/// <summary>
/// ExportToMOE
/// </summary>
/// <param name="mtName"></param>
/// <param name="mcName"></param>
/// <param name="url"></param>
void ExportToMOEMethod(
string url,
QueryManager qm,
ResultsFormatter fmtr,
ResultsField rfld)
{
List <string> fileList = ExportToFilesMethod(url, qm, fmtr, rfld); // download the files first
string moeExecutable, moeArgs = "";
if (!GetMoeExecutable(out moeExecutable, out moeArgs))
{
return; // failed
}
if (UseExistingMoeInstance.Checked) // -openfiles uses any existing instance, if not included then starts new instance
{
moeArgs += " -openfiles ";
}
for (int fi = 0; fi < fileList.Count; fi++)
{
moeArgs += Lex.AddDoubleQuotes(fileList[fi]) + " ";
}
try
{
Progress.Show("Passing data to MOE...");
Process p = Process.Start(moeExecutable, moeArgs);
Progress.Hide();
return;
}
catch (Exception ex)
{
try { Progress.Hide(); } catch { }
throw new Exception(ex.Message, ex);
}
}
public Cinemas()
{
_formatter = new ResultsFormatter();
}
public string Execute(CommandOption fetchScope, CommandOption sortOrder, CommandOption period)
{
FetchScope scope = FetchScope.All;
if (fetchScope.HasValue())
{
switch (fetchScope.Value().ToUpperInvariant())
{
case "MINE":
scope = FetchScope.Mine;
break;
case "ALL":
break;
default:
Console.WriteLine($"Fetch value {fetchScope.Value()} couldn't be parsed - fetching all");
scope = FetchScope.All;
break;
}
}
string[] cinemasToCheck = null;
if (scope == FetchScope.Mine)
{
cinemasToCheck = new SettingsReader().GetCinemas();
}
SortOrder sort = SortOrder.Date;
if (sortOrder.HasValue())
{
switch (sortOrder.Value().ToUpperInvariant())
{
case "D":
sort = SortOrder.Date;
break;
case "F":
sort = SortOrder.Film;
break;
case "C":
sort = SortOrder.Cinema;
break;
default:
Console.WriteLine($"Sort value {sortOrder.Value()} couldn't be parsed - sorting by Date");
sort = SortOrder.Date;
break;
}
}
Period periodToFetch = Period.All;
if (period.HasValue())
{
switch (period.Value().ToUpperInvariant())
{
case "T":
periodToFetch = Period.Today;
break;
case "M":
periodToFetch = Period.Tomorrow;
break;
default:
Console.WriteLine($"Period value {period.Value()} couldn't be parsed - fetching all");
periodToFetch = Period.All;
break;
}
}
var checker = new SiteChecker();
var result = checker.GetShowings(cinemasToCheck);
result = result.SortThisBy(sort);
result = result.JustThisPeriod(periodToFetch);
var formatter = new ResultsFormatter();
var toPrint = formatter.GetResultsTable(result);
return(toPrint.ToString());
//Console.WriteLine(toPrint);
//Console.ReadLine();
//return 0;
}
/// <summary>
/// Write Csv file of data
/// </summary>
/// <param name="csvFile"></param>
/// <param name="includeProtein"></param>
/// <param name="includeElectronDensity"></param>
void WriteCsvFile(
string csvFile,
bool exportSingle,
QueryColumn qcProtein,
QueryColumn qcDensity,
QueryColumn qcTarget,
QueryManager qm,
string url,
string densityMapUrl,
string target)
{
string rec;
DataRowMx dr;
StringMx sx;
List <int> markedRows;
//string finalUrl;
StreamWriter sw = new StreamWriter(csvFile);
rec = "BSL_XRAY_CMPLX_URL,BSL_XRAY_EDENSITY_URL,TRGT_LABEL";
sw.WriteLine(rec); // header
string filePath = DownloadFile(url);
string mapFilePath = DownloadFile(densityMapUrl);
if (qm == null) // export from HTML
{
rec = "";
//if (!Lex.Contains(url, "edensity")) // assume protein/ligand
rec += filePath;
rec += ",";
if (mapFilePath != null)
{
rec += mapFilePath;
}
rec += ","; // nothing for target for now
if (target != null)
{
rec += target;
}
sw.WriteLine(rec);
}
else // export from XtraGrid
{
ResultsFormatter fmtr = qm.ResultsFormatter;
if (exportSingle) // put single row to export in table
{
markedRows = new List <int>();
CellInfo cinf = qm.MoleculeGrid.LastMouseDownCellInfo;
markedRows.Add(cinf.DataRowIndex); // indicate current row
}
else
{
markedRows = fmtr.MarkedRowIndexes;
}
foreach (int ri in markedRows)
{
dr = qm.DataTable.Rows[ri];
rec = "";
if (qcProtein != null)
{
url = Lex.ToString(dr[qcProtein.VoPosition]);
filePath = DownloadFile(url);
if (String.IsNullOrEmpty(filePath))
{
continue;
}
rec += filePath;
}
rec += ",";
if (qcDensity != null)
{
string mapUrl = Lex.ToString(dr[qcDensity.VoPosition]);
mapFilePath = DownloadFile(mapUrl);
rec += mapFilePath;
}
else if (!IncludeElectronDensityPyMol.Checked)
{
// do nothing, user does not want map
}
else if (densityMapUrl == null && !exportSingle)
{
densityMapUrl = _xRay2Request ? GetXray2DensityMapUrl(url, _currentMetaTable, _currentPdbColumnName) : GetXray1DensityMapUrl(url, _currentMetaTable);
mapFilePath = DownloadFile(densityMapUrl);
rec += mapFilePath;
}
else if (densityMapUrl != null)
{
mapFilePath = DownloadFile(densityMapUrl);
rec += mapFilePath;
}
rec += ",";
if (qcTarget != null)
{
target = Lex.ToString(dr[qcTarget.VoPosition]);
rec += target;
}
densityMapUrl = null; //we only get the map from the first record
sw.WriteLine(rec);
}
}
sw.Close();
return;
}
/// <summary>
/// Export to Vida
/// </summary>
/// <param name="mtName"></param>
/// <param name="mcName"></param>
/// <param name="url"></param>
//void ExportToVidaMethod(
// string url,
// QueryManager qm)
//{
// StreamWriter sw;
// string scriptSourceFile = "", script;
// bool includeProtein = false; // IncludeProtein.Checked;
// if (!includeProtein) QcProtein = null;
// bool includeElectronDensity = false; // IncludeElectronDensityVida.Checked;
// if (!includeElectronDensity) QcDensity = null;
// if (!includeProtein && !includeElectronDensity)
// throw new Exception("Either the protein or the electron density must be selected for VIDA export");
// string csvFile = ClientDirs.TempDir + @"\VidaBatchLoad.csv";
// WriteCsvFile(csvFile, ExportSingle.Checked, QcProtein, QcDensity, QcTarget, qm, url);
// try
// {
// scriptSourceFile = CommonConfigInfo.MiscConfigDir + @"\VidaBatchLoad.py";
// StreamReader sr = new StreamReader(scriptSourceFile);
// script = sr.ReadToEnd();
// sr.Close();
// }
// catch (Exception ex)
// { throw new Exception("Error reading " + scriptSourceFile + ": " + ex.Message); }
// // Modify script & send to client for opening by VIDA
// script += "\r\nLoadMobiusExport(" + Lex.AddDoubleQuotes(csvFile) + ")\r\n";
// scriptSourceFile = ClientDirs.TempDir + @"\VidaBatchLoad.py";
// sw = new StreamWriter(scriptSourceFile);
// sw.Write(script);
// sw.Close();
// string vidaPaths = SS.I.ServicesIniFile.Read("VidaPaths", @"Software\Openeye\vida");
// scriptSourceFile = Lex.AddSingleQuotes(scriptSourceFile); // quote file name since it includes spaces
// string args = vidaPaths + "\t" + scriptSourceFile;
// Progress.Show("Passing data to VIDA...");
// StartVida(args);
// System.Threading.Thread.Sleep(3000); // leave message up a bit while VIDA is starting/being activated
// Progress.Hide();
//}
/// <summary>
/// ExportFiles
/// </summary>
List <string> ExportToFilesMethod(
string url,
QueryManager qm,
ResultsFormatter fmtr,
ResultsField rfld)
{
List <int> markedRows;
List <string> fileList = new List <string>();
DataRowMx dr;
StringMx sx;
string clientPath, clientFolder, clientFileName;
clientPath = FileName.Text; // path to file
clientFolder = Path.GetDirectoryName(clientPath);
if (Lex.IsUndefined(clientFolder) || !Directory.Exists(clientFolder))
{
clientFolder = Preferences.Get("DefaultExportFolder", ClientDirs.DefaultMobiusUserDocumentsFolder);
if (Lex.IsUndefined(clientFolder) || !Directory.Exists(clientFolder))
{
clientFolder = ClientDirs.TempDir;
}
}
clientFileName = Path.GetFileName(clientPath);
if (ExportSingle.Checked) // put single row to export in table
{
if (Lex.IsUndefined(clientFileName))
{
return(fileList);
}
Progress.Show("Retrieving " + clientFileName + " ...");
clientPath = clientFolder + @"\" + clientFileName;
try
{
bool downloadOk = DownloadFile(url, clientPath);
fileList.Add(clientPath);
}
catch (Exception ex)
{
throw new Exception(ex.Message, ex);
}
finally
{
Progress.Hide();
}
}
else // multiple files
{
markedRows = fmtr.MarkedRowIndexes;
foreach (int ri in markedRows)
{
if (ri < 0)
{
url = url; // single selected url
}
else
{
dr = qm.DataTable.Rows[ri];
sx = dr[rfld.VoPosition] as StringMx;
if (sx == null || sx.Hyperlink == null)
{
continue;
}
url = sx.Value; // link is in value rather than HyperLink currently
}
if (String.IsNullOrEmpty(url))
{
continue;
}
clientFileName = Path.GetFileName(url);
clientPath = clientFolder + @"\" + clientFileName;
Progress.Show("Retrieving " + clientFileName + " ...");
try
{
bool downloadOk = DownloadFile(url, clientPath);
fileList.Add(clientPath);
}
catch (Exception ex)
{
Progress.Hide();
throw ex;
}
}
Progress.Hide();
if (markedRows.Count > 0 && fileList.Count == 0)
{
throw new Exception("No files downloaded");
}
}
return(fileList);
}
/// <summary>
/// Handle a click on a link to a 3D structure & open in Vida
/// If clicked from an XtraGrid give the user a range of options for the data
/// to be exported. If clicked from a HTML page give limited options.
/// </summary>
/// <param name="mtName"></param>
/// <param name="mcName"></param>
/// <param name="url"></param>
public void ClickFunction(
string mtName,
string mcName,
string url)
{
ResultsFormatter fmtr = null;
ResultsField rfld = null;
//DataRowMx dr;
StringMx sx;
StreamWriter sw;
int markedCount = 0;
string densityMapUrl = null;
string target = null;
_currentMetaTable = mtName;
_currentPdbColumnName = mcName;
IncludeElectronDensityPyMol.Checked = false;
MetaTable mt = MetaTableCollection.Get(mtName);
if (mt == null)
{
return;
}
MetaColumn mc = mt.GetMetaColumnByName(mcName);
if (mc == null)
{
return;
}
_xRay2Request = Lex.Contains(mtName, "XRay2"); // newer XRay2 database table?
_urlFileName = Path.GetFileName(url); // extract file name from url
QueryManager qm = ClickFunctions.CurrentClickQueryManager;
if (qm != null)
{
Query q = qm.Query;
ResultsFormat rf = qm.ResultsFormat;
fmtr = qm.ResultsFormatter;
rfld = rf.GetResultsField(mc);
if (rfld == null)
{
return;
}
QueryTable qt = q.GetQueryTableByNameWithException(mtName);
_qcProtein = qt.GetQueryColumnByNameWithException(mcName);
if (_xRay2Request) // newer XRay2 database
{
string mapUrl = "";
if (mcName == "ALIGNED_SPLIT_COMPLEX_URL")
{
mapUrl = "ALIGNED_SPLIT_MAP_URL";
}
else if (mcName == "ALIGNED_FULL_COMPLEX_URL")
{
mapUrl = "ALIGNED_FULL_MAP_URL";
}
else if (mcName == "ORIGINAL_PDB_URL")
{
mapUrl = "ORIGINAL_MAP_URL";
} //{ mapUrl = "ORIGINAL_MAP_URL"; }
_qcDensity = qt.GetQueryColumnByName(mapUrl); //("ALIGNED_SPLIT_MAP_URL");
if (_qcDensity != null && !_qcDensity.Selected)
{
_qcDensity = null;
}
_qcTarget = qt.GetQueryColumnByName("primary_gene_name_alias");
if (_qcTarget != null && !_qcTarget.Selected)
{
_qcTarget = null;
}
}
if (_qcDensity != null)
{
// if there is a density map url located in the density column, enable the PyMol CheckEdit
DataRowMx dr = qm.DataTable.Rows[qm.MoleculeGrid.LastMouseDownCellInfo.DataRowIndex];
densityMapUrl = Lex.ToString(dr[_qcDensity.VoPosition]);
}
else
{
// user did not select the map column, try to retrieve the XRay1 or Xray2 density map url fromt he metatable
densityMapUrl = _xRay2Request ? GetXray2DensityMapUrl(url, qt.MetaTable.Name, mcName) : GetXray1DensityMapUrl(url, qt.MetaTable.Name);
}
// default checkbox to false so user does not load electron density maps everytime, since these take
// extra time to load.
IncludeElectronDensityPyMol.Checked = false;
IncludeElectronDensityPyMol.Enabled = !string.IsNullOrEmpty(densityMapUrl);
if (_qcProtein == null && _qcDensity == null)
{
throw new Exception("Neither the PDB nor the MAP column is selected in the query");
}
markedCount = fmtr.MarkedRowCount;
int unmarkedCount = fmtr.UnmarkedRowCount;
if (markedCount == 0 || unmarkedCount == 0) // if no specific selection assume user wants single structure
{
ExportSingle.Checked = true;
FileName.Text = _urlFileName;
}
else
{
ExportMarked.Checked = true; // assume wants marked structures
}
ExportMarked.Enabled = true;
}
else // simple setup for click from HTML display
{
ExportSingle.Checked = true;
ExportMarked.Enabled = false;
FileName.Text = _urlFileName;
densityMapUrl = GetXray2DensityMapUrl(url, _currentMetaTable, mcName);
target = GetTarget(url, _currentMetaTable, mcName);
////IncludeProtein.Enabled = IncludeElectronDensityEnabled = false;
////if (Lex.Eq(mcName, "bsl_xray_cmplx_url"))
//// IncludeProtein.Checked = true;
////else if (Lex.Eq(mcName, "bsl_xray_edensity_url"))
//// IncludeElectronDensityChecked = true;
}
if (mcName == "ALIGNED_SPLIT_MAP_URL" || mcName == "ALIGNED_FULL_MAP_URL" || mcName == "ORIGINAL_MAP_URL") // not viewable fileds
{
DisablePymol();
DisableMoe();
ExportToFile.Enabled = ExportToFile.Checked = true;
}
else if (mcName == "ALIGNED_FULL_COMPLEX_URL" || mcName == "ORIGINAL_PDB_URL" || mcName == "ALIGNED_SPLIT_COMPLEX_URL") // viewable by PyMol
{
EnableMoe();
EnablePymol();
ExportToFile.Enabled = true;
ExportToFile.Checked = false;
}
else //everything else should be viewable by MOE
{
EnableMoe();
DisablePymol();
ExportToFile.Enabled = true;
ExportToFile.Checked = false;
}
DialogResult dlgRslt = ShowDialog(SessionManager.ActiveForm);
if (dlgRslt == DialogResult.Cancel)
{
return;
}
bool exportSingle = ExportSingle.Checked;
bool exportMarked = !exportSingle;
if (!IncludeElectronDensityPyMol.Checked)
{
densityMapUrl = null;
}
if (exportMarked) // see if reasonable count if exporting marked rows
{
string msg;
if (markedCount == 0)
{
msg = "No rows have been marked for export";
MessageBoxMx.Show(msg, "Mobius", MessageBoxButtons.OK, MessageBoxIcon.Exclamation);
return;
}
if (markedCount > 10)
{
msg =
markedCount + " structures have been selected out export.\n" +
"Are you sure these are the structures you want to export?";
dlgRslt = MessageBoxMx.Show(msg, "Mobius", MessageBoxButtons.YesNoCancel, MessageBoxIcon.Question);
if (dlgRslt != DialogResult.Yes)
{
return;
}
}
}
// Export to PyMol (Schrodinger) - Collab with Paul Sprengeler and Ken Schwinn
// Relavant Files:
// 1. Plugin: CorpView.py (in Mobius config dir)
// 2. Script: CorpView.pml - Runs the plugin and then passes in the .csv file (in Mobius config dir)
// Expected content (note: <csv-file-name> gets replaced):
// import pymol
// pluginLocation = 'C:\Progra~1\PyMOL\PyMOL\modules\pmg_tk\startup\CorpView.py'
// cmd.do('run ' + pluginLocation)
// cmd.do('lv_create_environment')
// cmd.do('lv_import_mobius <csv-file-name>')
// cmd.do('lv_destroy_environment')
// 3. Csv file: PyMolBatchLoad.csv - Csv file in format expected by plugin (in Mobius temp dir)
if (ExportToPyMol.Checked)
{
ExportToPyMolMethod(url, densityMapUrl, target, qm);
}
else if (ExportToMOE.Checked) // Export to MOE
{
ExportToMOEMethod(url, qm, fmtr, rfld);
}
else
{
ExportToFilesMethod(url, qm, fmtr, rfld);
}
}
