/// <summary>
/// Validade the properties.
/// </summary>
internal static bool Validade()
{
if (!(Exceptions.Any() || Warnings.Any() || Messages.Any() || Successes.Any()))
{
//throw new ArgumentException("At least one Exception/Warning/Message/Success expected.");
return(false);
}
if (String.IsNullOrEmpty(ProjectName))
{
throw new ArgumentException("Project name must be declared.");
}
if (String.IsNullOrEmpty(Folder))
{
throw new ArgumentException("You must inform the Folder wich the Log will be writen.");
}
if (!Directory.Exists(Folder))
{
Directory.CreateDirectory(Folder);
}
if (!FileName.StartsWith("\\"))
{
FileName = "\\" + FileName;
}
if (!FileName.EndsWith(".htm"))
{
FileName += ".htm";
}
return(true);
}
void CheckAll()
{
bool clearRest = false;
foreach (var issue in IssueList)
{
if (clearRest)
{
issue.Severity = IssueSeverity.None;
}
else
{
issue.Check();
}
// If issue is critical then...
if (issue.Severity == IssueSeverity.Critical)
{
// Skip checking other issues.
clearRest = true;
}
// Try to get issue from warnings list.
var item = Warnings.FirstOrDefault(x => x.Name == issue.Name);
// If issue found and not a problem then...
if (item != null && issue.Severity == IssueSeverity.None)
{
// Remove from the list.
Warnings.Remove(item);
}
// If issue not found and there is a problem then...
else if (item != null && issue.Severity != IssueSeverity.None)
{
// Add to the list.
Warnings.Add(issue);
}
}
HasIssues = IgnoreAll
? false
: Warnings.Any(x => x.Severity > IssueSeverity.Moderate);
var ev = CheckCompleted;
if (ev != null)
{
CheckCompleted(this, new EventArgs());
}
}
private void UpdateErrors(INotifyDataErrorInfo viewModel)
{
ClearErrors();
var validations = GetErrors(viewModel).ToList();
foreach (var validation in validations.Where(x => x.Severity == Validation.IssueSeverity.Error))
{
Errors.Add(validation);
}
foreach (var validation in validations.Where(x => x.Severity == Validation.IssueSeverity.Warning))
{
Warnings.Add(validation);
}
HasIssues = validations.Any();
HasWarnings = Warnings.Any();
HasErrors = Errors.Any();
}
/// <summary>
/// Check if no warnings
/// </summary>
/// <returns></returns>
public bool HasWarnings()
{
return(Warnings.Any());
}
public void AssertWarningNotLogged(string warning)
{
var found = Warnings.Any(s => warning.Equals(s, System.StringComparison.CurrentCulture));
found.Should().BeFalse("Not expecting the warning to have been logged: '{0}'", warning);
}
/// <summary>
/// Creates the page and writes to disk using properties set before.
/// </summary>
public static void Me()
{
if (!Validade())
{
return;
}
var html = new Html();
#region Head
html.Head = new Head();
html.Head.Meta = new List <Meta>();
html.Head.Meta.Add(new Meta()
{
Content = "en-us", HttpEquiv = "Content-Language"
});
html.Head.Meta.Add(new Meta()
{
Content = "text/html; charset=utf-16", HttpEquiv = "Content-Type"
});
html.Head.Title = Title;
html.Head.Style = Style;
html.Head.Script = Script;
#endregion
#region Body
html.Body = new Body();
html.Body.H1 = Header;
html.Body.Div = new Div();
html.Body.Div.Id = "content";
#region Summary Table (Overview)
html.Body.Div.Div1 = new Div1();
html.Body.Div.Div1.H2 = "Overview";
html.Body.Div.Div1.Div2 = new Div2();
html.Body.Div.Div1.Div2.Id = "overview";
html.Body.Div.Div1.Div2.Table = new Table();
html.Body.Div.Div1.Div2.Table.Tr = new List <Tr>();
#region Header
var tableRow = new Tr();
tableRow.Th = new List <Th>();
tableRow.Th.Add(new Th());
tableRow.Th.Add(new Th("ProjectTableHeader", "Project"));
tableRow.Th.Add(new Th("PathTableHeader", "Path"));
tableRow.Th.Add(new Th("ErrorsTableHeader", "Errors"));
tableRow.Th.Add(new Th("WarningsTableHeader", "Warnings"));
tableRow.Th.Add(new Th("MessagesTableHeader", "Messages"));
tableRow.Th.Add(new Th("SuccessesTableHeader", "Successes"));
html.Body.Div.Div1.Div2.Table.Tr.Add(tableRow);
#endregion
#region Project Summary
var tableRowItem = new Tr();
tableRowItem.Td = new List <Td>();
#region Project Status Icon
if (Exceptions.Any())
{
tableRowItem.Td.Add(new Td("IconErrorEncoded", ""));
}
else if (Warnings.Any())
{
tableRowItem.Td.Add(new Td("IconWarningEncoded", ""));
}
else if (Messages.Any())
{
tableRowItem.Td.Add(new Td("IconInfoEncoded", ""));
}
else
{
tableRowItem.Td.Add(new Td("IconSuccessEncoded", ""));
}
#endregion
tableRowItem.Td.Add(new Td("", "<strong><a href=\"#" + ProjectName + "\">" + ProjectName + "</a></strong>"));
tableRowItem.Td.Add(new Td("", ProjectPath));
#region Counters
#region Exceptions
if (Exceptions.Any())
{
tableRowItem.Td.Add(new Td("textCentered", "<a href=\"#\" onclick=\"ScrollToFirstVisibleRow('" + ProjectName + "', 'Error'); return false;\">" + Exceptions.Count + "</a>"));
}
else
{
tableRowItem.Td.Add(new Td("textCentered", "<a>0</a>")); //If zero, no href
}
#endregion
#region Warnings
if (Warnings.Any())
{
tableRowItem.Td.Add(new Td("textCentered", "<a href=\"#\" onclick=\"ScrollToFirstVisibleRow('" + ProjectName + "', 'Warning'); return false;\">" + Warnings.Count + "</a>"));
}
else
{
tableRowItem.Td.Add(new Td("textCentered", "<a>0</a>")); //If zero, no href
}
#endregion
#region Messages
if (Messages.Any())
{
tableRowItem.Td.Add(new Td("textCentered", "<a href=\"#\" onclick=\"ScrollToFirstVisibleRow('" + ProjectName + "', 'Message'); return false;\">" + Messages.Count + "</a>"));
}
else
{
tableRowItem.Td.Add(new Td("textCentered", "<a>0</a>")); //If zero, no href
}
#endregion
#region Successes
if (Successes.Any())
{
tableRowItem.Td.Add(new Td("textCentered", "<a href=\"#\" onclick=\"ScrollToFirstVisibleRow('" + ProjectName + "', 'Success'); return false;\">" + Successes.Count + "</a>"));
}
else
{
tableRowItem.Td.Add(new Td("textCentered", "<a>0</a>")); //If zero, no href
}
#endregion
#endregion
html.Body.Div.Div1.Div2.Table.Tr.Add(tableRowItem);
#endregion
#endregion
#region Projects
html.Body.Div.H2 = "Details";
html.Body.Div.Div3 = new Div3();
html.Body.Div.Div3.Div4 = new List <Div4>();
#region For Each Project
var div4 = new Div4();
div4.A = new A();
div4.A.Name = ProjectName;
div4.H3 = ProjectName;
div4.Table = new Table();
div4.Table.Tr = new List <Tr>();
#region Header Row
var tr = new Tr();
tr.Id = div4.H3 + "HeaderRow";
tr.Th = new List <Th>();
tr.Th.Add(new Th("", "", ""));
tr.Th.Add(new Th("MessageTableHeader", "Messages", "messageCell"));
//First cell is empty.
//second cell is "Messages".
div4.Table.Tr.Add(tr);
#endregion
#region For each Error/Warning/Message/Success
#region Errors
foreach (Exception exce in Exceptions)
{
var trException = new Tr();
if (!ExpandErrors)
{
trException.Style = "display: none";
}
trException.Name = "ErrorRowClass" + ProjectName;
trException.Td = new List <Td>();
trException.Td.Add(new Td("IconErrorEncoded", "<a name=\"" + ProjectName + "Error\" />"));
trException.Td.Add(new Td("messageCell", "<span>" + exce.Message + "<br><code>" + exce.StackTrace + "</code>" + "</span>"));
div4.Table.Tr.Add(trException);
}
#region Show/Hide
if (Exceptions.Count > 0 && !ExpandErrors)
{
#region Singular/Plural
string singularPlural = "error";
if (Exceptions.Count > 1)
{
singularPlural += "s";
}
#endregion
var trShow = new Tr();
trShow.Name = "ErrorRowHeaderShow" + ProjectName;
trShow.Td = new List <Td>();
trShow.Td.Add(new Td("IconErrorEncoded", "<a name=\" " + div4.H3 + "Error\" />", "rgb(242,255,255)"));
trShow.Td.Add(new Td("messageCell", "<a _locid=\"ShowAdditionalErrors\" href=\"#\" name=\"" + ProjectName + "Error\" onclick=\"ToggleErrorVisibility('" + ProjectName + "'); return false;\">Show " + Exceptions.Count + " " + singularPlural + "</a>", "background-color: rgb(239,245,249);"));
div4.Table.Tr.Add(trShow);
var trHide = new Tr();
trHide.Name = "ErrorRowHeaderHide" + ProjectName;
trHide.Style = "display: none";
trHide.Td = new List <Td>();
trHide.Td.Add(new Td("IconErrorEncoded", "<a name=\" " + div4.H3 + "Error\" />", "rgb(242,255,255)"));
trHide.Td.Add(new Td("messageCell", "<a _locid=\"HideAdditionalErrors\" href=\"#\" name=\"" + ProjectName + "Error\" onclick=\"ToggleErrorVisibility('" + ProjectName + "'); return false;\">Hide " + Exceptions.Count + " " + singularPlural + "</a>", "background-color: rgb(239,245,249);"));
div4.Table.Tr.Add(trHide);
}
#endregion
#endregion
#region Warnings
foreach (string warning in Warnings)
{
var trWarnings = new Tr();
if (!ExpandWarnings)
{
trWarnings.Style = "display: none";
}
trWarnings.Name = "WarningRowClass" + ProjectName;
trWarnings.Td = new List <Td>();
trWarnings.Td.Add(new Td("IconWarningEncoded", "<a name=\"" + ProjectName + "Warning\" />"));
trWarnings.Td.Add(new Td("messageCell", "<span>" + warning + "</span>"));
div4.Table.Tr.Add(trWarnings);
}
#region Show/Hide
if (Warnings.Count > 0 && !ExpandWarnings)
{
#region Singular/Plural
string singularPlural = "warning";
if (Warnings.Count > 1)
{
singularPlural += "s";
}
#endregion
var trShow = new Tr();
trShow.Name = "WarningRowHeaderShow" + ProjectName;
trShow.Td = new List <Td>();
trShow.Td.Add(new Td("IconWarningEncoded", "<a name=\" " + div4.H3 + "Warning\" />", "rgb(242,255,255)"));
trShow.Td.Add(new Td("messageCell", "<a _locid=\"ShowAdditionalWarnings\" href=\"#\" name=\"" + ProjectName + "Error\" onclick=\"ToggleWarningVisibility('" + ProjectName + "'); return false;\">Show " + Warnings.Count + " " + singularPlural + "</a>", "background-color: rgb(239,245,249);"));
div4.Table.Tr.Add(trShow);
var trHide = new Tr();
trHide.Name = "WarningRowHeaderHide" + ProjectName;
trHide.Style = "display: none";
trHide.Td = new List <Td>();
trHide.Td.Add(new Td("IconWarningEncoded", "<a name=\" " + div4.H3 + "Warning\" />", "rgb(242,255,255)"));
trHide.Td.Add(new Td("messageCell", "<a _locid=\"HideAdditionalWarnings\" href=\"#\" name=\"" + ProjectName + "Error\" onclick=\"ToggleWarningVisibility('" + ProjectName + "'); return false;\">Hide " + Warnings.Count + " " + singularPlural + "</a>", "background-color: rgb(239,245,249);"));
div4.Table.Tr.Add(trHide);
}
#endregion
#endregion
#region Messages
foreach (string message in Messages)
{
var trMessages = new Tr();
if (!ExpandMessages)
{
trMessages.Style = "display: none";
}
trMessages.Name = "MessageRowClass" + ProjectName;
trMessages.Td = new List <Td>();
trMessages.Td.Add(new Td("IconInfoEncoded", "<a name=\"" + ProjectName + "Message\" />"));
trMessages.Td.Add(new Td("messageCell", "<span>" + message + "</span>"));
div4.Table.Tr.Add(trMessages);
}
#region Show/Hide
if (Messages.Count > 0 && !ExpandMessages)
{
#region Singular/Plural
string singularPlural = "message";
if (Messages.Count > 1)
{
singularPlural += "s";
}
#endregion
var trShow = new Tr();
trShow.Name = "MessageRowHeaderShow" + ProjectName;
trShow.Td = new List <Td>();
trShow.Td.Add(new Td("IconInfoEncoded", "<a name=\" " + div4.H3 + "Message\" />", "rgb(242,255,255)"));
trShow.Td.Add(new Td("messageCell", "<a _locid=\"ShowAdditionalMessages\" href=\"#\" name=\"" + ProjectName + "Message\" onclick=\"ToggleMessageVisibility('" + ProjectName + "'); return false;\">Show " + Messages.Count + " " + singularPlural + "</a>", "background-color: rgb(239,245,249);"));
div4.Table.Tr.Add(trShow);
var trHide = new Tr();
trHide.Name = "MessageRowHeaderHide" + ProjectName;
trHide.Style = "display: none";
trHide.Td = new List <Td>();
trHide.Td.Add(new Td("IconInfoEncoded", "<a name=\" " + div4.H3 + "Message\" />", "rgb(242,255,255)"));
trHide.Td.Add(new Td("messageCell", "<a _locid=\"HideAdditionalMessages\" href=\"#\" name=\"" + ProjectName + "Message\" onclick=\"ToggleMessageVisibility('" + ProjectName + "'); return false;\">Hide " + Messages.Count + " " + singularPlural + "</a>", "background-color: rgb(239,245,249);"));
div4.Table.Tr.Add(trHide);
}
#endregion
#endregion
#region Successes
foreach (string success in Successes)
{
var trSuccesses = new Tr();
if (!ExpandSuccesses)
{
trSuccesses.Style = "display: none";
}
trSuccesses.Name = "SuccessRowClass" + ProjectName;
trSuccesses.Td = new List <Td>();
trSuccesses.Td.Add(new Td("IconSuccessEncoded", "<a name=\"" + ProjectName + "Success\" />"));
trSuccesses.Td.Add(new Td("messageCell", "<span>" + success + "</span>"));
div4.Table.Tr.Add(trSuccesses);
}
#region Show/Hide
if (Successes.Count > 0 && !ExpandSuccesses)
{
#region Singular/Plural
string singularPlural = "success";
if (Successes.Count > 1)
{
singularPlural += "es";
}
#endregion
var trShow = new Tr();
trShow.Name = "SuccessRowHeaderShow" + ProjectName;
trShow.Td = new List <Td>();
trShow.Td.Add(new Td("IconSuccessEncoded", "<a name=\" " + div4.H3 + "Success\" />", "rgb(242,255,255)"));
trShow.Td.Add(new Td("messageCell", "<a _locid=\"ShowAdditionalSuccesses\" href=\"#\" name=\"" + ProjectName + "Success\" onclick=\"ToggleSuccessVisibility('" + ProjectName + "'); return false;\">Show " + Successes.Count + " " + singularPlural + "</a>", "background-color: rgb(239,245,249);"));
div4.Table.Tr.Add(trShow);
var trHide = new Tr();
trHide.Name = "SuccessRowHeaderHide" + ProjectName;
trHide.Style = "display: none";
trHide.Td = new List <Td>();
trHide.Td.Add(new Td("IconSuccessEncoded", "<a name=\" " + div4.H3 + "Success\" />", "rgb(242,255,255)"));
trHide.Td.Add(new Td("messageCell", "<a _locid=\"HideAdditionalSuccesses\" href=\"#\" name=\"" + ProjectName + "Success\" onclick=\"ToggleSuccessVisibility('" + ProjectName + "'); return false;\">Hide " + Successes.Count + " " + singularPlural + "</a>", "background-color: rgb(239,245,249);"));
div4.Table.Tr.Add(trHide);
}
#endregion
#endregion
#endregion
html.Body.Div.Div3.Div4.Add(div4);
#endregion
#endregion
#endregion
#region Serialize
XmlDocument doc = XmlUtils.Serializar <Html>(html);
string xmltext = XmlUtils.GetXmlTexto(doc);
#endregion
#region Replace's
xmltext = "<!DOCTYPE html>\r\n" +
"<!-- saved from url=(0014)about:internet -->\r\n" + xmltext;
xmltext = xmltext.Replace("<", "<").Replace(">", ">").Replace("&", "&");
xmltext = xmltext.Replace("<html>", "<html xmlns:msxsl=\"urn:schemas-microsoft-com:xslt\">\r\n").Replace("<script>", "<script type=\"text/javascript\" language=\"javascript\">").Replace("<value>", "").Replace("</value>", "");
#endregion
File.WriteAllText(Folder + FileName, xmltext);
}
public SnpEffAnnotation(string annotation)
{
bool isSnpEffAnnotation = annotation.StartsWith("ANN=") || annotation.StartsWith("EFF=");
Annotation = isSnpEffAnnotation ? annotation.Substring(4) : annotation;
if (!isSnpEffAnnotation)
{
return;
}
string[] a = Annotation.Split('|');
Allele = a[0];
Effects = a[1].Split('&');
PutativeImpact = a[2];
GeneName = a[3];
GeneID = a[4];
FeatureType = a[5];
FeatureID = a[6];
TranscriptBiotype = a[7];
if (a[8].Split('/').Length > 0 && int.TryParse(a[8].Split('/')[0], out int x))
{
ExonIntronRank = x;
}
if (a[8].Split('/').Length > 1 && int.TryParse(a[8].Split('/')[1], out int y))
{
ExonIntronTotal = y;
}
HGVSNotationDnaLevel = a[9];
HGVSNotationProteinLevel = a[10];
if (a[11].Split('/').Length > 0 && int.TryParse(a[11].Split('/')[0], out x))
{
OneBasedTranscriptCDNAPosition = x;
}
if (a[11].Split('/').Length > 1 && int.TryParse(a[11].Split('/')[1], out y))
{
TranscriptCDNALength = y;
}
if (a[12].Split('/').Length > 0 && int.TryParse(a[12].Split('/')[0], out x))
{
OneBasedCodingDomainSequencePosition = x;
}
if (a[12].Split('/').Length > 1 && int.TryParse(a[12].Split('/')[1], out y))
{
CodingDomainSequenceLengthIncludingStopCodon = y;
}
if (a[13].Split('/').Length > 0 && int.TryParse(a[13].Split('/')[0], out x))
{
OneBasedProteinPosition = x;
}
if (a[13].Split('/').Length > 1 && int.TryParse(a[13].Split('/')[1], out y))
{
ProteinLength = y;
}
if (int.TryParse(a[14], out y))
{
DistanceToFeature = y;
}
Warnings = a[15].Split('&');
Missense = Effects.Any(eff => eff == "missense_variant");
Synonymous = !Effects.Any(eff => NonSynonymousVariations.Contains(eff));
FrameshiftVariant = Effects.Contains("frameshift_variant");
BadTranscript = Warnings.Any(w => BadTranscriptWarnings.Contains(w));
}
public SnpEffAnnotation(Variant variant, string annotation)
{
Variant = variant;
Annotation = annotation;
string[] a = annotation.Split('|');
Allele = a[0];
Effects = a[1].Split('&');
PutativeImpact = a[2];
GeneName = a[3];
GeneID = a[4];
FeatureType = a[5];
FeatureID = a[6];
TranscriptBiotype = a[7];
if (a[8].Split('/').Length > 0 && int.TryParse(a[8].Split('/')[0], out int x))
{
ExonIntronRank = x;
}
if (a[8].Split('/').Length > 1 && int.TryParse(a[8].Split('/')[1], out int y))
{
ExonIntronTotal = y;
}
HGVSNotationDnaLevel = a[9];
HGVSNotationProteinLevel = a[10];
if (a[11].Split('/').Length > 0 && int.TryParse(a[11].Split('/')[0], out x))
{
OneBasedTranscriptCDNAPosition = x;
}
if (a[11].Split('/').Length > 1 && int.TryParse(a[11].Split('/')[1], out y))
{
TranscriptCDNALength = y;
}
if (a[12].Split('/').Length > 0 && int.TryParse(a[12].Split('/')[0], out x))
{
OneBasedCodingDomainSequencePosition = x;
}
if (a[12].Split('/').Length > 1 && int.TryParse(a[12].Split('/')[1], out y))
{
CodingDomainSequenceLengthIncludingStopCodon = y;
}
if (a[13].Split('/').Length > 0 && int.TryParse(a[13].Split('/')[0], out x))
{
OneBasedProteinPosition = x;
}
if (a[13].Split('/').Length > 1 && int.TryParse(a[13].Split('/')[1], out y))
{
ProteinLength = y;
}
if (int.TryParse(a[14], out y))
{
DistanceToFeature = y;
}
Warnings = a[15].Split('&');
if (HGVSNotationProteinLevel != null)
{
GroupCollection hgvsProteinMatch = HGVSProteinRegex.Match(HGVSNotationProteinLevel).Groups;
if (hgvsProteinMatch.Count > 2)
{
ReferenceAminoAcid = ProteogenomicsUtility.amino_acids_3to1[hgvsProteinMatch[2].Value];
}
if (hgvsProteinMatch.Count > 3 && int.TryParse(hgvsProteinMatch[3].Value, out int location))
{
AminoAcidLocation = location;
}
if (hgvsProteinMatch.Count > 4)
{
AlternateAminoAcid = ProteogenomicsUtility.amino_acids_3to1[hgvsProteinMatch[4].Value];
}
}
Missense = Effects.Any(eff => eff == "missense_variant");
Synonymous = !Effects.Any(eff => NonSynonymousVariations.Contains(eff));
FrameshiftVariant = Effects.Contains("frameshift_variant");
BadTranscript = Warnings.Any(w => BadTranscriptWarnings.Contains(w));
}
public bool WouldThrow()
{
return(Errors.Any() || (Warnings.Any() && !_ignoreWarnings));
}
public bool Any() => Warnings.Any() || SafetyConcerns.Any() || SanityChecks.Any();
