Merge pull request #285 from hapifhir/gg-v5016-work

fix evaluation of codes in code systems that are labelled content = fragment
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Grahame Grieve 2020-07-28 13:35:14 +10:00 committed by GitHub
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7 changed files with 17 additions and 216 deletions

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README.md
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# HAPI FHIR - HL7 FHIR Core Artifacts
| CI Status (master) |
| :---: |
| [![Build Status][Badge-BuildPipeline]][Link-BuildPipeline] |
### CI/CD
All intergration and delivery done on Azure pipelines. Azure project can be viewed [here][Link-AzureProject].
### Current Versions
| Project | Current Release | Latest SNAPSHOT |
| :---: | :---: | :---: |
| org.hl7.fhir.validation.cli | [![Release Artifacts][Badge-r4SonatypeRelease]][Link-cliSonatypeRelease] | [![Snapshot Artifact][Badge-cliSonatypeSnapshot]][Link-cliSonatypeSnapshot] |
| org.hl7.fhir.validation | [![Release Artifacts][Badge-validationSonatypeRelease]][Link-validationSonatypeRelease] | [![Snapshot Artifact][Badge-validationSonatypeSnapshot]][Link-validationSonatypeSnapshot] |
| org.hl7.fhir.dstu2 | [![Release Artifacts][Badge-dstu2SonatypeRelease]][Link-dstu2SonatypeRelease] | [![Snapshot Artifact][Badge-dstu2SonatypeSnapshot]][Link-dstu2SonatypeSnapshot] |
| org.hl7.fhir.dstu2016may | [![Release Artifacts][Badge-dstu2016maySonatypeRelease]][Link-dstu2016maySonatypeRelease] | [![Snapshot Artifact][Badge-dstu2016maySonatypeSnapshot]][Link-dstu2016maySonatypeSnapshot] |
| org.hl7.fhir.dstu3 | [![Release Artifacts][Badge-dstu3SonatypeRelease]][Link-dstu3SonatypeRelease] | [![Snapshot Artifact][Badge-dstu3SonatypeSnapshot]][Link-dstu3SonatypeSnapshot] |
| org.hl7.fhir.r4 | [![Release Artifacts][Badge-r4SonatypeRelease]][Link-r4SonatypeRelease] | [![Snapshot Artifact][Badge-r4SonatypeSnapshot]][Link-r4SonatypeSnapshot] |
| org.hl7.fhir.r5 | [![Release Artifacts][Badge-r5SonatypeRelease]][Link-r5SonatypeRelease] | [![Snapshot Artifact][Badge-r5SonatypeSnapshot]][Link-r5SonatypeSnapshot] |
### Building this Project
This project uses [Apache Maven](http://maven.apache.org) to build. To build:
```
mvn install
```
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.
To skip unit tests:
```
mvn -Dmaven.test.skip install
```
### Publishing Binaries
An brief overview of our publishing process is [here][Link-Publishing].
For more detailed instructions on cutting a release, please read [the wiki][Link-PublishingRelease]
### Download
##### org.hl7.fhir.validation.cli
###### Maven
```xml
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>org.hl7.fhir.validation.cli</artifactId>
<version>(latest version)</version>
</dependency>
```
###### Gradle
```groovy
compile group: 'ca.uhn.hapi.fhir', name: 'org.hl7.fhir.validation.cli', version: '(latest version)'
```
##### org.hl7.fhir.dstu2
###### Maven
```xml
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-structures-dstu2</artifactId>
<version>(latest version)</version>
</dependency>
```
###### Gradle
```groovy
compile group: 'ca.uhn.hapi.fhir', name: 'hapi-fhir-structures-dstu2', version: '(latest version)'
```
##### org.hl7.fhir.dstu3
###### Maven
```xml
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-structures-dstu3</artifactId>
<version>(latest version)</version>
</dependency>
```
###### Gradle
```groovy
compile group: 'ca.uhn.hapi.fhir', name: 'hapi-fhir-structures-dstu3', version: '(latest version)'
```
##### org.hl7.fhir.r4
###### Maven
```xml
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-structures-r4</artifactId>
<version>(latest version)</version>
</dependency>
```
###### Gradle
```groovy
compile group: 'ca.uhn.hapi.fhir', name: 'hapi-fhir-structures-r4', version: '(latest version)'
```
##### org.hl7.fhir.r5
###### Maven
```xml
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-structures-r5</artifactId>
<version>(latest version)</version>
</dependency>
```
###### Gradle
```groovy
compile group: 'ca.uhn.hapi.fhir', name: 'hapi-fhir-structures-r5', version: '(latest version)'
```
### Maintenance
This project is maintained by [Grahame Grieve][Link-grahameGithub] and [James Agnew][Link-jamesGithub] on behalf of the FHIR community.
[Link-AzureProject]: https://dev.azure.com/fhir-pipelines/fhir-core-library
[Link-BuildPipeline]: https://dev.azure.com/fhir-pipelines/fhir-core-library/_build/latest?definitionId=29&branchName=master
[Link-SnapshotPipeline]: https://dev.azure.com/fhir-pipelines/fhir-core-library/_build/latest?definitionId=17&branchName=master
[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"
[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"
[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"
[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"
[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"
[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"
[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"
[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"
[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"
[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"
[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"
[Link-cliSonatypeRelease]: https://github.com/hapifhir/org.hl7.fhir.core/releases/latest/download/validator_cli.jar
[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"
[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"
[Link-grahameGithub]: https://github.com/grahamegrieve
[Link-jamesGithub]: https://github.com/jamesagnew
[Link-Publishing]: https://github.com/FHIR/fhir-test-cases/wiki/Publishing-Binaries
[Link-PublishingRelease]: https://github.com/FHIR/fhir-test-cases/wiki/Detailed-Release-Instructions
[Badge-BuildPipeline]: https://dev.azure.com/fhir-pipelines/fhir-core-library/_apis/build/status/Master%20Branch%20Pipeline?branchName=master
[Badge-SnapshotPipeline]: https://dev.azure.com/fhir-pipelines/fhir-core-library/_apis/build/status/Module%20SNAPSHOT%20Publisher?branchName=master
[Badge-dstu2SonatypeRelease]: https://img.shields.io/nexus/r/https/oss.sonatype.org/ca.uhn.hapi.fhir/org.hl7.fhir.dstu2.svg "Sonatype Releases"
[Badge-dstu2SonatypeSnapshot]: https://img.shields.io/nexus/s/https/oss.sonatype.org/ca.uhn.hapi.fhir/org.hl7.fhir.dstu2.svg "Sonatype Snapshots"
[Badge-dstu2016maySonatypeRelease]: https://img.shields.io/nexus/r/https/oss.sonatype.org/ca.uhn.hapi.fhir/org.hl7.fhir.dstu2016may.svg "Sonatype Releases"
[Badge-dstu2016maySonatypeSnapshot]: https://img.shields.io/nexus/s/https/oss.sonatype.org/ca.uhn.hapi.fhir/org.hl7.fhir.dstu2016may.svg "Sonatype Snapshots"
[Badge-dstu3SonatypeRelease]: https://img.shields.io/nexus/r/https/oss.sonatype.org/ca.uhn.hapi.fhir/org.hl7.fhir.dstu3.svg "Sonatype Releases"
[Badge-dstu3SonatypeSnapshot]: https://img.shields.io/nexus/s/https/oss.sonatype.org/ca.uhn.hapi.fhir/org.hl7.fhir.dstu3.svg "Sonatype Snapshots"
[Badge-r4SonatypeRelease]: https://img.shields.io/nexus/r/https/oss.sonatype.org/ca.uhn.hapi.fhir/org.hl7.fhir.r4.svg "Sonatype Releases"
[Badge-r4SonatypeSnapshot]: https://img.shields.io/nexus/s/https/oss.sonatype.org/ca.uhn.hapi.fhir/org.hl7.fhir.r4.svg "Sonatype Snapshots"
[Badge-r5SonatypeRelease]: https://img.shields.io/nexus/r/https/oss.sonatype.org/ca.uhn.hapi.fhir/org.hl7.fhir.r5.svg "Sonatype Releases"
[Badge-r5SonatypeSnapshot]: https://img.shields.io/nexus/s/https/oss.sonatype.org/ca.uhn.hapi.fhir/org.hl7.fhir.r5.svg "Sonatype Snapshots"
[Badge-cliSonatypeRelease]: https://img.shields.io/nexus/r/https/oss.sonatype.org/ca.uhn.hapi.fhir/org.hl7.fhir.validation.cli.svg "Sonatype Releases"
[Badge-cliSonatypeSnapshot]: https://img.shields.io/nexus/s/https/oss.sonatype.org/ca.uhn.hapi.fhir/org.hl7.fhir.validation.cli.svg "Sonatype Snapshots"
[Badge-validationSonatypeRelease]: https://img.shields.io/nexus/r/https/oss.sonatype.org/ca.uhn.hapi.fhir/org.hl7.fhir.validation.svg "Sonatype Releases"
[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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* fix evaluation of codes in code systems that are labelled content = fragment
* fix url for cqfmeasures project
* change from error to warning for code system fragments

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@ -67,7 +67,6 @@ public class ComparisonRenderer implements IEvaluationContext {
b.append("</table>\r\n");
Map<String, Base> vars = new HashMap<>();
CodeSystemComparer cs = new CodeSystemComparer(session);
vars.put("title", new StringType(session.getTitle()));
vars.put("list", new StringType(b.toString()));
String template = templates.get("Index");
@ -147,8 +146,8 @@ public class ComparisonRenderer implements IEvaluationContext {
vars.put("concepts", new StringType(new XhtmlComposer(true).compose(cs.renderConcepts(comp, "", ""))));
String cnt = processTemplate(template, "CodeSystem", vars);
TextFile.stringToFile(cnt, file(comp.getId()+".html"));
new org.hl7.fhir.r5.formats.JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path("[tmp]", "comparison", comp.getId() + "-union.json")), comp.getUnion());
new org.hl7.fhir.r5.formats.JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path("[tmp]", "comparison", comp.getId() + "-intersection.json")), comp.getIntersection());
new org.hl7.fhir.r5.formats.JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path(folder, "comparison", comp.getId() + "-union.json")), comp.getUnion());
new org.hl7.fhir.r5.formats.JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path(folder, "comparison", comp.getId() + "-intersection.json")), comp.getIntersection());
}
private String file(String name) throws IOException {
@ -171,8 +170,8 @@ public class ComparisonRenderer implements IEvaluationContext {
vars.put("expansion", new StringType(new XhtmlComposer(true).compose(cs.renderExpansion(comp, "", ""))));
String cnt = processTemplate(template, "ValueSet", vars);
TextFile.stringToFile(cnt, file(comp.getId()+".html"));
new org.hl7.fhir.r5.formats.JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path("[tmp]", "comparison", comp.getId() + "-union.json")), comp.getUnion());
new org.hl7.fhir.r5.formats.JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path("[tmp]", "comparison", comp.getId() + "-intersection.json")), comp.getIntersection());
new org.hl7.fhir.r5.formats.JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path(folder, "comparison", comp.getId() + "-union.json")), comp.getUnion());
new org.hl7.fhir.r5.formats.JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path(folder, "comparison", comp.getId() + "-intersection.json")), comp.getIntersection());
}
private void renderProfile(String id, ProfileComparison comp) throws IOException {
@ -190,8 +189,8 @@ public class ComparisonRenderer implements IEvaluationContext {
vars.put("structure", new StringType(new XhtmlComposer(true).compose(cs.renderStructure(comp, "", "", "http://hl7.org/fhir"))));
String cnt = processTemplate(template, "CodeSystem", vars);
TextFile.stringToFile(cnt, file(comp.getId()+".html"));
new org.hl7.fhir.r5.formats.JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path("[tmp]", "comparison", comp.getId() + "-union.json")), comp.getUnion());
new org.hl7.fhir.r5.formats.JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path("[tmp]", "comparison", comp.getId() + "-intersection.json")), comp.getIntersection());
new org.hl7.fhir.r5.formats.JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path(folder, "comparison", comp.getId() + "-union.json")), comp.getUnion());
new org.hl7.fhir.r5.formats.JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path(folder, "comparison", comp.getId() + "-intersection.json")), comp.getIntersection());
}
private String processTemplate(String template, String name, Map<String, Base> vars) {

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@ -139,7 +139,7 @@ public class ValueSetCheckerSimple implements ValueSetChecker {
throw new FHIRException(warningMessage);
}
if (cs!=null && cs.getContent() != CodeSystemContentMode.COMPLETE) {
warningMessage = "Unable to resolve system "+system+" - system is not complete";
warningMessage = "Resolved system "+system+", but the definition is not complete";
if (!inExpansion && cs.getContent() != CodeSystemContentMode.FRAGMENT) // we're going to give it a go if it's a fragment
throw new FHIRException(warningMessage);
}
@ -224,7 +224,7 @@ public class ValueSetCheckerSimple implements ValueSetChecker {
ConceptDefinitionComponent cc = cs.hasUserData("tx.cs.special") ? ((SpecialCodeSystem) cs.getUserData("tx.cs.special")).findConcept(code) : findCodeInConcept(cs.getConcept(), code.getCode());
if (cc == null) {
if (cs.getContent() == CodeSystemContentMode.FRAGMENT) {
return new ValidationResult(IssueSeverity.ERROR, context.formatMessage(I18nConstants.UNKNOWN_CODE__IN_FRAGMENT, gen(code), cs.getUrl()));
return new ValidationResult(IssueSeverity.WARNING, context.formatMessage(I18nConstants.UNKNOWN_CODE__IN_FRAGMENT, gen(code), cs.getUrl()));
} else {
return new ValidationResult(IssueSeverity.ERROR, context.formatMessage(I18nConstants.UNKNOWN_CODE__IN_, gen(code), cs.getUrl()));
}
@ -420,7 +420,7 @@ public class ValueSetCheckerSimple implements ValueSetChecker {
return false;
// ok, we need the code system
CodeSystem cs = context.fetchCodeSystem(system);
if (cs == null || cs.getContent() != CodeSystemContentMode.COMPLETE) {
if (cs == null || (cs.getContent() != CodeSystemContentMode.COMPLETE && cs.getContent() != CodeSystemContentMode.FRAGMENT)) {
// make up a transient value set with
ValueSet vs = new ValueSet();
vs.setStatus(PublicationStatus.ACTIVE);

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@ -119,6 +119,9 @@ public class PackageHacker {
if (webref.equals("file://C:\\GitHub\\hl7.fhir.us.qicore#4.0.0\\output")) {
return "http://hl7.org/fhir/us/qicore/STU4";
}
if (webref.equals("file://C:\\GitHub\\hl7.fhir.us.cqfmeasures#2.0.0\\output")) {
return "http://hl7.org/fhir/us/cqfmeasures/STU2";
}
return webref;
}

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@ -1371,7 +1371,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
if (binding.hasExtension("http://hl7.org/fhir/StructureDefinition/elementdefinition-maxValueSet"))
checkMaxValueSet(errors, path, element, profile, ToolingExtensions.readStringExtension(binding, "http://hl7.org/fhir/StructureDefinition/elementdefinition-maxValueSet"), c, stack);
else
txWarning(errors, vr.getTxLink(), IssueType.CODEINVALID, element.line(), element.col(), path, false, I18nConstants.TERMINOLOGY_TX_NOVALID_13, describeReference(binding.getValueSet(), valueset), getErrorMessage(vr.getMessage()), gen(c));
txWarning(errors, vr.getTxLink(), IssueType.CODEINVALID, element.line(), element.col(), path, false, I18nConstants.TERMINOLOGY_TX_NOVALID_13, describeReference(binding.getValueSet(), valueset), getErrorMessage(vr.getMessage()), c.getSystem()+"#"+c.getCode());
} else if (binding.getStrength() == BindingStrength.PREFERRED) {
if (baseOnly) {
txHint(errors, vr.getTxLink(), IssueType.CODEINVALID, element.line(), element.col(), path, false, I18nConstants.TERMINOLOGY_TX_NOVALID_14, describeReference(binding.getValueSet(), valueset), getErrorMessage(vr.getMessage()));
@ -1395,10 +1395,6 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
}
}
private String gen(Coding c) {
return c.getSystem()+"#"+c.getCode()+ (c.hasDisplay() ? " \""+c.getDisplay()+"\"" : "");
}
private boolean isValueSet(String url) {
try {
ValueSet vs = context.fetchResourceWithException(ValueSet.class, url);

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@ -1,46 +0,0 @@
@echo off
set oldver=5.0.6
set newver=5.0.7
echo ..
echo =========================================================================
echo upgrade and release fhir.core from %oldver%-SNAPSHOT to %newver%-SNAPSHOT
echo =========================================================================
echo ..
call mvn versions:set -DnewVersion=%newver%-SNAPSHOT
call "C:\tools\fnr.exe" -dir "C:\work\org.hl7.fhir\build" -fileMask "*.xml" -find "%oldver%-SNAPSHOT" -replace "%newver%-SNAPSHOT" -count 8
call "C:\tools\fnr.exe" -dir "C:\work\org.hl7.fhir\fhir-ig-publisher" -fileMask "*.xml" -find "%oldver%-SNAPSHOT" -replace "%newver%-SNAPSHOT" -count 2
call "C:\tools\fnr.exe" -dir "C:\work\org.hl7.fhir\latest-ig-publisher" -fileMask "*.html" -find "%oldver%" -replace "%newver%" -count 1
call "C:\tools\fnr.exe" -dir "C:\work\org.hl7.fhir\latest-ig-publisher" -fileMask "*.json" -find "%oldver%" -replace "%newver%" -count 1
call mvn clean deploy -Dmaven.test.redirectTestOutputToFile=false -DdeployAtEnd=true
IF %ERRORLEVEL% NEQ 0 (
GOTO DONE
)
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
call git commit -t v%newver% -a -m "Release new version %newver%"
call git tag v%newver%
call git push origin master
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
cd ..\latest-ig-publisher
call git commit -a -m "Release new validator version %newver%-SNAPSHOT"
call git push origin master
cd ..\org.hl7.fhir.core
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
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
del C:\temp\current-release-notes-validator.md
:DONE
echo ===============================================================
echo all done
echo ===============================================================
pause