working aggregation code.
added tests for sql generation.
This commit is contained in:
Jason Kulatunga
parent
2c5133bef7
commit
6f56fa9c3b
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@ -24,8 +24,8 @@ const (
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SearchParameterTypeToken SearchParameterType = "token"
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SearchParameterTypeReference SearchParameterType = "reference"
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SearchParameterTypeUri SearchParameterType = "uri"
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SearchParameterTypeComposite SearchParameterType = "composite"
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SearchParameterTypeQuantity SearchParameterType = "quantity"
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SearchParameterTypeComposite SearchParameterType = "composite"
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SearchParameterTypeSpecial SearchParameterType = "special"
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)
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@ -131,23 +131,67 @@ func (sr *SqliteRepository) sqlQueryResources(ctx context.Context, query models.
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//defaults
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selectClauses := []string{fmt.Sprintf("%s.*", TABLE_ALIAS)}
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groupClause := fmt.Sprintf("%s.id", TABLE_ALIAS)
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orderClause := fmt.Sprintf("%s.sort_date asc", TABLE_ALIAS)
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orderClause := fmt.Sprintf("%s.sort_date ASC", TABLE_ALIAS)
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if query.Aggregations != nil {
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selectClauses = []string{}
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groupClause = ""
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orderClause = ""
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//Handle Aggregations
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if len(query.Aggregations.CountBy) > 0 {
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//populate the group by and order by clause with the count by values
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query.Aggregations.OrderBy = "count(*) DESC"
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query.Aggregations.GroupBy = query.Aggregations.CountBy
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}
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//TODO:
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//process order by clause
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if len(query.Aggregations.OrderBy) > 0 {
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orderAsc := true
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if !strings.HasPrefix(query.Aggregations.OrderBy, "count(*)") {
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orderAggregationParam, err := ProcessAggregationParameter(query.Aggregations.OrderBy, searchCodeToTypeLookup)
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if err != nil {
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return nil, err
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}
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orderAggregationFromClause, err := SearchCodeToFromClause(orderAggregationParam)
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if err != nil {
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return nil, err
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}
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fromClauses = append(fromClauses, orderAggregationFromClause)
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orderClause = AggregationParameterToClause(orderAggregationParam)
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if orderAsc {
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orderClause = fmt.Sprintf("%s ASC", orderClause)
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} else {
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orderClause = fmt.Sprintf("%s DESC", orderClause)
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}
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} else {
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orderClause = query.Aggregations.OrderBy
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}
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}
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//process group by clause
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if len(query.Aggregations.GroupBy) > 0 {
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groupAggregationParam, err := ProcessAggregationParameter(query.Aggregations.GroupBy, searchCodeToTypeLookup)
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if err != nil {
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return nil, err
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}
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groupAggregationFromClause, err := SearchCodeToFromClause(groupAggregationParam)
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if err != nil {
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return nil, err
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}
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fromClauses = append(fromClauses, groupAggregationFromClause)
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groupClause = AggregationParameterToClause(groupAggregationParam)
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selectClauses = []string{
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fmt.Sprintf("%s as %s", groupClause, "group_by"),
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"count(*) as count",
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}
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}
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}
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//ensure Where and From clauses are unique
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whereClauses = lo.Uniq(whereClauses)
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whereClauses = lo.Compact(whereClauses)
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fromClauses = lo.Uniq(fromClauses)
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fromClauses = lo.Compact(fromClauses)
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return sr.GormClient.WithContext(ctx).
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Select(strings.Join(selectClauses, ", ")).
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@ -158,6 +202,7 @@ func (sr *SqliteRepository) sqlQueryResources(ctx context.Context, query models.
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}
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/// INTERNAL functionality. These functions are exported for testing, but are not available in the Interface
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//TODO: dont export these, instead use casting to convert the interface to the SqliteRepository struct, then call ehese functions directly
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type SearchParameter struct {
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Name string
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@ -499,3 +544,56 @@ func SearchCodeToFromClause(searchParam SearchParameter) (string, error) {
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}
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return "", nil
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}
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func AggregationParameterToClause(aggParameter SearchParameter) string {
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switch aggParameter.Type {
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case SearchParameterTypeQuantity, SearchParameterTypeToken, SearchParameterTypeString:
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//setup the clause
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return fmt.Sprintf("(%sJson.value ->> '$.%s')", aggParameter.Name, aggParameter.Modifier)
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default:
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return fmt.Sprintf("%s.%s", TABLE_ALIAS, aggParameter.Name)
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}
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}
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//ProcessAggregationParameter processes the aggregation parameters which are fields with optional properties:
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// Fields that are primitive types (number, uri) must not have any property specified:
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// eg. `probability`
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//
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// Fields that are complex types (token, quantity) must have a property specified:
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// eg. `identifier:code`
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//
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// if the a property is specified, its set as the modifier, and used when generating the SQL query groupBy, orderBy, etc clause
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func ProcessAggregationParameter(aggregationFieldWithProperty string, searchParamTypeLookup map[string]string) (SearchParameter, error) {
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aggregationParameter := SearchParameter{}
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//determine the searchCode searchCodeModifier
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//TODO: this is only applicable to string, token, reference and uri type (however unknown names & modifiers are ignored)
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if aggregationFieldParts := strings.SplitN(aggregationFieldWithProperty, ":", 2); len(aggregationFieldParts) == 2 {
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aggregationParameter.Name = aggregationFieldParts[0]
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aggregationParameter.Modifier = aggregationFieldParts[1]
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} else {
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aggregationParameter.Name = aggregationFieldParts[0]
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aggregationParameter.Modifier = ""
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}
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//next, determine the searchCodeType for this Resource (or throw an error if it is unknown)
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searchParamTypeStr, searchParamTypeOk := searchParamTypeLookup[aggregationParameter.Name]
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if !searchParamTypeOk {
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return aggregationParameter, fmt.Errorf("unknown search parameter: %s", aggregationParameter.Name)
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} else {
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aggregationParameter.Type = SearchParameterType(searchParamTypeStr)
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}
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//primitive types should not have a modifier, we need to throw an error
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if aggregationParameter.Type == SearchParameterTypeNumber || aggregationParameter.Type == SearchParameterTypeUri {
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if len(aggregationParameter.Modifier) > 0 {
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return aggregationParameter, fmt.Errorf("primitive aggregation parameter %s cannot have a property (%s)", aggregationParameter.Name, aggregationParameter.Modifier)
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}
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} else {
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//complex types must have a modifier
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if len(aggregationParameter.Modifier) == 0 {
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return aggregationParameter, fmt.Errorf("complex aggregation parameter %s must have a property", aggregationParameter.Name)
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}
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}
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return aggregationParameter, nil
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}
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@ -0,0 +1,292 @@
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package database
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import (
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"context"
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"fmt"
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"github.com/fastenhealth/fastenhealth-onprem/backend/pkg"
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mock_config "github.com/fastenhealth/fastenhealth-onprem/backend/pkg/config/mock"
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"github.com/fastenhealth/fastenhealth-onprem/backend/pkg/models"
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"github.com/golang/mock/gomock"
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"github.com/sirupsen/logrus"
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"github.com/stretchr/testify/require"
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"github.com/stretchr/testify/suite"
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"gorm.io/gorm"
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"io/ioutil"
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"log"
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"os"
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"strings"
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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 RepositorySqlTestSuite struct {
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suite.Suite
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MockCtrl *gomock.Controller
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TestDatabase *os.File
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TestRepository DatabaseRepository
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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 *RepositorySqlTestSuite) BeforeTest(suiteName, testName string) {
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suite.MockCtrl = gomock.NewController(suite.T())
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dbFile, err := ioutil.TempFile("", fmt.Sprintf("%s.*.db", testName))
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if err != nil {
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log.Fatal(err)
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}
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suite.TestDatabase = dbFile
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fakeConfig := mock_config.NewMockInterface(suite.MockCtrl)
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fakeConfig.EXPECT().GetString("database.location").Return(suite.TestDatabase.Name()).AnyTimes()
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fakeConfig.EXPECT().GetString("log.level").Return("INFO").AnyTimes()
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dbRepo, err := NewRepository(fakeConfig, logrus.WithField("test", suite.T().Name()))
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require.NoError(suite.T(), err)
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suite.TestRepository = dbRepo
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userModel := &models.User{
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Username: "test_username",
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Password: "testpassword",
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Email: "test@test.com",
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}
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err = suite.TestRepository.CreateUser(context.Background(), userModel)
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require.NoError(suite.T(), err)
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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 *RepositorySqlTestSuite) AfterTest(suiteName, testName string) {
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suite.MockCtrl.Finish()
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os.Remove(suite.TestDatabase.Name())
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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 TestRepositorySqlTestSuite(t *testing.T) {
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suite.Run(t, new(RepositorySqlTestSuite))
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}
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func (suite *RepositorySqlTestSuite) TestQueryResources_SQL() {
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//setup
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sqliteRepo := suite.TestRepository.(*SqliteRepository)
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sqliteRepo.GormClient = sqliteRepo.GormClient.Session(&gorm.Session{DryRun: true})
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//test
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authContext := context.WithValue(context.Background(), pkg.ContextKeyTypeAuthUsername, "test_username")
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sqlQuery, err := sqliteRepo.sqlQueryResources(authContext, models.QueryResource{
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Select: []string{},
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Where: map[string]interface{}{
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"code": "test_code",
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},
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From: "Observation",
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})
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require.NoError(suite.T(), err)
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var results []map[string]interface{}
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statement := sqlQuery.Find(&results).Statement
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sqlString := statement.SQL.String()
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sqlParams := statement.Vars
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//assert
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require.NoError(suite.T(), err)
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require.Equal(suite.T(),
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strings.Join([]string{
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"SELECT fhir.*",
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"FROM fhir_observation as fhir, json_each(fhir.code) as codeJson",
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"WHERE ((codeJson.value ->> '$.code' = ?)) AND (user_id = ?)",
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"GROUP BY `fhir`.`id`",
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"ORDER BY fhir.sort_date ASC",
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}, " "),
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sqlString)
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require.Equal(suite.T(), sqlParams, []interface{}{
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"test_code", "00000000-0000-0000-0000-000000000000",
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})
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}
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func (suite *RepositorySqlTestSuite) TestQueryResources_SQL_WithMultipleWhereConditions() {
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//setup
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sqliteRepo := suite.TestRepository.(*SqliteRepository)
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sqliteRepo.GormClient = sqliteRepo.GormClient.Session(&gorm.Session{DryRun: true})
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//test
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authContext := context.WithValue(context.Background(), pkg.ContextKeyTypeAuthUsername, "test_username")
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sqlQuery, err := sqliteRepo.sqlQueryResources(authContext, models.QueryResource{
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Select: []string{},
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Where: map[string]interface{}{
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"code": "test_code",
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"category": "12345",
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},
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From: "Observation",
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})
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require.NoError(suite.T(), err)
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var results []map[string]interface{}
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statement := sqlQuery.Find(&results).Statement
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sqlString := statement.SQL.String()
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sqlParams := statement.Vars
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//assert
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require.NoError(suite.T(), err)
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require.Equal(suite.T(),
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strings.Join([]string{
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"SELECT fhir.*",
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"FROM fhir_observation as fhir, json_each(fhir.code) as codeJson",
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"WHERE ((codeJson.value ->> '$.code' = ?)) AND (user_id = ?)",
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"GROUP BY `fhir`.`id`",
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"ORDER BY fhir.sort_date ASC",
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}, " "),
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sqlString)
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require.Equal(suite.T(), sqlParams, []interface{}{
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"test_code", "00000000-0000-0000-0000-000000000000",
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})
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}
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func (suite *RepositorySqlTestSuite) TestQueryResources_SQL_WithPrimitiveOrderByAggregation() {
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//setup
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sqliteRepo := suite.TestRepository.(*SqliteRepository)
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sqliteRepo.GormClient = sqliteRepo.GormClient.Session(&gorm.Session{DryRun: true})
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//test
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authContext := context.WithValue(context.Background(), pkg.ContextKeyTypeAuthUsername, "test_username")
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sqlQuery, err := sqliteRepo.sqlQueryResources(authContext, models.QueryResource{
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Select: []string{},
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Where: map[string]interface{}{
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"code": "test_code",
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},
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From: "Observation",
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Aggregations: &models.QueryResourceAggregations{OrderBy: "sourceUri"},
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})
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require.NoError(suite.T(), err)
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var results []map[string]interface{}
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statement := sqlQuery.Find(&results).Statement
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sqlString := statement.SQL.String()
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sqlParams := statement.Vars
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//assert
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require.NoError(suite.T(), err)
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require.Equal(suite.T(),
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strings.Join([]string{
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"SELECT fhir.*",
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"FROM fhir_observation as fhir, json_each(fhir.code) as codeJson",
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"WHERE ((codeJson.value ->> '$.code' = ?)) AND (user_id = ?)",
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"GROUP BY `fhir`.`id`",
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"ORDER BY fhir.sourceUri ASC",
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}, " "), sqlString)
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require.Equal(suite.T(), sqlParams, []interface{}{
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"test_code", "00000000-0000-0000-0000-000000000000",
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})
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}
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func (suite *RepositorySqlTestSuite) TestQueryResources_SQL_WithComplexOrderByAggregation() {
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//setup
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sqliteRepo := suite.TestRepository.(*SqliteRepository)
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sqliteRepo.GormClient = sqliteRepo.GormClient.Session(&gorm.Session{DryRun: true})
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//test
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authContext := context.WithValue(context.Background(), pkg.ContextKeyTypeAuthUsername, "test_username")
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sqlQuery, err := sqliteRepo.sqlQueryResources(authContext, models.QueryResource{
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Select: []string{},
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Where: map[string]interface{}{
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"code": "test_code",
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},
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From: "Observation",
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Aggregations: &models.QueryResourceAggregations{OrderBy: "valueString:value"},
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})
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require.NoError(suite.T(), err)
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var results []map[string]interface{}
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statement := sqlQuery.Find(&results).Statement
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sqlString := statement.SQL.String()
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sqlParams := statement.Vars
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//assert
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require.NoError(suite.T(), err)
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require.Equal(suite.T(),
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strings.Join([]string{
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"SELECT fhir.*",
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"FROM fhir_observation as fhir, json_each(fhir.code) as codeJson, json_each(fhir.valueString) as valueStringJson",
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"WHERE ((codeJson.value ->> '$.code' = ?)) AND (user_id = ?)",
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"GROUP BY `fhir`.`id`",
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"ORDER BY (valueStringJson.value ->> '$.value') ASC",
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}, " "), sqlString)
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require.Equal(suite.T(), sqlParams, []interface{}{
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"test_code", "00000000-0000-0000-0000-000000000000",
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})
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}
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func (suite *RepositorySqlTestSuite) TestQueryResources_SQL_WithPrimitiveCountByAggregation() {
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//setup
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sqliteRepo := suite.TestRepository.(*SqliteRepository)
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sqliteRepo.GormClient = sqliteRepo.GormClient.Session(&gorm.Session{DryRun: true})
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//test
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authContext := context.WithValue(context.Background(), pkg.ContextKeyTypeAuthUsername, "test_username")
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sqlQuery, err := sqliteRepo.sqlQueryResources(authContext, models.QueryResource{
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Select: []string{},
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Where: map[string]interface{}{
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"code": "test_code",
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},
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From: "Observation",
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Aggregations: &models.QueryResourceAggregations{CountBy: "sourceUri"},
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})
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require.NoError(suite.T(), err)
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var results []map[string]interface{}
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statement := sqlQuery.Find(&results).Statement
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sqlString := statement.SQL.String()
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sqlParams := statement.Vars
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//assert
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require.NoError(suite.T(), err)
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require.Equal(suite.T(),
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strings.Join([]string{
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"SELECT fhir.sourceUri as group_by, count(*) as count",
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"FROM fhir_observation as fhir, json_each(fhir.code) as codeJson",
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"WHERE ((codeJson.value ->> '$.code' = ?)) AND (user_id = ?)",
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"GROUP BY `fhir`.`sourceUri`",
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"ORDER BY count(*) DESC",
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}, " "), sqlString)
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require.Equal(suite.T(), sqlParams, []interface{}{
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"test_code", "00000000-0000-0000-0000-000000000000",
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})
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}
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func (suite *RepositorySqlTestSuite) TestQueryResources_SQL_WithComplexCountByAggregation() {
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//setup
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sqliteRepo := suite.TestRepository.(*SqliteRepository)
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sqliteRepo.GormClient = sqliteRepo.GormClient.Session(&gorm.Session{DryRun: true})
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//test
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authContext := context.WithValue(context.Background(), pkg.ContextKeyTypeAuthUsername, "test_username")
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sqlQuery, err := sqliteRepo.sqlQueryResources(authContext, models.QueryResource{
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Select: []string{},
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Where: map[string]interface{}{
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"code": "test_code",
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},
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From: "Observation",
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Aggregations: &models.QueryResourceAggregations{CountBy: "code:code"},
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})
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require.NoError(suite.T(), err)
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var results []map[string]interface{}
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statement := sqlQuery.Find(&results).Statement
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sqlString := statement.SQL.String()
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sqlParams := statement.Vars
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//assert
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require.NoError(suite.T(), err)
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require.Equal(suite.T(),
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strings.Join([]string{
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"SELECT (codeJson.value ->> '$.code') as group_by, count(*) as count",
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"FROM fhir_observation as fhir, json_each(fhir.code) as codeJson",
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"WHERE ((codeJson.value ->> '$.code' = ?)) AND (user_id = ?)",
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"GROUP BY (codeJson.value ->> '$.code')",
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"ORDER BY count(*) DESC",
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}, " "), sqlString)
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require.Equal(suite.T(), sqlParams, []interface{}{
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"test_code", "00000000-0000-0000-0000-000000000000",
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})
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}
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|
|
@ -1,6 +1,9 @@
|
|||
package models
|
||||
|
||||
import "fmt"
|
||||
import (
|
||||
"fmt"
|
||||
"strings"
|
||||
)
|
||||
|
||||
// maps to frontend/src/app/models/widget/dashboard-widget-query.ts
|
||||
type QueryResource struct {
|
||||
|
|
@ -44,6 +47,15 @@ func (q *QueryResource) Validate() error {
|
|||
if len(q.Aggregations.CountBy) == 0 && len(q.Aggregations.OrderBy) == 0 && len(q.Aggregations.GroupBy) == 0 {
|
||||
return fmt.Errorf("aggregations must have at least one of 'count_by', 'group_by', or 'order_by'")
|
||||
}
|
||||
if strings.Contains(q.Aggregations.CountBy, " ") {
|
||||
return fmt.Errorf("count_by cannot have spaces (or aliases)")
|
||||
}
|
||||
if strings.Contains(q.Aggregations.GroupBy, " ") {
|
||||
return fmt.Errorf("group_by cannot have spaces (or aliases)")
|
||||
}
|
||||
if strings.Contains(q.Aggregations.OrderBy, " ") {
|
||||
return fmt.Errorf("order_by cannot have spaces (or aliases)")
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -18,6 +18,10 @@ func TestQueryResource_Validate(t *testing.T) {
|
|||
{QueryResource{From: "test", Aggregations: &QueryResourceAggregations{CountBy: "test", GroupBy: "test"}}, "cannot use 'count_by' and 'group_by' together", true},
|
||||
{QueryResource{From: "test", Aggregations: &QueryResourceAggregations{CountBy: "test", OrderBy: "test"}}, "cannot use 'count_by' and 'order_by' together", true},
|
||||
{QueryResource{From: "test", Aggregations: &QueryResourceAggregations{}}, "aggregations must have at least one of 'count_by', 'group_by', or 'order_by'", true},
|
||||
{QueryResource{From: "test", Aggregations: &QueryResourceAggregations{CountBy: "test:property"}}, "", false},
|
||||
{QueryResource{From: "test", Aggregations: &QueryResourceAggregations{CountBy: "test:property as HELLO"}}, "count_by cannot have spaces", true},
|
||||
{QueryResource{From: "test", Aggregations: &QueryResourceAggregations{GroupBy: "test:property as HELLO"}}, "group_by cannot have spaces", true},
|
||||
{QueryResource{From: "test", Aggregations: &QueryResourceAggregations{OrderBy: "test:property as HELLO"}}, "order_by cannot have spaces", true},
|
||||
}
|
||||
|
||||
//test && assert
|
||||
|
|
|
|||
Loading…
Reference in New Issue