Merge branch 'develop' into dependabot/npm_and_yarn/webdash/multi-321…

…339f732
ohsu-comp-bio · Sep 10, 2024 · 8c6068e · 8c6068e
2 parents c29d539 + d67a738
commit 8c6068e
Show file tree

Hide file tree

Showing 8 changed files with 2,933 additions and 2,132 deletions.
diff --git a/.github/workflows/compliance-test.yaml b/.github/workflows/compliance-test.yaml
@@ -66,7 +66,7 @@ jobs:
       - name: Check out code
         uses: actions/checkout@v2
 
-      - uses: actions/download-artifact@v3
+      - uses: actions/download-artifact@v4.1.7
         with:
           name: funnelBin
 

diff --git a/.github/workflows/nextflow.yaml b/.github/workflows/nextflow.yaml
@@ -29,13 +29,12 @@ jobs:
     needs: build
     steps:
     - name: Download Funnel
-      uses: actions/download-artifact@v2
+      uses: actions/download-artifact@v4.1.7
       with:
         name: funnelBin
         path: funnel
 
     - name: Start Funnel
-      working-directory: 
       run: |
         cd funnel/
         chmod +x ./funnel
@@ -44,7 +43,7 @@ jobs:
     - name: Install Nextflow
       run: |
         cd ..
-        git clone https://github.com/nextflow-io/nextflow/ -b tes-update-1.1
+        git clone https://github.com/nextflow-io/nextflow
         cd nextflow
         make compile
 

diff --git a/.github/workflows/tests.yaml b/.github/workflows/tests.yaml
@@ -16,7 +16,8 @@ jobs:
         uses: golangci/golangci-lint-action@v3
         with:
           version: latest
-          args: --timeout 3m --verbose -D unused -D errcheck -D staticcheck -D govet -D gosimple -D ineffassign
+          # TODO: Re-enable all linters
+          args: --timeout 3m --verbose -D unused -D errcheck -D staticcheck -D govet -D gosimple -D ineffassign -D typecheck
 
   build:
     runs-on: ubuntu-latest
@@ -64,7 +65,7 @@ jobs:
       uses: actions/checkout@v2
 
     - name: Download funnel bin
-      uses: actions/download-artifact@v2
+      uses: actions/download-artifact@v4.1.7
       with:
         name: funnelBin
 
@@ -87,7 +88,7 @@ jobs:
       uses: actions/checkout@v2
 
     - name: Download funnel bin
-      uses: actions/download-artifact@v2
+      uses: actions/download-artifact@v4.1.7
       with:
         name: funnelBin
     - name: Badger Test
@@ -107,7 +108,7 @@ jobs:
       uses: actions/checkout@v2
 
     - name: Download funnel bin
-      uses: actions/download-artifact@v2
+      uses: actions/download-artifact@v4.1.7
       with:
         name: funnelBin
 
@@ -128,7 +129,7 @@ jobs:
       uses: actions/checkout@v2
 
     - name: Download funnel bin
-      uses: actions/download-artifact@v2
+      uses: actions/download-artifact@v4.1.7
       with:
         name: funnelBin
 
@@ -138,4 +139,4 @@ jobs:
         make start-generic-s3
         sleep 10
         make test-generic-s3
-          
+          
diff --git a/go.mod b/go.mod
@@ -1,180 +1,185 @@
 module github.com/ohsu-comp-bio/funnel
 
-go 1.21
+go 1.22.0
 
-toolchain go1.21.5
+toolchain go1.22.2
 
 require (
-	cloud.google.com/go/datastore v1.15.0
-	cloud.google.com/go/pubsub v1.33.0
-	github.com/Microsoft/go-winio v0.6.1 // indirect
-	github.com/Shopify/sarama v1.26.1
-	github.com/alecthomas/units v0.0.0-20211218093645-b94a6e3cc137
+	cloud.google.com/go/datastore v1.17.1
+	cloud.google.com/go/pubsub v1.40.0
+	github.com/Microsoft/go-winio v0.6.2 // indirect
+	github.com/Shopify/sarama v1.38.1
+	github.com/alecthomas/units v0.0.0-20231202071711-9a357b53e9c9
 	github.com/andreyvit/diff v0.0.0-20170406064948-c7f18ee00883
 	github.com/armon/circbuf v0.0.0-20190214190532-5111143e8da2
-	github.com/aws/aws-sdk-go v1.44.314
+	github.com/aws/aws-sdk-go v1.55.2
 	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/dgraph-io/badger/v2 v2.2007.4
 	github.com/dgryski/go-farm v0.0.0-20200201041132-a6ae2369ad13 // indirect
-	github.com/docker/distribution v2.8.2+incompatible // indirect
-	github.com/docker/docker v24.0.7+incompatible
-	github.com/docker/go-connections v0.4.0 // indirect
+	github.com/docker/docker v27.1.1+incompatible
+	github.com/docker/go-connections v0.5.0 // indirect
 	github.com/docker/go-units v0.5.0 // indirect
-	github.com/elazarl/go-bindata-assetfs v1.0.0
-	github.com/gammazero/workerpool v0.0.0-20200206003619-019d125201ab
-	github.com/getkin/kin-openapi v0.98.0
+	github.com/elazarl/go-bindata-assetfs v1.0.1
+	github.com/gammazero/workerpool v1.1.3
+	github.com/getkin/kin-openapi v0.126.0
 	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/go-ini/ini v1.52.0 // indirect
-	github.com/go-ole/go-ole v1.2.6 // 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/imdario/mergo v0.3.8
-	github.com/jlaffaye/ftp v0.0.0-20191218041957-e1b8fdd0dcc3
+	github.com/go-ini/ini v1.67.0 // indirect
+	github.com/go-ole/go-ole v1.3.0 // indirect
+	github.com/go-test/deep v1.1.1
+	github.com/golang/gddo v0.0.0-20210115222349-20d68f94ee1f
+	github.com/golang/protobuf v1.5.4
+	github.com/grpc-ecosystem/go-grpc-middleware v1.4.0
+	github.com/imdario/mergo v0.3.16
+	github.com/jlaffaye/ftp v0.2.0
 	github.com/kballard/go-shellquote v0.0.0-20180428030007-95032a82bc51
 	github.com/kr/pretty v0.3.1
-	github.com/logrusorgru/aurora v0.0.0-20200102142835-e9ef32dff381
+	github.com/logrusorgru/aurora v2.0.3+incompatible
 	github.com/minio/minio-go v6.0.14+incompatible
 	github.com/mitchellh/go-wordwrap v1.0.1 // 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/ncw/swift v1.0.53
 	github.com/nu7hatch/gouuid v0.0.0-20131221200532-179d4d0c4d8d
-	github.com/prometheus/client_golang v1.15.1
-	github.com/prometheus/common v0.42.0
+	github.com/prometheus/client_golang v1.19.1
+	github.com/prometheus/common v0.55.0
 	github.com/rs/xid v1.5.0
 	github.com/shirou/gopsutil v3.21.11+incompatible
 	github.com/sirupsen/logrus v1.9.3
-	github.com/spf13/cobra v1.8.0
+	github.com/spf13/cobra v1.8.1
 	github.com/spf13/pflag v1.0.5
-	github.com/stretchr/testify v1.8.4
-	go.mongodb.org/mongo-driver v1.12.1
-	golang.org/x/crypto v0.18.0
-	golang.org/x/net v0.20.0
-	golang.org/x/oauth2 v0.16.0
-	golang.org/x/time v0.3.0
-	google.golang.org/api v0.149.0
-	google.golang.org/genproto v0.0.0-20240116215550-a9fa1716bcac // indirect
-	google.golang.org/grpc v1.61.0
-	gopkg.in/ini.v1 v1.67.0 // indirect
-	gopkg.in/olivere/elastic.v5 v5.0.84
-	k8s.io/api v0.28.0-alpha.2
-	k8s.io/apimachinery v0.28.2
-	k8s.io/client-go v0.28.0-alpha.2
+	github.com/stretchr/testify v1.9.0
+	go.mongodb.org/mongo-driver v1.16.0
+	golang.org/x/crypto v0.25.0
+	golang.org/x/net v0.27.0
+	golang.org/x/oauth2 v0.21.0
+	golang.org/x/time v0.5.0
+	google.golang.org/api v0.189.0
+	google.golang.org/genproto v0.0.0-20240722135656-d784300faade // indirect
+	google.golang.org/grpc v1.65.0
+	gopkg.in/olivere/elastic.v5 v5.0.86
+	k8s.io/api v0.31.0-beta.0
+	k8s.io/apimachinery v0.31.0-beta.0
+	k8s.io/client-go v0.31.0-beta.0
 )
 
 require (
 	github.com/gogo/protobuf v1.3.2
-	github.com/grpc-ecosystem/grpc-gateway/v2 v2.19.1
+	github.com/grpc-ecosystem/grpc-gateway/v2 v2.20.0
 	github.com/hashicorp/go-multierror v1.1.1
-	google.golang.org/genproto/googleapis/api v0.0.0-20240125205218-1f4bbc51befe
-	google.golang.org/protobuf v1.32.0
+	google.golang.org/genproto/googleapis/api v0.0.0-20240701130421-f6361c86f094
+	google.golang.org/protobuf v1.34.2
 )
 
 require (
-	cloud.google.com/go v0.111.0 // indirect
-	cloud.google.com/go/compute v1.23.3 // indirect
-	cloud.google.com/go/compute/metadata v0.2.3 // indirect
-	cloud.google.com/go/iam v1.1.5 // indirect
+	cloud.google.com/go v0.115.0 // indirect
+	cloud.google.com/go/auth v0.7.2 // indirect
+	cloud.google.com/go/auth/oauth2adapt v0.2.3 // indirect
+	cloud.google.com/go/compute/metadata v0.5.0 // indirect
+	cloud.google.com/go/iam v1.1.10 // indirect
 	github.com/Azure/go-ansiterm v0.0.0-20230124172434-306776ec8161 // indirect
-	github.com/DataDog/zstd v1.4.5 // indirect
 	github.com/OneOfOne/xxhash v1.2.8 // 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/v2 v2.0.3 // indirect
+	github.com/cespare/xxhash/v2 v2.3.0 // indirect
+	github.com/containerd/log v0.1.0 // indirect
+	github.com/cpuguy83/go-md2man/v2 v2.0.4 // indirect
 	github.com/davecgh/go-spew v1.1.2-0.20180830191138-d8f796af33cc // indirect
-	github.com/dgraph-io/ristretto v0.0.0-20191025175511-c1f00be0418e // indirect
+	github.com/dgraph-io/ristretto v0.1.1 // indirect
+	github.com/distribution/reference v0.6.0 // indirect
 	github.com/dustin/go-humanize v1.0.1 // 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/go-resiliency v1.6.0 // indirect
+	github.com/eapache/go-xerial-snappy v0.0.0-20230731223053-c322873962e3 // indirect
 	github.com/eapache/queue v1.1.0 // indirect
-	github.com/emicklei/go-restful/v3 v3.9.0 // indirect
-	github.com/frankban/quicktest v1.14.4 // indirect
-	github.com/gammazero/deque v0.0.0-20190521012701-46e4ffb7a622 // indirect
-	github.com/go-logr/logr v1.2.4 // indirect
+	github.com/emicklei/go-restful/v3 v3.12.0 // indirect
+	github.com/felixge/httpsnoop v1.0.4 // indirect
+	github.com/fxamacker/cbor/v2 v2.7.0 // indirect
+	github.com/gammazero/deque v0.2.1 // indirect
+	github.com/go-logr/logr v1.4.2 // indirect
 	github.com/go-logr/stdr v1.2.2 // indirect
-	github.com/go-openapi/jsonpointer v0.19.6 // indirect
-	github.com/go-openapi/jsonreference v0.20.2 // indirect
-	github.com/go-openapi/swag v0.22.4 // indirect
+	github.com/go-openapi/jsonpointer v0.21.0 // indirect
+	github.com/go-openapi/jsonreference v0.21.0 // indirect
+	github.com/go-openapi/swag v0.23.0 // indirect
+	github.com/golang/glog v1.2.1 // 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 v0.1.7 // indirect
-	github.com/google/uuid v1.5.0 // indirect
+	github.com/google/uuid v1.6.0 // indirect
 	github.com/googleapis/enterprise-certificate-proxy v0.3.2 // indirect
-	github.com/googleapis/gax-go/v2 v2.12.0 // indirect
+	github.com/googleapis/gax-go/v2 v2.12.5 // indirect
 	github.com/hashicorp/errwrap v1.1.0 // indirect
 	github.com/hashicorp/go-uuid v1.0.3 // indirect
 	github.com/inconshreveable/mousetrap v1.1.0 // indirect
-	github.com/invopop/yaml v0.1.0 // indirect
-	github.com/jcmturner/gofork v1.0.0 // indirect
+	github.com/invopop/yaml v0.3.1 // indirect
+	github.com/jcmturner/aescts/v2 v2.0.0 // indirect
+	github.com/jcmturner/dnsutils/v2 v2.0.0 // indirect
+	github.com/jcmturner/gofork v1.7.6 // indirect
+	github.com/jcmturner/gokrb5/v8 v8.4.4 // indirect
+	github.com/jcmturner/rpc/v2 v2.0.3 // indirect
 	github.com/jmespath/go-jmespath v0.4.0 // indirect
 	github.com/josharian/intern v1.0.0 // indirect
 	github.com/json-iterator/go v1.1.12 // indirect
-	github.com/klauspost/compress v1.17.4 // indirect
+	github.com/klauspost/compress v1.17.8 // indirect
 	github.com/kr/text v0.2.0 // indirect
 	github.com/mailru/easyjson v0.7.7 // indirect
 	github.com/maruel/panicparse v1.6.2 // indirect
 	github.com/mattn/go-runewidth v0.0.15 // indirect
-	github.com/matttproud/golang_protobuf_extensions v1.0.4 // indirect
 	github.com/mitchellh/go-homedir v1.1.0 // indirect
+	github.com/moby/docker-image-spec v1.3.1 // indirect
 	github.com/modern-go/concurrent v0.0.0-20180306012644-bacd9c7ef1dd // indirect
 	github.com/modern-go/reflect2 v1.0.2 // indirect
-	github.com/montanaflynn/stats v0.7.0 // indirect
+	github.com/mohae/deepcopy v0.0.0-20170929034955-c48cc78d4826 // indirect
+	github.com/montanaflynn/stats v0.7.1 // indirect
 	github.com/munnerz/goautoneg v0.0.0-20191010083416-a7dc8b61c822 // indirect
 	github.com/nsf/termbox-go v1.1.1 // indirect
 	github.com/opencontainers/go-digest v1.0.0 // indirect
-	github.com/opencontainers/image-spec v1.1.0-rc5 // indirect
-	github.com/pierrec/lz4 v2.6.1+incompatible // indirect
+	github.com/opencontainers/image-spec v1.1.0 // indirect
+	github.com/perimeterx/marshmallow v1.1.5 // indirect
+	github.com/pierrec/lz4/v4 v4.1.21 // indirect
 	github.com/pkg/errors v0.9.1 // indirect
 	github.com/pmezard/go-difflib v1.0.1-0.20181226105442-5d4384ee4fb2 // indirect
-	github.com/prometheus/client_model v0.4.0 // indirect
-	github.com/prometheus/procfs v0.9.0 // indirect
+	github.com/prometheus/client_model v0.6.1 // indirect
+	github.com/prometheus/procfs v0.15.1 // indirect
 	github.com/rcrowley/go-metrics v0.0.0-20201227073835-cf1acfcdf475 // indirect
-	github.com/rivo/uniseg v0.4.2 // indirect
-	github.com/rogpeppe/go-internal v1.10.0 // indirect
+	github.com/rivo/uniseg v0.4.7 // indirect
+	github.com/rogpeppe/go-internal v1.12.0 // indirect
 	github.com/russross/blackfriday/v2 v2.1.0 // indirect
 	github.com/sergi/go-diff v1.2.0 // indirect
-	github.com/smartystreets/goconvey v1.8.0 // indirect
-	github.com/stretchr/objx v0.5.0 // indirect
-	github.com/tklauser/go-sysconf v0.3.11 // indirect
-	github.com/tklauser/numcpus v0.6.0 // indirect
+	github.com/stretchr/objx v0.5.2 // indirect
+	github.com/tklauser/go-sysconf v0.3.14 // indirect
+	github.com/tklauser/numcpus v0.8.0 // indirect
+	github.com/x448/float16 v0.8.4 // indirect
 	github.com/xdg-go/pbkdf2 v1.0.0 // indirect
 	github.com/xdg-go/scram v1.1.2 // indirect
 	github.com/xdg-go/stringprep v1.0.4 // indirect
-	github.com/youmark/pkcs8 v0.0.0-20181117223130-1be2e3e5546d // indirect
-	github.com/yusufpapurcu/wmi v1.2.2 // indirect
+	github.com/youmark/pkcs8 v0.0.0-20240424034433-3c2c7870ae76 // indirect
+	github.com/yusufpapurcu/wmi v1.2.4 // indirect
 	go.opencensus.io v0.24.0 // indirect
-	go.opentelemetry.io/otel v1.19.0 // indirect
-	go.opentelemetry.io/otel/metric v1.19.0 // indirect
-	go.opentelemetry.io/otel/trace v1.19.0 // indirect
-	golang.org/x/mod v0.13.0 // indirect
-	golang.org/x/sync v0.5.0 // indirect
-	golang.org/x/sys v0.16.0 // indirect
-	golang.org/x/term v0.16.0 // indirect
-	golang.org/x/text v0.14.0 // indirect
-	golang.org/x/tools v0.14.0 // indirect
-	google.golang.org/appengine v1.6.8 // indirect
-	google.golang.org/genproto/googleapis/rpc v0.0.0-20240125205218-1f4bbc51befe // indirect
+	go.opentelemetry.io/contrib/instrumentation/google.golang.org/grpc/otelgrpc v0.51.0 // indirect
+	go.opentelemetry.io/contrib/instrumentation/net/http/otelhttp v0.51.0 // indirect
+	go.opentelemetry.io/otel v1.26.0 // indirect
+	go.opentelemetry.io/otel/exporters/otlp/otlptrace/otlptracehttp v1.26.0 // indirect
+	go.opentelemetry.io/otel/metric v1.26.0 // indirect
+	go.opentelemetry.io/otel/sdk v1.26.0 // indirect
+	go.opentelemetry.io/otel/trace v1.26.0 // indirect
+	golang.org/x/sync v0.7.0 // indirect
+	golang.org/x/sys v0.22.0 // indirect
+	golang.org/x/term v0.22.0 // indirect
+	golang.org/x/text v0.16.0 // indirect
+	google.golang.org/genproto/googleapis/rpc v0.0.0-20240722135656-d784300faade // indirect
 	gopkg.in/inf.v0 v0.9.1 // 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 v3.4.0 // indirect
-	k8s.io/klog/v2 v2.100.1 // indirect
-	k8s.io/kube-openapi v0.0.0-20230717233707-2695361300d9 // indirect
-	k8s.io/utils v0.0.0-20230406110748-d93618cff8a2 // indirect
+	k8s.io/klog/v2 v2.130.1 // indirect
+	k8s.io/kube-openapi v0.0.0-20240430033511-f0e62f92d13f // indirect
+	k8s.io/utils v0.0.0-20240711033017-18e509b52bc8 // indirect
 	sigs.k8s.io/json v0.0.0-20221116044647-bc3834ca7abd // indirect
-	sigs.k8s.io/structured-merge-diff/v4 v4.2.3 // indirect
-	sigs.k8s.io/yaml v1.3.0 // indirect
+	sigs.k8s.io/structured-merge-diff/v4 v4.4.1 // indirect
+	sigs.k8s.io/yaml v1.4.0 // indirect
 )