[Nmrshiftdb-devel] CVS: nmrshiftdb/src/java/org/openscience/nmrshiftdb/portlets ResultPortlet.java,1
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[Nmrshiftdb-devel] CVS: nmrshiftdb/src/java/org/openscience/nmrshiftdb/portlets ResultPortlet.java,1.71,1.72 SubmitPortlet.java,1.91,1.92
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From: Stefan K. <sh...@us...> - 2002-05-31 14:02:27
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/portlets
In directory usw-pr-cvs1:/tmp/cvs-serv666/src/java/org/openscience/nmrshiftdb/portlets
Modified Files:
ResultPortlet.java SubmitPortlet.java
Log Message:
Added the links to submit and results
Index: ResultPortlet.java
===================================================================
RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/portlets/ResultPortlet.java,v
retrieving revision 1.71
retrieving revision 1.72
diff -C2 -r1.71 -r1.72
*** ResultPortlet.java 30 May 2002 15:08:00 -0000 1.71
--- ResultPortlet.java 31 May 2002 14:02:20 -0000 1.72
***************
*** 184,190 ****
out.close();
}
! catch (Exception e)
{
! System.err.println(e.getMessage());
}
context.put("molfile", outputFile.getName());
--- 184,191 ----
out.close();
}
! catch (Exception ex)
{
! Log.error("Error in ResultPortlet/viewDetails: " + ex.getMessage());
! return new StringElement("An error occured. Please report that bug!");
}
context.put("molfile", outputFile.getName());
***************
*** 279,283 ****
Statement stmt = dbconn.createStatement();
query = "SELECT SPECTRUM.SPECTRUM_ID FROM SPECTRUM WHERE fingerprint_compare64(SPECTRUM.FINGERPRINT, " + "\"" + fingerprint + "\"" + ")" + " = \"Y\" AND SPECTRUM.REVIEW_FLAG = 'true';";
- System.err.println("Spectrum search query : " + query);
Statement stmt2 = dbconn.createStatement();
ResultSet rs2 = stmt2.executeQuery(query);
--- 280,283 ----
***************
*** 479,483 ****
return (new StringElement("You did not enter a valid formula!<a href=\"nmrshiftdb/nmrshiftdbhelp22.html#2232\" target=\"_blank\">Help</a>"));
}
- z1 = System.currentTimeMillis();
query = "SELECT DISTINCT MOLECULE.MOLECULE_ID, MOLECULE.STRUCTURE_FILE FROM SPECTRUM, MOLECULE";
--- 479,482 ----
***************
*** 512,521 ****
query += " AND MOLECULE.MOLECULE_ID = SPECTRUM.MOLECULE_ID;";
- System.err.println("searchByFuzzyFormula query : " + query);
-
ResultSet rs = stmt.executeQuery(query);
- z2 = System.currentTimeMillis();
- z2 = z2 - z1;
- System.err.println("Serach by fuzzy formula Zeit : " + z2);
String rstring = null;
while (rs.next())
--- 511,515 ----
***************
*** 524,531 ****
}
stmt.close();
- z2 = System.currentTimeMillis();
- z2 = z2 - z1;
- System.err.println("Serach by fuzzy formula Zeit : " + z2);
-
TurbineDB.releaseConnection(dbconn);
session.setAttribute("results", results);
--- 518,521 ----
***************
*** 570,579 ****
String fp = (SearchUtilities.getBitString(Fingerprinter.getFingerprint(mol)));
query = "SELECT DISTINCT MOLECULE.MOLECULE_ID, MOLECULE.STRUCTURE_FILE FROM MOLECULE, SPECTRUM WHERE SPECTRUM.REVIEW_FLAG = 'true' AND fingerprint_compare(MOLECULE.FINGERPRINT, " + "\"" + fp + "\"" + ")" + " = \"" + "Y" + "\" AND SPECTRUM.MOLECULE_ID = MOLECULE.MOLECULE_ID;";
- z1 = System.currentTimeMillis();
rs = stmt.executeQuery(query);
- z2 = System.currentTimeMillis();
- z2 = z2 - z1;
- System.err.println("UDF Zeit : " + z2);
- //System.err.println("searchBysubstructure query : " + query);
while (rs.next())
{
--- 560,564 ----
***************
*** 581,587 ****
}
stmt.close();
- z2 = System.currentTimeMillis();
- z2 = z2 - z1;
- System.err.println("Gesamtzeit : " + z2);
TurbineDB.releaseConnection(dbconn);
session.setAttribute("results", results);
--- 566,569 ----
***************
*** 597,606 ****
ResultSet rs;
- z1 = System.currentTimeMillis();
rs = stmt.executeQuery(query);
! z2 = System.currentTimeMillis();
! z2 = z2 - z1;
! System.err.println("SMILES_STRING Zeit : " + z2);
!
while (rs.next())
{
--- 579,584 ----
ResultSet rs;
rs = stmt.executeQuery(query);
!
while (rs.next())
{
Index: SubmitPortlet.java
===================================================================
RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/portlets/SubmitPortlet.java,v
retrieving revision 1.91
retrieving revision 1.92
diff -C2 -r1.91 -r1.92
*** SubmitPortlet.java 30 May 2002 16:12:19 -0000 1.91
--- SubmitPortlet.java 31 May 2002 14:02:21 -0000 1.92
***************
*** 359,365 ****
--- 359,385 ----
{
subData.setChemName(req.getParameter("chemName"));
+ subData.setMoleculeLinks(req.getParameter("moleculelinks"));
+ boolean lastWasEnd=true;
+ for(int i=0;i<subData.getMoleculeLinks().length();i++){
+ if(subData.getMoleculeLinks().charAt(i)!='\r')
+ {
+ if(lastWasEnd&&subData.getMoleculeLinks().charAt(i)=='\n')
+ messages += "<br>Your links for the molecule contains an empty line!";
+ lastWasEnd=subData.getMoleculeLinks().charAt(i)=='\n';
+ }
+ }
}
subData.setCasNumber(req.getParameter("casnumber"));
subData.setLiterature(req.getParameter("literature"));
+ subData.setSpectrumLinks(req.getParameter("spectrumlinks"));
+ boolean lastWasEnd=true;
+ for(int i=0;i<subData.getMoleculeLinks().length();i++){
+ if(subData.getMoleculeLinks().charAt(i)!='\r')
+ {
+ if(lastWasEnd&&subData.getMoleculeLinks().charAt(i)=='\n')
+ messages += "<br>Your links for the spectrum contains an empty line!";
+ lastWasEnd=subData.getMoleculeLinks().charAt(i)=='\n';
+ }
+ }
for (int i = 0; i < subData.getConditions().size(); i++)
{
***************
*** 603,607 ****
{
//If the molecule is new, we save it
! dbmol = subData.saveMolecule(mol, molWithH, subData.getMolecule(), now, subData.getCasNumber(), nmrshiftdbnr, userKey, subData.getChemName());
chemNames = subData.chemNames;
dbatoms = subData.dbatoms;
--- 623,627 ----
{
//If the molecule is new, we save it
! dbmol = subData.saveMolecule(mol, molWithH, subData.getMolecule(), now, subData.getCasNumber(), nmrshiftdbnr, userKey, subData.getChemName(), subData.getMoleculeLinks());
chemNames = subData.chemNames;
dbatoms = subData.dbatoms;
***************
*** 651,655 ****
}
//Add spectrum to DB
! spectrum = subData.saveSpectrum(now, subData.getLiterature(), dbmol, userKey, subData.getChoosenSpectrumType(), subData.getSpectrumForApplet(), nmrshiftdbnr, subData.getConditions(), subData.getSignalstable(), molWithH, "true");
session.removeAttribute("subData");
//Send an email to a reviewer
--- 671,675 ----
}
//Add spectrum to DB
! spectrum = subData.saveSpectrum(now, subData.getLiterature(), dbmol, userKey, subData.getChoosenSpectrumType(), subData.getSpectrumForApplet(), nmrshiftdbnr, subData.getConditions(), subData.getSignalstable(), molWithH, "true", subData.getSpectrumLinks());
session.removeAttribute("subData");
//Send an email to a reviewer
***************
*** 662,667 ****
catch (Throwable ex)
{
! Log.error("Error in SubmitPortlet/submitSpectrumForDB: " + ex.getMessage());
! returnValue = "An error occured. Please report that bug!";
}
//We need to remove some flags
--- 682,686 ----
catch (Throwable ex)
{
! Log.error("Error in SubmitPortlet when trying to read nmrshiftdbprtoperties: " + ex.getMessage());
}
//We need to remove some flags
***************
*** 705,709 ****
}
//Create the overall object for serializing
! AllInOne aio=new AllInOne(dbmol, spectrum, subData.dbconditions, subData.spectrumConditions, subData.signals, subData.shifts, subData.signalAtoms, dbatoms, bondAtoms, dbbonds, chemNames);
if (nmrprops.getProperty("writeserializedtodir").equals("true")) {
FileWriter out = new FileWriter(nmrprops.getProperty("serializeddir")+File.separatorChar+now.toString().replace(' ','_')+"_"+time.substring(time.length()-4)+"ms"+".ser");
--- 724,728 ----
}
//Create the overall object for serializing
! AllInOne aio=new AllInOne(dbmol, spectrum, subData.dbconditions, subData.spectrumConditions, subData.signals, subData.shifts, subData.signalAtoms, dbatoms, bondAtoms, dbbonds, chemNames, subData.moleculeHyperlinks, subData.spectrumHyperlinks);
if (nmrprops.getProperty("writeserializedtodir").equals("true")) {
FileWriter out = new FileWriter(nmrprops.getProperty("serializeddir")+File.separatorChar+now.toString().replace(' ','_')+"_"+time.substring(time.length()-4)+"ms"+".ser");
***************
*** 787,790 ****
--- 806,810 ----
else
{
+ mol=(Molecule)XMLTools.getFromXMLString(((DBMolecule) session.getAttribute("existingMolecule")).getSerializedMolecule());
}
}
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