honeymoose
/
org.hl7.fhir.core
mirror of https://github.com/hapifhir/org.hl7.fhir.core.git
1
0
Fork 0
Code Issues Packages Projects Releases Wiki Activity

Merge pull request #1155 from hapifhir/gg-202303-qa-sm-validation-4 

Gg 202303 qa sm validation 4
This commit is contained in:
Grahame Grieve 2023-03-07 23:28:35 +11:00 committed by GitHub
parent 5eca02f879 ed016ef9ed
commit 7a3825d9e8
No known key found for this signature in database
GPG Key ID: 4AEE18F83AFDEB23
28 changed files with 213 additions and 75 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

8
org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/loaders/loaderR5/BaseLoaderR5.java
View File

@ -17,6 +17,7 @@ import org.hl7.fhir.r5.model.StructureDefinition;
import org.hl7.fhir.r5.model.UriType;
import org.hl7.fhir.r5.model.ValueSet;
import org.hl7.fhir.r5.model.ValueSet.ConceptSetComponent;
import org.hl7.fhir.r5.utils.ToolingExtensions;
import org.hl7.fhir.r5.model.ElementDefinition.TypeRefComponent;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.VersionUtilities;
@ -158,7 +159,12 @@ public abstract class BaseLoaderR5 implements IContextResourceLoader {
tr.setCode(URL_BASE+versionString()+"/StructureDefinition/"+tr.getCode());
}
for (CanonicalType s : tr.getTargetProfile()) {
s.setValue(patchUrl(s.getValue(), "StructureDefinitino"));
s.setValue(patchUrl(s.getValue(), "StructureDefinition"));
}
if (tr.hasExtension(ToolingExtensions.EXT_FHIR_TYPE)) {
String code = ToolingExtensions.readStringExtension(tr, ToolingExtensions.EXT_FHIR_TYPE);
String url = URL_BASE+versionString()+"/StructureDefinition/"+code;
ToolingExtensions.setUrlExtension(tr, ToolingExtensions.EXT_FHIR_TYPE, url);
}
}
if (ed.hasBinding()) {

2
org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/misc/NpmPackageVersionConverter.java
View File

@ -84,7 +84,7 @@ public class NpmPackageVersionConverter {
output.put("package/other/spec.internals", convertSpec(content.get("package/other/spec.internals")));
for (Entry<String, byte[]> e : content.entrySet()) {
if (!e.getKey().equals("package/package.json") && !e.getKey().equals("package/other/spec.internals") && !e.getKey().endsWith("ig-r4.json")) {
if (!e.getKey().equals("package/package.json") && !e.getKey().equals("package/other/spec.internals") && !e.getKey().endsWith("ig-r4.json") && !e.getKey().endsWith("ig-r4.jsonX")) {
byte[] cnv = e.getValue();
try {
JsonObject json = JsonParser.parseObject(e.getValue());

2
org.hl7.fhir.dstu2/src/test/java/org/hl7/fhir/dstu2/test/TestingUtilities.java
View File

@ -134,7 +134,7 @@ public class TestingUtilities {
}
private static Node skipBlankText(Node node) {
while (node != null && (((node.getNodeType() == Node.TEXT_NODE) && Utilities.isWhitespace(node.getTextContent())) || (node.getNodeType() == Node.COMMENT_NODE)))
while (node != null && (((node.getNodeType() == Node.TEXT_NODE) && Utilities.isAllWhitespace(node.getTextContent())) || (node.getNodeType() == Node.COMMENT_NODE)))
node = node.getNextSibling();
return node;
}

2
org.hl7.fhir.dstu2016may/src/test/java/org/hl7/fhir/dstu2016may/test/TestingUtilities.java
View File

@ -134,7 +134,7 @@ public class TestingUtilities {
}
private static Node skipBlankText(Node node) {
while (node != null && (((node.getNodeType() == Node.TEXT_NODE) && Utilities.isWhitespace(node.getTextContent())) || (node.getNodeType() == Node.COMMENT_NODE)))
while (node != null && (((node.getNodeType() == Node.TEXT_NODE) && Utilities.isAllWhitespace(node.getTextContent())) || (node.getNodeType() == Node.COMMENT_NODE)))
node = node.getNextSibling();
return node;
}

2
org.hl7.fhir.dstu3/src/test/java/org/hl7/fhir/dstu3/test/support/TestingUtilities.java
View File

@ -164,7 +164,7 @@ public class TestingUtilities extends BaseTestingUtilities {
}
private static Node skipBlankText(Node node) {
while (node != null && (((node.getNodeType() == Node.TEXT_NODE) && Utilities.isWhitespace(node.getTextContent())) || (node.getNodeType() == Node.COMMENT_NODE)))
while (node != null && (((node.getNodeType() == Node.TEXT_NODE) && Utilities.isAllWhitespace(node.getTextContent())) || (node.getNodeType() == Node.COMMENT_NODE)))
node = node.getNextSibling();
return node;
}

2
org.hl7.fhir.r4/src/main/java/org/hl7/fhir/r4/test/utils/TestingUtilities.java
View File

@ -242,7 +242,7 @@ public class TestingUtilities {
}
private static Node skipBlankText(Node node) {
while (node != null && (((node.getNodeType() == Node.TEXT_NODE) && Utilities.isWhitespace(node.getTextContent())) || (node.getNodeType() == Node.COMMENT_NODE)))
while (node != null && (((node.getNodeType() == Node.TEXT_NODE) && Utilities.isAllWhitespace(node.getTextContent())) || (node.getNodeType() == Node.COMMENT_NODE)))
node = node.getNextSibling();
return node;
}

2
org.hl7.fhir.r4b/src/main/java/org/hl7/fhir/r4b/test/utils/TestingUtilities.java
View File

@ -257,7 +257,7 @@ public class TestingUtilities extends BaseTestingUtilities {
}
private static Node skipBlankText(Node node) {
while (node != null && (((node.getNodeType() == Node.TEXT_NODE) && Utilities.isWhitespace(node.getTextContent())) || (node.getNodeType() == Node.COMMENT_NODE)))
while (node != null && (((node.getNodeType() == Node.TEXT_NODE) && Utilities.isAllWhitespace(node.getTextContent())) || (node.getNodeType() == Node.COMMENT_NODE)))
node = node.getNextSibling();
return node;
}

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

@ -919,7 +919,7 @@ public class ProfileUtilities extends TranslatingUtilities {
throw new FHIRException(context.formatMessage(I18nConstants.ILLEGAL_PATH__IN_DIFFERENTIAL_IN__NAME_PORTION_EXCEEDS_64_CHARS_IN_LENGTH, p, url));
}
for (char ch : pp.toCharArray()) {
if (Character.isWhitespace(ch)) {
if (Utilities.isWhitespace(ch)) {
throw new FHIRException(context.formatMessage(I18nConstants.ILLEGAL_PATH__IN_DIFFERENTIAL_IN__NO_UNICODE_WHITESPACE, p, url));
}
if (Utilities.existsInList(ch, ',', ':', ';', '\'', '"', '/', '|', '?', '!', '@', '#', '$', '%', '^', '&', '*', '(', ')', '{', '}')) {

6
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/elementmodel/Element.java
View File

@ -659,6 +659,12 @@ public class Element extends Base {
return this;
}
public Element markLocation(Element src) {
this.line = src.line();
this.col = src.col();
return this;
}
public void clearDecorations() {
clearUserData("fhir.decorations");
for (Element e : children) {

10
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/elementmodel/FmlParser.java
View File

@ -361,10 +361,10 @@ public class FmlParser extends ParserBase {
rule.forceElement("source").makeElement("variable").setValue(StructureMapUtilities.AUTO_VAR_NAME);
rule.forceElement("target").makeElement("variable").setValue(StructureMapUtilities.AUTO_VAR_NAME);
rule.forceElement("target").makeElement("transform").setValue(StructureMapTransform.CREATE.toCode());
Element dep = rule.forceElement("dependent");
dep.makeElement("name").setValue(StructureMapUtilities.DEF_GROUP_NAME);
dep.addElement("parameter").makeElement("valueId").setValue(StructureMapUtilities.AUTO_VAR_NAME);
dep.addElement("parameter").makeElement("valueId").setValue(StructureMapUtilities.AUTO_VAR_NAME);
Element dep = rule.forceElement("dependent").markLocation(rule);
dep.makeElement("name").markLocation(rule).setValue(StructureMapUtilities.DEF_GROUP_NAME);
dep.addElement("parameter").markLocation(dep).makeElement("valueId").markLocation(dep).setValue(StructureMapUtilities.AUTO_VAR_NAME);
dep.addElement("parameter").markLocation(dep).makeElement("valueId").markLocation(dep).setValue(StructureMapUtilities.AUTO_VAR_NAME);
// no dependencies - imply what is to be done based on types
}
if (newFmt) {
@ -387,7 +387,7 @@ public class FmlParser extends ParserBase {
}
private void parseRuleReference(Element rule, FHIRLexer lexer) throws FHIRLexerException {
Element ref = rule.addElement("dependent");
Element ref = rule.addElement("dependent").markLocation(lexer.getCurrentLocation());
ref.makeElement("name").markLocation(lexer.getCurrentLocation()).setValue(lexer.take());
lexer.token("(");
boolean done = false;

3
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/test/utils/CompareUtilities.java
View File

@ -1,6 +1,7 @@
package org.hl7.fhir.r5.test.utils;
import org.apache.commons.codec.binary.Base64;
import org.apache.commons.lang3.StringUtils;
import org.hl7.fhir.utilities.CSFile;
import org.hl7.fhir.utilities.TextFile;
import org.hl7.fhir.utilities.ToolGlobalSettings;
@ -147,7 +148,7 @@ public class CompareUtilities extends BaseTestingUtilities {
}
private static Node skipBlankText(Node node) {
while (node != null && (((node.getNodeType() == Node.TEXT_NODE) && Utilities.isWhitespace(node.getTextContent())) || (node.getNodeType() == Node.COMMENT_NODE)))
while (node != null && (((node.getNodeType() == Node.TEXT_NODE) && StringUtils.isWhitespace(node.getTextContent())) || (node.getNodeType() == Node.COMMENT_NODE)))
node = node.getNextSibling();
return node;
}

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

@ -338,7 +338,7 @@ public class FHIRLexer {
comments.add(source.substring(start, cursor).trim());
cursor = cursor + 2;
}
} else if (Character.isWhitespace(source.charAt(cursor))) {
} else if (Utilities.isWhitespace(source.charAt(cursor))) {
last13 = currentLocation.checkChar(source.charAt(cursor), last13);
cursor++;
} else {

20
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/utils/ToolingExtensions.java
View File

@ -629,6 +629,26 @@ public class ToolingExtensions {
resource.getExtension().add(new Extension(uri).setValue(new UriType(value)));
}
public static void setUrlExtension(DomainResource resource, String uri, String value) {
if (Utilities.noString(value))
return;
Extension ext = getExtension(resource, uri);
if (ext != null)
ext.setValue(new UrlType(value));
else
resource.getExtension().add(new Extension(uri).setValue(new UrlType(value)));
}
public static void setUrlExtension(Element resource, String uri, String value) {
if (Utilities.noString(value))
return;
Extension ext = getExtension(resource, uri);
if (ext != null)
ext.setValue(new UrlType(value));
else
resource.getExtension().add(new Extension(uri).setValue(new UrlType(value)));
}
public static void setCodeExtension(DomainResource resource, String uri, String value) {
if (Utilities.noString(value))
return;

78
org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/Utilities.java
View File

@ -826,7 +826,7 @@ public class Utilities {
boolean isWhitespace = false;
for (int i = 0; i < s.length(); i++) {
char c = s.charAt(i);
if (!Character.isWhitespace(c)) {
if (!isWhitespace(c)) {
b.append(Character.toLowerCase(c));
isWhitespace = false;
} else if (!isWhitespace) {
@ -861,15 +861,6 @@ public class Utilities {
}
public static boolean isWhitespace(String s) {
boolean ok = true;
for (int i = 0; i < s.length(); i++)
ok = ok && Character.isWhitespace(s.charAt(i));
return ok;
}
public static String URLEncode(String string) {
try {
return URLEncoder.encode(string, "UTF-8");
@ -1002,7 +993,11 @@ public class Utilities {
b.append("\\\"");
else if (c == '\\')
b.append("\\\\");
else if (((int) c) < 32)
else if (c == ' ')
b.append(" ");
else if (isWhitespace(c)) {
b.append("\\u"+Utilities.padLeft(Integer.toHexString(c), '0', 4));
} else if (((int) c) < 32)
b.append("\\u" + Utilities.padLeft(String.valueOf((int) c), '0', 4));
else
b.append(c);
@ -1086,15 +1081,15 @@ public class Utilities {
int expectedByte = in1.read();
while (expectedByte != -1) {
boolean w1 = isWhitespace(expectedByte);
boolean w1 = Character.isWhitespace(expectedByte);
if (w1)
while (isWhitespace(expectedByte))
while (Character.isWhitespace(expectedByte))
expectedByte = in1.read();
int foundByte = in2.read();
if (w1) {
if (!isWhitespace(foundByte))
if (!Character.isWhitespace(foundByte))
return false;
while (isWhitespace(foundByte))
while (Character.isWhitespace(foundByte))
foundByte = in2.read();
}
if (expectedByte != foundByte)
@ -1121,10 +1116,6 @@ public class Utilities {
}
}
private static boolean isWhitespace(int b) {
return b == 9 || b == 10 || b == 13 || b == 32;
}
public static boolean compareIgnoreWhitespace(String fn1, String fn2) throws IOException {
return compareIgnoreWhitespace(new File(fn1), new File(fn2));
@ -1880,5 +1871,54 @@ public class Utilities {
public static boolean isValidCRName(String name) {
return name != null && name.matches("[A-Z]([A-Za-z0-9_]){1,254}");
}
public static boolean isAllWhitespace(String s) {
if (Utilities.noString(s)) {
return true;
}
for (char ch : s.toCharArray()) {
if (!isWhitespace(ch)) {
return false;
}
}
return true;
}
public static String trimWS(String s) {
if (Utilities.noString(s)) {
return s;
}
int start = 0;
while (start < s.length() && isWhitespace(s.charAt(start))) {
start++;
}
if (start == s.length()) {
return "";
}
int end = s.length() - 1;
while (end >= 0 && isWhitespace(s.charAt(end))) {
end--;
}
if (start > end) {
return "";
}
return s.substring(start, end+1);
}
// from https://en.wikipedia.org/wiki/Whitespace_character#Unicode
public static boolean isWhitespace(int ch) {
return Utilities.existsInList(ch, '\u0009', '\n', '\u000B','\u000C','\r','\u0020','\u0085','\u00A0',
'\u1680','\u2000','\u2001','\u2002','\u2003','\u2004','\u2005','\u2006','\u2007','\u2008','\u2009','\u200A',
'\u2028', '\u2029', '\u202F', '\u205F', '\u3000');
}
//public static boolean !isWhitespace(String s) {
//boolean ok = true;
//for (int i = 0; i < s.length(); i++)
// ok = ok && Character.isWhitespace(s.charAt(i));
//return ok;
//
//}
}

1
org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/i18n/I18nConstants.java
View File

@ -534,6 +534,7 @@ public class I18nConstants {
public static final String TYPE_SPECIFIC_CHECKS_DT_QTY_NO_ANNOTATIONS = "TYPE_SPECIFIC_CHECKS_DT_QTY_NO_ANNOTATIONS";
public static final String TYPE_SPECIFIC_CHECKS_DT_STRING_LENGTH = "Type_Specific_Checks_DT_String_Length";
public static final String TYPE_SPECIFIC_CHECKS_DT_STRING_WS = "Type_Specific_Checks_DT_String_WS";
public static final String TYPE_SPECIFIC_CHECKS_DT_STRING_WS_ALL = "Type_Specific_Checks_DT_String_WS_ALL";
public static final String TYPE_SPECIFIC_CHECKS_DT_TIME_VALID = "Type_Specific_Checks_DT_Time_Valid";
public static final String TYPE_SPECIFIC_CHECKS_DT_URI_OID = "Type_Specific_Checks_DT_URI_OID";
public static final String TYPE_SPECIFIC_CHECKS_DT_URI_UUID = "Type_Specific_Checks_DT_URI_UUID";

3
org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/xhtml/CDANarrativeFormat.java
View File

@ -33,6 +33,7 @@ package org.hl7.fhir.utilities.xhtml;
import java.io.IOException;
import org.apache.commons.lang3.StringUtils;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.xml.IXMLWriter;
@ -81,7 +82,7 @@ public class CDANarrativeFormat {
xn.addComment(n.getTextContent());
return;
case Node.TEXT_NODE:
if (!Utilities.isWhitespace(n.getTextContent()))
if (!StringUtils.isWhitespace(n.getTextContent()))
xn.addText(n.getTextContent());
return;
case Node.ELEMENT_NODE:

3
org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/xhtml/HierarchicalTableGenerator.java
View File

@ -77,6 +77,7 @@ import javax.imageio.ImageIO;
import org.apache.commons.codec.binary.Base64;
import org.apache.commons.io.FileUtils;
import org.apache.commons.lang3.StringUtils;
import org.commonmark.node.Node;
import org.commonmark.parser.Parser;
import org.commonmark.renderer.html.HtmlRenderer;
@ -303,7 +304,7 @@ public class HierarchicalTableGenerator extends TranslatingUtilities {
myPieces.add(new Piece("br"));
}
if (c.getNodeType() == NodeType.Text) {
if (!Utilities.isWhitespace(c.getContent()))
if (!StringUtils.isWhitespace(c.getContent()))
addNode(myPieces, c, style);
} else if ("p".equals(c.getName())) {
for (XhtmlNode g : c.getChildNodes()) {

5
org.hl7.fhir.utilities/src/main/resources/Messages.properties
View File

@ -218,6 +218,7 @@ Type_Specific_Checks_DT_Primitive_ValueExt = Primitive types must have a value o
Type_Specific_Checks_DT_Primitive_WS = Primitive types should not only be whitespace
Type_Specific_Checks_DT_String_Length = value is longer than permitted maximum length of 1 MB (1048576 bytes)
Type_Specific_Checks_DT_String_WS = value should not start or finish with whitespace ''{0}''
Type_Specific_Checks_DT_String_WS_ALL = value should not be all whitespace ''{0}''
Type_Specific_Checks_DT_Time_Valid = Not a valid time ({0})
Type_Specific_Checks_DT_URI_OID = URI values cannot start with oid:
Type_Specific_Checks_DT_URI_UUID = URI values cannot start with uuid:
@ -882,9 +883,9 @@ SM_TARGET_TRANSLATE_BINDING_VS_TARGET = The target variable refers to an unknown
SM_TARGET_TRANSLATE_BINDING_VSE_TARGET = There was an error expanding the target value set, so this concept map can''t be checked: ''{0}''
SM_TARGET_TRANSLATE_BINDING_TARGET_WRONG = The map produces one or more codes that the target value set does not include: {0}
CONCEPTMAP_GROUP_SOURCE_MISSING = No Source Code System, so the source codes cannot be checked
CONCEPTMAP_GROUP_SOURCE_UNKNOWN = Unknown Source Code System, so the source codes cannot be checked
CONCEPTMAP_GROUP_SOURCE_UNKNOWN = Unknown Source Code System {0}, so the source codes cannot be checked
CONCEPTMAP_GROUP_TARGET_MISSING = No Target Code System, so the source codes cannot be checked
CONCEPTMAP_GROUP_TARGET_UNKNOWN = Unknown Target Code System, so the source codes cannot be checked
CONCEPTMAP_GROUP_TARGET_UNKNOWN = Unknown Target Code System {0}, so the target codes cannot be checked
CONCEPTMAP_GROUP_SOURCE_CODE_INVALID = The source code ''{0}'' is not valid in the code system {1}
CONCEPTMAP_GROUP_SOURCE_DISPLAY_INVALID = The source display ''{0}'' is not valid. Possible codes {1}
CONCEPTMAP_GROUP_TARGET_CODE_INVALID =The target code ''{0}'' is not valid in the code system {1}

37
org.hl7.fhir.utilities/src/test/java/org/hl7/fhir/utilities/UtilitiesTest.java
View File

@ -229,5 +229,42 @@ class UtilitiesTest {
Assertions.assertEquals(17, Utilities.getDatePrecision("1900-06-06T14:00:00.000-10:00"));
}
@Test
@DisplayName("trimWS tests")
void testTrimWS() {
Assertions.assertEquals("", Utilities.trimWS(""));
Assertions.assertEquals("", Utilities.trimWS(" "));
Assertions.assertEquals("t", Utilities.trimWS(" t "));
Assertions.assertEquals(".", Utilities.trimWS("\r."));
Assertions.assertEquals("# %", Utilities.trimWS("# %"));
Assertions.assertEquals("", Utilities.trimWS("\u0009\n\u000B\u000C\r\u0020\u0085\u00A0\u1680\u2000\u2001\u2002\u2003\u2004\u2005\u2006\u2007\u2008\u2009\u200A\u2028\u2029\u202F\u205F\u3000"));
}
@Test
@DisplayName("regex tests")
void testRegex() {
Assertions.assertFalse("".matches(".+"));
Assertions.assertTrue(".".matches(".+"));
Assertions.assertTrue(" t ".matches(".+"));
Assertions.assertTrue(" ".matches(".+"));
Assertions.assertFalse("".matches("^.+$"));
Assertions.assertTrue(".".matches("^.+$"));
Assertions.assertTrue(" t ".matches("^.+$"));
Assertions.assertTrue(" ".matches("^.+$"));
Assertions.assertFalse("".matches("[\\s\\S]+"));
Assertions.assertTrue(".".matches("[\\s\\S]+"));
Assertions.assertTrue(" t ".matches("[\\s\\S]+"));
Assertions.assertTrue(" ".matches("[\\s\\S]+"));
Assertions.assertFalse("".matches("^[\\s\\S]+$"));
Assertions.assertTrue(".".matches("^[\\s\\S]+$"));
Assertions.assertTrue(" t ".matches("^[\\s\\S]+$"));
Assertions.assertTrue(" ".matches("^[\\s\\S]+$"));
Assertions.assertTrue("Example Requirements Set 2".matches("^[\\s\\S]+$"));
Assertions.assertTrue("\u0009\n\u000B\u000C\r\u0020\u0085\u00A0\u1680\u2000\u2001\u2002\u2003\u2004\u2005\u2006\u2007\u2008\u2009\u200A\u2028\u2029\u202F\u205F\u3000".matches("^[\\s\\S]+$"));
Assertions.assertFalse("\u0009\n\u000B\u000C\r\u0020\u0085\u00A0\u1680\u2000\u2001\u2002\u2003\u2004\u2005\u2006\u2007\u2008\u2009\u200A\u2028\u2029\u202F\u205F\u3000".matches(".+"));
Assertions.assertFalse("\u0009\n\u000B\u000C\r\u0020\u0085\u00A0\u1680\u2000\u2001\u2002\u2003\u2004\u2005\u2006\u2007\u2008\u2009\u200A\u2028\u2029\u202F\u205F\u3000".matches("^.+$"));
}
}

7
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/cli/renderers/CompactRenderer.java
View File

@ -4,6 +4,7 @@ import java.io.File;
import java.io.FileOutputStream;
import java.io.IOException;
import java.io.PrintStream;
import java.text.SimpleDateFormat;
import java.util.ArrayList;
import java.util.Collections;
import java.util.List;
@ -35,17 +36,17 @@ public class CompactRenderer extends ValidationOutputRenderer {
}
private void render(PrintStream d, OperationOutcome op) {
d.println(ToolingExtensions.readStringExtension(op, ToolingExtensions.EXT_OO_FILE));
d.println(ToolingExtensions.readStringExtension(op, ToolingExtensions.EXT_OO_FILE)+" "+getRunDate());
List<String> lines = new ArrayList<>();
for (OperationOutcome.OperationOutcomeIssueComponent issue : op.getIssue()) {
String path = issue.hasExpression() ? issue.getExpression().get(0).asStringValue() : "n/a";
int line = ToolingExtensions.readIntegerExtension(issue, ToolingExtensions.EXT_ISSUE_LINE, -1);
int col = ToolingExtensions.readIntegerExtension(issue, ToolingExtensions.EXT_ISSUE_COL, -1);
lines.add("["+Integer.toString(line) + ", " + Integer.toString(col)+"] "+path+": "+issue.getSeverity().getDisplay()+" - "+issue.getDetails().getText());
lines.add(Utilities.padLeft(Integer.toString(line), '0', 8) + ":" + Utilities.padLeft(Integer.toString(col), '0', 8)+":"+path+"|["+Integer.toString(line) + ", " + Integer.toString(col)+"] "+path+": "+issue.getSeverity().getDisplay()+" - "+issue.getDetails().getText());
}
Collections.sort(lines);
for (String s : lines) {
d.println(s);
d.println(s.substring(s.indexOf("|")+1));
}
}

9
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/cli/renderers/ValidationOutputRenderer.java
View File

@ -9,6 +9,7 @@ import org.hl7.fhir.r5.model.OperationOutcome;
public abstract class ValidationOutputRenderer {
private String runDate;
protected boolean crumbTrails;
protected boolean moreThanOne;
protected PrintStream dst;
@ -21,6 +22,14 @@ public abstract class ValidationOutputRenderer {
this.crumbTrails = crumbTrails;
}
public String getRunDate() {
return runDate;
}
public void setRunDate(String runDate) {
this.runDate = runDate;
}
public void start(boolean moreThanOne) {
this.moreThanOne = moreThanOne;
}

6
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/cli/services/ValidationService.java
View File

@ -5,8 +5,11 @@ import java.io.FileOutputStream;
import java.io.PrintStream;
import java.lang.management.ManagementFactory;
import java.lang.management.MemoryMXBean;
import java.text.SimpleDateFormat;
import java.util.ArrayList;
import java.util.Date;
import java.util.List;
import java.util.Locale;
import org.hl7.fhir.r5.conformance.R5ExtensionsLoader;
import org.hl7.fhir.r5.context.ContextUtilities;
@ -59,9 +62,11 @@ import org.hl7.fhir.validation.cli.utils.VersionSourceInformation;
public class ValidationService {
private final SessionCache sessionCache;
private String runDate;
public ValidationService() {
sessionCache = new SessionCache();
runDate = new SimpleDateFormat("hh:mm:ss", new Locale("en", "US")).format(new Date());
}
protected ValidationService(SessionCache cache) {
@ -123,6 +128,7 @@ public class ValidationService {
PrintStream dst = null;
ValidationOutputRenderer renderer = makeValidationOutputRenderer(cliContext);
renderer.setCrumbTrails(validator.isCrumbTrails());
renderer.setRunDate(runDate);
if (renderer.isSingleFile()) {
if (cliContext.getOutput() == null) {
dst = System.out;

37
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/instance/InstanceValidator.java
View File

@ -2258,7 +2258,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
ok = rule(errors, NO_RULE_DATE, IssueType.INVALID, e.line(), e.col(), path, e.hasChildren(), I18nConstants.TYPE_SPECIFIC_CHECKS_DT_PRIMITIVE_VALUEEXT) && ok;
else if (e.primitiveValue().length() == 0)
ok = rule(errors, NO_RULE_DATE, IssueType.INVALID, e.line(), e.col(), path, e.hasChildren(), I18nConstants.TYPE_SPECIFIC_CHECKS_DT_PRIMITIVE_NOTEMPTY) && ok;
else if (StringUtils.isWhitespace(e.primitiveValue()))
else if (Utilities.isAllWhitespace(e.primitiveValue()))
warning(errors, NO_RULE_DATE, IssueType.INVALID, e.line(), e.col(), path, e.hasChildren(), I18nConstants.TYPE_SPECIFIC_CHECKS_DT_PRIMITIVE_WS);
if (context.hasBinding()) {
ok = rule(errors, NO_RULE_DATE, IssueType.CODEINVALID, e.line(), e.col(), path, context.getBinding().getStrength() != BindingStrength.REQUIRED, I18nConstants.Terminology_TX_Code_ValueSet_MISSING) && ok;
@ -2306,7 +2306,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
String url = e.primitiveValue();
ok = rule(errors, NO_RULE_DATE, IssueType.INVALID, e.line(), e.col(), path, !url.startsWith("oid:"), I18nConstants.TYPE_SPECIFIC_CHECKS_DT_URI_OID) && ok;
ok = rule(errors, NO_RULE_DATE, IssueType.INVALID, e.line(), e.col(), path, !url.startsWith("uuid:"), I18nConstants.TYPE_SPECIFIC_CHECKS_DT_URI_UUID) && ok;
ok = rule(errors, NO_RULE_DATE, IssueType.INVALID, e.line(), e.col(), path, url.equals(url.trim().replace(" ", ""))
ok = rule(errors, NO_RULE_DATE, IssueType.INVALID, e.line(), e.col(), path, url.equals(Utilities.trimWS(url).replace(" ", ""))
// work around an old invalid example in a core package
|| "http://www.acme.com/identifiers/patient or urn:ietf:rfc:3986 if the Identifier.value itself is a full uri".equals(url), I18nConstants.TYPE_SPECIFIC_CHECKS_DT_URI_WS, url) && ok;
ok = rule(errors, NO_RULE_DATE, IssueType.INVALID, e.line(), e.col(), path, !context.hasMaxLength() || context.getMaxLength() == 0 || url.length() <= context.getMaxLength(), I18nConstants.TYPE_SPECIFIC_CHECKS_DT_PRIMITIVE_LENGTH, context.getMaxLength()) && ok;
@ -2353,7 +2353,9 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
}
if (type.equalsIgnoreCase("string") && e.hasPrimitiveValue()) {
if (rule(errors, NO_RULE_DATE, IssueType.INVALID, e.line(), e.col(), path, e.primitiveValue() == null || e.primitiveValue().length() > 0, I18nConstants.TYPE_SPECIFIC_CHECKS_DT_PRIMITIVE_NOTEMPTY)) {
warning(errors, NO_RULE_DATE, IssueType.INVALID, e.line(), e.col(), path, e.primitiveValue() == null || e.primitiveValue().trim().equals(e.primitiveValue()), I18nConstants.TYPE_SPECIFIC_CHECKS_DT_STRING_WS, prepWSPresentation(e.primitiveValue()));
if (warning(errors, NO_RULE_DATE, IssueType.INVALID, e.line(), e.col(), path, e.primitiveValue() == null || !Utilities.isAllWhitespace(e.primitiveValue()), I18nConstants.TYPE_SPECIFIC_CHECKS_DT_STRING_WS_ALL, prepWSPresentation(e.primitiveValue()))) {
warning(errors, NO_RULE_DATE, IssueType.INVALID, e.line(), e.col(), path, e.primitiveValue() == null || Utilities.trimWS(e.primitiveValue()).equals(e.primitiveValue()), I18nConstants.TYPE_SPECIFIC_CHECKS_DT_STRING_WS, prepWSPresentation(e.primitiveValue()));
}
if (rule(errors, NO_RULE_DATE, IssueType.INVALID, e.line(), e.col(), path, e.primitiveValue().length() <= 1048576, I18nConstants.TYPE_SPECIFIC_CHECKS_DT_STRING_LENGTH)) {
ok = rule(errors, NO_RULE_DATE, IssueType.INVALID, e.line(), e.col(), path, !context.hasMaxLength() || context.getMaxLength() == 0 || e.primitiveValue().length() <= context.getMaxLength(), I18nConstants.TYPE_SPECIFIC_CHECKS_DT_PRIMITIVE_LENGTH, context.getMaxLength()) && ok;
} else {
@ -2623,24 +2625,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
if (Utilities.noString(s)) {
return "";
}
if (!StringUtils.containsWhitespace(s.trim())) {
return s;
}
int b = 0;
while (Character.isWhitespace(s.charAt(b))) {
b++;
}
while (!Character.isWhitespace(s.charAt(b))) {
b++;
}
int e = s.length() - 1;
while (Character.isWhitespace(s.charAt(e))) {
e--;
}
while (!Character.isWhitespace(s.charAt(e))) {
e--;
}
return s.substring(0, b)+"..."+s.substring(e+1);
return Utilities.escapeJson(s);
}
public boolean validateReference(ValidatorHostContext hostContext, List<ValidationMessage> errors, String path, String type, ElementDefinition context, Element e, String url) {
@ -2803,7 +2788,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
boolean ok = true;
for (int i = 0; i < theEncoded.length(); i++) {
char nextChar = theEncoded.charAt(i);
if (Character.isWhitespace(nextChar)) {
if (Utilities.isWhitespace(nextChar)) {
continue;
}
if (Character.isLetterOrDigit(nextChar)) {
@ -2826,7 +2811,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
}
for (int i = 0; i < theEncoded.length(); i++) {
char nextChar = theEncoded.charAt(i);
if (Character.isWhitespace(nextChar)) {
if (Utilities.isWhitespace(nextChar)) {
return true;
}
}
@ -2930,7 +2915,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
return context.formatMessage(I18nConstants.XHTML_URL_DATA_DATA_INVALID, value);
} else {
if (p[0].startsWith(" ")) {
p[0] = p[0].trim();
p[0] = Utilities.trimWS(p[0]);
}
String mMsg = checkValidMimeType(p[0].substring(0, p[0].lastIndexOf(";")));
if (mMsg != null) {
@ -4039,7 +4024,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
}
private boolean passesCodeWhitespaceRules(String v) {
if (!v.trim().equals(v))
if (!Utilities.trimWS(v).equals(v))
return false;
boolean lastWasSpace = true;
for (char c : v.toCharArray()) {
@ -4048,7 +4033,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
return false;
else
lastWasSpace = true;
} else if (Character.isWhitespace(c) || c == '\u00A0')
} else if (Utilities.isWhitespace(c))
return false;
else
lastWasSpace = false;

29
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/instance/type/StructureMapValidator.java
View File

@ -160,6 +160,14 @@ public class StructureMapValidator extends BaseValidator {
public String getWorkingType() {
if (type != null) {
if (ed != null) {
for (TypeRefComponent td : ed.getType()) {
StructureDefinition sd = context.fetchTypeDefinition(td.getWorkingCode());
if (sd != null && sd.getType().equals(type)) {
return td.getWorkingCode();
}
}
}
return type;
}
if (ed != null && ed.getType().size() == 1) {
@ -558,7 +566,8 @@ public class StructureMapValidator extends BaseValidator {
private boolean hasType(ElementDefinition ed, String type) {
for (TypeRefComponent td : ed.getType()) {
if (type.equals(td.getWorkingCode())) {
StructureDefinition sd = context.fetchTypeDefinition(td.getWorkingCode());
if (sd != null && type.equals(sd.getType())) {
return true;
}
}
@ -802,12 +811,12 @@ public class StructureMapValidator extends BaseValidator {
// * there's a default type group for the type of the source type
// otherwise, we can't know the target type.
if (ruleInfo.getDefVariable() != null && "create".equals(transform) && params.isEmpty()) {
if (ruleInfo.getDefVariable() != null && Utilities.existsInList(transform, "create", "copy") && params.isEmpty()) {
VariableDefn v = variables.getVariable(ruleInfo.getDefVariable(), SOURCE);
if (v != null && v.getEd() != null && (v.getEd().getType().size() == 1 || v.getType() != null)) {
List<Element> dependents = rule.getChildrenByName("dependent");
if (dependents.size() == 1 && StructureMapUtilities.DEF_GROUP_NAME.equals(dependents.get(0).getChildValue("name"))) {
String type = v.getType() != null ? v.getType() : v.getEd().getTypeFirstRep().getWorkingCode();
String type = v.getType() != null ? getTypeFromDefn(v.getEd(), v.getType()) : v.getEd().getTypeFirstRep().getWorkingCode();
// now, we look for a default group.
// todo: look in this source
// now look through the inputs
@ -830,6 +839,16 @@ public class StructureMapValidator extends BaseValidator {
return null;
}
private String getTypeFromDefn(ElementDefinition ed, String type) {
for (TypeRefComponent td : ed.getType()) {
StructureDefinition sd = context.fetchTypeDefinition(td.getWorkingCode());
if (sd != null && type.equals(sd.getType())) {
return td.getWorkingCode();
}
}
return type;
}
private boolean sameTypes(String type1, String type2) {
if (type1 == null || type2 == null) {
return false;
@ -844,11 +863,11 @@ public class StructureMapValidator extends BaseValidator {
}
private String getTypeForGroupInput(StructureMap map, StructureMapGroupComponent grp, StructureMapGroupInputComponent input) {
String type = input.getType();
StructureMapModelMode mode = input.getMode() == StructureMapInputMode.SOURCE ? StructureMapModelMode.SOURCE : StructureMapModelMode.TARGET;
if (input == null) {
return null;
}
String type = input.getType();
StructureMapModelMode mode = input.getMode() == StructureMapInputMode.SOURCE ? StructureMapModelMode.SOURCE : StructureMapModelMode.TARGET;
for (StructureMapStructureComponent st : map.getStructure()) {
if (type.equals(st.getAlias()) && mode == st.getMode()) {
return st.getUrl();

3
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/instance/utils/FHIRPathExpressionFixer.java
View File

@ -134,6 +134,9 @@ public class FHIRPathExpressionFixer {
if (regex.equals("-?(0|[1-9][0-9]{0,17})(\\.[0-9]{1,17})?([eE][+-]?[0-9]{1,9}})?")) {
return "-?(0|[1-9][0-9]{0,17})(\\.[0-9]{1,17})?([eE](0|[+\\-]?[1-9][0-9]{0,9}))?";
}
if (regex.equals("[ \\r\\n\\t\\S]+")) {
return "^[\\s\\S]+$";
}
return regex;
}

2
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/packages/PackageValidator.java
View File

@ -33,7 +33,7 @@ public class PackageValidator {
NpmPackage pi = pcm.loadPackage(v.getId(), v.getVersion());
if (VersionUtilities.isR4Ver(pi.fhirVersion()) || VersionUtilities.isR3Ver(pi.fhirVersion()) || VersionUtilities.isR2Ver(pi.fhirVersion())) {
for (String n : pi.list("package")) {
if (n.endsWith(".json") && !n.equals("ig-r4.json")) {
if (n.endsWith(".json") && !n.equals("ig-r4.json") && !n.equals("ig-r4.jsonX")) {
InputStream s = pi.load("package", n);
try {
parseResource(s, pi.fhirVersion());

3
org.hl7.fhir.validation/src/test/java/org/hl7/fhir/conversion/tests/UtilitiesXTests.java
View File

@ -45,6 +45,7 @@ import javax.xml.parsers.DocumentBuilderFactory;
import org.apache.commons.codec.binary.Base64;
import org.apache.commons.io.IOUtils;
import org.apache.commons.lang3.StringUtils;
import org.fhir.ucum.UcumEssenceService;
import org.hl7.fhir.convertors.loaders.loaderR5.NullLoaderKnowledgeProviderR5;
import org.hl7.fhir.convertors.loaders.loaderR5.R2016MayToR5Loader;
@ -265,7 +266,7 @@ public class UtilitiesXTests {
}
private static Node skipBlankText(Node node) {
while (node != null && (((node.getNodeType() == Node.TEXT_NODE) && Utilities.isWhitespace(node.getTextContent())) || (node.getNodeType() == Node.COMMENT_NODE)))
while (node != null && (((node.getNodeType() == Node.TEXT_NODE) && StringUtils.isWhitespace(node.getTextContent())) || (node.getNodeType() == Node.COMMENT_NODE)))
node = node.getNextSibling();
return node;
}

2
pom.xml
View File

@ -19,7 +19,7 @@
<properties>
<hapi_fhir_version>6.2.1</hapi_fhir_version>
<validator_test_case_version>1.2.14</validator_test_case_version>
<validator_test_case_version>1.2.15-SNAPSHOT</validator_test_case_version>
<junit_jupiter_version>5.7.1</junit_jupiter_version>
<junit_platform_launcher_version>1.8.2</junit_platform_launcher_version>
<maven_surefire_version>3.0.0-M5</maven_surefire_version>