renamed

bin/owljs-diff.js

@@ -1,7 +1,7 @@
 var Parser = require('ringo/args').Parser;
 var system = require('system');
 var {OWL} = require("owl");
-var {Differ} = require("owl/Differ");
+var {Differ} = require("owljs/Differ");
 
 var owlA;
 var owlB;

bin/owljs-dlmatch.js

@@ -1,7 +1,7 @@
 var Parser = require('ringo/args').Parser;
 var system = require('system');
 var {OWL} = require("owl");
-var {DLMatch} = require("owl/dlmatch");
+var {DLMatch} = require("owljs/dlmatch");
 
 importPackage(Packages.org.semanticweb.owlapi.model);
 var owl;
@@ -45,7 +45,7 @@ function main(args) {
     owl.addCatalog();
     args.forEach(function(fn) { owl.loadFile(fn) } );
     var q = new DLMatch(owl);
-    var repl = require("owl/repl");
+    var repl = require("owljs/repl");
     repl.owlinit(owl);
     var o = repl.o;
 

bin/owljs-grep.js

@@ -68,7 +68,7 @@ function main(args) {
         owl.log("#filteredObjects = " + filteredObjects.length);
 
         if (options.jsFrames) {
-            var repl = require("owl/repl");
+            var repl = require("owljs/repl");
             repl.owlinit(owl);
             for (var k in filteredObjects) {
                 var obj = filteredObjects[k];
@@ -86,7 +86,7 @@ function main(args) {
         owl.log("#filteredAxioms = " + filteredAxioms.length);
 
         if (options.jsFrames) {
-            var repl = require("owl/repl");
+            var repl = require("owljs/repl");
             repl.owlinit(owl);
             //repl.owl = owl;
             for (var k in filteredAxioms) {

bin/owljs-obol.js

@@ -1,7 +1,7 @@
 var Parser = require('ringo/args').Parser;
 var system = require('system');
 var {OWL} = require("owl");
-var {Obol} = require("owl/obol");
+var {Obol} = require("owljs/obol");
 
 function main(args) {
     var script = args.shift();
@@ -11,7 +11,7 @@ function main(args) {
     parser.addOption('h', 'help', null, 'Display help');
     parser.addOption('q', 'query', 'String', 'sentence to parse');
     parser.addOption('r', 'rootClass', 'Class', 'root class to restrict search space. Can be IRI or name. E.g. "neuron" or "regulation of biological process"');
-    parser.addOption('m', 'module', 'Module', 'module in owl/obol to load. E.g. phenotype; E.g. anatomy; E.g. bp/involvedIn');
+    parser.addOption('m', 'module', 'Module', 'module in owljs/obol to load. E.g. phenotype; E.g. anatomy; E.g. bp/involvedIn');
     parser.addOption('o', 'outputFile', 'File', 'output OWL file where generated axioms are stored (defaults to stdout)');
     parser.addOption('t', 'toOutputFormat', 'OWLOntologyFormat', 'output format for generated axioms (defaults to RDFXML)');
     parser.addOption('F', 'forceGenerate', 'Variables', 'forces generation of classes for the given variable name or names (comma-separated). E.g. "part,whole"');
@@ -66,10 +66,10 @@ owljs-obol -p label,has_exact_synonym -T -v 1 -u -o xp.owl -t ofn -m bp/involved
         if (options.module.indexOf(".") == 0) {
             require(options.module);
         }
-        require("owl/obol/" + options.module);
+        require("owljs/obol/" + options.module);
     }
 
-    var repl = require("owl/repl");
+    var repl = require("owljs/repl");
     repl.owlinit(owl);
     var obol = new Obol(owl, repl.o);
 

bin/owljs-owlstats.js

@@ -1,7 +1,7 @@
 var Parser = require('ringo/args').Parser;
 var system = require('system');
 var {OWL} = require("owl");
-var stats = require("owl/Stats");
+var stats = require("owljs/Stats");
 
 var owl;
 function main(args) {

bin/owljs-refilter.js

@@ -47,7 +47,7 @@ function main(args) {
     owl.log("#filteredClasses = " + clist.length);
 
     if (options.jsFrames) {
-        var repl = require("owl/repl");
+        var repl = require("owljs/repl");
         repl.owlinit(owl);
         //repl.owl = owl;
         for (var ci in clist) {

bin/owljs-repl.js

@@ -1,13 +1,13 @@
 // we use include() rather than require(), deliberately polluting our namespace for convenience
-include("owl/repl"); 
+include("owljs/repl"); 
 
 var Parser = require('ringo/args').Parser;
 var system = require('system');
 var fs = require('fs');
 var {OWL} = require("owl");
-var {OWLFrame} = require("owl/owlframe");
-var {DLMatch} = require("owl/dlmatch");
-var {Obol} = require("owl/obol");
+var {OWLFrame} = require("owljs/owlframe");
+var {DLMatch} = require("owljs/dlmatch");
+var {Obol} = require("owljs/obol");
 var owl;
 var q;
 var obol;

lib/Differ.js

@@ -17,8 +17,8 @@
  *
  */
 
-var javautil = require("owl/javautil");
-var md = require("owl/io/markdown");
+var javautil = require("owljs/javautil");
+var md = require("owljs/io/markdown");
 
 importPackage(Packages.org.semanticweb.owlapi.model);
 

lib/Stats.js

@@ -1,4 +1,4 @@
-var obovocab = require("owl/vocab/obo");
+var obovocab = require("owljs/vocab/obo");
 
 var getOntologyStats = exports.getOntologyStats = function(owl, objs, gf) {
     return {

lib/dlmatch.js

@@ -3,7 +3,7 @@
  * Pattern matching system for OWL ontologies
  *
  * Example:
- * > var {DLMatcher} = require("owl/dlmatcher");
+ * > var {DLMatcher} = require("owljs/dlmatcher");
  * > var q = new DLMatcher(owl);
  * > var part_of = owl.find("part of");
  * >
@@ -62,7 +62,7 @@
  *
  */
 
-var javautil = require("owl/javautil");
+var javautil = require("owljs/javautil");
 importPackage(Packages.org.semanticweb.owlapi.model);
 
 /* Function: DLMatch
@@ -150,7 +150,7 @@ DLMatch.prototype.findAndReplace = function(q, rfunc) {
  * Example:
  *
  * > # Add definitions
- * > var obovocab = require("owl/vocab/obo");
+ * > var obovocab = require("owljs/vocab/obo");
  * > q.findAndExtend(
  * >    q.equivalentClassesMatch( "?x", q.intersectionOfMatch("?genus", q.objectSomeValuesFromMatch("?r", "?y"))),
  * >    function(m,owl) { 

lib/obol.js

@@ -37,7 +37,7 @@
 
 
 
-  See the directory owl/obol/ for a list of ready-made parse rules for bio-ontologies
+  See the directory owljs/obol/ for a list of ready-made parse rules for bio-ontologies
 
 
   Scripts:
@@ -60,7 +60,7 @@ export('Obol');
 function Obol(owl, labelObjectMap) {
     this.owl = owl;
     if (labelObjectMap == null) {
-        var repl = require("owl/repl");
+        var repl = require("owljs/repl");
         repl.owlinit(owl);
         labelObjectMap = repl.o;
     }
@@ -131,8 +131,8 @@ Obol.prototype.isRespectCase = function() {
  *
  */
 Obol.prototype.useOboVocab = function() {
-    var vocab = require("owl/vocab/obo");
-    var nif = require("owl/vocab/nif");
+    var vocab = require("owljs/vocab/obo");
+    var nif = require("owljs/vocab/nif");
     var owl = this.owl;
     this.setPropertyScore( vocab.hasBroadSynonym(owl), 5 );
     this.setPropertyScore( vocab.hasNarrowSynonym(owl), 5 );

lib/obol/anatomy.js

@@ -1,5 +1,5 @@
-var {Obol} = require("owl/obol");
-include("owl/repl");
+var {Obol} = require("owljs/obol");
+include("owljs/repl");
 
 Obol.add(
     {

lib/obol/bp.js

@@ -1 +1 @@
-require("owl/obol/bp/involvedIn");
+require("owljs/obol/bp/involvedIn");

lib/obol/bp/cellDevelopment.js

@@ -1,5 +1,5 @@
-var {Obol} = require("owl/obol");
-include("owl/repl");
+var {Obol} = require("owljs/obol");
+include("owljs/repl");
 
 Obol.add(
     {

lib/obol/bp/involvedIn.js

@@ -1,5 +1,5 @@
-var {Obol} = require("owl/obol");
-include("owl/repl");
+var {Obol} = require("owljs/obol");
+include("owljs/repl");
 
 Obol.add(
     {

lib/obol/bp/regulationOfQuality.js

@@ -1,5 +1,5 @@
-var {Obol} = require("owl/obol");
-include("owl/repl");
+var {Obol} = require("owljs/obol");
+include("owljs/repl");
 
 Obol.add(
     {

lib/obol/equiv.js

@@ -1,5 +1,5 @@
-var {Obol} = require("owl/obol");
-include("owl/repl");
+var {Obol} = require("owljs/obol");
+include("owljs/repl");
 
 Obol.add(
     {

lib/obol/phenotype.js

@@ -1,5 +1,5 @@
-var {Obol} = require("owl/obol");
-include("owl/repl");
+var {Obol} = require("owljs/obol");
+include("owljs/repl");
 
 Obol.add(
     {

lib/owl.js

@@ -1,5 +1,5 @@
-var {OWLFrame} = require("owl/owlframe"); 
-var javautil = require("owl/javautil");
+var {OWLFrame} = require("owljs/owlframe"); 
+var javautil = require("owljs/javautil");
 
 /* Namespace: OWL
  *

lib/owlframe.js

@@ -7,7 +7,7 @@ importPackage(org.semanticweb.elk.owlapi);
 importPackage(Packages.owltools.io);
 importPackage(Packages.com.google.gson);
 
-var javautil = require("owl/javautil");
+var javautil = require("owljs/javautil");
 
 /* 
  * 

lib/repl.js

@@ -1,6 +1,6 @@
 var {OWL} = require("owl");
-var {OWLFrame} = require("owl/owlframe"); 
-var javautil = require("owl/javautil");
+var {OWLFrame} = require("owljs/owlframe"); 
+var javautil = require("owljs/javautil");
 importPackage(java.io);
 importPackage(Packages.org.semanticweb.owlapi.model);
 importPackage(Packages.org.semanticweb.owlapi.io);
@@ -765,13 +765,13 @@ exports.ogw = function() {
     return getRunner().g; 
 };
 
-var obovocab = require("owl/vocab/obo");
+var obovocab = require("owljs/vocab/obo");
 var oboIdSpace = exports.oboIdSpace = function(obj) {
     return obovocab.getOboIdentifierPrefix(owl, obj);
 }
 
 exports.getStats = function() {
-    var stats = require("owl/stats");
+    var stats = require("owljs/stats");
     return stats.getOntologyStats(owl);
 }
 

server.js

@@ -24,8 +24,8 @@ app.configure('route');
 app.configure('params');
 app.configure('static');
 
-var owlservices = require('./lib/owl/owlservices.js');
-var addons = require('./lib/owl/addons.js');
+var owlservices = require('./lib/owljs/owlservices.js');
+var addons = require('./lib/owljs/addons.js');
 
 print("owl is :"+session.owl);
 var myOwlservices = new owlservices.OWLServices(app,session);

tests/differ/differ_test.js

@@ -1,5 +1,5 @@
 var {OWL} = require("owl");
-var {Differ} = require("owl/differ");
+var {Differ} = require("owljs/differ");
 var assert = require("assert");
 
 var differ;
@@ -17,8 +17,8 @@ function init() {
 
 exports.testDiffs = function() {
     init();
-    var ov = require("owl/vocab/obo");
-    var repl = require("owl/repl");
+    var ov = require("owljs/vocab/obo");
+    var repl = require("owljs/repl");
     var owlB = new OWL();
     repl.owlinit(owlB);
     owlB.loadOntology("tests/data/ceph.owl");

tests/dlmatch/dlmatch_test.js

@@ -1,7 +1,7 @@
 var {OWL} = require("owl");
-var {DLMatch} = require("owl/dlmatch");
+var {DLMatch} = require("owljs/dlmatch");
 var assert = require("assert");
-var repl = require("owl/repl");
+var repl = require("owljs/repl");
 
 var matcher;
 var owl;

tests/learner/mp_test.js

@@ -1,7 +1,7 @@
 var {OWL} = require("owl");
-var {Learner} = require("owl/learner");
+var {Learner} = require("owljs/learner");
 var assert = require("assert");
-var repl = require("owl/repl");
+var repl = require("owljs/repl");
 
 var learner;
 var owl;

tests/obol/obol_test.js

@@ -1,6 +1,6 @@
 var {OWL} = require("owl");
-var {Obol} = require("owl/obol");
-var repl = require("owl/repl");
+var {Obol} = require("owljs/obol");
+var repl = require("owljs/repl");
 var assert = require("assert");
 
 var owl;
@@ -22,7 +22,7 @@ exports.testOps = function() {
     var o = repl.o;
     obol = new Obol(owl, repl.o);
     owl.config.isCompareClasses = true;
-    require("owl/obol/anatomy");
+    require("owljs/obol/anatomy");
     var str = "cell of brain";
     var results = obol.parse(str, null);
     repl.pp(results);

tests/obol/obolsyn_test.js

@@ -1,6 +1,6 @@
 var {OWL} = require("owl");
-var {Obol} = require("owl/obol");
-var obovocab = require("owl/vocab/obo");
+var {Obol} = require("owljs/obol");
+var obovocab = require("owljs/vocab/obo");
 var assert = require("assert");
 
 var owl;
@@ -94,7 +94,7 @@ exports.testGenerateLastToken = function() {
 
     obol.generate("whole");
     matches = obol.parseClass(fbPyramidalCell);
-    var repl = require("owl/repl");
+    var repl = require("owljs/repl");
     repl.pp(matches);
     assert.equal(matches.length, 1);
 
@@ -115,7 +115,7 @@ exports.testGenerateInitialToken = function() {
 
     obol.generate("part");
     matches = obol.parseClass(capc);
-    var repl = require("owl/repl");
+    var repl = require("owljs/repl");
     repl.pp(matches);
     assert.equal(matches.length, 1);
 }
@@ -135,7 +135,7 @@ exports.testGenerateViaSynonym = function() {
 
     obol.generate("part");
     matches = obol.parseClass(capc);
-    var repl = require("owl/repl");
+    var repl = require("owljs/repl");
     repl.pp(matches);
     assert.equal(matches.length, 1);
 }
@@ -156,7 +156,7 @@ exports.testDoubleGenerate = function() {
     obol.generate("part");
     obol.generate("whole");
     matches = obol.parseClass(capc, "part of whole");
-    var repl = require("owl/repl");
+    var repl = require("owljs/repl");
     repl.pp(matches);
     assert.equal(matches.length, 1);
 }
@@ -167,7 +167,7 @@ function testParse(erule, escore) {
     obol.useOboVocab();
     obol.logLevel = 5;
     var matches = obol.parseClass(caPyramidalCell);
-    var repl = require("owl/repl");
+    var repl = require("owljs/repl");
     repl.pp(matches);
     if (escore == null) {
         assert.equal(matches.length, 0);