SO-4872: FHIR model harmonization, batch support #867

bbanfai · 2021-07-28T09:17:11Z

Please review so we can merge the improved domain objects and corresponding testing code to 8.x.

feature/SO-4872_FHIR_Batch_support Conflicts: fhir/com.b2international.snowowl.fhir.core/src/com/b2international/snowowl/fhir/core/model/OperationOutcome.java fhir/com.b2international.snowowl.fhir.core/src/com/b2international/snowowl/fhir/core/model/codesystem/CodeSystem.java fhir/com.b2international.snowowl.fhir.core/src/com/b2international/snowowl/fhir/core/provider/CodeSystemApiProvider.java fhir/com.b2international.snowowl.fhir.rest.tests/src/com/b2international/snowowl/fhir/tests/filter/FilterTest.java fhir/com.b2international.snowowl.fhir.rest.tests/src/com/b2international/snowowl/fhir/tests/serialization/domain/ModelSerializationTest.java fhir/com.b2international.snowowl.fhir.rest/src/com/b2international/snowowl/fhir/rest/FhirCodeSystemController.java fhir/com.b2international.snowowl.fhir.rest/src/com/b2international/snowowl/fhir/rest/FhirConceptMapController.java fhir/com.b2international.snowowl.fhir.rest/src/com/b2international/snowowl/fhir/rest/FhirValueSetController.java

…atch_support

...snowowl.fhir.core/src/com/b2international/snowowl/fhir/core/model/codesystem/CodeSystem.java

...nowowl.fhir.rest.tests/src/com/b2international/snowowl/fhir/rest/tests/AllFhirRestTests.java

....fhir.rest.tests/src/com/b2international/snowowl/fhir/rest/tests/batch/BatchApiRestTest.java

fhir/com.b2international.snowowl.fhir.rest/META-INF/MANIFEST.MF

...al.snowowl.fhir.rest/src/com/b2international/snowowl/fhir/rest/FhirCodeSystemController.java

lgtm-com · 2021-08-02T18:26:41Z

This pull request introduces 4 alerts when merging 3b9fbc7 into 33e66a0 - view on LGTM.com

new alerts:

3 for Server-side request forgery
1 for Container contents are never accessed

lgtm-com · 2021-08-03T14:17:18Z

This pull request introduces 4 alerts when merging bf5448c into bdcae0a - view on LGTM.com

new alerts:

3 for Server-side request forgery
1 for Container contents are never accessed

cmark

LGTM! Looks good so far.

Disable FHIR batch api tests.

codecov-commenter · 2021-08-05T20:53:05Z

Codecov Report

Merging #867 (5d1c931) into 8.x (1dea916) will increase coverage by 1.18%.
The diff coverage is 78.25%.

@@             Coverage Diff              @@
##                8.x     #867      +/-   ##
============================================
+ Coverage     60.20%   61.38%   +1.18%     
- Complexity    11061    11498     +437     
============================================
  Files          1656     1713      +57     
  Lines         54565    56210    +1645     
  Branches       5298     5389      +91     
============================================
+ Hits          32851    34505    +1654     
+ Misses        19598    19510      -88     
- Partials       2116     2195      +79

Impacted Files	Coverage Δ
...fhir/core/codesystems/ConditionalDeleteStatus.java	`0.00% <0.00%> (ø)`
...l/fhir/core/codesystems/ConditionalReadStatus.java	`0.00% <0.00%> (ø)`
.../snowowl/fhir/core/codesystems/FilterOperator.java	`83.87% <0.00%> (-5.79%)`	⬇️
...nowowl/fhir/core/codesystems/MessageTransport.java	`0.00% <0.00%> (ø)`
...al/snowowl/fhir/core/codesystems/PropertyType.java	`86.66% <0.00%> (+0.95%)`	⬆️
...owowl/fhir/core/codesystems/PublicationStatus.java	`87.50% <ø> (+12.50%)`	⬆️
...fhir/core/codesystems/ReferenceHandlingPolicy.java	`0.00% <0.00%> (ø)`
...wowl/fhir/core/codesystems/RestfulInteraction.java	`0.00% <0.00%> (ø)`
.../fhir/core/codesystems/RestfulSecurityService.java	`0.00% <0.00%> (ø)`
...nowowl/fhir/core/codesystems/VersioningPolicy.java	`0.00% <0.00%> (ø)`
... and 296 more

Continue to review full report at Codecov.

Legend - Click here to learn more
Δ = absolute <relative> (impact), ø = not affected, ? = missing data
Powered by Codecov. Last update 1dea916...5d1c931. Read the comment docs.

bbanfai added 30 commits June 23, 2021 15:29

SO-4872 Progress committed

5c35582

SO-4872 Request/Resource bundle.entry types implemented.

4896855

SO-4872 Initial server-side controller.

0d72d07

SO-4872 Test cases rearranged, deserialization issues solved.

5b1d258

SO-4872 Test code.

fda5872

SO-4872 Batch response created.

78c3dad

SO-4872 Request URI created for call.

c1ced02

SO-4872 Operation outcome for failed requests.

ba16a4f

SO-4872 Methods rearranged.

80a29cc

SO-4872 REST API test cases added.

5629508

SO-4872 Swagger doc added.

56fd4d5

SO-4872 Test cases for batch processing completed.

f6b9d25

SO-4872 Skeleton bundle REST API methods added.

8d3608a

SO-4872 FHIR bundle requests added.

65b278c

SO_4872 Builder added

033674b

SO-4872 Builder added

dac657f

SO-4872 Extension creation fixed.

5e1f963

SO-4872 Extension creation fixed

d956568

SO-4872 Deserialization support added to data types and domain objects.

1ad559c

SO-4872 Deserialization support added.

476c5d1

SO-4872 Compile errors fixed after merge with 8.x.

e5133f6

SO-4872 Minor changes.

85a2c98

SO-4872 Compile errors fixed.

27af4fc

SO-4872 Updated test json file.

c8c5a47

SO-4872 Data type rests rearranged.

2baa8f7

SO-4872 Test classes rearranged.

314ec09

SO-4872 Test case and skeleton endpoint added.

d1c2f53

SO-4872 Merged code.

9171d4f

SO-4872 Value set deserialization improvements.

2e73935

bbanfai self-assigned this Jul 28, 2021

cmark changed the base branch from 7.x to 8.x July 28, 2021 09:20

bbanfai added 2 commits July 28, 2021 15:15

SO-4872 StructureDefinition fixes.

39825fa

SO-4872 StructureDefinition deserialization support improved.

5139ab8

cmark changed the title ~~SO-4872: FHIR batch support~~ SO-4872: FHIR model harmonization, batch support Jul 30, 2021

Merge remote-tracking branch 'origin/8.x' into feature/SO-4872_FHIR_B…

20eff46

…atch_support

cmark requested changes Jul 30, 2021

View reviewed changes

bbanfai added 10 commits July 31, 2021 09:44

SO-4872 Base class deserializable.

19a6290

SO-4872 Typed property deserializer.

0f4a2cb

SO-4872 Structuredef tests and deserialization support improvements.

ee0576b

SO-4872 Improvements for the Example element.

2f5386d

SO-4872 Unwrapped serialization for typed properties.

9ac2036

SO-4872 ElementDefinition test and serialization support.

9984631

SO-4872 All resources are (de)serializable.

07fe38b

SO-4872 Tests are green.

a5a39c0

SO-4872 Test case bug fixed.

2456d86

SO-4872 PR comments addressed.

3b9fbc7

SO-4872 Capability Statement domain objects part1

bf5448c

bbanfai added 2 commits August 4, 2021 15:21

SO-4872 Capability statement domain model completed.

6433f26

SO-4872 Type corrected

7689031

cmark approved these changes Aug 4, 2021

View reviewed changes

bbanfai and others added 4 commits August 4, 2021 17:14

SO-4872 Test cases added.

79b23fa

SO-4872 Capability statement completed. All tests are green.

36f6e3d

fix(fhir): use proper class when extracting resource from entry

412b705

fix(fhir): properly deserialize test codesytem from file

5d1c931

Disable FHIR batch api tests.

cmark merged commit c6c3ca5 into 8.x Aug 6, 2021

cmark deleted the feature/SO-4872_FHIR_Batch_support branch August 6, 2021 06:46

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

SO-4872: FHIR model harmonization, batch support #867

SO-4872: FHIR model harmonization, batch support #867

bbanfai commented Jul 28, 2021

lgtm-com bot commented Aug 2, 2021

lgtm-com bot commented Aug 3, 2021

cmark left a comment

codecov-commenter commented Aug 5, 2021

SO-4872: FHIR model harmonization, batch support #867

SO-4872: FHIR model harmonization, batch support #867

Conversation

bbanfai commented Jul 28, 2021

lgtm-com bot commented Aug 2, 2021

lgtm-com bot commented Aug 3, 2021

cmark left a comment

Choose a reason for hiding this comment

codecov-commenter commented Aug 5, 2021

Codecov Report