Merge pull request #256 from fastenhealth/labwork_report_filtering

.gitignore

@@ -8,6 +8,7 @@
 .idea/**/tasks.xml
 .idea/**/dictionaries
 .idea/**/shelf
+.idea/dataSources.xml
 
 # Sensitive or high-churn files
 .idea/**/dataSources/

backend/pkg/database/sqlite_repository_query_sql_test.go

@@ -98,7 +98,7 @@ func (suite *RepositorySqlTestSuite) TestQueryResources_SQL() {
 			"FROM fhir_observation as fhir, json_each(fhir.code) as codeJson",
 			"WHERE ((codeJson.value ->> '$.code' = ?)) AND (user_id = ?)",
 			"GROUP BY `fhir`.`id`",
-			"ORDER BY fhir.sort_date ASC",
+			"ORDER BY fhir.sort_date DESC",
 		}, " "),
 		sqlString)
 	require.Equal(suite.T(), sqlParams, []interface{}{
@@ -136,7 +136,7 @@ func (suite *RepositorySqlTestSuite) TestQueryResources_SQL_WithMultipleWhereCon
 			"FROM fhir_observation as fhir, json_each(fhir.code) as codeJson, json_each(fhir.category) as categoryJson",
 			"WHERE ((codeJson.value ->> '$.code' = ?)) AND ((categoryJson.value ->> '$.code' = ?)) AND (user_id = ?)",
 			"GROUP BY `fhir`.`id`",
-			"ORDER BY fhir.sort_date ASC",
+			"ORDER BY fhir.sort_date DESC",
 		}, " "),
 		sqlString)
 	require.Equal(suite.T(), sqlParams, []interface{}{
@@ -158,7 +158,7 @@ func (suite *RepositorySqlTestSuite) TestQueryResources_SQL_WithPrimitiveOrderBy
 			"activityCode": "test_code",
 		},
 		From:         "CarePlan",
-		Aggregations: &models.QueryResourceAggregations{OrderBy: "instantiatesUri"},
+		Aggregations: &models.QueryResourceAggregations{OrderBy: &models.QueryResourceAggregation{Field: "instantiatesUri"}},
 	})
 	require.NoError(suite.T(), err)
 	var results []map[string]interface{}
@@ -193,7 +193,7 @@ func (suite *RepositorySqlTestSuite) TestQueryResources_SQL_WithKeywordOrderByAg
 		Select:       []string{},
 		Where:        map[string]interface{}{},
 		From:         "CarePlan",
-		Aggregations: &models.QueryResourceAggregations{OrderBy: "id"},
+		Aggregations: &models.QueryResourceAggregations{OrderBy: &models.QueryResourceAggregation{Field: "id"}},
 	})
 	require.NoError(suite.T(), err)
 	var results []map[string]interface{}
@@ -230,7 +230,7 @@ func (suite *RepositorySqlTestSuite) TestQueryResources_SQL_WithComplexOrderByAg
 			"code": "test_code",
 		},
 		From:         "Observation",
-		Aggregations: &models.QueryResourceAggregations{OrderBy: "valueString:value"},
+		Aggregations: &models.QueryResourceAggregations{OrderBy: &models.QueryResourceAggregation{Field: "valueString:value"}},
 	})
 	require.NoError(suite.T(), err)
 	var results []map[string]interface{}
@@ -267,7 +267,7 @@ func (suite *RepositorySqlTestSuite) TestQueryResources_SQL_WithPrimitiveCountBy
 			"activityCode": "test_code",
 		},
 		From:         "CarePlan",
-		Aggregations: &models.QueryResourceAggregations{CountBy: "instantiatesUri"},
+		Aggregations: &models.QueryResourceAggregations{CountBy: &models.QueryResourceAggregation{Field: "instantiatesUri"}},
 	})
 	require.NoError(suite.T(), err)
 	var results []map[string]interface{}
@@ -304,7 +304,7 @@ func (suite *RepositorySqlTestSuite) TestQueryResources_SQL_WithKeywordCountByAg
 			"activityCode": "test_code",
 		},
 		From:         "CarePlan",
-		Aggregations: &models.QueryResourceAggregations{CountBy: "source_resource_type"},
+		Aggregations: &models.QueryResourceAggregations{CountBy: &models.QueryResourceAggregation{Field: "source_resource_type"}},
 	})
 	require.NoError(suite.T(), err)
 	var results []map[string]interface{}
@@ -339,7 +339,7 @@ func (suite *RepositorySqlTestSuite) TestQueryResources_SQL_WithWildcardCountByA
 		Select:       []string{},
 		Where:        map[string]interface{}{},
 		From:         "CarePlan",
-		Aggregations: &models.QueryResourceAggregations{CountBy: "*"},
+		Aggregations: &models.QueryResourceAggregations{CountBy: &models.QueryResourceAggregation{Field: "*"}},
 	})
 	require.NoError(suite.T(), err)
 	var results []map[string]interface{}
@@ -376,7 +376,7 @@ func (suite *RepositorySqlTestSuite) TestQueryResources_SQL_WithComplexCountByAg
 			"code": "test_code",
 		},
 		From:         "Observation",
-		Aggregations: &models.QueryResourceAggregations{CountBy: "code:code"},
+		Aggregations: &models.QueryResourceAggregations{CountBy: &models.QueryResourceAggregation{Field: "code:code"}},
 	})
 	require.NoError(suite.T(), err)
 	var results []map[string]interface{}
@@ -398,3 +398,120 @@ func (suite *RepositorySqlTestSuite) TestQueryResources_SQL_WithComplexCountByAg
 		"test_code", "00000000-0000-0000-0000-000000000000",
 	})
 }
+
+func (suite *RepositorySqlTestSuite) TestQueryResources_SQL_WithComplexGroupByWithOrderByMaxFnAggregation() {
+	//setup
+	sqliteRepo := suite.TestRepository.(*SqliteRepository)
+	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",
+		},
+		From: "Observation",
+		Aggregations: &models.QueryResourceAggregations{
+			GroupBy: &models.QueryResourceAggregation{Field: "code:code"},
+			OrderBy: &models.QueryResourceAggregation{Field: "sort_date", Function: "max"},
+		},
+	})
+	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 (codeJson.value ->> '$.code') as label, max(fhir.sort_date) as value",
+			"FROM fhir_observation as fhir, json_each(fhir.code) as codeJson",
+			"WHERE ((codeJson.value ->> '$.code' = ?)) AND (user_id = ?)",
+			"GROUP BY (codeJson.value ->> '$.code')",
+			"ORDER BY max(fhir.sort_date) DESC",
+		}, " "), sqlString)
+	require.Equal(suite.T(), sqlParams, []interface{}{
+		"test_code", "00000000-0000-0000-0000-000000000000",
+	})
+}
+
+func (suite *RepositorySqlTestSuite) TestQueryResources_SQL_WithTokenGroupByNoModifier() {
+	//setup
+	sqliteRepo := suite.TestRepository.(*SqliteRepository)
+	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{}{},
+		From:   "Observation",
+		Aggregations: &models.QueryResourceAggregations{
+			GroupBy: &models.QueryResourceAggregation{Field: "code"},
+		},
+	})
+	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 ((codeJson.value ->> '$.system') || '|' || (codeJson.value ->> '$.code')) as label, count(*) as value",
+			"FROM fhir_observation as fhir, json_each(fhir.code) as codeJson",
+			"WHERE (user_id = ?)",
+			"GROUP BY ((codeJson.value ->> '$.system') || '|' || (codeJson.value ->> '$.code'))",
+			"ORDER BY count(*) DESC",
+		}, " "), sqlString)
+	require.Equal(suite.T(), sqlParams, []interface{}{
+		"00000000-0000-0000-0000-000000000000",
+	})
+}
+
+func (suite *RepositorySqlTestSuite) TestQueryResources_SQL_WithTokenGroupByNoModifierWithLimit() {
+	//setup
+	sqliteRepo := suite.TestRepository.(*SqliteRepository)
+	sqliteRepo.GormClient = sqliteRepo.GormClient.Session(&gorm.Session{DryRun: true})
+
+	//test
+	authContext := context.WithValue(context.Background(), pkg.ContextKeyTypeAuthUsername, "test_username")
+
+	limit := 10
+	sqlQuery, err := sqliteRepo.sqlQueryResources(authContext, models.QueryResource{
+		Select: []string{},
+		Where:  map[string]interface{}{},
+		From:   "Observation",
+		Limit:  &limit,
+		Aggregations: &models.QueryResourceAggregations{
+			GroupBy: &models.QueryResourceAggregation{Field: "code"},
+		},
+	})
+	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 ((codeJson.value ->> '$.system') || '|' || (codeJson.value ->> '$.code')) as label, count(*) as value",
+			"FROM fhir_observation as fhir, json_each(fhir.code) as codeJson",
+			"WHERE (user_id = ?)",
+			"GROUP BY ((codeJson.value ->> '$.system') || '|' || (codeJson.value ->> '$.code'))",
+			"ORDER BY count(*) DESC",
+			"LIMIT 10",
+		}, " "), sqlString)
+	require.Equal(suite.T(), sqlParams, []interface{}{
+		"00000000-0000-0000-0000-000000000000",
+	})
+}

backend/pkg/database/sqlite_repository_query_test.go

@@ -103,6 +103,8 @@ func TestProcessSearchParameterValue(t *testing.T) {
 		{SearchParameter{Type: "token", Name: "identifier", Modifier: "otype"}, "http://terminology.hl7.org/CodeSystem/v2-0203|MR|446053", SearchParameterValue{Value: "MR|446053", Prefix: "", SecondaryValues: map[string]interface{}{"identifierSystem": "http://terminology.hl7.org/CodeSystem/v2-0203"}}, false},
 		{SearchParameter{Type: "token", Name: "code", Modifier: ""}, "|", SearchParameterValue{}, true}, //empty value should throw an error
 		{SearchParameter{Type: "token", Name: "code", Modifier: ""}, "", SearchParameterValue{}, true},  //empty value should throw an error
+		{SearchParameter{Type: "token", Name: "code", Modifier: ""}, "http://acme.org/conditions/codes|", SearchParameterValue{Value: "", Prefix: "", SecondaryValues: map[string]interface{}{"codeSystem": "http://acme.org/conditions/codes"}}, false},
+		{SearchParameter{Type: "token", Name: "code", Modifier: ""}, "|807-1", SearchParameterValue{Value: "807-1", Prefix: "", SecondaryValues: map[string]interface{}{"codeSystem": ""}}, false},
 
 		{SearchParameter{Type: "quantity", Name: "valueQuantity", Modifier: ""}, "5.4|http://unitsofmeasure.org|mg", SearchParameterValue{Value: float64(5.4), Prefix: "", SecondaryValues: map[string]interface{}{"valueQuantitySystem": "http://unitsofmeasure.org", "valueQuantityCode": "mg"}}, false},
 		{SearchParameter{Type: "quantity", Name: "valueQuantity", Modifier: ""}, "5.40e-3|http://unitsofmeasure.org|g", SearchParameterValue{Value: float64(0.0054), Prefix: "", SecondaryValues: map[string]interface{}{"valueQuantitySystem": "http://unitsofmeasure.org", "valueQuantityCode": "g"}}, false},
@@ -204,6 +206,55 @@ func TestSearchCodeToFromClause(t *testing.T) {
 
 }
 
+//Aggregation tests
+
+// mimic tests from https://hl7.org/fhir/r4/search.html#token
+func TestProcessAggregationParameter(t *testing.T) {
+	//setup
+	t.Parallel()
+	var processSearchParameterTests = []struct {
+		aggregationFieldWithFn models.QueryResourceAggregation // input
+		searchParameterLookup  map[string]string               // input (allowed search parameters)
+		expected               AggregationParameter
+		expectedError          bool // expected result
+	}{
+		//primitive types
+		{models.QueryResourceAggregation{Field: "test"}, map[string]string{"test": "keyword"}, AggregationParameter{SearchParameter: SearchParameter{Type: "keyword", Name: "test", Modifier: ""}}, false},
+		{models.QueryResourceAggregation{Field: "test"}, map[string]string{"test": "number"}, AggregationParameter{SearchParameter: SearchParameter{Type: "number", Name: "test", Modifier: ""}}, false},
+		{models.QueryResourceAggregation{Field: "test"}, map[string]string{"test": "uri"}, AggregationParameter{SearchParameter: SearchParameter{Type: "uri", Name: "test", Modifier: ""}}, false},
+		{models.QueryResourceAggregation{Field: "test"}, map[string]string{"test": "date"}, AggregationParameter{SearchParameter: SearchParameter{Type: "date", Name: "test", Modifier: ""}}, false},
+
+		{models.QueryResourceAggregation{Field: "test:hello"}, map[string]string{"test": "keyword"}, AggregationParameter{SearchParameter: SearchParameter{Type: "date", Name: "test", Modifier: ""}}, true}, //cannot have a modifier
+		{models.QueryResourceAggregation{Field: "test:hello"}, map[string]string{"test": "number"}, AggregationParameter{SearchParameter: SearchParameter{Type: "date", Name: "test", Modifier: ""}}, true},  //cannot have a modifier
+		{models.QueryResourceAggregation{Field: "test:hello"}, map[string]string{"test": "uri"}, AggregationParameter{SearchParameter: SearchParameter{Type: "date", Name: "test", Modifier: ""}}, true},     //cannot have a modifier
+		{models.QueryResourceAggregation{Field: "test:hello"}, map[string]string{"test": "date"}, AggregationParameter{SearchParameter: SearchParameter{Type: "date", Name: "test", Modifier: ""}}, true},    //cannot have a modifier
+
+		//complex types
+		{models.QueryResourceAggregation{Field: "test"}, map[string]string{"test": "reference"}, AggregationParameter{SearchParameter: SearchParameter{Type: "reference", Name: "test", Modifier: ""}}, true}, //complex types should throw an error when missing modifier
+		{models.QueryResourceAggregation{Field: "test"}, map[string]string{"test": "string"}, AggregationParameter{SearchParameter: SearchParameter{Type: "string", Name: "test", Modifier: ""}}, true},       //complex types should throw an error when missing modifier
+		{models.QueryResourceAggregation{Field: "test"}, map[string]string{"test": "quantity"}, AggregationParameter{SearchParameter: SearchParameter{Type: "quantity", Name: "test", Modifier: ""}}, true},   //complex types should throw an error when missing modifier
+
+		{models.QueryResourceAggregation{Field: "test:hello"}, map[string]string{"test": "reference"}, AggregationParameter{SearchParameter: SearchParameter{Type: "reference", Name: "test", Modifier: "hello"}}, false},
+		{models.QueryResourceAggregation{Field: "test:hello"}, map[string]string{"test": "string"}, AggregationParameter{SearchParameter: SearchParameter{Type: "string", Name: "test", Modifier: "hello"}}, false},
+		{models.QueryResourceAggregation{Field: "test:hello"}, map[string]string{"test": "quantity"}, AggregationParameter{SearchParameter: SearchParameter{Type: "quantity", Name: "test", Modifier: "hello"}}, false},
+
+		//token type
+		{models.QueryResourceAggregation{Field: "code"}, map[string]string{"code": "token"}, AggregationParameter{SearchParameter: SearchParameter{Type: "token", Name: "code", Modifier: ""}}, false},
+		{models.QueryResourceAggregation{Field: "code:code"}, map[string]string{"code": "token"}, AggregationParameter{SearchParameter: SearchParameter{Type: "token", Name: "code", Modifier: "code"}}, false},
+	}
+
+	//test && assert
+	for ndx, tt := range processSearchParameterTests {
+		actual, actualErr := ProcessAggregationParameter(tt.aggregationFieldWithFn, tt.searchParameterLookup)
+		if tt.expectedError {
+			require.Error(t, actualErr, "Expected error but got none for processAggregationParameterTests[%d] %s", ndx, tt.aggregationFieldWithFn)
+		} else {
+			require.NoError(t, actualErr, "Expected no error but got one for processAggregationParameterTests[%d] %s", ndx, tt.aggregationFieldWithFn)
+			require.Equal(t, tt.expected, actual)
+		}
+	}
+}
+
 func (suite *RepositoryTestSuite) TestQueryResources_SQL() {
 	//setup
 	fakeConfig := mock_config.NewMockInterface(suite.MockCtrl)
@@ -245,7 +296,7 @@ func (suite *RepositoryTestSuite) TestQueryResources_SQL() {
 			"SELECT fhir.*",
 			"FROM fhir_observation as fhir, json_each(fhir.code) as codeJson",
 			"WHERE ((codeJson.value ->> '$.code' = ?)) AND (user_id = ?) GROUP BY `fhir`.`id`",
-			"ORDER BY fhir.sort_date ASC"}, " "))
+			"ORDER BY fhir.sort_date DESC"}, " "))
 	require.Equal(suite.T(), sqlParams, []interface{}{
 		"test_code", "00000000-0000-0000-0000-000000000000",
 	})

backend/pkg/models/database/fhir_account.go

@@ -62,6 +62,7 @@ func (s *FhirAccount) GetSearchParameters() map[string]string {
 		"owner":                "reference",
 		"period":               "date",
 		"profile":              "reference",
+		"sort_date":            "date",
 		"source_id":            "keyword",
 		"source_resource_id":   "keyword",
 		"source_resource_type": "keyword",

backend/pkg/models/database/fhir_adverse_event.go

@@ -85,6 +85,7 @@ func (s *FhirAdverseEvent) GetSearchParameters() map[string]string {
 		"resultingcondition":   "reference",
 		"seriousness":          "token",
 		"severity":             "token",
+		"sort_date":            "date",
 		"source_id":            "keyword",
 		"source_resource_id":   "keyword",
 		"source_resource_type": "keyword",

backend/pkg/models/database/fhir_allergy_intolerance.go

@@ -165,6 +165,7 @@ func (s *FhirAllergyIntolerance) GetSearchParameters() map[string]string {
 		"recorder":             "reference",
 		"route":                "token",
 		"severity":             "token",
+		"sort_date":            "date",
 		"source_id":            "keyword",
 		"source_resource_id":   "keyword",
 		"source_resource_type": "keyword",

backend/pkg/models/database/fhir_appointment.go

@@ -101,6 +101,7 @@ func (s *FhirAppointment) GetSearchParameters() map[string]string {
 		"serviceCategory":      "token",
 		"serviceType":          "token",
 		"slot":                 "reference",
+		"sort_date":            "date",
 		"source_id":            "keyword",
 		"source_resource_id":   "keyword",
 		"source_resource_type": "keyword",

backend/pkg/models/database/fhir_binary.go

@@ -40,6 +40,7 @@ func (s *FhirBinary) GetSearchParameters() map[string]string {
 		"language":             "token",
 		"lastUpdated":          "date",
 		"profile":              "reference",
+		"sort_date":            "date",
 		"source_id":            "keyword",
 		"source_resource_id":   "keyword",
 		"source_resource_type": "keyword",

backend/pkg/models/database/fhir_care_plan.go

@@ -167,6 +167,7 @@ func (s *FhirCarePlan) GetSearchParameters() map[string]string {
 		"performer":             "reference",
 		"profile":               "reference",
 		"replaces":              "reference",
+		"sort_date":             "date",
 		"source_id":             "keyword",
 		"source_resource_id":    "keyword",
 		"source_resource_type":  "keyword",

backend/pkg/models/database/fhir_care_team.go

@@ -119,6 +119,7 @@ func (s *FhirCareTeam) GetSearchParameters() map[string]string {
 		"lastUpdated":          "date",
 		"participant":          "reference",
 		"profile":              "reference",
+		"sort_date":            "date",
 		"source_id":            "keyword",
 		"source_resource_id":   "keyword",
 		"source_resource_type": "keyword",

backend/pkg/models/database/fhir_claim.go

@@ -101,6 +101,7 @@ func (s *FhirClaim) GetSearchParameters() map[string]string {
 		"procedureUdi":         "reference",
 		"profile":              "reference",
 		"provider":             "reference",
+		"sort_date":            "date",
 		"source_id":            "keyword",
 		"source_resource_id":   "keyword",
 		"source_resource_type": "keyword",

backend/pkg/models/database/fhir_claim_response.go

@@ -78,6 +78,7 @@ func (s *FhirClaimResponse) GetSearchParameters() map[string]string {
 		"profile":              "reference",
 		"request":              "reference",
 		"requestor":            "reference",
+		"sort_date":            "date",
 		"source_id":            "keyword",
 		"source_resource_id":   "keyword",
 		"source_resource_type": "keyword",

backend/pkg/models/database/fhir_composition.go

@@ -169,6 +169,7 @@ func (s *FhirComposition) GetSearchParameters() map[string]string {
 		"relatedId":            "token",
 		"relatedRef":           "reference",
 		"section":              "token",
+		"sort_date":            "date",
 		"source_id":            "keyword",
 		"source_resource_id":   "keyword",
 		"source_resource_type": "keyword",

backend/pkg/models/database/fhir_condition.go

@@ -167,6 +167,7 @@ func (s *FhirCondition) GetSearchParameters() map[string]string {
 		"profile":              "reference",
 		"recordedDate":         "date",
 		"severity":             "token",
+		"sort_date":            "date",
 		"source_id":            "keyword",
 		"source_resource_id":   "keyword",
 		"source_resource_type": "keyword",

backend/pkg/models/database/fhir_consent.go

@@ -147,6 +147,7 @@ func (s *FhirConsent) GetSearchParameters() map[string]string {
 		"purpose":              "token",
 		"scope":                "token",
 		"securityLabel":        "token",
+		"sort_date":            "date",
 		"sourceReference":      "reference",
 		"source_id":            "keyword",
 		"source_resource_id":   "keyword",

backend/pkg/models/database/fhir_coverage.go

@@ -74,6 +74,7 @@ func (s *FhirCoverage) GetSearchParameters() map[string]string {
 		"payor":                "reference",
 		"policyHolder":         "reference",
 		"profile":              "reference",
+		"sort_date":            "date",
 		"source_id":            "keyword",
 		"source_resource_id":   "keyword",
 		"source_resource_type": "keyword",