bio 1.0.0 → 1.1.0
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- data/bin/bioruby +14 -122
- data/bin/br_biofetch.rb +2 -2
- data/bin/br_bioflat.rb +2 -2
- data/bin/br_biogetseq.rb +2 -2
- data/bin/br_pmfetch.rb +3 -3
- data/doc/Changes-0.7.rd +77 -0
- data/doc/KEGG_API.rd +523 -232
- data/doc/KEGG_API.rd.ja +529 -207
- data/doc/Tutorial.rd +48 -11
- data/lib/bio.rb +59 -6
- data/lib/bio/alignment.rb +713 -103
- data/lib/bio/appl/bl2seq/report.rb +2 -18
- data/lib/bio/appl/blast.rb +108 -91
- data/lib/bio/appl/blast/format0.rb +33 -18
- data/lib/bio/appl/blast/format8.rb +6 -20
- data/lib/bio/appl/blast/report.rb +293 -429
- data/lib/bio/appl/blast/rexml.rb +8 -22
- data/lib/bio/appl/blast/wublast.rb +21 -12
- data/lib/bio/appl/blast/xmlparser.rb +180 -183
- data/lib/bio/appl/blat/report.rb +127 -30
- data/lib/bio/appl/clustalw.rb +87 -59
- data/lib/bio/appl/clustalw/report.rb +20 -22
- data/lib/bio/appl/emboss.rb +113 -20
- data/lib/bio/appl/fasta.rb +173 -198
- data/lib/bio/appl/fasta/format10.rb +244 -347
- data/lib/bio/appl/gcg/msf.rb +212 -0
- data/lib/bio/appl/gcg/seq.rb +195 -0
- data/lib/bio/appl/genscan/report.rb +5 -23
- data/lib/bio/appl/hmmer.rb +8 -45
- data/lib/bio/appl/hmmer/report.rb +2 -20
- data/lib/bio/appl/iprscan/report.rb +374 -0
- data/lib/bio/appl/mafft.rb +87 -50
- data/lib/bio/appl/mafft/report.rb +151 -44
- data/lib/bio/appl/muscle.rb +52 -0
- data/lib/bio/appl/phylip/alignment.rb +129 -0
- data/lib/bio/appl/phylip/distance_matrix.rb +96 -0
- data/lib/bio/appl/probcons.rb +41 -0
- data/lib/bio/appl/psort.rb +89 -96
- data/lib/bio/appl/psort/report.rb +6 -22
- data/lib/bio/appl/pts1.rb +263 -0
- data/lib/bio/appl/sim4.rb +26 -36
- data/lib/bio/appl/sim4/report.rb +2 -18
- data/lib/bio/appl/sosui/report.rb +5 -20
- data/lib/bio/appl/spidey/report.rb +2 -2
- data/lib/bio/appl/targetp/report.rb +4 -20
- data/lib/bio/appl/tcoffee.rb +55 -0
- data/lib/bio/appl/tmhmm/report.rb +4 -20
- data/lib/bio/command.rb +235 -64
- data/lib/bio/data/aa.rb +21 -26
- data/lib/bio/data/codontable.rb +2 -20
- data/lib/bio/data/na.rb +19 -4
- data/lib/bio/db.rb +27 -12
- data/lib/bio/db/aaindex.rb +2 -20
- data/lib/bio/db/embl/common.rb +4 -21
- data/lib/bio/db/embl/embl.rb +33 -85
- data/lib/bio/db/embl/sptr.rb +612 -302
- data/lib/bio/db/embl/swissprot.rb +10 -29
- data/lib/bio/db/embl/trembl.rb +10 -29
- data/lib/bio/db/embl/uniprot.rb +10 -29
- data/lib/bio/db/fantom.rb +15 -20
- data/lib/bio/db/fasta.rb +3 -3
- data/lib/bio/db/genbank/common.rb +37 -46
- data/lib/bio/db/genbank/ddbj.rb +6 -18
- data/lib/bio/db/genbank/genbank.rb +47 -186
- data/lib/bio/db/genbank/genpept.rb +4 -17
- data/lib/bio/db/genbank/refseq.rb +4 -17
- data/lib/bio/db/gff.rb +103 -35
- data/lib/bio/db/go.rb +4 -20
- data/lib/bio/db/kegg/brite.rb +26 -36
- data/lib/bio/db/kegg/compound.rb +81 -85
- data/lib/bio/db/kegg/drug.rb +98 -0
- data/lib/bio/db/kegg/enzyme.rb +133 -110
- data/lib/bio/db/kegg/expression.rb +2 -20
- data/lib/bio/db/kegg/genes.rb +208 -238
- data/lib/bio/db/kegg/genome.rb +164 -285
- data/lib/bio/db/kegg/glycan.rb +114 -157
- data/lib/bio/db/kegg/keggtab.rb +242 -303
- data/lib/bio/db/kegg/kgml.rb +117 -160
- data/lib/bio/db/kegg/orthology.rb +112 -0
- data/lib/bio/db/kegg/reaction.rb +54 -69
- data/lib/bio/db/kegg/taxonomy.rb +331 -0
- data/lib/bio/db/lasergene.rb +209 -0
- data/lib/bio/db/litdb.rb +3 -27
- data/lib/bio/db/medline.rb +228 -249
- data/lib/bio/db/nbrf.rb +3 -3
- data/lib/bio/db/newick.rb +510 -0
- data/lib/bio/db/nexus.rb +1854 -0
- data/lib/bio/db/pdb.rb +5 -17
- data/lib/bio/db/pdb/atom.rb +2 -18
- data/lib/bio/db/pdb/chain.rb +2 -18
- data/lib/bio/db/pdb/chemicalcomponent.rb +2 -18
- data/lib/bio/db/pdb/model.rb +2 -18
- data/lib/bio/db/pdb/pdb.rb +73 -34
- data/lib/bio/db/pdb/residue.rb +4 -20
- data/lib/bio/db/pdb/utils.rb +2 -18
- data/lib/bio/db/prosite.rb +403 -422
- data/lib/bio/db/rebase.rb +84 -40
- data/lib/bio/db/soft.rb +404 -0
- data/lib/bio/db/transfac.rb +5 -17
- data/lib/bio/feature.rb +106 -52
- data/lib/bio/io/das.rb +32 -42
- data/lib/bio/io/dbget.rb +2 -20
- data/lib/bio/io/ddbjxml.rb +77 -138
- data/lib/bio/io/ebisoap.rb +158 -0
- data/lib/bio/io/ensembl.rb +229 -0
- data/lib/bio/io/fastacmd.rb +89 -82
- data/lib/bio/io/fetch.rb +163 -96
- data/lib/bio/io/flatfile.rb +170 -73
- data/lib/bio/io/flatfile/bdb.rb +3 -16
- data/lib/bio/io/flatfile/index.rb +2 -2
- data/lib/bio/io/flatfile/indexer.rb +3 -2
- data/lib/bio/io/higet.rb +12 -31
- data/lib/bio/io/keggapi.rb +210 -269
- data/lib/bio/io/ncbisoap.rb +155 -0
- data/lib/bio/io/pubmed.rb +169 -147
- data/lib/bio/io/registry.rb +4 -20
- data/lib/bio/io/soapwsdl.rb +43 -38
- data/lib/bio/io/sql.rb +242 -305
- data/lib/bio/location.rb +407 -285
- data/lib/bio/map.rb +410 -0
- data/lib/bio/pathway.rb +558 -695
- data/lib/bio/reference.rb +272 -75
- data/lib/bio/sequence.rb +255 -13
- data/lib/bio/sequence/aa.rb +71 -10
- data/lib/bio/sequence/common.rb +187 -33
- data/lib/bio/sequence/compat.rb +59 -4
- data/lib/bio/sequence/format.rb +54 -7
- data/lib/bio/sequence/generic.rb +3 -3
- data/lib/bio/sequence/na.rb +328 -26
- data/lib/bio/shell.rb +11 -4
- data/lib/bio/shell/core.rb +221 -160
- data/lib/bio/shell/demo.rb +18 -15
- data/lib/bio/shell/interface.rb +14 -12
- data/lib/bio/shell/irb.rb +95 -0
- data/lib/bio/shell/object.rb +45 -26
- data/lib/bio/shell/plugin/blast.rb +42 -0
- data/lib/bio/shell/plugin/codon.rb +22 -14
- data/lib/bio/shell/plugin/das.rb +58 -0
- data/lib/bio/shell/plugin/emboss.rb +2 -2
- data/lib/bio/shell/plugin/entry.rb +22 -11
- data/lib/bio/shell/plugin/flatfile.rb +2 -2
- data/lib/bio/shell/plugin/keggapi.rb +13 -6
- data/lib/bio/shell/plugin/midi.rb +4 -4
- data/lib/bio/shell/plugin/obda.rb +2 -2
- data/lib/bio/shell/plugin/psort.rb +56 -0
- data/lib/bio/shell/plugin/seq.rb +35 -8
- data/lib/bio/shell/plugin/soap.rb +87 -0
- data/lib/bio/shell/rails/vendor/plugins/generators/bioruby/bioruby_generator.rb +29 -0
- data/lib/bio/shell/rails/vendor/plugins/generators/bioruby/templates/_classes.rhtml +4 -0
- data/lib/bio/shell/rails/vendor/plugins/generators/bioruby/templates/_log.rhtml +27 -0
- data/lib/bio/shell/rails/vendor/plugins/generators/bioruby/templates/_methods.rhtml +11 -0
- data/lib/bio/shell/rails/vendor/plugins/generators/bioruby/templates/_modules.rhtml +4 -0
- data/lib/bio/shell/rails/vendor/plugins/generators/bioruby/templates/_variables.rhtml +7 -0
- data/lib/bio/shell/rails/vendor/plugins/generators/bioruby/templates/bioruby-bg.gif +0 -0
- data/lib/bio/shell/rails/vendor/plugins/generators/bioruby/templates/bioruby-console.png +0 -0
- data/lib/bio/shell/rails/{public/images/icon.png → vendor/plugins/generators/bioruby/templates/bioruby-gem.png} +0 -0
- data/lib/bio/shell/rails/vendor/plugins/generators/bioruby/templates/bioruby-link.gif +0 -0
- data/lib/bio/shell/rails/vendor/plugins/generators/bioruby/templates/bioruby.css +369 -0
- data/lib/bio/shell/rails/vendor/plugins/generators/bioruby/templates/bioruby.rhtml +47 -0
- data/lib/bio/shell/rails/vendor/plugins/generators/bioruby/templates/bioruby_controller.rb +144 -0
- data/lib/bio/shell/rails/vendor/plugins/generators/bioruby/templates/bioruby_helper.rb +47 -0
- data/lib/bio/shell/rails/vendor/plugins/generators/bioruby/templates/commands.rhtml +8 -0
- data/lib/bio/shell/rails/vendor/plugins/generators/bioruby/templates/history.rhtml +10 -0
- data/lib/bio/shell/rails/vendor/plugins/generators/bioruby/templates/index.rhtml +22 -0
- data/lib/bio/shell/script.rb +25 -0
- data/lib/bio/shell/setup.rb +109 -0
- data/lib/bio/shell/web.rb +70 -58
- data/lib/bio/tree.rb +850 -0
- data/lib/bio/util/color_scheme.rb +84 -107
- data/lib/bio/util/color_scheme/buried.rb +5 -24
- data/lib/bio/util/color_scheme/helix.rb +5 -24
- data/lib/bio/util/color_scheme/hydropathy.rb +5 -24
- data/lib/bio/util/color_scheme/nucleotide.rb +5 -24
- data/lib/bio/util/color_scheme/strand.rb +5 -24
- data/lib/bio/util/color_scheme/taylor.rb +5 -24
- data/lib/bio/util/color_scheme/turn.rb +5 -24
- data/lib/bio/util/color_scheme/zappo.rb +5 -24
- data/lib/bio/util/contingency_table.rb +70 -43
- data/lib/bio/util/restriction_enzyme.rb +228 -0
- data/lib/bio/util/restriction_enzyme/analysis.rb +249 -0
- data/lib/bio/util/restriction_enzyme/analysis_basic.rb +217 -0
- data/lib/bio/util/restriction_enzyme/cut_symbol.rb +107 -0
- data/lib/bio/util/restriction_enzyme/double_stranded.rb +321 -0
- data/lib/bio/util/restriction_enzyme/double_stranded/aligned_strands.rb +130 -0
- data/lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair.rb +103 -0
- data/lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair_in_enzyme_notation.rb +38 -0
- data/lib/bio/util/restriction_enzyme/double_stranded/cut_locations.rb +76 -0
- data/lib/bio/util/restriction_enzyme/double_stranded/cut_locations_in_enzyme_notation.rb +107 -0
- data/lib/bio/util/restriction_enzyme/enzymes.yaml +7061 -0
- data/lib/bio/util/restriction_enzyme/range/cut_range.rb +24 -0
- data/lib/bio/util/restriction_enzyme/range/cut_ranges.rb +47 -0
- data/lib/bio/util/restriction_enzyme/range/horizontal_cut_range.rb +67 -0
- data/lib/bio/util/restriction_enzyme/range/sequence_range.rb +257 -0
- data/lib/bio/util/restriction_enzyme/range/sequence_range/calculated_cuts.rb +242 -0
- data/lib/bio/util/restriction_enzyme/range/sequence_range/fragment.rb +51 -0
- data/lib/bio/util/restriction_enzyme/range/sequence_range/fragments.rb +41 -0
- data/lib/bio/util/restriction_enzyme/range/vertical_cut_range.rb +77 -0
- data/lib/bio/util/restriction_enzyme/single_strand.rb +199 -0
- data/lib/bio/util/restriction_enzyme/single_strand/cut_locations_in_enzyme_notation.rb +135 -0
- data/lib/bio/util/restriction_enzyme/single_strand_complement.rb +23 -0
- data/lib/bio/util/restriction_enzyme/string_formatting.rb +111 -0
- data/lib/bio/util/sirna.rb +4 -22
- data/sample/color_scheme_na.rb +4 -12
- data/sample/enzymes.rb +78 -0
- data/sample/goslim.rb +5 -13
- data/sample/psortplot_html.rb +4 -12
- data/test/data/blast/2.2.15.blastp.m7 +876 -0
- data/test/data/embl/AB090716.embl.rel89 +63 -0
- data/test/data/fasta/example1.txt +75 -0
- data/test/data/fasta/example2.txt +21 -0
- data/test/data/iprscan/merged.raw +32 -0
- data/test/data/iprscan/merged.txt +74 -0
- data/test/data/soft/GDS100_partial.soft +92 -0
- data/test/data/soft/GSE3457_family_partial.soft +874 -0
- data/test/functional/bio/io/test_ensembl.rb +103 -0
- data/test/functional/bio/io/test_soapwsdl.rb +5 -17
- data/test/unit/bio/appl/bl2seq/test_report.rb +2 -2
- data/test/unit/bio/appl/blast/test_report.rb +3 -16
- data/test/unit/bio/appl/blast/test_xmlparser.rb +4 -16
- data/test/unit/bio/appl/genscan/test_report.rb +3 -16
- data/test/unit/bio/appl/hmmer/test_report.rb +3 -16
- data/test/unit/bio/appl/iprscan/test_report.rb +338 -0
- data/test/unit/bio/appl/mafft/test_report.rb +63 -0
- data/test/unit/bio/appl/sosui/test_report.rb +3 -16
- data/test/unit/bio/appl/targetp/test_report.rb +3 -16
- data/test/unit/bio/appl/test_blast.rb +3 -16
- data/test/unit/bio/appl/test_fasta.rb +4 -16
- data/test/unit/bio/appl/test_pts1.rb +140 -0
- data/test/unit/bio/appl/tmhmm/test_report.rb +3 -16
- data/test/unit/bio/data/test_aa.rb +4 -17
- data/test/unit/bio/data/test_codontable.rb +3 -16
- data/test/unit/bio/data/test_na.rb +3 -3
- data/test/unit/bio/db/embl/test_common.rb +3 -16
- data/test/unit/bio/db/embl/test_embl.rb +3 -16
- data/test/unit/bio/db/embl/test_embl_rel89.rb +219 -0
- data/test/unit/bio/db/embl/test_sptr.rb +1548 -41
- data/test/unit/bio/db/embl/test_uniprot.rb +3 -16
- data/test/unit/bio/db/kegg/test_genes.rb +3 -16
- data/test/unit/bio/db/pdb/test_pdb.rb +7 -24
- data/test/unit/bio/db/test_aaindex.rb +2 -2
- data/test/unit/bio/db/test_fasta.rb +3 -16
- data/test/unit/bio/db/test_gff.rb +3 -16
- data/test/unit/bio/db/test_lasergene.rb +95 -0
- data/test/unit/bio/db/test_newick.rb +56 -0
- data/test/unit/bio/db/test_nexus.rb +360 -0
- data/test/unit/bio/db/test_prosite.rb +5 -18
- data/test/unit/bio/db/test_rebase.rb +11 -25
- data/test/unit/bio/db/test_soft.rb +138 -0
- data/test/unit/bio/io/test_ddbjxml.rb +5 -17
- data/test/unit/bio/io/test_ensembl.rb +109 -0
- data/test/unit/bio/io/test_fastacmd.rb +3 -16
- data/test/unit/bio/io/test_flatfile.rb +237 -0
- data/test/unit/bio/io/test_soapwsdl.rb +4 -17
- data/test/unit/bio/sequence/test_aa.rb +3 -3
- data/test/unit/bio/sequence/test_common.rb +3 -16
- data/test/unit/bio/sequence/test_compat.rb +3 -16
- data/test/unit/bio/sequence/test_na.rb +29 -3
- data/test/unit/bio/shell/plugin/test_seq.rb +8 -8
- data/test/unit/bio/test_alignment.rb +16 -27
- data/test/unit/bio/test_command.rb +242 -25
- data/test/unit/bio/test_db.rb +3 -16
- data/test/unit/bio/test_feature.rb +4 -16
- data/test/unit/bio/test_location.rb +4 -16
- data/test/unit/bio/test_map.rb +230 -0
- data/test/unit/bio/test_pathway.rb +4 -16
- data/test/unit/bio/test_reference.rb +2 -2
- data/test/unit/bio/test_sequence.rb +7 -19
- data/test/unit/bio/test_shell.rb +3 -16
- data/test/unit/bio/test_tree.rb +593 -0
- data/test/unit/bio/util/restriction_enzyme/analysis/test_calculated_cuts.rb +299 -0
- data/test/unit/bio/util/restriction_enzyme/analysis/test_cut_ranges.rb +103 -0
- data/test/unit/bio/util/restriction_enzyme/analysis/test_sequence_range.rb +240 -0
- data/test/unit/bio/util/restriction_enzyme/double_stranded/test_aligned_strands.rb +100 -0
- data/test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_location_pair.rb +75 -0
- data/test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_location_pair_in_enzyme_notation.rb +73 -0
- data/test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations.rb +53 -0
- data/test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations_in_enzyme_notation.rb +104 -0
- data/test/unit/bio/util/restriction_enzyme/single_strand/test_cut_locations_in_enzyme_notation.rb +83 -0
- data/test/unit/bio/util/restriction_enzyme/test_analysis.rb +246 -0
- data/test/unit/bio/util/restriction_enzyme/test_cut_symbol.rb +44 -0
- data/test/unit/bio/util/restriction_enzyme/test_double_stranded.rb +115 -0
- data/test/unit/bio/util/restriction_enzyme/test_single_strand.rb +147 -0
- data/test/unit/bio/util/restriction_enzyme/test_single_strand_complement.rb +147 -0
- data/test/unit/bio/util/restriction_enzyme/test_string_formatting.rb +60 -0
- data/test/unit/bio/util/test_color_scheme.rb +6 -18
- data/test/unit/bio/util/test_contingency_table.rb +6 -18
- data/test/unit/bio/util/test_restriction_enzyme.rb +42 -0
- data/test/unit/bio/util/test_sirna.rb +3 -16
- metadata +228 -169
- data/doc/BioRuby.rd.ja +0 -225
- data/doc/Design.rd.ja +0 -341
- data/doc/TODO.rd.ja +0 -138
- data/lib/bio/appl/fasta/format6.rb +0 -37
- data/lib/bio/db/kegg/cell.rb +0 -88
- data/lib/bio/db/kegg/ko.rb +0 -178
- data/lib/bio/shell/rails/Rakefile +0 -10
- data/lib/bio/shell/rails/app/controllers/application.rb +0 -4
- data/lib/bio/shell/rails/app/controllers/shell_controller.rb +0 -94
- data/lib/bio/shell/rails/app/helpers/application_helper.rb +0 -3
- data/lib/bio/shell/rails/app/models/shell_connection.rb +0 -30
- data/lib/bio/shell/rails/app/views/layouts/shell.rhtml +0 -37
- data/lib/bio/shell/rails/app/views/shell/history.rhtml +0 -5
- data/lib/bio/shell/rails/app/views/shell/index.rhtml +0 -2
- data/lib/bio/shell/rails/app/views/shell/show.rhtml +0 -13
- data/lib/bio/shell/rails/config/boot.rb +0 -19
- data/lib/bio/shell/rails/config/database.yml +0 -85
- data/lib/bio/shell/rails/config/environment.rb +0 -53
- data/lib/bio/shell/rails/config/environments/development.rb +0 -19
- data/lib/bio/shell/rails/config/environments/production.rb +0 -19
- data/lib/bio/shell/rails/config/environments/test.rb +0 -19
- data/lib/bio/shell/rails/config/routes.rb +0 -19
- data/lib/bio/shell/rails/doc/README_FOR_APP +0 -2
- data/lib/bio/shell/rails/public/404.html +0 -8
- data/lib/bio/shell/rails/public/500.html +0 -8
- data/lib/bio/shell/rails/public/dispatch.cgi +0 -10
- data/lib/bio/shell/rails/public/dispatch.fcgi +0 -24
- data/lib/bio/shell/rails/public/dispatch.rb +0 -10
- data/lib/bio/shell/rails/public/favicon.ico +0 -0
- data/lib/bio/shell/rails/public/images/rails.png +0 -0
- data/lib/bio/shell/rails/public/index.html +0 -277
- data/lib/bio/shell/rails/public/javascripts/controls.js +0 -750
- data/lib/bio/shell/rails/public/javascripts/dragdrop.js +0 -584
- data/lib/bio/shell/rails/public/javascripts/effects.js +0 -854
- data/lib/bio/shell/rails/public/javascripts/prototype.js +0 -1785
- data/lib/bio/shell/rails/public/robots.txt +0 -1
- data/lib/bio/shell/rails/public/stylesheets/main.css +0 -187
- data/lib/bio/shell/rails/script/about +0 -3
- data/lib/bio/shell/rails/script/breakpointer +0 -3
- data/lib/bio/shell/rails/script/console +0 -3
- data/lib/bio/shell/rails/script/destroy +0 -3
- data/lib/bio/shell/rails/script/generate +0 -3
- data/lib/bio/shell/rails/script/performance/benchmarker +0 -3
- data/lib/bio/shell/rails/script/performance/profiler +0 -3
- data/lib/bio/shell/rails/script/plugin +0 -3
- data/lib/bio/shell/rails/script/process/reaper +0 -3
- data/lib/bio/shell/rails/script/process/spawner +0 -3
- data/lib/bio/shell/rails/script/process/spinner +0 -3
- data/lib/bio/shell/rails/script/runner +0 -3
- data/lib/bio/shell/rails/script/server +0 -42
- data/lib/bio/shell/rails/test/test_helper.rb +0 -28
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+
|
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10
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+
<body>
|
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11
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+
|
|
12
|
+
<div id="content">
|
|
13
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+
|
|
14
|
+
<div id="side">
|
|
15
|
+
<div class="title">Project</div>
|
|
16
|
+
<ul>
|
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17
|
+
<li><%= link_to "#{File.basename(project_workdir)}", "file://#{project_workdir}" %>
|
|
18
|
+
</ul>
|
|
19
|
+
|
|
20
|
+
<div class="title">Functions</div>
|
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+
<ul>
|
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22
|
+
<li><%= link_to "Console", :action => "index" %></li>
|
|
23
|
+
<li><%= link_to "History", :action => "history" %></li>
|
|
24
|
+
<li><%= link_to "Commands", :action => "commands" %></li>
|
|
25
|
+
</ul>
|
|
26
|
+
|
|
27
|
+
<div class="title">Local variables</div>
|
|
28
|
+
<%= render :partial => "variables" %>
|
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29
|
+
|
|
30
|
+
<br>
|
|
31
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+
<a href="http://bioruby.org/"><img src="/images/bioruby-link.gif" border=0></a>
|
|
32
|
+
</div><!-- side -->
|
|
33
|
+
|
|
34
|
+
<div id="title">
|
|
35
|
+
<p class="titletop">BioRuby shell on Rails</p>
|
|
36
|
+
<p class="titlesub">Web interface for the BioRuby library</p>
|
|
37
|
+
</div><!-- title -->
|
|
38
|
+
|
|
39
|
+
<div id="main">
|
|
40
|
+
<%= yield %>
|
|
41
|
+
</div><!-- main -->
|
|
42
|
+
|
|
43
|
+
</div><!-- content -->
|
|
44
|
+
|
|
45
|
+
</body>
|
|
46
|
+
|
|
47
|
+
</html>
|
|
@@ -0,0 +1,144 @@
|
|
|
1
|
+
class BiorubyController < ApplicationController
|
|
2
|
+
|
|
3
|
+
HIDE_METHODS = Object.methods + [ "singleton_method_added" ]
|
|
4
|
+
|
|
5
|
+
HIDE_MODULES = [
|
|
6
|
+
Base64::Deprecated, Base64, PP::ObjectMixin, Bio::Shell,
|
|
7
|
+
]
|
|
8
|
+
HIDE_MODULES << WEBrick if defined?(WEBrick)
|
|
9
|
+
|
|
10
|
+
HIDE_VARIABLES = [
|
|
11
|
+
"_", "irb", "_erbout",
|
|
12
|
+
]
|
|
13
|
+
|
|
14
|
+
SECURITY_NOTICE = "For security purposes, this functionality is only available to local requests."
|
|
15
|
+
|
|
16
|
+
def index
|
|
17
|
+
unless local_request?
|
|
18
|
+
flash[:notice] = SECURITY_NOTICE
|
|
19
|
+
end
|
|
20
|
+
end
|
|
21
|
+
|
|
22
|
+
def evaluate
|
|
23
|
+
if local_request?
|
|
24
|
+
begin
|
|
25
|
+
@script = params[:script].strip
|
|
26
|
+
|
|
27
|
+
# write out to history
|
|
28
|
+
Bio::Shell.store_history(@script)
|
|
29
|
+
|
|
30
|
+
# evaluate ruby script
|
|
31
|
+
@result = eval(@script, Bio::Shell.cache[:binding])
|
|
32
|
+
|
|
33
|
+
# *TODO* need to handle with output of print/puts/p/pp etc. here
|
|
34
|
+
@output = nil
|
|
35
|
+
rescue
|
|
36
|
+
@result = $!
|
|
37
|
+
@output = nil
|
|
38
|
+
end
|
|
39
|
+
else
|
|
40
|
+
@result = SECURITY_NOTICE
|
|
41
|
+
@output = nil
|
|
42
|
+
end
|
|
43
|
+
|
|
44
|
+
@number = Bio::Shell.cache[:results].store(@script, @result, @output)
|
|
45
|
+
|
|
46
|
+
render :update do |page|
|
|
47
|
+
render_log(page)
|
|
48
|
+
end
|
|
49
|
+
end
|
|
50
|
+
|
|
51
|
+
def list_methods
|
|
52
|
+
number = params[:number].to_i
|
|
53
|
+
|
|
54
|
+
script, result, output = Bio::Shell.cache[:results].restore(number)
|
|
55
|
+
@class = result.class
|
|
56
|
+
@methods = (result.methods - HIDE_METHODS).sort
|
|
57
|
+
|
|
58
|
+
render :update do |page|
|
|
59
|
+
page.replace_html "methods_#{number}", :partial => "methods"
|
|
60
|
+
page.visual_effect :toggle_blind, "methods_#{number}", :duration => 0.5
|
|
61
|
+
end
|
|
62
|
+
end
|
|
63
|
+
|
|
64
|
+
def list_classes
|
|
65
|
+
number = params[:number].to_i
|
|
66
|
+
|
|
67
|
+
script, result, output = Bio::Shell.cache[:results].restore(number)
|
|
68
|
+
class_name = result.class
|
|
69
|
+
@class = class_name
|
|
70
|
+
@classes = []
|
|
71
|
+
loop do
|
|
72
|
+
@classes.unshift(class_name)
|
|
73
|
+
if class_name == Object
|
|
74
|
+
break
|
|
75
|
+
else
|
|
76
|
+
class_name = class_name.superclass
|
|
77
|
+
end
|
|
78
|
+
end
|
|
79
|
+
|
|
80
|
+
render :update do |page|
|
|
81
|
+
page.replace_html "classes_#{number}", :partial => "classes"
|
|
82
|
+
page.visual_effect :toggle_blind, "classes_#{number}", :duration => 0.5
|
|
83
|
+
end
|
|
84
|
+
end
|
|
85
|
+
|
|
86
|
+
def list_modules
|
|
87
|
+
number = params[:number].to_i
|
|
88
|
+
|
|
89
|
+
script, result, output = Bio::Shell.cache[:results].restore(number)
|
|
90
|
+
@class = result.class
|
|
91
|
+
@modules = result.class.included_modules - HIDE_MODULES
|
|
92
|
+
|
|
93
|
+
render :update do |page|
|
|
94
|
+
page.replace_html "modules_#{number}", :partial => "modules"
|
|
95
|
+
page.visual_effect :toggle_blind, "modules_#{number}", :duration => 0.5
|
|
96
|
+
end
|
|
97
|
+
end
|
|
98
|
+
|
|
99
|
+
def reload_script
|
|
100
|
+
number = params[:number].to_i
|
|
101
|
+
|
|
102
|
+
script, result, output = Bio::Shell.cache[:results].restore(number)
|
|
103
|
+
|
|
104
|
+
render :update do |page|
|
|
105
|
+
page.replace_html :script, script
|
|
106
|
+
end
|
|
107
|
+
end
|
|
108
|
+
|
|
109
|
+
def results
|
|
110
|
+
if Bio::Shell.cache[:results].number > 0
|
|
111
|
+
limit = params[:limit].to_i
|
|
112
|
+
max_num = Bio::Shell.cache[:results].number
|
|
113
|
+
min_num = [ max_num - limit + 1, 1 ].max
|
|
114
|
+
min_num = 1 if limit == 0
|
|
115
|
+
|
|
116
|
+
render :update do |page|
|
|
117
|
+
# delete all existing results in the current DOM for clean up
|
|
118
|
+
page.select(".log").each do |element|
|
|
119
|
+
#page.hide element
|
|
120
|
+
page.remove element
|
|
121
|
+
end
|
|
122
|
+
|
|
123
|
+
# add selected results to the current DOM
|
|
124
|
+
min_num.upto(max_num) do |@number|
|
|
125
|
+
#page.show "log_#{@number}"
|
|
126
|
+
@script, @result, @output = Bio::Shell.cache[:results].restore(@number)
|
|
127
|
+
if @script
|
|
128
|
+
render_log(page)
|
|
129
|
+
end
|
|
130
|
+
end
|
|
131
|
+
end
|
|
132
|
+
end
|
|
133
|
+
end
|
|
134
|
+
|
|
135
|
+
def commands
|
|
136
|
+
@bioruby_commands = Bio::Shell.private_instance_methods.sort
|
|
137
|
+
end
|
|
138
|
+
|
|
139
|
+
def history
|
|
140
|
+
@history = File.readlines(Bio::Shell.history_file)
|
|
141
|
+
end
|
|
142
|
+
|
|
143
|
+
end
|
|
144
|
+
|
|
@@ -0,0 +1,47 @@
|
|
|
1
|
+
module BiorubyHelper
|
|
2
|
+
|
|
3
|
+
include Bio::Shell
|
|
4
|
+
|
|
5
|
+
def project_workdir
|
|
6
|
+
if Bio::Shell.cache[:savedir].match(/\.bioruby$/)
|
|
7
|
+
Bio::Shell.cache[:workdir]
|
|
8
|
+
else
|
|
9
|
+
Bio::Shell.cache[:savedir]
|
|
10
|
+
end
|
|
11
|
+
end
|
|
12
|
+
|
|
13
|
+
def have_results
|
|
14
|
+
Bio::Shell.cache[:results].number > 0
|
|
15
|
+
end
|
|
16
|
+
|
|
17
|
+
def local_variables
|
|
18
|
+
eval("local_variables", Bio::Shell.cache[:binding]) -
|
|
19
|
+
BiorubyController::HIDE_VARIABLES
|
|
20
|
+
end
|
|
21
|
+
|
|
22
|
+
def render_log(page)
|
|
23
|
+
page.insert_html :top, :logs, :partial => "log"
|
|
24
|
+
page.replace_html "variables", :partial => "variables"
|
|
25
|
+
page.hide "methods_#{@number}"
|
|
26
|
+
page.hide "classes_#{@number}"
|
|
27
|
+
page.hide "modules_#{@number}"
|
|
28
|
+
end
|
|
29
|
+
|
|
30
|
+
def reference_link(class_or_module)
|
|
31
|
+
name = class_or_module.to_s
|
|
32
|
+
case name
|
|
33
|
+
when /Bio::(.+)/
|
|
34
|
+
path = $1.split('::').join('/')
|
|
35
|
+
url = "http://bioruby.org/rdoc/classes/Bio/#{path}.html"
|
|
36
|
+
when /Chem::(.+)/
|
|
37
|
+
path = $1.split('::').join('/')
|
|
38
|
+
url = "http://chemruby.org/rdoc/classes/Chem/#{path}.html"
|
|
39
|
+
else
|
|
40
|
+
path = name.split('::').join('/')
|
|
41
|
+
url = "http://www.ruby-doc.org/core/classes/#{path}.html"
|
|
42
|
+
end
|
|
43
|
+
return "<a href='#{url}'>#{name}</a>"
|
|
44
|
+
end
|
|
45
|
+
|
|
46
|
+
end
|
|
47
|
+
|
|
@@ -0,0 +1,22 @@
|
|
|
1
|
+
<div id="console">
|
|
2
|
+
<%- if flash[:notice] -%>
|
|
3
|
+
<div id="notice"><p><%= flash[:notice] %></p></div><br>
|
|
4
|
+
<%- end -%>
|
|
5
|
+
<%= form_remote_tag(:url => {:action => "evaluate"}, :position => "top") %>
|
|
6
|
+
<b>BioRuby script:</b>
|
|
7
|
+
<textarea id="script" name="script" rows=10 cols=80></textarea><br>
|
|
8
|
+
<input type="submit" value="Evaluate">
|
|
9
|
+
<input type="reset" value="Clear">
|
|
10
|
+
|
|
11
|
+
Show [
|
|
12
|
+
<%= link_to_remote "All", :url => {:action => "results", :limit => 0} %> |
|
|
13
|
+
<%= link_to_remote "Last 5", :url => {:action => "results", :limit => 5} %> |
|
|
14
|
+
<%= link_to_remote "Previous", :url => {:action => "results", :limit => 1} %>
|
|
15
|
+
] or
|
|
16
|
+
<%= link_to "Hide", :action => "index" %>
|
|
17
|
+
results<br>
|
|
18
|
+
<%= end_form_tag %>
|
|
19
|
+
</div>
|
|
20
|
+
<div id="logs">
|
|
21
|
+
</div>
|
|
22
|
+
|
|
@@ -0,0 +1,25 @@
|
|
|
1
|
+
#
|
|
2
|
+
# = bio/shell/script.rb - script mode for the BioRuby shell
|
|
3
|
+
#
|
|
4
|
+
# Copyright:: Copyright (C) 2006
|
|
5
|
+
# Toshiaki Katayama <k@bioruby.org>
|
|
6
|
+
# License:: The Ruby License
|
|
7
|
+
#
|
|
8
|
+
# $Id: script.rb,v 1.3 2007/04/05 23:35:41 trevor Exp $
|
|
9
|
+
#
|
|
10
|
+
|
|
11
|
+
module Bio::Shell
|
|
12
|
+
|
|
13
|
+
class Script
|
|
14
|
+
|
|
15
|
+
def initialize(script)
|
|
16
|
+
Bio::Shell.cache[:binding] = TOPLEVEL_BINDING
|
|
17
|
+
Bio::Shell.load_session
|
|
18
|
+
eval(File.read(script), TOPLEVEL_BINDING)
|
|
19
|
+
exit
|
|
20
|
+
end
|
|
21
|
+
|
|
22
|
+
end # Script
|
|
23
|
+
|
|
24
|
+
end
|
|
25
|
+
|
|
@@ -0,0 +1,109 @@
|
|
|
1
|
+
#
|
|
2
|
+
# = bio/shell/setup.rb - setup initial environment for the BioRuby shell
|
|
3
|
+
#
|
|
4
|
+
# Copyright:: Copyright (C) 2006
|
|
5
|
+
# Toshiaki Katayama <k@bioruby.org>
|
|
6
|
+
# License:: The Ruby License
|
|
7
|
+
#
|
|
8
|
+
# $Id: setup.rb,v 1.8 2007/06/28 11:21:40 k Exp $
|
|
9
|
+
#
|
|
10
|
+
|
|
11
|
+
require 'getoptlong'
|
|
12
|
+
|
|
13
|
+
class Bio::Shell::Setup
|
|
14
|
+
|
|
15
|
+
def initialize
|
|
16
|
+
check_ruby_version
|
|
17
|
+
|
|
18
|
+
# command line options
|
|
19
|
+
getoptlong
|
|
20
|
+
|
|
21
|
+
# setup working directory
|
|
22
|
+
savedir = setup_savedir
|
|
23
|
+
|
|
24
|
+
# load configuration and plugins
|
|
25
|
+
Bio::Shell.configure(savedir)
|
|
26
|
+
|
|
27
|
+
# set default to irb mode
|
|
28
|
+
Bio::Shell.cache[:mode] = @mode || :irb
|
|
29
|
+
|
|
30
|
+
case Bio::Shell.cache[:mode]
|
|
31
|
+
when :web
|
|
32
|
+
# setup rails server
|
|
33
|
+
Bio::Shell::Web.new
|
|
34
|
+
when :irb
|
|
35
|
+
# setup irb server
|
|
36
|
+
Bio::Shell::Irb.new
|
|
37
|
+
when :script
|
|
38
|
+
# run bioruby shell script
|
|
39
|
+
Bio::Shell::Script.new(@script)
|
|
40
|
+
end
|
|
41
|
+
end
|
|
42
|
+
|
|
43
|
+
def check_ruby_version
|
|
44
|
+
if RUBY_VERSION < "1.8.2"
|
|
45
|
+
raise "BioRuby shell runs on Ruby version >= 1.8.2"
|
|
46
|
+
end
|
|
47
|
+
end
|
|
48
|
+
|
|
49
|
+
# command line argument (working directory or bioruby shell script file)
|
|
50
|
+
def getoptlong
|
|
51
|
+
opts = GetoptLong.new
|
|
52
|
+
opts.set_options(
|
|
53
|
+
[ '--rails', '-r', GetoptLong::NO_ARGUMENT ],
|
|
54
|
+
[ '--web', '-w', GetoptLong::NO_ARGUMENT ],
|
|
55
|
+
[ '--console', '-c', GetoptLong::NO_ARGUMENT ],
|
|
56
|
+
[ '--irb', '-i', GetoptLong::NO_ARGUMENT ]
|
|
57
|
+
)
|
|
58
|
+
opts.each_option do |opt, arg|
|
|
59
|
+
case opt
|
|
60
|
+
when /--rails/, /--web/
|
|
61
|
+
@mode = :web
|
|
62
|
+
when /--console/, /--irb/
|
|
63
|
+
@mode = :irb
|
|
64
|
+
end
|
|
65
|
+
end
|
|
66
|
+
end
|
|
67
|
+
|
|
68
|
+
def setup_savedir
|
|
69
|
+
arg = ARGV.shift
|
|
70
|
+
|
|
71
|
+
# Options after the '--' argument are not parsed by GetoptLong and
|
|
72
|
+
# are passed to irb or rails. This hack preserve the first option
|
|
73
|
+
# when working directory of the project is not given.
|
|
74
|
+
if arg and arg[/^-/]
|
|
75
|
+
ARGV.unshift arg
|
|
76
|
+
arg = nil
|
|
77
|
+
end
|
|
78
|
+
|
|
79
|
+
if arg.nil?
|
|
80
|
+
# run in the current directory
|
|
81
|
+
if File.exist?(Bio::Shell::Core::HISTORY)
|
|
82
|
+
savedir = Dir.pwd
|
|
83
|
+
else
|
|
84
|
+
savedir = File.join(ENV['HOME'].to_s, ".bioruby")
|
|
85
|
+
install_savedir(savedir)
|
|
86
|
+
end
|
|
87
|
+
elsif File.file?(arg)
|
|
88
|
+
# run file as a bioruby shell script
|
|
89
|
+
savedir = File.join(File.dirname(arg), "..")
|
|
90
|
+
@script = arg
|
|
91
|
+
@mode = :script
|
|
92
|
+
else
|
|
93
|
+
# run in new or existing directory
|
|
94
|
+
if arg[/^#{File::SEPARATOR}/]
|
|
95
|
+
savedir = arg
|
|
96
|
+
else
|
|
97
|
+
savedir = File.join(Dir.pwd, arg)
|
|
98
|
+
end
|
|
99
|
+
install_savedir(savedir)
|
|
100
|
+
end
|
|
101
|
+
|
|
102
|
+
return savedir
|
|
103
|
+
end
|
|
104
|
+
|
|
105
|
+
def install_savedir(savedir)
|
|
106
|
+
FileUtils.makedirs(savedir)
|
|
107
|
+
end
|
|
108
|
+
|
|
109
|
+
end # Setup
|
data/lib/bio/shell/web.rb
CHANGED
|
@@ -4,86 +4,98 @@
|
|
|
4
4
|
# Copyright:: Copyright (C) 2006
|
|
5
5
|
# Nobuya Tanaka <t@chemruby.org>,
|
|
6
6
|
# Toshiaki Katayama <k@bioruby.org>
|
|
7
|
-
# License:: Ruby
|
|
7
|
+
# License:: The Ruby License
|
|
8
8
|
#
|
|
9
|
-
# $Id: web.rb,v 1.
|
|
9
|
+
# $Id: web.rb,v 1.5 2007/06/26 08:38:38 k Exp $
|
|
10
10
|
#
|
|
11
11
|
|
|
12
12
|
|
|
13
13
|
module Bio::Shell
|
|
14
14
|
|
|
15
|
-
|
|
15
|
+
class Web
|
|
16
16
|
|
|
17
|
-
|
|
18
|
-
|
|
19
|
-
|
|
20
|
-
|
|
21
|
-
|
|
22
|
-
|
|
23
|
-
FileUtils.cp_r("#{basedir}/rails/.", ".")
|
|
24
|
-
puts "done"
|
|
17
|
+
def initialize
|
|
18
|
+
Bio::Shell.cache[:binding] = binding
|
|
19
|
+
Bio::Shell.cache[:results] ||= Results.new
|
|
20
|
+
install_rails
|
|
21
|
+
setup_rails
|
|
22
|
+
start_rails
|
|
25
23
|
end
|
|
26
|
-
end
|
|
27
24
|
|
|
28
|
-
|
|
29
|
-
require 'open3'
|
|
30
|
-
$web_server = Open3.popen3(server)
|
|
25
|
+
private
|
|
31
26
|
|
|
32
|
-
|
|
33
|
-
|
|
27
|
+
def setup_rails
|
|
28
|
+
puts
|
|
29
|
+
puts ">>>"
|
|
30
|
+
puts ">>> open http://localhost:3000/bioruby"
|
|
31
|
+
puts ">>>"
|
|
32
|
+
puts
|
|
33
|
+
puts '(You can change the port number by adding "-- -p 4000" option)'
|
|
34
|
+
puts
|
|
35
|
+
end
|
|
34
36
|
|
|
35
|
-
|
|
36
|
-
|
|
37
|
-
|
|
38
|
-
|
|
39
|
-
|
|
37
|
+
def install_rails
|
|
38
|
+
savedir = Bio::Shell.cache[:savedir]
|
|
39
|
+
path = File.join(savedir, "script", "generate")
|
|
40
|
+
unless File.exist?(path)
|
|
41
|
+
puts "Installing Rails application for BioRuby shell ... "
|
|
42
|
+
system("rails #{savedir}")
|
|
43
|
+
puts "done"
|
|
44
|
+
end
|
|
45
|
+
path = File.join(savedir, "app", "controllers", "bioruby_controller.rb")
|
|
46
|
+
unless File.exist?(path)
|
|
47
|
+
basedir = File.dirname(__FILE__)
|
|
48
|
+
puts "Installing Rails plugin for BioRuby shell ... "
|
|
49
|
+
FileUtils.cp_r("#{basedir}/rails/.", savedir)
|
|
50
|
+
Dir.chdir(savedir) do
|
|
51
|
+
system("./script/generate bioruby shell")
|
|
52
|
+
end
|
|
53
|
+
puts "done"
|
|
40
54
|
end
|
|
41
55
|
end
|
|
42
56
|
|
|
43
|
-
|
|
44
|
-
|
|
45
|
-
|
|
46
|
-
|
|
47
|
-
|
|
57
|
+
def start_rails
|
|
58
|
+
begin
|
|
59
|
+
Bio::Shell.cache[:rails] = Thread.new do
|
|
60
|
+
Dir.chdir(Bio::Shell.cache[:savedir]) do
|
|
61
|
+
require './config/boot'
|
|
62
|
+
require 'commands/server'
|
|
63
|
+
end
|
|
64
|
+
end
|
|
65
|
+
end
|
|
66
|
+
end
|
|
48
67
|
|
|
49
|
-
|
|
50
|
-
|
|
68
|
+
class Results
|
|
69
|
+
attr_accessor :number, :script, :result, :output
|
|
51
70
|
|
|
52
|
-
|
|
53
|
-
|
|
71
|
+
def initialize
|
|
72
|
+
@number = 0
|
|
73
|
+
@script = []
|
|
74
|
+
@result = []
|
|
75
|
+
@output = []
|
|
76
|
+
end
|
|
54
77
|
|
|
55
|
-
|
|
56
|
-
|
|
57
|
-
|
|
78
|
+
def store(script, result, output)
|
|
79
|
+
@number += 1
|
|
80
|
+
@script[@number] = script
|
|
81
|
+
@result[@number] = result
|
|
82
|
+
@output[@number] = output
|
|
83
|
+
return @number
|
|
84
|
+
end
|
|
58
85
|
|
|
59
|
-
|
|
60
|
-
|
|
86
|
+
def restore(number)
|
|
87
|
+
return @script[number], @result[number], @output[number]
|
|
88
|
+
end
|
|
89
|
+
end
|
|
61
90
|
|
|
62
|
-
|
|
63
|
-
puts "Open http://localhost:3000/shell/"
|
|
91
|
+
end
|
|
64
92
|
|
|
65
|
-
|
|
93
|
+
private
|
|
66
94
|
|
|
67
|
-
|
|
68
|
-
|
|
69
|
-
|
|
95
|
+
# *TODO* stop irb and start rails?
|
|
96
|
+
#def web
|
|
97
|
+
#end
|
|
70
98
|
|
|
71
|
-
def io.gets
|
|
72
|
-
bind = IRB.conf[:MAIN_CONTEXT].workspace.binding
|
|
73
|
-
vars = eval("local_variables", bind)
|
|
74
|
-
vars.each do |var|
|
|
75
|
-
next if var == "_"
|
|
76
|
-
if val = eval("#{var}", bind)
|
|
77
|
-
$drb_server[var] = val
|
|
78
|
-
else
|
|
79
|
-
$drb_server.delete(var)
|
|
80
|
-
end
|
|
81
|
-
end
|
|
82
|
-
line = shell_original_gets
|
|
83
|
-
line
|
|
84
|
-
end
|
|
85
|
-
end
|
|
86
|
-
|
|
87
99
|
end
|
|
88
100
|
|
|
89
101
|
|