Using Docker Hub and renaming the images

EGA-archive · Oct 28, 2018 · 36b09ff · 36b09ff
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commit 36b09ff
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diff --git a/deploy/Makefile b/deploy/Makefile
@@ -16,8 +16,8 @@ private/lega.yml private bootstrap bootstrap-dev:
 		    -v /dev/urandom:/dev/random \
                     ${ENVS} \
 		    -v ${PWD}:/ega \
-		    --entrypoint /ega/bootstrap/boot.sh \
-		    crg/ega-base --prefix $(PROJECT_NAME) ${ARGS}
+		    --entrypoint /ega/bootstrap/run.sh \
+		    egarchive/lega --prefix $(PROJECT_NAME) ${ARGS}
 
 
 up: private/lega.yml

diff --git a/deploy/README.md b/deploy/README.md
@@ -35,7 +35,13 @@ default).
 
 ## Docker images
 
-[Create the EGA docker images](images) with
+docker-compose will pull the appropriate images from [docker hub](https://hub.docker.com/u/egarchive/).
+However, before it can, you need to bootstrap the project, and the latter requires one image. So run, first:
+
+	docker pull egarchive/lega
+
+
+If you prefer, you can [create the EGA docker images](images), locally, with
 
 	make -C images
 

diff --git a/deploy/bootstrap/boot.sh b/deploy/bootstrap/boot.sh
diff --git a/deploy/bootstrap/lega.sh → deploy/bootstrap/run.sh b/deploy/bootstrap/lega.sh → deploy/bootstrap/run.sh
@@ -1,4 +1,70 @@
 #!/usr/bin/env bash
+set -e
+
+[ ${BASH_VERSINFO[0]} -lt 4 ] && echo 'Bash 4 (or higher) is required' 1>&2 && exit 1
+
+HERE=$(dirname ${BASH_SOURCE[0]})
+PRIVATE=${HERE}/../private
+DOT_ENV=${HERE}/../.env
+
+# Defaults
+VERBOSE=no
+FORCE=yes
+OPENSSL=openssl
+COMPOSE_PROJECT_NAME=crg
+
+function usage {
+    echo "Usage: $0 [options]"
+    echo -e "\nOptions are:"
+    echo -e "\t--openssl <value> \tPath to the Openssl executable [Default: ${OPENSSL}]"
+    echo -e "\t--prefix <value>  \tPrefix used for the project name [Default: ${COMPOSE_PROJECT_NAME}]"
+    echo ""
+    echo -e "\t--verbose, -v     \tShow verbose output"
+    echo -e "\t--polite, -p      \tDo not force the re-creation of the subfolders. Ask instead"
+    echo -e "\t--help, -h        \tOutputs this message and exits"
+    echo -e "\t-- ...            \tAny other options appearing after the -- will be ignored"
+    echo ""
+}
+
+
+# While there are arguments or '--' is reached
+while [[ $# -gt 0 ]]; do
+    case "$1" in
+        --help|-h) usage; exit 0;;
+        --verbose|-v) VERBOSE=yes;;
+        --polite|-p) FORCE=no;;
+        --openssl) OPENSSL=$2; shift;;
+        --prefix) COMPOSE_PROJECT_NAME=$2; shift;;
+	--) shift; break;;
+        *) echo "$0: error - unrecognized option $1" 1>&2; usage; exit 1;;    esac
+    shift
+done
+
+[[ $VERBOSE == 'no' ]] && echo -en "Bootstrapping "
+
+#########################################################################
+source ${HERE}/defs.sh
+
+[[ -x $(readlink ${OPENSSL}) ]] && echo "${OPENSSL} is not executable. Adjust the setting with --openssl" && exit 3
+
+rm_politely ${PRIVATE}
+mkdir -p ${PRIVATE}
+exec 2>${PRIVATE}/.err
+backup ${DOT_ENV}
+cat > ${DOT_ENV} <<EOF
+COMPOSE_PROJECT_NAME=${COMPOSE_PROJECT_NAME}
+COMPOSE_FILE=private/lega.yml
+#COMPOSE_IGNORE_ORPHANS=1
+EOF
+# Don't use ${PRIVATE}, since it's running in a container: wrong path then.
+
+#########################################################################
+source ${HERE}/settings.rc
+
+#########################################################################
+# Generate the configuration for each instance
+echomsg "Generating private data for a LocalEGA instance"
+#########################################################################
 
 echomsg "\t* the keys"
 
@@ -171,7 +237,7 @@ services:
     ports:
       - "${DOCKER_PORT_inbox}:9000"
     container_name: inbox
-    image: crg/ega-inbox
+    image: ${DOCKER_IMAGE_PREFIX:-egarchive/}inbox
     volumes:
       - ./conf.ini:/etc/ega/conf.ini:ro
       - inbox:/ega/inbox
@@ -186,7 +252,7 @@ services:
   ingest:
     # depends_on:
     #   - mq
-    image: crg/ega-base
+    image: ${DOCKER_IMAGE_PREFIX:-egarchive/}lega
     container_name: ingest
     environment:
       - S3_ACCESS_KEY=${S3_ACCESS_KEY}
@@ -206,7 +272,7 @@ services:
   verify:
     hostname: verify
     container_name: verify
-    image: crg/ega-base
+    image: ${DOCKER_IMAGE_PREFIX:-egarchive/}lega
     environment:
       - S3_ACCESS_KEY=${S3_ACCESS_KEY}
       - S3_SECRET_KEY=${S3_SECRET_KEY}
@@ -226,7 +292,7 @@ services:
   finalize:
     # depends_on:
     #   - mq
-    image: crg/ega-base
+    image: ${DOCKER_IMAGE_PREFIX:-egarchive/}lega
     container_name: finalize
     volumes:
       - ./conf.ini:/etc/ega/conf.ini:ro
@@ -253,7 +319,7 @@ services:
   outgest:
     hostname: outgest
     container_name: outgest
-    image: crg/ega-base
+    image: ${DOCKER_IMAGE_PREFIX:-egarchive/}lega
     ports:
       - "${DOCKER_PORT_outgest}:8443"
     volumes:
@@ -270,7 +336,7 @@ services:
   streamer:
     hostname: streamer
     container_name: streamer
-    image: crg/ega-base
+    image: ${DOCKER_IMAGE_PREFIX:-egarchive/}lega
     environment:
       - S3_ACCESS_KEY=${S3_ACCESS_KEY}
       - S3_SECRET_KEY=${S3_SECRET_KEY}
@@ -320,3 +386,5 @@ S3_SECRET_KEY             = ${S3_SECRET_KEY}
 DOCKER_PORT_inbox         = ${DOCKER_PORT_inbox}
 DOCKER_PORT_outgest       = ${DOCKER_PORT_outgest}
 EOF
+
+task_complete "Bootstrap complete"
diff --git a/deploy/images/Makefile b/deploy/images/Makefile
@@ -5,36 +5,36 @@ endif
 
 CHECKOUT=$(shell git rev-parse --abbrev-ref HEAD)
 TAG=$(shell git rev-parse --short HEAD)
-TARGET_PREFIX=crg/ega
+TARGET_PREFIX=egarchive/
 
 BUILD_ARGS=--build-arg checkout=$(CHECKOUT)
 
-.PHONY: all erase delete clean cleanall os base inbox
+.PHONY: all erase delete clean cleanall base lega inbox
 
-all: os base inbox
+all: base lega inbox
 
-os: BUILD_ARGS+=--build-arg DEV_PACKAGES="$(DEV_PACKAGES)"
-base: os
-inbox: os
+base: BUILD_ARGS+=--build-arg DEV_PACKAGES="$(DEV_PACKAGES)"
+lega: base
+inbox: base
 inbox: BUILD_ARGS+=--build-arg cryptor_checkout=master
-os base inbox:
+base lega inbox:
 	docker build ${BUILD_ARGS} \
-                     --cache-from $(TARGET_PREFIX)-$@:latest \
-                     --tag $(TARGET_PREFIX)-$@:$(TAG) \
-                     --tag $(TARGET_PREFIX)-$@:latest \
+                     --cache-from $(TARGET_PREFIX)$@:latest \
+                     --tag $(TARGET_PREFIX)$@:$(TAG) \
+                     --tag $(TARGET_PREFIX)$@:latest \
                      $@
 
 remove-%:
-	@docker rmi $(TARGET_PREFIX)-$(@:remove-%=%):latest
+	@docker rmi $(TARGET_PREFIX)$(@:remove-%=%):latest
 
 clean:
-	@docker images $(TARGET_PREFIX)-* -f "dangling=true" -q | uniq | while read n; do docker rmi -f $$n; done
+	@docker images $(TARGET_PREFIX)* -f "dangling=true" -q | uniq | while read n; do docker rmi -f $$n; done
 
 cleanall:
 	@docker images -f "dangling=true" -q | uniq | while read n; do docker rmi -f $$n; done
 
 delete:
-	@docker images $(TARGET_PREFIX)-* --format "{{.Repository}} {{.Tag}}" | awk '{ if ($$2 != "$(TAG)" && $$2 != "latest") print $$1":"$$2; }' | uniq | while read n; do docker rmi $$n; done
+	@docker images $(TARGET_PREFIX)* --format "{{.Repository}} {{.Tag}}" | awk '{ if ($$2 != "$(TAG)" && $$2 != "latest") print $$1":"$$2; }' | uniq | while read n; do docker rmi $$n; done
 
 erase: # erasing all including base
-	@docker images $(TARGET_PREFIX)-* -q | uniq | while read n; do docker rmi -f $$n; done
+	@docker images $(TARGET_PREFIX)* -q | uniq | while read n; do docker rmi -f $$n; done
diff --git a/deploy/images/base/Dockerfile b/deploy/images/base/Dockerfile
@@ -1,25 +1,55 @@
-FROM crg/ega-os
+FROM centos:7.5.1804
 LABEL maintainer "EGA System Developers"
 
 #################################################
 ##
-## Install LocalEGA stuff
+## Upgrade CentOS 7, and install Python 3.6
 ##
 #################################################
 
-RUN groupadd -r lega && \
-    useradd -M -r -g lega lega
+ARG DEV_PACKAGES=
+RUN yum -y install https://centos7.iuscommunity.org/ius-release.rpm && \
+    yum -y install epel-release && \
+    yum -y update && \
+    yum -y install git gcc make bzip2 curl ${DEV_PACKAGES} \
+                   zlib-devel bzip2-devel unzip \
+		   wget dpkg \
+                   openssl \
+		   python36u python36u-devel python36u-pip
 
-ARG checkout=master
-ARG cryptor_checkout=master
+RUN [[ -e /lib64/libpython3.6m.so ]] || ln -s /lib64/libpython3.6m.so.1.0 /lib64/libpython3.6m.so
 
-RUN git clone https://github.com/EGA-archive/LocalEGA.git /root/LocalEGA
-RUN git clone https://github.com/EGA-archive/crypt4gh.git /root/cryptor
+RUN pip3.6 install --upgrade pip && \
+    pip3.6 install PyYaml
 
-RUN cd /root/LocalEGA && git checkout ${checkout}
-RUN pip3.6 install -r /root/LocalEGA/requirements.txt
-RUN pip3.6 install /root/LocalEGA
+#################################################
+##
+## Install GOSU
+##
+#################################################
+
+ENV GOSU_VERSION 1.10
+ENV GPG_KEYS B42F6819007F00F88E364FD4036A9C25BF357DD4
+RUN set -ex && \
+    dpkgArch="$(dpkg --print-architecture | awk -F- '{ print $NF }')" && \
+    wget -O /usr/bin/gosu "https://github.com/tianon/gosu/releases/download/${GOSU_VERSION}/gosu-${dpkgArch}" && \
+    wget -O /tmp/gosu.asc "https://github.com/tianon/gosu/releases/download/${GOSU_VERSION}/gosu-${dpkgArch}.asc"
+
+# verify the signature
+RUN export GNUPGHOME="$(mktemp -d)" && \
+    (gpg --keyserver ha.pool.sks-keyservers.net --recv-keys "$GPG_KEYS" \
+    || gpg --keyserver pgp.mit.edu --recv-keys "$GPG_KEYS" \
+    || gpg --keyserver keyserver.pgp.com --recv-keys "$GPG_KEYS") && \
+    gpg --keyserver hkps://hkps.pool.sks-keyservers.net --recv-keys  && \
+    gpg --batch --verify /tmp/gosu.asc /usr/bin/gosu && \
+    rm -r "$GNUPGHOME" /tmp/gosu.asc && \
+    chmod +x /usr/bin/gosu
+
+# verify that the binary works
+RUN gosu nobody true && \
+    yum -y remove dpkg
+
+#################################################
+# Clean up
 
-RUN cd /root/cryptor && git checkout ${cryptor_checkout}
-RUN pip3.6 install -r /root/cryptor/requirements.txt
-RUN pip3.6 install /root/cryptor
+RUN yum clean all && rm -rf /var/cache/yum
diff --git a/deploy/images/inbox/Dockerfile b/deploy/images/inbox/Dockerfile
@@ -1,4 +1,4 @@
-FROM crg/ega-os
+FROM egarchive/base
 LABEL maintainer "EGA System Developers"
 
 RUN groupadd -r lega && \

diff --git a/deploy/images/lega/Dockerfile b/deploy/images/lega/Dockerfile
@@ -0,0 +1,22 @@
+FROM egarchive/base
+LABEL maintainer "EGA System Developers"
+
+#################################################
+##
+## Install LocalEGA stuff
+##
+#################################################
+
+RUN groupadd -r lega && \
+    useradd -M -r -g lega lega
+
+RUN git clone https://github.com/EGA-archive/LocalEGA.git /root/LocalEGA
+
+ARG checkout=master
+
+RUN cd /root/LocalEGA && git checkout ${checkout}
+
+# Requirements include crypt4gh (from https://github.com/EGA-archive/crypt4gh.git)
+RUN pip3.6 install -r /root/LocalEGA/requirements.txt && \
+    pip3.6 install /root/LocalEGA && \
+    rm -rf /root/LocalEGA