Running a reindex job
There are scenarios where you may have search parameters in the FHIR service in Azure Health Data Services that haven't yet been indexed. This scenario is relevant when you define your own custom search parameters. Until the search parameter is indexed, it can't be used in live production. This article covers how to run a reindex job to index any custom search parameters that haven't yet been indexed in your FHIR service database.
Warning
It's important that you read this entire article before getting started. A reindex job can be very performance intensive. This article discusses options for how to throttle and control a reindex job.
How to run a reindex job
Reindex job can be executed against entire FHIR service database and against specific custom search parameter.
Run reindex job on entire FHIR service database
To run reindex job, use the following POST call with the JSON formatted Parameters resource in the request body:
POST {{FHIR_URL}}/$reindex
content-type: application/fhir+json
{
"resourceType": "Parameters",
"parameter": []
}
Leave the "parameter": [] field blank (as shown) if you don't need to tweak the resources allocated to the reindex job.
If the request is successful, you receive a 201 Created status code in addition to a Parameters resource in the response.
HTTP/1.1 201 Created
Content-Location: https://{{FHIR URL}}/_operations/reindex/560c7c61-2c70-4c54-b86d-c53a9d29495e
{
"resourceType": "Parameters",
"id": "560c7c61-2c70-4c54-b86d-c53a9d29495e",
"meta": {
"versionId": "138035"
},
"parameter": [
{
"name": "id",
"valueString": "560c7c61-2c70-4c54-b86d-c53a9d29495e"
},
{
"name": "lastModified",
"valueDateTime": "2023-06-08T04:52:44.0974408+00:00"
},
{
"name": "queuedTime",
"valueDateTime": "2023-06-08T04:52:44.0974406+00:00"
},
{
"name": "totalResourcesToReindex",
"valueDecimal": 0.0
},
{
"name": "resourcesSuccessfullyReindexed",
"valueDecimal": 0.0
},
{
"name": "progress",
"valueDecimal": 0.0
},
{
"name": "status",
"valueString": "Queued"
},
{
"name": "maximumConcurrency",
"valueDecimal": 3.0
},
{
"name": "queryDelayIntervalInMilliseconds",
"valueDecimal": 500.0
},
{
"name": "maximumNumberOfResourcesPerQuery",
"valueDecimal": 100.0
}
]
}
Run reindex job against specific custom search parameter
To run reindex job against specific custom search parameter, use the following POST call with the JSON formatted Parameters resource in the request body:
POST {{FHIR_URL}}/$reindex
content-type: application/fhir+json
{
"resourceType": "Parameters",
"parameter": [
{
"name": "targetSearchParameterTypes",
"valueString": "{url of custom search parameter. In case of multiple custom search parameters, url list can be comma separated.}"
}
]
}
Note
To check the status of a reindex job or to cancel the job, you'll need the reindex ID. This is the "id" carried in the "parameter" value returned in the response. In the example above, the ID for the reindex job would be 560c7c61-2c70-4c54-b86d-c53a9d29495e.
How to check the status of a reindex job
Once you’ve started a reindex job, you can check the status of the job using the following call:
GET {{FHIR_URL}}/_operations/reindex/{{reindexJobId}}
An example response:
{
"resourceType": "Parameters",
"id": "560c7c61-2c70-4c54-b86d-c53a9d29495e",
"meta": {
"versionId": "138087"
},
"parameter": [
{
"name": "id",
"valueString": "560c7c61-2c70-4c54-b86d-c53a9d29495e"
},
{
"name": "startTime",
"valueDateTime": "2023-06-08T04:54:53.2943069+00:00"
},
{
"name": "endTime",
"valueDateTime": "2023-06-08T04:54:54.4052272+00:00"
},
{
"name": "lastModified",
"valueDateTime": "2023-06-08T04:54:54.4053002+00:00"
},
{
"name": "queuedTime",
"valueDateTime": "2023-06-08T04:52:44.0974406+00:00"
},
{
"name": "totalResourcesToReindex",
"valueDecimal": 2.0
},
{
"name": "resourcesSuccessfullyReindexed",
"valueDecimal": 2.0
},
{
"name": "progress",
"valueDecimal": 100.0
},
{
"name": "status",
"valueString": "Completed"
},
{
"name": "maximumConcurrency",
"valueDecimal": 3.0
},
{
"name": "resources",
"valueString": "{{LIST_OF_IMPACTED_RESOURCES}}"
},
{
"name": "resourceReindexProgressByResource (CountReindexed of Count)",
"valueString": "{{RESOURCE_TYPE:REINDEXED_COUNT OF TOTAL_COUNT}}"
},
{
"name": "searchParams",
"valueString": "{{LIST_OF_SEARCHPARAM_URLS}}"
},
{
"name": "queryDelayIntervalInMilliseconds",
"valueDecimal": 500.0
},
{
"name": "maximumNumberOfResourcesPerQuery",
"valueDecimal": 100.0
}
]
}
The following information is shown in the above response:
totalResourcesToReindex: Includes the total number of resources that are being reindexed in this job.resourcesSuccessfullyReindexed: The total number of resources that have already been reindexed in this job.progress: Reindex job percent complete. EqualsresourcesSuccessfullyReindexed/totalResourcesToReindexx 100.status: States if the reindex job is queued, running, complete, failed, or canceled.resources: Lists all the resource types impacted by the reindex job.'resourceReindexProgressByResource (CountReindexed of Count)': Provides reindexed count of the total count, per resource type. In cases where reindexing for a specific resource type is queued, only Count is provided.
'searchParams': Lists url of the search parameters impacted by the reindex job.
Delete a reindex job
If you need to cancel a reindex job, use a DELETE call and specify the reindex job ID:
DELETE {{FHIR URL}}/_operations/reindex/{{reindexJobId}}
Performance considerations
A reindex job can be quite performance intensive. The FHIR service offers some throttling controls to help you manage how a reindex job run on your database.
Note
It is not uncommon on large datasets for a reindex job to run for days.
Below is a table outlining the available parameters, defaults, and recommended ranges for controlling reindex job compute resources. You can use these parameters to either speed up the process (use more compute) or slow down the process (use less compute).
| Parameter | Description | Default | Available Range |
|---|---|---|---|
QueryDelayIntervalInMilliseconds |
The delay between each batch of resources being kicked off during the reindex job. A smaller number speeds up the job while a larger number slows it down. | 500 MS (.5 seconds) | 50 to 500000 |
MaximumResourcesPerQuery |
The maximum number of resources included in the batch of resources to be reindexed. | 100 | 1-5000 |
MaximumConcurrency |
The number of batches done at a time. | 1 | 1-10 |
If you want to use any of the parameters above, you can pass them into the Parameters resource when you send the initial POST request to start a reindex job.
POST {{FHIR_URL}}/$reindex
content-type: application/fhir+json
{
"resourceType": "Parameters",
"parameter": [
{
"name": "maximumConcurrency",
"valueInteger": "3"
},
{
"name": "queryDelayIntervalInMilliseconds",
"valueInteger": "1000"
},
{
"name": "maximumNumberOfResourcesPerQuery",
"valueInteger": "1"
}
]
}
Next steps
In this article, you've learned how to perform a reindex job in your FHIR service. To learn how to define custom search parameters, see
FHIR® is a registered trademark of HL7 and is used with the permission of HL7.
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