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Pyrophen generates a FHIR Code system representing the Human Phenotype Ontology

Home Page: https://pyrophen.readthedocs.io/en/latest/

License: GNU General Public License v3.0

Java 100.00%

hpo fhir-ig

pyrophen's Introduction

pyrophen

Pyrophen generates a FHIR Code system representing the Human Phenotype Ontology

See the documentation for more information.

pyrophen's People

Contributors

Stargazers

Watchers

Forkers

joeflack4 shahimessaid

pyrophen's Issues

CodeSystem properties should be declared

The "parent" property needs to be declared so its semantics can be applied by terminology servers that implement the property.

See:
https://hl7.org/fhir/R4/codesystem.html#properties
https://hl7.org/fhir/R4/codesystem-concept-properties.html

Will provide a PR.

New Feature: GitHub action for creating new release

Description

I think it would be pretty cool to:

1. Create a GitHub action to run the build and create a new release.
2. Set this to run on a regular schedule, ideally downloading the latest version of HPO to use as input.

update to phenol 2.0.0

Basically there would be minor changes but the input file would become hp.json

Generated CodeSystem contains codes other than HPO's

I'm just starting to look at pyrophen and noticed that the generated CodeSystem contains a lot of non-HPO codes. Is this intentional?

If not, I can try to have a PR that only includes HPO codes, and only HPO parent assertions.

Default JSON output has .xml file extension instead

Description

I built the .jar file, and then I ran:

java -jar target/pyrophen.jar --hpo ~/Desktop/hp.obo

The generated file was: hpo_fhir.xml

However, the format of this file is JSON (as expected).

Bug: Build issues: (i) failure on Java 17, (ii) issue w/ some `settings.xml`

Description

I cloned the project and tried to build via mvn package, but I get an error that appears to be related to how my ~/.m2/settings.xml is set up. @ShahimEssaid helped me fix that error, but now I'm getting an error when trying to build w/ Java 17 (docs say that 11+ is supported).

Sub-issue checklist

1. Java 17 incompatibility
2. Incompatibility w/ certain settings.xml setups

Issue 1: Java 17

Errors

[ERROR] Failed to execute goal org.springframework.experimental:spring-aot-maven-plugin:0.9.1:test-generate (test-generate) on project hpo-fhir-terminology: Build failed during Spring AOT test code generation: Unsupported class file major version 61 -> [Help 1]

Log:

mvn package
[INFO] Scanning for projects...
[INFO]
[INFO] -----------------< org.hpo.fhir:hpo-fhir-terminology >------------------
[INFO] Building hpo-fhir-terminology 0.0.3
[INFO] --------------------------------[ jar ]---------------------------------
[INFO]
[INFO] --- maven-resources-plugin:3.2.0:resources (default-resources) @ hpo-fhir-terminology ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Using 'UTF-8' encoding to copy filtered properties files.
[INFO] Copying 1 resource
[INFO] Copying 1 resource
[INFO]
[INFO] --- maven-compiler-plugin:3.8.1:compile (default-compile) @ hpo-fhir-terminology ---
[INFO] Nothing to compile - all classes are up to date
[INFO]
[INFO] --- maven-resources-plugin:3.2.0:testResources (default-testResources) @ hpo-fhir-terminology ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Using 'UTF-8' encoding to copy filtered properties files.
[INFO] Copying 1 resource
[INFO]
[INFO] --- maven-compiler-plugin:3.8.1:testCompile (default-testCompile) @ hpo-fhir-terminology ---
[INFO] Nothing to compile - all classes are up to date
[INFO]
[INFO] --- spring-aot-maven-plugin:0.9.1:test-generate (test-generate) @ hpo-fhir-terminology ---
[INFO] Spring Native operating mode: native
[ERROR] java.lang.IllegalArgumentException: Unsupported class file major version 61
[ERROR] [sbg.asm.ClassReader.<init>(ClassReader.java:189), sbg.asm.ClassReader.<init>(ClassReader.java:170), sbg.asm.ClassReader.<init>(ClassReader.java:156), org.springframework.nativex.type.TypeSystem.findType(TypeSystem.java:251), org.springframework.nativex.type.TypeSystem.resolveSlashed(TypeSystem.java:196), org.springframework.nativex.type.TypeSystem.resolveSlashed(TypeSystem.java:181), org.springframework.nativex.type.TypeSystem.resolveDotted(TypeSystem.java:151), org.springframework.nativex.type.TypeSystem.resolveDotted(TypeSystem.java:160), org.springframework.nativex.type.TypeSystem.resolveName(TypeSystem.java:155), org.springframework.nativex.type.Type.unpackTypeHint(Type.java:1820), org.springframework.nativex.type.Type.lambda$unpackNativeHint$21(Type.java:1707), org.springframework.nativex.type.Type.processHintList(Type.java:1737), org.springframework.nativex.type.Type.unpackNativeHint(Type.java:1707), org.springframework.nativex.type.Type.unpackNativeHints(Type.java:2075), org.springframework.nativex.type.Type.unpackHints(Type.java:1653), org.springframework.nativex.type.Type.getCompilationHints(Type.java:2099), org.springframework.nativex.type.SpringConfiguration.<init>(SpringConfiguration.java:58), org.springframework.nativex.type.TypeSystem.ensureSpringConfigurationDiscovered(TypeSystem.java:662), org.springframework.nativex.type.TypeSystem.getAccessCheckers(TypeSystem.java:1047), org.springframework.nativex.support.ReflectionHandler.addAccess(ReflectionHandler.java:135), org.springframework.nativex.support.ReflectionHandler.addAccess(ReflectionHandler.java:91), org.springframework.nativex.support.ReflectionHandler.register(ReflectionHandler.java:73), org.springframework.nativex.support.SpringAnalyzer.analyze(SpringAnalyzer.java:76), org.springframework.aot.nativex.ConfigurationContributor.contribute(ConfigurationContributor.java:51), org.springframework.aot.BootstrapCodeGenerator.generate(BootstrapCodeGenerator.java:74), org.springframework.aot.maven.TestGenerateMojo.execute(TestGenerateMojo.java:65), org.apache.maven.plugin.DefaultBuildPluginManager.executeMojo(DefaultBuildPluginManager.java:137), org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:210), org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:156), org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:148), org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject(LifecycleModuleBuilder.java:117), org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject(LifecycleModuleBuilder.java:81), org.apache.maven.lifecycle.internal.builder.singlethreaded.SingleThreadedBuilder.build(SingleThreadedBuilder.java:56), org.apache.maven.lifecycle.internal.LifecycleStarter.execute(LifecycleStarter.java:128), org.apache.maven.DefaultMaven.doExecute(DefaultMaven.java:305), org.apache.maven.DefaultMaven.doExecute(DefaultMaven.java:192), org.apache.maven.DefaultMaven.execute(DefaultMaven.java:105), org.apache.maven.cli.MavenCli.execute(MavenCli.java:972), org.apache.maven.cli.MavenCli.doMain(MavenCli.java:293), org.apache.maven.cli.MavenCli.main(MavenCli.java:196), java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method), java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77), java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43), java.base/java.lang.reflect.Method.invoke(Method.java:568), org.codehaus.plexus.classworlds.launcher.Launcher.launchEnhanced(Launcher.java:282), org.codehaus.plexus.classworlds.launcher.Launcher.launch(Launcher.java:225), org.codehaus.plexus.classworlds.launcher.Launcher.mainWithExitCode(Launcher.java:406), org.codehaus.plexus.classworlds.launcher.Launcher.main(Launcher.java:347)]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time:  1.608 s
[INFO] Finished at: 2022-02-10T18:06:59-05:00
[INFO] ------------------------------------------------------------------------
[ERROR] Failed to execute goal org.springframework.experimental:spring-aot-maven-plugin:0.9.1:test-generate (test-generate) on project hpo-fhir-terminology: Build failed during Spring AOT test code generation: Unsupported class file major version 61 -> [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

Causes

The cause was because I was running Java 17.

We determined this by looking at class numbers: https://stackoverflow.com/questions/9170832/list-of-java-class-file-format-major-version-numbers

Java 11 uses major version 55
Java 17 uses major version 61

After I installed and set Java 11 as my JAVA_HOME for the project, I got:
[INFO] BUILD SUCCESS :D

Possible solutions

As far as I can tell, the options are:
a. Update so that the project is compatible Java versions higher than 11.
b. Update the documentation to specifically require Java 11.

Issue 2: `settings.xml`

I have an ~/.m2/settings.xml that was causing problems for the build process, until I commented out the mirror section.

Errors

[ERROR] Plugin org.springframework.experimental:spring-aot-maven-plugin:0.9.1 or one of its dependencies could not be resolved: Could not find artifact org.springframework.experimental:spring-aot-maven-plugin:jar:0.9.1 in informatics (https://nexus.informatics.com/repository/komet/) -> [Help 1]

Here's the full log:

mvn package
[INFO] Scanning for projects...
Downloading from informatics: https://nexus.informatics.com/repository/komet/org/springframework/boot/spring-boot-starter-parent/2.4.4/spring-boot-starter-parent-2.4.4.pom
Downloaded from informatics: https://nexus.informatics.com/repository/komet/org/springframework/boot/spring-boot-starter-parent/2.4.4/spring-boot-starter-parent-2.4.4.pom (8.6 kB at 4.3 kB/s)
Downloading from informatics: https://nexus.informatics.com/repository/komet/org/springframework/boot/spring-boot-dependencies/2.4.4/spring-boot-dependencies-2.4.4.pom
Downloaded from informatics: https://nexus.informatics.com/repository/komet/org/springframework/boot/spring-boot-dependencies/2.4.4/spring-boot-dependencies-2.4.4.pom (108 kB at 101 kB/s)
Downloading from informatics: https://nexus.informatics.com/repository/komet/com/datastax/oss/java-driver-bom/4.9.0/java-driver-bom-4.9.0.pom
Downloaded from informatics: https://nexus.informatics.com/repository/komet/com/datastax/oss/java-driver-bom/4.9.0/java-driver-bom-4.9.0.pom (4.1 kB at 6.3 kB/s)
Downloading from informatics: https://nexus.informatics.com/repository/komet/io/dropwizard/metrics/metrics-bom/4.1.18/metrics-bom-4.1.18.pom
Downloaded from informatics: https://nexus.informatics.com/repository/komet/io/dropwizard/metrics/metrics-bom/4.1.18/metrics-bom-4.1.18.pom (5.3 kB at 8.3 kB/s)
Downloading from informatics: https://nexus.informatics.com/repository/komet/io/dropwizard/metrics/metrics-parent/4.1.18/metrics-parent-4.1.18.pom
Downloaded from informatics: https://nexus.informatics.com/repository/komet/io/dropwizard/metrics/metrics-parent/4.1.18/metrics-parent-4.1.18.pom (17 kB at 22 kB/s)
Downloading from informatics: https://nexus.informatics.com/repository/komet/org/codehaus/groovy/groovy-bom/2.5.14/groovy-bom-2.5.14.pom
Downloaded from informatics: https://nexus.informatics.com/repository/komet/org/codehaus/groovy/groovy-bom/2.5.14/groovy-bom-2.5.14.pom (26 kB at 36 kB/s)
Downloading from informatics: https://nexus.informatics.com/repository/komet/org/infinispan/infinispan-bom/11.0.10.Final/infinispan-bom-11.0.10.Final.pom
Downloaded from informatics: https://nexus.informatics.com/repository/komet/org/infinispan/infinispan-bom/11.0.10.Final/infinispan-bom-11.0.10.Final.pom (19 kB at 29 kB/s)
Downloading from informatics: https://nexus.informatics.com/repository/komet/org/infinispan/infinispan-build-configuration-parent/11.0.10.Final/infinispan-build-configuration-parent-11.0.10.Final.pom
Downloaded from informatics: https://nexus.informatics.com/repository/komet/org/infinispan/infinispan-build-configuration-parent/11.0.10.Final/infinispan-build-configuration-parent-11.0.10.Final.pom (13 kB at 22 kB/s)
Downloading from informatics: https://nexus.informatics.com/repository/komet/org/jboss/jboss-parent/36/jboss-parent-36.pom
Downloaded from informatics: https://nexus.informatics.com/repository/komet/org/jboss/jboss-parent/36/jboss-parent-36.pom (66 kB at 86 kB/s)
Downloading from informatics: https://nexus.informatics.com/repository/komet/com/fasterxml/jackson/jackson-bom/2.11.4/jackson-bom-2.11.4.pom
Downloaded from informatics: https://nexus.informatics.com/repository/komet/com/fasterxml/jackson/jackson-bom/2.11.4/jackson-bom-2.11.4.pom (0 B at 0 B/s)
Downloading from informatics: https://nexus.informatics.com/repository/komet/com/fasterxml/jackson/jackson-parent/2.11/jackson-parent-2.11.pom
Downloaded from informatics: https://nexus.informatics.com/repository/komet/com/fasterxml/jackson/jackson-parent/2.11/jackson-parent-2.11.pom (0 B at 0 B/s)
Downloading from informatics: https://nexus.informatics.com/repository/komet/org/glassfish/jersey/jersey-bom/2.32/jersey-bom-2.32.pom
Downloaded from informatics: https://nexus.informatics.com/repository/komet/org/glassfish/jersey/jersey-bom/2.32/jersey-bom-2.32.pom (19 kB at 30 kB/s)
Downloading from informatics: https://nexus.informatics.com/repository/komet/org/eclipse/jetty/jetty-bom/9.4.38.v20210224/jetty-bom-9.4.38.v20210224.pom
Downloaded from informatics: https://nexus.informatics.com/repository/komet/org/eclipse/jetty/jetty-bom/9.4.38.v20210224/jetty-bom-9.4.38.v20210224.pom (18 kB at 27 kB/s)
Downloading from informatics: https://nexus.informatics.com/repository/komet/org/jetbrains/kotlin/kotlin-bom/1.4.31/kotlin-bom-1.4.31.pom
Downloaded from informatics: https://nexus.informatics.com/repository/komet/org/jetbrains/kotlin/kotlin-bom/1.4.31/kotlin-bom-1.4.31.pom (9.3 kB at 15 kB/s)
Downloading from informatics: https://nexus.informatics.com/repository/komet/org/apache/logging/log4j/log4j-bom/2.13.3/log4j-bom-2.13.3.pom
Downloaded from informatics: https://nexus.informatics.com/repository/komet/org/apache/logging/log4j/log4j-bom/2.13.3/log4j-bom-2.13.3.pom (7.6 kB at 8.5 kB/s)
Downloading from informatics: https://nexus.informatics.com/repository/komet/io/micrometer/micrometer-bom/1.6.5/micrometer-bom-1.6.5.pom
Downloaded from informatics: https://nexus.informatics.com/repository/komet/io/micrometer/micrometer-bom/1.6.5/micrometer-bom-1.6.5.pom (6.8 kB at 8.2 kB/s)
Downloading from informatics: https://nexus.informatics.com/repository/komet/io/netty/netty-bom/4.1.60.Final/netty-bom-4.1.60.Final.pom
Downloaded from informatics: https://nexus.informatics.com/repository/komet/io/netty/netty-bom/4.1.60.Final/netty-bom-4.1.60.Final.pom (8.8 kB at 11 kB/s)
Downloading from informatics: https://nexus.informatics.com/repository/komet/com/oracle/database/jdbc/ojdbc-bom/19.8.0.0/ojdbc-bom-19.8.0.0.pom
Downloaded from informatics: https://nexus.informatics.com/repository/komet/com/oracle/database/jdbc/ojdbc-bom/19.8.0.0/ojdbc-bom-19.8.0.0.pom (12 kB at 18 kB/s)
Downloading from informatics: https://nexus.informatics.com/repository/komet/io/r2dbc/r2dbc-bom/Arabba-SR9/r2dbc-bom-Arabba-SR9.pom
Downloaded from informatics: https://nexus.informatics.com/repository/komet/io/r2dbc/r2dbc-bom/Arabba-SR9/r2dbc-bom-Arabba-SR9.pom (4.1 kB at 6.3 kB/s)
Downloading from informatics: https://nexus.informatics.com/repository/komet/io/projectreactor/reactor-bom/2020.0.5/reactor-bom-2020.0.5.pom
Downloaded from informatics: https://nexus.informatics.com/repository/komet/io/projectreactor/reactor-bom/2020.0.5/reactor-bom-2020.0.5.pom (4.5 kB at 7.4 kB/s)
Downloading from informatics: https://nexus.informatics.com/repository/komet/io/rsocket/rsocket-bom/1.1.0/rsocket-bom-1.1.0.pom
Downloaded from informatics: https://nexus.informatics.com/repository/komet/io/rsocket/rsocket-bom/1.1.0/rsocket-bom-1.1.0.pom (2.6 kB at 4.4 kB/s)
Downloading from informatics: https://nexus.informatics.com/repository/komet/org/springframework/data/spring-data-bom/2020.0.6/spring-data-bom-2020.0.6.pom
Downloaded from informatics: https://nexus.informatics.com/repository/komet/org/springframework/data/spring-data-bom/2020.0.6/spring-data-bom-2020.0.6.pom (5.9 kB at 9.5 kB/s)
Downloading from informatics: https://nexus.informatics.com/repository/komet/org/springframework/spring-framework-bom/5.3.5/spring-framework-bom-5.3.5.pom
Downloaded from informatics: https://nexus.informatics.com/repository/komet/org/springframework/spring-framework-bom/5.3.5/spring-framework-bom-5.3.5.pom (5.6 kB at 9.2 kB/s)
Downloading from informatics: https://nexus.informatics.com/repository/komet/org/springframework/integration/spring-integration-bom/5.4.5/spring-integration-bom-5.4.5.pom
Downloaded from informatics: https://nexus.informatics.com/repository/komet/org/springframework/integration/spring-integration-bom/5.4.5/spring-integration-bom-5.4.5.pom (9.5 kB at 15 kB/s)
Downloading from informatics: https://nexus.informatics.com/repository/komet/org/springframework/security/spring-security-bom/5.4.5/spring-security-bom-5.4.5.pom
Downloaded from informatics: https://nexus.informatics.com/repository/komet/org/springframework/security/spring-security-bom/5.4.5/spring-security-bom-5.4.5.pom (5.3 kB at 8.2 kB/s)
Downloading from informatics: https://nexus.informatics.com/repository/komet/org/springframework/session/spring-session-bom/2020.0.3/spring-session-bom-2020.0.3.pom
Downloaded from informatics: https://nexus.informatics.com/repository/komet/org/springframework/session/spring-session-bom/2020.0.3/spring-session-bom-2020.0.3.pom (2.7 kB at 4.0 kB/s)
[INFO]
[INFO] -----------------< org.hpo.fhir:hpo-fhir-terminology >------------------
[INFO] Building hpo-fhir-terminology 0.0.3
[INFO] --------------------------------[ jar ]---------------------------------
Downloading from informatics: https://nexus.informatics.com/repository/komet/org/springframework/boot/spring-boot-maven-plugin/2.4.4/spring-boot-maven-plugin-2.4.4.pom
Downloaded from informatics: https://nexus.informatics.com/repository/komet/org/springframework/boot/spring-boot-maven-plugin/2.4.4/spring-boot-maven-plugin-2.4.4.pom (2.9 kB at 4.7 kB/s)
Downloading from informatics: https://nexus.informatics.com/repository/komet/org/springframework/boot/spring-boot-maven-plugin/2.4.4/spring-boot-maven-plugin-2.4.4.jar
Downloaded from informatics: https://nexus.informatics.com/repository/komet/org/springframework/boot/spring-boot-maven-plugin/2.4.4/spring-boot-maven-plugin-2.4.4.jar (101 kB at 147 kB/s)
Downloading from informatics: https://nexus.informatics.com/repository/komet/org/springframework/experimental/spring-aot-maven-plugin/0.9.1/spring-aot-maven-plugin-0.9.1.pom
[WARNING] The POM for org.springframework.experimental:spring-aot-maven-plugin:jar:0.9.1 is missing, no dependency information available
Downloading from informatics: https://nexus.informatics.com/repository/komet/org/springframework/experimental/spring-aot-maven-plugin/0.9.1/spring-aot-maven-plugin-0.9.1.jar
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time:  42.248 s
[INFO] Finished at: 2022-02-10T15:24:15-05:00
[INFO] ------------------------------------------------------------------------
[ERROR] Plugin org.springframework.experimental:spring-aot-maven-plugin:0.9.1 or one of its dependencies could not be resolved: Could not find artifact org.springframework.experimental:spring-aot-maven-plugin:jar:0.9.1 in informatics (https://nexus.informatics.com/repository/komet/) -> [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/PluginResolutionException

Additional information

I am not the best at Java. I'm surprised that it's trying to pull from the 'komet' repository. It's in my settings.xml, but why are repositories in my settings.xml being used instead of what's defined in the Pyrophen pom.xml?

~/.m2/settings.xml:

<?xml version="1.0" encoding="UTF-8"?>
<settings xsi:schemaLocation="http://maven.apache.org/SETTINGS/1.1.0 http://maven.apache.org/xsd/settings-1.1.0.xsd"
          xmlns="http://maven.apache.org/SETTINGS/1.1.0"
          xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
    <offline>false</offline>
    <mirrors>
        <mirror>
            <!--This sends everything else to /public -->
            <id>informatics</id>
            <mirrorOf>*</mirrorOf>
            <url>https://nexus.informatics.com/repository/komet/</url>
        </mirror>
    </mirrors>
    <servers>
        <server>
            <username>jflack</username>
            <password>REDACTED</password>
            <id>informatics</id>
        </server>
        <server>
            <username>jflack</username>
            <password>REDACTED</password>
            <id>snapshots</id>
        </server>
     </servers>
    <profiles>
         <profile>
            <repositories>
                <repository>
                    <snapshots>
                        <enabled>false</enabled>
                    </snapshots>
                    <id>informatics</id>
                    <name>libs-release</name>
                    <url>https://nexus.informatics.com/repository/komet/</url>
                </repository>
                <repository>
                    <snapshots />
                    <id>snapshots</id>
                    <name>libs-snapshot</name>
                    <url>https://nexus.informatics.com/repository/komet-snapshot/</url>
                </repository>
            </repositories>
            <pluginRepositories>
                <pluginRepository>
                    <snapshots>
                        <enabled>false</enabled>
                    </snapshots>
                    <id>informatics</id>
                    <name>plugins-release</name>
                    <url>https://nexus.informatics.com/repository/komet/</url>
                </pluginRepository>
                <pluginRepository>
                    <snapshots />
                    <id>snapshots</id>
                    <name>plugins-snapshot</name>
                    <url>https://nexus.informatics.com/repository/komet-snapshot/</url>
                </pluginRepository>
            </pluginRepositories>
            <id>nexus</id>
        </profile>
        <profile>
            <id>release-deploy</id>
            <properties>
                <altDeploymentRepository>informatics::default::https://nexus.informatics.com/repository/komet-release/</altDeploymentRepository>
            </properties>
        </profile>
        <profile>
            <id>snapshot-deploy</id>
            <properties>
                <altDeploymentRepository>informatics::default::https://nexus.informatics.com/repository/komet-snapshot/</altDeploymentRepository>
            </properties>
        </profile>
        <profile>
            <id>plugins</id>
            <properties>
                <plugins>true</plugins>
            </properties>
        </profile>
    </profiles>
    <activeProfiles>
        <activeProfile>snapshot-deploy</activeProfile>
        <activeProfile>nexus</activeProfile>
    </activeProfiles>

</settings>

I see that pom.xml appears to have what is needed, but I suppose it seems to be overridden by the settings.xml. We also tried adding the maven central repository to it, but that didn't help:

    <repositories>
        <repository>
            <snapshots>
                <enabled>false</enabled>
            </snapshots>
            <id>central</id>
            <name>Central Repository</name>
            <url>https://repo.maven.apache.org/maven2</url>
        </repository>
        <repository>
            <id>spring-releases</id>
            <name>Spring Releases</name>
            <url>https://repo.spring.io/release</url>
        </repository>
    </repositories>
    <pluginRepositories>
        <pluginRepository>
            <id>spring-releases</id>
            <name>Spring Releases</name>
            <url>https://repo.spring.io/release</url>
        </pluginRepository>
    </pluginRepositories>

One article I read (Shahim agreed) even said that it is not a good practice to put repositories or pluginRepositories in pom.xml: https://blog.sonatype.com/2009/02/why-putting-repositories-in-your-poms-is-a-bad-idea/

Solution

We commented out the following in settings.xml, which fixed the problem:

        <mirror>
            <id>informatics</id>
            <mirrorOf>*</mirrorOf>
            <url>https://nexus.informatics.com/repository/komet/</url>
        </mirror>

However, I've decided to leave this open, because I am wondering if there is some way to work around whatever settings.xml someone has set up. I could be wrong though, in which case I should consider this problem solved.

set release in the metadata

What is the best way of setting the release?

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monarch-initiative / pyrophen Goto Github PK

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Issue 1: Java 17

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Issue 2: settings.xml

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Issue 2: `settings.xml`