Merge branch 'devel'

.github/workflows/run-tests.yml

@@ -19,16 +19,16 @@ jobs:
       matrix:
         include:
           # iRODS 4.2.11 clients vs 4.2.7 server
-          - go: "1.17"
+          - go: "1.18"
             irods: "4.2.11"
-            server_image: "wsinpg/ub-16.04-irods-4.2.7:latest"
-            baton: "4.0.0"
+            server_image: "ghcr.io/wtsi-npg/ub-16.04-irods-4.2.7:latest"
+            baton: "4.0.1"
             experimental: false
           # iRODS 4.2.11 clients vs 4.2.11 server
-          - go: "1.17"
+          - go: "1.18"
             irods: "4.2.11"
-            server_image: "wsinpg/ub-18.04-irods-4.2.11:latest"
-            baton: "4.0.0"
+            server_image: "ghcr.io/wtsi-npg/ub-18.04-irods-4.2.11:latest"
+            baton: "4.0.1"
             experimental: false
 
     services:
@@ -38,10 +38,10 @@ jobs:
           - 1247:1247
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
 
     - name: "Set up Go ${{ matrix.go }}"
-      uses: actions/setup-go@v2
+      uses: actions/setup-go@v3
       with:
         go-version: ${{ matrix.go }}
 
@@ -88,7 +88,7 @@ jobs:
         baton-do --version
 
     - name: "Cache Go modules"
-      uses: actions/cache@v2
+      uses: actions/cache@v3
       with:
         path: |
           "$HOME/go/pkg/mod"
@@ -99,7 +99,7 @@ jobs:
 
     - name: "Install test runner"
       run: |
-        go get github.com/onsi/ginkgo/v2/ginkgo
+        go install -mod=mod github.com/onsi/ginkgo/v2/ginkgo
         go get github.com/onsi/gomega/...
 
     - name: "Run tests"

CHANGELOG.md

@@ -6,13 +6,25 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [Unreleased] - [![Unit tests](https://github.com/wtsi-npg/extendo/actions/workflows/run-tests.yml/badge.svg)](https://github.com/wtsi-npg/extendo/actions/workflows/run-tests.yml)
 
+## [2.6.0] - 2023-04-17
+
+### Fixed
+
+- Hang when baton crashed
+
+### Changed
+
+- Bump github.com/onsi/ginkgo/v2 from 2.1.6 to 2.9.1
+- Bump github.com/onsi/gomega from 1.20.2 to 1.27.6
+- Bump github.com/stretchr/testify from 1.8.0 to 1.8.2
+- Bump github.com/rs/zerolog from 1.28.0 to 1.29.0
+
 ## [2.5.0] - 2022-10-13
 
 ### Added
 
 - Checksum verification on put
 
-
 Removal of a workaround that was created for iRODS 4.1.* now allows
 extendo to support iRODS' checksum verification feature for `put` operations.
 This feature calculates a checksum from the local file on disk and compares

Makefile

@@ -17,10 +17,10 @@ lint:
 check: test
 
 test:
-	ginkgo -r -slow-spec-threshold=30s -race
+	ginkgo -r -race
 
 coverage:
-	ginkgo -r -slow-spec-threshold=30s -cover -coverprofile=coverage.out
+	ginkgo -r -cover -coverprofile=coverage.out
 
 clean:
 	go clean

client.go

@@ -184,7 +184,7 @@ func RodsErrorCode(err error) (int32, error) {
 		return e.Code(), nil
 	default:
 		return int32(0),
-			errors.Errorf("cannot get an iRODS error code from %v", err)
+			errors.Errorf("cannot get an iRODS error code from error: '%v'", err)
 	}
 }
 
@@ -419,15 +419,16 @@ func (client *Client) Start(arg ...string) (*Client, error) {
 
 	// Watch for baton sub-process completion and capture any error
 	go func() {
-		inWg.Wait()
-		outWg.Wait()
 		err := cmd.Wait()
 
 		client.Lock()
 		client.isRunning = false
 		client.stopTime = time.Now()
 		client.Unlock()
 
+		inWg.Wait()
+		outWg.Wait()
+
 		client.err <- err
 		close(client.err)
 	}()
@@ -473,7 +474,7 @@ func (client *Client) Runtime() time.Duration {
 // error from the sub-process.
 func (client *Client) StopIgnoreError() {
 	if err := client.Stop(); err != nil {
-		logs.GetLogger().Error().Err(err).Int("pid", client.pid).
+		logs.GetLogger().Error().Err(err).Int("pid", client.ClientPid()).
 			Msg("stopped client")
 	}
 }
@@ -777,14 +778,13 @@ func (client *Client) putRecurse(args Args, item RodsItem) ([]RodsItem, error) {
 // iRODS server is being run.
 func (client *Client) execute(op string, args Args, item RodsItem) ([]RodsItem,
 	error) {
-	client.Lock()
-	defer client.Unlock()
-
-	if !client.isRunning {
+	if !client.IsRunning() {
 		return []RodsItem{}, errors.New("client is not running")
 	}
 
+	client.Lock()
 	client.activityTime = time.Now()
+	client.Unlock()
 
 	response, err := client.send(wrap(op, args, item))
 	if err != nil {
@@ -817,10 +817,13 @@ waitResponse:
 		case <-time.After(client.respTimeout):
 			// If the sub-process is running we just wait again, until either
 			// it responds or stops running.
-			if !client.isRunning {
-				return nil, errors.New("receiving failed")
+			if !client.IsRunning() {
+				ps := client.cmd.ProcessState
+				return nil, errors.Errorf("receiving failed because the client stopped. "+
+					"PID: %d, process state: %s", ps.Pid(), ps.String())
 			}
-			log.Debug().Str("executable", client.path).
+
+			log.Debug().Str("executable", client.path).Int("pid", client.ClientPid()).
 				Msg("receiving timed out, waiting again ...")
 		}
 	}

client_test.go

@@ -163,6 +163,21 @@ var _ = Describe("List an iRODS path", func() {
 		})
 	})
 
+	When("the path does not exist and contains printf placeholders", func() {
+		It("should return an iRODS -310000 error", func() {
+			path := filepath.Join(rootColl, "%s")
+			item := ex.RodsItem{IPath: path}
+
+			_, err := client.ListItem(ex.Args{}, item)
+			Expect(err).To(HaveOccurred())
+
+			code, e := ex.RodsErrorCode(err)
+			Expect(e).NotTo(HaveOccurred())
+
+			Expect(code).To(Equal(ex.RodsUserFileDoesNotExist))
+		})
+	})
+
 	When("the item is a collection", func() {
 		BeforeEach(func() {
 			testColl = ex.RodsItem{IPath: filepath.Join(workColl, "testdata")}
@@ -430,7 +445,6 @@ var _ = Describe("List an iRODS path", func() {
 	})
 })
 
-
 var _ = Describe("Put a file into iRODS", func() {
 	var (
 		client *ex.Client

go.mod

@@ -3,23 +3,27 @@ module github.com/wtsi-npg/extendo/v2
 go 1.17
 
 require (
-	github.com/onsi/ginkgo/v2 v2.1.6
-	github.com/onsi/gomega v1.20.2
+	github.com/onsi/ginkgo/v2 v2.9.2
+	github.com/onsi/gomega v1.27.6
 	github.com/pkg/errors v0.9.1
-	github.com/rs/zerolog v1.28.0
-	github.com/stretchr/testify v1.8.0
+	github.com/rs/zerolog v1.29.0
+	github.com/stretchr/testify v1.8.2
 	github.com/wtsi-npg/logshim v1.3.0
 	github.com/wtsi-npg/logshim-zerolog v1.3.0
 )
 
 require (
 	github.com/davecgh/go-spew v1.1.1 // indirect
-	github.com/google/go-cmp v0.5.8 // indirect
+	github.com/go-logr/logr v1.2.3 // indirect
+	github.com/go-task/slim-sprig v0.0.0-20230315185526-52ccab3ef572 // indirect
+	github.com/google/go-cmp v0.5.9 // indirect
+	github.com/google/pprof v0.0.0-20210407192527-94a9f03dee38 // indirect
 	github.com/mattn/go-colorable v0.1.12 // indirect
 	github.com/mattn/go-isatty v0.0.14 // indirect
 	github.com/pmezard/go-difflib v1.0.0 // indirect
-	golang.org/x/net v0.0.0-20220722155237-a158d28d115b // indirect
-	golang.org/x/sys v0.0.0-20220722155257-8c9f86f7a55f // indirect
-	golang.org/x/text v0.3.7 // indirect
+	golang.org/x/net v0.8.0 // indirect
+	golang.org/x/sys v0.6.0 // indirect
+	golang.org/x/text v0.8.0 // indirect
+	golang.org/x/tools v0.7.0 // indirect
 	gopkg.in/yaml.v3 v3.0.1 // indirect
 )