added codecov GH action

[bashir2]

Description of what I changed

Attempting to address issue #666.

E2E test

TESTED:

Ran mvn locally and verified that the Jacoco report generated locally makes sense.

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.

  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)

• 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

All modified and coverable lines are covered by tests ✅

Project coverage is 50.16%. Comparing base (a57f13b) to head (4bf1cf0).
Report is 154 commits behind head on master.

Additional details and impacted files

@@              Coverage Diff              @@
##             master     #973       +/-   ##
=============================================
+ Coverage     34.04%   50.16%   +16.11%     
- Complexity      291      606      +315     
=============================================
  Files            71       86       +15     
  Lines          3818     5073     +1255     
  Branches        437      632      +195     
=============================================
+ Hits           1300     2545     +1245     
+ Misses         2397     2282      -115     
- Partials        121      246      +125     

☔ View full report in Codecov by Sentry.
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[bashir2]

@chandrashekar-s please note that the numbers reported by Codecov are not accurate but I am guessing it is due to having a bad baseline. I like to merge this PR since the local Jacoco report makes sense; we will see if in future PRs the Codecov issue will be fixed or not.

[chandrashekar-s]

Hi @bashir2 thanks for the changes. I see that there are couple of errors during the Upload coverage to codecov phase of codecov run, can you please have a look.

[bashir2]

Hi @bashir2 thanks for the changes. I see that there are couple of errors during the Upload coverage to codecov phase of codecov run, can you please have a look.

Thanks @chandrashekar-s for the review and for noting the errors. I am not sure what the root cause of 500s are but when I was debugging this on Friday, there were certainly runs with no such errors. For example this is a codecov action run with no such errors (done before the Dockerfile commit). As commented above, my guess is that these are due to having a bad baseline, but I am not sure. So if you don't mind, I am going to merge this and if the issue does not go away, I'll resume debugging codecov's upload issue.

[chandrashekar-s]

Hi @bashir2 thanks for the changes. I see that there are couple of errors during the Upload coverage to codecov phase of codecov run, can you please have a look.

Thanks @chandrashekar-s for the review and for noting the errors. I am not sure what the root cause of 500s are but when I was debugging this on Friday, there were certainly runs with no such errors. For example this is a codecov action run with no such errors (done before the Dockerfile commit). As commented above, my guess is that these are due to having a bad baseline, but I am not sure. So if you don't mind, I am going to merge this and if the issue does not go away, I'll resume debugging codecov's upload issue.

Sure, please go ahead and merge the PR. Also, I see that the latest codecov build is successful and the test coverage reported now is ~50%. The incremental report is not accurate as of now, may be because as you pointed out the base report is lagging behind a lot.

[chandrashekar-s]

Thanks @bashir2 for enabling the codecov report. Later on, when the reporting is stabilized we should probably add some checks for min test coverage and others.

[LovjeetVyas]

@bashir2 , @chandrashekar-s guys needed your help with the authentication I am stuck in,
actually in token response am getting a key expires_in that is in string "3600"
but google oauth2 requires it in long and thus its generatig a error
after "fetching the first batch of (resouce)" in buildfhirsearchpipeline as when i traced it back
in the fetchUtil there is tokenresponse that is requiring expiresinsecond that is our expires_in field that is in string format but it requires it in long as per google's oauth2 doc
thus generating a value error and that field being catched as illegalargument

if you guys can make some time for this it would turn out to be much helpful for me

[chandrashekar-s]

@bashir2 , @chandrashekar-s guys needed your help with the authentication I am stuck in, actually in token response am getting a key expires_in that is in string "3600" but google oauth2 requires it in long and thus its generatig a error after "fetching the first batch of (resouce)" in buildfhirsearchpipeline as when i traced it back in the fetchUtil there is tokenresponse that is requiring expiresinsecond that is our expires_in field that is in string format but it requires it in long as per google's oauth2 doc thus generating a value error and that field being catched as illegalargument

if you guys can make some time for this it would turn out to be much helpful for me

Hi @LovjeetVyas, I have replied to your query in this issue. Also, can you please file a new issue, so that it can be discussed there.