mirror of
https://github.com/metabarcoding/obitools4.git
synced 2025-06-29 16:20:46 +00:00
b9bee5f426
modified: go.mod modified: go.sum modified: pkg/obilua/obilib.go modified: pkg/obilua/obiseq.go modified: pkg/obilua/obiseqslice.go new file: pkg/obilua/obitaxon.go new file: pkg/obilua/obitaxonomy.go modified: pkg/obioptions/version.go
140 lines
3.1 KiB
Go
140 lines
3.1 KiB
Go
package obilua
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import (
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"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitax"
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lua "github.com/yuin/gopher-lua"
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)
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const luaTaxonTypeName = "Taxon"
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func registerTaxonType(luaState *lua.LState) {
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taxonType := luaState.NewTypeMetatable(luaTaxonTypeName)
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luaState.SetGlobal(luaTaxonTypeName, taxonType)
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luaState.SetField(taxonType, "new", luaState.NewFunction(newTaxon))
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luaState.SetField(taxonType, "nil", taxonomy2Lua(luaState, nil))
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luaState.SetField(taxonType, "__index",
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luaState.SetFuncs(luaState.NewTable(),
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taxonMethods))
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}
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func taxon2Lua(interpreter *lua.LState,
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taxon *obitax.Taxon) lua.LValue {
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ud := interpreter.NewUserData()
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ud.Value = taxon
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interpreter.SetMetatable(ud, interpreter.GetTypeMetatable(luaTaxonTypeName))
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return ud
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}
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func newTaxon(luaState *lua.LState) int {
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taxonomy := checkTaxonomy(luaState)
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taxid := luaState.CheckString(2)
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parent := luaState.CheckString(3)
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sname := luaState.CheckString(4)
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rank := luaState.CheckString(5)
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isroot := false
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if luaState.GetTop() > 5 {
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isroot = luaState.CheckBool(6)
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}
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taxon, err := taxonomy.AddTaxon(taxid, parent, rank, isroot, false)
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if err != nil {
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luaState.RaiseError("(%v,%v,%v) : Error on taxon creation: %v", taxid, parent, sname, err)
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return 0
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}
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taxon.SetName(sname, "scientific name")
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luaState.Push(taxon2Lua(luaState, taxon))
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return 1
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}
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var taxonMethods = map[string]lua.LGFunction{
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"string": taxonAsString,
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"scientific_name": taxonGetSetScientificName,
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"parent": taxonGetParent,
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"taxon_at_rank": taxGetTaxonAtRank,
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"species": taxonGetSpecies,
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"genus": taxonGetGenus,
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"family": taxonGetFamily,
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}
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func checkTaxon(L *lua.LState, i int) *obitax.Taxon {
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ud := L.CheckUserData(i)
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if v, ok := ud.Value.(*obitax.Taxon); ok {
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return v
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}
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L.ArgError(i, "obitax.Taxon expected")
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return nil
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}
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func taxonAsString(luaState *lua.LState) int {
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taxon := checkTaxon(luaState, 1)
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luaState.Push(lua.LString(taxon.String()))
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return 1
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}
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func taxonGetSetScientificName(luaState *lua.LState) int {
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taxon := checkTaxon(luaState, 1)
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if luaState.GetTop() > 1 {
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sname := luaState.CheckString(2)
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taxon.SetName(sname, "scientific name")
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return 0
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}
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luaState.Push(lua.LString(taxon.ScientificName()))
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return 1
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}
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func taxonGetParent(luaState *lua.LState) int {
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taxon := checkTaxon(luaState, 1)
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parent := taxon.Parent()
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luaState.Push(taxon2Lua(luaState, parent))
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return 1
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}
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func taxonGetSpecies(luaState *lua.LState) int {
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taxon := checkTaxon(luaState, 1)
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species := taxon.Species()
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luaState.Push(taxon2Lua(luaState, species))
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return 1
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}
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func taxonGetGenus(luaState *lua.LState) int {
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taxon := checkTaxon(luaState, 1)
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genus := taxon.Genus()
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luaState.Push(taxon2Lua(luaState, genus))
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return 1
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}
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func taxonGetFamily(luaState *lua.LState) int {
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taxon := checkTaxon(luaState, 1)
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family := taxon.Family()
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luaState.Push(taxon2Lua(luaState, family))
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return 1
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}
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func taxGetTaxonAtRank(luaState *lua.LState) int {
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taxon := checkTaxon(luaState, 1)
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rank := luaState.CheckString(2)
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taxonAt := taxon.TaxonAtRank(rank)
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luaState.Push(taxon2Lua(luaState, taxonAt))
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return 1
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}
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