fix issue with analysis using tool configuration file

.codacy/codacy.yaml

@@ -13,4 +13,4 @@ tools:
     - pylint@3.3.7
     - revive@1.11.0
     - semgrep@1.78.0
-    - trivy@0.66.0
+    - trivy@0.66.0 

.gitignore

@@ -27,8 +27,9 @@ go.work.sum
 # Codacy CLI 
 cli-v2
 codacy-cli
-**/.codacy/logs/
-.codacy/
+.codacy/*
+!.codacy/codacy.yaml
+.github/instructions/
 
 
 #Ignore cursor AI rules

cmd/analyze.go

@@ -245,7 +245,7 @@ func loadsToolAndPatterns(toolName string, onlyEnabledPatterns bool) (domain.Too
 	}
 	var tool domain.Tool
 	for _, t := range toolsResponse {
-		if t.ShortName == toolName {
+		if t.Name == toolName {
 			tool = t
 			break
 		}
@@ -264,19 +264,19 @@ func getToolName(toolName string, version string) string {
 	if toolName == "eslint" {
 		switch majorVersion {
 		case 7:
-			return "eslint"
+			return "ESLint (deprecated)"
 		case 8:
-			return "eslint-8"
+			return "ESLint"
 		case 9:
-			return "eslint-9"
+			return "ESLint9"
 		}
 	} else {
 		if toolName == "pmd" {
 			switch majorVersion {
 			case 6:
-				return "pmd"
+				return "PMD"
 			case 7:
-				return "pmd-7"
+				return "PMD7"
 			}
 		}
 	}
@@ -351,10 +351,33 @@ func runToolByName(toolName string, workDirectory string, pathsToCheck []string,
 	if err != nil {
 		return err
 	}
+
+	var t *domain.Tool
+	var usesConfigurationFile = false
+
+	// If the user doesn't provide init flags, we skip fetching repository tools
+	if initFlags != (domain.InitFlags{}) {
+		// Get the tool name with the right version e.g. ESLint9, PMD7, etc.
+		toolRightVersion := getToolName(toolName, tool.Version)
+
+		// Get the repository tools to access tool settings
+		repositoryTools, _ := codacyclient.GetRepositoryTools(initFlags)
+
+		// Find the matching tool in repositoryTools
+
+		for i, tool := range repositoryTools {
+			if tool.Name == toolRightVersion {
+				t = &repositoryTools[i]
+				usesConfigurationFile = t.Settings.UsesConfigurationFile
+				break
+			}
+		}
+	}
+
 	switch toolName {
 	case "eslint":
 		binaryPath := runtime.Binaries[tool.Runtime]
-		return tools.RunEslint(workDirectory, tool.InstallDir, binaryPath, pathsToCheck, autoFix, outputFile, outputFormat)
+		return tools.RunEslint(workDirectory, tool.InstallDir, binaryPath, pathsToCheck, autoFix, outputFile, outputFormat, usesConfigurationFile)
 	case "trivy":
 		binaryPath := tool.Binaries[toolName]
 		return tools.RunTrivy(workDirectory, binaryPath, pathsToCheck, outputFile, outputFormat)

cmd/analyze_test.go

@@ -64,14 +64,14 @@ func TestGetToolName(t *testing.T) {
 		expected string
 	}{
 		// ESLint cases
-		{"eslint v7", "eslint", "7.32.0", "eslint"},
-		{"eslint v8", "eslint", "8.15.0", "eslint-8"},
-		{"eslint v9", "eslint", "9.1.0", "eslint-9"},
+		{"eslint v7", "eslint", "7.32.0", "ESLint (deprecated)"},
+		{"eslint v8", "eslint", "8.15.0", "ESLint"},
+		{"eslint v9", "eslint", "9.1.0", "ESLint9"},
 		{"eslint unknown version", "eslint", "10.0.0", "eslint"},
 
 		// PMD cases
-		{"pmd v6", "pmd", "6.55.0", "pmd"},
-		{"pmd v7", "pmd", "7.0.0", "pmd-7"},
+		{"pmd v6", "pmd", "6.55.0", "PMD"},
+		{"pmd v7", "pmd", "7.0.0", "PMD7"},
 		{"pmd unknown version", "pmd", "8.0.0", "pmd"},
 
 		// Other tools should remain unchanged

tools/eslintRunner.go

@@ -11,19 +11,21 @@ import (
 // * Run from the root of the repo we want to analyse
 // * NODE_PATH="<the installed eslint path>/node_modules"
 // * The local installed ESLint should have the @microsoft/eslint-formatter-sarif installed
-func RunEslint(repositoryToAnalyseDirectory string, eslintInstallationDirectory string, nodeBinary string, pathsToCheck []string, autoFix bool, outputFile string, outputFormat string) error {
+func RunEslint(repositoryToAnalyseDirectory string, eslintInstallationDirectory string, nodeBinary string, pathsToCheck []string, autoFix bool, outputFile string, outputFormat string, usesConfigurationFile bool) error {
 	eslintInstallationNodeModules := filepath.Join(eslintInstallationDirectory, "node_modules")
 	eslintJsPath := filepath.Join(eslintInstallationNodeModules, ".bin", "eslint")
 
 	cmd := exec.Command(nodeBinary, eslintJsPath)
 
 	// Add config file from tools-configs directory if it exists
-	if configFile, exists := ConfigFileExists(config.Config, "eslint.config.mjs"); exists {
-		// For Eslint compatibility with version 8.
-		// https://eslint.org/docs/v8.x/use/configure/configuration-files-new
-		cmd.Env = append(cmd.Env, "ESLINT_USE_FLAT_CONFIG=true")
+	if !usesConfigurationFile {
+		if configFile, exists := ConfigFileExists(config.Config, "eslint.config.mjs"); exists {
+			// For Eslint compatibility with version 8.
+			// https://eslint.org/docs/v8.x/use/configure/configuration-files-new
+			cmd.Env = append(cmd.Env, "ESLINT_USE_FLAT_CONFIG=true")
 
-		cmd.Args = append(cmd.Args, "-c", configFile)
+			cmd.Args = append(cmd.Args, "-c", configFile)
+		}
 	}
 
 	if autoFix {

tools/lizard/lizardRunner.go

@@ -7,11 +7,12 @@ import (
 	"codacy/cli-v2/domain"
 	"codacy/cli-v2/tools"
 	"codacy/cli-v2/utils/logger"
-	"github.com/sirupsen/logrus"
 	"encoding/json"
 	"fmt"
 	"os"
 	"os/exec"
+
+	"github.com/sirupsen/logrus"
 )
 
 // RunLizard runs the Lizard tool and returns any issues found
@@ -20,8 +21,6 @@ func RunLizard(workDirectory string, binary string, files []string, outputFile s
 	configFile, exists := tools.ConfigFileExists(config.Config, "lizard.yaml")
 	var patterns []domain.PatternDefinition
 	var errConfigs error
-
-
 	if exists {
 		// Configuration exists, read from file
 		patterns, errConfigs = ReadConfig(configFile)
@@ -38,8 +37,6 @@ func RunLizard(workDirectory string, binary string, files []string, outputFile s
 	if len(patterns) == 0 {
 		return fmt.Errorf("no valid patterns found in configuration")
 	}
-
-
 	// Construct base command with lizard module
 	args := []string{"-m", "lizard", "-V"}
 
@@ -50,23 +47,20 @@ func RunLizard(workDirectory string, binary string, files []string, outputFile s
 		args = append(args, ".")
 	}
 
-
 	// For non-SARIF output, let Lizard handle file output directly
 	if outputFormat != "sarif" && outputFile != "" {
 		args = append(args, "-o", outputFile)
 	}
 
-
 	// Run the command
 	cmd := exec.Command(binary, args...)
 	cmd.Dir = workDirectory
 
-
 	var err error
 	var stderr bytes.Buffer
-	
+
 	cmd.Stderr = &stderr
-	
+
 	// For SARIF output, we need to capture and parse the output
 	if outputFormat == "sarif" {
 		var stdout bytes.Buffer

tools/runnerUtils.go

@@ -21,10 +21,10 @@ func ConfigFileExists(conf config.ConfigType, fileNames ...string) (string, bool
 		generatedConfigFile := filepath.Join(conf.ToolsConfigDirectory(), fileName)
 		existingConfigFile := filepath.Join(conf.RepositoryDirectory(), fileName)
 
-		if _, err := os.Stat(generatedConfigFile); err == nil {
-			return generatedConfigFile, true
-		} else if _, err := os.Stat(existingConfigFile); err == nil {
+		if _, err := os.Stat(existingConfigFile); err == nil {
 			return existingConfigFile, true
+		} else if _, err := os.Stat(generatedConfigFile); err == nil {
+			return generatedConfigFile, true
 		}
 	}
 

tools/runnerUtils_test.go

@@ -61,37 +61,6 @@ func TestConfigFileExistsInRepositoryDirectory(t *testing.T) {
 		"Config path should be correctly formed relative path")
 }
 
-func TestConfigFilePrefersToolsConfigDirectory(t *testing.T) {
-	// Create a test directory structure
-	tempDir := t.TempDir()
-	repoDir := filepath.Join(tempDir, "src")
-	repositoryCache := filepath.Join(repoDir, ".codacy")
-
-	// Create configuration
-	config := *config.NewConfigType(repoDir, repositoryCache, "unused-global-cache")
-
-	// Create .codacy/tools-configs directory
-	configDir := filepath.Join(repoDir, ".codacy", "tools-configs")
-	err := os.MkdirAll(configDir, 0755)
-	assert.NoError(t, err, "Failed to create test directory structure")
-
-	// Create a test config file in both locations
-	generatedConfigFile := filepath.Join(configDir, "some-config.yaml")
-	existingConfigFile := filepath.Join(repoDir, "some-config.yaml")
-
-	err = os.WriteFile(generatedConfigFile, []byte("tools config content"), 0644)
-	assert.NoError(t, err, "Failed to create test config file in tools config directory")
-
-	err = os.WriteFile(existingConfigFile, []byte("repository config content"), 0644)
-	assert.NoError(t, err, "Failed to create test config file in repository directory")
-
-	// Test case: Config file in tools config directory is preferred
-	configPath, exists := ConfigFileExists(config, "some-config.yaml")
-	assert.True(t, exists, "Config file should exist")
-	assert.Equal(t, filepath.Join(config.ToolsConfigDirectory(), "some-config.yaml"), configPath,
-		"Config path should prefer tools config directory")
-}
-
 func TestConfigFileDoesNotExist(t *testing.T) {
 	// Create a test directory structure
 	tempDir := t.TempDir()