private void AddMissingEntries(AnalysisOutput output, AnalyzerLanguage language)
{
var foundKeys = output.Issues.Select(i => i.RuleId).ToList();
var notFoundKeys = RuleFinder.GetAnalyzerTypes(language)
.Select(t =>
new
{
Type = t,
RuleAttribute = t.GetCustomAttribute <RuleAttribute>()
})
.Select(rule =>
RuleFinder.IsRuleTemplate(rule.Type)
? string.Format(TemplateRuleIdPattern, rule.RuleAttribute.Key)
: rule.RuleAttribute.Key)
.Where(s => !foundKeys.Contains(s));
foreach (var notFoundKey in notFoundKeys)
{
output.Issues.Add(new Issue
{
RuleId = notFoundKey
});
}
}
private void SplitAndStoreOmstarByIssueType(AnalysisOutput omstar)
{
foreach (var issueGroup in omstar.Issues.GroupBy(issue => issue.RuleId))
{
var omstarForRule = new AnalysisOutput
{
ToolInfo = omstar.ToolInfo,
Version = omstar.Version,
Issues = issueGroup
.OrderBy(issue =>
{
var location = issue.Locations.FirstOrDefault();
return(location == null ? string.Empty : location.AnalysisTarget.Uri);
}, new InvariantCultureStringSortComparer())
.ThenBy(issue =>
{
var location = issue.Locations.FirstOrDefault();
return(location == null ? 0 : location.AnalysisTarget.Region.StartLine);
})
.ThenBy(issue =>
{
var location = issue.Locations.FirstOrDefault();
return(location == null ? 0 : location.AnalysisTarget.Region.EndLine);
})
.ThenBy(issue =>
{
return(issue.FullMessage);
}, new InvariantCultureStringSortComparer())
.ToList()
};
var content = JsonConvert.SerializeObject(omstarForRule,
new JsonSerializerSettings
{
NullValueHandling = NullValueHandling.Ignore,
Formatting = Formatting.Indented
});
File.WriteAllText(Path.Combine(
AnalysisOutputDirectory.FullName, string.Format("{0}.json", issueGroup.Key)), content);
}
}
private static AnalysisOutput GenerateOmstarOutput(ErrorModels.Xml.AnalysisOutput xml)
{
var assemblyName = xml.GetType().Assembly.GetName();
var omstar = new AnalysisOutput
{
Version = "0.1",
ToolInfo = new ToolInfo
{
FileVersion = "1.0.0",
ToolName = assemblyName.Name
},
Issues = xml.Files.SelectMany(f => f.Issues.Select(i => new Issue
{
FullMessage = i.Message,
RuleId = i.Id,
Properties = null,
Locations = new List <IssueLocation>
{
new IssueLocation
{
AnalysisTarget = new AnalysisTarget
{
Region = new Region
{
StartLine = i.Line,
EndLine = i.Line,
StartColumn = 0,
EndColumn = int.MaxValue
},
Uri = f.Path
}
}
}
})).ToList()
};
return(omstar);
}
public static async Task <string> Run([HttpTrigger(AuthorizationLevel.Anonymous, "post", Route = null)] HttpRequest req, ILogger log)
{
var defaultTimeLimit = TimeSpan.FromMinutes(2);
var content = await new StreamReader(req.Body).ReadToEndAsync();
var input = JsonConvert.DeserializeObject <AnalysisInput>(content);
try
{
var output = Utilities.RunWithTimeLimit(() => Analysis.Analyze(input), defaultTimeLimit);
return(JsonConvert.SerializeObject(output));
}
catch (BackendUtilities.TimeoutException ex)
{
var result = new AnalysisOutput
{
Error = "Operation was not completed in " + defaultTimeLimit.ToString(),
Status = BioModelAnalyzer.StatusType.Error
};
return(JsonConvert.SerializeObject(result));
}
}
/// <summary>
/// Clears the session state
/// </summary>
public void ClearState()
{
MemoryRegion.RemoveVariablesInScope(VariableType.Standard);
if (DataInfo != null)
{
DataInfo.Dispose();
}
OverriddenSetOptions = new Dictionary<string, string>(StringComparer.OrdinalIgnoreCase);
DataInfo = new DataSourceInfo();
Recodes.Clear();
Reset();
CurrentRead = null;
IsFirstStatement = false;
ProgramText.Length = 0;
DataTableRefreshNeeded = true;
AnalysisOut = new AnalysisOutput(this);
isCancelRequest = false;
GroupVariableList = new Dictionary<string, List<string>>();
}
private void Initialize()
{
GroupVariableList = new Dictionary<string, List<string>>(StringComparer.OrdinalIgnoreCase);
StatisticModuleList = new Dictionary<string, System.Reflection.Assembly>(StringComparer.OrdinalIgnoreCase);
CommandToAssemblyMap = new Dictionary<string, string>(StringComparer.OrdinalIgnoreCase);
DLLClassList = new Dictionary<string, IDLLClass>();
foreach (string s in System.Configuration.ConfigurationSettings.AppSettings)
{
switch (s.ToUpper())
{
case "FREQUENCY":
case "TABLES":
case "SUMMARIZE":
case "GRAPH":
case "MEANS":
case "MATCH":
case "LINEARREGRESSION":
case "LOGISTICREGRESSION":
case "COMPLEXSAMPLEMEANS":
case "COMPLEXSAMPLETABLES":
case "COMPLEXSAMPLEFREQUENCY":
case "KAPLANMEIERSURVIVAL":
case "COXPROPORTIONALHAZARDS":
string StatisticsAssembly = System.Configuration.ConfigurationSettings.AppSettings[s].ToString();
if (! StatisticModuleList.ContainsKey(StatisticsAssembly))
{
System.Reflection.Assembly a = System.Reflection.Assembly.Load(StatisticsAssembly);
StatisticModuleList.Add(StatisticsAssembly, a);
}
CommandToAssemblyMap.Add(s, StatisticsAssembly);
break;
}
}
ConnectionList = new Dictionary<string, IDataSource>(StringComparer.OrdinalIgnoreCase);
DataTableRefreshNeeded = true;
CurrentSelect = new StringBuilder();
PermanantVariables = new System.Collections.Specialized.NameValueCollection();
GlobalVariables = new System.Collections.Specialized.NameValueCollection();
StandardVariables = new Dictionary<string, string>(StringComparer.OrdinalIgnoreCase);
SelectString = new StringBuilder();
SelectExpression = new List<Epi.Core.AnalysisInterpreter.AnalysisRule>();
SortExpression = new StringBuilder();
DataSet = new System.Data.DataSet();
DataInfo = new DataSourceInfo();
ProgramText = new StringBuilder();
IsFirstStatement = false;
Recodes = new Dictionary<string, Epi.Core.AnalysisInterpreter.Rules.RecodeList>(StringComparer.OrdinalIgnoreCase);
VariableExpressionList = new Dictionary<string, AnalysisRule>(StringComparer.OrdinalIgnoreCase);
VariableValueList = new Dictionary<string, object>(StringComparer.OrdinalIgnoreCase);
AnalysisOut = new AnalysisOutput(this);
OverriddenSetOptions = new Dictionary<string, string>(StringComparer.OrdinalIgnoreCase);
SelectCommandList.Add(CommandNames.ABS);
SelectCommandList.Add(CommandNames.AND);
SelectCommandList.Add(CommandNames.ALWAYS);
SelectCommandList.Add(CommandNames.APPEND);
SelectCommandList.Add(CommandNames.MOD);
SelectCommandList.Add(CommandNames.LIKE);
SelectCommandList.Add(CommandNames.OR);
SelectCommandList.Add(CommandNames.XOR);
SelectCommandList.Add(CommandNames.NOT);
SelectCommandList.Add(CommandNames.EXP);
SelectCommandList.Add(CommandNames.LN);
SelectCommandList.Add(CommandNames.LOG);
SelectCommandList.Add(CommandNames.NUMTODATE);
SelectCommandList.Add(CommandNames.NUMTOTIME);
SelectCommandList.Add(CommandNames.RECORDCOUNT);
SelectCommandList.Add(CommandNames.RND);
SelectCommandList.Add(CommandNames.ROUND);
SelectCommandList.Add(CommandNames.STEP);
SelectCommandList.Add(CommandNames.SIN);
SelectCommandList.Add(CommandNames.COS);
SelectCommandList.Add(CommandNames.TAN);
SelectCommandList.Add(CommandNames.TRUNC);
SelectCommandList.Add(CommandNames.PFROMZ);
SelectCommandList.Add(CommandNames.ZSCORE);
SelectCommandList.Add(CommandNames.YEARS);
SelectCommandList.Add(CommandNames.MONTHS);
SelectCommandList.Add(CommandNames.DAYS);
SelectCommandList.Add(CommandNames.YEAR);
SelectCommandList.Add(CommandNames.MONTH);
SelectCommandList.Add(CommandNames.DAY);
SelectCommandList.Add(CommandNames.CURRENTUSER);
SelectCommandList.Add(CommandNames.EXISTS);
SelectCommandList.Add(CommandNames.FILEDATE);
SelectCommandList.Add(CommandNames.SYSTEMDATE);
SelectCommandList.Add(CommandNames.SYSTEMTIME);
SelectCommandList.Add(CommandNames.HOURS);
SelectCommandList.Add(CommandNames.MINUTES);
SelectCommandList.Add(CommandNames.SECONDS);
SelectCommandList.Add(CommandNames.HOUR);
SelectCommandList.Add(CommandNames.MINUTE);
SelectCommandList.Add(CommandNames.SECOND);
SelectCommandList.Add(CommandNames.FINDTEXT);
SelectCommandList.Add(CommandNames.FORMAT);
SelectCommandList.Add(CommandNames.LINEBREAK);
SelectCommandList.Add(CommandNames.STRLEN);
SelectCommandList.Add(CommandNames.SUBSTRING);
SelectCommandList.Add(CommandNames.TXTTONUM);
SelectCommandList.Add(CommandNames.TXTTODATE);
SelectCommandList.Add(CommandNames.UPPERCASE);
}
