dbt Models for CHT Applications

Overview

CHT Sync copies data from CouchDB to a relational database. It initially stores the document data from CouchDB in a jsonb column in a single PostgreSQL table. This is not possible to query for analytics, so it uses dbt to convert the document data to a relational database format.

The cht-pipeline repository defines a dbt project, which contains model files for the data schema described in the database schema conventions. Forms may be specific to each CHT application; additional models will need to be developed to analyze data from responses to these custom forms. One additional model will be needed for each form, and for any aggregations, dashboards, or reusable views that use those form responses as input. If using the configurable contact hierarchy, it may also be useful to add models for other contact types.

Prerequisites

• An existing install of CHT Sync via Docker or Kubernetes
• cht-pipeline GitHub repository (can be cloned via git clone https://github.com/medic/cht-pipeline).

Setup

To create application specific models, create a new dbt project. Edit the packages.yml in your new dbt project to add cht-pipeline as a dependency. Add your dbt new project in a GitHub repository (it may be public or private) so you can track changes in your models.

packages:
  - git: "https://github.com/medic/cht-pipeline"
    revision: "v1.2.0"

To avoid breaking changes in downstream models, include revision in the dependency, which should be a version tag for cht-pipeline.

In the CHT Sync config, set the URL of dbt GitHub repository to the CHT_PIPELINE_BRANCH_URL environment variable, either in .env if using Docker compose, or in values.yaml if using Kubernetes.

Deploying models

CHT Sync automatically checks for updates to the dbt project at CHT_PIPELINE_BRANCH_URL. Use the main branch for changes that should be released; they will be applied as soon as they are pushed to the repository. For models that are in development, any other branch can be used.

Rebuilding tables can take some time (a rough estimate is several hours for tables between 1M and 10M rows, up to 24H for tables between 10M and 100M rows), so plan for affected dashboards to be out of date when releasing new changes to models; only changed tables and their dependencies will be rebuilt.

New releases of the base models are rare, but schema changes to the CHT or new features may require changes. Generally, these changes will be backwards compatible so that a new release of the CHT, or to the base models, does not break application specific models.

When it is necessary to update the base models, update the version tag in the dependency that refers to cht-pipeline, make any changes to application specific models that are necessary, rerun any unit tests, and push to the main branch to release.

Testing models and dashboards

It is highly encouraged to write dbt tests for application-specific models to ensure that they are accurate and to avoid releasing broken models. Examples can be found in the cht-pipeline repository.

Base Models

All tables contain a uuid which is the primary key for the table; it is also the _id from the source CouchDB document.

couchdb

All documents are stored in the couchdb table; downstream models move fields from the document into columns and index them. Deleted documents will still be present in this table with the _deleted flag set to true. This table can be used to get any field from a CouchDB document; however, it is recommended that the columns from downstream models be used instead for performance reasons. The name is configurable using the POSTGRES_TABLE environment variable.

document_metadata

This table contains the metadata about all documents and is the root for all other models. It contains a type column describing the type of the document. Deleted documents do not appear as rows in this table and deletes from this table cascade to all other models. The document itself is not copied to this table; to use it requires joining to the couchdb table.

data_record

All form responses are stored in the data_record table; see more details in the database schema conventions. This table contains columns for the contact who made the report, the parent of that contact, and the date it was reported.

contact

See a description of contact documents in CouchDB in the database schema conventions. Every person and place is stored in the contact table. Persons and places are stored in their own tables, but because contact types are configurable, other contact types do not have their own tables by default. The contact hierarchy defines “is a” relationships between contact types; e.g., a patient is a person is a contact. This is modeled as one table per type, where the uuid is both the primary key for the child table and a foreign key to the parent table.

contact_type

This table stores metadata about contact types. It uses the configurable contact types from app settings, combined with all distinct values of contact_type from the contact table. The person column defines which contact types are persons and which are places. It uses the person field from the settings, or if the contact type is not in settings, it is assumed to be a place unless id is person

person

This table stores all contacts where the contact_type is person, and has additional fields that are relevant only for person contacts.

place

This table stores all contacts where the contact_type is place, and has additional columns that are relevant only for place contacts. The contact_id column contains a foreign key to a person contact who is the primary contact for the place.

Building App models

An overview of building dbt models can be found in the dbt documentation. The additional models that need to be developed for a CHT application are:

• One model for each form
• Models for contacts that are defined by the configurable hierarchy
• Models to contain aggregates that may be useful for dashboards or analysis.

Form models

For each form in the CHT application that is relevant for analysis, create a model using the cht_form_model macro. This macro creates a model that selects from data_record where form = 'theformyouwant', joins to the couchdb table to get the jsonb fields, moves the fields into columns, applies any convenient transformations, and, if necessary, adds indexes to them.

To use this macro, select the fields to move into columns and any indexes as in the example below.

cht_form_model

This example extracts Last Menstrual Period, Expected Delivery Date and ANC visit number from a typical pregnancy registration form.

-- add any indexes specific to this form
{%- set form_indexes = [
  {'columns': ['edd']},
  {'columns': ['danger_signs']}]
  {'columns': ['risk_factors']}]
-%}
-- add columns specific to this form
{% set form_columns %}
  NULLIF(couchdb.doc->'fields'->>'lmp_date','')::date as lmp, -- CAST lmp string to date or NULL if empty
  NULLIF(couchdb.doc->'fields' ->> 'edd','')::date as edd, -- CAST edd string to date or NULL if empty

  couchdb.doc->'fields' ->> 'lmp_method' as lmp_method,
  couchdb.doc->'fields' ->> 'danger_signs' AS danger_signs,
  couchdb.doc->'fields' ->> 'risk_factors' AS risk_factors,

  -- extract the ANC visit number
  CASE
    WHEN couchdb.doc->'fields' ->>'anc_visit_identifier' <> ''
      THEN (couchdb.doc->'fields' ->>'anc_visit_identifier')::int
    WHEN couchdb.doc->'fields' #>>'{group_repeat,anc_visit_repeat,anc_visit_identifier}' <> ''
      THEN RIGHT(couchdb.doc->'fields' #>>'{group_repeat,anc_visit_repeat,anc_visit_identifier}'::text[], 1)::int
    ELSE 0 -- if not included default to 0
  END AS anc_visit
{% endset %}

-- call the macro with the form name, the columns and indexes to create the actual model
{{ cht_form_model('pregnancy', form_columns, form_indexes) }}

This creates the following model:

  {{
    config(
      materialized='incremental',
      unique_key='uuid',
      on_schema_change='append_new_columns',
      indexes=[
        {'columns': ['uuid'], 'type': 'hash'}, 
        {'columns': ['saved_timestamp']},
        {'columns': ['reported_by']},
        {'columns': ['reported_by_parent']},
        {'columns': ['reported']}
      ]
    )
  }}

  SELECT
  data_record.uuid as uuid,
  data_record.saved_timestamp,
  data_record.contact_uuid as reported_by,
  data_record.parent_uuid as reported_by_parent,
  data_record.reported

  NULLIF(couchdb.doc->'fields'->>'lmp_date','')::date as lmp, -- CAST lmp string to date or NULL if empty
  NULLIF(couchdb.doc->'fields' ->> 'edd','')::date as edd, -- CAST edd string to date or NULL if empty

  couchdb.doc->'fields' ->> 'lmp_method' as lmp_method,
  couchdb.doc->'fields' ->> 'danger_signs' AS danger_signs,
  couchdb.doc->'fields' ->> 'risk_factors' AS risk_factors,

  -- extract the ANC visit number
  CASE
    WHEN couchdb.doc->'fields' ->>'anc_visit_identifier' <> ''
      THEN (couchdb.doc->'fields' ->>'anc_visit_identifier')::int
    WHEN couchdb.doc->'fields' #>>'{group_repeat,anc_visit_repeat,anc_visit_identifier}' <> ''
      THEN RIGHT(couchdb.doc->'fields' #>>'{group_repeat,anc_visit_repeat,anc_visit_identifier}'::text[], 1)::int
    ELSE 0 -- if not included default to 0
  END AS anc_visit

  FROM {{ ref('data_record') }} data_record
  INNER JOIN {{ env_var('POSTGRES_SCHEMA') }}.{{ env_var('POSTGRES_TABLE') }} couchdb ON couchdb._id = data_record.uuid
  WHERE
    data_record.form = 'pregnancy'
  {% if is_incremental() %}
    AND data_record.saved_timestamp >= {{ max_existing_timestamp('saved_timestamp') }}
  {% endif %}

Contacts hierarchy

The base models have tables for person and place, but it’s often useful for other contact types to have their own specialized tables, which can have additional columns specific to that type, and can have foreign keys to parents in the hierarchy. For example, households, patients, chws and supervisors are all common objects in data analysis, but do not have any definition common to all applications and so need to be built in application-specific models.

To do this, use the cht_contact_model macro, specifying the contact_type id, any custom fields and indexes, and a list of parent models.

cht_contact_model

This example shows how this macro can be used to build a household model which has some custom columns, a foreign key to its parent, and a community health area.

{% set custom_fields %}
  contact.name AS household_name,
  contact.contact_id AS household_contact_id,
  community_health_unit.uuid as chu_area_id,
  NULLIF(couchdb.doc ->> 'uses_treated_water', '')::boolean AS uses_treated_water,
  NULLIF(couchdb.doc ->> 'has_functional_latrine', '')::boolean AS has_functional_latrine
{% endset %}
{{ cht_contact_model('household', custom_fields, [{'id': 'community_health_unit', 'table': 'community_health_units'}]) }}

Aggregations

After defining the form and contact models, they can be joined together by subject (patient_id or place_id), reported_by, or any of the other contact fields, to build aggregates of form submissions grouped by report date, area, or reporter.

It may be useful to save some common queries as views, so that they can be reused in dashboards or downstream aggregations. For example, with the pregnancy form model above, if there was also a postnatal care form, they could be joined to view outcomes together with registrations.

{{
    config(materialized = 'materialized_view')
}}

SELECT
  pnc.uuid AS pnc_uuid,
  pregnancy.uuid AS pregnancy_uuid,

  pnc.patient_id AS patient_id,

  pnc_contact.uuid AS pnc_reported_by,
  pregnancy_contact.uuid AS pregnancy_reported_by,
  pnc.reported AS reported,
  pregnancy.reported AS pregnancy_reported,

  pregnancy.edd as edd,
  pnc.delivery_date AS delivery_date,
  pnc.pregnancy_outcome,
FROM
  {{ ref('postnatal_care') }} AS pnc
LEFT JOIN {{ ref('pregnancy') }} ON
  (pnc.reported > pregnancy.reported AND
   pnc.reported < (pregnancy.reported + '1 year'::INTERVAL) AND
   pnc.patient_id = pregnancy.patient_id)
WHERE
  (pnc.pregnancy_outcome IN (VALUES ('healthy'), ('still_birth')))
  AND pnc.patient_id IS NOT NULL AND pnc.patient_id <> ''

Views vs. Incremental Tables

There are two options for building models using dbt: views and incremental tables; see a full description in the dbt documentation. In short, views are normal SQL views, and incremental tables are actual tables, which are periodically updated as new data is created, updated or deleted.

For CHT dbt models, it is generally preferred to start with materialized views. Materialized views are refreshed on every dbt run, columns can still be indexed, and they don’t require much extra configuration. Non-materialized views or non-incremental tables are possible but not recommended because they are unavailable during dbt run and anything that depends on them (including dashboards) will also be unavailable. Some base models use incremental tables to ensure good performance for dbt run, because materialized views can take a long time to refresh.

To convert a view to an incremental table, change the materialization to incremental and add a condition to the WHERE clause:

{{
    config(materialized = 'incremental')
    unique_key='uuid',
    indexes=[
      {'columns': ['"uuid"'], 'type': 'hash'},
      {'columns': ['"saved_timestamp"'], 'type': 'btree'}
    ]
}}


SELECT
  uuid,
  "saved_timestamp",

  ...

FROM
  {{ ref("data_record") }} data_record
WHERE
  form = 'pregnancy'

{% if is_incremental() %}
  AND "data_record.saved_timestamp" >= {{ max_existing_timestamp('"saved_timestamp"') }}
{% endif %}

To be performant, the table from this model is reading form needs to have the saved_timestamp column indexed.

Database disk space requirements

The disk space required for the database depends on a few things including the size the of CouchDB databases being replicated, and the models defined. The database will grow over time as more data is added to CouchDB. The database should be monitored to ensure that it has enough space to accommodate the data. To get an idea of the size requirements of the database, you can replicate 10% of the data from CouchDB to Postgres and then run the following command to see disk usage:

SELECT pg_size_pretty(pg_database_size('your_database_name'));

If Postgres is running in a Kubernetes cluster, you can use the following command to get the disk usage:

kubectl exec -it postgres-pod-name -- psql -U postgres -c "SELECT pg_size_pretty(pg_database_size('your_database_name'));"

To get the percentage of documents that have synced you can run the following query in your Postgres database:

SELECT (COUNT(*) * 100 / (COUNT(*) + (SELECT SUM(pending) FROM v1.couchdb_progress))) AS sync_percentage FROM v1.couchdb;

This query selects the total number of documents that have been synced to the v1.couchdb table and divides it by the total number of documents that have been synced and the number of documents that are pending to be synced. This will give you the percentage of documents that have been synced. Please note that the schema and table name could differ according to the environment variables you set so update them accordingly. Run this query periodically to monitor the progress of the sync and stop the sync process once you get to the desired percentage. It’s okay if it is not exactly 10% as long as it is close enough to give you an idea of the disk space required.

You can then multiply this figure by 10 to get an estimate of the disk space required for the full dataset and then add some extra space for indexes and other overhead as well as future growth.

For example if the size of the database is 1GB, you can expect the full dataset to be around 10GB. If the CouchDB docs grow by 20% every year then you can compound this growth over 5 years to get an estimate of the disk space required: 10GB * 1.2^5 = 18.5GB. You can add an extra 20% for indexes and overhead to get an estimate of 22.2GB.

Please note that this is just an estimate and the actual disk space required may vary so actively monitoring the disk space usage and making necessary adjustments is recommended.

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