sequenceserver 2.0.0.rc7 → 2.0.0.rc8
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- checksums.yaml +4 -4
- data/bin/chromedriver +0 -0
- data/bin/geckodriver +0 -0
- data/bin/sequenceserver +31 -4
- data/lib/sequenceserver.rb +6 -1
- data/lib/sequenceserver/database.rb +7 -42
- data/lib/sequenceserver/exceptions.rb +14 -0
- data/lib/sequenceserver/makeblastdb.rb +121 -41
- data/lib/sequenceserver/routes.rb +1 -1
- data/lib/sequenceserver/version.rb +1 -1
- data/public/css/sequenceserver.css +8 -2
- data/public/css/sequenceserver.min.css +1 -1
- data/public/js/jquery_world.js +1 -1
- data/public/js/report.js +1 -2
- data/public/js/search.js +40 -18
- data/public/js/sidebar.js +50 -26
- data/public/sequenceserver-report.min.js +17 -17
- data/public/sequenceserver-search.min.js +2 -2
- data/views/layout.erb +1 -1
- data/views/report.erb +1 -1
- data/views/search.erb +1 -1
- metadata +4 -510
- data/.bootstrap/config.json +0 -433
- data/.codeclimate.yml +0 -31
- data/.csslintrc +0 -2
- data/.dockerignore +0 -1
- data/.eslintignore +0 -1
- data/.eslintrc.json +0 -36
- data/.gitignore +0 -56
- data/.mailmap +0 -5
- data/.rspec +0 -3
- data/.rubocop.yml +0 -61
- data/.travis.yml +0 -74
- data/AppImage/recipe.yml +0 -15
- data/AppImage/sequenceserver.desktop +0 -8
- data/AppImage/sequenceserver.png +0 -0
- data/AppImage/sequenceserver.sh +0 -16
- data/Dockerfile +0 -25
- data/LICENSE.txt +0 -661
- data/LICENSE/Apache.txt +0 -176
- data/LICENSE/d3.txt +0 -26
- data/README.md +0 -161
- data/package.json +0 -48
- data/public/vendor/.dependencies.json +0 -18
- data/public/vendor/.loaderversions +0 -1
- data/public/vendor/github/components/jquery@2.1.4/.gitignore +0 -1
- data/public/vendor/github/components/jquery@2.1.4/.jspm-hash +0 -1
- data/public/vendor/github/components/jquery@2.1.4/.jspm.json +0 -37
- data/public/vendor/github/components/jqueryui@1.11.4/.gitignore +0 -4
- data/public/vendor/github/components/jqueryui@1.11.4/.jspm-hash +0 -1
- data/public/vendor/github/components/jqueryui@1.11.4/.jspm.json +0 -136
- data/public/vendor/github/components/jqueryui@1.11.4/ui/.jshintrc +0 -24
- data/public/vendor/github/jspm/nodelibs-buffer@0.1.0/.jspm-hash +0 -1
- data/public/vendor/github/jspm/nodelibs-buffer@0.1.0/.jspm.json +0 -10
- data/public/vendor/github/jspm/nodelibs-events@0.1.1/.jspm-hash +0 -1
- data/public/vendor/github/jspm/nodelibs-events@0.1.1/.jspm.json +0 -10
- data/public/vendor/github/jspm/nodelibs-fs@0.1.2/.jspm-hash +0 -1
- data/public/vendor/github/jspm/nodelibs-module@0.1.0/.jspm-hash +0 -1
- data/public/vendor/github/jspm/nodelibs-module@0.1.0/.jspm.json +0 -3
- data/public/vendor/github/jspm/nodelibs-path@0.1.0/.jspm-hash +0 -1
- data/public/vendor/github/jspm/nodelibs-path@0.1.0/.jspm.json +0 -10
- data/public/vendor/github/jspm/nodelibs-process@0.1.1/.jspm-hash +0 -1
- data/public/vendor/github/jspm/nodelibs-stream@0.1.0/.jspm-hash +0 -1
- data/public/vendor/github/jspm/nodelibs-stream@0.1.0/.jspm.json +0 -10
- data/public/vendor/github/jspm/nodelibs-util@0.1.0/.jspm-hash +0 -1
- data/public/vendor/github/jspm/nodelibs-util@0.1.0/.jspm.json +0 -10
- data/public/vendor/github/mbostock/d3@3.5.6/.jspm-hash +0 -1
- data/public/vendor/github/mbostock/d3@3.5.6/.jspm.json +0 -76
- data/public/vendor/github/nicgirault/circosJs@1.7.0/.gitignore +0 -10
- data/public/vendor/github/nicgirault/circosJs@1.7.0/.jspm-hash +0 -1
- data/public/vendor/github/systemjs/plugin-css@0.1.15/.gitignore +0 -1
- data/public/vendor/github/systemjs/plugin-css@0.1.15/.jspm-hash +0 -1
- data/public/vendor/github/systemjs/plugin-css@0.1.15/.jspm.json +0 -4
- data/public/vendor/github/systemjs/plugin-json@0.1.0/.jspm-hash +0 -1
- data/public/vendor/github/twbs/bootstrap@3.3.5/.jspm-hash +0 -1
- data/public/vendor/github/twbs/bootstrap@3.3.5/.jspm.json +0 -100
- data/public/vendor/npm/amdefine@1.0.0/.jspm-hash +0 -1
- data/public/vendor/npm/amdefine@1.0.0/.jspm.json +0 -55
- data/public/vendor/npm/babel-core@5.8.23/.jspm-hash +0 -1
- data/public/vendor/npm/babel-runtime@5.8.20/.jspm-hash +0 -1
- data/public/vendor/npm/babel-runtime@5.8.20/.npmignore +0 -2
- data/public/vendor/npm/base62@0.1.1/.jspm-hash +0 -1
- data/public/vendor/npm/base62@0.1.1/.jspm.json +0 -49
- data/public/vendor/npm/base62@0.1.1/.travis.yml +0 -4
- data/public/vendor/npm/base64-js@0.0.8/.jspm-hash +0 -1
- data/public/vendor/npm/base64-js@0.0.8/.jspm.json +0 -77
- data/public/vendor/npm/base64-js@0.0.8/.travis.yml +0 -5
- data/public/vendor/npm/buffer@3.4.3/.jspm-hash +0 -1
- data/public/vendor/npm/buffer@3.4.3/.jspm.json +0 -105
- data/public/vendor/npm/buffer@3.4.3/.npmignore +0 -1
- data/public/vendor/npm/buffer@3.4.3/.travis.yml +0 -8
- data/public/vendor/npm/buffer@3.4.3/.zuul.yml +0 -20
- data/public/vendor/npm/core-js@1.1.2/.eslintrc +0 -36
- data/public/vendor/npm/core-js@1.1.2/.gitattributes +0 -1
- data/public/vendor/npm/core-js@1.1.2/.jspm-hash +0 -1
- data/public/vendor/npm/core-js@1.1.2/.npmignore +0 -10
- data/public/vendor/npm/core-js@1.1.2/.travis.yml +0 -3
- data/public/vendor/npm/core-util-is@1.0.1/.jspm-hash +0 -1
- data/public/vendor/npm/core-util-is@1.0.1/.jspm.json +0 -58
- data/public/vendor/npm/envify@3.4.0/.jspm-hash +0 -1
- data/public/vendor/npm/envify@3.4.0/.jspm.json +0 -72
- data/public/vendor/npm/envify@3.4.0/.npmignore +0 -2
- data/public/vendor/npm/esprima-fb@13001.1001.0-dev-harmony-fb/.jspm-hash +0 -1
- data/public/vendor/npm/esprima-fb@13001.1001.0-dev-harmony-fb/.jspm.json +0 -102
- data/public/vendor/npm/events@1.0.2/.jspm-hash +0 -1
- data/public/vendor/npm/events@1.0.2/.jspm.json +0 -67
- data/public/vendor/npm/events@1.0.2/.npmignore +0 -1
- data/public/vendor/npm/events@1.0.2/.travis.yml +0 -7
- data/public/vendor/npm/events@1.0.2/.zuul.yml +0 -12
- data/public/vendor/npm/font-awesome@4.4.0/.jspm-hash +0 -1
- data/public/vendor/npm/font-awesome@4.4.0/.jspm.json +0 -81
- data/public/vendor/npm/font-awesome@4.4.0/.npmignore +0 -42
- data/public/vendor/npm/ieee754@1.1.6/.jspm-hash +0 -1
- data/public/vendor/npm/ieee754@1.1.6/.jspm.json +0 -70
- data/public/vendor/npm/ieee754@1.1.6/.travis.yml +0 -7
- data/public/vendor/npm/ieee754@1.1.6/.zuul.yml +0 -20
- data/public/vendor/npm/inherits@2.0.1/.jspm-hash +0 -1
- data/public/vendor/npm/inherits@2.0.1/.jspm.json +0 -60
- data/public/vendor/npm/is-array@1.0.1/.jepso-ci.json +0 -3
- data/public/vendor/npm/is-array@1.0.1/.jspm-hash +0 -1
- data/public/vendor/npm/is-array@1.0.1/.jspm.json +0 -42
- data/public/vendor/npm/is-array@1.0.1/.npmignore +0 -0
- data/public/vendor/npm/isarray@0.0.1/.jspm-hash +0 -1
- data/public/vendor/npm/isarray@0.0.1/.jspm.json +0 -51
- data/public/vendor/npm/jstransform@10.1.0/.jshintrc +0 -28
- data/public/vendor/npm/jstransform@10.1.0/.jspm-hash +0 -1
- data/public/vendor/npm/jstransform@10.1.0/.jspm.json +0 -95
- data/public/vendor/npm/jstransform@10.1.0/.npmignore +0 -4
- data/public/vendor/npm/jstransform@10.1.0/.travis.yml +0 -8
- data/public/vendor/npm/path-browserify@0.0.0/.jspm-hash +0 -1
- data/public/vendor/npm/path-browserify@0.0.0/.jspm.json +0 -56
- data/public/vendor/npm/process@0.10.1/.jspm-hash +0 -1
- data/public/vendor/npm/react@0.13.3/.jspm-hash +0 -1
- data/public/vendor/npm/react@0.13.3/.jspm.json +0 -77
- data/public/vendor/npm/readable-stream@1.1.13/.jspm-hash +0 -1
- data/public/vendor/npm/readable-stream@1.1.13/.jspm.json +0 -95
- data/public/vendor/npm/readable-stream@1.1.13/.npmignore +0 -5
- data/public/vendor/npm/source-map@0.1.31/.jspm-hash +0 -1
- data/public/vendor/npm/source-map@0.1.31/.jspm.json +0 -133
- data/public/vendor/npm/source-map@0.1.31/.npmignore +0 -2
- data/public/vendor/npm/source-map@0.1.31/.travis.yml +0 -4
- data/public/vendor/npm/stream-browserify@1.0.0/.jspm-hash +0 -1
- data/public/vendor/npm/stream-browserify@1.0.0/.jspm.json +0 -77
- data/public/vendor/npm/stream-browserify@1.0.0/.travis.yml +0 -4
- data/public/vendor/npm/string_decoder@0.10.31/.jspm-hash +0 -1
- data/public/vendor/npm/string_decoder@0.10.31/.jspm.json +0 -58
- data/public/vendor/npm/string_decoder@0.10.31/.npmignore +0 -2
- data/public/vendor/npm/through@2.3.8/.jspm-hash +0 -1
- data/public/vendor/npm/through@2.3.8/.jspm.json +0 -72
- data/public/vendor/npm/through@2.3.8/.travis.yml +0 -5
- data/public/vendor/npm/underscore@1.8.3/.jspm-hash +0 -1
- data/public/vendor/npm/underscore@1.8.3/.jspm.json +0 -74
- data/public/vendor/npm/util@0.10.3/.jspm-hash +0 -1
- data/public/vendor/npm/util@0.10.3/.jspm.json +0 -58
- data/public/vendor/npm/util@0.10.3/.npmignore +0 -1
- data/public/vendor/npm/util@0.10.3/.travis.yml +0 -8
- data/public/vendor/npm/util@0.10.3/.zuul.yml +0 -10
- data/public/vendor/npm/webshim@1.15.8/.gitattributes +0 -12
- data/public/vendor/npm/webshim@1.15.8/.jspm-hash +0 -1
- data/public/vendor/npm/webshim@1.15.8/.jspm.json +0 -92
- data/public/vendor/npm/webshim@1.15.8/.npmignore +0 -16
- data/public/vendor/npm/webshim@1.15.8/.project +0 -12
- data/public/vendor/npm/webshim@1.15.8/demos/demos/filereader/upload/.keep +0 -0
- data/sequenceserver.gemspec +0 -55
- data/spec/blast_versions/blast_2.2.30/blast_2.2.30_spec.rb +0 -228
- data/spec/blast_versions/blast_2.2.30/import_spec_capybara_local_2.2.30.rb +0 -583
- data/spec/blast_versions/blast_2.2.31/blast_2.2.31_spec.rb +0 -228
- data/spec/blast_versions/blast_2.2.31/import_spec_capybara_local_2.2.31.rb +0 -587
- data/spec/blast_versions/blast_2.3.0/blast_2.3.0_spec.rb +0 -229
- data/spec/blast_versions/blast_2.3.0/import_spec_capybara_local_2.3.0.rb +0 -587
- data/spec/blast_versions/blast_2.4.0/blast_2.4.0_spec.rb +0 -228
- data/spec/blast_versions/blast_2.4.0/import_spec_capybara_local_2.4.0.rb +0 -588
- data/spec/blast_versions/blast_2.5.0/blast_2.5.0_spec.rb +0 -228
- data/spec/blast_versions/blast_2.5.0/import_spec_capybara_local_2.5.0.rb +0 -587
- data/spec/blast_versions/blast_2.6.0/blast_2.6.0_spec.rb +0 -228
- data/spec/blast_versions/blast_2.6.0/import_spec_capybara_local_2.6.0.rb +0 -587
- data/spec/blast_versions/blast_2.7.1/blast_2.7.1_spec.rb +0 -228
- data/spec/blast_versions/blast_2.7.1/import_spec_capybara_local_2.7.1.rb +0 -587
- data/spec/blast_versions/blast_2.8.1/blast_2.8.1_spec.rb +0 -228
- data/spec/blast_versions/blast_2.8.1/import_spec_capybara_local_2.8.1.rb +0 -587
- data/spec/blast_versions/blast_2.9.0/blast_2.9.0_spec.rb +0 -228
- data/spec/blast_versions/blast_2.9.0/import_spec_capybara_local_2.9.0.rb +0 -585
- data/spec/blast_versions/diamond_0.9.24/diamond_0.9.24_spec.rb +0 -176
- data/spec/blast_versions/diamond_0.9.24/import_spec_capybara_local_0.9.24.rb +0 -237
- data/spec/capybara_spec.rb +0 -345
- data/spec/config_spec.rb +0 -87
- data/spec/database/funky_ids/funky_ids.fa +0 -16
- data/spec/database/funky_ids/v4/funky_ids.fa.nhd +0 -8
- data/spec/database/funky_ids/v4/funky_ids.fa.nhi +0 -0
- data/spec/database/funky_ids/v4/funky_ids.fa.nhr +0 -0
- data/spec/database/funky_ids/v4/funky_ids.fa.nin +0 -0
- data/spec/database/funky_ids/v4/funky_ids.fa.nog +0 -0
- data/spec/database/funky_ids/v4/funky_ids.fa.nsd +0 -15
- data/spec/database/funky_ids/v4/funky_ids.fa.nsi +0 -0
- data/spec/database/funky_ids/v4/funky_ids.fa.nsq +0 -0
- data/spec/database/funky_ids/v5/funky_ids.fa.ndb +0 -0
- data/spec/database/funky_ids/v5/funky_ids.fa.nhd +0 -8
- data/spec/database/funky_ids/v5/funky_ids.fa.nhi +0 -0
- data/spec/database/funky_ids/v5/funky_ids.fa.nhr +0 -0
- data/spec/database/funky_ids/v5/funky_ids.fa.nin +0 -0
- data/spec/database/funky_ids/v5/funky_ids.fa.nog +0 -0
- data/spec/database/funky_ids/v5/funky_ids.fa.nos +0 -0
- data/spec/database/funky_ids/v5/funky_ids.fa.not +0 -0
- data/spec/database/funky_ids/v5/funky_ids.fa.nsq +0 -0
- data/spec/database/funky_ids/v5/funky_ids.fa.ntf +0 -0
- data/spec/database/funky_ids/v5/funky_ids.fa.nto +0 -0
- data/spec/database/funky_sequences/README.md +0 -14
- data/spec/database/funky_sequences/funky_aa_sequences.fa +0 -7
- data/spec/database/funky_sequences/funky_aa_sequences.fa.phd +0 -3
- data/spec/database/funky_sequences/funky_aa_sequences.fa.phi +0 -0
- data/spec/database/funky_sequences/funky_aa_sequences.fa.phr +0 -0
- data/spec/database/funky_sequences/funky_aa_sequences.fa.pin +0 -0
- data/spec/database/funky_sequences/funky_aa_sequences.fa.pog +0 -0
- data/spec/database/funky_sequences/funky_aa_sequences.fa.psd +0 -6
- data/spec/database/funky_sequences/funky_aa_sequences.fa.psi +0 -0
- data/spec/database/funky_sequences/funky_aa_sequences.fa.psq +0 -0
- data/spec/database/funky_sequences/funky_na_sequences.fa +0 -2
- data/spec/database/funky_sequences/funky_na_sequences.fa.nhr +0 -0
- data/spec/database/funky_sequences/funky_na_sequences.fa.nin +0 -0
- data/spec/database/funky_sequences/funky_na_sequences.fa.nog +0 -0
- data/spec/database/funky_sequences/funky_na_sequences.fa.nsd +0 -2
- data/spec/database/funky_sequences/funky_na_sequences.fa.nsi +0 -0
- data/spec/database/funky_sequences/funky_na_sequences.fa.nsq +0 -0
- data/spec/database/ox_parse_error/query.fa +0 -1
- data/spec/database/ox_parse_error/rand1.fa +0 -2
- data/spec/database/ox_parse_error/rand1.fa.nhd +0 -1
- data/spec/database/ox_parse_error/rand1.fa.nhi +0 -0
- data/spec/database/ox_parse_error/rand1.fa.nhr +0 -0
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- data/spec/database/ox_parse_error/rand2.fa +0 -2
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- data/spec/database/pipe_in_seqid/pipe_in_seqid.fa +0 -6
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- data/spec/database/sample/genome/Solenopsis_invicta/Solenopsis_invicta_gnG_subset.txt +0 -8
- data/spec/database/sample/links.rb +0 -23
- data/spec/database/sample/proteins/Solenopsis_invicta/Sinvicta2-2-3.prot.subset.fasta +0 -6449
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- data/spec/sequences/alignment-4_hits_tblastx.txt +0 -318
- data/spec/sequences/nucleotide_query.fa +0 -21
- data/spec/sequences/problematic_query.fa +0 -5
- data/spec/sequences/protein_query.fa +0 -9
- data/spec/sequences/sample_query_fire_ant_obps.fa +0 -44
- data/spec/sequences/sequenceserver-2_hits.fa +0 -10
- data/spec/sequences/sequenceserver-SI2.2.0_06267.fa +0 -5
- data/spec/sequences/sp_P04637_P53_HUMAN_gi_1099170394_ref_XP_018868681_1.txt +0 -6
- data/spec/sequences/sp_P04637_P53_HUMAN_gi_120407068_ref_NP_000537_3.txt +0 -6
- data/spec/sequences/sp_P04637_P53_HUMAN_gi_1484127324_gb_MG595988_1.txt +0 -6
- data/spec/sequences/sp_P04637_P53_HUMAN_gi_395440626_gb_JQ694049_1.txt +0 -6
- data/spec/sequences/sp_P04637_P53_HUMAN_sp_P04637_P53_HUMAN.txt +0 -6
- data/spec/sequenceserver_spec.rb +0 -90
- data/spec/spec_helper.rb +0 -63
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require 'spec_helper'
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# Test BLAST module.
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module SequenceServer
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with_hits = Job.fetch('diamond_0.9.24/blastx')
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no_hits = Job.fetch('diamond_0.9.24/blastx_nohits')
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init
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describe 'Report' do
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hits_report = BLAST::Report.new(with_hits)
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no_hits_report = BLAST::Report.new(no_hits)
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it 'will return an Array of queries' do
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hits_report.queries.should be_a Array
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no_hits_report.queries.should be_a Array
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end
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it 'will return a Hash of stats' do
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hits_report.stats.should be_a Hash
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no_hits_report.stats.should be_a Hash
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end
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it 'contains all the necessary stats' do
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hits_report.stats.length.should eql(7)
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no_hits_report.stats.length.should eql(7)
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end
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end
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describe 'Query' do
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hits_report = BLAST::Report.new(with_hits)
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no_hits_report = BLAST::Report.new(no_hits)
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it 'will return queries with valid length' do
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hits_report.queries.first.length.should be_a Integer
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hits_report.queries.first.length.should satisfy { |n| n > 0 }
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no_hits_report.queries.first.length.should be_a Integer
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no_hits_report.queries.first.length.should satisfy { |n| n > 0 }
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end
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it 'will return an Array of hits' do
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hits_report.queries.first.hits.should be_a Array
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no_hits_report.queries.first.hits.should be_a Array
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end
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end
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describe 'Hits' do
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hits_report = BLAST::Report.new(with_hits)
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no_hits_report = BLAST::Report.new(no_hits)
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it 'will have non zero length' do
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hits_report.queries.last.hits.first.length.should satisfy { |n| n > 0 }
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end
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it 'will return an Array of HSPs' do
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hits_report.queries.first.hits.first.hsps.should be_a Array
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end
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it 'will return an Array with atleast one HSP' do
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hits_report.queries.first.hits.first.hsps.length.should be >= 1
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end
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it 'will contain no element if no hits were obtained' do
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no_hits_report.queries.first.hits.length.should eql(0)
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end
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end
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# Test general features of HSPs. Algorithm specific customizations are
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# tested separetly.
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describe 'HSPs' do
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hits_report = BLAST::Report.new(with_hits)
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# Currently using all 17 HSP parameters in BLAST Report + 1 to refer to the
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# hit object it belongs to.
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it 'have all the necessary values' do
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hits_report.queries.last.hits.first.hsps.last.count.should eql(19)
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end
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# Test Random HSPs to ensure that all the values from HSP struct are valid.
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it 'have correct alignment values' do
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hits_report.queries.last.hits.first.hsps.last.bit_score.should be_a Float
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hits_report.queries.last.hits.first.hsps.last.score.should be_a Integer
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hits_report.queries.first.hits.first.hsps.first.evalue.should be_a Float
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hits_report.queries.first.hits.first.hsps.first.evalue
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.should_not satisfy { |n| n < 0 }
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hits_report.queries.first.hits.last.hsps.first.qstart.should be_a Integer
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hits_report.queries.first.hits.last.hsps.first.qstart
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.should_not satisfy { |n| n < 0 }
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hits_report.queries.first.hits.last.hsps.first.qend.should be_a Integer
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hits_report.queries.first.hits.last.hsps.first.qend
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.should_not satisfy { |n| n < 0 }
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hits_report.queries.last.hits.last.hsps.last.sstart.should be_a Integer
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hits_report.queries.last.hits.last.hsps.last.sstart
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.should_not satisfy { |n| n < 0 }
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hits_report.queries.first.hits.first.hsps.last.send.should be_a Integer
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hits_report.queries.first.hits.first.hsps.last.send
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.should_not satisfy { |n| n < 0 }
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hits_report.queries.first.hits.first.hsps.last.qframe.should be_a Integer
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hits_report.queries.first.hits.first.hsps.last.sframe.should be_a Integer
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hits_report.queries.first.hits.first.hsps.last.identity.should be_a Integer
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hits_report.queries.first.hits.first.hsps.last.identity
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.should_not satisfy { |n| n < 0 }
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hits_report.queries.first.hits.first.hsps.last.gaps.should be_a Integer
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hits_report.queries.first.hits.first.hsps.last.gaps
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.should_not satisfy { |n| n < 0 }
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hits_report.queries.first.hits.first.hsps.last.positives
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.should be_a Integer
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hits_report.queries.first.hits.first.hsps.last.positives
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.should_not satisfy { |n| n < 0 }
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hits_report.queries.first.hits.first.hsps.last.length.should be_a Integer
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hits_report.queries.first.hits.first.hsps.last.length
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.should satisfy { |n| n > 0 }
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hits_report.queries.last.hits.last.hsps.first.qseq.should be_a String
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hits_report.queries.last.hits.last.hsps.first.sseq.should be_a String
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hits_report.queries.last.hits.last.hsps.first.midline.should be_a String
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end
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it 'have correctly matched query, hit and midline alignments' do
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hsp = hits_report.queries.last.hits.last.hsps.first
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hsp.qseq.length.should eql(hsp.sseq.length)
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hsp.sseq.length.should eql(hsp.midline.length)
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hsp.midline.length.should eql(hsp.qseq.length)
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end
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end
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# Individually test different DIAMOND BLASTP/BLASTX algorithms
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#
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describe 'diamond BLASTP' do
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let 'hsp' do
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report = BLAST::Report.new(Job.fetch('diamond_0.9.24/blastp'))
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report.queries.first.hits.last.hsps.first
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end
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it 'have correct query and subject frame' do
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hsp.qframe.should eql(0)
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hsp.sframe.should eql(0)
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end
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it 'have correct qstart, qend, sstart, send values' do
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hsp.qstart.should be <= hsp.qend
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hsp.sstart.should be <= hsp.send
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end
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end
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describe 'diamond BLASTX' do
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let 'hsp' do
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report = BLAST::Report.new(Job.fetch('diamond_0.9.24/blastx'))
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report.queries.first.hits.last.hsps.first
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end
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it 'have correct query and subject frame' do
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hsp.qframe.should_not eql(0)
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hsp.sframe.should eql(0)
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end
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it 'have correct qstart, qend, sstart, send' do
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hsp.qstart.should be <= hsp.qend
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hsp.sstart.should be <= hsp.send
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end
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end
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end
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@@ -1,237 +0,0 @@
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describe 'report generated from imported XML', type: :feature, js: true do
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# Fasta files used for testing consist of TP53 and COX41 protein/nucleotide
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# sequences for reproducibility.
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it 'loads diamond BLASTP xml and tests hit alignment and sidebar Alignment download' do
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access_by_uuid('diamond_0.9.24/blastp')
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# Click on the first Alignment download button on the page and wait for the
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# download to finish.
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page.execute_script("$('.download-aln:eq(0)').click()")
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wait_for_download
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expect(File.basename(downloaded_file)).to eq('sp_P04637_P53_HUMAN_sp_P04637_P53_HUMAN.txt')
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expect(File.read(downloaded_file)).to eq(File.read('spec/sequences/sp_P04637_P53_HUMAN_sp_P04637_P53_HUMAN.txt'))
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clear_downloads
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# Click on the Alignment of all hits download and compare the downloaded
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# content
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page.click_link('Alignment of all hits')
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wait_for_download
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expect(File.basename(downloaded_file)).to eq('alignment-35_hits.txt')
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expect(File.read(downloaded_file)).to eq(File.read('spec/sequences/alignment-35_hits_diamond_blastp.txt'))
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clear_downloads
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# Check the cheboxes of indicted hits and click on the download of Alignment
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# of selected hits and compare the downloaded content
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page.check('Query_1_hit_1_checkbox')
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page.check('Query_1_hit_2_checkbox')
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page.check('Query_2_hit_1_checkbox')
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page.check('Query_2_hit_2_checkbox')
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page.click_link('Alignment of 4 selected hit(s)')
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wait_for_download
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expect(File.basename(downloaded_file)).to eq('alignment-4_hits.txt')
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expect(File.read(downloaded_file)).to eq(File.read('spec/sequences/alignment-4_hits_diamond_blastp.txt'))
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page.should have_content('BLASTP')
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end
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it 'loads diamond BLASTP XML and tests alignment overview and hit PNG/SVG download' do
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access_by_uuid('diamond_0.9.24/blastp')
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# Click on the PNG/SVG download button of the alignment overview and compare
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# the downloaded content.
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page.execute_script("$('.export-to-png:eq(0)').click()")
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wait_for_download
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expect(File.basename(downloaded_file)).to eq('Alignment-Overview-sp_P04637_P53_HUMAN.png')
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clear_downloads
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page.execute_script("$('.export-to-svg:eq(0)').click()")
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wait_for_download
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expect(File.basename(downloaded_file)).to eq('Alignment-Overview-sp_P04637_P53_HUMAN.svg')
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clear_downloads
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# Click on the PNG/SVG download button of the first hit available and
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# compare the downloaded content.
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page.execute_script("$('.export-to-png:eq(1)').click()")
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wait_for_download
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expect(File.basename(downloaded_file)).to eq('Kablammo-sp_P04637_P53_HUMAN-sp_P04637_P53_HUMAN.png')
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clear_downloads
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-
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page.execute_script("$('.export-to-svg:eq(1)').click()")
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wait_for_download
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expect(File.basename(downloaded_file)).to eq('Kablammo-sp_P04637_P53_HUMAN-sp_P04637_P53_HUMAN.svg')
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page.should have_content('BLASTP')
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end
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72
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it 'loads diamond BLASTP XML and tests Circos download' do
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access_by_uuid('diamond_0.9.24/blastp')
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# Click on the Circos expanding button, wait for animation, click on the
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# download of PNG/SVG file and test that it initiated a file download in a
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# right format.
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page.should have_content('Queries and their top hits: chord diagram')
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page.execute_script("$('.circos > .grapher-header > h4').click()")
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sleep 1
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page.execute_script("$('.export-to-png:eq(0)').click()")
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wait_for_download
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expect(File.basename(downloaded_file)).to eq('Circos-visualisation.png')
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-
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clear_downloads
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page.execute_script("$('.export-to-svg:eq(0)').click()")
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wait_for_download
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expect(File.basename(downloaded_file)).to eq('Circos-visualisation.svg')
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92
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end
|
93
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-
|
94
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it 'loads BLASTP XML and tests Length distribution download' do
|
95
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access_by_uuid('diamond_0.9.24/blastp')
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96
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97
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# Click on the Length distribution expanding button, wait for animation,
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# click on the download of PNG/SVG file and test that it initiated a file
|
99
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# download in a right format.
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100
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101
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page.should have_content('Length distribution of hits')
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page.execute_script("$('.length-distribution > .grapher-header > h4').click()")
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103
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sleep 1
|
104
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-
|
105
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page.execute_script("$('.export-to-png:eq(1)').click()")
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wait_for_download
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expect(File.basename(downloaded_file)).to eq('length-distribution-sp_P04637_P53_HUMAN.png')
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-
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109
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clear_downloads
|
110
|
-
|
111
|
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page.execute_script("$('.export-to-svg:eq(1)').click()")
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wait_for_download
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expect(File.basename(downloaded_file)).to eq('length-distribution-sp_P04637_P53_HUMAN.svg')
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|
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end
|
115
|
-
|
116
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# BLASTX test scenarios
|
117
|
-
|
118
|
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it 'loads diamond BLASTX XML and tests hit alignment and sidebar Alignment download' do
|
119
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access_by_uuid('diamond_0.9.24/blastx')
|
120
|
-
|
121
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# Click on the first Alignment download button on the page and wait for the
|
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# download to finish.
|
123
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page.execute_script("$('.download-aln:eq(0)').click()")
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wait_for_download
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125
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-
|
126
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expect(File.basename(downloaded_file)).to eq('MH011443_1_sp_P04637_P53_HUMAN.txt')
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expect(File.read(downloaded_file)).to eq(File.read('spec/sequences/MH011443_1_sp_P04637_P53_HUMAN.txt'))
|
128
|
-
|
129
|
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clear_downloads
|
130
|
-
|
131
|
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# Click on the Alignment of all hits download and compare the downloaded
|
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# content
|
133
|
-
|
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page.click_link('Alignment of all hits')
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wait_for_download
|
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|
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expect(File.basename(downloaded_file)).to eq('alignment-35_hits.txt')
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expect(File.read(downloaded_file)).to eq(File.read('spec/sequences/alignment-35_hits_diamond_blastx.txt'))
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clear_downloads
|
140
|
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|
141
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# Select four hit checkboxes and click on the Alignment of selected hits.
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142
|
-
# Compare the downloaded content.
|
143
|
-
page.check('Query_1_hit_3_checkbox')
|
144
|
-
page.check('Query_1_hit_4_checkbox')
|
145
|
-
page.check('Query_2_hit_3_checkbox')
|
146
|
-
page.check('Query_2_hit_4_checkbox')
|
147
|
-
page.click_link('Alignment of 4 selected hit(s)')
|
148
|
-
wait_for_download
|
149
|
-
|
150
|
-
expect(File.basename(downloaded_file)).to eq('alignment-4_hits.txt')
|
151
|
-
expect(File.read(downloaded_file)).to eq(File.read('spec/sequences/alignment-4_hits_diamond_blastx.txt'))
|
152
|
-
|
153
|
-
page.should have_content('BLASTX')
|
154
|
-
end
|
155
|
-
|
156
|
-
it 'loads diamond BLASTX XML and tests alignment overview and hit PNG/SVG download' do
|
157
|
-
access_by_uuid('diamond_0.9.24/blastx')
|
158
|
-
|
159
|
-
# Click on the PNG/SVG download button of the alignment overview and compare
|
160
|
-
# the downloaded content.
|
161
|
-
page.execute_script("$('.export-to-png:eq(0)').click()")
|
162
|
-
wait_for_download
|
163
|
-
expect(File.basename(downloaded_file)).to eq('Alignment-Overview-MH011443_1.png')
|
164
|
-
|
165
|
-
clear_downloads
|
166
|
-
|
167
|
-
page.execute_script("$('.export-to-svg:eq(0)').click()")
|
168
|
-
wait_for_download
|
169
|
-
expect(File.basename(downloaded_file)).to eq('Alignment-Overview-MH011443_1.svg')
|
170
|
-
|
171
|
-
clear_downloads
|
172
|
-
# Click on the PNG/SVG download button of the first hit available and
|
173
|
-
# compare the downloaded content.
|
174
|
-
page.execute_script("$('.export-to-png:eq(1)').click()")
|
175
|
-
|
176
|
-
wait_for_download
|
177
|
-
expect(File.basename(downloaded_file)).to eq('Kablammo-MH011443_1-sp_P04637_P53_HUMAN.png')
|
178
|
-
|
179
|
-
clear_downloads
|
180
|
-
|
181
|
-
page.execute_script("$('.export-to-svg:eq(1)').click()")
|
182
|
-
wait_for_download
|
183
|
-
expect(File.basename(downloaded_file)).to eq('Kablammo-MH011443_1-sp_P04637_P53_HUMAN.svg')
|
184
|
-
page.should have_content('BLASTX')
|
185
|
-
end
|
186
|
-
|
187
|
-
it 'loads diamond BLASTX XML and tests Circos download' do
|
188
|
-
access_by_uuid('diamond_0.9.24/blastx')
|
189
|
-
# Click on the Circos expanding button, wait for animation, click on the
|
190
|
-
# download of PNG/SVG file and test that it initiated a file download in a
|
191
|
-
# right format.
|
192
|
-
|
193
|
-
page.should have_content('Queries and their top hits: chord diagram')
|
194
|
-
page.execute_script("$('.circos > .grapher-header > h4').click()")
|
195
|
-
sleep 1
|
196
|
-
|
197
|
-
page.execute_script("$('.export-to-png:eq(0)').click()")
|
198
|
-
wait_for_download
|
199
|
-
expect(File.basename(downloaded_file)).to eq('Circos-visualisation.png')
|
200
|
-
|
201
|
-
clear_downloads
|
202
|
-
|
203
|
-
page.execute_script("$('.export-to-svg:eq(0)').click()")
|
204
|
-
wait_for_download
|
205
|
-
expect(File.basename(downloaded_file)).to eq('Circos-visualisation.svg')
|
206
|
-
end
|
207
|
-
|
208
|
-
it 'loads diamond BLASTX XML and tests Length distribution download' do
|
209
|
-
access_by_uuid('diamond_0.9.24/blastx')
|
210
|
-
|
211
|
-
# Click on the Length distribution expanding button, wait for animation,
|
212
|
-
# click on the download of PNG/SVG file and test that it initiated a file
|
213
|
-
# download in a right format.
|
214
|
-
|
215
|
-
page.should have_content('Length distribution of hits')
|
216
|
-
page.execute_script("$('.length-distribution > .grapher-header > h4').click()")
|
217
|
-
sleep 1
|
218
|
-
|
219
|
-
page.execute_script("$('.export-to-png:eq(1)').click()")
|
220
|
-
wait_for_download
|
221
|
-
expect(File.basename(downloaded_file)).to eq('length-distribution-MH011443_1.png')
|
222
|
-
|
223
|
-
clear_downloads
|
224
|
-
|
225
|
-
page.execute_script("$('.export-to-svg:eq(1)').click()")
|
226
|
-
wait_for_download
|
227
|
-
expect(File.basename(downloaded_file)).to eq('length-distribution-MH011443_1.svg')
|
228
|
-
end
|
229
|
-
|
230
|
-
## Helpers ##
|
231
|
-
|
232
|
-
def access_by_uuid(id)
|
233
|
-
url = url_encode(id)
|
234
|
-
visit "/#{url}"
|
235
|
-
page.should have_content('Query')
|
236
|
-
end
|
237
|
-
end
|
data/spec/capybara_spec.rb
DELETED
@@ -1,345 +0,0 @@
|
|
1
|
-
describe 'a browser', type: :feature, js: true do
|
2
|
-
it 'sorts databases alphabetically' do
|
3
|
-
visit '/'
|
4
|
-
fill_in('sequence', with: nucleotide_query)
|
5
|
-
|
6
|
-
prot = page.evaluate_script("$('.protein .database').text().trim()")
|
7
|
-
prot.should eq("2018-04 Swiss-Prot insecta Sinvicta 2-2-3 prot subset")
|
8
|
-
|
9
|
-
nucl = page.evaluate_script("$('.nucleotide .database').text().trim()")
|
10
|
-
nucl.should eq("Sinvicta 2-2-3 cdna subset Solenopsis invicta gnG subset")
|
11
|
-
end
|
12
|
-
|
13
|
-
it 'properly controls blast button' do
|
14
|
-
visit '/'
|
15
|
-
|
16
|
-
fill_in('sequence', with: nucleotide_query)
|
17
|
-
page.evaluate_script("$('#method').is(':disabled')").should eq(true)
|
18
|
-
|
19
|
-
check(nucleotide_databases.first)
|
20
|
-
page.evaluate_script("$('#method').is(':disabled')").should eq(false)
|
21
|
-
end
|
22
|
-
|
23
|
-
it 'properly controls interaction with database listing' do
|
24
|
-
visit '/'
|
25
|
-
fill_in('sequence', with: nucleotide_query)
|
26
|
-
check(nucleotide_databases.first)
|
27
|
-
page.evaluate_script("$('.protein .database').first().hasClass('disabled')")
|
28
|
-
.should eq(true)
|
29
|
-
end
|
30
|
-
|
31
|
-
it 'shows a dropdown menu when other blast methods are available' do
|
32
|
-
visit '/'
|
33
|
-
fill_in('sequence', with: nucleotide_query)
|
34
|
-
check(nucleotide_databases.first)
|
35
|
-
page.has_css?('button.dropdown-toggle').should eq(true)
|
36
|
-
end
|
37
|
-
|
38
|
-
it 'can run a simple blastn search' do
|
39
|
-
perform_search query: nucleotide_query,
|
40
|
-
databases: nucleotide_databases
|
41
|
-
page.should have_content('BLASTN')
|
42
|
-
end
|
43
|
-
|
44
|
-
it 'can run a simple blastp search' do
|
45
|
-
perform_search query: protein_query,
|
46
|
-
databases: protein_databases
|
47
|
-
page.should have_content('BLASTP')
|
48
|
-
end
|
49
|
-
|
50
|
-
it 'can run a simple blastx search' do
|
51
|
-
perform_search query: nucleotide_query,
|
52
|
-
databases: protein_databases
|
53
|
-
page.should have_content('BLASTX')
|
54
|
-
end
|
55
|
-
|
56
|
-
it 'can run a simple tblastx search' do
|
57
|
-
perform_search query: nucleotide_query,
|
58
|
-
databases: nucleotide_databases,
|
59
|
-
method: 'tblastx'
|
60
|
-
page.should have_content('TBLASTX')
|
61
|
-
end
|
62
|
-
|
63
|
-
it 'can run a simple tblastn search' do
|
64
|
-
perform_search query: protein_query,
|
65
|
-
databases: nucleotide_databases
|
66
|
-
page.should have_content('TBLASTN')
|
67
|
-
end
|
68
|
-
|
69
|
-
### Test aspects of the generated report.
|
70
|
-
|
71
|
-
it 'can download FASTA of each hit' do
|
72
|
-
# Do a BLASTP search. protein_query refers to the first two sequence in
|
73
|
-
# protein_databases[0], so the top hits are the query sequences themselves.
|
74
|
-
perform_search(query: protein_query,
|
75
|
-
databases: protein_databases.values_at(0))
|
76
|
-
|
77
|
-
# Click on the first FASTA download button on the page and wait for the
|
78
|
-
# download to finish.
|
79
|
-
page.execute_script("$('.download-fa:eq(0)').click()")
|
80
|
-
wait_for_download
|
81
|
-
|
82
|
-
# Test name and content of the downloaded file.
|
83
|
-
expect(File.basename(downloaded_file))
|
84
|
-
.to eq('sequenceserver-SI2.2.0_06267.fa')
|
85
|
-
expect(File.read(downloaded_file))
|
86
|
-
.to eq(File.read("#{__dir__}/sequences/sequenceserver-SI2.2.0_06267.fa"))
|
87
|
-
end
|
88
|
-
|
89
|
-
it 'can download FASTA of selected hits' do
|
90
|
-
# Do a BLASTP search. protein_query refers to the first two sequence in
|
91
|
-
# protein_databases[0], so the top hits are the query sequences themselves.
|
92
|
-
perform_search(query: protein_query,
|
93
|
-
databases: protein_databases.values_at(0))
|
94
|
-
|
95
|
-
# Select first hit for each query and click 'FASTA of 2 selected hits'.
|
96
|
-
page.check('Query_1_hit_1_checkbox')
|
97
|
-
page.check('Query_2_hit_1_checkbox')
|
98
|
-
page.click_link('FASTA of 2 selected hit(s)')
|
99
|
-
wait_for_download
|
100
|
-
|
101
|
-
expect(File.basename(downloaded_file)).to eq('sequenceserver-2_hits.fa')
|
102
|
-
expect(File.read(downloaded_file)).to eq(File.read('spec/sequences/sequenceserver-2_hits.fa'))
|
103
|
-
end
|
104
|
-
|
105
|
-
it 'can download FASTA of all hits' do
|
106
|
-
# Do a BLASTP search. protein_query refers to the first two sequence in
|
107
|
-
# protein_databases[0], so the top hits are the query sequences themselves.
|
108
|
-
perform_search(query: protein_query,
|
109
|
-
databases: protein_databases.values_at(0))
|
110
|
-
|
111
|
-
# Click 'FASTA of all hits'.
|
112
|
-
page.click_link('FASTA of all hits')
|
113
|
-
wait_for_download
|
114
|
-
|
115
|
-
expect(File.basename(downloaded_file)).to eq('sequenceserver-2_hits.fa')
|
116
|
-
expect(File.read(downloaded_file)).to eq(File.read('spec/sequences/sequenceserver-2_hits.fa'))
|
117
|
-
end
|
118
|
-
|
119
|
-
it 'can download alignment for each hit' do
|
120
|
-
# Do a BLASTP search. protein_query refers to the first two sequence in
|
121
|
-
# protein_databases[0], so the top hits are the query sequences themselves.
|
122
|
-
perform_search(query: protein_query,
|
123
|
-
databases: protein_databases.values_at(0))
|
124
|
-
|
125
|
-
# Click on the first Alignment download button on the page and wait for the
|
126
|
-
# download to finish.
|
127
|
-
page.execute_script("$('.download-aln:eq(0)').click()")
|
128
|
-
wait_for_download
|
129
|
-
|
130
|
-
# Test name and content of the downloaded file.
|
131
|
-
expect(File.basename(downloaded_file)).to eq('Query_1_SI2_2_0_06267.txt')
|
132
|
-
expect(File.read(downloaded_file))
|
133
|
-
.to eq(File.read("#{__dir__}/sequences/Query_1_SI2_2_0_06267.txt"))
|
134
|
-
end
|
135
|
-
|
136
|
-
it 'can download Alignment of selected hits' do
|
137
|
-
# Do a BLASTP search. protein_query refers to the first two sequence in
|
138
|
-
# protein_databases[0], so the top hits are the query sequences themselves.
|
139
|
-
perform_search(query: protein_query,
|
140
|
-
databases: protein_databases.values_at(0))
|
141
|
-
|
142
|
-
# Select first hit for each query and click 'Alignment of 2 selected hits'.
|
143
|
-
page.check('Query_1_hit_1_checkbox')
|
144
|
-
page.check('Query_2_hit_1_checkbox')
|
145
|
-
page.click_link('Alignment of 2 selected hit(s)')
|
146
|
-
wait_for_download
|
147
|
-
|
148
|
-
expect(File.basename(downloaded_file)).to eq('alignment-2_hits.txt')
|
149
|
-
expect(File.read(downloaded_file)).to eq(File.read('spec/sequences/alignment-2_hits.txt'))
|
150
|
-
end
|
151
|
-
|
152
|
-
it 'can download Alignment of all hits' do
|
153
|
-
# Do a BLASTP search. protein_query refers to the first two sequence in
|
154
|
-
# protein_databases[0], so the top hits are the query sequences themselves.
|
155
|
-
perform_search(query: protein_query,
|
156
|
-
databases: protein_databases.values_at(0))
|
157
|
-
|
158
|
-
# Click 'Alignment of all hits'.
|
159
|
-
page.click_link('Alignment of all hits')
|
160
|
-
wait_for_download
|
161
|
-
|
162
|
-
expect(File.basename(downloaded_file)).to eq('alignment-2_hits.txt')
|
163
|
-
expect(File.read(downloaded_file)).to eq(File.read('spec/sequences/alignment-2_hits.txt'))
|
164
|
-
end
|
165
|
-
|
166
|
-
it 'can download BLAST results in XML and tabular formats' do
|
167
|
-
# Do a BLASTP search. protein_query refers to the first two sequence in
|
168
|
-
# protein_databases[0], so the top hits are the query sequences themselves.
|
169
|
-
perform_search(query: protein_query,
|
170
|
-
databases: protein_databases.values_at(0))
|
171
|
-
|
172
|
-
page.click_link('Standard tabular report')
|
173
|
-
wait_for_download
|
174
|
-
expect(File.basename(downloaded_file)).to eq('sequenceserver-std_tsv_report.tsv')
|
175
|
-
clear_downloads
|
176
|
-
|
177
|
-
page.click_link('Full tabular report')
|
178
|
-
wait_for_download
|
179
|
-
expect(File.basename(downloaded_file)).to eq('sequenceserver-full_tsv_report.tsv')
|
180
|
-
clear_downloads
|
181
|
-
|
182
|
-
page.click_link('Full XML report')
|
183
|
-
wait_for_download
|
184
|
-
expect(File.basename(downloaded_file)).to eq('sequenceserver-xml_report.xml')
|
185
|
-
clear_downloads
|
186
|
-
end
|
187
|
-
|
188
|
-
it 'can show hit sequences in a modal' do
|
189
|
-
# Do a BLASTP search. protein_query refers to the first two sequence in
|
190
|
-
# protein_databases[0], so the top hits are the query sequences themselves.
|
191
|
-
perform_search(query: protein_query,
|
192
|
-
databases: protein_databases.values_at(0))
|
193
|
-
|
194
|
-
# Click on the first sequence viewer link in the report.
|
195
|
-
page.execute_script("$('.view-sequence:eq(0)').click()")
|
196
|
-
|
197
|
-
within('.sequence-viewer') do
|
198
|
-
page.should have_content('SI2.2.0_06267')
|
199
|
-
page.should have_content(<<~SEQ.chomp)
|
200
|
-
MNTLWLSLWDYPGKLPLNFMVFDTKDDLQAAYWRDPYSIP
|
201
|
-
LAVIFEDPQPISQRLIYEIRTNPSYTLPPPPTKLYSAPIS
|
202
|
-
CRKNKTGHWMDDILSIKTGESCPVNNYLHSGFLALQMITD
|
203
|
-
ITKIKLENSDVTIPDIKLIMFPKEPYTADWMLAFRVVIPL
|
204
|
-
YMVLALSQFITYLLILIVGEKENKIKEGMKMMGLNDSVF
|
205
|
-
SEQ
|
206
|
-
end
|
207
|
-
|
208
|
-
# Dismiss the first modal.
|
209
|
-
page.execute_script("$('.sequence-viewer').modal('hide')")
|
210
|
-
|
211
|
-
# Click on the second sequence viewer link in the report.
|
212
|
-
page.execute_script("$('.view-sequence:eq(1)').click()")
|
213
|
-
|
214
|
-
within('.sequence-viewer') do
|
215
|
-
page.should have_content('SI2.2.0_13722')
|
216
|
-
page.should have_content(<<~SEQ.chomp)
|
217
|
-
MSANRLNVLVTLMLAVALLVTESGNAQVDGYLQFNPKRSA
|
218
|
-
VSSPQKYCGKKLSNALQIICDGVYNSMFKKSGQDFPPQNK
|
219
|
-
RHIAHRINGNEEESFTTLKSNFLNWCVEVYHRHYRFVFVS
|
220
|
-
EMEMADYPLAYDISPYLPPFLSRARARGMLDGRFAGRRYR
|
221
|
-
RESRGIHEECCINGCTINELTSYCGP
|
222
|
-
SEQ
|
223
|
-
end
|
224
|
-
end
|
225
|
-
|
226
|
-
it 'disables sequence viewer links if hits are longer than 10kb' do
|
227
|
-
# BLASTN transcripts against genome. nucleotide_query refers to two fire
|
228
|
-
# ant transcripts and nucleotide_databases[0] is subset of the fire ant
|
229
|
-
# genome (few longest scaffolds). We expect sequence viewer links to be
|
230
|
-
# disabled for all hits of this search.
|
231
|
-
perform_search(query: nucleotide_query,
|
232
|
-
databases: nucleotide_databases.values_at(0))
|
233
|
-
|
234
|
-
# Check that the sequence viewer links are disabled.
|
235
|
-
page.evaluate_script("$('.view-sequence').is(':disabled')").should eq(true)
|
236
|
-
end
|
237
|
-
|
238
|
-
it 'can download visualisations in svg and png format' do
|
239
|
-
# Do a BLASTP search. protein_query refers to the first two sequence in
|
240
|
-
# protein_databases[0], so the top hits are the query sequences themselves.
|
241
|
-
perform_search(query: protein_query,
|
242
|
-
databases: protein_databases.values_at(0))
|
243
|
-
|
244
|
-
## Check that there is a circos vis and unfold it.
|
245
|
-
page.should have_content('Queries and their top hits: chord diagram')
|
246
|
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page.execute_script("$('.circos > .grapher-header > h4').click()")
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247
|
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sleep 1
|
248
|
-
|
249
|
-
page.execute_script("$('.export-to-svg:eq(0)').click()")
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250
|
-
wait_for_download
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251
|
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expect(File.basename(downloaded_file)).to eq('Circos-visualisation.svg')
|
252
|
-
clear_downloads
|
253
|
-
|
254
|
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page.execute_script("$('.export-to-png:eq(0)').click()")
|
255
|
-
wait_for_download
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256
|
-
expect(File.basename(downloaded_file)).to eq('Circos-visualisation.png')
|
257
|
-
clear_downloads
|
258
|
-
|
259
|
-
## Check that there is a graphical overview of hits.
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260
|
-
page.should have_content('Graphical overview of hits')
|
261
|
-
|
262
|
-
page.execute_script("$('.export-to-svg:eq(1)').click()")
|
263
|
-
wait_for_download
|
264
|
-
expect(File.basename(downloaded_file)).to eq('Alignment-Overview-Query_1.svg')
|
265
|
-
clear_downloads
|
266
|
-
|
267
|
-
page.execute_script("$('.export-to-png:eq(1)').click()")
|
268
|
-
wait_for_download
|
269
|
-
expect(File.basename(downloaded_file)).to eq('Alignment-Overview-Query_1.png')
|
270
|
-
clear_downloads
|
271
|
-
|
272
|
-
## Check that there is a length distribution of hits.
|
273
|
-
page.should have_content('Length distribution of hits')
|
274
|
-
page.execute_script("$('.length-distribution > .grapher-header > h4').click()")
|
275
|
-
sleep 1
|
276
|
-
|
277
|
-
page.execute_script("$('.export-to-svg:eq(2)').click()")
|
278
|
-
wait_for_download
|
279
|
-
expect(File.basename(downloaded_file)).to eq('length-distribution-Query_1.svg')
|
280
|
-
clear_downloads
|
281
|
-
|
282
|
-
page.execute_script("$('.export-to-png:eq(2)').click()")
|
283
|
-
wait_for_download
|
284
|
-
expect(File.basename(downloaded_file)).to eq('length-distribution-Query_1.png')
|
285
|
-
clear_downloads
|
286
|
-
|
287
|
-
## Check that there is a kablammo vis of query vs hit.
|
288
|
-
page.should have_content('Graphical overview of aligning region(s)')
|
289
|
-
|
290
|
-
page.execute_script("$('.export-to-svg:eq(3)').click()")
|
291
|
-
wait_for_download
|
292
|
-
expect(File.basename(downloaded_file)).to eq('Kablammo-Query_1-SI2_2_0_06267.svg')
|
293
|
-
clear_downloads
|
294
|
-
|
295
|
-
page.execute_script("$('.export-to-png:eq(3)').click()")
|
296
|
-
wait_for_download
|
297
|
-
expect(File.basename(downloaded_file)).to eq('Kablammo-Query_1-SI2_2_0_06267.png')
|
298
|
-
clear_downloads
|
299
|
-
end
|
300
|
-
|
301
|
-
## Helpers ##
|
302
|
-
|
303
|
-
def perform_search(query:, databases:, method: nil)
|
304
|
-
# Load search form.
|
305
|
-
visit '/'
|
306
|
-
|
307
|
-
# Fill in query, select databases, submit form.
|
308
|
-
fill_in('sequence', with: query)
|
309
|
-
databases.each { |db| check db }
|
310
|
-
if method == 'tblastx'
|
311
|
-
find('.dropdown-toggle').click
|
312
|
-
find('.dropdown-menu li').click
|
313
|
-
end
|
314
|
-
click_button('method')
|
315
|
-
|
316
|
-
# Switch to new window because link opens in new window
|
317
|
-
page.driver.browser.switch_to.window(page.driver.browser.window_handles.last)
|
318
|
-
|
319
|
-
# It is important to have this line or the examples end prematurely with a
|
320
|
-
# failure.
|
321
|
-
page.should have_content('Query')
|
322
|
-
end
|
323
|
-
|
324
|
-
def nucleotide_query
|
325
|
-
File.read File.join(__dir__, 'sequences', 'nucleotide_query.fa')
|
326
|
-
end
|
327
|
-
|
328
|
-
def protein_query
|
329
|
-
File.read File.join(__dir__, 'sequences', 'protein_query.fa')
|
330
|
-
end
|
331
|
-
|
332
|
-
def nucleotide_databases
|
333
|
-
[
|
334
|
-
'Solenopsis invicta gnG subset',
|
335
|
-
'Sinvicta 2-2-3 cdna subset'
|
336
|
-
]
|
337
|
-
end
|
338
|
-
|
339
|
-
def protein_databases
|
340
|
-
[
|
341
|
-
'Sinvicta 2-2-3 prot subset',
|
342
|
-
'2018-04 Swiss-Prot insecta'
|
343
|
-
]
|
344
|
-
end
|
345
|
-
end
|