public async Task RecognizeHealthcareEntitiesBatchConvenienceTest()
{
TextAnalyticsClient client = GetClient();
AnalyzeHealthcareEntitiesOperation operation = await client.StartAnalyzeHealthcareEntitiesAsync(s_batchConvenienceDocuments);
await operation.WaitForCompletionAsync(PollingInterval);
ValidateOperationProperties(operation);
//Take the first page
AnalyzeHealthcareEntitiesResultCollection resultCollection = operation.Value.ToEnumerableAsync().Result.FirstOrDefault();
var expectedOutput = new Dictionary <string, List <string> >()
{
{ "0", s_document1ExpectedEntitiesOutput },
{ "1", s_document2ExpectedEntitiesOutput },
};
ValidateBatchDocumentsResult(resultCollection, expectedOutput);
}
public async Task RecognizeHealthcareEntitiesBatchWithErrorTest()
{
TextAnalyticsClient client = GetClient();
var documents = new List <string>
{
"Subject is taking 100mg of ibuprofen twice daily",
"Can cause rapid or irregular heartbeat, delirium, panic, psychosis, and heart failure.",
"",
};
AnalyzeHealthcareEntitiesOperation operation = await client.StartAnalyzeHealthcareEntitiesAsync(documents);
await operation.WaitForCompletionAsync(PollingInterval);
AnalyzeHealthcareEntitiesResultCollection resultCollection = operation.Value;
Assert.IsNotNull(resultCollection[2].Id);
Assert.IsTrue(resultCollection[2].HasError);
Assert.AreEqual(TextAnalyticsErrorCode.InvalidDocument, resultCollection[2].Error.ErrorCode.ToString());
}
public async Task RecognizeHealthcareEntitiesWithTopParameter()
{
TextAnalyticsClient client = GetClient();
HealthcareOptions options = new HealthcareOptions()
{
Top = 1
};
AnalyzeHealthcareEntitiesOperation operation = await client.StartHealthcareBatchAsync(batchDocuments, options);
await operation.WaitForCompletionAsync(PollingInterval);
RecognizeHealthcareEntitiesResultCollection resultCollection = operation.Value;
Assert.AreEqual(1, resultCollection.Count);
Assert.AreEqual(3, resultCollection[0].Entities.Count);
Assert.IsNotNull(resultCollection[0].Id);
Assert.AreEqual("1", resultCollection[0].Id);
Assert.AreEqual("100mg", resultCollection[0].Entities.FirstOrDefault().Text);
Assert.AreEqual("Dosage", resultCollection[0].Entities.FirstOrDefault().Category);
}
public async Task RecognizeHealthcareEntitiesBatchWithStatisticsTest()
{
TextAnalyticsClient client = GetClient();
var documents = batchDocuments;
HealthcareOptions options = new HealthcareOptions()
{
IncludeStatistics = true
};
AnalyzeHealthcareEntitiesOperation operation = await client.StartHealthcareBatchAsync(documents, options);
await operation.WaitForCompletionAsync(PollingInterval);
RecognizeHealthcareEntitiesResultCollection resultCollection = operation.Value;
Assert.AreEqual(2, resultCollection.Count);
Assert.AreEqual(2, resultCollection.Statistics.DocumentCount);
Assert.AreEqual(2, resultCollection.Statistics.TransactionCount);
Assert.AreEqual(0, resultCollection.Statistics.InvalidDocumentCount);
}
public async Task HealthcareAsyncPagination()
{
string endpoint = TestEnvironment.Endpoint;
string apiKey = TestEnvironment.ApiKey;
var client = new TextAnalyticsClient(new Uri(endpoint), new AzureKeyCredential(apiKey));
#region Snippet:TextAnalyticsSampleHealthcareAsyncPagination
string document = @"RECORD #333582770390100 | MH | 85986313 | | 054351 | 2/14/2001 12:00:00 AM | CORONARY ARTERY DISEASE.";
var list = new List <string>();
for (int i = 0; i < 10; i++)
{
list.Add(document);
}
;
HealthcareOptions options = new HealthcareOptions()
{
Top = 2
};
AnalyzeHealthcareEntitiesOperation healthOperation = await client.StartHealthcareBatchAsync(list, "en", options);
AsyncPageable <DocumentHealthcareResult> results = client.GetHealthcareEntities(healthOperation);
Console.WriteLine($"Results of Azure Text Analytics \"Healthcare Async\"");
Console.WriteLine("");
int resultCount = 0;
await foreach (DocumentHealthcareResult result in results)
{
resultCount += 1;
}
Console.WriteLine("resultCount " + resultCount);
}
public async Task HealthcareOperationCanPollFromNewObject()
{
TextAnalyticsClient client = GetClient(out var nonInstrumentedClient);
var documents = new List <TextDocumentInput>
{
new TextDocumentInput("1", "Subject is taking 100mg of ibuprofen twice daily")
{
Language = "en",
},
new TextDocumentInput("2", "Can cause rapid or irregular heartbeat, delirium, panic, psychosis, and heart failure.")
{
Language = "en",
}
};
AnalyzeHealthcareEntitiesOperation operation = await client.StartAnalyzeHealthcareEntitiesAsync(documents);
var sameOperation = InstrumentOperation(new AnalyzeHealthcareEntitiesOperation(operation.Id, nonInstrumentedClient));
await sameOperation.WaitForCompletionAsync();
Assert.IsTrue(sameOperation.HasValue);
}
public async Task AnalyzeHealthcareEntitiesPagination()
{
TextAnalyticsClient client = GetClient();
AnalyzeHealthcareEntitiesOperation operation = await client.StartAnalyzeHealthcareEntitiesAsync(s_batchDocuments);
Assert.IsFalse(operation.HasCompleted);
Assert.IsFalse(operation.HasValue);
Assert.ThrowsAsync <InvalidOperationException>(async() => await Task.Run(() => operation.Value));
Assert.Throws <InvalidOperationException>(() => operation.GetValues());
await operation.WaitForCompletionAsync();
Assert.IsTrue(operation.HasCompleted);
Assert.IsTrue(operation.HasValue);
ValidateOperationProperties(operation);
// try async
//There most be 1 page
List <AnalyzeHealthcareEntitiesResultCollection> asyncPages = operation.Value.ToEnumerableAsync().Result;
Assert.AreEqual(1, asyncPages.Count);
// First page should have 2 results
Assert.AreEqual(2, asyncPages[0].Count);
// try sync
//There most be 1 page
List <AnalyzeHealthcareEntitiesResultCollection> pages = operation.GetValues().AsEnumerable().ToList();
Assert.AreEqual(1, pages.Count);
// First page should have 2 results
Assert.AreEqual(2, pages[0].Count);
}
public async Task RecognizeHealthcareEntitiesWithSkipParameter()
{
TextAnalyticsClient client = GetClient();
AnalyzeHealthcareEntitiesOptions options = new AnalyzeHealthcareEntitiesOptions()
{
Skip = 1
};
AnalyzeHealthcareEntitiesOperation operation = await client.StartAnalyzeHealthcareEntitiesAsync(batchDocuments, options);
await operation.WaitForCompletionAsync(PollingInterval);
AnalyzeHealthcareEntitiesResultCollection resultCollection = operation.Value;
Assert.IsFalse(resultCollection[0].HasError);
Assert.IsNotNull(resultCollection[0].Warnings);
Assert.AreEqual(1, resultCollection.Count);
Assert.AreEqual(6, resultCollection[0].Entities.Count);
Assert.IsNotNull(resultCollection[0].Id);
Assert.AreEqual("2", resultCollection[0].Id);
Assert.AreEqual("rapid", resultCollection[0].Entities.FirstOrDefault().Text);
Assert.AreEqual("SymptomOrSign", resultCollection[0].Entities.FirstOrDefault().Category);
}
public async Task GetValuesSample()
{
#region Snippet:PageableOperationGetValues
// create a client
var client = new TextAnalyticsClient(new Uri("http://example.com"), new DefaultAzureCredential());
var document = new List <string>()
{
"document with information"
};
// Start the operation
AnalyzeHealthcareEntitiesOperation healthOperation = client.StartAnalyzeHealthcareEntities(document);
await healthOperation.WaitForCompletionAsync();
foreach (AnalyzeHealthcareEntitiesResultCollection documentsInPage in healthOperation.GetValues())
{
foreach (HealthcareEntity entity in documentsInPage[0].Entities)
{
Console.WriteLine($" Entity: {entity.Text}");
}
}
#endregion
}
public async Task HealthcareAsync_ManualPolling()
{
string endpoint = TestEnvironment.Endpoint;
string apiKey = TestEnvironment.ApiKey;
var client = new TextAnalyticsClient(new Uri(endpoint), new AzureKeyCredential(apiKey));
#region Snippet:RecognizeHealthcareEntitiesAsyncManualPolling
string document = @"RECORD #333582770390100 | MH | 85986313 | | 054351 | 2/14/2001 12:00:00 AM | CORONARY ARTERY DISEASE | Signed | DIS | \
Admission Date: 5/22/2001 Report Status: Signed Discharge Date: 4/24/2001 ADMISSION DIAGNOSIS: CORONARY ARTERY DISEASE. \
HISTORY OF PRESENT ILLNESS: The patient is a 54-year-old gentleman with a history of progressive angina over the past several months. \
The patient had a cardiac catheterization in July of this year revealing total occlusion of the RCA and 50% left main disease ,\
with a strong family history of coronary artery disease with a brother dying at the age of 52 from a myocardial infarction and \
another brother who is status post coronary artery bypass grafting. The patient had a stress echocardiogram done on July , 2001 , \
which showed no wall motion abnormalities , but this was a difficult study due to body habitus. The patient went for six minutes with \
minimal ST depressions in the anterior lateral leads , thought due to fatigue and wrist pain , his anginal equivalent. Due to the patient's \
increased symptoms and family history and history left main disease with total occasional of his RCA was referred for revascularization with open heart surgery.";
AnalyzeHealthcareEntitiesOperation healthOperation = await client.StartAnalyzeHealthcareEntitiesAsync(new List <string>() { document });
TimeSpan pollingInterval = new TimeSpan(1000);
while (true)
{
await healthOperation.UpdateStatusAsync();
if (healthOperation.HasCompleted)
{
break;
}
await Task.Delay(pollingInterval);
}
await foreach (AnalyzeHealthcareEntitiesResultCollection documentsInPage in healthOperation.Value)
{
Console.WriteLine($"Results of Azure Text Analytics \"Healthcare Async\" Model, version: \"{documentsInPage.ModelVersion}\"");
Console.WriteLine("");
foreach (AnalyzeHealthcareEntitiesResult result in documentsInPage)
{
Console.WriteLine($" Recognized the following {result.Entities.Count} healthcare entities:");
foreach (HealthcareEntity entity in result.Entities)
{
Console.WriteLine($" Entity: {entity.Text}");
Console.WriteLine($" Category: {entity.Category}");
Console.WriteLine($" Offset: {entity.Offset}");
Console.WriteLine($" Length: {entity.Length}");
Console.WriteLine($" Links:");
foreach (EntityDataSource entityDataSource in entity.DataSources)
{
Console.WriteLine($" Entity ID in Data Source: {entityDataSource.EntityId}");
Console.WriteLine($" DataSource: {entityDataSource.Name}");
}
}
Console.WriteLine("");
}
}
}
public async Task Sample7_AnalyzeHealthcareEntitiesBatch_ManualPolling()
{
// create a text analytics client
string endpoint = TestEnvironment.Endpoint;
string apiKey = TestEnvironment.ApiKey;
var client = new TextAnalyticsClient(new Uri(endpoint), new AzureKeyCredential(apiKey));
#region Snippet:Sample7_AnalyzeHealthcareEntitiesBatch_ManualPolling
// get input documents
string document1 = @"RECORD #333582770390100 | MH | 85986313 | | 054351 | 2/14/2001 12:00:00 AM | CORONARY ARTERY DISEASE | Signed | DIS | \
Admission Date: 5/22/2001 Report Status: Signed Discharge Date: 4/24/2001 ADMISSION DIAGNOSIS: CORONARY ARTERY DISEASE. \
HISTORY OF PRESENT ILLNESS: The patient is a 54-year-old gentleman with a history of progressive angina over the past several months. \
The patient had a cardiac catheterization in July of this year revealing total occlusion of the RCA and 50% left main disease ,\
with a strong family history of coronary artery disease with a brother dying at the age of 52 from a myocardial infarction and \
another brother who is status post coronary artery bypass grafting. The patient had a stress echocardiogram done on July , 2001 , \
which showed no wall motion abnormalities , but this was a difficult study due to body habitus. The patient went for six minutes with \
minimal ST depressions in the anterior lateral leads , thought due to fatigue and wrist pain , his anginal equivalent. Due to the patient's \
increased symptoms and family history and history left main disease with total occasional of his RCA was referred for revascularization with open heart surgery.";
string document2 = "Prescribed 100mg ibuprofen, taken twice daily.";
// prepare analyze operation input
List <TextDocumentInput> batchInput = new List <TextDocumentInput>()
{
new TextDocumentInput("1", document1)
{
Language = "en"
},
new TextDocumentInput("2", document2)
{
Language = "en"
}
};
AnalyzeHealthcareEntitiesOptions options = new AnalyzeHealthcareEntitiesOptions()
{
IncludeStatistics = true
};
// start analysis process
AnalyzeHealthcareEntitiesOperation healthOperation = await client.StartAnalyzeHealthcareEntitiesAsync(batchInput, options);
TimeSpan pollingInterval = new TimeSpan(1000);
// wait for completion with manual polling
while (true)
{
await healthOperation.UpdateStatusAsync();
if (healthOperation.HasCompleted)
{
break;
}
await Task.Delay(pollingInterval);
}
// view operation results
await foreach (AnalyzeHealthcareEntitiesResultCollection documentsInPage in healthOperation.Value)
{
Console.WriteLine($"Results of Azure Text Analytics \"Healthcare Async\" Model, version: \"{documentsInPage.ModelVersion}\"");
Console.WriteLine("");
foreach (AnalyzeHealthcareEntitiesResult result in documentsInPage)
{
Console.WriteLine($" Recognized the following {result.Entities.Count} healthcare entities:");
// view recognized healthcare entities
foreach (HealthcareEntity entity in result.Entities)
{
Console.WriteLine($" Entity: {entity.Text}");
Console.WriteLine($" Category: {entity.Category}");
Console.WriteLine($" Offset: {entity.Offset}");
Console.WriteLine($" Length: {entity.Length}");
Console.WriteLine($" NormalizedText: {entity.NormalizedText}");
Console.WriteLine($" Links:");
// view entity data sources
foreach (EntityDataSource entityDataSource in entity.DataSources)
{
Console.WriteLine($" Entity ID in Data Source: {entityDataSource.EntityId}");
Console.WriteLine($" DataSource: {entityDataSource.Name}");
}
// view assertion
if (entity.Assertion != null)
{
Console.WriteLine($" Assertions:");
if (entity.Assertion?.Association != null)
{
Console.WriteLine($" Association: {entity.Assertion?.Association}");
}
if (entity.Assertion?.Certainty != null)
{
Console.WriteLine($" Certainty: {entity.Assertion?.Certainty}");
}
if (entity.Assertion?.Conditionality != null)
{
Console.WriteLine($" Conditionality: {entity.Assertion?.Conditionality}");
}
}
Console.WriteLine($" We found {result.EntityRelations.Count} relations in the current document:");
Console.WriteLine("");
// view recognized healthcare relations
foreach (HealthcareEntityRelation relations in result.EntityRelations)
{
Console.WriteLine($" Relation: {relations.RelationType}");
Console.WriteLine($" For this relation there are {relations.Roles.Count} roles");
// view relation roles
foreach (HealthcareEntityRelationRole role in relations.Roles)
{
Console.WriteLine($" Role Name: {role.Name}");
Console.WriteLine($" Associated Entity Text: {role.Entity.Text}");
Console.WriteLine($" Associated Entity Category: {role.Entity.Category}");
Console.WriteLine("");
}
Console.WriteLine("");
}
Console.WriteLine("");
}
Console.WriteLine("");
}
}
}
public static async Task <IActionResult> Run(
[HttpTrigger(AuthorizationLevel.Function, "post", Route = null)] HttpRequest req,
ILogger log,
ExecutionContext executionContext)
{
string skillName = executionContext.FunctionName;
IEnumerable <WebApiRequestRecord> requestRecords = WebApiSkillHelpers.GetRequestRecords(req);
if (requestRecords == null)
{
return(new BadRequestObjectResult($"{skillName} - Invalid request record array."));
}
// Get Endpoint and access key from App Settings
string apiKey = Environment.GetEnvironmentVariable(textAnalyticsApiKeySetting, EnvironmentVariableTarget.Process);
string apiEndpoint = Environment.GetEnvironmentVariable(textAnalyticsApiEndpointSetting, EnvironmentVariableTarget.Process);
if (apiKey == null || apiEndpoint == null)
{
return(new BadRequestObjectResult($"{skillName} - TextAnalyticsForHealth API key or Endpoint is missing. Make sure to set it in the Environment Variables."));
}
var client = new TextAnalyticsClient(new Uri(apiEndpoint), new AzureKeyCredential(apiKey));
// Get a custom timeout from the header, if it exists. If not use the default timeout.
int timeout;
if (!int.TryParse(req.Headers["timeout"].ToString(), out timeout))
{
timeout = defaultTimeout;
}
timeout = Math.Clamp(timeout - timeoutBuffer, 1, maxTimeout - timeoutBuffer);
var timeoutMiliseconds = timeout * 1000;
var timeoutTask = Task.Delay(timeoutMiliseconds);
// Get a custom default language, if none is provided, use english
string defaultLanguage = req.Headers.ContainsKey("defaultLanguageCode")? req.Headers["defaultLanguageCode"].ToString(): "en";
WebApiSkillResponse response = await WebApiSkillHelpers.ProcessRequestRecordsAsync(skillName, requestRecords,
async (inRecord, outRecord) => {
if (timeoutTask.IsCompleted)
{
// The time limit for all the skills has been met
outRecord.Errors.Add(new WebApiErrorWarningContract
{
Message = "TextAnalyticsForHealth Error: The Text Analysis Operation took too long to complete."
});
return(outRecord);
}
// Prepare analysis operation input
if (!inRecord.Data.ContainsKey("text"))
{
outRecord.Errors.Add(new WebApiErrorWarningContract
{
Message = "TextAnalyticsForHealth Error: The skill request did not contain 'text' in the input."
});
return(outRecord);
}
var document = inRecord.Data["text"] as string;
var language = inRecord.Data.ContainsKey("languageCode") ? inRecord.Data["languageCode"] as string : defaultLanguage;
var docInfo = new StringInfo(document);
if (docInfo.LengthInTextElements >= maxCharLength)
{
outRecord.Warnings.Add(new WebApiErrorWarningContract
{
Message = $"TextAnalyticsForHealth Warning: The submitted document was over {maxCharLength} elements. It has been truncated to fit this requirement."
});
document = docInfo.SubstringByTextElements(0, maxCharLength);
}
var options = new AnalyzeHealthcareEntitiesOptions {
};
List <string> batchInput = new List <string>()
{
document
};
// start analysis process
var timer = System.Diagnostics.Stopwatch.StartNew();
AnalyzeHealthcareEntitiesOperation healthOperation = await client.StartAnalyzeHealthcareEntitiesAsync(batchInput, language, options);
var healthOperationTask = healthOperation.WaitForCompletionAsync().AsTask();
if (await Task.WhenAny(healthOperationTask, timeoutTask) == healthOperationTask)
{
// Task Completed, now lets process the result.
outRecord.Data["status"] = healthOperation.Status.ToString();
if (healthOperation.Status != TextAnalyticsOperationStatus.Succeeded || !healthOperation.HasValue)
{
// The operation was not a success
outRecord.Errors.Add(new WebApiErrorWarningContract
{
Message = "TextAnalyticsForHealth Error: Health Operation returned a non-succeeded status."
});
}
else
{
// The operation was a success, so lets add the results to our output.
await ExtractEntityData(healthOperation.Value, outRecord);
}
}
else
{
// Timeout
outRecord.Errors.Add(new WebApiErrorWarningContract
{
Message = "TextAnalyticsForHealth Error: The Text Analysis Operation took too long to complete."
});
}
// Record how long this task took to complete.
timer.Stop();
var timeToComplete = timer.Elapsed.TotalSeconds;
log.LogInformation($"Time to complete request for document with ID {inRecord.RecordId}: {timeToComplete}");
return(outRecord);
});
return(new OkObjectResult(response));
}
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 async Task Sample7_AnalyzeHealthcareEntitiesBatchAsync()
{
string endpoint = TestEnvironment.Endpoint;
string apiKey = TestEnvironment.ApiKey;
var client = new TextAnalyticsClient(new Uri(endpoint), new AzureKeyCredential(apiKey));
#region Snippet:TextAnalyticsSampleHealthcareBatchAsync
string document1 = @"RECORD #333582770390100 | MH | 85986313 | | 054351 | 2/14/2001 12:00:00 AM | CORONARY ARTERY DISEASE | Signed | DIS |
Admission Date: 5/22/2001 Report Status: Signed Discharge Date: 4/24/2001 ADMISSION DIAGNOSIS: CORONARY ARTERY DISEASE.
HISTORY OF PRESENT ILLNESS: The patient is a 54-year-old gentleman with a history of progressive angina over the past several months.
The patient had a cardiac catheterization in July of this year revealing total occlusion of the RCA and 50% left main disease ,\
with a strong family history of coronary artery disease with a brother dying at the age of 52 from a myocardial infarction and \
another brother who is status post coronary artery bypass grafting. The patient had a stress echocardiogram done on July , 2001 , \
which showed no wall motion abnormalities , but this was a difficult study due to body habitus. The patient went for six minutes with \
minimal ST depressions in the anterior lateral leads , thought due to fatigue and wrist pain , his anginal equivalent. Due to the patient's \
increased symptoms and family history and history left main disease with total occasional of his RCA was referred for revascularization with open heart surgery.";
string document2 = "Prescribed 100mg ibuprofen, taken twice daily.";
List <TextDocumentInput> batchInput = new List <TextDocumentInput>()
{
new TextDocumentInput("1", document1)
{
Language = "en"
},
new TextDocumentInput("2", document2)
{
Language = "en"
},
new TextDocumentInput("3", string.Empty)
};
AnalyzeHealthcareEntitiesOptions options = new AnalyzeHealthcareEntitiesOptions()
{
IncludeStatistics = true
};
AnalyzeHealthcareEntitiesOperation healthOperation = await client.StartAnalyzeHealthcareEntitiesAsync(batchInput, options);
await healthOperation.WaitForCompletionAsync();
Console.WriteLine($"AnalyzeHealthcareEntities operation was completed");
Console.WriteLine($"Created On : {healthOperation.CreatedOn}");
Console.WriteLine($"Expires On : {healthOperation.ExpiresOn}");
Console.WriteLine($"Id : {healthOperation.Id}");
Console.WriteLine($"Status : {healthOperation.Status}");
Console.WriteLine($"Last Modified: {healthOperation.LastModified}");
foreach (AnalyzeHealthcareEntitiesResultCollection documentsInPage in healthOperation.GetValues())
{
Console.WriteLine($"Results of Azure Text Analytics \"Healthcare\" Model, version: \"{documentsInPage.ModelVersion}\"");
Console.WriteLine("");
int i = 0;
foreach (AnalyzeHealthcareEntitiesResult result in documentsInPage)
{
TextDocumentInput document = batchInput[i++];
Console.WriteLine($"On document (Id={document.Id}, Language=\"{document.Language}\"):");
if (result.HasError)
{
Console.WriteLine(" Error!");
Console.WriteLine($" Document error code: {result.Error.ErrorCode}.");
Console.WriteLine($" Message: {result.Error.Message}");
}
else
{
Console.WriteLine($" Recognized the following {result.Entities.Count} healthcare entities:");
foreach (HealthcareEntity entity in result.Entities)
{
Console.WriteLine($" Entity: {entity.Text}");
Console.WriteLine($" Category: {entity.Category}");
Console.WriteLine($" Offset: {entity.Offset}");
Console.WriteLine($" Length: {entity.Length}");
Console.WriteLine($" NormalizedText: {entity.NormalizedText}");
Console.WriteLine($" Links:");
foreach (EntityDataSource entityDataSource in entity.DataSources)
{
Console.WriteLine($" Entity ID in Data Source: {entityDataSource.EntityId}");
Console.WriteLine($" DataSource: {entityDataSource.Name}");
}
if (entity.Assertion != null)
{
Console.WriteLine($" Assertions:");
if (entity.Assertion?.Association != null)
{
Console.WriteLine($" Association: {entity.Assertion?.Association}");
}
if (entity.Assertion?.Certainty != null)
{
Console.WriteLine($" Certainty: {entity.Assertion?.Certainty}");
}
if (entity.Assertion?.Conditionality != null)
{
Console.WriteLine($" Conditionality: {entity.Assertion?.Conditionality}");
}
}
}
Console.WriteLine($" We found {result.EntityRelations.Count} relations in the current document:");
Console.WriteLine("");
foreach (HealthcareEntityRelation relations in result.EntityRelations)
{
Console.WriteLine($" Relation: {relations.RelationType}");
Console.WriteLine($" For this relation there are {relations.Roles.Count} roles");
foreach (HealthcareEntityRelationRole role in relations.Roles)
{
Console.WriteLine($" Role Name: {role.Name}");
Console.WriteLine($" Associated Entity Text: {role.Entity.Text}");
Console.WriteLine($" Associated Entity Category: {role.Entity.Category}");
Console.WriteLine("");
}
Console.WriteLine("");
}
Console.WriteLine("");
}
Console.WriteLine($"Batch operation statistics:");
Console.WriteLine($" Document count: {result.Statistics.CharacterCount}");
Console.WriteLine($" Valid document count: {result.Statistics.TransactionCount}");
Console.WriteLine("");
}
Console.WriteLine($"Batch operation statistics:");
Console.WriteLine($" Document count: {documentsInPage.Statistics.DocumentCount}");
Console.WriteLine($" Valid document count: {documentsInPage.Statistics.ValidDocumentCount}");
Console.WriteLine($" Invalid document count: {documentsInPage.Statistics.InvalidDocumentCount}");
Console.WriteLine($" Transaction count: {documentsInPage.Statistics.TransactionCount}");
Console.WriteLine("");
}
}
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());
}
}
public async Task AnalyzeHealthcareEntitiesConvenienceAsync()
{
// create a text analytics client
string endpoint = TestEnvironment.Endpoint;
string apiKey = TestEnvironment.ApiKey;
var client = new TextAnalyticsClient(new Uri(endpoint), new AzureKeyCredential(apiKey), CreateSampleOptions());
#region Snippet:TextAnalyticsAnalyzeHealthcareEntitiesConvenienceAsyncAll
#region Snippet:TextAnalyticsAnalyzeHealthcareEntitiesConvenienceAsync
// get input documents
string document1 = @"RECORD #333582770390100 | MH | 85986313 | | 054351 | 2/14/2001 12:00:00 AM | CORONARY ARTERY DISEASE | Signed | DIS | \
Admission Date: 5/22/2001 Report Status: Signed Discharge Date: 4/24/2001 ADMISSION DIAGNOSIS: CORONARY ARTERY DISEASE. \
HISTORY OF PRESENT ILLNESS: The patient is a 54-year-old gentleman with a history of progressive angina over the past several months. \
The patient had a cardiac catheterization in July of this year revealing total occlusion of the RCA and 50% left main disease ,\
with a strong family history of coronary artery disease with a brother dying at the age of 52 from a myocardial infarction and \
another brother who is status post coronary artery bypass grafting. The patient had a stress echocardiogram done on July , 2001 , \
which showed no wall motion abnormalities , but this was a difficult study due to body habitus. The patient went for six minutes with \
minimal ST depressions in the anterior lateral leads , thought due to fatigue and wrist pain , his anginal equivalent. Due to the patient's \
increased symptoms and family history and history left main disease with total occasional of his RCA was referred for revascularization with open heart surgery.";
string document2 = "Prescribed 100mg ibuprofen, taken twice daily.";
// prepare analyze operation input
List <string> batchInput = new List <string>()
{
document1,
document2
};
// start analysis process
AnalyzeHealthcareEntitiesOperation healthOperation = await client.StartAnalyzeHealthcareEntitiesAsync(batchInput);
await healthOperation.WaitForCompletionAsync();
#endregion Snippet:TextAnalyticsAnalyzeHealthcareEntitiesConvenienceAsync
#region Snippet:TextAnalyticsSampleHealthcareOperationStatus
// view operation status
Console.WriteLine($"Created On : {healthOperation.CreatedOn}");
Console.WriteLine($"Expires On : {healthOperation.ExpiresOn}");
Console.WriteLine($"Status : {healthOperation.Status}");
Console.WriteLine($"Last Modified: {healthOperation.LastModified}");
#endregion Snippet:TextAnalyticsSampleHealthcareOperationStatus
#region Snippet:TextAnalyticsSampleHealthcareConvenienceAsyncViewResults
// view operation results
await foreach (AnalyzeHealthcareEntitiesResultCollection documentsInPage in healthOperation.Value)
{
Console.WriteLine($"Results of Azure Text Analytics \"Healthcare Async\" Model, version: \"{documentsInPage.ModelVersion}\"");
Console.WriteLine("");
foreach (AnalyzeHealthcareEntitiesResult entitiesInDoc in documentsInPage)
{
if (!entitiesInDoc.HasError)
{
foreach (var entity in entitiesInDoc.Entities)
{
// view recognized healthcare entities
Console.WriteLine($" Entity: {entity.Text}");
Console.WriteLine($" Category: {entity.Category}");
Console.WriteLine($" Offset: {entity.Offset}");
Console.WriteLine($" Length: {entity.Length}");
Console.WriteLine($" NormalizedText: {entity.NormalizedText}");
Console.WriteLine($" Links:");
// view entity data sources
foreach (EntityDataSource entityDataSource in entity.DataSources)
{
Console.WriteLine($" Entity ID in Data Source: {entityDataSource.EntityId}");
Console.WriteLine($" DataSource: {entityDataSource.Name}");
}
// view assertion
if (entity.Assertion != null)
{
Console.WriteLine($" Assertions:");
if (entity.Assertion?.Association != null)
{
Console.WriteLine($" Association: {entity.Assertion?.Association}");
}
if (entity.Assertion?.Certainty != null)
{
Console.WriteLine($" Certainty: {entity.Assertion?.Certainty}");
}
if (entity.Assertion?.Conditionality != null)
{
Console.WriteLine($" Conditionality: {entity.Assertion?.Conditionality}");
}
}
}
Console.WriteLine($" We found {entitiesInDoc.EntityRelations.Count} relations in the current document:");
Console.WriteLine("");
// view recognized healthcare relations
foreach (HealthcareEntityRelation relations in entitiesInDoc.EntityRelations)
{
Console.WriteLine($" Relation: {relations.RelationType}");
Console.WriteLine($" For this relation there are {relations.Roles.Count} roles");
// view relation roles
foreach (HealthcareEntityRelationRole role in relations.Roles)
{
Console.WriteLine($" Role Name: {role.Name}");
Console.WriteLine($" Associated Entity Text: {role.Entity.Text}");
Console.WriteLine($" Associated Entity Category: {role.Entity.Category}");
Console.WriteLine("");
}
Console.WriteLine("");
}
}
else
{
Console.WriteLine(" Error!");
Console.WriteLine($" Document error code: {entitiesInDoc.Error.ErrorCode}.");
Console.WriteLine($" Message: {entitiesInDoc.Error.Message}");
}
Console.WriteLine("");
}
}
#endregion Snippet:TextAnalyticsSampleHealthcareConvenienceAsyncViewResults
#endregion Snippet:TextAnalyticsAnalyzeHealthcareEntitiesConvenienceAsyncAll
}
public async Task HealthcareBatch()
{
string endpoint = TestEnvironment.Endpoint;
string apiKey = TestEnvironment.ApiKey;
var client = new TextAnalyticsClient(new Uri(endpoint), new AzureKeyCredential(apiKey));
#region Snippet:TextAnalyticsSampleHealthcareBatch
string document = @"RECORD #333582770390100 | MH | 85986313 | | 054351 | 2/14/2001 12:00:00 AM | CORONARY ARTERY DISEASE | Signed | DIS | \
Admission Date: 5/22/2001 Report Status: Signed Discharge Date: 4/24/2001 ADMISSION DIAGNOSIS: CORONARY ARTERY DISEASE. \
HISTORY OF PRESENT ILLNESS: The patient is a 54-year-old gentleman with a history of progressive angina over the past several months. \
The patient had a cardiac catheterization in July of this year revealing total occlusion of the RCA and 50% left main disease ,\
with a strong family history of coronary artery disease with a brother dying at the age of 52 from a myocardial infarction and \
another brother who is status post coronary artery bypass grafting. The patient had a stress echocardiogram done on July , 2001 , \
which showed no wall motion abnormalities , but this was a difficult study due to body habitus. The patient went for six minutes with \
minimal ST depressions in the anterior lateral leads , thought due to fatigue and wrist pain , his anginal equivalent. Due to the patient's \
increased symptoms and family history and history left main disease with total occasional of his RCA was referred for revascularization with open heart surgery.";
List <string> batchInput = new List <string>()
{
document,
document,
};
AnalyzeHealthcareEntitiesOptions options = new AnalyzeHealthcareEntitiesOptions()
{
IncludeStatistics = true
};
AnalyzeHealthcareEntitiesOperation healthOperation = client.StartAnalyzeHealthcareEntities(batchInput, "en", options);
await healthOperation.WaitForCompletionAsync();
AnalyzeHealthcareEntitiesResultCollection results = healthOperation.Value;
Console.WriteLine($"Results of Azure Text Analytics \"Healthcare\" Model, version: \"{results.ModelVersion}\"");
Console.WriteLine("");
foreach (AnalyzeHealthcareEntitiesResult result in results)
{
Console.WriteLine($" Recognized the following {result.Entities.Count} healthcare entities:");
foreach (HealthcareEntity entity in result.Entities)
{
Console.WriteLine($" Entity: {entity.Text}");
Console.WriteLine($" Category: {entity.Category}");
Console.WriteLine($" Offset: {entity.Offset}");
Console.WriteLine($" Length: {entity.Length}");
Console.WriteLine($" Links:");
foreach (EntityDataSource entityDataSource in entity.DataSources)
{
Console.WriteLine($" Entity ID in Data Source: {entityDataSource.EntityId}");
Console.WriteLine($" DataSource: {entityDataSource.Name}");
}
}
Console.WriteLine($" Document statistics:");
Console.WriteLine($" Character count (in Unicode graphemes): {result.Statistics.CharacterCount}");
Console.WriteLine($" Transaction count: {result.Statistics.TransactionCount}");
Console.WriteLine("");
}
Console.WriteLine($"Request statistics:");
Console.WriteLine($" Document Count: {results.Statistics.DocumentCount}");
Console.WriteLine($" Valid Document Count: {results.Statistics.ValidDocumentCount}");
Console.WriteLine($" Transaction Count: {results.Statistics.TransactionCount}");
Console.WriteLine($" Invalid Document Count: {results.Statistics.InvalidDocumentCount}");
Console.WriteLine("");
}