object ISerializerInternal.DeserializeInternal(string data, DeserializationContext context)
{
if (data.Equals(EmptySymbol))
{
return(EmptyValue);
}
MainParser parser = new MainParser();
IList <INodeData> list;
parser.ExtractNodeData(data, out list);
Type instanceType;
Metadata metadata;
if (!CanDeserialize(list, out instanceType, out metadata, context))
{
return(EmptyValue);
}
if (context.TryGet(metadata.ReferenceTracker, out object cacheFound))
{
return(cacheFound);
}
ISerializer concreteSerializer = SerializerDependencies.SerializerCollection.GetOrAdd(instanceType);
return(((CustomSerializer)concreteSerializer).ReadObjectData(list, context, metadata.ReferenceTracker));
}
public void SetUp()
{
var rules = RuleFactory.CreateAllRules();
var sourceTags = rules.Select(rule => rule.SourceTag);
mainParser = new MainParser(sourceTags);
}
private static Parser<object> GetArrayParser(MainParser mainParser)
{
return
from openBracket in Parse.Char('[').Token()
from firstItem in Parse.Ref(() => mainParser.Value).Optional()
from otherItems in
(from comma in Parse.Char(',').Token()
from item in Parse.Ref(() => mainParser.Value)
select item).Many()
from closeBracket in Parse.Char(']').Token()
select GetObjectArray(firstItem, otherItems);
}
private static Parser <object> GetArrayParser(MainParser mainParser)
{
return
(from openSquare in Parse.Char('[').Token()
from first in Parse.Ref(() => mainParser.Value).Optional()
from rest in
(from comman in Parse.Char(',').Token()
from value in Parse.Ref(() => mainParser.Value)
select value).Many()
from closeSquare in Parse.Char(']').Token()
select GetObjectArray(first.GetOrDefault(), rest));
}
private static Parser<object> GetArrayParser(MainParser mainParser)
{
return
from openSquare in Parse.Char('[').Token()
from first in Parse.Ref(() => mainParser.Value).Optional()
from rest in
(from comman in Parse.Char(',').Token()
from value in Parse.Ref(() => mainParser.Value)
select value).Many()
from closeSquare in Parse.Char(']').Token()
select GetObjectArray(first.GetOrDefault(), rest);
}
public static Func <string, object> GetJsonParser()
{
var mainParser = new MainParser();
var literalParser = GetLiteralParser();
var stringParser = GetStringParser();
var objectParser = GetObjectParser(stringParser, mainParser);
var arrayParser = GetArrayParser(mainParser);
mainParser.Value = literalParser.Or(stringParser).Or(objectParser).Or(arrayParser);
return(mainParser.Value.Parse);
}
public static Func<string, object> GetJsonParser()
{
var mainParser = new MainParser();
var literalParser = GetLiteralParser();
var stringParser = GetStringParser();
var objectParser = GetObjectParser(stringParser, mainParser);
var arrayParser = GetArrayParser(mainParser);
mainParser.Value = literalParser.Or(stringParser).Or(objectParser).Or(arrayParser);
return mainParser.Value.Parse;
}
private static Parser<object> GetArrayParser(MainParser mainParser)
{
var remainderParser =
from comma in Parse.Char(',').Token()
from item in Parse.Ref(() => mainParser.Value)
select item;
return
from openBracket in Parse.Char('[').Token()
from item in Parse.Ref(() => mainParser.Value).Optional()
from rest in remainderParser.Many()
from closeBracket in Parse.Char(']').Token()
select GetObjectArray(item, rest);
}
/// <summary>
/// example code using the parser to index into mongo
/// </summary>
/// <param name="args"></param>
static void Main(string[] args)
{
DBAdapter mongoAdapter = new MongoAdapter();
MainParser mp = new MainParser();
string content1 = File.ReadAllText(path1);
string output1 = mp.ParseInput(content1);
mongoAdapter.Index(output1);
string content2 = File.ReadAllText(path2);
string output2 = mp.ParseInput(content2);
mongoAdapter.Index(output2);
}
public static int Main(string[] args)
{
var modeParser = new MainParser(CanvasVersionInfo.VersionString, CanvasVersionInfo.CopyrightString,
new GermlineWgsModeParser("Germline-WGS", "CNV calling of a germline sample from whole genome sequencing data"),
new SomaticEnrichmentModeParser("Somatic-Enrichment", "CNV calling of a somatic sample from targeted sequencing data"),
new TumorNormalWgsModeParser("Somatic-WGS", "CNV calling of a somatic sample from whole genome sequencing data"),
new TumorNormalEnrichmentModeParser("Tumor-normal-enrichment", "CNV calling of a tumor/normal pair from targeted sequencing data"));
var result = modeParser.Parse(args, Console.Out, Console.Error);
if (!result.Success)
{
return(-1);
}
return(result.Result.Launch());
}
public static string Render(string markdown)
{
var rules = RuleFactory.CreateAllRules();
var sourceTags = rules.Select(rule => rule.SourceTag);
var renderedLines = new List <string>();
var parser = new MainParser(sourceTags);
var render = new Render(rules);
var escapedText = EscapeSpecialSymbols(markdown);
foreach (var line in Regex.Split(escapedText, Environment.NewLine))
{
var tokens = parser.ParseLine(line);
var renderedLine = render.RenderLine(line, tokens);
renderedLines.Add(renderedLine);
}
return(string.Join(Environment.NewLine, renderedLines));
}
public void GermlineWgsParse_WithRequiredArguments_ReturnsSuccessfulCallsetResult(string name, string description, StringWriter standardWriter,
StringWriter errorWriter, TemporaryDirectoryFixture tempDirectory)
{
// arrange
GermlineWgsModeParser germlineWgsModeParser = new GermlineWgsModeParser(name, description);
MainParser parser = GetMainParser(germlineWgsModeParser);
string[] args =
{
"-h"
};
// act
var result = parser.Parse(args, standardWriter, errorWriter);
// assert
Assert.True(result.Success);
}
public static int Main(string[] args)
{
if (args.Length == 0)
{
return(Help());
}
if (File.Exists(args[0]))
{
XmlDocument doc = new XmlDocument();
doc.Load(args[0]);
IParser mainParser = new MainParser();
BaseParser.SourcePath = new FileInfo(args[0]).DirectoryName;
mainParser.Parse(doc.DocumentElement);
mainParser.Process();
doc.Save("Setup.wxs");
return(0);
}
return(-1);
}
object ISerializerInternal.DeserializeInternal(string data, DeserializationContext context)
{
if (data.Equals(EmptySymbol))
{
return(EmptyValue);
}
MainParser parser = new MainParser();
IList <INodeData> list;
parser.ExtractNodeData(data, out list);
// get the metadata
List <INodeData> validNodes = list[0].SubNodes[1].SubNodes.Where(n => !NodeUtils.IgnoreOnDeserialization(n.Type)).ToList();
INodeData typeNode = list[0].SubNodes[1].SubNodes.FirstOrDefault(n => n.Type == NodeType.METADATA);
CustomSerializer serializer = SerializerUtils.MetadataSerializer;
Metadata metadata = (Metadata)serializer.ReadObjectData(new List <INodeData>()
{
typeNode
}, context, -1);
// check if the object is already in cache
// if that's the case then return it
if (context.TryGet(metadata.ReferenceTracker, out object cacheFound))
{
return(cacheFound);
}
// validate the node structure
if (!ValidateNodes(list))
{
return(EmptyValue);
}
// else do the normal deserialization
object result = ReadObjectData(list, context, metadata.ReferenceTracker);
return(result);
}
public void Parse_ModeWithMissingRequiredArgument_DisplaysError(string messageToDisplay, string name, string description, StringWriter standardWriter,
StringWriter errorWriter)
{
// arrange
GermlineWgsModeParser germlineWgsModeParser = new GermlineWgsModeParser("WGS", "Run Canvas from WGS data");
MainParser parser = GetMainParser(germlineWgsModeParser);
string[] modeArgs =
{
"WGS"
};
// act
parser.Parse(modeArgs, standardWriter, errorWriter);
string errorOutput = errorWriter.ToString();
// assert
Assert.Contains(messageToDisplay, errorOutput);
Assert.Empty(standardWriter.ToString());
}
public void Parse_NoArguments_DisplaysError(string messageToDisplay, string name, string description, StringWriter standardWriter,
StringWriter errorWriter)
{
// arrange
GermlineWgsModeParser germlineWgsModeParser = new GermlineWgsModeParser(name, description);
MainParser parser = GetMainParser(germlineWgsModeParser);
string[] noArgs =
{
};
// act
var result = parser.Parse(noArgs, standardWriter, errorWriter);
string errorOutput = errorWriter.ToString();
// assert
Assert.False(result.Success);
Assert.Contains(messageToDisplay, errorOutput);
Assert.Empty(standardWriter.ToString());
}
public void Parse_WithHelpArgument_ReturnsSuccecssAndDisplaysHelp(string messageToDisplay, string name, string description, StringWriter standardWriter,
StringWriter errorWriter)
{
// arrange
GermlineWgsModeParser germlineWgsModeParser = new GermlineWgsModeParser(name, description);
MainParser parser = GetMainParser(germlineWgsModeParser);
string[] args =
{
"-h"
};
// act
var result = parser.Parse(args, standardWriter, errorWriter);
string standardOutput = standardWriter.ToString();
// assert
Assert.True(result.Success);
Assert.Contains(messageToDisplay, standardOutput);
Assert.Empty(errorWriter.ToString());
}
public void Parse_ModeWithVersion_ReturnsSuccecssAndDisplaysVersion(string messageToDisplay, string name, string description,
StringWriter standardWriter, StringWriter errorWriter)
{
// arrange
GermlineWgsModeParser germlineWgsModeParser = new GermlineWgsModeParser("WGS", "Run Canvas from WGS data");
MainParser parser = GetMainParser(germlineWgsModeParser);
string[] modeArgs =
{
"WGS", "-v"
};
// act
var result = parser.Parse(modeArgs, standardWriter, errorWriter);
string output = standardWriter.ToString().Trim();
// assert
Assert.True(result.Success);
Assert.Equal(Version, output);
Assert.Empty(errorWriter.ToString());
}
public void GermlineWgsParse_WithRequiredArguments_ReturnsSuccessfulCallsetResult()
{
string name = "Hello";
string description = "World";
StringWriter standardWriter = new StringWriter();
StringWriter errorWriter = new StringWriter();
// arrange
GermlineWgsModeParser germlineWgsModeParser = new GermlineWgsModeParser(name, description);
MainParser parser = GetMainParser(germlineWgsModeParser);
string[] args =
{
"-h"
};
// act
var result = parser.Run(args, standardWriter, errorWriter);
// assert
Assert.Equal(0, result);
}
private static Parser <object> GetObjectParser(
Parser <string> stringParser, MainParser mainParser)
{
var memberParser =
from name in stringParser
from colon in Parse.Char(':').Token()
from value in Parse.Ref(() => mainParser.Value)
select new Member {
Name = name, Value = value
};
var objectParser =
from openCurly in Parse.Char('{').Token()
from first in memberParser.Optional()
from rest in
(from comma in Parse.Char(',').Token()
from member in memberParser
select member).Many()
from closeCurly in Parse.Char('}').Token()
select GetExpandoObject(first.GetOrDefault(), rest);
return(objectParser);
}
public void Parse_WithHelpArgumentAndUnkownArgument_DisplaysError(string messageToDisplay, string name, string description)
{
StringWriter standardWriter = new StringWriter();
StringWriter errorWriter = new StringWriter();
// arrange
GermlineWgsModeParser germlineWgsModeParser = new GermlineWgsModeParser(name, description);
MainParser parser = GetMainParser(germlineWgsModeParser);
string[] args =
{
"-h", "--unknown-option"
};
// act
var result = parser.Run(args, standardWriter, errorWriter);
string errorOutput = errorWriter.ToString();
// assert
Assert.Equal(-1, result);
Assert.Contains(messageToDisplay, errorOutput);
Assert.Empty(standardWriter.ToString());
}
public void Parse_ModeWithHelp_ReturnsSuccessAndDisplaysHelp(string messageToDisplay)
{
StringWriter standardWriter = new StringWriter();
StringWriter errorWriter = new StringWriter();
// arrange
GermlineWgsModeParser germlineWgsModeParser = new GermlineWgsModeParser("WGS", "Run Canvas from WGS data");
MainParser parser = GetMainParser(germlineWgsModeParser);
string[] modeArgs =
{
"WGS", "-h"
};
// act
var result = parser.Run(modeArgs, standardWriter, errorWriter);
string output = standardWriter.ToString().Trim();
// assert
Assert.Equal(0, result);
Assert.Contains(messageToDisplay, output);
Assert.Empty(errorWriter.ToString());
}
public static int Main(string[] args)
{
try
{
var mainParser = new MainParser(CanvasVersionInfo.VersionString, CanvasVersionInfo.CopyrightString,
new GermlineWgsModeParser("Germline-WGS",
"CNV calling of a germline sample from whole genome sequencing data"),
new SomaticEnrichmentModeParser("Somatic-Enrichment",
"CNV calling of a somatic sample from targeted sequencing data"),
new TumorNormalWgsModeParser("Somatic-WGS",
"CNV calling of a somatic sample from whole genome sequencing data"),
new TumorNormalEnrichmentModeParser("Tumor-normal-enrichment",
"CNV calling of a tumor/normal pair from targeted sequencing data"),
new SmallPedigreeModeParser("SmallPedigree-WGS",
"CNV calling of a small pedigree from whole genome sequencing data"));
var result = mainParser.Run(args, Console.Out, Console.Error);
return(result);
}
catch (Exception e)
{
Console.Error.WriteLine(e);
return(-1);
}
}
public void Parse_SomaticEnrichmentModeWithMissingRequiredArgument_DisplaysError()
{
string messageToDisplay = "required";
StringWriter standardWriter = new StringWriter();
StringWriter errorWriter = new StringWriter();
// arrange
var modeParser = new SomaticEnrichmentModeParser("Somatic-Enrichment", "Run Canvas from somatic enrichment data");
MainParser parser = GetMainParser(modeParser);
string[] modeArgs =
{
"Somatic-Enrichment"
};
// act
var result = parser.Run(modeArgs, standardWriter, errorWriter);
string errorOutput = errorWriter.ToString();
// assert
Assert.NotEqual(0, result);
Assert.Contains(messageToDisplay, errorOutput);
Assert.Empty(standardWriter.ToString());
}
public void Parse_ModeWithMissingRequiredArgument_DisplaysError()
{
string messageToDisplay = "required";
StringWriter standardWriter = new StringWriter();
StringWriter errorWriter = new StringWriter();
// arrange
GermlineWgsModeParser germlineWgsModeParser = new GermlineWgsModeParser("WGS", "Run Canvas from WGS data");
MainParser parser = GetMainParser(germlineWgsModeParser);
string[] modeArgs =
{
"WGS"
};
// act
var result = parser.Run(modeArgs, standardWriter, errorWriter);
string errorOutput = errorWriter.ToString();
// assert
Assert.NotEqual(0, result);
Assert.Contains(messageToDisplay, errorOutput);
Assert.Empty(standardWriter.ToString());
}
public static void Main()
{
MainParser mainparse = new MainParser();
mainparse.Start();
}
public bool IsValid(string data, out IList <INodeData> nodeDatas, int position, out string patched)
{
if (string.IsNullOrEmpty(data))
{
nodeDatas = null;
patched = data;
return(false);
}
if (data.Length < 2)
{
nodeDatas = null;
patched = data;
return(false);
}
cachedList.Clear();
int startIndex;
int endIndex;
AllIndexesOf(data, START_SYMBOL, cachedList);
if (cachedList.Count == 0)
{
nodeDatas = null;
patched = data;
return(false);
}
startIndex = cachedList[0];
AllIndexesOf(data, END_SYMBOL, cachedList);
if (cachedList.Count == 0)
{
nodeDatas = null;
patched = data;
return(false);
}
endIndex = cachedList[0];
if (startIndex != 0)
{
patched = data;
nodeDatas = new List <INodeData>();
return(false);
}
var content = data.Substring(startIndex + 1, endIndex - startIndex - 1);
var fullText = data.Substring(startIndex, endIndex - startIndex + 1);
NodeDataBase obj = new NodeDataBase(NodeType, fullText, position);
nodeDatas = new List <INodeData>(1);
INodeData symbolStart = new NodeDataBase(NodeType.SYMBOL, START_SYMBOL, position);
INodeData nodeData = new NodeDataBase(NodeType.METADATA_CONTENT, content, position);
INodeData symbolEnd = new NodeDataBase(NodeType.SYMBOL, END_SYMBOL, position);
var firstPart = data.Substring(0, startIndex);
var secondPart = data.Substring(endIndex + 1, data.Length - 1 - endIndex);
patched = firstPart + secondPart;
MainParser mainParser = new MainParser();
IList <INodeData> list;
mainParser.ExtractNodeData(content, out list);
nodeData.SubNodes.AddRange(list);
obj.SubNodes.Add(symbolStart);
obj.SubNodes.Add(nodeData);
obj.SubNodes.Add(symbolEnd);
nodeDatas.Add(obj);
return(true);
}
public void Setup()
{
_mainParser = new MainParser(new MainVisitor());
}
private static Parser<object> GetObjectParser(Parser<string> stringParser, MainParser mainParser)
{
var memberParser =
from name in stringParser
from colon in Parse.Char(':').Token()
from value in Parse.Ref(() => mainParser.Value)
select new Member { Name = name, Value = value };
var objectParser =
from openBrace in Parse.Char('{').Token()
from firstMember in memberParser.Optional()
from otherMembers in
(from comma in Parse.Char(',').Token()
from member in memberParser
select member).Many()
from closeBrace in Parse.Char('}').Token()
select GetExpandoObject(firstMember, otherMembers);
return objectParser;
}
