static void UploadMedicalEntities(MedicalEntities medicaEntities, string id)
{
// Upload the specified entity to Azure Search
// Note it is much more efficient to upload content in batches
// Convert Concept ID's to actual Concept names
var MedicationMentionNames = new List <string>();
var AnatomicalSiteNames = new List <string>();
var DiseaseDisorderNames = new List <string>();
var SignSymptomNames = new List <string>();
foreach (var concept in medicaEntities.MedicationMentionConceptList.Select(x => x.ontologyConcept).Distinct())
{
MedicationMentionNames.Add(medicaEntities.ConceptNameDictionary.Where(x => x.Key == Convert.ToInt32(concept)).First().Value);
}
foreach (var concept in medicaEntities.AnatomicalSiteMentionConceptList.Select(x => x.ontologyConcept).Distinct())
{
AnatomicalSiteNames.Add(medicaEntities.ConceptNameDictionary.Where(x => x.Key == Convert.ToInt32(concept)).First().Value);
}
foreach (var concept in medicaEntities.DiseaseDisorderConceptList.Select(x => x.ontologyConcept).Distinct())
{
DiseaseDisorderNames.Add(medicaEntities.ConceptNameDictionary.Where(x => x.Key == Convert.ToInt32(concept)).First().Value);
}
foreach (var concept in medicaEntities.SignSymptomMentionConceptList.Select(x => x.ontologyConcept).Distinct())
{
SignSymptomNames.Add(medicaEntities.ConceptNameDictionary.Where(x => x.Key == Convert.ToInt32(concept)).First().Value);
}
try
{
var uploadBatch = new List <IndexSchema>();
var indexDoc = new IndexSchema();
// Get the key value so that we can merge content with the existing content
// The key is a url token encoding of the path (e.g. https://azsdemos.blob.core.windows.net/medical-tutorial/nihms637915.pdf)
//file = MedicalStorage + file.Substring(file.LastIndexOf("\\") + 1);
//indexDoc.metadata_storage_path = HttpServerUtility.UrlTokenEncode(Encoding.UTF8.GetBytes(file));
indexDoc.id = id;
indexDoc.medical_mentions = medicaEntities.MedicationMentionList.Select(x => x.term).Distinct().ToArray();
indexDoc.medical_mention_concepts = MedicationMentionNames.Distinct().ToArray();
indexDoc.sign_symptoms = medicaEntities.SignSymptomMentionList.Select(x => x.term).Distinct().ToArray();
indexDoc.sign_symptom_concepts = SignSymptomNames.Distinct().ToArray();
indexDoc.anatomical_sites = medicaEntities.AnatomicalSiteMentionList.Select(x => x.term).Distinct().ToArray();
indexDoc.anatomical_site_concepts = AnatomicalSiteNames.Distinct().ToArray();
indexDoc.disease_disorders = medicaEntities.DiseaseDisorderList.Select(x => x.term).Distinct().ToArray();
indexDoc.disease_disorder_concepts = DiseaseDisorderNames.Distinct().ToArray();
indexDoc.nihii = "87051718996";
uploadBatch.Add(indexDoc);
var batch = IndexBatch.MergeOrUpload(uploadBatch);
indexClient.Documents.Index(batch);
uploadBatch.Clear();
}
catch (Exception ex)
{
Console.WriteLine(ex.Message);
}
}
static MedicalEntities ProcessDoc(string text)
{
var medicalEntities = new MedicalEntities();
medicalEntities.DiseaseDisorderList = new List <Term>();
medicalEntities.MedicationMentionList = new List <Term>();
medicalEntities.SignSymptomMentionList = new List <Term>();
medicalEntities.AnatomicalSiteMentionList = new List <Term>();
medicalEntities.DiseaseDisorderConceptList = new List <OntologyConcept>();
medicalEntities.MedicationMentionConceptList = new List <OntologyConcept>();
medicalEntities.SignSymptomMentionConceptList = new List <OntologyConcept>();
medicalEntities.AnatomicalSiteMentionConceptList = new List <OntologyConcept>();
medicalEntities.ConceptNameDictionary = new Dictionary <int, string>();
try
{
var request = (HttpWebRequest)WebRequest.Create(url);
// Take a max of X KB of text
var subText = text.Substring(0, Math.Min(20480, text.Length));
var postData = "q=" + subText;
postData += "&format=" + format;
postData += "¨suser="******"¨spw=" + umlspw;
var data = Encoding.ASCII.GetBytes(postData);
request.Method = "POST";
request.ContentType = "application/x-www-form-urlencoded";
request.ContentLength = data.Length;
request.Timeout = 20 * 60 * 1000; // 20 min
using (var stream = request.GetRequestStream())
{
stream.Write(data, 0, data.Length);
}
var response = (HttpWebResponse)request.GetResponse();
var responseString = new StreamReader(response.GetResponseStream()).ReadToEnd();
if (responseString != "")
{
XmlDocument xml = new XmlDocument();
xml.LoadXml(responseString);
string parsedText = "";
int begin, end;
Guid termId;
foreach (var node in xml.ChildNodes[1])
{
//Sofa
if (((System.Xml.XmlElement)node).LocalName == "Sofa")
{
parsedText = ((XmlElement)node).GetAttribute("sofaString");
}
else if (((System.Xml.XmlElement)node).LocalName == "UmlsConcept")
{
medicalEntities.ConceptNameDictionary[Convert.ToInt32(((XmlElement)node).GetAttribute("xmi:id"))] =
((XmlElement)node).GetAttribute("preferredText");
}
else if (((System.Xml.XmlElement)node).LocalName == "DiseaseDisorderMention")
{
begin = Convert.ToInt32(((XmlElement)node).GetAttribute("begin"));
end = Convert.ToInt32(((XmlElement)node).GetAttribute("end"));
if (!(medicalEntities.DiseaseDisorderList.Any(t => t.term == parsedText.Substring(begin, end - begin).ToLower())))
{
termId = Guid.NewGuid();
medicalEntities.DiseaseDisorderList.Add(new Term
{
termId = termId,
term = parsedText.Substring(begin, end - begin).ToLower(),
});
var ontologyConceptArray = ((XmlElement)node).GetAttribute("ontologyConceptArr").ToString();
if (ontologyConceptArray.Length > 0)
{
foreach (var c in ontologyConceptArray.Split(' '))
{
medicalEntities.DiseaseDisorderConceptList.Add(new OntologyConcept
{
conceptId = Guid.NewGuid(),
termId = termId,
ontologyConcept = c
});
}
}
}
}
else if (((System.Xml.XmlElement)node).LocalName == "MedicationMention")
{
begin = Convert.ToInt32(((XmlElement)node).GetAttribute("begin"));
end = Convert.ToInt32(((XmlElement)node).GetAttribute("end"));
if (!(medicalEntities.MedicationMentionList.Any(t => t.term == parsedText.Substring(begin, end - begin).ToLower())))
{
termId = Guid.NewGuid();
medicalEntities.MedicationMentionList.Add(new Term
{
termId = termId,
term = parsedText.Substring(begin, end - begin).ToLower()
});
var ontologyConceptArray = ((XmlElement)node).GetAttribute("ontologyConceptArr").ToString();
if (ontologyConceptArray.Length > 0)
{
foreach (var c in ontologyConceptArray.Split(' '))
{
medicalEntities.MedicationMentionConceptList.Add(new OntologyConcept
{
conceptId = Guid.NewGuid(),
termId = termId,
ontologyConcept = c
});
}
}
}
}
else if (((System.Xml.XmlElement)node).LocalName == "SignSymptomMention")
{
begin = Convert.ToInt32(((XmlElement)node).GetAttribute("begin"));
end = Convert.ToInt32(((XmlElement)node).GetAttribute("end"));
if (!(medicalEntities.SignSymptomMentionList.Any(t => t.term == parsedText.Substring(begin, end - begin).ToLower())))
{
termId = Guid.NewGuid();
medicalEntities.SignSymptomMentionList.Add(new Term
{
termId = termId,
term = parsedText.Substring(begin, end - begin).ToLower()
});
var ontologyConceptArray = ((XmlElement)node).GetAttribute("ontologyConceptArr").ToString();
if (ontologyConceptArray.Length > 0)
{
foreach (var c in ontologyConceptArray.Split(' '))
{
medicalEntities.SignSymptomMentionConceptList.Add(new OntologyConcept
{
conceptId = Guid.NewGuid(),
termId = termId,
ontologyConcept = c
});
}
}
}
}
else if (((System.Xml.XmlElement)node).LocalName == "AnatomicalSiteMention")
{
begin = Convert.ToInt32(((XmlElement)node).GetAttribute("begin"));
end = Convert.ToInt32(((XmlElement)node).GetAttribute("end"));
if (!(medicalEntities.AnatomicalSiteMentionList.Any(t => t.term == parsedText.Substring(begin, end - begin).ToLower())))
{
termId = Guid.NewGuid();
medicalEntities.AnatomicalSiteMentionList.Add(new Term
{
termId = termId,
term = parsedText.Substring(begin, end - begin).ToLower()
});
var ontologyConceptArray = ((XmlElement)node).GetAttribute("ontologyConceptArr").ToString();
if (ontologyConceptArray.Length > 0)
{
foreach (var c in ontologyConceptArray.Split(' '))
{
medicalEntities.AnatomicalSiteMentionConceptList.Add(new OntologyConcept
{
conceptId = Guid.NewGuid(),
termId = termId,
ontologyConcept = c
});
}
}
}
}
}
}
}
catch (Exception ex)
{
Console.WriteLine(ex.Message);
}
return(medicalEntities);
}
