/// <summary>
/// Find snomed concept with indicated name.
/// </summary>
/// <param name="name"></param>
/// <returns></returns>
public RF2ConceptGroup FindSnomedConcept(String name)
{
name = name.ToUpper();
List <RF2ConceptGroup> retVal = new List <RF2ConceptGroup>();
foreach (RF2DescriptionGroup descriptionGroup in this.DescriptionGroups.Values)
{
foreach (RF2Description description in descriptionGroup.Items)
{
if (String.Compare(description?.Term.Trim().ToUpper(), name) == 0)
{
RF2ConceptGroup cg = this.GetConceptGroup(description.ConceptId);
if (retVal.Contains(cg) == false)
{
retVal.Add(cg);
}
}
}
}
if (retVal.Count == 0)
{
throw new ApplicationException("No Snomed CT Concept records found");
}
if (retVal.Count > 1)
{
throw new ApplicationException("Multiple Snomed CT Concept records found");
}
return(retVal[0]);
}
/// <summary>
/// Iterate over all rf2Parser concepts and create correct GcSnomedConcept derived class for each element.
/// </summary>
void CreateConceptRecords()
{
foreach (KeyValuePair <Int64, RF2ConceptGroup> kvp in this.rf2Parser.ConceptGroups)
{
RF2ConceptGroup rf2ConceptGroup = kvp.Value;
SnomedQueryConcept concept = this.CreateConceptRecord(rf2ConceptGroup);
if (concept != null)
{
this.modelManager.Add(concept);
}
}
}
/// <summary>
/// Pathc relationships.
/// This must be run after concepts are read in.
/// </summary>
/// <param name="path"></param>
void FixRelationships()
{
foreach (KeyValuePair <Int64, RF2RelationshipGroup> kvp in this.RelationshipGroups)
{
RF2RelationshipGroup relationshipGroup = kvp.Value;
RF2Relationship relationship = relationshipGroup.Active;
if (relationship != null)
{
RF2ConceptGroup sourceConcept = this.GetConceptGroup(relationship.SourceId);
RF2ConceptGroup destinationConcept = this.GetConceptGroup(relationship.DestinationId);
sourceConcept.AddSourceRelationship(relationshipGroup);
destinationConcept.AddDestinationRelationship(relationshipGroup);
}
}
}
/// <summary>
/// Iterate over all rf2Parser concepts and create correct GcSnomedConcept derived class for each element.
/// </summary>
SnomedQueryConcept CreateConceptRecord(RF2ConceptGroup rf2ConceptGroup)
{
RF2Concept rf2Concept = rf2ConceptGroup.Active;
if (rf2Concept == null)
{
return(null);
}
RF2ConceptGroup module = this.rf2Parser.GetConceptGroup(rf2Concept.ModuleId);
RF2ConceptGroup definitionStatus = this.rf2Parser.GetConceptGroup(rf2Concept.DefinitionStatusId);
List <String> synonyms = new List <string>();
foreach (RF2DescriptionGroup descriptionGroup in rf2ConceptGroup.DescriptionGroups)
{
RF2Description description = descriptionGroup.GetActiveEnglishDescription();
switch (description.TypeId)
{
case RF2Parser.SynonymTypeId:
synonyms.Add(description.Term);
break;
case RF2Parser.FullySpecifiedNameConceptId:
break;
default:
Console.WriteLine($"Unimplemented description type {this.rf2Parser.GetConceptGroup(description.TypeId).GetFullySpecifiedName()}");
break;
}
}
SnomedQueryConcept concept = new SnomedQueryConcept(
rf2Concept.Id, // conceptId,
rf2ConceptGroup.GetFullySpecifiedName(), // conceptFullyQualifiedName,
synonyms.ToArray(), // conceptSynonymns,
module.GetFullySpecifiedName(), // String conceptModule,
definitionStatus.GetFullySpecifiedName(), // String conceptDefinitionStatus,
rf2Concept.EffectiveTime // conceptEffectiveTime
);
return(concept);
}
/// <summary>
/// Load raw snomed description data into memory.
/// </summary>
/// <param name="path"></param>
public void LoadFromRF2Files(String conceptPath,
String relationshipPath,
String descriptionPath)
{
// Load main three snomed files (concepts, relationships, and descriptions).
// Load files concurrently
{
Thread loadConceptsTask = new Thread(() => this.LoadConcepts(conceptPath));
Thread loadRelationshipsTask = new Thread(() => this.LoadRelationships(relationshipPath));
Thread loadDescriptionsTask = new Thread(() => this.LoadDescriptions(descriptionPath));
loadConceptsTask.Start();
loadRelationshipsTask.Start();
loadDescriptionsTask.Start();
loadConceptsTask.Join();
loadRelationshipsTask.Join();
loadDescriptionsTask.Join();
}
// Perform cleanup on above loaded files.
{
Thread fixConceptsTask = new Thread(this.FixConcepts);
Thread fixRelationshipsTask = new Thread(this.FixRelationships);
Thread fixDescriptionsTask = new Thread(this.FixDescriptions);
fixConceptsTask.Start();
fixRelationshipsTask.Start();
fixDescriptionsTask.Start();
fixConceptsTask.Join();
fixRelationshipsTask.Join();
fixDescriptionsTask.Join();
}
this.RootConcept = this.FindSnomedConcept("SNOMED CT CONCEPT");
}
/// <summary>
/// Load raw snomed concept data into memory.
/// </summary>
/// <param name="path"></param>
void LoadConcepts(String path)
{
StreamReader reader = new StreamReader(File.OpenRead(path));
String[] parts = reader.ReadLine().Split('\t');
if (
(parts.Length != 5) ||
(String.Compare(parts[0], "id") != 0) ||
(String.Compare(parts[1], "effectiveTime") != 0) ||
(String.Compare(parts[2], "active") != 0) ||
(String.Compare(parts[3], "moduleId") != 0) ||
(String.Compare(parts[4], "definitionStatusId") != 0)
)
{
throw new ApplicationException("Invalid header line to concept file");
}
RF2ConceptGroup conceptGroup = null;
while (true)
{
String line = reader.ReadLine();
if (line == null)
{
break;
}
RF2Concept concept = RF2Concept.Parse(this, line);
if (concept != null)
{
/*
* Relationships in a common group are usually grouped together, so check
* last relationship to see if it is same group first.
*/
if ((conceptGroup != null) && (conceptGroup.Id != concept.Id))
{
conceptGroup = null;
}
if (
(conceptGroup == null) &&
(this.ConceptGroups.TryGetValue(concept.Id, out conceptGroup) == false)
)
{
conceptGroup = null;
}
if (conceptGroup == null)
{
conceptGroup = new RF2ConceptGroup()
{
Parser = this,
Id = concept.Id
};
if (this.ConceptGroups.TryAdd(concept.Id, conceptGroup) == false)
{
throw new ApplicationException("Error adding concept to dictionary");
}
}
conceptGroup.AddConcept(concept);
}
}
}