/// <summary>
/// Add snomed query concept to model manager.
/// </summary>
/// <param name="concept"></param>
public void Add(SnomedQueryConcept concept)
{
if (this.snomedConcepts.TryAdd(concept.ConceptId, concept) == false)
{
throw new ApplicationException($"Error adding concept {concept.ConceptId} to dictionary.`");
}
}
/// <summary>
/// Return true if parent is an ancestor of child
/// </summary>
/// <param name="parentID"></param>
/// <param name="childID"></param>
/// <returns></returns>
public bool IsChild(Int64 parentID, Int64 childID)
{
SnomedQueryConcept parent = this.GetConceptById(parentID);
ConcurrentDictionary <Int64, SnomedQueryConcept> visitedItems = new ConcurrentDictionary <long, SnomedQueryConcept>();
return(this.IsChild(visitedItems, parent, childID));
}
/// <summary>
/// Return Descendant concepts of parent, does not include parent.
/// </summary>
/// <param name="parentID"></param>
/// <returns></returns>
public SnomedQueryConcept[] FindDecendents(Int64 currentId)
{
SnomedQueryConcept currentConcept = this.GetConceptById(currentId);
ConcurrentDictionary <Int64, SnomedQueryConcept> decendentIDs = new ConcurrentDictionary <Int64, SnomedQueryConcept>();
this.FindDecendents(decendentIDs, currentConcept);
SnomedQueryConcept[] retVal = new SnomedQueryConcept[decendentIDs.Count];
decendentIDs.Values.CopyTo(retVal, 0);
return(retVal);
}
/// <summary>
/// Return Ancestors concepts of parent, does not include parent.
/// </summary>
/// <param name="parentID"></param>
/// <returns></returns>
public SnomedQueryConcept[] FindAncestors(Int64 currentId)
{
SnomedQueryConcept currentConcept = this.GetConceptById(currentId);
ConcurrentDictionary <Int64, SnomedQueryConcept> ancestorIDs = new ConcurrentDictionary <Int64, SnomedQueryConcept>();
this.FindAncestors(ancestorIDs, currentConcept);
SnomedQueryConcept[] retVal = new SnomedQueryConcept[ancestorIDs.Count];
ancestorIDs.Values.CopyTo(retVal, 0);
return(retVal);
}
/// <summary>
/// Link up parent/child relationships
/// </summary>
/// <param name="relationshipReader">Read relationship data from this stream</param>
/// <param name="concept">Concept to set child relationship data for</param>
/// <returns>Newly created snomed query concept instance</returns>
void DeserializeConceptRelationships(BinaryReader relationshipReader,
SnomedQueryConcept concept)
{
for (Int32 i = 0; i < concept.IsAChildren.Length; i++)
{
Int64 childConceptId = this.ReadInt64(relationshipReader);
SnomedQueryConcept child = this.GetConceptById(childConceptId);
concept.IsAChildren[i] = child;
child.IsAParents[this.ReadInt32(relationshipReader)] = concept;
}
}
/// <summary>
/// Collect child IDs of parent and continue visitor pattern onward with children.
/// </summary>
/// <param name="visitedItems">Items already visited. Dont go there again</param>
/// <param name="ancestors">All IDs of parents visited from public FindAncestors.</param>
/// <param name="parent">parent concept</param>
/// <returns></returns>
void FindAncestors(ConcurrentDictionary <Int64, SnomedQueryConcept> visitedItems,
SnomedQueryConcept thisConcept)
{
foreach (SnomedQueryConcept parent in thisConcept.IsAParents)
{
// If we have not visited this before.
if (visitedItems.TryAdd(parent.ConceptId, parent) == true)
{
this.FindAncestors(visitedItems, parent);
}
}
}
/// <summary>
/// Collect child IDs of parent and continue visitor pattern onward with children.
/// </summary>
/// <param name="visitedItems">Items already visited. Dont go there again</param>
/// <param name="decendents">All IDs of children visited from public FindDecendents.</param>
/// <param name="parent">parent concept</param>
/// <returns></returns>
void FindDecendents(ConcurrentDictionary <Int64, SnomedQueryConcept> visitedItems,
SnomedQueryConcept thisConcept)
{
foreach (SnomedQueryConcept child in thisConcept.IsAChildren)
{
// If we have not visited this before.
if (visitedItems.TryAdd(child.ConceptId, child) == true)
{
this.FindDecendents(visitedItems, child);
}
}
}
/// <summary>
/// Serialize the data part of the snomed concept instance.
/// </summary>
/// <param name="dataWriter">Write conept data to this stream</param>
/// <param name="relationshipWriter">Write IsA relationships to this stream</param>
/// <param name="snomedConcept"></param>
void SerializeConcept(BinaryWriter dataWriter,
BinaryWriter relationshipWriter,
SnomedQueryConcept snomedConcept)
{
this.Write(dataWriter, snomedConcept.ConceptId);
this.Write(dataWriter, snomedConcept.ConceptFullyQualifiedName);
this.Write(dataWriter, snomedConcept.ConceptSynonymns);
this.Write(dataWriter, snomedConcept.ConceptModule);
this.Write(dataWriter, snomedConcept.ConceptDefinitionStatus);
this.Write(dataWriter, snomedConcept.ConceptEffectiveTime.Ticks);
// Write out length of parent/child relationship arrays.
this.Write(dataWriter, snomedConcept.IsAParents.Length);
this.Write(dataWriter, snomedConcept.IsAChildren.Length);
/*
* This is a bit obtuse.
* To avoid unnecessary dictionary lookups, we serialize the isa data as follows.
* a) Only isa children are serialized. The parent fields are derived from the
* children values.
* b) The children id are serialized, and the offset in the childs parent relationship
* array is serialized. This makes it possible to deserialice quickly, but serialization
* is very much slower.
*/
// Output number of values in child list.
for (Int32 i = 0; i < snomedConcept.IsAChildren.Length; i++)
{
SnomedQueryConcept child = snomedConcept.IsAChildren[i];
this.Write(relationshipWriter, child.ConceptId);
Int32 reverseIndex = -1;
for (Int32 j = 0; j < child.IsAParents.Length; j++)
{
if (child.IsAParents[j] == snomedConcept)
{
reverseIndex = j;
break;
}
}
// If reverseIndex < 1, then the child record did not have a corresponding
// link to the parent. This is an error.
if (reverseIndex == -1)
{
throw new ApplicationException("Reverse snomed index not found");
}
this.Write(relationshipWriter, reverseIndex);
}
}
/// <summary>
/// Deserialize all records serialized in Serialize().
/// </summary>
public void Deserialize()
{
// Keep list of concepts read in, in the SAME ORDER they are read in.
// This is used later to link up relationships.
LinkedList <SnomedQueryConcept> list = new LinkedList <SnomedQueryConcept>();
// Read in conept data. This does not read in relationships, though the
// relationship arrays are resized properly.
String dataPath = Path.Combine(this.ParsedRecordsDir, "SnomedQueryConcepts.Data.ser");
dataPath = Path.GetFullPath(dataPath);
using (Stream inStream = new FileStream(dataPath, FileMode.Open, FileAccess.Read, FileShare.Read))
{
using (BinaryReader dataReader = new BinaryReader(inStream))
{
Int32 conceptCount = this.ReadInt32(dataReader);
for (Int32 i = 0; i < conceptCount; i++)
{
SnomedQueryConcept concept = this.DeserializeConceptData(dataReader);
this.Add(concept);
list.AddLast(concept);
}
}
}
// Read in relationship and link concepts togother. This must be done after all concepts
// have been created so we can access the parent and child objects (cant point to object
// that doesn't exist yet...)
using (Stream inStream = new FileStream(
Path.Combine(this.ParsedRecordsDir, "SnomedQueryConcepts.IsARelationships.ser"),
FileMode.Open,
FileAccess.Read,
FileShare.Read))
{
using (BinaryReader relationshipReader = new BinaryReader(inStream))
{
foreach (SnomedQueryConcept concept in list)
{
this.DeserializeConceptRelationships(relationshipReader, concept);
}
}
}
}
/// <summary>
/// Return true if concept with child id is a child of parent.
/// </summary>
/// <param name="visitedItems">Items already visited. Dont go there again</param>
/// <param name="parent">parent concept</param>
/// <param name="childID">child concept id to search for</param>
/// <returns></returns>
bool IsChild(ConcurrentDictionary <Int64, SnomedQueryConcept> visitedItems,
SnomedQueryConcept parent,
Int64 childID)
{
foreach (SnomedQueryConcept child in parent.IsAChildren)
{
// If we have not visited this before.
if (visitedItems.TryAdd(child.ConceptId, child) == true)
{
if (child.ConceptId == childID)
{
return(true);
}
if (this.IsChild(visitedItems, child, childID) == true)
{
return(true);
}
}
}
return(false);
}
/// <summary>
/// Return snomed concept record with its data initialized from the serial input file.
/// The is a links are not set yet.
/// </summary>
/// <param name="binaryReader"></param>
/// <returns>Newly created snomed query concept instance</returns>
SnomedQueryConcept DeserializeConceptData(BinaryReader binaryReader)
{
SnomedQueryConcept retVal = new SnomedQueryConcept(
this.ReadInt64(binaryReader), // conceptId
this.ReadString(binaryReader), // conceptFullyQualifiedName,
this.ReadStringArray(binaryReader), // conceptSynonymns,
this.ReadString(binaryReader), // conceptModule,
this.ReadString(binaryReader), // conceptDefinitionStatus,
this.ReadDateTime(binaryReader) // conceptEffectiveTime);
);
// Set length of parent/child arrays. The actual values in the array will be set later.
{
Int32 count = this.ReadInt32(binaryReader);
retVal.IsAParents = new SnomedQueryConcept[count];
}
{
Int32 count = this.ReadInt32(binaryReader);
retVal.IsAChildren = new SnomedQueryConcept[count];
}
return(retVal);
}