mirror of
https://github.com/fastenhealth/fasten-onprem.git
synced 2026-02-18 08:08:39 -06:00
dbd868c796
* adding meta prefix to all relevant meta keys. moved extractor functions into reusable script. * adding comprensive tests and types for extracted data stored in tables. * update with README. * using choiceTypePaths to correctly append types to the search parameter queries. * adding comment or `keyword` types * better extraction of Date information. * fix tests.
529 lines
16 KiB
Go
529 lines
16 KiB
Go
package database
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import (
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"encoding/json"
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"github.com/dop251/goja"
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"github.com/stretchr/testify/require"
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"github.com/stretchr/testify/suite"
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"os"
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"testing"
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)
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// Define the suite, and absorb the built-in basic suite
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// functionality from testify - including a T() method which
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// returns the current testing context
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type SearchParameterExtractorTestSuite struct {
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suite.Suite
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VM *goja.Runtime
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}
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// BeforeTest has a function to be executed right before the test starts and receives the suite and test names as input
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func (suite *SearchParameterExtractorTestSuite) BeforeTest(suiteName, testName string) {
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vm := goja.New()
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// setup the global window object
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vm.Set("window", vm.NewObject())
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// compile the fhirpath library
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fhirPathJsProgram, err := goja.Compile("fhirpath.min.js", fhirPathJs, true)
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if err != nil {
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require.NoError(suite.T(), err)
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}
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// compile the searchParametersExtractor library
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searchParametersExtractorJsProgram, err := goja.Compile("searchParameterExtractor.js", searchParameterExtractorJs, true)
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if err != nil {
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require.NoError(suite.T(), err)
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}
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// add the fhirpath library in the goja vm
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_, err = vm.RunProgram(fhirPathJsProgram)
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if err != nil {
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require.NoError(suite.T(), err)
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}
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// add the searchParametersExtractor library in the goja vm
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_, err = vm.RunProgram(searchParametersExtractorJsProgram)
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if err != nil {
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require.NoError(suite.T(), err)
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}
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suite.VM = vm
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}
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// AfterTest has a function to be executed right after the test finishes and receives the suite and test names as input
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func (suite *SearchParameterExtractorTestSuite) AfterTest(suiteName, testName string) {
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}
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// In order for 'go test' to run this suite, we need to create
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// a normal test function and pass our suite to suite.Run
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func TestSearchParameterExtractorTestSuite(t *testing.T) {
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suite.Run(t, new(SearchParameterExtractorTestSuite))
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}
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func (suite *SearchParameterExtractorTestSuite) TestFhirpathEvaluate() {
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//setup
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resourceRaw, err := os.ReadFile("../../../../frontend/src/lib/fixtures/r4/resources/observation/example1.json")
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require.NoError(suite.T(), err)
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var resourceRawMap map[string]interface{}
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err = json.Unmarshal(resourceRaw, &resourceRawMap)
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if err != nil {
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require.NoError(suite.T(), err)
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}
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err = suite.VM.Set("fhirResource", resourceRawMap)
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require.NoError(suite.T(), err)
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//test
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result, err := suite.VM.RunString("fhirpathEvaluate(fhirResource, 'Observation.status')")
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require.NoError(suite.T(), err)
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//assert
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require.Equal(suite.T(), "final", result.String())
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}
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// Testing Date extraction
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func (suite *SearchParameterExtractorTestSuite) TestExtractDateSearchParameters_Date() {
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//setup
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resourceRaw := []byte(`
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{
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"resourceType" : "Observation",
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"id" : "2",
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"effectiveDateTime": "2016-03-28"
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}
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`)
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var resourceRawMap map[string]interface{}
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err := json.Unmarshal(resourceRaw, &resourceRawMap)
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if err != nil {
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require.NoError(suite.T(), err)
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}
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err = suite.VM.Set("fhirResource", resourceRawMap)
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require.NoError(suite.T(), err)
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//test
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result, err := suite.VM.RunString("extractSimpleSearchParameters(fhirResource, 'AllergyIntolerance.recordedDate | CarePlan.period | CareTeam.period | ClinicalImpression.date | Composition.date | Consent.dateTime | DiagnosticReport.effectiveDateTime | DiagnosticReport.effectivePeriod | Encounter.period | EpisodeOfCare.period | FamilyMemberHistory.date | Flag.period | (Immunization.occurrenceDateTime) | List.date | Observation.effectiveDateTime | Observation.effectivePeriod | Observation.effectiveTiming | Observation.effectiveInstant | Procedure.performedDateTime | Procedure.performedPeriod | Procedure.performedString | Procedure.performedAge | Procedure.performedRange | (RiskAssessment.occurrenceDateTime) | SupplyRequest.authoredOn')")
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require.NoError(suite.T(), err)
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require.Equal(suite.T(), "2016-03-28", result.String())
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//TODO: this is broken
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}
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func (suite *SearchParameterExtractorTestSuite) TestExtractDateSearchParameters_Period() {
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//setup
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resourceRaw := []byte(`
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{
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"resourceType" : "Observation",
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"id" : "2",
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"effectivePeriod": {
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"start": "2013-04-02T09:30:10+01:00"
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}
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}
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`)
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var resourceRawMap map[string]interface{}
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err := json.Unmarshal(resourceRaw, &resourceRawMap)
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if err != nil {
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require.NoError(suite.T(), err)
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}
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err = suite.VM.Set("fhirResource", resourceRawMap)
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require.NoError(suite.T(), err)
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//test
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result, err := suite.VM.RunString("extractDateSearchParameters(fhirResource, 'AllergyIntolerance.recordedDate | CarePlan.period | CareTeam.period | ClinicalImpression.date | Composition.date | Consent.dateTime | DiagnosticReport.effectiveDateTime | DiagnosticReport.effectivePeriod | Encounter.period | EpisodeOfCare.period | FamilyMemberHistory.date | Flag.period | (Immunization.occurrenceDateTime) | List.date | Observation.effectiveDateTime | Observation.effectivePeriod | Observation.effectiveTiming | Observation.effectiveInstant | Procedure.performedDateTime | Procedure.performedPeriod | Procedure.performedString | Procedure.performedAge | Procedure.performedRange | (RiskAssessment.occurrenceDateTime) | SupplyRequest.authoredOn')")
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require.NoError(suite.T(), err)
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require.Equal(suite.T(), "2013-04-02T09:30:10+01:00", result.String())
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}
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// Testing String extraction
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func (suite *SearchParameterExtractorTestSuite) TestExtractStringSearchParameters_Simple() {
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//setup
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resourceRaw, err := os.ReadFile("../../../../frontend/src/lib/fixtures/r4/resources/patient/example1.json")
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require.NoError(suite.T(), err)
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var resourceRawMap map[string]interface{}
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err = json.Unmarshal(resourceRaw, &resourceRawMap)
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if err != nil {
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require.NoError(suite.T(), err)
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}
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err = suite.VM.Set("fhirResource", resourceRawMap)
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require.NoError(suite.T(), err)
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//test
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result, err := suite.VM.RunString("extractStringSearchParameters(fhirResource, 'Patient.address.city | Person.address.city | Practitioner.address.city | RelatedPerson.address.city')")
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require.NoError(suite.T(), err)
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var resultSearchParameter SearchParameterStringType
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err = json.Unmarshal([]byte(result.String()), &resultSearchParameter)
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//assert
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require.Equal(suite.T(), SearchParameterStringType{"PleasantVille"}, resultSearchParameter)
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}
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func (suite *SearchParameterExtractorTestSuite) TestExtractStringSearchParameters_SimpleWithMultipleValues() {
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//setup
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resourceRaw := []byte(`
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{
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"resourceType": "Patient",
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"id": "f001",
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"address": [
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{
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"use": "home",
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"line": ["Van Egmondkade 23"],
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"city": "Amsterdam",
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"postalCode": "1024 RJ",
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"country": "NLD"
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},
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{
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"use": "home",
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"line": ["Van Egmondkade 23"],
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"city": "England",
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"postalCode": "1024 RJ",
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"country": "NLD"
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}
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]
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}
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`)
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var resourceRawMap map[string]interface{}
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err := json.Unmarshal(resourceRaw, &resourceRawMap)
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if err != nil {
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require.NoError(suite.T(), err)
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}
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err = suite.VM.Set("fhirResource", resourceRawMap)
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require.NoError(suite.T(), err)
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//test
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result, err := suite.VM.RunString("extractStringSearchParameters(fhirResource, 'Patient.address.city | Person.address.city | Practitioner.address.city | RelatedPerson.address.city')")
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require.NoError(suite.T(), err)
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var resultSearchParameter SearchParameterStringType
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err = json.Unmarshal([]byte(result.String()), &resultSearchParameter)
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//assert
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require.Equal(suite.T(), SearchParameterStringType{"Amsterdam", "England"}, resultSearchParameter)
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}
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func (suite *SearchParameterExtractorTestSuite) TestExtractStringSearchParameters_SimpleWithNoResult() {
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//setup
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resourceRaw := []byte(`
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{
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"resourceType": "Patient",
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"id": "f001",
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"address": []
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}
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`)
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var resourceRawMap map[string]interface{}
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err := json.Unmarshal(resourceRaw, &resourceRawMap)
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if err != nil {
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require.NoError(suite.T(), err)
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}
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err = suite.VM.Set("fhirResource", resourceRawMap)
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require.NoError(suite.T(), err)
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//test
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result, err := suite.VM.RunString("extractStringSearchParameters(fhirResource, 'Patient.address.city | Person.address.city | Practitioner.address.city | RelatedPerson.address.city')")
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require.NoError(suite.T(), err)
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var resultSearchParameter SearchParameterStringType
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err = json.Unmarshal([]byte(result.String()), &resultSearchParameter)
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//assert
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require.Nil(suite.T(), resultSearchParameter)
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}
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func (suite *SearchParameterExtractorTestSuite) TestExtractStringSearchParameters_ComplexWithText() {
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//setup
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resourceRaw := []byte(`
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{
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"resourceType": "Patient",
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"id": "f001",
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"name": [
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{
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"use": "official",
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"family": "Chalmers",
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"given": ["Peter", "James"]
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},
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{
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"use": "usual",
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"given": ["Jim"]
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},
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{
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"use": "maiden",
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"family": "Windsor",
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"given": ["Peter", "James"],
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"period": {
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"end": "2002"
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}
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}
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]
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}
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`)
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var resourceRawMap map[string]interface{}
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err := json.Unmarshal(resourceRaw, &resourceRawMap)
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if err != nil {
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require.NoError(suite.T(), err)
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}
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err = suite.VM.Set("fhirResource", resourceRawMap)
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require.NoError(suite.T(), err)
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//test
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result, err := suite.VM.RunString("extractStringSearchParameters(fhirResource, 'Patient.name')")
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require.NoError(suite.T(), err)
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var resultSearchParameter SearchParameterStringType
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err = json.Unmarshal([]byte(result.String()), &resultSearchParameter)
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//assert
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require.Equal(suite.T(), SearchParameterStringType{"Peter James Chalmers", "Jim", "Peter James Windsor"}, resultSearchParameter)
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}
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// Testing Token extraction
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func (suite *SearchParameterExtractorTestSuite) TestExtractTokenSearchParameters_Coding() {
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//setup
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resourceRaw := []byte(`
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{
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"resourceType" : "Location",
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"id" : "2",
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"operationalStatus" : {
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"system" : "http://terminology.hl7.org/CodeSystem/v2-0116",
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"code" : "H",
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"display" : "Housekeeping"
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}
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}
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`)
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var resourceRawMap map[string]interface{}
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err := json.Unmarshal(resourceRaw, &resourceRawMap)
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if err != nil {
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require.NoError(suite.T(), err)
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}
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err = suite.VM.Set("fhirResource", resourceRawMap)
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require.NoError(suite.T(), err)
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//test
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result, err := suite.VM.RunString("extractTokenSearchParameters(fhirResource, 'Location.operationalStatus')")
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require.NoError(suite.T(), err)
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var resultSearchParameter SearchParameterTokenType
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err = json.Unmarshal([]byte(result.String()), &resultSearchParameter)
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//assert
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require.Equal(suite.T(), SearchParameterTokenType{{
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System: "http://terminology.hl7.org/CodeSystem/v2-0116",
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Code: "H",
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Text: "Housekeeping",
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}}, resultSearchParameter)
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}
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func (suite *SearchParameterExtractorTestSuite) TestExtractTokenSearchParameters_Nil() {
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//setup
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resourceRaw := []byte(`
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{
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"resourceType" : "Location",
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"id" : "2"
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}
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`)
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var resourceRawMap map[string]interface{}
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err := json.Unmarshal(resourceRaw, &resourceRawMap)
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if err != nil {
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require.NoError(suite.T(), err)
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}
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err = suite.VM.Set("fhirResource", resourceRawMap)
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require.NoError(suite.T(), err)
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//test
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result, err := suite.VM.RunString("extractTokenSearchParameters(fhirResource, 'Location.operationalStatus')")
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require.NoError(suite.T(), err)
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var resultSearchParameter SearchParameterTokenType
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err = json.Unmarshal([]byte(result.String()), &resultSearchParameter)
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//assert
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require.Nil(suite.T(), resultSearchParameter)
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}
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func (suite *SearchParameterExtractorTestSuite) TestExtractTokenSearchParameters_CodableConcept() {
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//setup
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resourceRaw := []byte(`
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{
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"resourceType": "Patient",
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"id": "f001",
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"communication": [
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{
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"language": {
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"coding": [
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{
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"system": "urn:ietf:bcp:47",
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"code": "nl",
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"display": "Dutch"
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}
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],
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"text": "Nederlands"
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},
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"preferred": true
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}
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]
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}
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`)
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var resourceRawMap map[string]interface{}
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err := json.Unmarshal(resourceRaw, &resourceRawMap)
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if err != nil {
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require.NoError(suite.T(), err)
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}
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err = suite.VM.Set("fhirResource", resourceRawMap)
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require.NoError(suite.T(), err)
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//test
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result, err := suite.VM.RunString("extractTokenSearchParameters(fhirResource, 'Patient.communication.language')")
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require.NoError(suite.T(), err)
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var resultSearchParameter SearchParameterTokenType
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err = json.Unmarshal([]byte(result.String()), &resultSearchParameter)
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//assert
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require.Equal(suite.T(), SearchParameterTokenType{{
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System: "urn:ietf:bcp:47",
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Code: "nl",
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Text: "Dutch",
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}}, resultSearchParameter)
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}
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func (suite *SearchParameterExtractorTestSuite) TestExtractTokenSearchParameters_Identifier() {
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//setup
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resourceRaw := []byte(`
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{
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"resourceType": "Patient",
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"id": "f001",
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"identifier": [
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{
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"use": "usual",
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"type": {
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"coding": [
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{
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"system": "http://terminology.hl7.org/CodeSystem/v2-0203",
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"code": "MR"
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}
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]
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},
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"system": "urn:oid:1.2.36.146.595.217.0.1",
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"value": "12345",
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"period": {
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"start": "2001-05-06"
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},
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"assigner": {
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"display": "Acme Healthcare"
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}
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}
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]
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}
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`)
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var resourceRawMap map[string]interface{}
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err := json.Unmarshal(resourceRaw, &resourceRawMap)
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if err != nil {
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require.NoError(suite.T(), err)
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}
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err = suite.VM.Set("fhirResource", resourceRawMap)
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require.NoError(suite.T(), err)
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//test
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result, err := suite.VM.RunString("extractTokenSearchParameters(fhirResource, 'Patient.identifier')")
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require.NoError(suite.T(), err)
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var resultSearchParameter SearchParameterTokenType
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err = json.Unmarshal([]byte(result.String()), &resultSearchParameter)
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//assert
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require.Equal(suite.T(), SearchParameterTokenType{{
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System: "urn:oid:1.2.36.146.595.217.0.1",
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Code: "12345",
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Text: "",
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}}, resultSearchParameter)
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}
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func (suite *SearchParameterExtractorTestSuite) TestExtractTokenSearchParameters_ContactPoint() {
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//setup
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resourceRaw := []byte(`
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{
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"resourceType": "Patient",
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"id": "f001",
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"telecom": [
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{
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"use": "home"
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},
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{
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"system": "phone",
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"value": "(03) 5555 6473",
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"use": "work",
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"rank": 1
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},
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{
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"system": "phone",
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"value": "(03) 3410 5613",
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"use": "mobile",
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"rank": 2
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},
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{
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"system": "phone",
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"value": "(03) 5555 8834",
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"use": "old",
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"period": {
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"end": "2014"
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}
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}
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]
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}
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`)
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var resourceRawMap map[string]interface{}
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err := json.Unmarshal(resourceRaw, &resourceRawMap)
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if err != nil {
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require.NoError(suite.T(), err)
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}
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err = suite.VM.Set("fhirResource", resourceRawMap)
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require.NoError(suite.T(), err)
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//test
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result, err := suite.VM.RunString("extractTokenSearchParameters(fhirResource, 'Patient.telecom | Person.telecom | Practitioner.telecom | PractitionerRole.telecom | RelatedPerson.telecom')")
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require.NoError(suite.T(), err)
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var resultSearchParameter SearchParameterTokenType
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err = json.Unmarshal([]byte(result.String()), &resultSearchParameter)
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//assert
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require.Equal(suite.T(), SearchParameterTokenType{
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{
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System: "phone",
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Code: "(03) 5555 6473",
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Text: "",
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},
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{
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System: "phone",
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Code: "(03) 3410 5613",
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Text: "",
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},
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{
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System: "phone",
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Code: "(03) 5555 8834",
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Text: "",
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},
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}, resultSearchParameter)
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}
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func (suite *SearchParameterExtractorTestSuite) TestExtractTokenSearchParameters_code() {
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//setup
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resourceRaw := []byte(`
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{
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"resourceType": "Patient",
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"id": "f001",
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"gender": "male"
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}
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`)
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var resourceRawMap map[string]interface{}
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err := json.Unmarshal(resourceRaw, &resourceRawMap)
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if err != nil {
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require.NoError(suite.T(), err)
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}
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err = suite.VM.Set("fhirResource", resourceRawMap)
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require.NoError(suite.T(), err)
|
|
|
|
//test
|
|
result, err := suite.VM.RunString("extractTokenSearchParameters(fhirResource, 'Patient.gender | Person.gender | Practitioner.gender | RelatedPerson.gender')")
|
|
require.NoError(suite.T(), err)
|
|
var resultSearchParameter SearchParameterTokenType
|
|
err = json.Unmarshal([]byte(result.String()), &resultSearchParameter)
|
|
//assert
|
|
require.Equal(suite.T(), SearchParameterTokenType{
|
|
{
|
|
System: "",
|
|
Code: "male",
|
|
Text: "",
|
|
},
|
|
}, resultSearchParameter)
|
|
}
|
|
|
|
// Testing Reference extraction
|
|
|
|
// Testing Quantity extraction
|
|
|
|
// Testing Uri extraction
|
|
|
|
// Testing Keyword extraction
|
|
|
|
// Testing Catchall extraction
|