/// <summary>
/// Write out the data and return the html/js to open the template .dxp file with the exported data file
/// </summary>
/// <param name="q"></param>
/// <param name="trvp"></param>
/// <returns></returns>
public static string CreateSpotfireAnalysisDocument(
Query q,
TargetSummaryOptions trvp)
{
ExportParms ep = new ExportParms();
ep.OutputDestination = OutputDest.TextFile;
ep.ExportFileFormat = ExportFileFormat.Csv;
ep.OutputFileName = TempFile.GetTempFileName(".csv"); // temp .csv file to export to
ep.IncludeDataTypes = true;
string result = UalUtil.IQueryExec.RunQuery(q, ep); // do the export
if (result == null)
{
return(null); // just return if cancelled
}
string templateLibFolder = // unc name of the lib folder (not currently used)
ServicesIniFile.Read("SpotfireLibraryFolder");
string templateLibUrl = // url of the library containing the Mobius templates
ServicesIniFile.Read("SpotfireLibraryUrl");
templateLibUrl = @"http://[server]/SpotfireWeb/Library.aspx?folder=DCRT%20(chemistry)%20users/Mobius/Templates";
string templateUrl = templateLibUrl + "/MultiDbView";
string html = templateUrl; // todo, build html/js to open the template with the specified file
return(html);
}
/// <summary>
/// Create a Spotfire Analysis Document displaying data for the specified
/// query using the template and other formatting info in the SpotfireParms.
/// </summary>
/// <param name="q"></param>
/// <param name="stp"></param>
/// <returns></returns>
public static string CreateSpotfireAnalysisDocument(
Query q,
TargetSummaryOptions trvp)
{
string serializedQuery = q.Serialize();
string serializedTrvp = trvp.Serialize();
if (ServiceFacade.UseRemoteServices)
{
Mobius.Services.Native.INativeSession nativeClient = ServiceFacade.CreateNativeSessionProxy();
Services.Native.NativeMethodTransportObject resultObject =
ServiceFacade.InvokeNativeMethod(nativeClient,
(int)Services.Native.ServiceCodes.MobiusTargetResultsViewerService,
(int)Services.Native.ServiceOpCodes.MobiusTargetResultsViewerService.CreateSpotfireAnalysisDocument,
new Services.Native.NativeMethodTransportObject(new object[] { serializedQuery, serializedTrvp }));
((System.ServiceModel.IClientChannel)nativeClient).Close();
if (resultObject == null || resultObject.Value == null)
{
return(null);
}
string path = resultObject.Value.ToString();
return(path);
}
else
{
q = Query.Deserialize(serializedQuery);
trvp = TargetSummaryOptions.Deserialize(serializedTrvp);
string path = Mobius.ToolServices.TargetResultsViewerService.CreateSpotfireAnalysisDocument(q, trvp);
return(path);
}
}
/// <summary>
/// Setup the form values
/// </summary>
/// <param name="tso"></param>
public void SetFormValues(
TargetSummaryOptions tso,
bool allowDbChange)
{
InSetup = true;
Tso = tso; // TargetSummaryOptions instance associated with this control
Cids.Text = tso.CidCriteria; // set initial cid criteria
InSetup = false;
return;
}
/// <summary>
/// Allocate & initialize a TargetResultsViewerParms instance
/// </summary>
/// <returns></returns>
public static TargetSummaryOptions GetPreferences()
{
TargetSummaryOptions tso;
string tsoString = Preferences.Get("MultiDbViewerPrefs");
if (Lex.Contains(tsoString, "MultiDbViewerPrefs"))
{
tso = TargetSummaryOptions.Deserialize(tsoString);
}
else
{
tso = new TargetSummaryOptions();
}
return(tso);
}
/// <summary>
/// Load any target map info
/// </summary>
void LoadTargetMap()
{
try
{
Tso = TargetSummaryOptions.GetFromMdbAssayOptionsColumn(Qt);
if (Tso == null || Lex.IsNullOrEmpty(Tso.TargetMapName))
{
return;
}
TargetMap = TargetMapDao.GetMapByLabel(Tso.TargetMapName); // get the basics
TargetMap = TargetMapDao.GetMapWithCoords(TargetMap.Name); // get the coords
return;
}
catch (Exception ex) { return; } // just return if "none" or no longer exists
}
object IInvokeServiceOps.InvokeServiceOperation(int opCode, object[] args)
{
MobiusTargetResultsViewerService op = (MobiusTargetResultsViewerService)opCode;
switch (op)
{
case MobiusTargetResultsViewerService.CreateSpotfireAnalysisDocument:
{
string serializedQuery = (string)args[0];
Mobius.Data.Query q = Mobius.Data.Query.Deserialize(serializedQuery);
string serializedTrvp = (string)args[1];
TargetSummaryOptions trvp = TargetSummaryOptions.Deserialize(serializedTrvp);
string path = Mobius.ToolServices.TargetResultsViewerService.CreateSpotfireAnalysisDocument(q, trvp);
return(path);
}
}
return(null);
}
/// <summary>
/// Summarize unpivoted unsummarized assay data by target
/// </summary>
/// <param name="parms"></param>
/// <param name="qm2"></param>
/// <returns></returns>
public QueryManager SummarizeByTargetUnpivoted(
TargetSummaryOptions summaryOptions,
QueryManager qm2)
{
// This method takes an unpivoted input query, summarizes it according to the summarization parameters
// and then formats the summarized data according to the specified output format.
// If a targetMap is specified then then coordinates are included in the output, the summarization
// level must be target, and the output format must be unpivoted.
QueryTable qt, qt2;
DataRowMx dr, dr2;
DataRowAttributes dra;
string cid = "", currentCid;
int rti, rfi;
AssayDict tad = TargetAssayDict; // be sure target assay dict has been loaded
TargetAssaySummarizationLevel sumLevel = TargetAssaySummarizationLevel.Target; // target level
SummarizationType sumMethod = summaryOptions.UseMeans ? SummarizationType.BioResponseMean : SummarizationType.MostPotent;
OutputDest outputDest = OutputDest.WinForms;
TargetMap targetMap = TargetMapDao.GetMapWithCoords(summaryOptions.TargetMapName);
qt = Query.GetQueryTableByName(MultiDbAssayDataNames.CombinedNonSumTableName);
if (qt == null)
{
throw new Exception("Query table not found: " + MultiDbAssayDataNames.CombinedNonSumTableName);
}
UnpivotedAssayResultFieldPositionMap voMap = UnpivotedAssayResultFieldPositionMap.NewOriginalMap(); // used for fast indexing of value by col name
voMap.InitializeFromQueryTableVoPositions(qt, 0);
if (qm2 == null) // need to create query manager?
{
qm2 = new QueryManager();
qm2 = InitializeSubqueryQm(MultiDbAssayDataNames.CombinedNonSumTableName);
}
Query q2 = qm2.Query;
qt2 = q2.GetQueryTableByNameWithException(MultiDbAssayDataNames.BaseTableName);
UnpivotedAssayResultFieldPositionMap voMap2 = UnpivotedAssayResultFieldPositionMap.NewOriginalMap(); // used for fast indexing of value by col name
voMap2.InitializeFromQueryTableVoPositions(qt2, 0);
// Summarize rows & store in DataSet
qm2.DataTable.Clear();
Dictionary <string, object> includedTargets = null;
if (summaryOptions.TargetsWithActivesOnly)
{ // scan data & make a list of targets to be included
includedTargets = new Dictionary <string, object>();
// ...
}
List <UnpivotedAssayResult> tars = new List <UnpivotedAssayResult>(); // build list of TA rows here
currentCid = "";
for (int dri = 0; dri <= DataTableMx.Rows.Count; dri++)
{
if (dri < DataTableMx.Rows.Count)
{
dr = DataTableMx.Rows[dri];
cid = dr[KeyValueVoPos] as string;
dra = GetRowAttributes(dr);
if (dra != null && dra.Filtered)
{
continue;
}
if (currentCid == "")
{
currentCid = cid;
}
}
else
{
dr = null;
}
if (dr == null || cid != currentCid)
{ // summarize rows for current cid & add to new datatable
if (tars.Count > 0) //
{
List <UnpivotedAssayResult> sumTars = TargetAssayUtil.SummarizeData(
tars,
sumLevel,
sumMethod,
true,
NullValue.NullNumber,
NullValue.NullNumber,
targetMap);
int voLength2 = qm2.DataTable.Columns.Count;
foreach (UnpivotedAssayResult sumTar in sumTars)
{
object[] vo2 = sumTar.ToValueObject(voLength2, voMap2);
dr2 = qm2.DataTable.NewRow();
dr2.ItemArrayRef = vo2; // copy ref for efficiency since vo won't be changed
qm2.DataTable.Rows.Add(dr2);
}
}
if (dr == null)
{
break;
}
tars.Clear();
currentCid = cid;
}
UnpivotedAssayResult tar = UnpivotedAssayResult.FromValueObjectNew(dr.ItemArray, voMap);
tars.Add(tar); // store in form for summarization
}
qm2.DataTableManager.InitializeRowAttributes();
return(qm2);
}
/// <summary>
/// Setup the form values
/// </summary>
/// <param name="tso"></param>
public void SetFormValues(
TargetSummaryOptions tso,
bool allowDbChange)
{
InSetup = true;
Tso = tso; // TargetSummaryOptions instance associated with this control
if (!Initialized)
{
InitializeTargetMapControl(tso);
}
Cids.Text = tso.CidCriteria; // set initial cid criteria
Targets.Text = tso.TargetList;
GeneFamilies.Text = tso.GeneFamilies;
if (Lex.Eq(tso.DbName, "CorpDb"))
{
CorpDb.Checked = true;
}
else
{
CorpDbAndChemblDb.Checked = true;
}
DatabaseGroupBox.Enabled = allowDbChange; // allow database changes only if no query so far
TableView.Checked = true; // default view
if (Lex.Eq(tso.PreferredView, "Table"))
{
TableView.Checked = true;
}
else if (Lex.Eq(tso.PreferredView, "Map"))
{
MapView.Checked = true;
}
else if (Lex.Eq(tso.PreferredView, "Network"))
{
NetworkView.Checked = true;
}
else if (Lex.Eq(tso.PreferredView, "Heatmap"))
{
HeatmapView.Checked = true;
}
else if (Lex.Eq(tso.PreferredView, "WebPlayer"))
{
WebPlayerView.Checked = true;
}
IncludeStructures.Checked = tso.IncludeStructures;
TargetsWithActivesOnly.Checked = tso.TargetsWithActivesOnly;
AssayTypes = tso.AssayTypesToInclude;
MaxCRC.Text = tso.CrcUpperBound;
MinSP.Text = tso.SpLowerBound;
if (tso.UseMeans)
{
MeanSummarization.Checked = true;
}
else
{
MinMaxSummarization.Checked = true;
}
FilterableTargets.Text = tso.FilterableTargets;
InSetup = false;
return;
}
/// <summary>
/// Save preferences
/// </summary>
/// <param name="tso"></param>
public static void SavePreferences(TargetSummaryOptions tso)
{
string tsoString = tso.Serialize();
Preferences.Set("MultiDbViewerPrefs", tsoString);
}
/// <summary>
/// GetFormValues
/// </summary>
/// <param name="tso"></param>
/// <returns></returns>
public bool GetFormValues(
TargetSummaryOptions tso)
{
tso.CidCriteria = Cids.Text;
tso.TargetList = Targets.Text;
tso.GeneFamilies = GeneFamilies.Text;
if (CorpDb.Checked)
{
tso.DbName = "CorpDb";
}
else
{
tso.DbName = "CorpDbChEMBL";
}
if (TableView.Checked)
{
tso.PreferredView = "Table";
}
else if (MapView.Checked)
{
tso.PreferredView = "Map";
}
else if (NetworkView.Checked)
{
tso.PreferredView = "Network";
}
else if (HeatmapView.Checked)
{
tso.PreferredView = "Heatmap";
}
else if (WebPlayerView.Checked)
{
tso.PreferredView = "WebPlayer";
}
else
{
throw new Exception("Unrecognized output format");
}
tso.IncludeStructures = IncludeStructures.Checked;
tso.TargetsWithActivesOnly = TargetsWithActivesOnly.Checked;
tso.CrcUpperBound = MaxCRC.Text;
tso.SpLowerBound = MinSP.Text;
tso.UseMeans = MeanSummarization.Checked;
tso.AssayTypesToInclude = AssayTypes;
tso.FilterableTargets = FilterableTargets.Text;
string mapLabel = TargetMap.Text;
tso.TargetMapName = "";
if (mapLabel != "")
{
foreach (string name0 in TargetMapNamesAndLabels.Keys)
{
if (Lex.Eq(TargetMapNamesAndLabels[name0], mapLabel))
{
tso.TargetMapName = name0;
break;
}
}
}
tso.UserMapNames = Csv.JoinCsvString(UserMapNames);
if (TargetsWithActivesOnly.Checked) // (not currently used)
{
double d;
if (!double.TryParse(MaxCRC.Text, out d))
{
MessageBoxMx.Show("You must supply a valid upper CRC bound value.", UmlautMobius.String);
MaxCRC.Focus();
return(false);
}
if (!double.TryParse(MinSP.Text, out d))
{
MessageBoxMx.Show("You must supply a valid lower SP bound value.", UmlautMobius.String);
MinSP.Focus();
return(false);
}
}
return(true);
}
/// <summary>
/// Initialize form with map info
/// </summary>
/// <param name="tso"></param>
void InitializeTargetMapControl(TargetSummaryOptions tso)
{
MapLabelList = new List <string>();
MapLabelDict = new Dictionary <string, object>();
UserMapNames = new List <string>(); // pathways specific to this user
TargetMapNamesAndLabels = TargetMapDao.GetTargetNamesAndLabels(); // get full list of maps
List <string> commonMapNames = TargetMapDao.GetCommonMapNames(); // get common maps
foreach (string mapName in commonMapNames)
{
if (!TargetMapNamesAndLabels.ContainsKey(mapName))
{
continue;
}
string mapLabel = TargetMapNamesAndLabels[mapName];
MapLabelList.Add(mapLabel);
MapLabelDict[mapLabel.ToUpper()] = null;
}
if (tso.UserMapNames.Length > 0) // get user-specific pathways
{
List <string> sa = Csv.SplitCsvString(tso.UserMapNames);
foreach (string mapName0 in sa)
{
if (!TargetMapNamesAndLabels.ContainsKey(mapName0))
{
continue;
}
string mapLabel = TargetMapNamesAndLabels[mapName0];
if (MapLabelDict.ContainsKey(mapLabel.ToUpper()))
{
continue; // don't add if already have
}
MapLabelList.Add(mapLabel);
MapLabelDict[mapLabel.ToUpper()] = null;
UserMapNames.Add(mapName0);
}
}
Lex.SortList(MapLabelList);
MapLabelList.Add("None");
MapLabelList.Add("---------------");
MapLabelList.Add("Retrieve KEGG Pathway..."); // allow addition of new pathway
TargetMap.Properties.Items.Clear();
TargetMap.Properties.Items.AddRange(MapLabelList);
if (Lex.IsNullOrEmpty(tso.TargetMapName))
{
tso.TargetMapName = "General Multi-platform Dendogram";
}
SelectedTargetMap = tso.TargetMapName;
if (String.IsNullOrEmpty(SelectedTargetMap))
{
SelectedTargetMap = MapLabelList[0];
}
if (TargetMapNamesAndLabels.ContainsKey(SelectedTargetMap))
{
SelectedTargetMap = TargetMapNamesAndLabels[SelectedTargetMap];
}
TargetMap.Text = SelectedTargetMap;
Initialized = true;
}
/// <summary>
/// GetFormValues
/// </summary>
/// <param name="tso"></param>
/// <returns></returns>
public bool GetFormValues(
TargetSummaryOptions tso)
{
tso.CidCriteria = Cids.Text;
return(true);
}