Merge pull request #1 from NBISweden/initial-push

Initial push

.github/workflows/go-linter.yaml

@@ -0,0 +1,32 @@
+name: golangci-lint
+on:
+  push:
+    branches:
+      - master
+      - main
+  pull_request:
+    branches:
+        - master
+
+permissions:
+  contents: read
+  # Optional: allow read access to pull request. Use with `only-new-issues` option.
+  # pull-requests: read
+
+jobs:
+  golangci:
+    name: lint
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - uses: actions/setup-go@v4
+        with:
+          go-version: '1.21'
+          cache: false
+      - name: golangci-lint
+        uses: golangci/golangci-lint-action@v3
+        with:
+          # Require: The version of golangci-lint to use.
+          # When `install-mode` is `binary` (default) the value can be v1.2 or v1.2.3 or `latest` to use the latest version.
+          # When `install-mode` is `goinstall` the value can be v1.2.3, `latest`, or the hash of a commit.
+          version: v1.54

.gitignore

@@ -0,0 +1 @@
+web/*

Dockerfile

@@ -0,0 +1,16 @@
+FROM golang:1.20.3-alpine3.17 as build
+WORKDIR /lp_app
+COPY . .
+ENV GO111MODULE=on
+ENV GOPATH=$PWD
+ENV GOOS=linux
+RUN go build -o /test .
+
+
+FROM alpine:3.17
+WORKDIR /gen_app
+RUN apk add  --repository=https://dl-cdn.alpinelinux.org/alpine/edge/community hugo
+COPY --from=build /test /gen_app/
+COPY dev_utils .
+CMD ["/gen_app/test"]
+COPY /web /web

config.go

@@ -0,0 +1,72 @@
+package main
+
+import (
+	"strings"
+
+	log "github.com/sirupsen/logrus"
+	"github.com/spf13/viper"
+)
+
+func getConfig() MetadataS3Config {
+	parseConfig()
+	S3Conf := configS3Storage()
+	return S3Conf
+
+}
+
+type MetadataS3Config struct {
+	URL               string
+	Port              int
+	AccessKey         string
+	SecretKey         string
+	Bucket            string
+	Region            string
+	Chunksize         int
+	Cacert            string
+	WebMetadataFolder string
+}
+
+func configS3Storage() MetadataS3Config {
+	s3 := MetadataS3Config{}
+	s3.URL = viper.GetString("S3MetadataBucket.url")
+	s3.AccessKey = viper.GetString("S3MetadataBucket.accesskey")
+	s3.SecretKey = viper.GetString("S3MetadataBucket.secretkey")
+	s3.Bucket = viper.GetString("S3MetadataBucket.bucket")
+	s3.Port = 9000
+	s3.WebMetadataFolder = viper.GetString("S3MetadataBucket.WebMetadataFolder")
+	if viper.IsSet("s3.port") {
+		s3.Port = viper.GetInt("S3MetadataBucket.port")
+	}
+
+	if viper.IsSet("s3.region") {
+		s3.Region = viper.GetString("S3MetadataBucket.region")
+	}
+
+	if viper.IsSet("s3.chunksize") {
+		s3.Chunksize = viper.GetInt("S3MetadataBucket.chunksize") * 1024 * 1024
+	}
+
+	if viper.IsSet("s3.cacert") {
+		s3.Cacert = viper.GetString("S3MetadataBucket.cacert")
+	}
+
+	return s3
+}
+
+func parseConfig() {
+	viper.SetConfigName("config")
+	viper.AddConfigPath(".")
+	viper.AutomaticEnv()
+	viper.SetEnvKeyReplacer(strings.NewReplacer(".", "_"))
+	viper.SetConfigType("yaml")
+	if viper.IsSet("configFile") {
+		viper.SetConfigFile(viper.GetString("configFile"))
+	}
+	if err := viper.ReadInConfig(); err != nil {
+		if _, ok := err.(viper.ConfigFileNotFoundError); ok {
+			log.Infoln("No config file found, using ENVs only")
+		} else {
+			log.Fatalf("Error when reading config file: '%s'", err)
+		}
+	}
+}

dev_utils/compose.yaml

@@ -0,0 +1,16 @@
+version: "3.7"
+services:
+  minio:
+    command: server /data
+    container_name: s3
+    environment:
+      - MINIO_ACCESS_KEY=myaccesskey
+      - MINIO_SECRET_KEY=mysecretkey
+    healthcheck:
+      test: ["CMD", "curl", "-fkq", "https://127.0.0.1:9000/minio/health/live"]
+      interval: 5s
+      timeout: 20s
+      retries: 3
+    image: minio/minio:RELEASE.2020-10-28T08-16-50Z
+    ports:
+      - "9000:9000"

dev_utils/config.yaml

@@ -0,0 +1,9 @@
+S3MetadataBucket:
+  url: "http://127.0.0.1:9000"
+  accesskey: "myaccesskey"
+  secretkey: "mysecretkey"
+  region: "us-east-1"
+  bucket: "test/"
+  WebMetadataFolder: "web/content/"
+
+

download_metadata.go

@@ -0,0 +1,66 @@
+package main
+
+import (
+	"context"
+	"os"
+	"path/filepath"
+
+	"github.com/aws/aws-sdk-go-v2/aws"
+	"github.com/aws/aws-sdk-go-v2/feature/s3/manager"
+	"github.com/aws/aws-sdk-go-v2/service/s3"
+	log "github.com/sirupsen/logrus"
+)
+
+func metadataDownloader(Metadataclient *MetadataBackend) {
+
+	var (
+		Bucket         = Metadataclient.Bucket // Download from this bucket
+		Prefix         = "datasets/"           // Using this key prefix
+		LocalDirectory = "web/content/"        // Into this directory
+	)
+	client := Metadataclient.Client
+
+	manager := manager.NewDownloader(client)
+	paginator := s3.NewListObjectsV2Paginator(client, &s3.ListObjectsV2Input{
+		Bucket: &Bucket,
+		Prefix: &Prefix,
+	})
+	log.Infoln("Started downloading metadata files")
+	for paginator.HasMorePages() {
+		page, err := paginator.NextPage(context.TODO())
+		if err != nil {
+			log.Fatalln("error:", err)
+		}
+		for _, obj := range page.Contents {
+			if err := downloadToFile(manager, LocalDirectory, Bucket, aws.ToString(obj.Key)); err != nil {
+				log.Fatalf("Error while getting next page from ListObjectsV2Paginator: %v", err)
+			}
+		}
+
+	}
+	log.Infoln("Completed downloading metadatafiles")
+
+}
+
+func downloadToFile(downloader *manager.Downloader, targetDirectory, bucket, key string) error {
+	// Create the directories in the path
+	file := filepath.Join(targetDirectory, key)
+	if err := os.MkdirAll(filepath.Dir(file), 0775); err != nil {
+		return err
+	}
+
+	// Set up the local file
+	fd, err := os.Create(file)
+	if err != nil {
+		return err
+	}
+	defer fd.Close()
+	// Download the file using the AWS SDK for Go
+	//fmt.Printf("Downloading s3://%s/%s to %s...\n", bucket, key, file)
+
+	_, err = downloader.Download(context.TODO(), fd, &s3.GetObjectInput{Bucket: &bucket, Key: &key})
+	if err != nil {
+		log.Infoln("Failed to download metadatafiles")
+	}
+	return err
+}

go.mod

@@ -0,0 +1,50 @@
+module lpg
+
+go 1.20
+
+require (
+	github.com/aws/aws-sdk-go-v2 v1.24.1
+	github.com/aws/aws-sdk-go-v2/config v1.26.5
+	github.com/aws/aws-sdk-go-v2/credentials v1.16.16
+	github.com/aws/aws-sdk-go-v2/feature/s3/manager v1.15.13
+	github.com/aws/aws-sdk-go-v2/service/s3 v1.48.0
+	github.com/sirupsen/logrus v1.9.3
+	github.com/spf13/viper v1.18.2
+)
+
+require (
+	github.com/aws/aws-sdk-go-v2/aws/protocol/eventstream v1.5.4 // indirect
+	github.com/aws/aws-sdk-go-v2/feature/ec2/imds v1.14.11 // indirect
+	github.com/aws/aws-sdk-go-v2/internal/configsources v1.2.10 // indirect
+	github.com/aws/aws-sdk-go-v2/internal/endpoints/v2 v2.5.10 // indirect
+	github.com/aws/aws-sdk-go-v2/internal/ini v1.7.2 // indirect
+	github.com/aws/aws-sdk-go-v2/internal/v4a v1.2.10 // indirect
+	github.com/aws/aws-sdk-go-v2/service/internal/accept-encoding v1.10.4 // indirect
+	github.com/aws/aws-sdk-go-v2/service/internal/checksum v1.2.10 // indirect
+	github.com/aws/aws-sdk-go-v2/service/internal/presigned-url v1.10.10 // indirect
+	github.com/aws/aws-sdk-go-v2/service/internal/s3shared v1.16.10 // indirect
+	github.com/aws/aws-sdk-go-v2/service/sso v1.18.7 // indirect
+	github.com/aws/aws-sdk-go-v2/service/ssooidc v1.21.7 // indirect
+	github.com/aws/aws-sdk-go-v2/service/sts v1.26.7 // indirect
+	github.com/aws/smithy-go v1.19.0 // indirect
+	github.com/fsnotify/fsnotify v1.7.0 // indirect
+	github.com/hashicorp/hcl v1.0.0 // indirect
+	github.com/jmespath/go-jmespath v0.4.0 // indirect
+	github.com/magiconair/properties v1.8.7 // indirect
+	github.com/mitchellh/mapstructure v1.5.0 // indirect
+	github.com/pelletier/go-toml/v2 v2.1.0 // indirect
+	github.com/sagikazarmark/locafero v0.4.0 // indirect
+	github.com/sagikazarmark/slog-shim v0.1.0 // indirect
+	github.com/sourcegraph/conc v0.3.0 // indirect
+	github.com/spf13/afero v1.11.0 // indirect
+	github.com/spf13/cast v1.6.0 // indirect
+	github.com/spf13/pflag v1.0.5 // indirect
+	github.com/subosito/gotenv v1.6.0 // indirect
+	go.uber.org/atomic v1.9.0 // indirect
+	go.uber.org/multierr v1.9.0 // indirect
+	golang.org/x/exp v0.0.0-20230905200255-921286631fa9 // indirect
+	golang.org/x/sys v0.15.0 // indirect
+	golang.org/x/text v0.14.0 // indirect
+	gopkg.in/ini.v1 v1.67.0 // indirect
+	gopkg.in/yaml.v3 v3.0.1 // indirect
+)

go.sum

@@ -0,0 +1,109 @@
+github.com/aws/aws-sdk-go-v2 v1.24.1 h1:xAojnj+ktS95YZlDf0zxWBkbFtymPeDP+rvUQIH3uAU=
+github.com/aws/aws-sdk-go-v2 v1.24.1/go.mod h1:LNh45Br1YAkEKaAqvmE1m8FUx6a5b/V0oAKV7of29b4=
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+github.com/aws/aws-sdk-go-v2/aws/protocol/eventstream v1.5.4/go.mod h1:usURWEKSNNAcAZuzRn/9ZYPT8aZQkR7xcCtunK/LkJo=
+github.com/aws/aws-sdk-go-v2/config v1.26.5 h1:lodGSevz7d+kkFJodfauThRxK9mdJbyutUxGq1NNhvw=
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+github.com/aws/aws-sdk-go-v2/credentials v1.16.16 h1:8q6Rliyv0aUFAVtzaldUEcS+T5gbadPbWdV1WcAddK8=
+github.com/aws/aws-sdk-go-v2/credentials v1.16.16/go.mod h1:UHVZrdUsv63hPXFo1H7c5fEneoVo9UXiz36QG1GEPi0=
+github.com/aws/aws-sdk-go-v2/feature/ec2/imds v1.14.11 h1:c5I5iH+DZcH3xOIMlz3/tCKJDaHFwYEmxvlh2fAcFo8=
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+github.com/aws/aws-sdk-go-v2/internal/configsources v1.2.10 h1:vF+Zgd9s+H4vOXd5BMaPWykta2a6Ih0AKLq/X6NYKn4=
+github.com/aws/aws-sdk-go-v2/internal/configsources v1.2.10/go.mod h1:6BkRjejp/GR4411UGqkX8+wFMbFbqsUIimfK4XjOKR4=
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main.go

@@ -0,0 +1,13 @@
+package main
+
+import (
+	log "github.com/sirupsen/logrus"
+)
+
+func main() {
+	log.Infoln("started app successfully")
+	mConf := getConfig()
+	Metadataclient := connect_to_s3(mConf)
+	log.Infof("Connection to the bucket established")
+	metadataDownloader(Metadataclient)
+}