ID3C: Infectious Disease Data Distribution Center
Data logistics system enabling real-time genomic epidemiology. Built for the Seattle Flu Study.
Initially aims to provide:
De-identified metadata for participants (age, sex, address token, etc.) and samples (tissue, date, location, etc.)
Sample diagnostic results (positive/negative for influenza, RSV, and more)
Sequencing read sets and genome assemblies stored in the cloud and referenced via URLs in database
Rich data types (key/value, JSON, geospatial, etc)
Strong data integrity and validation controls
Role-based authentication and restricted data fields using row and column-level access control
Encrypted at rest and TLS-only connections
Administration via standard command-line tools (and maybe later pgAdmin4)
The database is designed as a distribution center which receives data from external providers, repackages and stores it in a data warehouse, and ships data back out of the warehouse via views, web APIs, and other means. Each of these three conceptual areas are organized into their own PostgreSQL schemas within a single database.
The "receiving" area contains tables to accept minimally- or un-controlled data from external providers. The general expectation is that most tables here are logs (in the journaling sense) and will be processed later in sequential order. For example, participant enrollment documents from our consent and questionnaire app partner, Audere, are stored here when received by our web API.
The "warehouse" area contains a hybrid relational + document model utilizing
standard relational tables that each have a JSON column for additional details.
Data enters the warehouse primarily through extract-transform-load (ETL)
routines which process received data and copy it into suitable warehouse rows
and documents. These ETL routines are run via
bin/id3c etl subcommands, where
they're defined in Python (though lean heavily on Pg itself).
The "shipping" area contains views of the warehouse designed with specific data consumers and purposes in mind, such as the incidence modeling team.
While the receiving and shipping areas are expected to be fairly fluid and reactive to new and changing external requirements, the warehouse area is expected to change at a somewhat slower pace informed by longer-term vision for it.
General principles to follow when developing the schema.
- Do the ~simplest thing that meets our immediate needs. Aim for ease of modification in the future rather than trying to guess future needs in advance.
It can be really hard to stick to this principle, but it turns out that the best way to make something flexible for future needs is to make it as simple as possible now so it can be modified later.
Columns should be maximally typed and constrained, unless there exists a concrete use case for something less.
Consider if a column should ever be unknown (null).
Consider if a column should have a default.
Consider what constraints make sense at both a column- and table-level. Would a
CHECKconstraint be useful to express domain logic?
Write a description (comment) for all schemas, tables, columns, etc.
Grant only the minimal privileges necessary to the read-only and read-write roles. For example, if the read-write role isn't expected to
UPDATEexisting records, then only grant it
Consider expected data access patterns and create indexes to match.
Integration with other data systems
Although we're building our own data system, we want to design and create it with interoperability in mind. To this extent, our system should adopt or parallel practices and terminology from other systems when appropriate. For example:
- Nouns (tables, columns, etc) in our system should consider adopting the equivalent terms used by FHIR R4 resources.
This will aid with producing FHIR documents in the future and provides a consistent terminology on which to discuss concepts more broadly than our group. FHIR is a large specification and there is a lot to digest; it's easy to be daunted or confused by it, so please don't hesitate to ask questions.
- Value vocabulary (specimen types, organism names, diagnostic tests, etc) should consider using and/or referencing the preferred terms from an appropriate ontology like SNOMED CT, LOINC, or GenEpiO.
The database schema is deployed using Sqitch, a database change management tool that really shines. You can install it a large number of ways, so pick the one that makes most sense to you.
For development, you'll need a PostgreSQL server and superuser credentials for it. The following commands assume the database server is running locally and your local user account maps directly to a database superuser.
Create a database named
seattleflu using the standard Pg tools. (You can use
another name if you want, maybe to have different dev instances, but you'll
need to adjust the sqitch target you deploy to.)
createdb --encoding=UTF-8 seattleflu
sqitch to deploy to it. (
dev is a sqitch target configured in
sqitch.conf which points to a local database named
sqitch deploy dev
Now you can connect to it for interactive use with:
Testing and production
Our testing and production databases are configured as
production sqitch targets. When running sqitch against these
targets, you'll need to provide a username via
PGUSER and a password via an
entry in ~/.pgpass.
Python 3 + Flask
- Consumes and stores enrollment documents from the Audere backend systems
- Database connection details are set entirely using the standard libpq
PGDATABASE. You may provide these when starting the API server.
User authentication is performed against the database for each request, so you do not (and should not) provide a username and password when starting the API server.
The maximum accepted Content-Length defaults to 20MB. You can override this by setting the environment variable
LOG_LEVELenvironment variable controls the level of terminal output. Levels are strings:
Starting the server
pipenv run python -m id3c.api or
pipenv run flask run
will run the application's development server. To provide database
connection details while starting the development server, run the command
PGDATABASE=DB_NAME pipenv run flask run, substituting
DB_NAME with the name
of your database.
For production, a standard
api.wsgi file is provided which can be used by any
web server with WSGI support.
User authentication must be provided when making POST requests to the API. For
example, you can run the following
curl command to send JSON data named
enrollments.json to the
/enrollment endpoint on a local development server:
curl http://localhost:5000/enrollment \ --header "Content-Type: application/json" \ --data-binary @enrollments.json \ --user USERNAME
Substitute your own local database username for
USERNAME. This will prompt
you for a password; you can also specify it directly by using
"USERNAME:PASSWORD", though be aware it will be saved to your shell history.
Python 3 + click
Interact with the database on the command-line in your shell to:
Mint identifiers and barcodes
Run ETL routines, e.g. enrollments, to process received data into the warehouse
Parse, diff, and upload sample manifests.
Preprocess clinical data and upload it into receiving.
Send Slack notifications from the Reportable Conditions Notifications Slack App
bin/id3c command is the entry point. It must be run within the project
environment, for example by using
pipenv run bin/id3c.
LOG_LEVEL environment variable controls the level of terminal output.
Levels are strings:
Python dependencies are managed using Pipenv.
Install all the (locked, known-good) dependencies by running:
Add new dependencies to
pipenv install <name>
and then commit the changes to
For example, if you want to list the identifier sets available in the Seattle Flu Study testing database, you could create the following files:
[seattleflu-testing] host=testing.db.seattleflu.org user=your_username dbname=testing
Make sure the ~/.pgpass file is only readable by you since it contains your password:
chmod u=rw,og= ~/.pgpass
and then run:
PGSERVICE=seattleflu-testing pipenv run bin/id3c identifier set ls
These files will also allow you to connect using
Run type-checking tests with: