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From: Stefan K. <sh...@us...> - 2006-11-09 14:43:48
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/vmtemplates/exporttemplates In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv19751/src/vmtemplates/exporttemplates Modified Files: schmalz.vm Log Message: submits of h spectra also possible with h shifts assigned to heavy atoms Index: schmalz.vm =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/vmtemplates/exporttemplates/schmalz.vm,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -r1.1 -r1.2 *** schmalz.vm 7 Nov 2006 14:44:43 -0000 1.1 --- schmalz.vm 9 Nov 2006 14:43:42 -0000 1.2 *************** *** 1,3 **** #foreach($spectrum in $spectra) ! $spectrum.getDBSpectrumType().getName()-NMR ($spectrum.getMeasurementConditionWithName("Field Strength [MHz]").getValue(), $spectrum.getMeasurementConditionWithName("Solvent").getValue(), RT): delta [ppm] =#foreach($signal in $spectrum.getDBSignals())$signal.getFirstShift().getValue() ($signal.getMultiplicity(),#foreach($atom in $signal.getAtoms())#if($spectrum.getDBSpectrumType().getName()=="1H")an#end #if($atom.getIdentifier($spectrum.getSpectrumId())=="")C-$atom.getMdlNumberPlus1Heavy()#else$atom.getIdentifier($spectrum.getSpectrumId())#end#end), #end #end \ No newline at end of file --- 1,4 ---- #foreach($spectrum in $spectra) ! $spectrum.getDBSpectrumType().getName()-NMR ($spectrum.getMeasurementConditionWithName("Field Strength [MHz]").getValue(), $spectrum.getMeasurementConditionWithName("Solvent").getValue(), RT): delta [ppm] = #foreach($signal in $spectrum.getDBSignals())$signal.getFirstShift().getValue() ($signal.getMultiplicity(),#foreach($atom in $signal.getAtoms())#if($spectrum.getDBSpectrumType().getName()=="1H")an#end #if($atom.getIdentifier($spectrum.getSpectrumId())=="")C-$atom.getMdlNumberPlus1Heavy()#else$atom.getIdentifier($spectrum.getSpectrumId())#end#end), #end ! #end \ No newline at end of file |
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From: Stefan K. <sh...@us...> - 2006-11-07 14:44:53
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/vmtemplates/exporttemplates In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv30318/src/vmtemplates/exporttemplates Added Files: schmalz.vm Log Message: started a templates-based export --- NEW FILE: schmalz.vm --- #foreach($spectrum in $spectra) $spectrum.getDBSpectrumType().getName()-NMR ($spectrum.getMeasurementConditionWithName("Field Strength [MHz]").getValue(), $spectrum.getMeasurementConditionWithName("Solvent").getValue(), RT): delta [ppm] =#foreach($signal in $spectrum.getDBSignals())$signal.getFirstShift().getValue() ($signal.getMultiplicity(),#foreach($atom in $signal.getAtoms())#if($spectrum.getDBSpectrumType().getName()=="1H")an#end #if($atom.getIdentifier($spectrum.getSpectrumId())=="")C-$atom.getMdlNumberPlus1Heavy()#else$atom.getIdentifier($spectrum.getSpectrumId())#end#end), #end #end |
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From: Stefan K. <sh...@us...> - 2006-11-07 14:44:51
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/om In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv30318/src/java/org/openscience/nmrshiftdb/om Modified Files: DBAtom.java Log Message: started a templates-based export Index: DBAtom.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/om/DBAtom.java,v retrieving revision 1.55 retrieving revision 1.56 diff -C2 -r1.55 -r1.56 *** DBAtom.java 9 Oct 2006 13:24:37 -0000 1.55 --- DBAtom.java 7 Nov 2006 14:44:42 -0000 1.56 *************** *** 214,218 **** /** ! * Gets the mdlNumber + 1 attribute of the DBAtom object * * @return The mdlNumberPlus1 value --- 214,245 ---- /** ! * Gets the mdlNumber value + 1, if atom is a heavy atom of the atom itself, if a hydrogen, of the heavy atom it is attached to. ! * ! * @return The mdlNumberPlus1 value ! * @exception Exception Description of Exception ! */ ! public int getMdlNumberPlus1Heavy() throws Exception { ! if(this.getSymbol().equals("H")){ ! return ((DBAtom)this.getConnectedAtoms().get(0)).getMdlNumberPlus1(); ! }else{ ! return (getMdlNumber() + 1); ! } ! } ! ! public String getIdentifier(NumberKey spectrum) throws Exception{ ! Criteria crit=new Criteria(); ! crit.add(DBSpectrumDBLiteraturePeer.SPECTRUM_ID,spectrum); ! crit.addJoin(DBSpectrumDBLiteraturePeer.LITERATURE_ID, DBIdentifierPeer.LITERATURE_ID); ! crit.add(DBIdentifierPeer.ATOM_ID,this.getAtomId()); ! Vector v=DBIdentifierPeer.doSelect(crit); ! if(v.size()==0) ! return ""; ! else ! return ((DBIdentifier)v.get(0)).getIdentifier(); ! } ! ! ! /** ! * Gets the mdlNumber value + 1 * * @return The mdlNumberPlus1 value *************** *** 225,229 **** /** ! * Gets the mdl number of the DBAtom object. * * @return The mdlNumber value. --- 252,257 ---- /** ! * Gets the mdl number of the Atom. The mdl number is the number of the atom in the molecule, in the order as they were in ! * the mdl of the original submit. Starts with 0. * * @return The mdlNumber value. |
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From: Stefan K. <sh...@us...> - 2006-11-07 14:44:44
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/vmtemplates In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv30318/src/vmtemplates Modified Files: exportform.vm Log Message: started a templates-based export Index: exportform.vm =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/vmtemplates/exportform.vm,v retrieving revision 1.18 retrieving revision 1.19 diff -C2 -r1.18 -r1.19 *** exportform.vm 28 May 2006 15:27:09 -0000 1.18 --- exportform.vm 7 Nov 2006 14:44:42 -0000 1.19 *************** *** 20,25 **** else if(document.exportboth${myrandom}.format.value=="cmlboth") document.exportboth${myrandom}.action="download/NmrshiftdbServlet/${spectrum.getDBMolecule().getNmrshiftdbNumber()}.cml?spectrumid=${spectrum.getSpectrumId()}&nmrshiftdbaction=exportspec"; ! else document.exportboth${myrandom}.action="download/NmrshiftdbServlet/${spectrum.getDBMolecule().getNmrshiftdbNumber()}.zip?spectrumid=${spectrum.getSpectrumId()}&nmrshiftdbaction=exportspec"; } } --- 20,27 ---- else if(document.exportboth${myrandom}.format.value=="cmlboth") document.exportboth${myrandom}.action="download/NmrshiftdbServlet/${spectrum.getDBMolecule().getNmrshiftdbNumber()}.cml?spectrumid=${spectrum.getSpectrumId()}&nmrshiftdbaction=exportspec"; ! else if(document.exportboth${myrandom}.format.value=="docbook" || document.exportboth${myrandom}.format.value=="rtf") document.exportboth${myrandom}.action="download/NmrshiftdbServlet/${spectrum.getDBMolecule().getNmrshiftdbNumber()}.zip?spectrumid=${spectrum.getSpectrumId()}&nmrshiftdbaction=exportspec"; + else + document.exportboth${myrandom}.action="download/NmrshiftdbServlet/${spectrum.getDBMolecule().getNmrshiftdbNumber()}.txt?spectrumid=${spectrum.getSpectrumId()}&nmrshiftdbaction=exportspec"; } } *************** *** 55,63 **** Get this spectrum and its molecule as <select name="format" size="1"> ! <option value="simplehtml">simple html</option> <option value="pdf">pdf</option> <option value="docbook">docbook (zip file)</option> <option value="rtf">rtf</option> ! <option value="cmlboth">cml</option> </select> file --- 57,68 ---- Get this spectrum and its molecule as <select name="format" size="1"> ! <option value="simplehtml">simple html</option> <option value="pdf">pdf</option> <option value="docbook">docbook (zip file)</option> <option value="rtf">rtf</option> ! #foreach($template in $templates) ! <option value="exsection-$template.getName()">experimental section (format: $template.getName())</option> ! #end ! <option value="cmlboth">cml</option> </select> file |
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From: Stefan K. <sh...@us...> - 2006-11-07 14:44:44
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/portlets In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv30318/src/java/org/openscience/nmrshiftdb/portlets Modified Files: DetailPortlet.java Log Message: started a templates-based export Index: DetailPortlet.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/portlets/DetailPortlet.java,v retrieving revision 1.70 retrieving revision 1.71 diff -C2 -r1.70 -r1.71 *** DetailPortlet.java 30 Oct 2006 15:45:32 -0000 1.70 --- DetailPortlet.java 7 Nov 2006 14:44:42 -0000 1.71 *************** *** 295,298 **** --- 295,301 ---- context.put("query",query.toString()); } + //handle the export templates + File templatedir = new File(ServletUtils.expandRelative(runData.getServletConfig(), "/WEB-INF/templates/vm/exporttemplates")); + context.put("templates",templatedir.listFiles()); // lets render the template w = new StringWriter(); |
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From: Stefan K. <sh...@us...> - 2006-11-07 14:43:38
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/vmtemplates/exporttemplates In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv29938/src/vmtemplates/exporttemplates Log Message: Directory /cvsroot/nmrshiftdb/nmrshiftdb/src/vmtemplates/exporttemplates added to the repository |
Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/html In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv23565/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: if changing to/from java mode in lab system, the entered values are kept Index: jchempaint-applet-Jama.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-Jama.jar,v retrieving revision 1.20 retrieving revision 1.21 diff -C2 -r1.20 -r1.21 Binary files /tmp/cvsu1SOJT and /tmp/cvsOXA8bn differ Index: jchempaint-applet-com_ozten.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-com_ozten.jar,v retrieving revision 1.20 retrieving revision 1.21 diff -C2 -r1.20 -r1.21 Binary files /tmp/cvs6VAzsj and /tmp/cvsUEdLAN differ Index: jchempaint-applet-core.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-core.jar,v retrieving revision 1.49 retrieving revision 1.50 diff -C2 -r1.49 -r1.50 Binary files /tmp/cvsiE2b4v and /tmp/cvsDZ1xD2 differ Index: jchempaint-applet-editor-opts.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-editor-opts.jar,v retrieving revision 1.47 retrieving revision 1.48 diff -C2 -r1.47 -r1.48 Binary files /tmp/cvsXB2Slc and /tmp/cvsx5KE8L differ Index: jchempaint-applet-editor.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-editor.jar,v retrieving revision 1.50 retrieving revision 1.51 diff -C2 -r1.50 -r1.51 Binary files /tmp/cvsblbgEU and /tmp/cvskjTbOv differ Index: jchempaint-applet-jas.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-jas.jar,v retrieving revision 1.20 retrieving revision 1.21 diff -C2 -r1.20 -r1.21 Binary files /tmp/cvsSxX2Bi and /tmp/cvsviMBqU differ Index: jchempaint-applet-javax_media.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-javax_media.jar,v retrieving revision 1.20 retrieving revision 1.21 diff -C2 -r1.20 -r1.21 Binary files /tmp/cvsz0qonI and /tmp/cvsa9fTSk differ Index: jchempaint-applet-javax_vecmath.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-javax_vecmath.jar,v retrieving revision 1.20 retrieving revision 1.21 diff -C2 -r1.20 -r1.21 Binary files /tmp/cvsfYmgwz and /tmp/cvsMVNeKd differ Index: jchempaint-applet-nu.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-nu.jar,v retrieving revision 1.20 retrieving revision 1.21 diff -C2 -r1.20 -r1.21 Binary files /tmp/cvsuTtYxl and /tmp/cvsl0zAg1 differ Index: jchempaint-applet-org.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-org.jar,v retrieving revision 1.46 retrieving revision 1.47 diff -C2 -r1.46 -r1.47 Binary files /tmp/cvseSGBRM and /tmp/cvssK9fjt differ Index: jchempaint-applet-org_3pq.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-org_3pq.jar,v retrieving revision 1.20 retrieving revision 1.21 diff -C2 -r1.20 -r1.21 Binary files /tmp/cvsVYif6U and /tmp/cvsDw2bJD differ Index: jchempaint-applet-org_apache.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-org_apache.jar,v retrieving revision 1.20 retrieving revision 1.21 diff -C2 -r1.20 -r1.21 Binary files /tmp/cvsjpb0KU and /tmp/cvs6vBYqF differ Index: jchempaint-applet-org_omegahat.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-org_omegahat.jar,v retrieving revision 1.20 retrieving revision 1.21 diff -C2 -r1.20 -r1.21 Binary files /tmp/cvsJbLpfc and /tmp/cvslX0NsZ differ Index: jchempaint-applet-org_openscience.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-org_openscience.jar,v retrieving revision 1.46 retrieving revision 1.47 diff -C2 -r1.46 -r1.47 Binary files /tmp/cvsG3FJ4K and /tmp/cvs3qv36y differ Index: jchempaint-applet-org_openscience_cdk.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-org_openscience_cdk.jar,v retrieving revision 1.46 retrieving revision 1.47 diff -C2 -r1.46 -r1.47 Binary files /tmp/cvsubYOis and /tmp/cvsSm5ILj 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 1.46 retrieving revision 1.47 diff -C2 -r1.46 -r1.47 Binary files /tmp/cvsr4tZU2 and /tmp/cvsApAxhV 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 1.50 retrieving revision 1.51 diff -C2 -r1.50 -r1.51 Binary files /tmp/cvsHKSuak and /tmp/cvsvv7gef 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 1.19 retrieving revision 1.20 diff -C2 -r1.19 -r1.20 Binary files /tmp/cvsLnC23U and /tmp/cvsTzJ81Q 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 1.19 retrieving revision 1.20 diff -C2 -r1.19 -r1.20 Binary files /tmp/cvsFygDe8 and /tmp/cvs2Mjux6 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 1.19 retrieving revision 1.20 diff -C2 -r1.19 -r1.20 Binary files /tmp/cvsjUK0wU and /tmp/cvsWfMSlU 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 1.19 retrieving revision 1.20 diff -C2 -r1.19 -r1.20 Binary files /tmp/cvs0jIr9e and /tmp/cvspxFNyf 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 1.19 retrieving revision 1.20 diff -C2 -r1.19 -r1.20 Binary files /tmp/cvshcggfV and /tmp/cvs3DBO2W 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 1.7 retrieving revision 1.8 diff -C2 -r1.7 -r1.8 Binary files /tmp/cvsooGVcd and /tmp/cvsc3U6kh 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 1.19 retrieving revision 1.20 diff -C2 -r1.19 -r1.20 Binary files /tmp/cvsAwDTLU and /tmp/cvsZRhjo0 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 1.19 retrieving revision 1.20 diff -C2 -r1.19 -r1.20 Binary files /tmp/cvsJan3nz and /tmp/cvsTXzr6R 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 1.19 retrieving revision 1.20 diff -C2 -r1.19 -r1.20 Binary files /tmp/cvsOFQZiw and /tmp/cvsmOs4pQ differ Index: jchempaint-applet-org_w3c.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-org_w3c.jar,v retrieving revision 1.20 retrieving revision 1.21 diff -C2 -r1.20 -r1.21 Binary files /tmp/cvsUZcHoq and /tmp/cvswF5StM differ Index: jchempaint-applet-org_xmlcml.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-org_xmlcml.jar,v retrieving revision 1.20 retrieving revision 1.21 diff -C2 -r1.20 -r1.21 Binary files /tmp/cvsejm3Te and /tmp/cvsTOF9lC differ Index: jchempaint-applet-others.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-others.jar,v retrieving revision 1.50 retrieving revision 1.51 diff -C2 -r1.50 -r1.51 Binary files /tmp/cvsniSORf and /tmp/cvs6EvjFF differ Index: jchempaint-applet-resources.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-resources.jar,v retrieving revision 1.47 retrieving revision 1.48 diff -C2 -r1.47 -r1.48 Binary files /tmp/cvsZc3DIr and /tmp/cvsgZxqjT differ Index: jchempaint-applet-viewer-opts.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-viewer-opts.jar,v retrieving revision 1.46 retrieving revision 1.47 diff -C2 -r1.46 -r1.47 Binary files /tmp/cvsjB4BMt and /tmp/cvsY4eHnX differ |
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From: Stefan K. <sh...@us...> - 2006-11-06 13:40:50
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/om In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv23565/src/java/org/openscience/nmrshiftdb/om Modified Files: DBConditionPeer.java Log Message: if changing to/from java mode in lab system, the entered values are kept Index: DBConditionPeer.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/om/DBConditionPeer.java,v retrieving revision 1.8 retrieving revision 1.9 diff -C2 -r1.8 -r1.9 *** DBConditionPeer.java 4 Aug 2005 21:55:20 -0000 1.8 --- DBConditionPeer.java 6 Nov 2006 13:40:08 -0000 1.9 *************** *** 4,7 **** --- 4,8 ---- import java.util.Vector; + import org.apache.turbine.om.NumberKey; import org.apache.turbine.util.db.Criteria; *************** *** 43,46 **** --- 44,64 ---- return (DBConditionPeer.doSelect(crit)); } + + public static DBCondition makeNewOrGetExisting(NumberKey type, String value,NmrshiftdbUser user) throws Exception{ + Criteria crit=new Criteria(); + crit.add(DBConditionPeer.CONDITION_TYPE_ID, type); + crit.add(DBConditionPeer.VALUE, value); + Vector v=DBConditionPeer.doSelect(crit); + if(v.size()>0){ + return (DBCondition)v.get(0); + }else{ + DBCondition cond=new DBCondition(); + cond.setConditionTypeId(type); + cond.setValue(value); + cond.setUserId(user.getUserId()); + cond.save(); + return cond; + } + } } |
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From: Stefan K. <sh...@us...> - 2006-11-06 13:40:41
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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-serv23565/src/java/org/openscience/nmrshiftdb/modules/actions/portlets Modified Files: OrderAction.java Log Message: if changing to/from java mode in lab system, the entered values are kept Index: OrderAction.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/modules/actions/portlets/OrderAction.java,v retrieving revision 1.36 retrieving revision 1.37 diff -C2 -r1.36 -r1.37 *** OrderAction.java 30 Oct 2006 15:45:31 -0000 1.36 --- OrderAction.java 6 Nov 2006 13:40:07 -0000 1.37 *************** *** 81,90 **** protected void buildNormalContext(VelocityPortlet portlet, Context context, RunData data) { try{ - if(data.getParameters().get("applet") !=null && data.getParameters().get("applet").equals("applet")){ - data.getSession().setAttribute("applet","applet"); - } - if(data.getParameters().get("applet") !=null && data.getParameters().get("applet").equals("noapplet")){ - data.getSession().setAttribute("applet","noapplet"); - } context.put("ordertype",OrderAction.WORKER); buildOrderContext(context,data); --- 81,84 ---- *************** *** 283,286 **** --- 277,286 ---- } context.put("years",years ); + if(data.getParameters().get("applet") !=null && data.getParameters().get("applet").equals("applet")){ + data.getSession().setAttribute("applet","applet"); + } + if(data.getParameters().get("applet") !=null && data.getParameters().get("applet").equals("noapplet")){ + data.getSession().setAttribute("applet","noapplet"); + } } *************** *** 322,330 **** 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(); --- 322,326 ---- DBCondition solvent; if(data.getParameters().get("solvent")!=null && !data.getParameters().get("solvent").equals("")){ ! solvent=DBConditionPeer.makeNewOrGetExisting(new NumberKey(2),data.getParameters().get("solvent"),(NmrshiftdbUser)data.getUser()); }else{ Criteria crit=new Criteria(); *************** *** 375,378 **** --- 371,377 ---- sample.setAttachment(fi[0].get()); sample.setAttachmentName(fi[0].getFileName()); + }else{ + sample.setAttachmentName(""); + sample.setAttachment(new byte[0]); } String wishedSpectrum=""; *************** *** 397,400 **** --- 396,401 ---- }else if(oldsamples.size()>0){ message+="Your id has already been used. Choose a different one!"; + }else if(data.getParameters().get("applet") !=null && !data.getParameters().get("applet").equals("")){ + message+=" "; }else{ sample.save(); |
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From: Stefan K. <sh...@us...> - 2006-11-06 13:40:16
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/vmtemplates In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv23565/src/vmtemplates Modified Files: predict.vm searchByStructure.vm Log Message: if changing to/from java mode in lab system, the entered values are kept Index: predict.vm =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/vmtemplates/predict.vm,v retrieving revision 1.86 retrieving revision 1.87 diff -C2 -r1.86 -r1.87 *** predict.vm 30 Oct 2006 15:45:33 -0000 1.86 --- predict.vm 6 Nov 2006 13:40:08 -0000 1.87 *************** *** 17,21 **** <td> #if($session.getAttribute("applet")=="applet") ! <a href="$data.getRequest().getRequestURI();jsessionid=$data.getSession().getId()?$data.getRequest().getQueryString()&applet=noapplet" title="Switch off Java applets" style="color:white"><img src="images/nojava.png"></a> #if($input=="0") <span style="color:#0000AA">Double click to get resizeable window!</span><br> --- 17,21 ---- <td> #if($session.getAttribute("applet")=="applet") ! <a href="$request.getRequestURI();jsessionid=$session.getId()?$request.getQueryString()&applet=noapplet" title="Switch off Java applets" style="color:white"><img src="images/nojava.png"></a><br> #if($input=="0") <span style="color:#0000AA">Double click to get resizeable window!</span><br> Index: searchByStructure.vm =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/vmtemplates/searchByStructure.vm,v retrieving revision 1.63 retrieving revision 1.64 diff -C2 -r1.63 -r1.64 *** searchByStructure.vm 27 Jun 2006 14:29:17 -0000 1.63 --- searchByStructure.vm 6 Nov 2006 13:40:09 -0000 1.64 *************** *** 4,7 **** --- 4,8 ---- <td> #if($data.getSession().getAttribute("applet")=="applet") + <a href="$data.getRequest().getRequestURI();jsessionid=$data.getSession().getId()?$data.getRequest().getQueryString()&applet=noapplet" title="Switch off Java applets" style="color:white"><img src="images/nojava.png"></a><br> <script LANGUAGE="JavaScript1.1" SRC="nmrshiftdbhtml/marvin.js"></script> <script LANGUAGE="JavaScript1.1"> |
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From: Stefan K. <sh...@us...> - 2006-11-06 13:40:16
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/vmtemplates/portlets/html In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv23565/src/vmtemplates/portlets/html Modified Files: user-order.vm Log Message: if changing to/from java mode in lab system, the entered values are kept Index: user-order.vm =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/vmtemplates/portlets/html/user-order.vm,v retrieving revision 1.48 retrieving revision 1.49 diff -C2 -r1.48 -r1.49 *** user-order.vm 30 Oct 2006 15:45:35 -0000 1.48 --- user-order.vm 6 Nov 2006 13:40:09 -0000 1.49 *************** *** 146,150 **** #if($probablestructure) #if($data.getSession().getAttribute("applet")=="applet") ! <a href="$data.getRequest().getRequestURI();jsessionid=$data.getSession().getId()?$data.getRequest().getQueryString()&applet=noapplet" title="Switch off Java applets" style="color:white"><img src="images/nojava.png"></a><br> <script LANGUAGE="JavaScript1.1" SRC="nmrshiftdbhtml/marvin.js"></script> <script LANGUAGE="JavaScript1.1"> --- 146,150 ---- #if($probablestructure) #if($data.getSession().getAttribute("applet")=="applet") ! <a href="$data.getRequest().getRequestURI();jsessionid=$data.getSession().getId()?$data.getRequest().getQueryString()&applet=noapplet" title="Switch off Java applets" style="color:white"><img src="images/nojava.png"></a><br> <script LANGUAGE="JavaScript1.1" SRC="nmrshiftdbhtml/marvin.js"></script> <script LANGUAGE="JavaScript1.1"> *************** *** 167,171 **** #else #if($data.getSession().getAttribute("applet")=="applet") ! Probable Structure: <a href="$data.getRequest().getRequestURI();jsessionid=$data.getSession().getId()?$data.getRequest().getQueryString()&applet=noapplet" title="Switch off Java applets" style="color:white"><img src="images/nojava.png"></a><br> <script LANGUAGE="JavaScript1.1" SRC="nmrshiftdbhtml/marvin.js"></script> <script LANGUAGE="JavaScript1.1"> --- 167,171 ---- #else #if($data.getSession().getAttribute("applet")=="applet") ! Probable Structure: <input type="hidden" id="applet" name="applet" value=""/><input #if($submitorshow=="edit") name="eventSubmit_doEditsubmitorder" #else name="eventSubmit_doSubmitorder" #end type="image" src="images/nojava.png" style="color:white" alt="Switch to non-Java-mode" onClick="document.getElementById('applet').value='noapplet';exportMol();"> <script LANGUAGE="JavaScript1.1" SRC="nmrshiftdbhtml/marvin.js"></script> <script LANGUAGE="JavaScript1.1"> *************** *** 206,210 **** <input type="button" style="font-size:smaller" value="Import from structures history" onClick="openStructureHistory()"> #else ! <a href="$data.getRequest().getRequestURI();jsessionid=$data.getSession().getId()?$data.getRequest().getQueryString()&applet=applet" title="Switch on Java-Applets" style="color:white"><img src="images/java.png"></a><br><br> Choose a structure file for the probable structure: <input type="file" name="datei" size="40"> #end --- 206,211 ---- <input type="button" style="font-size:smaller" value="Import from structures history" onClick="openStructureHistory()"> #else ! <input type="hidden" id="applet" name="applet" value=""/> ! <input #if($submitorshow=="edit") name="eventSubmit_doEditsubmitorder" #else name="eventSubmit_doSubmitorder" #end type="image" src="images/java.png" style="color:white" alt="Switch to Java-mode" onClick="document.getElementById('applet').value='applet';exportMol();"><br><br> Choose a structure file for the probable structure: <input type="file" name="datei" size="40"> #end |
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From: Stefan K. <sh...@us...> - 2006-10-30 15:46:25
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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-serv3468/src/java/org/openscience/nmrshiftdb/modules/actions/portlets Modified Files: OrderAction.java OrderFullfillAction.java Log Message: this has the changes from the discussion with the lab system users Index: OrderAction.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/modules/actions/portlets/OrderAction.java,v retrieving revision 1.35 retrieving revision 1.36 diff -C2 -r1.35 -r1.36 *** OrderAction.java 27 Oct 2006 12:17:00 -0000 1.35 --- OrderAction.java 30 Oct 2006 15:45:31 -0000 1.36 *************** *** 318,321 **** --- 318,322 ---- DBSample sample=new DBSample(); sample.setUsersId(data.getParameters().get("sampleid")); + sample.setUsersIdComment(data.getParameters().get("sampleidcomment")); sample.setNmrshiftdbUser((NmrshiftdbUser)data.getUser()); DBCondition solvent; *************** *** 364,369 **** } } - if(mol!=null){ - } sample.setDate(new Date()); sample.setOtherNuclei(data.getParameters().get("othernuc")); --- 365,368 ---- *************** *** 371,374 **** --- 370,379 ---- sample.setFinished("false"); sample.setProcess(data.getParameters().get("process")); + FileItem[] fi = data.getParameters().getFileItems("datei2"); + if(fi!=null){ + StringBuffer messages=new StringBuffer(); + sample.setAttachment(fi[0].get()); + sample.setAttachmentName(fi[0].getFileName()); + } String wishedSpectrum=""; if(data.getParameters().get("othertext")!=null && !data.getParameters().get("othertext").equals("")){ *************** *** 388,392 **** crit2.add(DBSamplePeer.USERS_ID,sample.getUsersId()); Vector oldsamples=DBSamplePeer.doSelect(crit2); ! if(wishedSpectrum.equals("")){ message+="You did not enter a spectrum type!"; }else if(oldsamples.size()>0){ --- 393,397 ---- crit2.add(DBSamplePeer.USERS_ID,sample.getUsersId()); Vector oldsamples=DBSamplePeer.doSelect(crit2); ! if(wishedSpectrum.equals("") && sample.getOtherNuclei().equals("")){ message+="You did not enter a spectrum type!"; }else if(oldsamples.size()>0){ *************** *** 398,401 **** --- 403,407 ---- context.put("ordertype",data.getParameters().get("process")); context.put("usersid",data.getParameters().get("sampleid")); + context.put("usersidcomment",data.getParameters().get("sampleidcomment")); context.put("solvent", solvent.getValue()); context.put("other",data.getParameters().get("othertext")); *************** *** 477,480 **** --- 483,487 ---- context.put("ordertype",data.getParameters().get("process")); context.put("usersid",data.getParameters().get("sampleid")); + context.put("usersidcomment",data.getParameters().get("sampleidcomment")); context.put("solvent", solvent.getValue()); context.put("other",data.getParameters().get("othertext")); *************** *** 546,550 **** context.put("nuclei",""); context.put("strength",sample.getMachine()); ! if(!(sample.getDBMolecule()+"").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")); --- 553,558 ---- context.put("nuclei",""); context.put("strength",sample.getMachine()); ! System.err.println("_"+sample.getProbableStructure()+"_"); ! if(!(sample.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")); Index: OrderFullfillAction.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/modules/actions/portlets/OrderFullfillAction.java,v retrieving revision 1.25 retrieving revision 1.26 diff -C2 -r1.25 -r1.26 *** OrderFullfillAction.java 24 Oct 2006 13:19:37 -0000 1.25 --- OrderFullfillAction.java 30 Oct 2006 15:45:32 -0000 1.26 *************** *** 134,137 **** --- 134,138 ---- } context.put("files",files); + toshow.setFinished("pending"); } } |
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From: Stefan K. <sh...@us...> - 2006-10-30 15:46:25
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/daemons In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv3468/src/java/org/openscience/nmrshiftdb/daemons Modified Files: AssignRobotDaemon.java Log Message: this has the changes from the discussion with the lab system users Index: AssignRobotDaemon.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/daemons/AssignRobotDaemon.java,v retrieving revision 1.8 retrieving revision 1.9 diff -C2 -r1.8 -r1.9 *** AssignRobotDaemon.java 24 Oct 2006 13:19:36 -0000 1.8 --- AssignRobotDaemon.java 30 Oct 2006 15:45:31 -0000 1.9 *************** *** 28,32 **** Log.info("running robot stuff"); DBConnection dbconn=null; ! String query="select distinct SAMPLE.SAMPLE_ID, USERS_ID from SAMPLE left join RAW_FILE using (SAMPLE_ID) where URL is null and FINISHED=\"false\" and PROCESS=\""+OrderAction.ROBOT+"\""; try{ dbconn = TurbineDB.getConnection(); --- 28,32 ---- Log.info("running robot stuff"); DBConnection dbconn=null; ! String query="select distinct SAMPLE.SAMPLE_ID, USERS_ID from SAMPLE left join RAW_FILE using (SAMPLE_ID) where URL is null and FINISHED=\"false\" and (PROCESS=\""+OrderAction.ROBOT+"\" or PROCESS=\""+OrderAction.SELF+"\")"; try{ dbconn = TurbineDB.getConnection(); *************** *** 71,75 **** searchfiles(filesindir[i],usersid,zipoutputstream,attachedfiles, dirtoignore); }else if(filesindir[i].isDirectory() && filesindir[i].getName().indexOf(usersid)==0){ ! addfiles(filesindir[i], zipoutputstream, attachedfiles); }else{ if(filesindir[i].getName().indexOf(usersid)==0){ --- 71,77 ---- searchfiles(filesindir[i],usersid,zipoutputstream,attachedfiles, dirtoignore); }else if(filesindir[i].isDirectory() && filesindir[i].getName().indexOf(usersid)==0){ ! //in order to avoid to attach directories currently written by the spectrometer we take only files older than 5 minute ! if((System.currentTimeMillis()-filesindir[i].lastModified())>300000) ! addfiles(filesindir[i], zipoutputstream, attachedfiles); }else{ if(filesindir[i].getName().indexOf(usersid)==0){ |
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From: Stefan K. <sh...@us...> - 2006-10-30 15:46:18
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/util In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv3468/src/java/org/openscience/nmrshiftdb/util Modified Files: SubmittingData.java Log Message: this has the changes from the discussion with the lab system users Index: SubmittingData.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/util/SubmittingData.java,v retrieving revision 1.284 retrieving revision 1.285 diff -C2 -r1.284 -r1.285 *** SubmittingData.java 16 Oct 2006 20:43:46 -0000 1.284 --- SubmittingData.java 30 Oct 2006 15:45:32 -0000 1.285 *************** *** 68,71 **** --- 68,72 ---- import org.openscience.nmrshiftdb.om.DBMoleculeHyperlinkPeer; import org.openscience.nmrshiftdb.om.DBMoleculePeer; + import org.openscience.nmrshiftdb.om.DBRawFile; import org.openscience.nmrshiftdb.om.DBRawFileDBSpectrum; import org.openscience.nmrshiftdb.om.DBShift; *************** *** 171,174 **** --- 172,176 ---- String path; private IRingSet ringSet=null; + public DBRawFile rawfile=null;//this is only used with the lab sytem to invalidate a rawfile entry after assignment //These attributes represent the collected data of a submit process and need to be set in order to do a save() String molecule = ""; *************** *** 1291,1294 **** --- 1293,1300 ---- } } + if(rawfile!=null){ + rawfile.setAssigned("true"); + rawfile.save(); + } try { stmt.executeUpdate("COMMIT"); |
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From: Stefan K. <sh...@us...> - 2006-10-30 15:46:15
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/sql In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv3468/src/sql Modified Files: nmrshiftdb-schema.sql populate-mysql.sql Log Message: this has the changes from the discussion with the lab system users Index: nmrshiftdb-schema.sql =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/sql/nmrshiftdb-schema.sql,v retrieving revision 1.81 retrieving revision 1.82 diff -C2 -r1.81 -r1.82 *** nmrshiftdb-schema.sql 23 Oct 2006 11:58:09 -0000 1.81 --- nmrshiftdb-schema.sql 30 Oct 2006 15:45:32 -0000 1.82 *************** *** 834,837 **** --- 834,838 ---- SAMPLE_ID INTEGER NOT NULL, USERS_ID VARCHAR (20) NOT NULL, + USERS_ID_COMMENT VARCHAR (40) NOT NULL, USER_ID INTEGER NOT NULL, SOLVENT INTEGER NOT NULL, *************** *** 844,847 **** --- 845,850 ---- FINISHED VARCHAR (8) NOT NULL, PROCESS VARCHAR (8) NOT NULL, + ATTACHMENT LONGBLOB NOT NULL, + ATTACHMENT_NAME VARCHAR (20) NOT NULL, PRIMARY KEY(SAMPLE_ID), FOREIGN KEY (USER_ID) REFERENCES TURBINE_USER (USER_ID), Index: populate-mysql.sql =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/sql/populate-mysql.sql,v retrieving revision 1.61 retrieving revision 1.62 diff -C2 -r1.61 -r1.62 *** populate-mysql.sql 24 Oct 2006 10:48:44 -0000 1.61 --- populate-mysql.sql 30 Oct 2006 15:45:33 -0000 1.62 *************** *** 139,143 **** alter table BOND change IS_AROMATIC IS_AROMATIC enum("false","true") not null; alter table LITERATURE change ET_AL ET_AL enum("false","true") not null; ! alter table SAMPLE change FINISHED FINISHED enum("false","true") not null; alter table GUESTBOOK change VALID VALID enum("false","true") not null default "false"; alter table CONDITION_TYPE change CML_ENTRY_TYPE CML_ENTRY_TYPE enum("","metadata","substance","condition") not null default ""; --- 139,143 ---- alter table BOND change IS_AROMATIC IS_AROMATIC enum("false","true") not null; alter table LITERATURE change ET_AL ET_AL enum("false","true") not null; ! alter table SAMPLE change FINISHED FINISHED enum("false","true","pending") not null; alter table GUESTBOOK change VALID VALID enum("false","true") not null default "false"; alter table CONDITION_TYPE change CML_ENTRY_TYPE CML_ENTRY_TYPE enum("","metadata","substance","condition") not null default ""; |
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From: Stefan K. <sh...@us...> - 2006-10-30 15:46:12
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/om In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv3468/src/java/org/openscience/nmrshiftdb/om Modified Files: BaseDBSample.java BaseDBSamplePeer.java DBSample.java Log Message: this has the changes from the discussion with the lab system users Index: BaseDBSample.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/om/BaseDBSample.java,v retrieving revision 1.8 retrieving revision 1.9 diff -C2 -r1.8 -r1.9 *** BaseDBSample.java 10 Oct 2006 15:20:31 -0000 1.8 --- BaseDBSample.java 30 Oct 2006 15:45:32 -0000 1.9 *************** *** 2,17 **** ! import java.util.Date; ! import java.util.List; ! import java.util.Vector; ! ! import org.apache.turbine.om.BaseObject; ! import org.apache.turbine.om.NumberKey; ! import org.apache.turbine.om.ObjectKey; ! import org.apache.turbine.om.Persistent; ! import org.apache.turbine.om.Retrievable; import org.apache.turbine.om.peer.BasePeer; - import org.apache.turbine.util.ObjectUtils; import org.apache.turbine.util.db.Criteria; import org.apache.turbine.util.db.pool.DBConnection; --- 2,14 ---- ! import java.util.*; ! import java.math.*; ! import org.apache.turbine.om.*; import org.apache.turbine.om.peer.BasePeer; import org.apache.turbine.util.db.Criteria; + import org.apache.turbine.util.ObjectUtils; + import org.apache.turbine.util.StringUtils; + import org.apache.turbine.util.ParameterParser; + import org.apache.turbine.util.Log; import org.apache.turbine.util.db.pool.DBConnection; *************** *** 27,30 **** --- 24,29 ---- /** the value for the users_id field */ private String users_id; + /** the value for the users_id_comment field */ + private String users_id_comment; /** the value for the user_id field */ private NumberKey user_id; *************** *** 47,50 **** --- 46,53 ---- /** the value for the process field */ private String process; + /** the value for the attachment field */ + private byte[] attachment; + /** the value for the attachment_name field */ + private String attachment_name; *************** *** 128,131 **** --- 131,160 ---- /** + * Get the UsersIdComment + * @return String + */ + public String getUsersIdComment() + { + return users_id_comment; + } + + + /** + * Set the value of UsersIdComment + */ + public void setUsersIdComment(String v ) + { + + + + if ( !ObjectUtils.equals(this.users_id_comment, v) ) + { + this.users_id_comment = v; + setModified(true); + } + } + + + /** * Get the UserId * @return NumberKey *************** *** 447,450 **** --- 476,531 ---- + /** + * Get the Attachment + * @return byte[] + */ + public byte[] getAttachment() + { + return attachment; + } + + + /** + * Set the value of Attachment + */ + public void setAttachment(byte[] v ) + { + + + + if ( !ObjectUtils.equals(this.attachment, v) ) + { + this.attachment = v; + setModified(true); + } + } + + + /** + * Get the AttachmentName + * @return String + */ + public String getAttachmentName() + { + return attachment_name; + } + + + /** + * Set the value of AttachmentName + */ + public void setAttachmentName(String v ) + { + + + + if ( !ObjectUtils.equals(this.attachment_name, v) ) + { + this.attachment_name = v; + setModified(true); + } + } + + *************** *** 786,789 **** --- 867,871 ---- fieldNames_.add("SampleId"); fieldNames_.add("UsersId"); + fieldNames_.add("UsersIdComment"); fieldNames_.add("UserId"); fieldNames_.add("Solvent"); *************** *** 796,799 **** --- 878,883 ---- fieldNames_.add("Finished"); fieldNames_.add("Process"); + fieldNames_.add("Attachment"); + fieldNames_.add("AttachmentName"); } return fieldNames_; *************** *** 814,817 **** --- 898,905 ---- return getUsersId(); } + if (name.equals("UsersIdComment")) + { + return getUsersIdComment(); + } if (name.equals("UserId")) { *************** *** 854,857 **** --- 942,953 ---- return getProcess(); } + if (name.equals("Attachment")) + { + return getAttachment(); + } + if (name.equals("AttachmentName")) + { + return getAttachmentName(); + } return null; } *************** *** 871,874 **** --- 967,974 ---- return getUsersId(); } + if (name.equals(DBSamplePeer.USERS_ID_COMMENT )) + { + return getUsersIdComment(); + } if (name.equals(DBSamplePeer.USER_ID )) { *************** *** 911,914 **** --- 1011,1022 ---- return getProcess(); } + if (name.equals(DBSamplePeer.ATTACHMENT )) + { + return getAttachment(); + } + if (name.equals(DBSamplePeer.ATTACHMENT_NAME )) + { + return getAttachmentName(); + } return null; } *************** *** 930,971 **** if ( pos == 2 ) { ! return getUserId(); } if ( pos == 3 ) { ! return getSolvent(); } if ( pos == 4 ) { ! return getMachine(); } if ( pos == 5 ) { ! return getProbableStructure(); } if ( pos == 6 ) { ! return getDate(); } if ( pos == 7 ) { ! return getOtherNuclei(); } if ( pos == 8 ) { ! return getSpecialCare(); } if ( pos == 9 ) { ! return getWishedSpectrum(); } if ( pos == 10 ) { ! return getFinished(); } if ( pos == 11 ) { return getProcess(); } return null; } --- 1038,1091 ---- if ( pos == 2 ) { ! return getUsersIdComment(); } if ( pos == 3 ) { ! return getUserId(); } if ( pos == 4 ) { ! return getSolvent(); } if ( pos == 5 ) { ! return getMachine(); } if ( pos == 6 ) { ! return getProbableStructure(); } if ( pos == 7 ) { ! return getDate(); } if ( pos == 8 ) { ! return getOtherNuclei(); } if ( pos == 9 ) { ! return getSpecialCare(); } if ( pos == 10 ) { ! return getWishedSpectrum(); } if ( pos == 11 ) { + return getFinished(); + } + if ( pos == 12 ) + { return getProcess(); } + if ( pos == 13 ) + { + return getAttachment(); + } + if ( pos == 14 ) + { + return getAttachmentName(); + } return null; } *************** *** 1117,1120 **** --- 1237,1241 ---- copyObj.setSampleId(sample_id); copyObj.setUsersId(users_id); + copyObj.setUsersIdComment(users_id_comment); copyObj.setUserId(user_id); copyObj.setSolvent(solvent); *************** *** 1127,1130 **** --- 1248,1253 ---- copyObj.setFinished(finished); copyObj.setProcess(process); + copyObj.setAttachment(attachment); + copyObj.setAttachmentName(attachment_name); *************** *** 1138,1142 **** copyObj.setSampleId((NumberKey)null); ! return copyObj; } } --- 1261,1265 ---- copyObj.setSampleId((NumberKey)null); ! return copyObj; } } Index: BaseDBSamplePeer.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/om/BaseDBSamplePeer.java,v retrieving revision 1.7 retrieving revision 1.8 diff -C2 -r1.7 -r1.8 *** BaseDBSamplePeer.java 10 Oct 2006 15:20:31 -0000 1.7 --- BaseDBSamplePeer.java 30 Oct 2006 15:45:32 -0000 1.8 *************** *** 1,19 **** package org.openscience.nmrshiftdb.om; ! import java.util.Vector; ! ! import org.apache.turbine.om.NumberKey; ! import org.apache.turbine.om.ObjectKey; ! import org.apache.turbine.om.peer.BasePeer; ! import org.apache.turbine.services.db.TurbineDB; ! import org.apache.turbine.util.Log; ! import org.apache.turbine.util.db.Criteria; ! import org.apache.turbine.util.db.map.MapBuilder; ! import org.apache.turbine.util.db.map.TableMap; import org.apache.turbine.util.db.pool.DBConnection; ! import org.openscience.nmrshiftdb.om.map.DBSampleMapBuilder; ! import com.workingdogs.village.QueryDataSet; ! import com.workingdogs.village.Record; /** --- 1,19 ---- package org.openscience.nmrshiftdb.om; ! import java.util.*; ! import java.math.*; ! import java.sql.*; ! import com.workingdogs.village.*; ! import org.apache.turbine.om.*; ! import org.apache.turbine.om.peer.*; ! import org.apache.turbine.util.*; ! import org.apache.turbine.util.db.*; ! import org.apache.turbine.util.db.map.*; import org.apache.turbine.util.db.pool.DBConnection; ! import org.apache.turbine.services.db.TurbineDB; ! import org.apache.turbine.util.TurbineException; ! // Local classes ! import org.openscience.nmrshiftdb.om.map.*; /** *************** *** 42,45 **** --- 42,47 ---- /** the column name for the USERS_ID field */ public static final String USERS_ID = mapBuilder.getDBSample_UsersId(); + /** the column name for the USERS_ID_COMMENT field */ + public static final String USERS_ID_COMMENT = mapBuilder.getDBSample_UsersIdComment(); /** the column name for the USER_ID field */ public static final String USER_ID = mapBuilder.getDBSample_UserId(); *************** *** 62,69 **** /** the column name for the PROCESS field */ public static final String PROCESS = mapBuilder.getDBSample_Process(); /** number of columns for this peer */ ! public static final int numColumns = 12; /** A class that can be returned by this peer. */ --- 64,75 ---- /** the column name for the PROCESS field */ public static final String PROCESS = mapBuilder.getDBSample_Process(); + /** the column name for the ATTACHMENT field */ + public static final String ATTACHMENT = mapBuilder.getDBSample_Attachment(); + /** the column name for the ATTACHMENT_NAME field */ + public static final String ATTACHMENT_NAME = mapBuilder.getDBSample_AttachmentName(); /** number of columns for this peer */ ! public static final int numColumns = 15; /** A class that can be returned by this peer. */ *************** *** 121,125 **** public static ObjectKey doInsert( Criteria criteria ) throws Exception { ! return BasePeer.doInsert( criteria ); } --- 127,131 ---- public static ObjectKey doInsert( Criteria criteria ) throws Exception { ! return BasePeer.doInsert( criteria ); } *************** *** 132,136 **** throws Exception { ! return BasePeer.doInsert( criteria, dbCon ); } --- 138,142 ---- throws Exception { ! return BasePeer.doInsert( criteria, dbCon ); } *************** *** 140,143 **** --- 146,150 ---- criteria.addSelectColumn( SAMPLE_ID ); criteria.addSelectColumn( USERS_ID ); + criteria.addSelectColumn( USERS_ID_COMMENT ); criteria.addSelectColumn( USER_ID ); criteria.addSelectColumn( SOLVENT ); *************** *** 150,153 **** --- 157,162 ---- criteria.addSelectColumn( FINISHED ); criteria.addSelectColumn( PROCESS ); + criteria.addSelectColumn( ATTACHMENT ); + criteria.addSelectColumn( ATTACHMENT_NAME ); } *************** *** 186,203 **** new NumberKey(row.getValue(offset+0).asBigDecimal())); obj.setUsersId(row.getValue(offset+1).asString()); obj.setUserId( - new NumberKey(row.getValue(offset+2).asBigDecimal())); - obj.setSolvent( new NumberKey(row.getValue(offset+3).asBigDecimal())); ! obj.setMachine( new NumberKey(row.getValue(offset+4).asBigDecimal())); ! obj.setProbableStructure( new NumberKey(row.getValue(offset+5).asBigDecimal())); ! obj.setDate(row.getValue(offset+6).asUtilDate()); ! obj.setOtherNuclei(row.getValue(offset+7).asString()); ! obj.setSpecialCare(row.getValue(offset+8).asString()); ! obj.setWishedSpectrum(row.getValue(offset+9).asString()); ! obj.setFinished(row.getValue(offset+10).asString()); ! obj.setProcess(row.getValue(offset+11).asString()); } --- 195,215 ---- new NumberKey(row.getValue(offset+0).asBigDecimal())); obj.setUsersId(row.getValue(offset+1).asString()); + obj.setUsersIdComment(row.getValue(offset+2).asString()); obj.setUserId( new NumberKey(row.getValue(offset+3).asBigDecimal())); ! obj.setSolvent( new NumberKey(row.getValue(offset+4).asBigDecimal())); ! obj.setMachine( new NumberKey(row.getValue(offset+5).asBigDecimal())); ! obj.setProbableStructure( ! new NumberKey(row.getValue(offset+6).asBigDecimal())); ! obj.setDate(row.getValue(offset+7).asUtilDate()); ! obj.setOtherNuclei(row.getValue(offset+8).asString()); ! obj.setSpecialCare(row.getValue(offset+9).asString()); ! obj.setWishedSpectrum(row.getValue(offset+10).asString()); ! obj.setFinished(row.getValue(offset+11).asString()); ! obj.setProcess(row.getValue(offset+12).asString()); ! obj.setAttachment(row.getValue(offset+13).asBytes()); ! obj.setAttachmentName(row.getValue(offset+14).asString()); } *************** *** 232,236 **** } ! // BasePeer returns a Vector of Value (Village) arrays. The array // order follows the order columns were placed in the Select clause. --- 244,248 ---- } ! // BasePeer returns a Vector of Value (Village) arrays. The array // order follows the order columns were placed in the Select clause. *************** *** 252,256 **** } ! // BasePeer returns a Vector of Value (Village) arrays. The array // order follows the order columns were placed in the Select clause. --- 264,268 ---- } ! // BasePeer returns a Vector of Value (Village) arrays. The array // order follows the order columns were placed in the Select clause. *************** *** 300,304 **** Criteria(mapBuilder.getDatabaseMap().getName(), 2); selectCriteria.put( SAMPLE_ID, criteria.remove(SAMPLE_ID) ); ! BasePeer.doUpdate( selectCriteria, criteria ); } --- 312,316 ---- Criteria(mapBuilder.getDatabaseMap().getName(), 2); selectCriteria.put( SAMPLE_ID, criteria.remove(SAMPLE_ID) ); ! BasePeer.doUpdate( selectCriteria, criteria ); } *************** *** 315,319 **** Criteria(mapBuilder.getDatabaseMap().getName(), 2); selectCriteria.put( SAMPLE_ID, criteria.remove(SAMPLE_ID) ); ! BasePeer.doUpdate( selectCriteria, criteria, dbCon ); } --- 327,331 ---- Criteria(mapBuilder.getDatabaseMap().getName(), 2); selectCriteria.put( SAMPLE_ID, criteria.remove(SAMPLE_ID) ); ! BasePeer.doUpdate( selectCriteria, criteria, dbCon ); } *************** *** 325,329 **** public static void doDelete(Criteria criteria) throws Exception { ! BasePeer.doDelete ( criteria ); } --- 337,341 ---- public static void doDelete(Criteria criteria) throws Exception { ! BasePeer.doDelete ( criteria ); } *************** *** 337,341 **** public static void doDelete(Criteria criteria, DBConnection dbCon) throws Exception { ! BasePeer.doDelete ( criteria, dbCon ); } --- 349,353 ---- public static void doDelete(Criteria criteria, DBConnection dbCon) throws Exception { ! BasePeer.doDelete ( criteria, dbCon ); } *************** *** 405,408 **** --- 417,421 ---- criteria.add( SAMPLE_ID, obj.getSampleId() ); criteria.add( USERS_ID, obj.getUsersId() ); + criteria.add( USERS_ID_COMMENT, obj.getUsersIdComment() ); criteria.add( USER_ID, obj.getUserId() ); criteria.add( SOLVENT, obj.getSolvent() ); *************** *** 415,418 **** --- 428,433 ---- criteria.add( FINISHED, obj.getFinished() ); criteria.add( PROCESS, obj.getProcess() ); + criteria.add( ATTACHMENT, obj.getAttachment() ); + criteria.add( ATTACHMENT_NAME, obj.getAttachmentName() ); return criteria; } *************** *** 495,499 **** ! Vector rows = BasePeer.doSelect(c); Vector results = new Vector(); --- 510,514 ---- ! Vector rows = BasePeer.doSelect(c); Vector results = new Vector(); *************** *** 562,566 **** ! Vector rows = BasePeer.doSelect(c); Vector results = new Vector(); --- 577,581 ---- ! Vector rows = BasePeer.doSelect(c); Vector results = new Vector(); *************** *** 629,633 **** ! Vector rows = BasePeer.doSelect(c); Vector results = new Vector(); --- 644,648 ---- ! Vector rows = BasePeer.doSelect(c); Vector results = new Vector(); *************** *** 696,700 **** ! Vector rows = BasePeer.doSelect(c); Vector results = new Vector(); --- 711,715 ---- ! Vector rows = BasePeer.doSelect(c); Vector results = new Vector(); *************** *** 767,771 **** DBMoleculePeer.addSelectColumns(c); int offset5 = offset4 + DBMoleculePeer.numColumns; ! Vector rows = BasePeer.doSelect(c); Vector results = new Vector(); --- 782,786 ---- DBMoleculePeer.addSelectColumns(c); int offset5 = offset4 + DBMoleculePeer.numColumns; ! Vector rows = BasePeer.doSelect(c); Vector results = new Vector(); *************** *** 890,894 **** DBMoleculePeer.addSelectColumns(c); int offset5 = offset4 + DBMoleculePeer.numColumns; ! Vector rows = BasePeer.doSelect(c); Vector results = new Vector(); --- 905,909 ---- DBMoleculePeer.addSelectColumns(c); int offset5 = offset4 + DBMoleculePeer.numColumns; ! Vector rows = BasePeer.doSelect(c); Vector results = new Vector(); *************** *** 1013,1017 **** DBMoleculePeer.addSelectColumns(c); int offset5 = offset4 + DBMoleculePeer.numColumns; ! Vector rows = BasePeer.doSelect(c); Vector results = new Vector(); --- 1028,1032 ---- DBMoleculePeer.addSelectColumns(c); int offset5 = offset4 + DBMoleculePeer.numColumns; ! Vector rows = BasePeer.doSelect(c); Vector results = new Vector(); *************** *** 1136,1140 **** int offset5 = offset4 + DBMachinePeer.numColumns; ! Vector rows = BasePeer.doSelect(c); Vector results = new Vector(); --- 1151,1155 ---- int offset5 = offset4 + DBMachinePeer.numColumns; ! Vector rows = BasePeer.doSelect(c); Vector results = new Vector(); Index: DBSample.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/om/DBSample.java,v retrieving revision 1.5 retrieving revision 1.6 diff -C2 -r1.5 -r1.6 *** DBSample.java 21 Sep 2006 12:22:12 -0000 1.5 --- DBSample.java 30 Oct 2006 15:45:32 -0000 1.6 *************** *** 19,22 **** --- 19,24 ---- public boolean isDeletable() throws Exception{ + if(this.getFinished().equals("pending")) + return false; Criteria crit=new Criteria(); crit.add(DBRawFilePeer.SAMPLE_ID,this.getSampleId()); *************** *** 24,27 **** --- 26,40 ---- return v.size()==0; } + + public String getAttachmentStr(){ + return new String(this.getAttachment()); + } + public boolean getUsersIdCommentIsSet(){ + return !new String(this.getUsersIdComment()).equals(""); + } + + public boolean getAttachmentIsSet(){ + return !new String(this.getAttachment()).equals(""); + } } |
Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/portlets In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv3468/src/java/org/openscience/nmrshiftdb/portlets Modified Files: DetailPortlet.java PredictPortlet.java ReviewPortlet.java SubmitPortlet.java Log Message: this has the changes from the discussion with the lab system users Index: DetailPortlet.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/portlets/DetailPortlet.java,v retrieving revision 1.69 retrieving revision 1.70 diff -C2 -r1.69 -r1.70 *** DetailPortlet.java 27 Jun 2006 14:29:17 -0000 1.69 --- DetailPortlet.java 30 Oct 2006 15:45:32 -0000 1.70 *************** *** 67,70 **** --- 67,73 ---- session.setAttribute("applet","applet"); } + if(req.getParameter("applet") !=null && req.getParameter("applet").equals("noapplet")){ + runData.getSession().setAttribute("applet","noapplet"); + } //used for storing the results for browsing between result pages Vector results = (Vector) session.getAttribute("results"); Index: PredictPortlet.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/portlets/PredictPortlet.java,v retrieving revision 1.174 retrieving revision 1.175 diff -C2 -r1.174 -r1.175 *** PredictPortlet.java 9 Oct 2006 13:24:38 -0000 1.174 --- PredictPortlet.java 30 Oct 2006 15:45:32 -0000 1.175 *************** *** 680,683 **** --- 680,686 ---- session.setAttribute("applet", "applet"); } + if(req.getParameter("applet") !=null && req.getParameter("applet").equals("noapplet")){ + runData.getSession().setAttribute("applet","noapplet"); + } StringBuffer input = (StringBuffer) session.getAttribute(NmrshiftdbConstants.INPUT); String action = null; Index: ReviewPortlet.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/portlets/ReviewPortlet.java,v retrieving revision 1.118 retrieving revision 1.119 diff -C2 -r1.118 -r1.119 *** ReviewPortlet.java 8 Jun 2006 11:02:36 -0000 1.118 --- ReviewPortlet.java 30 Oct 2006 15:45:32 -0000 1.119 *************** *** 88,91 **** --- 88,94 ---- session.setAttribute("applet","applet"); } + if(req.getParameter("applet") !=null && req.getParameter("applet").equals("noapplet")){ + runData.getSession().setAttribute("applet","noapplet"); + } //No login necessary for reviewbyurl if (action != null && action.equals("reviewbyurl")) { Index: SubmitPortlet.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/portlets/SubmitPortlet.java,v retrieving revision 1.424 retrieving revision 1.425 diff -C2 -r1.424 -r1.425 *** SubmitPortlet.java 23 Oct 2006 11:58:09 -0000 1.424 --- SubmitPortlet.java 30 Oct 2006 15:45:32 -0000 1.425 *************** *** 270,273 **** --- 270,276 ---- session.setAttribute("applet","applet"); } + if(req.getParameter("applet") !=null && req.getParameter("applet").equals("noapplet")){ + runData.getSession().setAttribute("applet","noapplet"); + } if ((req.getContentType() != null && req.getContentType().indexOf("multipart/form-data") > -1 && runData.getParameters().getFileItems("Datei2") != null) || (req.getContentType() != null && req.getContentType().indexOf("multipart/form-data") > -1 && subData != null && subData.getLevel() == 2)) { action = "uploadjcamp"; *************** *** 332,339 **** 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")); --- 335,343 ---- crit.add(DBRawFilePeer.RAW_FILE_ID,runData.getParameters().get("id")); DBRawFile rawfile=((DBRawFile)DBRawFilePeer.doSelect(crit).get(0)); ! subData.rawfile=rawfile; DBSample sample=DBSamplePeer.retrieveByPK(rawfile.getSampleId()); ! if(!new String(sample.getProbableStructure()+"").equals("")){ ! sample.getDBMolecule().addValuesToSubmittingData(subData,null,false); ! } subData.setSpectrumKeywords(((NmrshiftdbUser)runData.getUser()).getDBLabGroup().getLabgroupName()); subData.fullfillsOrder=new NumberKey(runData.getParameters().get("id")); |
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From: Stefan K. <sh...@us...> - 2006-10-30 15:46:11
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/om/map In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv3468/src/java/org/openscience/nmrshiftdb/om/map Modified Files: DBSampleMapBuilder.java Log Message: this has the changes from the discussion with the lab system users Index: DBSampleMapBuilder.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/om/map/DBSampleMapBuilder.java,v retrieving revision 1.8 retrieving revision 1.9 diff -C2 -r1.8 -r1.9 *** DBSampleMapBuilder.java 10 Oct 2006 15:20:31 -0000 1.8 --- DBSampleMapBuilder.java 30 Oct 2006 15:45:32 -0000 1.9 *************** *** 1,9 **** package org.openscience.nmrshiftdb.om.map; ! import java.util.Date; ! 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; *************** *** 34,37 **** --- 35,44 ---- } + /** SAMPLE.USERS_ID_COMMENT */ + public static String getDBSample_UsersIdComment() + { + return getTable() + ".USERS_ID_COMMENT"; + } + /** SAMPLE.USER_ID */ public static String getDBSample_UserId() *************** *** 94,97 **** --- 101,116 ---- } + /** SAMPLE.ATTACHMENT */ + public static String getDBSample_Attachment() + { + return getTable() + ".ATTACHMENT"; + } + + /** SAMPLE.ATTACHMENT_NAME */ + public static String getDBSample_AttachmentName() + { + return getTable() + ".ATTACHMENT_NAME"; + } + /** the database map */ private DatabaseMap dbMap = null; *************** *** 129,132 **** --- 148,153 ---- tMap.addColumn ( getDBSample_UsersId(), new String() ); + tMap.addColumn ( getDBSample_UsersIdComment(), new String() ); + tMap.addForeignKey ( getDBSample_UserId(), new Integer(0) , "TURBINE_USER" , "USER_ID" ); *************** *** 149,152 **** --- 170,177 ---- tMap.addColumn ( getDBSample_Process(), new String() ); + tMap.addColumn ( getDBSample_Attachment(), new Object() ); + + tMap.addColumn ( getDBSample_AttachmentName(), new String() ); + } |
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From: Stefan K. <sh...@us...> - 2006-10-30 15:46:07
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv3468/src/java/org/openscience/nmrshiftdb Modified Files: NmrshiftdbServlet.java Log Message: this has the changes from the discussion with the lab system users Index: NmrshiftdbServlet.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/NmrshiftdbServlet.java,v retrieving revision 1.95 retrieving revision 1.96 diff -C2 -r1.95 -r1.96 *** NmrshiftdbServlet.java 24 Oct 2006 17:17:22 -0000 1.95 --- NmrshiftdbServlet.java 30 Oct 2006 15:45:31 -0000 1.96 *************** *** 66,69 **** --- 66,71 ---- import org.openscience.nmrshiftdb.om.DBMolecule; import org.openscience.nmrshiftdb.om.DBMoleculePeer; + import org.openscience.nmrshiftdb.om.DBSample; + import org.openscience.nmrshiftdb.om.DBSamplePeer; import org.openscience.nmrshiftdb.om.DBSpectrum; import org.openscience.nmrshiftdb.om.DBSpectrumPeer; *************** *** 180,183 **** --- 182,190 ---- } rssWriter.write(soac); + }else if(action.equals("getattachment")){ + res.setContentType("application/zip"); + outstream=res.getOutputStream(); + DBSample sample=DBSamplePeer.retrieveByPK(new NumberKey(req.getParameter("sampleid"))); + outstream.write(sample.getAttachment()); }else if(action.equals("exportcmlbyinchi")){ res.setContentType("text/xml"); |
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From: Stefan K. <sh...@us...> - 2006-10-30 15:46:07
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Update of /cvsroot/nmrshiftdb/nmrshiftdb In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv3468 Modified Files: CHANGELOG Log Message: this has the changes from the discussion with the lab system users Index: CHANGELOG =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/CHANGELOG,v retrieving revision 1.117 retrieving revision 1.118 diff -C2 -r1.117 -r1.118 *** CHANGELOG 25 Oct 2006 10:51:09 -0000 1.117 --- CHANGELOG 30 Oct 2006 15:45:31 -0000 1.118 *************** *** 9,12 **** --- 9,13 ---- * Peak table/structure/peak view combinations highlight the rows in table as well * The rating now longer includes default mark + * It is possible to switch back from java to non-java mode Fixes: |
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From: Stefan K. <sh...@us...> - 2006-10-30 15:45:45
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/vmtemplates/portlets/html In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv3468/src/vmtemplates/portlets/html Modified Files: user-order.vm worker-order.vm Log Message: this has the changes from the discussion with the lab system users Index: user-order.vm =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/vmtemplates/portlets/html/user-order.vm,v retrieving revision 1.47 retrieving revision 1.48 diff -C2 -r1.47 -r1.48 *** user-order.vm 27 Oct 2006 12:17:01 -0000 1.47 --- user-order.vm 30 Oct 2006 15:45:35 -0000 1.48 *************** *** 1,4 **** --- 1,7 ---- <a href="portal/pane0/Help;jsessionid=$data.getSession().getId()?URL=using.html#labadmin" style="color:white"><img src="images/help.png"></a> #if($data.User.isLabgroupUser($data)) + #if($submitorshow=="show") + <a href="portal/pane0/NMR+lab+administration;jsessionid=$data.getSession().getId()">Submit a new order</a> + #end <table align="center" border="3" rules="cols"> <tr> *************** *** 17,21 **** bgcolor="#D3D3D3" #end ! ><td><a href="portal/pane0/NMR+lab+administration;jsessionid=$data.getSession().getId()?submitorshow=show&id=$sample.getSampleId()">$sample.getUsersId()</a></td></tr> #end </table> --- 20,24 ---- bgcolor="#D3D3D3" #end ! ><td><a href="portal/pane0/NMR+lab+administration;jsessionid=$data.getSession().getId()?submitorshow=show&id=$sample.getSampleId()">$sample.getUsersId() #if($sample.getUsersIdCommentIsSet()) ($sample.getUsersIdComment()) #end</a></td></tr> #end </table> *************** *** 33,37 **** bgcolor="#D3D3D3" #end ! ><td><a href="portal/pane0/NMR+lab+administration;jsessionid=$data.getSession().getId()?submitorshow=show&id=$sample.getSampleId()">$sample.getUsersId()</a></td></tr> #end </table> --- 36,40 ---- bgcolor="#D3D3D3" #end ! ><td><a href="portal/pane0/NMR+lab+administration;jsessionid=$data.getSession().getId()?submitorshow=show&id=$sample.getSampleId()">$sample.getUsersId() #if($sample.getUsersIdCommentIsSet()) ($sample.getUsersIdComment()) #end</a></td></tr> #end </table> *************** *** 49,53 **** bgcolor="#D3D3D3" #end ! ><td><a href="portal/pane0/NMR+lab+administration;jsessionid=$data.getSession().getId()?submitorshow=show&id=$sample.getSampleId()">$sample.getUsersId()</a></td></tr> #end </table> --- 52,56 ---- bgcolor="#D3D3D3" #end ! ><td><a href="portal/pane0/NMR+lab+administration;jsessionid=$data.getSession().getId()?submitorshow=show&id=$sample.getSampleId()">$sample.getUsersId() #if($sample.getUsersIdCommentIsSet()) ($sample.getUsersIdComment()) #end</a></td></tr> #end </table> *************** *** 65,69 **** bgcolor="#D3D3D3" #end ! ><td><a href="portal/pane0/NMR+lab+administration;jsessionid=$data.getSession().getId()?submitorshow=show&id=$sample.getSampleId()">$sample.getUsersId()</a> ($sample.getDate())</td></tr> #end </table> --- 68,72 ---- bgcolor="#D3D3D3" #end ! ><td><a href="portal/pane0/NMR+lab+administration;jsessionid=$data.getSession().getId()?submitorshow=show&id=$sample.getSampleId()">$sample.getUsersId()</a> #if($sample.getUsersIdCommentIsSet()) ($sample.getUsersIdComment()) #end ($sample.getDate())</td></tr> #end </table> *************** *** 125,129 **** Name: $data.getUser().getFirstName() $data.getUser().getLastName()<br> Workgroup: $data.getUser().getAffiliation()<br> ! Sample I. D.: #if($submitorshow=="submit")<input name="sampleid" type="text" size="30" value="$!usersid">#else $sample.getUsersId() #end <br> Date: $date<br> <br> --- 128,132 ---- Name: $data.getUser().getFirstName() $data.getUser().getLastName()<br> Workgroup: $data.getUser().getAffiliation()<br> ! Sample I. D.: #if($submitorshow=="submit")<input name="sampleid" type="text" size="30" value="$!usersid"> (keyword for personal use: <input name="sampleidcomment" type="text" size="30" value="$!usersidcomment">)#else $sample.getUsersId() (personal keyword: $sample.getUsersIdComment()) #end <br> Date: $date<br> <br> *************** *** 172,178 **** if(document.JcpEditor != null) { var s = document.JcpEditor.getMolFile();; s = unix2local(s); ! document.orderform.MolTxt.value=s; } else --- 175,182 ---- if(document.JcpEditor != null) { + var s = document.JcpEditor.getMolFile();; s = unix2local(s); ! document.getElementById("MolTxt").value=s; } else *************** *** 198,202 **** --> </script> ! <input type="hidden" name="MolTxt"> <input type="button" style="font-size:smaller" value="Clear" onClick="document.JcpEditor.clear();"> <input type="button" style="font-size:smaller" value="Import from structures history" onClick="openStructureHistory()"> --- 202,206 ---- --> </script> ! <input type="hidden" name="MolTxt" id="MolTxt"> <input type="button" style="font-size:smaller" value="Clear" onClick="document.JcpEditor.clear();"> <input type="button" style="font-size:smaller" value="Import from structures history" onClick="openStructureHistory()"> *************** *** 245,248 **** --- 249,257 ---- Other nuclei (please specify): #if($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> + #if($submitorshow=="show") + #if($sample.getAttachmentIsSet()) <a href="download/NmrshiftdbServlet/$sample.getAttachmentName()?sampleid=$sample.getSampleId()&nmrshiftdbaction=getattachment">The user attached a file to the order</a> #end + #else + Here you can attach any file for the operator: <input type="file" name="datei2" size="40"><br> + #end #foreach($sample in $sample.getDBRawFiles()) <a href="$sample.getUrl()">Download the raw NMR file here</a> Index: worker-order.vm =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/vmtemplates/portlets/html/worker-order.vm,v retrieving revision 1.22 retrieving revision 1.23 diff -C2 -r1.22 -r1.23 *** worker-order.vm 11 Oct 2006 12:25:14 -0000 1.22 --- worker-order.vm 30 Oct 2006 15:45:35 -0000 1.23 *************** *** 43,46 **** --- 43,47 ---- Other nuclei (please specify): $sample.getOtherNuclei()<br> Special care for sample: $sample.getSpecialCare()<br> + #if($sample.getAttachmentIsSet()) <a href="download/NmrshiftdbServlet/$sample.getAttachmentName()?sampleid=$sample.getSampleId()&nmrshiftdbaction=getattachment">The user attached a file to the order</a> #end<br> </td> <td> |
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From: Stefan K. <sh...@us...> - 2006-10-30 15:45:45
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/vmtemplates In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv3468/src/vmtemplates Modified Files: confirm.vm details.vm predict.vm review.vm submit.vm Log Message: this has the changes from the discussion with the lab system users Index: confirm.vm =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/vmtemplates/confirm.vm,v retrieving revision 1.58 retrieving revision 1.59 diff -C2 -r1.58 -r1.59 *** confirm.vm 20 Oct 2006 14:42:05 -0000 1.58 --- confirm.vm 30 Oct 2006 15:45:33 -0000 1.59 *************** *** 44,48 **** <td> #if($data.getSession().getAttribute("applet")=="applet") ! <span style="color:#0000AA">Double click to get resizeable window!</span><br> <script LANGUAGE="JavaScript1.1" SRC="nmrshiftdbhtml/marvin.js"></script> <script LANGUAGE="JavaScript1.1"> --- 44,48 ---- <td> #if($data.getSession().getAttribute("applet")=="applet") ! <a href="$data.getRequest().getRequestURI();jsessionid=$data.getSession().getId()?$data.getRequest().getQueryString()&applet=noapplet" title="Switch off Java applets" style="color:white"><img src="images/nojava.png"></a><span style="color:#0000AA">Double click to get resizeable window!</span><br> <script LANGUAGE="JavaScript1.1" SRC="nmrshiftdbhtml/marvin.js"></script> <script LANGUAGE="JavaScript1.1"> Index: details.vm =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/vmtemplates/details.vm,v retrieving revision 1.162 retrieving revision 1.163 diff -C2 -r1.162 -r1.163 *** details.vm 20 Oct 2006 14:42:05 -0000 1.162 --- details.vm 30 Oct 2006 15:45:33 -0000 1.163 *************** *** 115,119 **** </script> #else ! <span style="color:#0000AA">Double click to get resizeable window!</span><br> <script LANGUAGE="JavaScript1.1"> mview_mayscript = true; --- 115,119 ---- </script> #else ! <a href="$data.getRequest().getRequestURI();jsessionid=$data.getSession().getId()?$data.getRequest().getQueryString()&applet=noapplet" title="Switch off Java applets" style="color:white"><img src="images/nojava.png"></a><span style="color:#0000AA">Double click to get resizeable window!</span><br> <script LANGUAGE="JavaScript1.1"> mview_mayscript = true; Index: predict.vm =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/vmtemplates/predict.vm,v retrieving revision 1.85 retrieving revision 1.86 diff -C2 -r1.85 -r1.86 *** predict.vm 20 Oct 2006 14:42:05 -0000 1.85 --- predict.vm 30 Oct 2006 15:45:33 -0000 1.86 *************** *** 17,20 **** --- 17,21 ---- <td> #if($session.getAttribute("applet")=="applet") + <a href="$data.getRequest().getRequestURI();jsessionid=$data.getSession().getId()?$data.getRequest().getQueryString()&applet=noapplet" title="Switch off Java applets" style="color:white"><img src="images/nojava.png"></a> #if($input=="0") <span style="color:#0000AA">Double click to get resizeable window!</span><br> Index: review.vm =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/vmtemplates/review.vm,v retrieving revision 1.75 retrieving revision 1.76 diff -C2 -r1.75 -r1.76 *** review.vm 20 Oct 2006 14:42:05 -0000 1.75 --- review.vm 30 Oct 2006 15:45:33 -0000 1.76 *************** *** 9,13 **** <td> #if($data.getSession().getAttribute("applet")=="applet") ! <span style="color:#0000AA">Double click to get resizeable window!</span><br> <script LANGUAGE="JavaScript1.1" SRC="nmrshiftdbhtml/marvin.js"></script> <script LANGUAGE="JavaScript1.1"> --- 9,13 ---- <td> #if($data.getSession().getAttribute("applet")=="applet") ! <a href="$data.getRequest().getRequestURI();jsessionid=$data.getSession().getId()?$data.getRequest().getQueryString()&applet=noapplet" title="Switch off Java applets" style="color:white"><img src="images/nojava.png"></a><span style="color:#0000AA">Double click to get resizeable window!</span><br> <script LANGUAGE="JavaScript1.1" SRC="nmrshiftdbhtml/marvin.js"></script> <script LANGUAGE="JavaScript1.1"> Index: submit.vm =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/vmtemplates/submit.vm,v retrieving revision 1.155 retrieving revision 1.156 diff -C2 -r1.155 -r1.156 *** submit.vm 27 Jun 2006 14:29:18 -0000 1.155 --- submit.vm 30 Oct 2006 15:45:33 -0000 1.156 *************** *** 273,276 **** --- 273,277 ---- </script> #if($session.getAttribute("applet")=="applet") + <a href="$data.getRequest().getRequestURI();jsessionid=$data.getSession().getId()?$data.getRequest().getQueryString()&applet=noapplet" title="Switch off Java applets" style="color:white"><img src="images/nojava.png"></a><br> <script LANGUAGE="JavaScript1.1" SRC="nmrshiftdbhtml/marvin.js"></script> <script LANGUAGE="JavaScript1.1"> |
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From: Stefan K. <sh...@us...> - 2006-10-27 12:17:05
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/vmtemplates/portlets/html In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv11377/src/vmtemplates/portlets/html Modified Files: user-order.vm Log Message: the search history should now work for the user as well Index: user-order.vm =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/vmtemplates/portlets/html/user-order.vm,v retrieving revision 1.46 retrieving revision 1.47 diff -C2 -r1.46 -r1.47 *** user-order.vm 26 Oct 2006 17:18:48 -0000 1.46 --- user-order.vm 27 Oct 2006 12:17:01 -0000 1.47 *************** *** 199,204 **** </script> <input type="hidden" name="MolTxt"> ! <input type="button" value="Clear" onClick="document.JcpEditor.clear();"> ! <input type="button" value="Import from structures history" onClick="openStructureHistory()"> #else <a href="$data.getRequest().getRequestURI();jsessionid=$data.getSession().getId()?$data.getRequest().getQueryString()&applet=applet" title="Switch on Java-Applets" style="color:white"><img src="images/java.png"></a><br><br> --- 199,204 ---- </script> <input type="hidden" name="MolTxt"> ! <input type="button" style="font-size:smaller" value="Clear" onClick="document.JcpEditor.clear();"> ! <input type="button" style="font-size:smaller" value="Import from structures history" onClick="openStructureHistory()"> #else <a href="$data.getRequest().getRequestURI();jsessionid=$data.getSession().getId()?$data.getRequest().getQueryString()&applet=applet" title="Switch on Java-Applets" style="color:white"><img src="images/java.png"></a><br><br> |
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From: Stefan K. <sh...@us...> - 2006-10-27 12:17:05
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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-serv11377/src/java/org/openscience/nmrshiftdb/modules/actions/portlets Modified Files: OrderAction.java Log Message: the search history should now work for the user as well Index: OrderAction.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/modules/actions/portlets/OrderAction.java,v retrieving revision 1.34 retrieving revision 1.35 diff -C2 -r1.34 -r1.35 *** OrderAction.java 26 Oct 2006 17:18:48 -0000 1.34 --- OrderAction.java 27 Oct 2006 12:17:00 -0000 1.35 *************** *** 87,91 **** data.getSession().setAttribute("applet","noapplet"); } ! context.put("ordertype",this.WORKER); buildOrderContext(context,data); } --- 87,91 ---- data.getSession().setAttribute("applet","noapplet"); } ! context.put("ordertype",OrderAction.WORKER); buildOrderContext(context,data); } *************** *** 343,349 **** SubmittingData sd=new SubmittingData(ServletUtils.expandRelative(data.getServletConfig(), "/WEB-INF/conf/normalizer.xml")); sample.setProbableStructure(sd.saveMoleculeOnly(molecule, data, (NmrshiftdbUser)data.getUser())); } }else{ - System.err.println(data.getRequest().getContentType()+" "+data.getParameters().getFileItems("datei")); if(data.getRequest().getContentType().indexOf("multipart/form-data")>-1){ FileItem[] fi = data.getParameters().getFileItems("datei"); --- 343,349 ---- SubmittingData sd=new SubmittingData(ServletUtils.expandRelative(data.getServletConfig(), "/WEB-INF/conf/normalizer.xml")); sample.setProbableStructure(sd.saveMoleculeOnly(molecule, data, (NmrshiftdbUser)data.getUser())); + GeneralUtils.addToStructureHistory(molecule, data.getSession()); } }else{ if(data.getRequest().getContentType().indexOf("multipart/form-data")>-1){ FileItem[] fi = data.getParameters().getFileItems("datei"); *************** *** 359,366 **** --- 359,369 ---- new MDLWriter(sw).writeMolecule(mol); sample.setProbableStructure(sd.saveMoleculeOnly(sw.toString(), data, (NmrshiftdbUser)data.getUser())); + GeneralUtils.addToStructureHistory(sw.toString(), data.getSession()); } } } } + if(mol!=null){ + } sample.setDate(new Date()); sample.setOtherNuclei(data.getParameters().get("othernuc")); |
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From: Stefan K. <sh...@us...> - 2006-10-26 19:38:49
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/conf/jetspeed/images In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv3848/src/conf/jetspeed/images Added Files: nojava.png Log Message: forgot to add this --- NEW FILE: nojava.png --- PNG ý¶¼n i´y+/)DBXy=ËÔÖìyþÏÿ÷üç¸?ãsu:u>:/U®U®üCiV¹:? &ðkÙ·¼bÀÏÀ¤F %áB@Â3µDsá¨g¯Úµ j´¡ o&éùC@¿çêìNPV<Lß |
