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Merge branch 'master' of https://github.com/hapifhir/org.hl7.fhir.core

This commit is contained in:
Lloyd McKenzie 2020-11-14 13:27:22 -07:00
parent 409bcfbecf b91e1dcade
commit 7064b70712
24 changed files with 532 additions and 298 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>5.1.21-SNAPSHOT</version>
<version>5.1.23-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>5.1.21-SNAPSHOT</version>
<version>5.1.23-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

2
org.hl7.fhir.dstu2016may/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>org.hl7.fhir.core</artifactId>
<version>5.1.21-SNAPSHOT</version>
<version>5.1.23-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>5.1.21-SNAPSHOT</version>
<version>5.1.23-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>5.1.21-SNAPSHOT</version>
<version>5.1.23-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>5.1.21-SNAPSHOT</version>
<version>5.1.23-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

290
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/conformance/ProfileUtilities.java
View File

@ -150,6 +150,26 @@ import org.hl7.fhir.utilities.xml.SchematronWriter.Section;
*/
public class ProfileUtilities extends TranslatingUtilities {
public class ElementDefinitionResolution {
private StructureDefinition source;
private ElementDefinition element;
public ElementDefinitionResolution(StructureDefinition source, ElementDefinition element) {
this.source = source;
this.element = element;
}
public StructureDefinition getSource() {
return source;
}
public ElementDefinition getElement() {
return element;
}
}
public class ElementRedirection {
private String path;
@ -590,7 +610,7 @@ public class ProfileUtilities extends TranslatingUtilities {
baseSnapshot = cloneSnapshot(baseSnapshot, base.getType(), derivedType);
}
processPaths("", derived.getSnapshot(), baseSnapshot, diff, baseCursor, diffCursor, baseSnapshot.getElement().size()-1,
derived.getDifferential().hasElement() ? derived.getDifferential().getElement().size()-1 : -1, url, webUrl, derived.present(), null, null, false, base.getUrl(), null, false, null, new ArrayList<ElementRedirection>(), base);
derived.getDifferential().hasElement() ? derived.getDifferential().getElement().size()-1 : -1, url, webUrl, derived.present(), null, null, false, base.getUrl(), null, false, null, null, new ArrayList<ElementRedirection>(), base);
checkGroupConstraints(derived);
if (derived.getDerivation() == TypeDerivationRule.SPECIALIZATION) {
for (ElementDefinition e : diff.getElement()) {
@ -968,7 +988,7 @@ public class ProfileUtilities extends TranslatingUtilities {
* @throws Exception
*/
private ElementDefinition processPaths(String indent, StructureDefinitionSnapshotComponent result, StructureDefinitionSnapshotComponent base, StructureDefinitionDifferentialComponent differential, int baseCursor, int diffCursor, int baseLimit,
int diffLimit, String url, String webUrl, String profileName, String contextPathSrc, String contextPathDst, boolean trimDifferential, String contextName, String resultPathBase, boolean slicingDone, String typeSlicingPath, List<ElementRedirection> redirector, StructureDefinition srcSD) throws DefinitionException, FHIRException {
int diffLimit, String url, String webUrl, String profileName, String contextPathSrc, String contextPathDst, boolean trimDifferential, String contextName, String resultPathBase, boolean slicingDone, ElementDefinition slicer, String typeSlicingPath, List<ElementRedirection> redirector, StructureDefinition srcSD) throws DefinitionException, FHIRException {
if (debug) {
System.out.println(indent+"PP @ "+resultPathBase+" / "+contextPathSrc+" : base = "+baseCursor+" to "+baseLimit+", diff = "+diffCursor+" to "+diffLimit+" (slicing = "+slicingDone+", redirector = "+(redirector == null ? "null" : redirector.toString())+")");
}
@ -1002,7 +1022,7 @@ public class ProfileUtilities extends TranslatingUtilities {
// well, the profile walks into this, so we need to as well
// did we implicitly step into a new type?
if (baseHasChildren(base, currentBase)) { // not a new type here
processPaths(indent+" ", result, base, differential, baseCursor+1, diffCursor, baseLimit, diffLimit, url, webUrl, profileName, contextPathSrc, contextPathDst, trimDifferential, contextName, resultPathBase, false, null, redirector, srcSD);
processPaths(indent+" ", result, base, differential, baseCursor+1, diffCursor, baseLimit, diffLimit, url, webUrl, profileName, contextPathSrc, contextPathDst, trimDifferential, contextName, resultPathBase, false, null, null, redirector, srcSD);
baseCursor = indexOfFirstNonChild(base, currentBase, baseCursor+1, baseLimit);
} else {
if (outcome.getType().size() == 0) {
@ -1032,7 +1052,7 @@ public class ProfileUtilities extends TranslatingUtilities {
while (differential.getElement().size() > diffCursor && pathStartsWith(differential.getElement().get(diffCursor).getPath(), cpath+"."))
diffCursor++;
processPaths(indent+" ", result, dt.getSnapshot(), differential, 1 /* starting again on the data type, but skip the root */, start, dt.getSnapshot().getElement().size()-1,
diffCursor-1, url, getWebUrl(dt, webUrl, indent), profileName, cpath, outcome.getPath(), trimDifferential, contextName, resultPathBase, false, null, redirector, srcSD);
diffCursor-1, url, getWebUrl(dt, webUrl, indent), profileName, cpath, outcome.getPath(), trimDifferential, contextName, resultPathBase, false, null, null, redirector, srcSD);
}
}
baseCursor++;
@ -1103,8 +1123,14 @@ public class ProfileUtilities extends TranslatingUtilities {
if (res == null)
res = outcome;
updateFromBase(outcome, currentBase);
if (diffMatches.get(0).hasSliceName())
if (diffMatches.get(0).hasSliceName()) {
outcome.setSliceName(diffMatches.get(0).getSliceName());
if (!diffMatches.get(0).hasMin() && (diffMatches.size() > 1 || slicer == null || slicer.getSlicing().getRules() != SlicingRules.CLOSED) && !currentBase.hasSliceName()) {
if (!cpath.endsWith("xtension.value[x]")) { // hack work around for problems with snapshots in official releases
outcome.setMin(0);
}
}
}
updateFromDefinition(outcome, diffMatches.get(0), profileName, trimDifferential, url, srcSD);
removeStatusExtensions(outcome);
// if (outcome.getPath().endsWith("[x]") && outcome.getType().size() == 1 && !outcome.getType().get(0).getCode().equals("*") && !diffMatches.get(0).hasSlicing()) // if the base profile allows multiple types, but the profile only allows one, rename it
@ -1148,22 +1174,31 @@ public class ProfileUtilities extends TranslatingUtilities {
while (diffCursor <= diffLimit && differential.getElement().size() > diffCursor && pathStartsWith(differential.getElement().get(diffCursor).getPath(), diffMatches.get(0).getPath()+"."))
diffCursor++;
if (outcome.hasContentReference()) {
ElementDefinition tgt = getElementById(base.getElement(), outcome.getContentReference());
ElementDefinitionResolution tgt = getElementById(srcSD, base.getElement(), outcome.getContentReference());
if (tgt == null)
throw new DefinitionException(context.formatMessage(I18nConstants.UNABLE_TO_RESOLVE_REFERENCE_TO_, outcome.getContentReference()));
replaceFromContentReference(outcome, tgt);
int nbc = base.getElement().indexOf(tgt)+1;
replaceFromContentReference(outcome, tgt.getElement());
if (tgt.getSource() != srcSD) {
base = tgt.getSource().getSnapshot();
int nbc = base.getElement().indexOf(tgt.getElement())+1;
int nbl = nbc;
while (nbl < base.getElement().size() && base.getElement().get(nbl).getPath().startsWith(tgt.getPath()+"."))
while (nbl < base.getElement().size() && base.getElement().get(nbl).getPath().startsWith(tgt.getElement().getPath()+"."))
nbl++;
processPaths(indent+" ", result, base, differential, nbc, start - 1, nbl-1, diffCursor - 1, url, webUrl, profileName, tgt.getPath(), diffMatches.get(0).getPath(), trimDifferential, contextName, resultPathBase, false, null, redirectorStack(redirector, outcome, cpath), srcSD);
processPaths(indent+" ", result, base, differential, nbc, start - 1, nbl-1, diffCursor - 1, url, webUrl, profileName, tgt.getElement().getPath(), diffMatches.get(0).getPath(), trimDifferential, contextName, resultPathBase, false, null, null, redirectorStack(redirector, outcome, cpath), tgt.getSource());
} else {
int nbc = base.getElement().indexOf(tgt.getElement())+1;
int nbl = nbc;
while (nbl < base.getElement().size() && base.getElement().get(nbl).getPath().startsWith(tgt.getElement().getPath()+"."))
nbl++;
processPaths(indent+" ", result, base, differential, nbc, start - 1, nbl-1, diffCursor - 1, url, webUrl, profileName, tgt.getElement().getPath(), diffMatches.get(0).getPath(), trimDifferential, contextName, resultPathBase, false, null, null, redirectorStack(redirector, outcome, cpath), srcSD);
}
} else {
StructureDefinition dt = outcome.getType().size() == 1 ? getProfileForDataType(outcome.getType().get(0)) : getProfileForDataType("Element");
if (dt == null)
throw new DefinitionException(context.formatMessage(I18nConstants._HAS_CHILDREN__FOR_TYPE__IN_PROFILE__BUT_CANT_FIND_TYPE, diffMatches.get(0).getPath(), differential.getElement().get(diffCursor).getPath(), typeCode(outcome.getType()), profileName));
contextName = dt.getUrl();
processPaths(indent+" ", result, dt.getSnapshot(), differential, 1 /* starting again on the data type, but skip the root */, start, dt.getSnapshot().getElement().size()-1,
diffCursor - 1, url, getWebUrl(dt, webUrl, indent), profileName+pathTail(diffMatches, 0), diffMatches.get(0).getPath(), outcome.getPath(), trimDifferential, contextName, resultPathBase, false, null, new ArrayList<ElementRedirection>(), srcSD);
diffCursor - 1, url, getWebUrl(dt, webUrl, indent), profileName+pathTail(diffMatches, 0), diffMatches.get(0).getPath(), outcome.getPath(), trimDifferential, contextName, resultPathBase, false, null, null, new ArrayList<ElementRedirection>(), srcSD);
}
}
}
@ -1249,7 +1284,7 @@ public class ProfileUtilities extends TranslatingUtilities {
// ok passed the checks.
// copy the root diff, and then process any children it has
ElementDefinition e = processPaths(indent+" ", result, base, differential, baseCursor, ndc, nbl, ndl, url, webUrl, profileName+pathTail(diffMatches, 0), contextPathSrc, contextPathDst,
trimDifferential, contextName, resultPathBase, true, null, redirector, srcSD);
trimDifferential, contextName, resultPathBase, true, null, null, redirector, srcSD);
if (e==null)
throw new FHIRException(context.formatMessage(I18nConstants.DID_NOT_FIND_TYPE_ROOT_, diffMatches.get(0).getPath()));
// now set up slicing on the e (cause it was wiped by what we called.
@ -1257,6 +1292,7 @@ public class ProfileUtilities extends TranslatingUtilities {
e.getSlicing().addDiscriminator().setType(DiscriminatorType.TYPE).setPath("$this");
e.getSlicing().setRules(SlicingRules.CLOSED); // type slicing is always closed; the differential might call it open, but that just means it's not constraining the slices it doesn't mention
e.getSlicing().setOrdered(false);
start++;
String fixedType = null;
@ -1274,7 +1310,7 @@ public class ProfileUtilities extends TranslatingUtilities {
}
ndc = differential.getElement().indexOf(diffMatches.get(i));
ndl = findEndOfElement(differential, ndc);
processPaths(indent+" ", result, base, differential, baseCursor, ndc, nbl, ndl, url, webUrl, profileName+pathTail(diffMatches, i), contextPathSrc, contextPathDst, trimDifferential, contextName, resultPathBase, true, null, redirector, srcSD);
processPaths(indent+" ", result, base, differential, baseCursor, ndc, nbl, ndl, url, webUrl, profileName+pathTail(diffMatches, i), contextPathSrc, contextPathDst, trimDifferential, contextName, resultPathBase, true, e, null, redirector, srcSD);
}
if (elementToRemove != null) {
differential.getElement().remove(elementToRemove);
@ -1288,7 +1324,32 @@ public class ProfileUtilities extends TranslatingUtilities {
}
}
}
if (!"0".equals(e.getMax())) {
// check that there's a slice for each allowed types
Set<String> allowedTypes = getListOfTypes(e);
for (TypeSlice t : typeList) {
if (t.type != null) {
allowedTypes.remove(t.type);
} else if (t.getDefn().hasSliceName() && t.getDefn().getType().size() == 1) {
allowedTypes.remove(t.getDefn().getType().get(0).getCode());
}
}
if (!allowedTypes.isEmpty()) {
if (cpath.contains("xtension.value")) {
for (Iterator<TypeRefComponent> iter = e.getType().iterator(); iter.hasNext(); ) {
TypeRefComponent tr = iter.next();
if (allowedTypes.contains(tr.getCode())) {
iter.remove();
}
}
// System.out.println("!!: Extension Error at "+cpath+": Allowed Types not sliced = "+allowedTypes+". !Extension!!");
// throw new Error("Extension Error at "+cpath+": Allowed Types not sliced = "+allowedTypes+". !Extension!!");
} else {
e.getSlicing().setRules(SlicingRules.OPEN);
}
}
}
// ok, done with that - next in the base list
baseCursor = nbl+1;
diffCursor = ndl+1;
@ -1306,14 +1367,16 @@ public class ProfileUtilities extends TranslatingUtilities {
int start = 0;
int nbl = findEndOfElement(base, baseCursor);
// if (diffMatches.size() > 1 && diffMatches.get(0).hasSlicing() && differential.getElement().indexOf(diffMatches.get(1)) > differential.getElement().indexOf(diffMatches.get(0))+1) {
ElementDefinition slicerElement;
if (diffMatches.size() > 1 && diffMatches.get(0).hasSlicing() && (nbl > baseCursor || differential.getElement().indexOf(diffMatches.get(1)) > differential.getElement().indexOf(diffMatches.get(0))+1)) { // there's a default set before the slices
int ndc = differential.getElement().indexOf(diffMatches.get(0));
int ndl = findEndOfElement(differential, ndc);
ElementDefinition e = processPaths(indent+" ", result, base, differential, baseCursor, ndc, nbl, ndl, url, webUrl, profileName+pathTail(diffMatches, 0), contextPathSrc, contextPathDst,
trimDifferential, contextName, resultPathBase, true, null, redirector, srcSD);
trimDifferential, contextName, resultPathBase, true, null, null, redirector, srcSD);
if (e==null)
throw new FHIRException(context.formatMessage(I18nConstants.DID_NOT_FIND_SINGLE_SLICE_, diffMatches.get(0).getPath()));
e.setSlicing(diffMatches.get(0).getSlicing());
slicerElement = e;
start++;
} else {
// we're just going to accept the differential slicing at face value
@ -1328,6 +1391,7 @@ public class ProfileUtilities extends TranslatingUtilities {
if (!outcome.getPath().startsWith(resultPathBase))
throw new DefinitionException(context.formatMessage(I18nConstants.ADDING_WRONG_PATH));
result.getElement().add(outcome);
slicerElement = outcome;
// differential - if the first one in the list has a name, we'll process it. Else we'll treat it as the base definition of the slice.
if (!diffMatches.get(0).hasSliceName()) {
@ -1348,7 +1412,7 @@ public class ProfileUtilities extends TranslatingUtilities {
diffCursor++;
diffCursor--;
processPaths(indent+" ", result, dt.getSnapshot(), differential, 1 /* starting again on the data type, but skip the root */, start, dt.getSnapshot().getElement().size()-1,
diffCursor, url, getWebUrl(dt, webUrl, indent), profileName, cpath, outcome.getPath(), trimDifferential, contextName, resultPathBase, false, null, redirector, srcSD);
diffCursor, url, getWebUrl(dt, webUrl, indent), profileName, cpath, outcome.getPath(), trimDifferential, contextName, resultPathBase, false, null, null, redirector, srcSD);
}
}
start++;
@ -1370,7 +1434,7 @@ public class ProfileUtilities extends TranslatingUtilities {
continue;
}*/
// now we process the base scope repeatedly for each instance of the item in the differential list
processPaths(indent+" ", result, base, differential, baseCursor, ndc, nbl, ndl, url, webUrl, profileName+pathTail(diffMatches, i), contextPathSrc, contextPathDst, trimDifferential, contextName, resultPathBase, true, null, redirector, srcSD);
processPaths(indent+" ", result, base, differential, baseCursor, ndc, nbl, ndl, url, webUrl, profileName+pathTail(diffMatches, i), contextPathSrc, contextPathDst, trimDifferential, contextName, resultPathBase, true, slicerElement, null, redirector, srcSD);
}
// ok, done with that - next in the base list
baseCursor = nbl+1;
@ -1403,7 +1467,7 @@ public class ProfileUtilities extends TranslatingUtilities {
// the profile walks into this, so we need to as well
// did we implicitly step into a new type?
if (baseHasChildren(base, currentBase)) { // not a new type here
processPaths(indent+" ", result, base, differential, baseCursor+1, diffCursor, baseLimit, diffLimit, url, webUrl, profileName, contextPathSrc, contextPathDst, trimDifferential, contextName, resultPathBase, false, null, redirector, srcSD);
processPaths(indent+" ", result, base, differential, baseCursor+1, diffCursor, baseLimit, diffLimit, url, webUrl, profileName, contextPathSrc, contextPathDst, trimDifferential, contextName, resultPathBase, false, null, null, redirector, srcSD);
baseCursor = indexOfFirstNonChild(base, currentBase, baseCursor, baseLimit);
} else {
StructureDefinition dt = getTypeForElement(differential, diffCursor, profileName, diffMatches, outcome);
@ -1412,7 +1476,7 @@ public class ProfileUtilities extends TranslatingUtilities {
while (differential.getElement().size() > diffCursor && pathStartsWith(differential.getElement().get(diffCursor).getPath(), cpath+"."))
diffCursor++;
processPaths(indent+" ", result, dt.getSnapshot(), differential, 1 /* starting again on the data type, but skip the root */, start, dt.getSnapshot().getElement().size()-1,
diffCursor-1, url, getWebUrl(dt, webUrl, indent), profileName, cpath, outcome.getPath(), trimDifferential, contextName, resultPathBase, false, null, redirector, srcSD);
diffCursor-1, url, getWebUrl(dt, webUrl, indent), profileName, cpath, outcome.getPath(), trimDifferential, contextName, resultPathBase, false, null, null, redirector, srcSD);
}
baseCursor++;
} else {
@ -1505,7 +1569,7 @@ public class ProfileUtilities extends TranslatingUtilities {
// ok passed the checks.
// copy the root diff, and then process any children it has
ElementDefinition e = processPaths(indent+" ", result, base, differential, baseCursor, ndc, nbl, ndl, url, webUrl, profileName+pathTail(diffMatches, 0), contextPathSrc, contextPathDst,
trimDifferential, contextName, resultPathBase, true, cpath, redirector, srcSD);
trimDifferential, contextName, resultPathBase, true, null, cpath, redirector, srcSD);
if (e==null)
throw new FHIRException(context.formatMessage(I18nConstants.DID_NOT_FIND_TYPE_ROOT_, diffMatches.get(0).getPath()));
// now set up slicing on the e (cause it was wiped by what we called.
@ -1538,7 +1602,7 @@ public class ProfileUtilities extends TranslatingUtilities {
sEnd = bs.end;
bs.handled = true;
}
processPaths(indent+" ", result, base, differential, sStart, ndc, sEnd, ndl, url, webUrl, profileName+pathTail(diffMatches, i), contextPathSrc, contextPathDst, trimDifferential, contextName, resultPathBase, true, cpath, redirector, srcSD);
processPaths(indent+" ", result, base, differential, sStart, ndc, sEnd, ndl, url, webUrl, profileName+pathTail(diffMatches, i), contextPathSrc, contextPathDst, trimDifferential, contextName, resultPathBase, true, e, cpath, redirector, srcSD);
}
if (elementToRemove != null) {
differential.getElement().remove(elementToRemove);
@ -1557,7 +1621,7 @@ public class ProfileUtilities extends TranslatingUtilities {
// ok we gimme up a fake differential that says nothing, and run that against the slice.
StructureDefinitionDifferentialComponent fakeDiff = new StructureDefinitionDifferentialComponent();
fakeDiff.getElementFirstRep().setPath(bs.defn.getPath());
processPaths(indent+" ", result, base, fakeDiff, bs.start, 0, bs.end, 0, url, webUrl, profileName+tail(bs.defn.getPath()), contextPathSrc, contextPathDst, trimDifferential, contextName, resultPathBase, true, cpath, redirector, srcSD);
processPaths(indent+" ", result, base, fakeDiff, bs.start, 0, bs.end, 0, url, webUrl, profileName+tail(bs.defn.getPath()), contextPathSrc, contextPathDst, trimDifferential, contextName, resultPathBase, true, e, cpath, redirector, srcSD);
}
}
@ -1614,10 +1678,10 @@ public class ProfileUtilities extends TranslatingUtilities {
while (differential.getElement().size() > diffCursor && pathStartsWith(differential.getElement().get(diffCursor).getPath(), cpath+"."))
diffCursor++;
processPaths(indent+" ", result, dt.getSnapshot(), differential, 1, ndc, dt.getSnapshot().getElement().size()-1, ndl,
url, getWebUrl(dt, webUrl, indent), profileName, cpath, outcome.getPath(), trimDifferential, contextName, resultPathBase, false, null, redirector, srcSD);
url, getWebUrl(dt, webUrl, indent), profileName, cpath, outcome.getPath(), trimDifferential, contextName, resultPathBase, false, null, null, redirector, srcSD);
} else {
processPaths(indent+" ", result, base, differential, baseCursor+1, ndc, nbl, ndl,
url, webUrl, profileName+pathTail(diffMatches, 0), contextPathSrc, contextPathDst, trimDifferential, contextName, resultPathBase, false, null, null, srcSD);
url, webUrl, profileName+pathTail(diffMatches, 0), contextPathSrc, contextPathDst, trimDifferential, contextName, resultPathBase, false, null, null, null, srcSD);
}
// throw new Error("Not done yet");
// } else if (currentBase.getType().get(0).getCode().equals("BackboneElement") && diffMatches.size() > 0 && diffMatches.get(0).hasSliceName()) {
@ -1648,7 +1712,7 @@ public class ProfileUtilities extends TranslatingUtilities {
int ndc = differential.getElement().indexOf(diffMatches.get(diffpos));
int ndl = findEndOfElement(differential, ndc);
// now we process the base scope repeatedly for each instance of the item in the differential list
processPaths(indent+" ", result, base, differential, baseCursor, ndc, nbl, ndl, url, webUrl, profileName+pathTail(diffMatches, diffpos), contextPathSrc, contextPathDst, closed, contextName, resultPathBase, true, null, redirector, srcSD);
processPaths(indent+" ", result, base, differential, baseCursor, ndc, nbl, ndl, url, webUrl, profileName+pathTail(diffMatches, diffpos), contextPathSrc, contextPathDst, closed, contextName, resultPathBase, true, null, null, redirector, srcSD);
// ok, done with that - now set the cursors for if this is the end
baseCursor = nbl;
diffCursor = ndl+1;
@ -1693,7 +1757,7 @@ public class ProfileUtilities extends TranslatingUtilities {
outcome.setPath(fixedPathDest(contextPathDst, outcome.getPath(), redirector, contextPathSrc));
updateFromBase(outcome, currentBase);
outcome.setSlicing(null);
outcome.setMin(0); // were in a slice, so it's only a mandatory if it's explicitly marked so
outcome.setMin(0); // we're in a slice, so it's only a mandatory if it's explicitly marked so
if (!outcome.getPath().startsWith(resultPathBase))
throw new DefinitionException(context.formatMessage(I18nConstants.ADDING_WRONG_PATH));
result.getElement().add(outcome);
@ -1719,7 +1783,7 @@ public class ProfileUtilities extends TranslatingUtilities {
while (differential.getElement().size() > diffCursor && pathStartsWith(differential.getElement().get(diffCursor).getPath(), diffMatches.get(0).getPath()+"."))
diffCursor++;
processPaths(indent+" ", result, base, differential, baseStart, start-1, baseMax-1,
diffCursor - 1, url, webUrl, profileName+pathTail(diffMatches, 0), base.getElement().get(0).getPath(), base.getElement().get(0).getPath(), trimDifferential, contextName, resultPathBase, false, null, redirector, srcSD);
diffCursor - 1, url, webUrl, profileName+pathTail(diffMatches, 0), base.getElement().get(0).getPath(), base.getElement().get(0).getPath(), trimDifferential, contextName, resultPathBase, false, null, null, redirector, srcSD);
} else {
StructureDefinition dt = getProfileForDataType(outcome.getType().get(0));
@ -1733,7 +1797,7 @@ public class ProfileUtilities extends TranslatingUtilities {
while (differential.getElement().size() > diffCursor && pathStartsWith(differential.getElement().get(diffCursor).getPath(), diffMatches.get(0).getPath()+"."))
diffCursor++;
processPaths(indent+" ", result, dt.getSnapshot(), differential, 1 /* starting again on the data type, but skip the root */, start-1, dt.getSnapshot().getElement().size()-1,
diffCursor - 1, url, getWebUrl(dt, webUrl, indent), profileName+pathTail(diffMatches, 0), diffMatches.get(0).getPath(), outcome.getPath(), trimDifferential, contextName, resultPathBase, false, null, redirector, srcSD);
diffCursor - 1, url, getWebUrl(dt, webUrl, indent), profileName+pathTail(diffMatches, 0), diffMatches.get(0).getPath(), outcome.getPath(), trimDifferential, contextName, resultPathBase, false, null, null, redirector, srcSD);
}
}
}
@ -1756,6 +1820,14 @@ public class ProfileUtilities extends TranslatingUtilities {
return res;
}
private Set<String> getListOfTypes(ElementDefinition e) {
Set<String> result = new HashSet<>();
for (TypeRefComponent t : e.getType()) {
result.add(t.getCode());
}
return result;
}
public StructureDefinition getTypeForElement(StructureDefinitionDifferentialComponent differential, int diffCursor, String profileName,
List<ElementDefinition> diffMatches, ElementDefinition outcome) {
if (outcome.getType().size() == 0) {
@ -1961,7 +2033,7 @@ public class ProfileUtilities extends TranslatingUtilities {
private boolean diffsConstrainTypes(List<ElementDefinition> diffMatches, String cPath, List<TypeSlice> typeList) {
// if (diffMatches.size() < 2)
// return false;
// return false;
String p = diffMatches.get(0).getPath();
if (!p.endsWith("[x]") && !cPath.endsWith("[x]"))
return false;
@ -1978,12 +2050,18 @@ public class ProfileUtilities extends TranslatingUtilities {
if (ed.hasSliceName() && ed.getType().size() == 1) {
typeList.add(new TypeSlice(ed, ed.getTypeFirstRep().getWorkingCode()));
} else if (ed.hasSliceName() && ed.getType().size() == 0) {
String tn = ed.getSliceName().substring(rn.length());
if (isDataType(s)) {
typeList.add(new TypeSlice(ed, s));
} else if (isPrimitive(Utilities.uncapitalize(s))) {
typeList.add(new TypeSlice(ed, Utilities.uncapitalize(s)));
} else {
String tn = ed.getSliceName().substring(n.length());
if (isDataType(tn)) {
typeList.add(new TypeSlice(ed, tn));
} else if (isPrimitive(Utilities.uncapitalize(tn))) {
typeList.add(new TypeSlice(ed, Utilities.uncapitalize(tn)));
}
}
} else if (!ed.hasSliceName() && !s.equals("[x]")) {
if (isDataType(s))
typeList.add(new TypeSlice(ed, s));
@ -3143,7 +3221,7 @@ public class ProfileUtilities extends TranslatingUtilities {
r1.getCells().add(gen.new Cell(null, defFile == null ? "" : defFile+"-definitions.html#extension."+ed.getName(), ((UriType) ued.getFixed()).getValue(), null, null));
r1.getCells().add(gen.new Cell());
r1.getCells().add(gen.new Cell(null, null, describeCardinality(c, null, new UnusedTracker()), null, null));
genTypes(gen, r1, ved, defFile, ed, corePath, imagePath, false);
genTypes(gen, r1, ved, defFile, ed, corePath, imagePath, false, false);
Cell cell = gen.new Cell();
cell.addMarkdown(c.getDefinition());
r1.getCells().add(cell);
@ -3156,7 +3234,7 @@ public class ProfileUtilities extends TranslatingUtilities {
ved = ted;
}
genTypes(gen, r, ved, defFile, ed, corePath, imagePath, false);
genTypes(gen, r, ved, defFile, ed, corePath, imagePath, false, false);
r.setIcon("icon_"+m+"extension_simple.png", HierarchicalTableGenerator.TEXT_ICON_EXTENSION_SIMPLE);
}
@ -3215,7 +3293,7 @@ public class ProfileUtilities extends TranslatingUtilities {
private static final int AGG_GR = 2;
private static final boolean TABLE_FORMAT_FOR_FIXED_VALUES = false;
private Cell genTypes(HierarchicalTableGenerator gen, Row r, ElementDefinition e, String profileBaseFileName, StructureDefinition profile, String corePath, String imagePath, boolean root) {
private Cell genTypes(HierarchicalTableGenerator gen, Row r, ElementDefinition e, String profileBaseFileName, StructureDefinition profile, String corePath, String imagePath, boolean root, boolean mustSupportMode) {
Cell c = gen.new Cell();
r.getCells().add(c);
if (e.hasContentReference()) {
@ -3266,6 +3344,7 @@ public class ProfileUtilities extends TranslatingUtilities {
TypeRefComponent tl = null;
for (TypeRefComponent t : types) {
if (!mustSupportMode || allTypesMustSupport(e) || isMustSupport(t)) {
if (first) {
first = false;
} else {
@ -3274,23 +3353,25 @@ public class ProfileUtilities extends TranslatingUtilities {
tl = t;
if (t.hasTarget()) {
c.getPieces().add(gen.new Piece(corePath+"references.html", t.getWorkingCode(), null));
if (isMustSupportDirect(t) && e.getMustSupport()) {
if (!mustSupportMode && isMustSupportDirect(t) && e.getMustSupport()) {
c.addPiece(gen.new Piece(null, " ", null));
c.addStyledText(translate("sd.table", "This type must be supported"), "S", "white", "red", null, false);
}
c.getPieces().add(gen.new Piece(null, "(", null));
boolean tfirst = true;
for (CanonicalType u : t.getTargetProfile()) {
if (!mustSupportMode || allProfilesMustSupport(t.getTargetProfile()) || isMustSupport(u)) {
if (tfirst)
tfirst = false;
else
c.addPiece(gen.new Piece(null, " | ", null));
genTargetLink(gen, profileBaseFileName, corePath, c, t, u.getValue());
if (isMustSupport(u) && e.getMustSupport()) {
if (!mustSupportMode && isMustSupport(u) && e.getMustSupport()) {
c.addPiece(gen.new Piece(null, " ", null));
c.addStyledText(translate("sd.table", "This target must be supported"), "S", "white", "red", null, false);
}
}
}
c.getPieces().add(gen.new Piece(null, ")", null));
if (t.getAggregation().size() > 0) {
c.getPieces().add(gen.new Piece(corePath+"valueset-resource-aggregation-mode.html", " {", null));
@ -3308,6 +3389,7 @@ public class ProfileUtilities extends TranslatingUtilities {
String ref;
boolean pfirst = true;
for (CanonicalType p : t.getProfile()) {
if (!mustSupportMode || allProfilesMustSupport(t.getProfile()) || isMustSupport(p)) {
if (pfirst) {
pfirst = false;
} else {
@ -3326,11 +3408,12 @@ public class ProfileUtilities extends TranslatingUtilities {
}
} else
c.addPiece(checkForNoChange(t, gen.new Piece((p.getValue().startsWith(corePath)? corePath: "")+ref, t.getWorkingCode(), null)));
if (isMustSupport(p) && e.getMustSupport()) {
if (!mustSupportMode && isMustSupport(p) && e.getMustSupport()) {
c.addPiece(gen.new Piece(null, " ", null));
c.addStyledText(translate("sd.table", "This profile must be supported"), "S", "white", "red", null, false);
}
}
}
} else {
String tc = t.getWorkingCode();
if (Utilities.isAbsoluteUrl(tc)) {
@ -3345,12 +3428,13 @@ public class ProfileUtilities extends TranslatingUtilities {
} else {
c.addPiece(checkForNoChange(t, gen.new Piece(null, tc, null)));
}
if (isMustSupportDirect(t) && e.getMustSupport()) {
if (!mustSupportMode && isMustSupportDirect(t) && e.getMustSupport()) {
c.addPiece(gen.new Piece(null, " ", null));
c.addStyledText(translate("sd.table", "This type must be supported"), "S", "white", "red", null, false);
}
}
}
}
return c;
}
@ -3457,10 +3541,21 @@ public class ProfileUtilities extends TranslatingUtilities {
// return null;
}
private ElementDefinition getElementById(List<ElementDefinition> elements, String contentReference) {
private ElementDefinitionResolution getElementById(StructureDefinition source, List<ElementDefinition> elements, String contentReference) {
if (!contentReference.startsWith("#") && contentReference.contains("#")) {
String url = contentReference.substring(0, contentReference.indexOf("#"));
contentReference = contentReference.substring(contentReference.indexOf("#"));
if (!url.equals(source.getUrl())){
source = context.fetchResource(StructureDefinition.class, url);
if (source == null) {
return null;
}
elements = source.getSnapshot().getElement();
}
}
for (ElementDefinition ed : elements)
if (ed.hasId() && ("#"+ed.getId()).equals(contentReference))
return ed;
return new ElementDefinitionResolution(source, ed);
return null;
}
@ -3549,6 +3644,25 @@ public class ProfileUtilities extends TranslatingUtilities {
return piece;
}
private String checkForNoChange(Element source) {
if (source.hasUserData(DERIVATION_EQUALS)) {
return "opacity: 0.5";
} else {
return null;
}
}
private Piece applyAsUnchanged(Piece piece) {
piece.addStyle("opacity: 0.5");
return piece;
}
private String applyAsUnchanged() {
return "opacity: 0.5";
}
private Piece checkForNoChange(Element src1, Element src2, Piece piece) {
if (src1.hasUserData(DERIVATION_EQUALS) && src2.hasUserData(DERIVATION_EQUALS)) {
piece.addStyle("opacity: 0.5");
@ -3824,7 +3938,7 @@ public class ProfileUtilities extends TranslatingUtilities {
// genElement(defPath, gen, row.getSubRows(), child, all, profiles, showMissing, profileBaseFileName, true, false, corePath, imagePath, false, logicalModel, isConstraintMode, allInvariants);
}
if (typesRow != null) {
makeChoiceRows(typesRow.getSubRows(), element, gen, corePath, profileBaseFileName);
makeChoiceRows(typesRow.getSubRows(), element, gen, corePath, profileBaseFileName, mustSupport);
}
}
return slicingRow;
@ -3909,7 +4023,7 @@ public class ProfileUtilities extends TranslatingUtilities {
res.add(genCardinality(gen, element, row, hasDef, used, extDefn.getElement()));
ElementDefinition valueDefn = extDefn.getExtensionValueDefinition();
if (valueDefn != null && !"0".equals(valueDefn.getMax()))
res.add(genTypes(gen, row, valueDefn, profileBaseFileName, profile, corePath, imagePath, root));
res.add(genTypes(gen, row, valueDefn, profileBaseFileName, profile, corePath, imagePath, root, mustSupport));
else // if it's complex, we just call it nothing
// genTypes(gen, row, extDefn.getSnapshot().getElement().get(0), profileBaseFileName, profile);
res.add(addCell(row, gen.new Cell(null, null, "("+translate("sd.table", "Complex")+")", null, null)));
@ -3920,7 +4034,7 @@ public class ProfileUtilities extends TranslatingUtilities {
if ("0".equals(element.getMax()))
res.add(addCell(row, gen.new Cell()));
else
res.add(genTypes(gen, row, element, profileBaseFileName, profile, corePath, imagePath, root));
res.add(genTypes(gen, row, element, profileBaseFileName, profile, corePath, imagePath, root, mustSupport));
res.add(generateDescription(gen, row, element, (ElementDefinition) element.getUserData(DERIVATION_POINTER), used.used, null, null, profile, corePath, imagePath, root, logicalModel, allInvariants, snapshot, mustSupport));
}
} else {
@ -3928,7 +4042,7 @@ public class ProfileUtilities extends TranslatingUtilities {
if (element.hasSlicing())
res.add(addCell(row, gen.new Cell(null, corePath+"profiling.html#slicing", "(Slice Definition)", null, null)));
else if (hasDef && !"0".equals(element.getMax()) && typesRow == null)
res.add(genTypes(gen, row, element, profileBaseFileName, profile, corePath, imagePath, root));
res.add(genTypes(gen, row, element, profileBaseFileName, profile, corePath, imagePath, root, mustSupport));
else
res.add(addCell(row, gen.new Cell()));
res.add(generateDescription(gen, row, element, (ElementDefinition) element.getUserData(DERIVATION_POINTER), used.used, null, null, profile, corePath, imagePath, root, logicalModel, allInvariants, snapshot, mustSupport));
@ -3990,9 +4104,10 @@ public class ProfileUtilities extends TranslatingUtilities {
return key.startsWith("ele-") || key.startsWith("res-") || key.startsWith("ext-") || key.startsWith("dom-") || key.startsWith("dr-");
}
private void makeChoiceRows(List<Row> subRows, ElementDefinition element, HierarchicalTableGenerator gen, String corePath, String profileBaseFileName) {
private void makeChoiceRows(List<Row> subRows, ElementDefinition element, HierarchicalTableGenerator gen, String corePath, String profileBaseFileName, boolean mustSupportMode) {
// create a child for each choice
for (TypeRefComponent tr : element.getType()) {
if (!mustSupportMode || allTypesMustSupport(element) || isMustSupport(tr)) {
Row choicerow = gen.new Row();
String t = tr.getWorkingCode();
if (isReference(t)) {
@ -4007,7 +4122,7 @@ public class ProfileUtilities extends TranslatingUtilities {
c.getPieces().add(gen.new Piece(corePath+"datatypes.html#canonical", "canonical", null));
else
c.getPieces().add(gen.new Piece(corePath+"references.html#Reference", "Reference", null));
if (isMustSupportDirect(tr) && element.getMustSupport()) {
if (!mustSupportMode && isMustSupportDirect(tr) && element.getMustSupport()) {
c.addPiece(gen.new Piece(null, " ", null));
c.addStyledText(translate("sd.table", "This type must be supported"), "S", "white", "red", null, false);
}
@ -4015,15 +4130,17 @@ public class ProfileUtilities extends TranslatingUtilities {
}
boolean first = true;
for (CanonicalType rt : tr.getTargetProfile()) {
if (!mustSupportMode || allProfilesMustSupport(tr.getTargetProfile()) || isMustSupport(rt)) {
if (!first)
c.getPieces().add(gen.new Piece(null, " | ", null));
genTargetLink(gen, profileBaseFileName, corePath, c, tr, rt.getValue());
if (isMustSupport(rt) && element.getMustSupport()) {
if (!mustSupportMode && isMustSupport(rt) && element.getMustSupport()) {
c.addPiece(gen.new Piece(null, " ", null));
c.addStyledText(translate("sd.table", "This target must be supported"), "S", "white", "red", null, false);
}
first = false;
}
}
if (first)
c.getPieces().add(gen.new Piece(null, "Any", null));
@ -4042,7 +4159,7 @@ public class ProfileUtilities extends TranslatingUtilities {
choicerow.setIcon("icon_primitive.png", HierarchicalTableGenerator.TEXT_ICON_PRIMITIVE);
Cell c = gen.new Cell(null, corePath+"datatypes.html#"+t, sd.getType(), null, null);
choicerow.getCells().add(c);
if (isMustSupport(tr) && element.getMustSupport()) {
if (!mustSupportMode && isMustSupport(tr) && element.getMustSupport()) {
c.addPiece(gen.new Piece(null, " ", null));
c.addStyledText(translate("sd.table", "This type must be supported"), "S", "white", "red", null, false);
}
@ -4053,7 +4170,7 @@ public class ProfileUtilities extends TranslatingUtilities {
choicerow.setIcon("icon_datatype.gif", HierarchicalTableGenerator.TEXT_ICON_DATATYPE);
Cell c = gen.new Cell(null, pkp.getLinkFor(corePath, t), sd.getType(), null, null);
choicerow.getCells().add(c);
if (isMustSupport(tr) && element.getMustSupport()) {
if (!mustSupportMode && isMustSupport(tr) && element.getMustSupport()) {
c.addPiece(gen.new Piece(null, " ", null));
c.addStyledText(translate("sd.table", "This type must be supported"), "S", "white", "red", null, false);
}
@ -4063,17 +4180,18 @@ public class ProfileUtilities extends TranslatingUtilities {
typeCell.addPiece(gen.new Piece(null, "(", null));
boolean first = true;
for (CanonicalType pt : tr.getProfile()) {
if (!mustSupportMode || allProfilesMustSupport(tr.getProfile()) || isMustSupport(pt)) {
if (first) first = false; else typeCell.addPiece(gen.new Piece(null, " | ", null));
StructureDefinition psd = context.fetchResource(StructureDefinition.class, pt.getValue());
if (psd == null)
typeCell.addPiece(gen.new Piece(null, "?gen-e2?", null));
else
typeCell.addPiece(gen.new Piece(psd.getUserString("path"), psd.getName(), psd.present()));
if (isMustSupport(pt) && element.getMustSupport()) {
if (!mustSupportMode && isMustSupport(pt) && element.getMustSupport()) {
typeCell.addPiece(gen.new Piece(null, " ", null));
typeCell.addStyledText(translate("sd.table", "This profile must be supported"), "S", "white", "red", null, false);
}
}
}
typeCell.addPiece(gen.new Piece(null, ")", null));
}
@ -4082,6 +4200,7 @@ public class ProfileUtilities extends TranslatingUtilities {
subRows.add(choicerow);
}
}
}
private boolean isReference(String t) {
return t.equals("Reference") || t.equals("canonical");
@ -4124,7 +4243,7 @@ public class ProfileUtilities extends TranslatingUtilities {
ExtensionContext extDefn = null;
genCardinality(gen, element, row, hasDef, used, null);
if (hasDef && !"0".equals(element.getMax()))
genTypes(gen, row, element, profileBaseFileName, profile, corePath, imagePath, root);
genTypes(gen, row, element, profileBaseFileName, profile, corePath, imagePath, root, false);
else
row.getCells().add(gen.new Cell());
generateGridDescription(gen, row, element, null, used.used, null, null, profile, corePath, imagePath, root, null);
@ -4314,20 +4433,19 @@ public class ProfileUtilities extends TranslatingUtilities {
if (definition != null) {
ElementDefinitionBindingComponent binding = null;
if (valueDefn != null && valueDefn.hasBinding() && !valueDefn.getBinding().isEmpty())
binding = valueDefn.getBinding();
binding = makeUnifiedBinding(valueDefn.getBinding(), valueDefn);
else if (definition.hasBinding())
binding = definition.getBinding();
binding = makeUnifiedBinding(definition.getBinding(), definition);
if (binding!=null && !binding.isEmpty()) {
if (!c.getPieces().isEmpty())
c.addPiece(gen.new Piece("br"));
BindingResolution br = pkp.resolveBinding(profile, binding, definition.getPath());
c.getPieces().add(checkForNoChange(binding, gen.new Piece(null, translate("sd.table", "Binding")+": ", null).addStyle("font-weight:bold")));
c.getPieces().add(checkForNoChange(binding, gen.new Piece(br.url == null ? null : Utilities.isAbsoluteUrl(br.url) || !pkp.prependLinks() ? br.url : corePath+br.url, br.display, null)));
c.getPieces().add(checkForNoChange(binding.getValueSetElement(), gen.new Piece(br.url == null ? null : Utilities.isAbsoluteUrl(br.url) || !pkp.prependLinks() ? br.url : corePath+br.url, br.display, null)));
if (binding.hasStrength()) {
c.getPieces().add(checkForNoChange(binding, gen.new Piece(null, " (", null)));
c.getPieces().add(checkForNoChange(binding, gen.new Piece(corePath+"terminologies.html#"+binding.getStrength().toCode(), egt(binding.getStrengthElement()), binding.getStrength().getDefinition())));
c.getPieces().add(gen.new Piece(null, ")", null));
c.getPieces().add(checkForNoChange(binding.getStrengthElement(), gen.new Piece(null, " (", null)));
c.getPieces().add(checkForNoChange(binding.getStrengthElement(), gen.new Piece(corePath+"terminologies.html#"+binding.getStrength().toCode(), egt(binding.getStrengthElement()), binding.getStrength().getDefinition())));
c.getPieces().add(checkForNoChange(binding.getStrengthElement(), gen.new Piece(null, ")", null)));
}
if (binding.hasExtension(ToolingExtensions.EXT_MAX_VALUESET)) {
br = pkp.resolveBinding(profile, ToolingExtensions.readStringExtension(binding, ToolingExtensions.EXT_MAX_VALUESET), definition.getPath());
@ -4343,7 +4461,7 @@ public class ProfileUtilities extends TranslatingUtilities {
}
if (binding.hasDescription() && MarkDownProcessor.isSimpleMarkdown(binding.getDescription())) {
c.getPieces().add(gen.new Piece(null, ": ", null));
c.addMarkdownNoPara(binding.getDescription());
c.addMarkdownNoPara(binding.getDescription(), checkForNoChange(binding.getDescriptionElement()));
}
}
for (ElementDefinitionConstraintComponent inv : definition.getConstraint()) {
@ -4424,6 +4542,38 @@ public class ProfileUtilities extends TranslatingUtilities {
return c;
}
private ElementDefinitionBindingComponent makeUnifiedBinding(ElementDefinitionBindingComponent binding, ElementDefinition element) {
if (!element.hasUserData(DERIVATION_POINTER)) {
return binding;
}
ElementDefinition base = (ElementDefinition) element.getUserData(DERIVATION_POINTER);
if (!base.hasBinding()) {
return binding;
}
ElementDefinitionBindingComponent o = base.getBinding();
ElementDefinitionBindingComponent b = new ElementDefinitionBindingComponent();
b.setUserData(DERIVATION_POINTER, o);
if (binding.hasValueSet()) {
b.setValueSet(binding.getValueSet());
} else if (o.hasValueSet()) {
b.setValueSet(o.getValueSet());
b.getValueSetElement().setUserData(DERIVATION_EQUALS, o.getValueSetElement());
}
if (binding.hasStrength()) {
b.setStrength(binding.getStrength());
} else if (o.hasStrength()) {
b.setStrength(o.getStrength());
b.getStrengthElement().setUserData(DERIVATION_EQUALS, o.getStrengthElement());
}
if (binding.hasDescription()) {
b.setDescription(binding.getDescription());
} else if (o.hasDescription()) {
b.setDescription(o.getDescription());
b.getDescriptionElement().setUserData(DERIVATION_EQUALS, o.getDescriptionElement());
}
return b;
}
private void genFixedValue(HierarchicalTableGenerator gen, Row erow, DataType value, boolean snapshot, boolean pattern, String corePath, boolean skipnoValue) {
String ref = pkp.getLinkFor(corePath, value.fhirType());
if (ref != null) {
@ -4983,6 +5133,9 @@ public class ProfileUtilities extends TranslatingUtilities {
if (ref.substring(1, 2).toUpperCase().equals(ref.substring(1,2))) {
actual = base+(ref.substring(1)+"."+path.substring(p.length()+1)).substring(prefixLength);
path = actual;
} else if (ref.startsWith("http:")) {
actual = base+(ref.substring(ref.indexOf("#")+1)+"."+path.substring(p.length()+1)).substring(prefixLength);
path = actual;
} else {
// Older versions of FHIR (e.g. 2016May) had reference of the style #parameter instead of #Parameters.parameter, so we have to handle that
actual = base+(path.substring(0, path.indexOf(".")+1) + ref.substring(1)+"."+path.substring(p.length()+1)).substring(prefixLength);
@ -6016,7 +6169,7 @@ public class ProfileUtilities extends TranslatingUtilities {
TableModel model = gen.new TableModel(id, true);
model.setDocoImg(prefix+"help16.png");
model.setDocoRef(prefix+"formats.html#table"); // todo: change to graph definition
model.setDocoRef(Utilities.pathURL(prefix, "formats.html#table")); // todo: change to graph definition
model.getTitles().add(gen.new Title(null, model.getDocoRef(), "Property", "A profiled resource", null, 0));
model.getTitles().add(gen.new Title(null, model.getDocoRef(), "Card.", "Minimum and Maximum # of times the the element can appear in the instance", null, 0));
model.getTitles().add(gen.new Title(null, model.getDocoRef(), "Content", "What goes here", null, 0));
@ -6276,6 +6429,25 @@ public class ProfileUtilities extends TranslatingUtilities {
return grp;
}
public static boolean allTypesMustSupport(ElementDefinition e) {
boolean all = true;
boolean any = false;
for (TypeRefComponent tr : e.getType()) {
all = all && isMustSupport(tr);
any = any || isMustSupport(tr);
}
return !all && !any;
}
public static boolean allProfilesMustSupport(List<CanonicalType> profiles) {
boolean all = true;
boolean any = false;
for (CanonicalType u : profiles) {
all = all && isMustSupport(u);
any = any || isMustSupport(u);
}
return !all && !any;
}
public static boolean isMustSupportDirect(TypeRefComponent tr) {
return ("true".equals(ToolingExtensions.readStringExtension(tr, ToolingExtensions.EXT_MUST_SUPPORT)));
}

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

@ -392,13 +392,18 @@ public class DataRenderer extends Renderer {
} else if (!getContext().isCanonicalUrlsAsLinks())
url = null;
}
if (url == null)
if (url == null) {
x.b().tx(uri.getValue());
else if (uri.getValue().startsWith("mailto:"))
} else if (uri.getValue().startsWith("mailto:")) {
x.ah(uri.getValue()).addText(uri.getValue().substring(7));
else
} else {
if (uri.getValue().contains("|")) {
x.ah(uri.getValue().substring(0, uri.getValue().indexOf("|"))).addText(uri.getValue());
} else {
x.ah(uri.getValue()).addText(uri.getValue());
}
}
}
protected void renderAnnotation(XhtmlNode x, Annotation annot) {
renderAnnotation(x, annot, false);

5
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/renderers/ProfileDrivenRenderer.java
View File

@ -824,7 +824,10 @@ public class ProfileDrivenRenderer extends ResourceRenderer {
if (p == null || p.getValues().size() == 0 || p.getValues().get(0) == null)
td.tx(" ");
else {
renderLeaf(res, p.getValues().get(0), e, td, td, false, showCodeDetails, displayHints, path, indent);
for (BaseWrapper vv : p.getValues()) {
td.sep(", ");
renderLeaf(res, vv, e, td, td, false, showCodeDetails, displayHints, path, indent);
}
}
}
}

4
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/renderers/QuestionnaireRenderer.java
View File

@ -142,7 +142,7 @@ public class QuestionnaireRenderer extends TerminologyRenderer {
rows.add(r);
boolean hasExt = false;
r.setIcon("icon-q-"+i.getType().toCode()+".png", i.getType().getDisplay());
r.setIcon("icon-q-"+i.getType().toCode().toLowerCase()+".png", i.getType().getDisplay());
r.getCells().add(gen.new Cell(null, context.getDefinitionsTarget() == null ? "" : context.getDefinitionsTarget()+"#item."+i.getLinkId(), i.getLinkId(), null, null));
String txt = (i.hasPrefix() ? i.getPrefix() + ". " : "") + i.getText();
r.getCells().add(gen.new Cell(null, null, txt, null, null));
@ -361,7 +361,7 @@ public class QuestionnaireRenderer extends TerminologyRenderer {
rows.add(r);
boolean hasExt = false;
r.setIcon("icon-q-"+i.getType().toCode()+".png", i.getType().getDisplay());
r.setIcon("icon-q-"+i.getType().toCode().toLowerCase()+".png", i.getType().getDisplay());
r.getCells().add(gen.new Cell(null, context.getDefinitionsTarget() == null ? "" : context.getDefinitionsTarget()+"#item."+i.getLinkId(), i.getLinkId(), null, null));
Cell defn = gen.new Cell();
r.getCells().add(defn);

5
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/terminologies/ValueSetCheckerSimple.java
View File

@ -523,14 +523,13 @@ public class ValueSetCheckerSimple implements ValueSetChecker {
} else {
if (vsi.hasFilter()) {
boolean ok = true;
for (ConceptSetFilterComponent f : vsi.getFilter())
for (ConceptSetFilterComponent f : vsi.getFilter()) {
if (!codeInFilter(cs, system, f, code)) {
ok = false;
break;
}
if (ok) {
return true;
}
return ok;
}
List<ConceptDefinitionComponent> list = cs.getConcept();

1
org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/test/SnapShotGenerationTests.java
View File

@ -465,6 +465,7 @@ public class SnapShotGenerationTests {
fp.setHostServices(context);
messages = new ArrayList<ValidationMessage>();
System.out.println("---- "+id+" -----------------------------------------");
if (test.isFail()) {
boolean failed = true;
try {

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>5.1.21-SNAPSHOT</version>
<version>5.1.23-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>5.1.21-SNAPSHOT</version>
<version>5.1.23-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

6
org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/VersionUtilities.java
View File

@ -229,8 +229,14 @@ public class VersionUtilities {
* @return Is {@literal current} later or equal to {@literal test}? For example, if <code>this = 0.5</code> and <code>current = 0.6</code> this method will return true
*/
public static boolean isThisOrLater(String test, String current) {
if (test == null || current == null) {
return false;
}
String t = getMajMin(test);
String c = getMajMin(current);
if (t == null || c == null) {
return false;
}
if (c.compareTo(t) == 0) {
return isMajMinOrLaterPatch(test, current);
}

22
org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/npm/FilesystemPackageCacheManager.java
View File

@ -41,6 +41,7 @@ import org.hl7.fhir.utilities.TextFile;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.VersionUtilities;
import org.hl7.fhir.utilities.json.JSONUtil;
import org.hl7.fhir.utilities.json.JsonTrackingParser;
import org.hl7.fhir.utilities.npm.NpmPackage.NpmPackageFolder;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
@ -352,7 +353,7 @@ public class FilesystemPackageCacheManager extends BasePackageCacheManager imple
System.out.print(" Installing: ");
}
if (npm.name() == null || id == null || !id.equals(npm.name())) {
if (npm.name() == null || id == null || !id.equalsIgnoreCase(npm.name())) {
if (!id.equals("hl7.fhir.r5.core")) {// temporary work around
throw new IOException("Attempt to import a mis-identified package. Expected " + id + ", got " + npm.name());
}
@ -549,7 +550,9 @@ public class FilesystemPackageCacheManager extends BasePackageCacheManager imple
@Override
public String getPackageId(String canonicalUrl) throws IOException {
String retVal = super.getPackageId(canonicalUrl);
String retVal = findCanonicalInLocalCache(canonicalUrl);
retVal = super.getPackageId(canonicalUrl);
if (retVal == null) {
retVal = getPackageIdFromBuildList(canonicalUrl);
@ -559,6 +562,21 @@ public class FilesystemPackageCacheManager extends BasePackageCacheManager imple
}
public String findCanonicalInLocalCache(String canonicalUrl) {
try {
for (String pf : listPackages()) {
if (new File(Utilities.path(cacheFolder, pf, "package", "package.json")).exists()) {
JsonObject npm = JsonTrackingParser.parseJsonFile(Utilities.path(cacheFolder, pf, "package", "package.json"));
if (canonicalUrl.equals(JSONUtil.str(npm, "canonical"))) {
return JSONUtil.str(npm, "name");
}
}
}
} catch (IOException e) {
}
return null;
}
// ========================= Package Mgmt API =======================================================================
private String getPackageIdFromBuildList(String canonical) throws IOException {

56
org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/xhtml/HierarchicalTableGenerator.java
View File

@ -247,7 +247,7 @@ public class HierarchicalTableGenerator extends TranslatingUtilities {
Node document = parser.parse(md);
HtmlRenderer renderer = HtmlRenderer.builder().escapeHtml(true).build();
String html = renderer.render(document);
pieces.addAll(htmlToParagraphPieces(html));
pieces.addAll(htmlToParagraphPieces(html, null));
} catch (Exception e) {
e.printStackTrace();
}
@ -255,19 +255,23 @@ public class HierarchicalTableGenerator extends TranslatingUtilities {
}
public Cell addMarkdownNoPara(String md) {
return addMarkdownNoPara(md, null);
}
public Cell addMarkdownNoPara(String md, String style) {
try {
Parser parser = Parser.builder().build();
Node document = parser.parse(md);
HtmlRenderer renderer = HtmlRenderer.builder().escapeHtml(true).build();
String html = renderer.render(document);
pieces.addAll(htmlToParagraphPieces(html));
pieces.addAll(htmlToParagraphPieces(html, style));
} catch (Exception e) {
e.printStackTrace();
}
return this;
}
private List<Piece> htmlToParagraphPieces(String html) {
private List<Piece> htmlToParagraphPieces(String html, String style) {
List<Piece> myPieces = new ArrayList<Piece>();
try {
XhtmlNode node = new XhtmlParser().parseFragment("<html>"+html+"</html>");
@ -281,14 +285,17 @@ public class HierarchicalTableGenerator extends TranslatingUtilities {
}
if (c.getNodeType() == NodeType.Text) {
if (!Utilities.isWhitespace(c.getContent()))
addNode(myPieces, c);
addNode(myPieces, c, style);
} else if ("p".equals(c.getName())) {
for (XhtmlNode g : c.getChildNodes()) {
addNode(myPieces, g);
addNode(myPieces, g, style);
}
} else {
Piece x = new Piece(c.getName());
x.getChildren().addAll(c.getChildNodes());
if (style != null) {
x.addStyle(style);
}
myPieces.add(x);
}
}
@ -314,49 +321,56 @@ public class HierarchicalTableGenerator extends TranslatingUtilities {
if (html.contains(("<"))) {
XhtmlNode node = new XhtmlParser().parseFragment("<p>"+html+"</p>");
for (XhtmlNode c : node.getChildNodes()) {
addNode(myPieces, c);
addNode(myPieces, c, null);
}
} else
myPieces.add(new Piece(null, html, null));
return myPieces;
}
private void addNode(List<Piece> list, XhtmlNode c) {
private void addNode(List<Piece> list, XhtmlNode c, String style) {
if (c.getNodeType() == NodeType.Text)
list.add(new Piece(null, c.getContent(), null));
list.add(styleIt(new Piece(null, c.getContent(), null), style));
else if (c.getNodeType() == NodeType.Element) {
if (c.getName().equals("a")) {
list.add(new Piece(c.getAttribute("href"), c.allText(), c.getAttribute("title")));
list.add(styleIt(new Piece(c.getAttribute("href"), c.allText(), c.getAttribute("title")), style));
} else if (c.getName().equals("b") || c.getName().equals("em") || c.getName().equals("strong")) {
list.add(new Piece(null, c.allText(), null).setStyle("font-face: bold"));
list.add(styleIt(new Piece(null, c.allText(), null).setStyle("font-face: bold"), style));
} else if (c.getName().equals("code")) {
list.add(new Piece(null, c.allText(), null).setStyle("padding: 2px 4px; color: #005c00; background-color: #f9f2f4; white-space: nowrap; border-radius: 4px"));
list.add(styleIt(new Piece(null, c.allText(), null).setStyle("padding: 2px 4px; color: #005c00; background-color: #f9f2f4; white-space: nowrap; border-radius: 4px"), style));
} else if (c.getName().equals("i")) {
list.add(new Piece(null, c.allText(), null).setStyle("font-style: italic"));
list.add(styleIt(new Piece(null, c.allText(), null).setStyle("font-style: italic"), style));
} else if (c.getName().equals("pre")) {
Piece p = new Piece(c.getName()).setStyle("white-space: pre; font-family: courier");
Piece p = styleIt(new Piece(c.getName()).setStyle("white-space: pre; font-family: courier"), style);
list.add(p);
p.getChildren().addAll(c.getChildNodes());
} else if (c.getName().equals("ul") || c.getName().equals("ol")) {
Piece p = new Piece(c.getName());
Piece p = styleIt(new Piece(c.getName()), style);
list.add(p);
p.getChildren().addAll(c.getChildNodes());
} else if (c.getName().equals("i")) {
list.add(new Piece(null, c.allText(), null).setStyle("font-style: italic"));
list.add(styleIt(new Piece(null, c.allText(), null).setStyle("font-style: italic"), style));
} else if (c.getName().equals("h1")||c.getName().equals("h2")||c.getName().equals("h3")||c.getName().equals("h4")) {
Piece p = new Piece(c.getName());
Piece p = styleIt(new Piece(c.getName()), style);
list.add(p);
p.getChildren().addAll(c.getChildNodes());
} else if (c.getName().equals("br")) {
list.add(new Piece(c.getName()));
list.add(styleIt(new Piece(c.getName()), style));
} else {
throw new Error("Not handled yet: "+c.getName());
}
} else
throw new Error("Unhandled type "+c.getNodeType().toString());
}
private Piece styleIt(Piece piece, String style) {
if (style != null) {
piece.addStyle(style);
}
return piece;
}
public Cell addStyle(String style) {
for (Piece p : pieces)
p.addStyle(style);
@ -583,7 +597,7 @@ public class HierarchicalTableGenerator extends TranslatingUtilities {
model.setAlternating(alternating);
model.setDocoImg(prefix+"help16.png");
model.setDocoRef(prefix+"formats.html#table");
model.setDocoRef(Utilities.pathURL(prefix, "formats.html#table"));
model.getTitles().add(new Title(null, model.getDocoRef(), translate("sd.head", "Name"), translate("sd.hint", "The logical name of the element"), null, 0));
model.getTitles().add(new Title(null, model.getDocoRef(), translate("sd.head", "Flags"), translate("sd.hint", "Information about the use of the element"), null, 0));
model.getTitles().add(new Title(null, model.getDocoRef(), translate("sd.head", "Card."), translate("sd.hint", "Minimum and Maximum # of times the the element can appear in the instance"), null, 0));
@ -600,7 +614,7 @@ public class HierarchicalTableGenerator extends TranslatingUtilities {
model.setAlternating(true);
model.setDocoImg(prefix+"help16.png");
model.setDocoRef(prefix+"formats.html#table");
model.setDocoRef(Utilities.pathURL(prefix, "formats.html#table"));
model.getTitles().add(new Title(null, model.getDocoRef(), translate("sd.head", "Name"), translate("sd.hint", "The logical name of the element"), null, 0));
model.getTitles().add(new Title(null, model.getDocoRef(), translate("sd.head", "L Flags"), translate("sd.hint", "Information about the use of the element - Left Structure"), null, 0).setStyle("border-left: 1px grey solid"));
model.getTitles().add(new Title(null, model.getDocoRef(), translate("sd.head", "L Card."), translate("sd.hint", "Minimum and Maximum # of times the the element can appear in the instance - Left Structure"), null, 0));

6
org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/xhtml/XhtmlNode.java
View File

@ -843,11 +843,11 @@ public class XhtmlNode implements IBaseXhtml {
public XhtmlNode sep(String separator) {
// if there's already text, add the separator
if (seperated) {
// if there's already text, add the separator. otherwise, we'll add it next time
if (!seperated) {
seperated = true;
return this;
}
seperated = true;
return tx(separator);
}

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>5.1.21-SNAPSHOT</version>
<version>5.1.23-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>5.1.21-SNAPSHOT</version>
<version>5.1.23-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

37
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/cli/services/StandAloneValidatorFetcher.java
View File

@ -25,7 +25,7 @@ public class StandAloneValidatorFetcher implements IValidatorResourceFetcher {
void loadPackage(String id, String ver) throws IOException, FHIRException;
}
private BasePackageCacheManager pcm;
private FilesystemPackageCacheManager pcm;
private IWorkerContext context;
private IPackageInstaller installer;
@ -51,19 +51,37 @@ public class StandAloneValidatorFetcher implements IValidatorResourceFetcher {
if (!Utilities.isAbsoluteUrl(url)) {
return false;
}
// if we've got to here, it's a reference to a FHIR URL. We're going to try to resolve it on the fly
// if we've got to here, it's a reference to a FHIR URL. We're going to try to resolve it on the fly
String pid = null;
String ver = null;
String base = findBaseUrl(url);
if (base == null) {
return false;
}
if (base.equals("http://terminology.hl7.org")) {
pid = "hl7.terminology";
} else if (url.startsWith("http://hl7.org/fhir")) {
pid = pcm.getPackageId(base);
} else {
pid = pcm.findCanonicalInLocalCache(base);
}
ver = url.contains("|") ? url.substring(url.indexOf("|")+1) : null;
if (pid == null) {
return false;
}
if (url.startsWith("http://hl7.org/fhir")) {
// first possibility: it's a reference to a version specific URL http://hl7.org/fhir/X.X/...
VersionURLInfo vu = VersionUtilities.parseVersionUrl(url);
if (vu != null) {
NpmPackage pi = pcm.loadPackage(VersionUtilities.packageForVersion(vu.getVersion()), VersionUtilities.getCurrentVersion(vu.getVersion()));
return pi.hasCanonical(vu.getUrl());
}
}
// ok maybe it's a reference to a package we know
String base = findBaseUrl(url);
String pid = pcm.getPackageId(base);
String ver = url.contains("|") ? url.substring(url.indexOf("|")+1) : null;
if (pid != null) {
if (installer.packageExists(pid, ver)) {
installer.loadPackage(pid, ver);
@ -72,13 +90,8 @@ public class StandAloneValidatorFetcher implements IValidatorResourceFetcher {
}
}
if (!url.startsWith("http://hl7.org/fhir")) {
return true; // we don't bother with those in the standalone validator - we assume they are valid
}
// we assume it's invalid at this point
return false;
// we don't bother with urls outside fhir space in the standalone validator - we assume they are valid
return !url.startsWith("http://hl7.org/fhir");
}
private String findBaseUrl(String url) {

1
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/cli/services/ValidationService.java
View File

@ -209,6 +209,7 @@ public class ValidationService {
FhirPublication ver = FhirPublication.fromCode(cliContext.getSv());
ValidationEngine validator = new ValidationEngine(definitions, ver, cliContext.getSv(), tt);
System.out.println(" - "+validator.getContext().countAllCaches()+" resources ("+tt.milestone()+")");
validator.loadIg("hl7.terminology", false);
System.out.print(" Terminology server " + cliContext.getTxServer());
String txver = validator.setTerminologyServer(cliContext.getTxServer(), cliContext.getTxLog(), ver);
System.out.println(" - Version "+txver+" ("+tt.milestone()+")");

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

@ -2419,9 +2419,11 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
String ref = reference.getReference();
if (Utilities.noString(ref)) {
if (!path.contains("element.pattern")) { // this business rule doesn't apply to patterns
if (Utilities.noString(reference.getIdentifier().getSystem()) && Utilities.noString(reference.getIdentifier().getValue())) {
warning(errors, IssueType.STRUCTURE, element.line(), element.col(), path, !Utilities.noString(element.getNamedChildValue("display")), I18nConstants.REFERENCE_REF_NODISPLAY);
}
}
return;
} else if (Utilities.existsInList(ref, "http://tools.ietf.org/html/bcp47")) {
// special known URLs that can't be validated but are known to be valid

4
pom.xml
View File

@ -14,12 +14,12 @@
HAPI FHIR.
-->
<artifactId>org.hl7.fhir.core</artifactId>
<version>5.1.21-SNAPSHOT</version>
<version>5.1.23-SNAPSHOT</version>
<packaging>pom</packaging>
<properties>
<hapi_fhir_version>5.1.0</hapi_fhir_version>
<validator_test_case_version>1.1.48-SNAPSHOT</validator_test_case_version>
<validator_test_case_version>1.1.50</validator_test_case_version>
<junit_jupiter_version>5.6.2</junit_jupiter_version>
<maven_surefire_version>3.0.0-M4</maven_surefire_version>
<jacoco_version>0.8.5</jacoco_version>