sequenceserver 1.1.0.beta12 → 2.0.0.beta1
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- checksums.yaml +4 -4
- data/.rspec +1 -0
- data/.travis.yml +5 -5
- data/README.md +86 -43
- data/bin/sequenceserver +29 -32
- data/lib/sequenceserver.rb +86 -123
- data/lib/sequenceserver/api_errors.rb +3 -1
- data/lib/sequenceserver/blast/hit.rb +48 -28
- data/lib/sequenceserver/blast/job.rb +28 -8
- data/lib/sequenceserver/blast/report.rb +52 -15
- data/lib/sequenceserver/database.rb +71 -0
- data/lib/sequenceserver/exceptions.rb +5 -10
- data/lib/sequenceserver/job.rb +8 -1
- data/lib/sequenceserver/links.rb +49 -17
- data/lib/sequenceserver/logger.rb +2 -2
- data/lib/sequenceserver/routes.rb +20 -14
- data/lib/sequenceserver/sys.rb +86 -0
- data/lib/sequenceserver/version.rb +1 -1
- data/public/css/sequenceserver.min.css +3 -3
- data/public/js/alignment_exporter.js +1 -1
- data/public/js/hsp.js +1 -1
- data/public/js/report.js +76 -63
- data/public/js/search.js +29 -6
- data/public/sequenceserver-report.min.js +4 -4
- data/public/sequenceserver-search.min.js +2 -2
- data/sequenceserver.gemspec +3 -2
- data/spec/blast_versions/blast_2.2.30/blast_2.2.30_spec.rb +228 -0
- data/spec/blast_versions/blast_2.2.30/import_spec_capybara_local_2.2.30.rb +53 -0
- data/spec/blast_versions/blast_2.2.31/blast_2.2.31_spec.rb +228 -0
- data/spec/blast_versions/blast_2.2.31/import_spec_capybara_local_2.2.31.rb +53 -0
- data/spec/{blast_spec.rb → blast_versions/blast_2.3.0/blast_2.3.0_spec.rb} +8 -37
- data/spec/blast_versions/blast_2.3.0/import_spec_capybara_local_2.3.0.rb +52 -0
- data/spec/blast_versions/blast_2.4.0/blast_2.4.0_spec.rb +228 -0
- data/spec/blast_versions/blast_2.4.0/import_spec_capybara_local_2.4.0.rb +52 -0
- data/spec/blast_versions/blast_2.5.0/blast_2.5.0_spec.rb +228 -0
- data/spec/blast_versions/blast_2.5.0/import_spec_capybara_local_2.5.0.rb +53 -0
- data/spec/blast_versions/blast_2.6.0/blast_2.6.0_spec.rb +228 -0
- data/spec/blast_versions/blast_2.6.0/import_spec_capybara_local_2.6.0.rb +52 -0
- data/spec/blast_versions/blast_2.7.1/blast_2.7.1_spec.rb +228 -0
- data/spec/blast_versions/blast_2.7.1/import_spec_capybara_local_2.7.1.rb +56 -0
- data/spec/blast_versions/blast_2.8.1/blast_2.8.1_spec.rb +228 -0
- data/spec/blast_versions/blast_2.8.1/import_spec_capybara_local_2.8.1.rb +55 -0
- data/spec/blast_versions/blast_2.9.0/blast_2.9.0_spec.rb +228 -0
- data/spec/blast_versions/blast_2.9.0/import_spec_capybara_local_2.9.0.rb +53 -0
- data/spec/blast_versions/diamond_0.9.24/diamond_0.9.24_spec.rb +176 -0
- data/spec/blast_versions/diamond_0.9.24/import_spec_capybara_local_0.9.24.rb +39 -0
- data/spec/capybara_spec.local.rb +190 -0
- data/spec/capybara_spec.rb +15 -13
- data/spec/config_spec.rb +1 -1
- data/spec/database/funky_ids/funky_ids.fa +2 -0
- data/spec/database/funky_ids/funky_ids.fa.nhd +8 -0
- data/spec/database/funky_ids/funky_ids.fa.nhi +0 -0
- data/spec/database/funky_ids/funky_ids.fa.nhr +0 -0
- data/spec/database/funky_ids/funky_ids.fa.nin +0 -0
- data/spec/database/funky_ids/funky_ids.fa.nog +0 -0
- data/spec/database/funky_ids/funky_ids.fa.nsd +15 -13
- data/spec/database/funky_ids/funky_ids.fa.nsi +0 -0
- data/spec/database/funky_ids/funky_ids.fa.nsq +0 -0
- data/spec/database_spec.rb +2 -2
- data/spec/dotdir/blast_2.2.30/blastn/BLASTN_XML_2.2.30.xml +1201 -0
- data/spec/dotdir/blast_2.2.30/blastn/job.yaml +8 -0
- data/spec/dotdir/blast_2.2.30/blastn_nohits/BLASTN_NO_HITS_XML_2.2.30.xml +866 -0
- data/spec/dotdir/blast_2.2.30/blastn_nohits/job.yaml +8 -0
- data/spec/dotdir/blast_2.2.30/blastp/BLASTP_XML_2.2.30.xml +1181 -0
- data/spec/dotdir/blast_2.2.30/blastp/job.yaml +8 -0
- data/spec/dotdir/blast_2.2.30/blastx/BLASTX_XML_2.2.30.xml +1181 -0
- data/spec/dotdir/blast_2.2.30/blastx/job.yaml +8 -0
- data/spec/dotdir/blast_2.2.30/tblastn/TBLASTN_XML_2.2.30.xml +1181 -0
- data/spec/dotdir/blast_2.2.30/tblastn/job.yaml +8 -0
- data/spec/dotdir/blast_2.2.30/tblastx/TBLASTX_XML_2.2.30.xml +8857 -0
- data/spec/dotdir/blast_2.2.30/tblastx/job.yaml +8 -0
- data/spec/dotdir/blast_2.2.31/blastn/BLASTN_XML_2.2.31.xml +1201 -0
- data/spec/dotdir/blast_2.2.31/blastn/job.yaml +8 -0
- data/spec/dotdir/blast_2.2.31/blastn_nohits/BLASTN_NO_HITS_XML_2.2.31.xml +866 -0
- data/spec/dotdir/blast_2.2.31/blastn_nohits/job.yaml +8 -0
- data/spec/dotdir/blast_2.2.31/blastp/BLASTP_XML_2.2.31.xml +1181 -0
- data/spec/dotdir/blast_2.2.31/blastp/job.yaml +8 -0
- data/spec/dotdir/blast_2.2.31/blastx/BLASTX_XML_2.2.31.xml +1181 -0
- data/spec/dotdir/blast_2.2.31/blastx/job.yaml +8 -0
- data/spec/dotdir/blast_2.2.31/tblastn/TBLASTN_XML_2.2.31.xml +1181 -0
- data/spec/dotdir/blast_2.2.31/tblastn/job.yaml +8 -0
- data/spec/dotdir/blast_2.2.31/tblastx/TBLASTX_XML_2.2.31.xml +8857 -0
- data/spec/dotdir/blast_2.2.31/tblastx/job.yaml +8 -0
- data/spec/dotdir/blast_2.3.0/blastn/BLASTN_XML_2.3.0.xml +1201 -0
- data/spec/dotdir/blast_2.3.0/blastn/job.yaml +8 -0
- data/spec/dotdir/blast_2.3.0/blastn_nohits/BLASTN_NO_HITS_XML_2.3.0.xml +866 -0
- data/spec/dotdir/blast_2.3.0/blastn_nohits/job.yaml +8 -0
- data/spec/dotdir/blast_2.3.0/blastp/BLASTP_XML_2.3.0.xml +1181 -0
- data/spec/dotdir/blast_2.3.0/blastp/job.yaml +8 -0
- data/spec/dotdir/blast_2.3.0/blastx/BLASTX_XML_2.3.0.xml +1181 -0
- data/spec/dotdir/blast_2.3.0/blastx/job.yaml +8 -0
- data/spec/dotdir/blast_2.3.0/tblastn/TBLASTN_XML_2.3.0.xml +1181 -0
- data/spec/dotdir/blast_2.3.0/tblastn/job.yaml +8 -0
- data/spec/dotdir/blast_2.3.0/tblastx/TBLASTX_XML_2.3.0.xml +8857 -0
- data/spec/dotdir/blast_2.3.0/tblastx/job.yaml +8 -0
- data/spec/dotdir/blast_2.4.0/blastn/BLASTN_XML_2.4.0.xml +1201 -0
- data/spec/dotdir/blast_2.4.0/blastn/TBLASTN_XML_2.4.0.xml +1181 -0
- data/spec/dotdir/blast_2.4.0/blastn/job.yaml +8 -0
- data/spec/dotdir/blast_2.4.0/blastn_nohits/BLASTN_NO_HITS_XML_2.4.0.xml +866 -0
- data/spec/dotdir/blast_2.4.0/blastn_nohits/job.yaml +8 -0
- data/spec/dotdir/blast_2.4.0/blastp/BLASTP_XML_2.4.0.xml +1181 -0
- data/spec/dotdir/blast_2.4.0/blastp/job.yaml +8 -0
- data/spec/dotdir/blast_2.4.0/blastx/BLASTX_XML_2.4.0.xml +1181 -0
- data/spec/dotdir/blast_2.4.0/blastx/job.yaml +8 -0
- data/spec/dotdir/blast_2.4.0/tblastn/TBLASTN_XML_2.4.0.xml +1181 -0
- data/spec/dotdir/blast_2.4.0/tblastn/job.yaml +8 -0
- data/spec/dotdir/blast_2.4.0/tblastx/TBLASTX_XML_2.4.0.xml +8857 -0
- data/spec/dotdir/blast_2.4.0/tblastx/job.yaml +8 -0
- data/spec/dotdir/blast_2.5.0/blastn/BLASTN_LONG_XML_2.5.0.xml +18813 -0
- data/spec/dotdir/blast_2.5.0/blastn/BLASTN_XML_2.5.0.xml +1201 -0
- data/spec/dotdir/blast_2.5.0/blastn/job.yaml +8 -0
- data/spec/dotdir/blast_2.5.0/blastn_nohits/BLASTN_NO_HITS_XML_2.5.0.xml +866 -0
- data/spec/dotdir/blast_2.5.0/blastn_nohits/job.yaml +8 -0
- data/spec/dotdir/blast_2.5.0/blastp/BLASTP +2161 -0
- data/spec/dotdir/blast_2.5.0/blastp/BLASTP_XML_2.5.0.xml +1181 -0
- data/spec/dotdir/blast_2.5.0/blastp/job.yaml +8 -0
- data/spec/dotdir/blast_2.5.0/blastx/BLASTX +28080 -0
- data/spec/dotdir/blast_2.5.0/blastx/BLASTX_XML_2.5.0.xml +1181 -0
- data/spec/dotdir/blast_2.5.0/blastx/job.yaml +8 -0
- data/spec/dotdir/blast_2.5.0/tblastn/TBLASTN +29486 -0
- data/spec/dotdir/blast_2.5.0/tblastn/TBLASTN_XML_2.5.0.xml +1181 -0
- data/spec/dotdir/blast_2.5.0/tblastn/job.yaml +8 -0
- data/spec/dotdir/blast_2.5.0/tblastx/TBLASTX +180859 -0
- data/spec/dotdir/blast_2.5.0/tblastx/TBLASTX_XML_2.5.0.xml +8857 -0
- data/spec/dotdir/blast_2.5.0/tblastx/job.yaml +8 -0
- data/spec/dotdir/blast_2.6.0/blastn/BLASTN_XML_2.6.0.xml +1201 -0
- data/spec/dotdir/blast_2.6.0/blastn/job.yaml +8 -0
- data/spec/dotdir/blast_2.6.0/blastn_nohits/BLASTN_NO_HITS_XML_2.6.0.xml +866 -0
- data/spec/dotdir/blast_2.6.0/blastn_nohits/job.yaml +8 -0
- data/spec/dotdir/blast_2.6.0/blastp/BLASTP_XML_2.6.0.xml +1181 -0
- data/spec/dotdir/blast_2.6.0/blastp/job.yaml +8 -0
- data/spec/dotdir/blast_2.6.0/blastx/BLASTX_XML_2.6.0.xml +1181 -0
- data/spec/dotdir/blast_2.6.0/blastx/job.yaml +8 -0
- data/spec/dotdir/blast_2.6.0/tblastn/TBLASTN_XML_2.6.0.xml +1181 -0
- data/spec/dotdir/blast_2.6.0/tblastn/job.yaml +8 -0
- data/spec/dotdir/blast_2.6.0/tblastx/TBLASTX_XML_2.6.0.xml +8857 -0
- data/spec/dotdir/blast_2.6.0/tblastx/job.yaml +8 -0
- data/spec/dotdir/blast_2.7.1/blastn/BLASTN_XML_2.7.1.xml +1201 -0
- data/spec/dotdir/blast_2.7.1/blastn/job.yaml +8 -0
- data/spec/dotdir/blast_2.7.1/blastn_nohits/BLASTN_NO_HITS_XML_2.7.1.xml +866 -0
- data/spec/dotdir/blast_2.7.1/blastn_nohits/job.yaml +8 -0
- data/spec/dotdir/blast_2.7.1/blastp/BLASTP_XML_2.7.1.xml +1181 -0
- data/spec/dotdir/blast_2.7.1/blastp/job.yaml +8 -0
- data/spec/dotdir/blast_2.7.1/blastx/BLASTX_XML_2.7.1.xml +1181 -0
- data/spec/dotdir/blast_2.7.1/blastx/job.yaml +8 -0
- data/spec/dotdir/blast_2.7.1/tblastn/TBLASTN_XML_2.7.1.xml +1181 -0
- data/spec/dotdir/blast_2.7.1/tblastn/job.yaml +8 -0
- data/spec/dotdir/blast_2.7.1/tblastx/TBLASTX_XML_2.7.1.xml +8857 -0
- data/spec/dotdir/blast_2.7.1/tblastx/job.yaml +8 -0
- data/spec/dotdir/blast_2.8.1/blastn/BLASTN_XML_2.8.1.xml +1201 -0
- data/spec/dotdir/blast_2.8.1/blastn/job.yaml +8 -0
- data/spec/dotdir/blast_2.8.1/blastn_nohits/BLASTN_NO_HITS_XML_2.8.1.xml +866 -0
- data/spec/dotdir/blast_2.8.1/blastn_nohits/job.yaml +8 -0
- data/spec/dotdir/blast_2.8.1/blastp/BLASTP_XML_2.8.1.xml +1181 -0
- data/spec/dotdir/blast_2.8.1/blastp/job.yaml +8 -0
- data/spec/dotdir/blast_2.8.1/blastx/BLASTX_XML_2.8.1.xml +1181 -0
- data/spec/dotdir/blast_2.8.1/blastx/job.yaml +8 -0
- data/spec/dotdir/blast_2.8.1/tblastn/TBLASTN_XML_2.8.1.xml +1181 -0
- data/spec/dotdir/blast_2.8.1/tblastn/job.yaml +8 -0
- data/spec/dotdir/blast_2.8.1/tblastx/TBLASTX_XML_2.8.1.xml +8857 -0
- data/spec/dotdir/blast_2.8.1/tblastx/job.yaml +8 -0
- data/spec/dotdir/blast_2.9.0/blastn/BLASTN_XML_2.9.0.xml +1201 -0
- data/spec/dotdir/blast_2.9.0/blastn/job.yaml +8 -0
- data/spec/dotdir/blast_2.9.0/blastn_nohits/BLASTN_NO_HITS_XML_2.9.0.xml +866 -0
- data/spec/dotdir/blast_2.9.0/blastn_nohits/job.yaml +8 -0
- data/spec/dotdir/blast_2.9.0/blastp/BLASTP_XML_2.9.0.xml +1181 -0
- data/spec/dotdir/blast_2.9.0/blastp/job.yaml +8 -0
- data/spec/dotdir/blast_2.9.0/blastx/BLASTX_XML_2.9.0.xml +1181 -0
- data/spec/dotdir/blast_2.9.0/blastx/job.yaml +8 -0
- data/spec/dotdir/blast_2.9.0/tblastn/TBLASTN_XML_2.9.0.xml +1181 -0
- data/spec/dotdir/blast_2.9.0/tblastn/job.yaml +8 -0
- data/spec/dotdir/blast_2.9.0/tblastx/TBLASTX_XML_2.9.0.xml +8857 -0
- data/spec/dotdir/blast_2.9.0/tblastx/job.yaml +8 -0
- data/spec/dotdir/diamond_0.9.24/blastp/DIAMOND_BLASTP_0.9.24.xml +1040 -0
- data/spec/dotdir/diamond_0.9.24/blastp/job.yaml +8 -0
- data/spec/dotdir/diamond_0.9.24/blastx/DIAMOND_BLASTX_0.9.24.xml +1040 -0
- data/spec/dotdir/diamond_0.9.24/blastx/job.yaml +8 -0
- data/spec/dotdir/diamond_0.9.24/blastx_nohits/DIAMOND_BLASTX_NOHITS_0.9.24.xml +41 -0
- data/spec/dotdir/diamond_0.9.24/blastx_nohits/job.yaml +8 -0
- data/spec/download_helper.rb +32 -0
- data/spec/import_spec_capybara_local.rb +61 -0
- data/spec/sequence_spec.rb +1 -2
- data/spec/sequences/Nucleotide_TP53_COX41.fasta +15 -0
- data/spec/sequences/Protein_TP53_COX41.fasta +12 -0
- data/spec/sequences/Query_1_SI2_2_0_06267.txt +6 -0
- data/spec/{nucleotide_query.fa → sequences/nucleotide_query.fa} +0 -0
- data/spec/sequences/problematic_query.fa +5 -0
- data/spec/sequences/protein_query.fa +9 -0
- data/spec/sequences/sample_query_fire_ant_obps.fa +44 -0
- data/spec/sequences/sequenceserver-SI2.2.0_06267.fa +5 -0
- data/spec/sequenceserver_spec.rb +3 -3
- data/spec/spec_helper.rb +59 -0
- metadata +185 -28
- data/spec/protein_query.fa +0 -21
- data/spec/sample_reports/blastn_sample/job.yaml +0 -10
- data/spec/sample_reports/blastn_sample/stdout +0 -144
- data/spec/sample_reports/blastp_sample/job.yaml +0 -10
- data/spec/sample_reports/blastp_sample/stdout +0 -1187
- data/spec/sample_reports/blastx_sample/job.yaml +0 -10
- data/spec/sample_reports/blastx_sample/stdout +0 -1191
- data/spec/sample_reports/no_hits_sample/job.yaml +0 -10
- data/spec/sample_reports/no_hits_sample/stdout +0 -130
- data/spec/sample_reports/tblastn_sample/job.yaml +0 -10
- data/spec/sample_reports/tblastn_sample/stdout +0 -1107
- data/spec/sample_reports/tblastx_sample/job.yaml +0 -10
- data/spec/sample_reports/tblastx_sample/stdout +0 -2422
- data/spec/sample_reports/with_hits_sample/job.yaml +0 -10
- data/spec/sample_reports/with_hits_sample/stdout +0 -1489
@@ -3,9 +3,9 @@ require 'logger'
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module SequenceServer
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# Extend stdlib's Logger class for custom initialization and log format.
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class Logger < Logger
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def initialize(dev,
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def initialize(dev, level = INFO)
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super dev
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self.level
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self.level = level
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self.formatter = Formatter.new
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end
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require 'tilt/erb'
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require 'sinatra/base'
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require 'sequenceserver/job'
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require 'sequenceserver/blast'
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require 'sequenceserver/report'
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require 'sequenceserver/database'
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require 'sequenceserver/sequence'
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module SequenceServer
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# Controller.
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class Routes < Sinatra::Base
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configure do
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# Public, and views directory will be found here.
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set :root,
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set :root, File.join(__dir__, '..', '..')
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# Allow :frame_options to be configured for Rack::Protection.
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#
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# Returns data that is used to render the search form client side. These
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# include available databases and user-defined search options.
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get '/searchdata.json' do
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{
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searchdata = {
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database: Database.all,
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options:
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options: SequenceServer.config[:options],
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query: Database.retrieve(params[:query])
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}
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searchdata.to_json
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end
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# Queues a search job and redirects to `/:jid`.
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erb :layout
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else
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job = Job.create(params)
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redirect "/#{job.id}"
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redirect to("/#{job.id}")
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end
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end
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# will be used as title. Otherwise name of the error class is used as
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# title.
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#
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#
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# is used as more_info. If an error class does not want to include
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# more_info (like for NotFound), the error class must undefine
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# `backtrace` method.
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# All error classes should define `message` instance method that provides
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# a short and simple explanation of the error.
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#
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# If the error class defines `more_info` instance method, its return value
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# will be used as more_info, otherwise `backtrace.join("\n")` is used as
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# more_info.
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error 400..500 do
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error = env['sinatra.error']
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error.class.name
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end
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# If error object has a more_info method, use that. If the error does
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#
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# more_info.
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# If error object has a more_info method, use that. If the error does not
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# have more_info, use backtrace.join("\n") as more_info.
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if error.respond_to? :more_info
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error_data[:more_info] = error.more_info
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elsif error.respond_to? :backtrace
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@@ -0,0 +1,86 @@
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1
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+
require 'tempfile'
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2
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+
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3
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+
module SequenceServer
|
4
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+
# 'sys' executes a shell command.
|
5
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+
#
|
6
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+
# 'sys' can write the stdout and/or stderr from a shell command to files, or
|
7
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+
# return these values.
|
8
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+
#
|
9
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+
# 'sys' can get from a failed shell command stdout, stderr, and exit status.
|
10
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+
#
|
11
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+
# Supply 'sys' with the shell command and optionally:
|
12
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+
# dir: A directory to change to for the duration of the execution of
|
13
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+
# the shell command.
|
14
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+
# path: A directory to change the PATH environment variable to for the
|
15
|
+
# duration of the execution of the shell command.
|
16
|
+
# stdout: A path to a file to store stdout.
|
17
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+
# stderr: A path to a file to store stderr.
|
18
|
+
#
|
19
|
+
# Usage:
|
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|
+
#
|
21
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+
# sys(command, dir: '/path/to/directory', path: '/path/to/directory',
|
22
|
+
# stdout: '/path/to/stdout_file', stderr: '/path/to/stderr_file')
|
23
|
+
#
|
24
|
+
# rubocop:disable Metrics/CyclomaticComplexity
|
25
|
+
def self.sys(command, options = {})
|
26
|
+
# Available output channels
|
27
|
+
channels = %i[stdout stderr]
|
28
|
+
|
29
|
+
# Make temporary files to store output from stdout and stderr.
|
30
|
+
temp_files = {
|
31
|
+
stdout: Tempfile.new('sequenceserver-sys'),
|
32
|
+
stderr: Tempfile.new('sequenceserver-sys')
|
33
|
+
}
|
34
|
+
|
35
|
+
# Log the command we are going to run - use -D option to view.
|
36
|
+
logger.debug("Executing: #{command}")
|
37
|
+
|
38
|
+
# Run command in a child process. This allows us to control PATH
|
39
|
+
# and pwd of the running process.
|
40
|
+
child_pid = fork do
|
41
|
+
# Set the PATH environment variable to the binary directory or
|
42
|
+
# safe directory.
|
43
|
+
ENV['PATH'] = options[:path] if options[:path]
|
44
|
+
|
45
|
+
# Change to the specified directory.
|
46
|
+
Dir.chdir(options[:dir]) if options[:dir] && Dir.exist?(options[:dir])
|
47
|
+
|
48
|
+
# Execute the shell command, redirect stdout and stderr to the
|
49
|
+
# temporary files.
|
50
|
+
exec("#{command} 1>#{temp_files[:stdout].path}" \
|
51
|
+
" 2>#{temp_files[:stderr].path}")
|
52
|
+
end
|
53
|
+
|
54
|
+
# Wait for the termination of the child process.
|
55
|
+
_, status = Process.wait2(child_pid)
|
56
|
+
|
57
|
+
# If a full path was given for stdout and stderr files, move the
|
58
|
+
# temporary files to this path. If the path given does not exist,
|
59
|
+
# create it.
|
60
|
+
channels.each do |channel|
|
61
|
+
filename = options[channel]
|
62
|
+
break unless filename
|
63
|
+
|
64
|
+
# If the given path has a directory component, ensure it exists.
|
65
|
+
file_dir = File.dirname(filename)
|
66
|
+
FileUtils.mkdir_p(file_dir) unless File.directory?(file_dir)
|
67
|
+
|
68
|
+
# Now move the temporary file to the given path.
|
69
|
+
# TODO: don't we need to explicitly close the temp file here?
|
70
|
+
FileUtils.mv(temp_files.delete(channel), filename)
|
71
|
+
end
|
72
|
+
|
73
|
+
# Read the remaining temp files into memory. For large outputs,
|
74
|
+
# the caller should supply a file path to prevent loading the
|
75
|
+
# output in memory.
|
76
|
+
temp_files.each do |channel, tempfile|
|
77
|
+
temp_files[channel] = tempfile.read
|
78
|
+
end
|
79
|
+
|
80
|
+
# Finally, return contents of the remaining temp files if the
|
81
|
+
# command completed successfully or raise CommandFailed error.
|
82
|
+
return temp_files.values if status.success?
|
83
|
+
raise CommandFailed.new(status.exitstatus, **temp_files)
|
84
|
+
end
|
85
|
+
# rubocop:enable Metrics/CyclomaticComplexity
|
86
|
+
end
|
@@ -1,8 +1,8 @@
|
|
1
|
-
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.q25-32{fill:var(--z)}svg .RdYlBu .q26-32{fill:var(--aa)}svg .RdYlBu .q27-32{fill:var(--ab)}svg .RdYlBu .q28-32{fill:var(--ac)}svg .RdYlBu .q29-32{fill:var(--ad)}svg .RdYlBu .q30-32{fill:var(--ae)}svg .RdYlBu .q31-32{fill:var(--af)}@font-face{font-family:'Source Sans Pro';font-style:normal;font-weight:400;src:local('Source Sans Pro'),local('SourceSansPro-Regular'),url(../fonts/Source_Sans_Pro_400.woff2) format('woff2'),url(../fonts/Source_Sans_Pro_400.woff) format('woff'),url(../fonts/Source_Sans_Pro_400.ttf) format('truetype'),url(../fonts/Source_Sans_Pro_400.svg) format('svg'),url(../fonts/Source_Sans_Pro_400.eot) format('embedded-opentype')}@font-face{font-family:'Source Sans Pro';font-style:normal;font-weight:700;src:local('Source Sans Pro Bold'),local('SourceSansPro-Bold'),url(../fonts/Source_Sans_Pro_700.woff2) format('woff2'),url(../fonts/Source_Sans_Pro_700.woff) format('woff'),url(../fonts/Source_Sans_Pro_700.ttf) format('truetype'),url(../fonts/Source_Sans_Pro_700.svg) format('svg'),url(../fonts/Source_Sans_Pro_700.eot) format('embedded-opentype')}body{font-family:"Source Sans Pro","Helvetica Neue",Helvetica,Arial,sans-serif;position:relative;color:#000}.btn-link:hover,a:hover{text-decoration:none}textarea{resize:vertical;min-height:214px}label{cursor:pointer;font-weight:400}small{color:inherit!important}.disabled{color:#ccc}.btn-link[disabled]:hover,a.disabled:hover{color:#ccc;cursor:not-allowed}#methods li,.cursor-pointer,.hit h4{cursor:pointer}.navbar{border-radius:0;border-bottom:1px solid #eee}.navbar-brand{height:auto;padding:20px 15px;font-size:32px;color:#333}.navbar-brand>small{font-size:50%}.navbar-nav>li>a{padding:24px 15px;font-size:14px;color:#333}.section-header{border-bottom:1px solid #ddd;padding-bottom:5px;display:table;width:100%}.section-header>*{display:table-cell}.section-header>:first-child{width:100%}.section-content{padding:5px 0 0}.panel{border:none;-webkit-box-shadow:none;-moz-box-shadow:none;box-shadow:none}.panel .panel-heading{padding:4px 0 5px}.panel .panel-heading h4{margin:0}.control-label[class*=col-]{padding-right:0}.input-group[class*=col-]{padding-left:15px;padding-right:15px}.table>tbody>tr>td,.table>tbody>tr>th,.table>tfoot>tr>td,.table>tfoot>tr>th,.table>thead>tr>td,.table>thead>tr>th{border-top:none;padding-left:0;font-weight:400}.nav.active-bold>.active>a,.text-bold{font-weight:700}.table>thead>tr>th{border-bottom:1px solid #ddd}.tooltip-inner{max-width:350px;font-family:"Source sans pro","Helvetica Neue",Helvetica,Arial,sans-serif}.text-capitalize{text-transform:capitalize}.text-uppercase{text-transform:uppercase}.text-monospace{font-family:monospace}.nowrap-ellipsis{overflow-x:hidden;white-space:nowrap;text-overflow:ellipsis}.label-reset{color:inherit;font-weight:400}.pre-reset{margin:0;border:none;padding:0;border-radius:0}.nojs-error{margin-top:10px;padding:10px;color:#fff;background-color:red}.dnd-errors{color:red;font-size:18px}.biojs-vis-sequence pre{margin:0;border:none;padding:0;border-radius:0;background-color:inherit}.query-container{margin-top:35px}.notifications{position:relative;height:32px;top:-16px}.notification{height:32px!important}.notification .alert-danger,.notification .alert-info{-webkit-border-radius:6px;-moz-border-radius:6px;border-radius:6px;-webkit-box-shadow:0 3px 7px rgba(0,0,0,.3);-moz-box-shadow:0 3px 7px rgba(0,0,0,.3);box-shadow:0 3px 7px rgba(0,0,0,.3);font-weight:700;text-shadow:0 1px 0 rgba(255,255,255,.5);text-align:center;padding:6px 12px}.databases .list-group-item{border:none;padding:3px 0 0}#help pre:hover{background-color:#FFC}label[for=advanced]{font-size:16px;display:table-cell;width:1%;white-space:nowrap;vertical-align:middle;padding:5px 12px 5px 0}input[name=advanced]{border-top-left-radius:4px!important;border-bottom-left-radius:4px!important}#method{letter-spacing:1px}#methods li{text-align:center;padding-top:4px;padding-bottom:4px;letter-spacing:1px}.dropdown-menu li{border-bottom:1px solid #ccc}.dropdown-menu li:last-child{border-bottom:0}.sidebar>div{margin-top:20px}.sidebar h4{font-size:14px}.sidebar li a{padding:7px 10px}.sidebar.affix{margin-top:0;top:0}@media (min-width:992px){.sidebar.affix{width:212.5px}}@media (min-width:1200px){.sidebar.affix{width:262.5px}}.overview{margin:20px 0}.resultn{margin-bottom:25px}.graphical-overview{font-size:12px;text-align:center}.graphical-overview .btn{padding-top:0;padding-bottom:0}.tabular-view{margin-top:14px;margin-left:6px;margin-bottom:14px}.hit{padding-top:14px;margin-top:4px}.hit:first-child{padding-top:0}.hit h4 span{cursor:text}.hit>p{margin-top:0;margin-bottom:0}.hsps{padding:0 0 10px 10px}.hsp{padding-bottom:14px}.hsp:last-child{padding-bottom:0}.hsp pre{font-size:12px}.hsp-stats{word-break:normal;white-space:pre-wrap}.hsp .hsp-lines{margin-top:5px;font-size:10px;letter-spacing:1.2px}.hsp .hsp-coords{color:#6e6e6e}.hit-links *{padding-left:3px;letter-spacing:1px}.btn-link{border:none;padding:0;letter-spacing:1px}.fastan>.section-header{padding-bottom:8px}.fastan>.section-content{padding-top:8px;padding-left:0}.footer a:first-child{vertical-align:super}.dnd-overlay{position:absolute;top:51px;left:0;right:0;bottom:0;z-index:1000;background-color:rgba(255,255,255,.75)}.dnd-overlay *{pointer-events:none}.dnd-overlay-container{padding-top:72px}.dnd-overlay-container p{font-size:48px}.glow{border-left:2px solid #f0ad4e}.downloads a{cursor:pointer}
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@@ -36,7 +36,7 @@ export default class AlignmentExporter {
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36
36
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export_alignments(hsps, filename_prefix) {
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37
37
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var fasta = this.generate_fasta(hsps);
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38
38
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39
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-
var blob = new Blob([fasta], { type: '
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39
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+
var blob = new Blob([fasta], { type: 'text/fasta' });
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40
40
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// var filename_prefix = query_def + '_' + subject_def;
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41
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// var filename_prefix = query_id + '_' + subject_id;
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42
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var filename = Exporter.sanitize_filename(filename_prefix) + '.txt';
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data/public/js/hsp.js
CHANGED
@@ -40,7 +40,7 @@ export default class HSP extends React.Component {
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|
40
40
|
|
41
41
|
draw () {
|
42
42
|
var $container = $(React.findDOMNode(this.refs.hsp));
|
43
|
-
this.chars = Math.floor($container.width() / 7.
|
43
|
+
this.chars = Math.floor($container.width() / 7.5);
|
44
44
|
this.forceUpdate();
|
45
45
|
}
|
46
46
|
|
data/public/js/report.js
CHANGED
@@ -206,7 +206,8 @@ var Report = React.createClass({
|
|
206
206
|
<Query key={"Query_"+query.id}
|
207
207
|
program={this.state.program} querydb={this.state.querydb}
|
208
208
|
query={query} num_queries={this.state.num_queries}
|
209
|
-
veryBig={this.state.veryBig} selectHit={this.selectHit}
|
209
|
+
veryBig={this.state.veryBig} selectHit={this.selectHit}
|
210
|
+
imported_xml={this.state.imported_xml} />
|
210
211
|
);
|
211
212
|
}, this))
|
212
213
|
}
|
@@ -238,7 +239,7 @@ var Report = React.createClass({
|
|
238
239
|
</pre>
|
239
240
|
</div>
|
240
241
|
);
|
241
|
-
|
242
|
+
},
|
242
243
|
|
243
244
|
|
244
245
|
// Controller //
|
@@ -326,6 +327,10 @@ var Report = React.createClass({
|
|
326
327
|
if (event.type === 'mouseup') {
|
327
328
|
// user wants to toggle
|
328
329
|
$this.attr('data-toggle', 'collapse');
|
330
|
+
// Get the element indicated in the data-target attribute
|
331
|
+
// and toggle the 'in' class for collapsing/expanding.
|
332
|
+
var target = $('#' + $this.attr('data-target'));
|
333
|
+
target.toggleClass('in');
|
329
334
|
$this.find('.fa-chevron-down').toggleClass('fa-rotate-270');
|
330
335
|
} else {
|
331
336
|
// user wants to select
|
@@ -450,17 +455,17 @@ var Query = React.createClass({
|
|
450
455
|
<div className="section-content">
|
451
456
|
<HitsOverview key={"GO_"+this.props.query.number} query={this.props.query} program={this.props.program} collapsed={this.props.veryBig}/>
|
452
457
|
<LengthDistribution key={"LD_"+this.props.query.id} query={this.props.query} algorithm={this.props.program} collapsed="true"/>
|
453
|
-
<HitsTable key={"HT_"+this.props.query.number} query={this.props.query}/>
|
458
|
+
<HitsTable key={"HT_"+this.props.query.number} query={this.props.query} imported_xml={this.props.imported_xml} />
|
454
459
|
<div id="hits">
|
455
460
|
{
|
456
461
|
_.map(this.props.query.hits, _.bind(function (hit) {
|
457
462
|
return (
|
458
|
-
<Hit
|
459
|
-
hit={hit}
|
463
|
+
<Hit hit={hit}
|
460
464
|
key={"HIT_"+hit.number}
|
461
465
|
algorithm={this.props.program}
|
462
466
|
querydb={this.props.querydb}
|
463
467
|
query={this.props.query}
|
468
|
+
imported_xml={this.props.imported_xml}
|
464
469
|
selectHit={this.props.selectHit}/>
|
465
470
|
);
|
466
471
|
}, this))
|
@@ -508,7 +513,7 @@ var HitsTable = React.createClass({
|
|
508
513
|
<th className="text-left">#</th>
|
509
514
|
<th>Similar sequences</th>
|
510
515
|
{hasName && <th className="text-left">Species</th>}
|
511
|
-
<th className="text-right">Query coverage (%)</th>
|
516
|
+
{!this.props.imported_xml && <th className="text-right">Query coverage (%)</th>}
|
512
517
|
<th className="text-right">Total score</th>
|
513
518
|
<th className="text-right">E value</th>
|
514
519
|
<th className="text-right" data-toggle="tooltip"
|
@@ -528,7 +533,7 @@ var HitsTable = React.createClass({
|
|
528
533
|
</a>
|
529
534
|
</td>
|
530
535
|
{hasName && <td className="text-left">{hit.sciname}</td>}
|
531
|
-
<td className="text-right">{hit.qcovs}</td>
|
536
|
+
{!this.props.imported_xml && <td className="text-right">{hit.qcovs}</td>}
|
532
537
|
<td className="text-right">{hit.score}</td>
|
533
538
|
<td className="text-right">{this.inExponential(hit.hsps[0].evalue)}</td>
|
534
539
|
<td className="text-right">{hit.identity}</td>
|
@@ -683,18 +688,24 @@ var Hit = React.createClass({
|
|
683
688
|
}.bind(this)} data-target={'#' + this.domID()}
|
684
689
|
/> Select
|
685
690
|
</label>
|
686
|
-
|
|
687
|
-
{ this.viewSequenceButton() }
|
688
691
|
{
|
689
|
-
this.
|
690
|
-
|
692
|
+
!this.props.imported_xml && [
|
693
|
+
<span> | </span>,
|
694
|
+
this.viewSequenceButton(),
|
695
|
+
this.state.showSequenceViewer && <SequenceViewer
|
696
|
+
url={this.viewSequenceLink()} onHide={this.hideSequenceViewer} />
|
697
|
+
]
|
691
698
|
}
|
692
|
-
|
693
|
-
|
694
|
-
|
695
|
-
|
696
|
-
|
697
|
-
|
699
|
+
{
|
700
|
+
!this.props.imported_xml && [
|
701
|
+
<span> | </span>,
|
702
|
+
<button className='btn btn-link download-fa'
|
703
|
+
onClick={this.downloadFASTA}>
|
704
|
+
<i className="fa fa-download"></i> FASTA
|
705
|
+
</button>
|
706
|
+
]
|
707
|
+
}
|
708
|
+
<span> | </span>
|
698
709
|
<button className='btn btn-link download-aln'
|
699
710
|
onClick={this.downloadAlignment}>
|
700
711
|
<i className="fa fa-download"></i> Alignment
|
@@ -1024,72 +1035,74 @@ var SideBar = React.createClass({
|
|
1024
1035
|
downloads: function () {
|
1025
1036
|
return (
|
1026
1037
|
<div className="downloads">
|
1027
|
-
<div
|
1028
|
-
className="section-header">
|
1038
|
+
<div className="section-header">
|
1029
1039
|
<h4>
|
1030
1040
|
Download FASTA, XML, TSV
|
1031
1041
|
</h4>
|
1032
1042
|
</div>
|
1033
|
-
<ul
|
1034
|
-
|
1035
|
-
|
1036
|
-
|
1037
|
-
|
1038
|
-
|
1039
|
-
|
1040
|
-
</
|
1041
|
-
|
1042
|
-
|
1043
|
+
<ul className="nav">
|
1044
|
+
{
|
1045
|
+
!this.props.data.imported_xml && <li>
|
1046
|
+
<a className="download-fasta-of-all"
|
1047
|
+
onClick={this.downloadFastaOfAll}>
|
1048
|
+
FASTA of all hits
|
1049
|
+
</a>
|
1050
|
+
</li>
|
1051
|
+
}
|
1052
|
+
{
|
1053
|
+
!this.props.data.imported_xml && <li>
|
1043
1054
|
<a
|
1044
1055
|
className="download-fasta-of-selected disabled"
|
1045
1056
|
onClick={this.downloadFastaOfSelected}>
|
1046
1057
|
FASTA of <span className="text-bold"></span> selected hit(s)
|
1047
1058
|
</a>
|
1048
1059
|
</li>
|
1060
|
+
}
|
1049
1061
|
<li>
|
1050
|
-
<a
|
1051
|
-
className="download-alignment-of-all"
|
1062
|
+
<a className="download-alignment-of-all"
|
1052
1063
|
onClick={this.downloadAlignmentOfAll}>
|
1053
1064
|
Alignment of all hits
|
1054
1065
|
</a>
|
1055
1066
|
</li>
|
1056
1067
|
<li>
|
1057
|
-
<a
|
1058
|
-
className="download-alignment-of-selected disabled"
|
1068
|
+
<a className="download-alignment-of-selected disabled"
|
1059
1069
|
onClick={this.downloadAlignmentOfSelected}>
|
1060
1070
|
Alignment of <span className="text-bold"></span> selected hit(s)
|
1061
1071
|
</a>
|
1062
1072
|
</li>
|
1063
|
-
|
1064
|
-
<
|
1065
|
-
className="download" data-toggle="tooltip"
|
1066
|
-
|
1067
|
-
|
1068
|
-
|
1069
|
-
|
1070
|
-
|
1071
|
-
|
1072
|
-
|
1073
|
-
|
1074
|
-
|
1075
|
-
|
1076
|
-
|
1077
|
-
|
1078
|
-
|
1079
|
-
|
1080
|
-
|
1081
|
-
|
1082
|
-
|
1083
|
-
|
1084
|
-
|
1085
|
-
|
1086
|
-
|
1087
|
-
|
1088
|
-
|
1089
|
-
|
1090
|
-
|
1091
|
-
|
1092
|
-
|
1073
|
+
{
|
1074
|
+
!this.props.data.imported_xml && <li>
|
1075
|
+
<a className="download" data-toggle="tooltip"
|
1076
|
+
title="15 columns: query and subject ID; scientific
|
1077
|
+
name, alignment length, mismatches, gaps, identity,
|
1078
|
+
start and end coordinates, e value, bitscore, query
|
1079
|
+
coverage per subject and per HSP."
|
1080
|
+
href={"download/" + this.props.data.search_id + ".std_tsv"}>
|
1081
|
+
Standard tabular report
|
1082
|
+
</a>
|
1083
|
+
</li>
|
1084
|
+
}
|
1085
|
+
{
|
1086
|
+
!this.props.data.imported_xml && <li>
|
1087
|
+
<a className="download" data-toggle="tooltip"
|
1088
|
+
title="44 columns: query and subject ID, GI,
|
1089
|
+
accessions, and length; alignment details;
|
1090
|
+
taxonomy details of subject sequence(s) and
|
1091
|
+
query coverage per subject and per HSP."
|
1092
|
+
href={"download/" + this.props.data.search_id + ".full_tsv"}>
|
1093
|
+
Full tabular report
|
1094
|
+
</a>
|
1095
|
+
</li>
|
1096
|
+
}
|
1097
|
+
{
|
1098
|
+
!this.props.data.imported_xml && <li>
|
1099
|
+
<a className="download" data-toggle="tooltip"
|
1100
|
+
title="Results in XML format."
|
1101
|
+
href={"download/" + this.props.data.search_id + ".xml"}>
|
1102
|
+
Full XML report
|
1103
|
+
</a>
|
1104
|
+
</li>
|
1105
|
+
}
|
1093
1106
|
</ul>
|
1094
1107
|
</div>
|
1095
1108
|
);
|
data/public/js/search.js
CHANGED
@@ -201,12 +201,28 @@ var Form = React.createClass({
|
|
201
201
|
},
|
202
202
|
|
203
203
|
componentDidMount: function () {
|
204
|
-
|
204
|
+
/* Fetch data to initialise the search interface from the server. These
|
205
|
+
* include list of databases to search against, advanced options to
|
206
|
+
* apply when an algorithm is selected, and a query sequenced that
|
207
|
+
* the user may want to search in the databases.
|
208
|
+
*/
|
209
|
+
$.getJSON("searchdata.json" + window.location.search, function(data) {
|
210
|
+
/* Update form state (i.e., list of databases and predefined
|
211
|
+
* advanced options.
|
212
|
+
*/
|
205
213
|
this.setState({
|
206
214
|
databases: data["database"], preDefinedOpts: data["options"]
|
207
215
|
});
|
208
|
-
}, this));
|
209
216
|
|
217
|
+
/* Pre-populate the form with server sent query sequences
|
218
|
+
* (if any).
|
219
|
+
*/
|
220
|
+
if (data["query"]) {
|
221
|
+
this.refs.query.value(data["query"]);
|
222
|
+
}
|
223
|
+
}.bind(this));
|
224
|
+
|
225
|
+
/* Enable submitting form on Cmd+Enter */
|
210
226
|
$(document).bind("keydown", _.bind(function (e) {
|
211
227
|
if (e.ctrlKey && e.keyCode === 13 &&
|
212
228
|
!$('#method').is(':disabled')) {
|
@@ -315,17 +331,24 @@ var Query = React.createClass({
|
|
315
331
|
// Kind of public API. //
|
316
332
|
|
317
333
|
/**
|
318
|
-
*
|
319
|
-
*
|
334
|
+
* Returns query sequence if no argument is provided (or null or undefined
|
335
|
+
* is provided as argument). Otherwise, sets query sequenced to the given
|
336
|
+
* value and returns `this`.
|
337
|
+
*
|
338
|
+
* Default/initial state of query sequence is an empty string. Caller must
|
339
|
+
* explicitly provide empty string as argument to "reset" query sequence.
|
320
340
|
*/
|
321
341
|
value: function (val) {
|
322
|
-
if (val
|
342
|
+
if (val == null) {
|
343
|
+
// i.e., val is null or undefined
|
344
|
+
return this.state.value;
|
345
|
+
}
|
346
|
+
else {
|
323
347
|
this.setState({
|
324
348
|
value: val
|
325
349
|
})
|
326
350
|
return this;
|
327
351
|
}
|
328
|
-
return this.state.value;
|
329
352
|
},
|
330
353
|
|
331
354
|
/**
|