Merge pull request #13 from bmeg/feature/bugfixes

bugfix schema translator

Author: matthewpeterkort

README.md

@@ -113,3 +113,11 @@ specify custom namespace for edge generation with "namespace" key in extra args,
 ```
 jsonschemagraph gen-dir ../iceberg/schemas/graph DATA OUT --extraArgs '{"auth_resource_path": "/programs/ohsu/projects/test", "namespace": "CALIPERIDP.org"}'
 ```
+
+### Example commands for generating graphql schema from jsonschema
+
+```
+jsonschemagraph gen-graphql --graphName CALIPER --jsonSchema graph-fhir.json  --configPath config.yaml --writeIntermediateFile
+```
+
+This translator does not support codeable references

graphql/convertSchema.go

@@ -3,9 +3,9 @@ package graphql
 import (
 	"encoding/json"
 	"fmt"
-	"log"
 	"os"
 	"path/filepath"
+	"reflect"
 	"slices"
 	"strings"
 	"unicode"
@@ -56,10 +56,14 @@ func LowerFirstLetter(s string) string {
 
 func generateQueryList(classes []string) {
 	for i, v := range classes {
-		classes[i] = LowerFirstLetter(classes[i]) + "(offset: Int first: Int filter: JSON sort: JSON accessibility: Accessibility = all format: Format = json): [" + v + "Type]"
+		classes[i] = LowerFirstLetter(classes[i]) + "(offset: Int first: Int filter: JSON sort: [SortInput]  accessibility: Accessibility = all): [" + v + "Type!]!"
 	}
 }
 
+func isSlice(v interface{}) bool {
+	return reflect.TypeOf(v).Kind() == reflect.Slice
+}
+
 func ParseIntoGraphqlSchema(relpath string, graphName string, vertexSubset []string, writeFile bool) ([]*gripql.Graph, error) {
 	out, err := graph.Load(relpath)
 	if err != nil {
@@ -85,31 +89,22 @@ func ParseIntoGraphqlSchema(relpath string, graphName string, vertexSubset []str
 				continue
 			}
 
-			vertVal := ParseSchema(sch)
-			switch vertVal.(type) {
-			case string:
-				vertexData[key] = vertVal.(string)
-			case int:
-				vertexData[key] = vertVal.(int)
-			case bool:
-				vertexData[key] = vertVal.(bool)
-			case float64:
-				vertexData[key] = vertVal.(float64)
-			case []any:
-				if vertVal.([]any)[0].(string) == "Resource" {
-					vertVal.([]any)[0] = "ResourceUnion"
-				}
-				vertexData[key] = vertVal.([]any)
-			case nil:
-			default:
-				log.Printf("ERR State for type: ", vertVal)
-				continue
+			value := ParseSchema(sch)
+
+			// Fields with edges that aren't defined in our internal schema are not present in the graphql schema either
+			if value == nil {
+				fmt.Printf("WARNING: key %s on type %s may not be supported\n", key, class.Title)
+			} else if isSlice(value) && value.([]any)[0] == "Resource" {
+				value.([]any)[0] = "ResourceUnion"
+				vertexData[key] = value
+			} else {
+				vertexData[key] = value
 			}
 		}
 
 		if ext, ok := class.Extensions[compile.GraphExtensionTag]; ok {
-			enumData := map[string][]string{}
-			enumSeen := map[string]bool{}
+			unionData := map[string][]string{}
+			unionSeen := map[string]bool{}
 			for _, target := range ext.(compile.GraphExtension).Targets {
 				parts := strings.Split(target.Rel, "_")
 				RegexMatch := target.TargetHints.RegexMatch[0][:len(target.TargetHints.RegexMatch[0])-2]
@@ -121,24 +116,39 @@ func ParseIntoGraphqlSchema(relpath string, graphName string, vertexSubset []str
 					}
 					vertexData[parts[0]] = RegexMatch
 					continue
+				} else if len(parts) == 2 {
+					base, targetType := parts[0], parts[len(parts)-1]
+					if targetType != RegexMatch {
+						if value, ok := vertexData[parts[0]]; ok && value != nil {
+							strValue := ""
+							if slice, isSlice := value.([]any); isSlice && len(slice) > 0 {
+								strValue = slice[0].(string)
+							} else if s, isString := value.(string); isString {
+								strValue = s
+							}
+							if len(strValue) >= 5 && strings.HasSuffix(strValue, "Union") {
+								vertexData[parts[0]] = strValue[:len(strValue)-5]
+							}
+						} else {
+							fmt.Printf("Key not found or value is nil: %s\n %s", parts[0], vertexData)
+						}
+						continue
+					}
+					unionTitle := fmt.Sprintf("%s%s", class.Title, cases.Title(language.Und, cases.NoLower).String(base)) + "Union"
+					if _, seen := unionSeen[targetType+unionTitle]; !seen {
+						vertexData[base] = unionTitle
+						unionSeen[targetType+unionTitle] = true
+						unionData[unionTitle] = append(unionData[unionTitle], targetType)
+					}
 				}
-				base, targetType := parts[0], parts[len(parts)-1]
-				// In places where there are in-node traversals before hitting an edge, need to
-				// continue with execution to avoid creating a redundant enum.
-				if targetType != RegexMatch {
-					continue
-				}
-				unionTitle := fmt.Sprintf("%s%s", class.Title, cases.Title(language.Und, cases.NoLower).String(base)) + "Union"
-				if _, seen := enumSeen[targetType+unionTitle]; !seen {
-					vertexData[base] = unionTitle
-					enumSeen[targetType+unionTitle] = true
-					enumData[unionTitle] = append(enumData[unionTitle], targetType)
-				}
+				/* else { base, targetType := parts[0], parts[len(parts)-1]
+				fmt.Println("BASE: ", base, "TARGET TYPE: ", targetType) */
+
 			}
-			if enumData != nil {
-				for k, v := range enumData {
-					enum := map[string]any{"data": map[string]any{k: v}, "label": "Vertex", "gid": "Union"}
-					graphSchema["vertices"] = append(graphSchema["vertices"].([]map[string]any), enum)
+			if unionData != nil {
+				for k, v := range unionData {
+					union := map[string]any{"data": map[string]any{k: v}, "label": "Vertex", "gid": "Union"}
+					graphSchema["vertices"] = append(graphSchema["vertices"].([]map[string]any), union)
 				}
 			}
 		}

graphql/griptographql.go

@@ -23,9 +23,11 @@ func GripGraphqltoGraphql(graph *gripql.Graph) string {
 	// Write gen3 style boiler plate to mirror thier args
 	schemaBuilder.WriteString("scalar JSON\n")
 	schemaBuilder.WriteString("enum Accessibility {\n  all\n  accessible\n  unaccessible\n}\n")
-	schemaBuilder.WriteString("enum Format {\n  json\n  tsv\n  csv\n}\n")
+	schemaBuilder.WriteString("input SortInput {\n  field: String!\n  descending: Boolean\n}\n")
 
 	for _, v := range graph.Vertices {
+		//fmt.Println("V: ", v)
+		//fmt.Printf("BREAK: \n\n")
 		if v.Gid != "Query" {
 			executedFirstBlock := false
 			for name, values := range v.Data.AsMap() {
@@ -51,11 +53,12 @@ func GripGraphqltoGraphql(graph *gripql.Graph) string {
 				for field, fieldType := range v.Data.AsMap() {
 					strFieldType, ok := fieldType.(string)
 					if ok && (strings.HasSuffix(strFieldType, "Type") || strings.HasSuffix(strFieldType, "Union")) {
-						schemaBuilder.WriteString(fmt.Sprintf("  %s(offset: Int first: Int filter: JSON sort: JSON accessibility: Accessibility = all format: Format = json): [%s]\n", field, strFieldType))
+						schemaBuilder.WriteString(fmt.Sprintf("  %s(offset: Int first: Int): %s!\n", field, strFieldType))
 					} else {
 						schemaBuilder.WriteString(fmt.Sprintf("  %s: %s\n", field, fieldType))
 					}
 				}
+				schemaBuilder.WriteString("  auth_resource_path: String\n")
 				schemaBuilder.WriteString("}\n")
 			}
 		} else {

graphql/parse.go

@@ -3,23 +3,20 @@ package graphql
 import (
 	"fmt"
 	"slices"
-	"strings"
 
 	"github.com/bmeg/jsonschema/v5"
 )
 
 func jsontographlprimitiveType(returnType any) any {
-	switch returnType.(type) {
-	case string:
+	switch returnType {
+	case "string":
 		return "String"
-	case int:
+	case "integer":
 		return "Int"
-	case bool:
+	case "boolean":
 		return "Boolean"
-	case float64:
+	case "number":
 		return "Float"
-	case []any:
-		return []any{[]any{strings.Title(returnType.([]any)[0].(string))}}
 	default:
 		fmt.Println("ERR State for jsontographlprimitiveType: ", returnType)
 		return ""
@@ -37,6 +34,7 @@ func ParseSchema(schema *jsonschema.Schema) any {
 	if schema.Items2020 != nil {
 		if schema.Items2020.Ref != nil &&
 			schema.Items2020.Ref.Title != "" {
+			// Don't include keys that contain references which types can't be discerned from reading the schema
 			if slices.Contains([]string{"Reference", "FHIRPrimitiveExtension"}, schema.Items2020.Ref.Title) {
 				return nil
 			}