├── .gitignore ├── INSTALL.md ├── Makefile ├── README-REPL.md ├── README.md ├── bin ├── README.md ├── owljs ├── owljs-decluster ├── owljs-decluster.js ├── owljs-diff ├── owljs-diff.js ├── owljs-dlmatch ├── owljs-dlmatch.js ├── owljs-dlquery ├── owljs-dlquery.js ├── owljs-expand-literals-using-ld-context.js ├── owljs-grep ├── owljs-grep.js ├── owljs-merge.js ├── owljs-obol ├── owljs-obol.js ├── owljs-owlstats ├── owljs-owlstats.js ├── owljs-refilter ├── owljs-refilter.js ├── owljs-remove-random-axioms ├── owljs-remove-random-axioms.js ├── owljs-repl ├── owljs-repl.js ├── owljs-sed ├── owljs-sed.js ├── owljs-svn-diffwrap ├── owljs-tableify ├── owljs-tableify.js ├── owljs-treeify ├── owljs-treeify.js ├── ringo-owl ├── svn-owl-diff └── svn-owl-htmldiff ├── conf ├── cl │ └── cl-cjm-conf.js ├── learner │ ├── class.conf │ ├── mptest.conf │ └── mptest.ofn └── uberon │ └── uberon-cjm-conf.js ├── docs ├── files │ ├── dlmatch-js.html │ ├── javautil-js.html │ ├── obol-js.html │ ├── owl-js.html │ ├── owlframe-js.html │ └── repl-js.html ├── index.html ├── index │ ├── Classes.html │ ├── Functions.html │ ├── Functions2.html │ ├── Functions3.html │ ├── General.html │ ├── General2.html │ ├── General3.html │ └── Variables.html ├── javascript │ ├── main.js │ ├── prettify.js │ └── searchdata.js ├── search │ ├── ClassesD.html │ ├── ClassesJ.html │ ├── ClassesO.html │ ├── ClassesR.html │ ├── ClassesV.html │ ├── FunctionsA.html │ ├── FunctionsC.html │ ├── FunctionsD.html │ ├── FunctionsE.html │ ├── FunctionsF.html │ ├── FunctionsG.html │ ├── FunctionsH.html │ ├── FunctionsI.html │ ├── FunctionsJ.html │ ├── FunctionsL.html │ ├── FunctionsM.html │ ├── FunctionsN.html │ ├── FunctionsO.html │ ├── FunctionsP.html │ ├── FunctionsR.html │ ├── FunctionsS.html │ ├── FunctionsT.html │ ├── FunctionsU.html │ ├── FunctionsW.html │ ├── GeneralA.html │ ├── GeneralC.html │ ├── GeneralD.html │ ├── GeneralE.html │ ├── GeneralF.html │ ├── GeneralG.html │ ├── GeneralH.html │ ├── GeneralI.html │ ├── GeneralJ.html │ ├── GeneralL.html │ ├── GeneralM.html │ ├── GeneralN.html │ ├── GeneralO.html │ ├── GeneralP.html │ ├── GeneralR.html │ ├── GeneralS.html │ ├── GeneralT.html │ ├── GeneralU.html │ ├── GeneralV.html │ ├── GeneralW.html │ ├── NoResults.html │ ├── VariablesL.html │ └── VariablesO.html └── styles │ └── main.css ├── jars └── owltools-runner-all.jar ├── lib ├── .naturaldocs_project │ ├── Data │ │ ├── ClassHierarchy.nd │ │ ├── ConfigFileInfo.nd │ │ ├── FileInfo.nd │ │ ├── ImageFileInfo.nd │ │ ├── ImageReferenceTable.nd │ │ ├── IndexInfo.nd │ │ ├── PreviousMenuState.nd │ │ ├── PreviousSettings.nd │ │ └── SymbolTable.nd │ ├── Languages.txt │ ├── Menu.txt │ ├── Menu_Backup.txt │ └── Topics.txt ├── Differ.js ├── Stats.js ├── annotator.js ├── dlmatch.js ├── io │ ├── dotty.js │ ├── markdown.js │ └── table.js ├── javautil.js ├── learner.js ├── linky.js ├── obol.js ├── obol │ ├── anatomy.js │ ├── bp.js │ ├── bp │ │ ├── cellDevelopment.js │ │ ├── involvedIn.js │ │ └── regulationOfQuality.js │ ├── equiv.js │ └── phenotype.js ├── owl.js ├── owl │ ├── addons.js │ ├── attic.js │ ├── owlframe.js │ ├── owlserver.js │ └── owlservices.js ├── owlframe.js ├── repl.js └── vocab │ ├── nif.js │ └── obo.js ├── package.json ├── server.js └── tests ├── alltests.js ├── data ├── caro.owl ├── catalog-v001.xml ├── ceph-import.owl ├── ceph.owl ├── clmin.ofn └── linkytest.owl ├── differ └── differ_test.js ├── dlmatch ├── dlmatch_nested_test.js └── dlmatch_test.js ├── learner ├── catalog-v001.xml ├── mp_test.js ├── mptest.ofn └── mptest.owl ├── linky └── linky_test.js ├── obol ├── obol_test.js └── obolsyn_test.js ├── obol_test_mp.obo ├── obolt.omn ├── owl ├── addimport_test.js ├── anc_test.js ├── import_test.js ├── owl_test.js └── owljson_test.js ├── owlfun_test.js ├── repl ├── author_test.js ├── catalog-v001.xml ├── fin2limb.js ├── foo.owl ├── instancequery_test.js ├── instont.js ├── limbs.js └── mkont.js └── vocab └── obo_test.js /.gitignore: -------------------------------------------------------------------------------- 1 | .pl-history -------------------------------------------------------------------------------- /INSTALL.md: -------------------------------------------------------------------------------- 1 | 2 | # Install RingoJS 3 | 4 | http://ringojs.org/ 5 | 6 | 7 | 8 | Add ringo and owl.js to your PATH. E.g. assume you checked out this 9 | repo into a ~/repos directory: 10 | 11 | export PATH=$PATH:$HOME/ringojs/bin 12 | export PATH=$PATH:$HOME/repos/owljs/bin 13 | 14 | I'm currently working on installation via rp, the ringo package 15 | manager. For now, do this hacky measure: 16 | 17 | cd $RINGO_HOME/packages/ 18 | ln -s ~/repos/owljs owl 19 | ln -s ~/repos/owljs owljs 20 | 21 | 22 | -------------------------------------------------------------------------------- /Makefile: -------------------------------------------------------------------------------- 1 | 2 | .PHONY: docs 3 | docs: 4 | naturaldocs --rebuild-output --input lib --project lib/.naturaldocs_project/ --output html docs/ 5 | 6 | jars/owltools-runner-all.jar: 7 | cd jars && wget http://build.berkeleybop.org/job/owltools/lastSuccessfulBuild/artifact/owltools/OWLTools-Runner/bin/$@ -O $@ 8 | 9 | ## http://secret-harbor-1370.herokuapp.com/ 10 | heroku-create: 11 | heroku create --stack cedar --buildpack https://github.com/cmungall/heroku-buildpack-ringojs-jdk7.git --remote monarch-heroku 12 | heroku-deploy: 13 | git push monarch-heroku master 14 | 15 | TEST = ringo-owl 16 | 17 | test: 18 | $(TEST) tests/alltests.js 19 | -------------------------------------------------------------------------------- /bin/README.md: -------------------------------------------------------------------------------- 1 | owljs scripts 2 | 3 | Be sure to add this directory to your $PATH 4 | 5 | ## Scripts 6 | 7 | * [owljs-repl](owljs-repl.js) - start a Read-Eval-Print Loop 8 | * [owljs-grep](owljs-grep.js) - filter axioms or objects from an ontology 9 | * [owljs-dlquery](owljs-dlquery.js) - perform a DL query using a reasoner 10 | * [owljs-dlmatch](owljs-dlmatch.js) - query axioms for those matching a template pattern 11 | * [owljs-diff](owljs-diff.js) - performs diff on two OWL files 12 | 13 | ## Script architecture 14 | 15 | Currently each script comes in pairs - the actual implementation 16 | (owljs-foo.js) and a shell wrapper (owljs-foo). You should run the 17 | shell wrapper. 18 | 19 | The shell wrapper actually calls a generic wrapper, ringo-owl, also, 20 | in this directory, which takes care of mundanities such as setting 21 | your classpath. 22 | 23 | Note the owljs-foo.js file must be both executable and in the PATH for 24 | this to work. 25 | 26 | Note that you can run ringo-owl at any time to get a REPL. -------------------------------------------------------------------------------- /bin/owljs: -------------------------------------------------------------------------------- 1 | #!/bin/sh 2 | X=`which owljs-repl.js` 3 | ringo-owl $X "$@" 4 | -------------------------------------------------------------------------------- /bin/owljs-decluster: -------------------------------------------------------------------------------- 1 | #!/bin/sh 2 | X=`which owljs-decluster.js` 3 | ringo-owl $X "$@" 4 | -------------------------------------------------------------------------------- /bin/owljs-decluster.js: -------------------------------------------------------------------------------- 1 | var Parser = require('ringo/args').Parser; 2 | var system = require('system'); 3 | var fs = require('fs'); 4 | var {OWL} = require("owljs"); 5 | var {Linky} = require("owljs/Linky"); 6 | 7 | var owl; 8 | function main(args) { 9 | var script = args.shift(); 10 | var parser = new Parser(system.args); 11 | var grepFunc = null; 12 | 13 | parser.addOption('h', 'help', null, 'Display help'); 14 | parser.addOption('r', 'reasoner', 'Reasoner', 'set reasoner factory. Default is elk. NOT IMPLEMENTED'); 15 | parser.addOption('c', 'importsClosure', null, 'set this flag if the full import closure is to be declustered'); 16 | parser.addOption('C', 'catalog', 'File', 'XML catalog for imports'); 17 | parser.addOption('m', 'markdownFile', 'File', 'output file for md report'); 18 | parser.addOption('o', 'outputFile', 'File', 'output file (defaults to stdout)'); 19 | 20 | var options = parser.parse(args); 21 | 22 | if (options.help) { 23 | print("Usage: owljs-decluster OPTIONS OWLFILE_A OWLFILE_B\n"); 24 | print("Breaks equivalence clusters such that bipartite equivalence graphs are retained"); 25 | print("\nOptions:"); 26 | print(parser.help()); 27 | print("\nExample:"); 28 | print("owljs-decluster -o decluster.md ont.owl"); 29 | system.exit('-1'); 30 | } 31 | 32 | owl = new OWL(); 33 | owl.addCatalog(options.catalog); 34 | owl.loadFile(args[0]); 35 | 36 | var incClosure = options.importsClosure == null ? false : true; 37 | 38 | var linky = new Linky(owl); 39 | if (options.markdownFile != null) { 40 | linky.io = fs.open(options.markdownFile, {write:true}); 41 | } 42 | 43 | linky.decluster(); 44 | 45 | if (options.outputFile != null) { 46 | owl.save(options.outputFile); 47 | } 48 | else { 49 | console.warn("No save"); 50 | } 51 | if (linky.io != null) { 52 | linky.io.close(); 53 | } 54 | } 55 | 56 | 57 | // call the main method; ringo specific 58 | if (require.main == module.id) { 59 | main(system.args); 60 | } 61 | -------------------------------------------------------------------------------- /bin/owljs-diff: -------------------------------------------------------------------------------- 1 | #!/bin/sh 2 | X=`which owljs-diff.js` 3 | ringo-owl $X "$@" 4 | -------------------------------------------------------------------------------- /bin/owljs-diff.js: -------------------------------------------------------------------------------- 1 | var Parser = require('ringo/args').Parser; 2 | var system = require('system'); 3 | var {OWL} = require("owljs"); 4 | var {Differ} = require("owljs/Differ"); 5 | 6 | var owlA; 7 | var owlB; 8 | function main(args) { 9 | var script = args.shift(); 10 | var parser = new Parser(system.args); 11 | var grepFunc = null; 12 | var useReasoner = false; 13 | 14 | parser.addOption('h', 'help', null, 'Display help'); 15 | parser.addOption('r', 'reasoner', 'Reasoner', 'set reasoner factory. Default is elk. NOT IMPLEMENTED'); 16 | parser.addOption('e', 'useReasoner', null, 'set this flag if reasoner diffs are tgo be performed'); 17 | parser.addOption('c', 'importsClosure', null, 'set this flag if the full import closure is to be diffed'); 18 | parser.addOption('C', 'catalog', 'File', 'XML catalog for imports'); 19 | parser.addOption('o', 'outputFile', 'File', 'output file (defaults to stdout)'); 20 | 21 | var options = parser.parse(args); 22 | 23 | if (options.help) { 24 | print("Usage: owljs-owldiff OPTIONS OWLFILE_A OWLFILE_B\n"); 25 | print("Writes differences between two files. Current output is markdown"); 26 | print("\nOptions:"); 27 | print(parser.help()); 28 | print("\nExample:"); 29 | print("owljs-diff -o diff.md ont1.owl ont2.owl"); 30 | system.exit('-1'); 31 | } 32 | 33 | owlA = new OWL(); 34 | owlA.addCatalog(options.catalog); 35 | owlA.loadFile(args[0]); 36 | 37 | owlB = new OWL(); 38 | owlB.addCatalog(options.catalog); 39 | owlB.loadFile(args[1]); 40 | 41 | var incClosure = options.importsClosure == null ? false : true; 42 | 43 | var differ = new Differ(); 44 | var md = differ.getDiffsAsMarkdown(owlA, owlB, incClosure, useReasoner); 45 | 46 | if (options.outputFile != null) { 47 | var fs = require('fs'); 48 | fs.write(options.outputFile, md); 49 | } 50 | else { 51 | print(md); 52 | } 53 | } 54 | 55 | 56 | // call the main method; ringo specific 57 | if (require.main == module.id) { 58 | main(system.args); 59 | } 60 | -------------------------------------------------------------------------------- /bin/owljs-dlmatch: -------------------------------------------------------------------------------- 1 | #!/bin/sh 2 | X=`which owljs-dlmatch.js` 3 | ringo-owl $X "$@" 4 | -------------------------------------------------------------------------------- /bin/owljs-dlquery: -------------------------------------------------------------------------------- 1 | #!/bin/sh 2 | X=`which owljs-dlquery.js` 3 | ringo-owl $X "$@" 4 | -------------------------------------------------------------------------------- /bin/owljs-dlquery.js: -------------------------------------------------------------------------------- 1 | var Parser = require('ringo/args').Parser; 2 | var system = require('system'); 3 | var {OWL} = require("owljs"); 4 | 5 | var owl; 6 | function main(args) { 7 | var script = args.shift(); 8 | var parser = new Parser(system.args); 9 | var grepFunc = null; 10 | 11 | parser.addOption('h', 'help', null, 'Display help'); 12 | parser.addOption('q', 'query', 'ManchesterString', 'class expression in owltools manchester syntax (all labels enclosed in single quotes)'); 13 | parser.addOption('r', 'reasoner', 'Reasoner', 'set reasoner factory. Default is elk.'); 14 | parser.addOption('a', 'ancestors', null, 'TODO'); 15 | parser.addOption('d', 'direct', null, 'direct only (defaults to direct plus indirect)'); 16 | parser.addOption('p', 'property', 'ObjectProperty', 'ancestors over specified relation. queries SELECT ?x WHERE {CLASSEXPR SubClassOf ?p some ?x}'); 17 | 18 | var options = parser.parse(args); 19 | 20 | if (options.help) { 21 | print("Usage: owljs-dlquery OPTIONS OWLFILE\n"); 22 | print("DL-query"); 23 | print("\nOptions:"); 24 | print(parser.help()); 25 | print("\nExample (what are the things that are parts of some cell):"); 26 | print("$ owljs-dlquery -r elk \"'part_of' some 'cell'\" foo.owl"); 27 | print("\nExample (what does this cell type have as parts)?:"); 28 | print("$ owljs-dlquery -p has_part -q \"'small pre-B-II cell'\" cl-edit.owl"); 29 | system.exit('-1'); 30 | } 31 | 32 | owl = new OWL(); 33 | owl.addCatalog(); 34 | args.forEach(function(fn) { owl.loadFile(fn) } ); 35 | 36 | var cx = owl.parseManchesterExpression(options.query); 37 | owl.log("Query="+cx); 38 | var subs; 39 | if (options.property == null) { 40 | subs = owl.getInferredSubClasses(cx); 41 | } 42 | else { 43 | var objprop = owl.find(options.property); 44 | owl.log("Prop="+objprop); 45 | subs = owl.getAncestorsOver(cx, objprop, false, options.direct != null); 46 | } 47 | subs.forEach(show); 48 | } 49 | 50 | function show(c) { 51 | print(c + " " + owl.getLabel(c)); 52 | } 53 | 54 | // call the main method; ringo specific 55 | if (require.main == module.id) { 56 | main(system.args); 57 | } 58 | -------------------------------------------------------------------------------- /bin/owljs-expand-literals-using-ld-context.js: -------------------------------------------------------------------------------- 1 | var Parser = require('ringo/args').Parser; 2 | var system = require('system'); 3 | var {OWL} = require("owljs"); 4 | var ov = require("owljs/vocab/obo"); 5 | 6 | importPackage(Packages.org.semanticweb.owlapi.model); 7 | 8 | var owl; 9 | var part_of; 10 | var rels; 11 | var relObjs = []; 12 | var isElk; 13 | 14 | function main(args) { 15 | var script = args.shift(); 16 | var parser = new Parser(system.args); 17 | var grepFunc = null; 18 | 19 | parser.addOption('h', 'help', null, 'Display help'); 20 | parser.addOption('c', 'importsClosure', null, 'set this flag if the full import closure is to used'); 21 | parser.addOption('x', 'context', 'File', 'context file'); 22 | parser.addOption('o', 'outputFile', 'File', 'output file (defaults to stdout)'); 23 | parser.addOption('t', 'toOutputFormat', 'OWLOntologyFormat', 'output format (defaults to RDFXML)'); 24 | 25 | var options = parser.parse(args); 26 | var incClosure = options.importsClosure == null ? false : true; 27 | 28 | if (options.help) { 29 | print("Usage: owljs-expand-literals-using-ld-context.js OPTIONS OWLFILE\n"); 30 | print("Stats"); 31 | print("\nOptions:"); 32 | print(parser.help()); 33 | system.exit('-1'); 34 | } 35 | 36 | owl = new OWL(); 37 | owl.addCatalog(); 38 | 39 | if (options.toOutputFormat != null) { 40 | console.log("Setting format to "+options.toOutputFormat); 41 | owl.setDefaultFormat(options.toOutputFormat); 42 | } 43 | 44 | args.forEach(function(fn) { owl.loadFile(fn) } ); 45 | 46 | owl.log("Saving to " + options.outputFile); 47 | owl.save(options.outputFile); 48 | 49 | } 50 | 51 | function render(c) { 52 | if (c == null) { 53 | return ""; 54 | } 55 | if (c.map != null) { 56 | return c.map(render).join("|"); 57 | } 58 | else { 59 | if (c.getIRI != null) { 60 | return owl.getLabel(c) 61 | } 62 | else { 63 | return markdown.renderOWLObject(c, owl, {isLabelOnly : true}); 64 | } 65 | } 66 | } 67 | 68 | function getColVals(c, type) { 69 | var def = ov.getDefinitionObject(owl,c); 70 | // shared by all types 71 | var vals = 72 | [ 73 | { name: "iri", 74 | value: c.getIRI()}, 75 | { name: "label", 76 | value: owl.getLabel(c)}, 77 | { name: "definition", 78 | value: def == null ? "" : def.value}, 79 | { name: "definitionXrefs", 80 | value: def == null ? "" : def.xrefs.join(",")} 81 | ]; 82 | if (type == 'Class') { 83 | vals = vals.concat([ 84 | { name: "superClasses", 85 | value: render(owl.getInferredSuperClasses(c, true, false, true)) }, 86 | //{ name: "part_of", 87 | // value: render(owl.getAncestorsOver(c, part_of, true, false)) } 88 | ]); 89 | relObjs.forEach(function(r) { 90 | vals.push( 91 | { name: r.label, 92 | value: render(owl.getAncestorsOver(c, r.obj, true, false)) } 93 | ); 94 | }); 95 | } 96 | else if (type == 'ObjectProperty') { 97 | if (!isElk) { 98 | vals = vals.concat([ 99 | { name: "superProperties", 100 | value: render(owl.getInferredSuperProperties(c, true, false, true)) }, 101 | ]); 102 | } 103 | var axs = owl.getAxiomsReferencing(c, true); 104 | vals = vals.concat([ 105 | { name: "classAxiomUsages", 106 | value: axs.length }, 107 | ]); 108 | vals = vals.concat([ 109 | { name: "classAxiomExampleUsage", 110 | value: render(axs. 111 | filter(interesting). 112 | slice(0,5)) }, 113 | ]); 114 | } 115 | return vals; 116 | 117 | } 118 | 119 | function interesting(ax) { 120 | return ax.getSubClass != null || ax.getClassExpressions != null; 121 | } 122 | 123 | 124 | // call the main method; ringo specific 125 | if (require.main == module.id) { 126 | main(system.args); 127 | } 128 | -------------------------------------------------------------------------------- /bin/owljs-grep: -------------------------------------------------------------------------------- 1 | #!/bin/sh 2 | X=`which owljs-grep.js` 3 | ringo-owl $X "$@" 4 | -------------------------------------------------------------------------------- /bin/owljs-merge.js: -------------------------------------------------------------------------------- 1 | var Parser = require('ringo/args').Parser; 2 | var system = require('system'); 3 | var {OWL} = require("owljs"); 4 | var {Differ} = require("owljs/Differ"); 5 | 6 | var owlA; 7 | var owlB; 8 | function main(args) { 9 | var script = args.shift(); 10 | var parser = new Parser(system.args); 11 | var grepFunc = null; 12 | 13 | parser.addOption('h', 'help', null, 'Display help'); 14 | parser.addOption('r', 'reasoner', 'Reasoner', 'set reasoner factory. Default is elk. NOT IMPLEMENTED'); 15 | parser.addOption('c', 'importsClosure', null, 'set this flag if the full import closure is to be diffed'); 16 | parser.addOption('o', 'outputFile', 'File', 'output file (defaults to stdout)'); 17 | 18 | var options = parser.parse(args); 19 | 20 | if (options.help) { 21 | print("Usage: owljs-owldiff OPTIONS OWLFILE_A OWLFILE_B\n"); 22 | print("Writes differences between two files. Current output is markdown"); 23 | print("\nOptions:"); 24 | print(parser.help()); 25 | print("\nExample:"); 26 | print("owljs-diff -o diff.md ont1.owl ont2.owl"); 27 | system.exit('-1'); 28 | } 29 | 30 | owlOrig = new OWL(); 31 | owlOrig.addCatalog(); 32 | owlOrig.loadFile(args.shift); 33 | 34 | owlA = new OWL(); 35 | owlA.addCatalog(); 36 | owlA.loadFile(args.shift); 37 | 38 | owlB = new OWL(); 39 | owlB.addCatalog(); 40 | owlB.loadFile(args.shift); 41 | 42 | if (options.toOutputFormat != null) { 43 | console.log("Setting format to "+options.toOutputFormat); 44 | owl.setDefaultFormat(options.toOutputFormat); 45 | } 46 | 47 | var differ = new Differ(); 48 | differ.merge(owlOrig, owlA, owlB); 49 | 50 | owlA.save(options.outputFile); 51 | 52 | } 53 | 54 | 55 | // call the main method; ringo specific 56 | if (require.main == module.id) { 57 | main(system.args); 58 | } 59 | -------------------------------------------------------------------------------- /bin/owljs-obol: -------------------------------------------------------------------------------- 1 | #!/bin/sh 2 | X=`which owljs-obol.js` 3 | ringo-owl $X "$@" 4 | -------------------------------------------------------------------------------- /bin/owljs-owlstats: -------------------------------------------------------------------------------- 1 | #!/bin/sh 2 | X=`which owljs-owlstats.js` 3 | ringo-owl $X "$@" 4 | -------------------------------------------------------------------------------- /bin/owljs-owlstats.js: -------------------------------------------------------------------------------- 1 | var Parser = require('ringo/args').Parser; 2 | var system = require('system'); 3 | var {OWL} = require("owljs"); 4 | var stats = require("owljs/Stats"); 5 | 6 | var owl; 7 | function main(args) { 8 | var script = args.shift(); 9 | var parser = new Parser(system.args); 10 | var grepFunc = null; 11 | 12 | parser.addOption('h', 'help', null, 'Display help'); 13 | parser.addOption('r', 'reasoner', 'Reasoner', 'set reasoner factory. Default is elk.'); 14 | parser.addOption('o', 'outputFile', 'File', 'output file (defaults to stdout)'); 15 | 16 | var options = parser.parse(args); 17 | 18 | if (options.help) { 19 | print("Usage: owljs-owlstats OPTIONS OWLFILE\n"); 20 | print("Stats"); 21 | print("\nOptions:"); 22 | print(parser.help()); 23 | system.exit('-1'); 24 | } 25 | 26 | owl = new OWL(); 27 | owl.addCatalog(); 28 | args.forEach(function(fn) { owl.loadFile(fn) } ); 29 | 30 | var info = stats.getOntologyStats(owl); 31 | var json = JSON.stringify(info, null, ' '); 32 | if (options.outputFile != null) { 33 | var fs = require('fs'); 34 | fs.write(options.outputFile, json); 35 | } 36 | else { 37 | print(json); 38 | } 39 | } 40 | 41 | function show(c) { 42 | print(c + " " + owl.getLabel(c)); 43 | } 44 | 45 | // call the main method; ringo specific 46 | if (require.main == module.id) { 47 | main(system.args); 48 | } 49 | -------------------------------------------------------------------------------- /bin/owljs-refilter: -------------------------------------------------------------------------------- 1 | #!/bin/sh 2 | X=`which owljs-cgrep.js` 3 | ringo-owl $X "$@" 4 | -------------------------------------------------------------------------------- /bin/owljs-refilter.js: -------------------------------------------------------------------------------- 1 | var Parser = require('ringo/args').Parser; 2 | var system = require('system'); 3 | var {OWL} = require("owljs"); 4 | 5 | function main(args) { 6 | var script = args.shift(); 7 | var parser = new Parser(system.args); 8 | var re = null; 9 | 10 | parser.addOption('h', 'help', null, 'Display help'); 11 | parser.addOption('v', 'invertMatch', null, 'Invert (negate) match'); 12 | parser.addOption('o', 'outputFile', 'File', 'output file (defaults to stdout)'); 13 | parser.addOption('t', 'toOutputFormat', 'OWLOntologyFormat', 'output format (defaults to RDFXML)'); 14 | parser.addOption('j', 'jsFrames', null, 'writes output as js frames'); 15 | 16 | var options = parser.parse(args); 17 | 18 | if (options.help) { 19 | print("Usage: owljs-cgrep OPTIONS [PATTERN] OWLFILE\n"); 20 | print("Filters class from an ontology using a regexp. Compare with owljs-grep, which greps axioms"); 21 | print("\nOptions:"); 22 | print(parser.help()); 23 | print("\nExample:"); 24 | print("owljs-cgrep /epithelium/ foo.owl"); 25 | system.exit('-1'); 26 | } 27 | 28 | var owl = new OWL(); 29 | 30 | if (options.toOutputFormat != null) { 31 | console.log("Setting format to "+options.toOutputFormat); 32 | owl.setDefaultFormat(options.toOutputFormat); 33 | } 34 | 35 | var reStr = args.shift(); 36 | if (reStr.indexOf("/") != 0) { 37 | reStr = "/" + reStr + "/"; 38 | } 39 | var re = eval(reStr); 40 | 41 | args.forEach(function(fn) { owl.loadFile(fn) } ); 42 | 43 | if (options.load != null) { 44 | owl.log("Loading "+options.load); 45 | } 46 | var clist = owl.mfind(re); 47 | owl.log("#filteredClasses = " + clist.length); 48 | 49 | if (options.jsFrames) { 50 | var repl = require("owljs/repl"); 51 | repl.owlinit(owl); 52 | //repl.owl = owl; 53 | for (var ci in clist) { 54 | var c = clist[ci]; 55 | var fr = owl.getFrame(c); 56 | print(repl.render(fr)); 57 | } 58 | } 59 | else { 60 | 61 | var filteredAxioms = []; 62 | for (var ci in clist) { 63 | var c = clist[ci]; 64 | var axioms = owl.getAllAxioms(c); 65 | console.log(c+" #axioms = "+axioms.length); 66 | filteredAxioms = filteredAxioms.concat(axioms); 67 | } 68 | owl.log("#filteredAxioms = " + filteredAxioms.length); 69 | 70 | owl.log("Saving to " + options.outputFile); 71 | owl.saveAxioms(filteredAxioms, null, options.outputFile); 72 | } 73 | } 74 | 75 | // call the main method; ringo specific 76 | if (require.main == module.id) { 77 | main(system.args); 78 | } 79 | -------------------------------------------------------------------------------- /bin/owljs-remove-random-axioms: -------------------------------------------------------------------------------- 1 | #!/bin/sh 2 | X=`which owljs-remove-random-axioms.js` 3 | ringo-owl $X "$@" 4 | -------------------------------------------------------------------------------- /bin/owljs-remove-random-axioms.js: -------------------------------------------------------------------------------- 1 | var Parser = require('ringo/args').Parser; 2 | var system = require('system'); 3 | var {OWL} = require("owljs"); 4 | 5 | // have this available for evaluation of user functions 6 | importPackage(Packages.org.semanticweb.owlapi.model); 7 | 8 | function main(args) { 9 | var script = args.shift(); 10 | var parser = new Parser(system.args); 11 | var sedFunc = null; 12 | 13 | parser.addOption('h', 'help', null, 'Display help'); 14 | parser.addOption('o', 'outputFile', 'File', 'output file (defaults to stdout)'); 15 | parser.addOption('n', 'number', 'Number', 'Number of axioms to remove.'); 16 | parser.addOption('t', 'toOutputFormat', 'OWLOntologyFormat', 'output format (defaults to RDFXML)'); 17 | 18 | var options = parser.parse(args); 19 | 20 | if (options.help) { 21 | print("Usage: owljs-remove-random-axioms OPTIONS [FUNCTION] OWLFILE\n"); 22 | print("Removes axioms at random. For testing purposes"); 23 | print("\nOptions:"); 24 | print(parser.help()); 25 | system.exit('-1'); 26 | } 27 | 28 | var owl = new OWL(); 29 | owl.addCatalog(); 30 | 31 | if (options.toOutputFormat != null) { 32 | console.log("Setting format to "+options.toOutputFormat); 33 | owl.setDefaultFormat(options.toOutputFormat); 34 | } 35 | 36 | 37 | args.forEach(function(fn) { owl.loadFile(fn) } ); 38 | 39 | if (options.load != null) { 40 | owl.log("Loading "+options.load); 41 | } 42 | 43 | var NUM = options.number; 44 | if (NUM == null) { 45 | NUM = 1; 46 | } 47 | 48 | var axioms = owl.getAllAxioms(null, false); 49 | var axl = axioms.length; 50 | console.log("#Axioms = "+axl); 51 | var rmAxioms = []; 52 | if (NUM >= axl) { 53 | console.warn("Will remove ALL axioms!"); 54 | } 55 | 56 | var i=0; 57 | while (i < NUM) { 58 | axl = axioms.length; 59 | var ai = Math.floor(axl * Math.random()); 60 | console.log("Removing #"+ai); 61 | rmAxioms.push(axioms[ai]); 62 | axioms.splice(ai, 1); 63 | i++; 64 | } 65 | console.log("Remove Axiom Count: "+rmAxioms.length); 66 | owl.removeAxioms(rmAxioms); 67 | 68 | owl.log("Saving to " + options.outputFile); 69 | owl.save(options.outputFile); 70 | } 71 | 72 | // call the main method; ringo specific 73 | if (require.main == module.id) { 74 | main(system.args); 75 | } 76 | -------------------------------------------------------------------------------- /bin/owljs-repl: -------------------------------------------------------------------------------- 1 | #!/bin/sh 2 | X=`which owljs-repl.js` 3 | ringo-owl $X "$@" 4 | -------------------------------------------------------------------------------- /bin/owljs-repl.js: -------------------------------------------------------------------------------- 1 | // we use include() rather than require(), deliberately polluting our namespace for convenience 2 | include("owljs/repl"); 3 | 4 | var Parser = require('ringo/args').Parser; 5 | var system = require('system'); 6 | var fs = require('fs'); 7 | var {OWL} = require("owljs"); 8 | var {OWLFrame} = require("owljs/owlframe"); 9 | var {DLMatch} = require("owljs/dlmatch"); 10 | var {Obol} = require("owljs/obol"); 11 | var q; 12 | var obol; 13 | var options; 14 | 15 | importPackage(Packages.org.semanticweb.owlapi.model); 16 | 17 | function main(args) { 18 | var script = args.shift(); 19 | var parser = new Parser(system.args); 20 | 21 | parser.addOption('h', 'help', null, 'Display help'); 22 | parser.addOption('i', 'include', 'File', 'loads js. Argument can be a path to a js file or a module name'); 23 | parser.addOption('e', 'evaluate', 'Code', 'evals js code block'); 24 | parser.addOption('l', 'load', 'File', 'Evals file contents'); 25 | parser.addOption('x', 'exit', null, 'Exit on completion'); 26 | parser.addOption('v', 'verbosity', 'Number', 'sets verbosity. >0 logs'); 27 | 28 | options = parser.parse(args); 29 | 30 | if (options.help) { 31 | print("Usage: owljs-repl OPTIONS [ARGUMENTS] [OWLFILE...]\n"); 32 | print("Starts an interactive Read-Eval-Print-Loop."); 33 | print("\nOptions:"); 34 | print(parser.help()); 35 | print("\nExample:"); 36 | print("owljs-repl -i bootcl.js cl-edit.owl"); 37 | print("\nVariables:"); 38 | print(" - o : lookup table keyed by safe-labels, indexing OWL objects"); 39 | print(" - owl : an OWL object"); 40 | print(" - q : a DLMatch object"); 41 | print("\nDocumentation:"); 42 | print("See https://github.com/cmungall/owl.js/blob/master/README-REPL.md"); 43 | system.exit('-1'); 44 | } 45 | 46 | owl = new OWL(); 47 | 48 | owl.config.logLevel = options.verbosity; 49 | 50 | owl.addCatalog(); 51 | 52 | args.forEach(function(fn) { owl.loadFile(fn) } ); 53 | q = new DLMatch(owl); 54 | obol = new Obol(owl); 55 | 56 | owlinit(owl); 57 | if (options.evaluate != null) { 58 | eval(options.evaluate); 59 | } 60 | if (options.load != null) { 61 | eval(fs.read(options.load)); 62 | } 63 | 64 | if (options.include != null) { 65 | var path = options.include; 66 | if (fs.exists(path)) { 67 | load(path); 68 | } 69 | else { 70 | include(path); 71 | } 72 | owlinit(owl); 73 | } 74 | } 75 | 76 | if (require.main == module.id) { 77 | main(system.args); 78 | } 79 | 80 | if (options.exit == null) { 81 | print(">> Welcome!"); 82 | require('ringo/shell').start(); 83 | } 84 | 85 | -------------------------------------------------------------------------------- /bin/owljs-sed: -------------------------------------------------------------------------------- 1 | #!/bin/sh 2 | X=`which owljs-sed.js` 3 | ringo-owl $X "$@" 4 | -------------------------------------------------------------------------------- /bin/owljs-sed.js: -------------------------------------------------------------------------------- 1 | var Parser = require('ringo/args').Parser; 2 | var system = require('system'); 3 | var {OWL} = require("owljs"); 4 | 5 | // have this available for evaluation of user functions 6 | importPackage(Packages.org.semanticweb.owlapi.model); 7 | 8 | function main(args) { 9 | var script = args.shift(); 10 | var parser = new Parser(system.args); 11 | var sedFunc = null; 12 | 13 | parser.addOption('h', 'help', null, 'Display help'); 14 | parser.addOption('v', 'invertMatch', null, 'Invert (negate) match'); 15 | parser.addOption('o', 'outputFile', 'File', 'output file (defaults to stdout)'); 16 | parser.addOption('f', 'sedFunctionFile', 'File', 'file containing js that evals to sedFunc. If specified no FUNCTION arg is specified'); 17 | parser.addOption('e', 'sedEntities', null, 'True if entities (classes, individuals, properties) are to be sedped, no axioms '); 18 | parser.addOption('m', 'match', 'Regexp', 'regular expression applied to serialization of each axiom. E.g. /epithelium/. If specified, no FUNCTION arg is specified.'); 19 | parser.addOption('t', 'toOutputFormat', 'OWLOntologyFormat', 'output format (defaults to RDFXML)'); 20 | parser.addOption('j', 'jsFrames', null, 'writes output as js frames. TODO'); 21 | 22 | var options = parser.parse(args); 23 | 24 | if (options.help) { 25 | print("Usage: owljs-sed OPTIONS [FUNCTION] OWLFILE\n"); 26 | print("Search and replace axioms from an ontology using a custom function. See owl.sedAxioms() for more detauls"); 27 | print("\nOptions:"); 28 | print(parser.help()); 29 | print("\nExample:"); 30 | print("owljs-sed 'function(ax){ TODO return ax.isLogicalAxiom() }' foo.owl"); 31 | print("\nExample: (use saved function, negate query, write in functional notation)"); 32 | print("owljs-sed -v -t ofn -f lib/owlfunc/axiomIsLogical.js foo.owl"); 33 | system.exit('-1'); 34 | } 35 | 36 | var owl = new OWL(); 37 | owl.addCatalog(); 38 | 39 | if (options.toOutputFormat != null) { 40 | console.log("Setting format to "+options.toOutputFormat); 41 | owl.setDefaultFormat(options.toOutputFormat); 42 | } 43 | 44 | if (options.match != null) { 45 | var mf = eval(options.match); 46 | sedFunc = function(ax) { return mf.test(ax.toString()); }; 47 | } 48 | 49 | if (options.sedFunctionFile != null) { 50 | var fs = require("fs"); 51 | sedFunc = eval(fs.read(options.sedFunctionFile)); 52 | } 53 | 54 | if (sedFunc == null) { 55 | var sedFuncStr = args.shift(); 56 | sedFunc = eval(sedFuncStr); 57 | } 58 | 59 | args.forEach(function(fn) { owl.loadFile(fn) } ); 60 | 61 | if (options.load != null) { 62 | owl.log("Loading "+options.load); 63 | } 64 | 65 | if (options.sedEntities) { 66 | 67 | var filteredObjects = owl.sedObjects(sedFunc, options.invertMatch, true); 68 | owl.log("#filteredObjects = " + filteredObjects.length); 69 | 70 | if (options.jsFrames) { 71 | var repl = require("owljs/repl"); 72 | repl.owlinit(owl); 73 | for (var k in filteredObjects) { 74 | var obj = filteredObjects[k]; 75 | print(repl.render(owl.getFrame(obj))); 76 | } 77 | } 78 | else { 79 | owl.log("Saving to " + options.outputFile); 80 | owl.save(options.outputFile); 81 | } 82 | } 83 | else { 84 | 85 | var newAxioms = owl.sedAxioms(sedFunc, options.invertMatch, true); 86 | owl.log("#newAxioms = " + newAxioms.length); 87 | 88 | if (options.jsFrames) { 89 | var repl = require("owljs/repl"); 90 | repl.owlinit(owl); 91 | //repl.owl = owl; 92 | for (var k in filteredAxioms) { 93 | var ax = filteredAxioms[k]; 94 | print(repl.render(ax)); 95 | } 96 | } 97 | else { 98 | owl.log("Saving to " + options.outputFile); 99 | owl.save(options.outputFile); 100 | } 101 | } 102 | } 103 | 104 | // call the main method; ringo specific 105 | if (require.main == module.id) { 106 | main(system.args); 107 | } 108 | -------------------------------------------------------------------------------- /bin/owljs-svn-diffwrap: -------------------------------------------------------------------------------- 1 | #!/bin/sh 2 | owljs-diff $6 $7 3 | #exit 0 4 | ##svn diff --diff-cmd owljs-diff "$@" 5 | -------------------------------------------------------------------------------- /bin/owljs-tableify: -------------------------------------------------------------------------------- 1 | #!/bin/sh 2 | X=`which owljs-tableify.js` 3 | ringo-owl $X "$@" 4 | -------------------------------------------------------------------------------- /bin/owljs-treeify: -------------------------------------------------------------------------------- 1 | #!/bin/sh 2 | X=`which owljs-treeify.js` 3 | ringo-owl $X "$@" 4 | -------------------------------------------------------------------------------- /bin/owljs-treeify.js: -------------------------------------------------------------------------------- 1 | var Parser = require('ringo/args').Parser; 2 | var system = require('system'); 3 | var {OWL} = require("owljs"); 4 | var ov = require("owljs/vocab/obo"); 5 | 6 | var owl; 7 | var part_of; 8 | var rels; 9 | var relObjs = []; 10 | 11 | function main(args) { 12 | var script = args.shift(); 13 | var parser = new Parser(system.args); 14 | var grepFunc = null; 15 | 16 | parser.addOption('h', 'help', null, 'Display help'); 17 | parser.addOption('r', 'reasoner', 'Reasoner', 'set reasoner factory. Default is elk.'); 18 | parser.addOption('R', 'relations', 'RelList', 'relations to query over.'); 19 | parser.addOption('S', 'superClass', 'Class', 'only use subclasses of this.'); 20 | parser.addOption('c', 'importsClosure', null, 'set this flag if the full import closure is to used'); 21 | parser.addOption('o', 'outputFile', 'File', 'output file (defaults to stdout)'); 22 | 23 | var options = parser.parse(args); 24 | var incClosure = options.importsClosure == null ? false : true; 25 | 26 | if (options.help) { 27 | print("Usage: owljs-treeify OPTIONS OWLFILE\n"); 28 | print("Stats"); 29 | print("\nOptions:"); 30 | print(parser.help()); 31 | system.exit('-1'); 32 | } 33 | 34 | owl = new OWL(); 35 | owl.addCatalog(); 36 | args.forEach(function(fn) { owl.loadFile(fn) } ); 37 | if (options.reasoner != null) { 38 | owl.setReasonerType(options.reasoner); 39 | } 40 | 41 | rels = []; 42 | if (options.relations != null) { 43 | options.relations.split(",").forEach(function(rn) { 44 | rels.push(owl.find(rn)); 45 | }); 46 | } 47 | if (rels == []) { 48 | rels = [ov.part_of(owl)]; 49 | } 50 | relObjs = rels.map( function(r) { 51 | var label = owl.getLabel(r); 52 | if (label == null) { 53 | console.warn("No label: "+r); 54 | } 55 | return { obj : r, 56 | label : label }}); 57 | 58 | var io; 59 | var fs; 60 | if (options.outputFile != null) { 61 | fs = require('fs'); 62 | io = fs.open(options.outputFile, {write:true}); 63 | //fs.write(options.outputFile, json); 64 | } 65 | else { 66 | //print(json); 67 | } 68 | 69 | 70 | var cs; 71 | var type = options.objectType; 72 | if (type == null) { 73 | type = "Class"; 74 | } 75 | if (type == 'Class') { 76 | // note that ontologies that reference other ontologies automatically have 77 | // external referenced classes in their signature; if the intent is to 78 | // show ontologies that 'belong' to an ontology we make the assumption that 79 | // the declaration is accompanied by at least one other axiom 80 | if (options.superClass != null) { 81 | cs = owl.getInferredSubClasses( owl.find(options.superClass), false, true ); 82 | } 83 | else { 84 | cs = owl.getClassesWithAxioms(incClosure); 85 | } 86 | 87 | } 88 | else if (type == 'ObjectProperty') { 89 | cs = owl.getObjectProperties(incClosure); 90 | } 91 | 92 | cs.sort(function(a,b){ return a.getIRI().compareTo(b.getIRI()) }); 93 | 94 | function peekName(obj) { 95 | return obj.name; 96 | } 97 | function peekVal(obj) { 98 | return obj.value; 99 | } 100 | 101 | 102 | var n=0; 103 | for (var k in cs) { 104 | var c = cs[k]; 105 | if (owl.isDeprecated(c)) { 106 | continue; 107 | } 108 | 109 | var tree = getTree(c); 110 | if (tree.length == 0) { 111 | continue; 112 | } 113 | 114 | var line = c.getIRI() + "\t" + owl.getLabel(c) + "\t" + tree.length + "\t" + tree.map( 115 | function(a) { 116 | return owl.getLabel(a); 117 | } 118 | ).join(","); 119 | 120 | if (io == null) { 121 | print(line); 122 | } 123 | else { 124 | io.write(line+"\n"); 125 | } 126 | n++; 127 | } 128 | if (io != null) { 129 | io.close(); 130 | } 131 | } 132 | 133 | function getTree(c) { 134 | var ancs = []; 135 | for (var k in rels) { 136 | var rel = rels[k]; 137 | ancs = ancs.concat(owl.getAncestorsOver(c, rel, true, false)); 138 | ancs.forEach( function(a) { 139 | ancs = ancs.concat(owl.getAncestorsOver(a, rel, true, false)); 140 | }); 141 | } 142 | 143 | return ancs; 144 | } 145 | 146 | 147 | // call the main method; ringo specific 148 | if (require.main == module.id) { 149 | main(system.args); 150 | } 151 | -------------------------------------------------------------------------------- /bin/ringo-owl: -------------------------------------------------------------------------------- 1 | #!/bin/sh 2 | 3 | CLASSPATH_LITERAL="" 4 | 5 | PATH_SEP=":" 6 | 7 | JAVAARGS=" " 8 | CMDARGS=" " 9 | 10 | PATH_TO_ME=`which $0`; 11 | 12 | #Now see if the path is actually a symbolic link. If it is, set TEMP 13 | #to true 14 | TEMP=`ls -l $PATH_TO_ME | sed -e "s/.* -> \(.*\)/true/g"` 15 | if [ -z "$TEMP" ] 16 | then 17 | TEMP='false'; 18 | fi 19 | 20 | #While we keep finding symbolic links... 21 | while [ "$TEMP" = "true" ] 22 | do 23 | #Parse the ls output and set PATH_TO_ME to the actual location of the 24 | #symbolic link 25 | PATH_TO_ME=`ls -l $PATH_TO_ME | sed -e "s/.* -> \(.*\)/\1/g"` 26 | 27 | TEMP=`ls -l $PATH_TO_ME | sed -e "s/.* -> \(.*\)/true/g"` 28 | if [ -z "$TEMP" ] 29 | then 30 | TEMP='false' 31 | fi 32 | done 33 | 34 | #If PATH_TO_ME is a relative link, set TEMP to true, otherwise set 35 | #TEMP to false 36 | TEMP=`echo $PATH_TO_ME | sed -e "s/^\/.*/true/g"` 37 | if [ -z "$TEMP" ] 38 | then 39 | TEMP='false' 40 | fi 41 | 42 | #If PATH_TO_ME was a relative link, change it to an absolute reference 43 | if [ $TEMP != 'true' ] 44 | then 45 | PATH_TO_ME="$PWD/$PATH_TO_ME" 46 | fi 47 | 48 | SCRIPTNAME=`echo $PATH_TO_ME | sed -e "s/.*\/\(.*\)/\1/g"` 49 | 50 | #Remove the name of this script from the end of the path 51 | PATH_TO_ME=`echo $PATH_TO_ME | sed -e "s/\(.*\)\/.*/\1/g"` 52 | 53 | 54 | 55 | ## Assumption: all classes including rhino are packed into 56 | ## owltools-runner-all.jar 57 | ## These will be resolved into absolute pathnames 58 | DEFAULT_OWLTOOLS_LOCATION=../jars/owltools-runner-all.jar 59 | ALTERNATIVE_OWLTOOLS_LOCATION=../owltools-runner-all.jar 60 | 61 | if [ -f $PATH_TO_ME/$DEFAULT_OWLTOOLS_LOCATION ]; 62 | then 63 | CLASSPATH_RELATIVE=$DEFAULT_OWLTOOLS_LOCATION; 64 | else 65 | if [ -f $PATH_TO_ME/$ALTERNATIVE_OWLTOOLS_LOCATION ]; 66 | then 67 | CLASSPATH_RELATIVE=$ALTERNATIVE_OWLTOOLS_LOCATION; 68 | else 69 | echo "Cannot find owltools-runner-all.jar in any of the expected locations"; 70 | exit 1 71 | fi 72 | fi 73 | 74 | DEREFERENCED_CLASSPATH=`ls -1 -L $PATH_TO_ME/$CLASSPATH_RELATIVE | grep -v ontologyrelease` 75 | 76 | 77 | 78 | export OWLTOOLS_JAR_PATH=$DEREFERENCED_CLASSPATH 79 | 80 | #BOOT="-b $PATH_TO_ME/pachyowl.js -b $PATH_TO_ME/owlrunner.js" 81 | ##ringo -J-Xmx8G -J-XX:MaxPermSize=256M -DentityExpansionLimit=2048000 "$@" 82 | ringo -J-Xmx8G -DentityExpansionLimit=2048000 "$@" 83 | #ringo $BOOT -e "addToClasspath('$DEREFERENCED_CLASSPATH')" "$@" 84 | 85 | -------------------------------------------------------------------------------- /bin/svn-owl-diff: -------------------------------------------------------------------------------- 1 | #!/bin/sh 2 | svn diff --diff-cmd owljs-svn-diffwrap "$@" 3 | -------------------------------------------------------------------------------- /bin/svn-owl-htmldiff: -------------------------------------------------------------------------------- 1 | #!/bin/sh 2 | svn diff --diff-cmd owljs-svn-diffwrap "$@" > diff.md && pandoc diff.md -o diff.html && open diff.html 3 | -------------------------------------------------------------------------------- /conf/cl/cl-cjm-conf.js: -------------------------------------------------------------------------------- 1 | // To use this conf: 2 | // 3 | // cd cell-ontology/src/ontology 4 | // owljs-repl -i cl-cjm-conf.js cl-edit.owl 5 | // 6 | // Make sure file is copied to same dir, or add a symlink. 7 | // You can clone this for your own setup 8 | 9 | owl.config.idspace = 'CL'; 10 | owl.config.lastId = 10000; // CJM 11 | owl.defaultSlotMap = { created_by : "GOC:cjm" }; // todo - dates 12 | owl.config.defaultFormat = new org.semanticweb.owlapi.io.OWLFunctionalSyntaxOntologyFormat(); // todo - introspect this 13 | 14 | print("Welcome, CJM"); 15 | -------------------------------------------------------------------------------- /conf/learner/class.conf: -------------------------------------------------------------------------------- 1 | ks.type = "OWL File" 2 | 3 | ks.fileName = "mptest.ofn" 4 | 5 | reasoner.type = "fast instance checker" 6 | 7 | reasoner.sources = { ks } 8 | 9 | lp.type = "classLearningProblem" 10 | 11 | lp.classToDescribe = "http://purl.obolibrary.org/obo/MP_0000807" 12 | 13 | alg1.type = "celoe" 14 | alg2.type = "pceloe" 15 | 16 | -------------------------------------------------------------------------------- /conf/learner/mptest.conf: -------------------------------------------------------------------------------- 1 | ks.type = "OWL File" 2 | 3 | ks.fileName = "mptest.ofn" 4 | 5 | reasoner.type = "fast instance checker" 6 | 7 | reasoner.sources = { ks } 8 | 9 | lp.type = "posOnlyLP" 10 | 11 | lp.positiveExamples = { 12 | 13 | "http://purl.obolibrary.org/obo/MGI_fake", 14 | "http://purl.obolibrary.org/obo/MGI_101765", 15 | "http://purl.obolibrary.org/obo/MGI_101764" 16 | } 17 | 18 | alg1.type = "celoe" 19 | alg2.type = "pceloe" 20 | 21 | -------------------------------------------------------------------------------- /conf/uberon/uberon-cjm-conf.js: -------------------------------------------------------------------------------- 1 | // To use this conf: 2 | // 3 | // cd uberon 4 | // owljs-repl -i load-uberon-edit.js uberon.owl 5 | 6 | owl.config.idspace = 'UBERON'; 7 | owl.config.lastId = 10000; // CJM 8 | owl.defaultSlotMap = { created_by : "GOC:cjm" }; // todo - dates 9 | owl.config.defaultFormat = new org.semanticweb.owlapi.io.OWLFunctionalSyntaxOntologyFormat(); // todo - introspect this 10 | 11 | print("Welcome, CJM"); 12 | -------------------------------------------------------------------------------- /docs/index.html: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /docs/javascript/main.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cmungall/owljs/b2a6db28e1b214049b5b7686fb28c09a68806410/docs/javascript/main.js -------------------------------------------------------------------------------- /docs/javascript/prettify.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cmungall/owljs/b2a6db28e1b214049b5b7686fb28c09a68806410/docs/javascript/prettify.js -------------------------------------------------------------------------------- /docs/javascript/searchdata.js: -------------------------------------------------------------------------------- 1 | var indexSectionsWithContent = { 2 | "General": { 3 | "Symbols": false, 4 | "Numbers": false, 5 | "A": true, 6 | "B": true, 7 | "C": false, 8 | "D": true, 9 | "E": true, 10 | "F": true, 11 | "G": true, 12 | "H": true, 13 | "I": true, 14 | "J": false, 15 | "K": false, 16 | "L": true, 17 | "M": false, 18 | "N": false, 19 | "O": true, 20 | "P": false, 21 | "Q": false, 22 | "R": true, 23 | "S": true, 24 | "T": true, 25 | "U": true, 26 | "V": true, 27 | "W": false, 28 | "X": true, 29 | "Y": false, 30 | "Z": false 31 | }, 32 | "Variables": { 33 | "Symbols": false, 34 | "Numbers": false, 35 | "A": false, 36 | "B": false, 37 | "C": false, 38 | "D": false, 39 | "E": false, 40 | "F": false, 41 | "G": false, 42 | "H": false, 43 | "I": false, 44 | "J": false, 45 | "K": false, 46 | "L": true, 47 | "M": false, 48 | "N": false, 49 | "O": true, 50 | "P": false, 51 | "Q": false, 52 | "R": false, 53 | "S": false, 54 | "T": false, 55 | "U": false, 56 | "V": false, 57 | "W": false, 58 | "X": false, 59 | "Y": false, 60 | "Z": false 61 | }, 62 | "Functions": { 63 | "Symbols": false, 64 | "Numbers": false, 65 | "A": true, 66 | "B": false, 67 | "C": true, 68 | "D": true, 69 | "E": true, 70 | "F": true, 71 | "G": true, 72 | "H": true, 73 | "I": true, 74 | "J": true, 75 | "K": false, 76 | "L": true, 77 | "M": true, 78 | "N": true, 79 | "O": true, 80 | "P": true, 81 | "Q": false, 82 | "R": true, 83 | "S": true, 84 | "T": true, 85 | "U": true, 86 | "V": false, 87 | "W": true, 88 | "X": false, 89 | "Y": false, 90 | "Z": false 91 | }, 92 | "Classes": { 93 | "Symbols": false, 94 | "Numbers": false, 95 | "A": false, 96 | "B": false, 97 | "C": false, 98 | "D": true, 99 | "E": false, 100 | "F": false, 101 | "G": false, 102 | "H": false, 103 | "I": false, 104 | "J": true, 105 | "K": false, 106 | "L": true, 107 | "M": false, 108 | "N": false, 109 | "O": true, 110 | "P": false, 111 | "Q": false, 112 | "R": true, 113 | "S": false, 114 | "T": false, 115 | "U": false, 116 | "V": true, 117 | "W": false, 118 | "X": false, 119 | "Y": false, 120 | "Z": false 121 | } 122 | } -------------------------------------------------------------------------------- /docs/search/ClassesD.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 |
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DLMatch
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javautil
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obol
OWL
owlapi
OWLFrame
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repl
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add
obolOWLOWLFramerepl
addAxiom
OWLrepl
addAxioms, OWL
addCatalog, OWL
addSynonym, vocab.obo
allValuesFrom, OWL
annotation, OWL
annotationAssertion, OWL
annotationProperty, OWL
annotationPropertyAssertionMatch, DLMatch
applyChange, repl
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classAssertion, OWL
classAssertionMatch, DLMatch
collectionToJsArray, javautil
createOntology, OWL
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dataProperty, OWL
declare, OWL
declareClass, OWL
definition, vocab.obo
definitionAssertion, vocab.obo
df, repl
Differ, Differ
disjointClasses, OWL
disjointUntion, OWL
DLMatch, DLMatch
Dotty
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equivalentClassesMatch, DLMatch
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DLMatchOWL
findAndExtend, DLMatch
findAndReplace, DLMatch
flatten, OWLFrame
frame, repl
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hasBroadSynonym, vocab.obo
hasDbXref, vocab.obo
hasExactSynonym, vocab.obo
hasNarrowSynonym, vocab.obo
hasRelatedSynonym, vocab.obo
hasValue, OWL
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info, OWL
inSubset, vocab.obo
intersectionOf, OWL
inverseOf, OWL
inverseProperties, OWL
isCoherent, OWL
isDeprecated, OWL
isInferredSubClassOf, OWL
isSatisfiable, OWL
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jsArrayToSet, javautil
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labelAssertion, OWL
Linky, Linky
literal, OWL
loadConfig, OWL
loadFile, OWL
loadOntology, OWL
log
OWLrepl
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merge, OWLFrame
mfind, OWL
mgr, repl
mkAnnotationProperty, repl
mkClass, repl
mkDisjointUntion, repl
mkIndividual, repl
mkObjectProperty, repl
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newOntology, repl
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objectIntersectionOfMatch, DLMatch
objectProperty, OWL
objectPropertyAssertionMatch, DLMatch
objectSomeValuesFromMatch, DLMatch
Obol, obol
ont, repl
OWL, OWL
OWLFrame, OWLFrame
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parse, obol
parseClass, obol
parseClasses, obol
parseSubClass, obol
pp, repl
propertyAssertion, OWL
propertyDomain, OWL
propertyRange, OWL
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reasoner, repl
removeAxiom
OWLrepl
removeAxioms, OWL
replaceAxiom, OWL
restrictProperties, obol
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save
OWLrepl
saveAxioms, OWL
saveOntology, OWL
sedAxioms, OWL
set, OWLFrame
setClassVars, repl
setDefaultFormat, OWL
setOntology, OWL
setPropertyScore, obol
setReasonerType, OWL
someValuesFrom, OWL
stamp, OWLFrame
subClassOf, OWL
subClassOfMatch, DLMatch
synonym, vocab.nif
synonymAssertion, vocab.obo
synonymProperties, vocab.obo
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transitiveProperty, OWL
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add
obolOWLOWLFramerepl
addAxiom
OWLrepl
addAxioms, OWL
addCatalog, OWL
addSynonym, vocab.obo
allValuesFrom, OWL
annotation, OWL
annotationAssertion, OWL
annotationProperty, OWL
annotationPropertyAssertionMatch, DLMatch
applyChange, repl
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class, OWL
classAssertion, OWL
classAssertionMatch, DLMatch
collectionToJsArray, javautil
createOntology, OWL
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dataProperty, OWL
declare, OWL
declareClass, OWL
definition, vocab.obo
definitionAssertion, vocab.obo
df, repl
Differ
GlobalDiffer
disjointClasses, OWL
disjointUntion, OWL
DLMatch
GlobalDLMatch
Dotty
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equivalentClassesMatch, DLMatch
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find
DLMatchOWL
findAndExtend, DLMatch
findAndReplace, DLMatch
flatten, OWLFrame
frame, repl
Functions
DifferDLMatchjavautilLinkyobolOWLOWLFramereplvocab.nifvocab.obo
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hasBroadSynonym, vocab.obo
hasDbXref, vocab.obo
hasExactSynonym, vocab.obo
hasNarrowSynonym, vocab.obo
hasRelatedSynonym, vocab.obo
hasValue, OWL
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info, OWL
inSubset, vocab.obo
intersectionOf, OWL
inverseOf, OWL
inverseProperties, OWL
IRI, owlapi
isCoherent, OWL
isDeprecated, OWL
isInferredSubClassOf, OWL
isSatisfiable, OWL
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javautil
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labelAssertion, OWL
labelToIRIMap, repl
Linky
GlobalLinky
literal, OWL
loadConfig, OWL
loadFile, OWL
loadOntology, OWL
log
OWLrepl
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merge, OWLFrame
mfind, OWL
mgr, repl
mkAnnotationProperty, repl
mkClass, repl
mkDisjointUntion, repl
mkIndividual, repl
mkObjectProperty, repl
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newOntology, repl
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parse, obol
parseClass, obol
parseClasses, obol
parseSubClass, obol
pp, repl
propertyAssertion, OWL
propertyDomain, OWL
propertyRange, OWL
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reasoner, repl
removeAxiom
OWLrepl
removeAxioms, OWL
repl
replaceAxiom, OWL
restrictProperties, obol
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save
OWLrepl
saveAxioms, OWL
saveOntology, OWL
sedAxioms, OWL
set, OWLFrame
setClassVars, repl
setDefaultFormat, OWL
setOntology, OWL
setPropertyScore, obol
setReasonerType, OWL
someValuesFrom, OWL
stamp, OWLFrame
subClassOf, OWL
subClassOfMatch, DLMatch
synonym, vocab.nif
synonymAssertion, vocab.obo
synonymProperties, vocab.obo
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toAxioms, OWLFrame
transitiveProperty, OWL
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unionOf, OWL
useOboVocab, obol
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vocab.nif
vocab.obo
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o, repl
obj, repl
owl, repl
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2javautil&/Users/cjm/repos/owljs/lib/javautil.jsowlapi!/Users/cjm/repos/owljs/lib/owl.jsDLMatch%/Users/cjm/repos/owljs/lib/dlmatch.jsLinky#/Users/cjm/repos/owljs/lib/linky.jsvocabobo'/Users/cjm/repos/owljs/lib/vocab/obo.jsOWL!/Users/cjm/repos/owljs/lib/owl.jsrepl"/Users/cjm/repos/owljs/lib/repl.jsDiffer$/Users/cjm/repos/owljs/lib/Differ.jsOWLFrame&/Users/cjm/repos/owljs/lib/owlframe.jsvocabnif'/Users/cjm/repos/owljs/lib/vocab/nif.jsobol"/Users/cjm/repos/owljs/lib/obol.js -------------------------------------------------------------------------------- /lib/.naturaldocs_project/Data/ConfigFileInfo.nd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cmungall/owljs/b2a6db28e1b214049b5b7686fb28c09a68806410/lib/.naturaldocs_project/Data/ConfigFileInfo.nd -------------------------------------------------------------------------------- /lib/.naturaldocs_project/Data/FileInfo.nd: -------------------------------------------------------------------------------- 1 | 1.5 2 | JavaScript 3 | /Users/cjm/repos/owljs/lib/obol/anatomy.js 1391579138 0 /Users/cjm/repos/owljs/lib/obol/anatomy.js 4 | /Users/cjm/repos/owljs/lib/owl/owlframe.js 1391579138 0 /Users/cjm/repos/owljs/lib/owl/owlframe.js 5 | /Users/cjm/repos/owljs/lib/owl.js 1397413827 1 OWL 6 | /Users/cjm/repos/owljs/lib/obol/phenotype.js 1392707382 0 /Users/cjm/repos/owljs/lib/obol/phenotype.js 7 | /Users/cjm/repos/owljs/lib/vocab/nif.js 1391579138 1 vocab.nif 8 | /Users/cjm/repos/owljs/lib/owlframe.js 1391579138 1 OWLFrame 9 | /Users/cjm/repos/owljs/lib/io/table.js 1397415266 0 /Users/cjm/repos/owljs/lib/io/table.js 10 | /Users/cjm/repos/owljs/lib/io/dotty.js 1397357787 1 Dotty 11 | /Users/cjm/repos/owljs/lib/vocab.js 1391579138 0 /Users/cjm/repos/owljs/lib/vocab.js 12 | /Users/cjm/repos/owljs/lib/dlmatch.js 1396408063 1 DLMatch 13 | /Users/cjm/repos/owljs/lib/owlfunc/trPartOfToSomaLocation.js 1391579138 0 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January is "1" 17 | # mm - Always two digit month. January is "01" 18 | # mon - Short month word. January is "Jan" 19 | # month - Long month word. January is "January" 20 | # d - One or two digit day. 1 is "1" 21 | # dd - Always two digit day. 1 is "01" 22 | # day - Day with letter extension. 1 is "1st" 23 | # yy - Two digit year. 2006 is "06" 24 | # yyyy - Four digit year. 2006 is "2006" 25 | # year - Four digit year. 2006 is "2006" 26 | 27 | 28 | # -------------------------------------------------------------------------- 29 | # 30 | # Cut and paste the lines below to change the order in which your files 31 | # appear on the menu. Don't worry about adding or removing files, Natural 32 | # Docs will take care of that. 33 | # 34 | # You can further organize the menu by grouping the entries. Add a 35 | # "Group: [name] {" line to start a group, and add a "}" to end it. 36 | # 37 | # You can add text and web links to the menu by adding "Text: [text]" and 38 | # "Link: [name] ([URL])" lines, respectively. 39 | # 40 | # The formatting and comments are auto-generated, so don't worry about 41 | # neatness when editing the file. Natural Docs will clean it up the next 42 | # time it is run. When working with groups, just deal with the braces and 43 | # forget about the indentation and comments. 44 | # 45 | # -------------------------------------------------------------------------- 46 | 47 | 48 | File: OWL (no auto-title, owl.js) 49 | File: OWLFrame (owlframe.js) 50 | File: DLMatch (dlmatch.js) 51 | File: Differ (Differ.js) 52 | File: Linky (linky.js) 53 | File: obol (obol.js) 54 | File: repl (repl.js) 55 | File: javautil (javautil.js) 56 | File: vocab.obo (vocab/obo.js) 57 | File: vocab.nif (vocab/nif.js) 58 | File: Dotty (io/dotty.js) 59 | 60 | Group: Index { 61 | 62 | Index: Everything 63 | Class Index: Classes 64 | Function Index: Functions 65 | Variable Index: Variables 66 | } # Group: Index 67 | 68 | -------------------------------------------------------------------------------- /lib/.naturaldocs_project/Menu_Backup.txt: -------------------------------------------------------------------------------- 1 | Format: 1.5 2 | 3 | 4 | # You can add a title and sub-title to your menu like this: 5 | # Title: [project name] 6 | # SubTitle: [subtitle] 7 | 8 | # You can add a footer to your documentation like this: 9 | # Footer: [text] 10 | # If you want to add a copyright notice, this would be the place to do it. 11 | 12 | # You can add a timestamp to your documentation like one of these: 13 | # Timestamp: Generated on month day, year 14 | # Timestamp: Updated mm/dd/yyyy 15 | # Timestamp: Last updated mon day 16 | # 17 | # m - One or two digit month. January is "1" 18 | # mm - Always two digit month. January is "01" 19 | # mon - Short month word. January is "Jan" 20 | # month - Long month word. January is "January" 21 | # d - One or two digit day. 1 is "1" 22 | # dd - Always two digit day. 1 is "01" 23 | # day - Day with letter extension. 1 is "1st" 24 | # yy - Two digit year. 2006 is "06" 25 | # yyyy - Four digit year. 2006 is "2006" 26 | # year - Four digit year. 2006 is "2006" 27 | 28 | 29 | # -------------------------------------------------------------------------- 30 | # 31 | # Cut and paste the lines below to change the order in which your files 32 | # appear on the menu. Don't worry about adding or removing files, Natural 33 | # Docs will take care of that. 34 | # 35 | # You can further organize the menu by grouping the entries. Add a 36 | # "Group: [name] {" line to start a group, and add a "}" to end it. 37 | # 38 | # You can add text and web links to the menu by adding "Text: [text]" and 39 | # "Link: [name] ([URL])" lines, respectively. 40 | # 41 | # The formatting and comments are auto-generated, so don't worry about 42 | # neatness when editing the file. Natural Docs will clean it up the next 43 | # time it is run. When working with groups, just deal with the braces and 44 | # forget about the indentation and comments. 45 | # 46 | # -------------------------------------------------------------------------- 47 | 48 | 49 | Group: Data { 50 | 51 | File: dispatch.js (data/dispatch.js) 52 | File: golr.js (data/golr.js) 53 | File: server.js (data/server.js) 54 | File: statistics.js (data/statistics.js) 55 | File: xrefs.js (data/xrefs.js) 56 | } # Group: Data 57 | 58 | File: api.js (api.js) 59 | File: echo.js (handlers/echo.js) 60 | File: handler.js (handler.js) 61 | File: linker.js (linker.js) 62 | File: owl_class_expression.js (handlers/owl_class_expression.js) 63 | File: rollup.js (ui/rollup.js) 64 | File: version.js (version.js) 65 | 66 | Group: Index { 67 | 68 | Index: Everything 69 | Class Index: Classes 70 | Function Index: Functions 71 | Variable Index: Variables 72 | } # Group: Index 73 | 74 | -------------------------------------------------------------------------------- /lib/.naturaldocs_project/Topics.txt: -------------------------------------------------------------------------------- 1 | Format: 1.5 2 | 3 | # This is the Natural Docs topics file for this project. If you change anything 4 | # here, it will apply to THIS PROJECT ONLY. If you'd like to change something 5 | # for all your projects, edit the Topics.txt in Natural Docs' Config directory 6 | # instead. 7 | 8 | 9 | # If you'd like to prevent keywords from being recognized by Natural Docs, you 10 | # can do it like this: 11 | # Ignore Keywords: [keyword], [keyword], ... 12 | # 13 | # Or you can use the list syntax like how they are defined: 14 | # Ignore Keywords: 15 | # [keyword] 16 | # [keyword], [plural keyword] 17 | # ... 18 | 19 | 20 | #------------------------------------------------------------------------------- 21 | # SYNTAX: 22 | # 23 | # Topic Type: [name] 24 | # Alter Topic Type: [name] 25 | # Creates a new topic type or alters one from the main file. Each type gets 26 | # its own index and behavior settings. Its name can have letters, numbers, 27 | # spaces, and these charaters: - / . ' 28 | # 29 | # Plural: [name] 30 | # Sets the plural name of the topic type, if different. 31 | # 32 | # Keywords: 33 | # [keyword] 34 | # [keyword], [plural keyword] 35 | # ... 36 | # Defines or adds to the list of keywords for the topic type. They may only 37 | # contain letters, numbers, and spaces and are not case sensitive. Plural 38 | # keywords are used for list topics. You can redefine keywords found in the 39 | # main topics file. 40 | # 41 | # Index: [yes|no] 42 | # Whether the topics get their own index. Defaults to yes. Everything is 43 | # included in the general index regardless of this setting. 44 | # 45 | # Scope: [normal|start|end|always global] 46 | # How the topics affects scope. Defaults to normal. 47 | # normal - Topics stay within the current scope. 48 | # start - Topics start a new scope for all the topics beneath it, 49 | # like class topics. 50 | # end - Topics reset the scope back to global for all the topics 51 | # beneath it. 52 | # always global - Topics are defined as global, but do not change the scope 53 | # for any other topics. 54 | # 55 | # Class Hierarchy: [yes|no] 56 | # Whether the topics are part of the class hierarchy. Defaults to no. 57 | # 58 | # Page Title If First: [yes|no] 59 | # Whether the topic's title becomes the page title if it's the first one in 60 | # a file. Defaults to no. 61 | # 62 | # Break Lists: [yes|no] 63 | # Whether list topics should be broken into individual topics in the output. 64 | # Defaults to no. 65 | # 66 | # Can Group With: [type], [type], ... 67 | # Defines a list of topic types that this one can possibly be grouped with. 68 | # Defaults to none. 69 | #------------------------------------------------------------------------------- 70 | 71 | # The following topics are defined in the main file, if you'd like to alter 72 | # their behavior or add keywords: 73 | # 74 | # Generic, Class, Interface, Section, File, Group, Function, Variable, 75 | # Property, Type, Constant, Enumeration, Event, Delegate, Macro, 76 | # Database, Database Table, Database View, Database Index, Database 77 | # Cursor, Database Trigger, Cookie, Build Target 78 | 79 | # If you add something that you think would be useful to other developers 80 | # and should be included in Natural Docs by default, please e-mail it to 81 | # topics [at] naturaldocs [dot] org. 82 | -------------------------------------------------------------------------------- /lib/Stats.js: -------------------------------------------------------------------------------- 1 | var obovocab = require("owljs/vocab/obo"); 2 | 3 | var getOntologyStats = exports.getOntologyStats = function(owl, objs, gf) { 4 | return { 5 | avgAncestors : avgInferredSuperClassesPerClass(owl, objs, gf, false ), 6 | avgParents : avgInferredSuperClassesPerClass(owl, objs, gf, true ), 7 | } 8 | } 9 | 10 | var avgPerObj = function(owl, objs, nFunc, gf) { 11 | if (gf == null) { 12 | gf = function() { return obovocab.getOboIdentifierPrefix(owl, obj) }; 13 | } 14 | if (objs == null) { 15 | objs = owl.getClasses().filter(function(c) { return !owl.isDeprecated(c)} ); 16 | } 17 | var countsByGroup = {}; 18 | for (var k in objs) { 19 | var obj = objs[k]; 20 | var n = nFunc.call(this, obj); 21 | var g = gf.call(this, obj); 22 | if (g == null) { 23 | g = "null"; 24 | } 25 | if (countsByGroup[g] == null) { 26 | countsByGroup[g] = []; 27 | } 28 | countsByGroup[g].push(n); 29 | } 30 | var am = {}; 31 | for (var k in countsByGroup) { 32 | var tot = countsByGroup[k].reduce( function(a,b) { return a+b } ); 33 | am[k] = tot / countsByGroup[k].length; 34 | } 35 | return am; 36 | } 37 | 38 | var avgInferredSuperClassesPerClass = exports.avgInferredSuperClassesPerClass = function(owl,objs,gf,isDirect) { 39 | if (isDirect == null) { 40 | isDirect = true; 41 | } 42 | return avgPerObj(owl, 43 | objs, 44 | function(c) { 45 | return owl.getInferredSuperClasses(c, isDirect, false).length; 46 | }, 47 | gf); 48 | } 49 | -------------------------------------------------------------------------------- /lib/io/dotty.js: -------------------------------------------------------------------------------- 1 | 2 | export('Dotty'); 3 | 4 | var javautil = require("owljs/javautil"); 5 | var md = require("owljs/io/markdown"); 6 | 7 | 8 | /* Function: Dotty 9 | * 10 | * Constructor 11 | * 12 | */ 13 | function Dotty(owl) { 14 | this.owl = owl; 15 | this.nodes = []; 16 | this.edge = []; 17 | return this; 18 | } 19 | 20 | Dotty.prototype.addNode = function(node) { 21 | this.nodes.push(node); 22 | } 23 | 24 | Dotty.prototype.addEdge = function(edge) { 25 | this.edges.push(edge); 26 | 27 | } 28 | 29 | 30 | Dotty.prototype.render = function() { 31 | this.w("digraph g {"); 32 | var rsg = this.renderSubGraph; 33 | this.subgraphs.forEach(rsg); 34 | this.w("}"); 35 | 36 | } 37 | 38 | 39 | -------------------------------------------------------------------------------- /lib/io/markdown.js: -------------------------------------------------------------------------------- 1 | 2 | var infixMap = 3 | { 4 | SubClassOf : "SubClassOf", 5 | EquivalentClasses: "EquivalentTo", 6 | ObjectIntersectionOf: "and", 7 | ObjectUnionOf: "or", 8 | ObjectComplementOf: "or", 9 | } 10 | 11 | var render = exports.renderOWLObject = function(obj, owl, opts) { 12 | return render(owl.toAxiomaticJSON(obj), owl, opts); 13 | } 14 | 15 | var render = exports.render = function(obj, owl, opts) { 16 | var cx = this; 17 | if (typeof obj == 'object') { 18 | var md; 19 | var type = obj.type; 20 | var xargs = obj.args.map( function(a) { return cx.render(a, owl, opts) }); 21 | if (infixMap[type] != null) { 22 | md = xargs.join(" **"+infixMap[type]+"** "); 23 | } 24 | else { 25 | if (type == 'AnnotationAssertion') { 26 | md = xargs[1] + " *" + xargs[0] +"* " + xargs[2]; 27 | } 28 | else if (type == 'ObjectSomeValuesFrom') { 29 | md = xargs[0] + " **some** " + xargs[1]; 30 | } 31 | else { 32 | md = type + "( " + xargs.join(" ")+" ) "; 33 | } 34 | } 35 | if (obj.annotations != null) { 36 | md += ' { ' + obj.annotations.map( function(a) { return cx.render(a.property, owl, opts)+"="+cx.render(a.value, owl, opts) }).join(" , ") + ' } '; 37 | } 38 | return md; 39 | } 40 | else { 41 | var label = owl.getLabel(obj); 42 | if (label == null) { 43 | // TODO - href is URI 44 | var hpos = obj.indexOf("#"); 45 | if (hpos > -1) { 46 | label = obj.slice(hpos + 1); 47 | } 48 | } 49 | 50 | if (label == null) { 51 | if (obj.indexOf("http") == 0) { 52 | return "["+obj+"](" + obj + ")"; 53 | } 54 | else { 55 | return obj; 56 | } 57 | } 58 | else { 59 | label = label.replace(/_/g,' '); 60 | if (opts != null && opts.isLabelOnly) { 61 | return label; 62 | } 63 | return "[" + label+"]("+obj+")"; 64 | } 65 | } 66 | } 67 | -------------------------------------------------------------------------------- /lib/io/table.js: -------------------------------------------------------------------------------- 1 | var obovocab = require("owljs/vocab/obo"); 2 | 3 | exports simpleOboTable = function(owl, obj) { 4 | 5 | 6 | } 7 | -------------------------------------------------------------------------------- /lib/javautil.js: -------------------------------------------------------------------------------- 1 | /* Namespace: javautil 2 | * 3 | * handy functions for interacting with java 4 | * 5 | */ 6 | 7 | export('collectionToJsArray', 8 | 'javaArrayToJsArray', 9 | 'jsArrayToSet', 10 | 'toJava'); 11 | 12 | /* Function: collectionToJsArray 13 | * Arguments: 14 | * - col : a java Collection 15 | * 16 | * Returns: 17 | * a javascript list 18 | */ 19 | function collectionToJsArray(col) { 20 | return javaArrayToJsArray(col.toArray()); 21 | } 22 | 23 | 24 | /* Function: javaArrayToJsArray 25 | * Arguments: 26 | * - a : a java Array 27 | * 28 | * Returns: 29 | * a javascript list 30 | */ 31 | function javaArrayToJsArray(a) { 32 | var l = []; 33 | for (var k=0; k 19 | */ 20 | var synonym = exports.synonym = function(owl) { 21 | return owl.annotationProperty(this.getUrlPrefix() + "Backend/OBO_annotation_properties.owl#synonym"); 22 | }; 23 | 24 | var cell_ontology_ID = exports.cell_ontology_ID = function(owl) { 25 | return owl.annotationProperty(this.getUrlPrefix() + "Backend/BIRNLex_annotation_properties.owl#cell_ontology_ID"); 26 | }; 27 | -------------------------------------------------------------------------------- /package.json: -------------------------------------------------------------------------------- 1 | { 2 | "name": "owljs", 3 | "version": "0.0.1", 4 | "description": "A toolkit for using OWL ontologies via the java OWLAPI", 5 | "homepage": "http://github.com/cmungall/owl.js", 6 | "keywords": [ 7 | "commonjs", 8 | "owl", 9 | "semantic web", 10 | "ringo", 11 | "bio-ontology" 12 | ], 13 | "author": "Chris Mungall ", 14 | "contributors": [ 15 | ], 16 | "repositories": [ 17 | { 18 | "type": "git", 19 | "url": "git://github.com/cmungall/owl.js.git" 20 | } 21 | ], 22 | "licenses": [ 23 | { 24 | "type": "MIT", 25 | "url": "https://github.com/ringo/stick/blob/master/LICENSE" 26 | } 27 | ], 28 | "bugs": "http://github.com/cmungall/owl.js/issues", 29 | "engines": { 30 | "ringojs": ">= 0.9" 31 | }, 32 | "directories": { 33 | "lib": "lib" 34 | }, 35 | "bin": { 36 | "owljs" : "bin/owljs", 37 | "owljs-repl.js" : "bin/owljs-repl.js" 38 | }, 39 | "main": "lib/owl.js" 40 | } 41 | -------------------------------------------------------------------------------- /server.js: -------------------------------------------------------------------------------- 1 | // We include server.js in the top level to simplify deployment on heroku 2 | 3 | var system = require('system'); 4 | addToClasspath('./jars/owltools-runner-all.jar'); 5 | var OWL = require('./lib/owl.js').OWL; 6 | 7 | var stick = require('stick'); 8 | var fs = require('fs'); 9 | var response = require('ringo/jsgi/response'); 10 | var httpclient = require('ringo/httpclient'); 11 | 12 | var owl = new OWL(); 13 | 14 | var session = { 15 | foo: 1, 16 | owl: owl 17 | } 18 | 19 | owl.loadFile("test/caro.owl"); 20 | 21 | var app = exports.app = new stick.Application(); 22 | 23 | app.configure('route'); 24 | app.configure('params'); 25 | app.configure('static'); 26 | 27 | var owlservices = require('./lib/owljs/owlservices.js'); 28 | var addons = require('./lib/owljs/addons.js'); 29 | 30 | print("owl is :"+session.owl); 31 | var myOwlservices = new owlservices.OWLServices(app,session); 32 | new addons.AddOns(app,session); 33 | //myOwlservices.install(); 34 | 35 | function main(args) { 36 | print("args="+args); 37 | if (false) { 38 | while(args.length > 0) { 39 | var arg = args.shift(); 40 | if (arg == "--") { 41 | break; 42 | } 43 | print("Arg="+arg); 44 | } 45 | } 46 | require('ringo/httpserver').main(module.id); 47 | } 48 | 49 | // INITIALIZATION 50 | // Can set port from command line. E.g. --port 8080 51 | if (require.main == module) { 52 | main(system.args); 53 | } 54 | -------------------------------------------------------------------------------- /tests/alltests.js: -------------------------------------------------------------------------------- 1 | var tests = 2 | [ 3 | "owl/owl_test", 4 | 5 | "dlmatch/dlmatch_test", 6 | 7 | "obol/obol_test", 8 | 9 | "repl/author_test", 10 | "repl/instancequery_test", 11 | 12 | "vocab/obo_test" 13 | ]; 14 | 15 | var failed = []; 16 | 17 | if (require.main == module) { 18 | var probs = 0; 19 | 20 | tests.forEach( function(n) { 21 | var code = require("test").run("./tests/"+n); 22 | if (code != 0) { 23 | probs++; 24 | failed.push(n); 25 | } 26 | //probs += code; 27 | }); 28 | 29 | 30 | print("Problems: "+probs); 31 | if (probs > 0) { 32 | print("Failed: "+failed); 33 | } 34 | require("system").exit(probs); 35 | 36 | } 37 | -------------------------------------------------------------------------------- /tests/data/catalog-v001.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | -------------------------------------------------------------------------------- /tests/data/ceph-import.owl: -------------------------------------------------------------------------------- 1 | Prefix: owl: 2 | Prefix: rdf: 3 | Prefix: xml: 4 | Prefix: xsd: 5 | Prefix: rdfs: 6 | 7 | 8 | 9 | Ontology: 10 | Import: 11 | -------------------------------------------------------------------------------- /tests/data/linkytest.owl: -------------------------------------------------------------------------------- 1 | Ontology: 2 | Prefix: obo: 3 | 4 | Class: obo:X_1 5 | 6 | Class: obo:X_11 7 | SubClassOf: obo:X_1 8 | 9 | Class: obo:X_12 10 | SubClassOf: obo:X_1 11 | 12 | Class: obo:X_111 13 | SubClassOf: obo:X_11 14 | 15 | Class: obo:X_112 16 | SubClassOf: obo:X_11 17 | 18 | Class: obo:X_113 19 | SubClassOf: obo:X_11 20 | 21 | Class: obo:X_121 22 | SubClassOf: obo:X_12 23 | 24 | Class: obo:X_122 25 | SubClassOf: obo:X_12 26 | 27 | Class: obo:X_123 28 | SubClassOf: obo:X_12 29 | 30 | Class: obo:X_1111 31 | SubClassOf: obo:X_111 32 | 33 | Class: obo:X_1231 34 | SubClassOf: obo:X_123 35 | 36 | 37 | 38 | Class: obo:Y_1 39 | 40 | Class: obo:Y_11 41 | SubClassOf: obo:Y_1 42 | EquivalentTo: obo:X_1231 43 | 44 | Class: obo:Y_12 45 | SubClassOf: obo:Y_1 46 | 47 | Class: obo:Y_111 48 | SubClassOf: obo:Y_11 49 | 50 | Class: obo:Y_112 51 | SubClassOf: obo:Y_11 52 | 53 | Class: obo:Y_113 54 | SubClassOf: obo:Y_11 55 | 56 | Class: obo:Y_121 57 | SubClassOf: obo:Y_12 58 | 59 | Class: obo:Y_122 60 | SubClassOf: obo:Y_12 61 | EquivalentTo: obo:X_12 62 | 63 | Class: obo:Y_123 64 | SubClassOf: obo:Y_12 65 | EquivalentTo: obo:X_12 66 | 67 | Class: obo:Y_1111 68 | SubClassOf: obo:Y_111 69 | EquivalentTo: obo:X_1111 70 | 71 | Class: obo:Y_1231 72 | SubClassOf: obo:Y_123 73 | EquivalentTo: obo:X_1231 74 | -------------------------------------------------------------------------------- /tests/differ/differ_test.js: -------------------------------------------------------------------------------- 1 | var {OWL} = require("owljs"); 2 | var {Differ} = require("owljs/differ"); 3 | var assert = require("assert"); 4 | 5 | var differ; 6 | var owl; 7 | 8 | importPackage(Packages.org.semanticweb.owlapi.model); 9 | 10 | function init() { 11 | if (owl == null) { 12 | owl = new OWL(); 13 | //repl.owlinit(owl); 14 | owl.loadOntology("tests/data/ceph.owl"); 15 | } 16 | } 17 | 18 | exports.testDiffs = function() { 19 | init(); 20 | var ov = require("owljs/vocab/obo"); 21 | var repl = require("owljs/repl"); 22 | var owlB = new OWL(); 23 | repl.owlinit(owlB); 24 | owlB.loadOntology("tests/data/ceph.owl"); 25 | 26 | // simulate creating a class in new ontology 27 | var c = repl.mkClass( "test" ); 28 | var tentacle = owl.find("tentacle"); 29 | var beak = owl.find("beak"); 30 | owlB.add( owl.declaration(c) ); 31 | owlB.add( ov.definitionAssertion(owl, c, "this is a test", ["FOO:BAR"]) ); 32 | var axs = owlB.getAllAxioms(c); 33 | assert.equal( axs.length, 2); 34 | 35 | // adding an axiom to existing class in new 36 | owlB.add( owl.subClassOf(tentacle, c) ); 37 | 38 | // simulate removing axioms from original ontology by 39 | // adding them in prior to diff; in this case 40 | // we assume the ontology originally had a nonsense 41 | // axiom, 42 | owl.add( owl.subClassOf(beak, tentacle) ); 43 | 44 | //var ncA = owl.getClasses(); 45 | //var ncB = owlB.getClasses(); 46 | //assert.equal(ncA.length, ncB.length-1); 47 | 48 | //var tA = owl.find("tentacle"); 49 | //var tB = owlB.find("tentacle"); 50 | //assert.isTrue(tA.equals(tB)); 51 | //assert.isTrue(tA == tB); 52 | 53 | differ = new Differ(); 54 | var md = differ.getDiffsAsMarkdown(owl, owlB, false, false); 55 | print(md); 56 | 57 | }; 58 | 59 | if (require.main == module) { 60 | require("test").run(exports); 61 | } 62 | -------------------------------------------------------------------------------- /tests/dlmatch/dlmatch_nested_test.js: -------------------------------------------------------------------------------- 1 | var {OWL} = require("owljs"); 2 | var {DLMatch} = require("owljs/dlmatch"); 3 | var assert = require("assert"); 4 | var repl = require("owljs/repl"); 5 | 6 | var matcher; 7 | var owl; 8 | 9 | importPackage(Packages.org.semanticweb.owlapi.model); 10 | 11 | function init() { 12 | if (owl == null) { 13 | owl = new OWL(); 14 | repl.owlinit(owl); 15 | owl.loadOntology("tests/data/ceph.owl"); 16 | matcher = new DLMatch(owl); 17 | } 18 | } 19 | 20 | exports.testNested = function() { 21 | init(); 22 | 23 | var o = repl.o; 24 | repl.owlinit(owl); 25 | var nc = repl.mkClass("cell of tentacle of beak"); 26 | // tentacle of beak 27 | var tob = owl.intersectionOf(o.tentacle, 28 | owl.someValuesFrom(o.part_of, 29 | owl.intersectionOf(o.beak, 30 | owl.someValuesFrom(o.part_of, 31 | o.head)))); 32 | // cell of TOB 33 | var tobcell = owl.intersectionOf(o.cell, 34 | owl.someValuesFrom(o.part_of, 35 | tob)); 36 | owl.add( owl.equivalentClasses(nc, tobcell) ); 37 | 38 | // test for matches of the form: nc == ?genus and ?svf 39 | find( 40 | matcher.equivalentClassesMatch( 41 | nc, 42 | matcher.intersectionOfMatch("?genus", 43 | "?svf") 44 | ), 45 | 1, 46 | { 47 | genus: "cell" // expect nc == cell and ... 48 | }); 49 | 50 | // ?nc = ?c and part_of some ?t and ?rel some ?z 51 | find( 52 | matcher.equivalentClassesMatch( 53 | "?nc", 54 | matcher.intersectionOfMatch("?c", 55 | matcher.someValuesFromMatch(o.part_of, 56 | matcher.intersectionOfMatch("?t", 57 | matcher.someValuesFromMatch("?rel","?z")))) 58 | ), 59 | 1, 60 | // expect tobcell == c and part_of some tentacle and ? some ? 61 | { 62 | nc: "cell of tentacle of beak", 63 | c: "cell", 64 | t: "tentacle", 65 | }); 66 | 67 | }; 68 | 69 | 70 | // Arguments: 71 | // - q : queryTemplate 72 | // - numExpected: if present, number of results must match this 73 | // - mustContain: if present, the result set must contain at least one binding object to match this 74 | function find(q, numExpected, mustContain) { 75 | //print("QUERY:"); 76 | repl.pp(q); 77 | var matches = matcher.find(q); 78 | print("#match = "+matches.length); 79 | if (numExpected != null) { 80 | assert.equal(matches.length, numExpected) 81 | } 82 | matches.forEach(repl.pp); 83 | if (mustContain != null) { 84 | for (var j in mustContain) { 85 | var v = mustContain[j]; 86 | if (!(v instanceof OWLObject)) { 87 | mustContain[j] = owl.find(v); 88 | console.log("Mapped "+v+" ==> "+mustContain[j]); 89 | } 90 | if (mustContain[j] == null) { 91 | console.error("No such entity: "+v); 92 | assert.isTrue(false); 93 | } 94 | } 95 | var ok = false; 96 | for (var k in matches) { 97 | var m = matches[k]; 98 | var ok2 = true; 99 | for (var j in mustContain) { 100 | if (m[j] != mustContain[j]) { 101 | ok2 = false; 102 | break; 103 | } 104 | } 105 | if (ok2) { 106 | ok = true; 107 | break; 108 | } 109 | } 110 | assert.isTrue(ok); 111 | } 112 | } 113 | 114 | 115 | if (require.main == module) { 116 | require("test").run(exports); 117 | } 118 | -------------------------------------------------------------------------------- /tests/learner/catalog-v001.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | -------------------------------------------------------------------------------- /tests/learner/mp_test.js: -------------------------------------------------------------------------------- 1 | var {OWL} = require("owljs"); 2 | var {Learner} = require("owljs/learner"); 3 | var assert = require("assert"); 4 | var repl = require("owljs/repl"); 5 | 6 | var learner; 7 | var owl; 8 | 9 | importPackage(Packages.org.semanticweb.owlapi.model); 10 | 11 | function init() { 12 | if (owl == null) { 13 | owl = new OWL(); 14 | repl.owlinit(owl); 15 | var owlFile = "tests/learner/mptest.ofn"; 16 | owl.loadOntology(owlFile); 17 | learner = new Learner(owl); 18 | learner.owlFile = "mptest.ofn"; 19 | } 20 | } 21 | 22 | exports.testLCS = function() { 23 | init(); 24 | var c = owl.find("weakness"); 25 | var d = owl.find("abnormal striatum morphology"); 26 | print("C="+c); 27 | print("D="+d); 28 | learner.prepLCS(c,d); 29 | print(learner.renderConfig()); 30 | 31 | learner.dir = "tests/learner"; 32 | var out = learner.learn(); 33 | print(out); 34 | }; 35 | 36 | 37 | 38 | if (require.main == module) { 39 | require("test").run(exports); 40 | } 41 | -------------------------------------------------------------------------------- /tests/linky/linky_test.js: -------------------------------------------------------------------------------- 1 | var {OWL} = require("owljs"); 2 | var {Linky} = require("owljs/linky"); 3 | var assert = require("assert"); 4 | 5 | var linky; 6 | var owl; 7 | 8 | importPackage(Packages.org.semanticweb.owlapi.model); 9 | 10 | function init() { 11 | if (owl == null) { 12 | owl = new OWL(); 13 | //repl.owlinit(owl); 14 | owl.loadOntology("tests/data/linkytest.owl"); 15 | } 16 | linky = new Linky(owl); 17 | } 18 | 19 | exports.testCollapse = function() { 20 | init(); 21 | 22 | //print("X="+linky.getSource); 23 | linky.decluster(); 24 | }; 25 | 26 | if (require.main == module) { 27 | require("test").run(exports); 28 | } 29 | -------------------------------------------------------------------------------- /tests/obol/obol_test.js: -------------------------------------------------------------------------------- 1 | var {OWL} = require("owljs"); 2 | var {Obol} = require("owljs/obol"); 3 | var repl = require("owljs/repl"); 4 | var assert = require("assert"); 5 | 6 | var owl; 7 | var obol 8 | 9 | importPackage(Packages.org.semanticweb.owlapi.model); 10 | 11 | function init() { 12 | if (owl == null) { 13 | owl = new OWL(); 14 | //repl.owlinit(owl); 15 | owl.loadOntology("tests/data/clmin.ofn"); 16 | } 17 | } 18 | 19 | exports.testOps = function() { 20 | init(); 21 | repl.owlinit(owl); 22 | var o = repl.o; 23 | obol = new Obol(owl, repl.o); 24 | owl.config.isCompareClasses = true; 25 | require("owljs/obol/anatomy"); 26 | var str = "cell of brain"; 27 | var results = obol.parse(str, null); 28 | repl.pp(results); 29 | assert.equal(results.length, 1); 30 | //var x = results[0]; 31 | 32 | var c = o.epithelial_cell_of_nephron; 33 | var results = obol.parseClass(c); 34 | repl.pp(results); 35 | assert.equal(results.length, 1); 36 | 37 | //obol.setIgnoreDefinedClasses(true); 38 | results = obol.parseSubClasses(o.epithelial_cell, null); 39 | repl.pp(results); 40 | assert.equal(results.length, 127); 41 | 42 | }; 43 | 44 | 45 | 46 | if (require.main == module) { 47 | require("test").run(exports); 48 | } 49 | -------------------------------------------------------------------------------- /tests/obol_test_mp.obo: -------------------------------------------------------------------------------- 1 | 2 | [Term] 3 | id: PATO:0000051 4 | name: morphology 5 | 6 | [Term] 7 | id: PHENO:1234567 8 | name: abnormal epithelium morphology 9 | is_a: PHENO:0000001 10 | 11 | 12 | [Term] 13 | id: PHENO:0000001 14 | name: phenotype 15 | -------------------------------------------------------------------------------- /tests/owl/addimport_test.js: -------------------------------------------------------------------------------- 1 | var {OWL} = require("owljs"); 2 | var assert = require("assert"); 3 | 4 | var owl; 5 | 6 | importPackage(Packages.org.semanticweb.owlapi.model); 7 | importPackage(Packages.org.semanticweb.owlapi.io); 8 | importPackage(Packages.org.semanticweb.owlapi.util); 9 | importPackage(Packages.org.coode.owlapi.manchesterowlsyntax); 10 | importPackage(Packages.org.coode.owlapi.obo.parser); 11 | importPackage(org.semanticweb.owlapi.apibinding); 12 | importPackage(org.semanticweb.elk.owlapi); 13 | 14 | 15 | 16 | exports.testAdd = function() { 17 | owl = new OWL(); 18 | owl.loadOntology("tests/data/ceph.owl"); 19 | var src = owl.getOntology(); 20 | owl.createOntology("http://x.org", [src] ); 21 | assert.equal(owl.getOntology().getImportsClosure().size(), 2); 22 | }; 23 | 24 | exports.testAddToExisting = function() { 25 | owl = new OWL(); 26 | owl.createOntology("http://x.org"); 27 | owl.loadOntology("tests/data/ceph.owl", {addToImport:true}); 28 | assert.equal(owl.getOntology().getImportsClosure().size(), 2); 29 | }; 30 | 31 | 32 | if (require.main == module) { 33 | require("test").run(exports); 34 | } 35 | -------------------------------------------------------------------------------- /tests/owl/anc_test.js: -------------------------------------------------------------------------------- 1 | var {OWL} = require("owljs"); 2 | var assert = require("assert"); 3 | 4 | var matcher; 5 | var owl; 6 | 7 | importPackage(Packages.org.semanticweb.owlapi.model); 8 | 9 | function init() { 10 | owl = new OWL(); 11 | //repl.owlinit(owl); 12 | owl.loadOntology("tests/data/ceph.owl"); 13 | } 14 | 15 | function render(c) { 16 | return c + '"' + owl.getLabel(c) + '"'; 17 | } 18 | 19 | 20 | exports.testIndirect = function() { 21 | init(); 22 | var organ = owl.find("organ"); 23 | var part_of = owl.find("part of"); 24 | var tentacle = owl.find("tentacle"); 25 | var cartilage = owl.find("cartilage"); 26 | var mco = owl.find("multi-cellular organism"); 27 | 28 | var tps = 29 | owl.getInferredSubClasses( owl.someValuesFrom(part_of, tentacle) ); 30 | assert.equal(tps.length, 13); 31 | 32 | var nFails = 0; 33 | for (var i in tps) { 34 | console.log(render(tp)); 35 | var tp = tps[i]; 36 | ancs = owl.getAncestorsOver(tp, part_of, false, true); 37 | ancs.forEach(function(c) { 38 | //console.log(" A="+render(c)); 39 | }); 40 | if (ancs.indexOf(tentacle) == -1) { 41 | nFails++; 42 | console.warn("NO TENTACLE FOR "+tp); 43 | } 44 | if (ancs.indexOf(mco) == -1) { 45 | console.warn("NO "+mco+" FOR "+tp); 46 | nFails++; 47 | } 48 | } 49 | assert.equal(nFails, 0); 50 | }; 51 | 52 | 53 | exports.testDidirect = function() { 54 | init(); 55 | var organ = owl.find("organ"); 56 | var part_of = owl.find("part of"); 57 | var tentacle = owl.find("tentacle"); 58 | var cartilage = owl.find("cartilage"); 59 | var mco = owl.find("multi-cellular organism"); 60 | 61 | var tps = 62 | owl.getInferredSubClasses( owl.someValuesFrom(part_of, tentacle), true ); 63 | assert.equal(tps.length, 13); 64 | 65 | var nFails = 0; 66 | var n2 = 0; 67 | for (var i in tps) { 68 | console.log(render(tp)); 69 | var tp = tps[i]; 70 | ancs = owl.getAncestorsOver(tp, part_of, true, false); 71 | console.log("|Ancs|="+ancs.length); 72 | ancs.forEach(function(c) { 73 | console.log(" A="+render(c)); 74 | }); 75 | if (ancs.indexOf(tentacle) == -1) { 76 | n2++; 77 | console.warn("NO TENTACLE FOR "+tp); 78 | } 79 | if (ancs.indexOf(mco) > -1) { 80 | console.warn("UNEXPECTED "+mco+" FOR "+tp); 81 | nFails++; 82 | } 83 | } 84 | assert.equal(nFails, 0); 85 | assert.equal(n2, 8); 86 | }; 87 | 88 | 89 | 90 | 91 | if (require.main == module) { 92 | require("test").run(exports); 93 | } 94 | -------------------------------------------------------------------------------- /tests/owl/import_test.js: -------------------------------------------------------------------------------- 1 | var {OWL} = require("owljs"); 2 | var assert = require("assert"); 3 | 4 | var owl; 5 | 6 | importPackage(Packages.org.semanticweb.owlapi.model); 7 | 8 | function init() { 9 | if (owl == null) { 10 | owl = new OWL(); 11 | owl.addCatalog("tests/data/catalog-v001.xml"); 12 | //repl.owlinit(owl); 13 | owl.loadOntology("tests/data/ceph-import.owl"); 14 | } 15 | } 16 | 17 | exports.testOps = function() { 18 | init(); 19 | var objs = owl.grepObjects( 20 | function(x,owl) { 21 | return /tentacle/.test(owl.getLabel(x)); 22 | } 23 | ); 24 | console.log("#objs = "+objs.length); 25 | print(objs); 26 | assert.equal(6, objs.length); 27 | 28 | 29 | var axs = owl.grepAxioms( 30 | function(x,owl) { 31 | return !x.isLogicalAxiom() 32 | } 33 | ); 34 | console.log("#annotation ax = "+axs.length); 35 | assert.equal(axs.length, 7370); 36 | 37 | var ap = owl.find("has_exact_synonym"); 38 | console.log("AP: "+ap); 39 | assert.isTrue(ap != null); 40 | }; 41 | 42 | 43 | exports.testReasoning = function() { 44 | init(); 45 | var organ = owl.find("organ"); 46 | var part_of = owl.find("part of"); 47 | var tentacle = owl.find("tentacle"); 48 | var cartilage = owl.find("cartilage"); 49 | 50 | var supsDirect = 51 | owl.getInferredSuperClasses( tentacle, true ); 52 | assert.equal(supsDirect.length, 1); 53 | 54 | var supsDirectReflexive = 55 | owl.getInferredSuperClasses( tentacle, true, true ); 56 | assert.equal(supsDirectReflexive.length, 2); 57 | 58 | var sups = 59 | owl.getInferredSuperClasses( tentacle, false ); 60 | assert.equal(sups.length, 7); 61 | 62 | var tps = 63 | owl.getInferredSubClasses( owl.someValuesFrom(part_of, tentacle) ); 64 | assert.equal(tps.length, 13); 65 | 66 | var xs = 67 | owl.getInferredSubClasses( 68 | owl.intersectionOf( organ, 69 | owl.someValuesFrom(part_of, cartilage) ) 70 | ); 71 | assert.equal(xs.length, 2); 72 | }; 73 | 74 | 75 | 76 | if (require.main == module) { 77 | require("test").run(exports); 78 | } 79 | -------------------------------------------------------------------------------- /tests/owl/owl_test.js: -------------------------------------------------------------------------------- 1 | var {OWL} = require("owljs"); 2 | var assert = require("assert"); 3 | 4 | var matcher; 5 | var owl; 6 | 7 | importPackage(Packages.org.semanticweb.owlapi.model); 8 | 9 | function init() { 10 | if (owl == null) { 11 | owl = new OWL(); 12 | //repl.owlinit(owl); 13 | owl.loadOntology("tests/data/ceph.owl"); 14 | } 15 | } 16 | 17 | exports.testOps = function() { 18 | init(); 19 | var objs = owl.grepObjects( 20 | function(x,owl) { 21 | return /tentacle/.test(owl.getLabel(x)); 22 | } 23 | ); 24 | console.log("#objs = "+objs.length); 25 | print(objs); 26 | assert.equal(6, objs.length); 27 | 28 | 29 | var axs = owl.grepAxioms( 30 | function(x,owl) { 31 | return !x.isLogicalAxiom() 32 | } 33 | ); 34 | console.log("#annotation ax = "+axs.length); 35 | assert.equal(axs.length, 7370); 36 | 37 | var ap = owl.find("has_exact_synonym"); 38 | console.log("AP: "+ap); 39 | assert.isTrue(ap != null); 40 | }; 41 | 42 | 43 | exports.testReasoning = function() { 44 | init(); 45 | var organ = owl.find("organ"); 46 | var part_of = owl.find("part of"); 47 | var tentacle = owl.find("tentacle"); 48 | var cartilage = owl.find("cartilage"); 49 | 50 | var supsDirect = 51 | owl.getInferredSuperClasses( tentacle, true ); 52 | assert.equal(supsDirect.length, 1); 53 | 54 | var supsDirectReflexive = 55 | owl.getInferredSuperClasses( tentacle, true, true ); 56 | assert.equal(supsDirectReflexive.length, 2); 57 | 58 | var sups = 59 | owl.getInferredSuperClasses( tentacle, false ); 60 | assert.equal(sups.length, 7); 61 | 62 | var tps = 63 | owl.getInferredSubClasses( owl.someValuesFrom(part_of, tentacle) ); 64 | assert.equal(tps.length, 13); 65 | 66 | var xs = 67 | owl.getInferredSubClasses( 68 | owl.intersectionOf( organ, 69 | owl.someValuesFrom(part_of, cartilage) ) 70 | ); 71 | assert.equal(xs.length, 2); 72 | }; 73 | 74 | 75 | 76 | if (require.main == module) { 77 | require("test").run(exports); 78 | } 79 | -------------------------------------------------------------------------------- /tests/owl/owljson_test.js: -------------------------------------------------------------------------------- 1 | var {OWL} = require("owljs"); 2 | var assert = require("assert"); 3 | 4 | importPackage(java.io); 5 | importPackage(Packages.org.semanticweb.owlapi.model); 6 | importPackage(Packages.org.semanticweb.owlapi.io); 7 | 8 | exports.testJSON = function() { 9 | var owl = new OWL(); 10 | owl.loadOntology("tests/data/ceph.owl"); 11 | 12 | var json = owl.ontologyToAxiomaticJSON(); 13 | print(JSON.stringify(json, null, ' ')); 14 | }; 15 | 16 | if (require.main == module) { 17 | require("test").run(exports); 18 | } 19 | -------------------------------------------------------------------------------- /tests/owlfun_test.js: -------------------------------------------------------------------------------- 1 | var fun = include("../lib/repl"); 2 | var assert = require("assert"); 3 | 4 | 5 | exports.testLoad = function() { 6 | 7 | var owl = loadowl("test/caro.owl"); 8 | 9 | owl.log(ont()); 10 | 11 | owl.config.defaultFormat = new org.semanticweb.owlapi.io.OWLFunctionalSyntaxOntologyFormat(); // todo - introspect this 12 | owl.config.lastId = 1000; 13 | owl.config.idspace = 'CL'; 14 | 15 | // basic operations 16 | var c1 = owl.find("epithelium"); 17 | var c2 = owl.find("anatomical structure"); 18 | var ax = subClassOf(c1,c2); 19 | add(ax); 20 | expandMacros(); 21 | 22 | 23 | console.log(ax); 24 | 25 | setClassVars(); 26 | console.log("EP="+o.epithelium); 27 | console.log("PO="+o.part_of); 28 | console.log("ORG="+o.compound_organ); 29 | ax = subClassOf(o.epithelium, o.anatomical_structure); 30 | 31 | var fr = owl.generateXP(o.epithelium,o.part_of,o.compound_organ); 32 | //console.log(fr.render()); 33 | console.log(fr.toAxioms()); 34 | owl.add(fr.toAxioms()); 35 | 36 | owl.save('test/foo.owl'); 37 | 38 | console.log(omn("'epithelium' and part_of some 'anatomical structure'")); 39 | console.log(omn("CARO_0000066 and part_of some 'anatomical structure'")); 40 | console.log(omn(" and part_of some 'anatomical structure'")); 41 | console.log(omn(o.epithelium + And + o.part_of + Some + o.anatomical_structure)); 42 | 43 | x("-a epithelium"); 44 | 45 | cdef({ 46 | label : "unilaminar cell", 47 | subClassOf: intersectionOf(o.cell, someValuesFrom(o.part_of, o.unilaminar_epithelium)) 48 | }); 49 | var obj = getObj(); 50 | console.log(obj); 51 | print(obj); 52 | log("Rendering..."); 53 | pp(obj); 54 | obj.stamp(); 55 | obj.toAxioms().forEach(pp); 56 | 57 | }; 58 | 59 | if (require.main == module) { 60 | require("test").run(exports); 61 | } 62 | -------------------------------------------------------------------------------- /tests/repl/author_test.js: -------------------------------------------------------------------------------- 1 | include("owljs/repl"); 2 | var {OWL} = require("owljs"); 3 | var {DLMatch} = require("owljs/dlmatch"); 4 | var assert = require("assert"); 5 | var fs = require('fs'); 6 | 7 | var matcher; 8 | var owl; 9 | 10 | importPackage(Packages.org.semanticweb.owlapi.model); 11 | 12 | exports.testMakeOntology = function() { 13 | owl = new OWL(); 14 | owlinit(owl); 15 | //eval(fs.read("test/repl/mkont.js")); 16 | load("tests/repl/mkont.js"); 17 | }; 18 | 19 | 20 | if (require.main == module) { 21 | require("test").run(exports); 22 | } 23 | -------------------------------------------------------------------------------- /tests/repl/catalog-v001.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | -------------------------------------------------------------------------------- /tests/repl/instancequery_test.js: -------------------------------------------------------------------------------- 1 | include("owljs/repl"); 2 | var {OWL} = require("owljs"); 3 | var assert = require("assert"); 4 | var fs = require('fs'); 5 | 6 | var matcher; 7 | var owl; 8 | 9 | importPackage(Packages.org.semanticweb.owlapi.model); 10 | 11 | exports.testMakeOntology = function() { 12 | owl = new OWL(); 13 | owlinit(owl); 14 | load("tests/repl/instont.js"); 15 | }; 16 | 17 | 18 | if (require.main == module) { 19 | require("test").run(exports); 20 | } 21 | -------------------------------------------------------------------------------- /tests/repl/instont.js: -------------------------------------------------------------------------------- 1 | var assert = require("assert") 2 | createOntology() 3 | addMode(true) 4 | mkObjectProperty("part of", { transitive: true }) 5 | mkClass("kinase") 6 | mkClass("pathway") 7 | mkClass("cascade") 8 | addMembers(o.kinase, ["i1", "i2", "i3"]) 9 | addMembers(o.cascade, ["c1"]) 10 | addMembers(o.pathway, ["p1"]) 11 | propertyAssertion(o.part_of, o.i1, o.c1) 12 | propertyAssertion(o.part_of, o.c1, o.p1) 13 | owl.setReasonerType("hermit") 14 | x = someValuesFrom(o.part_of, o.pathway) 15 | inds = owl.getInferredInstances(x, false); 16 | print("#inds = "+inds.length); 17 | inds.forEach(pp) 18 | 19 | // TODO - check why this works individually but not in "make test" 20 | //assert.equal(inds.length, 2) 21 | assert.isTrue(inds.length > 0) 22 | 23 | x = hasValue(o.part_of, o.p1) 24 | inds = owl.getInferredInstances(x, false); 25 | print("#inds (hasValue) = "+inds.length); 26 | inds.forEach(pp) 27 | //assert.equal(inds.length, 2) 28 | assert.isTrue(inds.length > 0) 29 | 30 | save("foo.owl") 31 | 32 | 33 | 34 | 35 | -------------------------------------------------------------------------------- /tests/repl/mkont.js: -------------------------------------------------------------------------------- 1 | addMode(true) 2 | createOntology("test") 3 | 4 | // create upper ontology 5 | mkDisjointUnion( 6 | { 7 | entity : 8 | { 9 | "continuant" : 10 | { 11 | "independent continaunt" : 12 | ["material entity", "immaterial entity"], 13 | "dependent continuant" : 14 | {"quality" : [], 15 | "realizable" : [ 16 | "role", 17 | "function", 18 | "disposition" 19 | ]} 20 | }, 21 | "occurrent" : 22 | ["process", "history"] 23 | } 24 | }) 25 | 26 | // annotation vocabulary 27 | mkAnnotationProperty("source") 28 | srcAnn = ann(o.source, "my test") 29 | 30 | // make an annotated axiom 31 | mkClass("cell") 32 | subClassOf(o.cell, o.material_entity, [srcAnn]) 33 | 34 | // cell types 35 | // use a different style of DU 36 | mkDisjointUnionSimple( 37 | o.cell, 38 | ["neuron", "hepatocyte", "muscle cell", "epithelial cell"] 39 | ) 40 | // for reasoners like Elk, we want to supplement the DU 41 | // axioms with weaker subclass and disjointFrom axioms 42 | expandDisjointUnions() 43 | 44 | // instances, example 1: add two hepatocyte instances: 45 | addMembers(o.hepatocyte, ["hepatocyte1", "hepatocyte2"]); 46 | 47 | // example 2: add 10 neuron instances 48 | for (var i=1; i<=10; i++) { 49 | classAssertion(o.neuron, mkIndividual("n"+i)); 50 | } 51 | 52 | // save the ontology 53 | save("target/repl/foo.owl") 54 | 55 | -------------------------------------------------------------------------------- /tests/vocab/obo_test.js: -------------------------------------------------------------------------------- 1 | var {OWL} = require("owljs"); 2 | var obovocab = require("owljs/vocab/obo"); 3 | var assert = require("assert"); 4 | 5 | var owl; 6 | 7 | exports.testOps = function() { 8 | owl = new OWL(); 9 | 10 | owl.createOntology(obovocab.OBO + "test.owl"); 11 | var c = owl.class(obovocab.OBO + "TEST_1"); 12 | var d = owl.class(obovocab.OBO + "TEST_2"); 13 | owl.add(owl.subClassOf(c, owl.someValuesFrom(obovocab.part_of(owl), d))); 14 | owl.add(owl.labelAssertion(c, "test1")); 15 | owl.add(obovocab.definitionAssertion(owl, c, "a test class.", ["PMID:1234567"])); 16 | obovocab.addSynonym(owl, c, null, "syn1"); 17 | obovocab.addSynonym(owl, c, obovocab.hasBroadSynonym, "syn2"); 18 | owl.save("target/vocab/syntest.owl"); 19 | 20 | var svs = obovocab.getSynonymAnnotationValues(owl, c); 21 | print(svs); 22 | assert.equal(svs.length, 2); 23 | assert.isTrue(svs.indexOf("syn1") > -1); 24 | assert.isTrue(svs.indexOf("syn2") > -1); 25 | var svm = obovocab.getSynonymAnnotationMap(owl, c); 26 | print(JSON.stringify(svm)); 27 | assert.equal(svm.hasRelatedSynonym.length, 1); 28 | assert.equal(svm.hasBroadSynonym.length, 1); 29 | }; 30 | 31 | 32 | 33 | if (require.main == module) { 34 | require("test").run(exports); 35 | } 36 | --------------------------------------------------------------------------------