Examples with ConceptSetComponent org.hl7.fhir.r4.model.ValueSet.ConceptSetComponent used on opensource projects

Example 41 with ConceptSetComponent

use of org.hl7.fhir.r4.model.ValueSet.ConceptSetComponent in project org.hl7.fhir.core by hapifhir.

the class ValueSetExpanderSimple method includeCodes.

private void includeCodes(ConceptSetComponent inc, List<ValueSetExpansionParameterComponent> params, ExpansionProfile profile) throws ETooCostly, FileNotFoundException, IOException, FHIRException {
    List<ValueSet> imports = new ArrayList<ValueSet>();
    for (UriType imp : inc.getValueSet()) imports.add(importValueSet(imp.getValue(), params, profile));
    if (!inc.hasSystem()) {
        if (// though this is not supposed to be the case
        imports.isEmpty())
            return;
        ValueSet base = imports.get(0);
        imports.remove(0);
        copyImportContains(base.getExpansion().getContains(), null, profile, imports);
    } else {
        CodeSystem cs = context.fetchCodeSystem(inc.getSystem());
        if ((cs == null || cs.getContent() != CodeSystemContentMode.COMPLETE) && context.supportsSystem(inc.getSystem())) {
            addCodes(context.expandVS(inc, canBeHeirarchy), params, profile, imports);
            return;
        }
        if (cs == null) {
            if (context.isNoTerminologyServer())
                throw new NoTerminologyServiceException("unable to find code system " + inc.getSystem().toString());
            else
                throw new TerminologyServiceException("unable to find code system " + inc.getSystem().toString());
        }
        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 (inc.getConcept().size() == 0 && inc.getFilter().size() == 0) {
            // special case - add all the code system
            for (ConceptDefinitionComponent def : cs.getConcept()) {
                addCodeAndDescendents(cs, inc.getSystem(), def, null, profile, imports);
            }
        }
        if (!inc.getConcept().isEmpty()) {
            canBeHeirarchy = false;
            for (ConceptReferenceComponent c : inc.getConcept()) {
                addCode(inc.getSystem(), c.getCode(), Utilities.noString(c.getDisplay()) ? getCodeDisplay(cs, c.getCode()) : c.getDisplay(), null, convertDesignations(c.getDesignation()), profile, false, CodeSystemUtilities.isInactive(cs, c.getCode()), imports);
            }
        }
        if (inc.getFilter().size() > 1) {
            // which will bt the case if we get around to supporting this
            canBeHeirarchy = false;
            // need to and them, and this isn't done yet. But this shouldn't arise in non loinc and snomed value sets
            throw new TerminologyServiceException("Multiple filters not handled yet");
        }
        if (inc.getFilter().size() == 1) {
            ConceptSetFilterComponent fc = inc.getFilter().get(0);
            if ("concept".equals(fc.getProperty()) && fc.getOp() == FilterOperator.ISA) {
                // special: all codes in the target code system under the value
                ConceptDefinitionComponent def = getConceptForCode(cs.getConcept(), fc.getValue());
                if (def == null)
                    throw new TerminologyServiceException("Code '" + fc.getValue() + "' not found in system '" + inc.getSystem() + "'");
                addCodeAndDescendents(cs, inc.getSystem(), def, null, profile, imports);
            } else if ("concept".equals(fc.getProperty()) && fc.getOp() == FilterOperator.DESCENDENTOF) {
                // special: all codes in the target code system under the value
                ConceptDefinitionComponent def = getConceptForCode(cs.getConcept(), fc.getValue());
                if (def == null)
                    throw new TerminologyServiceException("Code '" + fc.getValue() + "' not found in system '" + inc.getSystem() + "'");
                for (ConceptDefinitionComponent c : def.getConcept()) addCodeAndDescendents(cs, inc.getSystem(), c, null, profile, imports);
            } else if ("display".equals(fc.getProperty()) && fc.getOp() == FilterOperator.EQUAL) {
                // gg; note: wtf is this: if the filter is display=v, look up the code 'v', and see if it's diplsay is 'v'?
                canBeHeirarchy = false;
                ConceptDefinitionComponent def = getConceptForCode(cs.getConcept(), fc.getValue());
                if (def != null) {
                    if (isNotBlank(def.getDisplay()) && isNotBlank(fc.getValue())) {
                        if (def.getDisplay().contains(fc.getValue())) {
                            addCode(inc.getSystem(), def.getCode(), def.getDisplay(), null, def.getDesignation(), profile, CodeSystemUtilities.isNotSelectable(cs, def), CodeSystemUtilities.isInactive(cs, def), imports);
                        }
                    }
                }
            } else
                throw new NotImplementedException("Search by property[" + fc.getProperty() + "] and op[" + fc.getOp() + "] is not supported yet");
        }
    }
}

Example 42 with ConceptSetComponent

use of org.hl7.fhir.r4.model.ValueSet.ConceptSetComponent in project org.hl7.fhir.core by hapifhir.

the class ValueSetComparer method compareCompose.

private void compareCompose(ValueSetComposeComponent left, ValueSetComposeComponent right, ValueSetComparison res, ValueSetComposeComponent union, ValueSetComposeComponent intersection) {
    // first, the includes
    List<ConceptSetComponent> matchR = new ArrayList<>();
    for (ConceptSetComponent l : left.getInclude()) {
        ConceptSetComponent r = findInList(right.getInclude(), l, left.getInclude());
        if (r == null) {
            union.getInclude().add(l);
            res.getIncludes().getChildren().add(new StructuralMatch<Element>(l, vmI(IssueSeverity.INFORMATION, "Removed Include", "ValueSet.compose.include")));
        } else {
            matchR.add(r);
            ConceptSetComponent csM = new ConceptSetComponent();
            ConceptSetComponent csI = new ConceptSetComponent();
            union.getInclude().add(csM);
            intersection.getInclude().add(csI);
            StructuralMatch<Element> sm = new StructuralMatch<Element>(l, r);
            res.getIncludes().getChildren().add(sm);
            compareDefinitions(l, r, sm, csM, csI);
        }
    }
    for (ConceptSetComponent r : right.getInclude()) {
        if (!matchR.contains(r)) {
            union.getInclude().add(r);
            res.getIncludes().getChildren().add(new StructuralMatch<Element>(vmI(IssueSeverity.INFORMATION, "Added Include", "ValueSet.compose.include"), r));
        }
    }
    // now. the excludes
    matchR.clear();
    for (ConceptSetComponent l : left.getExclude()) {
        ConceptSetComponent r = findInList(right.getExclude(), l, left.getExclude());
        if (r == null) {
            union.getExclude().add(l);
            res.getExcludes().getChildren().add(new StructuralMatch<Element>(l, vmI(IssueSeverity.INFORMATION, "Removed Exclude", "ValueSet.compose.exclude")));
        } else {
            matchR.add(r);
            ConceptSetComponent csM = new ConceptSetComponent();
            ConceptSetComponent csI = new ConceptSetComponent();
            union.getExclude().add(csM);
            intersection.getExclude().add(csI);
            StructuralMatch<Element> sm = new StructuralMatch<Element>(l, r);
            res.getExcludes().getChildren().add(sm);
            compareDefinitions(l, r, sm, csM, csI);
        }
    }
    for (ConceptSetComponent r : right.getExclude()) {
        if (!matchR.contains(r)) {
            union.getExclude().add(r);
            res.getExcludes().getChildren().add(new StructuralMatch<Element>(vmI(IssueSeverity.INFORMATION, "Added Exclude", "ValueSet.compose.exclude"), r));
        }
    }
}

Example 43 with ConceptSetComponent

use of org.hl7.fhir.r4.model.ValueSet.ConceptSetComponent in project org.hl7.fhir.core by hapifhir.

the class TerminologyRenderer method addCsRef.

protected <T extends Resource> void addCsRef(ConceptSetComponent inc, XhtmlNode li, T cs) {
    String ref = null;
    boolean addHtml = true;
    if (cs != null) {
        ref = (String) cs.getUserData("external.url");
        if (Utilities.noString(ref))
            ref = (String) cs.getUserData("filename");
        else
            addHtml = false;
        if (Utilities.noString(ref)) {
            ref = (String) cs.getUserData("path");
            if (ref != null) {
                addHtml = false;
            }
        }
    }
    String spec = getSpecialReference(inc.getSystem());
    if (spec != null) {
        XhtmlNode a = li.ah(spec);
        a.code(inc.getSystem());
    } else if (cs != null && ref != null) {
        if (addHtml && !ref.contains(".html"))
            ref = ref + ".html";
        ref = context.fixReference(ref);
        XhtmlNode a = li.ah(ref.replace("\\", "/"));
        a.code(inc.getSystem());
    } else {
        li.code(inc.getSystem());
    }
}

Example 44 with ConceptSetComponent

use of org.hl7.fhir.r4.model.ValueSet.ConceptSetComponent in project org.hl7.fhir.core by hapifhir.

the class ValueSetComparer method addComposeRow.

private void addComposeRow(HierarchicalTableGenerator gen, List<Row> rows, StructuralMatch<Element> t, String name) {
    Row r = gen.new Row();
    rows.add(r);
    r.getCells().add(gen.new Cell(null, null, name, null, null));
    if (t.hasLeft() && t.hasRight()) {
        ConceptSetComponent csL = (ConceptSetComponent) t.getLeft();
        ConceptSetComponent csR = (ConceptSetComponent) t.getRight();
        if (csL.hasSystem() && csL.getSystem().equals(csR.getSystem())) {
            r.getCells().add(gen.new Cell(null, null, csL.getSystem(), null, null).span(2).center());
        } else {
            r.getCells().add(gen.new Cell(null, null, csL.getSystem(), null, null).setStyle("background-color: " + COLOR_DIFFERENT));
            r.getCells().add(gen.new Cell(null, null, csR.getSystem(), null, null).setStyle("background-color: " + COLOR_DIFFERENT));
        }
        if (csL.hasVersion() && csR.hasVersion()) {
            if (csL.getVersion().equals(csR.getVersion())) {
                r.getCells().add(gen.new Cell(null, null, csL.getVersion(), null, null).span(2).center());
            } else {
                r.getCells().add(gen.new Cell(null, null, csL.getVersion(), null, null).setStyle("background-color: " + COLOR_DIFFERENT));
                r.getCells().add(gen.new Cell(null, null, csR.getVersion(), null, null).setStyle("background-color: " + COLOR_DIFFERENT));
            }
        } else if (csL.hasVersion()) {
            r.getCells().add(gen.new Cell(null, null, csL.getVersion(), null, null));
            r.getCells().add(missingCell(gen, COLOR_NO_CELL_RIGHT));
        } else if (csR.hasVersion()) {
            r.getCells().add(missingCell(gen, COLOR_NO_CELL_LEFT));
            r.getCells().add(gen.new Cell(null, null, csR.getVersion(), null, null));
        } else {
            r.getCells().add(missingCell(gen).span(2).center());
        }
    } else if (t.hasLeft()) {
        r.setColor(COLOR_NO_ROW_RIGHT);
        ConceptSetComponent cs = (ConceptSetComponent) t.getLeft();
        r.getCells().add(gen.new Cell(null, null, cs.getSystem(), null, null));
        r.getCells().add(missingCell(gen));
        r.getCells().add(gen.new Cell(null, null, cs.hasVersion() ? "Version: " + cs.getVersion() : "", null, null));
        r.getCells().add(missingCell(gen));
    } else {
        r.setColor(COLOR_NO_ROW_LEFT);
        ConceptSetComponent cs = (ConceptSetComponent) t.getRight();
        r.getCells().add(missingCell(gen));
        r.getCells().add(gen.new Cell(null, null, cs.getSystem(), null, null));
        r.getCells().add(missingCell(gen));
        r.getCells().add(gen.new Cell(null, null, cs.hasVersion() ? "Version: " + cs.getVersion() : "", null, null));
    }
    r.getCells().add(cellForMessages(gen, t.getMessages()));
    for (StructuralMatch<Element> c : t.getChildren()) {
        if (c.either() instanceof ConceptReferenceComponent) {
            addSetConceptRow(gen, r.getSubRows(), c);
        } else {
            addSetFilterRow(gen, r.getSubRows(), c);
        }
    }
}

Example 45 with ConceptSetComponent

use of org.hl7.fhir.r4.model.ValueSet.ConceptSetComponent in project org.hl7.fhir.core by hapifhir.

the class ValueSetComparer method compareDefinitions.

private void compareDefinitions(ConceptSetComponent left, ConceptSetComponent right, StructuralMatch<Element> combined, ConceptSetComponent union, ConceptSetComponent intersection) {
    // system must match, but the rest might not. we're going to do the full comparison whatever, so the outcome looks consistent to the user
    List<CanonicalType> matchVSR = new ArrayList<>();
    for (CanonicalType l : left.getValueSet()) {
        CanonicalType r = findInList(right.getValueSet(), l, left.getValueSet());
        if (r == null) {
            union.getValueSet().add(l);
            combined.getChildren().add(new StructuralMatch<Element>(l, vmI(IssueSeverity.INFORMATION, "Removed ValueSet", "ValueSet.compose.include.valueSet")));
        } else {
            matchVSR.add(r);
            if (l.getValue().equals(r.getValue())) {
                union.getValueSet().add(l);
                intersection.getValueSet().add(l);
                StructuralMatch<Element> sm = new StructuralMatch<Element>(l, r, null);
                combined.getChildren().add(sm);
            } else {
                union.getValueSet().add(l);
                union.getValueSet().add(r);
                StructuralMatch<Element> sm = new StructuralMatch<Element>(l, r, vmI(IssueSeverity.INFORMATION, "Values are different", "ValueSet.compose.include.valueSet"));
                combined.getChildren().add(sm);
            }
        }
    }
    for (CanonicalType r : right.getValueSet()) {
        if (!matchVSR.contains(r)) {
            union.getValueSet().add(r);
            combined.getChildren().add(new StructuralMatch<Element>(vmI(IssueSeverity.INFORMATION, "Add ValueSet", "ValueSet.compose.include.valueSet"), r));
        }
    }
    List<ConceptReferenceComponent> matchCR = new ArrayList<>();
    for (ConceptReferenceComponent l : left.getConcept()) {
        ConceptReferenceComponent r = findInList(right.getConcept(), l, left.getConcept());
        if (r == null) {
            union.getConcept().add(l);
            combined.getChildren().add(new StructuralMatch<Element>(l, vmI(IssueSeverity.INFORMATION, "Removed this Concept", "ValueSet.compose.include.concept")));
        } else {
            matchCR.add(r);
            if (l.getCode().equals(r.getCode())) {
                ConceptReferenceComponent cu = new ConceptReferenceComponent();
                ConceptReferenceComponent ci = new ConceptReferenceComponent();
                union.getConcept().add(cu);
                intersection.getConcept().add(ci);
                StructuralMatch<Element> sm = new StructuralMatch<Element>(l, r);
                combined.getChildren().add(sm);
                compareConcepts(l, r, sm, cu, ci);
            } else {
                union.getConcept().add(l);
                union.getConcept().add(r);
                StructuralMatch<Element> sm = new StructuralMatch<Element>(l, r, vmI(IssueSeverity.INFORMATION, "Concepts are different", "ValueSet.compose.include.concept"));
                combined.getChildren().add(sm);
                compareConcepts(l, r, sm, null, null);
            }
        }
    }
    for (ConceptReferenceComponent r : right.getConcept()) {
        if (!matchCR.contains(r)) {
            union.getConcept().add(r);
            combined.getChildren().add(new StructuralMatch<Element>(vmI(IssueSeverity.INFORMATION, "Added this Concept", "ValueSet.compose.include.concept"), r));
        }
    }
    List<ConceptSetFilterComponent> matchFR = new ArrayList<>();
    for (ConceptSetFilterComponent l : left.getFilter()) {
        ConceptSetFilterComponent r = findInList(right.getFilter(), l, left.getFilter());
        if (r == null) {
            union.getFilter().add(l);
            combined.getChildren().add(new StructuralMatch<Element>(l, vmI(IssueSeverity.INFORMATION, "Removed this item", "ValueSet.compose.include.filter")));
        } else {
            matchFR.add(r);
            if (l.getProperty().equals(r.getProperty()) && l.getOp().equals(r.getOp())) {
                ConceptSetFilterComponent cu = new ConceptSetFilterComponent();
                ConceptSetFilterComponent ci = new ConceptSetFilterComponent();
                union.getFilter().add(cu);
                intersection.getFilter().add(ci);
                StructuralMatch<Element> sm = new StructuralMatch<Element>(l, r);
                combined.getChildren().add(sm);
                compareFilters(l, r, sm, cu, ci);
            } else {
                union.getFilter().add(l);
                union.getFilter().add(r);
                StructuralMatch<Element> sm = new StructuralMatch<Element>(l, r, vmI(IssueSeverity.INFORMATION, "Codes are different", "ValueSet.compose.include.filter"));
                combined.getChildren().add(sm);
                compareFilters(l, r, sm, null, null);
            }
        }
    }
    for (ConceptSetFilterComponent r : right.getFilter()) {
        if (!matchFR.contains(r)) {
            union.getFilter().add(r);
            combined.getChildren().add(new StructuralMatch<Element>(vmI(IssueSeverity.INFORMATION, "Added this item", "ValueSet.compose.include.filter"), r));
        }
    }
}