├── .gitignore ├── README.md ├── pom.xml └── src ├── main ├── java │ └── org │ │ └── reactome │ │ └── server │ │ └── service │ │ ├── ContentServiceApplication.java │ │ ├── config │ │ ├── CustomMessageConverter.java │ │ ├── ExporterConfig.java │ │ ├── ObjectMapperConfig.java │ │ ├── ServletConfig.java │ │ ├── SwaggerConfig.java │ │ └── WebConfig.java │ │ ├── controller │ │ ├── EntryPointController.java │ │ ├── GlobalExceptionHandler.java │ │ ├── citation │ │ │ └── CitationController.java │ │ ├── exporter │ │ │ ├── EventPdfController.java │ │ │ ├── FireworksImageExporterController.java │ │ │ ├── ImageExporterController.java │ │ │ ├── PptxExporterController.java │ │ │ └── SbxxExporterController.java │ │ ├── graph │ │ │ ├── AdvancedGeneralController.java │ │ │ ├── DiscoverController.java │ │ │ ├── DiseasesController.java │ │ │ ├── EventsController.java │ │ │ ├── GeneralController.java │ │ │ ├── HierarchyController.java │ │ │ ├── MappingController.java │ │ │ ├── OrthologyController.java │ │ │ ├── ParticipantsController.java │ │ │ ├── PathwaysController.java │ │ │ ├── PersonController.java │ │ │ ├── PhysicalEntityController.java │ │ │ ├── QueryObjectController.java │ │ │ ├── ReferenceEntityController.java │ │ │ ├── SchemaController.java │ │ │ ├── SpeciesController.java │ │ │ └── util │ │ │ │ ├── ControllerUtils.java │ │ │ │ ├── CrossReferenceResult.java │ │ │ │ └── ShortCrossReference.java │ │ ├── interactors │ │ │ ├── CustomInteractorsController.java │ │ │ ├── CustomPsicquicController.java │ │ │ ├── DownloadController.java │ │ │ ├── PsicquicInteractionsController.java │ │ │ ├── StaticInteractionsController.java │ │ │ └── TokenController.java │ │ └── search │ │ │ └── SearchController.java │ │ ├── exception │ │ ├── BadRequestException.java │ │ ├── DiagramExporterException.java │ │ ├── ErrorInfo.java │ │ ├── FireworksExporterException.java │ │ ├── InteractorResourceNotFound.java │ │ ├── MissingSBXXException.java │ │ ├── NoResultsFoundException.java │ │ ├── NotFoundException.java │ │ ├── NotFoundTextPlainException.java │ │ ├── PsicquicContentException.java │ │ ├── RequestEntityTooLargeException.java │ │ ├── StaticInteractionException.java │ │ ├── TokenNotFoundException.java │ │ ├── UnprocessableEntityException.java │ │ └── UnsupportedMediaTypeException.java │ │ ├── manager │ │ ├── CustomInteractorManager.java │ │ ├── ExportManager.java │ │ ├── InteractionManager.java │ │ └── SearchManager.java │ │ ├── model │ │ ├── README.md │ │ ├── citation │ │ │ ├── Citation.java │ │ │ ├── EventCitation.java │ │ │ └── StaticCitation.java │ │ ├── graph │ │ │ ├── AnalysedPathwayBrowserNode.java │ │ │ ├── SizedPathwayBrowserNode.java │ │ │ └── SummaryEntity.java │ │ └── interactors │ │ │ ├── Interactor.java │ │ │ ├── InteractorEntity.java │ │ │ └── Interactors.java │ │ └── utils │ │ ├── AspectLazyLoadingPrevention.java │ │ ├── CustomRequestFilter.java │ │ ├── GetterSetterMap.java │ │ ├── HeaderFooterCacher.java │ │ ├── MailService.java │ │ ├── PsicquicResourceCachingScheduler.java │ │ ├── ScheduledSMTPAppender.java │ │ ├── StartupNotifier.java │ │ ├── TupleManager.java │ │ └── TuplesFileCheckerController.java ├── resources │ ├── application.properties │ ├── log4j.properties │ ├── logback.xml │ └── service.properties └── webapp │ ├── WEB-INF │ └── pages │ │ ├── additional.jsp │ │ └── index.jsp │ └── resources │ ├── fonts │ ├── arial.ttf │ ├── arialbd.ttf │ ├── arialbi.ttf │ └── ariali.ttf │ └── swagger │ ├── custom.css │ ├── swagger-ui-bundle.js │ ├── swagger-ui-bundle.js.map │ ├── swagger-ui-standalone-preset.js │ ├── swagger-ui-standalone-preset.js.map │ ├── swagger-ui.css │ ├── swagger-ui.css.map │ ├── swagger-ui.js │ └── swagger-ui.js.map └── test ├── java └── org │ └── reactome │ └── server │ └── service │ ├── controller │ ├── citation │ │ └── CitationControllerTest.java │ ├── exporter │ │ ├── EventPdfControllerTest.java │ │ ├── FireworksImageExporterControllerTest.java │ │ ├── ImageExporterControllerTest.java │ │ ├── PptxExporterControllerTest.java │ │ └── SbxxExporterControllerTest.java │ ├── graph │ │ ├── DiscoverControllerTest.java │ │ ├── DiseasesControllerTest.java │ │ ├── EventsControllerTest.java │ │ ├── GeneralControllerTest.java │ │ ├── MappingControllerTest.java │ │ ├── OrthologyControllerTest.java │ │ ├── ParticipantsControllerTest.java │ │ ├── PathwaysControllerTest.java │ │ ├── PersonControllerTest.java │ │ ├── PhysicalEntityControllerTest.java │ │ ├── QueryObjectControllerTest.java │ │ ├── ReferenceEntityControllerTest.java │ │ ├── SchemaControllerTest.java │ │ └── SpeciesControllerTest.java │ ├── interactors │ │ ├── CustomInteractorsControllerTest.java │ │ ├── CustomPsicquicControllerTest.java │ │ ├── PsicquicInteractionsControllerTest.java │ │ ├── StaticInteractionsControllerTest.java │ │ └── TokenControllerTest.java │ └── search │ │ └── SearchControllerTest.java │ └── utils │ ├── BaseTest.java │ └── NewObjectsTest.java └── resources ├── logback-test.xml └── manual-tests.http /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/reactome/content-service/HEAD/.gitignore -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/reactome/content-service/HEAD/README.md -------------------------------------------------------------------------------- /pom.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/reactome/content-service/HEAD/pom.xml -------------------------------------------------------------------------------- /src/main/java/org/reactome/server/service/ContentServiceApplication.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/reactome/content-service/HEAD/src/main/java/org/reactome/server/service/ContentServiceApplication.java -------------------------------------------------------------------------------- /src/main/java/org/reactome/server/service/config/CustomMessageConverter.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/reactome/content-service/HEAD/src/main/java/org/reactome/server/service/config/CustomMessageConverter.java -------------------------------------------------------------------------------- /src/main/java/org/reactome/server/service/config/ExporterConfig.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/reactome/content-service/HEAD/src/main/java/org/reactome/server/service/config/ExporterConfig.java -------------------------------------------------------------------------------- /src/main/java/org/reactome/server/service/config/ObjectMapperConfig.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/reactome/content-service/HEAD/src/main/java/org/reactome/server/service/config/ObjectMapperConfig.java -------------------------------------------------------------------------------- /src/main/java/org/reactome/server/service/config/ServletConfig.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/reactome/content-service/HEAD/src/main/java/org/reactome/server/service/config/ServletConfig.java -------------------------------------------------------------------------------- /src/main/java/org/reactome/server/service/config/SwaggerConfig.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/reactome/content-service/HEAD/src/main/java/org/reactome/server/service/config/SwaggerConfig.java -------------------------------------------------------------------------------- /src/main/java/org/reactome/server/service/config/WebConfig.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/reactome/content-service/HEAD/src/main/java/org/reactome/server/service/config/WebConfig.java -------------------------------------------------------------------------------- /src/main/java/org/reactome/server/service/controller/EntryPointController.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/reactome/content-service/HEAD/src/main/java/org/reactome/server/service/controller/EntryPointController.java -------------------------------------------------------------------------------- /src/main/java/org/reactome/server/service/controller/GlobalExceptionHandler.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/reactome/content-service/HEAD/src/main/java/org/reactome/server/service/controller/GlobalExceptionHandler.java -------------------------------------------------------------------------------- /src/main/java/org/reactome/server/service/controller/citation/CitationController.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/reactome/content-service/HEAD/src/main/java/org/reactome/server/service/controller/citation/CitationController.java -------------------------------------------------------------------------------- /src/main/java/org/reactome/server/service/controller/exporter/EventPdfController.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/reactome/content-service/HEAD/src/main/java/org/reactome/server/service/controller/exporter/EventPdfController.java -------------------------------------------------------------------------------- /src/main/java/org/reactome/server/service/controller/exporter/FireworksImageExporterController.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/reactome/content-service/HEAD/src/main/java/org/reactome/server/service/controller/exporter/FireworksImageExporterController.java -------------------------------------------------------------------------------- /src/main/java/org/reactome/server/service/controller/exporter/ImageExporterController.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/reactome/content-service/HEAD/src/main/java/org/reactome/server/service/controller/exporter/ImageExporterController.java -------------------------------------------------------------------------------- /src/main/java/org/reactome/server/service/controller/exporter/PptxExporterController.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/reactome/content-service/HEAD/src/main/java/org/reactome/server/service/controller/exporter/PptxExporterController.java -------------------------------------------------------------------------------- /src/main/java/org/reactome/server/service/controller/exporter/SbxxExporterController.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/reactome/content-service/HEAD/src/main/java/org/reactome/server/service/controller/exporter/SbxxExporterController.java -------------------------------------------------------------------------------- /src/main/java/org/reactome/server/service/controller/graph/AdvancedGeneralController.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/reactome/content-service/HEAD/src/main/java/org/reactome/server/service/controller/graph/AdvancedGeneralController.java -------------------------------------------------------------------------------- /src/main/java/org/reactome/server/service/controller/graph/DiscoverController.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/reactome/content-service/HEAD/src/main/java/org/reactome/server/service/controller/graph/DiscoverController.java -------------------------------------------------------------------------------- /src/main/java/org/reactome/server/service/controller/graph/DiseasesController.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/reactome/content-service/HEAD/src/main/java/org/reactome/server/service/controller/graph/DiseasesController.java -------------------------------------------------------------------------------- /src/main/java/org/reactome/server/service/controller/graph/EventsController.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/reactome/content-service/HEAD/src/main/java/org/reactome/server/service/controller/graph/EventsController.java -------------------------------------------------------------------------------- /src/main/java/org/reactome/server/service/controller/graph/GeneralController.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/reactome/content-service/HEAD/src/main/java/org/reactome/server/service/controller/graph/GeneralController.java -------------------------------------------------------------------------------- /src/main/java/org/reactome/server/service/controller/graph/HierarchyController.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/reactome/content-service/HEAD/src/main/java/org/reactome/server/service/controller/graph/HierarchyController.java -------------------------------------------------------------------------------- /src/main/java/org/reactome/server/service/controller/graph/MappingController.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/reactome/content-service/HEAD/src/main/java/org/reactome/server/service/controller/graph/MappingController.java -------------------------------------------------------------------------------- /src/main/java/org/reactome/server/service/controller/graph/OrthologyController.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/reactome/content-service/HEAD/src/main/java/org/reactome/server/service/controller/graph/OrthologyController.java -------------------------------------------------------------------------------- /src/main/java/org/reactome/server/service/controller/graph/ParticipantsController.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/reactome/content-service/HEAD/src/main/java/org/reactome/server/service/controller/graph/ParticipantsController.java -------------------------------------------------------------------------------- /src/main/java/org/reactome/server/service/controller/graph/PathwaysController.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/reactome/content-service/HEAD/src/main/java/org/reactome/server/service/controller/graph/PathwaysController.java -------------------------------------------------------------------------------- /src/main/java/org/reactome/server/service/controller/graph/PersonController.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/reactome/content-service/HEAD/src/main/java/org/reactome/server/service/controller/graph/PersonController.java -------------------------------------------------------------------------------- /src/main/java/org/reactome/server/service/controller/graph/PhysicalEntityController.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/reactome/content-service/HEAD/src/main/java/org/reactome/server/service/controller/graph/PhysicalEntityController.java -------------------------------------------------------------------------------- /src/main/java/org/reactome/server/service/controller/graph/QueryObjectController.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/reactome/content-service/HEAD/src/main/java/org/reactome/server/service/controller/graph/QueryObjectController.java -------------------------------------------------------------------------------- /src/main/java/org/reactome/server/service/controller/graph/ReferenceEntityController.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/reactome/content-service/HEAD/src/main/java/org/reactome/server/service/controller/graph/ReferenceEntityController.java -------------------------------------------------------------------------------- /src/main/java/org/reactome/server/service/controller/graph/SchemaController.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/reactome/content-service/HEAD/src/main/java/org/reactome/server/service/controller/graph/SchemaController.java -------------------------------------------------------------------------------- /src/main/java/org/reactome/server/service/controller/graph/SpeciesController.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/reactome/content-service/HEAD/src/main/java/org/reactome/server/service/controller/graph/SpeciesController.java -------------------------------------------------------------------------------- /src/main/java/org/reactome/server/service/controller/graph/util/ControllerUtils.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/reactome/content-service/HEAD/src/main/java/org/reactome/server/service/controller/graph/util/ControllerUtils.java -------------------------------------------------------------------------------- /src/main/java/org/reactome/server/service/controller/graph/util/CrossReferenceResult.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/reactome/content-service/HEAD/src/main/java/org/reactome/server/service/controller/graph/util/CrossReferenceResult.java -------------------------------------------------------------------------------- /src/main/java/org/reactome/server/service/controller/graph/util/ShortCrossReference.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/reactome/content-service/HEAD/src/main/java/org/reactome/server/service/controller/graph/util/ShortCrossReference.java -------------------------------------------------------------------------------- /src/main/java/org/reactome/server/service/controller/interactors/CustomInteractorsController.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/reactome/content-service/HEAD/src/main/java/org/reactome/server/service/controller/interactors/CustomInteractorsController.java -------------------------------------------------------------------------------- /src/main/java/org/reactome/server/service/controller/interactors/CustomPsicquicController.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/reactome/content-service/HEAD/src/main/java/org/reactome/server/service/controller/interactors/CustomPsicquicController.java -------------------------------------------------------------------------------- /src/main/java/org/reactome/server/service/controller/interactors/DownloadController.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/reactome/content-service/HEAD/src/main/java/org/reactome/server/service/controller/interactors/DownloadController.java -------------------------------------------------------------------------------- /src/main/java/org/reactome/server/service/controller/interactors/PsicquicInteractionsController.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/reactome/content-service/HEAD/src/main/java/org/reactome/server/service/controller/interactors/PsicquicInteractionsController.java -------------------------------------------------------------------------------- /src/main/java/org/reactome/server/service/controller/interactors/StaticInteractionsController.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/reactome/content-service/HEAD/src/main/java/org/reactome/server/service/controller/interactors/StaticInteractionsController.java -------------------------------------------------------------------------------- /src/main/java/org/reactome/server/service/controller/interactors/TokenController.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/reactome/content-service/HEAD/src/main/java/org/reactome/server/service/controller/interactors/TokenController.java -------------------------------------------------------------------------------- /src/main/java/org/reactome/server/service/controller/search/SearchController.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/reactome/content-service/HEAD/src/main/java/org/reactome/server/service/controller/search/SearchController.java -------------------------------------------------------------------------------- /src/main/java/org/reactome/server/service/exception/BadRequestException.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/reactome/content-service/HEAD/src/main/java/org/reactome/server/service/exception/BadRequestException.java -------------------------------------------------------------------------------- /src/main/java/org/reactome/server/service/exception/DiagramExporterException.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/reactome/content-service/HEAD/src/main/java/org/reactome/server/service/exception/DiagramExporterException.java -------------------------------------------------------------------------------- /src/main/java/org/reactome/server/service/exception/ErrorInfo.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/reactome/content-service/HEAD/src/main/java/org/reactome/server/service/exception/ErrorInfo.java -------------------------------------------------------------------------------- /src/main/java/org/reactome/server/service/exception/FireworksExporterException.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/reactome/content-service/HEAD/src/main/java/org/reactome/server/service/exception/FireworksExporterException.java -------------------------------------------------------------------------------- /src/main/java/org/reactome/server/service/exception/InteractorResourceNotFound.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/reactome/content-service/HEAD/src/main/java/org/reactome/server/service/exception/InteractorResourceNotFound.java -------------------------------------------------------------------------------- /src/main/java/org/reactome/server/service/exception/MissingSBXXException.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/reactome/content-service/HEAD/src/main/java/org/reactome/server/service/exception/MissingSBXXException.java -------------------------------------------------------------------------------- /src/main/java/org/reactome/server/service/exception/NoResultsFoundException.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/reactome/content-service/HEAD/src/main/java/org/reactome/server/service/exception/NoResultsFoundException.java -------------------------------------------------------------------------------- /src/main/java/org/reactome/server/service/exception/NotFoundException.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/reactome/content-service/HEAD/src/main/java/org/reactome/server/service/exception/NotFoundException.java -------------------------------------------------------------------------------- /src/main/java/org/reactome/server/service/exception/NotFoundTextPlainException.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/reactome/content-service/HEAD/src/main/java/org/reactome/server/service/exception/NotFoundTextPlainException.java -------------------------------------------------------------------------------- /src/main/java/org/reactome/server/service/exception/PsicquicContentException.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/reactome/content-service/HEAD/src/main/java/org/reactome/server/service/exception/PsicquicContentException.java -------------------------------------------------------------------------------- /src/main/java/org/reactome/server/service/exception/RequestEntityTooLargeException.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/reactome/content-service/HEAD/src/main/java/org/reactome/server/service/exception/RequestEntityTooLargeException.java -------------------------------------------------------------------------------- /src/main/java/org/reactome/server/service/exception/StaticInteractionException.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/reactome/content-service/HEAD/src/main/java/org/reactome/server/service/exception/StaticInteractionException.java -------------------------------------------------------------------------------- /src/main/java/org/reactome/server/service/exception/TokenNotFoundException.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/reactome/content-service/HEAD/src/main/java/org/reactome/server/service/exception/TokenNotFoundException.java -------------------------------------------------------------------------------- /src/main/java/org/reactome/server/service/exception/UnprocessableEntityException.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/reactome/content-service/HEAD/src/main/java/org/reactome/server/service/exception/UnprocessableEntityException.java -------------------------------------------------------------------------------- /src/main/java/org/reactome/server/service/exception/UnsupportedMediaTypeException.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/reactome/content-service/HEAD/src/main/java/org/reactome/server/service/exception/UnsupportedMediaTypeException.java -------------------------------------------------------------------------------- /src/main/java/org/reactome/server/service/manager/CustomInteractorManager.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/reactome/content-service/HEAD/src/main/java/org/reactome/server/service/manager/CustomInteractorManager.java -------------------------------------------------------------------------------- /src/main/java/org/reactome/server/service/manager/ExportManager.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/reactome/content-service/HEAD/src/main/java/org/reactome/server/service/manager/ExportManager.java -------------------------------------------------------------------------------- /src/main/java/org/reactome/server/service/manager/InteractionManager.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/reactome/content-service/HEAD/src/main/java/org/reactome/server/service/manager/InteractionManager.java -------------------------------------------------------------------------------- /src/main/java/org/reactome/server/service/manager/SearchManager.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/reactome/content-service/HEAD/src/main/java/org/reactome/server/service/manager/SearchManager.java -------------------------------------------------------------------------------- /src/main/java/org/reactome/server/service/model/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/reactome/content-service/HEAD/src/main/java/org/reactome/server/service/model/README.md -------------------------------------------------------------------------------- /src/main/java/org/reactome/server/service/model/citation/Citation.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/reactome/content-service/HEAD/src/main/java/org/reactome/server/service/model/citation/Citation.java -------------------------------------------------------------------------------- /src/main/java/org/reactome/server/service/model/citation/EventCitation.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/reactome/content-service/HEAD/src/main/java/org/reactome/server/service/model/citation/EventCitation.java -------------------------------------------------------------------------------- /src/main/java/org/reactome/server/service/model/citation/StaticCitation.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/reactome/content-service/HEAD/src/main/java/org/reactome/server/service/model/citation/StaticCitation.java -------------------------------------------------------------------------------- /src/main/java/org/reactome/server/service/model/graph/AnalysedPathwayBrowserNode.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/reactome/content-service/HEAD/src/main/java/org/reactome/server/service/model/graph/AnalysedPathwayBrowserNode.java -------------------------------------------------------------------------------- /src/main/java/org/reactome/server/service/model/graph/SizedPathwayBrowserNode.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/reactome/content-service/HEAD/src/main/java/org/reactome/server/service/model/graph/SizedPathwayBrowserNode.java -------------------------------------------------------------------------------- /src/main/java/org/reactome/server/service/model/graph/SummaryEntity.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/reactome/content-service/HEAD/src/main/java/org/reactome/server/service/model/graph/SummaryEntity.java -------------------------------------------------------------------------------- /src/main/java/org/reactome/server/service/model/interactors/Interactor.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/reactome/content-service/HEAD/src/main/java/org/reactome/server/service/model/interactors/Interactor.java -------------------------------------------------------------------------------- /src/main/java/org/reactome/server/service/model/interactors/InteractorEntity.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/reactome/content-service/HEAD/src/main/java/org/reactome/server/service/model/interactors/InteractorEntity.java -------------------------------------------------------------------------------- /src/main/java/org/reactome/server/service/model/interactors/Interactors.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/reactome/content-service/HEAD/src/main/java/org/reactome/server/service/model/interactors/Interactors.java -------------------------------------------------------------------------------- /src/main/java/org/reactome/server/service/utils/AspectLazyLoadingPrevention.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/reactome/content-service/HEAD/src/main/java/org/reactome/server/service/utils/AspectLazyLoadingPrevention.java -------------------------------------------------------------------------------- /src/main/java/org/reactome/server/service/utils/CustomRequestFilter.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/reactome/content-service/HEAD/src/main/java/org/reactome/server/service/utils/CustomRequestFilter.java -------------------------------------------------------------------------------- /src/main/java/org/reactome/server/service/utils/GetterSetterMap.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/reactome/content-service/HEAD/src/main/java/org/reactome/server/service/utils/GetterSetterMap.java -------------------------------------------------------------------------------- /src/main/java/org/reactome/server/service/utils/HeaderFooterCacher.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/reactome/content-service/HEAD/src/main/java/org/reactome/server/service/utils/HeaderFooterCacher.java -------------------------------------------------------------------------------- /src/main/java/org/reactome/server/service/utils/MailService.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/reactome/content-service/HEAD/src/main/java/org/reactome/server/service/utils/MailService.java -------------------------------------------------------------------------------- /src/main/java/org/reactome/server/service/utils/PsicquicResourceCachingScheduler.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/reactome/content-service/HEAD/src/main/java/org/reactome/server/service/utils/PsicquicResourceCachingScheduler.java -------------------------------------------------------------------------------- /src/main/java/org/reactome/server/service/utils/ScheduledSMTPAppender.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/reactome/content-service/HEAD/src/main/java/org/reactome/server/service/utils/ScheduledSMTPAppender.java -------------------------------------------------------------------------------- /src/main/java/org/reactome/server/service/utils/StartupNotifier.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/reactome/content-service/HEAD/src/main/java/org/reactome/server/service/utils/StartupNotifier.java -------------------------------------------------------------------------------- /src/main/java/org/reactome/server/service/utils/TupleManager.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/reactome/content-service/HEAD/src/main/java/org/reactome/server/service/utils/TupleManager.java -------------------------------------------------------------------------------- /src/main/java/org/reactome/server/service/utils/TuplesFileCheckerController.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/reactome/content-service/HEAD/src/main/java/org/reactome/server/service/utils/TuplesFileCheckerController.java -------------------------------------------------------------------------------- /src/main/resources/application.properties: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/reactome/content-service/HEAD/src/main/resources/application.properties -------------------------------------------------------------------------------- /src/main/resources/log4j.properties: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/reactome/content-service/HEAD/src/main/resources/log4j.properties -------------------------------------------------------------------------------- /src/main/resources/logback.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/reactome/content-service/HEAD/src/main/resources/logback.xml -------------------------------------------------------------------------------- /src/main/resources/service.properties: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/reactome/content-service/HEAD/src/main/resources/service.properties -------------------------------------------------------------------------------- /src/main/webapp/WEB-INF/pages/additional.jsp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/reactome/content-service/HEAD/src/main/webapp/WEB-INF/pages/additional.jsp -------------------------------------------------------------------------------- /src/main/webapp/WEB-INF/pages/index.jsp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/reactome/content-service/HEAD/src/main/webapp/WEB-INF/pages/index.jsp -------------------------------------------------------------------------------- /src/main/webapp/resources/fonts/arial.ttf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/reactome/content-service/HEAD/src/main/webapp/resources/fonts/arial.ttf -------------------------------------------------------------------------------- /src/main/webapp/resources/fonts/arialbd.ttf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/reactome/content-service/HEAD/src/main/webapp/resources/fonts/arialbd.ttf -------------------------------------------------------------------------------- /src/main/webapp/resources/fonts/arialbi.ttf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/reactome/content-service/HEAD/src/main/webapp/resources/fonts/arialbi.ttf -------------------------------------------------------------------------------- /src/main/webapp/resources/fonts/ariali.ttf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/reactome/content-service/HEAD/src/main/webapp/resources/fonts/ariali.ttf -------------------------------------------------------------------------------- /src/main/webapp/resources/swagger/custom.css: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/reactome/content-service/HEAD/src/main/webapp/resources/swagger/custom.css -------------------------------------------------------------------------------- /src/main/webapp/resources/swagger/swagger-ui-bundle.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/reactome/content-service/HEAD/src/main/webapp/resources/swagger/swagger-ui-bundle.js -------------------------------------------------------------------------------- /src/main/webapp/resources/swagger/swagger-ui-bundle.js.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/reactome/content-service/HEAD/src/main/webapp/resources/swagger/swagger-ui-bundle.js.map -------------------------------------------------------------------------------- /src/main/webapp/resources/swagger/swagger-ui-standalone-preset.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/reactome/content-service/HEAD/src/main/webapp/resources/swagger/swagger-ui-standalone-preset.js -------------------------------------------------------------------------------- /src/main/webapp/resources/swagger/swagger-ui-standalone-preset.js.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/reactome/content-service/HEAD/src/main/webapp/resources/swagger/swagger-ui-standalone-preset.js.map -------------------------------------------------------------------------------- /src/main/webapp/resources/swagger/swagger-ui.css: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/reactome/content-service/HEAD/src/main/webapp/resources/swagger/swagger-ui.css -------------------------------------------------------------------------------- /src/main/webapp/resources/swagger/swagger-ui.css.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/reactome/content-service/HEAD/src/main/webapp/resources/swagger/swagger-ui.css.map -------------------------------------------------------------------------------- /src/main/webapp/resources/swagger/swagger-ui.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/reactome/content-service/HEAD/src/main/webapp/resources/swagger/swagger-ui.js -------------------------------------------------------------------------------- /src/main/webapp/resources/swagger/swagger-ui.js.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/reactome/content-service/HEAD/src/main/webapp/resources/swagger/swagger-ui.js.map -------------------------------------------------------------------------------- /src/test/java/org/reactome/server/service/controller/citation/CitationControllerTest.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/reactome/content-service/HEAD/src/test/java/org/reactome/server/service/controller/citation/CitationControllerTest.java -------------------------------------------------------------------------------- /src/test/java/org/reactome/server/service/controller/exporter/EventPdfControllerTest.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/reactome/content-service/HEAD/src/test/java/org/reactome/server/service/controller/exporter/EventPdfControllerTest.java -------------------------------------------------------------------------------- /src/test/java/org/reactome/server/service/controller/exporter/FireworksImageExporterControllerTest.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/reactome/content-service/HEAD/src/test/java/org/reactome/server/service/controller/exporter/FireworksImageExporterControllerTest.java -------------------------------------------------------------------------------- /src/test/java/org/reactome/server/service/controller/exporter/ImageExporterControllerTest.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/reactome/content-service/HEAD/src/test/java/org/reactome/server/service/controller/exporter/ImageExporterControllerTest.java -------------------------------------------------------------------------------- /src/test/java/org/reactome/server/service/controller/exporter/PptxExporterControllerTest.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/reactome/content-service/HEAD/src/test/java/org/reactome/server/service/controller/exporter/PptxExporterControllerTest.java -------------------------------------------------------------------------------- /src/test/java/org/reactome/server/service/controller/exporter/SbxxExporterControllerTest.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/reactome/content-service/HEAD/src/test/java/org/reactome/server/service/controller/exporter/SbxxExporterControllerTest.java -------------------------------------------------------------------------------- /src/test/java/org/reactome/server/service/controller/graph/DiscoverControllerTest.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/reactome/content-service/HEAD/src/test/java/org/reactome/server/service/controller/graph/DiscoverControllerTest.java -------------------------------------------------------------------------------- /src/test/java/org/reactome/server/service/controller/graph/DiseasesControllerTest.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/reactome/content-service/HEAD/src/test/java/org/reactome/server/service/controller/graph/DiseasesControllerTest.java -------------------------------------------------------------------------------- /src/test/java/org/reactome/server/service/controller/graph/EventsControllerTest.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/reactome/content-service/HEAD/src/test/java/org/reactome/server/service/controller/graph/EventsControllerTest.java -------------------------------------------------------------------------------- /src/test/java/org/reactome/server/service/controller/graph/GeneralControllerTest.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/reactome/content-service/HEAD/src/test/java/org/reactome/server/service/controller/graph/GeneralControllerTest.java -------------------------------------------------------------------------------- /src/test/java/org/reactome/server/service/controller/graph/MappingControllerTest.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/reactome/content-service/HEAD/src/test/java/org/reactome/server/service/controller/graph/MappingControllerTest.java -------------------------------------------------------------------------------- /src/test/java/org/reactome/server/service/controller/graph/OrthologyControllerTest.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/reactome/content-service/HEAD/src/test/java/org/reactome/server/service/controller/graph/OrthologyControllerTest.java -------------------------------------------------------------------------------- /src/test/java/org/reactome/server/service/controller/graph/ParticipantsControllerTest.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/reactome/content-service/HEAD/src/test/java/org/reactome/server/service/controller/graph/ParticipantsControllerTest.java -------------------------------------------------------------------------------- /src/test/java/org/reactome/server/service/controller/graph/PathwaysControllerTest.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/reactome/content-service/HEAD/src/test/java/org/reactome/server/service/controller/graph/PathwaysControllerTest.java -------------------------------------------------------------------------------- /src/test/java/org/reactome/server/service/controller/graph/PersonControllerTest.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/reactome/content-service/HEAD/src/test/java/org/reactome/server/service/controller/graph/PersonControllerTest.java -------------------------------------------------------------------------------- /src/test/java/org/reactome/server/service/controller/graph/PhysicalEntityControllerTest.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/reactome/content-service/HEAD/src/test/java/org/reactome/server/service/controller/graph/PhysicalEntityControllerTest.java -------------------------------------------------------------------------------- /src/test/java/org/reactome/server/service/controller/graph/QueryObjectControllerTest.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/reactome/content-service/HEAD/src/test/java/org/reactome/server/service/controller/graph/QueryObjectControllerTest.java -------------------------------------------------------------------------------- /src/test/java/org/reactome/server/service/controller/graph/ReferenceEntityControllerTest.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/reactome/content-service/HEAD/src/test/java/org/reactome/server/service/controller/graph/ReferenceEntityControllerTest.java -------------------------------------------------------------------------------- /src/test/java/org/reactome/server/service/controller/graph/SchemaControllerTest.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/reactome/content-service/HEAD/src/test/java/org/reactome/server/service/controller/graph/SchemaControllerTest.java -------------------------------------------------------------------------------- /src/test/java/org/reactome/server/service/controller/graph/SpeciesControllerTest.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/reactome/content-service/HEAD/src/test/java/org/reactome/server/service/controller/graph/SpeciesControllerTest.java -------------------------------------------------------------------------------- /src/test/java/org/reactome/server/service/controller/interactors/CustomInteractorsControllerTest.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/reactome/content-service/HEAD/src/test/java/org/reactome/server/service/controller/interactors/CustomInteractorsControllerTest.java -------------------------------------------------------------------------------- /src/test/java/org/reactome/server/service/controller/interactors/CustomPsicquicControllerTest.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/reactome/content-service/HEAD/src/test/java/org/reactome/server/service/controller/interactors/CustomPsicquicControllerTest.java -------------------------------------------------------------------------------- /src/test/java/org/reactome/server/service/controller/interactors/PsicquicInteractionsControllerTest.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/reactome/content-service/HEAD/src/test/java/org/reactome/server/service/controller/interactors/PsicquicInteractionsControllerTest.java -------------------------------------------------------------------------------- /src/test/java/org/reactome/server/service/controller/interactors/StaticInteractionsControllerTest.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/reactome/content-service/HEAD/src/test/java/org/reactome/server/service/controller/interactors/StaticInteractionsControllerTest.java -------------------------------------------------------------------------------- /src/test/java/org/reactome/server/service/controller/interactors/TokenControllerTest.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/reactome/content-service/HEAD/src/test/java/org/reactome/server/service/controller/interactors/TokenControllerTest.java -------------------------------------------------------------------------------- /src/test/java/org/reactome/server/service/controller/search/SearchControllerTest.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/reactome/content-service/HEAD/src/test/java/org/reactome/server/service/controller/search/SearchControllerTest.java -------------------------------------------------------------------------------- /src/test/java/org/reactome/server/service/utils/BaseTest.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/reactome/content-service/HEAD/src/test/java/org/reactome/server/service/utils/BaseTest.java -------------------------------------------------------------------------------- /src/test/java/org/reactome/server/service/utils/NewObjectsTest.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/reactome/content-service/HEAD/src/test/java/org/reactome/server/service/utils/NewObjectsTest.java -------------------------------------------------------------------------------- /src/test/resources/logback-test.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/reactome/content-service/HEAD/src/test/resources/logback-test.xml -------------------------------------------------------------------------------- /src/test/resources/manual-tests.http: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/reactome/content-service/HEAD/src/test/resources/manual-tests.http --------------------------------------------------------------------------------