public GenesRepository(
Neo4jDataService neo4jService,
EbiDataService ebiDataService,
EnsemblDataService ensemblDataService)
: base("Gene", neo4jService)
{
EbiDataService = ebiDataService;
EnsemblDataService = ensemblDataService;
}
private void PutProteinsAndRelatedData(string geneName)
{
var gene = new Gene()
{
Name = geneName
};
var relatedData = EbiDataService.GetGeneRelatedData(geneName);
foreach (var relatedItem in relatedData)
{
if (relatedItem["id"] == null ||
relatedItem["accession"] == null ||
relatedItem["protein"] == null)
{
continue;
}
var protein = new Protein()
{
Name = relatedItem["id"].ToString(),
Code = relatedItem["accession"].ToString(),
FullName = relatedItem["protein"]
?["submittedName"]?.FirstOrDefault()
?["fullName"]
?["value"]
?.ToString()
?? string.Empty
};
_neo4jService.Client.Cypher.MergeEntity(gene)
.MergeEntity(protein)
.MergeRelationship(new GeneProteinRelationship())
.ExecuteWithoutResults();
var relatedSequences = new Sequence[]
{
new Sequence()
{
Content = relatedItem["sequence"]["sequence"].ToString()
}
};
var relatedTaxons = relatedItem["organism"]["lineage"].Select(jt =>
new Taxon()
{
Name = jt.ToString()
}
);
var relatedComments = relatedItem["comments"] != null ? relatedItem["comments"].Select(jt =>
jt["text"] != null ? jt["text"].Select(jtt =>
new Comment()
{
Text = jtt["value"].ToString(),
Type = jt["type"].ToString()
}) : new Comment[] {}
).SelectMany(c => c) : new Comment[] {};
foreach (var sequence in relatedSequences)
{
_neo4jService.Client.Cypher.MergeEntity(protein)
.MergeEntity(sequence)
.MergeRelationship(new ProteinSequenceRelationship())
.ExecuteWithoutResults();
}
foreach (var taxon in relatedTaxons)
{
_neo4jService.Client.Cypher.MergeEntity(protein)
.MergeEntity(taxon)
.MergeRelationship(new ProteinTaxonRelationship())
.ExecuteWithoutResults();
}
foreach (var comment in relatedComments)
{
_neo4jService.Client.Cypher.MergeEntity(protein)
.MergeEntity(comment)
.MergeRelationship(new ProteinCommentRelationship())
.ExecuteWithoutResults();
}
}
}
