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Patch a small bug on json write

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This commit is contained in:
Eric Coissac
2024-11-29 18:39:18 +01:00
parent 00b0edc15a
commit f41a6fbb60
3 changed files with 12 additions and 2 deletions
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9
pkg/obiformats/json_writer.go
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@ -7,6 +7,7 @@ import (
"os" "os"
"strconv" "strconv"
"strings" "strings"
"sync/atomic"
"time" "time"
"github.com/goccy/go-json" "github.com/goccy/go-json"
@ -84,6 +85,7 @@ func FormatJSONBatch(batch obiiter.BioSequenceBatch) *bytes.Buffer {
func WriteJSON(iterator obiiter.IBioSequence, func WriteJSON(iterator obiiter.IBioSequence,
file io.WriteCloser, file io.WriteCloser,
options ...WithOption) (obiiter.IBioSequence, error) { options ...WithOption) (obiiter.IBioSequence, error) {
var latestChunk atomic.Int64
opt := MakeOptions(options) opt := MakeOptions(options)
@ -97,6 +99,12 @@ func WriteJSON(iterator obiiter.IBioSequence,
go func() { go func() {
newIter.WaitAndClose() newIter.WaitAndClose()
chunkchan <- FileChunk{
Source: "end",
Raw: bytes.NewBuffer([]byte("\n]\n")),
Order: int(latestChunk.Load()) + 1,
}
for len(chunkchan) > 0 { for len(chunkchan) > 0 {
time.Sleep(time.Millisecond) time.Sleep(time.Millisecond)
} }
@ -115,6 +123,7 @@ func WriteJSON(iterator obiiter.IBioSequence,
} }
chunkchan <- ss chunkchan <- ss
latestChunk.Store(int64(batch.Order()))
newIter.Push(batch) newIter.Push(batch)
} }
newIter.Done() newIter.Done()

2
pkg/obioptions/version.go
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@ -7,7 +7,7 @@ import (
// TODO: The version number is extracted from git. This induces that the version // TODO: The version number is extracted from git. This induces that the version
// 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 = "69ef175" var _Commit = "00b0edc"
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.

3
sample/AY189646
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@ -1,4 +1,3 @@
==> db_v05_idx_ori.fasta <==
>AY189646 {"count":1,"obitag_ref_index":{"0":"9606@Homo sapiens@species","10":"9526@Catarrhini@parvorder","12":"1437010@Boreoeutheria@clade","16":"9347@Eutheria@clade","17":"40674@Mammalia@class","2":"207598@Homininae@subfamily","22":"117571@Euteleostomi@clade","25":"7776@Gnathostomata@clade","29":"33213@Bilateria@clade","3":"9604@Hominidae@family","30":"6072@Eumetazoa@clade","8":"314295@Hominoidea@superfamily"},"species_name":"Homo sapiens","taxid":9606} Homo sapiens clone arCan119 12S ribosomal RNA gene, partial sequence; mitochondrial gene for mitochondrial product. >AY189646 {"count":1,"obitag_ref_index":{"0":"9606@Homo sapiens@species","10":"9526@Catarrhini@parvorder","12":"1437010@Boreoeutheria@clade","16":"9347@Eutheria@clade","17":"40674@Mammalia@class","2":"207598@Homininae@subfamily","22":"117571@Euteleostomi@clade","25":"7776@Gnathostomata@clade","29":"33213@Bilateria@clade","3":"9604@Hominidae@family","30":"6072@Eumetazoa@clade","8":"314295@Hominoidea@superfamily"},"species_name":"Homo sapiens","taxid":9606} Homo sapiens clone arCan119 12S ribosomal RNA gene, partial sequence; mitochondrial gene for mitochondrial product.
ttagccctaaacctcaacagttaaatcaacaaaactgctcgccagaacactacgrgccac ttagccctaaacctcaacagttaaatcaacaaaactgctcgccagaacactacgrgccac
agcttaaaactcaaaggacctggcggtgcttcatatccct agcttaaaactcaaaggacctggcggtgcttcatatccct
@ -9,3 +8,5 @@ cagcttaaaactcaaaggacctggcggtgcttcatatccct
ttagccctaaacttcaacagttaaattaacaaaactgctcgccagaacactacgagccac ttagccctaaacttcaacagttaaattaacaaaactgctcgccagaacactacgagccac
agcttaaaactcaaaggacctggcggtgcttcatatccct agcttaaaactcaaaggacctggcggtgcttcatatccct
>AC008512 {"count":5,"obitag_ref_index":{"0":"9606@Homo sapiens@species","10":"1437010@Boreoeutheria@clade","14":"40674@Mammalia@class","18":"117571@Euteleostomi@clade","2":"207598@Homininae@subfamily","22":"7776@Gnathostomata@clade","26":"33213@Bilateria@clade","28":"6072@Eumetazoa@clade","7":"9526@Catarrhini@parvorder"},"species_name":"Homo sapiens","taxid":9606} Homo sapiens chromosome 5 clone CTC-454K8, complete sequence. >AC008512 {"count":5,"obitag_ref_index":{"0":"9606@Homo sapiens@species","10":"1437010@Boreoeutheria@clade","14":"40674@Mammalia@class","18":"117571@Euteleostomi@clade","2":"207598@Homininae@subfamily","22":"7776@Gnathostomata@clade","26":"33213@Bilateria@clade","28":"6072@Eumetazoa@clade","7":"9526@Catarrhini@parvorder"},"species_name":"Homo sapiens","taxid":9606} Homo sapiens chromosome 5 clone CTC-454K8, complete sequence.
ttagccctaaacttcaacagttaaattaacaaaactgctcgccagaacactacgagccac
agcttaaaactcaaaggacctggcggtgcttcatatccct