Getting Started

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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 Scikit-learn

  • install numpy from pre-built binaries here (choose the filename with 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 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
  • 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 (replace PATH_TO_CONDA_PYTHON_EXE with the path for your system)
 > mkvirtualenv --python=PATH_TO_CONDA_PYTHON_EXE bids
    • for example, I put
 > mkvirtualenv --python=c:\Miniconda2\python.exe bids
    • you should now see (bids) in your command prompt
  • install the Visual C++ compiler for Python 2.7 (try not to cry)
  • install the requirements for the BIDS project using pip and the requirements.txt file
 > pip install -r requirements.txt
  • THIS MAY BREAK. Windows should tell you that the .NET 3.5 framework is needed, and offer to install it automatically. Do it, and once it finishes run the above "pip install" command again
    • If Windows doesn't do this for you, please let David know
  • 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

Mac

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