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Merge pull request #1125 from hapifhir/gg-202302-markdown 

Gg 202302 markdown
This commit is contained in:
Grahame Grieve 2023-02-21 18:50:29 +11:00 committed by GitHub
parent b5669231e8 1eeee429ce
commit bbd9c6b018
No known key found for this signature in database
GPG Key ID: 4AEE18F83AFDEB23
12 changed files with 327 additions and 26 deletions
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24
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/context/ContextUtilities.java
View File

@ -43,6 +43,8 @@ public class ContextUtilities implements ProfileKnowledgeProvider {
private XVerExtensionManager xverManager;
private Map<String, String> oidCache = new HashMap<>();
private List<StructureDefinition> allStructuresList = new ArrayList<StructureDefinition>();
private List<String> canonicalResourceNames;
private List<String> concreteResourceNames;
public ContextUtilities(IWorkerContext context) {
super();
@ -197,13 +199,17 @@ public class ContextUtilities implements ProfileKnowledgeProvider {
* @return a list of the resource names that are canonical resources defined for this version
*/
public List<String> getCanonicalResourceNames() {
List<String> names = new ArrayList<>();
if (canonicalResourceNames == null) {
canonicalResourceNames = new ArrayList<>();
Set<String> names = new HashSet<>();
for (StructureDefinition sd : allStructures()) {
if (sd.getKind() == StructureDefinitionKind.RESOURCE && !sd.getAbstract() && hasUrlProperty(sd)) {
names.add(sd.getType());
}
}
return names;
canonicalResourceNames.addAll(Utilities.sorted(names));
}
return canonicalResourceNames;
}
/**
@ -370,5 +376,19 @@ public class ContextUtilities implements ProfileKnowledgeProvider {
return null;
}
public List<String> getConcreteResources() {
if (concreteResourceNames == null) {
concreteResourceNames = new ArrayList<>();
Set<String> names = new HashSet<>();
for (StructureDefinition sd : allStructures()) {
if (sd.getKind() == StructureDefinitionKind.RESOURCE && !sd.getAbstract()) {
names.add(sd.getType());
}
}
concreteResourceNames.addAll(Utilities.sorted(names));
}
return concreteResourceNames;
}
}

55
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/model/TypeDetails.java
View File

@ -115,10 +115,13 @@ public class TypeDetails {
public boolean isSystemType() {
return uri.startsWith(FP_NS);
}
}
private List<ProfiledType> types = new ArrayList<ProfiledType>();
private CollectionStatus collectionStatus;
private Set<String> targets; // or, not and, canonical urls
public TypeDetails(CollectionStatus collectionStatus, String... names) {
super();
this.collectionStatus = collectionStatus;
@ -268,7 +271,14 @@ public class TypeDetails {
collectionStatus = source.collectionStatus;
else
collectionStatus = CollectionStatus.ORDERED;
if (source.targets != null) {
if (targets == null) {
targets = new HashSet<>();
}
targets.addAll(source.targets);
}
}
public TypeDetails union(TypeDetails right) {
TypeDetails result = new TypeDetails(null);
if (right.collectionStatus == CollectionStatus.UNORDERED || collectionStatus == CollectionStatus.UNORDERED)
@ -279,6 +289,16 @@ public class TypeDetails {
result.addType(pt);
for (ProfiledType pt : right.types)
result.addType(pt);
if (targets != null || right.targets != null) {
result.targets = new HashSet<>();
if (targets != null) {
result.targets.addAll(targets);
}
if (right.targets != null) {
result.targets.addAll(right.targets);
}
}
return result;
}
@ -297,6 +317,15 @@ public class TypeDetails {
}
for (ProfiledType pt : right.types)
result.addType(pt);
if (targets != null && right.targets != null) {
result.targets = new HashSet<>();
for (String s : targets) {
if (right.targets.contains(s)) {
result.targets.add(s);
}
}
}
return result;
}
@ -383,4 +412,30 @@ public class TypeDetails {
}
public void addTarget(String url) {
if (targets == null) {
targets = new HashSet<>();
}
targets.add(url);
}
public Set<String> getTargets() {
return targets;
}
public boolean typesHaveTargets() {
for (ProfiledType pt : types) {
if (Utilities.existsInList(pt.getUri(), "Reference", "CodeableReference", "canonical", "http://hl7.org/fhir/StructureDefinition/Reference", "http://hl7.org/fhir/StructureDefinition/CodeableReference", "http://hl7.org/fhir/StructureDefinition/canonical")) {
return true;
}
}
return false;
}
public void addTargets(Set<String> src) {
if (src != null) {
for (String s : src) {
addTarget(s);
}
}
}
}

11
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/renderers/ResourceRenderer.java
View File

@ -223,12 +223,15 @@ public abstract class ResourceRenderer extends DataRenderer {
tr = resolveReference(rw, r.getReference());
if (!r.getReference().startsWith("#")) {
if (tr != null && tr.getReference() != null)
if (tr != null && tr.getReference() != null) {
c = x.ah(tr.getReference());
else
c = x.ah(r.getReference());
} else if (r.getReference().contains("?")) {
x.tx("Conditional Reference: ");
c = x.code("");
} else {
c = x.ah(r.getReference());
}
} else {
c = x.ah(r.getReference());
}
} else {

52
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/utils/FHIRPathEngine.java
View File

@ -30,6 +30,7 @@ import org.hl7.fhir.r5.context.IWorkerContext.ValidationResult;
import org.hl7.fhir.r5.model.Base;
import org.hl7.fhir.r5.model.BaseDateTimeType;
import org.hl7.fhir.r5.model.BooleanType;
import org.hl7.fhir.r5.model.CanonicalType;
import org.hl7.fhir.r5.model.CodeableConcept;
import org.hl7.fhir.r5.model.Constants;
import org.hl7.fhir.r5.model.DateTimeType;
@ -1615,7 +1616,7 @@ public class FHIRPathEngine {
result.update(executeContextType(context, exp.getName(), exp));
} else {
for (String s : focus.getTypes()) {
result.update(executeType(s, exp, atEntry, elementDependencies));
result.update(executeType(s, exp, atEntry, focus, elementDependencies));
}
if (result.hasNoTypes()) {
throw makeException(exp, I18nConstants.FHIRPATH_UNKNOWN_NAME, exp.getName(), focus.describe());
@ -1961,7 +1962,12 @@ public class FHIRPathEngine {
case LessOrEqual: return new TypeDetails(CollectionStatus.SINGLETON, TypeDetails.FP_Boolean);
case GreaterOrEqual: return new TypeDetails(CollectionStatus.SINGLETON, TypeDetails.FP_Boolean);
case Is: return new TypeDetails(CollectionStatus.SINGLETON, TypeDetails.FP_Boolean);
case As: return new TypeDetails(CollectionStatus.SINGLETON, right.getTypes());
case As:
TypeDetails td = new TypeDetails(CollectionStatus.SINGLETON, right.getTypes());
if (td.typesHaveTargets()) {
td.addTargets(left.getTargets());
}
return td;
case Union: return left.union(right);
case Or: return new TypeDetails(CollectionStatus.SINGLETON, TypeDetails.FP_Boolean);
case And: return new TypeDetails(CollectionStatus.SINGLETON, TypeDetails.FP_Boolean);
@ -3146,12 +3152,12 @@ public class FHIRPathEngine {
return hostServices.resolveConstantType(context.appInfo, name);
}
private TypeDetails executeType(String type, ExpressionNode exp, boolean atEntry, Set<ElementDefinition> elementDependencies) throws PathEngineException, DefinitionException {
private TypeDetails executeType(String type, ExpressionNode exp, boolean atEntry, TypeDetails focus, Set<ElementDefinition> elementDependencies) throws PathEngineException, DefinitionException {
if (atEntry && Character.isUpperCase(exp.getName().charAt(0)) && hashTail(type).equals(exp.getName())) { // special case for start up
return new TypeDetails(CollectionStatus.SINGLETON, type);
}
TypeDetails result = new TypeDetails(null);
getChildTypesByName(type, exp.getName(), result, exp, elementDependencies);
getChildTypesByName(type, exp.getName(), result, exp, focus, elementDependencies);
return result;
}
@ -3217,11 +3223,19 @@ public class FHIRPathEngine {
}
case As : {
checkParamTypes(exp, exp.getFunction().toCode(), paramTypes, new TypeDetails(CollectionStatus.SINGLETON, TypeDetails.FP_String));
return new TypeDetails(CollectionStatus.SINGLETON, exp.getParameters().get(0).getName());
TypeDetails td = new TypeDetails(CollectionStatus.SINGLETON, exp.getParameters().get(0).getName());
if (td.typesHaveTargets()) {
td.addTargets(focus.getTargets());
}
return td;
}
case OfType : {
checkParamTypes(exp, exp.getFunction().toCode(), paramTypes, new TypeDetails(CollectionStatus.SINGLETON, TypeDetails.FP_String));
return new TypeDetails(CollectionStatus.SINGLETON, exp.getParameters().get(0).getName());
TypeDetails td = new TypeDetails(CollectionStatus.SINGLETON, exp.getParameters().get(0).getName());
if (td.typesHaveTargets()) {
td.addTargets(focus.getTargets());
}
return td;
}
case Type : {
boolean s = false;
@ -3624,7 +3638,7 @@ public class FHIRPathEngine {
private TypeDetails childTypes(TypeDetails focus, String mask, ExpressionNode expr) throws PathEngineException, DefinitionException {
TypeDetails result = new TypeDetails(CollectionStatus.UNORDERED);
for (String f : focus.getTypes()) {
getChildTypesByName(f, mask, result, expr, null);
getChildTypesByName(f, mask, result, expr, null, null);
}
return result;
}
@ -5746,7 +5760,7 @@ public class FHIRPathEngine {
}
private void getChildTypesByName(String type, String name, TypeDetails result, ExpressionNode expr, Set<ElementDefinition> elementDependencies) throws PathEngineException, DefinitionException {
private void getChildTypesByName(String type, String name, TypeDetails result, ExpressionNode expr, TypeDetails focus, Set<ElementDefinition> elementDependencies) throws PathEngineException, DefinitionException {
if (Utilities.noString(type)) {
throw makeException(expr, I18nConstants.FHIRPATH_NO_TYPE, "", "getChildTypesByName");
}
@ -5757,8 +5771,6 @@ public class FHIRPathEngine {
return;
}
if (type.equals(TypeDetails.FP_SimpleTypeInfo)) {
getSimpleTypeChildTypesByName(name, result);
} else if (type.equals(TypeDetails.FP_ClassInfo)) {
@ -5816,7 +5828,7 @@ public class FHIRPathEngine {
if (elementDependencies != null) {
elementDependencies.add(ed);
}
getChildTypesByName(result.addType(tn), "**", result, expr, elementDependencies);
getChildTypesByName(result.addType(tn), "**", result, expr, null, elementDependencies);
}
} else {
for (TypeRefComponent t : ed.getType()) {
@ -5833,14 +5845,14 @@ public class FHIRPathEngine {
if (elementDependencies != null) {
elementDependencies.add(ed);
}
getChildTypesByName(result.addType(rn), "**", result, expr, elementDependencies);
getChildTypesByName(result.addType(rn), "**", result, expr, null, elementDependencies);
}
}
} else if (!result.hasType(worker, tn)) {
if (elementDependencies != null) {
elementDependencies.add(ed);
}
getChildTypesByName(result.addType(tn), "**", result, expr, elementDependencies);
getChildTypesByName(result.addType(tn), "**", result, expr, null, elementDependencies);
}
}
}
@ -5872,6 +5884,7 @@ public class FHIRPathEngine {
elementDependencies.add(ed);
}
result.addType(t.getCode());
copyTargetProfiles(ed, t, focus, result);
}
}
}
@ -5919,6 +5932,7 @@ public class FHIRPathEngine {
elementDependencies.add(ed.definition);
}
result.addType(ed.definition.unbounded() ? CollectionStatus.ORDERED : CollectionStatus.SINGLETON, pt);
copyTargetProfiles(ed.getDefinition(), t, focus, result);
}
}
}
@ -5928,6 +5942,18 @@ public class FHIRPathEngine {
}
}
private void copyTargetProfiles(ElementDefinition ed, TypeRefComponent t, TypeDetails focus, TypeDetails result) {
if (t.hasTargetProfile()) {
for (CanonicalType u : t.getTargetProfile()) {
result.addTarget(u.primitiveValue());
}
} else if (focus != null && focus.hasType("CodeableReference") && ed.getPath().endsWith(".reference") && focus.getTargets() != null) { // special case, targets are on parent
for (String s : focus.getTargets()) {
result.addTarget(s);
}
}
}
private void addTypeAndDescendents(List<StructureDefinition> sdl, StructureDefinition dt, List<StructureDefinition> types) {
sdl.add(dt);
for (StructureDefinition sd : types) {

119
org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/MarkDownProcessor.java
View File

@ -69,6 +69,125 @@ public class MarkDownProcessor {
}
}
/**
* Returns true if this is intended to be processed as markdown
*
* this is guess, based on textual analysis of the content.
*
* Uses of this routine:
* In general, the main use of this is to decide to escape the string so erroneous markdown processing doesn't munge characters
* If it's a plain string, and it's being put into something that's markdown, then you should escape the content
* If it's markdown, but you're not sure whether to process it as markdown
*
* The underlying problem is that markdown processing plain strings is problematic because some technical characters might
* get lost. So it's good to escape them... but if it's meant to be markdown, then it'll get trashed.
*
* This method works by looking for character patterns that are unlikely to occur outside markdown - but it's still only unlikely
*
* @param content
* @return
*/
// todo: dialect dependency?
public boolean isProbablyMarkdown(String content, boolean mdIfParagrapghs) {
if (mdIfParagrapghs && content.contains("\n")) {
return true;
}
String[] lines = content.split("\\r?\\n");
for (String s : lines) {
if (s.startsWith("* ") || isHeading(s) || s.startsWith("1. ") || s.startsWith(" ")) {
return true;
}
if (s.contains("```") || s.contains("~~~") || s.contains("[[[")) {
return true;
}
if (hasLink(s)) {
return true;
}
if (hasTextSpecial(s, '*') || hasTextSpecial(s, '_') ) {
return true;
}
}
return false;
}
private boolean isHeading(String s) {
if (s.length() > 7 && s.startsWith("###### ") && !Character.isWhitespace(s.charAt(7))) {
return true;
}
if (s.length() > 6 && s.startsWith("##### ") && !Character.isWhitespace(s.charAt(6))) {
return true;
}
if (s.length() > 5 && s.startsWith("#### ") && !Character.isWhitespace(s.charAt(5))) {
return true;
}
if (s.length() > 4 && s.startsWith("### ") && !Character.isWhitespace(s.charAt(4))) {
return true;
}
if (s.length() > 3 && s.startsWith("## ") && !Character.isWhitespace(s.charAt(3))) {
return true;
}
//
// not sure about this one. # [string] is something that could easily arise in non-markdown,
// so this appearing isn't enough to call it markdown
//
// if (s.length() > 2 && s.startsWith("# ") && !Character.isWhitespace(s.charAt(2))) {
// return true;
// }
return false;
}
private boolean hasLink(String s) {
int left = -1;
int mid = -1;
for (int i = 0; i < s.length(); i++) {
char c = s.charAt(i);
if (c == '[') {
mid = -1;
left = i;
} else if (left > -1 && i < s.length()-1 && c == ']' && s.charAt(i+1) == '(') {
mid = i;
} else if (left > -1 && c == ']') {
left = -1;
} else if (left > -1 && mid > -1 && c == ')') {
return true;
} else if (mid > -1 && c == '[' || c == ']' || (c == '(' && i > mid+1)) {
left = -1;
mid = -1;
}
}
return false;
}
private boolean hasTextSpecial(String s, char c) {
boolean second = false;
for (int i = 0; i < s.length(); i++) {
char prev = i == 0 ? ' ' : s.charAt(i-1);
char next = i < s.length() - 1 ? s.charAt(i+1) : ' ';
if (s.charAt(i) != c) {
// nothing
} else if (second) {
if (Character.isWhitespace(next) && (isPunctation(prev) || Character.isLetterOrDigit(prev))) {
return true;
}
second = false;
} else {
if (Character.isWhitespace(prev) && (isPunctation(next) || Character.isLetterOrDigit(next))) {
second = true;
}
}
}
return false;
}
private boolean isPunctation(char ch) {
return Utilities.existsInList(ch, '.', ',', '!', '?');
}
/**
* This deals with a painful problem created by the intersection of previous publishing processes
* and the way commonmark specifies that < is handled in content. For control reasons, the FHIR specification does

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

@ -774,6 +774,7 @@ public class I18nConstants {
public static final String EXT_VER_URL_REVERSION = "EXT_VER_URL_REVERSION";
public static final String ILLEGAL_COMMENT_TYPE = "ILLEGAL_COMMENT_TYPE";
public static final String SD_NO_SLICING_ON_ROOT = "SD_NO_SLICING_ON_ROOT";
public static final String REFERENCE_REF_QUERY_INVALID = "REFERENCE_REF_QUERY_INVALID";
}

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

@ -150,7 +150,9 @@ public abstract class XhtmlFluent {
public XhtmlNode code(String text) {
return addTag("code").tx(text);
XhtmlNode code = addTag("code");
code.tx(text);
return code;
}
public XhtmlNode code() {

1
org.hl7.fhir.utilities/src/main/resources/Messages.properties
View File

@ -824,5 +824,6 @@ EXT_VER_URL_NOT_ALLOWED = The extension URL must not contain a version
EXT_VER_URL_REVERSION = The extension URL must not contain a version. The extension was validated against version {0} of the extension
ILLEGAL_COMMENT_TYPE = The fhir_comments property must be an array of strings
SD_NO_SLICING_ON_ROOT = Slicing is not allowed at the root of a profile
REFERENCE_REF_QUERY_INVALID = The query part of the conditional reference is not a valid query string ({0})

57
org.hl7.fhir.utilities/src/test/java/org/hl7/fhir/utilities/MarkdownTests.java
View File

@ -2,15 +2,72 @@ package org.hl7.fhir.utilities;
import static org.junit.jupiter.api.Assertions.*;
import org.hl7.fhir.utilities.MarkDownProcessor.Dialect;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.Test;
class MarkdownTests {
@Test
void testMarkdownDetection() {
testMarkdown("this is a test string", false);
testMarkdown("this is a \r\ntest string", false);
testMarkdown("this is a \r\ntest string", true, true);
testMarkdown("this is a t*est strin*g", false);
testMarkdown("this is a *test strin*g", false);
testMarkdown("this is a *test string*", true);
testMarkdown("this is a *test *string", false);
testMarkdown("this is a *test* string", true);
testMarkdown("this [is] a test string", false);
testMarkdown("this [is](link) a test string", true);
testMarkdown("this [is](link a test string", false);
testMarkdown("this [is] (link) a test string", false);
testMarkdown("this [is(link)] a test string", false);
testMarkdown("this [is](link a test string", false);
testMarkdown("this [i]s] (link) a test string", false);
testMarkdown("## heading", true);
testMarkdown("# heading", false);
testMarkdown("## heading", false);
testMarkdown("###", false);
}
private void testMarkdown(String content, boolean isMD) {
testMarkdown(content, isMD, false);
}
private void testMarkdown(String content, boolean isMD, boolean ifLines) {
boolean test = new MarkDownProcessor(Dialect.COMMON_MARK).isProbablyMarkdown(content, ifLines);
assertEquals(isMD, test);
}
@Test
void testStringToMarkdown() {
// first, we test the need for replacing
Assertions.assertEquals("<p>This is a string</p>", new MarkDownProcessor(Dialect.COMMON_MARK).process("This is a string", null).trim());
Assertions.assertEquals("<p>This is *a string</p>", new MarkDownProcessor(Dialect.COMMON_MARK).process("This is *a string", null).trim());
Assertions.assertNotEquals("<p>This is *a* string</p>", new MarkDownProcessor(Dialect.COMMON_MARK).process("This is *a* string", null).trim());
Assertions.assertEquals("<p>This is *a *string</p>", new MarkDownProcessor(Dialect.COMMON_MARK).process("This is *a *string", null).trim());
Assertions.assertNotEquals("<p>This genomic study analyzes CYP2D6*1 and CYP2D6*2</p>", new MarkDownProcessor(Dialect.COMMON_MARK).process("This genomic study analyzes CYP2D6*1 and CYP2D6*2", null).trim());
Assertions.assertEquals("<p>This genomic study analyzes CYP2D6*1 and CYP2D6*2</p>", new MarkDownProcessor(Dialect.COMMON_MARK).process("This genomic study analyzes CYP2D6*1 and CYP2D6\\*2", null).trim());
Assertions.assertEquals("This is \\*a test\\*", MarkDownProcessor.makeStringSafeAsMarkdown("This is *a test*"));
Assertions.assertEquals("This is *a test*", MarkDownProcessor.makeMarkdownForString("This is \\*a test\\*"));
}
}
//
//case '*':
//case '&':
//case '#':
//case '[':
//case '>':
//case '<':
//case '`':
// -
// |
// :
// ~
// ^
// =

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

@ -1065,7 +1065,7 @@ public class BaseValidator implements IValidationContextResourceLoader {
if (!context.getResourceNames().contains(tn)) {
return false;
} else {
return q.matches("([_a-zA-Z][_a-zA-Z0-9]*=[^=&]+)(&([_a-zA-Z][_a-zA-Z0-9]*=[^=&]+))*");
return q.matches("([_a-zA-Z][_a-zA-Z0-9]*=[^=&]*)(&([_a-zA-Z][_a-zA-Z0-9]*=[^=&]*))*");
}
}

9
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/instance/InstanceValidator.java
View File

@ -3262,6 +3262,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
refType = "bundled";
}
}
boolean conditional = ref.contains("?") && Utilities.existsInList(ref.substring(0, ref.indexOf("?")), context.getResourceNames());
ReferenceValidationPolicy pol;
if (refType.equals("contained") || refType.equals("bundled")) {
pol = ReferenceValidationPolicy.CHECK_VALID;
@ -3273,7 +3274,13 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
}
}
if (pol.checkExists()) {
if (conditional) {
String query = ref.substring(ref.indexOf("?"));
boolean test = !Utilities.noString(query) && query.matches("\\?([_a-zA-Z][_a-zA-Z0-9]*=[^=&]*)(&([_a-zA-Z][_a-zA-Z0-9]*=[^=&]*))*");
//("^\\?([\\w-]+(=[\\w-]*)?(&[\\w-]+(=[\\w-]*)?)*)?$"),
ok = rule(errors, "2023-02-20", IssueType.INVALID, element.line(), element.col(), path, test, I18nConstants.REFERENCE_REF_QUERY_INVALID, ref) && ok;
} else if (pol.checkExists()) {
if (we == null) {
if (!refType.equals("contained")) {
if (fetcher == null) {

10
org.hl7.fhir.validation/src/test/resources/txCache/org.hl7.fhir.validation/5.0.0/ucum.cache
View File

@ -79,3 +79,13 @@ v: {
"system" : "http://unitsofmeasure.org"
}
-------------------------------------------------------------------------------------
{"code" : {
"system" : "http://unitsofmeasure.org",
"code" : "cm"
}, "valueSet" :null, "lang":"null", "useServer":"true", "useClient":"true", "guessSystem":"false", "valueSetMode":"ALL_CHECKS", "versionFlexible":"false"}####
v: {
"display" : "cm",
"code" : "cm",
"system" : "http://unitsofmeasure.org"
}
-------------------------------------------------------------------------------------