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

Example 86 with ConceptSetComponent

use of org.hl7.fhir.r4.model.ValueSet.ConceptSetComponent in project kindling by HL7.

the class CodeListToValueSetParser method generateConceptMapV3.

private void generateConceptMapV3(String v3map, ValueSet vs, CodeSystem cs) throws Exception {
    if (!v3map.startsWith("http://terminology.hl7.org/ValueSet/v3-"))
        v3map = "http://terminology.hl7.org/ValueSet/v3-" + v3map;
    ConceptMap cm = new ConceptMap();
    cm.setVersion(version);
    cm.setId("cm-" + vs.getId() + "-v3");
    cm.setUserData("path", cm.getId() + ".html");
    cm.setUserData("generate", true);
    cm.setUrl("http://hl7.org/fhir/ConceptMap/" + cm.getId());
    cm.setName("v3." + vs.getName());
    cm.setTitle("v3 map for " + vs.present());
    cm.setPublisher("HL7 (FHIR Project)");
    for (ContactDetail cc : vs.getContact()) {
        ContactDetail cd = cm.addContact();
        cd.setName(cc.getName());
        for (ContactPoint ccs : cc.getTelecom()) cd.addTelecom(ccs.copy());
    }
    cm.setCopyright(vs.getCopyright());
    // until we publish DSTU, then .review
    cm.setStatus(vs.getStatus());
    cm.setDate(vs.getDate());
    cm.setSource(Factory.newCanonical(vs.getUrl()));
    cm.setTarget(Factory.newCanonical(v3map));
    if (cs != null)
        processV3ConceptDefs(cm, cs.getUrl(), cs.getConcept());
    for (ConceptSetComponent cc : vs.getCompose().getInclude()) for (ConceptReferenceComponent c : cc.getConcept()) {
        processV3Map(cm, cc.getSystem(), c.getCode(), c.getUserString("v2"));
    }
    maps.see(cm, packageInfo);
}

Example 87 with ConceptSetComponent

use of org.hl7.fhir.r4.model.ValueSet.ConceptSetComponent in project kindling by HL7.

the class CodeListToValueSetParser method execute.

public void execute(String v2map, String v3map, boolean utg) throws Exception {
    boolean hasDefine = false;
    for (int row = 0; row < sheet.rows.size(); row++) {
        hasDefine = hasDefine || Utilities.noString(sheet.getColumn(row, "System"));
    }
    Map<String, ConceptDefinitionComponent> codes = new HashMap<String, ConceptDefinitionComponent>();
    Map<String, ConceptDefinitionComponent> codesById = new HashMap<String, ConceptDefinitionComponent>();
    Map<String, ConceptSetComponent> includes = new HashMap<String, ConceptSetComponent>();
    CodeSystem cs = null;
    if (hasDefine) {
        cs = new CodeSystem();
        if (utg)
            cs.setUrl("http://terminology.hl7.org/CodeSystem/" + sheetName);
        else
            cs.setUrl("http://hl7.org/fhir/" + sheetName);
        if (!valueSet.hasCompose())
            valueSet.setCompose(new ValueSetComposeComponent());
        valueSet.getCompose().addInclude().setSystem(cs.getUrl());
        cs.setVersion(version);
        cs.setCaseSensitive(true);
        cs.setContent(CodeSystemContentMode.COMPLETE);
        codeSystems.see(cs, packageInfo);
        for (int row = 0; row < sheet.rows.size(); row++) {
            if (Utilities.noString(sheet.getColumn(row, "System"))) {
                ConceptDefinitionComponent cc = new ConceptDefinitionComponent();
                cc.setUserData("id", sheet.getColumn(row, "Id"));
                cc.setCode(sheet.getColumn(row, "Code"));
                if (codes.containsKey(cc.getCode()))
                    throw new Exception("Duplicate Code " + cc.getCode());
                codes.put(cc.getCode(), cc);
                codesById.put(cc.getUserString("id"), cc);
                cc.setDisplay(sheet.getColumn(row, "Display"));
                if (sheet.getColumn(row, "Abstract").toUpperCase().equals("Y"))
                    CodeSystemUtilities.setNotSelectable(cs, cc);
                if (cc.hasCode() && !cc.hasDisplay())
                    cc.setDisplay(Utilities.humanize(cc.getCode()));
                cc.setDefinition(Utilities.appendPeriod(sheet.getColumn(row, "Definition")));
                if (!Utilities.noString(sheet.getColumn(row, "Comment")))
                    ToolingExtensions.addCSComment(cc, sheet.getColumn(row, "Comment"));
                cc.setUserData("v2", sheet.getColumn(row, "v2"));
                cc.setUserData("v3", sheet.getColumn(row, "v3"));
                for (String ct : sheet.columns) if (ct.startsWith("Display:") && !Utilities.noString(sheet.getColumn(row, ct)))
                    cc.addDesignation().setLanguage(ct.substring(8)).setValue(sheet.getColumn(row, ct));
                String parent = sheet.getColumn(row, "Parent");
                if (Utilities.noString(parent))
                    cs.addConcept(cc);
                else if (parent.startsWith("#") && codesById.containsKey(parent.substring(1)))
                    codesById.get(parent.substring(1)).addConcept(cc);
                else if (codes.containsKey(parent))
                    codes.get(parent).addConcept(cc);
                else
                    throw new Exception("Parent " + parent + " not resolved in " + sheetName);
            }
        }
    }
    for (int row = 0; row < sheet.rows.size(); row++) {
        if (!Utilities.noString(sheet.getColumn(row, "System"))) {
            String system = sheet.getColumn(row, "System");
            ConceptSetComponent t = includes.get(system);
            if (t == null) {
                if (!valueSet.hasCompose())
                    valueSet.setCompose(new ValueSetComposeComponent());
                t = valueSet.getCompose().addInclude();
                t.setSystem(system);
                includes.put(system, t);
            }
            ConceptReferenceComponent cc = t.addConcept();
            cc.setCode(sheet.getColumn(row, "Code"));
            if (codes.containsKey(cc.getCode()))
                throw new Exception("Duplicate Code " + cc.getCode());
            codes.put(cc.getCode(), null);
            cc.setDisplay(sheet.getColumn(row, "Display"));
            if (!Utilities.noString(sheet.getColumn(row, "Definition")))
                ToolingExtensions.addDefinition(cc, sheet.getColumn(row, "Definition"));
            if (!Utilities.noString(sheet.getColumn(row, "Comment")))
                ToolingExtensions.addVSComment(cc, sheet.getColumn(row, "Comment"));
            cc.setUserDataINN("v2", sheet.getColumn(row, "v2"));
            cc.setUserDataINN("v3", sheet.getColumn(row, "v3"));
            for (String ct : sheet.columns) if (ct.startsWith("Display:") && !Utilities.noString(sheet.getColumn(row, ct)))
                cc.addDesignation().setLanguage(ct.substring(8)).setValue(sheet.getColumn(row, ct));
        }
    }
    if (!Utilities.noString(v2map)) {
        generateConceptMapV2(v2map, valueSet, cs);
    }
    if (!Utilities.noString(v3map)) {
        generateConceptMapV3(v3map, valueSet, cs);
    }
    if (cs != null)
        CodeSystemConvertor.populate(cs, valueSet);
}

Example 88 with ConceptSetComponent

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

the class ICD11Generator method makeFullVs.

private void makeFullVs(String dest, CodeSystem cs) throws IOException {
    String url = "http://id.who.int/icd11/ValueSet/all-MMS";
    ValueSet vs = new ValueSet();
    vs.setId("all-MMS");
    vs.setUrl(url);
    vs.setName("ICDMMSAll");
    vs.setTitle("Value Set for all ICD MMS Codes");
    vs.setStatus(PublicationStatus.ACTIVE);
    vs.setExperimental(false);
    vs.setDate(cs.getDate());
    vs.setPublisher("WHO");
    vs.setCopyright("Consult WHO For terms of use");
    vs.setVersion(cs.getVersion());
    vs.setStatus(cs.getStatus());
    ConceptSetComponent inc = vs.getCompose().addInclude();
    inc.setSystem(cs.getUrl());
    new XmlParser(XmlVersion.V1_1).setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path(dest, "vs-all-MMS.xml")), vs);
}

Example 89 with ConceptSetComponent

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

the class ICD11Generator method makeFullVs2.

private void makeFullVs2(String dest, CodeSystem cs) throws IOException {
    String url = "http://id.who.int/icd11/ValueSet/all-foundation";
    ValueSet vs = new ValueSet();
    vs.setId("all-foundation");
    vs.setUrl(url);
    vs.setName("ICDFoundationAll");
    vs.setTitle("Value Set for all ICD Foundation Concepts");
    vs.setStatus(PublicationStatus.ACTIVE);
    vs.setExperimental(false);
    vs.setDate(cs.getDate());
    vs.setPublisher("WHO");
    vs.setCopyright("Consult WHO For terms of use");
    vs.setVersion(cs.getVersion());
    vs.setStatus(cs.getStatus());
    ConceptSetComponent inc = vs.getCompose().addInclude();
    inc.setSystem(cs.getUrl());
    new XmlParser(XmlVersion.V1_1).setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path(dest, "vs-all-foundation.xml")), vs);
}

Example 90 with ConceptSetComponent

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

the class ProfileComparer method intersectByExpansion.

private ValueSet intersectByExpansion(ValueSet lvs, ValueSet rvs) {
    // this is pretty straight forward - we intersect the lists, and build a compose out of the intersection
    ValueSet vs = new ValueSet();
    vs.setStatus(PublicationStatus.DRAFT);
    Map<String, ValueSetExpansionContainsComponent> left = new HashMap<String, ValueSetExpansionContainsComponent>();
    scan(lvs.getExpansion().getContains(), left);
    Map<String, ValueSetExpansionContainsComponent> right = new HashMap<String, ValueSetExpansionContainsComponent>();
    scan(rvs.getExpansion().getContains(), right);
    Map<String, ConceptSetComponent> inc = new HashMap<String, ConceptSetComponent>();
    for (String s : left.keySet()) {
        if (right.containsKey(s)) {
            ValueSetExpansionContainsComponent cc = left.get(s);
            ConceptSetComponent c = inc.get(cc.getSystem());
            if (c == null) {
                c = vs.getCompose().addInclude().setSystem(cc.getSystem());
                inc.put(cc.getSystem(), c);
            }
            c.addConcept().setCode(cc.getCode()).setDisplay(cc.getDisplay());
        }
    }
    return vs;
}