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Merge pull request #15 from fastenhealth/ndjson_phr_support
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,91 @@ | ||
| package manual | ||
|
|
||
| import ( | ||
| "fmt" | ||
| "github.com/fastenhealth/fasten-sources/clients/internal/base" | ||
| "github.com/fastenhealth/fasten-sources/clients/models" | ||
| "github.com/fastenhealth/fasten-sources/pkg" | ||
| "github.com/fastenhealth/gofhir-models/fhir401" | ||
| fhir401utils "github.com/fastenhealth/gofhir-models/fhir401/utils" | ||
| "github.com/fastenhealth/gofhir-models/fhir430" | ||
| fhir430utils "github.com/fastenhealth/gofhir-models/fhir430/utils" | ||
| "github.com/samber/lo" | ||
| "io" | ||
| "os" | ||
| ) | ||
|
|
||
| func extractPatientIdBundle(bundleFile *os.File) (string, pkg.FhirVersion, error) { | ||
| defer bundleFile.Seek(0, io.SeekStart) | ||
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| // TODO: find a way to correctly detect bundle version | ||
|
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| bundleType := pkg.FhirVersion401 | ||
| patientIds, err := parse401Bundle(bundleFile) | ||
| bundleFile.Seek(0, io.SeekStart) | ||
|
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| //fallback to 430 bundle | ||
| if err != nil || patientIds == nil || len(patientIds) == 0 { | ||
| bundleType = pkg.FhirVersion430 | ||
|
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| patientIds, err = parse430Bundle(bundleFile) | ||
|
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| } | ||
| if err != nil { | ||
| //failed to parse the bundle as 401 and 430, return an error | ||
| return "", "", fmt.Errorf("could not determine bundle version: %v", err) | ||
| } else if patientIds == nil || len(patientIds) == 0 { | ||
| return "", "", fmt.Errorf("could not determine patient id") | ||
| } else { | ||
| return cleanPatientIdPrefix(patientIds[0]), bundleType, nil | ||
| } | ||
| } | ||
|
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| //TODO: find a better, more generic way to do this. | ||
|
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| func parse401Bundle(bundleFile *os.File) ([]string, error) { | ||
| bundle401Data := fhir401.Bundle{} | ||
| //try parsing the bundle as a 401 bundle | ||
| if err := base.UnmarshalJson(bundleFile, &bundle401Data); err == nil { | ||
| patientIds := lo.FilterMap[fhir401.BundleEntry, string](bundle401Data.Entry, func(bundleEntry fhir401.BundleEntry, _ int) (string, bool) { | ||
| parsedResource, err := fhir401utils.MapToResource(bundleEntry.Resource, false) | ||
| if err != nil { | ||
| return "", false | ||
| } | ||
| typedResource := parsedResource.(models.ResourceInterface) | ||
| resourceType, resourceId := typedResource.ResourceRef() | ||
|
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||
| if resourceId == nil || len(*resourceId) == 0 { | ||
| return "", false | ||
| } | ||
| return *resourceId, resourceType == fhir430.ResourceTypePatient.String() | ||
| }) | ||
|
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| return patientIds, nil | ||
| } else { | ||
| return nil, err | ||
| } | ||
|
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| } | ||
|
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| func parse430Bundle(bundleFile *os.File) ([]string, error) { | ||
| bundle430Data := fhir430.Bundle{} | ||
| //try parsing the bundle as a 430 bundle | ||
| if err := base.UnmarshalJson(bundleFile, &bundle430Data); err == nil { | ||
| patientIds := lo.FilterMap[fhir430.BundleEntry, string](bundle430Data.Entry, func(bundleEntry fhir430.BundleEntry, _ int) (string, bool) { | ||
| parsedResource, err := fhir430utils.MapToResource(bundleEntry.Resource, false) | ||
| if err != nil { | ||
| return "", false | ||
| } | ||
| typedResource := parsedResource.(models.ResourceInterface) | ||
| resourceType, resourceId := typedResource.ResourceRef() | ||
|
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| if resourceId == nil || len(*resourceId) == 0 { | ||
| return "", false | ||
| } | ||
| return *resourceId, resourceType == fhir430.ResourceTypePatient.String() | ||
| }) | ||
| return patientIds, nil | ||
| } else { | ||
| return nil, err | ||
| } | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,50 @@ | ||
| package manual | ||
|
|
||
| import ( | ||
| "encoding/json" | ||
| "fmt" | ||
| "github.com/fastenhealth/fasten-sources/clients/models" | ||
| "github.com/fastenhealth/fasten-sources/pkg" | ||
| fhir401utils "github.com/fastenhealth/gofhir-models/fhir401/utils" | ||
| "io" | ||
| "os" | ||
| ) | ||
|
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| func extractPatientIdNDJson(bundleFile *os.File) (string, pkg.FhirVersion, error) { | ||
| // TODO: find a way to correctly detect bundle version | ||
| defer bundleFile.Seek(0, io.SeekStart) | ||
|
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| patientIds := []string{} | ||
| d := json.NewDecoder(bundleFile) | ||
| for { | ||
|
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| var resource json.RawMessage | ||
| err := d.Decode(&resource) | ||
| if err != nil { | ||
| // io.EOF is expected at end of stream. | ||
| if err == io.EOF { | ||
| break //we're done | ||
| } else { | ||
| continue //skip this document, invalid json | ||
| } | ||
| } | ||
|
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| resourceObj, err := fhir401utils.MapToResource(resource, false) | ||
| if err != nil { | ||
| continue | ||
| } | ||
|
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| resourceObjTyped := resourceObj.(models.ResourceInterface) | ||
| currentResourceType, currentResourceId := resourceObjTyped.ResourceRef() | ||
|
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| if currentResourceType == "Patient" { | ||
| patientIds = append(patientIds, *currentResourceId) | ||
| } | ||
| } | ||
|
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| if len(patientIds) == 0 { | ||
| return "", "", fmt.Errorf("could not determine patient id") | ||
| } else { | ||
| return cleanPatientIdPrefix(patientIds[0]), pkg.FhirVersion401, nil | ||
| } | ||
| } |
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