public async Task WaterfallPrompt()
{
var activities = TranscriptUtilities.GetFromTestContext(TestContext);
var convState = new ConversationState(new MemoryStorage());
var testProperty = convState.CreateProperty <Dictionary <string, object> >("test", () => new Dictionary <string, object>());
TestAdapter adapter = new TestAdapter()
.Use(convState);
await new TestFlow(adapter, async(turnContext) =>
{
if (turnContext.Activity.Type == ActivityTypes.Message)
{
var state = await testProperty.GetAsync(turnContext);
var dialogs = new DialogSet();
dialogs.Add("test-waterfall", Create_Waterfall2());
dialogs.Add("number", new NumberPrompt <int>(Culture.English));
var dc = dialogs.CreateContext(turnContext, state);
await dc.ContinueAsync();
if (!turnContext.Responded)
{
await dc.BeginAsync("test-waterfall");
}
}
})
.Test(activities)
.StartTestAsync();
}
public async Task WaterfallNested()
{
var activities = TranscriptUtilities.GetFromTestContext(TestContext);
TestAdapter adapter = new TestAdapter()
.Use(new ConversationState <Dictionary <string, object> >(new MemoryStorage()));
await new TestFlow(adapter, async(turnContext) =>
{
var dialogs = new DialogSet();
dialogs.Add("test-waterfall-a", Create_Waterfall3());
dialogs.Add("test-waterfall-b", Create_Waterfall4());
dialogs.Add("test-waterfall-c", Create_Waterfall5());
var state = ConversationState <Dictionary <string, object> > .Get(turnContext);
var dc = dialogs.CreateContext(turnContext, state);
await dc.Continue();
if (!turnContext.Responded)
{
await dc.Begin("test-waterfall-a");
}
})
.Test(activities)
.StartTestAsync();
}
public async Task LocaleConvertToEnglish()
{
var botLocale = "en-us";
var activities = TranscriptUtilities.GetFromTestContext(TestContext);
var userState = new UserState(new MemoryStorage());
var userLangProp = userState.CreateProperty <string>("language", () => "en-us");
TestAdapter adapter = new TestAdapter()
.Use(userState)
.Use(new LocaleConverterMiddleware(userLangProp, botLocale, LocaleConverter.Converter));
var flow = new TestFlow(adapter, async(context, cancellationToken) =>
{
if (context.Activity.Type == ActivityTypes.Message)
{
var userMessage = context.Activity.Text.ToLowerInvariant();
if (userMessage.StartsWith("set language "))
{
await userLangProp.SetAsync(context, userMessage.Substring(13, 5));
}
else
{
await context.SendActivityAsync($"message: {context.Activity.Text}");
}
}
});
await flow.Test(activities, (expected, actual) =>
{
Assert.AreEqual(expected.AsMessageActivity().Text, actual.AsMessageActivity().Text);
}).StartTestAsync();
}
public async Task CustomStateTest()
{
var activities = TranscriptUtilities.GetFromTestContext(TestContext);
var storage = new MemoryStorage();
TestAdapter adapter = new TestAdapter()
.Use(new CustomState(storage));
var flow = new TestFlow(adapter, async(context) => {
var(command, value) = GetCommandValue(context);
switch (command)
{
case "delete":
CustomState.Get(context).Value = null;
break;
case "set":
CustomState.Get(context).Value = value;
break;
case "read":
await context.SendActivityAsync($"value:{CustomState.Get(context).Value}");
break;
default:
await context.SendActivityAsync("bot message");
break;
}
});
await flow.Test(activities).StartTestAsync();
}
public async Task TranslateToEnglish()
{
if (!EnvironmentVariablesDefined())
{
Assert.Inconclusive("Missing Translator Environment variables - Skipping test");
return;
}
var nativeLanguages = new string[] { "en-us" };
var patterns = new Dictionary <string, List <string> >();
var activities = TranscriptUtilities.GetFromTestContext(TestContext);
TestAdapter adapter = new TestAdapter()
.Use(new UserState <LanguageState>(new MemoryStorage()))
.Use(new TranslationMiddleware(nativeLanguages, translatorKey, patterns, new CustomDictionary(), GetUserLanguage, SetUserLanguage, false));
var flow = new TestFlow(adapter, async(context) => {
if (!context.Responded)
{
await context.SendActivityAsync($"message: {context.Activity.Text}");
}
});
await flow.Test(activities).StartTestAsync();
}
/// <summary>
/// reads the transcript from the binary reader
/// </summary>
public static Transcript Read(ExtendedBinaryReader reader, Gene[] cacheGenes, SimpleInterval[] cacheIntrons,
SimpleInterval[] cacheMirnas, string[] cachePeptideSeqs)
{
// transcript
var referenceIndex = reader.ReadUInt16();
var start = reader.ReadOptInt32();
var end = reader.ReadOptInt32();
var id = CompactId.Read(reader);
// gene
var geneIndex = reader.ReadOptInt32();
var gene = cacheGenes[geneIndex];
// encoded data
var encoded = new EncodedTranscriptData(reader.ReadUInt16(), reader.ReadByte());
// exons & introns
var introns = encoded.HasIntrons ? ReadIndices(reader, cacheIntrons) : null;
var cdnaMaps = encoded.HasCdnaMaps ? ReadCdnaMaps(reader) : null;
// protein function predictions
int siftIndex = encoded.HasSift ? reader.ReadOptInt32() : -1;
int polyphenIndex = encoded.HasPolyPhen ? reader.ReadOptInt32() : -1;
// translation
var translation = encoded.HasTranslation ? Translation.Read(reader, cachePeptideSeqs) : null;
// attributes
var mirnas = encoded.HasMirnas ? ReadIndices(reader, cacheMirnas) : null;
return(new Transcript(referenceIndex, start, end, id, encoded.Version, translation, encoded.BioType,
gene, TranscriptUtilities.GetTotalExonLength(cdnaMaps), encoded.StartExonPhase, encoded.IsCanonical,
introns, mirnas, cdnaMaps, siftIndex, polyphenIndex, encoded.TranscriptSource));
}
public async Task DateTimePrompt()
{
var activities = TranscriptUtilities.GetFromTestContext(TestContext);
TestAdapter adapter = new TestAdapter()
.Use(new ConversationState <Dictionary <string, object> >(new MemoryStorage()));
await new TestFlow(adapter, async(turnContext) =>
{
var state = ConversationState <Dictionary <string, object> > .Get(turnContext);
var prompt = new DateTimePrompt(Culture.English);
var dialogCompletion = await prompt.Continue(turnContext, state);
if (!dialogCompletion.IsActive && !dialogCompletion.IsCompleted)
{
await prompt.Begin(turnContext, state, new PromptOptions {
PromptString = "What date would you like?", RetryPromptString = "Sorry, but that is not a date. What date would you like?"
});
}
else if (dialogCompletion.IsCompleted)
{
var dateTimeResult = (DateTimeResult)dialogCompletion.Result;
var resolution = dateTimeResult.Resolution.First();
var reply = $"Timex:'{resolution.Timex}' Value:'{resolution.Value}'";
await turnContext.SendActivityAsync(reply);
}
})
.Test(activities)
.StartTestAsync();
}
public async Task AttachmentPrompt()
{
var activities = TranscriptUtilities.GetFromTestContext(TestContext);
TestAdapter adapter = new TestAdapter()
.Use(new ConversationState <Dictionary <string, object> >(new MemoryStorage()));
await new TestFlow(adapter, async(turnContext) =>
{
var state = ConversationState <Dictionary <string, object> > .Get(turnContext);
var prompt = new AttachmentPrompt();
var dialogCompletion = await prompt.Continue(turnContext, state);
if (!dialogCompletion.IsActive && !dialogCompletion.IsCompleted)
{
await prompt.Begin(turnContext, state, new PromptOptions {
PromptString = "please add an attachment."
});
}
else if (dialogCompletion.IsCompleted)
{
var attachmentResult = (AttachmentResult)dialogCompletion.Result;
var reply = (string)attachmentResult.Attachments.First().Content;
await turnContext.SendActivityAsync(reply);
}
})
.Test(activities)
.StartTestAsync();
}
public async Task WaterfallNested()
{
var activities = TranscriptUtilities.GetFromTestContext(TestContext);
var convState = new ConversationState(new MemoryStorage());
var testProperty = convState.CreateProperty <Dictionary <string, object> >("test");
var adapter = new TestAdapter()
.Use(convState);
await new TestFlow(adapter, async(turnContext, cancellationToken) =>
{
if (turnContext.Activity.Type == ActivityTypes.Message)
{
var state = await testProperty.GetAsync(turnContext, () => new Dictionary <string, object>());
var dialogs = new DialogSet();
dialogs.Add("test-waterfall-a", Create_Waterfall3());
dialogs.Add("test-waterfall-b", Create_Waterfall4());
dialogs.Add("test-waterfall-c", Create_Waterfall5());
var dc = dialogs.CreateContext(turnContext, state);
await dc.ContinueAsync();
if (!turnContext.Responded)
{
await dc.BeginAsync("test-waterfall-a");
}
}
})
.Test(activities)
.StartTestAsync();
}
public void FinalizeAndAddAnnotationObject(Transcript transcript, TranscriptAnnotation ta, string[] consequences)
{
if (!ta.AlternateAllele.IsStructuralVariant)
{
_currTranscript.ComplementaryDnaPosition = GetCdnaRangeString(ta);
_currTranscript.HgvsCodingSequenceName = ta.HgvsCodingSequenceName;
if (ta.HasValidCdnaCodingStart)
{
_currTranscript.ProteinID = TranscriptUtilities.GetProteinId(transcript);
}
}
else
{
_currTranscript.ProteinID = ta.HasValidCdnaCodingStart ? TranscriptUtilities.GetProteinId(transcript) : null;
if (ta.GeneFusionAnnotations != null && ta.GeneFusionAnnotations.Count == 1)
{
var sb = new StringBuilder();
ta.GeneFusionAnnotations.First().SerializeJson(sb);
_currTranscript.GeneFusion = sb.ToString();
}
else if (ta.GeneFusionAnnotations != null && ta.GeneFusionAnnotations.Count > 1)
{
throw new Exception("has mutiple gene fusions");
}
}
_currTranscript.Consequence = consequences;
_currJsonVariant.AddTranscript(_currTranscript, transcript.TranscriptSource);
}
public async Task Waterfall()
{
var activities = TranscriptUtilities.GetFromTestContext(TestContext);
var convState = new ConversationState(new MemoryStorage());
var testProperty = convState.CreateProperty <Dictionary <string, object> >("test");
var adapter = new TestAdapter()
.Use(convState);
await new TestFlow(adapter, async(turnContext, cancellationToken) =>
{
if (turnContext.Activity.Type == ActivityTypes.Message)
{
var state = await testProperty.GetAsync(turnContext, () => new Dictionary <string, object>());
var waterfall = new Waterfall(new WaterfallStep[]
{
async(dc, args, next) => { await dc.Context.SendActivityAsync("step1"); },
async(dc, args, next) => { await dc.Context.SendActivityAsync("step2"); },
async(dc, args, next) => { await dc.Context.SendActivityAsync("step3"); },
});
var dialogCompletion = await waterfall.ContinueAsync(turnContext, state);
if (!dialogCompletion.IsActive && !dialogCompletion.IsCompleted)
{
await waterfall.BeginAsync(turnContext, state);
}
}
})
.Test(activities)
.StartTestAsync();
}
/// <summary>
/// parses the relevant data from each mapper unit object
/// </summary>
public static (int Start, int End, MapperUnitType Type) Parse(ObjectValueNode objectValue)
{
int start = -1;
int end = -1;
var type = MapperUnitType.Unknown;
foreach (var node in objectValue.Values)
{
// sanity check: make sure we know about the keys are used for
if (!KnownKeys.Contains(node.Key))
{
throw new InvalidDataException($"Encountered an unknown key in the mapper unit object: {node.Key}");
}
switch (node.Key)
{
case ImportKeys.Id:
type = TranscriptUtilities.GetMapperUnitType(node);
break;
case ImportKeys.End:
end = node.GetInt32();
break;
case ImportKeys.Start:
start = node.GetInt32();
break;
default:
throw new InvalidDataException($"Unknown key found: {node.Key}");
}
}
return(start, end, type);
}
public async Task AttachmentPrompt()
{
var activities = TranscriptUtilities.GetFromTestContext(TestContext);
var convState = new ConversationState(new MemoryStorage());
var testProperty = convState.CreateProperty <Dictionary <string, object> >("test");
var adapter = new TestAdapter()
.Use(convState);
await new TestFlow(adapter, async(turnContext, cancellationToken) =>
{
if (turnContext.Activity.Type == ActivityTypes.Message)
{
var state = await testProperty.GetAsync(turnContext, () => new Dictionary <string, object>());
var prompt = new AttachmentPrompt();
var dialogCompletion = await prompt.ContinueAsync(turnContext, state);
if (!dialogCompletion.IsActive && !dialogCompletion.IsCompleted)
{
await prompt.BeginAsync(turnContext, state, new PromptOptions {
PromptString = "please add an attachment."
});
}
else if (dialogCompletion.IsCompleted)
{
var attachmentResult = (AttachmentResult)dialogCompletion.Result;
var reply = (string)attachmentResult.Attachments.First().Content;
await turnContext.SendActivityAsync(reply);
}
}
})
.Test(activities)
.StartTestAsync();
}
public async Task TranslateToUserLanguage()
{
if (!EnvironmentVariablesDefined())
{
Assert.Inconclusive("Missing Translator Environment variables - Skipping test");
return;
}
var nativeLanguages = new string[] { };
var patterns = new Dictionary <string, List <string> >();
var activities = TranscriptUtilities.GetFromTestContext(TestContext);
var userState = new UserState(new MemoryStorage());
var userLangProp = userState.CreateProperty <string>("language");
TestAdapter adapter = new TestAdapter()
.Use(userState)
.Use(new TranslationMiddleware(nativeLanguages, translatorKey, patterns, new CustomDictionary(), userLangProp, true));
var flow = new TestFlow(adapter, async(context, cancellationToken) =>
{
if (!context.Responded)
{
await context.SendActivityAsync($"message: {context.Activity.Text}");
}
});
await flow.Test(activities).StartTestAsync();
}
public async Task Waterfall()
{
var activities = TranscriptUtilities.GetFromTestContext(TestContext);
TestAdapter adapter = new TestAdapter()
.Use(new ConversationState <Dictionary <string, object> >(new MemoryStorage()));
await new TestFlow(adapter, async(turnContext) =>
{
var waterfall = new Waterfall(new WaterfallStep[]
{
async(dc, args, next) => { await dc.Context.SendActivityAsync("step1"); },
async(dc, args, next) => { await dc.Context.SendActivityAsync("step2"); },
async(dc, args, next) => { await dc.Context.SendActivityAsync("step3"); },
});
var state = ConversationState <Dictionary <string, object> > .Get(turnContext);
var dialogCompletion = await waterfall.Continue(turnContext, state);
if (!dialogCompletion.IsActive && !dialogCompletion.IsCompleted)
{
await waterfall.Begin(turnContext, state);
}
})
.Test(activities)
.StartTestAsync();
}
public SvOverlapTranscript(DataStructures.Transcript transcript, VariantAlternateAllele altAllele)
{
TranscriptID = TranscriptUtilities.GetTranscriptId(transcript);
IsCanonical = transcript.IsCanonical ? "true" : null;
Hgnc = transcript.Gene.Symbol;
var isFullOverlap = altAllele.Start <= transcript.Start && altAllele.End >= transcript.End;
IsPartialOverlap = isFullOverlap ? null : "true";
}
private void CreateTranscriptDictionary(List <Transcript> transcripts)
{
_transcriptsById.Clear();
foreach (var transcript in transcripts)
{
_transcriptsById[TranscriptUtilities.GetTranscriptId(transcript)] = transcript;
}
}
/// <summary>
/// returns a new exon given an ObjectValue
/// </summary>
public static DataStructures.VEP.Exon Parse(ObjectValue objectValue, ushort currentReferenceIndex)
{
bool onReverseStrand = false;
int end = -1;
byte?phase = null;
int start = -1;
string stableId = null;
// loop over all of the key/value pairs in the exon object
foreach (AbstractData ad in objectValue)
{
// sanity check: make sure we know about the keys are used for
if (!KnownKeys.Contains(ad.Key))
{
throw new GeneralException($"Encountered an unknown key in the dumper mapper object: {ad.Key}");
}
// handle each key
switch (ad.Key)
{
case Transcript.EndKey:
end = DumperUtilities.GetInt32(ad);
break;
case EndPhaseKey:
break;
case PhaseKey:
int phaseInt = DumperUtilities.GetInt32(ad);
if (phaseInt != -1)
{
phase = (byte)phaseInt;
}
break;
case Transcript.StableIdKey:
stableId = DumperUtilities.GetString(ad);
break;
case Transcript.StartKey:
start = DumperUtilities.GetInt32(ad);
break;
case Transcript.StrandKey:
onReverseStrand = TranscriptUtilities.GetStrand(ad);
break;
default:
throw new GeneralException($"Unknown key found: {ad.Key}");
}
}
return(new DataStructures.VEP.Exon(currentReferenceIndex, start, end, stableId, onReverseStrand, phase));
}
public async Task NumberPrompt()
{
var activities = TranscriptUtilities.GetFromTestContext(TestContext);
PromptValidatorEx.PromptValidator <NumberResult <int> > validator = async(ctx, result) =>
{
if (result.Value < 0)
{
result.Status = PromptStatus.TooSmall;
}
if (result.Value > 100)
{
result.Status = PromptStatus.TooBig;
}
await Task.CompletedTask;
};
var convState = new ConversationState(new MemoryStorage());
var testProperty = convState.CreateProperty <Dictionary <string, object> >("test");
var adapter = new TestAdapter()
.Use(convState);
await new TestFlow(adapter, async(turnContext, cancellationToken) =>
{
if (turnContext.Activity.Type == ActivityTypes.Message)
{
var state = await testProperty.GetAsync(turnContext, () => new Dictionary <string, object>());
var prompt = new NumberPrompt <int>(Culture.English, validator);
var dialogCompletion = await prompt.ContinueAsync(turnContext, state);
if (!dialogCompletion.IsActive && !dialogCompletion.IsCompleted)
{
await prompt.BeginAsync(turnContext, state,
new PromptOptions
{
PromptString = "Enter a number.",
RetryPromptString = "You must enter a valid positive number less than 100."
});
}
else if (dialogCompletion.IsCompleted)
{
var numberResult = (NumberResult <int>)dialogCompletion.Result;
await turnContext.SendActivityAsync($"Bot received the number '{numberResult.Value}'.");
}
}
})
.Test(activities)
.StartTestAsync();
}
public async Task ConversationStateTest()
{
var testName = "ConversationStateTest";
var activities = TranscriptUtilities.GetActivitiesFromFile(ClassName, testName);
var storage = new MemoryStorage();
var convoState = new ConversationState(new MemoryStorage());
var testProperty = convoState.CreateProperty <ConversationStateObject>("test");
var adapter = new TestAdapter(TestAdapter.CreateConversation(testName))
.Use(new AutoSaveStateMiddleware(convoState));
var flow = new TestFlow(adapter, async(context, cancellationToken) =>
{
if (context.Activity.Type == ActivityTypes.Message)
{
var(command, value) = GetCommandValue(context);
switch (command)
{
case "delete":
await testProperty.DeleteAsync(context);
break;
case "set":
{
var data = await testProperty.GetAsync(context, () => new ConversationStateObject());
data.Value = value;
await testProperty.SetAsync(context, data);
}
break;
case "read":
{
var data = await testProperty.GetAsync(context, () => new ConversationStateObject());
await context.SendActivityAsync($"value:{data.Value}");
}
break;
default:
await context.SendActivityAsync("bot message");
break;
}
}
});
await flow.Test(activities).StartTestAsync();
}
private static string GetAlternateCds(string cacheStub, string transcriptId, string ensemblRefName, int start, int end, string allele)
{
var transcript = DataUtilities.GetTranscript(cacheStub, transcriptId);
Assert.NotNull(transcript);
var sequence = DataUtilities.GetCompressedSequence(cacheStub, ensemblRefName);
Assert.NotNull(sequence);
return(TranscriptUtilities.GetAlternateCds(sequence, start, end, allele, transcript.CdnaMaps,
transcript.Gene.OnReverseStrand, transcript.StartExonPhase,
transcript.Translation.CodingRegion.CdnaStart));
}
public static (int Start, int End, string Id, bool OnReverseStrand) Parse(IImportNode importNode)
{
var objectValue = importNode.GetObjectValueNode();
if (objectValue == null)
{
throw new InvalidDataException("Encountered a gene import node that could not be converted to an object value node.");
}
int start = -1;
int end = -1;
string stableId = null;
var onReverseStrand = false;
foreach (var node in objectValue.Values)
{
// sanity check: make sure we know about the keys are used for
if (!KnownKeys.Contains(node.Key))
{
throw new InvalidDataException($"Encountered an unknown key in the dumper gene object: {node.Key}");
}
// handle each key
switch (node.Key)
{
case ImportKeys.End:
end = node.GetInt32();
break;
case ImportKeys.StableId:
stableId = node.GetString();
break;
case ImportKeys.Start:
start = node.GetInt32();
break;
case ImportKeys.Strand:
onReverseStrand = TranscriptUtilities.GetStrand(node);
break;
default:
throw new InvalidDataException($"Unknown key found: {node.Key}");
}
}
return(start, end, stableId, onReverseStrand);
}
public async Task TextPrompt()
{
var activities = TranscriptUtilities.GetFromTestContext(TestContext);
PromptValidatorEx.PromptValidator <TextResult> validator = async(ctx, result) =>
{
if (result.Value.Length <= 3)
{
result.Status = PromptStatus.TooSmall;
}
await Task.CompletedTask;
};
var convState = new ConversationState(new MemoryStorage());
var testProperty = convState.CreateProperty <Dictionary <string, object> >("test");
var adapter = new TestAdapter()
.Use(convState);
await new TestFlow(adapter, async(turnContext, cancellationToken) =>
{
if (turnContext.Activity.Type == ActivityTypes.Message)
{
var state = await testProperty.GetAsync(turnContext, () => new Dictionary <string, object>());
var prompt = new TextPrompt(validator);
var dialogCompletion = await prompt.ContinueAsync(turnContext, state);
if (!dialogCompletion.IsActive && !dialogCompletion.IsCompleted)
{
await prompt.BeginAsync(turnContext, state,
new PromptOptions
{
PromptString = "Enter some text.",
RetryPromptString = "Make sure the text is greater than three characters."
});
}
else if (dialogCompletion.IsCompleted)
{
var textResult = (TextResult)dialogCompletion.Result;
await turnContext.SendActivityAsync($"Bot received the text '{textResult.Value}'.");
}
}
})
.Test(activities)
.StartTestAsync();
}
public async Task ConfirmPrompt()
{
var activities = TranscriptUtilities.GetFromTestContext(TestContext);
var convState = new ConversationState(new MemoryStorage());
var testProperty = convState.CreateProperty <Dictionary <string, object> >("test");
var adapter = new TestAdapter()
.Use(convState);
await new TestFlow(adapter, async(turnContext, cancellationToken) =>
{
if (turnContext.Activity.Type == ActivityTypes.Message)
{
var state = await testProperty.GetAsync(turnContext, () => new Dictionary <string, object>());
var prompt = new ConfirmPrompt(Culture.English)
{
Style = ListStyle.None
};
var dialogCompletion = await prompt.ContinueAsync(turnContext, state);
if (!dialogCompletion.IsActive && !dialogCompletion.IsCompleted)
{
await prompt.BeginAsync(turnContext, state,
new PromptOptions
{
PromptString = "Please confirm.",
RetryPromptString = "Please confirm, say 'yes' or 'no' or something like that."
});
}
else if (dialogCompletion.IsCompleted)
{
if (((ConfirmResult)dialogCompletion.Result).Confirmation)
{
await turnContext.SendActivityAsync("Confirmed.");
}
else
{
await turnContext.SendActivityAsync("Not confirmed.");
}
}
}
})
.Test(activities)
.StartTestAsync();
}
public async Task UserStateTest()
{
var activities = TranscriptUtilities.GetFromTestContext(TestContext);
var userState = new UserState(new MemoryStorage());
var testProperty = userState.CreateProperty <UserStateObject>("test");
var adapter = new TestAdapter()
.Use(userState);
var flow = new TestFlow(adapter, async(context, cancellationToken) =>
{
if (context.Activity.Type == ActivityTypes.Message)
{
var(command, value) = GetCommandValue(context);
switch (command)
{
case "delete":
await testProperty.DeleteAsync(context);
break;
case "set":
{
var data = await testProperty.GetAsync(context, () => new UserStateObject());
data.Value = value;
await testProperty.SetAsync(context, data);
}
break;
case "read":
{
var data = await testProperty.GetAsync(context, () => new UserStateObject());
await context.SendActivityAsync($"value:{data.Value}");
}
break;
default:
await context.SendActivityAsync("bot message");
break;
}
}
});
await flow.Test(activities).StartTestAsync();
}
public async Task BotAdapted_Bracketing()
{
var testName = "BotAdapted_Bracketing";
var activities = TranscriptUtilities.GetActivitiesFromFile(ClassName, testName);
TestAdapter adapter = new TestAdapter(TestAdapter.CreateConversation(testName))
.Use(new BeforeAfterMiddleware());
adapter.OnTurnError = async(context, exception) =>
{
await context.SendActivityAsync($"Caught: {exception.Message}");
return;
};
var flow = new TestFlow(adapter, async(context, cancellationToken) =>
{
switch (context.Activity.Type)
{
case ActivityTypes.Message:
{
var userMessage = context.Activity.AsMessageActivity()?.Text;
switch (userMessage)
{
case "use middleware":
await context.SendActivityAsync("using middleware");
break;
case "catch exception":
await context.SendActivityAsync("generating exception");
throw new Exception("exception to catch");
}
}
break;
default:
await context.SendActivityAsync(context.Activity.Type);
break;
}
});
await flow.Test(activities).StartTestAsync();
}
public void AddFlankingTranscript(Transcript transcript, TranscriptAnnotation ta, string[] consequences)
{
_currTranscript = new JsonVariant.Transcript
{
IsCanonical = transcript.IsCanonical ? TrueTag : null,
Consequence = consequences,
ProteinID = ta.HasValidCdnaCodingStart ? TranscriptUtilities.GetProteinId(transcript) : null,
TranscriptID = TranscriptUtilities.GetTranscriptId(transcript),
BioType = BioTypeUtilities.GetBiotypeDescription(transcript.BioType),
Gene = transcript.TranscriptSource == TranscriptDataSource.Ensembl ? transcript.Gene.EnsemblId.ToString() : transcript.Gene.EntrezGeneId.ToString(),
Hgnc = transcript.Gene.Symbol
};
if (ta.HasValidCdnaStart && ta.HasValidCdnaEnd)
{
_currTranscript.ComplementaryDnaPosition = GetCdnaRangeString(ta);
}
_currJsonVariant.AddTranscript(_currTranscript, transcript.TranscriptSource);
}
public async Task LocaleConvertToEnglish()
{
var botLocale = "en-us";
var activities = TranscriptUtilities.GetFromTestContext(TestContext);
TestAdapter adapter = new TestAdapter()
.Use(new UserState <LanguageState>(new MemoryStorage()))
.Use(new LocaleConverterMiddleware(GetUserLanguage, SetUserLanguage, botLocale, LocaleConverter.Converter));
var flow = new TestFlow(adapter, async(context) => {
if (!context.Responded)
{
await context.SendActivityAsync($"message: {context.Activity.Text}");
}
});
await flow.Test(activities, (expected, actual) => {
Assert.AreEqual(expected.AsMessageActivity().Text, actual.AsMessageActivity().Text);
}).StartTestAsync();
}
public void CreateAnnotationObject(Transcript transcript, VariantAlternateAllele altAllele)
{
// while annotating alternate allele, the first output function to be called is AddExonData.
// So, we set the current json variant and transcript here.
// they will subsequently be used in other output functions.
FindCorrespondingJsonVariant(altAllele);
if (_currJsonVariant == null)
{
throw new GeneralException("Cannot find jsonVariant corresponding to alternate allele");
}
_currTranscript = new JsonVariant.Transcript
{
IsCanonical = transcript.IsCanonical ? TrueTag : null,
TranscriptID = TranscriptUtilities.GetTranscriptId(transcript),
BioType = BioTypeUtilities.GetBiotypeDescription(transcript.BioType),
Gene = transcript.TranscriptSource == TranscriptDataSource.Ensembl ? transcript.Gene.EnsemblId.ToString() : transcript.Gene.EntrezGeneId.ToString(),
Hgnc = transcript.Gene.Symbol
};
}
/// <summary>
/// constructor
/// </summary>
public Transcript(ushort referenceIndex, int start, int end, CompactId id, byte version,
Translation translation, BioType bioType, Gene gene, int totalExonLength, byte startExonPhase,
bool isCanonical, SimpleInterval[] introns, SimpleInterval[] microRnas, CdnaCoordinateMap[] cdnaMaps,
int siftIndex, int polyPhenIndex, TranscriptDataSource transcriptSource) : base(referenceIndex, start, end)
{
Id = id;
Version = version;
Translation = translation;
BioType = bioType;
Gene = gene;
TotalExonLength = totalExonLength;
StartExonPhase = startExonPhase;
IsCanonical = isCanonical;
Introns = introns;
MicroRnas = microRnas;
CdnaMaps = cdnaMaps;
SiftIndex = siftIndex;
PolyPhenIndex = polyPhenIndex;
TranscriptSource = transcriptSource;
TotalExonLength = TranscriptUtilities.GetTotalExonLength(cdnaMaps);
}
