, 'z');\n  return pow ? toLetters(pow) + out : out;\n}\n/**\n * Defines how ticks will be formatted.\n *\n * Examples: 200 aa, 2.4 kbp, 7.6 Mbp.\n *\n * Borrowed from Kablammo. Modified by Priyam based on https://github.com/mbostock/d3/issues/1722.\n */\n\nfunction tick_formatter(scale, seq_type) {\n  var ticks = scale.ticks();\n  var prefix = d3__WEBPACK_IMPORTED_MODULE_1___default().formatPrefix(ticks[ticks.length - 1]);\n  var suffixes = {\n    amino_acid: 'aa',\n    nucleic_acid: 'bp'\n  };\n  var digits = 0;\n  var format;\n\n  var _ticks;\n\n  do {\n    format = d3__WEBPACK_IMPORTED_MODULE_1___default().format('.' + digits + 'f');\n    _ticks = scale.ticks().map(function (d) {\n      return format(prefix.scale(d));\n    });\n    digits++;\n  } while (_ticks.length !== underscore__WEBPACK_IMPORTED_MODULE_0__[\"default\"].uniq(_ticks).length);\n\n  return function (d) {\n    if (!prefix.symbol || d === scale.domain()[0]) {\n      return d + ' ' + suffixes[seq_type];\n    } else {\n      return format(prefix.scale(d)) + ' ' + prefix.symbol + suffixes[seq_type];\n    }\n  };\n}\nfunction get_seq_type(algorithm) {\n  var SEQ_TYPES = {\n    blastn: {\n      query_seq_type: 'nucleic_acid',\n      subject_seq_type: 'nucleic_acid'\n    },\n    blastp: {\n      query_seq_type: 'amino_acid',\n      subject_seq_type: 'amino_acid'\n    },\n    blastx: {\n      query_seq_type: 'nucleic_acid',\n      subject_seq_type: 'amino_acid'\n    },\n    tblastx: {\n      query_seq_type: 'nucleic_acid',\n      subject_seq_type: 'nucleic_acid'\n    },\n    tblastn: {\n      query_seq_type: 'amino_acid',\n      subject_seq_type: 'nucleic_acid'\n    }\n  };\n  return SEQ_TYPES[algorithm];\n}\nfunction prettify_evalue(evalue) {\n  var matches = evalue.toString().split('e');\n  var base = matches[0];\n  var power = matches[1];\n\n  if (power) {\n    var s = parseFloat(base).toFixed(2);\n    var element = '<span>' + s + ' &times; 10<sup>' + power + '</sup></span>';\n    return element;\n  } else {\n    if (!(base % 1 == 0)) return parseFloat(base).toFixed(2);else return base;\n  }\n}\n\n//# sourceURL=webpack://SequenceServer/./public/js/visualisation_helpers.js?");
 
 /***/ }),
 

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: sequenceserver
 version: !ruby/object:Gem::Version
-  version: 2.1.0
+  version: 2.2.0
 platform: ruby
 authors:
 - Queen Mary University of London
@@ -9,7 +9,7 @@ authors:
 autorequire:
 bindir: bin
 cert_chain: []
-date: 2023-07-28 00:00:00.000000000 Z
+date: 2023-10-05 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: json_pure
@@ -398,9 +398,11 @@ files:
 - public/js/share_url.js
 - public/js/sidebar.js
 - public/js/svgExporter.js
+- public/js/tests/advanced_parameters.spec.js
 - public/js/tests/database.spec.js
 - public/js/tests/mock_data/databases.json
 - public/js/tests/mock_data/long_response.json
+- public/js/tests/mock_data/sequences.js
 - public/js/tests/mock_data/short_response.json
 - public/js/tests/report.spec.js
 - public/js/tests/search_button.spec.js