From 17bd9beaf7f358a44e5bf36a5855fe6727d506dc Mon Sep 17 00:00:00 2001 From: Federico Igne Date: Tue, 10 May 2022 18:17:06 +0100 Subject: [pagoda] Move project to Scala This commit includes a few changes: - The repository still uses Maven to manage dependency but it is now a Scala project. - The code has been ported from OWLAPI 3.4.10 to 5.1.20 - A proof of concept program using both RSAComb and PAGOdA has been added. --- test/uk/ac/ox/cs/pagoda/tester/PagodaTester.java | 318 ----------------------- 1 file changed, 318 deletions(-) delete mode 100644 test/uk/ac/ox/cs/pagoda/tester/PagodaTester.java (limited to 'test/uk/ac/ox/cs/pagoda/tester/PagodaTester.java') diff --git a/test/uk/ac/ox/cs/pagoda/tester/PagodaTester.java b/test/uk/ac/ox/cs/pagoda/tester/PagodaTester.java deleted file mode 100644 index d741d3b..0000000 --- a/test/uk/ac/ox/cs/pagoda/tester/PagodaTester.java +++ /dev/null @@ -1,318 +0,0 @@ -package uk.ac.ox.cs.pagoda.tester; - -import uk.ac.ox.cs.pagoda.query.AnswerTuple; -import uk.ac.ox.cs.pagoda.query.AnswerTuples; -import uk.ac.ox.cs.pagoda.reasoner.QueryReasoner; -import uk.ac.ox.cs.pagoda.util.PagodaProperties; -import uk.ac.ox.cs.pagoda.util.Timer; -import uk.ac.ox.cs.pagoda.util.Utility; - -import java.io.File; -import java.io.FileNotFoundException; -import java.io.IOException; -import java.util.Scanner; - -@Deprecated -public class PagodaTester { - - // public static final String onto_dir = "/media/RDFData/yzhou/"; -// public static final String onto_dir = "/users/yzhou/ontologies/"; -// public static final String onto_dir = "/home/scratch/yzhou/ontologies/"; - public static final String onto_dir = "/home/alessandro/Big_files/Ontologies/"; - - public static final String fly = onto_dir + "fly/fly_anatomy_XP_with_GJ_FC_individuals.owl"; - public static final String fly_query = onto_dir + "fly/queries/fly.sparql"; - - public static final String test_tbox = onto_dir + "smallExampleFromAna/dummy.owl"; - public static final String test_abox = onto_dir + "smallExampleFromAna/initialABox.ttl"; - public static final String test_query = onto_dir + "smallExampleFromAna/queries.dlog"; - - public static final int lubm_number = 1; - public static final String lubm_tbox = onto_dir + "lubm/univ-bench.owl"; - public static final String lubm_abox = onto_dir + "lubm/data/lubm" + lubm_number + ".ttl"; - public static final String lubm_abox_copy = onto_dir + "lubm/data/lubm" + lubm_number + " (copy).ttl"; - public static final String lubm_query = onto_dir + "lubm/queries/test.sparql"; - public static final String lubm_query6 = onto_dir + "lubm/queries/test_q6.sparql"; - public static final String lubm_query20 = onto_dir + "lubm/queries/test_q16.sparql"; - - public static final int uobm_number = 1; - public static final String uobm_tbox = onto_dir + "uobm/univ-bench-dl.owl"; - public static final String uobm_abox = onto_dir + "uobm/data/uobm" + uobm_number + ".ttl"; - public static final String uobm_query = onto_dir + "uobm/queries/test.sparql"; - public static final String uobm_query_temp = onto_dir + "uobm/queries/temp.sparql"; - public static final String uobm_query2 = onto_dir + "uobm/queries/standard_q2.sparql"; - public static final String uobm_query9 = onto_dir + "uobm/queries/standard_q9.sparql"; - public static final String uobm_query11 = onto_dir + "uobm/queries/standard_q11.sparql"; - public static final String uobm_query12 = onto_dir + "uobm/queries/standard_q12.sparql"; - public static final String uobm_query14 = onto_dir + "uobm/queries/standard_q14.sparql"; - public static final String uobm_query15 = onto_dir + "uobm/queries/standard_q15.sparql"; - public static final String uobm_query_multi = onto_dir + "uobm/queries/standard_multi.sparql"; - public static final String uobm_generated_query1 = onto_dir + "uobm/queries/generated_q1.sparql"; - public static final String uobm_query_group3 = onto_dir + "uobm/queries/standard_group3.sparql"; - - public static final String npd_tbox = onto_dir + "npd/npd-all-minus-datatype.owl"; - // "npd/npd-all.owl"; - // "npd-all-minus-datatype.owl"; - public static final String npd_abox = onto_dir + "npd/data/npd-data-dump-minus-datatype-new.ttl"; - // "npd/data/npd-data-dump-processed.ttl"; - // "npd-data-dump-minus-datatype-old.ttl"; - public static final String npd_query = onto_dir + "npd/queries/atomic.sparql"; - - public static final String npd_bench_tbox = onto_dir + "npd-benchmark/npd-v2-ql_a.owl"; - // npd-all-minus-datatype.owl"; - public static final String npd_bench_abox = onto_dir + "npd-benchmark/npd-v2-ql_a.ttl"; - // npd-data-dump-minus-datatype-old.ttl"; - public static final String npd_bench_query = onto_dir + "npd-benchmark/queries/all.sparql"; - - public static final String dbpedia_tbox = onto_dir + "dbpedia/integratedOntology-all-in-one-minus-datatype.owl"; - public static final String dbpedia_abox = onto_dir + "dbpedia/data/dbpedia-minus-datatype-new.ttl"; - public static final String dbpedia_query = onto_dir + "dbpedia/queries/atomic_ground.sparql"; - public static final String dbpedia_query274 = onto_dir + "dbpedia/atomic_q274.sparql"; - - public static final String dbpedia_latest_tbox = onto_dir + "dbpedia/dbpedia_2014.owl"; - public static final String travel_tbox = onto_dir + "dbpedia/travel.owl"; - public static final String dbpedia_tbox_simple = onto_dir + "dbpedia/dbpedia_simple.owl"; - - public static final String bioModels_tbox = onto_dir + "biomodels/biomodels-21.owl"; - public static final String bioModels_abox = onto_dir + "biomodels/data_processed_1.ttl"; - public static final String bioModels_queries = onto_dir + "biomodels/queries/queries.sparql"; - - public static final String chembl_tbox = onto_dir + "bio2rdf/chembl/cco-processed-noDPR-noDPD.ttl"; - public static final String chembl_abox = onto_dir + "bio2rdf/chembl/graph sampling old/sample_100.nt"; - public static final String chembl_queries = onto_dir + "bio2rdf/chembl/queries/problematic.sparql"; - //"bio2rdf/chembl/queries/atomic_one_filtered.sparql"; // - - public static final String reactome_tbox = onto_dir + "bio2rdf/reactome/biopax-level3-processed.owl"; - 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"; // - public static final String reactome_queries = onto_dir + "bio2rdf/reactome/queries/atomic.sparql"; - - public static final String uniprot_tbox = onto_dir + "bio2rdf/uniprot/core-processed.owl"; - public static final String uniprot_abox = onto_dir + "bio2rdf/uniprot/graph sampling/sample_1.nt"; - public static final String uniprot_queries = onto_dir + "bio2rdf/uniprot/queries/atomic_one.sparql"; - - public static final String atlas_tbox = onto_dir + "bio2rdf/atlas/gxaterms.owl"; - public static final String atlas_abox = onto_dir + "bio2rdf/atlas/graph sampling/sample_1.nt"; - public static final String atlas_queries = onto_dir + "bio2rdf/atlas/queries/atomic_one.sparql"; - QueryReasoner pagoda; - - // private void printPredicatesWithGap() { -// for (String p: ((MyQueryReasoner) pagoda).getPredicatesWithGap()) { -// System.out.println(p); -// } -// } - Timer timer = new Timer(); - - public PagodaTester(QueryReasoner reasoner) { - pagoda = reasoner; - } - - public static void main(String... args) { - if(args.length == 0) { -// args = new String[] {test_tbox, test_abox, test_query}; -// args = new String[] {lubm_tbox, lubm_abox, lubm_query}; -// args = new String[] {uobm_tbox, uobm_abox, uobm_query}; -// args = new String[] {fly, "null", fly_query}; -// args = new String[] {dbpedia_tbox, dbpedia_abox, dbpedia_query}; -// args = new String[] {travel_tbox, null, dbpedia_query274}; - args = new String[]{fly, fly_query}; -// args = new String[] {npd_tbox, npd_abox, npd_query}; -// args = new String[] {npd_bench_tbox, npd_bench_abox, npd_bench_query}; -// args = new String[] {"../SemFacet/WebContent/WEB-INF/data/dbpedia.owl", "../SemFacet/WebContent/WEB-INF/data/dbpediaA.nt", null}; -// args = new String[] {"../core/WebContent/WEB-INF/data/fly.owl", "../core/WebContent/WEB-INF/data/fly-data.nt", null}; -// args = new String[] {"data/lubm/univ-bench.owl", "data/lubm/lubm1.ttl", "data/lubm/lubm.sparql", "lubm.ans"}; -// args = new String[] {"data/uobm/univ-bench-dl.owl", "data/uobm/uobm1.ttl", "data/uobm/uobm.sparql", "uobm.ans"}; -// args = new String[] {"data/fly/fly_anatomy_XP_with_GJ_FC_individuals.owl", "data/fly/fly.sparql", "fly.ans"}; -// args = new String[] {bioModels_tbox, bioModels_abox, bioModels_queries}; -// args = new String[] {chembl_tbox, chembl_abox, chembl_queries}; -// args = new String[] {reactome_tbox, reactome_abox, reactome_queries}; -// args = new String[] {reactome_tbox, "/users/yzhou/temp/reactome_debug.ttl", onto_dir +"bio2rdf/reactome/queries/atomic_one_q65.sparql"}; -// args = new String[] {uniprot_tbox.replace(".owl", "-noDis.owl"), "/users/yzhou/temp/uniprot_debug/sample_1_string.nt", uniprot_queries}; -// args = new String[] {uniprot_tbox.replace(".owl", "-noDis.owl"), uniprot_abox, uniprot_queries}; -// args = new String[] {atlas_tbox, atlas_abox, atlas_queries}; -// args = new String[] {onto_dir + "test/unsatisfiable.owl", null, onto_dir + "test/unsatisfiable_queries.sparql"}; -// args = new String[] {onto_dir + "test/jair-example.owl", null, onto_dir + "test/jair-example_query.sparql"}; -// args[2] = args[2].replace(".sparql", "_all_pagoda.sparql"); -// args[2] = args[2].replace(".sparql", "_pellet.sparql"); - } - - PagodaProperties properties = new PagodaProperties("config/uobm.properties"); - - int index = 0; - if(args.length > index) properties.setOntologyPath(args[index++]); - if(args.length > index && (args[index].endsWith(".ttl") || args[index].endsWith(".nt"))) - properties.setDataPath(args[index++]); - if(args.length > index && args[index].endsWith(".sparql")) properties.setQueryPath(args[index++]); - if(args.length > index && !args[index].startsWith("-")) properties.setAnswerPath(args[index++]); - if(args.length > index) properties.setToClassify(Boolean.parseBoolean(args[index++].substring(1))); - if(args.length > index) properties.setToCallHermiT(Boolean.parseBoolean(args[index++].substring(1))); - - Utility.logInfo("Ontology file: " + properties.getOntologyPath()); - Utility.logInfo("Data files: " + properties.getDataPath()); - Utility.logInfo("Query files: " + properties.getQueryPath()); - Utility.logInfo("Answer file: " + properties.getAnswerPath()); - - QueryReasoner pagoda = null; - - try { - Timer t = new Timer(); - pagoda = QueryReasoner.getInstance(properties); - if (pagoda == null) return; - - Utility.logInfo("Preprocessing Done in " + t.duration() + " seconds."); - - if (properties.getQueryPath() != null) - for (String queryFile: properties.getQueryPath().split(";")) - pagoda.evaluate(pagoda.getQueryManager().collectQueryRecords(queryFile)); - - if(properties.getShellMode()) - try { - evaluateConsoleQuery(pagoda); - } catch(IOException e) { - e.printStackTrace(); - } - } finally { - if (pagoda != null) pagoda.dispose(); - } - -// Utility.closeCurrentOut(); - - if(properties.getShellMode()) System.exit(0); - } - - private static void evaluateConsoleQuery(QueryReasoner pagoda) throws IOException { - int ending = (int) '$', symbol; - while(true) { - Utility.logInfo("Input your query ending with $"); - StringBuilder queryBuilder = new StringBuilder(); - while((symbol = System.in.read()) != ending) { - queryBuilder.append((char) symbol); - } - System.in.read(); - if(queryBuilder.length() == 0) return; - pagoda.evaluate_shell(queryBuilder.toString()); - } - } - - void testReactomeQueries() { - evaluate("select ?x where { ?x . }"); - evaluate("select ?y ?z where { ?y ?z . }"); - evaluate("select ?y where { ?y . }", true); - - } - - void testSemFacetQueries() { -// try { -// BufferedReader reader = new BufferedReader(new InputStreamReader(new FileInputStream("query.line"))); -// for (String line; (line = reader.readLine()) != null && !line.isEmpty(); ) -// evaluate(line, true); -// reader.close(); -// } catch (FileNotFoundException e) { -// e.printStackTrace(); -// } catch (IOException e) { -// e.printStackTrace(); -// } - evaluate("select ?x ?z where { ?x ?z }", true); - evaluate("select distinct ?y where { ?x ?y ?z }", true); - evaluate("select distinct ?z where { ?x ?z }", true); - evaluate("select ?y ?z where { ?y ?z .}", true); - } - - void testISGQueries() { - evaluate("select ?z where { ?z .}", false); - evaluate("select ?x where {?x .}", false); - } - - void testSomeTravelQueries() { - evaluate("select ?y ?z where { ?y ?z. }", true); - evaluate("select ?x where {?x . }"); - evaluate("select ?x where {?x . }"); - } - - void testSomeFlyQueries() { - evaluate("select ?x where { ?x . }", false); - - evaluate("select DISTINCT ?z where { ?x ?any . ?any ?z . ?x . } ", true); - - evaluate("Select ?x where { ?x " - + ". ?x " - + " ?any . ?any " - + " " - + " . }", true); - - evaluate("Select ?x where {?x " - + " . ?x " - + " ?any . ?any " - + " " - + " . }", true); - -// evaluate("Select ?x where { " -// + "?x . " -// + "?x ?any . " -// + "?any . }", true); - - evaluate("select DISTINCT ?z where { ?x ?any . " - + "?any ?z . " - + "?x . } ", true); - - evaluate("Select * where {" - + " . " - + " ?z }", true); - - evaluate("SELECT DISTINCT ?x ?z WHERE {?x ?z}", true); - evaluate("SELECT DISTINCT ?x ?z WHERE {?x ?z}", true); - - evaluate("select DISTINCT ?y where { ?x ?y ?z . " - + "?x }", true); - - evaluateQueriesFromFile("/users/yzhou/Downloads/logs(1).log"); - evaluateQueriesFromFile("/users/yzhou/Downloads/logs.log"); - - evaluate("SELECT DISTINCT ?x ?z WHERE {?x ?z}", true); - evaluate("SELECT DISTINCT ?x ?z WHERE {?x ?z}", true); - - evaluate("select ?x ?z where { ?x ?z } ", true); - evaluate("select ?x ?z where { ?x ?z } ", true); - } - - public void evaluateQueriesFromFile(String fileName) { - Scanner scanner = null; - try { - scanner = new Scanner(new File(fileName)); - String line; - while(scanner.hasNextLine()) { - line = scanner.nextLine(); - if(line.startsWith("select")) - evaluate(line, true); - } - } catch(FileNotFoundException e) { - e.printStackTrace(); - } finally { - if(scanner != null) - scanner.close(); - } - } - - private void evaluate(String query) { - evaluate(query, false); - } - - private void evaluate(String query, boolean tag) { - timer.reset(); - AnswerTuples tuples = pagoda.evaluate(query, tag); - int arity = tuples.getArity(); - int count = 0; - for(AnswerTuple tuple; tuples.isValid(); tuples.moveNext()) { - tuple = tuples.getTuple(); - for(int i = 0; i < arity; ++i) - tuple.getGroundTerm(i).toString(); -// System.out.print(tuple.getGroundTerm(i).toString() + "\t"); -// System.out.println(); - ++count; - } - tuples.dispose(); - Utility.logInfo("The number of answers for this SemFacet query: " + count); - Utility.logInfo("Total time for this SemFacet query: " + timer.duration()); - } - -} -- cgit v1.2.3