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Record TFX output artifacts in Metadata store #884

Merged
merged 9 commits into from
Mar 6, 2019
Merged

Record TFX output artifacts in Metadata store #884

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fb34ae4
WIP: ML Metadata in KFP
neuromage Feb 21, 2019
077eb6e
Move metadata tracking to its own package.
neuromage Mar 1, 2019
6be9fb5
Clean up
neuromage Mar 1, 2019
1c404ad
Address review comments, update travis.yml
neuromage Mar 3, 2019
2dda3b1
Merge branch 'master' into ml-metadata
neuromage Mar 3, 2019
ead8bf3
Add dependencies for building in Dockerfile
neuromage Mar 4, 2019
c519d75
Log errors but continue to update run when metadata storing fails.
neuromage Mar 4, 2019
a115c21
Update workspace to get latest ml-metadata version.
neuromage Mar 5, 2019
446f3f3
Update errors
neuromage Mar 6, 2019
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10 changes: 8 additions & 2 deletions .travis.yml
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Expand Up @@ -31,8 +31,14 @@ matrix:
- cd $TRAVIS_BUILD_DIR/backend/src
- gimme -f 1.11.4
- source ~/.gimme/envs/go1.11.4.env
- go vet -all -shadow ./...
- go test ./...
- go vet -all -shadow ./agent/...
- go vet -all -shadow ./cmd/...
- go vet -all -shadow ./common/...
- go vet -all -shadow ./crd/...
- go test ./agent/...
- go test ./cmd/...
- go test ./common/...
- go test ./crd/...
- language: python
python: "2.7"
env: TOXENV=py27
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4 changes: 4 additions & 0 deletions BUILD.bazel
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Expand Up @@ -4,4 +4,8 @@ load("@bazel_gazelle//:def.bzl", "gazelle")
# gazelle:resolve proto protoc-gen-swagger/options/annotations.proto @com_github_grpc_ecosystem_grpc_gateway//protoc-gen-swagger/options:options_proto
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A couple questions;

  • What's the ETA to check this in?
  • Could you provide a quick step by step overview (5/6 sentences) of how it works? What does the DSL provide? Where to the types come from?
  • Is it a temporary implementation to speed things up for the dev summit? Or will we do some changes later? (Let's add TODOs if the latter)

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  1. ETA is ASAP, before dev summit.

  2. How this works roughly, is that we parse ml_metadata protos from any node that has an output parameter with the specified convention (/output/ml_metadata/*). This parsing happens when a Run is updated. If the step has such an output, we will parse it. Only true for TFX components right now. Otherwise, this is a no-op and no metadata tracking happens for other types of components.

  3. It's a temporary implementation. I will most likely move all of this out post dev-summit for a more complete solution for metadata tracking.

# gazelle:resolve proto go protoc-gen-swagger/options/annotations.proto @com_github_grpc_ecosystem_grpc_gateway//protoc-gen-swagger/options:go_default_library
# gazelle:resolve go github.com/kubeflow/pipelines/backend/api/go_client //backend/api:go_default_library
# gazelle:resolve go ml_metadata/metadata_store/mlmetadata @google_ml_metadata//ml_metadata/metadata_store:metadata_store_go
# gazelle:resolve go ml_metadata/proto/metadata_store_go_proto @google_ml_metadata//ml_metadata/proto:metadata_store_go_proto
# gazelle:resolve go ml_metadata/proto/metadata_store_service_go_proto @google_ml_metadata//ml_metadata/proto:metadata_store_service_go_proto
# gazelle:exclude vendor/
gazelle(name = "gazelle")
46 changes: 43 additions & 3 deletions WORKSPACE
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@@ -1,12 +1,13 @@
load("@bazel_tools//tools/build_defs/repo:http.bzl", "http_archive")
load("@bazel_tools//tools/build_defs/repo:http.bzl", "http_archive")

http_archive(
name = "io_bazel_rules_go",
sha256 = "7be7dc01f1e0afdba6c8eb2b43d2fa01c743be1b9273ab1eaf6c233df078d705",
urls = ["https://github.com/bazelbuild/rules_go/releases/download/0.16.5/rules_go-0.16.5.tar.gz"],
sha256 = "492c3ac68ed9dcf527a07e6a1b2dcbf199c6bf8b35517951467ac32e421c06c1",
urls = ["https://github.com/bazelbuild/rules_go/releases/download/0.17.0/rules_go-0.17.0.tar.gz"],
)

load("@io_bazel_rules_go//go:def.bzl", "go_register_toolchains", "go_rules_dependencies")
load("@io_bazel_rules_go//go:deps.bzl", "go_register_toolchains", "go_rules_dependencies")

go_rules_dependencies()

Expand All @@ -22,6 +23,45 @@ load("@bazel_gazelle//:deps.bzl", "gazelle_dependencies", "go_repository")

gazelle_dependencies()

http_archive(
name = "org_tensorflow",
sha256 = "24570d860d87dcfb936f53fb8dd30302452d0aa6b8b8537e4555c1bf839121a6",
strip_prefix = "tensorflow-1.13.0-rc0",
urls = [
"https://github.com/tensorflow/tensorflow/archive/v1.13.0-rc0.tar.gz",
],
)

http_archive(
name = "io_bazel_rules_closure",
sha256 = "43c9b882fa921923bcba764453f4058d102bece35a37c9f6383c713004aacff1",
strip_prefix = "rules_closure-9889e2348259a5aad7e805547c1a0cf311cfcd91",
urls = [
"https://mirror.bazel.build/github.com/bazelbuild/rules_closure/archive/9889e2348259a5aad7e805547c1a0cf311cfcd91.tar.gz",
"https://github.com/bazelbuild/rules_closure/archive/9889e2348259a5aad7e805547c1a0cf311cfcd91.tar.gz", # 2018-12-21
],
)

load("@org_tensorflow//tensorflow:workspace.bzl", "tf_workspace")

tf_workspace()

load("@bazel_tools//tools/build_defs/repo:git.bzl", "new_git_repository")

go_repository(
name = "google_ml_metadata",
commit = "becc26ab61f82bfe7c812894f56f597949ce0fdc",
importpath = "github.com/google/ml-metadata",
)

new_git_repository(
name = "libmysqlclient",
build_file = "@google_ml_metadata//ml_metadata:libmysqlclient.BUILD",
remote = "https://github.com/MariaDB/mariadb-connector-c.git",
tag = "v3.0.8-release",
workspace_file = "@google_ml_metadata//ml_metadata:libmysqlclient.WORKSPACE",
)

go_repository(
name = "io_k8s_client_go",
build_file_proto_mode = "disable_global",
Expand Down
31 changes: 17 additions & 14 deletions backend/Dockerfile
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@@ -1,25 +1,29 @@
FROM golang:1.11-alpine3.7 as builder
FROM l.gcr.io/google/bazel:0.21.0 as builder

RUN apt-get update && \
apt-get install -y cmake clang musl-dev openssl
WORKDIR /go/src/github.com/kubeflow/pipelines
COPY . .

# Needed musl-dev for github.com/mattn/go-sqlite3
RUN apk update && apk upgrade && \
apk add --no-cache bash git openssh gcc musl-dev
COPY WORKSPACE WORKSPACE
COPY backend/src backend/src
COPY backend/api backend/api

RUN GO111MODULE=on go build -o /bin/apiserver backend/src/apiserver/*.go
RUN bazel build -c opt --action_env=PATH --define=grpc_no_ares=true backend/src/apiserver:apiserver


# Compile
FROM python:3.5 as compiler

RUN apt-get update -y && \
apt-get install --no-install-recommends -y -q default-jdk wget

apt-get install --no-install-recommends -y -q default-jdk wget
RUN pip3 install setuptools==40.5.0

RUN wget http://central.maven.org/maven2/io/swagger/swagger-codegen-cli/2.4.1/swagger-codegen-cli-2.4.1.jar -O /tmp/swagger-codegen-cli.jar

# WORKDIR /go/src/github.com/kubeflow/pipelines
WORKDIR /go/src/github.com/kubeflow/pipelines
COPY . .
COPY backend/api backend/api
COPY sdk sdk
WORKDIR /go/src/github.com/kubeflow/pipelines/sdk/python
RUN ./build.sh /kfp.tar.gz
RUN pip3 install /kfp.tar.gz
Expand All @@ -36,22 +40,21 @@ COPY ./samples .
#The "for" loop breaks on all whitespace, so we either need to override IFS or use the "read" command instead.
RUN find . -maxdepth 2 -name '*.py' -type f | while read pipeline; do dsl-compile --py "$pipeline" --output "$pipeline.tar.gz"; done


FROM alpine:3.8
FROM debian:stretch

ARG COMMIT_SHA=unknown
ENV COMMIT_SHA=${COMMIT_SHA}

WORKDIR /bin

COPY --from=builder /bin/apiserver /bin/apiserver
COPY --from=builder /go/src/github.com/kubeflow/pipelines/third_party/license.txt /bin/license.txt
COPY third_party/license.txt /bin/license.txt
COPY --from=builder /go/src/github.com/kubeflow/pipelines/bazel-bin/backend/src/apiserver/linux_amd64_stripped/apiserver /bin/apiserver
COPY backend/src/apiserver/config/ /config

COPY --from=compiler /samples/ /samples/

# Adding CA certificate so API server can download pipeline through URL
RUN apk add ca-certificates
RUN apt-get update && apt-get install -y ca-certificates

# Expose apiserver port
EXPOSE 8888
Expand Down
5 changes: 5 additions & 0 deletions backend/src/apiserver/BUILD.bazel
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Expand Up @@ -13,6 +13,7 @@ go_library(
deps = [
"//backend/api:go_default_library",
"//backend/src/apiserver/client:go_default_library",
"//backend/src/apiserver/metadata:go_default_library",
"//backend/src/apiserver/model:go_default_library",
"//backend/src/apiserver/resource:go_default_library",
"//backend/src/apiserver/server:go_default_library",
Expand All @@ -23,12 +24,16 @@ go_library(
"@com_github_cenkalti_backoff//:go_default_library",
"@com_github_fsnotify_fsnotify//:go_default_library",
"@com_github_golang_glog//:go_default_library",
"@com_github_golang_protobuf//proto:go_default_library",
"@com_github_grpc_ecosystem_grpc_gateway//runtime:go_default_library",
"@com_github_jinzhu_gorm//:go_default_library",
"@com_github_jinzhu_gorm//dialects/sqlite:go_default_library",
"@com_github_minio_minio_go//:go_default_library",
"@com_github_pkg_errors//:go_default_library",
"@com_github_spf13_viper//:go_default_library",
"@google_ml_metadata//ml_metadata/metadata_store:metadata_store_go", # keep
"@google_ml_metadata//ml_metadata/proto:metadata_store_go_proto", # keep
"@google_ml_metadata//ml_metadata/proto:metadata_store_service_go_proto", # keep
"@org_golang_google_grpc//:go_default_library",
"@org_golang_google_grpc//reflection:go_default_library",
],
Expand Down
38 changes: 37 additions & 1 deletion backend/src/apiserver/client_manager.go
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Expand Up @@ -17,19 +17,25 @@ package main
import (
"database/sql"
"fmt"
"strconv"
"time"

workflowclient "github.com/argoproj/argo/pkg/client/clientset/versioned/typed/workflow/v1alpha1"
"github.com/cenkalti/backoff"
"github.com/golang/glog"
"github.com/golang/protobuf/proto"
"github.com/jinzhu/gorm"
_ "github.com/jinzhu/gorm/dialects/sqlite"
"github.com/kubeflow/pipelines/backend/src/apiserver/client"
"github.com/kubeflow/pipelines/backend/src/apiserver/metadata"
"github.com/kubeflow/pipelines/backend/src/apiserver/model"
"github.com/kubeflow/pipelines/backend/src/apiserver/storage"
"github.com/kubeflow/pipelines/backend/src/common/util"
scheduledworkflowclient "github.com/kubeflow/pipelines/backend/src/crd/pkg/client/clientset/versioned/typed/scheduledworkflow/v1beta1"
minio "github.com/minio/minio-go"

"ml_metadata/metadata_store/mlmetadata"
mlpb "ml_metadata/proto/metadata_store_go_proto"
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what does mlpb stands for?

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It's just an alias for the proto package I'm referring to here. Standard Go google3 practice.

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does it stands for ml protobuf?

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Yes, mlmd protobuf. I'm trying to be consistent with how it's used in mlmd Go client itself.

)

const (
Expand All @@ -56,6 +62,8 @@ type ClientManager struct {
swfClient scheduledworkflowclient.ScheduledWorkflowInterface
time util.TimeInterface
uuid util.UUIDGeneratorInterface

MetadataStore *mlmetadata.Store
}

func (c *ClientManager) ExperimentStore() storage.ExperimentStoreInterface {
Expand Down Expand Up @@ -117,7 +125,6 @@ func (c *ClientManager) init() {
c.experimentStore = storage.NewExperimentStore(db, c.time, c.uuid)
c.pipelineStore = storage.NewPipelineStore(db, c.time, c.uuid)
c.jobStore = storage.NewJobStore(db, c.time)
c.runStore = storage.NewRunStore(db, c.time)
c.resourceReferenceStore = storage.NewResourceReferenceStore(db)
c.dBStatusStore = storage.NewDBStatusStore(db)
c.objectStore = initMinioClient(getDurationConfig(initConnectionTimeout))
Expand All @@ -127,13 +134,42 @@ func (c *ClientManager) init() {

c.swfClient = client.CreateScheduledWorkflowClientOrFatal(
getStringConfig(podNamespace), getDurationConfig(initConnectionTimeout))

metadataStore := initMetadataStore()
runStore := storage.NewRunStore(db, c.time, metadataStore)
c.runStore = runStore

glog.Infof("Client manager initialized successfully")
}

func (c *ClientManager) Close() {
c.db.Close()
}

func initMetadataStore() *metadata.Store {
port, err := strconv.Atoi(getStringConfig(mysqlServicePort))
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Would it be possible to follow the pattern above and encapsulate the metadata store setup in a method? (storage.NewMetadataStore())

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Sure, move it to it's own method. It's not going to be in storage, as it's not part of that package. It's in it's own package.

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Sure, moved it to it's own function below.

if err != nil {
glog.Fatalf("Failed to parse valid MySQL service port from %q: %v", getStringConfig(mysqlServicePort), err)
}

cfg := &mlpb.ConnectionConfig{
Config: &mlpb.ConnectionConfig_Mysql{
&mlpb.MySQLDatabaseConfig{
Host: proto.String(getStringConfig(mysqlServiceHost)),
Port: proto.Uint32(uint32(port)),
Database: proto.String("mlmetadata"),
User: proto.String("root"),
},
},
}

mlmdStore, err := mlmetadata.NewStore(cfg)
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Is there support for a "fake" implementation using SQLLite so that we can run a lot of backend tests as go tests?

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Definitely. mlmetadata supports sqlite, so it should be possible.

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Is it possible to add support for SQLLite right away so that we can run tests quickly locally?

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Nope, sorry, I can't do it right now.
If it's any consolation, I plan to move all of this out to its own service soon, so API server can stay the same as before.

if err != nil {
glog.Fatalf("Failed to create ML Metadata store: %v", err)
}
return metadata.NewStore(mlmdStore)
}

func initDBClient(initConnectionTimeout time.Duration) *storage.DB {
driverName := getStringConfig("DBConfig.DriverName")
var arg string
Expand Down
5 changes: 4 additions & 1 deletion backend/src/apiserver/main.go
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Expand Up @@ -35,6 +35,10 @@ import (
"github.com/pkg/errors"
"google.golang.org/grpc"
"google.golang.org/grpc/reflection"

_ "ml_metadata/metadata_store/mlmetadata"
_ "ml_metadata/proto/metadata_store_go_proto"
_ "ml_metadata/proto/metadata_store_service_go_proto"
)

var (
Expand All @@ -48,7 +52,6 @@ type RegisterHttpHandlerFromEndpoint func(ctx context.Context, mux *runtime.Serv

func main() {
flag.Parse()
glog.Infof("starting API server")

initConfig()
clientManager := newClientManager()
Expand Down
27 changes: 27 additions & 0 deletions backend/src/apiserver/metadata/BUILD.bazel
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@@ -0,0 +1,27 @@
load("@io_bazel_rules_go//go:def.bzl", "go_library", "go_test")

go_library(
name = "go_default_library",
srcs = ["metadata_store.go"],
importpath = "github.com/kubeflow/pipelines/backend/src/apiserver/metadata",
visibility = ["//visibility:public"],
deps = [
"//backend/src/common/util:go_default_library",
"@com_github_argoproj_argo//pkg/apis/workflow/v1alpha1:go_default_library",
"@com_github_golang_protobuf//jsonpb:go_default_library_gen",
"@com_github_golang_protobuf//proto:go_default_library",
"@google_ml_metadata//ml_metadata/metadata_store:metadata_store_go",
"@google_ml_metadata//ml_metadata/proto:metadata_store_go_proto",
],
)

go_test(
name = "go_default_test",
srcs = ["metadata_store_test.go"],
embed = [":go_default_library"],
deps = [
"@com_github_golang_protobuf//proto:go_default_library",
"@com_github_google_go_cmp//cmp:go_default_library",
"@google_ml_metadata//ml_metadata/proto:metadata_store_go_proto",
],
)
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