/// <summary>
/// Get the root table associated with a compound id prefix
/// </summary>
/// <param name="prefix"></param>
/// <param name="rti"></param>
/// <param name="mtRoot"></param>
public static void GetRootMetaTableFromPrefix(
string prefix,
out RootTable rti,
out MetaTable mtRoot)
{
rti = null;
mtRoot = null;
if (prefix == "")
{
prefix = "none"; // no prefix
}
if (PrefixToRootTableDict.ContainsKey(prefix)) // already have root info?
{
rti = PrefixToRootTableDict[prefix];
mtRoot = PrefixToRootMetaTableDict[prefix];
return;
}
rti = RootTable.GetFromPrefix(prefix);
if (rti == null)
{
return;
}
string mtName = rti.MetaTableName;
mtRoot = MetaTableCollection.Get(mtName);
PrefixToRootTableDict[prefix] = rti;
PrefixToRootMetaTableDict[prefix] = mtRoot;
return;
}
/// <summary>
/// Build query to fetch all unsummarized assay data for a target
/// </summary>
/// <param name="geneSymbol"></param>
/// <returns></returns>
public static Query BuildTargetAssayUnsummarizedDataQuery(
string geneSymbol)
{
Query q = new Query();
MetaTable mt = MetaTableCollection.Get(UnsummarizedMetaTableName);
QueryTable qt = new QueryTable(mt);
q.AddQueryTable(qt);
q.SingleStepExecution = true; // for performance
q.KeySortOrder = 0; // no sorting
return(q);
}
/// <summary>
/// Deserialize old format conditional formatting.
/// </summary>
/// <param name="serializedForm"></param>
/// <returns></returns>
public static CondFormat DeserializeOld(
string serializedForm)
{
CondFormat cf = new CondFormat();
string[] sa = serializedForm.Split('\n');
string[] sa2 = sa[0].Split('\t');
// cf.IsCSF = Boolean.Parse(sa2[0]); // (obsolete)
if (sa2.Length >= 3)
{
MetaTable mt = MetaTableCollection.Get(sa2[1]);
if (mt == null)
{
return(null);
}
MetaColumn mc = mt.GetMetaColumnByName(sa2[2]);
if (mc != null)
{
cf.ColumnType = mc.DataType;
}
}
if (sa.Length > 1 && sa[1] != "")
{
cf.Rules.Add(CondFormatRules.DeserializeOld(sa[1]));
}
if (sa.Length > 2 && sa[2] != "")
{
cf.Rules.Add(CondFormatRules.DeserializeOld(sa[2]));
}
if (sa.Length > 3 && sa[3] != "")
{
cf.Rules.Add(CondFormatRules.DeserializeOld(sa[3]));
}
if (sa.Length > 4 && sa[4] != "")
{
cf.Rules.Add(CondFormatRules.DeserializeOld(sa[4]));
}
return(cf);
}
/// <summary>
/// Parse serialized form of calculated field
/// </summary>
/// <param name="content"></param>
/// <returns></returns>
public static CalcField DeserializeOld(
string content)
{
MetaTable mt, mt2;
string mtName;
CalcField cf = new CalcField();
CalcFieldColumn c1 = cf.Column1;
CalcFieldColumn c2 = cf.Column2;
string[] sa = content.Split('\t');
cf.CalcType = CalcTypeEnum.Basic; // assume basic type
if (sa[0] != "")
{
mt = MetaTableCollection.GetWithException(sa[0]);
if (mt.SummarizedExists && !mt.UseSummarizedData)
{ // use summarized form if exists
mtName = mt.Name + MetaTable.SummarySuffix;
mt2 = MetaTableCollection.Get(mtName);
if (mt2 != null && mt2.GetMetaColumnByName(sa[1]) != null)
{
mt = mt2;
}
}
c1.MetaColumn = mt.GetMetaColumnByNameWithException(sa[1]);
if (c1.MetaColumn == null)
{
return(null);
}
c1.Function = sa[2];
c1.Constant = sa[3];
cf.Operation = sa[4];
}
if (sa.Length <= 5 || // old form with only first field defined
(sa.Length == 6 && String.IsNullOrEmpty(sa[5])))
{
cf.SetDerivedValues();
return(cf);
}
if (sa[6] != "")
{
mt = MetaTableCollection.GetWithException(sa[5]);
if (mt == null)
{
return(null);
}
if (mt.SummarizedExists && !mt.UseSummarizedData)
{ // use summarized form if exists
mtName = mt.Name + MetaTable.SummarySuffix;
mt2 = MetaTableCollection.Get(mtName);
if (mt2 != null && mt2.GetMetaColumnByName(sa[6]) != null)
{
mt = mt2;
}
}
c2.MetaColumn = mt.GetMetaColumnByNameWithException(sa[6]);
if (c2.MetaColumn == null)
{
return(null);
}
c2.Function = sa[7];
c2.Constant = sa[8];
}
if (sa.Length >= 13) // get other values if new form
{
EnumUtil.TryParse(sa[9], out cf.CalcType);
cf.AdvancedExpr = sa[10];
string obsoleteIncludedQueryXml = sa[11]; // obsolete cf.IncludedQueryXml
cf.Description = sa[12];
}
cf.SetDerivedValues();
return(cf);
}
/// <summary>
/// Deserialize CalcField from an XmlTextReader
/// </summary>
/// <param name="tr"></param>
/// <returns></returns>
public static CalcField Deserialize(
XmlTextReader tr)
{
string mtName, mcName, txt, errMsg = "";
MetaTable mt;
MetaColumn mc;
CalcField cf = new CalcField();
XmlUtil.GetStringAttribute(tr, "Name", ref cf.UserObject.Name);
txt = tr.GetAttribute("CalcType");
EnumUtil.TryParse(txt, out cf.CalcType);
if (cf.CalcType != CalcTypeEnum.Basic && cf.CalcType != CalcTypeEnum.Advanced)
{
cf.CalcType = CalcTypeEnum.Basic; // default to basic type
}
txt = tr.GetAttribute("SourceColumnType");
if (txt != null)
{
cf.SourceColumnType = MetaColumn.ParseMetaColumnTypeString(txt);
}
txt = tr.GetAttribute("PreclassificationlResultType");
if (txt != null)
{
cf.PreclassificationlResultType = MetaColumn.ParseMetaColumnTypeString(txt);
}
for (int ci = 1; ; ci++) // get the set of columns
{
mtName = tr.GetAttribute("Table" + ci);
if (String.IsNullOrEmpty(mtName))
{
//if (ci == 1) continue; // first col may be undefined
//else
if (ci > 1)
{
break; // if beyond the first then col then all done
}
}
if (ci > cf.CfCols.Count)
{
cf.CfCols.Add(new CalcFieldColumn());
}
CalcFieldColumn cfc = cf.CfCols[ci - 1];
mt = MetaTableCollection.Get(mtName);
if (mt != null)
{
mcName = tr.GetAttribute("Column" + ci);
if (mcName != null)
{
cfc.MetaColumn = mt.GetMetaColumnByName(mcName);
if (cfc.MetaColumn == null)
{
errMsg += "Unable to find column: " + mcName + " in data table " + mt.Label + "(" + mt.Name + ")\r\n";
}
}
}
else if (ci != 1)
{
errMsg += "Unable to find data table: " + mtName + "\r\n";
}
txt = tr.GetAttribute("Function" + ci);
if (txt != null)
{
cfc.Function = txt;
}
txt = tr.GetAttribute("Constant" + ci);
if (txt != null)
{
cfc.Constant = txt;
}
}
txt = tr.GetAttribute("Operation");
if (txt != null)
{
cf.Operation = txt;
}
XmlUtil.GetStringAttribute(tr, "AdvancedExpr", ref cf.AdvancedExpr);
XmlUtil.GetStringAttribute(tr, "OuterJoinRoot", ref cf.OuterJoinRoot);
XmlUtil.GetStringAttribute(tr, "ColumnLabel", ref cf.ColumnLabel);
XmlUtil.GetStringAttribute(tr, "Description", ref cf.Description);
XmlUtil.GetStringAttribute(tr, "Prompt", ref cf.Prompt);
if (!tr.IsEmptyElement)
{
tr.Read();
tr.MoveToContent();
if (Lex.Eq(tr.Name, "CondFormat")) // and cond format
{
if (!tr.IsEmptyElement)
{
cf.Classification = CondFormat.Deserialize(tr);
}
tr.Read(); // get next element
tr.MoveToContent();
}
if (!Lex.Eq(tr.Name, "CalcField") || tr.NodeType != XmlNodeType.EndElement)
{
throw new Exception("CalcField.Deserialize - Expected CalcField end element");
}
}
cf.SetDerivedValues();
return(cf);
}
/// <summary>
/// Get default key MetaTable
/// </summary>
/// <returns></returns>
public static MetaTable GetDefaultRootMetaTable()
{
return(MetaTableCollection.Get("corp_structure")); // todo: set from parameter
}