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Functional Exploration of Natural Networks and Ecological Communities
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README.md

Fennec

About

FENNEC - Functional Exploration of Natural Networks and Ecological Communities.

The FENNEC is a tool that helps integrate trait data into ecological community analyses. For that purpose traits are aggregated from various sources. Those can then be mapped onto user provided community data.

What are you looking for?

  • I want to see FENNEC in action.Public instance
  • I want to learn how to use FENNEC.User manual
  • I want to host my own instance of FENNEC.Admin manual
  • I want to access FENNEC data via API.API doc
  • I want to improve/add features to FENNEC.Read on
  • I want to read/cite the article describing FENNEC.MEE
  • I want to reference the source code of FENNEC.DOI Please also cite our article.
  • I want to find the docker image of FENNEC.Docker Hub
  • I want to see the TravisCI build of FENNEC.Build Status
  • I want to test new features of FENNEC.Beta Version

Setup development environment

So you want to contribute to the development of FENNEC - awesome!

Local setup

As there are quite a few dependencies and setting everything up properly is highly dependent on the environment, we suggest using docker. We provide ready to use docker containers with all dependencies bundled for easy setup and usage. A local setup is not impossible but all current developers use the docker setup. Therefore, we are best able to assist with that. If you really need a local setup have a look at the dockerfile to see how things are installed there. Also feel free to open issues with all the problems you encounter.

Docker setup

You will clone the repository to your local computer and mount it in a fully functional FENNEC docker environment. This way you can develop locally (using your IDE of choice), view your changes immediately in a realistic running system. In addition you can transpile code and run the tests without installing additional dependencies.

Prerequisites:

Clone source code and initialize containers

git clone https://github.com/molbiodiv/fennec --recursive
cd fennec
# your UID is used to run processes in the docker container so files in your repo are not owned by root
export UID=$UID
docker-compose -f docker/fennec/docker-compose-dev.yml up -d

Congratulations! You are good to go. Point your browser to localhost:3141.

Important: The first time you run docker-compose up all installation/initialization steps will be performed and a database with example data is created. After that the file .docker.initialized is created in the root of your repository which will skip the initialization on subsequent runs of docker-compose up. If you need re-initialization remove this file but be aware that this might fail if the database already contains data.

Configuration

The default config files that were created with init_dev.sh should be ok to get started but you might want to update app/config/parameters.yml with:

  • github_client_id
  • github_client_secret
  • ga_tracking
  • secret

The first two are required for "Login with GitHub", see this guide for details. The third one is your Google Analytics tracking ID, with an empty ID, Google Analytics will be disabled. The secret should be replaced with a random string as documented by symfony.

If you need to modify the docker-compose file (e.g. hard code your user id for better integration into your IDE, or for changing the db volume locations) you can do this:

cp docker/fennec/docker-compose-dev.yml docker/fennec/docker-compose-dev.local.yml

This file is not under version control so you can modify it as you like and use this file after the -f parameter for all of the docker-compose commands.

Source code

php

The structure of the project is that of a default symfony 3 application. Changes to the php code should be served immediately on localhost:3141 as we are using the development server. If you need additional composer packages you can install them with

docker-compose -f ~/projects/fennec/docker/fennec/docker-compose-dev.local.yml exec web bash -c "cd /fennec-dev;COMPOSER_CACHE_DIR=/tmp composer require -n foo/bar:1.0.0"
javascript and css

The js(x) and (s)css code is located in app/Resources/client. Important: do not edit the js or css files in web/assets directly. They are generated with the following command (assuming your working directory is the fennec repo):

docker-compose -f docker/fennec/docker-compose-dev.yml exec web /fennec-dev/node_modules/.bin/encore dev

If you need additional npm packages you can install them with

docker-compose -f ~/projects/fennec/docker/fennec/docker-compose-dev.local.yml exec web bash -c "cd /fennec-dev;HOME=/tmp yarn add --non-interactive package@1.0.0"
phinch

Beware that phinch is included as a git submodule so changes there should not be FENNEC specific. However, if you change the .coffee files or checkout another version via git re-generate the js files with:

docker-compose -f ~/projects/fennec/docker/fennec/docker-compose-dev.yml exec web coffee -o /fennec-dev/web/assets/Phinch/scripts /fennec-dev/web/assets/Phinch/src

Tests

php

In order to run the php tests do this:

docker-compose -f ~/projects/fennec/docker/fennec/docker-compose-dev.yml exec web /fennec-dev/vendor/bin/simple-phpunit -c /fennec-dev/phpunit.xml.dist

This completely removes and re-creates the test database (this can take some time).

javascript

Currently, only the javascript helper files are unit tested. To run the tests execute this command:

docker-compose -f ~/projects/fennec/docker/fennec/docker-compose-dev.local.yml exec web yarn --cwd /fennec-dev test

Documentation

If you want to contribute documentation you can do so by modifying the content of the .rst files in the doc directory. In case you want to check how the converted html files look you can build with.

docker-compose -f ~/projects/fennec/docker/fennec/docker-compose-dev.local.yml exec web bash -c "cd /fennec-dev/doc; make html"

Then open the (local) html file doc/_build/html/index.html in your favorite browser. As documentation is hosted at readthedocs those files are not served by FENNEC.

The api doc on the other hand is dynamically created from the php annotations in src/AppBundle/Controller/APIController.php. Those are served from localhost:3141/api/doc.

Changes

1.0.5 <2018-06-22>

  • Fix graphical glitch on small screen (#201)
  • Improve Phinch navigation (#202, #203)

1.0.4 <2018-04-24>

  • Update startpage design
  • Add guide for new users (#194)
  • Change version to database (#190)

1.0.3 <2018-03-29>

  • Fix dbversion of mapping in import commands (#175)

1.0.2 <2018-03-28>

  • Fix login via GitHub (#172)

1.0.1 <2018-03-27>

  • Breaking change: Change method of listing scinames API to POST
  • Update biom-format to 2.1.6

1.0.0 <2018-03-23>

  • Breaking change: Split database into user and data dbs (update schemas)
  • Add user management (FOSUserBundle)
  • Add sharing capability for projects
  • Add permission management for projects (view/edit)
  • Add admin interface for user management
  • Improve data import documentation
  • Improve auto-generated API documentation (NelmioApiDocBundle)
  • Improve development setup via docker-compose
  • Improve basic documentation (README)
  • Fix trait proportions in table and charts (#103,#104)

0.9.0 <2017-11-03>

  • Add cron capability to docker (#101)
  • Add option to use google analytics
  • Breaking changes: docker container has to be pulled, ga_tracking has to be added to parameters.yml (can be empty)

0.8.4 <2017-09-27>

  • Add API documentation
  • Add cors header to make API accessible (#109)
  • Make content wrapper expand automatically (#99)
  • Fix dropdown on project details page (#98)
  • Add scientific name to trait citation export (#97)

0.8.3 <2017-08-23>

  • Fix bug (add sample trait to project from table via +)
  • Add documentation for SCALES bee traits

0.8.2 <2017-08-21>

  • Fix dialog problem on project details page

0.8.1 <2017-08-21>

  • Fix dropdown problem on project details page

0.8.0 <2017-08-09>

  • Add interactive metadata tables
  • Add scientific name to fennec metadata in projects (breaking change: projects from versions <0.8 need to be re-mapped)
  • Upgrade to Symfony 3.3 (from 3.1)
  • Replace bower and gulp with yarn and webpack

0.7.2 <2017-06-30>

  • Add attribution to text blocks on organism pages (#84)
  • Add boxes for texts on organism pages
  • Improve admin documentation

0.7.1 <2017-06-29>

  • Add Phinch to docker image (#90)
  • Add EPPO trait to docu

0.7.0 <2017-06-28>

  • Add php importers for organisms (#79)
  • Improve performance of trait importer
  • Clean up design of organism search (#76)
  • Make docker container ready to use (#66)
  • Improve tutorial (#67)

0.6.2 <2017-05-29>

  • Add long table import (#70)
  • Add local demo user
  • Add Quick Start documentation
  • Add basic admin documentation

0.6.1 <2017-05-05>

  • Improve design of project details (tabs)
  • Add trait table for samples (#72)
  • Add better handling of traits via table
  • Add capability to remove traits from project (#71)
  • Add unit for numerical traits to frontend (#73)
  • Fix github login timeout (#69)

0.6.0 <2017-04-10>

  • Add metadata overview to projects
  • Add possibility to upload metadata tsv files
  • Generalize mapping to fennec ids
  • Add contact page

0.5.1 <2017-04-04>

  • Add numerical trait format
  • Add trait citations to frontend
  • Allow upload of OTU tables as projects

0.5.0 <2017-03-10>

  • Update color scheme
  • Improve startpage layout
  • Initialize documentation
  • Fix bugs
  • Improve mapping to fennec ids
  • Add cli trait importer
  • Add console commands for db interaction
  • Use ORM for database connection

0.4.1 <2017-01-05>

  • Handle deleted traits properly
  • Add two versions of IUCN to test set
  • Replace Blackbird with patched Phinch
  • Add user selected trait to project (biom)
  • Merge multiple trait values for one organism

0.4.0 <2016-11-22>

  • Rename organism_id to fennec_id
  • Update webservices for db schema 0.4.0
  • Fix frontend for new data schema
  • Fix bugs (related to biom json export)

0.3.2 <2016-11-04>

  • Add organism_id mapping to project details page
  • Export project as biom (v1)
  • Download mapping results as csv
  • Mapping to organism_id by species name
  • Make project ID and comment editable
  • Improve project details page
  • Use pre-compilation of jsx files with babel
  • Re-write message system (using React)

0.3.1 <2016-10-20 Th>

  • Add exception handling to API
  • Add generalized WebserviceTestCase
  • Add fennec icon-font
  • Fix project overview table delete bug (#30)

0.3.0 <2016-10-17 Mo>

  • Use Symfony framework (symfony.com)

0.2.0 <2016-10-10 Mo>

  • Update navigation
  • Add trait details to projects
  • Update database schema for specific trait types
  • Add webservice to convert ncbi_taxids to organism_ids
  • Add trait overview table to projects
  • Update color scheme (fix scss)

0.1.5 <2016-06-01 Mi>

  • Integrate a phinch fork for inspection of projects
  • Add OTU table to project page
  • Add central dialog method
  • Add biom2 to biom1 conversion capability on the server
  • Add filename of imported file to project table
  • Add "remove project" capability
  • Remove communities from web interface

0.1.4 <2016-05-20 Fr>

  • Add proper redirects on login and logout
  • Add project upload capability
  • Add project overview table

0.1.3 <2016-04-29 Fr>

  • Add login with GitHub

0.1.2 <2016-04-28 Do>

  • Add gulp as build system
  • Add style-checks (phpcs, sassLint, jshint)
  • Add docu generation (apigen, jsdoc)
  • Add unit tests (phpunit, jasmine)
  • Add performance test (artillery)
  • Add ui test (selenium)
  • Add contribution guidelines

0.1.1 <2016-04-08 Fr>

  • Fix redirect on startpage

0.1.0 <2016-04-08 Fr>

  • add version picker
  • add support for multiple db versions
  • add project page design
  • add community page design
  • clean pages
  • add new level to interactive browse
  • add apigen documentation for webservices

0.0.5 <2016-03-23 Mi>

  • display all traits of an organism
  • add progress bar on organism page
  • display preffered name from eol on organism page
  • setup javascript testing

0.0.4 <2016-03-21 Mo>

  • add plotly graphs
  • add trait webservice for displaying trait information
  • display eol organism info (via API)
  • add db test fixtures

0.0.3 <2016-03-11 Fr>

  • add dynamic organism view
  • create layout for trait overview page
  • create layout for trait search page
  • add autocompletion for trait search form

0.0.2 <2016-02-26 Fr>

  • create layout for organism details
  • add autocompletion for organism search form
  • present organisms from database
  • add organism listing webservice
  • define general layout
  • setup general framework

0.0.1 <2016-02-15 Mo>

  • Initial release
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