From fbe7d15dc3700e99d41e59bfef24abf0b408e860 Mon Sep 17 00:00:00 2001 From: Eric Coissac Date: Thu, 6 Mar 2025 13:38:38 +0100 Subject: [PATCH] Changes to be committed: modified: pkg/obioptions/version.go modified: pkg/obitools/obicleandb/obicleandb.go modified: pkg/obitools/obicleandb/options.go --- pkg/obioptions/version.go | 2 +- pkg/obitools/obicleandb/obicleandb.go | 2 +- pkg/obitools/obicleandb/options.go | 15 ++------------- 3 files changed, 4 insertions(+), 15 deletions(-) diff --git a/pkg/obioptions/version.go b/pkg/obioptions/version.go index d89810d..cf9aaab 100644 --- a/pkg/obioptions/version.go +++ b/pkg/obioptions/version.go @@ -8,7 +8,7 @@ import ( // corresponds to the last commit, and not the one when the file will be // commited -var _Commit = "286e27d" +var _Commit = "b5cf586" var _Version = "Release 4.4.0" // Version returns the version of the obitools package. diff --git a/pkg/obitools/obicleandb/obicleandb.go b/pkg/obitools/obicleandb/obicleandb.go index 027361a..131d9bf 100644 --- a/pkg/obitools/obicleandb/obicleandb.go +++ b/pkg/obitools/obicleandb/obicleandb.go @@ -258,7 +258,7 @@ func ICleanDB(itertator obiiter.IBioSequence) obiiter.IBioSequence { )).And(obiseq.HasRequiredRank(taxonomy, "family")) } - goodTaxa := obiseq.IsAValidTaxon(taxonomy, CLIUpdateTaxids()).And(rankPredicate) + goodTaxa := obiseq.IsAValidTaxon(taxonomy, obidefault.UpdateTaxid()).And(rankPredicate) usable := unique.FilterOn(goodTaxa, obidefault.BatchSize(), diff --git a/pkg/obitools/obicleandb/options.go b/pkg/obitools/obicleandb/options.go index 886ae19..3168a31 100644 --- a/pkg/obitools/obicleandb/options.go +++ b/pkg/obitools/obicleandb/options.go @@ -1,26 +1,15 @@ package obicleandb import ( + "git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions" "git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obiconvert" "git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obigrep" "github.com/DavidGamba/go-getoptions" ) -var _UpdateTaxids = false - -func ObicleanDBOptionSet(options *getoptions.GetOpt) { - - options.BoolVar(&_UpdateTaxids, "update-taxids", _UpdateTaxids, - options.Description("Indicates if decrecated Taxids must be corrected.")) -} - func OptionSet(options *getoptions.GetOpt) { + obioptions.LoadTaxonomyOptionSet(options, true, false) obiconvert.InputOptionSet(options) obiconvert.OutputOptionSet(options) obigrep.TaxonomySelectionOptionSet(options) - ObicleanDBOptionSet(options) -} - -func CLIUpdateTaxids() bool { - return _UpdateTaxids }