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org.hl7.fhir.core
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Merge branch 'master' of https://github.com/hapifhir/org.hl7.fhir.core into junit_test_issues

This commit is contained in:
markiantorno 2020-05-28 14:16:19 -04:00
parent a8dcaca261 fb2a8c32be
commit a8176a841d
46 changed files with 539 additions and 182 deletions
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71
azure-pipelines.yml
View File

@ -1,16 +1,20 @@
trigger:
branches:
include:
- '*'
- master
- release
pr:
- master
- release
# Different users have different machine setups, we run the build three times, on ubuntu, osx, and windows
strategy:
matrix:
linux:
imageName: "ubuntu-16.04"
# mac:
# imageName: "macos-10.14"
# windows:
# imageName: "vs2017-win2016"
mac:
imageName: "macos-10.14"
windows:
imageName: "vs2017-win2016"
maxParallel: 3
pool:
@ -19,18 +23,47 @@ pool:
variables:
currentImage: $(imageName)
codecov: $(CODECOV_TOKEN)
VERSION:
steps:
- bash: ls -la
- bash: pwd
# This task pulls the <version> value from the org.hl7.fhir.r5 project pom.xml file. All modules are released as
# the same version, at the same time, as defined in the root level pom.xml.
- task: PowerShell@2
inputs:
targetType: 'inline'
script: |
[xml]$pomXml = Get-Content .\pom.xml
[xml]$pomXml = Get-Content -Path .\pom.xml
# version
Write-Host $pomXml.project.version
$version=$pomXml.project.version
Write-Host "##vso[task.setvariable variable=version]$version"
# Prints out the build version, for debugging purposes
- bash: echo Pulled version from pom.xml => $(version)
# Azure pipelines cannot pass variables between pipelines, but it can pass files, so we
# pass the build id (ex: 1.1.13-SNAPSHOT) as a string in a file.
# This is used in the release pipeline, so we create it here.
# This is only done for the release branch.
- bash: |
echo $(version)
VERSION=$(version)
echo "$VERSION" > $(System.DefaultWorkingDirectory)/VERSION
condition: and(eq(variables.currentImage, 'ubuntu-16.04'), eq(variables['Build.SourceBranch'], 'refs/heads/release'))
# Copies the VERSION file containing the build id (ex: 1.1.13-SNAPSHOT) to the staging directory
# This is done for release versions only.
- task: CopyFiles@2
condition: and(eq(variables.currentImage, 'ubuntu-16.04'), eq(variables['Build.SourceBranch'], 'refs/heads/release'))
displayName: 'Copy Files to: $(build.artifactstagingdirectory)'
inputs:
SourceFolder: '$(System.Defaultworkingdirectory)'
Contents: "$(System.DefaultWorkingDirectory)/VERSION"
TargetFolder: '$(build.artifactstagingdirectory)'
# Runs 'mvn clean package'
- task: Maven@3
inputs:
mavenPomFile: 'pom.xml'
@ -41,22 +74,34 @@ steps:
publishJUnitResults: true
testResultsFiles: '**/surefire-reports/TEST-*.xml'
goals: 'clean package'
- bash: echo Current version => $(version)
displayName: 'version'
# Upload test results to codecov
- script: bash <(curl https://codecov.io/bash) -t $(codecov)
displayName: 'codecov'
displayName: 'codecov Bash Uploader'
# Publishes the test results to build artifacts.
- task: PublishCodeCoverageResults@1
displayName: 'Publish JaCoCo test results '
inputs:
codeCoverageTool: 'JaCoCo'
summaryFileLocation: '$(System.DefaultWorkingDirectory)/org.hl7.fhir.report/target/site/jacoco-aggregate/jacoco.xml'
reportDirectory: '$(System.DefaultWorkingDirectory)/org.hl7.fhir.report/target/site/jacoco-aggregate/'
# Publishes the built Validator jar to build artifacts. Primarily for testing and debugging builds.
- task: PublishPipelineArtifact@1
condition: eq(variables.currentImage, 'ubuntu-16.04')
displayName: 'Publish Validator jar'
condition: and(eq(variables.currentImage, 'ubuntu-16.04'), eq(variables['Build.SourceBranch'], 'refs/heads/release'))
inputs:
targetPath: "$(System.DefaultWorkingDirectory)/org.hl7.fhir.validation/target/org.hl7.fhir.validation-$(version).jar"
artifactName: Validator
# Publishes the files we've moved into the staging directory, so they can be accessed by the
# release pipeline. You will notice that we only do this for the ubuntu build, as doing it
# for each of the three release pipelines will cause conflicts.
# This is done for release versions only.
- task: PublishBuildArtifacts@1
condition: and(eq(variables.currentImage, 'ubuntu-16.04'), eq(variables['Build.SourceBranch'], 'refs/heads/release'))
displayName: 'Publish Build Artifacts'
inputs:
PathtoPublish: '$(build.artifactstagingdirectory)'

106
module-snapshot-publishing.yml Normal file
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@ -0,0 +1,106 @@
# This pipeline produces a SNAPSHOT build for each of the sub modules in
# the core library, and publishes them to ossrh.
trigger:
- master
strategy:
matrix:
dstu2:
module: "org.hl7.fhir.dstu2"
dstu3:
module: "org.hl7.fhir.dstu3"
dstu2016may:
module: "org.hl7.fhir.dstu2016may"
r4:
module: "org.hl7.fhir.r4"
r5:
module: "org.hl7.fhir.r5"
validator:
module: "org.hl7.fhir.validation"
maxParallel: 3
pool:
vmImage: "ubuntu-16.04"
variables:
currentModule: $(module)
steps:
# Debugging output to identify current module.
- bash: echo Publishing SNAPSHOT for $(module)
displayName: 'Print module name.'
# Signing, for now, occurs for all builds, SNAPSHOT or release. So we need a valid
# signing key. The next two steps download the public and private keys from the
# secure library files.
- task: DownloadSecureFile@1
displayName: 'Download public key.'
inputs:
secureFile: public.key
- task: DownloadSecureFile@1
displayName: 'Download private key.'
inputs:
secureFile: private.key
# Import both the private and public keys into gpg for signing.
- bash: |
gpg --import --no-tty --batch --yes $(Agent.TempDirectory)/public.key
gpg --import --no-tty --batch --yes $(Agent.TempDirectory)/private.key
gpg --list-keys --keyid-format LONG
gpg --list-secret-keys --keyid-format LONG
displayName: 'Import signing keys.'
# For creating the snapshot release with maven, we need to build a fake settings.xml
# for it to read from. This is done for the master branch merges only.
- bash: |
cat >$(System.DefaultWorkingDirectory)/settings.xml <<EOL
<settings xmlns="http://maven.apache.org/SETTINGS/1.0.0"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://maven.apache.org/SETTINGS/1.0.0
https://maven.apache.org/xsd/settings-1.0.0.xsd">
<servers>
<server>
<id>ossrh</id>
<username>$(SONATYPE_USER)</username>
<password>$(SONATYPE_PASS)</password>
</server>
<server>
<id>sonatype-nexus-snapshots</id>
<username>$(SONATYPE_USER)</username>
<password>$(SONATYPE_PASS)</password>
</server>
<server>
<id>sonatype-nexus-staging</id>
<username>$(SONATYPE_USER)</username>
<password>$(SONATYPE_PASS)</password>
</server>
<server>
<id>$(PGP_KEYNAME)</id>
<passphrase>$(PGP_PASSPHRASE)</passphrase>
</server>
</servers>
<profiles>
<profile>
<id>release</id>
<activation>
<activeByDefault>true</activeByDefault>
</activation>
<properties>
<gpg.keyname>$(PGP_KEYNAME)</gpg.keyname>
</properties>
</profile>
</profiles>
</settings>
EOL
displayName: 'Create .mvn/settings.xml'
# Deploy the SNAPSHOT artifact to sonatype nexus.
# This is done for the master branch merges only.
- task: Maven@3
displayName: 'Deploy $(module) to Sonatype staging'
inputs:
mavenPomFile: '$(System.DefaultWorkingDirectory)/$(module)/pom.xml'
goals: deploy
options: '--settings $(System.DefaultWorkingDirectory)/settings.xml '
publishJUnitResults: false

2
org.hl7.fhir.convertors/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>org.hl7.fhir.core</artifactId>
<version>5.0.3-SNAPSHOT</version>
<version>5.0.4-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

2
org.hl7.fhir.dstu2/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>org.hl7.fhir.core</artifactId>
<version>5.0.3-SNAPSHOT</version>
<version>5.0.4-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

2
org.hl7.fhir.dstu2016may/pom.xml
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@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>org.hl7.fhir.core</artifactId>
<version>5.0.3-SNAPSHOT</version>
<version>5.0.4-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

2
org.hl7.fhir.dstu3/pom.xml
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@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>org.hl7.fhir.core</artifactId>
<version>5.0.3-SNAPSHOT</version>
<version>5.0.4-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

2
org.hl7.fhir.r4/pom.xml
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@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>org.hl7.fhir.core</artifactId>
<version>5.0.3-SNAPSHOT</version>
<version>5.0.4-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

2
org.hl7.fhir.r5/pom.xml
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@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>org.hl7.fhir.core</artifactId>
<version>5.0.3-SNAPSHOT</version>
<version>5.0.4-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

2
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/comparison/OldProfileComparer.java
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@ -1403,7 +1403,7 @@ public class OldProfileComparer implements ProfileKnowledgeProvider {
}
private void genValueSetFile(String filename, ValueSet vs) throws IOException, FHIRException, EOperationOutcome {
RenderingContext rc = new RenderingContext(context, null, null, "", "http://hl7.org/fhir", ResourceRendererMode.RESOURCE);
RenderingContext rc = new RenderingContext(context, null, null, "http://hl7.org/fhir", "", null, ResourceRendererMode.RESOURCE);
rc.setNoSlowLookup(true);
RendererFactory.factory(vs, rc).render(vs);
String s = new XhtmlComposer(XhtmlComposer.HTML).compose(vs.getText().getDiv());

2
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/conformance/ProfileComparer.java
View File

@ -1391,7 +1391,7 @@ public class ProfileComparer implements ProfileKnowledgeProvider {
}
private void genValueSetFile(String filename, ValueSet vs) throws IOException, FHIRException, EOperationOutcome {
RenderingContext rc = new RenderingContext(context, null, null, "", "http://hl7.org/fhir", ResourceRendererMode.RESOURCE);
RenderingContext rc = new RenderingContext(context, null, null, "http://hl7.org/fhir", "", null, ResourceRendererMode.RESOURCE);
rc.setNoSlowLookup(true);
RendererFactory.factory(vs, rc).render(vs);
String s = new XhtmlComposer(XhtmlComposer.HTML).compose(vs.getText().getDiv());

33
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/conformance/ProfileUtilities.java
View File

@ -898,6 +898,9 @@ public class ProfileUtilities extends TranslatingUtilities {
baseCursor++;
} else if (diffMatches.size() == 1 && (slicingDone || (!isImplicitSlicing(diffMatches.get(0), cpath) && !(diffMatches.get(0).hasSlicing() || (isExtension(diffMatches.get(0)) && diffMatches.get(0).hasSliceName()))))) {// one matching element in the differential
ElementDefinition template = null;
if (diffMatches.get(0).hasType() && "Reference".equals(diffMatches.get(0).getType().get(0).getWorkingCode()) && !isValidType(diffMatches.get(0).getType().get(0), currentBase)) {
throw new DefinitionException(context.formatMessage(I18nConstants.VALIDATION_VAL_ILLEGAL_TYPE_CONSTRAINT, url, diffMatches.get(0).getPath(), diffMatches.get(0).getType().get(0), currentBase.typeSummary()));
}
if (diffMatches.get(0).hasType() && diffMatches.get(0).getType().size() == 1 && diffMatches.get(0).getType().get(0).hasProfile() && !"Reference".equals(diffMatches.get(0).getType().get(0).getWorkingCode())) {
CanonicalType p = diffMatches.get(0).getType().get(0).getProfile().get(0);
StructureDefinition sd = context.fetchResource(StructureDefinition.class, p.getValue());
@ -912,6 +915,9 @@ public class ProfileUtilities extends TranslatingUtilities {
}
}
if (sd != null) {
if (!isMatchingType(sd, diffMatches.get(0).getType())) {
throw new DefinitionException(context.formatMessage(I18nConstants.VALIDATION_VAL_PROFILE_WRONGTYPE2, sd.getUrl(), diffMatches.get(0).getPath(), sd.getType(), p.getValue(), diffMatches.get(0).getType().get(0).getWorkingCode()));
}
if (isGenerating(sd)) {
// this is a special case, because we're only going to access the first element, and we can rely on the fact that it's already populated.
// but we check anyway
@ -1447,7 +1453,7 @@ public class ProfileUtilities extends TranslatingUtilities {
if (!diffMatches.get(0).hasSliceName()) { // it's not real content, just the slice
diffpos++;
}
if (hasInnerDiffMatches(differential, cpath, diffpos, diffLimit, base.getElement(), false)) {
if (hasInnerDiffMatches(differential, cpath, diffCursor, diffLimit, base.getElement(), false)) {
int nbl = findEndOfElement(base, baseCursor);
int ndx = differential.getElement().indexOf(diffMatches.get(0));
int ndc = ndx+(diffMatches.get(0).hasSlicing() ? 1 : 0);
@ -1605,6 +1611,31 @@ public class ProfileUtilities extends TranslatingUtilities {
return res;
}
private boolean isMatchingType(StructureDefinition sd, List<TypeRefComponent> types) {
while (sd != null) {
for (TypeRefComponent tr : types) {
if (sd.getType().equals(tr.getCode())) {
return true;
}
}
sd = context.fetchResource(StructureDefinition.class, sd.getBaseDefinition());
}
return false;
}
private boolean isValidType(TypeRefComponent t, ElementDefinition base) {
for (TypeRefComponent tr : base.getType()) {
if (tr.getCode().equals(t.getCode())) {
return true;
}
if (tr.getWorkingCode().equals(t.getCode())) {
System.out.println("Type error: use of a simple type \""+t.getCode()+"\" wrongly constraining "+base.getPath());
return true;
}
}
return false;
}
private boolean isGenerating(StructureDefinition sd) {
return sd.hasUserData("profileutils.snapshot.generating");
}

63
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/renderers/BundleRenderer.java
View File

@ -15,7 +15,10 @@ import org.hl7.fhir.r5.model.Bundle.BundleEntrySearchComponent;
import org.hl7.fhir.r5.model.Bundle.BundleType;
import org.hl7.fhir.r5.model.Composition;
import org.hl7.fhir.r5.model.DomainResource;
import org.hl7.fhir.r5.model.Provenance;
import org.hl7.fhir.r5.model.Resource;
import org.hl7.fhir.r5.renderers.utils.BaseWrappers.BaseWrapper;
import org.hl7.fhir.r5.renderers.utils.BaseWrappers.ResourceWrapper;
import org.hl7.fhir.r5.renderers.utils.RenderingContext;
import org.hl7.fhir.r5.renderers.utils.Resolver.ResourceContext;
import org.hl7.fhir.r5.utils.EOperationOutcome;
@ -42,13 +45,54 @@ public class BundleRenderer extends ResourceRenderer {
return null;
}
@Override
public boolean render(XhtmlNode x, ResourceWrapper b) throws FHIRFormatError, DefinitionException, IOException, FHIRException, EOperationOutcome {
List<BaseWrapper> entries = b.children("entry");
if ("document".equals(b.get("type").primitiveValue())) {
if (entries.isEmpty() || (entries.get(0).has("resource") && "Composition".equals(entries.get(0).get("resource").fhirType())))
throw new FHIRException("Invalid document - first entry is not a Composition");
ResourceWrapper r = (ResourceWrapper) entries.get(0).getChildByName("resource").getValues().get(0);
x.addChildren(r.getNarrative());
} else if ("collection".equals(b.get("type").primitiveValue()) && allEntriesAreHistoryProvenance(entries)) {
// nothing
} else {
XhtmlNode root = new XhtmlNode(NodeType.Element, "div");
root.para().addText("Bundle "+b.getId()+" of type "+b.get("type").primitiveValue());
int i = 0;
for (BaseWrapper be : entries) {
i++;
if (be.has("fullUrl")) {
root.an(makeInternalLink(be.get("fullUrl").primitiveValue()));
}
if (be.has("resource") && be.getChildByName("resource").getValues().get(0).has("id")) {
root.an(be.get("resource").fhirType().toLowerCase() + "_" + be.getChildByName("resource").getValues().get(0).get("id").primitiveValue());
}
root.hr();
root.para().addText("Entry "+Integer.toString(i)+(be.has("fullUrl") ? " - Full URL = " + be.get("fullUrl").primitiveValue() : ""));
// if (be.hasRequest())
// renderRequest(root, be.getRequest());
// if (be.hasSearch())
// renderSearch(root, be.getSearch());
// if (be.hasResponse())
// renderResponse(root, be.getResponse());
if (be.has("resource")) {
root.para().addText("Resource "+be.get("resource").fhirType()+":");
ResourceWrapper rw = be.getChildByName("resource").getAsResource();
root.blockquote().addChildren(rw.getNarrative());
}
}
}
return false;
}
public XhtmlNode render(Bundle b) throws FHIRFormatError, DefinitionException, IOException, FHIRException, EOperationOutcome {
if (b.getType() == BundleType.DOCUMENT) {
if (!b.hasEntry() || !(b.getEntryFirstRep().hasResource() && b.getEntryFirstRep().getResource() instanceof Composition))
throw new FHIRException("Invalid document - first entry is not a Composition");
Composition dr = (Composition) b.getEntryFirstRep().getResource();
return dr.getText().getDiv();
} else if ((b.getType() == BundleType.DOCUMENT && allEntresAreHistoryProvenance(b))) {
} else if ((b.getType() == BundleType.COLLECTION && allEntresAreHistoryProvenance(b))) {
return null;
} else {
XhtmlNode root = new XhtmlNode(NodeType.Element, "div");
@ -81,9 +125,22 @@ public class BundleRenderer extends ResourceRenderer {
}
}
private boolean allEntriesAreHistoryProvenance(List<BaseWrapper> entries) throws UnsupportedEncodingException, FHIRException, IOException {
for (BaseWrapper be : entries) {
if (!"Provenance".equals(be.get("resource").fhirType())) {
return false;
}
}
return !entries.isEmpty();
}
private boolean allEntresAreHistoryProvenance(Bundle b) {
return false;
for (BundleEntryComponent be : b.getEntry()) {
if (!(be.getResource() instanceof Provenance)) {
return false;
}
}
return !b.getEntry().isEmpty();
}
private List<XhtmlNode> checkInternalLinks(Bundle b, List<XhtmlNode> childNodes) {

2
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/renderers/CapabilityStatementRenderer.java
View File

@ -82,7 +82,7 @@ public class CapabilityStatementRenderer extends ResourceRenderer {
tr = t.tr();
tr.td().addText(r.getType());
if (r.hasProfile()) {
tr.td().ah(context.getSpecLink()+r.getProfile()).addText(r.getProfile());
tr.td().ah(r.getProfile()).addText(r.getProfile());
}
tr.td().addText(showOp(r, TypeRestfulInteraction.READ));
if (hasVRead)

2
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/renderers/CodeSystemRenderer.java
View File

@ -414,7 +414,7 @@ public class CodeSystemRenderer extends TerminologyRenderer {
first = false;
XhtmlNode span = td.span(null, mapping.comp.hasRelationship() ? mapping.comp.getRelationship().toCode() : "");
span.addText(getCharForRelationship(mapping.comp));
a = td.ah(getContext().getSpecLink()+m.getLink()+"#"+makeAnchor(mapping.group.getTarget(), mapping.comp.getCode()));
a = td.ah(getContext().getSpecificationLink()+m.getLink()+"#"+makeAnchor(mapping.group.getTarget(), mapping.comp.getCode()));
a.addText(mapping.comp.getCode());
if (!Utilities.noString(mapping.comp.getComment()))
td.i().tx("("+mapping.comp.getComment()+")");

2
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/renderers/ConceptMapRenderer.java
View File

@ -375,7 +375,7 @@ public class ConceptMapRenderer extends TerminologyRenderer {
if (cs == null)
td.tx(url);
else
td.ah(cs.getUserString("path")).attribute("title", url).tx(cs.present());
td.ah(context.fixReference(cs.getUserString("path"))).attribute("title", url).tx(cs.present());
}
private void addUnmapped(XhtmlNode tbl, ConceptMapGroupComponent grp) {

4
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/renderers/DataRenderer.java
View File

@ -61,7 +61,7 @@ public class DataRenderer {
public DataRenderer(IWorkerContext worker) {
super();
this.context = new RenderingContext(worker, new MarkDownProcessor(Dialect.COMMON_MARK), ValidationOptions.defaults(), "", null, ResourceRendererMode.RESOURCE);
this.context = new RenderingContext(worker, new MarkDownProcessor(Dialect.COMMON_MARK), ValidationOptions.defaults(), "http://hl7.org/fhir/R4", "", null, ResourceRendererMode.RESOURCE);
}
// -- 2. Markdown support -------------------------------------------------------
@ -218,7 +218,7 @@ public class DataRenderer {
// -- 5. Data type Rendering ----------------------------------------------
public static String display(IWorkerContext context, DataType type) {
return new DataRenderer(new RenderingContext(context, null, null, "", null, ResourceRendererMode.RESOURCE)).display(type);
return new DataRenderer(new RenderingContext(context, null, null, "http://hl7.org/fhir/R4", "", null, ResourceRendererMode.RESOURCE)).display(type);
}
public String displayBase(Base b) {

2
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/renderers/OperationDefinitionRenderer.java
View File

@ -105,7 +105,7 @@ public class OperationDefinitionRenderer extends TerminologyRenderer {
if (p.hasSearchType()) {
td.br();
td.tx("(");
td.ah( context.getSpecLink() == null ? "search.html#"+p.getSearchType().toCode() : Utilities.pathURL(context.getSpecLink(), "search.html#"+p.getSearchType().toCode())).tx(p.getSearchType().toCode());
td.ah( context.getSpecificationLink() == null ? "search.html#"+p.getSearchType().toCode() : Utilities.pathURL(context.getSpecificationLink(), "search.html#"+p.getSearchType().toCode())).tx(p.getSearchType().toCode());
td.tx(")");
}
td = tr.td();

16
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/renderers/QuestionnaireRenderer.java
View File

@ -59,8 +59,8 @@ public class QuestionnaireRenderer extends TerminologyRenderer {
HierarchicalTableGenerator gen = new HierarchicalTableGenerator(context.getDestDir(), context.isInlineGraphics(), true);
TableModel model = gen.new TableModel("qtree="+q.getId(), true);
model.setAlternating(true);
model.setDocoImg(context.getSpecLink() +"help16.png");
model.setDocoRef(context.getSpecLink()+"formats.html#table");
model.setDocoImg(context.getSpecificationLink() +"help16.png");
model.setDocoRef(context.getSpecificationLink()+"formats.html#table");
model.getTitles().add(gen.new Title(null, model.getDocoRef(), translate("sd.head", "LinkId"), translate("sd.hint", "The linkId for the item"), null, 0));
model.getTitles().add(gen.new Title(null, model.getDocoRef(), translate("sd.head", "Text"), translate("sd.hint", "Text for the item"), null, 0));
model.getTitles().add(gen.new Title(null, model.getDocoRef(), translate("sd.head", "Cardinality"), translate("sd.hint", "Minimum and Maximum # of times the the itemcan appear in the instance"), null, 0));
@ -87,19 +87,19 @@ public class QuestionnaireRenderer extends TerminologyRenderer {
String txt = (i.hasPrefix() ? i.getPrefix() + ". " : "") + i.getText();
r.getCells().add(gen.new Cell(null, null, txt, null, null));
r.getCells().add(gen.new Cell(null, null, (i.getRequired() ? "1" : "0")+".."+(i.getRepeats() ? "*" : "1"), null, null));
r.getCells().add(gen.new Cell(null, context.getSpecLink()+"codesystem-item-type.html#"+i.getType().toCode(), i.getType().toCode(), null, null));
r.getCells().add(gen.new Cell(null, context.getSpecificationLink()+"codesystem-item-type.html#"+i.getType().toCode(), i.getType().toCode(), null, null));
// flags:
Cell flags = gen.new Cell();
r.getCells().add(flags);
if (i.getReadOnly()) {
flags.addPiece(gen.new Piece(Utilities.pathURL(context.getSpecLink(), "questionnaire-definitions.html#Questionnaire.item.readOnly"), null, "Is Readonly").addHtml(new XhtmlNode(NodeType.Element, "img").attribute("src", Utilities.path(context.getDestDir(), "icon-qi-readonly.png"))));
flags.addPiece(gen.new Piece(Utilities.pathURL(context.getSpecificationLink(), "questionnaire-definitions.html#Questionnaire.item.readOnly"), null, "Is Readonly").addHtml(new XhtmlNode(NodeType.Element, "img").attribute("src", Utilities.path(context.getDestDir(), "icon-qi-readonly.png"))));
}
if (ToolingExtensions.readBoolExtension(i, "http://hl7.org/fhir/uv/sdc/StructureDefinition/sdc-questionnaire-isSubject")) {
flags.addPiece(gen.new Piece("http://hl7.org/fhir/uv/sdc/StructureDefinition/sdc-questionnaire-isSubject", null, "Can change the subject of the questionnaire").addHtml(new XhtmlNode(NodeType.Element, "img").attribute("src", Utilities.path(context.getDestDir(), "icon-qi-subject.png"))));
}
if (ToolingExtensions.readBoolExtension(i, "http://hl7.org/fhir/StructureDefinition/questionnaire-hidden")) {
flags.addPiece(gen.new Piece(Utilities.pathURL(context.getSpecLink(), "extension-questionnaire-hidden.html"), null, "Is a hidden item").addHtml(new XhtmlNode(NodeType.Element, "img").attribute("src", Utilities.path(context.getDestDir(), "icon-qi-hidden.png"))));
flags.addPiece(gen.new Piece(Utilities.pathURL(context.getSpecificationLink(), "extension-questionnaire-hidden.html"), null, "Is a hidden item").addHtml(new XhtmlNode(NodeType.Element, "img").attribute("src", Utilities.path(context.getDestDir(), "icon-qi-hidden.png"))));
}
if (ToolingExtensions.readBoolExtension(i, "http://hl7.org/fhir/uv/sdc/StructureDefinition/sdc-questionnaire-optionalDisplay")) {
flags.addPiece(gen.new Piece("http://hl7.org/fhir/uv/sdc/StructureDefinition/sdc-questionnaire-optionalDisplay", null, "Is optional to display").addHtml(new XhtmlNode(NodeType.Element, "img").attribute("src", Utilities.path(context.getDestDir(), "icon-qi-optional.png"))));
@ -225,8 +225,8 @@ public class QuestionnaireRenderer extends TerminologyRenderer {
HierarchicalTableGenerator gen = new HierarchicalTableGenerator(context.getDestDir(), context.isInlineGraphics(), true);
TableModel model = gen.new TableModel("qtree="+q.getId(), true);
model.setAlternating(true);
model.setDocoImg(context.getSpecLink() +"help16.png");
model.setDocoRef(context.getSpecLink()+"formats.html#table");
model.setDocoImg(context.getSpecificationLink() +"help16.png");
model.setDocoRef(context.getSpecificationLink()+"formats.html#table");
model.getTitles().add(gen.new Title(null, model.getDocoRef(), translate("sd.head", "LinkId"), translate("sd.hint", "The linkId for the item"), null, 0));
model.getTitles().add(gen.new Title(null, model.getDocoRef(), translate("sd.head", "Description & Constraints"), translate("sd.hint", "Additional information about the item"), null, 0));
@ -474,7 +474,7 @@ public class QuestionnaireRenderer extends TerminologyRenderer {
}
if (ToolingExtensions.readBoolExtension(i, "http://hl7.org/fhir/StructureDefinition/questionnaire-hidden")) {
hasFlag = true;
flags.ah(Utilities.pathURL(context.getSpecLink(), "extension-questionnaire-hidden.html"), "Is a hidden item").img(Utilities.path(context.getDestDir(), "icon-qi-hidden.png"));
flags.ah(Utilities.pathURL(context.getSpecificationLink(), "extension-questionnaire-hidden.html"), "Is a hidden item").img(Utilities.path(context.getDestDir(), "icon-qi-hidden.png"));
d.style("background-color: #eeeeee");
}
if (ToolingExtensions.readBoolExtension(i, "http://hl7.org/fhir/uv/sdc/StructureDefinition/sdc-questionnaire-optionalDisplay")) {

6
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/renderers/ResourceRenderer.java
View File

@ -74,14 +74,16 @@ public abstract class ResourceRenderer extends DataRenderer {
assert r.getContext() == context;
XhtmlNode x = new XhtmlNode(NodeType.Element, "div");
boolean hasExtensions = render(x, r);
r.injectNarrative(x, hasExtensions ? NarrativeStatus.EXTENSIONS : NarrativeStatus.GENERATED);
if (r.hasNarrative()) {
r.injectNarrative(x, hasExtensions ? NarrativeStatus.EXTENSIONS : NarrativeStatus.GENERATED);
}
return x;
}
public abstract boolean render(XhtmlNode x, DomainResource r) throws FHIRFormatError, DefinitionException, IOException, FHIRException, EOperationOutcome;
public boolean render(XhtmlNode x, ResourceWrapper r) throws FHIRFormatError, DefinitionException, IOException, FHIRException, EOperationOutcome {
throw new NotImplementedException("This is not implemented yet for resources of type "+r.getName());
throw new NotImplementedException("Rendering using the wrapper is not implemented yet for resources of type "+r.getName());
}
public void describe(XhtmlNode x, DomainResource r) throws UnsupportedEncodingException, IOException {

2
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/renderers/StructureDefinitionRenderer.java
View File

@ -27,7 +27,7 @@ public class StructureDefinitionRenderer extends ResourceRenderer {
}
public boolean render(XhtmlNode x, StructureDefinition sd) throws FHIRFormatError, DefinitionException, IOException {
x.getChildNodes().add(context.getProfileUtilities().generateTable(context.getDefinitionsTarget(), sd, true, context.getDestDir(), false, sd.getId(), false, context.getSpecLink(), "", false, false, null, false));
x.getChildNodes().add(context.getProfileUtilities().generateTable(context.getDefinitionsTarget(), sd, true, context.getDestDir(), false, sd.getId(), false, context.getSpecificationLink(), "", false, false, null, false));
return true;
}

26
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/renderers/TerminologyRenderer.java
View File

@ -103,7 +103,7 @@ public abstract class TerminologyRenderer extends ResourceRenderer {
for (UsedConceptMap m : maps) {
XhtmlNode td = tr.td();
XhtmlNode b = td.b();
XhtmlNode a = b.ah(getContext().getSpecLink()+m.getLink());
XhtmlNode a = b.ah(getContext().getSpecificationLink()+m.getLink());
a.addText(m.getDetails().getName());
if (m.getDetails().isDoDescription() && m.getMap().hasDescription())
addMarkdown(td, m.getMap().getDescription());
@ -155,19 +155,22 @@ public abstract class TerminologyRenderer extends ResourceRenderer {
ref = (String) cs.getUserData("filename");
else
addHtml = false;
if (Utilities.noString(ref))
if (Utilities.noString(ref)) {
ref = (String) cs.getUserData("path");
if (ref != null) {
addHtml = false;
}
}
}
String spec = getSpecialReference(inc.getSystem());
if (spec != null) {
XhtmlNode a = li.ah(spec);
a.code(inc.getSystem());
} else if (cs != null && ref != null) {
if (!Utilities.noString(getContext().getSpecLink()) && ref.startsWith("http://hl7.org/fhir/"))
ref = ref.substring(20)+"/index.html";
else if (addHtml && !ref.contains(".html"))
if (addHtml && !ref.contains(".html"))
ref = ref + ".html";
XhtmlNode a = li.ah(getContext().getSpecLink()+ref.replace("\\", "/"));
ref = context.fixReference(ref);
XhtmlNode a = li.ah(ref.replace("\\", "/"));
a.code(inc.getSystem());
} else {
li.code(inc.getSystem());
@ -260,14 +263,14 @@ public abstract class TerminologyRenderer extends ResourceRenderer {
if (vs != null) {
String ref = (String) vs.getUserData("path");
ref = adjustForPath(ref);
ref = context.fixReference(ref);
XhtmlNode a = li.ah(ref == null ? "?ngen-11?" : ref.replace("\\", "/"));
a.addText(value);
} else {
CodeSystem cs = getContext().getWorker().fetchCodeSystem(value);
if (cs != null) {
String ref = (String) cs.getUserData("path");
ref = adjustForPath(ref);
ref = context.fixReference(ref);
XhtmlNode a = li.ah(ref == null ? "?ngen-12?" : ref.replace("\\", "/"));
a.addText(value);
} else if (value.equals("http://snomed.info/sct") || value.equals("http://snomed.info/id")) {
@ -282,13 +285,6 @@ public abstract class TerminologyRenderer extends ResourceRenderer {
}
}
private String adjustForPath(String ref) {
if (getContext().getSpecLink() == null)
return ref;
else
return getContext().getSpecLink()+ref;
}
protected String getDisplayForConcept(String system, String value) {

10
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/renderers/ValueSetRenderer.java
View File

@ -207,7 +207,7 @@ public class ValueSetRenderer extends TerminologyRenderer {
if (ref == null)
p.code(vs.getExpansion().getContains().get(0).getSystem());
else
p.ah(getContext().getSpecLink()+ref).code(vs.getExpansion().getContains().get(0).getSystem());
p.ah(context.fixReference(ref)).code(vs.getExpansion().getContains().get(0).getSystem());
}
XhtmlNode t = x.table( "codes");
XhtmlNode tr = t.tr();
@ -638,7 +638,7 @@ public class ValueSetRenderer extends TerminologyRenderer {
} else
td.addText(code);
} else {
String href = getContext().getSpecLink()+getCsRef(e);
String href = context.fixReference(getCsRef(e));
if (href.contains("#"))
href = href + "-"+Utilities.nmtokenize(code);
else
@ -662,9 +662,9 @@ public class ValueSetRenderer extends TerminologyRenderer {
String cslink = getCsRef(cs);
XhtmlNode a = null;
if (cslink != null)
a = td.ah(getContext().getSpecLink()+cslink+"#"+cs.getId()+"-"+code);
a = td.ah(getContext().getSpecificationLink()+cslink+"#"+cs.getId()+"-"+code);
else
a = td.ah(getContext().getSpecLink()+vslink+"#"+code);
a = td.ah(getContext().getSpecificationLink()+vslink+"#"+code);
a.addText(code);
}
@ -796,7 +796,7 @@ public class ValueSetRenderer extends TerminologyRenderer {
} else {
li.tx(f.getProperty()+" "+describe(f.getOp())+" ");
if (e != null && codeExistsInValueSet(e, f.getValue())) {
String href = getContext().getSpecLink()+getCsRef(e);
String href = getContext().getSpecificationLink()+getCsRef(e);
if (href.contains("#"))
href = href + "-"+Utilities.nmtokenize(f.getValue());
else

2
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/renderers/utils/BaseWrappers.java
View File

@ -29,6 +29,7 @@ public class BaseWrappers {
public int getMaxCardinality();
public StructureDefinition getStructure();
public BaseWrapper value();
public ResourceWrapper getAsResource();
}
public interface WrapperBase extends RendererWrapper {
@ -48,6 +49,7 @@ public class BaseWrappers {
public void injectNarrative(XhtmlNode x, NarrativeStatus status) throws IOException;
public BaseWrapper root();
public StructureDefinition getDefinition();
public boolean hasNarrative();
}
public interface BaseWrapper extends WrapperBase {

17
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/renderers/utils/DOMWrappers.java
View File

@ -178,6 +178,11 @@ public class DOMWrappers {
return getValues().get(0);
}
@Override
public ResourceWrapper getAsResource() {
throw new Error("Not implemented yet");
}
}
public static class ResourceWrapperElement extends WrapperBaseImpl implements ResourceWrapper {
@ -312,6 +317,18 @@ public class DOMWrappers {
public Base getBase() {
throw new Error("Not Implemented yet");
}
@Override
public boolean hasNarrative() {
StructureDefinition sd = definition;
while (sd != null) {
if ("DomainResource".equals(sd.getType())) {
return true;
}
sd = context.getWorker().fetchResource(StructureDefinition.class, sd.getBaseDefinition());
}
return false;
}
}
}

18
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/renderers/utils/DirectWrappers.java
View File

@ -96,6 +96,11 @@ public class DirectWrappers {
public String toString() {
return "#."+wrapped.toString();
}
@Override
public ResourceWrapper getAsResource() {
throw new Error("Not implemented yet");
}
}
public static class BaseWrapperDirect extends WrapperBaseImpl implements BaseWrapper {
@ -219,6 +224,19 @@ public class DirectWrappers {
public Base getBase() {
return wrapped;
}
@Override
public boolean hasNarrative() {
StructureDefinition sd = context.getWorker().fetchTypeDefinition(wrapped.fhirType());
while (sd != null) {
if ("DomainResource".equals(sd.getType())) {
return true;
}
sd = context.getWorker().fetchResource(StructureDefinition.class, sd.getBaseDefinition());
}
return false;
}
}
}

24
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/renderers/utils/ElementWrappers.java
View File

@ -48,8 +48,9 @@ public class ElementWrappers {
if (type == null || type.equals("Resource") || type.equals("BackboneElement") || type.equals("Element"))
return null;
if (element.hasElementProperty())
return null;
if (element.hasElementProperty()) {
return element;
}
ByteArrayOutputStream xml = new ByteArrayOutputStream();
try {
new XmlParser(context.getWorker()).compose(element, xml, OutputStyle.PRETTY, null);
@ -57,7 +58,7 @@ public class ElementWrappers {
throw new FHIRException(e.getMessage(), e);
}
if (context.getParser() == null) {
System.out.println("huh?");
System.out.println("Noe version specific parser provided");
}
return context.getParser().parseType(xml.toString(), type);
}
@ -219,6 +220,18 @@ public class ElementWrappers {
public Base getBase() {
return wrapped;
}
@Override
public boolean hasNarrative() {
StructureDefinition sd = definition;
while (sd != null) {
if ("DomainResource".equals(sd.getType())) {
return true;
}
sd = context.getWorker().fetchResource(StructureDefinition.class, sd.getBaseDefinition());
}
return false;
}
}
public static class PropertyWrapperMetaElement extends RendererWrapperImpl implements PropertyWrapper {
@ -287,6 +300,11 @@ public class ElementWrappers {
return getValues().get(0);
}
@Override
public ResourceWrapper getAsResource() {
return new ElementWrappers.ResourceWrapperMetaElement(context, values.get(0));
}
}
}

29
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/renderers/utils/RenderingContext.java
View File

@ -16,6 +16,7 @@ import org.hl7.fhir.r5.renderers.utils.Resolver.ResourceContext;
import org.hl7.fhir.r5.utils.FHIRPathEngine.IEvaluationContext;
import org.hl7.fhir.utilities.MarkDownProcessor;
import org.hl7.fhir.utilities.MarkDownProcessor.Dialect;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.validation.ValidationOptions;
public class RenderingContext {
@ -71,7 +72,8 @@ public class RenderingContext {
private ITypeParser parser;
private String lang;
private String specLink;
private String localPrefix; // relative link within local context
private String specificationLink;
private String selfLink; // absolute link to where the content is to be found (only used in a few circumstances when making external references to tools)
private int headerLevelContext;
private boolean canonicalUrlsAsLinks;
@ -101,12 +103,13 @@ public class RenderingContext {
* @param specLink - path to FHIR specification
* @param lang - langauage to render in
*/
public RenderingContext(IWorkerContext worker, MarkDownProcessor markdown, ValidationOptions terminologyServiceOptions, String specLink, String lang, ResourceRendererMode mode) {
public RenderingContext(IWorkerContext worker, MarkDownProcessor markdown, ValidationOptions terminologyServiceOptions, String specLink, String localPrefix, String lang, ResourceRendererMode mode) {
super();
this.worker = worker;
this.markdown = markdown;
this.lang = lang;
this.specLink = specLink;
this.specificationLink = specLink;
this.localPrefix = localPrefix;
this.mode = mode;
this.terminologyServiceOptions = terminologyServiceOptions;
profileUtilities = new ProfileUtilities(worker, null, null);
@ -146,8 +149,12 @@ public class RenderingContext {
return lang;
}
public String getSpecLink() {
return specLink;
public String getSpecificationLink() {
return specificationLink;
}
public String getLocalPrefix() {
return localPrefix;
}
public ValidationOptions getTerminologyServiceOptions() {
@ -293,7 +300,7 @@ public class RenderingContext {
}
public RenderingContext copy() {
RenderingContext res = new RenderingContext(worker, markdown, terminologyServiceOptions, specLink, lang, mode);
RenderingContext res = new RenderingContext(worker, markdown, terminologyServiceOptions, specificationLink, localPrefix, lang, mode);
res.resolver = resolver;
res.templateProvider = templateProvider;
@ -349,6 +356,16 @@ public class RenderingContext {
public void setSelfLink(String selfLink) {
this.selfLink = selfLink;
}
public String fixReference(String ref) {
if (!Utilities.isAbsoluteUrl(ref)) {
return (localPrefix == null ? "" : localPrefix)+ref;
}
if (ref.startsWith("http://hl7.org/fhir") && !ref.substring(20).contains("/")) {
return specificationLink+ref.substring(20);
}
return ref;
}

2
org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/test/NarrativeGenerationTests.java
View File

@ -101,7 +101,7 @@ public class NarrativeGenerationTests {
@ParameterizedTest(name = "{index}: file {0}")
@MethodSource("data")
public void test(String id, TestDetails test) throws Exception {
RenderingContext rc = new RenderingContext(context, null, null, "http://hl7.org/fhir", null, ResourceRendererMode.RESOURCE);
RenderingContext rc = new RenderingContext(context, null, null, "http://hl7.org/fhir", "", null, ResourceRendererMode.RESOURCE);
rc.setDestDir("C:\\work\\org.hl7.fhir\\packages\\packages\\hl7.fhir.pubpack\\package\\other\\");
rc.setHeader(test.isHeader());
rc.setDefinitionsTarget("test.html");

2
org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/test/NarrativeGeneratorTests.java
View File

@ -24,7 +24,7 @@ public class NarrativeGeneratorTests {
@BeforeAll
public static void setUp() throws FHIRException {
rc = new RenderingContext(TestingUtilities.context(), null, null, "", "http://hl7.org/fhir", ResourceRendererMode.RESOURCE);
rc = new RenderingContext(TestingUtilities.context(), null, null, "http://hl7.org/fhir", "", null, ResourceRendererMode.RESOURCE);
}
@Test

2
org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/test/ResourceRoundTripTests.java
View File

@ -27,7 +27,7 @@ public class ResourceRoundTripTests {
@Test
public void test() throws IOException, FHIRException, EOperationOutcome {
DomainResource res = (DomainResource) new XmlParser().parse(TestingUtilities.loadTestResourceStream("r5", "unicode.xml"));
RenderingContext rc = new RenderingContext(TestingUtilities.context(), null, null, "", "http://hl7.org/fhir", ResourceRendererMode.RESOURCE);
RenderingContext rc = new RenderingContext(TestingUtilities.context(), null, null, "http://hl7.org/fhir", "", null, ResourceRendererMode.RESOURCE);
RendererFactory.factory(res, rc).render(res);
IOUtils.copy(TestingUtilities.loadTestResourceStream("r5", "unicode.xml"), new FileOutputStream(TestingUtilities.tempFile("gen", "unicode.xml")));
new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(TestingUtilities.tempFile("gen", "unicode.out.xml")), res);

2
org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/test/SnapShotGenerationTests.java
View File

@ -550,7 +550,7 @@ public class SnapShotGenerationTests {
throw e;
}
if (output.getDifferential().hasElement()) {
RenderingContext rc = new RenderingContext(TestingUtilities.context(), null, null, "", "http://hl7.org/fhir", ResourceRendererMode.RESOURCE);
RenderingContext rc = new RenderingContext(TestingUtilities.context(), null, null, "http://hl7.org/fhir", "", null, ResourceRendererMode.RESOURCE);
rc.setProfileUtilities(new ProfileUtilities(TestingUtilities.context(), null, new TestPKP()));
RendererFactory.factory(output, rc).render(output);
}

2
org.hl7.fhir.report/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>org.hl7.fhir.core</artifactId>
<version>5.0.3-SNAPSHOT</version>
<version>5.0.4-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

2
org.hl7.fhir.utilities/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>org.hl7.fhir.core</artifactId>
<version>5.0.3-SNAPSHOT</version>
<version>5.0.4-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

3
org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/cache/NpmPackage.java vendored
View File

@ -576,6 +576,9 @@ public class NpmPackage {
public boolean hasFile(String folder, String file) throws IOException {
NpmPackageFolder f = folders.get(folder);
if (f == null) {
f = folders.get(Utilities.path("package", folder));
}
return f != null && f.hasFile(file);
}

189
org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/cache/PackageCacheManager.java vendored
View File

@ -35,11 +35,15 @@ import java.io.BufferedOutputStream;
import java.io.ByteArrayOutputStream;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.io.InputStream;
import java.io.RandomAccessFile;
import java.net.HttpURLConnection;
import java.net.URL;
import java.net.URLConnection;
import java.nio.channels.FileChannel;
import java.nio.channels.FileLock;
import java.sql.Timestamp;
import java.text.ParseException;
import java.text.SimpleDateFormat;
@ -186,6 +190,37 @@ public class PackageCacheManager {
}
}
public interface CacheLockFunction<T> {
T get() throws IOException;
}
public class CacheLock {
private final File lockFile;
public CacheLock(String name) throws IOException {
this.lockFile = new File(cacheFolder, name + ".lock");
if (!lockFile.isFile()) {
TextFile.stringToFile("", lockFile);
}
}
public <T> T doWithLock(CacheLockFunction<T> f) throws FileNotFoundException, IOException {
try (FileChannel channel = new RandomAccessFile(lockFile, "rw").getChannel()) {
final FileLock fileLock = channel.lock();
T result = null;
try {
result = f.get();
} finally {
fileLock.release();
}
if (!lockFile.delete()) {
lockFile.deleteOnExit();
}
return result;
}
}
}
public static final String PRIMARY_SERVER = "http://packages.fhir.org";
public static final String SECONDARY_SERVER = "http://packages2.fhir.org/packages";
// private static final String SECONDARY_SERVER = "http://local.fhir.org:960/packages";
@ -256,16 +291,19 @@ public class PackageCacheManager {
private void clearCache() throws IOException {
for (File f : new File(cacheFolder).listFiles()) {
if (f.isDirectory()) {
Utilities.clearDirectory(f.getAbsolutePath());
try {
FileUtils.deleteDirectory(f);
} catch (Exception e1) {
new CacheLock(f.getName()).doWithLock(() -> {
Utilities.clearDirectory(f.getAbsolutePath());
try {
FileUtils.deleteDirectory(f);
} catch (Exception e1) {
try {
FileUtils.deleteDirectory(f);
} catch (Exception e2) {
// just give up
}
}
}
return null; // must return something
});
}
else if (!f.getName().equals("packages.ini"))
FileUtils.forceDelete(f);
@ -413,15 +451,18 @@ public class PackageCacheManager {
* @throws IOException
*/
public void removePackage(String id, String ver) throws IOException {
String f = Utilities.path(cacheFolder, id+"#"+ver);
File ff = new File(f);
if (ff.exists()) {
Utilities.clearDirectory(f);
IniFile ini = new IniFile(Utilities.path(cacheFolder, "packages.ini"));
ini.removeProperty("packages", id+"#"+ver);
ini.save();
ff.delete();
}
new CacheLock(id+"#"+ver).doWithLock(() -> {
String f = Utilities.path(cacheFolder, id+"#"+ver);
File ff = new File(f);
if (ff.exists()) {
Utilities.clearDirectory(f);
IniFile ini = new IniFile(Utilities.path(cacheFolder, "packages.ini"));
ini.removeProperty("packages", id+"#"+ver);
ini.save();
ff.delete();
}
return null;
});
}
/**
@ -494,70 +535,78 @@ public class PackageCacheManager {
if (version == null)
version = npm.version();
String packRoot = Utilities.path(cacheFolder, id+"#"+version);
try {
Utilities.createDirectory(packRoot);
Utilities.clearDirectory(packRoot);
String v = version;
return new CacheLock(id+"#"+version).doWithLock(() -> {
NpmPackage pck = null;
String packRoot = Utilities.path(cacheFolder, id+"#"+v);
try {
// ok, now we have a lock on it... check if something created it while we were waiting
if (!new File(packRoot).exists()) {
Utilities.createDirectory(packRoot);
Utilities.clearDirectory(packRoot);
int i = 0;
int c = 0;
int size = 0;
for (Entry<String, NpmPackageFolder> e : npm.getFolders().entrySet()) {
String dir = e.getKey().equals("package") ? Utilities.path(packRoot, "package") : Utilities.path(packRoot, "package", e.getKey());;
if (!(new File(dir).exists()))
Utilities.createDirectory(dir);
for (Entry<String, byte[]> fe : e.getValue().getContent().entrySet()) {
String fn = Utilities.path(dir, fe.getKey());
byte[] cnt = fe.getValue();
TextFile.bytesToFile(cnt, fn);
size = size + cnt.length;
i++;
if (progress && i % 50 == 0) {
c++;
System.out.print(".");
if (c == 120) {
System.out.println("");
System.out.print(" ");
c = 2;
int i = 0;
int c = 0;
int size = 0;
for (Entry<String, NpmPackageFolder> e : npm.getFolders().entrySet()) {
String dir = e.getKey().equals("package") ? Utilities.path(packRoot, "package") : Utilities.path(packRoot, "package", e.getKey());;
if (!(new File(dir).exists()))
Utilities.createDirectory(dir);
for (Entry<String, byte[]> fe : e.getValue().getContent().entrySet()) {
String fn = Utilities.path(dir, fe.getKey());
byte[] cnt = fe.getValue();
TextFile.bytesToFile(cnt, fn);
size = size + cnt.length;
i++;
if (progress && i % 50 == 0) {
c++;
System.out.print(".");
if (c == 120) {
System.out.println("");
System.out.print(" ");
c = 2;
}
}
}
}
}
}
}
IniFile ini = new IniFile(Utilities.path(cacheFolder, "packages.ini"));
ini.setTimeStampFormat("yyyyMMddhhmmss");
ini.setTimestampProperty("packages", id+"#"+version, Timestamp.from(Instant.now()), null);
ini.setIntegerProperty("package-sizes", id+"#"+version, size, null);
ini.save();
if (progress)
System.out.println(" done.");
NpmPackage pck = loadPackageInfo(packRoot);
if (!id.equals(JSONUtil.str(npm.getNpm(), "name")) || !version.equals(JSONUtil.str(npm.getNpm(), "version"))) {
if (!id.equals(JSONUtil.str(npm.getNpm(), "name"))) {
npm.getNpm().addProperty("original-name", JSONUtil.str(npm.getNpm(), "name"));
npm.getNpm().remove("name");
npm.getNpm().addProperty("name", id);
IniFile ini = new IniFile(Utilities.path(cacheFolder, "packages.ini"));
ini.setTimeStampFormat("yyyyMMddhhmmss");
ini.setTimestampProperty("packages", id+"#"+v, Timestamp.from(Instant.now()), null);
ini.setIntegerProperty("package-sizes", id+"#"+v, size, null);
ini.save();
if (progress)
System.out.println(" done.");
}
if (!version.equals(JSONUtil.str(npm.getNpm(), "version"))) {
npm.getNpm().addProperty("original-version", JSONUtil.str(npm.getNpm(), "version"));
npm.getNpm().remove("version");
npm.getNpm().addProperty("version", version);
pck = loadPackageInfo(packRoot);
if (!id.equals(JSONUtil.str(npm.getNpm(), "name")) || !v.equals(JSONUtil.str(npm.getNpm(), "version"))) {
if (!id.equals(JSONUtil.str(npm.getNpm(), "name"))) {
npm.getNpm().addProperty("original-name", JSONUtil.str(npm.getNpm(), "name"));
npm.getNpm().remove("name");
npm.getNpm().addProperty("name", id);
}
if (!v.equals(JSONUtil.str(npm.getNpm(), "version"))) {
npm.getNpm().addProperty("original-version", JSONUtil.str(npm.getNpm(), "version"));
npm.getNpm().remove("version");
npm.getNpm().addProperty("version", v);
}
TextFile.stringToFile(new GsonBuilder().setPrettyPrinting().create().toJson(npm.getNpm()), Utilities.path(cacheFolder, id+"#"+v, "package", "package.json"), false);
}
TextFile.stringToFile(new GsonBuilder().setPrettyPrinting().create().toJson(npm.getNpm()), Utilities.path(cacheFolder, id+"#"+version, "package", "package.json"), false);
} catch (Exception e) {
try {
// don't leave a half extracted package behind
System.out.println("Clean up package "+packRoot+" because installation failed: "+e.getMessage());
e.printStackTrace();
Utilities.clearDirectory(packRoot);
new File(packRoot).delete();
} catch (Exception ei) {
// nothing
}
throw e;
}
return pck;
} catch (Exception e) {
try {
// don't leave a half extracted package behind
Utilities.clearDirectory(packRoot);
new File(packRoot).delete();
} catch (Exception ei) {
// nothing
}
throw e;
}
});
}
public String getPackageId(String canonical) throws IOException {

24
org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/i18n/I18nConstants.java
View File

@ -491,30 +491,10 @@ public class I18nConstants {
public static final String MEASURE_M_CRITERIA_CQL_NO_ELM = "MEASURE_M_CRITERIA_CQL_NO_ELM";
public static final String MEASURE_M_CRITERIA_CQL_ELM_NOT_VALID = "MEASURE_M_CRITERIA_CQL_ELM_NOT_VALID";
public static final String MEASURE_M_CRITERIA_CQL_NOT_FOUND = "MEASURE_M_CRITERIA_CQL_NOT_FOUND";
//public static final String
//public static final String
//public static final String
//public static final String
//public static final String
//public static final String
//public static final String
//public static final String
//public static final String
//public static final String
//public static final String
//public static final String
//public static final String
//public static final String
//public static final String
//public static final String
//public static final String
//public static final String
//public static final String
//public static final String
//public static final String
//public static final String
public static final String VALIDATION_VAL_PROFILE_WRONGTYPE2 = "Validation_VAL_Profile_WrongType2";
public static final String XHTML_URL_EMPTY = "XHTML_URL_EMPTY";
public static final String XHTML_URL_INVALID_CHARS = "XHTML_URL_INVALID_CHARS";
public static final String TERMINOLOGY_TX_SYSTEM_HTTPS = "TERMINOLOGY_TX_SYSTEM_HTTPS";
public static final String CODESYSTEM_CS_NO_VS_NOTCOMPLETE = "CODESYSTEM_CS_NO_VS_NOTCOMPLETE";
public static final String VALIDATION_VAL_ILLEGAL_TYPE_CONSTRAINT = "VALIDATION_VAL_ILLEGAL_TYPE_CONSTRAINT";
}

7
org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/xhtml/XhtmlNode.java
View File

@ -681,6 +681,13 @@ public class XhtmlNode implements IBaseXhtml {
return this;
}
public XhtmlNode addChildren(XhtmlNode x) {
if (x != null) {
getChildNodes().addAll(x.getChildNodes());
}
return this;
}
public XhtmlNode input(String name, String type, String placeholder, int size) {
XhtmlNode p = new XhtmlNode(NodeType.Element, "input");

3
org.hl7.fhir.utilities/src/main/resources/Messages.properties
View File

@ -495,3 +495,6 @@ TYPE_SPECIFIC_CHECKS_DT_ATT_TOO_LONG = Attachment size is {0} bytes which exceed
TYPE_SPECIFIC_CHECKS_DT_ATT_NO_CONTENT = Attachments have data and/or url, or else must have either contentType and/oor language
TYPE_SPECIFIC_CHECKS_DT_BASE64_TOO_LONG = Base64 size is {0} bytes which exceeds the stated limit of {1} bytes
TYPE_SPECIFIC_CHECKS_DT_DECIMAL_CHARS = Found {0} decimal places which exceeds the stated limit of {1} digits
Validation_VAL_Profile_WrongType = Specified profile type was "{0}", but found type "{1}"
Validation_VAL_Profile_WrongType2 = Type mismatch processing profile {0} at path {1}: The element type is {4}, but the profile {3} is for a different type {2}
VALIDATION_VAL_ILLEGAL_TYPE_CONSTRAINT = Illegal constraint in profile {0} at path {1} - cannot constrain to type {2} from base types {3}

2
org.hl7.fhir.validation.cli/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>org.hl7.fhir.core</artifactId>
<version>5.0.3-SNAPSHOT</version>
<version>5.0.4-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

2
org.hl7.fhir.validation/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>org.hl7.fhir.core</artifactId>
<version>5.0.3-SNAPSHOT</version>
<version>5.0.4-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

8
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/ValidationEngine.java
View File

@ -1171,7 +1171,7 @@ public class ValidationEngine implements IValidatorResourceFetcher {
private OperationOutcome exceptionToOutcome(Exception ex) throws IOException, FHIRException, EOperationOutcome {
OperationOutcome op = new OperationOutcome();
op.addIssue().setCode(org.hl7.fhir.r5.model.OperationOutcome.IssueType.EXCEPTION).setSeverity(org.hl7.fhir.r5.model.OperationOutcome.IssueSeverity.FATAL).getDetails().setText(ex.getMessage());
RenderingContext rc = new RenderingContext(context, null, null, "", "http://hl7.org/fhir", ResourceRendererMode.RESOURCE);
RenderingContext rc = new RenderingContext(context, null, null, "http://hl7.org/fhir", "", null, ResourceRendererMode.RESOURCE);
RendererFactory.factory(op, rc).render(op);
return op;
}
@ -1187,7 +1187,7 @@ public class ValidationEngine implements IValidatorResourceFetcher {
}
op.getIssue().add(OperationOutcomeUtilities.convertToIssue(vm, op));
}
RenderingContext rc = new RenderingContext(context, null, null, "", "http://hl7.org/fhir", ResourceRendererMode.RESOURCE);
RenderingContext rc = new RenderingContext(context, null, null, "http://hl7.org/fhir", "", null, ResourceRendererMode.RESOURCE);
RendererFactory.factory(op, rc).render(op);
return op;
}
@ -1245,7 +1245,7 @@ public class ValidationEngine implements IValidatorResourceFetcher {
public DomainResource generate(String source, String version) throws Exception {
Content cnt = loadContent(source, "validate");
Resource res = loadResourceByVersion(version, cnt.focus, source);
RenderingContext rc = new RenderingContext(context, null, null, "", "http://hl7.org/fhir", ResourceRendererMode.RESOURCE);
RenderingContext rc = new RenderingContext(context, null, null, "http://hl7.org/fhir", "", null, ResourceRendererMode.RESOURCE);
RendererFactory.factory(res, rc).render((DomainResource) res);
return (DomainResource) res;
}
@ -1550,7 +1550,7 @@ public class ValidationEngine implements IValidatorResourceFetcher {
}
private void genScanOutputItem(ScanOutputItem item, String filename) throws IOException, FHIRException, EOperationOutcome {
RenderingContext rc = new RenderingContext(context, null, null, "", "http://hl7.org/fhir", ResourceRendererMode.RESOURCE);
RenderingContext rc = new RenderingContext(context, null, null, "http://hl7.org/fhir", "", null, ResourceRendererMode.RESOURCE);
rc.setNoSlowLookup(true);
RendererFactory.factory(item.outcome, rc).render(item.outcome);
String s = new XhtmlComposer(XhtmlComposer.HTML).compose(item.outcome.getText().getDiv());

2
org.hl7.fhir.validation/src/test/java/org/hl7/fhir/comparison/tests/ComparisonTests.java
View File

@ -103,7 +103,7 @@ public class ComparisonTests {
System.out.println("---- Set up Output ----------------------------------------------------------");
Utilities.createDirectory(Utilities.path("[tmp]", "comparison"));
PackageCacheManager pcm = new PackageCacheManager(true, ToolsVersion.TOOLS_VERSION);
NpmPackage npm = pcm.loadPackage("hl7.fhir.pubpack", "0.0.4");
NpmPackage npm = pcm.loadPackage("hl7.fhir.pubpack", "0.0.5");
for (String f : npm.list("other")) {
TextFile.streamToFile(npm.load("other", f), Utilities.path("[tmp]", "comparison", f));
}

2
org.hl7.fhir.validation/src/test/java/org/hl7/fhir/conversion/tests/SnapShotGenerationTestsX.java
View File

@ -520,7 +520,7 @@ public class SnapShotGenerationTestsX {
throw e;
}
if (output.getDifferential().hasElement()) {
RenderingContext rc = new RenderingContext(TestingUtilities.context(), null, null, "", "http://hl7.org/fhir", ResourceRendererMode.RESOURCE);
RenderingContext rc = new RenderingContext(TestingUtilities.context(), null, null, "http://hl7.org/fhir", "", null, ResourceRendererMode.RESOURCE);
rc.setProfileUtilities(new ProfileUtilities(TestingUtilities.context(), null, new TestPKP()));
RendererFactory.factory(output, rc).render(output);
}

3
pom.xml
View File

@ -13,7 +13,7 @@
each other. It is fine to bump the point version of this POM without affecting
HAPI FHIR.
-->
<version>5.0.3-SNAPSHOT</version>
<version>5.0.4-SNAPSHOT</version>
<properties>
<hapi_fhir_version>5.0.0</hapi_fhir_version>
@ -136,6 +136,7 @@
<module>org.hl7.fhir.report</module>
</modules>
<build>
<plugins>
<plugin>

7
release-notes-validator.md
View File

@ -6,6 +6,11 @@ title: FHIR Validator Release Notes
## Current (not released yet)
(no changes yet)
## v5.0.4 (2020-05-27)
(no changes yet)
## v5.0.3 (2020-05-26)
@ -199,4 +204,4 @@ title: FHIR Validator Release Notes
## v4.1.60 (2020-02-02)
* This
* This

6
release.bat
View File

@ -1,7 +1,7 @@
@echo off
set oldver=5.0.2
set newver=5.0.3
set oldver=5.0.3
set newver=5.0.4
echo ..
echo =========================================================================
@ -15,7 +15,7 @@ call "C:\tools\fnr.exe" -dir "C:\work\org.hl7.fhir\build" -fileMask "*.xml" -fin
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
rem call mvn clean deploy -Dmaven.test.redirectTestOutputToFile=false -DdeployAtEnd=true
IF %ERRORLEVEL% NEQ 0 (
GOTO DONE
)