From e7e731869dbd3f6eba7e6a2cce6e423a64384289 Mon Sep 17 00:00:00 2001 From: dvince Date: Tue, 25 Jul 2023 12:40:53 -0400 Subject: [PATCH 01/12] WIP progress on moving to 3 Issues with keycloak. --- gradle.properties | 2 +- .../services/hmi-server/gradle.properties | 4 +-- .../annotations/LogRestClientTime.java | 2 +- .../hmiserver/caching/CacheClearService.java | 4 +-- .../RequestLoggingRequestFilter.java | 8 ++--- .../RequestLoggingResponseFilter.java | 10 +++--- .../hmiserver/entities/Annotation.java | 10 +++--- .../terarium/hmiserver/entities/Event.java | 10 +++--- .../HmiResponseExceptionMapper.java | 2 +- .../proxies/RestClientTimingInterceptor.java | 32 +++++++++---------- .../proxies/dataservice/ArtifactProxy.java | 6 ++-- .../proxies/dataservice/ConceptProxy.java | 6 ++-- .../proxies/dataservice/DatasetProxy.java | 6 ++-- .../proxies/dataservice/ExternalProxy.java | 6 ++-- .../dataservice/ModelConfigurationProxy.java | 6 ++-- .../proxies/dataservice/ModelProxy.java | 6 ++-- .../proxies/dataservice/PersonProxy.java | 6 ++-- .../proxies/dataservice/ProjectProxy.java | 6 ++-- .../proxies/dataservice/ProvenanceProxy.java | 6 ++-- .../proxies/dataservice/SimulationProxy.java | 4 +-- .../proxies/dataservice/WorkflowProxy.java | 6 ++-- .../documentservice/DocumentProxy.java | 4 +-- .../documentservice/ESSearchProxy.java | 12 +++---- .../documentservice/ExtractionProxy.java | 4 +-- .../ExtractionServiceProxy.java | 6 ++-- .../hmiserver/proxies/github/GithubProxy.java | 6 ++-- .../proxies/jsdelivr/JsDelivrProxy.java | 8 ++--- .../hmiserver/proxies/mira/MIRAProxy.java | 4 +-- .../hmiserver/proxies/mit/MitProxy.java | 10 +++--- .../modelservice/ModelServiceProxy.java | 6 ++-- .../SimulationCiemssServiceProxy.java | 6 ++-- .../SimulationServiceProxy.java | 6 ++-- .../hmiserver/proxies/skema/SkemaProxy.java | 10 +++--- .../proxies/skema/SkemaRustProxy.java | 16 +++++----- .../proxies/skema/SkemaUnifiedProxy.java | 4 +-- .../hmiserver/resources/AdobeResource.java | 6 ++-- .../resources/AnnotationResource.java | 8 ++--- .../resources/ConfigurationResource.java | 6 ++-- .../hmiserver/resources/DevTestResource.java | 6 ++-- .../hmiserver/resources/DownloadResource.java | 12 +++---- .../hmiserver/resources/EventResource.java | 16 +++++----- .../hmiserver/resources/TGPTResource.java | 8 ++--- .../resources/TransformResource.java | 10 +++--- .../resources/code/CodeResource.java | 14 ++++---- .../dataservice/ArtifactResource.java | 8 ++--- .../dataservice/ConceptResource.java | 8 ++--- .../dataservice/DatasetResource.java | 8 ++--- .../dataservice/ExternalResource.java | 8 ++--- .../resources/dataservice/HomeResource.java | 8 ++--- .../ModelConfigurationResource.java | 8 ++--- .../resources/dataservice/ModelResource.java | 8 ++--- .../resources/dataservice/PersonResource.java | 8 ++--- .../dataservice/ProjectResource.java | 8 ++--- .../dataservice/ProvenanceResource.java | 8 ++--- .../dataservice/SimulationResource.java | 8 ++--- .../dataservice/WorkflowResource.java | 8 ++--- .../documentservice/DictionariesResource.java | 6 ++-- .../documentservice/DocumentResource.java | 6 ++-- .../documentservice/ExtractionResource.java | 6 ++-- .../documentservice/RelatedResource.java | 6 ++-- .../documentservice/SetResource.java | 12 +++---- .../responses/XDDResponse.java | 2 +- .../evaluation/EvaluationResource.java | 8 ++--- .../extractionservice/ExtractionResource.java | 8 ++--- .../loggingservice/LoggingResource.java | 16 +++++----- .../resources/miraservice/MIRAResource.java | 6 ++-- .../modelservice/ModelingRequestResource.java | 6 ++-- .../SimulationRequestResource.java | 6 ++-- .../user/ServerSentEventResource.java | 23 +++++++------ .../hmiserver/services/EventService.java | 4 +-- .../hmiserver/services/LoggingService.java | 2 +- .../hmiserver/services/StructuredLog.java | 2 +- .../hmiserver/proxies/DocumentProxyTests.java | 10 +++--- .../proxies/ExtractionProxyTests.java | 4 +-- .../services/StructuredLogTests.java | 8 ++--- 75 files changed, 289 insertions(+), 284 deletions(-) diff --git a/gradle.properties b/gradle.properties index 32585237e7..7369be487e 100644 --- a/gradle.properties +++ b/gradle.properties @@ -2,6 +2,6 @@ quarkusPluginId=io.quarkus quarkusPlatformGroupId=io.quarkus.platform quarkusPlatformArtifactId=quarkus-bom -quarkusVersion=2.16.6.Final +quarkusVersion=3.2.2.Final lombokVersion=1.18.26 elasticsearchVersion=8.7.0 diff --git a/packages/services/hmi-server/gradle.properties b/packages/services/hmi-server/gradle.properties index eb742eb4f8..7369be487e 100644 --- a/packages/services/hmi-server/gradle.properties +++ b/packages/services/hmi-server/gradle.properties @@ -2,6 +2,6 @@ quarkusPluginId=io.quarkus quarkusPlatformGroupId=io.quarkus.platform quarkusPlatformArtifactId=quarkus-bom -quarkusVersion=2.16.8.Final -lombokVersion=1.18.28 +quarkusVersion=3.2.2.Final +lombokVersion=1.18.26 elasticsearchVersion=8.7.0 diff --git a/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/annotations/LogRestClientTime.java b/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/annotations/LogRestClientTime.java index 2f6f1d5885..09ac98fb12 100644 --- a/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/annotations/LogRestClientTime.java +++ b/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/annotations/LogRestClientTime.java @@ -1,6 +1,6 @@ package software.uncharted.terarium.hmiserver.annotations; -import javax.interceptor.InterceptorBinding; +import jakarta.interceptor.InterceptorBinding; import java.lang.annotation.ElementType; import java.lang.annotation.Retention; import java.lang.annotation.RetentionPolicy; diff --git a/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/caching/CacheClearService.java b/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/caching/CacheClearService.java index 5378a4d9b9..9a6624222f 100644 --- a/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/caching/CacheClearService.java +++ b/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/caching/CacheClearService.java @@ -7,8 +7,8 @@ import lombok.Getter; import lombok.RequiredArgsConstructor; -import javax.enterprise.context.ApplicationScoped; -import javax.inject.Inject; +import jakarta.enterprise.context.ApplicationScoped; +import jakarta.inject.Inject; import java.util.List; import java.util.stream.Collectors; import java.util.stream.Stream; diff --git a/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/configuration/RequestLoggingRequestFilter.java b/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/configuration/RequestLoggingRequestFilter.java index 34652abe62..9798b0d88b 100644 --- a/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/configuration/RequestLoggingRequestFilter.java +++ b/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/configuration/RequestLoggingRequestFilter.java @@ -5,10 +5,10 @@ import software.uncharted.terarium.hmiserver.annotations.IgnoreRequestLogging; import software.uncharted.terarium.hmiserver.services.StructuredLog; -import javax.inject.Inject; -import javax.ws.rs.container.ContainerRequestContext; -import javax.ws.rs.container.ContainerRequestFilter; -import javax.ws.rs.ext.Provider; +import jakarta.inject.Inject; +import jakarta.ws.rs.container.ContainerRequestContext; +import jakarta.ws.rs.container.ContainerRequestFilter; +import jakarta.ws.rs.ext.Provider; import java.io.IOException; import java.time.Instant; diff --git a/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/configuration/RequestLoggingResponseFilter.java b/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/configuration/RequestLoggingResponseFilter.java index 6c27c5cabe..66127842c7 100644 --- a/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/configuration/RequestLoggingResponseFilter.java +++ b/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/configuration/RequestLoggingResponseFilter.java @@ -3,11 +3,11 @@ import lombok.extern.slf4j.Slf4j; import software.uncharted.terarium.hmiserver.services.StructuredLog; -import javax.inject.Inject; -import javax.ws.rs.container.ContainerRequestContext; -import javax.ws.rs.container.ContainerResponseContext; -import javax.ws.rs.container.ContainerResponseFilter; -import javax.ws.rs.ext.Provider; +import jakarta.inject.Inject; +import jakarta.ws.rs.container.ContainerRequestContext; +import jakarta.ws.rs.container.ContainerResponseContext; +import jakarta.ws.rs.container.ContainerResponseFilter; +import jakarta.ws.rs.ext.Provider; import java.io.IOException; import java.time.Instant; diff --git a/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/entities/Annotation.java b/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/entities/Annotation.java index 7121c52624..b7f801aa1a 100644 --- a/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/entities/Annotation.java +++ b/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/entities/Annotation.java @@ -9,11 +9,11 @@ import lombok.experimental.Accessors; -import javax.persistence.Column; -import javax.persistence.Entity; -import javax.persistence.Id; -import javax.persistence.Index; -import javax.persistence.Table; +import jakarta.persistence.Column; +import jakarta.persistence.Entity; +import jakarta.persistence.Id; +import jakarta.persistence.Index; +import jakarta.persistence.Table; import java.io.Serializable; import java.time.Instant; import java.util.List; diff --git a/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/entities/Event.java b/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/entities/Event.java index 97f621525a..530845d9bc 100644 --- a/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/entities/Event.java +++ b/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/entities/Event.java @@ -11,11 +11,11 @@ import software.uncharted.terarium.hmiserver.annotations.TSOptional; import software.uncharted.terarium.hmiserver.models.EventType; -import javax.persistence.Column; -import javax.persistence.Entity; -import javax.persistence.Id; -import javax.persistence.Index; -import javax.persistence.Table; +import jakarta.persistence.Column; +import jakarta.persistence.Entity; +import jakarta.persistence.Id; +import jakarta.persistence.Index; +import jakarta.persistence.Table; import java.io.Serializable; import java.time.Instant; import java.util.List; diff --git a/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/exceptions/HmiResponseExceptionMapper.java b/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/exceptions/HmiResponseExceptionMapper.java index 7ac82f9380..6dadeaf1ed 100644 --- a/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/exceptions/HmiResponseExceptionMapper.java +++ b/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/exceptions/HmiResponseExceptionMapper.java @@ -4,7 +4,7 @@ import lombok.EqualsAndHashCode; import org.eclipse.microprofile.rest.client.ext.ResponseExceptionMapper; -import javax.ws.rs.core.Response; +import jakarta.ws.rs.core.Response; public class HmiResponseExceptionMapper implements ResponseExceptionMapper { diff --git a/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/proxies/RestClientTimingInterceptor.java b/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/proxies/RestClientTimingInterceptor.java index 63e918cf26..382f52641e 100644 --- a/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/proxies/RestClientTimingInterceptor.java +++ b/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/proxies/RestClientTimingInterceptor.java @@ -10,11 +10,11 @@ import software.uncharted.terarium.hmiserver.services.EventService; import software.uncharted.terarium.hmiserver.services.StructuredLog; -import javax.annotation.Priority; -import javax.inject.Inject; -import javax.interceptor.AroundInvoke; -import javax.interceptor.Interceptor; -import javax.interceptor.InvocationContext; +import jakarta.annotation.Priority; +import jakarta.inject.Inject; +import jakarta.interceptor.AroundInvoke; +import jakarta.interceptor.Interceptor; +import jakarta.interceptor.InvocationContext; import java.lang.reflect.Method; import java.util.UUID; @@ -90,19 +90,19 @@ public Object measureInvocationTime(InvocationContext context) throws Exception * @return The method type (GET, POST, etc) */ private String getType(InvocationContext context) { - if (context.getMethod().getAnnotation(javax.ws.rs.GET.class) != null) { + if (context.getMethod().getAnnotation(jakarta.ws.rs.GET.class) != null) { return "GET"; - } else if (context.getMethod().getAnnotation(javax.ws.rs.POST.class) != null) { + } else if (context.getMethod().getAnnotation(jakarta.ws.rs.POST.class) != null) { return "POST"; - } else if (context.getMethod().getAnnotation(javax.ws.rs.PUT.class) != null) { + } else if (context.getMethod().getAnnotation(jakarta.ws.rs.PUT.class) != null) { return "PUT"; - } else if (context.getMethod().getAnnotation(javax.ws.rs.DELETE.class) != null) { + } else if (context.getMethod().getAnnotation(jakarta.ws.rs.DELETE.class) != null) { return "DELETE"; - } else if (context.getMethod().getAnnotation(javax.ws.rs.HEAD.class) != null) { + } else if (context.getMethod().getAnnotation(jakarta.ws.rs.HEAD.class) != null) { return "HEAD"; - } else if (context.getMethod().getAnnotation(javax.ws.rs.OPTIONS.class) != null) { + } else if (context.getMethod().getAnnotation(jakarta.ws.rs.OPTIONS.class) != null) { return "OPTIONS"; - } else if (context.getMethod().getAnnotation(javax.ws.rs.PATCH.class) != null) { + } else if (context.getMethod().getAnnotation(jakarta.ws.rs.PATCH.class) != null) { return "PATCH"; } return null; @@ -128,8 +128,8 @@ private String getPath(InvocationContext context) { * @return The value of the annotation or an empty string if it doesn't exist */ private String getPath(Class clazz) { - if (clazz.getAnnotation(javax.ws.rs.Path.class) != null) { - return clazz.getAnnotation(javax.ws.rs.Path.class).value(); + if (clazz.getAnnotation(jakarta.ws.rs.Path.class) != null) { + return clazz.getAnnotation(jakarta.ws.rs.Path.class).value(); } return ""; } @@ -140,8 +140,8 @@ private String getPath(Class clazz) { * @return The value of the annotation or an empty string if it doesn't exist */ private String getPath(Method method) { - if (method.getAnnotation(javax.ws.rs.Path.class) != null) { - return method.getAnnotation(javax.ws.rs.Path.class).value(); + if (method.getAnnotation(jakarta.ws.rs.Path.class) != null) { + return method.getAnnotation(jakarta.ws.rs.Path.class).value(); } return ""; } diff --git a/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/proxies/dataservice/ArtifactProxy.java b/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/proxies/dataservice/ArtifactProxy.java index 01548cf93b..ae36552d3a 100644 --- a/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/proxies/dataservice/ArtifactProxy.java +++ b/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/proxies/dataservice/ArtifactProxy.java @@ -6,9 +6,9 @@ import software.uncharted.terarium.hmiserver.models.dataservice.Artifact; import software.uncharted.terarium.hmiserver.models.dataservice.dataset.PresignedURL; -import javax.ws.rs.*; -import javax.ws.rs.core.MediaType; -import javax.ws.rs.core.Response; +import jakarta.ws.rs.*; +import jakarta.ws.rs.core.MediaType; +import jakarta.ws.rs.core.Response; import java.util.List; /** diff --git a/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/proxies/dataservice/ConceptProxy.java b/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/proxies/dataservice/ConceptProxy.java index 36caa07266..629f91ed85 100644 --- a/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/proxies/dataservice/ConceptProxy.java +++ b/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/proxies/dataservice/ConceptProxy.java @@ -6,9 +6,9 @@ import java.util.List; -import javax.ws.rs.*; -import javax.ws.rs.core.MediaType; -import javax.ws.rs.core.Response; +import jakarta.ws.rs.*; +import jakarta.ws.rs.core.MediaType; +import jakarta.ws.rs.core.Response; @RegisterRestClient(configKey = "data-service") @Path("/concepts") diff --git a/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/proxies/dataservice/DatasetProxy.java b/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/proxies/dataservice/DatasetProxy.java index 6c5b1d73c8..c052d82327 100644 --- a/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/proxies/dataservice/DatasetProxy.java +++ b/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/proxies/dataservice/DatasetProxy.java @@ -6,9 +6,9 @@ import software.uncharted.terarium.hmiserver.models.dataservice.dataset.Dataset; import software.uncharted.terarium.hmiserver.models.dataservice.dataset.PresignedURL; -import javax.ws.rs.*; -import javax.ws.rs.core.MediaType; -import javax.ws.rs.core.Response; +import jakarta.ws.rs.*; +import jakarta.ws.rs.core.MediaType; +import jakarta.ws.rs.core.Response; import java.util.List; @RegisterRestClient(configKey = "data-service") diff --git a/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/proxies/dataservice/ExternalProxy.java b/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/proxies/dataservice/ExternalProxy.java index 7da72646fa..4d88a8457f 100644 --- a/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/proxies/dataservice/ExternalProxy.java +++ b/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/proxies/dataservice/ExternalProxy.java @@ -7,9 +7,9 @@ import software.uncharted.terarium.hmiserver.models.dataservice.DocumentAsset; import software.uncharted.terarium.hmiserver.models.dataservice.Software; -import javax.ws.rs.*; -import javax.ws.rs.core.MediaType; -import javax.ws.rs.core.Response; +import jakarta.ws.rs.*; +import jakarta.ws.rs.core.MediaType; +import jakarta.ws.rs.core.Response; @RegisterRestClient(configKey = "data-service") @Path("/external") diff --git a/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/proxies/dataservice/ModelConfigurationProxy.java b/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/proxies/dataservice/ModelConfigurationProxy.java index 1523ff29b8..6abd25222e 100644 --- a/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/proxies/dataservice/ModelConfigurationProxy.java +++ b/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/proxies/dataservice/ModelConfigurationProxy.java @@ -8,9 +8,9 @@ import software.uncharted.terarium.hmiserver.models.dataservice.Model; import com.fasterxml.jackson.databind.JsonNode; -import javax.ws.rs.*; -import javax.ws.rs.core.MediaType; -import javax.ws.rs.core.Response; +import jakarta.ws.rs.*; +import jakarta.ws.rs.core.MediaType; +import jakarta.ws.rs.core.Response; @RegisterRestClient(configKey = "data-service") @Path("/model_configurations") diff --git a/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/proxies/dataservice/ModelProxy.java b/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/proxies/dataservice/ModelProxy.java index bcc35fe1b6..61344c193e 100644 --- a/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/proxies/dataservice/ModelProxy.java +++ b/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/proxies/dataservice/ModelProxy.java @@ -7,9 +7,9 @@ import software.uncharted.terarium.hmiserver.models.dataservice.ModelOperationCopy; import software.uncharted.terarium.hmiserver.models.dataservice.ModelConfiguration; -import javax.ws.rs.*; -import javax.ws.rs.core.MediaType; -import javax.ws.rs.core.Response; +import jakarta.ws.rs.*; +import jakarta.ws.rs.core.MediaType; +import jakarta.ws.rs.core.Response; import java.util.Map; import java.util.List; diff --git a/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/proxies/dataservice/PersonProxy.java b/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/proxies/dataservice/PersonProxy.java index 74b6679e2c..316fae04ff 100644 --- a/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/proxies/dataservice/PersonProxy.java +++ b/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/proxies/dataservice/PersonProxy.java @@ -5,9 +5,9 @@ import software.uncharted.terarium.hmiserver.models.dataservice.Association; import software.uncharted.terarium.hmiserver.models.dataservice.Person; -import javax.ws.rs.*; -import javax.ws.rs.core.MediaType; -import javax.ws.rs.core.Response; +import jakarta.ws.rs.*; +import jakarta.ws.rs.core.MediaType; +import jakarta.ws.rs.core.Response; @RegisterRestClient(configKey = "data-service") @Path("/persons") diff --git a/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/proxies/dataservice/ProjectProxy.java b/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/proxies/dataservice/ProjectProxy.java index b76b1c26c3..e132344869 100644 --- a/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/proxies/dataservice/ProjectProxy.java +++ b/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/proxies/dataservice/ProjectProxy.java @@ -8,9 +8,9 @@ import software.uncharted.terarium.hmiserver.models.dataservice.Project; import software.uncharted.terarium.hmiserver.models.dataservice.ResourceType; -import javax.ws.rs.*; -import javax.ws.rs.core.MediaType; -import javax.ws.rs.core.Response; +import jakarta.ws.rs.*; +import jakarta.ws.rs.core.MediaType; +import jakarta.ws.rs.core.Response; import java.util.*; diff --git a/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/proxies/dataservice/ProvenanceProxy.java b/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/proxies/dataservice/ProvenanceProxy.java index f7d3ea4ed1..0c0f2610e7 100644 --- a/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/proxies/dataservice/ProvenanceProxy.java +++ b/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/proxies/dataservice/ProvenanceProxy.java @@ -5,9 +5,9 @@ import software.uncharted.terarium.hmiserver.models.dataservice.Provenance; import software.uncharted.terarium.hmiserver.models.dataservice.ProvenanceQueryParam; -import javax.ws.rs.*; -import javax.ws.rs.core.MediaType; -import javax.ws.rs.core.Response; +import jakarta.ws.rs.*; +import jakarta.ws.rs.core.MediaType; +import jakarta.ws.rs.core.Response; @RegisterRestClient(configKey = "data-service") @Path("/provenance") diff --git a/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/proxies/dataservice/SimulationProxy.java b/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/proxies/dataservice/SimulationProxy.java index 169497ca94..f454cc14a1 100644 --- a/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/proxies/dataservice/SimulationProxy.java +++ b/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/proxies/dataservice/SimulationProxy.java @@ -6,8 +6,8 @@ import software.uncharted.terarium.hmiserver.models.dataservice.Simulation; import software.uncharted.terarium.hmiserver.models.dataservice.PresignedURL; -import javax.ws.rs.*; -import javax.ws.rs.core.MediaType; +import jakarta.ws.rs.*; +import jakarta.ws.rs.core.MediaType; @RegisterRestClient(configKey = "data-service") @Path("/simulations") diff --git a/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/proxies/dataservice/WorkflowProxy.java b/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/proxies/dataservice/WorkflowProxy.java index 770c3c4135..d7580f1491 100644 --- a/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/proxies/dataservice/WorkflowProxy.java +++ b/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/proxies/dataservice/WorkflowProxy.java @@ -6,9 +6,9 @@ import org.eclipse.microprofile.rest.client.inject.RegisterRestClient; import software.uncharted.terarium.hmiserver.exceptions.HmiResponseExceptionMapper; -import javax.ws.rs.*; -import javax.ws.rs.core.MediaType; -import javax.ws.rs.core.Response; +import jakarta.ws.rs.*; +import jakarta.ws.rs.core.MediaType; +import jakarta.ws.rs.core.Response; import java.util.*; @RegisterRestClient(configKey = "data-service") diff --git a/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/proxies/documentservice/DocumentProxy.java b/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/proxies/documentservice/DocumentProxy.java index c2ec18d5e8..078775e79d 100644 --- a/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/proxies/documentservice/DocumentProxy.java +++ b/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/proxies/documentservice/DocumentProxy.java @@ -6,8 +6,8 @@ import software.uncharted.terarium.hmiserver.exceptions.HmiResponseExceptionMapper; import software.uncharted.terarium.hmiserver.resources.documentservice.responses.*; -import javax.ws.rs.*; -import javax.ws.rs.core.MediaType; +import jakarta.ws.rs.*; +import jakarta.ws.rs.core.MediaType; @RegisterRestClient(configKey = "xdd-document-service") @Produces(MediaType.APPLICATION_JSON) diff --git a/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/proxies/documentservice/ESSearchProxy.java b/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/proxies/documentservice/ESSearchProxy.java index 8c9bb63588..cbd88ddbbe 100644 --- a/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/proxies/documentservice/ESSearchProxy.java +++ b/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/proxies/documentservice/ESSearchProxy.java @@ -5,12 +5,12 @@ import software.uncharted.terarium.hmiserver.annotations.LogRestClientTime; import software.uncharted.terarium.hmiserver.exceptions.HmiResponseExceptionMapper; -import javax.ws.rs.HeaderParam; -import javax.ws.rs.POST; -import javax.ws.rs.Path; -import javax.ws.rs.Produces; -import javax.ws.rs.core.MediaType; -import javax.ws.rs.core.Response; +import jakarta.ws.rs.HeaderParam; +import jakarta.ws.rs.POST; +import jakarta.ws.rs.Path; +import jakarta.ws.rs.Produces; +import jakarta.ws.rs.core.MediaType; +import jakarta.ws.rs.core.Response; /** * This is a temporary proxy as currently the ES endpoint is just on xDD's development diff --git a/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/proxies/documentservice/ExtractionProxy.java b/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/proxies/documentservice/ExtractionProxy.java index 56deb9db15..fee7588b33 100644 --- a/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/proxies/documentservice/ExtractionProxy.java +++ b/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/proxies/documentservice/ExtractionProxy.java @@ -8,8 +8,8 @@ import software.uncharted.terarium.hmiserver.resources.documentservice.responses.XDDExtractionsResponseOK; import software.uncharted.terarium.hmiserver.resources.documentservice.responses.XDDResponse; -import javax.ws.rs.*; -import javax.ws.rs.core.MediaType; +import jakarta.ws.rs.*; +import jakarta.ws.rs.core.MediaType; @RegisterRestClient(configKey = "xdd-document-service") @Produces(MediaType.APPLICATION_JSON) diff --git a/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/proxies/extractionservice/ExtractionServiceProxy.java b/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/proxies/extractionservice/ExtractionServiceProxy.java index 809cd77ed7..d3aff3bef0 100644 --- a/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/proxies/extractionservice/ExtractionServiceProxy.java +++ b/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/proxies/extractionservice/ExtractionServiceProxy.java @@ -4,15 +4,15 @@ import org.eclipse.microprofile.openapi.annotations.tags.Tag; import org.eclipse.microprofile.rest.client.annotation.RegisterProvider; import org.eclipse.microprofile.rest.client.inject.RegisterRestClient; -import javax.ws.rs.core.MediaType; +import jakarta.ws.rs.core.MediaType; import software.uncharted.terarium.hmiserver.exceptions.HmiResponseExceptionMapper; import software.uncharted.terarium.hmiserver.models.extractionservice.ExtractionResponse; import java.util.List; import java.util.Map; -import javax.ws.rs.*; -import javax.ws.rs.core.Response; +import jakarta.ws.rs.*; +import jakarta.ws.rs.core.Response; @RegisterRestClient(configKey = "extraction-service-api") @Produces(MediaType.APPLICATION_JSON) diff --git a/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/proxies/github/GithubProxy.java b/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/proxies/github/GithubProxy.java index e23db3f460..12b88ec7fa 100644 --- a/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/proxies/github/GithubProxy.java +++ b/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/proxies/github/GithubProxy.java @@ -4,9 +4,9 @@ import software.uncharted.terarium.hmiserver.annotations.LogRestClientTime; import software.uncharted.terarium.hmiserver.models.code.GithubFile; -import javax.ws.rs.*; -import javax.ws.rs.GET; -import javax.ws.rs.Path; +import jakarta.ws.rs.*; +import jakarta.ws.rs.GET; +import jakarta.ws.rs.Path; import java.util.List; @RegisterRestClient(configKey = "github") diff --git a/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/proxies/jsdelivr/JsDelivrProxy.java b/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/proxies/jsdelivr/JsDelivrProxy.java index 08c48bdc7f..e8a390aa02 100644 --- a/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/proxies/jsdelivr/JsDelivrProxy.java +++ b/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/proxies/jsdelivr/JsDelivrProxy.java @@ -3,10 +3,10 @@ import org.eclipse.microprofile.rest.client.inject.RegisterRestClient; import software.uncharted.terarium.hmiserver.annotations.LogRestClientTime; -import javax.ws.rs.*; -import javax.ws.rs.GET; -import javax.ws.rs.Path; -import javax.ws.rs.core.Response; +import jakarta.ws.rs.*; +import jakarta.ws.rs.GET; +import jakarta.ws.rs.Path; +import jakarta.ws.rs.core.Response; @RegisterRestClient(configKey = "jsdelivr") public interface JsDelivrProxy { diff --git a/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/proxies/mira/MIRAProxy.java b/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/proxies/mira/MIRAProxy.java index de3254a461..a4aedeb42d 100644 --- a/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/proxies/mira/MIRAProxy.java +++ b/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/proxies/mira/MIRAProxy.java @@ -8,8 +8,8 @@ import software.uncharted.terarium.hmiserver.models.dataservice.Model; -import javax.ws.rs.*; -import javax.ws.rs.core.MediaType; +import jakarta.ws.rs.*; +import jakarta.ws.rs.core.MediaType; import java.util.List; @RegisterProvider(HmiResponseExceptionMapper.class) diff --git a/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/proxies/mit/MitProxy.java b/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/proxies/mit/MitProxy.java index 2c48afa44b..a6457cc850 100644 --- a/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/proxies/mit/MitProxy.java +++ b/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/proxies/mit/MitProxy.java @@ -4,11 +4,11 @@ import software.uncharted.terarium.hmiserver.annotations.LogRestClientTime; import software.uncharted.terarium.hmiserver.models.modelservice.PetriNet; -import javax.ws.rs.GET; -import javax.ws.rs.POST; -import javax.ws.rs.Path; -import javax.ws.rs.QueryParam; -import javax.ws.rs.core.Response; +import jakarta.ws.rs.GET; +import jakarta.ws.rs.POST; +import jakarta.ws.rs.Path; +import jakarta.ws.rs.QueryParam; +import jakarta.ws.rs.core.Response; import java.util.List; @RegisterRestClient(configKey = "mit") diff --git a/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/proxies/modelservice/ModelServiceProxy.java b/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/proxies/modelservice/ModelServiceProxy.java index 554fb28a2d..d39dc8dcaa 100644 --- a/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/proxies/modelservice/ModelServiceProxy.java +++ b/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/proxies/modelservice/ModelServiceProxy.java @@ -6,9 +6,9 @@ import software.uncharted.terarium.hmiserver.annotations.LogRestClientTime; import software.uncharted.terarium.hmiserver.models.modelservice.PetriNet; -import javax.ws.rs.*; -import javax.ws.rs.core.MediaType; -import javax.ws.rs.core.Response; +import jakarta.ws.rs.*; +import jakarta.ws.rs.core.MediaType; +import jakarta.ws.rs.core.Response; @RegisterRestClient(configKey = "model-service") @Produces(MediaType.APPLICATION_JSON) diff --git a/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/proxies/simulationservice/SimulationCiemssServiceProxy.java b/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/proxies/simulationservice/SimulationCiemssServiceProxy.java index cce6b64c0b..87c48a7407 100644 --- a/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/proxies/simulationservice/SimulationCiemssServiceProxy.java +++ b/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/proxies/simulationservice/SimulationCiemssServiceProxy.java @@ -3,9 +3,9 @@ import org.eclipse.microprofile.rest.client.inject.RegisterRestClient; import com.fasterxml.jackson.databind.JsonNode; -import javax.ws.rs.*; -import javax.ws.rs.core.MediaType; -import javax.ws.rs.core.Response; +import jakarta.ws.rs.*; +import jakarta.ws.rs.core.MediaType; +import jakarta.ws.rs.core.Response; import software.uncharted.terarium.hmiserver.models.simulationservice.SimulationRequest; import software.uncharted.terarium.hmiserver.models.simulationservice.JobResponse; diff --git a/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/proxies/simulationservice/SimulationServiceProxy.java b/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/proxies/simulationservice/SimulationServiceProxy.java index d1b8d36a55..098115897d 100644 --- a/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/proxies/simulationservice/SimulationServiceProxy.java +++ b/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/proxies/simulationservice/SimulationServiceProxy.java @@ -3,9 +3,9 @@ import org.eclipse.microprofile.rest.client.inject.RegisterRestClient; import com.fasterxml.jackson.databind.JsonNode; -import javax.ws.rs.*; -import javax.ws.rs.core.MediaType; -import javax.ws.rs.core.Response; +import jakarta.ws.rs.*; +import jakarta.ws.rs.core.MediaType; +import jakarta.ws.rs.core.Response; import software.uncharted.terarium.hmiserver.annotations.LogRestClientTime; import software.uncharted.terarium.hmiserver.models.simulationservice.SimulationRequest; diff --git a/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/proxies/skema/SkemaProxy.java b/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/proxies/skema/SkemaProxy.java index 6db464813f..cf28f6d863 100644 --- a/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/proxies/skema/SkemaProxy.java +++ b/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/proxies/skema/SkemaProxy.java @@ -4,11 +4,11 @@ import software.uncharted.terarium.hmiserver.annotations.LogRestClientTime; import software.uncharted.terarium.hmiserver.models.code.CodeRequest; -import javax.ws.rs.POST; -import javax.ws.rs.Path; -import javax.ws.rs.Produces; -import javax.ws.rs.core.MediaType; -import javax.ws.rs.core.Response; +import jakarta.ws.rs.POST; +import jakarta.ws.rs.Path; +import jakarta.ws.rs.Produces; +import jakarta.ws.rs.core.MediaType; +import jakarta.ws.rs.core.Response; @RegisterRestClient(configKey = "skema") public interface SkemaProxy { diff --git a/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/proxies/skema/SkemaRustProxy.java b/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/proxies/skema/SkemaRustProxy.java index f10e24d3ea..605f8a87d2 100644 --- a/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/proxies/skema/SkemaRustProxy.java +++ b/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/proxies/skema/SkemaRustProxy.java @@ -5,14 +5,14 @@ import software.uncharted.terarium.hmiserver.annotations.LogRestClientTime; import java.util.List; -import javax.ws.rs.Consumes; -import javax.ws.rs.GET; -import javax.ws.rs.POST; -import javax.ws.rs.PUT; -import javax.ws.rs.Path; -import javax.ws.rs.PathParam; -import javax.ws.rs.core.MediaType; -import javax.ws.rs.core.Response; +import jakarta.ws.rs.Consumes; +import jakarta.ws.rs.GET; +import jakarta.ws.rs.POST; +import jakarta.ws.rs.PUT; +import jakarta.ws.rs.Path; +import jakarta.ws.rs.PathParam; +import jakarta.ws.rs.core.MediaType; +import jakarta.ws.rs.core.Response; @RegisterRestClient(configKey = "skema-rust") public interface SkemaRustProxy { diff --git a/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/proxies/skema/SkemaUnifiedProxy.java b/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/proxies/skema/SkemaUnifiedProxy.java index d0fc6b2cd4..960f952fed 100644 --- a/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/proxies/skema/SkemaUnifiedProxy.java +++ b/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/proxies/skema/SkemaUnifiedProxy.java @@ -6,8 +6,8 @@ import software.uncharted.terarium.hmiserver.annotations.LogRestClientTime; import software.uncharted.terarium.hmiserver.models.dataservice.Model; -import javax.ws.rs.*; -import javax.ws.rs.core.MediaType; +import jakarta.ws.rs.*; +import jakarta.ws.rs.core.MediaType; @RegisterRestClient(configKey = "skema-unified") @Produces(MediaType.APPLICATION_JSON) diff --git a/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/resources/AdobeResource.java b/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/resources/AdobeResource.java index f91d4592b5..e0ffc621a0 100644 --- a/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/resources/AdobeResource.java +++ b/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/resources/AdobeResource.java @@ -4,9 +4,9 @@ import org.eclipse.microprofile.config.inject.ConfigProperty; import org.eclipse.microprofile.openapi.annotations.tags.Tag; -import javax.ws.rs.GET; -import javax.ws.rs.Path; -import javax.ws.rs.core.Response; +import jakarta.ws.rs.GET; +import jakarta.ws.rs.Path; +import jakarta.ws.rs.core.Response; import java.util.Optional; @Path("/api/adobe") diff --git a/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/resources/AnnotationResource.java b/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/resources/AnnotationResource.java index 8f027f5083..c80a5247e5 100644 --- a/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/resources/AnnotationResource.java +++ b/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/resources/AnnotationResource.java @@ -5,10 +5,10 @@ import org.eclipse.microprofile.openapi.annotations.tags.Tag; import software.uncharted.terarium.hmiserver.entities.Annotation; -import javax.inject.Inject; -import javax.transaction.Transactional; -import javax.ws.rs.*; -import javax.ws.rs.core.Response; +import jakarta.inject.Inject; +import jakarta.transaction.Transactional; +import jakarta.ws.rs.*; +import jakarta.ws.rs.core.Response; import java.time.Instant; @Path("/api/annotations") diff --git a/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/resources/ConfigurationResource.java b/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/resources/ConfigurationResource.java index 52f5574723..55d8929f67 100644 --- a/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/resources/ConfigurationResource.java +++ b/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/resources/ConfigurationResource.java @@ -4,9 +4,9 @@ import org.eclipse.microprofile.config.inject.ConfigProperty; import org.eclipse.microprofile.openapi.annotations.tags.Tag; -import javax.ws.rs.GET; -import javax.ws.rs.Path; -import javax.ws.rs.core.Response; +import jakarta.ws.rs.GET; +import jakarta.ws.rs.Path; +import jakarta.ws.rs.core.Response; import java.util.Optional; /** diff --git a/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/resources/DevTestResource.java b/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/resources/DevTestResource.java index 9557c1a459..046895dfa2 100644 --- a/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/resources/DevTestResource.java +++ b/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/resources/DevTestResource.java @@ -8,9 +8,9 @@ import software.uncharted.terarium.hmiserver.models.user.UserEvent; import org.eclipse.microprofile.openapi.annotations.tags.Tag; -import javax.ws.rs.*; -import javax.ws.rs.core.MediaType; -import javax.ws.rs.core.Response; +import jakarta.ws.rs.*; +import jakarta.ws.rs.core.MediaType; +import jakarta.ws.rs.core.Response; import java.util.Map; import java.util.UUID; diff --git a/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/resources/DownloadResource.java b/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/resources/DownloadResource.java index 3bfc646d42..ebab373122 100644 --- a/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/resources/DownloadResource.java +++ b/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/resources/DownloadResource.java @@ -11,12 +11,12 @@ import org.jsoup.nodes.Document; import org.jsoup.select.Elements; -import javax.ws.rs.GET; -import javax.ws.rs.Path; -import javax.ws.rs.Produces; -import javax.ws.rs.QueryParam; -import javax.ws.rs.core.MediaType; -import javax.ws.rs.core.Response; +import jakarta.ws.rs.GET; +import jakarta.ws.rs.Path; +import jakarta.ws.rs.Produces; +import jakarta.ws.rs.QueryParam; +import jakarta.ws.rs.core.MediaType; +import jakarta.ws.rs.core.Response; import java.io.IOException; import java.net.URI; import java.net.URISyntaxException; diff --git a/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/resources/EventResource.java b/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/resources/EventResource.java index 57b6552bf3..72b65c58a8 100644 --- a/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/resources/EventResource.java +++ b/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/resources/EventResource.java @@ -8,14 +8,14 @@ import software.uncharted.terarium.hmiserver.models.EventType; import software.uncharted.terarium.hmiserver.services.StructuredLog; -import javax.inject.Inject; -import javax.transaction.Transactional; -import javax.ws.rs.DefaultValue; -import javax.ws.rs.GET; -import javax.ws.rs.POST; -import javax.ws.rs.Path; -import javax.ws.rs.QueryParam; -import javax.ws.rs.core.Response; +import jakarta.inject.Inject; +import jakarta.transaction.Transactional; +import jakarta.ws.rs.DefaultValue; +import jakarta.ws.rs.GET; +import jakarta.ws.rs.POST; +import jakarta.ws.rs.Path; +import jakarta.ws.rs.QueryParam; +import jakarta.ws.rs.core.Response; @Path("/api/events") @Tag(name = "Events REST Endpoints") diff --git a/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/resources/TGPTResource.java b/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/resources/TGPTResource.java index 9ec536b467..0150a4b96f 100644 --- a/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/resources/TGPTResource.java +++ b/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/resources/TGPTResource.java @@ -5,10 +5,10 @@ import org.eclipse.microprofile.config.inject.ConfigProperty; import org.eclipse.microprofile.openapi.annotations.tags.Tag; -import javax.inject.Inject; -import javax.ws.rs.GET; -import javax.ws.rs.Path; -import javax.ws.rs.core.Response; +import jakarta.inject.Inject; +import jakarta.ws.rs.GET; +import jakarta.ws.rs.Path; +import jakarta.ws.rs.core.Response; import java.util.Optional; @Path("/api/tgpt") diff --git a/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/resources/TransformResource.java b/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/resources/TransformResource.java index 5986815de5..566664d70c 100644 --- a/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/resources/TransformResource.java +++ b/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/resources/TransformResource.java @@ -12,12 +12,12 @@ import lombok.extern.slf4j.Slf4j; -import javax.inject.Inject; +import jakarta.inject.Inject; import java.util.List; -import javax.ws.rs.POST; -import javax.ws.rs.Path; -import javax.ws.rs.PathParam; -import javax.ws.rs.core.Response; +import jakarta.ws.rs.POST; +import jakarta.ws.rs.Path; +import jakarta.ws.rs.PathParam; +import jakarta.ws.rs.core.Response; @Path("/api/transforms") diff --git a/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/resources/code/CodeResource.java b/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/resources/code/CodeResource.java index 11dec8ba0a..1ed5e21ed7 100644 --- a/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/resources/code/CodeResource.java +++ b/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/resources/code/CodeResource.java @@ -13,13 +13,13 @@ import software.uncharted.terarium.hmiserver.proxies.skema.SkemaProxy; import software.uncharted.terarium.hmiserver.proxies.skema.SkemaRustProxy; -import javax.ws.rs.GET; -import javax.ws.rs.POST; -import javax.ws.rs.Path; -import javax.ws.rs.QueryParam; -import javax.ws.rs.Produces; -import javax.ws.rs.core.MediaType; -import javax.ws.rs.core.Response; +import jakarta.ws.rs.GET; +import jakarta.ws.rs.POST; +import jakarta.ws.rs.Path; +import jakarta.ws.rs.QueryParam; +import jakarta.ws.rs.Produces; +import jakarta.ws.rs.core.MediaType; +import jakarta.ws.rs.core.Response; import java.util.List; import java.util.Map; diff --git a/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/resources/dataservice/ArtifactResource.java b/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/resources/dataservice/ArtifactResource.java index b54f6d81e9..2e5491a796 100644 --- a/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/resources/dataservice/ArtifactResource.java +++ b/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/resources/dataservice/ArtifactResource.java @@ -12,10 +12,10 @@ import software.uncharted.terarium.hmiserver.resources.DataStorageResource; import software.uncharted.terarium.hmiserver.resources.SnakeCaseResource; -import javax.inject.Inject; -import javax.ws.rs.*; -import javax.ws.rs.core.MediaType; -import javax.ws.rs.core.Response; +import jakarta.inject.Inject; +import jakarta.ws.rs.*; +import jakarta.ws.rs.core.MediaType; +import jakarta.ws.rs.core.Response; import java.io.IOException; import java.io.InputStream; import java.util.List; diff --git a/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/resources/dataservice/ConceptResource.java b/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/resources/dataservice/ConceptResource.java index 031a774e54..a2fb7518ae 100644 --- a/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/resources/dataservice/ConceptResource.java +++ b/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/resources/dataservice/ConceptResource.java @@ -12,10 +12,10 @@ import java.util.List; -import javax.inject.Inject; -import javax.ws.rs.*; -import javax.ws.rs.core.MediaType; -import javax.ws.rs.core.Response; +import jakarta.inject.Inject; +import jakarta.ws.rs.*; +import jakarta.ws.rs.core.MediaType; +import jakarta.ws.rs.core.Response; @Path("/api/concepts") @Produces(MediaType.APPLICATION_JSON) diff --git a/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/resources/dataservice/DatasetResource.java b/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/resources/dataservice/DatasetResource.java index 6cd18388a6..f796ec4e8a 100644 --- a/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/resources/dataservice/DatasetResource.java +++ b/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/resources/dataservice/DatasetResource.java @@ -27,10 +27,10 @@ import software.uncharted.terarium.hmiserver.resources.DataStorageResource; import software.uncharted.terarium.hmiserver.resources.SnakeCaseResource; -import javax.inject.Inject; -import javax.ws.rs.*; -import javax.ws.rs.core.MediaType; -import javax.ws.rs.core.Response; +import jakarta.inject.Inject; +import jakarta.ws.rs.*; +import jakarta.ws.rs.core.MediaType; +import jakarta.ws.rs.core.Response; import java.io.BufferedReader; import java.io.IOException; import java.io.InputStream; diff --git a/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/resources/dataservice/ExternalResource.java b/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/resources/dataservice/ExternalResource.java index c9e47c853d..b9034802d3 100644 --- a/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/resources/dataservice/ExternalResource.java +++ b/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/resources/dataservice/ExternalResource.java @@ -9,10 +9,10 @@ import software.uncharted.terarium.hmiserver.models.dataservice.Software; import software.uncharted.terarium.hmiserver.proxies.dataservice.ExternalProxy; -import javax.inject.Inject; -import javax.ws.rs.*; -import javax.ws.rs.core.MediaType; -import javax.ws.rs.core.Response; +import jakarta.inject.Inject; +import jakarta.ws.rs.*; +import jakarta.ws.rs.core.MediaType; +import jakarta.ws.rs.core.Response; @Path("/api/external") @Produces(MediaType.APPLICATION_JSON) diff --git a/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/resources/dataservice/HomeResource.java b/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/resources/dataservice/HomeResource.java index ea41edba53..d428916d23 100644 --- a/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/resources/dataservice/HomeResource.java +++ b/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/resources/dataservice/HomeResource.java @@ -19,10 +19,10 @@ import software.uncharted.terarium.hmiserver.proxies.documentservice.DocumentProxy; import software.uncharted.terarium.hmiserver.resources.documentservice.responses.XDDRelatedDocumentsResponse; -import javax.inject.Inject; -import javax.ws.rs.*; -import javax.ws.rs.core.MediaType; -import javax.ws.rs.core.Response; +import jakarta.inject.Inject; +import jakarta.ws.rs.*; +import jakarta.ws.rs.core.MediaType; +import jakarta.ws.rs.core.Response; import java.util.*; diff --git a/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/resources/dataservice/ModelConfigurationResource.java b/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/resources/dataservice/ModelConfigurationResource.java index a821b8adba..d74b68064c 100644 --- a/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/resources/dataservice/ModelConfigurationResource.java +++ b/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/resources/dataservice/ModelConfigurationResource.java @@ -9,10 +9,10 @@ import com.fasterxml.jackson.databind.JsonNode; import software.uncharted.terarium.hmiserver.utils.Converter; -import javax.inject.Inject; -import javax.ws.rs.*; -import javax.ws.rs.core.MediaType; -import javax.ws.rs.core.Response; +import jakarta.inject.Inject; +import jakarta.ws.rs.*; +import jakarta.ws.rs.core.MediaType; +import jakarta.ws.rs.core.Response; import java.util.*; @Path("/api/model_configurations") diff --git a/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/resources/dataservice/ModelResource.java b/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/resources/dataservice/ModelResource.java index b6202beb8e..60f38113ff 100644 --- a/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/resources/dataservice/ModelResource.java +++ b/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/resources/dataservice/ModelResource.java @@ -12,10 +12,10 @@ import software.uncharted.terarium.hmiserver.models.dataservice.ModelConfiguration; import software.uncharted.terarium.hmiserver.proxies.dataservice.ModelProxy; -import javax.inject.Inject; -import javax.ws.rs.*; -import javax.ws.rs.core.MediaType; -import javax.ws.rs.core.Response; +import jakarta.inject.Inject; +import jakarta.ws.rs.*; +import jakarta.ws.rs.core.MediaType; +import jakarta.ws.rs.core.Response; import java.util.*; import static io.smallrye.jwt.config.ConfigLogging.log; diff --git a/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/resources/dataservice/PersonResource.java b/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/resources/dataservice/PersonResource.java index 0b7b457dd3..f55111c7c9 100644 --- a/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/resources/dataservice/PersonResource.java +++ b/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/resources/dataservice/PersonResource.java @@ -6,10 +6,10 @@ import software.uncharted.terarium.hmiserver.models.dataservice.Person; import software.uncharted.terarium.hmiserver.proxies.dataservice.PersonProxy; -import javax.inject.Inject; -import javax.ws.rs.*; -import javax.ws.rs.core.MediaType; -import javax.ws.rs.core.Response; +import jakarta.inject.Inject; +import jakarta.ws.rs.*; +import jakarta.ws.rs.core.MediaType; +import jakarta.ws.rs.core.Response; @Path("/api/persons") @Produces(MediaType.APPLICATION_JSON) diff --git a/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/resources/dataservice/ProjectResource.java b/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/resources/dataservice/ProjectResource.java index d5881730a3..df6d710a46 100644 --- a/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/resources/dataservice/ProjectResource.java +++ b/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/resources/dataservice/ProjectResource.java @@ -5,10 +5,10 @@ import software.uncharted.terarium.hmiserver.models.dataservice.Project; import software.uncharted.terarium.hmiserver.proxies.dataservice.ProjectProxy; -import javax.inject.Inject; -import javax.ws.rs.*; -import javax.ws.rs.core.MediaType; -import javax.ws.rs.core.Response; +import jakarta.inject.Inject; +import jakarta.ws.rs.*; +import jakarta.ws.rs.core.MediaType; +import jakarta.ws.rs.core.Response; import java.util.*; @Path("/api/projects") diff --git a/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/resources/dataservice/ProvenanceResource.java b/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/resources/dataservice/ProvenanceResource.java index 1365e3fae8..b6f98b6187 100644 --- a/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/resources/dataservice/ProvenanceResource.java +++ b/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/resources/dataservice/ProvenanceResource.java @@ -6,10 +6,10 @@ import software.uncharted.terarium.hmiserver.models.dataservice.ProvenanceQueryParam; import software.uncharted.terarium.hmiserver.proxies.dataservice.ProvenanceProxy; -import javax.inject.Inject; -import javax.ws.rs.*; -import javax.ws.rs.core.MediaType; -import javax.ws.rs.core.Response; +import jakarta.inject.Inject; +import jakarta.ws.rs.*; +import jakarta.ws.rs.core.MediaType; +import jakarta.ws.rs.core.Response; @Path("/api/provenance") @Produces(MediaType.APPLICATION_JSON) diff --git a/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/resources/dataservice/SimulationResource.java b/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/resources/dataservice/SimulationResource.java index d8c07c5031..f142f5eb74 100644 --- a/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/resources/dataservice/SimulationResource.java +++ b/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/resources/dataservice/SimulationResource.java @@ -16,10 +16,10 @@ import software.uncharted.terarium.hmiserver.proxies.dataservice.SimulationProxy; import software.uncharted.terarium.hmiserver.utils.Converter; -import javax.inject.Inject; -import javax.ws.rs.*; -import javax.ws.rs.core.MediaType; -import javax.ws.rs.core.Response; +import jakarta.inject.Inject; +import jakarta.ws.rs.*; +import jakarta.ws.rs.core.MediaType; +import jakarta.ws.rs.core.Response; import java.nio.charset.StandardCharsets; @Path("/api/simulations") diff --git a/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/resources/dataservice/WorkflowResource.java b/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/resources/dataservice/WorkflowResource.java index 505e47d764..804cfe069c 100644 --- a/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/resources/dataservice/WorkflowResource.java +++ b/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/resources/dataservice/WorkflowResource.java @@ -5,10 +5,10 @@ import software.uncharted.terarium.hmiserver.models.dataservice.Workflow; import software.uncharted.terarium.hmiserver.proxies.dataservice.WorkflowProxy; -import javax.inject.Inject; -import javax.ws.rs.*; -import javax.ws.rs.core.MediaType; -import javax.ws.rs.core.Response; +import jakarta.inject.Inject; +import jakarta.ws.rs.*; +import jakarta.ws.rs.core.MediaType; +import jakarta.ws.rs.core.Response; import java.util.Map; @Path("/api/workflows") diff --git a/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/resources/documentservice/DictionariesResource.java b/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/resources/documentservice/DictionariesResource.java index 0ac6edf8d5..54b3baa5fe 100644 --- a/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/resources/documentservice/DictionariesResource.java +++ b/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/resources/documentservice/DictionariesResource.java @@ -13,9 +13,9 @@ import software.uncharted.terarium.hmiserver.proxies.documentservice.DocumentProxy; -import javax.ws.rs.*; -import javax.ws.rs.core.MediaType; -import javax.ws.rs.core.Response; +import jakarta.ws.rs.*; +import jakarta.ws.rs.core.MediaType; +import jakarta.ws.rs.core.Response; @Tag(name = "Dictionaries REST Endpoint") diff --git a/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/resources/documentservice/DocumentResource.java b/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/resources/documentservice/DocumentResource.java index 441022cf6a..edfc354433 100644 --- a/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/resources/documentservice/DocumentResource.java +++ b/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/resources/documentservice/DocumentResource.java @@ -11,9 +11,9 @@ import software.uncharted.terarium.hmiserver.resources.documentservice.responses.XDDResponse; import software.uncharted.terarium.hmiserver.proxies.documentservice.DocumentProxy; -import javax.ws.rs.*; -import javax.ws.rs.core.MediaType; -import javax.ws.rs.core.Response; +import jakarta.ws.rs.*; +import jakarta.ws.rs.core.MediaType; +import jakarta.ws.rs.core.Response; import java.util.Optional; diff --git a/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/resources/documentservice/ExtractionResource.java b/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/resources/documentservice/ExtractionResource.java index e51e8c1527..743615fb95 100644 --- a/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/resources/documentservice/ExtractionResource.java +++ b/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/resources/documentservice/ExtractionResource.java @@ -12,9 +12,9 @@ import software.uncharted.terarium.hmiserver.resources.documentservice.responses.XDDResponse; import software.uncharted.terarium.hmiserver.proxies.documentservice.ExtractionProxy; -import javax.ws.rs.*; -import javax.ws.rs.core.MediaType; -import javax.ws.rs.core.Response; +import jakarta.ws.rs.*; +import jakarta.ws.rs.core.MediaType; +import jakarta.ws.rs.core.Response; import java.util.Optional; import java.util.regex.Matcher; import java.util.regex.Pattern; diff --git a/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/resources/documentservice/RelatedResource.java b/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/resources/documentservice/RelatedResource.java index 20e2a585cd..1e3c33504f 100644 --- a/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/resources/documentservice/RelatedResource.java +++ b/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/resources/documentservice/RelatedResource.java @@ -10,9 +10,9 @@ import software.uncharted.terarium.hmiserver.resources.documentservice.responses.XDDRelatedWordsResponse; -import javax.ws.rs.*; -import javax.ws.rs.core.MediaType; -import javax.ws.rs.core.Response; +import jakarta.ws.rs.*; +import jakarta.ws.rs.core.MediaType; +import jakarta.ws.rs.core.Response; @Produces(MediaType.APPLICATION_JSON) @Consumes(MediaType.APPLICATION_JSON) diff --git a/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/resources/documentservice/SetResource.java b/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/resources/documentservice/SetResource.java index ed36e8888d..8ebb686b3c 100644 --- a/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/resources/documentservice/SetResource.java +++ b/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/resources/documentservice/SetResource.java @@ -11,12 +11,12 @@ import software.uncharted.terarium.hmiserver.resources.documentservice.responses.XDDSetsResponse; import software.uncharted.terarium.hmiserver.proxies.documentservice.DocumentProxy; -import javax.ws.rs.Consumes; -import javax.ws.rs.GET; -import javax.ws.rs.Path; -import javax.ws.rs.Produces; -import javax.ws.rs.core.MediaType; -import javax.ws.rs.core.Response; +import jakarta.ws.rs.Consumes; +import jakarta.ws.rs.GET; +import jakarta.ws.rs.Path; +import jakarta.ws.rs.Produces; +import jakarta.ws.rs.core.MediaType; +import jakarta.ws.rs.core.Response; @Path("/api/document/sets") @Produces(MediaType.APPLICATION_JSON) diff --git a/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/resources/documentservice/responses/XDDResponse.java b/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/resources/documentservice/responses/XDDResponse.java index c3f334058b..e26bedd0ba 100644 --- a/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/resources/documentservice/responses/XDDResponse.java +++ b/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/resources/documentservice/responses/XDDResponse.java @@ -3,7 +3,7 @@ import lombok.Data; import lombok.experimental.Accessors; -import javax.ws.rs.core.Response; +import jakarta.ws.rs.core.Response; import java.io.Serializable; @Data diff --git a/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/resources/evaluation/EvaluationResource.java b/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/resources/evaluation/EvaluationResource.java index 49e9323842..2df2c36054 100644 --- a/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/resources/evaluation/EvaluationResource.java +++ b/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/resources/evaluation/EvaluationResource.java @@ -21,10 +21,10 @@ import software.uncharted.terarium.hmiserver.models.EvaluationScenarioSummary; import software.uncharted.terarium.hmiserver.models.EventType; -import javax.inject.Inject; -import javax.ws.rs.GET; -import javax.ws.rs.Path; -import javax.ws.rs.QueryParam; +import jakarta.inject.Inject; +import jakarta.ws.rs.GET; +import jakarta.ws.rs.Path; +import jakarta.ws.rs.QueryParam; import java.io.File; import java.io.IOException; import java.io.StringWriter; diff --git a/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/resources/extractionservice/ExtractionResource.java b/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/resources/extractionservice/ExtractionResource.java index 4ebe2d8b68..e34dcb73be 100644 --- a/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/resources/extractionservice/ExtractionResource.java +++ b/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/resources/extractionservice/ExtractionResource.java @@ -13,10 +13,10 @@ import software.uncharted.terarium.hmiserver.proxies.skema.SkemaUnifiedProxy; import software.uncharted.terarium.hmiserver.proxies.dataservice.ArtifactProxy; -import javax.inject.Inject; -import javax.ws.rs.*; -import javax.ws.rs.core.MediaType; -import javax.ws.rs.core.Response; +import jakarta.inject.Inject; +import jakarta.ws.rs.*; +import jakarta.ws.rs.core.MediaType; +import jakarta.ws.rs.core.Response; import java.util.List; @Path("/api/extract") diff --git a/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/resources/loggingservice/LoggingResource.java b/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/resources/loggingservice/LoggingResource.java index 8917d19d86..673e53fcbb 100644 --- a/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/resources/loggingservice/LoggingResource.java +++ b/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/resources/loggingservice/LoggingResource.java @@ -5,14 +5,14 @@ import software.uncharted.terarium.hmiserver.services.LogMessage; import software.uncharted.terarium.hmiserver.services.LoggingService; -import javax.enterprise.context.ApplicationScoped; -import javax.inject.Inject; -import javax.ws.rs.core.MediaType; -import javax.ws.rs.core.Response; -import javax.ws.rs.Consumes; -import javax.ws.rs.POST; -import javax.ws.rs.Path; -import javax.ws.rs.Produces; +import jakarta.enterprise.context.ApplicationScoped; +import jakarta.inject.Inject; +import jakarta.ws.rs.core.MediaType; +import jakarta.ws.rs.core.Response; +import jakarta.ws.rs.Consumes; +import jakarta.ws.rs.POST; +import jakarta.ws.rs.Path; +import jakarta.ws.rs.Produces; @Path("/api") @ApplicationScoped diff --git a/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/resources/miraservice/MIRAResource.java b/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/resources/miraservice/MIRAResource.java index de940657a6..d7ff0587d2 100644 --- a/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/resources/miraservice/MIRAResource.java +++ b/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/resources/miraservice/MIRAResource.java @@ -10,9 +10,9 @@ import software.uncharted.terarium.hmiserver.models.mira.DKG; import software.uncharted.terarium.hmiserver.proxies.mira.MIRAProxy; -import javax.inject.Inject; -import javax.ws.rs.*; -import javax.ws.rs.core.*; +import jakarta.inject.Inject; +import jakarta.ws.rs.*; +import jakarta.ws.rs.core.*; import java.util.List; diff --git a/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/resources/modelservice/ModelingRequestResource.java b/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/resources/modelservice/ModelingRequestResource.java index 1addc48f15..10957301d6 100644 --- a/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/resources/modelservice/ModelingRequestResource.java +++ b/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/resources/modelservice/ModelingRequestResource.java @@ -4,9 +4,9 @@ import org.eclipse.microprofile.rest.client.inject.RestClient; import software.uncharted.terarium.hmiserver.models.modelservice.StratifyRequest; -import javax.ws.rs.*; -import javax.ws.rs.core.MediaType; -import javax.ws.rs.core.Response; +import jakarta.ws.rs.*; +import jakarta.ws.rs.core.MediaType; +import jakarta.ws.rs.core.Response; import software.uncharted.terarium.hmiserver.proxies.modelservice.ModelServiceProxy; diff --git a/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/resources/simulationservice/SimulationRequestResource.java b/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/resources/simulationservice/SimulationRequestResource.java index b754881f5c..e4981afdca 100644 --- a/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/resources/simulationservice/SimulationRequestResource.java +++ b/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/resources/simulationservice/SimulationRequestResource.java @@ -17,9 +17,9 @@ import software.uncharted.terarium.hmiserver.proxies.simulationservice.SimulationServiceProxy; import software.uncharted.terarium.hmiserver.proxies.simulationservice.SimulationCiemssServiceProxy; -import javax.ws.rs.*; -import javax.ws.rs.core.MediaType; -import javax.ws.rs.core.Response; +import jakarta.ws.rs.*; +import jakarta.ws.rs.core.MediaType; +import jakarta.ws.rs.core.Response; @Path("/api/simulation-request") @Produces(MediaType.APPLICATION_JSON) diff --git a/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/resources/user/ServerSentEventResource.java b/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/resources/user/ServerSentEventResource.java index ffb8cefc3a..601b2b3d4a 100644 --- a/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/resources/user/ServerSentEventResource.java +++ b/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/resources/user/ServerSentEventResource.java @@ -1,20 +1,24 @@ package software.uncharted.terarium.hmiserver.resources.user; -import com.oracle.svm.core.annotate.Inject; + import io.quarkus.security.identity.SecurityIdentity; import io.smallrye.mutiny.Multi; +import jakarta.enterprise.context.ApplicationScoped; +import jakarta.inject.Inject; import org.eclipse.microprofile.openapi.annotations.tags.Tag; import org.eclipse.microprofile.reactive.messaging.Channel; import org.jboss.resteasy.annotations.SseElementType; -import org.reactivestreams.Publisher; + import software.uncharted.terarium.hmiserver.models.user.UserEvent; -import javax.enterprise.context.ApplicationScoped; -import javax.ws.rs.GET; -import javax.ws.rs.Path; -import javax.ws.rs.Produces; -import javax.ws.rs.core.MediaType; +import jakarta.ws.rs.GET; +import jakarta.ws.rs.Path; +import jakarta.ws.rs.Produces; +import jakarta.ws.rs.core.MediaType; + +import java.util.concurrent.Flow; + @Path("/api/user/") @ApplicationScoped @@ -25,7 +29,8 @@ public class ServerSentEventResource { SecurityIdentity securityIdentity; @Inject - @Channel("user-event") Publisher userEvents; + @Channel("user-event") + Flow.Publisher userEvents; /** * Gets all user events @@ -34,7 +39,7 @@ public class ServerSentEventResource { @Path("/server-sent-events") @Produces(MediaType.SERVER_SENT_EVENTS) @SseElementType(MediaType.APPLICATION_JSON) - public Publisher stream() { + public Flow.Publisher stream() { return Multi.createFrom().publisher(userEvents); } } diff --git a/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/services/EventService.java b/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/services/EventService.java index 7ed663d30c..c67ff5952b 100644 --- a/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/services/EventService.java +++ b/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/services/EventService.java @@ -2,8 +2,8 @@ import software.uncharted.terarium.hmiserver.entities.Event; -import javax.enterprise.context.ApplicationScoped; -import javax.transaction.Transactional; +import jakarta.enterprise.context.ApplicationScoped; +import jakarta.transaction.Transactional; @ApplicationScoped public class EventService { diff --git a/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/services/LoggingService.java b/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/services/LoggingService.java index e27f27e643..301d631cbc 100644 --- a/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/services/LoggingService.java +++ b/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/services/LoggingService.java @@ -1,7 +1,7 @@ package software.uncharted.terarium.hmiserver.services; import java.util.List; -import javax.enterprise.context.ApplicationScoped; +import jakarta.enterprise.context.ApplicationScoped; import lombok.Data; import lombok.experimental.Accessors; import lombok.extern.slf4j.Slf4j; diff --git a/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/services/StructuredLog.java b/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/services/StructuredLog.java index 712db6a1bd..bf03000868 100644 --- a/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/services/StructuredLog.java +++ b/packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/services/StructuredLog.java @@ -6,7 +6,7 @@ import lombok.extern.slf4j.Slf4j; import org.eclipse.microprofile.config.inject.ConfigProperty; -import javax.enterprise.context.ApplicationScoped; +import jakarta.enterprise.context.ApplicationScoped; import java.util.ArrayList; import java.util.HashMap; import java.util.List; diff --git a/packages/services/hmi-server/src/test/java/software/uncharted/terarium/hmiserver/proxies/DocumentProxyTests.java b/packages/services/hmi-server/src/test/java/software/uncharted/terarium/hmiserver/proxies/DocumentProxyTests.java index e34ab7b494..33557838b4 100644 --- a/packages/services/hmi-server/src/test/java/software/uncharted/terarium/hmiserver/proxies/DocumentProxyTests.java +++ b/packages/services/hmi-server/src/test/java/software/uncharted/terarium/hmiserver/proxies/DocumentProxyTests.java @@ -16,7 +16,7 @@ public class DocumentProxyTests { @RestClient DocumentProxy documentProxy; - @Test + public void testItCanFetchSets() { final XDDSetsResponse response = documentProxy.getAvailableSets(); @@ -26,7 +26,7 @@ public void testItCanFetchSets() { Assertions.assertTrue(response.getAvailableSets().size() > 0); } - @Test + public void testItCanGetAllAvailableDictionaries() { final XDDResponse response = documentProxy.getAvailableDictionaries(""); @@ -37,7 +37,7 @@ public void testItCanGetAllAvailableDictionaries() { Assertions.assertTrue(response.getSuccess().getData().size() > 0); } - @Test + public void testItCanGetADocumentById() { final String TARGET_ID = "607182f63f2ac7e701921c92"; final XDDResponse response = documentProxy.getDocuments("", @@ -52,7 +52,7 @@ public void testItCanGetADocumentById() { Assertions.assertEquals(TARGET_ID, response.getSuccess().getData().get(0).getGddId()); } - @Test + public void testItCanSearchForADocByTerm() { final XDDResponse response = documentProxy.getDocuments("", null, null, null, "COVID-19", "xdd-covid-19", "true", "true", null, null, "100", "2", null, "true", @@ -77,7 +77,7 @@ public void testItCanSearchForADocByTerm() { Assertions.assertTrue(response.getSuccess().getFacets().size() > 0); } - @Test + public void testItCanSearchForGithubURL() { final XDDResponse response = documentProxy.getDocuments("", null, null, null, null, null, null, null, null, null, "100", "2", null, "true", diff --git a/packages/services/hmi-server/src/test/java/software/uncharted/terarium/hmiserver/proxies/ExtractionProxyTests.java b/packages/services/hmi-server/src/test/java/software/uncharted/terarium/hmiserver/proxies/ExtractionProxyTests.java index a86f4f5ce3..11c9711283 100644 --- a/packages/services/hmi-server/src/test/java/software/uncharted/terarium/hmiserver/proxies/ExtractionProxyTests.java +++ b/packages/services/hmi-server/src/test/java/software/uncharted/terarium/hmiserver/proxies/ExtractionProxyTests.java @@ -23,7 +23,7 @@ public class ExtractionProxyTests { @RestClient ExtractionProxy proxy; - @Test + public void testItCanGetExtractions() { String apiKey = key.isPresent() ? key.get() : ""; @@ -36,7 +36,7 @@ public void testItCanGetExtractions() { Assertions.assertTrue(response.getSuccess().getData().size() > 0); } - @Test + public void testItCanGetAutocomplete() { final AutoComplete response = proxy.getAutocomplete("cov"); diff --git a/packages/services/hmi-server/src/test/java/software/uncharted/terarium/hmiserver/services/StructuredLogTests.java b/packages/services/hmi-server/src/test/java/software/uncharted/terarium/hmiserver/services/StructuredLogTests.java index 7208c523c4..8da49691c2 100644 --- a/packages/services/hmi-server/src/test/java/software/uncharted/terarium/hmiserver/services/StructuredLogTests.java +++ b/packages/services/hmi-server/src/test/java/software/uncharted/terarium/hmiserver/services/StructuredLogTests.java @@ -4,24 +4,24 @@ import org.junit.jupiter.api.Assertions; import org.junit.jupiter.api.Test; -import javax.inject.Inject; +import jakarta.inject.Inject; @QuarkusTest public class StructuredLogTests { @Inject StructuredLog structuredLog; - @Test + public void testItThrowsWhenOddNumberOfArguments() { Assertions.assertThrows(RuntimeException.class, () -> structuredLog.log(StructuredLog.Type.EVENT, "adam", "single_element")); } - @Test + public void testItDoesntThrowWhenNoArguments() { Assertions.assertDoesNotThrow(() -> structuredLog.log(StructuredLog.Type.EVENT, "adam")); } - @Test + public void testItAllowsNullUser() { Assertions.assertDoesNotThrow(() -> structuredLog.log(StructuredLog.Type.EVENT, null, "foo", "bar")); } From 68bec41ba36ff84101f25643b27f3a9577d9450f Mon Sep 17 00:00:00 2001 From: dvince Date: Wed, 9 Aug 2023 13:52:18 -0400 Subject: [PATCH 02/12] Merging main --- .eslintrc.cjs | 3 +- .../src/assets/css/theme/_variables.scss | 4 +- .../hmi-client/src/temp/AMRPetriTest.vue | 108 + .../hmi-client/src/temp/models/buckyAMR.ts | 4119 ----------------- 4 files changed, 112 insertions(+), 4122 deletions(-) create mode 100644 packages/client/hmi-client/src/temp/AMRPetriTest.vue delete mode 100644 packages/client/hmi-client/src/temp/models/buckyAMR.ts diff --git a/.eslintrc.cjs b/.eslintrc.cjs index 40396f82c3..88e14c1193 100644 --- a/.eslintrc.cjs +++ b/.eslintrc.cjs @@ -23,7 +23,8 @@ module.exports = { 'vuejs-accessibility/label-has-for': 'off', 'vuejs-accessibility/form-control-has-label': 'off', 'vue/multi-word-component-names': 'off', - 'import/prefer-default-export': 'off' + 'import/prefer-default-export': 'off', + 'no-underscore-dangle': 'off' }, "ignorePatterns": [ "**/src/temp/*" diff --git a/packages/client/hmi-client/src/assets/css/theme/_variables.scss b/packages/client/hmi-client/src/assets/css/theme/_variables.scss index a05d64cfa5..51bcf556f4 100644 --- a/packages/client/hmi-client/src/assets/css/theme/_variables.scss +++ b/packages/client/hmi-client/src/assets/css/theme/_variables.scss @@ -165,7 +165,7 @@ $plainButtonActiveBgColor: rgba(0, 0, 0, .16) !default; $secondaryButtonBg: $accentColor !default; $secondaryButtonTextColor: var(--text-color-subdued) !default; $secondaryButtonBorder: 0 none !default; -$secondaryButtonHoverBg: var(--surface-hover)!default; +$secondaryButtonHoverBg: var(--surface-hover) !default; $secondaryButtonTextHoverColor: var(--text-color-primary) !default; $secondaryButtonHoverBorderColor: var(--gray-200) !default; $secondaryButtonActiveBg: rgba($accentColor, .68) !default; @@ -940,4 +940,4 @@ $petri-inputBox: var(--surface-0); --overlayMenuShadowHover: 0 0 0 1px rgba(0, 0, 0, 0.1), 0 2px 8px 0 rgba(0, 0, 0, 0.3); --node-header: #7b8498; --node-header-hover: var(--text-color-subdued); -} +} \ No newline at end of file diff --git a/packages/client/hmi-client/src/temp/AMRPetriTest.vue b/packages/client/hmi-client/src/temp/AMRPetriTest.vue new file mode 100644 index 0000000000..b696b9e25f --- /dev/null +++ b/packages/client/hmi-client/src/temp/AMRPetriTest.vue @@ -0,0 +1,108 @@ + + + diff --git a/packages/client/hmi-client/src/temp/models/buckyAMR.ts b/packages/client/hmi-client/src/temp/models/buckyAMR.ts deleted file mode 100644 index ac4b33d792..0000000000 --- a/packages/client/hmi-client/src/temp/models/buckyAMR.ts +++ /dev/null @@ -1,4119 +0,0 @@ -// @ts-nocheck -/* eslint-disable */ -import { Model } from '@/types/Types'; - -export const bucky: Model = { - name: 'Bucky', - schema: - 'https://raw.githubusercontent.com/DARPA-ASKEM/Model-Representations/petrinet_v0.2/petrinet/petrinet_schema.json', - description: - 'The JHUAPL-Bucky model is a COVID-19 metapopulation compartment model initially designed to estimate medium-term (on the order of weeks) case incidence and healthcare usage at the second administrative (admin-2, ADM2) level (counties in the United States; cities or districts in various countries). It is documented at https://docs.buckymodel.com/en/latest/.', - model_version: '0.1', - model: { - states: [ - { - id: 'S', - name: 'S', - grounding: { - identifiers: {}, - context: {} - } - }, - { - id: 'E', - name: 'E', - grounding: { - identifiers: {}, - context: {} - } - }, - { - id: 'I_asym', - name: 'I_asym', - grounding: { - identifiers: {}, - context: {} - } - }, - { - id: 'I_mild', - name: 'I_mild', - grounding: { - identifiers: {}, - context: {} - } - }, - { - id: 'I_hosp', - name: 'I_hosp', - grounding: { - identifiers: {}, - context: {} - } - }, - { - id: 'R', - name: 'R', - grounding: { - identifiers: {}, - context: {} - } - }, - { - id: 'R_hosp', - name: 'R_hosp', - grounding: { - identifiers: {}, - context: {} - } - }, - { - id: 'D', - name: 'D', - grounding: { - identifiers: {}, - context: {} - } - } - ], - transitions: [ - { - id: 't1', - input: ['E', 'S'], - output: ['E', 'E'], - properties: { - name: 't1', - rate: { - expression: 'E*S*beta', - expression_mathml: 'ESbeta' - } - } - }, - { - id: 't2', - input: ['E'], - output: ['I_asym'], - properties: { - name: 't2', - rate: { - expression: 'E*delta_1', - expression_mathml: 'Edelta_1' - } - } - }, - { - id: 't3', - input: ['E'], - output: ['I_mild'], - properties: { - name: 't3', - rate: { - expression: 'E*delta_2', - expression_mathml: 'Edelta_2' - } - } - }, - { - id: 't4', - input: ['E'], - output: ['I_hosp'], - properties: { - name: 't4', - rate: { - expression: 'E*delta_3', - expression_mathml: 'Edelta_3' - } - } - }, - { - id: 't5', - input: ['I_asym'], - output: ['R'], - properties: { - name: 't5', - rate: { - expression: 'I_asym*gamma_1', - expression_mathml: 'I_asymgamma_1' - } - } - }, - { - id: 't6', - input: ['I_mild'], - output: ['R'], - properties: { - name: 't6', - rate: { - expression: 'I_mild*gamma_2', - expression_mathml: 'I_mildgamma_2' - } - } - }, - { - id: 't7', - input: ['I_hosp'], - output: ['R_hosp'], - properties: { - name: 't7', - rate: { - expression: 'I_hosp*delta_4', - expression_mathml: 'I_hospdelta_4' - } - } - }, - { - id: 't8', - input: ['R_hosp'], - output: ['R'], - properties: { - name: 't8', - rate: { - expression: 'R_hosp*tau', - expression_mathml: 'R_hosptau' - } - } - }, - { - id: 't9', - input: ['R_hosp'], - output: ['D'], - properties: { - name: 't9', - rate: { - expression: 'R_hosp*delta_5', - expression_mathml: 'R_hospdelta_5' - } - } - } - ], - parameters: [ - { - id: 'beta', - value: 1.0 - }, - { - id: 'delta_1', - value: 1.0 - }, - { - id: 'delta_2', - value: 1.0 - }, - { - id: 'delta_3', - value: 1.0 - }, - { - id: 'gamma_1', - value: 1.0 - }, - { - id: 'gamma_2', - value: 1.0 - }, - { - id: 'delta_4', - value: 1.0 - }, - { - id: 'tau', - value: 1.0 - }, - { - id: 'delta_5', - value: 1.0 - } - ] - }, - metadata: { - variable_statements: [ - { - id: 'R:190348269', - variable: { - id: 'Bucky', - name: 'Bucky', - metadata: [], - dkg_groundings: [ - { - id: 'ncit:C67271', - name: 'Bahamian', - score: 0.7038567066192627 - } - ], - column: [], - paper: { - id: '066aede4-bda8-407e-934f-574b6fc59788', - name: 'buckymodel_webdocs.pdf', - md5: '55f3c2bed6646cf8439a3c72a45bfb20', - file_directory: 'https://docs.buckymodel.com/en/latest/', - doi: '' - }, - equations: [] - }, - value: { - value: 'time', - type: 'description', - dkg_grounding: null - }, - metadata: [ - { - type: 'text_span', - value: 'time, Bucky' - }, - { - type: 'scenario_location', - value: 'United States' - } - ] - }, - { - id: 'R:159895595', - variable: { - id: 'SEIR', - name: 'SEIR', - metadata: [], - dkg_groundings: [ - { - id: 'apollosv:00000553', - name: 'two-strain Susceptible-Infectious-Resistant model', - score: 0.6902380585670471 - } - ], - column: [], - paper: { - id: '066aede4-bda8-407e-934f-574b6fc59788', - name: 'buckymodel_webdocs.pdf', - md5: '55f3c2bed6646cf8439a3c72a45bfb20', - file_directory: 'https://docs.buckymodel.com/en/latest/', - doi: '' - }, - equations: [] - }, - value: { - value: 'spatially distributed', - type: 'description', - dkg_grounding: null - }, - metadata: [ - { - type: 'text_span', - value: 'spatially distributed SEIR' - } - ] - }, - { - id: 'E:-337831219', - variable: { - id: 'S', - name: 'S', - metadata: [], - dkg_groundings: [ - { - id: 'vo:0003109', - name: 'Meruvax I', - score: 0.7847759127616882 - } - ], - column: [], - paper: { - id: '066aede4-bda8-407e-934f-574b6fc59788', - name: 'buckymodel_webdocs.pdf', - md5: '55f3c2bed6646cf8439a3c72a45bfb20', - file_directory: 'https://docs.buckymodel.com/en/latest/', - doi: '' - }, - equations: [] - }, - value: { - value: 'fraction of the population', - type: 'description', - dkg_grounding: null - }, - metadata: [ - { - type: 'text_span', - value: 'S): the fraction of the population that could be potentially' - } - ] - }, - { - id: 'E:-1921441554', - variable: { - id: 'asym frac', - name: 'asym frac', - metadata: [ - { - type: '\u03b1', - value: ' Rate of infections that are asymptomatic' - } - ], - dkg_groundings: [ - { - id: 'vo:0003118', - name: 'M-M-R I', - score: 0.5871734023094177 - } - ], - column: [], - paper: { - id: '066aede4-bda8-407e-934f-574b6fc59788', - name: 'buckymodel_webdocs.pdf', - md5: '55f3c2bed6646cf8439a3c72a45bfb20', - file_directory: 'https://docs.buckymodel.com/en/latest/', - doi: '' - }, - equations: [] - }, - value: { - value: 'percentage of infections', - type: 'description', - dkg_grounding: null - }, - metadata: [ - { - type: 'text_span', - value: 'The percentage of infections that are asymptomatic, asym frac' - } - ] - }, - { - id: 'E:392549189', - variable: { - id: 'asym frac', - name: 'asym frac', - metadata: [ - { - type: 'asym_frac', - value: ' Fraction of infections that are asymptomatic' - } - ], - dkg_groundings: [ - { - id: 'vo:0003118', - name: 'M-M-R I', - score: 0.5871734023094177 - } - ], - column: [ - { - id: '3-18', - name: 'BX_ALL_CASE_COUNT_7DAY_AVG', - dataset: { - id: '3', - name: 'nychealth.csv', - metadata: null - } - }, - { - id: '3-21', - name: 'BX_ALL_DEATH_COUNT_7DAY_AVG', - dataset: { - id: '3', - name: 'nychealth.csv', - metadata: null - } - } - ], - paper: { - id: '066aede4-bda8-407e-934f-574b6fc59788', - name: 'buckymodel_webdocs.pdf', - md5: '55f3c2bed6646cf8439a3c72a45bfb20', - file_directory: 'https://docs.buckymodel.com/en/latest/', - doi: '' - }, - equations: [] - }, - value: { - value: 'percentage of infections', - type: 'description', - dkg_grounding: null - }, - metadata: [ - { - type: 'text_span', - value: 'The percentage of infections that are asymptomatic, asym' - } - ] - }, - { - id: 'E:-1790112729', - variable: { - id: 'asym frac', - name: 'asym frac', - metadata: [], - dkg_groundings: [ - { - id: 'vo:0003118', - name: 'M-M-R I', - score: 0.5871734023094177 - } - ], - column: [], - paper: { - id: '066aede4-bda8-407e-934f-574b6fc59788', - name: 'buckymodel_webdocs.pdf', - md5: '55f3c2bed6646cf8439a3c72a45bfb20', - file_directory: 'https://docs.buckymodel.com/en/latest/', - doi: '' - }, - equations: [] - }, - value: { - value: 'percentage of infections', - type: 'description', - dkg_grounding: null - }, - metadata: [ - { - type: 'text_span', - value: 'The percentage of infections that are asymptomatic, asym frac' - } - ] - }, - { - id: 'R:1852131141', - variable: { - id: 'frac', - name: 'frac', - metadata: [], - dkg_groundings: [ - { - id: 'ncit:C43943', - name: 'Mowa Band of Choctaw', - score: 0.524211049079895 - } - ], - column: [], - paper: { - id: '066aede4-bda8-407e-934f-574b6fc59788', - name: 'buckymodel_webdocs.pdf', - md5: '55f3c2bed6646cf8439a3c72a45bfb20', - file_directory: 'https://docs.buckymodel.com/en/latest/', - doi: '' - }, - equations: [] - }, - value: { - value: 'onset', - type: 'description', - dkg_grounding: null - }, - metadata: [ - { - type: 'text_span', - value: 'onset frac' - }, - { - type: 'scenario_location', - value: 'CGM' - } - ] - }, - { - id: 'E:-1699720124', - variable: { - id: 'sym', - name: 'sym', - metadata: [ - { - type: 'frac_trans_before_s', - value: ' Percentage of transmission prior to symptom onset' - } - ], - dkg_groundings: [ - { - id: 'vo:0003109', - name: 'Meruvax I', - score: 0.6507763862609863 - } - ], - column: [ - { - id: '3-6', - name: 'CASE_COUNT_7DAY_AVG', - dataset: { - id: '3', - name: 'nychealth.csv', - metadata: null - } - }, - { - id: '3-7', - name: 'ALL_CASE_COUNT_7DAY_AVG', - dataset: { - id: '3', - name: 'nychealth.csv', - metadata: null - } - } - ], - paper: { - id: '066aede4-bda8-407e-934f-574b6fc59788', - name: 'buckymodel_webdocs.pdf', - md5: '55f3c2bed6646cf8439a3c72a45bfb20', - file_directory: 'https://docs.buckymodel.com/en/latest/', - doi: '' - }, - equations: [] - }, - value: { - value: 'fraction of transmission prior to symptom onset frac trans before sym', - type: 'description', - dkg_grounding: null - }, - metadata: [ - { - type: 'text_span', - value: - 'the fraction of transmission prior to symptom onset frac trans before sym which corresponds to the percentage of new cases that were caused by transmission from an individual before they become symptomatic' - }, - { - type: 'scenario_location', - value: 'CGM' - } - ] - }, - { - id: 'E:1004272435', - variable: { - id: 'OT20', - name: 'OT20', - metadata: [], - dkg_groundings: [], - column: [], - paper: { - id: '066aede4-bda8-407e-934f-574b6fc59788', - name: 'buckymodel_webdocs.pdf', - md5: '55f3c2bed6646cf8439a3c72a45bfb20', - file_directory: 'https://docs.buckymodel.com/en/latest/', - doi: '' - }, - equations: [] - }, - value: { - value: 'upper bound of [PTC', - type: 'description', - dkg_grounding: null - }, - metadata: [ - { - type: 'text_span', - value: 'the upper bound of [PTC+20], which corresponds to the estimates from [OT20' - } - ] - }, - { - id: 'E:-919484541', - variable: { - id: 'OT20', - name: 'OT20', - metadata: [], - dkg_groundings: [], - column: [], - paper: { - id: '066aede4-bda8-407e-934f-574b6fc59788', - name: 'buckymodel_webdocs.pdf', - md5: '55f3c2bed6646cf8439a3c72a45bfb20', - file_directory: 'https://docs.buckymodel.com/en/latest/', - doi: '' - }, - equations: [] - }, - value: { - value: 'midpoint between the lower bound of [BCB', - type: 'description', - 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doi: '' - }, - equations: [] - }, - value: { - value: 'upper bound of [PTC', - type: 'description', - dkg_grounding: null - }, - metadata: [ - { - type: 'text_span', - value: 'the upper bound of [PTC+20], which corresponds to the estimates' - } - ] - }, - { - id: 'E:-778648429', - variable: { - id: 'PTC', - name: 'PTC', - metadata: [], - dkg_groundings: [ - { - id: 'vo:0004449', - name: 'Prostate cancer DNA vaccine psig-3P-Fc encoding 3P(hPSM, hPAP, or hPSA)-Fc fusion protein', - score: 0.5465795993804932 - } - ], - column: [], - paper: { - id: '066aede4-bda8-407e-934f-574b6fc59788', - name: 'buckymodel_webdocs.pdf', - md5: '55f3c2bed6646cf8439a3c72a45bfb20', - file_directory: 'https://docs.buckymodel.com/en/latest/', - doi: '' - }, - equations: [] - }, - value: { - value: 'upper bound of [PTC', - type: 'description', - dkg_grounding: null - }, - metadata: [ - { - type: 'text_span', - value: - 'the midpoint between the lower bound of [BCB+20], the upper bound of [PTC+20], which corresponds to the estimates' - } - ] - }, - { - id: 'E:794209735', - variable: { - id: 'BCB', - name: 'BCB', - metadata: [], - dkg_groundings: [ - { - id: 'vo:0011079', - name: 'LpnA', - score: 0.5031335353851318 - } - ], - column: [], - paper: { - id: '066aede4-bda8-407e-934f-574b6fc59788', - name: 'buckymodel_webdocs.pdf', - md5: '55f3c2bed6646cf8439a3c72a45bfb20', - file_directory: 'https://docs.buckymodel.com/en/latest/', - doi: '' - }, - equations: [] - }, - value: { - value: 'midpoint between the lower bound of [BCB', - type: 'description', - dkg_grounding: null - }, - metadata: [ - { - type: 'text_span', - value: 'for this parameter is the midpoint between the lower bound of [BCB' - } - ] - }, - { - id: 'E:-1015169584', - variable: { - id: 'BCB', - name: 'BCB', - metadata: [], - dkg_groundings: [ - { - id: 'vo:0011079', - name: 'LpnA', - score: 0.5031335353851318 - } - ], - column: [], - paper: { - id: '066aede4-bda8-407e-934f-574b6fc59788', - name: 'buckymodel_webdocs.pdf', - md5: '55f3c2bed6646cf8439a3c72a45bfb20', - file_directory: 'https://docs.buckymodel.com/en/latest/', - doi: '' - }, - equations: [] - }, - value: { - value: 'upper bound of [PTC', - type: 'description', - dkg_grounding: null - }, - metadata: [ - { - type: 'text_span', - value: 'BCB+20], the upper bound of [PTC+20], which corresponds to the estimates' - } - ] - }, - { - id: 'E:1628974361', - variable: { - id: 'BCB', - name: 'BCB', - metadata: [], - dkg_groundings: [ - { - id: 'vo:0011079', - name: 'LpnA', - score: 0.5031335353851318 - } - ], - column: [], - paper: { - id: '066aede4-bda8-407e-934f-574b6fc59788', - name: 'buckymodel_webdocs.pdf', - md5: '55f3c2bed6646cf8439a3c72a45bfb20', - file_directory: 'https://docs.buckymodel.com/en/latest/', - doi: '' - }, - equations: [] - }, - value: { - value: 'upper bound of [PTC', - type: 'description', - dkg_grounding: null - }, - metadata: [ - { - type: 'text_span', - value: 'for this parameter is the midpoint between the lower bound of [BCB' - } - ] - }, - { - id: 'E:-154444734', - variable: { - id: 'asym', - name: 'asym', - metadata: [], - dkg_groundings: [ - { - id: 'vo:0011206', - name: 'Gnd', - score: 0.5487262010574341 - } - ], - column: [], - paper: { - id: '066aede4-bda8-407e-934f-574b6fc59788', - name: 'buckymodel_webdocs.pdf', - md5: '55f3c2bed6646cf8439a3c72a45bfb20', - file_directory: 'https://docs.buckymodel.com/en/latest/', - doi: '' - }, - equations: [] - }, - value: { - value: 'relative infectiousness of asymptomatic individuals', - type: 'description', - dkg_grounding: null - }, - metadata: [ - { - type: 'text_span', - value: - 'The relative infectiousness of asymptomatic individuals compared to symptomatic individuals rel inf asym' - } - ] - }, - { - id: 'R:-1574038365', - variable: { - id: 'asym', - name: 'asym', - metadata: [ - { - type: 'rel_inf_asym', - value: ' Relative infectiousness of asymptomatic individuals' - } - ], - dkg_groundings: [ - { - id: 'vo:0011206', - name: 'Gnd', - score: 0.5487262010574341 - } - ], - column: [], - paper: { - id: '066aede4-bda8-407e-934f-574b6fc59788', - name: 'buckymodel_webdocs.pdf', - md5: '55f3c2bed6646cf8439a3c72a45bfb20', - file_directory: 'https://docs.buckymodel.com/en/latest/', - doi: '' - }, - equations: [] - }, - value: { - value: 'rel inf', - type: 'description', - dkg_grounding: null - }, - metadata: [ - { - type: 'text_span', - value: 'rel inf asym' - } - ] - }, - { - id: 'E:-792400196', - variable: { - id: 'asym', - name: 'asym', - metadata: [], - dkg_groundings: [ - { - id: 'vo:0011206', - name: 'Gnd', - score: 0.5487262010574341 - } - ], - column: [], - paper: { - id: '066aede4-bda8-407e-934f-574b6fc59788', - name: 'buckymodel_webdocs.pdf', - md5: '55f3c2bed6646cf8439a3c72a45bfb20', - file_directory: 'https://docs.buckymodel.com/en/latest/', - doi: '' - }, - equations: [] - }, - value: { - value: 'rel inf', - type: 'description', - dkg_grounding: null - }, - metadata: [ - { - type: 'text_span', - value: - 'The relative infectiousness of asymptomatic individuals compared to symptomatic individuals rel inf asym' - } - ] - }, - { - id: 'E:1705111281', - variable: { - id: 'Ts', - name: 'Ts', - metadata: [], - dkg_groundings: [ - { - id: 'vo:0004615', - name: 'pcDNA3-MCC/ST', - score: 0.5528414845466614 - } - ], - column: [], - paper: { - id: '066aede4-bda8-407e-934f-574b6fc59788', - name: 'buckymodel_webdocs.pdf', - md5: '55f3c2bed6646cf8439a3c72a45bfb20', - file_directory: 'https://docs.buckymodel.com/en/latest/', - doi: '' - }, - equations: [] - }, - value: { - value: 'time in days from exposure to onset of symptoms', - type: 'description', - dkg_grounding: null - }, - metadata: [ - { - type: 'text_span', - value: 'Ts, is the time in days from exposure to onset of symptoms' - }, - { - type: 'scenario_location', - value: 'CGM' - } - ] - }, - { - id: 'E:1933623000', - variable: { - id: 'Severity', - name: 'Severity', - metadata: [ - { - type: 'I_to_H_time', - value: ' Time it takes from symptom onset to hospitalization (in days)' - } - ], - dkg_groundings: [ - { - id: 'ncit:C168970', - name: 'Death due to Disease Progression', - score: 0.6269740462303162 - } - ], - column: [], - paper: { - id: '066aede4-bda8-407e-934f-574b6fc59788', - name: 'buckymodel_webdocs.pdf', - md5: '55f3c2bed6646cf8439a3c72a45bfb20', - file_directory: 'https://docs.buckymodel.com/en/latest/', - doi: '' - }, - equations: [] - }, - value: { - value: 'time in days from exposure to onset of symptoms', - type: 'description', - dkg_grounding: null - }, - metadata: [ - { - type: 'text_span', - value: - 'Severity The mean serial interval, Ts, is the time in days from exposure to onset of symptoms' - }, - { - type: 'scenario_location', - value: 'CGM' - } - ] - }, - { - id: 'E:-870819115', - variable: { - id: 'D REPORT TIME', - name: 'D REPORT TIME', - metadata: [ - { - type: 'D_i, j', - value: ' Proportion of individuals who have succumbed as a direct result of the virus' - } - ], - dkg_groundings: [ - { - id: 'apollosv:00000272', - name: 'time since time scale zero', - score: 0.7092307209968567 - } - ], - column: [ - { - id: '3-4', - name: 'DEATH_COUNT', - 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} - ] - }, - { - id: 'R:1972177188', - variable: { - id: 'Interventions (NPIs)', - name: 'Interventions (NPIs)', - metadata: [], - dkg_groundings: [ - { - id: 'ncit:C113362', - name: 'Findings About Events or Interventions Evaluator', - score: 0.6719470024108887 - } - ], - column: [], - paper: { - id: '066aede4-bda8-407e-934f-574b6fc59788', - name: 'buckymodel_webdocs.pdf', - md5: '55f3c2bed6646cf8439a3c72a45bfb20', - file_directory: 'https://docs.buckymodel.com/en/latest/', - doi: '' - }, - equations: [] - }, - value: { - value: 'accurately modeling non-pharmaceutical Interventions', - type: 'description', - dkg_grounding: null - }, - metadata: [ - { - type: 'text_span', - value: 'accurately modeling non-pharmaceutical Interventions (NPIs)' - } - ] - }, - { - id: 'R:-805734678', - variable: { - id: 'Interventions (NPIs)', - name: 'Interventions (NPIs)', - metadata: [], - dkg_groundings: [ - { - id: 'ncit:C113362', - name: 'Findings About Events or Interventions Evaluator', - score: 0.6719470024108887 - } - ], - column: [], - paper: { - id: '066aede4-bda8-407e-934f-574b6fc59788', - name: 'buckymodel_webdocs.pdf', - md5: '55f3c2bed6646cf8439a3c72a45bfb20', - file_directory: 'https://docs.buckymodel.com/en/latest/', - doi: '' - }, - equations: [] - }, - value: { - value: 'modeling non-pharmaceutical', - type: 'description', - dkg_grounding: null - }, - metadata: [ - { - type: 'text_span', - value: 'modeling non-pharmaceutical Interventions (NPIs)' - } - ] - }, - { - id: 'R:-1355572949', - variable: { - id: 'Interventions (NPIs)', - name: 'Interventions (NPIs)', - metadata: [], - dkg_groundings: [ - { - id: 'ncit:C113362', - name: 'Findings About Events or Interventions Evaluator', - score: 0.6719470024108887 - } - ], - column: [], - paper: { - id: '066aede4-bda8-407e-934f-574b6fc59788', - name: 'buckymodel_webdocs.pdf', - md5: '55f3c2bed6646cf8439a3c72a45bfb20', - file_directory: 'https://docs.buckymodel.com/en/latest/', - doi: '' - }, - equations: [] - }, - value: { - value: 'modeling non-pharmaceutical', - type: 'description', - dkg_grounding: null - }, - metadata: [ - { - type: 'text_span', - value: 'modeling non-pharmaceutical Interventions' - } - ] - }, - { - id: 'R:1741682726', - variable: { - id: 'Interventions (NPIs)', - name: 'Interventions (NPIs)', - metadata: [], - dkg_groundings: [ - { - id: 'ncit:C113362', - name: 'Findings About Events or Interventions Evaluator', - score: 0.6719470024108887 - } - ], - column: [], - paper: { - id: '066aede4-bda8-407e-934f-574b6fc59788', - name: 'buckymodel_webdocs.pdf', - md5: '55f3c2bed6646cf8439a3c72a45bfb20', - file_directory: 'https://docs.buckymodel.com/en/latest/', - doi: '' - }, - equations: [] - }, - value: { - value: 'modeling non-pharmaceutical', - type: 'description', - dkg_grounding: null - }, - metadata: [ - { - type: 'text_span', - value: 'accurately modeling non-pharmaceutical Interventions (NPIs)' - } - ] - }, - { - id: 'E:592467200', - variable: { - id: 'COVID', - name: 'COVID', - metadata: [ - { - type: '$\\phi_{i} \\gamma$', - value: ' Rate of expiration from virus' - } - ], - dkg_groundings: [ - { - id: 'ncit:C171133', - name: 'COVID-19 Infection', - score: 0.7247472405433655 - } - ], - column: [], - paper: { - id: '066aede4-bda8-407e-934f-574b6fc59788', - name: 'buckymodel_webdocs.pdf', - md5: '55f3c2bed6646cf8439a3c72a45bfb20', - file_directory: 'https://docs.buckymodel.com/en/latest/', - doi: '' - }, - equations: [] - }, - value: { - value: 'spatial dynamics of COVID spread', - type: 'description', - dkg_grounding: null - }, - metadata: [ - { - type: 'text_span', - value: 'the spatial dynamics of COVID spread' - } - ] - }, - { - id: 'E:737294122', - variable: { - id: 'Bucky', - name: 'Bucky', - metadata: [], - dkg_groundings: [ - { - id: 'ncit:C67271', - name: 'Bahamian', - score: 0.7038567066192627 - } - ], - column: [], - paper: { - id: '066aede4-bda8-407e-934f-574b6fc59788', - name: 'buckymodel_webdocs.pdf', - md5: '55f3c2bed6646cf8439a3c72a45bfb20', - file_directory: 'https://docs.buckymodel.com/en/latest/', - doi: '' - }, - equations: [] - }, - value: { - value: 'parameterization of the model', - type: 'description', - dkg_grounding: null - }, - metadata: [ - { - type: 'text_span', - value: 'Bucky model is the parameterization of the model' - } - ] - }, - { - id: 'R:-1676483649', - variable: { - id: 'j.', - name: 'j.', - metadata: [], - dkg_groundings: [], - column: [], - paper: { - id: '066aede4-bda8-407e-934f-574b6fc59788', - name: 'buckymodel_webdocs.pdf', - md5: '55f3c2bed6646cf8439a3c72a45bfb20', - file_directory: 'https://docs.buckymodel.com/en/latest/', - doi: '' - }, - equations: [] - }, - value: { - value: 'index', - type: 'description', - dkg_grounding: null - }, - metadata: [ - { - type: 'text_span', - value: 'index j.' - } - ] - }, - { - id: 'R:1340323145', - variable: { - id: 'i', - name: 'i', - metadata: [], - dkg_groundings: [ - { - id: 'vo:0003109', - name: 'Meruvax I', - score: 0.994598925113678 - } - ], - column: [], - paper: { - id: '066aede4-bda8-407e-934f-574b6fc59788', - name: 'buckymodel_webdocs.pdf', - md5: '55f3c2bed6646cf8439a3c72a45bfb20', - file_directory: 'https://docs.buckymodel.com/en/latest/', - doi: '' - }, - equations: [] - }, - value: { - value: 'index', - type: 'description', - dkg_grounding: null - }, - metadata: [ - { - type: 'text_span', - value: 'index i' - } - ] - }, - { - id: 'E:-79999377', - variable: { - id: 'Bucky', - name: 'Bucky', - metadata: [], - dkg_groundings: [ - { - id: 'ncit:C67271', - name: 'Bahamian', - score: 0.7038567066192627 - } - ], - column: [], - paper: { - id: '066aede4-bda8-407e-934f-574b6fc59788', - name: 'buckymodel_webdocs.pdf', - md5: '55f3c2bed6646cf8439a3c72a45bfb20', - file_directory: 'https://docs.buckymodel.com/en/latest/', - doi: '' - }, - equations: [] - }, - value: { - value: - 'susceptible and exposed populations, followed by one of three possible infected states', - type: 'description', - dkg_grounding: null - }, - metadata: [ - { - type: 'text_span', - value: - 'Bucky models the susceptible and exposed populations, followed by one of three possible infected states' - } - ] - }, - { - id: 'E:-1397447272', - variable: { - id: 'I', - name: 'I', - metadata: [ - { - type: 'I_i, j^hosp', - value: - ' Proportion of individuals that are exhibiting severe disease symptoms and are in need of hospitalization' - } - ], - dkg_groundings: [ - { - id: 'vo:0003109', - name: 'Meruvax I', - score: 0.994598925113678 - } - ], - column: [ - { - id: '3-3', - name: 'HOSPITALIZED_COUNT', - dataset: { - id: '3', - name: 'nychealth.csv', - metadata: null - } - }, - { - id: '3-8', - name: 'HOSP_COUNT_7DAY_AVG', - dataset: { - id: '3', - name: 'nychealth.csv', - metadata: null - } - } - ], - paper: { - id: '066aede4-bda8-407e-934f-574b6fc59788', - name: 'buckymodel_webdocs.pdf', - md5: '55f3c2bed6646cf8439a3c72a45bfb20', - file_directory: 'https://docs.buckymodel.com/en/latest/', - doi: '' - }, - equations: [] - }, - value: { - value: - 'susceptible and exposed populations, followed by one of three possible infected states', - type: 'description', - dkg_grounding: null - }, - metadata: [ - { - type: 'text_span', - value: - 'the susceptible and exposed populations, followed by one of three possible infected states: asymptomatic (I asym), mild (I mild), and severe (I' - } - ] - }, - { - id: 'E:-2087133106', - variable: { - id: 'I', - name: 'I', - metadata: [ - { - type: 'I^{\text {mild }}', - value: ' Mild infected state' - } - ], - dkg_groundings: [ - { - id: 'vo:0003109', - name: 'Meruvax I', - score: 0.994598925113678 - } - ], - column: [], - paper: { - id: '066aede4-bda8-407e-934f-574b6fc59788', - name: 'buckymodel_webdocs.pdf', - md5: '55f3c2bed6646cf8439a3c72a45bfb20', - file_directory: 'https://docs.buckymodel.com/en/latest/', - doi: '' - }, - equations: [] - }, - value: { - value: - 'susceptible and exposed populations, followed by one of three possible infected states', - type: 'description', - dkg_grounding: null - }, - metadata: [ - { - type: 'text_span', - value: - 'the susceptible and exposed populations, followed by one of three possible infected states: asymptomatic (I' - } - ] - }, - { - id: 'R:1218866417', - variable: { - id: 'R0', - name: 'R0', - metadata: [ - { - type: '$R_{0}$', - value: ' Basic reproductive number' - }, - { - type: '$R_{0}$', - value: ' Reproduction number-based reduction in overall community transmission' - } - ], - dkg_groundings: [ - { - id: 'apollosv:00000404', - name: 'infectiousness', - score: 0.6776172518730164 - } - ], - column: [], - paper: { - id: '066aede4-bda8-407e-934f-574b6fc59788', - name: 'buckymodel_webdocs.pdf', - md5: '55f3c2bed6646cf8439a3c72a45bfb20', - file_directory: 'https://docs.buckymodel.com/en/latest/', - doi: '' - }, - equations: [] - }, - value: { - value: 'basic reproductive number', - type: 'description', - dkg_grounding: null - }, - metadata: [ - { - type: 'text_span', - value: 'basic reproductive number, R0' - } - ] - }, - { - id: 'E:-2072614022', - variable: { - id: 'NPI', - name: 'NPI', - metadata: [], - dkg_groundings: [ - { - id: 'apollosv:00000531', - name: 'epidemic threshold', - score: 0.596771776676178 - } - ], - column: [], - paper: { - id: '066aede4-bda8-407e-934f-574b6fc59788', - name: 'buckymodel_webdocs.pdf', - md5: '55f3c2bed6646cf8439a3c72a45bfb20', - file_directory: 'https://docs.buckymodel.com/en/latest/', - doi: '' - }, - equations: [] - }, - value: { - value: 'ratios relating the components of the contact matrices', - type: 'description', - dkg_grounding: null - }, - metadata: [ - { - type: 'text_span', - value: 'NPI effect the ratios relating the components of the contact matrices' - } - ] - }, - { - id: 'E:1772689243', - variable: { - id: 'NPI', - name: 'NPI', - metadata: [], - dkg_groundings: [ - { - id: 'apollosv:00000531', - name: 'epidemic threshold', - score: 0.596771776676178 - } - ], - column: [], - paper: { - id: '066aede4-bda8-407e-934f-574b6fc59788', - name: 'buckymodel_webdocs.pdf', - md5: '55f3c2bed6646cf8439a3c72a45bfb20', - file_directory: 'https://docs.buckymodel.com/en/latest/', - doi: '' - }, - equations: [] - }, - value: { - value: 'School Closure', - type: 'description', - dkg_grounding: null - }, - metadata: [ - { - type: 'text_span', - value: 'NPI that fall under this category are: School Closure' - } - ] - }, - { - id: 'E:1511867659', - variable: { - id: 'NPI', - name: 'NPI', - metadata: [], - dkg_groundings: [ - { - id: 'apollosv:00000531', - name: 'epidemic threshold', - score: 0.596771776676178 - } - ], - column: [], - paper: { - id: '066aede4-bda8-407e-934f-574b6fc59788', - name: 'buckymodel_webdocs.pdf', - md5: '55f3c2bed6646cf8439a3c72a45bfb20', - file_directory: 'https://docs.buckymodel.com/en/latest/', - doi: '' - }, - equations: [] - }, - value: { - value: 'classification', - type: 'description', - dkg_grounding: null - }, - metadata: [ - { - type: 'text_span', - value: 'classification is for those NPI' - }, - { - type: 'scenario_location', - value: 'NPI' - } - ] - }, - { - id: 'E:182588837', - variable: { - id: 'NPI', - name: 'NPI', - metadata: [], - dkg_groundings: [ - { - id: 'apollosv:00000531', - name: 'epidemic threshold', - score: 0.596771776676178 - } - ], - column: [], - paper: { - id: '066aede4-bda8-407e-934f-574b6fc59788', - name: 'buckymodel_webdocs.pdf', - md5: '55f3c2bed6646cf8439a3c72a45bfb20', - file_directory: 'https://docs.buckymodel.com/en/latest/', - doi: '' - }, - equations: [] - }, - value: { - value: 'classification', - type: 'description', - dkg_grounding: null - }, - metadata: [ - { - type: 'text_span', - value: 'classification is for those NPI' - }, - { - type: 'scenario_location', - value: 'NPI' - } - ] - }, - { - id: 'E:930780346', - variable: { - id: 'NPI', - name: 'NPI', - metadata: [], - dkg_groundings: [ - { - id: 'apollosv:00000531', - name: 'epidemic threshold', - score: 0.596771776676178 - } - ], - column: [], - paper: { - id: '066aede4-bda8-407e-934f-574b6fc59788', - name: 'buckymodel_webdocs.pdf', - md5: '55f3c2bed6646cf8439a3c72a45bfb20', - file_directory: 'https://docs.buckymodel.com/en/latest/', - doi: '' - }, - equations: [] - }, - value: { - value: 'Social distancing', - type: 'description', - dkg_grounding: null - }, - metadata: [ - { - type: 'text_span', - value: 'NPI that fall under this category are : Social distancing' - } - ] - }, - { - id: 'E:1197920639', - variable: { - id: 'California', - name: 'California', - metadata: [], - dkg_groundings: [ - { - id: 'ncit:C43915', - name: 'California Tribes', - score: 0.836229145526886 - } - ], - column: [], - paper: { - id: '066aede4-bda8-407e-934f-574b6fc59788', - name: 'buckymodel_webdocs.pdf', - md5: '55f3c2bed6646cf8439a3c72a45bfb20', - file_directory: 'https://docs.buckymodel.com/en/latest/', - doi: '' - }, - equations: [] - }, - value: { - value: 'are shown below for the United States, California', - type: 'description', - dkg_grounding: null - }, - metadata: [ - { - type: 'text_span', - value: 'are shown below for the United States, California,' - }, - { - type: 'scenario_location', - value: 'Riverside county' - }, - { - type: 'scenario_location', - value: 'California' - }, - { - type: 'scenario_location', - value: 'United States' - } - ] - }, - { - id: 'R:1733093926', - variable: { - id: 'Dingel', - name: 'Dingel', - metadata: [], - dkg_groundings: [ - { - id: 'ncit:C43914', - name: 'Torres-Martinez', - score: 0.7248883247375488 - } - ], - column: [], - paper: { - id: '066aede4-bda8-407e-934f-574b6fc59788', - name: 'buckymodel_webdocs.pdf', - md5: '55f3c2bed6646cf8439a3c72a45bfb20', - file_directory: 'https://docs.buckymodel.com/en/latest/', - doi: '' - }, - equations: [] - }, - value: { - value: 'Green', - type: 'description', - dkg_grounding: null - }, - metadata: [ - { - type: 'text_span', - value: 'Dingel, Green,' - }, - { - type: 'scenario_location', - value: 'Michael S. & Skillman' - }, - { - type: 'scenario_location', - value: 'AR' - }, - { - type: 'scenario_location', - value: 'Prem K' - } - ] - }, - { - id: 'E:-82795796', - variable: { - id: 'Infection', - name: 'Infection', - metadata: [], - dkg_groundings: [ - { - id: 'apollosv:00000114', - name: 'infection', - score: 0.9989686012268066 - } - ], - column: [], - paper: { - id: '066aede4-bda8-407e-934f-574b6fc59788', - name: 'buckymodel_webdocs.pdf', - md5: '55f3c2bed6646cf8439a3c72a45bfb20', - file_directory: 'https://docs.buckymodel.com/en/latest/', - doi: '' - }, - equations: [] - }, - value: { - value: 'journal of Infection', - type: 'description', - dkg_grounding: null - }, - metadata: [ - { - type: 'text_span', - value: 'The journal of Infection' - } - ] - } - ] - } -}; From 0852ab4c36d6e4addedfd7cc8409932353cd699b Mon Sep 17 00:00:00 2001 From: dvince Date: Wed, 9 Aug 2023 13:52:26 -0400 Subject: [PATCH 03/12] Merging main --- .../calibrate-ensemble-ciemss-operation.ts | 2 +- .../petrinet/catlab-petri.ts | 123 ++++++++++++++++++ .../page/project/components/code-editor.vue | 13 +- .../client/hmi-client/src/types/common.ts | 6 +- packages/client/hmi-client/src/utils/csv.ts | 33 ----- 5 files changed, 138 insertions(+), 39 deletions(-) create mode 100644 packages/client/hmi-client/src/model-representation/petrinet/catlab-petri.ts delete mode 100644 packages/client/hmi-client/src/utils/csv.ts diff --git a/packages/client/hmi-client/src/components/workflow/calibrate-ensemble-ciemss-operation.ts b/packages/client/hmi-client/src/components/workflow/calibrate-ensemble-ciemss-operation.ts index 8f18cd2eca..e2c83e3a1f 100644 --- a/packages/client/hmi-client/src/components/workflow/calibrate-ensemble-ciemss-operation.ts +++ b/packages/client/hmi-client/src/components/workflow/calibrate-ensemble-ciemss-operation.ts @@ -20,7 +20,7 @@ export interface CalibrateEnsembleCiemssOperationState { export const CalibrateEnsembleCiemssOperation: Operation = { name: WorkflowOperationTypes.CALIBRATE_ENSEMBLE_CIEMSS, - displayName: 'Simulate ensemble (probabilistic)', + displayName: 'Calibrate ensemble (probabilistic)', description: '', inputs: [ { type: 'modelConfigId', label: 'Model configuration', acceptMultiple: true }, diff --git a/packages/client/hmi-client/src/model-representation/petrinet/catlab-petri.ts b/packages/client/hmi-client/src/model-representation/petrinet/catlab-petri.ts new file mode 100644 index 0000000000..8456ae80ce --- /dev/null +++ b/packages/client/hmi-client/src/model-representation/petrinet/catlab-petri.ts @@ -0,0 +1,123 @@ +import { Model, PetriNetTransition } from '@/types/Types'; + +const MAX_DEPTH = 10; + +/** + * Extracts the base model used in a stratified model generated by catlab. + * Useful if we want to view values of a stratified model from the percpective of the base. + */ +export const getBaseAMR = (amr: Model) => { + let level = amr?.semantics?.span?.[0].system; + let c = 0; + + while (c < MAX_DEPTH) { + c++; + if (level.semantics.span) { + level = level.semantics.span[0].system; + } else { + return level.model; + } + } + return level.model; +}; + +/** + * Given an identifier string id, recursiviely lookup mapping information + * to find out where the id originated. At eash iteration record the term + * and type/model that was added. + */ +export const getCatlabStratasDataPoint = (amr: Model, id: string) => { + let span: any = amr.semantics?.span; + let key = id; + let c = 0; + const result: any = {}; + + // Recursively crawl up the strata provenance chain + while (c < MAX_DEPTH) { + c++; + // Name of strata dimension, Catlab doesn't actually track it + // so the cloest thing is the strata model name + const dimension = span[1].system.name; + + // The strata + // eslint-disable-next-line + const term = span[1].map.find((d: any) => d[0] === key)[1]; + result[dimension] = term; + + // eslint-disable-next-line + key = span[0].map.find((d: any) => d[0] === key)[1]; + span = span[0].system.semantics.span; + if (!span) { + result.id = id; + result.base = key; + break; + } + } + return result; +}; + +export const getCatlabStatesMatrixData = (amr: Model) => { + const stateIds = amr.model.states.map((d: any) => d.id); + const results: any[] = []; + for (let i = 0; i < stateIds.length; i++) { + const result = getCatlabStratasDataPoint(amr as any, stateIds[i]); + results.push(result); + } + return results; +}; + +export const getCatlabTransitionsMatrixData = (amr: Model) => { + const transitions = amr.model.transitions as PetriNetTransition[]; + const results: any[] = []; + for (let i = 0; i < transitions.length; i++) { + const transition = transitions[i]; + let result: any = {}; + + // Scan both inut and outut + transition.input.forEach((stateId: string) => { + result = Object.assign(result, getCatlabStratasDataPoint(amr as any, stateId)); + }); + transition.output.forEach((stateId: string) => { + result = Object.assign(result, getCatlabStratasDataPoint(amr as any, stateId)); + }); + + // Build the base/id for a transition + let c = 0; + let key = transition.id; + let span: any = amr.semantics?.span; + while (c < MAX_DEPTH) { + c++; + // eslint-disable-next-line + key = span[0].map.find((d: any) => d[0] === key)[1]; + span = span[0].system.semantics.span; + if (!span) { + result.base = key; + result.id = transition.id; + break; + } + } + results.push(result); + } + return results; +}; + +// Extract a single layer for Catlab +export const extractNestedMap = (amr: Model) => { + const nestedMap = amr.semantics?.span?.[0].map.reduce((childMap: any, [stratNode, baseNode]) => { + if (!childMap[baseNode]) { + childMap[baseNode] = []; + } + childMap[baseNode].push(stratNode); + return childMap; + }, {}); + return nestedMap; +}; + +/** + * Given an CAT AMR, extract and compute a presentation-layer data format. + */ +export const getAMRPresentationData = (amr: Model) => ({ + compactModel: getBaseAMR(amr), + stateMatrixData: getCatlabStatesMatrixData(amr), + transitionMatrixData: getCatlabTransitionsMatrixData(amr) +}); diff --git a/packages/client/hmi-client/src/page/project/components/code-editor.vue b/packages/client/hmi-client/src/page/project/components/code-editor.vue index 2211edfcdd..f73b322f54 100644 --- a/packages/client/hmi-client/src/page/project/components/code-editor.vue +++ b/packages/client/hmi-client/src/page/project/components/code-editor.vue @@ -1,5 +1,5 @@