thalamus 0.9.16

The GNU Health Federation Message and Authentication Server

The Thalamus project provides a RESTful API hub to all the GNU Health Federation nodes. The main functions are:

1. Message server: A concentrator and message relay from and to the participating nodes in the GNU Health Federation and the GNU Health Information System (PgSQL). Some of the participating nodes include the GNU Health HMIS, MyGNUHealth mobile PHR application, laboratories, research institutions and civil offices.

2. Authentication Server: Thalamus also serves as an authentication and authorization server to interact with the GNUHealth Information System

Thalamus is part of the GNU Health project, but it is a self contained, independent server that can be used in different health related scenarios.

Installation

Thalamus is pip-installable:

$ pip3 install --upgrade --user thalamus

Note on psycopg2: The package psycopg2-binary is a source of issues, so we have replaced it by psycopg2 since thalamus 0.9.16. You need to install the postgresql development libraries. look for the description like PostgreSQL shared libraries (development files) or header files in your operating system packages

Technology

RESTful API: Thalamus uses a REST (Representional State Transfer) architectural style, powered by Flask technology

Thalamus will perform CRUD (Create, Read, Update, Delete) operations. They will be achived via the following methods upon resources and their instances.

• GET : Read

• POST : Create

• PATCH : Update

• DELETE : Delete.

The DELETE operations will be minimal.

JSON: The information will be encoded in JSON format.

Resources

Some resources and end-points are:

• People (/people)

• Pages of Life (/pols)

• DomiciliaryUnits (/domiciliary-units)

• PersonalDocs (/personal_docs)

Running Thalamus from a WSGI Container

In production settings, for performance reasons you should use a HTTP server. We have chosen uWSGI , but you can use any WSGI server. We have also included the configuration file for Gunicorn if you prefer it instead of uWSGI.

For example, you can run the Thalamus application from uWSGI as follows. The default configuration file uses secure (SSL) connections:

$ uwsgi --ini etc/thalamus_uwsgi.ini

For development, ff you want to run it directly from the Flask Werkzeug server,:

$ python3 ./thalamus.py

Examples

Command-line, using httpie

Retrieve the demographic information of person:

$ http --verify no --auth ARGBUE111FAV:freedom https://federation.gnuhealth.org:8443/people/ESPGNU777ORG

Yields to:

HTTP/1.1 200 OK
Access-Control-Allow-Origin: *
Connection: close
Content-Length: 547
Content-Type: application/json
Date: Thu, 30 Jul 2020 12:01:37 GMT
Server: gunicorn/20.0.0

{
    "_id": "ESPGNU777ORG",
    "active": true,
    "dob": "1990-10-04",
    "education": "tertiary",
    "ethnicity": "latino",
    "gender": "f",
    "id": "ESPGNU777ORG",
    "lastname": "Betz",
    "marital_status": "married",
    "modification_info": {
        "node": "SPAIN-LASPALMAS-GNUSOLIDARIO-GRAL_HOSPITAL",
        "timestamp": "2018-11-06 19:24:43.662846",
        "user": "ITAPYT999HON"
    },
    "name": "Ana",
    "password": "$2b$12$cjrKVGYEKUwCmVDCtEnwcegcrmECTmeBz526AAD/ZqMGPWFpHJ4FW",
    "profession": "teacher",
    "roles": [
        "end_user"
    ]
}

Retrieve the demographics information globally:

$ http --verify no --auth ARGBUE111FAV:freedom https://federation.gnuhealth.org:8443/people

Yields to:

HTTP/1.1 200 OK
Access-Control-Allow-Origin: *
Connection: close
Content-Length: 2715
Content-Type: application/json
Date: Mon, 20 Jul 2020 18:03:24 GMT
Server: gunicorn/20.0.0

[
[
    {
        "active": true,
        "dob": "1984-10-05",
        "education": "tertiary",
        "ethnicity": "latino",
        "gender": "f",
        "id": "ITAPYT999HON",
        "lastname": "Cordara",
        "marital_status": "married",
        "name": "Cameron",
        "password": "$2b$12$Y9rX7PoTHRXhTO1H78Tan.8mVmyayGAUIveiYxu2Qeo0ZDRvJQ8/2",
        "profession": "teacher",
        "roles": [
            "end_user",
            "health_professional"
        ]
    }
],
[
    {
        "creation_info": {
            "node": "SPAIN-LASPALMAS-GNUSOLIDARIO-GRAL_HOSPITAL",
            "timestamp": "2019-11-20 10:39:21.162731",
            "user": "ITAPYT999HON"
        },
        "dob": "1999-10-12",
        "gender": "m",
        "id": "DEUMOP095IDI",
        "lastname": "Dillinger",
        "name": "John Doe",
        "roles": [
            "end_user"
        ]
    }
],


[
    {
        "active": true,
        "dob": "2008-10-12",
        "education": "tertiary",
        "ethnicity": "latino",
        "gender": "f",
        "id": "ARGBUE111FAV",
        "lastname": "Root",
        "marital_status": "married",
        "name": "Admin",
        "password": "$2b$12$McKDNgArdHKbUssD1fj64ecpdbJGMIt29ns7DGvqzqIT26W0dtJzi",
        "profession": "System Administrator",
        "roles": [
            "root"
        ]
    }
],
[
    {
        "_id": "ESPGNU777ORG",
        "active": true,
        "dob": "1990-10-04",
        "education": "tertiary",
        "ethnicity": "latino",
        "gender": "f",
        "id": "ESPGNU777ORG",
        "lastname": "Betz",
        "marital_status": "married",
        "modification_info": {
            "node": "SPAIN-LASPALMAS-GNUSOLIDARIO-GRAL_HOSPITAL",
            "timestamp": "2018-11-06 19:24:43.662846",
            "user": "ITAPYT999HON"
        },
        "name": "Ana",
        "password": "$2b$12$cjrKVGYEKUwCmVDCtEnwcegcrmECTmeBz526AAD/ZqMGPWFpHJ4FW",
        "profession": "teacher",
        "roles": [
            "end_user"
        ]
    }
],
]

Using Python requests:

>>> import requests
>>> person = requests.get('https://localhost:8443/people/ESPGNU777ORG', auth=('ITAPYT999HON', 'gnusolidario'), verify=False)
>>> person.json()
  {'_id': 'ESPGNU777ORG', 'active': True, 'biological_sex': 'female','dob': 'Fri, 04 Oct 1985 13:05:00 GMT',
  'education': 'tertiary', 'ethnicity': 'latino', 'gender': 'female', 'lastname': 'Betz', 'marital_status': 'married',
  'name': 'Ana', 'password': '$2b$12$cjrKVGYEKUwCmVDCtEnwcegcrmECTmeBz526AAD/ZqMGPWFpHJ4FW', 'profession': 'teacher',
  'roles': ['end_user']}

Note on roles The demo user “ITAPYT999HON” is a health professional (health_professional role), so she has global access to demographic information.

The user “ARGBUE111FAV”, password “freedom”. This is the “root” user for the demo database.

Check the roles.cfg file for examples information about roles and ACLs.

Development

Thalamus is part of the GNU Health project.

The development will be done on GNU Savannah, using the Mercurial repository.

Tasks, bugs and mailing lists will be on [e-mail] , for development.

General questions can be done on [e-mail] mailing list.

Homepage

https://www.gnuhealth.org

Release Cycle

Thalamus, as other GNU Health components, will follow its own release process.

Documentation

The Thalamus documentation will be at the corresponding chapter in the GNU Health documentation portal:

https://docs.gnuhealth.org

Author:

Luis Falcon <[e-mail]>