├── .github └── workflows │ ├── docs.yml │ ├── maven-test.yml │ └── snapshot-release.yml ├── .gitignore ├── .gitmodules ├── .mvn └── wrapper │ └── maven-wrapper.properties ├── Dockerfile ├── LICENSE.txt ├── NOTES.md ├── README.md ├── bin └── np ├── docs ├── assets │ ├── nanopub-icon.svg │ └── nanopub.png ├── getting-started │ ├── setup.md │ └── what-are-nanopubs.md ├── index.md └── quick-start │ ├── cli.md │ └── java.md ├── mkdocs.yml ├── mvnw ├── mvnw.cmd ├── poetry.lock ├── pom.xml ├── pyproject.toml ├── scripts ├── exec-class.sh └── run.sh └── src ├── integration-test ├── java │ └── org │ │ └── nanopub │ │ ├── FdoQueryIT.java │ │ ├── GeneralIntegrationTestsIT.java │ │ ├── MySandboxIT.java │ │ ├── RoCrateIT.java │ │ ├── RoHubImporter-Statistics.csv │ │ ├── RoHubImporter.java │ │ ├── extra │ │ └── server │ │ │ └── GetIndexIT.java │ │ └── ro-hub-imports.txt └── resources │ └── simplelogger.properties ├── main ├── java │ └── org │ │ └── nanopub │ │ ├── CheckNanopub.java │ │ ├── CliRunner.java │ │ ├── CustomTrigWriter.java │ │ ├── CustomTrigWriterFactory.java │ │ ├── HtmlWriter.java │ │ ├── MalformedNanopubException.java │ │ ├── MultiNanopubRdfHandler.java │ │ ├── Nanopub.java │ │ ├── Nanopub2Html.java │ │ ├── NanopubAlreadyFinalizedException.java │ │ ├── NanopubCreator.java │ │ ├── NanopubImpl.java │ │ ├── NanopubPattern.java │ │ ├── NanopubPatterns.java │ │ ├── NanopubProfile.java │ │ ├── NanopubRdfHandler.java │ │ ├── NanopubRetractor.java │ │ ├── NanopubRetractorCli.java │ │ ├── NanopubUtils.java │ │ ├── NanopubWithNs.java │ │ ├── PopularPrefixes.java │ │ ├── RoCrateImporter.java │ │ ├── RoCrateParser.java │ │ ├── Run.java │ │ ├── SimpleCreatorPattern.java │ │ ├── SimpleTimestampPattern.java │ │ ├── StripDown.java │ │ ├── TimestampNow.java │ │ ├── TimestampUpdater.java │ │ ├── extra │ │ ├── aida │ │ │ ├── AidaPattern.java │ │ │ └── package-info.java │ │ ├── index │ │ │ ├── IndexUtils.java │ │ │ ├── MakeIndex.java │ │ │ ├── NanopubIndex.java │ │ │ ├── NanopubIndexCreator.java │ │ │ ├── NanopubIndexImpl.java │ │ │ ├── NanopubIndexPattern.java │ │ │ ├── SimpleIndexCreator.java │ │ │ └── package-info.java │ │ ├── security │ │ │ ├── CryptoElement.java │ │ │ ├── DigitalSignaturePattern.java │ │ │ ├── KeyDeclaration.java │ │ │ ├── LegacySignatureUtils.java │ │ │ ├── MakeKeys.java │ │ │ ├── MalformedCryptoElementException.java │ │ │ ├── NanopubSignatureElement.java │ │ │ ├── SignNanopub.java │ │ │ ├── SignatureAlgorithm.java │ │ │ ├── SignatureUtils.java │ │ │ ├── TransformContext.java │ │ │ └── package-info.java │ │ ├── server │ │ │ ├── FetchIndex.java │ │ │ ├── FetchIndexFromDb.java │ │ │ ├── GetNanopub.java │ │ │ ├── GetServerInfo.java │ │ │ ├── NanopubDb.java │ │ │ ├── NanopubServerUtils.java │ │ │ ├── NanopubStatus.java │ │ │ ├── PublishNanopub.java │ │ │ ├── RegistryInfo.java │ │ │ ├── ServerIterator.java │ │ │ ├── UnreliableInputStream.java │ │ │ └── package-info.java │ │ ├── services │ │ │ ├── APINotReachableException.java │ │ │ ├── ApiResponse.java │ │ │ ├── ApiResponseEntry.java │ │ │ ├── FailedApiCallException.java │ │ │ ├── NotEnoughAPIInstancesException.java │ │ │ ├── QueryAccess.java │ │ │ ├── QueryCall.java │ │ │ ├── QueryRef.java │ │ │ ├── RunQuery.java │ │ │ └── package-info.java │ │ └── setting │ │ │ ├── GetIntroNanopub.java │ │ │ ├── IntroNanopub.java │ │ │ ├── NanopubSetting.java │ │ │ ├── ShowSetting.java │ │ │ └── package-info.java │ │ ├── fdo │ │ ├── FdoNanopubCreator.java │ │ ├── FdoNotFoundException.java │ │ ├── FdoQuery.java │ │ ├── FdoRecord.java │ │ ├── FdoUtils.java │ │ ├── RetrieveFdo.java │ │ ├── ShaclValidator.java │ │ ├── ValidateFdo.java │ │ ├── ValidationResult.java │ │ ├── package-info.java │ │ └── rest │ │ │ ├── HandleResolver.java │ │ │ ├── ResponsePrinter.java │ │ │ ├── gson │ │ │ ├── Data.java │ │ │ ├── ParsedJsonResponse.java │ │ │ ├── ParsedSchemaResponse.java │ │ │ ├── Value.java │ │ │ └── package-info.java │ │ │ ├── package-info.java │ │ │ └── rohub │ │ │ └── gson │ │ │ ├── Page.java │ │ │ ├── RoCrateIndex.java │ │ │ └── page1-2025-10-29_part0.json │ │ ├── jelly │ │ ├── JellyMetadataUtil.java │ │ ├── JellyUtils.java │ │ ├── JellyWriterRDFHandler.java │ │ ├── MaybeNanopub.java │ │ ├── NanopubStream.java │ │ └── package-info.java │ │ ├── op │ │ ├── Aggregate.java │ │ ├── Build.java │ │ ├── Count.java │ │ ├── Create.java │ │ ├── Decontextualize.java │ │ ├── ExportJson.java │ │ ├── Extract.java │ │ ├── Filter.java │ │ ├── Fingerprint.java │ │ ├── Gml.java │ │ ├── Import.java │ │ ├── IndexReuse.java │ │ ├── Namespaces.java │ │ ├── Reuse.java │ │ ├── Run.java │ │ ├── Tar.java │ │ ├── Topic.java │ │ ├── Union.java │ │ ├── fingerprint │ │ │ ├── AlwaysDifferentFingerprints.java │ │ │ ├── DefaultFingerprints.java │ │ │ ├── DisgenetFingerprints.java │ │ │ ├── FingerprintHandler.java │ │ │ ├── WikipathwaysFingerprints.java │ │ │ └── package-info.java │ │ ├── package-info.java │ │ └── topic │ │ │ ├── DefaultTopics.java │ │ │ ├── DisgenetTopics.java │ │ │ ├── MetaboliteSpeciesTopics.java │ │ │ ├── NoTopics.java │ │ │ ├── UriBaseTopics.java │ │ │ ├── UriTailTopics.java │ │ │ ├── WikipathwaysTopics.java │ │ │ └── package-info.java │ │ ├── package-info.java │ │ ├── trusty │ │ ├── CrossRefResolver.java │ │ ├── FixTrustyNanopub.java │ │ ├── MakeTrustyNanopub.java │ │ ├── TempUriReplacer.java │ │ ├── TrustyNanopubPattern.java │ │ ├── TrustyNanopubUtils.java │ │ └── package-info.java │ │ └── vocabulary │ │ ├── FDOC.java │ │ ├── FDOF.java │ │ ├── FIP.java │ │ ├── HDL.java │ │ ├── KPXL.java │ │ ├── NP.java │ │ ├── NPA.java │ │ ├── NPX.java │ │ ├── NTEMPLATE.java │ │ ├── PAV.java │ │ ├── RDFG.java │ │ ├── SCHEMA.java │ │ ├── Utils.java │ │ └── package-info.java └── resources │ ├── settings │ └── default.trig │ └── simplelogger.properties └── test ├── java └── org │ └── nanopub │ ├── CheckInvalidNanopubsTest.java │ ├── CheckValidNanopubsTest.java │ ├── Nanopub2HtmlTest.java │ ├── NanopubCreatorTest.java │ ├── NanopubImplTest.java │ ├── NanopubPatternsTest.java │ ├── NanopubProfileTest.java │ ├── NanopubRetractorTest.java │ ├── NanopubUtilsTest.java │ ├── PopularPrefixesTest.java │ ├── RoCrateTest.java │ ├── ShaclValidationTest.java │ ├── StripDownTest.java │ ├── TimestampNowTest.java │ ├── TimestampUpdaterTest.java │ ├── UsageExamples.java │ ├── extra │ ├── index │ │ ├── IndexUtilsTest.java │ │ ├── MakeIndexTest.java │ │ └── NanopubIndexPatternTest.java │ ├── security │ │ ├── DigitalSignaturePatternTest.java │ │ ├── KeyDeclarationTest.java │ │ ├── MakeKeysTest.java │ │ ├── MalformedCryptoElementExceptionTest.java │ │ ├── SignNanopubTest.java │ │ └── SignatureUtilsTest.java │ ├── server │ │ ├── GetNanopubTest.java │ │ ├── NanopubServerUtilsTest.java │ │ └── RegistryInfoTest.java │ ├── services │ │ ├── APINotReachableExceptionTest.java │ │ ├── ApiResponseEntryTest.java │ │ ├── ApiResponseTest.java │ │ ├── FailedApiCallExceptionTest.java │ │ ├── NotEnoughAPIInstancesExceptionTest.java │ │ ├── QueryCallTest.java │ │ ├── QueryRefTest.java │ │ └── RunQueryTest.java │ └── setting │ │ ├── IntroExtractorTest.java │ │ ├── IntroNanopubTest.java │ │ └── NanopubSettingTest.java │ ├── fdo │ ├── FdoNanopubCreatorTest.java │ ├── FdoNotFoundExceptionTest.java │ ├── FdoQueryTest.java │ ├── FdoRecordTest.java │ ├── FdoUtilsTest.java │ ├── RetrieveFdoTest.java │ ├── ValidateFdoTest.java │ ├── ValidationResultTest.java │ └── rest │ │ ├── ResponsePrinterTest.java │ │ └── gson │ │ ├── DataTest.java │ │ ├── ParsedSchemaResponseTest.java │ │ └── ValueTest.java │ ├── jelly │ ├── JellyMetadataUtilTest.java │ ├── JellyUtilsTest.java │ └── JellyWriterRDFHandlerTest.java │ ├── op │ ├── ExportJsonTest.java │ ├── fingerprint │ │ └── AlwaysDifferentFingerprintsTest.java │ └── topic │ │ ├── DefaultTopicsTest.java │ │ ├── NoTopicsTest.java │ │ ├── UriBaseTopicsTest.java │ │ └── UriTailTopicsTest.java │ ├── utils │ ├── MockFileService.java │ ├── MockFileServiceExtension.java │ ├── MockNanopubUtils.java │ ├── MockTrustyUriUtils.java 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