# HG changeset patch # User Mikel Egana Aranguren # Date 1349553039 -7200 # Node ID cc270db37d3370d6d0e2f25b398e1448ad387bff # Parent d3616fac4ca5a599a925d46331b6ae5343d6b38d Directories re-arranged diff -r d3616fac4ca5 -r cc270db37d33 FaCT++-OSX-v1.5.2/32bit/libFaCTPlusPlusJNI.jnilib Binary file FaCT++-OSX-v1.5.2/32bit/libFaCTPlusPlusJNI.jnilib has changed diff -r d3616fac4ca5 -r cc270db37d33 FaCT++-OSX-v1.5.2/64bit/libFaCTPlusPlusJNI.jnilib Binary file FaCT++-OSX-v1.5.2/64bit/libFaCTPlusPlusJNI.jnilib has changed diff -r d3616fac4ca5 -r cc270db37d33 FaCT++-linux-v1.5.2/32bit/FaCT++ Binary file FaCT++-linux-v1.5.2/32bit/FaCT++ has changed diff -r d3616fac4ca5 -r cc270db37d33 FaCT++-linux-v1.5.2/32bit/libFaCTPlusPlusJNI.so Binary file FaCT++-linux-v1.5.2/32bit/libFaCTPlusPlusJNI.so has changed diff -r d3616fac4ca5 -r cc270db37d33 FaCT++-linux-v1.5.2/64bit/FaCT++ Binary file FaCT++-linux-v1.5.2/64bit/FaCT++ has changed diff -r d3616fac4ca5 -r cc270db37d33 FaCT++-linux-v1.5.2/64bit/libFaCTPlusPlusJNI.so Binary file FaCT++-linux-v1.5.2/64bit/libFaCTPlusPlusJNI.so has changed diff -r d3616fac4ca5 -r cc270db37d33 FaCT++-linux-v1.5.2/Models.lisp/DataTypeTest/DataTypeTest.conf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/FaCT++-linux-v1.5.2/Models.lisp/DataTypeTest/DataTypeTest.conf Sat Oct 06 21:50:39 2012 +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 d3616fac4ca5 -r cc270db37d33 FaCT++-linux-v1.5.2/Models.lisp/DataTypeTest/DataTypeTest.tbox --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/FaCT++-linux-v1.5.2/Models.lisp/DataTypeTest/DataTypeTest.tbox Sat Oct 06 21:50:39 2012 +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 diff -r d3616fac4ca5 -r cc270db37d33 FaCT++-linux-v1.5.2/Models.lisp/DataTypeTest/Makefile --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/FaCT++-linux-v1.5.2/Models.lisp/DataTypeTest/Makefile Sat Oct 06 21:50:39 2012 +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 d3616fac4ca5 -r cc270db37d33 FaCT++-linux-v1.5.2/Models.lisp/Makefile.default --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/FaCT++-linux-v1.5.2/Models.lisp/Makefile.default Sat Oct 06 21:50:39 2012 +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 d3616fac4ca5 -r cc270db37d33 FaCT++-linux-v1.5.2/Models.lisp/create-new-test --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/FaCT++-linux-v1.5.2/Models.lisp/create-new-test Sat Oct 06 21:50:39 2012 +0200 @@ -0,0 +1,60 @@ +#!/bin/bash + +# Script for creating new test-suit. +# In parameters: +# output: +# - create directory +# - copy into /.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 " + echo " where: -- unique name for new suit" + echo " -- 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 d3616fac4ca5 -r cc270db37d33 FaCT++-linux-v1.5.2/Models.lisp/options.default --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/FaCT++-linux-v1.5.2/Models.lisp/options.default Sat Oct 06 21:50:39 2012 +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 d3616fac4ca5 -r cc270db37d33 FaCT++-linux-v1.5.2/Models.lisp/query.default --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/FaCT++-linux-v1.5.2/Models.lisp/query.default Sat Oct 06 21:50:39 2012 +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 d3616fac4ca5 -r cc270db37d33 FaCT++-linux-v1.5.2/licensing/FaCT++.license.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/FaCT++-linux-v1.5.2/licensing/FaCT++.license.txt Sat Oct 06 21:50:39 2012 +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. 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See the GNU + Lesser General Public License for more details. + + You should have received a copy of the GNU Lesser General Public + License along with this library; if not, write to the Free Software + Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA + +Also add information on how to contact you by electronic and paper mail. + +You should also get your employer (if you work as a programmer) or your +school, if any, to sign a "copyright disclaimer" for the library, if +necessary. Here is a sample; alter the names: + + Yoyodyne, Inc., hereby disclaims all copyright interest in the + library `Frob' (a library for tweaking knobs) written by James Random Hacker. + + , 1 April 1990 + Ty Coon, President of Vice + +That's all there is to it! + + diff -r d3616fac4ca5 -r cc270db37d33 OPPL/FaCT++-OSX-v1.5.2/32bit/libFaCTPlusPlusJNI.jnilib Binary file OPPL/FaCT++-OSX-v1.5.2/32bit/libFaCTPlusPlusJNI.jnilib has changed diff -r d3616fac4ca5 -r cc270db37d33 OPPL/FaCT++-OSX-v1.5.2/64bit/libFaCTPlusPlusJNI.jnilib Binary file OPPL/FaCT++-OSX-v1.5.2/64bit/libFaCTPlusPlusJNI.jnilib has changed diff -r d3616fac4ca5 -r cc270db37d33 OPPL/FaCT++-linux-v1.5.2/32bit/FaCT++ Binary file OPPL/FaCT++-linux-v1.5.2/32bit/FaCT++ has changed diff -r d3616fac4ca5 -r cc270db37d33 OPPL/FaCT++-linux-v1.5.2/32bit/libFaCTPlusPlusJNI.so Binary file OPPL/FaCT++-linux-v1.5.2/32bit/libFaCTPlusPlusJNI.so has changed diff -r d3616fac4ca5 -r cc270db37d33 OPPL/FaCT++-linux-v1.5.2/64bit/FaCT++ Binary file OPPL/FaCT++-linux-v1.5.2/64bit/FaCT++ has changed diff -r d3616fac4ca5 -r cc270db37d33 OPPL/FaCT++-linux-v1.5.2/64bit/libFaCTPlusPlusJNI.so Binary file OPPL/FaCT++-linux-v1.5.2/64bit/libFaCTPlusPlusJNI.so has changed diff -r d3616fac4ca5 -r cc270db37d33 OPPL/FaCT++-linux-v1.5.2/Models.lisp/DataTypeTest/DataTypeTest.conf --- a/OPPL/FaCT++-linux-v1.5.2/Models.lisp/DataTypeTest/DataTypeTest.conf Thu Sep 20 12:46:36 2012 +0200 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,148 +0,0 @@ -[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 d3616fac4ca5 -r cc270db37d33 OPPL/FaCT++-linux-v1.5.2/Models.lisp/DataTypeTest/DataTypeTest.tbox --- a/OPPL/FaCT++-linux-v1.5.2/Models.lisp/DataTypeTest/DataTypeTest.tbox Thu Sep 20 12:46:36 2012 +0200 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,201 +0,0 @@ -; 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 diff -r d3616fac4ca5 -r cc270db37d33 OPPL/FaCT++-linux-v1.5.2/Models.lisp/DataTypeTest/Makefile --- a/OPPL/FaCT++-linux-v1.5.2/Models.lisp/DataTypeTest/Makefile Thu Sep 20 12:46:36 2012 +0200 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,13 +0,0 @@ -# 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 d3616fac4ca5 -r cc270db37d33 OPPL/FaCT++-linux-v1.5.2/Models.lisp/Makefile.default --- a/OPPL/FaCT++-linux-v1.5.2/Models.lisp/Makefile.default Thu Sep 20 12:46:36 2012 +0200 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,8 +0,0 @@ -# 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 d3616fac4ca5 -r cc270db37d33 OPPL/FaCT++-linux-v1.5.2/Models.lisp/create-new-test --- a/OPPL/FaCT++-linux-v1.5.2/Models.lisp/create-new-test Thu Sep 20 12:46:36 2012 +0200 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,60 +0,0 @@ -#!/bin/bash - -# Script for creating new test-suit. -# In parameters: -# output: -# - create directory -# - copy into /.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 " - echo " where: -- unique name for new suit" - echo " -- 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 d3616fac4ca5 -r cc270db37d33 OPPL/FaCT++-linux-v1.5.2/Models.lisp/options.default --- a/OPPL/FaCT++-linux-v1.5.2/Models.lisp/options.default Thu Sep 20 12:46:36 2012 +0200 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,130 +0,0 @@ -[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 d3616fac4ca5 -r cc270db37d33 OPPL/FaCT++-linux-v1.5.2/Models.lisp/query.default --- a/OPPL/FaCT++-linux-v1.5.2/Models.lisp/query.default Thu Sep 20 12:46:36 2012 +0200 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,16 +0,0 @@ -[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 d3616fac4ca5 -r cc270db37d33 OPPL/FaCT++-linux-v1.5.2/README --- a/OPPL/FaCT++-linux-v1.5.2/README Thu Sep 20 12:46:36 2012 +0200 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,126 +0,0 @@ -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 ". Default value of - is 3490. - -This reasoner will avaliable at http://:, where 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://: - -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 d3616fac4ca5 -r cc270db37d33 OPPL/FaCT++-linux-v1.5.2/licensing/FaCT++.license.txt --- a/OPPL/FaCT++-linux-v1.5.2/licensing/FaCT++.license.txt Thu Sep 20 12:46:36 2012 +0200 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,30 +0,0 @@ -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 d3616fac4ca5 -r cc270db37d33 OPPL/FaCT++-linux-v1.5.2/licensing/gpl.txt --- a/OPPL/FaCT++-linux-v1.5.2/licensing/gpl.txt Thu Sep 20 12:46:36 2012 +0200 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,340 +0,0 @@ - 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. 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Here is a sample; alter the names: - - Yoyodyne, Inc., hereby disclaims all copyright interest in the - library `Frob' (a library for tweaking knobs) written by James Random Hacker. - - , 1 April 1990 - Ty Coon, President of Vice - -That's all there is to it! - - diff -r d3616fac4ca5 -r cc270db37d33 OPPL/README --- a/OPPL/README Thu Sep 20 12:46:36 2012 +0200 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,112 +0,0 @@ - - - -INSTALLATION -============ - -1.- Stop Galaxy. - -2.- Copy the following files and directories to -/galaxy-dist/tool-data/shared/jars/: - -oppl_galaxy_tool.jar -inference.jar -query.jar -oppl_query.jar -merge.jar -oppl_galaxy_lib/ -inference_lib/ -query_lib/ -oppl_query_lib/ -merge_lib/ -FaCT++-linux-v1.5.2/ -FaCT++-OSX-v1.5.2/ - -3.- Create directory /galaxy-dist/tools/OPPL/ - -4.- Copy oppl.xml, inference.xml, query.xml, oppl_query.xml and -merge.xml to /galaxy-dist/tools/OPPL/ - -5.- Add the following lines to /galaxy-dist/tool_conf.xml: - -
- - - - - -
- -6.- Start Galaxy. - - - -FORESEEN FEATURES -================= - -- Support for processing ontologies that import other ontologies loaded -in Galaxy (i.e. to resolve imports within galaxy). - -- Entities rendering definition (URI fragment, rdfs:label, QName, etc). - -- OWLLink and Racer support. - -- Standalone OPPL assertions parsing (e.g. ADD phagocyte subClassOf -cell). - -- Other output formats apart from RDF/XML. - -- Support for DataPropertyAssertion, DataPropertyHierarchy, -DifferentIndividuals, ... - - - -KNOWN BUGS AND ISSUES -===================== - -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 - - - -CONTACT -======= - -Please send any request or comment to mikel.egana.aranguren@gmail.com. - - - -ACKNOWLEDGEMENTS -================ - -This work is funded by the Marie Curie Cofund program of the EU, FP7. - - - -COPYRIGHT AND LICENSE -===================== - -Copyright (c) 2011 Mikel Egaña Aranguren. - -(OPPL|Inference|Query|OPPL-Query|Merge)-Galaxy -is free software: you can redistribute it and/or modify it under the -terms of the GNU General Public License as published by the Free -Software Foundation, either version 3 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, see . - -OPPL API, OWL API, Pellet, HermiT, Elk and FaCT++ have their own licenses. - - diff -r d3616fac4ca5 -r cc270db37d33 OPPL/inference.jar Binary file OPPL/inference.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 OPPL/inference.xml --- a/OPPL/inference.xml Thu Sep 20 12:46:36 2012 +0200 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,57 +0,0 @@ - - It performs inference in an OWL ontology and it generates a new ontology with the inferred axioms as asserted axioms - - - - - java -Xmx3000M -Xms250M -DentityExpansionLimit=1000000000 -jar ${__tool_data_path__}/shared/jars/inference.jar $input $reasoner $axioms > $output - - - - - - - - - - - - - - - - - - - - - - - - -**About Inference-Galaxy** - - Inference-Galaxy offers the possibility of performing automated reasoning in an ontology and then injecting the inferred axioms as asserted axioms, generating a new OWL ontology. - -**Usage** - - An ontology is needed as input: load it with Get Data >> Upload File from your computer or redirect the output of another galaxy tool. Inference-Galaxy uses the OWL API, and therefore it can load any ontology format that such API is able to load: OBO flat file, OWL (RDF/XML, OWL/XML, Functional, Manchester), turtle, and KRSS. In case the loaded ontology includes OWL imports, Inference-Galaxy will try to resolve them. - - The reasoner can be Pellet, HermiT, FaCT++ or Elk. - - The inferred axioms to add as asserted axioms can be chosen. - -**Contact** - - Please send any request or comment to mikel.egana.aranguren@gmail.com. - - - - diff -r d3616fac4ca5 -r cc270db37d33 OPPL/inference_lib/FaCTpp-OWLAPI-3.2-v1.5.2.jar Binary file OPPL/inference_lib/FaCTpp-OWLAPI-3.2-v1.5.2.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 OPPL/inference_lib/HermiT.jar Binary file OPPL/inference_lib/HermiT.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 OPPL/inference_lib/antlr-runtime-3.2.jar Binary file OPPL/inference_lib/antlr-runtime-3.2.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 OPPL/inference_lib/aterm-java-1.6.jar Binary file OPPL/inference_lib/aterm-java-1.6.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 OPPL/inference_lib/commons-logging-1.1.1.jar Binary file OPPL/inference_lib/commons-logging-1.1.1.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 OPPL/inference_lib/elk-owlapi.jar Binary file OPPL/inference_lib/elk-owlapi.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 OPPL/inference_lib/jgrapht-jdk1.5.jar Binary file OPPL/inference_lib/jgrapht-jdk1.5.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 OPPL/inference_lib/junit-4.8.2.jar Binary file OPPL/inference_lib/junit-4.8.2.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 OPPL/inference_lib/junit.jar Binary file OPPL/inference_lib/junit.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 OPPL/inference_lib/log4j-1.2.15.jar Binary file OPPL/inference_lib/log4j-1.2.15.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 OPPL/inference_lib/log4j-sources.jar Binary file OPPL/inference_lib/log4j-sources.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 OPPL/inference_lib/log4j.jar Binary file OPPL/inference_lib/log4j.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 OPPL/inference_lib/oboformat.jar Binary file OPPL/inference_lib/oboformat.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 OPPL/inference_lib/org.coode.oppl-API.jar Binary file OPPL/inference_lib/org.coode.oppl-API.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 OPPL/inference_lib/owlapi-bin.jar Binary file OPPL/inference_lib/owlapi-bin.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 OPPL/inference_lib/owlapi-bin_2.jar Binary file OPPL/inference_lib/owlapi-bin_2.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 OPPL/inference_lib/owllink-bin.jar Binary file OPPL/inference_lib/owllink-bin.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 OPPL/inference_lib/parsers.jar Binary file OPPL/inference_lib/parsers.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 OPPL/inference_lib/pellet-core.jar Binary file OPPL/inference_lib/pellet-core.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 OPPL/inference_lib/pellet-datatypes.jar Binary file OPPL/inference_lib/pellet-datatypes.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 OPPL/inference_lib/pellet-el.jar Binary file OPPL/inference_lib/pellet-el.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 OPPL/inference_lib/pellet-owlapiv3.jar Binary file OPPL/inference_lib/pellet-owlapiv3.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 OPPL/inference_lib/pellet-query.jar Binary file OPPL/inference_lib/pellet-query.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 OPPL/inference_lib/pellet-rules.jar Binary file OPPL/inference_lib/pellet-rules.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 OPPL/merge.jar Binary file OPPL/merge.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 OPPL/merge.xml --- a/OPPL/merge.xml Thu Sep 20 12:46:36 2012 +0200 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,44 +0,0 @@ - - If an ontology with import axioms is provided, it will merge the imported ontologies into the main ontology - - - - - - - java -Xmx3000M -Xms250M -DentityExpansionLimit=1000000000 -jar ${__tool_data_path__}/shared/jars/merge.jar $ontology "$uri" > $output - - - - - - - - - - - - -**About Merge-Galaxy** - - Merge-Galaxy can be used to merge any (resolvable) imported ontologies into the main ontology, creating a new ontology. - -**Usage** - - An ontology is needed as input: load it with Get Data >> Upload File from your computer or redirect the output of another galaxy tool. Merge-Galaxy uses the OWL API, and therefore it can load any ontology format that such API is able to load: OBO flat file, OWL (RDF/XML, OWL/XML, Functional, Manchester), turtle, and KRSS. - - An URI can be specified for the new merged ontology. In case non is specified, the following URI will be used: http://cbgp.upm.es/BiologicalInformatics/OPPLGalaxy/merged.owl. - -**Contact** - - Please send any request or comment to mikel.egana.aranguren@gmail.com. - - - - diff -r d3616fac4ca5 -r cc270db37d33 OPPL/merge_lib/FaCTpp-OWLAPI-3.2-v1.5.2.jar Binary file OPPL/merge_lib/FaCTpp-OWLAPI-3.2-v1.5.2.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 OPPL/merge_lib/HermiT.jar Binary file OPPL/merge_lib/HermiT.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 OPPL/merge_lib/antlr-runtime-3.2.jar Binary file OPPL/merge_lib/antlr-runtime-3.2.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 OPPL/merge_lib/aterm-java-1.6.jar Binary file OPPL/merge_lib/aterm-java-1.6.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 OPPL/merge_lib/elk-owlapi.jar Binary file OPPL/merge_lib/elk-owlapi.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 OPPL/merge_lib/jgrapht-jdk1.5.jar Binary file OPPL/merge_lib/jgrapht-jdk1.5.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 OPPL/merge_lib/log4j-sources.jar Binary file OPPL/merge_lib/log4j-sources.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 OPPL/merge_lib/log4j.jar Binary file OPPL/merge_lib/log4j.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 OPPL/merge_lib/org.coode.oppl-API.jar Binary file OPPL/merge_lib/org.coode.oppl-API.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 OPPL/merge_lib/owlapi-bin.jar Binary file OPPL/merge_lib/owlapi-bin.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 OPPL/merge_lib/parsers.jar Binary file OPPL/merge_lib/parsers.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 OPPL/merge_lib/pellet-core.jar Binary file OPPL/merge_lib/pellet-core.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 OPPL/merge_lib/pellet-datatypes.jar Binary file OPPL/merge_lib/pellet-datatypes.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 OPPL/merge_lib/pellet-el.jar Binary file OPPL/merge_lib/pellet-el.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 OPPL/merge_lib/pellet-owlapiv3.jar Binary file OPPL/merge_lib/pellet-owlapiv3.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 OPPL/merge_lib/pellet-query.jar Binary file OPPL/merge_lib/pellet-query.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 OPPL/merge_lib/pellet-rules.jar Binary file OPPL/merge_lib/pellet-rules.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 OPPL/oppl.xml --- a/OPPL/oppl.xml Thu Sep 20 12:46:36 2012 +0200 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,123 +0,0 @@ - - It executes an OPPL script against the input ontology and generates a new ontology with the changes described in the OPPL script - - - - - - - - - - - - - - - - - - - - java -Djava.library.path=${__tool_data_path__}/shared/jars/FaCT++-linux-v1.5.2/64bit -Xmx3000M -Xms250M -DentityExpansionLimit=1000000000 -jar ${__tool_data_path__}/shared/jars/oppl_galaxy.jar $input $reasoner $OPPL $format > $output 2>/dev/null - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -**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 energy. - -**Usage** - - An ontology and an OPPL file are needed (test.owl and test.oppl can be used as samples, both available in the bundle). Load both with Get Data >> Upload File from your computer, or redirect from another Galaxy tool. OPPL-Galaxy uses the OWL API, and therefore it can load any ontology format that such API is able to load: OBO flat file, OWL (RDF/XML, OWL/XML, Functional, Manchester), turtle, and KRSS. In case the loaded ontology includes OWL imports, OPPL-Galaxy will try to resolve them. - - The reasoner can be Pellet, HermiT, FaCT++ or Elk. - - The output ontology can be OBO or OWL (RDF/XML). - -**More information** - - Galaxy public instances with OPPL-Galaxy pre-installed: - - http://sele.inf.um.es:9080/ - - http://linkeddata2.dia.fi.upm.es:8080 - - OPPL-Galaxy Examples: - - http://miuras.inf.um.es/OPPL-Galaxy/ - - OPPL examples: - - http://oppl2.sourceforge.net/taggedexamples/ - - Links of interest: - - http://oppl.sf.net/ - - http://www.w3.org/TR/owl2-manchester-syntax/ - - http://clarkparsia.com/pellet - - http://hermit-reasoner.com/ - - http://code.google.com/p/factplusplus/ - - http://code.google.com/p/elk-reasoner/ - - http://owlapi.sourceforge.net/ - -**Citation** - - Mikel Egaña Aranguren, Jesualdo Tomás Fernández-Breis, Erick Antezana. OPPL-Galaxy: Enhancing ontology exploitation in Galaxy with OPPL. In Proceedings of the 4th International Workshop on Semantic Web Applications and Tools for the Life Sciences, SWAT4LS 2011, pages 12–19, ACM 2012. - -**Contact** - - Please send any request or comment to mikel.egana.aranguren@gmail.com. - - - - diff -r d3616fac4ca5 -r cc270db37d33 OPPL/oppl_galaxy.jar Binary file OPPL/oppl_galaxy.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 OPPL/oppl_galaxy_lib/FaCTpp-OWLAPI-3.2-v1.5.2.jar Binary file OPPL/oppl_galaxy_lib/FaCTpp-OWLAPI-3.2-v1.5.2.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 OPPL/oppl_galaxy_lib/HermiT.jar Binary file OPPL/oppl_galaxy_lib/HermiT.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 OPPL/oppl_galaxy_lib/antlr-runtime-3.2.jar Binary file OPPL/oppl_galaxy_lib/antlr-runtime-3.2.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 OPPL/oppl_galaxy_lib/aterm-java-1.6.jar Binary file OPPL/oppl_galaxy_lib/aterm-java-1.6.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 OPPL/oppl_galaxy_lib/commons-logging-1.1.1.jar Binary file OPPL/oppl_galaxy_lib/commons-logging-1.1.1.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 OPPL/oppl_galaxy_lib/elk-owlapi.jar Binary file OPPL/oppl_galaxy_lib/elk-owlapi.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 OPPL/oppl_galaxy_lib/jgrapht-jdk1.5.jar Binary file OPPL/oppl_galaxy_lib/jgrapht-jdk1.5.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 OPPL/oppl_galaxy_lib/junit-4.8.2.jar Binary file OPPL/oppl_galaxy_lib/junit-4.8.2.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 OPPL/oppl_galaxy_lib/junit.jar Binary file OPPL/oppl_galaxy_lib/junit.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 OPPL/oppl_galaxy_lib/log4j-1.2.15.jar Binary file OPPL/oppl_galaxy_lib/log4j-1.2.15.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 OPPL/oppl_galaxy_lib/log4j-sources.jar Binary file OPPL/oppl_galaxy_lib/log4j-sources.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 OPPL/oppl_galaxy_lib/log4j.jar Binary file OPPL/oppl_galaxy_lib/log4j.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 OPPL/oppl_galaxy_lib/oboformat.jar Binary file OPPL/oppl_galaxy_lib/oboformat.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 OPPL/oppl_galaxy_lib/org.coode.oppl-API.jar Binary file OPPL/oppl_galaxy_lib/org.coode.oppl-API.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 OPPL/oppl_galaxy_lib/owlapi-bin.jar Binary file OPPL/oppl_galaxy_lib/owlapi-bin.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 OPPL/oppl_galaxy_lib/owlapi-bin_2.jar Binary file OPPL/oppl_galaxy_lib/owlapi-bin_2.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 OPPL/oppl_galaxy_lib/owllink-bin.jar Binary file OPPL/oppl_galaxy_lib/owllink-bin.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 OPPL/oppl_galaxy_lib/parsers.jar Binary file OPPL/oppl_galaxy_lib/parsers.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 OPPL/oppl_galaxy_lib/pellet-core.jar Binary file OPPL/oppl_galaxy_lib/pellet-core.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 OPPL/oppl_galaxy_lib/pellet-datatypes.jar Binary file OPPL/oppl_galaxy_lib/pellet-datatypes.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 OPPL/oppl_galaxy_lib/pellet-el.jar Binary file OPPL/oppl_galaxy_lib/pellet-el.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 OPPL/oppl_galaxy_lib/pellet-owlapiv3.jar Binary file OPPL/oppl_galaxy_lib/pellet-owlapiv3.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 OPPL/oppl_galaxy_lib/pellet-query.jar Binary file OPPL/oppl_galaxy_lib/pellet-query.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 OPPL/oppl_galaxy_lib/pellet-rules.jar Binary file OPPL/oppl_galaxy_lib/pellet-rules.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 OPPL/oppl_query.jar Binary file OPPL/oppl_query.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 OPPL/oppl_query.xml --- a/OPPL/oppl_query.xml Thu Sep 20 12:46:36 2012 +0200 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,75 +0,0 @@ - - It performs a query, expressed in OPPL Syntax, against an OWL ontology - - - - - - - - - - - java -Xmx3000M -Xms250M -DentityExpansionLimit=1000000000 -jar ${__tool_data_path__}/shared/jars/oppl_query.jar $ontology $reasoner $answer_format "$query" > $output 2>/dev/null - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -**About OPPL-Query-Galaxy** - - OPPL-Query-Galaxy can be used to execute an OPPL query against an OWL ontology. The result is a two column table with the entities that have been bound by the variables. - -**Usage** - - An ontology is needed as input: load it with Get Data >> Upload File from your computer or redirect the output of another galaxy tool. OPPL-Query-Galaxy uses the OWL API, and therefore it can load any ontology format that such API is able to load: OBO flat file, OWL (RDF/XML, OWL/XML, Functional, Manchester), turtle, and KRSS. In case the loaded ontology includes OWL imports, OPPL-Query-Galaxy will try to resolve them. - - An OPPL query must be provided, e.g. ?whole:CLASS, ?part:CLASS SELECT ?part SubClassOf part_of some ?whole WHERE ?part != Nothing. - - The reasoner can be Pellet, HermiT, FaCT++ or Elk. - - The returned entities can be rendered using their URI, their URI fragment, or OBO type URI fragment (e.g. GO_0000022 to GO:0000022). - -**Contact** - - Please send any request or comment to mikel.egana.aranguren@gmail.com. - - - - diff -r d3616fac4ca5 -r cc270db37d33 OPPL/oppl_query_lib/FaCTpp-OWLAPI-3.2-v1.5.2.jar Binary file OPPL/oppl_query_lib/FaCTpp-OWLAPI-3.2-v1.5.2.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 OPPL/oppl_query_lib/HermiT.jar Binary file OPPL/oppl_query_lib/HermiT.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 OPPL/oppl_query_lib/antlr-runtime-3.2.jar Binary file OPPL/oppl_query_lib/antlr-runtime-3.2.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 OPPL/oppl_query_lib/aterm-java-1.6.jar Binary file OPPL/oppl_query_lib/aterm-java-1.6.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 OPPL/oppl_query_lib/elk-owlapi.jar Binary file OPPL/oppl_query_lib/elk-owlapi.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 OPPL/oppl_query_lib/jgrapht-jdk1.5.jar Binary file OPPL/oppl_query_lib/jgrapht-jdk1.5.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 OPPL/oppl_query_lib/log4j-sources.jar Binary file OPPL/oppl_query_lib/log4j-sources.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 OPPL/oppl_query_lib/log4j.jar Binary file OPPL/oppl_query_lib/log4j.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 OPPL/oppl_query_lib/org.coode.oppl-API.jar Binary file OPPL/oppl_query_lib/org.coode.oppl-API.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 OPPL/oppl_query_lib/owlapi-bin.jar Binary file OPPL/oppl_query_lib/owlapi-bin.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 OPPL/oppl_query_lib/parsers.jar Binary file OPPL/oppl_query_lib/parsers.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 OPPL/oppl_query_lib/pellet-core.jar Binary file OPPL/oppl_query_lib/pellet-core.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 OPPL/oppl_query_lib/pellet-datatypes.jar Binary file OPPL/oppl_query_lib/pellet-datatypes.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 OPPL/oppl_query_lib/pellet-el.jar Binary file OPPL/oppl_query_lib/pellet-el.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 OPPL/oppl_query_lib/pellet-owlapiv3.jar Binary file OPPL/oppl_query_lib/pellet-owlapiv3.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 OPPL/oppl_query_lib/pellet-query.jar Binary file OPPL/oppl_query_lib/pellet-query.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 OPPL/oppl_query_lib/pellet-rules.jar Binary file OPPL/oppl_query_lib/pellet-rules.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 OPPL/query.jar Binary file OPPL/query.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 OPPL/query.xml --- a/OPPL/query.xml Thu Sep 20 12:46:36 2012 +0200 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,82 +0,0 @@ - - It performs a query, expressed in Manchester OWL Syntax, against an OWL ontology - - - - - - - java -Xmx3000M -Xms250M -DentityExpansionLimit=1000000000 -jar ${__tool_data_path__}/shared/jars/query.jar $ontology $reasoner $answer_type $answer_format "$query" > $output - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -**About Query-Galaxy** - - Query-Galaxy can be used to execute a DL query against an OWL ontology. The result is a list of entities from the target ontology. - -**Usage** - - An ontology is needed as input: load it with Get Data >> Upload File from your computer or redirect the output of another galaxy tool. Query-Galaxy uses the OWL API, and therefore it can load any ontology format that such API is able to load: OBO flat file, OWL (RDF/XML, OWL/XML, Functional, Manchester), turtle, and KRSS. In case the loaded ontology includes OWL imports, Query-Galaxy will try to resolve them. - - A DL query must be provided, e.g. GO_0007049 or part_of some GO_0007049. - - The reasoner can be Pellet, HermiT, FaCT++ or Elk. - - How the retrieved entities relate to the query can be chosen: a DL query is just an anonymous OWL Class, and the retrieved entities can be descendant classes, direct sub-classes, ancestor classes, direct super-classes, equivalent classes, or member individuals. - - The returned entities can be rendered using their URI, their URI fragment, or OBO type URI fragment (e.g. GO_0000022 to GO:0000022). - -**Contact** - - Please send any request or comment to mikel.egana.aranguren@gmail.com. - - - - diff -r d3616fac4ca5 -r cc270db37d33 OPPL/query_lib/FaCTpp-OWLAPI-3.2-v1.5.2.jar Binary file OPPL/query_lib/FaCTpp-OWLAPI-3.2-v1.5.2.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 OPPL/query_lib/HermiT.jar Binary file OPPL/query_lib/HermiT.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 OPPL/query_lib/antlr-runtime-3.2.jar Binary file OPPL/query_lib/antlr-runtime-3.2.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 OPPL/query_lib/aterm-java-1.6.jar Binary file OPPL/query_lib/aterm-java-1.6.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 OPPL/query_lib/commons-logging-1.1.1.jar Binary file OPPL/query_lib/commons-logging-1.1.1.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 OPPL/query_lib/elk-owlapi.jar Binary file OPPL/query_lib/elk-owlapi.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 OPPL/query_lib/jgrapht-jdk1.5.jar Binary file OPPL/query_lib/jgrapht-jdk1.5.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 OPPL/query_lib/junit-4.8.2.jar Binary file OPPL/query_lib/junit-4.8.2.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 OPPL/query_lib/junit.jar Binary file OPPL/query_lib/junit.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 OPPL/query_lib/log4j-1.2.15.jar Binary file OPPL/query_lib/log4j-1.2.15.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 OPPL/query_lib/log4j-sources.jar Binary file OPPL/query_lib/log4j-sources.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 OPPL/query_lib/log4j.jar Binary file OPPL/query_lib/log4j.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 OPPL/query_lib/oboformat.jar Binary file OPPL/query_lib/oboformat.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 OPPL/query_lib/org.coode.oppl-API.jar Binary file OPPL/query_lib/org.coode.oppl-API.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 OPPL/query_lib/owlapi-bin.jar Binary file OPPL/query_lib/owlapi-bin.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 OPPL/query_lib/owlapi-bin_2.jar Binary file OPPL/query_lib/owlapi-bin_2.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 OPPL/query_lib/owllink-bin.jar Binary file OPPL/query_lib/owllink-bin.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 OPPL/query_lib/parsers.jar Binary file OPPL/query_lib/parsers.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 OPPL/query_lib/pellet-core.jar Binary file OPPL/query_lib/pellet-core.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 OPPL/query_lib/pellet-datatypes.jar Binary file OPPL/query_lib/pellet-datatypes.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 OPPL/query_lib/pellet-el.jar Binary file OPPL/query_lib/pellet-el.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 OPPL/query_lib/pellet-owlapiv3.jar Binary file OPPL/query_lib/pellet-owlapiv3.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 OPPL/query_lib/pellet-query.jar Binary file OPPL/query_lib/pellet-query.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 OPPL/query_lib/pellet-rules.jar Binary file OPPL/query_lib/pellet-rules.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 OPPL/src/GalaxyOWLAPI.java --- a/OPPL/src/GalaxyOWLAPI.java Thu Sep 20 12:46:36 2012 +0200 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,331 +0,0 @@ -/** - * - */ -package es.upm.fi.dia.oeg.oppl.galaxy; - -import java.io.BufferedWriter; -import java.io.File; -import java.io.IOException; -import java.io.OutputStreamWriter; -import java.util.ArrayList; -import java.util.List; -import java.util.Scanner; -import java.util.Set; - -import org.apache.log4j.Level; -import org.apache.log4j.Logger; -import org.coode.owlapi.manchesterowlsyntax.ManchesterOWLSyntaxEditorParser; -import org.coode.owlapi.obo.parser.OBOOntologyFormat; -import org.coode.parsers.BidirectionalShortFormProviderAdapter; -import org.semanticweb.HermiT.Reasoner; -import org.semanticweb.elk.owlapi.ElkReasonerFactory; -import org.semanticweb.owlapi.apibinding.OWLManager; -import org.semanticweb.owlapi.expression.OWLEntityChecker; -import org.semanticweb.owlapi.expression.ParserException; -import org.semanticweb.owlapi.expression.ShortFormEntityChecker; -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.OWLClass; -import org.semanticweb.owlapi.model.OWLClassExpression; -import org.semanticweb.owlapi.model.OWLDataFactory; -import org.semanticweb.owlapi.model.OWLLiteral; -import org.semanticweb.owlapi.model.OWLNamedIndividual; -import org.semanticweb.owlapi.model.OWLOntology; -import org.semanticweb.owlapi.model.OWLOntologyChange; -import org.semanticweb.owlapi.model.OWLOntologyCreationException; -import org.semanticweb.owlapi.model.OWLOntologyManager; -import org.semanticweb.owlapi.model.OWLOntologyStorageException; -import org.semanticweb.owlapi.reasoner.InferenceType; -import org.semanticweb.owlapi.reasoner.OWLReasoner; -import org.semanticweb.owlapi.reasoner.OWLReasonerFactory; -import org.semanticweb.owlapi.util.BidirectionalShortFormProvider; -import org.semanticweb.owlapi.util.InferredAxiomGenerator; -import org.semanticweb.owlapi.util.InferredClassAssertionAxiomGenerator; -import org.semanticweb.owlapi.util.InferredDisjointClassesAxiomGenerator; -import org.semanticweb.owlapi.util.InferredOntologyGenerator; -import org.semanticweb.owlapi.util.InferredSubClassAxiomGenerator; -import org.semanticweb.owlapi.util.InferredSubDataPropertyAxiomGenerator; -import org.semanticweb.owlapi.util.InferredSubObjectPropertyAxiomGenerator; -import org.semanticweb.owlapi.util.OWLEntityRenamer; -import org.semanticweb.owlapi.util.OWLOntologyImportsClosureSetProvider; -import org.semanticweb.owlapi.util.OWLOntologyMerger; -import org.semanticweb.owlapi.util.SimpleShortFormProvider; -import org.semanticweb.owlapi.vocab.OWL2Datatype; -import org.semanticweb.owlapi.vocab.OWLRDFVocabulary; -import org.semanticweb.owlapi.reasoner.Node; - -import uk.ac.manchester.cs.factplusplus.owlapiv3.FaCTPlusPlusReasonerFactory; - -import com.clarkparsia.pellet.owlapiv3.PelletReasonerFactory; - -/** - * A wrapper of the OWL API - * - * @author Mikel Egana Aranguren - */ -public class GalaxyOWLAPI { - private OWLOntologyManager manager; - private OWLOntology ontology; - private OWLReasonerFactory reasonerFactory; - private OWLReasoner reasoner; - - public GalaxyOWLAPI (){ - manager = OWLManager.createOWLOntologyManager(); - } - public OWLOntologyManager getOWLManager(){ - return manager; - } - public OWLOntology getMainOntology(){ - return ontology; - } - public OWLReasoner getReasoner(){ - return reasoner; - } - - public void loadMainOntology(String OWLFilePath) throws OWLOntologyCreationException{ - File owl_file = new File(OWLFilePath); - ontology = manager.loadOntologyFromOntologyDocument(owl_file); - } - -// public void loadImportedOntology(IRI importedOntologyIRI) throws OWLOntologyCreationException{ -// manager.loadOntologyFromOntologyDocument(importedOntologyIRI); -// } - - // 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); - - public void setReasonerPellet (){ - reasonerFactory = new PelletReasonerFactory(); - reasoner = reasonerFactory.createReasoner(ontology); - } - public void setReasonerFaCT (){ - reasonerFactory = new FaCTPlusPlusReasonerFactory(); - reasoner = reasonerFactory.createReasoner(ontology); - } - public void setReasonerHermit (){ - reasonerFactory = new Reasoner.ReasonerFactory(); - reasoner = reasonerFactory.createReasoner(ontology); - } - public void setReasonerElk (){ - reasonerFactory = new ElkReasonerFactory(); - Logger.getLogger("org.semanticweb.elk").setLevel(Level.OFF); - reasoner = reasonerFactory.createReasoner(ontology); - } - public void disposeReasoner(){ - reasoner.dispose(); - } - public void merge (String ontologyIRI) throws OWLOntologyCreationException, OWLOntologyStorageException{ - OWLOntologyMerger merger = new OWLOntologyMerger(manager); -// OWLOntologyMerger merger = new OWLOntologyMerger(new OWLOntologyImportsClosureSetProvider(manager, ontology)); - IRI mergedOntologyIRI = IRI.create(ontologyIRI); -// OWLOntology merged_ontology = merger.createMergedOntology(manager, mergedOntologyIRI); - ontology = merger.createMergedOntology(manager, mergedOntologyIRI); -// manager.saveOntology(ontology, new RDFXMLOntologyFormat(), new SystemOutDocumentTarget()); - } - - public OWLClassExpression parseMOSClassExpression (String expr) throws ParserException{ - Set importsClosure = ontology.getImportsClosure(); - BidirectionalShortFormProvider bidiShortFormProvider = new BidirectionalShortFormProviderAdapter(manager, importsClosure, new SimpleShortFormProvider()); - OWLEntityChecker entityChecker = new ShortFormEntityChecker(bidiShortFormProvider); - ManchesterOWLSyntaxEditorParser MOSparser = new ManchesterOWLSyntaxEditorParser(manager.getOWLDataFactory(), expr); - MOSparser.setOWLEntityChecker(entityChecker); - return MOSparser.parseClassExpression(); - } - - public Set getIndividuals (OWLClassExpression expr){ - return (reasoner.getInstances(expr, false)).getFlattened(); - } - public Set getEquivalentClasses (OWLClassExpression expr){ - Node equivalentClasses = reasoner.getEquivalentClasses(expr); - Set result; - if (expr.isAnonymous()) { - result = equivalentClasses.getEntities(); - } - else { - result = equivalentClasses.getEntitiesMinus(expr.asOWLClass()); - } - return result; - } - - public Set getDirectSuperClasses (OWLClassExpression expr){ - return (reasoner.getSuperClasses(expr, true)).getFlattened(); - } - - public Set getAncestors (OWLClassExpression expr){ - return (reasoner.getSuperClasses(expr, false)).getFlattened(); - } - - public Set getDirectSubClasses (OWLClassExpression expr){ - return (reasoner.getSubClasses(expr, true)).getFlattened(); - } - - public Set getDescendants (OWLClassExpression expr){ - return (reasoner.getSubClasses(expr, false)).getFlattened(); - } - - // CLASS_ASSERTIONS Denotes the computation of the direct types of individuals for each individual in the signature of the imports closure of the root ontology. - - public void addCLASS_ASSERTIONS(){ - reasoner.precomputeInferences(InferenceType.CLASS_ASSERTIONS); - List> gens = new ArrayList>(); - gens.add(new InferredClassAssertionAxiomGenerator()); - InferredOntologyGenerator iog = new InferredOntologyGenerator(reasoner, gens); - iog.fillOntology(manager, ontology); - } - - // CLASS_HIERARCHY Denotes the computation of the class hierarchy. - - public void addCLASS_HIERARCHY(){ - reasoner.precomputeInferences(InferenceType.CLASS_HIERARCHY); - List> gens = new ArrayList>(); - gens.add(new InferredSubClassAxiomGenerator()); - InferredOntologyGenerator iog = new InferredOntologyGenerator(reasoner, gens); - iog.fillOntology(manager, ontology); - } - - // DATA_PROPERTY_ASSERTIONS Denotes the computation of relationships between individuals and data property values for each individual in the signature of the imports closure of the root ontology. -// public void addDATA_PROPERTY_ASSERTIONS(){ -// reasoner.precomputeInferences(InferenceType.DATA_PROPERTY_ASSERTIONS); -// List> gens = new ArrayList>(); -// gens.add(new InferredDataPropertyAxiomGenerator()); -// InferredOntologyGenerator iog = new InferredOntologyGenerator(reasoner, gens); -// iog.fillOntology(manager, ontology); -// } - - // DATA_PROPERTY_HIERARCHY Denotes the computation of the data property hierarchy. - - public void addDATA_PROPERTY_HIERARCHY(){ - reasoner.precomputeInferences(InferenceType.DATA_PROPERTY_HIERARCHY); - List> gens = new ArrayList>(); - gens.add(new InferredSubDataPropertyAxiomGenerator()); - InferredOntologyGenerator iog = new InferredOntologyGenerator(reasoner, gens); - iog.fillOntology(manager, ontology); - } - - // DIFFERENT_INDIVIDUALS Denotes the computation of sets of individuals that are different from each individual in the signature of the imports closure of the root ontology. - -// public void addDIFFERENT_INDIVIDUALS(){ -// reasoner.precomputeInferences(InferenceType.DIFFERENT_INDIVIDUALS); -// List> gens = new ArrayList>(); -// gens.add(new Inferred); -// InferredOntologyGenerator iog = new InferredOntologyGenerator(reasoner, gens); -// iog.fillOntology(manager, ontology); -// } - - // DISJOINT_CLASSES Denotes the computation of sets of classes that are disjoint for each class in the signature of the imports closure of the root ontology. - - public void addDISJOINT_CLASSES(){ - reasoner.precomputeInferences(InferenceType.DISJOINT_CLASSES); - List> gens = new ArrayList>(); - gens.add(new InferredDisjointClassesAxiomGenerator()); - InferredOntologyGenerator iog = new InferredOntologyGenerator(reasoner, gens); - iog.fillOntology(manager, ontology); - } - - // OBJECT_PROPERTY_ASSERTIONS Denotes the computation of relationships between individuals in the signature of the imports closure of the root ontology. - -// public void addOBJECT_PROPERTY_ASSERTIONS(){ -// reasoner.precomputeInferences(InferenceType.OBJECT_PROPERTY_ASSERTIONS); -// List> gens = new ArrayList>(); -// gens.add(new InferredObjectPropertyAxiomGenerator() { -// };()); -// InferredOntologyGenerator iog = new InferredOntologyGenerator(reasoner, gens); -// iog.fillOntology(manager, ontology); -// } - - // OBJECT_PROPERTY_HIERARCHY Denotes the computation of the object property hierarchy. - - public void addOBJECT_PROPERTY_HIERARCHY(){ - reasoner.precomputeInferences(InferenceType.OBJECT_PROPERTY_HIERARCHY); - List> gens = new ArrayList>(); - gens.add(new InferredSubObjectPropertyAxiomGenerator()); - InferredOntologyGenerator iog = new InferredOntologyGenerator(reasoner, gens); - iog.fillOntology(manager, ontology); - } - - // SAME_INDIVIDUAL Denotes the computation of individuals that are interpreted as the same object for each individual in the imports closure of the root ontology. - -// public void addSAME_INDIVIDUAL(){ -// reasoner.precomputeInferences(InferenceType.SAME_INDIVIDUAL); -// List> gens = new ArrayList>(); -// gens.add(new Infer); -// InferredOntologyGenerator iog = new InferredOntologyGenerator(reasoner, gens); -// iog.fillOntology(manager, ontology); -// } - - public void saveOntology (boolean OWL) throws OWLOntologyStorageException, IOException, OWLOntologyCreationException{ - // OWL format - if(OWL){ - manager.saveOntology(ontology, new RDFXMLOntologyFormat(), new SystemOutDocumentTarget()); - } - // OBO format - else{ - // 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 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 = ""; - - 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(); - } - } -} diff -r d3616fac4ca5 -r cc270db37d33 OPPL/src/InferenceGalaxy.java --- a/OPPL/src/InferenceGalaxy.java Thu Sep 20 12:46:36 2012 +0200 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,111 +0,0 @@ -/** - * - */ -package es.upm.fi.dia.oeg.oppl.galaxy; - - -import java.io.IOException; - -import org.semanticweb.owlapi.model.OWLOntologyCreationException; -import org.semanticweb.owlapi.model.OWLOntologyStorageException; - - -/** - * @author Mikel Ega��a Aranguren - * - */ -public class InferenceGalaxy { - - /** - * @param args - * @throws IOException - * @throws OWLOntologyCreationException - * @throws OWLOntologyStorageException - */ - public static void main(String[] args) throws OWLOntologyStorageException, OWLOntologyCreationException, IOException { - // Get the arguments from command-line - String OWLFilePath = args [0]; - String reasoner_type = args [1]; // Pellet|FaCTPlusPlus|HermiT|Elk - String axioms_to_inject = args [2]; // CLASS_ASSERTIONS,CLASS_HIERARCHY,DATA_PROPERTY_ASSERTIONS - -// CLASS_ASSERTIONS Denotes the computation of the direct types of individuals for each individual in the signature of the imports closure of the root ontology. -// CLASS_HIERARCHY Denotes the computation of the class hierarchy. -// DATA_PROPERTY_ASSERTIONS Denotes the computation of relationships between individuals and data property values for each individual in the signature of the imports closure of the root ontology. -// DATA_PROPERTY_HIERARCHY Denotes the computation of the data property hierarchy. -// DIFFERENT_INDIVIDUALS Denotes the computation of sets of individuals that are different from each individual in the signature of the imports closure of the root ontology. -// DISJOINT_CLASSES Denotes the computation of sets of classes that are disjoint for each class in the signature of the imports closure of the root ontology. -// OBJECT_PROPERTY_ASSERTIONS Denotes the computation of relationships between individuals in the signature of the imports closure of the root ontology. -// OBJECT_PROPERTY_HIERARCHY Denotes the computation of the object property hierarchy. -// SAME_INDIVIDUAL Denotes the computation of individuals that are interpreted as the same object for each individual in the imports closure of the root ontology. - - // Create the manager - GalaxyOWLAPI galaxyowlapi = new GalaxyOWLAPI(); - - // Load the main ontology - galaxyowlapi.loadMainOntology(OWLFilePath); - - // Set the reasoner - - // Pellet - if(reasoner_type.equals("Pellet")){ - galaxyowlapi.setReasonerPellet(); - } - // FaCTPlusPlus - else if (reasoner_type.equals("FaCTPlusPlus")){ - galaxyowlapi.setReasonerFaCT(); - } - // Elk - else if (reasoner_type.equals("Elk")){ - galaxyowlapi.setReasonerElk(); - } - // HermiT - else{ - galaxyowlapi.setReasonerHermit(); - } - - // Add the inferred axioms as asserted axioms to the original ontology - - if(axioms_to_inject.contains(",")){ - String[] axioms = axioms_to_inject.split(","); - for(int i =0; i < axioms.length ; i++) - injectAxiom (axioms[i], galaxyowlapi); - } - else{ - injectAxiom (axioms_to_inject, galaxyowlapi); - } - - galaxyowlapi.disposeReasoner(); - - // Merge imported ontologies if requested -// if(merge.equals("Merge")){ -// galaxyowlapi.merge(); -// } - - // Save the ontology in OWL - galaxyowlapi.saveOntology(true); - - } - - static void injectAxiom (String axiom_to_inject, GalaxyOWLAPI galaxyowlapi){ - if(axiom_to_inject.equals("CLASS_HIERARCHY")){ - galaxyowlapi.addCLASS_HIERARCHY(); -// System.out.println("CLASS_HIERARCHY"); - } - if(axiom_to_inject.equals("CLASS_ASSERTIONS")){ - galaxyowlapi.addCLASS_ASSERTIONS(); -// System.out.println("CLASS_ASSERTIONS"); - } - if(axiom_to_inject.equals("DATA_PROPERTY_HIERARCHY")){ - galaxyowlapi.addDATA_PROPERTY_HIERARCHY(); -// System.out.println("DATA_PROPERTY_HIERARCHY"); - } - if(axiom_to_inject.equals("DISJOINT_CLASSES")){ - galaxyowlapi.addDISJOINT_CLASSES(); -// System.out.println("DISJOINT_CLASSES"); - } - if(axiom_to_inject.equals("OBJECT_PROPERTY_HIERARCHY")){ - galaxyowlapi.addOBJECT_PROPERTY_HIERARCHY(); -// System.out.println("OBJECT_PROPERTY_HIERARCHY"); - } - } -} diff -r d3616fac4ca5 -r cc270db37d33 OPPL/src/MergeImportedOntologies.java --- a/OPPL/src/MergeImportedOntologies.java Thu Sep 20 12:46:36 2012 +0200 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,39 +0,0 @@ -package es.upm.cbgp.opplquery.oppl.galaxy; - -import java.io.IOException; - -import org.semanticweb.owlapi.model.OWLOntologyCreationException; -import org.semanticweb.owlapi.model.OWLOntologyStorageException; - -import es.upm.fi.dia.oeg.oppl.galaxy.GalaxyOWLAPI; - -public class MergeImportedOntologies { - - /** - * @param args - * @throws OWLOntologyCreationException - * @throws IOException - * @throws OWLOntologyStorageException - */ - public static void main(String[] args) throws OWLOntologyCreationException, OWLOntologyStorageException, IOException { - String OWLFilePath = args [0]; - String MergedOntologyNewURI = args [1]; -// String OWLFilePath = "/home/mikel/UPM/OPPL_galaxy/OPPL/OPPL/test-data/ontology/imports/merge_test.owl"; -// String MergedOntologyNewURI = "http://cbgp.upm.es/merged.owl"; - - // Create the manager - GalaxyOWLAPI galaxyowlapi = new GalaxyOWLAPI(); - - // Load the main ontology and hope for the imported URIs to be resolvable - galaxyowlapi.loadMainOntology(OWLFilePath); - - // Merge and save - - if(MergedOntologyNewURI.isEmpty()){ - MergedOntologyNewURI = "http://cbgp.upm.es/BiologicalInformatics/OPPLGalaxy/merged.owl"; - } - - galaxyowlapi.merge(MergedOntologyNewURI); - galaxyowlapi.saveOntology(true); - } -} diff -r d3616fac4ca5 -r cc270db37d33 OPPL/src/OPPLGalaxy.java --- a/OPPL/src/OPPLGalaxy.java Thu Sep 20 12:46:36 2012 +0200 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,121 +0,0 @@ -/** - * - */ -package es.upm.fi.dia.oeg.oppl.galaxy; - -import java.io.File; -import java.io.IOException; -import java.util.List; -import java.util.Scanner; -import java.util.logging.Level; -import java.util.logging.Logger; - -//import org.apache.log4j.Level; -import org.coode.oppl.ChangeExtractor; -import org.coode.oppl.OPPLParser; -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.parsers.ErrorListener; -import org.coode.parsers.LoggerErrorListener; -import org.semanticweb.owlapi.model.OWLAxiomChange; -import org.semanticweb.owlapi.model.OWLOntology; -import org.semanticweb.owlapi.model.OWLOntologyCreationException; -import org.semanticweb.owlapi.model.OWLOntologyManager; -import org.semanticweb.owlapi.model.OWLOntologyStorageException; -import org.semanticweb.owlapi.reasoner.OWLReasoner; - - - - -/** - * @author Mikel Ega��a Aranguren - * - */ -public class OPPLGalaxy { - - /** - * @param args - * @throws OWLOntologyCreationException - * @throws OWLOntologyStorageException - * @throws IOException - */ - public static void main(String[] args) throws OWLOntologyCreationException, OWLOntologyStorageException, IOException { - // Get the arguments from command-line - String OWLFilePath = args [0]; - String reasoner_type = args [1]; // Pellet|FaCTPlusPlus|Elk|HermiT - - String OPPL_script_file = args [2]; - String OWL = args [3]; // OWL|OBO - - // Create the manager - GalaxyOWLAPI galaxyowlapi = new GalaxyOWLAPI(); - - // Load the main ontology and hope for the imported URIs to be resolvable - galaxyowlapi.loadMainOntology(OWLFilePath); - - // Set the reasoner - - // Pellet - if(reasoner_type.equals("Pellet")){ - galaxyowlapi.setReasonerPellet(); - } - // FaCTPlusPlus - else if (reasoner_type.equals("FaCTPlusPlus")){ - galaxyowlapi.setReasonerFaCT(); - } - // Elk - else if (reasoner_type.equals("Elk")){ - galaxyowlapi.setReasonerElk(); - } - // HermiT - else{ - galaxyowlapi.setReasonerHermit(); - } - - // Load the OPPL flat file with script in memory - String OPPL_script_source = ""; - File file = new File(OPPL_script_file); - Scanner input = new Scanner(file); - while(input.hasNext()) { - String nextToken = input.next(); - OPPL_script_source = OPPL_script_source + " " + nextToken; - } - input.close(); - - OWLOntologyManager manager = galaxyowlapi.getOWLManager(); - OWLOntology ontology = galaxyowlapi.getMainOntology(); - OWLReasoner reasoner = galaxyowlapi.getReasoner(); - - // Parse the OPPL script - ParserFactory parserFactory = new ParserFactory(manager, ontology, reasoner); - Logger logger = Logger.getLogger(OPPLGalaxy.class.getName()); -// logger.setLevel(Level.OFF); -// Logging.getQueryLogger().setLevel(Level.OFF); // The normal messages are errors for galaxy (Fixed in Galaxy by 2 > /dev/null) - - ErrorListener errorListener = (ErrorListener)new LoggerErrorListener(logger); - OPPLParser opplparser = parserFactory.build(errorListener); - OPPLScript OPPLscript = opplparser.parse(OPPL_script_source); - - // Execute the script - ChangeExtractor extractor = new ChangeExtractor(new QuickFailRuntimeExceptionHandler(), true); - List changes = extractor.visit(OPPLscript); - manager.applyChanges(changes); - - galaxyowlapi.disposeReasoner(); - - // Merge imported ontologies if requested -// if(merge.equals("Merge")){ -// galaxyowlapi.merge(); -// } - - // Save the ontology - if(OWL.equals("OWL")){ - galaxyowlapi.saveOntology(true); - } - else{ - galaxyowlapi.saveOntology(false); - } - } -} diff -r d3616fac4ca5 -r cc270db37d33 OPPL/src/OPPLQueryGalaxy.java --- a/OPPL/src/OPPLQueryGalaxy.java Thu Sep 20 12:46:36 2012 +0200 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,177 +0,0 @@ -/** - * - */ -package es.upm.cbgp.opplquery.oppl.galaxy; - -import java.io.File; -import java.io.FileNotFoundException; -import java.util.Iterator; -import java.util.Scanner; -import java.util.Set; -import java.util.logging.Logger; -import java.util.regex.Matcher; -import java.util.regex.Pattern; - -import org.semanticweb.owlapi.expression.ParserException; -import org.semanticweb.owlapi.model.IRI; -import org.semanticweb.owlapi.model.OWLObject; -import org.semanticweb.owlapi.model.OWLOntologyCreationException; - -import es.upm.fi.dia.oeg.oppl.galaxy.GalaxyOWLAPI; - -import org.coode.oppl.ChangeExtractor; -import org.coode.oppl.ConstraintSystem; -import org.coode.oppl.OPPLParser; -import org.coode.oppl.OPPLScript; -import org.coode.oppl.ParserFactory; -import org.coode.parsers.ErrorListener; -import org.coode.parsers.LoggerErrorListener; -import org.coode.oppl.bindingtree.Assignment; -import org.coode.oppl.bindingtree.BindingNode; -import org.coode.oppl.exceptions.QuickFailRuntimeExceptionHandler; -import org.coode.oppl.exceptions.RuntimeExceptionHandler; - -public class OPPLQueryGalaxy { - - /** - * @param args - * @throws OWLOntologyCreationException - * @throws ParserException - * @throws FileNotFoundException - */ - public static void main(String[] args) throws OWLOntologyCreationException, ParserException, FileNotFoundException { - // Get the arguments from command-line - String OWLFilePath = args [0]; // /home/mikel/UPM/OPPL_galaxy/OPPL/OPPL/test-data/ontology/single/test.owl - String reasoner_type = args [1]; // Pellet|FaCTPlusPlus|HermiT|Elk - String Answer_render = args [2]; // URI|URIfragment|URIfragment2OBO - String OPPL_script_source = args [3]; - -// String OPPL_script_file = args [3]; -// File OPPL_script_file = new File("/home/mikel/UPM/OPPL_galaxy/OPPL/OPPL/test-data/oppl_script/test_oppl_query.oppl"); -// File OPPL_script_file = new File("/home/mikel/UPM/OPPL_galaxy/OPPL/OPPL/test-data/oppl_script/test_oppl_query_object_prop.oppl"); -// File OPPL_script_file = new File("/home/mikel/UPM/OPPL_galaxy/OPPL/OPPL/test-data/oppl_script/test_oppl_query_object_ind.oppl"); - -// String OPPL_script_source = ""; -// Scanner input = new Scanner(OPPL_script_file); -// while(input.hasNext()) { -// String nextToken = input.next(); -// OPPL_script_source = OPPL_script_source + " " + nextToken; -// } -// input.close(); - - // Create the manager - GalaxyOWLAPI galaxyowlapi = new GalaxyOWLAPI(); - - // Load the main ontology and hope for the imported URIs to be resolvable - galaxyowlapi.loadMainOntology(OWLFilePath); - - // Set the reasoner - - // Pellet - if(reasoner_type.equals("Pellet")){ - galaxyowlapi.setReasonerPellet(); - } - // FaCTPlusPlus - else if (reasoner_type.equals("FaCTPlusPlus")){ - galaxyowlapi.setReasonerFaCT(); - } - // Elk - else if (reasoner_type.equals("Elk")){ - galaxyowlapi.setReasonerElk(); - } - // HermiT - else{ - galaxyowlapi.setReasonerHermit(); - } - - OPPL_script_source = completeOPPLScript(OPPL_script_source); -// System.out.println(OPPL_script_source); - - ParserFactory parserFactory = new ParserFactory(galaxyowlapi.getOWLManager(), galaxyowlapi.getMainOntology(), galaxyowlapi.getReasoner()); - Logger logger = Logger.getLogger(OPPLQueryGalaxy.class.getName()); - ErrorListener errorListener = (ErrorListener) new LoggerErrorListener(logger); - OPPLParser opplparser = parserFactory.build(errorListener); - OPPLScript OPPLscript = opplparser.parse(OPPL_script_source); - RuntimeExceptionHandler exceptionhandler = new QuickFailRuntimeExceptionHandler(); - ChangeExtractor extractor = new ChangeExtractor(exceptionhandler, true); - extractor.visit(OPPLscript); - ConstraintSystem cs = OPPLscript.getConstraintSystem(); - Set nodes = cs.getLeaves(); - - galaxyowlapi.disposeReasoner(); - - Iterator NodesIterator = nodes.iterator(); - while(NodesIterator.hasNext()){ - Set Assignments = ((BindingNode)NodesIterator.next()).getAssignments(); - Iterator AssignmentIterator = Assignments.iterator(); - while(AssignmentIterator.hasNext()){ - Assignment assignment = (Assignment)AssignmentIterator.next(); - System.out.print(assignment.getAssignedVariable().toString()); - System.out.print("\t"); - String OWLObjectString = ((OWLObject)assignment.getAssignment()).toString(); - IRI entityIRI = IRI.create(OWLObjectString.substring(1,OWLObjectString.length()-1)); - print_result_entity(entityIRI, Answer_render); - System.out.print("\n"); - } - } - } - - //URI|URIfragment|URIfragment2OBO - private static void print_result_entity (IRI iri, String Answer_render){ - if(Answer_render.equals("URI")){ - System.out.print(iri); - } - - // Weird bug: in eclipse it can print out the IRIs of every entity, but in Galaxy it can't! - // done manually - else if(Answer_render.equals("URIfragment")){ - if(iri.toString().contains("#")){ - System.out.print(iri.getFragment()); - } - else{ - String [] iri_tokens = iri.toString().split("/"); - System.out.print(iri_tokens[iri_tokens.length-1]); - } - } - else{ - if(iri.toString().contains("#")){ - System.out.print((iri.getFragment()).replace("_", ":")); - } - else{ - String [] iri_tokens = iri.toString().split("/"); - System.out.print((iri_tokens[iri_tokens.length-1]).replace("_", ":")); - } - } - } - - // Very crappy stuff: complete the query to make a whole OPPL script that can be parsed - private static String completeOPPLScript (String OPPLQuery){ - - // Get the first variable and add at least an axiom to make a whole script - Pattern p = Pattern.compile("(\\?\\w+):(CLASS|INDIVIDUAL|OBJECTPROPERTY|DATAPROPERTY|ANNOTATIONPROPERTY|CONSTANT)"); - Matcher m = p.matcher(OPPLQuery); - m.find(); - if (m.group(2).equals("CLASS")){ - OPPLQuery = OPPLQuery + " BEGIN ADD " + m.group(1) + " SubClassOf !A END;"; - } - else if (m.group(2).equals("INDIVIDUAL")){ - OPPLQuery = OPPLQuery + " BEGIN ADD " + m.group(1) + " !p !b END;"; - } - else if (m.group(2).equals("OBJECTPROPERTY")){ - OPPLQuery = OPPLQuery + " BEGIN ADD Transitive ?p END;"; - } -// else if (m.group(2).equals("DATAPROPERTY")){ -// OPPLQuery = OPPLQuery + " BEGIN ADD ?whole SubClassOf !A END;"; -// } -// else if (m.group(2).equals("ANNOTATIONPROPERTY")){ -// OPPLQuery = OPPLQuery + " BEGIN ADD ?whole SubClassOf !A END;"; -// } -// else if (m.group(2).equals("CONSTANT")){ -// OPPLQuery = OPPLQuery + " BEGIN ADD ?whole SubClassOf !A END;"; -// } - else{ - OPPLQuery = "Malformed OPPL query"; - } - return OPPLQuery; - } -} diff -r d3616fac4ca5 -r cc270db37d33 OPPL/src/OWLQueryGalaxy.java --- a/OPPL/src/OWLQueryGalaxy.java Thu Sep 20 12:46:36 2012 +0200 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,129 +0,0 @@ -package es.upm.fi.dia.oeg.oppl.galaxy; - -import java.util.Set; - -import org.semanticweb.owlapi.expression.ParserException; -import org.semanticweb.owlapi.model.IRI; -import org.semanticweb.owlapi.model.OWLClass; -import org.semanticweb.owlapi.model.OWLClassExpression; -import org.semanticweb.owlapi.model.OWLNamedIndividual; -import org.semanticweb.owlapi.model.OWLOntologyCreationException; - -public class OWLQueryGalaxy { - - /** - * @param args - * @throws OWLOntologyCreationException - * @throws ParserException - */ - public static void main(String[] args) throws OWLOntologyCreationException, ParserException { - // Get the arguments from command-line - String OWLFilePath = args [0]; // /home/pik/UPM/Paper/SWAT4LS_2011/JBS/Workflows_JBS/GO_module_transitive/go_no_trans.owl - String reasoner_type = args [1]; // Pellet|FaCTPlusPlus|HermiT|Elk - - String Answer_type = args [2]; // Individuals|EquivalentClasses|DirectSuperClasses|Ancestors|DirectSubClasses|Descendants - String Answer_render = args [3]; // URI|URIfragment|URIfragment2OBO - String MOS_query = args [4]; // GO_0007049 or part_of some GO_0007049 - - // Create the manager - GalaxyOWLAPI galaxyowlapi = new GalaxyOWLAPI(); - - // Load the main ontology and hope for the imported URIs to be resolvable - galaxyowlapi.loadMainOntology(OWLFilePath); - - // Set the reasoner - - // Pellet - if(reasoner_type.equals("Pellet")){ - galaxyowlapi.setReasonerPellet(); - } - // FaCTPlusPlus - else if (reasoner_type.equals("FaCTPlusPlus")){ - galaxyowlapi.setReasonerFaCT(); - } - // Elk - else if (reasoner_type.equals("Elk")){ - galaxyowlapi.setReasonerElk(); - } - // HermiT - else{ - galaxyowlapi.setReasonerHermit(); - } - - // Parse the expression to an OWLexpression - OWLClassExpression class_expr = galaxyowlapi.parseMOSClassExpression(MOS_query); - - // Execute query and print results - if(Answer_type.equals("Individuals")){ - Set inds = galaxyowlapi.getIndividuals(class_expr); - galaxyowlapi.disposeReasoner(); - for(OWLNamedIndividual ind : inds){ - print_result_entity(ind.getIRI(), Answer_render); - } - } - else if (Answer_type.equals("EquivalentClasses")) { - Set answer_classes = galaxyowlapi.getEquivalentClasses(class_expr); - galaxyowlapi.disposeReasoner(); - for(OWLClass cls : answer_classes){ - print_result_entity(cls.getIRI(), Answer_render); - } - } - else if (Answer_type.equals("DirectSuperClasses")) { - Set answer_classes = galaxyowlapi.getDirectSuperClasses(class_expr); - galaxyowlapi.disposeReasoner(); - for(OWLClass cls : answer_classes){ - print_result_entity(cls.getIRI(), Answer_render); - } - } - else if (Answer_type.equals("Ancestors")) { - Set answer_classes = galaxyowlapi.getAncestors(class_expr); - galaxyowlapi.disposeReasoner(); - for(OWLClass cls : answer_classes){ - print_result_entity(cls.getIRI(), Answer_render); - } - } - else if (Answer_type.equals("DirectSubClasses")) { - Set answer_classes = galaxyowlapi.getDirectSubClasses(class_expr); - galaxyowlapi.disposeReasoner(); - for(OWLClass cls : answer_classes){ - print_result_entity(cls.getIRI(), Answer_render); - } - } - // Descendants - else { - Set answer_classes = galaxyowlapi.getDescendants(class_expr); - galaxyowlapi.disposeReasoner(); - for(OWLClass cls : answer_classes){ - print_result_entity(cls.getIRI(), Answer_render); - } - } - } - - //URI|URIfragment|URIfragment2OBO - private static void print_result_entity (IRI iri, String Answer_render){ - if(Answer_render.equals("URI")){ - System.out.println(iri); - } - - // Weird bug: in eclipse it can print out the IRIs of every entity, but in Galaxy it can't! - // done manually - else if(Answer_render.equals("URIfragment")){ - if(iri.toString().contains("#")){ - System.out.println(iri.getFragment()); - } - else{ - String [] iri_tokens = iri.toString().split("/"); - System.out.println(iri_tokens[iri_tokens.length-1]); - } - } - else{ - if(iri.toString().contains("#")){ - System.out.println((iri.getFragment()).replace("_", ":")); - } - else{ - String [] iri_tokens = iri.toString().split("/"); - System.out.println((iri_tokens[iri_tokens.length-1]).replace("_", ":")); - } - } - } -} diff -r d3616fac4ca5 -r cc270db37d33 OPPL/test-data/ontology/imports/imports_inference_test.owl --- a/OPPL/test-data/ontology/imports/imports_inference_test.owl Thu Sep 20 12:46:36 2012 +0200 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,196 +0,0 @@ - - - - - - - - - -]> - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Expected inferences: - -aa memberOf a - -c subClassOf a - -(imports) - -d subClassOf e - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff -r d3616fac4ca5 -r cc270db37d33 OPPL/test-data/ontology/imports/imports_test.owl --- a/OPPL/test-data/ontology/imports/imports_test.owl Thu Sep 20 12:46:36 2012 +0200 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,208 +0,0 @@ - - - - - - - - - -]> - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Expected inferences: - -aa memberOf a - -c subClassOf a - -(imports) - -d subClassOf e - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff -r d3616fac4ca5 -r cc270db37d33 OPPL/test-data/ontology/imports/merge.owl --- a/OPPL/test-data/ontology/imports/merge.owl Thu Sep 20 12:46:36 2012 +0200 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,8824 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - NB Transitive - the ingredients of ingredients are ingredients of the whole - - - - - - - - - - - - A property created to be used with the ValuePartition - Spiciness. - - - - - - - - - - Note that hasTopping is inverse functional because isToppingOf is functional - - - - - - - - - - - - - - - - - - - - - - - - - The inverse property tree to hasIngredient - all subproperties and attributes of the properties should reflect those under hasIngredient. - - - - - - - - - - - Any given instance of topping should only be added to a single pizza (no cheap half-measures on our pizzas) - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Americana - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AmericanaPicante - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CoberturaDeAnchovies - - - - - - - - - - - CoberturaDeArtichoke - - - - - - - - - - - - - - - - - - - - - - - - - - - CoberturaDeAspargos - - - - - - - - - - - - - - - - - - - - - - - - - - Cajun - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CoberturaDeCajun - - - - - - - - - - - - - - - - CoberturaDeCaper - - - - - - - - - - - - - - - - - - - - - - - - - Capricciosa - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Caprina - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CoberturaDeQueijo - - - - - - - - - - - - - - - - PizzaComQueijo - - - - - - - - - - - - Any pizza that has at least 1 cheese topping. - - - - - - - - CoberturaDeQueijoComVegetais - - - This class will be inconsistent. This is because we have given it 2 disjoint parents, which means it could never have any members (as nothing can simultaneously be a CheeseTopping and a VegetableTopping). NB Called ProbeInconsistentTopping in the ProtegeOWL Tutorial. - - - - - - - - CoberturaDeFrango - - - - - - - - - - - - - - - - - - Pais - - - - - - - - - - - - - - - - - A class that is equivalent to the set of individuals that are described in the enumeration - ie Countries can only be either America, England, France, Germany or Italy and nothing else. Note that these individuals have been asserted to be allDifferent from each other. - - - - - - - - BaseEspessa - - - - - - - - - - - - - - - - - - Fiorentina - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CoberturaDePeixe - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CoberturaQuatroQueijos - - - - - - - - - - - - - - - - - - - QuatroQueijos - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CoberturaDeFrutas - - - - - - - - - - - - - - FrutosDoMar - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CoberturaDeAlho - - - - - - - - - - - - - - - - - - - - - - - - Giardiniera - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CoberturaDeQueijoDeCabra - - - - - - - - - - - - - - - - - - CoberturaDeGorgonzola - - - - - - - - - - - - - - - - - CoberturaDePimentaoVerde - - - - - - - - - - - - CoberturaDePresunto - - - - - - - - - - - CoberturaDeErvas - - - - - - - - - - - - - Picante - - - - - - - - - - - CoberturaDePimentaoVerdePicante - - - - - - - - - - - - - - - CoberturaDeBifePicante - - - - - - - - - - - - - - - - Sorvete - - - - - - - - - - - A class to demonstrate mistakes made with setting a property domain. The property hasTopping has a domain of Pizza. This means that the reasoner can infer that all individuals using the hasTopping property must be of type Pizza. Because of the restriction on this class, all members of IceCream must use the hasTopping property, and therefore must also be members of Pizza. However, Pizza and IceCream are disjoint, so this causes an inconsistency. If they were not disjoint, IceCream would be inferred to be a subclass of Pizza. - - - - - - - - PizzaInteressante - - - - - - - 3 - - - - - Any pizza that has at least 3 toppings. Note that this is a cardinality constraint on the hasTopping property and NOT a qualified cardinality constraint (QCR). A QCR would specify from which class the members in this relationship must be. eg has at least 3 toppings from PizzaTopping. This is currently not supported in OWL. - - - - - - - - CoberturaDeJalapeno - - - - - - - - - - - - - - - - - LaReine - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CoberturaDeLeek - - - - - - - - - - - - - - - - - - - - - - - Margherita - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CoberturaDeCarne - - - - - - - - - - - - PizzaDeCarne - - - - - - - - - - - - Any pizza that has at least one meat topping - - - - - - - - Media - - - - - - - - - - NaoPicante - - - - - - - - - CoberturaDeFrutosDoMarMistos - - - - - - - - - - CoberturaDeMozzarella - - - - - - - - - - - - - - - - - - - - - - Cogumelo - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CoberturaDeCogumelo - - - - - - - - - - - - - - - - - - - - - - PizzaComUmNome - - A pizza that can be found on a pizza menu - - - - - - - - Napoletana - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - PizzaNaoVegetariana - - - - - - - - - - - - Any Pizza that is not a VegetarianPizza - - - - - - - - CoberturaDeCastanha - - - - - - - - - - - - - - - - - CoberturaDeAzeitona - - - - - - - - - - - - - - - - - - - - - CoberturaDeCebola - - - - - - - - - - - - - - - - - - - - CoberturaDePrezuntoParma - - - - - - - - - - - - - - - Parmense - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CoberturaDeParmesao - - - - - - - - - - - - - - - CoberturaPeperonata - - - - - - - - - - - - - - - - CoberturaDeCalabreza - - - - - - - - - - - - - - - CoberturaDePimentao - - - - - - - - - - - - - CoberturaPetitPois - - - - - - - - - - - - - - - - - - CoberturaPineKernels - - - - - - - - - Pizza - - - - - - - - - - - - - - - - - BaseDaPizza - - - - - - - - - - CoberturaDaPizza - - - - - - - - - PolloAdAstra - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CoberturaDeCamarao - - - - - - - - - CoberturaPrinceCarlo - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - QuatroQueijos - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - PizzaItalianaReal - - - - - - - - - - - - - - - - - - This defined class has conditions that are part of the definition: ie any Pizza that has the country of origin, Italy is a RealItalianPizza. It also has conditions that merely describe the members - that all RealItalianPizzas must only have ThinAndCrispy bases. In essence, all pizzas from Italy must have ThinAndCrispy bases. - - - - - - - - CoberturaDeCebolaVermelha - - - - - - - - - CoberturaRocket - - - - - - - - - - - - - - - - - Rosa - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CoberturaRosemary - - - - - - - - - - - - - - - CoberturaEmMolho - - - - - - - - - - Siciliana - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CoberturaDeTomateFatiado - - - - - - - - - - - - - - - - SloppyGiuseppe - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Soho - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Tempero - - - - - - - - - - - A ValuePartition that describes only values from Hot, Medium or Mild. NB Subclasses can themselves be divided up into further partitions. - - - - - - - - PizzaTemperada - - - - - - - - - - - - Any pizza that has a spicy topping is a SpicyPizza - - - - - - - - PizzaTemperadaEquivalente - - - - - - - - - - - - - - - - - - - - - - An alternative definition for the SpicyPizza which does away with needing a definition of SpicyTopping and uses a slightly more complicated restriction: Pizzas that have at least one topping that is both a PizzaTopping and has spiciness hot are members of this class. - - - - - - - - CoberturaTemperada - - - - - - - - - - - - Any pizza topping that has spiciness Hot - - - - - - - - CoberturaDeEspinafre - - - - - - - - - - - - - - - - CoberturaSultana - - - - - - - - - - - - - - - CoberturaDeTomateRessecadoAoSol - - - - - - - - - - - - - - - CoberturaDePimentaoDoce - - - - - - - - - - - - - - - BaseFinaEQuebradica - - - - - - - - - - - - - - - - - - - - - - - - - - - MolhoTobascoPepper - - - - - - - - - - - - - - - CoberturaDeTomate - - - - - - - - - - - - - - - PizzaAberta - - - - - - - - - An unclosed Pizza cannot be inferred to be either a VegetarianPizza or a NonVegetarianPizza, because it might have other toppings. - - - - - - - - ValorDaParticao - A ValuePartition is a pattern that describes a restricted set of classes from which a property can be associated. The parent class is used in restrictions, and the covering axiom means that only members of the subclasses may be used as values. The possible subclasses cannot be extended without updating the ValuePartition class. - - - - - - - - CoberturaDeVegetais - - - - - - - - - PizzaVegetariana - - - - - - - - - - - - - - - - - - - - - - - - Any pizza that does not have fish topping and does not have meat topping is a VegetarianPizza. Members of this class do not need to have any toppings at all. - - - - - - - - PizzaVegetarianaEquivalente1 - - - - - - - - - - - - Any pizza that only has vegetarian toppings or no toppings is a VegetarianPizzaEquiv1. Should be inferred to be equivalent to VegetarianPizzaEquiv2. Not equivalent to VegetarianPizza because PizzaTopping is not covering - - - - - - - - PizzaVegetarianaEquivalente2 - - - - - - - - - - - - - - - - - - - - - - - An alternative to VegetarianPizzaEquiv1 that does not require a definition of VegetarianTopping. Perhaps more difficult to maintain. Not equivalent to VegetarianPizza - - - - - - - - CoberturaVegetariana - - - - - - - - - - - - - - - - - - An example of a covering axiom. VegetarianTopping is equivalent to the union of all toppings in the given axiom. VegetarianToppings can only be Cheese or Vegetable or....etc. - - - - - - - - Veneziana - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - - - - - - - 1 - - - - - - 1 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1998 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff -r d3616fac4ca5 -r cc270db37d33 OPPL/test-data/ontology/imports/merge_test.owl --- a/OPPL/test-data/ontology/imports/merge_test.owl Thu Sep 20 12:46:36 2012 +0200 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,74 +0,0 @@ - - - - - - - -]> - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff -r d3616fac4ca5 -r cc270db37d33 OPPL/test-data/ontology/single/OWLQueryGalaxyTest.owl --- a/OPPL/test-data/ontology/single/OWLQueryGalaxyTest.owl Thu Sep 20 12:46:36 2012 +0200 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,193 +0,0 @@ - - - - - - - - - -]> - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - p some d: - -equiv a -sub b -desc b,b1, -ind aa - -inv_p some c - -ances d,f -sup d - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff -r d3616fac4ca5 -r cc270db37d33 OPPL/test-data/ontology/single/elk.owl --- a/OPPL/test-data/ontology/single/elk.owl Thu Sep 20 12:46:36 2012 +0200 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,106 +0,0 @@ - - - - - - - - -]> - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff -r d3616fac4ca5 -r cc270db37d33 OPPL/test-data/ontology/single/inference_test.owl --- a/OPPL/test-data/ontology/single/inference_test.owl Thu Sep 20 12:46:36 2012 +0200 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,162 +0,0 @@ - - - - - - - - -]> - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Expected inferences: - -aa memberOf a - -c subClassOf a - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff -r d3616fac4ca5 -r cc270db37d33 OPPL/test-data/ontology/single/test.owl --- a/OPPL/test-data/ontology/single/test.owl Thu Sep 20 12:46:36 2012 +0200 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,172 +0,0 @@ - - - - - - - - -]> - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff -r d3616fac4ca5 -r cc270db37d33 OPPL/test-data/oppl_script/test.oppl --- a/OPPL/test-data/oppl_script/test.oppl Thu Sep 20 12:46:36 2012 +0200 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,7 +0,0 @@ -?whole:CLASS, -?part:CLASS -SELECT -?part SubClassOf part_of some ?whole WHERE ?part != Nothing -BEGIN -ADD ?part SubClassOf part_of only ?whole -END; \ No newline at end of file diff -r d3616fac4ca5 -r cc270db37d33 OPPL/test-data/oppl_script/test_oppl_query.oppl --- a/OPPL/test-data/oppl_script/test_oppl_query.oppl Thu Sep 20 12:46:36 2012 +0200 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ -?whole:CLASS, -?part:CLASS -SELECT -?part SubClassOf part_of some ?whole WHERE ?part != Nothing \ No newline at end of file diff -r d3616fac4ca5 -r cc270db37d33 OPPL/test-data/oppl_script/test_oppl_query_object_ind.oppl --- a/OPPL/test-data/oppl_script/test_oppl_query_object_ind.oppl Thu Sep 20 12:46:36 2012 +0200 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ -?a:INDIVIDUAL, -?part:CLASS, -?c:INDIVIDUAL -SELECT ?a prop ?c \ No newline at end of file diff -r d3616fac4ca5 -r cc270db37d33 OPPL/test-data/oppl_script/test_oppl_query_object_prop.oppl --- a/OPPL/test-data/oppl_script/test_oppl_query_object_prop.oppl Thu Sep 20 12:46:36 2012 +0200 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,2 +0,0 @@ -?p:OBJECTPROPERTY -SELECT Transitive ?p \ No newline at end of file diff -r d3616fac4ca5 -r cc270db37d33 README --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README Sat Oct 06 21:50:39 2012 +0200 @@ -0,0 +1,115 @@ + + + +MANUAL INSTALLATION +============ + +1.- Stop Galaxy. + +2.- Copy the following files and directories to +/galaxy-dist/tool-data/shared/jars/: + +oppl_galaxy_tool.jar +inference.jar +query.jar +oppl_query.jar +merge.jar +oppl_galaxy_lib/ +inference_lib/ +query_lib/ +oppl_query_lib/ +merge_lib/ +FaCT++-linux-v1.5.2/ +FaCT++-OSX-v1.5.2/ + +3.- Create directory /galaxy-dist/tools/OPPL/ + +4.- Copy oppl.xml, inference.xml, query.xml, oppl_query.xml and +merge.xml to /galaxy-dist/tools/OPPL/ + +5.- Add the following lines to /galaxy-dist/tool_conf.xml: + +
+ + + + + +
+ +6.- Start Galaxy. + + +INSTALLATION VIA MERCURIAL AND SHELL SCRIPT + + + +FORESEEN FEATURES +================= + +- Support for processing ontologies that import other ontologies loaded +in Galaxy (i.e. to resolve imports within galaxy). + +- Entities rendering definition (URI fragment, rdfs:label, QName, etc). + +- OWLLink and Racer support. + +- Standalone OPPL assertions parsing (e.g. ADD phagocyte subClassOf +cell). + +- Other output formats apart from RDF/XML. + +- Support for DataPropertyAssertion, DataPropertyHierarchy, +DifferentIndividuals, ... + + + +KNOWN BUGS AND ISSUES +===================== + +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 + + + +CONTACT +======= + +Please send any request or comment to mikel.egana.aranguren@gmail.com. + + + +ACKNOWLEDGEMENTS +================ + +This work is funded by the Marie Curie Cofund program of the EU, FP7. + + + +COPYRIGHT AND LICENSE +===================== + +Copyright (c) 2011 Mikel Egaña Aranguren. + +(OPPL|Inference|Query|OPPL-Query|Merge)-Galaxy +is free software: you can redistribute it and/or modify it under the +terms of the GNU General Public License as published by the Free +Software Foundation, either version 3 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, see . + +OPPL API, OWL API, Pellet, HermiT, Elk and FaCT++ have their own licenses. + + diff -r d3616fac4ca5 -r cc270db37d33 config_oppl_for_galaxy.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/config_oppl_for_galaxy.sh Sat Oct 06 21:50:39 2012 +0200 @@ -0,0 +1,58 @@ +#!/bin/sh + +# Remove Kate backup files +rm *~ + +# Wrapper does not work +# cp stderr_wrapper.py /home/mikel/galaxy/galaxy-dist/tools/OPPL/ + +# Local installation + +cp oppl.xml /home/mikel/galaxy/galaxy-dist/tools/OPPL/ +cp inference.xml /home/mikel/galaxy/galaxy-dist/tools/OPPL/ +cp query.xml /home/mikel/galaxy/galaxy-dist/tools/OPPL/ +cp oppl_query.xml /home/mikel/galaxy/galaxy-dist/tools/OPPL/ +cp merge.xml /home/mikel/galaxy/galaxy-dist/tools/OPPL/ + +cp oppl_galaxy.jar /home/mikel/galaxy/galaxy-dist/tool-data/shared/jars/ +cp inference.jar /home/mikel/galaxy/galaxy-dist/tool-data/shared/jars/ +cp query.jar /home/mikel/galaxy/galaxy-dist/tool-data/shared/jars/ +cp oppl_query.jar /home/mikel/galaxy/galaxy-dist/tool-data/shared/jars/ +cp merge.jar /home/mikel/galaxy/galaxy-dist/tool-data/shared/jars/ + +cp -r FaCT++-linux-v1.5.2 /home/mikel/galaxy/galaxy-dist/tool-data/shared/jars/ + +cp -r oppl_galaxy_lib /home/mikel/galaxy/galaxy-dist/tool-data/shared/jars/ +cp -r inference_lib /home/mikel/galaxy/galaxy-dist/tool-data/shared/jars/ +cp -r query_lib /home/mikel/galaxy/galaxy-dist/tool-data/shared/jars/ +cp -r oppl_query_lib /home/mikel/galaxy/galaxy-dist/tool-data/shared/jars/ +cp -r merge_lib /home/mikel/galaxy/galaxy-dist/tool-data/shared/jars/ + +# Copy src from Eclipse for release + +cp /home/mikel/UPM/Eclipse_Workspace/OPPL_Galaxy/src/es/upm/fi/dia/oeg/oppl/galaxy/OPPLGalaxy.java ./src/ +cp /home/mikel/UPM/Eclipse_Workspace/OPPL_Galaxy/src/es/upm/fi/dia/oeg/oppl/galaxy/GalaxyOWLAPI.java ./src/ +cp /home/mikel/UPM/Eclipse_Workspace/OPPL_Galaxy/src/es/upm/fi/dia/oeg/oppl/galaxy/InferenceGalaxy.java ./src/ +cp /home/mikel/UPM/Eclipse_Workspace/OPPL_Galaxy/src/es/upm/fi/dia/oeg/oppl/galaxy/OWLQueryGalaxy.java ./src/ +cp /home/mikel/UPM/Eclipse_Workspace/OPPL_Galaxy/src/es/upm/fi/dia/oeg/oppl/galaxy/OWLQueryGalaxy.java ./src/ +cp /home/mikel/UPM/Eclipse_Workspace/OPPL_Galaxy/src/es/upm/cbgp/opplquery/oppl/galaxy/OPPLQueryGalaxy.java ./src/ +cp /home/mikel/UPM/Eclipse_Workspace/OPPL_Galaxy/src/es/upm/cbgp/opplquery/oppl/galaxy/MergeImportedOntologies.java ./src/ + +# Copy files for google code release ('Backup' release, not open to public) + +cp *.jar /home/mikel/UPM/Paper/SWAT4LS_2011/JBS_review/oppl-galaxy.src/ +cp *.xml /home/mikel/UPM/Paper/SWAT4LS_2011/JBS_review/oppl-galaxy.src/ +cp -r *_lib /home/mikel/UPM/Paper/SWAT4LS_2011/JBS_review/oppl-galaxy.src/ +cp -r FaCT++-* /home/mikel/UPM/Paper/SWAT4LS_2011/JBS_review/oppl-galaxy.src/ +cp -r src /home/mikel/UPM/Paper/SWAT4LS_2011/JBS_review/oppl-galaxy.src/ +cp -r test-data /home/mikel/UPM/Paper/SWAT4LS_2011/JBS_review/oppl-galaxy.src/ +cp README /home/mikel/UPM/Paper/SWAT4LS_2011/JBS_review/oppl-galaxy.src/ + +# ##### NOTES + +# To kill Galaxy easily: ./run.sh --reload + +# Usual mercurial session: update, status, add, commit -m 'Changes', push + + + diff -r d3616fac4ca5 -r cc270db37d33 inference.jar Binary file inference.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 inference.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/inference.xml Sat Oct 06 21:50:39 2012 +0200 @@ -0,0 +1,57 @@ + + It performs inference in an OWL ontology and it generates a new ontology with the inferred axioms as asserted axioms + + + + + java -Xmx3000M -Xms250M -DentityExpansionLimit=1000000000 -jar ${__tool_data_path__}/shared/jars/inference.jar $input $reasoner $axioms > $output + + + + + + + + + + + + + + + + + + + + + + + + +**About Inference-Galaxy** + + Inference-Galaxy offers the possibility of performing automated reasoning in an ontology and then injecting the inferred axioms as asserted axioms, generating a new OWL ontology. + +**Usage** + + An ontology is needed as input: load it with Get Data >> Upload File from your computer or redirect the output of another galaxy tool. Inference-Galaxy uses the OWL API, and therefore it can load any ontology format that such API is able to load: OBO flat file, OWL (RDF/XML, OWL/XML, Functional, Manchester), turtle, and KRSS. In case the loaded ontology includes OWL imports, Inference-Galaxy will try to resolve them. + + The reasoner can be Pellet, HermiT, FaCT++ or Elk. + + The inferred axioms to add as asserted axioms can be chosen. + +**Contact** + + Please send any request or comment to mikel.egana.aranguren@gmail.com. + + + + diff -r d3616fac4ca5 -r cc270db37d33 inference_lib/FaCTpp-OWLAPI-3.2-v1.5.2.jar Binary file inference_lib/FaCTpp-OWLAPI-3.2-v1.5.2.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 inference_lib/HermiT.jar Binary file inference_lib/HermiT.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 inference_lib/antlr-runtime-3.2.jar Binary file inference_lib/antlr-runtime-3.2.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 inference_lib/aterm-java-1.6.jar Binary file inference_lib/aterm-java-1.6.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 inference_lib/elk-owlapi.jar Binary file inference_lib/elk-owlapi.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 inference_lib/jgrapht-jdk1.5.jar Binary file inference_lib/jgrapht-jdk1.5.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 inference_lib/log4j-sources.jar Binary file inference_lib/log4j-sources.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 inference_lib/log4j.jar Binary file inference_lib/log4j.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 inference_lib/org.coode.oppl-API.jar Binary file inference_lib/org.coode.oppl-API.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 inference_lib/owlapi-bin.jar Binary file inference_lib/owlapi-bin.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 inference_lib/parsers.jar Binary file inference_lib/parsers.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 inference_lib/pellet-core.jar Binary file inference_lib/pellet-core.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 inference_lib/pellet-datatypes.jar Binary file inference_lib/pellet-datatypes.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 inference_lib/pellet-el.jar Binary file inference_lib/pellet-el.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 inference_lib/pellet-owlapiv3.jar Binary file inference_lib/pellet-owlapiv3.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 inference_lib/pellet-query.jar Binary file inference_lib/pellet-query.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 inference_lib/pellet-rules.jar Binary file inference_lib/pellet-rules.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 install.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/install.sh Sat Oct 06 21:50:39 2012 +0200 @@ -0,0 +1,3 @@ +#!/bin/sh + +# Shell script for installing OPPL-Galaxy \ No newline at end of file diff -r d3616fac4ca5 -r cc270db37d33 merge.jar Binary file merge.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 merge.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/merge.xml Sat Oct 06 21:50:39 2012 +0200 @@ -0,0 +1,44 @@ + + If an ontology with import axioms is provided, it will merge the imported ontologies into the main ontology + + + + + + + java -Xmx3000M -Xms250M -DentityExpansionLimit=1000000000 -jar ${__tool_data_path__}/shared/jars/merge.jar $ontology "$uri" > $output + + + + + + + + + + + + +**About Merge-Galaxy** + + Merge-Galaxy can be used to merge any (resolvable) imported ontologies into the main ontology, creating a new ontology. + +**Usage** + + An ontology is needed as input: load it with Get Data >> Upload File from your computer or redirect the output of another galaxy tool. Merge-Galaxy uses the OWL API, and therefore it can load any ontology format that such API is able to load: OBO flat file, OWL (RDF/XML, OWL/XML, Functional, Manchester), turtle, and KRSS. + + An URI can be specified for the new merged ontology. In case non is specified, the following URI will be used: http://cbgp.upm.es/BiologicalInformatics/OPPLGalaxy/merged.owl. + +**Contact** + + Please send any request or comment to mikel.egana.aranguren@gmail.com. + + + + diff -r d3616fac4ca5 -r cc270db37d33 merge_lib/FaCTpp-OWLAPI-3.2-v1.5.2.jar Binary file merge_lib/FaCTpp-OWLAPI-3.2-v1.5.2.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 merge_lib/HermiT.jar Binary file merge_lib/HermiT.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 merge_lib/antlr-runtime-3.2.jar Binary file merge_lib/antlr-runtime-3.2.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 merge_lib/aterm-java-1.6.jar Binary file merge_lib/aterm-java-1.6.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 merge_lib/elk-owlapi.jar Binary file merge_lib/elk-owlapi.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 merge_lib/jgrapht-jdk1.5.jar Binary file merge_lib/jgrapht-jdk1.5.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 merge_lib/log4j-sources.jar Binary file merge_lib/log4j-sources.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 merge_lib/log4j.jar Binary file merge_lib/log4j.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 merge_lib/org.coode.oppl-API.jar Binary file merge_lib/org.coode.oppl-API.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 merge_lib/owlapi-bin.jar Binary file merge_lib/owlapi-bin.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 merge_lib/parsers.jar Binary file merge_lib/parsers.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 merge_lib/pellet-core.jar Binary file merge_lib/pellet-core.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 merge_lib/pellet-datatypes.jar Binary file merge_lib/pellet-datatypes.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 merge_lib/pellet-el.jar Binary file merge_lib/pellet-el.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 merge_lib/pellet-owlapiv3.jar Binary file merge_lib/pellet-owlapiv3.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 merge_lib/pellet-query.jar Binary file merge_lib/pellet-query.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 merge_lib/pellet-rules.jar Binary file merge_lib/pellet-rules.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 oppl.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/oppl.xml Sat Oct 06 21:50:39 2012 +0200 @@ -0,0 +1,123 @@ + + It executes an OPPL script against the input ontology and generates a new ontology with the changes described in the OPPL script + + + + + + + + + + + + + + + + + + + + java -Djava.library.path=${__tool_data_path__}/shared/jars/FaCT++-linux-v1.5.2/64bit -Xmx3000M -Xms250M -DentityExpansionLimit=1000000000 -jar ${__tool_data_path__}/shared/jars/oppl_galaxy.jar $input $reasoner $OPPL $format > $output 2>/dev/null + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +**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 energy. + +**Usage** + + An ontology and an OPPL file are needed (test.owl and test.oppl can be used as samples, both available in the bundle). Load both with Get Data >> Upload File from your computer, or redirect from another Galaxy tool. OPPL-Galaxy uses the OWL API, and therefore it can load any ontology format that such API is able to load: OBO flat file, OWL (RDF/XML, OWL/XML, Functional, Manchester), turtle, and KRSS. In case the loaded ontology includes OWL imports, OPPL-Galaxy will try to resolve them. + + The reasoner can be Pellet, HermiT, FaCT++ or Elk. + + The output ontology can be OBO or OWL (RDF/XML). + +**More information** + + Galaxy public instances with OPPL-Galaxy pre-installed: + + http://sele.inf.um.es:9080/ + + http://linkeddata2.dia.fi.upm.es:8080 + + OPPL-Galaxy Examples: + + http://miuras.inf.um.es/OPPL-Galaxy/ + + OPPL examples: + + http://oppl2.sourceforge.net/taggedexamples/ + + Links of interest: + + http://oppl.sf.net/ + + http://www.w3.org/TR/owl2-manchester-syntax/ + + http://clarkparsia.com/pellet + + http://hermit-reasoner.com/ + + http://code.google.com/p/factplusplus/ + + http://code.google.com/p/elk-reasoner/ + + http://owlapi.sourceforge.net/ + +**Citation** + + Mikel Egaña Aranguren, Jesualdo Tomás Fernández-Breis, Erick Antezana. OPPL-Galaxy: Enhancing ontology exploitation in Galaxy with OPPL. In Proceedings of the 4th International Workshop on Semantic Web Applications and Tools for the Life Sciences, SWAT4LS 2011, pages 12–19, ACM 2012. + +**Contact** + + Please send any request or comment to mikel.egana.aranguren@gmail.com. + + + + diff -r d3616fac4ca5 -r cc270db37d33 oppl_galaxy.jar Binary file oppl_galaxy.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 oppl_galaxy_lib/FaCTpp-OWLAPI-3.2-v1.5.2.jar Binary file oppl_galaxy_lib/FaCTpp-OWLAPI-3.2-v1.5.2.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 oppl_galaxy_lib/HermiT.jar Binary file oppl_galaxy_lib/HermiT.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 oppl_galaxy_lib/antlr-runtime-3.2.jar Binary file oppl_galaxy_lib/antlr-runtime-3.2.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 oppl_galaxy_lib/aterm-java-1.6.jar Binary file oppl_galaxy_lib/aterm-java-1.6.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 oppl_galaxy_lib/elk-owlapi.jar Binary file oppl_galaxy_lib/elk-owlapi.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 oppl_galaxy_lib/jgrapht-jdk1.5.jar Binary file oppl_galaxy_lib/jgrapht-jdk1.5.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 oppl_galaxy_lib/log4j-sources.jar Binary file oppl_galaxy_lib/log4j-sources.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 oppl_galaxy_lib/log4j.jar Binary file oppl_galaxy_lib/log4j.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 oppl_galaxy_lib/org.coode.oppl-API.jar Binary file oppl_galaxy_lib/org.coode.oppl-API.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 oppl_galaxy_lib/owlapi-bin.jar Binary file oppl_galaxy_lib/owlapi-bin.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 oppl_galaxy_lib/parsers.jar Binary file oppl_galaxy_lib/parsers.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 oppl_galaxy_lib/pellet-core.jar Binary file oppl_galaxy_lib/pellet-core.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 oppl_galaxy_lib/pellet-datatypes.jar Binary file oppl_galaxy_lib/pellet-datatypes.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 oppl_galaxy_lib/pellet-el.jar Binary file oppl_galaxy_lib/pellet-el.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 oppl_galaxy_lib/pellet-owlapiv3.jar Binary file oppl_galaxy_lib/pellet-owlapiv3.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 oppl_galaxy_lib/pellet-query.jar Binary file oppl_galaxy_lib/pellet-query.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 oppl_galaxy_lib/pellet-rules.jar Binary file oppl_galaxy_lib/pellet-rules.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 oppl_query.jar Binary file oppl_query.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 oppl_query.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/oppl_query.xml Sat Oct 06 21:50:39 2012 +0200 @@ -0,0 +1,75 @@ + + It performs a query, expressed in OPPL Syntax, against an OWL ontology + + + + + + + + + + + java -Xmx3000M -Xms250M -DentityExpansionLimit=1000000000 -jar ${__tool_data_path__}/shared/jars/oppl_query.jar $ontology $reasoner $answer_format $query > $output 2>/dev/null + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +**About OPPL-Query-Galaxy** + + OPPL-Query-Galaxy can be used to execute an OPPL query against an OWL ontology. The result is a two column table with the entities that have been bound by the variables. + +**Usage** + + An ontology is needed as input: load it with Get Data >> Upload File from your computer or redirect the output of another galaxy tool. OPPL-Query-Galaxy uses the OWL API, and therefore it can load any ontology format that such API is able to load: OBO flat file, OWL (RDF/XML, OWL/XML, Functional, Manchester), turtle, and KRSS. In case the loaded ontology includes OWL imports, OPPL-Query-Galaxy will try to resolve them. + + An OPPL query must be provided in a file: an OPPL query is an OPPL script without the actions part, e.g. ?whole:CLASS, ?part:CLASS SELECT ?part SubClassOf part_of some ?whole WHERE ?part != Nothing. + + The reasoner can be Pellet, HermiT, FaCT++ or Elk. + + The returned entities can be rendered using their URI, their URI fragment, or OBO type URI fragment (e.g. GO_0000022 to GO:0000022). + +**Contact** + + Please send any request or comment to mikel.egana.aranguren@gmail.com. + + + + diff -r d3616fac4ca5 -r cc270db37d33 oppl_query_lib/FaCTpp-OWLAPI-3.2-v1.5.2.jar Binary file oppl_query_lib/FaCTpp-OWLAPI-3.2-v1.5.2.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 oppl_query_lib/HermiT.jar Binary file oppl_query_lib/HermiT.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 oppl_query_lib/antlr-runtime-3.2.jar Binary file oppl_query_lib/antlr-runtime-3.2.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 oppl_query_lib/aterm-java-1.6.jar Binary file oppl_query_lib/aterm-java-1.6.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 oppl_query_lib/elk-owlapi.jar Binary file oppl_query_lib/elk-owlapi.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 oppl_query_lib/jgrapht-jdk1.5.jar Binary file oppl_query_lib/jgrapht-jdk1.5.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 oppl_query_lib/log4j-sources.jar Binary file oppl_query_lib/log4j-sources.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 oppl_query_lib/log4j.jar Binary file oppl_query_lib/log4j.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 oppl_query_lib/org.coode.oppl-API.jar Binary file oppl_query_lib/org.coode.oppl-API.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 oppl_query_lib/owlapi-bin.jar Binary file oppl_query_lib/owlapi-bin.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 oppl_query_lib/parsers.jar Binary file oppl_query_lib/parsers.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 oppl_query_lib/pellet-core.jar Binary file oppl_query_lib/pellet-core.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 oppl_query_lib/pellet-datatypes.jar Binary file oppl_query_lib/pellet-datatypes.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 oppl_query_lib/pellet-el.jar Binary file oppl_query_lib/pellet-el.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 oppl_query_lib/pellet-owlapiv3.jar Binary file oppl_query_lib/pellet-owlapiv3.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 oppl_query_lib/pellet-query.jar Binary file oppl_query_lib/pellet-query.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 oppl_query_lib/pellet-rules.jar Binary file oppl_query_lib/pellet-rules.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 query.jar Binary file query.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 query.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/query.xml Sat Oct 06 21:50:39 2012 +0200 @@ -0,0 +1,82 @@ + + It performs a query, expressed in Manchester OWL Syntax, against an OWL ontology + + + + + + + java -Xmx3000M -Xms250M -DentityExpansionLimit=1000000000 -jar ${__tool_data_path__}/shared/jars/query.jar $ontology $reasoner $answer_type $answer_format "$query" > $output + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +**About Query-Galaxy** + + Query-Galaxy can be used to execute a DL query against an OWL ontology. The result is a list of entities from the target ontology. + +**Usage** + + An ontology is needed as input: load it with Get Data >> Upload File from your computer or redirect the output of another galaxy tool. Query-Galaxy uses the OWL API, and therefore it can load any ontology format that such API is able to load: OBO flat file, OWL (RDF/XML, OWL/XML, Functional, Manchester), turtle, and KRSS. In case the loaded ontology includes OWL imports, Query-Galaxy will try to resolve them. + + A DL query must be provided, e.g. GO_0007049 or part_of some GO_0007049. + + The reasoner can be Pellet, HermiT, FaCT++ or Elk. + + How the retrieved entities relate to the query can be chosen: a DL query is just an anonymous OWL Class, and the retrieved entities can be descendant classes, direct sub-classes, ancestor classes, direct super-classes, equivalent classes, or member individuals. + + The returned entities can be rendered using their URI, their URI fragment, or OBO type URI fragment (e.g. GO_0000022 to GO:0000022). + +**Contact** + + Please send any request or comment to mikel.egana.aranguren@gmail.com. + + + + diff -r d3616fac4ca5 -r cc270db37d33 query_lib/FaCTpp-OWLAPI-3.2-v1.5.2.jar Binary file query_lib/FaCTpp-OWLAPI-3.2-v1.5.2.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 query_lib/HermiT.jar Binary file query_lib/HermiT.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 query_lib/antlr-runtime-3.2.jar Binary file query_lib/antlr-runtime-3.2.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 query_lib/aterm-java-1.6.jar Binary file query_lib/aterm-java-1.6.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 query_lib/elk-owlapi.jar Binary file query_lib/elk-owlapi.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 query_lib/jgrapht-jdk1.5.jar Binary file query_lib/jgrapht-jdk1.5.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 query_lib/log4j-sources.jar Binary file query_lib/log4j-sources.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 query_lib/log4j.jar Binary file query_lib/log4j.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 query_lib/org.coode.oppl-API.jar Binary file query_lib/org.coode.oppl-API.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 query_lib/owlapi-bin.jar Binary file query_lib/owlapi-bin.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 query_lib/parsers.jar Binary file query_lib/parsers.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 query_lib/pellet-core.jar Binary file query_lib/pellet-core.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 query_lib/pellet-datatypes.jar Binary file query_lib/pellet-datatypes.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 query_lib/pellet-el.jar Binary file query_lib/pellet-el.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 query_lib/pellet-owlapiv3.jar Binary file query_lib/pellet-owlapiv3.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 query_lib/pellet-query.jar Binary file query_lib/pellet-query.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 query_lib/pellet-rules.jar Binary file query_lib/pellet-rules.jar has changed diff -r d3616fac4ca5 -r cc270db37d33 sed_recipes --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/sed_recipes Sat Oct 06 21:50:39 2012 +0200 @@ -0,0 +1,8 @@ +less Elk_output.text | sed s/INFO/X/ > output +less Elk_output.text | sed s/.*org.semanticweb.elk.reasoner.*// > output +less Elk_output.text | sed /.*org.semanticweb.elk.reasoner.*/d > output + +| sed /.*org.semanticweb.elk.reasoner.*/d +less Elk_output.text | sed /^\s*\<.*\>/d + + diff -r d3616fac4ca5 -r cc270db37d33 src/GalaxyOWLAPI.java --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/src/GalaxyOWLAPI.java Sat Oct 06 21:50:39 2012 +0200 @@ -0,0 +1,331 @@ +/** + * + */ +package es.upm.fi.dia.oeg.oppl.galaxy; + +import java.io.BufferedWriter; +import java.io.File; +import java.io.IOException; +import java.io.OutputStreamWriter; +import java.util.ArrayList; +import java.util.List; +import java.util.Scanner; +import java.util.Set; + +import org.apache.log4j.Level; +import org.apache.log4j.Logger; +import org.coode.owlapi.manchesterowlsyntax.ManchesterOWLSyntaxEditorParser; +import org.coode.owlapi.obo.parser.OBOOntologyFormat; +import org.coode.parsers.BidirectionalShortFormProviderAdapter; +import org.semanticweb.HermiT.Reasoner; +import org.semanticweb.elk.owlapi.ElkReasonerFactory; +import org.semanticweb.owlapi.apibinding.OWLManager; +import org.semanticweb.owlapi.expression.OWLEntityChecker; +import org.semanticweb.owlapi.expression.ParserException; +import org.semanticweb.owlapi.expression.ShortFormEntityChecker; +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.OWLClass; +import org.semanticweb.owlapi.model.OWLClassExpression; +import org.semanticweb.owlapi.model.OWLDataFactory; +import org.semanticweb.owlapi.model.OWLLiteral; +import org.semanticweb.owlapi.model.OWLNamedIndividual; +import org.semanticweb.owlapi.model.OWLOntology; +import org.semanticweb.owlapi.model.OWLOntologyChange; +import org.semanticweb.owlapi.model.OWLOntologyCreationException; +import org.semanticweb.owlapi.model.OWLOntologyManager; +import org.semanticweb.owlapi.model.OWLOntologyStorageException; +import org.semanticweb.owlapi.reasoner.InferenceType; +import org.semanticweb.owlapi.reasoner.OWLReasoner; +import org.semanticweb.owlapi.reasoner.OWLReasonerFactory; +import org.semanticweb.owlapi.util.BidirectionalShortFormProvider; +import org.semanticweb.owlapi.util.InferredAxiomGenerator; +import org.semanticweb.owlapi.util.InferredClassAssertionAxiomGenerator; +import org.semanticweb.owlapi.util.InferredDisjointClassesAxiomGenerator; +import org.semanticweb.owlapi.util.InferredOntologyGenerator; +import org.semanticweb.owlapi.util.InferredSubClassAxiomGenerator; +import org.semanticweb.owlapi.util.InferredSubDataPropertyAxiomGenerator; +import org.semanticweb.owlapi.util.InferredSubObjectPropertyAxiomGenerator; +import org.semanticweb.owlapi.util.OWLEntityRenamer; +import org.semanticweb.owlapi.util.OWLOntologyImportsClosureSetProvider; +import org.semanticweb.owlapi.util.OWLOntologyMerger; +import org.semanticweb.owlapi.util.SimpleShortFormProvider; +import org.semanticweb.owlapi.vocab.OWL2Datatype; +import org.semanticweb.owlapi.vocab.OWLRDFVocabulary; +import org.semanticweb.owlapi.reasoner.Node; + +import uk.ac.manchester.cs.factplusplus.owlapiv3.FaCTPlusPlusReasonerFactory; + +import com.clarkparsia.pellet.owlapiv3.PelletReasonerFactory; + +/** + * A wrapper of the OWL API + * + * @author Mikel Egana Aranguren + */ +public class GalaxyOWLAPI { + private OWLOntologyManager manager; + private OWLOntology ontology; + private OWLReasonerFactory reasonerFactory; + private OWLReasoner reasoner; + + public GalaxyOWLAPI (){ + manager = OWLManager.createOWLOntologyManager(); + } + public OWLOntologyManager getOWLManager(){ + return manager; + } + public OWLOntology getMainOntology(){ + return ontology; + } + public OWLReasoner getReasoner(){ + return reasoner; + } + + public void loadMainOntology(String OWLFilePath) throws OWLOntologyCreationException{ + File owl_file = new File(OWLFilePath); + ontology = manager.loadOntologyFromOntologyDocument(owl_file); + } + +// public void loadImportedOntology(IRI importedOntologyIRI) throws OWLOntologyCreationException{ +// manager.loadOntologyFromOntologyDocument(importedOntologyIRI); +// } + + // 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); + + public void setReasonerPellet (){ + reasonerFactory = new PelletReasonerFactory(); + reasoner = reasonerFactory.createReasoner(ontology); + } + public void setReasonerFaCT (){ + reasonerFactory = new FaCTPlusPlusReasonerFactory(); + reasoner = reasonerFactory.createReasoner(ontology); + } + public void setReasonerHermit (){ + reasonerFactory = new Reasoner.ReasonerFactory(); + reasoner = reasonerFactory.createReasoner(ontology); + } + public void setReasonerElk (){ + reasonerFactory = new ElkReasonerFactory(); + Logger.getLogger("org.semanticweb.elk").setLevel(Level.OFF); + reasoner = reasonerFactory.createReasoner(ontology); + } + public void disposeReasoner(){ + reasoner.dispose(); + } + public void merge (String ontologyIRI) throws OWLOntologyCreationException, OWLOntologyStorageException{ + OWLOntologyMerger merger = new OWLOntologyMerger(manager); +// OWLOntologyMerger merger = new OWLOntologyMerger(new OWLOntologyImportsClosureSetProvider(manager, ontology)); + IRI mergedOntologyIRI = IRI.create(ontologyIRI); +// OWLOntology merged_ontology = merger.createMergedOntology(manager, mergedOntologyIRI); + ontology = merger.createMergedOntology(manager, mergedOntologyIRI); +// manager.saveOntology(ontology, new RDFXMLOntologyFormat(), new SystemOutDocumentTarget()); + } + + public OWLClassExpression parseMOSClassExpression (String expr) throws ParserException{ + Set importsClosure = ontology.getImportsClosure(); + BidirectionalShortFormProvider bidiShortFormProvider = new BidirectionalShortFormProviderAdapter(manager, importsClosure, new SimpleShortFormProvider()); + OWLEntityChecker entityChecker = new ShortFormEntityChecker(bidiShortFormProvider); + ManchesterOWLSyntaxEditorParser MOSparser = new ManchesterOWLSyntaxEditorParser(manager.getOWLDataFactory(), expr); + MOSparser.setOWLEntityChecker(entityChecker); + return MOSparser.parseClassExpression(); + } + + public Set getIndividuals (OWLClassExpression expr){ + return (reasoner.getInstances(expr, false)).getFlattened(); + } + public Set getEquivalentClasses (OWLClassExpression expr){ + Node equivalentClasses = reasoner.getEquivalentClasses(expr); + Set result; + if (expr.isAnonymous()) { + result = equivalentClasses.getEntities(); + } + else { + result = equivalentClasses.getEntitiesMinus(expr.asOWLClass()); + } + return result; + } + + public Set getDirectSuperClasses (OWLClassExpression expr){ + return (reasoner.getSuperClasses(expr, true)).getFlattened(); + } + + public Set getAncestors (OWLClassExpression expr){ + return (reasoner.getSuperClasses(expr, false)).getFlattened(); + } + + public Set getDirectSubClasses (OWLClassExpression expr){ + return (reasoner.getSubClasses(expr, true)).getFlattened(); + } + + public Set getDescendants (OWLClassExpression expr){ + return (reasoner.getSubClasses(expr, false)).getFlattened(); + } + + // CLASS_ASSERTIONS Denotes the computation of the direct types of individuals for each individual in the signature of the imports closure of the root ontology. + + public void addCLASS_ASSERTIONS(){ + reasoner.precomputeInferences(InferenceType.CLASS_ASSERTIONS); + List> gens = new ArrayList>(); + gens.add(new InferredClassAssertionAxiomGenerator()); + InferredOntologyGenerator iog = new InferredOntologyGenerator(reasoner, gens); + iog.fillOntology(manager, ontology); + } + + // CLASS_HIERARCHY Denotes the computation of the class hierarchy. + + public void addCLASS_HIERARCHY(){ + reasoner.precomputeInferences(InferenceType.CLASS_HIERARCHY); + List> gens = new ArrayList>(); + gens.add(new InferredSubClassAxiomGenerator()); + InferredOntologyGenerator iog = new InferredOntologyGenerator(reasoner, gens); + iog.fillOntology(manager, ontology); + } + + // DATA_PROPERTY_ASSERTIONS Denotes the computation of relationships between individuals and data property values for each individual in the signature of the imports closure of the root ontology. +// public void addDATA_PROPERTY_ASSERTIONS(){ +// reasoner.precomputeInferences(InferenceType.DATA_PROPERTY_ASSERTIONS); +// List> gens = new ArrayList>(); +// gens.add(new InferredDataPropertyAxiomGenerator()); +// InferredOntologyGenerator iog = new InferredOntologyGenerator(reasoner, gens); +// iog.fillOntology(manager, ontology); +// } + + // DATA_PROPERTY_HIERARCHY Denotes the computation of the data property hierarchy. + + public void addDATA_PROPERTY_HIERARCHY(){ + reasoner.precomputeInferences(InferenceType.DATA_PROPERTY_HIERARCHY); + List> gens = new ArrayList>(); + gens.add(new InferredSubDataPropertyAxiomGenerator()); + InferredOntologyGenerator iog = new InferredOntologyGenerator(reasoner, gens); + iog.fillOntology(manager, ontology); + } + + // DIFFERENT_INDIVIDUALS Denotes the computation of sets of individuals that are different from each individual in the signature of the imports closure of the root ontology. + +// public void addDIFFERENT_INDIVIDUALS(){ +// reasoner.precomputeInferences(InferenceType.DIFFERENT_INDIVIDUALS); +// List> gens = new ArrayList>(); +// gens.add(new Inferred); +// InferredOntologyGenerator iog = new InferredOntologyGenerator(reasoner, gens); +// iog.fillOntology(manager, ontology); +// } + + // DISJOINT_CLASSES Denotes the computation of sets of classes that are disjoint for each class in the signature of the imports closure of the root ontology. + + public void addDISJOINT_CLASSES(){ + reasoner.precomputeInferences(InferenceType.DISJOINT_CLASSES); + List> gens = new ArrayList>(); + gens.add(new InferredDisjointClassesAxiomGenerator()); + InferredOntologyGenerator iog = new InferredOntologyGenerator(reasoner, gens); + iog.fillOntology(manager, ontology); + } + + // OBJECT_PROPERTY_ASSERTIONS Denotes the computation of relationships between individuals in the signature of the imports closure of the root ontology. + +// public void addOBJECT_PROPERTY_ASSERTIONS(){ +// reasoner.precomputeInferences(InferenceType.OBJECT_PROPERTY_ASSERTIONS); +// List> gens = new ArrayList>(); +// gens.add(new InferredObjectPropertyAxiomGenerator() { +// };()); +// InferredOntologyGenerator iog = new InferredOntologyGenerator(reasoner, gens); +// iog.fillOntology(manager, ontology); +// } + + // OBJECT_PROPERTY_HIERARCHY Denotes the computation of the object property hierarchy. + + public void addOBJECT_PROPERTY_HIERARCHY(){ + reasoner.precomputeInferences(InferenceType.OBJECT_PROPERTY_HIERARCHY); + List> gens = new ArrayList>(); + gens.add(new InferredSubObjectPropertyAxiomGenerator()); + InferredOntologyGenerator iog = new InferredOntologyGenerator(reasoner, gens); + iog.fillOntology(manager, ontology); + } + + // SAME_INDIVIDUAL Denotes the computation of individuals that are interpreted as the same object for each individual in the imports closure of the root ontology. + +// public void addSAME_INDIVIDUAL(){ +// reasoner.precomputeInferences(InferenceType.SAME_INDIVIDUAL); +// List> gens = new ArrayList>(); +// gens.add(new Infer); +// InferredOntologyGenerator iog = new InferredOntologyGenerator(reasoner, gens); +// iog.fillOntology(manager, ontology); +// } + + public void saveOntology (boolean OWL) throws OWLOntologyStorageException, IOException, OWLOntologyCreationException{ + // OWL format + if(OWL){ + manager.saveOntology(ontology, new RDFXMLOntologyFormat(), new SystemOutDocumentTarget()); + } + // OBO format + else{ + // 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 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 = ""; + + 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(); + } + } +} diff -r d3616fac4ca5 -r cc270db37d33 src/InferenceGalaxy.java --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/src/InferenceGalaxy.java Sat Oct 06 21:50:39 2012 +0200 @@ -0,0 +1,111 @@ +/** + * + */ +package es.upm.fi.dia.oeg.oppl.galaxy; + + +import java.io.IOException; + +import org.semanticweb.owlapi.model.OWLOntologyCreationException; +import org.semanticweb.owlapi.model.OWLOntologyStorageException; + + +/** + * @author Mikel Ega��a Aranguren + * + */ +public class InferenceGalaxy { + + /** + * @param args + * @throws IOException + * @throws OWLOntologyCreationException + * @throws OWLOntologyStorageException + */ + public static void main(String[] args) throws OWLOntologyStorageException, OWLOntologyCreationException, IOException { + // Get the arguments from command-line + String OWLFilePath = args [0]; + String reasoner_type = args [1]; // Pellet|FaCTPlusPlus|HermiT|Elk + String axioms_to_inject = args [2]; // CLASS_ASSERTIONS,CLASS_HIERARCHY,DATA_PROPERTY_ASSERTIONS + +// CLASS_ASSERTIONS Denotes the computation of the direct types of individuals for each individual in the signature of the imports closure of the root ontology. +// CLASS_HIERARCHY Denotes the computation of the class hierarchy. +// DATA_PROPERTY_ASSERTIONS Denotes the computation of relationships between individuals and data property values for each individual in the signature of the imports closure of the root ontology. +// DATA_PROPERTY_HIERARCHY Denotes the computation of the data property hierarchy. +// DIFFERENT_INDIVIDUALS Denotes the computation of sets of individuals that are different from each individual in the signature of the imports closure of the root ontology. +// DISJOINT_CLASSES Denotes the computation of sets of classes that are disjoint for each class in the signature of the imports closure of the root ontology. +// OBJECT_PROPERTY_ASSERTIONS Denotes the computation of relationships between individuals in the signature of the imports closure of the root ontology. +// OBJECT_PROPERTY_HIERARCHY Denotes the computation of the object property hierarchy. +// SAME_INDIVIDUAL Denotes the computation of individuals that are interpreted as the same object for each individual in the imports closure of the root ontology. + + // Create the manager + GalaxyOWLAPI galaxyowlapi = new GalaxyOWLAPI(); + + // Load the main ontology + galaxyowlapi.loadMainOntology(OWLFilePath); + + // Set the reasoner + + // Pellet + if(reasoner_type.equals("Pellet")){ + galaxyowlapi.setReasonerPellet(); + } + // FaCTPlusPlus + else if (reasoner_type.equals("FaCTPlusPlus")){ + galaxyowlapi.setReasonerFaCT(); + } + // Elk + else if (reasoner_type.equals("Elk")){ + galaxyowlapi.setReasonerElk(); + } + // HermiT + else{ + galaxyowlapi.setReasonerHermit(); + } + + // Add the inferred axioms as asserted axioms to the original ontology + + if(axioms_to_inject.contains(",")){ + String[] axioms = axioms_to_inject.split(","); + for(int i =0; i < axioms.length ; i++) + injectAxiom (axioms[i], galaxyowlapi); + } + else{ + injectAxiom (axioms_to_inject, galaxyowlapi); + } + + galaxyowlapi.disposeReasoner(); + + // Merge imported ontologies if requested +// if(merge.equals("Merge")){ +// galaxyowlapi.merge(); +// } + + // Save the ontology in OWL + galaxyowlapi.saveOntology(true); + + } + + static void injectAxiom (String axiom_to_inject, GalaxyOWLAPI galaxyowlapi){ + if(axiom_to_inject.equals("CLASS_HIERARCHY")){ + galaxyowlapi.addCLASS_HIERARCHY(); +// System.out.println("CLASS_HIERARCHY"); + } + if(axiom_to_inject.equals("CLASS_ASSERTIONS")){ + galaxyowlapi.addCLASS_ASSERTIONS(); +// System.out.println("CLASS_ASSERTIONS"); + } + if(axiom_to_inject.equals("DATA_PROPERTY_HIERARCHY")){ + galaxyowlapi.addDATA_PROPERTY_HIERARCHY(); +// System.out.println("DATA_PROPERTY_HIERARCHY"); + } + if(axiom_to_inject.equals("DISJOINT_CLASSES")){ + galaxyowlapi.addDISJOINT_CLASSES(); +// System.out.println("DISJOINT_CLASSES"); + } + if(axiom_to_inject.equals("OBJECT_PROPERTY_HIERARCHY")){ + galaxyowlapi.addOBJECT_PROPERTY_HIERARCHY(); +// System.out.println("OBJECT_PROPERTY_HIERARCHY"); + } + } +} diff -r d3616fac4ca5 -r cc270db37d33 src/MergeImportedOntologies.java --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/src/MergeImportedOntologies.java Sat Oct 06 21:50:39 2012 +0200 @@ -0,0 +1,39 @@ +package es.upm.cbgp.opplquery.oppl.galaxy; + +import java.io.IOException; + +import org.semanticweb.owlapi.model.OWLOntologyCreationException; +import org.semanticweb.owlapi.model.OWLOntologyStorageException; + +import es.upm.fi.dia.oeg.oppl.galaxy.GalaxyOWLAPI; + +public class MergeImportedOntologies { + + /** + * @param args + * @throws OWLOntologyCreationException + * @throws IOException + * @throws OWLOntologyStorageException + */ + public static void main(String[] args) throws OWLOntologyCreationException, OWLOntologyStorageException, IOException { + String OWLFilePath = args [0]; + String MergedOntologyNewURI = args [1]; +// String OWLFilePath = "/home/mikel/UPM/OPPL_galaxy/OPPL/OPPL/test-data/ontology/imports/merge_test.owl"; +// String MergedOntologyNewURI = "http://cbgp.upm.es/merged.owl"; + + // Create the manager + GalaxyOWLAPI galaxyowlapi = new GalaxyOWLAPI(); + + // Load the main ontology and hope for the imported URIs to be resolvable + galaxyowlapi.loadMainOntology(OWLFilePath); + + // Merge and save + + if(MergedOntologyNewURI.isEmpty()){ + MergedOntologyNewURI = "http://cbgp.upm.es/BiologicalInformatics/OPPLGalaxy/merged.owl"; + } + + galaxyowlapi.merge(MergedOntologyNewURI); + galaxyowlapi.saveOntology(true); + } +} diff -r d3616fac4ca5 -r cc270db37d33 src/OPPLGalaxy.java --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/src/OPPLGalaxy.java Sat Oct 06 21:50:39 2012 +0200 @@ -0,0 +1,121 @@ +/** + * + */ +package es.upm.fi.dia.oeg.oppl.galaxy; + +import java.io.File; +import java.io.IOException; +import java.util.List; +import java.util.Scanner; +import java.util.logging.Level; +import java.util.logging.Logger; + +//import org.apache.log4j.Level; +import org.coode.oppl.ChangeExtractor; +import org.coode.oppl.OPPLParser; +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.parsers.ErrorListener; +import org.coode.parsers.LoggerErrorListener; +import org.semanticweb.owlapi.model.OWLAxiomChange; +import org.semanticweb.owlapi.model.OWLOntology; +import org.semanticweb.owlapi.model.OWLOntologyCreationException; +import org.semanticweb.owlapi.model.OWLOntologyManager; +import org.semanticweb.owlapi.model.OWLOntologyStorageException; +import org.semanticweb.owlapi.reasoner.OWLReasoner; + + + + +/** + * @author Mikel Ega��a Aranguren + * + */ +public class OPPLGalaxy { + + /** + * @param args + * @throws OWLOntologyCreationException + * @throws OWLOntologyStorageException + * @throws IOException + */ + public static void main(String[] args) throws OWLOntologyCreationException, OWLOntologyStorageException, IOException { + // Get the arguments from command-line + String OWLFilePath = args [0]; + String reasoner_type = args [1]; // Pellet|FaCTPlusPlus|Elk|HermiT + + String OPPL_script_file = args [2]; + String OWL = args [3]; // OWL|OBO + + // Create the manager + GalaxyOWLAPI galaxyowlapi = new GalaxyOWLAPI(); + + // Load the main ontology and hope for the imported URIs to be resolvable + galaxyowlapi.loadMainOntology(OWLFilePath); + + // Set the reasoner + + // Pellet + if(reasoner_type.equals("Pellet")){ + galaxyowlapi.setReasonerPellet(); + } + // FaCTPlusPlus + else if (reasoner_type.equals("FaCTPlusPlus")){ + galaxyowlapi.setReasonerFaCT(); + } + // Elk + else if (reasoner_type.equals("Elk")){ + galaxyowlapi.setReasonerElk(); + } + // HermiT + else{ + galaxyowlapi.setReasonerHermit(); + } + + // Load the OPPL flat file with script in memory + String OPPL_script_source = ""; + File file = new File(OPPL_script_file); + Scanner input = new Scanner(file); + while(input.hasNext()) { + String nextToken = input.next(); + OPPL_script_source = OPPL_script_source + " " + nextToken; + } + input.close(); + + OWLOntologyManager manager = galaxyowlapi.getOWLManager(); + OWLOntology ontology = galaxyowlapi.getMainOntology(); + OWLReasoner reasoner = galaxyowlapi.getReasoner(); + + // Parse the OPPL script + ParserFactory parserFactory = new ParserFactory(manager, ontology, reasoner); + Logger logger = Logger.getLogger(OPPLGalaxy.class.getName()); +// logger.setLevel(Level.OFF); +// Logging.getQueryLogger().setLevel(Level.OFF); // The normal messages are errors for galaxy (Fixed in Galaxy by 2 > /dev/null) + + ErrorListener errorListener = (ErrorListener)new LoggerErrorListener(logger); + OPPLParser opplparser = parserFactory.build(errorListener); + OPPLScript OPPLscript = opplparser.parse(OPPL_script_source); + + // Execute the script + ChangeExtractor extractor = new ChangeExtractor(new QuickFailRuntimeExceptionHandler(), true); + List changes = extractor.visit(OPPLscript); + manager.applyChanges(changes); + + galaxyowlapi.disposeReasoner(); + + // Merge imported ontologies if requested +// if(merge.equals("Merge")){ +// galaxyowlapi.merge(); +// } + + // Save the ontology + if(OWL.equals("OWL")){ + galaxyowlapi.saveOntology(true); + } + else{ + galaxyowlapi.saveOntology(false); + } + } +} diff -r d3616fac4ca5 -r cc270db37d33 src/OPPLQueryGalaxy.java --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/src/OPPLQueryGalaxy.java Sat Oct 06 21:50:39 2012 +0200 @@ -0,0 +1,180 @@ +/** + * + */ +package es.upm.cbgp.opplquery.oppl.galaxy; + +import java.io.File; +import java.io.FileNotFoundException; +import java.util.Iterator; +import java.util.Scanner; +import java.util.Set; +import java.util.logging.Logger; +import java.util.regex.Matcher; +import java.util.regex.Pattern; + +import org.semanticweb.owlapi.expression.ParserException; +import org.semanticweb.owlapi.model.IRI; +import org.semanticweb.owlapi.model.OWLObject; +import org.semanticweb.owlapi.model.OWLOntologyCreationException; + +import es.upm.fi.dia.oeg.oppl.galaxy.GalaxyOWLAPI; + +import org.coode.oppl.ChangeExtractor; +import org.coode.oppl.ConstraintSystem; +import org.coode.oppl.OPPLParser; +import org.coode.oppl.OPPLScript; +import org.coode.oppl.ParserFactory; +import org.coode.parsers.ErrorListener; +import org.coode.parsers.LoggerErrorListener; +import org.coode.oppl.bindingtree.Assignment; +import org.coode.oppl.bindingtree.BindingNode; +import org.coode.oppl.exceptions.QuickFailRuntimeExceptionHandler; +import org.coode.oppl.exceptions.RuntimeExceptionHandler; + +public class OPPLQueryGalaxy { + + /** + * @param args + * @throws OWLOntologyCreationException + * @throws ParserException + * @throws FileNotFoundException + */ + public static void main(String[] args) throws OWLOntologyCreationException, ParserException, FileNotFoundException { + // Get the arguments from command-line + String OWLFilePath = args [0]; // /home/mikel/UPM/OPPL_galaxy/OPPL/OPPL/test-data/ontology/single/test.owl + String reasoner_type = args [1]; // Pellet|FaCTPlusPlus|HermiT|Elk + String Answer_render = args [2]; // URI|URIfragment|URIfragment2OBO + String OPPL_script_file = args [3]; + +// String OPPL_script_file = args [3]; +// File OPPL_script_file = new File("/home/mikel/UPM/OPPL_galaxy/OPPL/OPPL/test-data/oppl_script/test_oppl_query.oppl"); +// File OPPL_script_file = new File("/home/mikel/UPM/OPPL_galaxy/OPPL/OPPL/test-data/oppl_script/test_oppl_query_object_prop.oppl"); +// File OPPL_script_file = new File("/home/mikel/UPM/OPPL_galaxy/OPPL/OPPL/test-data/oppl_script/test_oppl_query_object_ind.oppl"); + + + // Create the manager + GalaxyOWLAPI galaxyowlapi = new GalaxyOWLAPI(); + + // Load the main ontology and hope for the imported URIs to be resolvable + galaxyowlapi.loadMainOntology(OWLFilePath); + + // Set the reasoner + + // Pellet + if(reasoner_type.equals("Pellet")){ + galaxyowlapi.setReasonerPellet(); + } + // FaCTPlusPlus + else if (reasoner_type.equals("FaCTPlusPlus")){ + galaxyowlapi.setReasonerFaCT(); + } + // Elk + else if (reasoner_type.equals("Elk")){ + galaxyowlapi.setReasonerElk(); + } + // HermiT + else{ + galaxyowlapi.setReasonerHermit(); + } + + // Load the OPPL flat file with script in memory + String OPPL_script_source = ""; + File file = new File(OPPL_script_file); + Scanner input = new Scanner(file); + while(input.hasNext()) { + String nextToken = input.next(); + OPPL_script_source = OPPL_script_source + " " + nextToken; + } + input.close(); + + OPPL_script_source = completeOPPLScript(OPPL_script_source); +// System.out.println(OPPL_script_source); + + ParserFactory parserFactory = new ParserFactory(galaxyowlapi.getOWLManager(), galaxyowlapi.getMainOntology(), galaxyowlapi.getReasoner()); + Logger logger = Logger.getLogger(OPPLQueryGalaxy.class.getName()); + ErrorListener errorListener = (ErrorListener) new LoggerErrorListener(logger); + OPPLParser opplparser = parserFactory.build(errorListener); + OPPLScript OPPLscript = opplparser.parse(OPPL_script_source); + RuntimeExceptionHandler exceptionhandler = new QuickFailRuntimeExceptionHandler(); + ChangeExtractor extractor = new ChangeExtractor(exceptionhandler, true); + extractor.visit(OPPLscript); + ConstraintSystem cs = OPPLscript.getConstraintSystem(); + Set nodes = cs.getLeaves(); + + galaxyowlapi.disposeReasoner(); + + Iterator NodesIterator = nodes.iterator(); + while(NodesIterator.hasNext()){ + Set Assignments = ((BindingNode)NodesIterator.next()).getAssignments(); + Iterator AssignmentIterator = Assignments.iterator(); + while(AssignmentIterator.hasNext()){ + Assignment assignment = (Assignment)AssignmentIterator.next(); + System.out.print(assignment.getAssignedVariable().toString()); + System.out.print("\t"); + String OWLObjectString = ((OWLObject)assignment.getAssignment()).toString(); + IRI entityIRI = IRI.create(OWLObjectString.substring(1,OWLObjectString.length()-1)); + print_result_entity(entityIRI, Answer_render); + System.out.print("\n"); + } + } + } + + //URI|URIfragment|URIfragment2OBO + private static void print_result_entity (IRI iri, String Answer_render){ + if(Answer_render.equals("URI")){ + System.out.print(iri); + } + + // Weird bug: in eclipse it can print out the IRIs of every entity, but in Galaxy it can't! + // done manually + else if(Answer_render.equals("URIfragment")){ + if(iri.toString().contains("#")){ + System.out.print(iri.getFragment()); + } + else{ + String [] iri_tokens = iri.toString().split("/"); + System.out.print(iri_tokens[iri_tokens.length-1]); + } + } + else{ + if(iri.toString().contains("#")){ + System.out.print((iri.getFragment()).replace("_", ":")); + } + else{ + String [] iri_tokens = iri.toString().split("/"); + System.out.print((iri_tokens[iri_tokens.length-1]).replace("_", ":")); + } + } + } + + // Very crappy stuff: complete the query to make a whole OPPL script that can be parsed + private static String completeOPPLScript (String OPPLQuery){ +// System.out.println(OPPLQuery); + // Get the first variable and add at least an axiom to make a whole script + Pattern p = Pattern.compile("(\\?\\w+):(CLASS|INDIVIDUAL|OBJECTPROPERTY|DATAPROPERTY|ANNOTATIONPROPERTY|CONSTANT)"); + Matcher m = p.matcher(OPPLQuery); + m.find(); + if (m.group(2).equals("CLASS")){ + OPPLQuery = OPPLQuery + " BEGIN ADD " + m.group(1) + " SubClassOf !A END;"; + } + else if (m.group(2).equals("INDIVIDUAL")){ + OPPLQuery = OPPLQuery + " BEGIN ADD " + m.group(1) + " !p !b END;"; + } + else if (m.group(2).equals("OBJECTPROPERTY")){ + OPPLQuery = OPPLQuery + " BEGIN ADD Transitive ?p END;"; + } +// else if (m.group(2).equals("DATAPROPERTY")){ +// OPPLQuery = OPPLQuery + " BEGIN ADD ?whole SubClassOf !A END;"; +// } +// else if (m.group(2).equals("ANNOTATIONPROPERTY")){ +// OPPLQuery = OPPLQuery + " BEGIN ADD ?whole SubClassOf !A END;"; +// } +// else if (m.group(2).equals("CONSTANT")){ +// OPPLQuery = OPPLQuery + " BEGIN ADD ?whole SubClassOf !A END;"; +// } + else{ + OPPLQuery = "Malformed OPPL query"; + } + return OPPLQuery; + } +} diff -r d3616fac4ca5 -r cc270db37d33 src/OWLQueryGalaxy.java --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/src/OWLQueryGalaxy.java Sat Oct 06 21:50:39 2012 +0200 @@ -0,0 +1,129 @@ +package es.upm.fi.dia.oeg.oppl.galaxy; + +import java.util.Set; + +import org.semanticweb.owlapi.expression.ParserException; +import org.semanticweb.owlapi.model.IRI; +import org.semanticweb.owlapi.model.OWLClass; +import org.semanticweb.owlapi.model.OWLClassExpression; +import org.semanticweb.owlapi.model.OWLNamedIndividual; +import org.semanticweb.owlapi.model.OWLOntologyCreationException; + +public class OWLQueryGalaxy { + + /** + * @param args + * @throws OWLOntologyCreationException + * @throws ParserException + */ + public static void main(String[] args) throws OWLOntologyCreationException, ParserException { + // Get the arguments from command-line + String OWLFilePath = args [0]; // /home/pik/UPM/Paper/SWAT4LS_2011/JBS/Workflows_JBS/GO_module_transitive/go_no_trans.owl + String reasoner_type = args [1]; // Pellet|FaCTPlusPlus|HermiT|Elk + + String Answer_type = args [2]; // Individuals|EquivalentClasses|DirectSuperClasses|Ancestors|DirectSubClasses|Descendants + String Answer_render = args [3]; // URI|URIfragment|URIfragment2OBO + String MOS_query = args [4]; // GO_0007049 or part_of some GO_0007049 + + // Create the manager + GalaxyOWLAPI galaxyowlapi = new GalaxyOWLAPI(); + + // Load the main ontology and hope for the imported URIs to be resolvable + galaxyowlapi.loadMainOntology(OWLFilePath); + + // Set the reasoner + + // Pellet + if(reasoner_type.equals("Pellet")){ + galaxyowlapi.setReasonerPellet(); + } + // FaCTPlusPlus + else if (reasoner_type.equals("FaCTPlusPlus")){ + galaxyowlapi.setReasonerFaCT(); + } + // Elk + else if (reasoner_type.equals("Elk")){ + galaxyowlapi.setReasonerElk(); + } + // HermiT + else{ + galaxyowlapi.setReasonerHermit(); + } + + // Parse the expression to an OWLexpression + OWLClassExpression class_expr = galaxyowlapi.parseMOSClassExpression(MOS_query); + + // Execute query and print results + if(Answer_type.equals("Individuals")){ + Set inds = galaxyowlapi.getIndividuals(class_expr); + galaxyowlapi.disposeReasoner(); + for(OWLNamedIndividual ind : inds){ + print_result_entity(ind.getIRI(), Answer_render); + } + } + else if (Answer_type.equals("EquivalentClasses")) { + Set answer_classes = galaxyowlapi.getEquivalentClasses(class_expr); + galaxyowlapi.disposeReasoner(); + for(OWLClass cls : answer_classes){ + print_result_entity(cls.getIRI(), Answer_render); + } + } + else if (Answer_type.equals("DirectSuperClasses")) { + Set answer_classes = galaxyowlapi.getDirectSuperClasses(class_expr); + galaxyowlapi.disposeReasoner(); + for(OWLClass cls : answer_classes){ + print_result_entity(cls.getIRI(), Answer_render); + } + } + else if (Answer_type.equals("Ancestors")) { + Set answer_classes = galaxyowlapi.getAncestors(class_expr); + galaxyowlapi.disposeReasoner(); + for(OWLClass cls : answer_classes){ + print_result_entity(cls.getIRI(), Answer_render); + } + } + else if (Answer_type.equals("DirectSubClasses")) { + Set answer_classes = galaxyowlapi.getDirectSubClasses(class_expr); + galaxyowlapi.disposeReasoner(); + for(OWLClass cls : answer_classes){ + print_result_entity(cls.getIRI(), Answer_render); + } + } + // Descendants + else { + Set answer_classes = galaxyowlapi.getDescendants(class_expr); + galaxyowlapi.disposeReasoner(); + for(OWLClass cls : answer_classes){ + print_result_entity(cls.getIRI(), Answer_render); + } + } + } + + //URI|URIfragment|URIfragment2OBO + private static void print_result_entity (IRI iri, String Answer_render){ + if(Answer_render.equals("URI")){ + System.out.println(iri); + } + + // Weird bug: in eclipse it can print out the IRIs of every entity, but in Galaxy it can't! + // done manually + else if(Answer_render.equals("URIfragment")){ + if(iri.toString().contains("#")){ + System.out.println(iri.getFragment()); + } + else{ + String [] iri_tokens = iri.toString().split("/"); + System.out.println(iri_tokens[iri_tokens.length-1]); + } + } + else{ + if(iri.toString().contains("#")){ + System.out.println((iri.getFragment()).replace("_", ":")); + } + else{ + String [] iri_tokens = iri.toString().split("/"); + System.out.println((iri_tokens[iri_tokens.length-1]).replace("_", ":")); + } + } + } +} diff -r d3616fac4ca5 -r cc270db37d33 stderr_wrapper.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/stderr_wrapper.py Sat Oct 06 21:50:39 2012 +0200 @@ -0,0 +1,53 @@ +#!/usr/bin/env python + +""" +Wrapper that execute a program and its arguments but reports standard error +messages only if the program exit status was not 0 +Example: ./stderr_wrapper.py myprog arg1 -f arg2 +""" + +import sys, subprocess + +assert sys.version_info[:2] >= ( 2, 4 ) + +def stop_err( msg ): + sys.stderr.write( "%s\n" % msg ) + sys.exit() + +def __main__(): + # Get command-line arguments + args = sys.argv + # Remove name of calling program, i.e. ./stderr_wrapper.py + args.pop(0) + # If there are no arguments left, we're done + if len(args) == 0: + return + + # If one needs to silence stdout + #args.append( ">" ) + #args.append( "/dev/null" ) + + cmdline = " ".join(args) + try: + # Run program + proc = subprocess.Popen( args=cmdline, shell=True, stderr=subprocess.PIPE ) + returncode = proc.wait() + # Capture stderr, allowing for case where it's very large + stderr = '' + buffsize = 1048576 + try: + while True: + stderr += proc.stderr.read( buffsize ) + if not stderr or len( stderr ) % buffsize != 0: + break + except OverflowError: + pass + # Running Grinder failed: write error message to stderr + if returncode != 0: + raise Exception, stderr + except Exception, e: + # Running Grinder failed: write error message to stderr + stop_err( 'Error:\n' + str( e ) ) + + +if __name__ == "__main__": __main__() \ No newline at end of file diff -r d3616fac4ca5 -r cc270db37d33 test-data/ontology/imports/imports_inference_test.owl --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ontology/imports/imports_inference_test.owl Sat Oct 06 21:50:39 2012 +0200 @@ -0,0 +1,196 @@ + + + + + + + + + +]> + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Expected inferences: + +aa memberOf a + +c subClassOf a + +(imports) + +d subClassOf e + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff -r d3616fac4ca5 -r cc270db37d33 test-data/ontology/imports/imports_test.owl --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ontology/imports/imports_test.owl Sat Oct 06 21:50:39 2012 +0200 @@ -0,0 +1,208 @@ + + + + + + + + + +]> + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Expected inferences: + +aa memberOf a + +c subClassOf a + +(imports) + +d subClassOf e + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff -r d3616fac4ca5 -r cc270db37d33 test-data/ontology/imports/merge.owl --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ontology/imports/merge.owl Sat Oct 06 21:50:39 2012 +0200 @@ -0,0 +1,8824 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + NB Transitive - the ingredients of ingredients are ingredients of the whole + + + + + + + + + + + + A property created to be used with the ValuePartition - Spiciness. + + + + + + + + + + Note that hasTopping is inverse functional because isToppingOf is functional + + + + + + + + + + + + + + + + + + + + + + + + + The inverse property tree to hasIngredient - all subproperties and attributes of the properties should reflect those under hasIngredient. + + + + + + + + + + + Any given instance of topping should only be added to a single pizza (no cheap half-measures on our pizzas) + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Americana + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + AmericanaPicante + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + CoberturaDeAnchovies + + + + + + + + + + + CoberturaDeArtichoke + + + + + + + + + + + + + + + + + + + + + + + + + + + CoberturaDeAspargos + + + + + + + + + + + + + + + + + + + + + + + + + + Cajun + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + CoberturaDeCajun + + + + + + + + + + + + + + + + CoberturaDeCaper + + + + + + + + + + + + + + + + + + + + + + + + + Capricciosa + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Caprina + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + CoberturaDeQueijo + + + + + + + + + + + + + + + + PizzaComQueijo + + + + + + + + + + + + Any pizza that has at least 1 cheese topping. + + + + + + + + CoberturaDeQueijoComVegetais + + + This class will be inconsistent. This is because we have given it 2 disjoint parents, which means it could never have any members (as nothing can simultaneously be a CheeseTopping and a VegetableTopping). NB Called ProbeInconsistentTopping in the ProtegeOWL Tutorial. + + + + + + + + CoberturaDeFrango + + + + + + + + + + + + + + + + + + Pais + + + + + + + + + + + + + + + + + A class that is equivalent to the set of individuals that are described in the enumeration - ie Countries can only be either America, England, France, Germany or Italy and nothing else. Note that these individuals have been asserted to be allDifferent from each other. + + + + + + + + BaseEspessa + + + + + + + + + + + + + + + + + + Fiorentina + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + CoberturaDePeixe + + + + + + + + + + + + + + + + + + + + + + + + + + + + + CoberturaQuatroQueijos + + + + + + + + + + + + + + + + + + + QuatroQueijos + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + CoberturaDeFrutas + + + + + + + + + + + + + + FrutosDoMar + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + CoberturaDeAlho + + + + + + + + + + + + + + + + + + + + + + + + Giardiniera + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + CoberturaDeQueijoDeCabra + + + + + + + + + + + + + + + + + + CoberturaDeGorgonzola + + + + + + + + + + + + + + + + + CoberturaDePimentaoVerde + + + + + + + + + + + + CoberturaDePresunto + + + + + + + + + + + CoberturaDeErvas + + + + + + + + + + + + + Picante + + + + + + + + + + + CoberturaDePimentaoVerdePicante + + + + + + + + + + + + + + + CoberturaDeBifePicante + + + + + + + + + + + + + + + + Sorvete + + + + + + + + + + + A class to demonstrate mistakes made with setting a property domain. The property hasTopping has a domain of Pizza. This means that the reasoner can infer that all individuals using the hasTopping property must be of type Pizza. Because of the restriction on this class, all members of IceCream must use the hasTopping property, and therefore must also be members of Pizza. However, Pizza and IceCream are disjoint, so this causes an inconsistency. If they were not disjoint, IceCream would be inferred to be a subclass of Pizza. + + + + + + + + PizzaInteressante + + + + + + + 3 + + + + + Any pizza that has at least 3 toppings. Note that this is a cardinality constraint on the hasTopping property and NOT a qualified cardinality constraint (QCR). A QCR would specify from which class the members in this relationship must be. eg has at least 3 toppings from PizzaTopping. 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+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff -r d3616fac4ca5 -r cc270db37d33 test-data/ontology/single/inference_test.owl --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ontology/single/inference_test.owl Sat Oct 06 21:50:39 2012 +0200 @@ -0,0 +1,162 @@ + + + + + + + + +]> + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Expected inferences: + +aa memberOf a + +c subClassOf a + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff -r d3616fac4ca5 -r cc270db37d33 test-data/oppl_script/test_oppl_query.oppl --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/oppl_script/test_oppl_query.oppl Sat Oct 06 21:50:39 2012 +0200 @@ -0,0 +1,4 @@ +?whole:CLASS, +?part:CLASS +SELECT +?part SubClassOf part_of some ?whole WHERE ?part != Nothing \ No newline at end of file diff -r d3616fac4ca5 -r cc270db37d33 test-data/oppl_script/test_oppl_query_object_ind.oppl --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/oppl_script/test_oppl_query_object_ind.oppl Sat Oct 06 21:50:39 2012 +0200 @@ -0,0 +1,4 @@ +?a:INDIVIDUAL, +?part:CLASS, +?c:INDIVIDUAL +SELECT ?a prop ?c \ No newline at end of file diff -r d3616fac4ca5 -r cc270db37d33 test-data/oppl_script/test_oppl_query_object_prop.oppl --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/oppl_script/test_oppl_query_object_prop.oppl Sat Oct 06 21:50:39 2012 +0200 @@ -0,0 +1,2 @@ +?p:OBJECTPROPERTY +SELECT Transitive ?p \ No newline at end of file diff -r d3616fac4ca5 -r cc270db37d33 wrapper.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/wrapper.sh Sat Oct 06 21:50:39 2012 +0200 @@ -0,0 +1,33 @@ +#!/bin/sh + +# STDERR wrapper - discards STDERR if command execution was OK. + +# +# This script executes a given command line, +# while saving the STDERR in a temporary file. +# +# When the command is completed, it checks to see if the exit code was zero. +# if so - the command is assumed to have succeeded - the STDERR file is discarded. +# if not - the command is assumed to have failed, and the STDERR file is dumped to the real STDERR +# +# +# Use this wrapper for tools which insist on writting stuff to STDERR +# even if they succeeded - +# which throws galaxy off balance. +# +# +# Copyright 2009 (C) by Assaf Gordon +# This file is distributed under the BSD license. + +TMPFILE=$(mktemp) || exit 1 + +"$@" 2> $TMPFILE + +EXITCODE=$? +# Exitcode != 0 ? +if [ "$EXITCODE" -ne "0" ]; then + cat $TMPFILE >&2 +fi +rm $TMPFILE + +exit $EXITCODE