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chore: port more clinical implementation and improve dependency injec…
…tion Implement OCL as a service Improve FHIR repository dependency injection Signed-off-by: Otieno Calvine <nyarangaotieno@gmail.com>
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,102 +1,57 @@ | ||
| package fhir | ||
|
|
||
| import ( | ||
| "context" | ||
| "fmt" | ||
| "log" | ||
|
|
||
| "github.com/savannahghi/serverutils" | ||
| "google.golang.org/api/healthcare/v1" | ||
| ) | ||
|
|
||
| // constants used to configure the Google Cloud Healthcare API | ||
| const ( | ||
| DatasetLocation = "europe-west4" | ||
| ) | ||
|
|
||
| // CreateDataset creates a cloud healthcare dataset and returns it's name | ||
| func (s Service) CreateDataset() (*healthcare.Operation, error) { | ||
| s.checkPreconditions() | ||
| datasetsService := s.healthcareService.Projects.Locations.Datasets | ||
| parent := fmt.Sprintf("projects/%s/locations/%s", s.projectID, s.location) | ||
| resp, err := datasetsService.Create(parent, &healthcare.Dataset{}).DatasetId(s.datasetID).Do() | ||
| if err != nil { | ||
| return nil, fmt.Errorf("create Data Set: %v", err) | ||
| } | ||
| return resp, nil | ||
| // Repository accesses and updates patient data that is stored on Healthcare | ||
| // FHIR repository | ||
| type Repository struct { | ||
| Dataset DatasetExtension | ||
| } | ||
|
|
||
| // GetDataset gets a cloud healthcare dataset. | ||
| func (s Service) GetDataset() (*healthcare.Dataset, error) { | ||
| s.checkPreconditions() | ||
| datasetsService := s.healthcareService.Projects.Locations.Datasets | ||
| name := fmt.Sprintf("projects/%s/locations/%s/datasets/%s", s.projectID, s.location, s.datasetID) | ||
| resp, err := datasetsService.Get(name).Do() | ||
| if err != nil { | ||
| return nil, fmt.Errorf("get Data Set: %v", err) | ||
| // NewFHIRRepository initializes a FHIR repository | ||
| func NewFHIRRepository( | ||
| dataset DatasetExtension, | ||
| ) *Repository { | ||
| return &Repository{ | ||
| Dataset: dataset, | ||
| } | ||
| return resp, nil | ||
| } | ||
|
|
||
| // Service is an implementation of the healthcare fhir repository | ||
| // It is implementation agnostic i.e logic should be handled using | ||
| // the preferred datastore/database | ||
| type Service struct { | ||
| healthcareService *healthcare.Service | ||
| projectID, location, datasetID, fhirStoreID string | ||
| // CreateFHIRResource creates an FHIR resource. | ||
| // | ||
| // The payload should be the result of marshalling a resource to JSON | ||
| func (fr Repository) CreateFHIRResource(resourceType string, payload map[string]interface{}) ([]byte, error) { | ||
| return nil, nil | ||
| } | ||
|
|
||
| // NewService initializes a Google Cloud Healthcare API service | ||
| func NewService() *Service { | ||
| projectID := serverutils.MustGetEnvVar(serverutils.GoogleCloudProjectIDEnvVarName) | ||
| _ = serverutils.MustGetEnvVar("CLOUD_HEALTH_PUBSUB_TOPIC") | ||
| datasetID := serverutils.MustGetEnvVar("CLOUD_HEALTH_DATASET_ID") | ||
| fhirStoreID := serverutils.MustGetEnvVar("CLOUD_HEALTH_FHIRSTORE_ID") | ||
|
|
||
| ctx := context.Background() | ||
| hsv, err := healthcare.NewService(ctx) | ||
| if err != nil { | ||
| log.Panicf("unable to initialize new Google Cloud Healthcare Service: %s", err) | ||
| } | ||
| service := &Service{ | ||
| healthcareService: hsv, | ||
| projectID: projectID, | ||
| location: DatasetLocation, | ||
| datasetID: datasetID, | ||
| fhirStoreID: fhirStoreID, | ||
| } | ||
|
|
||
| // ensure that the dataset exists | ||
| _, err = service.GetDataset() | ||
| if err != nil { | ||
| _, err = service.CreateDataset() | ||
| if err != nil { | ||
| log.Printf( | ||
| "Unable to get or create dataset with projectID %s, "+ | ||
| "location %s, datasetID %s; got error %s", | ||
| service.projectID, service.location, service.datasetID, err, | ||
| ) | ||
| } | ||
| } | ||
| // DeleteFHIRResource deletes an FHIR resource. | ||
| func (fr Repository) DeleteFHIRResource(resourceType, fhirResourceID string) ([]byte, error) { | ||
| return nil, nil | ||
| } | ||
|
|
||
| // ensure that the FHIR store exists | ||
| _, err = service.GetFHIRStore() | ||
| if err != nil { | ||
| _, err = service.CreateFHIRStore() | ||
| if err != nil { | ||
| log.Printf( | ||
| "Unable to get or create FHIR store with projectID %s, "+ | ||
| "location %s, datasetID %s, fhirStoreID %s; got error %s", | ||
| service.projectID, service.location, service.datasetID, service.fhirStoreID, err, | ||
| ) | ||
| } | ||
| } | ||
| // PatchFHIRResource patches a FHIR resource. | ||
| // The payload is a JSON patch document that follows guidance on Patch from the | ||
| // FHIR standard. | ||
| // See: | ||
| // payload := []map[string]interface{}{ | ||
| // { | ||
| // "op": "replace", | ||
| // "path": "/active", | ||
| // "value": active, | ||
| // }, | ||
| // } | ||
| // See: https://www.hl7.org/fhir/http.html#patch | ||
| func (fr Repository) PatchFHIRResource( | ||
| resourceType, fhirResourceID string, payload []map[string]interface{}) ([]byte, error) { | ||
| return nil, nil | ||
| } | ||
|
|
||
| return service | ||
| // UpdateFHIRResource updates the entire contents of a resource. | ||
| func (fr Repository) UpdateFHIRResource( | ||
| resourceType, fhirResourceID string, payload map[string]interface{}) ([]byte, error) { | ||
| return nil, nil | ||
| } | ||
|
|
||
| func (s Service) checkPreconditions() { | ||
| if s.healthcareService == nil { | ||
| log.Panicf("cloudhealth.Service *healthcare.Service is nil") | ||
| } | ||
| // GetFHIRPatientEverything gets all resources associated with a particular | ||
| // patient compartment. | ||
| func (fr Repository) GetFHIRPatientEverything(fhirResourceID string) ([]byte, error) { | ||
| return nil, nil | ||
| } |
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