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org.hl7.fhir.core
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Merge remote-tracking branch 'origin/master'

This commit is contained in:
Grahame Grieve 2023-08-22 22:58:13 +10:00
parent 53a9829e20 2ab5919e2e
commit 7a7a85f08f
13 changed files with 100 additions and 28 deletions
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11
org.hl7.fhir.convertors/pom.xml
View File

@ -78,10 +78,19 @@
<dependency>
<groupId>org.fhir</groupId>
<artifactId>ucum</artifactId>
<version>1.0.3</version>
<optional>true</optional>
</dependency>
<dependency>
<groupId>xpp3</groupId>
<artifactId>xpp3</artifactId>
<optional>true</optional>
</dependency>
<dependency>
<groupId>xpp3</groupId>
<artifactId>xpp3_xpath</artifactId>
<optional>true</optional>
</dependency>
<!-- HTTP Client -->
<dependency>
<groupId>org.apache.httpcomponents</groupId>

1
org.hl7.fhir.dstu2/pom.xml
View File

@ -32,7 +32,6 @@
<dependency>
<groupId>org.fhir</groupId>
<artifactId>ucum</artifactId>
<version>1.0.3</version>
<optional>true</optional>
</dependency>

15
org.hl7.fhir.dstu2016may/pom.xml
View File

@ -32,22 +32,7 @@
<dependency>
<groupId>org.fhir</groupId>
<artifactId>ucum</artifactId>
<version>1.0.3</version>
<optional>true</optional>
<exclusions>
<exclusion>
<groupId>xpp3</groupId>
<artifactId>xpp3</artifactId>
</exclusion>
<exclusion>
<groupId>xpp3</groupId>
<artifactId>xpp3_xpath</artifactId>
</exclusion>
<exclusion>
<groupId>xpp3</groupId>
<artifactId>xpp3_min</artifactId>
</exclusion>
</exclusions>
</dependency>
<!-- XML Parsers -->

1
org.hl7.fhir.dstu3/pom.xml
View File

@ -32,7 +32,6 @@
<dependency>
<groupId>org.fhir</groupId>
<artifactId>ucum</artifactId>
<version>1.0.3</version>
<optional>true</optional>
</dependency>

1
org.hl7.fhir.r4/pom.xml
View File

@ -39,7 +39,6 @@
<dependency>
<groupId>org.fhir</groupId>
<artifactId>ucum</artifactId>
<version>1.0.3</version>
<optional>true</optional>
</dependency>

68
org.hl7.fhir.r4/src/main/java/org/hl7/fhir/r4/utils/ParametersBuilder.java Normal file
View File

@ -0,0 +1,68 @@
package org.hl7.fhir.r4.utils;
import java.io.File;
import java.io.FileOutputStream;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.util.Arrays;
import java.util.Set;
import java.util.HashSet;
import org.hl7.fhir.r4.formats.IParser.OutputStyle;
import org.hl7.fhir.r4.formats.JsonParser;
import org.hl7.fhir.r4.model.Resource;
import org.hl7.fhir.r4.model.MetadataResource;
import org.hl7.fhir.r4.model.Parameters;
import org.hl7.fhir.utilities.TextFile;
/**
* Used to take an overload dump from tx.fhir.org and turn it into a parameters resource
*
* @author grahamegrieve
*
*/
public class ParametersBuilder {
public static void main(String[] args) throws FileNotFoundException, IOException {
new ParametersBuilder(args[0], args[1]).process(args[2]);
}
private String folder;
private String baseId;
protected ParametersBuilder(String folder, String baseId) {
super();
this.folder = folder;
this.baseId = baseId;
}
private void process(String output) throws FileNotFoundException, IOException {
Parameters p = new Parameters();
Set<String> ids = new HashSet<>();
for (File f : new File(folder).listFiles()) {
if (f.getName().startsWith(baseId)) {
if (f.getName().startsWith(baseId)) {
byte[] cnt = TextFile.fileToBytes(f);
cnt = shaveZeros(cnt); // bug in tx.fhir.org
MetadataResource r = (MetadataResource) new JsonParser().parse(cnt);
if (!ids.contains(r.getUrl()+"|"+r.getVersion())) {
ids.add(r.getUrl()+"|"+r.getVersion());
p.addParameter().setName("tx-resource").setResource(r);
}
}
}
}
new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(output), p);
}
private byte[] shaveZeros(byte[] cnt) {
for (int i = 0; i < cnt.length; i++) {
if (cnt[i] == 0) {
return Arrays.copyOf(cnt, i-1);
}
}
return cnt;
}
}

1
org.hl7.fhir.r4b/pom.xml
View File

@ -38,7 +38,6 @@
<dependency>
<groupId>org.fhir</groupId>
<artifactId>ucum</artifactId>
<version>1.0.3</version>
<optional>true</optional>
</dependency>

14
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/context/BaseWorkerContext.java
View File

@ -1499,7 +1499,7 @@ public abstract class BaseWorkerContext extends I18nBase implements IWorkerConte
boolean cache = false;
for (CanonicalType c : inc.getValueSet()) {
ValueSet vs = fetchResource(ValueSet.class, c.getValue(), src);
if (vs != null) {
if (vs != null && !hasCanonicalResource(pin, "tx-resource", vs.getVUrl())) {
pin.addParameter().setName("tx-resource").setResource(vs);
if (tcc.isTxCaching() && tcc.getCacheId() == null || !tcc.getCached().contains(vs.getVUrl())) {
tcc.getCached().add(vs.getVUrl());
@ -1509,7 +1509,7 @@ public abstract class BaseWorkerContext extends I18nBase implements IWorkerConte
}
}
CodeSystem cs = fetchResource(CodeSystem.class, inc.getSystem(), src);
if (cs != null && (cs.getContent() == CodeSystemContentMode.COMPLETE || cs.getContent() == CodeSystemContentMode.FRAGMENT)) {
if (cs != null && !hasCanonicalResource(pin, "tx-resource", cs.getVUrl()) && (cs.getContent() == CodeSystemContentMode.COMPLETE || cs.getContent() == CodeSystemContentMode.FRAGMENT)) {
pin.addParameter().setName("tx-resource").setResource(cs);
if (tcc.isTxCaching() && tcc.getCacheId() == null || !tcc.getCached().contains(cs.getVUrl())) {
tcc.getCached().add(cs.getVUrl());
@ -1520,6 +1520,16 @@ public abstract class BaseWorkerContext extends I18nBase implements IWorkerConte
return cache;
}
private boolean hasCanonicalResource(Parameters pin, String name, String vUrl) {
for (ParametersParameterComponent p : pin.getParameter()) {
if (name.equals(p.getName()) && p.hasResource() &&
p.getResource() instanceof CanonicalResource && vUrl.equals(((CanonicalResource) p.getResource()).getVUrl())) {
return true;
}
}
return false;
}
public ValidationResult processValidationResult(Parameters pOut, String vs) {
boolean ok = false;
String message = "No Message returned";

4
org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/PathBuilder.java
View File

@ -150,7 +150,7 @@ public class PathBuilder {
return;
}
if (isPathRoot(args[0])) {
throw new RuntimeException("First entry cannot be root: " + args[0]);
throw new RuntimeException("First entry in file path cannot be root: " + args[0]+", full path = "+String.join(", ", args));
}
}
@ -159,7 +159,7 @@ public class PathBuilder {
return;
}
if (args[0] == null || Utilities.noString(args[0].trim())) {
throw new RuntimeException("First path entry cannot be null or empty");
throw new RuntimeException("First entry in file path cannot be null or empty, full path = "+String.join(", ", args));
}
}

4
org.hl7.fhir.utilities/src/test/java/org/hl7/fhir/utilities/UtilitiesTest.java
View File

@ -293,7 +293,7 @@ class UtilitiesTest {
RuntimeException thrown = Assertions.assertThrows(RuntimeException.class, () -> {
Utilities.path(pathStrings);
});
assertTrue(thrown.getMessage().endsWith(pathStrings[0]));
assertTrue(thrown.getMessage().endsWith(pathStrings[0]+", full path = "+String.join(", ", pathStrings)));
}
public static Stream<Arguments> macAndLinuxNonFirstElementStartPaths() {
@ -384,7 +384,7 @@ class UtilitiesTest {
RuntimeException thrown = Assertions.assertThrows(RuntimeException.class, () -> {
Utilities.path(pathsStrings);
});
assertEquals("First path entry cannot be null or empty",thrown.getMessage());
assertEquals("First entry in file path cannot be null or empty, full path = "+String.join(", ", pathsStrings),thrown.getMessage());
}
@Test

1
org.hl7.fhir.validation.cli/pom.xml
View File

@ -286,7 +286,6 @@
<dependency>
<groupId>org.fhir</groupId>
<artifactId>ucum</artifactId>
<version>1.0.3</version>
</dependency>
<dependency>
<groupId>xpp3</groupId>

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

@ -120,7 +120,7 @@
<dependency>
<groupId>org.fhir</groupId>
<artifactId>ucum</artifactId>
<version>1.0.3</version>
<optional>true</optional>
</dependency>
<!-- CQL-to-ELM -->

5
pom.xml
View File

@ -164,6 +164,11 @@
<artifactId>Saxon-HE</artifactId>
<version>${saxon_he_version}</version>
</dependency>
<dependency>
<groupId>org.fhir</groupId>
<artifactId>ucum</artifactId>
<version>1.0.8</version>
</dependency>
<dependency>
<groupId>mysql</groupId>