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fix issue with validating fixed values for primitive elements

This commit is contained in:
Grahame Grieve 2021-03-29 17:26:12 +11:00
parent 4e4885dc7d
commit 032b81a38e
3 changed files with 78 additions and 23 deletions
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9
RELEASE_NOTES.md
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@ -1,6 +1,13 @@
Version Conversion:
* add test for Observation conversion from 10 to 40
* add procedures conversion form dstu2 to r4
* add medication conversion from dstu2 to r4
* add copy of extension field for Enumeration fieldtype by Resource.copy
* minor fixes in code generators for R4B
* add default value to Medication Request during conversion from dstu2 to r4
* fix R2B/R5 ElementDefinition.type.code conversion
Other:
* minor fixes in code generators for R4B
* Fix null pointer exception in validator validating language codes
* fix issue with validating fixed values for primitive elements
* add utility to unzip file

47
org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/Utilities.java
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@ -50,6 +50,7 @@ import java.nio.channels.FileChannel;
import java.nio.file.Files;
import java.nio.file.Path;
import java.nio.file.Paths;
import java.nio.file.StandardCopyOption;
import java.time.Duration;
import java.util.ArrayList;
import java.util.Arrays;
@ -60,6 +61,8 @@ import java.util.List;
import java.util.Set;
import java.util.UUID;
import java.util.concurrent.TimeUnit;
import java.util.zip.ZipEntry;
import java.util.zip.ZipInputStream;
import static org.apache.commons.lang3.StringUtils.isBlank;
@ -1398,5 +1401,49 @@ public class Utilities {
return res;
}
public static void unzip(InputStream zip, Path target) throws IOException {
try (ZipInputStream zis = new ZipInputStream(zip)) {
ZipEntry zipEntry = zis.getNextEntry();
while (zipEntry != null) {
boolean isDirectory = false;
if (zipEntry.getName().endsWith("/") || zipEntry.getName().endsWith("\\")) {
isDirectory = true;
}
Path newPath = zipSlipProtect(zipEntry, target);
if (isDirectory) {
Files.createDirectories(newPath);
} else {
if (newPath.getParent() != null) {
if (Files.notExists(newPath.getParent())) {
Files.createDirectories(newPath.getParent());
}
}
Files.copy(zis, newPath, StandardCopyOption.REPLACE_EXISTING);
}
zipEntry = zis.getNextEntry();
}
zis.closeEntry();
}
}
private static Path zipSlipProtect(ZipEntry zipEntry, Path targetDir)
throws IOException {
// test zip slip vulnerability
// Path targetDirResolved = targetDir.resolve("../../" + zipEntry.getName());
Path targetDirResolved = targetDir.resolve(zipEntry.getName());
// make sure normalized file still has targetDir as its prefix
// else throws exception
Path normalizePath = targetDirResolved.normalize();
if (!normalizePath.startsWith(targetDir)) {
throw new IOException("Bad zip entry: " + zipEntry.getName());
}
return normalizePath;
}
}

45
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/instance/type/StructureDefinitionValidator.java
View File

@ -125,7 +125,16 @@ public class StructureDefinitionValidator extends BaseValidator {
if (hasMustSupportExtension(type)) {
typeMustSupport = true;
}
typeCodes.add(type.getChildValue("code"));
String tc = type.getChildValue("code");
if (type.hasExtension("http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type")) {
tc = type.getExtensionValue("http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type").primitiveValue();
}
if (Utilities.noString(tc) && type.hasChild("code")) {
if (type.getNamedChild("code").hasExtension("http://hl7.org/fhir/StructureDefinition/structuredefinition-json-type")) {
tc = "*";
}
}
typeCodes.add(tc);
// check the stated profile - must be a constraint on the type
if (snapshot || sd != null) {
validateElementType(errors, type, stack.push(type, -1, null, null), sd, element.getChildValue("path"));
@ -148,27 +157,19 @@ public class StructureDefinitionValidator extends BaseValidator {
}
// in a snapshot, we validate that fixedValue, pattern, and defaultValue, if present, are all of the right type
if (snapshot && element.getIdBase().contains(".")) {
if (rule(errors, IssueType.EXCEPTION, stack.getLiteralPath(), !typeCodes.isEmpty() || element.hasChild("contentReference"), I18nConstants.SD_NO_TYPES_OR_CONTENTREF, element.getIdBase())) {
/*
TODO Grahame, this is breaking the ig publisher for implementers
https://chat.fhir.org/#narrow/stream/215610-shorthand/topic/The.20element.20Extension.2Eurl.20has.20a.20fixed.20of.20type.20uri
https://chat.fhir.org/#narrow/stream/179252-IG-creation/topic/BUG.3A.20The.20element.20Extension.2Eurl.20has.20a.20fixed.20of.20type.20uri
https://github.com/HL7/fhir-ig-publisher/issues/240
This was brought up to Wayne, so I'm commenting it out for now. When you get back we can discuss how to
put the changes back in.
*/
// Element v = element.getNamedChild("defaultValue");
// if (v != null) {
// rule(errors, IssueType.EXCEPTION, stack.push(v, -1, null, null).getLiteralPath(), typeCodes.contains(v.fhirType()), I18nConstants.SD_VALUE_TYPE_IILEGAL, element.getIdBase(), "defaultValue", v.fhirType(), typeCodes);
// }
// v = element.getNamedChild("fixed");
// if (v != null) {
// rule(errors, IssueType.EXCEPTION, stack.push(v, -1, null, null).getLiteralPath(), typeCodes.contains(v.fhirType()), I18nConstants.SD_VALUE_TYPE_IILEGAL, element.getIdBase(), "fixed", v.fhirType(), typeCodes);
// }
// v = element.getNamedChild("pattern");
// if (v != null) {
// rule(errors, IssueType.EXCEPTION, stack.push(v, -1, null, null).getLiteralPath(), typeCodes.contains(v.fhirType()), I18nConstants.SD_VALUE_TYPE_IILEGAL, element.getIdBase(), "pattern", v.fhirType(), typeCodes);
// }
if (rule(errors, IssueType.EXCEPTION, stack.getLiteralPath(), !typeCodes.isEmpty() || element.hasChild("contentReference"), I18nConstants.SD_NO_TYPES_OR_CONTENTREF, element.getIdBase())) {
Element v = element.getNamedChild("defaultValue");
if (v != null) {
rule(errors, IssueType.EXCEPTION, stack.push(v, -1, null, null).getLiteralPath(), typeCodes.contains(v.fhirType()), I18nConstants.SD_VALUE_TYPE_IILEGAL, element.getIdBase(), "defaultValue", v.fhirType(), typeCodes);
}
v = element.getNamedChild("fixed");
if (v != null) {
rule(errors, IssueType.EXCEPTION, stack.push(v, -1, null, null).getLiteralPath(), typeCodes.contains(v.fhirType()), I18nConstants.SD_VALUE_TYPE_IILEGAL, element.getIdBase(), "fixed", v.fhirType(), typeCodes);
}
v = element.getNamedChild("pattern");
if (v != null) {
rule(errors, IssueType.EXCEPTION, stack.push(v, -1, null, null).getLiteralPath(), typeCodes.contains(v.fhirType()), I18nConstants.SD_VALUE_TYPE_IILEGAL, element.getIdBase(), "pattern", v.fhirType(), typeCodes);
}
}
}
}