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Fix UnsupportedOperationException while validating MHD Document Bundle #5925

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merged 2 commits into from May 16, 2024
Merged

Fix UnsupportedOperationException while validating MHD Document Bundle #5925

merged 2 commits into from May 16, 2024

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subigre
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@subigre subigre commented May 11, 2024

Changelog:

  • Fetch the ValueSet resource and call expandVS(ValueSet source, boolean cacheOk, boolean Hierarchical) method
  • Add unit test and resources

Fixes #5924

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subigre commented May 12, 2024 •
edited

Edit: rebasing on master did the job

Could someone from the team can retrigger the hapifhir.hapi-fhir (module-tests hapi_fhir_jpaserver_test_r4b) workflow step?

The build error comes from a connection timeout to Maven central:

11:47:35,773 [INFO] BUILD FAILURE
Could not retrieve code analysis results - Maven run failed.
11:47:35,773 [INFO] ------------------------------------------------------------------------
11:47:35,775 [INFO] Total time:  22.767 s
11:47:35,777 [INFO] Finished at: 2024-05-11T11:47:35-04:00
11:47:35,777 [INFO] ------------------------------------------------------------------------
11:47:35,779 [ERROR] Failed to execute goal org.apache.maven.plugins:maven-surefire-plugin:3.1.2:test (default-test) on project hapi-fhir-jpaserver-test-r4b: The following artifacts could not be resolved: org.junit.platform:junit-platform-engine:jar:1.9.2 (absent): Could not transfer artifact org.junit.platform:junit-platform-engine:jar:1.9.2 from/to central (https://repo.maven.apache.org/maven2): Connect to repo.maven.apache.org:443 [repo.maven.apache.org/151.101.124.215] failed: Connect timed out -> [Help 1]
org.apache.maven.lifecycle.LifecycleExecutionException: Failed to execute goal org.apache.maven.plugins:maven-surefire-plugin:3.1.2:test (default-test) on project hapi-fhir-jpaserver-test-r4b: The following artifacts could not be resolved: org.junit.platform:junit-platform-engine:jar:1.9.2 (absent): Could not transfer artifact org.junit.platform:junit-platform-engine:jar:1.9.2 from/to central (https://repo.maven.apache.org/maven2): Connect to repo.maven.apache.org:443 [repo.maven.apache.org/151.101.124.215] failed: Connect timed out
    at org.apache.maven.lifecycle.internal.MojoExecutor.doExecute2 (MojoExecutor.java:333)
    at org.apache.maven.lifecycle.internal.MojoExecutor.doExecute (MojoExecutor.java:316)
    at org.apache.maven.lifecycle.internal.MojoExecutor.execute (MojoExecutor.java:212)
    at org.apache.maven.lifecycle.internal.MojoExecutor.execute (MojoExecutor.java:174)
    at org.apache.maven.lifecycle.internal.MojoExecutor.access$000 (MojoExecutor.java:75)
    at org.apache.maven.lifecycle.internal.MojoExecutor$1.run (MojoExecutor.java:162)
    at org.apache.maven.plugin.DefaultMojosExecutionStrategy.execute (DefaultMojosExecutionStrategy.java:39)
    at org.apache.maven.lifecycle.internal.MojoExecutor.execute (MojoExecutor.java:159)
    at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject (LifecycleModuleBuilder.java:105)
    at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject (LifecycleModuleBuilder.java:73)
    at org.apache.maven.lifecycle.internal.builder.singlethreaded.SingleThreadedBuilder.build (SingleThreadedBuilder.java:53)
    at org.apache.maven.lifecycle.internal.LifecycleStarter.execute (LifecycleStarter.java:118)
    at org.apache.maven.DefaultMaven.doExecute (DefaultMaven.java:261)
    at org.apache.maven.DefaultMaven.doExecute (DefaultMaven.java:173)
    at org.apache.maven.DefaultMaven.execute (DefaultMaven.java:101)
    at org.apache.maven.cli.MavenCli.execute (MavenCli.java:906)
    at org.apache.maven.cli.MavenCli.doMain (MavenCli.java:283)
    at org.apache.maven.cli.MavenCli.main (MavenCli.java:206)
    at jdk.internal.reflect.DirectMethodHandleAccessor.invoke (DirectMethodHandleAccessor.java:103)
    at java.lang.reflect.Method.invoke (Method.java:580)
    at org.codehaus.plexus.classworlds.launcher.Launcher.launchEnhanced (Launcher.java:283)
    at org.codehaus.plexus.classworlds.launcher.Launcher.launch (Launcher.java:226)
    at org.codehaus.plexus.classworlds.launcher.Launcher.mainWithExitCode (Launcher.java:407)
    at org.codehaus.plexus.classworlds.launcher.Launcher.main (Launcher.java:348)

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codecov bot commented May 14, 2024 •
edited

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 83.44%. Comparing base (497b9f2) to head (ff66cd5).
Report is 62 commits behind head on master.

Additional details and impacted files 
@@             Coverage Diff              @@
##             master    #5925      +/-   ##
============================================
+ Coverage     83.39%   83.44%   +0.04%     
- Complexity    26927    27082     +155     
============================================
  Files          1681     1692      +11     
  Lines        103965   104543     +578     
  Branches      13189    13234      +45     
============================================
+ Hits          86702    87232     +530     
- Misses        11613    11645      +32     
- Partials       5650     5666      +16

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

@jamesagnew jamesagnew enabled auto-merge (squash) May 15, 2024 08:45
jamesagnew
jamesagnew approved these changes May 15, 2024
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Thanks for the contribution!

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subigre commented May 15, 2024

@jamesagnew I am not sure why it failed but I just run mvn spotless:check on the branch and everything went well:

[INFO] --- spotless:2.41.1:check (default-cli) @ hapi-fhir-server-cds-hooks ---
[INFO] Spotless.Java is keeping 73 files clean - 0 needs changes to be clean, 0 were already clean, 73 were skipped because caching determined they were already clean
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary for HAPI-FHIR 7.3.2-SNAPSHOT:
[INFO]
[INFO] HAPI-FHIR .......................................... SUCCESS [  1.099 s]
[INFO] HAPI FHIR - Checkstyle ............................. SUCCESS [  0.066 s]
[INFO] HAPI FHIR - Deployable Artifact Parent POM ......... SUCCESS [  0.033 s]
[INFO] HAPI FHIR BOM ...................................... SUCCESS [  0.033 s]
[INFO] HAPI FHIR - Core Library ........................... SUCCESS [  0.609 s]
[INFO] HAPI FHIR - ServiceLoaders ......................... SUCCESS [  0.031 s]
[INFO] HAPI FHIR - ServiceLoaders - Caching API ........... SUCCESS [  0.035 s]
[INFO] HAPI FHIR - ServiceLoaders - Caching Caffeine ...... SUCCESS [  0.037 s]
[INFO] HAPI FHIR - ServiceLoaders - Caching Testing ....... SUCCESS [  0.030 s]
[INFO] HAPI FHIR - Server Framework ....................... SUCCESS [  0.056 s]
[INFO] HAPI FHIR - Validation Resources (DSTU3) ........... SUCCESS [  0.031 s]
[INFO] HAPI FHIR - Client Framework ....................... SUCCESS [  0.038 s]
[INFO] HAPI FHIR Test Utilities ........................... SUCCESS [  0.037 s]
[INFO] HAPI FHIR Structures - DSTU3 ....................... SUCCESS [  0.037 s]
[INFO] HAPI FHIR - Validation Resources (FHIR R4) ......... SUCCESS [  0.030 s]
[INFO] HAPI FHIR Structures - FHIR R4 ..................... SUCCESS [  0.039 s]
[INFO] HAPI FHIR - Validation Resources (DSTU2) ........... SUCCESS [  0.029 s]
[INFO] HAPI FHIR JPA Model ................................ SUCCESS [  0.042 s]
[INFO] HAPI FHIR Structures - HL7.org DSTU2 ............... SUCCESS [  0.038 s]
[INFO] HAPI FHIR Structures - FHIR r4b .................... SUCCESS [  0.036 s]
[INFO] HAPI FHIR - Validation Resources (FHIR R5) ......... SUCCESS [  0.031 s]
[INFO] HAPI FHIR Structures - FHIR R5 ..................... SUCCESS [  0.035 s]
[INFO] HAPI Tinder Plugin ................................. SUCCESS [  0.045 s]
[INFO] HAPI FHIR Structures - DSTU2 (FHIR v1.0.0) ......... SUCCESS [  0.037 s]
[INFO] HAPI FHIR - Validation Resources DSTU2.1 (2016May) . SUCCESS [  0.029 s]
[INFO] HAPI FHIR Structures - DSTU2.1 (2016May) ........... SUCCESS [  0.034 s]
[INFO] HAPI FHIR - Converter .............................. SUCCESS [  0.035 s]
[INFO] HAPI FHIR - Validation Resources (FHIR R4B) ........ SUCCESS [  0.030 s]
[INFO] HAPI FHIR JPA Model ................................ SUCCESS [  0.035 s]
[INFO] HAPI FHIR - Validation ............................. SUCCESS [  0.037 s]
[INFO] HAPI FHIR OkHttp Client ............................ SUCCESS [  0.037 s]
[INFO] HAPI FHIR JAX-RS Server ............................ SUCCESS [  0.034 s]
[INFO] HAPI FHIR JPA - Search Parameters .................. SUCCESS [  0.036 s]
[INFO] HAPI FHIR Storage api .............................. SUCCESS [  0.053 s]
[INFO] HAPI FHIR - Master Data Management ................. SUCCESS [  0.044 s]
[INFO] HAPI FHIR Subscription Server ...................... SUCCESS [  0.040 s]
[INFO] HAPI FHIR Server - SQL Migration ................... SUCCESS [  0.037 s]
[INFO] HAPI FHIR JPA Server - Batch2 Task Processor ....... SUCCESS [  0.040 s]
[INFO] hapi-fhir-storage-batch2-jobs ...................... SUCCESS [  0.035 s]
[INFO] hapi-fhir-server-openapi ........................... SUCCESS [  0.031 s]
[INFO] HAPI FHIR JPA Server ............................... SUCCESS [  0.055 s]
[INFO] HAPI FHIR JPA Server - HFQL Driver ................. SUCCESS [  0.034 s]
[INFO] HAPI FHIR TestPage Overlay ......................... SUCCESS [  0.039 s]
[INFO] HAPI FHIR - Docs ................................... SUCCESS [  0.033 s]
[INFO] hapi-fhir-storage-test-utilities ................... SUCCESS [  0.030 s]
[INFO] HAPI FHIR JPA Server Test Utilities ................ SUCCESS [  0.038 s]
[INFO] HAPI FHIR JPA Server Test Dstu2 .................... SUCCESS [  0.031 s]
[INFO] HAPI FHIR JPA Server Test Dstu3 .................... SUCCESS [  0.031 s]
[INFO] HAPI FHIR JPA Server - Batch2 specification tests .. SUCCESS [  0.030 s]
[INFO] HAPI FHIR JPA Server Test R4 ....................... SUCCESS [  0.038 s]
[INFO] HAPI FHIR JPA Server Test R4B ...................... SUCCESS [  0.029 s]
[INFO] HAPI FHIR JPA Server Test R5 ....................... SUCCESS [  0.031 s]
[INFO] HAPI FHIR JPA Server Elastic Test Utilities ........ SUCCESS [  0.030 s]
[INFO] HAPI Tinder Plugin - Test Project .................. SUCCESS [  0.037 s]
[INFO] HAPI FHIR - ServiceLoaders - Caching Guava ......... SUCCESS [  0.030 s]
[INFO] HAPI FHIR - Clinical Reasoning ..................... SUCCESS [  0.035 s]
[INFO] hapi-fhir-storage-mdm .............................. SUCCESS [  0.031 s]
[INFO] HAPI FHIR JPA Server - International Patient Summary (IPS) SUCCESS [  0.032 s]
[INFO] HAPI FHIR JPA Server - Master Data Management ...... SUCCESS [  0.040 s]
[INFO] HAPI FHIR - fhirtest.uhn.ca Deployable WAR ......... SUCCESS [  0.045 s]
[INFO] HAPI FHIR - Android ................................ SUCCESS [  0.036 s]
[INFO] HAPI FHIR - Command Line Client - API .............. SUCCESS [  0.036 s]
[INFO] HAPI FHIR - Command Line Client - Base Project ..... SUCCESS [  0.033 s]
[INFO] HAPI FHIR - Command Line Client - Application ...... SUCCESS [  0.041 s]
[INFO] HAPI FHIR - Distribution Archive ................... SUCCESS [  0.033 s]
[INFO] HAPI FHIR JAX-RS Server Kotlin test ................ SUCCESS [  0.039 s]
[INFO] HAPI FHIR - Minimal Dependency Test - Client ....... SUCCESS [  0.030 s]
[INFO] HAPI FHIR - Minimal Dependency Test - Server ....... SUCCESS [  0.029 s]
[INFO] hapi-fhir-spring-boot-autoconfigure ................ SUCCESS [  0.030 s]
[INFO] hapi-fhir-spring-boot-starter ...................... SUCCESS [  0.028 s]
[INFO] hapi-fhir-spring-boot .............................. SUCCESS [  0.026 s]
[INFO] hapi-fhir-spring-boot-samples ...................... SUCCESS [  0.028 s]
[INFO] hapi-fhir-spring-boot-sample-client-apache ......... SUCCESS [  0.032 s]
[INFO] hapi-fhir-spring-boot-sample-client-okhttp ......... SUCCESS [  0.029 s]
[INFO] hapi-fhir-spring-boot-sample-server-jersey ......... SUCCESS [  0.029 s]
[INFO] HAPI FHIR - JaCoCo Test Coverage ................... SUCCESS [  0.030 s]
[INFO] HAPI FHIR - CDS Hooks .............................. SUCCESS [  0.036 s]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time:  5.958 s
[INFO] Finished at: 2024-05-15T19:07:22+02:00
[INFO] ------------------------------------------------------------------------

@jamesagnew jamesagnew disabled auto-merge May 16, 2024 06:20
@jamesagnew jamesagnew merged commit 446869b into hapifhir:master May 16, 2024
63 of 65 checks passed
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@subigre that is a false negative - because of some weird permissions issues we haven't yet figured out, external PRs always fail that check. Thanks again!

@subigre subigre deleted the fix-ihe-mhd-validation branch May 16, 2024 07:27
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