/// <summary>
/// Load raw snomed description data into memory.
/// </summary>
/// <param name="path"></param>
void FixDescription(RF2DescriptionGroup descriptionGroup)
{
RF2Description description = descriptionGroup.Active;
if (description == null)
{
return;
}
RF2ConceptGroup conceptGroup;
if (this.ConceptGroups.TryGetValue(description.ConceptId, out conceptGroup) == false)
{
throw new ApplicationException($"Concept {description.ConceptId} in Description {description.Id} not found");
}
else
{
RF2ConceptGroup typeConcept;
if (this.DescriptionTypes.TryGetValue(description.TypeId, out typeConcept) == false)
{
if (this.ConceptGroups.TryGetValue(description.TypeId, out typeConcept) == false)
{
throw new ApplicationException($"Description Type concept {description.TypeId} not found");
}
if (this.DescriptionTypes.TryAdd(description.TypeId, typeConcept) == false)
{
throw new ApplicationException($"Error adding {description.TypeId} to disctionary");
}
}
this.GetConceptGroup(description.ConceptId).AddDescriptionGroup(descriptionGroup);
}
}
/// <summary>
/// Iterate over all rf2Parser concepts and create correct GcSnomedConcept derived class for each element.
/// </summary>
SnomedQueryConcept CreateConceptRecord(RF2ConceptGroup rf2ConceptGroup)
{
RF2Concept rf2Concept = rf2ConceptGroup.Active;
if (rf2Concept == null)
{
return(null);
}
RF2ConceptGroup module = this.rf2Parser.GetConceptGroup(rf2Concept.ModuleId);
RF2ConceptGroup definitionStatus = this.rf2Parser.GetConceptGroup(rf2Concept.DefinitionStatusId);
List <String> synonyms = new List <string>();
foreach (RF2DescriptionGroup descriptionGroup in rf2ConceptGroup.DescriptionGroups)
{
RF2Description description = descriptionGroup.GetActiveEnglishDescription();
switch (description.TypeId)
{
case RF2Parser.SynonymTypeId:
synonyms.Add(description.Term);
break;
case RF2Parser.FullySpecifiedNameConceptId:
break;
default:
Console.WriteLine($"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>
void LoadDescriptions(String path)
{
StreamReader reader = new StreamReader(File.OpenRead(path));
String[] parts = reader.ReadLine().Split('\t');
if (
(parts.Length != 9) ||
(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], "conceptId") != 0) ||
(String.Compare(parts[5], "languageCode") != 0) ||
(String.Compare(parts[6], "typeId") != 0) ||
(String.Compare(parts[7], "term") != 0) ||
(String.Compare(parts[8], "caseSignificanceId") != 0)
)
{
throw new ApplicationException("Invalid header line to description file");
}
RF2DescriptionGroup descriptionGroup = null;
while (true)
{
String line = reader.ReadLine();
if (line == null)
{
break;
}
RF2Description description = RF2Description.Parse(this, line);
if (description != null)
{
/*
* Relationships in a common group are usually grouped together, so check
* last relationship to see if it is same group first.
*/
if ((descriptionGroup != null) && (descriptionGroup.Id != description.Id))
{
descriptionGroup = null;
}
if (
(descriptionGroup == null) &&
(this.DescriptionGroups.TryGetValue(description.Id, out descriptionGroup) == false)
)
{
descriptionGroup = null;
}
if (descriptionGroup == null)
{
descriptionGroup = new RF2DescriptionGroup()
{
Parser = this,
Id = description.Id
};
if (this.DescriptionGroups.TryAdd(description.Id, descriptionGroup) == false)
{
throw new ApplicationException("Error adding description to dictionary");
}
}
descriptionGroup.AddDescription(description);
}
}
}