streaming

OpenMRS Streaming Pipeline

Note: This pipeline is in maintenance mode and not actively developed. There are known issues with duplicated resources in Parquet files.

The streaming directory contains code to continuously listen for changes to an underlying OpenMRS database using Debezium.

The Debezium-based streaming mode provides real-time downstream consumption of incremental updates, even for operations that were performed outside the OpenMRS API, e.g., data cleaning, module operations, and data syncing/migration. It captures incremental updates from the MySQL database binlog then streams both FHIR and non-FHIR data for downstream consumption. It is not based on Hibernate Interceptor or Event Module; therefore, all events are captured from day 0 and can be used independently without the need for a batch pipeline. It also tolerates failures like application restarts or crashes, as the pipeline will resume from the last processed offset.

Streaming mode works only with OpenMRS; support for other data sources is not planned.

Prerequisites

• An OpenMRS instance with the latest version of the FHIR2 Module installed.
  • There is an OpenMRS Reference Application image with these prerequisites and demo data you can use to try things out.
• A target output for the data. Supported options are Apache Parquet files or a FHIR server such as HAPI FHIR or Google Cloud Platform FHIR stores.
  • You can use our HAPI FHIR server image for testing FHIR API targets.
  • Learn how to create a compatible GCP FHIR store, if you want to use this option.

Getting Started

1. Clone the FHIR Data Pipes project to your machine.

2. Set the utils directory to world-readable: chmod -R 755 ./utils.

3. Edit ../utils/dbz_event_to_fhir_config.json. Find the debeziumConfigurations section at the top of the file and edit the values to match your environment. See the documentation on Debezium MySQL Connector properties for more information.

4. Build binaries from the repo root with mvn clean package.

5. Run the pipeline to a FHIR server and Parquet files:

   $ java -jar ./pipelines/streaming/target/streaming-bundled.jar \
     com.google.fhir.analytics.Runner \
     --fhirServerUrl=http://localhost:8099/openmrs/ws/fhir2/R4 \
       --fhirServerUserName=admin --fhirServerPassword=Admin123 \
       --fhirSinkPath=http://localhost:8098/fhir \
       --sinkUserName=hapi --sinkPassword=hapi \
       --outputParquetPath=/tmp/TEST/ \
       --fhirDatabaseConfigPath=./utils/dbz_event_to_fhir_config.json

   Or to a GCP FHIR store:

   $ java -jar ./pipelines/streaming/target/streaming-bundled.jar \
     com.google.fhir.analytics.Runner \
     --fhirServerUrl=http://localhost:8099/openmrs/ws/fhir2/R4 \
       --fhirServerUserName=admin --fhirServerPassword=Admin123 \
       --fhirSinkPath=projects/PROJECT/locations/LOCATION/datasets/DATASET/fhirStores/FHIRSTORENAME \
       --fhirDatabaseConfigPath=../utils/dbz_event_to_fhir_config.json

Parameters

Basic parameters

• fhirServerUrl - The URL of the source FHIR server instance.
• fhirServerUserName - The HTTP Basic Auth username to access the fhir server APIs.
• fhirServerPassword - The HTTP Basic Auth password to access the fhir server APIs.

Debezium parameters

• fhirDatabaseConfigPath - The path to the configuration file containing MySQL parameters and FHIR mappings. This generally should not be changed. Instead, edit ../utils/dbz_event_to_fhir_config.json to match your configuration. Default: ../utils/dbz_event_to_fhir_config.json

Parquet output parameters

Parquet files are output when outputParquetPath is set.

• outputParquetPath - The file path to write Parquet files to, e.g., ./tmp/parquet/. Default: empty string, which does not output Parquet files.
• secondsToFlushParquetFiles - The number of seconds to wait before flushing all Parquet writers with non-empty content to files. Use 0 to disable. Default: 3600.
• rowGroupSizeForParquetFiles - The approximate size in bytes of the row-groups in Parquet files. When this size is reached, the content is flushed to disk. This is not used if there are less than 100 records. Use 0 to use the default Parquet row-group size. Default: 0.

FHIR output parameters

Resources will be copied to the FHIR server specified in fhirSinkPath if that field is set.

• fhirSinkPath - A base URL to a target FHIR server, or the relative path of a GCP FHIR store, e.g. http://localhost:8091/fhir for a FHIR server or projects/PROJECT/locations/LOCATION/datasets/DATASET/fhirStores/FHIR-STORE-NAME for a GCP FHIR store. If using a GCP FHIR store, see here for setup information. default: none, resources are not copied
• sinkUserName - The HTTP Basic Auth username to access the FHIR sink. Not used for GCP FHIR stores.
• sinkPassword - The HTTP Basic Auth password to access the FHIR sink. Not used for GCP FHIR stores.

Common questions

• Will this pipeline include historical data recorded before the mysql binlog was enabled? Yes. By default, the pipeline takes a snapshot of the entire database and will include all historical data.

• How do I stop Debezium from taking a snapshot of the entire database? Set snapshotMode in the config file to schema_only i.e., "snapshotMode" : "initial". Other options include: when_needed, schema_only, initial (default), never, e.t.c. See the debezium documentation for more details.