Merge branch 'feature/k8s-support' into feature/container-engines

ohsu-comp-bio · Oct 1, 2024 · 1a32f86 · 1a32f86
2 parents c0f5920 + f8db3a5
commit 1a32f86
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Showing 4 changed files with 615 additions and 63 deletions.
diff --git a/compute/kubernetes/backend_test.go b/compute/kubernetes/backend_test.go
@@ -1,79 +1,25 @@
 package kubernetes
 
 import (
-	"context"
 	"fmt"
-	"io/ioutil"
+	"os"
 	"testing"
 
-	"path/filepath"
-
 	"github.com/ohsu-comp-bio/funnel/config"
 	"github.com/ohsu-comp-bio/funnel/logger"
 	"github.com/ohsu-comp-bio/funnel/tes"
-	"k8s.io/client-go/kubernetes"
-	"k8s.io/client-go/rest"
-	"k8s.io/client-go/tools/clientcmd"
-	"k8s.io/client-go/util/homedir"
 )
 
-// getKubernetesClient creates a Kubernetes clientset for communication with the Kubernetes API
-func getKubernetesClient() (*kubernetes.Clientset, error) {
-	var config *rest.Config
-	var err error
-	var contextName string
-
-	// Try to create an in-cluster client
-	config, err = rest.InClusterConfig()
-	if err != nil {
-		// If in-cluster config fails, fallback to kubeconfig file for out-of-cluster
-		kubeconfig := filepath.Join(homedir.HomeDir(), ".kube", "config")
-		kubeConfig, err := clientcmd.LoadFromFile(kubeconfig)
-		if err != nil {
-			return nil, fmt.Errorf("failed to load kubeconfig: %v", err)
-		}
-
-		// Get the current context name
-		contextName = kubeConfig.CurrentContext
-
-		// Build config from flags or kubeconfig
-		config, err = clientcmd.BuildConfigFromFlags("", kubeconfig)
-		if err != nil {
-			return nil, fmt.Errorf("failed to create kubernetes config: %v", err)
-		}
-	} else {
-		contextName = "in-cluster"
-	}
-
-	// Create the clientset
-	clientset, err := kubernetes.NewForConfig(config)
-	if err != nil {
-		return nil, fmt.Errorf("failed to create kubernetes clientset: %v", err)
-	}
-
-	// Log or print the current context being used
-	fmt.Printf("Using Kubernetes context: %s\n", contextName)
-
-	return clientset, nil
-}
-
 func TestCreateJobc(t *testing.T) {
 	conf := config.DefaultConfig().Kubernetes
-	content, err := ioutil.ReadFile("../../config/kubernetes-template.yaml")
+	content, err := os.ReadFile("../../config/kubernetes-template.yaml")
 	if err != nil {
 		t.Fatal(fmt.Errorf("reading template: %v", err))
 	}
 	conf.Template = string(content)
 	log := logger.NewLogger("test", logger.DefaultConfig())
-
-	// Create Kubernetes client
-	clientset, err := getKubernetesClient()
-	if err != nil {
-		t.Fatal(fmt.Errorf("creating kubernetes client: %v", err))
-	}
-
 	b := &Backend{
-		client:    clientset.BatchV1().Jobs(conf.Namespace),
+		client:    nil,
 		namespace: conf.Namespace,
 		template:  conf.Template,
 		event:     nil,
@@ -96,9 +42,4 @@ func TestCreateJobc(t *testing.T) {
 		t.Fatal(err)
 	}
 	t.Logf("%+v", job)
-
-	err = b.Submit(context.Background(), task)
-	if err != nil {
-		t.Fatal(err)
-	}
 }
diff --git a/go.mod b/go.mod
@@ -80,42 +80,165 @@ require (
 	cloud.google.com/go/compute/metadata v0.5.0 // indirect
 	cloud.google.com/go/iam v1.1.13 // indirect
 	github.com/Azure/go-ansiterm v0.0.0-20230124172434-306776ec8161 // indirect
+	github.com/Azure/go-autorest v14.2.0+incompatible // indirect
+	github.com/Azure/go-autorest/autorest v0.11.29 // indirect
+	github.com/Azure/go-autorest/autorest/adal v0.9.23 // indirect
+	github.com/Azure/go-autorest/autorest/azure/auth v0.5.12 // indirect
+	github.com/Azure/go-autorest/autorest/azure/cli v0.4.6 // indirect
+	github.com/Azure/go-autorest/autorest/date v0.3.0 // indirect
+	github.com/Azure/go-autorest/autorest/to v0.4.0 // indirect
+	github.com/Azure/go-autorest/logger v0.2.1 // indirect
+	github.com/Azure/go-autorest/tracing v0.6.0 // indirect
+	github.com/AzureAD/microsoft-authentication-library-for-go v1.2.2 // indirect
+	github.com/BurntSushi/toml v1.2.1 // indirect
+	github.com/Masterminds/goutils v1.1.1 // indirect
+	github.com/Masterminds/semver/v3 v3.2.1 // indirect
+	github.com/Masterminds/sprig/v3 v3.2.3 // indirect
 	github.com/OneOfOne/xxhash v1.2.8 // indirect
+	github.com/ProtonMail/go-crypto v1.0.0 // indirect
+	github.com/alessio/shellescape v1.4.1 // indirect
+	github.com/anchore/bubbly v0.0.0-20230518153401-87b6af8ccf22 // indirect
+	github.com/anchore/go-logger v0.0.0-20230725134548-c21dafa1ec5a // indirect
+	github.com/anchore/go-macholibre v0.0.0-20220308212642-53e6d0aaf6fb // indirect
+	github.com/anchore/quill v0.4.1 // indirect
+	github.com/asaskevich/govalidator v0.0.0-20230301143203-a9d515a09cc2 // indirect
+	github.com/atc0005/go-teams-notify/v2 v2.10.0 // indirect
+	github.com/aws/aws-sdk-go-v2 v1.26.1 // indirect
+	github.com/aws/aws-sdk-go-v2/aws/protocol/eventstream v1.6.1 // indirect
+	github.com/aws/aws-sdk-go-v2/config v1.27.13 // indirect
+	github.com/aws/aws-sdk-go-v2/credentials v1.17.13 // indirect
+	github.com/aws/aws-sdk-go-v2/feature/ec2/imds v1.16.1 // indirect
+	github.com/aws/aws-sdk-go-v2/feature/s3/manager v1.16.9 // indirect
+	github.com/aws/aws-sdk-go-v2/internal/configsources v1.3.5 // indirect
+	github.com/aws/aws-sdk-go-v2/internal/endpoints/v2 v2.6.5 // indirect
+	github.com/aws/aws-sdk-go-v2/internal/ini v1.8.0 // indirect
+	github.com/aws/aws-sdk-go-v2/internal/v4a v1.3.3 // indirect
+	github.com/aws/aws-sdk-go-v2/service/ecr v1.28.0 // indirect
+	github.com/aws/aws-sdk-go-v2/service/ecrpublic v1.23.5 // indirect
+	github.com/aws/aws-sdk-go-v2/service/internal/accept-encoding v1.11.2 // indirect
+	github.com/aws/aws-sdk-go-v2/service/internal/checksum v1.3.5 // indirect
+	github.com/aws/aws-sdk-go-v2/service/internal/presigned-url v1.11.7 // indirect
+	github.com/aws/aws-sdk-go-v2/service/internal/s3shared v1.17.3 // indirect
+	github.com/aws/aws-sdk-go-v2/service/kms v1.30.0 // indirect
+	github.com/aws/aws-sdk-go-v2/service/s3 v1.51.4 // indirect
+	github.com/aws/aws-sdk-go-v2/service/sso v1.20.6 // indirect
+	github.com/aws/aws-sdk-go-v2/service/ssooidc v1.24.0 // indirect
+	github.com/aws/aws-sdk-go-v2/service/sts v1.28.7 // indirect
+	github.com/aws/smithy-go v1.20.2 // indirect
+	github.com/awslabs/amazon-ecr-credential-helper/ecr-login v0.0.0-20240514230400-03fa26f5508f // indirect
+	github.com/aymanbagabas/go-osc52/v2 v2.0.1 // indirect
+	github.com/bahlo/generic-list-go v0.2.0 // indirect
 	github.com/beorn7/perks v1.0.1 // indirect
+	github.com/blacktop/go-dwarf v1.0.9 // indirect
+	github.com/blacktop/go-macho v1.1.162 // indirect
+	github.com/blakesmith/ar v0.0.0-20190502131153-809d4375e1fb // indirect
+	github.com/bluesky-social/indigo v0.0.0-20240411170459-440932307e0d // indirect
+	github.com/buchanae/github-release-notes v0.0.0-20180827045457-200e1dacadbb // indirect
+	github.com/buger/jsonparser v1.1.1 // indirect
+	github.com/caarlos0/ctrlc v1.2.0 // indirect
+	github.com/caarlos0/env/v11 v11.0.1 // indirect
+	github.com/caarlos0/go-reddit/v3 v3.0.1 // indirect
+	github.com/caarlos0/go-shellwords v1.0.12 // indirect
+	github.com/caarlos0/go-version v0.1.1 // indirect
+	github.com/caarlos0/log v0.4.4 // indirect
+	github.com/carlmjohnson/versioninfo v0.22.5 // indirect
+	github.com/cavaliergopher/cpio v1.0.1 // indirect
+	github.com/cenkalti/backoff/v4 v4.3.0 // indirect
 	github.com/cespare/xxhash v1.1.0 // indirect
 	github.com/cespare/xxhash/v2 v2.3.0 // indirect
+	github.com/charmbracelet/bubbletea v0.22.1 // indirect
+	github.com/charmbracelet/lipgloss v0.10.0 // indirect
+	github.com/charmbracelet/x/exp/ordered v0.0.0-20231010190216-1cb11efc897d // indirect
+	github.com/chrismellard/docker-credential-acr-env v0.0.0-20230304212654-82a0ddb27589 // indirect
+	github.com/cloudflare/circl v1.3.8 // indirect
+	github.com/containerd/console v1.0.4 // indirect
 	github.com/containerd/log v0.1.0 // indirect
+	github.com/containerd/stargz-snapshotter/estargz v0.14.3 // indirect
 	github.com/cpuguy83/go-md2man/v2 v2.0.4 // indirect
+	github.com/cyphar/filepath-securejoin v0.2.4 // indirect
 	github.com/davecgh/go-spew v1.1.2-0.20180830191138-d8f796af33cc // indirect
+	github.com/davidmz/go-pageant v1.0.2 // indirect
+	github.com/dghubble/go-twitter v0.0.0-20211115160449-93a8679adecb // indirect
+	github.com/dghubble/oauth1 v0.7.3 // indirect
+	github.com/dghubble/sling v1.4.0 // indirect
 	github.com/dgraph-io/ristretto v0.1.1 // indirect
+	github.com/dimchansky/utfbom v1.1.1 // indirect
 	github.com/distribution/reference v0.6.0 // indirect
+	github.com/docker/cli v25.0.4+incompatible // indirect
+	github.com/docker/distribution v2.8.3+incompatible // indirect
+	github.com/docker/docker-credential-helpers v0.8.1 // indirect
 	github.com/dustin/go-humanize v1.0.1 // 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 v3.12.1 // indirect
 	github.com/felixge/httpsnoop v1.0.4 // indirect
+	github.com/fsnotify/fsnotify v1.7.0 // indirect
 	github.com/fxamacker/cbor/v2 v2.7.0 // indirect
+	github.com/gabriel-vasile/mimetype v1.4.2 // indirect
 	github.com/gammazero/deque v0.2.1 // indirect
+	github.com/github/smimesign v0.2.0 // indirect
+	github.com/go-fed/httpsig v1.1.0 // indirect
+	github.com/go-git/gcfg v1.5.1-0.20230307220236-3a3c6141e376 // indirect
+	github.com/go-git/go-billy/v5 v5.5.0 // indirect
+	github.com/go-git/go-git/v5 v5.12.0 // indirect
 	github.com/go-logr/logr v1.4.2 // indirect
 	github.com/go-logr/stdr v1.2.2 // indirect
+	github.com/go-openapi/analysis v0.23.0 // indirect
+	github.com/go-openapi/errors v0.22.0 // indirect
 	github.com/go-openapi/jsonpointer v0.21.0 // indirect
 	github.com/go-openapi/jsonreference v0.21.0 // indirect
+	github.com/go-openapi/loads v0.22.0 // indirect
+	github.com/go-openapi/runtime v0.28.0 // indirect
+	github.com/go-openapi/spec v0.21.0 // indirect
+	github.com/go-openapi/strfmt v0.23.0 // indirect
 	github.com/go-openapi/swag v0.23.0 // indirect
+	github.com/go-openapi/validate v0.24.0 // indirect
+	github.com/go-restruct/restruct v1.2.0-alpha // indirect
+	github.com/go-telegram-bot-api/telegram-bot-api/v5 v5.5.1 // indirect
+	github.com/gobwas/glob v0.2.3 // indirect
+	github.com/golang-jwt/jwt/v4 v4.5.0 // indirect
+	github.com/golang-jwt/jwt/v5 v5.2.1 // 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 v0.6.9-0.20230804172637-c7be7c783f49 // indirect
 	github.com/google/go-cmp v0.6.0 // indirect
+	github.com/google/go-containerregistry v0.19.1 // indirect
+	github.com/google/go-github v17.0.0+incompatible // indirect
+	github.com/google/go-github/v62 v62.0.0 // indirect
+	github.com/google/go-querystring v1.1.0 // indirect
 	github.com/google/gofuzz v1.2.0 // indirect
 	github.com/google/s2a-go v0.1.8 // indirect
 	github.com/google/uuid v1.6.0 // indirect
+	github.com/google/wire v0.6.0 // indirect
 	github.com/googleapis/enterprise-certificate-proxy v0.3.2 // indirect
 	github.com/googleapis/gax-go/v2 v2.13.0 // indirect
 	github.com/hashicorp/errwrap v1.1.0 // indirect
+	github.com/hashicorp/go-cleanhttp v0.5.2 // indirect
+	github.com/hashicorp/go-retryablehttp v0.7.5 // indirect
 	github.com/hashicorp/go-uuid v1.0.3 // indirect
+	github.com/hashicorp/go-version v1.6.0 // indirect
+	github.com/hashicorp/golang-lru v1.0.2 // indirect
+	github.com/hashicorp/hcl v1.0.1-vault-5 // indirect
+	github.com/huandu/xstrings v1.3.3 // indirect
 	github.com/inconshreveable/mousetrap v1.1.0 // indirect
+	github.com/invopop/jsonschema v0.12.0 // indirect
 	github.com/invopop/yaml v0.3.1 // indirect
+	github.com/ipfs/bbloom v0.0.4 // indirect
+	github.com/ipfs/go-block-format v0.2.0 // indirect
+	github.com/ipfs/go-cid v0.4.1 // indirect
+	github.com/ipfs/go-datastore v0.6.0 // indirect
+	github.com/ipfs/go-ipfs-blockstore v1.3.1 // indirect
+	github.com/ipfs/go-ipfs-ds-help v1.1.1 // indirect
+	github.com/ipfs/go-ipfs-util v0.0.3 // indirect
+	github.com/ipfs/go-ipld-cbor v0.1.0 // indirect
+	github.com/ipfs/go-ipld-format v0.6.0 // indirect
+	github.com/ipfs/go-log v1.0.5 // indirect
+	github.com/ipfs/go-log/v2 v2.5.1 // indirect
+	github.com/ipfs/go-metrics-interface v0.0.1 // indirect
+	github.com/jbenet/go-context v0.0.0-20150711004518-d14ea06fba99 // indirect
+	github.com/jbenet/goprocess v0.1.4 // 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
@@ -126,23 +249,55 @@ require (
 	github.com/json-iterator/go v1.1.12 // indirect
 	github.com/klauspost/compress v1.17.9 // indirect
 	github.com/kr/text v0.2.0 // indirect
+	github.com/kylelemons/godebug v1.1.0 // indirect
+	github.com/letsencrypt/boulder v0.0.0-20231026200631-000cd05d5491 // indirect
+	github.com/lucasb-eyer/go-colorful v1.2.0 // indirect
+	github.com/magiconair/properties v1.8.7 // indirect
 	github.com/mailru/easyjson v0.7.7 // indirect
 	github.com/maruel/panicparse v1.6.2 // indirect
+	github.com/mattn/go-isatty v0.0.20 // indirect
+	github.com/mattn/go-localereader v0.0.1 // indirect
+	github.com/mattn/go-mastodon v0.0.8 // indirect
 	github.com/mattn/go-runewidth v0.0.15 // indirect
+	github.com/minio/sha256-simd v1.0.1 // indirect
+	github.com/mitchellh/copystructure v1.2.0 // indirect
 	github.com/mitchellh/go-homedir v1.1.0 // indirect
+	github.com/mitchellh/mapstructure v1.5.0 // indirect
+	github.com/mitchellh/reflectwalk v1.0.2 // 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/mohae/deepcopy v0.0.0-20170929034955-c48cc78d4826 // indirect
 	github.com/montanaflynn/stats v0.7.1 // indirect
+	github.com/mr-tron/base58 v1.2.0 // indirect
+	github.com/muesli/ansi v0.0.0-20211031195517-c9f0611b6c70 // indirect
+	github.com/muesli/cancelreader v0.2.2 // indirect
+	github.com/muesli/mango v0.1.0 // indirect
+	github.com/muesli/mango-cobra v1.2.0 // indirect
+	github.com/muesli/mango-pflag v0.1.0 // indirect
+	github.com/muesli/reflow v0.3.0 // indirect
+	github.com/muesli/roff v0.1.0 // indirect
+	github.com/muesli/termenv v0.15.2 // indirect
+	github.com/multiformats/go-base32 v0.1.0 // indirect
+	github.com/multiformats/go-base36 v0.2.0 // indirect
+	github.com/multiformats/go-multibase v0.2.0 // indirect
+	github.com/multiformats/go-multihash v0.2.3 // indirect
+	github.com/multiformats/go-varint v0.0.7 // indirect
 	github.com/munnerz/goautoneg v0.0.0-20191010083416-a7dc8b61c822 // indirect
 	github.com/nsf/termbox-go v1.1.1 // indirect
+	github.com/oklog/ulid v1.3.1 // indirect
 	github.com/opencontainers/go-digest v1.0.0 // indirect
 	github.com/opencontainers/image-spec v1.1.0 // indirect
+	github.com/opentracing/opentracing-go v1.2.0 // indirect
+	github.com/pelletier/go-toml v1.9.5 // indirect
+	github.com/pelletier/go-toml/v2 v2.1.0 // indirect
 	github.com/perimeterx/marshmallow v1.1.5 // indirect
 	github.com/pierrec/lz4/v4 v4.1.21 // indirect
+	github.com/pjbgf/sha1cd v0.3.0 // indirect
+	github.com/pkg/browser v0.0.0-20240102092130-5ac0b6a4141c // indirect
 	github.com/pkg/errors v0.9.1 // indirect
 	github.com/pmezard/go-difflib v1.0.1-0.20181226105442-5d4384ee4fb2 // indirect
+	github.com/polydawn/refmt v0.89.1-0.20221221234430-40501e09de1f // 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
@@ -151,14 +306,26 @@ require (
 	github.com/russross/blackfriday/v2 v2.1.0 // indirect
 	github.com/sergi/go-diff v1.3.2-0.20230802210424-5b0b94c5c0d3 // indirect
 	github.com/stretchr/objx v0.5.2 // indirect
+	github.com/subosito/gotenv v1.6.0 // indirect
+	github.com/titanous/rocacheck v0.0.0-20171023193734-afe73141d399 // indirect
 	github.com/tklauser/go-sysconf v0.3.14 // indirect
 	github.com/tklauser/numcpus v0.8.0 // indirect
+	github.com/tomnomnom/linkheader v0.0.0-20180905144013-02ca5825eb80 // indirect
+	github.com/ulikunitz/xz v0.5.12 // indirect
+	github.com/vbatts/tar-split v0.11.5 // indirect
+	github.com/wagoodman/go-partybus v0.0.0-20230516145632-8ccac152c651 // indirect
+	github.com/wagoodman/go-progress v0.0.0-20220614130704-4b1c25a33c7c // indirect
+	github.com/whyrusleeping/cbor-gen v0.1.1-0.20240311221002-68b9f235c302 // indirect
+	github.com/wk8/go-ordered-map/v2 v2.1.8 // indirect
 	github.com/x448/float16 v0.8.4 // indirect
+	github.com/xanzy/go-gitlab v0.105.0 // indirect
+	github.com/xanzy/ssh-agent v0.3.3 // 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 v0.0.0-20240726163527-a2c0da244d78 // indirect
 	github.com/yusufpapurcu/wmi v1.2.4 // indirect
+	gitlab.com/digitalxero/go-conventional-commit v1.0.7 // indirect
 	go.opencensus.io v0.24.0 // indirect
 	go.opentelemetry.io/contrib/instrumentation/google.golang.org/grpc/otelgrpc v0.52.0 // indirect
 	go.opentelemetry.io/contrib/instrumentation/net/http/otelhttp v0.53.0 // indirect
@@ -172,13 +339,19 @@ require (
 	golang.org/x/text v0.17.0 // indirect
 	google.golang.org/genproto/googleapis/rpc v0.0.0-20240814211410-ddb44dafa142 // indirect
 	gopkg.in/inf.v0 v0.9.1 // indirect
+	gopkg.in/ini.v1 v1.67.0 // indirect
+	gopkg.in/mail.v2 v2.3.1 // indirect
+	gopkg.in/warnings.v0 v0.1.2 // 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 v2.130.1 // indirect
 	k8s.io/kube-openapi v0.0.0-20240430033511-f0e62f92d13f // indirect
 	k8s.io/utils v0.0.0-20240711033017-18e509b52bc8 // indirect
+	lukechampine.com/blake3 v1.2.1 // indirect
 	sigs.k8s.io/json v0.0.0-20221116044647-bc3834ca7abd // indirect
+	sigs.k8s.io/kind v0.23.0 // indirect
 	sigs.k8s.io/structured-merge-diff/v4 v4.4.1 // indirect
 	sigs.k8s.io/yaml v1.4.0 // indirect
+	software.sslmate.com/src/go-pkcs12 v0.4.0 // indirect
 )