use of org.hl7.fhir.dstu2.model.ConceptMap.TargetElementComponent in project org.hl7.fhir.core by hapifhir.
the class IEEE11073Convertor method generateLoincMdcMap.
private static ConceptMap generateLoincMdcMap(CodeSystem mdc, String dst, String src) throws IOException, FHIRException {
ConceptMap cm = new ConceptMap();
cm.setId("loinc-mdc");
cm.setUrl("http:/???/fhir/ConceptMap/loinc-mdc");
cm.setVersion("[todo]");
cm.setName("LoincMdcCrossMap");
cm.setTitle("Cross Map between LOINC and MDC");
cm.setStatus(PublicationStatus.DRAFT);
cm.setExperimental(true);
cm.setDateElement(new DateTimeType());
cm.setPublisher("HL7, Inc");
ContactDetail cd = cm.addContact();
cd.setName("LOINC + IEEE");
ContactPoint cp = cd.addTelecom();
cp.setSystem(ContactPointSystem.URL);
cp.setValue("http://loinc.org");
cm.setDescription("A Cross Map between the LOINC and MDC Code systems");
cm.setPurpose("To implementers map between medical device codes and LOINC codes");
cm.setCopyright("This content LOINC \u00ae is copyright \u00a9 1995 Regenstrief Institute, Inc. and the LOINC Committee, and available at no cost under the license at http://loinc.org/terms-of-use");
cm.setSource(new UriType("http://loinc.org/vs"));
cm.setTarget(new UriType(MDC_ALL_VALUES));
ConceptMapGroupComponent g = cm.addGroup();
g.setSource("urn:iso:std:iso:11073:10101");
g.setTarget("http://loinc.org");
CSVReader csv = new CSVReader(new FileInputStream(src));
csv.readHeaders();
while (csv.line()) {
SourceElementComponent e = g.addElement();
e.setCode(csv.cell("IEEE_CF_CODE10"));
e.setDisplay(csv.cell("IEEE_DESCRIPTION"));
TargetElementComponent t = e.addTarget();
t.setEquivalence(ConceptMapEquivalence.EQUIVALENT);
t.setCode(csv.cell("LOINC_NUM"));
t.setDisplay(csv.cell("LOINC_LONG_COMMON_NAME"));
}
new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path(dst, "conceptmap-" + cm.getId() + ".xml")), cm);
System.out.println("Done");
return cm;
}
use of org.hl7.fhir.dstu2.model.ConceptMap.TargetElementComponent in project org.hl7.fhir.core by hapifhir.
the class NarrativeGenerator method addDefineRowToTable.
private boolean addDefineRowToTable(XhtmlNode t, ConceptDefinitionComponent c, int i, boolean hasHierarchy, boolean hasDisplay, boolean comment, boolean deprecated, Map<ConceptMap, String> maps, String system) {
boolean hasExtensions = false;
XhtmlNode tr = t.addTag("tr");
XhtmlNode td = tr.addTag("td");
if (hasHierarchy) {
td.addText(Integer.toString(i + 1));
td = tr.addTag("td");
String s = Utilities.padLeft("", '\u00A0', i * 2);
td.addText(s);
}
td.addText(c.getCode());
XhtmlNode a;
if (c.hasCodeElement()) {
a = td.addTag("a");
a.setAttribute("name", Utilities.nmtokenize(c.getCode()));
a.addText(" ");
}
if (hasDisplay) {
td = tr.addTag("td");
if (c.hasDisplayElement())
td.addText(c.getDisplay());
}
td = tr.addTag("td");
if (c != null)
smartAddText(td, c.getDefinition());
if (deprecated) {
td = tr.addTag("td");
Boolean b = ToolingExtensions.getDeprecated(c);
if (b != null && b) {
smartAddText(td, "Deprecated");
hasExtensions = true;
if (ToolingExtensions.hasExtension(c, ToolingExtensions.EXT_REPLACED_BY)) {
Coding cc = (Coding) ToolingExtensions.getExtension(c, ToolingExtensions.EXT_REPLACED_BY).getValue();
td.addText(" (replaced by ");
String url = getCodingReference(cc, system);
if (url != null) {
td.addTag("a").setAttribute("href", url).addText(cc.getCode());
td.addText(": " + cc.getDisplay() + ")");
} else
td.addText(cc.getCode() + " '" + cc.getDisplay() + "' in " + cc.getSystem() + ")");
}
}
}
if (comment) {
td = tr.addTag("td");
String s = ToolingExtensions.getComment(c);
if (s != null) {
smartAddText(td, s);
hasExtensions = true;
}
}
for (ConceptMap m : maps.keySet()) {
td = tr.addTag("td");
List<TargetElementComponent> mappings = findMappingsForCode(c.getCode(), m);
boolean first = true;
for (TargetElementComponent mapping : mappings) {
if (!first)
td.addTag("br");
first = false;
XhtmlNode span = td.addTag("span");
span.setAttribute("title", mapping.hasEquivalence() ? mapping.getEquivalence().toCode() : "");
span.addText(getCharForEquivalence(mapping));
a = td.addTag("a");
a.setAttribute("href", prefix + maps.get(m) + "#" + makeAnchor(mapping.getCodeSystem(), mapping.getCode()));
a.addText(mapping.getCode());
if (!Utilities.noString(mapping.getComments()))
td.addTag("i").addText("(" + mapping.getComments() + ")");
}
}
for (CodeType e : ToolingExtensions.getSubsumes(c)) {
hasExtensions = true;
tr = t.addTag("tr");
td = tr.addTag("td");
String s = Utilities.padLeft("", '.', i * 2);
td.addText(s);
a = td.addTag("a");
a.setAttribute("href", "#" + Utilities.nmtokenize(e.getValue()));
a.addText(c.getCode());
}
for (ConceptDefinitionComponent cc : c.getConcept()) {
hasExtensions = addDefineRowToTable(t, cc, i + 1, hasHierarchy, hasDisplay, comment, deprecated, maps, system) || hasExtensions;
}
return hasExtensions;
}
use of org.hl7.fhir.dstu2.model.ConceptMap.TargetElementComponent in project org.hl7.fhir.core by hapifhir.
the class NarrativeGenerator method addExpansionRowToTable.
private void addExpansionRowToTable(XhtmlNode t, ValueSetExpansionContainsComponent c, int i, boolean doSystem, Map<ConceptMap, String> mymaps) {
XhtmlNode tr = t.addTag("tr");
XhtmlNode td = tr.addTag("td");
String tgt = makeAnchor(c.getSystem(), c.getCode());
td.addTag("a").setAttribute("name", tgt).addText(" ");
String s = Utilities.padLeft("", '.', i * 2);
td.addText(s);
Resource e = context.fetchCodeSystem(c.getSystem());
if (e == null)
td.addText(c.getCode());
else {
XhtmlNode a = td.addTag("a");
a.addText(c.getCode());
a.setAttribute("href", prefix + getCsRef(e) + "#" + Utilities.nmtokenize(c.getCode()));
}
if (doSystem) {
td = tr.addTag("td");
td.addText(c.getSystem());
}
td = tr.addTag("td");
if (c.hasDisplayElement())
td.addText(c.getDisplay());
for (ConceptMap m : mymaps.keySet()) {
td = tr.addTag("td");
List<TargetElementComponent> mappings = findMappingsForCode(c.getCode(), m);
boolean first = true;
for (TargetElementComponent mapping : mappings) {
if (!first)
td.addTag("br");
first = false;
XhtmlNode span = td.addTag("span");
span.setAttribute("title", mapping.getEquivalence().toString());
span.addText(getCharForEquivalence(mapping));
XhtmlNode a = td.addTag("a");
a.setAttribute("href", prefix + mymaps.get(m) + "#" + mapping.getCode());
a.addText(mapping.getCode());
if (!Utilities.noString(mapping.getComments()))
td.addTag("i").addText("(" + mapping.getComments() + ")");
}
}
for (ValueSetExpansionContainsComponent cc : c.getContains()) {
addExpansionRowToTable(t, cc, i + 1, doSystem, mymaps);
}
}
use of org.hl7.fhir.dstu2.model.ConceptMap.TargetElementComponent in project org.hl7.fhir.core by hapifhir.
the class NarrativeGenerator method generate.
public void generate(ConceptMap cm) {
XhtmlNode x = new XhtmlNode(NodeType.Element, "div");
x.addTag("h2").addText(cm.getName() + " (" + cm.getUrl() + ")");
XhtmlNode p = x.addTag("p");
p.addText("Mapping from ");
AddVsRef(((Reference) cm.getSource()).getReference(), p);
p.addText(" to ");
AddVsRef(((Reference) cm.getTarget()).getReference(), p);
p = x.addTag("p");
if (cm.getExperimental())
p.addText(Utilities.capitalize(cm.getStatus().toString()) + " (not intended for production usage). ");
else
p.addText(Utilities.capitalize(cm.getStatus().toString()) + ". ");
p.addText("Published on " + cm.getDateElement().toHumanDisplay() + " by " + cm.getPublisher());
if (!cm.getContact().isEmpty()) {
p.addText(" (");
boolean firsti = true;
for (ConceptMapContactComponent ci : cm.getContact()) {
if (firsti)
firsti = false;
else
p.addText(", ");
if (ci.hasName())
p.addText(ci.getName() + ": ");
boolean first = true;
for (ContactPoint c : ci.getTelecom()) {
if (first)
first = false;
else
p.addText(", ");
addTelecom(p, c);
}
p.addText("; ");
}
p.addText(")");
}
p.addText(". ");
p.addText(cm.getCopyright());
if (!Utilities.noString(cm.getDescription()))
x.addTag("p").addText(cm.getDescription());
x.addTag("br");
if (!cm.getElement().isEmpty()) {
SourceElementComponent cc = cm.getElement().get(0);
String src = cc.getSystem();
boolean comments = false;
boolean ok = cc.getTarget().size() == 1;
Map<String, HashSet<String>> sources = new HashMap<String, HashSet<String>>();
sources.put("code", new HashSet<String>());
Map<String, HashSet<String>> targets = new HashMap<String, HashSet<String>>();
targets.put("code", new HashSet<String>());
if (ok) {
String dst = cc.getTarget().get(0).getSystem();
for (SourceElementComponent ccl : cm.getElement()) {
ok = ok && src.equals(ccl.getSystem()) && ccl.getTarget().size() == 1 && dst.equals(ccl.getTarget().get(0).getSystem()) && ccl.getTarget().get(0).getDependsOn().isEmpty() && ccl.getTarget().get(0).getProduct().isEmpty();
if (ccl.hasSystem())
sources.get("code").add(ccl.getSystem());
for (TargetElementComponent ccm : ccl.getTarget()) {
comments = comments || !Utilities.noString(ccm.getComments());
for (OtherElementComponent d : ccm.getDependsOn()) {
if (!sources.containsKey(d.getElement()))
sources.put(d.getElement(), new HashSet<String>());
sources.get(d.getElement()).add(d.getSystem());
}
if (ccm.hasSystem())
targets.get("code").add(ccm.getSystem());
for (OtherElementComponent d : ccm.getProduct()) {
if (!targets.containsKey(d.getElement()))
targets.put(d.getElement(), new HashSet<String>());
targets.get(d.getElement()).add(d.getSystem());
}
}
}
}
String display;
if (ok) {
// simple
XhtmlNode tbl = x.addTag("table").setAttribute("class", "grid");
XhtmlNode tr = tbl.addTag("tr");
tr.addTag("td").addTag("b").addText("Source Code");
tr.addTag("td").addTag("b").addText("Equivalence");
tr.addTag("td").addTag("b").addText("Destination Code");
if (comments)
tr.addTag("td").addTag("b").addText("Comments");
for (SourceElementComponent ccl : cm.getElement()) {
tr = tbl.addTag("tr");
XhtmlNode td = tr.addTag("td");
td.addText(ccl.getCode());
display = getDisplayForConcept(ccl.getSystem(), ccl.getCode());
if (display != null)
td.addText(" (" + display + ")");
TargetElementComponent ccm = ccl.getTarget().get(0);
tr.addTag("td").addText(!ccm.hasEquivalence() ? "" : ccm.getEquivalence().toCode());
td = tr.addTag("td");
td.addText(ccm.getCode());
display = getDisplayForConcept(ccm.getSystem(), ccm.getCode());
if (display != null)
td.addText(" (" + display + ")");
if (comments)
tr.addTag("td").addText(ccm.getComments());
}
} else {
XhtmlNode tbl = x.addTag("table").setAttribute("class", "grid");
XhtmlNode tr = tbl.addTag("tr");
XhtmlNode td;
tr.addTag("td").setAttribute("colspan", Integer.toString(sources.size())).addTag("b").addText("Source Concept");
tr.addTag("td").addTag("b").addText("Equivalence");
tr.addTag("td").setAttribute("colspan", Integer.toString(targets.size())).addTag("b").addText("Destination Concept");
if (comments)
tr.addTag("td").addTag("b").addText("Comments");
tr = tbl.addTag("tr");
if (sources.get("code").size() == 1)
tr.addTag("td").addTag("b").addText("Code " + sources.get("code").toString() + "");
else
tr.addTag("td").addTag("b").addText("Code");
for (String s : sources.keySet()) {
if (!s.equals("code")) {
if (sources.get(s).size() == 1)
tr.addTag("td").addTag("b").addText(getDescForConcept(s) + " " + sources.get(s).toString());
else
tr.addTag("td").addTag("b").addText(getDescForConcept(s));
}
}
tr.addTag("td");
if (targets.get("code").size() == 1)
tr.addTag("td").addTag("b").addText("Code " + targets.get("code").toString());
else
tr.addTag("td").addTag("b").addText("Code");
for (String s : targets.keySet()) {
if (!s.equals("code")) {
if (targets.get(s).size() == 1)
tr.addTag("td").addTag("b").addText(getDescForConcept(s) + " " + targets.get(s).toString() + "");
else
tr.addTag("td").addTag("b").addText(getDescForConcept(s));
}
}
if (comments)
tr.addTag("td");
for (SourceElementComponent ccl : cm.getElement()) {
tr = tbl.addTag("tr");
td = tr.addTag("td");
if (sources.get("code").size() == 1)
td.addText(ccl.getCode());
else
td.addText(ccl.getSystem() + " / " + ccl.getCode());
display = getDisplayForConcept(ccl.getSystem(), ccl.getCode());
if (display != null)
td.addText(" (" + display + ")");
TargetElementComponent ccm = ccl.getTarget().get(0);
for (String s : sources.keySet()) {
if (!s.equals("code")) {
td = tr.addTag("td");
td.addText(getCode(ccm.getDependsOn(), s, sources.get(s).size() != 1));
display = getDisplay(ccm.getDependsOn(), s);
if (display != null)
td.addText(" (" + display + ")");
}
}
tr.addTag("td").addText(ccm.getEquivalence().toString());
td = tr.addTag("td");
if (targets.get("code").size() == 1)
td.addText(ccm.getCode());
else
td.addText(ccm.getSystem() + " / " + ccm.getCode());
display = getDisplayForConcept(ccm.getSystem(), ccm.getCode());
if (display != null)
td.addText(" (" + display + ")");
for (String s : targets.keySet()) {
if (!s.equals("code")) {
td = tr.addTag("td");
td.addText(getCode(ccm.getProduct(), s, targets.get(s).size() != 1));
display = getDisplay(ccm.getProduct(), s);
if (display != null)
td.addText(" (" + display + ")");
}
}
if (comments)
tr.addTag("td").addText(ccm.getComments());
}
}
}
inject(cm, x, NarrativeStatus.GENERATED);
}
use of org.hl7.fhir.dstu2.model.ConceptMap.TargetElementComponent in project org.hl7.fhir.core by hapifhir.
the class NarrativeGenerator method addDefineRowToTable.
private boolean addDefineRowToTable(XhtmlNode t, ConceptDefinitionComponent c, int i, boolean hasHierarchy, boolean hasDisplay, boolean comment, boolean deprecated, Map<ConceptMap, String> maps, String system, CodeSystem cs) {
boolean hasExtensions = false;
XhtmlNode tr = t.addTag("tr");
XhtmlNode td = tr.addTag("td");
if (hasHierarchy) {
td.addText(Integer.toString(i + 1));
td = tr.addTag("td");
String s = Utilities.padLeft("", '\u00A0', i * 2);
td.addText(s);
}
td.addText(c.getCode());
XhtmlNode a;
if (c.hasCodeElement()) {
a = td.addTag("a");
a.setAttribute("name", Utilities.nmtokenize(c.getCode()));
a.addText(" ");
}
if (hasDisplay) {
td = tr.addTag("td");
if (c.hasDisplayElement())
td.addText(c.getDisplay());
}
td = tr.addTag("td");
if (c != null)
smartAddText(td, c.getDefinition());
if (deprecated) {
td = tr.addTag("td");
Boolean b = CodeSystemUtilities.isDeprecated(cs, c);
if (b != null && b) {
smartAddText(td, "Deprecated");
hasExtensions = true;
if (ToolingExtensions.hasExtension(c, ToolingExtensions.EXT_REPLACED_BY)) {
Coding cc = (Coding) ToolingExtensions.getExtension(c, ToolingExtensions.EXT_REPLACED_BY).getValue();
td.addText(" (replaced by ");
String url = getCodingReference(cc, system);
if (url != null) {
td.addTag("a").setAttribute("href", url).addText(cc.getCode());
td.addText(": " + cc.getDisplay() + ")");
} else
td.addText(cc.getCode() + " '" + cc.getDisplay() + "' in " + cc.getSystem() + ")");
}
}
}
if (comment) {
td = tr.addTag("td");
String s = ToolingExtensions.getComment(c);
if (s != null) {
smartAddText(td, s);
hasExtensions = true;
}
}
for (ConceptMap m : maps.keySet()) {
td = tr.addTag("td");
List<TargetElementComponent> mappings = findMappingsForCode(c.getCode(), m);
boolean first = true;
for (TargetElementComponent mapping : mappings) {
if (!first)
td.addTag("br");
first = false;
XhtmlNode span = td.addTag("span");
span.setAttribute("title", mapping.hasEquivalence() ? mapping.getEquivalence().toCode() : "");
span.addText(getCharForEquivalence(mapping));
a = td.addTag("a");
a.setAttribute("href", prefix + maps.get(m) + "#" + makeAnchor(mapping.getSystem(), mapping.getCode()));
a.addText(mapping.getCode());
if (!Utilities.noString(mapping.getComments()))
td.addTag("i").addText("(" + mapping.getComments() + ")");
}
}
for (CodeType e : ToolingExtensions.getSubsumes(c)) {
hasExtensions = true;
tr = t.addTag("tr");
td = tr.addTag("td");
String s = Utilities.padLeft("", '.', i * 2);
td.addText(s);
a = td.addTag("a");
a.setAttribute("href", "#" + Utilities.nmtokenize(e.getValue()));
a.addText(c.getCode());
}
for (ConceptDefinitionComponent cc : c.getConcept()) {
hasExtensions = addDefineRowToTable(t, cc, i + 1, hasHierarchy, hasDisplay, comment, deprecated, maps, system, cs) || hasExtensions;
}
return hasExtensions;
}
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