Merge pull request #959 from suhasgumma/fix-command

fix: keep user formatting when autofixing

core/cautils/scaninfo.go

@@ -419,7 +419,7 @@ func metadataGitLocal(input string) (*reporthandlingv2.RepoContextMetadata, erro
 		Date:          commit.Committer.Date,
 		CommitterName: commit.Committer.Name,
 	}
-	context.LocalRootPath = getAbsPath(input)
+	context.LocalRootPath, _ = gitParser.GetRootDir()
 
 	return context, nil
 }

core/pkg/fixhandler/datastructures.go

@@ -5,6 +5,7 @@ import (
 	metav1 "github.com/kubescape/kubescape/v2/core/meta/datastructures/v1"
 	"github.com/kubescape/opa-utils/reporthandling"
 	reporthandlingv2 "github.com/kubescape/opa-utils/reporthandling/v2"
+	"gopkg.in/yaml.v3"
 )
 
 // FixHandler is a struct that holds the information of the report to be fixed
@@ -19,4 +20,44 @@ type ResourceFixInfo struct {
 	YamlExpressions map[string]*armotypes.FixPath
 	Resource        *reporthandling.Resource
 	FilePath        string
+	DocumentIndex   int
+}
+
+// NodeInfo holds extra information about the node
+type nodeInfo struct {
+	node   *yaml.Node
+	parent *yaml.Node
+
+	// position of the node among siblings
+	index int
+}
+
+// FixInfoMetadata holds the arguments "getFixInfo" function needs to pass to the
+// functions it uses
+type fixInfoMetadata struct {
+	originalList        *[]nodeInfo
+	fixedList           *[]nodeInfo
+	originalListTracker int
+	fixedListTracker    int
+	contentToAdd        *[]contentToAdd
+	linesToRemove       *[]linesToRemove
+}
+
+// ContentToAdd holds the information about where to insert the new changes in the existing yaml file
+type contentToAdd struct {
+	// Line where the fix should be applied to
+	line int
+	// Content is a string representation of the YAML node that describes a suggested fix
+	content string
+}
+
+// LinesToRemove holds the line numbers to remove from the existing yaml file
+type linesToRemove struct {
+	startLine int
+	endLine   int
+}
+
+type fileFixInfo struct {
+	contentsToAdd *[]contentToAdd
+	linesToRemove *[]linesToRemove
 }

core/pkg/fixhandler/fixhandler.go

@@ -145,6 +145,7 @@ func (h *FixHandler) PrepareResourcesToFix() []ResourceFixInfo {
 			FilePath:        absolutePath,
 			Resource:        resourceObj,
 			YamlExpressions: make(map[string]*armotypes.FixPath, 0),
+			DocumentIndex:   documentIndex,
 		}
 
 		for i := range result.AssociatedControls {
@@ -185,19 +186,34 @@ func (h *FixHandler) PrintExpectedChanges(resourcesToFix []ResourceFixInfo) {
 func (h *FixHandler) ApplyChanges(resourcesToFix []ResourceFixInfo) (int, []error) {
 	updatedFiles := make(map[string]bool)
 	errors := make([]error, 0)
-	for _, resourceToFix := range resourcesToFix {
-		singleExpression := reduceYamlExpressions(&resourceToFix)
-		if err := h.applyFixToFile(resourceToFix.FilePath, singleExpression); err != nil {
-			errors = append(errors,
-				fmt.Errorf("failed to fix resource [Name: '%s', Kind: '%s'] in '%s': %w ",
-					resourceToFix.Resource.GetName(),
-					resourceToFix.Resource.GetKind(),
-					resourceToFix.FilePath,
-					err))
+
+	fileYamlExpressions := h.getFileYamlExpressions(resourcesToFix)
+
+	for filepath, yamlExpression := range fileYamlExpressions {
+		fileAsString, err := getFileString(filepath)
+
+		if err != nil {
+			errors = append(errors, err)
+			continue
+		}
+
+		fixedYamlString, err := h.ApplyFixToContent(fileAsString, yamlExpression)
+
+		if err != nil {
+			errors = append(errors, fmt.Errorf("Failed to fix file %s: %w ", filepath, err))
+			continue
 		} else {
-			updatedFiles[resourceToFix.FilePath] = true
+			updatedFiles[filepath] = true
+		}
+
+		err = writeFixesToFile(filepath, fixedYamlString)
+
+		if err != nil {
+			logger.L().Error(fmt.Sprintf("Failed to write fixes to file %s, %v", filepath, err.Error()))
+			errors = append(errors, err)
 		}
 	}
+
 	return len(updatedFiles), errors
 }
 
@@ -215,34 +231,45 @@ func (h *FixHandler) getFilePathAndIndex(filePathWithIndex string) (filePath str
 	}
 }
 
-func (h *FixHandler) applyFixToFile(filePath, yamlExpression string) (cmdError error) {
-	var completedSuccessfully bool
-	writeInPlaceHandler := yqlib.NewWriteInPlaceHandler(filePath)
-	out, err := writeInPlaceHandler.CreateTempFile()
+func (h *FixHandler) ApplyFixToContent(yamlAsString, yamlExpression string) (fixedString string, err error) {
+	yamlLines := strings.Split(yamlAsString, "\n")
+
+	originalRootNodes, err := decodeDocumentRoots(yamlAsString)
+
 	if err != nil {
-		return fmt.Errorf("unable to create a tmp file for in-place YAML update: %s", err)
+		return "", err
 	}
 
-	defer func() {
-		if cmdError == nil {
-			cmdError = writeInPlaceHandler.FinishWriteInPlace(completedSuccessfully)
+	fixedRootNodes, err := getFixedNodes(yamlAsString, yamlExpression)
+
+	if err != nil {
+		return "", err
+	}
+
+	fileFixInfo := getFixInfo(originalRootNodes, fixedRootNodes)
+
+	fixedYamlLines := getFixedYamlLines(yamlLines, fileFixInfo)
+
+	fixedString = getStringFromSlice(fixedYamlLines)
+
+	return fixedString, nil
+}
+
+func (h *FixHandler) getFileYamlExpressions(resourcesToFix []ResourceFixInfo) map[string]string {
+	fileYamlExpressions := make(map[string]string, 0)
+	for _, resourceToFix := range resourcesToFix {
+		singleExpression := reduceYamlExpressions(&resourceToFix)
+		resourceFilePath := resourceToFix.FilePath
+
+		if _, pathExistsInMap := fileYamlExpressions[resourceFilePath]; !pathExistsInMap {
+			fileYamlExpressions[resourceFilePath] = singleExpression
+		} else {
+			fileYamlExpressions[resourceFilePath] = joinStrings(fileYamlExpressions[resourceFilePath], " | ", singleExpression)
 		}
-	}()
 
-	encoder := yqlib.NewYamlEncoder(2, false, yqlib.ConfiguredYamlPreferences)
+	}
 
-	printer := yqlib.NewPrinter(encoder, yqlib.NewSinglePrinterWriter(out))
-	allAtOnceEvaluator := yqlib.NewAllAtOnceEvaluator()
-
-	preferences := yqlib.ConfiguredYamlPreferences
-	preferences.EvaluateTogether = true
-	decoder := yqlib.NewYamlDecoder(preferences)
-
-	err = allAtOnceEvaluator.EvaluateFiles(yamlExpression, []string{filePath}, printer, decoder)
-
-	completedSuccessfully = err == nil
-
-	return err
+	return fileYamlExpressions
 }
 
 func (rfi *ResourceFixInfo) addYamlExpressionsFromResourceAssociatedControl(documentIndex int, ac *resourcesresults.ResourceAssociatedControl, skipUserValues bool) {
@@ -293,3 +320,27 @@ func fixPathToValidYamlExpression(fixPath, value string, documentIndexInYaml int
 	// select document index and add a dot for the root node
 	return fmt.Sprintf("select(di==%d).%s |= %s", documentIndexInYaml, fixPath, value)
 }
+
+func joinStrings(inputStrings ...string) string {
+	return strings.Join(inputStrings, "")
+}
+
+func getFileString(filepath string) (string, error) {
+	bytes, err := ioutil.ReadFile(filepath)
+
+	if err != nil {
+		return "", fmt.Errorf("Error reading file %s", filepath)
+	}
+
+	return string(bytes), nil
+}
+
+func writeFixesToFile(filepath, content string) error {
+	err := ioutil.WriteFile(filepath, []byte(content), 0644)
+
+	if err != nil {
+		return fmt.Errorf("Error writing fixes to file: %w", err)
+	}
+
+	return nil
+}

core/pkg/fixhandler/fixhandler_test.go

@@ -1,20 +1,24 @@
 package fixhandler
 
 import (
-	"io/ioutil"
 	"os"
 	"path/filepath"
 	"testing"
 
-	"github.com/stretchr/testify/assert"
-
 	logger "github.com/kubescape/go-logger"
 	metav1 "github.com/kubescape/kubescape/v2/core/meta/datastructures/v1"
 	reporthandlingv2 "github.com/kubescape/opa-utils/reporthandling/v2"
 	"github.com/mikefarah/yq/v4/pkg/yqlib"
+	"github.com/stretchr/testify/assert"
 	"gopkg.in/op/go-logging.v1"
 )
 
+type indentationTestCase struct {
+	inputFile      string
+	yamlExpression string
+	expectedFile   string
+}
+
 func NewFixHandlerMock() (*FixHandler, error) {
 	backendLoggerLeveled := logging.AddModuleLevel(logging.NewLogBackend(logger.L().GetWriter(), "", 0))
 	backendLoggerLeveled.SetLevel(logging.ERROR, "")
@@ -27,45 +31,172 @@ func NewFixHandlerMock() (*FixHandler, error) {
 	}, nil
 }
 
-func onlineBoutiquePath() string {
-	o, _ := os.Getwd()
-	return filepath.Join(filepath.Dir(o), "..", "..", "examples", "online-boutique")
+func getTestdataPath() string {
+	currentDir, _ := os.Getwd()
+	return filepath.Join(currentDir, "testdata")
 }
 
-func TestFixHandler_applyFixToFile(t *testing.T) {
-	originalFilePath := filepath.Join(onlineBoutiquePath(), "adservice.yaml")
-	// create temp file
-	tempFile, err := ioutil.TempFile("", "adservice.yaml")
-	if err != nil {
-		panic(err)
-	}
-	defer os.Remove(tempFile.Name())
+func getTestCases() []indentationTestCase {
+	indentationTestCases := []indentationTestCase{
+		// Insertion Scenarios
+		{
+			"inserts/tc-01-00-input-mapping-insert-mapping.yaml",
+			"select(di==0).spec.containers[0].securityContext.allowPrivilegeEscalation |= false",
+			"inserts/tc-01-01-expected.yaml",
+		},
+		{
+			"inserts/tc-02-00-input-mapping-insert-mapping-with-list.yaml",
+			"select(di==0).spec.containers[0].securityContext.capabilities.drop += [\"NET_RAW\"]",
+			"inserts/tc-02-01-expected.yaml",
+		},
+		{
+			"inserts/tc-03-00-input-list-append-scalar.yaml",
+			"select(di==0).spec.containers[0].securityContext.capabilities.drop += [\"SYS_ADM\"]",
+			"inserts/tc-03-01-expected.yaml",
+		},
+		{
+			"inserts/tc-04-00-input-multiple-inserts.yaml",
 
-	// read original file
-	b, err := ioutil.ReadFile(originalFilePath)
-	if err != nil {
-		panic(err)
-	}
-	assert.NotContains(t, string(b), "readOnlyRootFilesystem: true")
+			`select(di==0).spec.template.spec.securityContext.allowPrivilegeEscalation |= false |
+			 select(di==0).spec.template.spec.containers[0].securityContext.capabilities.drop += ["NET_RAW"] |
+			 select(di==0).spec.template.spec.containers[0].securityContext.seccompProfile.type |= "RuntimeDefault" |
+			 select(di==0).spec.template.spec.containers[0].securityContext.allowPrivilegeEscalation |= false |
+			 select(di==0).spec.template.spec.containers[0].securityContext.readOnlyRootFilesystem |= true`,
 
-	// write original file contents to temp file
-	err = ioutil.WriteFile(tempFile.Name(), b, 0644)
-	if err != nil {
-		panic(err)
+			"inserts/tc-04-01-expected.yaml",
+		},
+		{
+			"inserts/tc-05-00-input-comment-blank-line-single-insert.yaml",
+			"select(di==0).spec.containers[0].securityContext.allowPrivilegeEscalation |= false",
+			"inserts/tc-05-01-expected.yaml",
+		},
+		{
+			"inserts/tc-06-00-input-list-append-scalar-oneline.yaml",
+			"select(di==0).spec.containers[0].securityContext.capabilities.drop += [\"SYS_ADM\"]",
+			"inserts/tc-06-01-expected.yaml",
+		},
+		{
+			"inserts/tc-07-00-input-multiple-documents.yaml",
+
+			`select(di==0).spec.containers[0].securityContext.allowPrivilegeEscalation |= false |
+			 select(di==1).spec.containers[0].securityContext.allowPrivilegeEscalation |= false`,
+
+			"inserts/tc-07-01-expected.yaml",
+		},
+		{
+			"inserts/tc-08-00-input-mapping-insert-mapping-indented.yaml",
+			"select(di==0).spec.containers[0].securityContext.capabilities.drop += [\"NET_RAW\"]",
+			"inserts/tc-08-01-expected.yaml",
+		},
+		{
+			"inserts/tc-09-00-input-list-insert-new-mapping-indented.yaml",
+			`select(di==0).spec.containers += {"name": "redis", "image": "redis"}`,
+			"inserts/tc-09-01-expected.yaml",
+		},
+		{
+			"inserts/tc-10-00-input-list-insert-new-mapping.yaml",
+			`select(di==0).spec.containers += {"name": "redis", "image": "redis"}`,
+			"inserts/tc-10-01-expected.yaml",
+		},
+
+		// Removal Scenarios
+		{
+			"removals/tc-01-00-input.yaml",
+			"del(select(di==0).spec.containers[0].securityContext)",
+			"removals/tc-01-01-expected.yaml",
+		},
+		{
+			"removals/tc-02-00-input.yaml",
+			"del(select(di==0).spec.containers[1])",
+			"removals/tc-02-01-expected.yaml",
+		},
+		{
+			"removals/tc-03-00-input.yaml",
+			"del(select(di==0).spec.containers[0].securityContext.capabilities.drop[1])",
+			"removals/tc-03-01-expected.yaml",
+		},
+		{
+			"removes/tc-04-00-input.yaml",
+			`del(select(di==0).spec.containers[0].securityContext) | 
+			 del(select(di==1).spec.containers[1])`,
+			"removes/tc-04-01-expected.yaml",
+		},
+
+		// Replace Scenarios
+		{
+			"replaces/tc-01-00-input.yaml",
+			"select(di==0).spec.containers[0].securityContext.runAsRoot |= false",
+			"replaces/tc-01-01-expected.yaml",
+		},
+		{
+			"replaces/tc-02-00-input.yaml",
+			`select(di==0).spec.containers[0].securityContext.capabilities.drop[0] |= "SYS_ADM" |
+			 select(di==0).spec.containers[0].securityContext.capabilities.add[0] |= "NET_RAW"`,
+			"replaces/tc-02-01-expected.yaml",
+		},
+
+		// Hybrid Scenarios
+		{
+			"hybrids/tc-01-00-input.yaml",
+			`del(select(di==0).spec.containers[0].securityContext) |
+			 select(di==0).spec.securityContext.runAsRoot |= false`,
+			"hybrids/tc-01-01-expected.yaml",
+		},
+		{
+			"hybrids/tc-02-00-input-indented-list.yaml",
+			`del(select(di==0).spec.containers[0].securityContext) |
+			 select(di==0).spec.securityContext.runAsRoot |= false`,
+			"hybrids/tc-02-01-expected.yaml",
+		},
+		{
+			"hybrids/tc-03-00-input-comments.yaml",
+			`del(select(di==0).spec.containers[0].securityContext) |
+			 select(di==0).spec.securityContext.runAsRoot |= false`,
+			"hybrids/tc-03-01-expected.yaml",
+		},
+		{
+			"hybrids/tc-04-00-input-separated-keys.yaml",
+			`del(select(di==0).spec.containers[0].securityContext) |
+			 select(di==0).spec.securityContext.runAsRoot |= false`,
+			"hybrids/tc-04-01-expected.yaml",
+		},
 	}
 
-	// make changes to temp file
-	h, _ := NewFixHandlerMock()
-	yamlExpression := "select(di==0).spec.template.spec.containers[0].securityContext.readOnlyRootFilesystem |= true"
-	err = h.applyFixToFile(tempFile.Name(), yamlExpression)
-	assert.NoError(t, err)
+	return indentationTestCases
+}
+
+func TestApplyFixKeepsFormatting(t *testing.T) {
+	testCases := getTestCases()
+
+	for _, tc := range testCases {
+		t.Run(tc.inputFile, func(t *testing.T) {
+			getTestDataPath := func(filename string) string {
+				currentDir, _ := os.Getwd()
+				currentFile := "testdata/" + filename
+				return filepath.Join(currentDir, currentFile)
+			}
+
+			input, _ := os.ReadFile(getTestDataPath(tc.inputFile))
+			wantRaw, _ := os.ReadFile(getTestDataPath(tc.expectedFile))
+			want := string(wantRaw)
+			expression := tc.yamlExpression
+
+			h, _ := NewFixHandlerMock()
+
+			got, _ := h.ApplyFixToContent(string(input), expression)
+
+			assert.Equalf(
+				t, want, got,
+				"Contents of the fixed file don't match the expectation.\n"+
+					"Input file: %s\n\n"+
+					"Got: <%s>\n\n"+
+					"Want: <%s>",
+				tc.inputFile, got, want,
+			)
+		},
+		)
 
-	// Check temp file contents
-	b, err = ioutil.ReadFile(tempFile.Name())
-	if err != nil {
-		panic(err)
 	}
-	assert.Contains(t, string(b), "readOnlyRootFilesystem: true")
 }
 
 func Test_fixPathToValidYamlExpression(t *testing.T) {

core/pkg/fixhandler/testdata/hybrids/tc-01-00-input.yaml

@@ -0,0 +1,19 @@
+# Fix to Apply:
+# REMOVE:
+# "del(select(di==0).spec.containers[0].securityContext)"
+
+# INSERT:
+# select(di==0).spec.securityContext.runAsRoot: false
+
+
+apiVersion: v1
+kind: Pod
+metadata:
+  name: insert_to_mapping_node_1
+
+spec:
+  containers:
+  - name: nginx_container
+    image: nginx
+    securityContext:
+      runAsRoot: true

core/pkg/fixhandler/testdata/hybrids/tc-01-01-expected.yaml

@@ -0,0 +1,19 @@
+# Fix to Apply:
+# REMOVE:
+# "del(select(di==0).spec.containers[0].securityContext)"
+
+# INSERT:
+# select(di==0).spec.securityContext.runAsRoot: false
+
+
+apiVersion: v1
+kind: Pod
+metadata:
+  name: insert_to_mapping_node_1
+
+spec:
+  containers:
+  - name: nginx_container
+    image: nginx
+  securityContext:
+    runAsRoot: false

core/pkg/fixhandler/testdata/hybrids/tc-02-00-input-indented-list.yaml

@@ -0,0 +1,19 @@
+# Fix to Apply:
+# REMOVE:
+# "del(select(di==0).spec.containers[0].securityContext)"
+
+# INSERT:
+# select(di==0).spec.securityContext.runAsRoot: false
+
+
+apiVersion: v1
+kind: Pod
+metadata:
+  name: insert_to_mapping_node_1
+
+spec:
+  containers:
+    - name: nginx_container
+      image: nginx
+      securityContext:
+        runAsRoot: true

core/pkg/fixhandler/testdata/hybrids/tc-02-01-expected.yaml

@@ -0,0 +1,19 @@
+# Fix to Apply:
+# REMOVE:
+# "del(select(di==0).spec.containers[0].securityContext)"
+
+# INSERT:
+# select(di==0).spec.securityContext.runAsRoot: false
+
+
+apiVersion: v1
+kind: Pod
+metadata:
+  name: insert_to_mapping_node_1
+
+spec:
+  containers:
+    - name: nginx_container
+      image: nginx
+  securityContext:
+    runAsRoot: false

core/pkg/fixhandler/testdata/hybrids/tc-03-00-input-comments.yaml

@@ -0,0 +1,21 @@
+# Fix to Apply:
+# REMOVE:
+# "del(select(di==0).spec.containers[0].securityContext)"
+
+# INSERT:
+# select(di==0).spec.securityContext.runAsRoot: false
+
+
+apiVersion: v1
+kind: Pod
+metadata:
+  name: insert_to_mapping_node_1
+
+spec:
+  # These are the container comments
+  containers:
+    # These are the first containers comments
+    - name: nginx_container
+      image: nginx
+      securityContext:
+        runAsRoot: true

core/pkg/fixhandler/testdata/hybrids/tc-03-01-expected.yaml

@@ -0,0 +1,21 @@
+# Fix to Apply:
+# REMOVE:
+# "del(select(di==0).spec.containers[0].securityContext)"
+
+# INSERT:
+# select(di==0).spec.securityContext.runAsRoot: false
+
+
+apiVersion: v1
+kind: Pod
+metadata:
+  name: insert_to_mapping_node_1
+
+spec:
+  # These are the container comments
+  containers:
+    # These are the first containers comments
+    - name: nginx_container
+      image: nginx
+  securityContext:
+    runAsRoot: false

core/pkg/fixhandler/testdata/hybrids/tc-04-00-input-separated-keys.yaml

@@ -0,0 +1,21 @@
+# Fix to Apply:
+# REMOVE:
+# "del(select(di==0).spec.containers[0].securityContext)"
+
+# INSERT:
+# select(di==0).spec.securityContext.runAsRoot: false
+
+
+apiVersion: v1
+kind: Pod
+metadata:
+  name: insert_to_mapping_node_1
+
+spec:
+  containers:
+    - name: nginx_container
+
+      image: nginx
+
+      securityContext:
+        runAsRoot: true

core/pkg/fixhandler/testdata/hybrids/tc-04-01-expected.yaml

@@ -0,0 +1,21 @@
+# Fix to Apply:
+# REMOVE:
+# "del(select(di==0).spec.containers[0].securityContext)"
+
+# INSERT:
+# select(di==0).spec.securityContext.runAsRoot: false
+
+
+apiVersion: v1
+kind: Pod
+metadata:
+  name: insert_to_mapping_node_1
+
+spec:
+  containers:
+    - name: nginx_container
+
+      image: nginx
+  securityContext:
+    runAsRoot: false
+

core/pkg/fixhandler/testdata/inserts/tc-01-00-input-mapping-insert-mapping.yaml

@@ -0,0 +1,12 @@
+# Fix to Apply:
+# "select(di==0).spec.containers[0].securityContext.allowPrivilegeEscalation |= false"
+
+apiVersion: v1
+kind: Pod
+metadata:
+  name: insert_to_mapping_node_1
+
+spec:
+  containers:
+  - name: nginx_container
+    image: nginx

core/pkg/fixhandler/testdata/inserts/tc-01-01-expected.yaml

@@ -0,0 +1,14 @@
+# Fix to Apply:
+# "select(di==0).spec.containers[0].securityContext.allowPrivilegeEscalation |= false"
+
+apiVersion: v1
+kind: Pod
+metadata:
+  name: insert_to_mapping_node_1
+
+spec:
+  containers:
+  - name: nginx_container
+    image: nginx
+    securityContext:
+      allowPrivilegeEscalation: false

core/pkg/fixhandler/testdata/inserts/tc-02-00-input-mapping-insert-mapping-with-list.yaml

@@ -0,0 +1,11 @@
+# Fix to Apply:
+# select(di==0).spec.containers[0].securityContext.capabilities.drop += ["NET_RAW"]
+
+apiVersion: v1
+kind: Pod
+metadata:
+  name: insert_list
+spec:
+  containers:
+  - name: nginx_container
+    image: nginx

core/pkg/fixhandler/testdata/inserts/tc-02-01-expected.yaml

@@ -0,0 +1,15 @@
+# Fix to Apply:
+# select(di==0).spec.containers[0].securityContext.capabilities.drop += ["NET_RAW"]
+
+apiVersion: v1
+kind: Pod
+metadata:
+  name: insert_list
+spec:
+  containers:
+  - name: nginx_container
+    image: nginx
+    securityContext:
+      capabilities:
+        drop:
+          - NET_RAW

core/pkg/fixhandler/testdata/inserts/tc-03-00-input-list-append-scalar.yaml

@@ -0,0 +1,15 @@
+# Fix to Apply:
+# select(di==0).spec.containers[0].securityContext.capabilities.drop += ["SYS_ADM"]
+
+apiVersion: v1
+kind: Pod
+metadata:
+  name: insert_list
+spec:
+  containers:
+  - name: nginx_container
+    image: nginx
+    securityContext:
+      capabilities:
+        drop:
+        - NET_RAW

core/pkg/fixhandler/testdata/inserts/tc-03-01-expected.yaml

@@ -0,0 +1,16 @@
+# Fix to Apply:
+# select(di==0).spec.containers[0].securityContext.capabilities.drop += ["SYS_ADM"]
+
+apiVersion: v1
+kind: Pod
+metadata:
+  name: insert_list
+spec:
+  containers:
+  - name: nginx_container
+    image: nginx
+    securityContext:
+      capabilities:
+        drop:
+        - NET_RAW
+        - SYS_ADM

core/pkg/fixhandler/testdata/inserts/tc-04-00-input-multiple-inserts.yaml

@@ -0,0 +1,47 @@
+# Fixes to Apply:
+# 1) select(di==0).spec.template.spec.securityContext.allowPrivilegeEscalation = false
+# 2) select(di==0).spec.template.spec.containers[0].securityContext.capabilities.drop += ["NET_RAW"]
+# 3) select(di==0).spec.template.spec.containers[0].securityContext.seccompProfile.type = RuntimeDefault
+# 4) select(di==0).spec.template.spec.containers[0].securityContext.allowPrivilegeEscalation |= false
+# 5) select(di==0).spec.template.spec.containers[0].securityContext.readOnlyRootFilesystem |= true
+
+apiVersion: apps/v1
+kind: Deployment
+metadata:
+  name: multiple_inserts
+spec:
+  selector:
+    matchLabels:
+      app: example_4
+  template:
+    metadata:
+      labels:
+        app: example_4
+    spec:
+      serviceAccountName: default
+      terminationGracePeriodSeconds: 5
+      containers:
+      - name: example_4
+        image: nginx
+        ports:
+        - containerPort: 3000
+        env:
+        - name: PORT
+          value: "3000"
+        resources:
+          requests:
+            cpu: 200m
+            memory: 180Mi
+          limits:
+            cpu: 300m
+            memory: 300Mi
+        readinessProbe:
+          initialDelaySeconds: 20
+          periodSeconds: 15
+          exec:
+            command: ["/bin/grpc_health_probe", "-addr=:3000"]
+        livenessProbe:
+          initialDelaySeconds: 20
+          periodSeconds: 15
+          exec:
+            command: ["/bin/grpc_health_probe", "-addr=:3000"]

core/pkg/fixhandler/testdata/inserts/tc-04-01-expected.yaml

@@ -0,0 +1,57 @@
+# Fixes to Apply:
+# 1) select(di==0).spec.template.spec.securityContext.allowPrivilegeEscalation = false
+# 2) select(di==0).spec.template.spec.containers[0].securityContext.capabilities.drop += ["NET_RAW"]
+# 3) select(di==0).spec.template.spec.containers[0].securityContext.seccompProfile.type = RuntimeDefault
+# 4) select(di==0).spec.template.spec.containers[0].securityContext.allowPrivilegeEscalation |= false
+# 5) select(di==0).spec.template.spec.containers[0].securityContext.readOnlyRootFilesystem |= true
+
+apiVersion: apps/v1
+kind: Deployment
+metadata:
+  name: multiple_inserts
+spec:
+  selector:
+    matchLabels:
+      app: example_4
+  template:
+    metadata:
+      labels:
+        app: example_4
+    spec:
+      serviceAccountName: default
+      terminationGracePeriodSeconds: 5
+      containers:
+      - name: example_4
+        image: nginx
+        ports:
+        - containerPort: 3000
+        env:
+        - name: PORT
+          value: "3000"
+        resources:
+          requests:
+            cpu: 200m
+            memory: 180Mi
+          limits:
+            cpu: 300m
+            memory: 300Mi
+        readinessProbe:
+          initialDelaySeconds: 20
+          periodSeconds: 15
+          exec:
+            command: ["/bin/grpc_health_probe", "-addr=:3000"]
+        livenessProbe:
+          initialDelaySeconds: 20
+          periodSeconds: 15
+          exec:
+            command: ["/bin/grpc_health_probe", "-addr=:3000"]
+        securityContext:
+          capabilities:
+            drop:
+              - NET_RAW
+          seccompProfile:
+            type: RuntimeDefault
+          allowPrivilegeEscalation: false
+          readOnlyRootFilesystem: true
+      securityContext:
+        allowPrivilegeEscalation: false

core/pkg/fixhandler/testdata/inserts/tc-05-00-input-comment-blank-line-single-insert.yaml

@@ -0,0 +1,16 @@
+# Fix to Apply:
+# "select(di==0).spec.containers[0].securityContext.allowPrivilegeEscalation |= false"
+
+apiVersion: v1
+kind: Pod
+metadata:
+  name: insert_to_mapping_node_1
+
+spec:
+  containers:
+  - name: nginx_container
+    image: nginx
+
+  # Testing if comments are retained as intended
+  securityContext:
+    runAsRoot: false

core/pkg/fixhandler/testdata/inserts/tc-05-01-expected.yaml

@@ -0,0 +1,18 @@
+# Fix to Apply:
+# "select(di==0).spec.containers[0].securityContext.allowPrivilegeEscalation |= false"
+
+apiVersion: v1
+kind: Pod
+metadata:
+  name: insert_to_mapping_node_1
+
+spec:
+  containers:
+  - name: nginx_container
+    image: nginx
+    securityContext:
+      allowPrivilegeEscalation: false
+
+  # Testing if comments are retained as intended
+  securityContext:
+    runAsRoot: false

core/pkg/fixhandler/testdata/inserts/tc-06-00-input-list-append-scalar-oneline.yaml

@@ -0,0 +1,14 @@
+# Fix to Apply:
+# select(di==0).spec.containers[0].securityContext.capabilities.drop += ["SYS_ADM"]
+
+apiVersion: v1
+kind: Pod
+metadata:
+  name: insert_list
+spec:
+  containers:
+  - name: nginx1
+    image: nginx
+    securityContext:
+      capabilities:
+        drop: [NET_RAW]

core/pkg/fixhandler/testdata/inserts/tc-06-01-expected.yaml

@@ -0,0 +1,14 @@
+# Fix to Apply:
+# select(di==0).spec.containers[0].securityContext.capabilities.drop += ["SYS_ADM"]
+
+apiVersion: v1
+kind: Pod
+metadata:
+  name: insert_list
+spec:
+  containers:
+  - name: nginx1
+    image: nginx
+    securityContext:
+      capabilities:
+        drop: [NET_RAW, SYS_ADM]

core/pkg/fixhandler/testdata/inserts/tc-07-00-input-multiple-documents.yaml

@@ -0,0 +1,27 @@
+# Fix to Apply:
+# "select(di==0).spec.containers[0].securityContext.allowPrivilegeEscalation |= false"
+
+apiVersion: v1
+kind: Pod
+metadata:
+  name: insert_to_mapping_node_1
+
+spec:
+  containers:
+  - name: nginx_container
+    image: nginx
+
+---
+
+# Fix to Apply:
+# "select(di==1).spec.containers[0].securityContext.allowPrivilegeEscalation |= false"
+
+apiVersion: v1
+kind: Pod
+metadata:
+  name: insert_to_mapping_node_1
+
+spec:
+  containers:
+  - name: nginx_container
+    image: nginx

core/pkg/fixhandler/testdata/inserts/tc-07-01-expected.yaml

@@ -0,0 +1,31 @@
+# Fix to Apply:
+# "select(di==0).spec.containers[0].securityContext.allowPrivilegeEscalation |= false"
+
+apiVersion: v1
+kind: Pod
+metadata:
+  name: insert_to_mapping_node_1
+
+spec:
+  containers:
+  - name: nginx_container
+    image: nginx
+    securityContext:
+      allowPrivilegeEscalation: false
+
+---
+
+# Fix to Apply:
+# "select(di==1).spec.containers[0].securityContext.allowPrivilegeEscalation |= false"
+
+apiVersion: v1
+kind: Pod
+metadata:
+  name: insert_to_mapping_node_1
+
+spec:
+  containers:
+  - name: nginx_container
+    image: nginx
+    securityContext:
+      allowPrivilegeEscalation: false

core/pkg/fixhandler/testdata/inserts/tc-08-00-input-mapping-insert-mapping-indented.yaml

@@ -0,0 +1,11 @@
+# Fix to Apply:
+# select(di==0).spec.containers[0].securityContext.capabilities.drop += ["NET_RAW"]
+
+apiVersion: v1
+kind: Pod
+metadata:
+  name: indented-parent-list-insert-list-value
+spec:
+  containers:
+    - name: nginx_container
+      image: nginx

core/pkg/fixhandler/testdata/inserts/tc-08-01-expected.yaml

@@ -0,0 +1,15 @@
+# Fix to Apply:
+# select(di==0).spec.containers[0].securityContext.capabilities.drop += ["NET_RAW"]
+
+apiVersion: v1
+kind: Pod
+metadata:
+  name: indented-parent-list-insert-list-value
+spec:
+  containers:
+    - name: nginx_container
+      image: nginx
+      securityContext:
+        capabilities:
+          drop:
+            - NET_RAW

core/pkg/fixhandler/testdata/inserts/tc-09-00-input-list-insert-new-mapping-indented.yaml

@@ -0,0 +1,11 @@
+# Fix to Apply:
+# select(di==0).spec.containers += {"name": "redis", "image": "redis"}
+
+apiVersion: v1
+kind: Pod
+metadata:
+  name: indented-parent-list-insert-list-value
+spec:
+  containers:
+    - name: nginx_container
+      image: nginx

core/pkg/fixhandler/testdata/inserts/tc-09-01-expected.yaml

@@ -0,0 +1,13 @@
+# Fix to Apply:
+# select(di==0).spec.containers += {"name": "redis", "image": "redis"}
+
+apiVersion: v1
+kind: Pod
+metadata:
+  name: indented-parent-list-insert-list-value
+spec:
+  containers:
+    - name: nginx_container
+      image: nginx
+    - name: redis
+      image: redis

core/pkg/fixhandler/testdata/inserts/tc-10-00-input-list-insert-new-mapping.yaml

@@ -0,0 +1,11 @@
+# Fix to Apply:
+# select(di==0).spec.containers += {"name": "redis", "image": "redis"}
+
+apiVersion: v1
+kind: Pod
+metadata:
+  name: indented-list-insert-new-object
+spec:
+  containers:
+  - name: nginx_container
+    image: nginx

core/pkg/fixhandler/testdata/inserts/tc-10-01-expected.yaml

@@ -0,0 +1,13 @@
+# Fix to Apply:
+# select(di==0).spec.containers += {"name": "redis", "image": "redis"}
+
+apiVersion: v1
+kind: Pod
+metadata:
+  name: indented-list-insert-new-object
+spec:
+  containers:
+  - name: nginx_container
+    image: nginx
+  - name: redis
+    image: redis

core/pkg/fixhandler/testdata/removals/tc-01-00-input.yaml

@@ -0,0 +1,14 @@
+# Fix to Apply:
+# del(select(di==0).spec.containers[0].securityContext)
+
+apiVersion: v1
+kind: Pod
+metadata:
+  name: remove_example
+
+spec:
+  containers:
+  - name: nginx_container
+    image: nginx
+    securityContext:
+      runAsRoot: false

core/pkg/fixhandler/testdata/removals/tc-01-01-expected.yaml

@@ -0,0 +1,12 @@
+# Fix to Apply:
+# del(select(di==0).spec.containers[0].securityContext)
+
+apiVersion: v1
+kind: Pod
+metadata:
+  name: remove_example
+
+spec:
+  containers:
+  - name: nginx_container
+    image: nginx

core/pkg/fixhandler/testdata/removals/tc-02-00-input.yaml

@@ -0,0 +1,15 @@
+# Fix to Apply:
+# del(select(di==0).spec.containers[1])
+
+apiVersion: v1
+kind: Pod
+metadata:
+  name: remove_example
+
+spec:
+  containers:
+  - name: nginx_container
+    image: nginx
+
+  - name: container_with_security_issues
+    image: image_with_security_issues

core/pkg/fixhandler/testdata/removals/tc-02-01-expected.yaml

@@ -0,0 +1,12 @@
+# Fix to Apply:
+# del(select(di==0).spec.containers[1])
+
+apiVersion: v1
+kind: Pod
+metadata:
+  name: remove_example
+
+spec:
+  containers:
+  - name: nginx_container
+    image: nginx

core/pkg/fixhandler/testdata/removals/tc-03-00-input.yaml

@@ -0,0 +1,14 @@
+# Fix to Apply:
+# del(select(di==0).spec.containers[0].securityContext.capabilities.drop[1])
+
+apiVersion: v1
+kind: Pod
+metadata:
+  name: insert_list
+spec:
+  containers:
+  - name: nginx1
+    image: nginx
+    securityContext:
+      capabilities:
+        drop: ["NET_RAW", "SYS_ADM"]

core/pkg/fixhandler/testdata/removals/tc-03-01-expected.yaml

@@ -0,0 +1,14 @@
+# Fix to Apply:
+# del(select(di==0).spec.containers[0].securityContext.capabilities.drop[1])
+
+apiVersion: v1
+kind: Pod
+metadata:
+  name: insert_list
+spec:
+  containers:
+  - name: nginx1
+    image: nginx
+    securityContext:
+      capabilities:
+        drop: ["NET_RAW"]

core/pkg/fixhandler/testdata/removals/tc-04-00-input.yaml

@@ -0,0 +1,32 @@
+# Fix to Apply:
+# del(select(di==0).spec.containers[0].securityContext)
+
+apiVersion: v1
+kind: Pod
+metadata:
+  name: remove_example
+
+spec:
+  containers:
+  - name: nginx_container
+    image: nginx
+    securityContext:
+      runAsRoot: false
+
+---
+
+# Fix to Apply:
+# del(select(di==0).spec.containers[1])
+
+apiVersion: v1
+kind: Pod
+metadata:
+  name: remove_example
+
+spec:
+  containers:
+  - name: nginx_container
+    image: nginx
+
+  - name: container_with_security_issues
+    image: image_with_security_issues

core/pkg/fixhandler/testdata/removals/tc-04-01-expected.yaml

@@ -0,0 +1,27 @@
+# Fix to Apply:
+# del(select(di==0).spec.containers[0].securityContext)
+
+apiVersion: v1
+kind: Pod
+metadata:
+  name: remove_example
+
+spec:
+  containers:
+  - name: nginx_container
+    image: nginx
+
+---
+
+# Fix to Apply:
+# del(select(di==0).spec.containers[1])
+
+apiVersion: v1
+kind: Pod
+metadata:
+  name: remove_example
+
+spec:
+  containers:
+  - name: nginx_container
+    image: nginx

core/pkg/fixhandler/testdata/replaces/tc-01-00-input.yaml

@@ -0,0 +1,14 @@
+# Fix to Apply:
+# "select(di==0).spec.containers[0].securityContext.runAsRoot |= false"
+
+apiVersion: v1
+kind: Pod
+metadata:
+  name: insert_to_mapping_node_1
+
+spec:
+  containers:
+  - name: nginx_container
+    image: nginx
+    securityContext:
+      runAsRoot: true

core/pkg/fixhandler/testdata/replaces/tc-01-01-expected.yaml

@@ -0,0 +1,14 @@
+# Fix to Apply:
+# "select(di==0).spec.containers[0].securityContext.runAsRoot |= false"
+
+apiVersion: v1
+kind: Pod
+metadata:
+  name: insert_to_mapping_node_1
+
+spec:
+  containers:
+  - name: nginx_container
+    image: nginx
+    securityContext:
+      runAsRoot: false

core/pkg/fixhandler/testdata/replaces/tc-02-00-input.yaml

@@ -0,0 +1,18 @@
+# Fix to Apply:
+# select(di==0).spec.containers[0].securityContext.capabilities.drop[0] |= "SYS_ADM"
+# select(di==0).spec.containers[0].securityContext.capabilities.add[0] |= "NET_RAW"
+
+
+apiVersion: v1
+kind: Pod
+metadata:
+  name: insert_list
+spec:
+  containers:
+  - name: nginx1
+    image: nginx
+    securityContext:
+      capabilities:
+        drop:
+        - "NET_RAW"
+        add: ["SYS_ADM"]

core/pkg/fixhandler/testdata/replaces/tc-02-01-expected.yaml

@@ -0,0 +1,18 @@
+# Fix to Apply:
+# select(di==0).spec.containers[0].securityContext.capabilities.drop[0] |= "SYS_ADM"
+# select(di==0).spec.containers[0].securityContext.capabilities.add[0] |= "NET_RAW"
+
+
+apiVersion: v1
+kind: Pod
+metadata:
+  name: insert_list
+spec:
+  containers:
+  - name: nginx1
+    image: nginx
+    securityContext:
+      capabilities:
+        drop:
+        - "SYS_ADM"
+        add: ["NET_RAW"]

core/pkg/fixhandler/yamlhandler.go

@@ -0,0 +1,286 @@
+package fixhandler
+
+import (
+	"container/list"
+	"errors"
+	"fmt"
+	"io"
+	"strings"
+
+	"github.com/mikefarah/yq/v4/pkg/yqlib"
+
+	"gopkg.in/yaml.v3"
+)
+
+// decodeDocumentRoots decodes all YAML documents stored in a given `filepath` and returns a slice of their root nodes
+func decodeDocumentRoots(yamlAsString string) ([]yaml.Node, error) {
+	fileReader := strings.NewReader(yamlAsString)
+	dec := yaml.NewDecoder(fileReader)
+
+	nodes := make([]yaml.Node, 0)
+	for {
+		var node yaml.Node
+		err := dec.Decode(&node)
+
+		nodes = append(nodes, node)
+
+		if errors.Is(err, io.EOF) {
+			break
+		}
+		if err != nil {
+			return nil, fmt.Errorf("Cannot Decode File as YAML")
+
+		}
+	}
+
+	return nodes, nil
+}
+
+func getFixedNodes(yamlAsString, yamlExpression string) ([]yaml.Node, error) {
+	preferences := yqlib.ConfiguredYamlPreferences
+	preferences.EvaluateTogether = true
+	decoder := yqlib.NewYamlDecoder(preferences)
+
+	var allDocuments = list.New()
+	reader := strings.NewReader(yamlAsString)
+
+	fileDocuments, err := readDocuments(reader, decoder)
+	if err != nil {
+		return nil, err
+	}
+	allDocuments.PushBackList(fileDocuments)
+
+	allAtOnceEvaluator := yqlib.NewAllAtOnceEvaluator()
+
+	fixedCandidateNodes, err := allAtOnceEvaluator.EvaluateCandidateNodes(yamlExpression, allDocuments)
+
+	if err != nil {
+		return nil, fmt.Errorf("Error fixing YAML, %w", err)
+	}
+
+	fixedNodes := make([]yaml.Node, 0)
+	var fixedNode *yaml.Node
+	for fixedCandidateNode := fixedCandidateNodes.Front(); fixedCandidateNode != nil; fixedCandidateNode = fixedCandidateNode.Next() {
+		fixedNode = fixedCandidateNode.Value.(*yqlib.CandidateNode).Node
+		fixedNodes = append(fixedNodes, *fixedNode)
+	}
+
+	return fixedNodes, nil
+}
+
+func flattenWithDFS(node *yaml.Node) *[]nodeInfo {
+	dfsOrder := make([]nodeInfo, 0)
+	flattenWithDFSHelper(node, nil, &dfsOrder, 0)
+	return &dfsOrder
+}
+
+func flattenWithDFSHelper(node *yaml.Node, parent *yaml.Node, dfsOrder *[]nodeInfo, index int) {
+	dfsNode := nodeInfo{
+		node:   node,
+		parent: parent,
+		index:  index,
+	}
+	*dfsOrder = append(*dfsOrder, dfsNode)
+
+	for idx, child := range node.Content {
+		flattenWithDFSHelper(child, node, dfsOrder, idx)
+	}
+}
+
+func getFixInfo(originalRootNodes, fixedRootNodes []yaml.Node) fileFixInfo {
+	contentToAdd := make([]contentToAdd, 0)
+	linesToRemove := make([]linesToRemove, 0)
+
+	for idx := 0; idx < len(fixedRootNodes); idx++ {
+		originalList := flattenWithDFS(&originalRootNodes[idx])
+		fixedList := flattenWithDFS(&fixedRootNodes[idx])
+		nodeContentToAdd, nodeLinesToRemove := getFixInfoHelper(*originalList, *fixedList)
+		contentToAdd = append(contentToAdd, nodeContentToAdd...)
+		linesToRemove = append(linesToRemove, nodeLinesToRemove...)
+	}
+
+	return fileFixInfo{
+		contentsToAdd: &contentToAdd,
+		linesToRemove: &linesToRemove,
+	}
+}
+
+func getFixInfoHelper(originalList, fixedList []nodeInfo) ([]contentToAdd, []linesToRemove) {
+
+	// While obtaining fixedYamlNode, comments and empty lines at the top are ignored.
+	// This causes a difference in Line numbers across the tree structure. In order to
+	// counter this, line numbers are adjusted in fixed list.
+	adjustFixedListLines(&originalList, &fixedList)
+
+	contentToAdd := make([]contentToAdd, 0)
+	linesToRemove := make([]linesToRemove, 0)
+
+	originalListTracker, fixedListTracker := 0, 0
+
+	fixInfoMetadata := &fixInfoMetadata{
+		originalList:        &originalList,
+		fixedList:           &fixedList,
+		originalListTracker: originalListTracker,
+		fixedListTracker:    fixedListTracker,
+		contentToAdd:        &contentToAdd,
+		linesToRemove:       &linesToRemove,
+	}
+
+	for originalListTracker < len(originalList) && fixedListTracker < len(fixedList) {
+		matchNodeResult := matchNodes(originalList[originalListTracker].node, fixedList[fixedListTracker].node)
+
+		fixInfoMetadata.originalListTracker = originalListTracker
+		fixInfoMetadata.fixedListTracker = fixedListTracker
+
+		switch matchNodeResult {
+		case sameNodes:
+			originalListTracker += 1
+			fixedListTracker += 1
+
+		case removedNode:
+			originalListTracker, fixedListTracker = addLinesToRemove(fixInfoMetadata)
+
+		case insertedNode:
+			originalListTracker, fixedListTracker = addLinesToInsert(fixInfoMetadata)
+
+		case replacedNode:
+			originalListTracker, fixedListTracker = updateLinesToReplace(fixInfoMetadata)
+		}
+	}
+
+	// Some nodes are still not visited if they are removed at the end of the list
+	for originalListTracker < len(originalList) {
+		fixInfoMetadata.originalListTracker = originalListTracker
+		originalListTracker, _ = addLinesToRemove(fixInfoMetadata)
+	}
+
+	// Some nodes are still not visited if they are inserted at the end of the list
+	for fixedListTracker < len(fixedList) {
+		// Use negative index of last node in original list as a placeholder to determine the last line number later
+		fixInfoMetadata.originalListTracker = -(len(originalList) - 1)
+		fixInfoMetadata.fixedListTracker = fixedListTracker
+		_, fixedListTracker = addLinesToInsert(fixInfoMetadata)
+	}
+
+	return contentToAdd, linesToRemove
+
+}
+
+// Adds the lines to remove and returns the updated originalListTracker
+func addLinesToRemove(fixInfoMetadata *fixInfoMetadata) (int, int) {
+	isOneLine, line := isOneLineSequenceNode(fixInfoMetadata.originalList, fixInfoMetadata.originalListTracker)
+
+	if isOneLine {
+		// Remove the entire line and replace it with the sequence node in fixed info. This way,
+		// the original formatting is not lost.
+		return replaceSingleLineSequence(fixInfoMetadata, line)
+	}
+
+	currentDFSNode := (*fixInfoMetadata.originalList)[fixInfoMetadata.originalListTracker]
+
+	newOriginalListTracker := updateTracker(fixInfoMetadata.originalList, fixInfoMetadata.originalListTracker)
+	*fixInfoMetadata.linesToRemove = append(*fixInfoMetadata.linesToRemove, linesToRemove{
+		startLine: currentDFSNode.node.Line,
+		endLine:   getNodeLine(fixInfoMetadata.originalList, newOriginalListTracker),
+	})
+
+	return newOriginalListTracker, fixInfoMetadata.fixedListTracker
+}
+
+// Adds the lines to insert and returns the updated fixedListTracker
+func addLinesToInsert(fixInfoMetadata *fixInfoMetadata) (int, int) {
+
+	isOneLine, line := isOneLineSequenceNode(fixInfoMetadata.fixedList, fixInfoMetadata.fixedListTracker)
+
+	if isOneLine {
+		return replaceSingleLineSequence(fixInfoMetadata, line)
+	}
+
+	currentDFSNode := (*fixInfoMetadata.fixedList)[fixInfoMetadata.fixedListTracker]
+
+	lineToInsert := getLineToInsert(fixInfoMetadata)
+	contentToInsert := getContent(currentDFSNode.parent, fixInfoMetadata.fixedList, fixInfoMetadata.fixedListTracker)
+
+	newFixedTracker := updateTracker(fixInfoMetadata.fixedList, fixInfoMetadata.fixedListTracker)
+
+	*fixInfoMetadata.contentToAdd = append(*fixInfoMetadata.contentToAdd, contentToAdd{
+		line:    lineToInsert,
+		content: contentToInsert,
+	})
+
+	return fixInfoMetadata.originalListTracker, newFixedTracker
+}
+
+// Adds the lines to remove and insert and updates the fixedListTracker and originalListTracker
+func updateLinesToReplace(fixInfoMetadata *fixInfoMetadata) (int, int) {
+
+	isOneLine, line := isOneLineSequenceNode(fixInfoMetadata.fixedList, fixInfoMetadata.fixedListTracker)
+
+	if isOneLine {
+		return replaceSingleLineSequence(fixInfoMetadata, line)
+	}
+
+	currentDFSNode := (*fixInfoMetadata.fixedList)[fixInfoMetadata.fixedListTracker]
+
+	// If only the value node is changed, entire "key-value" pair is replaced
+	if isValueNodeinMapping(&currentDFSNode) {
+		fixInfoMetadata.originalListTracker -= 1
+		fixInfoMetadata.fixedListTracker -= 1
+	}
+
+	addLinesToRemove(fixInfoMetadata)
+	updatedOriginalTracker, updatedFixedTracker := addLinesToInsert(fixInfoMetadata)
+
+	return updatedOriginalTracker, updatedFixedTracker
+}
+
+func removeNewLinesAtTheEnd(yamlLines []string) []string {
+	for idx := 1; idx < len(yamlLines); idx++ {
+		if yamlLines[len(yamlLines)-idx] != "\n" {
+			yamlLines = yamlLines[:len(yamlLines)-idx+1]
+			break
+		}
+	}
+	return yamlLines
+}
+
+func getFixedYamlLines(yamlLines []string, fileFixInfo fileFixInfo) (fixedYamlLines []string) {
+
+	// Determining last line requires original yaml lines slice. The placeholder for last line is replaced with the real last line
+	assignLastLine(fileFixInfo.contentsToAdd, fileFixInfo.linesToRemove, &yamlLines)
+
+	removeLines(fileFixInfo.linesToRemove, &yamlLines)
+
+	fixedYamlLines = make([]string, 0)
+	lineIdx, lineToAddIdx := 1, 0
+
+	// Ideally, new node is inserted at line before the next node in DFS order. But, when the previous line contains a
+	// comment or empty line, we need to insert new nodes before them.
+	adjustContentLines(fileFixInfo.contentsToAdd, &yamlLines)
+
+	for lineToAddIdx < len(*fileFixInfo.contentsToAdd) {
+		for lineIdx <= (*fileFixInfo.contentsToAdd)[lineToAddIdx].line {
+			// Check if the current line is not removed
+			if yamlLines[lineIdx-1] != "*" {
+				fixedYamlLines = append(fixedYamlLines, yamlLines[lineIdx-1])
+			}
+			lineIdx += 1
+		}
+
+		content := (*fileFixInfo.contentsToAdd)[lineToAddIdx].content
+		fixedYamlLines = append(fixedYamlLines, content)
+
+		lineToAddIdx += 1
+	}
+
+	for lineIdx <= len(yamlLines) {
+		if yamlLines[lineIdx-1] != "*" {
+			fixedYamlLines = append(fixedYamlLines, yamlLines[lineIdx-1])
+		}
+		lineIdx += 1
+	}
+
+	fixedYamlLines = removeNewLinesAtTheEnd(fixedYamlLines)
+
+	return fixedYamlLines
+}

core/pkg/fixhandler/yamlhelper.go

@@ -0,0 +1,406 @@
+package fixhandler
+
+import (
+	"bufio"
+	"bytes"
+	"container/list"
+	"errors"
+	"fmt"
+	"io"
+	"math"
+	"os"
+	"strings"
+
+	logger "github.com/kubescape/go-logger"
+	"github.com/mikefarah/yq/v4/pkg/yqlib"
+	"gopkg.in/yaml.v3"
+)
+
+type NodeRelation int
+
+const (
+	sameNodes NodeRelation = iota
+	insertedNode
+	removedNode
+	replacedNode
+)
+
+func matchNodes(nodeOne, nodeTwo *yaml.Node) NodeRelation {
+
+	isNewNode := nodeTwo.Line == 0 && nodeTwo.Column == 0
+	sameLines := nodeOne.Line == nodeTwo.Line
+	sameColumns := nodeOne.Column == nodeTwo.Column
+
+	isSameNode := isSameNode(nodeOne, nodeTwo)
+
+	switch {
+	case isSameNode:
+		return sameNodes
+	case isNewNode:
+		return insertedNode
+	case sameLines && sameColumns:
+		return replacedNode
+	default:
+		return removedNode
+	}
+}
+
+func adjustContentLines(contentToAdd *[]contentToAdd, linesSlice *[]string) {
+	for contentIdx, content := range *contentToAdd {
+		line := content.line
+
+		// Adjust line numbers such that there are no "empty lines or comment lines of next nodes" before them
+		for idx := line - 1; idx >= 0; idx-- {
+			if isEmptyLineOrComment((*linesSlice)[idx]) {
+				(*contentToAdd)[contentIdx].line -= 1
+			} else {
+				break
+			}
+		}
+	}
+}
+
+func adjustFixedListLines(originalList, fixedList *[]nodeInfo) {
+	differenceAtTop := (*originalList)[0].node.Line - (*fixedList)[0].node.Line
+
+	if differenceAtTop <= 0 {
+		return
+	}
+
+	for _, node := range *fixedList {
+		// line numbers should not be changed for new nodes.
+		if node.node.Line != 0 {
+			node.node.Line += differenceAtTop
+		}
+	}
+
+	return
+
+}
+
+func enocodeIntoYaml(parentNode *yaml.Node, nodeList *[]nodeInfo, tracker int) (string, error) {
+	content := make([]*yaml.Node, 0)
+	currentNode := (*nodeList)[tracker].node
+	content = append(content, currentNode)
+
+	// Add the value in "key-value" pair to construct if the parent is mapping node
+	if parentNode.Kind == yaml.MappingNode {
+		valueNode := (*nodeList)[tracker+1].node
+		content = append(content, valueNode)
+	}
+
+	// The parent is added at the top to encode into YAML
+	parentForContent := yaml.Node{
+		Kind:    parentNode.Kind,
+		Content: content,
+	}
+
+	buf := new(bytes.Buffer)
+
+	encoder := yaml.NewEncoder(buf)
+	encoder.SetIndent(2)
+
+	errorEncoding := encoder.Encode(parentForContent)
+	if errorEncoding != nil {
+		return "", fmt.Errorf("Error debugging node, %v", errorEncoding.Error())
+	}
+	errorClosingEncoder := encoder.Close()
+	if errorClosingEncoder != nil {
+		return "", fmt.Errorf("Error closing encoder: %v", errorClosingEncoder.Error())
+	}
+	return fmt.Sprintf(`%v`, buf.String()), nil
+}
+
+func getContent(parentNode *yaml.Node, nodeList *[]nodeInfo, tracker int) string {
+	content, err := enocodeIntoYaml(parentNode, nodeList, tracker)
+	if err != nil {
+		logger.L().Fatal("Cannot Encode into YAML")
+	}
+
+	indentationSpaces := parentNode.Column - 1
+
+	content = indentContent(content, indentationSpaces)
+
+	return strings.TrimSuffix(content, "\n")
+}
+
+func indentContent(content string, indentationSpaces int) string {
+	indentedContent := ""
+	indentSpaces := strings.Repeat(" ", indentationSpaces)
+
+	scanner := bufio.NewScanner(strings.NewReader(content))
+	for scanner.Scan() {
+		line := scanner.Text()
+		indentedContent += (indentSpaces + line + "\n")
+	}
+	return indentedContent
+}
+
+func getLineToInsert(fixInfoMetadata *fixInfoMetadata) int {
+	var lineToInsert int
+	// Check if lineToInsert is last line
+	if fixInfoMetadata.originalListTracker < 0 {
+		originalListTracker := int(math.Abs(float64(fixInfoMetadata.originalListTracker)))
+		// Storing the negative value of line of last node as a placeholder to determine the last line later.
+		lineToInsert = -(*fixInfoMetadata.originalList)[originalListTracker].node.Line
+	} else {
+		lineToInsert = (*fixInfoMetadata.originalList)[fixInfoMetadata.originalListTracker].node.Line - 1
+	}
+	return lineToInsert
+}
+
+func assignLastLine(contentsToAdd *[]contentToAdd, linesToRemove *[]linesToRemove, linesSlice *[]string) {
+	for idx, contentToAdd := range *contentsToAdd {
+		if contentToAdd.line < 0 {
+			currentLine := int(math.Abs(float64(contentToAdd.line)))
+			(*contentsToAdd)[idx].line, _ = getLastLineOfResource(linesSlice, currentLine)
+		}
+	}
+
+	for idx, lineToRemove := range *linesToRemove {
+		if lineToRemove.endLine < 0 {
+			endLine, _ := getLastLineOfResource(linesSlice, lineToRemove.startLine)
+			(*linesToRemove)[idx].endLine = endLine
+		}
+	}
+}
+
+func getLastLineOfResource(linesSlice *[]string, currentLine int) (int, error) {
+	// Get lastlines of all resources...
+	lastLinesOfResources := make([]int, 0)
+	for lineNumber, lineContent := range *linesSlice {
+		if lineContent == "---" {
+			for lastLine := lineNumber - 1; lastLine >= 0; lastLine-- {
+				if !isEmptyLineOrComment((*linesSlice)[lastLine]) {
+					lastLinesOfResources = append(lastLinesOfResources, lastLine+1)
+					break
+				}
+			}
+		}
+	}
+
+	lastLine := len(*linesSlice)
+	for lastLine >= 0 {
+		if !isEmptyLineOrComment((*linesSlice)[lastLine-1]) {
+			lastLinesOfResources = append(lastLinesOfResources, lastLine)
+			break
+		} else {
+			lastLine--
+		}
+	}
+
+	// Get last line of the resource we need
+	for _, endLine := range lastLinesOfResources {
+		if currentLine <= endLine {
+			return endLine, nil
+		}
+	}
+
+	return 0, fmt.Errorf("Provided line is greater than the length of YAML file")
+}
+
+func getNodeLine(nodeList *[]nodeInfo, tracker int) int {
+	if tracker < len(*nodeList) {
+		return (*nodeList)[tracker].node.Line
+	} else {
+		return -1
+	}
+}
+
+// Checks if the node is value node in "key-value" pairs of mapping node
+func isValueNodeinMapping(node *nodeInfo) bool {
+	if node.parent.Kind == yaml.MappingNode && node.index%2 != 0 {
+		return true
+	}
+	return false
+}
+
+// Checks if the node is part of single line sequence node and returns the line
+func isOneLineSequenceNode(list *[]nodeInfo, currentTracker int) (bool, int) {
+	parentNode := (*list)[currentTracker].parent
+	if parentNode.Kind != yaml.SequenceNode {
+		return false, -1
+	}
+
+	var currentNode, prevNode nodeInfo
+	currentTracker -= 1
+
+	for (*list)[currentTracker].node != parentNode {
+		currentNode = (*list)[currentTracker]
+		prevNode = (*list)[currentTracker-1]
+
+		if currentNode.node.Line != prevNode.node.Line {
+			return false, -1
+		}
+		currentTracker -= 1
+	}
+
+	parentNodeInfo := (*list)[currentTracker]
+
+	if parentNodeInfo.parent.Kind == yaml.MappingNode {
+		keyNodeInfo := (*list)[currentTracker-1]
+		if keyNodeInfo.node.Line == parentNode.Line {
+			return true, parentNode.Line
+		} else {
+			return false, -1
+		}
+	} else {
+		if parentNodeInfo.parent.Line == parentNode.Line {
+			return true, parentNode.Line
+		} else {
+			return false, -1
+		}
+	}
+}
+
+// Checks if nodes are of same kind, value, line and column
+func isSameNode(nodeOne, nodeTwo *yaml.Node) bool {
+	sameLines := nodeOne.Line == nodeTwo.Line
+	sameColumns := nodeOne.Column == nodeTwo.Column
+	sameKinds := nodeOne.Kind == nodeTwo.Kind
+	sameValues := nodeOne.Value == nodeTwo.Value
+
+	return sameKinds && sameValues && sameLines && sameColumns
+}
+
+// Checks if the line is empty or a comment
+func isEmptyLineOrComment(lineContent string) bool {
+	lineContent = strings.TrimSpace(lineContent)
+	if lineContent == "" {
+		return true
+	} else if lineContent[0:1] == "#" {
+		return true
+	}
+	return false
+}
+
+func readDocuments(reader io.Reader, decoder yqlib.Decoder) (*list.List, error) {
+	err := decoder.Init(reader)
+	if err != nil {
+		return nil, fmt.Errorf("Error Initializing the decoder, %w", err)
+	}
+	inputList := list.New()
+
+	var currentIndex uint
+
+	for {
+		candidateNode, errorReading := decoder.Decode()
+
+		if errors.Is(errorReading, io.EOF) {
+			switch reader := reader.(type) {
+			case *os.File:
+				safelyCloseFile(reader)
+			}
+			return inputList, nil
+		} else if errorReading != nil {
+			return nil, fmt.Errorf("Error Decoding YAML file, %w", errorReading)
+		}
+
+		candidateNode.Document = currentIndex
+		candidateNode.EvaluateTogether = true
+
+		inputList.PushBack(candidateNode)
+
+		currentIndex = currentIndex + 1
+	}
+}
+
+func safelyCloseFile(file *os.File) {
+	err := file.Close()
+	if err != nil {
+		logger.L().Error("Error Closing File")
+	}
+}
+
+// Remove the entire line and replace it with the sequence node in fixed info. This way,
+// the original formatting is lost.
+func replaceSingleLineSequence(fixInfoMetadata *fixInfoMetadata, line int) (int, int) {
+	originalListTracker := getFirstNodeInLine(fixInfoMetadata.originalList, line)
+	fixedListTracker := getFirstNodeInLine(fixInfoMetadata.fixedList, line)
+
+	currentDFSNode := (*fixInfoMetadata.fixedList)[fixedListTracker]
+	contentToInsert := getContent(currentDFSNode.parent, fixInfoMetadata.fixedList, fixedListTracker)
+
+	// Remove the Single line
+	*fixInfoMetadata.linesToRemove = append(*fixInfoMetadata.linesToRemove, linesToRemove{
+		startLine: line,
+		endLine:   line,
+	})
+
+	// Encode entire Sequence Node and Insert
+	*fixInfoMetadata.contentToAdd = append(*fixInfoMetadata.contentToAdd, contentToAdd{
+		line:    line,
+		content: contentToInsert,
+	})
+
+	originalListTracker = updateTracker(fixInfoMetadata.originalList, originalListTracker)
+	fixedListTracker = updateTracker(fixInfoMetadata.fixedList, fixedListTracker)
+
+	return originalListTracker, fixedListTracker
+}
+
+// Returns the first node in the given line that is not mapping node
+func getFirstNodeInLine(list *[]nodeInfo, line int) int {
+	tracker := 0
+
+	currentNode := (*list)[tracker].node
+	for currentNode.Line != line || currentNode.Kind == yaml.MappingNode {
+		tracker += 1
+		currentNode = (*list)[tracker].node
+	}
+
+	return tracker
+}
+
+// To not mess with the line number while inserting, removed lines are not deleted but replaced with "*"
+func removeLines(linesToRemove *[]linesToRemove, linesSlice *[]string) {
+	var startLine, endLine int
+	for _, lineToRemove := range *linesToRemove {
+		startLine = lineToRemove.startLine - 1
+		endLine = lineToRemove.endLine - 1
+
+		for line := startLine; line <= endLine; line++ {
+			lineContent := (*linesSlice)[line]
+			// When determining the endLine, empty lines and comments which are not intended to be removed are included.
+			// To deal with that, we need to refrain from removing empty lines and comments
+			if isEmptyLineOrComment(lineContent) {
+				break
+			}
+			(*linesSlice)[line] = "*"
+		}
+	}
+}
+
+// Skips the current node including it's children in DFS order and returns the new tracker.
+func skipCurrentNode(node *yaml.Node, currentTracker int) int {
+	updatedTracker := currentTracker + getChildrenCount(node)
+	return updatedTracker
+}
+
+func getChildrenCount(node *yaml.Node) int {
+	totalChildren := 1
+	for _, child := range node.Content {
+		totalChildren += getChildrenCount(child)
+	}
+	return totalChildren
+}
+
+// The current node along with it's children is skipped and the tracker is moved to next sibling
+// of current node. If parent is mapping node, "value" in "key-value" pairs is also skipped.
+func updateTracker(nodeList *[]nodeInfo, tracker int) int {
+	currentNode := (*nodeList)[tracker]
+	var updatedTracker int
+
+	if currentNode.parent.Kind == yaml.MappingNode {
+		valueNode := (*nodeList)[tracker+1]
+		updatedTracker = skipCurrentNode(valueNode.node, tracker+1)
+	} else {
+		updatedTracker = skipCurrentNode(currentNode.node, tracker)
+	}
+
+	return updatedTracker
+}
+
+func getStringFromSlice(yamlLines []string) (fixedYamlString string) {
+	return strings.Join(yamlLines, "\n")
+}

core/pkg/resourcehandler/filesloader.go

@@ -103,6 +103,8 @@ func getResourcesFromPath(path string) (map[string]reporthandling.Source, []work
 	gitRepo, err := cautils.NewLocalGitRepository(path)
 	if err == nil && gitRepo != nil {
 		repoRoot, _ = gitRepo.GetRootDir()
+	} else {
+		repoRoot, _ = filepath.Abs(path)
 	}
 
 	// load resource from local file system
@@ -141,7 +143,7 @@ func getResourcesFromPath(path string) (map[string]reporthandling.Source, []work
 		}
 
 		workloadSource := reporthandling.Source{
-			RelativePath: source,
+			RelativePath: relSource,
 			FileType:     filetype,
 			LastCommit:   lastCommit,
 		}