Adding support for IPS Export/Summary

.github/workflows/docker.yaml

@@ -57,6 +57,14 @@ jobs:
             type=raw,value=${{ matrix.flavor }},enable=${{  github.ref_name == 'main' }}
             # if this is a (non main) branch build, tag it with the flavor and branch name (eg. main-branch and sandbox-branch)
             type=ref,event=branch,prefix=${{ matrix.flavor }}-,enable=${{ github.ref_name != 'main' }}
+          labels: |
+            maintainer=AnalogJ
+            org.opencontainers.image.title=Fasten Health - ${{ matrix.flavor }}
+            org.opencontainers.image.authors=Jason Kulatunga - [email protected]
+            org.opencontainers.image.description=An open-source personal medical record that never leaves the patients hands without their consent
+            org.opencontainers.image.vendor=Fasten Health, Inc.
+            org.opencontainers.image.source=https://github.com/fastenhealth/fasten-onprem/
+            org.opencontainers.image.revision=${{ github.sha }}
           images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
       # Build and push Docker image with Buildx (don't push on PR)
       # https://github.com/docker/build-push-action

backend/pkg/constants.go

@@ -10,6 +10,9 @@ type DatabaseRepositoryType string
 type InstallationVerificationStatus string
 type InstallationQuotaStatus string
 
+type IPSSections string
+type IPSSectionGroups string
+
 const (
 	ResourceListPageSize int = 20
 
@@ -50,4 +53,63 @@ 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"
+	IPSSectionsHistoryOfIllness      IPSSections = "history_of_illness"
+	IPSSectionsPregnancy             IPSSections = "pregnancy"
+	IPSSectionsSocialHistory         IPSSections = "social_history"
+	IPSSectionsPlanOfCare            IPSSections = "plan_of_care"
+	IPSSectionsFunctionalStatus      IPSSections = "functional_status"
+	IPSSectionsAdvanceDirectives     IPSSections = "advance_directives"
+
+	IPSSectionGroupsRequired    IPSSectionGroups = "required"
+	IPSSectionGroupsRecommended IPSSectionGroups = "recommended"
+	IPSSectionGroupsOptional    IPSSectionGroups = "optional"
 )
+
+var IPSSectionsList = []IPSSections{
+	IPSSectionsMedicationSummary,
+	IPSSectionsAllergiesIntolerances,
+	IPSSectionsProblemList,
+	IPSSectionsImmunizations,
+	IPSSectionsHistoryOfProcedures,
+	IPSSectionsMedicalDevices,
+	IPSSectionsDiagnosticResults,
+	IPSSectionsVitalSigns,
+	IPSSectionsHistoryOfIllness,
+	IPSSectionsPregnancy,
+	IPSSectionsSocialHistory,
+	IPSSectionsPlanOfCare,
+	IPSSectionsFunctionalStatus,
+	IPSSectionsAdvanceDirectives,
+}
+
+var IPSSectionGroupsOrdered = map[IPSSectionGroups][]IPSSections{
+	IPSSectionGroupsRequired: []IPSSections{
+		IPSSectionsMedicationSummary,
+		IPSSectionsAllergiesIntolerances,
+		IPSSectionsProblemList,
+	},
+	IPSSectionGroupsRecommended: []IPSSections{
+		IPSSectionsImmunizations,
+		IPSSectionsHistoryOfProcedures,
+		IPSSectionsMedicalDevices,
+		IPSSectionsDiagnosticResults,
+	},
+	IPSSectionGroupsOptional: []IPSSections{
+		IPSSectionsVitalSigns,
+		IPSSectionsHistoryOfIllness,
+		IPSSectionsPregnancy,
+		IPSSectionsSocialHistory,
+		IPSSectionsPlanOfCare,
+		IPSSectionsFunctionalStatus,
+		IPSSectionsAdvanceDirectives,
+	},
+}

backend/pkg/database/gorm_repository_query_sql_test.go

@@ -520,3 +520,231 @@ func (suite *RepositorySqlTestSuite) TestQueryResources_SQL_WithTokenGroupByNoMo
 		"00000000-0000-0000-0000-000000000000",
 	})
 }
+
+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 ->> '$.code' <> ?)) AND (user_id = ?)",
+			"GROUP BY `fhir`.`id`",
+			"ORDER BY fhir.sort_date DESC",
+		}, " "),
+		sqlString)
+	require.Equal(suite.T(), sqlParams, []interface{}{
+		"test_code", "00000000-0000-0000-0000-000000000000",
+	})
+}
+
+func (suite *RepositorySqlTestSuite) TestQueryResources_SQL_WithTokenMultipleANDValuesWithNotModifier() {
+	//setup
+	sqliteRepo := suite.TestRepository.(*GormRepository)
+	sqliteRepo.GormClient = sqliteRepo.GormClient.Session(&gorm.Session{DryRun: true})
+
+	//test
+	authContext := context.WithValue(context.Background(), pkg.ContextKeyTypeAuthUsername, "test_username")
+
+	sqlQuery, err := sqliteRepo.sqlQueryResources(authContext, models.QueryResource{
+		Select: []string{},
+		Where: map[string]interface{}{
+			"code:not": []string{"test_code", "test_code2"}, //AND condition
+		},
+		From: "Observation",
+	})
+	require.NoError(suite.T(), err)
+	var results []map[string]interface{}
+	statement := sqlQuery.Find(&results).Statement
+	sqlString := statement.SQL.String()
+	sqlParams := statement.Vars
+
+	//assert
+	require.NoError(suite.T(), err)
+	require.Equal(suite.T(),
+		strings.Join([]string{
+			"SELECT fhir.*",
+			"FROM fhir_observation as fhir, json_each(fhir.code) as codeJson",
+			"WHERE ((codeJson.value ->> '$.code' <> ?)) AND ((codeJson.value ->> '$.code' <> ?)) AND (user_id = ?)",
+			"GROUP BY `fhir`.`id`",
+			"ORDER BY fhir.sort_date DESC",
+		}, " "),
+		sqlString)
+	require.Equal(suite.T(), sqlParams, []interface{}{
+		"test_code", "test_code2", "00000000-0000-0000-0000-000000000000",
+	})
+}
+
+func (suite *RepositorySqlTestSuite) TestQueryResources_SQL_WithTokenMultipleORValues() {
+	//setup
+	sqliteRepo := suite.TestRepository.(*GormRepository)
+	sqliteRepo.GormClient = sqliteRepo.GormClient.Session(&gorm.Session{DryRun: true})
+
+	//test
+	authContext := context.WithValue(context.Background(), pkg.ContextKeyTypeAuthUsername, "test_username")
+
+	sqlQuery, err := sqliteRepo.sqlQueryResources(authContext, models.QueryResource{
+		Select: []string{},
+		Where: map[string]interface{}{
+			"code": "test_code,test_code2", //OR condition
+		},
+		From: "Observation",
+	})
+	require.NoError(suite.T(), err)
+	var results []map[string]interface{}
+	statement := sqlQuery.Find(&results).Statement
+	sqlString := statement.SQL.String()
+	sqlParams := statement.Vars
+
+	//assert
+	require.NoError(suite.T(), err)
+	require.Equal(suite.T(),
+		strings.Join([]string{
+			"SELECT fhir.*",
+			"FROM fhir_observation as fhir, json_each(fhir.code) as codeJson",
+			"WHERE ((codeJson.value ->> '$.code' = ?) OR (codeJson.value ->> '$.code' = ?)) AND (user_id = ?)",
+			"GROUP BY `fhir`.`id`",
+			"ORDER BY fhir.sort_date DESC",
+		}, " "),
+		sqlString)
+	require.Equal(suite.T(), sqlParams, []interface{}{
+		"test_code", "test_code2", "00000000-0000-0000-0000-000000000000",
+	})
+}
+
+func (suite *RepositorySqlTestSuite) TestQueryResources_SQL_WithTokenMultipleORANDValues() {
+	//setup
+	sqliteRepo := suite.TestRepository.(*GormRepository)
+	sqliteRepo.GormClient = sqliteRepo.GormClient.Session(&gorm.Session{DryRun: true})
+
+	//test
+	authContext := context.WithValue(context.Background(), pkg.ContextKeyTypeAuthUsername, "test_username")
+
+	sqlQuery, err := sqliteRepo.sqlQueryResources(authContext, models.QueryResource{
+		Select: []string{},
+		Where: map[string]interface{}{
+			"code": []string{"test_code,test_code2", "test_code3,test_code4"}, //OR-AND condition
+		},
+		From: "Observation",
+	})
+	require.NoError(suite.T(), err)
+	var results []map[string]interface{}
+	statement := sqlQuery.Find(&results).Statement
+	sqlString := statement.SQL.String()
+	sqlParams := statement.Vars
+
+	//assert
+	require.NoError(suite.T(), err)
+	require.Equal(suite.T(),
+		strings.Join([]string{
+			"SELECT fhir.*",
+			"FROM fhir_observation as fhir, json_each(fhir.code) as codeJson",
+			"WHERE ((codeJson.value ->> '$.code' = ?) OR (codeJson.value ->> '$.code' = ?)) AND ((codeJson.value ->> '$.code' = ?) OR (codeJson.value ->> '$.code' = ?)) AND (user_id = ?)",
+			"GROUP BY `fhir`.`id`",
+			"ORDER BY fhir.sort_date DESC",
+		}, " "),
+		sqlString)
+	require.Equal(suite.T(), sqlParams, []interface{}{
+		"test_code", "test_code2", "test_code3", "test_code4", "00000000-0000-0000-0000-000000000000",
+	})
+}
+
+func (suite *RepositorySqlTestSuite) TestQueryResources_SQL_WithTokenMultipleModifiersMultipleANDORValues() {
+	//setup
+	sqliteRepo := suite.TestRepository.(*GormRepository)
+	sqliteRepo.GormClient = sqliteRepo.GormClient.Session(&gorm.Session{DryRun: true})
+
+	//test
+	authContext := context.WithValue(context.Background(), pkg.ContextKeyTypeAuthUsername, "test_username")
+
+	sqlQuery, err := sqliteRepo.sqlQueryResources(authContext, models.QueryResource{
+		Select: []string{},
+		Where: map[string]interface{}{
+			"code:not": []string{"test_code", "test_code2,test_code3"}, //AND-OR condition
+			"code":     "test_code4,test_code5,test_code6",             //OR condition
+		},
+		From: "Observation",
+	})
+	require.NoError(suite.T(), err)
+	var results []map[string]interface{}
+	statement := sqlQuery.Find(&results).Statement
+	sqlString := statement.SQL.String()
+	sqlParams := statement.Vars
+
+	//assert
+	require.NoError(suite.T(), err)
+	require.Equal(suite.T(),
+		strings.Join([]string{
+			"SELECT fhir.*",
+			"FROM fhir_observation as fhir, json_each(fhir.code) as codeJson",
+			"WHERE ((codeJson.value ->> '$.code' <> ?)) AND ((codeJson.value ->> '$.code' <> ?) OR (codeJson.value ->> '$.code' <> ?)) AND ((codeJson.value ->> '$.code' = ?) OR (codeJson.value ->> '$.code' = ?) OR (codeJson.value ->> '$.code' = ?)) AND (user_id = ?)",
+			"GROUP BY `fhir`.`id`",
+			"ORDER BY fhir.sort_date DESC",
+		}, " "),
+		sqlString)
+	require.Equal(suite.T(), sqlParams, []interface{}{
+		"test_code", "test_code2", "test_code3", "test_code4", "test_code5", "test_code6", "00000000-0000-0000-0000-000000000000",
+	})
+}
+
+// Section Vital Signs Codes Lookup
+
+func (suite *RepositorySqlTestSuite) TestQueryResources_SQL_SectionVitalSigns_WithTokenGroupByNoModifier() {
+	//setup
+	sqliteRepo := suite.TestRepository.(*GormRepository)
+	sqliteRepo.GormClient = sqliteRepo.GormClient.Session(&gorm.Session{DryRun: true})
+
+	//test
+	authContext := context.WithValue(context.Background(), pkg.ContextKeyTypeAuthUsername, "test_username")
+
+	sqlQuery, err := sqliteRepo.sqlQueryResources(authContext, models.QueryResource{
+		Select: []string{},
+		Where: map[string]interface{}{
+			"category": "vital-signs",
+		},
+		From: "Observation",
+		Aggregations: &models.QueryResourceAggregations{
+			GroupBy: &models.QueryResourceAggregation{Field: "code:code"},
+		},
+	})
+	require.NoError(suite.T(), err)
+	var results []map[string]interface{}
+	statement := sqlQuery.Find(&results).Statement
+	sqlString := statement.SQL.String()
+	sqlParams := statement.Vars
+
+	//assert
+	require.NoError(suite.T(), err)
+	require.Equal(suite.T(),
+		strings.Join([]string{
+			"SELECT (codeJson.value ->> '$.code') as label, count(*) as value",
+			"FROM fhir_observation as fhir, json_each(fhir.category) as categoryJson, json_each(fhir.code) as codeJson",
+			"WHERE ((categoryJson.value ->> '$.code' = ?)) AND (user_id = ?)",
+			"GROUP BY (codeJson.value ->> '$.code')",
+			"ORDER BY count(*) DESC",
+		}, " "), sqlString)
+	require.Equal(suite.T(), sqlParams, []interface{}{
+		"vital-signs",
+		"00000000-0000-0000-0000-000000000000",
+	})
+}

backend/pkg/database/gorm_repository_query_test.go

@@ -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
@@ -147,10 +149,10 @@ func TestSearchCodeToWhereClause(t *testing.T) {
 		{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", "(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: "string", Name: "given", Modifier: "contains"}, SearchParameterValue{Value: "eve", Prefix: "", SecondaryValues: map[string]interface{}{}}, "0_0", "(givenJson.value LIKE @given_contains_0_0)", map[string]interface{}{"given_contains_0_0": "%eve%"}, false},
+		{SearchParameter{Type: "string", Name: "given", Modifier: "exact"}, SearchParameterValue{Value: "eve", Prefix: "", SecondaryValues: map[string]interface{}{}}, "0_0", "(givenJson.value = @given_exact_0_0)", map[string]interface{}{"given_exact_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: "below"}, SearchParameterValue{Value: "http://acme.org/fhir/", Prefix: "", SecondaryValues: map[string]interface{}{}}, "0_0", "(url LIKE @url_below_0_0)", map[string]interface{}{"url_below_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
 
 		{SearchParameter{Type: "quantity", Name: "valueQuantity", Modifier: ""}, SearchParameterValue{Value: float64(5.4), Prefix: "", SecondaryValues: map[string]interface{}{"valueQuantityCode": "mg"}}, "0_0", "(valueQuantityJson.value ->> '$.value' = @valueQuantity_0_0 AND valueQuantityJson.value ->> '$.code' = @valueQuantityCode_0_0)", map[string]interface{}{"valueQuantity_0_0": float64(5.4), "valueQuantityCode_0_0": "mg"}, false},
@@ -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_not_0_0 AND genderJson.value ->> '$.system' = @genderSystem_not_0_0)", map[string]interface{}{"gender_not_0_0": "male", "genderSystem_not_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},
 	}