MassBank3-10 Build tool to write/update MassBank records to database

Begin implementation of packages

cmd/mb3dbtool/main.go

@@ -0,0 +1,5 @@
+package main
+
+func main() {
+
+}

go.mod

@@ -3,4 +3,22 @@ module github.com/MassBank/MassBank3
 go 1.19
 
 require github.com/go-chi/chi/v5 v5.0.3
-require github.com/go-chi/cors v1.2.0
+
+require (
+	github.com/go-chi/cors v1.2.0
+	go.mongodb.org/mongo-driver v1.11.1
+)
+
+require (
+	github.com/golang/snappy v0.0.1 // indirect
+	github.com/klauspost/compress v1.13.6 // indirect
+	github.com/montanaflynn/stats v0.0.0-20171201202039-1bf9dbcd8cbe // indirect
+	github.com/pkg/errors v0.9.1 // indirect
+	github.com/xdg-go/pbkdf2 v1.0.0 // indirect
+	github.com/xdg-go/scram v1.1.1 // indirect
+	github.com/xdg-go/stringprep v1.0.3 // indirect
+	github.com/youmark/pkcs8 v0.0.0-20181117223130-1be2e3e5546d // indirect
+	golang.org/x/crypto v0.0.0-20220622213112-05595931fe9d // indirect
+	golang.org/x/sync v0.0.0-20210220032951-036812b2e83c // indirect
+	golang.org/x/text v0.3.7 // indirect
+)

go.sum

@@ -1,4 +1,59 @@
+github.com/davecgh/go-spew v1.1.0/go.mod h1:J7Y8YcW2NihsgmVo/mv3lAwl/skON4iLHjSsI+c5H38=
+github.com/davecgh/go-spew v1.1.1 h1:vj9j/u1bqnvCEfJOwUhtlOARqs3+rkHYY13jYWTU97c=
+github.com/davecgh/go-spew v1.1.1/go.mod h1:J7Y8YcW2NihsgmVo/mv3lAwl/skON4iLHjSsI+c5H38=
 github.com/go-chi/chi/v5 v5.0.3 h1:khYQBdPivkYG1s1TAzDQG1f6eX4kD2TItYVZexL5rS4=
 github.com/go-chi/chi/v5 v5.0.3/go.mod h1:DslCQbL2OYiznFReuXYUmQ2hGd1aDpCnlMNITLSKoi8=
 github.com/go-chi/cors v1.2.0 h1:tV1g1XENQ8ku4Bq3K9ub2AtgG+p16SmzeMSGTwrOKdE=
 github.com/go-chi/cors v1.2.0/go.mod h1:sSbTewc+6wYHBBCW7ytsFSn836hqM7JxpglAy2Vzc58=
+github.com/golang/snappy v0.0.1 h1:Qgr9rKW7uDUkrbSmQeiDsGa8SjGyCOGtuasMWwvp2P4=
+github.com/golang/snappy v0.0.1/go.mod h1:/XxbfmMg8lxefKM7IXC3fBNl/7bRcc72aCRzEWrmP2Q=
+github.com/google/go-cmp v0.5.2 h1:X2ev0eStA3AbceY54o37/0PQ/UWqKEiiO2dKL5OPaFM=
+github.com/google/go-cmp v0.5.2/go.mod h1:v8dTdLbMG2kIc/vJvl+f65V22dbkXbowE6jgT/gNBxE=
+github.com/klauspost/compress v1.13.6 h1:P76CopJELS0TiO2mebmnzgWaajssP/EszplttgQxcgc=
+github.com/klauspost/compress v1.13.6/go.mod h1:/3/Vjq9QcHkK5uEr5lBEmyoZ1iFhe47etQ6QUkpK6sk=
+github.com/kr/pretty v0.1.0 h1:L/CwN0zerZDmRFUapSPitk6f+Q3+0za1rQkzVuMiMFI=
+github.com/kr/pretty v0.1.0/go.mod h1:dAy3ld7l9f0ibDNOQOHHMYYIIbhfbHSm3C4ZsoJORNo=
+github.com/kr/pty v1.1.1/go.mod h1:pFQYn66WHrOpPYNljwOMqo10TkYh1fy3cYio2l3bCsQ=
+github.com/kr/text v0.1.0 h1:45sCR5RtlFHMR4UwH9sdQ5TC8v0qDQCHnXt+kaKSTVE=
+github.com/kr/text v0.1.0/go.mod h1:4Jbv+DJW3UT/LiOwJeYQe1efqtUx/iVham/4vfdArNI=
+github.com/montanaflynn/stats v0.0.0-20171201202039-1bf9dbcd8cbe h1:iruDEfMl2E6fbMZ9s0scYfZQ84/6SPL6zC8ACM2oIL0=
+github.com/montanaflynn/stats v0.0.0-20171201202039-1bf9dbcd8cbe/go.mod h1:wL8QJuTMNUDYhXwkmfOly8iTdp5TEcJFWZD2D7SIkUc=
+github.com/pkg/errors v0.9.1 h1:FEBLx1zS214owpjy7qsBeixbURkuhQAwrK5UwLGTwt4=
+github.com/pkg/errors v0.9.1/go.mod h1:bwawxfHBFNV+L2hUp1rHADufV3IMtnDRdf1r5NINEl0=
+github.com/pmezard/go-difflib v1.0.0 h1:4DBwDE0NGyQoBHbLQYPwSUPoCMWR5BEzIk/f1lZbAQM=
+github.com/pmezard/go-difflib v1.0.0/go.mod h1:iKH77koFhYxTK1pcRnkKkqfTogsbg7gZNVY4sRDYZ/4=
+github.com/stretchr/objx v0.1.0/go.mod h1:HFkY916IF+rwdDfMAkV7OtwuqBVzrE8GR6GFx+wExME=
+github.com/stretchr/testify v1.6.1 h1:hDPOHmpOpP40lSULcqw7IrRb/u7w6RpDC9399XyoNd0=
+github.com/stretchr/testify v1.6.1/go.mod h1:6Fq8oRcR53rry900zMqJjRRixrwX3KX962/h/Wwjteg=
+github.com/tidwall/pretty v1.0.0 h1:HsD+QiTn7sK6flMKIvNmpqz1qrpP3Ps6jOKIKMooyg4=
+github.com/tidwall/pretty v1.0.0/go.mod h1:XNkn88O1ChpSDQmQeStsy+sBenx6DDtFZJxhVysOjyk=
+github.com/xdg-go/pbkdf2 v1.0.0 h1:Su7DPu48wXMwC3bs7MCNG+z4FhcyEuz5dlvchbq0B0c=
+github.com/xdg-go/pbkdf2 v1.0.0/go.mod h1:jrpuAogTd400dnrH08LKmI/xc1MbPOebTwRqcT5RDeI=
+github.com/xdg-go/scram v1.1.1 h1:VOMT+81stJgXW3CpHyqHN3AXDYIMsx56mEFrB37Mb/E=
+github.com/xdg-go/scram v1.1.1/go.mod h1:RaEWvsqvNKKvBPvcKeFjrG2cJqOkHTiyTpzz23ni57g=
+github.com/xdg-go/stringprep v1.0.3 h1:kdwGpVNwPFtjs98xCGkHjQtGKh86rDcRZN17QEMCOIs=
+github.com/xdg-go/stringprep v1.0.3/go.mod h1:W3f5j4i+9rC0kuIEJL0ky1VpHXQU3ocBgklLGvcBnW8=
+github.com/youmark/pkcs8 v0.0.0-20181117223130-1be2e3e5546d h1:splanxYIlg+5LfHAM6xpdFEAYOk8iySO56hMFq6uLyA=
+github.com/youmark/pkcs8 v0.0.0-20181117223130-1be2e3e5546d/go.mod h1:rHwXgn7JulP+udvsHwJoVG1YGAP6VLg4y9I5dyZdqmA=
+go.mongodb.org/mongo-driver v1.11.1 h1:QP0znIRTuL0jf1oBQoAoM0C6ZJfBK4kx0Uumtv1A7w8=
+go.mongodb.org/mongo-driver v1.11.1/go.mod h1:s7p5vEtfbeR1gYi6pnj3c3/urpbLv2T5Sfd6Rp2HBB8=
+golang.org/x/crypto v0.0.0-20220622213112-05595931fe9d h1:sK3txAijHtOK88l68nt020reeT1ZdKLIYetKl95FzVY=
+golang.org/x/crypto v0.0.0-20220622213112-05595931fe9d/go.mod h1:IxCIyHEi3zRg3s0A5j5BB6A9Jmi73HwBIUl50j+osU4=
+golang.org/x/net v0.0.0-20211112202133-69e39bad7dc2/go.mod h1:9nx3DQGgdP8bBQD5qxJ1jj9UTztislL4KSBs9R2vV5Y=
+golang.org/x/sync v0.0.0-20210220032951-036812b2e83c h1:5KslGYwFpkhGh+Q16bwMP3cOontH8FOep7tGV86Y7SQ=
+golang.org/x/sync v0.0.0-20210220032951-036812b2e83c/go.mod h1:RxMgew5VJxzue5/jJTE5uejpjVlOe/izrB70Jof72aM=
+golang.org/x/sys v0.0.0-20201119102817-f84b799fce68/go.mod h1:h1NjWce9XRLGQEsW7wpKNCjG9DtNlClVuFLEZdDNbEs=
+golang.org/x/sys v0.0.0-20210423082822-04245dca01da/go.mod h1:h1NjWce9XRLGQEsW7wpKNCjG9DtNlClVuFLEZdDNbEs=
+golang.org/x/sys v0.0.0-20210615035016-665e8c7367d1/go.mod h1:oPkhp1MJrh7nUepCBck5+mAzfO9JrbApNNgaTdGDITg=
+golang.org/x/term v0.0.0-20201126162022-7de9c90e9dd1/go.mod h1:bj7SfCRtBDWHUb9snDiAeCFNEtKQo2Wmx5Cou7ajbmo=
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+gopkg.in/check.v1 v0.0.0-20161208181325-20d25e280405/go.mod h1:Co6ibVJAznAaIkqp8huTwlJQCZ016jof/cbN4VW5Yz0=
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+gopkg.in/yaml.v3 v3.0.0-20200313102051-9f266ea9e77c/go.mod h1:K4uyk7z7BCEPqu6E+C64Yfv1cQ7kz7rIZviUmN+EgEM=
+gopkg.in/yaml.v3 v3.0.1 h1:fxVm/GzAzEWqLHuvctI91KS9hhNmmWOoWu0XTYJS7CA=
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pkg/database/db_interface.go

@@ -0,0 +1,17 @@
+package database
+
+import "github.com/MassBank/MassBank3/pkg/massbank"
+
+type Filters struct {
+}
+
+type MB3Database interface {
+	Connect() error
+	Disconnect() error
+	GetRecord(*string) (massbank.Massbank, error)
+	GetRecords(filters Filters, limit uint64) ([]massbank.Massbank, error)
+	AddRecords(records []massbank.Massbank) error
+	UpdateRecords(records []massbank.Massbank, add bool) (uint64, error)
+	AddRecord(record massbank.Massbank) error
+	UpdateRecord(record massbank.Massbank, add bool) error
+}

pkg/database/mongodb.go

@@ -0,0 +1,124 @@
+package database
+
+import (
+	"github.com/MassBank/MassBank3/pkg/massbank"
+	"go.mongodb.org/mongo-driver/mongo"
+	"go.mongodb.org/mongo-driver/mongo/options"
+	"golang.org/x/net/context"
+	"strconv"
+)
+
+const connectionURIDefault = "mongodb://massbank3:massbank3password@localhost:27017"
+
+type Mb3MongoDB struct {
+	user     string
+	pwd      string
+	host     string
+	dbname   string
+	port     uint16
+	database *mongo.Database
+	dirty    bool
+}
+
+func (self *Mb3MongoDB) GetRecord(s *string) (massbank.Massbank, error) {
+	//TODO implement me
+	panic("implement me")
+}
+
+func (self *Mb3MongoDB) GetRecords(filters Filters, limit uint64) ([]massbank.Massbank, error) {
+	//TODO implement me
+	panic("implement me")
+}
+
+func (self *Mb3MongoDB) AddRecords(records []massbank.Massbank) error {
+	//TODO implement me
+	panic("implement me")
+}
+
+func (self *Mb3MongoDB) UpdateRecords(records []massbank.Massbank, add bool) (uint64, error) {
+	//TODO implement me
+	panic("implement me")
+}
+
+func (self *Mb3MongoDB) AddRecord(record massbank.Massbank) error {
+	//TODO implement me
+	panic("implement me")
+}
+
+func (self *Mb3MongoDB) UpdateRecord(record massbank.Massbank, add bool) error {
+	//TODO implement me
+	panic("implement me")
+}
+
+func newMongoDB() (*Mb3MongoDB, error) {
+	return &Mb3MongoDB{
+		user:     "massbank3",
+		pwd:      "massbank3password",
+		host:     "localhost",
+		dbname:   "massbank3",
+		port:     27017,
+		database: nil,
+		dirty:    true,
+	}, nil
+
+}
+
+func (self *Mb3MongoDB) SetUser(user string) *Mb3MongoDB {
+	self.dirty = self.dirty || user != self.user
+	self.user = user
+	return self
+}
+
+func (self *Mb3MongoDB) SetPassword(password string) *Mb3MongoDB {
+	self.dirty = self.dirty || password != self.pwd
+	self.pwd = password
+	return self
+}
+
+func (self *Mb3MongoDB) SetHost(host string) *Mb3MongoDB {
+	self.dirty = self.dirty || host != self.host
+	self.host = host
+	return self
+}
+
+func (self *Mb3MongoDB) SetDbName(dbname string) *Mb3MongoDB {
+	self.dirty = self.dirty || dbname == self.dbname
+	self.dbname = dbname
+	return self
+}
+
+func (self *Mb3MongoDB) SetPort(port uint16) *Mb3MongoDB {
+	self.dirty = self.dirty || port == self.port
+	self.port = port
+	return self
+}
+
+func (self *Mb3MongoDB) Connect() error {
+	ctx := context.TODO()
+	if self.dirty && self.database != nil {
+		self.database.Client().Disconnect(ctx)
+		self.database = nil
+	}
+	if self.database == nil {
+		clOptions := options.Client().SetAuth(options.Credential{
+			AuthMechanism:           "SCRAM-SHA-256",
+			AuthMechanismProperties: nil,
+			AuthSource:              "admin",
+			Username:                self.user,
+			Password:                self.pwd,
+			PasswordSet:             true,
+		}).SetAppName("Massbank3API").SetHosts([]string{self.host + ":" + strconv.FormatInt(int64(self.port), 10)})
+		dbclient, err := mongo.Connect(ctx, clOptions)
+		db := dbclient.Database(self.dbname)
+		if err != nil {
+			return err
+		}
+		self.database = db
+		self.dirty = false
+	}
+	return self.database.Client().Ping(ctx, nil)
+}
+
+func (self *Mb3MongoDB) Disconnect() error {
+	return self.database.Client().Disconnect(context.TODO())
+}