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Patch a small bug on json write

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This commit is contained in:
Eric Coissac
2024-12-20 19:42:03 +01:00
parent abfa8f357a
commit 5d0f996625
14 changed files with 458 additions and 79 deletions
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41
pkg/obiformats/ncbitaxdump/read.go
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@ -15,6 +15,19 @@ import (
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
)
// loadNodeTable reads a node table from the provided reader and populates the given taxonomy.
// It is an internal function and should not be called directly. It is part of the NCBI taxdump reader.
// The node table is expected to be in CSV format with a custom delimiter ('|') and comments
// starting with '#'. Each record in the table represents a taxon with its taxid, parent taxid,
// and rank.
//
// Parameters:
// - reader: An io.Reader from which the node table is read.
// - taxonomy: A pointer to an obitax.Taxonomy instance where the taxon data will be added.
//
// The function reads each record from the input, trims whitespace from the taxid, parent, and rank,
// and adds the taxon to the taxonomy. If an error occurs while adding a taxon, the function logs
// a fatal error and terminates the program.
func loadNodeTable(reader io.Reader, taxonomy *obitax.Taxonomy) {
file := csv.NewReader(reader)
file.Comma = '|'
@ -38,6 +51,21 @@ func loadNodeTable(reader io.Reader, taxonomy *obitax.Taxonomy) {
}
}
// loadNameTable reads a name table from the provided reader and populates the given taxonomy.
// It is an internal function and should not be called directly. It is part of the NCBI taxdump reader.
// The name table is expected to be in a custom format with fields separated by the '|' character.
// Each record in the table represents a taxon with its taxid, name, and class name.
//
// Parameters:
// - reader: An io.Reader from which the name table is read.
// - taxonomy: A pointer to an obitax.Taxonomy instance where the taxon names will be set.
// - onlysn: A boolean flag indicating whether to only process records with the class name "scientific name".
//
// Returns:
//
// The number of taxon names successfully loaded into the taxonomy. If a line is too long, -1 is returned.
// The function processes each line, trims whitespace from the taxid, name, and class name, and sets
// the name in the taxonomy if the conditions are met.
func loadNameTable(reader io.Reader, taxonomy *obitax.Taxonomy, onlysn bool) int {
// file := csv.NewReader(reader)
// file.Comma = '|'
@ -71,6 +99,19 @@ func loadNameTable(reader io.Reader, taxonomy *obitax.Taxonomy, onlysn bool) int
return n
}
// loadMergedTable reads a merged table from the provided reader and populates the given taxonomy.
// It is an internal function and should not be called directly. It is part of the NCBI taxdump reader.
// The merged table is expected to be in CSV format with a custom delimiter ('|') and comments
// starting with '#'. Each record in the table represents a mapping between an old taxid and a new taxid.
//
// Parameters:
// - reader: An io.Reader from which the merged table is read.
// - taxonomy: A pointer to an obitax.Taxonomy instance where the alias mappings will be added.
//
// Returns:
//
// The number of alias mappings successfully loaded into the taxonomy. The function processes
// each record, trims whitespace from the old and new taxid, and adds the alias to the taxonomy.
func loadMergedTable(reader io.Reader, taxonomy *obitax.Taxonomy) int {
file := csv.NewReader(reader)
file.Comma = '|'