/// <summary>
/// Constructor
/// </summary>
/// <param name="primaryKeySuffix">String appended to the ontology term identifier when creating the primary key for the Term_PK column</param>
public clsOwlConverter(string primaryKeySuffix = DEFAULT_PRIMARY_KEY_SUFFIX)
{
if (string.IsNullOrWhiteSpace(primaryKeySuffix))
{
mPrimaryKeySuffix = string.Empty;
}
else
{
mPrimaryKeySuffix = primaryKeySuffix;
}
OutputOptions = DefaultOutputOptions();
}
public static udtOutputOptions DefaultOutputOptions()
{
var outputOptions = new udtOutputOptions()
{
IncludeDefinition = false,
StripQuotesFromDefinition = false,
IncludeComment = false,
IncludeParentTerms = true,
IncludeGrandparentTerms = true
};
return(outputOptions);
}
private bool WriteOwlInfoToFile(IReadOnlyCollection <OwlEntry> ontologyEntries, FileSystemInfo outputFile)
{
try
{
OnStatusEvent("Creating " + outputFile.FullName);
using (var writer = new StreamWriter(new FileStream(outputFile.FullName, FileMode.Create, FileAccess.Write, FileShare.ReadWrite)))
{
var columnHeaders = new List <string>
{
"Term_PK",
"Term_Name",
"Identifier",
"Is_Leaf",
"Synonyms"
};
if (OutputOptions.IncludeDefinition)
{
columnHeaders.Add("Definition");
}
if (OutputOptions.IncludeComment)
{
columnHeaders.Add("Comment");
}
if (OutputOptions.IncludeGrandparentTerms && !OutputOptions.IncludeParentTerms)
{
// Force-enable inclusion of parent terms because grandparent terms will be included
var updatedOptions = OutputOptions;
updatedOptions.IncludeParentTerms = true;
OutputOptions = updatedOptions;
}
if (OutputOptions.IncludeParentTerms)
{
columnHeaders.Add("Parent_term_name");
columnHeaders.Add("Parent_term_ID");
}
if (OutputOptions.IncludeGrandparentTerms)
{
columnHeaders.Add("GrandParent_term_name");
columnHeaders.Add("GrandParent_term_ID");
}
writer.WriteLine(string.Join("\t", columnHeaders));
var idToNameMap = new Dictionary <string, string>();
// Make a map from term ID to term Name
var warningCount = 0;
foreach (var ontologyTerm in ontologyEntries)
{
if (idToNameMap.ContainsKey(ontologyTerm.Identifier))
{
warningCount++;
if (warningCount < 5)
{
OnWarningEvent(
$"Identifier {ontologyTerm.Identifier} is defined multiple times in th ontology entries; " +
"parent name lookup will use the first occurrence");
}
continue;
}
idToNameMap.Add(ontologyTerm.Identifier, ontologyTerm.Name);
}
foreach (var ontologyTerm in ontologyEntries)
{
if (ontologyTerm.ParentTerms.Count == 0 || !OutputOptions.IncludeParentTerms)
{
var lineOut = OntologyTermNoParents(ontologyTerm);
if (OutputOptions.IncludeParentTerms)
{
lineOut.Add(string.Empty); // Parent term name
lineOut.Add(string.Empty); // Parent term ID
}
writer.WriteLine(string.Join("\t", lineOut));
continue;
}
foreach (var parentTerm in ontologyTerm.ParentTerms)
{
var ancestor = GetAncestor(ontologyEntries, parentTerm.Key);
if (ancestor == null || ancestor.ParentTerms.Count == 0 || !OutputOptions.IncludeGrandparentTerms)
{
// No grandparents (or grandparents are disabled)
var lineOut = OntologyTermWithParents(ontologyTerm, parentTerm, idToNameMap);
if (OutputOptions.IncludeGrandparentTerms)
{
lineOut.Add(string.Empty); // Grandparent term name
lineOut.Add(string.Empty); // Grandparent term ID
}
writer.WriteLine(string.Join("\t", lineOut));
continue;
}
foreach (var grandParent in ancestor.ParentTerms)
{
var lineOut = OntologyTermWithParents(ontologyTerm, parentTerm, idToNameMap);
lineOut.Add(LookupNameById(idToNameMap, grandParent.Key)); // Get Grandparent Name using ID
lineOut.Add(grandParent.Key); // Grandparent ID
writer.WriteLine(string.Join("\t", lineOut));
}
} // ForEach
} // ForEach
} // Using
return(true);
}
catch (Exception ex)
{
OnErrorEvent("Error writing to file " + outputFile.FullName + ": " + ex.Message);
return(false);
}
}
