#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"