fix: Converts WDL log exit_code from string to int32 per WES spec

packages/cdk/go.mod

@@ -1,2 +1,14 @@
 // Exclude CDK directory from Go module parsing
 module ignore
+
+go 1.17
+
+require (
+	github.com/aws/aws-cdk-go/awscdk v1.149.0-devpreview
+	github.com/aws/aws-cdk-go/awscdk/v2 v2.17.0
+	github.com/aws/constructs-go/constructs/v10 v10.0.92
+	github.com/aws/constructs-go/constructs/v3 v3.3.246
+	github.com/aws/jsii-runtime-go v1.55.1
+)
+
+require github.com/Masterminds/semver/v3 v3.1.1 // indirect

packages/cdk/go.sum

@@ -0,0 +1,28 @@
+github.com/Masterminds/semver/v3 v3.1.1 h1:hLg3sBzpNErnxhQtUy/mmLR2I9foDujNK030IGemrRc=
+github.com/Masterminds/semver/v3 v3.1.1/go.mod h1:VPu/7SZ7ePZ3QOrcuXROw5FAcLl4a0cBrbBpGY/8hQs=
+github.com/aws/aws-cdk-go/awscdk v1.149.0-devpreview h1:gpdOA2oRX0MLXysVFJJUTVjmCFEdukYi3v48j0G93eI=
+github.com/aws/aws-cdk-go/awscdk v1.149.0-devpreview/go.mod h1:KsYzWfJFb/1ERW2gWbFTue6veTWoBygVCgy/pX2eMnU=
+github.com/aws/aws-cdk-go/awscdk/v2 v2.17.0 h1:nAdo4anojORKe2thFI7glrvixJCBs5XRYZDQ7EabhtM=
+github.com/aws/aws-cdk-go/awscdk/v2 v2.17.0/go.mod h1:EBLkGLkGx7DGQHTqth6V+0STQVzJbkrC7WlIQvy54Vs=
+github.com/aws/constructs-go/constructs/v10 v10.0.9/go.mod h1:RC6w8bOwxLmPX7Jfo9dkEZ9iVfgH4QnaVnfWvaNOHy0=
+github.com/aws/constructs-go/constructs/v10 v10.0.92 h1:D9WDPCUjQRa12yHexsL2PJ9zl4P9oa2yF/3nKNRwYg0=
+github.com/aws/constructs-go/constructs/v10 v10.0.92/go.mod h1:nJ+TOsvImM5avqQ9apT6TQaMlZt1LYdBS573ztfcr7k=
+github.com/aws/constructs-go/constructs/v3 v3.3.237/go.mod h1:tLZgYT2LxttX7vn2MkqDI/oXP3Kno4obsg6hN4ShfuA=
+github.com/aws/constructs-go/constructs/v3 v3.3.246 h1:RjcCROeM7B6wObOxN6TMUD+HAo5jG1J6qPk939ua9M4=
+github.com/aws/constructs-go/constructs/v3 v3.3.246/go.mod h1:4FvBHW1fYWFF+3421qEXzPFqJTEHzwvH17Sa0ZJwS6I=
+github.com/aws/jsii-runtime-go v1.37.0/go.mod h1:6tZnlstx8bAB3vnLFF9n8bbkI//LDblAek9zFyMXV3E=
+github.com/aws/jsii-runtime-go v1.54.0/go.mod h1:9htokR2a9XpRcbNf3fwqPaTs0CpC3KJCOUDMMJvEgZQ=
+github.com/aws/jsii-runtime-go v1.55.1 h1:naQzHp7NMVpQ6lElj5tn5HcnBvVjiP+g6XmNzs22Bvs=
+github.com/aws/jsii-runtime-go v1.55.1/go.mod h1:9htokR2a9XpRcbNf3fwqPaTs0CpC3KJCOUDMMJvEgZQ=
+github.com/davecgh/go-spew v1.1.0/go.mod h1:J7Y8YcW2NihsgmVo/mv3lAwl/skON4iLHjSsI+c5H38=
+github.com/davecgh/go-spew v1.1.1 h1:vj9j/u1bqnvCEfJOwUhtlOARqs3+rkHYY13jYWTU97c=
+github.com/davecgh/go-spew v1.1.1/go.mod h1:J7Y8YcW2NihsgmVo/mv3lAwl/skON4iLHjSsI+c5H38=
+github.com/pmezard/go-difflib v1.0.0 h1:4DBwDE0NGyQoBHbLQYPwSUPoCMWR5BEzIk/f1lZbAQM=
+github.com/pmezard/go-difflib v1.0.0/go.mod h1:iKH77koFhYxTK1pcRnkKkqfTogsbg7gZNVY4sRDYZ/4=
+github.com/stretchr/objx v0.1.0/go.mod h1:HFkY916IF+rwdDfMAkV7OtwuqBVzrE8GR6GFx+wExME=
+github.com/stretchr/testify v1.7.0 h1:nwc3DEeHmmLAfoZucVR881uASk0Mfjw8xYJ99tb5CcY=
+github.com/stretchr/testify v1.7.0/go.mod h1:6Fq8oRcR53rry900zMqJjRRixrwX3KX962/h/Wwjteg=
+gopkg.in/check.v1 v0.0.0-20161208181325-20d25e280405/go.mod h1:Co6ibVJAznAaIkqp8huTwlJQCZ016jof/cbN4VW5Yz0=
+gopkg.in/yaml.v3 v3.0.0-20200313102051-9f266ea9e77c/go.mod h1:K4uyk7z7BCEPqu6E+C64Yfv1cQ7kz7rIZviUmN+EgEM=
+gopkg.in/yaml.v3 v3.0.0-20210107192922-496545a6307b h1:h8qDotaEPuJATrMmW04NCwg7v22aHH28wwpauUhK9Oo=
+gopkg.in/yaml.v3 v3.0.0-20210107192922-496545a6307b/go.mod h1:K4uyk7z7BCEPqu6E+C64Yfv1cQ7kz7rIZviUmN+EgEM=

packages/cli/internal/pkg/cli/workflow/workflow_tasks.go

@@ -3,6 +3,7 @@ package workflow
 import (
 	"fmt"
 	"io"
+	"strconv"
 	"strings"
 	"time"
 
@@ -103,12 +104,18 @@ func (m *Manager) getTasks() ([]Task, error) {
 		if len(nameParts) != 2 {
 			return nil, fmt.Errorf("unable to parse job ID from task name '%s'", taskName)
 		}
+
+		exitCode := "NA"
+		if taskLog.ExitCode != nil {
+			exitCode = strconv.FormatInt(int64(*taskLog.ExitCode), 10)
+		}
+
 		tasks[i] = Task{
 			Name:      nameParts[0],
 			JobId:     nameParts[1],
 			StartTime: parseLogTime(taskLog.StartTime),
 			StopTime:  parseLogTime(taskLog.EndTime),
-			ExitCode:  taskLog.ExitCode,
+			ExitCode:  exitCode,
 		}
 	}
 

packages/cli/internal/pkg/cli/workflow/workflow_tasks_test.go

@@ -14,6 +14,7 @@ import (
 	storagemocks "github.com/aws/amazon-genomics-cli/internal/pkg/mocks/storage"
 	wesmocks "github.com/aws/amazon-genomics-cli/internal/pkg/mocks/wes"
 	"github.com/aws/amazon-genomics-cli/internal/pkg/wes"
+	"github.com/aws/aws-sdk-go-v2/aws"
 	"github.com/golang/mock/gomock"
 	"github.com/rsc/wes_client"
 	"github.com/stretchr/testify/suite"
@@ -97,7 +98,7 @@ func (s *GetWorkflowTasksTestSuite) TestGetWorkflowTasks_WithTask() {
 			Name:      testTaskCompositeName,
 			StartTime: testStartTime.UTC().Format("2006-01-02T15:04:05Z"),
 			EndTime:   testStopTime.UTC().Format("2006-01-02T15:04:05Z"),
-			ExitCode:  testExitCode,
+			ExitCode:  aws.Int32(0),
 		}},
 	}, nil)
 
@@ -200,6 +201,60 @@ func (s *GetWorkflowTasksTestSuite) TestGetWorkflowTasks_WithTaskNameFailure() {
 	}
 }
 
+func (s *GetWorkflowTasksTestSuite) TestGetWorkflowTasks_WithExitCodeNil() {
+	defer s.ctrl.Finish()
+	s.mockProjectClient.EXPECT().Read().Return(s.testProjSpec, nil)
+	s.mockConfigClient.EXPECT().GetUserId().Return(testUserId, nil)
+	s.mockDdb.EXPECT().GetWorkflowInstanceById(ctx.Background(), testProjectName, testUserId, testRunId).Return(ddb.WorkflowInstance{ContextName: testContext1Name}, nil)
+	s.mockCfn.EXPECT().GetStackInfo(testContext1Stack).Return(cfn.StackInfo{Outputs: map[string]string{"WesUrl": testWes1Url}}, nil)
+	s.mockWes.EXPECT().GetRunLog(ctx.Background(), testRunId).Return(wes_client.RunLog{
+		RunId: testRunId,
+		TaskLogs: []wes_client.Log{{
+			Name:      testTaskCompositeName,
+			StartTime: testStartTime.UTC().Format("2006-01-02T15:04:05Z"),
+			EndTime:   testStopTime.UTC().Format("2006-01-02T15:04:05Z"),
+			ExitCode:  nil,
+		}},
+	}, nil)
+
+	tasks, err := s.manager.GetWorkflowTasks(testRunId)
+	s.Assert().NoError(err)
+	{
+		s.Assert().Equal(testTaskName, tasks[0].Name)
+		s.Assert().Equal(testTaskJobId, tasks[0].JobId)
+		s.Assert().True(tasks[0].StartTime.Equal(testStartTime.Truncate(time.Second)))
+		s.Assert().True(tasks[0].StopTime.Equal(testStopTime.Truncate(time.Second)))
+		s.Assert().Equal(tasks[0].ExitCode, "NA")
+	}
+}
+
+func (s *GetWorkflowTasksTestSuite) TestGetWorkflowTasks_WithExitCodeExists() {
+	defer s.ctrl.Finish()
+	s.mockProjectClient.EXPECT().Read().Return(s.testProjSpec, nil)
+	s.mockConfigClient.EXPECT().GetUserId().Return(testUserId, nil)
+	s.mockDdb.EXPECT().GetWorkflowInstanceById(ctx.Background(), testProjectName, testUserId, testRunId).Return(ddb.WorkflowInstance{ContextName: testContext1Name}, nil)
+	s.mockCfn.EXPECT().GetStackInfo(testContext1Stack).Return(cfn.StackInfo{Outputs: map[string]string{"WesUrl": testWes1Url}}, nil)
+	s.mockWes.EXPECT().GetRunLog(ctx.Background(), testRunId).Return(wes_client.RunLog{
+		RunId: testRunId,
+		TaskLogs: []wes_client.Log{{
+			Name:      testTaskCompositeName,
+			StartTime: testStartTime.UTC().Format("2006-01-02T15:04:05Z"),
+			EndTime:   testStopTime.UTC().Format("2006-01-02T15:04:05Z"),
+			ExitCode:  aws.Int32(0),
+		}},
+	}, nil)
+
+	tasks, err := s.manager.GetWorkflowTasks(testRunId)
+	s.Assert().NoError(err)
+	{
+		s.Assert().Equal(testTaskName, tasks[0].Name)
+		s.Assert().Equal(testTaskJobId, tasks[0].JobId)
+		s.Assert().True(tasks[0].StartTime.Equal(testStartTime.Truncate(time.Second)))
+		s.Assert().True(tasks[0].StopTime.Equal(testStopTime.Truncate(time.Second)))
+		s.Assert().Equal(testExitCode, "0")
+	}
+}
+
 func TestGetWorkflowTasksTestSuite(t *testing.T) {
 	suite.Run(t, new(GetWorkflowTasksTestSuite))
 }

packages/wes_adapter/amazon_genomics/wes/adapters/BatchAdapter.py

@@ -230,15 +230,14 @@ def to_log(job_details: JobDetailTypeDef) -> Log:
 
         start_time = to_iso(job_details.get("startedAt"))
         end_time = to_iso(job_details.get("stoppedAt"))
-        exitCode = job_details["container"].get("exitCode")
 
         return Log(
             name=task_name,
             cmd=job_details["container"]["command"],
             start_time=start_time,
             end_time=end_time,
             stdout=job_details["container"].get("logStreamName"),
-            exit_code=("" if exitCode == None else str(exitCode)),
+            exit_code=job_details["container"].get("exitCode"),
         )
 
 

packages/wes_api/client/model_log.go

@@ -31,5 +31,5 @@ type Log struct {
 	Stderr string `json:"stderr,omitempty"`
 
 	// Exit code of the program
-	ExitCode string `json:"exit_code,omitempty"`
+	ExitCode *int32 `json:"exit_code,omitempty"`
 }