public async Task RecognizeHealthcareEntitiesTest()
{
TextAnalyticsClient client = GetClient();
AnalyzeHealthcareEntitiesOperation operation = await client.StartAnalyzeHealthcareEntitiesAsync(s_batchDocuments);
await operation.WaitForCompletionAsync(PollingInterval);
ValidateOperationProperties(operation);
List <AnalyzeHealthcareEntitiesResultCollection> resultInPages = operation.Value.ToEnumerableAsync().Result;
Assert.AreEqual(1, resultInPages.Count);
//Take the first page
var resultCollection = resultInPages.FirstOrDefault();
Assert.AreEqual(s_batchDocuments.Count, resultCollection.Count);
AnalyzeHealthcareEntitiesResult result1 = resultCollection[0];
Assert.AreEqual(s_document1ExpectedEntitiesOutput.Count, result1.Entities.Count);
Assert.IsNotNull(result1.Id);
Assert.AreEqual("1", result1.Id);
foreach (HealthcareEntity entity in result1.Entities)
{
Assert.IsTrue(s_document1ExpectedEntitiesOutput.Contains(entity.Text));
if (entity.Text == "ibuprofen")
{
var linksList = new List <string> {
"UMLS", "AOD", "ATC", "CCPSS", "CHV", "CSP", "DRUGBANK", "GS", "LCH_NW", "LNC", "MEDCIN", "MMSL", "MSH", "MTHSPL", "NCI", "NCI_CTRP", "NCI_DCP", "NCI_DTP", "NCI_FDA", "NCI_NCI-GLOSS", "NDDF", "PDQ", "RCD", "RXNORM", "SNM", "SNMI", "SNOMEDCT_US", "USP", "USPMG", "VANDF"
};
foreach (EntityDataSource entityDataSource in entity.DataSources)
{
Assert.IsTrue(linksList.Contains(entityDataSource.Name));
}
}
// TODO - Implement HC preview.4 https://github.com/Azure/azure-sdk-for-net/issues/18984
//if (entity.Text == "100mg")
//{
// Assert.IsTrue(entity.RelatedEntities.Count == 1);
// var relatedEntity = entity.RelatedEntities.FirstOrDefault().Key;
// Assert.AreEqual("ibuprofen", relatedEntity.Text);
// Assert.AreEqual("MedicationName", relatedEntity.Category);
// Assert.AreEqual(9, relatedEntity.Length);
// Assert.AreEqual(27, relatedEntity.Offset);
// Assert.AreEqual(1.0, relatedEntity.ConfidenceScore);
// Assert.AreEqual(HealthcareEntityRelationType.DosageOfMedication, entity.RelatedEntities.FirstOrDefault().Value);
//}
}
}
public async Task RecognizeHealthcareEntitiesTest()
{
TextAnalyticsClient client = GetClient();
AnalyzeHealthcareEntitiesOperation operation = await client.StartAnalyzeHealthcareEntitiesAsync(batchDocuments);
await operation.WaitForCompletionAsync(PollingInterval);
AnalyzeHealthcareEntitiesResultCollection resultCollection = operation.Value;
Assert.AreEqual(2, resultCollection.Count);
AnalyzeHealthcareEntitiesResult result = resultCollection[0];
var entitiesList = new List <string> {
"100mg", "ibuprofen", "twice daily"
};
Assert.AreEqual(3, result.Entities.Count);
Assert.IsNotNull(result.Id);
Assert.AreEqual("1", result.Id);
foreach (HealthcareEntity entity in result.Entities)
{
Assert.IsTrue(entitiesList.Contains(entity.Text));
if (entity.Text == "ibuprofen")
{
var linksList = new List <string> {
"UMLS", "AOD", "ATC", "CCPSS", "CHV", "CSP", "DRUGBANK", "GS", "LCH_NW", "LNC", "MEDCIN", "MMSL", "MSH", "MTHSPL", "NCI", "NCI_CTRP", "NCI_DCP", "NCI_DTP", "NCI_FDA", "NCI_NCI-GLOSS", "NDDF", "PDQ", "RCD", "RXNORM", "SNM", "SNMI", "SNOMEDCT_US", "USP", "USPMG", "VANDF"
};
foreach (EntityDataSource entityDataSource in entity.DataSources)
{
Assert.IsTrue(linksList.Contains(entityDataSource.Name));
}
}
if (entity.Text == "100mg")
{
Assert.IsTrue(entity.RelatedEntities.Count == 1);
var relatedEntity = entity.RelatedEntities.FirstOrDefault().Key;
Assert.AreEqual("ibuprofen", relatedEntity.Text);
Assert.AreEqual("MedicationName", relatedEntity.Category);
Assert.AreEqual(0, relatedEntity.Length);
Assert.AreEqual(27, relatedEntity.Offset);
Assert.AreEqual(1.0, relatedEntity.ConfidenceScore);
// TODO - DosageOfMedication is not in relation types and is returned from the service. Need to add to swagger.
//Assert.AreEqual(HealthcareEntityRelationType.DosageOfMedication, entity.RelatedEntities.ElementAt(0).Value);
}
}
}
public async Task RecognizeHealthcareEntitiesTest()
{
TextAnalyticsClient client = GetClient();
AnalyzeHealthcareEntitiesOperation operation = await client.StartAnalyzeHealthcareEntitiesAsync(s_batchDocuments);
await operation.WaitForCompletionAsync();
ValidateOperationProperties(operation);
List <AnalyzeHealthcareEntitiesResultCollection> resultInPages = operation.Value.ToEnumerableAsync().Result;
Assert.AreEqual(1, resultInPages.Count);
//Take the first page
var resultCollection = resultInPages.FirstOrDefault();
Assert.AreEqual(s_batchDocuments.Count, resultCollection.Count);
AnalyzeHealthcareEntitiesResult result1 = resultCollection[0];
Assert.AreEqual(s_document1ExpectedEntitiesOutput.Count, result1.Entities.Count);
Assert.IsNotNull(result1.Id);
Assert.AreEqual("1", result1.Id);
foreach (HealthcareEntity entity in result1.Entities)
{
Assert.IsTrue(s_document1ExpectedEntitiesOutput.Contains(entity.Text));
if (entity.Text == "ibuprofen")
{
var linksList = new List <string> {
"UMLS", "AOD", "ATC", "CCPSS", "CHV", "CSP", "DRUGBANK", "GS", "LCH_NW", "LNC", "MEDCIN", "MMSL", "MSH", "MTHSPL", "NCI", "NCI_CTRP", "NCI_DCP", "NCI_DTP", "NCI_FDA", "NCI_NCI-GLOSS", "NDDF", "PDQ", "RCD", "RXNORM", "SNM", "SNMI", "SNOMEDCT_US", "USP", "USPMG", "VANDF"
};
foreach (EntityDataSource entityDataSource in entity.DataSources)
{
Assert.IsTrue(linksList.Contains(entityDataSource.Name));
}
}
if (entity.Text == "100mg")
{
Assert.AreEqual(18, entity.Offset);
Assert.AreEqual("Dosage", entity.Category);
Assert.AreEqual(5, entity.Length);
}
}
Assert.AreEqual(2, result1.EntityRelations.Count());
foreach (HealthcareEntityRelation relation in result1.EntityRelations)
{
if (relation.RelationType == "DosageOfMedication")
{
var role = relation.Roles.ElementAt(0);
Assert.IsNotNull(relation.Roles);
Assert.AreEqual(2, relation.Roles.Count());
Assert.AreEqual("Dosage", role.Name);
Assert.AreEqual("100mg", role.Entity.Text);
Assert.AreEqual(18, role.Entity.Offset);
Assert.AreEqual("Dosage", role.Entity.Category);
Assert.AreEqual(5, role.Entity.Length);
}
}
}
public async Task RecognizeHealthcareEntitiesTestWithAssertions()
{
TextAnalyticsClient client = GetClient();
IReadOnlyCollection <string> batchDocuments = new List <string>()
{
"Baby not likely to have Meningitis. in case of fever in the mother, consider Penicillin for the baby too."
};
IReadOnlyCollection <string> expectedEntitiesOutput = new List <string>
{
"Baby",
"Meningitis",
"fever",
"mother",
"Penicillin",
"baby"
};
AnalyzeHealthcareEntitiesOperation operation = await client.StartAnalyzeHealthcareEntitiesAsync(batchDocuments);
await operation.WaitForCompletionAsync();
ValidateOperationProperties(operation);
List <AnalyzeHealthcareEntitiesResultCollection> resultInPages = operation.Value.ToEnumerableAsync().Result;
Assert.AreEqual(1, resultInPages.Count);
var resultCollection = resultInPages.FirstOrDefault();
Assert.AreEqual(batchDocuments.Count, resultCollection.Count);
AnalyzeHealthcareEntitiesResult result1 = resultCollection[0];
Assert.AreEqual(expectedEntitiesOutput.Count, result1.Entities.Count);
foreach (HealthcareEntity entity in result1.Entities)
{
Assert.IsTrue(expectedEntitiesOutput.Contains(entity.Text));
if (entity.Text == "Baby")
{
var linksList = new List <string> {
"UMLS", "AOD", "CCPSS", "CHV", "DXP", "LCH", "LCH_NW", "LNC", "MDR", "MSH", "NCI", "NCI_FDA", "NCI_NICHD", "SNOMEDCT_US"
};
foreach (EntityDataSource entityDataSource in entity.DataSources)
{
Assert.IsTrue(linksList.Contains(entityDataSource.Name));
}
Assert.AreEqual("Infant", entity.NormalizedText);
}
if (entity.Text == "Meningitis")
{
Assert.AreEqual(24, entity.Offset);
Assert.AreEqual("Diagnosis", entity.Category);
Assert.AreEqual(10, entity.Length);
Assert.IsNotNull(entity.Assertion);
Assert.AreEqual(EntityCertainty.NegativePossible, entity.Assertion.Certainty.Value);
}
if (entity.Text == "Penicillin")
{
Assert.AreEqual("MedicationName", entity.Category);
Assert.AreEqual(10, entity.Length);
Assert.IsNotNull(entity.Assertion);
Assert.AreEqual(EntityCertainty.NeutralPossible, entity.Assertion.Certainty.Value);
}
}
}
public static async Task RunAsync([EventGridTrigger] EventGridEvent eventGridEvent, ILogger log)
{
//Extracting content type and url of the blob triggering the function
var jsondata = JsonConvert.SerializeObject(eventGridEvent.Data);
var tmp = new { contentType = "", url = "" };
var data = JsonConvert.DeserializeAnonymousType(jsondata, tmp);
//Checking if the trigger was iniatiated for a WAV File.
if (data.contentType == "audio/wav")
{
var audioUrl = data.url;
string blobName = audioUrl.Split('/').Last();
string contosoStorageConnectionString = System.Environment.GetEnvironmentVariable("ContosoStorageConnectionString", EnvironmentVariableTarget.Process);
string speechRegion = System.Environment.GetEnvironmentVariable("SpeechRegion", EnvironmentVariableTarget.Process);
string speechKey = System.Environment.GetEnvironmentVariable("SpeechKey", EnvironmentVariableTarget.Process);
string translatorKey = System.Environment.GetEnvironmentVariable("TranslatorKey", EnvironmentVariableTarget.Process);
string translatorEndpoint = System.Environment.GetEnvironmentVariable("TranslatorEndpoint", EnvironmentVariableTarget.Process);
string translatorLocation = System.Environment.GetEnvironmentVariable("TranslatorLocation", EnvironmentVariableTarget.Process);
string cosmosEndpointUrl = System.Environment.GetEnvironmentVariable("CosmosDBEndpointUrl", EnvironmentVariableTarget.Process);
string cosmosPrimaryKey = System.Environment.GetEnvironmentVariable("CosmosDBPrimaryKey", EnvironmentVariableTarget.Process);
string textAnalyticsKey = System.Environment.GetEnvironmentVariable("TextAnalyticsKey", EnvironmentVariableTarget.Process);
string textAnalyticsEndpoint = System.Environment.GetEnvironmentVariable("TextAnalyticsEndpoint", EnvironmentVariableTarget.Process);
// Download audio file to a local temp directory
var tempPath = System.IO.Path.GetTempFileName();
BlobContainerClient container = new BlobContainerClient(contosoStorageConnectionString, "audiorecordings");
BlobClient blob = container.GetBlobClient(blobName);
await blob.DownloadToAsync(tempPath);
var speechConfig = SpeechConfig.FromSubscription(speechKey, speechRegion);
speechConfig.SetProperty(PropertyId.SpeechServiceConnection_SingleLanguageIdPriority, "Latency");
// Audio Language Identification
// Considering only two languages: English and Spanish
// Languages supported for language detection : https://docs.microsoft.com/azure/cognitive-services/speech-service/language-support
var autoDetectSourceLanguageConfig = AutoDetectSourceLanguageConfig.FromLanguages(new string[] { "en-US", "es-MX" });
string languageDetected = "en-US";
using (var audioInput = AudioConfig.FromWavFileInput(tempPath))
{
using (var recognizer = new SourceLanguageRecognizer(speechConfig, autoDetectSourceLanguageConfig, audioInput))
{
var result = await recognizer.RecognizeOnceAsync().ConfigureAwait(false);
if (result.Reason == ResultReason.RecognizedSpeech)
{
var lidResult = AutoDetectSourceLanguageResult.FromResult(result);
languageDetected = lidResult.Language;
}
}
}
speechConfig.SpeechRecognitionLanguage = languageDetected;
// Audio Transcription
StringBuilder sb = new StringBuilder();
using var audioConfig = AudioConfig.FromWavFileInput(tempPath);
{
using var recognizer = new SpeechRecognizer(speechConfig, audioConfig);
{
var stopRecognition = new TaskCompletionSource <int>();
recognizer.SessionStopped += (s, e) =>
{
stopRecognition.TrySetResult(0);
};
recognizer.Canceled += (s, e) =>
{
stopRecognition.TrySetResult(0);
};
recognizer.Recognized += (s, e) =>
{
if (e.Result.Reason == ResultReason.RecognizedSpeech)
{
sb.Append(e.Result.Text);
}
else if (e.Result.Reason == ResultReason.NoMatch)
{
log.LogInformation($"NOMATCH: Speech could not be recognized.");
}
};
await recognizer.StartContinuousRecognitionAsync();
Task.WaitAny(new[] { stopRecognition.Task });
}
}
string transcribedText = sb.ToString();
// If transcription is in Spanish we will translate it to English
if (!languageDetected.Contains("en"))
{
string route = $"/translate?api-version=3.0&to=en";
string textToTranslate = sb.ToString();
object[] body = new object[] { new { Text = textToTranslate } };
var requestBody = JsonConvert.SerializeObject(body);
using (var client = new HttpClient())
using (var request = new HttpRequestMessage())
{
request.Method = HttpMethod.Post;
request.RequestUri = new Uri(translatorEndpoint + route);
request.Content = new StringContent(requestBody, Encoding.UTF8, "application/json");
request.Headers.Add("Ocp-Apim-Subscription-Key", translatorKey);
request.Headers.Add("Ocp-Apim-Subscription-Region", translatorLocation);
HttpResponseMessage response = await client.SendAsync(request).ConfigureAwait(false);
var responseBody = await response.Content.ReadAsStringAsync();
List <Model.TranslatorService.Root> translatedDocuments = JsonConvert.DeserializeObject <List <Model.TranslatorService.Root> >(responseBody);
transcribedText = translatedDocuments.FirstOrDefault().Translations.FirstOrDefault().Text;
}
}
//Azure Text Analytics for Healthcare
List <string> healthDocuments = new List <string>
{
transcribedText
};
var textAnalyticsClient = new TextAnalyticsClient(new Uri(textAnalyticsEndpoint), new AzureKeyCredential(textAnalyticsKey));
AnalyzeHealthcareEntitiesOperation healthOperation = textAnalyticsClient.StartAnalyzeHealthcareEntities(healthDocuments, "en", new AnalyzeHealthcareEntitiesOptions {
});
await healthOperation.WaitForCompletionAsync();
AnalyzeHealthcareEntitiesResult healthcareResult = healthOperation.GetValues().FirstOrDefault().FirstOrDefault();
//Insert documents into CosmosDB
var cosmosClient = new CosmosClient(cosmosEndpointUrl, cosmosPrimaryKey);
var cosmosDatabase = (await cosmosClient.CreateDatabaseIfNotExistsAsync("Contoso")).Database;
var cosmosContainer = (await cosmosDatabase.CreateContainerIfNotExistsAsync("Transcriptions", "/id")).Container;
Model.Transcription newTranscription = new Model.Transcription();
newTranscription.Id = Guid.NewGuid().ToString();
newTranscription.DocumentDate = new DateTime(int.Parse(blobName.Substring(0, 4)),
int.Parse(blobName.Substring(4, 2)), int.Parse(blobName.Substring(6, 2)));
newTranscription.FileName = blobName;
newTranscription.TranscribedText = transcribedText;
foreach (var item in healthcareResult.Entities)
{
newTranscription.HealthcareEntities.Add(new Model.HealthcareEntity()
{
Category = item.Category, Text = item.Text
});
}
try
{
ItemResponse <Model.Transcription> cosmosResponse = await
cosmosContainer.CreateItemAsync(newTranscription, new PartitionKey(newTranscription.Id));
}
catch (CosmosException ex) when(ex.StatusCode == System.Net.HttpStatusCode.Conflict)
{
//Conflicting documents are silently ignored for demo purposes.
}
System.IO.File.Delete(tempPath);
log.LogInformation(eventGridEvent.Data.ToString());
}
}
