Vizier DB - Web API

This repository contains the code for the Vizier DB Web Server API. The Web API is the backend that manages Viztrails and provides the API that is used by the Vizier DB Web UI.

Install and Run

Installation is still a bit labor intensive. The following steps seem to work for now (requires Anaconda). If you want to use Mimir modules within your curation workflows a local installation of Mimir v0.2 is required. Refer to this guide for Mimir installation details.

Python Environment

To setup the Python environment clone the repository and run the following commands:

git clone https://github.com/VizierDB/web-api.git
cd web-api
conda env create -f environment.yml
source activate vizier
pip install git+https://github.com/VizierDB/Vistrails.git
pip install -e .

As an alternative the following sequence of steps might also work (e.g., for MacOS):

git clone https://github.com/VizierDB/web-api.git
cd web-api
conda create --name vizier pip
source activate vizier
pip install -r requirements.txt
pip install -e .
conda install pyqt=4.11.4=py27_4

Configuration

The web server is configured using a configuration file. There are two example configuration files in the (config directory)[https://github.com/VizierDB/web-api/tree/master/config] (depending on whether including Mimir config-mimir.yaml or not config-default.yaml).

The configuration paramaters are:

api

• server_url: Url of the server (e.g., http://localhost)
• server_port: Server port (e.g., 5000)
• app_path: Application path for Web API (e.g., /vizier-db/api/v1)
• app_base_url: Concatenation of server_url, server_port and app_path
• doc_url: Url to API documentation

fileserver

• directory: Path to base directory for file server
• max_file_size: Maximum size for file uploads

engines

• identifier: Engine type (i.e., DEFAULT or MIMIR)
• name: Engine printable name
• description: Descriptive text for engine
• datastore:
  • directory: Base directory for data store

viztrails

• directory: Base directory for storing viztrail information and meta data

name: Web Service name

debug: Flag indicating whether server is started in debug mode

logs: Path to log directory

When the Web server starts it first looks for the configuration file that is reference in the environment variable VIZIERSERVER_CONFIG. If the variable is not set the server looks for a file config.yaml in the current working directory.

Note that there is a config.yaml file in the working directory of the server that can be used for development mode.

Run Server

After adjusting the server configuration the server is run using the following command:

cd vizier
python server.py

Make sure that the conda environment has been activated using source activate vizier.

If using Mimir the gateway server sould be started before running the web server.

API Documentation

For development it can be helpful to have a local copy of the API documentation. The repository README contains information on how to install the UI locally.