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Implement FHIR Bulk Export client.#1781

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piotrszul wants to merge 88 commits intomainaehrc/pathling:mainfrom issue/1776aehrc/pathling:issue/1776Copy head branch name to clipboard

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Commits on Jan 29, 2024

• Fixing the R build (inclue Roxygen always as it is need to generate NAMESPACE file)

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• Initial version of the Bulk Export Client module.

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Commits on Feb 6, 2024

• Initial version of the Bulk Export Client

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• Adding support for '_type' parameter.

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• Adding basic python interface for bulk export.

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• Adding support for '_since' parameter.

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Commits on Feb 7, 2024

• Adding support for '_since' parameter to Python API.

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• Fixing support for '_since' parameter to Python API.

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• Moving the example of running the client to tests and fixing logging setup.

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• Added identification and handling of transient error while pooling for status.

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• Added support for http-date in retry-after header.

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Commits on Feb 8, 2024

• Added WireMock test cases for some error scenarios.

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Commits on Feb 9, 2024

• Added wiremock test scenario for persistent transient errors.

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• Migrating to Apache Http Client

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Commits on Feb 12, 2024

• Adding java and python code for setting the log level for Pathling (au.csiro.pathling logger)

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Commits on Feb 13, 2024

• Refactoring the FileSystem access abstraction.

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• Refactoring of the file download process.

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Commits on Feb 14, 2024

• Defining required FHIR resources and types

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• Refactoring: moving web service related classes to 'ws' package.

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• Refactoring: reimplementing web service using ResponseHandler.

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Commits on Feb 15, 2024

• Improving reporting of HTTP Errors.

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• Refactoring: exposing bulk export configuration (AsyncRequest configuration).

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• Adding support got System/Group and Patien level export in Java.

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• Adding wirmock test for Group level export.

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• Adding wiremock tests for Patient level export.

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Commits on Feb 16, 2024

• Refactoring: Improved creation and disposal of Closeable resources.

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• Refactoring: Extracting Async Config from BulkExport;

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• Refactoring: Adding native Gson deserialization for instant that can also support a timestamp (which is what we are getting from the test server).

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• Refactoring: Finalising the interface for the client.

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Commits on Feb 19, 2024

• Synchronizing Python API for Fhir Bulk Export with Java interface.

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• Refactoring of Bulk Export request Operations (replace member variables with function calls).

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• Fixing unit tests to pass.

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• Fixing javadocs issue with BulkExportClientBuilder.

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Commits on Feb 20, 2024

• Finalising and unifying processing of timeouts.

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• Refactoring: Unifying exception handling.

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• Refactoring: Moving HttpClientConfiguration to utils and adding a method to build a http client based on the configuration.

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• Refactoring: Removing bulkexport client dependencies on Spark, HDFS and HAPI.

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• Finishing python API for bulk export client.

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Commits on Feb 21, 2024

• Refactoring of the python API and adding python test cases for correct parameter passing to java.

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Commits on Feb 22, 2024

• Adding flask based mock http server to python tests and an integration test for python bulk client export API.

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• Improving docstrings and parameters names for BulkExport python API.

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• Moving timedate/java and FHIR conversion functions to 'jvm' and 'fhir' packages and adding unit tests.

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Commits on Feb 23, 2024

• Changing the pattern for filenames produced by bulkexport to match the NDJSON DataSource pattern.

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• Fixing javadocs generation for bulkclient module.

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Commits on Feb 27, 2024

• Adding implementation of symetric client authentication.

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• Fixing parsing of FHIR instants to allow for offset time zone specification.

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Commits on Feb 28, 2024

• Adding support for symmetric authentication to python API.

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Commits on Feb 29, 2024

• Updating notes with the list of builk export server to test against.

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• Adding 'max_concurent_downloads' parameter for bulk export python API.

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• Fixing python unit test with the new default for bulk export outputFormat parameter.

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Commits on Mar 1, 2024

• Adding basic authentication to token endpoint and authentication scope to support bulk export from cerner sandbox.

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Commits on Mar 4, 2024

• Adding support for '_elements' and '_typeFilter' parameters in java and python bulk export clients.

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• Adding an example bulk export from SmileCDR.

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Commits on Mar 5, 2024

• Fixing codefactor issues.

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Commits on Mar 21, 2024

• Refactoring: Using the HttpClient mechanism of CredentialProvider to provide credentials for token authentication.

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Commits on Mar 22, 2024

• Adding support for asymmetric client authentication with RSA384.

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• Adding unit tests for JWT signing helpers.

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• Adding javadocs main API classes.

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• Adding javadocs and unit test cases for FileStore abstraction classes.

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• Adding javadocs and unit test cases for FHIR related classes.

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Commits on Mar 25, 2024

• Adding javadocs and unit test cases for bulk client utility classes.

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• Adding javadocs and unit test cases for bulk client download classes.

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Commits on Mar 26, 2024

• Adding javadocs and unit test cases for bulk client web service classes.

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Commits on Mar 27, 2024

• Adding support for transactionTime expressed as a string with the epoch milliseconds, to support SMART Bulk Data Server.

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• Adding unit tests for bulk export web service client.

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Commits on Mar 28, 2024

• Refactoring and adding tests for BulkExport template (states for the async call protocol).

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• Refactoring and adding tests for authentication in bulkexport client.

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Commits on Apr 2, 2024

• Refactoring and adding tests for authentication request interceptor in bulkexport client.

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Commits on Apr 3, 2024

• Refactoring the authentication integration with HttpClient to use TokenCredentials.

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• Adding SMART authentication discovery capabilites.

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Commits on Apr 4, 2024

• Refactoring of the Token authentication for better testability.

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• Further refactoring and unit testing of SMART authentication methods.

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• Further refactoring and unit testing of SMART configuration discovery.

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• Further refactoring and unit testing of SMART configuration discovery.

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Commits on Apr 5, 2024

• Further refactoring and unit testing of SMART configuration and authentication.

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• Aligning the python API for bulkexport with Java implementation.

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• Refactoring and improving logging for AuthTokenProvider.

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Commits on Apr 8, 2024

• Add missing Javadoc comments, needs review

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• Update version to 6.6.0-SNAPSHOT

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Commits on Apr 14, 2024

• Refactoring out common code to read resources as strings.

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• Refactoring: Simplifying class hierarchy for bulk export authentication methods.

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• Refactoring: Redistributing client authentication constants to the authentication method classes.

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• Fixing an issues with accessing of test resources.

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Commits on Apr 15, 2024

• Adding support for 'includeAssociatedData' parameter in the bulk export Java API.

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• Adding support for 'includeAssociatedData' parameter in the bulk export Python API.

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Commits on Apr 16, 2024

• Adding support for cleaning up the export state on the server in case of an error or successful download.

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• Removing dependency of bulkclient on 'utilities'.

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Commits on Apr 17, 2024

• Removing dependency of bulkclient on amazon-sdk-bundle

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