# Overview

Cellxgene Gateway allows you to use the Cellxgene Server provided by the Chan Zuckerberg Institute (https://github.com/chanzuckerberg/cellxgene) with multiple datasets. It displays an index of available h5ad (anndata) files. When a user clicks on a file name, it launches a Cellxgene Server instance that loads that particular data file and once it is available  proxies requests to that server.

# Running locally

## Prequisites

0. This project requires python 3.6 or higher. Please check your version with

```bash
$ python --version
```

1. It is also a good idea to always set up a venv. 

```bash
python -m venv .cellxgene-gateway
source .cellxgene-gateway/bin/activate
```

2. Prepare a folder with .h5ad files, for example

```bash
mkdir ../cellxgene_data
wget https://github.com/chanzuckerberg/cellxgene/raw/master/example-dataset/pbmc3k.h5ad -O ../cellxgene_data/pbmc3k.h5ad
```


## Pip Install from Github

```bash
pip install git+https://github.com/Novartis/cellxgene-gateway
```

### Install from PyPI

```bash
# NOT YET DONE, COMING! STAY TUNED
```

### Developer Install

If you want to develop the code, you will need to clone the repo. We assume your current working directory is the directory into which you've cloned this repository.


1. Install requirements with

```bash
pip install -r requirements.txt
```

2. Install the gateway in developer mode

```bash
python setup.py develop
```

## Running cellxgene gateway

1. Set your environment variables correctly:

```bash
export CELLXGENE_LOCATION=`which cellxgene`
export CELLXGENE_DATA=../cellxgene_data  # change this directory if you put data in a different place.
export GATEWAY_HOST=localhost:5005
export GATEWAY_PROTOCOL=http
export GATEWAY_IP=127.0.0.1
```

2. Now, execute the cellxgene gateway:

```bash
cellxgene-gateway
```

For convenience, you can also change `run.sh.example` and execute it.

Here's what the environment variables mean:

* `CELLXGENE_LOCATION` - the location of the cellxgene executable, e.g. `~/anaconda2/envs/cellxgene/bin/cellxgene`
* `CELLXGENE_DATA` - a directory that can contain subdirectories with `.h5ad` data files, *without* trailing slash, e.g. `/mnt/cellxgene_data`
* `GATEWAY_HOST` - the hostname and port that the gateway will run on, typically `localhost:5005` if running locally
* `GATEWAY_PROTOCOL` - typically http when running locally, can be https when deployed if the gateway is behind a load balancer or reverse proxy.

The defaults should be fine if you set up a venv and cellxgene_data folder as above.

# Customization

The current paradigm for customization is to modify files during a build or deployment phase:

* To modify CSS or JS on particular gateway pages, overwrite or append to the templates
* To add script tags such as for user analytics to all pages, overwrite the extra_scripts.py file.
  * these scripts will also be run on the pages served by cellxgene server via the --scripts parameter
  * See https://github.com/chanzuckerberg/cellxgene/pull/680 for details on --scripts parameter

Currently we use a build.sh that copies the gateway to a "build" directory before modifying with sed and the like.

# Development

## Running Linters

pip install isort flake8 black

```bash
isort -rc .
flake8 .
black -l 79 .
```

# Getting Help

If you need help for any reason, please make a github ticket. One of the contributors should help you out.

# Contributors

* Niket Patel - https://github.com/NiketPatel9
* Alok Saldanha - https://github.com/alokito
* Yohann Potier - https://github.com/ypotier