Fixes for unit tests and golangci-lint

.github/workflows/tests.yaml

@@ -1,39 +1,39 @@
 name: Go
 
-on: [ pull_request ]
+on: [ pull_request, workflow_dispatch ]
 
 jobs:
 
   lint:
     name: lint
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/setup-go@v3
+      - uses: actions/checkout@v4
+      - uses: actions/setup-go@v5
         with:
-          go-version: 1.18
-      - uses: actions/checkout@v3
+          go-version: 1.21
       - name: golangci-lint
-        uses: golangci/golangci-lint-action@v3
+        uses: golangci/golangci-lint-action@v4
         with:
-          version: v1.52.2
-          args: --timeout 3m --verbose
+          version: v1.56.2
+          args: --skip-dirs tests --modules-download-mode mod --timeout 10m --verbose
 
   build:
     runs-on: ubuntu-latest
     steps:
     - name: Set up Go 1.x
-      uses: actions/setup-go@v2
+      uses: actions/setup-go@v5
       with:
-        go-version: ^1.18
+        go-version: ^1.21
 
     - name: Check out code
-      uses: actions/checkout@v2
+      uses: actions/checkout@v4
 
     - name: Build
       run: go build -v ./
 
     - name: Store funnel
-      uses: actions/upload-artifact@v2
+      uses: actions/upload-artifact@v4
       with:
         name: funnelBin
         path: funnel
@@ -42,11 +42,11 @@ jobs:
     runs-on: ubuntu-latest
     steps:
     - name: Set up Go 1.x
-      uses: actions/setup-go@v2
+      uses: actions/setup-go@v5
       with:
-        go-version: ^1.18
+        go-version: ^1.21
     - name: Check out code
-      uses: actions/checkout@v2
+      uses: actions/checkout@v4
     - name: Unit Tests
       run: make test
 
@@ -55,10 +55,10 @@ jobs:
     needs: build
     steps:
     - name: Check out code
-      uses: actions/checkout@v2
+      uses: actions/checkout@v4
 
     - name: Download funnel bin
-      uses: actions/download-artifact@v2
+      uses: actions/download-artifact@v4
       with:
         name: funnelBin
     - name: MongoTest
@@ -73,10 +73,10 @@ jobs:
     needs: build
     steps:
     - name: Check out code
-      uses: actions/checkout@v2
+      uses: actions/checkout@v4
 
     - name: Download funnel bin
-      uses: actions/download-artifact@v2
+      uses: actions/download-artifact@v4
       with:
         name: funnelBin
     - name: Badger Test

go.mod

@@ -1,77 +1,165 @@
 module github.com/ohsu-comp-bio/funnel
 
-go 1.13
+go 1.21
 
 require (
 	cloud.google.com/go/datastore v1.11.0
 	cloud.google.com/go/pubsub v1.30.0
-	github.com/Microsoft/go-winio v0.4.14 // indirect
 	github.com/Shopify/sarama v1.26.1
-	github.com/StackExchange/wmi v0.0.0-20180116203802-5d049714c4a6 // indirect
 	github.com/alecthomas/units v0.0.0-20190924025748-f65c72e2690d
 	github.com/andreyvit/diff v0.0.0-20170406064948-c7f18ee00883
 	github.com/armon/circbuf v0.0.0-20190214190532-5111143e8da2
 	github.com/aws/aws-sdk-go v1.13.54
 	github.com/boltdb/bolt v1.3.1
 	github.com/cenkalti/backoff v2.2.1+incompatible
 	github.com/dgraph-io/badger/v2 v2.0.1
-	github.com/dgryski/go-farm v0.0.0-20200201041132-a6ae2369ad13 // indirect
-	github.com/docker/distribution v2.7.1+incompatible // indirect
 	github.com/docker/docker v24.0.7+incompatible
-	github.com/docker/go-connections v0.4.0 // indirect
-	github.com/docker/go-units v0.4.0 // indirect
 	github.com/elazarl/go-bindata-assetfs v1.0.0
 	github.com/gammazero/workerpool v0.0.0-20200206003619-019d125201ab
 	github.com/getlantern/deepcopy v0.0.0-20160317154340-7f45deb8130a
 	github.com/ghodss/yaml v1.0.0
 	github.com/gizak/termui v2.3.0+incompatible
 	github.com/globalsign/mgo v0.0.0-20181015135952-eeefdecb41b8
-	github.com/go-ini/ini v1.52.0 // indirect
-	github.com/go-ole/go-ole v1.2.1 // indirect
 	github.com/go-test/deep v1.0.5
 	github.com/golang/gddo v0.0.0-20200219175727-df439dd5819e
 	github.com/golang/protobuf v1.5.3
 	github.com/grpc-ecosystem/go-grpc-middleware v1.2.0
 	github.com/grpc-ecosystem/grpc-gateway v1.16.0
 	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
 	github.com/kballard/go-shellquote v0.0.0-20180428030007-95032a82bc51
 	github.com/kr/pretty v0.3.1
-	github.com/lestrrat-go/jwx/v2 v2.0.19 // indirect
+	github.com/lestrrat-go/jwx/v2 v2.0.19
 	github.com/logrusorgru/aurora v0.0.0-20200102142835-e9ef32dff381
-	github.com/maruel/panicparse v1.3.0 // indirect
-	github.com/mattn/go-runewidth v0.0.8 // indirect
 	github.com/minio/minio-go v6.0.14+incompatible
-	github.com/mitchellh/go-wordwrap v1.0.0 // indirect
-	github.com/moby/term v0.5.0 // indirect
-	github.com/morikuni/aec v1.0.0 // indirect
 	github.com/ncw/swift v1.0.50
-	github.com/nsf/termbox-go v0.0.0-20200204031403-4d2b513ad8be // indirect
 	github.com/nu7hatch/gouuid v0.0.0-20131221200532-179d4d0c4d8d
-	github.com/opencontainers/go-digest v1.0.0-rc1 // indirect
-	github.com/opencontainers/image-spec v1.0.2 // indirect
 	github.com/prometheus/client_golang v1.4.1
 	github.com/prometheus/common v0.9.1
 	github.com/rs/xid v1.2.1
-	github.com/sergi/go-diff v1.1.0 // indirect
 	github.com/shirou/gopsutil v2.20.1+incompatible
 	github.com/sirupsen/logrus v1.5.0
-	github.com/smartystreets/goconvey v1.6.4 // indirect
 	github.com/spf13/cobra v0.0.5
 	github.com/spf13/pflag v1.0.5
 	github.com/stretchr/testify v1.8.4
 	golang.org/x/crypto v0.17.0
-	golang.org/x/net v0.17.0
-	golang.org/x/oauth2 v0.8.0
+	golang.org/x/net v0.19.0
+	golang.org/x/oauth2 v0.10.0
 	golang.org/x/time v0.3.0
-	google.golang.org/api v0.114.0
-	google.golang.org/genproto v0.0.0-20230410155749-daa745c078e1
+	google.golang.org/api v0.126.0
+	google.golang.org/genproto/googleapis/api v0.0.0-20230530153820-e85fd2cbaebc
 	google.golang.org/grpc v1.56.3
-	gopkg.in/ini.v1 v1.51.0 // indirect
 	gopkg.in/olivere/elastic.v5 v5.0.84
+	k8s.io/api v0.29.2
+	k8s.io/apimachinery v0.29.2
+	k8s.io/client-go v0.29.2
+)
+
+require (
+	cloud.google.com/go v0.110.2 // indirect
+	cloud.google.com/go/compute v1.20.1 // indirect
+	cloud.google.com/go/compute/metadata v0.2.3 // indirect
+	cloud.google.com/go/iam v0.13.0 // indirect
+	github.com/DataDog/zstd v1.4.1 // indirect
+	github.com/Microsoft/go-winio v0.4.14 // indirect
+	github.com/StackExchange/wmi v0.0.0-20180116203802-5d049714c4a6 // indirect
+	github.com/beorn7/perks v1.0.1 // indirect
+	github.com/cespare/xxhash v1.1.0 // indirect
+	github.com/cespare/xxhash/v2 v2.2.0 // indirect
+	github.com/cpuguy83/go-md2man v1.0.10 // indirect
+	github.com/davecgh/go-spew v1.1.1 // indirect
+	github.com/decred/dcrd/dcrec/secp256k1/v4 v4.2.0 // indirect
+	github.com/dgraph-io/ristretto v0.0.0-20191025175511-c1f00be0418e // indirect
+	github.com/dgryski/go-farm v0.0.0-20200201041132-a6ae2369ad13 // indirect
+	github.com/docker/distribution v2.7.1+incompatible // indirect
+	github.com/docker/go-connections v0.4.0 // indirect
+	github.com/docker/go-units v0.4.0 // indirect
+	github.com/dustin/go-humanize v1.0.0 // indirect
+	github.com/eapache/go-resiliency v1.2.0 // indirect
+	github.com/eapache/go-xerial-snappy v0.0.0-20180814174437-776d5712da21 // indirect
+	github.com/eapache/queue v1.1.0 // indirect
+	github.com/emicklei/go-restful/v3 v3.11.0 // indirect
+	github.com/gammazero/deque v0.0.0-20190521012701-46e4ffb7a622 // indirect
+	github.com/go-ini/ini v1.52.0 // indirect
+	github.com/go-logr/logr v1.3.0 // indirect
+	github.com/go-ole/go-ole v1.2.1 // indirect
+	github.com/go-openapi/jsonpointer v0.19.6 // indirect
+	github.com/go-openapi/jsonreference v0.20.2 // indirect
+	github.com/go-openapi/swag v0.22.3 // indirect
+	github.com/goccy/go-json v0.10.2 // indirect
+	github.com/gogo/protobuf v1.3.2 // indirect
+	github.com/golang/groupcache v0.0.0-20210331224755-41bb18bfe9da // indirect
+	github.com/golang/snappy v0.0.4 // indirect
+	github.com/google/gnostic-models v0.6.8 // indirect
+	github.com/google/go-cmp v0.6.0 // indirect
+	github.com/google/gofuzz v1.2.0 // indirect
+	github.com/google/s2a-go v0.1.4 // indirect
+	github.com/google/uuid v1.3.0 // indirect
+	github.com/googleapis/enterprise-certificate-proxy v0.2.3 // indirect
+	github.com/googleapis/gax-go/v2 v2.11.0 // indirect
+	github.com/hashicorp/go-uuid v1.0.2 // indirect
+	github.com/inconshreveable/mousetrap v1.0.0 // indirect
+	github.com/jcmturner/gofork v1.0.0 // indirect
+	github.com/jmespath/go-jmespath v0.0.0-20180206201540-c2b33e8439af // indirect
+	github.com/josharian/intern v1.0.0 // indirect
+	github.com/json-iterator/go v1.1.12 // indirect
+	github.com/klauspost/compress v1.9.8 // indirect
+	github.com/konsorten/go-windows-terminal-sequences v1.0.1 // indirect
+	github.com/kr/text v0.2.0 // indirect
+	github.com/lestrrat-go/blackmagic v1.0.2 // indirect
+	github.com/lestrrat-go/httpcc v1.0.1 // indirect
+	github.com/lestrrat-go/httprc v1.0.4 // indirect
+	github.com/lestrrat-go/iter v1.0.2 // indirect
+	github.com/lestrrat-go/option v1.0.1 // indirect
+	github.com/mailru/easyjson v0.7.7 // indirect
+	github.com/maruel/panicparse v1.3.0 // indirect
+	github.com/mattn/go-runewidth v0.0.8 // indirect
+	github.com/matttproud/golang_protobuf_extensions v1.0.1 // indirect
+	github.com/mitchellh/go-homedir v1.1.0 // indirect
+	github.com/mitchellh/go-wordwrap v1.0.0 // indirect
+	github.com/moby/term v0.5.0 // indirect
+	github.com/modern-go/concurrent v0.0.0-20180306012644-bacd9c7ef1dd // indirect
+	github.com/modern-go/reflect2 v1.0.2 // indirect
+	github.com/morikuni/aec v1.0.0 // indirect
+	github.com/munnerz/goautoneg v0.0.0-20191010083416-a7dc8b61c822 // indirect
+	github.com/nsf/termbox-go v0.0.0-20200204031403-4d2b513ad8be // indirect
+	github.com/opencontainers/go-digest v1.0.0-rc1 // indirect
+	github.com/opencontainers/image-spec v1.0.2 // indirect
+	github.com/pierrec/lz4 v2.4.1+incompatible // indirect
+	github.com/pkg/errors v0.9.1 // indirect
+	github.com/pmezard/go-difflib v1.0.0 // indirect
+	github.com/prometheus/client_model v0.2.0 // indirect
+	github.com/prometheus/procfs v0.0.8 // indirect
+	github.com/rcrowley/go-metrics v0.0.0-20190826022208-cac0b30c2563 // indirect
+	github.com/rogpeppe/go-internal v1.10.0 // indirect
+	github.com/russross/blackfriday v1.5.2 // indirect
+	github.com/segmentio/asm v1.2.0 // indirect
+	github.com/sergi/go-diff v1.1.0 // indirect
+	github.com/smartystreets/goconvey v1.6.4 // indirect
+	github.com/stretchr/objx v0.5.0 // indirect
+	go.opencensus.io v0.24.0 // indirect
+	golang.org/x/sync v0.2.0 // indirect
+	golang.org/x/sys v0.15.0 // indirect
+	golang.org/x/term v0.15.0 // indirect
+	golang.org/x/text v0.14.0 // indirect
+	golang.org/x/xerrors v0.0.0-20220907171357-04be3eba64a2 // indirect
+	google.golang.org/appengine v1.6.7 // indirect
+	google.golang.org/genproto v0.0.0-20230530153820-e85fd2cbaebc // indirect
+	google.golang.org/genproto/googleapis/rpc v0.0.0-20230530153820-e85fd2cbaebc // indirect
+	google.golang.org/protobuf v1.31.0 // indirect
+	gopkg.in/inf.v0 v0.9.1 // indirect
+	gopkg.in/ini.v1 v1.51.0 // indirect
+	gopkg.in/jcmturner/aescts.v1 v1.0.1 // indirect
+	gopkg.in/jcmturner/dnsutils.v1 v1.0.1 // indirect
+	gopkg.in/jcmturner/gokrb5.v7 v7.5.0 // indirect
+	gopkg.in/jcmturner/rpc.v1 v1.1.0 // indirect
+	gopkg.in/yaml.v2 v2.4.0 // indirect
+	gopkg.in/yaml.v3 v3.0.1 // indirect
 	gotest.tools/v3 v3.5.1 // indirect
-	k8s.io/api v0.28.4
-	k8s.io/apimachinery v0.28.4
-	k8s.io/client-go v0.28.4
+	k8s.io/klog/v2 v2.110.1 // indirect
+	k8s.io/kube-openapi v0.0.0-20231010175941-2dd684a91f00 // indirect
+	k8s.io/utils v0.0.0-20230726121419-3b25d923346b // indirect
+	sigs.k8s.io/json v0.0.0-20221116044647-bc3834ca7abd // indirect
+	sigs.k8s.io/structured-merge-diff/v4 v4.4.1 // indirect
+	sigs.k8s.io/yaml v1.3.0 // indirect
 )