BigChef/main.go

package main

import (
	"errors"
	"flag"
	"fmt"
	"os"
	"sort"
	"sync"
	"sync/atomic"
	"time"

	"cook/processor"
	"cook/utils"

	"gopkg.in/yaml.v3"

	logger "git.site.quack-lab.dev/dave/cylogger"
)

// mainLogger is a scoped logger for the main package.
var mainLogger = logger.Default.WithPrefix("main")

type GlobalStats struct {
	TotalMatches            int64
	TotalModifications      int64
	ProcessedFiles          int64
	FailedFiles             int64
	ModificationsPerCommand sync.Map
}

var (
	stats GlobalStats = GlobalStats{
		ModificationsPerCommand: sync.Map{},
	}
)

func main() {
	flag.Usage = func() {
		CreateExampleConfig()
		fmt.Fprintf(os.Stderr, "Usage: %s [options] <pattern> <lua_expression> <...files_or_globs>\n", os.Args[0])
		fmt.Fprintf(os.Stderr, "\nOptions:\n")
		fmt.Fprintf(os.Stderr, "  -reset\n")
		fmt.Fprintf(os.Stderr, "        Reset files to their original state\n")
		fmt.Fprintf(os.Stderr, "  -loglevel string\n")
		fmt.Fprintf(os.Stderr, "        Set logging level: ERROR, WARNING, INFO, DEBUG, TRACE (default \"INFO\")\n")
		fmt.Fprintf(os.Stderr, "  -json\n")
		fmt.Fprintf(os.Stderr, "        Enable JSON mode for processing JSON files\n")
		fmt.Fprintf(os.Stderr, "\nExamples:\n")
		fmt.Fprintf(os.Stderr, "  Regex mode (default):\n")
		fmt.Fprintf(os.Stderr, "    %s \"<value>(\\\\d+)</value>\" \"*1.5\" data.xml\n", os.Args[0])
		fmt.Fprintf(os.Stderr, "  JSON mode:\n")
		fmt.Fprintf(os.Stderr, "    %s -json data.json\n", os.Args[0])
		fmt.Fprintf(os.Stderr, "\nNote: v1, v2, etc. are used to refer to capture groups as numbers.\n")
		fmt.Fprintf(os.Stderr, "      s1, s2, etc. are used to refer to capture groups as strings.\n")
		fmt.Fprintf(os.Stderr, "      Helper functions: num(str) converts string to number, str(num) converts number to string\n")
		fmt.Fprintf(os.Stderr, "      is_number(str) checks if a string is numeric\n")
		fmt.Fprintf(os.Stderr, "      If expression starts with an operator like *, /, +, -, =, etc., v1 is automatically prepended\n")
		fmt.Fprintf(os.Stderr, "      You can use any valid Lua code, including if statements, loops, etc.\n")
		fmt.Fprintf(os.Stderr, "      Glob patterns are supported for file selection (*.xml, data/**.xml, etc.)\n")
		fmt.Fprintf(os.Stderr, "\nLua Functions Available:\n")
		fmt.Fprintf(os.Stderr, "%s\n", processor.GetLuaFunctionsHelp())
	}
	// TODO: Fix bed shitting when doing *.yml in barotrauma directory
	flag.Parse()
	args := flag.Args()

	logger.InitFlag()
	mainLogger.Info("Initializing with log level: %s", logger.GetLevel().String())
	mainLogger.Trace("Full argv: %v", os.Args)

	if flag.NArg() == 0 {
		flag.Usage()
		return
	}

	mainLogger.Debug("Getting database connection")
	db, err := utils.GetDB()
	if err != nil {
		mainLogger.Error("Failed to get database: %v", err)
		return
	}
	mainLogger.Debug("Database connection established")

	workdone, err := HandleSpecialArgs(args, err, db)
	if err != nil {
		mainLogger.Error("Failed to handle special args: %v", err)
		return
	}
	if workdone {
		mainLogger.Info("Special arguments handled, exiting.")
		return
	}

	// The plan is:
	// Load all commands
	mainLogger.Debug("Loading commands from arguments")
	mainLogger.Trace("Arguments: %v", args)
	commands, err := utils.LoadCommands(args)
	if err != nil || len(commands) == 0 {
		mainLogger.Error("Failed to load commands: %v", err)
		flag.Usage()
		return
	}
	// Collect global modifiers from special entries and filter them out
	vars := map[string]interface{}{}
	filtered := make([]utils.ModifyCommand, 0, len(commands))
	for _, c := range commands {
		if len(c.Modifiers) > 0 && c.Name == "" && c.Regex == "" && len(c.Regexes) == 0 && c.Lua == "" && len(c.Files) == 0 {
			for k, v := range c.Modifiers {
				vars[k] = v
			}
			continue
		}
		filtered = append(filtered, c)
	}
	if len(vars) > 0 {
		mainLogger.Info("Loaded %d global modifiers", len(vars))
		processor.SetVariables(vars)
	}
	commands = filtered
	mainLogger.Info("Loaded %d commands", len(commands))

	if *utils.Filter != "" {
		mainLogger.Info("Filtering commands by name: %s", *utils.Filter)
		commands = utils.FilterCommands(commands, *utils.Filter)
		mainLogger.Info("Filtered %d commands", len(commands))
	}

	// Then aggregate all the globs and deduplicate them
	mainLogger.Debug("Aggregating globs and deduplicating")
	globs := utils.AggregateGlobs(commands)
	mainLogger.Debug("Aggregated %d globs before deduplication", utils.CountGlobsBeforeDedup(commands))

	for _, command := range commands {
		mainLogger.Trace("Command: %s", command.Name)
		if len(command.Regexes) > 0 {
			mainLogger.Trace("Regexes: %v", command.Regexes)
		} else {
			mainLogger.Trace("Regex: %s", command.Regex)
		}
		mainLogger.Trace("Files: %v", command.Files)
		mainLogger.Trace("Lua: %s", command.Lua)
		mainLogger.Trace("Reset: %t", command.Reset)
		mainLogger.Trace("Isolate: %t", command.Isolate)
		mainLogger.Trace("LogLevel: %s", command.LogLevel)
	}

	// Resolve all the files for all the globs
	mainLogger.Info("Found %d unique file patterns", len(globs))
	mainLogger.Debug("Expanding glob patterns to files")
	files, err := utils.ExpandGLobs(globs)
	if err != nil {
		mainLogger.Error("Failed to expand file patterns: %v", err)
		return
	}
	mainLogger.Info("Found %d files to process", len(files))
	mainLogger.Trace("Files to process: %v", files)

	// Somehow connect files to commands via globs..
	// For each file check every glob of every command
	// Maybe memoize this part
	// That way we know what commands affect what files
	mainLogger.Debug("Associating files with commands")
	associations, err := utils.AssociateFilesWithCommands(files, commands)
	if err != nil {
		mainLogger.Error("Failed to associate files with commands: %v", err)
		return
	}
	mainLogger.Debug("Files associated with commands")
	mainLogger.Trace("File-command associations: %v", associations)
	// Per-file association summary for better visibility when debugging
	for file, assoc := range associations {
		cmdNames := make([]string, 0, len(assoc.Commands))
		for _, c := range assoc.Commands {
			cmdNames = append(cmdNames, c.Name)
		}
		isoNames := make([]string, 0, len(assoc.IsolateCommands))
		for _, c := range assoc.IsolateCommands {
			isoNames = append(isoNames, c.Name)
		}
		mainLogger.Debug("File %q has %d regular and %d isolate commands", file, len(assoc.Commands), len(assoc.IsolateCommands))
		mainLogger.Trace("\tRegular: %v", cmdNames)
		mainLogger.Trace("\tIsolate: %v", isoNames)
	}

	mainLogger.Debug("Resetting files where necessary")
	err = utils.ResetWhereNecessary(associations, db)
	if err != nil {
		mainLogger.Error("Failed to reset files where necessary: %v", err)
		return
	}
	mainLogger.Debug("Files reset where necessary")

	// Then for each file run all commands associated with the file
	workers := make(chan struct{}, *utils.ParallelFiles)
	wg := sync.WaitGroup{}
	mainLogger.Debug("Starting file processing with %d parallel workers", *utils.ParallelFiles)

	// Add performance tracking
	startTime := time.Now()

	// Create a map to store loggers for each command
	commandLoggers := make(map[string]*logger.Logger)
	for _, command := range commands {
		// Create a named logger for each command
		cmdName := command.Name
		if cmdName == "" {
			// If no name is provided, use a short version of the regex pattern
			if len(command.Regex) > 20 {
				cmdName = command.Regex[:17] + "..."
			} else {
				cmdName = command.Regex
			}
		}

		// Parse the log level for this specific command
		cmdLogLevel := logger.ParseLevel(command.LogLevel)

		// Create a logger with the command name as a field
		commandLoggers[command.Name] = logger.Default.WithField("command", cmdName)
		commandLoggers[command.Name].SetLevel(cmdLogLevel)

		mainLogger.Debug("Created logger for command %q with log level %s", cmdName, cmdLogLevel.String())
	}

	for file, association := range associations {
		workers <- struct{}{}
		wg.Add(1)
		logger.SafeGoWithArgs(func(args ...interface{}) {
			defer func() { <-workers }()
			defer wg.Done()
			// Track per-file processing time
			fileStartTime := time.Now()

			mainLogger.Debug("Reading file %q", file)
			fileData, err := os.ReadFile(file)
			if err != nil {
				mainLogger.Error("Failed to read file %q: %v", file, err)
				atomic.AddInt64(&stats.FailedFiles, 1)
				return
			}
			fileDataStr := string(fileData)
			mainLogger.Trace("File %q content: %s", file, utils.LimitString(fileDataStr, 500))

			isChanged := false
			mainLogger.Debug("Running isolate commands for file %q", file)
			fileDataStr, err = RunIsolateCommands(association, file, fileDataStr)
			if err != nil && err != NothingToDo {
				mainLogger.Error("Failed to run isolate commands for file %q: %v", file, err)
				atomic.AddInt64(&stats.FailedFiles, 1)
				return
			}
			if err != NothingToDo {
				isChanged = true
			}

			mainLogger.Debug("Running other commands for file %q", file)
			fileDataStr, err = RunOtherCommands(file, fileDataStr, association, commandLoggers)
			if err != nil && err != NothingToDo {
				mainLogger.Error("Failed to run other commands for file %q: %v", file, err)
				atomic.AddInt64(&stats.FailedFiles, 1)
				return
			}
			if err != NothingToDo {
				isChanged = true
			}

			if isChanged {
				mainLogger.Debug("Saving file %q to database", file)
				err = db.SaveFile(file, fileData)
				if err != nil {
					mainLogger.Error("Failed to save file %q to database: %v", file, err)
					atomic.AddInt64(&stats.FailedFiles, 1)
					return
				}
				mainLogger.Debug("File %q saved to database", file)
			}

			mainLogger.Debug("Writing file %q", file)
			err = os.WriteFile(file, []byte(fileDataStr), 0644)
			if err != nil {
				mainLogger.Error("Failed to write file %q: %v", file, err)
				atomic.AddInt64(&stats.FailedFiles, 1)
				return
			}
			mainLogger.Debug("File %q written", file)

			// Only increment ProcessedFiles once per file, after all processing is complete
			atomic.AddInt64(&stats.ProcessedFiles, 1)

			mainLogger.Debug("File %q processed in %v", file, time.Since(fileStartTime))
		}, file, commands)
	}
	wg.Wait()

	processingTime := time.Since(startTime)
	mainLogger.Info("Processing completed in %v", processingTime)
	processedFiles := atomic.LoadInt64(&stats.ProcessedFiles)
	if processedFiles > 0 {
		mainLogger.Info("Average time per file: %v", processingTime/time.Duration(processedFiles))
	}

	// TODO: Also give each command its own logger, maybe prefix it with something... Maybe give commands a name?
	// Do that with logger.WithField("loglevel", level.String())
	// Since each command also has its own log level
	// TODO: Maybe even figure out how to run individual commands...?
	// TODO: What to do with git? Figure it out ....

	// if *gitFlag {
	// 	mainLogger.Info("Git integration enabled, setting up git repository")
	// 	err := setupGit()
	// 	if err != nil {
	// 		mainLogger.Error("Failed to setup git: %v", err)
	// 		fmt.Fprintf(os.Stderr, "Error setting up git: %v\n", err)
	// 		return
	// 	}
	// }

	// mainLogger.Debug("Expanding file patterns")
	// files, err := expandFilePatterns(filePatterns)
	// if err != nil {
	// 	mainLogger.Error("Failed to expand file patterns: %v", err)
	// 	fmt.Fprintf(os.Stderr, "Error expanding file patterns: %v\n", err)
	// 	return
	// }

	// if *gitFlag {
	// 	mainLogger.Info("Cleaning up git files before processing")
	// 	err := cleanupGitFiles(files)
	// 	if err != nil {
	// 		mainLogger.Error("Failed to cleanup git files: %v", err)
	// 		fmt.Fprintf(os.Stderr, "Error cleaning up git files: %v\n", err)
	// 		return
	// 	}
	// }
	// if *resetFlag {
	// 	mainLogger.Info("Files reset to their original state, nothing more to do")
	// 	log.Printf("Files reset to their original state, nothing more to do")
	// 	return
	// }

	// Print summary
	totalModifications := atomic.LoadInt64(&stats.TotalModifications)
	if totalModifications == 0 {
		mainLogger.Warning("No modifications were made in any files")
	} else {
		failedFiles := atomic.LoadInt64(&stats.FailedFiles)
		mainLogger.Info("Operation complete! Modified %d values in %d/%d files",
			totalModifications, processedFiles, processedFiles+failedFiles)
		sortedCommands := []string{}
		stats.ModificationsPerCommand.Range(func(key, value interface{}) bool {
			sortedCommands = append(sortedCommands, key.(string))
			return true
		})
		sort.Strings(sortedCommands)

		for _, command := range sortedCommands {
			count, _ := stats.ModificationsPerCommand.Load(command)
			if count.(int) > 0 {
				mainLogger.Info("\tCommand %q made %d modifications", command, count)
			} else {
				mainLogger.Warning("\tCommand %q made no modifications", command)
			}
		}
	}
}

func HandleSpecialArgs(args []string, err error, db utils.DB) (bool, error) {
	handleSpecialArgsLogger := logger.Default.WithPrefix("HandleSpecialArgs")
	handleSpecialArgsLogger.Debug("Handling special arguments: %v", args)
	switch args[0] {
	case "reset":
		handleSpecialArgsLogger.Info("Resetting all files")
		err = utils.ResetAllFiles(db)
		if err != nil {
			handleSpecialArgsLogger.Error("Failed to reset all files: %v", err)
			return true, err
		}
		handleSpecialArgsLogger.Info("All files reset")
		return true, nil
	case "dump":
		handleSpecialArgsLogger.Info("Dumping all files from database")
		err = db.RemoveAllFiles()
		if err != nil {
			handleSpecialArgsLogger.Error("Failed to remove all files from database: %v", err)
			return true, err
		}
		handleSpecialArgsLogger.Info("All files removed from database")
		return true, nil
	}
	handleSpecialArgsLogger.Debug("No special arguments handled, returning false")
	return false, nil
}

func CreateExampleConfig() {
	createExampleConfigLogger := logger.Default.WithPrefix("CreateExampleConfig")
	createExampleConfigLogger.Debug("Creating example configuration file")
	commands := []utils.ModifyCommand{
		// Global modifiers only entry (no name/regex/lua/files)
		{
			Modifiers: map[string]interface{}{
				"foobar":   4,
				"multiply": 1.5,
				"prefix":   "NEW_",
				"enabled":  true,
			},
		},
		// Multi-regex example using $variable in Lua
		{
			Name:    "RFToolsMultiply",
			Regexes: []string{"generatePerTick = !num", "ticksPer\\w+ = !num", "generatorRFPerTick = !num"},
			Lua:     "* $foobar",
			Files:   []string{"polymc/instances/**/rftools*.toml", `polymc\\instances\\**\\rftools*.toml`},
			Reset:   true,
			// LogLevel defaults to INFO
		},
		// Named capture groups with arithmetic and string ops
		{
			Name:  "UpdateAmountsAndItems",
			Regex: `(?P<amount>!num)\s+units\s+of\s+(?P<item>[A-Za-z_\-]+)`,
			Lua:   `amount = amount * $multiply; item = upper(item); return true`,
			Files: []string{"data/**/*.txt"},
			// INFO log level
		},
		// Full replacement via Lua 'replacement' variable
		{
			Name:  "BumpMinorVersion",
			Regex: `version\s*=\s*"(?P<major>!num)\.(?P<minor>!num)\.(?P<patch>!num)"`,
			Lua:   `replacement = format("version=\"%s.%s.%s\"", major, num(minor)+1, 0); return true`,
			Files: []string{"config/*.ini", "config/*.cfg"},
		},
		// Multiline regex example (DOTALL is auto-enabled). Captures numeric in nested XML.
		{
			Name:  "XMLNestedValueMultiply",
			Regex: `<item>\s*\s*<name>!any<\/name>\s*\s*<value>(!num)<\/value>\s*\s*<\/item>`,
			Lua:   `* $multiply`,
			Files: []string{"data/**/*.xml"},
			// Demonstrates multiline regex in YAML
		},
		// Multiline regexES array, with different patterns handled by same Lua
		{
			Name: "MultiLinePatterns",
			Regexes: []string{
				`<entry>\s*\n\s*<id>(?P<id>!num)</id>\s*\n\s*<score>(?P<score>!num)</score>\s*\n\s*</entry>`,
				`\[block\]\nkey=(?P<key>[A-Za-z_]+)\nvalue=(?P<val>!num)`,
			},
			Lua:      `if is_number(score) then score = score * 2 end; if is_number(val) then val = val * 3 end; return true`,
			Files:    []string{"examples/**/*.*"},
			LogLevel: "DEBUG",
		},
		// Use equals operator shorthand and boolean variable
		{
			Name:  "EnableFlags",
			Regex: `enabled\s*=\s*(true|false)`,
			Lua:   `= $enabled`,
			Files: []string{"**/*.toml"},
		},
		// Demonstrate NoDedup to allow overlapping replacements
		{
			Name:    "OverlappingGroups",
			Regex:   `(?P<a>!num)(?P<b>!num)`,
			Lua:     `a = num(a) + 1; b = num(b) + 1; return true`,
			Files:   []string{"overlap/**/*.txt"},
			NoDedup: true,
		},
		// Isolate command example operating on entire matched block
		{
			Name:     "IsolateUppercaseBlock",
			Regex:    `BEGIN\n(?P<block>!any)\nEND`,
			Lua:      `block = upper(block); return true`,
			Files:    []string{"logs/**/*.log"},
			Isolate:  true,
			LogLevel: "TRACE",
		},
		// Using !rep placeholder and arrays of files
		{
			Name:  "RepeatPlaceholderExample",
			Regex: `name: (.*) !rep(, .* , 2)`,
			Lua:   `-- no-op, just demonstrate placeholder; return false`,
			Files: []string{"lists/**/*.yml", "lists/**/*.yaml"},
		},
		// Using string variable in Lua expression
		{
			Name:  "PrefixKeys",
			Regex: `(?P<key>[A-Za-z0-9_]+)\s*=`,
			Lua:   `key = $prefix .. key; return true`,
			Files: []string{"**/*.properties"},
		},
		// JSON mode examples
		{
			Name:  "JSONArrayMultiply",
			JSON:  true,
			Lua:   `for i, item in ipairs(data.items) do data.items[i].value = item.value * 2 end; return true`,
			Files: []string{"data/**/*.json"},
		},
		{
			Name:  "JSONObjectUpdate",
			JSON:  true,
			Lua:   `data.version = "2.0.0"; data.enabled = true; return true`,
			Files: []string{"config/**/*.json"},
		},
		{
			Name:  "JSONNestedModify",
			JSON:  true,
			Lua:   `if data.settings and data.settings.performance then data.settings.performance.multiplier = data.settings.performance.multiplier * 1.5 end; return true`,
			Files: []string{"settings/**/*.json"},
		},
	}

	data, err := yaml.Marshal(commands)
	if err != nil {
		createExampleConfigLogger.Error("Failed to marshal example config: %v", err)
		return
	}

	createExampleConfigLogger.Debug("Writing example_cook.yml")
	err = os.WriteFile("example_cook.yml", data, 0644)
	if err != nil {
		createExampleConfigLogger.Error("Failed to write example_cook.yml: %v", err)
		return
	}

	createExampleConfigLogger.Info("Wrote example_cook.yml")
}

var NothingToDo = errors.New("nothing to do")

func RunOtherCommands(file string, fileDataStr string, association utils.FileCommandAssociation, commandLoggers map[string]*logger.Logger) (string, error) {
	runOtherCommandsLogger := mainLogger.WithPrefix("RunOtherCommands").WithField("file", file)
	runOtherCommandsLogger.Debug("Running other commands for file")
	runOtherCommandsLogger.Trace("File data before modifications: %s", utils.LimitString(fileDataStr, 200))

	// Separate JSON and regex commands for different processing approaches
	jsonCommands := []utils.ModifyCommand{}
	regexCommands := []utils.ModifyCommand{}

	for _, command := range association.Commands {
		if command.JSON || *utils.JSON {
			jsonCommands = append(jsonCommands, command)
		} else {
			regexCommands = append(regexCommands, command)
		}
	}

	// Process JSON commands sequentially (each operates on the entire file)
	for _, command := range jsonCommands {
		cmdLogger := logger.Default
		if cmdLog, ok := commandLoggers[command.Name]; ok {
			cmdLogger = cmdLog
		}

		cmdLogger.Debug("Processing file with JSON mode for command %q", command.Name)
		newModifications, err := processor.ProcessJSON(fileDataStr, command, file)
		if err != nil {
			runOtherCommandsLogger.Error("Failed to process file with JSON command %q: %v", command.Name, err)
			continue
		}

		// Apply JSON modifications immediately
		if len(newModifications) > 0 {
			var count int
			fileDataStr, count = utils.ExecuteModifications(newModifications, fileDataStr)
			atomic.AddInt64(&stats.TotalModifications, int64(count))
			cmdLogger.Debug("Applied %d JSON modifications for command %q", count, command.Name)
		}

		count, ok := stats.ModificationsPerCommand.Load(command.Name)
		if !ok {
			count = 0
		}
		stats.ModificationsPerCommand.Store(command.Name, count.(int)+len(newModifications))
	}

	// Aggregate regex modifications and execute them
	modifications := []utils.ReplaceCommand{}
	numCommandsConsidered := 0
	for _, command := range regexCommands {
		cmdLogger := logger.Default
		if cmdLog, ok := commandLoggers[command.Name]; ok {
			cmdLogger = cmdLog
		}

		patterns := command.Regexes
		if len(patterns) == 0 {
			patterns = []string{command.Regex}
		}
		for idx, pattern := range patterns {
			tmpCmd := command
			tmpCmd.Regex = pattern
			cmdLogger.Debug("Begin processing file with command %q (pattern %d/%d)", command.Name, idx+1, len(patterns))
			numCommandsConsidered++
			newModifications, err := processor.ProcessRegex(fileDataStr, tmpCmd, file)
			if err != nil {
				runOtherCommandsLogger.Error("Failed to process file with command %q: %v", command.Name, err)
				continue
			}
			modifications = append(modifications, newModifications...)
			count, ok := stats.ModificationsPerCommand.Load(command.Name)
			if !ok {
				count = 0
			}
			stats.ModificationsPerCommand.Store(command.Name, count.(int)+len(newModifications))

			cmdLogger.Debug("Command %q generated %d modifications (pattern %d/%d)", command.Name, len(newModifications), idx+1, len(patterns))
			cmdLogger.Trace("Modifications generated by command %q: %v", command.Name, newModifications)
			if len(newModifications) == 0 {
				cmdLogger.Debug("No modifications yielded by command %q (pattern %d/%d)", command.Name, idx+1, len(patterns))
			}
		}
	}

	runOtherCommandsLogger.Debug("Aggregated %d modifications from %d command-pattern runs", len(modifications), numCommandsConsidered)
	runOtherCommandsLogger.Trace("All aggregated modifications: %v", modifications)

	if len(modifications) == 0 {
		runOtherCommandsLogger.Warning("No modifications found for file")
		return fileDataStr, NothingToDo
	}
	runOtherCommandsLogger.Debug("Executing %d modifications for file", len(modifications))

	// Sort commands in reverse order for safe replacements
	var count int
	fileDataStr, count = utils.ExecuteModifications(modifications, fileDataStr)
	runOtherCommandsLogger.Trace("File data after modifications: %s", utils.LimitString(fileDataStr, 200))

	atomic.AddInt64(&stats.TotalModifications, int64(count))

	runOtherCommandsLogger.Info("Executed %d modifications for file", count)
	return fileDataStr, nil
}

func RunIsolateCommands(association utils.FileCommandAssociation, file string, fileDataStr string) (string, error) {
	runIsolateCommandsLogger := mainLogger.WithPrefix("RunIsolateCommands").WithField("file", file)
	runIsolateCommandsLogger.Debug("Running isolate commands for file")
	runIsolateCommandsLogger.Trace("File data before isolate modifications: %s", utils.LimitString(fileDataStr, 200))

	anythingDone := false
	for _, isolateCommand := range association.IsolateCommands {
		// Check if this isolate command should use JSON mode
		if isolateCommand.JSON || *utils.JSON {
			runIsolateCommandsLogger.Debug("Begin processing file with JSON isolate command %q", isolateCommand.Name)
			modifications, err := processor.ProcessJSON(fileDataStr, isolateCommand, file)
			if err != nil {
				runIsolateCommandsLogger.Error("Failed to process file with JSON isolate command %q: %v", isolateCommand.Name, err)
				continue
			}

			if len(modifications) == 0 {
				runIsolateCommandsLogger.Debug("JSON isolate command %q produced no modifications", isolateCommand.Name)
				continue
			}
			anythingDone = true

			runIsolateCommandsLogger.Debug("Executing %d JSON isolate modifications for file", len(modifications))
			runIsolateCommandsLogger.Trace("JSON isolate modifications: %v", modifications)
			var count int
			fileDataStr, count = utils.ExecuteModifications(modifications, fileDataStr)
			runIsolateCommandsLogger.Trace("File data after JSON isolate modifications: %s", utils.LimitString(fileDataStr, 200))

			atomic.AddInt64(&stats.TotalModifications, int64(count))

			runIsolateCommandsLogger.Info("Executed %d JSON isolate modifications for file", count)
		} else {
			// Regular regex processing for isolate commands
			runIsolateCommandsLogger.Debug("Begin processing file with isolate command %q", isolateCommand.Regex)
			patterns := isolateCommand.Regexes
			if len(patterns) == 0 {
				patterns = []string{isolateCommand.Regex}
			}
			for idx, pattern := range patterns {
				tmpCmd := isolateCommand
				tmpCmd.Regex = pattern
				modifications, err := processor.ProcessRegex(fileDataStr, tmpCmd, file)
				if err != nil {
					runIsolateCommandsLogger.Error("Failed to process file with isolate command %q (pattern %d/%d): %v", isolateCommand.Name, idx+1, len(patterns), err)
					continue
				}

				if len(modifications) == 0 {
					runIsolateCommandsLogger.Debug("Isolate command %q produced no modifications (pattern %d/%d)", isolateCommand.Name, idx+1, len(patterns))
					continue
				}
				anythingDone = true

				runIsolateCommandsLogger.Debug("Executing %d isolate modifications for file", len(modifications))
				runIsolateCommandsLogger.Trace("Isolate modifications: %v", modifications)
				var count int
				fileDataStr, count = utils.ExecuteModifications(modifications, fileDataStr)
				runIsolateCommandsLogger.Trace("File data after isolate modifications: %s", utils.LimitString(fileDataStr, 200))

				atomic.AddInt64(&stats.TotalModifications, int64(count))

				runIsolateCommandsLogger.Info("Executed %d isolate modifications for file", count)
			}
		}
	}
	if !anythingDone {
		runIsolateCommandsLogger.Debug("No isolate modifications were made for file")
		return fileDataStr, NothingToDo
	}
	return fileDataStr, nil
}