public async Task <IActionResult> PostData([FromBody] ConceptMap data)
{
if (!ModelState.IsValid)
{
return(BadRequest(ModelState));
}
bool versionExists = await _conceptmapservice.VersionExists(data.Version, data.Domain);
if (versionExists)
{
return(BadRequest(error: "Version already exists"));
}
var result = await _conceptmapservice.PostConceptMap(data);
if (result.Equals(data))
{
using (var connection = factoryformessagebus.CreateConnection())
using (var channel = connection.CreateModel())
{
channel.QueueDeclare(queue: "Concepts",
durable: false,
exclusive: false,
autoDelete: false,
arguments: null);
string bodydata = JsonConvert.SerializeObject(data);
channel.BasicPublish(exchange: "",
routingKey: "Concepts",
mandatory: true,
basicProperties: null,
body: Encoding.UTF8.GetBytes(bodydata));
}
}
return(CreatedAtAction("GetData", new { result.Domain, result.Version }, result));
}
private static XElement renderConceptMapList(ConceptMap conceptMap, XNamespace ns)
{
XElement xConceptMapList = null;
if (conceptMap.Group.Count > 0)
{
xConceptMapList = new XElement(ns + "table",
new XElement(ns + "tr",
new XElement(ns + "th", "Source Code"),
new XElement(ns + "th", "Source Display"),
new XElement(ns + "th", "Source Code System"),
new XElement(ns + "th", "Equivalence"),
new XElement(ns + "th", "Target Code"),
new XElement(ns + "th", "Target Display"),
new XElement(ns + "th", "Target Code System"),
new XElement(ns + "th", "Comments")
),
from cmg in conceptMap.Group
from exp in cmg.Element
select new XElement(ns + "tr",
new XElement(ns + "td", exp.Code),
new XElement(ns + "td", exp.Display),
new XElement(ns + "td", cmg.Source),
new XElement(ns + "td", exp.Target[0].Equivalence.ToString()),
new XElement(ns + "td", exp.Target[0].Code),
new XElement(ns + "td", exp.Target[0].Display),
new XElement(ns + "td", cmg.Target),
new XElement(ns + "td", exp.Target[0].Comment)
)
);
}
return(xConceptMapList);
}
private static Resource GetConceptMaps(string identifier, NameValueCollection queryParam)
{
Bundle cmBundle = new Bundle();
cmBundle.Id = Guid.NewGuid().ToString();
cmBundle.Type = Bundle.BundleType.Searchset;
cmBundle.Link.Add(new Bundle.LinkComponent {
Url = ServerCapability.TERMINZ_CANONICAL + "/ConceptMap", Relation = "self"
});
if (string.IsNullOrEmpty(identifier) && queryParam.Count < 1)
{
cmBundle.AddResourceEntry(GetRequest("NZREAD_SCT", queryParam), ServerCapability.TERMINZ_CANONICAL + "/ConceptMap/NzRead_Sct");
cmBundle.AddResourceEntry(GetRequest("SCT_NZREAD", queryParam), ServerCapability.TERMINZ_CANONICAL + "ConceptMap/Sct_NzRead");
cmBundle.AddResourceEntry(GetRequest("NZMP_SCT", queryParam), ServerCapability.TERMINZ_CANONICAL + "/ConceptMap/NzMp_Sct");
cmBundle.AddResourceEntry(GetRequest("NZ_ETHNICITY", queryParam), ServerCapability.TERMINZ_CANONICAL + "/ConceptMap/NzEthnicity");
cmBundle.AddResourceEntry(GetRequest("DELPHIC_LOINC", queryParam), "http://sysmex.co.nz/LIS/Observation/Mapping");
cmBundle.AddResourceEntry(GetRequest("101", queryParam), "http://hl7.org/fhir/ConceptMap/101");
cmBundle.AddResourceEntry(GetRequest("102", queryParam), "http://hl7.org/fhir/ConceptMap/102");
}
else
{
ConceptMap cm = (ConceptMap)GetRequest(identifier, queryParam);
cmBundle.AddResourceEntry(cm, cm.Url);
}
cmBundle.Total = cmBundle.Entry.Count();
return(cmBundle);
}
public async Task <ConceptMap> PostConceptMap(ConceptMap map)
{
await _context.Concepts.InsertOneAsync(map);
ConceptMapDomain conceptMapDomain = new ConceptMapDomain();
conceptMapDomain.Domain = map.Domain;
conceptMapDomain.Version = map.Version;
var result = GetConceptMapbyVersionandDomain(map.Version, map.Domain).Result;
conceptMapDomain.ConceptMapId = result.Select(x => x.ID).ToString();
await _context.ConceptMapDomain.InsertOneAsync(conceptMapDomain);
return(map);
}
private static Resource GetRequest(string identifier, NameValueCollection queryParam)
{
//if (string.IsNullOrEmpty(identifier))
//{
// throw new Exception(MISSING_CONCEPTMAP_IDENTIFIER);
//}
string url = Utilities.GetQueryValue("url", queryParam);
ConceptMap conceptMap = new ConceptMap();
string sourceSystem = Utilities.GetQueryValue("source", queryParam);
string targetSystem = Utilities.GetQueryValue("target", queryParam);
string versionVal = Utilities.GetQueryValue("version", queryParam);
conceptMap = GetConceptMap(identifier, string.Empty, sourceSystem, targetSystem, versionVal);
AddNarrative(conceptMap);
return(conceptMap);
}
private object[] GenerateDefinition(ConceptMap conceptMap)
{
List <object> result = new List <object>();
List <object> table = new List <object>();
table.Add(Html.Tr(new object[]
{
Html.Td(Html.B("Source")),
Html.Td(""),
Html.Td(Html.B("Target")),
Html.Td("")
}
));
ValueSet sourceValueSet = null;
ValueSet targetValueSet = null;
if (conceptMap.Item != null && conceptMap.Item.GetType() == typeof(Reference))
{
// Cheating a little here at the mo. Not safe
Reference source = (Reference)conceptMap.Item;
Reference target = (Reference)conceptMap.Item1;
Link sourceValuesetLink = _profileSet.GetValueSetLink(source.reference.GetValueAsString());
Link targetValuesetLink = _profileSet.GetValueSetLink(target.reference.GetValueAsString());
sourceValueSet = _profileSet.GetValueSet(source.reference.GetValueAsString());
targetValueSet = _profileSet.GetValueSet(target.reference.GetValueAsString());
table.Add(Html.Tr(new object[]
{
Html.Td(Html.P(GetLabelAndValue("Valueset", new object[]
{
Html.A(sourceValuesetLink.Url, sourceValuesetLink.Display)
}))),
Html.Td(""),
Html.Td(Html.P(GetLabelAndValue("Valueset", new object[]
{
Html.A(targetValuesetLink.Url, targetValuesetLink.Display)
}))),
Html.Td("")
}
));
}
if (conceptMap.element != null && sourceValueSet != null && targetValueSet != null)
{
foreach (ConceptMapElement element in conceptMap.element)
{
string sourceCode = element.code.GetValueAsString(); // GetExtensionValueAsString(FhirConstants.ValueSetSystemNameExtensionUrl);
string sourceName = "";
foreach (ValueSetInclude include in sourceValueSet.compose.include)
{
foreach (ValueSetConcept1 concept in include.concept)
{
if (concept.code.value.Equals(sourceCode))
{
sourceName = concept.display.GetValueAsString();
}
}
}
if (element.code.WhenNotNull(t => t.ToString().Length) > 0)
{
if (element.target != null)
{
bool isFirstTarget = true;
foreach (ConceptMapTarget target in element.target)
{
if (!isFirstTarget)
{
sourceCode = "";
}
isFirstTarget = true;
string targetCode = target.code.GetValueAsString();
string targetName = "";
foreach (ValueSetInclude include in targetValueSet.compose.include)
{
foreach (ValueSetConcept1 concept in include.concept)
{
if (concept.code.value.Equals(targetCode))
{
targetName = concept.display.GetValueAsString();
}
}
}
// Need to check codeSystem is SNOMED
if (float.Parse(targetCode) > 0 && targetCode.Length > 7)
{
table.Add(Html.Tr(new object[]
{
Html.Td(sourceCode),
Html.Td(sourceName),
Html.Td(Html.A(SnomedHelper.GetBrowserUrl(targetCode), targetCode)),
Html.Td(targetName)
}
));
}
else
{
table.Add(Html.Tr(new object[]
{
Html.Td(sourceCode),
Html.Td(sourceName),
Html.Td(targetCode),
Html.Td(targetName)
}
));
}
}
}
else
{
table.Add(Html.Tr(new object[]
{
Html.Td(sourceCode),
Html.Td(""),
Html.Td(""),
Html.Td("")
}
)
);
}
}
}
}
result.Add(Html.Table(new object[] { table, Html.Class(Styles.ValueSetReferenceTableClassName) }));
return(result.ToArray());
}
private void FillValues(string version, string nzmpCode)
{
this.conceptMap = new ConceptMap();
this.conceptMap.Id = "NZMP_SCT";
this.conceptMap.Url = ServerCapability.TERMINZ_CANONICAL + "/ConceptMap/NzMp_Sct";
this.conceptMap.Name = this.conceptMap.Id;
this.conceptMap.Title = "NZMT medicinal product to SNOMED CT map";
this.conceptMap.Description = new Markdown("A mapping between NZMT Medicinal Products and SNOMED CT, published by NZMT in May 2018.");
this.conceptMap.Version = "20180501";
this.conceptMap.Status = PublicationStatus.Draft;
this.conceptMap.Experimental = true;
this.conceptMap.Publisher = "Ministry of Health";
this.conceptMap.Date = new FhirDateTime(2018, 05, 1).Value;
this.conceptMap.Purpose = new Markdown("To begin alignment between NZMT and SNOMED CT");
this.conceptMap.Copyright = new Markdown("© 2018+ New Zealand Crown Copyright");
ContactPoint cp = new ContactPoint {
System = ContactPoint.ContactPointSystem.Email, Value = "*****@*****.**"
};
ContactDetail cd = new ContactDetail();
cd.Telecom.Add(cp);
cd.Name = "Patients First Ltd";
this.conceptMap.Contact.Add(cd);
string sourceCodeSystemUri = NzMt.URI;
string sourceValueSetUri = @"http://itp.patientsfirst.org.nz/ValueSet/NzulmMp";
string targetCodeSystemUri = FhirSnomed.URI;
string targetValueSetUri = @"http://snomed.info/sct?fhir_vs";
this.conceptMap.Source = new FhirUri(sourceValueSetUri);
this.conceptMap.Target = new FhirUri(targetValueSetUri);
if ((string.IsNullOrEmpty(version) || version == this.conceptMap.Version))
{
List <Coding> map = SnomedCtSearch.GetConceptMap_NZ(REFSET_ID, nzmpCode);
ConceptMap.GroupComponent gc = new ConceptMap.GroupComponent();
gc.Source = sourceCodeSystemUri;
gc.Target = targetCodeSystemUri;
foreach (Coding mv in map)
{
ConceptMap.ConceptMapEquivalence cme = ConceptMap.ConceptMapEquivalence.Equivalent;
ConceptMap.SourceElementComponent sec = new ConceptMap.SourceElementComponent {
Code = mv.Version, Display = mv.System
};
ConceptMap.TargetElementComponent tec = new ConceptMap.TargetElementComponent {
Code = mv.Code, Equivalence = cme, Display = mv.Display
};
sec.Target.Add(tec);
gc.Element.Add(sec);
}
this.conceptMap.Group.Add(gc);
}
}
private void FillValues(string version)
{
this.conceptMap = new ConceptMap();
this.conceptMap.Id = "101";
this.conceptMap.Url = "http://hl7.org/fhir/ConceptMap/101";
this.conceptMap.Identifier = new Identifier {
System = "urn:ietf:rfc:3986", Value = "urn:uuid:53cd62ee-033e-414c-9f58-3ca97b5ffc3b"
};
this.conceptMap.Name = this.conceptMap.Id;
this.conceptMap.Title = "FHIR/v3 Address Use Mapping";
this.conceptMap.Description = new Markdown("A mapping between the FHIR and HL7 v3 AddressUse Code systems");
this.conceptMap.Version = "R4";
this.conceptMap.Status = PublicationStatus.Draft;
this.conceptMap.Experimental = true;
this.conceptMap.Publisher = "HL7, Inc";
this.conceptMap.Date = new FhirDateTime(2012, 6, 13).Value;
this.conceptMap.Purpose = new Markdown("To help implementers map from HL7 v3/CDA to FHIR");
this.conceptMap.Copyright = new Markdown("Creative Commons 0");
ContactPoint cp = new ContactPoint {
System = ContactPoint.ContactPointSystem.Other, Value = "http://hl7.org/fhir"
};
ContactDetail cd = new ContactDetail();
cd.Telecom.Add(cp);
cd.Name = "FHIR project team (example)";
this.conceptMap.Contact.Add(cd);
string sourceUri = @"http://hl7.org/fhir/ValueSet/address-use";
string targetUri = @"http://terminology.hl7.org/ValueSet/v3-AddressUse";
this.conceptMap.Source = new FhirUri(sourceUri); // Value Set
this.conceptMap.Target = new FhirUri(targetUri); // Value Set
Dictionary <string, string> mapVals = new Dictionary <string, string>();
mapVals.Add("home", "H");
mapVals.Add("work", "WP");
mapVals.Add("temp", "TMP");
mapVals.Add("old", "BAD");
if (string.IsNullOrEmpty(version) || version == this.conceptMap.Version)
{
ConceptMap.GroupComponent gc = new ConceptMap.GroupComponent();
gc.Source = "http://hl7.org/fhir/address-use"; // Code System
gc.Target = "http://terminology.hl7.org/CodeSystem/v3-AddressUse"; // Code System
foreach (KeyValuePair <string, string> mapVal in mapVals)
{
ConceptMap.ConceptMapEquivalence cme = ConceptMap.ConceptMapEquivalence.Equivalent;
string comments = "";
string display = mapVal.Value.Replace("H", "home address").Replace("WP", "work place").Replace("TMP", "temporary address");
if (mapVal.Key == "old")
{
cme = ConceptMap.ConceptMapEquivalence.Disjoint;
comments = "In the HL7 v3 AD, old is handled by the usablePeriod element, but you have to provide a time, there's no simple equivalent of flagging an address as old";
display = "bad address";
}
ConceptMap.SourceElementComponent sec = new ConceptMap.SourceElementComponent {
Code = mapVal.Key, Display = mapVal.Key
};
ConceptMap.TargetElementComponent tec = new ConceptMap.TargetElementComponent {
Code = mapVal.Value, Display = display, Equivalence = cme, Comment = comments
};
sec.Target.Add(tec);
gc.Element.Add(sec);
}
this.conceptMap.Group.Add(gc);
}
else
{
throw new Exception(TerminologyConceptMap.UNSUPPORTED_VERSION);
}
}
internal static ConceptMap AddNarrative(ConceptMap conceptMap)
{
// create display text for ConceptMap Resource
string textString = string.Empty;
//string nameTitle = conceptMap.Name.ToString() + (!string.IsNullOrEmpty(conceptMap.Title) ? " | " + conceptMap.Title : "");
try
{
XNamespace ns = "http://www.w3.org/1999/xhtml";
var summary = new XElement(ns + "div",
new XElement(ns + "h2", conceptMap.Title),
new XElement(ns + "p", conceptMap.Description),
new XElement(ns + "table",
new XElement(ns + "tr",
new XElement(ns + "td", "Id"),
new XElement(ns + "td", conceptMap.Id)
),
new XElement(ns + "tr",
new XElement(ns + "td", "Url"),
new XElement(ns + "td", conceptMap.Url)
),
new XElement(ns + "tr",
new XElement(ns + "td", "Version"),
new XElement(ns + "td", conceptMap.Version)
),
new XElement(ns + "tr",
new XElement(ns + "td", "Publisher"),
new XElement(ns + "td", conceptMap.Publisher)
),
new XElement(ns + "tr",
new XElement(ns + "td", "Status"),
new XElement(ns + "td", conceptMap.Status.ToString())
),
new XElement(ns + "tr",
new XElement(ns + "td", "Status Date"),
new XElement(ns + "td", conceptMap.Date)
),
new XElement(ns + "tr",
new XElement(ns + "td", "Experimental"),
new XElement(ns + "td", conceptMap.Experimental.ToString())
)
),
renderConceptMapList(conceptMap, ns)
);
textString = summary.ToString();
}
catch
{
throw new Exception(UNRECOGNISED_CONCEPTMAP);
}
conceptMap.Text = new Narrative();
conceptMap.Text.Status = Narrative.NarrativeStatus.Generated;
conceptMap.Text.Div = textString;
// format Name property correctly
conceptMap.Name = conceptMap.Name.First().ToString().ToUpper() + conceptMap.Name.Substring(1).Replace('-', '_');
return(conceptMap);
}
private static Resource ClosureOperation(NameValueCollection queryParam)
{
bool outcome = true;
int spReturn = 0;
bool resync = false;
string nameVal = Utilities.GetQueryValue("name", queryParam);
string versionVal = Utilities.GetQueryValue("version", queryParam);
string codeVals = Utilities.GetQueryValue("code", queryParam);
string systemVal = Utilities.GetQueryValue("system", queryParam);
// need to determine task (initialise /add concept / version check / resync) from what is passed
// nb client can pass a version or concept(s), but not both
if (string.IsNullOrEmpty(nameVal))
{
throw new Exception(MISSING_CLOSURE_NAME);
}
// nb if versionVal = 0 will re-synch entire table (BUT if >0 changes since certain version OR specific version?)
resync = !string.IsNullOrEmpty(versionVal);
if (resync && !string.IsNullOrEmpty(codeVals))
{
throw new Exception(INVALID_CLOSURE_PARAMS);
}
if (!string.IsNullOrEmpty(codeVals) || resync)
{
if (systemVal != FhirSnomed.URI && !resync)
{
throw new Exception(UNSUPPORTED_CODE_SYSTEM);
}
string newConcepts = string.Empty;
short dbVer = 0;
string storedConcepts = Closure.GetClosureConcepts(nameVal, (short)spReturn, out dbVer);
bool codesToAdd = false;
foreach (string cd in codeVals.Split(';'))
{
if (!string.IsNullOrEmpty(cd))
{
string newCode = cd.Trim() + "|";
if (storedConcepts.IndexOf(newCode) < 0)
{
storedConcepts += newCode;
codesToAdd = true;
}
}
}
if (codesToAdd)
{
spReturn = Closure.UpdateClosureTable(nameVal, storedConcepts, CLOSURE_CODE_SYSTEM_ID, CLOSURE_CODE_SYSTEM_VERSION);
}
if (spReturn == -1)
{
throw new Exception(INVALID_CLOSURE_NAME);
}
else if (spReturn == 99)
{
throw new Exception(REINITIALISE_CLOSURE);
}
ConceptMap cMap = new ConceptMap();
cMap.Id = Guid.NewGuid().ToString();
cMap.Version = dbVer.ToString();
cMap.Name = "Updates for Closure Table " + nameVal;
cMap.Status = PublicationStatus.Active;
cMap.Experimental = true;
cMap.Date = Hl7.Fhir.Model.Date.Today().Value;
ConceptMap.GroupComponent gc = new ConceptMap.GroupComponent();
gc.Source = CLOSURE_CODE_SYSTEM_ID;
gc.SourceVersion = CLOSURE_CODE_SYSTEM_VERSION;
gc.Target = CLOSURE_CODE_SYSTEM_ID;
gc.TargetVersion = CLOSURE_CODE_SYSTEM_VERSION;
if (resync)
{
codeVals = storedConcepts.Replace("|", ";");
}
string subSuper = string.Empty;
// look for sub-type / super-type relationships between existing codes and new codes
foreach (string newCode in codeVals.Split(';'))
{
foreach (string storedCode in storedConcepts.Split('|'))
{
if (!string.IsNullOrEmpty(newCode) && newCode != storedCode)
{
// does one of these codes subsume another?
string relat = TerminologyCodeSystem.GetRelationship(storedCode, newCode);
string supertype = string.Empty;
string subType = string.Empty;
if (relat == TerminologyCodeSystem.CODE_RELATIONSHIP_SUBSUMED_BY)
{
subType = storedCode;
supertype = newCode;
}
else if (relat == TerminologyCodeSystem.CODE_RELATIONSHIP_SUBSUMES)
{
subType = newCode;
supertype = storedCode;
}
// check if this combination used already (reSync)
string combo = subType + "+" + supertype + "|";
bool newPair = false;
if (!string.IsNullOrEmpty(supertype))
{
if (subSuper.IndexOf(combo) < 0)
{
subSuper += combo;
newPair = true;
}
}
if (newPair)
{
ConceptMap.SourceElementComponent sec = new ConceptMap.SourceElementComponent {
Code = subType
};
ConceptMap.TargetElementComponent tec = new ConceptMap.TargetElementComponent {
Code = supertype, Equivalence = ConceptMap.ConceptMapEquivalence.Subsumes
};
sec.Target.Add(tec);
gc.Element.Add(sec);
}
}
}
}
cMap.Group.Add(gc);
return(cMap);
}
else
{
// initialise Closure Table
outcome = Closure.AddClosureTable(nameVal, CLOSURE_CODE_SYSTEM_ID, CLOSURE_CODE_SYSTEM_VERSION);
if (outcome == false)
{
throw new Exception(INVALID_CLOSURE_NAME);
}
}
Parameters param = new Parameters();
param.Add("outcome", new FhirBoolean(outcome));
return(param);
}
private static ConceptMap GetConceptMap(string identifier, string sourceCode, string sourceSystem, string targetSystem, string mapVersion)
{
string resourceFilePath = Path.GetDirectoryName(new Uri(Assembly.GetExecutingAssembly().CodeBase).LocalPath) + @"\Test Files\";
// <TODO> need a factory method here
ConceptMap conceptMap = new ConceptMap();
if (identifier == "101" || identifier == "http://hl7.org/fhir/ConceptMap/101" || (sourceSystem == "http://hl7.org/fhir/ValueSet/address-use" && targetSystem == "http://terminology.hl7.org/ValueSet/v3-AddressUse"))
{
AddressUseV3Fhir cm = new AddressUseV3Fhir(mapVersion);
conceptMap = cm.conceptMap;
}
else if (identifier == "102" || identifier == "http://hl7.org/fhir/ConceptMap/102" || (sourceSystem == "http://hl7.org/fhir/v2/0487" && targetSystem.StartsWith(FhirSnomed.URI)))
{
FhirXmlParser fxp = new FhirXmlParser();
conceptMap = fxp.Parse <ConceptMap>(File.ReadAllText(resourceFilePath + "SpecimenType_v2_SCT_Map.xml"));
}
else if (identifier == "NZREAD_SCT" || identifier == "http://itp.patientsfirst.org.nz/ConceptMap/NzRead_Sct" || (sourceSystem.StartsWith("http://health.govt.nz/read-codes") && targetSystem.StartsWith(FhirSnomed.URI)))
{
NZReadToSCT cm = new NZReadToSCT(mapVersion, sourceCode);
conceptMap = cm.conceptMap;
}
else if (identifier == "SCT_NZREAD" || identifier == "http://itp.patientsfirst.org.nz/ConceptMap/Sct_NzRead" || (sourceSystem.StartsWith(FhirSnomed.URI) && targetSystem.StartsWith("http://health.govt.nz/read-codes")))
{
SctToNZRead cm = new SctToNZRead(mapVersion, sourceCode);
conceptMap = cm.conceptMap;
}
else if (identifier == "NZMP_SCT" || identifier == "http://itp.patientsfirst.org.nz/ConceptMap/NzMp_Sct" || (sourceSystem.StartsWith(NzMt.URI) && targetSystem.StartsWith(FhirSnomed.URI)))
{
NzMpToSCT cm = new NzMpToSCT(mapVersion, sourceCode);
conceptMap = cm.conceptMap;
}
else if (identifier == "NZ_ETHNICITY" || identifier == "http://itp.patientsfirst.org.nz/ConceptMap/NzEthnicity" || (sourceSystem.StartsWith("https://standards.digital.health.nz/codesystem/ethnic-group-level-") && targetSystem.StartsWith("https://standards.digital.health.nz/codesystem/ethnic-group-level-")))
{
sourceSystem = string.IsNullOrEmpty(sourceSystem) ? "https://standards.digital.health.nz/codesystem/ethnic-group-level-" : sourceSystem;
targetSystem = string.IsNullOrEmpty(targetSystem) ? "https://standards.digital.health.nz/codesystem/ethnic-group-level-" : targetSystem;
// as this facilitates a generic map to/from levels 2-4, prevent use of an invalid ethnicity level
string invalidLevels = "0156789";
string sourceLevel = sourceSystem.Substring(sourceSystem.Length - 1, 1);
string targetLevel = targetSystem.Substring(targetSystem.Length - 1, 1);
if (invalidLevels.Contains(sourceLevel) && invalidLevels.Contains(targetLevel))
{
throw new Exception(UNSUPPORTED_CODE_SYSTEM);
}
NZEthnicityLevels cm = new NZEthnicityLevels(mapVersion, sourceCode, sourceSystem, targetSystem);
conceptMap = cm.conceptMap;
}
else if (identifier == "DELPHIC_LOINC" || identifier == "http://sysmex.co.nz/LIS/Observation/Mapping" || identifier == "f9f7e8f3-4d81-4291-8534-538fecd6f554")
{
FhirXmlParser fxp = new FhirXmlParser();
conceptMap = fxp.Parse <ConceptMap>(File.ReadAllText(resourceFilePath + "DELPHIC_LOINC_Map.xml"));
}
//else if (identifier == "NZMP_SCT" || (sourceSystem == "http://nzmt.org.nz" && targetSystem == "http://snomed.info/sct"))
//{
// NZMpToSCT cm = new NZMpToSCT(mapVersion, sourceCode);
// conceptMap = cm.conceptMap;
//}
else
{
throw new Exception(UNRECOGNISED_CONCEPTMAP);
}
return(conceptMap);
}
private static Resource TranslateOperation(string id, NameValueCollection queryParam)
{
string systemVal = Utilities.GetQueryValue("system", queryParam);
string sourceSystemVal = Utilities.GetQueryValue("source", queryParam);
string sourceCodeVal = Utilities.GetQueryValue("code", queryParam);
//string codingVal = Utilities.GetQueryValue("coding", queryParam);
string versionVal = Utilities.GetQueryValue("conceptMapVersion", queryParam);
string targetVal = Utilities.GetQueryValue("target", queryParam); // ValueSet
string targetSystemVal = Utilities.GetQueryValue("targetSystem", queryParam); // Code System
if (string.IsNullOrEmpty(sourceSystemVal))
{
sourceSystemVal = systemVal;
}
if (string.IsNullOrEmpty(targetSystemVal))
{
targetSystemVal = targetVal;
}
// if id supplied - just require source code to be translated, otherwise both source and target code systems must also be supplied
if (string.IsNullOrEmpty(sourceCodeVal))
{
throw new Exception(MISSING_SOURCE_CODE_CODING);
}
else if (string.IsNullOrEmpty(id) && string.IsNullOrEmpty(sourceSystemVal))
{
throw new Exception(MISSING_SOURCE_SYSTEM);
}
else if (string.IsNullOrEmpty(id) && string.IsNullOrEmpty(targetSystemVal))
{
throw new Exception(MISSING_TARGET_SYSTEM);
}
// get Mapping(s)
ConceptMap conceptMap = GetConceptMap(id, sourceCodeVal, sourceSystemVal, targetSystemVal, versionVal);
// iterate through Mappings storing any results
List <Tuple <string, Base> > tuples = new List <Tuple <string, Base> >();
string matchMessage = string.Empty;
Dictionary <string, string> targetCodes = new Dictionary <string, string>();
foreach (ConceptMap.GroupComponent cmGroup in conceptMap.Group)
{
foreach (ConceptMap.SourceElementComponent se in cmGroup.Element)
{
if (se.Code.Trim() == sourceCodeVal.Trim())
{
foreach (ConceptMap.TargetElementComponent te in se.Target)
{
if (!string.IsNullOrEmpty(se.Display))
{
matchMessage += string.IsNullOrEmpty(matchMessage) ? "Source Code Description(s): " : " | ";
matchMessage += se.Display;
}
// prevent duplicate targets (e.g. Read to SCT maps with >1 description mapped per code)
if (!targetCodes.ContainsKey(te.Code.Trim()))
{
tuples.Add(new Tuple <string, Base>("equivalence", new FhirString(te.Equivalence.ToString())));
tuples.Add(new Tuple <string, Base>("concept", new Coding {
Code = te.Code.Trim(), Display = te.Display, System = cmGroup.Target
}));
targetCodes.Add(te.Code.Trim(), te.Display);
}
foreach (ConceptMap.OtherElementComponent prod in te.Product)
{
tuples.Add(new Tuple <string, Base>("product", new Coding {
Code = prod.Value.Trim(), Display = prod.Display, System = prod.System, ElementId = prod.Property
}));
}
}
}
}
}
Parameters param = new Parameters();
param.Add("result", new FhirBoolean(tuples.Count > 0));
if (tuples.Count < 1)
{
throw new Exception("No mappings could be found for " + sourceCodeVal + " / " + systemVal);
//param.Add("message", new FhirString("No mappings could be found for " + sourceCodeVal + " / " + systemVal));
}
else
{
if (!string.IsNullOrEmpty(matchMessage))
{
param.Add("message", new FhirString(matchMessage));
}
param.Add("match", tuples);
}
return(param);
}
private object[] GenerateContent(ConceptMapFile conceptMapFile, string displayName)
{
List <object> content = new List <object>();
ConceptMap conceptMap = conceptMapFile.ConceptMap;
string name = conceptMap.name.value;
string url = "";
if (conceptMap.url != null)
{
url = conceptMap.url.value;
}
content.AddRange(new object[]
{
Html.H3(GetConceptMapNameLabel(name)),
Html.P("The official URL for this value set is: "),
Html.Pre(url),
Html.P(GetMaturity(conceptMapFile.Maturity)),
});
string description = conceptMap.description.WhenNotNull(t => t.value);
string referenceUrl = conceptMap.GetExtensionValueAsString(FhirConstants.ValueSetSourceReferenceExtensionUrl);
string oid = conceptMap.GetExtensionValueAsString(FhirConstants.ValueSetOidExtensionUrl);
if ((!string.IsNullOrWhiteSpace(description)) || (!string.IsNullOrWhiteSpace(referenceUrl)) || (!string.IsNullOrWhiteSpace(oid)))
{
content.AddRange(new object[]
{
Html.H3("Description"),
GetFormattedDescription(description, referenceUrl, oid)
});
}
content.AddRange(new object[]
{
Html.H3("Definition"),
GenerateDefinition(conceptMap)
});
string copyright = conceptMap.copyright.WhenNotNull(t => t.value);
if (!string.IsNullOrEmpty(copyright))
{
content.AddRange(new object[]
{
Html.H3("Copyright"),
Html.P(copyright)
});
}
content.AddRange(new object[]
{
Html.H3("Schemas"),
StructureDefinitionHtmlGenerator.GetSchemasList(new object[]
{
Html.A(_outputPaths.GetRelativePath(OutputFileType.ConceptMap, conceptMapFile.OutputXmlFilename), "ConceptMap XML"),
Html.A(_outputPaths.GetRelativePath(OutputFileType.ConceptMap, conceptMapFile.OutputJsonFilename), "ConceptMap JSON")
})
});
return(content.ToArray());
}
private void FillValues(string version, string sctid)
{
this.conceptMap = new ConceptMap();
this.conceptMap.Id = "SCT_NZREAD";
this.conceptMap.Url = ServerCapability.TERMINZ_CANONICAL + "/ConceptMap/Sct_NzRead";
//this.conceptMap.Identifier = new Identifier { System = "urn:ietf:rfc:3986", Value = "urn:uuid:53cd62ee-033e-414c-9f58-3ca97b5ffc3b" };
this.conceptMap.Name = this.conceptMap.Id;
this.conceptMap.Title = "SNOMED CT to NZ Read Codes";
string caveat = string.Empty;
if (string.IsNullOrEmpty(sctid))
{
caveat = " Definition only - complete map too large to download (over 100k elements).";
}
this.conceptMap.Description = new Markdown("A mapping between SNOMED CT and the NZ Read Codes, published by NHS Digital and augmented for use in NZ." + caveat);
this.conceptMap.Version = "20190501";
this.conceptMap.Status = PublicationStatus.Draft;
this.conceptMap.Experimental = true;
this.conceptMap.Publisher = "Ministry of Health";
this.conceptMap.Date = new FhirDateTime(2019, 05, 01).Value;
this.conceptMap.Purpose = new Markdown("Used by the NZ Ministry of Social Development to help process SNOMED - coded work capacity medical certificates.");
this.conceptMap.Copyright = new Markdown("© 2010+ New Zealand Crown Copyright");
ContactPoint cp = new ContactPoint {
System = ContactPoint.ContactPointSystem.Email, Value = "*****@*****.**"
};
ContactDetail cd = new ContactDetail();
cd.Telecom.Add(cp);
cd.Name = "Patients First Ltd";
this.conceptMap.Contact.Add(cd);
string sourceCodeSystemUri = FhirSnomed.URI;
string sourceValueSetUri = @"http://snomed.info/sct?fhir_vs";
string targetCodeSystemUri = @"http://health.govt.nz/read-codes";
string targetValueSetUri = @"http://health.govt.nz/read-codes/fhir_vs";
this.conceptMap.Source = new FhirUri(sourceValueSetUri);
this.conceptMap.Target = new FhirUri(targetValueSetUri);
if ((string.IsNullOrEmpty(version) || version == this.conceptMap.Version) && !string.IsNullOrEmpty(sctid))
{
List <Coding> map = SnomedCtSearch.GetConceptMap_NZ(REFSET_ID, sctid);
ConceptMap.GroupComponent gc = new ConceptMap.GroupComponent();
gc.Source = sourceCodeSystemUri;
gc.Target = targetCodeSystemUri;
foreach (Coding mv in map)
{
ConceptMap.ConceptMapEquivalence cme = ConceptMap.ConceptMapEquivalence.Equivalent;
ConceptMap.SourceElementComponent sec = new ConceptMap.SourceElementComponent {
Code = mv.Version, Display = mv.System
};
ConceptMap.TargetElementComponent tec = new ConceptMap.TargetElementComponent {
Code = mv.Code, Equivalence = cme, Display = mv.Display
};
sec.Target.Add(tec);
gc.Element.Add(sec);
}
this.conceptMap.Group.Add(gc);
}
}
private void FillValues(string version, string readcode)
{
this.conceptMap = new ConceptMap();
this.conceptMap.Id = "NZREAD_SCT";
this.conceptMap.Url = ServerCapability.TERMINZ_CANONICAL + "/ConceptMap/NzRead_Sct";
//this.conceptMap.Identifier = new Identifier { System = "urn:ietf:rfc:3986", Value = "urn:uuid:53cd62ee-033e-414c-9f58-3ca97b5ffc3b" };
this.conceptMap.Name = this.conceptMap.Id;
this.conceptMap.Title = "NZ Read Codes to SNOMED CT";
string caveat = string.Empty;
if (string.IsNullOrEmpty(readcode))
{
caveat = " Definition only - complete map too large to download (over 100k elements).";
}
this.conceptMap.Description = new Markdown("A mapping between the NZ Read Codes and SNOMED CT, published by NHS Digital and augmented for use in NZ." + caveat);
this.conceptMap.Version = "20190501";
this.conceptMap.Status = PublicationStatus.Draft;
this.conceptMap.Experimental = true;
this.conceptMap.Publisher = "Ministry of Health";
this.conceptMap.Date = new FhirDateTime(2019, 05, 01).Value;
this.conceptMap.Purpose = new Markdown("To help primary care facilities translate legacy Read Codes");
this.conceptMap.Copyright = new Markdown("© 2010+ New Zealand Crown Copyright");
ContactPoint cp = new ContactPoint {
System = ContactPoint.ContactPointSystem.Email, Value = "*****@*****.**"
};
ContactDetail cd = new ContactDetail();
cd.Telecom.Add(cp);
cd.Name = "Patients First Ltd";
this.conceptMap.Contact.Add(cd);
string sourceCodeSystemUri = @"http://health.govt.nz/read-codes";
string sourceValueSetUri = @"http://health.govt.nz/read-codes/fhir_vs";
string targetCodeSystemUri = FhirSnomed.URI;
string targetValueSetUri = @"http://snomed.info/sct?fhir_vs";
this.conceptMap.Source = new FhirUri(sourceValueSetUri);
this.conceptMap.Target = new FhirUri(targetValueSetUri);
if ((string.IsNullOrEmpty(version) || version == this.conceptMap.Version) && !string.IsNullOrEmpty(readcode))
{
// add any missing periods to end of code and default Term ID of '00'
//readcode = readcode.PadRight(5, '.');
//readcode = readcode + (readcode.Length == 5 ? "00" : "");
List <Coding> map = SnomedCtSearch.GetConceptMap_NZ(REFSET_ID, readcode);
ConceptMap.GroupComponent gc = new ConceptMap.GroupComponent();
gc.Source = sourceCodeSystemUri;
gc.Target = targetCodeSystemUri;
foreach (Coding mv in map)
{
ConceptMap.ConceptMapEquivalence cme = ConceptMap.ConceptMapEquivalence.Equivalent;
ConceptMap.SourceElementComponent sec = new ConceptMap.SourceElementComponent {
Code = mv.Version, Display = mv.System
};
ConceptMap.TargetElementComponent tec = new ConceptMap.TargetElementComponent {
Code = mv.Code, Equivalence = cme, Display = mv.Display
};
sec.Target.Add(tec);
gc.Element.Add(sec);
}
this.conceptMap.Group.Add(gc);
}
}
private void Validate(string filename, ConceptMap profile)
{
_logger.Log("Validating ConceptMap" + filename);
_logger.LogError("ConceptMap validation not currently supported.");
}
private void FillValues(string version, string ethcode, string sourceSystem, string targetSystem)
{
this.conceptMap = new ConceptMap();
this.conceptMap.Id = "NZ_ETHNICITY";
this.conceptMap.Url = ServerCapability.TERMINZ_CANONICAL + "/ConceptMap/NzEthnicityLevels";
this.conceptMap.Name = this.conceptMap.Id;
this.conceptMap.Title = "NZ Ethnicity Level (2-4) Mappings";
this.conceptMap.Description = new Markdown("Mappings between NZ Ethnicity Levels 2, 3 and 4.");
this.conceptMap.Version = "20161209";
this.conceptMap.Status = PublicationStatus.Draft;
this.conceptMap.Experimental = true;
this.conceptMap.Publisher = "Ministry of Health";
this.conceptMap.Date = new FhirDateTime(2016, 10, 26).Value;
this.conceptMap.Purpose = new Markdown("To aid conversions of Ethnicity Codes held at different levels.");
this.conceptMap.Copyright = new Markdown("© 2010+ New Zealand Crown Copyright");
ContactPoint cp = new ContactPoint {
System = ContactPoint.ContactPointSystem.Email, Value = "*****@*****.**"
};
ContactDetail cd = new ContactDetail();
cd.Telecom.Add(cp);
cd.Name = "Patients First Ltd";
this.conceptMap.Contact.Add(cd);
this.conceptMap.Source = new FhirUri(sourceSystem);
this.conceptMap.Target = new FhirUri(targetSystem);
// determine which maps have been requested or all
bool allMaps = true;
string mapping = string.Empty;
string levels = "234";
string sourceLevel = sourceSystem.Substring(sourceSystem.Length - 1, 1);
string targetLevel = targetSystem.Substring(targetSystem.Length - 1, 1);
if (levels.Contains(sourceLevel) && levels.Contains(targetLevel))
{
mapping = sourceLevel + targetLevel;
allMaps = false;
}
// get ValueSets for Levels 2-4
NameValueCollection queryParams = new NameValueCollection();
ValueSet vsL2 = (ValueSet)TerminologyValueSet.PerformOperation("NzEthnicityL2", "$expand", queryParams);
ValueSet vsL3 = (ValueSet)TerminologyValueSet.PerformOperation("NzEthnicityL3", "$expand", queryParams);
ValueSet vsL4 = (ValueSet)TerminologyValueSet.PerformOperation("NzEthnicityL4", "$expand", queryParams);
// Level 2-3 mappings
Dictionary <string, string> mapVals23 = new Dictionary <string, string>();
mapVals23.Add("10", "100");
mapVals23.Add("11", "111");
mapVals23.Add("12", "129");
mapVals23.Add("21", "211");
mapVals23.Add("30", "300");
mapVals23.Add("31", "311");
mapVals23.Add("32", "321");
mapVals23.Add("33", "331");
mapVals23.Add("34", "341");
mapVals23.Add("35", "351");
mapVals23.Add("36", "361");
mapVals23.Add("37", "371");
mapVals23.Add("40", "400");
mapVals23.Add("41", "414");
mapVals23.Add("42", "421");
mapVals23.Add("43", "431");
mapVals23.Add("44", "444");
mapVals23.Add("51", "511");
mapVals23.Add("52", "521");
mapVals23.Add("53", "531");
mapVals23.Add("61", "611");
mapVals23.Add("94", "944");
mapVals23.Add("95", "955");
mapVals23.Add("96", "966");
mapVals23.Add("97", "977");
mapVals23.Add("98", "988");
mapVals23.Add("99", "999");
ConceptMap.GroupComponent gc23 = new ConceptMap.GroupComponent();
gc23.Source = NzEthnicityL2.URI;
gc23.Target = NzEthnicityL3.URI;
foreach (KeyValuePair <string, string> mapVal in mapVals23)
{
ConceptMap.ConceptMapEquivalence cme = ConceptMap.ConceptMapEquivalence.Narrower;
ConceptMap.SourceElementComponent sec = new ConceptMap.SourceElementComponent {
Code = mapVal.Key, Display = GetCodeDisplay(vsL2, mapVal.Key)
};
ConceptMap.TargetElementComponent tec = new ConceptMap.TargetElementComponent {
Code = mapVal.Value, Equivalence = cme, Display = GetCodeDisplay(vsL3, mapVal.Value)
};
sec.Target.Add(tec);
gc23.Element.Add(sec);
}
if (allMaps || mapping == "23")
{
this.conceptMap.Group.Add(gc23);
}
// Level 2-4 mappings
Dictionary <string, string> mapVals24 = new Dictionary <string, string>();
mapVals24.Add("10", "10000");
mapVals24.Add("11", "11111");
mapVals24.Add("12", "12999");
mapVals24.Add("21", "21111");
mapVals24.Add("30", "30000");
mapVals24.Add("31", "31111");
mapVals24.Add("32", "32100");
mapVals24.Add("33", "33111");
mapVals24.Add("34", "34111");
mapVals24.Add("35", "35111");
mapVals24.Add("36", "36111");
mapVals24.Add("37", "37199");
mapVals24.Add("40", "40000");
mapVals24.Add("41", "41499");
mapVals24.Add("42", "42199");
mapVals24.Add("43", "43199");
mapVals24.Add("44", "44499");
mapVals24.Add("51", "51199");
mapVals24.Add("52", "52199");
mapVals24.Add("53", "53199");
mapVals24.Add("61", "61199");
mapVals24.Add("94", "94444");
mapVals24.Add("95", "95555");
mapVals24.Add("96", "96666");
mapVals24.Add("97", "97777");
mapVals24.Add("98", "98888");
mapVals24.Add("99", "99999");
ConceptMap.GroupComponent gc24 = new ConceptMap.GroupComponent();
gc24.Source = NzEthnicityL2.URI;
gc24.Target = NzEthnicityL4.URI;
foreach (KeyValuePair <string, string> mapVal in mapVals24)
{
ConceptMap.ConceptMapEquivalence cme = ConceptMap.ConceptMapEquivalence.Narrower;
ConceptMap.SourceElementComponent sec = new ConceptMap.SourceElementComponent {
Code = mapVal.Key, Display = GetCodeDisplay(vsL2, mapVal.Key)
};
ConceptMap.TargetElementComponent tec = new ConceptMap.TargetElementComponent {
Code = mapVal.Value, Equivalence = cme, Display = GetCodeDisplay(vsL4, mapVal.Value)
};
sec.Target.Add(tec);
gc24.Element.Add(sec);
}
if (allMaps || mapping == "24")
{
this.conceptMap.Group.Add(gc24);
}
// Level 3 to 4
ConceptMap.GroupComponent gc34 = new ConceptMap.GroupComponent();
gc34.Source = NzEthnicityL3.URI;
gc34.Target = NzEthnicityL4.URI;
foreach (ValueSet.ContainsComponent ec in vsL3.Expansion.Contains)
{
ConceptMap.ConceptMapEquivalence cme = ConceptMap.ConceptMapEquivalence.Narrower;
string targetCode = ec.Code + ec.Code.Substring(2, 1) + ec.Code.Substring(2, 1);
ConceptMap.SourceElementComponent sec = new ConceptMap.SourceElementComponent {
Code = ec.Code, Display = ec.Display
};
ConceptMap.TargetElementComponent tec = new ConceptMap.TargetElementComponent {
Code = targetCode, Equivalence = cme, Display = GetCodeDisplay(vsL4, targetCode)
};
sec.Target.Add(tec);
gc34.Element.Add(sec);
}
if (allMaps || mapping == "34")
{
this.conceptMap.Group.Add(gc34);
}
// Level 3 to 2
ConceptMap.GroupComponent gc32 = new ConceptMap.GroupComponent();
gc32.Source = NzEthnicityL3.URI;
gc32.Target = NzEthnicityL2.URI;
foreach (ValueSet.ContainsComponent ec in vsL3.Expansion.Contains)
{
ConceptMap.ConceptMapEquivalence cme = ConceptMap.ConceptMapEquivalence.Wider;
ConceptMap.SourceElementComponent sec = new ConceptMap.SourceElementComponent {
Code = ec.Code, Display = ec.Display
};
ConceptMap.TargetElementComponent tec = new ConceptMap.TargetElementComponent {
Code = ec.Code.Substring(0, 2), Equivalence = cme, Display = GetCodeDisplay(vsL2, ec.Code.Substring(0, 2))
};
sec.Target.Add(tec);
gc32.Element.Add(sec);
}
if (allMaps || mapping == "32")
{
this.conceptMap.Group.Add(gc32);
}
// Level 4 to 3
ConceptMap.GroupComponent gc43 = new ConceptMap.GroupComponent();
gc43.Source = NzEthnicityL4.URI;
gc43.Target = NzEthnicityL3.URI;
foreach (ValueSet.ContainsComponent ec in vsL4.Expansion.Contains)
{
string targetCode = (ec.Code == "61118") ? "111" : ec.Code.Substring(0, 3);
ConceptMap.ConceptMapEquivalence cme = ConceptMap.ConceptMapEquivalence.Wider;
ConceptMap.SourceElementComponent sec = new ConceptMap.SourceElementComponent {
Code = ec.Code, Display = ec.Display
};
ConceptMap.TargetElementComponent tec = new ConceptMap.TargetElementComponent {
Code = targetCode, Equivalence = cme, Display = GetCodeDisplay(vsL3, targetCode)
};
sec.Target.Add(tec);
gc43.Element.Add(sec);
}
if (allMaps || mapping == "43")
{
this.conceptMap.Group.Add(gc43);
}
// Level 4 to 2
ConceptMap.GroupComponent gc42 = new ConceptMap.GroupComponent();
gc42.Source = NzEthnicityL4.URI;
gc42.Target = NzEthnicityL2.URI;
foreach (ValueSet.ContainsComponent ec in vsL4.Expansion.Contains)
{
string targetCode = (ec.Code == "61118") ? "11" : ec.Code.Substring(0, 2);
ConceptMap.ConceptMapEquivalence cme = ConceptMap.ConceptMapEquivalence.Wider;
ConceptMap.SourceElementComponent sec = new ConceptMap.SourceElementComponent {
Code = ec.Code, Display = ec.Display
};
ConceptMap.TargetElementComponent tec = new ConceptMap.TargetElementComponent {
Code = targetCode, Equivalence = cme, Display = GetCodeDisplay(vsL2, targetCode)
};
sec.Target.Add(tec);
gc42.Element.Add(sec);
}
if (allMaps || mapping == "42")
{
this.conceptMap.Group.Add(gc42);
}
}
