public IEnumerable <OmimItem> GetItems()
{
var mimToGeneSymbol = GetMimNumberToGeneSymbol();
foreach (var entry in GetEntryItems())
{
int mimNumber = entry.mimNumber;
string description = entry.textSectionList?[0].textSection.textSectionContent.RemoveLinks().RemoveFormatControl();
string geneName = entry.geneMap?.geneName;
var phenotypes = entry.geneMap?.phenotypeMapList?.Select(x => OmimUtilities.GetPhenotype(x, _jsonSchema.GetSubSchema("phenotypes")))
.ToList() ?? new List <OmimItem.Phenotype>();
yield return(new OmimItem(mimToGeneSymbol[mimNumber.ToString()], geneName, description, mimNumber, phenotypes, _jsonSchema));
}
}
private IEnumerable <OmimItem> GetOmimItems(EntryRoot entryRoot, IDictionary <int, string> mimToGeneSymbol, IDictionary <int, string> phenotypeDescriptions)
{
foreach (var entry in entryRoot.omim.entryList)
{
var item = entry.entry;
var mimNumber = item.mimNumber;
//skip if not a supported gene symbol
if (!mimToGeneSymbol.TryGetValue(mimNumber, out var geneSymbol))
{
continue;
}
string description = OmimUtilities.ExtractAndProcessItemDescription(item);
string geneName = item.geneMap?.geneName;
var phenotypes = item.geneMap?.phenotypeMapList?.Select(x => OmimUtilities.GetPhenotype(x, phenotypeDescriptions, _jsonSchema.GetSubSchema("phenotypes")))
.ToList() ?? new List <OmimItem.Phenotype>();
yield return(new OmimItem(geneSymbol, geneName, description, mimNumber, phenotypes, _jsonSchema));
}
}
private IEnumerable <OmimItem> GetOmimItemsFromMinNumbers(IDictionary <string, string> mimToGeneSymbol, ZipArchive zipArchive)
{
var i = 0;
var queryIndex = 1;
var mimNumbers = mimToGeneSymbol.Select(x => x.Key).ToArray();
while (i < mimNumbers.Length)
{
int endMimNumberIndex = Math.Min(i + EntryQueryLimit - 1, mimNumbers.Length - 1);
string mimNumberString = GetMimNumbersString(mimNumbers, i, endMimNumberIndex);
string queryUrl = GetApiQueryUrl(OmimApiUrl, EntryHandler, ("mimNumber", mimNumberString), ("include", "text:description"), ("include", "externalLinks"), ("include", "geneMap"), ("format", ReturnDataFormat));
using (StreamWriter writer = zipArchive == null ? null : new StreamWriter(zipArchive.CreateEntry($"EntryQueryResponses/response{queryIndex}.txt").Open()))
using (var response = _httpClient.GetAsync(queryUrl).Result)
{
string responseContent = response.Content.ReadAsStringAsync().Result;
writer?.Write(responseContent);
var entryResponse = JsonConvert.DeserializeObject <EntryRoot>(responseContent);
var entryIndex = 0;
foreach (var entry in entryResponse.omim.entryList)
{
int mimNumber = entry.entry.mimNumber;
string description = OmimUtilities.RemoveLinksInText(entry.entry.textSectionList?[0].textSection.textSectionContent);
string geneName = entry.entry.geneMap?.geneName;
var phenotypes = entry.entry.geneMap?.phenotypeMapList?.Select(x => OmimUtilities.GetPhenotype(x, _jsonSchema.GetSubSchema("phenotypes"))).ToList() ??
new List <OmimItem.Phenotype>();
yield return(new OmimItem(mimToGeneSymbol[mimNumber.ToString()], geneName, description, mimNumber, phenotypes, _jsonSchema));
entryIndex++;
}
}
i = endMimNumberIndex + 1;
queryIndex++;
}
}
