warning not error on code system fragment
This commit is contained in:
Grahame Grieve
parent
b256965738
commit
62b70947b8
155
README.md
155
README.md
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# HAPI FHIR - HL7 FHIR Core Artifacts
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| CI Status (master) |
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| :---: |
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| [![Build Status][Badge-BuildPipeline]][Link-BuildPipeline] |
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### CI/CD
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All intergration and delivery done on Azure pipelines. Azure project can be viewed [here][Link-AzureProject].
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### Current Versions
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| Project | Current Release | Latest SNAPSHOT |
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| :---: | :---: | :---: |
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| org.hl7.fhir.validation.cli | [![Release Artifacts][Badge-r4SonatypeRelease]][Link-cliSonatypeRelease] | [![Snapshot Artifact][Badge-cliSonatypeSnapshot]][Link-cliSonatypeSnapshot] |
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| org.hl7.fhir.validation | [![Release Artifacts][Badge-validationSonatypeRelease]][Link-validationSonatypeRelease] | [![Snapshot Artifact][Badge-validationSonatypeSnapshot]][Link-validationSonatypeSnapshot] |
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| org.hl7.fhir.dstu2 | [![Release Artifacts][Badge-dstu2SonatypeRelease]][Link-dstu2SonatypeRelease] | [![Snapshot Artifact][Badge-dstu2SonatypeSnapshot]][Link-dstu2SonatypeSnapshot] |
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| org.hl7.fhir.dstu2016may | [![Release Artifacts][Badge-dstu2016maySonatypeRelease]][Link-dstu2016maySonatypeRelease] | [![Snapshot Artifact][Badge-dstu2016maySonatypeSnapshot]][Link-dstu2016maySonatypeSnapshot] |
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| org.hl7.fhir.dstu3 | [![Release Artifacts][Badge-dstu3SonatypeRelease]][Link-dstu3SonatypeRelease] | [![Snapshot Artifact][Badge-dstu3SonatypeSnapshot]][Link-dstu3SonatypeSnapshot] |
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| org.hl7.fhir.r4 | [![Release Artifacts][Badge-r4SonatypeRelease]][Link-r4SonatypeRelease] | [![Snapshot Artifact][Badge-r4SonatypeSnapshot]][Link-r4SonatypeSnapshot] |
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| org.hl7.fhir.r5 | [![Release Artifacts][Badge-r5SonatypeRelease]][Link-r5SonatypeRelease] | [![Snapshot Artifact][Badge-r5SonatypeSnapshot]][Link-r5SonatypeSnapshot] |
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### Building this Project
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This project uses [Apache Maven](http://maven.apache.org) to build. To build:
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```
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mvn install
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```
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Note that unit tests will run, but are currently not set to fail the build as they do not all pass. This is being worked on.
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To skip unit tests:
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```
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mvn -Dmaven.test.skip install
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```
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### Publishing Binaries
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An brief overview of our publishing process is [here][Link-Publishing].
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For more detailed instructions on cutting a release, please read [the wiki][Link-PublishingRelease]
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### Download
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##### org.hl7.fhir.validation.cli
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###### Maven
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```xml
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<dependency>
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<groupId>ca.uhn.hapi.fhir</groupId>
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<artifactId>org.hl7.fhir.validation.cli</artifactId>
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<version>(latest version)</version>
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</dependency>
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```
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###### Gradle
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```groovy
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compile group: 'ca.uhn.hapi.fhir', name: 'org.hl7.fhir.validation.cli', version: '(latest version)'
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```
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##### org.hl7.fhir.dstu2
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###### Maven
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```xml
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<dependency>
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<groupId>ca.uhn.hapi.fhir</groupId>
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<artifactId>hapi-fhir-structures-dstu2</artifactId>
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<version>(latest version)</version>
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</dependency>
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```
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###### Gradle
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```groovy
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compile group: 'ca.uhn.hapi.fhir', name: 'hapi-fhir-structures-dstu2', version: '(latest version)'
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```
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##### org.hl7.fhir.dstu3
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###### Maven
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```xml
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<dependency>
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<groupId>ca.uhn.hapi.fhir</groupId>
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<artifactId>hapi-fhir-structures-dstu3</artifactId>
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<version>(latest version)</version>
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</dependency>
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```
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###### Gradle
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```groovy
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compile group: 'ca.uhn.hapi.fhir', name: 'hapi-fhir-structures-dstu3', version: '(latest version)'
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```
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##### org.hl7.fhir.r4
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###### Maven
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```xml
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<dependency>
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<groupId>ca.uhn.hapi.fhir</groupId>
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<artifactId>hapi-fhir-structures-r4</artifactId>
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<version>(latest version)</version>
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</dependency>
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```
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###### Gradle
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```groovy
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compile group: 'ca.uhn.hapi.fhir', name: 'hapi-fhir-structures-r4', version: '(latest version)'
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```
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##### org.hl7.fhir.r5
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###### Maven
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```xml
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<dependency>
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<groupId>ca.uhn.hapi.fhir</groupId>
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<artifactId>hapi-fhir-structures-r5</artifactId>
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<version>(latest version)</version>
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</dependency>
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```
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###### Gradle
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```groovy
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compile group: 'ca.uhn.hapi.fhir', name: 'hapi-fhir-structures-r5', version: '(latest version)'
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```
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### Maintenance
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This project is maintained by [Grahame Grieve][Link-grahameGithub] and [James Agnew][Link-jamesGithub] on behalf of the FHIR community.
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[Link-AzureProject]: https://dev.azure.com/fhir-pipelines/fhir-core-library
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[Link-BuildPipeline]: https://dev.azure.com/fhir-pipelines/fhir-core-library/_build/latest?definitionId=29&branchName=master
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[Link-SnapshotPipeline]: https://dev.azure.com/fhir-pipelines/fhir-core-library/_build/latest?definitionId=17&branchName=master
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[Link-dstu2SonatypeSnapshot]: https://oss.sonatype.org/service/local/artifact/maven/redirect?r=snapshots&g=ca.uhn.hapi.fhir&a=org.hl7.fhir.dstu2&v=LATEST "Sonatype Snapshot"
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[Link-dstu2SonatypeRelease]: https://oss.sonatype.org/service/local/artifact/maven/redirect?r=releases&g=ca.uhn.hapi.fhir&a=org.hl7.fhir.dstu2&v=LATEST "Sonatype Release"
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[Link-dstu2016maySonatypeSnapshot]: https://oss.sonatype.org/service/local/artifact/maven/redirect?r=snapshots&g=ca.uhn.hapi.fhir&a=org.hl7.fhir.dstu2016may&v=LATEST "Sonatype Snapshot"
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[Link-dstu2016maySonatypeRelease]: https://oss.sonatype.org/service/local/artifact/maven/redirect?r=releases&g=ca.uhn.hapi.fhir&a=org.hl7.fhir.dstu2016may&v=LATEST "Sonatype Release"
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[Link-dstu3SonatypeSnapshot]: https://oss.sonatype.org/service/local/artifact/maven/redirect?r=snapshots&g=ca.uhn.hapi.fhir&a=org.hl7.fhir.dstu3&v=LATEST "Sonatype Snapshot"
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[Link-dstu3SonatypeRelease]: https://oss.sonatype.org/service/local/artifact/maven/redirect?r=releases&g=ca.uhn.hapi.fhir&a=org.hl7.fhir.dstu3&v=LATEST "Sonatype Release"
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[Link-r4SonatypeSnapshot]: https://oss.sonatype.org/service/local/artifact/maven/redirect?r=snapshots&g=ca.uhn.hapi.fhir&a=org.hl7.fhir.r4&v=LATEST "Sonatype Snapshot"
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[Link-r4SonatypeRelease]: https://oss.sonatype.org/service/local/artifact/maven/redirect?r=releases&g=ca.uhn.hapi.fhir&a=org.hl7.fhir.r4&v=LATEST "Sonatype Release"
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[Link-r5SonatypeSnapshot]: https://oss.sonatype.org/service/local/artifact/maven/redirect?r=snapshots&g=ca.uhn.hapi.fhir&a=org.hl7.fhir.r5&v=LATEST "Sonatype Snapshot"
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[Link-r5SonatypeRelease]: https://oss.sonatype.org/service/local/artifact/maven/redirect?r=releases&g=ca.uhn.hapi.fhir&a=org.hl7.fhir.r5&v=LATEST "Sonatype Release"
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[Link-cliSonatypeSnapshot]: https://oss.sonatype.org/service/local/artifact/maven/redirect?r=snapshots&g=ca.uhn.hapi.fhir&a=org.hl7.fhir.validation.cli&v=LATEST "Sonatype Snapshot"
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[Link-cliSonatypeRelease]: https://github.com/hapifhir/org.hl7.fhir.core/releases/latest/download/validator_cli.jar
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[Link-validationSonatypeSnapshot]: https://oss.sonatype.org/service/local/artifact/maven/redirect?r=snapshots&g=ca.uhn.hapi.fhir&a=org.hl7.fhir.validation&v=LATEST "Sonatype Snapshot"
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[Link-validationSonatypeRelease]: https://oss.sonatype.org/service/local/artifact/maven/redirect?r=releases&g=ca.uhn.hapi.fhir&a=org.hl7.fhir.validation&v=LATEST "Sonatype Release"
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[Link-grahameGithub]: https://github.com/grahamegrieve
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[Link-jamesGithub]: https://github.com/jamesagnew
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[Link-Publishing]: https://github.com/FHIR/fhir-test-cases/wiki/Publishing-Binaries
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[Link-PublishingRelease]: https://github.com/FHIR/fhir-test-cases/wiki/Detailed-Release-Instructions
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[Badge-BuildPipeline]: https://dev.azure.com/fhir-pipelines/fhir-core-library/_apis/build/status/Master%20Branch%20Pipeline?branchName=master
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[Badge-SnapshotPipeline]: https://dev.azure.com/fhir-pipelines/fhir-core-library/_apis/build/status/Module%20SNAPSHOT%20Publisher?branchName=master
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[Badge-dstu2SonatypeRelease]: https://img.shields.io/nexus/r/https/oss.sonatype.org/ca.uhn.hapi.fhir/org.hl7.fhir.dstu2.svg "Sonatype Releases"
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[Badge-dstu2SonatypeSnapshot]: https://img.shields.io/nexus/s/https/oss.sonatype.org/ca.uhn.hapi.fhir/org.hl7.fhir.dstu2.svg "Sonatype Snapshots"
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[Badge-dstu2016maySonatypeRelease]: https://img.shields.io/nexus/r/https/oss.sonatype.org/ca.uhn.hapi.fhir/org.hl7.fhir.dstu2016may.svg "Sonatype Releases"
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[Badge-dstu2016maySonatypeSnapshot]: https://img.shields.io/nexus/s/https/oss.sonatype.org/ca.uhn.hapi.fhir/org.hl7.fhir.dstu2016may.svg "Sonatype Snapshots"
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[Badge-dstu3SonatypeRelease]: https://img.shields.io/nexus/r/https/oss.sonatype.org/ca.uhn.hapi.fhir/org.hl7.fhir.dstu3.svg "Sonatype Releases"
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[Badge-dstu3SonatypeSnapshot]: https://img.shields.io/nexus/s/https/oss.sonatype.org/ca.uhn.hapi.fhir/org.hl7.fhir.dstu3.svg "Sonatype Snapshots"
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[Badge-r4SonatypeRelease]: https://img.shields.io/nexus/r/https/oss.sonatype.org/ca.uhn.hapi.fhir/org.hl7.fhir.r4.svg "Sonatype Releases"
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[Badge-r4SonatypeSnapshot]: https://img.shields.io/nexus/s/https/oss.sonatype.org/ca.uhn.hapi.fhir/org.hl7.fhir.r4.svg "Sonatype Snapshots"
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[Badge-r5SonatypeRelease]: https://img.shields.io/nexus/r/https/oss.sonatype.org/ca.uhn.hapi.fhir/org.hl7.fhir.r5.svg "Sonatype Releases"
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[Badge-r5SonatypeSnapshot]: https://img.shields.io/nexus/s/https/oss.sonatype.org/ca.uhn.hapi.fhir/org.hl7.fhir.r5.svg "Sonatype Snapshots"
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[Badge-cliSonatypeRelease]: https://img.shields.io/nexus/r/https/oss.sonatype.org/ca.uhn.hapi.fhir/org.hl7.fhir.validation.cli.svg "Sonatype Releases"
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[Badge-cliSonatypeSnapshot]: https://img.shields.io/nexus/s/https/oss.sonatype.org/ca.uhn.hapi.fhir/org.hl7.fhir.validation.cli.svg "Sonatype Snapshots"
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[Badge-validationSonatypeRelease]: https://img.shields.io/nexus/r/https/oss.sonatype.org/ca.uhn.hapi.fhir/org.hl7.fhir.validation.svg "Sonatype Releases"
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[Badge-validationSonatypeSnapshot]: https://img.shields.io/nexus/s/https/oss.sonatype.org/ca.uhn.hapi.fhir/org.hl7.fhir.validation.svg "Sonatype Snapshots"
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@ -67,7 +67,6 @@ public class ComparisonRenderer implements IEvaluationContext {
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b.append("</table>\r\n");
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Map<String, Base> vars = new HashMap<>();
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CodeSystemComparer cs = new CodeSystemComparer(session);
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vars.put("title", new StringType(session.getTitle()));
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vars.put("list", new StringType(b.toString()));
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String template = templates.get("Index");
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@ -147,8 +146,8 @@ public class ComparisonRenderer implements IEvaluationContext {
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vars.put("concepts", new StringType(new XhtmlComposer(true).compose(cs.renderConcepts(comp, "", ""))));
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String cnt = processTemplate(template, "CodeSystem", vars);
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TextFile.stringToFile(cnt, file(comp.getId()+".html"));
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new org.hl7.fhir.r5.formats.JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path("[tmp]", "comparison", comp.getId() + "-union.json")), comp.getUnion());
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new org.hl7.fhir.r5.formats.JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path("[tmp]", "comparison", comp.getId() + "-intersection.json")), comp.getIntersection());
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new org.hl7.fhir.r5.formats.JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path(folder, "comparison", comp.getId() + "-union.json")), comp.getUnion());
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new org.hl7.fhir.r5.formats.JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path(folder, "comparison", comp.getId() + "-intersection.json")), comp.getIntersection());
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}
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private String file(String name) throws IOException {
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vars.put("expansion", new StringType(new XhtmlComposer(true).compose(cs.renderExpansion(comp, "", ""))));
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String cnt = processTemplate(template, "ValueSet", vars);
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TextFile.stringToFile(cnt, file(comp.getId()+".html"));
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new org.hl7.fhir.r5.formats.JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path("[tmp]", "comparison", comp.getId() + "-union.json")), comp.getUnion());
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new org.hl7.fhir.r5.formats.JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path("[tmp]", "comparison", comp.getId() + "-intersection.json")), comp.getIntersection());
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new org.hl7.fhir.r5.formats.JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path(folder, "comparison", comp.getId() + "-union.json")), comp.getUnion());
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new org.hl7.fhir.r5.formats.JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path(folder, "comparison", comp.getId() + "-intersection.json")), comp.getIntersection());
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}
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private void renderProfile(String id, ProfileComparison comp) throws IOException {
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vars.put("structure", new StringType(new XhtmlComposer(true).compose(cs.renderStructure(comp, "", "", "http://hl7.org/fhir"))));
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String cnt = processTemplate(template, "CodeSystem", vars);
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TextFile.stringToFile(cnt, file(comp.getId()+".html"));
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new org.hl7.fhir.r5.formats.JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path("[tmp]", "comparison", comp.getId() + "-union.json")), comp.getUnion());
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new org.hl7.fhir.r5.formats.JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path("[tmp]", "comparison", comp.getId() + "-intersection.json")), comp.getIntersection());
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new org.hl7.fhir.r5.formats.JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path(folder, "comparison", comp.getId() + "-union.json")), comp.getUnion());
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new org.hl7.fhir.r5.formats.JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path(folder, "comparison", comp.getId() + "-intersection.json")), comp.getIntersection());
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}
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private String processTemplate(String template, String name, Map<String, Base> vars) {
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@ -224,7 +224,7 @@ public class ValueSetCheckerSimple implements ValueSetChecker {
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ConceptDefinitionComponent cc = cs.hasUserData("tx.cs.special") ? ((SpecialCodeSystem) cs.getUserData("tx.cs.special")).findConcept(code) : findCodeInConcept(cs.getConcept(), code.getCode());
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if (cc == null) {
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if (cs.getContent() == CodeSystemContentMode.FRAGMENT) {
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return new ValidationResult(IssueSeverity.ERROR, context.formatMessage(I18nConstants.UNKNOWN_CODE__IN_FRAGMENT, gen(code), cs.getUrl()));
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return new ValidationResult(IssueSeverity.WARNING, context.formatMessage(I18nConstants.UNKNOWN_CODE__IN_FRAGMENT, gen(code), cs.getUrl()));
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} else {
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return new ValidationResult(IssueSeverity.ERROR, context.formatMessage(I18nConstants.UNKNOWN_CODE__IN_, gen(code), cs.getUrl()));
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}
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46
release.bat
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release.bat
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@echo off
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set oldver=5.0.6
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set newver=5.0.7
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echo ..
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echo =========================================================================
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echo upgrade and release fhir.core from %oldver%-SNAPSHOT to %newver%-SNAPSHOT
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echo =========================================================================
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echo ..
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call mvn versions:set -DnewVersion=%newver%-SNAPSHOT
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call "C:\tools\fnr.exe" -dir "C:\work\org.hl7.fhir\build" -fileMask "*.xml" -find "%oldver%-SNAPSHOT" -replace "%newver%-SNAPSHOT" -count 8
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call "C:\tools\fnr.exe" -dir "C:\work\org.hl7.fhir\fhir-ig-publisher" -fileMask "*.xml" -find "%oldver%-SNAPSHOT" -replace "%newver%-SNAPSHOT" -count 2
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call "C:\tools\fnr.exe" -dir "C:\work\org.hl7.fhir\latest-ig-publisher" -fileMask "*.html" -find "%oldver%" -replace "%newver%" -count 1
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call "C:\tools\fnr.exe" -dir "C:\work\org.hl7.fhir\latest-ig-publisher" -fileMask "*.json" -find "%oldver%" -replace "%newver%" -count 1
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call mvn clean deploy -Dmaven.test.redirectTestOutputToFile=false -DdeployAtEnd=true
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IF %ERRORLEVEL% NEQ 0 (
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GOTO DONE
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)
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call "C:\tools\versionNotes.exe" -fileName C:\work\org.hl7.fhir\org.hl7.fhir.core\release-notes-validator.md -version %newver% -fileDest C:\temp\current-release-notes-validator.md -url https://storage.googleapis.com/ig-build/org.hl7.fhir.validator.jar -maven https://oss.sonatype.org/service/local/artifact/maven/redirect?r=snapshots&g=ca.uhn.hapi.fhir&a=org.hl7.fhir.validation.cli&v=%newver%-SNAPSHOT&e=jar
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call git commit -t v%newver% -a -m "Release new version %newver%"
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call git tag v%newver%
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call git push origin master
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call gsutil cp -a public-read org.hl7.fhir.validation.cli\target\org.hl7.fhir.validation.cli-%newver%-SNAPSHOT.jar gs://ig-build/org.hl7.fhir.validator.jar
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cd ..\latest-ig-publisher
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call git commit -a -m "Release new validator version %newver%-SNAPSHOT"
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call git push origin master
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cd ..\org.hl7.fhir.core
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call python c:\tools\zulip-api\zulip\zulip\send.py --stream committers/notification --subject "java core" -m "New Java Core v%newver%-SNAPSHOT released. New Validator at https://oss.sonatype.org/service/local/artifact/maven/redirect?r=snapshots&g=ca.uhn.hapi.fhir&a=org.hl7.fhir.validation.cli&v=%newver%-SNAPSHOT&e=jar, and also deployed at https://storage.googleapis.com/ig-build/org.hl7.fhir.validator.jar" --config-file zuliprc
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call python c:\tools\zulip-api\zulip\zulip\send.py --stream tooling/releases --subject "Validator" --config-file zuliprc < C:\temp\current-release-notes-validator.md
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del C:\temp\current-release-notes-validator.md
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:DONE
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echo ===============================================================
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echo all done
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echo ===============================================================
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pause
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