first preliminary version of obiscript.

Former-commit-id: 0d2c0fc5e33e0873ba5c04aca4cf7dd69aa83c90

pkg/obilua/obiseq.go

@@ -0,0 +1,154 @@
+package obilua
+
+import (
+	log "github.com/sirupsen/logrus"
+
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
+	lua "github.com/yuin/gopher-lua"
+)
+
+func RegisterObiSeq(luaState *lua.LState) {
+	registerBioSequenceType(luaState)
+}
+
+const luaBioSequenceTypeName = "BioSequence"
+
+func registerBioSequenceType(luaState *lua.LState) {
+	bioSequenceType := luaState.NewTypeMetatable(luaBioSequenceTypeName)
+	luaState.SetGlobal(luaBioSequenceTypeName, bioSequenceType)
+	luaState.SetField(bioSequenceType, "new", luaState.NewFunction(newObiSeq))
+
+	luaState.SetField(bioSequenceType, "__index",
+		luaState.SetFuncs(luaState.NewTable(),
+			bioSequenceMethods))
+}
+
+func obiseq2Lua(interpreter *lua.LState,
+	sequence *obiseq.BioSequence) lua.LValue {
+	ud := interpreter.NewUserData()
+	ud.Value = sequence
+	interpreter.SetMetatable(ud, interpreter.GetTypeMetatable(luaBioSequenceTypeName))
+
+	return ud
+}
+func newObiSeq(luaState *lua.LState) int {
+	seqid := luaState.CheckString(1)
+	seq := []byte(luaState.CheckString(2))
+
+	definition := ""
+	if luaState.GetTop() > 2 {
+		definition = luaState.CheckString(3)
+	}
+
+	sequence := obiseq.NewBioSequence(seqid, seq, definition)
+
+	luaState.Push(obiseq2Lua(luaState, sequence))
+	return 1
+}
+
+var bioSequenceMethods = map[string]lua.LGFunction{
+	"id":         bioSequenceGetSetId,
+	"sequence":   bioSequenceGetSetSequence,
+	"definition": bioSequenceGetSetDefinition,
+	"count":      bioSequenceGetSetCount,
+	"taxid":      bioSequenceGetSetTaxid,
+	"attribute":  bioSequenceGetSetAttribute,
+}
+
+// checkBioSequence checks if the first argument in the Lua stack is a *obiseq.BioSequence.
+//
+// This function accepts a pointer to the Lua state and attempts to retrieve a userdata
+// that holds a pointer to a BioSequence. If the conversion is successful, it returns
+// the *BioSequence. If the conversion fails, it raises a Lua argument error.
+// Returns a pointer to obiseq.BioSequence or nil if the argument is not of the expected type.
+func checkBioSequence(L *lua.LState) *obiseq.BioSequence {
+	ud := L.CheckUserData(1)
+	if v, ok := ud.Value.(*obiseq.BioSequence); ok {
+		return v
+	}
+	L.ArgError(1, "obiseq.BioSequence expected")
+	return nil
+}
+
+// bioSequenceGetSetId gets the ID of a biosequence or sets a new ID if provided.
+//
+// This function expects a *lua.LState pointer as its only parameter.
+// If a second argument is provided, it sets the new ID for the biosequence.
+// It returns 0 if a new ID is set, or 1 after pushing the current ID onto the stack.
+func bioSequenceGetSetId(luaState *lua.LState) int {
+	s := checkBioSequence(luaState)
+	if luaState.GetTop() == 2 {
+		s.SetId(luaState.CheckString(2))
+		return 0
+	}
+	luaState.Push(lua.LString(s.Id()))
+	return 1
+}
+
+func bioSequenceGetSetSequence(luaState *lua.LState) int {
+	s := checkBioSequence(luaState)
+	if luaState.GetTop() == 2 {
+		s.SetSequence([]byte(luaState.CheckString(2)))
+		return 0
+	}
+	luaState.Push(lua.LString(s.String()))
+	return 1
+}
+
+func bioSequenceGetSetDefinition(luaState *lua.LState) int {
+	s := checkBioSequence(luaState)
+	if luaState.GetTop() == 2 {
+		s.SetDefinition(luaState.CheckString(2))
+		return 0
+	}
+	luaState.Push(lua.LString(s.Definition()))
+	return 1
+}
+
+func bioSequenceGetSetCount(luaState *lua.LState) int {
+	s := checkBioSequence(luaState)
+	if luaState.GetTop() == 2 {
+		s.SetCount(luaState.CheckInt(2))
+		return 0
+	}
+	luaState.Push(lua.LNumber(s.Count()))
+	return 1
+}
+
+func bioSequenceGetSetTaxid(luaState *lua.LState) int {
+	s := checkBioSequence(luaState)
+	if luaState.GetTop() == 2 {
+		s.SetTaxid(luaState.CheckInt(2))
+		return 0
+	}
+	luaState.Push(lua.LNumber(s.Taxid()))
+	return 1
+}
+
+func bioSequenceGetSetAttribute(luaState *lua.LState) int {
+	s := checkBioSequence(luaState)
+	attName := luaState.CheckString(2)
+
+	if luaState.GetTop() == 3 {
+		ud := luaState.CheckAny(3)
+
+		log.Infof("ud : %v [%v]", ud, ud.Type())
+		//
+		// Perhaps the code needs some type checking on ud.Value
+		// It's a first test
+		//
+
+		s.SetAttribute(attName, ud)
+		return 0
+	}
+
+	value, ok := s.GetAttribute(attName)
+
+	if !ok {
+		luaState.Push(lua.LNil)
+	} else {
+		pushInterfaceToLua(luaState, value)
+	}
+
+	return 1
+}