Update the expression language

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 = "13ff892"
+var _Commit = "e065e29"
 var _Version = "Release 4.4.0"
 
 // Version returns the version of the obitools package.

pkg/obiseq/language.go

@@ -1,6 +1,7 @@
 package obiseq
 
 import (
+	"errors"
 	"fmt"
 	"reflect"
 	"regexp"
@@ -145,14 +146,14 @@ var OBILang = gval.NewLanguage(
 		ismap := obiutils.IsAMap(args[0])
 		return ismap, nil
 	}),
+	gval.Function("isvector", func(args ...interface{}) (interface{}, error) {
+		isvector := obiutils.IsASlice(args[0])
+		return isvector, nil
+	}),
 	gval.Function("sprintf", func(args ...interface{}) (interface{}, error) {
 		text := fmt.Sprintf(args[0].(string), args[1:]...)
 		return text, nil
 	}),
-	gval.Function("gsub", func(args ...interface{}) (interface{}, error) {
-		text := strings.ReplaceAll(args[0].(string), args[1].(string), args[2].(string))
-		return text, nil
-	}),
 	gval.Function("subspc", func(args ...interface{}) (interface{}, error) {
 		text := strings.ReplaceAll(args[0].(string), " ", "_")
 		return text, nil
@@ -181,6 +182,14 @@ var OBILang = gval.NewLanguage(
 		}
 		return val, nil
 	}),
+	gval.Function("string", func(args ...interface{}) (interface{}, error) {
+		val, err := obiutils.InterfaceToString(args[0])
+
+		if err != nil {
+			log.Fatalf("%v cannot be converted to a string value", args[0])
+		}
+		return val, nil
+	}),
 	gval.Function("ifelse", func(args ...interface{}) (interface{}, error) {
 		if args[0].(bool) {
 			return args[1], nil
@@ -192,13 +201,52 @@ var OBILang = gval.NewLanguage(
 		composition := (args[0].(*BioSequence)).Composition()
 		return float64(composition['g']-composition['c']) / float64(composition['g']+composition['c']), nil
 	}),
+	gval.Function("qualities", func(args ...interface{}) (interface{}, error) {
+		qualities := (args[0].(*BioSequence)).Qualities()
+		rep := make([]interface{}, len(qualities))
+		for i, q := range qualities {
+			rep[i] = float64(q)
+		}
+		return rep, nil
+	}),
+	gval.Function("elementof", func(args ...interface{}) (interface{}, error) {
+		if obiutils.IsASlice(args[0]) {
+			pos, err := obiutils.InterfaceToInt(args[1])
+			if err != nil {
+				return nil, err
+			}
+			if slice, ok := args[0].([]interface{}); ok {
+				return slice[pos], nil
+			} else {
+				return nil, errors.New("obi: first argument incorrect slice")
+			}
+
+		} else if obiutils.IsAMap(args[0]) {
+			pos, err := obiutils.InterfaceToString(args[1])
+			if err != nil {
+				return nil, err
+			}
+			if m, ok := args[0].(map[string]interface{}); ok {
+				return m[pos], nil
+			} else {
+				return nil, errors.New("obi: first argument incorrect map")
+			}
+		} else if s, ok := args[0].(string); ok {
+			pos, err := obiutils.InterfaceToInt(args[1])
+			if err != nil {
+				return nil, err
+			}
+			return string(s[pos]), nil
+		}
+		return nil, fmt.Errorf("invalid arguments")
+	}),
 	gval.Function("gc", func(args ...interface{}) (interface{}, error) {
 		composition := (args[0].(*BioSequence)).Composition()
-		return float64(composition['g']+composition['c']) / float64(args[0].(*BioSequence).Len()), nil
+		return float64(composition['g']+composition['c']) / float64(args[0].(*BioSequence).Len()-composition['o']), nil
 	}),
 	gval.Function("composition", func(args ...interface{}) (interface{}, error) {
 		comp := (args[0].(*BioSequence)).Composition()
-		scomp := make(map[string]float64)
+		scomp := make(map[string]interface{}, 5)
 		for k, v := range comp {
 			scomp[string(k)] = float64(v)
 		}
@@ -209,4 +257,22 @@ var OBILang = gval.NewLanguage(
 		results := pattern.ReplaceAllString(args[0].(string), args[2].(string))
 		return results, nil
 	}),
+	gval.Function("substr", func(args ...interface{}) (interface{}, error) {
+		str, ok1 := args[0].(string)
+		start, ok2 := args[1].(float64) // Gval utilise float64 pour les nombres
+		length, ok3 := args[2].(float64)
+
+		if !ok1 || !ok2 || !ok3 {
+			return nil, fmt.Errorf("invalid arguments")
+		}
+
+		startIndex := int(start)
+		endIndex := startIndex + int(length)
+
+		if startIndex < 0 || endIndex > len(str) {
+			return nil, fmt.Errorf("index out of range")
+		}
+
+		return str[startIndex:endIndex], nil
+	}),
 )

pkg/obiutils/cast_interface.go

@@ -4,6 +4,7 @@ import (
 	"fmt"
 	"reflect"
 	"strconv"
+	"strings"
 
 	log "github.com/sirupsen/logrus"
 )
@@ -14,7 +15,12 @@ import (
 // It returns the string representation and an error if any occurred during the conversion process.
 func InterfaceToString(i interface{}) (val string, err error) {
 	err = nil
-	val = fmt.Sprintf("%v", i)
+	if vc, ok := i.(interface{ String() string }); ok {
+		val = vc.String()
+	} else {
+		val = fmt.Sprintf("%v", i)
+	}
+
 	return
 }
 
@@ -67,6 +73,10 @@ func InterfaceToBool(i interface{}) (val bool, err error) {
 		val = t != 0 // standardizes across systems
 	case uint64:
 		val = t != 0 // standardizes across systems
+	case string:
+		val = strings.ToLower(t) == "true" || t == "1" || strings.ToLower(t) == "yes" || strings.ToLower(t) == "on" || strings.ToLower(t) == "t"
+	case nil:
+		val = false
 	default:
 		err = &NotABoolean{"value attribute cannot be casted to a boolean"}
 	}