diff --git a/clients/internal/manual/client.go b/clients/internal/manual/client.go index 899ac35aa..845dbdd65 100644 --- a/clients/internal/manual/client.go +++ b/clients/internal/manual/client.go @@ -2,15 +2,13 @@ package manual import ( "context" + "encoding/json" "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" "github.com/sirupsen/logrus" "io" "net/http" @@ -77,39 +75,27 @@ func (m ManualClient) SyncAllBundle(db models.DatabaseRepository, bundleFile *os //lookup table for bundle internal references -> relative references (used heavily by file Bundles) internalFragmentReferenceLookup := map[string]string{} - switch bundleType { - case pkg.FhirVersion430: - bundle430Data := fhir430.Bundle{} - err := base.UnmarshalJson(bundleFile, &bundle430Data) - if err != nil { - return summary, fmt.Errorf("an error occurred while parsing 4.3.0 bundle: %w", err) - } - client, err := base.GetSourceClientFHIR430(m.FastenEnv, m.Context, m.Logger, m.SourceCredential, http.DefaultClient) - if err != nil { - return summary, fmt.Errorf("an error occurred while creating 4.3.0 client: %w", err) - } - rawResourceList, err = client.ProcessBundle(bundle430Data) - if err != nil { - return summary, fmt.Errorf("an error occurred while processing 4.3.0 resources: %w", err) - } + //retrieve the FHIR client + client, err := base.GetSourceClientFHIR401(m.FastenEnv, m.Context, m.Logger, m.SourceCredential, http.DefaultClient) + if err != nil { + return summary, fmt.Errorf("an error occurred while creating 4.0.1 client: %w", err) + } + + //parse the document + documentType, err := GetFileDocumentType(bundleFile) + if err != nil { + return summary, err + } + m.Logger.Infof("Begin processing document: %s", documentType) + switch documentType { + case pkg.DocumentTypeFhirBundle: - //for _, apiModel := range rawResourceList { - // err = client.ProcessResource(db, apiModel, lookupResourceReferences, &summary) - // if err != nil { - // syncErrors[apiModel.SourceResourceType] = err - // continue - // } - //} - case pkg.FhirVersion401: bundle401Data := fhir401.Bundle{} err := base.UnmarshalJson(bundleFile, &bundle401Data) if err != nil { return summary, fmt.Errorf("an error occurred while parsing 4.0.1 bundle: %w", err) } - client, err := base.GetSourceClientFHIR401(m.FastenEnv, m.Context, m.Logger, m.SourceCredential, http.DefaultClient) - if err != nil { - return summary, fmt.Errorf("an error occurred while creating 4.0.1 client: %w", err) - } + rawResourceList, internalFragmentReferenceLookup, err = client.ProcessBundle(bundle401Data) if err != nil { return summary, fmt.Errorf("an error occurred while processing 4.0.1 resources: %w", err) @@ -123,9 +109,54 @@ func (m ManualClient) SyncAllBundle(db models.DatabaseRepository, bundleFile *os } } + case pkg.DocumentTypeFhirNDJSON: + d := json.NewDecoder(bundleFile) + counter := 0 + for { + + 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 + } + } + + resourceObj, err := fhir401utils.MapToResource(resource, false) + if err != nil { + syncErrors[fmt.Sprintf("index: %d", counter)] = err + continue + } + + resourceObjTyped := resourceObj.(models.ResourceInterface) + resourceType, resourceId := resourceObjTyped.ResourceRef() + if resourceId == nil { + syncErrors[fmt.Sprintf("%s (index: %d)", resourceType, counter)] = fmt.Errorf("resource ID is nil, skipping") + continue + } + + apiModel := models.RawResourceFhir{ + SourceResourceID: *resourceId, + SourceResourceType: resourceType, + ResourceRaw: resource, + } + rawResourceList = append(rawResourceList, apiModel) + err = client.ProcessResource(db, apiModel, lookupResourceReferences, internalFragmentReferenceLookup, &summary) + if err != nil { + syncErrors[apiModel.SourceResourceType] = err + continue + } + + counter += 1 + } } summary.TotalResources = len(rawResourceList) + m.Logger.Infof("Completed document processing: %d resources", summary.TotalResources) + if len(syncErrors) > 0 { //TODO: ignore errors. m.Logger.Errorf("%d error(s) occurred during sync. \n %v", len(syncErrors), syncErrors) @@ -134,29 +165,18 @@ func (m ManualClient) SyncAllBundle(db models.DatabaseRepository, bundleFile *os } func (m ManualClient) ExtractPatientId(bundleFile *os.File) (string, pkg.FhirVersion, error) { - // TODO: find a way to correctly detect bundle version - - bundleType := pkg.FhirVersion401 - patientIds, err := parse401Bundle(bundleFile) - bundleFile.Seek(0, io.SeekStart) - - //fallback to 430 bundle - if err != nil || patientIds == nil || len(patientIds) == 0 { - bundleType = pkg.FhirVersion430 - - patientIds, err = parse430Bundle(bundleFile) - bundleFile.Seek(0, io.SeekStart) - - } + documentType, err := GetFileDocumentType(bundleFile) 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 { - //reset reader - - return strings.TrimLeft(patientIds[0], "Patient/"), bundleType, nil + return "", pkg.FhirVersion401, err + } + + switch documentType { + case pkg.DocumentTypeFhirBundle: + return extractPatientIdBundle(bundleFile) + case pkg.DocumentTypeFhirNDJSON: + return extractPatientIdNDJson(bundleFile) + default: + return "", pkg.FhirVersion401, fmt.Errorf("unsupported document type: %s", documentType) } } @@ -169,52 +189,6 @@ func GetSourceClientManual(env pkg.FastenLighthouseEnvType, ctx context.Context, }, nil } -//TODO: find a better, more generic way to do this. - -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() - - if resourceId == nil || len(*resourceId) == 0 { - return "", false - } - return *resourceId, resourceType == fhir430.ResourceTypePatient.String() - }) - - return patientIds, nil - } else { - return nil, err - } - -} - -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() - - if resourceId == nil || len(*resourceId) == 0 { - return "", false - } - return *resourceId, resourceType == fhir430.ResourceTypePatient.String() - }) - return patientIds, nil - } else { - return nil, err - } +func cleanPatientIdPrefix(patientId string) string { + return strings.TrimLeft(patientId, "Patient/") } diff --git a/clients/internal/manual/client_bundle.go b/clients/internal/manual/client_bundle.go new file mode 100644 index 000000000..b44e8be08 --- /dev/null +++ b/clients/internal/manual/client_bundle.go @@ -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) + + // TODO: find a way to correctly detect bundle version + + bundleType := pkg.FhirVersion401 + patientIds, err := parse401Bundle(bundleFile) + bundleFile.Seek(0, io.SeekStart) + + //fallback to 430 bundle + if err != nil || patientIds == nil || len(patientIds) == 0 { + bundleType = pkg.FhirVersion430 + + patientIds, err = parse430Bundle(bundleFile) + + } + 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 + } +} + +//TODO: find a better, more generic way to do this. + +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() + + if resourceId == nil || len(*resourceId) == 0 { + return "", false + } + return *resourceId, resourceType == fhir430.ResourceTypePatient.String() + }) + + return patientIds, nil + } else { + return nil, err + } + +} + +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() + + if resourceId == nil || len(*resourceId) == 0 { + return "", false + } + return *resourceId, resourceType == fhir430.ResourceTypePatient.String() + }) + return patientIds, nil + } else { + return nil, err + } +} diff --git a/clients/internal/manual/client_ndjson.go b/clients/internal/manual/client_ndjson.go new file mode 100644 index 000000000..377c88aaf --- /dev/null +++ b/clients/internal/manual/client_ndjson.go @@ -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" +) + +func extractPatientIdNDJson(bundleFile *os.File) (string, pkg.FhirVersion, error) { + // TODO: find a way to correctly detect bundle version + defer bundleFile.Seek(0, io.SeekStart) + + patientIds := []string{} + d := json.NewDecoder(bundleFile) + for { + + 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 + } + } + + resourceObj, err := fhir401utils.MapToResource(resource, false) + if err != nil { + continue + } + + resourceObjTyped := resourceObj.(models.ResourceInterface) + currentResourceType, currentResourceId := resourceObjTyped.ResourceRef() + + if currentResourceType == "Patient" { + patientIds = append(patientIds, *currentResourceId) + } + } + + if len(patientIds) == 0 { + return "", "", fmt.Errorf("could not determine patient id") + } else { + return cleanPatientIdPrefix(patientIds[0]), pkg.FhirVersion401, nil + } +} diff --git a/clients/internal/manual/client_test.go b/clients/internal/manual/client_test.go index 5a3f27fc4..88615d75f 100644 --- a/clients/internal/manual/client_test.go +++ b/clients/internal/manual/client_test.go @@ -11,6 +11,78 @@ import ( "testing" ) +func TestGetSourceClientManual_ExtractPatientId_Bundle(t *testing.T) { + t.Parallel() + //setup + testLogger := logrus.WithFields(logrus.Fields{ + "type": "test", + }) + mockCtrl := gomock.NewController(t) + defer mockCtrl.Finish() + fakeSourceCredential := mock_models.NewMockSourceCredential(mockCtrl) + fakeSourceCredential.EXPECT().GetSourceType().AnyTimes().Return(pkg.SourceTypeManual) + client, err := GetSourceClientManual(pkg.FastenLighthouseEnvSandbox, context.Background(), testLogger, fakeSourceCredential) + + bundleFile, err := os.Open("testdata/fixtures/401-R4/bundle/synthea_Tania553_Harris789_545c2380-b77f-4919-ab5d-0f615f877250.json") + require.NoError(t, err) + + //test + resp, ver, err := client.ExtractPatientId(bundleFile) + + //assert + require.NoError(t, err) + require.Equal(t, pkg.FhirVersion401, ver) + require.Equal(t, "57959813-8cd2-4e3c-8970-e4364b74980a", resp) +} + +func TestGetSourceClientManual_ExtractPatientId_BundleIPS(t *testing.T) { + t.Parallel() + //setup + testLogger := logrus.WithFields(logrus.Fields{ + "type": "test", + }) + mockCtrl := gomock.NewController(t) + defer mockCtrl.Finish() + fakeSourceCredential := mock_models.NewMockSourceCredential(mockCtrl) + fakeSourceCredential.EXPECT().GetSourceType().AnyTimes().Return(pkg.SourceTypeManual) + client, err := GetSourceClientManual(pkg.FastenLighthouseEnvSandbox, context.Background(), testLogger, fakeSourceCredential) + + bundleFile, err := os.Open("testdata/fixtures/401-R4/international-patient-summary/IPS-bundle-01.json") + require.NoError(t, err) + + //test + resp, ver, err := client.ExtractPatientId(bundleFile) + + //assert + require.NoError(t, err) + require.Equal(t, pkg.FhirVersion401, ver) + require.Equal(t, "2b90dd2b-2dab-4c75-9bb9-a355e07401e8", resp) +} + +func TestGetSourceClientManual_ExtractPatientId_NDJSON(t *testing.T) { + t.Parallel() + //setup + testLogger := logrus.WithFields(logrus.Fields{ + "type": "test", + }) + mockCtrl := gomock.NewController(t) + defer mockCtrl.Finish() + fakeSourceCredential := mock_models.NewMockSourceCredential(mockCtrl) + fakeSourceCredential.EXPECT().GetSourceType().AnyTimes().Return(pkg.SourceTypeManual) + client, err := GetSourceClientManual(pkg.FastenLighthouseEnvSandbox, context.Background(), testLogger, fakeSourceCredential) + + bundleFile, err := os.Open("testdata/fixtures/401-R4/phr-ndjson-jsonl/TimmySmart-FosterCareTimeline.phr") + require.NoError(t, err) + + //test + resp, ver, err := client.ExtractPatientId(bundleFile) + + //assert + require.NoError(t, err) + require.Equal(t, pkg.FhirVersion401, ver) + require.Equal(t, "12724069", resp) +} + func TestGetSourceClientManual_SyncAllBundle(t *testing.T) { t.Parallel() //setup @@ -20,7 +92,7 @@ func TestGetSourceClientManual_SyncAllBundle(t *testing.T) { mockCtrl := gomock.NewController(t) defer mockCtrl.Finish() fakeDatabase := mock_models.NewMockDatabaseRepository(mockCtrl) - fakeDatabase.EXPECT().UpsertRawResource(gomock.Any(), gomock.Any(), gomock.Any()).Times(195+1).Return(true, nil) + fakeDatabase.EXPECT().UpsertRawResource(gomock.Any(), gomock.Any(), gomock.Any()).Times(234).Return(true, nil) fakeSourceCredential := mock_models.NewMockSourceCredential(mockCtrl) fakeSourceCredential.EXPECT().GetSourceType().AnyTimes().Return(pkg.SourceTypeManual) @@ -35,6 +107,90 @@ func TestGetSourceClientManual_SyncAllBundle(t *testing.T) { //assert require.Equal(t, 195+1, resp.TotalResources) - require.Equal(t, 195+1, len(resp.UpdatedResources)) + require.Equal(t, 234, len(resp.UpdatedResources)) + require.NoError(t, err) +} + +func TestGetSourceClientManual_SyncAllBundle_IPS(t *testing.T) { + t.Parallel() + //setup + testLogger := logrus.WithFields(logrus.Fields{ + "type": "test", + }) + mockCtrl := gomock.NewController(t) + defer mockCtrl.Finish() + fakeDatabase := mock_models.NewMockDatabaseRepository(mockCtrl) + fakeDatabase.EXPECT().UpsertRawResource(gomock.Any(), gomock.Any(), gomock.Any()).Times(234).Return(true, nil) + + fakeSourceCredential := mock_models.NewMockSourceCredential(mockCtrl) + fakeSourceCredential.EXPECT().GetSourceType().AnyTimes().Return(pkg.SourceTypeManual) + client, err := GetSourceClientManual(pkg.FastenLighthouseEnvSandbox, context.Background(), testLogger, fakeSourceCredential) + + bundleFile, err := os.Open("testdata/fixtures/401-R4/international-patient-summary/IPS-bundle-01.json") + require.NoError(t, err) + + //test + resp, err := client.SyncAllBundle(fakeDatabase, bundleFile, pkg.FhirVersion401) + require.NoError(t, err) + + //assert + require.Equal(t, 20, resp.TotalResources) + require.Equal(t, 20, len(resp.UpdatedResources)) + require.NoError(t, err) +} + +func TestGetSourceClientManual_SyncAllBundle_NDJSON(t *testing.T) { + t.Parallel() + //setup + testLogger := logrus.WithFields(logrus.Fields{ + "type": "test", + }) + mockCtrl := gomock.NewController(t) + defer mockCtrl.Finish() + fakeDatabase := mock_models.NewMockDatabaseRepository(mockCtrl) + fakeDatabase.EXPECT().UpsertRawResource(gomock.Any(), gomock.Any(), gomock.Any()).AnyTimes().Return(true, nil) + + fakeSourceCredential := mock_models.NewMockSourceCredential(mockCtrl) + fakeSourceCredential.EXPECT().GetSourceType().AnyTimes().Return(pkg.SourceTypeManual) + client, err := GetSourceClientManual(pkg.FastenLighthouseEnvSandbox, context.Background(), testLogger, fakeSourceCredential) + + bundleFile, err := os.Open("testdata/fixtures/401-R4/phr-ndjson-jsonl/TimmySmart-FosterCareTimeline.phr") + require.NoError(t, err) + + //test + resp, err := client.SyncAllBundle(fakeDatabase, bundleFile, pkg.FhirVersion401) + require.NoError(t, err) + + //assert + require.Equal(t, 123, resp.TotalResources) + require.Equal(t, 123, len(resp.UpdatedResources)) + require.NoError(t, err) +} + +func TestGetSourceClientManual_SyncAllBundle_NDJSON2(t *testing.T) { + t.Parallel() + //setup + testLogger := logrus.WithFields(logrus.Fields{ + "type": "test", + }) + mockCtrl := gomock.NewController(t) + defer mockCtrl.Finish() + fakeDatabase := mock_models.NewMockDatabaseRepository(mockCtrl) + fakeDatabase.EXPECT().UpsertRawResource(gomock.Any(), gomock.Any(), gomock.Any()).AnyTimes().Return(true, nil) + + fakeSourceCredential := mock_models.NewMockSourceCredential(mockCtrl) + fakeSourceCredential.EXPECT().GetSourceType().AnyTimes().Return(pkg.SourceTypeManual) + client, err := GetSourceClientManual(pkg.FastenLighthouseEnvSandbox, context.Background(), testLogger, fakeSourceCredential) + + bundleFile, err := os.Open("testdata/fixtures/401-R4/phr-ndjson-jsonl/JohnDoe.phr") + require.NoError(t, err) + + //test + resp, err := client.SyncAllBundle(fakeDatabase, bundleFile, pkg.FhirVersion401) + require.NoError(t, err) + + //assert + require.Equal(t, 12, resp.TotalResources) + require.Equal(t, 12, len(resp.UpdatedResources)) require.NoError(t, err) } diff --git a/clients/internal/manual/testdata/fixtures/401-R4/ccda/MaryGrant-ClinicalSummary.xml b/clients/internal/manual/testdata/fixtures/401-R4/ccda/MaryGrant-ClinicalSummary.xml new file mode 100644 index 000000000..89e9e507b --- /dev/null +++ b/clients/internal/manual/testdata/fixtures/401-R4/ccda/MaryGrant-ClinicalSummary.xml @@ -0,0 +1,686 @@ + + + + + + + +Summary of Care + + + + + + +No Address IndicatedNo City IndicatedCA99999United States of America + + +MaryGrant + + + + + + + + + + +Get Well Clinic + +1002 Healthcare Dr.BeavertonOR97005United States of America + + + + + + +Get Well Clinic Facility1002 Healthcare Dr.PortlandOR97005United States of America + + +MartinGreen + + +Get Well Clinic +1002 Healthcare Dr.PortlandOR97005United States of America + + + + + + +Get Well Clinic Facility1002 Healthcare Dr.PortlandOR97005United States of America + + +FnameLname + + +Get Well Clinic +1002 Healthcare Dr.PortlandOR97005United States of America + + + +1002 Healthcare Dr.PortlandOR97005United States of America + + +FnameLname + + + + +Get Well Clinic + +1002 Healthcare Dr.BeavertonOR97005United States of America + + + + + +1002 Healthcare Dr.PortlandOR97005United States of America + + +FnameLname + + + + + + + + + + + + +1002 Healthcare Dr.PortlandOR97005United States of America + + +FnameLname + + +Get Well Clinic +1002 Healthcare Dr.PortlandOR97005United States of America + + + + + + + + + +
+ + +Allergies + + + + + + + + + + + + + + + + + +
AllergyDateReaction StatusSeverity Status
Bicillin L-AOnset: Not IndicatedHivesVery Mild
AspirinOnset: Not IndicatedNauseaMild
 + + + + + + + + + + + + + + + + + + + + +1002 Healthcare Dr.PortlandOR97005United States of America + + +MartinGreen + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +1002 Healthcare Dr.PortlandOR97005United States of America + + +MartinGreen + + + + + + + + + + + + + + + + + + + + + + + + +
 + +
+ + +Assessment and Plan + + + + + + +
Assessment and Plan
Goal: weight loss +Instructions: diet and exercise counseling provided during visit
 + + + + + + + +
 + +
+ + +Chief Complaint and Reason For Visit + + + + + + +
Chief Complaint or Reason for Visit
2014-01-01 : No Chief Complaint or Reason for Visit given
+ +
+ + +Encounters + + + + + + + + + + + + +
Encounter Type Location NamePerformerDate of Service
Encounter: Encounter for "check-up" (procedure)Get Well Clinic, 1002 Healthcare Dr., Beaverton, OR 97005 Phone: (415) 427-2132 Fname Lname 2014-01-01
 + + + + + + + + + + + + +1002 Healthcare Dr.BeavertonOR97005United States of America + + +FnameLname + + + + +United States of America +
 + +
+ + +Immunizations + + + + + + + + + + +
VaccineDateDelivery Status
No immunizations administered during visitNot ApplicableNot Applicable
 + + + + + + + + + + + + + + +
 + +
+ + +Instructions + + + + + + +
Instructions
Education resources were given to the patient during the visit
 + + + + + +
 + +
+ + +Medications + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
MaterialRXnormCodeGenericNameProductStrengthStartDateStopDateSIG
Keflex (cephalexin) oral capsuleRxNorm: 212339cephalexin500 mg2012-09-20Not Indicated4 times daily for 10 days
PROzac (FLUoxetine) oral capsuleRxNorm: 261287FLUoxetine40 mg2011-11-10Not Indicatedonce daily
Synthroid (levothyroxine) oral tabletRxNorm: 966247levothyroxine50 mcg (0.05 mg)2010-04-15Not Indicatedonce daily
 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
 + +
+ + +Problem List + + + + + + + + + + +
Problem DescriptionProblem StartDateStatus
No Problems indicated
+ + + + + + + + + + + + + + + + +
 + +
+ + +Procedures + + + + + + + + +
ProcedureDate
Standard chest X-ray (procedure)Performed: 2013-12-18
 + + + + + + + + + + + + + +Get Well Clinic Facility1002 Healthcare Dr.PortlandOR97005United States of America + + +FnameLname + + + + +Get Well Clinic Facility1002 Healthcare Dr.PortlandOR97005United States of America + +
 + +
+ + +Results +Not indicated + + + + + + + + + + + + + + +
 + +
+ + +Social History + + + + + + + + +
Social HistoryEffective Date
Never smoker2013-12-17
 + + + + + + + + +
 + +
+ + +Vital Signs + + + + + + + + + + + + + + + + + + + + + + + + +
Date:TimeRespiratoryRate /minHeartRate /minSystolicBP mm[Hg]DiastolicBP mm[Hg]BodyTemperature [degF]Height [in_us]Head Circumference [in_us]Weight [lb_av]BMI kg/m2
2014-01-010011672064016027.4609
 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
 diff --git a/clients/internal/manual/testdata/fixtures/401-R4/international-patient-summary/IPS-bundle-01.json b/clients/internal/manual/testdata/fixtures/401-R4/international-patient-summary/IPS-bundle-01.json new file mode 100644 index 000000000..f9a9b06a6 --- /dev/null +++ b/clients/internal/manual/testdata/fixtures/401-R4/international-patient-summary/IPS-bundle-01.json @@ -0,0 +1,1216 @@ +{ + "resourceType": "Bundle", + "id": "IPS-examples-Bundle-01", + "language": "en-GB", + "identifier": { + "system": "urn:oid:2.16.724.4.8.10.200.10", + "value": "175bd032-8b00-4728-b2dc-748bb1501aed" + }, + "type": "document", + "timestamp": "2017-12-11T14:30:00+01:00", + "entry": [ + { + "fullUrl": "urn:uuid:30551ce1-5a28-4356-b684-1e639094ad4d", + "resource": { + "resourceType": "Composition", + "id": "30551ce1-5a28-4356-b684-1e639094ad4d", + "text": { + "status": "generated", + "div": "

Generated Narrative

Resource \"30551ce1-5a28-4356-b684-1e639094ad4d\"

identifier: id: 3f69e0a5-2177-4540-baab-7a5d0877428f

status: final

type: Patient summary Document (LOINC#60591-5)

date: 2017-12-11T14:30:00+01:00

author: See above (Practitioner/1c616b24-3895-48c4-9a02-9a64110351ef)

title: Patient Summary as of December 11, 2017 14:30

confidentiality: N

attester

mode: legal

time: 2017-12-11T14:30:00+01:00

party: See above (Practitioner/1c616b24-3895-48c4-9a02-9a64110351ef)

attester

mode: legal

time: 2017-12-11T14:30:00+01:00

party: See above (Organization/890751f4-2924-4636-bab7-efffc7f3cf15)

custodian: See above (Organization/890751f4-2924-4636-bab7-efffc7f3cf15)

RelatesTos

-CodeTarget[x]
*appendsid: c2277753-9f90-4a95-8ddb-a0b3f6e7d292

Events

-CodePeriod
*care provision (ActClass#PCPR)?? --> 2017-12-11T14:30:00+01:00
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Hot flushes
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MedicationStrengthFormDosageComment
Anastrozole1 mgtabletonce dailytreatment for breast cancer
Black Cohosh Extract pil herbal supplement
\n\t\t\t\t\t\t
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Allergy to penicillin, high criticality, active\n\t\t\t\t\t\t\tNo known food allergies\n\t\t\t\t\t\t
" + }, + "entry": [ + { + "reference": "AllergyIntolerance/72884cad-ebe6-4f43-a51a-2f978275f132" + }, + { + "reference": "AllergyIntolerance/c7781f44-6df8-4a8b-9e06-0b34263a47c5" + } + ] + }, + { + "title": "History of Past Illness", + "code": { + "coding": [ + { + "system": "http://loinc.org", + "code": "11348-0", + "display": "Hx of Past illness" + } + ] + }, + "text": { + "status": "generated", + "div": "
Breast cancer Stage II with no evidence of recurrence following treatment
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Continue hormone medication with Anastrozole for total of 5 years and monitor for potential breast cancer recurrence
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Blood typing
Blood groupA+\n\t\t\t\t\t\t\t\t\t
C Ab [Presence] in Serum or PlasmaPositive\n\t\t\t\t\t\t\t\t\t
E Ab [Presence] in Serum or PlasmaPositive\n\t\t\t\t\t\t\t\t\t
Little c Ab [Presence] in Serum or PlasmaNegative\n\t\t\t\t\t\t\t\t\t
\n\t\t\t\t\t\t\t\n\t\t\t\t\t\t\t\t\n\t\t\t\t\t\t\t\t\t\n\t\t\t\t\t\t\t\t\t\t\n\t\t\t\t\t\t\t\t\t\n\t\t\t\t\t\t\t\t\n\t\t\t\t\t\t\t\t\n\t\t\t\t\t\t\t\t\t\n\t\t\t\t\t\t\t\t\t\t\n\t\t\t\t\t\t\t\t\t\t\n\t\t\t\t\t\t\t\t\t\t\n\t\t\t\t\t\t\t\t\n\t\t\t\t\t\t\t
Hemoglobin A1c monitoring
Hemoglobin A1c/Hemoglobin.total in Blood by HPLC7.5 %\n\t\t\t\t\t\t\t\t\t
\n\t\t\t\t\t\t\t\n\t\t\t\t\t\t\t\t\n\t\t\t\t\t\t\t\t\t\n\t\t\t\t\t\t\t\t\t\t\n\t\t\t\t\t\t\t\t\t\n\t\t\t\t\t\t\t\t\n\t\t\t\t\t\t\t\t\n\t\t\t\t\t\t\t\t\t\n\t\t\t\t\t\t\t\t\t\t\n\t\t\t\t\t\t\t\t\t\n\t\t\t\t\t\t\t\t\t\n\t\t\t\t\t\t\t\t\t\t\n\t\t\t\t\t\t\t\t\t\n\t\t\t\t\t\t\t\t\n\t\t\t\t\t\t\t
Bacteriology
Methicillin resistant Staphylococcus aureus
Healthy carrier of MRSA
\n\t\t\t\t\t\t
" + }, + "entry": [ + { + "reference": "Observation/2639657a-c19a-48e2-82cc-471e13b8ad94" + }, + { + "reference": "Observation/cc354e00-a419-47ea-8b6c-1768b2a01646" + }, + { + "reference": "Observation/26bee0a9-5997-4557-ab9d-c6adbb05b572" + } + ] + } + ] + } + }, + { + "fullUrl": "urn:uuid:2b90dd2b-2dab-4c75-9bb9-a355e07401e8", + "resource": { + "resourceType": "Patient", + "id": "2b90dd2b-2dab-4c75-9bb9-a355e07401e8", + "text": { + "status": "generated", + "div": "

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identifier: id: 574687583

active: true

name: Martha DeLarosa

telecom: +31788700800

gender: female

birthDate: 1972-05-01

address: Laan Van Europa 1600 Dordrecht 3317 DB NL

Contacts

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*mother (RoleCode#MTH)Martha Mum +33-555-20036Promenade des Anglais 111 Lyon 69001 FR
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identifier: id: 129854633

active: true

name: Beetje van Hulp

Qualifications

-Code
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identifier: id: 564738757

active: true

name: Anorg Aniza Tion BV / The best custodian ever

telecom: +31-51-34343400

address: Houttuinen 27 Dordrecht 3311 CE NL (WORK)

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identifier: id: c87bf51c-e53c-4bfe-b8b7-aa62bdd93002

clinicalStatus: Active (Condition Clinical Status Codes#active)

verificationStatus: Confirmed (ConditionVerificationStatus#confirmed)

category: Problem (LOINC#75326-9)

severity: Moderate (LOINC#LA6751-7)

code: Menopausal flushing (finding) (SNOMED CT#198436008; ICD-10#N95.1 \"Menopausal and female climacteric states\")

subject: See above (Patient/2b90dd2b-2dab-4c75-9bb9-a355e07401e8)

onset: 2015-01-01

recordedDate: 2016-10-01

" + }, + "identifier": [ + { + "system": "urn:oid:1.2.3.999", + "value": "c87bf51c-e53c-4bfe-b8b7-aa62bdd93002" + } + ], + "clinicalStatus": { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/condition-clinical", + "code": "active" + } + ] + }, + "verificationStatus": { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/condition-ver-status", + "code": "confirmed" + } + ] + }, + "category": [ + { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/condition-category", + "code": "problem-list-item", + "display": "Problem List Item" + }, + { + "system": "http://loinc.org", + "code": "75326-9", + "display": "Problem" + } + ] + } + ], + "severity": { + "coding": [ + { + "system": "http://loinc.org", + "code": "LA6751-7", + "display": "Moderate" + } + ] + }, + "code": { + "coding": [ + { + "system": "http://snomed.info/sct", + "code": "198436008", + "display": "Menopausal flushing (finding)", + "_display": { + "extension": [ + { + "url": "http://hl7.org/fhir/StructureDefinition/translation", + "extension": [ + { + "url": "lang", + "valueCode": "nl-NL" + }, + { + "url": "content", + "valueString": "opvliegers" + } + ] + } + ] + } + }, + { + "system": "http://hl7.org/fhir/sid/icd-10", + "code": "N95.1", + "display": "Menopausal and female climacteric states" + } + ] + }, + "subject": { + "reference": "Patient/2b90dd2b-2dab-4c75-9bb9-a355e07401e8" + }, + "onsetDateTime": "2015", + "recordedDate": "2016-10" + } + }, + { + "fullUrl": "urn:uuid:c220e36c-eb67-4fc4-9ba1-2fabc52acec6", + "resource": { + "resourceType": "MedicationStatement", + "id": "c220e36c-eb67-4fc4-9ba1-2fabc52acec6", + "text": { + "status": "generated", + "div": "

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status: active

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subject: See above (Patient/2b90dd2b-2dab-4c75-9bb9-a355e07401e8)

effective: 2015-03-01 --> (ongoing)

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identifier: id: 9e312d6b-c6b6-439a-a730-6efaa5dcf8bc

status: active

medication: See above (Medication/8adc0999-9468-4ac9-9557-680fa133d626)

subject: See above (Patient/2b90dd2b-2dab-4c75-9bb9-a355e07401e8)

effective: 2016-01-01 --> (ongoing)

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Generated Narrative

Resource \"976d0804-cae0-45ae-afe3-a19f3ceba6bc\"

code: Product containing anastrozole (medicinal product) (SNOMED CT#108774000; unknown#99872 \"ANASTROZOL 1MG TABLET\"; unknown#2076667 \"ANASTROZOL CF TABLET FILMOMHULD 1MG\"; WHO ATC#L02BG03 \"anastrozole\")

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Generated Narrative

Resource \"8adc0999-9468-4ac9-9557-680fa133d626\"

code: Black Cohosh Extract herbal supplement (SNOMED CT#412588001 \"Cimicifuga racemosa extract (substance)\"; WHO ATC#G02CX04 \"Cimicifugae rhizoma\")

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category: medication

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code: Substance with penicillin structure and antibacterial mechanism of action (substance) (SNOMED CT#373270004)

patient: See above (Patient/2b90dd2b-2dab-4c75-9bb9-a355e07401e8)

onset: 2010-01-01

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verificationStatus: Confirmed (ConditionVerificationStatus#confirmed)

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severity: Severe (LOINC#LA6750-9)

code: Malignant tumor of breast (SNOMED CT#254837009; unknown#8500/3 \"Infiltrating duct carcinoma, NOS\")

subject: See above (Patient/2b90dd2b-2dab-4c75-9bb9-a355e07401e8)

onset: 2015-01-01

abatement: 2015-03-01

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active: true

type: Other (Organization type#other)

name: Laboratoire de charme

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Generated Narrative

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performer: See above (Organization/45a5c5b1-4ec1-4d60-b4b2-ff5a84a41fd7)

value: Blood group A Rh(D) positive (SNOMED CT#278149003)

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effective: 2015-10-10T09:35:00+01:00

performer: See above (Organization/45a5c5b1-4ec1-4d60-b4b2-ff5a84a41fd7)

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performer: See above (Organization/45a5c5b1-4ec1-4d60-b4b2-ff5a84a41fd7)

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performer: See above (Organization/45a5c5b1-4ec1-4d60-b4b2-ff5a84a41fd7)

value: Negative (SNOMED CT#260385009)

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category: Laboratory (Observation Category Codes#laboratory)

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performer: See above (Organization/45a5c5b1-4ec1-4d60-b4b2-ff5a84a41fd7)

value: 7.5 % (Details: UCUM code % = '%')

note: Above stated goal of 7.0 %

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Resource \"26bee0a9-5997-4557-ab9d-c6adbb05b572\"

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category: Laboratory (Observation Category Codes#laboratory)

code: Bacteria identified in Isolate (LOINC#42803-7)

subject: See above (Patient/2b90dd2b-2dab-4c75-9bb9-a355e07401e8)

effective: 2017-12-10T08:20:00+01:00

performer: See above (Organization/45a5c5b1-4ec1-4d60-b4b2-ff5a84a41fd7)

value: Methicillin resistant Staphylococcus aureus (SNOMED CT#115329001)

note: Healthy carrier of MRSA

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patient: See above (Patient/2b90dd2b-2dab-4c75-9bb9-a355e07401e8)

" + }, + "clinicalStatus": { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/allergyintolerance-clinical", + "code": "active" + } + ] + }, + "code": { + "coding": [ + { + "system": "http://hl7.org/fhir/uv/ips/CodeSystem/absent-unknown-uv-ips", + "code": "no-known-food-allergies" + } + ] + }, + "patient": { + "reference": "Patient/2b90dd2b-2dab-4c75-9bb9-a355e07401e8" + } + } + } + ] +} \ No newline at end of file diff --git a/clients/internal/manual/testdata/fixtures/401-R4/phr-ndjson-jsonl/JohnDoe.phr b/clients/internal/manual/testdata/fixtures/401-R4/phr-ndjson-jsonl/JohnDoe.phr new file mode 100644 index 000000000..2a0120525 --- /dev/null +++ b/clients/internal/manual/testdata/fixtures/401-R4/phr-ndjson-jsonl/JohnDoe.phr @@ -0,0 +1,18 @@ + +{"resourceType":"Composition","status":"preliminary","subject":{"display":"","reference":""},"date":"2022-09-20","author":[{"display":"","reference":""}],"title":"Continuity of Care Document","section":[{"reference":"Patient/john-doe"},{"reference":"CarePlan/ExampleCarePlan"},{"reference":"Condition/JohnDoe-diabetes"},{"reference":"Consent/ExampleConsent"},{"reference":"Communication/ExampleCommunication"},{"reference":"Device/ExampleDevice"},{"reference":"DiagnosticReport/ExampleDiagnosticReport"},{"reference":"Immunization/immunization"},{"reference":"Medication/Medication-1"},{"reference":"MedicationStatement/medication-statement"},{"reference":"Observation/observation-lab-urine"},{"reference":"Observation/observation-smoker"},{"reference":"Observation/observation-vitals-temp"},{"reference":"Organization/organization-1"},{"reference":"Procedure/procedure-rehab"}]} +{"resourceType":"DocumentManifest","status":"current"} +{"resourceType":"Patient","id":"john-doe","text":{"status":"generated","div":"

Johnny male, DoB: 1954-09-17

"},"active":true,"name":[{"use":"official","family":"Doe","given":["John"]},{"use":"usual","given":["Johnny"]}],"telecom":[{"use":"home"},{"system":"phone","value":"(+1) 555 6473","use":"work","rank":1}],"gender":"male","birthDate":"1954-09-17","deceasedBoolean":false,"_id":"K7GNYY39v2tTNHtHg"} +{"resourceType":"CarePlan","id":"ExampleCarePlan","meta":{"profile":["https://gitlab.mitre.org/awatson/sphr/StructureDefinition/PhrCarePlan"]},"text":{"status":"generated","div":"

Generated Narrative

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intent: plan

subject: Patient/john-doe: John Doe \" DOE\"

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Generated Narrative

Resource \"JohnDoe-diabetes\"

clinicalStatus: active ([not stated]#active)

verificationStatus: differential ([not stated]#differential)

category: Problem (SNOMED CT#55607006; condition-category#problem-list-item)

severity: Severe (SNOMED CT#24484000)

code: Diabetes Type 2 (SNOMED CT#44054006)

subject: Patient/Anyman/Bob: John Doe

onset: 2018-09-16

abatement: 2018-09-16

asserter: Provider/Primary/Patricia

note: The patient is now diagnosed with type 2 diabetes.

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Profile: PhrConsent

status: active

scope: Patient Privacy (Consent Scope Codes#patient-privacy)

category: Advanced Directive (valueset-consent-category.html#acd)

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Profile: PhrCommunication

status: completed

"},"status":"completed","_id":"EYRnh96huaSF3TQCq"} +{"resourceType":"Device","id":"ExampleDevice","meta":{"profile":["https://gitlab.mitre.org/awatson/sphr/StructureDefinition/PhrDevice"]},"text":{"status":"generated","div":"

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Resource \"ExampleDevice\"

Profile: PhrDevice

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Withdrawal arrhythmia

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Generated Narrative

Resource \"immunization\" Version \"1\" Updated \"2018-10-04 07:42:52-0400\"

status: completed

vaccineCode: influenza, injectable, quadrivalent (PH_VaccinesAdministeredCVX_CDC_NIP#158; National drug codes#49281-0623-78 \"FLUZONE QUADRIVALENT\")

patient: Patient/john-doe: John Doe \" DOE\"

occurrence: 2016-01-08

primarySource: false

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Resource \"Medication-1\"

code: Glipizide and Metformin Hydrochloride (National drug codes#68382-185)

manufacturer: : Zydus Pharmaceuticals (USA) Inc.

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Resource \"medication-statement\" Version \"1\" Updated \"2018-10-04 07:42:52-0400\"

Profile: http://hl7.org/fhir/us/core/StructureDefinition/us-core-medicationstatement

status: active

medication: lisinopril oral 10 mg (RxNorm#206765 \"Lisinopril 10 MG Oral Tablet [Prinivil]\")

subject: Patient/john-doe: John Doe \" DOE\"

effective: 2010-05-01 --> (ongoing)

dateAsserted: 2016-05-01 04:13:03+0000

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Generated Narrative

Resource \"observation-lab-urine\" Version \"1\" Updated \"2018-10-04 07:42:52-0400\"

Profile: http://hl7.org/fhir/us/core/StructureDefinition/us-core-observationresults

status: final

category: Laboratory (observation-category#laboratory)

code: SPEC GRAV (LOINC#5811-5 \"Specific gravity of Urine by Test strip\")

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Generated Narrative

Resource \"observation-smoker\" Version \"1\" Updated \"2018-10-04 07:42:52-0400\"

status: final

category: Social History (observation-category#social-history)

code: Tobacco smoking status (LOINC#72166-2)

subject: Patient/john-doe: John Doe \" DOE\"

issued: Mar 17, 2016, 10:27:04 PM

value: Current some day smoker (SNOMED CT#428041000124106)

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Generated Narrative

Resource \"observation-vitals-temp\" Version \"1\" Updated \"2018-10-04 07:42:52-0400\"

Profile: Vital Signs Profile

status: final

category: Vital Signs (observation-category#vital-signs)

code: temperature (LOINC#8310-5 \"Body temperature\")

subject: Patient/john-doe: John Doe \" DOE\"

effective: 1999-07-02

value: 36.55556 Cel (Details: UCUM code Cel = 'Cel')

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Generated Narrative

Resource \"organization-1\" Version \"3\" Updated \"2019-01-25 04:39:57-0500\"

Profile: http://hl7.org/fhir/us/core/StructureDefinition/us-core-organization

identifier: id: 1144221847, id: 2523423456

active: true

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name: Acme Labs

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Generated Narrative

Resource \"procedure-rehab\" Version \"1\" Updated \"2018-10-04 07:42:52-0400\"

Profile: http://hl7.org/fhir/us/core/StructureDefinition/us-core-procedure

status: completed

code: Alcohol rehabilitation (SNOMED CT#38670004 \"Patient referral for alcoholism rehabilitation (procedure)\")

subject: Patient/john-doe: John Doe \" DOE\"

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Printed and reviewed Do-Not-Resuscitate Order, Michigan."}],"notDone":true,"_id":"CQi7pLPSijAL2jRxh"} +{"resourceType":"Procedure","id":"183432009","status":"completed","code":{"coding":[{"system":"http://snomed.info/sct","code":"183432009","display":"Application to foster a child (procedure)","userSelected":true}],"text":"Application to foster a child (procedure)"},"subject":{"reference":"Patient/john-caring","display":"CARING, JOHN"},"encounter":{"reference":"Encounter/97953492"},"performedDateTime":"2019-06-01T00:00:00.000Z","recorder":{"reference":"Practitioner/maggie-caseworker","display":"Caseworker, Maggie - Social Worker"},"notDone":false,"_id":"qEe7DjAkPwoW9xLts"} diff --git a/clients/internal/manual/testdata/fixtures/README.md b/clients/internal/manual/testdata/fixtures/README.md new file mode 100644 index 000000000..e7e972e33 --- /dev/null +++ b/clients/internal/manual/testdata/fixtures/README.md @@ -0,0 +1,19 @@ +# Manual Test Data + +## Bundle + +- https://synthea.mitre.org/downloads + +## Standard Personal Health Record (PHR) + +- https://build.fhir.org/ig/HL7/standard-patient-health-record-ig/branches/master/personas-index.html + +## CCDA + +- https://github.com/jmandel/sample_ccdas +- https://github.com/chunli866/CCDAtoFHIRSamples +- https://github.com/microsoft/FHIR-Converter/tree/main/data/SampleData/Ccda + +## IPS + +- https://github.com/HL7/fhir-ips-ri/blob/main/examples/example_bundle/IPS-bundle-01.json diff --git a/clients/internal/manual/utils.go b/clients/internal/manual/utils.go new file mode 100644 index 000000000..db305023a --- /dev/null +++ b/clients/internal/manual/utils.go @@ -0,0 +1,96 @@ +package manual + +import ( + "encoding/json" + "fmt" + "github.com/fastenhealth/fasten-sources/pkg" + fhir401utils "github.com/fastenhealth/gofhir-models/fhir401/utils" + "io" + "net/http" + "os" + "strings" +) + +/* +GetFileDocumentType returns the document type of given file. +We'll use various techniques to determine if the file is XML or JSON-like first. +If the file is JSON, we'll determine if it's a FHIR bundle. +If the file is NDJson, we'll parse the first entry to ensure it's a valid fhir resource. +We can't depend on just http.DetectContentType because it doesn't detect the difference between JSON, NDJSON, FHIR, XML and CCDAs. +*/ +func GetFileDocumentType(file *os.File) (pkg.DocumentType, error) { + + // Only the first 512 bytes are used to sniff the content type. + buffer := make([]byte, 512) + _, err := file.Read(buffer) + if err != nil { + return "", err + } + defer file.Seek(0, io.SeekStart) + + contentType := http.DetectContentType(buffer) + contentTypeParts := strings.Split(contentType, ";") + + if contentTypeParts[0] == "text/plain" { + firstNonWS := 0 + //find first non-whitespace character + for ; firstNonWS < len(buffer) && isWhitespaceChar(buffer[firstNonWS]); firstNonWS++ { + } + + //determine the content-type using buffer + if firstNonWS == len(buffer) { + return pkg.DocumentType(contentTypeParts[0]), fmt.Errorf("file is empty") + } else if buffer[firstNonWS] == '<' { + //TODO: we should do some additional parsing to confirm + return pkg.DocumentTypeCCDA, nil + } else if buffer[firstNonWS] == '{' { + //reset file to beginning + file.Seek(0, io.SeekStart) + + //this is 1 or more json documents + documentCount := 0 + containsFhirResource := false + d := json.NewDecoder(file) + for { + + 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, don't add it to the documentCount + } + } + + //we have a valid json document, lets check if it's a FHIR resource + if !containsFhirResource { + _, err := fhir401utils.MapToResource(resource, false) + if err == nil { + containsFhirResource = true + } + } + + documentCount++ + } + + if containsFhirResource && documentCount > 1 { + return pkg.DocumentTypeFhirNDJSON, nil + } else if containsFhirResource && documentCount == 1 { + return pkg.DocumentTypeFhirBundle, nil + } + } + } + return pkg.DocumentType(contentTypeParts[0]), fmt.Errorf("unknown document type, content-type: %s", contentTypeParts[0]) +} + +// isWhitespaceChar reports whether the provided byte is a whitespace byte (0xWS) +// as defined in https://mimesniff.spec.whatwg.org/#terminology. +func isWhitespaceChar(b byte) bool { + switch b { + case '\t', '\n', '\x0c', '\r', ' ': + return true + } + return false +} diff --git a/clients/internal/manual/utils_test.go b/clients/internal/manual/utils_test.go new file mode 100644 index 000000000..91548e18e --- /dev/null +++ b/clients/internal/manual/utils_test.go @@ -0,0 +1,38 @@ +package manual + +import ( + "github.com/fastenhealth/fasten-sources/pkg" + "github.com/stretchr/testify/require" + "os" + "testing" +) + +func TestGetFileDocumentType(t *testing.T) { + + var documentTypeTests = []struct { + fixturePath string // input + expectedSuccess bool // expected result + expectedDocumentType pkg.DocumentType // expected result + }{ + {"testdata/fixtures/401-R4/bundle/synthea_Tania553_Harris789_545c2380-b77f-4919-ab5d-0f615f877250.json", true, pkg.DocumentTypeFhirBundle}, + {"testdata/fixtures/401-R4/ccda/MaryGrant-ClinicalSummary.xml", true, pkg.DocumentTypeCCDA}, + {"testdata/fixtures/401-R4/international-patient-summary/IPS-bundle-01.json", true, pkg.DocumentTypeFhirBundle}, + {"testdata/fixtures/401-R4/phr-ndjson-jsonl/JohnDoe.phr", true, pkg.DocumentTypeFhirNDJSON}, + {"testdata/fixtures/401-R4/phr-ndjson-jsonl/TimmySmart-FosterCareTimeline.phr", true, pkg.DocumentTypeFhirNDJSON}, + {"testdata/fixtures/README.md", false, pkg.DocumentType("")}, + } + + for _, tt := range documentTypeTests { + file, err := os.OpenFile(tt.fixturePath, os.O_RDONLY, 0644) + require.NoError(t, err) + + //test + contentType, err := GetFileDocumentType(file) + if tt.expectedSuccess { + require.NoError(t, err) + require.Equal(t, contentType, tt.expectedDocumentType, "fixture: %s", tt.fixturePath) + } else { + require.Error(t, err, "fixture: %s", tt.fixturePath) + } + } +} diff --git a/clients/models/mock/mock_database_repository.go b/clients/models/mock/mock_database_repository.go index 149d4a7a9..f90bb57f9 100644 --- a/clients/models/mock/mock_database_repository.go +++ b/clients/models/mock/mock_database_repository.go @@ -35,6 +35,18 @@ func (m *MockDatabaseRepository) EXPECT() *MockDatabaseRepositoryMockRecorder { return m.recorder } +// BackgroundJobCheckpoint mocks base method. +func (m *MockDatabaseRepository) BackgroundJobCheckpoint(ctx context.Context, checkpointData, errorData map[string]interface{}) { + m.ctrl.T.Helper() + m.ctrl.Call(m, "BackgroundJobCheckpoint", ctx, checkpointData, errorData) +} + +// BackgroundJobCheckpoint indicates an expected call of BackgroundJobCheckpoint. +func (mr *MockDatabaseRepositoryMockRecorder) BackgroundJobCheckpoint(ctx, checkpointData, errorData interface{}) *gomock.Call { + mr.mock.ctrl.T.Helper() + return mr.mock.ctrl.RecordCallWithMethodType(mr.mock, "BackgroundJobCheckpoint", reflect.TypeOf((*MockDatabaseRepository)(nil).BackgroundJobCheckpoint), ctx, checkpointData, errorData) +} + // UpsertRawResource mocks base method. func (m *MockDatabaseRepository) UpsertRawResource(ctx context.Context, sourceCredentials models.SourceCredential, rawResource models.RawResourceFhir) (bool, error) { m.ctrl.T.Helper() diff --git a/go.mod b/go.mod index 5ea6b5060..78a628d24 100644 --- a/go.mod +++ b/go.mod @@ -9,7 +9,7 @@ require ( github.com/seborama/govcr v4.5.0+incompatible github.com/sirupsen/logrus v1.9.0 github.com/skratchdot/open-golang v0.0.0-20200116055534-eef842397966 - github.com/stretchr/testify v1.8.1 + github.com/stretchr/testify v1.8.4 golang.org/x/exp v0.0.0-20220303212507-bbda1eaf7a17 golang.org/x/oauth2 v0.2.0 ) diff --git a/go.sum b/go.sum index cb361fb23..84b9dae20 100644 --- a/go.sum +++ b/go.sum @@ -24,13 +24,9 @@ github.com/sirupsen/logrus v1.9.0/go.mod h1:naHLuLoDiP4jHNo9R0sCBMtWGeIprob74mVs github.com/skratchdot/open-golang v0.0.0-20200116055534-eef842397966 h1:JIAuq3EEf9cgbU6AtGPK4CTG3Zf6CKMNqf0MHTggAUA= github.com/skratchdot/open-golang v0.0.0-20200116055534-eef842397966/go.mod h1:sUM3LWHvSMaG192sy56D9F7CNvL7jUJVXoqM1QKLnog= github.com/stretchr/objx v0.1.0/go.mod h1:HFkY916IF+rwdDfMAkV7OtwuqBVzrE8GR6GFx+wExME= -github.com/stretchr/objx v0.4.0/go.mod h1:YvHI0jy2hoMjB+UWwv71VJQ9isScKT/TqJzVSSt89Yw= -github.com/stretchr/objx v0.5.0/go.mod h1:Yh+to48EsGEfYuaHDzXPcE3xhTkx73EhmCGUpEOglKo= github.com/stretchr/testify v1.7.0/go.mod h1:6Fq8oRcR53rry900zMqJjRRixrwX3KX962/h/Wwjteg= -github.com/stretchr/testify v1.7.1/go.mod h1:6Fq8oRcR53rry900zMqJjRRixrwX3KX962/h/Wwjteg= -github.com/stretchr/testify v1.8.0/go.mod h1:yNjHg4UonilssWZ8iaSj1OCr/vHnekPRkoO+kdMU+MU= -github.com/stretchr/testify v1.8.1 h1:w7B6lhMri9wdJUVmEZPGGhZzrYTPvgJArz7wNPgYKsk= -github.com/stretchr/testify v1.8.1/go.mod h1:w2LPCIKwWwSfY2zedu0+kehJoqGctiVI29o6fzry7u4= +github.com/stretchr/testify v1.8.4 h1:CcVxjf3Q8PM0mHUKJCdn+eZZtm5yQwehR5yeSVQQcUk= +github.com/stretchr/testify v1.8.4/go.mod h1:sz/lmYIOXD/1dqDmKjjqLyZ2RngseejIcXlSw2iwfAo= github.com/thoas/go-funk v0.9.1 h1:O549iLZqPpTUQ10ykd26sZhzD+rmR5pWhuElrhbC20M= github.com/yuin/goldmark v1.3.5/go.mod h1:mwnBkeHKe2W/ZEtQ+71ViKU8L12m81fl3OWwC1Zlc8k= golang.org/x/crypto v0.0.0-20190308221718-c2843e01d9a2/go.mod h1:djNgcEr1/C05ACkg1iLfiJU5Ep61QUkGW8qpdssI0+w= diff --git a/pkg/document_type.go b/pkg/document_type.go new file mode 100644 index 000000000..36a41fe8a --- /dev/null +++ b/pkg/document_type.go @@ -0,0 +1,9 @@ +package pkg + +type DocumentType string + +const ( + DocumentTypeCCDA DocumentType = "CCDA" + DocumentTypeFhirBundle DocumentType = "FHIR_BUNDLE" + DocumentTypeFhirNDJSON DocumentType = "NDJSON" +) diff --git a/testutils/oauth_cli.go b/testutils/oauth_cli.go index 48bcdabe5..2b0dd3e6b 100644 --- a/testutils/oauth_cli.go +++ b/testutils/oauth_cli.go @@ -86,7 +86,7 @@ func main() { //get the source defintiion sourceConfig, err := defFactory.GetSourceConfig(pkg.FastenLighthouseEnvType(requestData.SourceMode), pkg.SourceType(requestData.SourceType), map[pkg.SourceType]string{}) if err != nil { - JSONError(res, fmt.Errorf("an error occurred while initializing source config", err), http.StatusBadRequest) + JSONError(res, fmt.Errorf("an error occurred while initializing source config: %w", err), http.StatusBadRequest) return }