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monarch-initiative / phenopacket2prompt

GA4GH Phenopacket to LLM prompt
https://monarch-initiative.github.io/phenopacket2prompt/
MIT License
3 stars 2 forks source link

Cannot install, HpInternationalOboParserTest fails #37

Closed cmungall closed 4 months ago

cmungall commented 5 months ago

[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.008 s - in org.monarchinitiative.phenopacket2prompt.international.HpInternationalOboParserTest

➜ phenopacket2prompt git:(main) ✗ mvn --version Apache Maven 3.9.8 (36645f6c9b5079805ea5009217e36f2cffd34256) Maven home: /opt/homebrew/Cellar/maven/3.9.8/libexec Java version: 22.0.1, vendor: Homebrew, runtime: /opt/homebrew/Cellar/openjdk/22.0.1/libexec/openjdk.jdk/Contents/Home Default locale: en_US, platform encoding: UTF-8 OS name: "mac os x", version: "12.6", arch: "aarch64", family: "mac" ➜ phenopacket2prompt git:(main) ✗ mvn test [INFO] Scanning for projects... [INFO] [INFO] --------------< org.monarchinitiative:phenopacket2prompt >-------------- [INFO] Building phenopacket2prompt 0.4.6 [INFO] from pom.xml [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- enforcer:3.3.0:enforce (enforce-maven) @ phenopacket2prompt --- [INFO] Rule 0: org.apache.maven.enforcer.rules.version.RequireMavenVersion passed [INFO] [INFO] --- resources:3.3.0:resources (default-resources) @ phenopacket2prompt --- [INFO] Copying 1 resource [INFO] [INFO] --- compiler:3.8.1:compile (default-compile) @ phenopacket2prompt --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- resources:3.3.0:testResources (default-testResources) @ phenopacket2prompt --- [INFO] Copying 2 resources [INFO] [INFO] --- compiler:3.8.1:testCompile (default-testCompile) @ phenopacket2prompt --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- surefire:3.0.0-M5:test (default-test) @ phenopacket2prompt --- [INFO] [INFO] ------------------------------------------------------- [INFO] T E S T S [INFO] ------------------------------------------------------- [INFO] Running org.monarchinitiative.phenopacket2prompt.output.impl.german.PpktIndividualGermanTest SLF4J(W): No SLF4J providers were found. SLF4J(W): Defaulting to no-operation (NOP) logger implementation SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details. SLF4J(W): Class path contains SLF4J bindings targeting slf4j-api versions 1.7.x or earlier. SLF4J(W): Ignoring binding found at [jar:file:/Users/cjm/.m2/repository/org/apache/logging/log4j/log4j-slf4j-impl/2.23.1/log4j-slf4j-impl-2.23.1.jar!/org/slf4j/impl/StaticLoggerBinder.class] SLF4J(W): See https://www.slf4j.org/codes.html#ignoredBindings for an explanation. [INFO] Tests run: 13, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.128 s - in org.monarchinitiative.phenopacket2prompt.output.impl.german.PpktIndividualGermanTest [INFO] Running org.monarchinitiative.phenopacket2prompt.output.impl.italian.PpktIndividualItalianTest [WARNING] Tests run: 13, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.015 s - in org.monarchinitiative.phenopacket2prompt.output.impl.italian.PpktIndividualItalianTest [INFO] Running org.monarchinitiative.phenopacket2prompt.output.impl.english.PPKtEnglishBuildingBlocksTest [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.monarchinitiative.phenopacket2prompt.output.impl.english.PPKtEnglishBuildingBlocksTest [INFO] Running org.monarchinitiative.phenopacket2prompt.output.impl.english.PpktPhenotypicFeatureEnglishTest [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.012 s - in org.monarchinitiative.phenopacket2prompt.output.impl.english.PpktPhenotypicFeatureEnglishTest [INFO] Running org.monarchinitiative.phenopacket2prompt.output.impl.english.PpktIndividualEnglishTest [INFO] Tests run: 13, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.017 s - in org.monarchinitiative.phenopacket2prompt.output.impl.english.PpktIndividualEnglishTest [INFO] Running org.monarchinitiative.phenopacket2prompt.output.impl.spanish.PpktIndividualSpanishTest [ERROR] Tests run: 12, Failures: 4, Errors: 0, Skipped: 0, Time elapsed: 0.026 s <<< FAILURE! - in org.monarchinitiative.phenopacket2prompt.output.impl.spanish.PpktIndividualSpanishTest [ERROR] org.monarchinitiative.phenopacket2prompt.output.impl.spanish.PpktIndividualSpanishTest.testEvaluateExpression(TestIndividual)[1] Time elapsed: 0.004 s <<< FAILURE! org.opentest4j.AssertionFailedError: Incorrect evaluation for: 46 year olf female, infantile onset ==> expected: but was: at org.monarchinitiative.phenopacket2prompt.output.impl.spanish.PpktIndividualSpanishTest.testEvaluateExpression(PpktIndividualSpanishTest.java:45) [ERROR] org.monarchinitiative.phenopacket2prompt.output.impl.spanish.PpktIndividualSpanishTest.testEvaluateExpression(TestIndividual)[2] Time elapsed: 0.001 s <<< FAILURE! org.opentest4j.AssertionFailedError: Incorrect evaluation for: male 4 months, congenital onset ==> expected: but was: at org.monarchinitiative.phenopacket2prompt.output.impl.spanish.PpktIndividualSpanishTest.testEvaluateExpression(PpktIndividualSpanishTest.java:45) [ERROR] org.monarchinitiative.phenopacket2prompt.output.impl.spanish.PpktIndividualSpanishTest.testEvaluateExpression(TestIndividual)[3] Time elapsed: 0.001 s <<< FAILURE! org.opentest4j.AssertionFailedError: Incorrect evaluation for: female, no onset ==> expected: but was: at org.monarchinitiative.phenopacket2prompt.output.impl.spanish.PpktIndividualSpanishTest.testEvaluateExpression(PpktIndividualSpanishTest.java:45) [ERROR] org.monarchinitiative.phenopacket2prompt.output.impl.spanish.PpktIndividualSpanishTest.testEvaluateExpression(TestIndividual)[5] Time elapsed: 0 s <<< FAILURE! org.opentest4j.AssertionFailedError: Incorrect evaluation for: unknown sex, no 4yo ==> expected: but was: at org.monarchinitiative.phenopacket2prompt.output.impl.spanish.PpktIndividualSpanishTest.testEvaluateExpression(PpktIndividualSpanishTest.java:45) [INFO] Running org.monarchinitiative.phenopacket2prompt.international.HpInternationalOboParserTest [WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.007 s - in org.monarchinitiative.phenopacket2prompt.international.HpInternationalOboParserTest [INFO] [INFO] Results: [INFO] [ERROR] Failures: [ERROR] PpktIndividualSpanishTest.testEvaluateExpression:45 Incorrect evaluation for: 46 year olf female, infantile onset ==> expected: but was: [ERROR] PpktIndividualSpanishTest.testEvaluateExpression:45 Incorrect evaluation for: male 4 months, congenital onset ==> expected: but was: [ERROR] PpktIndividualSpanishTest.testEvaluateExpression:45 Incorrect evaluation for: female, no onset ==> expected: but was: [ERROR] PpktIndividualSpanishTest.testEvaluateExpression:45 Incorrect evaluation for: unknown sex, no 4yo ==> expected: but was: [INFO] [ERROR] Tests run: 57, Failures: 4, Errors: 0, Skipped: 2 [INFO] [INFO] ------------------------------------------------------------------------ [INFO] BUILD FAILURE [INFO] ------------------------------------------------------------------------ [INFO] Total time: 1.580 s [INFO] Finished at: 2024-06-24T11:14:47-07:00 [INFO] ------------------------------------------------------------------------ [ERROR] Failed to execute goal org.apache.maven.plugins:maven-surefire-plugin:3.0.0-M5:test (default-test) on project phenopacket2prompt: There are test failures. [ERROR] [ERROR] Please refer to /Users/cjm/repos/phenopacket2prompt/target/surefire-reports for the individual test results. [ERROR] Please refer to dump files (if any exist) [date].dump, [date]-jvmRun[N].dump and [date].dumpstream. [ERROR] -> [Help 1] [ERROR] [ERROR] To see the full stack trace of the errors, re-run Maven with the -e switch. [ERROR] Re-run Maven using the -X switch to enable full debug logging. [ERROR] [ERROR] For more information about the errors and possible solutions, please read the following articles: [ERROR] [Help 1] http://cwiki.apache.org/confluence/display/MAVEN/MojoFailureException
pnrobinson commented 4 months ago

@cmungall we are still in a pre-alpha phase with this software, sorry for the crash. The issue with this error is that Nico made a few final updates to the format of the hp-international.obo file. The tests are working now. If you have previously downloaded files, please delete the "data" directory and re-run the "download" command, then things should work.