sequenceserver 2.0.0.rc7 → 2.0.0.rc8
Sign up to get free protection for your applications and to get access to all the features.
- 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
- data/spec/database/ox_parse_error/rand1.fa.nin +0 -0
- data/spec/database/ox_parse_error/rand1.fa.nog +0 -0
- data/spec/database/ox_parse_error/rand1.fa.nsd +0 -2
- data/spec/database/ox_parse_error/rand1.fa.nsi +0 -0
- data/spec/database/ox_parse_error/rand1.fa.nsq +0 -0
- data/spec/database/ox_parse_error/rand2.fa +0 -2
- data/spec/database/ox_parse_error/rand2.fa.nhd +0 -1
- data/spec/database/ox_parse_error/rand2.fa.nhi +0 -0
- data/spec/database/ox_parse_error/rand2.fa.nhr +0 -0
- data/spec/database/ox_parse_error/rand2.fa.nin +0 -0
- data/spec/database/ox_parse_error/rand2.fa.nog +0 -0
- data/spec/database/ox_parse_error/rand2.fa.nsd +0 -2
- data/spec/database/ox_parse_error/rand2.fa.nsi +0 -0
- data/spec/database/ox_parse_error/rand2.fa.nsq +0 -0
- data/spec/database/ox_parse_error_unique_ids/query.fa +0 -1
- data/spec/database/ox_parse_error_unique_ids/rand1.fa +0 -2
- data/spec/database/ox_parse_error_unique_ids/rand1.fa.nhd +0 -1
- data/spec/database/ox_parse_error_unique_ids/rand1.fa.nhi +0 -0
- data/spec/database/ox_parse_error_unique_ids/rand1.fa.nhr +0 -0
- data/spec/database/ox_parse_error_unique_ids/rand1.fa.nin +0 -0
- data/spec/database/ox_parse_error_unique_ids/rand1.fa.nog +0 -0
- data/spec/database/ox_parse_error_unique_ids/rand1.fa.nsd +0 -2
- data/spec/database/ox_parse_error_unique_ids/rand1.fa.nsi +0 -0
- data/spec/database/ox_parse_error_unique_ids/rand1.fa.nsq +0 -0
- data/spec/database/ox_parse_error_unique_ids/rand2.fa +0 -2
- data/spec/database/ox_parse_error_unique_ids/rand2.fa.nhd +0 -1
- data/spec/database/ox_parse_error_unique_ids/rand2.fa.nhi +0 -0
- data/spec/database/ox_parse_error_unique_ids/rand2.fa.nhr +0 -0
- data/spec/database/ox_parse_error_unique_ids/rand2.fa.nin +0 -0
- data/spec/database/ox_parse_error_unique_ids/rand2.fa.nog +0 -0
- data/spec/database/ox_parse_error_unique_ids/rand2.fa.nsd +0 -2
- data/spec/database/ox_parse_error_unique_ids/rand2.fa.nsi +0 -0
- data/spec/database/ox_parse_error_unique_ids/rand2.fa.nsq +0 -0
- data/spec/database/pipe_in_seqid/pipe_in_seqid.fa +0 -6
- data/spec/database/pipe_in_seqid/pipe_in_seqid.fa.nhd +0 -1
- data/spec/database/pipe_in_seqid/pipe_in_seqid.fa.nhi +0 -0
- data/spec/database/pipe_in_seqid/pipe_in_seqid.fa.nhr +0 -0
- data/spec/database/pipe_in_seqid/pipe_in_seqid.fa.nin +0 -0
- data/spec/database/pipe_in_seqid/pipe_in_seqid.fa.nog +0 -0
- data/spec/database/pipe_in_seqid/pipe_in_seqid.fa.nsd +0 -2
- data/spec/database/pipe_in_seqid/pipe_in_seqid.fa.nsi +0 -0
- data/spec/database/pipe_in_seqid/pipe_in_seqid.fa.nsq +0 -0
- data/spec/database/sample/genome/Solenopsis_invicta/Solenopsis_invicta_gnG_subset.fasta.ndb +0 -0
- data/spec/database/sample/genome/Solenopsis_invicta/Solenopsis_invicta_gnG_subset.fasta.nhd +0 -8
- data/spec/database/sample/genome/Solenopsis_invicta/Solenopsis_invicta_gnG_subset.fasta.nhi +0 -0
- data/spec/database/sample/genome/Solenopsis_invicta/Solenopsis_invicta_gnG_subset.fasta.nhr +0 -0
- data/spec/database/sample/genome/Solenopsis_invicta/Solenopsis_invicta_gnG_subset.fasta.nin +0 -0
- data/spec/database/sample/genome/Solenopsis_invicta/Solenopsis_invicta_gnG_subset.fasta.nog +0 -0
- data/spec/database/sample/genome/Solenopsis_invicta/Solenopsis_invicta_gnG_subset.fasta.nos +0 -0
- data/spec/database/sample/genome/Solenopsis_invicta/Solenopsis_invicta_gnG_subset.fasta.not +0 -0
- data/spec/database/sample/genome/Solenopsis_invicta/Solenopsis_invicta_gnG_subset.fasta.nsq +0 -0
- data/spec/database/sample/genome/Solenopsis_invicta/Solenopsis_invicta_gnG_subset.fasta.ntf +0 -0
- data/spec/database/sample/genome/Solenopsis_invicta/Solenopsis_invicta_gnG_subset.fasta.nto +0 -0
- 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
- data/spec/database/sample/proteins/Solenopsis_invicta/Sinvicta2-2-3.prot.subset.fasta.pdb +0 -0
- data/spec/database/sample/proteins/Solenopsis_invicta/Sinvicta2-2-3.prot.subset.fasta.phd +0 -1189
- data/spec/database/sample/proteins/Solenopsis_invicta/Sinvicta2-2-3.prot.subset.fasta.phi +0 -0
- data/spec/database/sample/proteins/Solenopsis_invicta/Sinvicta2-2-3.prot.subset.fasta.phr +0 -0
- data/spec/database/sample/proteins/Solenopsis_invicta/Sinvicta2-2-3.prot.subset.fasta.pin +0 -0
- data/spec/database/sample/proteins/Solenopsis_invicta/Sinvicta2-2-3.prot.subset.fasta.pog +0 -0
- data/spec/database/sample/proteins/Solenopsis_invicta/Sinvicta2-2-3.prot.subset.fasta.pos +0 -0
- data/spec/database/sample/proteins/Solenopsis_invicta/Sinvicta2-2-3.prot.subset.fasta.pot +0 -0
- data/spec/database/sample/proteins/Solenopsis_invicta/Sinvicta2-2-3.prot.subset.fasta.psq +0 -0
- data/spec/database/sample/proteins/Solenopsis_invicta/Sinvicta2-2-3.prot.subset.fasta.ptf +0 -0
- data/spec/database/sample/proteins/Solenopsis_invicta/Sinvicta2-2-3.prot.subset.fasta.pto +0 -0
- data/spec/database/sample/proteins/uniprot/2018-04-Swiss-Prot_insecta.fasta.pdb +0 -0
- data/spec/database/sample/proteins/uniprot/2018-04-Swiss-Prot_insecta.fasta.phd +0 -9140
- data/spec/database/sample/proteins/uniprot/2018-04-Swiss-Prot_insecta.fasta.phi +0 -0
- data/spec/database/sample/proteins/uniprot/2018-04-Swiss-Prot_insecta.fasta.phr +0 -0
- data/spec/database/sample/proteins/uniprot/2018-04-Swiss-Prot_insecta.fasta.pin +0 -0
- data/spec/database/sample/proteins/uniprot/2018-04-Swiss-Prot_insecta.fasta.pog +0 -0
- data/spec/database/sample/proteins/uniprot/2018-04-Swiss-Prot_insecta.fasta.pos +0 -0
- data/spec/database/sample/proteins/uniprot/2018-04-Swiss-Prot_insecta.fasta.pot +0 -0
- data/spec/database/sample/proteins/uniprot/2018-04-Swiss-Prot_insecta.fasta.psq +0 -0
- data/spec/database/sample/proteins/uniprot/2018-04-Swiss-Prot_insecta.fasta.ptf +0 -0
- data/spec/database/sample/proteins/uniprot/2018-04-Swiss-Prot_insecta.fasta.pto +0 -0
- data/spec/database/sample/proteins/uniprot/URL +0 -1
- data/spec/database/sample/si_uniprot_idmap.yml +0 -14180
- data/spec/database/sample/transcripts/Solenopsis_invicta/Sinvicta2-2-3.cdna.subset.fasta +0 -5486
- data/spec/database/sample/transcripts/Solenopsis_invicta/Sinvicta2-2-3.cdna.subset.fasta.ndb +0 -0
- data/spec/database/sample/transcripts/Solenopsis_invicta/Sinvicta2-2-3.cdna.subset.fasta.nhd +0 -473
- data/spec/database/sample/transcripts/Solenopsis_invicta/Sinvicta2-2-3.cdna.subset.fasta.nhi +0 -0
- data/spec/database/sample/transcripts/Solenopsis_invicta/Sinvicta2-2-3.cdna.subset.fasta.nhr +0 -0
- data/spec/database/sample/transcripts/Solenopsis_invicta/Sinvicta2-2-3.cdna.subset.fasta.nin +0 -0
- data/spec/database/sample/transcripts/Solenopsis_invicta/Sinvicta2-2-3.cdna.subset.fasta.nog +0 -0
- data/spec/database/sample/transcripts/Solenopsis_invicta/Sinvicta2-2-3.cdna.subset.fasta.nos +0 -0
- data/spec/database/sample/transcripts/Solenopsis_invicta/Sinvicta2-2-3.cdna.subset.fasta.not +0 -0
- data/spec/database/sample/transcripts/Solenopsis_invicta/Sinvicta2-2-3.cdna.subset.fasta.nsq +0 -0
- data/spec/database/sample/transcripts/Solenopsis_invicta/Sinvicta2-2-3.cdna.subset.fasta.ntf +0 -0
- data/spec/database/sample/transcripts/Solenopsis_invicta/Sinvicta2-2-3.cdna.subset.fasta.nto +0 -0
- data/spec/database/unformatted/Cardiocondyla_obscurior/Cobs1.4.proteins.fa +0 -148303
- data/spec/database/v4/genome/Solenopsis_invicta/Solenopsis_invicta_gnG_subset.fasta.nhd +0 -8
- data/spec/database/v4/genome/Solenopsis_invicta/Solenopsis_invicta_gnG_subset.fasta.nhi +0 -0
- data/spec/database/v4/genome/Solenopsis_invicta/Solenopsis_invicta_gnG_subset.fasta.nhr +0 -0
- data/spec/database/v4/genome/Solenopsis_invicta/Solenopsis_invicta_gnG_subset.fasta.nin +0 -0
- data/spec/database/v4/genome/Solenopsis_invicta/Solenopsis_invicta_gnG_subset.fasta.nog +0 -0
- data/spec/database/v4/genome/Solenopsis_invicta/Solenopsis_invicta_gnG_subset.fasta.nsd +0 -16
- data/spec/database/v4/genome/Solenopsis_invicta/Solenopsis_invicta_gnG_subset.fasta.nsi +0 -0
- data/spec/database/v4/genome/Solenopsis_invicta/Solenopsis_invicta_gnG_subset.fasta.nsq +0 -0
- data/spec/database/v4/genome/Solenopsis_invicta/Solenopsis_invicta_gnG_subset.txt +0 -8
- data/spec/database/v4/links.rb +0 -23
- data/spec/database/v4/proteins/Solenopsis_invicta/Sinvicta2-2-3.prot.subset.fasta +0 -6449
- data/spec/database/v4/proteins/Solenopsis_invicta/Sinvicta2-2-3.prot.subset.fasta.phd +0 -1189
- data/spec/database/v4/proteins/Solenopsis_invicta/Sinvicta2-2-3.prot.subset.fasta.phi +0 -0
- data/spec/database/v4/proteins/Solenopsis_invicta/Sinvicta2-2-3.prot.subset.fasta.phr +0 -0
- data/spec/database/v4/proteins/Solenopsis_invicta/Sinvicta2-2-3.prot.subset.fasta.pin +0 -0
- data/spec/database/v4/proteins/Solenopsis_invicta/Sinvicta2-2-3.prot.subset.fasta.pog +0 -0
- data/spec/database/v4/proteins/Solenopsis_invicta/Sinvicta2-2-3.prot.subset.fasta.psd +0 -2378
- data/spec/database/v4/proteins/Solenopsis_invicta/Sinvicta2-2-3.prot.subset.fasta.psi +0 -0
- data/spec/database/v4/proteins/Solenopsis_invicta/Sinvicta2-2-3.prot.subset.fasta.psq +0 -0
- data/spec/database/v4/proteins/uniprot/2018-04-Swiss-Prot_insecta.fasta.phd +0 -9140
- data/spec/database/v4/proteins/uniprot/2018-04-Swiss-Prot_insecta.fasta.phi +0 -0
- data/spec/database/v4/proteins/uniprot/2018-04-Swiss-Prot_insecta.fasta.phr +0 -0
- data/spec/database/v4/proteins/uniprot/2018-04-Swiss-Prot_insecta.fasta.pin +0 -0
- data/spec/database/v4/proteins/uniprot/2018-04-Swiss-Prot_insecta.fasta.pog +0 -0
- data/spec/database/v4/proteins/uniprot/2018-04-Swiss-Prot_insecta.fasta.psd +0 -18280
- data/spec/database/v4/proteins/uniprot/2018-04-Swiss-Prot_insecta.fasta.psi +0 -0
- data/spec/database/v4/proteins/uniprot/2018-04-Swiss-Prot_insecta.fasta.psq +0 -0
- data/spec/database/v4/proteins/uniprot/URL +0 -1
- data/spec/database/v4/si_uniprot_idmap.yml +0 -14180
- data/spec/database/v4/transcripts/Solenopsis_invicta/Sinvicta2-2-3.cdna.subset.fasta +0 -5486
- data/spec/database/v4/transcripts/Solenopsis_invicta/Sinvicta2-2-3.cdna.subset.fasta.nhd +0 -473
- data/spec/database/v4/transcripts/Solenopsis_invicta/Sinvicta2-2-3.cdna.subset.fasta.nhi +0 -0
- data/spec/database/v4/transcripts/Solenopsis_invicta/Sinvicta2-2-3.cdna.subset.fasta.nhr +0 -0
- data/spec/database/v4/transcripts/Solenopsis_invicta/Sinvicta2-2-3.cdna.subset.fasta.nin +0 -0
- data/spec/database/v4/transcripts/Solenopsis_invicta/Sinvicta2-2-3.cdna.subset.fasta.nog +0 -0
- data/spec/database/v4/transcripts/Solenopsis_invicta/Sinvicta2-2-3.cdna.subset.fasta.nsd +0 -946
- data/spec/database/v4/transcripts/Solenopsis_invicta/Sinvicta2-2-3.cdna.subset.fasta.nsi +0 -0
- data/spec/database/v4/transcripts/Solenopsis_invicta/Sinvicta2-2-3.cdna.subset.fasta.nsq +0 -0
- data/spec/database/without_parse_seqids/without_parse_seqids.fa +0 -10
- data/spec/database/without_parse_seqids/without_parse_seqids.fa.phr +0 -0
- data/spec/database/without_parse_seqids/without_parse_seqids.fa.pin +0 -0
- data/spec/database/without_parse_seqids/without_parse_seqids.fa.psq +0 -0
- data/spec/database_spec.rb +0 -51
- data/spec/doctor_spec.disabled.rb +0 -107
- data/spec/dotdir/blast_2.2.30/blastn/BLASTN_XML_2.2.30.xml +0 -1201
- data/spec/dotdir/blast_2.2.30/blastn/job.yaml +0 -8
- data/spec/dotdir/blast_2.2.30/blastn_nohits/BLASTN_NO_HITS_XML_2.2.30.xml +0 -866
- data/spec/dotdir/blast_2.2.30/blastn_nohits/job.yaml +0 -8
- data/spec/dotdir/blast_2.2.30/blastp/BLASTP_XML_2.2.30.xml +0 -1181
- data/spec/dotdir/blast_2.2.30/blastp/job.yaml +0 -8
- data/spec/dotdir/blast_2.2.30/blastx/BLASTX_XML_2.2.30.xml +0 -1181
- data/spec/dotdir/blast_2.2.30/blastx/job.yaml +0 -8
- data/spec/dotdir/blast_2.2.30/tblastn/TBLASTN_XML_2.2.30.xml +0 -1181
- data/spec/dotdir/blast_2.2.30/tblastn/job.yaml +0 -8
- data/spec/dotdir/blast_2.2.30/tblastx/TBLASTX_XML_2.2.30.xml +0 -8857
- data/spec/dotdir/blast_2.2.30/tblastx/job.yaml +0 -8
- data/spec/dotdir/blast_2.2.31/blastn/BLASTN_XML_2.2.31.xml +0 -1201
- data/spec/dotdir/blast_2.2.31/blastn/job.yaml +0 -8
- data/spec/dotdir/blast_2.2.31/blastn_nohits/BLASTN_NO_HITS_XML_2.2.31.xml +0 -866
- data/spec/dotdir/blast_2.2.31/blastn_nohits/job.yaml +0 -8
- data/spec/dotdir/blast_2.2.31/blastp/BLASTP_XML_2.2.31.xml +0 -1181
- data/spec/dotdir/blast_2.2.31/blastp/job.yaml +0 -8
- data/spec/dotdir/blast_2.2.31/blastx/BLASTX_XML_2.2.31.xml +0 -1181
- data/spec/dotdir/blast_2.2.31/blastx/job.yaml +0 -8
- data/spec/dotdir/blast_2.2.31/tblastn/TBLASTN_XML_2.2.31.xml +0 -1181
- data/spec/dotdir/blast_2.2.31/tblastn/job.yaml +0 -8
- data/spec/dotdir/blast_2.2.31/tblastx/TBLASTX_XML_2.2.31.xml +0 -8857
- data/spec/dotdir/blast_2.2.31/tblastx/job.yaml +0 -8
- data/spec/dotdir/blast_2.3.0/blastn/BLASTN_XML_2.3.0.xml +0 -1201
- data/spec/dotdir/blast_2.3.0/blastn/job.yaml +0 -8
- data/spec/dotdir/blast_2.3.0/blastn_nohits/BLASTN_NO_HITS_XML_2.3.0.xml +0 -866
- data/spec/dotdir/blast_2.3.0/blastn_nohits/job.yaml +0 -8
- data/spec/dotdir/blast_2.3.0/blastp/BLASTP_XML_2.3.0.xml +0 -1181
- data/spec/dotdir/blast_2.3.0/blastp/job.yaml +0 -8
- data/spec/dotdir/blast_2.3.0/blastx/BLASTX_XML_2.3.0.xml +0 -1181
- data/spec/dotdir/blast_2.3.0/blastx/job.yaml +0 -8
- data/spec/dotdir/blast_2.3.0/tblastn/TBLASTN_XML_2.3.0.xml +0 -1181
- data/spec/dotdir/blast_2.3.0/tblastn/job.yaml +0 -8
- data/spec/dotdir/blast_2.3.0/tblastx/TBLASTX_XML_2.3.0.xml +0 -8857
- data/spec/dotdir/blast_2.3.0/tblastx/job.yaml +0 -8
- data/spec/dotdir/blast_2.4.0/blastn/BLASTN_XML_2.4.0.xml +0 -1201
- data/spec/dotdir/blast_2.4.0/blastn/job.yaml +0 -8
- data/spec/dotdir/blast_2.4.0/blastn_nohits/BLASTN_NO_HITS_XML_2.4.0.xml +0 -866
- data/spec/dotdir/blast_2.4.0/blastn_nohits/job.yaml +0 -8
- data/spec/dotdir/blast_2.4.0/blastp/BLASTP_XML_2.4.0.xml +0 -1181
- data/spec/dotdir/blast_2.4.0/blastp/job.yaml +0 -8
- data/spec/dotdir/blast_2.4.0/blastx/BLASTX_XML_2.4.0.xml +0 -1181
- data/spec/dotdir/blast_2.4.0/blastx/job.yaml +0 -8
- data/spec/dotdir/blast_2.4.0/tblastn/TBLASTN_XML_2.4.0.xml +0 -1181
- data/spec/dotdir/blast_2.4.0/tblastn/job.yaml +0 -8
- data/spec/dotdir/blast_2.4.0/tblastx/TBLASTX_XML_2.4.0.xml +0 -8857
- data/spec/dotdir/blast_2.4.0/tblastx/job.yaml +0 -8
- data/spec/dotdir/blast_2.5.0/blastn/BLASTN_XML_2.5.0.xml +0 -1201
- data/spec/dotdir/blast_2.5.0/blastn/job.yaml +0 -8
- data/spec/dotdir/blast_2.5.0/blastn_nohits/BLASTN_NO_HITS_XML_2.5.0.xml +0 -866
- data/spec/dotdir/blast_2.5.0/blastn_nohits/job.yaml +0 -8
- data/spec/dotdir/blast_2.5.0/blastp/BLASTP +0 -2161
- data/spec/dotdir/blast_2.5.0/blastp/BLASTP_XML_2.5.0.xml +0 -1181
- data/spec/dotdir/blast_2.5.0/blastp/job.yaml +0 -8
- data/spec/dotdir/blast_2.5.0/blastx/BLASTX +0 -28080
- data/spec/dotdir/blast_2.5.0/blastx/BLASTX_XML_2.5.0.xml +0 -1181
- data/spec/dotdir/blast_2.5.0/blastx/job.yaml +0 -8
- data/spec/dotdir/blast_2.5.0/tblastn/TBLASTN +0 -29486
- data/spec/dotdir/blast_2.5.0/tblastn/TBLASTN_XML_2.5.0.xml +0 -1181
- data/spec/dotdir/blast_2.5.0/tblastn/job.yaml +0 -8
- data/spec/dotdir/blast_2.5.0/tblastx/TBLASTX +0 -180859
- data/spec/dotdir/blast_2.5.0/tblastx/TBLASTX_XML_2.5.0.xml +0 -8857
- data/spec/dotdir/blast_2.5.0/tblastx/job.yaml +0 -8
- data/spec/dotdir/blast_2.6.0/blastn/BLASTN_XML_2.6.0.xml +0 -1201
- data/spec/dotdir/blast_2.6.0/blastn/job.yaml +0 -8
- data/spec/dotdir/blast_2.6.0/blastn_nohits/BLASTN_NO_HITS_XML_2.6.0.xml +0 -866
- data/spec/dotdir/blast_2.6.0/blastn_nohits/job.yaml +0 -8
- data/spec/dotdir/blast_2.6.0/blastp/BLASTP_XML_2.6.0.xml +0 -1181
- data/spec/dotdir/blast_2.6.0/blastp/job.yaml +0 -8
- data/spec/dotdir/blast_2.6.0/blastx/BLASTX_XML_2.6.0.xml +0 -1181
- data/spec/dotdir/blast_2.6.0/blastx/job.yaml +0 -8
- data/spec/dotdir/blast_2.6.0/tblastn/TBLASTN_XML_2.6.0.xml +0 -1181
- data/spec/dotdir/blast_2.6.0/tblastn/job.yaml +0 -8
- data/spec/dotdir/blast_2.6.0/tblastx/TBLASTX_XML_2.6.0.xml +0 -8857
- data/spec/dotdir/blast_2.6.0/tblastx/job.yaml +0 -8
- data/spec/dotdir/blast_2.7.1/blastn/BLASTN_XML_2.7.1.xml +0 -1201
- data/spec/dotdir/blast_2.7.1/blastn/job.yaml +0 -8
- data/spec/dotdir/blast_2.7.1/blastn_nohits/BLASTN_NO_HITS_XML_2.7.1.xml +0 -866
- data/spec/dotdir/blast_2.7.1/blastn_nohits/job.yaml +0 -8
- data/spec/dotdir/blast_2.7.1/blastp/BLASTP_XML_2.7.1.xml +0 -1181
- data/spec/dotdir/blast_2.7.1/blastp/job.yaml +0 -8
- data/spec/dotdir/blast_2.7.1/blastx/BLASTX_XML_2.7.1.xml +0 -1181
- data/spec/dotdir/blast_2.7.1/blastx/job.yaml +0 -8
- data/spec/dotdir/blast_2.7.1/tblastn/TBLASTN_XML_2.7.1.xml +0 -1181
- data/spec/dotdir/blast_2.7.1/tblastn/job.yaml +0 -8
- data/spec/dotdir/blast_2.7.1/tblastx/TBLASTX_XML_2.7.1.xml +0 -8857
- data/spec/dotdir/blast_2.7.1/tblastx/job.yaml +0 -8
- data/spec/dotdir/blast_2.8.1/blastn/BLASTN_XML_2.8.1.xml +0 -1201
- data/spec/dotdir/blast_2.8.1/blastn/job.yaml +0 -8
- data/spec/dotdir/blast_2.8.1/blastn_nohits/BLASTN_NO_HITS_XML_2.8.1.xml +0 -866
- data/spec/dotdir/blast_2.8.1/blastn_nohits/job.yaml +0 -8
- data/spec/dotdir/blast_2.8.1/blastp/BLASTP_XML_2.8.1.xml +0 -1181
- data/spec/dotdir/blast_2.8.1/blastp/job.yaml +0 -8
- data/spec/dotdir/blast_2.8.1/blastx/BLASTX_XML_2.8.1.xml +0 -1181
- data/spec/dotdir/blast_2.8.1/blastx/job.yaml +0 -8
- data/spec/dotdir/blast_2.8.1/tblastn/TBLASTN_XML_2.8.1.xml +0 -1181
- data/spec/dotdir/blast_2.8.1/tblastn/job.yaml +0 -8
- data/spec/dotdir/blast_2.8.1/tblastx/TBLASTX_XML_2.8.1.xml +0 -8857
- data/spec/dotdir/blast_2.8.1/tblastx/job.yaml +0 -8
- data/spec/dotdir/blast_2.9.0/blastn/BLASTN_XML_2.9.0.xml +0 -1201
- data/spec/dotdir/blast_2.9.0/blastn/job.yaml +0 -8
- data/spec/dotdir/blast_2.9.0/blastn_nohits/BLASTN_NO_HITS_XML_2.9.0.xml +0 -866
- data/spec/dotdir/blast_2.9.0/blastn_nohits/job.yaml +0 -8
- data/spec/dotdir/blast_2.9.0/blastp/BLASTP_XML_2.9.0.xml +0 -1181
- data/spec/dotdir/blast_2.9.0/blastp/job.yaml +0 -8
- data/spec/dotdir/blast_2.9.0/blastx/BLASTX_XML_2.9.0.xml +0 -1181
- data/spec/dotdir/blast_2.9.0/blastx/job.yaml +0 -8
- data/spec/dotdir/blast_2.9.0/tblastn/TBLASTN_XML_2.9.0.xml +0 -1181
- data/spec/dotdir/blast_2.9.0/tblastn/job.yaml +0 -8
- data/spec/dotdir/blast_2.9.0/tblastx/TBLASTX_XML_2.9.0.xml +0 -8857
- data/spec/dotdir/blast_2.9.0/tblastx/job.yaml +0 -8
- data/spec/dotdir/diamond_0.9.24/blastp/DIAMOND_BLASTP_0.9.24.xml +0 -1040
- data/spec/dotdir/diamond_0.9.24/blastp/job.yaml +0 -8
- data/spec/dotdir/diamond_0.9.24/blastx/DIAMOND_BLASTX_0.9.24.xml +0 -1040
- data/spec/dotdir/diamond_0.9.24/blastx/job.yaml +0 -8
- data/spec/dotdir/diamond_0.9.24/blastx_nohits/DIAMOND_BLASTX_NOHITS_0.9.24.xml +0 -41
- data/spec/dotdir/diamond_0.9.24/blastx_nohits/job.yaml +0 -8
- data/spec/download_helper.rb +0 -35
- data/spec/empty_config.yml +0 -0
- data/spec/makeblastdb_spec.rb +0 -121
- data/spec/routes_spec.rb +0 -93
- data/spec/sample.conf +0 -2
- data/spec/sequence_spec.rb +0 -99
- data/spec/sequences/MH011443_1_gi_1486783306_gb_MH011443_1.txt +0 -6
- data/spec/sequences/MH011443_1_gi_1486783307_gb_AYF55702_1.txt +0 -6
- data/spec/sequences/MH011443_1_gi_1528997474_gb_MH447967_1.txt +0 -30
- data/spec/sequences/MH011443_1_sp_P04637_P53_HUMAN.txt +0 -6
- data/spec/sequences/Nucleotide_TP53_COX41.fasta +0 -15
- data/spec/sequences/Protein_TP53_COX41.fasta +0 -12
- data/spec/sequences/Query_1_SI2_2_0_06267.txt +0 -6
- data/spec/sequences/alignment-2_hits.txt +0 -12
- data/spec/sequences/alignment-35_hits_diamond_blastp.txt +0 -210
- data/spec/sequences/alignment-35_hits_diamond_blastx.txt +0 -210
- data/spec/sequences/alignment-3_hits.txt +0 -18
- data/spec/sequences/alignment-40_hits_blastn.txt +0 -246
- data/spec/sequences/alignment-40_hits_blastp.txt +0 -240
- data/spec/sequences/alignment-40_hits_blastp_2.2.30.txt +0 -240
- data/spec/sequences/alignment-40_hits_blastx.txt +0 -240
- data/spec/sequences/alignment-40_hits_tblastn.txt +0 -240
- data/spec/sequences/alignment-40_hits_tblastn_2.2.30.txt +0 -240
- data/spec/sequences/alignment-40_hits_tblastx.txt +0 -2664
- data/spec/sequences/alignment-4_hits.txt +0 -24
- data/spec/sequences/alignment-4_hits_blastn.txt +0 -24
- data/spec/sequences/alignment-4_hits_blastp.txt +0 -24
- data/spec/sequences/alignment-4_hits_blastp_2.2.30.txt +0 -24
- data/spec/sequences/alignment-4_hits_blastx.txt +0 -24
- data/spec/sequences/alignment-4_hits_diamond_blastp.txt +0 -24
- data/spec/sequences/alignment-4_hits_diamond_blastx.txt +0 -24
- data/spec/sequences/alignment-4_hits_tblastn.txt +0 -24
- data/spec/sequences/alignment-4_hits_tblastn_2.2.30.txt +0 -24
- 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
@@ -1,228 +0,0 @@
|
|
1
|
-
require 'spec_helper'
|
2
|
-
|
3
|
-
# Test BLAST module.
|
4
|
-
module SequenceServer
|
5
|
-
with_hits = Job.fetch('blast_2.5.0/blastn')
|
6
|
-
no_hits = Job.fetch('blast_2.5.0/blastn_nohits')
|
7
|
-
|
8
|
-
init
|
9
|
-
|
10
|
-
describe 'Report' do
|
11
|
-
hits_report = BLAST::Report.new(with_hits)
|
12
|
-
no_hits_report = BLAST::Report.new(no_hits)
|
13
|
-
|
14
|
-
it 'will return an Array of queries' do
|
15
|
-
hits_report.queries.should be_a Array
|
16
|
-
no_hits_report.queries.should be_a Array
|
17
|
-
end
|
18
|
-
|
19
|
-
it 'will return a Hash of stats' do
|
20
|
-
hits_report.stats.should be_a Hash
|
21
|
-
no_hits_report.stats.should be_a Hash
|
22
|
-
end
|
23
|
-
|
24
|
-
it 'contains all the necessary stats' do
|
25
|
-
hits_report.stats.length.should eql(7)
|
26
|
-
no_hits_report.stats.length.should eql(7)
|
27
|
-
end
|
28
|
-
end
|
29
|
-
|
30
|
-
describe 'Query' do
|
31
|
-
hits_report = BLAST::Report.new(with_hits)
|
32
|
-
no_hits_report = BLAST::Report.new(no_hits)
|
33
|
-
|
34
|
-
it 'will return queries with valid length' do
|
35
|
-
hits_report.queries.first.length.should be_a Integer
|
36
|
-
hits_report.queries.first.length.should satisfy { |n| n > 0 }
|
37
|
-
no_hits_report.queries.first.length.should be_a Integer
|
38
|
-
no_hits_report.queries.first.length.should satisfy { |n| n > 0 }
|
39
|
-
end
|
40
|
-
|
41
|
-
it 'will return an Array of hits' do
|
42
|
-
hits_report.queries.first.hits.should be_a Array
|
43
|
-
no_hits_report.queries.first.hits.should be_a Array
|
44
|
-
end
|
45
|
-
end
|
46
|
-
|
47
|
-
describe 'Hits' do
|
48
|
-
hits_report = BLAST::Report.new(with_hits)
|
49
|
-
no_hits_report = BLAST::Report.new(no_hits)
|
50
|
-
|
51
|
-
it 'will have non zero length' do
|
52
|
-
hits_report.queries.last.hits.first.length.should satisfy { |n| n > 0 }
|
53
|
-
end
|
54
|
-
|
55
|
-
it 'will return an Array of HSPs' do
|
56
|
-
hits_report.queries.first.hits.first.hsps.should be_a Array
|
57
|
-
end
|
58
|
-
|
59
|
-
it 'will return an Array with atleast one HSP' do
|
60
|
-
hits_report.queries.first.hits.first.hsps.length.should be >= 1
|
61
|
-
end
|
62
|
-
|
63
|
-
it 'will contain no element if no hits were obtained' do
|
64
|
-
no_hits_report.queries.first.hits.length.should eql(0)
|
65
|
-
end
|
66
|
-
end
|
67
|
-
|
68
|
-
# Test general features of HSPs. Algorithm specific customizations are
|
69
|
-
# tested separetly.
|
70
|
-
describe 'HSPs' do
|
71
|
-
hits_report = BLAST::Report.new(with_hits)
|
72
|
-
|
73
|
-
# Currently using all 17 HSP parameters in BLAST Report + 1 to refer to the
|
74
|
-
# hit object it belongs to.
|
75
|
-
it 'have all the necessary values' do
|
76
|
-
hits_report.queries.last.hits.first.hsps.last.count.should eql(19)
|
77
|
-
end
|
78
|
-
|
79
|
-
# Test Random HSPs to ensure that all the values from HSP struct are valid.
|
80
|
-
it 'have correct alignment values' do
|
81
|
-
hits_report.queries.last.hits.first.hsps.last.bit_score.should be_a Float
|
82
|
-
hits_report.queries.last.hits.first.hsps.last.score.should be_a Integer
|
83
|
-
|
84
|
-
hits_report.queries.first.hits.first.hsps.first.evalue.should be_a Float
|
85
|
-
hits_report.queries.first.hits.first.hsps.first.evalue
|
86
|
-
.should_not satisfy { |n| n < 0 }
|
87
|
-
|
88
|
-
hits_report.queries.first.hits.last.hsps.first.qstart.should be_a Integer
|
89
|
-
hits_report.queries.first.hits.last.hsps.first.qstart
|
90
|
-
.should_not satisfy { |n| n < 0 }
|
91
|
-
|
92
|
-
hits_report.queries.first.hits.last.hsps.first.qend.should be_a Integer
|
93
|
-
hits_report.queries.first.hits.last.hsps.first.qend
|
94
|
-
.should_not satisfy { |n| n < 0 }
|
95
|
-
|
96
|
-
hits_report.queries.last.hits.last.hsps.last.sstart.should be_a Integer
|
97
|
-
hits_report.queries.last.hits.last.hsps.last.sstart
|
98
|
-
.should_not satisfy { |n| n < 0 }
|
99
|
-
|
100
|
-
hits_report.queries.first.hits.first.hsps.last.send.should be_a Integer
|
101
|
-
hits_report.queries.first.hits.first.hsps.last.send
|
102
|
-
.should_not satisfy { |n| n < 0 }
|
103
|
-
|
104
|
-
hits_report.queries.first.hits.first.hsps.last.qframe.should be_a Integer
|
105
|
-
hits_report.queries.first.hits.first.hsps.last.sframe.should be_a Integer
|
106
|
-
|
107
|
-
hits_report.queries.first.hits.first.hsps.last.identity.should be_a Integer
|
108
|
-
hits_report.queries.first.hits.first.hsps.last.identity
|
109
|
-
.should_not satisfy { |n| n < 0 }
|
110
|
-
|
111
|
-
hits_report.queries.first.hits.first.hsps.last.gaps.should be_a Integer
|
112
|
-
hits_report.queries.first.hits.first.hsps.last.gaps
|
113
|
-
.should_not satisfy { |n| n < 0 }
|
114
|
-
|
115
|
-
hits_report.queries.first.hits.first.hsps.last.positives
|
116
|
-
.should be_a Integer
|
117
|
-
hits_report.queries.first.hits.first.hsps.last.positives
|
118
|
-
.should_not satisfy { |n| n < 0 }
|
119
|
-
|
120
|
-
hits_report.queries.first.hits.first.hsps.last.length.should be_a Integer
|
121
|
-
hits_report.queries.first.hits.first.hsps.last.length
|
122
|
-
.should satisfy { |n| n > 0 }
|
123
|
-
|
124
|
-
hits_report.queries.last.hits.last.hsps.first.qseq.should be_a String
|
125
|
-
hits_report.queries.last.hits.last.hsps.first.sseq.should be_a String
|
126
|
-
hits_report.queries.last.hits.last.hsps.first.midline.should be_a String
|
127
|
-
end
|
128
|
-
|
129
|
-
it 'have correctly matched query, hit and midline alignments' do
|
130
|
-
hsp = hits_report.queries.last.hits.last.hsps.first
|
131
|
-
hsp.qseq.length.should eql(hsp.sseq.length)
|
132
|
-
hsp.sseq.length.should eql(hsp.midline.length)
|
133
|
-
hsp.midline.length.should eql(hsp.qseq.length)
|
134
|
-
end
|
135
|
-
end
|
136
|
-
|
137
|
-
# Individually test different BLAST+ algorithms
|
138
|
-
#
|
139
|
-
describe 'BLASTN' do
|
140
|
-
let 'hsp' do
|
141
|
-
report = BLAST::Report.new(Job.fetch('blast_2.5.0/blastn'))
|
142
|
-
report.queries.first.hits.last.hsps.first
|
143
|
-
end
|
144
|
-
|
145
|
-
it 'have correct query and subject frame' do
|
146
|
-
[1, -1].should include(hsp.qframe)
|
147
|
-
[1, -1].should include(hsp.sframe)
|
148
|
-
end
|
149
|
-
|
150
|
-
it 'have correct qstart, qend, sstart, send' do
|
151
|
-
if hsp.sframe > 0
|
152
|
-
hsp.sstart.should be <= hsp.send
|
153
|
-
else
|
154
|
-
hsp.sstart.should be >= hsp.send
|
155
|
-
end
|
156
|
-
end
|
157
|
-
end
|
158
|
-
|
159
|
-
describe 'BLASTP' do
|
160
|
-
let 'hsp' do
|
161
|
-
report = BLAST::Report.new(Job.fetch('blast_2.5.0/blastp'))
|
162
|
-
report.queries.first.hits.last.hsps.first
|
163
|
-
end
|
164
|
-
|
165
|
-
it 'have correct query and subject frame' do
|
166
|
-
hsp.qframe.should eql(0)
|
167
|
-
hsp.sframe.should eql(0)
|
168
|
-
end
|
169
|
-
|
170
|
-
it 'have correct qstart, qend, sstart, send values' do
|
171
|
-
hsp.qstart.should be <= hsp.qend
|
172
|
-
hsp.sstart.should be <= hsp.send
|
173
|
-
end
|
174
|
-
|
175
|
-
end
|
176
|
-
|
177
|
-
describe 'BLASTX' do
|
178
|
-
let 'hsp' do
|
179
|
-
report = BLAST::Report.new(Job.fetch('blast_2.5.0/blastx'))
|
180
|
-
|
181
|
-
report.queries.first.hits.last.hsps.first
|
182
|
-
end
|
183
|
-
|
184
|
-
it 'have correct query and subject frame' do
|
185
|
-
hsp.qframe.should_not eql(0)
|
186
|
-
hsp.sframe.should eql(0)
|
187
|
-
end
|
188
|
-
|
189
|
-
it 'have correct qstart, qend, sstart, send' do
|
190
|
-
hsp.qstart.should be <= hsp.qend
|
191
|
-
hsp.sstart.should be <= hsp.send
|
192
|
-
end
|
193
|
-
end
|
194
|
-
|
195
|
-
describe 'TBLASTX' do
|
196
|
-
let 'hsp' do
|
197
|
-
report = BLAST::Report.new(Job.fetch('blast_2.5.0/tblastx'))
|
198
|
-
report.queries.first.hits.last.hsps.first
|
199
|
-
end
|
200
|
-
|
201
|
-
it 'have correct query and subject frame' do
|
202
|
-
hsp.qframe.should_not eql(0)
|
203
|
-
hsp.sframe.should_not eql(0)
|
204
|
-
end
|
205
|
-
|
206
|
-
it 'have correct qstart, qend, sstart, send' do
|
207
|
-
hsp.qstart.should be <= hsp.qend
|
208
|
-
hsp.sstart.should be <= hsp.send
|
209
|
-
end
|
210
|
-
end
|
211
|
-
|
212
|
-
describe 'TBLASTN' do
|
213
|
-
let 'hsp' do
|
214
|
-
report = BLAST::Report.new(Job.fetch('blast_2.5.0/tblastn'))
|
215
|
-
report.queries.first.hits.last.hsps.first
|
216
|
-
end
|
217
|
-
|
218
|
-
it 'have correct query and subject frame' do
|
219
|
-
hsp.qframe.should eql(0)
|
220
|
-
hsp.sframe.should_not eql(0)
|
221
|
-
end
|
222
|
-
|
223
|
-
it 'have correct qstart, qend, sstart, send' do
|
224
|
-
hsp.qstart.should be <= hsp.qend
|
225
|
-
hsp.sstart.should be <= hsp.send
|
226
|
-
end
|
227
|
-
end
|
228
|
-
end
|
@@ -1,587 +0,0 @@
|
|
1
|
-
describe 'report generated from imported XML', type: :feature, js: true do
|
2
|
-
# Test suite to test features of imported XML report. Fasta files used for
|
3
|
-
# testing consist of TP53 and COX41 protein/nucleotide sequences for
|
4
|
-
# reproducibility. Each query was limited to 20 hits to not to overload the
|
5
|
-
# test suite.
|
6
|
-
|
7
|
-
# BLASTP test scenarios
|
8
|
-
it 'loads BLASTP XML and tests hit alignment and sidebar Alignment download' do
|
9
|
-
access_by_uuid('blast_2.5.0/blastp')
|
10
|
-
|
11
|
-
# Click on the first hit Alignment download button on the page and wait for
|
12
|
-
# the download to finish.
|
13
|
-
|
14
|
-
page.execute_script("$('.download-aln:eq(0)').click()")
|
15
|
-
wait_for_download
|
16
|
-
|
17
|
-
expect(File.basename(downloaded_file)).to eq('sp_P04637_P53_HUMAN_gi_1099170394_ref_XP_018868681_1.txt')
|
18
|
-
expect(File.read(downloaded_file)).to eq(File.read('spec/sequences/sp_P04637_P53_HUMAN_gi_1099170394_ref_XP_018868681_1.txt'))
|
19
|
-
|
20
|
-
clear_downloads
|
21
|
-
|
22
|
-
# Click on the Alignment of all hits download and compare the downloaded
|
23
|
-
# content
|
24
|
-
|
25
|
-
page.click_link('Alignment of all hits')
|
26
|
-
wait_for_download
|
27
|
-
|
28
|
-
expect(File.basename(downloaded_file)).to eq('alignment-40_hits.txt')
|
29
|
-
expect(File.read(downloaded_file)).to eq(File.read('spec/sequences/alignment-40_hits_blastp.txt'))
|
30
|
-
|
31
|
-
clear_downloads
|
32
|
-
|
33
|
-
# Check the cheboxes of indicted hits and click on the download of Alignment
|
34
|
-
# of selected hits and compare the downloaded content
|
35
|
-
|
36
|
-
page.check('Query_1_hit_1_checkbox')
|
37
|
-
page.check('Query_1_hit_2_checkbox')
|
38
|
-
page.check('Query_2_hit_1_checkbox')
|
39
|
-
page.check('Query_2_hit_2_checkbox')
|
40
|
-
page.click_link('Alignment of 4 selected hit(s)')
|
41
|
-
wait_for_download
|
42
|
-
|
43
|
-
expect(File.basename(downloaded_file)).to eq('alignment-4_hits.txt')
|
44
|
-
expect(File.read(downloaded_file)).to eq(File.read('spec/sequences/alignment-4_hits_blastp.txt'))
|
45
|
-
end
|
46
|
-
|
47
|
-
it 'loads BLASTP XML and tests alignment overview and hit PNG/SVG download' do
|
48
|
-
access_by_uuid('blast_2.5.0/blastp')
|
49
|
-
|
50
|
-
# Click on the PNG/SVG download button of the alignment overview and compare
|
51
|
-
# the downloaded content.
|
52
|
-
|
53
|
-
page.execute_script("$('.export-to-png:eq(0)').click()")
|
54
|
-
wait_for_download
|
55
|
-
expect(File.basename(downloaded_file)).to eq('Alignment-Overview-sp_P04637_P53_HUMAN.png')
|
56
|
-
|
57
|
-
clear_downloads
|
58
|
-
|
59
|
-
page.execute_script("$('.export-to-svg:eq(0)').click()")
|
60
|
-
wait_for_download
|
61
|
-
expect(File.basename(downloaded_file)).to eq('Alignment-Overview-sp_P04637_P53_HUMAN.svg')
|
62
|
-
|
63
|
-
clear_downloads
|
64
|
-
|
65
|
-
# Click on the PNG/SVG download button of the first hit available and
|
66
|
-
# compare the downloaded content.
|
67
|
-
|
68
|
-
page.execute_script("$('.export-to-png:eq(1)').click()")
|
69
|
-
wait_for_download
|
70
|
-
expect(File.basename(downloaded_file)).to eq('Kablammo-sp_P04637_P53_HUMAN-gi_1099170394_ref_XP_018868681_1.png')
|
71
|
-
|
72
|
-
clear_downloads
|
73
|
-
|
74
|
-
page.execute_script("$('.export-to-svg:eq(1)').click()")
|
75
|
-
wait_for_download
|
76
|
-
expect(File.basename(downloaded_file)).to eq('Kablammo-sp_P04637_P53_HUMAN-gi_1099170394_ref_XP_018868681_1.svg')
|
77
|
-
page.should have_content('BLASTP')
|
78
|
-
end
|
79
|
-
|
80
|
-
it 'loads BLASTP XML and tests Circos download' do
|
81
|
-
access_by_uuid('blast_2.5.0/blastp')
|
82
|
-
|
83
|
-
# Click on the Circos expanding button, wait for animation, click on the
|
84
|
-
# download of PNG/SVG file and test that it initiated a file download in a
|
85
|
-
# right format.
|
86
|
-
|
87
|
-
page.should have_content('Queries and their top hits: chord diagram')
|
88
|
-
page.execute_script("$('.circos > .grapher-header > h4').click()")
|
89
|
-
sleep 1
|
90
|
-
|
91
|
-
page.execute_script("$('.export-to-png:eq(0)').click()")
|
92
|
-
wait_for_download
|
93
|
-
expect(File.basename(downloaded_file)).to eq('Circos-visualisation.png')
|
94
|
-
|
95
|
-
clear_downloads
|
96
|
-
|
97
|
-
page.execute_script("$('.export-to-svg:eq(0)').click()")
|
98
|
-
wait_for_download
|
99
|
-
expect(File.basename(downloaded_file)).to eq('Circos-visualisation.svg')
|
100
|
-
end
|
101
|
-
|
102
|
-
it 'loads BLASTP XML and tests Length distribution download' do
|
103
|
-
access_by_uuid('blast_2.5.0/blastp')
|
104
|
-
|
105
|
-
# Click on the Length distribution expanding button, wait for animation,
|
106
|
-
# click on the download of PNG/SVG file and test that it initiated a file
|
107
|
-
# download in a right format.
|
108
|
-
|
109
|
-
page.should have_content('Length distribution of hits')
|
110
|
-
page.execute_script("$('.length-distribution > .grapher-header > h4').click()")
|
111
|
-
sleep 1
|
112
|
-
|
113
|
-
page.execute_script("$('.export-to-png:eq(1)').click()")
|
114
|
-
wait_for_download
|
115
|
-
expect(File.basename(downloaded_file)).to eq('length-distribution-sp_P04637_P53_HUMAN.png')
|
116
|
-
|
117
|
-
clear_downloads
|
118
|
-
|
119
|
-
page.execute_script("$('.export-to-svg:eq(1)').click()")
|
120
|
-
wait_for_download
|
121
|
-
expect(File.basename(downloaded_file)).to eq('length-distribution-sp_P04637_P53_HUMAN.svg')
|
122
|
-
end
|
123
|
-
|
124
|
-
# BLASTX test scenarios
|
125
|
-
|
126
|
-
it 'loads BLASTX XML and tests hit alignment and sidebar Alignment download' do
|
127
|
-
access_by_uuid('blast_2.5.0/blastx')
|
128
|
-
|
129
|
-
# Click on the first Alignment download button on the page and wait for the
|
130
|
-
# download to finish.
|
131
|
-
|
132
|
-
page.execute_script("$('.download-aln:eq(0)').click()")
|
133
|
-
wait_for_download
|
134
|
-
|
135
|
-
expect(File.basename(downloaded_file)).to eq('MH011443_1_gi_1486783307_gb_AYF55702_1.txt')
|
136
|
-
expect(File.read(downloaded_file)).to eq(File.read('spec/sequences/MH011443_1_gi_1486783307_gb_AYF55702_1.txt'))
|
137
|
-
|
138
|
-
clear_downloads
|
139
|
-
|
140
|
-
# Click on the Alignment of all hits download and compare the downloaded
|
141
|
-
# content
|
142
|
-
|
143
|
-
page.click_link('Alignment of all hits')
|
144
|
-
wait_for_download
|
145
|
-
expect(File.basename(downloaded_file)).to eq('alignment-40_hits.txt')
|
146
|
-
expect(File.read(downloaded_file)).to eq(File.read('spec/sequences/alignment-40_hits_blastx.txt'))
|
147
|
-
|
148
|
-
clear_downloads
|
149
|
-
|
150
|
-
# Select four hit checkboxes and click on the Alignment of selected hits.
|
151
|
-
# Compare the downloaded content.
|
152
|
-
|
153
|
-
page.check('Query_1_hit_3_checkbox')
|
154
|
-
page.check('Query_1_hit_4_checkbox')
|
155
|
-
page.check('Query_2_hit_3_checkbox')
|
156
|
-
page.check('Query_2_hit_4_checkbox')
|
157
|
-
page.click_link('Alignment of 4 selected hit(s)')
|
158
|
-
wait_for_download
|
159
|
-
|
160
|
-
expect(File.basename(downloaded_file)).to eq('alignment-4_hits.txt')
|
161
|
-
expect(File.read(downloaded_file)).to eq(File.read('spec/sequences/alignment-4_hits_blastx.txt'))
|
162
|
-
|
163
|
-
page.should have_content('BLASTX')
|
164
|
-
end
|
165
|
-
|
166
|
-
it 'loads BLASTX XML and tests hit PNG/SVG download' do
|
167
|
-
access_by_uuid('blast_2.5.0/blastx')
|
168
|
-
|
169
|
-
# Click on the PNG/SVG download button of the alignment overview and compare
|
170
|
-
# the downloaded content.
|
171
|
-
page.execute_script("$('.export-to-png:eq(0)').click()")
|
172
|
-
wait_for_download
|
173
|
-
expect(File.basename(downloaded_file)).to eq('Alignment-Overview-MH011443_1.png')
|
174
|
-
|
175
|
-
clear_downloads
|
176
|
-
|
177
|
-
page.execute_script("$('.export-to-svg:eq(0)').click()")
|
178
|
-
wait_for_download
|
179
|
-
expect(File.basename(downloaded_file)).to eq('Alignment-Overview-MH011443_1.svg')
|
180
|
-
|
181
|
-
clear_downloads
|
182
|
-
|
183
|
-
# Click on the PNG/SVG download button of the first hit available and
|
184
|
-
# compare the downloaded content.
|
185
|
-
page.execute_script("$('.export-to-png:eq(1)').click()")
|
186
|
-
wait_for_download
|
187
|
-
expect(File.basename(downloaded_file)).to eq('Kablammo-MH011443_1-gi_1486783307_gb_AYF55702_1.png')
|
188
|
-
|
189
|
-
clear_downloads
|
190
|
-
|
191
|
-
page.execute_script("$('.export-to-svg:eq(1)').click()")
|
192
|
-
wait_for_download
|
193
|
-
expect(File.basename(downloaded_file)).to eq('Kablammo-MH011443_1-gi_1486783307_gb_AYF55702_1.svg')
|
194
|
-
page.should have_content('BLASTX')
|
195
|
-
end
|
196
|
-
|
197
|
-
it 'loads BLASTX XML and tests Circos download' do
|
198
|
-
access_by_uuid('blast_2.5.0/blastx')
|
199
|
-
# Click on the Circos expanding button, wait for animation, click on the
|
200
|
-
# download of PNG/SVG file and test that it initiated a file download in a
|
201
|
-
# right format.
|
202
|
-
|
203
|
-
page.should have_content('Queries and their top hits: chord diagram')
|
204
|
-
page.execute_script("$('.circos > .grapher-header > h4').click()")
|
205
|
-
sleep 1
|
206
|
-
|
207
|
-
page.execute_script("$('.export-to-png:eq(0)').click()")
|
208
|
-
wait_for_download
|
209
|
-
expect(File.basename(downloaded_file)).to eq('Circos-visualisation.png')
|
210
|
-
clear_downloads
|
211
|
-
|
212
|
-
page.execute_script("$('.export-to-svg:eq(0)').click()")
|
213
|
-
wait_for_download
|
214
|
-
expect(File.basename(downloaded_file)).to eq('Circos-visualisation.svg')
|
215
|
-
end
|
216
|
-
|
217
|
-
it 'loads BLASTX XML and tests Length distribution download' do
|
218
|
-
access_by_uuid('blast_2.5.0/blastx')
|
219
|
-
# Click on the Length distribution expanding button, wait for animation,
|
220
|
-
# click on the download of PNG/SVG file and test that it initiated a file
|
221
|
-
# download in a right format.
|
222
|
-
|
223
|
-
page.should have_content('Length distribution of hits')
|
224
|
-
page.execute_script("$('.length-distribution > .grapher-header > h4').click()")
|
225
|
-
sleep 1
|
226
|
-
|
227
|
-
page.execute_script("$('.export-to-png:eq(1)').click()")
|
228
|
-
wait_for_download
|
229
|
-
expect(File.basename(downloaded_file)).to eq('length-distribution-MH011443_1.png')
|
230
|
-
|
231
|
-
clear_downloads
|
232
|
-
|
233
|
-
page.execute_script("$('.export-to-svg:eq(1)').click()")
|
234
|
-
wait_for_download
|
235
|
-
expect(File.basename(downloaded_file)).to eq('length-distribution-MH011443_1.svg')
|
236
|
-
end
|
237
|
-
|
238
|
-
# BLASTN Test scenarios
|
239
|
-
|
240
|
-
it 'loads BLASTN XML and tests hit alignment and sidebar Alignment download' do
|
241
|
-
access_by_uuid('blast_2.5.0/blastn')
|
242
|
-
# Click on the first Alignment download button on the page and wait for the
|
243
|
-
# download to finish.
|
244
|
-
|
245
|
-
page.execute_script("$('.download-aln:eq(0)').click()")
|
246
|
-
wait_for_download
|
247
|
-
expect(File.basename(downloaded_file)).to eq('MH011443_1_gi_1486783306_gb_MH011443_1.txt')
|
248
|
-
expect(File.read(downloaded_file)).to eq(File.read('spec/sequences/MH011443_1_gi_1486783306_gb_MH011443_1.txt'))
|
249
|
-
|
250
|
-
clear_downloads
|
251
|
-
|
252
|
-
# Click on the Alignment of all hits download and compare the downloaded
|
253
|
-
# content
|
254
|
-
|
255
|
-
page.click_link('Alignment of all hits')
|
256
|
-
wait_for_download
|
257
|
-
expect(File.basename(downloaded_file)).to eq('alignment-40_hits.txt')
|
258
|
-
expect(File.read(downloaded_file)).to eq(File.read('spec/sequences/alignment-40_hits_blastn.txt'))
|
259
|
-
|
260
|
-
clear_downloads
|
261
|
-
|
262
|
-
# Select four hit checkboxes and click on the Alignment of selected hits.
|
263
|
-
# Compare the downloaded content.
|
264
|
-
page.check('Query_1_hit_5_checkbox')
|
265
|
-
page.check('Query_1_hit_6_checkbox')
|
266
|
-
page.check('Query_2_hit_5_checkbox')
|
267
|
-
page.check('Query_2_hit_6_checkbox')
|
268
|
-
page.click_link('Alignment of 4 selected hit(s)')
|
269
|
-
wait_for_download
|
270
|
-
|
271
|
-
expect(File.basename(downloaded_file)).to eq('alignment-4_hits.txt')
|
272
|
-
expect(File.read(downloaded_file)).to eq(File.read('spec/sequences/alignment-4_hits_blastn.txt'))
|
273
|
-
page.should have_content('BLASTN')
|
274
|
-
end
|
275
|
-
|
276
|
-
it 'loads BLASTN XML and tests hit PNG/SVG download' do
|
277
|
-
access_by_uuid('blast_2.5.0/blastn')
|
278
|
-
|
279
|
-
# Click on the PNG/SVG download button of the alignment overview and compare
|
280
|
-
# the downloaded content.
|
281
|
-
page.execute_script("$('.export-to-png:eq(0)').click()")
|
282
|
-
wait_for_download
|
283
|
-
expect(File.basename(downloaded_file)).to eq('Alignment-Overview-MH011443_1.png')
|
284
|
-
|
285
|
-
clear_downloads
|
286
|
-
|
287
|
-
page.execute_script("$('.export-to-svg:eq(0)').click()")
|
288
|
-
wait_for_download
|
289
|
-
expect(File.basename(downloaded_file)).to eq('Alignment-Overview-MH011443_1.svg')
|
290
|
-
|
291
|
-
clear_downloads
|
292
|
-
# Click on the PNG download button of the first hit available and compare
|
293
|
-
# the downloaded content.
|
294
|
-
|
295
|
-
page.execute_script("$('.export-to-png:eq(2)').click()")
|
296
|
-
wait_for_download
|
297
|
-
expect(File.basename(downloaded_file)).to eq('Kablammo-MH011443_1-gi_1528997474_gb_MH447967_1.png')
|
298
|
-
|
299
|
-
clear_downloads
|
300
|
-
|
301
|
-
# Click on the SVG download button of the first hit available and compare
|
302
|
-
# the downloaded content.
|
303
|
-
|
304
|
-
page.execute_script("$('.export-to-svg:eq(2)').click()")
|
305
|
-
wait_for_download
|
306
|
-
expect(File.basename(downloaded_file)).to eq('Kablammo-MH011443_1-gi_1528997474_gb_MH447967_1.svg')
|
307
|
-
page.should have_content('BLASTN')
|
308
|
-
end
|
309
|
-
|
310
|
-
it 'loads BLASTN XML and tests Circos download' do
|
311
|
-
access_by_uuid('blast_2.5.0/blastn')
|
312
|
-
|
313
|
-
# Click on the Circos expanding button, wait for animation, click on the
|
314
|
-
# download of PNG/SVG file and test that it initiated a file download in a
|
315
|
-
# right format.
|
316
|
-
|
317
|
-
page.should have_content('Queries and their top hits: chord diagram')
|
318
|
-
page.execute_script("$('.circos > .grapher-header > h4').click()")
|
319
|
-
sleep 1
|
320
|
-
|
321
|
-
page.execute_script("$('.export-to-png:eq(0)').click()")
|
322
|
-
wait_for_download
|
323
|
-
expect(File.basename(downloaded_file)).to eq('Circos-visualisation.png')
|
324
|
-
clear_downloads
|
325
|
-
|
326
|
-
page.execute_script("$('.export-to-svg:eq(0)').click()")
|
327
|
-
wait_for_download
|
328
|
-
expect(File.basename(downloaded_file)).to eq('Circos-visualisation.svg')
|
329
|
-
end
|
330
|
-
|
331
|
-
it 'loads BLASTN XML and tests Length distribution download' do
|
332
|
-
access_by_uuid('blast_2.5.0/blastn')
|
333
|
-
# Click on the Length distribution expanding button, wait for animation,
|
334
|
-
# click on the download of PNG/SVG file and test that it initiated a file
|
335
|
-
# download in a right format.
|
336
|
-
|
337
|
-
page.should have_content('Length distribution of hits')
|
338
|
-
page.execute_script("$('.length-distribution > .grapher-header > h4').click()")
|
339
|
-
sleep 1
|
340
|
-
|
341
|
-
page.execute_script("$('.export-to-png:eq(1)').click()")
|
342
|
-
wait_for_download
|
343
|
-
expect(File.basename(downloaded_file)).to eq('length-distribution-MH011443_1.png')
|
344
|
-
clear_downloads
|
345
|
-
|
346
|
-
page.execute_script("$('.export-to-svg:eq(1)').click()")
|
347
|
-
wait_for_download
|
348
|
-
expect(File.basename(downloaded_file)).to eq('length-distribution-MH011443_1.svg')
|
349
|
-
end
|
350
|
-
|
351
|
-
# TBLASTN Test scenarios
|
352
|
-
|
353
|
-
it 'loads TBLASTN XML and tests hit alignment and sidebar Alignment download' do
|
354
|
-
access_by_uuid('blast_2.5.0/tblastn')
|
355
|
-
# Click on the first Alignment download button on the page and wait for the
|
356
|
-
# download to finish.
|
357
|
-
|
358
|
-
page.execute_script("$('.download-aln:eq(0)').click()")
|
359
|
-
wait_for_download
|
360
|
-
expect(File.basename(downloaded_file)).to eq('sp_P04637_P53_HUMAN_gi_395440626_gb_JQ694049_1.txt')
|
361
|
-
expect(File.read(downloaded_file)).to eq(File.read('spec/sequences/sp_P04637_P53_HUMAN_gi_395440626_gb_JQ694049_1.txt'))
|
362
|
-
|
363
|
-
clear_downloads
|
364
|
-
|
365
|
-
# Click on the Alignment of all hits download and compare the downloaded
|
366
|
-
# content
|
367
|
-
|
368
|
-
page.click_link('Alignment of all hits')
|
369
|
-
wait_for_download
|
370
|
-
expect(File.basename(downloaded_file)).to eq('alignment-40_hits.txt')
|
371
|
-
expect(File.read(downloaded_file)).to eq(File.read('spec/sequences/alignment-40_hits_tblastn.txt'))
|
372
|
-
|
373
|
-
clear_downloads
|
374
|
-
|
375
|
-
# Select four hit checkboxes and click on the Alignment of selected hits.
|
376
|
-
# Compare the downloaded content.
|
377
|
-
page.check('Query_1_hit_7_checkbox')
|
378
|
-
page.check('Query_1_hit_8_checkbox')
|
379
|
-
page.check('Query_2_hit_7_checkbox')
|
380
|
-
page.check('Query_2_hit_8_checkbox')
|
381
|
-
page.click_link('Alignment of 4 selected hit(s)')
|
382
|
-
wait_for_download
|
383
|
-
|
384
|
-
expect(File.basename(downloaded_file)).to eq('alignment-4_hits.txt')
|
385
|
-
expect(File.read(downloaded_file)).to eq(File.read('spec/sequences/alignment-4_hits_tblastn.txt'))
|
386
|
-
page.should have_content('TBLASTN')
|
387
|
-
end
|
388
|
-
|
389
|
-
it 'loads TBLASTN XML and tests hit PNG/SVG download' do
|
390
|
-
access_by_uuid('blast_2.5.0/tblastn')
|
391
|
-
|
392
|
-
# Click on the PNG/SVG download button of the alignment overview and compare
|
393
|
-
# the downloaded content.
|
394
|
-
page.execute_script("$('.export-to-png:eq(0)').click()")
|
395
|
-
wait_for_download
|
396
|
-
expect(File.basename(downloaded_file)).to eq('Alignment-Overview-sp_P04637_P53_HUMAN.png')
|
397
|
-
|
398
|
-
clear_downloads
|
399
|
-
|
400
|
-
page.execute_script("$('.export-to-svg:eq(0)').click()")
|
401
|
-
wait_for_download
|
402
|
-
expect(File.basename(downloaded_file)).to eq('Alignment-Overview-sp_P04637_P53_HUMAN.svg')
|
403
|
-
clear_downloads
|
404
|
-
# Click on the PNG download button of the first hit available and compare
|
405
|
-
# the downloaded content.
|
406
|
-
|
407
|
-
page.execute_script("$('.export-to-png:eq(1)').click()")
|
408
|
-
wait_for_download
|
409
|
-
expect(File.basename(downloaded_file)).to eq('Kablammo-sp_P04637_P53_HUMAN-gi_395440626_gb_JQ694049_1.png')
|
410
|
-
|
411
|
-
clear_downloads
|
412
|
-
|
413
|
-
# Click on the SVG download button of the first hit available and compare
|
414
|
-
# the downloaded content.
|
415
|
-
|
416
|
-
page.execute_script("$('.export-to-svg:eq(1)').click()")
|
417
|
-
wait_for_download
|
418
|
-
expect(File.basename(downloaded_file)).to eq('Kablammo-sp_P04637_P53_HUMAN-gi_395440626_gb_JQ694049_1.svg')
|
419
|
-
page.should have_content('TBLASTN')
|
420
|
-
end
|
421
|
-
|
422
|
-
it 'loads TBLASTN XML and tests Circos download' do
|
423
|
-
access_by_uuid('blast_2.5.0/tblastn')
|
424
|
-
# Click on the Circos expanding button, wait for animation, click on the
|
425
|
-
# download of PNG/SVG file and test that it initiated a file download in a
|
426
|
-
# right format.
|
427
|
-
|
428
|
-
page.should have_content('Queries and their top hits: chord diagram')
|
429
|
-
page.execute_script("$('.circos > .grapher-header > h4').click()")
|
430
|
-
sleep 1
|
431
|
-
|
432
|
-
page.execute_script("$('.export-to-png:eq(0)').click()")
|
433
|
-
wait_for_download
|
434
|
-
expect(File.basename(downloaded_file)).to eq('Circos-visualisation.png')
|
435
|
-
|
436
|
-
clear_downloads
|
437
|
-
|
438
|
-
page.execute_script("$('.export-to-svg:eq(0)').click()")
|
439
|
-
wait_for_download
|
440
|
-
expect(File.basename(downloaded_file)).to eq('Circos-visualisation.svg')
|
441
|
-
end
|
442
|
-
|
443
|
-
it 'loads TBLASTN XML and tests Length distribution download' do
|
444
|
-
access_by_uuid('blast_2.5.0/tblastn')
|
445
|
-
# Click on the Length distribution expanding button, wait for animation,
|
446
|
-
# click on the download of PNG/SVG file and test that it initiated a file
|
447
|
-
# download in a right format.
|
448
|
-
|
449
|
-
page.should have_content('Length distribution of hits')
|
450
|
-
page.execute_script("$('.length-distribution > .grapher-header > h4').click()")
|
451
|
-
sleep 1
|
452
|
-
|
453
|
-
page.execute_script("$('.export-to-png:eq(1)').click()")
|
454
|
-
wait_for_download
|
455
|
-
expect(File.basename(downloaded_file)).to eq('length-distribution-sp_P04637_P53_HUMAN.png')
|
456
|
-
|
457
|
-
clear_downloads
|
458
|
-
|
459
|
-
page.execute_script("$('.export-to-svg:eq(1)').click()")
|
460
|
-
wait_for_download
|
461
|
-
expect(File.basename(downloaded_file)).to eq('length-distribution-sp_P04637_P53_HUMAN.svg')
|
462
|
-
end
|
463
|
-
|
464
|
-
# TBLASTX Test scenarios
|
465
|
-
|
466
|
-
it 'loads TBLASTX XML and tests hit alignment and sidebar Alignment download' do
|
467
|
-
access_by_uuid('blast_2.5.0/tblastx')
|
468
|
-
# Click on the first Alignment download button on the page and wait for the
|
469
|
-
# download to finish.
|
470
|
-
|
471
|
-
page.execute_script("$('.download-aln:eq(1)').click()")
|
472
|
-
wait_for_download
|
473
|
-
expect(File.basename(downloaded_file)).to eq('MH011443_1_gi_1528997474_gb_MH447967_1.txt')
|
474
|
-
expect(File.read(downloaded_file)). to eq(File.read('spec/sequences/MH011443_1_gi_1528997474_gb_MH447967_1.txt'))
|
475
|
-
|
476
|
-
clear_downloads
|
477
|
-
|
478
|
-
# Click on the Alignment of all hits download and compare the downloaded
|
479
|
-
# content
|
480
|
-
|
481
|
-
page.click_link('Alignment of all hits')
|
482
|
-
wait_for_download
|
483
|
-
expect(File.basename(downloaded_file)).to eq('alignment-40_hits.txt')
|
484
|
-
expect(File.read(downloaded_file)).to eq(File.read('spec/sequences/alignment-40_hits_tblastx.txt'))
|
485
|
-
|
486
|
-
clear_downloads
|
487
|
-
|
488
|
-
# Select four hit checkboxes and click on the Alignment of selected hits.
|
489
|
-
# Compare the downloaded content.
|
490
|
-
page.check('Query_1_hit_9_checkbox')
|
491
|
-
page.check('Query_1_hit_10_checkbox')
|
492
|
-
page.check('Query_2_hit_9_checkbox')
|
493
|
-
page.check('Query_2_hit_10_checkbox')
|
494
|
-
page.click_link('Alignment of 4 selected hit(s)')
|
495
|
-
wait_for_download
|
496
|
-
|
497
|
-
expect(File.basename(downloaded_file)).to eq('alignment-4_hits.txt')
|
498
|
-
expect(File.read(downloaded_file)).to eq(File.read('spec/sequences/alignment-4_hits_tblastx.txt'))
|
499
|
-
page.should have_content('TBLASTX')
|
500
|
-
end
|
501
|
-
|
502
|
-
it 'loads TBLASTX XML and tests hit PNG/SVG download' do
|
503
|
-
access_by_uuid('blast_2.5.0/tblastx')
|
504
|
-
|
505
|
-
# Click on the PNG/SVG download button of the alignment overview and compare
|
506
|
-
# the downloaded content.
|
507
|
-
page.execute_script("$('.export-to-png:eq(0)').click()")
|
508
|
-
wait_for_download
|
509
|
-
expect(File.basename(downloaded_file)).to eq('Alignment-Overview-MH011443_1.png')
|
510
|
-
|
511
|
-
clear_downloads
|
512
|
-
|
513
|
-
page.execute_script("$('.export-to-svg:eq(0)').click()")
|
514
|
-
wait_for_download
|
515
|
-
expect(File.basename(downloaded_file)).to eq('Alignment-Overview-MH011443_1.svg')
|
516
|
-
|
517
|
-
clear_downloads
|
518
|
-
# Click on the PNG download button of the first hit available and compare
|
519
|
-
# the downloaded content.
|
520
|
-
|
521
|
-
page.execute_script("$('.export-to-png:eq(1)').click()")
|
522
|
-
wait_for_download
|
523
|
-
expect(File.basename(downloaded_file)).to eq('Kablammo-MH011443_1-gi_1486783306_gb_MH011443_1.png')
|
524
|
-
|
525
|
-
clear_downloads
|
526
|
-
|
527
|
-
# Click on the SVG download button of the first hit available and compare
|
528
|
-
# the downloaded content.
|
529
|
-
|
530
|
-
page.execute_script("$('.export-to-svg:eq(1)').click()")
|
531
|
-
wait_for_download
|
532
|
-
expect(File.basename(downloaded_file)).to eq('Kablammo-MH011443_1-gi_1486783306_gb_MH011443_1.svg')
|
533
|
-
|
534
|
-
page.should have_content('TBLASTX')
|
535
|
-
end
|
536
|
-
|
537
|
-
it 'loads TBLASTX XML and tests Circos download' do
|
538
|
-
access_by_uuid('blast_2.5.0/tblastx')
|
539
|
-
# Click on the Circos expanding button, wait for animation, click on the
|
540
|
-
# download of PNG/SVG file and test that it initiated a file download in a
|
541
|
-
# right format.
|
542
|
-
|
543
|
-
page.should have_content('Queries and their top hits: chord diagram')
|
544
|
-
page.execute_script("$('.circos > .grapher-header > h4').click()")
|
545
|
-
sleep 1
|
546
|
-
|
547
|
-
page.execute_script("$('.export-to-png:eq(0)').click()")
|
548
|
-
wait_for_download
|
549
|
-
expect(File.basename(downloaded_file)).to eq('Circos-visualisation.png')
|
550
|
-
|
551
|
-
clear_downloads
|
552
|
-
|
553
|
-
page.execute_script("$('.export-to-svg:eq(0)').click()")
|
554
|
-
wait_for_download
|
555
|
-
expect(File.basename(downloaded_file)).to eq('Circos-visualisation.svg')
|
556
|
-
end
|
557
|
-
|
558
|
-
it 'loads TBLASTX XML and tests Length distribution download' do
|
559
|
-
access_by_uuid('blast_2.5.0/tblastx')
|
560
|
-
# Click on the Length distribution expanding button, wait for animation,
|
561
|
-
# click on the download of PNG/SVG file and test that it initiated a file
|
562
|
-
# download in a right format.
|
563
|
-
|
564
|
-
page.should have_content('Length distribution of hits')
|
565
|
-
page.execute_script("$('.length-distribution > .grapher-header > h4').click()")
|
566
|
-
sleep 1
|
567
|
-
|
568
|
-
page.execute_script("$('.export-to-png:eq(1)').click()")
|
569
|
-
wait_for_download
|
570
|
-
expect(File.basename(downloaded_file)).to eq('length-distribution-MH011443_1.png')
|
571
|
-
|
572
|
-
clear_downloads
|
573
|
-
|
574
|
-
page.execute_script("$('.export-to-svg:eq(1)').click()")
|
575
|
-
wait_for_download
|
576
|
-
expect(File.basename(downloaded_file)).to eq('length-distribution-MH011443_1.svg')
|
577
|
-
end
|
578
|
-
|
579
|
-
## Helpers ##
|
580
|
-
|
581
|
-
def access_by_uuid(id)
|
582
|
-
# Method to access the XML report in the browser
|
583
|
-
url = url_encode(id)
|
584
|
-
visit "/#{url}"
|
585
|
-
page.should have_content('Query')
|
586
|
-
end
|
587
|
-
end
|