// Use this for initialization
void Start()
{
JsonSample.PersonToJson();
object message = ((new TestDemoMessage()).TryXmlDemo());
//string myString = Newtonsoft.Json.JsonConvert.SerializeXmlNode(message);
string myString = Newtonsoft.Json.JsonConvert.SerializeObject(message);
//string myString = UnitySerializer.JSONSerialize(message);
//Newtonsoft.Json.Linq.JObject test = Newtonsoft.Json.Linq.JObject.Parse(myString);
//string jsonString = JsonConvert.SerializeObject(test);
Debug.Log("HH = " + myString);
//Debug.Log("jsonString = " + jsonString);
// var s = new SerializationWrapper();
// string serializedObject;
// using(var ms = new MemoryStream())
// {
// s.Serialize(ms, message);
// TextReader reader = new StreamReader(ms);
// serializedObject = reader.ReadToEnd();
// Debug.Log("serializedObject = " + serializedObject);
// }
//LitJson.JsonWriter writer1 = new LitJson.JsonWriter(Console.Out);
//string LitTest = LitJson.JsonMapper.ToJson(message);
//Debug.Log("LitTest = " + LitTest);
//LitJson.JsonMapper.t
//JsonFx.Json.JsonWriter writer = new JsonFx.Json.JsonWriter();
//string fxTest = writer.
//Debug.Log("fxTest = " + fxTest);
}
public JEVisSampleWS(JEVisDataSourceWS ds, JsonSample json, JEVisAttribute att)
{
this.attribute = att;
this.ds = ds;
this.json = json;
ObjectifyValue();
ObjectifyTimeStamp();
}
static void btn_onclick()
{
var jso = new JsonSample {
Prop1 = "111", Prop2 = "222"
};
alert("New Json was created: {Prop1:\"" + jso.Prop1 + "\", Prop2:\"" + jso.Prop2 + "\"}");
}
public JEVisSampleWS(JEVisDataSourceWS ds, JsonSample json, JEVisAttribute att, JEVisFile file)
{
this.attribute = att;
this.ds = ds;
this.json = json;
this.file = file;
try
{
SetValue(file.getFilename());
}
catch (Exception ex)
{
logger.Error(ex);
}
}
public JEVisSample buildSample(DateTime ts, Object value, String note)
{
JsonSample newJson = new JsonSample();
newJson.setTs(attDTF.print(ts));
JEVisSample newSample = null;
//TODO: replace this , the getPrimitiveType() is very bad because it will call the Webservice for every sample
// if (getPrimitiveType() == JEVisConstants.PrimitiveType.FILE) {
if (value instanceof JEVisFile)// workaround
{
JEVisFile file = (JEVisFile)value;
newSample = new JEVisSampleWS(ds, newJson, this, file);
}
public void Sample()
{
var sampleEntry = new JsonSample
{
AlleleDepths = new[] { "92", "21" },
VariantFrequency = "1",
TotalDepth = "10",
FailedFilter = true,
GenotypeQuality = "790"
};
var observedJson = sampleEntry.ToString();
const string expectedJson =
"{\"variantFreq\":1,\"totalDepth\":10,\"genotypeQuality\":790,\"alleleDepths\":[92,21],\"failedFilter\":true}";
Assert.Equal(expectedJson, observedJson);
}
/// <summary>
/// returns a JsonSample object given the data contained within the sample genotype
/// field.
/// </summary>
private JsonSample ExtractSample(string sampleColumn, bool fixGatkGenomeVcf = false)
{
// sanity check: make sure we have a format column
if (_formatIndices == null || string.IsNullOrEmpty(sampleColumn))
{
return(EmptySample());
}
var sampleColumns = sampleColumn.Split(':');
// handle missing sample columns
if (sampleColumns.Length == 1 && sampleColumns[0] == ".")
{
return(EmptySample());
}
var tmp = new IntermediateSampleFields(_vcfColumns, _formatIndices, sampleColumns, fixGatkGenomeVcf);
var sample = new JsonSample
{
AlleleDepths = new AlleleDepths(tmp).GetAlleleDepths(),
FailedFilter = new FailedFilter(tmp).GetFailedFilter(),
Genotype = new Genotype(tmp).GetGenotype(),
GenotypeQuality = new GenotypeQuality(tmp).GetGenotypeQuality(),
TotalDepth = new TotalDepth(tmp).GetTotalDepth(_infoDepth),
VariantFrequency = new VariantFrequency(tmp).GetVariantFrequency(),
CopyNumber = tmp.CopyNumber?.ToString(),
IsLossOfHeterozygosity = tmp.MajorChromosomeCount != null && tmp.CopyNumber != null &&
tmp.MajorChromosomeCount.Value == tmp.CopyNumber.Value,
DenovoQuality = tmp.DenovoQuality?.ToString(),
SplitReadCounts = new ReadCounts(tmp).GetSplitReadCounts(),
PairEndReadCounts = new ReadCounts(tmp).GetPairEndReadCounts()
};
// sanity check: handle empty samples
if (sample.IsNull())
{
sample.IsEmpty = true;
}
return(sample);
}
static void btn_onclick()
{
var jso = new JsonSample { Prop1 = "111", Prop2 = "222"};
alert("New Json was created: {Prop1:\"" + jso.Prop1 + "\", Prop2:\"" + jso.Prop2 + "\"}");
}
// This method gets called by the runtime. Use this method to configure the HTTP request pipeline.
public void Configure(IApplicationBuilder app)
{
app.UseStaticFiles();
// app.UseH1Middleware(new H1MiddlewareOptions { NeverStop = false });
app.UseSession();
app.Map("/session", app1 =>
{
app1.Run(async(context) =>
{
try
{
string sessionInfo = context.Session.GetString("MySession");
if (string.IsNullOrEmpty(sessionInfo))
{
context.Session.SetString("MySession", $"session created at {DateTime.Now:T}");
await context.Session.CommitAsync();
await context.Response.WriteAsync($"session created at {DateTime.Now:T}");
}
else
{
await context.Response.WriteAsync($"session exists with this information: {sessionInfo}");
}
}
catch (Exception ex)
{
await context.Response.WriteAsync(ex.ToString());
}
});
});
app.MapWhen(context => context.Request.Path.Value.Contains("one"), app1 =>
{
app1.Run(async(context) =>
{
await context.Response.WriteAsync("path contains 'one'");
});
});
app.Map("/mycontroller", app1 =>
{
app1.Run(async(context) =>
{
var controller = Container.GetService <HelloController>();
string html = controller.Greeting("Katharina");
await context.Response.WriteAsync(html);
});
});
app.Map("/book", app1 =>
{
app1.Run(async(context) =>
{
try
{
var book = new JsonSample().GetABook();
string json = JsonConvert.SerializeObject(book);
await context.Response.WriteAsync(json);
}
catch (Exception ex)
{
await context.Response.WriteAsync(ex.ToString());
}
});
});
app.Map("/Cookies", app1 =>
{
app1.Run(async(context) =>
{
context.Response.Cookies.Append("Mycookie", "mycookieVal", new CookieOptions {
Expires = DateTime.Now.AddDays(3)
});
await context.Response.WriteAsync(HtmlEncoder.Default.Encode("cookie written"));
});
});
app.Map("/FormSample", app1 =>
{
app1.Run(async(context) =>
{
if (context.Request.Method == "POST")
{
string val1 = context.Request.Form["text1"];
await context.Response.WriteAsync($"received from the user: {HtmlEncoder.Default.Encode(val1)}");
return;
}
await MyForm.ReturnFormAsync(context);
});
});
app.Map("/Sample2", app1 =>
{
app1.Run(async(context) =>
{
string valx = context.Request.Query["x"].FirstOrDefault();
await context.Response.WriteAsync(HtmlEncoder.Default.Encode(valx));
});
});
app.Map("/Sample1", app1 =>
{
app1.Run(async(context) =>
{
await context.Response.WriteAsync("<h2>Mapped to Sample1</h2>");
});
});
app.Run(async(context) =>
{
await context.Response.WriteAsync("<h2>Hello World!</h2>");
});
}
public int addSamples(List <JEVisSample> samples)
{
List <JsonSample> jsonSamples = new ArrayList <>();
int imported = 0;
int primType = getPrimitiveType();
if (primType != JEVisConstants.PrimitiveType.FILE)
{
try {
for (JEVisSample s : samples)
{
JsonSample jsonSample = JsonFactory.buildSample(s, primType);
jsonSamples.add(jsonSample);
}
//JEWebService/v1/files/8598/attributes/File/samples/files/20180604T141441?filename=nb-configuration.xml
//JEWebService/v1/objects/{id}/attributes/{attribute}/samples
String resource = REQUEST.API_PATH_V1
+ REQUEST.OBJECTS.PATH
+ getObjectID() + "/"
+ REQUEST.OBJECTS.ATTRIBUTES.PATH
+ getName() + "/"
+ REQUEST.OBJECTS.ATTRIBUTES.SAMPLES.PATH;
// String requestjson = new Gson().toJson(jsonSamples, new TypeToken<List<JsonSample>>() {
// }.getType());
String json = this.ds.getObjectMapper().writeValueAsString(jsonSamples);
// logger.debug("Payload. {}", requestjson);
/** TODO: implement this function into ws **/
StringBuffer response = ds.getHTTPConnection().postRequest(resource, json);
logger.debug("Response.payload: {}", response);
} catch (Exception ex)
{
logger.catching(ex);
}
}
else
{
//Also upload die byte file, filename is in json
for (JEVisSample s : samples)
{
try
{
String resource = REQUEST.API_PATH_V1
+ REQUEST.OBJECTS.PATH
+ getObjectID() + "/"
+ REQUEST.OBJECTS.ATTRIBUTES.PATH
+ getName() + "/"
+ REQUEST.OBJECTS.ATTRIBUTES.SAMPLES.PATH
+ REQUEST.OBJECTS.ATTRIBUTES.SAMPLES.FILES.PATH
+ HTTPConnection.FMT.print(s.getTimestamp())
+ "?" + REQUEST.OBJECTS.ATTRIBUTES.SAMPLES.FILES.OPTIONS.FILENAME + s.getValueAsFile().getFilename();
HttpURLConnection connection = ds.getHTTPConnection().getPostFileConnection(resource);
// logger.trace("Upload file-------------: {}", s.getValueAsFile().getBytes().length);
try (OutputStream os = connection.getOutputStream()) {
os.write(s.getValueAsFile().getBytes());
os.flush();
os.close();
}
int responseCode = connection.getResponseCode();
imported = 1;/** TODO: fix server side, missing response **/
} catch (Exception ex)
{
logger.catching(ex);
}
}
//
}
ds.reloadAttribute(this);
/**
* cast needs to be removed
*/
JEVisObjectWS obj = (JEVisObjectWS)getObject();
obj.notifyListeners(new JEVisEvent(this, JEVisEvent.TYPE.ATTRIBUTE_UPDATE, this));
return(imported);
}
