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

Pass too-costly note on when including value sets + Improve rendering of value set version dependencies

This commit is contained in:
Grahame Grieve 2020-04-11 19:28:12 +10:00
parent dd78fa7f07
commit 8431a12195
3 changed files with 173 additions and 63 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

52
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/terminologies/ValueSetExpanderSimple.java
View File

@ -68,6 +68,7 @@ import org.hl7.fhir.exceptions.FHIRFormatError;
import org.hl7.fhir.exceptions.NoTerminologyServiceException;
import org.hl7.fhir.exceptions.TerminologyServiceException;
import org.hl7.fhir.r5.context.IWorkerContext;
import org.hl7.fhir.r5.model.BooleanType;
import org.hl7.fhir.r5.model.CodeSystem;
import org.hl7.fhir.r5.model.CodeSystem.CodeSystemContentMode;
import org.hl7.fhir.r5.model.CodeSystem.ConceptDefinitionComponent;
@ -319,7 +320,7 @@ public class ValueSetExpanderSimple implements ValueSetExpander {
}
if (source.hasCompose())
handleCompose(source.getCompose(), focus.getExpansion().getParameter(), expParams, source.getUrl(), focus.getExpansion().getExtension());
handleCompose(source.getCompose(), focus.getExpansion(), expParams, source.getUrl(), focus.getExpansion().getExtension());
if (canBeHeirarchy) {
for (ValueSetExpansionContainsComponent c : roots) {
@ -372,12 +373,12 @@ public class ValueSetExpanderSimple implements ValueSetExpander {
return null;
}
private void handleCompose(ValueSetComposeComponent compose, List<ValueSetExpansionParameterComponent> params, Parameters expParams, String ctxt, List<Extension> extensions)
private void handleCompose(ValueSetComposeComponent compose, ValueSetExpansionComponent exp, Parameters expParams, String ctxt, List<Extension> extensions)
throws ETooCostly, FileNotFoundException, IOException, FHIRException {
compose.checkNoModifiers("ValueSet.compose", "expanding");
// Exclude comes first because we build up a map of things to exclude
for (ConceptSetComponent inc : compose.getExclude())
excludeCodes(inc, params, ctxt);
excludeCodes(inc, exp.getParameter(), ctxt);
canBeHeirarchy = !expParams.getParameterBool("excludeNested") && excludeKeys.isEmpty() && excludeSystems.isEmpty();
boolean first = true;
for (ConceptSetComponent inc : compose.getInclude()) {
@ -385,12 +386,12 @@ public class ValueSetExpanderSimple implements ValueSetExpander {
first = false;
else
canBeHeirarchy = false;
includeCodes(inc, params, expParams, canBeHeirarchy, extensions);
includeCodes(inc, exp, expParams, canBeHeirarchy, extensions);
}
}
private ValueSet importValueSet(String value, List<ValueSetExpansionParameterComponent> params, Parameters expParams) throws ETooCostly, TerminologyServiceException, FileNotFoundException, IOException, FHIRFormatError {
private ValueSet importValueSet(String value, ValueSetExpansionComponent exp, Parameters expParams) throws ETooCostly, TerminologyServiceException, FileNotFoundException, IOException, FHIRFormatError {
if (value == null)
throw new TerminologyServiceException("unable to find value set with no identity");
ValueSet vs = context.fetchResource(ValueSet.class, value);
@ -400,11 +401,20 @@ public class ValueSetExpanderSimple implements ValueSetExpander {
if (vso.getError() != null)
throw new TerminologyServiceException("Unable to expand imported value set: " + vso.getError());
if (vs.hasVersion())
if (!existsInParams(params, "version", new UriType(vs.getUrl() + "|" + vs.getVersion())))
params.add(new ValueSetExpansionParameterComponent().setName("version").setValue(new UriType(vs.getUrl() + "|" + vs.getVersion())));
if (!existsInParams(exp.getParameter(), "version", new UriType(vs.getUrl() + "|" + vs.getVersion())))
exp.getParameter().add(new ValueSetExpansionParameterComponent().setName("version").setValue(new UriType(vs.getUrl() + "|" + vs.getVersion())));
for (Extension ex : vso.getValueset().getExpansion().getExtension()) {
if (ex.getUrl().equals("http://hl7.org/fhir/StructureDefinition/valueset-toocostly")) {
if (ex.getValue() instanceof BooleanType) {
exp.getExtension().add(new Extension("http://hl7.org/fhir/StructureDefinition/valueset-toocostly").setValue(new UriType(value)));
} else {
exp.getExtension().add(ex);
}
}
}
for (ValueSetExpansionParameterComponent p : vso.getValueset().getExpansion().getParameter()) {
if (!existsInParams(params, p.getName(), p.getValue()))
params.add(p);
if (!existsInParams(exp.getParameter(), p.getName(), p.getValue()))
exp.getParameter().add(p);
}
canBeHeirarchy = false; // if we're importing a value set, we have to be combining, so we won't try for a heirarchy
return vso.getValueset();
@ -418,11 +428,11 @@ public class ValueSetExpanderSimple implements ValueSetExpander {
}
}
private void includeCodes(ConceptSetComponent inc, List<ValueSetExpansionParameterComponent> params, Parameters expParams, boolean heirarchical, List<Extension> extensions) throws ETooCostly, FileNotFoundException, IOException, FHIRException {
private void includeCodes(ConceptSetComponent inc, ValueSetExpansionComponent exp, Parameters expParams, boolean heirarchical, List<Extension> extensions) throws ETooCostly, FileNotFoundException, IOException, FHIRException {
inc.checkNoModifiers("Compose.include", "expanding");
List<ValueSet> imports = new ArrayList<ValueSet>();
for (UriType imp : inc.getValueSet()) {
imports.add(importValueSet(imp.getValue(), params, expParams));
imports.add(importValueSet(imp.getValue(), exp, expParams));
}
if (!inc.hasSystem()) {
@ -435,27 +445,27 @@ public class ValueSetExpanderSimple implements ValueSetExpander {
} else {
CodeSystem cs = context.fetchCodeSystem(inc.getSystem());
if ((cs == null || cs.getContent() != CodeSystemContentMode.COMPLETE)) {
doServerIncludeCodes(inc, heirarchical, params, imports, expParams, extensions);
doServerIncludeCodes(inc, heirarchical, exp, imports, expParams, extensions);
} else {
doInternalIncludeCodes(inc, params, expParams, imports, cs);
doInternalIncludeCodes(inc, exp, expParams, imports, cs);
}
}
}
private void doServerIncludeCodes(ConceptSetComponent inc, boolean heirarchical, List<ValueSetExpansionParameterComponent> params, List<ValueSet> imports, Parameters expParams, List<Extension> extensions) throws FHIRException {
private void doServerIncludeCodes(ConceptSetComponent inc, boolean heirarchical, ValueSetExpansionComponent exp, List<ValueSet> imports, Parameters expParams, List<Extension> extensions) throws FHIRException {
ValueSetExpansionOutcome vso = context.expandVS(inc, heirarchical);
if (vso.getError() != null) {
throw new TerminologyServiceException("Unable to expand imported value set: " + vso.getError());
}
ValueSet vs = vso.getValueset();
if (vs.hasVersion()) {
if (!existsInParams(params, "version", new UriType(vs.getUrl() + "|" + vs.getVersion()))) {
params.add(new ValueSetExpansionParameterComponent().setName("version").setValue(new UriType(vs.getUrl() + "|" + vs.getVersion())));
if (!existsInParams(exp.getParameter(), "version", new UriType(vs.getUrl() + "|" + vs.getVersion()))) {
exp.getParameter().add(new ValueSetExpansionParameterComponent().setName("version").setValue(new UriType(vs.getUrl() + "|" + vs.getVersion())));
}
}
for (ValueSetExpansionParameterComponent p : vso.getValueset().getExpansion().getParameter()) {
if (!existsInParams(params, p.getName(), p.getValue())) {
params.add(p);
if (!existsInParams(exp.getParameter(), p.getName(), p.getValue())) {
exp.getParameter().add(p);
}
}
for (Extension ex : vs.getExpansion().getExtension()) {
@ -479,7 +489,7 @@ public class ValueSetExpanderSimple implements ValueSetExpander {
return false;
}
public void doInternalIncludeCodes(ConceptSetComponent inc, List<ValueSetExpansionParameterComponent> params, Parameters expParams, List<ValueSet> imports,
public void doInternalIncludeCodes(ConceptSetComponent inc, ValueSetExpansionComponent exp, Parameters expParams, List<ValueSet> imports,
CodeSystem cs) throws NoTerminologyServiceException, TerminologyServiceException, FHIRException {
if (cs == null) {
if (context.isNoTerminologyServer())
@ -491,8 +501,8 @@ public class ValueSetExpanderSimple implements ValueSetExpander {
if (cs.getContent() != CodeSystemContentMode.COMPLETE)
throw new TerminologyServiceException("Code system " + inc.getSystem().toString() + " is incomplete");
if (cs.hasVersion())
if (!existsInParams(params, "version", new UriType(cs.getUrl() + "|" + cs.getVersion())))
params.add(new ValueSetExpansionParameterComponent().setName("version").setValue(new UriType(cs.getUrl() + "|" + cs.getVersion())));
if (!existsInParams(exp.getParameter(), "version", new UriType(cs.getUrl() + "|" + cs.getVersion())))
exp.getParameter().add(new ValueSetExpansionParameterComponent().setName("version").setValue(new UriType(cs.getUrl() + "|" + cs.getVersion())));
if (inc.getConcept().size() == 0 && inc.getFilter().size() == 0) {
// special case - add all the code system

180
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/utils/NarrativeGenerator.java
View File

@ -422,7 +422,7 @@ public class NarrativeGenerator implements INarrativeGenerator {
throw new FHIRException("Error in template: Root element is not 'div'");
} catch (FHIRException | IOException e) {
x = new XhtmlNode(NodeType.Element, "div");
x.para().b().setAttribute("style", "color: maroon").tx("Exception generating Narrative: "+e.getMessage());
x.para().b().style("color: maroon").tx("Exception generating Narrative: "+e.getMessage());
}
inject(r, x, NarrativeStatus.GENERATED);
return true;
@ -1109,6 +1109,8 @@ public class NarrativeGenerator implements INarrativeGenerator {
private String basePath;
private String tooCostlyNoteEmpty;
private String tooCostlyNoteNotEmpty;
private String tooCostlyNoteEmptyDependent;
private String tooCostlyNoteNotEmptyDependent;
private IReferenceResolver resolver;
private int headerLevelContext;
private List<ConceptMapRenderInstructions> renderingMaps = new ArrayList<ConceptMapRenderInstructions>();
@ -1190,6 +1192,22 @@ public class NarrativeGenerator implements INarrativeGenerator {
}
public String getTooCostlyNoteEmptyDependent() {
return tooCostlyNoteEmptyDependent;
}
public void setTooCostlyNoteEmptyDependent(String tooCostlyNoteEmptyDependent) {
this.tooCostlyNoteEmptyDependent = tooCostlyNoteEmptyDependent;
}
public String getTooCostlyNoteNotEmptyDependent() {
return tooCostlyNoteNotEmptyDependent;
}
public void setTooCostlyNoteNotEmptyDependent(String tooCostlyNoteNotEmptyDependent) {
this.tooCostlyNoteNotEmptyDependent = tooCostlyNoteNotEmptyDependent;
}
// dom based version, for build program
public String generate(Element doc) throws IOException, org.hl7.fhir.exceptions.FHIRException {
return generate(null, doc);
@ -1225,7 +1243,7 @@ public class NarrativeGenerator implements INarrativeGenerator {
} catch (Exception e) {
e.printStackTrace();
x.para().b().setAttribute("style", "color: maroon").tx("Exception generating Narrative: "+e.getMessage());
x.para().b().style("color: maroon").tx("Exception generating Narrative: "+e.getMessage());
}
}
inject(er, x, NarrativeStatus.GENERATED);
@ -1239,7 +1257,7 @@ public class NarrativeGenerator implements INarrativeGenerator {
generateByProfile(rc.resourceResource, profile, rc.resourceResource, profile.getSnapshot().getElement(), profile.getSnapshot().getElement().get(0), getChildrenForPath(profile.getSnapshot().getElement(), rc.resourceResource.getResourceType().toString()), x, rc.resourceResource.getResourceType().toString(), showCodeDetails, rc);
} catch (Exception e) {
e.printStackTrace();
x.para().b().setAttribute("style", "color: maroon").tx("Exception generating Narrative: "+e.getMessage());
x.para().b().style("color: maroon").tx("Exception generating Narrative: "+e.getMessage());
}
inject(rc.resourceResource, x, NarrativeStatus.GENERATED);
return true;
@ -1252,7 +1270,7 @@ public class NarrativeGenerator implements INarrativeGenerator {
generateByProfile(er, profile, er, profile.getSnapshot().getElement(), profile.getSnapshot().getElement().get(0), getChildrenForPath(profile.getSnapshot().getElement(), er.getLocalName()), x, er.getLocalName(), showCodeDetails);
} catch (Exception e) {
e.printStackTrace();
x.para().b().setAttribute("style", "color: maroon").tx("Exception generating Narrative: "+e.getMessage());
x.para().b().style("color: maroon").tx("Exception generating Narrative: "+e.getMessage());
}
inject(er, x, NarrativeStatus.GENERATED);
String b = new XhtmlComposer(XhtmlComposer.XML, pretty).compose(x);
@ -3240,9 +3258,18 @@ public class NarrativeGenerator implements INarrativeGenerator {
if (vs.hasCopyright())
generateCopyright(x, vs);
}
if (ToolingExtensions.hasExtension(vs.getExpansion(), "http://hl7.org/fhir/StructureDefinition/valueset-toocostly"))
x.para().setAttribute("style", "border: maroon 1px solid; background-color: #FFCCCC; font-weight: bold; padding: 8px").addText(vs.getExpansion().getContains().isEmpty() ? tooCostlyNoteEmpty : tooCostlyNoteNotEmpty );
else {
if (ToolingExtensions.hasExtension(vs.getExpansion(), "http://hl7.org/fhir/StructureDefinition/valueset-toocostly")) {
List<Extension> exl = vs.getExpansion().getExtensionsByUrl("http://hl7.org/fhir/StructureDefinition/valueset-toocostly");
boolean other = false;
for (Extension ex : exl) {
if (ex.getValue() instanceof BooleanType) {
x.para().style("border: maroon 1px solid; background-color: #FFCCCC; font-weight: bold; padding: 8px").addText(vs.getExpansion().getContains().isEmpty() ? tooCostlyNoteEmpty : tooCostlyNoteNotEmpty );
} else if (!other) {
x.para().style("border: maroon 1px solid; background-color: #FFCCCC; font-weight: bold; padding: 8px").addText(vs.getExpansion().getContains().isEmpty() ? tooCostlyNoteEmptyDependent : tooCostlyNoteNotEmptyDependent );
other = true;
}
}
} else {
Integer count = countMembership(vs);
if (count == null)
x.para().tx("This value set does not contain a fixed number of concepts");
@ -3313,48 +3340,117 @@ public class NarrativeGenerator implements INarrativeGenerator {
@SuppressWarnings("rawtypes")
private void generateVersionNotice(XhtmlNode x, ValueSetExpansionComponent expansion) {
Map<String, String> versions = new HashMap<String, String>();
boolean firstVersion = true;
for (ValueSetExpansionParameterComponent p : expansion.getParameter()) {
if (p.getName().equals("version")) {
String[] parts = ((PrimitiveType) p.getValue()).asStringValue().split("\\|");
if (parts.length == 2)
versions.put(parts[0], parts[1]);
if (!versions.isEmpty()) {
StringBuilder b = new StringBuilder();
if (firstVersion) {
// the first version
// set the <p> tag and style attribute
x.para().setAttribute("style", "border: black 1px dotted; background-color: #EEEEEE; padding: 8px");
firstVersion = false;
} else {
// the second (or greater) version
x.br(); // add line break before the version text
}
b.append("Expansion based on ");
boolean firstPart = true;
for (String s : versions.keySet()) {
if (firstPart)
firstPart = false;
else
b.append(", ");
if (!s.equals("http://snomed.info/sct"))
b.append(describeSystem(s)+" version "+versions.get(s));
else {
parts = versions.get(s).split("\\/");
if (parts.length >= 5) {
String m = describeModule(parts[4]);
if (parts.length == 7)
b.append("SNOMED CT "+m+" edition "+formatSCTDate(parts[6]));
else
b.append("SNOMED CT "+m+" edition");
} else
b.append(describeSystem(s)+" version "+versions.get(s));
}
}
x.addText(b.toString()); // add the version text
}
}
}
if (versions.size() > 1) {
XhtmlNode div = x.div().style("border: black 1px dotted; background-color: #EEEEEE; padding: 8px; margin-bottom: 8px");
div.para().tx("Expansion based on: ");
XhtmlNode ul = div.ul();
for (String s : versions.keySet()) { // though there'll only be one
expRef(ul.li(), s, versions.get(s));
}
} else if (versions.size() == 1) {
XhtmlNode p = x.para().style("border: black 1px dotted; background-color: #EEEEEE; padding: 8px; margin-bottom: 8px");
p.tx("Expansion based on ");
for (String s : versions.keySet()) { // though there'll only be one
expRef(p, s, versions.get(s));
}
}
}
private void expRef(XhtmlNode x, String u, String v) {
// TODO Auto-generated method stub
if (u.equals("http://snomed.info/sct")) {
String[] parts = v.split("\\/");
if (parts.length >= 5) {
String m = describeModule(parts[4]);
if (parts.length == 7) {
x.tx("SNOMED CT "+m+" edition "+formatSCTDate(parts[6]));
} else {
x.tx("SNOMED CT "+m+" edition");
}
} else {
x.tx(describeSystem(u)+" version "+v);
}
} else if (u.equals("http://loinc.org")) {
String vd = describeLoincVer(v);
if (vd != null) {
x.tx("Loinc v"+v+" ("+vd+")");
} else {
x.tx("Loinc v"+v);
}
} else {
CanonicalResource cr = (CanonicalResource) context.fetchResource(Resource.class, u+"|"+v);
if (cr != null) {
if (cr.hasUserData("path")) {
x.ah(cr.getUserString("path")).tx(cr.present()+" v"+v+" ("+cr.fhirType()+")");
} else {
x.tx(describeSystem(u)+" v"+v+" ("+cr.fhirType()+")");
}
} else {
x.tx(describeSystem(u)+" version "+v);
}
}
}
private String describeLoincVer(String v) {
if ("2.67".equals(v)) return "Dec 2019";
if ("2.66".equals(v)) return "Jun 2019";
if ("2.65".equals(v)) return "Dec 2018";
if ("2.64".equals(v)) return "Jun 2018";
if ("2.63".equals(v)) return "Dec 2017";
if ("2.61".equals(v)) return "Jun 2017";
if ("2.59".equals(v)) return "Feb 2017";
if ("2.58".equals(v)) return "Dec 2016";
if ("2.56".equals(v)) return "Jun 2016";
if ("2.54".equals(v)) return "Dec 2015";
if ("2.52".equals(v)) return "Jun 2015";
if ("2.50".equals(v)) return "Dec 2014";
if ("2.48".equals(v)) return "Jun 2014";
if ("2.46".equals(v)) return "Dec 2013";
if ("2.44".equals(v)) return "Jun 2013";
if ("2.42".equals(v)) return "Dec 2012";
if ("2.40".equals(v)) return "Jun 2012";
if ("2.38".equals(v)) return "Dec 2011";
if ("2.36".equals(v)) return "Jun 2011";
if ("2.34".equals(v)) return "Dec 2010";
if ("2.32".equals(v)) return "Jun 2010";
if ("2.30".equals(v)) return "Feb 2010";
if ("2.29".equals(v)) return "Dec 2009";
if ("2.27".equals(v)) return "Jul 2009";
if ("2.26".equals(v)) return "Jan 2009";
if ("2.24".equals(v)) return "Jul 2008";
if ("2.22".equals(v)) return "Dec 2007";
if ("2.21".equals(v)) return "Jun 2007";
if ("2.19".equals(v)) return "Dec 2006";
if ("2.17".equals(v)) return "Jun 2006";
if ("2.16".equals(v)) return "Dec 2005";
if ("2.15".equals(v)) return "Jun 2005";
if ("2.14".equals(v)) return "Dec 2004";
if ("2.13".equals(v)) return "Aug 2004";
if ("2.12".equals(v)) return "Feb 2004";
if ("2.10".equals(v)) return "Oct 2003";
if ("2.09".equals(v)) return "May 2003";
if ("2.08 ".equals(v)) return "Sep 2002";
if ("2.07".equals(v)) return "Aug 2002";
if ("2.05".equals(v)) return "Feb 2002";
if ("2.04".equals(v)) return "Jan 2002";
if ("2.03".equals(v)) return "Jul 2001";
if ("2.02".equals(v)) return "May 2001";
if ("2.01".equals(v)) return "Jan 2001";
if ("2.00".equals(v)) return "Jan 2001";
if ("1.0n".equals(v)) return "Feb 2000";
if ("1.0ma".equals(v)) return "Aug 1999";
if ("1.0m".equals(v)) return "Jul 1999";
if ("1.0l".equals(v)) return "Jan 1998";
if ("1.0ja".equals(v)) return "Oct 1997";
return null;
}
private String formatSCTDate(String ds) {

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

@ -526,6 +526,10 @@ public class XhtmlNode implements IBaseXhtml {
return setAttribute("colspan", n);
}
public XhtmlNode div() {
return addTag("div");
}
public XhtmlNode para() {
return addTag("p");
}