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-rw-r--r--README.md48
-rw-r--r--pom.xml42
-rw-r--r--repo/uk/ac/ox/cs/jrdfox/jrdfox/1.0/jrdfox-1.0.jarbin0 -> 5015178 bytes
-rw-r--r--repo/uk/ac/ox/cs/jrdfox/jrdfox/1.0/jrdfox-1.0.jar.md51
-rw-r--r--repo/uk/ac/ox/cs/jrdfox/jrdfox/1.0/jrdfox-1.0.jar.sha11
-rw-r--r--repo/uk/ac/ox/cs/jrdfox/jrdfox/1.0/jrdfox-1.0.pom8
-rw-r--r--repo/uk/ac/ox/cs/jrdfox/jrdfox/1.0/jrdfox-1.0.pom.md51
-rw-r--r--repo/uk/ac/ox/cs/jrdfox/jrdfox/1.0/jrdfox-1.0.pom.sha11
-rw-r--r--repo/uk/ac/ox/cs/jrdfox/jrdfox/maven-metadata.xml12
-rw-r--r--repo/uk/ac/ox/cs/jrdfox/jrdfox/maven-metadata.xml.md51
-rw-r--r--repo/uk/ac/ox/cs/jrdfox/jrdfox/maven-metadata.xml.sha11
-rw-r--r--src/uk/ac/ox/cs/pagoda/reasoner/MyQueryReasoner.java2
-rw-r--r--test/resources/MainTests.xml5
-rw-r--r--test/uk/ac/ox/cs/pagoda/global_tests/TestPagodaFLY.java7
-rw-r--r--test/uk/ac/ox/cs/pagoda/global_tests/TestPagodaLUBM.java2
15 files changed, 93 insertions, 39 deletions
diff --git a/README.md b/README.md
index 5e908fb..663b6cb 100644
--- a/README.md
+++ b/README.md
@@ -1,35 +1,47 @@
1PAGOdA 1PAGOdA
2===== 2======
3 3
4PAGOdA is a conjunctive query answering engine for OWL 2 ontologies. The instruction how to use it can be found on the following website: http://www.cs.ox.ac.uk/isg/tools/PAGOdA/. 4PAGOdA is a conjunctive query answering engine for OWL 2 ontologies.
5 5
6 6
7Project dependencies/requirements 7Project dependencies/requirements
8===== 8=================================
9 9
10- This software has been developed for Linux
10- JavaSE 8 11- JavaSE 8
11- Maven 12- Maven
12 13
13 14
14How to compile the project from source in Eclipse? 15Building and packaging
15===== 16======================
16 17
17- In order to compile the project make sure that you have JavaSE 8 and Maven installed on your computer. 18This is a Maven project, hence Maven should be used for building and packaging.
18- After cloning the repository by command git clone https://github.com/yujiaoz/PAGOdA.git, you need to install it using the command "maven install". 19* Compile `mvn compile`
19- The project depends on a library JRDFox.jar that is not in central maven repository. The library for different operating systems can be found in lib directory. You need to include the correct one for your computer and add it to the build path. Alternative, if you have maven installed on your computer, you could add it into your local maven repository, modify maven dependencies and make sure that you remove it from the build path. If the provided JRDFox.jar doesn't work, you might need to follow the instruction below to compile the project JRDFox by yourself. 20* Create jars `mvn package`;
21you will get a jar without dependencies *target/pagoda-x.y.z.jar* and a runnable jar with dependencies *target/pagoda-x.y.z-jar-with-dependencies.jar*.
22* Execute tests `mvn test -DskipTests=false`;
20 23
21 24
22How to compile RDFox? 25Configuring the engine
23=== 26======================
24 27
25- Download https://github.com/yujiaoz/PAGOdA/blob/master/lib/RDFox/RDFox.zip. 28The engine provides a standard configuration, but it is most likely that is not suitable for your purposes.
26- Extract all files in the zip. 29You should provide your own configuration in a file called `pagoda.properties` including it in the classpath.
27- Go to the directory RDFox/RDFox. 30Such a file should resemble the file `src/resources/_default_pagoda.properties`.
28- Run command "ant".
29- You will find JRDFox.jar in the directory build/release/lib.
30 31
31 32
32How to run the project? 33Executing
33=== 34=========
34 35
35To run PAGOdA inside your java project, please check the simple example in src/example/simpleExample.jar. To run PAGOdA in command line once you have a jar package, follow the instruction on the following website https://www.cs.ox.ac.uk/isg/tools/PAGOdA/. \ No newline at end of file 36Once you have the runnable jar, you can make the system answer queries through the command line interface.
37
38Run `java -jar pagoda-x.y.z-jar-with-dependencies.jar` for getting a list of the mandatory arguments and optional parameters.
39
40Run `java -cp pagoda-x.y.z-jar-with-dependencies.jar:<your_path_to_properties>/pagoda.properties arg [arg]...` for executing the engine with a custom configuration.
41
42Using it as a library
43=====================
44
45The API is offered by the class `QueryReasoner`, however we provide a more handy wrapper, that is the class `Pagoda`.
46Thanks to such a wrapper, you can build an instance of `Pagoda` by specifying different parameters and after that you will get
47a runnable `Pagoda` object.
diff --git a/pom.xml b/pom.xml
index ffe18ce..466383a 100644
--- a/pom.xml
+++ b/pom.xml
@@ -6,7 +6,19 @@
6 <version>2.1.2</version> 6 <version>2.1.2</version>
7 <packaging>jar</packaging> 7 <packaging>jar</packaging>
8 <name>PAGOdA</name> 8 <name>PAGOdA</name>
9 <build> 9 <properties>
10 <skipTests>true</skipTests>
11 </properties>
12 <repositories>
13 <!--other repositories if any-->
14 <repository>
15 <id>project.local</id>
16 <name>pagoda</name>
17 <url>file:${project.basedir}/repo</url>
18 </repository>
19 </repositories>
20
21 <build>
10 <sourceDirectory>src</sourceDirectory> 22 <sourceDirectory>src</sourceDirectory>
11 <testSourceDirectory>test</testSourceDirectory> 23 <testSourceDirectory>test</testSourceDirectory>
12 <resources> 24 <resources>
@@ -101,20 +113,20 @@
101 <artifactId>dashboard-maven-plugin</artifactId> 113 <artifactId>dashboard-maven-plugin</artifactId>
102 <version>1.0.0-beta-1</version> 114 <version>1.0.0-beta-1</version>
103 </plugin> 115 </plugin>
104 <plugin> 116 <!--<plugin>-->
105 <groupId>org.apache.maven.plugins</groupId> 117 <!--<groupId>org.apache.maven.plugins</groupId>-->
106 <artifactId>maven-surefire-plugin</artifactId> 118 <!--<artifactId>maven-surefire-plugin</artifactId>-->
107 <version>2.13</version> 119 <!--<version>2.13</version>-->
108 <configuration> 120 <!--<configuration>-->
109 <forkMode>always</forkMode> 121 <!--<forkMode>always</forkMode>-->
110 <systemPropertyVariables> 122 <!--<systemPropertyVariables>-->
111 <reporter.debug>false</reporter.debug> 123 <!--<reporter.debug>false</reporter.debug>-->
112 </systemPropertyVariables> 124 <!--</systemPropertyVariables>-->
113 <suiteXmlFiles> 125 <!--<suiteXmlFiles>-->
114 <suiteXmlFile>testResources/LightTests.xml</suiteXmlFile> 126 <!--<suiteXmlFile>testResources/LightTests.xml</suiteXmlFile>-->
115 </suiteXmlFiles> 127 <!--</suiteXmlFiles>-->
116 </configuration> 128 <!--</configuration>-->
117 </plugin> 129 <!--</plugin>-->
118 </plugins> 130 </plugins>
119 </reporting> 131 </reporting>
120 <dependencies> 132 <dependencies>
diff --git a/repo/uk/ac/ox/cs/jrdfox/jrdfox/1.0/jrdfox-1.0.jar b/repo/uk/ac/ox/cs/jrdfox/jrdfox/1.0/jrdfox-1.0.jar
new file mode 100644
index 0000000..3339750
--- /dev/null
+++ b/repo/uk/ac/ox/cs/jrdfox/jrdfox/1.0/jrdfox-1.0.jar
Binary files differ
diff --git a/repo/uk/ac/ox/cs/jrdfox/jrdfox/1.0/jrdfox-1.0.jar.md5 b/repo/uk/ac/ox/cs/jrdfox/jrdfox/1.0/jrdfox-1.0.jar.md5
new file mode 100644
index 0000000..8b1c104
--- /dev/null
+++ b/repo/uk/ac/ox/cs/jrdfox/jrdfox/1.0/jrdfox-1.0.jar.md5
@@ -0,0 +1 @@
599f8f78d5c3aaa3c40b5bfc329b5849 \ No newline at end of file
diff --git a/repo/uk/ac/ox/cs/jrdfox/jrdfox/1.0/jrdfox-1.0.jar.sha1 b/repo/uk/ac/ox/cs/jrdfox/jrdfox/1.0/jrdfox-1.0.jar.sha1
new file mode 100644
index 0000000..5cd2924
--- /dev/null
+++ b/repo/uk/ac/ox/cs/jrdfox/jrdfox/1.0/jrdfox-1.0.jar.sha1
@@ -0,0 +1 @@
9ef62e415ff8a0ee95163886aaf38fc4ec4282a2 \ No newline at end of file
diff --git a/repo/uk/ac/ox/cs/jrdfox/jrdfox/1.0/jrdfox-1.0.pom b/repo/uk/ac/ox/cs/jrdfox/jrdfox/1.0/jrdfox-1.0.pom
new file mode 100644
index 0000000..ab34e46
--- /dev/null
+++ b/repo/uk/ac/ox/cs/jrdfox/jrdfox/1.0/jrdfox-1.0.pom
@@ -0,0 +1,8 @@
1<?xml version="1.0" encoding="UTF-8"?>
2<project xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd" xmlns="http://maven.apache.org/POM/4.0.0"
3 xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
4 <modelVersion>4.0.0</modelVersion>
5 <groupId>uk.ac.ox.cs.jrdfox</groupId>
6 <artifactId>jrdfox</artifactId>
7 <version>1.0</version>
8</project>
diff --git a/repo/uk/ac/ox/cs/jrdfox/jrdfox/1.0/jrdfox-1.0.pom.md5 b/repo/uk/ac/ox/cs/jrdfox/jrdfox/1.0/jrdfox-1.0.pom.md5
new file mode 100644
index 0000000..3ac0611
--- /dev/null
+++ b/repo/uk/ac/ox/cs/jrdfox/jrdfox/1.0/jrdfox-1.0.pom.md5
@@ -0,0 +1 @@
bb280362ba41e5f882ad4dd865b46ec0 \ No newline at end of file
diff --git a/repo/uk/ac/ox/cs/jrdfox/jrdfox/1.0/jrdfox-1.0.pom.sha1 b/repo/uk/ac/ox/cs/jrdfox/jrdfox/1.0/jrdfox-1.0.pom.sha1
new file mode 100644
index 0000000..7496630
--- /dev/null
+++ b/repo/uk/ac/ox/cs/jrdfox/jrdfox/1.0/jrdfox-1.0.pom.sha1
@@ -0,0 +1 @@
a6d405a3643296699d87f1626ebe802419065ffc \ No newline at end of file
diff --git a/repo/uk/ac/ox/cs/jrdfox/jrdfox/maven-metadata.xml b/repo/uk/ac/ox/cs/jrdfox/jrdfox/maven-metadata.xml
new file mode 100644
index 0000000..ed39b4d
--- /dev/null
+++ b/repo/uk/ac/ox/cs/jrdfox/jrdfox/maven-metadata.xml
@@ -0,0 +1,12 @@
1<?xml version="1.0" encoding="UTF-8"?>
2<metadata>
3 <groupId>uk.ac.ox.cs.jrdfox</groupId>
4 <artifactId>jrdfox</artifactId>
5 <versioning>
6 <release>1.0</release>
7 <versions>
8 <version>1.0</version>
9 </versions>
10 <lastUpdated>20151012092905</lastUpdated>
11 </versioning>
12</metadata>
diff --git a/repo/uk/ac/ox/cs/jrdfox/jrdfox/maven-metadata.xml.md5 b/repo/uk/ac/ox/cs/jrdfox/jrdfox/maven-metadata.xml.md5
new file mode 100644
index 0000000..d182e74
--- /dev/null
+++ b/repo/uk/ac/ox/cs/jrdfox/jrdfox/maven-metadata.xml.md5
@@ -0,0 +1 @@
1dafbe30a98fe9f5d0ec6d140ca79a6d \ No newline at end of file
diff --git a/repo/uk/ac/ox/cs/jrdfox/jrdfox/maven-metadata.xml.sha1 b/repo/uk/ac/ox/cs/jrdfox/jrdfox/maven-metadata.xml.sha1
new file mode 100644
index 0000000..952c15e
--- /dev/null
+++ b/repo/uk/ac/ox/cs/jrdfox/jrdfox/maven-metadata.xml.sha1
@@ -0,0 +1 @@
a476004dd5eae7023ae322c56e4c964750eafb34 \ No newline at end of file
diff --git a/src/uk/ac/ox/cs/pagoda/reasoner/MyQueryReasoner.java b/src/uk/ac/ox/cs/pagoda/reasoner/MyQueryReasoner.java
index ae57670..8cc9209 100644
--- a/src/uk/ac/ox/cs/pagoda/reasoner/MyQueryReasoner.java
+++ b/src/uk/ac/ox/cs/pagoda/reasoner/MyQueryReasoner.java
@@ -74,7 +74,7 @@ class MyQueryReasoner extends QueryReasoner {
74 program = new DatalogProgram(ontology); 74 program = new DatalogProgram(ontology);
75// program.getLower().save(); 75// program.getLower().save();
76// program.getUpper().save(); 76// program.getUpper().save();
77// program.getGeneral().save(); 77 program.getGeneral().save();
78 78
79 if(!program.getGeneral().isHorn()) 79 if(!program.getGeneral().isHorn())
80 lazyUpperStore = new MultiStageQueryEngine("lazy-upper-bound", true); 80 lazyUpperStore = new MultiStageQueryEngine("lazy-upper-bound", true);
diff --git a/test/resources/MainTests.xml b/test/resources/MainTests.xml
index ec299b5..fdecc72 100644
--- a/test/resources/MainTests.xml
+++ b/test/resources/MainTests.xml
@@ -6,10 +6,11 @@
6 <groups> 6 <groups>
7 <run> 7 <run>
8 <!--<include name="correctness"/>--> 8 <!--<include name="correctness"/>-->
9 <include name="light"/> 9 <!--<include name="light"/>-->
10 <!--<include name="justExecute"/>--> 10 <!--<include name="justExecute"/>-->
11 <exclude name="heavy"/> 11 <!--<exclude name="heavy"/>-->
12 <!--<include name="nonOriginal"/>--> 12 <!--<include name="nonOriginal"/>-->
13 <include name="existential"/>
13 </run> 14 </run>
14 </groups> 15 </groups>
15 <classes> 16 <classes>
diff --git a/test/uk/ac/ox/cs/pagoda/global_tests/TestPagodaFLY.java b/test/uk/ac/ox/cs/pagoda/global_tests/TestPagodaFLY.java
index 42f0ac1..3eb956f 100644
--- a/test/uk/ac/ox/cs/pagoda/global_tests/TestPagodaFLY.java
+++ b/test/uk/ac/ox/cs/pagoda/global_tests/TestPagodaFLY.java
@@ -51,17 +51,20 @@ public class TestPagodaFLY {
51 CheckAnswers.assertSameAnswers(answers, givenAnswers); 51 CheckAnswers.assertSameAnswers(answers, givenAnswers);
52 } 52 }
53 53
54 @Test(groups = {"light", "justExecute", "nonOriginal"}) 54 @Test(groups = {"light", "justExecute", "nonOriginal", "existential"})
55 public void justExecute_newQueries() throws IOException { 55 public void justExecute_newQueries() throws IOException {
56 String ontoDir = TestUtil.getConfig().getProperty("ontoDir"); 56 String ontoDir = TestUtil.getConfig().getProperty("ontoDir");
57 57
58 Pagoda.builder() 58 Pagoda.builder()
59// .ontology(Paths.get(ontoDir, "fly/fly_rolledUp.owl")) 59// .ontology(Paths.get(ontoDir, "fly/fly_rolledUp.owl"))
60 .ontology(Paths.get(ontoDir, "fly/fly_anatomy_XP_with_GJ_FC_individuals.owl")) 60 .ontology(Paths.get(ontoDir, "fly/fly_anatomy_XP_with_GJ_FC_individuals.owl"))
61 .query(Paths.get(ontoDir, "fly/queries/new_queries.sparql")) 61// .query(Paths.get(ontoDir, "fly/queries/fly_rolledUp.sparql"))
62// .query(Paths.get(ontoDir, "fly/queries/new_queries.sparql"))
63 .query("/home/alessandro/Desktop/query-8.sparql")
62// .answer(Paths.get("/home/alessandro/Desktop/answers.json")) 64// .answer(Paths.get("/home/alessandro/Desktop/answers.json"))
63 .classify(false) 65 .classify(false)
64 .hermit(true) 66 .hermit(true)
67 .skolemDepth(3)
65 .skolem(PagodaProperties.SkolemUpperBoundOptions.BEFORE_SUMMARISATION) 68 .skolem(PagodaProperties.SkolemUpperBoundOptions.BEFORE_SUMMARISATION)
66 .build() 69 .build()
67 .run(); 70 .run();
diff --git a/test/uk/ac/ox/cs/pagoda/global_tests/TestPagodaLUBM.java b/test/uk/ac/ox/cs/pagoda/global_tests/TestPagodaLUBM.java
index 2d95e5f..019fafa 100644
--- a/test/uk/ac/ox/cs/pagoda/global_tests/TestPagodaLUBM.java
+++ b/test/uk/ac/ox/cs/pagoda/global_tests/TestPagodaLUBM.java
@@ -85,7 +85,7 @@ public class TestPagodaLUBM {
85 Pagoda.builder() 85 Pagoda.builder()
86 .ontology(Paths.get(ontoDir, "lubm/univ-bench.owl")) 86 .ontology(Paths.get(ontoDir, "lubm/univ-bench.owl"))
87 .data(Paths.get(ontoDir, "lubm/data/lubm1.ttl")) 87 .data(Paths.get(ontoDir, "lubm/data/lubm1.ttl"))
88 .query(Paths.get(ontoDir, "lubm/queries/queries_from_feier-et-al.sparql")) 88 .query(Paths.get(ontoDir, "lubm/queries/queries_from_rules.sparql"))
89 .build() 89 .build()
90 .run(); 90 .run();
91 } 91 }
generated by cgit v1.2.3 (git 2.25.1) at 2025-11-05 15:12:09 +0000