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Fix pre sort cmd (#2222)
* make ndjson pre_sort parallel, fix several bugs, test * remove json tags (not needed), rename pre_sort -> presort
This commit is contained in:
Matthew Jaffee
GitHub
parent
468461fbcf
commit
8f1f3c6d06
3 changed files with 132 additions and 71 deletions
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@ -10,7 +10,7 @@ import (
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func newPreSortCommand(logdest logger.Logger) *cobra.Command {
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cmd := ctl.NewPreSortCommand(logdest)
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ccmd := &cobra.Command{
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Use: "pre_sort",
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Use: "presort",
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Short: "Sort records within files into files by FB partition for more efficient ingest",
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Long: `
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Takes all input files and writes PartitionN numbered files to a directory, where each file contains only records that will go into the partition it is named for.
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@ -22,8 +22,11 @@ Takes all input files and writes PartitionN numbered files to a directory, where
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flags.StringVarP(&cmd.File, "file", "", "", "Input file or directory.")
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flags.StringVarP(&cmd.Table, "table", "", "", "Name of table (used to hash keys to determine partition).")
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flags.StringVarP(&cmd.Type, "type", "", cmd.Type, "Input file type (csv or ndjson).")
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flags.StringSliceVar(&cmd.PrimaryKeyFields, "primary-key-fields", []string{}, "Names of primary key fields. For CSV there must be a header row and these pulled from there.")
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flags.StringSliceVar(&cmd.PrimaryKeyFields, "primary-key-fields", []string{}, "Names of primary key fields. For CSV there must be a header row and these are pulled from there.")
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flags.IntVar(&cmd.PartitionN, "partition-n", cmd.PartitionN, "Number of partitions.")
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flags.StringVarP(&cmd.OutputDir, "output-dir", "", cmd.OutputDir, "Directory name to write output to.")
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flags.StringVarP(&cmd.PrimaryKeySeparator, "primary-key-separator", "", cmd.PrimaryKeySeparator, "Separator to write in between primary key fields, can be empty.")
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flags.IntVar(&cmd.JobSize, "job-size", cmd.JobSize, "Number of lines to put into each job (purely a performance tuning parameter, only supported by ndjson mode).")
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flags.IntVar(&cmd.NumWorkers, "num-workers", cmd.NumWorkers, "Number of parallel worker routines doing decode->hash->encode. Only supported by ndjson mode.")
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return ccmd
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}
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@ -1,6 +1,7 @@
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package ctl
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import (
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"bufio"
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"context"
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"encoding/csv"
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"encoding/json"
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@ -10,22 +11,28 @@ import (
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"io/fs"
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"os"
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"path/filepath"
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"sync"
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"github.com/featurebasedb/featurebase/v3/logger"
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"github.com/pkg/errors"
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"golang.org/x/sync/errgroup"
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)
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type PreSortCommand struct {
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// Optional Index filter
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File string `json:"file"`
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File string
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Type string `json:"type"`
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Type string
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Table string `json:"table"`
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Table string
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PrimaryKeyFields []string `json:"primary-key-fields"`
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PrimaryKeyFields []string
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PrimaryKeySeparator string
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PartitionN int `json:"partition-n"`
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PartitionN int
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JobSize int
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NumWorkers int
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// Path to write sorted files to
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OutputDir string
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@ -33,17 +40,23 @@ type PreSortCommand struct {
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// Standard input/output
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logDest logger.Logger
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outputFiles map[int]*os.File
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outputLocks []sync.Mutex
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outputFiles map[int]*os.File
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outputEncoders map[int]*json.Encoder
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outputWriters map[int]*csv.Writer
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}
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// NewPreSortCommand returns a new instance of PreSortCommand.
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func NewPreSortCommand(logdest logger.Logger) *PreSortCommand {
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return &PreSortCommand{
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logDest: logdest,
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Type: "ndjson",
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OutputDir: "presorted_files",
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PartitionN: 256,
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outputFiles: make(map[int]*os.File),
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logDest: logdest,
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Type: "ndjson",
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OutputDir: "presorted_files",
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PartitionN: 256,
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JobSize: 1000,
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NumWorkers: 4,
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PrimaryKeySeparator: "|",
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outputFiles: make(map[int]*os.File),
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}
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}
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@ -58,6 +71,7 @@ func (cmd *PreSortCommand) Run(ctx context.Context) error {
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if cmd.Table == "" {
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return errors.New("must set a table name")
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}
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cmd.outputLocks = make([]sync.Mutex, cmd.PartitionN)
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filelist := []string{}
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walkfunc := func(path string, d fs.DirEntry, err error) error {
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if !d.IsDir() {
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@ -67,7 +81,7 @@ func (cmd *PreSortCommand) Run(ctx context.Context) error {
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}
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err := filepath.WalkDir(cmd.File, walkfunc)
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if err != nil {
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return errors.Wrapf(err, "wakling %s", cmd.File)
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return errors.Wrapf(err, "walking %s", cmd.File)
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}
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if len(filelist) > 3 {
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cmd.logDest.Printf("%d files: %v...", len(filelist), filelist[:3])
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@ -89,58 +103,111 @@ func (cmd *PreSortCommand) Run(ctx context.Context) error {
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}
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defer func() {
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for _, f := range cmd.outputFiles {
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_ = f.Sync()
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_ = f.Close()
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}
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}()
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linech := make(chan [][]byte, 16)
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var eg *errgroup.Group
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switch cmd.Type {
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case "ndjson":
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if err := cmd.RunNDJSON(filelist); err != nil {
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return errors.Wrap(err, "running ndjson")
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}
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eg = cmd.setupNDJSON(linech)
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case "csv":
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if err := cmd.RunCSV(filelist); err != nil {
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return errors.Wrap(err, "running csv")
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}
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// CSV ends here
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return errors.Wrap(cmd.RunCSV(filelist), "running CSV command")
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default:
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return errors.Errorf("unsupported type %s, try ndjson or csv", cmd.Type)
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}
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// The rest of this is just for NDJSON... CSV doesn't currently
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// support multiple workers. It needs to do the file reading
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// differently in order to handle potential newlines within
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// fields.
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for _, fname := range filelist {
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f, err := os.Open(fname)
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if err != nil {
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return errors.Wrapf(err, "opening %s", fname)
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}
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sc := bufio.NewScanner(f)
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batch:
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for {
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lines := make([][]byte, 0, cmd.JobSize)
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for i := 0; i < cmd.JobSize; i++ {
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if !sc.Scan() {
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linech <- lines
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break batch
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}
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line := sc.Bytes()
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// must copy line as scanner will reuse the buffer it's given us
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lc := make([]byte, len(line))
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copy(lc, line)
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lines = append(lines, lc)
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}
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linech <- lines
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}
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if err := sc.Err(); err != nil {
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return errors.Wrap(err, "scanning file")
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}
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}
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close(linech)
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if err := eg.Wait(); err != nil {
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return err
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}
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return nil
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}
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func (cmd *PreSortCommand) RunNDJSON(filelist []string) error {
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outputEncoders := make(map[int]*json.Encoder)
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func (cmd *PreSortCommand) setupNDJSON(linech chan [][]byte) *errgroup.Group {
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cmd.outputEncoders = make(map[int]*json.Encoder)
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for i, f := range cmd.outputFiles {
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outputEncoders[i] = json.NewEncoder(f)
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outputEncoders[i].SetIndent("", "")
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outputEncoders[i].SetEscapeHTML(false)
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cmd.outputEncoders[i] = json.NewEncoder(f)
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cmd.outputEncoders[i].SetIndent("", "")
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cmd.outputEncoders[i].SetEscapeHTML(false)
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}
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for _, fname := range filelist {
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f, err := os.Open(fname)
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if err != nil {
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cmd.logDest.Warnf("Could not open %s, skipping", fname)
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}
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dec := json.NewDecoder(f)
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// start workers
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eg := &errgroup.Group{}
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for i := 0; i < cmd.NumWorkers; i++ {
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eg.Go(func() error {
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return cmd.ndjsonWorker(linech)
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})
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}
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return eg
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}
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func (cmd *PreSortCommand) ndjsonWorker(linech chan [][]byte) error {
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for lines := range linech {
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rec := map[string]interface{}{}
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for err = dec.Decode(&rec); err == nil; err = dec.Decode(&rec) {
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for _, line := range lines {
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err := json.Unmarshal(line, &rec)
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if err != nil {
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return errors.Wrapf(err, "unmarshaling '%s'", line)
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}
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partition, err := cmd.ndjsonPartition(rec)
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if err != nil {
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return err
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}
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err = outputEncoders[partition].Encode(rec)
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if err != nil {
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return errors.Wrapf(err, "writing record to partition %d", partition)
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if err := cmd.outputNDJSON(partition, rec); err != nil {
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return errors.Wrap(err, "outputting ndjson")
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}
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for k := range rec {
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delete(rec, k)
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}
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}
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if err != io.EOF && err != nil {
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return errors.Wrapf(err, "error attempting to decode json from %s", fname)
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}
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}
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return nil
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}
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func (cmd *PreSortCommand) outputNDJSON(partition int, record map[string]interface{}) error {
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cmd.outputLocks[partition].Lock()
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defer cmd.outputLocks[partition].Unlock()
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return cmd.outputEncoders[partition].Encode(record)
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}
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func (cmd *PreSortCommand) ndjsonPartition(rec map[string]interface{}) (int, error) {
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h := fnv.New64a()
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_, _ = h.Write([]byte(cmd.Table))
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@ -152,12 +219,23 @@ func (cmd *PreSortCommand) ndjsonPartition(rec map[string]interface{}) (int, err
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}
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h.Write([]byte(toString(val)))
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if i < len(cmd.PrimaryKeyFields)-1 {
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h.Write([]byte{'|'})
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h.Write([]byte(cmd.PrimaryKeySeparator))
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}
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}
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return int(h.Sum64() % uint64(cmd.PartitionN)), nil
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}
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func toString(val interface{}) string {
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switch valt := val.(type) {
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case string:
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return valt
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case float64, int, int64, uint64, float32, uint:
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return fmt.Sprintf("%d", valt)
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default:
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return fmt.Sprintf("%v", valt)
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}
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}
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func (cmd *PreSortCommand) RunCSV(filelist []string) error {
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outputWriters := make(map[int]*csv.Writer)
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for i, f := range cmd.outputFiles {
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@ -209,37 +287,10 @@ func (cmd *PreSortCommand) csvPartition(header map[string]int, rec []string) (in
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if !ok {
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return 0, errors.Errorf("couldn't find primary key part '%s' in header: %+v", name, header)
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}
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val := rec[pos]
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h.Write([]byte(toString(val)))
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h.Write([]byte(rec[pos]))
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if i < len(cmd.PrimaryKeyFields)-1 {
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h.Write([]byte{'|'})
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h.Write([]byte(cmd.PrimaryKeySeparator))
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}
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}
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return int(h.Sum64() % uint64(cmd.PartitionN)), nil
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}
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func toString(val interface{}) string {
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switch valt := val.(type) {
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case string:
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return valt
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case float64, int, int64, uint64, float32, uint:
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return fmt.Sprintf("%d", valt)
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default:
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return fmt.Sprintf("%v", valt)
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}
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}
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func (cmd *PreSortCommand) partition(key string) int {
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h := fnv.New64a()
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_, _ = h.Write([]byte(cmd.Table))
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_, _ = h.Write([]byte(key))
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return int(h.Sum64() % uint64(cmd.PartitionN))
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}
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func partition(key string) int {
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indexName := "karambit"
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h := fnv.New64a()
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_, _ = h.Write([]byte(indexName))
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_, _ = h.Write([]byte(key))
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return int(h.Sum64() % uint64(256))
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}
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@ -22,6 +22,7 @@ func TestPreSort(t *testing.T) {
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com.File = "sample.ndjson"
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com.Table = "blah"
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com.PartitionN = 5
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com.JobSize = 2
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com.PrimaryKeyFields = []string{"url"}
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os.Chdir(td)
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@ -64,11 +65,12 @@ func TestPreSort(t *testing.T) {
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com.File = "sample.csv"
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com.Table = "blah"
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com.PartitionN = 5
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com.JobSize = 2
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com.PrimaryKeyFields = []string{"a", "b"}
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err = com.Run(context.Background())
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if err != nil {
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t.Fatalf("running ndjson: %v", err)
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t.Fatalf("running csv: %v", err)
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}
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entries, err = os.ReadDir(filepath.Join(td, com.OutputDir))
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@ -120,11 +122,12 @@ func testFile(t *testing.T, name, dir, contents string) {
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}
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}
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var sampleNDJSON string = `{"url":"https://www.yelp.com/search?find_desc=Desserts&find_loc=San+Jose,+CA&start=0","result":{"extractorData":{"url":"https://www.yelp.com/search?find_desc=Desserts&find_loc=San+Jose,+CA&start=0","data":[{"group":[{"Business":[{"href":"https://www.yelp.com/biz/milk-and-wood-san-jose?osq=Desserts","text":"Milk & Wood"}]},{"Business":[{"href":"https://www.yelp.com/biz/dzuis-cakes-and-desserts-san-jose?osq=Desserts","text":"Dzui’s Cakes & Desserts"}]},{"Business":[{"href":"https://www.yelp.com/biz/recess-italian-ice-and-desserts-san-jose?osq=Desserts","text":"Recess Italian Ice and Desserts"}]},{"Business":[{"href":"https://www.yelp.com/biz/icicles-san-jose-7?osq=Desserts","text":"ICICLES"}]},{"Business":[{"href":"https://www.yelp.com/biz/sweet-rendezvous-san-jose?osq=Desserts","text":"Sweet Rendezvous"}]},{"Business":[{"href":"https://www.yelp.com/biz/passion-t-snacks-and-desserts-san-jose?osq=Desserts","text":"Passion-T Snacks and Desserts"}]},{"Business":[{"href":"https://www.yelp.com/biz/vampire-penguin-featuring-jastea-san-jose?osq=Desserts","text":"Vampire Penguin featuring Jastea"}]},{"Business":[{"href":"https://www.yelp.com/biz/sweet-gelato-tea-lounge-san-jose?osq=Desserts","text":"Sweet Gelato Tea Lounge"}]},{"Business":[{"href":"https://www.yelp.com/biz/matcha-love-san-jose-6?osq=Desserts","text":"Matcha Love"}]},{"Business":[{"href":"https://www.yelp.com/biz/anton-sv-p%C3%A2tisserie-san-jose-2?osq=Desserts","text":"Anton SV Pâtisserie"}]}]}]},"pageData":{"statusCode":200,"timestamp":1513286383006},"timestamp":1513286383006,"sequenceNumber":0}}
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var sampleNDJSON string = `{"url":"https://www.yelp.com/search?find_desc=Desserts&find_loc=San+Jose,+CA&start=0","anything":"somedata","result":{"stuff":"blahhhhhhhhh","blufff":"hahahahah"}}
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{"url":"https://www.yelp.com/search?find_desc=Desserts&find_loc=San+Jose,+CA&start=10","result":{"extractorData":{"url":"https://www.yelp.com/search?find_desc=Desserts&find_loc=San+Jose,+CA&start=10","data":[{"group":[{"Business":[{"href":"https://www.yelp.com/biz/oooh-san-jose-4?osq=Desserts","text":"Oooh"}]},{"Business":[{"href":"https://www.yelp.com/biz/hannah-san-jose?osq=Desserts","text":"Hannah"}]},{"Business":[{"href":"https://www.yelp.com/biz/chocatoo-san-jose?osq=Desserts","text":"Chocatoo"}]},{"Business":[{"href":"https://www.yelp.com/biz/nox-cookie-bar-san-jose?osq=Desserts","text":"Nox Cookie Bar"}]},{"Business":[{"href":"https://www.yelp.com/biz/sweet-fix-creamery-san-jose?osq=Desserts","text":"Sweet Fix Creamery"}]},{"Business":[{"href":"https://www.yelp.com/biz/my-milkshake-san-jose?osq=Desserts","text":"My Milkshake"}]},{"Business":[{"href":"https://www.yelp.com/biz/matcha-love-san-jose-6?osq=Desserts","text":"Matcha Love"}]},{"Business":[{"href":"https://www.yelp.com/biz/banana-cr%C3%AApe-san-jose-2?osq=Desserts","text":"Banana Crêpe"}]},{"Business":[{"href":"https://www.yelp.com/biz/marco-polo-italian-ice-cream-san-jose-4?osq=Desserts","text":"Marco Polo Italian Ice Cream"}]},{"Business":[{"href":"https://www.yelp.com/biz/blackball-desserts-san-jose-san-jose?osq=Desserts","text":"BlackBall Desserts San Jose"}]}]}]},"pageData":{"statusCode":200,"timestamp":1513286384917},"timestamp":1513286384917,"sequenceNumber":1}}
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{"url":"https://www.yelp.com/search?find_desc=Desserts&find_loc=San+Jose,+CA&start=20","result":{"extractorData":{"url":"https://www.yelp.com/search?find_desc=Desserts&find_loc=San+Jose,+CA&start=20","data":[{"group":[{"Business":[{"href":"https://www.yelp.com/biz/anton-sv-p%C3%A2tisserie-san-jose-2?osq=Desserts","text":"Anton SV Pâtisserie"}]},{"Business":[{"href":"https://www.yelp.com/biz/soyful-desserts-san-jose-8?osq=Desserts","text":"Soyful Desserts"}]},{"Business":[{"href":"https://www.yelp.com/biz/cocola-bakery-san-jose?osq=Desserts","text":"Cocola Bakery"}]},{"Business":[{"href":"https://www.yelp.com/biz/charlies-cheesecake-works-san-jose?osq=Desserts","text":"Charlie’s Cheesecake Works"}]},{"Business":[{"href":"https://www.yelp.com/biz/jt-express-san-jose-2?osq=Desserts","text":"JT Express"}]},{"Business":[{"href":"https://www.yelp.com/biz/nox-cookie-bar-san-jose?osq=Desserts","text":"Nox Cookie Bar"}]},{"Business":[{"href":"https://www.yelp.com/biz/shuei-do-manju-shop-san-jose?osq=Desserts","text":"Shuei-Do Manju Shop"}]},{"Business":[{"href":"https://www.yelp.com/biz/churros-el-guero-san-jose?osq=Desserts","text":"Churros El Guero"}]},{"Business":[{"href":"https://www.yelp.com/biz/sno-crave-tea-house-san-jose-4?osq=Desserts","text":"Sno-Crave Tea House"}]},{"Business":[{"href":"https://www.yelp.com/biz/j-sweets-san-jose-3?osq=Desserts","text":"J.Sweets"}]}]}]},"pageData":{"statusCode":200,"timestamp":1513286395948},"timestamp":1513286395948,"sequenceNumber":2}}
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{"url":"https://www.yelp.com/search?find_desc=Desserts&find_loc=San+Jose,+CA&start=30","result":{"extractorData":{"url":"https://www.yelp.com/search?find_desc=Desserts&find_loc=San+Jose,+CA&start=30","data":[{"group":[{"Business":[{"href":"https://www.yelp.com/biz/treatbot-san-jose-2?osq=Desserts","text":"Treatbot"}]},{"Business":[{"href":"https://www.yelp.com/biz/cream-san-jose?osq=Desserts","text":"CREAM"}]},{"Business":[{"href":"https://www.yelp.com/biz/my-milkshake-san-jose?osq=Desserts","text":"My Milkshake"}]},{"Business":[{"href":"https://www.yelp.com/biz/peters-bakery-san-jose?osq=Desserts","text":"Peters’ Bakery"}]},{"Business":[{"href":"https://www.yelp.com/biz/the-charming-kitchen-san-jose-5?osq=Desserts","text":"The Charming Kitchen"}]},{"Business":[{"href":"https://www.yelp.com/biz/sweet-fix-creamery-san-jose?osq=Desserts","text":"Sweet Fix Creamery"}]},{"Business":[{"href":"https://www.yelp.com/biz/california-mochi-santa-clara-4?osq=Desserts","text":"California Mochi"}]},{"Business":[{"href":"https://www.yelp.com/biz/raw-sugar-milpitas-2?osq=Desserts","text":"Raw Sugar"}]},{"Business":[{"href":"https://www.yelp.com/biz/chola-desserts-san-jose?osq=Desserts","text":"Chola Desserts"}]},{"Business":[{"href":"https://www.yelp.com/biz/san-jose-tofu-company-san-jose?osq=Desserts","text":"San Jose Tofu Company"}]}]}]},"pageData":{"statusCode":200,"timestamp":1513286386420},"timestamp":1513286386420,"sequenceNumber":3}}
|
||||
{"url":"https://www.yelp.com/search?find_desc=Desserts&find_loc=San+Jose,+CA&start=30","result":{}}
|
||||
{"url":"https://www.yelp.com/search?find_desc=Desserts&find_loc=San+Jose,+CA&start=40","result":{"extractorData":{"url":"https://www.yelp.com/search?find_desc=Desserts&find_loc=San+Jose,+CA&start=40","data":[{"group":[{"Business":[{"href":"https://www.yelp.com/biz/the-sweet-corner-san-jose?osq=Desserts","text":"The Sweet Corner"}]},{"Business":[{"href":"https://www.yelp.com/biz/marco-polo-italian-ice-cream-san-jose-4?osq=Desserts","text":"Marco Polo Italian Ice Cream"}]},{"Business":[{"href":"https://www.yelp.com/biz/honeyberry-san-jose-9?osq=Desserts","text":"Honeyberry"}]},{"Business":[{"href":"https://www.yelp.com/biz/my-ch%C3%A8-san-jose?osq=Desserts","text":"My Chè"}]},{"Business":[{"href":"https://www.yelp.com/biz/creme-paris-san-jose-3?osq=Desserts","text":"Cre’Me Paris"}]},{"Business":[{"href":"https://www.yelp.com/biz/snowflake-san-jose?osq=Desserts","text":"Snowflake"}]},{"Business":[{"href":"https://www.yelp.com/biz/willow-glen-creamery-san-jose-4?osq=Desserts","text":"Willow Glen Creamery"}]},{"Business":[{"href":"https://www.yelp.com/biz/vans-bakery-san-jose?osq=Desserts","text":"Van’s Bakery"}]},{"Business":[{"href":"https://www.yelp.com/biz/happiness-cafe-san-jose?osq=Desserts","text":"Happiness Cafe"}]},{"Business":[{"href":"https://www.yelp.com/biz/la-original-paleteria-y-neveria-san-jose?osq=Desserts","text":"La Original Paleteria Y Neveria"}]}]}]},"pageData":{"statusCode":200,"timestamp":1513286387763},"timestamp":1513286387763,"sequenceNumber":4}}
|
||||
{"url":"https://www.yelp.com/search?find_desc=Desserts&find_loc=San+Jose,+CA&start=0","result":{}}
|
||||
`
|
||||
|
||||
var sampleCSV string = `a,b,c,d,e,f,g
|
||||
|
|
@ -133,4 +136,8 @@ var sampleCSV string = `a,b,c,d,e,f,g
|
|||
3,4,5,6,7,8,9
|
||||
4,5,6,7,8,9,0
|
||||
0,1,2,3,4,5,6
|
||||
1,3,3,4,5,6,7
|
||||
4,5,6,7,8,9,0
|
||||
3,4,5,8,7,8,9
|
||||
2,3,4,9,6,7,8
|
||||
`
|
||||
Loading…
Add table
Reference in a new issue