Public Health EHR Message Engine (PHEME), Web API

The pheme.webAPI exposes RESTful web services to act on documents. The documents typically represent generated public health reports. Available endpoints provide the standard document store, update, delete and retrieve mechanisms, supporting an unlimited set of meta-data on each document. Versioning of documents is also supported. Additional endpoints implement transfer protocols for secure transfer of stored reports to configured entities.

pheme.webAPI, a Pyramid application, uses the MongoDB as a backing store. Mongo must be installed and running for pheme.webAPI to properly function. Connection details are specified in the development and production initiation files at the root of this project. Alter these defaults if necessary:

[app:main]
db_uri = mongodb://localhost/
db_name = report_archive

For transmission via PHIN Messaging System additional entries in the pheme config file (see pheme.util.config) must specify the polled directories per report type. Configure PHIN-MS accordingly, and detail the locations such as:

[phinms]
essence=/opt/PHINms/shared/essence/outgoing/
essence_pcE=/opt/PHINms/shared/essence_er/outgoing/
essence_pcI=/opt/PHINms/shared/essence_in/outgoing/
essence_pcO=/opt/PHINms/shared/essence_out/outgoing/
longitudinal=/opt/PHINms/shared/longitudinal/outgoing/

Finally, to protect from sending test data to production servers, like most pheme modules, safeguards are in place. When ready for production, add to the pheme.util.config file. Note also the need for a log directory writable by the same user running the app:

[general]
in_production=True
log_dir=/var/log/pheme

Beyond the requirements listed above, pheme.webAPI is dependent on the pheme.util module. Although future builds may automatically pick it up, for now, clone and build it in the same virtual environment (or native environment) being used for pheme.webAPI:

git clone https://github.com/pbugni/pheme.util.git
cd pheme.util
./setup.py develop
cd ..

Then clone and build this web app:

git clone https://github.com/pbugni/pheme.webAPI.git
cd pheme.webAPI
./setup.py develop

The following invocation, run from the root directory of the pheme.webAPI project, uses the debug settings and captures logging information in the configured directory. The production initialization file should be used when ready:

pserve development.ini &> `configvar general log_dir`/webAPI.log

Many of the tests expect the web app to be running (see Running above). It is also strongly suggested that in_production be set to False before invoking the tests. Run the tests from the pheme.webAPI as follows:

./setup.py test

To completely clean up any testing artifacts, destroy and recreate the mongo database named in the initialization files.

At this time, no security measures are built into pheme.webAPI. It is expected that the port hosting this web app (see [servers:main]port in the development and production initiation files) is only accessible from localhost requests. Localhost access should be limited appropriately.

BSD 3 clause license - See LICENSE.txt