/// <summary>
/// Build platform / target / assay metatree
/// </summary>
public static void BuildPlatformMetaTree()
{
string assayId, assayDb;
string sql = @"
select gene_fmly, gene_symbl, assy_nm, assy_db, assy_id_txt
from mbs_owner.cmn_assy_atrbts
where gene_fmly is not null and gene_symbl is not null and assy_nm is not null
order by lower(gene_fmly), lower(gene_symbl), lower(assy_nm)" ;
sql = AssayAttributesDao.AdjustAssayAttrsTableName(sql);
try
{
DbCommandMx drd = new DbCommandMx();
drd.Prepare(sql);
drd.ExecuteReader();
string family = "";
string targetSymbol = "";
string assayName = "";
MetaTreeNode familyMtn = null, targetMtn = null, tsMtn = null, assayMtn = null;
while (drd.Read())
{
string nextFamily = drd.GetString(0);
if (Lex.Ne(family, nextFamily)) // get current family node
{
family = nextFamily;
string familyNodeName = "GFTA_" + family.Replace(" ", "_"); // build name to match node
familyMtn = MetaTreeFactory.GetNode(familyNodeName);
}
string nextTargetSymbol = drd.GetString(1);
// if (Lex.Eq(nextTargetSymbol, "Adr1a")) nextTargetSymbol = nextTargetSymbol; // debug
if (Lex.Ne(targetSymbol, nextTargetSymbol)) // add new target node if going to new target
{
targetSymbol = nextTargetSymbol;
targetMtn = new MetaTreeNode();
targetMtn.Type = MetaTreeNodeType.Target;
targetMtn.Name = "TGT_ASSYS_" + targetSymbol.ToUpper();
targetMtn.Label = targetSymbol;
targetMtn.Target = targetMtn.Name;
MetaTreeFactory.AddNode(targetMtn);
if (familyMtn != null)
{
familyMtn.Nodes.Add(targetMtn);
}
tsMtn = new MetaTreeNode(); // add node for summary view by gene symbol
tsMtn.Type = MetaTreeNodeType.MetaTable;
tsMtn.Name = MultiDbAssayDataNames.BasePivotTablePrefix + targetSymbol.ToUpper();
tsMtn.Label = targetSymbol + " Assay Results Summary";
tsMtn.Target = tsMtn.Name;
MetaTreeNode mtn2 = MetaTreeFactory.GetNode(tsMtn.Name); // node with this name already exist?
if (mtn2 == null)
{
MetaTreeFactory.AddNode(tsMtn); // add to tree if doesn't exist
}
else
{
tsMtn = mtn2; // use existing node otherwise since this label doesn't have priority
}
if (targetMtn != null)
{
targetMtn.Nodes.Add(tsMtn);
}
}
string nextAssayName = drd.GetString(2);
if (Lex.Ne(assayName, nextAssayName))
{
assayName = nextAssayName;
assayDb = drd.GetString(3);
assayId = drd.GetString(4);
assayMtn = new MetaTreeNode();
assayMtn.Type = MetaTreeNodeType.MetaTable;
assayMtn.Name = assayId;
assayMtn.Target = assayMtn.Name;
assayMtn.Label = assayName;
MetaTreeNode mtn2 = MetaTreeFactory.GetNode(assayMtn.Name); // node with this name already exist?
if (mtn2 == null)
{
MetaTreeFactory.AddNode(assayMtn); // add to tree if doesn't exist
}
else
{
assayMtn = mtn2; // use existing node otherwise since this label doesn't have priority
}
if (targetMtn != null)
{
targetMtn.Nodes.Add(assayMtn);
}
}
}
drd.CloseReader();
drd.Dispose();
}
catch (Exception ex)
{
DebugLog.Message("TargetAssayMetafactory.Build Error:\r\n" + DebugLog.FormatExceptionMessage(ex));
return;
}
}
/// <summary>
/// Build pathway / target / assay metatree
/// Depends on BuildPlatformMetaTree being called first
/// and a node named Pathway_View already existing in the tree.
/// </summary>
public static void BuildPathwayMetaTree()
{
MetaTreeNode pathwayMtn = null, targetMtn;
StreamReader sr;
MetaTreeNode pathwayViewRoot = MetaTreeFactory.GetNode("Pathway_View");
if (pathwayViewRoot == null)
{
return;
}
string fileName = TargetMapDao.TargetMapDir + @"\pathway2gene.csv";
if (!File.Exists(fileName))
{
return;
}
try { sr = new StreamReader(fileName); }
catch (Exception ex) { return; }
string rec = sr.ReadLine(); // read header line
if (rec == null)
{
sr.Close();
return;
}
while (true)
{
rec = sr.ReadLine();
if (rec == null)
{
break;
}
List <string> toks = // Rec format: pathway, pathway_name, Target_Entrez_Gene_Id, target_gene_symbol, gene_family
Csv.SplitCsvString(rec);
string pathwayName = toks[0].Trim();
string pathwayCaption = toks[1].Trim();
string targetSymbol = toks[3].Trim();
string nodeName = "PATHWAY_" + pathwayName;
pathwayMtn = MetaTreeFactory.GetNode(nodeName); // node with this name already exist?
if (pathwayMtn == null) // add new pathway node
{
pathwayMtn = new MetaTreeNode();
pathwayMtn.Type = MetaTreeNodeType.SystemFolder;
pathwayMtn.Name = nodeName;
pathwayMtn.Label = pathwayCaption + " (" + pathwayName + ")";
MetaTreeFactory.AddNode(pathwayMtn);
pathwayViewRoot.Nodes.Add(pathwayMtn);
}
nodeName = "TGT_ASSYS_" + targetSymbol.ToUpper();
targetMtn = MetaTreeFactory.GetNode(nodeName);
if (targetMtn == null)
{
continue;
}
pathwayMtn.Nodes.Add(targetMtn);
}
sr.Close();
return;
}
