Merge pull request #4 from medtune/dev-rest-capsuls

Support custom REST capsules

.circleci/config.yml

@@ -8,13 +8,16 @@ jobs:
 
       - run: 
           name: build capsul image
-          command: docker build -t medtune/capsul:dev-v0.0.1 .
+          command: make capsul
 
       - run: 
           name: login docker engine
           command: docker login -u $DOCKER_USER -p $DOCKER_PASS
 
       - run:
           name: push image to registry
-          command: docker push medtune/capsul:dev-v0.0.1
+          command: |
+            docker push medtune/capsul:v0.0.2
+            docker push medtune/capsul:latest
+
 

.gitignore

@@ -1,11 +1,138 @@
 .dev/
 
+# compiled cmd
 main
+capsul
+capsul-cmd
 
+# exported model
+weights/
+
+# before exporting models weights
+weights-bexp/
+
+# github.com/tensorflow/models repo --depth=1
+models/
+
+# bins
 *.so
 *.o
 
+# tensorflow pacakges
 tensorflow
 serving
 tensorflow_serving
-vendor
+vendor
+
+# Weights
+weights/
+# Weights subdir
+1/
+2/
+3/
+
+# python gitignore
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+.hypothesis/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# pyenv
+.python-version
+
+# celery beat schedule file
+celerybeat-schedule
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/

Makefile

@@ -1,3 +1,138 @@
-build-image:
-	docker build -t medtune/capsul .
+CONTAINER_ENGINE=docker
+CAPSUL_VERSION=0.0.2
+CAPSUL_CMD_VERSION=0.0.1
+MAINTAINERS=AEB MAHs
 
+GOCMD=go
+GOVERSION=$(GOCMD) version
+GOBUILD=$(GOCMD) build
+GOCLEAN=$(GOCMD) clean
+GOTEST=$(GOCMD) test
+GOGET=$(GOCMD) get
+
+BINARY_FILE=cmd/main.go
+BINARY_NAME=capsul
+
+build: 
+	CGO_ENABLED=0 GOOS=linux GOARCH=amd64 $(GOBUILD) -o $(BINARY_NAME) -v $(BINARY_FILE)
+
+test: 
+	$(GOTEST) -v ./...
+
+clean: 
+	$(GOCLEAN)
+	rm -f $(BINARY_NAME)
+
+
+test-clean:
+	rm -f test/testdata/*_cam.png
+
+
+# build base container image 
+# does not compile binaries
+build-base:
+	@echo building base capsul library ...
+	docker build \
+		-t medtune/capsul:base \
+		-f build/base.Dockerfile \
+		.
+
+
+# build capsul package and tag version/latest
+capsul: build-base
+	docker tag medtune/capsul:base medtune/capsul:v0.0.2
+	docker tag medtune/capsul:base medtune/capsul:latest
+
+
+# alias capsul
+capsul-base: capsul
+
+
+# build capsul command line tool
+build-cmd:
+	@echo building base capsul library ...
+	docker build \
+		-t medtune/capsul:cmd \
+		-f build/cmd.Dockerfile \
+		.
+
+
+# build capsul cmd & tag version/latest
+capsul-cmd: build-cmd
+	docker tag medtune/capsul:cmd medtune/capsul:cmd-v0.0.2
+	docker tag medtune/capsul:cmd medtune/capsul:cmd-latest
+
+
+# Build mnist tf server image
+build-mnist:
+	@echo building model capsul mnist ...
+	docker build \
+		-t medtune/capsul:mnist \
+		-f build/capsules/mnist.Dockerfile \
+		.
+
+
+# Build inception tf server image
+build-inception:
+	@echo building model capsul inception ...
+	docker build \
+		-t medtune/capsul:inception \
+		-f build/capsules/inception.Dockerfile \
+		.
+
+
+# Build mura inception restnet v2 tf server image
+build-mura-irn-v2:
+	@echo building model capsul mura inception resnet v2 ...
+	docker build \
+		-t medtune/capsul:mura-irn-v2 \
+		-f build/capsules/mura_irn_v2.Dockerfile \
+		.
+
+
+# Build mura mobilenet v2 tf server image
+build-mura-mn-v2:
+	@echo building model capsul mura mobilenet v2 ...
+	docker build \
+		-t medtune/capsul:mura-mn-v2 \
+		-f build/capsules/mura_mobilenet_v2.Dockerfile \
+		.
+
+
+# Build mura mobile net grad cam customized server
+build-mura-mn-v2-cam:
+	@echo building grad cam server for mura mobilenet v2
+	docker build \
+		-t medtune/capsul:mura-mn-v2-cam \
+		-f build/csflask/mura_mn_v2_cam.Dockerfile \
+		.
+
+
+# build mura main image
+build-mura: build-mura-mn-v2
+	@echo taging mura-mn-v2 with mura
+	docker tag medtune/capsul:mura-mn-v2 medtune/capsul:mura
+
+
+# Build mura 
+build-mura-cam: build-mura-mn-v2-cam
+	@echo building model capsul mura-cam ...
+	docker tag medtune/capsul:mura-mn-v2-cam medtune/capsul:mura-cam
+
+
+# Build chexray
+build-chexray:
+	@echo building model capsul chexray ...
+	docker build \
+		-t medtune/capsul:chexray \
+		-f build/capsules/chexray.Dockerfile \
+		.
+
+
+build-csflask: build-mura-mn-v2-cam
+
+
+build-capsules: build-mnist \
+	build-inception \
+	build-mura-mn-v2 \
+	build-mura-irn-v2

README.md

@@ -5,7 +5,7 @@
 ## Build status
 
 | branch | Build status |
-| --- | --- | 
+| --- | --- |
 | Master | [![CircleCI](https://circleci.com/gh/medtune/capsul/tree/master.svg?style=svg)](https://circleci.com/gh/medtune/capsul/tree/master) |
 | Dev | [![CircleCI](https://circleci.com/gh/medtune/capsul/tree/dev.svg?style=svg)](https://circleci.com/gh/medtune/capsul/tree/dev) |
 

build/base.Dockerfile

@@ -0,0 +1,64 @@
+FROM golang:1.10
+
+# Update system (ubuntu)
+RUN apt-get update && apt update
+
+# Add project to default GOPATH
+ADD cmd /go/src/github.com/medtune/capsul/cmd
+ADD csflask /go/src/github.com/medtune/capsul/csflask
+ADD pkg /go/src/github.com/medtune/capsul/pkg
+ADD hack /go/src/github.com/medtune/capsul/hack
+ADD plugins /go/src/github.com/medtune/capsul/plugins
+ADD examples /go/src/github.com/medtune/capsul/examples
+ADD test /go/src/github.com/medtune/capsul/test
+
+# install unzip
+RUN apt install unzip -y
+
+# Download protoc binaries
+RUN curl -OL https://github.com/google/protobuf/releases/download/v3.6.1/protoc-3.6.1-linux-x86_64.zip
+
+# unzip
+RUN unzip ./protoc-3.6.1-linux-x86_64.zip -d protoc3
+
+# Move protoc binaries
+RUN mv protoc3/bin/* /usr/local/bin/ && \
+    mv protoc3/include/* /usr/local/include/
+
+# Install golang protoc & grpc
+RUN go get github.com/golang/protobuf/ptypes/wrappers
+RUN go get google.golang.org/grpc
+RUN go get github.com/golang/protobuf/protoc-gen-go
+
+# Git clone tensorflow/tensorflow and tensorflow/serving version 1.7 
+#NOTE: earlier version (>1.7) fail to compile ?
+RUN git clone \
+    --depth 1 \
+    -b r1.7 \
+    https://github.com/tensorflow/serving.git 
+
+RUN git clone \
+    --depth 1 \
+     -b r1.7 \
+     https://github.com/tensorflow/tensorflow.git 
+
+# Compile proto files using gRPC plugin 
+RUN PROTOC_OPTS='-I tensorflow -I serving --go_out=plugins=grpc:src' && \
+    eval "protoc $PROTOC_OPTS serving/tensorflow_serving/apis/*.proto" && \
+    eval "protoc $PROTOC_OPTS serving/tensorflow_serving/config/*.proto" && \
+    eval "protoc $PROTOC_OPTS serving/tensorflow_serving/util/*.proto" && \
+    eval "protoc $PROTOC_OPTS serving/tensorflow_serving/sources/storage_path/*.proto" && \
+    eval "protoc $PROTOC_OPTS tensorflow/tensorflow/core/framework/*.proto" && \
+    eval "protoc $PROTOC_OPTS tensorflow/tensorflow/core/example/*.proto" && \
+    eval "protoc $PROTOC_OPTS tensorflow/tensorflow/core/lib/core/*.proto" && \
+    eval "protoc $PROTOC_OPTS tensorflow/tensorflow/core/protobuf/meta_graph.proto" && \
+    eval "protoc $PROTOC_OPTS tensorflow/tensorflow/core/protobuf/saver.proto"
+
+#TODO: Install gocv: opencv bindings
+
+# Set work dir
+WORKDIR /go/src/github.com/medtune/capsul
+
+#RUN go install ./example/inception-inference
+#RUN go install ./example/model-status
+#RUN go install ./example/mnist-inference/main.go

build/base/tf-flask.Dockerfile

@@ -0,0 +1 @@
+FROM baseImage

build/base/tf-serving.bazel-cpu.Dockerfile

@@ -0,0 +1 @@
+FROM baseImage

images/src/inception.Dockerfile → build/capsules/chexray.Dockerfile

@@ -1,2 +1,3 @@
 FROM medtune/tensorflow-serving:bazel-cpu
 
+RUN mkdir -p /models/chexray