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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,185 @@ | ||
| // Copyright © 2016-2021 Wei Shen <[email protected]> | ||
| // | ||
| // Permission is hereby granted, free of charge, to any person obtaining a copy | ||
| // of this software and associated documentation files (the "Software"), to deal | ||
| // in the Software without restriction, including without limitation the rights | ||
| // to use, copy, modify, merge, publish, distribute, sublicense, and/or sell | ||
| // copies of the Software, and to permit persons to whom the Software is | ||
| // furnished to do so, subject to the following conditions: | ||
| // | ||
| // The above copyright notice and this permission notice shall be included in | ||
| // all copies or substantial portions of the Software. | ||
| // | ||
| // THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR | ||
| // IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, | ||
| // FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE | ||
| // AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER | ||
| // LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, | ||
| // OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN | ||
| // THE SOFTWARE. | ||
|
|
||
| package cmd | ||
|
|
||
| import ( | ||
| "encoding/csv" | ||
| "fmt" | ||
| "runtime" | ||
|
|
||
| "github.com/shenwei356/xopen" | ||
| "github.com/spf13/cobra" | ||
| ) | ||
|
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| // fixCmd represents the pretty command | ||
| var fixCmd = &cobra.Command{ | ||
| Use: "fix", | ||
| Short: "fix CSV/TSV with different numbers of columns in rows", | ||
| Long: `fix CSV/TSV with different numbers of columns in rows | ||
| How to: | ||
| 1. First -n/--buf-rows rows are read to check the maximum number of columns. | ||
| The default value 0 means all rows will be read. | ||
| 2. Buffered and remaining rows with fewer columns are appended with empty | ||
| cells before output. | ||
| 3. An error will be reported if the number of columns of any remaining row | ||
| is larger than the maximum number of columns. | ||
| `, | ||
| Run: func(cmd *cobra.Command, args []string) { | ||
| config := getConfigs(cmd) | ||
| files := getFileListFromArgsAndFile(cmd, args, true, "infile-list", true) | ||
| if len(files) > 1 { | ||
| checkError(fmt.Errorf("no more than one file should be given")) | ||
| } | ||
| runtime.GOMAXPROCS(config.NumCPUs) | ||
|
|
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| bufRows := getFlagNonNegativeInt(cmd, "buf-rows") | ||
|
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| var buf [][]string | ||
| var readAll bool | ||
| if bufRows > 0 { | ||
| buf = make([][]string, 0, bufRows) | ||
| } else { | ||
| readAll = true | ||
| buf = make([][]string, 0, 1024) | ||
| } | ||
|
|
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| outfh, err := xopen.Wopen(config.OutFile) | ||
| checkError(err) | ||
| defer outfh.Close() | ||
|
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| writer := csv.NewWriter(outfh) | ||
| if config.OutTabs || config.Tabs { | ||
| if config.OutDelimiter == ',' { // default value, no other value given | ||
| writer.Comma = '\t' | ||
| } else { | ||
| writer.Comma = config.OutDelimiter | ||
| } | ||
| } else { | ||
| writer.Comma = config.OutDelimiter | ||
| } | ||
|
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| file := files[0] | ||
|
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| csvReader, err := newCSVReaderByConfig(config, file) | ||
|
|
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| if err != nil { | ||
| if err == xopen.ErrNoContent { | ||
| log.Warningf("csvtk pretty: skipping empty input file: %s", file) | ||
| return | ||
| } | ||
| checkError(err) | ||
| } | ||
|
|
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| // very important. | ||
| // If FieldsPerRecord is negative, no check is made and | ||
| // records may have a variable number of fields. | ||
| csvReader.Reader.FieldsPerRecord = -1 | ||
|
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| csvReader.Run() | ||
|
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| var record []string | ||
| var n int // number of loaded rows | ||
| var maxN int | ||
| var checkedMaxNcols bool | ||
| var row []string | ||
| var ncol int | ||
| var empty []string | ||
| for chunk := range csvReader.Ch { | ||
| checkError(chunk.Err) | ||
|
|
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| for _, record = range chunk.Data { | ||
| n++ | ||
|
|
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| if readAll { | ||
| buf = append(buf, record) | ||
| continue | ||
| } | ||
|
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| buf = append(buf, record) | ||
| if !checkedMaxNcols { | ||
| if n == bufRows { | ||
| maxN = maxNcols(buf) | ||
| log.Infof("the maximum number of columns in first %d rows: %d", bufRows, maxN) | ||
| checkedMaxNcols = true | ||
| empty = make([]string, maxN) | ||
|
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| for _, row = range buf { | ||
| ncol = len(row) | ||
| if ncol < maxN { | ||
| row = append(row, empty[0:maxN-ncol]...) | ||
| } | ||
| writer.Write(row) | ||
| } | ||
| } | ||
|
|
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| continue | ||
| } | ||
|
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| ncol = len(record) | ||
| if ncol > maxN { | ||
| checkError(fmt.Errorf("line %d: the number of columns is larger than %d, please increase the value of -n/--buf-rows (%d)", n, maxN, bufRows)) | ||
| } else if ncol < maxN { | ||
| record = append(record, empty[0:maxN-ncol]...) | ||
| } | ||
| writer.Write(record) | ||
| } | ||
| } | ||
|
|
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| if readAll || !checkedMaxNcols { | ||
| maxN = maxNcols(buf) | ||
| empty = make([]string, maxN) | ||
| log.Infof("the maximum number of columns in all %d rows: %d", len(buf), maxN) | ||
|
|
||
| for _, row = range buf { | ||
| ncol = len(row) | ||
| if ncol < maxN { | ||
| row = append(row, empty[0:maxN-ncol]...) | ||
| } | ||
| writer.Write(row) | ||
| } | ||
| } | ||
|
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| writer.Flush() | ||
| checkError(writer.Error()) | ||
|
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| readerReport(&config, csvReader, file) | ||
| }, | ||
| } | ||
|
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| func maxNcols(buf [][]string) int { | ||
| maxN := 0 | ||
| var ncol int | ||
| for _, row := range buf { | ||
| ncol = len(row) | ||
| if ncol > maxN { | ||
| maxN = ncol | ||
| } | ||
| } | ||
| return maxN | ||
| } | ||
|
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| func init() { | ||
| RootCmd.AddCommand(fixCmd) | ||
|
|
||
| fixCmd.Flags().IntP("buf-rows", "n", 0, "the number of rows to determine the maximum number of columns. 0 for all rows.") | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,6 @@ | ||
| id,first_name,last_name | ||
| 11,"Rob","Pike" | ||
| 2,Ken,Thompson | ||
| 4,"Robert","Griesemer","gri" | ||
| 1,"Robert","Thompson","abc" | ||
| NA,"Robert" |