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feat: support for SQL database connection settings#539

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RadovanTomik wants to merge 7 commits into
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feat/omop
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feat: support for SQL database connection settings#539
RadovanTomik wants to merge 7 commits into
masterfrom
feat/omop

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@RadovanTomik
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Pull Request:

Description:

Please provide a short description of what this PR is supposed to accomplish...

Checklist:

Make sure you tick all the boxes below if they are true or do not apply before you ask for review

  • I have performed a self-review of my code
  • I have made my code as simple as possible
  • I have added relevant tests for my changes and the code coverage has not dropped substantially
  • I have removed all commented code
  • I have updated the documentation in all relevant places (Javadoc, Swagger, MDs...)
  • I have described the PR and added a meaningful title in the Conventional Commits format

@RadovanTomik RadovanTomik self-assigned this May 22, 2026
@RadovanTomik RadovanTomik linked an issue May 22, 2026 that may be closed by this pull request
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codecov Bot commented May 22, 2026

Codecov Report

❌ Patch coverage is 53.67647% with 63 lines in your changes missing coverage. Please review.
✅ Project coverage is 58.68%. Comparing base (c85b05c) to head (aed26ec).

Files with missing lines Patch % Lines
...quality/agent/dataquality/impl/BlazeFHIRStore.java 8.00% 22 Missing and 1 partial ⚠️
...lity/agent/dataquality/impl/QualityChecksStep.java 38.88% 10 Missing and 1 partial ⚠️
...c/quality/agent/dataquality/impl/SqlDataStore.java 12.50% 7 Missing ⚠️
...i_eric/quality/agent/dataquality/dto/DBStatus.java 0.00% 3 Missing ⚠️
...y/agent/dataquality/impl/DataStoreFactoryImpl.java 85.00% 1 Missing and 2 partials ⚠️
...uality/agent/dataquality/impl/EntityCountStep.java 50.00% 2 Missing and 1 partial ⚠️
...quality/agent/dataquality/domain/QualityCheck.java 50.00% 1 Missing and 1 partial ⚠️
...ent/dataquality/impl/DuplicateIdentifierCheck.java 0.00% 2 Missing ⚠️
...y/agent/dataquality/impl/FhirCqlQueryExecutor.java 92.59% 0 Missing and 2 partials ⚠️
...ent/dataquality/impl/InvalidConditionICDCheck.java 0.00% 2 Missing ⚠️
... and 3 more
Additional details and impacted files

Impacted file tree graph

@@             Coverage Diff              @@
##             master     #539      +/-   ##
============================================
- Coverage     59.38%   58.68%   -0.71%     
- Complexity      345      357      +12     
============================================
  Files            85       88       +3     
  Lines          1726     1791      +65     
  Branches        141      149       +8     
============================================
+ Hits           1025     1051      +26     
- Misses          652      686      +34     
- Partials         49       54       +5     
Flag Coverage Δ
agent 58.68% <53.67%> (-0.71%) ⬇️

Flags with carried forward coverage won't be shown. Click here to find out more.

Files with missing lines Coverage Δ
...ity/agent/dataquality/domain/QualityCheckType.java 100.00% <100.00%> (ø)
...bmri_eric/quality/agent/settings/DatabaseType.java 100.00% <100.00%> (ø)
...agent/dataquality/controller/EntityController.java 31.25% <75.00%> (+1.25%) ⬆️
...quality/agent/dataquality/domain/QualityCheck.java 81.81% <50.00%> (-13.54%) ⬇️
...ent/dataquality/impl/DuplicateIdentifierCheck.java 0.00% <0.00%> (ø)
...y/agent/dataquality/impl/FhirCqlQueryExecutor.java 92.59% <92.59%> (ø)
...ent/dataquality/impl/InvalidConditionICDCheck.java 0.00% <0.00%> (ø)
...lity/agent/dataquality/impl/SurvivalRateCheck.java 0.00% <0.00%> (ø)
...ic/quality/agent/dataquality/impl/UpdateCheck.java 0.00% <0.00%> (ø)
...i_eric/quality/agent/dataquality/dto/DBStatus.java 0.00% <0.00%> (ø)
... and 5 more
Files with missing lines Coverage Δ
...ity/agent/dataquality/domain/QualityCheckType.java 100.00% <100.00%> (ø)
...bmri_eric/quality/agent/settings/DatabaseType.java 100.00% <100.00%> (ø)
...agent/dataquality/controller/EntityController.java 31.25% <75.00%> (+1.25%) ⬆️
...quality/agent/dataquality/domain/QualityCheck.java 81.81% <50.00%> (-13.54%) ⬇️
...ent/dataquality/impl/DuplicateIdentifierCheck.java 0.00% <0.00%> (ø)
...y/agent/dataquality/impl/FhirCqlQueryExecutor.java 92.59% <92.59%> (ø)
...ent/dataquality/impl/InvalidConditionICDCheck.java 0.00% <0.00%> (ø)
...lity/agent/dataquality/impl/SurvivalRateCheck.java 0.00% <0.00%> (ø)
...ic/quality/agent/dataquality/impl/UpdateCheck.java 0.00% <0.00%> (ø)
...i_eric/quality/agent/dataquality/dto/DBStatus.java 0.00% <0.00%> (ø)
... and 5 more
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Add SQL support

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