# Docker container (base) for the converter software

This directory contains all the files needed to create the base [Docker](https://www.docker.com) image used for the converter software in [`projects`](projects/).

A specific project's translation script can be executed either in an app like manner (*I.O.U. a link to the anchor here*), calling it directly from within the container, using a local copy executed by the container (*I.O.U. a link to the anchor here*), or in an interactive shell within the container (*I.O.U. a link to the anchor here*).

[[_TOC_]]


## Building & running the Docker container

This is a quick tour on how to build and run the Docker container through different scenarios. This is not a lecture on containerisation in general, nor Linux/ Unix, shell scripting or programming. But if you encounter a specific problem, feel free to ping the [MA team](https://modelarchive.org/contact).

This section describes four use cases of the Docker container (including a build-how to per use case) but starts with a short primer of what is common to all scenarios described here.


### Prerequisites

For building the Docker image, you need a local copy of the [Git repository](/.). After that, this guide assumes you are in the [`projects`](projects/) subdirectory (we skip the output of the commands here):

```terminal
$ git clone https://git.scicore.unibas.ch/schwede/modelcif-converters.git modelcif-converters.git
$ cd modelcif-converters.git/projects
$
```

Since the Docker container will run as a dedicated, non-root user, it is advisable to create this user with the ID of your local user. That way, file permission issues will be avoided. Get your user ID with the following command and note it down - it will be needed in the build steps:

```terminal
$ whoami
localuser
$ id
uid=(localuser) ...
$
```

Look for the `uid` in the output of `id`. In the example above, `1234` is the ID of user `localuser`, currently logged in and executing the commands.

One last thing that is needed for the example runs of the Docker container is data. For simplicity, we assume that a directory `/home/user/models` exists on the local computer executing a converter, full of modelling data.

### Run a fixed converter from within the Docker container (app-like)

This use case comes closest to having a Docker container that works like a [ModelCIF](https://mmcif.wwpdb.org/dictionaries/mmcif_ma.dic/Index/) converter app, that you can

- hand over to others

- send to a compute cluster

- turn into a [Singularity](https://sylabs.io/singularity/) image

and it works out of the box.

The idea is to copy a translation script from one of the [projects](projects/) into the Docker image along with all the software needed to run it. That enables you to start the script as a command with [`docker run`](https://docs.docker.com/engine/reference/run/).

The whole build of the Docker image, including installing necessary software and copying the translation script, is covered by our [Dockerfile](./Dockerfile). You just need to specify the translation script by [build time argument](https://docs.docker.com/engine/reference/commandline/build/#set-build-time-variables---build-arg) `CONVERTERSCRIPT` during [`docker build`](https://docs.docker.com/engine/reference/commandline/build/). By default, the translation script is renamed to `convert2modelcif` to be called as a command. This can be overwritten using build time argument `CONVERTERCMD`. There is also an alias `2cif` to the converter command, which is immutable.

The following command will build a Docker image named `converter` (with tag `latest`). The translation script will be copied from [`USDA-ASFVG/translate2modelcif.py`](projects/USDA-ASFVG/translate2modelcif.py) and made available as `convert2modelcif` in the Docker image/ `docker run`. By `MMCIF_USER_ID`, we use UID `1234` for the internal user of the Docker image, so mounted files have the right owner inside and outside of the Docker container (assuming the example user from above). Pay attention to the alternative Dockerfile location specified by `-f docker/Dockerfile`, as we are calling `docker build` from the [projects](projects/) subdirectory to get the right build context:

```terminal
$ # DOCKER_BUILDKIT=1 is only needed for older versions of Docker.
$ DOCKER_BUILDKIT=1 docker build -f docker/Dockerfile --build-arg MMCIF_USER_ID=1234 --build-arg CONVERTERSCRIPT=USDA-ASFVG/translate2modelcif.py -t converter .
$
```


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1. App like
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2. Local copy
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- own run command
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3. Interactive shell
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4. Development environment
- include pylint, black and pyproject.toml
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build:
- execute: docker build -f docker/Dockerfile -t converter .
- explain how to install a dedicated converter script in the container
- mention how to change user
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- mention .dockerignore in projects readme, like when adding projects consider..., add a reference to it, here

run interactive shell for development:
- make sure files exist: /Users/stefan/Projects/ma-converters.git/projects/pointmutations-haddock/.docker-bash-history
- execute:
docker run --rm -i -v /Users/stefan/.bash_profile:/home/mmcif/.bash_profile -v /Users/stefan/.bash_aliases:/home/mmcif/.bash_aliases -v /Users/stefan/.bashrc:/home/mmcif/.bashrc -v /Users/stefan/Projects/ma-converters.git/projects/pointmutations-haddock/.docker-bash-history:/home/mmcif/.bash_history -v /Users/stefan/Projects/ma-converters.git/:/develop -t mmcifconverter:20220427 bash

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