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- total_time: 56.650167584 - models_per_second: 81.02359085158959 + - total_time: 54.546511417 + models_per_second: 84.14836954301495 inconsistent: 56 - - total_time: 57.180463041 - models_per_second: 80.27217262491982 + - total_time: 54.342072417 + models_per_second: 84.46494209455464 inconsistent: 56 - - total_time: 57.018156083 - models_per_second: 80.50067408911723 + - total_time: 54.815056667 + models_per_second: 83.73611702865011 inconsistent: 56 -average: 80.59881252187556 +average: 84.11647622207325 diff --git a/perf/abox-consistency-whelk-4.yaml b/perf/abox-consistency-whelk-4.yaml index 028d92b..edb4fb4 100644 --- a/perf/abox-consistency-whelk-4.yaml +++ b/perf/abox-consistency-whelk-4.yaml @@ -1,11 +1,11 @@ runs: - - total_time: 16.875291583 - models_per_second: 271.99530019522274 + - total_time: 16.042678875 + models_per_second: 286.11181684580094 inconsistent: 56 - - total_time: 16.94443625 - models_per_second: 270.8853769035839 + - total_time: 16.0373305 + models_per_second: 286.2072338036558 inconsistent: 56 - - total_time: 16.934858167 - models_per_second: 271.0385853094579 + - total_time: 16.004304 + models_per_second: 286.7978513779793 inconsistent: 56 -average: 271.3064208027549 +average: 286.372300675812 diff --git a/perf/abox-consistency-whelk-8.yaml b/perf/abox-consistency-whelk-8.yaml index 58ee4a3..0084b23 100644 --- a/perf/abox-consistency-whelk-8.yaml +++ b/perf/abox-consistency-whelk-8.yaml @@ -1,11 +1,11 @@ runs: - - total_time: 9.816001041 - models_per_second: 467.6038623904217 + - total_time: 9.186279834 + models_per_second: 499.65819493236216 inconsistent: 56 - - total_time: 9.787052375 - models_per_second: 468.98696605779634 + - total_time: 9.146737333 + models_per_second: 501.81828043099 inconsistent: 56 - - total_time: 9.767001458 - models_per_second: 469.9497609105405 + - total_time: 9.343586417 + models_per_second: 491.2460585422336 inconsistent: 56 -average: 468.8468631195862 +average: 497.5741779685286 diff --git a/perf/classification-time-whelk-UNIV-BENCH-OWL2EL.yaml b/perf/classification-time-whelk-UNIV-BENCH-OWL2EL.yaml index e99ae2d..4bd9a4f 100644 --- a/perf/classification-time-whelk-UNIV-BENCH-OWL2EL.yaml +++ b/perf/classification-time-whelk-UNIV-BENCH-OWL2EL.yaml @@ -1,12 +1,12 @@ runs: - - 0.023376416 - - 0.017829458 - - 0.016220333 - - 0.015398166 - - 0.02136725 - - 0.014344833 - - 0.01400725 - - 0.0131655 - - 0.011981084 - - 0.011522709 -average: 0.0159212999 + - 0.134700833 + - 0.108798917 + - 0.094067375 + - 0.089982959 + - 0.105331583 + - 0.087947042 + - 0.085902084 + - 0.090490583 + - 0.088173417 + - 0.090485375 +average: 0.0975880168 diff --git a/perf/classification-time-whelk-nci-thesaurus.yaml b/perf/classification-time-whelk-nci-thesaurus.yaml index 23423e1..38a87fd 100644 --- a/perf/classification-time-whelk-nci-thesaurus.yaml +++ b/perf/classification-time-whelk-nci-thesaurus.yaml @@ -1,12 +1,12 @@ runs: - - 22.387721959 - - 22.761425459 - - 22.809044208 - - 22.439145292 - - 22.804195083 - - 22.389184875 - - 22.349211292 - - 22.04404675 - - 22.177009167 - - 22.461063625 -average: 22.462204771000003 + - 24.481516959 + - 24.316990291 + - 24.058775166 + - 24.101831292 + - 24.101316416 + - 24.099577208 + - 24.363836375 + - 24.037085625 + - 23.875729292 + - 24.184336292 +average: 24.162099491600003 diff --git a/perf/classification-time-whelk-uberon-go-cl-ro.yaml b/perf/classification-time-whelk-uberon-go-cl-ro.yaml index 43863e0..ff3b7ac 100644 --- a/perf/classification-time-whelk-uberon-go-cl-ro.yaml +++ b/perf/classification-time-whelk-uberon-go-cl-ro.yaml @@ -1,12 +1,12 @@ runs: - - 49.655627666 - - 50.658481708 - - 48.933700625 - - 48.814521334 - - 50.720092209 - - 49.260320417 - - 51.949872209 - - 49.832813583 - - 48.901309041 - - 49.114506333 -average: 49.7841245125 + - 47.667387708 + - 46.336307334 + - 46.455133125 + - 46.073700667 + - 47.180885042 + - 47.140810292 + - 47.177818333 + - 46.760034042 + - 46.5129415 + - 46.771035208 +average: 46.8076053251 diff --git a/perf/dl-query-speed-elk-0.4.3-UNIV-BENCH-OWL2EL-1.yaml b/perf/dl-query-speed-elk-0.4.3-UNIV-BENCH-OWL2EL-1.yaml index 6db0094..e55ff06 100644 --- a/perf/dl-query-speed-elk-0.4.3-UNIV-BENCH-OWL2EL-1.yaml +++ b/perf/dl-query-speed-elk-0.4.3-UNIV-BENCH-OWL2EL-1.yaml @@ -1,12 +1,12 @@ query_count: 23 - - total_time: 0.033326042 - queries_per_second: 690.1509636217826 + - total_time: 0.036842375 + queries_per_second: 624.2811436559126 total_subclasses_result: 72 - - total_time: 0.024107292 - queries_per_second: 954.0681715723193 + - total_time: 0.0271025 + queries_per_second: 848.6302001660363 total_subclasses_result: 72 - - total_time: 0.023228708 - queries_per_second: 990.1540800289022 + - total_time: 0.028098792 + queries_per_second: 818.540526582068 total_subclasses_result: 72 -average: 878.1244050743347 +average: 763.8172901346721 parallelism: 1 diff --git a/perf/dl-query-speed-elk-0.4.3-UNIV-BENCH-OWL2EL-4.yaml b/perf/dl-query-speed-elk-0.4.3-UNIV-BENCH-OWL2EL-4.yaml index 71b8e65..b8afda8 100644 --- a/perf/dl-query-speed-elk-0.4.3-UNIV-BENCH-OWL2EL-4.yaml +++ b/perf/dl-query-speed-elk-0.4.3-UNIV-BENCH-OWL2EL-4.yaml @@ -1,12 +1,12 @@ query_count: 23 - - total_time: 0.035640291 - queries_per_second: 645.3370428428882 + - total_time: 0.0381825 + queries_per_second: 602.3701957703136 total_subclasses_result: 72 - - total_time: 0.028687959 - queries_per_second: 801.7300917085109 + - total_time: 0.0317515 + queries_per_second: 724.3752263672582 total_subclasses_result: 72 - - total_time: 0.024369166 - queries_per_second: 943.8156398130326 + - total_time: 0.03137925 + queries_per_second: 732.9684425217301 total_subclasses_result: 72 -average: 796.960924788144 +average: 686.5712882197673 parallelism: 4 diff --git a/perf/dl-query-speed-elk-0.4.3-UNIV-BENCH-OWL2EL-8.yaml b/perf/dl-query-speed-elk-0.4.3-UNIV-BENCH-OWL2EL-8.yaml index 6a2a32e..5602a9f 100644 --- a/perf/dl-query-speed-elk-0.4.3-UNIV-BENCH-OWL2EL-8.yaml +++ b/perf/dl-query-speed-elk-0.4.3-UNIV-BENCH-OWL2EL-8.yaml @@ -1,12 +1,12 @@ query_count: 23 - - total_time: 0.03611925 - queries_per_second: 636.7795566076262 + - total_time: 0.036390125 + queries_per_second: 632.0395986548548 total_subclasses_result: 72 - - total_time: 0.028288291 - queries_per_second: 813.0572469012002 + - total_time: 0.030471542 + queries_per_second: 754.8026286296899 total_subclasses_result: 72 - - total_time: 0.02278675 - queries_per_second: 1009.3585087825161 + - total_time: 0.02361925 + queries_per_second: 973.7819786826423 total_subclasses_result: 72 -average: 819.7317707637809 +average: 786.8747353223956 parallelism: 8 diff --git a/perf/dl-query-speed-whelk-UNIV-BENCH-OWL2EL-1.yaml b/perf/dl-query-speed-whelk-UNIV-BENCH-OWL2EL-1.yaml index d40e59f..f02a3e3 100644 --- a/perf/dl-query-speed-whelk-UNIV-BENCH-OWL2EL-1.yaml +++ b/perf/dl-query-speed-whelk-UNIV-BENCH-OWL2EL-1.yaml @@ -1,12 +1,12 @@ query_count: 23 - - total_time: 0.0085205 - queries_per_second: 2699.3721025761397 + - total_time: 0.009323 + queries_per_second: 2467.01705459616 total_subclasses_result: 72 - - total_time: 0.010691417 - queries_per_second: 2151.2583411534692 + - total_time: 0.024174875 + queries_per_second: 951.4009896638556 total_subclasses_result: 72 - - total_time: 0.006617833 - queries_per_second: 3475.4579029117235 + - total_time: 0.011119583 + queries_per_second: 2068.422889599367 total_subclasses_result: 72 -average: 2775.3627822137773 +average: 1828.9469779531275 parallelism: 1 diff --git a/perf/dl-query-speed-whelk-UNIV-BENCH-OWL2EL-4.yaml b/perf/dl-query-speed-whelk-UNIV-BENCH-OWL2EL-4.yaml index 04cab3d..98b6114 100644 --- a/perf/dl-query-speed-whelk-UNIV-BENCH-OWL2EL-4.yaml +++ b/perf/dl-query-speed-whelk-UNIV-BENCH-OWL2EL-4.yaml @@ -1,12 +1,12 @@ query_count: 23 - - total_time: 0.008109084 - queries_per_second: 2836.3252865551767 + - total_time: 0.0080655 + queries_per_second: 2851.65209844399 total_subclasses_result: 72 - - total_time: 0.007255833 - queries_per_second: 3169.863473980176 + - total_time: 0.010693292 + queries_per_second: 2150.881131834799 total_subclasses_result: 72 - - total_time: 0.009988875 - queries_per_second: 2302.561599779755 + - total_time: 0.008216458 + queries_per_second: 2799.259729679139 total_subclasses_result: 72 -average: 2769.58345343837 +average: 2600.5976533193093 parallelism: 4 diff --git a/perf/dl-query-speed-whelk-UNIV-BENCH-OWL2EL-8.yaml b/perf/dl-query-speed-whelk-UNIV-BENCH-OWL2EL-8.yaml index 64d5848..61f658f 100644 --- a/perf/dl-query-speed-whelk-UNIV-BENCH-OWL2EL-8.yaml +++ b/perf/dl-query-speed-whelk-UNIV-BENCH-OWL2EL-8.yaml @@ -1,12 +1,12 @@ query_count: 23 - - total_time: 0.00756625 - queries_per_second: 3039.8149677845695 + - total_time: 0.007768375 + queries_per_second: 2960.7221587526346 total_subclasses_result: 72 - - total_time: 0.006511792 - queries_per_second: 3532.0538493858526 + - total_time: 0.008376708 + queries_per_second: 2745.708696065328 total_subclasses_result: 72 - - total_time: 0.0060965 - queries_per_second: 3772.6564422209462 + - total_time: 0.016743375 + queries_per_second: 1373.677648622216 total_subclasses_result: 72 -average: 3448.1750864637893 +average: 2360.0361678133927 parallelism: 8 diff --git a/perf/dl-query-speed-whelk-nci-thesaurus-1.yaml b/perf/dl-query-speed-whelk-nci-thesaurus-1.yaml index 2e0529f..d857909 100644 --- a/perf/dl-query-speed-whelk-nci-thesaurus-1.yaml +++ b/perf/dl-query-speed-whelk-nci-thesaurus-1.yaml @@ -1,12 +1,12 @@ query_count: 46685 - - total_time: 20.628322417 - queries_per_second: 2263.150587637046 + - total_time: 20.329595916 + queries_per_second: 2296.4057029415676 total_subclasses_result: 1091699 - - total_time: 20.258945625 - queries_per_second: 2304.414102498486 + - total_time: 20.266477042 + queries_per_second: 2303.5577374030313 total_subclasses_result: 1091699 - - total_time: 20.595273584 - queries_per_second: 2266.782221153329 + - total_time: 20.1381925 + queries_per_second: 2318.231886997803 total_subclasses_result: 1091699 -average: 2278.115637096287 +average: 2306.065109114134 parallelism: 1 diff --git a/perf/dl-query-speed-whelk-nci-thesaurus-4.yaml b/perf/dl-query-speed-whelk-nci-thesaurus-4.yaml index f110fdb..365024a 100644 --- a/perf/dl-query-speed-whelk-nci-thesaurus-4.yaml +++ b/perf/dl-query-speed-whelk-nci-thesaurus-4.yaml @@ -1,12 +1,12 @@ query_count: 46685 - - total_time: 5.554484 - queries_per_second: 8404.921141189712 + - total_time: 5.839449375 + queries_per_second: 7994.760636143027 total_subclasses_result: 1091699 - - total_time: 6.113228667 - queries_per_second: 7636.717443928063 + - total_time: 5.750739417 + queries_per_second: 8118.086495450051 total_subclasses_result: 1091699 - - total_time: 5.972687458 - queries_per_second: 7816.4143575717635 + - total_time: 5.580635167 + queries_per_second: 8365.535212920326 total_subclasses_result: 1091699 -average: 7952.684314229847 +average: 8159.460781504468 parallelism: 4 diff --git a/perf/dl-query-speed-whelk-nci-thesaurus-8.yaml b/perf/dl-query-speed-whelk-nci-thesaurus-8.yaml index 040ed59..fff77f7 100644 --- a/perf/dl-query-speed-whelk-nci-thesaurus-8.yaml +++ b/perf/dl-query-speed-whelk-nci-thesaurus-8.yaml @@ -1,12 +1,12 @@ query_count: 46685 - - total_time: 3.215000208 - queries_per_second: 14520.994394909227 + - total_time: 3.45496675 + queries_per_second: 13512.431053062955 total_subclasses_result: 1091699 - - total_time: 3.414133625 - queries_per_second: 13674.040072172043 + - total_time: 3.623531542 + queries_per_second: 12883.839828321827 total_subclasses_result: 1091699 - - total_time: 3.152783625 - queries_per_second: 14807.549630051126 + - total_time: 3.18878 + queries_per_second: 14640.395386323296 total_subclasses_result: 1091699 -average: 14334.19469904413 +average: 13678.888755902692 parallelism: 8 diff --git a/perf/dl-query-speed-whelk-uberon-go-cl-ro-1.yaml b/perf/dl-query-speed-whelk-uberon-go-cl-ro-1.yaml index c01b034..06feeaf 100644 --- a/perf/dl-query-speed-whelk-uberon-go-cl-ro-1.yaml +++ b/perf/dl-query-speed-whelk-uberon-go-cl-ro-1.yaml @@ -1,12 +1,12 @@ query_count: 66169 - - total_time: 48.787401625 - queries_per_second: 1356.272271038374 + - total_time: 47.107266167 + queries_per_second: 1404.6452996322105 total_subclasses_result: 1526774 - - total_time: 50.1838915 - queries_per_second: 1318.5306683520148 + - total_time: 47.262312917 + queries_per_second: 1400.0372795170454 total_subclasses_result: 1526774 - - total_time: 50.021178667 - queries_per_second: 1322.8196888461775 + - total_time: 47.762115625 + queries_per_second: 1385.3867052188396 total_subclasses_result: 1526774 -average: 1332.5408760788555 +average: 1396.6897614560319 parallelism: 1 diff --git a/perf/dl-query-speed-whelk-uberon-go-cl-ro-4.yaml b/perf/dl-query-speed-whelk-uberon-go-cl-ro-4.yaml index 320fb7b..130c4cb 100644 --- a/perf/dl-query-speed-whelk-uberon-go-cl-ro-4.yaml +++ b/perf/dl-query-speed-whelk-uberon-go-cl-ro-4.yaml @@ -1,12 +1,12 @@ query_count: 66169 - - total_time: 13.852153625 - queries_per_second: 4776.80235083301 + - total_time: 12.9397415 + queries_per_second: 5113.626110691624 total_subclasses_result: 1526774 - - total_time: 14.0974355 - queries_per_second: 4693.690565209537 + - total_time: 13.250811125 + queries_per_second: 4993.58110049282 total_subclasses_result: 1526774 - - total_time: 14.255504291 - queries_per_second: 4641.645686415654 + - total_time: 13.214369417 + queries_per_second: 5007.352065916593 total_subclasses_result: 1526774 -average: 4704.046200819401 +average: 5038.186425700345 parallelism: 4 diff --git a/perf/dl-query-speed-whelk-uberon-go-cl-ro-8.yaml b/perf/dl-query-speed-whelk-uberon-go-cl-ro-8.yaml index 28677dc..dcfccaa 100644 --- a/perf/dl-query-speed-whelk-uberon-go-cl-ro-8.yaml +++ b/perf/dl-query-speed-whelk-uberon-go-cl-ro-8.yaml @@ -1,12 +1,12 @@ query_count: 66169 - - total_time: 7.757764208 - queries_per_second: 8529.390456565421 + - total_time: 7.615574542 + queries_per_second: 8688.641892358488 total_subclasses_result: 1526774 - - total_time: 7.672512875 - queries_per_second: 8624.16278447757 + - total_time: 7.567250667 + queries_per_second: 8744.126884623525 total_subclasses_result: 1526774 - - total_time: 7.397184667 - queries_per_second: 8945.159946484813 + - total_time: 7.542833333 + queries_per_second: 8772.432994178687 total_subclasses_result: 1526774 -average: 8699.571062509269 +average: 8735.067257053566 parallelism: 8 diff --git a/scala/abox-consistency-whelk.sc b/scala/abox-consistency-whelk.sc index 4d85ae8..5fbbb3d 100644 --- a/scala/abox-consistency-whelk.sc +++ b/scala/abox-consistency-whelk.sc @@ -1,7 +1,7 @@ //> using scala "2.13" //> using dep "net.sourceforge.owlapi:owlapi-distribution:4.5.29" //> using dep "com.outr::scribe-slf4j2:3.15.0" -//> using dep "org.geneontology::whelk-owlapi:1.1.2" +//> using dep "org.geneontology::whelk-owlapi:1.2.1" //> using dep "dev.zio::zio-streams:2.1.4" import scala.jdk.CollectionConverters._ diff --git a/scala/classify-compare-elk-0.6.0.sc b/scala/classify-compare-elk-0.6.0.sc index 9b50e29..1e2cd47 100644 --- a/scala/classify-compare-elk-0.6.0.sc +++ b/scala/classify-compare-elk-0.6.0.sc @@ -1,5 +1,5 @@ //> using scala "2.13" -//> using dep "org.geneontology::whelk-owlapi:1.1.2" +//> using dep "org.geneontology::whelk-owlapi:1.2.1" //> using dep "io.github.liveontologies:elk-owlapi:0.6.0" //> using dep "com.outr::scribe-slf4j2:3.15.0" @@ -12,6 +12,7 @@ import org.semanticweb.elk.owlapi.ElkReasonerFactory //import au.csiro.snorocket.owlapi.SnorocketReasonerFactory import org.semanticweb.owlapi.apibinding.OWLManager import org.semanticweb.owlapi.reasoner.InferenceType +import org.semanticweb.owlapi.model.IRI scribe.Logger.root .clearHandlers() @@ -30,7 +31,7 @@ def time[T](operation: => T): (T, Double) = { val ontologyFile = args(0) val ontology = OWLManager .createOWLOntologyManager() - .loadOntologyFromOntologyDocument(new File(ontologyFile)) + .loadOntology(IRI.create(new File(ontologyFile))) val elk = new ElkReasonerFactory().createReasoner(ontology) val classes = ontology.getClassesInSignature().asScala.toSet val elkSubsumptions = classes.flatMap { c => diff --git a/scala/classify-compare.sc b/scala/classify-compare.sc index 8b4562d..5b7ea0c 100644 --- a/scala/classify-compare.sc +++ b/scala/classify-compare.sc @@ -1,5 +1,5 @@ //> using scala "2.13" -//> using dep "org.geneontology::whelk-owlapi:1.1.2" +//> using dep "org.geneontology::whelk-owlapi:1.2.1" //> using dep "org.semanticweb.elk:elk-owlapi:0.4.3" //> using dep "com.outr::scribe-slf4j2:3.15.0" @@ -13,6 +13,7 @@ import org.semanticweb.elk.owlapi.ElkReasonerFactory //import au.csiro.snorocket.owlapi.SnorocketReasonerFactory import org.semanticweb.owlapi.apibinding.OWLManager import org.semanticweb.owlapi.reasoner.InferenceType +import org.semanticweb.owlapi.model.IRI scribe.Logger.root .clearHandlers() @@ -31,7 +32,7 @@ def time[T](operation: => T): (T, Double) = { val ontologyFile = args(0) val ontology = OWLManager .createOWLOntologyManager() - .loadOntologyFromOntologyDocument(new File(ontologyFile)) + .loadOntology(IRI.create(new File(ontologyFile))) val elk = new ElkReasonerFactory().createReasoner(ontology) val classes = ontology.getClassesInSignature().asScala.toSet val elkSubsumptions = classes.flatMap { c => diff --git a/scala/classify-speed-whelk.sc b/scala/classify-speed-whelk.sc index 08d49e0..df93170 100644 --- a/scala/classify-speed-whelk.sc +++ b/scala/classify-speed-whelk.sc @@ -1,5 +1,5 @@ //> using scala "2.13" -//> using dep "org.geneontology::whelk-owlapi:1.1.2" +//> using dep "org.geneontology::whelk-owlapi:1.2.1" //> using file classify-speed.scala import org.geneontology.whelk.owlapi.WhelkOWLReasonerFactory diff --git a/scala/dl-query-speed-whelk-scala.sc b/scala/dl-query-speed-whelk-scala.sc index ba0a904..7903d03 100644 --- a/scala/dl-query-speed-whelk-scala.sc +++ b/scala/dl-query-speed-whelk-scala.sc @@ -2,7 +2,7 @@ //> using dep "net.sourceforge.owlapi:owlapi-distribution:4.5.29" //> using dep "com.outr::scribe-slf4j2:3.15.0" //> using dep "dev.zio::zio-streams:2.1.4" -//> using dep "org.geneontology::whelk-owlapi:1.1.2" +//> using dep "org.geneontology::whelk-owlapi:1.2.1" import org.geneontology.whelk.owlapi.WhelkOWLReasonerFactory import scala.jdk.CollectionConverters._ diff --git a/scala/dl-query-speed-whelk.sc b/scala/dl-query-speed-whelk.sc index 5c7d449..14a30ec 100644 --- a/scala/dl-query-speed-whelk.sc +++ b/scala/dl-query-speed-whelk.sc @@ -1,5 +1,5 @@ //> using scala "2.13" -//> using dep "org.geneontology::whelk-owlapi:1.1.2" +//> using dep "org.geneontology::whelk-owlapi:1.2.1" //> using file dl-query-speed.scala import org.geneontology.whelk.owlapi.WhelkOWLReasonerFactory