Rhizi

A collaborative graph editor for organizing, communicating, and analyzing data in graph form.

Screencast tutorial

Live demo

It is licensed under the GNU AGPL v3, see LICENSE for more details.

Patches or pull requests are welcome but we require a contributor license agreement, see TBU

Dependencies

Database:

• Neo4J DB server >= 2.1.5 - http://neo4j.com/download/

Server:

• Python 2.7
• Apache Ant >= 1.9.0
• Python dependencies as described in requirements.txt

Client All of the following are already bundled but noted here for reference:

• jquery
• d3
• Bacon.js
• underscore
• feedback - https://github.com/ivoviz/feedback (it also bundles html2canvas)
• FileSaver

For rebuilding client css from scss saource files you will need:

• sass (scss tool)

Build dependencies:

• ant
• make

Installation

Apt based systems: Debian / Ubuntu

# apt-get install
ant
python-pip
ruby-sass

Generic

use pip to install all requirements

$ pip install -r requirements.txt

Use npm for javascript (client) requirements, currently for development (testing) only, all other external dependencies are part of the repository:

$ npm install

Running instructions

Running Rhizi Locally

To run Rhizi locally:

• Run neo4j locally on the default 7474 port neo4j console or neo4j server after installing neo4j: we use 2.2.1 from http://neo4j.com
• Launch run-local.sh:
  $ ./run-local.sh

Or perform the following by hand:

• Invoke the local deployment Ant target:
  ant -f ./build.ant deploy-local
• Run rhizi-server.py:
  $ cd deploy-local && python bin/rz_server.py --config-dir=etc

Command line use documentation can be viewed with: :$ python rz_server.py -h

Configuration

Rhizi configuration is currently documented in code, see src/server/rz_server.py#Config

User addition

Through the sign up page you can add users.

Changing users roles

This is possible through the src/local/rz_cli_tool as follows: ./src/local/rz_cli_tool.py --config-dir res/etc --user-db-path res/user_db.db --email [email protected] --role-add admin

Development

Build currently uses Apache Ant(http://ant.apache.org/) and make

To update the css files you need sass. To rebuild the css files issue make from the top level directory:

$ make

For dev mode(debbuging, manual file load) use ?debug=1 at end of URL: e.g. file://rhizifolder/html.index?debug=1

Client testing:

$ npm install $ karma start

Coding Conventions - Ant Scripts

• use underscore as delimiter in var name, eg: pkg_foo_bar

Coding Conventions - CSS / SCSS

• assume use of modern browsers
• indent files using 4 space characters
• apply alphabetical ordering whenever possible: selectors, directives, etc.
• use a combination of CSS classes / IDs to draw common/unique styling, eg. class=form-Foo_input-field id=email-field
• minimize use of CSS directives, remove directives which have no effect
• avoid using browser-specific CSS directives when hand-writing CSS code

Neo4J DB management

• Clean Neo4J instances are auto-initialized by the rhizi server
• to reset the DB manually: $ neo4j-shell -file res/neo4j/reset-db__clean.cypher

Running server tests

Test code makes use of Python's unittest - run by invoking them with python, or by creating a launch configuration in your IDE of choice.

Note: server test-cases do not yet support pre-run DB state validation and are likely to leave DB side-effects.

Random data generation

Taks a look at src/server-tests/test_util__rzdoc#DBO_RDG__skill_graph as a starting point for random data generation.

Installing on windows (WIP)

mingw doesn't have python support, so using mingw (I want a unix native python)

• www.cygwin.com setup-x86_64.exe
• use correct mirror (i.e. mirror.isoc.org.il)
• defaults (c:\cygwin64)
• python + gvim + vim + python-six + git + git-completion + tig + ruby + ruby-sass + make + gcc-core + autoconf + automake
• start cygwin shell
• cd to directory of install
• git clone or extract tarball
• cd rhizi
• install neo4j from neo4j.com community eddition (neo4j-community_windows_2_1_6.exe)
• install python prerequisites:
• download get-pip.py from http://pip.pypa.io/en/latest/installing.html
• $ python get-pip.py
• install JDK: java SE development Kit 8 jdk-8u31-windows-x64.exe
• install ant: winant.googlecode.com/files/winant-install-v7.exe
  • specify JDK install directory, i.e. C:\Program Files\Java\jdk1.8.0_31
• Current ant bug: /usr/bin/rhizi is translated by ant to \usr\bin\rhizi and so it fails to find rhizi.
  • solution 1: replace /usr/bin/rhizi with rhizi, it will find rhizi in PATH
  • solution 2: ?
• pip install flask
• pip install gevent-websocket
  • pip install gevent never completes setup.py stage
    • solution 1: pip install cython git+git://github.com/surfly/gevent.git#egg=gevent
    • didn't complete.

Deployment

Deployment, that is installation on a different server that has none of the development prerequisites installed, takes two forms currently:

• development mode, in which flask handles all resource serving, including client/server code, resources & fragments
• reverse proxy mode, in which a reverse proxy, eg. Apache is used to serve all static content

These modes impost a slightly different resource layout, and require the following values to be correcly set/injected:

• app.js: fragment_d_path, handled by jinja
• rhizi-server.conf: fragment_d_path
• rhizi-server.conf: template_d_path

Deployment Steps

• obtain a server configuration by either adjusting res/etc/rhizi-server.conf.example or reusing an already active one.

• the following configuration keys will likely need changing: DEBUG, SECRET_KEY, root_path, access_control, etc.

• let targetDomain be the target domain (i.e. rhizi.example.com)

• place configuration at res/production-patch-set/${targetDomain}/rhizi-server.production.conf

• use the build.ant deploy-remote target:

  • adjust targetDomain path: should point at the configuration's file dir
  • adjust remoteDeployServer to point at the target server

• use res/debian/rhizi.init to run rhizi as a system process: rz_server.py will need chmod'ing to +x

• Deploying: $ ant -v -f build.ant -DremoteDeployServer=rhizi.example.com -Drsync_module=/srv/www/rhizi.example.com deploy-remote

getting the current config file from the server:

$ targetDomain="cri.rhizi.net" $ mkdir res/production-patch-set/${targetDomain} $ scp rz-1:/etc/rhizi/rhizi-server.conf res/production-patch-set/${targetDomain}/rhizi-server.production.conf

Tools

rz-doc

This is the only way to merge a number of documents right now. Here is how:

It is installed by default to /srv/www//tools/rz-doc, lets call that rz-doc for short.

rz-doc --list-names

• will show all available documents. uses default config in /etc/rhizi/rhizi-server.conf, can be overridden with --config-dir

1. rz-doc --list-names > merge.file
2. rz-doc --merge-file merge.file --merge-target "All Documents"

creates a new doc called "All Documents" with the contents of all rzdocs in merge.file.

API(WIP)

[url]/api/rzdoc/[doc-title]/delete