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more work on value set renderer (designations, expand-groups)

This commit is contained in:
Grahame Grieve 2022-01-17 10:51:48 +11:00
parent f368b021e3
commit c13c291949
5 changed files with 207 additions and 23 deletions
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2
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/renderers/CodeSystemRenderer.java
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@ -175,7 +175,7 @@ public class CodeSystemRenderer extends TerminologyRenderer {
hierarchy = hierarchy || csNav.isRestructure();
List<String> langs = new ArrayList<>();
addMapHeaders(addTableHeaderRowStandard(t, hierarchy, display, definitions, commentS, version, deprecated, properties, null, false), maps);
addMapHeaders(addTableHeaderRowStandard(t, hierarchy, display, definitions, commentS, version, deprecated, properties, null, null, false), maps);
for (ConceptDefinitionComponent c : csNav.getConcepts(null)) {
hasExtensions = addDefineRowToTable(t, c, 0, hierarchy, display, definitions, commentS, version, deprecated, maps, cs.getUrl(), cs, properties, csNav, langs, isSupplement) || hasExtensions;
}

13
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/renderers/ResourceRenderer.java
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@ -20,6 +20,7 @@ import org.hl7.fhir.r5.model.Narrative;
import org.hl7.fhir.r5.model.Narrative.NarrativeStatus;
import org.hl7.fhir.r5.model.Reference;
import org.hl7.fhir.r5.model.Resource;
import org.hl7.fhir.r5.model.ValueSet;
import org.hl7.fhir.r5.renderers.utils.BaseWrappers.BaseWrapper;
import org.hl7.fhir.r5.renderers.utils.BaseWrappers.PropertyWrapper;
import org.hl7.fhir.r5.renderers.utils.BaseWrappers.ResourceWrapper;
@ -488,4 +489,16 @@ public abstract class ResourceRenderer extends DataRenderer {
private String getPrimitiveValue(ResourceWrapper r, String name) throws UnsupportedEncodingException, FHIRException, IOException {
return r.has(name) && r.getChildByName(name).hasValues() ? r.getChildByName(name).getValues().get(0).getBase().primitiveValue() : null;
}
public void renderOrError(DomainResource dr) {
try {
render(dr);
} catch (Exception e) {
XhtmlNode x = new XhtmlNode(NodeType.Element, "div");
x.para().tx("Error rendering: "+e.getMessage());
dr.setText(null);
inject(dr, x, NarrativeStatus.GENERATED);
}
}
}

8
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/renderers/TerminologyRenderer.java
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@ -4,6 +4,7 @@ import java.io.IOException;
import java.io.UnsupportedEncodingException;
import java.util.ArrayList;
import java.util.List;
import java.util.Map;
import org.hl7.fhir.exceptions.DefinitionException;
import org.hl7.fhir.exceptions.FHIRFormatError;
@ -201,7 +202,7 @@ public abstract class TerminologyRenderer extends ResourceRenderer {
return null;
}
protected XhtmlNode addTableHeaderRowStandard(XhtmlNode t, boolean hasHierarchy, boolean hasDisplay, boolean definitions, boolean comments, boolean version, boolean deprecated, List<PropertyComponent> properties, List<String> langs, boolean doLangs) {
protected XhtmlNode addTableHeaderRowStandard(XhtmlNode t, boolean hasHierarchy, boolean hasDisplay, boolean definitions, boolean comments, boolean version, boolean deprecated, List<PropertyComponent> properties, List<String> langs, Map<String, String> designations, boolean doDesignations) {
XhtmlNode tr = t.tr();
if (hasHierarchy) {
tr.td().b().tx("Lvl");
@ -234,7 +235,10 @@ public abstract class TerminologyRenderer extends ResourceRenderer {
tr.td().b().tx(getContext().getWorker().translator().translate("xhtml-gen-cs", display, getContext().getLang()));
}
}
if (doLangs) {
if (doDesignations) {
for (String url : designations.keySet()) {
tr.td().b().addText(designations.get(url));
}
for (String lang : langs) {
tr.td().b().addText(describeLang(lang));
}

199
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/renderers/ValueSetRenderer.java
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@ -29,6 +29,7 @@ import org.hl7.fhir.r5.model.ConceptMap;
import org.hl7.fhir.r5.model.DataType;
import org.hl7.fhir.r5.model.DomainResource;
import org.hl7.fhir.r5.model.Enumerations.FilterOperator;
import org.hl7.fhir.r5.model.Questionnaire.QuestionnaireItemComponent;
import org.hl7.fhir.r5.model.Extension;
import org.hl7.fhir.r5.model.ExtensionHelper;
import org.hl7.fhir.r5.model.PrimitiveType;
@ -39,6 +40,7 @@ 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;
@ -48,7 +50,11 @@ import org.hl7.fhir.r5.terminologies.CodeSystemUtilities;
import org.hl7.fhir.r5.terminologies.ValueSetExpander.ValueSetExpansionOutcome;
import org.hl7.fhir.r5.utils.ToolingExtensions;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.xhtml.HierarchicalTableGenerator;
import org.hl7.fhir.utilities.xhtml.XhtmlNode;
import org.hl7.fhir.utilities.xhtml.HierarchicalTableGenerator.Row;
import org.hl7.fhir.utilities.xhtml.HierarchicalTableGenerator.TableModel;
import org.hl7.fhir.utilities.xhtml.HierarchicalTableGenerator.Title;
import com.google.common.collect.HashMultimap;
import com.google.common.collect.Multimap;
@ -65,7 +71,7 @@ public class ValueSetRenderer extends TerminologyRenderer {
private static final String ABSTRACT_CODE_HINT = "This code is not selectable ('Abstract')";
private static final int MAX_LANGS_IN_LINE = 5;
private static final int MAX_DESIGNATIONS_IN_LINE = 5;
private List<ConceptMapRenderInstructions> renderingMaps = new ArrayList<ConceptMapRenderInstructions>();
@ -222,7 +228,7 @@ public class ValueSetRenderer extends TerminologyRenderer {
doLangs = false;
} else {
// if we're not doing definitions and we don't have too many languages, we'll do them in line
if (langs.size() < MAX_LANGS_IN_LINE) {
if (langs.size() < MAX_DESIGNATIONS_IN_LINE) {
doLangs = true;
if (vs.hasLanguage()) {
tdDisp.tx(" - "+describeLang(vs.getLanguage()));
@ -586,8 +592,12 @@ public class ValueSetRenderer extends TerminologyRenderer {
private boolean checkDoDefinition(List<ValueSetExpansionContainsComponent> contains) {
for (ValueSetExpansionContainsComponent c : contains) {
CodeSystem cs = getContext().getWorker().fetchCodeSystem(c.getSystem());
if (cs != null)
if (cs != null) {
ConceptDefinitionComponent cd = CodeSystemUtilities.getCode(cs, c.getCode());
if (cd != null && cd.hasDefinition()) {
return true;
}
}
if (checkDoDefinition(c.getContains()))
return true;
}
@ -754,13 +764,14 @@ public class ValueSetRenderer extends TerminologyRenderer {
private boolean generateComposition(XhtmlNode x, ValueSet vs, boolean header, List<UsedConceptMap> maps) throws FHIRException, IOException {
boolean hasExtensions = false;
List<String> langs = new ArrayList<String>();
Map<String, String> 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()) {
scanForLangs(inc, langs);
scanDesignations(inc, langs, designations);
}
for (ConceptSetComponent inc : vs.getCompose().getExclude()) {
scanForLangs(inc, langs);
scanDesignations(inc, langs, designations);
}
boolean doLangs = langs.size() < MAX_LANGS_IN_LINE;
boolean doDesignations = langs.size() + designations.size() < MAX_DESIGNATIONS_IN_LINE;
if (header) {
XhtmlNode h = x.h2();
@ -769,35 +780,48 @@ public class ValueSetRenderer extends TerminologyRenderer {
if (vs.hasCopyrightElement())
generateCopyright(x, vs);
}
int index = 0;
if (vs.getCompose().getInclude().size() == 1 && vs.getCompose().getExclude().size() == 0) {
hasExtensions = genInclude(x.ul(), vs.getCompose().getInclude().get(0), "Include", langs, doLangs, maps) || hasExtensions;
hasExtensions = genInclude(x.ul(), vs.getCompose().getInclude().get(0), "Include", langs, doDesignations, maps, designations, index) || hasExtensions;
} else {
XhtmlNode p = x.para();
p.tx("This value set includes codes based on the following rules:");
XhtmlNode ul = x.ul();
for (ConceptSetComponent inc : vs.getCompose().getInclude()) {
hasExtensions = genInclude(ul, inc, "Include", langs, doLangs, maps) || hasExtensions;
hasExtensions = genInclude(ul, inc, "Include", langs, doDesignations, maps, designations, index) || hasExtensions;
index++;
}
if (vs.getCompose().hasExclude()) {
p = x.para();
p.tx("This value set excludes codes based on the following rules:");
ul = x.ul();
for (ConceptSetComponent exc : vs.getCompose().getExclude()) {
hasExtensions = genInclude(ul, exc, "Exclude", langs, doLangs, maps) || hasExtensions;
hasExtensions = genInclude(ul, exc, "Exclude", langs, doDesignations, maps, designations, index) || hasExtensions;
index++;
}
}
}
// now, build observed languages
if (!doLangs && langs.size() > 0) {
if (!doDesignations && langs.size() + designations.size() > 0) {
Collections.sort(langs);
if (designations.size() == 0) {
x.para().b().tx("Additional Language Displays");
XhtmlNode t = x.table( "codes");
} else if (langs.size() == 0) {
x.para().b().tx("Additional Designations");
} else {
x.para().b().tx("Additional Designations and Language Displays");
}
XhtmlNode t = x.table("codes");
XhtmlNode tr = t.tr();
tr.td().b().tx("Code");
for (String lang : langs)
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()) {
addLanguageRow(cc, t, langs);
@ -805,10 +829,102 @@ public class ValueSetRenderer extends TerminologyRenderer {
}
}
return hasExtensions;
}
private void scanForLangs(ConceptSetComponent inc, List<String> langs) {
private void renderExpansionRules(XhtmlNode x, ConceptSetComponent inc, int index, Map<String, ConceptDefinitionComponent> definitions) throws FHIRException, IOException {
String s = "This include specifies a heirarchy for when value sets are generated for use in a User Interface, but the rules are not properly defined";
if (inc.hasExtension(ToolingExtensions.EXT_EXPAND_RULES)) {
String rule = inc.getExtensionString(ToolingExtensions.EXT_EXPAND_RULES);
if (rule != null) {
switch (rule) {
case "all-codes": s = "This include specifies a heirarchy for when value sets are generated for use in a User Interface. The expansion contains all the codes, and also this structure:";
case "ungrouped": s = "This include specifies a heirarchy for when value sets are generated for use in a User Interface. The expansion contains this structure, and any codes not found in the structure:";
case "groups-only": s = "This include specifies a heirarchy for when value sets are generated for use in a User Interface. The expansion contains this structure:";
}
}
}
x.br();
x.tx(s);
HierarchicalTableGenerator gen = new HierarchicalTableGenerator(context.getDestDir(), context.isInlineGraphics(), true);
TableModel model = gen.new TableModel("exp.h="+index, !forResource);
model.setAlternating(true);
model.getTitles().add(gen.new Title(null, model.getDocoRef(), translate("vs.exp.header", "Code"), translate("vs.exp.hint", "The code for the item"), null, 0));
model.getTitles().add(gen.new Title(null, model.getDocoRef(), translate("vs.exp.header", "Display"), translate("vs.exp.hint", "The display for the 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.getChildNodes().add(xn);
}
private void renderExpandGroup(HierarchicalTableGenerator gen, TableModel model, Extension ext, ConceptSetComponent inc, Map<String, ConceptDefinitionComponent> 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<String, ConceptDefinitionComponent> 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<String> langs, Map<String, String> designations) {
for (ConceptReferenceComponent cc : inc.getConcept()) {
for (Extension ext : cc.getExtension()) {
if (ToolingExtensions.EXT_TRANSLATION.equals(ext.getUrl())) {
@ -822,16 +938,46 @@ public class ValueSetRenderer extends TerminologyRenderer {
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 url = getUrlForDesignation(d);
String disp = getDisplayForUrl(url);
if (disp != null && !designations.containsKey(url)) {
designations.put(url, disp);
}
}
}
}
}
private boolean genInclude(XhtmlNode ul, ConceptSetComponent inc, String type, List<String> langs, boolean doLangs, List<UsedConceptMap> maps) throws FHIRException, IOException {
private String getDisplayForUrl(String url) {
if (url == null) {
return null;
}
switch (url) {
case "http://snomed.info/sct#900000000000003001":
return "Fully specified name";
case "http://snomed.info/sct#900000000000013009":
return "Synonym";
default:
return null;
}
}
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 boolean genInclude(XhtmlNode ul, ConceptSetComponent inc, String type, List<String> langs, boolean doDesignations, List<UsedConceptMap> maps, Map<String, String> designations, int index) throws FHIRException, IOException {
boolean hasExtensions = false;
XhtmlNode li;
li = ul.li();
CodeSystem e = getContext().getWorker().fetchCodeSystem(inc.getSystem());
Map<String, ConceptDefinitionComponent> definitions = new HashMap<>();
if (inc.hasSystem()) {
if (inc.getConcept().size() == 0 && inc.getFilter().size() == 0) {
@ -847,7 +993,7 @@ public class ValueSetRenderer extends TerminologyRenderer {
}
// for performance reasons, we do all the fetching in one batch
Map<String, ConceptDefinitionComponent> definitions = getConceptsForCodes(e, inc);
definitions = getConceptsForCodes(e, inc);
XhtmlNode t = li.table("none");
boolean hasComments = false;
@ -859,7 +1005,7 @@ public class ValueSetRenderer extends TerminologyRenderer {
}
if (hasComments || hasDefinition)
hasExtensions = true;
addMapHeaders(addTableHeaderRowStandard(t, false, true, hasDefinition, hasComments, false, false, null, langs, doLangs), maps);
addMapHeaders(addTableHeaderRowStandard(t, false, true, hasDefinition, hasComments, false, false, null, langs, designations, doDesignations), maps);
for (ConceptReferenceComponent c : inc.getConcept()) {
XhtmlNode tr = t.tr();
XhtmlNode td = tr.td();
@ -886,7 +1032,8 @@ public class ValueSetRenderer extends TerminologyRenderer {
smartAddText(td, "Note: "+ToolingExtensions.readStringExtension(c, ToolingExtensions.EXT_VS_COMMENT));
}
}
if (doLangs) {
if (doDesignations) {
addDesignationsToRow(c, designations, tr);
addLangaugesToRow(c, langs, tr);
}
}
@ -946,6 +1093,10 @@ public class ValueSetRenderer extends TerminologyRenderer {
AddVsRef(vs.asStringValue(), li);
}
}
if (inc.hasExtension(ToolingExtensions.EXT_EXPAND_RULES) || inc.hasExtension(ToolingExtensions.EXT_EXPAND_GROUP)) {
hasExtensions = true;
renderExpansionRules(li, inc, index, definitions);
}
} else {
li.tx("Import all the codes that are contained in ");
if (inc.getValueSet().size() < 4) {
@ -968,6 +1119,20 @@ public class ValueSetRenderer extends TerminologyRenderer {
return hasExtensions;
}
public void addDesignationsToRow(ConceptReferenceComponent c, Map<String, String> 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<String> langs, XhtmlNode tr) {
for (String lang : langs) {
String d = null;

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

@ -198,6 +198,8 @@ public class ToolingExtensions {
public static final String EXT_TARGET_ID = "http://hl7.org/fhir/StructureDefinition/targetElement";
public static final String EXT_TARGET_PATH = "http://hl7.org/fhir/StructureDefinition/targetPath";
public static final String EXT_VALUESET_SYSTEM = "http://hl7.org/fhir/StructureDefinition/valueset-system";
public static final String EXT_EXPAND_RULES = "http://hl7.org/fhir/StructureDefinition/valueset-expand-rules";
public static final String EXT_EXPAND_GROUP = "http://hl7.org/fhir/StructureDefinition/valueset-expand-group";
// specific extension helpers