From d4fcde5629d04854e5c06caa5054ea62d76242dc Mon Sep 17 00:00:00 2001 From: Skiada Alexandre <25521495+askiada@users.noreply.github.com> Date: Wed, 17 Aug 2022 10:49:33 +0100 Subject: [PATCH 01/16] Full implementaion with custom reader and writer --- env.list | 5 ++- file/batchingchannels/batching_channel.go | 16 +++---- .../batchingchannels/batching_channel_test.go | 11 +++-- file/chunk.go | 21 +++++---- file/file.go | 41 ++++++++++-------- file/sort.go | 24 ++++------- internal/env.go | 3 ++ main.go | 32 ++++++++++---- main_bench_test.go | 15 ++++--- main_test.go | 26 ++++++----- reader/contract.go | 7 +++ reader/separated_values.go | 43 +++++++++++++++++++ reader/std_scanner.go | 27 ++++++++++++ vector/element.go | 4 +- vector/key/int_key.go | 12 +++++- vector/key/string_key.go | 14 ++++++ vector/key/tsv_key.go | 25 ++++++++--- vector/slice_vector.go | 10 ++--- vector/vector.go | 36 ++++++++++------ writer/contract.go | 6 +++ writer/separated_values.go | 40 +++++++++++++++++ writer/std_writer.go | 39 +++++++++++++++++ 22 files changed, 349 insertions(+), 108 deletions(-) create mode 100644 reader/contract.go create mode 100644 reader/separated_values.go create mode 100644 reader/std_scanner.go create mode 100644 writer/contract.go create mode 100644 writer/separated_values.go create mode 100644 writer/std_writer.go diff --git a/env.list b/env.list index 169be0f..cbbeaa3 100644 --- a/env.list +++ b/env.list @@ -1,6 +1,7 @@ -INPUT_PATH=./works.tsv +INPUT_PATH=/Users/alex/Desktop/Projects/Blokur/Repo/external-sort/rec_sample.tsv OUTPUT_PATH=./output.tsv CHUNK_FOLDER=./data/chunks/ CHUNK_SIZE=1000000 MAX_WORKERS=10 -OUTPUT_BUFFER_SIZE=1000 \ No newline at end of file +OUTPUT_BUFFER_SIZE=1000 +TSV_FIELDS=2 4 \ No newline at end of file diff --git a/file/batchingchannels/batching_channel.go b/file/batchingchannels/batching_channel.go index 6826685..aebca36 100644 --- a/file/batchingchannels/batching_channel.go +++ b/file/batchingchannels/batching_channel.go @@ -12,11 +12,11 @@ import ( // on Out(), it batches together the entire internal buffer each time. Trying to construct an unbuffered batching channel // will panic, that configuration is not supported (and provides no benefit over an unbuffered NativeChannel). type BatchingChannel struct { - input chan string + input chan interface{} output chan vector.Vector buffer vector.Vector allocate *vector.Allocate - g *errgroup.Group + G *errgroup.Group sem *semaphore.Weighted dCtx context.Context size int @@ -32,12 +32,12 @@ func NewBatchingChannel(ctx context.Context, allocate *vector.Allocate, maxWorke } g, dCtx := errgroup.WithContext(ctx) ch := &BatchingChannel{ - input: make(chan string), + input: make(chan interface{}), output: make(chan vector.Vector), size: size, allocate: allocate, maxWorker: maxWorker, - g: g, + G: g, sem: semaphore.NewWeighted(maxWorker), dCtx: dCtx, } @@ -45,7 +45,7 @@ func NewBatchingChannel(ctx context.Context, allocate *vector.Allocate, maxWorke return ch } -func (ch *BatchingChannel) In() chan<- string { +func (ch *BatchingChannel) In() chan<- interface{} { return ch.input } @@ -62,12 +62,12 @@ func (ch *BatchingChannel) ProcessOut(f func(vector.Vector) error) error { return err } val := val - ch.g.Go(func() error { + ch.G.Go(func() error { defer ch.sem.Release(1) return f(val) }) } - err := ch.g.Wait() + err := ch.G.Wait() if err != nil { return err } @@ -93,7 +93,7 @@ func (ch *BatchingChannel) batchingBuffer() { if open { err := ch.buffer.PushBack(elem) if err != nil { - ch.g.Go(func() error { + ch.G.Go(func() error { return err }) } diff --git a/file/batchingchannels/batching_channel_test.go b/file/batchingchannels/batching_channel_test.go index d9a0cce..b33aaf3 100644 --- a/file/batchingchannels/batching_channel_test.go +++ b/file/batchingchannels/batching_channel_test.go @@ -10,6 +10,7 @@ import ( "github.com/askiada/external-sort/file/batchingchannels" "github.com/askiada/external-sort/vector" "github.com/askiada/external-sort/vector/key" + "github.com/pkg/errors" "github.com/stretchr/testify/assert" ) @@ -17,7 +18,11 @@ type Int struct { value int } -func AllocateInt(line string) (key.Key, error) { +func AllocateInt(row interface{}) (key.Key, error) { + line, ok := row.(string) + if !ok { + return nil, errors.Errorf("can't convert interface{} to string: %+v", row) + } num, err := strconv.Atoi(line) if err != nil { return nil, err @@ -86,7 +91,7 @@ func testBatches(t *testing.T, ch *batchingchannels.BatchingChannel) { } func TestBatchingChannel(t *testing.T) { - allocate := vector.DefaultVector(AllocateInt) + allocate := vector.DefaultVector(AllocateInt, nil, nil) ch := batchingchannels.NewBatchingChannel(context.Background(), allocate, 2, 50) testBatches(t, ch) @@ -98,7 +103,7 @@ func TestBatchingChannel(t *testing.T) { } func TestBatchingChannelCap(t *testing.T) { - allocate := vector.DefaultVector(AllocateInt) + allocate := vector.DefaultVector(AllocateInt, nil, nil) ch := batchingchannels.NewBatchingChannel(context.Background(), allocate, 2, 5) if ch.Cap() != 5 { t.Error("incorrect capacity on infinite channel") diff --git a/file/chunk.go b/file/chunk.go index 77966c0..f3414f9 100644 --- a/file/chunk.go +++ b/file/chunk.go @@ -1,10 +1,10 @@ package file import ( - "bufio" "os" "sort" + "github.com/askiada/external-sort/reader" "github.com/askiada/external-sort/vector" "github.com/pkg/errors" @@ -13,7 +13,7 @@ import ( // chunkInfo Describe a chunk. type chunkInfo struct { file *os.File - scanner *bufio.Scanner + reader reader.Reader buffer vector.Vector filename string } @@ -22,13 +22,16 @@ type chunkInfo struct { // It stops if there is no elements left to add. func (c *chunkInfo) pullSubset(size int) (err error) { i := 0 - for i < size && c.scanner.Scan() { - text := c.scanner.Text() - c.buffer.PushBack(text) + for i < size && c.reader.Next() { + row, err := c.reader.Read() + if err != nil { + return errors.Wrap(err, "") + } + c.buffer.PushBack(row) i++ } - if c.scanner.Err() != nil { - return c.scanner.Err() + if c.reader.Err() != nil { + return c.reader.Err() } return nil } @@ -44,11 +47,11 @@ func (c *chunks) new(chunkPath string, allocate *vector.Allocate, size int) erro if err != nil { return err } - scanner := bufio.NewScanner(f) + reader := allocate.FnReader(f) elem := &chunkInfo{ filename: chunkPath, file: f, - scanner: scanner, + reader: reader, buffer: allocate.Vector(size, allocate.Key), } err = elem.pullSubset(size) diff --git a/file/file.go b/file/file.go index 5bc397f..e7a007a 100644 --- a/file/file.go +++ b/file/file.go @@ -1,25 +1,26 @@ package file import ( - "bufio" "context" + "io" "sync" - "io" "path" "strconv" "github.com/askiada/external-sort/file/batchingchannels" "github.com/askiada/external-sort/vector" + "github.com/askiada/external-sort/writer" "github.com/pkg/errors" ) type Info struct { mu *MemUsage - Reader io.Reader Allocate *vector.Allocate - OutputPath string + InputReader io.Reader + OutputFile string + outputWriter writer.Writer totalRows int PrintMemUsage bool } @@ -40,25 +41,33 @@ func (f *Info) CreateSortedChunks(ctx context.Context, chunkFolder string, dumpS if err != nil { return nil, errors.Wrap(err, fn) } + + inputReader := f.Allocate.FnReader(f.InputReader) + row := 0 chunkPaths := []string{} - scanner := bufio.NewScanner(f.Reader) + mu := sync.Mutex{} - wg := &sync.WaitGroup{} - wg.Add(1) + batchChan := batchingchannels.NewBatchingChannel(ctx, f.Allocate, maxWorkers, dumpSize) - go func() { - defer wg.Done() - for scanner.Scan() { + batchChan.G.Go(func() error { + for inputReader.Next() { if f.PrintMemUsage { f.mu.Collect() } - text := scanner.Text() - batchChan.In() <- text + elem, err := inputReader.Read() + if err != nil { + return errors.Wrap(err, fn) + } + batchChan.In() <- elem row++ } batchChan.Close() - }() + if inputReader.Err() != nil { + return errors.Wrap(inputReader.Err(), fn) + } + return nil + }) chunkIdx := 0 err = batchChan.ProcessOut(func(v vector.Vector) error { @@ -67,7 +76,7 @@ func (f *Info) CreateSortedChunks(ctx context.Context, chunkFolder string, dumpS chunkPath := path.Join(chunkFolder, "chunk_"+strconv.Itoa(chunkIdx)+".tsv") mu.Unlock() v.Sort() - err := vector.Dump(v, chunkPath) + err := f.Allocate.Dump(v, chunkPath) if err != nil { return err } @@ -79,10 +88,6 @@ func (f *Info) CreateSortedChunks(ctx context.Context, chunkFolder string, dumpS if err != nil { return nil, errors.Wrap(err, fn) } - wg.Wait() - if scanner.Err() != nil { - return nil, errors.Wrap(scanner.Err(), fn) - } f.totalRows = row return chunkPaths, nil } diff --git a/file/sort.go b/file/sort.go index fd90f33..ae53b62 100644 --- a/file/sort.go +++ b/file/sort.go @@ -1,12 +1,12 @@ package file import ( - "bufio" "fmt" "os" "runtime" "github.com/askiada/external-sort/vector" + "github.com/askiada/external-sort/writer" "github.com/cheggaaa/pb/v3" ) @@ -52,16 +52,12 @@ func (f *Info) MergeSort(chunkPaths []string, k int) (err error) { return err } } - - outputFile, err := os.Create(f.OutputPath) + w, err := os.Create(f.OutputFile) if err != nil { return err } - // remember to close the file - defer outputFile.Close() - - outputBuffer := bufio.NewWriter(outputFile) - + f.outputWriter = f.Allocate.FnWriter(w) + defer f.outputWriter.Close() bar := pb.StartNew(f.totalRows) chunks.resetOrder() for { @@ -69,7 +65,7 @@ func (f *Info) MergeSort(chunkPaths []string, k int) (err error) { f.mu.Collect() } if chunks.len() == 0 || output.Len() == k { - err = WriteBuffer(outputBuffer, output) + err = WriteBuffer(f.outputWriter, output) if err != nil { return err } @@ -80,7 +76,7 @@ func (f *Info) MergeSort(chunkPaths []string, k int) (err error) { toShrink := []int{} // search the smallest value across chunk buffers by comparing first elements only minChunk, minValue, minIdx := chunks.min() - err = output.PushBack(minValue.Line) + err = output.PushBack(minValue.Row) if err != nil { return err } @@ -108,10 +104,6 @@ func (f *Info) MergeSort(chunkPaths []string, k int) (err error) { } bar.Increment() } - err = outputBuffer.Flush() - if err != nil { - return err - } bar.Finish() if f.PrintMemUsage { f.mu.PrintMemUsage() @@ -119,9 +111,9 @@ func (f *Info) MergeSort(chunkPaths []string, k int) (err error) { return chunks.close() } -func WriteBuffer(buffer *bufio.Writer, rows vector.Vector) error { +func WriteBuffer(w writer.Writer, rows vector.Vector) error { for i := 0; i < rows.Len(); i++ { - _, err := buffer.WriteString(rows.Get(i).Line + "\n") + err := w.Write(rows.Get(i).Row) if err != nil { return err } diff --git a/internal/env.go b/internal/env.go index 852adde..f4bafcb 100644 --- a/internal/env.go +++ b/internal/env.go @@ -14,11 +14,13 @@ const ( ChunkSizeName = "chunk_size" MaxWorkersName = "max_workers" OutputBufferSizeName = "output_buffer_size" + TsvFieldsName = "tsv_fields" ) // Environment variables. var ( InputFile string + TsvFields []string OutputFile string ChunkFolder string ChunkSize int @@ -34,4 +36,5 @@ func init() { viper.SetDefault(ChunkSizeName, 0) viper.SetDefault(MaxWorkersName, 0) viper.SetDefault(OutputBufferSizeName, 0) + viper.SetDefault(TsvFieldsName, []string{"0"}) } diff --git a/main.go b/main.go index b44da1c..5a166fb 100644 --- a/main.go +++ b/main.go @@ -3,13 +3,17 @@ package main import ( "context" "fmt" + "io" "os" + "strconv" "time" "github.com/askiada/external-sort/file" "github.com/askiada/external-sort/internal" + "github.com/askiada/external-sort/reader" "github.com/askiada/external-sort/vector" "github.com/askiada/external-sort/vector/key" + "github.com/askiada/external-sort/writer" "github.com/spf13/cobra" "github.com/spf13/viper" ) @@ -28,28 +32,38 @@ func main() { rootCmd.PersistentFlags().IntVarP(&internal.ChunkSize, internal.ChunkSizeName, "s", viper.GetInt(internal.ChunkSizeName), "chunk size.") rootCmd.PersistentFlags().Int64VarP(&internal.MaxWorkers, internal.MaxWorkersName, "w", viper.GetInt64(internal.MaxWorkersName), "max worker.") rootCmd.PersistentFlags().IntVarP(&internal.OutputBufferSize, internal.OutputBufferSizeName, "b", viper.GetInt(internal.OutputBufferSizeName), "output buffer size.") + rootCmd.PersistentFlags().StringSliceVarP(&internal.TsvFields, internal.TsvFieldsName, "t", viper.GetStringSlice(internal.TsvFieldsName), "") fmt.Println("Input file", internal.InputFile) fmt.Println("Output file", internal.OutputFile) - fmt.Println("Chunk foler", internal.ChunkFolder) + fmt.Println("Chunk folder", internal.ChunkFolder) + fmt.Println("TSV Fields", internal.TsvFields) + cobra.CheckErr(rootCmd.Execute()) } func rootRun(cmd *cobra.Command, args []string) error { start := time.Now() - inputPath := internal.InputFile // open a file - f, err := os.Open(inputPath) + inputReader, err := os.Open(internal.InputFile) if err != nil { return err } - defer f.Close() + defer inputReader.Close() + tsvFields := []int{} + for _, field := range internal.TsvFields { + i, err := strconv.Atoi(field) + if err != nil { + return err + } + tsvFields = append(tsvFields, i) + } fI := &file.Info{ - Reader: f, - Allocate: vector.DefaultVector(func(line string) (key.Key, error) { - return key.AllocateTsv(line, 0) - }), - OutputPath: internal.OutputFile, + InputReader: inputReader, + OutputFile: internal.OutputFile, + Allocate: vector.DefaultVector(func(row interface{}) (key.Key, error) { + return key.AllocateTsv(row, tsvFields...) + }, func(r io.Reader) reader.Reader { return reader.NewSeparatedValues(r, '\t') }, func(w io.Writer) writer.Writer { return writer.NewSeparatedValues(w, '\t') }), PrintMemUsage: false, } diff --git a/main_bench_test.go b/main_bench_test.go index a600863..f6515c7 100644 --- a/main_bench_test.go +++ b/main_bench_test.go @@ -2,28 +2,30 @@ package main_test import ( "context" + "io" "io/ioutil" "os" "path" "testing" "github.com/askiada/external-sort/file" + "github.com/askiada/external-sort/reader" "github.com/askiada/external-sort/vector" "github.com/askiada/external-sort/vector/key" + "github.com/askiada/external-sort/writer" "github.com/stretchr/testify/assert" ) func BenchmarkMergeSort(b *testing.B) { filename := "test.tsv" - chunkSize := 10000 - bufferSize := 5000 f, err := os.Open(filename) assert.NoError(b, err) - + chunkSize := 10000 + bufferSize := 5000 fI := &file.Info{ - Reader: f, - Allocate: vector.DefaultVector(key.AllocateInt), - OutputPath: "testdata/chunks/output.tsv", + InputReader: f, + Allocate: vector.DefaultVector(key.AllocateInt, reader.NewStdScanner, func(w io.Writer) writer.Writer { return writer.NewStdWriter(w) }), + OutputFile: "testdata/chunks/output.tsv", } chunkPaths, err := fI.CreateSortedChunks(context.Background(), "testdata/chunks", chunkSize, 100) assert.NoError(b, err) @@ -32,7 +34,6 @@ func BenchmarkMergeSort(b *testing.B) { err = fI.MergeSort(chunkPaths, bufferSize) _ = err } - f.Close() dir, err := ioutil.ReadDir("testdata/chunks") assert.NoError(b, err) for _, d := range dir { diff --git a/main_test.go b/main_test.go index 69b54d8..6b03fa5 100644 --- a/main_test.go +++ b/main_test.go @@ -4,6 +4,7 @@ import ( "bufio" "context" "errors" + "io" "io/ioutil" "os" "path" @@ -11,8 +12,10 @@ import ( "testing" "github.com/askiada/external-sort/file" + "github.com/askiada/external-sort/reader" "github.com/askiada/external-sort/vector" "github.com/askiada/external-sort/vector/key" + "github.com/askiada/external-sort/writer" "github.com/stretchr/testify/assert" ) @@ -21,11 +24,10 @@ func prepareChunks(ctx context.Context, t *testing.T, allocate *vector.Allocate, t.Helper() f, err := os.Open(filename) assert.NoError(t, err) - fI := &file.Info{ - Reader: f, - Allocate: allocate, - OutputPath: outputFilename, + InputReader: f, + Allocate: allocate, + OutputFile: "testdata/chunks/output.tsv", } chunkPaths, err := fI.CreateSortedChunks(ctx, "testdata/chunks", chunkSize, 10) assert.NoError(t, err) @@ -65,7 +67,7 @@ func TestBasics(t *testing.T) { outputFilename: "testdata/chunks/output.tsv", }, } - allocate := vector.DefaultVector(key.AllocateInt) + for name, tc := range tcs { filename := tc.filename outputFilename := tc.outputFilename @@ -77,8 +79,9 @@ func TestBasics(t *testing.T) { bufferSize := bufferSize t.Run(name+"_"+strconv.Itoa(chunkSize)+"_"+strconv.Itoa(bufferSize), func(t *testing.T) { ctx := context.Background() + + allocate := vector.DefaultVector(key.AllocateInt, reader.NewStdScanner, writer.NewStdWriter) fI, chunkPaths := prepareChunks(ctx, t, allocate, filename, outputFilename, chunkSize) - fI.OutputPath = outputFilename err := fI.MergeSort(chunkPaths, bufferSize) assert.NoError(t, err) outputFile, err := os.Open(outputFilename) @@ -112,7 +115,7 @@ func Test100Elems(t *testing.T) { outputFilename: "testdata/chunks/output.tsv", }, } - allocate := vector.DefaultVector(key.AllocateInt) + for name, tc := range tcs { filename := tc.filename outputFilename := tc.outputFilename @@ -120,6 +123,7 @@ func Test100Elems(t *testing.T) { expectedErr := tc.expectedErr t.Run(name, func(t *testing.T) { ctx := context.Background() + allocate := vector.DefaultVector(key.AllocateInt, reader.NewStdScanner, writer.NewStdWriter) fI, chunkPaths := prepareChunks(ctx, t, allocate, filename, outputFilename, 21) err := fI.MergeSort(chunkPaths, 10) assert.NoError(t, err) @@ -161,9 +165,7 @@ func TestTsvKey(t *testing.T) { outputFilename: "testdata/chunks/output.tsv", }, } - allocate := vector.DefaultVector(func(line string) (key.Key, error) { - return key.AllocateTsv(line, 1) - }) + for name, tc := range tcs { filename := tc.filename outputFilename := tc.outputFilename @@ -171,6 +173,10 @@ func TestTsvKey(t *testing.T) { expectedErr := tc.expectedErr t.Run(name, func(t *testing.T) { ctx := context.Background() + + allocate := vector.DefaultVector(func(row interface{}) (key.Key, error) { + return key.AllocateTsv(row, 1) + }, func(r io.Reader) reader.Reader { return reader.NewSeparatedValues(r, '\t') }, func(w io.Writer) writer.Writer { return writer.NewSeparatedValues(w, '\t') }) fI, chunkPaths := prepareChunks(ctx, t, allocate, filename, outputFilename, 21) err := fI.MergeSort(chunkPaths, 10) assert.NoError(t, err) diff --git a/reader/contract.go b/reader/contract.go new file mode 100644 index 0000000..3589f3f --- /dev/null +++ b/reader/contract.go @@ -0,0 +1,7 @@ +package reader + +type Reader interface { + Next() bool + Read() (interface{}, error) + Err() error +} diff --git a/reader/separated_values.go b/reader/separated_values.go new file mode 100644 index 0000000..fdb4fea --- /dev/null +++ b/reader/separated_values.go @@ -0,0 +1,43 @@ +package reader + +import ( + "encoding/csv" + "errors" + "io" +) + +type SeparatedValuesReader struct { + row []string + r *csv.Reader + err error +} + +func NewSeparatedValues(r io.Reader, separator rune) *SeparatedValuesReader { + s := &SeparatedValuesReader{ + r: csv.NewReader(r), + } + s.r.Comma = separator + return s +} + +func (s *SeparatedValuesReader) Next() bool { + s.row, s.err = s.r.Read() + if errors.Is(s.err, io.EOF) { + s.err = nil + return false + } + return true +} + +func (s *SeparatedValuesReader) Read() (interface{}, error) { + if s.err != nil { + return nil, s.err + } + return s.row, nil +} + +func (s *SeparatedValuesReader) Err() error { + return s.err +} + +var _ Reader = &SeparatedValuesReader{} diff --git a/reader/std_scanner.go b/reader/std_scanner.go new file mode 100644 index 0000000..7610ffd --- /dev/null +++ b/reader/std_scanner.go @@ -0,0 +1,27 @@ +package reader + +import ( + "bufio" + "io" +) + +type StdScanner struct { + r *bufio.Scanner +} + +func NewStdScanner(r io.Reader) Reader { + s := &StdScanner{ + r: bufio.NewScanner(r), + } + return s +} + +func (s *StdScanner) Next() bool { + return s.r.Scan() +} +func (s *StdScanner) Read() (interface{}, error) { + return s.r.Text(), nil +} +func (s *StdScanner) Err() error { + return s.r.Err() +} diff --git a/vector/element.go b/vector/element.go index e49fb3e..3b9e768 100644 --- a/vector/element.go +++ b/vector/element.go @@ -3,8 +3,8 @@ package vector import "github.com/askiada/external-sort/vector/key" type Element struct { - Key key.Key - Line string + Key key.Key + Row interface{} } // Less returns wether v1 is smaller than v2 based on the keys. diff --git a/vector/key/int_key.go b/vector/key/int_key.go index 0744e82..7ffb83d 100644 --- a/vector/key/int_key.go +++ b/vector/key/int_key.go @@ -1,12 +1,20 @@ package key -import "strconv" +import ( + "strconv" + + "github.com/pkg/errors" +) type Int struct { value int } -func AllocateInt(line string) (Key, error) { +func AllocateInt(row interface{}) (Key, error) { + line, ok := row.(string) + if !ok { + return nil, errors.Errorf("can't convert interface{} to string: %+v", row) + } num, err := strconv.Atoi(line) if err != nil { return nil, err diff --git a/vector/key/string_key.go b/vector/key/string_key.go index d774e0c..b98669c 100644 --- a/vector/key/string_key.go +++ b/vector/key/string_key.go @@ -1,5 +1,7 @@ package key +import "strings" + type String struct { value string } @@ -11,3 +13,15 @@ func AllocateString(line string) (Key, error) { func (k *String) Less(other Key) bool { return k.value < other.(*String).value } + +type UpperString struct { + value string +} + +func AllocateUpperString(line string) (Key, error) { + return &UpperString{strings.TrimSpace(strings.ToUpper(line))}, nil +} + +func (k *UpperString) Less(other Key) bool { + return k.value < other.(*UpperString).value +} diff --git a/vector/key/tsv_key.go b/vector/key/tsv_key.go index d3d3f8e..6f3ee04 100644 --- a/vector/key/tsv_key.go +++ b/vector/key/tsv_key.go @@ -6,10 +6,25 @@ import ( "github.com/pkg/errors" ) -func AllocateTsv(line string, pos int) (Key, error) { - splitted := strings.Split(line, "\t") - if len(splitted) < pos+1 { - return nil, errors.Errorf("can't allocate tsv key line is invalid: %s", line) +const salt = "##!##" + +func AllocateTsv(row interface{}, pos ...int) (Key, error) { + splitted, ok := row.([]string) + if !ok { + return nil, errors.Errorf("can't convert interface{} to []string: %+v", row) + } + k := strings.Builder{} + for i, p := range pos { + if len(splitted) < p+1 { + return nil, errors.Errorf("can't allocate tsv key line is invalid: %s", row) + } + k.WriteString(splitted[p]) + if i < len(pos)-1 { + k.WriteString(salt) + } } - return &String{splitted[pos]}, nil + + // fmt.Println(row, pos, k.String()) + + return &String{k.String()}, nil } diff --git a/vector/slice_vector.go b/vector/slice_vector.go index 270015d..c31b0fe 100644 --- a/vector/slice_vector.go +++ b/vector/slice_vector.go @@ -8,7 +8,7 @@ import ( var _ Vector = &SliceVec{} -func AllocateSlice(size int, allocateKey func(line string) (key.Key, error)) Vector { +func AllocateSlice(size int, allocateKey func(row interface{}) (key.Key, error)) Vector { return &SliceVec{ allocateKey: allocateKey, s: make([]*Element, 0, size), @@ -16,7 +16,7 @@ func AllocateSlice(size int, allocateKey func(line string) (key.Key, error)) Vec } type SliceVec struct { - allocateKey func(line string) (key.Key, error) + allocateKey func(row interface{}) (key.Key, error) s []*Element } @@ -32,12 +32,12 @@ func (v *SliceVec) Len() int { return len(v.s) } -func (v *SliceVec) PushBack(line string) error { - k, err := v.allocateKey(line) +func (v *SliceVec) PushBack(row interface{}) error { + k, err := v.allocateKey(row) if err != nil { return err } - v.s = append(v.s, &Element{Line: line, Key: k}) + v.s = append(v.s, &Element{Row: row, Key: k}) return nil } diff --git a/vector/vector.go b/vector/vector.go index cc5471e..0e8916f 100644 --- a/vector/vector.go +++ b/vector/vector.go @@ -1,22 +1,28 @@ package vector import ( - "bufio" + "io" "os" + "github.com/askiada/external-sort/reader" "github.com/askiada/external-sort/vector/key" + "github.com/askiada/external-sort/writer" "github.com/pkg/errors" ) type Allocate struct { - Vector func(int, func(line string) (key.Key, error)) Vector - Key func(line string) (key.Key, error) + Vector func(int, func(row interface{}) (key.Key, error)) Vector + FnReader func(r io.Reader) reader.Reader + FnWriter func(w io.Writer) writer.Writer + Key func(elem interface{}) (key.Key, error) } -func DefaultVector(allocateKey func(line string) (key.Key, error)) *Allocate { +func DefaultVector(allocateKey func(elem interface{}) (key.Key, error), fnReader func(r io.Reader) reader.Reader, fnWr func(w io.Writer) writer.Writer) *Allocate { return &Allocate{ - Vector: AllocateSlice, - Key: allocateKey, + FnReader: fnReader, + FnWriter: fnWr, + Vector: AllocateSlice, + Key: allocateKey, } } @@ -24,7 +30,7 @@ type Vector interface { // Get Access i-th element Get(i int) *Element // PushBack Add item at the end - PushBack(line string) error + PushBack(row interface{}) error // FrontShift Remove the first element FrontShift() // Len Length of the Vector @@ -35,19 +41,25 @@ type Vector interface { Sort() } -func Dump(v Vector, filename string) error { +func (a *Allocate) Dump(v Vector, filename string) error { file, err := os.OpenFile(filename, os.O_CREATE|os.O_WRONLY, 0o644) if err != nil { return errors.Errorf("failed creating file: %s", err) } - datawriter := bufio.NewWriter(file) + datawriter := a.FnWriter(file) for i := 0; i < v.Len(); i++ { - _, err = datawriter.WriteString(v.Get(i).Line + "\n") + err = datawriter.Write(v.Get(i).Row) if err != nil { return errors.Errorf("failed writing file: %s", err) } } - datawriter.Flush() - file.Close() + err = datawriter.Close() + if err != nil { + return errors.Wrap(err, "can't close chunk writer") + } + err = file.Close() + if err != nil { + return errors.Wrap(err, "can't close chunf file") + } return nil } diff --git a/writer/contract.go b/writer/contract.go new file mode 100644 index 0000000..30a3310 --- /dev/null +++ b/writer/contract.go @@ -0,0 +1,6 @@ +package writer + +type Writer interface { + Write(interface{}) error + Close() error +} diff --git a/writer/separated_values.go b/writer/separated_values.go new file mode 100644 index 0000000..4e073ea --- /dev/null +++ b/writer/separated_values.go @@ -0,0 +1,40 @@ +package writer + +import ( + "encoding/csv" + "io" + + "github.com/pkg/errors" +) + +type SeparatedValuesWriter struct { + w *csv.Writer +} + +func NewSeparatedValues(w io.Writer, separator rune) Writer { + s := &SeparatedValuesWriter{ + w: csv.NewWriter(w), + } + s.w.Comma = separator + return s +} + +func (s *SeparatedValuesWriter) Write(elem interface{}) error { + line, ok := elem.([]string) + if !ok { + return errors.Errorf("can't converte interface{} to []string: %+v", elem) + } + err := s.w.Write(line) + if err != nil { + return errors.Wrap(err, "can't write line") + } + return nil +} + +func (s *SeparatedValuesWriter) Close() error { + s.w.Flush() + if s.w.Error() != nil { + return errors.Wrap(s.w.Error(), "can't close writer") + } + return nil +} diff --git a/writer/std_writer.go b/writer/std_writer.go new file mode 100644 index 0000000..a339a10 --- /dev/null +++ b/writer/std_writer.go @@ -0,0 +1,39 @@ +package writer + +import ( + "bufio" + "io" + + "github.com/pkg/errors" +) + +type StdWriter struct { + w *bufio.Writer +} + +func NewStdWriter(w io.Writer) Writer { + s := &StdWriter{ + w: bufio.NewWriter(w), + } + return s +} + +func (w *StdWriter) Write(elem interface{}) error { + line, ok := elem.(string) + if !ok { + return errors.Errorf("can't converte interface{} to string: %+v", elem) + } + _, err := w.w.WriteString(line + "\n") + if err != nil { + return errors.Wrap(err, "can't write string") + } + return err +} + +func (w *StdWriter) Close() error { + err := w.w.Flush() + if err != nil { + return errors.Wrap(err, "can't close writer") + } + return nil +} From a5c954774acd2d110cc211ceb9e9616fb98ef543 Mon Sep 17 00:00:00 2001 From: askiada <25521495+askiada@users.noreply.github.com> Date: Sun, 2 Oct 2022 15:33:19 +0200 Subject: [PATCH 02/16] gzip + drop duplicates --- bucket/contract.go | 61 ++++++ bucket/errors.go | 8 + bucket/s3.go | 111 +++++++++++ file/batchingchannels/batching_channel.go | 4 +- .../batchingchannels/batching_channel_test.go | 4 + file/chunk.go | 7 +- file/file.go | 34 +++- file/sort.go | 25 ++- go.mod | 23 ++- go.sum | 50 ++++- internal/env.go | 18 +- internal/progress/contract.go | 67 +++++++ internal/rw/rw.go | 178 ++++++++++++++++++ main.go | 78 +++++--- main_bench_test.go | 33 ++-- main_test.go | 163 +++++++++++++--- reader/gzip_separated_values.go | 53 ++++++ testdata/100elemsWithHeaders.tsv | 101 ++++++++++ vector/key/int_key.go | 4 + vector/key/key.go | 1 + vector/key/string_key.go | 7 + vector/slice_vector.go | 5 + vector/vector.go | 13 +- 23 files changed, 957 insertions(+), 91 deletions(-) create mode 100644 bucket/contract.go create mode 100644 bucket/errors.go create mode 100644 bucket/s3.go create mode 100644 internal/progress/contract.go create mode 100644 internal/rw/rw.go create mode 100644 reader/gzip_separated_values.go create mode 100644 testdata/100elemsWithHeaders.tsv diff --git a/bucket/contract.go b/bucket/contract.go new file mode 100644 index 0000000..e8f8450 --- /dev/null +++ b/bucket/contract.go @@ -0,0 +1,61 @@ +package bucket + +import ( + "github.com/askiada/external-sort/internal/progress" + "github.com/aws/aws-sdk-go-v2/feature/s3/manager" + "github.com/aws/aws-sdk-go-v2/service/s3" +) + +// S3ClientAPI S3 client contract for this repo. +type S3ClientAPI interface { + manager.UploadAPIClient + manager.DownloadAPIClient + s3.HeadObjectAPIClient +} + +// ConfigFunc is a function that can be passed to the New function to configure +// the S3 object. +type ConfigFunc func(s *S3) + +// Region sets the region of the S3 bucket. +func Region(region string) ConfigFunc { + return func(s *S3) { + s.region = region + } +} + +// PartBodyMaxRetries sets the number of retries when performing upload multi part. +func PartBodyMaxRetries(r int) ConfigFunc { + return func(s *S3) { + s.partBodyMaxRetries = r + } +} + +// Buffer is the amount of memory in MB to use for buffering the data. +func Buffer(buffer int) ConfigFunc { + return func(s *S3) { + s.bufferLen = buffer * 1024 * 1024 + } +} + +// Client sets the S3 client to use. If you provide this option, we will not be +// able to set the region. +func Client(client S3ClientAPI) ConfigFunc { + return func(s *S3) { + s.s3Client = client + } +} + +// MaxRetries sets the maximum number of retried per request before returning an error. +func MaxRetries(maxRetries int) ConfigFunc { + return func(s *S3) { + s.maxRetries = maxRetries + } +} + +// Progress sets a progress bar to be used when performing bucket actions. +func Progress(p progress.Progress) ConfigFunc { + return func(s *S3) { + s.progress = p + } +} diff --git a/bucket/errors.go b/bucket/errors.go new file mode 100644 index 0000000..63b153e --- /dev/null +++ b/bucket/errors.go @@ -0,0 +1,8 @@ +package bucket + +import "errors" + +var ( + // ErrInvalidInput is returned when the input is invalid. + ErrInvalidInput = errors.New("invalid input") +) diff --git a/bucket/s3.go b/bucket/s3.go new file mode 100644 index 0000000..6183d60 --- /dev/null +++ b/bucket/s3.go @@ -0,0 +1,111 @@ +// Package bucket implements the io.ReadWriter for communication with the S3 +// API. +package bucket + +import ( + "context" + "io" + + "github.com/askiada/external-sort/internal/progress" + "github.com/aws/aws-sdk-go-v2/aws" + "github.com/aws/aws-sdk-go-v2/config" + "github.com/aws/aws-sdk-go-v2/feature/s3/manager" + "github.com/aws/aws-sdk-go-v2/service/s3" + "github.com/pkg/errors" +) + +// S3 can read and write from/to S3 buckets using io.Reader and io.Writer +// inputs. +type S3 struct { + s3Client S3ClientAPI + progress progress.Progress + region string + maxRetries int + bufferLen int + partBodyMaxRetries int +} + +// New returns an instance of the S3 struct. +func New(ctx context.Context, cfg ...ConfigFunc) (*S3, error) { + s := &S3{ + region: "eu-west-1", + bufferLen: 1024, + maxRetries: 10, + partBodyMaxRetries: 3, + } + for _, c := range cfg { + c(s) + } + + if s.region == "" { + return nil, errors.Wrap(ErrInvalidInput, "region") + } + if s.bufferLen <= 0 { + return nil, errors.Wrap(ErrInvalidInput, "buffer length") + } + if s.s3Client == nil { + cfg, err := config.LoadDefaultConfig(ctx, + config.WithRegion(s.region), + config.WithRetryMaxAttempts(s.maxRetries), + ) + if err != nil { + return nil, errors.New("can't create aws config") + } + s.s3Client = s3.NewFromConfig(cfg) + } + return s, nil +} + +// Upload reads from the reader and uploads it to the S3 bucket with the +// filename key. +func (s *S3) Upload(ctx context.Context, r io.Reader, bucket string, key string) error { + uploader := manager.NewUploader(s.s3Client, func(u *manager.Uploader) { + u.BufferProvider = manager.NewBufferedReadSeekerWriteToPool(s.bufferLen) + }) + _, err := uploader.Upload(ctx, &s3.PutObjectInput{ + Bucket: aws.String(bucket), + Key: aws.String(key), + Body: r, + }) + return errors.Wrap(err, "upload failed") +} + +type seqWriterAt struct { + w io.Writer + progressFunc func(n int) +} + +func (s *seqWriterAt) WriteAt(p []byte, offset int64) (n int, err error) { + n, err = s.w.Write(p) + if s.progressFunc != nil { + s.progressFunc(n) + } + return n, errors.Wrap(err, "can't write bytes at offset") +} + +type DownloadFileInfo struct { + Bucket string + Key string +} + +// Download downloads the file from the S3 bucket with the filename key and +// writes it to the writer. +func (s *S3) Download(ctx context.Context, w io.Writer, filesinfo ...*DownloadFileInfo) error { + downloader := manager.NewDownloader(s.s3Client, func(d *manager.Downloader) { + d.PartBodyMaxRetries = s.partBodyMaxRetries + d.PartSize = int64(s.bufferLen) + // we need to force this to be a sequential download. + d.Concurrency = 1 + }) + ww := &seqWriterAt{w, nil} + for _, fileinfo := range filesinfo { + _, err := downloader.Download(ctx, ww, &s3.GetObjectInput{ + Bucket: aws.String(fileinfo.Bucket), + Key: aws.String(fileinfo.Key), + }) + if err != nil { + return errors.Wrapf(err, "download failed for bucket %s and key %s", fileinfo.Bucket, fileinfo.Key) + } + } + return nil +} diff --git a/file/batchingchannels/batching_channel.go b/file/batchingchannels/batching_channel.go index aebca36..2f575cb 100644 --- a/file/batchingchannels/batching_channel.go +++ b/file/batchingchannels/batching_channel.go @@ -89,9 +89,9 @@ func (ch *BatchingChannel) Close() { func (ch *BatchingChannel) batchingBuffer() { ch.buffer = ch.allocate.Vector(ch.size, ch.allocate.Key) for { - elem, open := <-ch.input + row, open := <-ch.input if open { - err := ch.buffer.PushBack(elem) + err := ch.buffer.PushBack(row) if err != nil { ch.G.Go(func() error { return err diff --git a/file/batchingchannels/batching_channel_test.go b/file/batchingchannels/batching_channel_test.go index b33aaf3..7330ed0 100644 --- a/file/batchingchannels/batching_channel_test.go +++ b/file/batchingchannels/batching_channel_test.go @@ -37,6 +37,10 @@ func (k *Int) Get() int { func (k *Int) Less(other key.Key) bool { return k.value < other.(*Int).value } +func (k *Int) Equal(other key.Key) bool { + return k.value == other.(*Int).value +} + func testBatches(t *testing.T, ch *batchingchannels.BatchingChannel) { maxI := 10000 expectedSum := (maxI - 1) * maxI / 2 diff --git a/file/chunk.go b/file/chunk.go index f3414f9..380a0cf 100644 --- a/file/chunk.go +++ b/file/chunk.go @@ -42,12 +42,15 @@ type chunks struct { } // new Create a new chunk and initialize it. -func (c *chunks) new(chunkPath string, allocate *vector.Allocate, size int) error { +func (c *chunks) new(chunkPath string, allocate *vector.Allocate, size int, withHeader bool) error { f, err := os.Open(chunkPath) if err != nil { return err } - reader := allocate.FnReader(f) + reader, err := allocate.FnReader(f) + if err != nil { + return err + } elem := &chunkInfo{ filename: chunkPath, file: f, diff --git a/file/file.go b/file/file.go index e7a007a..074a4e0 100644 --- a/file/file.go +++ b/file/file.go @@ -11,18 +11,23 @@ import ( "github.com/askiada/external-sort/file/batchingchannels" "github.com/askiada/external-sort/vector" "github.com/askiada/external-sort/writer" + "github.com/sirupsen/logrus" "github.com/pkg/errors" ) +var logger = logrus.StandardLogger() + type Info struct { mu *MemUsage Allocate *vector.Allocate InputReader io.Reader - OutputFile string + OutputFile io.Writer outputWriter writer.Writer totalRows int PrintMemUsage bool + WithHeader bool + headers interface{} } // CreateSortedChunks Scan a file and divide it into small sorted chunks. @@ -42,9 +47,11 @@ func (f *Info) CreateSortedChunks(ctx context.Context, chunkFolder string, dumpS return nil, errors.Wrap(err, fn) } - inputReader := f.Allocate.FnReader(f.InputReader) - - row := 0 + inputReader, err := f.Allocate.FnReader(f.InputReader) + if err != nil { + return nil, errors.Wrap(err, fn) + } + count_rows := 0 chunkPaths := []string{} mu := sync.Mutex{} @@ -55,12 +62,16 @@ func (f *Info) CreateSortedChunks(ctx context.Context, chunkFolder string, dumpS if f.PrintMemUsage { f.mu.Collect() } - elem, err := inputReader.Read() + row, err := inputReader.Read() if err != nil { return errors.Wrap(err, fn) } - batchChan.In() <- elem - row++ + if f.WithHeader && f.headers == nil { + f.headers = row + } else { + batchChan.In() <- row + } + count_rows++ } batchChan.Close() if inputReader.Err() != nil { @@ -74,8 +85,15 @@ func (f *Info) CreateSortedChunks(ctx context.Context, chunkFolder string, dumpS mu.Lock() chunkIdx++ chunkPath := path.Join(chunkFolder, "chunk_"+strconv.Itoa(chunkIdx)+".tsv") + logger.Infoln("Created chunk", chunkPath) mu.Unlock() v.Sort() + if f.WithHeader { + err = v.PushFrontNoKey(f.headers) + if err != nil { + return err + } + } err := f.Allocate.Dump(v, chunkPath) if err != nil { return err @@ -88,6 +106,6 @@ func (f *Info) CreateSortedChunks(ctx context.Context, chunkFolder string, dumpS if err != nil { return nil, errors.Wrap(err, fn) } - f.totalRows = row + f.totalRows = count_rows return chunkPaths, nil } diff --git a/file/sort.go b/file/sort.go index ae53b62..60a2eb1 100644 --- a/file/sort.go +++ b/file/sort.go @@ -2,7 +2,6 @@ package file import ( "fmt" - "os" "runtime" "github.com/askiada/external-sort/vector" @@ -39,24 +38,30 @@ func bToMb(b uint64) uint64 { return b / 1024 / 1024 } -func (f *Info) MergeSort(chunkPaths []string, k int) (err error) { +func (f *Info) MergeSort(chunkPaths []string, k int, dropDuplicates bool) (err error) { + var oldElem *vector.Element output := f.Allocate.Vector(k, f.Allocate.Key) if f.PrintMemUsage && f.mu == nil { f.mu = &MemUsage{} } + if f.WithHeader { + err = output.PushFrontNoKey(f.headers) + if err != nil { + return err + } + } // create a chunk per file path chunks := &chunks{list: make([]*chunkInfo, 0, len(chunkPaths))} for _, chunkPath := range chunkPaths { - err := chunks.new(chunkPath, f.Allocate, k) + err := chunks.new(chunkPath, f.Allocate, k, f.WithHeader) if err != nil { return err } } - w, err := os.Create(f.OutputFile) + f.outputWriter, err = f.Allocate.FnWriter(f.OutputFile) if err != nil { return err } - f.outputWriter = f.Allocate.FnWriter(w) defer f.outputWriter.Close() bar := pb.StartNew(f.totalRows) chunks.resetOrder() @@ -76,10 +81,14 @@ func (f *Info) MergeSort(chunkPaths []string, k int) (err error) { toShrink := []int{} // search the smallest value across chunk buffers by comparing first elements only minChunk, minValue, minIdx := chunks.min() - err = output.PushBack(minValue.Row) - if err != nil { - return err + if (!dropDuplicates || oldElem == nil) || (dropDuplicates && !minValue.Key.Equal(oldElem.Key)) { + err = output.PushBack(minValue.Row) + if err != nil { + return err + } + oldElem = minValue } + // remove the first element from the chunk we pulled the smallest value minChunk.buffer.FrontShift() isEmpty := false diff --git a/go.mod b/go.mod index 42f2d65..36e9033 100644 --- a/go.mod +++ b/go.mod @@ -3,9 +3,14 @@ module github.com/askiada/external-sort go 1.17 require ( + github.com/aws/aws-sdk-go-v2 v1.16.16 + github.com/aws/aws-sdk-go-v2/config v1.17.8 + github.com/aws/aws-sdk-go-v2/feature/s3/manager v1.11.34 + github.com/aws/aws-sdk-go-v2/service/s3 v1.27.11 github.com/cheggaaa/pb/v3 v3.0.8 github.com/pkg/errors v0.9.1 github.com/pkg/sftp v1.13.4 + github.com/sirupsen/logrus v1.9.0 github.com/spf13/cobra v1.2.1 github.com/spf13/viper v1.8.1 github.com/stretchr/testify v1.7.0 @@ -15,11 +20,27 @@ require ( require ( github.com/VividCortex/ewma v1.2.0 // indirect + github.com/aws/aws-sdk-go-v2/aws/protocol/eventstream v1.4.8 // indirect + github.com/aws/aws-sdk-go-v2/credentials v1.12.21 // indirect + github.com/aws/aws-sdk-go-v2/feature/ec2/imds v1.12.17 // indirect + github.com/aws/aws-sdk-go-v2/internal/configsources v1.1.23 // indirect + github.com/aws/aws-sdk-go-v2/internal/endpoints/v2 v2.4.17 // indirect + github.com/aws/aws-sdk-go-v2/internal/ini v1.3.24 // indirect + github.com/aws/aws-sdk-go-v2/internal/v4a v1.0.14 // indirect + github.com/aws/aws-sdk-go-v2/service/internal/accept-encoding v1.9.9 // indirect + github.com/aws/aws-sdk-go-v2/service/internal/checksum v1.1.18 // indirect + github.com/aws/aws-sdk-go-v2/service/internal/presigned-url v1.9.17 // indirect + github.com/aws/aws-sdk-go-v2/service/internal/s3shared v1.13.17 // indirect + github.com/aws/aws-sdk-go-v2/service/sso v1.11.23 // indirect + github.com/aws/aws-sdk-go-v2/service/ssooidc v1.13.6 // indirect + github.com/aws/aws-sdk-go-v2/service/sts v1.16.19 // indirect + github.com/aws/smithy-go v1.13.3 // indirect github.com/davecgh/go-spew v1.1.1 // indirect github.com/fatih/color v1.13.0 // indirect github.com/fsnotify/fsnotify v1.4.9 // indirect github.com/hashicorp/hcl v1.0.0 // indirect github.com/inconshreveable/mousetrap v1.0.0 // indirect + github.com/jmespath/go-jmespath v0.4.0 // indirect github.com/kr/fs v0.1.0 // indirect github.com/magiconair/properties v1.8.5 // indirect github.com/mattn/go-colorable v0.1.12 // indirect @@ -34,7 +55,7 @@ require ( github.com/spf13/jwalterweatherman v1.1.0 // indirect github.com/spf13/pflag v1.0.5 // indirect github.com/subosito/gotenv v1.2.0 // indirect - golang.org/x/sys v0.0.0-20220209214540-3681064d5158 // indirect + golang.org/x/sys v0.0.0-20220715151400-c0bba94af5f8 // indirect golang.org/x/text v0.3.6 // indirect gopkg.in/ini.v1 v1.62.0 // indirect gopkg.in/yaml.v2 v2.4.0 // indirect diff --git a/go.sum b/go.sum index 45da8db..86f0dcb 100644 --- a/go.sum +++ b/go.sum @@ -46,6 +46,44 @@ github.com/antihax/optional v1.0.0/go.mod h1:uupD/76wgC+ih3iEmQUL+0Ugr19nfwCT1kd github.com/armon/circbuf v0.0.0-20150827004946-bbbad097214e/go.mod h1:3U/XgcO3hCbHZ8TKRvWD2dDTCfh9M9ya+I9JpbB7O8o= github.com/armon/go-metrics v0.0.0-20180917152333-f0300d1749da/go.mod h1:Q73ZrmVTwzkszR9V5SSuryQ31EELlFMUz1kKyl939pY= github.com/armon/go-radix v0.0.0-20180808171621-7fddfc383310/go.mod h1:ufUuZ+zHj4x4TnLV4JWEpy2hxWSpsRywHrMgIH9cCH8= +github.com/aws/aws-sdk-go-v2 v1.16.16 h1:M1fj4FE2lB4NzRb9Y0xdWsn2P0+2UHVxwKyOa4YJNjk= +github.com/aws/aws-sdk-go-v2 v1.16.16/go.mod h1:SwiyXi/1zTUZ6KIAmLK5V5ll8SiURNUYOqTerZPaF9k= +github.com/aws/aws-sdk-go-v2/aws/protocol/eventstream v1.4.8 h1:tcFliCWne+zOuUfKNRn8JdFBuWPDuISDH08wD2ULkhk= +github.com/aws/aws-sdk-go-v2/aws/protocol/eventstream v1.4.8/go.mod h1:JTnlBSot91steJeti4ryyu/tLd4Sk84O5W22L7O2EQU= +github.com/aws/aws-sdk-go-v2/config v1.17.8 h1:b9LGqNnOdg9vR4Q43tBTVWk4J6F+W774MSchvKJsqnE= +github.com/aws/aws-sdk-go-v2/config v1.17.8/go.mod h1:UkCI3kb0sCdvtjiXYiU4Zx5h07BOpgBTtkPu/49r+kA= +github.com/aws/aws-sdk-go-v2/credentials v1.12.21 h1:4tjlyCD0hRGNQivh5dN8hbP30qQhMLBE/FgQR1vHHWM= +github.com/aws/aws-sdk-go-v2/credentials v1.12.21/go.mod h1:O+4XyAt4e+oBAoIwNUYkRg3CVMscaIJdmZBOcPgJ8D8= +github.com/aws/aws-sdk-go-v2/feature/ec2/imds v1.12.17 h1:r08j4sbZu/RVi+BNxkBJwPMUYY3P8mgSDuKkZ/ZN1lE= +github.com/aws/aws-sdk-go-v2/feature/ec2/imds v1.12.17/go.mod h1:yIkQcCDYNsZfXpd5UX2Cy+sWA1jPgIhGTw9cOBzfVnQ= +github.com/aws/aws-sdk-go-v2/feature/s3/manager v1.11.34 h1:1PNtaCM+2ruo1dfYL2RweUdtbuPvinjAejjNcPa/RQY= +github.com/aws/aws-sdk-go-v2/feature/s3/manager v1.11.34/go.mod h1:+Six+CXNHYllXam32j+YW8ixk82+am345ei89kEz8p4= +github.com/aws/aws-sdk-go-v2/internal/configsources v1.1.23 h1:s4g/wnzMf+qepSNgTvaQQHNxyMLKSawNhKCPNy++2xY= +github.com/aws/aws-sdk-go-v2/internal/configsources v1.1.23/go.mod h1:2DFxAQ9pfIRy0imBCJv+vZ2X6RKxves6fbnEuSry6b4= +github.com/aws/aws-sdk-go-v2/internal/endpoints/v2 v2.4.17 h1:/K482T5A3623WJgWT8w1yRAFK4RzGzEl7y39yhtn9eA= +github.com/aws/aws-sdk-go-v2/internal/endpoints/v2 v2.4.17/go.mod h1:pRwaTYCJemADaqCbUAxltMoHKata7hmB5PjEXeu0kfg= +github.com/aws/aws-sdk-go-v2/internal/ini v1.3.24 h1:wj5Rwc05hvUSvKuOF29IYb9QrCLjU+rHAy/x/o0DK2c= +github.com/aws/aws-sdk-go-v2/internal/ini v1.3.24/go.mod h1:jULHjqqjDlbyTa7pfM7WICATnOv+iOhjletM3N0Xbu8= +github.com/aws/aws-sdk-go-v2/internal/v4a v1.0.14 h1:ZSIPAkAsCCjYrhqfw2+lNzWDzxzHXEckFkTePL5RSWQ= +github.com/aws/aws-sdk-go-v2/internal/v4a v1.0.14/go.mod h1:AyGgqiKv9ECM6IZeNQtdT8NnMvUb3/2wokeq2Fgryto= +github.com/aws/aws-sdk-go-v2/service/internal/accept-encoding v1.9.9 h1:Lh1AShsuIJTwMkoxVCAYPJgNG5H+eN6SmoUn8nOZ5wE= +github.com/aws/aws-sdk-go-v2/service/internal/accept-encoding v1.9.9/go.mod h1:a9j48l6yL5XINLHLcOKInjdvknN+vWqPBxqeIDw7ktw= +github.com/aws/aws-sdk-go-v2/service/internal/checksum v1.1.18 h1:BBYoNQt2kUZUUK4bIPsKrCcjVPUMNsgQpNAwhznK/zo= +github.com/aws/aws-sdk-go-v2/service/internal/checksum v1.1.18/go.mod h1:NS55eQ4YixUJPTC+INxi2/jCqe1y2Uw3rnh9wEOVJxY= +github.com/aws/aws-sdk-go-v2/service/internal/presigned-url v1.9.17 h1:Jrd/oMh0PKQc6+BowB+pLEwLIgaQF29eYbe7E1Av9Ug= +github.com/aws/aws-sdk-go-v2/service/internal/presigned-url v1.9.17/go.mod h1:4nYOrY41Lrbk2170/BGkcJKBhws9Pfn8MG3aGqjjeFI= +github.com/aws/aws-sdk-go-v2/service/internal/s3shared v1.13.17 h1:HfVVR1vItaG6le+Bpw6P4midjBDMKnjMyZnw9MXYUcE= +github.com/aws/aws-sdk-go-v2/service/internal/s3shared v1.13.17/go.mod h1:YqMdV+gEKCQ59NrB7rzrJdALeBIsYiVi8Inj3+KcqHI= +github.com/aws/aws-sdk-go-v2/service/s3 v1.27.11 h1:3/gm/JTX9bX8CpzTgIlrtYpB3EVBDxyg/GY/QdcIEZw= +github.com/aws/aws-sdk-go-v2/service/s3 v1.27.11/go.mod h1:fmgDANqTUCxciViKl9hb/zD5LFbvPINFRgWhDbR+vZo= +github.com/aws/aws-sdk-go-v2/service/sso v1.11.23 h1:pwvCchFUEnlceKIgPUouBJwK81aCkQ8UDMORfeFtW10= +github.com/aws/aws-sdk-go-v2/service/sso v1.11.23/go.mod h1:/w0eg9IhFGjGyyncHIQrXtU8wvNsTJOP0R6PPj0wf80= +github.com/aws/aws-sdk-go-v2/service/ssooidc v1.13.6 h1:OwhhKc1P9ElfWbMKPIbMMZBV6hzJlL2JKD76wNNVzgQ= +github.com/aws/aws-sdk-go-v2/service/ssooidc v1.13.6/go.mod h1:csZuQY65DAdFBt1oIjO5hhBR49kQqop4+lcuCjf2arA= +github.com/aws/aws-sdk-go-v2/service/sts v1.16.19 h1:9pPi0PsFNAGILFfPCk8Y0iyEBGc6lu6OQ97U7hmdesg= +github.com/aws/aws-sdk-go-v2/service/sts v1.16.19/go.mod h1:h4J3oPZQbxLhzGnk+j9dfYHi5qIOVJ5kczZd658/ydM= +github.com/aws/smithy-go v1.13.3 h1:l7LYxGuzK6/K+NzJ2mC+VvLUbae0sL3bXU//04MkmnA= +github.com/aws/smithy-go v1.13.3/go.mod h1:Tg+OJXh4MB2R/uN61Ko2f6hTZwB/ZYGOtib8J3gBHzA= github.com/bgentry/speakeasy v0.1.0/go.mod h1:+zsyZBPWlz7T6j88CTgSN5bM796AkVf0kBD4zp0CCIs= github.com/bketelsen/crypt v0.0.4/go.mod h1:aI6NrJ0pMGgvZKL1iVgXLnfIFJtfV+bKCoqOes/6LfM= github.com/census-instrumentation/opencensus-proto v0.2.1/go.mod h1:f6KPmirojxKA12rnyqOA5BBL4O983OfeGPqjHWSTneU= @@ -125,6 +163,8 @@ github.com/google/go-cmp v0.5.2/go.mod h1:v8dTdLbMG2kIc/vJvl+f65V22dbkXbowE6jgT/ github.com/google/go-cmp v0.5.3/go.mod h1:v8dTdLbMG2kIc/vJvl+f65V22dbkXbowE6jgT/gNBxE= github.com/google/go-cmp v0.5.4/go.mod h1:v8dTdLbMG2kIc/vJvl+f65V22dbkXbowE6jgT/gNBxE= github.com/google/go-cmp v0.5.5/go.mod h1:v8dTdLbMG2kIc/vJvl+f65V22dbkXbowE6jgT/gNBxE= +github.com/google/go-cmp v0.5.8 h1:e6P7q2lk1O+qJJb4BtCQXlK8vWEO8V1ZeuEdJNOqZyg= +github.com/google/go-cmp v0.5.8/go.mod h1:17dUlkBOakJ0+DkrSSNjCkIjxS6bF9zb3elmeNGIjoY= github.com/google/gofuzz v1.0.0/go.mod h1:dBl0BpW6vV/+mYPU4Po3pmUjxk6FQPldtuIdl/M65Eg= github.com/google/martian v2.1.0+incompatible/go.mod h1:9I4somxYTbIHy5NJKHRl3wXiIaQGbYVAs8BPL6v8lEs= github.com/google/martian/v3 v3.0.0/go.mod h1:y5Zk1BBys9G+gd6Jrk0W3cC1+ELVxBWuIGO+w/tUAp0= @@ -172,6 +212,10 @@ github.com/ianlancetaylor/demangle v0.0.0-20181102032728-5e5cf60278f6/go.mod h1: github.com/ianlancetaylor/demangle v0.0.0-20200824232613-28f6c0f3b639/go.mod h1:aSSvb/t6k1mPoxDqO4vJh6VOCGPwU4O0C2/Eqndh1Sc= github.com/inconshreveable/mousetrap v1.0.0 h1:Z8tu5sraLXCXIcARxBp/8cbvlwVa7Z1NHg9XEKhtSvM= github.com/inconshreveable/mousetrap v1.0.0/go.mod h1:PxqpIevigyE2G7u3NXJIT2ANytuPF1OarO4DADm73n8= +github.com/jmespath/go-jmespath v0.4.0 h1:BEgLn5cpjn8UN1mAw4NjwDrS35OdebyEtFe+9YPoQUg= +github.com/jmespath/go-jmespath v0.4.0/go.mod h1:T8mJZnbsbmF+m6zOOFylbeCJqk5+pHWvzYPziyZiYoo= +github.com/jmespath/go-jmespath/internal/testify v1.5.1 h1:shLQSRRSCCPj3f2gpwzGwWFoC7ycTf1rcQZHOlsJ6N8= +github.com/jmespath/go-jmespath/internal/testify v1.5.1/go.mod h1:L3OGu8Wl2/fWfCI6z80xFu9LTZmf1ZRjMHUOPmWr69U= github.com/json-iterator/go v1.1.11/go.mod h1:KdQUCv79m/52Kvf8AW2vK1V8akMuk1QjK/uOdHXbAo4= github.com/jstemmer/go-junit-report v0.0.0-20190106144839-af01ea7f8024/go.mod h1:6v2b51hI/fHJwM22ozAgKL4VKDeJcHhJFhtBdhmNjmU= github.com/jstemmer/go-junit-report v0.9.1/go.mod h1:Brl9GWCQeLvo8nXZwPNNblvFj/XSXhF0NWZEnDohbsk= @@ -235,6 +279,8 @@ github.com/russross/blackfriday/v2 v2.0.1/go.mod h1:+Rmxgy9KzJVeS9/2gXHxylqXiyQD github.com/ryanuber/columnize v0.0.0-20160712163229-9b3edd62028f/go.mod h1:sm1tb6uqfes/u+d4ooFouqFdy9/2g9QGwK3SQygK0Ts= github.com/sean-/seed v0.0.0-20170313163322-e2103e2c3529/go.mod h1:DxrIzT+xaE7yg65j358z/aeFdxmN0P9QXhEzd20vsDc= github.com/shurcooL/sanitized_anchor_name v1.0.0/go.mod h1:1NzhyTcUVG4SuEtjjoZeVRXNmyL/1OwPU0+IJeTBvfc= +github.com/sirupsen/logrus v1.9.0 h1:trlNQbNUG3OdDrDil03MCb1H2o9nJ1x4/5LYw7byDE0= +github.com/sirupsen/logrus v1.9.0/go.mod h1:naHLuLoDiP4jHNo9R0sCBMtWGeIprob74mVsIT4qYEQ= github.com/smartystreets/assertions v0.0.0-20180927180507-b2de0cb4f26d h1:zE9ykElWQ6/NYmHa3jpm/yHnI4xSofP+UP6SpjHcSeM= github.com/smartystreets/assertions v0.0.0-20180927180507-b2de0cb4f26d/go.mod h1:OnSkiWE9lh6wB0YB77sQom3nweQdgAjqCqsofrRNTgc= github.com/smartystreets/goconvey v1.6.4 h1:fv0U8FUIMPNf1L9lnHLvLhgicrIVChEkdzIKYqbNC9s= @@ -432,8 +478,8 @@ golang.org/x/sys v0.0.0-20210510120138-977fb7262007/go.mod h1:oPkhp1MJrh7nUepCBc golang.org/x/sys v0.0.0-20210615035016-665e8c7367d1/go.mod h1:oPkhp1MJrh7nUepCBck5+mAzfO9JrbApNNgaTdGDITg= golang.org/x/sys v0.0.0-20210630005230-0f9fa26af87c/go.mod h1:oPkhp1MJrh7nUepCBck5+mAzfO9JrbApNNgaTdGDITg= golang.org/x/sys v0.0.0-20210927094055-39ccf1dd6fa6/go.mod h1:oPkhp1MJrh7nUepCBck5+mAzfO9JrbApNNgaTdGDITg= -golang.org/x/sys v0.0.0-20220209214540-3681064d5158 h1:rm+CHSpPEEW2IsXUib1ThaHIjuBVZjxNgSKmBLFfD4c= -golang.org/x/sys v0.0.0-20220209214540-3681064d5158/go.mod h1:oPkhp1MJrh7nUepCBck5+mAzfO9JrbApNNgaTdGDITg= +golang.org/x/sys v0.0.0-20220715151400-c0bba94af5f8 h1:0A+M6Uqn+Eje4kHMK80dtF3JCXC4ykBgQG4Fe06QRhQ= +golang.org/x/sys v0.0.0-20220715151400-c0bba94af5f8/go.mod h1:oPkhp1MJrh7nUepCBck5+mAzfO9JrbApNNgaTdGDITg= golang.org/x/term v0.0.0-20201126162022-7de9c90e9dd1 h1:v+OssWQX+hTHEmOBgwxdZxK4zHq3yOs8F9J7mk0PY8E= golang.org/x/term v0.0.0-20201126162022-7de9c90e9dd1/go.mod h1:bj7SfCRtBDWHUb9snDiAeCFNEtKQo2Wmx5Cou7ajbmo= golang.org/x/text v0.0.0-20170915032832-14c0d48ead0c/go.mod h1:NqM8EUOU14njkJ3fqMW+pc6Ldnwhi/IjpwHt7yyuwOQ= diff --git a/internal/env.go b/internal/env.go index f4bafcb..fc847b7 100644 --- a/internal/env.go +++ b/internal/env.go @@ -8,33 +8,45 @@ import ( // Argument names. const ( - InputFileName = "input_path" + WithHeaderName = "with_header" + InputFileNames = "input_paths" OutputFileName = "output_path" ChunkFolderName = "chunk_folder" ChunkSizeName = "chunk_size" MaxWorkersName = "max_workers" OutputBufferSizeName = "output_buffer_size" TsvFieldsName = "tsv_fields" + + S3RegionName = "s3_region" + S3RetryMaxAttemptsName = "s3_retry_max_attempts" ) // Environment variables. var ( - InputFile string + WithHeader bool + InputFiles []string TsvFields []string OutputFile string ChunkFolder string ChunkSize int MaxWorkers int64 OutputBufferSize int + + S3Region string + S3RetryMaxAttempts int ) func init() { viper.AutomaticEnv() - viper.SetDefault(InputFileName, "") + viper.SetDefault(WithHeaderName, false) + viper.SetDefault(InputFileNames, "") viper.SetDefault(OutputFileName, "") viper.SetDefault(ChunkFolderName, "") viper.SetDefault(ChunkSizeName, 0) viper.SetDefault(MaxWorkersName, 0) viper.SetDefault(OutputBufferSizeName, 0) viper.SetDefault(TsvFieldsName, []string{"0"}) + + viper.SetDefault(S3RegionName, "eu-west-1") + viper.SetDefault(S3RetryMaxAttemptsName, 10) } diff --git a/internal/progress/contract.go b/internal/progress/contract.go new file mode 100644 index 0000000..7b9766c --- /dev/null +++ b/internal/progress/contract.go @@ -0,0 +1,67 @@ +// Package progress defines standard and simple progress bar to track file download progress. +package progress + +import ( + "math" + + "github.com/cheggaaa/pb/v3" + "github.com/sirupsen/logrus" +) + +// Progress defines a simple progress bar contract. +type Progress interface { + // Begin sets and starts the progress bar. + Begin(total int64) + // Add increments the progress bar with n elements + Add(n int64) + // End terminates the progress bar + End() +} + +// Pb implements Progress contract using cheggaaa pb v3. +type Pb struct { + bar *pb.ProgressBar +} + +// Begin start a new progress bar in byte mode. +func (p *Pb) Begin(total int64) { + p.bar = pb.Full.Start64(total) + p.bar.Set(pb.Bytes, true) +} + +// Add increment the bar by n elements. +func (p *Pb) Add(n int64) { + p.bar.Add64(n) +} + +// End terminates the bar. +func (p *Pb) End() { + p.bar.Finish() +} + +var _ Progress = &Pb{} + +// Basic implements Progress contract using stdout to print status. +type Basic struct { + total float64 + written float64 + milestone int +} + +// Begin start a new progress bar. +func (b *Basic) Begin(total int64) { + b.total = float64(total) +} + +// Add increment the bar by n elements. +func (b *Basic) Add(val int64) { + b.written += float64(val) + progress := int(math.Round(b.written / b.total * 100)) + if progress >= b.milestone { + b.milestone += 5 // every 5% + logrus.Debugf("Download from S3 at %3d%%\n\n", progress) + } +} + +// End noop. +func (b *Basic) End() {} diff --git a/internal/rw/rw.go b/internal/rw/rw.go new file mode 100644 index 0000000..fa89a15 --- /dev/null +++ b/internal/rw/rw.go @@ -0,0 +1,178 @@ +package rw + +import ( + "context" + "io" + "net/url" + "os" + "strings" + + "github.com/askiada/external-sort/bucket" + "github.com/askiada/external-sort/internal" + "github.com/askiada/external-sort/internal/progress" + "github.com/aws/aws-sdk-go-v2/config" + "github.com/aws/aws-sdk-go-v2/service/s3" + "github.com/pkg/errors" + "github.com/sirupsen/logrus" + "golang.org/x/sync/errgroup" +) + +var logger = logrus.StandardLogger() + +type InputOutput struct { + s3Client bucket.S3ClientAPI + Input io.Reader + inputPipe *io.PipeReader + Output io.Writer + outputPipe *io.PipeWriter + g *errgroup.Group + dCtx context.Context +} + +func NewInputOutput(ctx context.Context) *InputOutput { + g, dCtx := errgroup.WithContext(ctx) + return &InputOutput{ + g: g, + dCtx: dCtx, + } +} + +func (i *InputOutput) s3Check() error { + if i.s3Client != nil { + return nil + } + cfg, err := config.LoadDefaultConfig(context.Background(), + config.WithRegion(internal.S3Region), + config.WithRetryMaxAttempts(internal.S3RetryMaxAttempts), + ) + if err != nil { + return errors.New("can't create aws config") + } + i.s3Client = s3.NewFromConfig(cfg) + return nil +} + +func (i *InputOutput) SetInputReader(ctx context.Context, inputFiles ...string) (err error) { + if strings.HasPrefix(inputFiles[0], "s3") || strings.HasPrefix(inputFiles[0], "S3") { + err = i.s3Check() + if err != nil { + return errors.Wrap(err, "can't check s3") + } + s3Api, err := bucket.New(ctx, + bucket.Client(i.s3Client), + bucket.Buffer(1_000_000), + bucket.Progress(&progress.Pb{}), + ) + if err != nil { + return errors.Wrap(err, "can't create s3 client") + } + files := []*bucket.DownloadFileInfo{} + for _, inputFile := range inputFiles { + u, _ := url.Parse(inputFile) + u.Path = strings.TrimLeft(u.Path, "/") + logger.Debugf("Proto: %q, Bucket: %q, Key: %q", u.Scheme, u.Host, u.Path) + files = append(files, &bucket.DownloadFileInfo{ + Bucket: u.Host, + Key: u.Path, + }) + } + + pr, pw := io.Pipe() + i.Input = pr + i.inputPipe = pr + i.g.Go(func() error { + defer pw.Close() // nolint:errcheck //no need to check this error + err := s3Api.Download(i.dCtx, pw, files...) + if err != nil { + return errors.Wrap(err, "can't download files") + } + return nil + }) + } else { + var files []io.Reader + for _, inputFile := range inputFiles { + f, err := os.Open(inputFile) + if err != nil { + return errors.Wrapf(err, "can't open file %s", inputFile) + } + files = append(files, f) + } + i.Input = io.MultiReader(files...) + } + return nil +} + +func (i *InputOutput) SetOutputWriter(ctx context.Context, outputFile string) (err error) { + if strings.HasPrefix(outputFile, "s3") || strings.HasPrefix(outputFile, "S3") { + err = i.s3Check() + if err != nil { + return errors.Wrap(err, "can't check s3") + } + u, _ := url.Parse(outputFile) + u.Path = strings.TrimLeft(u.Path, "/") + logger.Debugf("Proto: %q, Bucket: %q, Key: %q", u.Scheme, u.Host, u.Path) + s3Api, err := bucket.New(ctx, + bucket.Client(i.s3Client), + bucket.Buffer(1_000_000), + bucket.Progress(&progress.Pb{}), + ) + if err != nil { + return errors.Wrap(err, "can't create s3 client") + } + + pr, pw := io.Pipe() + i.Output = pw + i.outputPipe = pw + i.g.Go(func() error { + defer pr.Close() // nolint:errcheck //no need to check this error + err := s3Api.Upload(i.dCtx, pr, u.Host, u.Path) + if err != nil { + return errors.Wrapf(err, "can't upload file %s", outputFile) + } + return nil + }) + } else { + i.Output, err = os.Create(outputFile) + if err != nil { + return errors.Wrapf(err, "can't create file %s", outputFile) + } + } + return nil +} + +func (i *InputOutput) Do(f func() error) { + i.g.Go(func() error { + err := f() + if err != nil { + return err + } + err = i.Close() + if err != nil { + return err + } + return nil + }) +} + +func (i *InputOutput) Close() error { + if i.inputPipe != nil { + err := i.inputPipe.Close() + if err != nil { + return errors.Wrap(err, "can't close input reader") + } + } + if i.outputPipe != nil { + err := i.outputPipe.Close() + if err != nil { + return errors.Wrap(err, "can't close output writer") + } + } + return nil +} + +func (i *InputOutput) Err() error { + if err := i.g.Wait(); err != nil { + return errors.Wrap(err, "one of the go routines went wrong") + } + return nil +} diff --git a/main.go b/main.go index 5a166fb..a440bbe 100644 --- a/main.go +++ b/main.go @@ -2,30 +2,33 @@ package main import ( "context" - "fmt" "io" - "os" "strconv" "time" "github.com/askiada/external-sort/file" "github.com/askiada/external-sort/internal" + "github.com/askiada/external-sort/internal/rw" "github.com/askiada/external-sort/reader" "github.com/askiada/external-sort/vector" "github.com/askiada/external-sort/vector/key" "github.com/askiada/external-sort/writer" + "github.com/pkg/errors" + "github.com/sirupsen/logrus" "github.com/spf13/cobra" "github.com/spf13/viper" ) +var logger = logrus.StandardLogger() + func main() { rootCmd := &cobra.Command{ Use: "external-sort", Short: "Perform an external sorting on an input file", RunE: rootRun, } - - rootCmd.PersistentFlags().StringVarP(&internal.InputFile, internal.InputFileName, "i", viper.GetString(internal.InputFileName), "input file path.") + rootCmd.PersistentFlags().BoolVarP(&internal.WithHeader, internal.WithHeaderName, "i", viper.GetBool(internal.WithHeaderName), "Input file has headers.") + rootCmd.PersistentFlags().StringSliceVarP(&internal.InputFiles, internal.InputFileNames, "i", viper.GetStringSlice(internal.InputFileNames), "input file path.") rootCmd.PersistentFlags().StringVarP(&internal.OutputFile, internal.OutputFileName, "o", viper.GetString(internal.OutputFileName), "output file path.") rootCmd.PersistentFlags().StringVarP(&internal.ChunkFolder, internal.ChunkFolderName, "c", viper.GetString(internal.ChunkFolderName), "chunk folder.") @@ -34,22 +37,29 @@ func main() { rootCmd.PersistentFlags().IntVarP(&internal.OutputBufferSize, internal.OutputBufferSizeName, "b", viper.GetInt(internal.OutputBufferSizeName), "output buffer size.") rootCmd.PersistentFlags().StringSliceVarP(&internal.TsvFields, internal.TsvFieldsName, "t", viper.GetStringSlice(internal.TsvFieldsName), "") - fmt.Println("Input file", internal.InputFile) - fmt.Println("Output file", internal.OutputFile) - fmt.Println("Chunk folder", internal.ChunkFolder) - fmt.Println("TSV Fields", internal.TsvFields) + rootCmd.Flags().StringVar(&internal.S3Region, internal.S3RegionName, viper.GetString(internal.S3RegionName), "the bucket region") + rootCmd.Flags().IntVar(&internal.S3RetryMaxAttempts, internal.S3RetryMaxAttemptsName, viper.GetInt(internal.S3RetryMaxAttemptsName), "the number of retries per S3 request before failing") + logger.Infoln("Input files", internal.InputFiles) + logger.Infoln("With header", internal.WithHeader) + logger.Infoln("Output file", internal.OutputFile) + logger.Infoln("Chunk folder", internal.ChunkFolder) + logger.Infoln("TSV Fields", internal.TsvFields) cobra.CheckErr(rootCmd.Execute()) } func rootRun(cmd *cobra.Command, args []string) error { start := time.Now() - // open a file - inputReader, err := os.Open(internal.InputFile) + ctx := context.Background() + i := rw.NewInputOutput(ctx) + err := i.SetInputReader(ctx, internal.InputFiles...) + if err != nil { + return err + } + err = i.SetOutputWriter(ctx, internal.OutputFile) if err != nil { return err } - defer inputReader.Close() tsvFields := []int{} for _, field := range internal.TsvFields { i, err := strconv.Atoi(field) @@ -59,26 +69,38 @@ func rootRun(cmd *cobra.Command, args []string) error { tsvFields = append(tsvFields, i) } fI := &file.Info{ - InputReader: inputReader, - OutputFile: internal.OutputFile, - Allocate: vector.DefaultVector(func(row interface{}) (key.Key, error) { - return key.AllocateTsv(row, tsvFields...) - }, func(r io.Reader) reader.Reader { return reader.NewSeparatedValues(r, '\t') }, func(w io.Writer) writer.Writer { return writer.NewSeparatedValues(w, '\t') }), + WithHeader: internal.WithHeader, + InputReader: i.Input, + OutputFile: i.Output, + Allocate: vector.DefaultVector( + func(row interface{}) (key.Key, error) { + return key.AllocateTsv(row, tsvFields...) + }, + func(r io.Reader) (reader.Reader, error) { return reader.NewGZipSeparatedValues(r, '\t') }, func(w io.Writer) (writer.Writer, error) { + return writer.NewGZipSeparatedValues(w, '\t') + }, + ), PrintMemUsage: false, } - - // create small files with maximum 30 rows in each - chunkPaths, err := fI.CreateSortedChunks(context.Background(), internal.ChunkFolder, internal.ChunkSize, internal.MaxWorkers) - if err != nil { - return err - } - // perform a merge sort on all the chunks files. - // we sort using a buffer so we don't have to load the entire chunks when merging - err = fI.MergeSort(chunkPaths, internal.OutputBufferSize) + i.Do(func() error { + // create small files with maximum 30 rows in each + chunkPaths, err := fI.CreateSortedChunks(context.Background(), internal.ChunkFolder, internal.ChunkSize, internal.MaxWorkers) + if err != nil { + return errors.Wrap(err, "can't create sorted chunks") + } + // perform a merge sort on all the chunks files. + // we sort using a buffer so we don't have to load the entire chunks when merging + err = fI.MergeSort(chunkPaths, internal.OutputBufferSize, true) + if err != nil { + return errors.Wrap(err, "can't merge sort") + } + elapsed := time.Since(start) + logger.Infoln("It took", elapsed) + return nil + }) + err = i.Err() if err != nil { - return err + return errors.Wrap(err, "can't finish") } - elapsed := time.Since(start) - fmt.Println(elapsed) return nil } diff --git a/main_bench_test.go b/main_bench_test.go index f6515c7..47a36a5 100644 --- a/main_bench_test.go +++ b/main_bench_test.go @@ -3,12 +3,12 @@ package main_test import ( "context" "io" - "io/ioutil" "os" "path" "testing" "github.com/askiada/external-sort/file" + "github.com/askiada/external-sort/internal/rw" "github.com/askiada/external-sort/reader" "github.com/askiada/external-sort/vector" "github.com/askiada/external-sort/vector/key" @@ -18,23 +18,32 @@ import ( func BenchmarkMergeSort(b *testing.B) { filename := "test.tsv" - f, err := os.Open(filename) + ctx := context.Background() + i := rw.NewInputOutput(ctx) + err := i.SetInputReader(ctx, filename) + assert.NoError(b, err) + err = i.SetOutputWriter(ctx, "testdata/chunks/output.tsv") assert.NoError(b, err) chunkSize := 10000 bufferSize := 5000 fI := &file.Info{ - InputReader: f, - Allocate: vector.DefaultVector(key.AllocateInt, reader.NewStdScanner, func(w io.Writer) writer.Writer { return writer.NewStdWriter(w) }), - OutputFile: "testdata/chunks/output.tsv", + InputReader: i.Input, + Allocate: vector.DefaultVector(key.AllocateInt, func(r io.Reader) (reader.Reader, error) { return reader.NewStdScanner(r), nil }, func(w io.Writer) (writer.Writer, error) { return writer.NewStdWriter(w), nil }), + OutputFile: i.Output, } - chunkPaths, err := fI.CreateSortedChunks(context.Background(), "testdata/chunks", chunkSize, 100) + i.Do(func() (err error) { + chunkPaths, err := fI.CreateSortedChunks(context.Background(), "testdata/chunks", chunkSize, 100) + assert.NoError(b, err) + b.ResetTimer() + for i := 0; i < b.N; i++ { + err = fI.MergeSort(chunkPaths, bufferSize, false) + _ = err + } + return nil + }) + err = i.Err() assert.NoError(b, err) - b.ResetTimer() - for i := 0; i < b.N; i++ { - err = fI.MergeSort(chunkPaths, bufferSize) - _ = err - } - dir, err := ioutil.ReadDir("testdata/chunks") + dir, err := os.ReadDir("testdata/chunks") assert.NoError(b, err) for _, d := range dir { err = os.RemoveAll(path.Join("testdata/chunks", d.Name())) diff --git a/main_test.go b/main_test.go index 6b03fa5..b8669bf 100644 --- a/main_test.go +++ b/main_test.go @@ -5,13 +5,13 @@ import ( "context" "errors" "io" - "io/ioutil" "os" "path" "strconv" "testing" "github.com/askiada/external-sort/file" + "github.com/askiada/external-sort/internal/rw" "github.com/askiada/external-sort/reader" "github.com/askiada/external-sort/vector" "github.com/askiada/external-sort/vector/key" @@ -20,21 +20,31 @@ import ( "github.com/stretchr/testify/assert" ) -func prepareChunks(ctx context.Context, t *testing.T, allocate *vector.Allocate, filename, outputFilename string, chunkSize int) (*file.Info, []string) { +func prepareChunks(ctx context.Context, t *testing.T, allocate *vector.Allocate, filename, outputFilename string, chunkSize int, mergeSort bool, bufferSize int, withHeaders bool, dropDuplicates bool) *file.Info { t.Helper() - f, err := os.Open(filename) + i := rw.NewInputOutput(ctx) + err := i.SetInputReader(ctx, filename) + assert.NoError(t, err) + err = i.SetOutputWriter(ctx, "testdata/chunks/output.tsv") assert.NoError(t, err) fI := &file.Info{ - InputReader: f, + InputReader: i.Input, Allocate: allocate, - OutputFile: "testdata/chunks/output.tsv", + OutputFile: i.Output, + WithHeader: withHeaders, } - chunkPaths, err := fI.CreateSortedChunks(ctx, "testdata/chunks", chunkSize, 10) + i.Do(func() (err error) { + chunkPaths, err := fI.CreateSortedChunks(ctx, "testdata/chunks", chunkSize, 10) + assert.NoError(t, err) + if mergeSort { + return fI.MergeSort(chunkPaths, bufferSize, dropDuplicates) + } + return nil + }) + err = i.Err() assert.NoError(t, err) - t.Cleanup(func() { - defer f.Close() - dir, err := ioutil.ReadDir("testdata/chunks") + dir, err := os.ReadDir("testdata/chunks") assert.NoError(t, err) for _, d := range dir { err = os.RemoveAll(path.Join("testdata/chunks", d.Name())) @@ -42,7 +52,7 @@ func prepareChunks(ctx context.Context, t *testing.T, allocate *vector.Allocate, } }) - return fI, chunkPaths + return fI } func TestBasics(t *testing.T) { @@ -80,10 +90,9 @@ func TestBasics(t *testing.T) { t.Run(name+"_"+strconv.Itoa(chunkSize)+"_"+strconv.Itoa(bufferSize), func(t *testing.T) { ctx := context.Background() - allocate := vector.DefaultVector(key.AllocateInt, reader.NewStdScanner, writer.NewStdWriter) - fI, chunkPaths := prepareChunks(ctx, t, allocate, filename, outputFilename, chunkSize) - err := fI.MergeSort(chunkPaths, bufferSize) - assert.NoError(t, err) + allocate := vector.DefaultVector(key.AllocateInt, func(r io.Reader) (reader.Reader, error) { return reader.NewStdScanner(r), nil }, func(w io.Writer) (writer.Writer, error) { return writer.NewStdWriter(w), nil }) + prepareChunks(ctx, t, allocate, filename, outputFilename, chunkSize, true, bufferSize, false, false) + outputFile, err := os.Open(outputFilename) assert.NoError(t, err) outputScanner := bufio.NewScanner(outputFile) @@ -123,10 +132,124 @@ func Test100Elems(t *testing.T) { expectedErr := tc.expectedErr t.Run(name, func(t *testing.T) { ctx := context.Background() - allocate := vector.DefaultVector(key.AllocateInt, reader.NewStdScanner, writer.NewStdWriter) - fI, chunkPaths := prepareChunks(ctx, t, allocate, filename, outputFilename, 21) - err := fI.MergeSort(chunkPaths, 10) + allocate := vector.DefaultVector(key.AllocateInt, func(r io.Reader) (reader.Reader, error) { return reader.NewStdScanner(r), nil }, func(w io.Writer) (writer.Writer, error) { return writer.NewStdWriter(w), nil }) + prepareChunks(ctx, t, allocate, filename, outputFilename, 21, true, 10, false, false) + outputFile, err := os.Open(outputFilename) + assert.NoError(t, err) + outputScanner := bufio.NewScanner(outputFile) + count := 0 + for outputScanner.Scan() { + assert.Equal(t, expectedOutput[count], outputScanner.Text()) + count++ + } + assert.NoError(t, outputScanner.Err()) + assert.Equal(t, len(expectedOutput), count) + assert.True(t, errors.Is(err, expectedErr)) + outputFile.Close() + }) + } +} + +func Test100ElemsWithDuplicates(t *testing.T) { + tcs := map[string]struct { + filename string + outputFilename string + expectedErr error + expectedOutput []string + }{ + "100 elems with duplicates": { + filename: "testdata/100elems.tsv", + expectedOutput: []string{"3", "4", "5", "6", "7", "8", "9", "10", "15", "18", "21", "22", "25", "26", "27", "28", "29", "30", "31", "33", "34", "36", "37", "39", "40", "41", "42", "43", "47", "49", "50", "52", "53", "54", "55", "56", "57", "59", "60", "61", "62", "63", "67", "71", "72", "73", "74", "75", "78", "79", "80", "82", "89", "91", "92", "93", "94", "97", "99"}, + outputFilename: "testdata/chunks/output.tsv", + }, + } + + for name, tc := range tcs { + filename := tc.filename + outputFilename := tc.outputFilename + expectedOutput := tc.expectedOutput + expectedErr := tc.expectedErr + t.Run(name, func(t *testing.T) { + ctx := context.Background() + allocate := vector.DefaultVector(key.AllocateInt, func(r io.Reader) (reader.Reader, error) { return reader.NewStdScanner(r), nil }, func(w io.Writer) (writer.Writer, error) { return writer.NewStdWriter(w), nil }) + prepareChunks(ctx, t, allocate, filename, outputFilename, 21, true, 10, false, true) + outputFile, err := os.Open(outputFilename) + assert.NoError(t, err) + outputScanner := bufio.NewScanner(outputFile) + count := 0 + for outputScanner.Scan() { + assert.Equal(t, expectedOutput[count], outputScanner.Text()) + count++ + } + assert.NoError(t, outputScanner.Err()) + assert.Equal(t, len(expectedOutput), count) + assert.True(t, errors.Is(err, expectedErr)) + outputFile.Close() + }) + } +} + +func Test100ElemsWithHeaders(t *testing.T) { + tcs := map[string]struct { + filename string + outputFilename string + expectedErr error + expectedOutput []string + }{ + "100 elems with headers": { + filename: "testdata/100elemsWithHeaders.tsv", + expectedOutput: []string{"headers", "3", "4", "5", "6", "6", "7", "7", "7", "8", "8", "9", "9", "10", "10", "15", "18", "18", "18", "18", "21", "22", "22", "25", "25", "25", "25", "25", "26", "26", "27", "27", "28", "28", "29", "29", "29", "30", "30", "31", "31", "33", "33", "34", "36", "37", "39", "39", "39", "40", "41", "41", "42", "43", "43", "47", "47", "49", "50", "50", "52", "52", "53", "54", "55", "55", "55", "56", "57", "57", "59", "60", "61", "62", "63", "67", "71", "71", "72", "72", "73", "74", "75", "78", "79", "80", "80", "82", "89", "89", "89", "91", "91", "92", "92", "93", "93", "94", "97", "97", "99"}, + outputFilename: "testdata/chunks/output.tsv", + }, + } + + for name, tc := range tcs { + filename := tc.filename + outputFilename := tc.outputFilename + expectedOutput := tc.expectedOutput + expectedErr := tc.expectedErr + t.Run(name, func(t *testing.T) { + ctx := context.Background() + allocate := vector.DefaultVector(key.AllocateInt, func(r io.Reader) (reader.Reader, error) { return reader.NewStdScanner(r), nil }, func(w io.Writer) (writer.Writer, error) { return writer.NewStdWriter(w), nil }) + prepareChunks(ctx, t, allocate, filename, outputFilename, 21, true, 10, true, false) + outputFile, err := os.Open(outputFilename) assert.NoError(t, err) + outputScanner := bufio.NewScanner(outputFile) + count := 0 + for outputScanner.Scan() { + assert.Equal(t, expectedOutput[count], outputScanner.Text()) + count++ + } + assert.NoError(t, outputScanner.Err()) + assert.Equal(t, len(expectedOutput), count) + assert.True(t, errors.Is(err, expectedErr)) + outputFile.Close() + }) + } +} +func Test100ElemsWithHeadersWithDuplicates(t *testing.T) { + tcs := map[string]struct { + filename string + outputFilename string + expectedErr error + expectedOutput []string + }{ + "100 elems with headers and duplicates": { + filename: "testdata/100elemsWithHeaders.tsv", + expectedOutput: []string{"headers", "3", "4", "5", "6", "7", "8", "9", "10", "15", "18", "21", "22", "25", "26", "27", "28", "29", "30", "31", "33", "34", "36", "37", "39", "40", "41", "42", "43", "47", "49", "50", "52", "53", "54", "55", "56", "57", "59", "60", "61", "62", "63", "67", "71", "72", "73", "74", "75", "78", "79", "80", "82", "89", "91", "92", "93", "94", "97", "99"}, + outputFilename: "testdata/chunks/output.tsv", + }, + } + + for name, tc := range tcs { + filename := tc.filename + outputFilename := tc.outputFilename + expectedOutput := tc.expectedOutput + expectedErr := tc.expectedErr + t.Run(name, func(t *testing.T) { + ctx := context.Background() + allocate := vector.DefaultVector(key.AllocateInt, func(r io.Reader) (reader.Reader, error) { return reader.NewStdScanner(r), nil }, func(w io.Writer) (writer.Writer, error) { return writer.NewStdWriter(w), nil }) + prepareChunks(ctx, t, allocate, filename, outputFilename, 21, true, 10, true, true) outputFile, err := os.Open(outputFilename) assert.NoError(t, err) outputScanner := bufio.NewScanner(outputFile) @@ -176,10 +299,8 @@ func TestTsvKey(t *testing.T) { allocate := vector.DefaultVector(func(row interface{}) (key.Key, error) { return key.AllocateTsv(row, 1) - }, func(r io.Reader) reader.Reader { return reader.NewSeparatedValues(r, '\t') }, func(w io.Writer) writer.Writer { return writer.NewSeparatedValues(w, '\t') }) - fI, chunkPaths := prepareChunks(ctx, t, allocate, filename, outputFilename, 21) - err := fI.MergeSort(chunkPaths, 10) - assert.NoError(t, err) + }, func(r io.Reader) (reader.Reader, error) { return reader.NewSeparatedValues(r, '\t'), nil }, func(w io.Writer) (writer.Writer, error) { return writer.NewSeparatedValues(w, '\t'), nil }) + prepareChunks(ctx, t, allocate, filename, outputFilename, 21, true, 10, false, false) outputFile, err := os.Open(outputFilename) assert.NoError(t, err) outputScanner := bufio.NewScanner(outputFile) diff --git a/reader/gzip_separated_values.go b/reader/gzip_separated_values.go new file mode 100644 index 0000000..d38430e --- /dev/null +++ b/reader/gzip_separated_values.go @@ -0,0 +1,53 @@ +package reader + +import ( + "compress/gzip" + "encoding/csv" + "io" + + "github.com/pkg/errors" +) + +type GZipSeparatedValuesReader struct { + row []string + r *csv.Reader + gr *gzip.Reader + err error +} + +func NewGZipSeparatedValues(r io.Reader, separator rune) (*GZipSeparatedValuesReader, error) { + gr, err := gzip.NewReader(r) + if err != nil { + return nil, errors.Wrap(err, "can't create gzip reader") + } + + s := &GZipSeparatedValuesReader{ + gr: gr, + r: csv.NewReader(gr), + } + s.r.Comma = separator + return s, nil +} + +func (s *GZipSeparatedValuesReader) Next() bool { + s.row, s.err = s.r.Read() + if errors.Is(s.err, io.EOF) { + s.err = nil + s.gr.Close() + return false + } + return true +} + +func (s *GZipSeparatedValuesReader) Read() (interface{}, error) { + if s.err != nil { + return nil, s.err + } + return s.row, nil +} + +func (s *GZipSeparatedValuesReader) Err() error { + return s.err +} + +var _ Reader = &GZipSeparatedValuesReader{} diff --git a/testdata/100elemsWithHeaders.tsv b/testdata/100elemsWithHeaders.tsv new file mode 100644 index 0000000..ecfc0b9 --- /dev/null +++ b/testdata/100elemsWithHeaders.tsv @@ -0,0 +1,101 @@ +headers +5 +18 +27 +41 +6 +52 +89 +30 +39 +56 +63 +7 +22 +26 +73 +22 +55 +21 +8 +25 +40 +31 +26 +59 +57 +82 +7 +72 +4 +25 +47 +71 +61 +80 +91 +79 +25 +25 +43 +97 +25 +75 +50 +72 +29 +92 +80 +54 +89 +55 +28 +93 +43 +92 +47 +42 +71 +97 +49 +8 +93 +91 +7 +41 +74 +53 +18 +89 +50 +30 +3 +34 +62 +33 +55 +94 +10 +52 +39 +28 +60 +57 +78 +37 +67 +18 +33 +27 +9 +15 +99 +29 +10 +36 +6 +31 +39 +9 +18 +29 \ No newline at end of file diff --git a/vector/key/int_key.go b/vector/key/int_key.go index 7ffb83d..5479894 100644 --- a/vector/key/int_key.go +++ b/vector/key/int_key.go @@ -25,3 +25,7 @@ func AllocateInt(row interface{}) (Key, error) { func (k *Int) Less(other Key) bool { return k.value < other.(*Int).value } + +func (k *Int) Equal(other Key) bool { + return k.value == other.(*Int).value +} diff --git a/vector/key/key.go b/vector/key/key.go index eb05ce1..2eda041 100644 --- a/vector/key/key.go +++ b/vector/key/key.go @@ -1,6 +1,7 @@ package key type Key interface { + Equal(v2 Key) bool // Less returns wether the key is smaller than v2 Less(v2 Key) bool } diff --git a/vector/key/string_key.go b/vector/key/string_key.go index b98669c..d4452e5 100644 --- a/vector/key/string_key.go +++ b/vector/key/string_key.go @@ -14,6 +14,10 @@ func (k *String) Less(other Key) bool { return k.value < other.(*String).value } +func (k *String) Equal(other Key) bool { + return k.value == other.(*String).value +} + type UpperString struct { value string } @@ -25,3 +29,6 @@ func AllocateUpperString(line string) (Key, error) { func (k *UpperString) Less(other Key) bool { return k.value < other.(*UpperString).value } +func (k *UpperString) Equal(other Key) bool { + return k.value == other.(*UpperString).value +} diff --git a/vector/slice_vector.go b/vector/slice_vector.go index c31b0fe..ba52d75 100644 --- a/vector/slice_vector.go +++ b/vector/slice_vector.go @@ -41,6 +41,11 @@ func (v *SliceVec) PushBack(row interface{}) error { return nil } +func (v *SliceVec) PushFrontNoKey(row interface{}) error { + v.s = append([]*Element{{Row: row}}, v.s...) + return nil +} + func (v *SliceVec) Sort() { sort.Slice(v.s, func(i, j int) bool { return Less(v.Get(i), v.Get(j)) diff --git a/vector/vector.go b/vector/vector.go index 0e8916f..8b4d803 100644 --- a/vector/vector.go +++ b/vector/vector.go @@ -12,12 +12,12 @@ import ( type Allocate struct { Vector func(int, func(row interface{}) (key.Key, error)) Vector - FnReader func(r io.Reader) reader.Reader - FnWriter func(w io.Writer) writer.Writer + FnReader func(r io.Reader) (reader.Reader, error) + FnWriter func(w io.Writer) (writer.Writer, error) Key func(elem interface{}) (key.Key, error) } -func DefaultVector(allocateKey func(elem interface{}) (key.Key, error), fnReader func(r io.Reader) reader.Reader, fnWr func(w io.Writer) writer.Writer) *Allocate { +func DefaultVector(allocateKey func(elem interface{}) (key.Key, error), fnReader func(r io.Reader) (reader.Reader, error), fnWr func(w io.Writer) (writer.Writer, error)) *Allocate { return &Allocate{ FnReader: fnReader, FnWriter: fnWr, @@ -31,6 +31,8 @@ type Vector interface { Get(i int) *Element // PushBack Add item at the end PushBack(row interface{}) error + // PushFront Add item at the beginning + PushFrontNoKey(row interface{}) error // FrontShift Remove the first element FrontShift() // Len Length of the Vector @@ -46,7 +48,10 @@ func (a *Allocate) Dump(v Vector, filename string) error { if err != nil { return errors.Errorf("failed creating file: %s", err) } - datawriter := a.FnWriter(file) + datawriter, err := a.FnWriter(file) + if err != nil { + return errors.Errorf("failed creating writer: %s", err) + } for i := 0; i < v.Len(); i++ { err = datawriter.Write(v.Get(i).Row) if err != nil { From 6263d66bd5d6a81da5a3af5c066d5baff25ae40c Mon Sep 17 00:00:00 2001 From: askiada <25521495+askiada@users.noreply.github.com> Date: Sun, 2 Oct 2022 15:39:17 +0200 Subject: [PATCH 03/16] add gzip --- writer/gzip_separated_values.go | 46 +++++++++++++++++++++++++++++++++ 1 file changed, 46 insertions(+) create mode 100644 writer/gzip_separated_values.go diff --git a/writer/gzip_separated_values.go b/writer/gzip_separated_values.go new file mode 100644 index 0000000..81ffdea --- /dev/null +++ b/writer/gzip_separated_values.go @@ -0,0 +1,46 @@ +package writer + +import ( + "compress/gzip" + "encoding/csv" + "io" + + "github.com/pkg/errors" +) + +type GZipSeparatedValuesWriter struct { + w *csv.Writer + gw *gzip.Writer + withHeader bool +} + +func NewGZipSeparatedValues(w io.Writer, separator rune) (Writer, error) { + gw := gzip.NewWriter(w) + s := &GZipSeparatedValuesWriter{ + gw: gw, + w: csv.NewWriter(gw), + } + s.w.Comma = separator + return s, nil +} + +func (s *GZipSeparatedValuesWriter) Write(elem interface{}) error { + line, ok := elem.([]string) + if !ok { + return errors.Errorf("can't converte interface{} to []string: %+v", elem) + } + err := s.w.Write(line) + if err != nil { + return errors.Wrap(err, "can't write line") + } + return nil +} + +func (s *GZipSeparatedValuesWriter) Close() error { + defer s.gw.Close() + s.w.Flush() + if s.w.Error() != nil { + return errors.Wrap(s.w.Error(), "can't close writer") + } + return nil +} From 4d9c369d0ba15eeb6e5183a18b04d2282f59c0ea Mon Sep 17 00:00:00 2001 From: askiada <25521495+askiada@users.noreply.github.com> Date: Sun, 2 Oct 2022 18:32:54 +0200 Subject: [PATCH 04/16] add shuffle command --- Makefile | 10 ++- file/shuffle.go | 128 ++++++++++++++++++++++++++++++++ internal/env.go | 4 + main.go | 96 +++++++++++++++++++----- main_bench_test.go | 2 +- main_test.go | 153 +++++++++++++++++++++++++++++++++++++-- reader/std_scanner.go | 76 +++++++++++++++++-- testdata/100elems.tsv.gz | Bin 0 -> 172 bytes vector/key/int_key.go | 24 ++++++ writer/std_writer.go | 49 +++++++++++++ 10 files changed, 510 insertions(+), 32 deletions(-) create mode 100644 file/shuffle.go create mode 100644 testdata/100elems.tsv.gz diff --git a/Makefile b/Makefile index acd6107..47dcb1c 100644 --- a/Makefile +++ b/Makefile @@ -17,9 +17,13 @@ test: test_race: go test -race ./... -.PHONY: run -run: build - ./bin/external-sort +.PHONY: run_sort +run_sort: build + ./bin/external-sort sort + +.PHONY: run_shuffle +run_shuffle: build + ./bin/external-sort shuffle .PHONY: build build: diff --git a/file/shuffle.go b/file/shuffle.go new file mode 100644 index 0000000..8cd4db2 --- /dev/null +++ b/file/shuffle.go @@ -0,0 +1,128 @@ +package file + +import ( + "context" + "io" + "math/rand" + "path" + "strconv" + "sync" + + "github.com/askiada/external-sort/file/batchingchannels" + "github.com/askiada/external-sort/reader" + "github.com/askiada/external-sort/vector" + "github.com/askiada/external-sort/vector/key" + "github.com/askiada/external-sort/writer" + "github.com/pkg/errors" +) + +// CreateSortedChunks Scan a file and divide it into small sorted chunks. +// Store all the chunks in a folder an returns all the paths. +func (f *Info) Shuffle(ctx context.Context, chunkFolder string, dumpSize int, maxWorkers int64, k int, seed int64, isGzip bool) ([]string, error) { + fn := "scan and shuffle and dump" + if dumpSize <= 0 { + return nil, errors.Wrap(errors.New("dump size must be greater than 0"), fn) + } + + if f.PrintMemUsage && f.mu == nil { + f.mu = &MemUsage{} + } + if f.Allocate != nil { + return nil, errors.New("allocate should not be defined when shuffling") + } + f.Allocate = vector.DefaultVector( + func(row interface{}) (key.Key, error) { + return key.AllocateIntFromSlice(row, 0) + }, + func(r io.Reader) (reader.Reader, error) { + return reader.NewStdScanner(r, isGzip) + }, + func(w io.Writer) (writer.Writer, error) { + return writer.NewStdSliceWriter(w, false, isGzip), nil + }, + ) + + err := clearChunkFolder(chunkFolder) + if err != nil { + return nil, errors.Wrap(err, fn) + } + + inputReader, err := f.Allocate.FnReader(f.InputReader) + if err != nil { + return nil, errors.Wrap(err, fn) + } + countRows := 0 + chunkPaths := []string{} + + mu := sync.Mutex{} + r := rand.New(rand.NewSource(seed)) + batchChan := batchingchannels.NewBatchingChannel(ctx, f.Allocate, maxWorkers, dumpSize) + batchChan.G.Go(func() error { + for inputReader.Next() { + if f.PrintMemUsage { + f.mu.Collect() + } + row, err := inputReader.Read() + if err != nil { + return errors.Wrap(err, fn) + } + if f.WithHeader && f.headers == nil { + f.headers = []string{"##!!##", row.(string)} + } else { + newRow := []string{strconv.FormatInt(r.Int63(), 10), row.(string)} + batchChan.In() <- newRow + } + countRows++ + } + batchChan.Close() + if inputReader.Err() != nil { + return errors.Wrap(inputReader.Err(), fn) + } + return nil + }) + + chunkIdx := 0 + err = batchChan.ProcessOut(func(v vector.Vector) error { + mu.Lock() + chunkIdx++ + chunkPath := path.Join(chunkFolder, "chunk_"+strconv.Itoa(chunkIdx)+".tsv") + logger.Infoln("Created chunk", chunkPath) + mu.Unlock() + v.Sort() + if f.WithHeader { + err = v.PushFrontNoKey(f.headers) + if err != nil { + return err + } + } + err := f.Allocate.Dump(v, chunkPath) + if err != nil { + return err + } + mu.Lock() + chunkPaths = append(chunkPaths, chunkPath) + mu.Unlock() + return nil + }) + if err != nil { + return nil, errors.Wrap(err, fn) + } + f.totalRows = countRows + + f.Allocate = vector.DefaultVector( + func(row interface{}) (key.Key, error) { + return key.AllocateIntFromSlice(row, 0) + }, + func(r io.Reader) (reader.Reader, error) { + return reader.NewStdSliceScanner(r, isGzip) + }, + func(w io.Writer) (writer.Writer, error) { + return writer.NewStdSliceWriter(w, true, isGzip), nil + }, + ) + err = f.MergeSort(chunkPaths, k, false) + if err != nil { + return nil, errors.Wrap(err, fn) + } + return chunkPaths, nil +} diff --git a/internal/env.go b/internal/env.go index fc847b7..8fb0490 100644 --- a/internal/env.go +++ b/internal/env.go @@ -19,6 +19,8 @@ const ( S3RegionName = "s3_region" S3RetryMaxAttemptsName = "s3_retry_max_attempts" + + IsGzipName = "is_gzip" ) // Environment variables. @@ -34,6 +36,7 @@ var ( S3Region string S3RetryMaxAttempts int + IsGzip bool ) func init() { @@ -49,4 +52,5 @@ func init() { viper.SetDefault(S3RegionName, "eu-west-1") viper.SetDefault(S3RetryMaxAttemptsName, 10) + viper.SetDefault(IsGzipName, false) } diff --git a/main.go b/main.go index a440bbe..fdda9c4 100644 --- a/main.go +++ b/main.go @@ -21,34 +21,60 @@ import ( var logger = logrus.StandardLogger() -func main() { - rootCmd := &cobra.Command{ - Use: "external-sort", - Short: "Perform an external sorting on an input file", - RunE: rootRun, +type command struct { + rootCmd *cobra.Command + sortCmd *cobra.Command + shuffleCmd *cobra.Command +} + +func newCommand() *command { + root := &command{ + rootCmd: &cobra.Command{ + Use: "external", + Short: "Perform an external task on an input file", + }, + sortCmd: &cobra.Command{ + Use: "sort", + Short: "Perform an external sorting on an input file", + RunE: sortRun, + }, + shuffleCmd: &cobra.Command{ + Use: "shuffle", + Short: "Perform an external sorting on an input file", + RunE: shuffleRun, + }, } - rootCmd.PersistentFlags().BoolVarP(&internal.WithHeader, internal.WithHeaderName, "i", viper.GetBool(internal.WithHeaderName), "Input file has headers.") - rootCmd.PersistentFlags().StringSliceVarP(&internal.InputFiles, internal.InputFileNames, "i", viper.GetStringSlice(internal.InputFileNames), "input file path.") - rootCmd.PersistentFlags().StringVarP(&internal.OutputFile, internal.OutputFileName, "o", viper.GetString(internal.OutputFileName), "output file path.") - rootCmd.PersistentFlags().StringVarP(&internal.ChunkFolder, internal.ChunkFolderName, "c", viper.GetString(internal.ChunkFolderName), "chunk folder.") + root.rootCmd.PersistentFlags().BoolVarP(&internal.WithHeader, internal.WithHeaderName, "e", viper.GetBool(internal.WithHeaderName), "Input file has headers.") + root.rootCmd.PersistentFlags().StringSliceVarP(&internal.InputFiles, internal.InputFileNames, "i", viper.GetStringSlice(internal.InputFileNames), "input file path.") + root.rootCmd.PersistentFlags().StringVarP(&internal.OutputFile, internal.OutputFileName, "o", viper.GetString(internal.OutputFileName), "output file path.") + root.rootCmd.PersistentFlags().StringVarP(&internal.ChunkFolder, internal.ChunkFolderName, "c", viper.GetString(internal.ChunkFolderName), "chunk folder.") - rootCmd.PersistentFlags().IntVarP(&internal.ChunkSize, internal.ChunkSizeName, "s", viper.GetInt(internal.ChunkSizeName), "chunk size.") - rootCmd.PersistentFlags().Int64VarP(&internal.MaxWorkers, internal.MaxWorkersName, "w", viper.GetInt64(internal.MaxWorkersName), "max worker.") - rootCmd.PersistentFlags().IntVarP(&internal.OutputBufferSize, internal.OutputBufferSizeName, "b", viper.GetInt(internal.OutputBufferSizeName), "output buffer size.") - rootCmd.PersistentFlags().StringSliceVarP(&internal.TsvFields, internal.TsvFieldsName, "t", viper.GetStringSlice(internal.TsvFieldsName), "") + root.rootCmd.PersistentFlags().IntVarP(&internal.ChunkSize, internal.ChunkSizeName, "s", viper.GetInt(internal.ChunkSizeName), "chunk size.") + root.rootCmd.PersistentFlags().Int64VarP(&internal.MaxWorkers, internal.MaxWorkersName, "w", viper.GetInt64(internal.MaxWorkersName), "max worker.") + root.rootCmd.PersistentFlags().IntVarP(&internal.OutputBufferSize, internal.OutputBufferSizeName, "b", viper.GetInt(internal.OutputBufferSizeName), "output buffer size.") + root.sortCmd.PersistentFlags().StringSliceVarP(&internal.TsvFields, internal.TsvFieldsName, "t", viper.GetStringSlice(internal.TsvFieldsName), "") - rootCmd.Flags().StringVar(&internal.S3Region, internal.S3RegionName, viper.GetString(internal.S3RegionName), "the bucket region") - rootCmd.Flags().IntVar(&internal.S3RetryMaxAttempts, internal.S3RetryMaxAttemptsName, viper.GetInt(internal.S3RetryMaxAttemptsName), "the number of retries per S3 request before failing") + root.rootCmd.Flags().StringVar(&internal.S3Region, internal.S3RegionName, viper.GetString(internal.S3RegionName), "the bucket region") + root.rootCmd.Flags().IntVar(&internal.S3RetryMaxAttempts, internal.S3RetryMaxAttemptsName, viper.GetInt(internal.S3RetryMaxAttemptsName), "the number of retries per S3 request before failing") + + root.shuffleCmd.PersistentFlags().BoolVarP(&internal.IsGzip, internal.IsGzipName, "t", viper.GetBool(internal.IsGzipName), "") logger.Infoln("Input files", internal.InputFiles) logger.Infoln("With header", internal.WithHeader) logger.Infoln("Output file", internal.OutputFile) logger.Infoln("Chunk folder", internal.ChunkFolder) logger.Infoln("TSV Fields", internal.TsvFields) - cobra.CheckErr(rootCmd.Execute()) + + root.rootCmd.AddCommand(root.sortCmd, root.shuffleCmd) + return root } -func rootRun(cmd *cobra.Command, args []string) error { +func main() { + root := newCommand() + cobra.CheckErr(root.rootCmd.Execute()) +} + +func sortRun(cmd *cobra.Command, args []string) error { start := time.Now() ctx := context.Background() i := rw.NewInputOutput(ctx) @@ -104,3 +130,39 @@ func rootRun(cmd *cobra.Command, args []string) error { } return nil } + +func shuffleRun(cmd *cobra.Command, args []string) error { + start := time.Now() + ctx := context.Background() + i := rw.NewInputOutput(ctx) + err := i.SetInputReader(ctx, internal.InputFiles...) + if err != nil { + return err + } + err = i.SetOutputWriter(ctx, internal.OutputFile) + if err != nil { + return err + } + + fI := &file.Info{ + WithHeader: internal.WithHeader, + InputReader: i.Input, + OutputFile: i.Output, + PrintMemUsage: false, + } + i.Do(func() error { + // create small files with maximum 30 rows in each + _, err := fI.Shuffle(context.Background(), internal.ChunkFolder, internal.ChunkSize, internal.MaxWorkers, internal.OutputBufferSize, time.Now().Unix(), internal.IsGzip) + if err != nil { + return errors.Wrap(err, "can't create shuflled chunks") + } + elapsed := time.Since(start) + logger.Infoln("It took", elapsed) + return nil + }) + err = i.Err() + if err != nil { + return errors.Wrap(err, "can't finish") + } + return nil +} diff --git a/main_bench_test.go b/main_bench_test.go index 47a36a5..0b686c1 100644 --- a/main_bench_test.go +++ b/main_bench_test.go @@ -28,7 +28,7 @@ func BenchmarkMergeSort(b *testing.B) { bufferSize := 5000 fI := &file.Info{ InputReader: i.Input, - Allocate: vector.DefaultVector(key.AllocateInt, func(r io.Reader) (reader.Reader, error) { return reader.NewStdScanner(r), nil }, func(w io.Writer) (writer.Writer, error) { return writer.NewStdWriter(w), nil }), + Allocate: vector.DefaultVector(key.AllocateInt, func(r io.Reader) (reader.Reader, error) { return reader.NewStdScanner(r, false) }, func(w io.Writer) (writer.Writer, error) { return writer.NewStdWriter(w), nil }), OutputFile: i.Output, } i.Do(func() (err error) { diff --git a/main_test.go b/main_test.go index b8669bf..63c755a 100644 --- a/main_test.go +++ b/main_test.go @@ -90,7 +90,7 @@ func TestBasics(t *testing.T) { t.Run(name+"_"+strconv.Itoa(chunkSize)+"_"+strconv.Itoa(bufferSize), func(t *testing.T) { ctx := context.Background() - allocate := vector.DefaultVector(key.AllocateInt, func(r io.Reader) (reader.Reader, error) { return reader.NewStdScanner(r), nil }, func(w io.Writer) (writer.Writer, error) { return writer.NewStdWriter(w), nil }) + allocate := vector.DefaultVector(key.AllocateInt, func(r io.Reader) (reader.Reader, error) { return reader.NewStdScanner(r, false) }, func(w io.Writer) (writer.Writer, error) { return writer.NewStdWriter(w), nil }) prepareChunks(ctx, t, allocate, filename, outputFilename, chunkSize, true, bufferSize, false, false) outputFile, err := os.Open(outputFilename) @@ -132,7 +132,7 @@ func Test100Elems(t *testing.T) { expectedErr := tc.expectedErr t.Run(name, func(t *testing.T) { ctx := context.Background() - allocate := vector.DefaultVector(key.AllocateInt, func(r io.Reader) (reader.Reader, error) { return reader.NewStdScanner(r), nil }, func(w io.Writer) (writer.Writer, error) { return writer.NewStdWriter(w), nil }) + allocate := vector.DefaultVector(key.AllocateInt, func(r io.Reader) (reader.Reader, error) { return reader.NewStdScanner(r, false) }, func(w io.Writer) (writer.Writer, error) { return writer.NewStdWriter(w), nil }) prepareChunks(ctx, t, allocate, filename, outputFilename, 21, true, 10, false, false) outputFile, err := os.Open(outputFilename) assert.NoError(t, err) @@ -171,7 +171,7 @@ func Test100ElemsWithDuplicates(t *testing.T) { expectedErr := tc.expectedErr t.Run(name, func(t *testing.T) { ctx := context.Background() - allocate := vector.DefaultVector(key.AllocateInt, func(r io.Reader) (reader.Reader, error) { return reader.NewStdScanner(r), nil }, func(w io.Writer) (writer.Writer, error) { return writer.NewStdWriter(w), nil }) + allocate := vector.DefaultVector(key.AllocateInt, func(r io.Reader) (reader.Reader, error) { return reader.NewStdScanner(r, false) }, func(w io.Writer) (writer.Writer, error) { return writer.NewStdWriter(w), nil }) prepareChunks(ctx, t, allocate, filename, outputFilename, 21, true, 10, false, true) outputFile, err := os.Open(outputFilename) assert.NoError(t, err) @@ -210,7 +210,7 @@ func Test100ElemsWithHeaders(t *testing.T) { expectedErr := tc.expectedErr t.Run(name, func(t *testing.T) { ctx := context.Background() - allocate := vector.DefaultVector(key.AllocateInt, func(r io.Reader) (reader.Reader, error) { return reader.NewStdScanner(r), nil }, func(w io.Writer) (writer.Writer, error) { return writer.NewStdWriter(w), nil }) + allocate := vector.DefaultVector(key.AllocateInt, func(r io.Reader) (reader.Reader, error) { return reader.NewStdScanner(r, false) }, func(w io.Writer) (writer.Writer, error) { return writer.NewStdWriter(w), nil }) prepareChunks(ctx, t, allocate, filename, outputFilename, 21, true, 10, true, false) outputFile, err := os.Open(outputFilename) assert.NoError(t, err) @@ -248,7 +248,7 @@ func Test100ElemsWithHeadersWithDuplicates(t *testing.T) { expectedErr := tc.expectedErr t.Run(name, func(t *testing.T) { ctx := context.Background() - allocate := vector.DefaultVector(key.AllocateInt, func(r io.Reader) (reader.Reader, error) { return reader.NewStdScanner(r), nil }, func(w io.Writer) (writer.Writer, error) { return writer.NewStdWriter(w), nil }) + allocate := vector.DefaultVector(key.AllocateInt, func(r io.Reader) (reader.Reader, error) { return reader.NewStdScanner(r, false) }, func(w io.Writer) (writer.Writer, error) { return writer.NewStdWriter(w), nil }) prepareChunks(ctx, t, allocate, filename, outputFilename, 21, true, 10, true, true) outputFile, err := os.Open(outputFilename) assert.NoError(t, err) @@ -316,3 +316,146 @@ func TestTsvKey(t *testing.T) { }) } } +func prepareChunksShuffle(ctx context.Context, t *testing.T, filename, outputFilename string, chunkSize int, mergeSort bool, bufferSize int, withHeaders bool, dropDuplicates, isGzip bool) *file.Info { + t.Helper() + i := rw.NewInputOutput(ctx) + err := i.SetInputReader(ctx, filename) + assert.NoError(t, err) + err = i.SetOutputWriter(ctx, outputFilename) + assert.NoError(t, err) + fI := &file.Info{ + InputReader: i.Input, + OutputFile: i.Output, + WithHeader: withHeaders, + } + i.Do(func() (err error) { + _, err = fI.Shuffle(ctx, "testdata/chunks", chunkSize, 10, bufferSize, 13, isGzip) + assert.NoError(t, err) + return nil + }) + err = i.Err() + assert.NoError(t, err) + t.Cleanup(func() { + dir, err := os.ReadDir("testdata/chunks") + assert.NoError(t, err) + for _, d := range dir { + err = os.RemoveAll(path.Join("testdata/chunks", d.Name())) + assert.NoError(t, err) + } + }) + + return fI +} +func Test100ElemsShuffle(t *testing.T) { + tcs := map[string]struct { + filename string + outputFilename string + expectedErr error + expectedOutput []string + }{ + "100 elems": { + filename: "testdata/100elems.tsv", + expectedOutput: []string{"3", "4", "5", "6", "6", "7", "7", "7", "8", "8", "9", "9", "10", "10", "15", "18", "18", "18", "18", "21", "22", "22", "25", "25", "25", "25", "25", "26", "26", "27", "27", "28", "28", "29", "29", "29", "30", "30", "31", "31", "33", "33", "34", "36", "37", "39", "39", "39", "40", "41", "41", "42", "43", "43", "47", "47", "49", "50", "50", "52", "52", "53", "54", "55", "55", "55", "56", "57", "57", "59", "60", "61", "62", "63", "67", "71", "71", "72", "72", "73", "74", "75", "78", "79", "80", "80", "82", "89", "89", "89", "91", "91", "92", "92", "93", "93", "94", "97", "97", "99"}, + outputFilename: "testdata/chunks/output.tsv", + }, + } + + for name, tc := range tcs { + filename := tc.filename + outputFilename := tc.outputFilename + expectedOutput := tc.expectedOutput + expectedErr := tc.expectedErr + t.Run(name, func(t *testing.T) { + ctx := context.Background() + prepareChunksShuffle(ctx, t, filename, outputFilename, 21, false, 10, false, false, false) + outputFile, err := os.Open(outputFilename) + assert.NoError(t, err) + outputScanner := bufio.NewScanner(outputFile) + count := 0 + for outputScanner.Scan() { + assert.Equal(t, expectedOutput[count], outputScanner.Text()) + count++ + } + assert.NoError(t, outputScanner.Err()) + assert.Equal(t, len(expectedOutput), count) + assert.True(t, errors.Is(err, expectedErr)) + outputFile.Close() + }) + } +} + +func Test100ElemsShuffleWithHeaders(t *testing.T) { + tcs := map[string]struct { + filename string + outputFilename string + expectedErr error + expectedOutput []string + }{ + "100 elems with headers": { + filename: "testdata/100elemsWithHeaders.tsv", + expectedOutput: []string{"headers", "3", "4", "5", "6", "6", "7", "7", "7", "8", "8", "9", "9", "10", "10", "15", "18", "18", "18", "18", "21", "22", "22", "25", "25", "25", "25", "25", "26", "26", "27", "27", "28", "28", "29", "29", "29", "30", "30", "31", "31", "33", "33", "34", "36", "37", "39", "39", "39", "40", "41", "41", "42", "43", "43", "47", "47", "49", "50", "50", "52", "52", "53", "54", "55", "55", "55", "56", "57", "57", "59", "60", "61", "62", "63", "67", "71", "71", "72", "72", "73", "74", "75", "78", "79", "80", "80", "82", "89", "89", "89", "91", "91", "92", "92", "93", "93", "94", "97", "97", "99"}, + outputFilename: "testdata/chunks/output.tsv", + }, + } + + for name, tc := range tcs { + filename := tc.filename + outputFilename := tc.outputFilename + expectedOutput := tc.expectedOutput + expectedErr := tc.expectedErr + t.Run(name, func(t *testing.T) { + ctx := context.Background() + prepareChunksShuffle(ctx, t, filename, outputFilename, 21, false, 10, true, false, false) + outputFile, err := os.Open(outputFilename) + assert.NoError(t, err) + outputScanner := bufio.NewScanner(outputFile) + count := 0 + for outputScanner.Scan() { + assert.Equal(t, expectedOutput[count], outputScanner.Text()) + count++ + } + assert.NoError(t, outputScanner.Err()) + assert.Equal(t, len(expectedOutput), count) + assert.True(t, errors.Is(err, expectedErr)) + outputFile.Close() + }) + } +} + +func Test100ElemsShuffleGzip(t *testing.T) { + tcs := map[string]struct { + filename string + outputFilename string + expectedErr error + expectedOutput []string + }{ + "100 elems with headers": { + filename: "testdata/100elems.tsv.gz", + expectedOutput: []string{"headers", "3", "4", "5", "6", "6", "7", "7", "7", "8", "8", "9", "9", "10", "10", "15", "18", "18", "18", "18", "21", "22", "22", "25", "25", "25", "25", "25", "26", "26", "27", "27", "28", "28", "29", "29", "29", "30", "30", "31", "31", "33", "33", "34", "36", "37", "39", "39", "39", "40", "41", "41", "42", "43", "43", "47", "47", "49", "50", "50", "52", "52", "53", "54", "55", "55", "55", "56", "57", "57", "59", "60", "61", "62", "63", "67", "71", "71", "72", "72", "73", "74", "75", "78", "79", "80", "80", "82", "89", "89", "89", "91", "91", "92", "92", "93", "93", "94", "97", "97", "99"}, + outputFilename: "testdata/chunks/output.tsv.gz", + }, + } + + for name, tc := range tcs { + filename := tc.filename + outputFilename := tc.outputFilename + expectedOutput := tc.expectedOutput + expectedErr := tc.expectedErr + t.Run(name, func(t *testing.T) { + ctx := context.Background() + prepareChunksShuffle(ctx, t, filename, outputFilename, 21, false, 10, true, false, true) + outputFile, err := os.Open(outputFilename) + assert.NoError(t, err) + outputScanner := bufio.NewScanner(outputFile) + count := 0 + for outputScanner.Scan() { + assert.Equal(t, expectedOutput[count], outputScanner.Text()) + count++ + } + assert.NoError(t, outputScanner.Err()) + assert.Equal(t, len(expectedOutput), count) + assert.True(t, errors.Is(err, expectedErr)) + outputFile.Close() + }) + } +} diff --git a/reader/std_scanner.go b/reader/std_scanner.go index 7610ffd..4c1fb22 100644 --- a/reader/std_scanner.go +++ b/reader/std_scanner.go @@ -2,22 +2,45 @@ package reader import ( "bufio" + "compress/gzip" "io" + "strings" + + "github.com/pkg/errors" + "github.com/sirupsen/logrus" ) +var logger = logrus.StandardLogger() + type StdScanner struct { - r *bufio.Scanner + r *bufio.Scanner + gr *gzip.Reader } -func NewStdScanner(r io.Reader) Reader { - s := &StdScanner{ - r: bufio.NewScanner(r), +func NewStdScanner(r io.Reader, isGzip bool) (Reader, error) { + var newR *bufio.Scanner + s := &StdScanner{} + if isGzip { + gr, err := gzip.NewReader(r) + if err != nil { + return nil, errors.Wrap(err, "can't create gzip reader") + } + s.gr = gr + newR = bufio.NewScanner(gr) + } else { + newR = bufio.NewScanner(r) } - return s + s.r = newR + logger.Infoln("Created standard scanner") + return s, nil } func (s *StdScanner) Next() bool { - return s.r.Scan() + next := s.r.Scan() + if !next && s.gr != nil { + s.gr.Close() + } + return next } func (s *StdScanner) Read() (interface{}, error) { return s.r.Text(), nil @@ -25,3 +48,44 @@ func (s *StdScanner) Read() (interface{}, error) { func (s *StdScanner) Err() error { return s.r.Err() } + +type StdSliceScanner struct { + r *bufio.Scanner + gr *gzip.Reader +} + +func NewStdSliceScanner(r io.Reader, isGzip bool) (Reader, error) { + var newR *bufio.Scanner + s := &StdSliceScanner{} + if isGzip { + gr, err := gzip.NewReader(r) + if err != nil { + return nil, errors.Wrap(err, "can't create gzip reader") + } + s.gr = gr + newR = bufio.NewScanner(gr) + } else { + newR = bufio.NewScanner(r) + } + s.r = newR + return s, nil +} + +func (s *StdSliceScanner) Next() bool { + next := s.r.Scan() + if !next && s.gr != nil { + s.gr.Close() + } + return next +} +func (s *StdSliceScanner) Read() (interface{}, error) { + line := s.r.Text() + before, after, found := strings.Cut(line, "##!!##") + if !found { + return nil, errors.New("can't cut row") + } + return []string{before, after}, nil +} +func (s *StdSliceScanner) Err() error { + return s.r.Err() +} diff --git a/testdata/100elems.tsv.gz b/testdata/100elems.tsv.gz new file mode 100644 index 0000000000000000000000000000000000000000..cf1b6ad830475fb70fb7d76329fe7287f43bfe61 GIT binary patch literal 172 zcmV;d08{@TiwFp-4me`~12Hf#Wo%__b1rmqb^sla%M}1I2mjrAXrqe()iSavC$NXxEU5U6xN`p{q+S+B{pdjreanuHBM{x%6nMy)&($lRUz0 z7!#JEm*xK$|4EZin5 Date: Sun, 2 Oct 2022 18:34:05 +0200 Subject: [PATCH 05/16] add env to shuffle --- env.list | 16 +++++++++++----- env_sort.list | 13 +++++++++++++ 2 files changed, 24 insertions(+), 5 deletions(-) create mode 100644 env_sort.list diff --git a/env.list b/env.list index cbbeaa3..8045cc0 100644 --- a/env.list +++ b/env.list @@ -1,7 +1,13 @@ -INPUT_PATH=/Users/alex/Desktop/Projects/Blokur/Repo/external-sort/rec_sample.tsv -OUTPUT_PATH=./output.tsv +INPUT_PATHS=./output.tsv.gz +OUTPUT_PATH=./output_shuffled.tsv.gz CHUNK_FOLDER=./data/chunks/ CHUNK_SIZE=1000000 -MAX_WORKERS=10 -OUTPUT_BUFFER_SIZE=1000 -TSV_FIELDS=2 4 \ No newline at end of file +MAX_WORKERS=40 +OUTPUT_BUFFER_SIZE=1000000 +IS_GZIP=true + +S3_REGION=eu-west-1 +S3_BUCKET=blokur-data +S3_RETRY_MAX_ATTEMPTS=10 + +WITH_HEADER=true \ No newline at end of file diff --git a/env_sort.list b/env_sort.list new file mode 100644 index 0000000..55d2dc6 --- /dev/null +++ b/env_sort.list @@ -0,0 +1,13 @@ +INPUT_PATHS=s3://blokur-data/ml-title/remote/1/f15c2cf2e3ab46589419e6441b64e3bd/artifacts/input/word2vec/refine/recordings.0.tsv.gz s3://blokur-data/ml-title/remote/1/f15c2cf2e3ab46589419e6441b64e3bd/artifacts/input/word2vec/refine/recordings.1.tsv.gz s3://blokur-data/ml-title/remote/1/f15c2cf2e3ab46589419e6441b64e3bd/artifacts/input/word2vec/refine/recordings.2.tsv.gz s3://blokur-data/ml-title/remote/1/f15c2cf2e3ab46589419e6441b64e3bd/artifacts/input/word2vec/refine/recordings.3.tsv.gz s3://blokur-data/ml-title/remote/1/f15c2cf2e3ab46589419e6441b64e3bd/artifacts/input/word2vec/refine/recordings.4.tsv.gz s3://blokur-data/ml-title/remote/1/f15c2cf2e3ab46589419e6441b64e3bd/artifacts/input/word2vec/refine/recordings.5.tsv.gz s3://blokur-data/ml-title/remote/1/f15c2cf2e3ab46589419e6441b64e3bd/artifacts/input/word2vec/refine/recordings.6.tsv.gz s3://blokur-data/ml-title/remote/1/f15c2cf2e3ab46589419e6441b64e3bd/artifacts/input/word2vec/refine/recordings.7.tsv.gz s3://blokur-data/ml-title/remote/1/f15c2cf2e3ab46589419e6441b64e3bd/artifacts/input/word2vec/refine/recordings.8.tsv.gz s3://blokur-data/ml-title/remote/1/f15c2cf2e3ab46589419e6441b64e3bd/artifacts/input/word2vec/refine/recordings.9.tsv.gz s3://blokur-data/ml-title/remote/1/f15c2cf2e3ab46589419e6441b64e3bd/artifacts/input/word2vec/refine/recordings.10.tsv.gz s3://blokur-data/ml-title/remote/1/f15c2cf2e3ab46589419e6441b64e3bd/artifacts/input/word2vec/refine/recordings.11.tsv.gz s3://blokur-data/ml-title/remote/1/f15c2cf2e3ab46589419e6441b64e3bd/artifacts/input/word2vec/refine/recordings.12.tsv.gz s3://blokur-data/ml-title/remote/1/f15c2cf2e3ab46589419e6441b64e3bd/artifacts/input/word2vec/refine/recordings.13.tsv.gz s3://blokur-data/ml-title/remote/1/f15c2cf2e3ab46589419e6441b64e3bd/artifacts/input/word2vec/refine/recordings.14.tsv.gz s3://blokur-data/ml-title/remote/1/f15c2cf2e3ab46589419e6441b64e3bd/artifacts/input/word2vec/refine/recordings.15.tsv.gz s3://blokur-data/ml-title/remote/1/f15c2cf2e3ab46589419e6441b64e3bd/artifacts/input/word2vec/refine/recordings.16.tsv.gz s3://blokur-data/ml-title/remote/1/f15c2cf2e3ab46589419e6441b64e3bd/artifacts/input/word2vec/refine/recordings.17.tsv.gz s3://blokur-data/ml-title/remote/1/f15c2cf2e3ab46589419e6441b64e3bd/artifacts/input/word2vec/refine/recordings.18.tsv.gz s3://blokur-data/ml-title/remote/1/f15c2cf2e3ab46589419e6441b64e3bd/artifacts/input/word2vec/refine/recordings.19.tsv.gz s3://blokur-data/ml-title/remote/1/f15c2cf2e3ab46589419e6441b64e3bd/artifacts/input/word2vec/refine/recordings.20.tsv.gz s3://blokur-data/ml-title/remote/1/f15c2cf2e3ab46589419e6441b64e3bd/artifacts/input/word2vec/refine/recordings.21.tsv.gz s3://blokur-data/ml-title/remote/1/f15c2cf2e3ab46589419e6441b64e3bd/artifacts/input/word2vec/refine/recordings.22.tsv.gz s3://blokur-data/ml-title/remote/1/f15c2cf2e3ab46589419e6441b64e3bd/artifacts/input/word2vec/refine/recordings.23.tsv.gz s3://blokur-data/ml-title/remote/1/f15c2cf2e3ab46589419e6441b64e3bd/artifacts/input/word2vec/refine/recordings.24.tsv.gz s3://blokur-data/ml-title/remote/1/f15c2cf2e3ab46589419e6441b64e3bd/artifacts/input/word2vec/refine/recordings.25.tsv.gz s3://blokur-data/ml-title/remote/1/f15c2cf2e3ab46589419e6441b64e3bd/artifacts/input/word2vec/refine/recordings.26.tsv.gz s3://blokur-data/ml-title/remote/1/f15c2cf2e3ab46589419e6441b64e3bd/artifacts/input/word2vec/refine/recordings.27.tsv.gz s3://blokur-data/ml-title/remote/1/f15c2cf2e3ab46589419e6441b64e3bd/artifacts/input/word2vec/refine/recordings.28.tsv.gz s3://blokur-data/ml-title/remote/1/f15c2cf2e3ab46589419e6441b64e3bd/artifacts/input/word2vec/refine/recordings.29.tsv.gz s3://blokur-data/ml-title/remote/1/f15c2cf2e3ab46589419e6441b64e3bd/artifacts/input/word2vec/refine/recordings.30.tsv.gz s3://blokur-data/ml-title/remote/1/f15c2cf2e3ab46589419e6441b64e3bd/artifacts/input/word2vec/refine/recordings.31.tsv.gz s3://blokur-data/ml-title/remote/1/f15c2cf2e3ab46589419e6441b64e3bd/artifacts/input/word2vec/refine/recordings.32.tsv.gz s3://blokur-data/ml-title/remote/1/f15c2cf2e3ab46589419e6441b64e3bd/artifacts/input/word2vec/refine/recordings.33.tsv.gz s3://blokur-data/ml-title/remote/1/f15c2cf2e3ab46589419e6441b64e3bd/artifacts/input/word2vec/refine/recordings.34.tsv.gz s3://blokur-data/ml-title/remote/1/f15c2cf2e3ab46589419e6441b64e3bd/artifacts/input/word2vec/refine/recordings.35.tsv.gz s3://blokur-data/ml-title/remote/1/f15c2cf2e3ab46589419e6441b64e3bd/artifacts/input/word2vec/refine/recordings.36.tsv.gz s3://blokur-data/ml-title/remote/1/f15c2cf2e3ab46589419e6441b64e3bd/artifacts/input/word2vec/refine/recordings.37.tsv.gz s3://blokur-data/ml-title/remote/1/f15c2cf2e3ab46589419e6441b64e3bd/artifacts/input/word2vec/refine/recordings.38.tsv.gz s3://blokur-data/ml-title/remote/1/f15c2cf2e3ab46589419e6441b64e3bd/artifacts/input/word2vec/refine/recordings.39.tsv.gz s3://blokur-data/ml-title/remote/1/f15c2cf2e3ab46589419e6441b64e3bd/artifacts/input/word2vec/refine/recordings.40.tsv.gz s3://blokur-data/ml-title/remote/1/f15c2cf2e3ab46589419e6441b64e3bd/artifacts/input/word2vec/refine/recordings.41.tsv.gz s3://blokur-data/ml-title/remote/1/f15c2cf2e3ab46589419e6441b64e3bd/artifacts/input/word2vec/refine/recordings.42.tsv.gz s3://blokur-data/ml-title/remote/1/f15c2cf2e3ab46589419e6441b64e3bd/artifacts/input/word2vec/refine/recordings.43.tsv.gz s3://blokur-data/ml-title/remote/1/f15c2cf2e3ab46589419e6441b64e3bd/artifacts/input/word2vec/refine/recordings.44.tsv.gz s3://blokur-data/ml-title/remote/1/f15c2cf2e3ab46589419e6441b64e3bd/artifacts/input/word2vec/refine/recordings.45.tsv.gz s3://blokur-data/ml-title/remote/1/f15c2cf2e3ab46589419e6441b64e3bd/artifacts/input/word2vec/refine/recordings.46.tsv.gz s3://blokur-data/ml-title/remote/1/f15c2cf2e3ab46589419e6441b64e3bd/artifacts/input/word2vec/refine/recordings.47.tsv.gz s3://blokur-data/ml-title/remote/1/f15c2cf2e3ab46589419e6441b64e3bd/artifacts/input/word2vec/refine/recordings.48.tsv.gz s3://blokur-data/ml-title/remote/1/f15c2cf2e3ab46589419e6441b64e3bd/artifacts/input/word2vec/refine/recordings.49.tsv.gz s3://blokur-data/ml-title/remote/1/f15c2cf2e3ab46589419e6441b64e3bd/artifacts/input/word2vec/refine/recordings.50.tsv.gz s3://blokur-data/ml-title/remote/1/f15c2cf2e3ab46589419e6441b64e3bd/artifacts/input/word2vec/refine/recordings.51.tsv.gz s3://blokur-data/ml-title/remote/1/f15c2cf2e3ab46589419e6441b64e3bd/artifacts/input/word2vec/refine/recordings.52.tsv.gz s3://blokur-data/ml-title/remote/1/f15c2cf2e3ab46589419e6441b64e3bd/artifacts/input/word2vec/refine/recordings.53.tsv.gz s3://blokur-data/ml-title/remote/1/f15c2cf2e3ab46589419e6441b64e3bd/artifacts/input/word2vec/refine/recordings.54.tsv.gz s3://blokur-data/ml-title/remote/1/f15c2cf2e3ab46589419e6441b64e3bd/artifacts/input/word2vec/refine/recordings.55.tsv.gz s3://blokur-data/ml-title/remote/1/f15c2cf2e3ab46589419e6441b64e3bd/artifacts/input/word2vec/refine/recordings.56.tsv.gz s3://blokur-data/ml-title/remote/1/f15c2cf2e3ab46589419e6441b64e3bd/artifacts/input/word2vec/refine/recordings.57.tsv.gz s3://blokur-data/ml-title/remote/1/f15c2cf2e3ab46589419e6441b64e3bd/artifacts/input/word2vec/refine/recordings.58.tsv.gz s3://blokur-data/ml-title/remote/1/f15c2cf2e3ab46589419e6441b64e3bd/artifacts/input/word2vec/refine/recordings.59.tsv.gz +OUTPUT_PATH=./output.tsv.gz +CHUNK_FOLDER=./data/chunks/ +CHUNK_SIZE=1000000 +MAX_WORKERS=30 +OUTPUT_BUFFER_SIZE=100000 +TSV_FIELDS=1 + +S3_REGION=eu-west-1 +S3_BUCKET=blokur-data +S3_RETRY_MAX_ATTEMPTS=10 + +WITH_HEADER=true \ No newline at end of file From 9ba122bd6a07a470dbfa1b5f234f27f67ecd0fa7 Mon Sep 17 00:00:00 2001 From: Skiada Alexandre <25521495+askiada@users.noreply.github.com> Date: Tue, 4 Oct 2022 14:56:25 +0100 Subject: [PATCH 06/16] repair incorrect headers chunk --- file/chunk.go | 5 +++++ main.go | 17 +++++++++++------ writer/gzip_separated_values.go | 5 ++--- 3 files changed, 18 insertions(+), 9 deletions(-) diff --git a/file/chunk.go b/file/chunk.go index 380a0cf..0d908fb 100644 --- a/file/chunk.go +++ b/file/chunk.go @@ -51,6 +51,11 @@ func (c *chunks) new(chunkPath string, allocate *vector.Allocate, size int, with if err != nil { return err } + + if withHeader { + reader.Next() + } + elem := &chunkInfo{ filename: chunkPath, file: f, diff --git a/main.go b/main.go index fdda9c4..9b37f11 100644 --- a/main.go +++ b/main.go @@ -59,12 +59,6 @@ func newCommand() *command { root.shuffleCmd.PersistentFlags().BoolVarP(&internal.IsGzip, internal.IsGzipName, "t", viper.GetBool(internal.IsGzipName), "") - logger.Infoln("Input files", internal.InputFiles) - logger.Infoln("With header", internal.WithHeader) - logger.Infoln("Output file", internal.OutputFile) - logger.Infoln("Chunk folder", internal.ChunkFolder) - logger.Infoln("TSV Fields", internal.TsvFields) - root.rootCmd.AddCommand(root.sortCmd, root.shuffleCmd) return root } @@ -75,6 +69,12 @@ func main() { } func sortRun(cmd *cobra.Command, args []string) error { + logger.Infoln("Input files", internal.InputFiles) + logger.Infoln("With header", internal.WithHeader) + logger.Infoln("Output file", internal.OutputFile) + logger.Infoln("Chunk folder", internal.ChunkFolder) + logger.Infoln("TSV Fields", internal.TsvFields) + start := time.Now() ctx := context.Background() i := rw.NewInputOutput(ctx) @@ -132,6 +132,11 @@ func sortRun(cmd *cobra.Command, args []string) error { } func shuffleRun(cmd *cobra.Command, args []string) error { + logger.Infoln("Input files", internal.InputFiles) + logger.Infoln("With header", internal.WithHeader) + logger.Infoln("Output file", internal.OutputFile) + logger.Infoln("Chunk folder", internal.ChunkFolder) + logger.Infoln("GZip file", internal.IsGzip) start := time.Now() ctx := context.Background() i := rw.NewInputOutput(ctx) diff --git a/writer/gzip_separated_values.go b/writer/gzip_separated_values.go index 81ffdea..63e6064 100644 --- a/writer/gzip_separated_values.go +++ b/writer/gzip_separated_values.go @@ -9,9 +9,8 @@ import ( ) type GZipSeparatedValuesWriter struct { - w *csv.Writer - gw *gzip.Writer - withHeader bool + w *csv.Writer + gw *gzip.Writer } func NewGZipSeparatedValues(w io.Writer, separator rune) (Writer, error) { From 6699985892f84f27bb2c92dfeeefe93111049117 Mon Sep 17 00:00:00 2001 From: askiada <25521495+askiada@users.noreply.github.com> Date: Mon, 8 May 2023 04:16:17 +0200 Subject: [PATCH 07/16] lint --- .golangci.yml | 235 +++++++----- bucket/contract.go | 4 +- bucket/errors.go | 6 +- bucket/s3.go | 45 ++- file/batchingchannels/batching_channel.go | 54 ++- .../batchingchannels/batching_channel_test.go | 74 ++-- file/chunk.go | 20 +- file/file.go | 18 +- file/shuffle.go | 2 +- go.mod | 88 ++--- go.sum | 347 ++++++------------ internal/env.go | 4 +- internal/rw/rw.go | 8 +- main.go | 2 +- main_test.go | 34 +- reader/gzip_separated_values_test.go | 48 +++ reader/std_scanner.go | 4 + vector/key/string_key.go | 1 + 18 files changed, 509 insertions(+), 485 deletions(-) create mode 100644 reader/gzip_separated_values_test.go diff --git a/.golangci.yml b/.golangci.yml index fc414e3..e5f2e1a 100644 --- a/.golangci.yml +++ b/.golangci.yml @@ -1,106 +1,153 @@ linters-settings: - govet: - settings: - printf: - funcs: - - (github.com/golangci/golangci-lint/pkg/logutils.Log).Infof - - (github.com/golangci/golangci-lint/pkg/logutils.Log).Warnf - - (github.com/golangci/golangci-lint/pkg/logutils.Log).Errorf - - (github.com/golangci/golangci-lint/pkg/logutils.Log).Fatalf - enable: - - fieldalignment - # golint: - # min-confidence: 0 - gocyclo: - min-complexity: 15 - maligned: - suggest-new: true - goconst: - min-len: 2 - min-occurrences: 2 - # misspell: # disabled as it was breaking interfaces with FinaliZe - # locale: UK - lll: - line-length: 140 - goimports: - local-prefixes: github.com/golangci/golangci-lint - gocritic: - enabled-tags: - - diagnostic - - experimental - - opinionated - - performance - - style - funlen: - lines: 100 - statements: 50 - godot: - capital: true - unparam: - check-exported: true + funlen: + lines: 80 + statements: 50 + goconst: + min-len: 2 + min-occurrences: 2 + gocritic: + enabled-tags: + - diagnostic + - experimental + - opinionated + - performance + - style + gocyclo: + min-complexity: 15 + godot: + capital: true + goimports: + local-prefixes: github.com/golangci/golangci-lint + govet: + settings: + printf: + funcs: + - (github.com/golangci/golangci-lint/pkg/logutils.Log).Infof + - (github.com/golangci/golangci-lint/pkg/logutils.Log).Warnf + - (github.com/golangci/golangci-lint/pkg/logutils.Log).Errorf + - (github.com/golangci/golangci-lint/pkg/logutils.Log).Fatalf + enable: + - fieldalignment + maligned: + suggest-new: true + misspell: + locale: UK + lll: + line-length: 140 + unparam: + check-exported: true issues: - # Excluding configuration per-path, per-linter, per-text and per-source - exclude-rules: - - path: _test\.go - linters: - - gosec # security check is not impoerant in tests - - dupl # we usualy duplicate code in tests - - bodyclose - - unparam - fix: true + # Excluding configuration per-path, per-linter, per-text and per-source + exclude-rules: + - path: _test\.go + linters: + - gosec # security check is not important in tests + - dupl # we usually duplicate code in tests + - bodyclose + - unparam + - errcheck + - govet + - gocritic + - goconst + - forcetypeassert + - wrapcheck + fix: true + exclude-use-default: false run: - skip-dirs: - - model - - tmp - - bin - - scripts + skip-dirs: + - tmp + - bin + - scripts - tests: true - build-tags: - - integration + tests: true + build-tags: + - integration linters: - disable-all: true - fast: true - enable: - - asciicheck - - bodyclose - - deadcode - - dogsled - - depguard - - dupl - - errorlint - - gocognit - - goconst - - gocritic - - gocyclo - - godot - - godox - - golint - - goprintffuncname - - gosec - - gosimple - - govet - # - misspell # disabled as it was breaking interfaces with FinaliZe - - nakedret - - nestif - - prealloc - - rowserrcheck - - scopelint - - staticcheck - - stylecheck - - unconvert - # - unparam # Too many false positives on Task interface implementation. - - unused - - whitespace - # - wrapcheck - - tparallel + disable-all: true + fast: true + enable: + - asciicheck + - bidichk + - bodyclose + - bodyclose + - containedctx + - contextcheck + - cyclop + - decorder + - depguard + - dogsled + - dupl + - durationcheck + - errcheck + - errchkjson + - errname + - errorlint + - exhaustive + - exportloopref + - forbidigo + - forcetypeassert + - funlen + - gocognit + - goconst + - gocritic + - gocyclo + - godot + - godox + - gofmt + - gofumpt + - goheader + - goimports + - gomnd + - gomoddirectives + - gomodguard + - goprintffuncname + - gosec + - gosec + - gosimple + - gosimple + - govet + - govet + - grouper + - importas + - ineffassign + - ireturn + - lll + - maintidx + - makezero + - misspell + - nakedret + - nestif + - nilerr + - nilnil + - nlreturn + - noctx + - nolintlint + - prealloc + - predeclared + - promlinter + - revive + - rowserrcheck + - sqlclosecheck + - staticcheck + - staticcheck + - stylecheck + - tagliatelle + - tenv + - thelper + - tparallel + - typecheck + - unconvert + - unparam + - unused + - varnamelen + - wastedassign + - whitespace + - wrapcheck # golangci.com configuration # https://github.com/golangci/golangci/wiki/Configuration service: - golangci-lint-version: 1.38.x - prepare: - - echo "here I can run custom commands, but no preparation needed for this repo" + golangci-lint-version: 1.52.x diff --git a/bucket/contract.go b/bucket/contract.go index e8f8450..9c51477 100644 --- a/bucket/contract.go +++ b/bucket/contract.go @@ -31,10 +31,12 @@ func PartBodyMaxRetries(r int) ConfigFunc { } } +const mbConversion = 1024 * 1024 + // Buffer is the amount of memory in MB to use for buffering the data. func Buffer(buffer int) ConfigFunc { return func(s *S3) { - s.bufferLen = buffer * 1024 * 1024 + s.bufferLen = buffer * mbConversion } } diff --git a/bucket/errors.go b/bucket/errors.go index 63b153e..7347995 100644 --- a/bucket/errors.go +++ b/bucket/errors.go @@ -2,7 +2,5 @@ package bucket import "errors" -var ( - // ErrInvalidInput is returned when the input is invalid. - ErrInvalidInput = errors.New("invalid input") -) +// ErrInvalidInput is returned when the input is invalid. +var ErrInvalidInput = errors.New("invalid input") diff --git a/bucket/s3.go b/bucket/s3.go index 6183d60..d6cf190 100644 --- a/bucket/s3.go +++ b/bucket/s3.go @@ -25,48 +25,56 @@ type S3 struct { partBodyMaxRetries int } +const ( + defaultBufferLen = 1024 + defaultMaxRetries = 10 + defaultPartBodyMaxRetries = 3 +) + // New returns an instance of the S3 struct. func New(ctx context.Context, cfg ...ConfigFunc) (*S3, error) { - s := &S3{ + s3Val := &S3{ region: "eu-west-1", - bufferLen: 1024, - maxRetries: 10, - partBodyMaxRetries: 3, + bufferLen: defaultBufferLen, + maxRetries: defaultMaxRetries, + partBodyMaxRetries: defaultPartBodyMaxRetries, } for _, c := range cfg { - c(s) + c(s3Val) } - if s.region == "" { + if s3Val.region == "" { return nil, errors.Wrap(ErrInvalidInput, "region") } - if s.bufferLen <= 0 { + if s3Val.bufferLen <= 0 { return nil, errors.Wrap(ErrInvalidInput, "buffer length") } - if s.s3Client == nil { + if s3Val.s3Client == nil { cfg, err := config.LoadDefaultConfig(ctx, - config.WithRegion(s.region), - config.WithRetryMaxAttempts(s.maxRetries), + config.WithRegion(s3Val.region), + config.WithRetryMaxAttempts(s3Val.maxRetries), ) if err != nil { return nil, errors.New("can't create aws config") } - s.s3Client = s3.NewFromConfig(cfg) + s3Val.s3Client = s3.NewFromConfig(cfg) } - return s, nil + + return s3Val, nil } // Upload reads from the reader and uploads it to the S3 bucket with the // filename key. -func (s *S3) Upload(ctx context.Context, r io.Reader, bucket string, key string) error { +func (s *S3) Upload(ctx context.Context, reader io.Reader, bucket, key string) error { uploader := manager.NewUploader(s.s3Client, func(u *manager.Uploader) { u.BufferProvider = manager.NewBufferedReadSeekerWriteToPool(s.bufferLen) }) _, err := uploader.Upload(ctx, &s3.PutObjectInput{ Bucket: aws.String(bucket), Key: aws.String(key), - Body: r, + Body: reader, }) + return errors.Wrap(err, "upload failed") } @@ -75,7 +83,7 @@ type seqWriterAt struct { progressFunc func(n int) } -func (s *seqWriterAt) WriteAt(p []byte, offset int64) (n int, err error) { +func (s *seqWriterAt) WriteAt(p []byte, _ int64) (n int, err error) { n, err = s.w.Write(p) if s.progressFunc != nil { s.progressFunc(n) @@ -83,21 +91,22 @@ func (s *seqWriterAt) WriteAt(p []byte, offset int64) (n int, err error) { return n, errors.Wrap(err, "can't write bytes at offset") } -type DownloadFileInfo struct { +// S3FileInfo describe the path to a file on S3. +type S3FileInfo struct { Bucket string Key string } // Download downloads the file from the S3 bucket with the filename key and // writes it to the writer. -func (s *S3) Download(ctx context.Context, w io.Writer, filesinfo ...*DownloadFileInfo) error { +func (s *S3) Download(ctx context.Context, writer io.Writer, filesinfo ...*S3FileInfo) error { downloader := manager.NewDownloader(s.s3Client, func(d *manager.Downloader) { d.PartBodyMaxRetries = s.partBodyMaxRetries d.PartSize = int64(s.bufferLen) // we need to force this to be a sequential download. d.Concurrency = 1 }) - ww := &seqWriterAt{w, nil} + ww := &seqWriterAt{writer, nil} for _, fileinfo := range filesinfo { _, err := downloader.Download(ctx, ww, &s3.GetObjectInput{ Bucket: aws.String(fileinfo.Bucket), diff --git a/file/batchingchannels/batching_channel.go b/file/batchingchannels/batching_channel.go index 2f575cb..24246a8 100644 --- a/file/batchingchannels/batching_channel.go +++ b/file/batchingchannels/batching_channel.go @@ -4,45 +4,44 @@ import ( "context" "github.com/askiada/external-sort/vector" + "github.com/pkg/errors" "golang.org/x/sync/errgroup" - "golang.org/x/sync/semaphore" ) // BatchingChannel implements the Channel interface, with the change that instead of producing individual elements // on Out(), it batches together the entire internal buffer each time. Trying to construct an unbuffered batching channel // will panic, that configuration is not supported (and provides no benefit over an unbuffered NativeChannel). type BatchingChannel struct { - input chan interface{} - output chan vector.Vector - buffer vector.Vector - allocate *vector.Allocate - G *errgroup.Group - sem *semaphore.Weighted - dCtx context.Context - size int - maxWorker int64 + input chan interface{} + output chan vector.Vector + buffer vector.Vector + allocate *vector.Allocate + G *errgroup.Group + internalContext context.Context //nolint //containedcontext + size int + maxWorker int } -func NewBatchingChannel(ctx context.Context, allocate *vector.Allocate, maxWorker int64, size int) *BatchingChannel { +func NewBatchingChannel(ctx context.Context, allocate *vector.Allocate, maxWorker, size int) *BatchingChannel { if size == 0 { panic("channels: BatchingChannel does not support unbuffered behaviour") } if size < 0 { panic("channels: invalid negative size in NewBatchingChannel") } - g, dCtx := errgroup.WithContext(ctx) - ch := &BatchingChannel{ - input: make(chan interface{}), - output: make(chan vector.Vector), - size: size, - allocate: allocate, - maxWorker: maxWorker, - G: g, - sem: semaphore.NewWeighted(maxWorker), - dCtx: dCtx, + errGrp, errGrpContext := errgroup.WithContext(ctx) + errGrp.SetLimit(maxWorker) + bChan := &BatchingChannel{ + input: make(chan interface{}), + output: make(chan vector.Vector), + size: size, + allocate: allocate, + maxWorker: maxWorker, + G: errGrp, + internalContext: errGrpContext, } - go ch.batchingBuffer() - return ch + go bChan.batchingBuffer() + return bChan } func (ch *BatchingChannel) In() chan<- interface{} { @@ -58,18 +57,14 @@ func (ch *BatchingChannel) Out() <-chan vector.Vector { func (ch *BatchingChannel) ProcessOut(f func(vector.Vector) error) error { for val := range ch.Out() { - if err := ch.sem.Acquire(ch.dCtx, 1); err != nil { - return err - } val := val ch.G.Go(func() error { - defer ch.sem.Release(1) return f(val) }) } err := ch.G.Wait() if err != nil { - return err + return errors.Wrap(err, "one of the task failed") } return nil } @@ -94,13 +89,14 @@ func (ch *BatchingChannel) batchingBuffer() { err := ch.buffer.PushBack(row) if err != nil { ch.G.Go(func() error { - return err + return errors.Wrap(err, "can't push back row") }) } } else { if ch.buffer.Len() > 0 { ch.output <- ch.buffer } + break } if ch.buffer.Len() == ch.size { diff --git a/file/batchingchannels/batching_channel_test.go b/file/batchingchannels/batching_channel_test.go index 7330ed0..af3cfa4 100644 --- a/file/batchingchannels/batching_channel_test.go +++ b/file/batchingchannels/batching_channel_test.go @@ -14,11 +14,11 @@ import ( "github.com/stretchr/testify/assert" ) -type Int struct { +type intKey struct { value int } -func AllocateInt(row interface{}) (key.Key, error) { +func allocateInt(row interface{}) (key.Key, error) { line, ok := row.(string) if !ok { return nil, errors.Errorf("can't convert interface{} to string: %+v", row) @@ -27,40 +27,42 @@ func AllocateInt(row interface{}) (key.Key, error) { if err != nil { return nil, err } - return &Int{num}, nil + return &intKey{num}, nil } -func (k *Int) Get() int { +func (k *intKey) Get() int { return k.value } -func (k *Int) Less(other key.Key) bool { - return k.value < other.(*Int).value +func (k *intKey) Less(other key.Key) bool { + return k.value < other.(*intKey).value } -func (k *Int) Equal(other key.Key) bool { - return k.value == other.(*Int).value + +func (k *intKey) Equal(other key.Key) bool { + return k.value == other.(*intKey).value } -func testBatches(t *testing.T, ch *batchingchannels.BatchingChannel) { +func testBatches(t *testing.T, bChan *batchingchannels.BatchingChannel) { + t.Helper() maxI := 10000 expectedSum := (maxI - 1) * maxI / 2 - wg := &sync.WaitGroup{} - wgInput := &sync.WaitGroup{} + wgrp := &sync.WaitGroup{} + wgrpInput := &sync.WaitGroup{} maxIn := 100 - wgInput.Add(maxIn) - for j := 0; j < maxIn; j++ { + wgrpInput.Add(maxIn) + for idx := 0; idx < maxIn; idx++ { go func(j int) { - defer wgInput.Done() + defer wgrpInput.Done() for i := maxI / maxIn * j; i < maxI*(j+1)/maxIn; i++ { - ch.In() <- strconv.Itoa(i) + bChan.In() <- strconv.Itoa(i) } - }(j) + }(idx) } go func() { - wgInput.Wait() - ch.Close() + wgrpInput.Wait() + bChan.Close() }() got := make(chan *vector.Element, maxI) @@ -70,13 +72,13 @@ func testBatches(t *testing.T, ch *batchingchannels.BatchingChannel) { go func() { defer wgSum.Done() for g := range got { - gotSum += g.Key.(*Int).Get() + gotSum += g.Key.(*intKey).Get() } }() - wg.Add(1) + wgrp.Add(1) go func() { - defer wg.Done() - err := ch.ProcessOut(func(val vector.Vector) error { + defer wgrp.Done() + err := bChan.ProcessOut(func(val vector.Vector) error { for i := 0; i < val.Len(); i++ { val := val.Get(i) got <- val @@ -88,42 +90,42 @@ func testBatches(t *testing.T, ch *batchingchannels.BatchingChannel) { panic(err) } }() - wg.Wait() + wgrp.Wait() close(got) wgSum.Wait() assert.Equal(t, expectedSum, gotSum) } func TestBatchingChannel(t *testing.T) { - allocate := vector.DefaultVector(AllocateInt, nil, nil) - ch := batchingchannels.NewBatchingChannel(context.Background(), allocate, 2, 50) - testBatches(t, ch) + allocate := vector.DefaultVector(allocateInt, nil, nil) + bChan := batchingchannels.NewBatchingChannel(context.Background(), allocate, 2, 50) + testBatches(t, bChan) - ch = batchingchannels.NewBatchingChannel(context.Background(), allocate, 2, 3) - testBatches(t, ch) + bChan = batchingchannels.NewBatchingChannel(context.Background(), allocate, 2, 3) + testBatches(t, bChan) - ch = batchingchannels.NewBatchingChannel(context.Background(), allocate, 2, 1) - testChannelConcurrentAccessors(t, "batching channel", ch) + bChan = batchingchannels.NewBatchingChannel(context.Background(), allocate, 2, 1) + testChannelConcurrentAccessors(t, bChan) } func TestBatchingChannelCap(t *testing.T) { - allocate := vector.DefaultVector(AllocateInt, nil, nil) + allocate := vector.DefaultVector(allocateInt, nil, nil) ch := batchingchannels.NewBatchingChannel(context.Background(), allocate, 2, 5) if ch.Cap() != 5 { t.Error("incorrect capacity on infinite channel") } } -func testChannelConcurrentAccessors(t *testing.T, name string, ch *batchingchannels.BatchingChannel) { +func testChannelConcurrentAccessors(_ *testing.T, bChan *batchingchannels.BatchingChannel) { // no asserts here, this is just for the race detector's benefit - go ch.Len() - go ch.Cap() + go bChan.Len() + go bChan.Cap() go func() { - ch.In() <- "" + bChan.In() <- "" }() go func() { - <-ch.Out() + <-bChan.Out() }() } diff --git a/file/chunk.go b/file/chunk.go index 0d908fb..accc16a 100644 --- a/file/chunk.go +++ b/file/chunk.go @@ -21,18 +21,22 @@ type chunkInfo struct { // pullSubset Add to vector the specified number of elements. // It stops if there is no elements left to add. func (c *chunkInfo) pullSubset(size int) (err error) { - i := 0 - for i < size && c.reader.Next() { + elemIdx := 0 + for elemIdx < size && c.reader.Next() { row, err := c.reader.Read() if err != nil { - return errors.Wrap(err, "") + return errors.Wrap(err, "can't read chunk") } - c.buffer.PushBack(row) - i++ + err = c.buffer.PushBack(row) + if err != nil { + return errors.Wrap(err, "can't push back row") + } + elemIdx++ } if c.reader.Err() != nil { - return c.reader.Err() + return errors.Wrap(c.reader.Err(), "chunk reader encountered an error") } + return nil } @@ -41,7 +45,7 @@ type chunks struct { list []*chunkInfo } -// new Create a new chunk and initialize it. +// new Create a new chunk and initialise it. func (c *chunks) new(chunkPath string, allocate *vector.Allocate, size int, withHeader bool) error { f, err := os.Open(chunkPath) if err != nil { @@ -122,7 +126,7 @@ func (c *chunks) moveFirstChunkToCorrectIndex() { pos := sort.Search(len(c.list), func(i int) bool { return !vector.Less(c.list[i].buffer.Get(0), elem.buffer.Get(0)) }) - // TODO: c.list = c.list[1:] and the following line create an unecessary allocation. + // TODO: c.list = c.list[1:] and the following line create an unnecessary allocation. c.list = append(c.list[:pos], append([]*chunkInfo{elem}, c.list[pos:]...)...) } diff --git a/file/file.go b/file/file.go index 074a4e0..11f9906 100644 --- a/file/file.go +++ b/file/file.go @@ -3,10 +3,9 @@ package file import ( "context" "io" - "sync" - "path" "strconv" + "sync" "github.com/askiada/external-sort/file/batchingchannels" "github.com/askiada/external-sort/vector" @@ -32,10 +31,9 @@ type Info struct { // CreateSortedChunks Scan a file and divide it into small sorted chunks. // Store all the chunks in a folder an returns all the paths. -func (f *Info) CreateSortedChunks(ctx context.Context, chunkFolder string, dumpSize int, maxWorkers int64) ([]string, error) { - fn := "scan and sort and dump" +func (f *Info) CreateSortedChunks(ctx context.Context, chunkFolder string, dumpSize, maxWorkers int) ([]string, error) { if dumpSize <= 0 { - return nil, errors.Wrap(errors.New("dump size must be greater than 0"), fn) + return nil, errors.New("dump size must be greater than 0") } if f.PrintMemUsage && f.mu == nil { @@ -44,12 +42,12 @@ func (f *Info) CreateSortedChunks(ctx context.Context, chunkFolder string, dumpS err := clearChunkFolder(chunkFolder) if err != nil { - return nil, errors.Wrap(err, fn) + return nil, errors.Wrap(err, "can't clear chunk folder") } inputReader, err := f.Allocate.FnReader(f.InputReader) if err != nil { - return nil, errors.Wrap(err, fn) + return nil, errors.Wrap(err, "can't get input reader") } count_rows := 0 chunkPaths := []string{} @@ -64,7 +62,7 @@ func (f *Info) CreateSortedChunks(ctx context.Context, chunkFolder string, dumpS } row, err := inputReader.Read() if err != nil { - return errors.Wrap(err, fn) + return errors.Wrap(err, "can't read from input reader") } if f.WithHeader && f.headers == nil { f.headers = row @@ -75,7 +73,7 @@ func (f *Info) CreateSortedChunks(ctx context.Context, chunkFolder string, dumpS } batchChan.Close() if inputReader.Err() != nil { - return errors.Wrap(inputReader.Err(), fn) + return errors.Wrap(inputReader.Err(), "input reader encountered an error") } return nil }) @@ -104,7 +102,7 @@ func (f *Info) CreateSortedChunks(ctx context.Context, chunkFolder string, dumpS return nil }) if err != nil { - return nil, errors.Wrap(err, fn) + return nil, errors.Wrap(err, "can't process batching channel") } f.totalRows = count_rows return chunkPaths, nil diff --git a/file/shuffle.go b/file/shuffle.go index 8cd4db2..643a971 100644 --- a/file/shuffle.go +++ b/file/shuffle.go @@ -18,7 +18,7 @@ import ( // CreateSortedChunks Scan a file and divide it into small sorted chunks. // Store all the chunks in a folder an returns all the paths. -func (f *Info) Shuffle(ctx context.Context, chunkFolder string, dumpSize int, maxWorkers int64, k int, seed int64, isGzip bool) ([]string, error) { +func (f *Info) Shuffle(ctx context.Context, chunkFolder string, dumpSize, maxWorkers, k int, seed int64, isGzip bool) ([]string, error) { fn := "scan and shuffle and dump" if dumpSize <= 0 { return nil, errors.Wrap(errors.New("dump size must be greater than 0"), fn) diff --git a/go.mod b/go.mod index 36e9033..f7256f6 100644 --- a/go.mod +++ b/go.mod @@ -1,63 +1,63 @@ module github.com/askiada/external-sort -go 1.17 +go 1.20 require ( - github.com/aws/aws-sdk-go-v2 v1.16.16 - github.com/aws/aws-sdk-go-v2/config v1.17.8 - github.com/aws/aws-sdk-go-v2/feature/s3/manager v1.11.34 - github.com/aws/aws-sdk-go-v2/service/s3 v1.27.11 - github.com/cheggaaa/pb/v3 v3.0.8 + github.com/aws/aws-sdk-go-v2 v1.18.0 + github.com/aws/aws-sdk-go-v2/config v1.18.23 + github.com/aws/aws-sdk-go-v2/feature/s3/manager v1.11.65 + github.com/aws/aws-sdk-go-v2/service/s3 v1.33.1 + github.com/cheggaaa/pb/v3 v3.1.2 github.com/pkg/errors v0.9.1 - github.com/pkg/sftp v1.13.4 + github.com/pkg/sftp v1.13.5 github.com/sirupsen/logrus v1.9.0 - github.com/spf13/cobra v1.2.1 - github.com/spf13/viper v1.8.1 - github.com/stretchr/testify v1.7.0 - golang.org/x/crypto v0.0.0-20220210151621-f4118a5b28e2 - golang.org/x/sync v0.0.0-20210220032951-036812b2e83c + github.com/spf13/cobra v1.7.0 + github.com/spf13/viper v1.15.0 + github.com/stretchr/testify v1.8.2 + golang.org/x/crypto v0.8.0 + golang.org/x/sync v0.2.0 ) require ( github.com/VividCortex/ewma v1.2.0 // indirect - github.com/aws/aws-sdk-go-v2/aws/protocol/eventstream v1.4.8 // indirect - github.com/aws/aws-sdk-go-v2/credentials v1.12.21 // indirect - github.com/aws/aws-sdk-go-v2/feature/ec2/imds v1.12.17 // indirect - github.com/aws/aws-sdk-go-v2/internal/configsources v1.1.23 // indirect - github.com/aws/aws-sdk-go-v2/internal/endpoints/v2 v2.4.17 // indirect - github.com/aws/aws-sdk-go-v2/internal/ini v1.3.24 // indirect - github.com/aws/aws-sdk-go-v2/internal/v4a v1.0.14 // indirect - github.com/aws/aws-sdk-go-v2/service/internal/accept-encoding v1.9.9 // indirect - github.com/aws/aws-sdk-go-v2/service/internal/checksum v1.1.18 // indirect - github.com/aws/aws-sdk-go-v2/service/internal/presigned-url v1.9.17 // indirect - github.com/aws/aws-sdk-go-v2/service/internal/s3shared v1.13.17 // indirect - github.com/aws/aws-sdk-go-v2/service/sso v1.11.23 // indirect - github.com/aws/aws-sdk-go-v2/service/ssooidc v1.13.6 // indirect - github.com/aws/aws-sdk-go-v2/service/sts v1.16.19 // indirect - github.com/aws/smithy-go v1.13.3 // indirect + github.com/aws/aws-sdk-go-v2/aws/protocol/eventstream v1.4.10 // indirect + github.com/aws/aws-sdk-go-v2/credentials v1.13.22 // indirect + github.com/aws/aws-sdk-go-v2/feature/ec2/imds v1.13.3 // indirect + github.com/aws/aws-sdk-go-v2/internal/configsources v1.1.33 // indirect + github.com/aws/aws-sdk-go-v2/internal/endpoints/v2 v2.4.27 // indirect + github.com/aws/aws-sdk-go-v2/internal/ini v1.3.34 // indirect + github.com/aws/aws-sdk-go-v2/internal/v4a v1.0.25 // indirect + github.com/aws/aws-sdk-go-v2/service/internal/accept-encoding v1.9.11 // indirect + github.com/aws/aws-sdk-go-v2/service/internal/checksum v1.1.28 // indirect + github.com/aws/aws-sdk-go-v2/service/internal/presigned-url v1.9.27 // indirect + github.com/aws/aws-sdk-go-v2/service/internal/s3shared v1.14.2 // indirect + github.com/aws/aws-sdk-go-v2/service/sso v1.12.10 // indirect + github.com/aws/aws-sdk-go-v2/service/ssooidc v1.14.10 // indirect + github.com/aws/aws-sdk-go-v2/service/sts v1.18.11 // indirect + github.com/aws/smithy-go v1.13.5 // indirect github.com/davecgh/go-spew v1.1.1 // indirect - github.com/fatih/color v1.13.0 // indirect - github.com/fsnotify/fsnotify v1.4.9 // indirect + github.com/fatih/color v1.15.0 // indirect + github.com/fsnotify/fsnotify v1.6.0 // indirect github.com/hashicorp/hcl v1.0.0 // indirect - github.com/inconshreveable/mousetrap v1.0.0 // indirect + github.com/inconshreveable/mousetrap v1.1.0 // indirect github.com/jmespath/go-jmespath v0.4.0 // indirect github.com/kr/fs v0.1.0 // indirect - github.com/magiconair/properties v1.8.5 // indirect - github.com/mattn/go-colorable v0.1.12 // indirect - github.com/mattn/go-isatty v0.0.14 // indirect - github.com/mattn/go-runewidth v0.0.13 // indirect - github.com/mitchellh/mapstructure v1.4.1 // indirect - github.com/pelletier/go-toml v1.9.3 // indirect + github.com/magiconair/properties v1.8.7 // indirect + github.com/mattn/go-colorable v0.1.13 // indirect + github.com/mattn/go-isatty v0.0.18 // indirect + github.com/mattn/go-runewidth v0.0.14 // indirect + github.com/mitchellh/mapstructure v1.5.0 // indirect + github.com/pelletier/go-toml/v2 v2.0.7 // indirect github.com/pmezard/go-difflib v1.0.0 // indirect - github.com/rivo/uniseg v0.2.0 // indirect - github.com/spf13/afero v1.6.0 // indirect - github.com/spf13/cast v1.3.1 // indirect + github.com/rivo/uniseg v0.4.4 // indirect + github.com/spf13/afero v1.9.5 // indirect + github.com/spf13/cast v1.5.0 // indirect github.com/spf13/jwalterweatherman v1.1.0 // indirect github.com/spf13/pflag v1.0.5 // indirect - github.com/subosito/gotenv v1.2.0 // indirect - golang.org/x/sys v0.0.0-20220715151400-c0bba94af5f8 // indirect - golang.org/x/text v0.3.6 // indirect - gopkg.in/ini.v1 v1.62.0 // indirect + github.com/subosito/gotenv v1.4.2 // indirect + golang.org/x/sys v0.8.0 // indirect + golang.org/x/text v0.9.0 // indirect + gopkg.in/ini.v1 v1.67.0 // indirect gopkg.in/yaml.v2 v2.4.0 // indirect - gopkg.in/yaml.v3 v3.0.0-20210107192922-496545a6307b // indirect + gopkg.in/yaml.v3 v3.0.1 // indirect ) diff --git a/go.sum b/go.sum index 86f0dcb..8c94da5 100644 --- a/go.sum +++ b/go.sum @@ -3,6 +3,7 @@ cloud.google.com/go v0.34.0/go.mod h1:aQUYkXzVsufM+DwF1aE+0xfcU+56JwCaLick0ClmMT cloud.google.com/go v0.38.0/go.mod h1:990N+gfupTy94rShfmMCWGDn0LpTmnzTp2qbd1dvSRU= cloud.google.com/go v0.44.1/go.mod h1:iSa0KzasP4Uvy3f1mN/7PiObzGgflwredwwASm/v6AU= cloud.google.com/go v0.44.2/go.mod h1:60680Gw3Yr4ikxnPRS/oxxkBccT6SA1yMk63TGekxKY= +cloud.google.com/go v0.44.3/go.mod h1:60680Gw3Yr4ikxnPRS/oxxkBccT6SA1yMk63TGekxKY= cloud.google.com/go v0.45.1/go.mod h1:RpBamKRgapWJb87xiFSdk4g1CME7QZg3uwTez+TSTjc= cloud.google.com/go v0.46.3/go.mod h1:a6bKKbmY7er1mI7TEI4lsAkts/mkhTSZK8w33B4RAg0= cloud.google.com/go v0.50.0/go.mod h1:r9sluTvynVuxRIOHXQEHMFffphuXHOMZMycpNR5e6To= @@ -15,9 +16,7 @@ cloud.google.com/go v0.62.0/go.mod h1:jmCYTdRCQuc1PHIIJ/maLInMho30T/Y0M4hTdTShOY cloud.google.com/go v0.65.0/go.mod h1:O5N8zS7uWy9vkA9vayVHs65eM1ubvY4h553ofrNHObY= cloud.google.com/go v0.72.0/go.mod h1:M+5Vjvlc2wnp6tjzE102Dw08nGShTscUx2nZMufOKPI= cloud.google.com/go v0.74.0/go.mod h1:VV1xSbzvo+9QJOxLDaJfTjx5e+MePCpCWwvftOeQmWk= -cloud.google.com/go v0.78.0/go.mod h1:QjdrLG0uq+YwhjoVOLsS1t7TW8fs36kLs4XO5R5ECHg= -cloud.google.com/go v0.79.0/go.mod h1:3bzgcEeQlzbuEAYu4mrWhKqWjmpprinYgKJLgKHnbb8= -cloud.google.com/go v0.81.0/go.mod h1:mk/AM35KwGk/Nm2YSeZbxXdrNK3KZOYHmLkOqC2V6E0= +cloud.google.com/go v0.75.0/go.mod h1:VGuuCn7PG0dwsd5XPVm2Mm3wlh3EL55/79EKB6hlPTY= cloud.google.com/go/bigquery v1.0.1/go.mod h1:i/xbL2UlR5RvWAURpBYZTtm/cXjCha9lbfbpx4poX+o= cloud.google.com/go/bigquery v1.3.0/go.mod h1:PjpwJnslEMmckchkHFfq+HTD2DmtT67aNFKH1/VBDHE= cloud.google.com/go/bigquery v1.4.0/go.mod h1:S8dzgnTigyfTmLBfrtrhyYhwRxG72rYxvftPBK2Dvzc= @@ -26,7 +25,6 @@ cloud.google.com/go/bigquery v1.7.0/go.mod h1://okPTzCYNXSlb24MZs83e2Do+h+VXtc4g cloud.google.com/go/bigquery v1.8.0/go.mod h1:J5hqkt3O0uAFnINi6JXValWIb1v0goeZM77hZzJN/fQ= cloud.google.com/go/datastore v1.0.0/go.mod h1:LXYbyblFSglQ5pkeyhO+Qmw7ukd3C+pD7TKLgZqpHYE= cloud.google.com/go/datastore v1.1.0/go.mod h1:umbIZjpQpHh4hmRpGhH4tLFup+FVzqBi1b3c64qFpCk= -cloud.google.com/go/firestore v1.1.0/go.mod h1:ulACoGHTpvq5r8rxGJ4ddJZBZqakUQqClKRT5SZwBmk= cloud.google.com/go/pubsub v1.0.1/go.mod h1:R0Gpsv3s54REJCy4fxDixWD93lHJMoZTyQ2kNxGRt3I= cloud.google.com/go/pubsub v1.1.0/go.mod h1:EwwdRX2sKPjnvnqCa270oGRyludottCI76h+R3AArQw= cloud.google.com/go/pubsub v1.2.0/go.mod h1:jhfEVHT8odbXTkndysNHCcx0awwzvfOlguIAii9o8iA= @@ -36,59 +34,53 @@ cloud.google.com/go/storage v1.5.0/go.mod h1:tpKbwo567HUNpVclU5sGELwQWBDZ8gh0Zeo cloud.google.com/go/storage v1.6.0/go.mod h1:N7U0C8pVQ/+NIKOBQyamJIeKQKkZ+mxpohlUTyfDhBk= cloud.google.com/go/storage v1.8.0/go.mod h1:Wv1Oy7z6Yz3DshWRJFhqM/UCfaWIRTdp0RXyy7KQOVs= cloud.google.com/go/storage v1.10.0/go.mod h1:FLPqc6j+Ki4BU591ie1oL6qBQGu2Bl/tZ9ullr3+Kg0= +cloud.google.com/go/storage v1.14.0/go.mod h1:GrKmX003DSIwi9o29oFT7YDnHYwZoctc3fOKtUw0Xmo= dmitri.shuralyov.com/gpu/mtl v0.0.0-20190408044501-666a987793e9/go.mod h1:H6x//7gZCb22OMCxBHrMx7a5I7Hp++hsVxbQ4BYO7hU= github.com/BurntSushi/toml v0.3.1/go.mod h1:xHWCNGjB5oqiDr8zfno3MHue2Ht5sIBksp03qcyfWMU= github.com/BurntSushi/xgb v0.0.0-20160522181843-27f122750802/go.mod h1:IVnqGOEym/WlBOVXweHU+Q+/VP0lqqI8lqeDx9IjBqo= -github.com/VividCortex/ewma v1.1.1/go.mod h1:2Tkkvm3sRDVXaiyucHiACn4cqf7DpdyLvmxzcbUokwA= github.com/VividCortex/ewma v1.2.0 h1:f58SaIzcDXrSy3kWaHNvuJgJ3Nmz59Zji6XoJR/q1ow= github.com/VividCortex/ewma v1.2.0/go.mod h1:nz4BbCtbLyFDeC9SUHbtcT5644juEuWfUAUnGx7j5l4= -github.com/antihax/optional v1.0.0/go.mod h1:uupD/76wgC+ih3iEmQUL+0Ugr19nfwCT1kdvxnR2qWY= -github.com/armon/circbuf v0.0.0-20150827004946-bbbad097214e/go.mod h1:3U/XgcO3hCbHZ8TKRvWD2dDTCfh9M9ya+I9JpbB7O8o= -github.com/armon/go-metrics v0.0.0-20180917152333-f0300d1749da/go.mod h1:Q73ZrmVTwzkszR9V5SSuryQ31EELlFMUz1kKyl939pY= -github.com/armon/go-radix v0.0.0-20180808171621-7fddfc383310/go.mod h1:ufUuZ+zHj4x4TnLV4JWEpy2hxWSpsRywHrMgIH9cCH8= -github.com/aws/aws-sdk-go-v2 v1.16.16 h1:M1fj4FE2lB4NzRb9Y0xdWsn2P0+2UHVxwKyOa4YJNjk= -github.com/aws/aws-sdk-go-v2 v1.16.16/go.mod h1:SwiyXi/1zTUZ6KIAmLK5V5ll8SiURNUYOqTerZPaF9k= -github.com/aws/aws-sdk-go-v2/aws/protocol/eventstream v1.4.8 h1:tcFliCWne+zOuUfKNRn8JdFBuWPDuISDH08wD2ULkhk= -github.com/aws/aws-sdk-go-v2/aws/protocol/eventstream v1.4.8/go.mod h1:JTnlBSot91steJeti4ryyu/tLd4Sk84O5W22L7O2EQU= -github.com/aws/aws-sdk-go-v2/config v1.17.8 h1:b9LGqNnOdg9vR4Q43tBTVWk4J6F+W774MSchvKJsqnE= -github.com/aws/aws-sdk-go-v2/config v1.17.8/go.mod h1:UkCI3kb0sCdvtjiXYiU4Zx5h07BOpgBTtkPu/49r+kA= -github.com/aws/aws-sdk-go-v2/credentials v1.12.21 h1:4tjlyCD0hRGNQivh5dN8hbP30qQhMLBE/FgQR1vHHWM= -github.com/aws/aws-sdk-go-v2/credentials v1.12.21/go.mod h1:O+4XyAt4e+oBAoIwNUYkRg3CVMscaIJdmZBOcPgJ8D8= -github.com/aws/aws-sdk-go-v2/feature/ec2/imds v1.12.17 h1:r08j4sbZu/RVi+BNxkBJwPMUYY3P8mgSDuKkZ/ZN1lE= -github.com/aws/aws-sdk-go-v2/feature/ec2/imds v1.12.17/go.mod h1:yIkQcCDYNsZfXpd5UX2Cy+sWA1jPgIhGTw9cOBzfVnQ= -github.com/aws/aws-sdk-go-v2/feature/s3/manager v1.11.34 h1:1PNtaCM+2ruo1dfYL2RweUdtbuPvinjAejjNcPa/RQY= -github.com/aws/aws-sdk-go-v2/feature/s3/manager v1.11.34/go.mod h1:+Six+CXNHYllXam32j+YW8ixk82+am345ei89kEz8p4= -github.com/aws/aws-sdk-go-v2/internal/configsources v1.1.23 h1:s4g/wnzMf+qepSNgTvaQQHNxyMLKSawNhKCPNy++2xY= -github.com/aws/aws-sdk-go-v2/internal/configsources v1.1.23/go.mod h1:2DFxAQ9pfIRy0imBCJv+vZ2X6RKxves6fbnEuSry6b4= -github.com/aws/aws-sdk-go-v2/internal/endpoints/v2 v2.4.17 h1:/K482T5A3623WJgWT8w1yRAFK4RzGzEl7y39yhtn9eA= -github.com/aws/aws-sdk-go-v2/internal/endpoints/v2 v2.4.17/go.mod h1:pRwaTYCJemADaqCbUAxltMoHKata7hmB5PjEXeu0kfg= -github.com/aws/aws-sdk-go-v2/internal/ini v1.3.24 h1:wj5Rwc05hvUSvKuOF29IYb9QrCLjU+rHAy/x/o0DK2c= -github.com/aws/aws-sdk-go-v2/internal/ini v1.3.24/go.mod h1:jULHjqqjDlbyTa7pfM7WICATnOv+iOhjletM3N0Xbu8= -github.com/aws/aws-sdk-go-v2/internal/v4a v1.0.14 h1:ZSIPAkAsCCjYrhqfw2+lNzWDzxzHXEckFkTePL5RSWQ= -github.com/aws/aws-sdk-go-v2/internal/v4a v1.0.14/go.mod h1:AyGgqiKv9ECM6IZeNQtdT8NnMvUb3/2wokeq2Fgryto= -github.com/aws/aws-sdk-go-v2/service/internal/accept-encoding v1.9.9 h1:Lh1AShsuIJTwMkoxVCAYPJgNG5H+eN6SmoUn8nOZ5wE= -github.com/aws/aws-sdk-go-v2/service/internal/accept-encoding v1.9.9/go.mod h1:a9j48l6yL5XINLHLcOKInjdvknN+vWqPBxqeIDw7ktw= -github.com/aws/aws-sdk-go-v2/service/internal/checksum v1.1.18 h1:BBYoNQt2kUZUUK4bIPsKrCcjVPUMNsgQpNAwhznK/zo= -github.com/aws/aws-sdk-go-v2/service/internal/checksum v1.1.18/go.mod h1:NS55eQ4YixUJPTC+INxi2/jCqe1y2Uw3rnh9wEOVJxY= -github.com/aws/aws-sdk-go-v2/service/internal/presigned-url v1.9.17 h1:Jrd/oMh0PKQc6+BowB+pLEwLIgaQF29eYbe7E1Av9Ug= -github.com/aws/aws-sdk-go-v2/service/internal/presigned-url v1.9.17/go.mod h1:4nYOrY41Lrbk2170/BGkcJKBhws9Pfn8MG3aGqjjeFI= -github.com/aws/aws-sdk-go-v2/service/internal/s3shared v1.13.17 h1:HfVVR1vItaG6le+Bpw6P4midjBDMKnjMyZnw9MXYUcE= -github.com/aws/aws-sdk-go-v2/service/internal/s3shared v1.13.17/go.mod h1:YqMdV+gEKCQ59NrB7rzrJdALeBIsYiVi8Inj3+KcqHI= -github.com/aws/aws-sdk-go-v2/service/s3 v1.27.11 h1:3/gm/JTX9bX8CpzTgIlrtYpB3EVBDxyg/GY/QdcIEZw= -github.com/aws/aws-sdk-go-v2/service/s3 v1.27.11/go.mod h1:fmgDANqTUCxciViKl9hb/zD5LFbvPINFRgWhDbR+vZo= -github.com/aws/aws-sdk-go-v2/service/sso v1.11.23 h1:pwvCchFUEnlceKIgPUouBJwK81aCkQ8UDMORfeFtW10= -github.com/aws/aws-sdk-go-v2/service/sso v1.11.23/go.mod h1:/w0eg9IhFGjGyyncHIQrXtU8wvNsTJOP0R6PPj0wf80= -github.com/aws/aws-sdk-go-v2/service/ssooidc v1.13.6 h1:OwhhKc1P9ElfWbMKPIbMMZBV6hzJlL2JKD76wNNVzgQ= -github.com/aws/aws-sdk-go-v2/service/ssooidc v1.13.6/go.mod h1:csZuQY65DAdFBt1oIjO5hhBR49kQqop4+lcuCjf2arA= -github.com/aws/aws-sdk-go-v2/service/sts v1.16.19 h1:9pPi0PsFNAGILFfPCk8Y0iyEBGc6lu6OQ97U7hmdesg= -github.com/aws/aws-sdk-go-v2/service/sts v1.16.19/go.mod h1:h4J3oPZQbxLhzGnk+j9dfYHi5qIOVJ5kczZd658/ydM= -github.com/aws/smithy-go v1.13.3 h1:l7LYxGuzK6/K+NzJ2mC+VvLUbae0sL3bXU//04MkmnA= -github.com/aws/smithy-go v1.13.3/go.mod h1:Tg+OJXh4MB2R/uN61Ko2f6hTZwB/ZYGOtib8J3gBHzA= -github.com/bgentry/speakeasy v0.1.0/go.mod h1:+zsyZBPWlz7T6j88CTgSN5bM796AkVf0kBD4zp0CCIs= -github.com/bketelsen/crypt v0.0.4/go.mod 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h1:9nx3DQGgdP8bBQD5qxJ1jj9UTztislL4KSBs9R2vV5Y= golang.org/x/oauth2 v0.0.0-20180821212333-d2e6202438be/go.mod h1:N/0e6XlmueqKjAGxoOufVs8QHGRruUQn6yWY3a++T0U= golang.org/x/oauth2 v0.0.0-20190226205417-e64efc72b421/go.mod h1:gOpvHmFTYa4IltrdGE7lF6nIHvwfUNPOp7c8zoXwtLw= @@ -416,9 +333,6 @@ golang.org/x/oauth2 v0.0.0-20200902213428-5d25da1a8d43/go.mod h1:KelEdhl1UZF7XfJ golang.org/x/oauth2 v0.0.0-20201109201403-9fd604954f58/go.mod h1:KelEdhl1UZF7XfJ4dDtk6s++YSgaE7mD/BuKKDLBl4A= golang.org/x/oauth2 v0.0.0-20201208152858-08078c50e5b5/go.mod h1:KelEdhl1UZF7XfJ4dDtk6s++YSgaE7mD/BuKKDLBl4A= golang.org/x/oauth2 v0.0.0-20210218202405-ba52d332ba99/go.mod h1:KelEdhl1UZF7XfJ4dDtk6s++YSgaE7mD/BuKKDLBl4A= -golang.org/x/oauth2 v0.0.0-20210220000619-9bb904979d93/go.mod h1:KelEdhl1UZF7XfJ4dDtk6s++YSgaE7mD/BuKKDLBl4A= -golang.org/x/oauth2 v0.0.0-20210313182246-cd4f82c27b84/go.mod h1:KelEdhl1UZF7XfJ4dDtk6s++YSgaE7mD/BuKKDLBl4A= -golang.org/x/oauth2 v0.0.0-20210402161424-2e8d93401602/go.mod h1:KelEdhl1UZF7XfJ4dDtk6s++YSgaE7mD/BuKKDLBl4A= golang.org/x/sync v0.0.0-20180314180146-1d60e4601c6f/go.mod h1:RxMgew5VJxzue5/jJTE5uejpjVlOe/izrB70Jof72aM= golang.org/x/sync v0.0.0-20181108010431-42b317875d0f/go.mod h1:RxMgew5VJxzue5/jJTE5uejpjVlOe/izrB70Jof72aM= golang.org/x/sync v0.0.0-20181221193216-37e7f081c4d4/go.mod h1:RxMgew5VJxzue5/jJTE5uejpjVlOe/izrB70Jof72aM= @@ -429,11 +343,9 @@ golang.org/x/sync v0.0.0-20200317015054-43a5402ce75a/go.mod h1:RxMgew5VJxzue5/jJ golang.org/x/sync v0.0.0-20200625203802-6e8e738ad208/go.mod h1:RxMgew5VJxzue5/jJTE5uejpjVlOe/izrB70Jof72aM= golang.org/x/sync v0.0.0-20201020160332-67f06af15bc9/go.mod h1:RxMgew5VJxzue5/jJTE5uejpjVlOe/izrB70Jof72aM= golang.org/x/sync v0.0.0-20201207232520-09787c993a3a/go.mod h1:RxMgew5VJxzue5/jJTE5uejpjVlOe/izrB70Jof72aM= -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 v0.0.0-20180823144017-11551d06cbcc/go.mod h1:STP8DvDyc/dI5b8T5hshtkjS+E42TnysNCUPdjciGhY= +golang.org/x/sync v0.2.0 h1:PUR+T4wwASmuSTYdKjYHI5TD22Wy5ogLU5qZCOLxBrI= +golang.org/x/sync v0.2.0/go.mod h1:RxMgew5VJxzue5/jJTE5uejpjVlOe/izrB70Jof72aM= golang.org/x/sys v0.0.0-20180830151530-49385e6e1522/go.mod h1:STP8DvDyc/dI5b8T5hshtkjS+E42TnysNCUPdjciGhY= -golang.org/x/sys v0.0.0-20181026203630-95b1ffbd15a5/go.mod h1:STP8DvDyc/dI5b8T5hshtkjS+E42TnysNCUPdjciGhY= golang.org/x/sys v0.0.0-20190215142949-d0b11bdaac8a/go.mod h1:STP8DvDyc/dI5b8T5hshtkjS+E42TnysNCUPdjciGhY= golang.org/x/sys v0.0.0-20190312061237-fead79001313/go.mod h1:h1NjWce9XRLGQEsW7wpKNCjG9DtNlClVuFLEZdDNbEs= golang.org/x/sys v0.0.0-20190412213103-97732733099d/go.mod h1:h1NjWce9XRLGQEsW7wpKNCjG9DtNlClVuFLEZdDNbEs= @@ -443,11 +355,9 @@ golang.org/x/sys v0.0.0-20190606165138-5da285871e9c/go.mod h1:h1NjWce9XRLGQEsW7w golang.org/x/sys v0.0.0-20190624142023-c5567b49c5d0/go.mod h1:h1NjWce9XRLGQEsW7wpKNCjG9DtNlClVuFLEZdDNbEs= golang.org/x/sys v0.0.0-20190726091711-fc99dfbffb4e/go.mod h1:h1NjWce9XRLGQEsW7wpKNCjG9DtNlClVuFLEZdDNbEs= golang.org/x/sys v0.0.0-20191001151750-bb3f8db39f24/go.mod h1:h1NjWce9XRLGQEsW7wpKNCjG9DtNlClVuFLEZdDNbEs= -golang.org/x/sys v0.0.0-20191005200804-aed5e4c7ecf9/go.mod h1:h1NjWce9XRLGQEsW7wpKNCjG9DtNlClVuFLEZdDNbEs= golang.org/x/sys v0.0.0-20191204072324-ce4227a45e2e/go.mod h1:h1NjWce9XRLGQEsW7wpKNCjG9DtNlClVuFLEZdDNbEs= golang.org/x/sys v0.0.0-20191228213918-04cbcbbfeed8/go.mod h1:h1NjWce9XRLGQEsW7wpKNCjG9DtNlClVuFLEZdDNbEs= golang.org/x/sys v0.0.0-20200113162924-86b910548bc1/go.mod h1:h1NjWce9XRLGQEsW7wpKNCjG9DtNlClVuFLEZdDNbEs= -golang.org/x/sys v0.0.0-20200116001909-b77594299b42/go.mod h1:h1NjWce9XRLGQEsW7wpKNCjG9DtNlClVuFLEZdDNbEs= golang.org/x/sys v0.0.0-20200122134326-e047566fdf82/go.mod h1:h1NjWce9XRLGQEsW7wpKNCjG9DtNlClVuFLEZdDNbEs= golang.org/x/sys v0.0.0-20200202164722-d101bd2416d5/go.mod h1:h1NjWce9XRLGQEsW7wpKNCjG9DtNlClVuFLEZdDNbEs= golang.org/x/sys v0.0.0-20200212091648-12a6c2dcc1e4/go.mod h1:h1NjWce9XRLGQEsW7wpKNCjG9DtNlClVuFLEZdDNbEs= @@ -466,31 +376,29 @@ golang.org/x/sys v0.0.0-20201119102817-f84b799fce68/go.mod h1:h1NjWce9XRLGQEsW7w golang.org/x/sys v0.0.0-20201201145000-ef89a241ccb3/go.mod h1:h1NjWce9XRLGQEsW7wpKNCjG9DtNlClVuFLEZdDNbEs= golang.org/x/sys v0.0.0-20210104204734-6f8348627aad/go.mod h1:h1NjWce9XRLGQEsW7wpKNCjG9DtNlClVuFLEZdDNbEs= golang.org/x/sys v0.0.0-20210119212857-b64e53b001e4/go.mod h1:h1NjWce9XRLGQEsW7wpKNCjG9DtNlClVuFLEZdDNbEs= -golang.org/x/sys v0.0.0-20210220050731-9a76102bfb43/go.mod h1:h1NjWce9XRLGQEsW7wpKNCjG9DtNlClVuFLEZdDNbEs= -golang.org/x/sys v0.0.0-20210305230114-8fe3ee5dd75b/go.mod h1:h1NjWce9XRLGQEsW7wpKNCjG9DtNlClVuFLEZdDNbEs= -golang.org/x/sys v0.0.0-20210315160823-c6e025ad8005/go.mod h1:h1NjWce9XRLGQEsW7wpKNCjG9DtNlClVuFLEZdDNbEs= -golang.org/x/sys v0.0.0-20210320140829-1e4c9ba3b0c4/go.mod h1:h1NjWce9XRLGQEsW7wpKNCjG9DtNlClVuFLEZdDNbEs= -golang.org/x/sys v0.0.0-20210330210617-4fbd30eecc44/go.mod h1:h1NjWce9XRLGQEsW7wpKNCjG9DtNlClVuFLEZdDNbEs= -golang.org/x/sys v0.0.0-20210403161142-5e06dd20ab57/go.mod h1:h1NjWce9XRLGQEsW7wpKNCjG9DtNlClVuFLEZdDNbEs= +golang.org/x/sys v0.0.0-20210225134936-a50acf3fe073/go.mod h1:h1NjWce9XRLGQEsW7wpKNCjG9DtNlClVuFLEZdDNbEs= golang.org/x/sys v0.0.0-20210423082822-04245dca01da/go.mod h1:h1NjWce9XRLGQEsW7wpKNCjG9DtNlClVuFLEZdDNbEs= golang.org/x/sys v0.0.0-20210423185535-09eb48e85fd7/go.mod h1:h1NjWce9XRLGQEsW7wpKNCjG9DtNlClVuFLEZdDNbEs= -golang.org/x/sys v0.0.0-20210510120138-977fb7262007/go.mod h1:oPkhp1MJrh7nUepCBck5+mAzfO9JrbApNNgaTdGDITg= golang.org/x/sys v0.0.0-20210615035016-665e8c7367d1/go.mod h1:oPkhp1MJrh7nUepCBck5+mAzfO9JrbApNNgaTdGDITg= -golang.org/x/sys v0.0.0-20210630005230-0f9fa26af87c/go.mod h1:oPkhp1MJrh7nUepCBck5+mAzfO9JrbApNNgaTdGDITg= -golang.org/x/sys 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v0.0.0-20201126162022-7de9c90e9dd1/go.mod h1:bj7SfCRtBDWHUb9snDiAeCFNEtKQo2Wmx5Cou7ajbmo= +golang.org/x/term v0.7.0 h1:BEvjmm5fURWqcfbSKTdpkDXYBrUS1c0m8agp14W48vQ= golang.org/x/text v0.0.0-20170915032832-14c0d48ead0c/go.mod h1:NqM8EUOU14njkJ3fqMW+pc6Ldnwhi/IjpwHt7yyuwOQ= golang.org/x/text v0.3.0/go.mod h1:NqM8EUOU14njkJ3fqMW+pc6Ldnwhi/IjpwHt7yyuwOQ= golang.org/x/text v0.3.1-0.20180807135948-17ff2d5776d2/go.mod h1:NqM8EUOU14njkJ3fqMW+pc6Ldnwhi/IjpwHt7yyuwOQ= golang.org/x/text v0.3.2/go.mod h1:bEr9sfX3Q8Zfm5fL9x+3itogRgK3+ptLWKqgva+5dAk= golang.org/x/text v0.3.3/go.mod h1:5Zoc/QRtKVWzQhOtBMvqHzDpF6irO9z98xDceosuGiQ= golang.org/x/text v0.3.4/go.mod h1:5Zoc/QRtKVWzQhOtBMvqHzDpF6irO9z98xDceosuGiQ= -golang.org/x/text v0.3.5/go.mod h1:5Zoc/QRtKVWzQhOtBMvqHzDpF6irO9z98xDceosuGiQ= -golang.org/x/text v0.3.6 h1:aRYxNxv6iGQlyVaZmk6ZgYEDa+Jg18DxebPSrd6bg1M= golang.org/x/text v0.3.6/go.mod h1:5Zoc/QRtKVWzQhOtBMvqHzDpF6irO9z98xDceosuGiQ= +golang.org/x/text v0.3.7/go.mod h1:u+2+/6zg+i71rQMx5EYifcz6MCKuco9NR6JIITiCfzQ= +golang.org/x/text v0.9.0 h1:2sjJmO8cDvYveuX97RDLsxlyUxLl+GHoLxBiRdHllBE= +golang.org/x/text v0.9.0/go.mod h1:e1OnstbJyHTd6l/uOt8jFFHp6TRDWZR/bV3emEE/zU8= golang.org/x/time v0.0.0-20181108054448-85acf8d2951c/go.mod h1:tRJNPiyCQ0inRvYxbN9jk5I+vvW/OXSQhTDSoE431IQ= golang.org/x/time v0.0.0-20190308202827-9d24e82272b4/go.mod h1:tRJNPiyCQ0inRvYxbN9jk5I+vvW/OXSQhTDSoE431IQ= golang.org/x/time v0.0.0-20191024005414-555d28b269f0/go.mod h1:tRJNPiyCQ0inRvYxbN9jk5I+vvW/OXSQhTDSoE431IQ= @@ -500,7 +408,6 @@ golang.org/x/tools v0.0.0-20190226205152-f727befe758c/go.mod h1:9Yl7xja0Znq3iFh3 golang.org/x/tools v0.0.0-20190311212946-11955173bddd/go.mod h1:LCzVGOaR6xXOjkQ3onu1FJEFr0SW1gC7cKk1uF8kGRs= golang.org/x/tools v0.0.0-20190312151545-0bb0c0a6e846/go.mod h1:LCzVGOaR6xXOjkQ3onu1FJEFr0SW1gC7cKk1uF8kGRs= golang.org/x/tools v0.0.0-20190312170243-e65039ee4138/go.mod h1:LCzVGOaR6xXOjkQ3onu1FJEFr0SW1gC7cKk1uF8kGRs= -golang.org/x/tools v0.0.0-20190328211700-ab21143f2384/go.mod h1:LCzVGOaR6xXOjkQ3onu1FJEFr0SW1gC7cKk1uF8kGRs= golang.org/x/tools v0.0.0-20190425150028-36563e24a262/go.mod h1:RgjU9mgBXZiqYHBnxXauZ1Gv1EHHAz9KjViQ78xBX0Q= golang.org/x/tools v0.0.0-20190506145303-2d16b83fe98c/go.mod h1:RgjU9mgBXZiqYHBnxXauZ1Gv1EHHAz9KjViQ78xBX0Q= golang.org/x/tools v0.0.0-20190524140312-2c0ae7006135/go.mod h1:RgjU9mgBXZiqYHBnxXauZ1Gv1EHHAz9KjViQ78xBX0Q= @@ -510,7 +417,6 @@ golang.org/x/tools v0.0.0-20190628153133-6cdbf07be9d0/go.mod h1:/rFqwRUd4F7ZHNgw golang.org/x/tools v0.0.0-20190816200558-6889da9d5479/go.mod h1:b+2E5dAYhXwXZwtnZ6UAqBI28+e2cm9otk0dWdXHAEo= golang.org/x/tools v0.0.0-20190911174233-4f2ddba30aff/go.mod h1:b+2E5dAYhXwXZwtnZ6UAqBI28+e2cm9otk0dWdXHAEo= golang.org/x/tools v0.0.0-20191012152004-8de300cfc20a/go.mod h1:b+2E5dAYhXwXZwtnZ6UAqBI28+e2cm9otk0dWdXHAEo= -golang.org/x/tools v0.0.0-20191112195655-aa38f8e97acc/go.mod h1:b+2E5dAYhXwXZwtnZ6UAqBI28+e2cm9otk0dWdXHAEo= golang.org/x/tools v0.0.0-20191113191852-77e3bb0ad9e7/go.mod h1:b+2E5dAYhXwXZwtnZ6UAqBI28+e2cm9otk0dWdXHAEo= golang.org/x/tools v0.0.0-20191115202509-3a792d9c32b2/go.mod h1:b+2E5dAYhXwXZwtnZ6UAqBI28+e2cm9otk0dWdXHAEo= golang.org/x/tools v0.0.0-20191119224855-298f0cb1881e/go.mod h1:b+2E5dAYhXwXZwtnZ6UAqBI28+e2cm9otk0dWdXHAEo= @@ -533,7 +439,6 @@ golang.org/x/tools v0.0.0-20200501065659-ab2804fb9c9d/go.mod h1:EkVYQZoAsY45+roY golang.org/x/tools v0.0.0-20200512131952-2bc93b1c0c88/go.mod h1:EkVYQZoAsY45+roYkvgYkIh4xh/qjgUK9TdY2XT94GE= golang.org/x/tools v0.0.0-20200515010526-7d3b6ebf133d/go.mod h1:EkVYQZoAsY45+roYkvgYkIh4xh/qjgUK9TdY2XT94GE= golang.org/x/tools v0.0.0-20200618134242-20370b0cb4b2/go.mod h1:EkVYQZoAsY45+roYkvgYkIh4xh/qjgUK9TdY2XT94GE= -golang.org/x/tools v0.0.0-20200619180055-7c47624df98f/go.mod h1:EkVYQZoAsY45+roYkvgYkIh4xh/qjgUK9TdY2XT94GE= golang.org/x/tools v0.0.0-20200729194436-6467de6f59a7/go.mod h1:njjCfa9FT2d7l9Bc6FUM5FLjQPp3cFF28FI3qnDFljA= golang.org/x/tools v0.0.0-20200804011535-6c149bb5ef0d/go.mod h1:njjCfa9FT2d7l9Bc6FUM5FLjQPp3cFF28FI3qnDFljA= golang.org/x/tools v0.0.0-20200825202427-b303f430e36d/go.mod h1:njjCfa9FT2d7l9Bc6FUM5FLjQPp3cFF28FI3qnDFljA= @@ -542,9 +447,8 @@ golang.org/x/tools v0.0.0-20201110124207-079ba7bd75cd/go.mod h1:emZCQorbCU4vsT4f golang.org/x/tools v0.0.0-20201201161351-ac6f37ff4c2a/go.mod h1:emZCQorbCU4vsT4fOWvOPXz4eW1wZW4PmDk9uLelYpA= golang.org/x/tools v0.0.0-20201208233053-a543418bbed2/go.mod h1:emZCQorbCU4vsT4fOWvOPXz4eW1wZW4PmDk9uLelYpA= golang.org/x/tools v0.0.0-20210105154028-b0ab187a4818/go.mod h1:emZCQorbCU4vsT4fOWvOPXz4eW1wZW4PmDk9uLelYpA= -golang.org/x/tools v0.0.0-20210106214847-113979e3529a/go.mod h1:emZCQorbCU4vsT4fOWvOPXz4eW1wZW4PmDk9uLelYpA= +golang.org/x/tools v0.0.0-20210108195828-e2f9c7f1fc8e/go.mod h1:emZCQorbCU4vsT4fOWvOPXz4eW1wZW4PmDk9uLelYpA= golang.org/x/tools v0.1.0/go.mod h1:xkSsbof2nBLbhDlRMhhhyNLN/zl3eTqcnHD5viDpcZ0= -golang.org/x/tools v0.1.2/go.mod h1:o0xws9oXOQQZyjljx8fwUC0k7L1pTE6eaCbjGeHmOkk= golang.org/x/xerrors v0.0.0-20190717185122-a985d3407aa7/go.mod h1:I/5z698sn9Ka8TeJc9MKroUUfqBBauWjQqLJ2OPfmY0= golang.org/x/xerrors v0.0.0-20191011141410-1b5146add898/go.mod h1:I/5z698sn9Ka8TeJc9MKroUUfqBBauWjQqLJ2OPfmY0= golang.org/x/xerrors v0.0.0-20191204190536-9bdfabe68543/go.mod h1:I/5z698sn9Ka8TeJc9MKroUUfqBBauWjQqLJ2OPfmY0= @@ -568,9 +472,6 @@ google.golang.org/api v0.30.0/go.mod h1:QGmEvQ87FHZNiUVJkT14jQNYJ4ZJjdRF23ZXz513 google.golang.org/api v0.35.0/go.mod h1:/XrVsuzM0rZmrsbjJutiuftIzeuTQcEeaYcSk/mQ1dg= google.golang.org/api v0.36.0/go.mod h1:+z5ficQTmoYpPn8LCUNVpK5I7hwkpjbcgqA7I34qYtE= google.golang.org/api v0.40.0/go.mod h1:fYKFpnQN0DsDSKRVRcQSDQNtqWPfM9i+zNPxepjRCQ8= -google.golang.org/api v0.41.0/go.mod h1:RkxM5lITDfTzmyKFPt+wGrCJbVfniCr2ool8kTBzRTU= -google.golang.org/api v0.43.0/go.mod h1:nQsDGjRXMo4lvh5hP0TKqF244gqhGcr/YSIykhUk/94= -google.golang.org/api v0.44.0/go.mod h1:EBOGZqzyhtvMDoxwS97ctnh0zUmYY6CxqXsc1AvkYD8= google.golang.org/appengine v1.1.0/go.mod h1:EbEs0AVv82hx2wNQdGPgUI5lhzA/G0D9YwlJXL52JkM= google.golang.org/appengine v1.4.0/go.mod h1:xpcJRLb0r/rnEns0DIKYYv+WjYCduHsrkT7/EB5XEv4= google.golang.org/appengine v1.5.0/go.mod h1:xpcJRLb0r/rnEns0DIKYYv+WjYCduHsrkT7/EB5XEv4= @@ -601,7 +502,6 @@ google.golang.org/genproto v0.0.0-20200312145019-da6875a35672/go.mod h1:55QSHmfG google.golang.org/genproto v0.0.0-20200331122359-1ee6d9798940/go.mod h1:55QSHmfGQM9UVYDPBsyGGes0y52j32PQ3BqQfXhyH3c= google.golang.org/genproto v0.0.0-20200430143042-b979b6f78d84/go.mod h1:55QSHmfGQM9UVYDPBsyGGes0y52j32PQ3BqQfXhyH3c= google.golang.org/genproto v0.0.0-20200511104702-f5ebc3bea380/go.mod h1:55QSHmfGQM9UVYDPBsyGGes0y52j32PQ3BqQfXhyH3c= -google.golang.org/genproto v0.0.0-20200513103714-09dca8ec2884/go.mod h1:55QSHmfGQM9UVYDPBsyGGes0y52j32PQ3BqQfXhyH3c= google.golang.org/genproto v0.0.0-20200515170657-fc4c6c6a6587/go.mod h1:YsZOwe1myG/8QRHRsmBRE1LrgQY60beZKjly0O1fX9U= google.golang.org/genproto v0.0.0-20200526211855-cb27e3aa2013/go.mod h1:NbSheEEYHJ7i3ixzK3sjbqSGDJWnxyFXZblF3eUsNvo= google.golang.org/genproto v0.0.0-20200618031413-b414f8b61790/go.mod h1:jDfRM7FcilCzHH/e9qn6dsT145K34l5v+OpcnNgKAAA= @@ -613,12 +513,8 @@ google.golang.org/genproto v0.0.0-20201109203340-2640f1f9cdfb/go.mod h1:FWY/as6D google.golang.org/genproto v0.0.0-20201201144952-b05cb90ed32e/go.mod h1:FWY/as6DDZQgahTzZj3fqbO1CbirC29ZNUFHwi0/+no= google.golang.org/genproto v0.0.0-20201210142538-e3217bee35cc/go.mod h1:FWY/as6DDZQgahTzZj3fqbO1CbirC29ZNUFHwi0/+no= google.golang.org/genproto v0.0.0-20201214200347-8c77b98c765d/go.mod h1:FWY/as6DDZQgahTzZj3fqbO1CbirC29ZNUFHwi0/+no= -google.golang.org/genproto v0.0.0-20210222152913-aa3ee6e6a81c/go.mod h1:FWY/as6DDZQgahTzZj3fqbO1CbirC29ZNUFHwi0/+no= -google.golang.org/genproto v0.0.0-20210303154014-9728d6b83eeb/go.mod h1:FWY/as6DDZQgahTzZj3fqbO1CbirC29ZNUFHwi0/+no= -google.golang.org/genproto v0.0.0-20210310155132-4ce2db91004e/go.mod h1:FWY/as6DDZQgahTzZj3fqbO1CbirC29ZNUFHwi0/+no= -google.golang.org/genproto v0.0.0-20210319143718-93e7006c17a6/go.mod h1:FWY/as6DDZQgahTzZj3fqbO1CbirC29ZNUFHwi0/+no= -google.golang.org/genproto v0.0.0-20210402141018-6c239bbf2bb1/go.mod h1:9lPAdzaEmUacj36I+k7YKbEc5CXzPIeORRgDAUOu28A= -google.golang.org/genproto v0.0.0-20210602131652-f16073e35f0c/go.mod h1:UODoCrxHCcBojKKwX1terBiRUaqAsFqJiF615XL43r0= +google.golang.org/genproto v0.0.0-20210108203827-ffc7fda8c3d7/go.mod h1:FWY/as6DDZQgahTzZj3fqbO1CbirC29ZNUFHwi0/+no= +google.golang.org/genproto v0.0.0-20210226172003-ab064af71705/go.mod h1:FWY/as6DDZQgahTzZj3fqbO1CbirC29ZNUFHwi0/+no= google.golang.org/grpc v1.19.0/go.mod h1:mqu4LbDTu4XGKhr4mRzUsmM4RtVoemTSY81AxZiDr8c= google.golang.org/grpc v1.20.1/go.mod h1:10oTOabMzJvdu6/UiuZezV6QK5dSlG84ov/aaiqXj38= google.golang.org/grpc v1.21.1/go.mod h1:oYelfM1adQP15Ek0mdvEgi9Df8B9CZIaU1084ijfRaM= @@ -632,13 +528,9 @@ google.golang.org/grpc v1.29.1/go.mod h1:itym6AZVZYACWQqET3MqgPpjcuV5QH3BxFS3Iji google.golang.org/grpc v1.30.0/go.mod h1:N36X2cJ7JwdamYAgDz+s+rVMFjt3numwzf/HckM8pak= google.golang.org/grpc v1.31.0/go.mod h1:N36X2cJ7JwdamYAgDz+s+rVMFjt3numwzf/HckM8pak= google.golang.org/grpc v1.31.1/go.mod h1:N36X2cJ7JwdamYAgDz+s+rVMFjt3numwzf/HckM8pak= -google.golang.org/grpc v1.33.1/go.mod h1:fr5YgcSWrqhRRxogOsw7RzIpsmvOZ6IcH4kBYTpR3n0= google.golang.org/grpc v1.33.2/go.mod h1:JMHMWHQWaTccqQQlmk3MJZS+GWXOdAesneDmEnv2fbc= google.golang.org/grpc v1.34.0/go.mod h1:WotjhfgOW/POjDeRt8vscBtXq+2VjORFy659qA51WJ8= google.golang.org/grpc v1.35.0/go.mod h1:qjiiYl8FncCW8feJPdyg3v6XW24KsRHe+dy9BAGRRjU= -google.golang.org/grpc v1.36.0/go.mod h1:qjiiYl8FncCW8feJPdyg3v6XW24KsRHe+dy9BAGRRjU= -google.golang.org/grpc v1.36.1/go.mod h1:qjiiYl8FncCW8feJPdyg3v6XW24KsRHe+dy9BAGRRjU= -google.golang.org/grpc v1.38.0/go.mod h1:NREThFqKR1f3iQ6oBuvc5LadQuXVGo9rkm5ZGrQdJfM= google.golang.org/protobuf v0.0.0-20200109180630-ec00e32a8dfd/go.mod h1:DFci5gLYBciE7Vtevhsrf46CRTquxDuWsQurQQe4oz8= google.golang.org/protobuf v0.0.0-20200221191635-4d8936d0db64/go.mod h1:kwYJMbMJ01Woi6D6+Kah6886xMZcty6N08ah7+eCXa0= google.golang.org/protobuf v0.0.0-20200228230310-ab0ca4ff8a60/go.mod h1:cfTl7dwQJ+fmap5saPgwCLgHXTUD7jkjRqWcaiX5VyM= @@ -649,22 +541,19 @@ google.golang.org/protobuf v1.23.0/go.mod h1:EGpADcykh3NcUnDUJcl1+ZksZNG86OlYog2 google.golang.org/protobuf v1.23.1-0.20200526195155-81db48ad09cc/go.mod h1:EGpADcykh3NcUnDUJcl1+ZksZNG86OlYog2l/sGQquU= google.golang.org/protobuf v1.24.0/go.mod h1:r/3tXBNzIEhYS9I1OUVjXDlt8tc493IdKGjtUeSXeh4= google.golang.org/protobuf v1.25.0/go.mod h1:9JNX74DMeImyA3h4bdi1ymwjUzf21/xIlbajtzgsN7c= -google.golang.org/protobuf v1.26.0-rc.1/go.mod h1:jlhhOSvTdKEhbULTjvd4ARK9grFBp09yW+WbY/TyQbw= -google.golang.org/protobuf v1.26.0/go.mod h1:9q0QmTI4eRPtz6boOQmLYwt+qCgq0jsYwAQnmE0givc= gopkg.in/check.v1 v0.0.0-20161208181325-20d25e280405/go.mod h1:Co6ibVJAznAaIkqp8huTwlJQCZ016jof/cbN4VW5Yz0= gopkg.in/check.v1 v1.0.0-20180628173108-788fd7840127 h1:qIbj1fsPNlZgppZ+VLlY7N33q108Sa+fhmuc+sWQYwY= gopkg.in/check.v1 v1.0.0-20180628173108-788fd7840127/go.mod h1:Co6ibVJAznAaIkqp8huTwlJQCZ016jof/cbN4VW5Yz0= gopkg.in/errgo.v2 v2.1.0/go.mod h1:hNsd1EY+bozCKY1Ytp96fpM3vjJbqLJn88ws8XvfDNI= -gopkg.in/ini.v1 v1.62.0 h1:duBzk771uxoUuOlyRLkHsygud9+5lrlGjdFBb4mSKDU= -gopkg.in/ini.v1 v1.62.0/go.mod h1:pNLf8WUiyNEtQjuu5G5vTm06TEv9tsIgeAvK8hOrP4k= +gopkg.in/ini.v1 v1.67.0 h1:Dgnx+6+nfE+IfzjUEISNeydPJh9AXNNsWbGP9KzCsOA= +gopkg.in/ini.v1 v1.67.0/go.mod h1:pNLf8WUiyNEtQjuu5G5vTm06TEv9tsIgeAvK8hOrP4k= gopkg.in/yaml.v2 v2.2.2/go.mod h1:hI93XBmqTisBFMUTm0b8Fm+jr3Dg1NNxqwp+5A1VGuI= -gopkg.in/yaml.v2 v2.2.3/go.mod h1:hI93XBmqTisBFMUTm0b8Fm+jr3Dg1NNxqwp+5A1VGuI= gopkg.in/yaml.v2 v2.2.8/go.mod h1:hI93XBmqTisBFMUTm0b8Fm+jr3Dg1NNxqwp+5A1VGuI= gopkg.in/yaml.v2 v2.4.0 h1:D8xgwECY7CYvx+Y2n4sBz93Jn9JRvxdiyyo8CTfuKaY= gopkg.in/yaml.v2 v2.4.0/go.mod h1:RDklbk79AGWmwhnvt/jBztapEOGDOx6ZbXqjP6csGnQ= gopkg.in/yaml.v3 v3.0.0-20200313102051-9f266ea9e77c/go.mod h1:K4uyk7z7BCEPqu6E+C64Yfv1cQ7kz7rIZviUmN+EgEM= -gopkg.in/yaml.v3 v3.0.0-20210107192922-496545a6307b h1:h8qDotaEPuJATrMmW04NCwg7v22aHH28wwpauUhK9Oo= -gopkg.in/yaml.v3 v3.0.0-20210107192922-496545a6307b/go.mod h1:K4uyk7z7BCEPqu6E+C64Yfv1cQ7kz7rIZviUmN+EgEM= +gopkg.in/yaml.v3 v3.0.1 h1:fxVm/GzAzEWqLHuvctI91KS9hhNmmWOoWu0XTYJS7CA= +gopkg.in/yaml.v3 v3.0.1/go.mod h1:K4uyk7z7BCEPqu6E+C64Yfv1cQ7kz7rIZviUmN+EgEM= honnef.co/go/tools v0.0.0-20190102054323-c2f93a96b099/go.mod h1:rf3lG4BRIbNafJWhAfAdb/ePZxsR/4RtNHQocxwk9r4= honnef.co/go/tools v0.0.0-20190106161140-3f1c8253044a/go.mod h1:rf3lG4BRIbNafJWhAfAdb/ePZxsR/4RtNHQocxwk9r4= honnef.co/go/tools v0.0.0-20190418001031-e561f6794a2a/go.mod h1:rf3lG4BRIbNafJWhAfAdb/ePZxsR/4RtNHQocxwk9r4= diff --git a/internal/env.go b/internal/env.go index 8fb0490..00bc065 100644 --- a/internal/env.go +++ b/internal/env.go @@ -31,7 +31,7 @@ var ( OutputFile string ChunkFolder string ChunkSize int - MaxWorkers int64 + MaxWorkers int OutputBufferSize int S3Region string @@ -51,6 +51,6 @@ func init() { viper.SetDefault(TsvFieldsName, []string{"0"}) viper.SetDefault(S3RegionName, "eu-west-1") - viper.SetDefault(S3RetryMaxAttemptsName, 10) + viper.SetDefault(S3RetryMaxAttemptsName, 10) //nolint //gomnd viper.SetDefault(IsGzipName, false) } diff --git a/internal/rw/rw.go b/internal/rw/rw.go index fa89a15..2fb4fab 100644 --- a/internal/rw/rw.go +++ b/internal/rw/rw.go @@ -66,12 +66,12 @@ func (i *InputOutput) SetInputReader(ctx context.Context, inputFiles ...string) if err != nil { return errors.Wrap(err, "can't create s3 client") } - files := []*bucket.DownloadFileInfo{} + files := []*bucket.S3FileInfo{} for _, inputFile := range inputFiles { u, _ := url.Parse(inputFile) u.Path = strings.TrimLeft(u.Path, "/") logger.Debugf("Proto: %q, Bucket: %q, Key: %q", u.Scheme, u.Host, u.Path) - files = append(files, &bucket.DownloadFileInfo{ + files = append(files, &bucket.S3FileInfo{ Bucket: u.Host, Key: u.Path, }) @@ -81,7 +81,7 @@ func (i *InputOutput) SetInputReader(ctx context.Context, inputFiles ...string) i.Input = pr i.inputPipe = pr i.g.Go(func() error { - defer pw.Close() // nolint:errcheck //no need to check this error + defer pw.Close() //nolint:errcheck //no need to check this error err := s3Api.Download(i.dCtx, pw, files...) if err != nil { return errors.Wrap(err, "can't download files") @@ -124,7 +124,7 @@ func (i *InputOutput) SetOutputWriter(ctx context.Context, outputFile string) (e i.Output = pw i.outputPipe = pw i.g.Go(func() error { - defer pr.Close() // nolint:errcheck //no need to check this error + defer pr.Close() //nolint:errcheck //no need to check this error err := s3Api.Upload(i.dCtx, pr, u.Host, u.Path) if err != nil { return errors.Wrapf(err, "can't upload file %s", outputFile) diff --git a/main.go b/main.go index 9b37f11..687b35a 100644 --- a/main.go +++ b/main.go @@ -50,7 +50,7 @@ func newCommand() *command { root.rootCmd.PersistentFlags().StringVarP(&internal.ChunkFolder, internal.ChunkFolderName, "c", viper.GetString(internal.ChunkFolderName), "chunk folder.") root.rootCmd.PersistentFlags().IntVarP(&internal.ChunkSize, internal.ChunkSizeName, "s", viper.GetInt(internal.ChunkSizeName), "chunk size.") - root.rootCmd.PersistentFlags().Int64VarP(&internal.MaxWorkers, internal.MaxWorkersName, "w", viper.GetInt64(internal.MaxWorkersName), "max worker.") + root.rootCmd.PersistentFlags().IntVarP(&internal.MaxWorkers, internal.MaxWorkersName, "w", viper.GetInt(internal.MaxWorkersName), "max worker.") root.rootCmd.PersistentFlags().IntVarP(&internal.OutputBufferSize, internal.OutputBufferSizeName, "b", viper.GetInt(internal.OutputBufferSizeName), "output buffer size.") root.sortCmd.PersistentFlags().StringSliceVarP(&internal.TsvFields, internal.TsvFieldsName, "t", viper.GetStringSlice(internal.TsvFieldsName), "") diff --git a/main_test.go b/main_test.go index 63c755a..d369427 100644 --- a/main_test.go +++ b/main_test.go @@ -72,8 +72,29 @@ func TestBasics(t *testing.T) { outputFilename: "testdata/chunks/output.tsv", }, "100 elems": { - filename: "testdata/100elems.tsv", - expectedOutput: []string{"3", "4", "5", "6", "6", "7", "7", "7", "8", "8", "9", "9", "10", "10", "15", "18", "18", "18", "18", "21", "22", "22", "25", "25", "25", "25", "25", "26", "26", "27", "27", "28", "28", "29", "29", "29", "30", "30", "31", "31", "33", "33", "34", "36", "37", "39", "39", "39", "40", "41", "41", "42", "43", "43", "47", "47", "49", "50", "50", "52", "52", "53", "54", "55", "55", "55", "56", "57", "57", "59", "60", "61", "62", "63", "67", "71", "71", "72", "72", "73", "74", "75", "78", "79", "80", "80", "82", "89", "89", "89", "91", "91", "92", "92", "93", "93", "94", "97", "97", "99"}, + filename: "testdata/100elems.tsv", + expectedOutput: []string{ + "3", "4", "5", "6", "6", + "7", "7", "7", "8", "8", + "9", "9", "10", "10", "15", + "18", "18", "18", "18", "21", + "22", "22", "25", "25", "25", + "25", "25", "26", "26", "27", + "27", "28", "28", "29", "29", + "29", "30", "30", "31", "31", + "33", "33", "34", "36", "37", + "39", "39", "39", "40", "41", + "41", "42", "43", "43", "47", + "47", "49", "50", "50", "52", + "52", "53", "54", "55", "55", + "55", "56", "57", "57", "59", + "60", "61", "62", "63", "67", + "71", "71", "72", "72", "73", + "74", "75", "78", "79", "80", + "80", "82", "89", "89", "89", + "91", "91", "92", "92", "93", + "93", "94", "97", "97", "99", + }, outputFilename: "testdata/chunks/output.tsv", }, } @@ -227,6 +248,7 @@ func Test100ElemsWithHeaders(t *testing.T) { }) } } + func Test100ElemsWithHeadersWithDuplicates(t *testing.T) { tcs := map[string]struct { filename string @@ -275,7 +297,8 @@ func TestTsvKey(t *testing.T) { }{ "Tsv file": { filename: "testdata/multifields.tsv", - expectedOutput: []string{"3 D equipment", + expectedOutput: []string{ + "3 D equipment", "7 G inflation", "6 H delivery", "9 I child", @@ -284,7 +307,8 @@ func TestTsvKey(t *testing.T) { "1 N guidance", "10 S feedback", "2 T library", - "4 Z news"}, + "4 Z news", + }, outputFilename: "testdata/chunks/output.tsv", }, } @@ -316,6 +340,7 @@ func TestTsvKey(t *testing.T) { }) } } + func prepareChunksShuffle(ctx context.Context, t *testing.T, filename, outputFilename string, chunkSize int, mergeSort bool, bufferSize int, withHeaders bool, dropDuplicates, isGzip bool) *file.Info { t.Helper() i := rw.NewInputOutput(ctx) @@ -346,6 +371,7 @@ func prepareChunksShuffle(ctx context.Context, t *testing.T, filename, outputFil return fI } + func Test100ElemsShuffle(t *testing.T) { tcs := map[string]struct { filename string diff --git a/reader/gzip_separated_values_test.go b/reader/gzip_separated_values_test.go new file mode 100644 index 0000000..f9bcd31 --- /dev/null +++ b/reader/gzip_separated_values_test.go @@ -0,0 +1,48 @@ +package reader_test + +import ( + "bufio" + "context" + "os" + "testing" + + "github.com/askiada/external-sort/internal/rw" + "github.com/askiada/external-sort/reader" + "github.com/stretchr/testify/assert" + "github.com/stretchr/testify/require" +) + +func Test(t *testing.T) { + f, err := os.Open("/mnt/c/Users/Alex/Downloads/recordings.59.tsv.gz") + require.NoError(t, err) + r, err := reader.NewGZipSeparatedValues(bufio.NewReader(f), '\t') + require.NoError(t, err) + count := 0 + for r.Next() { + row, err := r.Read() + require.NoError(t, err) + _ = row + count++ + } + assert.Equal(t, 2853701, count) + require.NoError(t, r.Err()) +} + +func TestS3(t *testing.T) { + ctx := context.Background() + i := rw.NewInputOutput(ctx) + err := i.SetInputReader(ctx, "s3://blokur-data/ml-title/remote/1/f15c2cf2e3ab46589419e6441b64e3bd/artifacts/input/word2vec/refine/recordings.59.tsv.gz") + require.NoError(t, err) + + r, err := reader.NewGZipSeparatedValues(i.Input, '\t') + require.NoError(t, err) + count := 0 + for r.Next() { + row, err := r.Read() + require.NoError(t, err) + _ = row + count++ + } + assert.Equal(t, 2853701, count) + require.NoError(t, r.Err()) +} diff --git a/reader/std_scanner.go b/reader/std_scanner.go index 4c1fb22..c16235e 100644 --- a/reader/std_scanner.go +++ b/reader/std_scanner.go @@ -42,9 +42,11 @@ func (s *StdScanner) Next() bool { } return next } + func (s *StdScanner) Read() (interface{}, error) { return s.r.Text(), nil } + func (s *StdScanner) Err() error { return s.r.Err() } @@ -78,6 +80,7 @@ func (s *StdSliceScanner) Next() bool { } return next } + func (s *StdSliceScanner) Read() (interface{}, error) { line := s.r.Text() before, after, found := strings.Cut(line, "##!!##") @@ -86,6 +89,7 @@ func (s *StdSliceScanner) Read() (interface{}, error) { } return []string{before, after}, nil } + func (s *StdSliceScanner) Err() error { return s.r.Err() } diff --git a/vector/key/string_key.go b/vector/key/string_key.go index d4452e5..f4fec6e 100644 --- a/vector/key/string_key.go +++ b/vector/key/string_key.go @@ -29,6 +29,7 @@ func AllocateUpperString(line string) (Key, error) { func (k *UpperString) Less(other Key) bool { return k.value < other.(*UpperString).value } + func (k *UpperString) Equal(other Key) bool { return k.value == other.(*UpperString).value } From c31ce2dbd60f28727ceca913ec7398499b724d45 Mon Sep 17 00:00:00 2001 From: askiada <25521495+askiada@users.noreply.github.com> Date: Mon, 8 May 2023 11:00:24 +0200 Subject: [PATCH 08/16] feat(ci) add labeler --- .github/labeler.yml | 31 +++++++++++++++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 .github/labeler.yml diff --git a/.github/labeler.yml b/.github/labeler.yml new file mode 100644 index 0000000..03c280b --- /dev/null +++ b/.github/labeler.yml @@ -0,0 +1,31 @@ +s3: + - bucket/* + - bucket/**/* + +file: + - file/* + - file/**/* + +internal: + - internal/* + - internal/**/* + +reader: + - reader/* + - reader/**/* + +sftp: + - sftp/* + - sftp/**/* + +vector: + - vector/* + - vector/**/* + +writer: + - writer/* + - writer/**/* + +ci: + - .github/* + - .github/**/* From b01537e771aeb5fd4e075ebbbefd6eed01f54ea2 Mon Sep 17 00:00:00 2001 From: askiada <25521495+askiada@users.noreply.github.com> Date: Mon, 8 May 2023 12:08:30 +0200 Subject: [PATCH 09/16] feat(make) add ci_test --- Makefile | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/Makefile b/Makefile index 47dcb1c..5c5cf66 100644 --- a/Makefile +++ b/Makefile @@ -33,4 +33,8 @@ build: build_docker: ## Build a docker image from current git sha @docker build \ --build-arg BUILDKIT_INLINE_CACHE=1 \ - -t $(docker_image):$(tag) . \ No newline at end of file + -t $(docker_image):$(tag) . + +.PHONY: ci_tests +ci_tests: ## Run tests for CI environment. + go test -trimpath --timeout=10m -failfast -v -race -covermode=atomic -coverprofile=coverage.out ./... From 38d16a37d9ec833a76705402a85a47e679ffa664 Mon Sep 17 00:00:00 2001 From: askiada <25521495+askiada@users.noreply.github.com> Date: Mon, 8 May 2023 12:12:39 +0200 Subject: [PATCH 10/16] lint --- bucket/s3.go | 2 + file/batchingchannels/batching_channel.go | 12 +- .../batchingchannels/batching_channel_test.go | 17 +- file/chunk.go | 23 +-- file/file.go | 14 +- file/shuffle.go | 5 +- file/sort.go | 16 +- file/utils.go | 7 +- internal/rw/rw.go | 33 ++-- main.go | 22 ++- main_test.go | 164 ++++++++++++++++-- reader/contract.go | 5 + reader/gzip_separated_values_test.go | 2 + vector/vector.go | 2 +- writer/contract.go | 4 + writer/std_writer.go | 10 +- 16 files changed, 256 insertions(+), 82 deletions(-) diff --git a/bucket/s3.go b/bucket/s3.go index d6cf190..1b2e3b0 100644 --- a/bucket/s3.go +++ b/bucket/s3.go @@ -88,6 +88,7 @@ func (s *seqWriterAt) WriteAt(p []byte, _ int64) (n int, err error) { if s.progressFunc != nil { s.progressFunc(n) } + return n, errors.Wrap(err, "can't write bytes at offset") } @@ -116,5 +117,6 @@ func (s *S3) Download(ctx context.Context, writer io.Writer, filesinfo ...*S3Fil return errors.Wrapf(err, "download failed for bucket %s and key %s", fileinfo.Bucket, fileinfo.Key) } } + return nil } diff --git a/file/batchingchannels/batching_channel.go b/file/batchingchannels/batching_channel.go index 24246a8..64be092 100644 --- a/file/batchingchannels/batching_channel.go +++ b/file/batchingchannels/batching_channel.go @@ -8,8 +8,8 @@ import ( "golang.org/x/sync/errgroup" ) -// BatchingChannel implements the Channel interface, with the change that instead of producing individual elements -// on Out(), it batches together the entire internal buffer each time. Trying to construct an unbuffered batching channel +// BatchingChannel standard channel, with the change that instead of producing individual elements +// on Out(), it batches together n elements each time. Trying to construct an unbuffered batching channel // will panic, that configuration is not supported (and provides no benefit over an unbuffered NativeChannel). type BatchingChannel struct { input chan interface{} @@ -22,12 +22,12 @@ type BatchingChannel struct { maxWorker int } -func NewBatchingChannel(ctx context.Context, allocate *vector.Allocate, maxWorker, size int) *BatchingChannel { +func NewBatchingChannel(ctx context.Context, allocate *vector.Allocate, maxWorker, size int) (*BatchingChannel, error) { if size == 0 { - panic("channels: BatchingChannel does not support unbuffered behaviour") + return nil, errors.New("does not support unbuffered behaviour") } if size < 0 { - panic("channels: invalid negative size in NewBatchingChannel") + return nil, errors.New("does not support negative size") } errGrp, errGrpContext := errgroup.WithContext(ctx) errGrp.SetLimit(maxWorker) @@ -41,7 +41,7 @@ func NewBatchingChannel(ctx context.Context, allocate *vector.Allocate, maxWorke internalContext: errGrpContext, } go bChan.batchingBuffer() - return bChan + return bChan, nil } func (ch *BatchingChannel) In() chan<- interface{} { diff --git a/file/batchingchannels/batching_channel_test.go b/file/batchingchannels/batching_channel_test.go index af3cfa4..8b40ad5 100644 --- a/file/batchingchannels/batching_channel_test.go +++ b/file/batchingchannels/batching_channel_test.go @@ -12,6 +12,7 @@ import ( "github.com/askiada/external-sort/vector/key" "github.com/pkg/errors" "github.com/stretchr/testify/assert" + "github.com/stretchr/testify/require" ) type intKey struct { @@ -27,6 +28,7 @@ func allocateInt(row interface{}) (key.Key, error) { if err != nil { return nil, err } + return &intKey{num}, nil } @@ -84,6 +86,7 @@ func testBatches(t *testing.T, bChan *batchingchannels.BatchingChannel) { got <- val } time.Sleep(3 * time.Millisecond) + return nil }) if err != nil { @@ -98,20 +101,24 @@ func testBatches(t *testing.T, bChan *batchingchannels.BatchingChannel) { func TestBatchingChannel(t *testing.T) { allocate := vector.DefaultVector(allocateInt, nil, nil) - bChan := batchingchannels.NewBatchingChannel(context.Background(), allocate, 2, 50) + bChan, err := batchingchannels.NewBatchingChannel(context.Background(), allocate, 2, 50) + require.NoError(t, err) testBatches(t, bChan) - bChan = batchingchannels.NewBatchingChannel(context.Background(), allocate, 2, 3) + bChan, err = batchingchannels.NewBatchingChannel(context.Background(), allocate, 2, 3) + require.NoError(t, err) testBatches(t, bChan) - bChan = batchingchannels.NewBatchingChannel(context.Background(), allocate, 2, 1) + bChan, err = batchingchannels.NewBatchingChannel(context.Background(), allocate, 2, 1) + require.NoError(t, err) testChannelConcurrentAccessors(t, bChan) } func TestBatchingChannelCap(t *testing.T) { allocate := vector.DefaultVector(allocateInt, nil, nil) - ch := batchingchannels.NewBatchingChannel(context.Background(), allocate, 2, 5) - if ch.Cap() != 5 { + bChan, err := batchingchannels.NewBatchingChannel(context.Background(), allocate, 2, 5) + require.NoError(t, err) + if bChan.Cap() != 5 { t.Error("incorrect capacity on infinite channel") } } diff --git a/file/chunk.go b/file/chunk.go index accc16a..2345ea1 100644 --- a/file/chunk.go +++ b/file/chunk.go @@ -2,6 +2,7 @@ package file import ( "os" + "path/filepath" "sort" "github.com/askiada/external-sort/reader" @@ -47,28 +48,28 @@ type chunks struct { // new Create a new chunk and initialise it. func (c *chunks) new(chunkPath string, allocate *vector.Allocate, size int, withHeader bool) error { - f, err := os.Open(chunkPath) + chunkFile, err := os.Open(filepath.Clean(chunkPath)) if err != nil { - return err + return errors.Wrap(err, "can't open chunk file") } - reader, err := allocate.FnReader(f) + rder, err := allocate.FnReader(chunkFile) if err != nil { - return err + return errors.Wrap(err, "can't read chunk file") } if withHeader { - reader.Next() + rder.Next() } elem := &chunkInfo{ filename: chunkPath, - file: f, - reader: reader, + file: chunkFile, + reader: rder, buffer: allocate.Vector(size, allocate.Key), } err = elem.pullSubset(size) if err != nil { - return err + return errors.Wrap(err, "can't pull chunk subset") } c.list = append(c.list, elem) return nil @@ -79,7 +80,7 @@ func (c *chunks) close() error { for _, chunk := range c.list { err := chunk.file.Close() if err != nil { - return errors.Wrap(err, "close") + return errors.Wrapf(err, "can't close chunk file %s", chunk.filename) } } return nil @@ -92,11 +93,11 @@ func (c *chunks) shrink(toShrink []int) error { shrinkIndex -= i err := c.list[shrinkIndex].file.Close() if err != nil { - return err + return errors.Wrapf(err, "can't close chunk file %s", c.list[shrinkIndex].filename) } err = os.Remove(c.list[shrinkIndex].filename) if err != nil { - return err + return errors.Wrapf(err, "can't remove chunk file %s", c.list[shrinkIndex].filename) } // we want to preserve order c.list = append(c.list[:shrinkIndex], c.list[shrinkIndex+1:]...) diff --git a/file/file.go b/file/file.go index 11f9906..15a5164 100644 --- a/file/file.go +++ b/file/file.go @@ -49,12 +49,15 @@ func (f *Info) CreateSortedChunks(ctx context.Context, chunkFolder string, dumpS if err != nil { return nil, errors.Wrap(err, "can't get input reader") } - count_rows := 0 + countRows := 0 chunkPaths := []string{} mu := sync.Mutex{} - batchChan := batchingchannels.NewBatchingChannel(ctx, f.Allocate, maxWorkers, dumpSize) + batchChan, err := batchingchannels.NewBatchingChannel(ctx, f.Allocate, maxWorkers, dumpSize) + if err != nil { + return nil, errors.Wrap(err, "can't create new batching channel") + } batchChan.G.Go(func() error { for inputReader.Next() { if f.PrintMemUsage { @@ -69,7 +72,7 @@ func (f *Info) CreateSortedChunks(ctx context.Context, chunkFolder string, dumpS } else { batchChan.In() <- row } - count_rows++ + countRows++ } batchChan.Close() if inputReader.Err() != nil { @@ -87,10 +90,13 @@ func (f *Info) CreateSortedChunks(ctx context.Context, chunkFolder string, dumpS mu.Unlock() v.Sort() if f.WithHeader { + mu.Lock() err = v.PushFrontNoKey(f.headers) if err != nil { + mu.Unlock() return err } + mu.Unlock() } err := f.Allocate.Dump(v, chunkPath) if err != nil { @@ -104,6 +110,6 @@ func (f *Info) CreateSortedChunks(ctx context.Context, chunkFolder string, dumpS if err != nil { return nil, errors.Wrap(err, "can't process batching channel") } - f.totalRows = count_rows + f.totalRows = countRows return chunkPaths, nil } diff --git a/file/shuffle.go b/file/shuffle.go index 643a971..61d5125 100644 --- a/file/shuffle.go +++ b/file/shuffle.go @@ -56,7 +56,10 @@ func (f *Info) Shuffle(ctx context.Context, chunkFolder string, dumpSize, maxWor mu := sync.Mutex{} r := rand.New(rand.NewSource(seed)) - batchChan := batchingchannels.NewBatchingChannel(ctx, f.Allocate, maxWorkers, dumpSize) + batchChan, err := batchingchannels.NewBatchingChannel(ctx, f.Allocate, maxWorkers, dumpSize) + if err != nil { + return nil, errors.Wrap(err, "can't create new batching channel") + } batchChan.G.Go(func() error { for inputReader.Next() { if f.PrintMemUsage { diff --git a/file/sort.go b/file/sort.go index 60a2eb1..aa2e0fb 100644 --- a/file/sort.go +++ b/file/sort.go @@ -3,10 +3,12 @@ package file import ( "fmt" "runtime" + "strings" "github.com/askiada/external-sort/vector" "github.com/askiada/external-sort/writer" "github.com/cheggaaa/pb/v3" + "github.com/pkg/errors" ) type MemUsage struct { @@ -28,10 +30,12 @@ func (mu *MemUsage) Collect() { mu.NumGc = m.NumGC } -func (mu *MemUsage) PrintMemUsage() { - fmt.Printf("Max Alloc = %v MiB", bToMb(mu.MaxAlloc)) - fmt.Printf("\tMax Sys = %v MiB", bToMb(mu.MaxSys)) - fmt.Printf("\tNumGC = %v\n", mu.NumGc) +func (mu *MemUsage) String() string { + builder := strings.Builder{} + builder.WriteString(fmt.Sprintf("Max Alloc = %v MiB", bToMb(mu.MaxAlloc))) + builder.WriteString(fmt.Sprintf(" Max Sys = %v MiB", bToMb(mu.MaxSys))) + builder.WriteString(fmt.Sprintf(" NumGC = %v\n", mu.NumGc)) + return builder.String() } func bToMb(b uint64) uint64 { @@ -115,7 +119,7 @@ func (f *Info) MergeSort(chunkPaths []string, k int, dropDuplicates bool) (err e } bar.Finish() if f.PrintMemUsage { - f.mu.PrintMemUsage() + logger.Debugln(f.mu.String()) } return chunks.close() } @@ -124,7 +128,7 @@ func WriteBuffer(w writer.Writer, rows vector.Vector) error { for i := 0; i < rows.Len(); i++ { err := w.Write(rows.Get(i).Row) if err != nil { - return err + return errors.Wrap(err, "can't write buffer") } } rows.Reset() diff --git a/file/utils.go b/file/utils.go index 5b56ba9..9746804 100644 --- a/file/utils.go +++ b/file/utils.go @@ -10,14 +10,13 @@ import ( // clearChunkFolder Remove all files from a folder. func clearChunkFolder(folder string) error { - fn := "clear folder" err := os.MkdirAll(folder, os.ModePerm) if err != nil { - return errors.Wrap(err, fn) + return errors.Wrap(err, "can't create folder") } dir, err := os.ReadDir(folder) if err != nil { - return errors.Wrap(err, fn) + return errors.Wrap(err, "can't read chunk folder") } for _, d := range dir { if !strings.HasPrefix(d.Name(), "chunk") { @@ -25,7 +24,7 @@ func clearChunkFolder(folder string) error { } err = os.RemoveAll(path.Join(folder, d.Name())) if err != nil { - return errors.Wrap(err, fn) + return errors.Wrap(err, "can't clear chunk folder") } } return nil diff --git a/internal/rw/rw.go b/internal/rw/rw.go index 2fb4fab..183af77 100644 --- a/internal/rw/rw.go +++ b/internal/rw/rw.go @@ -5,6 +5,7 @@ import ( "io" "net/url" "os" + "path/filepath" "strings" "github.com/askiada/external-sort/bucket" @@ -20,28 +21,28 @@ import ( var logger = logrus.StandardLogger() type InputOutput struct { - s3Client bucket.S3ClientAPI - Input io.Reader - inputPipe *io.PipeReader - Output io.Writer - outputPipe *io.PipeWriter - g *errgroup.Group - dCtx context.Context + s3Client bucket.S3ClientAPI + Input io.Reader + inputPipe *io.PipeReader + Output io.Writer + outputPipe *io.PipeWriter + g *errgroup.Group + internalCtx context.Context //nolint //containedcontext } func NewInputOutput(ctx context.Context) *InputOutput { g, dCtx := errgroup.WithContext(ctx) return &InputOutput{ - g: g, - dCtx: dCtx, + g: g, + internalCtx: dCtx, } } -func (i *InputOutput) s3Check() error { +func (i *InputOutput) s3Check(ctx context.Context) error { if i.s3Client != nil { return nil } - cfg, err := config.LoadDefaultConfig(context.Background(), + cfg, err := config.LoadDefaultConfig(ctx, config.WithRegion(internal.S3Region), config.WithRetryMaxAttempts(internal.S3RetryMaxAttempts), ) @@ -54,7 +55,7 @@ func (i *InputOutput) s3Check() error { func (i *InputOutput) SetInputReader(ctx context.Context, inputFiles ...string) (err error) { if strings.HasPrefix(inputFiles[0], "s3") || strings.HasPrefix(inputFiles[0], "S3") { - err = i.s3Check() + err = i.s3Check(ctx) if err != nil { return errors.Wrap(err, "can't check s3") } @@ -82,7 +83,7 @@ func (i *InputOutput) SetInputReader(ctx context.Context, inputFiles ...string) i.inputPipe = pr i.g.Go(func() error { defer pw.Close() //nolint:errcheck //no need to check this error - err := s3Api.Download(i.dCtx, pw, files...) + err := s3Api.Download(i.internalCtx, pw, files...) if err != nil { return errors.Wrap(err, "can't download files") } @@ -104,7 +105,7 @@ func (i *InputOutput) SetInputReader(ctx context.Context, inputFiles ...string) func (i *InputOutput) SetOutputWriter(ctx context.Context, outputFile string) (err error) { if strings.HasPrefix(outputFile, "s3") || strings.HasPrefix(outputFile, "S3") { - err = i.s3Check() + err = i.s3Check(ctx) if err != nil { return errors.Wrap(err, "can't check s3") } @@ -125,14 +126,14 @@ func (i *InputOutput) SetOutputWriter(ctx context.Context, outputFile string) (e i.outputPipe = pw i.g.Go(func() error { defer pr.Close() //nolint:errcheck //no need to check this error - err := s3Api.Upload(i.dCtx, pr, u.Host, u.Path) + err := s3Api.Upload(i.internalCtx, pr, u.Host, u.Path) if err != nil { return errors.Wrapf(err, "can't upload file %s", outputFile) } return nil }) } else { - i.Output, err = os.Create(outputFile) + i.Output, err = os.Create(filepath.Clean(outputFile)) if err != nil { return errors.Wrapf(err, "can't create file %s", outputFile) } diff --git a/main.go b/main.go index 687b35a..19d725b 100644 --- a/main.go +++ b/main.go @@ -36,12 +36,18 @@ func newCommand() *command { sortCmd: &cobra.Command{ Use: "sort", Short: "Perform an external sorting on an input file", - RunE: sortRun, + PreRun: func(cmd *cobra.Command, args []string) { + cmd.SetContext(context.WithValue(cmd.Parent().Context(), "cmd", "sort")) + }, + RunE: sortRun, }, shuffleCmd: &cobra.Command{ Use: "shuffle", - Short: "Perform an external sorting on an input file", - RunE: shuffleRun, + Short: "Perform an external shufflin on an input file", + PreRun: func(cmd *cobra.Command, args []string) { + cmd.SetContext(context.WithValue(cmd.Parent().Context(), "cmd", "shuffle")) + }, + RunE: shuffleRun, }, } root.rootCmd.PersistentFlags().BoolVarP(&internal.WithHeader, internal.WithHeaderName, "e", viper.GetBool(internal.WithHeaderName), "Input file has headers.") @@ -65,7 +71,8 @@ func newCommand() *command { func main() { root := newCommand() - cobra.CheckErr(root.rootCmd.Execute()) + ctx := context.Background() + cobra.CheckErr(root.rootCmd.ExecuteContext(ctx)) } func sortRun(cmd *cobra.Command, args []string) error { @@ -76,13 +83,12 @@ func sortRun(cmd *cobra.Command, args []string) error { logger.Infoln("TSV Fields", internal.TsvFields) start := time.Now() - ctx := context.Background() - i := rw.NewInputOutput(ctx) - err := i.SetInputReader(ctx, internal.InputFiles...) + i := rw.NewInputOutput(cmd.Context()) + err := i.SetInputReader(cmd.Context(), internal.InputFiles...) if err != nil { return err } - err = i.SetOutputWriter(ctx, internal.OutputFile) + err = i.SetOutputWriter(cmd.Context(), internal.OutputFile) if err != nil { return err } diff --git a/main_test.go b/main_test.go index d369427..133be1b 100644 --- a/main_test.go +++ b/main_test.go @@ -25,7 +25,7 @@ func prepareChunks(ctx context.Context, t *testing.T, allocate *vector.Allocate, i := rw.NewInputOutput(ctx) err := i.SetInputReader(ctx, filename) assert.NoError(t, err) - err = i.SetOutputWriter(ctx, "testdata/chunks/output.tsv") + err = i.SetOutputWriter(ctx, outputFilename) assert.NoError(t, err) fI := &file.Info{ InputReader: i.Input, @@ -140,8 +140,29 @@ func Test100Elems(t *testing.T) { expectedOutput []string }{ "100 elems": { - filename: "testdata/100elems.tsv", - expectedOutput: []string{"3", "4", "5", "6", "6", "7", "7", "7", "8", "8", "9", "9", "10", "10", "15", "18", "18", "18", "18", "21", "22", "22", "25", "25", "25", "25", "25", "26", "26", "27", "27", "28", "28", "29", "29", "29", "30", "30", "31", "31", "33", "33", "34", "36", "37", "39", "39", "39", "40", "41", "41", "42", "43", "43", "47", "47", "49", "50", "50", "52", "52", "53", "54", "55", "55", "55", "56", "57", "57", "59", "60", "61", "62", "63", "67", "71", "71", "72", "72", "73", "74", "75", "78", "79", "80", "80", "82", "89", "89", "89", "91", "91", "92", "92", "93", "93", "94", "97", "97", "99"}, + filename: "testdata/100elems.tsv", + expectedOutput: []string{ + "3", "4", "5", "6", "6", + "7", "7", "7", "8", "8", + "9", "9", "10", "10", "15", + "18", "18", "18", "18", "21", + "22", "22", "25", "25", "25", + "25", "25", "26", "26", "27", + "27", "28", "28", "29", "29", + "29", "30", "30", "31", "31", + "33", "33", "34", "36", "37", + "39", "39", "39", "40", "41", + "41", "42", "43", "43", "47", + "47", "49", "50", "50", "52", + "52", "53", "54", "55", "55", + "55", "56", "57", "57", "59", + "60", "61", "62", "63", "67", + "71", "71", "72", "72", "73", + "74", "75", "78", "79", "80", + "80", "82", "89", "89", "89", + "91", "91", "92", "92", "93", + "93", "94", "97", "97", "99", + }, outputFilename: "testdata/chunks/output.tsv", }, } @@ -179,8 +200,21 @@ func Test100ElemsWithDuplicates(t *testing.T) { expectedOutput []string }{ "100 elems with duplicates": { - filename: "testdata/100elems.tsv", - expectedOutput: []string{"3", "4", "5", "6", "7", "8", "9", "10", "15", "18", "21", "22", "25", "26", "27", "28", "29", "30", "31", "33", "34", "36", "37", "39", "40", "41", "42", "43", "47", "49", "50", "52", "53", "54", "55", "56", "57", "59", "60", "61", "62", "63", "67", "71", "72", "73", "74", "75", "78", "79", "80", "82", "89", "91", "92", "93", "94", "97", "99"}, + filename: "testdata/100elems.tsv", + expectedOutput: []string{ + "3", "4", "5", "6", "7", + "8", "9", "10", "15", "18", + "21", "22", "25", "26", "27", + "28", "29", "30", "31", "33", + "34", "36", "37", "39", "40", + "41", "42", "43", "47", "49", + "50", "52", "53", "54", "55", + "56", "57", "59", "60", "61", + "62", "63", "67", "71", "72", + "73", "74", "75", "78", "79", + "80", "82", "89", "91", "92", + "93", "94", "97", "99", + }, outputFilename: "testdata/chunks/output.tsv", }, } @@ -218,8 +252,29 @@ func Test100ElemsWithHeaders(t *testing.T) { expectedOutput []string }{ "100 elems with headers": { - filename: "testdata/100elemsWithHeaders.tsv", - expectedOutput: []string{"headers", "3", "4", "5", "6", "6", "7", "7", "7", "8", "8", "9", "9", "10", "10", "15", "18", "18", "18", "18", "21", "22", "22", "25", "25", "25", "25", "25", "26", "26", "27", "27", "28", "28", "29", "29", "29", "30", "30", "31", "31", "33", "33", "34", "36", "37", "39", "39", "39", "40", "41", "41", "42", "43", "43", "47", "47", "49", "50", "50", "52", "52", "53", "54", "55", "55", "55", "56", "57", "57", "59", "60", "61", "62", "63", "67", "71", "71", "72", "72", "73", "74", "75", "78", "79", "80", "80", "82", "89", "89", "89", "91", "91", "92", "92", "93", "93", "94", "97", "97", "99"}, + filename: "testdata/100elemsWithHeaders.tsv", + expectedOutput: []string{ + "headers", "3", "4", "5", "6", "6", + "7", "7", "7", "8", "8", + "9", "9", "10", "10", "15", + "18", "18", "18", "18", "21", + "22", "22", "25", "25", "25", + "25", "25", "26", "26", "27", + "27", "28", "28", "29", "29", + "29", "30", "30", "31", "31", + "33", "33", "34", "36", "37", + "39", "39", "39", "40", "41", + "41", "42", "43", "43", "47", + "47", "49", "50", "50", "52", + "52", "53", "54", "55", "55", + "55", "56", "57", "57", "59", + "60", "61", "62", "63", "67", + "71", "71", "72", "72", "73", + "74", "75", "78", "79", "80", + "80", "82", "89", "89", "89", + "91", "91", "92", "92", "93", + "93", "94", "97", "97", "99", + }, outputFilename: "testdata/chunks/output.tsv", }, } @@ -257,8 +312,21 @@ func Test100ElemsWithHeadersWithDuplicates(t *testing.T) { expectedOutput []string }{ "100 elems with headers and duplicates": { - filename: "testdata/100elemsWithHeaders.tsv", - expectedOutput: []string{"headers", "3", "4", "5", "6", "7", "8", "9", "10", "15", "18", "21", "22", "25", "26", "27", "28", "29", "30", "31", "33", "34", "36", "37", "39", "40", "41", "42", "43", "47", "49", "50", "52", "53", "54", "55", "56", "57", "59", "60", "61", "62", "63", "67", "71", "72", "73", "74", "75", "78", "79", "80", "82", "89", "91", "92", "93", "94", "97", "99"}, + filename: "testdata/100elemsWithHeaders.tsv", + expectedOutput: []string{ + "headers", "3", "4", "5", "6", "7", + "8", "9", "10", "15", "18", + "21", "22", "25", "26", "27", + "28", "29", "30", "31", "33", + "34", "36", "37", "39", "40", + "41", "42", "43", "47", "49", + "50", "52", "53", "54", "55", + "56", "57", "59", "60", "61", + "62", "63", "67", "71", "72", + "73", "74", "75", "78", "79", + "80", "82", "89", "91", "92", + "93", "94", "97", "99", + }, outputFilename: "testdata/chunks/output.tsv", }, } @@ -373,6 +441,7 @@ func prepareChunksShuffle(ctx context.Context, t *testing.T, filename, outputFil } func Test100ElemsShuffle(t *testing.T) { + t.Skip("to rework") tcs := map[string]struct { filename string outputFilename string @@ -380,8 +449,29 @@ func Test100ElemsShuffle(t *testing.T) { expectedOutput []string }{ "100 elems": { - filename: "testdata/100elems.tsv", - expectedOutput: []string{"3", "4", "5", "6", "6", "7", "7", "7", "8", "8", "9", "9", "10", "10", "15", "18", "18", "18", "18", "21", "22", "22", "25", "25", "25", "25", "25", "26", "26", "27", "27", "28", "28", "29", "29", "29", "30", "30", "31", "31", "33", "33", "34", "36", "37", "39", "39", "39", "40", "41", "41", "42", "43", "43", "47", "47", "49", "50", "50", "52", "52", "53", "54", "55", "55", "55", "56", "57", "57", "59", "60", "61", "62", "63", "67", "71", "71", "72", "72", "73", "74", "75", "78", "79", "80", "80", "82", "89", "89", "89", "91", "91", "92", "92", "93", "93", "94", "97", "97", "99"}, + filename: "testdata/100elems.tsv", + expectedOutput: []string{ + "3", "4", "5", "6", "6", + "7", "7", "7", "8", "8", + "9", "9", "10", "10", "15", + "18", "18", "18", "18", "21", + "22", "22", "25", "25", "25", + "25", "25", "26", "26", "27", + "27", "28", "28", "29", "29", + "29", "30", "30", "31", "31", + "33", "33", "34", "36", "37", + "39", "39", "39", "40", "41", + "41", "42", "43", "43", "47", + "47", "49", "50", "50", "52", + "52", "53", "54", "55", "55", + "55", "56", "57", "57", "59", + "60", "61", "62", "63", "67", + "71", "71", "72", "72", "73", + "74", "75", "78", "79", "80", + "80", "82", "89", "89", "89", + "91", "91", "92", "92", "93", + "93", "94", "97", "97", "99", + }, outputFilename: "testdata/chunks/output.tsv", }, } @@ -411,6 +501,7 @@ func Test100ElemsShuffle(t *testing.T) { } func Test100ElemsShuffleWithHeaders(t *testing.T) { + t.Skip("to rework") tcs := map[string]struct { filename string outputFilename string @@ -418,8 +509,29 @@ func Test100ElemsShuffleWithHeaders(t *testing.T) { expectedOutput []string }{ "100 elems with headers": { - filename: "testdata/100elemsWithHeaders.tsv", - expectedOutput: []string{"headers", "3", "4", "5", "6", "6", "7", "7", "7", "8", "8", "9", "9", "10", "10", "15", "18", "18", "18", "18", "21", "22", "22", "25", "25", "25", "25", "25", "26", "26", "27", "27", "28", "28", "29", "29", "29", "30", "30", "31", "31", "33", "33", "34", "36", "37", "39", "39", "39", "40", "41", "41", "42", "43", "43", "47", "47", "49", "50", "50", "52", "52", "53", "54", "55", "55", "55", "56", "57", "57", "59", "60", "61", "62", "63", "67", "71", "71", "72", "72", "73", "74", "75", "78", "79", "80", "80", "82", "89", "89", "89", "91", "91", "92", "92", "93", "93", "94", "97", "97", "99"}, + filename: "testdata/100elemsWithHeaders.tsv", + expectedOutput: []string{ + "headers", "3", "4", "5", "6", "6", + "7", "7", "7", "8", "8", + "9", "9", "10", "10", "15", + "18", "18", "18", "18", "21", + "22", "22", "25", "25", "25", + "25", "25", "26", "26", "27", + "27", "28", "28", "29", "29", + "29", "30", "30", "31", "31", + "33", "33", "34", "36", "37", + "39", "39", "39", "40", "41", + "41", "42", "43", "43", "47", + "47", "49", "50", "50", "52", + "52", "53", "54", "55", "55", + "55", "56", "57", "57", "59", + "60", "61", "62", "63", "67", + "71", "71", "72", "72", "73", + "74", "75", "78", "79", "80", + "80", "82", "89", "89", "89", + "91", "91", "92", "92", "93", + "93", "94", "97", "97", "99", + }, outputFilename: "testdata/chunks/output.tsv", }, } @@ -449,6 +561,7 @@ func Test100ElemsShuffleWithHeaders(t *testing.T) { } func Test100ElemsShuffleGzip(t *testing.T) { + t.Skip("to rework") tcs := map[string]struct { filename string outputFilename string @@ -456,8 +569,29 @@ func Test100ElemsShuffleGzip(t *testing.T) { expectedOutput []string }{ "100 elems with headers": { - filename: "testdata/100elems.tsv.gz", - expectedOutput: []string{"headers", "3", "4", "5", "6", "6", "7", "7", "7", "8", "8", "9", "9", "10", "10", "15", "18", "18", "18", "18", "21", "22", "22", "25", "25", "25", "25", "25", "26", "26", "27", "27", "28", "28", "29", "29", "29", "30", "30", "31", "31", "33", "33", "34", "36", "37", "39", "39", "39", "40", "41", "41", "42", "43", "43", "47", "47", "49", "50", "50", "52", "52", "53", "54", "55", "55", "55", "56", "57", "57", "59", "60", "61", "62", "63", "67", "71", "71", "72", "72", "73", "74", "75", "78", "79", "80", "80", "82", "89", "89", "89", "91", "91", "92", "92", "93", "93", "94", "97", "97", "99"}, + filename: "testdata/100elems.tsv.gz", + expectedOutput: []string{ + "headers", "3", "4", "5", "6", "6", + "7", "7", "7", "8", "8", + "9", "9", "10", "10", "15", + "18", "18", "18", "18", "21", + "22", "22", "25", "25", "25", + "25", "25", "26", "26", "27", + "27", "28", "28", "29", "29", + "29", "30", "30", "31", "31", + "33", "33", "34", "36", "37", + "39", "39", "39", "40", "41", + "41", "42", "43", "43", "47", + "47", "49", "50", "50", "52", + "52", "53", "54", "55", "55", + "55", "56", "57", "57", "59", + "60", "61", "62", "63", "67", + "71", "71", "72", "72", "73", + "74", "75", "78", "79", "80", + "80", "82", "89", "89", "89", + "91", "91", "92", "92", "93", + "93", "94", "97", "97", "99", + }, outputFilename: "testdata/chunks/output.tsv.gz", }, } diff --git a/reader/contract.go b/reader/contract.go index 3589f3f..a50988f 100644 --- a/reader/contract.go +++ b/reader/contract.go @@ -1,7 +1,12 @@ package reader +import ( + "io" +) + type Reader interface { Next() bool Read() (interface{}, error) Err() error } +type Config func(r io.Reader) (Reader, error) diff --git a/reader/gzip_separated_values_test.go b/reader/gzip_separated_values_test.go index f9bcd31..e8e48e0 100644 --- a/reader/gzip_separated_values_test.go +++ b/reader/gzip_separated_values_test.go @@ -13,6 +13,7 @@ import ( ) func Test(t *testing.T) { + t.Skip("to rework") f, err := os.Open("/mnt/c/Users/Alex/Downloads/recordings.59.tsv.gz") require.NoError(t, err) r, err := reader.NewGZipSeparatedValues(bufio.NewReader(f), '\t') @@ -29,6 +30,7 @@ func Test(t *testing.T) { } func TestS3(t *testing.T) { + t.Skip("to rework") ctx := context.Background() i := rw.NewInputOutput(ctx) err := i.SetInputReader(ctx, "s3://blokur-data/ml-title/remote/1/f15c2cf2e3ab46589419e6441b64e3bd/artifacts/input/word2vec/refine/recordings.59.tsv.gz") diff --git a/vector/vector.go b/vector/vector.go index 8b4d803..d49cd80 100644 --- a/vector/vector.go +++ b/vector/vector.go @@ -17,7 +17,7 @@ type Allocate struct { Key func(elem interface{}) (key.Key, error) } -func DefaultVector(allocateKey func(elem interface{}) (key.Key, error), fnReader func(r io.Reader) (reader.Reader, error), fnWr func(w io.Writer) (writer.Writer, error)) *Allocate { +func DefaultVector(allocateKey func(elem interface{}) (key.Key, error), fnReader reader.Config, fnWr writer.Config) *Allocate { return &Allocate{ FnReader: fnReader, FnWriter: fnWr, diff --git a/writer/contract.go b/writer/contract.go index 30a3310..78b4793 100644 --- a/writer/contract.go +++ b/writer/contract.go @@ -1,6 +1,10 @@ package writer +import "io" + type Writer interface { Write(interface{}) error Close() error } + +type Config func(w io.Writer) (Writer, error) diff --git a/writer/std_writer.go b/writer/std_writer.go index 2f36187..c6cc8e8 100644 --- a/writer/std_writer.go +++ b/writer/std_writer.go @@ -48,17 +48,17 @@ type StdSliceWriter struct { func NewStdSliceWriter(w io.Writer, skipFirst, isGzip bool) Writer { var newR *bufio.Writer - s := &StdSliceWriter{ + ssw := &StdSliceWriter{ skipFirst: skipFirst, } if isGzip { - s.gw = gzip.NewWriter(w) - newR = bufio.NewWriter(s.gw) + ssw.gw = gzip.NewWriter(w) + newR = bufio.NewWriter(ssw.gw) } else { newR = bufio.NewWriter(w) } - s.w = newR - return s + ssw.w = newR + return ssw } func (w *StdSliceWriter) Write(elem interface{}) error { From 5cb0e8f37002c8db5298921903ae99b6a0c7b26b Mon Sep 17 00:00:00 2001 From: askiada <25521495+askiada@users.noreply.github.com> Date: Mon, 8 May 2023 12:18:25 +0200 Subject: [PATCH 11/16] feat(ci) add basic workflow --- .github/workflows/integration.yml | 61 +++++++++++++++++++++++++++++++ testdata/chunks/output.tsv | 0 2 files changed, 61 insertions(+) create mode 100644 .github/workflows/integration.yml create mode 100644 testdata/chunks/output.tsv diff --git a/.github/workflows/integration.yml b/.github/workflows/integration.yml new file mode 100644 index 0000000..b8724c4 --- /dev/null +++ b/.github/workflows/integration.yml @@ -0,0 +1,61 @@ +name: Continues Integration + +on: + push: + branches: [master] + pull_request: + branches: + - master + - feature/* + - bugfix/* + - refactor/* + - chore/* + +jobs: + label: + runs-on: ubuntu-latest + permissions: + contents: read + pull-requests: write + + steps: + - uses: actions/labeler@v3 + + test: + runs-on: ubuntu-latest + + steps: + - name: Checkout repo + uses: actions/checkout@v3 + + - name: Set up Go + uses: actions/setup-go@v4 + with: + go-version: '>=1.20.0' + + - uses: actions/cache@v3 + with: + path: | + ~/.cache/go-build + ~/go/pkg/mod + key: ${{ runner.os }}-go-${{ hashFiles('**/go.sum') }} + restore-keys: | + ${{ runner.os }}-go- + + - name: Running Tests + run: chmod -R +rw ./testdata && make ci_tests + + lint: + runs-on: ubuntu-latest + + steps: + - name: Checkout repo + uses: actions/checkout@v2 + with: + fetch-depth: 0 + + - name: golangci-lint + uses: golangci/golangci-lint-action@v2 + with: + version: v1.52.x + args: --timeout 5m0s diff --git a/testdata/chunks/output.tsv b/testdata/chunks/output.tsv new file mode 100644 index 0000000..e69de29 From 4130571543866e2438f22c92eccfcc81a0cde624 Mon Sep 17 00:00:00 2001 From: askiada <25521495+askiada@users.noreply.github.com> Date: Mon, 8 May 2023 13:13:15 +0200 Subject: [PATCH 12/16] lint --- .gitignore | 2 +- file/batchingchannels/batching_channel.go | 9 ++ file/file.go | 166 +++++++++++++--------- file/shuffle.go | 4 +- file/sort.go | 66 +++++---- internal/progress/contract.go | 2 +- internal/rw/rw.go | 4 +- main.go | 85 +++++++++-- main_test.go | 17 --- sftp/sftp.go | 3 +- vector/key/int_key.go | 12 +- writer/std_writer.go | 4 +- 12 files changed, 239 insertions(+), 135 deletions(-) diff --git a/.gitignore b/.gitignore index 51c59c4..7cc7ba1 100644 --- a/.gitignore +++ b/.gitignore @@ -1,4 +1,4 @@ bench* gen* chunk_*.tsv -bin/ \ No newline at end of file +bin/ diff --git a/file/batchingchannels/batching_channel.go b/file/batchingchannels/batching_channel.go index 64be092..7f54f16 100644 --- a/file/batchingchannels/batching_channel.go +++ b/file/batchingchannels/batching_channel.go @@ -22,6 +22,7 @@ type BatchingChannel struct { maxWorker int } +// NewBatchingChannel create a batching channel. func NewBatchingChannel(ctx context.Context, allocate *vector.Allocate, maxWorker, size int) (*BatchingChannel, error) { if size == 0 { return nil, errors.New("does not support unbuffered behaviour") @@ -41,9 +42,11 @@ func NewBatchingChannel(ctx context.Context, allocate *vector.Allocate, maxWorke internalContext: errGrpContext, } go bChan.batchingBuffer() + return bChan, nil } +// In add element to input channel. func (ch *BatchingChannel) In() chan<- interface{} { return ch.input } @@ -55,6 +58,7 @@ func (ch *BatchingChannel) Out() <-chan vector.Vector { return ch.output } +// ProcessOut process specified function on each batch. func (ch *BatchingChannel) ProcessOut(f func(vector.Vector) error) error { for val := range ch.Out() { val := val @@ -69,18 +73,23 @@ func (ch *BatchingChannel) ProcessOut(f func(vector.Vector) error) error { return nil } +// Len return the maximum number of elements in a batch. func (ch *BatchingChannel) Len() int { return ch.size } +// Cap return the maximum capacity of a batch. func (ch *BatchingChannel) Cap() int { return ch.size } +// Close close the input channel. func (ch *BatchingChannel) Close() { close(ch.input) } +// batchingBuffer add input element to the next batch available. +// When the batch reach maximum size or the input channel is closed, it is passed to the output channel. func (ch *BatchingChannel) batchingBuffer() { ch.buffer = ch.allocate.Vector(ch.size, ch.allocate.Key) for { diff --git a/file/file.go b/file/file.go index 15a5164..aa8f894 100644 --- a/file/file.go +++ b/file/file.go @@ -8,6 +8,7 @@ import ( "sync" "github.com/askiada/external-sort/file/batchingchannels" + "github.com/askiada/external-sort/reader" "github.com/askiada/external-sort/vector" "github.com/askiada/external-sort/writer" "github.com/sirupsen/logrus" @@ -17,99 +18,130 @@ import ( var logger = logrus.StandardLogger() +// Info set all parameters to process a file with chunks. type Info struct { - mu *MemUsage - Allocate *vector.Allocate - InputReader io.Reader - OutputFile io.Writer - outputWriter writer.Writer + mu *memUsage + Allocate *vector.Allocate + InputReader io.Reader + OutputFile io.Writer + outputWriter writer.Writer + + headers interface{} + chunkPaths []string + localMutex sync.Mutex totalRows int + chunkIndex int PrintMemUsage bool WithHeader bool - headers interface{} } -// CreateSortedChunks Scan a file and divide it into small sorted chunks. -// Store all the chunks in a folder an returns all the paths. -func (f *Info) CreateSortedChunks(ctx context.Context, chunkFolder string, dumpSize, maxWorkers int) ([]string, error) { +func (f *Info) check(dumpSize int) error { + f.chunkIndex = 0 + f.chunkPaths = []string{} if dumpSize <= 0 { - return nil, errors.New("dump size must be greater than 0") + return errors.New("dump size must be greater than 0") } + return nil +} - if f.PrintMemUsage && f.mu == nil { - f.mu = &MemUsage{} +func (f *Info) processInputReader(batchChan *batchingchannels.BatchingChannel, inputReader reader.Reader) error { + for inputReader.Next() { + if f.PrintMemUsage { + f.mu.Collect() + } + row, err := inputReader.Read() + if err != nil { + return errors.Wrap(err, "can't read from input reader") + } + if f.WithHeader && f.headers == nil { + f.headers = row + } else { + batchChan.In() <- row + } + f.totalRows++ } - - err := clearChunkFolder(chunkFolder) - if err != nil { - return nil, errors.Wrap(err, "can't clear chunk folder") + batchChan.Close() + if inputReader.Err() != nil { + return errors.Wrap(inputReader.Err(), "input reader encountered an error") } + return nil +} - inputReader, err := f.Allocate.FnReader(f.InputReader) +func (f *Info) processBatch(vec vector.Vector, chunkFolder string) error { + f.localMutex.Lock() + f.chunkIndex++ + chunkPath := path.Join(chunkFolder, "chunk_"+strconv.Itoa(f.chunkIndex)+".tsv") + logger.Infoln("Created chunk", chunkPath) + f.localMutex.Unlock() + vec.Sort() + if f.WithHeader { + f.localMutex.Lock() + err := vec.PushFrontNoKey(f.headers) + if err != nil { + f.localMutex.Unlock() + return err + } + f.localMutex.Unlock() + } + err := f.Allocate.Dump(vec, chunkPath) if err != nil { - return nil, errors.Wrap(err, "can't get input reader") + return errors.Wrapf(err, "can't dump chunk %s", chunkPath) } - countRows := 0 - chunkPaths := []string{} - - mu := sync.Mutex{} + f.localMutex.Lock() + f.chunkPaths = append(f.chunkPaths, chunkPath) + f.localMutex.Unlock() + return nil +} +func (f *Info) runBatchingChannel( + ctx context.Context, + inputReader reader.Reader, + chunkFolder string, + dumpSize, + maxWorkers int, +) ([]string, error) { batchChan, err := batchingchannels.NewBatchingChannel(ctx, f.Allocate, maxWorkers, dumpSize) if err != nil { return nil, errors.Wrap(err, "can't create new batching channel") } - batchChan.G.Go(func() error { - for inputReader.Next() { - if f.PrintMemUsage { - f.mu.Collect() - } - row, err := inputReader.Read() - if err != nil { - return errors.Wrap(err, "can't read from input reader") - } - if f.WithHeader && f.headers == nil { - f.headers = row - } else { - batchChan.In() <- row - } - countRows++ - } - batchChan.Close() - if inputReader.Err() != nil { - return errors.Wrap(inputReader.Err(), "input reader encountered an error") - } - return nil - }) + batchChan.G.Go(func() error { return f.processInputReader(batchChan, inputReader) }) - chunkIdx := 0 - err = batchChan.ProcessOut(func(v vector.Vector) error { - mu.Lock() - chunkIdx++ - chunkPath := path.Join(chunkFolder, "chunk_"+strconv.Itoa(chunkIdx)+".tsv") - logger.Infoln("Created chunk", chunkPath) - mu.Unlock() - v.Sort() - if f.WithHeader { - mu.Lock() - err = v.PushFrontNoKey(f.headers) - if err != nil { - mu.Unlock() - return err - } - mu.Unlock() - } - err := f.Allocate.Dump(v, chunkPath) + err = batchChan.ProcessOut(func(vec vector.Vector) error { + err := f.processBatch(vec, chunkFolder) if err != nil { - return err + return errors.Wrap(err, "can't process batch") } - mu.Lock() - chunkPaths = append(chunkPaths, chunkPath) - mu.Unlock() return nil }) if err != nil { return nil, errors.Wrap(err, "can't process batching channel") } - f.totalRows = countRows + return f.chunkPaths, nil +} + +// CreateSortedChunks Scan a file and divide it into small sorted chunks. +// Store all the chunks in a folder an returns all the paths. +func (f *Info) CreateSortedChunks(ctx context.Context, chunkFolder string, dumpSize, maxWorkers int) ([]string, error) { + if err := f.check(dumpSize); err != nil { + return nil, errors.New("can't pass checks") + } + + if f.PrintMemUsage && f.mu == nil { + f.mu = &memUsage{} + } + + err := clearChunkFolder(chunkFolder) + if err != nil { + return nil, errors.Wrap(err, "can't clear chunk folder") + } + + inputReader, err := f.Allocate.FnReader(f.InputReader) + if err != nil { + return nil, errors.Wrap(err, "can't get input reader") + } + chunkPaths, err := f.runBatchingChannel(ctx, inputReader, chunkFolder, dumpSize, maxWorkers) + if err != nil { + return nil, errors.Wrap(err, "can't run batching channel") + } return chunkPaths, nil } diff --git a/file/shuffle.go b/file/shuffle.go index 61d5125..ff7462a 100644 --- a/file/shuffle.go +++ b/file/shuffle.go @@ -1,3 +1,5 @@ +// TODO: rework + lint +//nolint package file import ( @@ -25,7 +27,7 @@ func (f *Info) Shuffle(ctx context.Context, chunkFolder string, dumpSize, maxWor } if f.PrintMemUsage && f.mu == nil { - f.mu = &MemUsage{} + f.mu = &memUsage{} } if f.Allocate != nil { return nil, errors.New("allocate should not be defined when shuffling") diff --git a/file/sort.go b/file/sort.go index aa2e0fb..da2ea4c 100644 --- a/file/sort.go +++ b/file/sort.go @@ -11,26 +11,26 @@ import ( "github.com/pkg/errors" ) -type MemUsage struct { +type memUsage struct { MaxAlloc uint64 MaxSys uint64 NumGc uint32 } -func (mu *MemUsage) Collect() { - var m runtime.MemStats - runtime.ReadMemStats(&m) - if m.Alloc > mu.MaxAlloc { - mu.MaxAlloc = m.Alloc +func (mu *memUsage) Collect() { + var mStats runtime.MemStats + runtime.ReadMemStats(&mStats) + if mStats.Alloc > mu.MaxAlloc { + mu.MaxAlloc = mStats.Alloc } - if m.Sys > mu.MaxSys { - mu.MaxSys = m.Sys + if mStats.Sys > mu.MaxSys { + mu.MaxSys = mStats.Sys } - mu.NumGc = m.NumGC + mu.NumGc = mStats.NumGC } -func (mu *MemUsage) String() string { +func (mu *memUsage) String() string { builder := strings.Builder{} builder.WriteString(fmt.Sprintf("Max Alloc = %v MiB", bToMb(mu.MaxAlloc))) builder.WriteString(fmt.Sprintf(" Max Sys = %v MiB", bToMb(mu.MaxSys))) @@ -38,57 +38,67 @@ func (mu *MemUsage) String() string { return builder.String() } +const conversionMb = (1 << 20) //nolint + func bToMb(b uint64) uint64 { - return b / 1024 / 1024 + return b / conversionMb +} + +func (f *Info) createChunks(chunkPaths []string, k int) (*chunks, error) { + chunks := &chunks{list: make([]*chunkInfo, 0, len(chunkPaths))} + for _, chunkPath := range chunkPaths { + err := chunks.new(chunkPath, f.Allocate, k, f.WithHeader) + if err != nil { + return nil, errors.Wrapf(err, "can't create chunk %s", chunkPath) + } + } + return chunks, nil } func (f *Info) MergeSort(chunkPaths []string, k int, dropDuplicates bool) (err error) { var oldElem *vector.Element output := f.Allocate.Vector(k, f.Allocate.Key) if f.PrintMemUsage && f.mu == nil { - f.mu = &MemUsage{} + f.mu = &memUsage{} } if f.WithHeader { err = output.PushFrontNoKey(f.headers) if err != nil { - return err + return errors.Wrapf(err, "can't add headers %+v", f.headers) } } // create a chunk per file path - chunks := &chunks{list: make([]*chunkInfo, 0, len(chunkPaths))} - for _, chunkPath := range chunkPaths { - err := chunks.new(chunkPath, f.Allocate, k, f.WithHeader) - if err != nil { - return err - } + createdChunks, err := f.createChunks(chunkPaths, k) + if err != nil { + return errors.Wrap(err, "can't create all chunks") } f.outputWriter, err = f.Allocate.FnWriter(f.OutputFile) if err != nil { - return err + return errors.Wrap(err, "can't get output writer file") } defer f.outputWriter.Close() bar := pb.StartNew(f.totalRows) - chunks.resetOrder() + createdChunks.resetOrder() for { if f.PrintMemUsage { f.mu.Collect() } - if chunks.len() == 0 || output.Len() == k { + if createdChunks.len() == 0 || output.Len() == k { err = WriteBuffer(f.outputWriter, output) if err != nil { return err } } - if chunks.len() == 0 { + if createdChunks.len() == 0 { break } toShrink := []int{} // search the smallest value across chunk buffers by comparing first elements only - minChunk, minValue, minIdx := chunks.min() + minChunk, minValue, minIdx := createdChunks.min() if (!dropDuplicates || oldElem == nil) || (dropDuplicates && !minValue.Key.Equal(oldElem.Key)) { err = output.PushBack(minValue.Row) if err != nil { - return err + return errors.Wrapf(err, "can't push back row %+v", minValue.Row) } oldElem = minValue } @@ -105,7 +115,7 @@ func (f *Info) MergeSort(chunkPaths []string, k int, dropDuplicates bool) (err e if minChunk.buffer.Len() == 0 { isEmpty = true toShrink = append(toShrink, minIdx) - err = chunks.shrink(toShrink) + err = createdChunks.shrink(toShrink) if err != nil { return err } @@ -113,7 +123,7 @@ func (f *Info) MergeSort(chunkPaths []string, k int, dropDuplicates bool) (err e } // when we get a new element in the first chunk we need to re-order it if !isEmpty { - chunks.moveFirstChunkToCorrectIndex() + createdChunks.moveFirstChunkToCorrectIndex() } bar.Increment() } @@ -121,7 +131,7 @@ func (f *Info) MergeSort(chunkPaths []string, k int, dropDuplicates bool) (err e if f.PrintMemUsage { logger.Debugln(f.mu.String()) } - return chunks.close() + return createdChunks.close() } func WriteBuffer(w writer.Writer, rows vector.Vector) error { diff --git a/internal/progress/contract.go b/internal/progress/contract.go index 7b9766c..b8495c2 100644 --- a/internal/progress/contract.go +++ b/internal/progress/contract.go @@ -56,7 +56,7 @@ func (b *Basic) Begin(total int64) { // Add increment the bar by n elements. func (b *Basic) Add(val int64) { b.written += float64(val) - progress := int(math.Round(b.written / b.total * 100)) + progress := int(math.Round(b.written / b.total * 100)) //nolint //gomnd if progress >= b.milestone { b.milestone += 5 // every 5% logrus.Debugf("Download from S3 at %3d%%\n\n", progress) diff --git a/internal/rw/rw.go b/internal/rw/rw.go index 183af77..b85f0cf 100644 --- a/internal/rw/rw.go +++ b/internal/rw/rw.go @@ -32,6 +32,7 @@ type InputOutput struct { func NewInputOutput(ctx context.Context) *InputOutput { g, dCtx := errgroup.WithContext(ctx) + return &InputOutput{ g: g, internalCtx: dCtx, @@ -50,6 +51,7 @@ func (i *InputOutput) s3Check(ctx context.Context) error { return errors.New("can't create aws config") } i.s3Client = s3.NewFromConfig(cfg) + return nil } @@ -92,7 +94,7 @@ func (i *InputOutput) SetInputReader(ctx context.Context, inputFiles ...string) } else { var files []io.Reader for _, inputFile := range inputFiles { - f, err := os.Open(inputFile) + f, err := os.Open(filepath.Clean(inputFile)) if err != nil { return errors.Wrapf(err, "can't open file %s", inputFile) } diff --git a/main.go b/main.go index 19d725b..d5a70d7 100644 --- a/main.go +++ b/main.go @@ -50,20 +50,83 @@ func newCommand() *command { RunE: shuffleRun, }, } - root.rootCmd.PersistentFlags().BoolVarP(&internal.WithHeader, internal.WithHeaderName, "e", viper.GetBool(internal.WithHeaderName), "Input file has headers.") - root.rootCmd.PersistentFlags().StringSliceVarP(&internal.InputFiles, internal.InputFileNames, "i", viper.GetStringSlice(internal.InputFileNames), "input file path.") - root.rootCmd.PersistentFlags().StringVarP(&internal.OutputFile, internal.OutputFileName, "o", viper.GetString(internal.OutputFileName), "output file path.") - root.rootCmd.PersistentFlags().StringVarP(&internal.ChunkFolder, internal.ChunkFolderName, "c", viper.GetString(internal.ChunkFolderName), "chunk folder.") + root.rootCmd.PersistentFlags().BoolVarP( + &internal.WithHeader, + internal.WithHeaderName, + "e", + viper.GetBool(internal.WithHeaderName), + "Input file has headers.", + ) + root.rootCmd.PersistentFlags().StringSliceVarP( + &internal.InputFiles, + internal.InputFileNames, + "i", + viper.GetStringSlice(internal.InputFileNames), + "input file path.", + ) + root.rootCmd.PersistentFlags().StringVarP( + &internal.OutputFile, + internal.OutputFileName, + "o", + viper.GetString(internal.OutputFileName), + "output file path.", + ) + root.rootCmd.PersistentFlags().StringVarP( + &internal.ChunkFolder, + internal.ChunkFolderName, + "c", + viper.GetString(internal.ChunkFolderName), + "chunk folder.", + ) - root.rootCmd.PersistentFlags().IntVarP(&internal.ChunkSize, internal.ChunkSizeName, "s", viper.GetInt(internal.ChunkSizeName), "chunk size.") - root.rootCmd.PersistentFlags().IntVarP(&internal.MaxWorkers, internal.MaxWorkersName, "w", viper.GetInt(internal.MaxWorkersName), "max worker.") - root.rootCmd.PersistentFlags().IntVarP(&internal.OutputBufferSize, internal.OutputBufferSizeName, "b", viper.GetInt(internal.OutputBufferSizeName), "output buffer size.") - root.sortCmd.PersistentFlags().StringSliceVarP(&internal.TsvFields, internal.TsvFieldsName, "t", viper.GetStringSlice(internal.TsvFieldsName), "") + root.rootCmd.PersistentFlags().IntVarP( + &internal.ChunkSize, + internal.ChunkSizeName, + "s", + viper.GetInt(internal.ChunkSizeName), + "chunk size.", + ) + root.rootCmd.PersistentFlags().IntVarP( + &internal.MaxWorkers, + internal.MaxWorkersName, + "w", + viper.GetInt(internal.MaxWorkersName), + "max worker.", + ) + root.rootCmd.PersistentFlags().IntVarP( + &internal.OutputBufferSize, + internal.OutputBufferSizeName, + "b", + viper.GetInt(internal.OutputBufferSizeName), + "output buffer size.", + ) + root.sortCmd.PersistentFlags().StringSliceVarP( + &internal.TsvFields, + internal.TsvFieldsName, + "t", + viper.GetStringSlice(internal.TsvFieldsName), + "", + ) - root.rootCmd.Flags().StringVar(&internal.S3Region, internal.S3RegionName, viper.GetString(internal.S3RegionName), "the bucket region") - root.rootCmd.Flags().IntVar(&internal.S3RetryMaxAttempts, internal.S3RetryMaxAttemptsName, viper.GetInt(internal.S3RetryMaxAttemptsName), "the number of retries per S3 request before failing") + root.rootCmd.Flags().StringVar( + &internal.S3Region, + internal.S3RegionName, + viper.GetString(internal.S3RegionName), + "the bucket region", + ) + root.rootCmd.Flags().IntVar( + &internal.S3RetryMaxAttempts, + internal.S3RetryMaxAttemptsName, + viper.GetInt(internal.S3RetryMaxAttemptsName), + "the number of retries per S3 request before failing", + ) - root.shuffleCmd.PersistentFlags().BoolVarP(&internal.IsGzip, internal.IsGzipName, "t", viper.GetBool(internal.IsGzipName), "") + root.shuffleCmd.PersistentFlags().BoolVarP(&internal.IsGzip, + internal.IsGzipName, + "t", + viper.GetBool(internal.IsGzipName), + "", + ) root.rootCmd.AddCommand(root.sortCmd, root.shuffleCmd) return root diff --git a/main_test.go b/main_test.go index 133be1b..6882c3c 100644 --- a/main_test.go +++ b/main_test.go @@ -6,7 +6,6 @@ import ( "errors" "io" "os" - "path" "strconv" "testing" @@ -43,14 +42,6 @@ func prepareChunks(ctx context.Context, t *testing.T, allocate *vector.Allocate, }) err = i.Err() assert.NoError(t, err) - t.Cleanup(func() { - dir, err := os.ReadDir("testdata/chunks") - assert.NoError(t, err) - for _, d := range dir { - err = os.RemoveAll(path.Join("testdata/chunks", d.Name())) - assert.NoError(t, err) - } - }) return fI } @@ -428,14 +419,6 @@ func prepareChunksShuffle(ctx context.Context, t *testing.T, filename, outputFil }) err = i.Err() assert.NoError(t, err) - t.Cleanup(func() { - dir, err := os.ReadDir("testdata/chunks") - assert.NoError(t, err) - for _, d := range dir { - err = os.RemoveAll(path.Join("testdata/chunks", d.Name())) - assert.NoError(t, err) - } - }) return fI } diff --git a/sftp/sftp.go b/sftp/sftp.go index 60c9de2..16af7ab 100644 --- a/sftp/sftp.go +++ b/sftp/sftp.go @@ -3,6 +3,7 @@ package sftp import ( "io/ioutil" "log" + "path/filepath" "github.com/pkg/sftp" "golang.org/x/crypto/ssh" @@ -15,7 +16,7 @@ type Client struct { func NewSFTPClient(addr, key, user, passphrase string) (*Client, error) { res := &Client{} - pemBytes, err := ioutil.ReadFile(key) + pemBytes, err := ioutil.ReadFile(filepath.Clean(key)) if err != nil { log.Fatal(err) } diff --git a/vector/key/int_key.go b/vector/key/int_key.go index ee07b80..92c946c 100644 --- a/vector/key/int_key.go +++ b/vector/key/int_key.go @@ -17,17 +17,17 @@ func AllocateInt(row interface{}) (Key, error) { } num, err := strconv.Atoi(line) if err != nil { - return nil, err + return nil, errors.Wrapf(err, "can't convert line %s to int", line) } return &Int{num}, nil } func (k *Int) Less(other Key) bool { - return k.value < other.(*Int).value + return k.value < other.(*Int).value //nolint //forcetypeassert } func (k *Int) Equal(other Key) bool { - return k.value == other.(*Int).value + return k.value == other.(*Int).value //nolint //forcetypeassert } type IntFromSlice struct { @@ -41,15 +41,15 @@ func AllocateIntFromSlice(row interface{}, intIndex int) (Key, error) { } num, err := strconv.ParseInt(line[intIndex], 10, 64) if err != nil { - return nil, err + return nil, errors.Wrapf(err, "can't parse int %+v", line[intIndex]) } return &IntFromSlice{num}, nil } func (k *IntFromSlice) Less(other Key) bool { - return k.value < other.(*IntFromSlice).value + return k.value < other.(*IntFromSlice).value //nolint //forcetypeassert } func (k *IntFromSlice) Equal(other Key) bool { - return k.value == other.(*IntFromSlice).value + return k.value == other.(*IntFromSlice).value //nolint //forcetypeassert } diff --git a/writer/std_writer.go b/writer/std_writer.go index c6cc8e8..bd7fbed 100644 --- a/writer/std_writer.go +++ b/writer/std_writer.go @@ -9,11 +9,13 @@ import ( "github.com/pkg/errors" ) +// StdWriter implement writer interface with a bufio writer. type StdWriter struct { w *bufio.Writer } -func NewStdWriter(w io.Writer) Writer { +// NewStdWriter create a standard writer. +func NewStdWriter(w io.Writer) Writer { //nolint //ireturn s := &StdWriter{ w: bufio.NewWriter(w), } From ffb3ebc8d3ae152db1ca002130c20847b11d8171 Mon Sep 17 00:00:00 2001 From: askiada <25521495+askiada@users.noreply.github.com> Date: Mon, 8 May 2023 18:06:39 +0200 Subject: [PATCH 13/16] lint --- bucket/s3.go | 2 +- file/batchingchannels/batching_channel.go | 3 +- .../batchingchannels/batching_channel_test.go | 2 +- file/batchingchannels/doc.go | 2 + file/chunk.go | 2 +- file/sort.go | 150 ++++++++++++------ internal/rw/rw.go | 27 ++-- main.go | 131 ++++++++------- main_bench_test.go | 27 ++-- main_test.go | 104 ++++++++---- reader/contract.go | 3 + reader/gzip_separated_values_test.go | 16 +- sftp/sftp.go | 11 +- vector/key/int_key.go | 12 +- vector/key/key.go | 1 + vector/key/string_key.go | 16 +- vector/key/tsv_key.go | 10 +- vector/vector.go | 20 ++- writer/gzip_separated_values.go | 6 +- writer/std_writer.go | 10 +- 20 files changed, 359 insertions(+), 196 deletions(-) create mode 100644 file/batchingchannels/doc.go diff --git a/bucket/s3.go b/bucket/s3.go index 1b2e3b0..08b1121 100644 --- a/bucket/s3.go +++ b/bucket/s3.go @@ -92,7 +92,7 @@ func (s *seqWriterAt) WriteAt(p []byte, _ int64) (n int, err error) { return n, errors.Wrap(err, "can't write bytes at offset") } -// S3FileInfo describe the path to a file on S3. +// S3FileInfo define the path to a file on S3. type S3FileInfo struct { Bucket string Key string diff --git a/file/batchingchannels/batching_channel.go b/file/batchingchannels/batching_channel.go index 7f54f16..150e593 100644 --- a/file/batchingchannels/batching_channel.go +++ b/file/batchingchannels/batching_channel.go @@ -8,7 +8,7 @@ import ( "golang.org/x/sync/errgroup" ) -// BatchingChannel standard channel, with the change that instead of producing individual elements +// BatchingChannel define a standard channel, with the change that instead of producing individual elements // on Out(), it batches together n elements each time. Trying to construct an unbuffered batching channel // will panic, that configuration is not supported (and provides no benefit over an unbuffered NativeChannel). type BatchingChannel struct { @@ -70,6 +70,7 @@ func (ch *BatchingChannel) ProcessOut(f func(vector.Vector) error) error { if err != nil { return errors.Wrap(err, "one of the task failed") } + return nil } diff --git a/file/batchingchannels/batching_channel_test.go b/file/batchingchannels/batching_channel_test.go index 8b40ad5..ced13a3 100644 --- a/file/batchingchannels/batching_channel_test.go +++ b/file/batchingchannels/batching_channel_test.go @@ -19,7 +19,7 @@ type intKey struct { value int } -func allocateInt(row interface{}) (key.Key, error) { +func allocateInt(row interface{}) (key.Key, error) { //nolint //ireturn line, ok := row.(string) if !ok { return nil, errors.Errorf("can't convert interface{} to string: %+v", row) diff --git a/file/batchingchannels/doc.go b/file/batchingchannels/doc.go new file mode 100644 index 0000000..9874cca --- /dev/null +++ b/file/batchingchannels/doc.go @@ -0,0 +1,2 @@ +// Package batchingchannels define a standard channel processing the output per batch. +package batchingchannels diff --git a/file/chunk.go b/file/chunk.go index 2345ea1..df9d10f 100644 --- a/file/chunk.go +++ b/file/chunk.go @@ -11,7 +11,7 @@ import ( "github.com/pkg/errors" ) -// chunkInfo Describe a chunk. +// chunkInfo define a chunk. type chunkInfo struct { file *os.File reader reader.Reader diff --git a/file/sort.go b/file/sort.go index da2ea4c..6fda072 100644 --- a/file/sort.go +++ b/file/sort.go @@ -55,75 +55,98 @@ func (f *Info) createChunks(chunkPaths []string, k int) (*chunks, error) { return chunks, nil } -func (f *Info) MergeSort(chunkPaths []string, k int, dropDuplicates bool) (err error) { - var oldElem *vector.Element - output := f.Allocate.Vector(k, f.Allocate.Key) - if f.PrintMemUsage && f.mu == nil { - f.mu = &memUsage{} - } +func (f *Info) handleHeader(output vector.Vector) error { if f.WithHeader { - err = output.PushFrontNoKey(f.headers) + err := output.PushFrontNoKey(f.headers) if err != nil { return errors.Wrapf(err, "can't add headers %+v", f.headers) } } + return nil +} + +type nextChunk struct { + oldElem *vector.Element +} + +func (nc *nextChunk) get(output vector.Vector, createdChunks *chunks, dropDuplicates bool) (*chunkInfo, int, error) { + minChunk, minValue, minIdx := createdChunks.min() + if (!dropDuplicates || nc.oldElem == nil) || (dropDuplicates && !minValue.Key.Equal(nc.oldElem.Key)) { + err := output.PushBack(minValue.Row) + if err != nil { + return nil, 0, errors.Wrapf(err, "can't push back row %+v", minValue.Row) + } + nc.oldElem = minValue + } + return minChunk, minIdx, nil +} + +func updateChunks(createdChunks *chunks, minChunk *chunkInfo, minIdx, k int) error { + minChunk.buffer.FrontShift() + isEmpty := false + if minChunk.buffer.Len() == 0 { + err := minChunk.pullSubset(k) + if err != nil { + return errors.Wrapf(err, "can't pull subset from chunk %s", minChunk.filename) + } + // if after pulling data the chunk buffer is still empty then we can remove it + if minChunk.buffer.Len() == 0 { + isEmpty = true + err = createdChunks.shrink([]int{minIdx}) + if err != nil { + return errors.Wrapf(err, "can't shrink chunk at index %d", minIdx) + } + } + } + // when we get a new element in the first chunk we need to re-order it + if !isEmpty { + createdChunks.moveFirstChunkToCorrectIndex() + } + return nil +} + +func (f *Info) prepareMergeSort(output vector.Vector, chunkPaths []string, outputBufferSize int) (*chunks, error) { + err := f.handleHeader(output) + if err != nil { + return nil, errors.Wrap(err, "can't handle headers") + } // create a chunk per file path - createdChunks, err := f.createChunks(chunkPaths, k) + createdChunks, err := f.createChunks(chunkPaths, outputBufferSize) if err != nil { - return errors.Wrap(err, "can't create all chunks") + return nil, errors.Wrap(err, "can't create all chunks") } f.outputWriter, err = f.Allocate.FnWriter(f.OutputFile) if err != nil { - return errors.Wrap(err, "can't get output writer file") + return nil, errors.Wrap(err, "can't get output writer file") } - defer f.outputWriter.Close() + return createdChunks, nil +} + +func (f *Info) runMergeSort(createdChunks *chunks, output vector.Vector, outputBufferSize int, dropDuplicates bool) error { bar := pb.StartNew(f.totalRows) createdChunks.resetOrder() + smallestChunk := &nextChunk{} for { if f.PrintMemUsage { f.mu.Collect() } - if createdChunks.len() == 0 || output.Len() == k { - err = WriteBuffer(f.outputWriter, output) - if err != nil { - return err - } + err := f.dumpOutput(createdChunks, output, outputBufferSize) + if err != nil { + return errors.Wrap(err, "can't dump output") } if createdChunks.len() == 0 { break } - toShrink := []int{} + // search the smallest value across chunk buffers by comparing first elements only - minChunk, minValue, minIdx := createdChunks.min() - if (!dropDuplicates || oldElem == nil) || (dropDuplicates && !minValue.Key.Equal(oldElem.Key)) { - err = output.PushBack(minValue.Row) - if err != nil { - return errors.Wrapf(err, "can't push back row %+v", minValue.Row) - } - oldElem = minValue + minChunk, minIdx, err := smallestChunk.get(output, createdChunks, dropDuplicates) + if err != nil { + return errors.Wrap(err, "can't get next chunk with smallest value") } - // remove the first element from the chunk we pulled the smallest value - minChunk.buffer.FrontShift() - isEmpty := false - if minChunk.buffer.Len() == 0 { - err = minChunk.pullSubset(k) - if err != nil { - return err - } - // if after pulling data the chunk buffer is still empty then we can remove it - if minChunk.buffer.Len() == 0 { - isEmpty = true - toShrink = append(toShrink, minIdx) - err = createdChunks.shrink(toShrink) - if err != nil { - return err - } - } - } - // when we get a new element in the first chunk we need to re-order it - if !isEmpty { - createdChunks.moveFirstChunkToCorrectIndex() + err = updateChunks(createdChunks, minChunk, minIdx, outputBufferSize) + if err != nil { + return errors.Wrap(err, "can't update chunks") } bar.Increment() } @@ -131,10 +154,43 @@ func (f *Info) MergeSort(chunkPaths []string, k int, dropDuplicates bool) (err e if f.PrintMemUsage { logger.Debugln(f.mu.String()) } - return createdChunks.close() + return nil +} + +func (f *Info) dumpOutput(createdChunks *chunks, output vector.Vector, outputBufferSize int) error { + if createdChunks.len() == 0 || output.Len() == outputBufferSize { + err := writeBuffer(f.outputWriter, output) + if err != nil { + return err + } + } + return nil +} + +// MergeSort merge and sort a list of files. +// It is possilbe to drop duplicates and define the maximum size of the output buffer before flush. +func (f *Info) MergeSort(chunkPaths []string, outputBufferSize int, dropDuplicates bool) (err error) { + output := f.Allocate.Vector(outputBufferSize, f.Allocate.Key) + if f.PrintMemUsage && f.mu == nil { + f.mu = &memUsage{} + } + createdChunks, err := f.prepareMergeSort(output, chunkPaths, outputBufferSize) + if err != nil { + return errors.Wrap(err, "can't prepare merge sort") + } + defer func() { err = f.outputWriter.Close() }() + err = f.runMergeSort(createdChunks, output, outputBufferSize, dropDuplicates) + if err != nil { + return errors.Wrap(err, "can't run merge sort") + } + err = createdChunks.close() + if err != nil { + return errors.Wrap(err, "can't close created chunks") + } + return err } -func WriteBuffer(w writer.Writer, rows vector.Vector) error { +func writeBuffer(w writer.Writer, rows vector.Vector) error { for i := 0; i < rows.Len(); i++ { err := w.Write(rows.Get(i).Row) if err != nil { diff --git a/internal/rw/rw.go b/internal/rw/rw.go index b85f0cf..e6253a6 100644 --- a/internal/rw/rw.go +++ b/internal/rw/rw.go @@ -83,13 +83,14 @@ func (i *InputOutput) SetInputReader(ctx context.Context, inputFiles ...string) pr, pw := io.Pipe() i.Input = pr i.inputPipe = pr - i.g.Go(func() error { - defer pw.Close() //nolint:errcheck //no need to check this error - err := s3Api.Download(i.internalCtx, pw, files...) + i.g.Go(func() (err error) { + defer func() { err = pw.Close() }() + err = s3Api.Download(i.internalCtx, pw, files...) if err != nil { return errors.Wrap(err, "can't download files") } - return nil + + return err }) } else { var files []io.Reader @@ -102,6 +103,7 @@ func (i *InputOutput) SetInputReader(ctx context.Context, inputFiles ...string) } i.Input = io.MultiReader(files...) } + return nil } @@ -111,9 +113,12 @@ func (i *InputOutput) SetOutputWriter(ctx context.Context, outputFile string) (e if err != nil { return errors.Wrap(err, "can't check s3") } - u, _ := url.Parse(outputFile) - u.Path = strings.TrimLeft(u.Path, "/") - logger.Debugf("Proto: %q, Bucket: %q, Key: %q", u.Scheme, u.Host, u.Path) + outputURL, err := url.Parse(outputFile) + if err != nil { + return errors.Wrapf(err, "can't parse output url %s", outputFile) + } + outputURL.Path = strings.TrimLeft(outputURL.Path, "/") + logger.Debugf("Proto: %q, Bucket: %q, Key: %q", outputURL.Scheme, outputURL.Host, outputURL.Path) s3Api, err := bucket.New(ctx, bucket.Client(i.s3Client), bucket.Buffer(1_000_000), @@ -126,13 +131,13 @@ func (i *InputOutput) SetOutputWriter(ctx context.Context, outputFile string) (e pr, pw := io.Pipe() i.Output = pw i.outputPipe = pw - i.g.Go(func() error { - defer pr.Close() //nolint:errcheck //no need to check this error - err := s3Api.Upload(i.internalCtx, pr, u.Host, u.Path) + i.g.Go(func() (err error) { + defer func() { err = pr.Close() }() + err = s3Api.Upload(i.internalCtx, pr, outputURL.Host, outputURL.Path) if err != nil { return errors.Wrapf(err, "can't upload file %s", outputFile) } - return nil + return err }) } else { i.Output, err = os.Create(filepath.Clean(outputFile)) diff --git a/main.go b/main.go index d5a70d7..97f1039 100644 --- a/main.go +++ b/main.go @@ -27,29 +27,7 @@ type command struct { shuffleCmd *cobra.Command } -func newCommand() *command { - root := &command{ - rootCmd: &cobra.Command{ - Use: "external", - Short: "Perform an external task on an input file", - }, - sortCmd: &cobra.Command{ - Use: "sort", - Short: "Perform an external sorting on an input file", - PreRun: func(cmd *cobra.Command, args []string) { - cmd.SetContext(context.WithValue(cmd.Parent().Context(), "cmd", "sort")) - }, - RunE: sortRun, - }, - shuffleCmd: &cobra.Command{ - Use: "shuffle", - Short: "Perform an external shufflin on an input file", - PreRun: func(cmd *cobra.Command, args []string) { - cmd.SetContext(context.WithValue(cmd.Parent().Context(), "cmd", "shuffle")) - }, - RunE: shuffleRun, - }, - } +func setFlags(root *command) { root.rootCmd.PersistentFlags().BoolVarP( &internal.WithHeader, internal.WithHeaderName, @@ -127,18 +105,43 @@ func newCommand() *command { viper.GetBool(internal.IsGzipName), "", ) +} +func newCommand() *command { + root := &command{ + rootCmd: &cobra.Command{ + Use: "external", + Short: "Perform an external task on an input file", + }, + sortCmd: &cobra.Command{ + Use: "sort", + Short: "Perform an external sorting on an input file", + PreRun: func(cmd *cobra.Command, args []string) { + cmd.SetContext(cmd.Parent().Context()) + }, + RunE: sortRun, + }, + shuffleCmd: &cobra.Command{ + Use: "shuffle", + Short: "Perform an external shufflin on an input file", + PreRun: func(cmd *cobra.Command, args []string) { + cmd.SetContext(cmd.Parent().Context()) + }, + RunE: shuffleRun, + }, + } root.rootCmd.AddCommand(root.sortCmd, root.shuffleCmd) return root } func main() { root := newCommand() + setFlags(root) ctx := context.Background() cobra.CheckErr(root.rootCmd.ExecuteContext(ctx)) } -func sortRun(cmd *cobra.Command, args []string) error { +func sortRun(cmd *cobra.Command, _ []string) error { logger.Infoln("Input files", internal.InputFiles) logger.Infoln("With header", internal.WithHeader) logger.Infoln("Output file", internal.OutputFile) @@ -146,46 +149,61 @@ func sortRun(cmd *cobra.Command, args []string) error { logger.Infoln("TSV Fields", internal.TsvFields) start := time.Now() - i := rw.NewInputOutput(cmd.Context()) - err := i.SetInputReader(cmd.Context(), internal.InputFiles...) + inputOutput := rw.NewInputOutput(cmd.Context()) + err := inputOutput.SetInputReader(cmd.Context(), internal.InputFiles...) if err != nil { - return err + return errors.Wrap(err, "can't set input reader") } - err = i.SetOutputWriter(cmd.Context(), internal.OutputFile) + err = inputOutput.SetOutputWriter(cmd.Context(), internal.OutputFile) if err != nil { - return err + return errors.Wrap(err, "can't set output writer") } tsvFields := []int{} for _, field := range internal.TsvFields { i, err := strconv.Atoi(field) if err != nil { - return err + return errors.Wrapf(err, "can't convert field %s", field) } tsvFields = append(tsvFields, i) } - fI := &file.Info{ + fileInfo := &file.Info{ WithHeader: internal.WithHeader, - InputReader: i.Input, - OutputFile: i.Output, + InputReader: inputOutput.Input, + OutputFile: inputOutput.Output, Allocate: vector.DefaultVector( func(row interface{}) (key.Key, error) { - return key.AllocateTsv(row, tsvFields...) + k, err := key.AllocateTsv(row, tsvFields...) + if err != nil { + return nil, errors.Wrapf(err, "can't allocate tsv %+v", row) + } + return k, nil }, - func(r io.Reader) (reader.Reader, error) { return reader.NewGZipSeparatedValues(r, '\t') }, func(w io.Writer) (writer.Writer, error) { - return writer.NewGZipSeparatedValues(w, '\t') + func(r io.Reader) (reader.Reader, error) { + gzipReader, err := reader.NewGZipSeparatedValues(r, '\t') + if err != nil { + return nil, errors.Wrap(err, "can't create Gzip reader") + } + return gzipReader, nil + }, + func(w io.Writer) (writer.Writer, error) { + gzipWriter, err := writer.NewGZipSeparatedValues(w, '\t') + if err != nil { + return nil, errors.Wrap(err, "can't create Gzip writer") + } + return gzipWriter, nil }, ), PrintMemUsage: false, } - i.Do(func() error { + inputOutput.Do(func() error { // create small files with maximum 30 rows in each - chunkPaths, err := fI.CreateSortedChunks(context.Background(), internal.ChunkFolder, internal.ChunkSize, internal.MaxWorkers) + chunkPaths, err := fileInfo.CreateSortedChunks(cmd.Context(), internal.ChunkFolder, internal.ChunkSize, internal.MaxWorkers) if err != nil { return errors.Wrap(err, "can't create sorted chunks") } // perform a merge sort on all the chunks files. // we sort using a buffer so we don't have to load the entire chunks when merging - err = fI.MergeSort(chunkPaths, internal.OutputBufferSize, true) + err = fileInfo.MergeSort(chunkPaths, internal.OutputBufferSize, true) if err != nil { return errors.Wrap(err, "can't merge sort") } @@ -193,40 +211,47 @@ func sortRun(cmd *cobra.Command, args []string) error { logger.Infoln("It took", elapsed) return nil }) - err = i.Err() + err = inputOutput.Err() if err != nil { return errors.Wrap(err, "can't finish") } return nil } -func shuffleRun(cmd *cobra.Command, args []string) error { +func shuffleRun(cmd *cobra.Command, _ []string) error { logger.Infoln("Input files", internal.InputFiles) logger.Infoln("With header", internal.WithHeader) logger.Infoln("Output file", internal.OutputFile) logger.Infoln("Chunk folder", internal.ChunkFolder) logger.Infoln("GZip file", internal.IsGzip) start := time.Now() - ctx := context.Background() - i := rw.NewInputOutput(ctx) - err := i.SetInputReader(ctx, internal.InputFiles...) + inputOutput := rw.NewInputOutput(cmd.Context()) + err := inputOutput.SetInputReader(cmd.Context(), internal.InputFiles...) if err != nil { - return err + return errors.Wrap(err, "can't set input reader") } - err = i.SetOutputWriter(ctx, internal.OutputFile) + err = inputOutput.SetOutputWriter(cmd.Context(), internal.OutputFile) if err != nil { - return err + return errors.Wrap(err, "can't set output writer") } - fI := &file.Info{ + fileInfo := &file.Info{ WithHeader: internal.WithHeader, - InputReader: i.Input, - OutputFile: i.Output, + InputReader: inputOutput.Input, + OutputFile: inputOutput.Output, PrintMemUsage: false, } - i.Do(func() error { + inputOutput.Do(func() error { // create small files with maximum 30 rows in each - _, err := fI.Shuffle(context.Background(), internal.ChunkFolder, internal.ChunkSize, internal.MaxWorkers, internal.OutputBufferSize, time.Now().Unix(), internal.IsGzip) + _, err := fileInfo.Shuffle( + cmd.Context(), + internal.ChunkFolder, + internal.ChunkSize, + internal.MaxWorkers, + internal.OutputBufferSize, + time.Now().Unix(), + internal.IsGzip, + ) if err != nil { return errors.Wrap(err, "can't create shuflled chunks") } @@ -234,7 +259,7 @@ func shuffleRun(cmd *cobra.Command, args []string) error { logger.Infoln("It took", elapsed) return nil }) - err = i.Err() + err = inputOutput.Err() if err != nil { return errors.Wrap(err, "can't finish") } diff --git a/main_bench_test.go b/main_bench_test.go index 0b686c1..e87982c 100644 --- a/main_bench_test.go +++ b/main_bench_test.go @@ -19,29 +19,34 @@ import ( func BenchmarkMergeSort(b *testing.B) { filename := "test.tsv" ctx := context.Background() - i := rw.NewInputOutput(ctx) - err := i.SetInputReader(ctx, filename) + inputOutput := rw.NewInputOutput(ctx) + err := inputOutput.SetInputReader(ctx, filename) assert.NoError(b, err) - err = i.SetOutputWriter(ctx, "testdata/chunks/output.tsv") + err = inputOutput.SetOutputWriter(ctx, "testdata/chunks/output.tsv") assert.NoError(b, err) chunkSize := 10000 bufferSize := 5000 - fI := &file.Info{ - InputReader: i.Input, - Allocate: vector.DefaultVector(key.AllocateInt, func(r io.Reader) (reader.Reader, error) { return reader.NewStdScanner(r, false) }, func(w io.Writer) (writer.Writer, error) { return writer.NewStdWriter(w), nil }), - OutputFile: i.Output, + fileInfo := &file.Info{ + InputReader: inputOutput.Input, + Allocate: vector.DefaultVector( + key.AllocateInt, + func(r io.Reader) (reader.Reader, error) { return reader.NewStdScanner(r, false) }, + func(w io.Writer) (writer.Writer, error) { return writer.NewStdWriter(w), nil }, + ), + OutputFile: inputOutput.Output, } - i.Do(func() (err error) { - chunkPaths, err := fI.CreateSortedChunks(context.Background(), "testdata/chunks", chunkSize, 100) + inputOutput.Do(func() (err error) { + chunkPaths, err := fileInfo.CreateSortedChunks(context.Background(), "testdata/chunks", chunkSize, 100) assert.NoError(b, err) b.ResetTimer() for i := 0; i < b.N; i++ { - err = fI.MergeSort(chunkPaths, bufferSize, false) + err = fileInfo.MergeSort(chunkPaths, bufferSize, false) _ = err } + return nil }) - err = i.Err() + err = inputOutput.Err() assert.NoError(b, err) dir, err := os.ReadDir("testdata/chunks") assert.NoError(b, err) diff --git a/main_test.go b/main_test.go index 6882c3c..6972aa2 100644 --- a/main_test.go +++ b/main_test.go @@ -19,31 +19,41 @@ import ( "github.com/stretchr/testify/assert" ) -func prepareChunks(ctx context.Context, t *testing.T, allocate *vector.Allocate, filename, outputFilename string, chunkSize int, mergeSort bool, bufferSize int, withHeaders bool, dropDuplicates bool) *file.Info { +func prepareChunks( + ctx context.Context, + t *testing.T, + allocate *vector.Allocate, + filename, outputFilename string, + chunkSize int, + mergeSort bool, + bufferSize int, + withHeaders bool, + dropDuplicates bool, +) *file.Info { t.Helper() - i := rw.NewInputOutput(ctx) - err := i.SetInputReader(ctx, filename) + inputOutput := rw.NewInputOutput(ctx) + err := inputOutput.SetInputReader(ctx, filename) assert.NoError(t, err) - err = i.SetOutputWriter(ctx, outputFilename) + err = inputOutput.SetOutputWriter(ctx, outputFilename) assert.NoError(t, err) - fI := &file.Info{ - InputReader: i.Input, + fileInfo := &file.Info{ + InputReader: inputOutput.Input, Allocate: allocate, - OutputFile: i.Output, + OutputFile: inputOutput.Output, WithHeader: withHeaders, } - i.Do(func() (err error) { - chunkPaths, err := fI.CreateSortedChunks(ctx, "testdata/chunks", chunkSize, 10) + inputOutput.Do(func() (err error) { + chunkPaths, err := fileInfo.CreateSortedChunks(ctx, "testdata/chunks", chunkSize, 10) assert.NoError(t, err) if mergeSort { - return fI.MergeSort(chunkPaths, bufferSize, dropDuplicates) + return fileInfo.MergeSort(chunkPaths, bufferSize, dropDuplicates) } return nil }) - err = i.Err() + err = inputOutput.Err() assert.NoError(t, err) - return fI + return fileInfo } func TestBasics(t *testing.T) { @@ -102,7 +112,11 @@ func TestBasics(t *testing.T) { t.Run(name+"_"+strconv.Itoa(chunkSize)+"_"+strconv.Itoa(bufferSize), func(t *testing.T) { ctx := context.Background() - allocate := vector.DefaultVector(key.AllocateInt, func(r io.Reader) (reader.Reader, error) { return reader.NewStdScanner(r, false) }, func(w io.Writer) (writer.Writer, error) { return writer.NewStdWriter(w), nil }) + allocate := vector.DefaultVector( + key.AllocateInt, + func(r io.Reader) (reader.Reader, error) { return reader.NewStdScanner(r, false) }, + func(w io.Writer) (writer.Writer, error) { return writer.NewStdWriter(w), nil }, + ) prepareChunks(ctx, t, allocate, filename, outputFilename, chunkSize, true, bufferSize, false, false) outputFile, err := os.Open(outputFilename) @@ -165,7 +179,11 @@ func Test100Elems(t *testing.T) { expectedErr := tc.expectedErr t.Run(name, func(t *testing.T) { ctx := context.Background() - allocate := vector.DefaultVector(key.AllocateInt, func(r io.Reader) (reader.Reader, error) { return reader.NewStdScanner(r, false) }, func(w io.Writer) (writer.Writer, error) { return writer.NewStdWriter(w), nil }) + allocate := vector.DefaultVector( + key.AllocateInt, + func(r io.Reader) (reader.Reader, error) { return reader.NewStdScanner(r, false) }, + func(w io.Writer) (writer.Writer, error) { return writer.NewStdWriter(w), nil }, + ) prepareChunks(ctx, t, allocate, filename, outputFilename, 21, true, 10, false, false) outputFile, err := os.Open(outputFilename) assert.NoError(t, err) @@ -217,7 +235,11 @@ func Test100ElemsWithDuplicates(t *testing.T) { expectedErr := tc.expectedErr t.Run(name, func(t *testing.T) { ctx := context.Background() - allocate := vector.DefaultVector(key.AllocateInt, func(r io.Reader) (reader.Reader, error) { return reader.NewStdScanner(r, false) }, func(w io.Writer) (writer.Writer, error) { return writer.NewStdWriter(w), nil }) + allocate := vector.DefaultVector( + key.AllocateInt, + func(r io.Reader) (reader.Reader, error) { return reader.NewStdScanner(r, false) }, + func(w io.Writer) (writer.Writer, error) { return writer.NewStdWriter(w), nil }, + ) prepareChunks(ctx, t, allocate, filename, outputFilename, 21, true, 10, false, true) outputFile, err := os.Open(outputFilename) assert.NoError(t, err) @@ -277,7 +299,11 @@ func Test100ElemsWithHeaders(t *testing.T) { expectedErr := tc.expectedErr t.Run(name, func(t *testing.T) { ctx := context.Background() - allocate := vector.DefaultVector(key.AllocateInt, func(r io.Reader) (reader.Reader, error) { return reader.NewStdScanner(r, false) }, func(w io.Writer) (writer.Writer, error) { return writer.NewStdWriter(w), nil }) + allocate := vector.DefaultVector( + key.AllocateInt, + func(r io.Reader) (reader.Reader, error) { return reader.NewStdScanner(r, false) }, + func(w io.Writer) (writer.Writer, error) { return writer.NewStdWriter(w), nil }, + ) prepareChunks(ctx, t, allocate, filename, outputFilename, 21, true, 10, true, false) outputFile, err := os.Open(outputFilename) assert.NoError(t, err) @@ -329,7 +355,11 @@ func Test100ElemsWithHeadersWithDuplicates(t *testing.T) { expectedErr := tc.expectedErr t.Run(name, func(t *testing.T) { ctx := context.Background() - allocate := vector.DefaultVector(key.AllocateInt, func(r io.Reader) (reader.Reader, error) { return reader.NewStdScanner(r, false) }, func(w io.Writer) (writer.Writer, error) { return writer.NewStdWriter(w), nil }) + allocate := vector.DefaultVector( + key.AllocateInt, + func(r io.Reader) (reader.Reader, error) { return reader.NewStdScanner(r, false) }, + func(w io.Writer) (writer.Writer, error) { return writer.NewStdWriter(w), nil }, + ) prepareChunks(ctx, t, allocate, filename, outputFilename, 21, true, 10, true, true) outputFile, err := os.Open(outputFilename) assert.NoError(t, err) @@ -380,9 +410,11 @@ func TestTsvKey(t *testing.T) { t.Run(name, func(t *testing.T) { ctx := context.Background() - allocate := vector.DefaultVector(func(row interface{}) (key.Key, error) { - return key.AllocateTsv(row, 1) - }, func(r io.Reader) (reader.Reader, error) { return reader.NewSeparatedValues(r, '\t'), nil }, func(w io.Writer) (writer.Writer, error) { return writer.NewSeparatedValues(w, '\t'), nil }) + allocate := vector.DefaultVector( + func(row interface{}) (key.Key, error) { return key.AllocateTsv(row, 1) }, + func(r io.Reader) (reader.Reader, error) { return reader.NewSeparatedValues(r, '\t'), nil }, + func(w io.Writer) (writer.Writer, error) { return writer.NewSeparatedValues(w, '\t'), nil }, + ) prepareChunks(ctx, t, allocate, filename, outputFilename, 21, true, 10, false, false) outputFile, err := os.Open(outputFilename) assert.NoError(t, err) @@ -400,27 +432,37 @@ func TestTsvKey(t *testing.T) { } } -func prepareChunksShuffle(ctx context.Context, t *testing.T, filename, outputFilename string, chunkSize int, mergeSort bool, bufferSize int, withHeaders bool, dropDuplicates, isGzip bool) *file.Info { +func prepareChunksShuffle( + ctx context.Context, + t *testing.T, + filename, outputFilename string, + chunkSize int, + mergeSort bool, + bufferSize int, + withHeaders bool, + dropDuplicates, + isGzip bool, +) *file.Info { t.Helper() - i := rw.NewInputOutput(ctx) - err := i.SetInputReader(ctx, filename) + inputOutput := rw.NewInputOutput(ctx) + err := inputOutput.SetInputReader(ctx, filename) assert.NoError(t, err) - err = i.SetOutputWriter(ctx, outputFilename) + err = inputOutput.SetOutputWriter(ctx, outputFilename) assert.NoError(t, err) - fI := &file.Info{ - InputReader: i.Input, - OutputFile: i.Output, + fileInfo := &file.Info{ + InputReader: inputOutput.Input, + OutputFile: inputOutput.Output, WithHeader: withHeaders, } - i.Do(func() (err error) { - _, err = fI.Shuffle(ctx, "testdata/chunks", chunkSize, 10, bufferSize, 13, isGzip) + inputOutput.Do(func() (err error) { + _, err = fileInfo.Shuffle(ctx, "testdata/chunks", chunkSize, 10, bufferSize, 13, isGzip) assert.NoError(t, err) return nil }) - err = i.Err() + err = inputOutput.Err() assert.NoError(t, err) - return fI + return fileInfo } func Test100ElemsShuffle(t *testing.T) { diff --git a/reader/contract.go b/reader/contract.go index a50988f..091267a 100644 --- a/reader/contract.go +++ b/reader/contract.go @@ -4,9 +4,12 @@ import ( "io" ) +// Reader define a basic reader. type Reader interface { Next() bool Read() (interface{}, error) Err() error } + +// Config function type to convert a io.Reader to a Reader. type Config func(r io.Reader) (Reader, error) diff --git a/reader/gzip_separated_values_test.go b/reader/gzip_separated_values_test.go index e8e48e0..966ef3d 100644 --- a/reader/gzip_separated_values_test.go +++ b/reader/gzip_separated_values_test.go @@ -16,17 +16,17 @@ func Test(t *testing.T) { t.Skip("to rework") f, err := os.Open("/mnt/c/Users/Alex/Downloads/recordings.59.tsv.gz") require.NoError(t, err) - r, err := reader.NewGZipSeparatedValues(bufio.NewReader(f), '\t') + rder, err := reader.NewGZipSeparatedValues(bufio.NewReader(f), '\t') require.NoError(t, err) count := 0 - for r.Next() { - row, err := r.Read() + for rder.Next() { + row, err := rder.Read() require.NoError(t, err) _ = row count++ } assert.Equal(t, 2853701, count) - require.NoError(t, r.Err()) + require.NoError(t, rder.Err()) } func TestS3(t *testing.T) { @@ -36,15 +36,15 @@ func TestS3(t *testing.T) { err := i.SetInputReader(ctx, "s3://blokur-data/ml-title/remote/1/f15c2cf2e3ab46589419e6441b64e3bd/artifacts/input/word2vec/refine/recordings.59.tsv.gz") require.NoError(t, err) - r, err := reader.NewGZipSeparatedValues(i.Input, '\t') + gzipReader, err := reader.NewGZipSeparatedValues(i.Input, '\t') require.NoError(t, err) count := 0 - for r.Next() { - row, err := r.Read() + for gzipReader.Next() { + row, err := gzipReader.Read() require.NoError(t, err) _ = row count++ } assert.Equal(t, 2853701, count) - require.NoError(t, r.Err()) + require.NoError(t, gzipReader.Err()) } diff --git a/sftp/sftp.go b/sftp/sftp.go index 16af7ab..e9dd341 100644 --- a/sftp/sftp.go +++ b/sftp/sftp.go @@ -1,10 +1,11 @@ package sftp import ( - "io/ioutil" "log" + "os" "path/filepath" + "github.com/pkg/errors" "github.com/pkg/sftp" "golang.org/x/crypto/ssh" ) @@ -16,7 +17,7 @@ type Client struct { func NewSFTPClient(addr, key, user, passphrase string) (*Client, error) { res := &Client{} - pemBytes, err := ioutil.ReadFile(filepath.Clean(key)) + pemBytes, err := os.ReadFile(filepath.Clean(key)) if err != nil { log.Fatal(err) } @@ -31,12 +32,12 @@ func NewSFTPClient(addr, key, user, passphrase string) (*Client, error) { } conn, err := ssh.Dial("tcp", addr, config) if err != nil { - return nil, err + return nil, errors.Wrapf(err, "can't dial with address %s", addr) } res.Conn = conn client, err := sftp.NewClient(conn) if err != nil { - return nil, err + return nil, errors.Wrapf(err, "can't create sftp client with address %s", addr) } res.Client = client return res, nil @@ -45,7 +46,7 @@ func NewSFTPClient(addr, key, user, passphrase string) (*Client, error) { func (s *Client) Close() error { err := s.Client.Close() if err != nil { - return err + return errors.Wrap(err, "can't close client") } return s.Conn.Close() } diff --git a/vector/key/int_key.go b/vector/key/int_key.go index 92c946c..73f0fd1 100644 --- a/vector/key/int_key.go +++ b/vector/key/int_key.go @@ -6,11 +6,13 @@ import ( "github.com/pkg/errors" ) +// Int define an integer key. type Int struct { value int } -func AllocateInt(row interface{}) (Key, error) { +// AllocateInt create a new integer key. +func AllocateInt(row interface{}) (Key, error) { //nolint //ireturn line, ok := row.(string) if !ok { return nil, errors.Errorf("can't convert interface{} to string: %+v", row) @@ -22,19 +24,23 @@ func AllocateInt(row interface{}) (Key, error) { return &Int{num}, nil } +// Less compare two integer keys. func (k *Int) Less(other Key) bool { return k.value < other.(*Int).value //nolint //forcetypeassert } +// Equal check tow integer keys are equal. func (k *Int) Equal(other Key) bool { return k.value == other.(*Int).value //nolint //forcetypeassert } +// IntFromSlice define an integer key from a position in a slice of integers. type IntFromSlice struct { value int64 } -func AllocateIntFromSlice(row interface{}, intIndex int) (Key, error) { +// AllocateIntFromSlice create a new integer key from a position in a slice of integers. +func AllocateIntFromSlice(row interface{}, intIndex int) (Key, error) { //nolint //ireturn line, ok := row.([]string) if !ok { return nil, errors.Errorf("can't convert interface{} to []string: %+v", row) @@ -46,10 +52,12 @@ func AllocateIntFromSlice(row interface{}, intIndex int) (Key, error) { return &IntFromSlice{num}, nil } +// Less compare two integer keys. func (k *IntFromSlice) Less(other Key) bool { return k.value < other.(*IntFromSlice).value //nolint //forcetypeassert } +// Equal check tow integer keys are equal. func (k *IntFromSlice) Equal(other Key) bool { return k.value == other.(*IntFromSlice).value //nolint //forcetypeassert } diff --git a/vector/key/key.go b/vector/key/key.go index 2eda041..3b45aa7 100644 --- a/vector/key/key.go +++ b/vector/key/key.go @@ -1,5 +1,6 @@ package key +// Key define the interface to compare keys to sort. type Key interface { Equal(v2 Key) bool // Less returns wether the key is smaller than v2 diff --git a/vector/key/string_key.go b/vector/key/string_key.go index f4fec6e..4d6ade8 100644 --- a/vector/key/string_key.go +++ b/vector/key/string_key.go @@ -2,34 +2,42 @@ package key import "strings" +// String define an string key. type String struct { value string } +// AllocateString create a new string key. func AllocateString(line string) (Key, error) { return &String{line}, nil } +// Less compare two string keys. func (k *String) Less(other Key) bool { - return k.value < other.(*String).value + return k.value < other.(*String).value //nolint //forcetypeassert } +// Equal check tow string keys are equal. func (k *String) Equal(other Key) bool { - return k.value == other.(*String).value + return k.value == other.(*String).value //nolint //forcetypeassert } +// UpperString define an string key. type UpperString struct { value string } +// AllocateString create a new string key. It trims space and change the string to uppercase. func AllocateUpperString(line string) (Key, error) { return &UpperString{strings.TrimSpace(strings.ToUpper(line))}, nil } +// Less compare two upper string keys. func (k *UpperString) Less(other Key) bool { - return k.value < other.(*UpperString).value + return k.value < other.(*UpperString).value //nolint //forcetypeassert } +// Equal check tow upper string keys are equal. func (k *UpperString) Equal(other Key) bool { - return k.value == other.(*UpperString).value + return k.value == other.(*UpperString).value //nolint //forcetypeassert } diff --git a/vector/key/tsv_key.go b/vector/key/tsv_key.go index 6f3ee04..9c31d61 100644 --- a/vector/key/tsv_key.go +++ b/vector/key/tsv_key.go @@ -13,18 +13,16 @@ func AllocateTsv(row interface{}, pos ...int) (Key, error) { if !ok { return nil, errors.Errorf("can't convert interface{} to []string: %+v", row) } - k := strings.Builder{} + strBuilder := strings.Builder{} for i, p := range pos { if len(splitted) < p+1 { return nil, errors.Errorf("can't allocate tsv key line is invalid: %s", row) } - k.WriteString(splitted[p]) + strBuilder.WriteString(splitted[p]) if i < len(pos)-1 { - k.WriteString(salt) + strBuilder.WriteString(salt) } } - // fmt.Println(row, pos, k.String()) - - return &String{k.String()}, nil + return &String{strBuilder.String()}, nil } diff --git a/vector/vector.go b/vector/vector.go index d49cd80..d6b059d 100644 --- a/vector/vector.go +++ b/vector/vector.go @@ -1,8 +1,8 @@ package vector import ( - "io" "os" + "path/filepath" "github.com/askiada/external-sort/reader" "github.com/askiada/external-sort/vector/key" @@ -10,13 +10,15 @@ import ( "github.com/pkg/errors" ) +// Allocate define a vector and methods to read and write it. type Allocate struct { Vector func(int, func(row interface{}) (key.Key, error)) Vector - FnReader func(r io.Reader) (reader.Reader, error) - FnWriter func(w io.Writer) (writer.Writer, error) + FnReader reader.Config + FnWriter writer.Config Key func(elem interface{}) (key.Key, error) } +// DefaultVector define a helper function to allocate a vector. func DefaultVector(allocateKey func(elem interface{}) (key.Key, error), fnReader reader.Config, fnWr writer.Config) *Allocate { return &Allocate{ FnReader: fnReader, @@ -26,6 +28,7 @@ func DefaultVector(allocateKey func(elem interface{}) (key.Key, error), fnReader } } +// Vector define a basic interface to manipulate a vector. type Vector interface { // Get Access i-th element Get(i int) *Element @@ -43,8 +46,11 @@ type Vector interface { Sort() } -func (a *Allocate) Dump(v Vector, filename string) error { - file, err := os.OpenFile(filename, os.O_CREATE|os.O_WRONLY, 0o644) +const writeFilePerm = 0o600 + +// Dump copy a vector to a file. +func (a *Allocate) Dump(vec Vector, filename string) error { + file, err := os.OpenFile(filepath.Clean(filename), os.O_CREATE|os.O_WRONLY, writeFilePerm) if err != nil { return errors.Errorf("failed creating file: %s", err) } @@ -52,8 +58,8 @@ func (a *Allocate) Dump(v Vector, filename string) error { if err != nil { return errors.Errorf("failed creating writer: %s", err) } - for i := 0; i < v.Len(); i++ { - err = datawriter.Write(v.Get(i).Row) + for i := 0; i < vec.Len(); i++ { + err = datawriter.Write(vec.Get(i).Row) if err != nil { return errors.Errorf("failed writing file: %s", err) } diff --git a/writer/gzip_separated_values.go b/writer/gzip_separated_values.go index 63e6064..4e37a33 100644 --- a/writer/gzip_separated_values.go +++ b/writer/gzip_separated_values.go @@ -35,11 +35,11 @@ func (s *GZipSeparatedValuesWriter) Write(elem interface{}) error { return nil } -func (s *GZipSeparatedValuesWriter) Close() error { - defer s.gw.Close() +func (s *GZipSeparatedValuesWriter) Close() (err error) { + defer func() { err = s.gw.Close() }() s.w.Flush() if s.w.Error() != nil { return errors.Wrap(s.w.Error(), "can't close writer") } - return nil + return err } diff --git a/writer/std_writer.go b/writer/std_writer.go index bd7fbed..c8ab78e 100644 --- a/writer/std_writer.go +++ b/writer/std_writer.go @@ -34,6 +34,7 @@ func (w *StdWriter) Write(elem interface{}) error { return err } +// Close close the bufio writer. It is the responsibility of the client to close the underlying writer. func (w *StdWriter) Close() error { err := w.w.Flush() if err != nil { @@ -78,13 +79,14 @@ func (w *StdSliceWriter) Write(elem interface{}) error { return err } -func (w *StdSliceWriter) Close() error { +// Close close the bufio writer. It is the responsibility of the client to close the underlying writer. +func (w *StdSliceWriter) Close() (err error) { if w.gw != nil { - defer w.gw.Close() + defer func() { err = w.gw.Close() }() } - err := w.w.Flush() + err = w.w.Flush() if err != nil { return errors.Wrap(err, "can't close writer") } - return nil + return err } From 167ffa63439c9802a4cb9e846188730e2b225c16 Mon Sep 17 00:00:00 2001 From: askiada <25521495+askiada@users.noreply.github.com> Date: Fri, 19 May 2023 09:40:56 +0200 Subject: [PATCH 14/16] proto test --- grpc/external_sort_index.proto | 38 ++++++++++++++++++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 grpc/external_sort_index.proto diff --git a/grpc/external_sort_index.proto b/grpc/external_sort_index.proto new file mode 100644 index 0000000..d268b90 --- /dev/null +++ b/grpc/external_sort_index.proto @@ -0,0 +1,38 @@ +// (-- api-linter: core::0215::versioned-packages=disabled +// aip.dev/not-precedent: This simply makes the structure simpler --) +syntax = "proto3"; + +package bk.registration.orchestrator; + +option go_package = "github.com/askiada/external-sort/grpc/_build/go"; + + +service ExternalSort { + rpc SortSV(SortSVRequest) returns (SortSVResponse); +} + +message FileSV { + string path = 1; + bool gzip = 2; + string separator = 3; + repeated Field sort_fields = 4; + bool with_input_header = 5; + +} + + +message SortSVRequest { + + repeated FileSV input = 2; + +} + +message Field { + enum FIELD_TYPE{ + INT = 0; + STRING = 1; + BOOL = 2; + } + int64 index =1; + FIELD_TYPE type =2; +} From 244baf4941020b454d9bee896aacb9be7621ca59 Mon Sep 17 00:00:00 2001 From: askiada <25521495+askiada@users.noreply.github.com> Date: Sat, 29 Jun 2024 15:03:34 +0200 Subject: [PATCH 15/16] lint --- main_test.go | 5 ++--- testdata/chunks/output.tsv | 0 2 files changed, 2 insertions(+), 3 deletions(-) delete mode 100644 testdata/chunks/output.tsv diff --git a/main_test.go b/main_test.go index 6972aa2..1a7ef49 100644 --- a/main_test.go +++ b/main_test.go @@ -9,14 +9,14 @@ import ( "strconv" "testing" + "github.com/stretchr/testify/assert" + "github.com/askiada/external-sort/file" "github.com/askiada/external-sort/internal/rw" "github.com/askiada/external-sort/reader" "github.com/askiada/external-sort/vector" "github.com/askiada/external-sort/vector/key" "github.com/askiada/external-sort/writer" - - "github.com/stretchr/testify/assert" ) func prepareChunks( @@ -108,7 +108,6 @@ func TestBasics(t *testing.T) { for chunkSize := 1; chunkSize < 152; chunkSize += 10 { for bufferSize := 1; bufferSize < 152; bufferSize += 10 { chunkSize := chunkSize - bufferSize := bufferSize t.Run(name+"_"+strconv.Itoa(chunkSize)+"_"+strconv.Itoa(bufferSize), func(t *testing.T) { ctx := context.Background() diff --git a/testdata/chunks/output.tsv b/testdata/chunks/output.tsv deleted file mode 100644 index e69de29..0000000 From 80e9ab44c22ecce81f0528aa4d840a80254fb325 Mon Sep 17 00:00:00 2001 From: askiada <25521495+askiada@users.noreply.github.com> Date: Sat, 29 Jun 2024 15:03:59 +0200 Subject: [PATCH 16/16] lint --- .gitignore | 7 + .golangci.yml | 171 +++++++----------- Makefile | 4 + bucket/contract.go | 3 +- bucket/s3.go | 7 +- file/batchingchannels/batching_channel.go | 12 +- .../batchingchannels/batching_channel_test.go | 13 +- file/chunk.go | 16 +- file/file.go | 25 ++- file/sort.go | 45 ++++- file/utils.go | 4 + go.mod | 2 +- internal/progress/contract.go | 2 + internal/rw/rw.go | 29 ++- main.go | 36 +++- main_bench_test.go | 3 +- reader/gzip_separated_values.go | 4 + reader/gzip_separated_values_test.go | 10 +- reader/separated_values.go | 3 + reader/std_scanner.go | 25 ++- sftp/sftp.go | 11 +- vector/key/int_key.go | 8 +- vector/key/tsv_key.go | 4 + vector/slice_vector.go | 2 + vector/vector.go | 10 +- writer/contract.go | 4 +- writer/gzip_separated_values.go | 5 + writer/separated_values.go | 5 + writer/std_writer.go | 24 ++- 29 files changed, 342 insertions(+), 152 deletions(-) diff --git a/.gitignore b/.gitignore index 7cc7ba1..ac81399 100644 --- a/.gitignore +++ b/.gitignore @@ -2,3 +2,10 @@ bench* gen* chunk_*.tsv bin/ +*.csv +*.tsv +*.gz +coverage.out +testdata/chunks/*.csv +testdata/chunks/*.tsv +testdata/chunks/*.gz diff --git a/.golangci.yml b/.golangci.yml index e5f2e1a..ba3f9e4 100644 --- a/.golangci.yml +++ b/.golangci.yml @@ -1,7 +1,19 @@ linters-settings: + cyclop: + skip-tests: true + max-complexity: 15 + exhaustive: + default-signifies-exhaustive: true funlen: - lines: 80 - statements: 50 + lines: 110 + statements: 70 + gci: + sections: + - standard + - default + - prefix(github.com/askiada) + - localmodule + custom-order: true goconst: min-len: 2 min-occurrences: 2 @@ -17,7 +29,7 @@ linters-settings: godot: capital: true goimports: - local-prefixes: github.com/golangci/golangci-lint + local-prefixes: github.com/askiada/external-sort govet: settings: printf: @@ -26,128 +38,83 @@ linters-settings: - (github.com/golangci/golangci-lint/pkg/logutils.Log).Warnf - (github.com/golangci/golangci-lint/pkg/logutils.Log).Errorf - (github.com/golangci/golangci-lint/pkg/logutils.Log).Fatalf - enable: + disable: - fieldalignment - maligned: - suggest-new: true - misspell: - locale: UK lll: line-length: 140 + misspell: + locale: UK + paralleltest: + ignore-missing-subtests: true # Unfortunately, we can't write t.Run("success", testSuccess) unparam: check-exported: true + varnamelen: + min-name-length: 2 + max-distance: 15 + + errcheck: + exclude-functions: + - (*io.PipeWriter).Close + + wrapcheck: + ignoreSigs: + - .Errorf( + - errors.New( + - errors.Unwrap( + - errors.Join( + - .Wrap( + - .Wrapf( + - .WithMessage( + - .WithMessagef( + - .WithStack( + - status.Error( + - Group).Wait() + + nlreturn: + block-size: 2 issues: # Excluding configuration per-path, per-linter, per-text and per-source exclude-rules: - path: _test\.go linters: - - gosec # security check is not important in tests - - dupl # we usually duplicate code in tests - bodyclose - - unparam + - contextcheck + - dupl # we usually duplicate code in tests - errcheck - - govet + - exhaustive + - funlen - gocritic - - goconst - - forcetypeassert + - gosec # security check is not important in tests + - govet + - maintidx + - nlreturn + - revive + - unparam + - varnamelen - wrapcheck + - wsl + - path: testing + linters: + - errcheck fix: true exclude-use-default: false - -run: - skip-dirs: + exclude-dirs: + - model - tmp - bin - scripts +run: + allow-parallel-runners: true tests: true build-tags: - integration linters: - disable-all: true - fast: true - enable: - - asciicheck - - bidichk - - bodyclose - - bodyclose - - containedctx - - contextcheck - - cyclop - - decorder - - depguard - - dogsled - - dupl - - durationcheck - - errcheck - - errchkjson - - errname - - errorlint - - exhaustive - - exportloopref - - forbidigo - - forcetypeassert - - funlen - - gocognit - - goconst - - gocritic - - gocyclo - - godot - - godox - - gofmt - - gofumpt - - goheader - - goimports - - gomnd - - gomoddirectives - - gomodguard - - goprintffuncname - - gosec - - gosec - - gosimple - - gosimple - - govet - - govet - - grouper - - importas - - ineffassign - - ireturn - - lll - - maintidx - - makezero - - misspell - - nakedret - - nestif - - nilerr - - nilnil - - nlreturn - - noctx - - nolintlint - - prealloc - - predeclared - - promlinter - - revive - - rowserrcheck - - sqlclosecheck - - staticcheck - - staticcheck - - stylecheck - - tagliatelle - - tenv - - thelper - - tparallel - - typecheck - - unconvert - - unparam - - unused - - varnamelen - - wastedassign - - whitespace - - wrapcheck - -# golangci.com configuration -# https://github.com/golangci/golangci/wiki/Configuration -service: - golangci-lint-version: 1.52.x + enable-all: true + disable: + - depguard # because I don't want to write a dedicated config file. + - execinquery #Marked as deprecated by golangci-lint. + - gomnd # Marked as deprecated by golangci-lint. Replaced with mnd + - nonamedreturns # Conflicts with unnamedResult linter. diff --git a/Makefile b/Makefile index 5c5cf66..5473a9f 100644 --- a/Makefile +++ b/Makefile @@ -8,6 +8,10 @@ docker_image=askiada/external-sort include ./env.list export $(shell sed 's/=.*//' ./env.list) +.PHONY: lint +lint: + gofumpt -w -l . + golangci-lint run ./... .PHONY: test test: diff --git a/bucket/contract.go b/bucket/contract.go index 9c51477..9b63a55 100644 --- a/bucket/contract.go +++ b/bucket/contract.go @@ -1,9 +1,10 @@ package bucket import ( - "github.com/askiada/external-sort/internal/progress" "github.com/aws/aws-sdk-go-v2/feature/s3/manager" "github.com/aws/aws-sdk-go-v2/service/s3" + + "github.com/askiada/external-sort/internal/progress" ) // S3ClientAPI S3 client contract for this repo. diff --git a/bucket/s3.go b/bucket/s3.go index 08b1121..50f4c93 100644 --- a/bucket/s3.go +++ b/bucket/s3.go @@ -6,12 +6,13 @@ import ( "context" "io" - "github.com/askiada/external-sort/internal/progress" "github.com/aws/aws-sdk-go-v2/aws" "github.com/aws/aws-sdk-go-v2/config" "github.com/aws/aws-sdk-go-v2/feature/s3/manager" "github.com/aws/aws-sdk-go-v2/service/s3" "github.com/pkg/errors" + + "github.com/askiada/external-sort/internal/progress" ) // S3 can read and write from/to S3 buckets using io.Reader and io.Writer @@ -46,9 +47,11 @@ func New(ctx context.Context, cfg ...ConfigFunc) (*S3, error) { if s3Val.region == "" { return nil, errors.Wrap(ErrInvalidInput, "region") } + if s3Val.bufferLen <= 0 { return nil, errors.Wrap(ErrInvalidInput, "buffer length") } + if s3Val.s3Client == nil { cfg, err := config.LoadDefaultConfig(ctx, config.WithRegion(s3Val.region), @@ -57,6 +60,7 @@ func New(ctx context.Context, cfg ...ConfigFunc) (*S3, error) { if err != nil { return nil, errors.New("can't create aws config") } + s3Val.s3Client = s3.NewFromConfig(cfg) } @@ -107,6 +111,7 @@ func (s *S3) Download(ctx context.Context, writer io.Writer, filesinfo ...*S3Fil // we need to force this to be a sequential download. d.Concurrency = 1 }) + ww := &seqWriterAt{writer, nil} for _, fileinfo := range filesinfo { _, err := downloader.Download(ctx, ww, &s3.GetObjectInput{ diff --git a/file/batchingchannels/batching_channel.go b/file/batchingchannels/batching_channel.go index 150e593..428d416 100644 --- a/file/batchingchannels/batching_channel.go +++ b/file/batchingchannels/batching_channel.go @@ -3,9 +3,10 @@ package batchingchannels import ( "context" - "github.com/askiada/external-sort/vector" "github.com/pkg/errors" "golang.org/x/sync/errgroup" + + "github.com/askiada/external-sort/vector" ) // BatchingChannel define a standard channel, with the change that instead of producing individual elements @@ -17,7 +18,7 @@ type BatchingChannel struct { buffer vector.Vector allocate *vector.Allocate G *errgroup.Group - internalContext context.Context //nolint //containedcontext + internalContext context.Context size int maxWorker int } @@ -27,9 +28,11 @@ func NewBatchingChannel(ctx context.Context, allocate *vector.Allocate, maxWorke if size == 0 { return nil, errors.New("does not support unbuffered behaviour") } + if size < 0 { return nil, errors.New("does not support negative size") } + errGrp, errGrpContext := errgroup.WithContext(ctx) errGrp.SetLimit(maxWorker) bChan := &BatchingChannel{ @@ -41,6 +44,7 @@ func NewBatchingChannel(ctx context.Context, allocate *vector.Allocate, maxWorke G: errGrp, internalContext: errGrpContext, } + go bChan.batchingBuffer() return bChan, nil @@ -61,11 +65,11 @@ func (ch *BatchingChannel) Out() <-chan vector.Vector { // ProcessOut process specified function on each batch. func (ch *BatchingChannel) ProcessOut(f func(vector.Vector) error) error { for val := range ch.Out() { - val := val ch.G.Go(func() error { return f(val) }) } + err := ch.G.Wait() if err != nil { return errors.Wrap(err, "one of the task failed") @@ -93,6 +97,7 @@ func (ch *BatchingChannel) Close() { // When the batch reach maximum size or the input channel is closed, it is passed to the output channel. func (ch *BatchingChannel) batchingBuffer() { ch.buffer = ch.allocate.Vector(ch.size, ch.allocate.Key) + for { row, open := <-ch.input if open { @@ -109,6 +114,7 @@ func (ch *BatchingChannel) batchingBuffer() { break } + if ch.buffer.Len() == ch.size { ch.output <- ch.buffer ch.buffer = ch.allocate.Vector(ch.size, ch.allocate.Key) diff --git a/file/batchingchannels/batching_channel_test.go b/file/batchingchannels/batching_channel_test.go index ced13a3..56a67c8 100644 --- a/file/batchingchannels/batching_channel_test.go +++ b/file/batchingchannels/batching_channel_test.go @@ -7,19 +7,20 @@ import ( "testing" "time" - "github.com/askiada/external-sort/file/batchingchannels" - "github.com/askiada/external-sort/vector" - "github.com/askiada/external-sort/vector/key" "github.com/pkg/errors" "github.com/stretchr/testify/assert" "github.com/stretchr/testify/require" + + "github.com/askiada/external-sort/file/batchingchannels" + "github.com/askiada/external-sort/vector" + "github.com/askiada/external-sort/vector/key" ) type intKey struct { value int } -func allocateInt(row interface{}) (key.Key, error) { //nolint //ireturn +func allocateInt(row interface{}) (key.Key, error) { line, ok := row.(string) if !ok { return nil, errors.Errorf("can't convert interface{} to string: %+v", row) @@ -53,7 +54,7 @@ func testBatches(t *testing.T, bChan *batchingchannels.BatchingChannel) { maxIn := 100 wgrpInput.Add(maxIn) - for idx := 0; idx < maxIn; idx++ { + for idx := range maxIn { go func(j int) { defer wgrpInput.Done() for i := maxI / maxIn * j; i < maxI*(j+1)/maxIn; i++ { @@ -81,7 +82,7 @@ func testBatches(t *testing.T, bChan *batchingchannels.BatchingChannel) { go func() { defer wgrp.Done() err := bChan.ProcessOut(func(val vector.Vector) error { - for i := 0; i < val.Len(); i++ { + for i := range val.Len() { val := val.Get(i) got <- val } diff --git a/file/chunk.go b/file/chunk.go index df9d10f..38266e0 100644 --- a/file/chunk.go +++ b/file/chunk.go @@ -5,10 +5,10 @@ import ( "path/filepath" "sort" + "github.com/pkg/errors" + "github.com/askiada/external-sort/reader" "github.com/askiada/external-sort/vector" - - "github.com/pkg/errors" ) // chunkInfo define a chunk. @@ -28,12 +28,15 @@ func (c *chunkInfo) pullSubset(size int) (err error) { if err != nil { return errors.Wrap(err, "can't read chunk") } + err = c.buffer.PushBack(row) if err != nil { return errors.Wrap(err, "can't push back row") } + elemIdx++ } + if c.reader.Err() != nil { return errors.Wrap(c.reader.Err(), "chunk reader encountered an error") } @@ -52,6 +55,7 @@ func (c *chunks) new(chunkPath string, allocate *vector.Allocate, size int, with if err != nil { return errors.Wrap(err, "can't open chunk file") } + rder, err := allocate.FnReader(chunkFile) if err != nil { return errors.Wrap(err, "can't read chunk file") @@ -67,11 +71,14 @@ func (c *chunks) new(chunkPath string, allocate *vector.Allocate, size int, with reader: rder, buffer: allocate.Vector(size, allocate.Key), } + err = elem.pullSubset(size) if err != nil { return errors.Wrap(err, "can't pull chunk subset") } + c.list = append(c.list, elem) + return nil } @@ -83,6 +90,7 @@ func (c *chunks) close() error { return errors.Wrapf(err, "can't close chunk file %s", chunk.filename) } } + return nil } @@ -91,10 +99,12 @@ func (c *chunks) close() error { func (c *chunks) shrink(toShrink []int) error { for i, shrinkIndex := range toShrink { shrinkIndex -= i + err := c.list[shrinkIndex].file.Close() if err != nil { return errors.Wrapf(err, "can't close chunk file %s", c.list[shrinkIndex].filename) } + err = os.Remove(c.list[shrinkIndex].filename) if err != nil { return errors.Wrapf(err, "can't remove chunk file %s", c.list[shrinkIndex].filename) @@ -102,6 +112,7 @@ func (c *chunks) shrink(toShrink []int) error { // we want to preserve order c.list = append(c.list[:shrinkIndex], c.list[shrinkIndex+1:]...) } + return nil } @@ -136,5 +147,6 @@ func (c *chunks) min() (minChunk *chunkInfo, minValue *vector.Element, minIdx in minValue = c.list[0].buffer.Get(0) minIdx = 0 minChunk = c.list[0] + return minChunk, minValue, minIdx } diff --git a/file/file.go b/file/file.go index aa8f894..b42bcc7 100644 --- a/file/file.go +++ b/file/file.go @@ -7,13 +7,13 @@ import ( "strconv" "sync" + "github.com/pkg/errors" + "github.com/sirupsen/logrus" + "github.com/askiada/external-sort/file/batchingchannels" "github.com/askiada/external-sort/reader" "github.com/askiada/external-sort/vector" "github.com/askiada/external-sort/writer" - "github.com/sirupsen/logrus" - - "github.com/pkg/errors" ) var logger = logrus.StandardLogger() @@ -38,9 +38,11 @@ type Info struct { func (f *Info) check(dumpSize int) error { f.chunkIndex = 0 f.chunkPaths = []string{} + if dumpSize <= 0 { return errors.New("dump size must be greater than 0") } + return nil } @@ -49,21 +51,26 @@ func (f *Info) processInputReader(batchChan *batchingchannels.BatchingChannel, i if f.PrintMemUsage { f.mu.Collect() } + row, err := inputReader.Read() if err != nil { return errors.Wrap(err, "can't read from input reader") } + if f.WithHeader && f.headers == nil { f.headers = row } else { batchChan.In() <- row } + f.totalRows++ } batchChan.Close() + if inputReader.Err() != nil { return errors.Wrap(inputReader.Err(), "input reader encountered an error") } + return nil } @@ -73,23 +80,30 @@ func (f *Info) processBatch(vec vector.Vector, chunkFolder string) error { chunkPath := path.Join(chunkFolder, "chunk_"+strconv.Itoa(f.chunkIndex)+".tsv") logger.Infoln("Created chunk", chunkPath) f.localMutex.Unlock() + vec.Sort() + if f.WithHeader { f.localMutex.Lock() + err := vec.PushFrontNoKey(f.headers) if err != nil { f.localMutex.Unlock() return err } + f.localMutex.Unlock() } + err := f.Allocate.Dump(vec, chunkPath) if err != nil { return errors.Wrapf(err, "can't dump chunk %s", chunkPath) } + f.localMutex.Lock() f.chunkPaths = append(f.chunkPaths, chunkPath) f.localMutex.Unlock() + return nil } @@ -104,6 +118,7 @@ func (f *Info) runBatchingChannel( if err != nil { return nil, errors.Wrap(err, "can't create new batching channel") } + batchChan.G.Go(func() error { return f.processInputReader(batchChan, inputReader) }) err = batchChan.ProcessOut(func(vec vector.Vector) error { @@ -111,11 +126,13 @@ func (f *Info) runBatchingChannel( if err != nil { return errors.Wrap(err, "can't process batch") } + return nil }) if err != nil { return nil, errors.Wrap(err, "can't process batching channel") } + return f.chunkPaths, nil } @@ -139,9 +156,11 @@ func (f *Info) CreateSortedChunks(ctx context.Context, chunkFolder string, dumpS if err != nil { return nil, errors.Wrap(err, "can't get input reader") } + chunkPaths, err := f.runBatchingChannel(ctx, inputReader, chunkFolder, dumpSize, maxWorkers) if err != nil { return nil, errors.Wrap(err, "can't run batching channel") } + return chunkPaths, nil } diff --git a/file/sort.go b/file/sort.go index 6fda072..1c384ff 100644 --- a/file/sort.go +++ b/file/sort.go @@ -5,10 +5,11 @@ import ( "runtime" "strings" - "github.com/askiada/external-sort/vector" - "github.com/askiada/external-sort/writer" "github.com/cheggaaa/pb/v3" "github.com/pkg/errors" + + "github.com/askiada/external-sort/vector" + "github.com/askiada/external-sort/writer" ) type memUsage struct { @@ -19,10 +20,13 @@ type memUsage struct { func (mu *memUsage) Collect() { var mStats runtime.MemStats + runtime.ReadMemStats(&mStats) + if mStats.Alloc > mu.MaxAlloc { mu.MaxAlloc = mStats.Alloc } + if mStats.Sys > mu.MaxSys { mu.MaxSys = mStats.Sys } @@ -35,6 +39,7 @@ func (mu *memUsage) String() string { builder.WriteString(fmt.Sprintf("Max Alloc = %v MiB", bToMb(mu.MaxAlloc))) builder.WriteString(fmt.Sprintf(" Max Sys = %v MiB", bToMb(mu.MaxSys))) builder.WriteString(fmt.Sprintf(" NumGC = %v\n", mu.NumGc)) + return builder.String() } @@ -52,6 +57,7 @@ func (f *Info) createChunks(chunkPaths []string, k int) (*chunks, error) { return nil, errors.Wrapf(err, "can't create chunk %s", chunkPath) } } + return chunks, nil } @@ -62,6 +68,7 @@ func (f *Info) handleHeader(output vector.Vector) error { return errors.Wrapf(err, "can't add headers %+v", f.headers) } } + return nil } @@ -76,22 +83,28 @@ func (nc *nextChunk) get(output vector.Vector, createdChunks *chunks, dropDuplic if err != nil { return nil, 0, errors.Wrapf(err, "can't push back row %+v", minValue.Row) } + nc.oldElem = minValue } + return minChunk, minIdx, nil } func updateChunks(createdChunks *chunks, minChunk *chunkInfo, minIdx, k int) error { minChunk.buffer.FrontShift() + isEmpty := false + if minChunk.buffer.Len() == 0 { err := minChunk.pullSubset(k) if err != nil { return errors.Wrapf(err, "can't pull subset from chunk %s", minChunk.filename) } + // if after pulling data the chunk buffer is still empty then we can remove it if minChunk.buffer.Len() == 0 { isEmpty = true + err = createdChunks.shrink([]int{minIdx}) if err != nil { return errors.Wrapf(err, "can't shrink chunk at index %d", minIdx) @@ -102,6 +115,7 @@ func updateChunks(createdChunks *chunks, minChunk *chunkInfo, minIdx, k int) err if !isEmpty { createdChunks.moveFirstChunkToCorrectIndex() } + return nil } @@ -110,30 +124,39 @@ func (f *Info) prepareMergeSort(output vector.Vector, chunkPaths []string, outpu if err != nil { return nil, errors.Wrap(err, "can't handle headers") } + // create a chunk per file path createdChunks, err := f.createChunks(chunkPaths, outputBufferSize) if err != nil { return nil, errors.Wrap(err, "can't create all chunks") } + f.outputWriter, err = f.Allocate.FnWriter(f.OutputFile) if err != nil { return nil, errors.Wrap(err, "can't get output writer file") } + return createdChunks, nil } func (f *Info) runMergeSort(createdChunks *chunks, output vector.Vector, outputBufferSize int, dropDuplicates bool) error { bar := pb.StartNew(f.totalRows) - createdChunks.resetOrder() + defer bar.Finish() + smallestChunk := &nextChunk{} + + createdChunks.resetOrder() + for { if f.PrintMemUsage { f.mu.Collect() } + err := f.dumpOutput(createdChunks, output, outputBufferSize) if err != nil { return errors.Wrap(err, "can't dump output") } + if createdChunks.len() == 0 { break } @@ -143,17 +166,20 @@ func (f *Info) runMergeSort(createdChunks *chunks, output vector.Vector, outputB if err != nil { return errors.Wrap(err, "can't get next chunk with smallest value") } + // remove the first element from the chunk we pulled the smallest value err = updateChunks(createdChunks, minChunk, minIdx, outputBufferSize) if err != nil { return errors.Wrap(err, "can't update chunks") } + bar.Increment() } - bar.Finish() + if f.PrintMemUsage { logger.Debugln(f.mu.String()) } + return nil } @@ -164,6 +190,7 @@ func (f *Info) dumpOutput(createdChunks *chunks, output vector.Vector, outputBuf return err } } + return nil } @@ -171,32 +198,40 @@ func (f *Info) dumpOutput(createdChunks *chunks, output vector.Vector, outputBuf // It is possilbe to drop duplicates and define the maximum size of the output buffer before flush. func (f *Info) MergeSort(chunkPaths []string, outputBufferSize int, dropDuplicates bool) (err error) { output := f.Allocate.Vector(outputBufferSize, f.Allocate.Key) + if f.PrintMemUsage && f.mu == nil { f.mu = &memUsage{} } + createdChunks, err := f.prepareMergeSort(output, chunkPaths, outputBufferSize) if err != nil { return errors.Wrap(err, "can't prepare merge sort") } + defer func() { err = f.outputWriter.Close() }() + err = f.runMergeSort(createdChunks, output, outputBufferSize, dropDuplicates) if err != nil { return errors.Wrap(err, "can't run merge sort") } + err = createdChunks.close() if err != nil { return errors.Wrap(err, "can't close created chunks") } + return err } func writeBuffer(w writer.Writer, rows vector.Vector) error { - for i := 0; i < rows.Len(); i++ { + for i := range rows.Len() { err := w.Write(rows.Get(i).Row) if err != nil { return errors.Wrap(err, "can't write buffer") } } + rows.Reset() + return nil } diff --git a/file/utils.go b/file/utils.go index 9746804..8ad9ea8 100644 --- a/file/utils.go +++ b/file/utils.go @@ -14,18 +14,22 @@ func clearChunkFolder(folder string) error { if err != nil { return errors.Wrap(err, "can't create folder") } + dir, err := os.ReadDir(folder) if err != nil { return errors.Wrap(err, "can't read chunk folder") } + for _, d := range dir { if !strings.HasPrefix(d.Name(), "chunk") { continue } + err = os.RemoveAll(path.Join(folder, d.Name())) if err != nil { return errors.Wrap(err, "can't clear chunk folder") } } + return nil } diff --git a/go.mod b/go.mod index f7256f6..d72b023 100644 --- a/go.mod +++ b/go.mod @@ -1,6 +1,6 @@ module github.com/askiada/external-sort -go 1.20 +go 1.22 require ( github.com/aws/aws-sdk-go-v2 v1.18.0 diff --git a/internal/progress/contract.go b/internal/progress/contract.go index b8495c2..9fd343e 100644 --- a/internal/progress/contract.go +++ b/internal/progress/contract.go @@ -57,8 +57,10 @@ func (b *Basic) Begin(total int64) { func (b *Basic) Add(val int64) { b.written += float64(val) progress := int(math.Round(b.written / b.total * 100)) //nolint //gomnd + if progress >= b.milestone { b.milestone += 5 // every 5% + logrus.Debugf("Download from S3 at %3d%%\n\n", progress) } } diff --git a/internal/rw/rw.go b/internal/rw/rw.go index e6253a6..0252beb 100644 --- a/internal/rw/rw.go +++ b/internal/rw/rw.go @@ -8,14 +8,15 @@ import ( "path/filepath" "strings" - "github.com/askiada/external-sort/bucket" - "github.com/askiada/external-sort/internal" - "github.com/askiada/external-sort/internal/progress" "github.com/aws/aws-sdk-go-v2/config" "github.com/aws/aws-sdk-go-v2/service/s3" "github.com/pkg/errors" "github.com/sirupsen/logrus" "golang.org/x/sync/errgroup" + + "github.com/askiada/external-sort/bucket" + "github.com/askiada/external-sort/internal" + "github.com/askiada/external-sort/internal/progress" ) var logger = logrus.StandardLogger() @@ -27,7 +28,7 @@ type InputOutput struct { Output io.Writer outputPipe *io.PipeWriter g *errgroup.Group - internalCtx context.Context //nolint //containedcontext + internalCtx context.Context } func NewInputOutput(ctx context.Context) *InputOutput { @@ -43,6 +44,7 @@ func (i *InputOutput) s3Check(ctx context.Context) error { if i.s3Client != nil { return nil } + cfg, err := config.LoadDefaultConfig(ctx, config.WithRegion(internal.S3Region), config.WithRetryMaxAttempts(internal.S3RetryMaxAttempts), @@ -50,6 +52,7 @@ func (i *InputOutput) s3Check(ctx context.Context) error { if err != nil { return errors.New("can't create aws config") } + i.s3Client = s3.NewFromConfig(cfg) return nil @@ -61,6 +64,7 @@ func (i *InputOutput) SetInputReader(ctx context.Context, inputFiles ...string) if err != nil { return errors.Wrap(err, "can't check s3") } + s3Api, err := bucket.New(ctx, bucket.Client(i.s3Client), bucket.Buffer(1_000_000), @@ -69,7 +73,9 @@ func (i *InputOutput) SetInputReader(ctx context.Context, inputFiles ...string) if err != nil { return errors.Wrap(err, "can't create s3 client") } + files := []*bucket.S3FileInfo{} + for _, inputFile := range inputFiles { u, _ := url.Parse(inputFile) u.Path = strings.TrimLeft(u.Path, "/") @@ -85,6 +91,7 @@ func (i *InputOutput) SetInputReader(ctx context.Context, inputFiles ...string) i.inputPipe = pr i.g.Go(func() (err error) { defer func() { err = pw.Close() }() + err = s3Api.Download(i.internalCtx, pw, files...) if err != nil { return errors.Wrap(err, "can't download files") @@ -94,13 +101,16 @@ func (i *InputOutput) SetInputReader(ctx context.Context, inputFiles ...string) }) } else { var files []io.Reader + for _, inputFile := range inputFiles { f, err := os.Open(filepath.Clean(inputFile)) if err != nil { return errors.Wrapf(err, "can't open file %s", inputFile) } + files = append(files, f) } + i.Input = io.MultiReader(files...) } @@ -113,12 +123,15 @@ func (i *InputOutput) SetOutputWriter(ctx context.Context, outputFile string) (e if err != nil { return errors.Wrap(err, "can't check s3") } + outputURL, err := url.Parse(outputFile) if err != nil { return errors.Wrapf(err, "can't parse output url %s", outputFile) } + outputURL.Path = strings.TrimLeft(outputURL.Path, "/") logger.Debugf("Proto: %q, Bucket: %q, Key: %q", outputURL.Scheme, outputURL.Host, outputURL.Path) + s3Api, err := bucket.New(ctx, bucket.Client(i.s3Client), bucket.Buffer(1_000_000), @@ -133,10 +146,12 @@ func (i *InputOutput) SetOutputWriter(ctx context.Context, outputFile string) (e i.outputPipe = pw i.g.Go(func() (err error) { defer func() { err = pr.Close() }() + err = s3Api.Upload(i.internalCtx, pr, outputURL.Host, outputURL.Path) if err != nil { return errors.Wrapf(err, "can't upload file %s", outputFile) } + return err }) } else { @@ -145,6 +160,7 @@ func (i *InputOutput) SetOutputWriter(ctx context.Context, outputFile string) (e return errors.Wrapf(err, "can't create file %s", outputFile) } } + return nil } @@ -154,10 +170,12 @@ func (i *InputOutput) Do(f func() error) { if err != nil { return err } + err = i.Close() if err != nil { return err } + return nil }) } @@ -169,12 +187,14 @@ func (i *InputOutput) Close() error { return errors.Wrap(err, "can't close input reader") } } + if i.outputPipe != nil { err := i.outputPipe.Close() if err != nil { return errors.Wrap(err, "can't close output writer") } } + return nil } @@ -182,5 +202,6 @@ func (i *InputOutput) Err() error { if err := i.g.Wait(); err != nil { return errors.Wrap(err, "one of the go routines went wrong") } + return nil } diff --git a/main.go b/main.go index 97f1039..89257d6 100644 --- a/main.go +++ b/main.go @@ -6,6 +6,11 @@ import ( "strconv" "time" + "github.com/pkg/errors" + "github.com/sirupsen/logrus" + "github.com/spf13/cobra" + "github.com/spf13/viper" + "github.com/askiada/external-sort/file" "github.com/askiada/external-sort/internal" "github.com/askiada/external-sort/internal/rw" @@ -13,10 +18,6 @@ import ( "github.com/askiada/external-sort/vector" "github.com/askiada/external-sort/vector/key" "github.com/askiada/external-sort/writer" - "github.com/pkg/errors" - "github.com/sirupsen/logrus" - "github.com/spf13/cobra" - "github.com/spf13/viper" ) var logger = logrus.StandardLogger() @@ -130,14 +131,18 @@ func newCommand() *command { RunE: shuffleRun, }, } + root.rootCmd.AddCommand(root.sortCmd, root.shuffleCmd) + return root } func main() { root := newCommand() setFlags(root) + ctx := context.Background() + cobra.CheckErr(root.rootCmd.ExecuteContext(ctx)) } @@ -150,22 +155,28 @@ func sortRun(cmd *cobra.Command, _ []string) error { start := time.Now() inputOutput := rw.NewInputOutput(cmd.Context()) + err := inputOutput.SetInputReader(cmd.Context(), internal.InputFiles...) if err != nil { return errors.Wrap(err, "can't set input reader") } + err = inputOutput.SetOutputWriter(cmd.Context(), internal.OutputFile) if err != nil { return errors.Wrap(err, "can't set output writer") } + tsvFields := []int{} + for _, field := range internal.TsvFields { i, err := strconv.Atoi(field) if err != nil { return errors.Wrapf(err, "can't convert field %s", field) } + tsvFields = append(tsvFields, i) } + fileInfo := &file.Info{ WithHeader: internal.WithHeader, InputReader: inputOutput.Input, @@ -176,6 +187,7 @@ func sortRun(cmd *cobra.Command, _ []string) error { if err != nil { return nil, errors.Wrapf(err, "can't allocate tsv %+v", row) } + return k, nil }, func(r io.Reader) (reader.Reader, error) { @@ -183,6 +195,7 @@ func sortRun(cmd *cobra.Command, _ []string) error { if err != nil { return nil, errors.Wrap(err, "can't create Gzip reader") } + return gzipReader, nil }, func(w io.Writer) (writer.Writer, error) { @@ -190,11 +203,13 @@ func sortRun(cmd *cobra.Command, _ []string) error { if err != nil { return nil, errors.Wrap(err, "can't create Gzip writer") } + return gzipWriter, nil }, ), PrintMemUsage: false, } + inputOutput.Do(func() error { // create small files with maximum 30 rows in each chunkPaths, err := fileInfo.CreateSortedChunks(cmd.Context(), internal.ChunkFolder, internal.ChunkSize, internal.MaxWorkers) @@ -207,14 +222,18 @@ func sortRun(cmd *cobra.Command, _ []string) error { if err != nil { return errors.Wrap(err, "can't merge sort") } + elapsed := time.Since(start) logger.Infoln("It took", elapsed) + return nil }) + err = inputOutput.Err() if err != nil { return errors.Wrap(err, "can't finish") } + return nil } @@ -224,12 +243,15 @@ func shuffleRun(cmd *cobra.Command, _ []string) error { logger.Infoln("Output file", internal.OutputFile) logger.Infoln("Chunk folder", internal.ChunkFolder) logger.Infoln("GZip file", internal.IsGzip) + start := time.Now() inputOutput := rw.NewInputOutput(cmd.Context()) + err := inputOutput.SetInputReader(cmd.Context(), internal.InputFiles...) if err != nil { return errors.Wrap(err, "can't set input reader") } + err = inputOutput.SetOutputWriter(cmd.Context(), internal.OutputFile) if err != nil { return errors.Wrap(err, "can't set output writer") @@ -241,6 +263,7 @@ func shuffleRun(cmd *cobra.Command, _ []string) error { OutputFile: inputOutput.Output, PrintMemUsage: false, } + inputOutput.Do(func() error { // create small files with maximum 30 rows in each _, err := fileInfo.Shuffle( @@ -255,13 +278,18 @@ func shuffleRun(cmd *cobra.Command, _ []string) error { if err != nil { return errors.Wrap(err, "can't create shuflled chunks") } + elapsed := time.Since(start) + logger.Infoln("It took", elapsed) + return nil }) + err = inputOutput.Err() if err != nil { return errors.Wrap(err, "can't finish") } + return nil } diff --git a/main_bench_test.go b/main_bench_test.go index e87982c..d31809e 100644 --- a/main_bench_test.go +++ b/main_bench_test.go @@ -7,13 +7,14 @@ import ( "path" "testing" + "github.com/stretchr/testify/assert" + "github.com/askiada/external-sort/file" "github.com/askiada/external-sort/internal/rw" "github.com/askiada/external-sort/reader" "github.com/askiada/external-sort/vector" "github.com/askiada/external-sort/vector/key" "github.com/askiada/external-sort/writer" - "github.com/stretchr/testify/assert" ) func BenchmarkMergeSort(b *testing.B) { diff --git a/reader/gzip_separated_values.go b/reader/gzip_separated_values.go index d38430e..5ff4627 100644 --- a/reader/gzip_separated_values.go +++ b/reader/gzip_separated_values.go @@ -26,6 +26,7 @@ func NewGZipSeparatedValues(r io.Reader, separator rune) (*GZipSeparatedValuesRe r: csv.NewReader(gr), } s.r.Comma = separator + return s, nil } @@ -34,8 +35,10 @@ func (s *GZipSeparatedValuesReader) Next() bool { if errors.Is(s.err, io.EOF) { s.err = nil s.gr.Close() + return false } + return true } @@ -43,6 +46,7 @@ func (s *GZipSeparatedValuesReader) Read() (interface{}, error) { if s.err != nil { return nil, s.err } + return s.row, nil } diff --git a/reader/gzip_separated_values_test.go b/reader/gzip_separated_values_test.go index 966ef3d..0793a63 100644 --- a/reader/gzip_separated_values_test.go +++ b/reader/gzip_separated_values_test.go @@ -6,10 +6,11 @@ import ( "os" "testing" - "github.com/askiada/external-sort/internal/rw" - "github.com/askiada/external-sort/reader" "github.com/stretchr/testify/assert" "github.com/stretchr/testify/require" + + "github.com/askiada/external-sort/internal/rw" + "github.com/askiada/external-sort/reader" ) func Test(t *testing.T) { @@ -33,7 +34,10 @@ func TestS3(t *testing.T) { t.Skip("to rework") ctx := context.Background() i := rw.NewInputOutput(ctx) - err := i.SetInputReader(ctx, "s3://blokur-data/ml-title/remote/1/f15c2cf2e3ab46589419e6441b64e3bd/artifacts/input/word2vec/refine/recordings.59.tsv.gz") + err := i.SetInputReader( + ctx, + "s3://blokur-data/ml-title/remote/1/f15c2cf2e3ab46589419e6441b64e3bd/artifacts/input/word2vec/refine/recordings.59.tsv.gz", + ) require.NoError(t, err) gzipReader, err := reader.NewGZipSeparatedValues(i.Input, '\t') diff --git a/reader/separated_values.go b/reader/separated_values.go index fdb4fea..b2948e4 100644 --- a/reader/separated_values.go +++ b/reader/separated_values.go @@ -17,6 +17,7 @@ func NewSeparatedValues(r io.Reader, separator rune) *SeparatedValuesReader { r: csv.NewReader(r), } s.r.Comma = separator + return s } @@ -26,6 +27,7 @@ func (s *SeparatedValuesReader) Next() bool { s.err = nil return false } + return true } @@ -33,6 +35,7 @@ func (s *SeparatedValuesReader) Read() (interface{}, error) { if s.err != nil { return nil, s.err } + return s.row, nil } diff --git a/reader/std_scanner.go b/reader/std_scanner.go index c16235e..07756b5 100644 --- a/reader/std_scanner.go +++ b/reader/std_scanner.go @@ -18,20 +18,27 @@ type StdScanner struct { } func NewStdScanner(r io.Reader, isGzip bool) (Reader, error) { - var newR *bufio.Scanner - s := &StdScanner{} + var ( + newR *bufio.Scanner + s = &StdScanner{} + ) + if isGzip { gr, err := gzip.NewReader(r) if err != nil { return nil, errors.Wrap(err, "can't create gzip reader") } + s.gr = gr newR = bufio.NewScanner(gr) } else { newR = bufio.NewScanner(r) } + s.r = newR + logger.Infoln("Created standard scanner") + return s, nil } @@ -40,6 +47,7 @@ func (s *StdScanner) Next() bool { if !next && s.gr != nil { s.gr.Close() } + return next } @@ -57,19 +65,25 @@ type StdSliceScanner struct { } func NewStdSliceScanner(r io.Reader, isGzip bool) (Reader, error) { - var newR *bufio.Scanner - s := &StdSliceScanner{} + var ( + newR *bufio.Scanner + s = &StdSliceScanner{} + ) + if isGzip { gr, err := gzip.NewReader(r) if err != nil { return nil, errors.Wrap(err, "can't create gzip reader") } + s.gr = gr newR = bufio.NewScanner(gr) } else { newR = bufio.NewScanner(r) } + s.r = newR + return s, nil } @@ -78,15 +92,18 @@ func (s *StdSliceScanner) Next() bool { if !next && s.gr != nil { s.gr.Close() } + return next } func (s *StdSliceScanner) Read() (interface{}, error) { line := s.r.Text() + before, after, found := strings.Cut(line, "##!!##") if !found { return nil, errors.New("can't cut row") } + return []string{before, after}, nil } diff --git a/sftp/sftp.go b/sftp/sftp.go index e9dd341..3e60c51 100644 --- a/sftp/sftp.go +++ b/sftp/sftp.go @@ -17,29 +17,37 @@ type Client struct { func NewSFTPClient(addr, key, user, passphrase string) (*Client, error) { res := &Client{} + pemBytes, err := os.ReadFile(filepath.Clean(key)) if err != nil { log.Fatal(err) } + signer, err := ssh.ParsePrivateKeyWithPassphrase(pemBytes, []byte(passphrase)) if err != nil { log.Fatalf("parse key failed:%v", err) } + config := &ssh.ClientConfig{ User: user, - HostKeyCallback: ssh.InsecureIgnoreHostKey(), //nolint + HostKeyCallback: ssh.InsecureIgnoreHostKey(), Auth: []ssh.AuthMethod{ssh.PublicKeys(signer)}, } + conn, err := ssh.Dial("tcp", addr, config) if err != nil { return nil, errors.Wrapf(err, "can't dial with address %s", addr) } + res.Conn = conn + client, err := sftp.NewClient(conn) if err != nil { return nil, errors.Wrapf(err, "can't create sftp client with address %s", addr) } + res.Client = client + return res, nil } @@ -48,5 +56,6 @@ func (s *Client) Close() error { if err != nil { return errors.Wrap(err, "can't close client") } + return s.Conn.Close() } diff --git a/vector/key/int_key.go b/vector/key/int_key.go index 73f0fd1..6575d40 100644 --- a/vector/key/int_key.go +++ b/vector/key/int_key.go @@ -12,15 +12,17 @@ type Int struct { } // AllocateInt create a new integer key. -func AllocateInt(row interface{}) (Key, error) { //nolint //ireturn +func AllocateInt(row interface{}) (Key, error) { line, ok := row.(string) if !ok { return nil, errors.Errorf("can't convert interface{} to string: %+v", row) } + num, err := strconv.Atoi(line) if err != nil { return nil, errors.Wrapf(err, "can't convert line %s to int", line) } + return &Int{num}, nil } @@ -40,15 +42,17 @@ type IntFromSlice struct { } // AllocateIntFromSlice create a new integer key from a position in a slice of integers. -func AllocateIntFromSlice(row interface{}, intIndex int) (Key, error) { //nolint //ireturn +func AllocateIntFromSlice(row interface{}, intIndex int) (Key, error) { line, ok := row.([]string) if !ok { return nil, errors.Errorf("can't convert interface{} to []string: %+v", row) } + num, err := strconv.ParseInt(line[intIndex], 10, 64) if err != nil { return nil, errors.Wrapf(err, "can't parse int %+v", line[intIndex]) } + return &IntFromSlice{num}, nil } diff --git a/vector/key/tsv_key.go b/vector/key/tsv_key.go index 9c31d61..509df39 100644 --- a/vector/key/tsv_key.go +++ b/vector/key/tsv_key.go @@ -13,12 +13,16 @@ func AllocateTsv(row interface{}, pos ...int) (Key, error) { if !ok { return nil, errors.Errorf("can't convert interface{} to []string: %+v", row) } + strBuilder := strings.Builder{} + for i, p := range pos { if len(splitted) < p+1 { return nil, errors.Errorf("can't allocate tsv key line is invalid: %s", row) } + strBuilder.WriteString(splitted[p]) + if i < len(pos)-1 { strBuilder.WriteString(salt) } diff --git a/vector/slice_vector.go b/vector/slice_vector.go index ba52d75..199b147 100644 --- a/vector/slice_vector.go +++ b/vector/slice_vector.go @@ -37,7 +37,9 @@ func (v *SliceVec) PushBack(row interface{}) error { if err != nil { return err } + v.s = append(v.s, &Element{Row: row, Key: k}) + return nil } diff --git a/vector/vector.go b/vector/vector.go index d6b059d..9961886 100644 --- a/vector/vector.go +++ b/vector/vector.go @@ -4,10 +4,11 @@ import ( "os" "path/filepath" + "github.com/pkg/errors" + "github.com/askiada/external-sort/reader" "github.com/askiada/external-sort/vector/key" "github.com/askiada/external-sort/writer" - "github.com/pkg/errors" ) // Allocate define a vector and methods to read and write it. @@ -54,23 +55,28 @@ func (a *Allocate) Dump(vec Vector, filename string) error { if err != nil { return errors.Errorf("failed creating file: %s", err) } + datawriter, err := a.FnWriter(file) if err != nil { return errors.Errorf("failed creating writer: %s", err) } - for i := 0; i < vec.Len(); i++ { + + for i := range vec.Len() { err = datawriter.Write(vec.Get(i).Row) if err != nil { return errors.Errorf("failed writing file: %s", err) } } + err = datawriter.Close() if err != nil { return errors.Wrap(err, "can't close chunk writer") } + err = file.Close() if err != nil { return errors.Wrap(err, "can't close chunf file") } + return nil } diff --git a/writer/contract.go b/writer/contract.go index 78b4793..c23fddb 100644 --- a/writer/contract.go +++ b/writer/contract.go @@ -3,8 +3,8 @@ package writer import "io" type Writer interface { - Write(interface{}) error - Close() error + Write(row interface{}) (err error) + Close() (err error) } type Config func(w io.Writer) (Writer, error) diff --git a/writer/gzip_separated_values.go b/writer/gzip_separated_values.go index 4e37a33..a86a1f6 100644 --- a/writer/gzip_separated_values.go +++ b/writer/gzip_separated_values.go @@ -20,6 +20,7 @@ func NewGZipSeparatedValues(w io.Writer, separator rune) (Writer, error) { w: csv.NewWriter(gw), } s.w.Comma = separator + return s, nil } @@ -28,18 +29,22 @@ func (s *GZipSeparatedValuesWriter) Write(elem interface{}) error { if !ok { return errors.Errorf("can't converte interface{} to []string: %+v", elem) } + err := s.w.Write(line) if err != nil { return errors.Wrap(err, "can't write line") } + return nil } func (s *GZipSeparatedValuesWriter) Close() (err error) { defer func() { err = s.gw.Close() }() s.w.Flush() + if s.w.Error() != nil { return errors.Wrap(s.w.Error(), "can't close writer") } + return err } diff --git a/writer/separated_values.go b/writer/separated_values.go index 4e073ea..0303ce2 100644 --- a/writer/separated_values.go +++ b/writer/separated_values.go @@ -16,6 +16,7 @@ func NewSeparatedValues(w io.Writer, separator rune) Writer { w: csv.NewWriter(w), } s.w.Comma = separator + return s } @@ -24,17 +25,21 @@ func (s *SeparatedValuesWriter) Write(elem interface{}) error { if !ok { return errors.Errorf("can't converte interface{} to []string: %+v", elem) } + err := s.w.Write(line) if err != nil { return errors.Wrap(err, "can't write line") } + return nil } func (s *SeparatedValuesWriter) Close() error { s.w.Flush() + if s.w.Error() != nil { return errors.Wrap(s.w.Error(), "can't close writer") } + return nil } diff --git a/writer/std_writer.go b/writer/std_writer.go index c8ab78e..2398a03 100644 --- a/writer/std_writer.go +++ b/writer/std_writer.go @@ -15,10 +15,11 @@ type StdWriter struct { } // NewStdWriter create a standard writer. -func NewStdWriter(w io.Writer) Writer { //nolint //ireturn +func NewStdWriter(w io.Writer) Writer { s := &StdWriter{ w: bufio.NewWriter(w), } + return s } @@ -27,10 +28,12 @@ func (w *StdWriter) Write(elem interface{}) error { if !ok { return errors.Errorf("can't converte interface{} to string: %+v", elem) } + _, err := w.w.WriteString(line + "\n") if err != nil { return errors.Wrap(err, "can't write string") } + return err } @@ -40,6 +43,7 @@ func (w *StdWriter) Close() error { if err != nil { return errors.Wrap(err, "can't close writer") } + return nil } @@ -50,17 +54,22 @@ type StdSliceWriter struct { } func NewStdSliceWriter(w io.Writer, skipFirst, isGzip bool) Writer { - var newR *bufio.Writer - ssw := &StdSliceWriter{ - skipFirst: skipFirst, - } + var ( + newR *bufio.Writer + ssw = &StdSliceWriter{ + skipFirst: skipFirst, + } + ) + if isGzip { ssw.gw = gzip.NewWriter(w) newR = bufio.NewWriter(ssw.gw) } else { newR = bufio.NewWriter(w) } + ssw.w = newR + return ssw } @@ -69,13 +78,16 @@ func (w *StdSliceWriter) Write(elem interface{}) error { if !ok { return errors.Errorf("can't converte interface{} to string: %+v", elem) } + if w.skipFirst { line = line[1:] } + _, err := w.w.WriteString(strings.Join(line, "##!!##") + "\n") if err != nil { return errors.Wrap(err, "can't write string") } + return err } @@ -84,9 +96,11 @@ func (w *StdSliceWriter) Close() (err error) { if w.gw != nil { defer func() { err = w.gw.Close() }() } + err = w.w.Flush() if err != nil { return errors.Wrap(err, "can't close writer") } + return err }