first preliminary version of obiscript.

Former-commit-id: 0d2c0fc5e33e0873ba5c04aca4cf7dd69aa83c90

pkg/obilua/lua.go

@@ -0,0 +1,140 @@
+package obilua
+
+import (
+	"bytes"
+	"os"
+
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
+	log "github.com/sirupsen/logrus"
+	lua "github.com/yuin/gopher-lua"
+	"github.com/yuin/gopher-lua/parse"
+)
+
+func NewInterpreter() *lua.LState {
+	lua := lua.NewState()
+
+	RegisterObilib(lua)
+
+	return lua
+}
+
+func Compile(program []byte, name string) (*lua.FunctionProto, error) {
+
+	reader := bytes.NewReader(program)
+	chunk, err := parse.Parse(reader, name)
+	if err != nil {
+		return nil, err
+	}
+
+	proto, err := lua.Compile(chunk, name)
+	if err != nil {
+		return nil, err
+	}
+	return proto, nil
+}
+
+func CompileScript(filePath string) (*lua.FunctionProto, error) {
+	program, err := os.ReadFile(filePath)
+
+	if err != nil {
+		return nil, err
+	}
+
+	return Compile(program, filePath)
+}
+
+func LuaWorker(proto *lua.FunctionProto) obiseq.SeqWorker {
+	interpreter := NewInterpreter()
+	lfunc := interpreter.NewFunctionFromProto(proto)
+
+	f := func(sequence *obiseq.BioSequence) (obiseq.BioSequenceSlice, error) {
+		interpreter.SetGlobal("sequence", obiseq2Lua(interpreter, sequence))
+		interpreter.Push(lfunc)
+		err := interpreter.PCall(0, lua.MultRet, nil)
+
+		return obiseq.BioSequenceSlice{sequence}, err
+	}
+
+	return f
+}
+
+func LuaProcessor(iterator obiiter.IBioSequence, name, program string, breakOnError bool, nworkers int) obiiter.IBioSequence {
+	newIter := obiiter.MakeIBioSequence()
+
+	if nworkers <= 0 {
+		nworkers = obioptions.CLIParallelWorkers()
+	}
+
+	newIter.Add(nworkers)
+
+	go func() {
+		newIter.WaitAndClose()
+	}()
+
+	bp := []byte(program)
+	proto, err := Compile(bp, name)
+
+	if err != nil {
+		log.Fatalf("Cannot compile script %s : %v", name, err)
+	}
+
+	ff := func(iterator obiiter.IBioSequence) {
+		w := LuaWorker(proto)
+		sw := obiseq.SeqToSliceWorker(w, false)
+
+		// iterator = iterator.SortBatches()
+
+		for iterator.Next() {
+			seqs := iterator.Get()
+			slice := seqs.Slice()
+			ns, err := sw(slice)
+
+			if err != nil {
+				if breakOnError {
+					log.Fatalf("Error during Lua sequence processing : %v", err)
+				} else {
+					log.Warnf("Error during Lua sequence processing : %v", err)
+				}
+			}
+
+			newIter.Push(obiiter.MakeBioSequenceBatch(seqs.Order(), ns))
+			seqs.Recycle(false)
+		}
+
+		newIter.Done()
+	}
+
+	for i := 1; i < nworkers; i++ {
+		go ff(iterator.Split())
+	}
+
+	go ff(iterator)
+
+	if iterator.IsPaired() {
+		newIter.MarkAsPaired()
+	}
+
+	return newIter
+
+}
+
+func LuaPipe(name, program string, breakOnError bool, nworkers int) obiiter.Pipeable {
+
+	f := func(input obiiter.IBioSequence) obiiter.IBioSequence {
+		return LuaProcessor(input, name, program, breakOnError, nworkers)
+	}
+
+	return f
+}
+
+func LuaScriptPipe(filename string, breakOnError bool, nworkers int) obiiter.Pipeable {
+	program, err := os.ReadFile(filename)
+
+	if err != nil {
+		log.Fatalf("Cannot read script file %s", filename)
+	}
+
+	return LuaPipe(filename, string(program), breakOnError, nworkers)
+}