Mercurial > repos > mikel-egana-aranguren > oppl
changeset 8:40adbcb2a7cc
Added merge function and FaCT++ support. Improved OBO render
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--- /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 +
--- /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 @@ -0,0 +1,201 @@ +; updated 05-04-06 + +;;TEST DATA +(defdatarole R); + +;GT and LT +;testing simple satisfiable and unsatisfiable ranges +(defconcept TTa1 (and (some R(gt (number 18))) (some R(lt(number 60))))) +(defconcept TTa2 (and (some R(gt (number 60))) (some R(lt(number 18)))));unsat +(defconcept TTa3 (and (some R(lt (number 18))) (some R(gt(number 60)))));unsat +(defconcept TTa4 (and (some R(lt (number 60))) (some R(gt(number 18))))) +(defconcept TTa5 (and (some R(gt (number 18))) (some R(lt(number 18)))));unsat +(defconcept TTa6 (and (some R(lt (number 60))) (some R(gt(number 60)))));unsat +;the 4 below should eventually simplify +(defconcept TTb1 (and (some R(gt (number 18))) (some R(gt(number 60))))) +(defconcept TTb2 (and (some R(gt (number 60))) (some R(gt(number 18))))) +(defconcept TTb3 (and (some R(lt (number 18))) (some R(lt(number 60))))) +(defconcept TTb4 (and (some R(lt (number 60))) (some R(lt(number 18))))) +(defconcept TTb5 (and (some R(gt (number 18))) (some R(gt(number 18))))) +(defconcept TTb6 (and (some R(lt (number 60))) (some R(lt(number 60))))) +;testing ranges together with specific values +(defconcept TTc1 (and (some R(gt (number 18))) (some R(number 60)))) +(defconcept TTc2 (and (some R(gt (number 60))) (some R(number 18))));unsat +(defconcept TTc3 (and (some R(lt (number 18))) (some R(number 60))));unsat +(defconcept TTc4 (and (some R(lt (number 60))) (some R(number 18)))) +(defconcept TTd1 (and (some R(number 18)) (some R(gt (number 60)))));unsat +(defconcept TTd2 (and (some R(number 60)) (some R(gt (number 18))))) +(defconcept TTd3 (and (some R(number 18)) (some R(lt (number 60))))) +(defconcept TTd4 (and (some R(number 60)) (some R(lt (number 18)))));unsat +(defconcept TTe1 (and (some R(number 18)) (some R(lt(number 18)))));unsat +(defconcept TTe2 (and (some R(number 60)) (some R(gt(number 60)))));unsat +(defconcept TTe3 (and (some R(lt (number 60))) (some R(number 60))));unsat +(defconcept TTe4 (and (some R(gt (number 18))) (some R(number 18))));unsat + +;GE and LT +;testing simple satisfiable and unsatisfiable ranges +(defconcept ETa1 (and (some R(ge (number 18))) (some R(lt(number 60))))) +(defconcept ETa2 (and (some R(ge (number 60))) (some R(lt(number 18)))));unsat +(defconcept ETa3 (and (some R(le (number 18))) (some R(gt(number 60)))));unsat +(defconcept ETa4 (and (some R(le (number 60))) (some R(gt(number 18))))) +(defconcept ETa5 (and (some R(ge (number 18))) (some R(lt(number 18)))));unsat +(defconcept ETa6 (and (some R(le (number 60))) (some R(gt(number 60)))));unsat +;the 4 below should eventually simplify +(defconcept ETb1 (and (some R(ge (number 18))) (some R(gt(number 60))))) +(defconcept ETb2 (and (some R(ge (number 60))) (some R(gt(number 18))))) +(defconcept ETb3 (and (some R(le (number 18))) (some R(lt(number 60))))) +(defconcept ETb4 (and (some R(le (number 60))) (some R(lt(number 18))))) +(defconcept ETb5 (and (some R(ge (number 18))) (some R(gt(number 18))))) +(defconcept ETb6 (and (some R(le (number 60))) (some R(lt(number 60))))) +;testing ranges together with specific values +(defconcept ETc1 (and (some R(ge (number 18))) (some R(number 60)))) +(defconcept ETc2 (and (some R(ge (number 60))) (some R(number 18))));unsat +(defconcept ETc3 (and (some R(le (number 18))) (some R(number 60))));unsat +(defconcept ETc4 (and (some R(le (number 60))) (some R(number 18)))) +(defconcept ETd1 (and (some R(number 18)) (some R(gt (number 60)))));unsat +(defconcept ETd2 (and (some R(number 60)) (some R(gt (number 18))))) +(defconcept ETd3 (and (some R(number 18)) (some R(lt (number 60))))) +(defconcept ETd4 (and (some R(number 60)) (some R(lt (number 18)))));unsat +(defconcept ETe1 (and (some R(number 18)) (some R(lt(number 18)))));unsat +(defconcept ETe2 (and (some R(number 60)) (some R(gt(number 60)))));unsat +(defconcept ETe3 (and (some R(le (number 60))) (some R(number 60)))) +(defconcept ETe4 (and (some R(ge (number 18))) (some R(number 18)))) + +;GE and LE +;testing simple satisfiable and unsatisfiable ranges +(defconcept EEa1 (and (some R(ge (number 18))) (some R(le(number 60))))) +(defconcept EEa2 (and (some R(ge (number 60))) (some R(le(number 18)))));unsat +(defconcept EEa3 (and (some R(le (number 18))) (some R(ge(number 60)))));unsat +(defconcept EEa4 (and (some R(le (number 60))) (some R(ge(number 18))))) +(defconcept EEa5 (and (some R(ge (number 18))) (some R(le(number 18))))) +(defconcept EEa6 (and (some R(le (number 60))) (some R(ge(number 60))))) +;the 4 below should eventually simplify +(defconcept EEb1 (and (some R(ge (number 18))) (some R(ge(number 60))))) +(defconcept EEb2 (and (some R(ge (number 60))) (some R(ge(number 18))))) +(defconcept EEb3 (and (some R(le (number 18))) (some R(le(number 60))))) +(defconcept EEb4 (and (some R(le (number 60))) (some R(le(number 18))))) +(defconcept EEb5 (and (some R(ge (number 18))) (some R(ge(number 18))))) +(defconcept EEb6 (and (some R(le (number 60))) (some R(le(number 60))))) +;testing ranges together with specific values +(defconcept EEc1 (and (some R(ge (number 18))) (some R(number 60)))) +(defconcept EEc2 (and (some R(ge (number 60))) (some R(number 18))));unsat +(defconcept EEc3 (and (some R(le (number 18))) (some R(number 60))));unsat +(defconcept EEc4 (and (some R(le (number 60))) (some R(number 18)))) +(defconcept EEd1 (and (some R(number 18)) (some R(ge (number 60)))));unsat +(defconcept EEd2 (and (some R(number 60)) (some R(ge (number 18))))) +(defconcept EEd3 (and (some R(number 18)) (some R(le (number 60))))) +(defconcept EEd4 (and (some R(number 60)) (some R(le (number 18)))));unsat +(defconcept EEe1 (and (some R(number 18)) (some R(le(number 18))))) +(defconcept EEe2 (and (some R(number 60)) (some R(ge(number 60))))) +(defconcept EEe3 (and (some R(le (number 60))) (some R(number 60)))) +(defconcept EEe4 (and (some R(ge (number 18))) (some R(number 18)))) + +;GT and LE +;testing simple satisfiable and unsatisfiable ranges +(defconcept TEa1 (and (some R(gt (number 18))) (some R(le(number 60))))) +(defconcept TEa2 (and (some R(gt (number 60))) (some R(le(number 18)))));unsat +(defconcept TEa3 (and (some R(lt (number 18))) (some R(ge(number 60)))));unsat +(defconcept TEa4 (and (some R(lt (number 60))) (some R(ge(number 18))))) +(defconcept TEa5 (and (some R(gt (number 18))) (some R(le(number 18)))));unsat +(defconcept TEa6 (and (some R(lt (number 60))) (some R(ge(number 60)))));unsat +;the 4 below should eventually simplify +(defconcept TEb1 (and (some R(gt (number 18))) (some R(ge(number 60))))) +(defconcept TEb2 (and (some R(gt (number 60))) (some R(ge(number 18))))) +(defconcept TEb3 (and (some R(lt (number 18))) (some R(le(number 60))))) +(defconcept TEb4 (and (some R(lt (number 60))) (some R(le(number 18))))) +(defconcept TEb5 (and (some R(gt (number 18))) (some R(ge(number 18))))) +(defconcept TEb6 (and (some R(lt (number 60))) (some R(le(number 60))))) +;testing ranges together with specific values +(defconcept TEc1 (and (some R(gt (number 18))) (some R(number 60)))) +(defconcept TEc2 (and (some R(gt (number 60))) (some R(number 18))));unsat +(defconcept TEc3 (and (some R(lt (number 18))) (some R(number 60))));unsat +(defconcept TEc4 (and (some R(lt (number 60))) (some R(number 18)))) +(defconcept TEd1 (and (some R(number 18)) (some R(ge (number 60)))));unsat +(defconcept TEd2 (and (some R(number 60)) (some R(ge (number 18))))) +(defconcept TEd3 (and (some R(number 18)) (some R(le (number 60))))) +(defconcept TEd4 (and (some R(number 60)) (some R(le (number 18)))));unsat +(defconcept TEe1 (and (some R(number 18)) (some R(le(number 18))))) +(defconcept TEe2 (and (some R(number 60)) (some R(ge(number 60))))) +(defconcept TEe3 (and (some R(lt (number 60))) (some R(number 60))));unsat +(defconcept TEe4 (and (some R(gt (number 18))) (some R(number 18))));unsat + +;Doubles - not supported +(defconcept double1 (and (some R(gt (number 18.4))) (some R(lt (number 18.5)))));unsat +(defconcept double2 (and (some R(lt (number 18.4))) (some R(gt (number 18.5)))));unsat + +;Testing range cross-over +(defconcept between1 (and (some R(between (number 28) (number 60))) (some R(between (number 18) (number 50))))) +(defconcept inrange1 (and (some R(in-range (number 18) (number 50))) (some R(in-range (number 28) (number 60))))) +(defconcept between2 (and (some R(between (number 18) (number 28))) (some R(between (number 50) (number 60)))));unsat +(defconcept inrange2 (and (some R(in-range (number 50) (number 60))) (some R(in-range (number 18) (number 28)))));unsat + +;Check that 1a and 1b, and 2a and 2b are equivalent +(defconcept equiv1a (and (some R(gt (number 18))) (some R(lt (number 60))))) +(defconcept equiv1b (some R(between (number 18) (number 60)))) +(defconcept equiv2a (and (some R(ge (number 18))) (some R(le (number 60))))) +(defconcept equiv2b (some R(in-range (number 18) (number 60)))) + +;Strings +(defconcept str01 (and (some R(gt(string AWord))) (some R(lt(string BWord))))) +(defconcept str02 (and (some R(lt(string AWord))) (some R(gt(string BWord)))));unsat +(defconcept str03 (and (some R(gt(string WordA))) (some R(lt(string WordB))))) +(defconcept str04 (and (some R(lt(string WordA))) (some R(gt(string WordB)))));unsat +(defconcept str05 (and (some R(gt(string A))) (some R(lt(string A)))));unsat +(defconcept str06 (and (some R(ge(string A))) (some R(le(string A))))) +(defconcept str07 (and (some R(gt(string A))) (some R(gt(string B))))) +(defconcept str08 (and (some R(lt(string A))) (some R(lt(string B))))) +(defconcept str09 (and (some R(gt(string aa))) (some R(lt(string aaa))))) +(defconcept str10 (and (some R(gt(string aaa))) (some R(lt(string aa)))));unsat +(defconcept str11 (and (some R(gt(string AWord))) (some R(string BWord)))) +(defconcept str12 (and (some R(lt(string AWord))) (some R(string BWord))));unsat + +;Subsumption tests +(defconcept subNumA (and (some R (ge (number 5))) (some R (le (number 10))))) ; subsumes TOP +(defconcept subNumB (and (some R (ge (number 5))) (some R (lt (number 10))))) ; subsumes a +(defconcept subNumC (and (some R (gt (number 5))) (some R (le (number 10))))) ; subsumes a +(defconcept subNumD (and (some R (gt (number 5))) (some R (lt (number 10))))) ; subsumes b, c (a) +(defconcept subNumE (some R (number 5))) ; subsumes b (a) +(defconcept subNumF (some R (number 10))) ; subsumes c (a) +(defconcept subStrA (and (some R (ge (string a))) (some R (le (string b))))) ; subsumes TOP +(defconcept subStrB (and (some R (ge (string a))) (some R (lt (string b))))) ; subsumes a +(defconcept subStrC (and (some R (gt (string a))) (some R (le (string b))))) ; subsumes a +(defconcept subStrD (and (some R (gt (string a))) (some R (lt (string b))))) ; subsumes b, c (a) +(defconcept subStrE (some R (string a))) ; subsumes b (a) +(defconcept subStrF (some R (string b))) ; subsumes c (a) + +;Mix of types unsatisfiability test +(defconcept mix1 (and (some R (gt (number 5))) (some R (lt (string five)))));unsat +(defconcept mix2 (and (some R (gt (number 5))) (some R (lt (string 5)))));unsat + +;Check that negative type saturation works correcly +(defconcept negSat1N (and (some R (number)) (not (some R (le (number 5)))) (not (some R (number 6))) (not(some R (ge (number 7))))));unsat +(defconcept negSat2N (and (some R (number)) (not (some R (lt (number 5)))) (not (some R (number 6))) (not(some R (ge (number 7)))))) +(defconcept negSat3N (and (some R (number)) (not (some R (le (number 5)))) (not (some R (number 6))) (not(some R (gt (number 7)))))) +(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 +(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 +(defconcept negSat1S (and (some R (string)) (not (some R (le (string a)))) (not (some R (string b))) (not(some R (ge (string c)))))) + +;negative subsumption tests +;C = E +;D = F +;I subsumes A +;J subsumes C +;H subsumes B +;G subsumes D +;F subsumes B +;E subsumes A +;M subsumes L +(defconcept subSumpA (not (some R(lt (number 2))))) +(defconcept subSumpB (not (some R(gt (number 5))))) +(defconcept subSumpC (not (some R(le (number 2))))) +(defconcept subSumpD (not (some R(ge (number 5))))) +(defconcept subSumpE (and (not (some R(lt (number 2)))) (not (some R (number 2))))) +(defconcept subSumpF (and (not (some R(gt (number 5)))) (not (some R (number 5))))) +(defconcept subSumpG (and (some R(lt (number 5))))) +(defconcept subSumpH (and (some R(le (number 5))))) +(defconcept subSumpI (and (some R(ge (number 2))))) +(defconcept subSumpJ (and (some R(gt (number 2))))) +(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 +(defconcept subSumpL (and (not (some R(number 2))) (not (some R(number 3))) (not (some R(number 4))))) +(defconcept subSumpM (some R(le (number 1)))) +(defconcept subSumpN (and (not (some R(number 2))) (some R (number 2))));unsat
--- /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)
--- /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 +
--- /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!"
--- /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 +
--- /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 +;--
--- /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
--- /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
--- /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 @@ -0,0 +1,340 @@ + GNU GENERAL PUBLIC LICENSE + Version 2, June 1991 + + Copyright (C) 1989, 1991 Free Software Foundation, Inc. + 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA + Everyone is permitted to copy and distribute verbatim copies + of this license document, but changing it is not allowed. + + Preamble + + The licenses for most software are designed to take away your +freedom to share and change it. By contrast, the GNU General Public +License is intended to guarantee your freedom to share and change free +software--to make sure the software is free for all its users. This +General Public License applies to most of the Free Software +Foundation's software and to any other program whose authors commit to +using it. (Some other Free Software Foundation software is covered by +the GNU Library General Public License instead.) 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--- /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 @@ -0,0 +1,504 @@ + GNU LESSER GENERAL PUBLIC LICENSE + Version 2.1, February 1999 + + Copyright (C) 1991, 1999 Free Software Foundation, Inc. + 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA + Everyone is permitted to copy and distribute verbatim copies + of this license document, but changing it is not allowed. + +[This is the first released version of the Lesser GPL. It also counts + as the successor of the GNU Library Public License, version 2, hence + the version number 2.1.] + + Preamble + + The licenses for most software are designed to take away your +freedom to share and change it. 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--- 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).
--- a/OPPL/Tool.java Sun Sep 18 12:57:22 2011 +0200 +++ b/OPPL/Tool.java Tue Oct 11 11:09:52 2011 +0200 @@ -17,12 +17,17 @@ package es.upm.fi.dia.oeg.oppl.galaxy; +import java.io.BufferedWriter; import java.io.File; -import java.io.FileNotFoundException; +//import java.io.PrintWriter; +//import java.io.FileNotFoundException; +import java.io.IOException; +import java.io.OutputStreamWriter; +import java.net.URISyntaxException; import java.util.ArrayList; import java.util.List; import java.util.Scanner; -import java.util.logging.Level; +//import java.util.logging.Level; import java.util.logging.Logger; import org.coode.oppl.ChangeExtractor; @@ -30,29 +35,46 @@ import org.coode.oppl.OPPLScript; import org.coode.oppl.ParserFactory; import org.coode.oppl.exceptions.QuickFailRuntimeExceptionHandler; -import org.coode.oppl.log.Logging; +//import org.coode.oppl.log.Logging; import org.coode.owlapi.obo.parser.OBOOntologyFormat; import org.coode.parsers.ErrorListener; import org.coode.parsers.LoggerErrorListener; +//import org.obolibrary.obo2owl.Owl2Obo; +//import org.obolibrary.oboformat.model.OBODoc; +//import org.obolibrary.oboformat.writer.OBOFormatWriter; import org.semanticweb.owlapi.apibinding.OWLManager; import org.semanticweb.owlapi.io.RDFXMLOntologyFormat; import org.semanticweb.owlapi.io.SystemOutDocumentTarget; +import org.semanticweb.owlapi.model.AddAxiom; import org.semanticweb.owlapi.model.IRI; +import org.semanticweb.owlapi.model.OWLAnnotation; +import org.semanticweb.owlapi.model.OWLAnnotationProperty; import org.semanticweb.owlapi.model.OWLAxiom; import org.semanticweb.owlapi.model.OWLAxiomChange; +import org.semanticweb.owlapi.model.OWLClass; import org.semanticweb.owlapi.model.OWLDataFactory; +import org.semanticweb.owlapi.model.OWLLiteral; +//import org.semanticweb.owlapi.model.OWLObjectProperty; import org.semanticweb.owlapi.model.OWLOntology; +import org.semanticweb.owlapi.model.OWLOntologyChange; import org.semanticweb.owlapi.model.OWLOntologyCreationException; import org.semanticweb.owlapi.model.OWLOntologyIRIMapper; import org.semanticweb.owlapi.model.OWLOntologyManager; import org.semanticweb.owlapi.model.OWLOntologyStorageException; +//import org.semanticweb.owlapi.owllink.OWLlinkHTTPXMLReasonerFactory; import org.semanticweb.owlapi.reasoner.InferenceType; import org.semanticweb.owlapi.reasoner.OWLReasoner; import org.semanticweb.owlapi.reasoner.OWLReasonerFactory; import org.semanticweb.owlapi.util.InferredAxiomGenerator; import org.semanticweb.owlapi.util.InferredOntologyGenerator; import org.semanticweb.owlapi.util.InferredSubClassAxiomGenerator; +import org.semanticweb.owlapi.util.OWLEntityRenamer; +import org.semanticweb.owlapi.util.OWLOntologyMerger; import org.semanticweb.owlapi.util.SimpleIRIMapper; +import org.semanticweb.owlapi.vocab.OWL2Datatype; +import org.semanticweb.owlapi.vocab.OWLRDFVocabulary; + +import uk.ac.manchester.cs.factplusplus.owlapiv3.FaCTPlusPlusReasonerFactory; import com.clarkparsia.pellet.owlapiv3.PelletReasonerFactory; @@ -64,18 +86,20 @@ public class Tool { /** - * @throws FileNotFoundException * @throws OWLOntologyCreationException * @throws OWLOntologyStorageException + * @throws IOException + * @throws URISyntaxException */ - public static void main(String[] args) throws FileNotFoundException, OWLOntologyCreationException, OWLOntologyStorageException { + public static void main(String[] args) throws OWLOntologyCreationException, OWLOntologyStorageException, IOException, URISyntaxException { // Get the arguments from command-line String OWLFilePath = args [0]; String OPPL_script_file = args [1]; String Output_format = args [2]; // OWL|OBO - String Add_inferred = args [3]; // Add_inferred|Whatever - String imports_file_path = args [4]; // Flat tab delimited file: URI Document URI - String reasoner_type = args [5]; // Pellet|HermiT + String Add_inferred = args [3]; // AddInferred|Whatever + String imports_file_path = args [4]; // NoImports|Flat tab delimited file: URI Document URI + String reasoner_type = args [5]; // Pellet|FaCTPlusPlus|HermiT + String merge_URI = args [6]; // NoMerge|URI for merged ontology // Load the main ontology File owl_file = new File(OWLFilePath); @@ -97,21 +121,33 @@ } imports_input.close(); } - OWLDataFactory factory = manager.getOWLDataFactory(); OWLOntology OWL_ontology = manager.loadOntologyFromOntologyDocument(owl_file); // Reasoner OWLReasonerFactory reasonerFactory = null; OWLReasoner reasoner = null; + + // Pellet if(reasoner_type.equals("Pellet")){ reasonerFactory = new PelletReasonerFactory(); reasoner = reasonerFactory.createReasoner(OWL_ontology); } + // FaCTPlusPlus + else if (reasoner_type.equals("FaCTPlusPlus")){ + reasonerFactory = new FaCTPlusPlusReasonerFactory(); + reasoner = reasonerFactory.createReasoner(OWL_ontology); + } + // HermiT else{ reasonerFactory = new Reasoner.ReasonerFactory(); reasoner = reasonerFactory.createReasoner(OWL_ontology); } + // OWLLink: The problem is that Racer, for example, listens in 8080, the same port as Galaxy + // I have to change Racer settings and OWLLink settings +// OWLlinkHTTPXMLReasonerFactory factory = new OWLlinkHTTPXMLReasonerFactory(); +// reasoner = factory.createReasoner(OWL_ontology); + // Load the flat file with script in memory String OPPL_script_source = ""; File file = new File(OPPL_script_file); @@ -136,20 +172,100 @@ manager.applyChanges(changes); // Add the inferred axioms as asserted axioms to the original ontology - if(Add_inferred.equals("Add_inferred")){ + if(Add_inferred.equals("AddInferred")){ reasoner.precomputeInferences(InferenceType.CLASS_HIERARCHY); List<InferredAxiomGenerator<? extends OWLAxiom>> gens = new ArrayList<InferredAxiomGenerator<? extends OWLAxiom>>(); gens.add(new InferredSubClassAxiomGenerator()); InferredOntologyGenerator iog = new InferredOntologyGenerator(reasoner, gens); iog.fillOntology(manager, OWL_ontology); } + + // Print the ontology to the standard output so other galaxy tools can operate on it + + // Do not merge ontologies + if(merge_URI.equals("NoMerge")){ + saveOntology(manager, OWL_ontology, Output_format); + } + // Merge ontologies + else{ + OWLOntologyMerger merger = new OWLOntologyMerger(manager); + IRI mergedOntologyIRI = IRI.create(merge_URI); + OWLOntology merged = merger.createMergedOntology(manager, mergedOntologyIRI); + saveOntology(manager, merged, Output_format); + } + } + + private static void saveOntology (OWLOntologyManager manager, OWLOntology ontology, String Format) throws OWLOntologyStorageException, IOException, URISyntaxException { + + // OBO format + if(Format.equals("OBO")){ + + // OWL API generates bad OBO but OBOformat doesn't work either so I correct the OWL API problems (More predictable) in a temporary file + // Very inefficient but no time for another solution + + OWLDataFactory factory = manager.getOWLDataFactory(); + + OWLEntityRenamer renamer = new OWLEntityRenamer (manager, manager.getOntologies()); + OWLAnnotationProperty label = factory.getOWLAnnotationProperty(OWLRDFVocabulary.RDFS_LABEL.getIRI()); + + for(OWLClass cls : ontology.getClassesInSignature()){ + // Remove annotations (OWL API generates bad OBO annotations) + + // Keep rdfs:label + String class_name = null; + for (OWLAnnotation annotation : cls.getAnnotations(ontology, label)) { + if (annotation.getValue() instanceof OWLLiteral) { + OWLLiteral val = (OWLLiteral) annotation.getValue(); + class_name = val.getLiteral(); + } + } + +// I have to remove all the annotations cause I don't know which ones are rendered properly + manager.removeAxioms(ontology,ontology.getAnnotationAssertionAxioms(cls.getIRI())); + + // Add rdfs:label again + OWLAnnotation labelAnno = factory.getOWLAnnotation(factory.getOWLAnnotationProperty( + OWLRDFVocabulary.RDFS_LABEL.getIRI()),factory.getOWLLiteral(class_name,OWL2Datatype.XSD_STRING)); + OWLAxiom ax = factory.getOWLAnnotationAssertionAxiom(cls.getIRI(), labelAnno); + manager.applyChange(new AddAxiom(ontology, ax)); + + // Rename entities + String cls_IRI = cls.getIRI().toString(); + String cls_proper_IRI = cls_IRI.replace("_", ":"); + List<OWLOntologyChange> changes = renamer.changeIRI(cls, IRI.create(cls_proper_IRI)); + manager.applyChanges(changes); + } + + File file = new File("tmp.obo"); + manager.saveOntology(ontology, new OBOOntologyFormat(), IRI.create(file.toURI())); + BufferedWriter bw = new BufferedWriter(new OutputStreamWriter(System.out)); + Scanner input = new Scanner(file); + String buffer = ""; - // Print the ontology to the standard output so other galaxy tools can operate on the output - if(Output_format.equals("OBO")){ - manager.saveOntology(OWL_ontology, new OBOOntologyFormat(), new SystemOutDocumentTarget()); + while(input.hasNext()){ + String nextLine = input.nextLine(); + if(nextLine.contains("[Term]") || nextLine.contains("[Typedef]")){ + if(buffer.isEmpty()){ + bw.write(buffer); + bw.newLine(); + } + } + if(!nextLine.contains("is_a: Thing") && !nextLine.contains("auto-generated-by:") && !nextLine.contains("id_space:") && !nextLine.contains("! ----")){ + if(!nextLine.isEmpty() && !buffer.contains("relationship:")){ + bw.write(nextLine); + bw.newLine(); + } + } + buffer = nextLine; + } + input.close(); + bw.close(); + file.delete(); } + + //OWL format else{ - manager.saveOntology(OWL_ontology, new RDFXMLOntologyFormat(), new SystemOutDocumentTarget()); + manager.saveOntology(ontology, new RDFXMLOntologyFormat(), new SystemOutDocumentTarget()); } } }
--- a/OPPL/oppl.xml Sun Sep 18 12:57:22 2011 +0200 +++ b/OPPL/oppl.xml Tue Oct 11 11:09:52 2011 +0200 @@ -1,39 +1,87 @@ -<tool id="oppl" name="Execute an OPPL file against an ontology" version="1.0.4"> +<tool id="oppl" name="Execute an OPPL file against an ontology" version="1.0.5"> <description>It executes an OPPL script against the input ontology and generates a new ontology with the changes described in the OPPL script</description> <!-- The command execution of the conditional is tacky, I think, but it works! --> <!-- Galaxy is not happy with OPPL throwing info into stderr, and I have redirected stderr to /dev/null, which is a bad solution since OPPL galaxy does not inform properly when it fails --> <!-- More info on the stderr issue: http://wiki.g2.bx.psu.edu/Future/Job%20Failure%20When%20stderr --> + + + <!-- For big ontologies I use -Xmx7000M -Xms250M -DentityExpansionLimit=1000000000 If that's too much for your machine simply delete or modify at will --> <command> - #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 - #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 + #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 + #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 + #end if + </command> + + + <!-- If you are planning to use FaCT++ you have to uncomment bellow (And comment the one above) and replace the -Djava.library.path with the appropiate JNI library path for your platform:FaCT++-linux-v1.5.2/64bit, FaCT++-linux-v1.5.2/32bit, FaCT++-OSX-v1.5.2/64bit, ...... --> + <!-- Using this setting doesn't upset the rest of the reasoners so you may as well leave it on if you plan to switch between FaCT++, Pellet and HermiT --> + + <!--<command> + #if $import_opts.imports_select==False #java -Djava.library.path=${__tool_data_path__}/shared/jars/FaCT++-linux-v1.5.2/64bit -Xmx7000M -Xms250M -DentityExpansionLimit=1000000000 -jar ${__tool_data_path__}/shared/jars/oppl_galaxy_tool.jar $input $OPPL $format $inferred NoImports $reasoner NoMerge > $output 2>/dev/null + #else #java -Djava.library.path=${__tool_data_path__}/shared/jars/FaCT++-linux-v1.5.2/64bit -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 #end if - </command> + </command>--> + + + <!-- For debugging simply remove 2>/dev/null Or uncomment bellow. It will fail always (Due to OPPL messages) but at least it will be informative --> + + <!--<command> + #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 no_merge > $output + #else #java -Xmx7000M -Xms250M -DentityExpansionLimit=1000000000 -jar ${__tool_data_path__}/shared/jars/oppl_galaxy_tool.jar $input $OPPL $format $inferred $imports $reasoner $merged > $output + #end if + </command>--> + - <!-- For big ontologies use something like java -Xmx7000M -Xms250M -DentityExpansionLimit=1000000000 -jar --> + <!-- EXPERIMENTS AND HOUSE KEEPING--> + <!--<command>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</command> --> + <!--<command> + #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 + #else + #if $merge_opts.merge_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 + #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 + #end if + #end if + </command>--> <inputs> <param format="text" name="input" type="data" label="Input ontology file"/> <param format="text" name="OPPL" type="data" label="OPPL file"/> <conditional name="import_opts"> <param name="imports_select" type="boolean" value="False" truevalue="imports_yes" falsevalue="imports_no" label="Tick the box if the loaded ontology includes OWL imports"/> - <when value="imports_no"/> + + <!-- EXPERIMENTS AND HOUSE KEEPING--> + <!--<when value="imports_no"/> --> <!--<when value="imports_no"> - <param type="hidden" name="imports" value="NoImports"/> + <param type="hidden" name="merged" value="no_merge"/> </when>--> + <when value="imports_yes"> - <param format="text" name="imports" type="data" label="OWL imports URI mapping file"/> + + <param format="text" name="imports" type="data" label="OWL imports URI mapping file"/> + + <!-- EXPERIMENTS AND HOUSE KEEPING--> + <!--<conditional name="merge_opts"> + <param name="merge_select" type="boolean" value="False" truevalue="merge_yes" falsevalue="merge_no" label="Tick the box to merge ontologies"/> + <when value="merge_yes"> + <param name="merged" type="text" size="100" value="http://oppl-galaxy/merged" label="Type an URI or use the default URI" /> + </when> + </conditional>--> + <!--<param format="text" name="merged" type="data" label="OWL "/>--> + </when> </conditional> <param name="format" type="select" label="Choose ontology output format"> <option value="OWL" selected="true">OWL</option> <option value="OBO">OBO</option> </param> - <param name="inferred" type="boolean" value="False" truevalue="Add_inferred" falsevalue="Gora_ni" label="Add inferred subsumption axioms to output ontology"/> + <param name="inferred" type="boolean" value="False" truevalue="AddInferred" falsevalue="Gora_ni" label="Add inferred subsumption axioms to output ontology"/> + <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)" /> <param name="reasoner" type="select" label="Choose reasoner"> <option value="Pellet" selected="true">Pellet</option> <option value="HermiT">HermiT</option> + <option value="FaCTPlusPlus">FaCT++</option> </param> </inputs> @@ -48,6 +96,7 @@ <param name="format" value="OWL"/> <param name="inferred" value="False"/> <param name="reasoner" value="Pellet"/> + <param name="merged" value="no_merge"/> <output name="out_file" file="test_new.owl"/> </test> </tests> @@ -55,7 +104,7 @@ **About OPPL-Galaxy** - 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. + 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. **Formats** @@ -77,7 +126,9 @@ The inferred subsumption axioms can be added to the output ontology as asserted axioms. - The reasoner can be Pellet or HermiT. Sometimes, if an execution fails it can be fixed by using a different reasoner. + The reasoner can be Pellet, HermiT FaCT++. Sometimes, if an execution fails it can be fixed by using a different reasoner. + + If OWL imports are used, all the ontologies (Main one and imported ones) can be merged in a single ontology for the output. **More information** @@ -90,6 +141,10 @@ http://clarkparsia.com/pellet http://hermit-reasoner.com/ + + http://code.google.com/p/factplusplus/ + + http://code.google.com/p/oboformat/ **Contact**