public static IReadOnlyCollection <dataKeyevent> MapToSchema(
this IQueryable <Event> events,
IReadOnlyDictionary <int, biologicaltermtype> organTermsByWikiId,
IReadOnlyDictionary <int, biologicaltermtype> cellTermsByWikiId,
IReadOnlyDictionary <int, dataBiologicalobject> biologicalObjectsByWikiId,
IReadOnlyDictionary <int, dataBiologicalprocess> biologicalProcessesByWikiId,
IReadOnlyDictionary <int, dataBiologicalaction> biologicalActionsByWikiId,
EnumsByWikiId enumsByWikiId,
TaxonomyMapper taxonomies,
IReadOnlyDictionary <int, dataStressor> stressorsByWikiId)
{
if (events == null)
{
throw new ArgumentNullException(nameof(events));
}
if (organTermsByWikiId == null)
{
throw new ArgumentNullException(nameof(organTermsByWikiId));
}
if (cellTermsByWikiId == null)
{
throw new ArgumentNullException(nameof(cellTermsByWikiId));
}
if (biologicalObjectsByWikiId == null)
{
throw new ArgumentNullException(nameof(biologicalObjectsByWikiId));
}
if (biologicalProcessesByWikiId == null)
{
throw new ArgumentNullException(nameof(biologicalProcessesByWikiId));
}
if (biologicalActionsByWikiId == null)
{
throw new ArgumentNullException(nameof(biologicalActionsByWikiId));
}
if (enumsByWikiId == null)
{
throw new ArgumentNullException(nameof(enumsByWikiId));
}
if (taxonomies == null)
{
throw new ArgumentNullException(nameof(taxonomies));
}
if (stressorsByWikiId == null)
{
throw new ArgumentNullException(nameof(stressorsByWikiId));
}
return(events.Select(
x => new dataKeyevent
{
id = Guid.NewGuid().ToString(),
title = x.Title,
shortname = x.ShortName,
description = x.HowItWorks,
measurementmethodology = x.MeasuredOrDetected,
evidencesupportingtaxonomicapplicability = x.SupportingTaxEvidence,
references = x.References,
organterm = x.OrganTermId.HasValue
? organTermsByWikiId[x.OrganTermId.Value]
: null,
cellterm = x.CellTermId.HasValue
? cellTermsByWikiId[x.CellTermId.Value]
: null,
biologicalevents = x.EventSubEvents.Select(
s => new dataKeyeventBiologicalevent
{
objectid = s.SubEvent.BiologicalObjectId.HasValue
? biologicalObjectsByWikiId[s.SubEvent.BiologicalObjectId.Value].id
.SetWikiId(s.SubEvent.BiologicalObjectId.Value)
: null,
processid = s.SubEvent.BiologicalProcessId.HasValue
? biologicalProcessesByWikiId[s.SubEvent.BiologicalProcessId.Value].id
.SetWikiId(s.SubEvent.BiologicalProcessId.Value)
: null,
actionid = s.SubEvent.BiologicalActionId.HasValue
? biologicalActionsByWikiId[s.SubEvent.BiologicalActionId.Value].id
.SetWikiId(s.SubEvent.BiologicalActionId.Value)
: null
})
.ToArray(),
biologicalorganizationlevel = x.BiologicalOrganizationId.HasValue
? enumsByWikiId.BiologicalOrganizations[x.BiologicalOrganizationId.Value]
: default(biologicalorganizationleveltype),
biologicalorganizationlevelSpecified = x.BiologicalOrganizationId.HasValue,
applicability = new applicabilitytype
{
sex = x.EventSexes
.Where(s => s.SexTermId.HasValue)
.Select(
s => new applicabilitytypeSex
{
sex = enumsByWikiId.Sexes[s.SexTermId.Value],
evidence = s.EvidenceId.HasValue
? enumsByWikiId.ConfidenceLevels[s.EvidenceId.Value]
: confidenceleveltype.NotSpecified
})
.ToArray(),
lifestage = x.EventLifeStages
.Where(l => l.LifeStageTermId.HasValue)
.Select(
l => new applicabilitytypeLifestage
{
lifestage = enumsByWikiId.LifeStages[l.LifeStageTermId.Value],
evidence = l.EvidenceId.HasValue
? enumsByWikiId.ConfidenceLevels[l.EvidenceId.Value]
: confidenceleveltype.NotSpecified
})
.ToArray(),
taxonomy = x.EventTaxons
.Where(t => t.TaxonTermId.HasValue)
.Select(
t => new applicabilitytypeTaxonomy
{
taxonomyid =
taxonomies.GetByAopWikiId(t.TaxonTermId.Value).id,
evidence = t.EvidenceId.HasValue
? enumsByWikiId.ConfidenceLevels[t.EvidenceId.Value]
: confidenceleveltype.NotSpecified
})
.ToArray()
},
keyeventstressors = x.EventStressors
.Where(s => s.StressorId.HasValue)
.Select(
s => new dataKeyeventKeyeventstressor
{
stressorid = stressorsByWikiId[s.StressorId.Value].id,
description = s.EvidenceText
}.SetWikiId(s.StressorId.Value))
.ToArray(),
creationtimestamp = x.CreatedAt,
creationtimestampSpecified = x.CreatedAt != default(DateTime),
lastmodificationtimestamp = x.UpdatedAt,
lastmodificationtimestampSpecified = x.UpdatedAt != default(DateTime),
evidencesupportingchemicalinitiation = x.EvidenceForChemicalInitiation, // Extension for mie
examplesusingadverseoutcome = x.ExamplesUsingAo // Extension for ao
}.SetWikiId(x.Id)
)
.ToList());
}
public static IReadOnlyCollection <dataAop> MapToSchema(
this IQueryable <Aop> aops,
IQueryable <AopEvent> aopEvents,
IReadOnlyDictionary <int, dataKeyevent> keyEventsByWikiId,
IReadOnlyDictionary <int, dataKeyeventrelationship> keyEventRelationshipsByWikiId,
IReadOnlyDictionary <int, dataStressor> stressorsByWikiId,
TaxonomyMapper taxonomies,
EnumsByWikiId enumsByWikiId)
{
if (aops == null)
{
throw new ArgumentNullException(nameof(aops));
}
if (aopEvents == null)
{
throw new ArgumentNullException(nameof(aopEvents));
}
if (keyEventsByWikiId == null)
{
throw new ArgumentNullException(nameof(keyEventsByWikiId));
}
if (keyEventRelationshipsByWikiId == null)
{
throw new ArgumentNullException(nameof(keyEventRelationshipsByWikiId));
}
if (stressorsByWikiId == null)
{
throw new ArgumentNullException(nameof(stressorsByWikiId));
}
if (taxonomies == null)
{
throw new ArgumentNullException(nameof(taxonomies));
}
if (enumsByWikiId == null)
{
throw new ArgumentNullException(nameof(enumsByWikiId));
}
return(aops.Select(
x => new dataAop
{
id = Guid.NewGuid().ToString(),
title = x.Title,
shortname = x.ShortName,
@abstract = x.Abstract,
authors = x.Authors,
overallassessment = new dataAopOverallassessment
{
description = x.OverallAssessment,
applicability = x.ApplicabilityOfTheAop,
keyeventessentialitysummary = x.KeyEventEssentiality,
weightofevidencesummary = x.WeightOfEvidenceSummary,
quantitativeconsiderations = x.QuantitativeConsiderations
},
background = x.Background,
potentialapplications = x.OptionalConsiderations,
references = x.References,
status = new status
{
wikistatus = x.StatusId.HasValue
? enumsByWikiId.WikiStatuses[x.StatusId.Value]
: statusWikistatus.UnderdevelopmentNotopenforcommentDonotcite,
oecdstatus = x.OecdStatusId.HasValue
? enumsByWikiId.OecdStatuses[x.OecdStatusId.Value]
: statusOecdstatus.UnderDevelopment,
oecdstatusSpecified = x.OecdStatusId.HasValue,
saaopstatus = x.SaaopStatusId.HasValue
? enumsByWikiId.SaaopStatuses[x.SaaopStatusId.Value]
: statusSaaopstatus.UnderDevelopment,
saaopstatusSpecified = x.SaaopStatusId.HasValue
},
applicability = new applicabilitytype
{
sex = x.AopSexes
.Where(s => s.SexTermId.HasValue)
.Select(
s => new applicabilitytypeSex
{
sex = enumsByWikiId.Sexes[s.SexTermId.Value],
evidence = s.EvidenceId.HasValue
? enumsByWikiId.ConfidenceLevels[s.EvidenceId.Value]
: confidenceleveltype.NotSpecified
})
.ToArray(),
lifestage = x.AopLifeStages
.Where(l => l.LifeStageTermId.HasValue)
.Select(
l => new applicabilitytypeLifestage
{
lifestage = enumsByWikiId.LifeStages[l.LifeStageTermId.Value],
evidence = l.EvidenceId.HasValue
? enumsByWikiId.ConfidenceLevels[l.EvidenceId.Value]
: confidenceleveltype.NotSpecified
})
.ToArray(),
taxonomy = x.AopTaxons
.Where(t => t.TaxonTermId.HasValue)
.Select(
t => new applicabilitytypeTaxonomy
{
taxonomyid =
taxonomies.GetByAopWikiId(t.TaxonTermId.Value).id,
evidence = t.EvidenceId.HasValue
? enumsByWikiId.ConfidenceLevels[t.EvidenceId.Value]
: confidenceleveltype.NotSpecified
})
.ToArray()
},
molecularinitiatingevent = aopEvents
.Where(
e => e.AopId == x.Id &&
e.Type == RelationshipType.MolecularInitiatingEvent.ToString() &&
e.EventId.HasValue)
.Select(
e => new dataAopMolecularinitiatingevent
{
keyeventid = keyEventsByWikiId[e.EventId.Value].id,
evidencesupportingchemicalinitiation = keyEventsByWikiId[e.EventId.Value]
.evidencesupportingchemicalinitiation
}.SetWikiId(e.EventId.Value))
.ToArray(),
adverseoutcome = aopEvents
.Where(
e => e.AopId == x.Id &&
e.Type == RelationshipType.AdverseOutcome.ToString() &&
e.EventId.HasValue)
.Select(
e => new dataAopAdverseoutcome
{
keyeventid = keyEventsByWikiId[e.EventId.Value].id,
examples = keyEventsByWikiId[e.EventId.Value].examplesusingadverseoutcome
}.SetWikiId(e.EventId.Value))
.ToArray(),
keyeventrelationships = x.AopRelationships
.Where(r => r.RelationshipId.HasValue && r.Directness.HasValue)
.OrderBy(r => r.RowOrder)
.Select(
r => new dataAopRelationship
{
id = keyEventRelationshipsByWikiId[r.RelationshipId.Value].id,
directness = r.Directness.Value == 0 // inverted in the sql
? dataAopRelationshipDirectness.direct
: dataAopRelationshipDirectness.indirect,
evidence = r.EvidenceId.HasValue
? enumsByWikiId.ConfidenceLevels[r.EvidenceId.Value]
: confidenceleveltype.NotSpecified,
quantitativeunderstandingvalue =
r.QuantitativeUnderstandingId.HasValue
? enumsByWikiId.ConfidenceLevels[r.QuantitativeUnderstandingId.Value]
: confidenceleveltype.NotSpecified
}.SetWikiId(r.RelationshipId.Value))
.ToArray(),
keyeventessentialities = aopEvents
.Where(e => e.AopId == x.Id && e.EventId.HasValue)
.Select(
s => new dataAopEssentiality
{
keyeventid = keyEventsByWikiId[s.EventId.Value].id,
essentialitylevel = s.EssentialityId.HasValue
? enumsByWikiId.ConfidenceLevels[s.EssentialityId.Value]
: confidenceleveltype.NotSpecified,
}.SetWikiId(s.EventId.Value)).ToArray(),
aopstressors = x.AopStressors
.Where(s => s.StressorId.HasValue)
.Select(
s => new dataAopAopstressor
{
stressorid = stressorsByWikiId[s.StressorId.Value].id,
evidence = s.EvidenceId.HasValue
? enumsByWikiId.ConfidenceLevels[s.EvidenceId.Value]
: confidenceleveltype.NotSpecified
}.SetWikiId(s.StressorId.Value))
.ToArray(),
creationtimestamp = x.CreatedAt,
lastmodificationtimestamp = x.UpdatedAt
}.SetWikiId(x.Id))
.ToList());
}
