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From: Stefan K. <sh...@us...> - 2006-10-23 11:58:16
|
Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/sql In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv27992/src/sql Modified Files: nmrshiftdb-schema.sql populate-mysql.sql Log Message: changes in the lab system Index: nmrshiftdb-schema.sql =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/sql/nmrshiftdb-schema.sql,v retrieving revision 1.80 retrieving revision 1.81 diff -C2 -r1.80 -r1.81 *** nmrshiftdb-schema.sql 6 Oct 2006 20:12:11 -0000 1.80 --- nmrshiftdb-schema.sql 23 Oct 2006 11:58:09 -0000 1.81 *************** *** 863,866 **** --- 863,867 ---- URL VARCHAR (255) NOT NULL, CONTAINED_FILES MEDIUMTEXT NOT NULL, + ASSIGNED VARCHAR (8) NOT NULL, PRIMARY KEY(RAW_FILE_ID), FOREIGN KEY (SAMPLE_ID) REFERENCES SAMPLE (SAMPLE_ID) Index: populate-mysql.sql =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/sql/populate-mysql.sql,v retrieving revision 1.59 retrieving revision 1.60 diff -C2 -r1.59 -r1.60 *** populate-mysql.sql 11 Sep 2006 14:21:16 -0000 1.59 --- populate-mysql.sql 23 Oct 2006 11:58:09 -0000 1.60 *************** *** 143,146 **** --- 143,147 ---- alter table CONDITION_TYPE change CML_ENTRY_TYPE CML_ENTRY_TYPE enum("","metadata","substance","condition") not null default ""; alter table SAMPLE change PROCESS PROCESS enum("self","worker","robot") not null default "self"; + alter table RAW_FILE change ASSIGNED ASSIGNED enum("self","worker","robot") not null default "self"; alter table MOLECULE change fp0 fp0 BIGINT UNSIGNED; alter table MOLECULE change fp1 fp1 BIGINT UNSIGNED; |
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From: Stefan K. <sh...@us...> - 2006-10-23 11:58:15
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/doc In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv27992/doc Modified Files: nmrshiftdbhelp.pdf nmrshiftdbhelp.xml Log Message: changes in the lab system Index: nmrshiftdbhelp.pdf =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/doc/nmrshiftdbhelp.pdf,v retrieving revision 1.66 retrieving revision 1.67 diff -C2 -r1.66 -r1.67 Binary files /tmp/cvsxdLnC9 and /tmp/cvsNPsYzZ differ Index: nmrshiftdbhelp.xml =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/doc/nmrshiftdbhelp.xml,v retrieving revision 1.80 retrieving revision 1.81 diff -C2 -r1.80 -r1.81 *** nmrshiftdbhelp.xml 21 Sep 2006 12:22:11 -0000 1.80 --- nmrshiftdbhelp.xml 23 Oct 2006 11:58:08 -0000 1.81 *************** *** 290,294 **** <listitem>By the user via a sample changer: Here the user needs to put his probe into the sample changer and it will be measured during the next night. The data files get attached automatically and the order goes to the fullfilled orders list.</listitem> </itemizedlist> ! The user can delete orders which have not yet been processed.</para> <para>An operator, when logged in, also has the "NMR lab administration" tab. He sees a list of open orders. When clicking on one, he can assign raw data files to it and declare the order to be finished. It will then disappear from the list.</para> </sect2> --- 290,294 ---- <listitem>By the user via a sample changer: Here the user needs to put his probe into the sample changer and it will be measured during the next night. The data files get attached automatically and the order goes to the fullfilled orders list.</listitem> </itemizedlist> ! The user can delete (=cancel) orders which have not yet been processed. Once an order is processed (i. e. has files assigned to it) it can not be deleted, because it is needed for statistcs. It stays in the "done orders" till a peak assignment is done. If the user does not want to do a peak assignment, he can view the order by clicking it and choose "I do not want to assign th spectra", having checked "confirm" before, which will take the order from the list as well. If the user wants to see the the orders which either have a peak assignment or where the user decided not to do it, he can choose "Also show orders already assigned" and press "Change dates/show alreayd assigned".</para> <para>An operator, when logged in, also has the "NMR lab administration" tab. He sees a list of open orders. When clicking on one, he can assign raw data files to it and declare the order to be finished. It will then disappear from the list.</para> </sect2> |
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From: Stefan K. <sh...@us...> - 2006-10-23 11:58:13
|
Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/html In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv27992/src/html Modified Files: using.html Log Message: changes in the lab system Index: using.html =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/using.html,v retrieving revision 1.48 retrieving revision 1.49 diff -C2 -r1.48 -r1.49 *** using.html 21 Sep 2006 12:22:11 -0000 1.48 --- using.html 23 Oct 2006 11:58:09 -0000 1.49 *************** *** 737,741 **** ></UL > ! The user can delete orders which have not yet been processed.</P ><P >An operator, when logged in, also has the "NMR lab administration" tab. He sees a list of open orders. When clicking on one, he can assign raw data files to it and declare the order to be finished. It will then disappear from the list.</P --- 737,741 ---- ></UL > ! The user can delete (=cancel) orders which have not yet been processed. Once an order is processed (i. e. has files assigned to it) it can not be deleted, because it is needed for statistcs. It stays in the "done orders" till a peak assignment is done. If the user does not want to do a peak assignment, he can view the order by clicking it and choose "I do not want to assign th spectra", having checked "confirm" before, which will take the order from the list as well. If the user wants to see the the orders which either have a peak assignment or where the user decided not to do it, he can choose "Also show orders already assigned" and press "Change dates/show alreayd assigned".</P ><P >An operator, when logged in, also has the "NMR lab administration" tab. He sees a list of open orders. When clicking on one, he can assign raw data files to it and declare the order to be finished. It will then disappear from the list.</P |
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From: Stefan K. <sh...@us...> - 2006-10-23 11:58:13
|
Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/modules/actions/portlets In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv27992/src/java/org/openscience/nmrshiftdb/modules/actions/portlets Modified Files: OrderAction.java Log Message: changes in the lab system Index: OrderAction.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/modules/actions/portlets/OrderAction.java,v retrieving revision 1.30 retrieving revision 1.31 diff -C2 -r1.30 -r1.31 *** OrderAction.java 16 Oct 2006 20:43:46 -0000 1.30 --- OrderAction.java 23 Oct 2006 11:58:09 -0000 1.31 *************** *** 104,107 **** --- 104,112 ---- Vector v3=new Vector(); SimpleDateFormat formatter = new SimpleDateFormat("yyyy-MM-dd", Locale.US); + Boolean showassigned=(Boolean)data.getSession().getAttribute("showassigned"); + if(showassigned==null){ + showassigned=new Boolean(false); + data.getSession().setAttribute("showassigned",showassigned); + } Date end=(Date)data.getSession().getAttribute("end"); if(end==null){ *************** *** 117,122 **** context.put("start",start); context.put("end",end); for(int i=0;i<v.size();i++){ ! sql="select distinct SAMPLE.SAMPLE_ID from SAMPLE join RAW_FILE using(SAMPLE_ID) left join RAW_FILE_SPECTRUM using (RAW_FILE_ID) where SAMPLE.SAMPLE_ID ="+((DBSample)v.get(i)).getSampleId()+" and RAW_FILE_SPECTRUM.SPECTRUM_ID is null and SAMPLE.DATE>='"+formatter.format(start)+"' and SAMPLE.DATE<='"+formatter.format(end)+"'"; Vector v4=DBSamplePeer.executeQuery(sql); if(v4.size()>0) --- 122,128 ---- context.put("start",start); context.put("end",end); + context.put("showassigned", showassigned); for(int i=0;i<v.size();i++){ ! sql="select distinct SAMPLE.SAMPLE_ID from SAMPLE join RAW_FILE using(SAMPLE_ID) left join RAW_FILE_SPECTRUM using (RAW_FILE_ID) where SAMPLE.SAMPLE_ID ="+((DBSample)v.get(i)).getSampleId()+" and RAW_FILE_SPECTRUM.SPECTRUM_ID is null and SAMPLE.DATE>='"+formatter.format(start)+"' and SAMPLE.DATE<='"+formatter.format(end)+"'" +(showassigned.booleanValue() ? "" : "and RAW_FILE.ASSIGNED='false'"); Vector v4=DBSamplePeer.executeQuery(sql); if(v4.size()>0) *************** *** 274,277 **** --- 280,284 ---- end.setYear(Integer.parseInt(data.getParameters().get("toyear"))-1900); data.getSession().setAttribute("end",end); + data.getSession().setAttribute("showassigned",new Boolean(data.getParameters().get("showassigned")!=null)); buildOrderContext(context,data); } *************** *** 457,460 **** --- 464,489 ---- } + public void doNoassignment(RunData data, Context context) throws Exception { + try{ + if(data.getParameters().get("confirm")!=null && data.getParameters().get("confirm").equals("confirm")){ + Criteria crit=new Criteria(); + crit.add(DBRawFilePeer.SAMPLE_ID,data.getParameters().get("id")); + Vector v=DBRawFilePeer.doSelect(crit); + for(int i=0;i<v.size();i++){ + DBRawFile rf=(DBRawFile)v.get(i); + rf.setAssigned("true"); + rf.save(); + } + DBRawFilePeer.doDelete(crit); + DBSamplePeer.doDelete(crit); + buildOrderContext(context,data); + } + }catch(Exception ex){ + ex.printStackTrace(); + GeneralUtils.logError(ex,"guestbook/doentry",data,true); + } + } + + public void doDeleteorder(RunData data, Context context) throws Exception { try{ |
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From: Stefan K. <sh...@us...> - 2006-10-23 11:58:13
|
Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/om/map In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv27992/src/java/org/openscience/nmrshiftdb/om/map Modified Files: DBRawFileMapBuilder.java Log Message: changes in the lab system Index: DBRawFileMapBuilder.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/om/map/DBRawFileMapBuilder.java,v retrieving revision 1.4 retrieving revision 1.5 diff -C2 -r1.4 -r1.5 *** DBRawFileMapBuilder.java 7 Jun 2006 19:13:50 -0000 1.4 --- DBRawFileMapBuilder.java 23 Oct 2006 11:58:09 -0000 1.5 *************** *** 1,7 **** package org.openscience.nmrshiftdb.om.map; import org.apache.turbine.services.db.TurbineDB; - import org.apache.turbine.util.db.map.DatabaseMap; import org.apache.turbine.util.db.map.MapBuilder; import org.apache.turbine.util.db.map.TableMap; --- 1,10 ---- package org.openscience.nmrshiftdb.om.map; + import java.util.*; + import java.math.*; + import org.apache.turbine.services.db.PoolBrokerService; import org.apache.turbine.services.db.TurbineDB; import org.apache.turbine.util.db.map.MapBuilder; + import org.apache.turbine.util.db.map.DatabaseMap; import org.apache.turbine.util.db.map.TableMap; *************** *** 44,47 **** --- 47,56 ---- } + /** RAW_FILE.ASSIGNED */ + public static String getDBRawFile_Assigned() + { + return getTable() + ".ASSIGNED"; + } + /** the database map */ private DatabaseMap dbMap = null; *************** *** 83,86 **** --- 92,97 ---- tMap.addColumn ( getDBRawFile_ContainedFiles(), new String() ); + tMap.addColumn ( getDBRawFile_Assigned(), new String() ); + } |
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From: Stefan K. <sh...@us...> - 2006-10-23 11:58:13
|
Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/vmtemplates/portlets/html In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv27992/src/vmtemplates/portlets/html Modified Files: user-order.vm Log Message: changes in the lab system Index: user-order.vm =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/vmtemplates/portlets/html/user-order.vm,v retrieving revision 1.43 retrieving revision 1.44 diff -C2 -r1.43 -r1.44 *** user-order.vm 16 Oct 2006 20:43:46 -0000 1.43 --- user-order.vm 23 Oct 2006 11:58:09 -0000 1.44 *************** *** 102,106 **** #end </select> ! <input type="submit" name="eventSubmit_doChangedates" value="Change dates"/> </form> </td> --- 102,107 ---- #end </select> ! <input type="checkbox" name="showassigned" value="showassigned" #if($showassigned) checked #end>Also show orders already assigned<br> ! <input type="submit" name="eventSubmit_doChangedates" value="Change dates/show alreayd assigned"/> </form> </td> *************** *** 241,244 **** --- 242,247 ---- <form name="orderform" method="post" action="portal/pane0/NMR+lab+administration"><input type="hidden" name="id" value="$sample.getSampleId()"><input type="submit" name="eventSubmit_doDeleteorder" value="Delete order"/> Confirm deletion by checking <input type="checkbox" name="confirm" value="confirm"></form> <form name="orderform" method="post" action="portal/pane0/NMR+lab+administration"><input type="hidden" name="id" value="$sample.getSampleId()"><input type="hidden" name="submitorshow" value="edit"><input type="submit" name="eventSubmit_doEditorder" value="Edit order"/></form> + #else + <form name="orderform" method="post" action="portal/pane0/NMR+lab+administration"><input type="hidden" name="id" value="$sample.getSampleId()"><input type="submit" name="eventSubmit_doNoassignment" value="I do not want to assign the spectra"/> Confirm this by checking <input type="checkbox" name="confirm" value="confirm"></form> #end #elseif($submitorshow=="edit") |
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From: Stefan K. <sh...@us...> - 2006-10-23 11:58:13
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/portlets In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv27992/src/java/org/openscience/nmrshiftdb/portlets Modified Files: SubmitPortlet.java Log Message: changes in the lab system Index: SubmitPortlet.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/portlets/SubmitPortlet.java,v retrieving revision 1.423 retrieving revision 1.424 diff -C2 -r1.423 -r1.424 *** SubmitPortlet.java 12 Oct 2006 14:34:13 -0000 1.423 --- SubmitPortlet.java 23 Oct 2006 11:58:09 -0000 1.424 *************** *** 67,70 **** --- 67,71 ---- import org.openscience.nmrshiftdb.om.DBBookPeer; import org.openscience.nmrshiftdb.om.DBCanonicalName; + import org.openscience.nmrshiftdb.om.DBCondition; import org.openscience.nmrshiftdb.om.DBConditionPeer; import org.openscience.nmrshiftdb.om.DBConditionType; *************** *** 330,338 **** Criteria crit=new Criteria(); crit.add(DBRawFilePeer.RAW_FILE_ID,runData.getParameters().get("id")); ! DBSample sample=DBSamplePeer.retrieveByPK(((DBRawFile)DBRawFilePeer.doSelect(crit).get(0)).getSampleId()); sample.getDBMolecule().addValuesToSubmittingData(subData,null,false); subData.setSpectrumKeywords(((NmrshiftdbUser)runData.getUser()).getDBLabGroup().getLabgroupName()); subData.fullfillsOrder=new NumberKey(runData.getParameters().get("id")); subData.noreview=true; } catch (Exception ex) { return new StringElement(GeneralUtils.logError(ex, "SubmitPortlet/Edit/populate subData", runData,true)); --- 331,353 ---- Criteria crit=new Criteria(); crit.add(DBRawFilePeer.RAW_FILE_ID,runData.getParameters().get("id")); ! DBRawFile rawfile=((DBRawFile)DBRawFilePeer.doSelect(crit).get(0)); ! rawfile.setAssigned("true"); ! rawfile.save(); ! DBSample sample=DBSamplePeer.retrieveByPK(rawfile.getSampleId()); sample.getDBMolecule().addValuesToSubmittingData(subData,null,false); subData.setSpectrumKeywords(((NmrshiftdbUser)runData.getUser()).getDBLabGroup().getLabgroupName()); subData.fullfillsOrder=new NumberKey(runData.getParameters().get("id")); subData.noreview=true; + for(int i=0;i<subData.getConditions().size();i++){ + DBConditionType cond=(DBConditionType)subData.getConditions().get(i); + if(cond.getConditionTypeId().getBigDecimal().intValue()==2){ + //solvent + cond.setCurrentValue(sample.getDBCondition().getValue()); + } + if(cond.getConditionTypeId().getBigDecimal().intValue()==3){ + //frequency + cond.setCurrentValue(sample.getDBMachine().getDBCondition().getValue()); + } + } } catch (Exception ex) { return new StringElement(GeneralUtils.logError(ex, "SubmitPortlet/Edit/populate subData", runData,true)); |
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From: Stefan K. <sh...@us...> - 2006-10-20 14:42:10
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/webservices In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv6528/src/java/org/openscience/nmrshiftdb/webservices Modified Files: NMRShiftDBServiceBindingImpl.java Log Message: minor changes Index: NMRShiftDBServiceBindingImpl.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/webservices/NMRShiftDBServiceBindingImpl.java,v retrieving revision 1.28 retrieving revision 1.29 diff -C2 -r1.28 -r1.29 *** NMRShiftDBServiceBindingImpl.java 19 Oct 2006 19:39:36 -0000 1.28 --- NMRShiftDBServiceBindingImpl.java 20 Oct 2006 14:42:04 -0000 1.29 *************** *** 410,415 **** metadata.setName("qname:similarity"); metadata.setContent(format.format(((Double)similarities.get(i)).doubleValue(), s, f) + " %"); mdl.addMetadata(metadata); ! mdl.addMetadata(metadata); cmlmol.appendChild(mdl); cmlcml.appendChild(cmlmol); --- 410,418 ---- metadata.setName("qname:similarity"); metadata.setContent(format.format(((Double)similarities.get(i)).doubleValue(), s, f) + " %"); + CMLMetadata metadata2=new CMLMetadata(); + metadata.setName("qname:name"); + metadata.setContent(mol.getChemicalNamesAsOneStringWithFallback()); mdl.addMetadata(metadata); ! mdl.addMetadata(metadata2); cmlmol.appendChild(mdl); cmlcml.appendChild(cmlmol); |
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From: Stefan K. <sh...@us...> - 2006-10-20 14:42:09
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/vmtemplates In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv6528/src/vmtemplates Modified Files: confirm.vm details.vm predict.vm predicttable.vm review.vm Log Message: minor changes Index: confirm.vm =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/vmtemplates/confirm.vm,v retrieving revision 1.57 retrieving revision 1.58 diff -C2 -r1.57 -r1.58 *** confirm.vm 11 Sep 2006 15:06:44 -0000 1.57 --- confirm.vm 20 Oct 2006 14:42:05 -0000 1.58 *************** *** 66,69 **** --- 66,70 ---- mview_param("background","12632256"); mview_param("detachable","true"); + mview_param("highlightTable","true"); mview_end(); //--> *************** *** 81,85 **** spectrumapplet_begin("/nmrshiftdbhtml", 350, 250); spectrumapplet_param("spectrum","$subdata.getSpectrumForApplet()"); ! pectrumapplet_param("spectrumTyp","$subdata.getChoosenSpectrumType()"); spectrumapplet_end(); </script> --- 82,87 ---- spectrumapplet_begin("/nmrshiftdbhtml", 350, 250); spectrumapplet_param("spectrum","$subdata.getSpectrumForApplet()"); ! spectrumapplet_param("spectrumTyp","$subdata.getChoosenSpectrumType()"); ! spectrumapplet_param("highlightTable","true"); spectrumapplet_end(); </script> *************** *** 95,104 **** #foreach($atom in $atoms) #set($greyorwhite=$velocityCount%2) ! <tr #if($greyorwhite==0) bgcolor="#D3D3D3" #end #if($data.getSession().getAttribute("applet")=="applet") ! onMouseover="select($atom.getValue().intValue())" #end ><td>$atom.getDisplayText()</td><td>$atom.getRange()</td><td>$atom.getMultiplicity()</td><td align="center">$!atom.getIdentifier()</td></tr> --- 97,106 ---- #foreach($atom in $atoms) #set($greyorwhite=$velocityCount%2) ! <tr id="tableid$option.getValue().intValue()" #if($greyorwhite==0) bgcolor="#D3D3D3" #end #if($data.getSession().getAttribute("applet")=="applet") ! onMouseover="select($atom.getValue().intValue());style.backgroundColor='red';" onmouseout="style.backgroundColor='#if($greyorwhite==0) #D3D3D3 #else white #end';" #end ><td>$atom.getDisplayText()</td><td>$atom.getRange()</td><td>$atom.getMultiplicity()</td><td align="center">$!atom.getIdentifier()</td></tr> Index: details.vm =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/vmtemplates/details.vm,v retrieving revision 1.161 retrieving revision 1.162 diff -C2 -r1.161 -r1.162 *** details.vm 11 Oct 2006 16:32:00 -0000 1.161 --- details.vm 20 Oct 2006 14:42:05 -0000 1.162 *************** *** 232,236 **** spectrumapplet_param("spectrum","$spectrum.getSpectrumForAppletNewFormat()"); spectrumapplet_param("spectrumTyp","$spectrum.getDBSpectrumType().getNameAsString()"); ! mview_param("highlightTable","true"); #if($spectrum.getConditionType()=="m" && !$spectrum.getMeasurementConditionWithName("Field Strength [MHz]").getValue().equals("unknown") && !$spectrum.getMeasurementConditionWithName("Field Strength [MHz]").getValue().equals("Unreported")) spectrumapplet_param("frequency","$spectrum.getMeasurementConditionWithName("Field Strength [MHz]").getValue()"); --- 232,236 ---- spectrumapplet_param("spectrum","$spectrum.getSpectrumForAppletNewFormat()"); spectrumapplet_param("spectrumTyp","$spectrum.getDBSpectrumType().getNameAsString()"); ! spectrumapplet_param("highlightTable","true"); #if($spectrum.getConditionType()=="m" && !$spectrum.getMeasurementConditionWithName("Field Strength [MHz]").getValue().equals("unknown") && !$spectrum.getMeasurementConditionWithName("Field Strength [MHz]").getValue().equals("Unreported")) spectrumapplet_param("frequency","$spectrum.getMeasurementConditionWithName("Field Strength [MHz]").getValue()"); Index: predict.vm =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/vmtemplates/predict.vm,v retrieving revision 1.84 retrieving revision 1.85 diff -C2 -r1.84 -r1.85 *** predict.vm 15 Sep 2006 09:38:11 -0000 1.84 --- predict.vm 20 Oct 2006 14:42:05 -0000 1.85 *************** *** 109,112 **** --- 109,113 ---- #end mview_name = "JcpViewer"; + mview_mayscript = true; mview_begin("/nmrshiftdbhtml", 300, 300); mview_param("load","$molfile"); *************** *** 116,119 **** --- 117,121 ---- mview_param("detachable","true"); mview_param("tooltips","$tooltips"); + mview_param("highlightTable","true"); mview_end(); //--> *************** *** 139,142 **** --- 141,145 ---- spectrumapplet_param("spectrumTyp","$spectrumtype"); spectrumapplet_param("predictions","$predictionValuesForApplet"); + spectrumapplet_param("highlightTable","true"); #if($typeid=="100") spectrumapplet_param("frequency","125"); Index: predicttable.vm =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/vmtemplates/predicttable.vm,v retrieving revision 1.21 retrieving revision 1.22 diff -C2 -r1.21 -r1.22 *** predicttable.vm 18 May 2006 16:14:18 -0000 1.21 --- predicttable.vm 20 Oct 2006 14:42:05 -0000 1.22 *************** *** 7,11 **** </tr> #foreach($element in $elements) ! <tr bgcolor= #set($evenorodd=$velocityCount % 2) #if($evenorodd==1) --- 7,11 ---- </tr> #foreach($element in $elements) ! <tr id="tableid$element.getValue().intValue()" bgcolor= #set($evenorodd=$velocityCount % 2) #if($evenorodd==1) *************** *** 20,25 **** jmolScript('select atomno=$element.getCurrentSelectedNumber();set display selected;',0);document.Spectrum.paintLine($element.getNameForElements()); #end ! unselectandselect($element.getNameForElements()) ! " #end > --- 20,25 ---- jmolScript('select atomno=$element.getCurrentSelectedNumber();set display selected;',0);document.Spectrum.paintLine($element.getNameForElements()); #end ! unselectandselect($element.getNameForElements()); ! style.backgroundColor='red';" onmouseout="style.backgroundColor='#if($evenorodd==0) #D3D3D3 #else white #end';" #end > Index: review.vm =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/vmtemplates/review.vm,v retrieving revision 1.74 retrieving revision 1.75 diff -C2 -r1.74 -r1.75 *** review.vm 20 Jul 2006 10:52:52 -0000 1.74 --- review.vm 20 Oct 2006 14:42:05 -0000 1.75 *************** *** 31,34 **** --- 31,35 ---- mview_param("background","12632256"); mview_param("detachable","true"); + mview_param("highlightTable","true"); mview_end(); //--> *************** *** 47,50 **** --- 48,52 ---- spectrumapplet_param("spectrumTyp","$spectrum.getDBSpectrumType().getNameAsString()"); spectrumapplet_param("spectrum","$spectrum.getSpectrumForAppletNewFormat()"); + spectrumapplet_param("highlightTable","true"); spectrumapplet_end(); </script> *************** *** 61,69 **** #foreach($atom in $spectrum.getOptions()) #set($greyorwhite=$velocityCount%2) ! <tr #if($greyorwhite==0) bgcolor="#D3D3D3" #end ! onMouseover="select($atom.getValue().intValue())"> <td>$atom.getDisplayText() #if($atom.getIdentifier()=="") --- 63,71 ---- #foreach($atom in $spectrum.getOptions()) #set($greyorwhite=$velocityCount%2) ! <tr id="tableid$option.getValue().intValue()" #if($greyorwhite==0) bgcolor="#D3D3D3" #end ! onMouseover="select($atom.getValue().intValue());style.backgroundColor='red'";onmouseout="style.backgroundColor='#if($greyorwhite==0) #D3D3D3 #else white #end';"> <td>$atom.getDisplayText() #if($atom.getIdentifier()=="") |
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From: Stefan K. <sh...@us...> - 2006-10-19 19:39:46
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/webservices In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv8437/src/java/org/openscience/nmrshiftdb/webservices Modified Files: NMRShiftDBServiceBindingImpl.java Log Message: web service finally works Index: NMRShiftDBServiceBindingImpl.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/webservices/NMRShiftDBServiceBindingImpl.java,v retrieving revision 1.27 retrieving revision 1.28 diff -C2 -r1.27 -r1.28 *** NMRShiftDBServiceBindingImpl.java 19 Oct 2006 10:46:51 -0000 1.27 --- NMRShiftDBServiceBindingImpl.java 19 Oct 2006 19:39:36 -0000 1.28 *************** *** 391,394 **** --- 391,395 ---- v.add(new ValuesForVelocityBean(NmrshiftdbConstants.TOTALSPECTRUM, "--", searchSpectrumBuffer.toString())); } + GeneralUtils.logToSql("Search - SELECT DISTINCT FINGERPRINTS.MOLECULE_ID, spectrumsimilarity(SPECTRUM_FINGERPRINTS.SIMPLE_SPECFILE,'"+searchSpectrumBuffer.toString()+"','total') FROM SPECTRUM_FINGERPRINTS, FINGERPRINTS WHERE SPECTRUM_FINGERPRINTS.MOLECULE_ID = FINGERPRINTS.MOLECULE_ID AND (SPECTRUM_FINGERPRINTS.NAME='13C' OR SPECTRUM_FINGERPRINTS.NAME='1H' OR SPECTRUM_FINGERPRINTS.NAME='15N' OR SPECTRUM_FINGERPRINTS.NAME='31P' OR SPECTRUM_FINGERPRINTS.NAME='19F' OR SPECTRUM_FINGERPRINTS.NAME='11B' OR SPECTRUM_FINGERPRINTS.NAME='29Si' OR SPECTRUM_FINGERPRINTS.NAME='17O' OR SPECTRUM_FINGERPRINTS.NAME='73Ge' OR SPECTRUM_FINGERPRINTS.NAME='195Pt' OR SPECTRUM_FINGERPRINTS.NAME='33S' OR false) and spectrumsimilarity(SPECTRUM_FINGERPRINTS.SIMPLE_SPECFILE, '"+searchSpectrumBuffer.toString()+"', 'total') order by spectrumsimilarity(SPECTRUM_FINGERPRINTS.SIMPLE_SPECFILE,'"+searchSpectrumBuffer.toString()+"', 'total') desc;",null); //And we do the search Vector similarities=new Vector(); *************** *** 399,402 **** --- 400,405 ---- StringBuffer s=new StringBuffer(); for(int i=0;i<results.size();i++){ + if(i>50) + break; DBMolecule mol=DBMoleculePeer.retrieveByPK((NumberKey)results.get(i)); CMLCml parent=(CMLCml)mol.getCML(1); *************** *** 405,409 **** CMLMetadataList mdl=new CMLMetadataList(); CMLMetadata metadata=new CMLMetadata(); ! metadata.setName("similarity"); metadata.setContent(format.format(((Double)similarities.get(i)).doubleValue(), s, f) + " %"); mdl.addMetadata(metadata); --- 408,412 ---- CMLMetadataList mdl=new CMLMetadataList(); CMLMetadata metadata=new CMLMetadata(); ! metadata.setName("qname:similarity"); metadata.setContent(format.format(((Double)similarities.get(i)).doubleValue(), s, f) + " %"); mdl.addMetadata(metadata); |
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From: Stefan K. <sh...@us...> - 2006-10-19 11:17:55
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/lib In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv20098/lib Modified Files: cdk-smiles.jar Log Message: change in cdk Index: cdk-smiles.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/lib/cdk-smiles.jar,v retrieving revision 1.10 retrieving revision 1.11 diff -C2 -r1.10 -r1.11 Binary files /tmp/cvssLgdyz and /tmp/cvsEGLS5e differ |
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From: Stefan K. <sh...@us...> - 2006-10-19 10:46:53
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/webservices In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv5233/src/java/org/openscience/nmrshiftdb/webservices Modified Files: NMRShiftDBServiceBindingImpl.java Log Message: modification in web service Index: NMRShiftDBServiceBindingImpl.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/webservices/NMRShiftDBServiceBindingImpl.java,v retrieving revision 1.26 retrieving revision 1.27 diff -C2 -r1.26 -r1.27 *** NMRShiftDBServiceBindingImpl.java 18 Oct 2006 16:29:11 -0000 1.26 --- NMRShiftDBServiceBindingImpl.java 19 Oct 2006 10:46:51 -0000 1.27 *************** *** 43,48 **** import org.openscience.nmrshiftdb.om.DBMolecule; import org.openscience.nmrshiftdb.om.DBMoleculePeer; - import org.openscience.nmrshiftdb.om.DBShift; - import org.openscience.nmrshiftdb.om.DBSignal; import org.openscience.nmrshiftdb.om.DBSpectrumPeer; import org.openscience.nmrshiftdb.om.DBSpectrumType; --- 43,46 ---- *************** *** 58,61 **** --- 56,60 ---- import org.openscience.nmrshiftdb.util.ValuesForVelocityBean; import org.openscience.nmrshiftdb.util.exception.NmrshiftdbException; + import org.xmlcml.cml.base.CMLElement; import org.xmlcml.cml.base.CMLElements; import org.xmlcml.cml.base.CMLUtil; *************** *** 401,405 **** for(int i=0;i<results.size();i++){ DBMolecule mol=DBMoleculePeer.retrieveByPK((NumberKey)results.get(i)); ! CMLMolecule cmlmol=(CMLMolecule)mol.getCML(1); CMLMetadataList mdl=new CMLMetadataList(); CMLMetadata metadata=new CMLMetadata(); --- 400,406 ---- for(int i=0;i<results.size();i++){ DBMolecule mol=DBMoleculePeer.retrieveByPK((NumberKey)results.get(i)); ! CMLCml parent=(CMLCml)mol.getCML(1); ! CMLElement cmlmol = parent.getChildCMLElements().get(0); ! parent.removeChildren(); CMLMetadataList mdl=new CMLMetadataList(); CMLMetadata metadata=new CMLMetadata(); *************** *** 408,412 **** mdl.addMetadata(metadata); mdl.addMetadata(metadata); ! cmlmol.addMetadataList(mdl); cmlcml.appendChild(cmlmol); } --- 409,413 ---- mdl.addMetadata(metadata); mdl.addMetadata(metadata); ! cmlmol.appendChild(mdl); cmlcml.appendChild(cmlmol); } |
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From: Stefan K. <sh...@us...> - 2006-10-18 16:29:14
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/webservices In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv22354/src/java/org/openscience/nmrshiftdb/webservices Modified Files: NMRShiftDBServiceBindingImpl.java Log Message: the spectrum search web service seems to work basically Index: NMRShiftDBServiceBindingImpl.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/webservices/NMRShiftDBServiceBindingImpl.java,v retrieving revision 1.25 retrieving revision 1.26 diff -C2 -r1.25 -r1.26 *** NMRShiftDBServiceBindingImpl.java 18 Oct 2006 13:07:27 -0000 1.25 --- NMRShiftDBServiceBindingImpl.java 18 Oct 2006 16:29:11 -0000 1.26 *************** *** 380,401 **** CMLSpectrum cmlspectrum = (CMLSpectrum) builder.parseString(element.toXML()); CMLPeakList peaklist=cmlspectrum.getPeakListElements().get(0); - DBSignal[] searchSpectrum = new DBSignal[peaklist.getPeakElements().size()]; - for (int i = 0; i < peaklist.getPeakElements().size(); i++) { - DBSignal sig = new DBSignal(); - DBShift[] shifts = new DBShift[1]; - DBShift shift = new DBShift(); - shift.setAxis("" + 1); - shift.setValue((float)peaklist.getPeakElements().get(i).getXValue()); - shifts[0] = shift; - sig.setDBShiftsArray(shifts); - sig.addDBShift(shift); - if(peaklist.getPeakElements().get(i).getYValueAttribute()!=null) - sig.setIntensity((float)peaklist.getPeakElements().get(i).getYValue()); - searchSpectrum[i] = sig; - } //For the UDF the spectrum is needed as a string like the specFile StringBuffer searchSpectrumBuffer = new StringBuffer(); for (int i = 0; i < peaklist.getPeakElements().size(); i++) { ! searchSpectrumBuffer.append((float) peaklist.getPeakElements().get(i).getXValue() + ";" + (float) peaklist.getPeakElements().get(i).getYValue() + peaklist.getPeakElements().get(i).getPeakMultiplicity()!=null ? peaklist.getPeakElements().get(i).getPeakMultiplicity() : ""+";0|"); } boolean sub = complete.getValue().equals("sub"); --- 380,387 ---- CMLSpectrum cmlspectrum = (CMLSpectrum) builder.parseString(element.toXML()); CMLPeakList peaklist=cmlspectrum.getPeakListElements().get(0); //For the UDF the spectrum is needed as a string like the specFile StringBuffer searchSpectrumBuffer = new StringBuffer(); for (int i = 0; i < peaklist.getPeakElements().size(); i++) { ! searchSpectrumBuffer.append((float) peaklist.getPeakElements().get(i).getXValue() + ";" + (Double.isNaN(peaklist.getPeakElements().get(i).getYValue()) ? "0" : (float) peaklist.getPeakElements().get(i).getYValue()) + (peaklist.getPeakElements().get(i).getPeakMultiplicity()!=null ? peaklist.getPeakElements().get(i).getPeakMultiplicity() : "")+";0|"); } boolean sub = complete.getValue().equals("sub"); |
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From: Stefan K. <sh...@us...> - 2006-10-18 13:07:30
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/portlets In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv31719/src/java/org/openscience/nmrshiftdb/portlets Modified Files: ResultPortlet.java Log Message: improved web service Index: ResultPortlet.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/portlets/ResultPortlet.java,v retrieving revision 1.284 retrieving revision 1.285 diff -C2 -r1.284 -r1.285 *** ResultPortlet.java 28 Aug 2006 14:33:58 -0000 1.284 --- ResultPortlet.java 18 Oct 2006 13:07:27 -0000 1.285 *************** *** 922,926 **** Vector similarities = new Vector(); session.setAttribute("similarities",similarities); ! return (GeneralUtils.executeSearch(searchHistory, searches, chiralMessage, similarities, session.getAttribute(NmrshiftdbConstants.CALCULATEDONLY)!=null, session.getAttribute(NmrshiftdbConstants.MEASUREDONLY)!=null, runData, ServletUtils.expandRelative(runData.getServletConfig(), "/WEB-INF/conf/normalizer.xml"), not, andor, session.getAttribute("otherspecified")!=null,(Vector)runData.getSession().getAttribute("choosenspectrumtypes"))); } } --- 922,926 ---- Vector similarities = new Vector(); session.setAttribute("similarities",similarities); ! return (GeneralUtils.executeSearch(searchHistory, searches, chiralMessage, similarities, session.getAttribute(NmrshiftdbConstants.CALCULATEDONLY)!=null, session.getAttribute(NmrshiftdbConstants.MEASUREDONLY)!=null, runData, ServletUtils.expandRelative(runData.getServletConfig(), "/WEB-INF/conf/normalizer.xml"), not, andor, session.getAttribute("otherspecified")!=null,(Vector)runData.getSession().getAttribute("choosenspectrumtypes"),true)); } } |
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From: Stefan K. <sh...@us...> - 2006-10-18 13:07:30
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/util In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv31719/src/java/org/openscience/nmrshiftdb/util Modified Files: GeneralUtils.java Log Message: improved web service Index: GeneralUtils.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/util/GeneralUtils.java,v retrieving revision 1.188 retrieving revision 1.189 diff -C2 -r1.188 -r1.189 *** GeneralUtils.java 9 Oct 2006 13:24:38 -0000 1.188 --- GeneralUtils.java 18 Oct 2006 13:07:27 -0000 1.189 *************** *** 867,871 **** * @exception NmrshiftdbException Description of Exception */ ! public static Vector executeSearch(Vector searchHistory, int[] searches, StringAndInt chiralMessage, Vector similarities, boolean calculatedonly, boolean measuredonly, RunData runData, String path, boolean not, boolean andor, boolean otherspecified, Vector spectrumTypes) throws NmrshiftdbException, Exception { //This is to avoid errors in case somebody has not got the spectrum choice portlet in his ui if(spectrumTypes==null) --- 867,871 ---- * @exception NmrshiftdbException Description of Exception */ ! public static Vector executeSearch(Vector searchHistory, int[] searches, StringAndInt chiralMessage, Vector similarities, boolean calculatedonly, boolean measuredonly, RunData runData, String path, boolean not, boolean andor, boolean otherspecified, Vector spectrumTypes, boolean logtosql) throws NmrshiftdbException, Exception { //This is to avoid errors in case somebody has not got the spectrum choice portlet in his ui if(spectrumTypes==null) *************** *** 1453,1457 **** } Log.info(query.toString()); ! if (runData != null) { GeneralUtils.logToSql("Search - " + query, runData); } --- 1453,1457 ---- } Log.info(query.toString()); ! if (runData != null && logtosql) { GeneralUtils.logToSql("Search - " + query, runData); } |
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From: Stefan K. <sh...@us...> - 2006-10-18 13:07:30
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/webservices In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv31719/src/java/org/openscience/nmrshiftdb/webservices Modified Files: MyNmrshiftdbServices.java NMRShiftDBServiceBindingImpl.java Log Message: improved web service Index: MyNmrshiftdbServices.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/webservices/MyNmrshiftdbServices.java,v retrieving revision 1.36 retrieving revision 1.37 diff -C2 -r1.36 -r1.37 *** MyNmrshiftdbServices.java 28 Aug 2006 14:33:58 -0000 1.36 --- MyNmrshiftdbServices.java 18 Oct 2006 13:07:27 -0000 1.37 *************** *** 183,187 **** ObjectInputStream ois = new ObjectInputStream(bais); Vector sh = (Vector) ois.readObject(); ! Vector v = GeneralUtils.executeSearch(sh, searches, new StringAndInt(), new Vector(), calculatedonly, measuredonly, null, "/usr/local/jakarta-tomcat/webapps/jetspeed/WEB-INF/conf/normalizer.xml", false, true, otherspecified, DBSpectrumTypePeer.doSelect(new Criteria())); Vector results = new Vector(); for (int i = 0; i < v.size(); i++) { --- 183,187 ---- ObjectInputStream ois = new ObjectInputStream(bais); Vector sh = (Vector) ois.readObject(); ! Vector v = GeneralUtils.executeSearch(sh, searches, new StringAndInt(), new Vector(), calculatedonly, measuredonly, null, "/usr/local/jakarta-tomcat/webapps/jetspeed/WEB-INF/conf/normalizer.xml", false, true, otherspecified, DBSpectrumTypePeer.doSelect(new Criteria()),true); Vector results = new Vector(); for (int i = 0; i < v.size(); i++) { Index: NMRShiftDBServiceBindingImpl.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/webservices/NMRShiftDBServiceBindingImpl.java,v retrieving revision 1.24 retrieving revision 1.25 diff -C2 -r1.24 -r1.25 *** NMRShiftDBServiceBindingImpl.java 18 Oct 2006 09:27:02 -0000 1.24 --- NMRShiftDBServiceBindingImpl.java 18 Oct 2006 13:07:27 -0000 1.25 *************** *** 23,26 **** --- 23,27 ---- import nu.xom.converters.DOMConverter; + import org.apache.jetspeed.services.rundata.DefaultJetspeedRunData; import org.apache.turbine.om.NumberKey; import org.apache.turbine.om.security.User; *************** *** 399,403 **** } boolean sub = complete.getValue().equals("sub"); ! Vector v=null; if (sub) { v.add(new ValuesForVelocityBean(NmrshiftdbConstants.SUBSPECTRUM, "--", searchSpectrumBuffer.toString())); --- 400,404 ---- } boolean sub = complete.getValue().equals("sub"); ! Vector v=new Vector(); if (sub) { v.add(new ValuesForVelocityBean(NmrshiftdbConstants.SUBSPECTRUM, "--", searchSpectrumBuffer.toString())); *************** *** 407,411 **** //And we do the search Vector similarities=new Vector(); ! Vector results=GeneralUtils.executeSearch(v, new int[1], new StringAndInt(), similarities, true, true, null, null, false, false, false, DBSpectrumTypePeer.doSelect(new Criteria())); CMLCml cmlcml=new CMLCml(); DecimalFormat format = new DecimalFormat("0.00"); --- 408,412 ---- //And we do the search Vector similarities=new Vector(); ! Vector results=GeneralUtils.executeSearch(v, new int[1], new StringAndInt(), similarities, true, true, new DefaultJetspeedRunData(), null, false, false, false, DBSpectrumTypePeer.doSelect(new Criteria()),false); CMLCml cmlcml=new CMLCml(); DecimalFormat format = new DecimalFormat("0.00"); |
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From: Stefan K. <sh...@us...> - 2006-10-18 09:27:07
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/deploymentdescriptors In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv4558/src/deploymentdescriptors Added Files: NMRShiftDBelucidate.wsdl Log Message: started a web service for spectrum search --- NEW FILE: NMRShiftDBelucidate.wsdl --- <?xml version="1.0" encoding="UTF-8"?> <wsdl:definitions xmlns:soap="http://schemas.xmlsoap.org/wsdl/soap/" xmlns:tns="http://www.nmrshiftdb.org/ws/NMRShiftDB/" xmlns:wsdl="http://schemas.xmlsoap.org/wsdl/" xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns:cml="http://www.xml-cml.org/schema" xmlns:soapenc="http://schemas.xmlsoap.org/soap/encoding/" name="NMRShiftDB" targetNamespace="http://www.nmrshiftdb.org/ws/NMRShiftDB/"> <wsdl:types> <xsd:schema targetNamespace="http://www.nmrshiftdb.org/ws/NMRShiftDB/" xmlns:cml="http://www.xml-cml.org/schema"> <xsd:import namespace="http://schemas.xmlsoap.org/soap/encoding/" /> <xsd:import namespace="http://schemas.xmlsoap.org/wsdl/" /> <xsd:import namespace="http://www.w3.org/2001/XMLSchema" /> <xsd:import namespace="http://www.xml-cml.org/schema" schemaLocation="http://almost.cubic.uni-koeln.de/schema.xsd" /> <xsd:element name="doElucidateResponse" type="cml:cml" /> <xsd:element name="doElucidateRequest" type="tns:DoElucidateParameters" /> <xsd:complexType name="DoElucidateParameters"> <xsd:sequence> <xsd:element ref="cml:spectrum" minOccurs="1" maxOccurs="1" /> <xsd:element name="suborwhole" type="xsd:string" /> </xsd:sequence> </xsd:complexType> </xsd:schema> </wsdl:types> <wsdl:message name="doElucidateResponse"> <wsdl:part element="tns:doElucidateResponse" name="doElucidateResponse" /> </wsdl:message> <wsdl:message name="doElucidateRequest"> <wsdl:part element="tns:doElucidateRequest" name="doElucidateRequest" /> </wsdl:message> <wsdl:portType name="NMRShiftDB"> <wsdl:operation name="doElucidate"> <wsdl:input message="tns:doElucidateRequest" /> <wsdl:output message="tns:doElucidateResponse" /> </wsdl:operation> </wsdl:portType> <wsdl:binding name="NMRShiftDBSOAP" type="tns:NMRShiftDB"> <soap:binding style="document" transport="http://schemas.xmlsoap.org/soap/http" /> <wsdl:operation name="doPrediction"> <soap:operation soapAction="http://www.nmrshiftdb.org/axis/services/NMRShiftDB?method=doElucidate" /> <wsdl:input> <soap:body use="literal" /> </wsdl:input> <wsdl:output> <soap:body use="literal" /> </wsdl:output> </wsdl:operation> </wsdl:binding> <wsdl:service name="NMRShiftDBElucidate"> <wsdl:port binding="tns:NMRShiftDBSOAP" name="NMRShiftDBSOAP"> <soap:address location="http://almost.cubic.uni-koeln.de/axis/services/NMRShiftDBelucidate" /> </wsdl:port> </wsdl:service> </wsdl:definitions> |
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From: Stefan K. <sh...@us...> - 2006-10-18 09:27:04
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/util In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv4558/src/java/org/openscience/nmrshiftdb/util Modified Files: AtomUtils.java Log Message: started a web service for spectrum search Index: AtomUtils.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/util/AtomUtils.java,v retrieving revision 1.164 retrieving revision 1.165 diff -C2 -r1.164 -r1.165 *** AtomUtils.java 9 Oct 2006 13:24:38 -0000 1.164 --- AtomUtils.java 18 Oct 2006 09:27:02 -0000 1.165 *************** *** 664,667 **** --- 664,669 ---- */ public static boolean normalize(IAtomContainer ac, String path){ + if(path==null) + return false; try{ UniversalIsomorphismTester.timeout = -1; |
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From: Stefan K. <sh...@us...> - 2006-10-18 09:27:04
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/webservices In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv4558/src/java/org/openscience/nmrshiftdb/webservices Modified Files: NMRShiftDB.java NMRShiftDBServiceBindingImpl.java Log Message: started a web service for spectrum search Index: NMRShiftDB.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/webservices/NMRShiftDB.java,v retrieving revision 1.4 retrieving revision 1.5 diff -C2 -r1.4 -r1.5 *** NMRShiftDB.java 28 Aug 2006 14:33:58 -0000 1.4 --- NMRShiftDB.java 18 Oct 2006 09:27:02 -0000 1.5 *************** *** 14,16 **** --- 14,18 ---- throws java.rmi.RemoteException; + public Document doElucidate(Document request) + throws java.rmi.RemoteException; } Index: NMRShiftDBServiceBindingImpl.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/webservices/NMRShiftDBServiceBindingImpl.java,v retrieving revision 1.23 retrieving revision 1.24 diff -C2 -r1.23 -r1.24 *** NMRShiftDBServiceBindingImpl.java 12 Oct 2006 14:34:13 -0000 1.23 --- NMRShiftDBServiceBindingImpl.java 18 Oct 2006 09:27:02 -0000 1.24 *************** *** 6,9 **** --- 6,11 ---- import java.io.StringWriter; import java.rmi.RemoteException; + import java.text.DecimalFormat; + import java.text.FieldPosition; import java.util.Date; import java.util.HashMap; *************** *** 38,41 **** --- 40,47 ---- import org.openscience.nmrshiftdb.om.DBConditionType; import org.openscience.nmrshiftdb.om.DBLiterature; + import org.openscience.nmrshiftdb.om.DBMolecule; + import org.openscience.nmrshiftdb.om.DBMoleculePeer; + import org.openscience.nmrshiftdb.om.DBShift; + import org.openscience.nmrshiftdb.om.DBSignal; import org.openscience.nmrshiftdb.om.DBSpectrumPeer; import org.openscience.nmrshiftdb.om.DBSpectrumType; *************** *** 46,51 **** --- 52,59 ---- import org.openscience.nmrshiftdb.util.GeneralUtils; import org.openscience.nmrshiftdb.util.NmrshiftdbConstants; + import org.openscience.nmrshiftdb.util.StringAndInt; import org.openscience.nmrshiftdb.util.SubmittingData; import org.openscience.nmrshiftdb.util.ValueTriple; + import org.openscience.nmrshiftdb.util.ValuesForVelocityBean; import org.openscience.nmrshiftdb.util.exception.NmrshiftdbException; import org.xmlcml.cml.base.CMLElements; *************** *** 54,57 **** --- 62,67 ---- import org.xmlcml.cml.element.CMLBuilder; import org.xmlcml.cml.element.CMLCml; + import org.xmlcml.cml.element.CMLMetadata; + import org.xmlcml.cml.element.CMLMetadataList; import org.xmlcml.cml.element.CMLMolecule; import org.xmlcml.cml.element.CMLPeak; *************** *** 346,348 **** --- 356,434 ---- } + + public org.w3c.dom.Document doElucidate(org.w3c.dom.Document request) throws RemoteException { + StringBuffer sb=new StringBuffer(); + org.w3c.dom.Document document; + try{ + TurbineConfig tc = new TurbineConfig("", webinfdir+"conf/TurbineResources.properties"); + File nmrpropsFile = new File(webinfdir+"conf/NMRShiftDB.properties"); + Properties nmrprops = new Properties(); + nmrprops.load(new FileInputStream(nmrpropsFile)); + GeneralUtils.nmrprops=nmrprops; + tc.init(); + System.err.println(request); + Document doc=DOMConverter.convert(request); + System.err.println(doc); + Node spectrum=doc.getChild(0).getChild(0); + Node complete=doc.getChild(0).getChild(1); + //Node elpassword=doc.getChild(0).getChild(2); + CMLBuilder builder = new CMLBuilder(false); + Element element = (Element) builder.parseString(spectrum.toXML()); + namespaceThemAll(element.getChildElements()); + element.setNamespaceURI(CMLUtil.CML_NS); + CMLSpectrum cmlspectrum = (CMLSpectrum) builder.parseString(element.toXML()); + CMLPeakList peaklist=cmlspectrum.getPeakListElements().get(0); + DBSignal[] searchSpectrum = new DBSignal[peaklist.getPeakElements().size()]; + for (int i = 0; i < peaklist.getPeakElements().size(); i++) { + DBSignal sig = new DBSignal(); + DBShift[] shifts = new DBShift[1]; + DBShift shift = new DBShift(); + shift.setAxis("" + 1); + shift.setValue((float)peaklist.getPeakElements().get(i).getXValue()); + shifts[0] = shift; + sig.setDBShiftsArray(shifts); + sig.addDBShift(shift); + if(peaklist.getPeakElements().get(i).getYValueAttribute()!=null) + sig.setIntensity((float)peaklist.getPeakElements().get(i).getYValue()); + searchSpectrum[i] = sig; + } + //For the UDF the spectrum is needed as a string like the specFile + StringBuffer searchSpectrumBuffer = new StringBuffer(); + for (int i = 0; i < peaklist.getPeakElements().size(); i++) { + searchSpectrumBuffer.append((float) peaklist.getPeakElements().get(i).getXValue() + ";" + (float) peaklist.getPeakElements().get(i).getYValue() + peaklist.getPeakElements().get(i).getPeakMultiplicity()!=null ? peaklist.getPeakElements().get(i).getPeakMultiplicity() : ""+";0|"); + } + boolean sub = complete.getValue().equals("sub"); + Vector v=null; + if (sub) { + v.add(new ValuesForVelocityBean(NmrshiftdbConstants.SUBSPECTRUM, "--", searchSpectrumBuffer.toString())); + } else { + v.add(new ValuesForVelocityBean(NmrshiftdbConstants.TOTALSPECTRUM, "--", searchSpectrumBuffer.toString())); + } + //And we do the search + Vector similarities=new Vector(); + Vector results=GeneralUtils.executeSearch(v, new int[1], new StringAndInt(), similarities, true, true, null, null, false, false, false, DBSpectrumTypePeer.doSelect(new Criteria())); + CMLCml cmlcml=new CMLCml(); + DecimalFormat format = new DecimalFormat("0.00"); + FieldPosition f = new FieldPosition(0); + StringBuffer s=new StringBuffer(); + for(int i=0;i<results.size();i++){ + DBMolecule mol=DBMoleculePeer.retrieveByPK((NumberKey)results.get(i)); + CMLMolecule cmlmol=(CMLMolecule)mol.getCML(1); + CMLMetadataList mdl=new CMLMetadataList(); + CMLMetadata metadata=new CMLMetadata(); + metadata.setName("similarity"); + metadata.setContent(format.format(((Double)similarities.get(i)).doubleValue(), s, f) + " %"); + mdl.addMetadata(metadata); + mdl.addMetadata(metadata); + cmlmol.addMetadataList(mdl); + cmlcml.appendChild(cmlmol); + } + DocumentBuilder docbuilder = DocumentBuilderFactory.newInstance().newDocumentBuilder(); + document = docbuilder.parse(new ByteArrayInputStream(cmlcml.toXML().getBytes())); + return document; + }catch(Exception ex){ + ex.printStackTrace(); + throw new RemoteException(ex.getMessage(),ex); + } + } } |
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From: Stefan K. <sh...@us...> - 2006-10-17 13:19:19
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/conf/jetspeed/WEB-INF/templates/vm/screens/html In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv31903/src/conf/jetspeed/WEB-INF/templates/vm/screens/html Modified Files: EditAccount.vm Log Message: new jcp Index: EditAccount.vm =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/conf/jetspeed/WEB-INF/templates/vm/screens/html/EditAccount.vm,v retrieving revision 1.15 retrieving revision 1.16 diff -C2 -r1.15 -r1.16 *** EditAccount.vm 21 Jun 2005 12:57:34 -0000 1.15 --- EditAccount.vm 17 Oct 2006 13:18:47 -0000 1.16 *************** *** 20,24 **** <td><img src="images/blank.gif" width="20"></td> <td> ! <p align="center"><a href="$urltool.getBaseUrl()/nmrshiftdb">Back to Home</a></p> <p align="center"><a href="portal/pane0/Results?nmrshiftdbaction=my spectra">Show all my contributions</a></p> <div align="left"> --- 20,24 ---- <td><img src="images/blank.gif" width="20"></td> <td> ! <p align="center"><a href="nmrshiftdb">Back to Home</a></p> <p align="center"><a href="portal/pane0/Results?nmrshiftdbaction=my spectra">Show all my contributions</a></p> <div align="left"> |
Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/html In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv31903/src/html Modified Files: jchempaint-applet-Jama.jar jchempaint-applet-com_ozten.jar jchempaint-applet-core.jar jchempaint-applet-editor-opts.jar jchempaint-applet-editor.jar jchempaint-applet-jas.jar jchempaint-applet-javax_media.jar jchempaint-applet-javax_vecmath.jar jchempaint-applet-nu.jar jchempaint-applet-org.jar jchempaint-applet-org_3pq.jar jchempaint-applet-org_apache.jar jchempaint-applet-org_omegahat.jar jchempaint-applet-org_openscience.jar jchempaint-applet-org_openscience_cdk.jar jchempaint-applet-org_openscience_cdk_applications.jar jchempaint-applet-org_openscience_cdk_applications_jchempaint.jar jchempaint-applet-org_openscience_cdk_config.jar jchempaint-applet-org_openscience_cdk_dict.jar jchempaint-applet-org_openscience_cdk_io.jar jchempaint-applet-org_openscience_cdk_iupac.jar jchempaint-applet-org_openscience_cdk_math.jar jchempaint-applet-org_openscience_cdk_nonotify.jar jchempaint-applet-org_openscience_cdk_qsar.jar jchempaint-applet-org_openscience_cdk_structgen.jar jchempaint-applet-org_openscience_cdk_tools.jar jchempaint-applet-org_w3c.jar jchempaint-applet-org_xmlcml.jar jchempaint-applet-others.jar jchempaint-applet-resources.jar jchempaint-applet-viewer-opts.jar Log Message: new jcp Index: jchempaint-applet-Jama.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-Jama.jar,v retrieving revision 1.19 retrieving revision 1.20 diff -C2 -r1.19 -r1.20 Binary files /tmp/cvsVOj8C1 and /tmp/cvszpHASf differ Index: jchempaint-applet-com_ozten.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-com_ozten.jar,v retrieving revision 1.19 retrieving revision 1.20 diff -C2 -r1.19 -r1.20 Binary files /tmp/cvsNjBOH3 and /tmp/cvsgpO00h differ Index: jchempaint-applet-core.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-core.jar,v retrieving revision 1.48 retrieving revision 1.49 diff -C2 -r1.48 -r1.49 Binary files /tmp/cvs1HwdM5 and /tmp/cvsvx2sek differ Index: jchempaint-applet-editor-opts.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-editor-opts.jar,v retrieving revision 1.46 retrieving revision 1.47 diff -C2 -r1.46 -r1.47 Binary files /tmp/cvstUuxC9 and /tmp/cvsow2Kao differ Index: jchempaint-applet-editor.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-editor.jar,v retrieving revision 1.49 retrieving revision 1.50 diff -C2 -r1.49 -r1.50 Binary files /tmp/cvsTS7KUc and /tmp/cvsPbiOxr differ Index: jchempaint-applet-jas.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-jas.jar,v retrieving revision 1.19 retrieving revision 1.20 diff -C2 -r1.19 -r1.20 Binary files /tmp/cvsfPwe1h and /tmp/cvsPOf4Hw differ Index: jchempaint-applet-javax_media.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-javax_media.jar,v retrieving revision 1.19 retrieving revision 1.20 diff -C2 -r1.19 -r1.20 Binary files /tmp/cvspbIpVh and /tmp/cvsBTnGHw differ Index: jchempaint-applet-javax_vecmath.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-javax_vecmath.jar,v retrieving revision 1.19 retrieving revision 1.20 diff -C2 -r1.19 -r1.20 Binary files /tmp/cvsO45eRn and /tmp/cvszz0dIC differ Index: jchempaint-applet-nu.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-nu.jar,v retrieving revision 1.19 retrieving revision 1.20 diff -C2 -r1.19 -r1.20 Binary files /tmp/cvswURfiq and /tmp/cvsMi8WdF differ Index: jchempaint-applet-org.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-org.jar,v retrieving revision 1.45 retrieving revision 1.46 diff -C2 -r1.45 -r1.46 Binary files /tmp/cvsOurh3q and /tmp/cvsWiEP3F differ Index: jchempaint-applet-org_3pq.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-org_3pq.jar,v retrieving revision 1.19 retrieving revision 1.20 diff -C2 -r1.19 -r1.20 Binary files /tmp/cvsSCGm2t and /tmp/cvsTJg46I differ Index: jchempaint-applet-org_apache.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-org_apache.jar,v retrieving revision 1.19 retrieving revision 1.20 diff -C2 -r1.19 -r1.20 Binary files /tmp/cvsHomKaw and /tmp/cvs0IF0oL differ Index: jchempaint-applet-org_omegahat.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-org_omegahat.jar,v retrieving revision 1.19 retrieving revision 1.20 diff -C2 -r1.19 -r1.20 Binary files /tmp/cvsOo6vEu and /tmp/cvskwdV2J differ Index: jchempaint-applet-org_openscience.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-org_openscience.jar,v retrieving revision 1.45 retrieving revision 1.46 diff -C2 -r1.45 -r1.46 Binary files /tmp/cvsSj9rcz and /tmp/cvsYoVPFO differ Index: jchempaint-applet-org_openscience_cdk.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-org_openscience_cdk.jar,v retrieving revision 1.45 retrieving revision 1.46 diff -C2 -r1.45 -r1.46 Binary files /tmp/cvs2HjeFB and /tmp/cvsty0KdR differ Index: jchempaint-applet-org_openscience_cdk_applications.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-org_openscience_cdk_applications.jar,v retrieving revision 1.45 retrieving revision 1.46 diff -C2 -r1.45 -r1.46 Binary files /tmp/cvseZnDYE and /tmp/cvsCqrwBU differ Index: jchempaint-applet-org_openscience_cdk_applications_jchempaint.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-org_openscience_cdk_applications_jchempaint.jar,v retrieving revision 1.49 retrieving revision 1.50 diff -C2 -r1.49 -r1.50 Binary files /tmp/cvsEX9ZfH and /tmp/cvsqffRWW differ Index: jchempaint-applet-org_openscience_cdk_config.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-org_openscience_cdk_config.jar,v retrieving revision 1.18 retrieving revision 1.19 diff -C2 -r1.18 -r1.19 Binary files /tmp/cvsh1oFBJ and /tmp/cvsAS59lZ differ Index: jchempaint-applet-org_openscience_cdk_dict.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-org_openscience_cdk_dict.jar,v retrieving revision 1.18 retrieving revision 1.19 diff -C2 -r1.18 -r1.19 Binary files /tmp/cvsVO0JEL and /tmp/cvsFXDJs1 differ Index: jchempaint-applet-org_openscience_cdk_io.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-org_openscience_cdk_io.jar,v retrieving revision 1.18 retrieving revision 1.19 diff -C2 -r1.18 -r1.19 Binary files /tmp/cvswHX3ON and /tmp/cvsZXcfI3 differ Index: jchempaint-applet-org_openscience_cdk_iupac.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-org_openscience_cdk_iupac.jar,v retrieving revision 1.18 retrieving revision 1.19 diff -C2 -r1.18 -r1.19 Binary files /tmp/cvsuCyUIT and /tmp/cvspfuAG9 differ Index: jchempaint-applet-org_openscience_cdk_math.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-org_openscience_cdk_math.jar,v retrieving revision 1.18 retrieving revision 1.19 diff -C2 -r1.18 -r1.19 Binary files /tmp/cvsMMaJrW and /tmp/cvsoOkMtc differ Index: jchempaint-applet-org_openscience_cdk_nonotify.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-org_openscience_cdk_nonotify.jar,v retrieving revision 1.6 retrieving revision 1.7 diff -C2 -r1.6 -r1.7 Binary files /tmp/cvslYn0TY and /tmp/cvs9EA3Ze differ Index: jchempaint-applet-org_openscience_cdk_qsar.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-org_openscience_cdk_qsar.jar,v retrieving revision 1.18 retrieving revision 1.19 diff -C2 -r1.18 -r1.19 Binary files /tmp/cvs9DCj7Z and /tmp/cvsFIFDkg differ Index: jchempaint-applet-org_openscience_cdk_structgen.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-org_openscience_cdk_structgen.jar,v retrieving revision 1.18 retrieving revision 1.19 diff -C2 -r1.18 -r1.19 Binary files /tmp/cvsJ3pOX5 and /tmp/cvszTwDfm differ Index: jchempaint-applet-org_openscience_cdk_tools.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-org_openscience_cdk_tools.jar,v retrieving revision 1.18 retrieving revision 1.19 diff -C2 -r1.18 -r1.19 Binary files /tmp/cvsJGQ2N7 and /tmp/cvsTHD6co differ Index: jchempaint-applet-org_w3c.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-org_w3c.jar,v retrieving revision 1.19 retrieving revision 1.20 diff -C2 -r1.19 -r1.20 Binary files /tmp/cvsFLXfvd and /tmp/cvswMpoZt differ Index: jchempaint-applet-org_xmlcml.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-org_xmlcml.jar,v retrieving revision 1.19 retrieving revision 1.20 diff -C2 -r1.19 -r1.20 Binary files /tmp/cvsbDpaLe and /tmp/cvs8Nwssv differ Index: jchempaint-applet-others.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-others.jar,v retrieving revision 1.49 retrieving revision 1.50 diff -C2 -r1.49 -r1.50 Binary files /tmp/cvsVLaYhp and /tmp/cvsxRJ8qG differ Index: jchempaint-applet-resources.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-resources.jar,v retrieving revision 1.46 retrieving revision 1.47 diff -C2 -r1.46 -r1.47 Binary files /tmp/cvsJEgMuB and /tmp/cvsFqSYWS differ Index: jchempaint-applet-viewer-opts.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-viewer-opts.jar,v retrieving revision 1.45 retrieving revision 1.46 diff -C2 -r1.45 -r1.46 Binary files /tmp/cvsudhtXD and /tmp/cvs3lv7sV differ |
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From: Stefan K. <sh...@us...> - 2006-10-16 20:44:00
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/util In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv11717/src/java/org/openscience/nmrshiftdb/util Modified Files: SubmittingData.java Log Message: added an edit to orders in lab system Index: SubmittingData.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/util/SubmittingData.java,v retrieving revision 1.283 retrieving revision 1.284 diff -C2 -r1.283 -r1.284 *** SubmittingData.java 9 Oct 2006 13:24:38 -0000 1.283 --- SubmittingData.java 16 Oct 2006 20:43:46 -0000 1.284 *************** *** 1455,1459 **** while(atoms.hasNext()){ IAtom atom=(IAtom)atoms.next(); ! if (atom.getPoint2d()!=null && atom.getPoint2d().equals(atom.getPoint2d())) { return (i); } --- 1455,1459 ---- while(atoms.hasNext()){ IAtom atom=(IAtom)atoms.next(); ! if (atom.getPoint2d()!=null && atom.getPoint2d().equals(atomcompare.getPoint2d())) { return (i); } |
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From: Stefan K. <sh...@us...> - 2006-10-16 20:43:59
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/vmtemplates/portlets/html In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv11717/src/vmtemplates/portlets/html Modified Files: user-order.vm Log Message: added an edit to orders in lab system Index: user-order.vm =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/vmtemplates/portlets/html/user-order.vm,v retrieving revision 1.42 retrieving revision 1.43 diff -C2 -r1.42 -r1.43 *** user-order.vm 11 Oct 2006 12:24:07 -0000 1.42 --- user-order.vm 16 Oct 2006 20:43:46 -0000 1.43 *************** *** 115,118 **** --- 115,122 ---- Here you can submit a <b>new order</b>:<br> I want this order to be processed by <input type="radio" name="process" #if($ordertype=="worker") checked #end value="worker"> a lab operator <input type="radio" name="process" #if($ordertype=="self") checked #end value="self"> myself <input type="radio" name="process" #if($ordertype=="robot") checked #end value="robot"> myself via sample changer<br> + #elseif($submitorshow=="edit") + <form name="orderform" method="post" action="portal/pane0/NMR+lab+administration"> + Here you can edit your submit:<br> + I want this order to be processed by <input type="radio" name="process" #if($ordertype=="worker") checked #end value="worker"> a lab operator <input type="radio" name="process" #if($ordertype=="self") checked #end value="self"> myself <input type="radio" name="process" #if($ordertype=="robot") checked #end value="robot"> myself via sample changer<br> #else <b>Order $sample.getUsersId()</b> has the following properties: *************** *** 124,128 **** <br> Solvent ! #if($submitorshow=="submit") (enter or choose): <input type="text" name="solvent" size="15" value="$!solvent"> <select name="solvents" size="1" onChange="document.restform.elements['solvent'].value=''"> --- 128,134 ---- <br> Solvent ! #if($submitorshow=="show") ! : $sample.getDBCondition().getValue() ! #else (enter or choose): <input type="text" name="solvent" size="15" value="$!solvent"> <select name="solvents" size="1" onChange="document.restform.elements['solvent'].value=''"> *************** *** 131,140 **** #end </select> - #else - : $sample.getDBCondition().getValue() #end <br> ! #if($submitorshow=="submit") ! Probable Structure (click the field to open a sketcher):<br> <script LANGUAGE="JavaScript1.1" SRC="nmrshiftdbhtml/marvin.js"></script> <script LANGUAGE="JavaScript1.1"> --- 137,160 ---- #end </select> #end <br> ! #if($submitorshow=="show") ! #if($probablestructure) ! <script LANGUAGE="JavaScript1.1" SRC="nmrshiftdbhtml/marvin.js"></script> ! <script LANGUAGE="JavaScript1.1"> ! mview_mayscript = true; ! mview_name = "JcpViewer"; ! mview_begin("/nmrshiftdbhtml", 300, 300); ! mview_param("load","$molfile"); ! mview_param("atomNumbersVisible","true"); ! mview_param("background","12632256"); ! mview_param("detachable","true"); ! mview_end(); ! </script> ! #else ! No probable structure suggested! ! #end ! #else ! Probable Structure (click the field to open a sketcher):<br> <script LANGUAGE="JavaScript1.1" SRC="nmrshiftdbhtml/marvin.js"></script> <script LANGUAGE="JavaScript1.1"> *************** *** 173,196 **** <input type="button" value="Clear" onClick="document.JcpEditor.clear();"> <input type="button" value="Import from structures history" onClick="openStructureHistory()"> - #else - #if($probablestructure) - <script LANGUAGE="JavaScript1.1" SRC="nmrshiftdbhtml/marvin.js"></script> - <script LANGUAGE="JavaScript1.1"> - mview_mayscript = true; - mview_name = "JcpViewer"; - mview_begin("/nmrshiftdbhtml", 300, 300); - mview_param("load","$molfile"); - mview_param("atomNumbersVisible","true"); - mview_param("background","12632256"); - mview_param("detachable","true"); - mview_end(); - </script> - #else - No probable structure suggested! - #end #end <br> Spectrometer ! #if($submitorshow=="submit") : <select name="fstrengths" size="1" onChange="document.restform.elements['fstrength'].value=''"> #foreach($existingcondition in $fstrengths) --- 193,202 ---- <input type="button" value="Clear" onClick="document.JcpEditor.clear();"> <input type="button" value="Import from structures history" onClick="openStructureHistory()"> #end <br> Spectrometer ! #if($submitorshow=="show") ! : $sample.getDBMachine().getName() ($sample.getDBMachine().getDBCondition().getValue() Mhz) ! #else : <select name="fstrengths" size="1" onChange="document.restform.elements['fstrength'].value=''"> #foreach($existingcondition in $fstrengths) *************** *** 198,203 **** #end </select> - #else - : $sample.getDBMachine().getName() ($sample.getDBMachine().getDBCondition().getValue() Mhz) #end <br> --- 204,207 ---- *************** *** 206,223 **** <tr> <td> ! #if($submitorshow=="submit") ! #foreach($type in $typesc) ! $type <input type="checkbox" name="$type" value="$type" #if($nuclei.indexOf($type)>-1) checked #end><br> ! #end ! </td> ! <td> ! #foreach($type in $typesh) ! $type <input type="checkbox" name="$type" value="$type" #if($nuclei.indexOf($type)>-1) checked #end><br> ! #end ! </td> ! </tr> ! <tr><td>other<input name="othertext" type="text" size="30" value="$!other"></td> ! #else ! $sample.getWishedSpectrum() #end </td> --- 210,229 ---- <tr> <td> ! Spectrum types ! #if($submitorshow=="show") ! : $sample.getWishedSpectrum() ! #else ! <br> ! #foreach($type in $typesc) ! $type <input type="checkbox" name="$type" value="$type" #if($nuclei.indexOf($type)>-1) checked #end><br> ! #end ! </td> ! <td> ! #foreach($type in $typesh) ! $type <input type="checkbox" name="$type" value="$type" #if($nuclei.indexOf($type)>-1) checked #end><br> ! #end ! </td> ! </tr> ! <tr><td>other<input name="othertext" type="text" size="30" value="$!other"></td> #end </td> *************** *** 225,241 **** <tr> <td colspan="2"> ! Other nuclei (please specify): #if($submitorshow=="submit") <input name="othernuc" type="text" size="30" value="$!othernuc"> #else $sample.getOtherNuclei() #end <br> ! Special care for sample: #if($submitorshow=="submit") <input name="specialcare" type="text" size="30" value="$!care"> #else $sample.getSpecialCare() #end <br> #foreach($sample in $sample.getDBRawFiles()) <a href="$sample.getUrl()">Download the raw NMR file here</a> <form name="orderform" method="post" action="portal/pane0/Submit"><input type="hidden" name="id" value="$sample.getRawFileId()"><input type="hidden" name="nmrshiftdbaction" value="assignrawdata"><input type="submit" name="eventSubmit_doAssign" value="Assign spectrum"/></form> #end ! #if($submitorshow=="submit") ! <input type="submit" name="eventSubmit_doSubmitorder" value="Submit order" onClick="exportMol()"/> ! </form> ! #else #if($sample.isDeletable()) <form name="orderform" method="post" action="portal/pane0/NMR+lab+administration"><input type="hidden" name="id" value="$sample.getSampleId()"><input type="submit" name="eventSubmit_doDeleteorder" value="Delete order"/> Confirm deletion by checking <input type="checkbox" name="confirm" value="confirm"></form> #end #end </td> --- 231,252 ---- <tr> <td colspan="2"> ! Other nuclei (please specify): #if($submitorshow=="show") $sample.getOtherNuclei() #else <input name="othernuc" type="text" size="30" value="$!othernuc"> #end <br> ! Special care for sample: #if($submitorshow=="show") $sample.getSpecialCare() #else <input name="specialcare" type="text" size="30" value="$!care"> #end <br> #foreach($sample in $sample.getDBRawFiles()) <a href="$sample.getUrl()">Download the raw NMR file here</a> <form name="orderform" method="post" action="portal/pane0/Submit"><input type="hidden" name="id" value="$sample.getRawFileId()"><input type="hidden" name="nmrshiftdbaction" value="assignrawdata"><input type="submit" name="eventSubmit_doAssign" value="Assign spectrum"/></form> #end ! #if($submitorshow=="show") #if($sample.isDeletable()) <form name="orderform" method="post" action="portal/pane0/NMR+lab+administration"><input type="hidden" name="id" value="$sample.getSampleId()"><input type="submit" name="eventSubmit_doDeleteorder" value="Delete order"/> Confirm deletion by checking <input type="checkbox" name="confirm" value="confirm"></form> + <form name="orderform" method="post" action="portal/pane0/NMR+lab+administration"><input type="hidden" name="id" value="$sample.getSampleId()"><input type="hidden" name="submitorshow" value="edit"><input type="submit" name="eventSubmit_doEditorder" value="Edit order"/></form> #end + #elseif($submitorshow=="edit") + <input type="hidden" name="editid" value="$sample.getSampleId()"/> + <input type="submit" name="eventSubmit_doEditsubmitorder" value="Submit order" onClick="exportMol()"/> + </form> + #else + <input type="submit" name="eventSubmit_doSubmitorder" value="Submit order" onClick="exportMol()"/> + </form> #end </td> |
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From: Stefan K. <sh...@us...> - 2006-10-16 20:43:59
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/modules/actions/portlets In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv11717/src/java/org/openscience/nmrshiftdb/modules/actions/portlets Modified Files: OrderAction.java Log Message: added an edit to orders in lab system Index: OrderAction.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/modules/actions/portlets/OrderAction.java,v retrieving revision 1.29 retrieving revision 1.30 diff -C2 -r1.29 -r1.30 *** OrderAction.java 9 Oct 2006 13:24:37 -0000 1.29 --- OrderAction.java 16 Oct 2006 20:43:46 -0000 1.30 *************** *** 141,148 **** context.put("samplesrobot",v8); context.put("data", data); ! if(data.getParameters().get("submitorshow")!=null && data.getParameters().get("submitorshow").equals("show")){ DBSample toshow=DBSamplePeer.retrieveByPK(new NumberKey(data.getParameters().get("id"))); context.put("date", toshow.getDate()); ! context.put("submitorshow","show"); context.put("sample",toshow); if(new String(toshow.getProbableStructure()+"").equals("")) --- 141,148 ---- context.put("samplesrobot",v8); context.put("data", data); ! if(data.getParameters().get("submitorshow")!=null && (data.getParameters().get("submitorshow").equals("show") || data.getParameters().get("submitorshow").equals("edit"))){ DBSample toshow=DBSamplePeer.retrieveByPK(new NumberKey(data.getParameters().get("id"))); context.put("date", toshow.getDate()); ! context.put("submitorshow",data.getParameters().get("submitorshow")); context.put("sample",toshow); if(new String(toshow.getProbableStructure()+"").equals("")) *************** *** 210,213 **** --- 210,236 ---- context.put("files",files); } + if(data.getParameters().get("submitorshow").equals("edit")){ + context.put("ordertype",toshow.getProcess()); + context.put("usersid",toshow.getUsersId()); + context.put("solvent", toshow.getDBCondition().getValue()); + context.put("other",toshow.getWishedSpectrum()); + context.put("othernuc",toshow.getOtherNuclei()); + context.put("care",toshow.getSpecialCare()); + context.put("nuclei",toshow.getWishedSpectrum()); + context.put("strength",toshow.getMachine()); + crit=new Criteria(); + crit.add(DBConditionPeer.CONDITION_TYPE_ID,"2"); + context.put("solvents", DBConditionPeer.doSelect(crit)); + context.put("fstrengths", DBMachinePeer.doSelect(new Criteria())); + if(!new String(toshow.getProbableStructure()+"").equals("")){ + //The mol is put into the MView applet via a file + File outputFile = new File(ServletUtils.expandRelative(data.getServletConfig(), "/nmrshiftdbhtml/" + System.currentTimeMillis() + "order.mol")); + FileWriter out = new FileWriter(outputFile); + out.write(toshow.getDBMolecule().getStructureFile(1,false)); + out.close(); + context.put("molfile", "/nmrshiftdbhtml/" + outputFile.getName()); + context.put("import","true"); + } + } }else{ context.put("date", new Date()); *************** *** 349,354 **** --- 372,460 ---- } } + + public void doEditsubmitorder(RunData data, Context context) throws Exception { + try{ + String message=""; + DBSample sample=DBSamplePeer.retrieveByPK(new NumberKey(data.getParameters().get("editid"))); + DBCondition solvent; + if(data.getParameters().get("solvent")!=null && !data.getParameters().get("solvent").equals("")){ + solvent = new DBCondition(); + solvent.setDBConditionTypeKey(new NumberKey(2)); + solvent.setValue(data.getParameters().get("solvent")); + solvent.setNmrshiftdbUser((NmrshiftdbUser)data.getUser()); + solvent.save(); + }else{ + Criteria crit=new Criteria(); + crit.add(DBConditionPeer.CONDITION_ID,data.getParameters().get("solvents")); + solvent=(DBCondition)DBConditionPeer.doSelect(crit).get(0); + } + sample.setDBCondition(solvent); + Criteria crit=new Criteria(); + crit.add(DBMachinePeer.MACHINE_ID,data.getParameters().get("fstrengths")); + DBMachine fstrength=(DBMachine)DBMachinePeer.doSelect(crit).get(0); + sample.setDBMachine(fstrength); + String molecule = data.getParameters().get("MolTxt"); + Molecule mol = (Molecule) new MDLReader(new StringReader(molecule)).read(new Molecule()); + if(mol!= null && mol.getAtomCount()>0){ + SubmittingData sd=new SubmittingData(ServletUtils.expandRelative(data.getServletConfig(), "/WEB-INF/conf/normalizer.xml")); + sample.setProbableStructure(sd.saveMoleculeOnly(molecule, data, (NmrshiftdbUser)data.getUser())); + } + sample.setDate(new Date()); + sample.setOtherNuclei(data.getParameters().get("othernuc")); + sample.setSpecialCare(data.getParameters().get("specialcare")); + sample.setFinished("false"); + sample.setProcess(data.getParameters().get("process")); + String wishedSpectrum=""; + if(data.getParameters().get("othertext")!=null && !data.getParameters().get("othertext").equals("")){ + wishedSpectrum+=data.getParameters().get("othertext")+", "; + } + Vector v=new Vector(); + v.addAll(getTypesC()); + v.addAll(getTypesH()); + for(int i=0;i<v.size();i++){ + String type=(String)v.get(i); + if(data.getParameters().get(type)!=null && data.getParameters().get(type).equals(type)){ + wishedSpectrum+=type+", "; + } + } + sample.setWishedSpectrum(wishedSpectrum); + if(wishedSpectrum.equals("")){ + message+="You did not enter a spectrum type!"; + }else{ + sample.save(); + } + if(!message.equals("")){ + context.put("ordertype",data.getParameters().get("process")); + context.put("usersid",data.getParameters().get("sampleid")); + context.put("solvent", solvent.getValue()); + context.put("other",data.getParameters().get("othertext")); + context.put("othernuc",sample.getOtherNuclei()); + context.put("care",sample.getSpecialCare()); + context.put("nuclei",wishedSpectrum); + context.put("strength",fstrength.getMachineId()); + if(mol!= null && mol.getAtomCount()>0){ + //The mol is put into the MView applet via a file + File outputFile = new File(ServletUtils.expandRelative(data.getServletConfig(), "/nmrshiftdbhtml/" + System.currentTimeMillis() + "order.mol")); + FileWriter out = new FileWriter(outputFile); + out.write(sample.getDBMolecule().getStructureFile(1,false)); + out.close(); + context.put("molfile", "/nmrshiftdbhtml/" + outputFile.getName()); + context.put("import","true"); + } + } + context.put("message",message); + buildOrderContext(context,data); + } + catch(Exception ex){ + GeneralUtils.logError(ex,"guestbook/doentry",data,true); + } + } + + public void doEditorder(RunData data, Context context) throws Exception { + this.buildOrderContext(context, data); + } + public void doDeleteorder(RunData data, Context context) throws Exception { try{ |
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From: Stefan K. <sh...@us...> - 2006-10-12 14:34:26
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/portlets In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv14380/src/java/org/openscience/nmrshiftdb/portlets Modified Files: SubmitPortlet.java Log Message: changes in lab system Index: SubmitPortlet.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/portlets/SubmitPortlet.java,v retrieving revision 1.422 retrieving revision 1.423 diff -C2 -r1.422 -r1.423 *** SubmitPortlet.java 9 Oct 2006 13:24:38 -0000 1.422 --- SubmitPortlet.java 12 Oct 2006 14:34:13 -0000 1.423 *************** *** 141,144 **** --- 141,145 ---- url.append(urltool.getBaseUrl()); } + String url2=url+"pane0/Results?nmrshiftdbaction=showDetailsFromHome&unreviewed=true&molNumber="+subData.dbmol; url.append("pane0/Review?nmrshiftdbaction=reviewbyurl&id=" + subData.spectrumid + "&reviewkey=" + spectrum.getReviewKey() + "&userId=" + ((NumberKey) reviewer.getPrimaryKey()).getBigDecimal().intValue()); MailMessage email = new org.apache.turbine.util.mail.MailMessage(GeneralUtils.getSmtpServer(runData), reviewer.getEmail(), GeneralUtils.getAdminEmail(runData), "Review this input!", "Some input to NMRShiftDB has been assigned to you for review, the id is " + spectrum.getSpectrumId() + ", the URL " + url + ". For contacting the submitter please quote " + spectrum.getNmrshiftdbNumber() + "." + GeneralUtils.getEmailSignature(runData)); *************** *** 146,150 **** Log.error("Sending email to reviewer failed for spectrum " + spectrum.getSpectrumId()); } ! email = new org.apache.turbine.util.mail.MailMessage(GeneralUtils.getSmtpServer(runData), spectrum.getContributor().getEmail(), GeneralUtils.getAdminEmail(runData), "Your input "+subData.timeformatted+" is assigned for review", "The spectrum for " + DBMoleculePeer.retrieveByPK(subData.dbmol).getChemicalNamesAsOneString(false) + " you submitted at " + spectrum.getDate() + " has been assigned to for review to <href=\"mailto:" + reviewer.getEmail() + "\">" + reviewer.getUserName() + "</a> (email: " + reviewer.getEmail() + "). For enquiries about the status of the review process, please contact the reviewer. You will be notified automatically if the spectrum is accepted or rejected!\n\rThe full ID is "+spectrum.getNmrshiftdbNumber()+"\n\rIf you want to have a look at your submitted data, use this link "+javax.servlet.http.HttpUtils.getRequestURL(runData.getRequest())+"pane0/Results?nmrshiftdbaction=showDetailsFromHome&unreviewed=true&molNumber="+subData.dbmol +"" + GeneralUtils.getEmailSignature(runData)); if (email.send() == false) { Log.error("Sending email to contributor failed for spectrum " + spectrum.getSpectrumId()); --- 147,151 ---- Log.error("Sending email to reviewer failed for spectrum " + spectrum.getSpectrumId()); } ! email = new org.apache.turbine.util.mail.MailMessage(GeneralUtils.getSmtpServer(runData), spectrum.getContributor().getEmail(), GeneralUtils.getAdminEmail(runData), "Your input "+subData.timeformatted+" is assigned for review", "The spectrum for " + DBMoleculePeer.retrieveByPK(subData.dbmol).getChemicalNamesAsOneString(false) + " you submitted at " + spectrum.getDate() + " has been assigned to for review to <href=\"mailto:" + reviewer.getEmail() + "\">" + reviewer.getUserName() + "</a> (email: " + reviewer.getEmail() + "). For enquiries about the status of the review process, please contact the reviewer. You will be notified automatically if the spectrum is accepted or rejected!\n\rThe full ID is "+spectrum.getNmrshiftdbNumber()+"\n\rIf you want to have a look at your submitted data, use this link "+javax.servlet.http.HttpUtils.getRequestURL(runData.getRequest())+ url2 +"" + GeneralUtils.getEmailSignature(runData)); if (email.send() == false) { Log.error("Sending email to contributor failed for spectrum " + spectrum.getSpectrumId()); |
