Support for multiple FHIR profile extensions

[chandrashekar-s]

Description of what I changed

Fixes #980

This is an extension to the PR #924. In this PR we provide support for multiple FHIR profile extension for a given resource type. This is achieved by creating a Master AvroConverter for the given resource type by merging all the individual AvroConverters against the configured extensions profiles including the base profile. The merging includes a deep merge of the nested elements under the AvroConverter.

E2E test

Tested the changes with the default US Core FHIR profile extensions and verified that the extension fields are properly populated in the parquet files.

TESTED:

Please replace this with a description of how you tested your PR beyond the automated e2e/unit tests.

Checklist: I completed these to help reviewers :)

• [x] I have read and will follow the review process.

• [x] I am familiar with Google Style Guides for the language I have coded in.

  No? Please take some time and review Java and Python style guides.

• [x] My IDE is configured to follow the Google code styles.

  No? Unsure? -> configure your IDE.

• [ ] I have added tests to cover my changes. (If you refactored existing code that was well tested you do not have to add tests)

• [x] I ran mvn clean package right before creating this pull request and added all formatting changes to my commit.

• [x] All new and existing tests passed.

• [x] My pull request is based on the latest changes of the master branch.

  No? Unsure? -> execute command git pull --rebase upstream master

[codecov-commenter]

Codecov Report

Attention: Patch coverage is 59.20578% with 113 lines in your changes are missing coverage. Please review.

Project coverage is 50.52%. Comparing base (b354beb) to head (178366b).

Files	Patch %	Lines
...r/bunsen/avro/tools/GenerateAggregatedSchemas.java	0.00%	55 Missing :warning:
...unsen/avro/converters/DefinitionToAvroVisitor.java	88.18%	9 Missing and 4 partials :warning:
.../cerner/bunsen/definitions/PrimitiveConverter.java	38.46%	6 Missing and 2 partials :warning:
...m/cerner/bunsen/definitions/HapiConverterUtil.java	12.50%	5 Missing and 2 partials :warning:
...ner/bunsen/definitions/LeafExtensionConverter.java	40.00%	3 Missing and 3 partials :warning:
.../com/cerner/bunsen/avro/tools/GenerateSchemas.java	44.44%	4 Missing and 1 partial :warning:
.../com/google/fhir/analytics/AvroConversionUtil.java	44.44%	4 Missing and 1 partial :warning:
...java/com/cerner/bunsen/ProfileMappingProvider.java	66.66%	3 Missing :warning:
...m/cerner/bunsen/avro/converters/NoOpConverter.java	0.00%	2 Missing :warning:
...a/com/cerner/bunsen/ProfileMapperFhirContexts.java	50.00%	2 Missing :warning:
... and 6 more

Additional details and impacted files

```diff @@ Coverage Diff @@ ## master #986 +/- ## ============================================ + Coverage 50.36% 50.52% +0.16% - Complexity 644 663 +19 ============================================ Files 87 91 +4 Lines 5266 5465 +199 Branches 669 701 +32 ============================================ + Hits 2652 2761 +109 - Misses 2366 2444 +78 - Partials 248 260 +12 ```

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[chandrashekar-s]

@bashir2 The PR is ready for the first round of review, can you please have a look and let me know if the approach taken is good. In the meanwhile, I will add unit tests.

[chandrashekar-s]

@bashir2 Please have a look at the latest commits containing more unit tests and some minor fixes.

[chandrashekar-s]

Thanks @bashir2 for the detailed review. I have addressed most of the comments, there are only 2 comments left which we can discuss in our tomorrow's meeting.