Getting Started

Setting up BIDS

Linux

Debian, Ubuntu, Mint

• TODO

Arch

• TODO

Windows

Do all of the following in cmd (that is what is meant by terminal)

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
• set JAVA_OPTS

 > set JAVA_OPTS=-server -Xms3g -Xmx6g

• 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
 > cd 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. (NOTE: this may be replaced with setx at the command line in the future. I need to look into it. -David)
  • In a terminal, do (you may need to replace jdk1.8.0_91 with something similar but different) <source lang=winbatch>

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

</source>

• • now highlight the path to the left of the ">" (not including the ">") and do <ctrl><c> to copy it
  • right click the cmd icon on the task bar, and click "run as administrator"
    • set the path <source lang=winbatch>

 > setx path "%path%;<ctrl><v> /M" 

</source> where <ctrl><v> is you pressing those keys to paste in the path you just copied.

• 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 Scikit-learn

• install numpy from pre-built binaries here (choose the filename with both '27' in it [for Python 2.7.x] and either 'amd64' (if you're 64 bit architecture) or 'win32' (otherwise)
• install scipy from pre-built binaries here (choose the filename with both '27' in it [for Python 2.7.x] and either 'amd64' (if you're 64 bit architecture) or 'win32' (otherwise)
• install scikit-learn from pre-built binaries here (choose the filename with both '27' in it [for Python 2.7.x] and either 'amd64' (if you're 64 bit architecture) or 'win32' (otherwise)
• 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. If you do not use Python 2.7.x as your python interpreter (calling <source lang=winbatch>python --version</source> on the command line will tell you), you'll need to do

 > mkvirtualenv --python=C:\Python27\python.exe bids

possibly substituting a different path to the python.exe for Python2.7.x if it's not in the default location. If you do use python 2.7.x, you can just do

 > 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 modified 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 <source lang=winbatch> > cd Src\BIDS\bigmech\bioIncrementalDistantSupervision </source>
    • 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 test.test_IncrementalDistantSupervision.IncrementalDistantSupervisionTests.test_train

• If you see "Training classifier..." followed by an error about a .pkl file missing, you are good (this will be fixed very shortly)