/// <summary>
/// Get subtree starting at specified node
/// </summary>
/// <param name="rootNodeName"></param>
/// <returns></returns>
public MetaTreeNode GetAfsSubtree(string rootNodeName)
{
if (ServiceFacade.UseRemoteServices)
{
NativeMethodTransportObject resultObject = ServiceFacade.CallServiceMethod(
ServiceCodes.MobiusMetaDataService,
MobiusMetaDataService.GetAfsSubtree,
new object[] { rootNodeName });
if (resultObject == null)
{
return(null);
}
MetaTreeNode mtn = resultObject.Value as MetaTreeNode;
return(mtn);
}
else
{
if (MetaTreeFactoryInstance == null)
{
MetaTreeFactoryInstance = new Mobius.MetaFactoryNamespace.MetaTreeFactory();
}
return(MetaTreeFactoryInstance.GetAfsSubtree(rootNodeName));
}
}
/// <summary>
/// Mark the MetaTree cache for rebuilding
/// </summary>
public void MarkCacheForRebuild()
{
if (ServiceFacade.UseRemoteServices)
{
NativeMethodTransportObject resultObject = ServiceFacade.CallServiceMethod(
ServiceCodes.MobiusMetaDataService,
MobiusMetaDataService.MarkCacheForRebuild,
null);
return;
}
else
{
if (MetaTreeFactoryInstance == null)
{
MetaTreeFactoryInstance = new Mobius.MetaFactoryNamespace.MetaTreeFactory();
}
MetaTreeFactoryInstance.MarkCacheForRebuild();
}
}
/// <summary>
/// Build & return the full MetaTree
/// </summary>
public Dictionary <string, MetaTreeNode> ReloadMetaTree()
{
if (ServiceFacade.UseRemoteServices)
{
NativeMethodTransportObject resultObject = ServiceFacade.CallServiceMethod(
ServiceCodes.MobiusMetaDataService,
MobiusMetaDataService.GetFullTree,
null);
Dictionary <string, MetaTreeNode> metaTree = (resultObject != null) ? (Dictionary <string, MetaTreeNode>)resultObject.Value : null;
return(metaTree);
}
else
{
if (MetaTreeFactoryInstance == null)
{
MetaTreeFactoryInstance = new Mobius.MetaFactoryNamespace.MetaTreeFactory();
}
return(MetaTreeFactoryInstance.ReloadMetaTree());
}
}
/// <summary>
/// Create MetaTable for a PubChem assay
/// </summary>
public MetaTable GetMetaTable(
string name)
{
MetaTable mt = null, mt2 = null, mt3 = null;
MetaColumn mc, mcc;
string txt, tok;
string aid;
string prefix = "pubchem_aid_";
if (!name.ToLower().StartsWith(prefix))
{
return(null);
}
int t0 = TimeOfDay.Milliseconds();
aid = name.Substring(prefix.Length);
XmlNode node;
XmlNodeList nodes;
TextReader rdr = GetAssayXml(aid);
if (rdr == null)
{
return(null);
}
XmlDocument doc = new XmlDocument();
doc.Load(rdr);
mt = new MetaTable();
mt.Name = "PUBCHEM_AID_" + aid.ToString();
mt.TableMap =
"(select * " +
"from mbs_owner.mbs_pbchm_rslt)";
mt.MetaBrokerType = MetaBrokerType.Pivot;
mt.Parent = MetaTableCollection.Get("pubchem_structure");
mt.TableFilterColumns = Csv.SplitCsvString("mthd_vrsn_id");
mt.TableFilterValues = Csv.SplitCsvString(aid);
mt.PivotMergeColumns = Csv.SplitCsvString("ext_cmpnd_id_nbr, rslt_grp_id");
mt.PivotColumns = Csv.SplitCsvString("rslt_typ_id");
XmlNamespaceManager nsmgr = new XmlNamespaceManager(doc.NameTable);
nsmgr.AddNamespace("ab", "http://www.ncbi.nlm.nih.gov"); // must look within this namespace
MetaTreeNode mtn = MetaTreeFactory.GetNode(mt.Name); // try to get label from contents tree
mtn = null;
if (mtn != null)
{
mt.Label = mtn.Label;
}
else
{
string dataSource = SelectNodeValue(doc, nsmgr, "//ab:PC-DBTracking_name");
string assayName = SelectNodeValue(doc, nsmgr, "//ab:PC-AssayDescription_name");
string outcomeMethod = SelectNodeValue(doc, nsmgr, "//ab:PC-AssayDescription_activity-outcome-method");
mt.Label = assayName;
if (outcomeMethod == "1")
{
outcomeMethod = "Primary";
}
else if (outcomeMethod == "2")
{
outcomeMethod = "Dose-Response";
}
else if (outcomeMethod == "3")
{
outcomeMethod = "Probe Summary";
}
else
{
outcomeMethod = "";
}
if (outcomeMethod.Length > 0)
{
mt.Label += " (" + outcomeMethod + ")";
}
}
if (mt.Label == "")
{
mt.Label = mt.Name;
}
mt.Description = // reference PubChem description page
"http://pubchem.ncbi.nlm.nih.gov/assay/assay.cgi?aid=" + aid;
nodes = doc.SelectNodes("//ab:PC-ResultType", nsmgr); // result types
// Build common metacolumns
mc = mt.AddMetaColumn("PUBCHEM_CID", "CID", MetaColumnType.CompoundId, ColumnSelectionEnum.Selected, 14);
mc.ColumnMap = "ext_cmpnd_id_nbr";
mc = mt.AddMetaColumn("PUBCHEM_SID", "SID", MetaColumnType.Integer, ColumnSelectionEnum.Selected, 7);
mc.ColumnMap = "rslt_val_nbr";
mc.PivotValues = Csv.SplitCsvString("1001"); // assign codes that won't interfere with assay-specific codes
mc = mt.AddMetaColumn("PUBCHEM_ACTIVITY_SCORE", "Activity Score", MetaColumnType.Integer, ColumnSelectionEnum.Selected, 7);
mc.ColumnMap = "rslt_val_nbr";
mc.PivotValues = Csv.SplitCsvString("1002");
mc = mt.AddMetaColumn("PUBCHEM_ACTIVITY_OUTCOME", "Activity Outcome", MetaColumnType.DictionaryId, ColumnSelectionEnum.Selected, 7);
mc.ColumnMap = "rslt_val_nbr";
mc.Dictionary = "PubChemActivityOutcome"; // code stored in db must be translated via dictionary
mc.PivotValues = Csv.SplitCsvString("1003");
mc = mt.AddMetaColumn("PUBCHEM_ACTIVITY_URL", "Activity URL", MetaColumnType.Hyperlink, ColumnSelectionEnum.Selected, 7);
mc.ColumnMap = "rslt_val_txt";
mc.PivotValues = Csv.SplitCsvString("1004");
// Build assay-specific metacolumns
for (int ci = 0; ci < nodes.Count; ci++)
{
node = nodes[ci];
string typeId = SelectNodeValue(node, nsmgr, ".//ab:PC-ResultType_tid"); // get values relative to node (need "." in xpath string)
string typeName = SelectNodeValue(node, nsmgr, ".//ab:PC-ResultType_type");
string colName = SelectNodeValue(node, nsmgr, ".//ab:PC-ResultType_name");
string desc = SelectNodeValue(node, nsmgr, ".//ab:PC-ResultType_description_E");
if (desc.IndexOf(", unit: ") > 0) // shorten label a bit
{
desc = desc.Replace(", unit: ", " (");
if (desc.EndsWith("."))
{
desc = desc.Substring(0, desc.Length - 1);
}
desc += ")";
}
string unit = SelectNodeValue(node, nsmgr, ".//ab:PC-ResultType_unit");
if (unit == "")
{
unit = SelectNodeValue(node, nsmgr, ".//ab:PC-ResultType_sunit");
}
if (Lex.Eq(unit, "none") || Lex.Eq(unit, "unspecified"))
{
unit = "";
}
if (unit.EndsWith("ml"))
{
unit = unit.Substring(0, unit.Length - 2) + "/mL";
}
string transform = SelectNodeValue(node, nsmgr, ".//ab:PC-ResultType_transform");
mc = new MetaColumn();
mc.PivotValues = Csv.SplitCsvString(typeId);
mc.Name = "R_" + typeId;
mc.Label = colName;
if (unit != "")
{
mc.Label += " (" + unit + ")";
}
if (mc.Label == "")
{
mc.Label = mc.Name;
}
//mc.Label = desc; // user longer description for label
//if (mc.Label == "") mc.Label = mc.Label;
mc.Format = ColumnFormatEnum.Default;
mc.Decimals = -1;
mc.InitialSelection = ColumnSelectionEnum.Selected;
if (Lex.Eq(typeName, "float"))
{
mc.DataType = MetaColumnType.Number;
mc.Width = 8;
mc.ColumnMap = "rslt_val_nbr";
}
else if (Lex.Eq(typeName, "int"))
{
mc.DataType = MetaColumnType.Number;
mc.Width = 8;
mc.Format = ColumnFormatEnum.Decimal;
mc.Decimals = 0;
mc.ColumnMap = "rslt_val_nbr";
}
else if (Lex.Eq(typeName, "bool"))
{
mc.DataType = MetaColumnType.Number;
mc.Width = 8;
mc.ColumnMap = "rslt_val_nbr";
}
else if (Lex.Eq(typeName, "string"))
{
mc.DataType = MetaColumnType.String;
mc.Width = 8;
mc.ColumnMap = "rslt_val_txt";
}
else
{
throw new Exception("Invalid type" + typeName);
}
mc.MetaTable = mt;
mt.AddMetaColumn(mc);
}
mc = mt.AddMetaColumn("PUBCHEM_ASSAYDATA_COMMENT", "Comment", MetaColumnType.String, ColumnSelectionEnum.Unselected, 7);
mc.ColumnMap = "rslt_val_txt";
mc.PivotValues = Csv.SplitCsvString("1005");
mc = mt.AddMetaColumn("PUBCHEM_EXT_DATASOURCE_REG", "Ext. Source. Reg. Id", MetaColumnType.String, ColumnSelectionEnum.Unselected, 7);
mc.ColumnMap = "rslt_val_txt";
mc.PivotValues = Csv.SplitCsvString("1006");
mc = mt.AddMetaColumn("PUBCHEM_ASSAYDATA_REVOKE", "Revoked", MetaColumnType.String, ColumnSelectionEnum.Hidden, 7);
mc.ColumnMap = "rslt_val_txt";
mc.PivotValues = Csv.SplitCsvString("1007");
MetaTableFactory.SetAnyNewMetaTableLabel(mt); // if table has been renamed the set new label
foreach (MetaColumn mc2 in mt.MetaColumns)
{
MetaTableFactory.SetAnyNewMetaColumnLabel(mc2); // if col has been renamed then set new label
}
GetMetaTableCount++;
t0 = TimeOfDay.Milliseconds() - t0;
GetMetaTableTime += t0;
GetMetaTableAvgTime = GetMetaTableTime / GetMetaTableCount;
return(mt);
}
/// <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;
}
