Index (jaxrs-container-core 9.4.0 API)

A B C D E F G H I J K L M N O P R S T U V W X
All Classes and Interfaces|All Packages|Constant Field Values|Serialized Form

A

AbstractDependency - Class in org.veupathdb.lib.container.jaxrs.health
AbstractDependency(String) - Constructor for class org.veupathdb.lib.container.jaxrs.health.AbstractDependency
accountDatabase() - Static method in class org.veupathdb.lib.container.jaxrs.utils.db.DbManager: Gets the current account database connection or throws an exception if the connection has not yet been established.
additionalInfo - Variable in class org.veupathdb.lib.container.jaxrs.health.Dependency.TestResult
ADMIN_TOKEN_HEADER - Static variable in class org.veupathdb.lib.container.jaxrs.utils.RequestKeys
adminOverride() - Element in annotation interface org.veupathdb.lib.container.jaxrs.server.annotations.Authenticated: Applies an override option to this resource.
AdminRequired - Annotation Interface in org.veupathdb.lib.container.jaxrs.server.annotations: Annotation that flags a resource as requiring an admin token value before processing.
ALLOW_ALWAYS - Enum constant in enum class org.veupathdb.lib.container.jaxrs.server.annotations.Authenticated.AdminOverrideOption: allow access only if admin token is present; proxied user discovery will be attempted via proxied-user-id header/query-param but resource will be visited with an empty user if missing
ALLOW_WITH_USER - Enum constant in enum class org.veupathdb.lib.container.jaxrs.server.annotations.Authenticated.AdminOverrideOption: allow access only if admin token is present and valid and proxied-user-id header/query-param is present
allowGuests() - Element in annotation interface org.veupathdb.lib.container.jaxrs.server.annotations.Authenticated: Whether to allow guest users to access this resource.
AnnotationUtil - Class in org.veupathdb.lib.container.jaxrs.utils
AnnotationUtil() - Constructor for class org.veupathdb.lib.container.jaxrs.utils.AnnotationUtil
anyIsEmpty(Optional<String>...) - Static method in class org.veupathdb.lib.container.jaxrs.server.middleware.AuthFilter
ApiDocService - Class in org.veupathdb.lib.container.jaxrs.server.controller
ApiDocService() - Constructor for class org.veupathdb.lib.container.jaxrs.server.controller.ApiDocService
applicationDatabase() - Static method in class org.veupathdb.lib.container.jaxrs.utils.db.DbManager: Gets the current application database connection or throws an exception if the connection has not yet been established.
aroundWriteTo(WriterInterceptorContext) - Method in class org.veupathdb.lib.container.jaxrs.server.middleware.PrometheusFilter
aroundWriteTo(WriterInterceptorContext) - Method in class org.veupathdb.lib.container.jaxrs.server.middleware.RequestIdFilter
Authenticated - Annotation Interface in org.veupathdb.lib.container.jaxrs.server.annotations: Annotation that flags a resource as requiring valid user authentication to execute.
Authenticated.AdminOverrideOption - Enum Class in org.veupathdb.lib.container.jaxrs.server.annotations
AuthFilter - Class in org.veupathdb.lib.container.jaxrs.server.middleware: Provides client authentication checks for resource classes or methods annotated with @Authenticated.
AuthFilter(Options) - Constructor for class org.veupathdb.lib.container.jaxrs.server.middleware.AuthFilter
authRequirementsCache - Variable in class org.veupathdb.lib.container.jaxrs.server.middleware.AuthFilter: Cache of resource references to AuthInfo details describing the auth requirements and allowances of specific resources.

B

BAD_METHOD - Enum constant in enum class org.veupathdb.lib.container.jaxrs.view.error.ErrorStatus
BAD_REQUEST - Enum constant in enum class org.veupathdb.lib.container.jaxrs.view.error.ErrorStatus
BadContentTypeError - Class in org.veupathdb.lib.container.jaxrs.view.error
BadContentTypeError() - Constructor for class org.veupathdb.lib.container.jaxrs.view.error.BadContentTypeError
BadContentTypeError(String) - Constructor for class org.veupathdb.lib.container.jaxrs.view.error.BadContentTypeError
BadContentTypeError(Throwable) - Constructor for class org.veupathdb.lib.container.jaxrs.view.error.BadContentTypeError
BadMethodError - Class in org.veupathdb.lib.container.jaxrs.view.error
BadMethodError() - Constructor for class org.veupathdb.lib.container.jaxrs.view.error.BadMethodError
BadMethodError(String) - Constructor for class org.veupathdb.lib.container.jaxrs.view.error.BadMethodError
BadMethodError(Throwable) - Constructor for class org.veupathdb.lib.container.jaxrs.view.error.BadMethodError
BadRequestError - Class in org.veupathdb.lib.container.jaxrs.view.error
BadRequestError() - Constructor for class org.veupathdb.lib.container.jaxrs.view.error.BadRequestError
BadRequestError(String) - Constructor for class org.veupathdb.lib.container.jaxrs.view.error.BadRequestError
BadRequestError(Throwable) - Constructor for class org.veupathdb.lib.container.jaxrs.view.error.BadRequestError
baseDn() - Method in class org.veupathdb.lib.container.jaxrs.utils.ldap.OracleLDAPConfig
BEARER_TOKEN_HEADER - Static variable in class org.veupathdb.lib.container.jaxrs.utils.RequestKeys
BEARER_TOKEN_QUERY_PARAM - Static variable in class org.veupathdb.lib.container.jaxrs.utils.RequestKeys

C

clear() - Static method in class org.veupathdb.lib.container.jaxrs.utils.logging.LoggingVars
Cli - Class in org.veupathdb.lib.container.jaxrs.utils
close() - Method in class org.veupathdb.lib.container.jaxrs.health.DatabaseDependency
close() - Method in class org.veupathdb.lib.container.jaxrs.health.FgpDatabaseDependency
close() - Method in class org.veupathdb.lib.container.jaxrs.health.ServiceDependency
close() - Method in class org.veupathdb.lib.container.jaxrs.utils.db.DatabaseInstance
closeAndRemove(String) - Method in class org.veupathdb.lib.container.jaxrs.providers.DependencyProvider: Removes and closes the dependency with the given name.
CONFLICT - Enum constant in enum class org.veupathdb.lib.container.jaxrs.view.error.ErrorStatus
ConflictError - Class in org.veupathdb.lib.container.jaxrs.view.error
ConflictError() - Constructor for class org.veupathdb.lib.container.jaxrs.view.error.ConflictError
ConflictError(String) - Constructor for class org.veupathdb.lib.container.jaxrs.view.error.ConflictError
ConflictError(Throwable) - Constructor for class org.veupathdb.lib.container.jaxrs.view.error.ConflictError
ConnectionDetails - Interface in org.veupathdb.lib.container.jaxrs.utils.db
ContainerResources - Class in org.veupathdb.lib.container.jaxrs.server: Container Meta Resources
ContainerResources(Options) - Constructor for class org.veupathdb.lib.container.jaxrs.server.ContainerResources
CONTEXT_ID - Static variable in class org.veupathdb.lib.container.jaxrs.Globals
CorsFilter - Class in org.veupathdb.lib.container.jaxrs.server.middleware: CORS Header Filter
CorsFilter() - Constructor for class org.veupathdb.lib.container.jaxrs.server.middleware.CorsFilter
currentThreadCount() - Static method in class org.veupathdb.lib.container.jaxrs.utils.Threads
CUSTOM_HEADERS_KEY - Static variable in class org.veupathdb.lib.container.jaxrs.server.middleware.CustomResponseHeadersFilter: Attribute service classes should fill on the ContainerRequestContext to set custom headers on the response.
CustomResponseHeadersFilter - Class in org.veupathdb.lib.container.jaxrs.server.middleware: Provides a mechanism for services classes that implement generated service interfaces (via RAML) to set response headers.
CustomResponseHeadersFilter() - Constructor for class org.veupathdb.lib.container.jaxrs.server.middleware.CustomResponseHeadersFilter

D

DatabaseDependency - Class in org.veupathdb.lib.container.jaxrs.health
DatabaseDependency(String, String, int, DataSource) - Constructor for class org.veupathdb.lib.container.jaxrs.health.DatabaseDependency
DatabaseInstance - Class in org.veupathdb.lib.container.jaxrs.utils.db
DatabaseInstance(ConnectionPoolConfig, String) - Constructor for class org.veupathdb.lib.container.jaxrs.utils.db.DatabaseInstance
DB_ACCOUNT_SCHEMA - Static variable in class org.veupathdb.lib.container.jaxrs.Globals
DbManager - Class in org.veupathdb.lib.container.jaxrs.utils.db: Database Manager.
dbName() - Method in interface org.veupathdb.lib.container.jaxrs.utils.db.ConnectionDetails: Returns the name of the database.
dbName() - Method in class org.veupathdb.lib.container.jaxrs.utils.db.OracleConnectionDetails
dbName() - Method in class org.veupathdb.lib.container.jaxrs.utils.db.PostgresConnectionDetails
dbName(String) - Method in class org.veupathdb.lib.container.jaxrs.utils.db.OracleConnectionDetails
dbName(String) - Method in class org.veupathdb.lib.container.jaxrs.utils.db.PostgresConnectionDetails
DbOptions - Interface in org.veupathdb.lib.container.jaxrs.config
DbOptionsImpl - Class in org.veupathdb.lib.container.jaxrs.config
DbOptionsImpl(String, String, Integer, String, String, String, SupportedPlatform, Integer, String) - Constructor for class org.veupathdb.lib.container.jaxrs.config.DbOptionsImpl
DBPrometheus - Class in org.veupathdb.lib.container.jaxrs.utils.db
DBPrometheus() - Constructor for class org.veupathdb.lib.container.jaxrs.utils.db.DBPrometheus
dependencies() - Method in class org.veupathdb.lib.container.jaxrs.server.Server: Extension point for registering external dependencies.
dependency - Variable in class org.veupathdb.lib.container.jaxrs.health.Dependency.TestResult
Dependency - Interface in org.veupathdb.lib.container.jaxrs.health: Service Dependency
Dependency.Status - Enum Class in org.veupathdb.lib.container.jaxrs.health
Dependency.TestResult - Class in org.veupathdb.lib.container.jaxrs.health
DependencyHealth - Class in org.veupathdb.lib.container.jaxrs.view.health
DependencyHealth(Dependency.TestResult) - Constructor for class org.veupathdb.lib.container.jaxrs.view.health.DependencyHealth
DependencyProvider - Class in org.veupathdb.lib.container.jaxrs.providers
DependencySource - Interface in org.veupathdb.lib.container.jaxrs.health: Defines a mechanism for supplying extra or ephemeral dependencies that cannot or should not be registered as a permanent dependency.
DisableJackson - Annotation Interface in org.veupathdb.lib.container.jaxrs.server.annotations: Annotation that marks a resource method as not to be serialized by Jackson.
DISALLOW - Enum constant in enum class org.veupathdb.lib.container.jaxrs.server.annotations.Authenticated.AdminOverrideOption: (default if missing) admin is irrelevant
displayName() - Method in interface org.veupathdb.lib.container.jaxrs.config.DbOptions: Returns the display name for the database connection details.
displayName() - Method in class org.veupathdb.lib.container.jaxrs.config.DbOptionsImpl
doFilter(ContainerRequestContext, Request) - Method in class org.veupathdb.lib.container.jaxrs.server.middleware.RequestIdFilter
DuplicateDependencyException - Exception Class in org.veupathdb.lib.container.jaxrs.errors
DuplicateDependencyException(String) - Constructor for exception class org.veupathdb.lib.container.jaxrs.errors.DuplicateDependencyException

E

enableAccountDB() - Method in class org.veupathdb.lib.container.jaxrs.server.Server: Enables access to the account database.
enableApplicationDB() - Method in class org.veupathdb.lib.container.jaxrs.server.Server: Enables access to the application database.
enableAuth() - Method in class org.veupathdb.lib.container.jaxrs.server.ContainerResources: Enable OAuth authentication checks for annotated resources.
enableCors() - Method in class org.veupathdb.lib.container.jaxrs.server.ContainerResources: Enable cross-origin request allowance headers.
enableJerseyTrace() - Method in class org.veupathdb.lib.container.jaxrs.server.ContainerResources: Enable Jersey trace response headers.
enableUserDB() - Method in class org.veupathdb.lib.container.jaxrs.server.Server: Enables access to the user database.
enableUserQuerying() - Method in class org.veupathdb.lib.container.jaxrs.server.Server: Enables querying of users' data on the OAuth server by either user IDs or by user emails.
err400BadRequest(String) - Method in class org.veupathdb.lib.container.jaxrs.server.middleware.AuthFilter
err401Unauthorized(String) - Method in class org.veupathdb.lib.container.jaxrs.server.middleware.AuthFilter
err403Forbidden(String) - Method in class org.veupathdb.lib.container.jaxrs.server.middleware.AuthFilter
err500Internal(String, Exception) - Method in class org.veupathdb.lib.container.jaxrs.server.middleware.AuthFilter
ErrorMapper - Class in org.veupathdb.lib.container.jaxrs.server.middleware
ErrorMapper() - Constructor for class org.veupathdb.lib.container.jaxrs.server.middleware.ErrorMapper
ErrorResponse - Class in org.veupathdb.lib.container.jaxrs.view.error
ErrorResponse(ErrorStatus) - Constructor for class org.veupathdb.lib.container.jaxrs.view.error.ErrorResponse
Errors(List<String>, Map<String, List<String>>) - Constructor for class org.veupathdb.lib.container.jaxrs.view.error.InvalidInputError.Errors
ErrorStatus - Enum Class in org.veupathdb.lib.container.jaxrs.view.error
ExternalDependency - Class in org.veupathdb.lib.container.jaxrs.health
ExternalDependency(String) - Constructor for class org.veupathdb.lib.container.jaxrs.health.ExternalDependency

F

FAILED_DEPENDENCY - Enum constant in enum class org.veupathdb.lib.container.jaxrs.view.error.ErrorStatus
FailedDependencyError - Class in org.veupathdb.lib.container.jaxrs.view.error
FailedDependencyError(String, String) - Constructor for class org.veupathdb.lib.container.jaxrs.view.error.FailedDependencyError
FailedDependencyError(String, Throwable) - Constructor for class org.veupathdb.lib.container.jaxrs.view.error.FailedDependencyError
FailedDependencyError(Throwable) - Constructor for class org.veupathdb.lib.container.jaxrs.view.error.FailedDependencyError
FailedDependencyException - Exception Class in org.veupathdb.lib.container.jaxrs.errors
FailedDependencyException(String, String) - Constructor for exception class org.veupathdb.lib.container.jaxrs.errors.FailedDependencyException
FailedDependencyException(String, String, Throwable) - Constructor for exception class org.veupathdb.lib.container.jaxrs.errors.FailedDependencyException
FgpDatabaseDependency - Class in org.veupathdb.lib.container.jaxrs.health: Database Dependency
FgpDatabaseDependency(String, String, int, DatabaseInstance) - Constructor for class org.veupathdb.lib.container.jaxrs.health.FgpDatabaseDependency
filter(ContainerRequestContext) - Method in class org.veupathdb.lib.container.jaxrs.server.middleware.AuthFilter
filter(ContainerRequestContext) - Method in class org.veupathdb.lib.container.jaxrs.server.middleware.PrometheusFilter
filter(ContainerRequestContext) - Method in class org.veupathdb.lib.container.jaxrs.server.middleware.RequestIdFilter
filter(ContainerRequestContext, ContainerResponseContext) - Method in class org.veupathdb.lib.container.jaxrs.server.middleware.CorsFilter
filter(ContainerRequestContext, ContainerResponseContext) - Method in class org.veupathdb.lib.container.jaxrs.server.middleware.CustomResponseHeadersFilter
filter(ContainerRequestContext, ContainerResponseContext) - Method in class org.veupathdb.lib.container.jaxrs.server.middleware.PrometheusFilter
filter(ContainerRequestContext, ContainerResponseContext) - Method in class org.veupathdb.lib.container.jaxrs.server.middleware.RequestIdFilter
findResourceAnnotation(ResourceInfo, Class<T>) - Static method in class org.veupathdb.lib.container.jaxrs.utils.AnnotationUtil
findSubmittedValue(ContainerRequestContext, String) - Method in class org.veupathdb.lib.container.jaxrs.server.middleware.AuthFilter
firstGroup(Matcher) - Static method in class org.veupathdb.lib.container.jaxrs.utils.Patterns
firstGroup(Pattern, String) - Static method in class org.veupathdb.lib.container.jaxrs.utils.Patterns
FORBIDDEN - Enum constant in enum class org.veupathdb.lib.container.jaxrs.view.error.ErrorStatus
ForbiddenError - Class in org.veupathdb.lib.container.jaxrs.view.error
ForbiddenError() - Constructor for class org.veupathdb.lib.container.jaxrs.view.error.ForbiddenError
ForbiddenError(String) - Constructor for class org.veupathdb.lib.container.jaxrs.view.error.ForbiddenError
ForbiddenError(Throwable) - Constructor for class org.veupathdb.lib.container.jaxrs.view.error.ForbiddenError
format(LogEvent, StringBuilder) - Method in class org.veupathdb.lib.container.jaxrs.utils.logging.RequestDurationPatternConverter
fromOptions(DbOptions) - Static method in interface org.veupathdb.lib.container.jaxrs.utils.db.ConnectionDetails: Returns a ConnectionDetails instance from the input options.
fromOptions(DbOptions) - Static method in class org.veupathdb.lib.container.jaxrs.utils.db.OracleConnectionDetails
fromOptions(DbOptions) - Static method in class org.veupathdb.lib.container.jaxrs.utils.db.PostgresConnectionDetails

G

getAccountDatabase() - Method in class org.veupathdb.lib.container.jaxrs.utils.db.DbManager: Gets the current account database connection or throws an exception if the connection has not yet been established.
getAcctDbOpts() - Method in class org.veupathdb.lib.container.jaxrs.config.Options
getAdminAuthToken() - Method in class org.veupathdb.lib.container.jaxrs.config.Options
getApi() - Method in class org.veupathdb.lib.container.jaxrs.server.controller.ApiDocService
getAppDbOpts() - Method in class org.veupathdb.lib.container.jaxrs.config.Options
getApplicationDatabase() - Method in class org.veupathdb.lib.container.jaxrs.utils.db.DbManager: Gets the current application database connection or throws an exception if the connection has not yet been established.
getAuthenticationTokenValue() - Method in interface org.veupathdb.lib.container.jaxrs.model.User
getByKey() - Method in exception class org.veupathdb.lib.container.jaxrs.errors.UnprocessableEntityException
getByKey() - Method in class org.veupathdb.lib.container.jaxrs.view.error.InvalidInputError.Errors
getCorsEnabled() - Method in class org.veupathdb.lib.container.jaxrs.config.Options
getCurrentThreadCount() - Method in class org.veupathdb.lib.container.jaxrs.utils.Threads: Get the total current active thread count.
getDependencies() - Method in class org.veupathdb.lib.container.jaxrs.view.health.ServiceHealth
getDependency() - Method in exception class org.veupathdb.lib.container.jaxrs.errors.FailedDependencyException
getDependency() - Method in class org.veupathdb.lib.container.jaxrs.view.error.FailedDependencyError
getErrors() - Method in class org.veupathdb.lib.container.jaxrs.view.error.InvalidInputError
getExtraFields() - Method in class org.veupathdb.lib.container.jaxrs.view.health.DependencyHealth
getGeneral() - Method in exception class org.veupathdb.lib.container.jaxrs.errors.UnprocessableEntityException
getGeneral() - Method in class org.veupathdb.lib.container.jaxrs.view.error.InvalidInputError.Errors
getGrizzlyServer() - Method in class org.veupathdb.lib.container.jaxrs.server.Server
getHealth() - Method in class org.veupathdb.lib.container.jaxrs.server.controller.HealthController
getInfo() - Method in class org.veupathdb.lib.container.jaxrs.view.health.ServiceHealth
getInstance() - Static method in class org.veupathdb.lib.container.jaxrs.providers.DependencyProvider
getInstance() - Static method in class org.veupathdb.lib.container.jaxrs.providers.LogProvider
getInstance() - Static method in class org.veupathdb.lib.container.jaxrs.providers.RuntimeProvider
getInstance() - Static method in class org.veupathdb.lib.container.jaxrs.server.Server
getInstance() - Static method in class org.veupathdb.lib.container.jaxrs.utils.db.DbManager
getInstance() - Static method in class org.veupathdb.lib.container.jaxrs.utils.ldap.OracleLDAPConfig
getInstance() - Static method in class org.veupathdb.lib.container.jaxrs.utils.Threads
getKeyStoreFile() - Method in class org.veupathdb.lib.container.jaxrs.config.Options
getKeyStorePassPhrase() - Method in class org.veupathdb.lib.container.jaxrs.config.Options
getLdapServers() - Method in class org.veupathdb.lib.container.jaxrs.config.Options
getLogger(Class<?>) - Method in class org.veupathdb.lib.container.jaxrs.providers.LogProvider
getLogger(String) - Method in class org.veupathdb.lib.container.jaxrs.providers.LogProvider
getMessage() - Method in class org.veupathdb.lib.container.jaxrs.view.error.ErrorResponse
getMetrics() - Method in class org.veupathdb.lib.container.jaxrs.server.controller.MetricsService
getName() - Method in class org.veupathdb.lib.container.jaxrs.health.AbstractDependency
getName() - Method in interface org.veupathdb.lib.container.jaxrs.health.Dependency: Get the unique name of this dependency
getName() - Method in class org.veupathdb.lib.container.jaxrs.view.health.DependencyHealth
getOAuthClient() - Static method in class org.veupathdb.lib.container.jaxrs.providers.OAuthProvider
getOAuthClientId() - Method in class org.veupathdb.lib.container.jaxrs.config.Options
getOAuthClientSecret() - Method in class org.veupathdb.lib.container.jaxrs.config.Options
getOAuthConfig() - Static method in class org.veupathdb.lib.container.jaxrs.providers.OAuthProvider
getOAuthUrl() - Method in class org.veupathdb.lib.container.jaxrs.config.Options
getOAuthUrl() - Static method in class org.veupathdb.lib.container.jaxrs.providers.OAuthProvider
getOptions() - Static method in class org.veupathdb.lib.container.jaxrs.providers.OptionsProvider
getOracleBaseDn() - Method in class org.veupathdb.lib.container.jaxrs.config.Options
getOrCreateOptions() - Method in class org.veupathdb.lib.container.jaxrs.providers.OptionsProvider
getPort() - Method in class org.veupathdb.lib.container.jaxrs.health.ServiceDependency
getRequestDuration(Object) - Static method in class org.veupathdb.lib.container.jaxrs.utils.logging.RequestDurationPatternConverter: Converts the object passed to a String first, then tries to convert to a Long for comparison against the current system time (millisecs) in order to calculate the duration from a start time to now.
getRequestId() - Method in class org.veupathdb.lib.container.jaxrs.view.error.ServerError
getRequestId(Request) - Static method in class org.veupathdb.lib.container.jaxrs.providers.RequestIdProvider
getRuntime() - Method in class org.veupathdb.lib.container.jaxrs.providers.RuntimeProvider
getServerPort() - Method in class org.veupathdb.lib.container.jaxrs.config.Options
getStatus() - Method in class org.veupathdb.lib.container.jaxrs.view.error.ErrorResponse
getStatus() - Method in class org.veupathdb.lib.container.jaxrs.view.health.DependencyHealth
getStatus() - Method in class org.veupathdb.lib.container.jaxrs.view.health.ServiceHealth
getSubmittedAuth(ContainerRequest) - Static method in class org.veupathdb.lib.container.jaxrs.providers.UserProvider
getThreads() - Method in class org.veupathdb.lib.container.jaxrs.view.health.ServiceInfo
getUptime() - Method in class org.veupathdb.lib.container.jaxrs.view.health.ServiceInfo
getUptimeMillis() - Method in class org.veupathdb.lib.container.jaxrs.view.health.ServiceInfo
getUrl() - Method in class org.veupathdb.lib.container.jaxrs.health.ServiceDependency
getUserDatabase() - Method in class org.veupathdb.lib.container.jaxrs.utils.db.DbManager: Gets the current user database connection or throws an exception if the connection has not yet been established.
getUserDbOpts() - Method in class org.veupathdb.lib.container.jaxrs.config.Options
getUserDbSchema() - Method in class org.veupathdb.lib.container.jaxrs.config.Options: Retrieves either the configured user schema or the default value userlogins5 if none was configured.
getUsersByEmail(Collection<String>) - Static method in class org.veupathdb.lib.container.jaxrs.providers.UserProvider
getUsersById(Collection<Long>) - Static method in class org.veupathdb.lib.container.jaxrs.providers.UserProvider
Globals - Class in org.veupathdb.lib.container.jaxrs
GONE - Enum constant in enum class org.veupathdb.lib.container.jaxrs.view.error.ErrorStatus
GoneError - Class in org.veupathdb.lib.container.jaxrs.view.error
GoneError() - Constructor for class org.veupathdb.lib.container.jaxrs.view.error.GoneError
GoneError(String) - Constructor for class org.veupathdb.lib.container.jaxrs.view.error.GoneError
GoneError(Throwable) - Constructor for class org.veupathdb.lib.container.jaxrs.view.error.GoneError
group(int, Matcher) - Static method in class org.veupathdb.lib.container.jaxrs.utils.Patterns
group(int, Pattern, String) - Static method in class org.veupathdb.lib.container.jaxrs.utils.Patterns

H

has(String) - Method in class org.veupathdb.lib.container.jaxrs.providers.DependencyProvider: Returns whether there is a dependency registered with the given name.
hasAccountDatabase() - Static method in class org.veupathdb.lib.container.jaxrs.utils.db.DbManager
hasApplicationDatabase() - Static method in class org.veupathdb.lib.container.jaxrs.utils.db.DbManager
hasUserDatabase() - Static method in class org.veupathdb.lib.container.jaxrs.utils.db.DbManager
HealthController - Class in org.veupathdb.lib.container.jaxrs.server.controller
HealthController() - Constructor for class org.veupathdb.lib.container.jaxrs.server.controller.HealthController
HEALTHY - Enum constant in enum class org.veupathdb.lib.container.jaxrs.health.ServerStatus
host() - Method in interface org.veupathdb.lib.container.jaxrs.config.DbOptions: Returns an option of a host name for a database server.
host() - Method in class org.veupathdb.lib.container.jaxrs.config.DbOptionsImpl
host() - Method in interface org.veupathdb.lib.container.jaxrs.utils.db.ConnectionDetails: Returns the host address for the connection.
host() - Method in class org.veupathdb.lib.container.jaxrs.utils.db.OracleConnectionDetails
host() - Method in class org.veupathdb.lib.container.jaxrs.utils.db.PostgresConnectionDetails
host(String) - Method in class org.veupathdb.lib.container.jaxrs.utils.db.OracleConnectionDetails
host(String) - Method in class org.veupathdb.lib.container.jaxrs.utils.db.PostgresConnectionDetails
hosts() - Method in class org.veupathdb.lib.container.jaxrs.utils.ldap.OracleLDAPConfig

I

initAccountDatabase(Options) - Static method in class org.veupathdb.lib.container.jaxrs.utils.db.DbManager: Initialize a connection wrapper to the user account database.
initApplicationDatabase(Options) - Static method in class org.veupathdb.lib.container.jaxrs.utils.db.DbManager: Initialize a connection wrapper to the user account database.
InitFailedException - Exception Class in org.veupathdb.lib.container.jaxrs.errors
InitFailedException(Throwable) - Constructor for exception class org.veupathdb.lib.container.jaxrs.errors.InitFailedException
initialize() - Static method in class org.veupathdb.lib.container.jaxrs.utils.logging.Log: Routes all logging through Log4J2 and applies the configuration from resources.
initialize(Options) - Static method in class org.veupathdb.lib.container.jaxrs.utils.ldap.OracleLDAPConfig
initUserDatabase(Options) - Static method in class org.veupathdb.lib.container.jaxrs.utils.db.DbManager: Initialize a connection wrapper to the user account database.
INTERNAL_ERROR_COUNT - Static variable in class org.veupathdb.lib.container.jaxrs.server.middleware.ErrorMapper
InvalidConfigException - Exception Class in org.veupathdb.lib.container.jaxrs.config
InvalidConfigException(String) - Constructor for exception class org.veupathdb.lib.container.jaxrs.config.InvalidConfigException
InvalidInputError - Class in org.veupathdb.lib.container.jaxrs.view.error
InvalidInputError() - Constructor for class org.veupathdb.lib.container.jaxrs.view.error.InvalidInputError
InvalidInputError(String) - Constructor for class org.veupathdb.lib.container.jaxrs.view.error.InvalidInputError
InvalidInputError(Throwable) - Constructor for class org.veupathdb.lib.container.jaxrs.view.error.InvalidInputError
InvalidInputError.Errors - Class in org.veupathdb.lib.container.jaxrs.view.error
isClosed() - Method in class org.veupathdb.lib.container.jaxrs.utils.db.DatabaseInstance
isReachable() - Method in class org.veupathdb.lib.container.jaxrs.view.health.DependencyHealth
isReachable(String, int) - Method in class org.veupathdb.lib.container.jaxrs.utils.net.Pinger
isReadable(Class<?>, Type, Annotation[], MediaType) - Method in class org.veupathdb.lib.container.jaxrs.server.middleware.JacksonFilter
isWriteable(Class<?>, Type, Annotation[], MediaType) - Method in class org.veupathdb.lib.container.jaxrs.server.middleware.JacksonFilter

J

JacksonFilter - Class in org.veupathdb.lib.container.jaxrs.server.middleware: Jackson JSON (De)Serialization Filter
JacksonFilter() - Constructor for class org.veupathdb.lib.container.jaxrs.server.middleware.JacksonFilter
JSON_KEY_BY_KEY - Static variable in class org.veupathdb.lib.container.jaxrs.view.error.InvalidInputError.Errors
JSON_KEY_DEPENDENCY - Static variable in class org.veupathdb.lib.container.jaxrs.view.error.FailedDependencyError
JSON_KEY_ERRORS - Static variable in class org.veupathdb.lib.container.jaxrs.view.error.InvalidInputError
JSON_KEY_GENERAL - Static variable in class org.veupathdb.lib.container.jaxrs.view.error.InvalidInputError.Errors
JSON_KEY_MESSAGE - Static variable in class org.veupathdb.lib.container.jaxrs.view.error.ErrorResponse
JSON_KEY_REQUEST_ID - Static variable in class org.veupathdb.lib.container.jaxrs.view.error.ServerError
JSON_KEY_STATUS - Static variable in class org.veupathdb.lib.container.jaxrs.view.error.ErrorResponse

K

keyedSingle(String, String) - Static method in exception class org.veupathdb.lib.container.jaxrs.errors.UnprocessableEntityException: Keyed Single returns a new UnprocessableEntityException with a single error key mapped to a single error message.
keyedSingles(String, String, String, String) - Static method in exception class org.veupathdb.lib.container.jaxrs.errors.UnprocessableEntityException: Keyed singles returns a new UnprocessableEntityException with two error keys, each mapped to a single error message.
keyedSingles(String, String, String, String, String, String) - Static method in exception class org.veupathdb.lib.container.jaxrs.errors.UnprocessableEntityException: Keyed singles returns a new UnprocessableEntityException with three error keys, each mapped to a single error message.

L

LDAP - Class in org.veupathdb.lib.container.jaxrs.utils.ldap
LDAP() - Constructor for class org.veupathdb.lib.container.jaxrs.utils.ldap.LDAP
Log - Class in org.veupathdb.lib.container.jaxrs.utils.logging
Log() - Constructor for class org.veupathdb.lib.container.jaxrs.utils.logging.Log
logger - Variable in class org.veupathdb.lib.container.jaxrs.server.middleware.AuthFilter
logger(Class<?>) - Static method in class org.veupathdb.lib.container.jaxrs.providers.LogProvider
logger(String) - Static method in class org.veupathdb.lib.container.jaxrs.providers.LogProvider
LoggingVars - Class in org.veupathdb.lib.container.jaxrs.utils.logging: Centralizes the assigning of log line vars (referenced in log4j2.yml patterns)
LoggingVars() - Constructor for class org.veupathdb.lib.container.jaxrs.utils.logging.LoggingVars
LogProvider - Class in org.veupathdb.lib.container.jaxrs.providers: Mockable Wrapper for SLF4J's LoggerFactory.
lookup(String) - Method in class org.veupathdb.lib.container.jaxrs.providers.DependencyProvider: Attempts to fetch a dependency by name.
lookupUser(ContainerRequest) - Static method in class org.veupathdb.lib.container.jaxrs.providers.UserProvider

M

MetricsService - Class in org.veupathdb.lib.container.jaxrs.server.controller
MetricsService() - Constructor for class org.veupathdb.lib.container.jaxrs.server.controller.MetricsService
missingPropErr(DbOptions) - Static method in class org.veupathdb.lib.container.jaxrs.utils.db.OracleConnectionDetails
missingPropErr(DbOptions) - Static method in class org.veupathdb.lib.container.jaxrs.utils.db.PostgresConnectionDetails

N

name - Variable in class org.veupathdb.lib.container.jaxrs.health.AbstractDependency
name() - Method in interface org.veupathdb.lib.container.jaxrs.config.DbOptions: Returns an option of a name of a database to connect to.
name() - Method in class org.veupathdb.lib.container.jaxrs.config.DbOptionsImpl
newAccountDatabase(Options) - Method in class org.veupathdb.lib.container.jaxrs.utils.db.DbManager
newApplicationDatabase(Options) - Method in class org.veupathdb.lib.container.jaxrs.utils.db.DbManager
newInstance(String[]) - Static method in class org.veupathdb.lib.container.jaxrs.utils.logging.RequestDurationPatternConverter: Obtains an instance of PropertiesPatternConverter.
newOptions() - Method in class org.veupathdb.lib.container.jaxrs.server.Server: Creates a new Options object and returns it.
newResourceConfig(Options) - Method in class org.veupathdb.lib.container.jaxrs.server.Server: Creates a new ContainerResources object which will be used to configure the Grizzly HttpServer.
newUserDatabase(Options) - Method in class org.veupathdb.lib.container.jaxrs.utils.db.DbManager
NOT_FOUND - Enum constant in enum class org.veupathdb.lib.container.jaxrs.view.error.ErrorStatus
NotFoundError - Class in org.veupathdb.lib.container.jaxrs.view.error
NotFoundError() - Constructor for class org.veupathdb.lib.container.jaxrs.view.error.NotFoundError
NotFoundError(String) - Constructor for class org.veupathdb.lib.container.jaxrs.view.error.NotFoundError
NotFoundError(Throwable) - Constructor for class org.veupathdb.lib.container.jaxrs.view.error.NotFoundError

O

OAuthProvider - Class in org.veupathdb.lib.container.jaxrs.providers
OAuthProvider() - Constructor for class org.veupathdb.lib.container.jaxrs.providers.OAuthProvider
OFFLINE - Enum constant in enum class org.veupathdb.lib.container.jaxrs.health.Dependency.Status
ONLINE - Enum constant in enum class org.veupathdb.lib.container.jaxrs.health.Dependency.Status
onShutdown() - Method in class org.veupathdb.lib.container.jaxrs.server.Server: Called on server shutdown to perform any tasks assigned by the overriding subclass.
Options - Class in org.veupathdb.lib.container.jaxrs.config: CLI Options.
Options() - Constructor for class org.veupathdb.lib.container.jaxrs.config.Options
OptionsProvider - Class in org.veupathdb.lib.container.jaxrs.providers
ORA_ATTR - Static variable in class org.veupathdb.lib.container.jaxrs.utils.ldap.LDAP
ORA_CONTEXT - Static variable in class org.veupathdb.lib.container.jaxrs.utils.ldap.LDAP
ORA_CTX_PATTERN - Static variable in class org.veupathdb.lib.container.jaxrs.utils.ldap.LDAP
ORA_FILTER - Static variable in class org.veupathdb.lib.container.jaxrs.utils.ldap.LDAP
OracleConnectionDetails - Class in org.veupathdb.lib.container.jaxrs.utils.db
OracleLDAPConfig - Class in org.veupathdb.lib.container.jaxrs.utils.ldap
OracleLDAPConfig() - Constructor for class org.veupathdb.lib.container.jaxrs.utils.ldap.OracleLDAPConfig
org.veupathdb.lib.container.jaxrs - package org.veupathdb.lib.container.jaxrs
org.veupathdb.lib.container.jaxrs.config - package org.veupathdb.lib.container.jaxrs.config
org.veupathdb.lib.container.jaxrs.errors - package org.veupathdb.lib.container.jaxrs.errors
org.veupathdb.lib.container.jaxrs.health - package org.veupathdb.lib.container.jaxrs.health
org.veupathdb.lib.container.jaxrs.model - package org.veupathdb.lib.container.jaxrs.model
org.veupathdb.lib.container.jaxrs.providers - package org.veupathdb.lib.container.jaxrs.providers
org.veupathdb.lib.container.jaxrs.server - package org.veupathdb.lib.container.jaxrs.server
org.veupathdb.lib.container.jaxrs.server.annotations - package org.veupathdb.lib.container.jaxrs.server.annotations
org.veupathdb.lib.container.jaxrs.server.controller - package org.veupathdb.lib.container.jaxrs.server.controller
org.veupathdb.lib.container.jaxrs.server.middleware - package org.veupathdb.lib.container.jaxrs.server.middleware
org.veupathdb.lib.container.jaxrs.utils - package org.veupathdb.lib.container.jaxrs.utils
org.veupathdb.lib.container.jaxrs.utils.db - package org.veupathdb.lib.container.jaxrs.utils.db
org.veupathdb.lib.container.jaxrs.utils.ldap - package org.veupathdb.lib.container.jaxrs.utils.ldap
org.veupathdb.lib.container.jaxrs.utils.logging - package org.veupathdb.lib.container.jaxrs.utils.logging
org.veupathdb.lib.container.jaxrs.utils.net - package org.veupathdb.lib.container.jaxrs.utils.net
org.veupathdb.lib.container.jaxrs.view.error - package org.veupathdb.lib.container.jaxrs.view.error
org.veupathdb.lib.container.jaxrs.view.health - package org.veupathdb.lib.container.jaxrs.view.health

P

parseCLI(String[], T) - Static method in class org.veupathdb.lib.container.jaxrs.utils.Cli: Parses the given arguments into the given annotated type.
pass() - Method in interface org.veupathdb.lib.container.jaxrs.config.DbOptions: Returns an option of a database credentials password.
pass() - Method in class org.veupathdb.lib.container.jaxrs.config.DbOptionsImpl
pass(String) - Method in class org.veupathdb.lib.container.jaxrs.utils.db.OracleConnectionDetails
pass(String) - Method in class org.veupathdb.lib.container.jaxrs.utils.db.PostgresConnectionDetails
password() - Method in interface org.veupathdb.lib.container.jaxrs.utils.db.ConnectionDetails: Returns the connection credentials password.
password() - Method in class org.veupathdb.lib.container.jaxrs.utils.db.OracleConnectionDetails
password() - Method in class org.veupathdb.lib.container.jaxrs.utils.db.PostgresConnectionDetails
Patterns - Class in org.veupathdb.lib.container.jaxrs.utils
Patterns() - Constructor for class org.veupathdb.lib.container.jaxrs.utils.Patterns
pinger - Variable in class org.veupathdb.lib.container.jaxrs.health.ExternalDependency
Pinger - Class in org.veupathdb.lib.container.jaxrs.utils.net
Pinger() - Constructor for class org.veupathdb.lib.container.jaxrs.utils.net.Pinger
platform() - Method in interface org.veupathdb.lib.container.jaxrs.config.DbOptions: Returns an option of a database platform type.
platform() - Method in class org.veupathdb.lib.container.jaxrs.config.DbOptionsImpl
poolSize() - Method in interface org.veupathdb.lib.container.jaxrs.config.DbOptions: Returns an option of a database connection pool size value.
poolSize() - Method in class org.veupathdb.lib.container.jaxrs.config.DbOptionsImpl
poolSize() - Method in interface org.veupathdb.lib.container.jaxrs.utils.db.ConnectionDetails: Returns the connection pool size for this connection.
poolSize() - Method in class org.veupathdb.lib.container.jaxrs.utils.db.OracleConnectionDetails
poolSize() - Method in class org.veupathdb.lib.container.jaxrs.utils.db.PostgresConnectionDetails
poolSize(int) - Method in class org.veupathdb.lib.container.jaxrs.utils.db.OracleConnectionDetails
poolSize(int) - Method in class org.veupathdb.lib.container.jaxrs.utils.db.PostgresConnectionDetails
port() - Method in interface org.veupathdb.lib.container.jaxrs.config.DbOptions: Returns an option of a port number for a database server.
port() - Method in class org.veupathdb.lib.container.jaxrs.config.DbOptionsImpl
port() - Method in interface org.veupathdb.lib.container.jaxrs.utils.db.ConnectionDetails: Returns the host port for the connection.
port() - Method in class org.veupathdb.lib.container.jaxrs.utils.db.OracleConnectionDetails
port() - Method in class org.veupathdb.lib.container.jaxrs.utils.db.PostgresConnectionDetails
port(int) - Method in class org.veupathdb.lib.container.jaxrs.utils.db.OracleConnectionDetails
port(int) - Method in class org.veupathdb.lib.container.jaxrs.utils.db.PostgresConnectionDetails
postAcctDb() - Method in class org.veupathdb.lib.container.jaxrs.server.Server
postAppDb() - Method in class org.veupathdb.lib.container.jaxrs.server.Server
postCliParse(Options) - Method in class org.veupathdb.lib.container.jaxrs.server.Server: Hook-point for performing tasks after the CLI/Environment configuration has been parsed.
PostgresConnectionDetails - Class in org.veupathdb.lib.container.jaxrs.utils.db
PostgresConnectionDetails(String, int, String, String, String, int) - Constructor for class org.veupathdb.lib.container.jaxrs.utils.db.PostgresConnectionDetails
postStartup() - Method in class org.veupathdb.lib.container.jaxrs.server.Server: Hook-point for performing tasks after the service has started up.
postUserDb() - Method in class org.veupathdb.lib.container.jaxrs.server.Server
PrometheusFilter - Class in org.veupathdb.lib.container.jaxrs.server.middleware: Prometheus Metrics Filter
PrometheusFilter() - Constructor for class org.veupathdb.lib.container.jaxrs.server.middleware.PrometheusFilter
PROXIED_USER_ID_HEADER - Static variable in class org.veupathdb.lib.container.jaxrs.utils.RequestKeys

R

reachable - Variable in class org.veupathdb.lib.container.jaxrs.health.Dependency.TestResult
readFrom(Class<Object>, Type, Annotation[], MediaType, MultivaluedMap<String, String>, InputStream) - Method in class org.veupathdb.lib.container.jaxrs.server.middleware.JacksonFilter
register(String, DatabaseInstance) - Static method in class org.veupathdb.lib.container.jaxrs.utils.db.DBPrometheus
register(Dependency) - Method in class org.veupathdb.lib.container.jaxrs.providers.DependencyProvider: Register a new dependency.
registerDependencySource(DependencySource) - Method in class org.veupathdb.lib.container.jaxrs.providers.DependencyProvider: Registers a source of extra or ephemeral dependencies that should not or cannot be registered normally.
REQUEST_ID - Static variable in class org.veupathdb.lib.container.jaxrs.utils.RequestKeys
REQUEST_USER - Static variable in class org.veupathdb.lib.container.jaxrs.Globals
RequestDurationPatternConverter - Class in org.veupathdb.lib.container.jaxrs.utils.logging: This class is identical to Log4J 2.x's MdcPatternConverter EXCEPT for a change to the format() method where we convert the request start time into a request duration at the time this line is being logged.
RequestIdFilter - Class in org.veupathdb.lib.container.jaxrs.server.middleware: Assigns a unique ID to each request for logging, error tracing purposes.
RequestIdFilter() - Constructor for class org.veupathdb.lib.container.jaxrs.server.middleware.RequestIdFilter
RequestIdProvider - Class in org.veupathdb.lib.container.jaxrs.providers
RequestIdProvider() - Constructor for class org.veupathdb.lib.container.jaxrs.providers.RequestIdProvider
RequestKeys - Class in org.veupathdb.lib.container.jaxrs.utils
requireOracleDetails(String) - Method in class org.veupathdb.lib.container.jaxrs.utils.ldap.LDAP
resolveSingleValue(String, String, String) - Method in class org.veupathdb.lib.container.jaxrs.server.middleware.AuthFilter
resource - Variable in class org.veupathdb.lib.container.jaxrs.server.middleware.AuthFilter
resources() - Method in class org.veupathdb.lib.container.jaxrs.server.ContainerResources: Returns an array of JaxRS endpoints, providers, and contexts.
runtime() - Static method in class org.veupathdb.lib.container.jaxrs.providers.RuntimeProvider
RuntimeProvider - Class in org.veupathdb.lib.container.jaxrs.providers: Mockable wrapper for the Java Runtime class.

S

Server - Class in org.veupathdb.lib.container.jaxrs.server
Server() - Constructor for class org.veupathdb.lib.container.jaxrs.server.Server
SERVER_ERROR - Enum constant in enum class org.veupathdb.lib.container.jaxrs.view.error.ErrorStatus
ServerError - Class in org.veupathdb.lib.container.jaxrs.view.error
ServerError(String) - Constructor for class org.veupathdb.lib.container.jaxrs.view.error.ServerError
ServerError(String, String) - Constructor for class org.veupathdb.lib.container.jaxrs.view.error.ServerError
ServerError(String, Throwable) - Constructor for class org.veupathdb.lib.container.jaxrs.view.error.ServerError
ServerStatus - Enum Class in org.veupathdb.lib.container.jaxrs.health
ServiceDependency - Class in org.veupathdb.lib.container.jaxrs.health: Service Dependency
ServiceDependency(String, String, int) - Constructor for class org.veupathdb.lib.container.jaxrs.health.ServiceDependency
ServiceHealth - Class in org.veupathdb.lib.container.jaxrs.view.health
ServiceHealth() - Constructor for class org.veupathdb.lib.container.jaxrs.view.health.ServiceHealth
ServiceInfo - Class in org.veupathdb.lib.container.jaxrs.view.health
ServiceInfo() - Constructor for class org.veupathdb.lib.container.jaxrs.view.health.ServiceInfo
serviceOptions - Variable in class org.veupathdb.lib.container.jaxrs.server.middleware.AuthFilter
serviceTest() - Method in class org.veupathdb.lib.container.jaxrs.health.ServiceDependency
setDependencies(List<Dependency.TestResult>) - Method in class org.veupathdb.lib.container.jaxrs.view.health.ServiceHealth
setInfo(ServiceInfo) - Method in class org.veupathdb.lib.container.jaxrs.view.health.ServiceHealth
setMessage(String) - Method in class org.veupathdb.lib.container.jaxrs.view.error.ErrorResponse
setNonRequestThreadVars(String) - Static method in class org.veupathdb.lib.container.jaxrs.utils.logging.LoggingVars
setPinger(Pinger) - Method in class org.veupathdb.lib.container.jaxrs.health.ExternalDependency
setProvider(Supplier<Options>) - Static method in class org.veupathdb.lib.container.jaxrs.providers.OptionsProvider
setRequestThreadVars(String, String, String, String) - Static method in class org.veupathdb.lib.container.jaxrs.utils.logging.LoggingVars
setStatus(ServerStatus) - Method in class org.veupathdb.lib.container.jaxrs.view.health.ServiceHealth
setTestQuery(String) - Method in class org.veupathdb.lib.container.jaxrs.health.DatabaseDependency
setTestQuery(String) - Method in class org.veupathdb.lib.container.jaxrs.health.FgpDatabaseDependency
setThreads(int) - Method in class org.veupathdb.lib.container.jaxrs.view.health.ServiceInfo
setUptime(long) - Method in class org.veupathdb.lib.container.jaxrs.view.health.ServiceInfo
shutDown() - Method in class org.veupathdb.lib.container.jaxrs.providers.DependencyProvider: Attempts to shut down all dependencies currently registered.
start(String[]) - Method in class org.veupathdb.lib.container.jaxrs.server.Server: Start up the HTTP server.
status - Variable in class org.veupathdb.lib.container.jaxrs.health.Dependency.TestResult
STATUS_CODE - Static variable in exception class org.veupathdb.lib.container.jaxrs.errors.FailedDependencyException

T

TEAPOT - Enum constant in enum class org.veupathdb.lib.container.jaxrs.view.error.ErrorStatus
test() - Method in class org.veupathdb.lib.container.jaxrs.health.DatabaseDependency
test() - Method in interface org.veupathdb.lib.container.jaxrs.health.Dependency: Test the resource availability
test() - Method in class org.veupathdb.lib.container.jaxrs.health.FgpDatabaseDependency
test() - Method in class org.veupathdb.lib.container.jaxrs.health.ServiceDependency
testDependencies() - Method in class org.veupathdb.lib.container.jaxrs.providers.DependencyProvider: Runs the test method on all currently registered dependencies and returns a map of the test results keyed on dependency name.
TestResult(Dependency, boolean, Dependency.Status) - Constructor for class org.veupathdb.lib.container.jaxrs.health.Dependency.TestResult
TestResult(Dependency, boolean, Dependency.Status, Map<String, Object>) - Constructor for class org.veupathdb.lib.container.jaxrs.health.Dependency.TestResult
Threads - Class in org.veupathdb.lib.container.jaxrs.utils: Utilities for dealing with threads.
tnsName() - Method in interface org.veupathdb.lib.container.jaxrs.config.DbOptions: Returns an option of a TNS Name for an Oracle database.
tnsName() - Method in class org.veupathdb.lib.container.jaxrs.config.DbOptionsImpl
toFgpUtilConfig() - Method in interface org.veupathdb.lib.container.jaxrs.utils.db.ConnectionDetails: Returns an FgpUtil DatabaseInstance configuration based on the current connection details.
toFgpUtilConfig() - Method in class org.veupathdb.lib.container.jaxrs.utils.db.OracleConnectionDetails
toFgpUtilConfig() - Method in class org.veupathdb.lib.container.jaxrs.utils.db.PostgresConnectionDetails
toJdbcString() - Method in interface org.veupathdb.lib.container.jaxrs.utils.db.ConnectionDetails: Returns a JDBC connection string based on the current connection details.
toJdbcString() - Method in class org.veupathdb.lib.container.jaxrs.utils.db.OracleConnectionDetails
toJdbcString() - Method in class org.veupathdb.lib.container.jaxrs.utils.db.PostgresConnectionDetails
toResponse(Throwable) - Method in class org.veupathdb.lib.container.jaxrs.server.middleware.ErrorMapper
toString() - Method in enum class org.veupathdb.lib.container.jaxrs.health.ServerStatus
toString() - Method in enum class org.veupathdb.lib.container.jaxrs.view.error.ErrorStatus
TRACE_ID_HEADER - Static variable in class org.veupathdb.lib.container.jaxrs.Globals
tsName() - Method in class org.veupathdb.lib.container.jaxrs.utils.db.OracleConnectionDetails

U

UNAUTHORIZED - Enum constant in enum class org.veupathdb.lib.container.jaxrs.view.error.ErrorStatus
UnauthorizedError - Class in org.veupathdb.lib.container.jaxrs.view.error
UnauthorizedError() - Constructor for class org.veupathdb.lib.container.jaxrs.view.error.UnauthorizedError
UnauthorizedError(String) - Constructor for class org.veupathdb.lib.container.jaxrs.view.error.UnauthorizedError
UnauthorizedError(Throwable) - Constructor for class org.veupathdb.lib.container.jaxrs.view.error.UnauthorizedError
UNHEALTHY - Enum constant in enum class org.veupathdb.lib.container.jaxrs.health.ServerStatus
UNKNOWN - Enum constant in enum class org.veupathdb.lib.container.jaxrs.health.Dependency.Status
UNPROCESSABLE_ENTITY - Enum constant in enum class org.veupathdb.lib.container.jaxrs.view.error.ErrorStatus
UNPROCESSABLE_ENTITY - Static variable in exception class org.veupathdb.lib.container.jaxrs.errors.UnprocessableEntityException
UnprocessableEntityException - Exception Class in org.veupathdb.lib.container.jaxrs.errors: Extension for the JaxRS exceptions for 422 errors.
UnprocessableEntityException(String) - Constructor for exception class org.veupathdb.lib.container.jaxrs.errors.UnprocessableEntityException
UnprocessableEntityException(String, Throwable) - Constructor for exception class org.veupathdb.lib.container.jaxrs.errors.UnprocessableEntityException
UnprocessableEntityException(Throwable) - Constructor for exception class org.veupathdb.lib.container.jaxrs.errors.UnprocessableEntityException
UnprocessableEntityException(List<String>, Map<String, List<String>>) - Constructor for exception class org.veupathdb.lib.container.jaxrs.errors.UnprocessableEntityException
UnprocessableEntityException(Map<String, List<String>>) - Constructor for exception class org.veupathdb.lib.container.jaxrs.errors.UnprocessableEntityException
UNSUPPORTED_MEDIA - Enum constant in enum class org.veupathdb.lib.container.jaxrs.view.error.ErrorStatus
user() - Method in interface org.veupathdb.lib.container.jaxrs.config.DbOptions: Returns an option of a database credentials username.
user() - Method in class org.veupathdb.lib.container.jaxrs.config.DbOptionsImpl
user() - Method in interface org.veupathdb.lib.container.jaxrs.utils.db.ConnectionDetails: Returns the connection credentials username.
user() - Method in class org.veupathdb.lib.container.jaxrs.utils.db.OracleConnectionDetails
user() - Method in class org.veupathdb.lib.container.jaxrs.utils.db.PostgresConnectionDetails
user(String) - Method in class org.veupathdb.lib.container.jaxrs.utils.db.OracleConnectionDetails
user(String) - Method in class org.veupathdb.lib.container.jaxrs.utils.db.PostgresConnectionDetails
User - Interface in org.veupathdb.lib.container.jaxrs.model: Interface for container core users serves two purposes: 1.
User.UserImpl - Class in org.veupathdb.lib.container.jaxrs.model
userDatabase() - Static method in class org.veupathdb.lib.container.jaxrs.utils.db.DbManager: Gets the current user database connection or throws an exception if the connection has not yet been established.
UserImpl(OAuthClient, String, ValidatedToken) - Constructor for class org.veupathdb.lib.container.jaxrs.model.User.UserImpl
UserInfo - Interface in org.veupathdb.lib.container.jaxrs.model: Interface for container core users serves two purposes: 1.
UserInfo.UserInfoImpl - Class in org.veupathdb.lib.container.jaxrs.model
UserInfoImpl(JSONObject) - Constructor for class org.veupathdb.lib.container.jaxrs.model.UserInfo.UserInfoImpl
UserProvider - Class in org.veupathdb.lib.container.jaxrs.providers
UserProvider() - Constructor for class org.veupathdb.lib.container.jaxrs.providers.UserProvider

V

valueOf(String) - Static method in enum class org.veupathdb.lib.container.jaxrs.health.Dependency.Status: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class org.veupathdb.lib.container.jaxrs.health.ServerStatus: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class org.veupathdb.lib.container.jaxrs.server.annotations.Authenticated.AdminOverrideOption: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class org.veupathdb.lib.container.jaxrs.view.error.ErrorStatus: Returns the enum constant of this class with the specified name.
values() - Static method in enum class org.veupathdb.lib.container.jaxrs.health.Dependency.Status: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class org.veupathdb.lib.container.jaxrs.health.ServerStatus: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class org.veupathdb.lib.container.jaxrs.server.annotations.Authenticated.AdminOverrideOption: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class org.veupathdb.lib.container.jaxrs.view.error.ErrorStatus: Returns an array containing the constants of this enum class, in the order they are declared.

W

writeTo(Object, Class<?>, Type, Annotation[], MediaType, MultivaluedMap<String, Object>, OutputStream) - Method in class org.veupathdb.lib.container.jaxrs.server.middleware.JacksonFilter

X

X_CONTEXT_ID - Static variable in class org.veupathdb.lib.container.jaxrs.Globals

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