Galaxy |

Changeset 8:40adbcb2a7cc (2011-10-11)

Previous changeset 7:756f1f5798bf (2011-09-18) Next changeset 9:14bfd77f8520 (2011-10-18)

Commit message:
Added merge function and FaCT++ support. Improved OBO render

modified:
OPPL/README
OPPL/Tool.java
OPPL/oppl.xml
OPPL/oppl_galaxy_tool.jar

diff -r 756f1f5798bf -r 40adbcb2a7cc OPPL/FaCT++-OSX-v1.5.2/32bit/libFaCTPlusPlusJNI.jnilib

Binary file OPPL/FaCT++-OSX-v1.5.2/32bit/libFaCTPlusPlusJNI.jnilib has changed

diff -r 756f1f5798bf -r 40adbcb2a7cc OPPL/FaCT++-OSX-v1.5.2/64bit/libFaCTPlusPlusJNI.jnilib

Binary file OPPL/FaCT++-OSX-v1.5.2/64bit/libFaCTPlusPlusJNI.jnilib has changed

diff -r 756f1f5798bf -r 40adbcb2a7cc OPPL/FaCT++-linux-v1.5.2/32bit/FaCT++

Binary file OPPL/FaCT++-linux-v1.5.2/32bit/FaCT++ has changed

diff -r 756f1f5798bf -r 40adbcb2a7cc OPPL/FaCT++-linux-v1.5.2/32bit/libFaCTPlusPlusJNI.so

Binary file OPPL/FaCT++-linux-v1.5.2/32bit/libFaCTPlusPlusJNI.so has changed

diff -r 756f1f5798bf -r 40adbcb2a7cc OPPL/FaCT++-linux-v1.5.2/64bit/FaCT++

Binary file OPPL/FaCT++-linux-v1.5.2/64bit/FaCT++ has changed

diff -r 756f1f5798bf -r 40adbcb2a7cc OPPL/FaCT++-linux-v1.5.2/64bit/libFaCTPlusPlusJNI.so

Binary file OPPL/FaCT++-linux-v1.5.2/64bit/libFaCTPlusPlusJNI.so has changed

diff -r 756f1f5798bf -r 40adbcb2a7cc OPPL/FaCT++-linux-v1.5.2/Models.lisp/DataTypeTest/DataTypeTest.conf
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/OPPL/FaCT++-linux-v1.5.2/Models.lisp/DataTypeTest/DataTypeTest.conf Tue Oct 11 11:09:52 2011 +0200

[

@@ -0,0 +1,148 @@
+[LeveLogger]
+
+;--- Logging file name
+ file = reasoning.log
+;--- Logging level (the less level you give, the less information will be logged)
+ allowedLevel = 0
+
+
+[Tuning]
+
+;---
+;--- Option 'IAOEFLG': text ---
+;---
+;* Option 'IAOEFLG' define the priorities of different operations in TODO list. Possible values are 7-digit strings with ony possible digit are 0-6. The digits on the places 1, 2, ..., 7 are for priority of Id, And, Or, Exists, Forall, LE and GE operations respectively. The smaller number means the higher priority. All other constructions (TOP, BOTTOM, etc) has priority 0.
+;* Default value: '1263005'
+
+; IAOEFLG = 1263005
+
+;---
+;--- Option 'absorptionFlags': text ---
+;---
+;* Option 'absorptionFlags' sets up absorption process for general axioms. It is 5-letters text field; 1st symbol -- 'n' or 'c' -- (doN't) use Concept absorption; 2nd symbol -- 'n', 'r' or 'e' -- (doN't) use (Extended) Role absorption; the rest is symbols C,R,S; their order setup order of Simplification, Concept and Role absorptions performed (if possible).
+;* Default value: 'ceSCR'
+
+; absorptionFlags = ceSCR
+
+;---
+;--- Option 'alwaysPreferEquals': boolean ---
+;---
+;* Option 'alwaysPreferEquals' allows user to enforce usage of C=D definition instead of C[=D during absorption, even if implication appeares earlier in stream of axioms.
+;* Default value: 'true'
+
+; alwaysPreferEquals = 1
+
+;---
+;--- Option 'dumpQuery': boolean ---
+;---
+;* Option 'dumpQuery' dumps sub-TBox relevant to given satisfiability/subsumption query.
+;* Default value: 'false'
+
+; dumpQuery = 0
+
+;---
+;--- Option 'orSortSat': text ---
+;---
+;* Option 'orSortSat' define the sorting order of OR vertices in the DAG used in satisfiability tests (used mostly in caching). Option has form of string 'Mop', see orSortSub for details.
+;* Default value: '0'
+
+; orSortSat = 0
+
+;---
+;--- Option 'orSortSub': text ---
+;---
+;* Option 'orSortSub' define the sorting order of OR vertices in the DAG used in subsumption tests. Option has form of string 'Mop', where 'M' is a sort field (could be 'D' for depth, 'S' for size, 'F' for frequency, and '0' for no sorting), 'o' is a order field (could be 'a' for ascending and 'd' for descending mode), and 'p' is a preference field (could be 'p' for preferencing non-generating rules and 'n' for not doing so).
+;* Default value: '0'
+
+; orSortSub = 0
+
+;---
+;--- Option 'testTimeout': integer ---
+;---
+;* Option 'testTimeout' sets timeout for a single reasoning test in milliseconds.
+;* Default value: '0'
+
+; testTimeout = 0
+
+;---
+;--- Option 'useAnywhereBlocking': boolean ---
+;---
+;* Option 'useAnywhereBlocking' allow user to choose between Anywhere and Ancestor blocking.
+;* Default value: 'true'
+
+; useAnywhereBlocking = 1
+
+;---
+;--- Option 'useBackjumping': boolean ---
+;---
+;* Option 'useBackjumping' switch backjumping on and off. The usage of backjumping usually leads to much faster reasoning.
+;* Default value: 'true'
+
+; useBackjumping = 1
+
+;---
+;--- Option 'useCompletelyDefined': boolean ---
+;---
+;* Option 'useCompletelyDefined' leads to simpler Taxonomy creation if TBox contains no non-primitive concepts. Unfortunately, it is quite rare case.
+;* Default value: 'true'
+
+; useCompletelyDefined = 1
+
+;---
+;--- Option 'useLazyBlocking': boolean ---
+;---
+;* Option 'useLazyBlocking' makes checking of blocking status as small as possible. This greatly increase speed of reasoning.
+;* Default value: 'true'
+
+; useLazyBlocking = 1
+
+;---
+;--- Option 'usePrecompletion': boolean ---
+;---
+;* Option 'usePrecompletion' switchs on and off precompletion process for ABox.
+;* Default value: 'false'
+
+; usePrecompletion = 0
+
+;---
+;--- Option 'useRangeDomain': boolean ---
+;---
+;* Option 'useRangeDomain' switch on and off native support for the range and domain. This option is of internal use only. It is crusial for reasoning performance to leave this option true.
+;* Default value: 'true'
+
+; useRangeDomain = 1
+
+;---
+;--- Option 'useRelevantOnly': boolean ---
+;---
+;* Option 'useRelevantOnly' is used when creating internal DAG representation for externally given TBox. If true, DAG contains only concepts, relevant to query. It is safe to leave this option false.
+;* Default value: 'false'
+
+; useRelevantOnly = 0
+
+;---
+;--- Option 'useSemanticBranching': boolean ---
+;---
+;* Option 'useSemanticBranching' switch semantic branching on and off. The usage of semantic branching usually leads to faster reasoning, but sometime could give small overhead.
+;* Default value: 'true'
+
+; useSemanticBranching = 1
+
+[Query]
+
+;--
+;-- targets for single satisfiability (is Target sat) or subsumption (if Target [= Target2 holds) test
+;--
+
+; Target = *TOP*
+; Target2 = *BOTTOM*
+
+;***
+;*** please do not change lines below
+;***
+
+;--
+;-- target KB
+;--
+TBox = DataTypeTest.tbox
+

diff -r 756f1f5798bf -r 40adbcb2a7cc OPPL/FaCT++-linux-v1.5.2/Models.lisp/DataTypeTest/DataTypeTest.tbox
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/OPPL/FaCT++-linux-v1.5.2/Models.lisp/DataTypeTest/DataTypeTest.tbox Tue Oct 11 11:09:52 2011 +0200

b'@@ -0,0 +1,201 @@\n+; updated 05-04-06\n+\n+;;TEST DATA \n+(defdatarole R);\n+\n+;GT and LT\n+;testing simple satisfiable and unsatisfiable ranges\n+(defconcept TTa1 (and (some R(gt (number 18))) (some R(lt(number 60)))))\n+(defconcept TTa2 (and (some R(gt (number 60))) (some R(lt(number 18)))));unsat\n+(defconcept TTa3 (and (some R(lt (number 18))) (some R(gt(number 60)))));unsat\n+(defconcept TTa4 (and (some R(lt (number 60))) (some R(gt(number 18)))))\n+(defconcept TTa5 (and (some R(gt (number 18))) (some R(lt(number 18)))));unsat\n+(defconcept TTa6 (and (some R(lt (number 60))) (some R(gt(number 60)))));unsat\n+;the 4 below should eventually simplify\n+(defconcept TTb1 (and (some R(gt (number 18))) (some R(gt(number 60)))))\n+(defconcept TTb2 (and (some R(gt (number 60))) (some R(gt(number 18)))))\n+(defconcept TTb3 (and (some R(lt (number 18))) (some R(lt(number 60)))))\n+(defconcept TTb4 (and (some R(lt (number 60))) (some R(lt(number 18)))))\n+(defconcept TTb5 (and (some R(gt (number 18))) (some R(gt(number 18)))))\n+(defconcept TTb6 (and (some R(lt (number 60))) (some R(lt(number 60)))))\n+;testing ranges together with specific values\n+(defconcept TTc1 (and (some R(gt (number 18))) (some R(number 60))))\n+(defconcept TTc2 (and (some R(gt (number 60))) (some R(number 18))));unsat\n+(defconcept TTc3 (and (some R(lt (number 18))) (some R(number 60))));unsat\n+(defconcept TTc4 (and (some R(lt (number 60))) (some R(number 18))))\n+(defconcept TTd1 (and (some R(number 18)) (some R(gt (number 60)))));unsat\n+(defconcept TTd2 (and (some R(number 60)) (some R(gt (number 18)))))\n+(defconcept TTd3 (and (some R(number 18)) (some R(lt (number 60)))))\n+(defconcept TTd4 (and (some R(number 60)) (some R(lt (number 18)))));unsat\n+(defconcept TTe1 (and (some R(number 18)) (some R(lt(number 18)))));unsat\n+(defconcept TTe2 (and (some R(number 60)) (some R(gt(number 60)))));unsat\n+(defconcept TTe3 (and (some R(lt (number 60))) (some R(number 60))));unsat\n+(defconcept TTe4 (and (some R(gt (number 18))) (some R(number 18))));unsat\n+\n+;GE and LT\n+;testing simple satisfiable and unsatisfiable ranges\n+(defconcept ETa1 (and (some R(ge (number 18))) (some R(lt(number 60)))))\n+(defconcept ETa2 (and (some R(ge (number 60))) (some R(lt(number 18)))));unsat\n+(defconcept ETa3 (and (some R(le (number 18))) (some R(gt(number 60)))));unsat\n+(defconcept ETa4 (and (some R(le (number 60))) (some R(gt(number 18)))))\n+(defconcept ETa5 (and (some R(ge (number 18))) (some R(lt(number 18)))));unsat\n+(defconcept ETa6 (and (some R(le (number 60))) (some R(gt(number 60)))));unsat\n+;the 4 below should eventually simplify\n+(defconcept ETb1 (and (some R(ge (number 18))) (some R(gt(number 60)))))\n+(defconcept ETb2 (and (some R(ge (number 60))) (some R(gt(number 18)))))\n+(defconcept ETb3 (and (some R(le (number 18))) (some R(lt(number 60)))))\n+(defconcept ETb4 (and (some R(le (number 60))) (some R(lt(number 18)))))\n+(defconcept ETb5 (and (some R(ge (number 18))) (some R(gt(number 18)))))\n+(defconcept ETb6 (and (some R(le (number 60))) (some R(lt(number 60)))))\n+;testing ranges together with specific values\n+(defconcept ETc1 (and (some R(ge (number 18))) (some R(number 60))))\n+(defconcept ETc2 (and (some R(ge (number 60))) (some R(number 18))));unsat\n+(defconcept ETc3 (and (some R(le (number 18))) (some R(number 60))));unsat\n+(defconcept ETc4 (and (some R(le (number 60))) (some R(number 18))))\n+(defconcept ETd1 (and (some R(number 18)) (some R(gt (number 60)))));unsat\n+(defconcept ETd2 (and (some R(number 60)) (some R(gt (number 18)))))\n+(defconcept ETd3 (and (some R(number 18)) (some R(lt (number 60)))))\n+(defconcept ETd4 (and (some R(number 60)) (some R(lt (number 18)))));unsat\n+(defconcept ETe1 (and (some R(number 18)) (some R(lt(number 18)))));unsat\n+(defconcept ETe2 (and (some R(number 60)) (some R(gt(number 60)))));unsat\n+(defconcept ETe3 (and (some R(le (number 60))) (some R(number 60))))\n+(defconcept ETe4 (and (some R(ge (number 18))) (some R(number 18))))\n+\n+;GE and LE\n+;testing simple '..b'efconcept str04 (and (some R(lt(string WordA))) (some R(gt(string WordB)))));unsat\n+(defconcept str05 (and (some R(gt(string A))) (some R(lt(string A)))));unsat\n+(defconcept str06 (and (some R(ge(string A))) (some R(le(string A)))))\n+(defconcept str07 (and (some R(gt(string A))) (some R(gt(string B)))))\n+(defconcept str08 (and (some R(lt(string A))) (some R(lt(string B)))))\n+(defconcept str09 (and (some R(gt(string aa))) (some R(lt(string aaa)))))\n+(defconcept str10 (and (some R(gt(string aaa))) (some R(lt(string aa)))));unsat\n+(defconcept str11 (and (some R(gt(string AWord))) (some R(string BWord))))\n+(defconcept str12 (and (some R(lt(string AWord))) (some R(string BWord))));unsat\n+\n+;Subsumption tests\n+(defconcept subNumA (and (some R (ge (number 5))) (some R (le (number 10))))) ; subsumes TOP\n+(defconcept subNumB (and (some R (ge (number 5))) (some R (lt (number 10))))) ; subsumes a\n+(defconcept subNumC (and (some R (gt (number 5))) (some R (le (number 10))))) ; subsumes a\n+(defconcept subNumD (and (some R (gt (number 5))) (some R (lt (number 10))))) ; subsumes b, c (a)\n+(defconcept subNumE (some R (number 5)))\t\t\t\t ; subsumes b (a)\n+(defconcept subNumF (some R (number 10)))\t\t\t ; subsumes c (a)\n+(defconcept subStrA (and (some R (ge (string a))) (some R (le (string b))))) ; subsumes TOP\n+(defconcept subStrB (and (some R (ge (string a))) (some R (lt (string b))))) ; subsumes a\n+(defconcept subStrC (and (some R (gt (string a))) (some R (le (string b))))) ; subsumes a\n+(defconcept subStrD (and (some R (gt (string a))) (some R (lt (string b))))) ; subsumes b, c (a)\n+(defconcept subStrE (some R (string a)))\t\t\t\t ; subsumes b (a)\n+(defconcept subStrF (some R (string b)))\t\t\t\t ; subsumes c (a)\n+\n+;Mix of types unsatisfiability test\n+(defconcept mix1 (and (some R (gt (number 5))) (some R (lt (string five)))));unsat\n+(defconcept mix2 (and (some R (gt (number 5))) (some R (lt (string 5)))));unsat\n+\n+;Check that negative type saturation works correcly\n+(defconcept negSat1N (and (some R (number)) (not (some R (le (number 5)))) (not (some R (number 6))) (not(some R (ge (number 7))))));unsat\n+(defconcept negSat2N (and (some R (number)) (not (some R (lt (number 5)))) (not (some R (number 6))) (not(some R (ge (number 7))))))\n+(defconcept negSat3N (and (some R (number)) (not (some R (le (number 5)))) (not (some R (number 6))) (not(some R (gt (number 7))))))\n+(defconcept negSat4N (and (some R (number)) (not (some R (lt (number 5)))) (not (some R (number 6))) (not (some R (number 5))) (not(some R (ge (number 7))))));unsat\n+(defconcept negSat5N (and (some R (number)) (not (some R (le (number 5)))) (not (some R (number 6))) (not (some R (number 7))) (not(some R (gt (number 7))))));unsat\n+(defconcept negSat1S (and (some R (string)) (not (some R (le (string a)))) (not (some R (string b))) (not(some R (ge (string c))))))\n+\n+;negative subsumption tests\n+;C = E\n+;D = F\n+;I subsumes A\n+;J subsumes C\n+;H subsumes B\n+;G subsumes D\n+;F subsumes B\n+;E subsumes A\n+;M subsumes L\n+(defconcept subSumpA (not (some R(lt (number 2)))))\n+(defconcept subSumpB (not (some R(gt (number 5)))))\n+(defconcept subSumpC (not (some R(le (number 2)))))\n+(defconcept subSumpD (not (some R(ge (number 5)))))\n+(defconcept subSumpE (and (not (some R(lt (number 2)))) (not (some R (number 2)))))\n+(defconcept subSumpF (and (not (some R(gt (number 5)))) (not (some R (number 5)))))\n+(defconcept subSumpG (and (some R(lt (number 5)))))\n+(defconcept subSumpH (and (some R(le (number 5)))))\n+(defconcept subSumpI (and (some R(ge (number 2)))))\n+(defconcept subSumpJ (and (some R(gt (number 2)))))\n+(defconcept subSumpK (and (not (some R(number 2))) (not (some R(number 3))) (not (some R(number 4))) (some R (ge (number 2))) (some R (le (number 4)))));unsat\n+(defconcept subSumpL (and (not (some R(number 2))) (not (some R(number 3))) (not (some R(number 4)))))\n+(defconcept subSumpM (some R(le (number 1))))\n+(defconcept subSumpN (and (not (some R(number 2))) (some R (number 2))));unsat\n'

diff -r 756f1f5798bf -r 40adbcb2a7cc OPPL/FaCT++-linux-v1.5.2/Models.lisp/DataTypeTest/Makefile
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/OPPL/FaCT++-linux-v1.5.2/Models.lisp/DataTypeTest/Makefile Tue Oct 11 11:09:52 2011 +0200

@@ -0,0 +1,13 @@
+# this is automatically generate makefile for KB
+
+all: sat
+
+clean:
+ rm -f dl.res Taxonomy.Roles Taxonomy.log reasoning.log
+ rm -f dl.res.diff Taxonomy.Roles.diff Taxonomy.log.diff reasoning.log.diff
+
+KB_CONF = DataTypeTest.conf
+KB = DataTypeTest.tbox
+
+sat classify:
+ FaCT++ $(KB_CONF)

diff -r 756f1f5798bf -r 40adbcb2a7cc OPPL/FaCT++-linux-v1.5.2/Models.lisp/Makefile.default
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/OPPL/FaCT++-linux-v1.5.2/Models.lisp/Makefile.default Tue Oct 11 11:09:52 2011 +0200

@@ -0,0 +1,8 @@
+# this is automatically generate makefile for KB
+
+all: sat
+
+clean:
+ rm -f dl.res Taxonomy.Roles Taxonomy.log reasoning.log
+ rm -f dl.res.diff Taxonomy.Roles.diff Taxonomy.log.diff reasoning.log.diff
+

diff -r 756f1f5798bf -r 40adbcb2a7cc OPPL/FaCT++-linux-v1.5.2/Models.lisp/create-new-test
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/OPPL/FaCT++-linux-v1.5.2/Models.lisp/create-new-test Tue Oct 11 11:09:52 2011 +0200

@@ -0,0 +1,60 @@
+#!/bin/bash
+
+# Script for creating new test-suit.
+# In parameters: <suit-name> <source-tbox>
+# output:
+#  - create <suit-name> directory
+#  - copy <source-tbox> into <suit-name>/<suit-name>.tbox
+#  - create Makefile and conf-file
+
+# file names
+MKNAME=./$1/Makefile
+TBOXNAME=./$1/$1.tbox
+CONFNAME=./$1/$1.conf
+
+# .orig files path
+OFP=.
+
+Usage()
+{
+ echo
+ echo "Usage: create-new-test <suit-name> <source-tbox>"
+ echo " where: <suit-name>   -- unique name for new suit"
+ echo "        <source-tbox> -- test TBox file"
+ exit 1
+}
+
+Fatal()
+{
+  echo "Fatal: directory $1 already exists"
+  exit 1
+}
+
+# check for the parameters
+if test "$1" = ""; then
+  Usage
+elif test "$2" = ""; then
+  Usage
+fi
+
+# create new subdir
+mkdir $1 || Fatal
+
+# create Makefile for the test suit
+cp $OFP/Makefile.default $MKNAME
+echo "KB_CONF = $1.conf" >> $MKNAME
+echo "KB = $1.tbox" >> $MKNAME
+echo >> $MKNAME
+echo "sat classify:" >> $MKNAME
+echo " FaCT++ \$(KB_CONF)" >> $MKNAME
+
+# create TBox file for the test suit
+cp $2 $TBOXNAME
+
+# create Config file for the test suit
+cp $OFP/options.default $CONFNAME
+cat $OFP/query.default >> $CONFNAME
+echo "TBox = $1.tbox" >> $CONFNAME
+echo >> $CONFNAME
+
+echo "Finished!"

diff -r 756f1f5798bf -r 40adbcb2a7cc OPPL/FaCT++-linux-v1.5.2/Models.lisp/options.default
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/OPPL/FaCT++-linux-v1.5.2/Models.lisp/options.default Tue Oct 11 11:09:52 2011 +0200

[

@@ -0,0 +1,130 @@
+[LeveLogger]
+
+;--- Logging file name
+ file = reasoning.log
+;--- Logging level (the less level you give, the less information will be logged)
+ allowedLevel = 0
+
+
+[Tuning]
+
+;---
+;--- Option 'IAOEFLG': text ---
+;---
+;* Option 'IAOEFLG' define the priorities of different operations in TODO list. Possible values are 7-digit strings with ony possible digit are 0-6. The digits on the places 1, 2, ..., 7 are for priority of Id, And, Or, Exists, Forall, LE and GE operations respectively. The smaller number means the higher priority. All other constructions (TOP, BOTTOM, etc) has priority 0.
+;* Default value: '1263005'
+
+; IAOEFLG = 1263005
+
+;---
+;--- Option 'absorptionFlags': text ---
+;---
+;* Option 'absorptionFlags' sets up absorption process for general axioms. It is 5-letters text field; 1st symbol -- 'n' or 'c' -- (doN't) use Concept absorption; 2nd symbol -- 'n', 'r' or 'e' -- (doN't) use (Extended) Role absorption; the rest is symbols C,R,S; their order setup order of Simplification, Concept and Role absorptions performed (if possible).
+;* Default value: 'ceSCR'
+
+; absorptionFlags = ceSCR
+
+;---
+;--- Option 'alwaysPreferEquals': boolean ---
+;---
+;* Option 'alwaysPreferEquals' allows user to enforce usage of C=D definition instead of C[=D during absorption, even if implication appeares earlier in stream of axioms.
+;* Default value: 'true'
+
+; alwaysPreferEquals = 1
+
+;---
+;--- Option 'dumpQuery': boolean ---
+;---
+;* Option 'dumpQuery' dumps sub-TBox relevant to given satisfiability/subsumption query.
+;* Default value: 'false'
+
+; dumpQuery = 0
+
+;---
+;--- Option 'orSortSat': text ---
+;---
+;* Option 'orSortSat' define the sorting order of OR vertices in the DAG used in satisfiability tests (used mostly in caching). Option has form of string 'Mop', see orSortSub for details.
+;* Default value: '0'
+
+; orSortSat = 0
+
+;---
+;--- Option 'orSortSub': text ---
+;---
+;* Option 'orSortSub' define the sorting order of OR vertices in the DAG used in subsumption tests. Option has form of string 'Mop', where 'M' is a sort field (could be 'D' for depth, 'S' for size, 'F' for frequency, and '0' for no sorting), 'o' is a order field (could be 'a' for ascending and 'd' for descending mode), and 'p' is a preference field (could be 'p' for preferencing non-generating rules and 'n' for not doing so).
+;* Default value: '0'
+
+; orSortSub = 0
+
+;---
+;--- Option 'testTimeout': integer ---
+;---
+;* Option 'testTimeout' sets timeout for a single reasoning test in milliseconds.
+;* Default value: '0'
+
+; testTimeout = 0
+
+;---
+;--- Option 'useAnywhereBlocking': boolean ---
+;---
+;* Option 'useAnywhereBlocking' allow user to choose between Anywhere and Ancestor blocking.
+;* Default value: 'true'
+
+; useAnywhereBlocking = 1
+
+;---
+;--- Option 'useBackjumping': boolean ---
+;---
+;* Option 'useBackjumping' switch backjumping on and off. The usage of backjumping usually leads to much faster reasoning.
+;* Default value: 'true'
+
+; useBackjumping = 1
+
+;---
+;--- Option 'useCompletelyDefined': boolean ---
+;---
+;* Option 'useCompletelyDefined' leads to simpler Taxonomy creation if TBox contains no non-primitive concepts. Unfortunately, it is quite rare case.
+;* Default value: 'true'
+
+; useCompletelyDefined = 1
+
+;---
+;--- Option 'useLazyBlocking': boolean ---
+;---
+;* Option 'useLazyBlocking' makes checking of blocking status as small as possible. This greatly increase speed of reasoning.
+;* Default value: 'true'
+
+; useLazyBlocking = 1
+
+;---
+;--- Option 'usePrecompletion': boolean ---
+;---
+;* Option 'usePrecompletion' switchs on and off precompletion process for ABox.
+;* Default value: 'false'
+
+; usePrecompletion = 0
+
+;---
+;--- Option 'useRangeDomain': boolean ---
+;---
+;* Option 'useRangeDomain' switch on and off native support for the range and domain. This option is of internal use only. It is crusial for reasoning performance to leave this option true.
+;* Default value: 'true'
+
+; useRangeDomain = 1
+
+;---
+;--- Option 'useRelevantOnly': boolean ---
+;---
+;* Option 'useRelevantOnly' is used when creating internal DAG representation for externally given TBox. If true, DAG contains only concepts, relevant to query. It is safe to leave this option false.
+;* Default value: 'false'
+
+; useRelevantOnly = 0
+
+;---
+;--- Option 'useSemanticBranching': boolean ---
+;---
+;* Option 'useSemanticBranching' switch semantic branching on and off. The usage of semantic branching usually leads to faster reasoning, but sometime could give small overhead.
+;* Default value: 'true'
+
+; useSemanticBranching = 1
+

diff -r 756f1f5798bf -r 40adbcb2a7cc OPPL/FaCT++-linux-v1.5.2/Models.lisp/query.default
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/OPPL/FaCT++-linux-v1.5.2/Models.lisp/query.default Tue Oct 11 11:09:52 2011 +0200

[

@@ -0,0 +1,16 @@
+[Query]
+
+;--
+;-- targets for single satisfiability (is Target sat) or subsumption (if Target [= Target2 holds) test
+;--
+
+; Target = *TOP*
+; Target2 = *BOTTOM*
+
+;***
+;*** please do not change lines below
+;***
+
+;--
+;-- target KB
+;--

diff -r 756f1f5798bf -r 40adbcb2a7cc OPPL/FaCT++-linux-v1.5.2/README
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/OPPL/FaCT++-linux-v1.5.2/README Tue Oct 11 11:09:52 2011 +0200

@@ -0,0 +1,126 @@
+This is a README file for the FaCT++ v1.1.6 reasoner distribution.
+
+This file contains following information
+
+1. Introduction
+2. Contents of distribution
+3. Installation
+4. Usage
+5. Known problems
+6. Contact information
+
+1. Introduction
+---------------
+
+FaCT++ is re-implementation of the well-known FaCT Description Logic (DL)
+Reasoner. This reasoner currently supports the SROIQ(D) description Logic
+language, which corresponds to OWL DL ontology language standard.
+The current version is 1.1.6. This is source distribution package so it can
+be used on different platforms. It was tested on Windows, Linux and MacOS X.
+
+FaCT++ is distributed under GNU Public License (GPL). Full text of license
+can be found at http://www.gnu.org/licenses/gpl.txt. Libraries that are
+provided by the FaCT++ are distributed under the GNU Lesser Public License
+(LGPL).
+
+2. Contents of distribution
+---------------------------
+
+  file              description
+
+- src/             FaCT++ source code
+- bin/ and lib/    FaCT++ precompiled binaries
+- Models.lisp/     examples and infrastructure for FaCT++ lisp reasoner
+- licensing/       license information
+- README           this file
+
+3. Installation
+---------------
+
+3.1 Building system from sources
+--------------------------------
+
+For building system you will need GNU c++ compiler and GNU make (version 3.3
+and higher were tested). Change GENERAL_DEFINES macro in src/Makefile.include
+to make it suitable for your computer. Then just run "make".
+
+In order to compile DIG part you will also need an XML parsing library
+Xerces-c (freely avaliable at http://xml.apache.org/xerces-c/). Make sure
+that Xerces-c package is installed system-wide or you have environment
+variable XERCESCROOT which points to Xerces-c root directory.
+
+In order to compile OWL-API interface (src/FaCTPlusPlusJNI/) it is necessary
+to have JNI development files (jni.h) available.
+
+4. Usage
+--------
+
+4.1 Standalone FaCT++ with lisp-like interface
+----------------------------------------------
+
+Models.lisp directory of this distribution contains some files that
+support FaCT++ reasoning as well as examples of KBs.
+
+To use standalone reasoner user should usually perform the following steps:
+- create an ontology using the FaCT++ input language
+- create a working directory (i.e. TEST) for FaCT++ using the command
+        create-new-test TEST ontology
+  where "ontology" is the name of the file containing your FaCT++ ontology
+- inside TEST directory run
+        make
+
+This will run FaCT++ reasoner on the newly created config-file for the
+given ontology. The results of FaCT++'s reasoning appear in following files:
+
+- Taxonomy.Roles contains information about the roles taxonomy;
+- Taxonomy.log contains information about the concept taxonomy (if it was requested);
+- dl.res contains full information about the ontology and some statistical
+  information about the reasoning process;
+
+4.1.1 Ontology creation
+-----------------------
+
+There are three ways of creating an ontology for FaCT++
+
+- Hand-made ontology. This way is not recommended for the end user.
+- Using OilEd (http://oiled.man.ac.uk). Load an ontology to the OilEd
+  then choose Export|FaCT++ lisp.
+- From the OWL source using the OWL Ontology Converter
+  (http://phoebus.cs.man.ac.uk:9999/OWL/Converter). Set the ontology URL to
+  the OWL ontology, choose FaCT++ as the output language, press Convert and then
+  copy the resulting ontology text to the FaCT++ ontology file.
+
+4.1.2 Reasoning process
+-----------------------
+
+There are a number of options that could influence the reasoning process. All
+options, their format and description are given in the config file, which is
+generated by the create-new-test script.
+
+4.2 FaCT++ as an HTTP DIG reasoner
+----------------------------------
+
+Run FaCT++.Server with optional parameter "-port <port>". Default value of
+<port> is 3490.
+
+This reasoner will avaliable at http://<host>:<port>, where <host> is
+a name of a computer running FaCT++.Server.
+
+4.3 FaCT++ as an HTTP OWL reasoner
+---------------------------------
+
+Use FaCT++ as describe in section 4.2. Then connect your OWL editor like
+Protege (http://protege.stanford.edu/) to the FaCT++ using address
+http://<host>:<port>
+
+5. Known problems
+-----------------
+
+6. Contact information
+----------------------
+
+For any problems concerning FaCT++ please contact Dmitry Tsarkov
+(tsarkov@cs.man.ac.uk).  Any questions, suggestions or bug reports are
+welcome!
+
+Last updated: 01/05/2007

diff -r 756f1f5798bf -r 40adbcb2a7cc OPPL/FaCT++-linux-v1.5.2/licensing/FaCT++.license.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/OPPL/FaCT++-linux-v1.5.2/licensing/FaCT++.license.txt Tue Oct 11 11:09:52 2011 +0200

@@ -0,0 +1,30 @@
+Copyright (c) The Victoria University of Manchester 2004
+
+This program is free software; you can redistribute it and/or modif y
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation; either version 2 of the License, or (at
+your option) any later version.
+
+This program is distributed in the hope that it will be useful, but
+WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+General Public License for more details.
+
+You should have received a copy of the GNU General Public License
+along with this program; if not, write to the Free Software
+Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+USA
+
+Any questions relating to this software should be directed to:
+
+Dmitry Tsarkov
+Department of Computer Science
+University of Manchester
+Room 2.90
+Kilburn Building
+Oxford Road
+Manchester
+M13 9PL
+UK
+
+email: tsarkov@cs.man.ac.uk

diff -r 756f1f5798bf -r 40adbcb2a7cc OPPL/FaCT++-linux-v1.5.2/licensing/gpl.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/OPPL/FaCT++-linux-v1.5.2/licensing/gpl.txt Tue Oct 11 11:09:52 2011 +0200

b'@@ -0,0 +1,340 @@\n+\t\t GNU GENERAL PUBLIC LICENSE\n+\t\t Version 2, June 1991\n+\n+ Copyright (C) 1989, 1991 Free Software Foundation, Inc.\n+ 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA\n+ Everyone is permitted to copy and distribute verbatim copies\n+ of this license document, but changing it is not allowed.\n+\n+\t\t\t Preamble\n+\n+ The licenses for most software are designed to take away your\n+freedom to share and change it. By contrast, the GNU General Public\n+License is intended to guarantee your freedom to share and change free\n+software--to make sure the software is free for all its users. This\n+General Public License applies to most of the Free Software\n+Foundation\'s software and to any other program whose authors commit to\n+using it. (Some other Free Software Foundation software is covered by\n+the GNU Library General Public License instead.) You can apply it to\n+your programs, too.\n+\n+ When we speak of free software, we are referring to freedom, not\n+price. Our General Public Licenses are designed to make sure that you\n+have the freedom to distribute copies of free software (and charge for\n+this service if you wish), that you receive source code or can get it\n+if you want it, that you can change the software or use pieces of it\n+in new free programs; and that you know you can do these things.\n+\n+ To protect your rights, we need to make restrictions that forbid\n+anyone to deny you these rights or to ask you to surrender the rights.\n+These restrictions translate to certain responsibilities for you if you\n+distribute copies of the software, or if you modify it.\n+\n+ For example, if you distribute copies of such a program, whether\n+gratis or for a fee, you must give the recipients all the rights that\n+you have. You must make sure that they, too, receive or can get the\n+source code. And you must show them these terms so they know their\n+rights.\n+\n+ We protect your rights with two steps: (1) copyright the software, and\n+(2) offer you this license which gives you legal permission to copy,\n+distribute and/or modify the software.\n+\n+ Also, for each author\'s protection and ours, we want to make certain\n+that everyone understands that there is no warranty for this free\n+software. If the software is modified by someone else and passed on, we\n+want its recipients to know that what they have is not the original, so\n+that any problems introduced by others will not reflect on the original\n+authors\' reputations.\n+\n+ Finally, any free program is threatened constantly by software\n+patents. We wish to avoid the danger that redistributors of a free\n+program will individually obtain patent licenses, in effect making the\n+program proprietary. To prevent this, we have made it clear that any\n+patent must be licensed for everyone\'s free use or not licensed at all.\n+\n+ The precise terms and conditions for copying, distribution and\n+modification follow.\n+\x0c\n+\t\t GNU GENERAL PUBLIC LICENSE\n+ TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION\n+\n+ 0. This License applies to any program or other work which contains\n+a notice placed by the copyright holder saying it may be distributed\n+under the terms of this General Public License. The "Program", below,\n+refers to any such program or work, and a "work based on the Program"\n+means either the Program or any derivative work under copyright law:\n+that is to say, a work containing the Program or a portion of it,\n+either verbatim or with modifications and/or translated into another\n+language. (Hereinafter, translation is included without limitation in\n+the term "modification".) Each licensee is addressed as "you".\n+\n+Activities other than copying, distribution and modification are not\n+covered by this License; they are outside its scope. The act of\n+running the Program is not restricted, and the output from the Program\n+is covered only if its contents constitute a work based on the\n+Program (independent of having been made by running t'..b'ND/OR OTHER PARTIES\n+PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED\n+OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF\n+MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS\n+TO THE QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE\n+PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING,\n+REPAIR OR CORRECTION.\n+\n+ 12. IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING\n+WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR\n+REDISTRIBUTE THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES,\n+INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING\n+OUT OF THE USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED\n+TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY\n+YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER\n+PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE\n+POSSIBILITY OF SUCH DAMAGES.\n+\n+\t\t END OF TERMS AND CONDITIONS\n+\x0c\n+\t How to Apply These Terms to Your New Programs\n+\n+ If you develop a new program, and you want it to be of the greatest\n+possible use to the public, the best way to achieve this is to make it\n+free software which everyone can redistribute and change under these terms.\n+\n+ To do so, attach the following notices to the program. It is safest\n+to attach them to the start of each source file to most effectively\n+convey the exclusion of warranty; and each file should have at least\n+the "copyright" line and a pointer to where the full notice is found.\n+\n+ <one line to give the program\'s name and a brief idea of what it does.>\n+ Copyright (C) <year> <name of author>\n+\n+ This program is free software; you can redistribute it and/or modify\n+ it under the terms of the GNU General Public License as published by\n+ the Free Software Foundation; either version 2 of the License, or\n+ (at your option) any later version.\n+\n+ This program is distributed in the hope that it will be useful,\n+ but WITHOUT ANY WARRANTY; without even the implied warranty of\n+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\n+ GNU General Public License for more details.\n+\n+ You should have received a copy of the GNU General Public License\n+ along with this program; if not, write to the Free Software\n+ Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA\n+\n+\n+Also add information on how to contact you by electronic and paper mail.\n+\n+If the program is interactive, make it output a short notice like this\n+when it starts in an interactive mode:\n+\n+ Gnomovision version 69, Copyright (C) year name of author\n+ Gnomovision comes with ABSOLUTELY NO WARRANTY; for details type `show w\'.\n+ This is free software, and you are welcome to redistribute it\n+ under certain conditions; type `show c\' for details.\n+\n+The hypothetical commands `show w\' and `show c\' should show the appropriate\n+parts of the General Public License. Of course, the commands you use may\n+be called something other than `show w\' and `show c\'; they could even be\n+mouse-clicks or menu items--whatever suits your program.\n+\n+You should also get your employer (if you work as a programmer) or your\n+school, if any, to sign a "copyright disclaimer" for the program, if\n+necessary. Here is a sample; alter the names:\n+\n+ Yoyodyne, Inc., hereby disclaims all copyright interest in the program\n+ `Gnomovision\' (which makes passes at compilers) written by James Hacker.\n+\n+ <signature of Ty Coon>, 1 April 1989\n+ Ty Coon, President of Vice\n+\n+This General Public License does not permit incorporating your program into\n+proprietary programs. If your program is a subroutine library, you may\n+consider it more useful to permit linking proprietary applications with the\n+library. If this is what you want to do, use the GNU Library General\n+Public License instead of this License.\n'

diff -r 756f1f5798bf -r 40adbcb2a7cc OPPL/FaCT++-linux-v1.5.2/licensing/lgpl-2.1.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/OPPL/FaCT++-linux-v1.5.2/licensing/lgpl-2.1.txt Tue Oct 11 11:09:52 2011 +0200

[

b"@@ -0,0 +1,504 @@\n+\t\t GNU LESSER GENERAL PUBLIC LICENSE\n+\t\t Version 2.1, February 1999\n+\n+ Copyright (C) 1991, 1999 Free Software Foundation, Inc.\n+ 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA\n+ Everyone is permitted to copy and distribute verbatim copies\n+ of this license document, but changing it is not allowed.\n+\n+[This is the first released version of the Lesser GPL. It also counts\n+ as the successor of the GNU Library Public License, version 2, hence\n+ the version number 2.1.]\n+\n+\t\t\t Preamble\n+\n+ The licenses for most software are designed to take away your\n+freedom to share and change it. By contrast, the GNU General Public\n+Licenses are intended to guarantee your freedom to share and change\n+free software--to make sure the software is free for all its users.\n+\n+ This license, the Lesser General Public License, applies to some\n+specially designated software packages--typically libraries--of the\n+Free Software Foundation and other authors who decide to use it. You\n+can use it too, but we suggest you first think carefully about whether\n+this license or the ordinary General Public License is the better\n+strategy to use in any particular case, based on the explanations below.\n+\n+ When we speak of free software, we are referring to freedom of use,\n+not price. Our General Public Licenses are designed to make sure that\n+you have the freedom to distribute copies of free software (and charge\n+for this service if you wish); that you receive source code or can get\n+it if you want it; that you can change the software and use pieces of\n+it in new free programs; and that you are informed that you can do\n+these things.\n+\n+ To protect your rights, we need to make restrictions that forbid\n+distributors to deny you these rights or to ask you to surrender these\n+rights. These restrictions translate to certain responsibilities for\n+you if you distribute copies of the library or if you modify it.\n+\n+ For example, if you distribute copies of the library, whether gratis\n+or for a fee, you must give the recipients all the rights that we gave\n+you. You must make sure that they, too, receive or can get the source\n+code. If you link other code with the library, you must provide\n+complete object files to the recipients, so that they can relink them\n+with the library after making changes to the library and recompiling\n+it. And you must show them these terms so they know their rights.\n+\n+ We protect your rights with a two-step method: (1) we copyright the\n+library, and (2) we offer you this license, which gives you legal\n+permission to copy, distribute and/or modify the library.\n+\n+ To protect each distributor, we want to make it very clear that\n+there is no warranty for the free library. Also, if the library is\n+modified by someone else and passed on, the recipients should know\n+that what they have is not the original version, so that the original\n+author's reputation will not be affected by problems that might be\n+introduced by others.\n+\x0c\n+ Finally, software patents pose a constant threat to the existence of\n+any free program. We wish to make sure that a company cannot\n+effectively restrict the users of a free program by obtaining a\n+restrictive license from a patent holder. Therefore, we insist that\n+any patent license obtained for a version of the library must be\n+consistent with the full freedom of use specified in this license.\n+\n+ Most GNU software, including some libraries, is covered by the\n+ordinary GNU General Public License. This license, the GNU Lesser\n+General Public License, applies to certain designated libraries, and\n+is quite different from the ordinary General Public License. We use\n+this license for certain libraries in order to permit linking those\n+libraries into non-free programs.\n+\n+ When a program is linked with a library, whether statically or using\n+a shared library, the combination of the two is legally speaking a\n+combined work, a derivative of the original library. The "..b'rsion number, you may choose any version ever published by\n+the Free Software Foundation.\n+\x0c\n+ 14. If you wish to incorporate parts of the Library into other free\n+programs whose distribution conditions are incompatible with these,\n+write to the author to ask for permission. For software which is\n+copyrighted by the Free Software Foundation, write to the Free\n+Software Foundation; we sometimes make exceptions for this. Our\n+decision will be guided by the two goals of preserving the free status\n+of all derivatives of our free software and of promoting the sharing\n+and reuse of software generally.\n+\n+\t\t\t NO WARRANTY\n+\n+ 15. BECAUSE THE LIBRARY IS LICENSED FREE OF CHARGE, THERE IS NO\n+WARRANTY FOR THE LIBRARY, TO THE EXTENT PERMITTED BY APPLICABLE LAW.\n+EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR\n+OTHER PARTIES PROVIDE THE LIBRARY "AS IS" WITHOUT WARRANTY OF ANY\n+KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE\n+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR\n+PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE\n+LIBRARY IS WITH YOU. SHOULD THE LIBRARY PROVE DEFECTIVE, YOU ASSUME\n+THE COST OF ALL NECESSARY SERVICING, REPAIR OR CORRECTION.\n+\n+ 16. IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN\n+WRITING WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY\n+AND/OR REDISTRIBUTE THE LIBRARY AS PERMITTED ABOVE, BE LIABLE TO YOU\n+FOR DAMAGES, INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR\n+CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OR INABILITY TO USE THE\n+LIBRARY (INCLUDING BUT NOT LIMITED TO LOSS OF DATA OR DATA BEING\n+RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A\n+FAILURE OF THE LIBRARY TO OPERATE WITH ANY OTHER SOFTWARE), EVEN IF\n+SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH\n+DAMAGES.\n+\n+\t\t END OF TERMS AND CONDITIONS\n+\x0c\n+ How to Apply These Terms to Your New Libraries\n+\n+ If you develop a new library, and you want it to be of the greatest\n+possible use to the public, we recommend making it free software that\n+everyone can redistribute and change. You can do so by permitting\n+redistribution under these terms (or, alternatively, under the terms of the\n+ordinary General Public License).\n+\n+ To apply these terms, attach the following notices to the library. It is\n+safest to attach them to the start of each source file to most effectively\n+convey the exclusion of warranty; and each file should have at least the\n+"copyright" line and a pointer to where the full notice is found.\n+\n+ <one line to give the library\'s name and a brief idea of what it does.>\n+ Copyright (C) <year> <name of author>\n+\n+ This library is free software; you can redistribute it and/or\n+ modify it under the terms of the GNU Lesser General Public\n+ License as published by the Free Software Foundation; either\n+ version 2.1 of the License, or (at your option) any later version.\n+\n+ This library is distributed in the hope that it will be useful,\n+ but WITHOUT ANY WARRANTY; without even the implied warranty of\n+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU\n+ Lesser General Public License for more details.\n+\n+ You should have received a copy of the GNU Lesser General Public\n+ License along with this library; if not, write to the Free Software\n+ Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA\n+\n+Also add information on how to contact you by electronic and paper mail.\n+\n+You should also get your employer (if you work as a programmer) or your\n+school, if any, to sign a "copyright disclaimer" for the library, if\n+necessary. Here is a sample; alter the names:\n+\n+ Yoyodyne, Inc., hereby disclaims all copyright interest in the\n+ library `Frob\' (a library for tweaking knobs) written by James Random Hacker.\n+\n+ <signature of Ty Coon>, 1 April 1990\n+ Ty Coon, President of Vice\n+\n+That\'s all there is to it!\n+\n+\n'

diff -r 756f1f5798bf -r 40adbcb2a7cc OPPL/README
--- a/OPPL/README Sun Sep 18 12:57:22 2011 +0200
+++ b/OPPL/README Tue Oct 11 11:09:52 2011 +0200

@@ -12,8 +12,8 @@

1.- Stop galaxy.

-2.- Copy oppl_galaxy_tool.jar and oppl_galaxy_tool_lib/ to
-/galaxy-dist/tool-data/shared/jars/.
+2.- Copy oppl_galaxy_tool.jar, FaCT++-linux-v1.5.2/ FaCT++-OSX-v1.5.2/
+and oppl_galaxy_tool_lib/ to /galaxy-dist/tool-data/shared/jars/.

3.- Create directory /galaxy-dist/tools/OPPL/.

@@ -43,15 +43,33 @@
Ontology Pre Processor Language
>> Execute an OPPL file against an OWL file

+An ontology produced by another galaxy tools can also be used
+

FORESEEN FEATURES
=================

Choose which inferred axioms to add to the output ontology (Right now
-only subsumption is available).
+only subsumption between named classes is available).
+
+OWLLink support.
+
+
+
+KNOWN BUGS AND ISSUES
+=====================

-FaCT++ and OWLLink support.
+Currently Galaxy interprets any information thrown to stderr as a tool
+error, which is bad since OPPL (And many other tools) throw info to
+sdterr even if working properly. In OPPL Galaxy, stderr is redirected to
+/dev/null to avoid the problem, but that means that OPPL Galaxy does not
+fail gracefully (It simply stops). A wrapper will be implemented.
+
+http://wiki.g2.bx.psu.edu/Future/Job%20Failure%20When%20stderr
+
+OBO rendering does not work properly if the URIs lack the fragment or
+if an object property lacks an rdfs:label.

@@ -104,7 +122,8 @@
You should have received a copy of the GNU General Public License
along with this program. If not, see <http://www.gnu.org/licenses/>.

-OPPL, OWL API and Pellet have their own licenses.
+OPPL API, OWL API, Pellet, HermiT, FaCT++ and OBOformat have their own
+licenses.

Galaxy is distributed as open source under the conditions of the
Academic Free License (http://www.opensource.org/licenses/academic.php).

diff -r 756f1f5798bf -r 40adbcb2a7cc OPPL/Tool.java
--- a/OPPL/Tool.java Sun Sep 18 12:57:22 2011 +0200
+++ b/OPPL/Tool.java Tue Oct 11 11:09:52 2011 +0200

[

b'@@ -17,12 +17,17 @@\n \n package es.upm.fi.dia.oeg.oppl.galaxy;\n \n+import java.io.BufferedWriter;\n import java.io.File;\n-import java.io.FileNotFoundException;\n+//import java.io.PrintWriter;\n+//import java.io.FileNotFoundException;\n+import java.io.IOException;\n+import java.io.OutputStreamWriter;\n+import java.net.URISyntaxException;\n import java.util.ArrayList;\n import java.util.List;\n import java.util.Scanner;\n-import java.util.logging.Level;\n+//import java.util.logging.Level;\n import java.util.logging.Logger;\n \n import org.coode.oppl.ChangeExtractor;\n@@ -30,29 +35,46 @@\n import org.coode.oppl.OPPLScript;\n import org.coode.oppl.ParserFactory;\n import org.coode.oppl.exceptions.QuickFailRuntimeExceptionHandler;\n-import org.coode.oppl.log.Logging;\n+//import org.coode.oppl.log.Logging;\n import org.coode.owlapi.obo.parser.OBOOntologyFormat;\n import org.coode.parsers.ErrorListener;\n import org.coode.parsers.LoggerErrorListener;\n+//import org.obolibrary.obo2owl.Owl2Obo;\n+//import org.obolibrary.oboformat.model.OBODoc;\n+//import org.obolibrary.oboformat.writer.OBOFormatWriter;\n import org.semanticweb.owlapi.apibinding.OWLManager;\n import org.semanticweb.owlapi.io.RDFXMLOntologyFormat;\n import org.semanticweb.owlapi.io.SystemOutDocumentTarget;\n+import org.semanticweb.owlapi.model.AddAxiom;\n import org.semanticweb.owlapi.model.IRI;\n+import org.semanticweb.owlapi.model.OWLAnnotation;\n+import org.semanticweb.owlapi.model.OWLAnnotationProperty;\n import org.semanticweb.owlapi.model.OWLAxiom;\n import org.semanticweb.owlapi.model.OWLAxiomChange;\n+import org.semanticweb.owlapi.model.OWLClass;\n import org.semanticweb.owlapi.model.OWLDataFactory;\n+import org.semanticweb.owlapi.model.OWLLiteral;\n+//import org.semanticweb.owlapi.model.OWLObjectProperty;\n import org.semanticweb.owlapi.model.OWLOntology;\n+import org.semanticweb.owlapi.model.OWLOntologyChange;\n import org.semanticweb.owlapi.model.OWLOntologyCreationException;\n import org.semanticweb.owlapi.model.OWLOntologyIRIMapper;\n import org.semanticweb.owlapi.model.OWLOntologyManager;\n import org.semanticweb.owlapi.model.OWLOntologyStorageException;\n+//import org.semanticweb.owlapi.owllink.OWLlinkHTTPXMLReasonerFactory;\n import org.semanticweb.owlapi.reasoner.InferenceType;\n import org.semanticweb.owlapi.reasoner.OWLReasoner;\n import org.semanticweb.owlapi.reasoner.OWLReasonerFactory;\n import org.semanticweb.owlapi.util.InferredAxiomGenerator;\n import org.semanticweb.owlapi.util.InferredOntologyGenerator;\n import org.semanticweb.owlapi.util.InferredSubClassAxiomGenerator;\n+import org.semanticweb.owlapi.util.OWLEntityRenamer;\n+import org.semanticweb.owlapi.util.OWLOntologyMerger;\n import org.semanticweb.owlapi.util.SimpleIRIMapper;\n+import org.semanticweb.owlapi.vocab.OWL2Datatype;\n+import org.semanticweb.owlapi.vocab.OWLRDFVocabulary;\n+\n+import uk.ac.manchester.cs.factplusplus.owlapiv3.FaCTPlusPlusReasonerFactory;\n \n import com.clarkparsia.pellet.owlapiv3.PelletReasonerFactory;\n \n@@ -64,18 +86,20 @@\n public class Tool {\n \n \t/**\n-\t * @throws FileNotFoundException \n \t * @throws OWLOntologyCreationException \n \t * @throws OWLOntologyStorageException \n+\t * @throws IOException \n+\t * @throws URISyntaxException \n \t */\n-\tpublic static void main(String[] args) throws FileNotFoundException, OWLOntologyCreationException, OWLOntologyStorageException {\t\t\n+\tpublic static void main(String[] args) throws OWLOntologyCreationException, OWLOntologyStorageException, IOException, URISyntaxException {\t\t\n \t\t// Get the arguments from command-line\n \t\tString OWLFilePath = args [0]; \n \t\tString OPPL_script_file = args [1];\n \t\tString Output_format = args [2]; // OWL|OBO\n-\t\tString Add_inferred = args [3]; // Add_inferred|Whatever\n-\t\tString imports_file_path = args [4]; // Flat tab delimited file: URI\tDocument URI\n-\t\tString reasoner_type = args [5]; // Pellet|HermiT\n+\t\tString Add_inferred = args [3]; // AddInferred|Whatever\n+\t\tString imports_file_path = args [4]; // NoImports|Flat tab delimited file: URI\tDocument URI\n+\t\tString r'..b'nferredOntologyGenerator iog = new InferredOntologyGenerator(reasoner, gens);\n \t\t\tiog.fillOntology(manager, OWL_ontology);\t\n \t\t}\n+\t\t\n+\t\t// Print the ontology to the standard output so other galaxy tools can operate on it\n+\t\t\n+\t\t// Do not merge ontologies\n+\t\tif(merge_URI.equals("NoMerge")){\n+\t\t\tsaveOntology(manager, OWL_ontology, Output_format);\n+\t\t}\n+\t\t// Merge ontologies\n+\t\telse{\t\n+\t\t\tOWLOntologyMerger merger = new OWLOntologyMerger(manager);\n+\t\t\tIRI mergedOntologyIRI = IRI.create(merge_URI);\n+\t\t\tOWLOntology merged = merger.createMergedOntology(manager, mergedOntologyIRI);\n+\t\t\tsaveOntology(manager, merged, Output_format);\n+\t\t}\n+\t}\n+\t\n+\tprivate static void saveOntology (OWLOntologyManager manager, OWLOntology ontology, String Format) throws OWLOntologyStorageException, IOException, URISyntaxException {\n+\t\t\n+\t\t// OBO format\n+\t\tif(Format.equals("OBO")){\n+\t\t\t\n+\t\t\t// OWL API generates bad OBO but OBOformat doesn\'t work either so I correct the OWL API problems (More predictable) in a temporary file\n+\t\t\t// Very inefficient but no time for another solution\n+\t\t\t\n+\t\t\tOWLDataFactory factory = manager.getOWLDataFactory();\n+\t\t\t\n+\t\t\tOWLEntityRenamer renamer = new OWLEntityRenamer (manager, manager.getOntologies());\n+\t\t\tOWLAnnotationProperty label = factory.getOWLAnnotationProperty(OWLRDFVocabulary.RDFS_LABEL.getIRI());\n+\t\t\t\n+\t\t\tfor(OWLClass cls : ontology.getClassesInSignature()){\n+\t\t\t\t// Remove annotations (OWL API generates bad OBO annotations)\n+\t\t\t\t\n+\t\t\t\t// Keep rdfs:label\n+\t\t\t\tString class_name = null;\n+\t\t\t\tfor (OWLAnnotation annotation : cls.getAnnotations(ontology, label)) {\n+\t if (annotation.getValue() instanceof OWLLiteral) {\n+\t OWLLiteral val = (OWLLiteral) annotation.getValue();\n+\t class_name = val.getLiteral();\n+\t }\n+\t }\n+\t\t\t\t\t\t\t\n+//\t\t\t\tI have to remove all the annotations cause I don\'t know which ones are rendered properly\n+\t\t\t\tmanager.removeAxioms(ontology,ontology.getAnnotationAssertionAxioms(cls.getIRI()));\n+\t\t\t\t\n+\t\t\t\t// Add rdfs:label again\n+\t\t\t\tOWLAnnotation labelAnno = factory.getOWLAnnotation(factory.getOWLAnnotationProperty(\n+\t\t\t\tOWLRDFVocabulary.RDFS_LABEL.getIRI()),factory.getOWLLiteral(class_name,OWL2Datatype.XSD_STRING));\n+\t\t\t\tOWLAxiom ax = factory.getOWLAnnotationAssertionAxiom(cls.getIRI(), labelAnno);\n+\t\t\t\tmanager.applyChange(new AddAxiom(ontology, ax));\n+\t\t\t\t\n+\t\t\t\t// Rename entities\n+\t\t\t\tString cls_IRI = cls.getIRI().toString();\n+\t\t\t\tString cls_proper_IRI = cls_IRI.replace("_", ":");\n+\t\t\t\tList<OWLOntologyChange> changes = renamer.changeIRI(cls, IRI.create(cls_proper_IRI));\n+\t\t\t\tmanager.applyChanges(changes);\n+\t\t\t}\n+\t\t\t\n+\t\t\tFile file = new File("tmp.obo");\n+\t\t\tmanager.saveOntology(ontology, new OBOOntologyFormat(), IRI.create(file.toURI()));\n+\t\t\tBufferedWriter bw = new BufferedWriter(new OutputStreamWriter(System.out));\t\t\n+\t\t\tScanner input = new Scanner(file);\n+\t\t\tString buffer = "";\n \n-\t\t// Print the ontology to the standard output so other galaxy tools can operate on the output\t\n-\t\tif(Output_format.equals("OBO")){\n-\t\t\tmanager.saveOntology(OWL_ontology, new OBOOntologyFormat(), new SystemOutDocumentTarget());\n+\t\t\twhile(input.hasNext()){\n+\t\t\t\tString nextLine = input.nextLine();\n+\t\t\t\tif(nextLine.contains("[Term]") || nextLine.contains("[Typedef]")){\n+\t\t\t\t\tif(buffer.isEmpty()){\n+\t\t\t\t\t\tbw.write(buffer);\n+\t\t\t\t\t\tbw.newLine();\n+\t\t\t\t\t}\n+\t\t\t\t}\n+\t\t\t\tif(!nextLine.contains("is_a: Thing") && !nextLine.contains("auto-generated-by:") && !nextLine.contains("id_space:") && !nextLine.contains("! ----")){\n+\t\t\t\t\tif(!nextLine.isEmpty() && !buffer.contains("relationship:")){\n+\t\t\t\t\t\tbw.write(nextLine);\n+\t\t\t\t\t\tbw.newLine();\n+\t\t\t\t\t}\n+\t\t\t\t}\n+\t\t\t\tbuffer = nextLine;\n+\t\t\t}\n+\t\t\tinput.close();\n+\t\t\tbw.close();\n+\t\t\tfile.delete();\n \t\t}\n+\t\t\n+\t\t//OWL format\n \t\telse{\n-\t\t\tmanager.saveOntology(OWL_ontology, new RDFXMLOntologyFormat(), new SystemOutDocumentTarget());\n+\t\t\tmanager.saveOntology(ontology, new RDFXMLOntologyFormat(), new SystemOutDocumentTarget());\n \t\t}\n \t}\n }\n'

diff -r 756f1f5798bf -r 40adbcb2a7cc OPPL/oppl.xml
--- a/OPPL/oppl.xml Sun Sep 18 12:57:22 2011 +0200
+++ b/OPPL/oppl.xml Tue Oct 11 11:09:52 2011 +0200

b'@@ -1,39 +1,87 @@\n-<tool id="oppl" name="Execute an OPPL file against an ontology" version="1.0.4">\n+\xef\xbb\xbf<tool id="oppl" name="Execute an OPPL file against an ontology" version="1.0.5">\n \t<description>It executes an OPPL script against the input ontology and generates a new ontology with the changes described in the OPPL script</description>\n \n \t\n \t\n \t\n+\t\n+\n+\t\n \n \t<command>\n-\t\t#if $import_opts.imports_select==False #java -Xmx7000M -Xms250M -DentityExpansionLimit=1000000000 -jar ${__tool_data_path__}/shared/jars/oppl_galaxy_tool.jar $input $OPPL $format $inferred NoImports $reasoner > $output 2>/dev/null\n-\t\t#else #java -Xmx7000M -Xms250M -DentityExpansionLimit=1000000000 -jar ${__tool_data_path__}/shared/jars/oppl_galaxy_tool.jar $input $OPPL $format $inferred $imports $reasoner > $output 2>/dev/null\n+\t\t#if $import_opts.imports_select==False #java -Xmx7000M -Xms250M -DentityExpansionLimit=1000000000 -jar ${__tool_data_path__}/shared/jars/oppl_galaxy_tool.jar $input $OPPL $format $inferred NoImports $reasoner NoMerge > $output 2>/dev/null\n+\t\t#else #java -Xmx7000M -Xms250M -DentityExpansionLimit=1000000000 -jar ${__tool_data_path__}/shared/jars/oppl_galaxy_tool.jar $input $OPPL $format $inferred $imports $reasoner $merged > $output 2>/dev/null\n+\t\t#end if\n+\t</command> \n+\t\n+\t\n+\t\n+\t\n+\t\n+\t\n+\t\n+\t\n+\t\n+\t\n+\t\n+\t\n \t\t\n-\t\n+\t\n+\t\n+\t\n+\t\t\t\t \n+\t\t\t\t\n+\t\t\t\t\n \t\t</when>\n \t\t</conditional>\n \t\t<param name="format" type="select" label="Choose ontology output format">\n \t\t\t<option value="OWL" selected="true">OWL</option>\n \t\t\t<option value="OBO">OBO</option>\n \t\t</param>\n-\t\t<param name="inferred" type="boolean" value="False" truevalue="Add_inferred" falsevalue="Gora_ni" label="Add inferred subsumption axioms to output ontology"/>\n+\t\t<param name="inferred" type="boolean" value="False" truevalue="AddInferred" falsevalue="Gora_ni" label="Add inferred subsumption axioms to output ontology"/>\n+\t\t<param name="merged" type="text" size="100" value="NoMerge" label="To merge the ontologies, type an URI for the new ontology (Leave NoMerge for not merging)" />\n \t\t<param name="reasoner" type="select" label="Choose reasoner">\n \t\t\t<option value="Pellet" selected="true">Pellet</option>\n \t\t\t<option value="HermiT">HermiT</option>\n+\t\t\t<option value="FaCTPlusPlus">FaCT++</option>\n \t\t</param>\n \n \t</inputs>\n@@ -48,6 +96,7 @@\n \t\t\t<param name="format" value="OWL"/>\n \t\t\t<param name="inferred" value="False"/>\n \t\t\t<param name="reasoner" value="Pellet"/>\n+\t\t\t<param name="merged" value="no_merge"/>\n \t\t\t<output name="out_file" file="test_new.owl"/>\t\n \t\t</test>\n \t</tests>\n@@ -55,7 +104,7 @@\n \n **About OPPL-Galaxy**\n \n- OPPL-Galaxy can be used to execute an OPPL script against an ontology, generating a new ontology. OPPL (Ontology Pre Processor Language) is a high level scripting language, based in the Manchester OWL Syntax, to automate the manipulation of an ontology. An OPPL script (See test.oppl) defines a query to be performed against the ontology, and some actions (Adding or removing axioms) that affect the entities that will be retrieved. Those entities can be named or defined by a variable. OPPL is a powerful method for defining and executing modelling patterns that are repeated in an ontology, saving time and effort. \n+ OPPL-Galaxy can be used to execute an OPPL script against an ontology, generating a new ontology. OPPL (Ontology Pre Processor Language) is a high level scripting language, based in the Manchester OWL Syntax, to automate the manipulation of an ontology. An OPPL script (See test.oppl) defines a query to be performed against the ontology, and some actions (Adding or removing axioms) that affect the entities that will be retrieved. Those entities can be named or defined by a variable. OPPL is a powerful method for defining and executing modelling patterns that are repeated in an ontology, saving time and efforts. \n \n **Formats**\n \n@@ -77,7 +126,9 @@\n \n The inferred subsumption axioms can be added to the output ontology as asserted axioms. \n \n- The reasoner can be Pellet or HermiT. Sometimes, if an execution fails it can be fixed by using a different reasoner. \n+ The reasoner can be Pellet, HermiT FaCT++. Sometimes, if an execution fails it can be fixed by using a different reasoner. \n+\n+ If OWL imports are used, all the ontologies (Main one and imported ones) can be merged in a single ontology for the output.\n \n **More information**\n \n@@ -90,6 +141,10 @@\n http://clarkparsia.com/pellet\n \n http://hermit-reasoner.com/\n+ \n+ http://code.google.com/p/factplusplus/\n+ \n+ http://code.google.com/p/oboformat/\n \n **Contact**\n \n'

diff -r 756f1f5798bf -r 40adbcb2a7cc OPPL/oppl_galaxy_tool.jar

Binary file OPPL/oppl_galaxy_tool.jar has changed

diff -r 756f1f5798bf -r 40adbcb2a7cc OPPL/oppl_galaxy_tool_lib/FaCTpp-OWLAPI-3.2-v1.5.2.jar

Binary file OPPL/oppl_galaxy_tool_lib/FaCTpp-OWLAPI-3.2-v1.5.2.jar has changed

diff -r 756f1f5798bf -r 40adbcb2a7cc OPPL/oppl_galaxy_tool_lib/commons-logging-1.1.1.jar

Binary file OPPL/oppl_galaxy_tool_lib/commons-logging-1.1.1.jar has changed

diff -r 756f1f5798bf -r 40adbcb2a7cc OPPL/oppl_galaxy_tool_lib/junit-4.8.2.jar

Binary file OPPL/oppl_galaxy_tool_lib/junit-4.8.2.jar has changed

diff -r 756f1f5798bf -r 40adbcb2a7cc OPPL/oppl_galaxy_tool_lib/junit.jar

Binary file OPPL/oppl_galaxy_tool_lib/junit.jar has changed

diff -r 756f1f5798bf -r 40adbcb2a7cc OPPL/oppl_galaxy_tool_lib/log4j-1.2.15.jar

Binary file OPPL/oppl_galaxy_tool_lib/log4j-1.2.15.jar has changed

diff -r 756f1f5798bf -r 40adbcb2a7cc OPPL/oppl_galaxy_tool_lib/oboformat.jar

Binary file OPPL/oppl_galaxy_tool_lib/oboformat.jar has changed

diff -r 756f1f5798bf -r 40adbcb2a7cc OPPL/oppl_galaxy_tool_lib/owlapi-bin_2.jar

Binary file OPPL/oppl_galaxy_tool_lib/owlapi-bin_2.jar has changed

diff -r 756f1f5798bf -r 40adbcb2a7cc OPPL/oppl_galaxy_tool_lib/owllink-bin.jar

Binary file OPPL/oppl_galaxy_tool_lib/owllink-bin.jar has changed