Merge pull request #129 from GMOD/docker-updates

Docker updates

README.md

@@ -83,13 +83,65 @@ are currently using PostgreSQL.
 Please read the included [chado/INSTALL.Chado.md](./chado/INSTALL.Chado.md) document for instructions on how to
 install the Chado schema.
 
-### Running the Docker Image
+### Using the Chado Docker Image
+#### Locally Build the Docker Image
+To build the docker image run the following:
+```bash
+
+cd docker
+make v<version>
+```
+Replace `<version>` with a specific version of Chado that you want to use (e.g.  `1.31`).  This will create a Docker image with the tag: `gmod/chado:<version>` where <version> is the same version used above (e.g. `gmod/chado:1.31`).
+
+#### Using the Chado Docker
+You can start and work within the Chado container by using the following command.
+```bash
+docker run -it gmod/chado:<version>
+```
+Replace `<version>` with the specific version of Chado that you want to use (e.g. `1.31`). This will start the PostgreSQL server and give you access to a bash terminal.
+
+As a test, you can run the `flyway info` command after starting the container:
 
 ```bash
+flyway info
+```
+
+You can explore the Chado tables using the `psql` command in the following way:
 
-docker build -t chado .
-docker run -it -d chado
+```bash
+psql -U postgres -h localhost -d chado
 ```
+You will be prompted for a password. The default password is `chadotest`
+
+##### Testing a Pull Request
+You can test any pull request or other Git branch of Chado by navigating to the Chado directory in the image and changing the branch:
+```bash
+cd Chado/chado
+git checkout <branch>
+```
+If the branch has any FlyWay migrations you can test those by running these flyway commans:
+
+Use this command to see what needs to be applied
+```bash
+flyway info
+```
+
+For testing of a PR you can set the baseline to the current installation of Chado provided by the image:
+```bash
+flyway baseline
+```
+
+To update Chado you can apply the Flyway migrations:
+```bash
+flyway migrate
+```
+
+As long as no errors occured you will see success for all updates:
+
+```bash
+flyway info
+```
+
 
 
 ## Chado Support

docker/Dockerfile

@@ -0,0 +1,45 @@
+FROM ubuntu:20.04
+MAINTAINER Scott Cain <[email protected]>
+
+RUN apt-get update
+
+#for some reason, this has to be installed by itself
+RUN apt-get install -y tzdata
+
+RUN apt-get install -y apt-utils
+
+RUN apt-get install -y wget \
+                       unzip \
+                       git \
+                       make \
+                       gcc \
+                       vim \
+                       uuid-dev
+
+RUN apt-get install -y postgresql-all
+
+RUN cd /usr/local \
+   && wget -qO- https://repo1.maven.org/maven2/org/flywaydb/flyway-commandline/8.5.2/flyway-commandline-8.5.2-linux-x64.tar.gz | tar xvz \
+   && ln -s `pwd`/flyway-8.5.2/flyway /usr/local/bin
+
+ARG CHADO_BRANCH=${CHADO_BRANCH}
+ARG CHADO_VERSION=${CHADO_VERSION}
+
+RUN cd / \
+   && git clone https://github.com/GMOD/Chado.git  \
+   && cd Chado \
+   && git checkout ${CHADO_BRANCH}
+
+RUN /etc/init.d/postgresql start \
+   && su -c "createdb chado" - postgres \
+   && su -c "psql chado < /Chado/chado/schemas/${CHADO_VERSION}/default_schema.sql" - postgres \
+   && su -c "psql -c \"ALTER USER postgres PASSWORD 'chadotest';\"" - postgres \
+   && /etc/init.d/postgresql stop;
+
+ADD flyway.conf /root/flyway.conf
+ADD entrypoint.sh entrypoint.sh
+ADD motd /etc/motd
+
+RUN echo '[ ! -z "$TERM" -a -r /etc/motd ] && cat /etc/issue && cat /etc/motd' >> /etc/bash.bashrc
+
+ENTRYPOINT ["sh", "entrypoint.sh"]

docker/entrypoint.sh

@@ -0,0 +1,2 @@
+/etc/init.d/postgresql start
+/bin/bash

docker/flyway.conf

@@ -0,0 +1,6 @@
+flyway.url=jdbc:postgresql://localhost:5432/chado
+flyway.user=postgres
+flyway.password=chadotest
+flyway.schemas=public
+flyway.locations=filesystem:/Chado
+flyway.validateOnMigrate=false

docker/makefile

@@ -0,0 +1,8 @@
+all: v1.31
+
+v1.31:
+	docker build \
+		-t gmod/chado:1.31 \
+		--build-arg CHADO_BRANCH=1.31-release \
+		--build-arg CHADO_VERSION=1.31 \
+		.

docker/motd

@@ -0,0 +1,10 @@
+   ________  _____    ____  ____
+  / ____/ / / /   |  / __ \/ __ \
+ / /   / /_/ / /| | / / / / / / /
+/ /___/ __  / ___ |/ /_/ / /_/ /
+\____/_/ /_/_/  |_/_____/\____/
+
+This Chado docker image uses default security settings for
+PostgreSQL and has a hard-coded password for the postgres
+user.  Do not use this image for a production service without
+first correcting