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Re-implementation of the combined approach for CQ answering over RSA ontologies

Home Page: https://www.cs.ox.ac.uk/isg/tools/RSAComb

License: Apache License 2.0

Scala 97.79% Shell 2.21%

conjunctive-query-answering cq cq-answering rsa role-safety-acyclic

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rsacomb's Issues

DBpedia causes RDFox crash

Trying to run RSAComb on DBpedia result in a crash with JRDFox reporting back a stack trace.

Here is an example

#
# A fatal error has been detected by the Java Runtime Environment:
#
#  SIGSEGV (0xb) at pc=0x00007f87b73075ab, pid=3763, tid=0x00007f87b49c5640
#
# JRE version: OpenJDK Runtime Environment (8.0_252-b09) (build 1.8.0_252-b09)
# Java VM: OpenJDK 64-Bit Server VM (25.252-b09 mixed mode linux-amd64 compressed oops)
# Derivative: IcedTea 3.16.0
# Distribution: Gentoo Base System release 2.6, package Gentoo icedtea-3.16.0
# Problematic frame:
# C  [libRDFox3103994948759367886.so+0x113e5ab]  Stratum::getPatternIndexEx(PatternIndexType, unsigned int)+0x1b
#
# Failed to write core dump. Core dumps have been disabled. To enable core dumping, try "ulimit -c unlimited" before starting Java again
#
# If you would like to submit a bug report, please include
# instructions on how to reproduce the bug and visit:
#   https://icedtea.classpath.org/bugzilla
#

---------------  T H R E A D  ---------------

Current thread is native thread

siginfo: si_signo: 11 (SIGSEGV), si_code: 1 (SEGV_MAPERR), si_addr: 0x00000000000000a0

Registers:
RAX=0x00007f7a180ba890, RBX=0x00007f7a180ba820, RCX=0x00007f7a1c5cc498, RDX=0x000000048233b680
RSP=0x00007f87b49c3b60, RBP=0x00007f87b49c3ba0, RSI=0x0000000000000004, RDI=0x0000000000000000
R8 =0x0000000000000007, R9 =0x00007f7a184c6830, R10=0x0000000000000000, R11=0x00000000000000b0
R12=0x00000000000000c8, R13=0x0000000000000000, R14=0x00007f7a1c5cc458, R15=0x00007f7a1c5cb940
RIP=0x00007f87b73075ab, EFLAGS=0x0000000000010206, CSGSFS=0x002b000000000033, ERR=0x0000000000000004
  TRAPNO=0x000000000000000e

Top of Stack: (sp=0x00007f87b49c3b60)
0x00007f87b49c3b60:   000002bfb49c3ba0 00007f7a1c657b50
0x00007f87b49c3b70:   0000000000000000 0000000000000000
0x00007f87b49c3b80:   0000000000000000 00007f7a180ba820
0x00007f87b49c3b90:   00000000000000c8 00007f7a1c5cc458
0x00007f87b49c3ba0:   00007f7a285e2000 00007f87b72d6bec
0x00007f87b49c3bb0:   0000000000000000 00007f7a181aa930
0x00007f87b49c3bc0:   00007f7a285e2000 00007f7a181aab60
0x00007f87b49c3bd0:   0000000000000000 00007f7a1c5cc458
0x00007f87b49c3be0:   00007f7a1c5cb940 00007f87b72e6253
0x00007f87b49c3bf0:   00007f7a1c5cc428 00007f87b49c4d40
0x00007f87b49c3c00:   00007f87d8369ec0 00007f87b71ff4a5
0x00007f87b49c3c10:   0001000000000000 0000000000000000
0x00007f87b49c3c20:   0000000000000000 00007f7a180b9210
0x00007f87b49c3c30:   0000000000000000 00007f87d863ca08
0x00007f87b49c3c40:   0000000000000000 0000000000000000
0x00007f87b49c3c50:   0000000000000000 0000000000000000
0x00007f87b49c3c60:   00007f7a1cb6bbe8 00007f7a180b91e8
0x00007f87b49c3c70:   00007f87d8636178 0000000000000000
0x00007f87b49c3c80:   00007f87d863c900 00007f7a180ba820
0x00007f87b49c3c90:   00007f7a184c6980 00007f87b7e332e8
0x00007f87b49c3ca0:   00007f7a180ba8a8 00007f7a180ba820
0x00007f87b49c3cb0:   00007f87d863c8d0 0000000000000000
0x00007f87b49c3cc0:   00007f7a180f8550 00007f7a1c5cc430
0x00007f87b49c3cd0:   0000000000000000 0000000000000000
0x00007f87b49c3ce0:   0000000000000000 0000000000000000
0x00007f87b49c3cf0:   0000000000000000 0000000000000000
0x00007f87b49c3d00:   0000000000000000 0000000000000000
0x00007f87b49c3d10:   0000000000000000 0000000000000000
0x00007f87b49c3d20:   00007f87b7e33320 0000000000000000
0x00007f87b49c3d30:   00007f87d8635850 00007f87b62ae605
0x00007f87b49c3d40:   00007f87b7e33348 00007f87b65244db
0x00007f87b49c3d50:   00007f87d8635850 00007f87dd62ca06 

Instructions: (pc=0x00007f87b73075ab)
0x00007f87b730758b:   00 00 00 00 00 55 89 d2 40 0f b6 f6 48 8d 14 52
0x00007f87b730759b:   48 89 e5 41 56 41 54 53 48 c1 e2 04 48 83 ec 28
0x00007f87b73075ab:   48 03 97 a0 00 00 00 48 8d 5c f2 08 48 8b 03 48
0x00007f87b73075bb:   85 c0 74 11 48 8d 65 e8 5b 41 5c 41 5e 5d c3 66 

Register to memory mapping:

RAX=0x00007f7a180ba890 is an unknown value
RBX=0x00007f7a180ba820 is an unknown value
RCX=0x00007f7a1c5cc498 is an unknown value
RDX=0x000000048233b680 is an unknown value
RSP=0x00007f87b49c3b60 is an unknown value
RBP=0x00007f87b49c3ba0 is an unknown value
RSI=0x0000000000000004 is an unknown value
RDI=0x0000000000000000 is an unknown value
R8 =0x0000000000000007 is an unknown value
R9 =0x00007f7a184c6830 is an unknown value
R10=0x0000000000000000 is an unknown value
R11=0x00000000000000b0 is an unknown value
R12=0x00000000000000c8 is an unknown value
R13=0x0000000000000000 is an unknown value
R14=0x00007f7a1c5cc458 is an unknown value
R15=0x00007f7a1c5cb940 is an unknown value


Stack: [0x00007f87b41c6000,0x00007f87b49c6000],  sp=0x00007f87b49c3b60,  free space=8182k
Native frames: (J=compiled Java code, j=interpreted, Vv=VM code, C=native code)
C  [libRDFox3103994948759367886.so+0x113e5ab]  Stratum::getPatternIndexEx(PatternIndexType, unsigned int)+0x1b


---------------  P R O C E S S  ---------------

VM state:not at safepoint (normal execution)

VM Mutex/Monitor currently owned by a thread: None

heap address: 0x0000000085600000, size: 1962 MB, Compressed Oops mode: 32-bit
Narrow klass base: 0x0000000000000000, Narrow klass shift: 3
Compressed class space size: 1073741824 Address: 0x0000000100000000

Heap:
 PSYoungGen      total 36864K, used 25003K [0x00000000d7200000, 0x00000000d9b00000, 0x0000000100000000)
  eden space 31744K, 62% used [0x00000000d7200000,0x00000000d8572e38,0x00000000d9100000)
  from space 5120K, 99% used [0x00000000d9100000,0x00000000d95f80e0,0x00000000d9600000)
  to   space 5120K, 0% used [0x00000000d9600000,0x00000000d9600000,0x00000000d9b00000)
 ParOldGen       total 84992K, used 2814K [0x0000000085600000, 0x000000008a900000, 0x00000000d7200000)
  object space 84992K, 3% used [0x0000000085600000,0x00000000858bfa20,0x000000008a900000)
 Metaspace       used 19878K, capacity 20920K, committed 21120K, reserved 1067008K
  class space    used 2609K, capacity 2817K, committed 2944K, reserved 1048576K

Card table byte_map: [0x00007f87c83bc000,0x00007f87c8792000] byte_map_base: 0x00007f87c7f91000

Marking Bits: (ParMarkBitMap*) 0x00007f87dd3e14a0
 Begin Bits: [0x00007f87c4268000, 0x00007f87c6110000)
 End Bits:   [0x00007f87c6110000, 0x00007f87c7fb8000)

Polling page: 0x00007f87dd5fe000

CodeCache: size=245760Kb used=3189Kb max_used=3189Kb free=242571Kb
 bounds [0x00007f87c8b52000, 0x00007f87c8e72000, 0x00007f87d7b52000]
 total_blobs=1338 nmethods=951 adapters=310
 compilation: enabled

Compilation events (10 events):
Event: 344.803 Thread 0x00007f87d80e1800  944       4       com.github.benmanes.caffeine.cache.AbstractLinkedDeque::add (6 bytes)
Event: 344.804 Thread 0x00007f87d80e1800 nmethod 944 0x00007f87c8e64a10 code [0x00007f87c8e64b60, 0x00007f87c8e64cf8]
Event: 344.817 Thread 0x00007f87d80de800  945       4       java.util.concurrent.locks.AbstractQueuedSynchronizer::release (33 bytes)
Event: 344.819 Thread 0x00007f87d80de800 nmethod 945 0x00007f87c8e64650 code [0x00007f87c8e647a0, 0x00007f87c8e648e8]
Event: 344.833 Thread 0x00007f87d80e3800  946       3       com.github.benmanes.caffeine.cache.BoundedLocalCache::reorderProbation (63 bytes)
Event: 344.834 Thread 0x00007f87d80e3800 nmethod 946 0x00007f87c8e68610 code [0x00007f87c8e688a0, 0x00007f87c8e69de8]
Event: 344.834 Thread 0x00007f87d80e3800  947       3       com.github.benmanes.caffeine.cache.WSMS::setMainProtectedWeightedSize (6 bytes)
Event: 344.834 Thread 0x00007f87d80e3800 nmethod 947 0x00007f87c8e682d0 code [0x00007f87c8e68420, 0x00007f87c8e68570]
Event: 346.800 Thread 0x00007f87d80e1800  951       4       com.github.benmanes.caffeine.cache.BaseMpscLinkedArrayQueue::poll (108 bytes)
Event: 346.801 Thread 0x00007f87d80e1800 nmethod 951 0x00007f87c8e6d710 code [0x00007f87c8e6d860, 0x00007f87c8e6d978]

GC Heap History (6 events):
Event: 341.590 GC heap before
{Heap before GC invocations=1 (full 0):
 PSYoungGen      total 36864K, used 31744K [0x00000000d7200000, 0x00000000d9b00000, 0x0000000100000000)
  eden space 31744K, 100% used [0x00000000d7200000,0x00000000d9100000,0x00000000d9100000)
  from space 5120K, 0% used [0x00000000d9600000,0x00000000d9600000,0x00000000d9b00000)
  to   space 5120K, 0% used [0x00000000d9100000,0x00000000d9100000,0x00000000d9600000)
 ParOldGen       total 84992K, used 0K [0x0000000085600000, 0x000000008a900000, 0x00000000d7200000)
  object space 84992K, 0% used [0x0000000085600000,0x0000000085600000,0x000000008a900000)
 Metaspace       used 13940K, capacity 14332K, committed 14464K, reserved 1062912K
  class space    used 1754K, capacity 1894K, committed 1920K, reserved 1048576K
Event: 341.610 GC heap after
Heap after GC invocations=1 (full 0):
 PSYoungGen      total 36864K, used 5088K [0x00000000d7200000, 0x00000000d9b00000, 0x0000000100000000)
  eden space 31744K, 0% used [0x00000000d7200000,0x00000000d7200000,0x00000000d9100000)
  from space 5120K, 99% used [0x00000000d9100000,0x00000000d95f83d8,0x00000000d9600000)
  to   space 5120K, 0% used [0x00000000d9600000,0x00000000d9600000,0x00000000d9b00000)
 ParOldGen       total 84992K, used 2023K [0x0000000085600000, 0x000000008a900000, 0x00000000d7200000)
  object space 84992K, 2% used [0x0000000085600000,0x00000000857f9c30,0x000000008a900000)
 Metaspace       used 13940K, capacity 14332K, committed 14464K, reserved 1062912K
  class space    used 1754K, capacity 1894K, committed 1920K, reserved 1048576K
}
Event: 346.255 GC heap before
{Heap before GC invocations=2 (full 0):
 PSYoungGen      total 36864K, used 36832K [0x00000000d7200000, 0x00000000d9b00000, 0x0000000100000000)
  eden space 31744K, 100% used [0x00000000d7200000,0x00000000d9100000,0x00000000d9100000)
  from space 5120K, 99% used [0x00000000d9100000,0x00000000d95f83d8,0x00000000d9600000)
  to   space 5120K, 0% used [0x00000000d9600000,0x00000000d9600000,0x00000000d9b00000)
 ParOldGen       total 84992K, used 2023K [0x0000000085600000, 0x000000008a900000, 0x00000000d7200000)
  object space 84992K, 2% used [0x0000000085600000,0x00000000857f9c30,0x000000008a900000)
 Metaspace       used 17266K, capacity 18124K, committed 18176K, reserved 1064960K
  class space    used 2320K, capacity 2514K, committed 2560K, reserved 1048576K
Event: 346.265 GC heap after
Heap after GC invocations=2 (full 0):
 PSYoungGen      total 36864K, used 5112K [0x00000000d7200000, 0x00000000d9b00000, 0x0000000100000000)
  eden space 31744K, 0% used [0x00000000d7200000,0x00000000d7200000,0x00000000d9100000)
  from space 5120K, 99% used [0x00000000d9600000,0x00000000d9afe260,0x00000000d9b00000)
  to   space 5120K, 0% used [0x00000000d9100000,0x00000000d9100000,0x00000000d9600000)
 ParOldGen       total 84992K, used 2190K [0x0000000085600000, 0x000000008a900000, 0x00000000d7200000)
  object space 84992K, 2% used [0x0000000085600000,0x0000000085823bc8,0x000000008a900000)
 Metaspace       used 17266K, capacity 18124K, committed 18176K, reserved 1064960K
  class space    used 2320K, capacity 2514K, committed 2560K, reserved 1048576K
}
Event: 350.758 GC heap before
{Heap before GC invocations=3 (full 0):
 PSYoungGen      total 36864K, used 36856K [0x00000000d7200000, 0x00000000d9b00000, 0x0000000100000000)
  eden space 31744K, 99% used [0x00000000d7200000,0x00000000d90ffff0,0x00000000d9100000)
  from space 5120K, 99% used [0x00000000d9600000,0x00000000d9afe260,0x00000000d9b00000)
  to   space 5120K, 0% used [0x00000000d9100000,0x00000000d9100000,0x00000000d9600000)
 ParOldGen       total 84992K, used 2190K [0x0000000085600000, 0x000000008a900000, 0x00000000d7200000)
  object space 84992K, 2% used [0x0000000085600000,0x0000000085823bc8,0x000000008a900000)
 Metaspace       used 17945K, capacity 18954K, committed 19072K, reserved 1064960K
  class space    used 2451K, capacity 2641K, committed 2688K, reserved 1048576K
Event: 350.767 GC heap after
Heap after GC invocations=3 (full 0):
 PSYoungGen      total 36864K, used 5088K [0x00000000d7200000, 0x00000000d9b00000, 0x0000000100000000)
  eden space 31744K, 0% used [0x00000000d7200000,0x00000000d7200000,0x00000000d9100000)
  from space 5120K, 99% used [0x00000000d9100000,0x00000000d95f80e0,0x00000000d9600000)
  to   space 5120K, 0% used [0x00000000d9600000,0x00000000d9600000,0x00000000d9b00000)
 ParOldGen       total 84992K, used 2814K [0x0000000085600000, 0x000000008a900000, 0x00000000d7200000)
  object space 84992K, 3% used [0x0000000085600000,0x00000000858bfa20,0x000000008a900000)
 Metaspace       used 17945K, capacity 18954K, committed 19072K, reserved 1064960K
  class space    used 2451K, capacity 2641K, committed 2688K, reserved 1048576K
}

Deoptimization events (3 events):
Event: 0.926 Thread 0x00007f87d800d000 Uncommon trap: reason=unstable_if action=reinterpret pc=0x00007f87c8d02d58 method=java.lang.String.indexOf([CII[CIII)I @ 134
Event: 0.980 Thread 0x00007f87d800d000 Uncommon trap: reason=unstable_if action=reinterpret pc=0x00007f87c8cf794c method=java.lang.String.replace(CC)Ljava/lang/String; @ 2
Event: 1.385 Thread 0x00007f87d800d000 Uncommon trap: reason=range_check action=make_not_entrant pc=0x00007f87c8e132b0 method=sun.reflect.generics.parser.SignatureParser.current()C @ 34

Classes redefined (0 events):
No events

Internal exceptions (10 events):
Event: 348.440 Thread 0x00007f87d800d000 Exception <a 'java/lang/ArrayIndexOutOfBoundsException': 69> (0x00000000d827bc60) thrown at [/var/tmp/portage/dev-java/icedtea-3.16.0/work/icedtea-3.16.0/openjdk/hotspot/src/share/vm/interpreter/interpreterRuntime.cpp, line 371]
Event: 348.442 Thread 0x00007f87d800d000 Exception <a 'java/lang/ArrayIndexOutOfBoundsException': 67> (0x00000000d827f3d8) thrown at [/var/tmp/portage/dev-java/icedtea-3.16.0/work/icedtea-3.16.0/openjdk/hotspot/src/share/vm/interpreter/interpreterRuntime.cpp, line 371]
Event: 350.814 Thread 0x00007f87d800d000 Exception <a 'java/lang/ArrayIndexOutOfBoundsException': 71> (0x00000000d72c3068) thrown at [/var/tmp/portage/dev-java/icedtea-3.16.0/work/icedtea-3.16.0/openjdk/hotspot/src/share/vm/interpreter/interpreterRuntime.cpp, line 371]
Event: 350.815 Thread 0x00007f87d800d000 Exception <a 'java/lang/ArrayIndexOutOfBoundsException': 64> (0x00000000d72c5688) thrown at [/var/tmp/portage/dev-java/icedtea-3.16.0/work/icedtea-3.16.0/openjdk/hotspot/src/share/vm/interpreter/interpreterRuntime.cpp, line 371]
Event: 350.818 Thread 0x00007f87d800d000 Exception <a 'java/lang/ArrayIndexOutOfBoundsException': 69> (0x00000000d72c8d08) thrown at [/var/tmp/portage/dev-java/icedtea-3.16.0/work/icedtea-3.16.0/openjdk/hotspot/src/share/vm/interpreter/interpreterRuntime.cpp, line 371]
Event: 350.820 Thread 0x00007f87d800d000 Exception <a 'java/lang/ArrayIndexOutOfBoundsException': 67> (0x00000000d72cc480) thrown at [/var/tmp/portage/dev-java/icedtea-3.16.0/work/icedtea-3.16.0/openjdk/hotspot/src/share/vm/interpreter/interpreterRuntime.cpp, line 371]
Event: 350.847 Thread 0x00007f87d800d000 Exception <a 'java/lang/NoSuchMethodError': java.lang.Object.$anonfun$convert$9(Luk/ac/ox/cs/rsacomb/converter/RDFoxConverter;Ltech/oxfordsemantic/jrdfox/logic/expression/Term;Lscala/collection/immutable/List;Luk/ac/ox/cs/rsacomb/converter/SkolemStrategy;
Event: 350.856 Thread 0x00007f87d800d000 Exception <a 'java/lang/NoSuchMethodError': java.lang.Object.$anonfun$unzip$1(Lscala/Function1;Lscala/collection/mutable/Builder;Lscala/collection/mutable/Builder;Ljava/lang/Object;)Lscala/collection/mutable/Builder;> (0x00000000d7337a98) thrown at [/var/
Event: 352.022 Thread 0x00007f87d800d000 Exception <a 'java/lang/NoSuchMethodError': java.lang.Object.$anonfun$convert$8(Luk/ac/ox/cs/rsacomb/converter/RDFoxConverter;Luk/ac/ox/cs/rsacomb/util/DataFactory;Luk/ac/ox/cs/rsacomb/suffix/RSASuffix;Lscala/Tuple2;Lorg/semanticweb/owlapi/model/OWLObject
Event: 352.135 Thread 0x00007f87d800d000 Exception <a 'java/io/FileNotFoundException'> (0x00000000d7c28570) thrown at [/var/tmp/portage/dev-java/icedtea-3.16.0/work/icedtea-3.16.0/openjdk/hotspot/src/share/vm/prims/jni.cpp, line 710]

Events (10 events):
Event: 353.175 loading class scala/collection/immutable/Seq
Event: 353.175 loading class scala/collection/immutable/Seq done
Event: 353.175 loading class scala/collection/immutable/Seq
Event: 353.175 loading class scala/collection/immutable/Seq done
Event: 353.189 loading class tech/oxfordsemantic/jrdfox/logic/datalog/Rule
Event: 353.189 loading class tech/oxfordsemantic/jrdfox/logic/datalog/Rule done
Event: 353.190 loading class tech/oxfordsemantic/jrdfox/logic/datalog/Rule
Event: 353.190 loading class tech/oxfordsemantic/jrdfox/logic/datalog/Rule done
Event: 353.190 loading class scala/Function1
Event: 353.190 loading class scala/Function1 done


Dynamic libraries:
85600000-8a900000 rw-p 00000000 00:00 0 
8a900000-d7200000 ---p 00000000 00:00 0 
d7200000-d9b00000 rw-p 00000000 00:00 0 
d9b00000-100000000 ---p 00000000 00:00 0 
100000000-1002e0000 rw-p 00000000 00:00 0 
1002e0000-140000000 ---p 00000000 00:00 0 
55aa70fec000-55aa70fed000 r--p 00000000 08:04 3828714                    /opt/icedtea-bin-3.16.0/jre/bin/java
55aa70fed000-55aa70fee000 r-xp 00001000 08:04 3828714                    /opt/icedtea-bin-3.16.0/jre/bin/java
55aa70fee000-55aa70fef000 r--p 00002000 08:04 3828714                    /opt/icedtea-bin-3.16.0/jre/bin/java
55aa70fef000-55aa70ff0000 r--p 00002000 08:04 3828714                    /opt/icedtea-bin-3.16.0/jre/bin/java
55aa70ff0000-55aa70ff1000 rw-p 00003000 08:04 3828714                    /opt/icedtea-bin-3.16.0/jre/bin/java
55aa720ab000-55aa720cc000 rw-p 00000000 00:00 0                          [heap]
7f7a10000000-7f7a1008e000 rw-p 00000000 00:00 0 
7f7a1008e000-7f7a14000000 ---p 00000000 00:00 0 
7f7a18000000-7f7a1862a000 rw-p 00000000 00:00 0 
7f7a1862a000-7f7a1c000000 ---p 00000000 00:00 0 
7f7a1c000000-7f7a1cb6e000 rw-p 00000000 00:00 0 
7f7a1cb6e000-7f7a20000000 ---p 00000000 00:00 0 
7f7a20000000-7f7a2008e000 rw-p 00000000 00:00 0 
7f7a2008e000-7f7a24000000 ---p 00000000 00:00 0 
7f7a24000000-7f7a28000000 rw-p 00000000 00:00 0 
7f7a2856c000-7f7a289fe000 rw-p 00000000 00:00 0 
7f7a28a02000-7f7a28a04000 rw-p 00000000 00:00 0 
7f7a28a04000-7f7a28a0c000 ---p 00000000 00:00 0 
7f7a28a0c000-7f7a28a0e000 rw-p 00000000 00:00 0 
7f7a28a0e000-7f7a28a16000 ---p 00000000 00:00 0 
7f7a28a16000-7f7a28a18000 rw-p 00000000 00:00 0 
7f7a28a18000-7f7a28a20000 ---p 00000000 00:00 0 
7f7a28a20000-7f7a28a22000 rw-p 00000000 00:00 0 
7f7a28a22000-7f7a28a2a000 ---p 00000000 00:00 0 
7f7a28a2a000-7f7a28a2d000 rw-p 00000000 00:00 0 
7f7a28a2d000-7f7a4bece000 ---p 00000000 00:00 0 
7f7a4bece000-7f7a4becf000 rw-p 00000000 00:00 0 
7f7a4becf000-7f7b287cb000 ---p 00000000 00:00 0 
7f7b287cb000-7f7b287cc000 rw-p 00000000 00:00 0 
7f7b287cc000-7f7c050c8000 ---p 00000000 00:00 0 
7f7c050c8000-7f7c050c9000 rw-p 00000000 00:00 0 
7f7c050c9000-7f7ce19c5000 ---p 00000000 00:00 0 
7f7ce19c5000-7f7ce19cd000 rw-p 00000000 00:00 0 
7f7ce19cd000-7f7e9abc5000 ---p 00000000 00:00 0 
7f7e9abc5000-7f7e9abcd000 rw-p 00000000 00:00 0 
7f7e9abcd000-7f8053dc5000 ---p 00000000 00:00 0 
7f8053dc5000-7f8053dcd000 rw-p 00000000 00:00 0 
7f8053dcd000-7f820cfc5000 ---p 00000000 00:00 0 
7f820cfc5000-7f820cfcd000 rw-p 00000000 00:00 0 
7f820cfcd000-7f821ea1d000 ---p 00000000 00:00 0 
7f821ea1d000-7f821ea35000 rw-p 00000000 00:00 0 
7f821ea35000-7f82f25f5000 ---p 00000000 00:00 0 
7f82f25f5000-7f82f260d000 rw-p 00000000 00:00 0 
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7f87dd5a5000-7f87dd5f0000 r--p 00165000 08:04 4391599                    /lib64/libc-2.33.so
7f87dd5f0000-7f87dd5f4000 r--p 001af000 08:04 4391599                    /lib64/libc-2.33.so
7f87dd5f4000-7f87dd5f6000 rw-p 001b3000 08:04 4391599                    /lib64/libc-2.33.so
7f87dd5f6000-7f87dd5fc000 rw-p 00000000 00:00 0 
7f87dd5fc000-7f87dd5fd000 r--p 00000000 08:04 4387178                    /usr/share/locale/en_GB/LC_MESSAGES/libc.mo
7f87dd5fd000-7f87dd5fe000 rw-p 00000000 00:00 0 
7f87dd5fe000-7f87dd5ff000 r--p 00000000 00:00 0 
7f87dd5ff000-7f87dd603000 r--p 00000000 08:04 3828822                    /opt/icedtea-bin-3.16.0/jre/lib/amd64/libverify.so
7f87dd603000-7f87dd60a000 r-xp 00004000 08:04 3828822                    /opt/icedtea-bin-3.16.0/jre/lib/amd64/libverify.so
7f87dd60a000-7f87dd60c000 r--p 0000b000 08:04 3828822                    /opt/icedtea-bin-3.16.0/jre/lib/amd64/libverify.so
7f87dd60c000-7f87dd60d000 ---p 0000d000 08:04 3828822                    /opt/icedtea-bin-3.16.0/jre/lib/amd64/libverify.so
7f87dd60d000-7f87dd60f000 r--p 0000d000 08:04 3828822                    /opt/icedtea-bin-3.16.0/jre/lib/amd64/libverify.so
7f87dd60f000-7f87dd610000 rw-p 0000f000 08:04 3828822                    /opt/icedtea-bin-3.16.0/jre/lib/amd64/libverify.so
7f87dd610000-7f87dd612000 r--p 00000000 08:04 3828827                    /opt/icedtea-bin-3.16.0/jre/lib/amd64/jli/libjli.so
7f87dd612000-7f87dd61b000 r-xp 00002000 08:04 3828827                    /opt/icedtea-bin-3.16.0/jre/lib/amd64/jli/libjli.so
7f87dd61b000-7f87dd61e000 r--p 0000b000 08:04 3828827                    /opt/icedtea-bin-3.16.0/jre/lib/amd64/jli/libjli.so
7f87dd61e000-7f87dd61f000 r--p 0000d000 08:04 3828827                    /opt/icedtea-bin-3.16.0/jre/lib/amd64/jli/libjli.so
7f87dd61f000-7f87dd620000 rw-p 0000e000 08:04 3828827                    /opt/icedtea-bin-3.16.0/jre/lib/amd64/jli/libjli.so
7f87dd620000-7f87dd622000 rw-p 00000000 00:00 0 
7f87dd622000-7f87dd623000 r--p 00000000 08:04 4387024                    /lib64/ld-2.33.so
7f87dd623000-7f87dd647000 r-xp 00001000 08:04 4387024                    /lib64/ld-2.33.so
7f87dd647000-7f87dd651000 r--p 00025000 08:04 4387024                    /lib64/ld-2.33.so
7f87dd651000-7f87dd653000 r--p 0002e000 08:04 4387024                    /lib64/ld-2.33.so
7f87dd653000-7f87dd655000 rw-p 00030000 08:04 4387024                    /lib64/ld-2.33.so
7fff27794000-7fff277b6000 rw-p 00000000 00:00 0                          [stack]
7fff277db000-7fff277df000 r--p 00000000 00:00 0                          [vvar]
7fff277df000-7fff277e1000 r-xp 00000000 00:00 0                          [vdso]
ffffffffff600000-ffffffffff601000 --xp 00000000 00:00 0                  [vsyscall]

Using jdb to inspect the issue it seems like the crash happens when trying to load the datalog rules (DBpedia TBox) to RDFox. Printing the rules just before the crash results in a list of Datalog rules with some syntactic errors.

Here they are

Note the missing > on some atoms.

<X21[?X] :- <http://www.owl-ontologies.com/travel.owl#AccommodationRating>[?X].
<http://schema.org/StadiumOrArena>[?X] :- <http://dbpedia.org/ontology/Stadium[?X].
<http://www.owl-ontologies.com/travel.owl#FamilyDestination>[?X] :- <X23>[?X], <X24>[?X], <http://www.owl-ontologies.com/travel.owl#Destination[?X].
<http://dbpedia.org/ontology/Artwork[?X] :- <http://dbpedia.org/ontology/Painting>[?X].
<http://dbpedia.org/ontology/Organisation[?X] :- <http://dbpedia.org/ontology/GeopoliticalOrganisation>[?X].
<http://www.owl-ontologies.com/travel.owl#Activity>[?X] :- <http://www.owl-ontologies.com/travel.owl#Sports[?X].
<http://dbpedia.org/ontology/Royalty[?X] :- <http://dbpedia.org/ontology/PolishKing>[?X].
<http://dbpedia.org/ontology/SportsLeague[?X] :- <http://dbpedia.org/ontology/TennisLeague>[?X].
<http://dbpedia.org/ontology/SportsEvent[?X] :- <http://dbpedia.org/ontology/WrestlingEvent>[?X].
<http://dbpedia.org/ontology/Company>[?X] :- <http://dbpedia.org/ontology/Airline[?X].
<http://dbpedia.org/ontology/Country[?X] :- <http://dbpedia.org/ontology/locationCountry>[?I00206,?X], owl:Thing[?I00206].
<http://dbpedia.org/ontology/Person[?X] :- <http://dbpedia.org/ontology/memberOfParliament>[?I00265,?X], owl:Thing[?I00265].
<http://dbpedia.org/ontology/Person[?X] :- <http://dbpedia.org/ontology/medalist>[?I00401,?X], owl:Thing[?I00401].
<http://dbpedia.org/ontology/EducationalInstitution[?X] :- <http://dbpedia.org/ontology/training>[?I00433,?X], owl:Thing[?I00433].
<http://dbpedia.org/ontology/SoccerClub[?X] :- <http://dbpedia.org/ontology/soccerTournamentMostSuccesfull>[?I00518,?X], owl:Thing[?I00518].
<http://dbpedia.org/ontology/Award>[?X] :- <http://dbpedia.org/ontology/polishFilmAward[?I00569,?X], owl:Thing[?I00569].
<http://dbpedia.org/ontology/MeanOfTransportation>[?X] :- <http://dbpedia.org/ontology/aircraftHelicopterObservation[?I00576,?X], owl:Thing[?I00576].
<http://dbpedia.org/ontology/Language>[?X] :- <http://dbpedia.org/ontology/languageCode[?X,?I00646], owl:Thing[?I00646].
<http://dbpedia.org/ontology/Organisation[?X] :- <http://dbpedia.org/ontology/affiliation>[?X,?I00648], owl:Thing[?I00648].
<http://dbpedia.org/ontology/FigureSkater[?X] :- <http://dbpedia.org/ontology/formerCoach>[?X,?I00656], owl:Thing[?I00656].
<http://dbpedia.org/ontology/WaterwayTunnel[?X] :- <http://dbpedia.org/ontology/waterwayThroughTunnel>[?X,?I00685], owl:Thing[?I00685].
<http://dbpedia.org/ontology/SoccerLeagueSeason[?X] :- <http://dbpedia.org/ontology/soocerLeaguePromoted>[?X,?I00688], owl:Thing[?I00688].
<http://dbpedia.org/ontology/SoccerPlayer[?X] :- <http://dbpedia.org/ontology/managerClub>[?X,?I00738], owl:Thing[?I00738].
<http://dbpedia.org/ontology/RouteOfTransportation[?X] :- <http://dbpedia.org/ontology/routeStartLocation>[?X,?I00754], owl:Thing[?I00754].
<http://dbpedia.org/ontology/FictionalCharacter[?X] :- <http://dbpedia.org/ontology/firstAppearance>[?X,?I00912], owl:Thing[?I00912].
<http://dbpedia.org/ontology/Artist>[?X] :- <http://dbpedia.org/ontology/goyaAward[?X,?I01124], owl:Thing[?I01124].
<http://dbpedia.org/ontology/SpaceMission>[?X] :- <http://dbpedia.org/ontology/landingVehicle[?X,?I01185], owl:Thing[?I01185].
<http://dbpedia.org/ontology/Athlete[?X] :- <http://dbpedia.org/ontology/youthClub>[?X,?I01261], owl:Thing[?I01261].
<http://dbpedia.org/ontology/Film[?X] :- <http://dbpedia.org/ontology/narrator>[?X,?I01278], owl:Thing[?I01278].

Note the broken :- symbol printed as :

<http://dbpedia.org/ontology/Work>[?X] : <http://dbpedia.org/ontology/Website>[?X].
owl:Thing[?X] : <http://dbpedia.org/ontology/TopicalConcept>[?X].
<http://dbpedia.org/ontology/Building>[?X] : <http://dbpedia.org/ontology/Hospital>[?X].
<http://dbpedia.org/ontology/Award>[?X] : <http://dbpedia.org/ontology/tonyAward>[?I00108,?X], owl:Thing[?I00108].
<http://dbpedia.org/ontology/PopulatedPlace>[?X] : <http://dbpedia.org/ontology/sourceState>[?I00468,?X], owl:Thing[?I00468].
<http://dbpedia.org/ontology/Person>[?X] : <http://dbpedia.org/ontology/cinematography>[?I00571,?X], owl:Thing[?I00571].
<http://dbpedia.org/ontology/Person>[?X] : <http://dbpedia.org/ontology/formerCoach>[?I00575,?X], owl:Thing[?I00575].
<http://dbpedia.org/ontology/Person>[?X] : <http://dbpedia.org/ontology/vicePrincipal>[?I00624,?X], owl:Thing[?I00624].
<http://dbpedia.org/ontology/Magazine>[?X] : <http://dbpedia.org/ontology/previousEditor>[?X,?I00782], owl:Thing[?I00782].
<http://dbpedia.org/ontology/Software>[?X] : <http://dbpedia.org/ontology/cpu>[?X,?I00849], owl:Thing[?I00849].
<http://dbpedia.org/ontology/EducationalInstitution>[?X] : <http://dbpedia.org/ontology/principal>[?X,?I00959], owl:Thing[?I00959].
<http://dbpedia.org/ontology/Place>[?X] : <http://dbpedia.org/ontology/river>[?X,?I01111], owl:Thing[?I01111].
<http://dbpedia.org/ontology/River>[?X] : <http://dbpedia.org/ontology/sourceConfluenceState>[?X,?I01163], owl:Thing[?I01163].
<http://dbpedia.org/ontology/River>[?X] : <http://dbpedia.org/ontology/sourceConfluencePosition>[?X,?I01190], owl:Thing[?I01190].
<http://dbpedia.org/ontology/Person>[?X] : <http://dbpedia.org/ontology/partner>[?X,?I01289], owl:Thing[?I01289].

This is hardly a bug in our code since we are using Rule.toString(Prefixes)

Loading data via OWLAPI is slow

Manipulation of data (ABox) is minimal and we need a way to avoid importing it in memory before loading it in RDFox.

At the moment data is involved in the following:

Computation of rules for the canonical model often involve cycling through "all concepts and roles". This might be a problem if the abox introduces concepts/roles that are not named in the tbox. Processes that require this are: computation of additional rules per role, top axiomatization, equality axiomatization.
The filtering program introduces a predicate named on all constants in the original ontology.

Solution to (2)

Given that:

An anonymous term is defined as a functional term or a skolem constant not equal to a constant in the original ontology;
not NI(x) can be interpreted as x is anonymous;
we can introduce a new predicate skolem whenever we introduce a functional term or a skolem constant.

We can generate named and NI instances with the following rules:

named(x) <- top(x), not skolem(x) .
NI(x) <- congruent(x, y), named(y) .

Equality and \top axiomatisation

The RSA check needs additional LP rules:

Equality axiomatization:
I thought this could be solved just using RDFox built-in equality features. Still, looking at this it seems like there is no way to both enable the equality feature and use other features like aggregates or negation-as-failure.
\top axiomatization:
It seems like RDFox supports owl:Nothing out of the box but it doesn't seem to recognize owl:Thing. It seems weird...
E predicate derivation

RSAComb testing suite

We clearly need to automate testing better that how it is atm.

Unit testing

Unit testing is almost useless when it comes to modules that depend on generating "fresh names" since we can't predict the names of the generated names.

The simple solution is to put the code that generates fresh names into its own class and keep track of the seed as an implicit parameter to the generation function. This won't break the existing code, will keep the seed "out of the way" when we don't need it, but will give us the ability to run unit tests on the same seed.

Note: unit testing is also incomplete on most modules so it might be worth spending some time on that.

Test cases

Along the way we collected a fair amount of interesting (and correct) test cases. We should integrate them with some GitHub Action so that we don't break the existing code while introducing new features.

Unsound cases in PAGOdA

The following queries return an empty set of answers in PAGOdA. RSAComb on the other hand is able to find the right set of answer. It might be possible that we are using an unsound version of PAGOdA.

Query 15 has 39 answers but none is found by PAGOdA:

RSAComb/tests/lubm/queries.sparql

Lines 143 to 151 in 2a3b515

 ^[query15] 

 PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> 

 PREFIX ub: <http://www.lehigh.edu/~zhp2/2004/0401/univ-bench.owl#> 

 SELECT ?X 

 WHERE { 

 ?X ub:memberOf ?Y . 

 ?Y rdf:type ub:ResearchGroup . 

 ?X ub:memberOf <http://www.Department0.University0.edu> 

 }

Query 16 has 1 answer but it's not returned by PAGOdA:

RSAComb/tests/lubm/queries.sparql

Lines 153 to 162 in 2a3b515

 ^[query16] 

 PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> 

 PREFIX ub: <http://www.lehigh.edu/~zhp2/2004/0401/univ-bench.owl#> 

 SELECT ?X 

 WHERE { 

 ?X ub:memberOf ?Z . 

 ?Z rdf:type ub:ResearchGroup . 

 ?X ub:takesCourse ?Y . 

 <http://www.Department0.University0.edu/FullProfessor0> ub:teacherOf ?Y 

 }

RDFox debugging script

The RDFox debugging script simulate can be slightly improved generating different files during execution.

we should generate everything in the debug folder created when running in verbose mode. This avoids the need to pass the folder as an argument.
we should generate a sub-script to handle the canonical model generation.
we should generate sub-scripts to import a single query's filtering program (can be parameteric) and a script to import them all.

Answers should be stored in their own named graph.

This, logically, makes sense and might simplify the code slightly.
I don't think there will be any improvement performance-wise.

RDFox 5.2.1 exposes dependency graph in reserved named graph

evaluateUpdate now has an additional first parameter baseIRI that corresponds to "the base IRI for the query (if null, a default is used)". I'm not entirely sure what this is but we set it to null for now.
The changelog mentions a new "tuple table rdfox:DependencyGraph, which can be used to analyse the dependency graphs of Datalog programs". This might be usefull but it doesn't seem to be exposed by the Java API.

RSAComb as a library

As part of the effort of integrating RSAComb into PAGOdA, it would be beneficial if RSAComb would behave more like a library than a standalone application.

This might be relevant to integrate sbt with Github packages.

Maven, packages and dependences

We should:

generate pom.xml (see sbt makePom). Can we automate this somehow? Yes, have a look here:
- https://docs.github.com/en/actions/learn-github-actions/workflow-syntax-for-github-actions#onpushpull_requestpaths
- https://github.com/marketplace/actions/git-auto-commit
activate dependabot
automate releases, packaging and releasing to Maven (with GitHub Actions?)
set up better integration with Zenodo
update thanks section in README for new dependences

EXPLICIT vs rsacomb:Named

In RDFox, it is possible to specify when a match in a SPARQL query has to be restricted to explicit facts (see https://docs.oxfordsemantic.tech/querying.html#distinguishing-explicit-and-derived-facts-in-queries).

Can we use this to simplify the use/instantiation of rsacomb:Named or remove the redundancy altogether?

Complete RSA check

Add a library capable of managing graphs
Build RSA graph and check acyclicity
Implement additional checks (look at def.3 of the main paper)

See #11.

Concurrent execution of the filtering step

We could easily execute the filtering steps for different queries in parallel, but we need to understand how this affects RDFox performance and execution. In particular we should ask ourselves:

Is RDFox able to undestand that each connection (filtering step) will work on a different named graph?
Is RDFox going to parallelise the materialisation of all open connection? Or maybe the materialisation is restricted to a single materialisation step and request from different connections are handled in sequence?

The easiest way to find out is probably ask the developers.

NI predicate

This is just to keep track of the discussion about the instantiation of NI predicates in the RSA canonical model.
In the paper NI in mentioned multiple times.

During the definition of canonical model for O:

[Definition 4] [...] Let P be the smallest program with a rule -> NI(a) for each constant a and all rules in Table 2 [...]

During the definition of filtering program:

[Table 3 - rules 3a, 5a, 5b, 5c]

we refer to all functional terms and Skolem constants in the model that are not equal to constant in O as anonymous

We keep track of identities in the model relative to a match using a fresh predicate id. It is initialised as the minimal congruence relation over the positions of the existential variables in the query which are mapped to anonymous terms (rules (3)).

Furthermore the predicate named is introduced in the filtering program seemingly with the same semantics.

At the time of writing we agreed on the following:

predicate named is instantiated on all constants appearing in the original ontology O;
Such predicates can be computed (in the code) before the filtering program, since they don't directly depend on the submitted query;
predicate NI is defined as the set of constants in O along with any fresh constant introduced during the canonical model computation that are equivalent to a constant in O;
given the canonical model we can retrieve all instances of NI with the following rule:

NI(X) <- X rsa:EquivTo Y, named(Y).

Despite this decision we are still not sure why the paper introduces NI during the definition of the logic program used to compute the canonical model, since its instantiation depend on the canonical model itself.

Answer Filtering

We need to find a way to read and parse SPARQL queries. This is because we need to derive a filtering program from a query.

So far we have this:

OWLAPI does not provide an interface to import queries;
RDFox understands (a subset of?) SPARQL. Queries can either be provided as Strings or built using the internal abstract syntax. There is no bridge between the two, i.e., there is no way to provide a String/file and parse it into the internal representation;
We can use another library to manage the query import. We ignore the RDFox internal represention of a query and instead generate the filtering program directly. Here are a few libraries that should be good to use
- OpenRDF Sesame (javadocs)
- RDF4J (javadoc)
- Graal

Another option for now is to just ignore all of this and embed the queries in the code using the RDFox internal representation.

Update: it seems like RDFox functions that take a Query as a parameter usually provide alternative signatures that accept the query as a String. This most likely means that they have a method to parse Querys from Strings but it's not exposed. Maybe ask Valerio about this.

Apart from importing the query we still need to:

implement all filtering rules
refactor code for the generation of the filtering program (a.k.a. make it easier to use it later on when putting all the pieces together)
write a function to retrieve all bounded variables in a query. In a SELECT-FROM-WHERE SPARQL query this corresponds to all variables that are not named in the SELECT statement (a.k.a. answer variables);
write a function to obtain all invividuals in an ontology. Note that this is worth doing before any convertion into LP rules since the convertion introduces newly generated constants that we don't want in the set;
Import query from file (see above).

Automatic testing in develop

Add automatic testing in develop as well. Now that we have functional tests as well we need to set up everything properly.

Related to #9

Implementation of builtin predicate `notIn`

This might be a problem since we can't change how RDFox performs its materialisation.

Possible solutions are:

Find a way to encode the predicate using RDFox aggregates and/or builtin functions;
Create a predicate in (specifying its instances during role creation) and than use negation-as-failure to simulate notIn. Since in cannot be deduced anywhere using NaF should be equivalent to having normal negation.

Datalog rules and triples in RDFox

Setting

The problem came up while investigating why RDFox didn't seem to provide any automatic derivation of some obvious axioms (e.g., every class in a subclass of owl:Thing, every role is a subrole of owl:topObjectProperty, etc.).

Relevant documentation

RDFox docs

Problem

Let's say we have an axiom stating that A is a subclass of B.

Importing this axiom in RDFox as a triple ([:A rdfs:subClassOf :B]) will cause the solver to derive also some additional information, such as

[owl:Nothing, rdfs:subClassOf, :A], [owl:Nothing, rdfs:subClassOf, :B], 
[:A, rdfs:subClassOf, :A], [:B, rdfs:subClassOf, :B],
[:B, rdfs:subClassOf, owl:Thing], [:A, rdfs:subClassOf, owl:Thing]

The problem is that we are converting axioms into Datalog rules and hence we have something like this

[?X a :B] :- [?X a :A]

Doing this we lose the esplicit information about class subsumption and we don't get the same additional derivations as before.

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	^[query15]
	PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
	PREFIX ub: <http://www.lehigh.edu/~zhp2/2004/0401/univ-bench.owl#>
	SELECT ?X
	WHERE {
	?X ub:memberOf ?Y .
	?Y rdf:type ub:ResearchGroup .
	?X ub:memberOf <http://www.Department0.University0.edu>
	}

	^[query16]
	PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
	PREFIX ub: <http://www.lehigh.edu/~zhp2/2004/0401/univ-bench.owl#>
	SELECT ?X
	WHERE {
	?X ub:memberOf ?Z .
	?Z rdf:type ub:ResearchGroup .
	?X ub:takesCourse ?Y .
	<http://www.Department0.University0.edu/FullProfessor0> ub:teacherOf ?Y
	}