org.hl7.fhir.r5.renderers.ValueSetRenderer Maven / Gradle / Ivy
package org.hl7.fhir.r5.renderers;
import java.io.IOException;
import java.io.UnsupportedEncodingException;
import java.text.ParseException;
import java.text.SimpleDateFormat;
import java.util.ArrayList;
import java.util.Collections;
import java.util.Date;
import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
import java.util.Set;
import org.hl7.fhir.exceptions.DefinitionException;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.exceptions.FHIRFormatError;
import org.hl7.fhir.exceptions.TerminologyServiceException;
import org.hl7.fhir.r5.comparison.VersionComparisonAnnotation;
import org.hl7.fhir.r5.model.Base;
import org.hl7.fhir.r5.model.CanonicalResource;
import org.hl7.fhir.r5.model.CodeSystem;
import org.hl7.fhir.r5.model.CodeSystem.ConceptDefinitionComponent;
import org.hl7.fhir.r5.model.Coding;
import org.hl7.fhir.r5.model.ConceptMap;
import org.hl7.fhir.r5.model.DataType;
import org.hl7.fhir.r5.model.Enumerations.FilterOperator;
import org.hl7.fhir.r5.model.Enumerations.PublicationStatus;
import org.hl7.fhir.r5.model.Expression;
import org.hl7.fhir.r5.model.Extension;
import org.hl7.fhir.r5.model.ExtensionHelper;
import org.hl7.fhir.r5.model.PrimitiveType;
import org.hl7.fhir.r5.model.Resource;
import org.hl7.fhir.r5.model.StringType;
import org.hl7.fhir.r5.model.UriType;
import org.hl7.fhir.r5.model.ValueSet;
import org.hl7.fhir.r5.model.ValueSet.ConceptPropertyComponent;
import org.hl7.fhir.r5.model.ValueSet.ConceptReferenceComponent;
import org.hl7.fhir.r5.model.ValueSet.ConceptReferenceDesignationComponent;
import org.hl7.fhir.r5.model.ValueSet.ConceptSetComponent;
import org.hl7.fhir.r5.model.ValueSet.ConceptSetFilterComponent;
import org.hl7.fhir.r5.model.ValueSet.ValueSetComposeComponent;
import org.hl7.fhir.r5.model.ValueSet.ValueSetExpansionComponent;
import org.hl7.fhir.r5.model.ValueSet.ValueSetExpansionContainsComponent;
import org.hl7.fhir.r5.model.ValueSet.ValueSetExpansionParameterComponent;
import org.hl7.fhir.r5.model.ValueSet.ValueSetExpansionPropertyComponent;
import org.hl7.fhir.r5.renderers.utils.RenderingContext;
import org.hl7.fhir.r5.renderers.utils.RenderingContext.DesignationMode;
import org.hl7.fhir.r5.renderers.utils.RenderingContext.GenerationRules;
import org.hl7.fhir.r5.renderers.utils.ResourceWrapper;
import org.hl7.fhir.r5.terminologies.CodeSystemUtilities;
import org.hl7.fhir.r5.terminologies.ValueSetUtilities;
import org.hl7.fhir.r5.terminologies.expansion.ValueSetExpansionOutcome;
import org.hl7.fhir.r5.terminologies.utilities.CodingValidationRequest;
import org.hl7.fhir.r5.terminologies.utilities.SnomedUtilities;
import org.hl7.fhir.r5.terminologies.utilities.ValidationResult;
import org.hl7.fhir.r5.utils.EOperationOutcome;
import org.hl7.fhir.r5.utils.ToolingExtensions;
import org.hl7.fhir.r5.utils.UserDataNames;
import org.hl7.fhir.utilities.LoincLinker;
import org.hl7.fhir.utilities.MarkedToMoveToAdjunctPackage;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.xhtml.HierarchicalTableGenerator;
import org.hl7.fhir.utilities.xhtml.HierarchicalTableGenerator.Row;
import org.hl7.fhir.utilities.xhtml.HierarchicalTableGenerator.TableModel;
import org.hl7.fhir.utilities.xhtml.XhtmlNode;
import com.google.common.collect.HashMultimap;
import com.google.common.collect.Multimap;
@MarkedToMoveToAdjunctPackage
public class ValueSetRenderer extends TerminologyRenderer {
public ValueSetRenderer(RenderingContext context) {
super(context);
}
@Override
public void buildNarrative(RenderingStatus status, XhtmlNode x, ResourceWrapper r) throws FHIRFormatError, DefinitionException, IOException, FHIRException, EOperationOutcome {
if (!r.isDirect()) {
// the intention is to change this in the future
x.para().tx("ValueSetRenderer only renders native resources directly");
} else {
renderResourceTechDetails(r, x);
ValueSet vs = (ValueSet) r.getBase();
genSummaryTable(status, x, vs);
List maps = findReleventMaps(vs);
if (context.isShowSummaryTable()) {
XhtmlNode h = x.h2();
h.addText(vs.hasTitle() ? vs.getTitle() : vs.getName());
addMarkdown(x, vs.getDescription());
if (vs.hasCopyright())
generateCopyright(x, r);
}
if (vs.hasExtension(ToolingExtensions.EXT_VS_CS_SUPPL_NEEDED)) {
var p = x.para();
p.tx("This ValueSet requires the Code system Supplement ");
String u = ToolingExtensions.readStringExtension(vs, ToolingExtensions.EXT_VS_CS_SUPPL_NEEDED);
CodeSystem cs = context.getContext().fetchResource(CodeSystem.class, u);
if (cs == null) {
p.code().tx(u);
} else if (!cs.hasWebPath()) {
p.ah(u).tx(cs.present());
} else {
p.ah(cs.getWebPath()).tx(cs.present());
}
p.tx(".");
}
if (vs.hasExtension(ToolingExtensions.EXT_VALUESET_PARAMETER)) {
x.para().b().tx("This ValueSet has parameters");
XhtmlNode tbl = x.table("grid");
XhtmlNode tr = tbl.tr();
tr.th().tx("Name");
tr.th().tx("Documentation");
for (Extension ext : vs.getExtensionsByUrl(ToolingExtensions.EXT_VALUESET_PARAMETER)) {
tr = tbl.tr();
tr.td().tx(ext.getExtensionString("name"));
tr.td().markdown(ext.getExtensionString("documentation"), "parameter.documentation");
}
}
if (vs.hasExpansion()) {
// for now, we just accept an expansion if there is one
generateExpansion(status, r, x, vs, false, maps);
} else {
generateComposition(status, r, x, vs, false, maps);
}
}
}
@Override
public String buildSummary(ResourceWrapper r) throws UnsupportedEncodingException, IOException {
return canonicalTitle(r);
}
private static final int MAX_DESIGNATIONS_IN_LINE = 5;
private static final int MAX_BATCH_VALIDATION_SIZE = 1000;
private List renderingMaps = new ArrayList();
public void render(RenderingStatus status, XhtmlNode x, ValueSet vs, boolean header) throws FHIRFormatError, DefinitionException, IOException {
}
public void describe(XhtmlNode x, ValueSet vs) {
x.tx(display(vs));
}
public String display(ValueSet vs) {
return vs.present();
}
private List findReleventMaps(ValueSet vs) throws FHIRException {
List res = new ArrayList();
for (ConceptMap cm : getContext().getWorker().fetchResourcesByType(ConceptMap.class)) {
if (isSource(vs, cm.getSourceScope())) {
ConceptMapRenderInstructions re = findByTarget(cm.getTargetScope());
if (re == null) {
re = new ConceptMapRenderInstructions(cm.present(), cm.getUrl(), false);
}
if (re != null) {
ValueSet vst = cm.hasTargetScope() ? getContext().getWorker().findTxResource(ValueSet.class, cm.hasTargetScopeCanonicalType() ? cm.getTargetScopeCanonicalType().getValue() : cm.getTargetScopeUriType().asStringValue(), cm) : null;
res.add(new UsedConceptMap(re, vst == null ? cm.getWebPath() : vst.getWebPath(), cm));
}
}
}
return res;
// @Override
// public List findMapsForSource(String url) throws FHIRException {
// synchronized (lock) {
// List res = new ArrayList();
// for (ConceptMap map : maps.getList()) {
// if (((Reference) map.getSourceScope()).getReference().equals(url)) {
// res.add(map);
// }
// }
// return res;
// }
// }
// Map mymaps = new HashMap();
// for (ConceptMap a : context.getWorker().findMapsForSource(vs.getUrl())) {
// String url = "";
// ValueSet vsr = context.getWorker().findTxResource(ValueSet.class, ((Reference) a.getTarget()).getReference());
// if (vsr != null)
// url = (String) vsr.getUserData(UserDataNames.filename);
// mymaps.put(a, url);
// }
// Map mymaps = new HashMap();
// for (ConceptMap a : context.getWorker().findMapsForSource(cs.getValueSet())) {
// String url = "";
// ValueSet vsr = context.getWorker().fetchResource(ValueSet.class, ((Reference) a.getTarget()).getReference());
// if (vsr != null)
// url = (String) vsr.getUserData(UserDataNames.filename);
// mymaps.put(a, url);
// }
// also, look in the contained resources for a concept map
// for (Resource r : cs.getContained()) {
// if (r instanceof ConceptMap) {
// ConceptMap cm = (ConceptMap) r;
// if (((Reference) cm.getSource()).getReference().equals(cs.getValueSet())) {
// String url = "";
// ValueSet vsr = context.getWorker().findTxResource(ValueSet.class, ((Reference) cm.getTarget()).getReference());
// if (vsr != null)
// url = (String) vsr.getUserData(UserDataNames.filename);
// mymaps.put(cm, url);
// }
// }
// }
}
private boolean isSource(ValueSet vs, DataType source) {
return vs.hasUrl() && source != null && vs.getUrl().equals(source.primitiveValue());
}
private void generateExpansion(RenderingStatus status, ResourceWrapper res, XhtmlNode x, ValueSet vs, boolean header, List maps) throws FHIRFormatError, DefinitionException, IOException {
List langs = new ArrayList();
Map designations = new HashMap<>(); // map of url = description, where url is the designation code. Designations that are for languages won't make it into this list
Map properties = new HashMap<>(); // map of url = description, where url is the designation code. Designations that are for languages won't make it into this list
if (header) {
XhtmlNode h = x.addTag(getHeader());
h.tx(context.formatPhrase(RenderingContext.VALUE_SET_CONT));
if (IsNotFixedExpansion(vs))
addMarkdown(x, vs.getDescription());
if (vs.hasCopyright())
generateCopyright(x, res);
}
boolean hasFragment = generateContentModeNotices(x, vs.getExpansion(), vs);
generateVersionNotice(x, vs.getExpansion(), vs);
if (ToolingExtensions.hasExtension(vs.getExpansion(), ToolingExtensions.EXT_EXP_TOOCOSTLY)) {
String msg = null;
if (vs.getExpansion().getContains().isEmpty()) {
msg = context.formatPhrase(RenderingContext.VALUE_SET_TOO_COSTLY);
} else {
msg = context.formatPhrase(RenderingContext.VALUE_SET_CODE_SELEC, countMembership(vs));
}
x.para().style("border: maroon 1px solid; background-color: #FFCCCC; font-weight: bold; padding: 8px").addText(msg);
} else {
int count = ValueSetUtilities.countExpansion(vs);
if (vs.getExpansion().hasTotal()) {
if (count != vs.getExpansion().getTotal()) {
x.para().style("border: maroon 1px solid; background-color: #FFCCCC; font-weight: bold; padding: 8px")
.addText(context.formatPhrase(hasFragment ? RenderingContext.VALUE_SET_HAS_AT_LEAST : RenderingContext.VALUE_SET_HAS, vs.getExpansion().getTotal(), count));
} else {
x.para().tx(context.formatPhrase(hasFragment ? RenderingContext.VALUE_SET_CONTAINS_AT_LEAST : RenderingContext.VALUE_SET_CONTAINS, vs.getExpansion().getTotal()));
}
} else if (count == 1000) {
// it's possible that there's exactly 1000 codes, in which case wht we're about to do is wrong
// work in progress to tighten up the terminology system to always return a total...
String msg = context.formatPhrase(RenderingContext.VALUE_SET_SEL);
x.para().style("border: maroon 1px solid; background-color: #FFCCCC; font-weight: bold; padding: 8px").addText(msg);
} else {
x.para().tx(context.formatPhrase(RenderingContext.VALUE_SET_NUMBER_CONCEPTS, count));
}
}
boolean doLevel = false;
for (ValueSetExpansionContainsComponent cc : vs.getExpansion().getContains()) {
if (cc.hasContains()) {
doLevel = true;
break;
}
}
boolean doInactive = checkDoInactive(vs.getExpansion().getContains());
boolean doDefinition = checkDoDefinition(vs.getExpansion().getContains());
XhtmlNode t = x.table("codes", false);
XhtmlNode tr = t.tr();
if (doLevel)
tr.td().b().tx(context.formatPhrase(RenderingContext.VALUE_SET_LEVEL));
tr.td().attribute("style", "white-space:nowrap").b().tx(context.formatPhrase(RenderingContext.GENERAL_CODE));
tr.td().b().tx(context.formatPhrase(RenderingContext.VALUE_SET_SYSTEM));
XhtmlNode tdDisp = tr.td();
String displang = vs.getLanguage();
if (displang == null) {
displang = findParamValue(vs.getExpansion().getParameter(), "displayLanguage");
}
if (displang == null) {
tdDisp.b().tx(context.formatPhrase(RenderingContext.TX_DISPLAY));
} else {
tdDisp.b().tx(context.formatPhrase(RenderingContext.TX_DISPLAY_LANG, displang));
}
boolean doDesignations = false;
for (ValueSetExpansionContainsComponent c : vs.getExpansion().getContains()) {
scanForDesignations(vs, c, langs, designations);
}
scanForProperties(vs.getExpansion(), langs, properties);
if (doInactive) {
tr.td().b().tx(context.formatPhrase(RenderingContext.VALUE_SET_INACTIVE));
}
if (doDefinition) {
tr.td().b().tx(context.formatPhrase(RenderingContext.GENERAL_DEFINITION));
doDesignations = false;
for (String n : Utilities.sorted(properties.keySet())) {
tr.td().b().ah(context.prefixLocalHref(properties.get(n))).addText(n);
}
} else {
for (String n : Utilities.sorted(properties.keySet())) {
tr.td().b().ah(context.prefixLocalHref(properties.get(n))).addText(n);
}
// if we're not doing definitions and we don't have too many languages, we'll do them in line
doDesignations = langs.size() + properties.size() + designations.size() < MAX_DESIGNATIONS_IN_LINE;
if (doDesignations) {
if (vs.hasLanguage()) {
tdDisp.tx(" - "+describeLang(vs.getLanguage()));
}
for (String url : designations.keySet()) {
tr.td().b().addText(designations.get(url));
}
for (String lang : langs) {
tr.td().b().addText(describeVSLang(lang, displang));
}
}
}
addMapHeaders(tr, maps);
for (ValueSetExpansionContainsComponent c : vs.getExpansion().getContains()) {
addExpansionRowToTable(t, vs, c, 1, doLevel, doDefinition, doInactive, maps, langs, designations, doDesignations, properties, res);
}
// now, build observed languages
if (!doDesignations && langs.size() + designations.size() > 0) {
Collections.sort(langs);
if (designations.size() == 0) {
x.para().b().tx(context.formatPhrase(RenderingContext.GENERAL_ADD_LANG));
} else if (langs.size() == 0) {
x.para().b().tx(context.formatPhrase(RenderingContext.VALUE_SET_DESIG));
} else {
x.para().b().tx(context.formatPhrase(RenderingContext.VALUE_SET_ADD_DESIG));
}
t = x.table("codes", false);
tr = t.tr();
tr.td().b().tx(context.formatPhrase(RenderingContext.GENERAL_CODE));
for (String url : designations.keySet()) {
tr.td().b().addText(designations.get(url));
}
for (String lang : langs) {
tr.td().b().addText(describeLang(lang));
}
for (ValueSetExpansionContainsComponent c : vs.getExpansion().getContains()) {
addDesignationRow(c, t, langs, designations);
}
}
}
protected String describeVSLang(String lang, String displang) {
// special cases:
if ("fr-CA".equals(lang)) {
return "French (Canadian)"; // this one was omitted from the value set
}
ValueSet v = getContext().getWorker().findTxResource(ValueSet.class, "http://hl7.org/fhir/ValueSet/languages");
if (v != null) {
ConceptReferenceComponent l = null;
for (ConceptReferenceComponent cc : v.getCompose().getIncludeFirstRep().getConcept()) {
if (cc.getCode().equals(lang))
l = cc;
}
if (l == null) {
if (lang.contains("-")) {
lang = lang.substring(0, lang.indexOf("-"));
}
for (ConceptReferenceComponent cc : v.getCompose().getIncludeFirstRep().getConcept()) {
if (cc.getCode().equals(lang)) {
l = cc;
break;
}
}
if (l == null) {
for (ConceptReferenceComponent cc : v.getCompose().getIncludeFirstRep().getConcept()) {
if (cc.getCode().startsWith(lang+"-")) {
l = cc;
break;
}
}
}
}
if (l != null) {
if (lang.contains("-"))
lang = lang.substring(0, lang.indexOf("-"));
String en = l.getDisplay();
String nativelang = null;
for (ConceptReferenceDesignationComponent cd : l.getDesignation()) {
if (cd.getLanguage().equals(lang))
nativelang = cd.getValue();
}
return context.formatPhrase(langsMatch(lang, displang) ? RenderingContext.VALUE_SET_OTHER_DISPLAY : RenderingContext.TX_DISPLAY_LANG, nativelang == null ? en : nativelang);
}
}
return lang;
}
private boolean langsMatch(String lang, String displang) {
if (lang == null) {
return displang == null;
} else if (lang.equals(displang)) {
return true;
} else if (displang == null) {
return false;
} else {
String l1 = lang.contains("-") ? lang.substring(0, lang.indexOf("-")) : lang;
String l2 = displang.contains("-") ? displang.substring(0, displang.indexOf("-")) : displang;
return l1.equals(l2);
}
}
private void scanForProperties(ValueSetExpansionComponent exp, List langs, Map properties) {
properties.clear();
for (ValueSetExpansionPropertyComponent pp : exp.getProperty()) {
if (pp.hasCode() && pp.hasUri() && anyActualproperties(exp.getContains(), pp.getCode())) {
properties.put(pp.getCode(), pp.getUri());
}
}
}
private boolean anyActualproperties(List contains, String pp) {
for (ValueSetExpansionContainsComponent c : contains) {
for (ConceptPropertyComponent cp : c.getProperty()) {
if (pp.equals(cp.getCode())) {
return true;
}
}
if (anyActualproperties(c.getContains(), pp)) {
return true;
}
}
return false;
}
private boolean generateContentModeNotices(XhtmlNode x, ValueSetExpansionComponent expansion, Resource vs) {
generateContentModeNotice(x, expansion, "example", context.formatPhrase(RenderingContext.VALUE_SET_EXP), vs);
return generateContentModeNotice(x, expansion, "fragment", context.formatPhrase(RenderingContext.VALUE_SET_EXP_FRAG), vs);
}
private boolean generateContentModeNotice(XhtmlNode x, ValueSetExpansionComponent expansion, String mode, String text, Resource vs) {
boolean res = false;
Multimap versions = HashMultimap.create();
for (ValueSetExpansionParameterComponent p : expansion.getParameter()) {
if (p.getName().equals(mode)) {
String[] parts = ((PrimitiveType) p.getValue()).asStringValue().split("\\|");
if (parts.length == 2 && !Utilities.noString(parts[0]))
versions.put(parts[0], parts[1]);
}
}
if (versions.size() > 0) {
XhtmlNode div = null;
XhtmlNode ul = null;
boolean first = true;
for (String s : versions.keySet()) {
if (versions.size() == 1 && versions.get(s).size() == 1) {
for (String v : versions.get(s)) { // though there'll only be one
XhtmlNode p = x.para().style("border: black 1px dotted; background-color: #ffcccc; padding: 8px; margin-bottom: 8px");
p.tx(text+" ");
expRef(p, s, v, vs);
res = true;
}
} else {
for (String v : versions.get(s)) {
if (first) {
div = x.div().style("border: black 1px dotted; background-color: #EEEEEE; padding: 8px; margin-bottom: 8px");
div.para().tx(text+"s: ");
ul = div.ul();
first = false;
res = true;
}
expRef(ul.li(), s, v, vs);
}
}
}
}
return res;
}
private boolean checkDoSystem(ValueSet vs, ValueSet src) {
if (src != null)
vs = src;
return vs.hasCompose();
}
private boolean IsNotFixedExpansion(ValueSet vs) {
if (vs.hasCompose())
return false;
// it's not fixed if it has any includes that are not version fixed
for (ConceptSetComponent cc : vs.getCompose().getInclude()) {
if (cc.hasValueSet())
return true;
if (!cc.hasVersion())
return true;
}
return false;
}
private ConceptMapRenderInstructions findByTarget(DataType source) {
if (source == null) {
return null;
}
String src = source.primitiveValue();
if (src == null) {
return null;
}
for (ConceptMapRenderInstructions t : renderingMaps) {
if (src.equals(t.getUrl()))
return t;
}
return null;
}
private Integer countMembership(ValueSet vs) {
int count = 0;
if (vs.hasExpansion())
count = count + ValueSetUtilities.countExpansion(vs);
else {
if (vs.hasCompose()) {
if (vs.getCompose().hasExclude()) {
try {
ValueSetExpansionOutcome vse = getContext().getWorker().expandVS(vs, true, false);
count = 0;
count += ValueSetUtilities.countExpansion(vse.getValueset());
return count;
} catch (Exception e) {
return null;
}
}
for (ConceptSetComponent inc : vs.getCompose().getInclude()) {
if (inc.hasFilter())
return null;
if (!inc.hasConcept())
return null;
count = count + inc.getConcept().size();
}
}
}
return count;
}
private void addCSRef(XhtmlNode x, String url) {
CodeSystem cs = getContext().getWorker().fetchCodeSystem(url);
if (cs == null) {
x.code(url);
} else if (cs.hasWebPath()) {
x.ah(context.prefixLocalHref(cs.getWebPath())).tx(cs.present());
} else {
x.code(url);
x.tx(" ("+cs.present()+")");
}
}
@SuppressWarnings("rawtypes")
private void generateVersionNotice(XhtmlNode x, ValueSetExpansionComponent expansion, Resource vs) {
Multimap versions = HashMultimap.create();
Set vlist = new HashSet<>();
for (ValueSetExpansionParameterComponent p : expansion.getParameter()) {
if ((p.getName().startsWith("used-") || p.getName().equals("version")) && !vlist.contains(p.getValue().primitiveValue())) {
String name = p.getName().equals("version") ? "system" : p.getName().substring(5);
vlist.add(p.getValue().primitiveValue());
String[] parts = ((PrimitiveType) p.getValue()).asStringValue().split("\\|");
if (parts.length == 2 && !Utilities.noString(parts[0]))
versions.put(name+"|"+parts[0], parts[1]);
}
}
if (versions.size() > 0) {
XhtmlNode div = null;
XhtmlNode ul = null;
boolean first = true;
for (String s : Utilities.sorted(versions.keySet())) {
if (versions.size() == 1 && versions.get(s).size() == 1) {
for (String v : versions.get(s)) { // though there'll only be one
XhtmlNode p = x.para().style("border: black 1px dotted; background-color: #EEEEEE; padding: 8px; margin-bottom: 8px");
if (!vs.hasUserData(UserDataNames.VS_EXPANSION_SOURCE)) {
p.tx(context.formatPhrase(RenderingContext.VALUE_SET_EXPANSION)+" ");
} else if ("internal".equals(vs.getUserString(UserDataNames.VS_EXPANSION_SOURCE))) {
p.tx(context.formatPhrase(RenderingContext.VALUE_SET_EXPANSION_INTERNAL)+" ");
} else {
p.tx(context.formatPhrase(RenderingContext.VALUE_SET_EXPANSION_SRVR, vs.getUserString(UserDataNames.VS_EXPANSION_SOURCE))+" ");
}
expRef(p, s, v, vs);
}
} else {
for (String v : versions.get(s)) {
if (first) {
div = x.div().style("border: black 1px dotted; background-color: #EEEEEE; padding: 8px; margin-bottom: 8px");
if (!vs.hasUserData(UserDataNames.VS_EXPANSION_SOURCE)) {
div.para().tx(context.formatPhrase(RenderingContext.VALUE_SET_EXPANSIONS));
} else if ("internal".equals(vs.getUserString(UserDataNames.VS_EXPANSION_SOURCE))) {
div.para().tx(context.formatPhrase(RenderingContext.VALUE_SET_EXPANSIONS_INTERNAL));
} else {
div.para().tx(context.formatPhrase(RenderingContext.VALUE_SET_EXPANSIONS_SRVR, vs.getUserString(UserDataNames.VS_EXPANSION_SOURCE)));
}
ul = div.ul();
first = false;
}
expRef(ul.li(), s, v, vs);
}
}
}
}
}
private String findParamValue(List list, String name) {
for (ValueSetExpansionParameterComponent p : list) {
if (name.equals(p.getName())) {
return p.getValue().primitiveValue();
}
}
return null;
}
private void expRef(XhtmlNode x, String u, String v, Resource source) {
String t = u.contains("|") ? u.substring(0, u.indexOf("|")) : u;
u = u.substring(u.indexOf("|")+1);
// 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(context.formatPhrase(RenderingContext.VALUE_SET_SNOMED_ADD, m, formatSCTDate(parts[6])));
} else {
x.tx(context.formatPhrase(RenderingContext.VALUE_SET_SNOMED, m));
}
} else {
x.tx(displaySystem(u)+" "+ context.formatPhrase(RenderingContext.GENERAL_VER_LOW) + " " +v);
}
} else if (u.equals("http://loinc.org")) {
String vd = describeLoincVer(v);
if (vd != null) {
x.tx(context.formatPhrase(RenderingContext.VALUE_SET_LOINCV)+v+" ("+vd+")");
} else {
x.tx(context.formatPhrase(RenderingContext.VALUE_SET_LOINCV)+v);
}
} else if (Utilities.noString(v)) {
CanonicalResource cr = (CanonicalResource) getContext().getWorker().fetchResource(Resource.class, u, source);
if (cr != null) {
if (cr.hasWebPath()) {
x.ah(context.prefixLocalHref(cr.getWebPath())).tx(t+" "+cr.present()+" "+ context.formatPhrase(RenderingContext.VALUE_SET_NO_VERSION)+cr.fhirType()+")");
} else {
x.tx(t+" "+displaySystem(u)+" "+context.formatPhrase(RenderingContext.VALUE_SET_NO_VERSION)+cr.fhirType()+")");
}
} else {
x.tx(t+" "+displaySystem(u)+" "+ context.formatPhrase(RenderingContext.VALUE_SET_NO_VER));
}
} else {
CanonicalResource cr = (CanonicalResource) getContext().getWorker().fetchResource(Resource.class, u+"|"+v, source);
if (cr != null) {
if (cr.hasWebPath()) {
x.ah(context.prefixLocalHref(cr.getWebPath())).tx(t+" "+cr.present()+" v"+v+" ("+cr.fhirType()+")");
} else {
x.tx(t+" "+displaySystem(u)+" v"+v+" ("+cr.fhirType()+")");
}
} else {
x.tx(t+" "+displaySystem(u)+" "+ context.formatPhrase(RenderingContext.GENERAL_VER_LOW)+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) {
SimpleDateFormat format = new SimpleDateFormat("yyyyMMdd");
Date date;
try {
date = format.parse(ds);
} catch (ParseException e) {
return ds;
}
return new SimpleDateFormat("dd-MMM yyyy").format(date);
}
private String describeModule(String module) {
switch (module) {
case "900000000000207008" : return context.formatPhrase(RenderingContext.VALUE_SET_INT);
case "449081005" : return context.formatPhrase(RenderingContext.VALUE_SET_SPAN);
case "11000221109" : return context.formatPhrase(RenderingContext.VALUE_SET_AR);
case "32506021000036107" : return context.formatPhrase(RenderingContext.VALUE_SET_AUS);
case "11000234105" : return context.formatPhrase(RenderingContext.VALUE_SET_AT);
case "11000172109" : return context.formatPhrase(RenderingContext.VALUE_SET_BE);
case "20621000087109" : return context.formatPhrase(RenderingContext.VALUE_SET_CA_EN);
case "20611000087101" : return context.formatPhrase(RenderingContext.VALUE_SET_CA_FR);
case "554471000005108" : return context.formatPhrase(RenderingContext.VALUE_SET_DANISH);
case "11000181102 " : return context.formatPhrase(RenderingContext.VALUE_SET_EE);
case "11000229106" : return context.formatPhrase(RenderingContext.VALUE_SET_FI);
case "11000274103" : return context.formatPhrase(RenderingContext.VALUE_SET_DE);
case "1121000189102" : return context.formatPhrase(RenderingContext.VALUE_SET_IN);
case "11000220105" : return context.formatPhrase(RenderingContext.VALUE_SET_IE);
case "11000146104" : return context.formatPhrase(RenderingContext.VALUE_SET_DUTCH);
case "21000210109" : return context.formatPhrase(RenderingContext.VALUE_SET_NZ);
case "51000202101 " : return context.formatPhrase(RenderingContext.VALUE_SET_NO);
case "11000267109" : return context.formatPhrase(RenderingContext.VALUE_SET_KR);
case "900000001000122104" : return context.formatPhrase(RenderingContext.VALUE_ES_ES);
case "45991000052106" : return context.formatPhrase(RenderingContext.VALUE_SET_SWEDISH);
case "2011000195101" : return context.formatPhrase(RenderingContext.VALUE_SET_CH);
case "83821000000107" : return context.formatPhrase(RenderingContext.VALUE_SET_UK);
case "999000021000000109" : return context.formatPhrase(RenderingContext.VALUE_SET_UK_CLIN);
case "5631000179106" : return context.formatPhrase(RenderingContext.VALUE_SET_UY);
case "731000124108" : return context.formatPhrase(RenderingContext.VALUE_SET_US);
case "5991000124107" : return context.formatPhrase(RenderingContext.VALUE_SET_US_ICD10CM);
default:
return module;
}
}
private boolean hasVersionParameter(ValueSetExpansionComponent expansion) {
for (ValueSetExpansionParameterComponent p : expansion.getParameter()) {
if (p.getName().equals("version"))
return true;
}
return false;
}
private void addDesignationRow(ValueSetExpansionContainsComponent c, XhtmlNode t, List langs, Map designations) {
XhtmlNode tr = t.tr();
tr.td().addText(c.getCode());
addDesignationsToRow(c, designations, tr);
addLangaugesToRow(c, langs, tr);
for (ValueSetExpansionContainsComponent cc : c.getContains()) {
addDesignationRow(cc, t, langs, designations);
}
}
public void addDesignationsToRow(ValueSetExpansionContainsComponent c, Map designations, XhtmlNode tr) {
for (String url : designations.keySet()) {
String d = null;
if (d == null) {
for (ConceptReferenceDesignationComponent dd : c.getDesignation()) {
if (url.equals(getUrlForDesignation(dd))) {
d = dd.getValue();
}
}
}
tr.td().addText(d == null ? "" : d);
}
}
public void addLangaugesToRow(ValueSetExpansionContainsComponent c, List langs, XhtmlNode tr) {
for (String lang : langs) {
String d = null;
for (Extension ext : c.getExtension()) {
if (ToolingExtensions.EXT_TRANSLATION.equals(ext.getUrl())) {
String l = ToolingExtensions.readStringExtension(ext, "lang");
if (lang.equals(l)) {
d = ToolingExtensions.readStringExtension(ext, "content");
}
}
}
if (d == null) {
for (ConceptReferenceDesignationComponent dd : c.getDesignation()) {
String l = dd.getLanguage();
if (lang.equals(l)) {
d = dd.getValue();
}
}
}
tr.td().addText(d == null ? "" : d);
}
}
private boolean checkDoDefinition(List contains) {
for (ValueSetExpansionContainsComponent c : contains) {
CodeSystem cs = getContext().getWorker().fetchCodeSystem(c.getSystem());
if (cs != null) {
ConceptDefinitionComponent cd = CodeSystemUtilities.getCode(cs, c.getCode());
if (cd != null && cd.hasDefinition()) {
return true;
}
}
if (checkDoDefinition(c.getContains()))
return true;
}
return false;
}
private boolean checkDoInactive(List contains) {
for (ValueSetExpansionContainsComponent c : contains) {
if (c.hasInactive()) {
return true;
}
if (checkDoInactive(c.getContains()))
return true;
}
return false;
}
private boolean allFromOneSystem(ValueSet vs) {
if (vs.getExpansion().getContains().isEmpty())
return false;
String system = vs.getExpansion().getContains().get(0).getSystem();
for (ValueSetExpansionContainsComponent cc : vs.getExpansion().getContains()) {
if (!checkSystemMatches(system, cc))
return false;
}
return true;
}
private String getCsRef(String system) {
CodeSystem cs = getContext().getWorker().fetchCodeSystem(system);
return getCsRef(cs);
}
private String getCsRef(T cs) {
if (cs == null) {
return "?cs-n?";
}
String ref = cs.getWebPath();
if (ref == null) {
ref = cs.getUserString(UserDataNames.render_filename);
}
return ref == null ? null : ref.replace("\\", "/");
}
private void scanForDesignations(ValueSet vs, ValueSetExpansionContainsComponent c, List langs, Map designations) {
for (Extension ext : c.getExtension()) {
if (ToolingExtensions.EXT_TRANSLATION.equals(ext.getUrl())) {
String lang = ToolingExtensions.readStringExtension(ext, "lang");
if (!Utilities.noString(lang) && !langs.contains(lang) && !isBaseLang(vs, lang)) {
langs.add(lang);
}
}
}
if (context.getDesignationMode() != DesignationMode.NONE) {
for (ConceptReferenceDesignationComponent d : c.getDesignation()) {
String lang = d.getLanguage();
if (!Utilities.noString(lang)) {
if (!langs.contains(lang)) {
langs.add(lang);
}
} else if (context.getDesignationMode() == DesignationMode.ALL) {
// can we present this as a designation that we know?
String disp = getDisplayForDesignation(d);
String url = getUrlForDesignation(d);
if (disp == null) {
disp = getDisplayForUrl(url);
}
if (disp != null && !designations.containsKey(url) && url != null) {
designations.put(url, disp);
}
}
}
}
for (ValueSetExpansionContainsComponent cc : c.getContains()) {
scanForDesignations(vs, cc, langs, designations);
}
}
private boolean isBaseLang(ValueSet vs, String lang) {
return (isDefLang(lang) && isDefLang(vs.getLanguage())) || langsMatch(lang, vs.getLanguage());
}
private boolean isDefLang(String lang) {
return lang == null || "en".equals(lang) || "en-US".equals(lang);
}
private void scanForLangs(ValueSetExpansionContainsComponent c, List langs) {
for (Extension ext : c.getExtension()) {
if (ToolingExtensions.EXT_TRANSLATION.equals(ext.getUrl())) {
String lang = ToolingExtensions.readStringExtension(ext, "lang");
if (!Utilities.noString(lang) && !langs.contains(lang)) {
langs.add(lang);
}
}
}
for (ConceptReferenceDesignationComponent d : c.getDesignation()) {
String lang = d.getLanguage();
if (!Utilities.noString(lang) && !langs.contains(lang)) {
langs.add(lang);
}
}
for (ValueSetExpansionContainsComponent cc : c.getContains()) {
scanForLangs(cc, langs);
}
}
private void addExpansionRowToTable(XhtmlNode t, ValueSet vs, ValueSetExpansionContainsComponent c, int i, boolean doLevel, boolean doDefinition, boolean doInactive, List maps, List langs, Map designations, boolean doDesignations, Map properties, ResourceWrapper res) throws FHIRFormatError, DefinitionException, IOException {
XhtmlNode tr = t.tr();
if (ValueSetUtilities.isDeprecated(vs, c)) {
tr.setAttribute("style", "background-color: #ffeeee");
}
XhtmlNode td = tr.td();
String tgt = makeAnchor(c.getSystem(), c.getCode());
String pfx = res.getScopedId();
td.an((context.prefixAnchor(pfx == null ? "" : pfx+"-")+tgt));
if (doLevel) {
td.addText(Integer.toString(i));
td = tr.td();
}
String s = Utilities.padLeft("", '\u00A0', i*2);
td.attribute("style", "white-space:nowrap").addText(s);
addCodeToTable(c.getAbstract(), c.getSystem(), c.getVersion(), c.getCode(), c.getDisplay(), td);
td = tr.td();
td.addText(c.getSystem());
td = tr.td();
if (c.hasDisplayElement())
td.addText(c.getDisplay());
if (doInactive) {
td = tr.td();
if (c.getInactive()) {
td.tx(context.formatPhrase(RenderingContext.VALUE_SET_INACT));
}
}
if (doDefinition) {
td = tr.td();
CodeSystem cs = getContext().getWorker().fetchCodeSystem(c.getSystem());
if (cs != null) {
String defn = CodeSystemUtilities.getCodeDefinition(cs, c.getCode());
addMarkdown(td, defn, cs.getWebPath());
}
}
for (String n : Utilities.sorted(properties.keySet())) {
td = tr.td();
String ps = getPropertyValue(c, n);
if (!Utilities.noString(ps)) {
td.addText(ps);
}
}
for (UsedConceptMap m : maps) {
td = tr.td();
List mappings = findMappingsForCode(c.getCode(), m.getMap());
boolean first = true;
for (TargetElementComponentWrapper mapping : mappings) {
if (!first)
td.br();
first = false;
XhtmlNode span = td.span(null, mapping.comp.getRelationship().toString());
span.addText(getCharForRelationship(mapping.comp));
addRefToCode(td, mapping.group.getTarget(), null, m.getLink(), mapping.comp.getCode());
if (!Utilities.noString(mapping.comp.getComment()))
td.i().tx("("+mapping.comp.getComment()+")");
}
}
if (doDesignations) {
addDesignationsToRow(c, designations, tr);
addLangaugesToRow(c, langs, tr);
}
for (ValueSetExpansionContainsComponent cc : c.getContains()) {
addExpansionRowToTable(t, vs, cc, i+1, doLevel, doDefinition, doInactive, maps, langs, designations, doDesignations, properties, res);
}
}
private String getPropertyValue(ValueSetExpansionContainsComponent c, String n) {
for (ConceptPropertyComponent cp : c.getProperty()) {
if (n.equals(cp.getCode())) {
return cp.getValue().primitiveValue();
}
}
return null;
}
private boolean checkSystemMatches(String system, ValueSetExpansionContainsComponent cc) {
if (!system.equals(cc.getSystem()))
return false;
for (ValueSetExpansionContainsComponent cc1 : cc.getContains()) {
if (!checkSystemMatches(system, cc1))
return false;
}
return true;
}
private void addCodeToTable(boolean isAbstract, String system, String version, String code, String display, XhtmlNode td) {
CodeSystem e = getContext().getWorker().fetchCodeSystem(system);
if (e == null || (e.getContent() != org.hl7.fhir.r5.model.Enumerations.CodeSystemContentMode.COMPLETE && e.getContent() != org.hl7.fhir.r5.model.Enumerations.CodeSystemContentMode.FRAGMENT)) {
if (isAbstract)
td.i().setAttribute("title", context.formatPhrase(RenderingContext.VS_ABSTRACT_CODE_HINT)).addText(code);
else if ("http://snomed.info/sct".equals(system)) {
td.ah(context.prefixLocalHref(SnomedUtilities.getSctLink(version, code, context.getContext().getExpansionParameters()))).addText(code);
} else if ("http://loinc.org".equals(system)) {
td.ah(context.prefixLocalHref(LoincLinker.getLinkForCode(code))).addText(code);
} else
td.addText(code);
} else {
String href = context.fixReference(getCsRef(e));
if (href == null) {
td.code().tx(code);
} else {
if (href.contains("#"))
href = href + "-"+Utilities.nmtokenize(code);
else
href = href + "#"+e.getId()+"-"+Utilities.nmtokenize(code);
if (isAbstract)
td.ah(context.prefixLocalHref(href)).setAttribute("title", context.formatPhrase(RenderingContext.VS_ABSTRACT_CODE_HINT)).i().addText(code);
else
td.ah(context.prefixLocalHref(href)).addText(code);
}
}
}
private void addRefToCode(XhtmlNode td, String target, String vslink, String code, String version) {
addCodeToTable(false, target, version, code, null, td);
// CodeSystem cs = getContext().getWorker().fetchCodeSystem(target);
// String cslink = getCsRef(cs);
// String link = cslink != null ? cslink+"#"+cs.getId()+"-"+code : vslink+"#"+code;
// if (!Utilities.isAbsoluteUrl(link)) {
// link = getContext().getSpecificationLink()+link;
// }
// XhtmlNode a = td.ah(context.prefixLocalHref(link));
// a.addText(code);
}
private void generateComposition(RenderingStatus status, ResourceWrapper res, XhtmlNode x, ValueSet vs, boolean header, List maps) throws FHIRException, IOException {
List langs = new ArrayList();
Map designations = new HashMap<>(); // map of url = description, where url is the designation code. Designations that are for languages won't make it into this list
for (ConceptSetComponent inc : vs.getCompose().getInclude()) {
scanDesignations(inc, langs, designations);
}
for (ConceptSetComponent inc : vs.getCompose().getExclude()) {
scanDesignations(inc, langs, designations);
}
boolean doDesignations = langs.size() + designations.size() < MAX_DESIGNATIONS_IN_LINE;
if (header) {
XhtmlNode h = x.h2();
h.addText(vs.present());
addMarkdown(x, vs.getDescription());
if (vs.hasCopyrightElement())
generateCopyright(x, res);
}
int index = 0;
if (vs.getCompose().getInclude().size() == 1 && vs.getCompose().getExclude().size() == 0 && !VersionComparisonAnnotation.hasDeleted(vs.getCompose(), "include", "exclude")) {
genInclude(status, x.ul(), vs.getCompose().getInclude().get(0), "Include", langs, doDesignations, maps, designations, index, vs);
} else {
XhtmlNode p = x.para();
p.tx(context.formatPhrase(RenderingContext.VALUE_SET_RULES_INC));
XhtmlNode ul = x.ul();
for (ConceptSetComponent inc : vs.getCompose().getInclude()) {
genInclude(status, ul, inc, context.formatPhrase(RenderingContext.VALUE_SET_INC), langs, doDesignations, maps, designations, index, vs);
index++;
}
for (Base inc : VersionComparisonAnnotation.getDeleted(vs.getCompose(), "include")) {
genInclude(status, ul, (ConceptSetComponent) inc, context.formatPhrase(RenderingContext.VALUE_SET_INC), langs, doDesignations, maps, designations, index, vs);
index++;
}
if (vs.getCompose().hasExclude() || VersionComparisonAnnotation.hasDeleted(vs.getCompose(), "exclude")) {
p = x.para();
p.tx(context.formatPhrase(RenderingContext.VALUE_SET_RULES_EXC));
ul = x.ul();
for (ConceptSetComponent exc : vs.getCompose().getExclude()) {
genInclude(status, ul, exc, context.formatPhrase(RenderingContext.VALUE_SET_EXCL), langs, doDesignations, maps, designations, index, vs);
index++;
}
for (Base inc : VersionComparisonAnnotation.getDeleted(vs.getCompose(), "exclude")) {
genInclude(status, ul, (ConceptSetComponent) inc, context.formatPhrase(RenderingContext.VALUE_SET_EXCL), langs, doDesignations, maps, designations, index, vs);
index++;
}
}
}
// now, build observed languages
if (!doDesignations && langs.size() + designations.size() > 0) {
Collections.sort(langs);
if (designations.size() == 0) {
x.para().b().tx(context.formatPhrase(RenderingContext.GENERAL_ADD_LANG));
} else if (langs.size() == 0) {
x.para().b().tx(context.formatPhrase(RenderingContext.VALUE_SET_DESIG));
} else {
x.para().b().tx(context.formatPhrase(RenderingContext.VALUE_SET_ADD_DESIG));
}
XhtmlNode t = x.table("codes", false);
XhtmlNode tr = t.tr();
tr.td().b().tx(context.formatPhrase(RenderingContext.GENERAL_CODE));
for (String url : designations.keySet()) {
tr.td().b().addText(designations.get(url));
}
for (String lang : langs) {
tr.td().b().addText(describeLang(lang));
}
for (ConceptSetComponent c : vs.getCompose().getInclude()) {
for (ConceptReferenceComponent cc : c.getConcept()) {
addDesignationRow(cc, t, langs, designations);
}
}
}
}
private void renderExpansionRules(XhtmlNode x, ConceptSetComponent inc, int index, Map definitions) throws FHIRException, IOException {
String s = context.formatPhrase(RenderingContext.VALUE_SET_NOT_DEF);
if (inc.hasExtension(ToolingExtensions.EXT_EXPAND_RULES)) {
String rule = inc.getExtensionString(ToolingExtensions.EXT_EXPAND_RULES);
if (rule != null) {
switch (rule) {
case "all-codes": s = context.formatPhrase(RenderingContext.VALUE_SET_ALL_CODE);
case "ungrouped": s = context.formatPhrase(RenderingContext.VALUE_SET_NOT_FOUND);
case "groups-only": s = context.formatPhrase(RenderingContext.VALUE_SET_CONT_STRUC);
}
}
}
x.br();
x.tx(s);
HierarchicalTableGenerator gen = new HierarchicalTableGenerator(context, context.getDestDir(), context.isInlineGraphics(), true, "exp");
TableModel model = gen.new TableModel("exp.h="+index, context.getRules() == GenerationRules.IG_PUBLISHER);
model.setAlternating(true);
model.getTitles().add(gen.new Title(null, model.getDocoRef(), context.formatPhrase(RenderingContext.GENERAL_CODE), context.formatPhrase(RenderingContext.VALUE_SET_CODE_ITEM), null, 0));
model.getTitles().add(gen.new Title(null, model.getDocoRef(), context.formatPhrase(RenderingContext.TX_DISPLAY), context.formatPhrase(RenderingContext.VALUE_SET_DISPLAY_ITEM), null, 0));
for (Extension ext : inc.getExtensionsByUrl(ToolingExtensions.EXT_EXPAND_GROUP)) {
renderExpandGroup(gen, model, ext, inc, definitions);
}
x.br();
x.tx("table");
XhtmlNode xn = gen.generate(model, context.getLocalPrefix(), 1, null);
x.addChildNode(xn);
}
private void renderExpandGroup(HierarchicalTableGenerator gen, TableModel model, Extension ext, ConceptSetComponent inc, Map definitions) {
Row row = gen.new Row();
model.getRows().add(row);
row.setIcon("icon_entry_blue.png", "entry");
String code = ext.getExtensionString("code");
if (code != null) {
row.getCells().add(gen.new Cell(null, null, code, null, null));
row.getCells().add(gen.new Cell(null, null, getDisplayForCode(inc, code, definitions), null, null));
} else if (ext.hasId()) {
row.getCells().add(gen.new Cell(null, null, "(#"+ext.getId()+")", null, null));
row.getCells().add(gen.new Cell(null, null, ext.getExtensionString("display"), null, null));
} else {
row.getCells().add(gen.new Cell(null, null, null, null, null));
row.getCells().add(gen.new Cell(null, null, ext.getExtensionString("display"), null, null));
}
for (Extension member : ext.getExtensionsByUrl("member")) {
Row subRow = gen.new Row();
row.getSubRows().add(subRow);
subRow.setIcon("icon_entry_blue.png", "entry");
String mc = member.getValue().primitiveValue();
// mc might be a reference to another expansion group - we check that first, or to a code in the compose
if (mc.startsWith("#")) {
// it's a reference by id
subRow.getCells().add(gen.new Cell(null, null, "("+mc+")", null, null));
subRow.getCells().add(gen.new Cell(null, null, "group reference by id", null, null));
} else {
Extension tgt = findTargetByCode(inc, mc);
if (tgt != null) {
subRow.getCells().add(gen.new Cell(null, null, mc, null, null));
subRow.getCells().add(gen.new Cell(null, null, "group reference by code", null, null));
} else {
subRow.getCells().add(gen.new Cell(null, null, mc, null, null));
subRow.getCells().add(gen.new Cell(null, null, getDisplayForCode(inc, mc, definitions), null, null));
}
}
}
}
private Extension findTargetByCode(ConceptSetComponent inc, String mc) {
for (Extension ext : inc.getExtensionsByUrl(ToolingExtensions.EXT_EXPAND_GROUP)) {
String code = ext.getExtensionString("code");
if (mc.equals(code)) {
return ext;
}
}
return null;
}
private String getDisplayForCode(ConceptSetComponent inc, String code, Map definitions) {
for (ConceptReferenceComponent cc : inc.getConcept()) {
if (code.equals(cc.getCode())) {
if (cc.hasDisplay()) {
return cc.getDisplay();
}
}
}
if (definitions.containsKey(code)) {
return definitions.get(code).getDisplay();
}
return null;
}
private void scanDesignations(ConceptSetComponent inc, List langs, Map designations) {
for (ConceptReferenceComponent cc : inc.getConcept()) {
for (Extension ext : cc.getExtension()) {
if (ToolingExtensions.EXT_TRANSLATION.equals(ext.getUrl())) {
String lang = ToolingExtensions.readStringExtension(ext, "lang");
if (!Utilities.noString(lang) && !langs.contains(lang)) {
langs.add(lang);
}
}
}
for (ConceptReferenceDesignationComponent d : cc.getDesignation()) {
String lang = d.getLanguage();
if (!Utilities.noString(lang) && !langs.contains(lang)) {
langs.add(lang);
} else {
// can we present this as a designation that we know?
String disp = getDisplayForDesignation(d);
String url = getUrlForDesignation(d);
if (disp == null) {
disp = getDisplayForUrl(url);
}
if (disp != null && !designations.containsKey(url)) {
designations.put(url, disp);
}
}
}
}
}
private String getDisplayForUrl(String url) {
if (url == null) {
return null;
}
switch (url) {
case "http://snomed.info/sct#900000000000003001":
return context.formatPhrase(RenderingContext.VALUE_SET_SPEC_NAME);
case "http://snomed.info/sct#900000000000013009":
return context.formatPhrase(RenderingContext.VALUE_SET_SYNONYM);
case "http://terminology.hl7.org/CodeSystem/designation-usage#display":
return context.formatPhrase(RenderingContext.VALUE_SET_OTHER_DISPLAY);
default:
// As specified in http://www.hl7.org/fhir/valueset-definitions.html#ValueSet.compose.include.concept.designation.use and in http://www.hl7.org/fhir/codesystem-definitions.html#CodeSystem.concept.designation.use the terminology binding is extensible.
return url;
}
}
private String getUrlForDesignation(ConceptReferenceDesignationComponent d) {
if (d.hasUse() && d.getUse().hasSystem() && d.getUse().hasCode()) {
return d.getUse().getSystem()+"#"+d.getUse().getCode();
} else {
return null;
}
}
private String getDisplayForDesignation(ConceptReferenceDesignationComponent d) {
if (d.hasUse() && d.getUse().hasDisplay()) {
return d.getUse().getDisplay();
} else {
return null;
}
}
private void genInclude(RenderingStatus status, XhtmlNode ul, ConceptSetComponent inc, String type, List langs, boolean doDesignations, List maps, Map designations, int index, ValueSet vsRes) throws FHIRException, IOException {
XhtmlNode li;
li = ul.li();
li = renderStatus(inc, li);
Map definitions = new HashMap<>();
if (inc.hasSystem()) {
CodeSystem e = getContext().getWorker().fetchCodeSystem(inc.getSystem());
if (inc.getConcept().size() == 0 && inc.getFilter().size() == 0) {
li.addText(type+" "+ context.formatPhrase(RenderingContext.VALUE_SET_ALL_CODES_DEF) + " ");
addCsRef(inc, li, e);
} else {
if (inc.getConcept().size() > 0) {
li.addText(type+" "+ context.formatPhrase(RenderingContext.VALUE_SET_THESE_CODES_DEF) + " ");
addCsRef(inc, li, e);
if (inc.hasVersion()) {
li.addText(" "+ context.formatPhrase(RenderingContext.GENERAL_VER_LOW) + " ");
li.code(inc.getVersion());
}
// for performance reasons, we do all the fetching in one batch
definitions = getConceptsForCodes(e, inc, vsRes, index);
XhtmlNode t = li.table("none", false);
boolean hasComments = false;
boolean hasDefinition = false;
for (ConceptReferenceComponent c : inc.getConcept()) {
hasComments = hasComments || ExtensionHelper.hasExtension(c, ToolingExtensions.EXT_VS_COMMENT);
ConceptDefinitionComponent cc = definitions == null ? null : definitions.get(c.getCode());
hasDefinition = hasDefinition || ((cc != null && cc.hasDefinition()) || ExtensionHelper.hasExtension(c, ToolingExtensions.EXT_DEFINITION));
}
if (hasComments || hasDefinition) {
status.setExtensions(true);
}
addMapHeaders(addTableHeaderRowStandard(t, false, true, hasDefinition, hasComments, false, false, null, langs, designations, doDesignations), maps);
for (ConceptReferenceComponent c : inc.getConcept()) {
renderConcept(inc, langs, doDesignations, maps, designations, definitions, t, hasComments, hasDefinition, c, inc.getVersion());
}
for (Base b : VersionComparisonAnnotation.getDeleted(inc, "concept" )) {
renderConcept(inc, langs, doDesignations, maps, designations, definitions, t, hasComments, hasDefinition, (ConceptReferenceComponent) b, inc.getVersion());
}
}
if (inc.getFilter().size() > 0) {
li.addText(type+" "+ context.formatPhrase(RenderingContext.VALUE_SET_CODES_FROM));
addCsRef(inc, li, e);
li.tx(" "+ context.formatPhrase(RenderingContext.VALUE_SET_WHERE)+" ");
for (int i = 0; i < inc.getFilter().size(); i++) {
ConceptSetFilterComponent f = inc.getFilter().get(i);
if (i > 0) {
if (i == inc.getFilter().size()-1) {
li.tx(" "+ context.formatPhrase(RenderingContext.VALUE_SET_AND)+" ");
} else {
li.tx(context.formatPhrase(RenderingContext.VALUE_SET_COMMA)+" ");
}
}
XhtmlNode wli = renderStatus(f, li);
if (f.getOp() == FilterOperator.EXISTS) {
if (f.getValue().equals("true")) {
wli.tx(f.getProperty()+" "+ context.formatPhrase(RenderingContext.VALUE_SET_EXISTS));
} else {
wli.tx(f.getProperty()+" "+ context.formatPhrase(RenderingContext.VALUE_SET_DOESNT_EXIST));
}
} else {
wli.tx(f.getProperty()+" "+describe(f.getOp())+" ");
if (f.getValueElement().hasExtension(ToolingExtensions.EXT_CQF_EXP)) {
Extension expE = f.getValueElement().getExtensionByUrl(ToolingExtensions.EXT_CQF_EXP);
Expression exp = expE.getValueExpression();
wli.addText("(as calculated by ");
wli.code().tx(exp.getExpression());
wli.addText(")");
} else {
if (e != null && codeExistsInValueSet(e, f.getValue())) {
String href = getContext().fixReference(getCsRef(e));
if (href == null) {
wli.code().tx(f.getValue());
} else {
if (href.contains("#"))
href = href + "-"+Utilities.nmtokenize(f.getValue());
else
href = href + "#"+e.getId()+"-"+Utilities.nmtokenize(f.getValue());
wli.ah(context.prefixLocalHref(href)).addText(f.getValue());
}
} else if (inc.hasSystem()) {
wli.addText(f.getValue());
ValidationResult vr = getContext().getWorker().validateCode(getContext().getTerminologyServiceOptions(), inc.getSystem(), inc.getVersion(), f.getValue(), null);
if (vr.isOk() && vr.getDisplay() != null) {
wli.tx(" ("+vr.getDisplay()+")");
}
} else {
wli.addText(f.getValue());
}
}
String disp = ToolingExtensions.getDisplayHint(f);
if (disp != null)
wli.tx(" ("+disp+")");
}
}
}
}
if (inc.hasValueSet()) {
li.tx(context.formatPhrase(RenderingContext.VALUE_SET_WHERE_CODES)+" ");
boolean first = true;
for (UriType vs : inc.getValueSet()) {
if (first)
first = false;
else
li.tx(", ");
XhtmlNode wli = renderStatus(vs, li);
AddVsRef(vs.asStringValue(), wli, vsRes);
}
}
if (inc.hasExtension(ToolingExtensions.EXT_EXPAND_RULES) || inc.hasExtension(ToolingExtensions.EXT_EXPAND_GROUP)) {
status.setExtensions(true);
renderExpansionRules(li, inc, index, definitions);
}
} else {
li.tx(context.formatMessagePlural(inc.getValueSet().size(), RenderingContext.VALUE_SET_IMPORT)+" ");
if (inc.getValueSet().size() <= 2) {
int i = 0;
for (UriType vs : inc.getValueSet()) {
if (i > 0) {
if ( i < inc.getValueSet().size() - 1) {
li.tx(", ");
} else {
li.tx(" and ");
}
}
i++;
XhtmlNode wli = renderStatus(vs, li);
AddVsRef(vs.asStringValue(), wli, vsRes);
}
} else {
XhtmlNode xul = li.ul();
for (UriType vs : inc.getValueSet()) {
XhtmlNode wli = renderStatus(vs, xul.li());
AddVsRef(vs.asStringValue(), wli, vsRes);
}
}
}
}
private void renderConcept(ConceptSetComponent inc, List langs, boolean doDesignations,
List maps, Map designations, Map definitions,
XhtmlNode t, boolean hasComments, boolean hasDefinition, ConceptReferenceComponent c, String version) {
XhtmlNode tr = t.tr();
XhtmlNode td = renderStatusRow(c, t, tr);
ConceptDefinitionComponent cc = definitions == null ? null : definitions.get(c.getCode());
addCodeToTable(false, inc.getSystem(), version, c.getCode(), c.hasDisplay()? c.getDisplay() : cc != null ? cc.getDisplay() : "", td);
td = tr.td();
if (!Utilities.noString(c.getDisplay()))
renderStatus(c.getDisplayElement(), td).addText(c.getDisplay());
else if (VersionComparisonAnnotation.hasDeleted(c, "display")) {
StringType d = (StringType) VersionComparisonAnnotation.getDeletedItem(c, "display");
renderStatus(d, td).addText(d.primitiveValue());
} else if (cc != null && !Utilities.noString(cc.getDisplay()))
td.style("color: #cccccc").addText(cc.getDisplay());
if (hasDefinition) {
td = tr.td();
if (ExtensionHelper.hasExtension(c, ToolingExtensions.EXT_DEFINITION)) {
smartAddText(td, ToolingExtensions.readStringExtension(c, ToolingExtensions.EXT_DEFINITION));
} else if (cc != null && !Utilities.noString(cc.getDefinition())) {
smartAddText(td, cc.getDefinition());
}
}
if (hasComments) {
td = tr.td();
if (ExtensionHelper.hasExtension(c, ToolingExtensions.EXT_VS_COMMENT)) {
smartAddText(td, context.formatPhrase(RenderingContext.VALUE_SET_NOTE, ToolingExtensions.readStringExtension(c, ToolingExtensions.EXT_VS_COMMENT)+" "));
}
}
if (doDesignations) {
addDesignationsToRow(c, designations, tr);
addLangaugesToRow(c, langs, tr);
}
for (UsedConceptMap m : maps) {
td = tr.td();
List mappings = findMappingsForCode(c.getCode(), m.getMap());
boolean first = true;
for (TargetElementComponentWrapper mapping : mappings) {
if (!first)
td.br();
first = false;
XhtmlNode span = td.span(null, mapping.comp.getRelationship().toString());
span.addText(getCharForRelationship(mapping.comp));
addRefToCode(td, mapping.group.getTarget(), m.getLink(), mapping.comp.getCode(), version);
if (!Utilities.noString(mapping.comp.getComment()))
td.i().tx("("+mapping.comp.getComment()+")");
}
}
}
public void addDesignationsToRow(ConceptReferenceComponent c, Map designations, XhtmlNode tr) {
for (String url : designations.keySet()) {
String d = null;
if (d == null) {
for (ConceptReferenceDesignationComponent dd : c.getDesignation()) {
if (url.equals(getUrlForDesignation(dd))) {
d = dd.getValue();
}
}
}
tr.td().addText(d == null ? "" : d);
}
}
public void addLangaugesToRow(ConceptReferenceComponent c, List langs, XhtmlNode tr) {
for (String lang : langs) {
String d = null;
for (Extension ext : c.getExtension()) {
if (ToolingExtensions.EXT_TRANSLATION.equals(ext.getUrl())) {
String l = ToolingExtensions.readStringExtension(ext, "lang");
if (lang.equals(l)) {
d = ToolingExtensions.readStringExtension(ext, "content");
}
}
}
if (d == null) {
for (ConceptReferenceDesignationComponent dd : c.getDesignation()) {
String l = dd.getLanguage();
if (lang.equals(l)) {
d = dd.getValue();
}
}
}
tr.td().addText(d == null ? "" : d);
}
}
private Map getConceptsForCodes(CodeSystem e, ConceptSetComponent inc, ValueSet source, int index) {
if (e == null) {
e = getContext().getWorker().fetchCodeSystem(inc.getSystem());
}
ValueSetExpansionComponent vse = null;
if (!context.isNoSlowLookup()) { // && !getContext().getWorker().hasCache()) { removed GG 20220107 like what is this trying to do?
try {
ValueSet vs = new ValueSet();
vs.setUrl(source.getUrl()+"-inc-"+index);
vs.setStatus(PublicationStatus.ACTIVE);
vs.setCompose(new ValueSetComposeComponent());
vs.getCompose().setInactive(false);
vs.getCompose().getInclude().add(inc);
ValueSetExpansionOutcome vso = getContext().getWorker().expandVS(vs, true, false);
ValueSet valueset = vso.getValueset();
if (valueset == null)
throw new TerminologyServiceException(context.formatPhrase(RenderingContext.VALUE_SET_ERROR, vso.getError()+" "));
vse = valueset.getExpansion();
} catch (Exception e1) {
return null;
}
}
Map results = new HashMap<>();
List serverList = new ArrayList<>();
// 1st pass, anything we can resolve internally
for (ConceptReferenceComponent cc : inc.getConcept()) {
String code = cc.getCode();
ConceptDefinitionComponent v = null;
if (e != null && code != null) {
v = getConceptForCode(e.getConcept(), code);
}
if (v == null && vse != null) {
v = getConceptForCodeFromExpansion(vse.getContains(), code);
}
if (v != null) {
results.put(code, v);
} else {
serverList.add(new CodingValidationRequest(new Coding(inc.getSystem(), code, null)));
}
}
if (!context.isNoSlowLookup() && !serverList.isEmpty()) {
try {
// todo: split this into 10k batches
int i = 0;
while (serverList.size() > i) {
int len = Integer.min(serverList.size(), MAX_BATCH_VALIDATION_SIZE);
List list = serverList.subList(i, i+len);
i += len;
getContext().getWorker().validateCodeBatch(getContext().getTerminologyServiceOptions(), list, null);
for (CodingValidationRequest vr : list) {
ConceptDefinitionComponent v = vr.getResult().asConceptDefinition();
if (v != null) {
results.put(vr.getCoding().getCode(), v);
}
}
}
} catch (Exception e1) {
return null;
}
}
return results;
}
private ConceptDefinitionComponent getConceptForCode(List list, String code) {
for (ConceptDefinitionComponent c : list) {
if (code.equals(c.getCode()))
return c;
ConceptDefinitionComponent v = getConceptForCode(c.getConcept(), code);
if (v != null)
return v;
}
return null;
}
private ConceptDefinitionComponent getConceptForCodeFromExpansion(List list, String code) {
for (ValueSetExpansionContainsComponent c : list) {
if (code.equals(c.getCode())) {
ConceptDefinitionComponent res = new ConceptDefinitionComponent();
res.setCode(c.getCode());
res.setDisplay(c.getDisplay());
return res;
}
ConceptDefinitionComponent v = getConceptForCodeFromExpansion(c.getContains(), code);
if (v != null)
return v;
}
return null;
}
private boolean codeExistsInValueSet(CodeSystem cs, String code) {
for (ConceptDefinitionComponent c : cs.getConcept()) {
if (inConcept(code, c))
return true;
}
return false;
}
private void addDesignationRow(ConceptReferenceComponent c, XhtmlNode t, List langs, Map designations) {
XhtmlNode tr = t.tr();
tr.td().addText(c.getCode());
addDesignationsToRow(c, designations, tr);
addLangaugesToRow(c, langs, tr);
}
private String describe(FilterOperator op) {
if (op == null)
return " "+ context.formatPhrase(RenderingContext.VALUE_SET_NULL);
switch (op) {
case EQUAL: return " "+ context.formatPhrase(RenderingContext.VALUE_SET_EQUAL);
case ISA: return " "+ context.formatPhrase(RenderingContext.VALUE_SET_ISA);
case ISNOTA: return " "+ context.formatPhrase(RenderingContext.VALUE_SET_ISNOTA);
case REGEX: return " "+ context.formatPhrase(RenderingContext.VALUE_SET_REGEX);
case NULL: return " "+ context.formatPhrase(RenderingContext.VALUE_SET_NULLS);
case IN: return " "+ context.formatPhrase(RenderingContext.VALUE_SET_IN);
case NOTIN: return " "+ context.formatPhrase(RenderingContext.VALUE_SET_NOTIN);
case DESCENDENTOF: return " "+ context.formatPhrase(RenderingContext.VALUE_SET_DESCENDENTOF);
case EXISTS: return " "+ context.formatPhrase(RenderingContext.VALUE_SET_EXISTS);
case GENERALIZES: return " "+ context.formatPhrase(RenderingContext.VALUE_SET_GENERALIZES);
}
return null;
}
private boolean inConcept(String code, ConceptDefinitionComponent c) {
if (c.hasCodeElement() && c.getCode().equals(code))
return true;
for (ConceptDefinitionComponent g : c.getConcept()) {
if (inConcept(code, g))
return true;
}
return false;
}
@Override
protected void genSummaryTableContent(RenderingStatus status, XhtmlNode tbl, CanonicalResource cr) throws IOException {
super.genSummaryTableContent(status, tbl, cr);
ValueSet vs = (ValueSet) cr;
XhtmlNode tr;
if (CodeSystemUtilities.hasOID(vs)) {
tr = tbl.tr();
tr.td().tx(context.formatPhrase(RenderingContext.GENERAL_OID)+":");
tr.td().tx(context.formatPhrase(RenderingContext.CODE_SYS_FOR_OID, CodeSystemUtilities.getOID(vs)));
}
}
} © 2015 - 2025 Weber Informatics LLC | Privacy Policy