adding tests to ensure that the same field with multiple modifiers is correctly handled.

adding IPS query logic. Adding IPS sections. TODO: tests broken.
2024-02-20 10:22:19 -08:00 · 2024-02-20 10:22:19 -08:00 · 68859546c0
parent a5eba794b5
commit 68859546c0
4 changed files with 345 additions and 2 deletions
--- a/backend/pkg/constants.go
+++ b/backend/pkg/constants.go
@ -10,6 +10,8 @@ type DatabaseRepositoryType string
 type InstallationVerificationStatus string
 type InstallationQuotaStatus string

+type IPSSections string
+
 const (
 	ResourceListPageSize int = 20

@ -50,4 +52,19 @@ const (
 	InstallationVerificationStatusVerified InstallationVerificationStatus = "VERIFIED" //email has been verified
 	InstallationQuotaStatusActive          InstallationQuotaStatus        = "ACTIVE"
 	InstallationQuotaStatusConsumed        InstallationQuotaStatus        = "CONSUMED"
+
+	IPSSectionsMedicationSummary     IPSSections = "medication_summary"
+	IPSSectionsAllergiesIntolerances IPSSections = "allergies_intolerances"
+	IPSSectionsProblemList           IPSSections = "problem_list"
+	IPSSectionsImmunizations         IPSSections = "immunizations"
+	IPSSectionsHistoryOfProcedures   IPSSections = "history_of_procedures"
+	IPSSectionsMedicalDevices        IPSSections = "medical_devices"
+	IPSSectionsDiagnosticResults     IPSSections = "diagnostic_results"
+	IPSSectionsVitalSigns            IPSSections = "vital_signs"
+	IPSSectionsHistoryOfIllnesses    IPSSections = "history_of_illnesses"
+	IPSSectionsPregnancy             IPSSections = "pregnancy"
+	IPSSectionsSocialHistory         IPSSections = "social_history"
+	IPSSectionsPlanOfCare            IPSSections = "plan_of_care"
+	IPSSectionsFunctionalStatus      IPSSections = "functional_status"
+	IPSSectionsAdvanceDirectives     IPSSections = "advance_directives"
 )
--- a/backend/pkg/database/gorm_repository_query.go
+++ b/backend/pkg/database/gorm_repository_query.go
@ -3,6 +3,7 @@ package database
 import (
 	"context"
 	"fmt"
+	"log"
 	"sort"
 	"strconv"
 	"strings"
@ -230,6 +231,15 @@ func (gr *GormRepository) sqlQueryResources(ctx context.Context, query models.Qu
 		}
 	}

+	log.Printf("!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!")
+	log.Printf("!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!")
+	log.Printf("!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!")
+	log.Printf("!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!")
+	log.Printf("!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!")
+	log.Printf("!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!")
+	log.Printf("whereClauses: %v", whereClauses)
+	log.Printf("whereNamedParameters: %v", whereNamedParameters)
+
 	//ensure Where and From clauses are unique
 	whereClauses = lo.Uniq(whereClauses)
 	whereClauses = lo.Compact(whereClauses)
--- a/backend/pkg/database/gorm_repository_query_sql_test.go
+++ b/backend/pkg/database/gorm_repository_query_sql_test.go
@ -186,7 +186,7 @@ func (suite *RepositorySqlTestSuite) TestQueryResources_SQL_WithTokenWithNotModi
 	})
 }

-func (suite *RepositorySqlTestSuite) TestQueryResources_SQL_WithTokenMultipleValuesWithNotModifier() {
+func (suite *RepositorySqlTestSuite) TestQueryResources_SQL_WithTokenMultipleANDValuesWithNotModifier() {
 	//setup
 	sqliteRepo := suite.TestRepository.(*GormRepository)
 	sqliteRepo.GormClient = sqliteRepo.GormClient.Session(&gorm.Session{DryRun: true})
@ -197,7 +197,7 @@ func (suite *RepositorySqlTestSuite) TestQueryResources_SQL_WithTokenMultipleVal
 	sqlQuery, err := sqliteRepo.sqlQueryResources(authContext, models.QueryResource{
 		Select: []string{},
 		Where: map[string]interface{}{
-			"code:not": []string{"test_code", "test_code2"},
+			"code:not": []string{"test_code", "test_code2"}, //AND condition
 		},
 		From: "Observation",
 	})
@ -223,6 +223,81 @@ func (suite *RepositorySqlTestSuite) TestQueryResources_SQL_WithTokenMultipleVal
 	})
 }

+func (suite *RepositorySqlTestSuite) TestQueryResources_SQL_WithTokenMultipleORValues() {
+	//setup
+	sqliteRepo := suite.TestRepository.(*GormRepository)
+	sqliteRepo.GormClient = sqliteRepo.GormClient.Session(&gorm.Session{DryRun: true})
+
+	//test
+	authContext := context.WithValue(context.Background(), pkg.ContextKeyTypeAuthUsername, "test_username")
+
+	sqlQuery, err := sqliteRepo.sqlQueryResources(authContext, models.QueryResource{
+		Select: []string{},
+		Where: map[string]interface{}{
+			"code": "test_code,test_code2", //OR condition
+		},
+		From: "Observation",
+	})
+	require.NoError(suite.T(), err)
+	var results []map[string]interface{}
+	statement := sqlQuery.Find(&results).Statement
+	sqlString := statement.SQL.String()
+	sqlParams := statement.Vars
+
+	//assert
+	require.NoError(suite.T(), err)
+	require.Equal(suite.T(),
+		strings.Join([]string{
+			"SELECT fhir.*",
+			"FROM fhir_observation as fhir, json_each(fhir.code) as codeJson",
+			"WHERE ((codeJson.value ->> '$.code' = ?)) OR ((codeJson.value ->> '$.code' = ?)) AND (user_id = ?)",
+			"GROUP BY `fhir`.`id`",
+			"ORDER BY fhir.sort_date DESC",
+		}, " "),
+		sqlString)
+	require.Equal(suite.T(), sqlParams, []interface{}{
+		"test_code", "test_code2", "00000000-0000-0000-0000-000000000000",
+	})
+}
+
+func (suite *RepositorySqlTestSuite) TestQueryResources_SQL_WithTokenMixedMultipleANDORValues() {
+	//setup
+	sqliteRepo := suite.TestRepository.(*GormRepository)
+	sqliteRepo.GormClient = sqliteRepo.GormClient.Session(&gorm.Session{DryRun: true})
+
+	//test
+	authContext := context.WithValue(context.Background(), pkg.ContextKeyTypeAuthUsername, "test_username")
+
+	sqlQuery, err := sqliteRepo.sqlQueryResources(authContext, models.QueryResource{
+		Select: []string{},
+		Where: map[string]interface{}{
+			"code:not": []string{"test_code", "test_code2", "test_code3"}, //AND condition
+			"code":     "test_code4,test_code5,test_code6",                //OR condition
+		},
+		From: "Observation",
+	})
+	require.NoError(suite.T(), err)
+	var results []map[string]interface{}
+	statement := sqlQuery.Find(&results).Statement
+	sqlString := statement.SQL.String()
+	sqlParams := statement.Vars
+
+	//assert
+	require.NoError(suite.T(), err)
+	require.Equal(suite.T(),
+		strings.Join([]string{
+			"SELECT fhir.*",
+			"FROM fhir_observation as fhir, json_each(fhir.code) as codeJson",
+			"WHERE ((codeJson.value ->> '$.code' <> ?)) AND ((codeJson.value ->> '$.code' <> ?)) AND ((codeJson.value ->> '$.code' <> ?)) AND ((codeJson.value ->> '$.code' = ?) OR (codeJson.value ->> '$.code' = ?) OR (codeJson.value ->> '$.code' = ?)) AND (user_id = ?)",
+			"GROUP BY `fhir`.`id`",
+			"ORDER BY fhir.sort_date DESC",
+		}, " "),
+		sqlString)
+	require.Equal(suite.T(), sqlParams, []interface{}{
+		"test_code", "test_code2", "test_code3", "test_code4", "00000000-0000-0000-0000-000000000000",
+	})
+}
+
 func (suite *RepositorySqlTestSuite) TestQueryResources_SQL_WithPrimitiveOrderByAggregation() {
 	//setup
 	sqliteRepo := suite.TestRepository.(*GormRepository)
--- a/backend/pkg/database/gorm_repository_summary.go
+++ b/backend/pkg/database/gorm_repository_summary.go
@ -0,0 +1,241 @@
+package database
+
+import (
+	"context"
+	"github.com/fastenhealth/fasten-onprem/backend/pkg"
+	"github.com/fastenhealth/fasten-onprem/backend/pkg/models"
+	databaseModel "github.com/fastenhealth/fasten-onprem/backend/pkg/models/database"
+)
+
+// GetInternationalPatientSummary will generate an IPS bundle, which can then be used to generate a IPS QR code, PDF or JSON bundle
+// The IPS bundle will contain a summary of all the data in the system, including a list of all sources, and the main Patient
+// See: https://github.com/fastenhealth/fasten-onprem/issues/170
+// See: https://github.com/jddamore/fhir-ips-server/blob/main/docs/Summary_Creation_Steps.md
+func (gr *GormRepository) GetInternationalPatientSummary(ctx context.Context) (*models.Summary, error) {
+	currentUser, currentUserErr := gr.GetCurrentUser(ctx)
+	if currentUserErr != nil {
+		return nil, currentUserErr
+	}
+
+	// we want a count of all resources for this user by type
+	var resourceCountResults []map[string]interface{}
+
+	resourceTypes := databaseModel.GetAllowedResourceTypes()
+	for _, resourceType := range resourceTypes {
+		tableName, err := databaseModel.GetTableNameByResourceType(resourceType)
+		if err != nil {
+			return nil, err
+		}
+		var count int64
+
+		gr.QueryResources(ctx, models.QueryResource{
+			Use:          "",
+			Select:       nil,
+			From:         "",
+			Where:        nil,
+			Limit:        nil,
+			Offset:       nil,
+			Aggregations: nil,
+		})
+
+		result := gr.GormClient.WithContext(ctx).
+			Table(tableName).
+			Where(models.OriginBase{
+				UserID: currentUser.ID,
+			}).
+			Count(&count)
+		if result.Error != nil {
+			return nil, result.Error
+		}
+		if count == 0 {
+			continue //don't add resource counts if the count is 0
+		}
+		resourceCountResults = append(resourceCountResults, map[string]interface{}{
+			"resource_type": resourceType,
+			"count":         count,
+		})
+	}
+
+	// we want a list of all sources (when they were last updated)
+	sources, err := gr.GetSources(ctx)
+	if err != nil {
+		return nil, err
+	}
+
+	// we want the main Patient for each source
+	patients, err := gr.GetPatientForSources(ctx)
+	if err != nil {
+		return nil, err
+	}
+
+	if resourceCountResults == nil {
+		resourceCountResults = []map[string]interface{}{}
+	}
+	summary := &models.Summary{
+		Sources:            sources,
+		ResourceTypeCounts: resourceCountResults,
+		Patients:           patients,
+	}
+
+	return summary, nil
+}
+
+// https://github.com/jddamore/fhir-ips-server/blob/main/docs/Summary_Creation_Steps.md
+func generateIPSSectionQueries(sectionType pkg.IPSSections) ([]models.QueryResource, error) {
+
+	queries := []models.QueryResource{}
+	switch sectionType {
+	case pkg.IPSSectionsAllergiesIntolerances:
+		queries = append(queries, models.QueryResource{
+			Select: nil,
+			From:   "AllergyIntolerance",
+			Where: map[string]interface{}{
+				"clinicalStatus:not":     []string{"inactive", "resolved"},
+				"verificationStatus:not": []string{"entered-in-error"},
+			},
+		})
+		break
+	case pkg.IPSSectionsProblemList:
+		queries = append(queries, models.QueryResource{
+			Select: nil,
+			From:   "Condition",
+			Where: map[string]interface{}{
+				"clinicalStatus:not":     []string{"inactive", "resolved"},
+				"verificationStatus:not": []string{"entered-in-error"},
+			},
+		})
+		break
+	case pkg.IPSSectionsMedicationSummary:
+		queries = append(queries, models.QueryResource{
+			Select: nil,
+			From:   "MedicationStatement",
+			Where: map[string]interface{}{
+				"status": "active,intended,unknown,on-hold",
+			},
+		})
+		queries = append(queries, models.QueryResource{
+			Select: nil,
+			From:   "MedicationRequest",
+			Where: map[string]interface{}{
+				"status": "active,unknown,on-hold",
+			},
+		})
+		break
+	case pkg.IPSSectionsDiagnosticResults:
+		queries = append(queries, models.QueryResource{
+			Select: nil,
+			From:   "DiagnosticReport",
+			Where: map[string]interface{}{
+				"category": "LAB",
+			},
+		})
+
+		//TODO: group by code, sort by date, limit to the most recent 3
+		queries = append(queries, models.QueryResource{
+			Select: nil,
+			From:   "Observation",
+			Where: map[string]interface{}{
+				"category":   "laboratory",
+				"status:not": "preliminary",
+			},
+		})
+		break
+	case pkg.IPSSectionsVitalSigns:
+		//TODO: group by code, sort by date, limit to the most recent 3
+		queries = append(queries, models.QueryResource{
+			Select: nil,
+			From:   "Observation",
+			Where: map[string]interface{}{
+				"category": "vital-signs",
+			},
+		})
+		break
+	case pkg.IPSSectionsSocialHistory:
+		queries = append(queries, models.QueryResource{
+			Select: nil,
+			From:   "Observation",
+			Where: map[string]interface{}{
+				"category":   "social-history",
+				"status:not": "preliminary",
+			},
+		})
+		break
+	case pkg.IPSSectionsPregnancy:
+		//TODO: determine the code for pregnancy from IPS specification
+		queries = append(queries, models.QueryResource{
+			Select: nil,
+			From:   "Observation",
+			Where: map[string]interface{}{
+				"status:not": "preliminary",
+			},
+		})
+		break
+	case pkg.IPSSectionsImmunizations:
+		queries = append(queries, models.QueryResource{
+			Select: nil,
+			From:   "Immunization",
+			Where: map[string]interface{}{
+				"status:not": "entered-in-error",
+			},
+		})
+		break
+	case pkg.IPSSectionsAdvanceDirectives:
+		queries = append(queries, models.QueryResource{
+			Select: nil,
+			From:   "Consent",
+			Where: map[string]interface{}{
+				"status": "active",
+			},
+		})
+		break
+	case pkg.IPSSectionsFunctionalStatus:
+		queries = append(queries, models.QueryResource{
+			Select: nil,
+			From:   "ClinicalImpression",
+			Where: map[string]interface{}{
+				"status": "in-progress,completed",
+			},
+		})
+		break
+	case pkg.IPSSectionsMedicalDevices:
+		queries = append(queries, models.QueryResource{
+			Select: nil,
+			From:   "Device",
+			Where: map[string]interface{}{
+				"status": "entered-in-error",
+			},
+		})
+		break
+	case pkg.IPSSectionsHistoryOfIllnesses:
+		//TODO: last updated date should be older than 5 years (dateTime or period.high)
+		//TODO: check if where clause with multiple modifiers for the same field works as expected
+		queries = append(queries, models.QueryResource{
+			Select: nil,
+			From:   "Condition",
+			Where: map[string]interface{}{
+				"clinicalStatus:not": []string{"entered-in-error"},
+				"clinicalStatus":     "inactive,remission,resolved",
+			},
+		})
+		break
+	case pkg.IPSSectionsPlanOfCare:
+		queries = append(queries, models.QueryResource{
+			Select: nil,
+			From:   "CarePlan",
+			Where: map[string]interface{}{
+				"status": "active,on-hold,unknown",
+			},
+		})
+		break
+	case pkg.IPSSectionsHistoryOfProcedures:
+		queries = append(queries, models.QueryResource{
+			Select: nil,
+			From:   "Procedure",
+			Where: map[string]interface{}{
+				"status:not": []string{"entered-in-error", "not-done"},
+			},
+		})
+	}
+
+	return queries, nil
+}