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-rw-r--r--test/uk/ac/ox/cs/pagoda/tester/PagodaTester.java276
1 files changed, 4 insertions, 272 deletions
diff --git a/test/uk/ac/ox/cs/pagoda/tester/PagodaTester.java b/test/uk/ac/ox/cs/pagoda/tester/PagodaTester.java
index b97d85e..7d9b49c 100644
--- a/test/uk/ac/ox/cs/pagoda/tester/PagodaTester.java
+++ b/test/uk/ac/ox/cs/pagoda/tester/PagodaTester.java
@@ -1,126 +1,18 @@
1package uk.ac.ox.cs.pagoda.tester; 1package uk.ac.ox.cs.pagoda.tester;
2 2
3import uk.ac.ox.cs.pagoda.query.AnswerTuple;
4import uk.ac.ox.cs.pagoda.query.AnswerTuples;
5import uk.ac.ox.cs.pagoda.reasoner.QueryReasoner; 3import uk.ac.ox.cs.pagoda.reasoner.QueryReasoner;
6import uk.ac.ox.cs.pagoda.util.Properties; 4import uk.ac.ox.cs.pagoda.util.Properties;
7import uk.ac.ox.cs.pagoda.util.Timer; 5import uk.ac.ox.cs.pagoda.util.Timer;
8import uk.ac.ox.cs.pagoda.util.Utility; 6import uk.ac.ox.cs.pagoda.util.Utility;
9 7
10import java.io.File; 8// TODO clean it, or code another one
11import java.io.FileNotFoundException;
12import java.io.IOException;
13import java.util.Scanner;
14
15public class PagodaTester { 9public class PagodaTester {
16 10
17// public static final String onto_dir = "/media/RDFData/yzhou/";
18// public static final String onto_dir = "/users/yzhou/ontologies/";
19// public static final String onto_dir = "/home/scratch/yzhou/ontologies/";
20 public static final String onto_dir = "/home/alessandro/Big_files/Ontologies/";
21
22 public static final String fly = onto_dir + "fly/fly_anatomy_XP_with_GJ_FC_individuals.owl";
23 public static final String fly_query = onto_dir + "fly/queries/fly.sparql";
24
25 public static final String test_tbox = onto_dir + "smallExampleFromAna/dummy.owl";
26 public static final String test_abox = onto_dir + "smallExampleFromAna/initialABox.ttl";
27 public static final String test_query = onto_dir + "smallExampleFromAna/queries.dlog";
28
29 public static final int lubm_number = 1;
30 public static final String lubm_tbox = onto_dir + "lubm/univ-bench.owl";
31 public static final String lubm_abox = onto_dir + "lubm/data/lubm" + lubm_number + ".ttl";
32 public static final String lubm_abox_copy = onto_dir + "lubm/data/lubm" + lubm_number + " (copy).ttl";
33 public static final String lubm_query = onto_dir + "lubm/queries/test.sparql";
34 public static final String lubm_query6 = onto_dir + "lubm/queries/test_q6.sparql";
35 public static final String lubm_query20 = onto_dir + "lubm/queries/test_q16.sparql";
36
37 public static final int uobm_number = 1;
38 public static final String uobm_tbox = onto_dir + "uobm/univ-bench-dl.owl";
39 public static final String uobm_abox = onto_dir + "uobm/data/uobm" + uobm_number + ".ttl";
40 public static final String uobm_query = onto_dir + "uobm/queries/test.sparql";
41 public static final String uobm_query_temp = onto_dir + "uobm/queries/temp.sparql";
42 public static final String uobm_query2 = onto_dir + "uobm/queries/standard_q2.sparql";
43 public static final String uobm_query9 = onto_dir + "uobm/queries/standard_q9.sparql";
44 public static final String uobm_query11 = onto_dir + "uobm/queries/standard_q11.sparql";
45 public static final String uobm_query12 = onto_dir + "uobm/queries/standard_q12.sparql";
46 public static final String uobm_query14 = onto_dir + "uobm/queries/standard_q14.sparql";
47 public static final String uobm_query15 = onto_dir + "uobm/queries/standard_q15.sparql";
48 public static final String uobm_query_multi = onto_dir + "uobm/queries/standard_multi.sparql";
49 public static final String uobm_generated_query1 = onto_dir + "uobm/queries/generated_q1.sparql";
50 public static final String uobm_query_group3 = onto_dir + "uobm/queries/standard_group3.sparql";
51
52 public static final String npd_tbox = onto_dir + "npd/npd-all-minus-datatype.owl";
53 // "npd/npd-all.owl";
54 // "npd-all-minus-datatype.owl";
55 public static final String npd_abox = onto_dir + "npd/data/npd-data-dump-minus-datatype-new.ttl";
56 // "npd/data/npd-data-dump-processed.ttl";
57 // "npd-data-dump-minus-datatype-old.ttl";
58 public static final String npd_query = onto_dir + "npd/queries/atomic.sparql";
59
60 public static final String npd_bench_tbox = onto_dir + "npd-benchmark/npd-v2-ql_a.owl"; // npd-all-minus-datatype.owl";
61 public static final String npd_bench_abox = onto_dir + "npd-benchmark/npd-v2-ql_a.ttl"; // npd-data-dump-minus-datatype-old.ttl";
62 public static final String npd_bench_query = onto_dir + "npd-benchmark/queries/all.sparql";
63
64 public static final String dbpedia_tbox = onto_dir + "dbpedia/integratedOntology-all-in-one-minus-datatype.owl";
65 public static final String dbpedia_abox = onto_dir + "dbpedia/data/dbpedia-minus-datatype-new.ttl";
66 public static final String dbpedia_query = onto_dir + "dbpedia/queries/atomic_ground.sparql";
67 public static final String dbpedia_query274 = onto_dir + "dbpedia/atomic_q274.sparql";
68
69 public static final String dbpedia_latest_tbox = onto_dir + "dbpedia/dbpedia_2014.owl";
70 public static final String travel_tbox = onto_dir + "dbpedia/travel.owl";
71 public static final String dbpedia_tbox_simple = onto_dir + "dbpedia/dbpedia_simple.owl";
72
73 public static final String bioModels_tbox = onto_dir + "biomodels/biomodels-21.owl";
74 public static final String bioModels_abox = onto_dir + "biomodels/data_processed_1.ttl";
75 public static final String bioModels_queries = onto_dir + "biomodels/queries/queries.sparql";
76
77 public static final String chembl_tbox = onto_dir + "bio2rdf/chembl/cco-processed-noDPR-noDPD.ttl";
78 public static final String chembl_abox = onto_dir + "bio2rdf/chembl/graph sampling old/sample_100.nt";
79 public static final String chembl_queries = onto_dir + "bio2rdf/chembl/queries/problematic.sparql"; //"bio2rdf/chembl/queries/atomic_one_filtered.sparql"; //
80
81 public static final String reactome_tbox = onto_dir + "bio2rdf/reactome/biopax-level3-processed.owl";
82 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"; //
83 public static final String reactome_queries = onto_dir +"bio2rdf/reactome/queries/atomic.sparql";
84
85 public static final String uniprot_tbox = onto_dir + "bio2rdf/uniprot/core-processed.owl";
86 public static final String uniprot_abox = onto_dir + "bio2rdf/uniprot/graph sampling/sample_1.nt";
87 public static final String uniprot_queries = onto_dir + "bio2rdf/uniprot/queries/atomic_one.sparql";
88
89 public static final String atlas_tbox = onto_dir + "bio2rdf/atlas/gxaterms.owl";
90 public static final String atlas_abox = onto_dir + "bio2rdf/atlas/graph sampling/sample_1.nt";
91 public static final String atlas_queries = onto_dir + "bio2rdf/atlas/queries/atomic_one.sparql";
92
93 public static void main(String... args) { 11 public static void main(String... args) {
94 if (args.length == 0) { 12// Properties properties = new Properties(PagodaTester.class.
95// args = new String[] {test_tbox, test_abox, test_query}; 13// getClassLoader().getResource("uobm.properties").getPath());
96// args = new String[] {lubm_tbox, lubm_abox, lubm_query}; 14 Properties properties = new Properties();
97// args = new String[] {uobm_tbox, uobm_abox, uobm_query};
98// args = new String[] {fly, "null", fly_query};
99// args = new String[] {dbpedia_tbox, dbpedia_abox, dbpedia_query};
100// args = new String[] {travel_tbox, null, dbpedia_query274};
101 args = new String[] {fly, fly_query};
102// args = new String[] {npd_tbox, npd_abox, npd_query};
103// args = new String[] {npd_bench_tbox, npd_bench_abox, npd_bench_query};
104// args = new String[] {"../SemFacet/WebContent/WEB-INF/data/dbpedia.owl", "../SemFacet/WebContent/WEB-INF/data/dbpediaA.nt", null};
105// args = new String[] {"../core/WebContent/WEB-INF/data/fly.owl", "../core/WebContent/WEB-INF/data/fly-data.nt", null};
106// args = new String[] {"data/lubm/univ-bench.owl", "data/lubm/lubm1.ttl", "data/lubm/lubm.sparql", "lubm.ans"};
107// args = new String[] {"data/uobm/univ-bench-dl.owl", "data/uobm/uobm1.ttl", "data/uobm/uobm.sparql", "uobm.ans"};
108// args = new String[] {"data/fly/fly_anatomy_XP_with_GJ_FC_individuals.owl", "data/fly/fly.sparql", "fly.ans"};
109// args = new String[] {bioModels_tbox, bioModels_abox, bioModels_queries};
110// args = new String[] {chembl_tbox, chembl_abox, chembl_queries};
111// args = new String[] {reactome_tbox, reactome_abox, reactome_queries};
112// args = new String[] {reactome_tbox, "/users/yzhou/temp/reactome_debug.ttl", onto_dir +"bio2rdf/reactome/queries/atomic_one_q65.sparql"};
113// args = new String[] {uniprot_tbox.replace(".owl", "-noDis.owl"), "/users/yzhou/temp/uniprot_debug/sample_1_string.nt", uniprot_queries};
114// args = new String[] {uniprot_tbox.replace(".owl", "-noDis.owl"), uniprot_abox, uniprot_queries};
115// args = new String[] {atlas_tbox, atlas_abox, atlas_queries};
116// args = new String[] {onto_dir + "test/unsatisfiable.owl", null, onto_dir + "test/unsatisfiable_queries.sparql"};
117// args = new String[] {onto_dir + "test/jair-example.owl", null, onto_dir + "test/jair-example_query.sparql"};
118// args[2] = args[2].replace(".sparql", "_all_pagoda.sparql");
119// args[2] = args[2].replace(".sparql", "_pellet.sparql");
120 }
121 15
122 Properties properties = new Properties("config/uobm.properties");
123
124 int index = 0; 16 int index = 0;
125 if (args.length > index) properties.setOntologyPath(args[index++]); 17 if (args.length > index) properties.setOntologyPath(args[index++]);
126 if (args.length > index && (args[index].endsWith(".ttl") || args[index].endsWith(".nt"))) properties.setDataPath(args[index++]); 18 if (args.length > index && (args[index].endsWith(".ttl") || args[index].endsWith(".nt"))) properties.setDataPath(args[index++]);
@@ -146,169 +38,9 @@ public class PagodaTester {
146 if (properties.getQueryPath() != null) 38 if (properties.getQueryPath() != null)
147 for (String queryFile: properties.getQueryPath().split(";")) 39 for (String queryFile: properties.getQueryPath().split(";"))
148 pagoda.evaluate(pagoda.getQueryManager().collectQueryRecords(queryFile)); 40 pagoda.evaluate(pagoda.getQueryManager().collectQueryRecords(queryFile));
149
150 if (properties.getShellMode())
151 try {
152 evaluateConsoleQuery(pagoda);
153 } catch (IOException e) {
154 e.printStackTrace();
155 }
156 } finally { 41 } finally {
157 if (pagoda != null) pagoda.dispose(); 42 if (pagoda != null) pagoda.dispose();
158 } 43 }
159
160// Utility.closeCurrentOut();
161
162 if (properties.getShellMode()) System.exit(0);
163 }
164
165// private void printPredicatesWithGap() {
166// for (String p: ((MyQueryReasoner) pagoda).getPredicatesWithGap()) {
167// System.out.println(p);
168// }
169// }
170
171 private static void evaluateConsoleQuery(QueryReasoner pagoda) throws IOException {
172 int ending = (int) '$', symbol;
173 while (true) {
174 Utility.logInfo("Input your query ending with $");
175 StringBuilder queryBuilder = new StringBuilder();
176 while ((symbol = System.in.read()) != ending) {
177 queryBuilder.append((char) symbol);
178 }
179 System.in.read();
180 if (queryBuilder.length() == 0) return ;
181 pagoda.evaluate_shell(queryBuilder.toString());
182 }
183 }
184
185 void testReactomeQueries() {
186 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> . }");
187 evaluate("select ?y ?z where { <http://identifiers.org/ensembl/ENSG00000157557> ?y ?z . }");
188 evaluate("select ?y where { <http://identifiers.org/ensembl/ENSG00000157557> <http://www.biopax.org/release/biopax-level3.owl#name> ?y . }", true);
189
190 }
191
192 void testSemFacetQueries() {
193// try {
194// BufferedReader reader = new BufferedReader(new InputStreamReader(new FileInputStream("query.line")));
195// for (String line; (line = reader.readLine()) != null && !line.isEmpty(); )
196// evaluate(line, true);
197// reader.close();
198// } catch (FileNotFoundException e) {
199// e.printStackTrace();
200// } catch (IOException e) {
201// e.printStackTrace();
202// }
203 evaluate("select ?x ?z where { ?x <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> ?z }", true);
204 evaluate("select distinct ?y where { ?x ?y ?z }", true);
205 evaluate("select distinct ?z where { ?x <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> ?z }", true);
206 evaluate("select ?y ?z where { <http://www.reactome.org/biopax/46/49633#Protein3885> ?y ?z .}", true);
207 }
208
209 void testISGQueries() {
210 evaluate("select ?z where {<http://cs.ox.ac.uk/Evgeny_Kharlamov> <http://cs.ox.ac.uk/lat> ?z .}", false);
211 evaluate("select ?x where {?x <http://cs.ox.ac.uk/type> <http://cs.ox.ac.uk/person> .}", false);
212 }
213
214 void testSomeTravelQueries() {
215 evaluate("select ?y ?z where {<http://www.owl-ontologies.com/travel.owl#BlueMountains> ?y ?z. }", true);
216 evaluate("select ?x where {?x <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.owl-ontologies.com/travel.owl#RetireeDestination>. }");
217 evaluate("select ?x where {?x <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.owl-ontologies.com/travel.owl#BackpackersDestination>. }");
218 }
219
220 void testSomeFlyQueries() {
221 evaluate("select ?x where { ?x <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://purl.obolibrary.org/obo/FBbt_00005106> . }", false);
222
223 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);
224
225 evaluate("Select ?x where { ?x <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> "
226 + "<http://purl.obolibrary.org/obo/FBbt_00067123>. ?x "
227 + "<http://purl.obolibrary.org/obo/RO_0002131> ?any . ?any "
228 + "<http://www.w3.org/1999/02/22-rdf-syntax-ns#type> "
229 + "<http://purl.obolibrary.org/obo/FBbt_00005140> . }", true);
230
231 evaluate("Select ?x where {?x <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> "
232 + "<http://purl.obolibrary.org/obo/FBbt_00067363> . ?x "
233 + "<http://purl.obolibrary.org/obo/RO_0002131> ?any . ?any "
234 + "<http://www.w3.org/1999/02/22-rdf-syntax-ns#type> "
235 + "<http://purl.obolibrary.org/obo/FBbt_00005140> . }", true);
236
237// evaluate("Select ?x where { "
238// + "?x <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://purl.obolibrary.org/obo/FBbt_00003660>. "
239// + "?x <http://purl.obolibrary.org/obo/FBbt#develops_from> ?any . "
240// + "?any <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://purl.obolibrary.org/obo/FBbt_00001446> . }", true);
241
242 evaluate("select DISTINCT ?z where { ?x <http://purl.obolibrary.org/obo/RO_0002110> ?any . "
243 + "?any <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> ?z . "
244 + "?x <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://purl.obolibrary.org/obo/FBbt_00007016> . } ", true);
245
246 evaluate("Select * where {"
247 + "<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>. "
248 + "<http://www.virtualflybrain.org/ontologies/individuals/VFB_00100607> <http://www.w3.org/2002/07/owl#sameAs> ?z }", true);
249
250 evaluate("SELECT DISTINCT ?x ?z WHERE {?x <http://www.w3.org/2002/07/owl#sameAs> ?z}", true);
251 evaluate("SELECT DISTINCT ?x ?z WHERE {?x <http://purl.obolibrary.org/obo/BFO_0000051> ?z}", true);
252
253 evaluate("select DISTINCT ?y where { ?x ?y ?z . "
254 + "?x <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://purl.obolibrary.org/obo/FBbt_00007364> }", true);
255
256 evaluateQueriesFromFile("/users/yzhou/Downloads/logs(1).log");
257 evaluateQueriesFromFile("/users/yzhou/Downloads/logs.log");
258
259 evaluate("SELECT DISTINCT ?x ?z WHERE {?x <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> ?z}", true);
260 evaluate("SELECT DISTINCT ?x ?z WHERE {?x <http://xmlns.com/foaf/0.1/depicts> ?z}", true);
261
262 evaluate("select ?x ?z where { ?x <http://www.w3.org/2002/07/owl#sameAs> ?z } ", true);
263 evaluate("select ?x ?z where { ?x <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> ?z } ", true);
264 }
265
266 public void evaluateQueriesFromFile(String fileName) {
267 Scanner scanner = null;
268 try {
269 scanner = new Scanner(new File(fileName));
270 String line;
271 while (scanner.hasNextLine()) {
272 line = scanner.nextLine();
273 if (line.startsWith("select"))
274 evaluate(line, true);
275 }
276 } catch (FileNotFoundException e) {
277 e.printStackTrace();
278 } finally {
279 if (scanner != null)
280 scanner.close();
281 }
282 }
283
284 QueryReasoner pagoda;
285
286 public PagodaTester(QueryReasoner reasoner) {
287 pagoda = reasoner;
288 }
289
290 Timer timer = new Timer();
291
292 private void evaluate(String query) {
293 evaluate(query, false);
294 }
295
296 private void evaluate(String query, boolean tag) {
297 timer.reset();
298 AnswerTuples tuples = pagoda.evaluate(query, tag);
299 int arity = tuples.getArity();
300 int count = 0;
301 for (AnswerTuple tuple; tuples.isValid(); tuples.moveNext()) {
302 tuple = tuples.getTuple();
303 for (int i = 0; i < arity; ++i)
304 tuple.getGroundTerm(i).toString();
305// System.out.print(tuple.getGroundTerm(i).toString() + "\t");
306// System.out.println();
307 ++count;
308 }
309 tuples.dispose();
310 Utility.logInfo("The number of answers for this SemFacet query: " + count);
311 Utility.logInfo("Total time for this SemFacet query: " + timer.duration());
312 } 44 }
313 45
314} 46}
generated by cgit v1.2.3 (git 2.25.1) at 2025-11-05 14:52:10 +0000