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A program that dumps Natural Language Search text/PDF results for anatomic pathology reports into spreadsheet tabular format.

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PathISTabs

A program that dumps Natural Language Search text/PDF results into spreadsheet tabular and json formats.

README for non-developers

The webapp program is multi-platform and has been tested on the following systems (Windows 10, Ubuntu 16.04 and MacOS Sierra).

Download repository

Repository: https://github.com/gcampuzano14/PathISTabs

Green button "Clone or download" (top right)

Download zip

Extract contents to preferred folder (i.e. Desktop, Documents, etc.). You should have a path like this (root path for application): C:\Peferred_folder\PathISTabs.

Windows-specific instructions

Check python version

You need python 3.5+ to run this program. Version should be 3.5 (tested version) but may run on Python 3.6. This version hasn't been tested on Python 2x.

Access Windows command prompt (CMD) as administrator from within the PathISTabs parent directory (PathISTabs) (http://www.thewindowsclub.com/how-to-run-command-prompt-as-an-administrator)

Type the following command inside the CMD:

python

If python is installed i your system you should see something like this: Python 3.5.2 (v3.5.2:4def2a2901a5, Jun 25 2016, 22:18:55) [MSC v.1900 64 bit (AMD64)] on win32

If installed, take note of the version; it should be 3.5.x (see below for further explanation).

If python is not installed i your system you will get a message similar or equal to this: 'python' is not recognized as an internal or external command operable program or batch file

Exit the python console with control+c or type exit()

If no python version is installed or the version is python 2.7 you will need to get and install python 3.5.3 (https://www.python.org/downloads/release/python-353/). Download links:

Execute python-3.5.3.exe setup file and follow setup instructions.

First setup screen

Bottom, select Add Python 3.5 to PATH
Leave all other options as they are
Select: Install Now option

Let installation finish and hit close button

Open a new CMD and verify installation by typing following command:

python

Results should be as stated above in previous section, something like this: Python 3.5.2 (v3.5.2:4def2a2901a5, Jun 25 2016, 22:18:55) [MSC v.1900 64 bit (AMD64)] on win32

Setup python virtual environment

Once python is installed, within the and still inside a new CMD, inside the program's root folder (PathISTabs) you need to setup a virtual environment:

  • Install virtualenv

If default python is 3+

pip install virtualenv

If default python is not 3+

pip3 install virtualenv

Create virtual environment

virtualenv venv

Activate virtualenvironmetn

venv\Scripts\activate

Start application

-clean placeholders go to webapp\temp\lock folder an delete "placeholder" file

  • In CMD (inside program folder) go to webapp folder

cd webapp

  • Start app

python pathis_nls_parser.py

Access app in browser

  • Use chrome or firefox

in the address bar type the following

127.0.0.1:5000

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A program that dumps Natural Language Search text/PDF results for anatomic pathology reports into spreadsheet tabular format.

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