Skip to content

[s3inbox] store uploaded file size in db #1571

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
merged 7 commits into from
Apr 16, 2025
Merged

[s3inbox] store uploaded file size in db #1571

Show file tree
Hide file tree
Changes from 5 commits
Commits
Show all changes
7 commits
Select commit Hold shift + click to select a range
6383ce5
[s3inbox] add function to get size of object from backend
jbygdell Apr 7, 2025
a6f98cf
[s3inbox_tests] Add tests for get object size function
jbygdell Apr 7, 2025
2158387
[s3inbox] get object size, handle DB reconnects
jbygdell Apr 7, 2025
30aba3a
[s3inbox_test] Add test for rapid check of file size
jbygdell Apr 8, 2025
e88d3b0
[s3inbox] store upload size in DB on completion #minor
jbygdell Apr 7, 2025
1248101
[s3inbox] Use Predefined S3 client
jbygdell Apr 11, 2025
153fa67
[s3inbox test] Add comments to S3 backend test
jbygdell Apr 11, 2025
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
39 changes: 39 additions & 0 deletions sda/cmd/s3inbox/proxy.go
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -16,6 +16,8 @@ import (
"time"

"github.com/aws/aws-sdk-go-v2/aws"
"github.com/aws/aws-sdk-go-v2/config"
"github.com/aws/aws-sdk-go-v2/credentials"
"github.com/aws/aws-sdk-go-v2/service/s3"
"github.com/lestrrat-go/jwx/v2/jwt"
"github.com/minio/minio-go/v6/pkg/signer"
Expand Down Expand Up @@ -225,6 +227,13 @@ func (p *Proxy) allowedResponse(w http.ResponseWriter, r *http.Request, token jw
log.Debugf("resuming work on file with fileId: %v", p.fileIds[r.URL.Path])
}

if err := p.storeObjectSizeInDB(rawFilepath, p.fileIds[r.URL.Path]); err != nil {
log.Errorf("storeObjectSizeInDB failed because: %s", err.Error())
p.internalServerError(w, r, "storeObjectSizeInDB failed")

return
}

log.Debugf("marking file %v as 'uploaded' in database", p.fileIds[r.URL.Path])
err = p.database.UpdateFileEventLog(p.fileIds[r.URL.Path], "uploaded", p.fileIds[r.URL.Path], "inbox", "{}", string(jsonMessage))
if err != nil {
Expand Down Expand Up @@ -624,3 +633,33 @@ func reportError(errorCode int, message string, w http.ResponseWriter) {
log.Error(err)
}
}

func (p *Proxy) storeObjectSizeInDB(path, fileID string) error {
s3cfg, _ := config.LoadDefaultConfig(context.TODO(), config.WithCredentialsProvider(credentials.NewStaticCredentialsProvider(p.s3.AccessKey, p.s3.SecretKey, "")))
client := s3.NewFromConfig(
s3cfg,
func(o *s3.Options) {
o.BaseEndpoint = aws.String(fmt.Sprintf("%s:%d", p.s3.URL, p.s3.Port))
o.EndpointOptions.DisableHTTPS = strings.HasPrefix(p.s3.URL, "http:")
o.Region = p.s3.Region
o.UsePathStyle = true
},
)
o, err := client.HeadObject(context.TODO(), &s3.HeadObjectInput{
Bucket: &p.s3.Bucket,
Key: &path,
})
if err != nil {
return err
}

if err := p.database.DB.Ping(); err != nil {
p.database.Close()
_ = p.database.Connect()
}

const setObjectSize = "UPDATE sda.files set submission_file_size = $1 where id = $2;"
_, err = p.database.DB.Exec(setObjectSize, *o.ContentLength, fileID)

return err
}
112 changes: 112 additions & 0 deletions sda/cmd/s3inbox/proxy_test.go
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -614,3 +614,115 @@ func (suite *ProxyTests) TestCheckFileExists_unresponsive() {
assert.NotNil(suite.T(), err)
assert.Contains(suite.T(), err.Error(), "StatusCode: 403")
}

func (suite *ProxyTests) TestStoreObjectSizeInDB() {
db, err := database.NewSDAdb(suite.DBConf)
assert.NoError(suite.T(), err)
defer db.Close()

mq, err := broker.NewMQ(suite.MQConf)
assert.NoError(suite.T(), err)
defer mq.Connection.Close()

p := NewProxy(suite.S3conf, helper.NewAlwaysAllow(), suite.messenger, suite.database, new(tls.Config))
p.database = db

fileID, err := db.RegisterFile("/dummy/file", "test-user")
assert.NoError(suite.T(), err)
assert.NotNil(suite.T(), fileID)

assert.NoError(suite.T(), p.storeObjectSizeInDB("/dummy/file", fileID))

const getObjectSize = "SELECT submission_file_size FROM sda.files WHERE id = $1;"
var objectSize int64
assert.NoError(suite.T(), p.database.DB.QueryRow(getObjectSize, fileID).Scan(&objectSize))
assert.Equal(suite.T(), int64(14), objectSize)
}

func (suite *ProxyTests) TestStoreObjectSizeInDB_dbFailure() {
db, err := database.NewSDAdb(suite.DBConf)
assert.NoError(suite.T(), err)

mq, err := broker.NewMQ(suite.MQConf)
assert.NoError(suite.T(), err)
defer mq.Connection.Close()

p := NewProxy(suite.S3conf, helper.NewAlwaysAllow(), suite.messenger, suite.database, new(tls.Config))
p.database = db

fileID, err := db.RegisterFile("/dummy/file", "test-user")
assert.NoError(suite.T(), err)
assert.NotNil(suite.T(), fileID)

db.Close()
assert.NoError(suite.T(), p.storeObjectSizeInDB("/dummy/file", fileID))
}

func (suite *ProxyTests) TestStoreObjectSizeInDB_s3Failure() {
db, err := database.NewSDAdb(suite.DBConf)
assert.NoError(suite.T(), err)
defer db.Close()
mq, err := broker.NewMQ(suite.MQConf)
assert.NoError(suite.T(), err)
defer mq.Connection.Close()

p := NewProxy(suite.S3conf, helper.NewAlwaysAllow(), suite.messenger, suite.database, new(tls.Config))
p.database = db

fileID, err := db.RegisterFile("/dummy/file", "test-user")
assert.NoError(suite.T(), err)
assert.NotNil(suite.T(), fileID)

p.s3.AccessKey = "badKey"
assert.Error(suite.T(), p.storeObjectSizeInDB("/dummy/file", fileID))

p.s3.Port = 1234
assert.Error(suite.T(), p.storeObjectSizeInDB("/dummy/file", fileID))
}

func (suite *ProxyTests) TestStoreObjectSizeInDB_fastCheck() {
db, err := database.NewSDAdb(suite.DBConf)
assert.NoError(suite.T(), err)
defer db.Close()

mq, err := broker.NewMQ(suite.MQConf)
assert.NoError(suite.T(), err)
defer mq.Connection.Close()

p := NewProxy(suite.S3conf, helper.NewAlwaysAllow(), suite.messenger, suite.database, new(tls.Config))
p.database = db

fileID, err := db.RegisterFile("/test/new_file", "test-user")
assert.NoError(suite.T(), err)
assert.NotNil(suite.T(), fileID)

s3cfg, err := config.LoadDefaultConfig(context.TODO(), config.WithCredentialsProvider(credentials.NewStaticCredentialsProvider(suite.S3conf.AccessKey, suite.S3conf.SecretKey, "")))
if err != nil {
suite.FailNow("bad")
}
s3Client := s3.NewFromConfig(
s3cfg,
func(o *s3.Options) {
o.BaseEndpoint = aws.String(fmt.Sprintf("%s:%d", suite.S3conf.URL, suite.S3conf.Port))
o.EndpointOptions.DisableHTTPS = strings.HasPrefix(suite.S3conf.URL, "http:")
o.Region = suite.S3conf.Region
o.UsePathStyle = true
},
)

output, err := s3Client.PutObject(context.TODO(), &s3.PutObjectInput{
Body: strings.NewReader(strings.Repeat("A", 10*1024*1024)),
Bucket: aws.String(suite.S3conf.Bucket),
Key: aws.String("/test/new_file"),
ContentEncoding: aws.String("application/octet-stream"),
})
assert.NoError(suite.T(), err)
assert.NotNil(suite.T(), output, output)

assert.NoError(suite.T(), p.storeObjectSizeInDB("/test/new_file", fileID))

const getObjectSize = "SELECT submission_file_size FROM sda.files WHERE id = $1;"
var objectSize int64
assert.NoError(suite.T(), p.database.DB.QueryRow(getObjectSize, fileID).Scan(&objectSize))
assert.Equal(suite.T(), int64(10*1024*1024), objectSize)
}
Loading