Getting Started

Setting up BIDS

Linux

Debian, Ubuntu, Mint

• TODO

Arch

• TODO

Windows

Install Reach-Examples

• download the JDK for Java 8 (or choose the latest Java version) from the java website
• install the JDK with default options
• download SBT from the scala website
• run the installer with default options
• close and reopen any terminals you have open
• In a terminal run SBT (ensure your network remains connected, as things will be downloaded from maven repos.)

 > sbt

• download git from the git website
• install git with default options
• close and reopen any terminals you have open
• In a terminal make a directory to store the BIDS project. We will create a directory 'Src' (intended to store all source code we work on, including BIDS) with a directory 'BIDS' inside

 > mkdir Src
 > cd Src
 > mkdir BIDS

• clone the reach-examples repository

 > git clone https://github.com/dsidi/reach-examples

• change to the reach-examples directory

 > cd reach-examples

• edit your PATH variable.
  • In a terminal, do (you may need to replace jdk1.8.0_91 with something similar but different)

 > cd c:\Program Files\Java\jdk1.8.0_91\bin

• • now highlight the path to the left of the ">" (not including the ">") and do <ctrl><c> to copy it
  • Click Start, then Settings. Type "environment" into the search box in the corner of the settings window
    • Click "edit the system environment variables"
    • Click the "Environment Variables..." button
    • Select "Path" from the "System variables" box, and click "Edit..."
    • Click at the end of the Variable value field to edit the text.
    • Add a semicolon ";", then right click and select paste.
    • Click OK in all windows, close the settings window, and close all open terminals
• In a new terminal, change to the reach-examples directory. For my case, this is

 > cd Src\BIDS\reach-examples

• run reach-examples with sbt (again sbt will download several things, so ensure your connection to the internet is up)

 > sbt run

• when prompted, type the number of the selection for com.yourorg.GroundStringsEntryPoint
• If no errors are shown, move to the next section

Install BIDS

Install miniconda

• download miniconda from the conda website (choose the version for Python 2.7, and your architecture
• install miniconda (install for the whole system, not just the current user, if possible) with default options
• install scikit-learn package

 > conda install scikit-learn

• close all terminals (including the one with SBT running in it, if you left it open)

Get the BIDS code

• in a new terminal change to the directory containing reach-examples, then clone the BIDS repository (so that the BIDS directory and the reach-examples directory are siblings:

 > cd Src\BIDS
 > git clone https://github.com/ua-sista/bigmech.git

Install BIDS dependencies

• in a new terminal, install virtual env from pip:

 > pip install virtualenvwrapper-win

• make a bids environment

 > mkvirtualenv bids

• • you should now see (bids) in your command prompt
• install the Visual C++ compiler for Python 2.7 (try not to cry)
  • download from the microsoft website, run the installer with default options
• install the requirements for the BIDS project using pip and the requirements.txt file

 > pip install -r requirements.txt

• now change to the BIDS directory. In my case

 > cd Src\BIDS\bigmech

Add BIDS paths to PYTHONPATH

• we need to add the path to bioCausalRelationLearner to your path (similar to what we did before to add javac to the path)
  • first get the path to the bioCausalRelationLearner
    • in a new terminal, go to the directory containing the file bioCausalRelationLearner.py. This file is in the directory for BIDS that you cloned earlier. For me it is in

 > cd Src\BIDS\bioIncrementalDistantSupervision

• • • highlight the path to the left of the ">" (not including the ">"), and copy with <ctrl><c>
    • close the terminal
  • Click Start, then Settings. Type "environment" into the search box in the corner of the settings window
  • Click "edit the system environment variables"
  • Click the "Environment Variables..." button
  • Try to find "PYTHONPATH" in the "System variables" box. If it is there, click "Edit..." and add a semicolon, then paste from the clipboard. If it is not, click New... and name the variable PYTHONPATH, and paste from the clipboard into the Variable value field.
  • Click OK to save the settings, then OK again in the next window

Run the unit tests

• now we'll run the unit test for training the classifier. First we run the reach server.
• In a new terminal, go to the reach-examples directory and do

 > run sbt 

selecting the entry point exactly as above

• In a second new terminal, go to the BIDS source directory and run the python unittest test_train:

 > cd Src\BIDS\bigmech
 > python -m unittest