aboutsummaryrefslogtreecommitdiff
path: root/test/uk/ac/ox/cs/pagoda/tester/PagodaTester.java
diff options
context:
space:
mode:
Diffstat (limited to 'test/uk/ac/ox/cs/pagoda/tester/PagodaTester.java')
-rw-r--r--test/uk/ac/ox/cs/pagoda/tester/PagodaTester.java336
1 files changed, 336 insertions, 0 deletions
diff --git a/test/uk/ac/ox/cs/pagoda/tester/PagodaTester.java b/test/uk/ac/ox/cs/pagoda/tester/PagodaTester.java
new file mode 100644
index 0000000..e040c18
--- /dev/null
+++ b/test/uk/ac/ox/cs/pagoda/tester/PagodaTester.java
@@ -0,0 +1,336 @@
1package uk.ac.ox.cs.pagoda.tester;
2
3import java.io.File;
4import java.io.FileNotFoundException;
5import java.io.IOException;
6import java.util.Scanner;
7
8import org.semanticweb.owlapi.model.OWLOntology;
9
10import uk.ac.ox.cs.pagoda.owl.OWLHelper;
11import uk.ac.ox.cs.pagoda.query.AnswerTuple;
12import uk.ac.ox.cs.pagoda.query.AnswerTuples;
13import uk.ac.ox.cs.pagoda.reasoner.*;
14import uk.ac.ox.cs.pagoda.reasoner.QueryReasoner.Type;
15import uk.ac.ox.cs.pagoda.util.Timer;
16import uk.ac.ox.cs.pagoda.util.Utility;
17
18public class PagodaTester {
19
20// public static final String onto_dir = "/media/RDFData/yzhou/";
21// public static final String onto_dir = "/users/yzhou/ontologies/";
22// public static final String onto_dir = "/home/scratch/yzhou/ontologies/";
23 public static final String onto_dir = "/home/yzhou/krr-nas-share/Yujiao/ontologies/";
24
25 public static final String fly = onto_dir + "fly/fly_anatomy_XP_with_GJ_FC_individuals.owl";
26 public static final String fly_query = onto_dir + "fly/queries/fly.sparql";
27
28 public static final String test_tbox = onto_dir + "smallExampleFromAna/dummy.owl";
29 public static final String test_abox = onto_dir + "smallExampleFromAna/initialABox.ttl";
30 public static final String test_query = onto_dir + "smallExampleFromAna/queries.dlog";
31
32 public static final int lubm_number = 1;
33 public static final String lubm_tbox = onto_dir + "lubm/univ-bench.owl";
34 public static final String lubm_abox = onto_dir + "lubm/data/lubm" + lubm_number + ".ttl";
35 public static final String lubm_abox_copy = onto_dir + "lubm/data/lubm" + lubm_number + " (copy).ttl";
36 public static final String lubm_query = onto_dir + "lubm/queries/test.sparql";
37 public static final String lubm_query6 = onto_dir + "lubm/queries/test_q6.sparql";
38 public static final String lubm_query20 = onto_dir + "lubm/queries/test_q16.sparql";
39
40 public static final int uobm_number = 1;
41 public static final String uobm_tbox = onto_dir + "uobm/univ-bench-dl.owl";
42 public static final String uobm_abox = onto_dir + "uobm/data/uobm" + uobm_number + ".ttl";
43 public static final String uobm_query = onto_dir + "uobm/queries/standard.sparql";
44 public static final String uobm_query_temp = onto_dir + "uobm/queries/temp.sparql";
45 public static final String uobm_query2 = onto_dir + "uobm/queries/standard_q2.sparql";
46 public static final String uobm_query9 = onto_dir + "uobm/queries/standard_q9.sparql";
47 public static final String uobm_query11 = onto_dir + "uobm/queries/standard_q11.sparql";
48 public static final String uobm_query12 = onto_dir + "uobm/queries/standard_q12.sparql";
49 public static final String uobm_query14 = onto_dir + "uobm/queries/standard_q14.sparql";
50 public static final String uobm_query15 = onto_dir + "uobm/queries/standard_q15.sparql";
51 public static final String uobm_query_multi = onto_dir + "uobm/queries/standard_multi.sparql";
52 public static final String uobm_generated_query1 = onto_dir + "uobm/queries/generated_q1.sparql";
53 public static final String uobm_query_group3 = onto_dir + "uobm/queries/standard_group3.sparql";
54
55 public static final String npd_tbox = onto_dir + "npd/npd-all-minus-datatype.owl";
56 // "npd/npd-all.owl";
57 // "npd-all-minus-datatype.owl";
58 public static final String npd_abox = onto_dir + "npd/data/npd-data-dump-minus-datatype-new.ttl";
59 // "npd/data/npd-data-dump-processed.ttl";
60 // "npd-data-dump-minus-datatype-old.ttl";
61 public static final String npd_query = onto_dir + "npd/queries/atomic.sparql";
62
63 public static final String npd_bench_tbox = onto_dir + "npd-benchmark/npd-v2-ql_a.owl"; // npd-all-minus-datatype.owl";
64 public static final String npd_bench_abox = onto_dir + "npd-benchmark/npd-v2-ql_a.ttl"; // npd-data-dump-minus-datatype-old.ttl";
65 public static final String npd_bench_query = onto_dir + "npd-benchmark/queries/all.sparql";
66
67 public static final String dbpedia_tbox = onto_dir + "dbpedia/integratedOntology-all-in-one-minus-datatype.owl";
68 public static final String dbpedia_abox = onto_dir + "dbpedia/data/dbpedia-minus-datatype-new.ttl";
69 public static final String dbpedia_query = onto_dir + "dbpedia/queries/atomic_ground.sparql";
70 public static final String dbpedia_query274 = onto_dir + "dbpedia/atomic_q274.sparql";
71
72 public static final String dbpedia_latest_tbox = onto_dir + "dbpedia/dbpedia_2014.owl";
73 public static final String travel_tbox = onto_dir + "dbpedia/travel.owl";
74 public static final String dbpedia_tbox_simple = onto_dir + "dbpedia/dbpedia_simple.owl";
75
76 public static final String bioModels_tbox = onto_dir + "biomodels/biomodels-21.owl";
77 public static final String bioModels_abox = onto_dir + "biomodels/data_processed_1.ttl";
78 public static final String bioModels_queries = onto_dir + "biomodels/queries/queries.sparql";
79
80 public static final String chembl_tbox = onto_dir + "bio2rdf/chembl/cco-processed-noDPR-noDPD.ttl";
81 public static final String chembl_abox = onto_dir + "bio2rdf/chembl/graph sampling old/sample_100.nt";
82 public static final String chembl_queries = onto_dir + "bio2rdf/chembl/queries/problematic.sparql"; //"bio2rdf/chembl/queries/atomic_one_filtered.sparql"; //
83
84 public static final String reactome_tbox = onto_dir + "bio2rdf/reactome/biopax-level3-processed.owl";
85 public static final String reactome_abox = onto_dir + "bio2rdf/reactome/graph sampling old/sample.ttl"; //data/data.ttl"; //graph sampling old/reactome_sample_10.ttl"; //
86 public static final String reactome_queries = onto_dir +"bio2rdf/reactome/queries/atomic.sparql";
87
88 public static final String uniprot_tbox = onto_dir + "bio2rdf/uniprot/core-processed.owl";
89 public static final String uniprot_abox = onto_dir + "bio2rdf/uniprot/graph sampling/sample_1.nt";
90 public static final String uniprot_queries = onto_dir + "bio2rdf/uniprot/queries/atomic_one.sparql";
91
92 public static final String atlas_tbox = onto_dir + "bio2rdf/atlas/gxaterms.owl";
93 public static final String atlas_abox = onto_dir + "bio2rdf/atlas/graph sampling/sample_1.nt";
94 public static final String atlas_queries = onto_dir + "bio2rdf/atlas/queries/atomic_one.sparql";
95
96 public static boolean ShellMode = false;
97
98 public static void main(String... args) {
99 if (args.length == 0) {
100// args = new String[] {test_tbox, test_abox, test_query};
101// args = new String[] {lubm_tbox, lubm_abox, lubm_query.replace(".sparql", "_all_pagoda.sparql")};
102// args = new String[] {uobm_tbox, uobm_abox, uobm_query.replace(".sparql", "_all_pagoda.sparql")};
103// args = new String[] {fly, "null", fly_query.replace(".sparql", "_pellet.sparql") };
104// args = new String[] {dbpedia_tbox, dbpedia_abox, dbpedia_query};
105// args = new String[] {travel_tbox, null, dbpedia_query274};
106// args = new String[] {fly, null, fly_query};
107// args = new String[] {npd_tbox, npd_abox, npd_query};
108// args = new String[] {npd_bench_tbox, npd_bench_abox, npd_bench_query};
109// args = new String[] {"../SemFacet/WebContent/WEB-INF/data/dbpedia.owl", "../SemFacet/WebContent/WEB-INF/data/dbpediaA.nt", null};
110// args = new String[] {"../SemFacet/WebContent/WEB-INF/data/isg.owl", "../SemFacet/WebContent/WEB-INF/data/isg.nt", null};
111 args = new String[] {"..\\core\\WebContent\\WEB-INF\\data\\fly.owl", "..\\core\\WebContent\\WEB-INF\\data\\fly-data.nt", null};
112// args = new String[] {bioModels_tbox, bioModels_abox, bioModels_queries};
113// args = new String[] {chembl_tbox, chembl_abox, chembl_queries};
114// args = new String[] {reactome_tbox, reactome_abox, reactome_queries};
115// args = new String[] {reactome_tbox, "/users/yzhou/temp/reactome_debug.ttl", onto_dir +"bio2rdf/reactome/queries/atomic_one_q65.sparql"};
116// args = new String[] {uniprot_tbox.replace(".owl", "-noDis.owl"), "/users/yzhou/temp/uniprot_debug/sample_1_string.nt", uniprot_queries};
117// args = new String[] {uniprot_tbox.replace(".owl", "-noDis.owl"), uniprot_abox, uniprot_queries};
118// args = new String[] {atlas_tbox, atlas_abox, atlas_queries};
119// args = new String[] {onto_dir + "test/unsatisfiable.owl", null, onto_dir + "test/unsatisfiable_queries.sparql"};
120// args = new String[] {onto_dir + "test/jair-example.owl", null, onto_dir + "test/jair-example_query.sparql"};
121// args[2] = args[2].replace(".sparql", "_all_pagoda.sparql");
122// args[2] = args[2].replace(".sparql", "_pellet.sparql");
123 }
124
125 int ontoIndex = 0, dataIndex = 1, queryIndex = 2;
126
127 if (args.length > dataIndex && args[dataIndex] != null && args[dataIndex].endsWith(".sparql")) {
128 String[] inputArgs = args;
129 args = new String[inputArgs.length + 1];
130 for (int i = 0; i < dataIndex; ++i)
131 args[i] = inputArgs[i];
132 args[dataIndex] = null;
133 args[queryIndex] = inputArgs[dataIndex];
134 for (int i = dataIndex + 1; i < inputArgs.length; ++i)
135 args[i + 1] = inputArgs[i];
136 }
137
138 StringBuilder info = new StringBuilder();
139 info.append("System started with \n");
140 for (int i = 0; i < args.length; ++i)
141 info.append("Arg " + (i + 1) + ": " + args[i] + "\n");
142 Utility.logInfo(info);
143
144// Utility.redirectCurrentOut("temp.out");
145
146 OWLOntology ontology = OWLHelper.loadOntology(args[ontoIndex]);
147
148 QueryReasoner pagoda = QueryReasoner.getInstance(Type.Full, ontology, true, true);
149// QueryReasoner pagoda = QueryReasoner.getInstance(Type.ELHOU, ontology, true, true);
150
151// QueryReasoner pagoda = QueryReasoner.getInstanceForSemFacet(ontology);
152// QueryReasoner pagoda = QueryReasoner.getHermiTReasoner(false);
153
154// PagodaTester tester = new PagodaTester(pagoda);
155 String ansFile = args.length > 3 ? args[3] : null;
156 try {
157 Timer t = new Timer();
158 pagoda.loadOntology(ontology);
159 pagoda.importData(args[dataIndex]);
160 if (!pagoda.preprocess())
161 return;
162 Utility.logInfo("Preprocessing Done in " + t.duration() + " seconds.");
163// tester.printPredicatesWithGap();
164// tester.testSemFacetQueries();
165// tester.testSomeFlyQueries();
166// tester.testISGQueries();
167// tester.testReactomeQueries();
168 if (args[queryIndex] != null)
169 for (String queryFile: args[queryIndex].split(";"))
170 pagoda.evaluate(pagoda.getQueryManager().collectQueryRecords(queryFile), ansFile);
171
172 if (ShellMode)
173 try {
174 evaluateConsoleQuery(pagoda);
175 } catch (IOException e) {
176 e.printStackTrace();
177 }
178 } finally {
179 pagoda.dispose();
180 }
181
182 Utility.closeCurrentOut();
183
184 if (ShellMode) System.exit(0);
185 }
186
187// private void printPredicatesWithGap() {
188// for (String p: ((MyQueryReasoner) pagoda).getPredicatesWithGap()) {
189// System.out.println(p);
190// }
191// }
192
193 private static void evaluateConsoleQuery(QueryReasoner pagoda) throws IOException {
194 int ending = (int) '$', symbol;
195 while (true) {
196 Utility.logInfo("Input your query ending with $");
197 StringBuilder queryBuilder = new StringBuilder();
198 while ((symbol = System.in.read()) != ending) {
199 queryBuilder.append((char) symbol);
200 }
201 System.in.read();
202 if (queryBuilder.length() == 0) return ;
203 pagoda.evaluate_shell(queryBuilder.toString());
204 }
205 }
206
207 void testReactomeQueries() {
208 evaluate("select ?x where { ?x <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.biopax.org/release/biopax-level3.owl#DnaReference> . }");
209 evaluate("select ?y ?z where { <http://identifiers.org/ensembl/ENSG00000157557> ?y ?z . }");
210 evaluate("select ?y where { <http://identifiers.org/ensembl/ENSG00000157557> <http://www.biopax.org/release/biopax-level3.owl#name> ?y . }", true);
211
212 }
213
214 void testSemFacetQueries() {
215// try {
216// BufferedReader reader = new BufferedReader(new InputStreamReader(new FileInputStream("query.line")));
217// for (String line; (line = reader.readLine()) != null && !line.isEmpty(); )
218// evaluate(line, true);
219// reader.close();
220// } catch (FileNotFoundException e) {
221// e.printStackTrace();
222// } catch (IOException e) {
223// e.printStackTrace();
224// }
225 evaluate("select ?x ?z where { ?x <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> ?z }", true);
226 evaluate("select distinct ?y where { ?x ?y ?z }", true);
227 evaluate("select distinct ?z where { ?x <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> ?z }", true);
228 evaluate("select ?y ?z where { <http://www.reactome.org/biopax/46/49633#Protein3885> ?y ?z .}", true);
229 }
230
231 void testISGQueries() {
232 evaluate("select ?z where {<http://cs.ox.ac.uk/Evgeny_Kharlamov> <http://cs.ox.ac.uk/lat> ?z .}", false);
233 evaluate("select ?x where {?x <http://cs.ox.ac.uk/type> <http://cs.ox.ac.uk/person> .}", false);
234 }
235
236 void testSomeTravelQueries() {
237 evaluate("select ?y ?z where {<http://www.owl-ontologies.com/travel.owl#BlueMountains> ?y ?z. }", true);
238 evaluate("select ?x where {?x <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.owl-ontologies.com/travel.owl#RetireeDestination>. }");
239 evaluate("select ?x where {?x <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.owl-ontologies.com/travel.owl#BackpackersDestination>. }");
240 }
241
242 void testSomeFlyQueries() {
243 evaluate("select ?x where { ?x <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://purl.obolibrary.org/obo/FBbt_00005106> . }", false);
244
245 evaluate("select DISTINCT ?z where { ?x <http://purl.obolibrary.org/obo/FBbt#develops_from> ?any . ?any <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> ?z . ?x <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://purl.obolibrary.org/obo/FBbt_00067123> . } ", true);
246
247 evaluate("Select ?x where { ?x <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> "
248 + "<http://purl.obolibrary.org/obo/FBbt_00067123>. ?x "
249 + "<http://purl.obolibrary.org/obo/RO_0002131> ?any . ?any "
250 + "<http://www.w3.org/1999/02/22-rdf-syntax-ns#type> "
251 + "<http://purl.obolibrary.org/obo/FBbt_00005140> . }", true);
252
253 evaluate("Select ?x where {?x <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> "
254 + "<http://purl.obolibrary.org/obo/FBbt_00067363> . ?x "
255 + "<http://purl.obolibrary.org/obo/RO_0002131> ?any . ?any "
256 + "<http://www.w3.org/1999/02/22-rdf-syntax-ns#type> "
257 + "<http://purl.obolibrary.org/obo/FBbt_00005140> . }", true);
258
259// evaluate("Select ?x where { "
260// + "?x <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://purl.obolibrary.org/obo/FBbt_00003660>. "
261// + "?x <http://purl.obolibrary.org/obo/FBbt#develops_from> ?any . "
262// + "?any <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://purl.obolibrary.org/obo/FBbt_00001446> . }", true);
263
264 evaluate("select DISTINCT ?z where { ?x <http://purl.obolibrary.org/obo/RO_0002110> ?any . "
265 + "?any <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> ?z . "
266 + "?x <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://purl.obolibrary.org/obo/FBbt_00007016> . } ", true);
267
268 evaluate("Select * where {"
269 + "<http://www.virtualflybrain.org/ontologies/individuals/VFB_00100607> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://purl.obolibrary.org/obo/FBbt_00007364>. "
270 + "<http://www.virtualflybrain.org/ontologies/individuals/VFB_00100607> <http://www.w3.org/2002/07/owl#sameAs> ?z }", true);
271
272 evaluate("SELECT DISTINCT ?x ?z WHERE {?x <http://www.w3.org/2002/07/owl#sameAs> ?z}", true);
273 evaluate("SELECT DISTINCT ?x ?z WHERE {?x <http://purl.obolibrary.org/obo/BFO_0000051> ?z}", true);
274
275 evaluate("select DISTINCT ?y where { ?x ?y ?z . "
276 + "?x <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://purl.obolibrary.org/obo/FBbt_00007364> }", true);
277
278 evaluateQueriesFromFile("/users/yzhou/Downloads/logs(1).log");
279 evaluateQueriesFromFile("/users/yzhou/Downloads/logs.log");
280
281 evaluate("SELECT DISTINCT ?x ?z WHERE {?x <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> ?z}", true);
282 evaluate("SELECT DISTINCT ?x ?z WHERE {?x <http://xmlns.com/foaf/0.1/depicts> ?z}", true);
283
284 evaluate("select ?x ?z where { ?x <http://www.w3.org/2002/07/owl#sameAs> ?z } ", true);
285 evaluate("select ?x ?z where { ?x <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> ?z } ", true);
286 }
287
288 public void evaluateQueriesFromFile(String fileName) {
289 Scanner scanner = null;
290 try {
291 scanner = new Scanner(new File(fileName));
292 String line;
293 while (scanner.hasNextLine()) {
294 line = scanner.nextLine();
295 if (line.startsWith("select"))
296 evaluate(line, true);
297 }
298 } catch (FileNotFoundException e) {
299 e.printStackTrace();
300 } finally {
301 if (scanner != null)
302 scanner.close();
303 }
304 }
305
306 QueryReasoner pagoda;
307
308 public PagodaTester(QueryReasoner reasoner) {
309 pagoda = reasoner;
310 }
311
312 Timer timer = new Timer();
313
314 private void evaluate(String query) {
315 evaluate(query, false);
316 }
317
318 private void evaluate(String query, boolean tag) {
319 timer.reset();
320 AnswerTuples tuples = pagoda.evaluate(query, tag);
321 int arity = tuples.getArity();
322 int count = 0;
323 for (AnswerTuple tuple; tuples.isValid(); tuples.moveNext()) {
324 tuple = tuples.getTuple();
325 for (int i = 0; i < arity; ++i)
326 tuple.getGroundTerm(i).toString();
327// System.out.print(tuple.getGroundTerm(i).toString() + "\t");
328// System.out.println();
329 ++count;
330 }
331 tuples.dispose();
332 Utility.logInfo("The number of answers for this SemFacet query: " + count);
333 Utility.logInfo("Total time for this SemFacet query: " + timer.duration());
334 }
335
336}
generated by cgit v1.2.3 (git 2.25.1) at 2025-11-05 18:22:34 +0000