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authorRncLsn <rnc.lsn@gmail.com>2015-05-06 18:11:08 +0100
committerRonca <alessandro.a.ronca@gmail.com>2015-05-06 18:20:58 +0100
commitf2909a748a300f94cf6067fc84416e408d3e6de8 (patch)
tree02962a710fe27ea1c7a2704a356b7f663a42cb52
parent58e6d87cb604702e7b307bad73c4fd42a694c3ec (diff)
downloadACQuA-f2909a748a300f94cf6067fc84416e408d3e6de8.tar.gz
ACQuA-f2909a748a300f94cf6067fc84416e408d3e6de8.zip
Switch from JUnit to TestNG.
Plus minor fixes.
-rw-r--r--.idea/libraries/Maven__com_beust_jcommander_1_12.xml13
-rw-r--r--.idea/libraries/Maven__com_fasterxml_jackson_core_jackson_core_2_2_1.xml13
-rw-r--r--.idea/libraries/Maven__commons_codec_commons_codec_1_4.xml13
-rw-r--r--.idea/libraries/Maven__commons_dbcp_commons_dbcp_1_3.xml13
-rw-r--r--.idea/libraries/Maven__commons_httpclient_commons_httpclient_3_1.xml13
-rw-r--r--.idea/libraries/Maven__junit_junit_4_10.xml13
-rw-r--r--.idea/libraries/Maven__net_sf_opencsv_opencsv_2_0.xml13
-rw-r--r--.idea/libraries/Maven__net_sourceforge_owlapi_owlapi_api_3_4_10.xml13
-rw-r--r--.idea/libraries/Maven__net_sourceforge_owlapi_owlapi_apibinding_3_4_10.xml13
-rw-r--r--.idea/libraries/Maven__net_sourceforge_owlapi_owlapi_contract_3_4_10.xml13
-rw-r--r--.idea/libraries/Maven__net_sourceforge_owlapi_owlapi_distribution_3_4_10.xml13
-rw-r--r--.idea/libraries/Maven__net_sourceforge_owlapi_owlapi_impl_3_4_10.xml13
-rw-r--r--.idea/libraries/Maven__net_sourceforge_owlapi_owlapi_oboformat_3_4_10.xml13
-rw-r--r--.idea/libraries/Maven__net_sourceforge_owlapi_owlapi_parsers_3_4_10.xml13
-rw-r--r--.idea/libraries/Maven__net_sourceforge_owlapi_owlapi_tools_3_4_10.xml13
-rw-r--r--.idea/libraries/Maven__org_beanshell_bsh_2_0b4.xml13
-rw-r--r--.idea/libraries/Maven__org_hamcrest_hamcrest_core_1_1.xml13
-rw-r--r--.idea/libraries/Maven__org_openrdf_sesame_sesame_http_client_2_7_13.xml13
-rw-r--r--.idea/libraries/Maven__org_openrdf_sesame_sesame_http_protocol_2_7_13.xml13
-rw-r--r--.idea/libraries/Maven__org_openrdf_sesame_sesame_model_2_7_13.xml13
-rw-r--r--.idea/libraries/Maven__org_openrdf_sesame_sesame_query_2_7_13.xml13
-rw-r--r--.idea/libraries/Maven__org_openrdf_sesame_sesame_queryalgebra_evaluation_2_7_13.xml13
-rw-r--r--.idea/libraries/Maven__org_openrdf_sesame_sesame_queryalgebra_model_2_7_13.xml13
-rw-r--r--.idea/libraries/Maven__org_openrdf_sesame_sesame_queryparser_api_2_7_13.xml13
-rw-r--r--.idea/libraries/Maven__org_openrdf_sesame_sesame_queryparser_serql_2_7_13.xml13
-rw-r--r--.idea/libraries/Maven__org_openrdf_sesame_sesame_queryparser_sparql_2_7_13.xml13
-rw-r--r--.idea/libraries/Maven__org_openrdf_sesame_sesame_queryresultio_api_2_7_13.xml13
-rw-r--r--.idea/libraries/Maven__org_openrdf_sesame_sesame_queryresultio_binary_2_7_13.xml13
-rw-r--r--.idea/libraries/Maven__org_openrdf_sesame_sesame_queryresultio_sparqljson_2_7_13.xml13
-rw-r--r--.idea/libraries/Maven__org_openrdf_sesame_sesame_queryresultio_sparqlxml_2_7_13.xml13
-rw-r--r--.idea/libraries/Maven__org_openrdf_sesame_sesame_queryresultio_text_2_7_13.xml13
-rw-r--r--.idea/libraries/Maven__org_openrdf_sesame_sesame_repository_api_2_7_13.xml13
-rw-r--r--.idea/libraries/Maven__org_openrdf_sesame_sesame_repository_contextaware_2_7_13.xml13
-rw-r--r--.idea/libraries/Maven__org_openrdf_sesame_sesame_repository_dataset_2_7_13.xml13
-rw-r--r--.idea/libraries/Maven__org_openrdf_sesame_sesame_repository_event_2_7_13.xml13
-rw-r--r--.idea/libraries/Maven__org_openrdf_sesame_sesame_repository_http_2_7_13.xml13
-rw-r--r--.idea/libraries/Maven__org_openrdf_sesame_sesame_repository_manager_2_7_13.xml13
-rw-r--r--.idea/libraries/Maven__org_openrdf_sesame_sesame_repository_sail_2_7_13.xml13
-rw-r--r--.idea/libraries/Maven__org_openrdf_sesame_sesame_repository_sparql_2_7_13.xml13
-rw-r--r--.idea/libraries/Maven__org_openrdf_sesame_sesame_rio_api_2_7_13.xml13
-rw-r--r--.idea/libraries/Maven__org_openrdf_sesame_sesame_rio_binary_2_7_13.xml13
-rw-r--r--.idea/libraries/Maven__org_openrdf_sesame_sesame_rio_datatypes_2_7_13.xml13
-rw-r--r--.idea/libraries/Maven__org_openrdf_sesame_sesame_rio_languages_2_7_13.xml13
-rw-r--r--.idea/libraries/Maven__org_openrdf_sesame_sesame_rio_n3_2_7_13.xml13
-rw-r--r--.idea/libraries/Maven__org_openrdf_sesame_sesame_rio_nquads_2_7_13.xml13
-rw-r--r--.idea/libraries/Maven__org_openrdf_sesame_sesame_rio_ntriples_2_7_13.xml13
-rw-r--r--.idea/libraries/Maven__org_openrdf_sesame_sesame_rio_rdfjson_2_7_13.xml13
-rw-r--r--.idea/libraries/Maven__org_openrdf_sesame_sesame_rio_rdfxml_2_7_13.xml13
-rw-r--r--.idea/libraries/Maven__org_openrdf_sesame_sesame_rio_trig_2_7_13.xml13
-rw-r--r--.idea/libraries/Maven__org_openrdf_sesame_sesame_rio_trix_2_7_13.xml13
-rw-r--r--.idea/libraries/Maven__org_openrdf_sesame_sesame_rio_turtle_2_7_13.xml13
-rw-r--r--.idea/libraries/Maven__org_openrdf_sesame_sesame_runtime_2_7_13.xml13
-rw-r--r--.idea/libraries/Maven__org_openrdf_sesame_sesame_sail_api_2_7_13.xml13
-rw-r--r--.idea/libraries/Maven__org_openrdf_sesame_sesame_sail_federation_2_7_13.xml13
-rw-r--r--.idea/libraries/Maven__org_openrdf_sesame_sesame_sail_inferencer_2_7_13.xml13
-rw-r--r--.idea/libraries/Maven__org_openrdf_sesame_sesame_sail_memory_2_7_13.xml13
-rw-r--r--.idea/libraries/Maven__org_openrdf_sesame_sesame_sail_nativerdf_2_7_13.xml13
-rw-r--r--.idea/libraries/Maven__org_openrdf_sesame_sesame_sail_rdbms_2_7_13.xml13
-rw-r--r--.idea/libraries/Maven__org_openrdf_sesame_sesame_util_2_7_13.xml13
-rw-r--r--.idea/libraries/Maven__org_slf4j_slf4j_api_1_6_1.xml13
-rw-r--r--.idea/libraries/Maven__org_testng_testng_6_7.xml13
-rw-r--r--.idea/libraries/Maven__org_yaml_snakeyaml_1_6.xml13
-rw-r--r--config/log4j.properties (renamed from src/log4j.properties)0
-rw-r--r--config/test.properties1
-rw-r--r--pom.xml11
-rw-r--r--src/org/semanticweb/karma2/model/cqparser/ConjunctiveQueryWalker.java2
-rw-r--r--src/uk/ac/ox/cs/pagoda/util/Utility.java16
-rw-r--r--target/.gitignore2
-rw-r--r--test/AllTests.xml12
-rw-r--r--test/FullEvaluation.xml18
-rw-r--r--test/uk/ac/ox/cs/pagoda/junit/AllTests.java48
-rw-r--r--test/uk/ac/ox/cs/pagoda/junit/FullEvaluation.java14
-rw-r--r--test/uk/ac/ox/cs/pagoda/junit/PagodaLUBM.java38
-rw-r--r--test/uk/ac/ox/cs/pagoda/junit/PagodaUOBM.java48
-rw-r--r--test/uk/ac/ox/cs/pagoda/test_units/ClauseTester.java (renamed from test/uk/ac/ox/cs/pagoda/junit/ClauseTester.java)17
-rw-r--r--test/uk/ac/ox/cs/pagoda/test_units/CostEvaluation.java (renamed from test/uk/ac/ox/cs/pagoda/junit/CostEvaluation.java)4
-rw-r--r--test/uk/ac/ox/cs/pagoda/test_units/JAIR_PAGOdA.java (renamed from test/uk/ac/ox/cs/pagoda/junit/JAIR_PAGOdA.java)151
-rw-r--r--test/uk/ac/ox/cs/pagoda/test_units/JAIR_Scalability.java (renamed from test/uk/ac/ox/cs/pagoda/junit/JAIR_Scalability.java)28
-rw-r--r--test/uk/ac/ox/cs/pagoda/test_units/LightEvaluation.java (renamed from test/uk/ac/ox/cs/pagoda/junit/LightEvaluation.java)33
-rw-r--r--test/uk/ac/ox/cs/pagoda/test_units/PagodaDBPedia.java (renamed from test/uk/ac/ox/cs/pagoda/junit/PagodaDBPedia.java)11
-rw-r--r--test/uk/ac/ox/cs/pagoda/test_units/PagodaELU.java (renamed from test/uk/ac/ox/cs/pagoda/junit/PagodaELU.java)2
-rw-r--r--test/uk/ac/ox/cs/pagoda/test_units/PagodaFLY.java (renamed from test/uk/ac/ox/cs/pagoda/junit/PagodaFLY.java)2
-rw-r--r--test/uk/ac/ox/cs/pagoda/test_units/PagodaLUBM.java68
-rw-r--r--test/uk/ac/ox/cs/pagoda/test_units/PagodaNPD.java (renamed from test/uk/ac/ox/cs/pagoda/junit/PagodaNPD.java)17
-rw-r--r--test/uk/ac/ox/cs/pagoda/test_units/PagodaNPD_bench.java (renamed from test/uk/ac/ox/cs/pagoda/junit/PagodaNPD_bench.java)11
-rw-r--r--test/uk/ac/ox/cs/pagoda/test_units/PagodaRLU.java (renamed from test/uk/ac/ox/cs/pagoda/junit/PagodaRLU.java)2
-rw-r--r--test/uk/ac/ox/cs/pagoda/test_units/PagodaUOBM.java79
-rw-r--r--test/uk/ac/ox/cs/pagoda/tester/PagodaTester.java16
88 files changed, 1168 insertions, 289 deletions
diff --git a/.idea/libraries/Maven__com_beust_jcommander_1_12.xml b/.idea/libraries/Maven__com_beust_jcommander_1_12.xml
new file mode 100644
index 0000000..2b9ea17
--- /dev/null
+++ b/.idea/libraries/Maven__com_beust_jcommander_1_12.xml
@@ -0,0 +1,13 @@
1<component name="libraryTable">
2 <library name="Maven: com.beust:jcommander:1.12">
3 <CLASSES>
4 <root url="jar://$MAVEN_REPOSITORY$/com/beust/jcommander/1.12/jcommander-1.12.jar!/" />
5 </CLASSES>
6 <JAVADOC>
7 <root url="jar://$MAVEN_REPOSITORY$/com/beust/jcommander/1.12/jcommander-1.12-javadoc.jar!/" />
8 </JAVADOC>
9 <SOURCES>
10 <root url="jar://$MAVEN_REPOSITORY$/com/beust/jcommander/1.12/jcommander-1.12-sources.jar!/" />
11 </SOURCES>
12 </library>
13</component> \ No newline at end of file
diff --git a/.idea/libraries/Maven__com_fasterxml_jackson_core_jackson_core_2_2_1.xml b/.idea/libraries/Maven__com_fasterxml_jackson_core_jackson_core_2_2_1.xml
new file mode 100644
index 0000000..c8360e5
--- /dev/null
+++ b/.idea/libraries/Maven__com_fasterxml_jackson_core_jackson_core_2_2_1.xml
@@ -0,0 +1,13 @@
1<component name="libraryTable">
2 <library name="Maven: com.fasterxml.jackson.core:jackson-core:2.2.1">
3 <CLASSES>
4 <root url="jar://$MAVEN_REPOSITORY$/com/fasterxml/jackson/core/jackson-core/2.2.1/jackson-core-2.2.1.jar!/" />
5 </CLASSES>
6 <JAVADOC>
7 <root url="jar://$MAVEN_REPOSITORY$/com/fasterxml/jackson/core/jackson-core/2.2.1/jackson-core-2.2.1-javadoc.jar!/" />
8 </JAVADOC>
9 <SOURCES>
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11 </SOURCES>
12 </library>
13</component> \ No newline at end of file
diff --git a/.idea/libraries/Maven__commons_codec_commons_codec_1_4.xml b/.idea/libraries/Maven__commons_codec_commons_codec_1_4.xml
new file mode 100644
index 0000000..2b149c4
--- /dev/null
+++ b/.idea/libraries/Maven__commons_codec_commons_codec_1_4.xml
@@ -0,0 +1,13 @@
1<component name="libraryTable">
2 <library name="Maven: commons-codec:commons-codec:1.4">
3 <CLASSES>
4 <root url="jar://$MAVEN_REPOSITORY$/commons-codec/commons-codec/1.4/commons-codec-1.4.jar!/" />
5 </CLASSES>
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11 </SOURCES>
12 </library>
13</component> \ No newline at end of file
diff --git a/.idea/libraries/Maven__commons_dbcp_commons_dbcp_1_3.xml b/.idea/libraries/Maven__commons_dbcp_commons_dbcp_1_3.xml
new file mode 100644
index 0000000..ebd31e4
--- /dev/null
+++ b/.idea/libraries/Maven__commons_dbcp_commons_dbcp_1_3.xml
@@ -0,0 +1,13 @@
1<component name="libraryTable">
2 <library name="Maven: commons-dbcp:commons-dbcp:1.3">
3 <CLASSES>
4 <root url="jar://$MAVEN_REPOSITORY$/commons-dbcp/commons-dbcp/1.3/commons-dbcp-1.3.jar!/" />
5 </CLASSES>
6 <JAVADOC>
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9 <SOURCES>
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11 </SOURCES>
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13</component> \ No newline at end of file
diff --git a/.idea/libraries/Maven__commons_httpclient_commons_httpclient_3_1.xml b/.idea/libraries/Maven__commons_httpclient_commons_httpclient_3_1.xml
new file mode 100644
index 0000000..66e6537
--- /dev/null
+++ b/.idea/libraries/Maven__commons_httpclient_commons_httpclient_3_1.xml
@@ -0,0 +1,13 @@
1<component name="libraryTable">
2 <library name="Maven: commons-httpclient:commons-httpclient:3.1">
3 <CLASSES>
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5 </CLASSES>
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11 </SOURCES>
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13</component> \ No newline at end of file
diff --git a/.idea/libraries/Maven__junit_junit_4_10.xml b/.idea/libraries/Maven__junit_junit_4_10.xml
new file mode 100644
index 0000000..ed8bf5f
--- /dev/null
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diff --git a/.idea/libraries/Maven__net_sf_opencsv_opencsv_2_0.xml b/.idea/libraries/Maven__net_sf_opencsv_opencsv_2_0.xml
new file mode 100644
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diff --git a/.idea/libraries/Maven__net_sourceforge_owlapi_owlapi_api_3_4_10.xml b/.idea/libraries/Maven__net_sourceforge_owlapi_owlapi_api_3_4_10.xml
new file mode 100644
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+++ b/.idea/libraries/Maven__net_sourceforge_owlapi_owlapi_api_3_4_10.xml
@@ -0,0 +1,13 @@
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3 <CLASSES>
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5 </CLASSES>
6 <JAVADOC>
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11 </SOURCES>
12 </library>
13</component> \ No newline at end of file
diff --git a/.idea/libraries/Maven__net_sourceforge_owlapi_owlapi_apibinding_3_4_10.xml b/.idea/libraries/Maven__net_sourceforge_owlapi_owlapi_apibinding_3_4_10.xml
new file mode 100644
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--- /dev/null
+++ b/.idea/libraries/Maven__net_sourceforge_owlapi_owlapi_apibinding_3_4_10.xml
@@ -0,0 +1,13 @@
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13</component> \ No newline at end of file
diff --git a/.idea/libraries/Maven__net_sourceforge_owlapi_owlapi_contract_3_4_10.xml b/.idea/libraries/Maven__net_sourceforge_owlapi_owlapi_contract_3_4_10.xml
new file mode 100644
index 0000000..ff992a4
--- /dev/null
+++ b/.idea/libraries/Maven__net_sourceforge_owlapi_owlapi_contract_3_4_10.xml
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9 <SOURCES>
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13</component> \ No newline at end of file
diff --git a/.idea/libraries/Maven__net_sourceforge_owlapi_owlapi_distribution_3_4_10.xml b/.idea/libraries/Maven__net_sourceforge_owlapi_owlapi_distribution_3_4_10.xml
new file mode 100644
index 0000000..dbe2cb6
--- /dev/null
+++ b/.idea/libraries/Maven__net_sourceforge_owlapi_owlapi_distribution_3_4_10.xml
@@ -0,0 +1,13 @@
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3 <CLASSES>
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5 </CLASSES>
6 <JAVADOC>
7 <root url="jar://$MAVEN_REPOSITORY$/net/sourceforge/owlapi/owlapi-distribution/3.4.10/owlapi-distribution-3.4.10-javadoc.jar!/" />
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12 </library>
13</component> \ No newline at end of file
diff --git a/.idea/libraries/Maven__net_sourceforge_owlapi_owlapi_impl_3_4_10.xml b/.idea/libraries/Maven__net_sourceforge_owlapi_owlapi_impl_3_4_10.xml
new file mode 100644
index 0000000..38600b6
--- /dev/null
+++ b/.idea/libraries/Maven__net_sourceforge_owlapi_owlapi_impl_3_4_10.xml
@@ -0,0 +1,13 @@
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new file mode 100644
index 0000000..b223003
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diff --git a/.idea/libraries/Maven__net_sourceforge_owlapi_owlapi_parsers_3_4_10.xml b/.idea/libraries/Maven__net_sourceforge_owlapi_owlapi_parsers_3_4_10.xml
new file mode 100644
index 0000000..1576413
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new file mode 100644
index 0000000..bf8a4d0
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new file mode 100644
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new file mode 100644
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new file mode 100644
index 0000000..dd22d4a
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new file mode 100644
index 0000000..7889ad6
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new file mode 100644
index 0000000..45725f9
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diff --git a/.idea/libraries/Maven__org_openrdf_sesame_sesame_query_2_7_13.xml b/.idea/libraries/Maven__org_openrdf_sesame_sesame_query_2_7_13.xml
new file mode 100644
index 0000000..889e8b1
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new file mode 100644
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new file mode 100644
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new file mode 100644
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new file mode 100644
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new file mode 100644
index 0000000..a60664a
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diff --git a/.idea/libraries/Maven__org_openrdf_sesame_sesame_repository_api_2_7_13.xml b/.idea/libraries/Maven__org_openrdf_sesame_sesame_repository_api_2_7_13.xml
new file mode 100644
index 0000000..3898d28
--- /dev/null
+++ b/.idea/libraries/Maven__org_openrdf_sesame_sesame_repository_api_2_7_13.xml
@@ -0,0 +1,13 @@
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13</component> \ No newline at end of file
diff --git a/.idea/libraries/Maven__org_openrdf_sesame_sesame_repository_contextaware_2_7_13.xml b/.idea/libraries/Maven__org_openrdf_sesame_sesame_repository_contextaware_2_7_13.xml
new file mode 100644
index 0000000..ff88a73
--- /dev/null
+++ b/.idea/libraries/Maven__org_openrdf_sesame_sesame_repository_contextaware_2_7_13.xml
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diff --git a/.idea/libraries/Maven__org_openrdf_sesame_sesame_repository_dataset_2_7_13.xml b/.idea/libraries/Maven__org_openrdf_sesame_sesame_repository_dataset_2_7_13.xml
new file mode 100644
index 0000000..e6a6616
--- /dev/null
+++ b/.idea/libraries/Maven__org_openrdf_sesame_sesame_repository_dataset_2_7_13.xml
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12 </library>
13</component> \ No newline at end of file
diff --git a/.idea/libraries/Maven__org_openrdf_sesame_sesame_repository_event_2_7_13.xml b/.idea/libraries/Maven__org_openrdf_sesame_sesame_repository_event_2_7_13.xml
new file mode 100644
index 0000000..15a5630
--- /dev/null
+++ b/.idea/libraries/Maven__org_openrdf_sesame_sesame_repository_event_2_7_13.xml
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13</component> \ No newline at end of file
diff --git a/.idea/libraries/Maven__org_openrdf_sesame_sesame_repository_http_2_7_13.xml b/.idea/libraries/Maven__org_openrdf_sesame_sesame_repository_http_2_7_13.xml
new file mode 100644
index 0000000..38165f2
--- /dev/null
+++ b/.idea/libraries/Maven__org_openrdf_sesame_sesame_repository_http_2_7_13.xml
@@ -0,0 +1,13 @@
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6 <JAVADOC>
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12 </library>
13</component> \ No newline at end of file
diff --git a/.idea/libraries/Maven__org_openrdf_sesame_sesame_repository_manager_2_7_13.xml b/.idea/libraries/Maven__org_openrdf_sesame_sesame_repository_manager_2_7_13.xml
new file mode 100644
index 0000000..cb9ecc6
--- /dev/null
+++ b/.idea/libraries/Maven__org_openrdf_sesame_sesame_repository_manager_2_7_13.xml
@@ -0,0 +1,13 @@
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13</component> \ No newline at end of file
diff --git a/.idea/libraries/Maven__org_openrdf_sesame_sesame_repository_sail_2_7_13.xml b/.idea/libraries/Maven__org_openrdf_sesame_sesame_repository_sail_2_7_13.xml
new file mode 100644
index 0000000..0bdac86
--- /dev/null
+++ b/.idea/libraries/Maven__org_openrdf_sesame_sesame_repository_sail_2_7_13.xml
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2 <library name="Maven: org.openrdf.sesame:sesame-repository-sail:2.7.13">
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12 </library>
13</component> \ No newline at end of file
diff --git a/.idea/libraries/Maven__org_openrdf_sesame_sesame_repository_sparql_2_7_13.xml b/.idea/libraries/Maven__org_openrdf_sesame_sesame_repository_sparql_2_7_13.xml
new file mode 100644
index 0000000..bf6a5e1
--- /dev/null
+++ b/.idea/libraries/Maven__org_openrdf_sesame_sesame_repository_sparql_2_7_13.xml
@@ -0,0 +1,13 @@
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diff --git a/.idea/libraries/Maven__org_openrdf_sesame_sesame_rio_api_2_7_13.xml b/.idea/libraries/Maven__org_openrdf_sesame_sesame_rio_api_2_7_13.xml
new file mode 100644
index 0000000..2db30bf
--- /dev/null
+++ b/.idea/libraries/Maven__org_openrdf_sesame_sesame_rio_api_2_7_13.xml
@@ -0,0 +1,13 @@
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13</component> \ No newline at end of file
diff --git a/.idea/libraries/Maven__org_openrdf_sesame_sesame_rio_binary_2_7_13.xml b/.idea/libraries/Maven__org_openrdf_sesame_sesame_rio_binary_2_7_13.xml
new file mode 100644
index 0000000..03c46cf
--- /dev/null
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@@ -0,0 +1,13 @@
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12 </library>
13</component> \ No newline at end of file
diff --git a/.idea/libraries/Maven__org_openrdf_sesame_sesame_rio_datatypes_2_7_13.xml b/.idea/libraries/Maven__org_openrdf_sesame_sesame_rio_datatypes_2_7_13.xml
new file mode 100644
index 0000000..c5c5088
--- /dev/null
+++ b/.idea/libraries/Maven__org_openrdf_sesame_sesame_rio_datatypes_2_7_13.xml
@@ -0,0 +1,13 @@
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13</component> \ No newline at end of file
diff --git a/.idea/libraries/Maven__org_openrdf_sesame_sesame_rio_languages_2_7_13.xml b/.idea/libraries/Maven__org_openrdf_sesame_sesame_rio_languages_2_7_13.xml
new file mode 100644
index 0000000..825799e
--- /dev/null
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@@ -0,0 +1,13 @@
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2 <library name="Maven: org.openrdf.sesame:sesame-rio-languages:2.7.13">
3 <CLASSES>
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6 <JAVADOC>
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8 </JAVADOC>
9 <SOURCES>
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13</component> \ No newline at end of file
diff --git a/.idea/libraries/Maven__org_openrdf_sesame_sesame_rio_n3_2_7_13.xml b/.idea/libraries/Maven__org_openrdf_sesame_sesame_rio_n3_2_7_13.xml
new file mode 100644
index 0000000..287d1c8
--- /dev/null
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diff --git a/.idea/libraries/Maven__org_openrdf_sesame_sesame_rio_nquads_2_7_13.xml b/.idea/libraries/Maven__org_openrdf_sesame_sesame_rio_nquads_2_7_13.xml
new file mode 100644
index 0000000..a6de600
--- /dev/null
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diff --git a/.idea/libraries/Maven__org_openrdf_sesame_sesame_rio_ntriples_2_7_13.xml b/.idea/libraries/Maven__org_openrdf_sesame_sesame_rio_ntriples_2_7_13.xml
new file mode 100644
index 0000000..4a2ef50
--- /dev/null
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diff --git a/.idea/libraries/Maven__org_openrdf_sesame_sesame_rio_rdfjson_2_7_13.xml b/.idea/libraries/Maven__org_openrdf_sesame_sesame_rio_rdfjson_2_7_13.xml
new file mode 100644
index 0000000..8a6d5a4
--- /dev/null
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6 <JAVADOC>
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diff --git a/.idea/libraries/Maven__org_openrdf_sesame_sesame_rio_rdfxml_2_7_13.xml b/.idea/libraries/Maven__org_openrdf_sesame_sesame_rio_rdfxml_2_7_13.xml
new file mode 100644
index 0000000..53bdb15
--- /dev/null
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diff --git a/.idea/libraries/Maven__org_openrdf_sesame_sesame_rio_trig_2_7_13.xml b/.idea/libraries/Maven__org_openrdf_sesame_sesame_rio_trig_2_7_13.xml
new file mode 100644
index 0000000..736a55d
--- /dev/null
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@@ -0,0 +1,13 @@
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12 </library>
13</component> \ No newline at end of file
diff --git a/.idea/libraries/Maven__org_openrdf_sesame_sesame_rio_trix_2_7_13.xml b/.idea/libraries/Maven__org_openrdf_sesame_sesame_rio_trix_2_7_13.xml
new file mode 100644
index 0000000..8045595
--- /dev/null
+++ b/.idea/libraries/Maven__org_openrdf_sesame_sesame_rio_trix_2_7_13.xml
@@ -0,0 +1,13 @@
1<component name="libraryTable">
2 <library name="Maven: org.openrdf.sesame:sesame-rio-trix:2.7.13">
3 <CLASSES>
4 <root url="jar://$MAVEN_REPOSITORY$/org/openrdf/sesame/sesame-rio-trix/2.7.13/sesame-rio-trix-2.7.13.jar!/" />
5 </CLASSES>
6 <JAVADOC>
7 <root url="jar://$MAVEN_REPOSITORY$/org/openrdf/sesame/sesame-rio-trix/2.7.13/sesame-rio-trix-2.7.13-javadoc.jar!/" />
8 </JAVADOC>
9 <SOURCES>
10 <root url="jar://$MAVEN_REPOSITORY$/org/openrdf/sesame/sesame-rio-trix/2.7.13/sesame-rio-trix-2.7.13-sources.jar!/" />
11 </SOURCES>
12 </library>
13</component> \ No newline at end of file
diff --git a/.idea/libraries/Maven__org_openrdf_sesame_sesame_rio_turtle_2_7_13.xml b/.idea/libraries/Maven__org_openrdf_sesame_sesame_rio_turtle_2_7_13.xml
new file mode 100644
index 0000000..857a710
--- /dev/null
+++ b/.idea/libraries/Maven__org_openrdf_sesame_sesame_rio_turtle_2_7_13.xml
@@ -0,0 +1,13 @@
1<component name="libraryTable">
2 <library name="Maven: org.openrdf.sesame:sesame-rio-turtle:2.7.13">
3 <CLASSES>
4 <root url="jar://$MAVEN_REPOSITORY$/org/openrdf/sesame/sesame-rio-turtle/2.7.13/sesame-rio-turtle-2.7.13.jar!/" />
5 </CLASSES>
6 <JAVADOC>
7 <root url="jar://$MAVEN_REPOSITORY$/org/openrdf/sesame/sesame-rio-turtle/2.7.13/sesame-rio-turtle-2.7.13-javadoc.jar!/" />
8 </JAVADOC>
9 <SOURCES>
10 <root url="jar://$MAVEN_REPOSITORY$/org/openrdf/sesame/sesame-rio-turtle/2.7.13/sesame-rio-turtle-2.7.13-sources.jar!/" />
11 </SOURCES>
12 </library>
13</component> \ No newline at end of file
diff --git a/.idea/libraries/Maven__org_openrdf_sesame_sesame_runtime_2_7_13.xml b/.idea/libraries/Maven__org_openrdf_sesame_sesame_runtime_2_7_13.xml
new file mode 100644
index 0000000..fbbc6ab
--- /dev/null
+++ b/.idea/libraries/Maven__org_openrdf_sesame_sesame_runtime_2_7_13.xml
@@ -0,0 +1,13 @@
1<component name="libraryTable">
2 <library name="Maven: org.openrdf.sesame:sesame-runtime:2.7.13">
3 <CLASSES>
4 <root url="jar://$MAVEN_REPOSITORY$/org/openrdf/sesame/sesame-runtime/2.7.13/sesame-runtime-2.7.13.jar!/" />
5 </CLASSES>
6 <JAVADOC>
7 <root url="jar://$MAVEN_REPOSITORY$/org/openrdf/sesame/sesame-runtime/2.7.13/sesame-runtime-2.7.13-javadoc.jar!/" />
8 </JAVADOC>
9 <SOURCES>
10 <root url="jar://$MAVEN_REPOSITORY$/org/openrdf/sesame/sesame-runtime/2.7.13/sesame-runtime-2.7.13-sources.jar!/" />
11 </SOURCES>
12 </library>
13</component> \ No newline at end of file
diff --git a/.idea/libraries/Maven__org_openrdf_sesame_sesame_sail_api_2_7_13.xml b/.idea/libraries/Maven__org_openrdf_sesame_sesame_sail_api_2_7_13.xml
new file mode 100644
index 0000000..e8ba5bc
--- /dev/null
+++ b/.idea/libraries/Maven__org_openrdf_sesame_sesame_sail_api_2_7_13.xml
@@ -0,0 +1,13 @@
1<component name="libraryTable">
2 <library name="Maven: org.openrdf.sesame:sesame-sail-api:2.7.13">
3 <CLASSES>
4 <root url="jar://$MAVEN_REPOSITORY$/org/openrdf/sesame/sesame-sail-api/2.7.13/sesame-sail-api-2.7.13.jar!/" />
5 </CLASSES>
6 <JAVADOC>
7 <root url="jar://$MAVEN_REPOSITORY$/org/openrdf/sesame/sesame-sail-api/2.7.13/sesame-sail-api-2.7.13-javadoc.jar!/" />
8 </JAVADOC>
9 <SOURCES>
10 <root url="jar://$MAVEN_REPOSITORY$/org/openrdf/sesame/sesame-sail-api/2.7.13/sesame-sail-api-2.7.13-sources.jar!/" />
11 </SOURCES>
12 </library>
13</component> \ No newline at end of file
diff --git a/.idea/libraries/Maven__org_openrdf_sesame_sesame_sail_federation_2_7_13.xml b/.idea/libraries/Maven__org_openrdf_sesame_sesame_sail_federation_2_7_13.xml
new file mode 100644
index 0000000..9483bf5
--- /dev/null
+++ b/.idea/libraries/Maven__org_openrdf_sesame_sesame_sail_federation_2_7_13.xml
@@ -0,0 +1,13 @@
1<component name="libraryTable">
2 <library name="Maven: org.openrdf.sesame:sesame-sail-federation:2.7.13">
3 <CLASSES>
4 <root url="jar://$MAVEN_REPOSITORY$/org/openrdf/sesame/sesame-sail-federation/2.7.13/sesame-sail-federation-2.7.13.jar!/" />
5 </CLASSES>
6 <JAVADOC>
7 <root url="jar://$MAVEN_REPOSITORY$/org/openrdf/sesame/sesame-sail-federation/2.7.13/sesame-sail-federation-2.7.13-javadoc.jar!/" />
8 </JAVADOC>
9 <SOURCES>
10 <root url="jar://$MAVEN_REPOSITORY$/org/openrdf/sesame/sesame-sail-federation/2.7.13/sesame-sail-federation-2.7.13-sources.jar!/" />
11 </SOURCES>
12 </library>
13</component> \ No newline at end of file
diff --git a/.idea/libraries/Maven__org_openrdf_sesame_sesame_sail_inferencer_2_7_13.xml b/.idea/libraries/Maven__org_openrdf_sesame_sesame_sail_inferencer_2_7_13.xml
new file mode 100644
index 0000000..4d09415
--- /dev/null
+++ b/.idea/libraries/Maven__org_openrdf_sesame_sesame_sail_inferencer_2_7_13.xml
@@ -0,0 +1,13 @@
1<component name="libraryTable">
2 <library name="Maven: org.openrdf.sesame:sesame-sail-inferencer:2.7.13">
3 <CLASSES>
4 <root url="jar://$MAVEN_REPOSITORY$/org/openrdf/sesame/sesame-sail-inferencer/2.7.13/sesame-sail-inferencer-2.7.13.jar!/" />
5 </CLASSES>
6 <JAVADOC>
7 <root url="jar://$MAVEN_REPOSITORY$/org/openrdf/sesame/sesame-sail-inferencer/2.7.13/sesame-sail-inferencer-2.7.13-javadoc.jar!/" />
8 </JAVADOC>
9 <SOURCES>
10 <root url="jar://$MAVEN_REPOSITORY$/org/openrdf/sesame/sesame-sail-inferencer/2.7.13/sesame-sail-inferencer-2.7.13-sources.jar!/" />
11 </SOURCES>
12 </library>
13</component> \ No newline at end of file
diff --git a/.idea/libraries/Maven__org_openrdf_sesame_sesame_sail_memory_2_7_13.xml b/.idea/libraries/Maven__org_openrdf_sesame_sesame_sail_memory_2_7_13.xml
new file mode 100644
index 0000000..1bbe45c
--- /dev/null
+++ b/.idea/libraries/Maven__org_openrdf_sesame_sesame_sail_memory_2_7_13.xml
@@ -0,0 +1,13 @@
1<component name="libraryTable">
2 <library name="Maven: org.openrdf.sesame:sesame-sail-memory:2.7.13">
3 <CLASSES>
4 <root url="jar://$MAVEN_REPOSITORY$/org/openrdf/sesame/sesame-sail-memory/2.7.13/sesame-sail-memory-2.7.13.jar!/" />
5 </CLASSES>
6 <JAVADOC>
7 <root url="jar://$MAVEN_REPOSITORY$/org/openrdf/sesame/sesame-sail-memory/2.7.13/sesame-sail-memory-2.7.13-javadoc.jar!/" />
8 </JAVADOC>
9 <SOURCES>
10 <root url="jar://$MAVEN_REPOSITORY$/org/openrdf/sesame/sesame-sail-memory/2.7.13/sesame-sail-memory-2.7.13-sources.jar!/" />
11 </SOURCES>
12 </library>
13</component> \ No newline at end of file
diff --git a/.idea/libraries/Maven__org_openrdf_sesame_sesame_sail_nativerdf_2_7_13.xml b/.idea/libraries/Maven__org_openrdf_sesame_sesame_sail_nativerdf_2_7_13.xml
new file mode 100644
index 0000000..da24cb2
--- /dev/null
+++ b/.idea/libraries/Maven__org_openrdf_sesame_sesame_sail_nativerdf_2_7_13.xml
@@ -0,0 +1,13 @@
1<component name="libraryTable">
2 <library name="Maven: org.openrdf.sesame:sesame-sail-nativerdf:2.7.13">
3 <CLASSES>
4 <root url="jar://$MAVEN_REPOSITORY$/org/openrdf/sesame/sesame-sail-nativerdf/2.7.13/sesame-sail-nativerdf-2.7.13.jar!/" />
5 </CLASSES>
6 <JAVADOC>
7 <root url="jar://$MAVEN_REPOSITORY$/org/openrdf/sesame/sesame-sail-nativerdf/2.7.13/sesame-sail-nativerdf-2.7.13-javadoc.jar!/" />
8 </JAVADOC>
9 <SOURCES>
10 <root url="jar://$MAVEN_REPOSITORY$/org/openrdf/sesame/sesame-sail-nativerdf/2.7.13/sesame-sail-nativerdf-2.7.13-sources.jar!/" />
11 </SOURCES>
12 </library>
13</component> \ No newline at end of file
diff --git a/.idea/libraries/Maven__org_openrdf_sesame_sesame_sail_rdbms_2_7_13.xml b/.idea/libraries/Maven__org_openrdf_sesame_sesame_sail_rdbms_2_7_13.xml
new file mode 100644
index 0000000..b378c3f
--- /dev/null
+++ b/.idea/libraries/Maven__org_openrdf_sesame_sesame_sail_rdbms_2_7_13.xml
@@ -0,0 +1,13 @@
1<component name="libraryTable">
2 <library name="Maven: org.openrdf.sesame:sesame-sail-rdbms:2.7.13">
3 <CLASSES>
4 <root url="jar://$MAVEN_REPOSITORY$/org/openrdf/sesame/sesame-sail-rdbms/2.7.13/sesame-sail-rdbms-2.7.13.jar!/" />
5 </CLASSES>
6 <JAVADOC>
7 <root url="jar://$MAVEN_REPOSITORY$/org/openrdf/sesame/sesame-sail-rdbms/2.7.13/sesame-sail-rdbms-2.7.13-javadoc.jar!/" />
8 </JAVADOC>
9 <SOURCES>
10 <root url="jar://$MAVEN_REPOSITORY$/org/openrdf/sesame/sesame-sail-rdbms/2.7.13/sesame-sail-rdbms-2.7.13-sources.jar!/" />
11 </SOURCES>
12 </library>
13</component> \ No newline at end of file
diff --git a/.idea/libraries/Maven__org_openrdf_sesame_sesame_util_2_7_13.xml b/.idea/libraries/Maven__org_openrdf_sesame_sesame_util_2_7_13.xml
new file mode 100644
index 0000000..5c7b506
--- /dev/null
+++ b/.idea/libraries/Maven__org_openrdf_sesame_sesame_util_2_7_13.xml
@@ -0,0 +1,13 @@
1<component name="libraryTable">
2 <library name="Maven: org.openrdf.sesame:sesame-util:2.7.13">
3 <CLASSES>
4 <root url="jar://$MAVEN_REPOSITORY$/org/openrdf/sesame/sesame-util/2.7.13/sesame-util-2.7.13.jar!/" />
5 </CLASSES>
6 <JAVADOC>
7 <root url="jar://$MAVEN_REPOSITORY$/org/openrdf/sesame/sesame-util/2.7.13/sesame-util-2.7.13-javadoc.jar!/" />
8 </JAVADOC>
9 <SOURCES>
10 <root url="jar://$MAVEN_REPOSITORY$/org/openrdf/sesame/sesame-util/2.7.13/sesame-util-2.7.13-sources.jar!/" />
11 </SOURCES>
12 </library>
13</component> \ No newline at end of file
diff --git a/.idea/libraries/Maven__org_slf4j_slf4j_api_1_6_1.xml b/.idea/libraries/Maven__org_slf4j_slf4j_api_1_6_1.xml
new file mode 100644
index 0000000..38036e9
--- /dev/null
+++ b/.idea/libraries/Maven__org_slf4j_slf4j_api_1_6_1.xml
@@ -0,0 +1,13 @@
1<component name="libraryTable">
2 <library name="Maven: org.slf4j:slf4j-api:1.6.1">
3 <CLASSES>
4 <root url="jar://$MAVEN_REPOSITORY$/org/slf4j/slf4j-api/1.6.1/slf4j-api-1.6.1.jar!/" />
5 </CLASSES>
6 <JAVADOC>
7 <root url="jar://$MAVEN_REPOSITORY$/org/slf4j/slf4j-api/1.6.1/slf4j-api-1.6.1-javadoc.jar!/" />
8 </JAVADOC>
9 <SOURCES>
10 <root url="jar://$MAVEN_REPOSITORY$/org/slf4j/slf4j-api/1.6.1/slf4j-api-1.6.1-sources.jar!/" />
11 </SOURCES>
12 </library>
13</component> \ No newline at end of file
diff --git a/.idea/libraries/Maven__org_testng_testng_6_7.xml b/.idea/libraries/Maven__org_testng_testng_6_7.xml
new file mode 100644
index 0000000..264ea06
--- /dev/null
+++ b/.idea/libraries/Maven__org_testng_testng_6_7.xml
@@ -0,0 +1,13 @@
1<component name="libraryTable">
2 <library name="Maven: org.testng:testng:6.7">
3 <CLASSES>
4 <root url="jar://$MAVEN_REPOSITORY$/org/testng/testng/6.7/testng-6.7.jar!/" />
5 </CLASSES>
6 <JAVADOC>
7 <root url="jar://$MAVEN_REPOSITORY$/org/testng/testng/6.7/testng-6.7-javadoc.jar!/" />
8 </JAVADOC>
9 <SOURCES>
10 <root url="jar://$MAVEN_REPOSITORY$/org/testng/testng/6.7/testng-6.7-sources.jar!/" />
11 </SOURCES>
12 </library>
13</component> \ No newline at end of file
diff --git a/.idea/libraries/Maven__org_yaml_snakeyaml_1_6.xml b/.idea/libraries/Maven__org_yaml_snakeyaml_1_6.xml
new file mode 100644
index 0000000..0f8bd19
--- /dev/null
+++ b/.idea/libraries/Maven__org_yaml_snakeyaml_1_6.xml
@@ -0,0 +1,13 @@
1<component name="libraryTable">
2 <library name="Maven: org.yaml:snakeyaml:1.6">
3 <CLASSES>
4 <root url="jar://$MAVEN_REPOSITORY$/org/yaml/snakeyaml/1.6/snakeyaml-1.6.jar!/" />
5 </CLASSES>
6 <JAVADOC>
7 <root url="jar://$MAVEN_REPOSITORY$/org/yaml/snakeyaml/1.6/snakeyaml-1.6-javadoc.jar!/" />
8 </JAVADOC>
9 <SOURCES>
10 <root url="jar://$MAVEN_REPOSITORY$/org/yaml/snakeyaml/1.6/snakeyaml-1.6-sources.jar!/" />
11 </SOURCES>
12 </library>
13</component> \ No newline at end of file
diff --git a/src/log4j.properties b/config/log4j.properties
index 25da4d4..25da4d4 100644
--- a/src/log4j.properties
+++ b/config/log4j.properties
diff --git a/config/test.properties b/config/test.properties
new file mode 100644
index 0000000..c4a25d0
--- /dev/null
+++ b/config/test.properties
@@ -0,0 +1 @@
ontoDir=/home/alessandro/Big_files/Ontologies/ \ No newline at end of file
diff --git a/pom.xml b/pom.xml
index fad1545..096a14d 100644
--- a/pom.xml
+++ b/pom.xml
@@ -83,6 +83,12 @@
83 <version>2.7.13</version> 83 <version>2.7.13</version>
84 </dependency> 84 </dependency>
85 <dependency> 85 <dependency>
86 <groupId>org.openrdf.sesame</groupId>
87 <artifactId>sesame-rio-rdfxml</artifactId>
88 <version>2.7.13</version>
89 <scope>compile</scope>
90 </dependency>
91 <dependency>
86 <groupId>org.apache.jena</groupId> 92 <groupId>org.apache.jena</groupId>
87 <artifactId>jena-arq</artifactId> 93 <artifactId>jena-arq</artifactId>
88 <version>2.12.0</version> 94 <version>2.12.0</version>
@@ -97,5 +103,10 @@
97 <artifactId>jgrapht-jdk1.5</artifactId> 103 <artifactId>jgrapht-jdk1.5</artifactId>
98 <version>0.7.3</version> 104 <version>0.7.3</version>
99 </dependency> 105 </dependency>
106 <dependency>
107 <groupId>org.testng</groupId>
108 <artifactId>testng</artifactId>
109 <version>6.7</version>
110 </dependency>
100 </dependencies> 111 </dependencies>
101</project> 112</project>
diff --git a/src/org/semanticweb/karma2/model/cqparser/ConjunctiveQueryWalker.java b/src/org/semanticweb/karma2/model/cqparser/ConjunctiveQueryWalker.java
index f95ac12..f10b761 100644
--- a/src/org/semanticweb/karma2/model/cqparser/ConjunctiveQueryWalker.java
+++ b/src/org/semanticweb/karma2/model/cqparser/ConjunctiveQueryWalker.java
@@ -67,7 +67,7 @@ public class ConjunctiveQueryWalker {
67 assert (prefixList.getType() == ConjunctiveQueryLexer.PREFIX_LIST); 67 assert (prefixList.getType() == ConjunctiveQueryLexer.PREFIX_LIST);
68 Prefixes prefixes = walkPrefixList(prefixList); 68 Prefixes prefixes = walkPrefixList(prefixList);
69 CommonTree rulebody = iterator.next(); 69 CommonTree rulebody = iterator.next();
70 assert (prefixList.getType() == ConjunctiveQueryLexer.RULE); 70 assert (rulebody.getType() == ConjunctiveQueryLexer.RULE);
71 return walkRuleNode(rulebody, prefixes); 71 return walkRuleNode(rulebody, prefixes);
72 72
73 } 73 }
diff --git a/src/uk/ac/ox/cs/pagoda/util/Utility.java b/src/uk/ac/ox/cs/pagoda/util/Utility.java
index cb05de4..7138ca9 100644
--- a/src/uk/ac/ox/cs/pagoda/util/Utility.java
+++ b/src/uk/ac/ox/cs/pagoda/util/Utility.java
@@ -10,6 +10,8 @@ import java.io.IOException;
10import java.io.InputStreamReader; 10import java.io.InputStreamReader;
11import java.io.OutputStreamWriter; 11import java.io.OutputStreamWriter;
12import java.io.PrintStream; 12import java.io.PrintStream;
13import java.nio.file.Files;
14import java.nio.file.Paths;
13import java.text.SimpleDateFormat; 15import java.text.SimpleDateFormat;
14import java.time.LocalDateTime; 16import java.time.LocalDateTime;
15import java.time.format.DateTimeFormatter; 17import java.time.format.DateTimeFormatter;
@@ -24,9 +26,11 @@ import java.util.Stack;
24import org.apache.log4j.Logger; 26import org.apache.log4j.Logger;
25import org.semanticweb.HermiT.model.Atom; 27import org.semanticweb.HermiT.model.Atom;
26 28
29import static java.nio.file.StandardCopyOption.REPLACE_EXISTING;
30
27public class Utility { 31public class Utility {
28 32
29 private static final Logger LOGS = null; // Logger.getLogger(""); 33 private static final Logger LOGS = Logger.getLogger("PAGOdA");
30 34
31 public static final String JAVA_FILE_SEPARATOR = "/"; 35 public static final String JAVA_FILE_SEPARATOR = "/";
32 public static final String FILE_SEPARATOR = System.getProperty("file.separator"); 36 public static final String FILE_SEPARATOR = System.getProperty("file.separator");
@@ -255,4 +259,14 @@ public class Utility {
255 return iri.replace(FILE_SEPARATOR, JAVA_FILE_SEPARATOR).replace(" ", "%20"); 259 return iri.replace(FILE_SEPARATOR, JAVA_FILE_SEPARATOR).replace(" ", "%20");
256 } 260 }
257 261
262 public static String combinePaths(String path1, String path2) {
263 File file1 = new File(path1);
264 File file2 = new File(file1, path2);
265 return file2.getPath();
266 }
267
268 public static void copyFile(String src, String dst) throws IOException {
269 Files.copy(Paths.get(src), Paths.get(dst), REPLACE_EXISTING);
270 }
271
258} 272}
diff --git a/target/.gitignore b/target/.gitignore
deleted file mode 100644
index 4569837..0000000
--- a/target/.gitignore
+++ /dev/null
@@ -1,2 +0,0 @@
1/classes/
2/test-classes/
diff --git a/test/AllTests.xml b/test/AllTests.xml
new file mode 100644
index 0000000..8ce5fcf
--- /dev/null
+++ b/test/AllTests.xml
@@ -0,0 +1,12 @@
1<?xml version="1.0" encoding="UTF-8"?>
2<!DOCTYPE suite SYSTEM "http://testng.org/testng-1.0.dtd" >
3
4<suite name="AllTests">
5
6 <test name="PagodaUOBM">
7 <classes>
8 <class name="uk.ac.ox.cs.pagoda.test_units.PagodaUOBM" />
9 </classes>
10 </test>
11
12</suite> \ No newline at end of file
diff --git a/test/FullEvaluation.xml b/test/FullEvaluation.xml
new file mode 100644
index 0000000..f0f047d
--- /dev/null
+++ b/test/FullEvaluation.xml
@@ -0,0 +1,18 @@
1<?xml version="1.0" encoding="UTF-8"?>
2<!DOCTYPE suite SYSTEM "http://testng.org/testng-1.0.dtd" >
3
4<suite name="AllTests">
5
6 <test name="LightEvaluation">
7 <classes>
8 <class name="uk.ac.ox.cs.pagoda.test_units.LightEvaluation" />
9 </classes>
10 </test>
11
12 <test name="CostEvaluation">
13 <classes>
14 <class name="uk.ac.ox.cs.pagoda.test_units.CostEvaluation" />
15 </classes>
16 </test>
17
18</suite> \ No newline at end of file
diff --git a/test/uk/ac/ox/cs/pagoda/junit/AllTests.java b/test/uk/ac/ox/cs/pagoda/junit/AllTests.java
deleted file mode 100644
index fb38787..0000000
--- a/test/uk/ac/ox/cs/pagoda/junit/AllTests.java
+++ /dev/null
@@ -1,48 +0,0 @@
1package uk.ac.ox.cs.pagoda.junit;
2
3import java.io.BufferedWriter;
4import java.io.FileInputStream;
5import java.io.FileNotFoundException;
6import java.io.FileOutputStream;
7import java.io.IOException;
8import java.io.InputStream;
9import java.io.OutputStream;
10import java.io.OutputStreamWriter;
11
12import org.junit.runner.RunWith;
13import org.junit.runners.Suite;
14import org.junit.runners.Suite.SuiteClasses;
15
16@RunWith(Suite.class)
17@SuiteClasses({ PagodaUOBM.class
18 })
19public class AllTests {
20
21 public static void copy(String source, String dest) {
22 InputStream is = null;
23 OutputStream os = null;
24 try {
25 is = new FileInputStream(source);
26 os = new FileOutputStream(dest);
27 byte[] buffer = new byte[1024];
28 int length;
29 while ((length = is.read(buffer)) > 0) {
30 os.write(buffer, 0, length);
31 }
32 is.close();
33 os.close();
34
35 BufferedWriter writer = new BufferedWriter(new OutputStreamWriter(new FileOutputStream(source)));
36 writer.write("");
37 writer.close();
38 } catch (FileNotFoundException e) {
39 e.printStackTrace();
40 } catch (IOException e) {
41 e.printStackTrace();
42 }
43
44// File src = new File(source);
45// src.delete();
46 }
47
48}
diff --git a/test/uk/ac/ox/cs/pagoda/junit/FullEvaluation.java b/test/uk/ac/ox/cs/pagoda/junit/FullEvaluation.java
deleted file mode 100644
index 3406ed2..0000000
--- a/test/uk/ac/ox/cs/pagoda/junit/FullEvaluation.java
+++ /dev/null
@@ -1,14 +0,0 @@
1package uk.ac.ox.cs.pagoda.junit;
2
3import org.junit.runner.RunWith;
4import org.junit.runners.Suite;
5import org.junit.runners.Suite.SuiteClasses;
6
7@RunWith(Suite.class)
8@SuiteClasses({ LightEvaluation.class,
9 CostEvaluation.class
10 })
11
12public class FullEvaluation {
13
14}
diff --git a/test/uk/ac/ox/cs/pagoda/junit/PagodaLUBM.java b/test/uk/ac/ox/cs/pagoda/junit/PagodaLUBM.java
deleted file mode 100644
index f8fef0e..0000000
--- a/test/uk/ac/ox/cs/pagoda/junit/PagodaLUBM.java
+++ /dev/null
@@ -1,38 +0,0 @@
1package uk.ac.ox.cs.pagoda.junit;
2
3import static org.junit.Assert.*;
4
5import org.junit.Test;
6
7import uk.ac.ox.cs.pagoda.tester.PagodaTester;
8import uk.ac.ox.cs.pagoda.tester.Statistics;
9
10public class PagodaLUBM {
11
12 public void test_all(int number) {
13 PagodaTester.main(
14 PagodaTester.onto_dir + "lubm/univ-bench.owl",
15 PagodaTester.onto_dir + "lubm/data/lubm" + number + ".ttl",
16 PagodaTester.onto_dir + "lubm/queries/test_all_pagoda.sparql"
17 );
18
19 AllTests.copy("log4j.log", "output/jair/lubm" + number + ".out");
20 }
21
22 @Test
23 public void test1() { test_all(1); }
24
25 public void test() {
26 int number = 100;
27 test_all(number);
28 }
29
30 public void check(int number) {
31 Statistics stat = new Statistics("output/log4j.log");
32 String diff = stat.diff("results-backup/benchmark/lubm" + number + ".out");
33 AllTests.copy("output/log4j.log", "results-backup/current/lubm" + number + ".out");
34 if (!diff.isEmpty())
35 fail(diff);
36 }
37
38}
diff --git a/test/uk/ac/ox/cs/pagoda/junit/PagodaUOBM.java b/test/uk/ac/ox/cs/pagoda/junit/PagodaUOBM.java
deleted file mode 100644
index 5b56c6d..0000000
--- a/test/uk/ac/ox/cs/pagoda/junit/PagodaUOBM.java
+++ /dev/null
@@ -1,48 +0,0 @@
1package uk.ac.ox.cs.pagoda.junit;
2
3import org.junit.Test;
4
5import uk.ac.ox.cs.pagoda.tester.PagodaTester;
6import uk.ac.ox.cs.pagoda.tester.Statistics;
7
8public class PagodaUOBM {
9
10 public void test_all(int number ) {
11 PagodaTester.main(
12 PagodaTester.onto_dir + "uobm/univ-bench-dl.owl",
13 PagodaTester.onto_dir + "uobm/data/uobm" + number + ".ttl",
14 PagodaTester.onto_dir + "uobm/queries/standard_all_pagoda.sparql"
15// PagodaTester.onto_dir + "uobm/queries/standard_group3_all_less.sparql;" +
16// PagodaTester.onto_dir + "uobm/queries/G3.sparql;" +
17// PagodaTester.onto_dir + "uobm/queries/last.sparql"
18 );
19
20 AllTests.copy("log4j.log", "output/jair/newuobm/uobm" + number + ".out");
21 }
22
23 public void test_upToSum(int number) {
24 PagodaTester.main(
25 PagodaTester.onto_dir + "uobm/univ-bench-dl.owl",
26 PagodaTester.onto_dir + "uobm/data/uobm" + number + ".ttl",
27 PagodaTester.onto_dir + "uobm/queries/standard_group3_all.sparql"
28 );
29
30// AllTests.copy("log4j.log", "output/jair/uobm" + number + ".out");
31 }
32
33 @Test
34 public void test1() { test_all(1); }
35
36 public void test500() { test_upToSum(500); }
37
38 public static void main(String... args) {
39 new PagodaUOBM().test_all(1);
40 }
41
42 public void check() {
43 Statistics stat = new Statistics("results-backup/current/uobm1.out");
44 String diff = stat.diff("results-backup/benchmark/uobm1.out");
45 System.out.println(diff);
46 }
47
48}
diff --git a/test/uk/ac/ox/cs/pagoda/junit/ClauseTester.java b/test/uk/ac/ox/cs/pagoda/test_units/ClauseTester.java
index d23f186..a0f16d4 100644
--- a/test/uk/ac/ox/cs/pagoda/junit/ClauseTester.java
+++ b/test/uk/ac/ox/cs/pagoda/test_units/ClauseTester.java
@@ -1,8 +1,5 @@
1package uk.ac.ox.cs.pagoda.junit; 1package uk.ac.ox.cs.pagoda.test_units;
2 2
3import static org.junit.Assert.*;
4
5import org.junit.Test;
6import org.semanticweb.HermiT.model.Atom; 3import org.semanticweb.HermiT.model.Atom;
7import org.semanticweb.HermiT.model.AtomicConcept; 4import org.semanticweb.HermiT.model.AtomicConcept;
8import org.semanticweb.HermiT.model.AtomicRole; 5import org.semanticweb.HermiT.model.AtomicRole;
@@ -13,6 +10,8 @@ import org.semanticweb.owlapi.apibinding.OWLManager;
13import org.semanticweb.owlapi.model.OWLOntology; 10import org.semanticweb.owlapi.model.OWLOntology;
14import org.semanticweb.owlapi.model.OWLOntologyManager; 11import org.semanticweb.owlapi.model.OWLOntologyManager;
15 12
13import org.testng.Assert;
14import org.testng.annotations.Test;
16import uk.ac.ox.cs.pagoda.approx.Clause; 15import uk.ac.ox.cs.pagoda.approx.Clause;
17import uk.ac.ox.cs.pagoda.approx.Clausifier; 16import uk.ac.ox.cs.pagoda.approx.Clausifier;
18 17
@@ -39,7 +38,7 @@ public class ClauseTester {
39 emptyOntology = m.createOntology(); 38 emptyOntology = m.createOntology();
40 } catch (Exception e) { 39 } catch (Exception e) {
41 e.printStackTrace(); 40 e.printStackTrace();
42 fail("failed to create a new ontology"); 41 Assert.fail("failed to create a new ontology");
43 } 42 }
44 Clause c = new Clause(Clausifier.getInstance(emptyOntology), DLClause.create(headAtoms, bodyAtoms)); 43 Clause c = new Clause(Clausifier.getInstance(emptyOntology), DLClause.create(headAtoms, bodyAtoms));
45 System.out.println(c.toString()); 44 System.out.println(c.toString());
@@ -69,7 +68,7 @@ public class ClauseTester {
69 emptyOntology = m.createOntology(); 68 emptyOntology = m.createOntology();
70 } catch (Exception e) { 69 } catch (Exception e) {
71 e.printStackTrace(); 70 e.printStackTrace();
72 fail("failed to create a new ontology"); 71 Assert.fail("failed to create a new ontology");
73 } 72 }
74 Clause c = new Clause(Clausifier.getInstance(emptyOntology), DLClause.create(headAtoms, bodyAtoms)); 73 Clause c = new Clause(Clausifier.getInstance(emptyOntology), DLClause.create(headAtoms, bodyAtoms));
75 System.out.println(c.toString()); 74 System.out.println(c.toString());
@@ -96,7 +95,7 @@ public class ClauseTester {
96 emptyOntology = m.createOntology(); 95 emptyOntology = m.createOntology();
97 } catch (Exception e) { 96 } catch (Exception e) {
98 e.printStackTrace(); 97 e.printStackTrace();
99 fail("failed to create a new ontology"); 98 Assert.fail("failed to create a new ontology");
100 } 99 }
101 Clause c = new Clause(Clausifier.getInstance(emptyOntology), DLClause.create(headAtoms, bodyAtoms)); 100 Clause c = new Clause(Clausifier.getInstance(emptyOntology), DLClause.create(headAtoms, bodyAtoms));
102 System.out.println(c.toString()); 101 System.out.println(c.toString());
@@ -126,7 +125,7 @@ public class ClauseTester {
126 emptyOntology = m.createOntology(); 125 emptyOntology = m.createOntology();
127 } catch (Exception e) { 126 } catch (Exception e) {
128 e.printStackTrace(); 127 e.printStackTrace();
129 fail("failed to create a new ontology"); 128 Assert.fail("failed to create a new ontology");
130 } 129 }
131 Clause c = new Clause(Clausifier.getInstance(emptyOntology), DLClause.create(headAtoms, bodyAtoms)); 130 Clause c = new Clause(Clausifier.getInstance(emptyOntology), DLClause.create(headAtoms, bodyAtoms));
132 System.out.println(c.toString()); 131 System.out.println(c.toString());
@@ -156,7 +155,7 @@ public class ClauseTester {
156 emptyOntology = m.createOntology(); 155 emptyOntology = m.createOntology();
157 } catch (Exception e) { 156 } catch (Exception e) {
158 e.printStackTrace(); 157 e.printStackTrace();
159 fail("failed to create a new ontology"); 158 Assert.fail("failed to create a new ontology");
160 } 159 }
161 Clause c = new Clause(Clausifier.getInstance(emptyOntology), DLClause.create(headAtoms, bodyAtoms)); 160 Clause c = new Clause(Clausifier.getInstance(emptyOntology), DLClause.create(headAtoms, bodyAtoms));
162 System.out.println(c.toString()); 161 System.out.println(c.toString());
diff --git a/test/uk/ac/ox/cs/pagoda/junit/CostEvaluation.java b/test/uk/ac/ox/cs/pagoda/test_units/CostEvaluation.java
index 87b01ed..4e32297 100644
--- a/test/uk/ac/ox/cs/pagoda/junit/CostEvaluation.java
+++ b/test/uk/ac/ox/cs/pagoda/test_units/CostEvaluation.java
@@ -1,8 +1,8 @@
1package uk.ac.ox.cs.pagoda.junit; 1package uk.ac.ox.cs.pagoda.test_units;
2 2
3import org.junit.Test;
4import org.semanticweb.owlapi.model.OWLOntology; 3import org.semanticweb.owlapi.model.OWLOntology;
5 4
5import org.testng.annotations.Test;
6import uk.ac.ox.cs.pagoda.owl.OWLHelper; 6import uk.ac.ox.cs.pagoda.owl.OWLHelper;
7import uk.ac.ox.cs.pagoda.reasoner.QueryReasoner; 7import uk.ac.ox.cs.pagoda.reasoner.QueryReasoner;
8import uk.ac.ox.cs.pagoda.reasoner.QueryReasoner.Type; 8import uk.ac.ox.cs.pagoda.reasoner.QueryReasoner.Type;
diff --git a/test/uk/ac/ox/cs/pagoda/junit/JAIR_PAGOdA.java b/test/uk/ac/ox/cs/pagoda/test_units/JAIR_PAGOdA.java
index 2a148cc..ff616f7 100644
--- a/test/uk/ac/ox/cs/pagoda/junit/JAIR_PAGOdA.java
+++ b/test/uk/ac/ox/cs/pagoda/test_units/JAIR_PAGOdA.java
@@ -1,173 +1,180 @@
1package uk.ac.ox.cs.pagoda.junit; 1package uk.ac.ox.cs.pagoda.test_units;
2
3import org.junit.Test;
4 2
3import org.testng.annotations.Test;
5import uk.ac.ox.cs.pagoda.tester.PagodaTester; 4import uk.ac.ox.cs.pagoda.tester.PagodaTester;
5import uk.ac.ox.cs.pagoda.util.Utility;
6
7import java.io.IOException;
6 8
7public class JAIR_PAGOdA { 9public class JAIR_PAGOdA {
8 10
9 public void lubm1() { 11 @Test
12 public void lubm1() throws IOException {
10 String[] args = new String[] { 13 String[] args = new String[] {
11 PagodaTester.onto_dir + "lubm/univ-bench.owl", 14 PagodaTester.onto_dir + "lubm/univ-bench.owl",
12 PagodaTester.onto_dir + "lubm/data/lubm1.ttl", 15 PagodaTester.onto_dir + "lubm/data/lubm1.ttl",
13 PagodaTester.onto_dir + "lubm/queries/test.sparql" 16 PagodaTester.onto_dir + "lubm/queries/test.sparql"
14 }; 17 };
15 PagodaTester.main(args); 18 PagodaTester.main(args);
16 AllTests.copy("output/log4j.log", "/home/yzhou/java-workspace/test-share/results_new/lubm1/pagoda"); 19 Utility.copyFile("output/log4j.log", "/home/yzhou/java-workspace/test-share/results_new/lubm1/pagoda");
17 } 20 }
18 21
19 22 @Test
20 public void lubm1_conj() { 23 public void lubm1_conj() throws IOException {
21 String[] args = new String[] { 24 String[] args = new String[] {
22 PagodaTester.onto_dir + "lubm/univ-bench.owl", 25 PagodaTester.onto_dir + "lubm/univ-bench.owl",
23 PagodaTester.onto_dir + "lubm/data/lubm1.ttl", 26 PagodaTester.onto_dir + "lubm/data/lubm1.ttl",
24 PagodaTester.onto_dir + "lubm/queries/test_pellet.sparql" 27 PagodaTester.onto_dir + "lubm/queries/test_pellet.sparql"
25 }; 28 };
26 PagodaTester.main(args); 29 PagodaTester.main(args);
27 AllTests.copy("output/log4j.log", "/home/yzhou/java-workspace/test-share/results_new/lubm1/pagoda_conj"); 30 Utility.copyFile("output/log4j.log", "/home/yzhou/java-workspace/test-share/results_new/lubm1/pagoda_conj");
28 } 31 }
29 32
30 33 @Test
31 public void lubm1_rolledUp() { 34 public void lubm1_rolledUp() throws IOException {
32 String[] args = new String[] { 35 String[] args = new String[] {
33 "/home/yzhou/backup/20141212/univ-bench-queries.owl", 36 "/home/yzhou/backup/20141212/univ-bench-queries.owl",
34 PagodaTester.onto_dir + "lubm/data/lubm1.ttl", 37 PagodaTester.onto_dir + "lubm/data/lubm1.ttl",
35 PagodaTester.onto_dir + "lubm/queries/atomic_lubm.sparql" 38 PagodaTester.onto_dir + "lubm/queries/atomic_lubm.sparql"
36 }; 39 };
37 PagodaTester.main(args); 40 PagodaTester.main(args);
38 AllTests.copy("output/log4j.log", "/home/yzhou/java-workspace/test-share/results_new/lubm1/pagoda_rolledUp"); 41 Utility.copyFile("output/log4j.log", "/home/yzhou/java-workspace/test-share/results_new/lubm1/pagoda_rolledUp");
39 } 42 }
40 43
41 44 @Test
42 public void uobm1() { 45 public void uobm1() throws IOException {
43 String[] args = new String[] { 46 String[] args = new String[] {
44 PagodaTester.onto_dir + "uobm/univ-bench-dl.owl", 47 PagodaTester.onto_dir + "uobm/univ-bench-dl.owl",
45 PagodaTester.onto_dir + "uobm/data/uobm1.ttl", 48 PagodaTester.onto_dir + "uobm/data/uobm1.ttl",
46 PagodaTester.onto_dir + "uobm/queries/standard.sparql" 49 PagodaTester.onto_dir + "uobm/queries/standard.sparql"
47 }; 50 };
48 PagodaTester.main(args); 51 PagodaTester.main(args);
49 AllTests.copy("output/log4j.log", "/home/yzhou/java-workspace/test-share/results_new/uobm1/pagoda"); 52 Utility.copyFile("output/log4j.log", "/home/yzhou/java-workspace/test-share/results_new/uobm1/pagoda");
50 } 53 }
51 54
52 55 @Test
53 public void uobm1_conj() { 56 public void uobm1_conj() throws IOException {
54 String[] args = new String[] { 57 String[] args = new String[] {
55 PagodaTester.onto_dir + "uobm/univ-bench-dl.owl", 58 PagodaTester.onto_dir + "uobm/univ-bench-dl.owl",
56 PagodaTester.onto_dir + "uobm/data/uobm1.ttl", 59 PagodaTester.onto_dir + "uobm/data/uobm1.ttl",
57 PagodaTester.onto_dir + "uobm/queries/standard_pellet.sparql" 60 PagodaTester.onto_dir + "uobm/queries/standard_pellet.sparql"
58 }; 61 };
59 PagodaTester.main(args); 62 PagodaTester.main(args);
60 AllTests.copy("output/log4j.log", "/home/yzhou/java-workspace/test-share/results_new/uobm1/pagoda_conj"); 63 Utility.copyFile("output/log4j.log", "/home/yzhou/java-workspace/test-share/results_new/uobm1/pagoda_conj");
61 } 64 }
62 65
63 66 @Test
64 public void uobm1_rolledUp() { 67 public void uobm1_rolledUp() {
65 String[] args = new String[] { 68 String[] args = new String[] {
66 "/home/yzhou/backup/20141212/univ-bench-dl-queries.owl", 69 "/home/yzhou/backup/20141212/univ-bench-dl-queries.owl",
67 PagodaTester.onto_dir + "uobm/data/uobm1.ttl", 70 PagodaTester.onto_dir + "uobm/data/uobm1.ttl",
68 PagodaTester.onto_dir + "uobm/queries/atomic_uobm.sparql" 71 PagodaTester.onto_dir + "uobm/queries/atomic_uobm.sparql"
69 }; 72 };
70 PagodaTester.main(args); 73 PagodaTester.main(args);
71// AllTests.copy("output/log4j.log", "/home/yzhou/java-workspace/test-share/results_new/uobm1/pagoda_rolledUp"); 74// AllTests.copy("output/log4j.log", "/home/yzhou/java-workspace/test-share/results_new/uobm1/pagoda_rolledUp");
72 } 75 }
73 76
74 77 @Test
75 public void fly() { 78 public void fly() {
76 String[] args = new String[] { 79 String[] args = new String[] {
77 PagodaTester.onto_dir + "fly/fly_anatomy_XP_with_GJ_FC_individuals.owl", 80 PagodaTester.onto_dir + "fly/fly_anatomy_XP_with_GJ_FC_individuals.owl",
78 null, 81 null,
79 PagodaTester.onto_dir + "fly/queries/fly_pellet.sparql" 82 PagodaTester.onto_dir + "fly/queries/fly_pellet.sparql"
80 }; 83 };
81 PagodaTester.main(args); 84 PagodaTester.main(args);
82// AllTests.copy("output/log4j.log", "/home/yzhou/java-workspace/test-share/results_new/fly/pagoda"); 85// AllTests.copy("output/log4j.log", "/home/yzhou/java-workspace/test-share/results_new/fly/pagoda");
83 } 86 }
84 87
85 @Test 88 @Test
86 public void fly_conj() { 89 public void fly_conj() throws IOException {
87 String[] args = new String[] { 90 String[] args = new String[] {
88 PagodaTester.onto_dir + "fly/fly_anatomy_XP_with_GJ_FC_individuals.owl", 91 PagodaTester.onto_dir + "fly/fly_anatomy_XP_with_GJ_FC_individuals.owl",
89 null, 92 null,
90 PagodaTester.onto_dir + "fly/queries/fly_pellet.sparql" 93 PagodaTester.onto_dir + "fly/queries/fly_pellet.sparql"
91 }; 94 };
92 PagodaTester.main(args); 95 PagodaTester.main(args);
93 AllTests.copy("output/log4j.log", "/home/yzhou/java-workspace/test-share/results_new/fly/pagoda_conj"); 96 Utility.copyFile("output/log4j.log", "/home/yzhou/java-workspace/test-share/results_new/fly/pagoda_conj");
94 } 97 }
95 98
96 99
97 public void fly_rolledUp() { 100 public void fly_rolledUp() {
98 PagodaTester.main(new String[] { 101 PagodaTester.main(new String[] {
99// PagodaTester.onto_dir + "fly/fly_anatomy_XP_with_GJ_FC_individuals.owl", 102// PagodaTester.onto_dir + "fly/fly_anatomy_XP_with_GJ_FC_individuals.owl",
100 PagodaTester.onto_dir + "fly/fly-all-in-one_rolledUp.owl", 103 PagodaTester.onto_dir + "fly/fly-all-in-one_rolledUp.owl",
101 null, 104 null,
102 PagodaTester.onto_dir + "fly/queries/fly_atomic.sparql" 105 PagodaTester.onto_dir + "fly/queries/fly_atomic.sparql"
103 }); 106 });
104// AllTests.copy("output/log4j.log", "/home/yzhou/java-workspace/test-share/results_new/fly/pagoda_rolledUp"); 107// Utility.copyFile("output/log4j.log", "/home/yzhou/java-workspace/test-share/results_new/fly/pagoda_rolledUp");
105 } 108 }
106 109
107 public void dbpedia() { 110 public void dbpedia() {
108 PagodaTester.main( 111 PagodaTester.main(
109 PagodaTester.onto_dir + "dbpedia/integratedOntology-all-in-one-minus-datatype.owl", 112 PagodaTester.onto_dir + "dbpedia/integratedOntology-all-in-one-minus-datatype.owl",
110 PagodaTester.onto_dir + "dbpedia/data/dbpedia-minus-datatype-new.ttl", 113 PagodaTester.onto_dir + "dbpedia/data/dbpedia-minus-datatype-new.ttl",
111 PagodaTester.onto_dir + "dbpedia/queries/atomic_ground.sparql" 114 PagodaTester.onto_dir + "dbpedia/queries/atomic_ground.sparql"
112 , "dbpedia.ans" 115 , "dbpedia.ans"
113 ); 116 );
114 117
115// AllTests.copy("output/log4j.log", "/home/yzhou/java-workspace/test-share/results_new/dbpedia/pagoda"); 118// Utility.copyFile("output/log4j.log", "/home/yzhou/java-workspace/test-share/results_new/dbpedia/pagoda");
116 } 119 }
117 120
118 public void npd() { 121 public void npd() {
119 PagodaTester.main( 122 PagodaTester.main(
120 PagodaTester.onto_dir + "npd/npd-all-minus-datatype.owl", 123 PagodaTester.onto_dir + "npd/npd-all-minus-datatype.owl",
121 PagodaTester.onto_dir + "npd/data/npd-data-dump-minus-datatype-new.ttl", 124 PagodaTester.onto_dir + "npd/data/npd-data-dump-minus-datatype-new.ttl",
122 PagodaTester.onto_dir + "npd/queries/atomic_ground.sparql" 125 PagodaTester.onto_dir + "npd/queries/atomic_ground.sparql"
123 , "npd.ans" 126 , "npd.ans"
124 ); 127 );
125 128
126// AllTests.copy("output/log4j.log", "/home/yzhou/java-workspace/test-share/results_new/npd/pagoda"); 129// Utility.copyFile("output/log4j.log", "/home/yzhou/java-workspace/test-share/results_new/npd/pagoda");
127 } 130 }
128 131
129 public void reactome() { 132 public void reactome() throws IOException {
130 PagodaTester.main( 133 PagodaTester.main(
131 PagodaTester.onto_dir + "bio2rdf/reactome/biopax-level3-processed.owl", 134 PagodaTester.onto_dir + "bio2rdf/reactome/biopax-level3-processed.owl",
132 PagodaTester.onto_dir + "bio2rdf/reactome/graph sampling/reactome_sample_10.ttl", 135 PagodaTester.onto_dir + "bio2rdf/reactome/graph sampling/reactome_sample_10.ttl",
133// null, 136// null,
134// PagodaTester.onto_dir + "bio2rdf/reactome/queries/atomic_ground.sparql" 137// PagodaTester.onto_dir + "bio2rdf/reactome/queries/atomic_ground.sparql"
135 PagodaTester.onto_dir + "bio2rdf/reactome/queries/example.sparql" 138 PagodaTester.onto_dir + "bio2rdf/reactome/queries/example.sparql"
136 , "pagoda_reactome.ans" 139 , "pagoda_reactome.ans"
137 ); 140 );
138 AllTests.copy("log4j.log", "output/jair/pagoda_reactome.example"); 141 Utility.copyFile("log4j.log", "output/jair/pagoda_reactome.example");
139 142
140// AllTests.copy("output/log4j.log", "/home/yzhou/java-workspace/test-share/results_new/reactome/pagoda_10p"); 143// AllTests.copy("output/log4j.log", "/home/yzhou/java-workspace/test-share/results_new/reactome/pagoda_10p");
141 } 144 }
142 145
143 public void chembl() { 146 public void chembl() throws IOException {
144 PagodaTester.main( 147 PagodaTester.main(
145 PagodaTester.onto_dir + "bio2rdf/chembl/cco-noDPR.ttl", 148 PagodaTester.onto_dir + "bio2rdf/chembl/cco-noDPR.ttl",
146 PagodaTester.onto_dir + "bio2rdf/chembl/graph sampling/sample_1.nt", 149 PagodaTester.onto_dir + "bio2rdf/chembl/graph sampling/sample_1.nt",
147// PagodaTester.onto_dir + "bio2rdf/chembl/queries/atomic_ground.sparql" 150// PagodaTester.onto_dir + "bio2rdf/chembl/queries/atomic_ground.sparql"
148 PagodaTester.onto_dir + "bio2rdf/chembl/queries/example.sparql" 151 PagodaTester.onto_dir + "bio2rdf/chembl/queries/example.sparql"
149 , "pagoda_chembl.ans" 152 , "pagoda_chembl.ans"
150 ); 153 );
151 AllTests.copy("log4j.log", "output/jair/pagoda_chembl.example"); 154 Utility.copyFile("log4j.log", "output/jair/pagoda_chembl.example");
152// AllTests.copy("output/log4j.log", "/home/yzhou/java-workspace/test-share/results_new/chembl/pagoda_1p"); 155// Utility.copyFile("output/log4j.log", "/home/yzhou/java-workspace/test-share/results_new/chembl/pagoda_1p");
153 } 156 }
154 157
155 public void uniprot() { 158 public void uniprot() throws IOException {
156 PagodaTester.main( 159 PagodaTester.main(
157 PagodaTester.onto_dir + "bio2rdf/uniprot/core-sat-processed.owl", 160 PagodaTester.onto_dir + "bio2rdf/uniprot/core-sat-processed.owl",
158 PagodaTester.onto_dir + "bio2rdf/uniprot/graph sampling/sample_1.nt", 161 PagodaTester.onto_dir + "bio2rdf/uniprot/graph sampling/sample_1.nt",
159// null, 162// null,
160// PagodaTester.onto_dir + "bio2rdf/uniprot/queries/atomic_ground.sparql" 163// PagodaTester.onto_dir + "bio2rdf/uniprot/queries/atomic_ground.sparql"
161 PagodaTester.onto_dir + "bio2rdf/uniprot/queries/example.sparql" 164 PagodaTester.onto_dir + "bio2rdf/uniprot/queries/example.sparql"
162 , "pagoda_uniprot.ans" 165 , "pagoda_uniprot.ans"
163 ); 166 );
164 AllTests.copy("log4j.log", "output/jair/pagoda_uniprot.example"); 167 Utility.copyFile("log4j.log", "output/jair/pagoda_uniprot.example");
165// AllTests.copy("output/log4j.log", "/home/yzhou/java-workspace/test-share/results_new/uniprot/pagoda_1p"); 168// AllTests.copy("output/log4j.log", "/home/yzhou/java-workspace/test-share/results_new/uniprot/pagoda_1p");
166 } 169 }
167 170
168 171
169 public static void main(String... args) { 172 public static void main(String... args) {
170 new JAIR_PAGOdA().fly(); 173 try {
174 new JAIR_PAGOdA().lubm1();
175 } catch (IOException e) {
176 e.printStackTrace();
177 }
171 } 178 }
172 179
173} 180}
diff --git a/test/uk/ac/ox/cs/pagoda/junit/JAIR_Scalability.java b/test/uk/ac/ox/cs/pagoda/test_units/JAIR_Scalability.java
index 5e2b1d7..43cb810 100644
--- a/test/uk/ac/ox/cs/pagoda/junit/JAIR_Scalability.java
+++ b/test/uk/ac/ox/cs/pagoda/test_units/JAIR_Scalability.java
@@ -1,30 +1,32 @@
1package uk.ac.ox.cs.pagoda.junit; 1package uk.ac.ox.cs.pagoda.test_units;
2
3import org.junit.Test;
4 2
3import org.testng.annotations.Test;
5import uk.ac.ox.cs.pagoda.tester.PagodaTester; 4import uk.ac.ox.cs.pagoda.tester.PagodaTester;
6import uk.ac.ox.cs.pagoda.util.Properties; 5import uk.ac.ox.cs.pagoda.util.Properties;
6import uk.ac.ox.cs.pagoda.util.Utility;
7
8import java.io.IOException;
7 9
8public class JAIR_Scalability { 10public class JAIR_Scalability {
9 11
10 private static final String date = "_0123"; 12 private static final String date = "_0123";
11 13
12 @Test 14 @Test
13 public void reactome() { 15 public void reactome() throws IOException {
14 testReactome(10, false); 16 testReactome(10, false);
15 } 17 }
16 18
17 @Test 19 @Test
18 public void chembl() { 20 public void chembl() throws IOException {
19 testChEMBL(1, false); 21 testChEMBL(1, false);
20 } 22 }
21 23
22 @Test 24 @Test
23 public void uniprot() { 25 public void uniprot() throws IOException {
24 testUniProt(1, false); 26 testUniProt(1, false);
25 } 27 }
26 28
27 public void testReactome(int percentage, boolean save) { 29 public void testReactome(int percentage, boolean save) throws IOException {
28 String[] args = new String[] { 30 String[] args = new String[] {
29 PagodaTester.onto_dir + "bio2rdf/reactome/biopax-level3-processed.owl", 31 PagodaTester.onto_dir + "bio2rdf/reactome/biopax-level3-processed.owl",
30 PagodaTester.onto_dir + "bio2rdf/reactome/graph sampling/simplifed_sample_" + percentage + ".ttl", 32 PagodaTester.onto_dir + "bio2rdf/reactome/graph sampling/simplifed_sample_" + percentage + ".ttl",
@@ -36,10 +38,10 @@ public class JAIR_Scalability {
36 38
37 PagodaTester.main(args); 39 PagodaTester.main(args);
38 if (save) 40 if (save)
39 AllTests.copy("log4j.log", "/home/yzhou/java-workspace/test-share/results_new/reactome/pagoda_" + percentage + "p" + date); 41 Utility.copyFile("log4j.log", "/home/yzhou/java-workspace/test-share/results_new/reactome/pagoda_" + percentage + "p" + date);
40 } 42 }
41 43
42 public void testChEMBL(int percentage, boolean save) { 44 public void testChEMBL(int percentage, boolean save) throws IOException {
43 String[] args = new String[] { 45 String[] args = new String[] {
44 PagodaTester.onto_dir + "bio2rdf/chembl/cco-noDPR.ttl", 46 PagodaTester.onto_dir + "bio2rdf/chembl/cco-noDPR.ttl",
45 PagodaTester.onto_dir + "bio2rdf/chembl/sample_" + percentage + ".nt", 47 PagodaTester.onto_dir + "bio2rdf/chembl/sample_" + percentage + ".nt",
@@ -55,10 +57,10 @@ public class JAIR_Scalability {
55 57
56 PagodaTester.main(args); 58 PagodaTester.main(args);
57 if (save) 59 if (save)
58 AllTests.copy("log4j.log", "/home/yzhou/java-workspace/test-share/results_new/chembl/pagoda_" + percentage + "p" + date); 60 Utility.copyFile("log4j.log", "/home/yzhou/java-workspace/test-share/results_new/chembl/pagoda_" + percentage + "p" + date);
59 } 61 }
60 62
61 public void testUniProt(int percentage, boolean save) { 63 public void testUniProt(int percentage, boolean save) throws IOException {
62 String[] args = new String[] { 64 String[] args = new String[] {
63 PagodaTester.onto_dir + "bio2rdf/uniprot/core-sat-processed.owl", 65 PagodaTester.onto_dir + "bio2rdf/uniprot/core-sat-processed.owl",
64 PagodaTester.onto_dir + "bio2rdf/uniprot/sample_" + percentage + ".nt", 66 PagodaTester.onto_dir + "bio2rdf/uniprot/sample_" + percentage + ".nt",
@@ -75,10 +77,10 @@ public class JAIR_Scalability {
75 77
76 PagodaTester.main(args); 78 PagodaTester.main(args);
77 if (save) 79 if (save)
78 AllTests.copy("log4j.log", "/home/yzhou/java-workspace/test-share/results_new/uniprot/pagoda_" + percentage + "p" + date); 80 Utility.copyFile("log4j.log", "/home/yzhou/java-workspace/test-share/results_new/uniprot/pagoda_" + percentage + "p" + date);
79 } 81 }
80 82
81 public static void main(String... args) { 83 public static void main(String... args) throws IOException {
82 Properties.ShellModeDefault = true; 84 Properties.ShellModeDefault = true;
83 new JAIR_Scalability().testUniProt(50, false); 85 new JAIR_Scalability().testUniProt(50, false);
84 } 86 }
diff --git a/test/uk/ac/ox/cs/pagoda/junit/LightEvaluation.java b/test/uk/ac/ox/cs/pagoda/test_units/LightEvaluation.java
index 1ddca15..29006de 100644
--- a/test/uk/ac/ox/cs/pagoda/junit/LightEvaluation.java
+++ b/test/uk/ac/ox/cs/pagoda/test_units/LightEvaluation.java
@@ -1,59 +1,62 @@
1package uk.ac.ox.cs.pagoda.junit; 1package uk.ac.ox.cs.pagoda.test_units;
2 2
3import org.junit.Test; 3import org.junit.Test;
4import uk.ac.ox.cs.pagoda.tester.PagodaTester; 4import uk.ac.ox.cs.pagoda.tester.PagodaTester;
5import uk.ac.ox.cs.pagoda.util.Utility;
6
7import java.io.IOException;
5 8
6public class LightEvaluation { 9public class LightEvaluation {
7 10
8 @Test 11 @Test
9 public void uobm1() { 12 public void uobm1() throws IOException {
10 int number = 1; 13 int number = 1;
11 PagodaTester.main( 14 PagodaTester.main(
12 PagodaTester.onto_dir + "uobm/univ-bench-dl.owl", 15 PagodaTester.onto_dir + "uobm/univ-bench-dl.owl",
13 PagodaTester.onto_dir + "uobm/data/uobm" + number + ".ttl", 16 PagodaTester.onto_dir + "uobm/data/uobm" + number + ".ttl",
14 PagodaTester.onto_dir + "uobm/queries/standard.sparql" 17 PagodaTester.onto_dir + "uobm/queries/standard.sparql"
15 ); 18 );
16 AllTests.copy("log4j.log", "output/jair/uobm1.out"); 19 Utility.copyFile("log4j.log", "output/jair/uobm1.out");
17 } 20 }
18 21
19 @Test 22 @Test
20 public void lubm100() { 23 public void lubm100() throws IOException {
21 int number = 100; 24 int number = 100;
22 PagodaTester.main( 25 PagodaTester.main(
23 PagodaTester.onto_dir + "lubm/univ-bench.owl", 26 PagodaTester.onto_dir + "lubm/univ-bench.owl",
24 PagodaTester.onto_dir + "lubm/data/lubm" + number + ".ttl", 27 PagodaTester.onto_dir + "lubm/data/lubm" + number + ".ttl",
25 PagodaTester.onto_dir + "lubm/queries/test.sparql" 28 PagodaTester.onto_dir + "lubm/queries/test.sparql"
26 ); 29 );
27 AllTests.copy("log4j.log", "results-backup/current/lubm100.out"); 30 Utility.copyFile("log4j.log", "results-backup/current/lubm100.out");
28 } 31 }
29 32
30 @Test 33 @Test
31 public void fly() { 34 public void fly() throws IOException {
32 PagodaTester.main( 35 PagodaTester.main(
33 PagodaTester.onto_dir + "fly/fly_anatomy_XP_with_GJ_FC_individuals.owl", 36 PagodaTester.onto_dir + "fly/fly_anatomy_XP_with_GJ_FC_individuals.owl",
34 PagodaTester.onto_dir + "fly/queries/fly.sparql" 37 PagodaTester.onto_dir + "fly/queries/fly.sparql"
35 ); 38 );
36 AllTests.copy("log4j.log", "results-backup/current/fly.out"); 39 Utility.copyFile("log4j.log", "results-backup/current/fly.out");
37 } 40 }
38 41
39 @Test 42 @Test
40 public void dbpedia() { 43 public void dbpedia() throws IOException {
41 PagodaTester.main( 44 PagodaTester.main(
42 PagodaTester.onto_dir + "dbpedia/integratedOntology-all-in-one-minus-datatype.owl", 45 PagodaTester.onto_dir + "dbpedia/integratedOntology-all-in-one-minus-datatype.owl",
43 PagodaTester.onto_dir + "dbpedia/data/dbpedia-minus-datatype-new.ttl", 46 PagodaTester.onto_dir + "dbpedia/data/dbpedia-minus-datatype-new.ttl",
44 PagodaTester.onto_dir + "dbpedia/atomic.sparql" 47 PagodaTester.onto_dir + "dbpedia/atomic.sparql"
45 ); 48 );
46 AllTests.copy("log4j.log", "results-backup/current/dbpedia.out"); 49 Utility.copyFile("log4j.log", "results-backup/current/dbpedia.out");
47 } 50 }
48 51
49 @Test 52 @Test
50 public void npdWithoutDataType() { 53 public void npdWithoutDataType() throws IOException {
51 PagodaTester.main( 54 PagodaTester.main(
52 PagodaTester.onto_dir + "npd/npd-all-minus-datatype.owl", 55 PagodaTester.onto_dir + "npd/npd-all-minus-datatype.owl",
53 PagodaTester.onto_dir + "npd/data/npd-data-dump-minus-datatype-new.ttl", 56 PagodaTester.onto_dir + "npd/data/npd-data-dump-minus-datatype-new.ttl",
54 PagodaTester.onto_dir + "npd/queries/atomic.sparql" 57 PagodaTester.onto_dir + "npd/queries/atomic.sparql"
55 ); 58 );
56 AllTests.copy("log4j.log", "results-backup/current/npd_minus.out"); 59 Utility.copyFile("log4j.log", "results-backup/current/npd_minus.out");
57 } 60 }
58 61
59} 62}
diff --git a/test/uk/ac/ox/cs/pagoda/junit/PagodaDBPedia.java b/test/uk/ac/ox/cs/pagoda/test_units/PagodaDBPedia.java
index 37ffb44..aaf542e 100644
--- a/test/uk/ac/ox/cs/pagoda/junit/PagodaDBPedia.java
+++ b/test/uk/ac/ox/cs/pagoda/test_units/PagodaDBPedia.java
@@ -1,4 +1,4 @@
1package uk.ac.ox.cs.pagoda.junit; 1package uk.ac.ox.cs.pagoda.test_units;
2 2
3import static org.junit.Assert.fail; 3import static org.junit.Assert.fail;
4 4
@@ -6,11 +6,14 @@ import org.junit.Test;
6 6
7import uk.ac.ox.cs.pagoda.tester.PagodaTester; 7import uk.ac.ox.cs.pagoda.tester.PagodaTester;
8import uk.ac.ox.cs.pagoda.tester.Statistics; 8import uk.ac.ox.cs.pagoda.tester.Statistics;
9import uk.ac.ox.cs.pagoda.util.Utility;
10
11import java.io.IOException;
9 12
10public class PagodaDBPedia { 13public class PagodaDBPedia {
11 14
12 @Test 15 @Test
13 public void test() { 16 public void test() throws IOException {
14 PagodaTester.main( 17 PagodaTester.main(
15 PagodaTester.onto_dir + "dbpedia/integratedOntology-all-in-one-minus-datatype.owl", 18 PagodaTester.onto_dir + "dbpedia/integratedOntology-all-in-one-minus-datatype.owl",
16 PagodaTester.onto_dir + "dbpedia/data/dbpedia-minus-datatype-new.ttl", 19 PagodaTester.onto_dir + "dbpedia/data/dbpedia-minus-datatype-new.ttl",
@@ -18,8 +21,8 @@ public class PagodaDBPedia {
18 ); 21 );
19 22
20 Statistics stat = new Statistics("output/log4j.log"); 23 Statistics stat = new Statistics("output/log4j.log");
21 String diff = stat.diff("results-backup/benchmark/dbpedia.out"); 24 String diff = stat.diff("results-backup/benchmark/dbpedia.out");
22 AllTests.copy("output/log4j.log", "results-backup/current/dbpedia.out"); 25 Utility.copyFile("output/log4j.log", "results-backup/current/dbpedia.out");
23 if (!diff.isEmpty()) 26 if (!diff.isEmpty())
24 fail(diff); 27 fail(diff);
25 } 28 }
diff --git a/test/uk/ac/ox/cs/pagoda/junit/PagodaELU.java b/test/uk/ac/ox/cs/pagoda/test_units/PagodaELU.java
index d999a6e..c2fa838 100644
--- a/test/uk/ac/ox/cs/pagoda/junit/PagodaELU.java
+++ b/test/uk/ac/ox/cs/pagoda/test_units/PagodaELU.java
@@ -1,4 +1,4 @@
1package uk.ac.ox.cs.pagoda.junit; 1package uk.ac.ox.cs.pagoda.test_units;
2 2
3import org.junit.Test; 3import org.junit.Test;
4import uk.ac.ox.cs.pagoda.tester.PagodaTester; 4import uk.ac.ox.cs.pagoda.tester.PagodaTester;
diff --git a/test/uk/ac/ox/cs/pagoda/junit/PagodaFLY.java b/test/uk/ac/ox/cs/pagoda/test_units/PagodaFLY.java
index 4631837..2fe07f0 100644
--- a/test/uk/ac/ox/cs/pagoda/junit/PagodaFLY.java
+++ b/test/uk/ac/ox/cs/pagoda/test_units/PagodaFLY.java
@@ -1,4 +1,4 @@
1package uk.ac.ox.cs.pagoda.junit; 1package uk.ac.ox.cs.pagoda.test_units;
2 2
3import org.junit.Test; 3import org.junit.Test;
4 4
diff --git a/test/uk/ac/ox/cs/pagoda/test_units/PagodaLUBM.java b/test/uk/ac/ox/cs/pagoda/test_units/PagodaLUBM.java
new file mode 100644
index 0000000..f40e41b
--- /dev/null
+++ b/test/uk/ac/ox/cs/pagoda/test_units/PagodaLUBM.java
@@ -0,0 +1,68 @@
1package uk.ac.ox.cs.pagoda.test_units;
2
3import org.testng.Assert;
4import org.testng.annotations.Test;
5import uk.ac.ox.cs.pagoda.tester.PagodaTester;
6import uk.ac.ox.cs.pagoda.tester.Statistics;
7import uk.ac.ox.cs.pagoda.util.Utility;
8
9import java.io.FileInputStream;
10import java.io.IOException;
11import java.util.Properties;
12
13public class PagodaLUBM {
14
15 public static final String CONFIG_FILE = "config/test.properties";
16
17 private static boolean isInit = false;
18 private static String ontoDir;
19
20 private static void init() {
21 if(isInit) return;
22 isInit = true;
23
24 Properties config = new Properties();
25
26 try(FileInputStream in = new FileInputStream(CONFIG_FILE)) {
27 config.load(in);
28 in.close();
29 } catch (IOException e) {
30 e.printStackTrace();
31 }
32
33 ontoDir = config.getProperty("ontoDir");
34 }
35
36 private void test_all(int number) {
37 init();
38 PagodaTester.main(
39 Utility.combinePaths(ontoDir, "lubm/univ-bench.owl"),
40 Utility.combinePaths(ontoDir, "lubm/data/lubm" + number + ".ttl"),
41 Utility.combinePaths(ontoDir, "lubm/queries/test.sparql")
42 );
43
44// assertTrue(false);
45// AllTests.copy("log4j.log", "output/jair/lubm" + number + ".out");
46 }
47
48 @Test
49 public void test1() {
50 test_all(1);
51 }
52
53// @Test
54// public void test() {
55// int number = 100;
56// test_all(number);
57// }
58
59 private void check(int number) throws IOException {
60 Statistics stat = new Statistics("output/log4j.log");
61 // TODO insert proper file
62 String diff = stat.diff("results-backup/benchmark/lubm" + number + ".out");
63 Utility.copyFile("output/log4j.log", "results-backup/current/lubm" + number + ".out");
64 if (!diff.isEmpty())
65 Assert.fail(diff);
66 }
67
68}
diff --git a/test/uk/ac/ox/cs/pagoda/junit/PagodaNPD.java b/test/uk/ac/ox/cs/pagoda/test_units/PagodaNPD.java
index 96edbb4..8fbe793 100644
--- a/test/uk/ac/ox/cs/pagoda/junit/PagodaNPD.java
+++ b/test/uk/ac/ox/cs/pagoda/test_units/PagodaNPD.java
@@ -1,4 +1,4 @@
1package uk.ac.ox.cs.pagoda.junit; 1package uk.ac.ox.cs.pagoda.test_units;
2 2
3import static org.junit.Assert.fail; 3import static org.junit.Assert.fail;
4 4
@@ -6,11 +6,14 @@ import org.junit.Test;
6 6
7import uk.ac.ox.cs.pagoda.tester.PagodaTester; 7import uk.ac.ox.cs.pagoda.tester.PagodaTester;
8import uk.ac.ox.cs.pagoda.tester.Statistics; 8import uk.ac.ox.cs.pagoda.tester.Statistics;
9import uk.ac.ox.cs.pagoda.util.Utility;
10
11import java.io.IOException;
9 12
10public class PagodaNPD { 13public class PagodaNPD {
11 14
12 @Test 15 @Test
13 public void testNPDwithoutDataType() { 16 public void testNPDwithoutDataType() throws IOException {
14 PagodaTester.main( 17 PagodaTester.main(
15 PagodaTester.onto_dir + "npd/npd-all-minus-datatype.owl", 18 PagodaTester.onto_dir + "npd/npd-all-minus-datatype.owl",
16 PagodaTester.onto_dir + "npd/data/npd-data-dump-minus-datatype-new.ttl", 19 PagodaTester.onto_dir + "npd/data/npd-data-dump-minus-datatype-new.ttl",
@@ -18,14 +21,14 @@ public class PagodaNPD {
18 ); 21 );
19 22
20 Statistics stat = new Statistics("output/log4j.log"); 23 Statistics stat = new Statistics("output/log4j.log");
21 String diff = stat.diff("results-backup/benchmark/npd_minus.out"); 24 String diff = stat.diff("results-backup/benchmark/npd_minus.out");
22 AllTests.copy("output/log4j.log", "results-backup/current/npd_minus.out"); 25 Utility.copyFile("output/log4j.log", "results-backup/current/npd_minus.out");
23 if (!diff.isEmpty()) 26 if (!diff.isEmpty())
24 fail(diff); 27 fail(diff);
25 } 28 }
26 29
27 @Test 30 @Test
28 public void testNPD() { 31 public void testNPD() throws IOException {
29 PagodaTester.main( 32 PagodaTester.main(
30 PagodaTester.onto_dir + "npd/npd-all.owl", 33 PagodaTester.onto_dir + "npd/npd-all.owl",
31 PagodaTester.onto_dir + "npd/data/npd-data-dump-processed.ttl", 34 PagodaTester.onto_dir + "npd/data/npd-data-dump-processed.ttl",
@@ -33,8 +36,8 @@ public class PagodaNPD {
33 ); 36 );
34 37
35 Statistics stat = new Statistics("output/log4j.log"); 38 Statistics stat = new Statistics("output/log4j.log");
36 String diff = stat.diff("results-backup/benchmark/npd.out"); 39 String diff = stat.diff("results-backup/benchmark/npd.out");
37 AllTests.copy("output/log4j.log", "results-backup/current/npd.out"); 40 Utility.copyFile("output/log4j.log", "results-backup/current/npd.out");
38 if (!diff.isEmpty()) 41 if (!diff.isEmpty())
39 fail(diff); 42 fail(diff);
40 } 43 }
diff --git a/test/uk/ac/ox/cs/pagoda/junit/PagodaNPD_bench.java b/test/uk/ac/ox/cs/pagoda/test_units/PagodaNPD_bench.java
index df1a57d..1243180 100644
--- a/test/uk/ac/ox/cs/pagoda/junit/PagodaNPD_bench.java
+++ b/test/uk/ac/ox/cs/pagoda/test_units/PagodaNPD_bench.java
@@ -1,4 +1,4 @@
1package uk.ac.ox.cs.pagoda.junit; 1package uk.ac.ox.cs.pagoda.test_units;
2 2
3import static org.junit.Assert.fail; 3import static org.junit.Assert.fail;
4 4
@@ -6,11 +6,14 @@ import org.junit.Test;
6 6
7import uk.ac.ox.cs.pagoda.tester.PagodaTester; 7import uk.ac.ox.cs.pagoda.tester.PagodaTester;
8import uk.ac.ox.cs.pagoda.tester.Statistics; 8import uk.ac.ox.cs.pagoda.tester.Statistics;
9import uk.ac.ox.cs.pagoda.util.Utility;
10
11import java.io.IOException;
9 12
10public class PagodaNPD_bench { 13public class PagodaNPD_bench {
11 14
12 @Test 15 @Test
13 public void test() { 16 public void test() throws IOException {
14 PagodaTester.main( 17 PagodaTester.main(
15 PagodaTester.onto_dir + "npd-benchmark/npd-v2-ql_a.owl", 18 PagodaTester.onto_dir + "npd-benchmark/npd-v2-ql_a.owl",
16 PagodaTester.onto_dir + "npd-benchmark/npd-v2-ql_a.ttl", 19 PagodaTester.onto_dir + "npd-benchmark/npd-v2-ql_a.ttl",
@@ -18,8 +21,8 @@ public class PagodaNPD_bench {
18 ); 21 );
19 22
20 Statistics stat = new Statistics("output/log4j.log"); 23 Statistics stat = new Statistics("output/log4j.log");
21 String diff = stat.diff("results-backup/benchmark/npd-bench.out"); 24 String diff = stat.diff("results-backup/benchmark/npd-bench.out");
22 AllTests.copy("output/log4j.log", "results-backup/current/npd-bench.out"); 25 Utility.copyFile("output/log4j.log", "results-backup/current/npd-bench.out");
23 if (!diff.isEmpty()) 26 if (!diff.isEmpty())
24 fail(diff); 27 fail(diff);
25 } 28 }
diff --git a/test/uk/ac/ox/cs/pagoda/junit/PagodaRLU.java b/test/uk/ac/ox/cs/pagoda/test_units/PagodaRLU.java
index 5d93302..8b31c99 100644
--- a/test/uk/ac/ox/cs/pagoda/junit/PagodaRLU.java
+++ b/test/uk/ac/ox/cs/pagoda/test_units/PagodaRLU.java
@@ -1,4 +1,4 @@
1package uk.ac.ox.cs.pagoda.junit; 1package uk.ac.ox.cs.pagoda.test_units;
2 2
3import org.junit.Test; 3import org.junit.Test;
4import uk.ac.ox.cs.pagoda.tester.PagodaTester; 4import uk.ac.ox.cs.pagoda.tester.PagodaTester;
diff --git a/test/uk/ac/ox/cs/pagoda/test_units/PagodaUOBM.java b/test/uk/ac/ox/cs/pagoda/test_units/PagodaUOBM.java
new file mode 100644
index 0000000..29a9056
--- /dev/null
+++ b/test/uk/ac/ox/cs/pagoda/test_units/PagodaUOBM.java
@@ -0,0 +1,79 @@
1package uk.ac.ox.cs.pagoda.test_units;
2
3import org.testng.annotations.Test;
4import uk.ac.ox.cs.pagoda.tester.PagodaTester;
5import uk.ac.ox.cs.pagoda.tester.Statistics;
6import uk.ac.ox.cs.pagoda.util.Utility;
7
8import java.io.FileInputStream;
9import java.io.IOException;
10import java.util.Properties;
11
12public class PagodaUOBM {
13
14 public static final String CONFIG_FILE = "config/test.properties";
15
16 private static boolean isInit = false;
17 private static String ontoDir;
18
19 private static void init() {
20 if(isInit) return;
21 isInit = true;
22
23 Properties config = new Properties();
24
25 try(FileInputStream in = new FileInputStream(CONFIG_FILE)) {
26 config.load(in);
27 in.close();
28 } catch (IOException e) {
29 e.printStackTrace();
30 }
31
32 ontoDir = config.getProperty("ontoDir");
33 }
34
35 private void test_all(int number ) {
36 init();
37
38 PagodaTester.main(
39 Utility.combinePaths(ontoDir, "uobm/univ-bench-dl.owl"),
40 Utility.combinePaths(ontoDir, "uobm/data/uobm" + number + ".ttl"),
41 Utility.combinePaths(ontoDir, "uobm/queries/test.sparql")
42// + ";" +
43// Utility.combinePaths(ontoDir, "uobm/queries/standard_group3_all_less.sparql") + ";" +
44// Utility.combinePaths(ontoDir, "uobm/queries/G3.sparql") + ";" +
45// Utility.combinePaths(ontoDir, "uobm/queries/last.sparql")
46 );
47
48// AllTests.copy("log4j.log", "output/jair/newuobm/uobm" + number + ".out");
49 }
50
51 private void test_upToSum(int number) {
52 init();
53
54 PagodaTester.main(
55 PagodaTester.onto_dir + "uobm/univ-bench-dl.owl",
56 PagodaTester.onto_dir + "uobm/data/uobm" + number + ".ttl",
57 PagodaTester.onto_dir + "uobm/queries/standard_group3_all.sparql"
58 );
59
60// AllTests.copy("log4j.log", "output/jair/uobm" + number + ".out");
61 }
62
63 @Test
64 public void test1() { test_all(1); }
65
66// @Test
67 public void test500() { test_upToSum(500); }
68
69// public static void main(String... args) {
70// new PagodaUOBM().test_all(1);
71// }
72
73 private void check() {
74 Statistics stat = new Statistics("results-backup/current/uobm1.out");
75 String diff = stat.diff("results-backup/benchmark/uobm1.out");
76 System.out.println(diff);
77 }
78
79}
diff --git a/test/uk/ac/ox/cs/pagoda/tester/PagodaTester.java b/test/uk/ac/ox/cs/pagoda/tester/PagodaTester.java
index 05a7d70..51b41f9 100644
--- a/test/uk/ac/ox/cs/pagoda/tester/PagodaTester.java
+++ b/test/uk/ac/ox/cs/pagoda/tester/PagodaTester.java
@@ -17,7 +17,7 @@ public class PagodaTester {
17// public static final String onto_dir = "/media/RDFData/yzhou/"; 17// public static final String onto_dir = "/media/RDFData/yzhou/";
18// public static final String onto_dir = "/users/yzhou/ontologies/"; 18// public static final String onto_dir = "/users/yzhou/ontologies/";
19// public static final String onto_dir = "/home/scratch/yzhou/ontologies/"; 19// public static final String onto_dir = "/home/scratch/yzhou/ontologies/";
20 public static final String onto_dir = "/home/yzhou/krr-nas-share/Yujiao/ontologies/"; 20 public static final String onto_dir = "/home/alessandro/Big_files/Ontologies/";
21 21
22 public static final String fly = onto_dir + "fly/fly_anatomy_XP_with_GJ_FC_individuals.owl"; 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"; 23 public static final String fly_query = onto_dir + "fly/queries/fly.sparql";
@@ -88,12 +88,12 @@ public class PagodaTester {
88 88
89 public static final String atlas_tbox = onto_dir + "bio2rdf/atlas/gxaterms.owl"; 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"; 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"; 91 public static final String atlas_queries = onto_dir + "bio2rdf/atlas/queries/atomic_one.sparql";
92 92
93 public static void main(String... args) { 93 public static void main(String... args) {
94 if (args.length == 0) { 94 if (args.length == 0) {
95// args = new String[] {test_tbox, test_abox, test_query}; 95// args = new String[] {test_tbox, test_abox, test_query};
96// args = new String[] {lubm_tbox, lubm_abox, lubm_query.replace(".sparql", "_all_pagoda.sparql")}; 96 args = new String[] {lubm_tbox, lubm_abox, lubm_query};
97// args = new String[] {uobm_tbox, uobm_abox, uobm_query.replace(".sparql", "_all_pagoda.sparql")}; 97// args = new String[] {uobm_tbox, uobm_abox, uobm_query.replace(".sparql", "_all_pagoda.sparql")};
98// args = new String[] {fly, "null", fly_query.replace(".sparql", "_pellet.sparql") }; 98// args = new String[] {fly, "null", fly_query.replace(".sparql", "_pellet.sparql") };
99// args = new String[] {dbpedia_tbox, dbpedia_abox, dbpedia_query}; 99// args = new String[] {dbpedia_tbox, dbpedia_abox, dbpedia_query};
@@ -129,10 +129,10 @@ public class PagodaTester {
129 if (args.length > index) properties.setToClassify(Boolean.parseBoolean(args[index++].substring(1))); 129 if (args.length > index) properties.setToClassify(Boolean.parseBoolean(args[index++].substring(1)));
130 if (args.length > index) properties.setToCallHermiT(Boolean.parseBoolean(args[index++].substring(1))); 130 if (args.length > index) properties.setToCallHermiT(Boolean.parseBoolean(args[index++].substring(1)));
131 131
132 System.out.println("Ontology file: " + properties.getOntologyPath()); 132 Utility.logInfo("Ontology file: " + properties.getOntologyPath());
133 System.out.println("Data files: " + properties.getDataPath()); 133 Utility.logInfo("Data files: " + properties.getDataPath());
134 System.out.println("Query files: " + properties.getQueryPath()); 134 Utility.logInfo("Query files: " + properties.getQueryPath());
135 System.out.println("Answer file: " + properties.getAnswerPath()); 135 Utility.logInfo("Answer file: " + properties.getAnswerPath());
136 136
137 QueryReasoner pagoda = null; 137 QueryReasoner pagoda = null;
138 138