Update to latest deps for sec vulns. (#38)

* Update to latest deps for sec vulns. * Test with latest version of go. * Lint with latest linters.
wtsi-ssg · Jul 2, 2024 · 5b77863 · 5b77863
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commit 5b77863
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Showing 9 changed files with 158 additions and 119 deletions.
diff --git a/.github/workflows/golangci-lint.yml b/.github/workflows/golangci-lint.yml
@@ -17,10 +17,10 @@ jobs:
     steps:
       - uses: actions/setup-go@v3
         with:
-          go-version: 1.20.4
+          go-version: 1.22.4
       - uses: actions/checkout@v3
       - name: golangci-lint
         uses: golangci/golangci-lint-action@v3
         with:
-          version: v1.50.1
+          version: v1.59.1
           only-new-issues: true
diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
@@ -20,7 +20,7 @@ jobs:
     - name: Setup Go
       uses: actions/setup-go@v3
       with:
-        go-version: '1.20.4'
+        go-version: '1.22.4'
 
     - name: Run tests
       run: make test

diff --git a/.golangci.yml b/.golangci.yml
@@ -6,7 +6,7 @@ run:
 
 linters-settings:
   dupl:
-    threshold: 50
+    threshold: 100
   errcheck:
     check-type-assertions: true
     check-blank: true
@@ -16,13 +16,14 @@ linters-settings:
     lines: 30
     statements: 20
   gocognit:
-    min-complexity: 8
-  nestif:
-    min-complexity: 2
+    min-complexity: 9
   gocyclo:
-    min-complexity: 5
+    min-complexity: 7
+  gomnd:
+    ignored-functions:
+      - 'strconv.Parse*'
   govet:
-    check-shadowing: true
+    shadow: true
     enable-all: true
     disable-all: false
     disable:
@@ -33,6 +34,8 @@ linters-settings:
     locale: UK
   nakedret:
     max-func-lines: 20
+  nestif:
+    min-complexity: 2
   prealloc:
     simple: true
     range-loops: true
@@ -54,56 +57,85 @@ issues:
       linters:
         - funlen
         - maintidx
-    - path: clog.go
+        - contextcheck
+        - gocognit
+        - gocyclo
+        - cyclop
+        - revive
+    - path: cmd
       linters:
         - gochecknoinits
         - gochecknoglobals
-        - contextcheck
+        - dupl
+        - forbidigo
+    - path: version\.go
+      linters:
+        - forbidigo
+    - path: groupuser\.go
+      linters:
+        - dupl
+    - path: usergroup\.go
+      linters:
+        - dupl
   max-issues-per-linter: 0
   max-same-issues: 0
   new-from-rev: master
 
 linters:
   disable-all: true
   enable:
+    # defaults
     - errcheck
     - gosimple
     - govet
     - ineffassign
     - staticcheck
-    - typecheck
     - unused
+    # extras
     - containedctx
     - contextcheck
+    #- copyloopvar
     - cyclop
     - dogsled
     - dupl
+    - dupword
     - durationcheck
+    - err113
+    - errchkjson
     - errname
     - errorlint
     - exhaustive
     - exportloopref
+    - fatcontext
     - forbidigo
     - forcetypeassert
     - funlen
     - gci
+    - gocheckcompilerdirectives
     - gochecknoglobals
     - gochecknoinits
+    - gochecksumtype
     - gocognit
     - goconst
     - gocritic
     - gocyclo
     - godot
     - godox
-    - goerr113
     - goimports
-    - gomnd
     - gosec
+    - gosmopolitan
+    - grouper
     - importas
+    - inamedparam
+    - interfacebloat
+    #- intrange
+    - ireturn
     - lll
     - maintidx
     - makezero
+    - mirror
     - misspell
+    - mnd
     - nakedret
     - nestif
     - nilerr
@@ -112,56 +144,53 @@ linters:
     - noctx
     - nolintlint
     - nosprintfhostport
+    - perfsprint
     - prealloc
     - predeclared
     - reassign
     - revive
+    - sloglint
     - stylecheck
+    - tagalign
     - tenv
     - thelper
+    - tparallel
     - unconvert
     - unparam
     - usestdlibvars
-    #- wastedassign
+    - wastedassign
     - whitespace
     - wsl
-  # disable:
+
+  #disable:
   #   - asasalint
   #   - asciicheck
   #   - bidichk
   #   - bodyclose
+  #   - canonicalheader
   #   - decorder
   #   - depguard
-  #   - errchkjson
-  #   - execinquery
-  #   - exhaustivestruct
   #   - exhaustruct
   #   - ginkgolinter
   #   - gofmt
   #   - gofumpt
   #   - goheader
-  #   - golint
   #   - gomoddirectives
   #   - gomodguard
   #   - goprintffuncname
-  #   - grouper
-  #   - ifshort
-  #   - interfacer
-  #   - ireturn
   #   - loggercheck
-  #   - maligned
+  #   - musttag
   #   - nonamedreturns
-  #   - nosnakecase
   #   - paralleltest
   #   - promlinter
+  #   - protogetter
   #   - rowserrcheck
-  #   - scopeline
+  #   - spancheck
   #   - sqlclosecheck
-  #   - structcheck
   #   - tagliatelle
   #   - testableexamples
+  #   - testifylint
   #   - testpackage
-  #   - tparallel
-  #   - varcheck
   #   - varnamelen
   #   - wrapcheck
+  #   - zerologlint
diff --git a/.vscode/settings.json b/.vscode/settings.json
@@ -2,8 +2,8 @@
     "[go]": {
         "editor.formatOnSave": true,
         "editor.codeActionsOnSave": {
-            "source.organizeImports": true
-        },
+			"source.organizeImports": "explicit"
+		},
     },
     "go.formatTool": "goimports",
     "go.formatFlags": [

diff --git a/README.md b/README.md
@@ -29,7 +29,7 @@ To run the benchmarks:
 
 Before committing any code, you should make sure you haven't introduced any
 linting errors. First install the linters:
-`curl -sSfL https://raw.githubusercontent.com/golangci/golangci-lint/master/install.sh | sh -s -- -b $(go env GOPATH)/bin v1.39.0`
+`curl -sSfL https://raw.githubusercontent.com/golangci/golangci-lint/master/install.sh | sh -s -- -b $(go env GOPATH)/bin v1.59.1`
 
 Then:
 `make lint`
diff --git a/container/docker/docker.go b/container/docker/docker.go
@@ -28,7 +28,7 @@ import (
 	"context"
 	"encoding/json"
 
-	"github.com/docker/docker/api/types"
+	cn "github.com/docker/docker/api/types/container"
 	"github.com/docker/docker/client"
 	"github.com/wtsi-ssg/wr/container"
 	"github.com/wtsi-ssg/wr/math/convert"
@@ -50,7 +50,7 @@ func NewInteractor(cl *client.Client) *Interactor {
 // ContainerList implements the Interactor interface method, which returns the
 // list of containers.
 func (i *Interactor) ContainerList(ctx context.Context) ([]*container.Container, error) {
-	containerList, err := i.dockerClient.ContainerList(ctx, types.ContainerListOptions{})
+	containerList, err := i.dockerClient.ContainerList(ctx, cn.ListOptions{})
 	if err != nil {
 		return nil, err
 	}
@@ -80,8 +80,8 @@ func (i *Interactor) ContainerStats(ctx context.Context,
 
 // decodeDockerContainerStats takes type.ContainerStats and decodes it to return
 // the current memory usage (RSS, in MB) and total CPU (in seconds).
-func decodeDockerContainerStats(containerStats types.ContainerStats) (*container.Stats, error) {
-	var ds *types.Stats
+func decodeDockerContainerStats(containerStats cn.StatsResponseReader) (*container.Stats, error) {
+	var ds *cn.Stats
 
 	err := json.NewDecoder(containerStats.Body).Decode(&ds)
 	if err != nil {

diff --git a/container/docker/docker_test.go b/container/docker/docker_test.go
@@ -34,6 +34,7 @@ import (
 
 	"github.com/docker/docker/api/types"
 	cn "github.com/docker/docker/api/types/container"
+	"github.com/docker/docker/api/types/image"
 	nw "github.com/docker/docker/api/types/network"
 	"github.com/docker/docker/client"
 	specs "github.com/opencontainers/image-spec/specs-go/v1"
@@ -116,7 +117,7 @@ func createContainers(ctx context.Context, cli *client.Client, containerNames []
 }
 
 func pullUbuntuImage(ctx context.Context, cli *client.Client) error {
-	rc, err := cli.ImagePull(ctx, "ubuntu", types.ImagePullOptions{})
+	rc, err := cli.ImagePull(ctx, "ubuntu", image.PullOptions{})
 	if err != nil {
 		return err
 	}
@@ -153,14 +154,14 @@ func createContainer(ctx context.Context, cli *client.Client, cname string) (str
 }
 
 func startContainer(ctx context.Context, cli *client.Client, containerID string) error {
-	return cli.ContainerStart(ctx, containerID, types.ContainerStartOptions{})
+	return cli.ContainerStart(ctx, containerID, cn.StartOptions{})
 }
 
 // removeContainers removes all the containers given a list of containers as a
 // part of clean up step.
 func removeContainers(ctx context.Context, cli *client.Client, containerIDs []string) error {
 	for _, cid := range containerIDs {
-		err := cli.ContainerRemove(ctx, cid, types.ContainerRemoveOptions{Force: true})
+		err := cli.ContainerRemove(ctx, cid, cn.RemoveOptions{Force: true})
 		if err != nil {
 			return err
 		}

diff --git a/go.mod b/go.mod
@@ -1,46 +1,54 @@
 module github.com/wtsi-ssg/wr
 
-go 1.17
+go 1.21
+
+toolchain go1.22.0
 
 require (
-	github.com/Microsoft/go-winio v0.6.1 // indirect
+	github.com/Microsoft/go-winio v0.6.2 // indirect
 	github.com/acarl005/stripansi v0.0.0-20180116102854-5a71ef0e047d
-	github.com/docker/docker v24.0.2+incompatible
-	github.com/docker/go-connections v0.4.0 // indirect
+	github.com/docker/docker v27.0.3+incompatible
+	github.com/docker/go-connections v0.5.0 // indirect
 	github.com/go-stack/stack v1.8.1
 	github.com/hpcloud/tail v1.0.0
 	github.com/inconshreveable/log15 v2.16.0+incompatible
 	github.com/mattn/go-colorable v0.1.13 // indirect
 	github.com/morikuni/aec v1.0.0 // indirect
-	github.com/opencontainers/image-spec v1.1.0-rc3
+	github.com/opencontainers/image-spec v1.1.0
 	github.com/ricochet2200/go-disk-usage/du v0.0.0-20210707232629-ac9918953285
 	github.com/rs/xid v1.5.0
 	github.com/sb10/l15h v0.0.0-20170510122137-64c488bf8e22
 	github.com/smartystreets/goconvey v1.6.4
-	golang.org/x/net v0.10.0 // indirect
-	golang.org/x/sys v0.8.0 // indirect
+	golang.org/x/net v0.26.0 // indirect
+	golang.org/x/sys v0.21.0 // indirect
 )
 
 require (
-	github.com/docker/distribution v2.8.2+incompatible // indirect
+	github.com/containerd/log v0.1.0 // indirect
+	github.com/distribution/reference v0.6.0 // indirect
 	github.com/docker/go-units v0.5.0 // indirect
+	github.com/felixge/httpsnoop v1.0.4 // indirect
 	github.com/fsnotify/fsnotify v1.4.9 // indirect
+	github.com/go-logr/logr v1.4.2 // indirect
+	github.com/go-logr/stdr v1.2.2 // indirect
 	github.com/gogo/protobuf v1.3.2 // indirect
-	github.com/google/go-cmp v0.5.9 // indirect
 	github.com/gopherjs/gopherjs v0.0.0-20181017120253-0766667cb4d1 // indirect
 	github.com/jtolds/gls v4.20.0+incompatible // indirect
-	github.com/mattn/go-isatty v0.0.19 // indirect
+	github.com/mattn/go-isatty v0.0.20 // indirect
+	github.com/moby/docker-image-spec v1.3.1 // indirect
 	github.com/moby/term v0.0.0-20200312100748-672ec06f55cd // indirect
 	github.com/opencontainers/go-digest v1.0.0 // indirect
 	github.com/pkg/errors v0.9.1 // indirect
-	github.com/pmezard/go-difflib v1.0.0 // indirect
 	github.com/smartystreets/assertions v0.0.0-20180927180507-b2de0cb4f26d // indirect
-	golang.org/x/mod v0.10.0 // indirect
-	golang.org/x/term v0.8.0 // indirect
+	go.opentelemetry.io/contrib/instrumentation/net/http/otelhttp v0.52.0 // indirect
+	go.opentelemetry.io/otel v1.27.0 // indirect
+	go.opentelemetry.io/otel/exporters/otlp/otlptrace/otlptracehttp v1.27.0 // indirect
+	go.opentelemetry.io/otel/metric v1.27.0 // indirect
+	go.opentelemetry.io/otel/sdk v1.27.0 // indirect
+	go.opentelemetry.io/otel/trace v1.27.0 // indirect
+	golang.org/x/term v0.21.0 // indirect
 	golang.org/x/time v0.0.0-20210723032227-1f47c861a9ac // indirect
-	golang.org/x/tools v0.9.1 // indirect
 	gopkg.in/fsnotify.v1 v1.4.7 // indirect
 	gopkg.in/tomb.v1 v1.0.0-20141024135613-dd632973f1e7 // indirect
-	gopkg.in/yaml.v3 v3.0.1 // indirect
 	gotest.tools/v3 v3.0.3 // indirect
 )