#21 Add basic contents page

Dockerfile-debug

@@ -2,6 +2,7 @@ FROM docker.io/golang:1.20 AS build
 WORKDIR /go/src
 COPY cmd/mb3server/src ./cmd/mb3server/src
 COPY cmd/mb3server/main.go ./cmd/mb3server
+COPY pkg ./pkg
 COPY go.mod .
 
 ENV CGO_ENABLED=0
@@ -16,5 +17,5 @@ VOLUME /var/log
 COPY --from=build /go/src/mb3server ./
 COPY --from=build /go/bin/dlv /
 EXPOSE 8080/tcp 40000
-CMD ["/dlv", "--log", "--log-dest", "/var/log/delve.log", "--log-output", "rpc","--listen=:40000", "--headless=true", "--api-version=2", "--accept-multiclient", "exec", "./mb3server"]
+CMD ["/dlv", "--log", "--log-dest", "/var/log/delve.log", "--log-output", "debugger","--listen=:40000", "--headless=true", "--api-version=2", "--accept-multiclient", "exec", "./mb3server"]
 

api/schemas/FilterOptions.yaml

@@ -1,15 +1,15 @@
 components:
   schemas:
     StringCount:
-      type: object
-      properties:
-        values:
-          type: array
-          items:
+      type: array
+      items:
+        type: object
+        properties:
+          value:
             type: string
-        count:
-          type: integer
-          minimum: 0
+          count:
+            type: integer
+            minimum: 0
     FilterOptions:
       type: object
       properties:

cmd/mb3server/.openapi-generator/FILES

@@ -3,7 +3,6 @@ api/openapi.yaml
 main.go
 src/api.go
 src/api_default.go
-src/api_default_service.go
 src/error.go
 src/helpers.go
 src/impl.go
@@ -38,5 +37,5 @@ src/model_ms_focused_ion_inner.go
 src/model_search_result.go
 src/model_search_result_data_inner.go
 src/model_search_result_data_inner_spectra_inner.go
-src/model_string_count.go
+src/model_string_count_inner.go
 src/routers.go

cmd/mb3server/.openapi-generator/VERSION

@@ -1 +1 @@
-6.3.0
+6.5.0

cmd/mb3server/api/openapi.yaml

@@ -594,59 +594,58 @@ components:
           result_count: 0
           timestamp: timestamp
         compound_start:
-          values:
-          - values
-          - values
-          count: 0
+        - count: 0
+          value: value
+        - count: 0
+          value: value
         contributor:
-          values:
-          - values
-          - values
-          count: 0
+        - count: 0
+          value: value
+        - count: 0
+          value: value
         ms_type:
-          values:
-          - values
-          - values
-          count: 0
+        - count: 0
+          value: value
+        - count: 0
+          value: value
         ion_mode:
-          values:
-          - values
-          - values
-          count: 0
+        - count: 0
+          value: value
+        - count: 0
+          value: value
         instrument_type:
-          values:
-          - values
-          - values
-          count: 0
+        - count: 0
+          value: value
+        - count: 0
+          value: value
       properties:
         metadata:
           $ref: '#/components/schemas/Metadata'
         contributor:
-          $ref: '#/components/schemas/StringCount'
+          items:
+            $ref: '#/components/schemas/StringCount_inner'
+          type: array
         instrument_type:
-          $ref: '#/components/schemas/StringCount'
+          items:
+            $ref: '#/components/schemas/StringCount_inner'
+          type: array
         ms_type:
-          $ref: '#/components/schemas/StringCount'
+          items:
+            $ref: '#/components/schemas/StringCount_inner'
+          type: array
         ion_mode:
-          $ref: '#/components/schemas/StringCount'
+          items:
+            $ref: '#/components/schemas/StringCount_inner'
+          type: array
         compound_start:
-          $ref: '#/components/schemas/StringCount'
-      type: object
-    StringCount:
-      example:
-        values:
-        - values
-        - values
-        count: 0
-      properties:
-        values:
           items:
-            type: string
+            $ref: '#/components/schemas/StringCount_inner'
           type: array
-        count:
-          minimum: 0
-          type: integer
       type: object
+    StringCount:
+      items:
+        $ref: '#/components/schemas/StringCount_inner'
+      type: array
     Authors:
       items:
         $ref: '#/components/schemas/Authors_inner'
@@ -1154,6 +1153,17 @@ components:
           default: 100
           type: integer
       type: object
+    StringCount_inner:
+      example:
+        count: 0
+        value: value
+      properties:
+        value:
+          type: string
+        count:
+          minimum: 0
+          type: integer
+      type: object
     Authors_inner:
       description: Name of the author or affiliation
       example:

cmd/mb3server/main.go

@@ -12,13 +12,15 @@ package main
 import (
 	"log"
 	"net/http"
+	"time"
 
 	mb3server "github.com/MassBank/MassBank3/cmd/mb3server/src"
 )
 
 func main() {
 	log.Printf("Server started")
-
+	time.Sleep(5 * time.Second)
+	log.Printf("Server started 5")
 	DefaultApiService := mb3server.NewDefaultApiService()
 	DefaultApiController := mb3server.NewDefaultApiController(DefaultApiService)
 

cmd/mb3server/src/api-impl.go

@@ -0,0 +1,81 @@
+package mb3server
+
+import (
+	"github.com/MassBank/MassBank3/pkg/database"
+	"log"
+	"os"
+)
+
+var db database.MB3Database = nil
+
+func initDB() error {
+	if db == nil {
+		var mongo_uri = os.Getenv("MONGO_URI")
+		var mongo_name = os.Getenv("MONGO_DB_NAME")
+		log.Println("MongoDB URI: ", mongo_uri)
+		log.Println("Database_Name", mongo_name)
+		var err error = nil
+		var config = database.DBConfig{
+			Database:  database.MongoDB,
+			DbUser:    "",
+			DbPwd:     "",
+			DbHost:    "",
+			DbName:    os.Getenv("MONGO_DB_NAME"),
+			DbPort:    0,
+			DbConnStr: os.Getenv("MONGO_URI"),
+		}
+
+		db, err = database.NewMongoDB(config)
+		if err != nil {
+			return err
+		}
+		err = db.Connect()
+		if err != nil {
+			return err
+		}
+	}
+	return db.Ping()
+
+}
+
+func GetBrowseOptions() (*BrowseOptions, error) {
+	if err := initDB(); err != nil {
+		return nil, err
+	}
+	vals, err := db.GetUniqueValues(database.Filters{})
+	if err != nil {
+		return nil, err
+	}
+	var result = BrowseOptions{}
+	result.Metadata = Metadata{
+		Version:       "",
+		Timestamp:     "",
+		GitCommit:     "",
+		SpectraCount:  0,
+		CompoundCount: 0,
+		IsomerCount:   0,
+		ResultCount:   0,
+		Page:          0,
+		Limit:         0,
+	}
+	for _, val := range vals.IonMode {
+		result.IonMode = append(result.IonMode, StringCountInner{
+			Value: val.Val,
+			Count: int32(val.Count),
+		})
+	}
+	for _, val := range vals.MSType {
+		result.MsType = append(result.MsType, StringCountInner{
+			Value: val.Val,
+			Count: int32(val.Count),
+		})
+	}
+	for _, val := range vals.InstrumentType {
+		result.InstrumentType = append(result.InstrumentType, StringCountInner{
+			Value: val.Val,
+			Count: int32(val.Count),
+		})
+	}
+
+	return &result, nil
+}

cmd/mb3server/src/api_default_service.go

@@ -28,24 +28,22 @@ func NewDefaultApiService() DefaultApiServicer {
 
 // GetBrowseOptions - get browse options
 func (s *DefaultApiService) GetBrowseOptions(ctx context.Context) (ImplResponse, error) {
-	// TODO - update GetBrowseOptions with the required logic for this service method.
-	// Add api_default_service.go to the .openapi-generator-ignore to avoid overwriting this service implementation when updating open api generation.
-
-	//TODO: Uncomment the next line to return response Response(200, BrowseOptions{}) or use other options such as http.Ok ...
-	//return Response(200, BrowseOptions{}), nil
-
-	return Response(http.StatusNotImplemented, nil), errors.New("GetBrowseOptions method not implemented")
+	opt, err := GetBrowseOptions()
+	if err != nil {
+		return Response(http.StatusInternalServerError, nil), errors.New("Could not get results")
+	}
+	return Response(http.StatusOK, opt), nil
 }
 
 // GetFilterOptions - get filter options
 func (s *DefaultApiService) GetFilterOptions(ctx context.Context) (ImplResponse, error) {
-	// TODO - update GetFilterOptions with the required logic for this service method.
-	// Add api_default_service.go to the .openapi-generator-ignore to avoid overwriting this service implementation when updating open api generation.
 
-	//TODO: Uncomment the next line to return response Response(200, FilterOptions{}) or use other options such as http.Ok ...
-	//return Response(200, FilterOptions{}), nil
+	opt, err := GetBrowseOptions()
+	if err != nil {
+		return Response(http.StatusInternalServerError, nil), errors.New("Could not get results")
+	}
+	return Response(http.StatusOK, opt), nil
 
-	return Response(http.StatusNotImplemented, nil), errors.New("GetFilterOptions method not implemented")
 }
 
 // GetMetadata - get massbank metadata

cmd/mb3server/src/model_browse_options.go

@@ -12,36 +12,46 @@ package mb3server
 type BrowseOptions struct {
 	Metadata Metadata `json:"metadata,omitempty"`
 
-	Contributor StringCount `json:"contributor,omitempty"`
+	Contributor []StringCountInner `json:"contributor,omitempty"`
 
-	InstrumentType StringCount `json:"instrument_type,omitempty"`
+	InstrumentType []StringCountInner `json:"instrument_type,omitempty"`
 
-	MsType StringCount `json:"ms_type,omitempty"`
+	MsType []StringCountInner `json:"ms_type,omitempty"`
 
-	IonMode StringCount `json:"ion_mode,omitempty"`
+	IonMode []StringCountInner `json:"ion_mode,omitempty"`
 
-	CompoundStart StringCount `json:"compound_start,omitempty"`
+	CompoundStart []StringCountInner `json:"compound_start,omitempty"`
 }
 
 // AssertBrowseOptionsRequired checks if the required fields are not zero-ed
 func AssertBrowseOptionsRequired(obj BrowseOptions) error {
 	if err := AssertMetadataRequired(obj.Metadata); err != nil {
 		return err
 	}
-	if err := AssertStringCountRequired(obj.Contributor); err != nil {
-		return err
+	for _, el := range obj.Contributor {
+		if err := AssertStringCountInnerRequired(el); err != nil {
+			return err
+		}
 	}
-	if err := AssertStringCountRequired(obj.InstrumentType); err != nil {
-		return err
+	for _, el := range obj.InstrumentType {
+		if err := AssertStringCountInnerRequired(el); err != nil {
+			return err
+		}
 	}
-	if err := AssertStringCountRequired(obj.MsType); err != nil {
-		return err
+	for _, el := range obj.MsType {
+		if err := AssertStringCountInnerRequired(el); err != nil {
+			return err
+		}
 	}
-	if err := AssertStringCountRequired(obj.IonMode); err != nil {
-		return err
+	for _, el := range obj.IonMode {
+		if err := AssertStringCountInnerRequired(el); err != nil {
+			return err
+		}
 	}
-	if err := AssertStringCountRequired(obj.CompoundStart); err != nil {
-		return err
+	for _, el := range obj.CompoundStart {
+		if err := AssertStringCountInnerRequired(el); err != nil {
+			return err
+		}
 	}
 	return nil
 }

cmd/mb3server/src/routers.go

@@ -192,7 +192,7 @@ func parseBoolParameter(param string, required bool) (bool, error) {
 		return false, err
 	}
 
-	return val, nil
+	return bool(val), nil
 }
 
 // parseInt64ArrayParameter parses a string parameter containing array of values to []int64.

docker/docker-compose.yaml

@@ -34,11 +34,13 @@ services:
     ports:
       - "${MB3_API_PORT}:8080"
     environment:
-      MONGO_URI: "mongodb://${MONGODB_USER}:${MONGODB_PWD}@mongo:27017"
+      MONGO_URI: "mongodb://${MONGODB_USER}:${MONGODB_PWD}@mongodb:27017"
       MONGO_DB_NAME: "massbank3"
     depends_on:
       - mongodb
       - postgres
 
   mb3frontend:
     restart: always
+    environment:
+      VITE_SERVER_API_URL: "http://localhost:8081"