public static EnumsByWikiId CreateFrom(AopWikiDbContext context)
{
return(new EnumsByWikiId
{
LifeStages = context
.LifeStageTerms
.MapToLookupTable <LifeStageTerm, applicabilitytypeLifestageLifestage>(),
Sexes = context
.SexTerms
.MapToLookupTable <SexTerm, applicabilitytypeSexSex>(),
BiologicalOrganizations = context
.BiologicalOrganizations
.MapToLookupTable <BiologicalOrganization, biologicalorganizationleveltype>(),
ConfidenceLevels = context
.ConfidenceLevels
.MapToLookupTable <ConfidenceLevel, confidenceleveltype>(),
WikiStatuses = context
.Statuses
.MapToLookupTable(
new Dictionary <string, statusWikistatus>
{
["Open for adopton"] = statusWikistatus.Openforadoption
}),
OecdStatuses = context
.OecdStatuses
.MapToLookupTable <OecdStatus, statusOecdstatus>(),
SaaopStatuses = context
.SaaopStatuses
.MapToLookupTable <SaaopStatus, statusSaaopstatus>()
});
}
public void WriteToOutput(Stream output)
{
if (output == null)
{
throw new ArgumentNullException(nameof(output));
}
using (var context = new AopWikiDbContext(this._connectionString)
{
ChangeTracker = { AutoDetectChangesEnabled = false }
})
using (var tx = context.Database.BeginTransaction())
{
var enumsByWikiId = EnumsByWikiId.CreateFrom(context);
var data = new data();
var biologicalProcessesByWikiId = context.BiologicalProcesses
.Select(x => x.MapToSchema())
.ToList()
.ToDictionary(x => x.GetWikiId(), x => x);
var biologicalActionsByWikiId = context.BiologicalActions
.Select(x => x.MapToSchema())
.ToList()
.ToDictionary(x => x.GetWikiId(), x => x);
var taxonomyMapper = new TaxonomyMapper(context.TaxonTerms);
var uniqueTaxonomiesByXmlId = taxonomyMapper.GetUniqueMappedObjectsByXmlId();
var uniqueTaxonomies = uniqueTaxonomiesByXmlId.Values;
var chemicalsByWikiId = context.Chemicals
.MapToSchema(context.ChemicalSynonyms)
.ToDictionary(x => x.GetWikiId(), x => x);
var stressorsByWikiId = context.Stressors
.MapToSchema(chemicalsByWikiId)
.ToDictionary(x => x.GetWikiId(), x => x);
var cellTermsByWikiId = context.CellTerms
.ToList()
.Select(x => x.MapToSchema())
.ToDictionary(x => x.GetWikiId(), x => x);
var organTermsByWikiId = context.OrganTerms
.ToList()
.Select(x => x.MapToSchema())
.ToDictionary(x => x.GetWikiId(), x => x);
var biologicalObjectsByWikiId = context.BiologicalObjects
.Select(x => x.MapToSchema(enumsByWikiId.BiologicalOrganizations))
.ToList()
.ToDictionary(x => x.GetWikiId(), x => x);
var keyEventsByWikiId = context
.Events
.MapToSchema(
organTermsByWikiId,
cellTermsByWikiId,
biologicalObjectsByWikiId,
biologicalProcessesByWikiId,
biologicalActionsByWikiId,
enumsByWikiId,
taxonomyMapper,
stressorsByWikiId)
.ToDictionary(x => x.GetWikiId(), x => x);
var keyEventRelationshipsByWikiId = context
.Relationships
.MapToSchema(keyEventsByWikiId)
.ToDictionary(x => x.GetWikiId(), x => x);
var aopsByWikiId = context
.Aops
.MapToSchema(
context.AopEvents,
keyEventsByWikiId,
keyEventRelationshipsByWikiId,
stressorsByWikiId,
taxonomyMapper,
enumsByWikiId)
.ToDictionary(x => x.GetWikiId(), x => x);
IReadOnlyCollection <dataAop> targetAops = aopsByWikiId.Values;
if (this._excludeUnreferencedElements)
{
if (this._targetType == TargetType.Aop &&
this._targetId.HasValue &&
aopsByWikiId.TryGetValue(this._targetId.Value, out var matchedAop))
{
targetAops = new[] { matchedAop };
}
else if (this._targetType == TargetType.KeyEvent)
{
targetAops = new dataAop[0];
}
keyEventRelationshipsByWikiId = targetAops.SelectMany(x => x.keyeventrelationships)
.Where(x => x != null)
.GroupBy(x => x.id)
.Select(x => x.First())
.ToDictionary(x => x.GetWikiId(), x => keyEventRelationshipsByWikiId[x.GetWikiId()]);
keyEventsByWikiId = this._targetType == TargetType.KeyEvent &&
this._targetId.HasValue &&
keyEventsByWikiId.TryGetValue(this._targetId.Value, out var matchedKeyEvent)
? new Dictionary <int, dataKeyevent> {
[this._targetId.Value] = matchedKeyEvent
}
: targetAops
.SelectMany(
x => (x.molecularinitiatingevent?.Select(m => m?.GetWikiId() ?? 0) ?? new int[0])
.Union(x.adverseoutcome?.Select(a => a?.GetWikiId() ?? 0) ?? new int[0])
.Union(x.keyeventessentialities?.Select(e => e?.GetWikiId() ?? 0) ?? new int[0]))
.Union(
keyEventRelationshipsByWikiId
.Values
.SelectMany(
k => new[]
{
k.title?.upstreamid?.GetWikiId(), k.title?.downstreamid?.GetWikiId()
})
.Where(v => v != null).Select(v => v.Value))
.Distinct()
.ToDictionary(x => x, x => keyEventsByWikiId[x]);
uniqueTaxonomies = targetAops
.SelectMany(x => x.applicability?.taxonomy.Select(t => t?.taxonomyid))
.Union(
keyEventsByWikiId.Values.SelectMany(
x => x.applicability?.taxonomy.Select(t => t?.taxonomyid)))
.Distinct()
.Select(x => uniqueTaxonomiesByXmlId.TryGetValue(x, out var taxonomy) ? taxonomy : null)
.Where(x => x != null)
.ToList();
biologicalActionsByWikiId = keyEventsByWikiId.Values
.SelectMany(x => x.biologicalevents?.Select(e => e?.actionid?.GetWikiId()))
.Where(x => x.HasValue)
.Select(x => x.Value)
.Distinct()
.ToDictionary(x => x, x => biologicalActionsByWikiId[x]);
biologicalProcessesByWikiId = keyEventsByWikiId.Values
.SelectMany(x => x.biologicalevents?.Select(e => e?.processid?.GetWikiId()))
.Where(x => x.HasValue)
.Select(x => x.Value)
.Distinct()
.ToDictionary(x => x, x => biologicalProcessesByWikiId[x]);
biologicalObjectsByWikiId = keyEventsByWikiId.Values
.SelectMany(x => x.biologicalevents?.Select(e => e?.objectid?.GetWikiId()))
.Where(x => x.HasValue)
.Select(x => x.Value)
.Distinct()
.ToDictionary(x => x, x => biologicalObjectsByWikiId[x]);
stressorsByWikiId = targetAops
.SelectMany(x => x.aopstressors?.Select(s => s.GetWikiId()) ?? new int[0])
.Union(keyEventsByWikiId.Values.SelectMany(k => k.keyeventstressors?.Select(s => s.GetWikiId())))
.Distinct()
.ToDictionary(x => x, x => stressorsByWikiId[x]);
chemicalsByWikiId = stressorsByWikiId
.Values
.SelectMany(x => x.chemicals?.Select(c => c.GetWikiId()) ?? new int[0])
.Distinct()
.ToDictionary(x => x, x => chemicalsByWikiId[x]);
}
var referenceLists = new List <IEnumerable <IXmlIdentifiable> >();
biologicalProcessesByWikiId.Values.AddToReferencesAndAssignToRoot(referenceLists, data);
biologicalActionsByWikiId.Values.AddToReferencesAndAssignToRoot(referenceLists, data);
uniqueTaxonomies.AddToReferencesAndAssignToRoot(referenceLists, data);
chemicalsByWikiId.Values.AddToReferencesAndAssignToRoot(referenceLists, data);
stressorsByWikiId.Values.AddToReferencesAndAssignToRoot(referenceLists, data);
biologicalObjectsByWikiId.Values.AddToReferencesAndAssignToRoot(referenceLists, data);
keyEventsByWikiId.Values.AddToReferencesAndAssignToRoot(referenceLists, data);
keyEventRelationshipsByWikiId.Values.AddToReferencesAndAssignToRoot(referenceLists, data);
targetAops.AddToReferencesAndAssignToRoot(referenceLists, data);
data.vendorspecific = new dataVendorspecific
{
id = Guid.NewGuid().ToString(),
name = "AopWiki",
version = DateTime.UtcNow.ToString("O"),
Any = referenceLists.SelectMany(x => x, (x, i) => i.ToXmlElement()).ToArray()
};
using (var writer = XmlWriter.Create(
output,
new XmlWriterSettings
{
Indent = true,
IndentChars = " ",
ConformanceLevel = ConformanceLevel.Document,
WriteEndDocumentOnClose = true,
NamespaceHandling = NamespaceHandling.OmitDuplicates,
NewLineChars = "\n",
Encoding = Encoding.UTF8,
CloseOutput = false,
NewLineOnAttributes = false
}))
{
// Gets rid of xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:xsd="http://www.w3.org/2001/XMLSchema"
var namespaces = new XmlSerializerNamespaces();
namespaces.Add(
string.Empty,
typeof(data).GetTypeInfo().GetCustomAttribute <XmlTypeAttribute>()?.Namespace
?? string.Empty);
var rootSerializer = new XmlSerializer(data.GetType());
rootSerializer.Serialize(writer, data, namespaces);
}
tx.Commit();
}
}
