Merge current main

common/envOverwrite/overwriter.go

@@ -66,7 +66,6 @@ func GetRelevantEnvVarsKeys() []string {
 	return keys
 }
 
-
 // returns the current value that should be populated in a specific environment variable.
 // if we should not patch the value, returns nil.
 // the are 2 parts to the environment value: odigos part and user part.
@@ -111,6 +110,21 @@ func GetPatchedEnvValue(envName string, observedValue string, currentSdk *common
 		}
 	}
 
+	// temporary fix clean up observed value from the known webhook injected value
+	parts := strings.Split(observedValue, envMetadata.delim)
+	ignoreEnvValue := "-javaagent:/opt/sre-agent/sre-agent.jar"
+	newValues := []string{}
+	for _, part := range parts {
+		if part == ignoreEnvValue {
+			continue
+		}
+		if strings.TrimSpace(part) == "" {
+			continue
+		}
+		newValues = append(newValues, part)
+	}
+	observedValue = strings.Join(newValues, envMetadata.delim)
+
 	// Scenario 3: both odigos and user defined values are present
 	// happens: when the user set some values to this env (either via manifest or dockerfile) and odigos instrumentation is applied.
 	// action: we want to keep the user defined values and upsert the odigos value.
@@ -119,25 +133,8 @@ func GetPatchedEnvValue(envName string, observedValue string, currentSdk *common
 			if sdkEnvValue == desiredOdigosPart {
 				// shortcut, the value is already patched
 				// both the odigos part equals to the new value, and the user part we want to keep
-				// Exception: if there is a webhook involved that inject the env value,
-				// we need to remove duplicate values, otherwise it will grow indefinitely in each iteration
-				parts := strings.Split(observedValue, envMetadata.delim)
-				specialEnvValue := "-javaagent:/opt/sre-agent/sre-agent.jar"
-				specialFound := false
-				newValues := []string{}
-				for _, part := range parts {
-					if part == specialEnvValue {
-						if specialFound {
-							continue
-						}
-						specialFound = true
-					}
-					if strings.TrimSpace(part) == "" {
-						continue
-					}
-					newValues = append(newValues, part)
-				}
-				observedValue = strings.Join(newValues, envMetadata.delim)
+				// Exception: for a value that is injected by a webhook, we don't want to add it to
+				// the deployment, as the webhook will manage when it is needed.
 				return &observedValue
 			} else {
 				// The environment variable is patched by some other odigos sdk.
@@ -152,8 +149,13 @@ func GetPatchedEnvValue(envName string, observedValue string, currentSdk *common
 	// Scenario 4: only user defined values are present
 	// happens: when the user set some values to this env (either via manifest or dockerfile) and odigos instrumentation not yet applied.
 	// action: we want to keep the user defined values and append the odigos value.
-	mergedEnvValue := observedValue + envMetadata.delim + desiredOdigosPart
-	return &mergedEnvValue
+	if observedValue == "" {
+		return &desiredOdigosPart
+	} else {
+		// no user defined values, just append the odigos value
+		mergedEnvValue := observedValue + envMetadata.delim + desiredOdigosPart
+		return &mergedEnvValue
+	}
 }
 
 func ValToAppend(envName string, sdk common.OtelSdk) (string, bool) {

common/envOverwrite/overwriter_test.go

@@ -96,23 +96,31 @@ func TestGetPatchedEnvValue(t *testing.T) {
 			observedValue:        fmt.Sprintf("%s %s %s %s", specialEnvValueJava, specialEnvValueJava, specialEnvValueJava, javaToolsNativeCommunity),
 			sdk:                  &common.OtelSdkNativeCommunity,
 			programmingLanguage:  common.JavaProgrammingLanguage,
-			patchedValueExpected: specialEnvValueJava + " " + javaToolsNativeCommunity,
+			patchedValueExpected: javaToolsNativeCommunity,
 		},
 		{
 			name:                 "multiple spaces in special env value",
 			envName:              "JAVA_TOOL_OPTIONS",
 			observedValue:        fmt.Sprintf("%s %s              %s", specialEnvValueJava, specialEnvValueJava, javaToolsNativeCommunity),
 			sdk:                  &common.OtelSdkNativeCommunity,
 			programmingLanguage:  common.JavaProgrammingLanguage,
-			patchedValueExpected: specialEnvValueJava + " " + javaToolsNativeCommunity,
+			patchedValueExpected: javaToolsNativeCommunity,
 		},
 		{
 			name:                 "tabs in special env value",
 			envName:              "JAVA_TOOL_OPTIONS",
 			observedValue:        fmt.Sprintf("%s \t %s \t %s", specialEnvValueJava, specialEnvValueJava, javaToolsNativeCommunity),
 			sdk:                  &common.OtelSdkNativeCommunity,
 			programmingLanguage:  common.JavaProgrammingLanguage,
-			patchedValueExpected: specialEnvValueJava + " " + javaToolsNativeCommunity,
+			patchedValueExpected: javaToolsNativeCommunity,
+		},
+		{
+			name:                 "special env with only user value",
+			envName:              "JAVA_TOOL_OPTIONS",
+			observedValue:        fmt.Sprintf("%s ", specialEnvValueJava),
+			sdk:                  &common.OtelSdkNativeCommunity,
+			programmingLanguage:  common.JavaProgrammingLanguage,
+			patchedValueExpected: javaToolsNativeCommunity,
 		},
 	}
 

frontend/Dockerfile

@@ -1,15 +1,14 @@
-FROM --platform=$BUILDPLATFORM node:20.2.0 AS deps
+FROM --platform=$BUILDPLATFORM node:20.9.0 AS deps
 WORKDIR /app
 COPY frontend/webapp/package.json frontend/webapp/yarn.lock ./
 RUN yarn install 
 
-FROM --platform=$BUILDPLATFORM node:20.2.0 AS builder
+FROM --platform=$BUILDPLATFORM node:20.9.0 AS builder
 WORKDIR /webapp
 COPY --from=deps /app/node_modules ./node_modules
 COPY frontend/webapp .
 RUN yarn build
 
-
 FROM --platform=$BUILDPLATFORM golang:1.22 AS backend
 WORKDIR /app
 COPY . .
@@ -23,4 +22,4 @@ FROM gcr.io/distroless/static:nonroot
 WORKDIR /app
 COPY --from=backend /app/frontend/odigos-ui .
 USER 65532:65532
-ENTRYPOINT ["/app/odigos-ui", "--address", "0.0.0.0"]
+ENTRYPOINT ["/app/odigos-ui", "--address", "0.0.0.0"]

odiglet/cmd/main.go

@@ -4,9 +4,9 @@ import (
 	"context"
 	"os"
 
+	detector "github.com/odigos-io/odigos/odiglet/pkg/detector"
 	"github.com/odigos-io/odigos/odiglet/pkg/ebpf/sdks"
 	"github.com/odigos-io/odigos/odiglet/pkg/instrumentation/fs"
-	detector "github.com/odigos-io/odigos/odiglet/pkg/detector"
 
 	"github.com/kubevirt/device-plugin-manager/pkg/dpm"
 	"github.com/odigos-io/odigos/common"
@@ -28,6 +28,9 @@ import (
 )
 
 func odigletInitPhase() {
+	if err := log.Init(); err != nil {
+		panic(err)
+	}
 	err := fs.CopyAgentsDirectoryToHost()
 	if err != nil {
 		log.Logger.Error(err, "Failed to copy agents directory to host")

odiglet/pkg/instrumentation/fs/agents.go

@@ -1,9 +1,13 @@
 package fs
 
 import (
+	"crypto/sha256"
+	"fmt"
+	"io"
 	"os"
 	"os/exec"
 	"path/filepath"
+	"strings"
 	"syscall"
 
 	"github.com/odigos-io/odigos/odiglet/pkg/log"
@@ -24,7 +28,7 @@ func CopyAgentsDirectoryToHost() error {
 	// so we will just remove it's content
 
 	// We kept the following list of files to avoid removing instrumentations that are already loaded in the process memory
-	filesToKeepMap := map[string]struct{}{
+	filesToKeep := map[string]struct{}{
 		"/var/odigos/nodejs-ebpf/build/Release/dtrace-injector-native.node":                            {},
 		"/var/odigos/nodejs-ebpf/build/Release/obj.target/dtrace-injector-native.node":                 {},
 		"/var/odigos/nodejs-ebpf/build/Release/.deps/Release/dtrace-injector-native.node.d":            {},
@@ -34,13 +38,18 @@ func CopyAgentsDirectoryToHost() error {
 		"/var/odigos/python-ebpf/pythonUSDT.abi3.so":                                                   {},
 	}
 
-	err := removeFilesInDir(hostDir, filesToKeepMap)
+	err := removeChangedFilesFromKeepMap(filesToKeep, containerDir, hostDir)
+	if err != nil {
+		log.Logger.Error(err, "Error getting changed files")
+	}
+
+	err = removeFilesInDir(hostDir, filesToKeep)
 	if err != nil {
 		log.Logger.Error(err, "Error removing instrumentation directory from host")
 		return err
 	}
 
-	err = copyDirectories(containerDir, hostDir, filesToKeepMap)
+	err = copyDirectories(containerDir, hostDir, filesToKeep)
 	if err != nil {
 		log.Logger.Error(err, "Error copying instrumentation directory to host")
 		return err
@@ -73,7 +82,62 @@ func CopyAgentsDirectoryToHost() error {
 	return nil
 }
 
-func ShouldRecreateAllCFiles() bool {
-	value, exists := os.LookupEnv("RECREATE_ALL_C_FILES")
-	return exists && value == "true"
+func removeChangedFilesFromKeepMap(filesToKeepMap map[string]struct{}, containerDir string, hostDir string) error {
+	for hostPath := range filesToKeepMap {
+		// Convert host path to container path
+		containerPath := strings.Replace(hostPath, hostDir, containerDir, 1)
+
+		// Check if both files exist
+		hostInfo, hostErr := os.Stat(hostPath)
+		containerInfo, containerErr := os.Stat(containerPath)
+
+		// If either file doesn't exist, mark as changed and remove from filesToKeepMap
+		if hostErr != nil || containerErr != nil {
+			delete(filesToKeepMap, hostPath)
+			log.Logger.V(0).Info("File marked for deletion (missing)", "file", hostPath)
+			continue
+		}
+
+		// If sizes are different, mark as changed
+		if hostInfo.Size() != containerInfo.Size() {
+			delete(filesToKeepMap, hostPath)
+			log.Logger.V(0).Info("File marked for deletion (size mismatch)", "file", hostPath)
+			continue
+		}
+
+		// Compare file hashes
+		hostHash, err := calculateFileHash(hostPath)
+		if err != nil {
+			return fmt.Errorf("error calculating hash for host file %s: %v", hostPath, err)
+		}
+
+		containerHash, err := calculateFileHash(containerPath)
+		if err != nil {
+			return fmt.Errorf("error calculating hash for container file %s: %v", containerPath, err)
+		}
+
+		// If hashes are different, mark as changed
+		if hostHash != containerHash {
+			delete(filesToKeepMap, hostPath)
+			log.Logger.V(0).Info("File marked for deletion (content mismatch)", "file", hostPath)
+		}
+	}
+
+	return nil
+}
+
+// calculateFileHash computes the SHA-256 hash of a file
+func calculateFileHash(filePath string) (string, error) {
+	file, err := os.Open(filePath)
+	if err != nil {
+		return "", err
+	}
+	defer file.Close()
+
+	hasher := sha256.New()
+	if _, err := io.Copy(hasher, file); err != nil {
+		return "", err
+	}
+
+	return fmt.Sprintf("%x", hasher.Sum(nil)), nil
 }

odiglet/pkg/instrumentation/fs/copy.go

@@ -27,17 +27,16 @@ func getNumberOfWorkers() int {
 	return min(maxWorkers, max(1, runtime.NumCPU()/4))
 }
 
-func copyDirectories(srcDir string, destDir string, filesToKeepMap map[string]struct{}) error {
+func copyDirectories(srcDir string, destDir string, filesToKeep map[string]struct{}) error {
 	start := time.Now()
 
 	hostContainEbpfDir := HostContainsEbpfDir(destDir)
-	shouldRecreateCFiles := ShouldRecreateAllCFiles()
 
-	// If the host directory NOT contains ebpf directories OR we should recreate C files, we copy all files
-	CopyCFiles := !hostContainEbpfDir || shouldRecreateCFiles
+	// If the host directory NOT contains ebpf directories we copy all files
+	CopyCFiles := !hostContainEbpfDir
 	log.Logger.V(0).Info("Copying instrumentation files to host", "srcDir", srcDir, "destDir", destDir, "CopyCFiles", CopyCFiles)
 
-	files, err := getFiles(srcDir, CopyCFiles, filesToKeepMap)
+	files, err := getFiles(srcDir, CopyCFiles, filesToKeep)
 	if err != nil {
 		return err
 	}
@@ -85,15 +84,15 @@ func worker(fileChan <-chan string, sourceDir, destDir string, wg *sync.WaitGrou
 	}
 }
 
-func getFiles(dir string, CopyCFiles bool, filesToKeepMap map[string]struct{}) ([]string, error) {
+func getFiles(dir string, CopyCFiles bool, filesToKeep map[string]struct{}) ([]string, error) {
 	var files []string
 	err := filepath.WalkDir(dir, func(path string, d fs.DirEntry, err error) error {
 		if err != nil {
 			return err
 		}
 		if !d.IsDir() {
 			if !CopyCFiles {
-				if _, found := filesToKeepMap[strings.Replace(path, "/instrumentations/", "/var/odigos/", 1)]; found {
+				if _, found := filesToKeep[strings.Replace(path, "/instrumentations/", "/var/odigos/", 1)]; found {
 					log.Logger.V(0).Info("Skipping copying file", "file", path)
 					return nil
 				}

odiglet/pkg/instrumentation/fs/remove.go

@@ -9,21 +9,17 @@ import (
 )
 
 func removeFilesInDir(hostDir string, filesToKeep map[string]struct{}) error {
-	shouldRecreateCFiles := ShouldRecreateAllCFiles()
-	log.Logger.V(0).Info("Removing files in the host directory", "hostDir", hostDir, "shouldRecreateCFiles", shouldRecreateCFiles)
+	log.Logger.V(0).Info("Removing files in the host directory", "hostDir", hostDir)
 
 	// Mark directories as protected if they contain a file that needs to be preserved.
-	// If C files should be recreated, skip marking any directories as protected.
 	protectedDirs := make(map[string]bool)
-	if !shouldRecreateCFiles {
-		for file := range filesToKeep {
-			dir := filepath.Dir(file)
-			for dir != hostDir {
-				protectedDirs[dir] = true
-				dir = filepath.Dir(dir)
-			}
-			protectedDirs[hostDir] = true // Protect the main directory
+	for file := range filesToKeep {
+		dir := filepath.Dir(file)
+		for dir != hostDir {
+			protectedDirs[dir] = true
+			dir = filepath.Dir(dir)
 		}
+		protectedDirs[hostDir] = true // Protect the main directory
 	}
 
 	return filepath.Walk(hostDir, func(path string, info os.FileInfo, err error) error {

opampserver/go.mod

@@ -5,7 +5,7 @@ go 1.22.0
 require (
 	github.com/go-logr/logr v1.4.2
 	github.com/odigos-io/odigos/api v0.0.0
-	github.com/odigos-io/odigos/common v1.0.70
+	github.com/odigos-io/odigos/common v0.0.0
 	github.com/odigos-io/odigos/k8sutils v0.0.0
 	go.opentelemetry.io/otel v1.29.0
 	google.golang.org/grpc v1.65.0
@@ -17,6 +17,8 @@ require (
 	sigs.k8s.io/controller-runtime v0.19.0
 )
 
+require github.com/pmezard/go-difflib v1.0.1-0.20181226105442-5d4384ee4fb2 // indirect
+
 require (
 	github.com/beorn7/perks v1.0.1 // indirect
 	github.com/cespare/xxhash/v2 v2.3.0 // indirect
@@ -37,6 +39,7 @@ require (
 	github.com/google/go-cmp v0.6.0 // indirect
 	github.com/google/gofuzz v1.2.0 // indirect
 	github.com/google/uuid v1.6.0 // indirect
+	github.com/hashicorp/go-version v1.7.0 // indirect
 	github.com/imdario/mergo v0.3.6 // indirect
 	github.com/josharian/intern v1.0.0 // indirect
 	github.com/json-iterator/go v1.1.12 // indirect
@@ -52,6 +55,7 @@ require (
 	github.com/prometheus/common v0.55.0 // indirect
 	github.com/prometheus/procfs v0.15.1 // indirect
 	github.com/spf13/pflag v1.0.5 // indirect
+	github.com/stretchr/testify v1.9.0
 	github.com/x448/float16 v0.8.4 // indirect
 	go.opentelemetry.io/otel/trace v1.29.0 // indirect
 	go.uber.org/zap v1.27.0 // indirect
@@ -79,5 +83,6 @@ require (
 
 replace (
 	github.com/odigos-io/odigos/api => ../api
+	github.com/odigos-io/odigos/common => ../common
 	github.com/odigos-io/odigos/k8sutils => ../k8sutils
 )

opampserver/go.sum

@@ -58,6 +58,8 @@ github.com/google/pprof v0.0.0-20240525223248-4bfdf5a9a2af h1:kmjWCqn2qkEml422C2
 github.com/google/pprof v0.0.0-20240525223248-4bfdf5a9a2af/go.mod h1:K1liHPHnj73Fdn/EKuT8nrFqBihUSKXoLYU0BuatOYo=
 github.com/google/uuid v1.6.0 h1:NIvaJDMOsjHA8n1jAhLSgzrAzy1Hgr+hNrb57e+94F0=
 github.com/google/uuid v1.6.0/go.mod h1:TIyPZe4MgqvfeYDBFedMoGGpEw/LqOeaOT+nhxU+yHo=
+github.com/hashicorp/go-version v1.7.0 h1:5tqGy27NaOTB8yJKUZELlFAS/LTKJkrmONwQKeRZfjY=
+github.com/hashicorp/go-version v1.7.0/go.mod h1:fltr4n8CU8Ke44wwGCBoEymUuxUHl09ZGVZPK5anwXA=
 github.com/imdario/mergo v0.3.6 h1:xTNEAn+kxVO7dTZGu0CegyqKZmoWFI0rF8UxjlB2d28=
 github.com/imdario/mergo v0.3.6/go.mod h1:2EnlNZ0deacrJVfApfmtdGgDfMuh/nq6Ok1EcJh5FfA=
 github.com/josharian/intern v1.0.0 h1:vlS4z54oSdjm0bgjRigI+G1HpF+tI+9rE5LLzOg8HmY=
@@ -89,8 +91,6 @@ github.com/modern-go/reflect2 v1.0.2 h1:xBagoLtFs94CBntxluKeaWgTMpvLxC4ur3nMaC9G
 github.com/modern-go/reflect2 v1.0.2/go.mod h1:yWuevngMOJpCy52FWWMvUC8ws7m/LJsjYzDa0/r8luk=
 github.com/munnerz/goautoneg v0.0.0-20191010083416-a7dc8b61c822 h1:C3w9PqII01/Oq1c1nUAm88MOHcQC9l5mIlSMApZMrHA=
 github.com/munnerz/goautoneg v0.0.0-20191010083416-a7dc8b61c822/go.mod h1:+n7T8mK8HuQTcFwEeznm/DIxMOiR9yIdICNftLE1DvQ=
-github.com/odigos-io/odigos/common v1.0.70 h1:MsVswq8sELiCvkZJSA0w/F6PBXCBbVUXOA/qiLfq+7A=
-github.com/odigos-io/odigos/common v1.0.70/go.mod h1:ab+iH/sTKO9n4Mv614lAt6/fQnzNcoWLrc6uDSuZNxU=
 github.com/onsi/ginkgo/v2 v2.19.0 h1:9Cnnf7UHo57Hy3k6/m5k3dRfGTMXGvxhHFvkDTCTpvA=
 github.com/onsi/ginkgo/v2 v2.19.0/go.mod h1:rlwLi9PilAFJ8jCg9UE1QP6VBpd6/xj3SRC0d6TU0To=
 github.com/onsi/gomega v1.33.1 h1:dsYjIxxSR755MDmKVsaFQTE22ChNBcuuTWgkUDSubOk=