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Development environment setup

MIQA has two components, a server and a client.. They are located under the server and client directories respectively.

Prerequisites

  • Python 3.5+
  • Mongodb running at the default port
  • Node 8

Server

Setup

  • git clone https://github.com/OpenImaging/miqa.git
  • pip install -e miqa/server/
  • girder build
  • girder serve Now a running girder instance should be available at localhost:8080/girder

Setup Girder with Miqa Server

  • Navigate to localhost:8080/girder
  • Create a user
  • Navigate to Admin Console, System configuration
  • Populate fields under Email Delivery of appropriate values to enable girder to send emails
  • under Advanced Settings, Set CORS Allowed Origins to *, then click Save

Client

Miqa client is a Vue CLI based application. All Vue-CLI options are available.

  • keep the server running and open a new terminal
  • cd miqa/client
  • npm install
  • npm run serve
  • Navigate to localhost:8081
  • and login with the user created above

Data

The repo has a sample dataset. By default, it needs to be put under user home directory. Sample data is attributed to: OpenNeuro To put the sample data somewhere other than the user home directory, the json data description must be edited, probably just to update the data_root value to match the location of the data on your system. For more information on importing arbitrary datasets, see IMPORTING_DATA.md.

Prepare data store

  • Navigate to localhost:8080 and click the third tab to open girder interface
  • Navigate to Collection
  • Create a collection named miqa
  • Navigate to Admin Console, Assetstores
  • Create a Filesystem assetstore

Populate data

  • Navigate back to localhost:8081 and navigate to Settings tab
  • Suppose the repo is located at home diretory.
  • Set import path to ~/miqa/sample_data/sample.json and set export path to something like ~/miqa/sample_data/sample-output.json