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make sure tokens support modifiers during query 

make sure we can use multiple AND clauses in query.
This commit is contained in:
Jason Kulatunga 2024-02-19 18:31:18 -08:00
parent d0f2080d09
commit a5eba794b5
No known key found for this signature in database
4 changed files with 97 additions and 8 deletions
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22
backend/pkg/database/gorm_repository_query.go
View File

@ -313,9 +313,10 @@ func ProcessSearchParameter(searchCodeWithModifier string, searchParamTypeLookup
searchParameter.Type = SearchParameterType(searchParamTypeStr)
}
//if this is a token search parameter with a modifier, we need to throw an error
if searchParameter.Type == SearchParameterTypeToken && len(searchParameter.Modifier) > 0 {
return searchParameter, fmt.Errorf("token search parameter %s cannot have a modifier", searchParameter.Name)
//only a limited set of token modifiers are allowed. Otherwise we need to throw an error
allowedTokenModifiers := []string{"not"}
if searchParameter.Type == SearchParameterTypeToken && len(searchParameter.Modifier) > 0 && !lo.Contains(allowedTokenModifiers, searchParameter.Modifier) {
return searchParameter, fmt.Errorf("token search parameter %s does not support this modifier: %s", searchParameter.Name, searchParameter.Modifier)
}
return searchParameter, nil
@ -332,8 +333,8 @@ func ProcessSearchParameter(searchCodeWithModifier string, searchParamTypeLookup
//
// For example, searchParamCodeValueOrValuesWithPrefix may be:
//
// "code": "29463-7,3141-9,27113001"
// "code": ["le29463-7", "gt3141-9", "27113001"]
// "code": "29463-7,3141-9,27113001" = OR
// "code": ["le29463-7", "gt3141-9", "27113001"] = AND
func ProcessSearchParameterValueIntoOperatorTree(searchParameter SearchParameter, searchParamCodeValueOrValuesWithPrefix interface{}) (SearchParameterValueOperatorTree, error) {
searchParamCodeValuesWithPrefix := []string{}
@ -344,6 +345,11 @@ func ProcessSearchParameterValueIntoOperatorTree(searchParameter SearchParameter
case []string:
searchParamCodeValuesWithPrefix = v
break
case []interface{}:
for _, searchParamCodeValue := range v {
searchParamCodeValuesWithPrefix = append(searchParamCodeValuesWithPrefix, fmt.Sprintf("%v", searchParamCodeValue))
}
break
default:
return nil, fmt.Errorf("invalid search parameter value type %T, must be a string or a list of strings (%s=%v)", v, searchParameter.Name, searchParamCodeValueOrValuesWithPrefix)
}
@ -574,7 +580,11 @@ func SearchCodeToWhereClause(searchParam SearchParameter, searchParamValue Searc
//setup the clause
clause := []string{}
if searchParamValue.Value.(string) != "" {
clause = append(clause, fmt.Sprintf("%sJson.value ->> '$.code' = @%s", searchParam.Name, NamedParameterWithSuffix(searchParam.Name, namedParameterSuffix)))
if searchParam.Modifier == "" {
clause = append(clause, fmt.Sprintf("%sJson.value ->> '$.code' = @%s", searchParam.Name, NamedParameterWithSuffix(searchParam.Name, namedParameterSuffix)))
} else if searchParam.Modifier == "not" {
clause = append(clause, fmt.Sprintf("%sJson.value ->> '$.code' <> @%s", searchParam.Name, NamedParameterWithSuffix(searchParam.Name, namedParameterSuffix)))
}
}
//append the code and/or system clauses (if required)

74
backend/pkg/database/gorm_repository_query_sql_test.go
View File

@ -149,6 +149,80 @@ func (suite *RepositorySqlTestSuite) TestQueryResources_SQL_WithMultipleWhereCon
})
}
func (suite *RepositorySqlTestSuite) TestQueryResources_SQL_WithTokenWithNotModifier() {
//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": "test_code",
},
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 ->> '$.code' <> ?)) AND (user_id = ?)",
"GROUP BY `fhir`.`id`",
"ORDER BY fhir.sort_date DESC",
}, " "),
sqlString)
require.Equal(suite.T(), sqlParams, []interface{}{
"test_code", "00000000-0000-0000-0000-000000000000",
})
}
func (suite *RepositorySqlTestSuite) TestQueryResources_SQL_WithTokenMultipleValuesWithNotModifier() {
//setup
sqliteRepo := suite.TestRepository.(*GormRepository)
sqliteRepo.GormClient = sqliteRepo.GormClient.Session(&gorm.Session{DryRun: true})
//test
authContext := context.WithValue(context.Background(), pkg.ContextKeyTypeAuthUsername, "test_username")
sqlQuery, err := sqliteRepo.sqlQueryResources(authContext, models.QueryResource{
Select: []string{},
Where: map[string]interface{}{
"code:not": []string{"test_code", "test_code2"},
},
From: "Observation",
})
require.NoError(suite.T(), err)
var results []map[string]interface{}
statement := sqlQuery.Find(&results).Statement
sqlString := statement.SQL.String()
sqlParams := statement.Vars
//assert
require.NoError(suite.T(), err)
require.Equal(suite.T(),
strings.Join([]string{
"SELECT fhir.*",
"FROM fhir_observation as fhir, json_each(fhir.code) as codeJson",
"WHERE ((codeJson.value ->> '$.code' <> ?)) AND ((codeJson.value ->> '$.code' <> ?)) AND (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_WithPrimitiveOrderByAggregation() {
//setup
sqliteRepo := suite.TestRepository.(*GormRepository)

8
backend/pkg/database/gorm_repository_query_test.go
View File

@ -38,7 +38,9 @@ func TestProcessSearchParameter(t *testing.T) {
{"url:below", map[string]string{"url": "string"}, SearchParameter{Type: "string", Name: "url", Modifier: "below"}, false},
{"url:above", map[string]string{"url": "string"}, SearchParameter{Type: "string", Name: "url", Modifier: "above"}, false},
{"display:text", map[string]string{"display": "token"}, SearchParameter{}, true},
{"display", map[string]string{"display": "token"}, SearchParameter{Type: "token", Name: "display", Modifier: ""}, false},
{"display:not", map[string]string{"display": "token"}, SearchParameter{Type: "token", Name: "display", Modifier: "not"}, false},
{"display:unsupported", map[string]string{"display": "token"}, SearchParameter{}, true},
}
//test && assert
@ -161,7 +163,9 @@ func TestSearchCodeToWhereClause(t *testing.T) {
{SearchParameter{Type: "token", Name: "code", Modifier: ""}, SearchParameterValue{Value: "ha125", Prefix: "", SecondaryValues: map[string]interface{}{"codeSystem": "http://acme.org/conditions/codes"}}, "0_0", "(codeJson.value ->> '$.code' = @code_0_0 AND codeJson.value ->> '$.system' = @codeSystem_0_0)", map[string]interface{}{"code_0_0": "ha125", "codeSystem_0_0": "http://acme.org/conditions/codes"}, false},
{SearchParameter{Type: "token", Name: "code", Modifier: ""}, SearchParameterValue{Value: "ha125", Prefix: "", SecondaryValues: map[string]interface{}{}}, "0_0", "(codeJson.value ->> '$.code' = @code_0_0)", map[string]interface{}{"code_0_0": "ha125"}, false},
{SearchParameter{Type: "token", Name: "identifier", Modifier: "otype"}, SearchParameterValue{Value: "MR|446053", Prefix: "", SecondaryValues: map[string]interface{}{"identifierSystem": "http://terminology.hl7.org/CodeSystem/v2-0203"}}, "0_0", "(identifierJson.value ->> '$.code' = @identifier_0_0 AND identifierJson.value ->> '$.system' = @identifierSystem_0_0)", map[string]interface{}{"identifier_0_0": "MR|446053", "identifierSystem_0_0": "http://terminology.hl7.org/CodeSystem/v2-0203"}, false},
{SearchParameter{Type: "token", Name: "identifier", Modifier: ""}, SearchParameterValue{Value: "MR|446053", Prefix: "", SecondaryValues: map[string]interface{}{"identifierSystem": "http://terminology.hl7.org/CodeSystem/v2-0203"}}, "0_0", "(identifierJson.value ->> '$.code' = @identifier_0_0 AND identifierJson.value ->> '$.system' = @identifierSystem_0_0)", map[string]interface{}{"identifier_0_0": "MR|446053", "identifierSystem_0_0": "http://terminology.hl7.org/CodeSystem/v2-0203"}, false},
{SearchParameter{Type: "token", Name: "gender", Modifier: ""}, SearchParameterValue{Value: "male", Prefix: "", SecondaryValues: map[string]interface{}{"genderSystem": "http://terminology.hl7.org/CodeSystem/v2-0203"}}, "0_0", "(genderJson.value ->> '$.code' = @gender_0_0 AND genderJson.value ->> '$.system' = @genderSystem_0_0)", map[string]interface{}{"gender_0_0": "male", "genderSystem_0_0": "http://terminology.hl7.org/CodeSystem/v2-0203"}, false},
{SearchParameter{Type: "token", Name: "gender", Modifier: "not"}, SearchParameterValue{Value: "male", Prefix: "", SecondaryValues: map[string]interface{}{"genderSystem": "http://terminology.hl7.org/CodeSystem/v2-0203"}}, "0_0", "(genderJson.value ->> '$.code' <> @gender_0_0 AND genderJson.value ->> '$.system' = @genderSystem_0_0)", map[string]interface{}{"gender_0_0": "male", "genderSystem_0_0": "http://terminology.hl7.org/CodeSystem/v2-0203"}, false},
{SearchParameter{Type: "keyword", Name: "id", Modifier: ""}, SearchParameterValue{Value: "1234", Prefix: "", SecondaryValues: map[string]interface{}{}}, "0_0", "(id = @id_0_0)", map[string]interface{}{"id_0_0": "1234"}, false},
}

1
backend/pkg/database/interface.go
View File

@ -19,6 +19,7 @@ type DatabaseRepository interface {
GetCurrentUser(ctx context.Context) (*models.User, error)
DeleteCurrentUser(ctx context.Context) error
//get a count of every resource type
GetSummary(ctx context.Context) (*models.Summary, error)
GetResourceByResourceTypeAndId(context.Context, string, string) (*models.ResourceBase, error)