public DatabaseObjectMultipartName(string?currentDatabase, string?name)
{
if (name != null)
{
var parser = new IdentifierParser(new StringReader(name));
string?[] parts = parser.Parse().ToArray();
var i = parts.Length - 1;
var commandBuilder = new SqlCommandBuilder();
if (i >= 0)
{
Name = parts[i];
i--;
if (i >= 0)
{
Schema = parts[i];
i--;
if (i >= 0)
{
Database = parts[i];
i--;
if (i >= 0)
{
_server = parts[i];
}
}
}
}
}
if (Database == null)
{
Database = currentDatabase;
}
if (string.IsNullOrEmpty(Schema))
{
Schema = null;
}
if (Name != null)
{
var length = Name.Length;
if (length > 0 && Name[0] == '[')
{
Name = Name.Substring(1);
length--;
}
if (length > 0 && Name[length - 1] == ']')
{
Name = Name.Substring(0, length - 1);
}
}
}
private void AddCode(Composition header, XElement element)
{
if (header == null || element == null)
{
return;
}
header.Type = new CodeableConceptParser().FromXml(element, Errors);
var type = header.Type?.Coding.FirstOrDefault()?.Code;
if (string.IsNullOrEmpty(type))
{
return;
}
if (type == "34133-9")
{
header.Meta.ProfileElement.Add(new FhirUri(
"http://hl7.org/fhir/us/ccda/StructureDefinition/CCDA-on-FHIR-Continuity-of-Care-Document"));
}
else
{
var templateIdElement = element.Parent.CdaElement("templateId");
var templateId = new IdentifierParser().FromXml(templateIdElement)?.System;
if (!string.IsNullOrEmpty(templateId) && header.Meta.ProfileElement.All(p => p.Value != templateId))
{
header.Meta.ProfileElement.Add(new FhirUri(templateId));
}
}
}
public void Parse_empty_string_returns_empty_list()
{
var parser = new IdentifierParser();
var result = parser.Parse("");
Assert.IsNotNull(result);
Assert.IsFalse(result.Any());
}
public void Parse_ShouldParseLocalIdentifier()
{
var expected = new LocalIdentifier("123");
var actual = IdentifierParser.Parse("lcl|123") as LocalIdentifier;
Assert.IsNotNull(actual);
Assert.AreEqual(expected.Code, actual.Code);
Assert.AreEqual(expected.Value, actual.Value);
}
public void Parse_ShouldParseIntegratedDatabaseIdentifier()
{
var expected = new IntegratedDatabaseIdentifier(123);
var actual = IdentifierParser.Parse("gi|123") as IntegratedDatabaseIdentifier;
Assert.IsNotNull(actual);
Assert.AreEqual(expected.Code, actual.Code);
Assert.AreEqual(expected.Value, actual.Value);
}
public void Identifer_VariableArgument_IsValidIdentifier()
{
IdentifierParser parser = new IdentifierParser();
string token = "...";
IdentifierNode node = (IdentifierNode)parser.Parse(token);
Assert.AreEqual(token, node.Name);
}
void AddIdentifierTokens()
{
IdentifierParser ip = new IdentifierParser();
foreach (var item in codeTxtBox.Lines)
{
lstIdTokens = ip.GenerateTokens(item);
}
}
public void Parse_ShouldParseImportIdIdentifier()
{
var expected = new ImportIdIdentifier(123);
var actual = IdentifierParser.Parse("gim|123") as ImportIdIdentifier;
Assert.IsNotNull(actual);
Assert.AreEqual(expected.Code, actual.Code);
Assert.AreEqual(expected.Value, actual.Value);
}
public void Identifer_CannotContain_CloseParenthesis()
{
IdentifierParser parser = new IdentifierParser();
string token = ")";
IdentifierNode node = (IdentifierNode)parser.Parse(token);
Assert.IsNull(node);
}
public void Identifer_CannotStartWithDash()
{
IdentifierParser parser = new IdentifierParser();
string token = "-";
IdentifierNode node = (IdentifierNode)parser.Parse(token);
Assert.AreEqual(token, node.Name);
}
public void Identifer_MultipleCharacters_IsValidIdentifier()
{
IdentifierParser parser = new IdentifierParser();
string token = "ab";
IdentifierNode node = (IdentifierNode)parser.Parse(token);
Assert.AreEqual(token, node.Name);
}
public void Parse_ShouldParseBackboneSeqIdIdentifier()
{
var expected = new BackboneSeqIdIdentifier(123);
var actual = IdentifierParser.Parse("bbs|123") as BackboneSeqIdIdentifier;
Assert.IsNotNull(actual);
Assert.AreEqual(expected.Code, actual.Code);
Assert.AreEqual(expected.Value, actual.Value);
}
public void Identifer_Operator_IsValidIdentifer()
{
IdentifierParser parser = new IdentifierParser();
string token = "<=";
IdentifierNode node = (IdentifierNode)parser.Parse(token);
Assert.AreEqual(token, node.Name);
}
public void Identifer_CanContainQuestionMark_IsValidIdentifier()
{
IdentifierParser parser = new IdentifierParser();
string token = "ab?";
IdentifierNode node = (IdentifierNode)parser.Parse(token);
Assert.AreEqual(token, node.Name);
}
public void Identifer_CannotContain_SingleNumber()
{
IdentifierParser parser = new IdentifierParser();
string token = "2";
IdentifierNode node = (IdentifierNode)parser.Parse(token);
Assert.IsNull(node);
}
public void ElementWithoutCodeSystemAttributeShallRenturnNull()
{
var xml =
@"<id extension=""TT988""/>";
var element = XElement.Parse(xml);
var result = new IdentifierParser().FromXml(element);
result.Should().BeNull();
}
public void Parse_word()
{
var parser = new IdentifierParser();
var result = parser.Parse("word").ToArray();
Assert.IsNotNull(result);
Assert.AreEqual(1, result.Count());
Assert.AreEqual(IdentifierPartTypeEnum.Word, result[0].Type);
Assert.AreEqual("word", result[0].Value);
}
public void Parse_ShouldParseSWISSPROTIdentifier()
{
var expected = new SWISSPROTIdentifier("M73307", "AGMA13GT");
var actual = IdentifierParser.Parse("sp|M73307|AGMA13GT") as SWISSPROTIdentifier;
Assert.IsNotNull(actual);
Assert.AreEqual(expected.Code, actual.Code);
Assert.AreEqual(expected.Accession, actual.Accession);
Assert.AreEqual(expected.Name, actual.Name);
}
public void Parse_ShouldParsePRFIdentifier()
{
var expected = new PRFIdentifier("ACCESSION", "0806162C");
var actual = IdentifierParser.Parse("prf|ACCESSION|0806162C") as PRFIdentifier;
Assert.IsNotNull(actual);
Assert.AreEqual(expected.Code, actual.Code);
Assert.AreEqual(expected.Accession, actual.Accession);
Assert.AreEqual(expected.Name, actual.Name);
}
public void Parse_ShouldParseEMBLIdentifier()
{
var expected = new EMBLIdentifier("M73307", "AGMA13GT");
var actual = IdentifierParser.Parse("emb|M73307|AGMA13GT") as EMBLIdentifier;
Assert.IsNotNull(actual);
Assert.AreEqual(expected.Code, actual.Code);
Assert.AreEqual(expected.Accession, actual.Accession);
Assert.AreEqual(expected.Locus, actual.Locus);
}
public void Parse_ShouldParseDDBJIdentifier()
{
var expected = new DDBJIdentifier("BAC85684.1", "1");
var actual = IdentifierParser.Parse("dbj|BAC85684.1|1") as DDBJIdentifier;
Assert.IsNotNull(actual);
Assert.AreEqual(expected.Code, actual.Code);
Assert.AreEqual(expected.Accession, actual.Accession);
Assert.AreEqual(expected.Locus, actual.Locus);
}
public void Parse_ShouldParseTrEMBLIdentifier()
{
var expected = new TrEMBLIdentifier("Q90RT2", "Q90RT2_9HIV1");
var actual = IdentifierParser.Parse("tr|Q90RT2|Q90RT2_9HIV1") as TrEMBLIdentifier;
Assert.IsNotNull(actual);
Assert.AreEqual(expected.Code, actual.Code);
Assert.AreEqual(expected.Accession, actual.Accession);
Assert.AreEqual(expected.Name, actual.Name);
}
public void Parse_ShouldParseThirdPartyGenBankIdentifier()
{
var expected = new ThirdPartyGenBankIdentifier("BK003456", "NAME");
var actual = IdentifierParser.Parse("tpg|BK003456|NAME") as ThirdPartyGenBankIdentifier;
Assert.IsNotNull(actual);
Assert.AreEqual(expected.Code, actual.Code);
Assert.AreEqual(expected.Accession, actual.Accession);
Assert.AreEqual(expected.Name, actual.Name);
}
public void Parse_ShouldParseThirdPartyEMBLIdentifier()
{
var expected = new ThirdPartyEMBLIdentifier("BN000123", "NAME");
var actual = IdentifierParser.Parse("tpe|BN000123|NAME") as ThirdPartyEMBLIdentifier;
Assert.IsNotNull(actual);
Assert.AreEqual(expected.Code, actual.Code);
Assert.AreEqual(expected.Accession, actual.Accession);
Assert.AreEqual(expected.Name, actual.Name);
}
public void Parse_ShouldParsePDBIdentifier()
{
var expected = new PDBIdentifier("1I4L", "D");
var actual = IdentifierParser.Parse("pdb|1I4L|D") as PDBIdentifier;
Assert.IsNotNull(actual);
Assert.AreEqual(expected.Code, actual.Code);
Assert.AreEqual(expected.Entry, actual.Entry);
Assert.AreEqual(expected.Chain, actual.Chain);
}
public void Parse_ShouldParseGeneralDatabaseReferenceIdentifier()
{
var expected = new GeneralDatabaseReferenceIdentifier("taxon", "9606");
var actual = IdentifierParser.Parse("gnl|taxon|9606") as GeneralDatabaseReferenceIdentifier;
Assert.IsNotNull(actual);
Assert.AreEqual(expected.Code, actual.Code);
Assert.AreEqual(expected.Database, actual.Database);
Assert.AreEqual(expected.Value, actual.Value);
}
public void Parse_ShouldParsePatentIdentifier()
{
var expected = new PatentIdentifier("US", "RE33188", "1");
var actual = IdentifierParser.Parse("pat|US|RE33188|1") as PatentIdentifier;
Assert.IsNotNull(actual);
Assert.AreEqual(expected.Code, actual.Code);
Assert.AreEqual(expected.Country, actual.Country);
Assert.AreEqual(expected.Patent, actual.Patent);
Assert.AreEqual(expected.SequenceNumber, actual.SequenceNumber);
}
public void ShallRenturnIdentifier()
{
var xml =
@"<id extension=""TT988"" root=""2.16.840.1.113883.19.5.99999.1""/>";
var element = XElement.Parse(xml);
var result = new IdentifierParser().FromXml(element);
result.Should().NotBeNull();
result.Value.Should().Be("TT988");
result.System.Should().Be("urn:oid:2.16.840.1.113883.19.5.99999.1");
}
public void Parse_ShouldParsePreGrantPatentIdentifier()
{
var expected = new PreGrantPatentIdentifier("EP", "0238993", "7");
var actual = IdentifierParser.Parse("pgp|EP|0238993|7") as PreGrantPatentIdentifier;
Assert.IsNotNull(actual);
Assert.AreEqual(expected.Code, actual.Code);
Assert.AreEqual(expected.Country, actual.Country);
Assert.AreEqual(expected.ApplicationNumber, actual.ApplicationNumber);
Assert.AreEqual(expected.SequenceNumber, actual.SequenceNumber);
}
public override bool TryBypass(CompilationPool compilationPool)
{
var line = 1;
while (compilationPool.CodePosition < compilationPool.Code.Length)
{
if (Constraints.Instance.Tokens.SkippedSymbols.Contains(
compilationPool.Code[compilationPool.CodePosition]))
{
if (compilationPool.Code[compilationPool.CodePosition] == '\n')
{
line++;
}
compilationPool.CodePosition++;
continue;
}
if (_stateMachines.Any(stateMachine => stateMachine.FindToken(compilationPool)))
{
OnTokenFounded(compilationPool.Tokens.Last(), compilationPool.FileName, line);
continue;
}
if (LiteralParser.IsLiteral(compilationPool))
{
OnTokenFounded(compilationPool.Tokens.Last(), compilationPool.FileName, line);
continue;
}
if (IdentifierParser.IsIndentifier(compilationPool))
{
OnTokenFounded(compilationPool.Tokens.Last(), compilationPool.FileName, line);
continue;
}
Errors.Add(string.Format(Resources.Messages.UnexpectedSymbol, compilationPool.FileName,
GetNextPartOfLexem(compilationPool), line));
return(false);
}
DetermineIdentifierTypes(compilationPool);
compilationPool.Identifiers.ForEach(identifier =>
{
Messages.Add(string.Format(Resources.Messages.IndentifierFounded,
compilationPool.FileName,
identifier.Type,
identifier.Identity));
});
return(true);
}
