#10 add files to database

cmd/mb3dbtool/main.go

@@ -48,6 +48,10 @@ func main() {
  panic(err)
  }
  }
+ err = db.AddRecords(mbfiles)
+ if err != nil {
+ println("Could not add records: " + err.Error())
+ }
  if mbfiles == nil {
  panic("No files found")
  }

pkg/database/db_interface.go

@@ -19,8 +19,8 @@ type MB3Database interface {
  Disconnect() error
  GetRecord(*string) (massbank.Massbank, error)
  GetRecords(filters Filters, limit uint64) ([]massbank.Massbank, error)
- AddRecords(records []massbank.Massbank) error
+ AddRecords(records []*massbank.Massbank) error
  UpdateRecords(records []massbank.Massbank, add bool) (uint64, error)
- AddRecord(record massbank.Massbank) error
+ AddRecord(record *massbank.Massbank) error
  UpdateRecord(record massbank.Massbank, add bool) error
 }

pkg/database/mongodb.go

@@ -1,10 +1,13 @@
 package database
 
 import (
+ "errors"
  "github.com/MassBank/MassBank3/pkg/massbank"
+ "go.mongodb.org/mongo-driver/bson"
  "go.mongodb.org/mongo-driver/mongo"
  "go.mongodb.org/mongo-driver/mongo/options"
  "golang.org/x/net/context"
+ "log"
  "strconv"
 )
 
@@ -30,19 +33,37 @@ func (db *Mb3MongoDB) GetRecords(filters Filters, limit uint64) ([]massbank.Mass
  panic("implement me")
 }
 
-func (db *Mb3MongoDB) AddRecords(records []massbank.Massbank) error {
- //TODO implement me
- panic("implement me")
+func (db *Mb3MongoDB) AddRecords(records []*massbank.Massbank) error {
+ if db.database == nil {
+ return errors.New("database not ready")
+ }
+ var recordsI = make([]interface{}, len(records))
+ for i, record := range records {
+ recordsI[i] = record
+ }
+ _, err := db.database.Collection("massbank").InsertMany(context.Background(), recordsI)
+ if err != nil {
+ log.Println(err)
+ return err
+ }
+ return nil
 }
 
 func (db *Mb3MongoDB) UpdateRecords(records []massbank.Massbank, add bool) (uint64, error) {
  //TODO implement me
  panic("implement me")
 }
 
-func (db *Mb3MongoDB) AddRecord(record massbank.Massbank) error {
- //TODO implement me
- panic("implement me")
+func (db *Mb3MongoDB) AddRecord(record *massbank.Massbank) error {
+ if db.database == nil {
+ return errors.New("database not ready")
+ }
+ _, err := db.database.Collection("massbank").InsertOne(context.Background(), *record)
+ if err != nil {
+ log.Println(err)
+ return err
+ }
+ return nil
 }
 
 func (db *Mb3MongoDB) UpdateRecord(record massbank.Massbank, add bool) error {
@@ -118,9 +139,23 @@ func (db *Mb3MongoDB) Connect() error {
  db.database = mongoDb
  db.dirty = false
  }
+ db.init()
  return db.database.Client().Ping(ctx, nil)
 }
 
+func (db *Mb3MongoDB) init() error {
+ opt := options.IndexOptions{}
+ _, err := db.database.Collection("massbank").Indexes().CreateOne(context.Background(),
+ mongo.IndexModel{bson.D{{"accession", 1}},
+ opt.SetName("accession_1").SetUnique(true)})
+ indeces := []string{"compound.names", "compound.mass", "compound.formula", "acquisition.instrumenttype", "acquisition.massspectrometry.ION_MODE", "acquisition.massspectrometry.MS_TYPE"}
+ for _, index := range indeces {
+ db.database.Collection("massbank").Indexes().CreateOne(context.Background(), mongo.IndexModel{bson.D{{index, 1}}, &options.IndexOptions{}})
+
+ }
+ return err
+}
+
 func (db *Mb3MongoDB) Disconnect() error {
  return db.database.Client().Disconnect(context.TODO())
 }

pkg/massbank/bson.go

@@ -0,0 +1,71 @@
+package massbank
+
+import (
+ "go.mongodb.org/mongo-driver/bson"
+ "go.mongodb.org/mongo-driver/bson/bsontype"
+ "time"
+)
+
+func (p StringProperty) MarshalBSONValue() (bsontype.Type, []byte, error) {
+ return bson.MarshalValue(p.string)
+}
+
+func (p SubtagProperty) MarshalBSONValue() (bsontype.Type, []byte, error) {
+ m := map[string]string{p.subtag: p.string}
+ return bson.MarshalValue(m)
+}
+
+func (p DatabaseProperty) MarshalBSONValue() (bsontype.Type, []byte, error) {
+ m := map[string]string{p.Database: p.Identifier}
+ return bson.MarshalValue(m)
+}
+
+func (p RecordDeprecated) MarshalBSONValue() (bsontype.Type, []byte, error) {
+ return bson.MarshalValue(struct {
+ Date time.Time
+ reason string
+ }{p.Date, p.Reason})
+}
+
+func (p RecordDate) MarshalBSONValue() (bsontype.Type, []byte, error) {
+ return bson.MarshalValue(struct {
+ updated time.Time
+ created time.Time
+ }{p.Updated, p.Created})
+}
+
+func (p RecordAuthorNames) MarshalBSONValue() (bsontype.Type, []byte, error) {
+ return bson.MarshalValue(p.value)
+}
+
+func (p ChCompoundClasses) MarshalBSONValue() (bsontype.Type, []byte, error) {
+ return bson.MarshalValue(p.value)
+}
+
+func (p ChMass) MarshalBSONValue() (bsontype.Type, []byte, error) {
+ return bson.MarshalValue(p.value)
+}
+
+func (p SpLineage) MarshalBSONValue() (bsontype.Type, []byte, error) {
+ return bson.MarshalValue(p.value)
+}
+
+func (p PkPeak) MarshalBSONValue() (bsontype.Type, []byte, error) {
+ return bson.MarshalValue(struct {
+ Header []string
+ Mz []float64
+ Intensity []float64
+ Rel []uint
+ }{p.Header, p.Mz, p.Intensity, p.Rel})
+}
+
+func (p PkNumPeak) MarshalBSONValue() (bsontype.Type, []byte, error) {
+ return bson.MarshalValue(p.Value)
+}
+
+func (p PkAnnotation) MarshalBSONValue() (bsontype.Type, []byte, error) {
+ return bson.MarshalValue(struct {
+ Header []string
+ Values map[string][]interface{}
+ }{p.Header, p.Values})
+}