Changes to fix issues of missing extensions and others

[chandrashekar-s]

Description of what I changed

Fixes #1027
The below mentioned changes have been made as part of this PR

• Handled the error properly when the StructureDefinitions for extensions are missing.
• The DoubleConverter for decimal data types has been fixed, which was failing for Leaf Extensions containing Decimal data types.
• The avro schema name for the Reference types have been changed to contain a full path name from root, so that it is unique for each path.

E2E test

• Tested the changes by referencing an extension whose StructureDefinition was not available and ensure proper error message is thrown instead of NPE.
• Ingested an QuestionnaireResponse fhir resource and ran a Full Run and checked if the QuestionnaireResponse is converted to Avro record properly

TESTED:

• Added a unit test case

Checklist: I completed these to help reviewers :)

• I have read and will follow the review process.

• 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.

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

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

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

• All new and existing tests passed.

• 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 70.00000% with 6 lines in your changes are missing coverage. Please review.

Project coverage is 50.60%. Comparing base (498d7c1) to head (bebc984).

Files	Patch %	Lines
.../bunsen/definitions/r4/R4StructureDefinitions.java	50.00%	2 Missing and 1 partial ⚠️
...sen/definitions/stu3/Stu3StructureDefinitions.java	50.00%	2 Missing and 1 partial ⚠️

Additional details and impacted files

@@             Coverage Diff              @@
##             master    #1050      +/-   ##
============================================
- Coverage     50.60%   50.60%   -0.01%     
- Complexity      673      674       +1     
============================================
  Files            91       91              
  Lines          5505     5511       +6     
  Branches        707      707              
============================================
+ Hits           2786     2789       +3     
- Misses         2457     2461       +4     
+ Partials        262      261       -1     

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[bashir2]

Thanks @chandrashekar-s for fixing these issues. All of my comments are either minor or questions, so please feel free to merge this after you address them and the e2e issue is fixed.

[chandrashekar-s]

Hi @bashir2, thanks for the review. I have updated my comments and I have also created these 2 issues (Relook at the recursive depth and Fix the number of parquet files for DirectRunner) which can be resolved in different PRs.

[bashir2]

Thanks @chandrashekar-s for the detailed responses. My only main remaining issue is the null return value. Otherwise, please feel free to merge this.

[chandrashekar-s]

Thanks @bashir2 for the review, I have addressed the review comments and will be merging the PR. Please let me know if you see any discrepancies and I will take them up in a separate PR.