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Merge pull request #107 from MetaCell/release/0.2.0
Release/0.2.0
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‎.coveragerc‎

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[report]
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exclude_lines =
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pytest: no cover
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omit =
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nwb_explorer/nwb_main.py

‎.dockerignore‎

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.idea/
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.vscode/
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*pyc
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/static/
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/dependencies/
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/webapp/build/
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/webapp/node_modules/
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/webapp/geppetto-client/
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.DS_Store
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*.egg-info/
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*.nwb
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.ipynb_checkpoints
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*.log
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holoviews_plots
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nwb_files_cache
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test_data
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*.ipynb
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.pytest_cache
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.tox
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tox.ini
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.coverage
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/src
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geppetto-client
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.git
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**/__pycache__

‎.gitignore‎

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.idea/
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.vscode/
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*pyc
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static/org.geppetto.frontend/
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/static/
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/dependencies/
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/webapp/build/
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/webapp/node_modules/
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/webapp/geppetto-client/
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.DS_Store
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*.nwb
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*.egg-info/
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*.nwb
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.ipynb_checkpoints
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*.log
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holoviews_plots
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nwb_files_cache
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test_data
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*.ipynb
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.pytest_cache
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.tox
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tox.ini
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.coverage
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/src
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geppetto-client

‎.travis.yml‎

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language: node_js
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node_js:
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- "9"
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cache:
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- pip
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- npm
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before_install:
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- pyenv local 3.7.1
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install:
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- pip install --upgrade pip
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- pip install codecov
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script:
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- cd utilities
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- python install.py branch ${TRAVIS_BRANCH}
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- cd ..
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- python -m pytest --cov=nwb_explorer --cov-report term
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after_success:
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- codecov

‎Dockerfile‎

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FROM metacell/jupyter-neuron:development
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ENV FOLDER=nwb-explorer
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USER root
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RUN apt-get update -qq &&\
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apt-get install python3-tk vim nano unzip -qq
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USER $NB_UID
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RUN jupyter labextension disable @jupyterlab/hub-extension
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COPY --chown=1000:1000 . ${FOLDER}
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RUN python $FOLDER/utilities/install.py
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WORKDIR $HOME/$FOLDER
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EXPOSE 8000
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CMD ./NWBE

‎GeppettoConfiguration.json‎

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‎LICENSE‎

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The MIT License (MIT)
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Copyright © 2018, 2019 MetaCell LLC, Ltd.
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http://metacell.us
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All rights reserved. This program and the accompanying materials
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are made available under the terms of the MIT License
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which accompanies this distribution, and is available at
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http://opensource.org/licenses/MIT
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Permission is hereby granted, free of charge, to any person obtaining a copy
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of this software and associated documentation files (the "Software"), to deal
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in the Software without restriction, including without limitation the rights
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to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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copies of the Software, and to permit persons to whom the Software is
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furnished to do so, subject to the following conditions:
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The above copyright notice and this permission notice shall be included in all
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copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
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IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,
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DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR
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OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE
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USE OR OTHER DEALINGS IN THE SOFTWARE.

‎NWBE‎

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#!/bin/sh
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exec jupyter notebook --NotebookApp.default_url=/geppetto --NotebookApp.token='' --library=nwb_explorer

‎README.md‎

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[![Build Status](https://travis-ci.org/MetaCell/nwb-explorer.svg?branch=master)](https://travis-ci.org/MetaCell/nwb-explorer)
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[![codecov](https://codecov.io/gh/MetaCell/nwb-explorer/branch/master/graph/badge.svg)](https://codecov.io/gh/MetaCell/nwb-explorer)
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[![Twitter Follow](https://img.shields.io/twitter/follow/metacell.svg?label=follow&style=social)](https://twitter.com/metacell)
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# NWB Explorer
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NWB Explorer is an application that can be used by scientists to read, visualize and explore
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the content of NWB 2 files.
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NWB Explorer is a web application that can be used by scientists to read, visualize and explore
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the content of NWB:N 2 files.
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Learn more about the [Neurodata Without Borders](https://www.nwb.org/).
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## Getting Started
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These instructions will get you a copy of the project up and running on your local machine for development and testing purposes. See deployment for notes on how to deploy the project on a live system.
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These instructions will get you a copy of the project up and running on your local machine for development and testing purposes. See deployment for notes on how to deploy the project on a live system.
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### Prerequisites
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Below you will find the software you need to install to use nwb explorer (and the versions we used):
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### Prerequisites
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Below you will find the software you need to install to use nwb explorer (and the versions we used)
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* Git (2.17.0).
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* Node (9.11.1) and npm (6.0.0).
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* Redis-Server (4.0.9).
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* Python 3 (3.6.5), pip (10.0.1) and Python3-tk.
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* Python 3 (3.6+), pip (10.0.1)
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#### Python Dependencies
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`pip install -r requirements.txt`
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or
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We recommend the use of a new python 3 virtual environment:
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* Django (1.11.7). `pip install django`
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* Pygeppeto_server. ```git clone https://github.com/MetaCell/pygeppetto-django.git && cd pygeppetto-django && git checkout development && pip install -e . ```
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* Pygeppeto_model.```git clone https://github.com/openworm/pygeppetto.git && cd pygeppetto && git checkout manager && pip install -e . ```
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* Pyecore (0.8.1). `pip install pyecore`
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* Pynwb. ```git clone https://github.com/NeurodataWithoutBorders/pynwb.git && cd pynwb && git checkout dev && pip install -e . ```
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* Seaborn (0.8.1). `pip install seaborn`
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### Installing
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```bash
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python3 -m venv nwb-explorer
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source nwb-explorer/bin/activate
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```
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A step by step instructions to get a development env running
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Or, with conda
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```bash
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conda create -n nwb-explorer python=3.7
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conda activate nwb-explorer
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```
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git clone https://github.com/tarelli/nwb-explorer
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### Local installation
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Instructions to get a development environment running.
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```bash
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git clone -b development https://github.com/MetaCell/nwb-explorer
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cd nwb-explorer
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mkdir static
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cd static
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git clone https://github.com/openworm/org.geppetto.frontend
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cd org.geppetto.frontend/src/main/webapp/extensions
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git clone https://github.com/tarelli/geppetto-nwbexplorer
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cd ..
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/bin/cp -rf ../../../../../GeppettoConfiguration.json .
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npm install
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npm run build-dev-noTest
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python utilities/install.py
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```
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## Deployment
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Run the redis-server manually:
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## How to run NWB Explorer
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OSX
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```
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nohup redis-server &
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```
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Linux
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```
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redis-server &
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```
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Then, on the nwb-explorer folder, run :
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```
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python manage.py runserver
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After the installation is complete, run the script:
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```bash
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cd nwb-explorer
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./NWBE
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```
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## How to use
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If everything worked, the default browser will open on `http://localhost:8888/geppetto`
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![Real plots](https://github.com/NeurodataWithoutBorders/nwb_hackathons/raw/master/HCK04_2018_Seattle/Projects/NWBExplorer/nwbexplorer.gif)
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## How to develop
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## Getting started with NWB Explorer
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Any change you make in the python code will be automatically redeployed by the Django server.
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When the application is started, no file will be loaded.
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JS/HTML code can be found inside `static/org.geppetto.frontend/src/main/webapp/`. The code needs to be rebuilt with webpack everytime there is a change. The recommended way is to run in `/static/org.geppetto.frontend/src/main/webapp/` this command:
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1. Use the interface to load the file from a public url or just load a sample
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1. Specify the parameter nwbfile in your browser. Example: `http://localhost:8888/geppetto?nwbfile=https://github.com/OpenSourceBrain/NWBShowcase/raw/master/NWB/time_series_data.nwb`
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After the file is loaded, a Jupyter notebook will be available.
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From the notebook the current loaded file can be accessed through the variable `nwbfile`.
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For further information about the Python API, see the [PyNWB docs](https://pynwb.readthedocs.io/en/stable/)
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### Python code from sources
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In order to have all the Python files NWB:N 2 ed from sources, the application and the dependencies must be installed in development mode, i.e. with the command
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```bash
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pip install -e .
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```
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### Javascript code from sources
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JS/HTML code can be found inside `static/org.geppetto.frontend/src/main/webapp/`. The code needs to be rebuilt with webpack everytime there is a change. To avoid having to do so you can use the Webpack development server running in `/static/org.geppetto.frontend/src/main/webapp/` this command:
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```bash
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npm run build-dev-noTest:watch
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```
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## Running the tests
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This will spawn a process that while left running will watch for any changes on the `webapp` folder and automatically deploy them each time a file is saved.
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To check if a dependency is installed in development mode, run `pip list`.
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### Run via Docker
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There is a dockerfile ready to build a container for NWB-Explorer:
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```bash
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cd nwb-explorer/k8s
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docker build -t nwb-explorer .
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docker run -it -p8888:8888 nwb-explorer
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```
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python manage.py test
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```
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Then, after the docker contained has started, the application is ready http://localhost:8888/geppetto
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## Built With
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* [Django](https://www.djangoproject.com/) - The web framework used
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* [Geppetto](http://www.geppetto.org/) - Used to build a web-based application to visualize and simulate the NWB 2.0 files.
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* [Geppetto](http://www.geppetto.org/) - Used to build a web-based application to interpret and visualize the NWB:N 2 files.
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* [PyNWB](https://github.com/NeurodataWithoutBorders/pynwb) - Used to read and manipulate NWB:N 2 files
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* [Jupyter notebook](https://jupyter.org/) - Jupyter notebook is used as a backend.
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## Background
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The NWB Explorer was initially created by MetaCell to showcase the features of the Geppetto platform to share
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neurophysiological data in Neurodata Without Borders format. It was further developed as part of a
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Google Summer of Code project with the OpenWorm project. It is currently being extended as part of the Open Source Brain
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project to provide both a standalone and online application for visualising and analysing the contents of NWB:N 2 files.
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This work is currently funded by the Wellcome Trust.
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## Authors
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* Matteo Cantarelli ([MetaCell](http://metacell.us))
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* Giovanni Idili ([MetaCell](http://metacell.us))
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* Afonso Pinto
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See also the list of [contributors](https://github.com/tarelli/nwb-explorer/contributors) who participated in this project.
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* Filippo Ledda ([MetaCell](http://metacell.us))
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* Rodriguez Facundo ([MetaCell](http://metacell.us))
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* Afonso Pinto ([MetaCell](http://metacell.us))
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See also the list of [contributors](https://github.com/Metacell/nwb-explorer/contributors) who participated in this project.

‎db.sqlite3‎

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