/
gather.go
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/
gather.go
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// Copyright © 2016-2023 Wei Shen <shenwei356@gmail.com>
//
// 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"
)
// gatherCmd represents the gather command
var gatherCmd = &cobra.Command{
GroupID: "transform",
Use: "gather",
Aliases: []string{"longer"},
Short: "gather columns into key-value pairs, like tidyr::gather/pivot_longer",
Long: `gather columns into key-value pairs, like tidyr::gather/pivot_longer
`,
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)
if config.NoHeaderRow {
checkError(fmt.Errorf("flag -H/--no-header-row not allowed"))
}
fieldKey := getFlagString(cmd, "key")
fieldValue := getFlagString(cmd, "value")
if !config.NoHeaderRow {
if fieldKey == "" {
checkError(fmt.Errorf("flag -k/--key needed"))
}
if fieldValue == "" {
checkError(fmt.Errorf("flag -v/--value needed"))
}
}
fieldStr := getFlagString(cmd, "fields")
if fieldStr == "" {
checkError(fmt.Errorf("flag -f (--fields) needed"))
}
fuzzyFields := getFlagBool(cmd, "fuzzy-fields")
outfh, err := xopen.Wopen(config.OutFile)
checkError(err)
defer outfh.Close()
writer := csv.NewWriter(outfh)
if config.OutTabs || config.Tabs {
if config.OutDelimiter == ',' {
writer.Comma = '\t'
} else {
writer.Comma = config.OutDelimiter
}
} else {
writer.Comma = config.OutDelimiter
}
defer func() {
writer.Flush()
checkError(writer.Error())
}()
file := files[0]
csvReader, err := newCSVReaderByConfig(config, file)
if err != nil {
if err == xopen.ErrNoContent {
if config.Verbose {
log.Warningf("csvtk gather: skipping empty input file: %s", file)
}
writer.Flush()
checkError(writer.Error())
readerReport(&config, csvReader, file)
return
}
checkError(err)
}
csvReader.Read(ReadOption{
FieldStr: fieldStr,
FuzzyFields: fuzzyFields,
DoNotAllowDuplicatedColumnName: true,
})
var i, f int
var ok bool
var fieldsMap map[int]interface{}
var items []string
var fieldsLeft []int
var HeaderRow []string
var nFieldsLeft int
checkFirstLine := true
var handleHeaderRow bool
for record := range csvReader.Ch {
if record.Err != nil {
checkError(record.Err)
}
if checkFirstLine {
checkFirstLine = false
if len(record.Fields) == 0 {
checkError(fmt.Errorf("no fields matched in file: %s", file))
}
fieldsMap = make(map[int]interface{}, len(record.Selected))
for _, f = range record.Fields {
fieldsMap[f-1] = struct{}{}
}
for f = range record.All {
if _, ok = fieldsMap[f]; !ok {
fieldsLeft = append(fieldsLeft, f+1)
}
}
nFieldsLeft = len(fieldsLeft)
items = make([]string, nFieldsLeft+2)
if !config.NoHeaderRow || record.IsHeaderRow { // do not replace head line
handleHeaderRow = true
HeaderRow = record.All
}
}
// fill columns that are not key or value column
for i, f = range fieldsLeft {
items[i] = record.All[f-1]
}
if handleHeaderRow {
items[nFieldsLeft] = fieldKey
items[nFieldsLeft+1] = fieldValue
if !config.NoOutHeader {
checkError(writer.Write(items))
}
handleHeaderRow = false
} else {
for _, f = range record.Fields {
items[nFieldsLeft] = HeaderRow[f-1]
items[nFieldsLeft+1] = record.All[f-1]
checkError(writer.Write(items))
}
}
}
readerReport(&config, csvReader, file)
},
}
func init() {
RootCmd.AddCommand(gatherCmd)
gatherCmd.Flags().StringP("fields", "f", "", `fields for gathering. e.g -f 1,2 or -f columnA,columnB, or -f -columnA for unselect columnA`)
gatherCmd.Flags().BoolP("fuzzy-fields", "F", false, `using fuzzy fields, e.g., -F -f "*name" or -F -f "id123*"`)
gatherCmd.Flags().StringP("key", "k", "", `name of key column to create in output`)
gatherCmd.Flags().StringP("value", "v", "", `name of value column to create in output`)
}