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break the import cyccle

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This commit is contained in:
Eric Coissac
2025-01-27 17:23:07 +01:00
parent 7c4042df6b
commit c50a0f409d
9 changed files with 46 additions and 44 deletions
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2
pkg/obiiter/csv.go → pkg/obiitercsv/csv.go
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@ -1,4 +1,4 @@
package obiiter package obiitercsv
import ( import (
"fmt" "fmt"

2
pkg/obioptions/version.go
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@ -8,7 +8,7 @@ import (
// corresponds to the last commit, and not the one when the file will be // corresponds to the last commit, and not the one when the file will be
// commited // commited
var _Commit = "0a567f6" var _Commit = "7c4042d"
var _Version = "Release 4.2.0" var _Version = "Release 4.2.0"
// Version returns the version of the obitools package. // Version returns the version of the obitools package.

14
pkg/obitax/csvtaxdump_write.go
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@ -1,11 +1,11 @@
package obitax package obitax
// import ( import (
// "git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter" "git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiitercsv"
// ) )
// func WriteTaxonomyCSV(iterator obiiter.IBioSequence, func WriteTaxonomyCSV(iterator ITaxon,
// terminalAction bool, filenames ...string) *obiiter.ICSVRecord { terminalAction bool, filenames ...string) *obiitercsv.ICSVRecord {
// return nil return nil
// } }

4
pkg/obitools/obicsv/csvoption.go
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@ -2,7 +2,7 @@ package obicsv
import ( import (
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obidefault" "git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obidefault"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter" "git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiitercsv"
) )
// __options__ holds configuration options for processing. // __options__ holds configuration options for processing.
@ -70,7 +70,7 @@ func MakeOptions(setters []WithOption) Options {
csv_quality: false, csv_quality: false,
csv_separator: ",", csv_separator: ",",
csv_navalue: "NA", csv_navalue: "NA",
csv_keys: make(obiiter.CSVHeader, 0), csv_keys: make(obiitercsv.CSVHeader, 0),
csv_auto: false, csv_auto: false,
source: "unknown", source: "unknown",
} }

9
pkg/obitools/obicsv/obicsv.go
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@ -5,11 +5,12 @@ import (
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obidefault" "git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obidefault"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter" "git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiitercsv"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obiconvert" "git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obiconvert"
) )
func CLIWriteSequenceCSV(iterator obiiter.IBioSequence, func CLIWriteSequenceCSV(iterator obiiter.IBioSequence,
terminalAction bool, filenames ...string) *obiiter.ICSVRecord { terminalAction bool, filenames ...string) *obiitercsv.ICSVRecord {
if obiconvert.CLIProgressBar() { if obiconvert.CLIProgressBar() {
iterator = iterator.Speed("Writing CSV") iterator = iterator.Speed("Writing CSV")
@ -42,12 +43,12 @@ func CLIWriteSequenceCSV(iterator obiiter.IBioSequence,
} }
func CLICSVWriter(iterator *obiiter.ICSVRecord, func CLICSVWriter(iterator *obiitercsv.ICSVRecord,
terminalAction bool, terminalAction bool,
options ...WithOption) *obiiter.ICSVRecord { options ...WithOption) *obiitercsv.ICSVRecord {
var err error var err error
var newIter *obiiter.ICSVRecord var newIter *obiitercsv.ICSVRecord
if obiconvert.CLIOutPutFileName() != "-" { if obiconvert.CLIOutPutFileName() != "-" {
options = append(options, OptionFileName(obiconvert.CLIOutPutFileName())) options = append(options, OptionFileName(obiconvert.CLIOutPutFileName()))

17
pkg/obitools/obicsv/sequence.go
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@ -6,11 +6,12 @@ import (
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obidefault" "git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obidefault"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter" "git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiitercsv"
) )
func CSVSequenceHeader(opt Options) obiiter.CSVHeader { func CSVSequenceHeader(opt Options) obiitercsv.CSVHeader {
keys := opt.CSVKeys() keys := opt.CSVKeys()
record := make(obiiter.CSVHeader, 0, len(keys)+4) record := make(obiitercsv.CSVHeader, 0, len(keys)+4)
if opt.CSVId() { if opt.CSVId() {
record.AppendField("id") record.AppendField("id")
@ -45,12 +46,12 @@ func CSVSequenceHeader(opt Options) obiiter.CSVHeader {
return record return record
} }
func CSVBatchFromSequences(batch obiiter.BioSequenceBatch, opt Options) obiiter.CSVRecordBatch { func CSVBatchFromSequences(batch obiiter.BioSequenceBatch, opt Options) obiitercsv.CSVRecordBatch {
keys := opt.CSVKeys() keys := opt.CSVKeys()
csvslice := make([]obiiter.CSVRecord, batch.Len()) csvslice := make([]obiitercsv.CSVRecord, batch.Len())
for i, sequence := range batch.Slice() { for i, sequence := range batch.Slice() {
record := make(obiiter.CSVRecord) record := make(obiitercsv.CSVRecord)
if opt.CSVId() { if opt.CSVId() {
record["id"] = sequence.Id() record["id"] = sequence.Id()
@ -108,10 +109,10 @@ func CSVBatchFromSequences(batch obiiter.BioSequenceBatch, opt Options) obiiter.
csvslice[i] = record csvslice[i] = record
} }
return obiiter.MakeCSVRecordBatch(batch.Source(), batch.Order(), csvslice) return obiitercsv.MakeCSVRecordBatch(batch.Source(), batch.Order(), csvslice)
} }
func NewCSVSequenceIterator(iter obiiter.IBioSequence, options ...WithOption) *obiiter.ICSVRecord { func NewCSVSequenceIterator(iter obiiter.IBioSequence, options ...WithOption) *obiitercsv.ICSVRecord {
opt := MakeOptions(options) opt := MakeOptions(options)
@ -128,7 +129,7 @@ func NewCSVSequenceIterator(iter obiiter.IBioSequence, options ...WithOption) *o
} }
} }
newIter := obiiter.NewICSVRecord() newIter := obiitercsv.NewICSVRecord()
newIter.SetHeader(CSVSequenceHeader(opt)) newIter.SetHeader(CSVSequenceHeader(opt))
nwriters := opt.ParallelWorkers() nwriters := opt.ParallelWorkers()

20
pkg/obitools/obicsv/writer.go
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@ -7,13 +7,13 @@ import (
"os" "os"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiformats" "git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiformats"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter" "git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiitercsv"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils" "git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
log "github.com/sirupsen/logrus" log "github.com/sirupsen/logrus"
) )
func FormatCVSBatch(batch obiiter.CSVRecordBatch, header obiiter.CSVHeader, navalue string) *bytes.Buffer { func FormatCVSBatch(batch obiitercsv.CSVRecordBatch, header obiitercsv.CSVHeader, navalue string) *bytes.Buffer {
buff := new(bytes.Buffer) buff := new(bytes.Buffer)
csv := csv.NewWriter(buff) csv := csv.NewWriter(buff)
@ -45,14 +45,14 @@ func FormatCVSBatch(batch obiiter.CSVRecordBatch, header obiiter.CSVHeader, nava
return buff return buff
} }
func WriteCSV(iterator *obiiter.ICSVRecord, func WriteCSV(iterator *obiitercsv.ICSVRecord,
file io.WriteCloser, file io.WriteCloser,
options ...WithOption) (*obiiter.ICSVRecord, error) { options ...WithOption) (*obiitercsv.ICSVRecord, error) {
opt := MakeOptions(options) opt := MakeOptions(options)
file, _ = obiutils.CompressStream(file, opt.CompressedFile(), opt.CloseFile()) file, _ = obiutils.CompressStream(file, opt.CompressedFile(), opt.CloseFile())
newIter := obiiter.NewICSVRecord() newIter := obiitercsv.NewICSVRecord()
nwriters := opt.ParallelWorkers() nwriters := opt.ParallelWorkers()
@ -66,7 +66,7 @@ func WriteCSV(iterator *obiiter.ICSVRecord,
log.Debugf("Writing CSV file done") log.Debugf("Writing CSV file done")
}() }()
ff := func(iterator *obiiter.ICSVRecord) { ff := func(iterator *obiitercsv.ICSVRecord) {
for iterator.Next() { for iterator.Next() {
batch := iterator.Get() batch := iterator.Get()
@ -109,8 +109,8 @@ func WriteCSV(iterator *obiiter.ICSVRecord,
// os.Stdout as the output file, and the options slice. // os.Stdout as the output file, and the options slice.
// //
// The function returns the same bio sequence iterator and an error if any occurred. // The function returns the same bio sequence iterator and an error if any occurred.
func WriteCSVToStdout(iterator *obiiter.ICSVRecord, func WriteCSVToStdout(iterator *obiitercsv.ICSVRecord,
options ...WithOption) (*obiiter.ICSVRecord, error) { options ...WithOption) (*obiitercsv.ICSVRecord, error) {
// options = append(options, OptionDontCloseFile()) // options = append(options, OptionDontCloseFile())
options = append(options, OptionCloseFile()) options = append(options, OptionCloseFile())
return WriteCSV(iterator, os.Stdout, options...) return WriteCSV(iterator, os.Stdout, options...)
@ -127,9 +127,9 @@ func WriteCSVToStdout(iterator *obiiter.ICSVRecord,
// Returns: // Returns:
// - obiiter.IBioSequence: The updated biosequence iterator. // - obiiter.IBioSequence: The updated biosequence iterator.
// - error: Any error that occurred during the writing process. // - error: Any error that occurred during the writing process.
func WriteCSVToFile(iterator *obiiter.ICSVRecord, func WriteCSVToFile(iterator *obiitercsv.ICSVRecord,
filename string, filename string,
options ...WithOption) (*obiiter.ICSVRecord, error) { options ...WithOption) (*obiitercsv.ICSVRecord, error) {
opt := MakeOptions(options) opt := MakeOptions(options)
flags := os.O_WRONLY | os.O_CREATE flags := os.O_WRONLY | os.O_CREATE

16
pkg/obitools/obifind/iterator.go
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@ -4,7 +4,7 @@ import (
"slices" "slices"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obidefault" "git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obidefault"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter" "git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiitercsv"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitax" "git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitax"
) )
@ -192,12 +192,12 @@ func OptionsWithMetadata(values ...string) WithOption {
return f return f
} }
func NewCSVTaxaIterator(iterator *obitax.ITaxon, options ...WithOption) *obiiter.ICSVRecord { func NewCSVTaxaIterator(iterator *obitax.ITaxon, options ...WithOption) *obiitercsv.ICSVRecord {
opt := MakeOptions(options) opt := MakeOptions(options)
metakeys := make([]string, 0) metakeys := make([]string, 0)
newIter := obiiter.NewICSVRecord() newIter := obiitercsv.NewICSVRecord()
newIter.Add(1) newIter.Add(1)
@ -240,11 +240,11 @@ func NewCSVTaxaIterator(iterator *obitax.ITaxon, options ...WithOption) *obiiter
go func() { go func() {
o := 0 o := 0
data := make([]obiiter.CSVRecord, 0, batch_size) data := make([]obiitercsv.CSVRecord, 0, batch_size)
for iterator.Next() { for iterator.Next() {
taxon := iterator.Get() taxon := iterator.Get()
record := make(obiiter.CSVRecord) record := make(obiitercsv.CSVRecord)
if opt.WithPattern() { if opt.WithPattern() {
record["query"] = taxon.MetadataAsString("query") record["query"] = taxon.MetadataAsString("query")
@ -282,15 +282,15 @@ func NewCSVTaxaIterator(iterator *obitax.ITaxon, options ...WithOption) *obiiter
data = append(data, record) data = append(data, record)
if len(data) >= batch_size { if len(data) >= batch_size {
newIter.Push(obiiter.MakeCSVRecordBatch(opt.Source(), o, data)) newIter.Push(obiitercsv.MakeCSVRecordBatch(opt.Source(), o, data))
data = make([]obiiter.CSVRecord, 0, batch_size) data = make([]obiitercsv.CSVRecord, 0, batch_size)
o++ o++
} }
} }
if len(data) > 0 { if len(data) > 0 {
newIter.Push(obiiter.MakeCSVRecordBatch(opt.Source(), o, data)) newIter.Push(obiitercsv.MakeCSVRecordBatch(opt.Source(), o, data))
} }
newIter.Done() newIter.Done()

6
pkg/obitools/obifind/obifind.go
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@ -2,7 +2,7 @@ package obifind
import ( import (
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obidefault" "git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obidefault"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter" "git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiitercsv"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitax" "git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitax"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obicsv" "git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obicsv"
@ -40,7 +40,7 @@ func CLIFilterRankRestriction(iterator *obitax.ITaxon) *obitax.ITaxon {
return iterator return iterator
} }
func CLICSVTaxaIterator(iterator *obitax.ITaxon) *obiiter.ICSVRecord { func CLICSVTaxaIterator(iterator *obitax.ITaxon) *obiitercsv.ICSVRecord {
if iterator == nil { if iterator == nil {
return nil return nil
} }
@ -60,6 +60,6 @@ func CLICSVTaxaIterator(iterator *obitax.ITaxon) *obiiter.ICSVRecord {
return NewCSVTaxaIterator(iterator, options...) return NewCSVTaxaIterator(iterator, options...)
} }
func CLICSVTaxaWriter(iterator *obitax.ITaxon, terminalAction bool) *obiiter.ICSVRecord { func CLICSVTaxaWriter(iterator *obitax.ITaxon, terminalAction bool) *obiitercsv.ICSVRecord {
return obicsv.CLICSVWriter(CLICSVTaxaIterator(iterator), terminalAction) return obicsv.CLICSVWriter(CLICSVTaxaIterator(iterator), terminalAction)
} }