mirror of
https://github.com/metabarcoding/obitools4.git
synced 2026-04-30 03:50:39 +00:00
⬆️ version bump to v4.5
- Update obioptions.Version from "Release 4.4.29" to "/v/ Release v5" - Update version.txt from 4.29 → .30 (automated by Makefile)
This commit is contained in:
Eric Coissac
@@ -0,0 +1,222 @@
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//go:build ignore
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package main
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import (
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"encoding/json"
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"fmt"
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"os"
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"os/exec"
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"path/filepath"
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"regexp"
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"sort"
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"strconv"
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"strings"
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)
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type Reference struct {
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File string `json:"file"`
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Line int `json:"line"`
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Column int `json:"column"`
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Key string `json:"key"`
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Function string `json:"function"`
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Context string `json:"context"`
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}
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type Result struct {
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Method string `json:"method"`
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Signature string `json:"signature"`
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Definition string `json:"definition"`
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References []Reference `json:"references"`
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Total int `json:"total"`
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}
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var basePath = "/Users/coissac/Sync/travail/__MOI__/GO/obitools4"
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func main() {
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cmd := exec.Command("rg", "-n", `\.SetAttribute\(`, basePath+"/pkg", "--type", "go")
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output, err := cmd.Output()
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if err != nil {
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fmt.Fprintf(os.Stderr, "Error running rg: %v\n", err)
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os.Exit(1)
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}
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lines := strings.Split(string(output), "\n")
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lineRe := regexp.MustCompile(`^(.+?):(\d+):\s*(.+)$`)
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keyRe := regexp.MustCompile(`SetAttribute\("([^"]+)"`)
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templateKeyRe := regexp.MustCompile(`SetAttribute\("([^"]+)[^"]*"\s*,`)
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var refs []Reference
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seen := make(map[string]bool)
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for _, line := range lines {
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line = strings.TrimSpace(line)
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if line == "" {
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continue
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}
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matches := lineRe.FindStringSubmatch(line)
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if matches == nil {
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continue
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}
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file := matches[1]
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lineNum, _ := strconv.Atoi(matches[2])
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context := strings.TrimSpace(matches[3])
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// Skip definition
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if strings.Contains(file, "obiseq/attributes.go") && lineNum == 132 {
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continue
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}
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// Extract key
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var key string
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if keyMatches := keyRe.FindStringSubmatch(context); keyMatches != nil {
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key = keyMatches[1]
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} else if tmplMatches := templateKeyRe.FindStringSubmatch(context); tmplMatches != nil {
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key = tmplMatches[1]
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} else {
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continue
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}
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// Get function name using treesitter
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funcName := getFunctionNameTreesitter(file, lineNum)
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uniqueKey := fmt.Sprintf("%s:%d", file, lineNum)
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if seen[uniqueKey] {
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continue
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}
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seen[uniqueKey] = true
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refs = append(refs, Reference{
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File: filepath.Base(file),
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Line: lineNum,
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Column: 0,
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Key: key,
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Function: funcName,
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Context: context,
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})
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}
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sort.Slice(refs, func(i, j int) bool {
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if refs[i].File != refs[j].File {
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return refs[i].File < refs[j].File
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}
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return refs[i].Line < refs[j].Line
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})
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result := Result{
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Method: "SetAttribute",
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Signature: "func (s *BioSequence) SetAttribute(key string, value interface{})",
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Definition: basePath + "/pkg/obiseq/attributes.go:132",
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References: refs,
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Total: len(refs),
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}
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outputJSON, err := json.MarshalIndent(result, "", " ")
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if err != nil {
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fmt.Fprintf(os.Stderr, "Error marshaling JSON: %v\n", err)
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os.Exit(1)
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}
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fmt.Println(string(outputJSON))
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}
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// getFunctionNameTreesitter uses the treesitter_cursor_walk tool to get the containing function
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func getFunctionNameTreesitter(file string, targetLine int) string {
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// Convert to 0-based for treesitter
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row := targetLine - 1
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// Use treesitter cursor walk to get ancestors
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cmd := exec.Command("bash", "-c",
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fmt.Sprintf(`kilo treesitter_cursor_walk --file_path %q --row %d --column 0 --max_depth 10 2>/dev/null`, file, row))
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output, err := cmd.Output()
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if err != nil {
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return findContainingFunction(file, targetLine)
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}
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// Parse the JSON output to find function_declaration or method_declaration
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var result map[string]interface{}
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if err := json.Unmarshal(output, &result); err != nil {
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return findContainingFunction(file, targetLine)
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}
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// Check ancestors for function declaration
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if ancestors, ok := result["ancestors"].([]interface{}); ok {
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for _, a := range ancestors {
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if anc, ok := a.(map[string]interface{}); ok {
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nodeType, _ := anc["type"].(string)
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if nodeType == "function_declaration" || nodeType == "method_declaration" {
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// Try to get the function name from children
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if children, ok := anc["children"].([]interface{}); ok {
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for _, c := range children {
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if child, ok := c.(map[string]interface{}); ok {
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childType, _ := child["type"].(string)
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if childType == "identifier" {
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if text, ok := child["text"].(string); ok {
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return text
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}
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}
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if childType == "field_identifier" {
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if text, ok := child["text"].(string); ok {
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return text
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}
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}
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}
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}
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}
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}
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if nodeType == "func_literal" {
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return "closure"
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}
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}
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}
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}
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return findContainingFunction(file, targetLine)
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}
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func findContainingFunction(file string, targetLine int) string {
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data, err := os.ReadFile(file)
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if err != nil {
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return ""
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}
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lines := strings.Split(string(data), "\n")
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for i := targetLine - 1; i >= 0 && i >= targetLine-200; i-- {
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if i >= len(lines) {
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continue
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}
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line := strings.TrimSpace(lines[i])
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if line == "}" && i > 0 {
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for j := i - 1; j >= 0 && j >= i-50; j-- {
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if j >= len(lines) {
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continue
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}
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funcLine := strings.TrimSpace(lines[j])
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if strings.HasPrefix(funcLine, "func ") {
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if match := regexp.MustCompile(`func\s+\([^)]+\)\s+([a-zA-Z_][a-zA-Z0-9_]*)\s*\(`).FindStringSubmatch(funcLine); match != nil {
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return match[1]
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}
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if match := regexp.MustCompile(`func\s+([a-zA-Z_][a-zA-Z0-9_]*)\s*\(`).FindStringSubmatch(funcLine); match != nil {
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return match[1]
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}
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}
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}
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continue
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}
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if strings.HasPrefix(line, "func ") {
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if match := regexp.MustCompile(`func\s+\([^)]+\)\s+([a-zA-Z_][a-zA-Z0-9_]*)\s*\(`).FindStringSubmatch(line); match != nil {
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return match[1]
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}
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if match := regexp.MustCompile(`func\s+([a-zA-Z_][a-zA-Z0-9_]*)\s*\(`).FindStringSubmatch(line); match != nil {
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return match[1]
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}
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}
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}
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return ""
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}
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Executable
+36
@@ -0,0 +1,36 @@
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#!/bin/bash
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basePath="/Users/coissac/Sync/travail/__MOI__/GO/obitools4"
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OUTPUT_FILE="${1:-/dev/stdout}"
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# Get all SetAttribute calls
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rg -n '\.SetAttribute\(' "$basePath/pkg" --type go | while read -r line; do
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file="${line%%:*}"
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line_num="${line%:*}"
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line_num="${line_num##*:}"
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context="${line##*: }"
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# Extract key (only literal strings)
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key=$(echo "$context" | sed -n 's/.*SetAttribute("\([^"]*\)".*/\1/p')
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[ -z "$key" ] && continue
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# Get function name using treesitter
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func=$(kilo treesitter_cursor_walk \
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--file_path "$file" \
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--row "$((line_num - 1))" \
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--column 0 \
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--max_depth 10 2>/dev/null |
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jq -r '.ancestors[] | select(.type == "function_declaration" or .type == "method_declaration") | .children[] | select(.type == "identifier" or .type == "field_identifier") | .text' 2>/dev/null)
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# Fallback to func_literal for closures
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if [ -z "$func" ]; then
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func=$(kilo treesitter_cursor_walk \
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--file_path "$file" \
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--row "$((line_num - 1))" \
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--column 0 \
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--max_depth 10 2>/dev/null |
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jq -r '.ancestors[] | select(.type == "func_literal") | "closure"' 2>/dev/null)
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fi
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echo "$(basename "$file")|$line_num|$key|${func:-unknown}|$context"
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done | sort -t'|' -k1,1 -k2,2n
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