Working on code formatting and lintint

Makefile

@@ -82,12 +82,12 @@ tidy:
 	@find . \( -path ./vendor -o -path ./webdash/node_modules -o -path ./venv -o -path ./.git \) -prune -o -type f -print | grep -v "\.pb\." | grep -v "web.go" | grep -E '.*\.go$$' | xargs gofmt -w -s
 
 lint-depends:
-	go get github.com/golangci/golangci-lint/cmd/golangci-lint@v1.22.2
+	go install github.com/golangci/golangci-lint/cmd/golangci-lint@v1.50.1
 	go install golang.org/x/tools/cmd/goimports
 
 # Run code style and other checks
 lint:
-	@golangci-lint run --timeout 3m --disable-all --enable=vet --enable=golint --enable=gofmt --enable=goimports --enable=misspell \
+	@golangci-lint run --timeout 3m --disable-all --enable=golint --enable=gofmt --enable=goimports --enable=misspell \
 		--skip-dirs "vendor" \
 		--skip-dirs "webdash" \
 		--skip-dirs "cmd/webdash" \

compute/scheduler/node.go

@@ -125,7 +125,8 @@ func (n *NodeProcess) checkConnection(ctx context.Context) {
 // handles signals from the server (new task, cancel task, etc), reports resources, etc.
 //
 // TODO Sync should probably use a channel to sync data access.
-//      Probably only a problem for test code, where Sync is called directly.
+//
+//	Probably only a problem for test code, where Sync is called directly.
 func (n *NodeProcess) sync(ctx context.Context) {
 	var r *Node
 	var err error

database/boltdb/new.go

@@ -40,7 +40,8 @@ var ExecutorStderr = []byte("executor-stderr")
 var Nodes = []byte("nodes")
 
 // SysLogs defeines the name of a bucket with maps
-//  task ID -> tes.TaskLog.SystemLogs
+//
+//	task ID -> tes.TaskLog.SystemLogs
 var SysLogs = []byte("system-logs")
 
 // BoltDB provides handlers for gRPC endpoints.

go.mod

@@ -33,6 +33,7 @@ require (
 	github.com/golang/protobuf v1.5.2
 	github.com/grpc-ecosystem/go-grpc-middleware v1.2.0
 	github.com/grpc-ecosystem/grpc-gateway/v2 v2.5.0
+	github.com/hashicorp/go-multierror v1.1.1 // indirect
 	github.com/imdario/mergo v0.3.8
 	github.com/jlaffaye/ftp v0.0.0-20191218041957-e1b8fdd0dcc3
 	github.com/jmespath/go-jmespath v0.0.0-20180206201540-c2b33e8439af // indirect

go.sum

@@ -280,6 +280,10 @@ github.com/grpc-ecosystem/go-grpc-middleware v1.2.0 h1:0IKlLyQ3Hs9nDaiK5cSHAGmcQ
 github.com/grpc-ecosystem/go-grpc-middleware v1.2.0/go.mod h1:mJzapYve32yjrKlk9GbyCZHuPgZsrbyIbyKhSzOpg6s=
 github.com/grpc-ecosystem/grpc-gateway/v2 v2.5.0 h1:ajue7SzQMywqRjg2fK7dcpc0QhFGpTR2plWfV4EZWR4=
 github.com/grpc-ecosystem/grpc-gateway/v2 v2.5.0/go.mod h1:r1hZAcvfFXuYmcKyCJI9wlyOPIZUJl6FCB8Cpca/NLE=
+github.com/hashicorp/errwrap v1.0.0 h1:hLrqtEDnRye3+sgx6z4qVLNuviH3MR5aQ0ykNJa/UYA=
+github.com/hashicorp/errwrap v1.0.0/go.mod h1:YH+1FKiLXxHSkmPseP+kNlulaMuP3n2brvKWEqk/Jc4=
+github.com/hashicorp/go-multierror v1.1.1 h1:H5DkEtf6CXdFp0N0Em5UCwQpXMWke8IA0+lD48awMYo=
+github.com/hashicorp/go-multierror v1.1.1/go.mod h1:iw975J/qwKPdAO1clOe2L8331t/9/fmwbPZ6JB6eMoM=
 github.com/hashicorp/go-uuid v1.0.2 h1:cfejS+Tpcp13yd5nYHWDI6qVCny6wyX2Mt5SGur2IGE=
 github.com/hashicorp/go-uuid v1.0.2/go.mod h1:6SBZvOh/SIDV7/2o3Jml5SYk/TvGqwFJ/bN7x4byOro=
 github.com/hashicorp/golang-lru v0.5.0/go.mod h1:/m3WP610KZHVQ1SGc6re/UDhFvYD7pJ4Ao+sR/qLZy8=

logger/log.go

@@ -80,7 +80,8 @@ func (l *Logger) Discard() {
 // Debug logs a debug message.
 //
 // After the first argument, arguments are key-value pairs which are written as structured logs.
-//     log.Debug("Some message here", "key1", value1, "key2", value2)
+//
+//	log.Debug("Some message here", "key1", value1, "key2", value2)
 func (l *Logger) Debug(msg string, args ...interface{}) {
 	if l == nil {
 		return
@@ -93,7 +94,8 @@ func (l *Logger) Debug(msg string, args ...interface{}) {
 // Info logs an info message
 //
 // After the first argument, arguments are key-value pairs which are written as structured logs.
-//     log.Info("Some message here", "key1", value1, "key2", value2)
+//
+//	log.Info("Some message here", "key1", value1, "key2", value2)
 func (l *Logger) Info(msg string, args ...interface{}) {
 	if l == nil {
 		return
@@ -106,11 +108,13 @@ func (l *Logger) Info(msg string, args ...interface{}) {
 // Error logs an error message
 //
 // After the first argument, arguments are key-value pairs which are written as structured logs.
-//     log.Error("Some message here", "key1", value1, "key2", value2)
+//
+//	log.Error("Some message here", "key1", value1, "key2", value2)
 //
 // Error has a two-argument version that can be used as a shortcut.
-//     err := startServer()
-//     log.Error("Couldn't start server", err)
+//
+//	err := startServer()
+//	log.Error("Couldn't start server", err)
 func (l *Logger) Error(msg string, args ...interface{}) {
 	if l == nil {
 		return
@@ -136,7 +140,8 @@ func (l *Logger) Error(msg string, args ...interface{}) {
 // Warn logs an warning message
 //
 // After the first argument, arguments are key-value pairs which are written as structured logs.
-//     log.Info("Some message here", "key1", value1, "key2", value2)
+//
+//	log.Info("Some message here", "key1", value1, "key2", value2)
 func (l *Logger) Warn(msg string, args ...interface{}) {
 	if l == nil {
 		return

tests/core/basic_test.go

@@ -6,6 +6,7 @@ import (
 	"testing"
 	"time"
 
+	"github.com/hashicorp/go-multierror"
 	workerCmd "github.com/ohsu-comp-bio/funnel/cmd/worker"
 	"github.com/ohsu-comp-bio/funnel/events"
 	"github.com/ohsu-comp-bio/funnel/tes"
@@ -280,9 +281,10 @@ func TestGetTaskView(t *testing.T) {
 }
 
 // TODO this is a bit hacky for now because we're reusing the same
-//      server + DB for all the e2e tests, so ListTasks gets the
-//      results of all of those. It works for the moment, but
-//      should probably run against a clean environment.
+//
+//	server + DB for all the e2e tests, so ListTasks gets the
+//	results of all of those. It works for the moment, but
+//	should probably run against a clean environment.
 func TestListTaskView(t *testing.T) {
 	tests.SetLogOutput(log, t)
 	var tasks []*tes.Task
@@ -1117,6 +1119,8 @@ func TestConcurrentStateUpdate(t *testing.T) {
 	f := tests.NewFunnel(c)
 	f.StartServer()
 
+	var result *multierror.Error
+
 	ids := []string{}
 	for i := 0; i < 10; i++ {
 		id := f.Run(`--sh 'echo hello'`)
@@ -1126,12 +1130,14 @@ func TestConcurrentStateUpdate(t *testing.T) {
 			opts := &workerCmd.Options{TaskID: id}
 			w, err := workerCmd.NewWorker(ctx, c, log, opts)
 			if err != nil {
-				t.Fatal(err)
+				result = multierror.Append(result, err)
+				return
 			}
 
 			log.Info("writing state initializing event", "taskID", id)
 			err = w.EventWriter.WriteEvent(ctx, events.NewState(id, tes.Initializing))
 			if err != nil {
+				result = multierror.Append(result, err)
 				log.Error("error writing event", err)
 			}
 		}(id)
@@ -1140,17 +1146,23 @@ func TestConcurrentStateUpdate(t *testing.T) {
 			opts := &workerCmd.Options{TaskID: id}
 			w, err := workerCmd.NewWorker(ctx, c, log, opts)
 			if err != nil {
-				t.Fatal(err)
+				result = multierror.Append(result, err)
+				return
 			}
 
 			log.Info("writing state canceled event", "taskID", id)
 			err = w.EventWriter.WriteEvent(ctx, events.NewState(id, tes.Canceled))
 			if err != nil {
+				result = multierror.Append(result, err)
 				log.Error("error writing event", "error", err, "taskID", id)
 			}
 		}(id)
 	}
 
+	if result != nil {
+		t.Error(result)
+	}
+
 	for _, i := range ids {
 		log.Info("waiting for task", "taskID", i)
 		task := f.Wait(i)

tests/pubsub/pubsub_test.go

@@ -6,6 +6,7 @@ import (
 	"testing"
 	"time"
 
+	"github.com/hashicorp/go-multierror"
 	workerCmd "github.com/ohsu-comp-bio/funnel/cmd/worker"
 	"github.com/ohsu-comp-bio/funnel/config"
 	"github.com/ohsu-comp-bio/funnel/events"
@@ -50,12 +51,14 @@ func TestPubSubWorkerRun(t *testing.T) {
 	task := &tes.Task{}
 	b := events.TaskBuilder{Task: task}
 
+	var result *multierror.Error
+
 	// Read events from pubsub, write into task builder.
 	subname := "test-pubsub-" + tests.RandomString(10)
 	go func() {
 		err := events.ReadPubSub(ctx, conf.PubSub, subname, b)
 		if err != nil {
-			t.Fatal(err)
+			result = multierror.Append(result, err)
 		}
 	}()
 
@@ -70,6 +73,10 @@ func TestPubSubWorkerRun(t *testing.T) {
 	fun.Wait(id)
 	time.Sleep(time.Second)
 
+	if result != nil {
+		t.Fatal(result)
+	}
+
 	// Check the task (built from a stream of kafka events).
 	if task.State != tes.State_COMPLETE {
 		t.Fatal("unexpected state", task.State)

tests/storage/storage_test.go

@@ -95,13 +95,13 @@ func TestBrokenSymlinkInput(t *testing.T) {
 }
 
 /*
-  Test the case where a container creates a symlink in an output path.
-  From the view of the host system where Funnel is running, this creates
-  a broken link, because the source of the symlink is a path relative
-  to the container filesystem.
+Test the case where a container creates a symlink in an output path.
+From the view of the host system where Funnel is running, this creates
+a broken link, because the source of the symlink is a path relative
+to the container filesystem.
 
-  Funnel can fix some of these cases using volume definitions, which
-  is being tested here.
+Funnel can fix some of these cases using volume definitions, which
+is being tested here.
 */
 func TestSymlinkOutput(t *testing.T) {
 	tests.SetLogOutput(log, t)

util/idle_timeout.go

@@ -6,18 +6,18 @@ import "time"
 // Start() and Stop() are used to control the timer, and Done() is used to
 // detect when the timeout has been reached.
 //
-//     in := make(chan int)
-//     requestInput(in)
-//     t := IdleTimeoutAfter(time.Second * 10)
-//     for {
-//       select {
-//       case <-t.Done():
-//         // ... code to respond to timeout
-//       case <-in:
-//         // Reset the timeout.
-//         t.Start()
-//       }
-//    }
+//	 in := make(chan int)
+//	 requestInput(in)
+//	 t := IdleTimeoutAfter(time.Second * 10)
+//	 for {
+//	   select {
+//	   case <-t.Done():
+//	     // ... code to respond to timeout
+//	   case <-in:
+//	     // Reset the timeout.
+//	     t.Start()
+//	   }
+//	}
 type IdleTimeout interface {
 	Done() <-chan time.Time
 	Start()
@@ -51,13 +51,13 @@ type timerTimeout struct {
 
 // Done returns a channel which can be used to wait for the timeout.
 //
-//     t := IdleTimeoutAfter(time.Second * 10)
-//     for {
-//       select {
-//       case <-t.Done():
-//         // ... code to respond to timeout
-//       }
-//    }
+//	 t := IdleTimeoutAfter(time.Second * 10)
+//	 for {
+//	   select {
+//	   case <-t.Done():
+//	     // ... code to respond to timeout
+//	   }
+//	}
 func (t *timerTimeout) Done() <-chan time.Time {
 	if t.timer != nil {
 		return t.timer.C

util/openapi2proto/main.go

@@ -16,7 +16,7 @@ type Field struct {
 	Name     string
 	Type     string
 	Repeated bool
-	Id       int
+	ID       int
 	Source   *openapi3.SchemaRef
 }
 
@@ -98,7 +98,7 @@ func getFields(schema *openapi3.SchemaRef) []Field {
 	}
 	sort.SliceStable(fields, func(i, j int) bool { return fields[i].Name < fields[j].Name })
 	for i := range fields {
-		fields[i].Id = i + 1
+		fields[i].ID = i + 1
 	}
 	return fields
 }
@@ -133,7 +133,7 @@ func parseMessageSchema(name string, schema *openapi3.SchemaRef) (Message, error
 		//fmt.Printf("Fields: %#vs\n", fields)
 		sort.SliceStable(fields, func(i, j int) bool { return fields[i].Name < fields[j].Name })
 		for i := range fields {
-			fields[i].Id = i + 1
+			fields[i].ID = i + 1
 		}
 		m := Message{Name: name, Fields: fields}
 		return m, nil
@@ -227,7 +227,7 @@ func main() {
 					reqFields = append(reqFields, Field{Name: param.Value.Name, Type: t, Repeated: r})
 				}
 				for i := range reqFields {
-					reqFields[i].Id = i + 1
+					reqFields[i].ID = i + 1
 				}
 				m := Message{Name: req.Get.OperationID + "Request", Fields: reqFields}
 				messages = append(messages, m)
@@ -241,7 +241,7 @@ func main() {
 					reqFields = append(reqFields, Field{Name: param.Value.Name, Type: t, Repeated: r})
 				}
 				for i := range reqFields {
-					reqFields[i].Id = i + 1
+					reqFields[i].ID = i + 1
 				}
 				if req.Post.RequestBody != nil {
 					//if not a reference to schema, build it

worker/file_mapper.go

@@ -151,7 +151,7 @@ func (mapper *FileMapper) HostPath(src string) (string, error) {
 // OpenHostFile opens a file on the host file system at a mapped path.
 // "src" is an unmapped path. This function will handle mapping the path.
 //
-// This function calls os.Open
+// # This function calls os.Open
 //
 // If the path can't be mapped or the file can't be opened, an error is returned.
 func (mapper *FileMapper) OpenHostFile(src string) (*os.File, error) {
@@ -169,7 +169,7 @@ func (mapper *FileMapper) OpenHostFile(src string) (*os.File, error) {
 // CreateHostFile creates a file on the host file system at a mapped path.
 // "src" is an unmapped path. This function will handle mapping the path.
 //
-// This function calls os.Create
+// # This function calls os.Create
 //
 // If the path can't be mapped or the file can't be created, an error is returned.
 func (mapper *FileMapper) CreateHostFile(src string) (*os.File, error) {