first preliminary version of obiscript.

Former-commit-id: 0d2c0fc5e33e0873ba5c04aca4cf7dd69aa83c90

pkg/obitools/obiscript/obiscript.go

@@ -0,0 +1,14 @@
+package obiscript
+
+import (
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obilua"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
+)
+
+func CLIScriptPipeline() obiiter.Pipeable {
+
+	pipe := obilua.LuaScriptPipe(CLIScriptFilename(), true, obioptions.CLIParallelWorkers())
+
+	return pipe
+}

pkg/obitools/obiscript/options.go

@@ -0,0 +1,83 @@
+package obiscript
+
+import (
+	"log"
+	"os"
+
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obiconvert"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obigrep"
+	"github.com/DavidGamba/go-getoptions"
+)
+
+var _script = ""
+var _askTemplate = false
+
+func ScriptOptionSet(options *getoptions.GetOpt) {
+
+	options.StringVar(&_script, "script", _script,
+		options.Description("The script to execute."),
+		options.Alias("S"),
+		options.Description("Name of a map attribute."))
+
+	options.BoolVar(&_askTemplate, "template", _askTemplate,
+		options.Description("Print on the standard output a script template."),
+	)
+}
+
+func OptionSet(options *getoptions.GetOpt) {
+	ScriptOptionSet(options)
+	obiconvert.OptionSet(options)
+	obigrep.SequenceSelectionOptionSet(options)
+}
+
+func CLIScriptFilename() string {
+	return _script
+}
+
+func CLIScript() string {
+	file, err := os.ReadFile(_script) // Reads the script
+	if err != nil {
+		log.Fatalf("cannot read the script file : %s", _script)
+	}
+	return string(file)
+}
+
+func CLIAskScriptTemplate() bool {
+	return _askTemplate
+}
+
+func CLIScriptTemplate() string {
+	return `
+	import {
+		"sync"
+		"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
+	}
+	//
+	// Begin function run before the first sequence being processed
+	//
+
+	func Begin(environment *sync.Map) {
+
+	}
+
+	//
+	// Begin function run after the last sequence being processed
+	//
+
+	func End(environment *sync.Map) {
+
+	}
+
+	//
+	// Worker function run for each sequence validating the selection predicat as specified by 
+	// the command line options.
+	//
+	// The function must return the altered sequence.
+	// If the function returns nil, the sequence is discarded from the output
+	func Worker(sequence *obiseq.BioSequence, environment *sync.Map) *obiseq.BioSequence {
+
+
+		return sequence
+	}
+	`
+}