Documentation ¶
Index ¶
- Constants
- Variables
- func AbortNonFhirXMLorJSONRequestsMiddleware(c *gin.Context)
- func AbortNonJSONRequestsMiddleware(c *gin.Context)
- func CreateCollections(db *mongo.Database)
- func EnableXmlToJsonConversionMiddleware() gin.HandlerFunc
- func ErrorToOpOutcome(err interface{}) (statusCode int, outcome *models.OperationOutcome)
- func FHIRBind(c *gin.Context, validatorURL string) (resource *models2.Resource, err error)
- func FhirJsFormatConverterJavascript() string
- func ReadOnlyMiddleware(c *gin.Context)
- func RegisterController(name string, e *gin.Engine, m []gin.HandlerFunc, dal DataAccessLayer, ...)
- func RegisterRoutes(e *gin.Engine, config map[string][]gin.HandlerFunc, dal DataAccessLayer, ...)
- func RequestLoggerHandler(c *gin.Context)
- type AfterRoutes
- type BatchController
- type Config
- type CurrentOp
- type CurrentOps
- type CustomFhirRenderer
- type DataAccessLayer
- type DataAccessSession
- type ErrConflict
- type ErrMultipleMatches
- type FHIRServer
- type FhirFormatConverter
- type IndexMap
- type Indexer
- type Interceptor
- type InterceptorHandler
- type InterceptorList
- type Reply
- type ResourceController
- func (rc *ResourceController) ConditionalDeleteHandler(c *gin.Context)
- func (rc *ResourceController) ConditionalUpdateHandler(c *gin.Context)
- func (rc *ResourceController) CreateHandler(c *gin.Context)
- func (rc *ResourceController) DeleteHandler(c *gin.Context)
- func (rc *ResourceController) EverythingHandler(c *gin.Context)
- func (rc *ResourceController) HistoryHandler(c *gin.Context)
- func (rc *ResourceController) IndexHandler(c *gin.Context)
- func (rc *ResourceController) LoadResource(c *gin.Context) (resourceId string, resource *models2.Resource, err error)
- func (rc *ResourceController) ShowHandler(c *gin.Context)
- func (rc *ResourceController) UpdateHandler(c *gin.Context)
Constants ¶
const ( // OK when returned by MongoDB is really a float (0.0 = false, 1.0 = true) OK = float64(1) )
Variables ¶
var DefaultConfig = Config{ ServerURL: "", IndexConfigPath: "config/indexes.conf", DatabaseURI: "mongodb://localhost:27017/?replicaSet=rs0", DatabaseSuffix: "_fhir", DatabaseSocketTimeout: 2 * time.Minute, DatabaseOpTimeout: 90 * time.Second, DatabaseKillOpPeriod: 10 * time.Second, Auth: auth.None(), EnableCISearches: true, EnableHistory: true, EnableXML: true, CountTotalResults: true, ReadOnly: false, Debug: false, }
DefaultConfig is the default server configuration
var ErrDeleted = errors.New("Resource deleted")
ErrDeleted indicates that the resource has been deleted (HTTP 410)
var ErrNotFound = errors.New("Resource Not Found")
ErrNotFound indicates that the resource was not found (HTTP 404)
var ErrOpInterrupted = errors.New("Operation Interrupted")
ErrOpInterrupted indicates that the query was interrupted by a killOp() operation
Functions ¶
func AbortNonFhirXMLorJSONRequestsMiddleware ¶
AbortNonFhirXMLorJSONRequestsMiddleware is middleware that responds to any request that Accepts a Content-Type other than FHIR JSON or XML with a 406 Not Acceptable status.
func AbortNonJSONRequestsMiddleware ¶
AbortNonJSONRequestsMiddleware is middleware that responds to any request that Accepts a Content-Type other than JSON (or a JSON flavor) with a 406 Not Acceptable status.
func CreateCollections ¶
func EnableXmlToJsonConversionMiddleware ¶
func EnableXmlToJsonConversionMiddleware() gin.HandlerFunc
func ErrorToOpOutcome ¶
func ErrorToOpOutcome(err interface{}) (statusCode int, outcome *models.OperationOutcome)
func FhirJsFormatConverterJavascript ¶
func FhirJsFormatConverterJavascript() string
func ReadOnlyMiddleware ¶
ReadOnlyMiddleware makes the API read-only and responds to any requests that are not GET, HEAD, or OPTIONS with a 405 Method Not Allowed error.
func RegisterController ¶
func RegisterController(name string, e *gin.Engine, m []gin.HandlerFunc, dal DataAccessLayer, config Config)
RegisterController registers the CRUD routes (and middleware) for a FHIR resource
func RegisterRoutes ¶
func RegisterRoutes(e *gin.Engine, config map[string][]gin.HandlerFunc, dal DataAccessLayer, serverConfig Config)
RegisterRoutes registers the routes for each of the FHIR resources
func RequestLoggerHandler ¶
RequestLoggerHandler is a handler intended to be used during debugging to log out the request details including the request headers and the request body. This should not be used in production as it has performance implications.
Types ¶
type AfterRoutes ¶
type BatchController ¶
type BatchController struct { DAL DataAccessLayer Config Config }
BatchController handles FHIR batch operations via input bundles
func NewBatchController ¶
func NewBatchController(dal DataAccessLayer, config Config) *BatchController
NewBatchController creates a new BatchController based on the passed in DAL
func (*BatchController) Post ¶
func (b *BatchController) Post(c *gin.Context)
Handles batch and transaction requests
type Config ¶
type Config struct { // ServerURL is the full URL for the root of the server. This may be used // by other middleware to compute redirect URLs ServerURL string // Auth determines what, if any authentication and authorization will be used // by the FHIR server Auth auth.Config // IndexConfigPath is the path to an indexes.conf configuration file, specifying // what mongo indexes the server should create (or verify) on startup IndexConfigPath string // DatabaseURI is the url of the mongo replica set to use for the FHIR database. // A replica set is required for transactions support // e.g. mongodb://db1:27017,db2:27017/?replicaSet=rs1 DatabaseURI string // DatabaseName is the name of the mongo database used for the fhir database by default. // Typically this will be the "fhir". DefaultDatabaseName string // EnableMultiDB allows requests to specify a specific Mongo database instead of the default // e.g. to use test4_fhir http://fhir-server/db/test4_fhir/Patient?name=alex EnableMultiDB bool // All custom database names should end with this suffix (default is "_fhir") DatabaseSuffix string // DatabaseSocketTimeout is the amount of time the mgo driver will wait for a response // from mongo before timing out. DatabaseSocketTimeout time.Duration // DatabaseOpTimeout is the amount of time GoFHIR will wait before killing a long-running // database process. This defaults to a reasonable upper bound for slow, pipelined queries: 30s. DatabaseOpTimeout time.Duration // DatabaseKillOpPeriod is the length of time between scans of the database to kill long-running ops. DatabaseKillOpPeriod time.Duration // CountTotalResults toggles whether the searcher should also get a total // count of the total results of a search. In practice this is a performance hit // for large datasets. CountTotalResults bool // EnableCISearches toggles whether the mongo searches uses regexes to maintain // case-insesitivity when performing searches on string fields, codes, etc. EnableCISearches bool // Whether to support storing previous versions of each resource EnableHistory bool // Whether to allow retrieving resources with no meta component, // meaning Last-Modified & ETag headers can't be generated (breaking spec compliance) // May be needed to support previous databases AllowResourcesWithoutMeta bool // ValidatorURL is an endpoint to which validation requests will be sent ValidatorURL string // ReadOnly toggles whether the server is in read-only mode. In read-only // mode any HTTP verb other than GET, HEAD or OPTIONS is rejected. ReadOnly bool // Enables requests and responses using FHIR XML MIME-types EnableXML bool // Debug toggles debug-level logging. Debug bool }
Config is used to hold information about the configuration of the FHIR server.
type CurrentOp ¶
type CurrentOp struct { Active bool `bson:"active" json:"active"` OpID uint32 `bson:"opid" json:"opid"` SecsRunning uint32 `bson:"secs_running" json:"secs_running"` MicrosecsRunning uint64 `bson:"microsecs_running" json:"microsecs_running"` OpType string `bson:"op" json:"op"` Namespace string `bson:"ns" json:"ns"` KillPending bool `bson:"killPending" json:"killPending"` Query bson.D `bson:"query" json:"query"` }
CurrentOp is a database operation currently in-progress.
type CurrentOps ¶
type CurrentOps struct { InProg []CurrentOp `bson:"inprog" json:"inprog"` Info string `bson:"info,omitempty" json:"info,omitempty"` Ok float64 `bson:"ok" json:"ok"` }
CurrentOps is returned by db.currentOp() and contains a list of all operations currently in-progress. The db.currentOp() operation will itself be an element of InProg[].
type CustomFhirRenderer ¶
type CustomFhirRenderer struct {
// contains filtered or unexported fields
}
CustomFhirRenderer replaces gin's default JSON renderer and ensures that the special characters "<", ">", and "&" are not escaped after the the JSON is marshaled. Escaping these special HTML characters is the default behavior of Go's json.Marshal(). It also outputs XML if that is required
func (CustomFhirRenderer) Render ¶
func (u CustomFhirRenderer) Render(w http.ResponseWriter) (err error)
func (CustomFhirRenderer) WriteContentType ¶
func (u CustomFhirRenderer) WriteContentType(w http.ResponseWriter)
type DataAccessLayer ¶
type DataAccessLayer interface {
StartSession(dbname string) DataAccessSession
}
func NewMongoDataAccessLayer ¶
func NewMongoDataAccessLayer(client *mongo.Client, defaultDbName string, enableMultiDB bool, dbSuffix string, interceptors map[string]InterceptorList, config Config) DataAccessLayer
NewMongoDataAccessLayer returns an implementation of DataAccessLayer that is backed by a Mongo database
type DataAccessSession ¶
type DataAccessSession interface { // Starts a transaction StartTransaction() error // Commits a transaction CommmitIfTransaction() error // Ends the session (aborts any running transactions) - for use in defer statements after StartSession Finish() // Get retrieves a single resource instance identified by its resource type and ID Get(id, resourceType string) (resource *models2.Resource, err error) // GetVersion retrieves a single resource instance identified by its resource type, ID and versionId GetVersion(id, versionId, resourceType string) (resource *models2.Resource, err error) // Post creates a resource instance, returning its new ID. Post(resource *models2.Resource) (id string, err error) // ConditionalPost creates a resource if the query finds no matches ConditionalPost(query search.Query, resource *models2.Resource) (httpStatus int, id string, outputResource *models2.Resource, err error) // PostWithID creates a resource instance with the given ID. PostWithID(id string, resource *models2.Resource) error // Put creates or updates a resource instance with the given ID. Put(id string, conditionalVersionId string, resource *models2.Resource) (createdNew bool, err error) // ConditionalPut creates or updates a resource based on search criteria. If the criteria results in zero matches, // the resource is created. If the criteria results in one match, it is updated. Otherwise, a ErrMultipleMatches // error is returned. ConditionalPut(query search.Query, conditionalVersionId string, resource *models2.Resource) (id string, createdNew bool, err error) // Delete removes the resource instance with the given ID. This operation cannot be undone. Delete(id, resourceType string) (newVersionId string, err error) // ConditionalDelete removes zero or more resources matching the passed in search criteria. This operation cannot // be undone. ConditionalDelete(query search.Query) (count int64, err error) // Search executes a search given the baseURL and searchQuery. Search(baseURL url.URL, searchQuery search.Query) (bundle *models2.ShallowBundle, err error) // FindIDs executes a search given the searchQuery and returns only the matching IDs. This function ignores // search options that don't make sense in this context: _include, _revinclude, _summary, _elements, _contained, // and _containedType. It honors search options such as _count, _sort, and _offset. FindIDs(searchQuery search.Query) (result []string, err error) // History executes the history operation (partial support) History(baseURL url.URL, resoureType string, id string) (bundle *models2.ShallowBundle, err error) }
DataAccessLayer is an interface for the various interactions that can occur on a FHIR data store.
type ErrConflict ¶
type ErrConflict struct {
// contains filtered or unexported fields
}
func (ErrConflict) Error ¶
func (e ErrConflict) Error() string
type ErrMultipleMatches ¶
type ErrMultipleMatches struct {
// contains filtered or unexported fields
}
ErrMultipleMatches indicates that the conditional update query returned multiple matches
func (ErrMultipleMatches) Error ¶
func (e ErrMultipleMatches) Error() string
type FHIRServer ¶
type FHIRServer struct { Config Config Engine *gin.Engine MiddlewareConfig map[string][]gin.HandlerFunc AfterRoutes []AfterRoutes Interceptors map[string]InterceptorList }
func NewServer ¶
func NewServer(config Config) *FHIRServer
func (*FHIRServer) AddInterceptor ¶
func (f *FHIRServer) AddInterceptor(op, resourceType string, handler InterceptorHandler) error
AddInterceptor adds a new interceptor for a particular database operation and FHIR resource. For example: AddInterceptor("Create", "Patient", patientInterceptorHandler) would register the patientInterceptorHandler methods to be run against a Patient resource when it is created.
To run a handler against ALL resources pass "*" as the resourceType.
Supported database operations are: "Create", "Update", "Delete"
func (*FHIRServer) AddMiddleware ¶
func (f *FHIRServer) AddMiddleware(key string, middleware gin.HandlerFunc)
func (*FHIRServer) InitDB ¶
func (f *FHIRServer) InitDB(databaseName string)
func (*FHIRServer) Run ¶
func (f *FHIRServer) Run()
type FhirFormatConverter ¶
type FhirFormatConverter struct {
// contains filtered or unexported fields
}
Converts between FHIR JSON and XML encodings using the FHIR.js library developed by the Lantana Consulting Group (https://github.com/lantanagroup/FHIR.js) It is executed using the goja JavaScript engine
func NewFhirFormatConverter ¶
func NewFhirFormatConverter() *FhirFormatConverter
func (*FhirFormatConverter) JsonToXml ¶
func (c *FhirFormatConverter) JsonToXml(json string) (xml string, err error)
type IndexMap ¶
type IndexMap map[string][]mongo.IndexModel
IndexMap is a map of index arrays with the collection name as the key. Each index array contains one or more indexes.
type Indexer ¶
type Indexer struct {
// contains filtered or unexported fields
}
Indexer is the top-level interface for managing MongoDB indexes.
func NewIndexer ¶
NewIndexer returns a pointer to a newly configured Indexer.
func (*Indexer) ConfigureIndexes ¶
ConfigureIndexes ensures that all indexes listed in the provided indexes.conf file are part of the Mongodb fhir database. If an index does not exist yet ConfigureIndexes creates a new index in the background using mgo.collection.EnsureIndex(). Depending on the size of the collection it may take some time before the index is created. This will block the current thread until the indexing completes, but will not block other connections to the mongo database.
type Interceptor ¶
type Interceptor struct { ResourceType string Handler InterceptorHandler }
Interceptor optionally executes functions on a specified resource type before and after a database operation involving that resource. To register an interceptor for ALL resource types use a "*" as the resourceType.
type InterceptorHandler ¶
type InterceptorHandler interface { Before(resource interface{}) After(resource interface{}) OnError(err error, resource interface{}) }
InterceptorHandler is an interface that defines three methods that are executed on a resource before the database operation, after the database operation SUCCEEDS, and after the database operation FAILS.
type InterceptorList ¶
type InterceptorList []Interceptor
InterceptorList is a list of interceptors registered for a given database operation
type Reply ¶
type Reply struct { Info string `bson:"info,omitempty" json:"info,omitempty"` Ok float64 `bson:"ok" json:"ok"` }
Reply is a response from a MongoDB command that doesn't return any results.
type ResourceController ¶
type ResourceController struct { Name string DAL DataAccessLayer Config Config }
ResourceController provides the necessary CRUD handlers for a given resource.
func NewResourceController ¶
func NewResourceController(name string, dal DataAccessLayer, config Config) *ResourceController
NewResourceController creates a new resource controller for the passed in resource name and the passed in DataAccessLayer.
func (*ResourceController) ConditionalDeleteHandler ¶
func (rc *ResourceController) ConditionalDeleteHandler(c *gin.Context)
ConditionalDeleteHandler handles requests to delete resources identified by search criteria. All resources matching the search criteria will be deleted.
func (*ResourceController) ConditionalUpdateHandler ¶
func (rc *ResourceController) ConditionalUpdateHandler(c *gin.Context)
ConditionalUpdateHandler handles requests for conditional updates. These requests contain search criteria for the resource to update. If the criteria results in no found resources, a new resource is created. If the criteria results in one found resource, that resource will be updated. Criteria resulting in more than one found resource is considered an error.
func (*ResourceController) CreateHandler ¶
func (rc *ResourceController) CreateHandler(c *gin.Context)
CreateHandler handles requests to create a new resource instance, assigning it a new ID.
func (*ResourceController) DeleteHandler ¶
func (rc *ResourceController) DeleteHandler(c *gin.Context)
DeleteHandler handles requests to delete a resource instance identified by its ID.
func (*ResourceController) EverythingHandler ¶
func (rc *ResourceController) EverythingHandler(c *gin.Context)
EverythingHandler handles requests for everything related to a Patient or Encounter resource.
func (*ResourceController) HistoryHandler ¶
func (rc *ResourceController) HistoryHandler(c *gin.Context)
func (*ResourceController) IndexHandler ¶
func (rc *ResourceController) IndexHandler(c *gin.Context)
IndexHandler handles requests to list resource instances or search for them.
func (*ResourceController) LoadResource ¶
func (rc *ResourceController) LoadResource(c *gin.Context) (resourceId string, resource *models2.Resource, err error)
LoadResource uses the resource id in the request to get a resource from the DataAccessLayer and store it in the context.
func (*ResourceController) ShowHandler ¶
func (rc *ResourceController) ShowHandler(c *gin.Context)
ShowHandler handles requests to get a particular resource by ID.
func (*ResourceController) UpdateHandler ¶
func (rc *ResourceController) UpdateHandler(c *gin.Context)
UpdateHandler handles requests to update a resource having a given ID. If the resource with that ID does not exist, a new resource is created with that ID.