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Add more error checks on taxonomy reading

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Former-commit-id: 30c848d8e61214afcc7d92f0d3a3f5a1474fc720
This commit is contained in:
Eric Coissac
2023-12-14 08:09:06 +01:00
parent 2caaa62485
commit b9a7961c91
3 changed files with 25 additions and 3 deletions
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17
pkg/obiformats/ncbitaxdump/read.go
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@@ -22,9 +22,22 @@ func loadNodeTable(reader io.Reader, taxonomy *obitax.Taxonomy) {
file.TrimLeadingSpace = true
file.ReuseRecord = true
n := 0
for record, err := file.Read(); err == nil; record, err = file.Read() {
taxid, _ := strconv.Atoi(strings.TrimSpace(record[0]))
parent, _ := strconv.Atoi(strings.TrimSpace(record[1]))
n++
taxid, err := strconv.Atoi(strings.TrimSpace(record[0]))
if err != nil {
log.Panicf("Cannot read taxid at line %d: %v", n, err)
}
parent, err := strconv.Atoi(strings.TrimSpace(record[1]))
if err != nil {
log.Panicf("Cannot read parent taxid at line %d: %v", n, err)
}
rank := strings.TrimSpace(record[2])
taxonomy.AddNewTaxa(taxid, parent, rank, true, true)