private static IQueryable <ProteinSearchValue> GetNameSearchValues(this FaToolDbEntities entities)
{
return(entities
.GetProteinNameValues()
.Union(entities.GetSynonymValues())
.Union(entities.GetTranscriptIDValues()));
}
public static TEntity Init <TEntity, TKey>(this FaToolDbEntities ctx, TKey id)
where TEntity : class, IEntity <TKey>
{
var entity = ctx.Create <TEntity>();
entity.ID = id;
entity.RowVersion = new byte[8];
return(entity);
}
public static IQueryable <ProteinSearchValue> GetProteinSearchValues(
this FaToolDbEntities entities,
ProteinSearchOption option,
string organismId)
{
return(from p in entities.GetSourceProteins()
join pv in entities.GetProteinSearchValues(option) on p.ProteinID equals pv.ProteinID
where p.SourceOrganismID == organismId
select pv);
}
private static IQueryable <SourceProtein> GetSourceProteins(this FaToolDbEntities entities)
{
var query = from gm in entities.GeneModels
select new SourceProtein()
{
SourceOrganismID = gm.GeneModelSource.Organism.ID,
ProteinID = gm.Protein.ID
};
return(query.Distinct());
}
private static IQueryable <ProteinSearchValue> GetProteinNameValues(this FaToolDbEntities entities)
{
return(from p in entities.Proteins
select new ProteinSearchValue()
{
ProteinID = p.ID,
ProteinName = p.Name,
TermID = null,
TermName = null,
OntologyID = null,
OntologyName = null,
Value = p.Name
});
}
private static IQueryable <ProteinSearchValue> GetTranscriptIDValues(this FaToolDbEntities entities)
{
return(from gm in entities.GeneModels
select new ProteinSearchValue()
{
ProteinID = gm.Protein.ID,
ProteinName = gm.Protein.Name,
TermID = null,
TermName = null,
OntologyID = null,
OntologyName = null,
Value = gm.TranscriptID
});
}
private static IQueryable <ProteinSearchValue> GetDescriptionValues(this FaToolDbEntities entities)
{
return(from param in entities.ProteinParams
select new ProteinSearchValue()
{
ProteinID = param.ParamContainer.ID,
ProteinName = param.ParamContainer.Name,
TermID = param.Term.ID,
TermName = param.Term.Name,
OntologyID = param.Term.Ontology.ID,
OntologyName = param.Term.Ontology.Name,
Value = param.Value
});
}
private static IQueryable <ProteinSearchValue> GetSynonymValues(this FaToolDbEntities entities)
{
return(from s in entities.Synonyms
select new ProteinSearchValue()
{
ProteinID = s.Protein.ID,
ProteinName = s.Protein.Name,
TermID = s.SynonymType.ID,
TermName = s.SynonymType.Name,
OntologyID = s.SynonymType.Ontology.ID,
OntologyName = s.SynonymType.Ontology.Name,
Value = s.SynonymValue
});
}
private static IQueryable <ProteinSearchValue> GetFunctionValues(this FaToolDbEntities entities)
{
return(from a in entities.Annotations
select new ProteinSearchValue()
{
ProteinID = a.Protein.ID,
ProteinName = a.Protein.Name,
TermID = a.Term.ID,
TermName = a.Term.Name,
OntologyID = a.Term.Ontology.ID,
OntologyName = a.Term.Ontology.Name,
Value = a.Term.Name
});
}
public static IQueryable <ProteinSearchValue> GetProteinSearchValues(
this FaToolDbEntities entities,
ProteinSearchOption option)
{
switch (option)
{
case ProteinSearchOption.Function:
return(GetFunctionValues(entities));
case ProteinSearchOption.Description:
return(GetDescriptionValues(entities));
default:
return(GetNameSearchValues(entities));
}
}
public static Task LoadCollection <TEntity, TElement>(
this FaToolDbEntities ctx,
TEntity entity,
Expression <Func <TEntity, ICollection <TElement> > > navigationProperty,
params string[] includes)
where TEntity : class, IEntity
where TElement : class, IEntity
{
var query = ctx
.Entry(entity)
.Collection(navigationProperty)
.Query();
foreach (var include in includes)
{
query = query.Include(include);
}
return(query.LoadAsync());
}
public static TEntity Create <TEntity>(this FaToolDbEntities ctx)
where TEntity : class, IEntity
{
return(ctx.Core.CreateObject <TEntity>());
}
public static Task <TEntity> Find <TEntity>(this FaToolDbEntities ctx, object id)
where TEntity : class, IEntity
{
return(ctx.Set <TEntity>().FindAsync(id));
}
public static async Task <bool> Exists <TEntity>(this FaToolDbEntities ctx, string id)
where TEntity : class, IEntity <string>
{
return(await ctx.Exists <TEntity>(x => x.ID == id));
}
public static async Task <bool> Exists <TEntity>(this FaToolDbEntities ctx, Expression <Func <TEntity, bool> > predicate)
where TEntity : class, IEntity
{
return(await ctx.Set <TEntity>().AnyAsync(predicate));
}
