change the parsing library for yaml case

ATTRIBUTIONS-Go.md

@@ -1484,7 +1484,7 @@ Subdependencies:
 * `golang.org/x/net`
 * `golang.org/x/text`
 * `gopkg.in/inf.v0`
-* `gopkg.in/yaml.v2`
+* `github.com/goccy/go-yaml`
 * `k8s.io/klog/v2`
 * `k8s.io/utils`
 * `sigs.k8s.io/json`
@@ -3179,7 +3179,7 @@ THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
 OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 ```
 
-### gopkg.in/yaml.v2
+### github.com/goccy/go-yaml
 
 License Identifier: Apache-2.0
 License Text:
@@ -4864,7 +4864,7 @@ Subdependencies:
 * `google.golang.org/genproto/googleapis/api`
 * `google.golang.org/genproto/googleapis/rpc`
 * `google.golang.org/protobuf`
-* `gopkg.in/yaml.v2`
+* `github.com/goccy/go-yaml`
 
 ### github.com/dustin/go-humanize
 
@@ -8180,7 +8180,7 @@ Subdependencies:
 * `golang.org/x/text`
 * `google.golang.org/genproto/googleapis/rpc`
 * `gopkg.in/inf.v0`
-* `gopkg.in/yaml.v2`
+* `github.com/goccy/go-yaml`
 * `k8s.io/klog/v2`
 * `k8s.io/utils`
 * `sigs.k8s.io/json`
@@ -9056,7 +9056,7 @@ Subdependencies:
 * `google.golang.org/genproto/googleapis/api`
 * `google.golang.org/protobuf`
 * `gopkg.in/inf.v0`
-* `gopkg.in/yaml.v2`
+* `github.com/goccy/go-yaml`
 * `gopkg.in/yaml.v3`
 * `k8s.io/api`
 * `k8s.io/klog/v2`
@@ -22970,7 +22970,7 @@ Subdependencies:
 * `google.golang.org/protobuf`
 * `gopkg.in/evanphx/json-patch.v4`
 * `gopkg.in/inf.v0`
-* `gopkg.in/yaml.v2`
+* `github.com/goccy/go-yaml`
 * `gopkg.in/yaml.v3`
 * `k8s.io/component-base`
 * `k8s.io/gengo/v2`

deploy/cloud/operator/go.mod

@@ -11,6 +11,7 @@ require (
 	github.com/awslabs/amazon-ecr-credential-helper/ecr-login v0.9.1
 	github.com/bsm/gomega v1.27.10
 	github.com/chrismellard/docker-credential-acr-env v0.0.0-20230304212654-82a0ddb27589
+	github.com/goccy/go-yaml v1.18.0
 	github.com/google/go-cmp v0.7.0
 	github.com/google/go-containerregistry v0.20.5
 	github.com/huandu/xstrings v1.4.0
@@ -22,7 +23,6 @@ require (
 	github.com/sergeymakinen/go-quote v1.1.0
 	github.com/sirupsen/logrus v1.9.3
 	go.etcd.io/etcd/client/v3 v3.5.16
-	gopkg.in/yaml.v2 v2.4.0
 	istio.io/api v1.23.1
 	istio.io/client-go v1.23.1
 	k8s.io/api v0.32.3

deploy/cloud/operator/go.sum

@@ -111,6 +111,8 @@ github.com/go-openapi/swag v0.23.0 h1:vsEVJDUo2hPJ2tu0/Xc+4noaxyEffXNIs3cOULZ+Gr
 github.com/go-openapi/swag v0.23.0/go.mod h1:esZ8ITTYEsH1V2trKHjAN8Ai7xHb8RV+YSZ577vPjgQ=
 github.com/go-task/slim-sprig/v3 v3.0.0 h1:sUs3vkvUymDpBKi3qH1YSqBQk9+9D/8M2mN1vB6EwHI=
 github.com/go-task/slim-sprig/v3 v3.0.0/go.mod h1:W848ghGpv3Qj3dhTPRyJypKRiqCdHZiAzKg9hl15HA8=
+github.com/goccy/go-yaml v1.18.0 h1:8W7wMFS12Pcas7KU+VVkaiCng+kG8QiFeFwzFb+rwuw=
+github.com/goccy/go-yaml v1.18.0/go.mod h1:XBurs7gK8ATbW4ZPGKgcbrY1Br56PdM69F7LkFRi1kA=
 github.com/godbus/dbus/v5 v5.0.4/go.mod h1:xhWf0FNVPg57R7Z0UbKHbJfkEywrmjJnf7w5xrFpKfA=
 github.com/gogo/protobuf v1.3.2 h1:Ov1cvc58UF3b5XjBnZv7+opcTcQFZebYjWzi34vdm4Q=
 github.com/gogo/protobuf v1.3.2/go.mod h1:P1XiOD3dCwIKUDQYPy72D8LYyHL2YPYrpS2s69NZV8Q=
@@ -310,8 +312,6 @@ gopkg.in/evanphx/json-patch.v4 v4.12.0 h1:n6jtcsulIzXPJaxegRbvFNNrZDjbij7ny3gmSP
 gopkg.in/evanphx/json-patch.v4 v4.12.0/go.mod h1:p8EYWUEYMpynmqDbY58zCKCFZw8pRWMG4EsWvDvM72M=
 gopkg.in/inf.v0 v0.9.1 h1:73M5CoZyi3ZLMOyDlQh031Cx6N9NDJ2Vvfl76EDAgDc=
 gopkg.in/inf.v0 v0.9.1/go.mod h1:cWUDdTG/fYaXco+Dcufb5Vnc6Gp2YChqWtbxRZE0mXw=
-gopkg.in/yaml.v2 v2.4.0 h1:D8xgwECY7CYvx+Y2n4sBz93Jn9JRvxdiyyo8CTfuKaY=
-gopkg.in/yaml.v2 v2.4.0/go.mod h1:RDklbk79AGWmwhnvt/jBztapEOGDOx6ZbXqjP6csGnQ=
 gopkg.in/yaml.v3 v3.0.0-20200313102051-9f266ea9e77c/go.mod h1:K4uyk7z7BCEPqu6E+C64Yfv1cQ7kz7rIZviUmN+EgEM=
 gopkg.in/yaml.v3 v3.0.1 h1:fxVm/GzAzEWqLHuvctI91KS9hhNmmWOoWu0XTYJS7CA=
 gopkg.in/yaml.v3 v3.0.1/go.mod h1:K4uyk7z7BCEPqu6E+C64Yfv1cQ7kz7rIZviUmN+EgEM=

deploy/cloud/operator/internal/controller/dynamocomponent_controller.go

@@ -40,6 +40,7 @@ import (
 	"github.com/apparentlymart/go-shquot/shquot"
 	"github.com/awslabs/amazon-ecr-credential-helper/ecr-login"
 	"github.com/chrismellard/docker-credential-acr-env/pkg/credhelper"
+	"github.com/goccy/go-yaml"
 	"github.com/google/go-containerregistry/pkg/authn"
 	"github.com/google/go-containerregistry/pkg/name"
 	"github.com/google/go-containerregistry/pkg/v1/google"
@@ -49,7 +50,6 @@ import (
 	"github.com/rs/xid"
 	"github.com/sergeymakinen/go-quote/unix"
 	"github.com/sirupsen/logrus"
-	"gopkg.in/yaml.v2"
 	batchv1 "k8s.io/api/batch/v1"
 	corev1 "k8s.io/api/core/v1"
 	k8serrors "k8s.io/apimachinery/pkg/api/errors"

deploy/cloud/operator/internal/dynamo/graph.go

@@ -42,7 +42,7 @@ import (
 	"sigs.k8s.io/controller-runtime/pkg/log"
 
 	"github.com/ai-dynamo/dynamo/deploy/cloud/operator/internal/archive"
-	"gopkg.in/yaml.v2"
+	"github.com/goccy/go-yaml"
 )
 
 const (
@@ -237,7 +237,25 @@ func ParseDynamoGraphConfig(ctx context.Context, yamlContent *bytes.Buffer) (*Dy
 	logger := log.FromContext(ctx)
 	logger.Info("trying to parse dynamo graph config", "yamlContent", yamlContent.String())
 	err := yaml.Unmarshal(yamlContent.Bytes(), &config)
-	return &config, err
+	if err != nil {
+		return nil, err
+	}
+
+	// Add debug logging for ExtraPodSpec
+	for _, service := range config.Services {
+		if service.Config.ExtraPodSpec != nil {
+			extraPodSpecBytes, err := json.MarshalIndent(service.Config.ExtraPodSpec, "", "  ")
+			if err != nil {
+				logger.Error(err, "failed to marshal ExtraPodSpec for logging", "service", service.Name)
+			} else {
+				logger.Info("Parsed ExtraPodSpec for service", "service", service.Name, "ExtraPodSpec", string(extraPodSpecBytes))
+			}
+		} else {
+			logger.Info("No ExtraPodSpec found for service", "service", service.Name)
+		}
+	}
+
+	return &config, nil
 }
 
 func ParseDynDeploymentConfig(ctx context.Context, jsonContent []byte) (DynDeploymentConfig, error) {
@@ -371,15 +389,6 @@ func GenerateDynamoComponentsDeployments(ctx context.Context, parentDynamoGraphD
 			deployment.Spec.Autoscaling.MinReplicas = service.Config.Autoscaling.MinReplicas
 			deployment.Spec.Autoscaling.MaxReplicas = service.Config.Autoscaling.MaxReplicas
 		}
-
-		// override the component config with the component config that is in the parent deployment
-		if configOverride, ok := parentDynamoGraphDeployment.Spec.Services[service.Name]; ok {
-			err := mergo.Merge(&deployment.Spec.DynamoComponentDeploymentSharedSpec, configOverride.DynamoComponentDeploymentSharedSpec, mergo.WithOverride)
-			if err != nil {
-				return nil, err
-			}
-		}
-
 		// Override command and args if provided.
 		if service.Config.ExtraPodSpec != nil && service.Config.ExtraPodSpec.MainContainer != nil {
 			if deployment.Spec.DynamoComponentDeploymentSharedSpec.ExtraPodSpec == nil {
@@ -411,6 +420,14 @@ func GenerateDynamoComponentsDeployments(ctx context.Context, parentDynamoGraphD
 			}
 		}
 
+		// override the component config with the component config that is in the parent deployment
+		if configOverride, ok := parentDynamoGraphDeployment.Spec.Services[service.Name]; ok {
+			err := mergo.Merge(&deployment.Spec.DynamoComponentDeploymentSharedSpec, configOverride.DynamoComponentDeploymentSharedSpec, mergo.WithOverride)
+			if err != nil {
+				return nil, err
+			}
+		}
+
 		// merge the envs from the parent deployment with the envs from the service
 		if len(parentDynamoGraphDeployment.Spec.Envs) > 0 {
 			deployment.Spec.Envs = mergeEnvs(parentDynamoGraphDeployment.Spec.Envs, deployment.Spec.Envs)