citeclaw 2.0.0

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Files changed (1723) hide show
  1. package/LICENSE +202 -0
  2. package/README.md +152 -0
  3. package/app.js +318 -0
  4. package/config.dev.yaml +124 -0
  5. package/config.prod.yaml +123 -0
  6. package/config.yaml +0 -0
  7. package/lib/Citation.js +101 -0
  8. package/lib/CitoidError.js +61 -0
  9. package/lib/CitoidRequest.js +150 -0
  10. package/lib/CitoidResponse.js +44 -0
  11. package/lib/CitoidService.js +1118 -0
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  14. package/lib/Scraper.js +617 -0
  15. package/lib/Translator.js +76 -0
  16. package/lib/ZoteroService.js +220 -0
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  19. package/lib/external-apis/OpenAlexService.js +245 -0
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  37. package/package.json +121 -0
  38. package/routes/citoid.js +101 -0
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  41. package/scripts/botcite.js +5021 -0
  42. package/scripts/citeclaw.js +10 -0
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@@ -0,0 +1,578 @@
1
+ /**
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+ * @fileoverview
3
+ * TABULATOR RDF PARSER
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+ *
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+ * Version 0.1
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+ * Parser believed to be in full positive RDF/XML parsing compliance
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+ * with the possible exception of handling deprecated RDF attributes
8
+ * appropriately. Parser is believed to comply fully with other W3C
9
+ * and industry standards where appropriate (DOM, ECMAScript, &c.)
10
+ *
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+ * Author: David Sheets <dsheets@mit.edu>
12
+ * SVN ID: $Id$
13
+ *
14
+ * W3C® SOFTWARE NOTICE AND LICENSE
15
+ * http://www.w3.org/Consortium/Legal/2002/copyright-software-20021231
16
+ * This work (and included software, documentation such as READMEs, or
17
+ * other related items) is being provided by the copyright holders under
18
+ * the following license. By obtaining, using and/or copying this work,
19
+ * you (the licensee) agree that you have read, understood, and will
20
+ * comply with the following terms and conditions.
21
+ *
22
+ * Permission to copy, modify, and distribute this software and its
23
+ * documentation, with or without modification, for any purpose and
24
+ * without fee or royalty is hereby granted, provided that you include
25
+ * the following on ALL copies of the software and documentation or
26
+ * portions thereof, including modifications:
27
+ *
28
+ * 1. The full text of this NOTICE in a location viewable to users of
29
+ * the redistributed or derivative work.
30
+ * 2. Any pre-existing intellectual property disclaimers, notices, or terms and
31
+ * conditions. If none exist, the W3C Software Short Notice should be
32
+ * included (hypertext is preferred, text is permitted) within the body
33
+ * of any redistributed or derivative code.
34
+ * 3. Notice of any changes or modifications to the files, including the
35
+ * date changes were made. (We recommend you provide URIs to the location
36
+ * from which the code is derived.)
37
+ *
38
+ * THIS SOFTWARE AND DOCUMENTATION IS PROVIDED "AS IS," AND COPYRIGHT
39
+ * HOLDERS MAKE NO REPRESENTATIONS OR WARRANTIES, EXPRESS OR IMPLIED,
40
+ * INCLUDING BUT NOT LIMITED TO, WARRANTIES OF MERCHANTABILITY OR FITNESS
41
+ * FOR ANY PARTICULAR PURPOSE OR THAT THE USE OF THE SOFTWARE OR
42
+ * DOCUMENTATION WILL NOT INFRINGE ANY THIRD PARTY PATENTS, COPYRIGHTS,
43
+ * TRADEMARKS OR OTHER RIGHTS.
44
+ *
45
+ * COPYRIGHT HOLDERS WILL NOT BE LIABLE FOR ANY DIRECT, INDIRECT, SPECIAL
46
+ * OR CONSEQUENTIAL DAMAGES ARISING OUT OF ANY USE OF THE SOFTWARE OR
47
+ * DOCUMENTATION.
48
+ *
49
+ * The name and trademarks of copyright holders may NOT be used in
50
+ * advertising or publicity pertaining to the software without specific,
51
+ * written prior permission. Title to copyright in this software and any
52
+ * associated documentation will at all times remain with copyright
53
+ * holders.
54
+ */
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+
56
+ if (typeof process === 'object' && process + '' === '[object process]'){
57
+ var $rdf = require('./init');
58
+ }
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+
60
+ /**
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+ * @class Class defining an RDFParser resource object tied to an RDFStore
62
+ *
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+ * @author David Sheets <dsheets@mit.edu>
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+ * @version 0.1
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+ *
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+ * @constructor
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+ * @param {RDFStore} store An RDFStore object
68
+ */
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+ $rdf.RDFParser = function (store) {
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+ var RDFParser = {};
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+
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+ /** Standard namespaces that we know how to handle @final
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+ * @member RDFParser
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+ */
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+ RDFParser['ns'] = {
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+ 'RDF': "http://www.w3.org/1999/02/22-rdf-syntax-ns#",
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+ 'RDFS': "http://www.w3.org/2000/01/rdf-schema#"
78
+ }
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+ /** DOM Level 2 node type magic numbers @final
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+ * @member RDFParser
81
+ */
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+ RDFParser['nodeType'] = {
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+ 'ELEMENT': 1,
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+ 'ATTRIBUTE': 2,
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+ 'TEXT': 3,
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+ 'CDATA_SECTION': 4,
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+ 'ENTITY_REFERENCE': 5,
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+ 'ENTITY': 6,
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+ 'PROCESSING_INSTRUCTION': 7,
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+ 'COMMENT': 8,
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+ 'DOCUMENT': 9,
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+ 'DOCUMENT_TYPE': 10,
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+ 'DOCUMENT_FRAGMENT': 11,
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+ 'NOTATION': 12
95
+ }
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+
97
+ /**
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+ * Frame class for namespace and base URI lookups
99
+ * Base lookups will always resolve because the parser knows
100
+ * the default base.
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+ *
102
+ * @private
103
+ */
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+ this['frameFactory'] = function (parser, parent, element) {
105
+ return {
106
+ 'NODE': 1,
107
+ 'ARC': 2,
108
+ 'parent': parent,
109
+ 'parser': parser,
110
+ 'store': parser['store'],
111
+ 'element': element,
112
+ 'lastChild': 0,
113
+ 'base': null,
114
+ 'lang': null,
115
+ 'node': null,
116
+ 'nodeType': null,
117
+ 'listIndex': 1,
118
+ 'rdfid': null,
119
+ 'datatype': null,
120
+ 'collection': false,
121
+
122
+ /** Terminate the frame and notify the store that we're done */
123
+ 'terminateFrame': function () {
124
+ if(this['collection']) {
125
+ this['node']['close']()
126
+ }
127
+ },
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+
129
+ /** Add a symbol of a certain type to the this frame */
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+ 'addSymbol': function (type, uri) {
131
+ uri = $rdf.Util.uri.join(uri, this['base'])
132
+ this['node'] = this['store']['sym'](uri)
133
+ this['nodeType'] = type
134
+ },
135
+
136
+ /** Load any constructed triples into the store */
137
+ 'loadTriple': function () {
138
+ if(this['parent']['parent']['collection']) {
139
+ this['parent']['parent']['node']['append'](this['node'])
140
+ } else {
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+ this['store']['add'](this['parent']['parent']['node'],
142
+ this['parent']['node'],
143
+ this['node'],
144
+ this['parser']['why'])
145
+ }
146
+ if(this['parent']['rdfid'] != null) { // reify
147
+ var triple = this['store']['sym'](
148
+ $rdf.Util.uri.join("#" + this['parent']['rdfid'], this['base']))
149
+ this['store']['add'](triple,
150
+ this['store']['sym'](RDFParser['ns']['RDF'] + "type"),
151
+ this['store']['sym'](RDFParser['ns']['RDF'] + "Statement"),
152
+ this['parser']['why'])
153
+ this['store']['add'](triple,
154
+ this['store']['sym'](RDFParser['ns']['RDF'] + "subject"),
155
+ this['parent']['parent']['node'],
156
+ this['parser']['why'])
157
+ this['store']['add'](triple,
158
+ this['store']['sym'](RDFParser['ns']['RDF'] + "predicate"),
159
+ this['parent']['node'],
160
+ this['parser']['why'])
161
+ this['store']['add'](triple,
162
+ this['store']['sym'](RDFParser['ns']['RDF'] + "object"),
163
+ this['node'],
164
+ this['parser']['why'])
165
+ }
166
+ },
167
+
168
+ /** Check if it's OK to load a triple */
169
+ 'isTripleToLoad': function () {
170
+ return (this['parent'] != null
171
+ && this['parent']['parent'] != null
172
+ && this['nodeType'] == this['NODE']
173
+ && this['parent']['nodeType'] == this['ARC']
174
+ && this['parent']['parent']['nodeType'] == this['NODE'])
175
+ },
176
+
177
+ /** Add a symbolic node to this frame */
178
+ 'addNode': function (uri) {
179
+ this['addSymbol'](this['NODE'], uri)
180
+ if(this['isTripleToLoad']()) {
181
+ this['loadTriple']()
182
+ }
183
+ },
184
+
185
+ /** Add a collection node to this frame */
186
+ 'addCollection': function () {
187
+ this['nodeType'] = this['NODE']
188
+ this['node'] = this['store']['collection']()
189
+ this['collection'] = true
190
+ if(this['isTripleToLoad']()) {
191
+ this['loadTriple']()
192
+ }
193
+ },
194
+
195
+ /** Add a collection arc to this frame */
196
+ 'addCollectionArc': function () {
197
+ this['nodeType'] = this['ARC']
198
+ },
199
+
200
+ /** Add a bnode to this frame */
201
+ 'addBNode': function (id) {
202
+ if(id != null) {
203
+ if(this['parser']['bnodes'][id] != null) {
204
+ this['node'] = this['parser']['bnodes'][id]
205
+ } else {
206
+ this['node'] = this['parser']['bnodes'][id] = this['store']['bnode']()
207
+ }
208
+ } else {
209
+ this['node'] = this['store']['bnode']()
210
+ }
211
+
212
+ this['nodeType'] = this['NODE']
213
+ if(this['isTripleToLoad']()) {
214
+ this['loadTriple']()
215
+ }
216
+ },
217
+
218
+ /** Add an arc or property to this frame */
219
+ 'addArc': function (uri) {
220
+ if(uri == RDFParser['ns']['RDF'] + "li") {
221
+ uri = RDFParser['ns']['RDF'] + "_" + this['parent']['listIndex']++
222
+ }
223
+ this['addSymbol'](this['ARC'], uri)
224
+ },
225
+
226
+ /** Add a literal to this frame */
227
+ 'addLiteral': function (value) {
228
+ if(this['parent']['datatype']) {
229
+ this['node'] = this['store']['literal'](
230
+ value, "", this['store']['sym'](
231
+ this['parent']['datatype']))
232
+ } else {
233
+ this['node'] = this['store']['literal'](
234
+ value, this['lang'])
235
+ }
236
+ this['nodeType'] = this['NODE']
237
+ if(this['isTripleToLoad']()) {
238
+ this['loadTriple']()
239
+ }
240
+ }
241
+ }
242
+ }
243
+
244
+ //from the OpenLayers source .. needed to get around IE problems.
245
+ this['getAttributeNodeNS'] = function (node, uri, name) {
246
+ var attributeNode = null;
247
+ if(node.getAttributeNodeNS) {
248
+ attributeNode = node.getAttributeNodeNS(uri, name);
249
+ } else {
250
+ var attributes = node.attributes;
251
+ var potentialNode, fullName;
252
+ for(var i = 0; i < attributes.length; ++i) {
253
+ potentialNode = attributes[i];
254
+ if(potentialNode.namespaceURI == uri) {
255
+ fullName = (potentialNode.prefix) ? (potentialNode.prefix + ":" + name) : name;
256
+ if(fullName == potentialNode.nodeName) {
257
+ attributeNode = potentialNode;
258
+ break;
259
+ }
260
+ }
261
+ }
262
+ }
263
+ return attributeNode;
264
+ }
265
+
266
+ /** Our triple store reference @private */
267
+ this['store'] = store
268
+ /** Our identified blank nodes @private */
269
+ this['bnodes'] = {}
270
+ /** A context for context-aware stores @private */
271
+ this['why'] = null
272
+ /** Reification flag */
273
+ this['reify'] = false
274
+
275
+ /**
276
+ * Build our initial scope frame and parse the DOM into triples
277
+ * @param {DOMTree} document The DOM to parse
278
+ * @param {String} base The base URL to use
279
+ * @param {Object} why The context to which this resource belongs
280
+ */
281
+ this['parse'] = function (document, base, why) {
282
+ // $rdf.log('parse base:'+base);
283
+ var children = document['childNodes']
284
+
285
+ // clean up for the next run
286
+ this['cleanParser']()
287
+
288
+ // figure out the root element
289
+ //var root = document.documentElement; //this is faster, I think, cross-browser issue? well, DOM 2
290
+ if(document['nodeType'] == RDFParser['nodeType']['DOCUMENT']) {
291
+ for(var c = 0; c < children['length']; c++) {
292
+ if(children[c]['nodeType'] == RDFParser['nodeType']['ELEMENT']) {
293
+ var root = children[c]
294
+ break
295
+ }
296
+ }
297
+ } else if(document['nodeType'] == RDFParser['nodeType']['ELEMENT']) {
298
+ var root = document
299
+ } else {
300
+ throw new Error("RDFParser: can't find root in " + base + ". Halting. ")
301
+ return false
302
+ }
303
+
304
+ this['why'] = why
305
+
306
+
307
+ // our topmost frame
308
+ var f = this['frameFactory'](this)
309
+ this['base'] = base
310
+ f['base'] = base
311
+ f['lang'] = ''
312
+
313
+ this['parseDOM'](this['buildFrame'](f, root))
314
+ return true
315
+ }
316
+ this['parseDOM'] = function (frame) {
317
+ // a DOM utility function used in parsing
318
+ var elementURI = function (el) {
319
+ var result = "";
320
+ if(el['namespaceURI'] == null) {
321
+ throw new Error("RDF/XML syntax error: No namespace for "
322
+ + el['localName'] + " in " + this.base)
323
+ }
324
+ if(el['namespaceURI']) {
325
+ result = result + el['namespaceURI'];
326
+ }
327
+ if(el['localName']) {
328
+ result = result + el['localName'];
329
+ } else if(el['nodeName']) {
330
+ if(el['nodeName'].indexOf(":") >= 0)
331
+ result = result + el['nodeName'].split(":")[1];
332
+ else
333
+ result = result + el['nodeName'];
334
+ }
335
+ return result;
336
+ }
337
+ var dig = true // if we'll dig down in the tree on the next iter
338
+ while(frame['parent']) {
339
+ var dom = frame['element']
340
+ var attrs = dom['attributes']
341
+
342
+ if(dom['nodeType'] == RDFParser['nodeType']['TEXT']
343
+ || dom['nodeType'] == RDFParser['nodeType']['CDATA_SECTION']) {
344
+ //we have a literal
345
+ if(frame['parent']['nodeType'] == frame['NODE']) {
346
+ //must have had attributes, store as rdf:value
347
+ frame['addArc'](RDFParser['ns']['RDF'] + 'value');
348
+ frame = this['buildFrame'](frame);
349
+ }
350
+ frame['addLiteral'](dom['nodeValue'])
351
+ } else if(elementURI(dom) != RDFParser['ns']['RDF'] + "RDF") {
352
+ // not root
353
+ if(frame['parent'] && frame['parent']['collection']) {
354
+ // we're a collection element
355
+ frame['addCollectionArc']()
356
+ frame = this['buildFrame'](frame, frame['element'])
357
+ frame['parent']['element'] = null
358
+ }
359
+ if(!frame['parent'] || !frame['parent']['nodeType']
360
+ || frame['parent']['nodeType'] == frame['ARC']) {
361
+ // we need a node
362
+ var about = this['getAttributeNodeNS'](dom, RDFParser['ns']['RDF'], "about")
363
+ var rdfid = this['getAttributeNodeNS'](dom, RDFParser['ns']['RDF'], "ID")
364
+ if(about && rdfid) {
365
+ throw new Error("RDFParser: " + dom['nodeName']
366
+ + " has both rdf:id and rdf:about." + " Halting. Only one of these"
367
+ + " properties may be specified on a" + " node.");
368
+ }
369
+ if(about == null && rdfid) {
370
+ frame['addNode']("#" + rdfid['nodeValue'])
371
+ dom['removeAttributeNode'](rdfid)
372
+ } else if(about == null && rdfid == null) {
373
+ var bnid = this['getAttributeNodeNS'](dom, RDFParser['ns']['RDF'], "nodeID")
374
+ if(bnid) {
375
+ frame['addBNode'](bnid['nodeValue'])
376
+ dom['removeAttributeNode'](bnid)
377
+ } else {
378
+ frame['addBNode']()
379
+ }
380
+ } else {
381
+ frame['addNode'](about['nodeValue'])
382
+ dom['removeAttributeNode'](about)
383
+ }
384
+
385
+ // Typed nodes
386
+ var rdftype = this['getAttributeNodeNS'](dom, RDFParser['ns']['RDF'], "type")
387
+ if(RDFParser['ns']['RDF'] + "Description" != elementURI(dom)) {
388
+ rdftype = {
389
+ 'nodeValue': elementURI(dom)
390
+ }
391
+ }
392
+ if(rdftype != null) {
393
+ this['store']['add'](frame['node'],
394
+ this['store']['sym'](RDFParser['ns']['RDF'] + "type"),
395
+ this['store']['sym'](
396
+ $rdf.Util.uri.join(
397
+ rdftype['nodeValue'],
398
+ frame['base'])),
399
+ this['why'])
400
+ if(rdftype['nodeName']) {
401
+ dom['removeAttributeNode'](rdftype)
402
+ }
403
+ }
404
+
405
+ // Property Attributes
406
+ for(var x = attrs['length'] - 1; x >= 0; x--) {
407
+ this['store']['add'](frame['node'],
408
+ this['store']['sym'](elementURI(attrs[x])),
409
+ this['store']['literal'](
410
+ attrs[x]['nodeValue'],
411
+ frame['lang']),
412
+ this['why'])
413
+ }
414
+ } else {
415
+ // we should add an arc (or implicit bnode+arc)
416
+ frame['addArc'](elementURI(dom))
417
+
418
+ // save the arc's rdf:ID if it has one
419
+ if(this['reify']) {
420
+ var rdfid = this['getAttributeNodeNS'](dom, RDFParser['ns']['RDF'], "ID")
421
+ if(rdfid) {
422
+ frame['rdfid'] = rdfid['nodeValue']
423
+ dom['removeAttributeNode'](rdfid)
424
+ }
425
+ }
426
+
427
+ var parsetype = this['getAttributeNodeNS'](dom, RDFParser['ns']['RDF'], "parseType")
428
+ var datatype = this['getAttributeNodeNS'](dom, RDFParser['ns']['RDF'], "datatype")
429
+ if(datatype) {
430
+ frame['datatype'] = datatype['nodeValue']
431
+ dom['removeAttributeNode'](datatype)
432
+ }
433
+
434
+ if(parsetype) {
435
+ var nv = parsetype['nodeValue']
436
+ if(nv == "Literal") {
437
+ frame['datatype'] = RDFParser['ns']['RDF'] + "XMLLiteral"
438
+ // (this.buildFrame(frame)).addLiteral(dom)
439
+ // should work but doesn't
440
+ frame = this['buildFrame'](frame)
441
+ frame['addLiteral'](dom)
442
+ dig = false
443
+ } else if(nv == "Resource") {
444
+ frame = this['buildFrame'](frame, frame['element'])
445
+ frame['parent']['element'] = null
446
+ frame['addBNode']()
447
+ } else if(nv == "Collection") {
448
+ frame = this['buildFrame'](frame, frame['element'])
449
+ frame['parent']['element'] = null
450
+ frame['addCollection']()
451
+ }
452
+ dom['removeAttributeNode'](parsetype)
453
+ }
454
+
455
+ if(attrs['length'] != 0) {
456
+ var resource = this['getAttributeNodeNS'](dom, RDFParser['ns']['RDF'], "resource")
457
+ var bnid = this['getAttributeNodeNS'](dom, RDFParser['ns']['RDF'], "nodeID")
458
+
459
+ frame = this['buildFrame'](frame)
460
+ if(resource) {
461
+ frame['addNode'](resource['nodeValue'])
462
+ dom['removeAttributeNode'](resource)
463
+ } else {
464
+ if(bnid) {
465
+ frame['addBNode'](bnid['nodeValue'])
466
+ dom['removeAttributeNode'](bnid)
467
+ } else {
468
+ frame['addBNode']()
469
+ }
470
+ }
471
+
472
+ for(var x = attrs['length'] - 1; x >= 0; x--) {
473
+ var f = this['buildFrame'](frame)
474
+ f['addArc'](elementURI(attrs[x]))
475
+ if(elementURI(attrs[x]) == RDFParser['ns']['RDF'] + "type") {
476
+ (this['buildFrame'](f))['addNode'](
477
+ attrs[x]['nodeValue'])
478
+ } else {
479
+ (this['buildFrame'](f))['addLiteral'](
480
+ attrs[x]['nodeValue'])
481
+ }
482
+ }
483
+ } else if(dom['childNodes']['length'] == 0) {
484
+ (this['buildFrame'](frame))['addLiteral']("")
485
+ }
486
+ }
487
+ } // rdf:RDF
488
+ // dig dug
489
+ dom = frame['element']
490
+ while(frame['parent']) {
491
+ var pframe = frame
492
+ while(dom == null) {
493
+ frame = frame['parent']
494
+ dom = frame['element']
495
+ }
496
+ var candidate = dom['childNodes'][frame['lastChild']]
497
+ if(candidate == null || !dig) {
498
+ frame['terminateFrame']()
499
+ if(!(frame = frame['parent'])) {
500
+ break
501
+ } // done
502
+ dom = frame['element']
503
+ dig = true
504
+ } else if((candidate['nodeType'] != RDFParser['nodeType']['ELEMENT']
505
+ && candidate['nodeType'] != RDFParser['nodeType']['TEXT']
506
+ && candidate['nodeType'] != RDFParser['nodeType']['CDATA_SECTION'])
507
+ || ((candidate['nodeType'] == RDFParser['nodeType']['TEXT']
508
+ || candidate['nodeType'] == RDFParser['nodeType']['CDATA_SECTION'])
509
+ && dom['childNodes']['length'] != 1)) {
510
+ frame['lastChild']++
511
+ } else {
512
+ // not a leaf
513
+ frame['lastChild']++;
514
+ frame = this['buildFrame'](pframe, dom['childNodes'][frame['lastChild'] - 1])
515
+ break
516
+ }
517
+ }
518
+ } // while
519
+ }
520
+
521
+ /**
522
+ * Cleans out state from a previous parse run
523
+ * @private
524
+ */
525
+ this['cleanParser'] = function () {
526
+ this['bnodes'] = {}
527
+ this['why'] = null
528
+ }
529
+
530
+ /**
531
+ * Builds scope frame
532
+ * @private
533
+ */
534
+ this['buildFrame'] = function (parent, element) {
535
+ var frame = this['frameFactory'](this, parent, element)
536
+ if(parent) {
537
+ frame['base'] = parent['base']
538
+ frame['lang'] = parent['lang']
539
+ }
540
+ if(element == null
541
+ || element['nodeType'] == RDFParser['nodeType']['TEXT']
542
+ || element['nodeType'] == RDFParser['nodeType']['CDATA_SECTION']) {
543
+ return frame
544
+ }
545
+
546
+ var attrs = element['attributes']
547
+
548
+ var base = element['getAttributeNode']("xml:base")
549
+ if(base != null) {
550
+ frame['base'] = base['nodeValue']
551
+ element['removeAttribute']("xml:base")
552
+ }
553
+ var lang = element['getAttributeNode']("xml:lang")
554
+ if(lang != null) {
555
+ frame['lang'] = lang['nodeValue']
556
+ element['removeAttribute']("xml:lang")
557
+ }
558
+
559
+ // remove all extraneous xml and xmlns attributes
560
+ for(var x = attrs['length'] - 1; x >= 0; x--) {
561
+ if(attrs[x]['nodeName']['substr'](0, 3) == "xml") {
562
+ if(attrs[x].name.slice(0, 6) == 'xmlns:') {
563
+ var uri = attrs[x].nodeValue;
564
+ // $rdf.log('base for namespac attr:'+this.base);
565
+ if(this.base) uri = $rdf.Util.uri.join(uri, this.base);
566
+ this.store.setPrefixForURI(attrs[x].name.slice(6), uri);
567
+ }
568
+ // $rdf.log('rdfparser: xml atribute: '+attrs[x].name) //@@
569
+ element['removeAttributeNode'](attrs[x])
570
+ }
571
+ }
572
+ return frame
573
+ }
574
+ }
575
+
576
+ if (typeof process === 'object' && process + '' === '[object process]'){
577
+ module.exports = $rdf.RDFParser;
578
+ }