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make sure HumanName and Address types are correctly extracted as sear…
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…chable strings.

Make sure they can be searched against using the query endpoint.
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@AnalogJ
AnalogJ committed Aug 1, 2023
1 parent 94fa479 commit 9e776c6
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Showing 2 changed files with 46 additions and 16 deletions.
56 changes: 43 additions & 13 deletions backend/pkg/database/sqlite_repository_query.go
View file
Original file line number Diff line number Diff line change
Expand Up @@ -30,6 +30,21 @@ const (
const TABLE_ALIAS = "fhir"

//Allows users to use SearchParameters to query resources
// Can generate simple or complex queries, depending on the SearchParameter type:
//
// eg. Simple
//
//
// eg. Complex
// SELECT fhir.*
// FROM fhir_observation as fhir, json_each(fhir.code) as codeJson
// WHERE (
// (codeJson.value ->> '$.code' = "29463-7" AND codeJson.value ->> '$.system' = "http://loinc.org")
// OR (codeJson.value ->> '$.code' = "3141-9" AND codeJson.value ->> '$.system' = "http://loinc.org")
// OR (codeJson.value ->> '$.code' = "27113001" AND codeJson.value ->> '$.system' = "http://snomed.info/sct")
// )
// AND (user_id = "6efcd7c5-3f29-4f0d-926d-a66ff68bbfc2")
// GROUP BY `fhir`.`id`
func (sr *SqliteRepository) QueryResources(ctx context.Context, query models.QueryResource) ([]models.ResourceBase, error) {
//todo, until we actually parse the select statement, we will just return all resources based on "from"

Expand Down Expand Up @@ -112,7 +127,7 @@ type SearchParameter struct {
Modifier string
}

//Items in the SearchParameterValueOperatorTree are AND'd together, and items within each SearchParameterValueOperatorTree are OR'd together
//Lists in the SearchParameterValueOperatorTree are AND'd together, and items within each SearchParameterValueOperatorTree list are OR'd together
//For example, the following would be AND'd together, and then OR'd with the next SearchParameterValueOperatorTree
// {
// {SearchParameterValue{Value: "foo"}, SearchParameterValue{Value: "bar"}}
Expand All @@ -128,6 +143,8 @@ type SearchParameterValue struct {
SecondaryValues map[string]interface{}
}

//SearchParameters are made up of parameter names and modifiers. For example, "name" and "name:exact" are both valid search parameters
// This function will parse the searchCodeWithModifier and return the SearchParameter
func ProcessSearchParameter(searchCodeWithModifier string, searchParamTypeLookup map[string]string) (SearchParameter, error) {
searchParameter := SearchParameter{}

Expand Down Expand Up @@ -165,6 +182,10 @@ func ProcessSearchParameter(searchCodeWithModifier string, searchParamTypeLookup
// 3. use the ProcessSearchParameterValue function to split each value into a list of prefixes and values
// these are then stored in a multidimentional list of SearchParameterValueOperatorTree
// top level is AND'd together, and each item within the lists are OR'd together
//
// For example, searchParamCodeValueOrValuesWithPrefix may be:
// "code": "29463-7,3141-9,27113001"
// "code": ["le29463-7", "gt3141-9", "27113001"]
func ProcessSearchParameterValueIntoOperatorTree(searchParameter SearchParameter, searchParamCodeValueOrValuesWithPrefix interface{}) (SearchParameterValueOperatorTree, error) {

searchParamCodeValuesWithPrefix := []string{}
Expand Down Expand Up @@ -198,6 +219,13 @@ func ProcessSearchParameterValueIntoOperatorTree(searchParameter SearchParameter
return searchParamCodeValueOperatorTree, nil
}

// ProcessSearchParameterValue searchValueWithPrefix may or may not have a prefix which needs to be parsed
// this function will parse the searchValueWithPrefix and return the SearchParameterValue
// for example, "eq2018-01-01" would return a SearchParameterValue with a prefix of "eq" and a value of "2018-01-01"
// and "2018-01-01" would return a SearchParameterValue with a value of "2018-01-01"
//
// some query types, like token, quantity and reference, have secondary values that need to be parsed
// for example, code="http://loinc.org|29463-7" would return a SearchParameterValue with a value of "29463-7" and a secondary value of { "codeSystem": "http://loinc.org" }
func ProcessSearchParameterValue(searchParameter SearchParameter, searchValueWithPrefix string) (SearchParameterValue, error) {
searchParameterValue := SearchParameterValue{
SecondaryValues: map[string]interface{}{},
Expand Down Expand Up @@ -288,6 +316,7 @@ func NamedParameterWithSuffix(parameterName string, suffix string) string {
return fmt.Sprintf("%s_%s", parameterName, suffix)
}

//SearchCodeToWhereClause converts a searchCode and searchCodeValue to a where clause and a map of named parameters
func SearchCodeToWhereClause(searchParam SearchParameter, searchParamValue SearchParameterValue, namedParameterSuffix string) (string, map[string]interface{}, error) {

//add named parameters to the lookup map. Basically, this is a map of all the named parameters that will be used in the where clause we're generating
Expand Down Expand Up @@ -320,17 +349,7 @@ func SearchCodeToWhereClause(searchParam SearchParameter, searchParamValue Searc
} else if searchParam.Modifier == "ap" {
return "", nil, fmt.Errorf("search modifier 'ap' not supported for search parameter type %s (%s=%s)", searchParam.Type, searchParam.Name, searchParamValue.Value)
}
case SearchParameterTypeString:
if searchParam.Modifier == "" {
searchClauseNamedParams[NamedParameterWithSuffix(searchParam.Name, namedParameterSuffix)] = searchParamValue.Value.(string) + "%" // "eve" matches "Eve" and "Evelyn"
return fmt.Sprintf("(%s LIKE @%s)", searchParam.Name, NamedParameterWithSuffix(searchParam.Name, namedParameterSuffix)), searchClauseNamedParams, nil
} else if searchParam.Modifier == "exact" {
// "eve" matches "eve" (not "Eve" or "EVE")
return fmt.Sprintf("(%s = @%s)", searchParam.Name, NamedParameterWithSuffix(searchParam.Name, namedParameterSuffix)), searchClauseNamedParams, nil
} else if searchParam.Modifier == "contains" {
searchClauseNamedParams[NamedParameterWithSuffix(searchParam.Name, namedParameterSuffix)] = "%" + searchParamValue.Value.(string) + "%" // "eve" matches "Eve", "Evelyn" and "Severine"
return fmt.Sprintf("(%s LIKE @%s)", searchParam.Name, NamedParameterWithSuffix(searchParam.Name, namedParameterSuffix)), searchClauseNamedParams, nil
}

case SearchParameterTypeUri:
if searchParam.Modifier == "" {
return fmt.Sprintf("(%s = @%s)", searchParam.Name, NamedParameterWithSuffix(searchParam.Name, namedParameterSuffix)), searchClauseNamedParams, nil
Expand All @@ -343,6 +362,17 @@ func SearchCodeToWhereClause(searchParam SearchParameter, searchParamValue Searc
////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
//COMPLEX SEARCH PARAMETERS
////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
case SearchParameterTypeString:
if searchParam.Modifier == "" {
searchClauseNamedParams[NamedParameterWithSuffix(searchParam.Name, namedParameterSuffix)] = searchParamValue.Value.(string) + "%" // "eve" matches "Eve" and "Evelyn"
return fmt.Sprintf("(%sJson.value LIKE @%s)", searchParam.Name, NamedParameterWithSuffix(searchParam.Name, namedParameterSuffix)), searchClauseNamedParams, nil
} else if searchParam.Modifier == "exact" {
// "eve" matches "eve" (not "Eve" or "EVE")
return fmt.Sprintf("(%sJson.value = @%s)", searchParam.Name, NamedParameterWithSuffix(searchParam.Name, namedParameterSuffix)), searchClauseNamedParams, nil
} else if searchParam.Modifier == "contains" {
searchClauseNamedParams[NamedParameterWithSuffix(searchParam.Name, namedParameterSuffix)] = "%" + searchParamValue.Value.(string) + "%" // "eve" matches "Eve", "Evelyn" and "Severine"
return fmt.Sprintf("(%sJson.value LIKE @%s)", searchParam.Name, NamedParameterWithSuffix(searchParam.Name, namedParameterSuffix)), searchClauseNamedParams, nil
}
case SearchParameterTypeQuantity:

//setup the clause
Expand Down Expand Up @@ -425,7 +455,7 @@ func SearchCodeToFromClause(searchParam SearchParameter) (string, error) {
//COMPLEX SEARCH PARAMETERS
////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
switch searchParam.Type {
case SearchParameterTypeQuantity, SearchParameterTypeToken:
case SearchParameterTypeQuantity, SearchParameterTypeToken, SearchParameterTypeString:
//setup the clause
return fmt.Sprintf("json_each(%s.%s) as %sJson", TABLE_ALIAS, searchParam.Name, searchParam.Name), nil
}
Expand Down
6 changes: 3 additions & 3 deletions backend/pkg/database/sqlite_repository_query_test.go
View file
Original file line number Diff line number Diff line change
Expand Up @@ -132,9 +132,9 @@ func TestSearchCodeToWhereClause(t *testing.T) {
{SearchParameter{Type: "number", Name: "probability", Modifier: ""}, SearchParameterValue{Value: float64(100), Prefix: "gt", SecondaryValues: map[string]interface{}{}}, "0_0", "(probability > @probability_0_0)", map[string]interface{}{"probability_0_0": float64(100)}, false},
{SearchParameter{Type: "date", Name: "issueDate", Modifier: ""}, SearchParameterValue{Value: time.Date(2013, time.January, 14, 10, 0, 0, 0, time.UTC), Prefix: "lt", SecondaryValues: map[string]interface{}{}}, "1_1", "(issueDate < @issueDate_1_1)", map[string]interface{}{"issueDate_1_1": time.Date(2013, time.January, 14, 10, 0, 0, 0, time.UTC)}, false},

{SearchParameter{Type: "string", Name: "given", Modifier: ""}, SearchParameterValue{Value: "eve", Prefix: "", SecondaryValues: map[string]interface{}{}}, "0_0", "(given LIKE @given_0_0)", map[string]interface{}{"given_0_0": "eve%"}, false},
{SearchParameter{Type: "string", Name: "given", Modifier: "contains"}, SearchParameterValue{Value: "eve", Prefix: "", SecondaryValues: map[string]interface{}{}}, "0_0", "(given LIKE @given_0_0)", map[string]interface{}{"given_0_0": "%eve%"}, false},
{SearchParameter{Type: "string", Name: "given", Modifier: "exact"}, SearchParameterValue{Value: "eve", Prefix: "", SecondaryValues: map[string]interface{}{}}, "0_0", "(given = @given_0_0)", map[string]interface{}{"given_0_0": "eve"}, false},
{SearchParameter{Type: "string", Name: "given", Modifier: ""}, SearchParameterValue{Value: "eve", Prefix: "", SecondaryValues: map[string]interface{}{}}, "0_0", "(givenJson.value LIKE @given_0_0)", map[string]interface{}{"given_0_0": "eve%"}, false},
{SearchParameter{Type: "string", Name: "given", Modifier: "contains"}, SearchParameterValue{Value: "eve", Prefix: "", SecondaryValues: map[string]interface{}{}}, "0_0", "(givenJson.value LIKE @given_0_0)", map[string]interface{}{"given_0_0": "%eve%"}, false},
{SearchParameter{Type: "string", Name: "given", Modifier: "exact"}, SearchParameterValue{Value: "eve", Prefix: "", SecondaryValues: map[string]interface{}{}}, "0_0", "(givenJson.value = @given_0_0)", map[string]interface{}{"given_0_0": "eve"}, false},

{SearchParameter{Type: "uri", Name: "url", Modifier: "below"}, SearchParameterValue{Value: "http://acme.org/fhir/", Prefix: "", SecondaryValues: map[string]interface{}{}}, "0_0", "(url LIKE @url_0_0)", map[string]interface{}{"url_0_0": "http://acme.org/fhir/%"}, false},
{SearchParameter{Type: "uri", Name: "url", Modifier: "above"}, SearchParameterValue{Value: "http://acme.org/fhir/", Prefix: "", SecondaryValues: map[string]interface{}{}}, "0_0", "", map[string]interface{}{}, true}, //above modifier not supported
Expand Down

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