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

This commit is contained in:
dotasek 2023-03-28 15:19:56 -04:00
parent c88c8762c8 7928c858bb
commit 56f99e4872
20 changed files with 251 additions and 122 deletions
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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>5.6.116-SNAPSHOT</version>
<version>5.6.117-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>5.6.116-SNAPSHOT</version>
<version>5.6.117-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>5.6.116-SNAPSHOT</version>
<version>5.6.117-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

2
org.hl7.fhir.dstu3/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>org.hl7.fhir.core</artifactId>
<version>5.6.116-SNAPSHOT</version>
<version>5.6.117-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

2
org.hl7.fhir.r4/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>org.hl7.fhir.core</artifactId>
<version>5.6.116-SNAPSHOT</version>
<version>5.6.117-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

2
org.hl7.fhir.r4b/.classpath
View File

@ -19,7 +19,7 @@
<attribute name="maven.pomderived" value="true"/>
</attributes>
</classpathentry>
<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-17">
<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-11">
<attributes>
<attribute name="maven.pomderived" value="true"/>
</attributes>

1
org.hl7.fhir.r4b/.project
View File

@ -17,6 +17,7 @@
</buildCommand>
</buildSpec>
<natures>
<nature>org.eclipse.pde.PluginNature</nature>
<nature>org.eclipse.jdt.core.javanature</nature>
<nature>org.eclipse.m2e.core.maven2Nature</nature>
</natures>

2
org.hl7.fhir.r4b/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>org.hl7.fhir.core</artifactId>
<version>5.6.116-SNAPSHOT</version>
<version>5.6.117-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

2
org.hl7.fhir.r5/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>org.hl7.fhir.core</artifactId>
<version>5.6.116-SNAPSHOT</version>
<version>5.6.117-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

8
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/elementmodel/FmlParser.java
View File

@ -108,10 +108,18 @@ public class FmlParser extends ParserBase {
parseGroup(result, lexer);
}
} catch (FHIRLexerException e) {
if (policy == ValidationPolicy.NONE) {
throw e;
} else {
logError("2023-02-24", e.getLocation().getLine(), e.getLocation().getColumn(), "??", IssueType.INVALID, e.getMessage(), IssueSeverity.FATAL);
}
} catch (Exception e) {
if (policy == ValidationPolicy.NONE) {
throw e;
} else {
logError("2023-02-24", -1, -1, "?", IssueType.INVALID, e.getMessage(), IssueSeverity.FATAL);
}
}
result.setIgnorePropertyOrder(true);
return result;
}

10
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/terminologies/CodeSystemUtilities.java
View File

@ -698,5 +698,15 @@ public class CodeSystemUtilities {
}
return list;
}
public static boolean checkDisplay(CodeSystem cs, ConceptDefinitionComponent cd, String display) {
List<String> displays = getDisplays(cs, cd);
for (String s : displays) {
if (s.equalsIgnoreCase(display)) {
return true;
}
}
return false;
}
}

2
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/test/utils/TestingUtilities.java
View File

@ -93,7 +93,7 @@ public class TestingUtilities extends BaseTestingUtilities {
fcontext.loadFromPackage(utg, new TestPackageLoader(Utilities.strings("CodeSystem", "ValueSet")));
}
if (!fcontext.hasPackage("hl7.fhir.uv.extensions", null)) {
NpmPackage ext = pcm.loadPackage("hl7.fhir.uv.extensions", "current");
NpmPackage ext = pcm.loadPackage("hl7.fhir.uv.extensions", "1.0.0");
System.out.println("Loading Extensions: "+ext.name()+"#"+ext.version());
fcontext.loadFromPackage(ext, new TestPackageLoader(Utilities.strings("CodeSystem", "ValueSet", "StructureDefinition")));
}

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>5.6.116-SNAPSHOT</version>
<version>5.6.117-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>5.6.116-SNAPSHOT</version>
<version>5.6.117-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

202
org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/PathBuilder.java Normal file
View File

@ -0,0 +1,202 @@
package org.hl7.fhir.utilities;
import lombok.AccessLevel;
import lombok.AllArgsConstructor;
import lombok.With;
import java.io.File;
import java.nio.file.Path;
import java.nio.file.Paths;
@AllArgsConstructor(access = AccessLevel.PRIVATE)
public class PathBuilder {
/**
* By default, the normalized built path must be a child of the first entry of the buildPath arguments. If a
* different parent is desired, this can be set via <code>withRequiredTarget</code>
*/
@With
private final String requiredTarget;
/**
* By default, the first entry of the buildPath argument cannot be null or an empty string. Setting this to false will
* disable this check.
*/
@With
private final boolean requireNonNullNonEmptyFirstEntry;
/**
* By default, the first entry of the buildPath argument cannot be a root directory (<code>"/", "C:\", etc. </code>. Setting this to false will disable this check.
*/
@With
private final boolean requireNonRootFirstEntry;
/**
* By default, the normalized built path must be a child of the first entry of the buildPath arguments. Setting this
* to false will disable this check.
*/
@With
private final boolean requirePathIsChildOfTarget;
/**
* Returns an instance of PathBuilder with all checks enabled (recommended).
*
* @return
*/
public static PathBuilder getPathBuilder() {
return new PathBuilder(null, true, true, true);
}
/**
* <p>Builds a path from the passed argument strings. This path will be compatible with the local filesystem.
* </p>
*
* <p>
* If the args contain variables enclosed in square brackets (<code>[ ]</code>), they will be replaced with values in
* the built path. There are several built-in variables available, listed below. Any text between square brackets that
* does not match these will be replaced by a matching System environment variable if one is available.
* </p>
*
* <p>
* Built-in variables include:
* <ul>
* <li><i>[tmp]</i> An available temp directory (Java Temp directory, <code>c:\\temp, $TMPDIR, %TEMP%</code>, etc.) </li>
* <li><i>[user]</i> The OS user directory (~, user.home, etc) </li>
* </ul>
* </p>
*
* <p>
* This method will run several checks by default to ensure that the built path does not point to unintended areas of
* the filesystem. If these checks are violated, a RuntimeException will be thrown. If needed in special cases, the
* behavior of these checks can be modified via the linked fluent constructor methods below.
* </p>
*
* @param args entries with which to construct the filesystem path
* @throws RuntimeException
* @return a local filesystem path
*
* @see this#withRequiredTarget(String)
* @see this#withRequireNonNullNonEmptyFirstEntry(boolean)
* @see this#withRequireNonRootFirstEntry(boolean)
* @see this#withRequirePathIsChildOfTarget(boolean)
*/
public String buildPath(String... args) {
checkNonNullNonEmptyFirstEntry(args);
checkNonRootFirstEntry(args);
StringBuilder stringBuilder = new StringBuilder();
boolean argIsNotEmptyOrNull = false;
boolean first = true;
for (String arg : args) {
if (first && arg == null)
continue;
first = false;
if (!argIsNotEmptyOrNull)
argIsNotEmptyOrNull = !Utilities.noString(arg);
else if (!stringBuilder.toString().endsWith(File.separator))
stringBuilder.append(File.separator);
String a = arg;
if (stringBuilder.length() == 0) {
a = replaceVariables(a);
}
a = a.replace("\\", File.separator);
a = a.replace("/", File.separator);
if (stringBuilder.length() > 0 && a.startsWith(File.separator))
a = a.substring(File.separator.length());
while (a.startsWith(".." + File.separator)) {
if (stringBuilder.length() == 0) {
stringBuilder = new StringBuilder(Paths.get(".").toAbsolutePath().normalize().toString());
} else {
String p = stringBuilder.toString().substring(0, stringBuilder.length() - 1);
if (!p.contains(File.separator)) {
stringBuilder = new StringBuilder();
} else {
stringBuilder = new StringBuilder(p.substring(0, p.lastIndexOf(File.separator)) + File.separator);
}
}
a = a.substring(3);
}
if ("..".equals(a)) {
int i = stringBuilder.substring(0, stringBuilder.length() - 1).lastIndexOf(File.separator);
stringBuilder = new StringBuilder(stringBuilder.substring(0, i + 1));
} else
stringBuilder.append(a);
}
checkPathIsChildOfTarget(stringBuilder.toString(), args);
return stringBuilder.toString();
}
private void checkPathIsChildOfTarget(String path, String[] args) {
if (!requirePathIsChildOfTarget) {
return;
}
final String target = requiredTarget != null
? requiredTarget
: args[0];
if (!Path.of(path).normalize().startsWith(Path.of(replaceVariables(target)).normalize())) {
throw new RuntimeException("Computed path does not start with first element: " + String.join(", ", args));
}
}
private void checkNonRootFirstEntry(String[] args) {
if (!requireNonRootFirstEntry) {
return;
}
if (isPathRoot(args[0])) {
throw new RuntimeException("First entry cannot be root: " + args[0]);
}
}
private void checkNonNullNonEmptyFirstEntry(String[] args) {
if (!requireNonNullNonEmptyFirstEntry) {
return;
}
if (args[0] == null || Utilities.noString(args[0].trim())) {
throw new RuntimeException("First entry cannot be null or empty");
}
}
private String replaceVariables(String a) {
if ("[tmp]".equals(a)) {
if (hasCTempDir()) {
return Utilities.C_TEMP_DIR;
} else if (ToolGlobalSettings.hasTempPath()) {
return ToolGlobalSettings.getTempPath();
} else {
return System.getProperty("java.io.tmpdir");
}
} else if ("[user]".equals(a)) {
return System.getProperty("user.home");
} else if (a.startsWith("[") && a.endsWith("]")) {
String ev = System.getenv(a.replace("[", "").replace("]", ""));
if (ev != null) {
return ev;
} else {
return "null";
}
}
return a;
}
protected static boolean hasCTempDir() {
if (!System.getProperty("os.name").toLowerCase().contains("win")) {
return false;
}
File tmp = new File(Utilities.C_TEMP_DIR);
return tmp.exists() && tmp.isDirectory() && tmp.canWrite();
}
protected static boolean isPathRoot(String pathString) {
boolean actual;
Path path = Path.of(pathString);
Path normalizedPath = path.normalize();
actual = normalizedPath.equals(path.getRoot());
return actual;
}
}

112
org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/Utilities.java
View File

@ -613,47 +613,22 @@ public class Utilities {
return s.toString();
}
private static boolean isPathRoot(String pathString) {
boolean actual;
Path path = Path.of(pathString);
Path normalizedPath = path.normalize();
actual = normalizedPath.equals(path.getRoot());
return actual;
}
/**
* Composes a path string using by concatenating the passed arguments.
* Variables such as [tmp] and [user] are replaced.
*
* In order to prevent unintentional access to areas of the file system
* outside of the first entry, this method will throw exceptions in situations
* where the constructed path is at a higher level than the first entry, or
* where the first entry is null or empty.
* This method enables all checks for unintended path locations.
*
* @param args
* @return
* @throws IOException
* @see PathBuilder#buildPath(String...)
*/
public static String path(String... args) throws IOException {
if (args[0] == null || noString(args[0].trim())) {
throw new RuntimeException("First entry cannot be null or empty");
}
if (isPathRoot(args[0])) {
throw new RuntimeException("First entry cannot be root: " + args[0]);
}
String output = uncheckedPath(args);
if (!Path.of(output.toString()).normalize().startsWith(Path.of(replaceVariables(args[0])).normalize())) {
throw new RuntimeException("Computed path does not start with first element: " + String.join(", ", args));
}
return output.toString();
return PathBuilder.getPathBuilder().buildPath(args);
}
/**
* Composes a path string using by concatenating the passed arguments.
* Variables such as [tmp] and [user] are replaced.
*
* This method does not check for unintentional access to areas of the file
* system outside of the first entry. ONLY USE THIS METHOD IN CASES WHERE YOU
@ -662,83 +637,18 @@ public class Utilities {
* @param args
* @return
* @throws IOException
*
* @see PathBuilder#buildPath(String...)
*/
@Deprecated
public static String uncheckedPath(String... args) {
StringBuilder s = new StringBuilder();
boolean argIsNotEmptyOrNull = false;
boolean first = true;
for (String arg : args) {
if (first && arg == null)
continue;
first = false;
if (!argIsNotEmptyOrNull)
argIsNotEmptyOrNull = !noString(arg);
else if (!s.toString().endsWith(File.separator))
s.append(File.separator);
String a = arg;
if (s.length() == 0) {
a = replaceVariables(a);
}
a = a.replace("\\", File.separator);
a = a.replace("/", File.separator);
if (s.length() > 0 && a.startsWith(File.separator))
a = a.substring(File.separator.length());
while (a.startsWith(".." + File.separator)) {
if (s.length() == 0) {
s = new StringBuilder(Paths.get(".").toAbsolutePath().normalize().toString());
} else {
String p = s.toString().substring(0, s.length() - 1);
if (!p.contains(File.separator)) {
s = new StringBuilder();
} else {
s = new StringBuilder(p.substring(0, p.lastIndexOf(File.separator)) + File.separator);
}
}
a = a.substring(3);
}
if ("..".equals(a)) {
int i = s.substring(0, s.length() - 1).lastIndexOf(File.separator);
s = new StringBuilder(s.substring(0, i + 1));
} else
s.append(a);
}
// if (!Path.of(s.toString()).normalize().startsWith(Path.of(replaceVariables(args[0])).normalize())) {
// throw new RuntimeException("Computed path '"+s.toString()+"' normalised to '"+Path.of(s.toString()).normalize()+"' does not start with first element: " + String.join(", ", args));
// }
return s.toString();
return PathBuilder.getPathBuilder()
.withRequireNonRootFirstEntry(false)
.withRequireNonNullNonEmptyFirstEntry(false)
.withRequirePathIsChildOfTarget(false)
.buildPath(args);
}
private static String replaceVariables(String a) {
if ("[tmp]".equals(a)) {
if (hasCTempDir()) {
return C_TEMP_DIR;
} else if (ToolGlobalSettings.hasTempPath()) {
return ToolGlobalSettings.getTempPath();
} else {
return System.getProperty("java.io.tmpdir");
}
} else if ("[user]".equals(a)) {
return System.getProperty("user.home");
} else if (a.startsWith("[") && a.endsWith("]")) {
String ev = System.getenv(a.replace("[", "").replace("]", ""));
if (ev != null) {
return ev;
} else {
return "null";
}
}
return a;
}
private static boolean hasCTempDir() {
if (!System.getProperty("os.name").toLowerCase().contains("win")) {
return false;
}
File tmp = new File(C_TEMP_DIR);
return tmp.exists() && tmp.isDirectory() && tmp.canWrite();
}
public static String pathURL(String... args) {
StringBuilder s = new StringBuilder();

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>5.6.116-SNAPSHOT</version>
<version>5.6.117-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>5.6.116-SNAPSHOT</version>
<version>5.6.117-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

6
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/instance/type/ConceptMapValidator.java
View File

@ -157,8 +157,7 @@ public class ConceptMapValidator extends BaseValidator {
if (warningOrError(srcCS.getContent() == CodeSystemContentMode.COMPLETE, errors, "2023-03-05", IssueType.REQUIRED, code.line(), code.col(), stack.push(code, -1, null, null).getLiteralPath(), cd != null, I18nConstants.CONCEPTMAP_GROUP_SOURCE_CODE_INVALID, c, srcCS.getVersionedUrl())) {
Element display = src.getNamedChild("display");
if (display != null) {
List<String> displays = CodeSystemUtilities.getDisplays(srcCS, cd);
ok = rule(errors, "2023-03-05", IssueType.REQUIRED, code.line(), code.col(), stack.push(code, -1, null, null).getLiteralPath(), displays.contains(display.getValue()), I18nConstants.CONCEPTMAP_GROUP_SOURCE_DISPLAY_INVALID, display.getValue(), displays) && ok;
warning(errors, "2023-03-05", IssueType.REQUIRED, code.line(), code.col(), stack.push(code, -1, null, null).getLiteralPath(), CodeSystemUtilities.checkDisplay(srcCS, cd, display.getValue()), I18nConstants.CONCEPTMAP_GROUP_SOURCE_DISPLAY_INVALID, display.getValue(), CodeSystemUtilities.getDisplays(srcCS, cd));
}
} else {
ok = false;
@ -184,8 +183,7 @@ public class ConceptMapValidator extends BaseValidator {
if (warningOrError(tgtCS.getContent() == CodeSystemContentMode.COMPLETE, errors, "2023-03-05", IssueType.REQUIRED, code.line(), code.col(), stack.push(code, -1, null, null).getLiteralPath(), cd != null, I18nConstants.CONCEPTMAP_GROUP_TARGET_CODE_INVALID, c, tgtCS.getVersionedUrl())) {
Element display = tgt.getNamedChild("display");
if (display != null) {
List<String> displays = CodeSystemUtilities.getDisplays(tgtCS, cd);
ok = rule(errors, "2023-03-05", IssueType.REQUIRED, code.line(), code.col(), stack.push(code, -1, null, null).getLiteralPath(), displays.contains(display.getValue()), I18nConstants.CONCEPTMAP_GROUP_TARGET_DISPLAY_INVALID, display.getValue(), displays) && ok;
warning(errors, "2023-03-05", IssueType.REQUIRED, code.line(), code.col(), stack.push(code, -1, null, null).getLiteralPath(), CodeSystemUtilities.checkDisplay(tgtCS, cd, display.getValue()), I18nConstants.CONCEPTMAP_GROUP_TARGET_DISPLAY_INVALID, display.getValue(), CodeSystemUtilities.getDisplays(tgtCS, cd));
}
} else {
ok = false;

2
pom.xml
View File

@ -14,7 +14,7 @@
HAPI FHIR
-->
<artifactId>org.hl7.fhir.core</artifactId>
<version>5.6.116-SNAPSHOT</version>
<version>5.6.117-SNAPSHOT</version>
<packaging>pom</packaging>
<properties>