Welcome to the AB2D Python Sample Repo

Our API Clients are open source. This repo contains sample Python script which demonstrate how to pull data from the AB2D API Production environment.

This may be a great starting point for your engineering or development teams however it is important to note that the AB2D team does not regularly maintain the sample clients. Additionally, a best-effort was made to ensure the clients are secure, but they have not undergone comprehensive formal security testing. Each user/organization is responsible for conducting their own review and testing prior to implementation

Use of these clients in the sandbox environment allows for safe testing and ensures no PII/PHI will not be compromised if a mistake is made. The sandbox environment is publicly available and all the data in it is synthetic (not real)

AB2D supports both R4 and STU3 versions of the FHIR standard. FHIR R4 is available using v2 of AB2D while FHIR STU3 can be accessed via AB2D v1. Accordingly, this client supports both R4/ v2 and STU3/ v1.

Production Use Disclaimer:

These clients are provided as examples, but they are fully functioning (with some modifications) in the production environment. Feel free to use them as a reference. When used in production (even for testing purposes), these clients have the ability to download PII/PHI information. You should therefore ensure the environment in which these scripts are run is secured in a way to allow for storage of PII/PHI. Additionally, when used in the production environment the scripts will require use of your production credentials. As such, please ensure that your credentials are handled in a secure manner and not printed to logs or the terminal. Ensuring the privacy of data is the responsibility of each user and/or organization.

Prerequisites

Python requests module must be installed

python3 -m pip install requests

Python Client

A simple client for starting a job in sandbox or production, monitor that job, and download the results. To prevent issues these scripts persist the job id and list of files generated. This client supports both FHIR version R4 (v2) and STU3 (v1) of the standard.

This script will not overwrite already existing export files.

Usage: 
  python job-cli.py (-prod | -sandbox) --auth <authfile.base64> [--directory <dir>] [--since <since>] --fhir (R4 | STU3)
        [(--only_start|--only_monitor|--only_download)]

Help (for an explanation of the arguments): 
   python job-cli.py --help
   
Arguments:
  -sandbox        -- if running against ab2d sandbox environment
  -prod           -- if running against ab2d production environment
  --auth          -- path to base64 file containing auth token
  --directory     -- if you want files and job info saved to specific directory
  --get_token     -- if you only want to get bearer token
  --only_start    -- if you only want to start a job
  --only_monitor  -- if you only want to monitor an already started a job
  --only_download -- if you only want to download an already finished job
  --since         -- if you only want to pull claims data added after a certain date.
                     The expected format is yyyy-MM-dd'T'HH:mm:ss.SSSXXX+/-ZZ:ZZ.
                     Example March 1, 2020 at 3 PM EST -> 2020-03-01T15:00:00.000-05:00. More below.
  --fhir          -- FHIR version

Help

Run python job-cli.py --help to get a full list of arguments and explanations.

Since Parameter

If you only want to pull claims data added to the CMS system after a certain date use the --since parameter. The expected format follows the typical ISO date time format of yyyy-MM-dd'T'HH:mm:ss.SSSXXX+/-ZZ:ZZ.

The earliest date that _since works for is February 13th, 2020. Specifically: 2020-02-13T00:00:00.000-05:00

For requests using FHIR R4, a default _since value is supplied if one is not provided. The value of the default _since parameter is set to the creation date and time of a contract's last successfully searched and downloaded job.

Examples:

1. March 1, 2020 at 3 PM EST -> 2020-03-01T15:00:00.000-05:00
2. May 31, 2020 at 4 AM PST -> 2020-05-31T04:00:00-08:00

Files

1. /directory/jobId.txt -- id of the job created
2. /directory/response.json -- list of files created
3. /directory/*.ndjson -- downloaded results of exports

Limitations

1. Assumes all scripts use the same directory
2. Assumes all scripts use the same base64 encoded AUTH token

Example

If you want to:

1. Start a job running against production
2. Using base64 encoded credentials stored in auth-credentials.base64
3. And save all results for this job to the directory /opt/foo

Then run the following command: python job-cli.py -prod --auth auth-credentials.base64 --directory /opt/foo

Install or verify python 3, pip, and required pip modules

1. If you are using Linux, jump to the following section:

   Install or verify python 3, pip, and required pip modules on Linux

2. If you are using Mac, jump to the following section:

   Install or verify python 3, pip, and required pip modules on Mac

3. If you are using Windows, jump to the following section:

   Install or verify python 3, pip, and required pip modules on Windows

Install or verify python 3, pip, and required pip modules on Linux

*** TO DO ***

Install or verify python 3, pip, and required pip modules on Mac

*** TO DO ***

Install or verify python 3, pip, and required pip modules on Windows

Determine if python 3 is already installed on Windows

1. Check to see if python 3 is installed

   where python

2. Note the output

   Example:

   {your user directory\AppData\Local\Microsoft\WindowsApps\python3.exe
   

3. Note the following

   • if you only see one line of output displaying "python3.exe" under the "WindowsApps" directory, this means python3 is NOT installed

   • these instructions will install from the official python site instead of the Windows Store (which is often locked by administrators)

4. If you only had one line of "...\WindowsApps\python3.exe" output, jump to the following section:

   Install python 3 on Windows

5. If more than one line was displayed in the output and includes a "...\Python\Python3{version}\python.exe" line, jump to the following section:

   Verify python and pip work from the command prompt on Windows

Install python 3 on Windows

1. Open a web browser

2. Enter the following in the address bar

   https://www.python.org/downloads

3. Select the following under "Download the latest version of Windows"

   Format:

   Download Python 3.{version}
   

   Example:

   Download Python 3.9.0
   

4. Wait for the download to complete

5. Open the downloaded file

   Format:

   python-3.{version}
   

   Example:

   python-3.{version}-amd64.exe
   

6. Check the following

   Format:

   Add Python 3.{version} to PATH
   

   Example:

   Add Python 3.9 to PATH
   

7. Select Install Now

8. Wait for the installation to complete

9. Select Close

Verify python and pip work from the command prompt on Windows

1. Select the Windows icon (likely in the bottom left of your window)

2. Type the following in the search text box

   command
   

3. Select Command Prompt from the results

4. Verify that python is installed properly, by checking its version

   1. Check the python3 version

      python --version

   2. Verify that the version of python that you installed is displayed

      Python 3.9.0
      

5. Verify that pip is installed properly, by checking its version

   1. Check the python3 version

      pip --version

   2. Verify that the version of python that you installed is displayed

      Format:

      pip {version} from {installation directory}\pip (python 3.{version}
      

Install required pip modules on Windows

1. Install the "requests" pip module

   pip install requests

2. Verify that the requests module installed correctly

   1. Show the request pip module

      pip show requests

   2. Verify that a description of the "requests" module is displayed

Get your data files

Choose the method you want to use to get your data files

Note that for this example we are running an export job on sandbox.

1. If you want to run the process stages individually in order to understand the process, jump to the following section:

   Running Stages Individually

2. If you just want all process stages to run automatically, jump to the following section:

   Running All Stages

Running Stages Individually

1. Set the AUTH_FILE value

   On Mac or Linux:

   AUTH_FILE=<auth credentials file>

   On Windows from command prompt:

   SET AUTH_FILE=<auth credentials file>

2. Write the credentials to the auth file

   On Mac or Linux:

   echo -n "${OKTA_CLIENT_ID}:${OKTA_CLIENT_PASSWORD}" | base64 > $AUTH_FILE

   On Windows from command prompt:

   $BASE64_ENCODED_ID_PASSWORD='{Base64-encoded id:password}'
   Set-Content -Path $AUTH_FILE $BASE64_ENCODED_ID_PASSWORD

3. Exit your current terminal and open a new terminal

4. Repeat setting the AUTH_FILE value

5. Set a variable with today's date

   Example on Mac or Linux:

   TODAYS_DATE=2020-10-30

   Example on Windows from command prompt:

   SET TODAYS_DATE=2020-10-30

6. Create a directory for downloading export files

   Make sure to change the directory using today's date (YYYY-MM-DD):

   Example on Mac or Linux:

   mkdir -p ~/ab2d/$TODAYS_DATE && TARGET_DIR=~/ab2d/$TODAYS_DATE

   Example on Windows from command prompt:

   mkdir "%HOMEPATH%/documents/%TODAYS_DATE%" && SET TARGET_DIR="%HOMEPATH%/documents/%TODAYS_DATE%"

7. Start the export job

   On Mac or Linux:

   python job-cli.py -sandbox --auth $AUTH_FILE --directory $TARGET_DIR --only_start --fhir R4

   On Windows from command prompt:

   python job-cli.py -sandbox --auth %AUTH_FILE% --directory %TARGET_DIR% --only_start --fhir R4

8. Verify that a job id was created

   On Mac or Linux:

   cat $TARGET_DIR/job_id.txt

   On Windows from command prompt:

   type %TARGET_DIR%\job_id.txt

9. Monitor the job

   On Mac or Linux:

   python job-cli.py -sandbox --auth $AUTH --directory $TARGET_DIR --only_monitor

   On Windows from command prompt:

   python job-cli.py -sandbox --auth %AUTH% --directory %TARGET_DIR% --only_monitor

10. Verify that a job completed by verifying the list of files in the response

    On Mac or Linux:

    cat $TARGET_DIR/response.json

    On Windows from command prompt:

    type %TARGET_DIR%\response.json

11. Download the files

    Note that this process will only download the files once. Running again will not overwrite the files but will also not download anything.

    On Mac or Linux:

    python job-cli.py -sandbox --auth $AUTH --directory $TARGET_DIR --only_download

    On Windows from command prompt:

    python job-cli.py -sandbox --auth %AUTH% --directory %TARGET_DIR% --only_download

12. List the files that you have downloaded

    On Mac or Linux:

    ls $TARGET_DIR/*.ndjson

    On Windows from command prompt:

    dir %TARGET_DIR%\*.ndjson

13. Stop here, you have completed the file download

Running All Stages

1. Set the AUTH value

   On Mac or Linux:

   AUTH=<auth value>

   On Windows from command prompt:

   SET AUTH=<auth value>

2. Set a variable with today's date

   Example on Mac or Linux:

   TODAYS_DATE=2020-10-30

   On Windows from command prompt:

   SET TODAYS_DATE=2020-10-30

3. Create a directory for downloading export files

   Make sure to change the directory using today's date (YYYY-MM-DD):

   Example on Mac or Linux:

   mkdir -p ~/ab2d/$TODAYS_DATE && TARGET_DIR=~/ab2d/$TODAYS_DATE

   Example on Windows from command prompt:

   mkdir "%HOMEPATH%/documents/%TODAYS_DATE%" && SET TARGET_DIR="%HOMEPATH%/documents/%TODAYS_DATE%"

4. Start the export job, monitor the job, and download the files

   On Mac or Linux:

   python job-cli.py -sandbox --auth $AUTH_FILE --directory $TARGET_DIR --fhir R4

   On Windows from command prompt:

   python job-cli.py -sandbox --auth %AUTH_FILE% --directory %TARGET_DIR% --fhir R4

5. List the files that you have downloaded

   On Mac or Linux:

   ls $TARGET_DIR/*.ndjson

   On Windows from command prompt:

   dir %TARGET_DIR%\*.ndjson

6. Stop here, you have completed the file download

Bundling Python and Script

Build Python in Source

1. Download the latest version of Python as a tar file
2. Unpack the tar file tar -xvf python-tar
3. Change directory to the folder created cd python-tar
4. Configure the installer ./configurer --prefix /path/to/ab2d/examples/python/python --with-openssl=$(brew --prefix openssl)
5. Run make
6. Run make install
7. Check that the following directories exist in /path/to/ab2d/examples/python/python: bin, lib, share, include

Setup Virtual Environment

Before zipping up Python we need to create a virtual environment. This part assumes access to IntelliJ or PyCharm.

In IntelliJ these are the steps

1. Go to File -> Project Structure
2. Look for Platform Settings -> SDKs and click on it
3. Add a new Python SDK, set the python interpreter as ab2d/examples/python/python/bin/python3, and set the venv home as examples/python/venv
4. Open a terminal in IntelliJ and in that terminal change directories to ab2d/examples/python/
5. Then install the requests library by running venv/bin/pip3 install requests

Zip

1. Change directory cd examples
2. zip -r client.zip python

Unzip and Run

When developing move /path/to/ab2d/examples/python/python and /path/to/ab2d/examples/python/venv to different directories to check that no symbolic links

1. Unzip unzip client.zip
2. Change directory to the python directory
3. Export the path to the python folder PYTHONPATH=./python
4. Run a job by using /venv/bin/python3 job-cli.py ...