/// <summary>
/// Determine if the concept set contains the specified concept
/// </summary>
public bool IsMember(ConceptSet set, Concept concept)
{
var persistence = ApplicationContext.Current.GetService <IDataPersistenceService <ConceptSet> >();
if (persistence == null)
{
throw new InvalidOperationException("Cannot locate concept set persistence service");
}
return(persistence.Count(o => o.Concepts.Any(c => c.Key == concept.Key)) > 0);
}
/// <summary>
/// Initializes a new instance of the <see cref="EditConceptSetModel"/> class
/// with a specific <see cref="ConceptSet"/> instance.
/// </summary>
/// <param name="conceptSet">The <see cref="ConceptSet"/> instance.</param>
public EditConceptSetModel(ConceptSet conceptSet) : this()
{
Concepts = conceptSet.Concepts.Select(c => new ConceptViewModel(c, conceptSet.Key ?? Guid.Empty)).ToList();
CreationTime = conceptSet.CreationTime.DateTime;
Id = conceptSet.Key ?? Guid.Empty;
Mnemonic = conceptSet.Mnemonic;
Name = conceptSet.Name;
Oid = conceptSet.Oid;
Url = conceptSet.Url;
}
public bool IsMember(ConceptSet set, Concept concept)
{
var persistence = ApplicationServiceContext.Current.GetService <IDataPersistenceService <ConceptSet> >();
if (persistence == null)
{
throw new InvalidOperationException($"{nameof(IDataPersistenceService<ConceptSet>)} not found");
}
return(persistence.Count(o => o.Key == set.Key && o.ConceptsXml.Any(c => c == concept.Key)) > 0);
}
public ConceptSet InsertConceptSet(ConceptSet set)
{
var persistenceService = ApplicationContext.Current.GetService <IDataPersistenceService <ConceptSet> >();
if (persistenceService == null)
{
throw new InvalidOperationException($"{nameof(IDataPersistenceService<ConceptSet>)} not found");
}
return(persistenceService.Insert(set, AuthenticationContext.Current.Principal, TransactionMode.Commit));
}
/// <summary>
/// Initializes a new instance of the <see cref="ConceptSetViewModel"/> class.
/// </summary>
/// <param name="conceptSet"></param>
/// <param name="loadConcepts">State that determines if Concepts associated with a Concept Set are loaded</param>
public ConceptSetViewModel(ConceptSet conceptSet, bool loadConcepts = false) : this()
{
if (loadConcepts)
{
Concepts = conceptSet.Concepts.Select(c => new ConceptViewModel(c)).ToList();
}
CreationTime = conceptSet.CreationTime.DateTime;
Id = conceptSet.Key ?? Guid.Empty;
Mnemonic = conceptSet.Mnemonic;
Name = conceptSet.Name;
Oid = conceptSet.Oid;
Url = conceptSet.Url;
}
public bool IsMember(ConceptSet set, Concept concept)
{
var persistence = ApplicationServiceContext.Current.GetService <IDataPersistenceService <ConceptSet> >();
if (persistence == null)
{
throw new InvalidOperationException(this.m_localizationService.FormatString("error.server.core.servicePersistence", new
{
param = nameof(IDataPersistenceService <ConceptSet>)
}));
}
return(persistence.Count(o => o.Key == set.Key && o.ConceptsXml.Any(c => c == concept.Key)) > 0);
}
public ActionResult Create(CreateConceptSetModel model)
{
try
{
var exists = this.ImsiClient.Query <ConceptSet>(c => c.Oid == model.Oid).Item.OfType <ConceptSet>().Any();
if (exists)
{
ModelState.AddModelError("Oid", Locale.OidMustBeUnique);
}
var duplicate = this.ImsiClient.Query <ConceptSet>(c => c.Mnemonic == model.Mnemonic).Item.OfType <ConceptSet>().Any();
if (duplicate)
{
ModelState.AddModelError("Mnemonic", Locale.MnemonicMustBeUnique);
}
if (ModelState.IsValid)
{
var conceptSet = new ConceptSet
{
Mnemonic = model.Mnemonic,
Name = model.Name,
Url = model.Url,
Oid = model.Oid,
Key = Guid.NewGuid()
};
var result = this.ImsiClient.Create <ConceptSet>(conceptSet);
TempData["success"] = Locale.ConceptSetCreatedSuccessfully;
return(RedirectToAction("ViewConceptSet", new { id = result.Key }));
}
}
catch (Exception e)
{
Trace.TraceError($"Unable to create concept set: {e}");
}
TempData["error"] = Locale.UnableToCreateConceptSet;
return(View(model));
}
/// <summary>
/// Converts an <see cref="EditConceptSetModel" /> instance to a <see cref="ConceptSet" /> instance.
/// </summary>
/// <param name="conceptSet">The concept set.</param>
/// <returns>Returns the converted concept set.</returns>
public ConceptSet ToConceptSet(ConceptSet conceptSet)
{
conceptSet.Mnemonic = this.Mnemonic;
conceptSet.Name = this.Name;
conceptSet.Oid = this.Oid;
conceptSet.Url = this.Url;
if (!this.AddConcepts.Any())
{
return(conceptSet);
}
foreach (var concept in this.AddConcepts)
{
Guid id;
if (Guid.TryParse(concept, out id))
{
conceptSet.ConceptsXml.Add(id);
}
}
return(conceptSet);
}
public static void PhinVadsToDataset(String[] args)
{
var options = new ParameterParser <CvxOptions>().Parse(args);
DatasetInstall conceptDataset = new DatasetInstall();
using (var sr = File.OpenText(options.Input))
{
// Consume the first line
sr.ReadLine();
var components = sr.ReadLine().Split('\t');
// Next line is the value set information
// Create code concept set
var conceptSet = new ConceptSet()
{
Key = Guid.NewGuid(),
Mnemonic = options.ConceptSetName ?? components[1],
Name = options.ConceptSetDescription ?? components[0],
Oid = options.ConceptSetOid ?? components[2],
CreationTime = DateTime.Parse(String.IsNullOrEmpty(components[6]) ? DateTime.Now.ToString() : components[6]),
Url = !String.IsNullOrEmpty(options.ConceptSetName) ? "http://openiz.org/conceptset/" + options.ConceptSetName :
"http://openiz.org/conceptsets/contrib/" + components[1]
};
Dictionary <String, CodeSystem> codeSystems = new Dictionary <string, CodeSystem>();
// Consume the next set of lines
while (!sr.ReadLine().StartsWith("Concept Code"))
{
;
}
while (!sr.EndOfStream)
{
components = sr.ReadLine().Split('\t');
// Try to get the code system
CodeSystem codeSys = null;
if (!codeSystems.TryGetValue(components[4], out codeSys))
{
codeSys = new CodeSystem()
{
Key = Guid.NewGuid(),
Authority = components[8],
Name = components[6],
Oid = components[4],
Description = components[5],
CreationTime = conceptSet.CreationTime
};
codeSystems.Add(codeSys.Oid, codeSys);
conceptDataset.Action.Add(new DataUpdate()
{
InsertIfNotExists = true,
Element = codeSys
});
}
// Insert the code
var refTerm = new ReferenceTerm()
{
Key = Guid.NewGuid(),
CodeSystemKey = codeSys.Key,
CreationTime = conceptSet.CreationTime,
DisplayNames = new List <ReferenceTermName>()
{
new ReferenceTermName()
{
Name = components[1],
Language = "en"
}
},
Mnemonic = components[0]
};
var concept = new Concept()
{
Key = Guid.NewGuid(),
Mnemonic = components[6] + "-" + components[1].Replace("[", "").Replace("]", "").Replace("-", "").Replace(" ", ""),
CreationTime = conceptSet.CreationTime,
StatusConceptKey = StatusKeys.Active,
ClassKey = ConceptClassKeys.Other,
ConceptNames = new List <ConceptName>()
{
new ConceptName()
{
Name = components[1],
Language = "en"
}
},
ReferenceTerms = new List <ConceptReferenceTerm>()
{
new ConceptReferenceTerm()
{
ReferenceTermKey = refTerm.Key,
RelationshipTypeKey = ConceptRelationshipTypeKeys.SameAs
}
}
};
conceptDataset.Action.Add(new DataUpdate()
{
InsertIfNotExists = true, Element = refTerm
});
conceptDataset.Action.Add(new DataUpdate()
{
InsertIfNotExists = true, Element = concept
});
conceptSet.ConceptsXml.Add(concept.Key.Value);
}
conceptDataset.Action.Add(new DataUpdate()
{
InsertIfNotExists = true, Element = conceptSet
});
}
XmlSerializer xsz = new XmlSerializer(typeof(DatasetInstall));
using (FileStream fs = File.Create(options.Output))
xsz.Serialize(fs, conceptDataset);
}
public ConceptSet SaveConceptSet(ConceptSet set)
{
throw new NotImplementedException();
}
/// <summary>
/// Create the specified concept st
/// </summary>
public ConceptSet InsertConceptSet(ConceptSet set)
{
throw new NotImplementedException();
}
/// <summary>
/// Create a value from an Everest enum
/// </summary>
/// TODO: Optimize this
private ValueSet CreateValueFromEverestEnum(Type enumType)
{
StructureAttribute structAtt = enumType.GetCustomAttribute <StructureAttribute>();
var baseUri = WebOperationContext.Current.IncomingRequest.UriTemplateMatch.BaseUri.ToString();
ValueSet retVal = new ValueSet();
retVal.Name = structAtt.Name;
retVal.Identifier = structAtt.CodeSystem;
retVal.Id = retVal.Identifier;
// Use the company attribute
var companyAtt = enumType.Assembly.GetCustomAttribute <AssemblyCompanyAttribute>();
if (companyAtt != null)
{
retVal.Publisher = companyAtt.Company;
}
var versionAtt = enumType.Assembly.GetCustomAttribute <AssemblyInformationalVersionAttribute>();
if (versionAtt != null)
{
retVal.Version = versionAtt.InformationalVersion;
}
retVal.VersionId = retVal.Version;
// Date of the assembly file
if (!String.IsNullOrEmpty(enumType.Assembly.Location) && File.Exists(enumType.Assembly.Location))
{
retVal.Date = new SVC.Messaging.FHIR.DataTypes.DateOnly()
{
DateValue = new FileInfo(enumType.Assembly.Location).LastWriteTime
}
}
;
retVal.Timestamp = retVal.Date.DateValue.Value;
retVal.Status = new SVC.Messaging.FHIR.DataTypes.PrimitiveCode <string>("published");
// Compose the codes if it has codes from a known code system
var enumFields = enumType.GetFields();
bool hasRegisteredCodes = Array.Exists(enumFields, (f) =>
{
var enumAtt = f.GetCustomAttribute <EnumerationAttribute>();
if (enumAtt != null)
{
return(ApplicationContext.ConfigurationService.OidRegistrar.FindData(enumAtt.SupplierDomain) != null);
}
else
{
return(false);
}
}), hasDifferentSuppliers = Array.Exists(enumFields, (f) => {
var enumAtt = f.GetCustomAttribute <EnumerationAttribute>();
if (enumAtt != null)
{
return(Array.Exists(enumFields, (fi) =>
{
var ienumAtt = fi.GetCustomAttribute <EnumerationAttribute>();
if (ienumAtt != null)
{
return ienumAtt.SupplierDomain != enumAtt.SupplierDomain;
}
return false;
}));
}
else
{
return(false);
}
});
// Compose or define
var sysOid = ApplicationContext.ConfigurationService.OidRegistrar.FindData(retVal.Identifier);
if (sysOid != null)
{
retVal.Compose = new ComposeDefinition();
retVal.Compose.Import.Add(new SVC.Messaging.FHIR.DataTypes.FhirUri(sysOid.Ref));
}
else if (hasRegisteredCodes || hasDifferentSuppliers)
{
retVal.Compose = new ComposeDefinition();
// Group like items
Array.Sort(enumFields, (a, b) =>
{
EnumerationAttribute aAtt = a.GetCustomAttribute <EnumerationAttribute>(),
bAtt = b.GetCustomAttribute <EnumerationAttribute>();
if ((aAtt == null) ^ (bAtt == null))
{
return(aAtt == null ? -1 : 1);
}
else if (aAtt == bAtt)
{
return(0);
}
return(aAtt.SupplierDomain.CompareTo(bAtt.SupplierDomain));
});
// Build the concept sets
ConceptSet currentSet = null;
foreach (var itm in enumFields)
{
EnumerationAttribute enumValue = itm.GetCustomAttribute <EnumerationAttribute>();
if (enumValue == null)
{
continue;
}
// Extract code system
var oidData = ApplicationContext.ConfigurationService.OidRegistrar.FindData(enumValue.SupplierDomain);
Uri codeSystem = oidData == null ? new Uri(String.Format("urn:oid:{0}", enumValue.SupplierDomain)) : oidData.Ref;
// add current set and construct
if (currentSet == null || !currentSet.System.Value.Equals(codeSystem))
{
currentSet = new ConceptSet()
{
System = codeSystem
};
retVal.Compose.Include.Add(currentSet);
}
// Now add mnemonic
currentSet.Code.Add(new SVC.Messaging.FHIR.DataTypes.PrimitiveCode <string>(enumValue.Value));
}
}
else
{
// Create a definition for a valueset
retVal.Define = new ValueSetDefinition();
retVal.Define.System = new Uri(String.Format("{0}/ValueSet/@v3-{1}", baseUri, structAtt.Name));
foreach (var itm in enumFields)
{
EnumerationAttribute enumValue = itm.GetCustomAttribute <EnumerationAttribute>();
if (enumValue == null)
{
continue;
}
DescriptionAttribute description = itm.GetCustomAttribute <DescriptionAttribute>();
retVal.Define.Concept.Add(new ConceptDefinition()
{
Code = new SVC.Messaging.FHIR.DataTypes.PrimitiveCode <string>(enumValue.Value),
Abstract = false,
Display = description == null ? itm.Name : description.Description
});
}
}
return(retVal);
}
}
/// <summary>
/// Checks of the selected concept is already in the concept set list
/// </summary>
/// <returns>Returns true if the selected concept exists, false if not found</returns>
public bool HasSelectedConcept(ConceptSet conceptSet)
{
return(AddConcepts.Any() && conceptSet.Concepts.Any(c => c.Key.ToString().Equals(AddConcepts[0])));
}