sequenceserver 2.0.0.rc3 → 2.0.0.rc8
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- checksums.yaml +4 -4
- data/bin/chromedriver +0 -0
- data/bin/geckodriver +0 -0
- data/bin/sequenceserver +39 -29
- data/lib/sequenceserver.rb +48 -22
- data/lib/sequenceserver/blast/job.rb +11 -1
- data/lib/sequenceserver/database.rb +7 -168
- data/lib/sequenceserver/exceptions.rb +14 -0
- data/lib/sequenceserver/makeblastdb.rb +323 -0
- data/lib/sequenceserver/routes.rb +6 -1
- data/lib/sequenceserver/sequence.rb +1 -1
- data/lib/sequenceserver/version.rb +1 -1
- data/public/css/sequenceserver.css +10 -3
- data/public/css/sequenceserver.min.css +1 -1
- data/public/js/error_modal.js +27 -29
- data/public/js/hit.js +14 -5
- data/public/js/jquery_world.js +1 -1
- data/public/js/query.js +31 -15
- data/public/js/report.js +13 -6
- data/public/js/search.js +44 -24
- data/public/js/sequence_modal.js +10 -5
- data/public/js/sidebar.js +52 -28
- data/public/sequenceserver-report.min.js +17 -17
- data/public/sequenceserver-search.min.js +2 -2
- data/views/layout.erb +5 -1
- data/views/report.erb +1 -1
- data/views/search.erb +1 -1
- metadata +9 -450
- data/.bootstrap/config.json +0 -433
- data/.codeclimate.yml +0 -31
- data/.csslintrc +0 -2
- 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 -23
- 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 -334
- data/spec/config_spec.rb +0 -87
- data/spec/database/funky_ids/funky_ids.fa +0 -16
- data/spec/database/funky_ids/funky_ids.fa.nhd +0 -8
- data/spec/database/funky_ids/funky_ids.fa.nhi +0 -0
- data/spec/database/funky_ids/funky_ids.fa.nhr +0 -0
- data/spec/database/funky_ids/funky_ids.fa.nin +0 -0
- data/spec/database/funky_ids/funky_ids.fa.nog +0 -0
- data/spec/database/funky_ids/funky_ids.fa.nsd +0 -15
- data/spec/database/funky_ids/funky_ids.fa.nsi +0 -0
- data/spec/database/funky_ids/funky_ids.fa.nsq +0 -0
- data/spec/database/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.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.nsd +0 -16
- data/spec/database/sample/genome/Solenopsis_invicta/Solenopsis_invicta_gnG_subset.fasta.nsi +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.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.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.psd +0 -2378
- data/spec/database/sample/proteins/Solenopsis_invicta/Sinvicta2-2-3.prot.subset.fasta.psi +0 -0
- data/spec/database/sample/proteins/Solenopsis_invicta/Sinvicta2-2-3.prot.subset.fasta.psq +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.psd +0 -18280
- data/spec/database/sample/proteins/uniprot/2018-04-Swiss-Prot_insecta.fasta.psi +0 -0
- data/spec/database/sample/proteins/uniprot/2018-04-Swiss-Prot_insecta.fasta.psq +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.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.nsd +0 -946
- data/spec/database/sample/transcripts/Solenopsis_invicta/Sinvicta2-2-3.cdna.subset.fasta.nsi +0 -0
- data/spec/database/sample/transcripts/Solenopsis_invicta/Sinvicta2-2-3.cdna.subset.fasta.nsq +0 -0
- data/spec/database/unformatted/Cardiocondyla_obscurior/Cobs1.4.proteins.fa +0 -148303
- 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 -127
- 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/routes_spec.rb +0 -93
- data/spec/sample.conf +0 -2
- data/spec/sequence_spec.rb +0 -100
- 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
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describe 'report generated from imported XML', type: :feature, js: true do
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# Test suite to test features of imported XML report. Fasta files used for
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# testing consist of TP53 and COX41 protein/nucleotide sequences for
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# reproducibility. Each query was limited to 20 hits to not to overload the
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# test suite. BLAST 2.2.30 displays hits in a different order than versions
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# 2.2.31 upwards for protein queries (BLASTP, TBLASTN), hence the test takes
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# different files for comparison.
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it 'loads BLASTP XML and tests hit alignment and sidebar Alignment download' do
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access_by_uuid('blast_2.2.30/blastp')
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# Click on the first hit Alignment download button on the page and wait for
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# the 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_gi_120407068_ref_NP_000537_3.txt')
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expect(File.read(downloaded_file)).to eq(File.read('spec/sequences/sp_P04637_P53_HUMAN_gi_120407068_ref_NP_000537_3.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-40_hits.txt')
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expect(File.read(downloaded_file)).to eq(File.read('spec/sequences/alignment-40_hits_blastp_2.2.30.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_blastp_2.2.30.txt'))
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end
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it 'loads BLASTP XML and tests alignment overiview and hit PNG/SVG download' do
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access_by_uuid('blast_2.2.30/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-gi_120407068_ref_NP_000537_3.png')
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70
|
-
clear_downloads
|
|
71
|
-
|
|
72
|
-
page.execute_script("$('.export-to-svg:eq(1)').click()")
|
|
73
|
-
wait_for_download
|
|
74
|
-
expect(File.basename(downloaded_file)).to eq('Kablammo-sp_P04637_P53_HUMAN-gi_120407068_ref_NP_000537_3.svg')
|
|
75
|
-
page.should have_content('BLASTP')
|
|
76
|
-
end
|
|
77
|
-
|
|
78
|
-
it 'loads BLASTP XML and tests Circos download' do
|
|
79
|
-
access_by_uuid('blast_2.2.30/blastp')
|
|
80
|
-
|
|
81
|
-
# Click on the Circos expanding button, wait for animation, click on the
|
|
82
|
-
# download of PNG/SVG file and test that it initiated a file download in a
|
|
83
|
-
# right format.
|
|
84
|
-
page.should have_content('Queries and their top hits: chord diagram')
|
|
85
|
-
page.execute_script("$('.circos > .grapher-header > h5').click()")
|
|
86
|
-
sleep 1
|
|
87
|
-
|
|
88
|
-
page.execute_script("$('.export-to-png:eq(0)').click()")
|
|
89
|
-
wait_for_download
|
|
90
|
-
expect(File.basename(downloaded_file)).to eq('Circos-visualisation.png')
|
|
91
|
-
clear_downloads
|
|
92
|
-
|
|
93
|
-
page.execute_script("$('.export-to-svg:eq(0)').click()")
|
|
94
|
-
wait_for_download
|
|
95
|
-
expect(File.basename(downloaded_file)).to eq('Circos-visualisation.svg')
|
|
96
|
-
end
|
|
97
|
-
|
|
98
|
-
it 'loads BLASTP XML and tests Length distribution download' do
|
|
99
|
-
access_by_uuid('blast_2.2.30/blastp')
|
|
100
|
-
|
|
101
|
-
# Click on the Length distribution expanding button, wait for animation,
|
|
102
|
-
# click on the download of PNG/SVG file and test that it initiated a file
|
|
103
|
-
# download in a right format.
|
|
104
|
-
page.should have_content('Length distribution of hits')
|
|
105
|
-
page.execute_script("$('.length-distribution > .grapher-header > h5').click()")
|
|
106
|
-
sleep 1
|
|
107
|
-
|
|
108
|
-
page.execute_script("$('.export-to-png:eq(1)').click()")
|
|
109
|
-
wait_for_download
|
|
110
|
-
expect(File.basename(downloaded_file)).to eq('length-distribution-sp_P04637_P53_HUMAN.png')
|
|
111
|
-
|
|
112
|
-
clear_downloads
|
|
113
|
-
|
|
114
|
-
page.execute_script("$('.export-to-svg:eq(1)').click()")
|
|
115
|
-
wait_for_download
|
|
116
|
-
expect(File.basename(downloaded_file)).to eq('length-distribution-sp_P04637_P53_HUMAN.svg')
|
|
117
|
-
end
|
|
118
|
-
|
|
119
|
-
# BLASTX test scenarios
|
|
120
|
-
|
|
121
|
-
it 'loads BLASTX XML and tests hit alignment and sidebar Alignment download' do
|
|
122
|
-
access_by_uuid('blast_2.2.30/blastx')
|
|
123
|
-
|
|
124
|
-
# Click on the first Alignment download button on the page and wait for the
|
|
125
|
-
# download to finish.
|
|
126
|
-
page.execute_script("$('.download-aln:eq(0)').click()")
|
|
127
|
-
wait_for_download
|
|
128
|
-
expect(File.basename(downloaded_file)).to eq('MH011443_1_gi_1486783307_gb_AYF55702_1.txt')
|
|
129
|
-
expect(File.read(downloaded_file)).to eq(File.read('spec/sequences/MH011443_1_gi_1486783307_gb_AYF55702_1.txt'))
|
|
130
|
-
|
|
131
|
-
clear_downloads
|
|
132
|
-
|
|
133
|
-
# Click on the Alignment of all hits download and compare the downloaded
|
|
134
|
-
# content
|
|
135
|
-
|
|
136
|
-
page.click_link('Alignment of all hits')
|
|
137
|
-
wait_for_download
|
|
138
|
-
expect(File.basename(downloaded_file)).to eq('alignment-40_hits.txt')
|
|
139
|
-
expect(File.read(downloaded_file)).to eq(File.read('spec/sequences/alignment-40_hits_blastx.txt'))
|
|
140
|
-
|
|
141
|
-
clear_downloads
|
|
142
|
-
|
|
143
|
-
# Select four hit checkboxes and click on the Alignment of selected hits.
|
|
144
|
-
# Compare the downloaded content.
|
|
145
|
-
page.check('Query_1_hit_3_checkbox')
|
|
146
|
-
page.check('Query_1_hit_4_checkbox')
|
|
147
|
-
page.check('Query_2_hit_3_checkbox')
|
|
148
|
-
page.check('Query_2_hit_4_checkbox')
|
|
149
|
-
page.click_link('Alignment of 4 selected hit(s)')
|
|
150
|
-
wait_for_download
|
|
151
|
-
|
|
152
|
-
expect(File.basename(downloaded_file)).to eq('alignment-4_hits.txt')
|
|
153
|
-
expect(File.read(downloaded_file)).to eq(File.read('spec/sequences/alignment-4_hits_blastx.txt'))
|
|
154
|
-
|
|
155
|
-
page.should have_content('BLASTX')
|
|
156
|
-
end
|
|
157
|
-
|
|
158
|
-
it 'loads BLASTX XML and tests hit PNG/SVG download' do
|
|
159
|
-
access_by_uuid('blast_2.2.30/blastx')
|
|
160
|
-
|
|
161
|
-
# Click on the PNG/SVG download button of the alignment overview and compare
|
|
162
|
-
# the downloaded content.
|
|
163
|
-
page.execute_script("$('.export-to-png:eq(0)').click()")
|
|
164
|
-
wait_for_download
|
|
165
|
-
expect(File.basename(downloaded_file)).to eq('Alignment-Overview-MH011443_1.png')
|
|
166
|
-
|
|
167
|
-
clear_downloads
|
|
168
|
-
|
|
169
|
-
page.execute_script("$('.export-to-svg:eq(0)').click()")
|
|
170
|
-
wait_for_download
|
|
171
|
-
expect(File.basename(downloaded_file)).to eq('Alignment-Overview-MH011443_1.svg')
|
|
172
|
-
|
|
173
|
-
clear_downloads
|
|
174
|
-
|
|
175
|
-
# Click on the PNG/SVG download button of the first hit available and
|
|
176
|
-
# compare the downloaded content.
|
|
177
|
-
page.execute_script("$('.export-to-png:eq(1)').click()")
|
|
178
|
-
wait_for_download
|
|
179
|
-
expect(File.basename(downloaded_file)).to eq('Kablammo-MH011443_1-gi_1486783307_gb_AYF55702_1.png')
|
|
180
|
-
|
|
181
|
-
clear_downloads
|
|
182
|
-
|
|
183
|
-
page.execute_script("$('.export-to-svg:eq(1)').click()")
|
|
184
|
-
wait_for_download
|
|
185
|
-
expect(File.basename(downloaded_file)).to eq('Kablammo-MH011443_1-gi_1486783307_gb_AYF55702_1.svg')
|
|
186
|
-
page.should have_content('BLASTX')
|
|
187
|
-
end
|
|
188
|
-
|
|
189
|
-
it 'loads BLASTX XML and tests Circos download' do
|
|
190
|
-
access_by_uuid('blast_2.2.30/blastx')
|
|
191
|
-
# Click on the Circos expanding button, wait for animation, click on the
|
|
192
|
-
# download of PNG/SVG file and test that it initiated a file download in a
|
|
193
|
-
# right format.
|
|
194
|
-
|
|
195
|
-
page.should have_content('Queries and their top hits: chord diagram')
|
|
196
|
-
page.execute_script("$('.circos > .grapher-header > h5').click()")
|
|
197
|
-
sleep 1
|
|
198
|
-
|
|
199
|
-
page.execute_script("$('.export-to-png:eq(0)').click()")
|
|
200
|
-
wait_for_download
|
|
201
|
-
expect(File.basename(downloaded_file)).to eq('Circos-visualisation.png')
|
|
202
|
-
clear_downloads
|
|
203
|
-
|
|
204
|
-
page.execute_script("$('.export-to-svg:eq(0)').click()")
|
|
205
|
-
wait_for_download
|
|
206
|
-
expect(File.basename(downloaded_file)).to eq('Circos-visualisation.svg')
|
|
207
|
-
end
|
|
208
|
-
|
|
209
|
-
it 'loads BLASTX XML and tests Length distribution download' do
|
|
210
|
-
access_by_uuid('blast_2.2.30/blastx')
|
|
211
|
-
# Click on the Length distribution expanding button, wait for animation,
|
|
212
|
-
# click on the download of PNG/SVG file and test that it initiated a file
|
|
213
|
-
# download in a right format.
|
|
214
|
-
|
|
215
|
-
page.should have_content('Length distribution of hits')
|
|
216
|
-
page.execute_script("$('.length-distribution > .grapher-header > h5').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
|
-
# BLASTN Test scenarios
|
|
231
|
-
|
|
232
|
-
it 'loads BLASTN XML and tests hit alignment and sidebar Alignment download' do
|
|
233
|
-
access_by_uuid('blast_2.2.30/blastn')
|
|
234
|
-
|
|
235
|
-
# Click on the first Alignment download button on the page and wait for the
|
|
236
|
-
# download to finish.
|
|
237
|
-
|
|
238
|
-
page.execute_script("$('.download-aln:eq(0)').click()")
|
|
239
|
-
wait_for_download
|
|
240
|
-
expect(File.basename(downloaded_file)).to eq('MH011443_1_gi_1486783306_gb_MH011443_1.txt')
|
|
241
|
-
expect(File.read(downloaded_file)).to eq(File.read('spec/sequences/MH011443_1_gi_1486783306_gb_MH011443_1.txt'))
|
|
242
|
-
|
|
243
|
-
clear_downloads
|
|
244
|
-
|
|
245
|
-
# Click on the Alignment of all hits download and compare the downloaded
|
|
246
|
-
# content
|
|
247
|
-
|
|
248
|
-
page.click_link('Alignment of all hits')
|
|
249
|
-
wait_for_download
|
|
250
|
-
expect(File.basename(downloaded_file)).to eq('alignment-40_hits.txt')
|
|
251
|
-
expect(File.read(downloaded_file)).to eq(File.read('spec/sequences/alignment-40_hits_blastn.txt'))
|
|
252
|
-
|
|
253
|
-
clear_downloads
|
|
254
|
-
|
|
255
|
-
# Select four hit checkboxes and click on the Alignment of selected hits.
|
|
256
|
-
# Compare the downloaded content.
|
|
257
|
-
page.check('Query_1_hit_5_checkbox')
|
|
258
|
-
page.check('Query_1_hit_6_checkbox')
|
|
259
|
-
page.check('Query_2_hit_5_checkbox')
|
|
260
|
-
page.check('Query_2_hit_6_checkbox')
|
|
261
|
-
page.click_link('Alignment of 4 selected hit(s)')
|
|
262
|
-
wait_for_download
|
|
263
|
-
|
|
264
|
-
expect(File.basename(downloaded_file)).to eq('alignment-4_hits.txt')
|
|
265
|
-
expect(File.read(downloaded_file)).to eq(File.read('spec/sequences/alignment-4_hits_blastn.txt'))
|
|
266
|
-
page.should have_content('BLASTN')
|
|
267
|
-
end
|
|
268
|
-
|
|
269
|
-
it 'loads BLASTN XML and tests alignment overview and hit PNG/SVG download' do
|
|
270
|
-
access_by_uuid('blast_2.2.30/blastn')
|
|
271
|
-
|
|
272
|
-
# Click on the PNG/SVG download button of the alignment overview and compare
|
|
273
|
-
# the downloaded content.
|
|
274
|
-
page.execute_script("$('.export-to-png:eq(0)').click()")
|
|
275
|
-
wait_for_download
|
|
276
|
-
expect(File.basename(downloaded_file)).to eq('Alignment-Overview-MH011443_1.png')
|
|
277
|
-
|
|
278
|
-
clear_downloads
|
|
279
|
-
|
|
280
|
-
page.execute_script("$('.export-to-svg:eq(0)').click()")
|
|
281
|
-
wait_for_download
|
|
282
|
-
expect(File.basename(downloaded_file)).to eq('Alignment-Overview-MH011443_1.svg')
|
|
283
|
-
|
|
284
|
-
clear_downloads
|
|
285
|
-
# Click on the PNG download button of the first hit available and compare
|
|
286
|
-
# the downloaded content.
|
|
287
|
-
|
|
288
|
-
page.execute_script("$('.export-to-png:eq(2)').click()")
|
|
289
|
-
wait_for_download
|
|
290
|
-
expect(File.basename(downloaded_file)).to eq('Kablammo-MH011443_1-gi_1528997474_gb_MH447967_1.png')
|
|
291
|
-
|
|
292
|
-
clear_downloads
|
|
293
|
-
|
|
294
|
-
# Click on the SVG download button of the first hit available and compare
|
|
295
|
-
# the downloaded content.
|
|
296
|
-
|
|
297
|
-
page.execute_script("$('.export-to-svg:eq(2)').click()")
|
|
298
|
-
wait_for_download
|
|
299
|
-
expect(File.basename(downloaded_file)).to eq('Kablammo-MH011443_1-gi_1528997474_gb_MH447967_1.svg')
|
|
300
|
-
page.should have_content('BLASTN')
|
|
301
|
-
end
|
|
302
|
-
|
|
303
|
-
it 'loads BLASTN XML and tests Circos download' do
|
|
304
|
-
access_by_uuid('blast_2.2.30/blastn')
|
|
305
|
-
# Click on the Circos expanding button, wait for animation, click on the
|
|
306
|
-
# download of PNG/SVG file and test that it initiated a file download in a
|
|
307
|
-
# right format.
|
|
308
|
-
|
|
309
|
-
page.should have_content('Queries and their top hits: chord diagram')
|
|
310
|
-
page.execute_script("$('.circos > .grapher-header > h5').click()")
|
|
311
|
-
sleep 1
|
|
312
|
-
|
|
313
|
-
page.execute_script("$('.export-to-png:eq(0)').click()")
|
|
314
|
-
wait_for_download
|
|
315
|
-
expect(File.basename(downloaded_file)).to eq('Circos-visualisation.png')
|
|
316
|
-
clear_downloads
|
|
317
|
-
|
|
318
|
-
page.execute_script("$('.export-to-svg:eq(0)').click()")
|
|
319
|
-
wait_for_download
|
|
320
|
-
expect(File.basename(downloaded_file)).to eq('Circos-visualisation.svg')
|
|
321
|
-
end
|
|
322
|
-
|
|
323
|
-
it 'loads BLASTN XML and tests Length distribution download' do
|
|
324
|
-
access_by_uuid('blast_2.2.30/blastn')
|
|
325
|
-
# Click on the Length distribution expanding button, wait for animation,
|
|
326
|
-
# click on the download of PNG/SVG file and test that it initiated a file
|
|
327
|
-
# download in a right format.
|
|
328
|
-
|
|
329
|
-
page.should have_content('Length distribution of hits')
|
|
330
|
-
page.execute_script("$('.length-distribution > .grapher-header > h5').click()")
|
|
331
|
-
sleep 1
|
|
332
|
-
|
|
333
|
-
page.execute_script("$('.export-to-png:eq(1)').click()")
|
|
334
|
-
wait_for_download
|
|
335
|
-
expect(File.basename(downloaded_file)).to eq('length-distribution-MH011443_1.png')
|
|
336
|
-
clear_downloads
|
|
337
|
-
|
|
338
|
-
page.execute_script("$('.export-to-svg:eq(1)').click()")
|
|
339
|
-
wait_for_download
|
|
340
|
-
expect(File.basename(downloaded_file)).to eq('length-distribution-MH011443_1.svg')
|
|
341
|
-
end
|
|
342
|
-
|
|
343
|
-
# TBLASTN Test scenarios
|
|
344
|
-
|
|
345
|
-
it 'loads TBLASTN XML and tests hit alignment and sidebar Alignment download' do
|
|
346
|
-
access_by_uuid('blast_2.2.30/tblastn')
|
|
347
|
-
|
|
348
|
-
# Click on the first Alignment download button on the page and wait for the
|
|
349
|
-
# download to finish.
|
|
350
|
-
|
|
351
|
-
page.execute_script("$('.download-aln:eq(0)').click()")
|
|
352
|
-
wait_for_download
|
|
353
|
-
expect(File.basename(downloaded_file)).to eq('sp_P04637_P53_HUMAN_gi_1484127324_gb_MG595988_1.txt')
|
|
354
|
-
expect(File.read(downloaded_file)).to eq(File.read('spec/sequences/sp_P04637_P53_HUMAN_gi_1484127324_gb_MG595988_1.txt'))
|
|
355
|
-
|
|
356
|
-
clear_downloads
|
|
357
|
-
|
|
358
|
-
# Click on the Alignment of all hits download and compare the downloaded
|
|
359
|
-
# content
|
|
360
|
-
|
|
361
|
-
page.click_link('Alignment of all hits')
|
|
362
|
-
wait_for_download
|
|
363
|
-
expect(File.basename(downloaded_file)).to eq('alignment-40_hits.txt')
|
|
364
|
-
expect(File.read(downloaded_file)).to eq(File.read('spec/sequences/alignment-40_hits_tblastn_2.2.30.txt'))
|
|
365
|
-
|
|
366
|
-
clear_downloads
|
|
367
|
-
|
|
368
|
-
# Select four hit checkboxes and click on the Alignment of selected hits.
|
|
369
|
-
# Compare the downloaded content.
|
|
370
|
-
page.check('Query_1_hit_7_checkbox')
|
|
371
|
-
page.check('Query_1_hit_8_checkbox')
|
|
372
|
-
page.check('Query_2_hit_7_checkbox')
|
|
373
|
-
page.check('Query_2_hit_8_checkbox')
|
|
374
|
-
page.click_link('Alignment of 4 selected hit(s)')
|
|
375
|
-
wait_for_download
|
|
376
|
-
|
|
377
|
-
expect(File.basename(downloaded_file)).to eq('alignment-4_hits.txt')
|
|
378
|
-
expect(File.read(downloaded_file)).to eq(File.read('spec/sequences/alignment-4_hits_tblastn_2.2.30.txt'))
|
|
379
|
-
page.should have_content('TBLASTN')
|
|
380
|
-
end
|
|
381
|
-
|
|
382
|
-
it 'loads TBLASTN XML and tests alignment overview and hit PNG/SVG download' do
|
|
383
|
-
access_by_uuid('blast_2.2.30/tblastn')
|
|
384
|
-
|
|
385
|
-
# Click on the PNG/SVG download button of the alignment overview and compare
|
|
386
|
-
# the downloaded content.
|
|
387
|
-
|
|
388
|
-
page.execute_script("$('.export-to-png:eq(0)').click()")
|
|
389
|
-
wait_for_download
|
|
390
|
-
expect(File.basename(downloaded_file)).to eq('Alignment-Overview-sp_P04637_P53_HUMAN.png')
|
|
391
|
-
|
|
392
|
-
clear_downloads
|
|
393
|
-
|
|
394
|
-
page.execute_script("$('.export-to-svg:eq(0)').click()")
|
|
395
|
-
wait_for_download
|
|
396
|
-
expect(File.basename(downloaded_file)).to eq('Alignment-Overview-sp_P04637_P53_HUMAN.svg')
|
|
397
|
-
|
|
398
|
-
clear_downloads
|
|
399
|
-
|
|
400
|
-
# Click on the PNG download button of the first hit available and compare
|
|
401
|
-
# the downloaded content.
|
|
402
|
-
|
|
403
|
-
page.execute_script("$('.export-to-png:eq(1)').click()")
|
|
404
|
-
wait_for_download
|
|
405
|
-
expect(File.basename(downloaded_file)).to eq('Kablammo-sp_P04637_P53_HUMAN-gi_1484127324_gb_MG595988_1.png')
|
|
406
|
-
|
|
407
|
-
clear_downloads
|
|
408
|
-
|
|
409
|
-
# Click on the SVG download button of the first hit available and compare
|
|
410
|
-
# the downloaded content.
|
|
411
|
-
|
|
412
|
-
page.execute_script("$('.export-to-svg:eq(1)').click()")
|
|
413
|
-
wait_for_download
|
|
414
|
-
expect(File.basename(downloaded_file)).to eq('Kablammo-sp_P04637_P53_HUMAN-gi_1484127324_gb_MG595988_1.svg')
|
|
415
|
-
page.should have_content('TBLASTN')
|
|
416
|
-
end
|
|
417
|
-
|
|
418
|
-
it 'loads TBLASTN XML and tests Circos download' do
|
|
419
|
-
access_by_uuid('blast_2.2.30/tblastn')
|
|
420
|
-
# Click on the Circos expanding button, wait for animation, click on the
|
|
421
|
-
# download of PNG/SVG file and test that it initiated a file download in a
|
|
422
|
-
# right format.
|
|
423
|
-
|
|
424
|
-
page.should have_content('Queries and their top hits: chord diagram')
|
|
425
|
-
page.execute_script("$('.circos > .grapher-header > h5').click()")
|
|
426
|
-
sleep 1
|
|
427
|
-
|
|
428
|
-
page.execute_script("$('.export-to-png:eq(0)').click()")
|
|
429
|
-
wait_for_download
|
|
430
|
-
expect(File.basename(downloaded_file)).to eq('Circos-visualisation.png')
|
|
431
|
-
|
|
432
|
-
clear_downloads
|
|
433
|
-
|
|
434
|
-
page.execute_script("$('.export-to-svg:eq(0)').click()")
|
|
435
|
-
wait_for_download
|
|
436
|
-
expect(File.basename(downloaded_file)).to eq('Circos-visualisation.svg')
|
|
437
|
-
end
|
|
438
|
-
|
|
439
|
-
it 'loads TBLASTN XML and tests Length distribution download' do
|
|
440
|
-
access_by_uuid('blast_2.2.30/tblastn')
|
|
441
|
-
# Click on the Length distribution expanding button, wait for animation,
|
|
442
|
-
# click on the download of PNG/SVG file and test that it initiated a file
|
|
443
|
-
# download in a right format.
|
|
444
|
-
|
|
445
|
-
page.should have_content('Length distribution of hits')
|
|
446
|
-
page.execute_script("$('.length-distribution > .grapher-header > h5').click()")
|
|
447
|
-
sleep 1
|
|
448
|
-
|
|
449
|
-
page.execute_script("$('.export-to-png:eq(1)').click()")
|
|
450
|
-
wait_for_download
|
|
451
|
-
expect(File.basename(downloaded_file)).to eq('length-distribution-sp_P04637_P53_HUMAN.png')
|
|
452
|
-
|
|
453
|
-
clear_downloads
|
|
454
|
-
|
|
455
|
-
page.execute_script("$('.export-to-svg:eq(1)').click()")
|
|
456
|
-
wait_for_download
|
|
457
|
-
expect(File.basename(downloaded_file)).to eq('length-distribution-sp_P04637_P53_HUMAN.svg')
|
|
458
|
-
end
|
|
459
|
-
|
|
460
|
-
# TBLASTX Test scenarios
|
|
461
|
-
|
|
462
|
-
it 'loads TBLASTX XML and tests hit alignment and sidebar Alignment download' do
|
|
463
|
-
access_by_uuid('blast_2.2.30/tblastx')
|
|
464
|
-
# Click on the first Alignment download button on the page and wait for the
|
|
465
|
-
# download to finish.
|
|
466
|
-
|
|
467
|
-
page.execute_script("$('.download-aln:eq(1)').click()")
|
|
468
|
-
wait_for_download
|
|
469
|
-
expect(File.basename(downloaded_file)).to eq('MH011443_1_gi_1528997474_gb_MH447967_1.txt')
|
|
470
|
-
expect(File.read(downloaded_file)). to eq(File.read('spec/sequences/MH011443_1_gi_1528997474_gb_MH447967_1.txt'))
|
|
471
|
-
|
|
472
|
-
clear_downloads
|
|
473
|
-
|
|
474
|
-
# Click on the Alignment of all hits download and compare the downloaded
|
|
475
|
-
# content
|
|
476
|
-
|
|
477
|
-
page.click_link('Alignment of all hits')
|
|
478
|
-
wait_for_download
|
|
479
|
-
expect(File.basename(downloaded_file)).to eq('alignment-40_hits.txt')
|
|
480
|
-
expect(File.read(downloaded_file)).to eq(File.read('spec/sequences/alignment-40_hits_tblastx.txt'))
|
|
481
|
-
|
|
482
|
-
clear_downloads
|
|
483
|
-
|
|
484
|
-
# Select four hit checkboxes and click on the Alignment of selected hits.
|
|
485
|
-
# Compare the downloaded content.
|
|
486
|
-
page.check('Query_1_hit_9_checkbox')
|
|
487
|
-
page.check('Query_1_hit_10_checkbox')
|
|
488
|
-
page.check('Query_2_hit_9_checkbox')
|
|
489
|
-
page.check('Query_2_hit_10_checkbox')
|
|
490
|
-
page.click_link('Alignment of 4 selected hit(s)')
|
|
491
|
-
wait_for_download
|
|
492
|
-
|
|
493
|
-
expect(File.basename(downloaded_file)).to eq('alignment-4_hits.txt')
|
|
494
|
-
expect(File.read(downloaded_file)).to eq(File.read('spec/sequences/alignment-4_hits_tblastx.txt'))
|
|
495
|
-
page.should have_content('TBLASTX')
|
|
496
|
-
end
|
|
497
|
-
|
|
498
|
-
it 'loads TBLASTX XML and tests hit PNG/SVG download' do
|
|
499
|
-
access_by_uuid('blast_2.2.30/tblastx')
|
|
500
|
-
|
|
501
|
-
# Click on the PNG/SVG download button of the alignment overview and compare
|
|
502
|
-
# the downloaded content.
|
|
503
|
-
page.execute_script("$('.export-to-png:eq(0)').click()")
|
|
504
|
-
wait_for_download
|
|
505
|
-
expect(File.basename(downloaded_file)).to eq('Alignment-Overview-MH011443_1.png')
|
|
506
|
-
|
|
507
|
-
clear_downloads
|
|
508
|
-
|
|
509
|
-
page.execute_script("$('.export-to-svg:eq(0)').click()")
|
|
510
|
-
wait_for_download
|
|
511
|
-
expect(File.basename(downloaded_file)).to eq('Alignment-Overview-MH011443_1.svg')
|
|
512
|
-
|
|
513
|
-
clear_downloads
|
|
514
|
-
|
|
515
|
-
# Click on the PNG download button of the first hit available and compare
|
|
516
|
-
# the downloaded content.
|
|
517
|
-
|
|
518
|
-
page.execute_script("$('.export-to-png:eq(1)').click()")
|
|
519
|
-
wait_for_download
|
|
520
|
-
expect(File.basename(downloaded_file)).to eq('Kablammo-MH011443_1-gi_1486783306_gb_MH011443_1.png')
|
|
521
|
-
|
|
522
|
-
clear_downloads
|
|
523
|
-
|
|
524
|
-
# Click on the SVG download button of the first hit available and compare
|
|
525
|
-
# the downloaded content.
|
|
526
|
-
|
|
527
|
-
page.execute_script("$('.export-to-svg:eq(1)').click()")
|
|
528
|
-
wait_for_download
|
|
529
|
-
expect(File.basename(downloaded_file)).to eq('Kablammo-MH011443_1-gi_1486783306_gb_MH011443_1.svg')
|
|
530
|
-
page.should have_content('TBLASTX')
|
|
531
|
-
end
|
|
532
|
-
|
|
533
|
-
it 'loads TBLASTX XML and tests Circos download' do
|
|
534
|
-
access_by_uuid('blast_2.2.30/tblastx')
|
|
535
|
-
# Click on the Circos expanding button, wait for animation, click on the
|
|
536
|
-
# download of PNG/SVG file and test that it initiated a file download in a
|
|
537
|
-
# right format.
|
|
538
|
-
|
|
539
|
-
page.should have_content('Queries and their top hits: chord diagram')
|
|
540
|
-
page.execute_script("$('.circos > .grapher-header > h5').click()")
|
|
541
|
-
sleep 1
|
|
542
|
-
|
|
543
|
-
page.execute_script("$('.export-to-png:eq(0)').click()")
|
|
544
|
-
wait_for_download
|
|
545
|
-
expect(File.basename(downloaded_file)).to eq('Circos-visualisation.png')
|
|
546
|
-
|
|
547
|
-
clear_downloads
|
|
548
|
-
|
|
549
|
-
page.execute_script("$('.export-to-svg:eq(0)').click()")
|
|
550
|
-
wait_for_download
|
|
551
|
-
expect(File.basename(downloaded_file)).to eq('Circos-visualisation.svg')
|
|
552
|
-
end
|
|
553
|
-
|
|
554
|
-
it 'loads TBLASTX XML and tests Length distribution download' do
|
|
555
|
-
access_by_uuid('blast_2.2.30/tblastx')
|
|
556
|
-
# Click on the Length distribution expanding button, wait for animation,
|
|
557
|
-
# click on the download of PNG/SVG file and test that it initiated a file
|
|
558
|
-
# download in a right format.
|
|
559
|
-
|
|
560
|
-
page.should have_content('Length distribution of hits')
|
|
561
|
-
page.execute_script("$('.length-distribution > .grapher-header > h5').click()")
|
|
562
|
-
sleep 1
|
|
563
|
-
|
|
564
|
-
page.execute_script("$('.export-to-png:eq(1)').click()")
|
|
565
|
-
wait_for_download
|
|
566
|
-
expect(File.basename(downloaded_file)).to eq('length-distribution-MH011443_1.png')
|
|
567
|
-
|
|
568
|
-
clear_downloads
|
|
569
|
-
|
|
570
|
-
page.execute_script("$('.export-to-svg:eq(1)').click()")
|
|
571
|
-
wait_for_download
|
|
572
|
-
expect(File.basename(downloaded_file)).to eq('length-distribution-MH011443_1.svg')
|
|
573
|
-
end
|
|
574
|
-
|
|
575
|
-
## Helpers ##
|
|
576
|
-
|
|
577
|
-
def access_by_uuid(id)
|
|
578
|
-
# Method to access the XML report in the browser
|
|
579
|
-
url = url_encode(id)
|
|
580
|
-
visit "/#{url}"
|
|
581
|
-
page.should have_content('Query')
|
|
582
|
-
end
|
|
583
|
-
end
|