Update Nextflow support tests

.github/workflows/compliance-test.yaml

@@ -13,10 +13,6 @@
 # output a ssh address associated with the Github action worker. Helpful for debugging build steps and
 # and intermediary files/artifacts.
 #
-# Example:
-#   Web shell: https://tmate.io/t/q8FU3U9SvmMVxAhMHRyExNhr8
-#   SSH: ssh q8FU3U9SvmMVxAhMHRyExNhr8@sfo2.tmate.io
-#
 # - name: "Debug: Package dependancies for tmate (CentOS)"
 #   run: |
 #     yum install -y xz

.github/workflows/nextflow.yaml

@@ -28,9 +28,6 @@ jobs:
     runs-on: ubuntu-latest
     needs: build
     steps:
-    - name: Check out code
-      uses: actions/checkout@v2
-
     - name: Download funnel
       uses: actions/download-artifact@v2
       with:
@@ -40,10 +37,29 @@ jobs:
     - name: Setup tmate session
       uses: mxschmitt/action-tmate@v3
 
-    - name: Run Nextflow test (nf-canary)
+    - name: Install Nextflow
+      run: |
+        git clone https://github.com/nextflow-io/nextflow -b tes-update-1.1
+        cd nextflow
+        make compile
+
+    - name: Install Nextflow GA4GH-TES plugin
+      run: |
+        cat <<EOF >> nextflow.config
+          plugins {
+            id 'nf-ga4gh'
+          }
+          process.executor = 'tes'
+          tes.endpoint = 'http://localhost:8000'
+        EOF
+
+    - name: Start Funnel
       run: |
         chmod +x funnel
         ./funnel server run &
+
+    - name: Run Nextflow test (nf-canary)
+      run: |
         git clone https://github.com/ohsu-comp-bio/nf-canary
         cd nf-canary
         nextflow run main.nf

Makefile

@@ -11,7 +11,7 @@ git_upstream := $(shell git remote get-url $(shell git config branch.$(shell git
 export GIT_BRANCH = $(git_branch)
 export GIT_UPSTREAM = $(git_upstream)
 
-export FUNNEL_VERSION=0.11.0-rc.1
+export FUNNEL_VERSION=0.11.0
 
 # LAST_PR_NUMBER is used by the release notes builder to generate notes
 # based on pull requests (PR) up until the last release.

cmd/task/get.go

@@ -19,7 +19,8 @@ func Get(server string, ids []string, taskView string, w io.Writer) error {
 
 	res := []string{}
 
-	_, err = getTaskView(taskView)
+	taskValue, err := getTaskView(taskView)
+	taskView = tes.View_name[taskValue]
 	if err != nil {
 		return err
 	}

funnel.config → funnel.config.yml

@@ -6,4 +6,3 @@ LocalStorage:
 
 Worker:
   LeaveWorkDir: true
-

go.mod

@@ -1,6 +1,8 @@
 module github.com/ohsu-comp-bio/funnel
 
-go 1.18
+go 1.21
+
+toolchain go1.21.5
 
 require (
 	cloud.google.com/go/datastore v1.13.0
@@ -13,7 +15,7 @@ require (
 	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/docker/docker v24.0.2+incompatible
+	github.com/docker/docker v24.0.7+incompatible
 	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
@@ -39,23 +41,23 @@ require (
 	github.com/prometheus/common v0.42.0
 	github.com/rs/xid v1.2.1
 	github.com/shirou/gopsutil v3.21.11+incompatible
-	github.com/sirupsen/logrus v1.9.1
-	github.com/spf13/cobra v1.7.0
+	github.com/sirupsen/logrus v1.9.3
+	github.com/spf13/cobra v1.8.0
 	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 v0.13.0
-	golang.org/x/net v0.15.0
-	golang.org/x/oauth2 v0.12.0
+	golang.org/x/crypto v0.14.0
+	golang.org/x/net v0.17.0
+	golang.org/x/oauth2 v0.13.0
 	golang.org/x/time v0.3.0
-	google.golang.org/api v0.134.0
-	google.golang.org/genproto/googleapis/api v0.0.0-20230731193218-e0aa005b6bdf
-	google.golang.org/grpc v1.57.0
+	google.golang.org/api v0.143.0
+	google.golang.org/genproto/googleapis/api v0.0.0-20230913181813-007df8e322eb
+	google.golang.org/grpc v1.58.3
 	google.golang.org/protobuf v1.31.0
 	gopkg.in/olivere/elastic.v5 v5.0.84
-	k8s.io/api v0.26.3
-	k8s.io/apimachinery v0.27.3
-	k8s.io/client-go v0.26.1
+	k8s.io/api v0.28.0-alpha.2
+	k8s.io/apimachinery v0.28.2
+	k8s.io/client-go v0.28.0-alpha.2
 )
 
 require (
@@ -70,8 +72,8 @@ require (
 	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 v2.0.2 // indirect
-	github.com/davecgh/go-spew v1.1.1 // indirect
+	github.com/cpuguy83/go-md2man/v2 v2.0.3 // 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/dgryski/go-farm v0.0.0-20200201041132-a6ae2369ad13 // indirect
 	github.com/docker/distribution v2.8.2+incompatible // indirect
@@ -89,15 +91,15 @@ require (
 	github.com/go-ole/go-ole v1.2.6 // 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/go-openapi/swag v0.22.4 // indirect
 	github.com/golang/groupcache v0.0.0-20210331224755-41bb18bfe9da // indirect
 	github.com/golang/snappy v0.0.4 // indirect
-	github.com/google/gnostic v0.5.7-v3refs // indirect
-	github.com/google/go-cmp v0.5.9 // 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 v1.3.1 // indirect
-	github.com/googleapis/enterprise-certificate-proxy v0.2.5 // indirect
+	github.com/google/s2a-go v0.1.7 // indirect
+	github.com/google/uuid v1.4.0 // indirect
+	github.com/googleapis/enterprise-certificate-proxy v0.3.1 // indirect
 	github.com/googleapis/gax-go/v2 v2.12.0 // indirect
 	github.com/hashicorp/errwrap v1.1.0 // indirect
 	github.com/hashicorp/go-uuid v1.0.3 // indirect
@@ -107,11 +109,11 @@ require (
 	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 v1.17.0 // indirect
+	github.com/klauspost/compress v1.17.2 // 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 v0.0.14 // 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/mitchellh/go-wordwrap v1.0.1 // indirect
@@ -123,10 +125,10 @@ require (
 	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-rc3 // indirect
+	github.com/opencontainers/image-spec v1.1.0-rc5 // indirect
 	github.com/pierrec/lz4 v2.6.1+incompatible // indirect
 	github.com/pkg/errors v0.9.1 // indirect
-	github.com/pmezard/go-difflib v1.0.0 // 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/rcrowley/go-metrics v0.0.0-20201227073835-cf1acfcdf475 // indirect
@@ -144,16 +146,16 @@ require (
 	github.com/youmark/pkcs8 v0.0.0-20181117223130-1be2e3e5546d // indirect
 	github.com/yusufpapurcu/wmi v1.2.2 // indirect
 	go.opencensus.io v0.24.0 // indirect
-	golang.org/x/mod v0.12.0 // indirect
-	golang.org/x/sync v0.3.0 // indirect
-	golang.org/x/sys v0.12.0 // indirect
-	golang.org/x/term v0.12.0 // indirect
-	golang.org/x/text v0.13.0 // indirect
-	golang.org/x/tools v0.13.0 // indirect
+	golang.org/x/mod v0.13.0 // indirect
+	golang.org/x/sync v0.5.0 // indirect
+	golang.org/x/sys v0.13.0 // indirect
+	golang.org/x/term v0.13.0 // indirect
+	golang.org/x/text v0.14.0 // indirect
+	golang.org/x/tools 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 v0.0.0-20230731193218-e0aa005b6bdf // indirect
-	google.golang.org/genproto/googleapis/rpc v0.0.0-20230731193218-e0aa005b6bdf // indirect
+	google.golang.org/genproto v0.0.0-20230913181813-007df8e322eb // indirect
+	google.golang.org/genproto/googleapis/rpc v0.0.0-20230920204549-e6e6cdab5c13 // indirect
 	gopkg.in/inf.v0 v0.9.1 // indirect
 	gopkg.in/ini.v1 v1.67.0 // indirect
 	gopkg.in/jcmturner/aescts.v1 v1.0.1 // indirect
@@ -164,7 +166,7 @@ require (
 	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 v0.0.0-20230501164219-8b0f38b5fd1f // indirect
+	k8s.io/kube-openapi v0.0.0-20230717233707-2695361300d9 // indirect
 	k8s.io/utils v0.0.0-20230406110748-d93618cff8a2 // indirect
 	sigs.k8s.io/json v0.0.0-20221116044647-bc3834ca7abd // indirect
 	sigs.k8s.io/structured-merge-diff/v4 v4.2.3 // indirect