GraphQL service for exposing OMOP CDM records.
.. code-block:: shell
python3 -m venv venv
.. code-block:: shell
source venv/bin/activate
.. code-block:: shell
pip install omop-cdm-graphql
.. code-block:: yaml
---
port: 8081
url: http://localhost
database_file: /tmp/omop-cdm-graphql/omop-cdm-v1.db
.. code-block:: bash
cp venv/lib/python3.10/site-packages/omop_cdm_graphql/conf/config.yaml .
Run the loader to load mock records.
.. code-block:: bash
load-omop-cdm-db-records
.. code-block:: bash
run-omop-cdm-graphql-app
http://localhost:8080/graphql <http://localhost:8080/graphql>_
.. code-block:: graphql
query {
person(personId: 1) {
personId
genderConceptId
birthDatetime
observations {
observationId
observationConceptId
observationDate
}
conditions {
conditionOccurrenceId
conditionConceptId
conditionStartDate
}
}
}
Result:
.. code-block:: json
{
"data": {
"person": {
"personId": 1,
"genderConceptId": 8507,
"birthDatetime": "1990-01-01T00:00:00",
"observations": [
{
"observationId": 1,
"observationConceptId": 123,
"observationDate": "2023-01-01T00:00:00"
},
{
"observationId": 7,
"observationConceptId": 129,
"observationDate": "2023-07-10T00:00:00"
}
],
"conditions": [
{
"conditionOccurrenceId": 1,
"conditionConceptId": 456,
"conditionStartDate": "2023-02-01T00:00:00"
},
{
"conditionOccurrenceId": 7,
"conditionConceptId": 462,
"conditionStartDate": "2023-08-20T00:00:00"
}
]
}
}
}
.. code-block:: graphql
query {
allPersons {
personId
genderConceptId
birthDatetime
}
}
Result:
.. code-block:: json
{
"data": {
"allPersons": [
{
"personId": 1,
"genderConceptId": 8507,
"birthDatetime": "1990-01-01T00:00:00"
},
{
"personId": 2,
"genderConceptId": 8532,
"birthDatetime": "1985-05-15T00:00:00"
},
{
"personId": 3,
"genderConceptId": 8507,
"birthDatetime": "1978-03-22T00:00:00"
},
{
"personId": 4,
"genderConceptId": 8532,
"birthDatetime": "1995-07-10T00:00:00"
},
{
"personId": 5,
"genderConceptId": 8507,
"birthDatetime": "1982-11-30T00:00:00"
},
{
"personId": 6,
"genderConceptId": 8532,
"birthDatetime": "2000-04-15T00:00:00"
}
]
}
}
Purpose: Shows how GraphQL lets clients filter data without needing a separate endpoint.
.. code-block:: graphql
query {
personsByGender(genderConceptId: 8532) {
personId
birthDatetime
observations {
observationId
observationDate
}
}
}
Returns only female persons (gender_concept_id = 8532) with their observations. Client specifies exactly what fields they want (e.g., skipping conditions or genderConceptId), avoiding over-fetching.
Result:
.. code-block:: json
{
"data": {
"personsByGender": [
{
"personId": 2,
"birthDatetime": "1985-05-15T00:00:00",
"observations": [
{
"observationId": 2,
"observationDate": "2023-03-15T00:00:00"
}
]
},
{
"personId": 4,
"birthDatetime": "1995-07-10T00:00:00",
"observations": [
{
"observationId": 4,
"observationDate": "2023-05-20T00:00:00"
}
]
},
{
"personId": 6,
"birthDatetime": "2000-04-15T00:00:00",
"observations": [
{
"observationId": 6,
"observationDate": "2023-06-01T00:00:00"
}
]
}
]
}
}
Purpose: Demonstrates time-based filtering and standalone access to related entities.
.. code-block:: graphql
query {
recentObservations(afterDate: "2023-03-01") {
observationId
observationConceptId
observationDate
}
}
Returns observations after March 1, 2023 (e.g., observation IDs 2, 4, 6, 7). No need to fetch persons first; GraphQL lets you query related data directly, reducing round trips.
Result:
.. code-block:: json
{
"data": {
"recentObservations": [
{
"observationId": 2,
"observationConceptId": 124,
"observationDate": "2023-03-15T00:00:00"
},
{
"observationId": 4,
"observationConceptId": 126,
"observationDate": "2023-05-20T00:00:00"
},
{
"observationId": 6,
"observationConceptId": 128,
"observationDate": "2023-06-01T00:00:00"
},
{
"observationId": 7,
"observationConceptId": 129,
"observationDate": "2023-07-10T00:00:00"
}
]
}
}
Purpose: Highlights nested relationship traversal and conditional filtering.
.. code-block:: graphql
query {
personsWithCondition(conditionConceptId: 456) {
personId
genderConceptId
conditions {
conditionOccurrenceId
conditionStartDate
}
observations {
observationId
}
}
}
Returns persons with condition_concept_id 456 (just person 1) and their conditions and observations. Combines filtering with flexible field selection across relationships in one request—impossible in REST without multiple calls or a custom endpoint.
Purpose: Shows how clients can pick and choose fields across relationships.
.. code-block:: graphql
query {
allPersons {
personId
birthDatetime
observations {
observationDate
}
conditions {
conditionConceptId
}
}
}
Returns all 6 persons with only their birth dates, observation dates, and condition concept IDs. Avoids over-fetching unused fields (e.g., gender_concept_id, observation_id) and simplifies frontend logic—no need to parse bloated responses.
Results:
.. code-block:: json
{
"data": {
"allPersons": [
{
"personId": 1,
"birthDatetime": "1990-01-01T00:00:00",
"observations": [
{
"observationDate": "2023-01-01T00:00:00"
},
{
"observationDate": "2023-07-10T00:00:00"
}
],
"conditions": [
{
"conditionConceptId": 456
},
{
"conditionConceptId": 462
}
]
},
{
"personId": 2,
"birthDatetime": "1985-05-15T00:00:00",
"observations": [
{
"observationDate": "2023-03-15T00:00:00"
}
],
"conditions": [
{
"conditionConceptId": 457
}
]
},
{
"personId": 3,
"birthDatetime": "1978-03-22T00:00:00",
"observations": [
{
"observationDate": "2022-12-10T00:00:00"
}
],
"conditions": [
{
"conditionConceptId": 458
}
]
},
{
"personId": 4,
"birthDatetime": "1995-07-10T00:00:00",
"observations": [
{
"observationDate": "2023-05-20T00:00:00"
}
],
"conditions": [
{
"conditionConceptId": 459
}
]
},
{
"personId": 5,
"birthDatetime": "1982-11-30T00:00:00",
"observations": [
{
"observationDate": "2023-01-25T00:00:00"
}
],
"conditions": [
{
"conditionConceptId": 460
}
]
},
{
"personId": 6,
"birthDatetime": "2000-04-15T00:00:00",
"observations": [
{
"observationDate": "2023-06-01T00:00:00"
}
],
"conditions": [
{
"conditionConceptId": 461
}
]
}
]
}
}
Purpose: Demonstrates deep nesting and customization.
.. code-block:: graphql
query {
person(personId: 1) {
personId
birthDatetime
observations {
observationId
observationConceptId
observationDate
}
conditions {
conditionOccurrenceId
conditionConceptId
conditionStartDate
}
}
}
Returns person 1 with all observation and condition details. Replaces multiple REST calls (e.g., /persons/1, /persons/1/observations, /persons/1/conditions) with one precise query.
Result:
.. code-block:: json
{
"data": {
"person": {
"personId": 1,
"birthDatetime": "1990-01-01T00:00:00",
"observations": [
{
"observationId": 1,
"observationConceptId": 123,
"observationDate": "2023-01-01T00:00:00"
},
{
"observationId": 7,
"observationConceptId": 129,
"observationDate": "2023-07-10T00:00:00"
}
],
"conditions": [
{
"conditionOccurrenceId": 1,
"conditionConceptId": 456,
"conditionStartDate": "2023-02-01T00:00:00"
},
{
"conditionOccurrenceId": 7,
"conditionConceptId": 462,
"conditionStartDate": "2023-08-20T00:00:00"
}
]
}
}
}
.. code-block:: shell
http POST http://localhost:8081/graphql query=@examples/query1.graphql
Result:
.. code-block:: shell
http POST http://localhost:8081/graphql query=@examples/query2.graphql
.. code-block:: shell
http POST http://localhost:8081/graphql query=@examples/query3.graphql
.. code-block:: shell
http POST http://localhost:8081/graphql query=@examples/query4.graphql
.. code-block:: shell
http POST http://localhost:8081/graphql query=@examples/query5.graphql
.. code-block:: shell
http POST http://localhost:8081/graphql query=@examples/query6.graphql
.. code-block:: shell
http POST http://localhost:8081/graphql query=@examples/query7.graphql
GitHub <https://github.com/jai-python3/omop-cdm-graphql>_PYPI <https://pypi.org/project/omop-cdm-graphql/>_FAQs
GraphQL service for exposing OMOP CDM records.
We found that omop-cdm-graphql demonstrated a healthy version release cadence and project activity because the last version was released less than a year ago. It has 1 open source maintainer collaborating on the project.
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