mirror of
https://github.com/metabarcoding/obitools4.git
synced 2026-03-25 21:40:52 +00:00
1a28d5ed64
This commit introduces a new configuration module `obidefault` to manage progress bar settings, allowing users to disable progress bars via a `--no-progressbar` option. It updates various packages to conditionally display progress bars based on this new configuration, improving user experience by providing control over progress bar output. The changes also include improvements to progress bar handling in several packages, ensuring they are only displayed when appropriate (e.g., when stderr is a terminal and stdout is not piped).
81 lines
1.9 KiB
Go
81 lines
1.9 KiB
Go
package obicsv
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import (
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log "github.com/sirupsen/logrus"
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"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obidefault"
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"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
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"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiitercsv"
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"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obiconvert"
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)
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func CLIWriteSequenceCSV(iterator obiiter.IBioSequence,
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terminalAction bool, filenames ...string) *obiitercsv.ICSVRecord {
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iterator = iterator.Speed("Writing CSV")
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opts := make([]WithOption, 0, 10)
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nworkers := obidefault.ParallelWorkers() / 4
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if nworkers < 2 {
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nworkers = 2
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}
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opts = append(opts, OptionsParallelWorkers(nworkers))
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opts = append(opts, OptionsBatchSize(obidefault.BatchSize()))
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opts = append(opts, OptionsCompressed(obidefault.CompressOutput()))
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opts = append(opts, CSVId(CLIPrintId()),
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CSVCount(CLIPrintCount()),
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CSVTaxon(CLIPrintTaxon()),
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CSVDefinition(CLIPrintDefinition()),
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CSVKeys(CLIToBeKeptAttributes()),
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CSVSequence(CLIPrintSequence()),
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CSVQuality(CLIPrintQuality()),
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CSVAutoColumn(CLIAutoColumns()),
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)
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csvIter := NewCSVSequenceIterator(iterator, opts...)
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newIter := CLICSVWriter(csvIter, terminalAction, opts...)
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return newIter
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}
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func CLICSVWriter(iterator *obiitercsv.ICSVRecord,
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terminalAction bool,
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options ...WithOption) *obiitercsv.ICSVRecord {
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var err error
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var newIter *obiitercsv.ICSVRecord
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if obiconvert.CLIOutPutFileName() != "-" {
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options = append(options, OptionFileName(obiconvert.CLIOutPutFileName()))
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}
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opt := MakeOptions(options)
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if opt.FileName() != "-" {
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newIter, err = WriteCSVToFile(iterator, opt.FileName(), options...)
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if err != nil {
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log.Fatalf("Cannot write to file : %+v", err)
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}
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} else {
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newIter, err = WriteCSVToStdout(iterator, options...)
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if err != nil {
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log.Fatalf("Cannot write to stdout : %+v", err)
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}
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}
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if terminalAction {
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newIter.Consume()
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return nil
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}
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return newIter
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}
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