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From: Stefan K. <sh...@us...> - 2006-07-06 10:49:35
|
Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/portlets In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv9900/src/java/org/openscience/nmrshiftdb/portlets Modified Files: PredictPortlet.java Log Message: fixes bug #1516607 Index: PredictPortlet.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/portlets/PredictPortlet.java,v retrieving revision 1.168 retrieving revision 1.169 diff -C2 -r1.168 -r1.169 *** PredictPortlet.java 28 Jun 2006 08:49:48 -0000 1.168 --- PredictPortlet.java 6 Jul 2006 10:49:31 -0000 1.169 *************** *** 513,516 **** --- 513,517 ---- } context.put("spectrumtype", predictAtomType.equals("Hsvm") ? "1H" : (predictAtomType.equals("All") ? "All" : DBSpectrumTypePeer.retrieveByPK(new NumberKey((String) session.getAttribute("spectype"))).getName())); + try{ String smilesNonChiral = new SmilesGenerator(DefaultChemObjectBuilder.getInstance()).createSMILES(mol); Criteria crit = new Criteria(); *************** *** 522,525 **** --- 523,529 ---- context.put("linkmessage", "none"); } + }catch(Exception ex){ + context.put("linkmessage", "none"); + } context.put("spectype", session.getAttribute("spectype")); if (!predictAtomType.equals("Hsvm")) { *************** *** 645,648 **** --- 649,656 ---- IMolecule molh=(IMolecule)AtomContainerManipulator.removeHydrogens(mol); new HydrogenAdder().addImplicitHydrogensToSatisfyValency(mol); + for(int i=0;i<mol.getAtomCount();i++){ + if(mol.getAtomAt(i).getHydrogenCount()<0) + mol.getAtomAt(i).setHydrogenCount(0); + } HueckelAromaticityDetector.detectAromaticity(mol, false); runData.getSession().setAttribute("mol", mol); |
|
From: Stefan K. <sh...@us...> - 2006-07-06 10:49:35
|
Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/vmtemplates In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv9900/src/vmtemplates Modified Files: details.vm Log Message: fixes bug #1516607 Index: details.vm =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/vmtemplates/details.vm,v retrieving revision 1.156 retrieving revision 1.157 diff -C2 -r1.156 -r1.157 *** details.vm 27 Jun 2006 14:59:28 -0000 1.156 --- details.vm 6 Jul 2006 10:49:32 -0000 1.157 *************** *** 244,252 **** #end <br><span style="color:#0000AA"> - #if ($viewingaction=="searchbyspectrum") - #if($spectrum.isSimilarityNot0()) - Input shift positions for search are shown by <span style="color:red">red arrows</span>. - #end - #end </span></br> </td> --- 244,247 ---- |
Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/deploymentdescriptors In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv27286/src/deploymentdescriptors Modified Files: NMRShiftDB.wsdd Added Files: NMRShiftDBpredict.wsdl NMRShiftDBrpc.wsdl NMRShiftDBsubmit.wsdl Removed Files: NMRShiftDB.wsdl Log Message: continuing web services --- NEW FILE: NMRShiftDBpredict.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="doPredictionResponse" type="cml:spectrumTypeType" /> <xsd:element name="doPredictionRequest" type="tns:DoPredictionParameters" /> <xsd:complexType name="DoPredictionParameters"> <xsd:sequence> <xsd:element ref="cml:molecule" minOccurs="1" maxOccurs="1" /> <xsd:element name="spectrumTypeName" type="xsd:string" /> </xsd:sequence> </xsd:complexType> </xsd:schema> </wsdl:types> <wsdl:message name="doPredictionResponse"> <wsdl:part element="tns:doPredictionResponse" name="doPredictionResponse" /> </wsdl:message> <wsdl:message name="doPredictionRequest"> <wsdl:part element="tns:doPredictionRequest" name="doPredictionRequest" /> </wsdl:message> <wsdl:portType name="NMRShiftDB"> <wsdl:operation name="doPrediction"> <wsdl:input message="tns:doPredictionRequest" /> <wsdl:output message="tns:doPredictionResponse" /> </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=doPrediction" /> <wsdl:input> <soap:body use="literal" /> </wsdl:input> <wsdl:output> <soap:body use="literal" /> </wsdl:output> </wsdl:operation> </wsdl:binding> <wsdl:service name="NMRShiftDBpredict"> <wsdl:port binding="tns:NMRShiftDBSOAP" name="NMRShiftDBSOAP"> <soap:address location="http://almost.cubic.uni-koeln.de/axis/services/NMRShiftDBpredict" /> </wsdl:port> </wsdl:definitions> --- NEW FILE: NMRShiftDBrpc.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:message name="getSpectrumTypesResponse"> <wsdl:part type="xsd:string" name="getSpectrumTypesResponse" /> </wsdl:message> <wsdl:portType name="NMRShiftDBOneWay"> <wsdl:operation name="getSpectrumTypes"> <wsdl:output message="tns:getSpectrumTypesResponse"></wsdl:output> </wsdl:operation> </wsdl:portType> <wsdl:binding name="NMRShiftDBOneWaySOAP" type="tns:NMRShiftDBOneWay"> <soap:binding style="document" transport="http://schemas.xmlsoap.org/soap/http" /> <wsdl:operation name="getSpectrumTypes"> <soap:operation soapAction="http://www.nmrshiftdb.org/ws/NMRShiftDB/getSpectrumTypes" /> <wsdl:output> <soap:body use="literal" /> </wsdl:output> </wsdl:operation> </wsdl:binding> <wsdl:service name="NMRShiftDBrpc"> <wsdl:port binding="tns:NMRShiftDBOneWaySOAP" name="NMRShiftDBOneWaySOAP"> <soap:address location="http://almost.cubic.uni-koeln.de/axis/services/NMRShiftDBrpc" /> </wsdl:port> </wsdl:service> </wsdl:definitions> --- NEW FILE: NMRShiftDBsubmit.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="doSubmitResponse" type="xsd:string" /> <xsd:element name="doSubmitRequest" type="tns:DoSubmitParameters" /> <xsd:complexType name="DoSubmitParameters"> <xsd:sequence> <xsd:element ref="cml:cml" minOccurs="1" maxOccurs="1" /> <xsd:element name="username" type="xsd:string" /> <xsd:element name="password" type="xsd:string" /> </xsd:sequence> </xsd:complexType> </xsd:schema> </wsdl:types> <wsdl:message name="doSubmitResponse"> <wsdl:part element="tns:doSubmitResponse" name="doSubmitResponse" /> </wsdl:message> <wsdl:message name="doSubmitRequest"> <wsdl:part element="tns:doSubmitRequest" name="doSubmitRequest" /> </wsdl:message> <wsdl:portType name="NMRShiftDB"> <wsdl:operation name="doSubmit"> <wsdl:input message="tns:doSubmitRequest" /> <wsdl:output message="tns:doSubmitResponse" /> </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=doPrediction" /> <wsdl:input> <soap:body use="literal" /> </wsdl:input> <wsdl:output> <soap:body use="literal" /> </wsdl:output> </wsdl:operation> </wsdl:binding> <wsdl:service name="NMRShiftDBsubmit"> <wsdl:port binding="tns:NMRShiftDBSOAP" name="NMRShiftDBSOAP"> <soap:address location="http://almost.cubic.uni-koeln.de/axis/services/NMRShiftDBsubmit" /> </wsdl:port> </wsdl:definitions> Index: NMRShiftDB.wsdd =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/deploymentdescriptors/NMRShiftDB.wsdd,v retrieving revision 1.2 retrieving revision 1.3 diff -C2 -r1.2 -r1.3 *** NMRShiftDB.wsdd 14 Jun 2006 20:42:17 -0000 1.2 --- NMRShiftDB.wsdd 4 Jul 2006 13:38:54 -0000 1.3 *************** *** 4,8 **** <!-- Services from serviceName WSDL service -->; ! <service name="NMRShiftDB" provider="java:MSG" use="literal"> <!-- Definitions for the SOAPMonitor (optional) --> <!--<requestFlow> --- 4,8 ---- <!-- Services from serviceName WSDL service -->; ! <service name="NMRShiftDBpredict" provider="java:MSG" use="literal"> <!-- Definitions for the SOAPMonitor (optional) --> <!--<requestFlow> *************** *** 15,20 **** <parameter name="className" value="org.openscience.nmrshiftdb.webservices.NMRShiftDBServiceBindingImpl"/> ! <parameter name="allowedMethods" value="*"/> ! <wsdlFile>NMRShiftDB.wsdl</wsdlFile> </service> </deployment> --- 15,48 ---- <parameter name="className" value="org.openscience.nmrshiftdb.webservices.NMRShiftDBServiceBindingImpl"/> ! <parameter name="allowedMethods" value="doPrediction"/> ! <wsdlFile>NMRShiftDBpredict.wsdl</wsdlFile> ! </service> ! <service name="NMRShiftDBrpc" provider="java:RPC" use="literal"> ! <!-- Definitions for the SOAPMonitor (optional) --> ! <!--<requestFlow> ! <handler type="soapmonitor"/> ! </requestFlow> ! <responseFlow> ! <handler type="soapmonitor"/> ! </responseFlow>--> ! <!-- End of the definitions for the SOAPMonitor --> ! <parameter name="className" ! value="org.openscience.nmrshiftdb.webservices.NMRShiftDBServiceBindingImpl"/> ! <parameter name="allowedMethods" value="getSpectrumTypes"/> ! <wsdlFile>NMRShiftDBrpc.wsdl</wsdlFile> ! </service> ! <service name="NMRShiftDBsubmit" provider="java:MSG" use="literal"> ! <!-- Definitions for the SOAPMonitor (optional) --> ! <!--<requestFlow> ! <handler type="soapmonitor"/> ! </requestFlow> ! <responseFlow> ! <handler type="soapmonitor"/> ! </responseFlow>--> ! <!-- End of the definitions for the SOAPMonitor --> ! <parameter name="className" ! value="org.openscience.nmrshiftdb.webservices.NMRShiftDBServiceBindingImpl"/> ! <parameter name="allowedMethods" value="getSpectrumTypes"/> ! <wsdlFile>NMRShiftDBrpc.wsdl</wsdlFile> </service> </deployment> --- NMRShiftDB.wsdl DELETED --- |
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From: Stefan K. <sh...@us...> - 2006-07-04 13:39:03
|
Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/webservices In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv27286/src/java/org/openscience/nmrshiftdb/webservices Modified Files: NMRShiftDB.java NMRShiftDBServiceBindingImpl.java Log Message: continuing web services Index: NMRShiftDB.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/webservices/NMRShiftDB.java,v retrieving revision 1.2 retrieving revision 1.3 diff -C2 -r1.2 -r1.3 *** NMRShiftDB.java 22 Jun 2006 16:33:24 -0000 1.2 --- NMRShiftDB.java 4 Jul 2006 13:38:55 -0000 1.3 *************** *** 12,15 **** --- 12,18 ---- public String getSpectrumTypes() throws java.rmi.RemoteException; + + public Document doSubmit(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 1.5 retrieving revision 1.6 diff -C2 -r1.5 -r1.6 *** NMRShiftDBServiceBindingImpl.java 23 Jun 2006 12:16:43 -0000 1.5 --- NMRShiftDBServiceBindingImpl.java 4 Jul 2006 13:38:55 -0000 1.6 *************** *** 4,8 **** --- 4,10 ---- import java.io.File; import java.io.FileInputStream; + import java.io.StringWriter; import java.rmi.RemoteException; + import java.util.Date; import java.util.HashMap; import java.util.Properties; *************** *** 13,33 **** import nu.xom.Document; import nu.xom.Node; import nu.xom.converters.DOMConverter; import org.apache.turbine.util.TurbineConfig; import org.apache.turbine.util.db.Criteria; import org.openscience.cdk.ChemFile; import org.openscience.cdk.interfaces.IChemFile; import org.openscience.cdk.interfaces.IMolecule; import org.openscience.cdk.io.CMLReader; import org.openscience.nmrshiftdb.PredictionTool; - import org.openscience.nmrshiftdb.om.DBSpectrum; import org.openscience.nmrshiftdb.om.DBSpectrumType; import org.openscience.nmrshiftdb.om.DBSpectrumTypePeer; import org.openscience.nmrshiftdb.util.GeneralUtils; import org.xmlcml.cml.element.CMLPeak; import org.xmlcml.cml.element.CMLPeakList; import org.xmlcml.cml.element.CMLSpectrum; public class NMRShiftDBServiceBindingImpl implements NMRShiftDB { --- 15,50 ---- import nu.xom.Document; + import nu.xom.Element; + import nu.xom.Elements; import nu.xom.Node; import nu.xom.converters.DOMConverter; + import org.apache.turbine.om.security.User; + import org.apache.turbine.services.security.TurbineSecurity; import org.apache.turbine.util.TurbineConfig; import org.apache.turbine.util.db.Criteria; + import org.apache.turbine.util.security.PasswordMismatchException; + import org.apache.turbine.util.security.UnknownEntityException; import org.openscience.cdk.ChemFile; import org.openscience.cdk.interfaces.IChemFile; import org.openscience.cdk.interfaces.IMolecule; import org.openscience.cdk.io.CMLReader; + import org.openscience.cdk.tools.manipulator.AtomContainerManipulator; import org.openscience.nmrshiftdb.PredictionTool; import org.openscience.nmrshiftdb.om.DBSpectrumType; import org.openscience.nmrshiftdb.om.DBSpectrumTypePeer; + import org.openscience.nmrshiftdb.om.NmrshiftdbUser; + import org.openscience.nmrshiftdb.om.NmrshiftdbUserPeer; import org.openscience.nmrshiftdb.util.GeneralUtils; + import org.openscience.nmrshiftdb.util.SubmittingData; + import org.openscience.nmrshiftdb.util.ValueTriple; + import org.openscience.nmrshiftdb.util.exception.NmrshiftdbException; + import org.xmlcml.cml.base.CMLElements; + import org.xmlcml.cml.element.CMLCml; + import org.xmlcml.cml.element.CMLMolecule; import org.xmlcml.cml.element.CMLPeak; import org.xmlcml.cml.element.CMLPeakList; import org.xmlcml.cml.element.CMLSpectrum; + import org.xmlcml.cml.legacy.molecule.MDLConverter; public class NMRShiftDBServiceBindingImpl implements NMRShiftDB { *************** *** 36,41 **** public org.w3c.dom.Document doPrediction(org.w3c.dom.Document request) throws RemoteException { ! System.err.println("lkj2222"); ! org.w3c.dom.Document document = null; try{ Document doc=DOMConverter.convert(request); --- 53,57 ---- public org.w3c.dom.Document doPrediction(org.w3c.dom.Document request) throws RemoteException { ! org.w3c.dom.Document document = null; try{ Document doc=DOMConverter.convert(request); *************** *** 103,105 **** --- 119,173 ---- return sb.toString().trim(); } + + public org.w3c.dom.Document doSubmit(org.w3c.dom.Document request) throws RemoteException { + org.w3c.dom.Document document = null; + 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(); + Document doc=DOMConverter.convert(request); + Node elcml=doc.getChild(0).getChild(0); + Node eluser=doc.getChild(0).getChild(1); + Node elpassword=doc.getChild(0).getChild(1); + CMLCml cmlcml=CMLCml.makeElementInContext((Element)elcml); + if(cmlcml.getCMLChildCount("molecule")!=1){ + throw new NmrshiftdbException("There must be exactly one molcule in cml"); + } + CMLMolecule cmlmol=(CMLMolecule)cmlcml.getChildCMLElement("molecule",0); + Elements spectra=cmlcml.getChildCMLElements("spectrum"); + if(spectra.size()==0){ + throw new NmrshiftdbException("There must be at least one spectrum in cml"); + } + NmrshiftdbUser user; + User turbineuser = TurbineSecurity.getAuthenticatedUser(eluser.getValue(), elpassword.getValue()); + user = NmrshiftdbUserPeer.getByName(turbineuser.getUserName()); + for(int i=0;i<spectra.size();i++){ + SubmittingData subData=new SubmittingData(webinfdir+"conf/normalizer.xml"); + StringWriter writer=new StringWriter(); + MDLConverter mdlconv=new MDLConverter(); + mdlconv.setVersion("V2000"); + mdlconv.writeMOL(writer,cmlmol); + subData.setMol(writer.toString(),false,true,true); + CMLSpectrum spectrum=(CMLSpectrum)spectra.get(i); + CMLElements<CMLPeak> peaks=spectrum.getPeakListElements().get(0).getPeakElements(); + for(int k=0;k<peaks.size();k++){ + CMLPeak peak=peaks.get(k); + ValueTriple vt=new ValueTriple(); + vt.value1=(float)peak.getXValue(); + vt.value2=(float)peak.getYValue(); + String[] atomrefs=peak.getAtomRefs(); + for(int l=0;l<atomrefs.length;l++){ + vt.atoms.add(AtomContainerManipulator.getAtomById(subData.getMolWithH(),atomrefs[l])); + } + } + subData.save(user.getUserId(),"false","bioclipse", new Date(),null,Integer.parseInt(GeneralUtils.getNmrshiftdbProperty("hosecode.spheres")), false); + } + }catch(Exception ex){ + throw new RemoteException(ex.getMessage(),ex); + } + return document; + } } |
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From: Stefan K. <sh...@us...> - 2006-07-04 13:39:02
|
Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/util In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv27286/src/java/org/openscience/nmrshiftdb/util Modified Files: NmrshiftdbConstants.java Log Message: continuing web services Index: NmrshiftdbConstants.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/util/NmrshiftdbConstants.java,v retrieving revision 1.32 retrieving revision 1.33 diff -C2 -r1.32 -r1.33 *** NmrshiftdbConstants.java 8 Jun 2006 12:22:46 -0000 1.32 --- NmrshiftdbConstants.java 4 Jul 2006 13:38:55 -0000 1.33 *************** *** 45,49 **** public static String SPECTRUM_NR="spectrum id"; public static String HOSECODE="HOSE code"; ! public static String DBE="dobule bond equivalents"; public static String SSSR="number of rings in smallest set of smallest rings"; public static String DBE_RINGS="double bond equivalents/smallest set of smallest rings"; --- 45,49 ---- public static String SPECTRUM_NR="spectrum id"; public static String HOSECODE="HOSE code"; ! public static String DBE="double bond equivalents"; public static String SSSR="number of rings in smallest set of smallest rings"; public static String DBE_RINGS="double bond equivalents/smallest set of smallest rings"; |
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From: Stefan K. <sh...@us...> - 2006-07-04 13:39:02
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv27286/src/java/org/openscience/nmrshiftdb Modified Files: AdminPanel.java Log Message: continuing web services Index: AdminPanel.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/AdminPanel.java,v retrieving revision 1.229 retrieving revision 1.230 diff -C2 -r1.229 -r1.230 *** AdminPanel.java 29 Jun 2006 14:06:28 -0000 1.229 --- AdminPanel.java 4 Jul 2006 13:38:54 -0000 1.230 *************** *** 78,81 **** --- 78,82 ---- import org.openscience.nmrshiftdb.om.DBCoordinateSet3d; import org.openscience.nmrshiftdb.om.DBIsotopePeer; + import org.openscience.nmrshiftdb.om.DBLiterature; import org.openscience.nmrshiftdb.om.DBMolecule; import org.openscience.nmrshiftdb.om.DBMoleculeHyperlink; *************** *** 87,90 **** --- 88,92 ---- import org.openscience.nmrshiftdb.om.DBSignalPeer; import org.openscience.nmrshiftdb.om.DBSpectrum; + import org.openscience.nmrshiftdb.om.DBSpectrumDBLiterature; import org.openscience.nmrshiftdb.om.DBSpectrumPeer; import org.openscience.nmrshiftdb.om.DBSpectrumType; |
Update of /cvsroot/nmrshiftdb/nmrshiftdb/lib In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv27286/lib Modified Files: cdk-builder3d.jar cdk-charges.jar cdk-core.jar cdk-data.jar cdk-extra.jar cdk-forcefield.jar cdk-interfaces.jar cdk-io.jar cdk-libio-cml.jar cdk-pdb-cml.jar cdk-pdb.jar cdk-qsar-cml.jar cdk-qsar.jar cdk-render.jar cdk-smiles.jar cdk-standard.jar cdk-valencycheck.jar Log Message: continuing web services Index: cdk-builder3d.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/lib/cdk-builder3d.jar,v retrieving revision 1.49 retrieving revision 1.50 diff -C2 -r1.49 -r1.50 Binary files /tmp/cvsVA42B8 and /tmp/cvs6Trkfm differ Index: cdk-charges.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/lib/cdk-charges.jar,v retrieving revision 1.4 retrieving revision 1.5 diff -C2 -r1.4 -r1.5 Binary files /tmp/cvsAryfIM and /tmp/cvsHMEel1 differ Index: cdk-core.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/lib/cdk-core.jar,v retrieving revision 1.121 retrieving revision 1.122 diff -C2 -r1.121 -r1.122 Binary files /tmp/cvspvlmR0 and /tmp/cvs4dq9Of differ Index: cdk-data.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/lib/cdk-data.jar,v retrieving revision 1.45 retrieving revision 1.46 diff -C2 -r1.45 -r1.46 Binary files /tmp/cvsPZhSzp and /tmp/cvs7mARcF differ Index: cdk-extra.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/lib/cdk-extra.jar,v retrieving revision 1.159 retrieving revision 1.160 diff -C2 -r1.159 -r1.160 Binary files /tmp/cvsATOQ8L and /tmp/cvsQFoIN2 differ Index: cdk-forcefield.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/lib/cdk-forcefield.jar,v retrieving revision 1.4 retrieving revision 1.5 diff -C2 -r1.4 -r1.5 Binary files /tmp/cvsuyUK90 and /tmp/cvswDMmai differ Index: cdk-interfaces.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/lib/cdk-interfaces.jar,v retrieving revision 1.37 retrieving revision 1.38 diff -C2 -r1.37 -r1.38 Binary files /tmp/cvsXWtSfg and /tmp/cvs07oPvx differ Index: cdk-io.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/lib/cdk-io.jar,v retrieving revision 1.111 retrieving revision 1.112 diff -C2 -r1.111 -r1.112 Binary files /tmp/cvs4bsGVs and /tmp/cvsF8lQyK differ Index: cdk-libio-cml.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/lib/cdk-libio-cml.jar,v retrieving revision 1.37 retrieving revision 1.38 diff -C2 -r1.37 -r1.38 Binary files /tmp/cvszmzodA and /tmp/cvsnNZJYR differ Index: cdk-pdb-cml.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/lib/cdk-pdb-cml.jar,v retrieving revision 1.37 retrieving revision 1.38 diff -C2 -r1.37 -r1.38 Binary files /tmp/cvs81czeA and /tmp/cvsdtREjS differ Index: cdk-pdb.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/lib/cdk-pdb.jar,v retrieving revision 1.37 retrieving revision 1.38 diff -C2 -r1.37 -r1.38 Binary files /tmp/cvsxR8inJ and /tmp/cvsnIvcI1 differ Index: cdk-qsar-cml.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/lib/cdk-qsar-cml.jar,v retrieving revision 1.37 retrieving revision 1.38 diff -C2 -r1.37 -r1.38 Binary files /tmp/cvsQws4CP and /tmp/cvseHLY37 differ Index: cdk-qsar.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/lib/cdk-qsar.jar,v retrieving revision 1.52 retrieving revision 1.53 diff -C2 -r1.52 -r1.53 Binary files /tmp/cvsHrUXdS and /tmp/cvsiS2sLa differ Index: cdk-render.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/lib/cdk-render.jar,v retrieving revision 1.92 retrieving revision 1.93 diff -C2 -r1.92 -r1.93 Binary files /tmp/cvsH0ZFXW and /tmp/cvsOUvJAf differ Index: cdk-smiles.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/lib/cdk-smiles.jar,v retrieving revision 1.7 retrieving revision 1.8 diff -C2 -r1.7 -r1.8 Binary files /tmp/cvs8ZtB43 and /tmp/cvsLt6FTm differ Index: cdk-standard.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/lib/cdk-standard.jar,v retrieving revision 1.106 retrieving revision 1.107 diff -C2 -r1.106 -r1.107 Binary files /tmp/cvsFl0Fj5 and /tmp/cvs3e2Nfo differ Index: cdk-valencycheck.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/lib/cdk-valencycheck.jar,v retrieving revision 1.7 retrieving revision 1.8 diff -C2 -r1.7 -r1.8 Binary files /tmp/cvsQR2127 and /tmp/cvsEVzu2q differ |
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From: Stefan K. <sh...@us...> - 2006-06-29 15:05:03
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Update of /cvsroot/nmrshiftdb/nmrshiftdb In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv9842 Modified Files: CHANGELOG RELNOTES Log Message: changelog Index: CHANGELOG =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/CHANGELOG,v retrieving revision 1.111 retrieving revision 1.112 diff -C2 -r1.111 -r1.112 *** CHANGELOG 27 Jun 2006 14:29:17 -0000 1.111 --- CHANGELOG 29 Jun 2006 15:04:59 -0000 1.112 *************** *** 2,5 **** --- 2,8 ---- ---------------- + 1.2 Release + ----------- + New: * CML export contains properties Index: RELNOTES =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/RELNOTES,v retrieving revision 1.14 retrieving revision 1.15 diff -C2 -r1.14 -r1.15 *** RELNOTES 20 Jan 2006 15:24:58 -0000 1.14 --- RELNOTES 29 Jun 2006 15:04:59 -0000 1.15 *************** *** 4,7 **** --- 4,11 ---- Release 1.2 ------------- + This has some new features and bugfixes. Major change of user interface. No known bugs. + + Release 1.2 + ------------- This has some new features and bugfixes. Applets changed to JChemPaint. No known bugs. |
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From: Stefan K. <sh...@us...> - 2006-06-29 14:07:14
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/om In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv15615/src/java/org/openscience/nmrshiftdb/om Modified Files: DBCoordinateSet3d.java Log Message: some changes for the release Index: DBCoordinateSet3d.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/om/DBCoordinateSet3d.java,v retrieving revision 1.5 retrieving revision 1.6 diff -C2 -r1.5 -r1.6 *** DBCoordinateSet3d.java 4 Aug 2005 21:55:20 -0000 1.5 --- DBCoordinateSet3d.java 29 Jun 2006 14:06:29 -0000 1.6 *************** *** 23,27 **** super(); } ! /** --- 23,27 ---- super(); } ! /** |
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From: Stefan K. <sh...@us...> - 2006-06-29 14:07:08
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/util In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv15615/src/java/org/openscience/nmrshiftdb/util Modified Files: GeneralUtils.java Log Message: some changes for the release Index: GeneralUtils.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/util/GeneralUtils.java,v retrieving revision 1.181 retrieving revision 1.182 diff -C2 -r1.181 -r1.182 *** GeneralUtils.java 27 Jun 2006 14:59:28 -0000 1.181 --- GeneralUtils.java 29 Jun 2006 14:06:30 -0000 1.182 *************** *** 179,183 **** return input; }else{ ! return "<a href=\"javascript:alert('"+input+"')\">"+input.substring(0,30)+"... (trunkated)</a>"; } } --- 179,183 ---- return input; }else{ ! return "<a href=\"javascript:alert('"+input+"')\">"+input.substring(0,30)+"... (truncated)</a>"; } } |
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From: Stefan K. <sh...@us...> - 2006-06-29 14:07:08
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv15615/src/java/org/openscience/nmrshiftdb Modified Files: AdminPanel.java Log Message: some changes for the release Index: AdminPanel.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/AdminPanel.java,v retrieving revision 1.228 retrieving revision 1.229 diff -C2 -r1.228 -r1.229 *** AdminPanel.java 9 Jun 2006 14:25:56 -0000 1.228 --- AdminPanel.java 29 Jun 2006 14:06:28 -0000 1.229 *************** *** 1600,1604 **** } subData.save(user.getUserId(), "true", args[2], new Date(), null, Integer.parseInt(nmrprops.getProperty("hosecode.spheres")), true); ! }catch(Exception ex){ ex.printStackTrace(); } --- 1600,1604 ---- } subData.save(user.getUserId(), "true", args[2], new Date(), null, Integer.parseInt(nmrprops.getProperty("hosecode.spheres")), true); ! }catch(Exception ex){ ex.printStackTrace(); } |
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From: Stefan K. <sh...@us...> - 2006-06-28 13:57:43
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/om In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv32399/src/java/org/openscience/nmrshiftdb/om Modified Files: DBSpectrum.java Log Message: a fix Index: DBSpectrum.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/om/DBSpectrum.java,v retrieving revision 1.178 retrieving revision 1.179 diff -C2 -r1.178 -r1.179 *** DBSpectrum.java 27 Jun 2006 15:35:34 -0000 1.178 --- DBSpectrum.java 28 Jun 2006 13:57:40 -0000 1.179 *************** *** 1462,1467 **** crit2.add(DBSignalDBAtomPeer.ATOM_ID,assignedTo.getAtomId()); crit2.add(DBSignalPeer.SPECTRUM_ID,spectrum.getSpectrumId()); ! DBSignal signal=(DBSignal)DBSignalPeer.doSelect(crit2).get(0); ! sb.append("<td bgcolor=\"#E8E8E8\">"+signal.getFirstShift().getValue()+"</td>"); } } --- 1462,1470 ---- crit2.add(DBSignalDBAtomPeer.ATOM_ID,assignedTo.getAtomId()); crit2.add(DBSignalPeer.SPECTRUM_ID,spectrum.getSpectrumId()); ! Vector v=DBSignalPeer.doSelect(crit2); ! if(v.size()>0){ ! DBSignal signal=(DBSignal)v.get(0); ! sb.append("<td bgcolor=\"#E8E8E8\">"+signal.getFirstShift().getValue()+"</td>"); ! } } } |
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From: Stefan K. <sh...@us...> - 2006-06-28 10:40:53
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/portlets In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv19326/src/java/org/openscience/nmrshiftdb/portlets Modified Files: PredictPortlet.java Log Message: more formatting stuff Index: PredictPortlet.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/portlets/PredictPortlet.java,v retrieving revision 1.167 retrieving revision 1.168 diff -C2 -r1.167 -r1.168 *** PredictPortlet.java 28 Jun 2006 07:48:05 -0000 1.167 --- PredictPortlet.java 28 Jun 2006 08:49:48 -0000 1.168 *************** *** 18,21 **** --- 18,22 ---- import java.sql.Statement; import java.text.DecimalFormat; + import java.text.DecimalFormatSymbols; import java.util.Collections; import java.util.HashMap; *************** *** 120,125 **** */ public static VelocityContext getContext(HttpSession session, boolean calculated, boolean measured, StringBuffer messages, Object servconorrundata, HttpServletRequest request, boolean print) throws IOException, FileNotFoundException, Exception { ! DecimalFormat myFormatter = (DecimalFormat)DecimalFormat.getInstance(Locale.US); ! myFormatter.applyPattern("0.00"); VelocityContext context = new VelocityContext(); ServletConfig servcon; --- 121,125 ---- */ public static VelocityContext getContext(HttpSession session, boolean calculated, boolean measured, StringBuffer messages, Object servconorrundata, HttpServletRequest request, boolean print) throws IOException, FileNotFoundException, Exception { ! DecimalFormat myFormatter = new DecimalFormat( "0.00", new DecimalFormatSymbols(Locale.US)); VelocityContext context = new VelocityContext(); ServletConfig servcon; |
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From: Stefan K. <sh...@us...> - 2006-06-28 09:01:23
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/util In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv19326/src/java/org/openscience/nmrshiftdb/util Modified Files: ValuesForVelocityBean.java Log Message: more formatting stuff Index: ValuesForVelocityBean.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/util/ValuesForVelocityBean.java,v retrieving revision 1.45 retrieving revision 1.46 diff -C2 -r1.45 -r1.46 *** ValuesForVelocityBean.java 2 Feb 2006 17:49:59 -0000 1.45 --- ValuesForVelocityBean.java 28 Jun 2006 08:49:48 -0000 1.46 *************** *** 3,6 **** --- 3,8 ---- import java.io.Serializable; import java.text.DecimalFormat; + import java.text.DecimalFormatSymbols; + import java.util.Locale; import java.util.Vector; *************** *** 543,549 **** DecimalFormat format; if (i == 4 || i == 5) { ! format = new DecimalFormat("0"); } else { ! format = new DecimalFormat("0.00"); } if (statistics[4] == -1 && i == 4) { --- 545,551 ---- DecimalFormat format; if (i == 4 || i == 5) { ! format = new DecimalFormat("0", new DecimalFormatSymbols(Locale.US)); } else { ! format = new DecimalFormat("0.00", new DecimalFormatSymbols(Locale.US)); } if (statistics[4] == -1 && i == 4) { *************** *** 569,575 **** DecimalFormat format; if (i == 4 || i == 5) { ! format = new DecimalFormat("0"); } else { ! format = new DecimalFormat("0.00"); } if (statistics2[4] == -1 && i == 4) { --- 571,577 ---- DecimalFormat format; if (i == 4 || i == 5) { ! format = new DecimalFormat("0", new DecimalFormatSymbols(Locale.US)); } else { ! format = new DecimalFormat("0.00", new DecimalFormatSymbols(Locale.US)); } if (statistics2[4] == -1 && i == 4) { |
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From: Stefan K. <sh...@us...> - 2006-06-28 07:48:09
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/portlets In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv22689/src/java/org/openscience/nmrshiftdb/portlets Modified Files: PredictPortlet.java Log Message: corrects formatting Index: PredictPortlet.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/portlets/PredictPortlet.java,v retrieving revision 1.166 retrieving revision 1.167 diff -C2 -r1.166 -r1.167 *** PredictPortlet.java 27 Jun 2006 10:43:10 -0000 1.166 --- PredictPortlet.java 28 Jun 2006 07:48:05 -0000 1.167 *************** *** 22,25 **** --- 22,26 ---- import java.util.Iterator; import java.util.List; + import java.util.Locale; import java.util.Map; import java.util.Vector; *************** *** 119,123 **** */ public static VelocityContext getContext(HttpSession session, boolean calculated, boolean measured, StringBuffer messages, Object servconorrundata, HttpServletRequest request, boolean print) throws IOException, FileNotFoundException, Exception { ! DecimalFormat myFormatter = new DecimalFormat("0.00"); VelocityContext context = new VelocityContext(); ServletConfig servcon; --- 120,125 ---- */ public static VelocityContext getContext(HttpSession session, boolean calculated, boolean measured, StringBuffer messages, Object servconorrundata, HttpServletRequest request, boolean print) throws IOException, FileNotFoundException, Exception { ! DecimalFormat myFormatter = (DecimalFormat)DecimalFormat.getInstance(Locale.US); ! myFormatter.applyPattern("0.00"); VelocityContext context = new VelocityContext(); ServletConfig servcon; |
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From: Stefan K. <sh...@us...> - 2006-06-27 16:40:25
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/vmtemplates In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv23047/src/vmtemplates Modified Files: halloffame.vm Log Message: redesign Index: halloffame.vm =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/vmtemplates/halloffame.vm,v retrieving revision 1.14 retrieving revision 1.15 diff -C2 -r1.14 -r1.15 *** halloffame.vm 27 Jun 2006 14:59:28 -0000 1.14 --- halloffame.vm 27 Jun 2006 16:40:18 -0000 1.15 *************** *** 2,6 **** <p><table cellpadding="2" cellspacing="0"> <tr> ! <th> </th><th bgcolor="#999999"><div style="color:white">Name</div></th><th bgcolor="#BB0000"><div style="color:white">Contributions</div></th> </tr> #foreach($user in $users) --- 2,6 ---- <p><table cellpadding="2" cellspacing="0"> <tr> ! <th> </th><th bgcolor="#999999"><div style="color:white">Name</div></th><th bgcolor="#999999"><div style="color:white">Contributions</div></th> </tr> #foreach($user in $users) |
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From: Stefan K. <sh...@us...> - 2006-06-27 15:35:42
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/om In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv24119/src/java/org/openscience/nmrshiftdb/om Modified Files: DBSpectrum.java Log Message: change in spectrum export Index: DBSpectrum.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/om/DBSpectrum.java,v retrieving revision 1.177 retrieving revision 1.178 diff -C2 -r1.177 -r1.178 *** DBSpectrum.java 20 Jun 2006 11:14:57 -0000 1.177 --- DBSpectrum.java 27 Jun 2006 15:35:34 -0000 1.178 *************** *** 890,894 **** spectrum.setId("nmrshiftdb"+dbspectrum.getSpectrumId().toString()); spectrum.setMoleculeRef("nmrshiftdb"+dbspectrum.getDBMolecule().getMoleculeId().toString()); ! spectrum.setType(dbspectrum.getDBSpectrumType().getName()); Vector signals = dbspectrum.getDBSignals(); for (int i = 0; i < signals.size(); i++) { --- 890,894 ---- spectrum.setId("nmrshiftdb"+dbspectrum.getSpectrumId().toString()); spectrum.setMoleculeRef("nmrshiftdb"+dbspectrum.getDBMolecule().getMoleculeId().toString()); ! spectrum.setType("NMR"); Vector signals = dbspectrum.getDBSignals(); for (int i = 0; i < signals.size(); i++) { |
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From: Stefan K. <sh...@us...> - 2006-06-27 14:59:31
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/vmtemplates In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv6332/src/vmtemplates Modified Files: details.vm halloffame.vm Log Message: redesign Index: details.vm =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/vmtemplates/details.vm,v retrieving revision 1.155 retrieving revision 1.156 diff -C2 -r1.155 -r1.156 *** details.vm 27 Jun 2006 14:29:17 -0000 1.155 --- details.vm 27 Jun 2006 14:59:28 -0000 1.156 *************** *** 47,51 **** </td> #else ! <td valign="middle" class="TitleStyleClass" style="background-color: #BB0000; color: #FFFFFF;" > <a href="$data.getRequest().getRequestURI();jsessionid=$data.getSession().getId()?$query&tab=0" style="color: #FFFFFF" >Spectral Data</a> </td> --- 47,51 ---- </td> #else ! <td valign="middle" class="TitleStyleClass" style="background-color: #999999; color: #FFFFFF;" > <a href="$data.getRequest().getRequestURI();jsessionid=$data.getSession().getId()?$query&tab=0" style="color: #FFFFFF" >Spectral Data</a> </td> *************** *** 57,61 **** </td> #else ! <td valign="middle" class="TitleStyleClass" style="background-color: #BB0000; color: #FFFFFF;" > <a href="$data.getRequest().getRequestURI();jsessionid=$data.getSession().getId()?$query&tab=1" style="color: #FFFFFF" >Additional Data</a> </td> --- 57,61 ---- </td> #else ! <td valign="middle" class="TitleStyleClass" style="background-color: #999999; color: #FFFFFF;" > <a href="$data.getRequest().getRequestURI();jsessionid=$data.getSession().getId()?$query&tab=1" style="color: #FFFFFF" >Additional Data</a> </td> Index: halloffame.vm =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/vmtemplates/halloffame.vm,v retrieving revision 1.13 retrieving revision 1.14 diff -C2 -r1.13 -r1.14 *** halloffame.vm 23 Jun 2006 12:16:43 -0000 1.13 --- halloffame.vm 27 Jun 2006 14:59:28 -0000 1.14 *************** *** 2,6 **** <p><table cellpadding="2" cellspacing="0"> <tr> ! <th> </th><th bgcolor="#BB0000"><div style="color:white">Name</div></th><th bgcolor="#BB0000"><div style="color:white">Contributions</div></th> </tr> #foreach($user in $users) --- 2,6 ---- <p><table cellpadding="2" cellspacing="0"> <tr> ! <th> </th><th bgcolor="#999999"><div style="color:white">Name</div></th><th bgcolor="#BB0000"><div style="color:white">Contributions</div></th> </tr> #foreach($user in $users) |
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From: Stefan K. <sh...@us...> - 2006-06-27 14:59:31
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/util In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv6332/src/java/org/openscience/nmrshiftdb/util Modified Files: GeneralUtils.java Log Message: redesign Index: GeneralUtils.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/util/GeneralUtils.java,v retrieving revision 1.180 retrieving revision 1.181 diff -C2 -r1.180 -r1.181 *** GeneralUtils.java 27 Jun 2006 14:29:17 -0000 1.180 --- GeneralUtils.java 27 Jun 2006 14:59:28 -0000 1.181 *************** *** 179,183 **** return input; }else{ ! return "<a href=\"javascript:alert('"+input+"')\""+input.substring(0,30)+"... (trunkated)</a>"; } } --- 179,183 ---- return input; }else{ ! return "<a href=\"javascript:alert('"+input+"')\">"+input.substring(0,30)+"... (trunkated)</a>"; } } |
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From: Stefan K. <sh...@us...> - 2006-06-27 14:29:23
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/vmtemplates In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv25355/src/vmtemplates Modified Files: details.vm keyword.vm measuredornot.vm predict.vm results.vm review.vm searchBySpectrum.vm searchByStructure.vm searchhistory.vm submit.vm Log Message: more redesign Index: details.vm =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/vmtemplates/details.vm,v retrieving revision 1.154 retrieving revision 1.155 diff -C2 -r1.154 -r1.155 *** details.vm 13 Jun 2006 08:53:00 -0000 1.154 --- details.vm 27 Jun 2006 14:29:17 -0000 1.155 *************** *** 23,27 **** #if($data.getSession().getAttribute("applet")=="applet") <form action="portal/pane0/Results;jsessionid=$data.getSession().getId()?startMolecule=$startmolecule&nmrshiftdbaction=$lastaction&molNumber=$molNumber" method="post"> - Choose coordinate set: <select name="coordinateselect"> #foreach($set in $mol.getCoordinateSetNames()) --- 23,26 ---- *************** *** 266,275 **** <tr bgcolor="#D3D3D3"><td>Canonical name(s)</td><td> <ul> ! <li>$mol.getSmilesStringStr() (SMILES)</li> #if($mol.isChiral()) ! <li>$mol.getSmilesStringChiralStr() (chiral SMILES)</li> #end #foreach($canname in $mol.getDBCanonicalNames()) ! <li>#if($canname.getDBCanonicalNameType().getCanonicalNameType()=="INChI") INChI=#end$canname.getName() ($canname.getDBCanonicalNameType().getCanonicalNameType())</li> #end </ul></td></tr> --- 265,274 ---- <tr bgcolor="#D3D3D3"><td>Canonical name(s)</td><td> <ul> ! <li>$genutil.getShort($mol.getSmilesStringStr()) (SMILES)</li> #if($mol.isChiral()) ! <li>$genutil.getShort($mol.getSmilesStringChiralStr()) (chiral SMILES)</li> #end #foreach($canname in $mol.getDBCanonicalNames()) ! <li>#if($canname.getDBCanonicalNameType().getCanonicalNameType()=="INChI") INChI=#end$genutil.getShort($canname.getName()) ($canname.getDBCanonicalNameType().getCanonicalNameType())</li> #end </ul></td></tr> *************** *** 327,330 **** --- 326,330 ---- There is a spectrum which seems to be wrong (rating: $spectrum.getMark()). If you want to see it nevertheless, <a href="portal/pane0/Results;jsessionid=$data.getSession().getId()?spectrum=${spectrum.getSpectrumId()}&nmrshiftdbaction=$lastaction&displayall=displayall&molNumber=$molNumber&startMolecule=$startmolecule">click here</a>.<br> #end + <hr> #end <br> Index: keyword.vm =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/vmtemplates/keyword.vm,v retrieving revision 1.19 retrieving revision 1.20 diff -C2 -r1.19 -r1.20 *** keyword.vm 18 May 2006 13:15:37 -0000 1.19 --- keyword.vm 27 Jun 2006 14:29:17 -0000 1.20 *************** *** 3,9 **** <table> <tr> - <td colspan="5">Hold <ctrl> to choose multiple keywords.</td> - </tr> - <tr> <td width="20"></td> <th>Spectrum categories:</th> --- 3,6 ---- Index: measuredornot.vm =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/vmtemplates/measuredornot.vm,v retrieving revision 1.11 retrieving revision 1.12 diff -C2 -r1.11 -r1.12 *** measuredornot.vm 16 May 2006 10:58:42 -0000 1.11 --- measuredornot.vm 27 Jun 2006 14:29:17 -0000 1.12 *************** *** 1,5 **** <form name="exactnameform" action="portal/pane0/Search;jsessionid=$data.getSession().getId()" method="post"> <input type="hidden" name="nmrshiftdbaction" value="measuredornot"> - Specify if you want to look for calculated or measured spectra only. This will be valid for all searches till you change it.<br> <input type="checkbox" name="measured" value="measured" #if($measured=="true") --- 1,4 ---- Index: predict.vm =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/vmtemplates/predict.vm,v retrieving revision 1.80 retrieving revision 1.81 diff -C2 -r1.80 -r1.81 *** predict.vm 13 Jun 2006 08:53:00 -0000 1.80 --- predict.vm 27 Jun 2006 14:29:17 -0000 1.81 *************** *** 1,6 **** <a href="portal/pane0/Help;jsessionid=$session.getId()?URL=using.html#predict" title="Help for results"><img src="images/help.png" style="color:white"></a> ! <p style="color:red"> $messages ! </p> <table><tr> #if($method=="hose") <td> <form action="portal/pane0/Predict;jsessionid=$session.getId()"> --- 1,6 ---- <a href="portal/pane0/Help;jsessionid=$session.getId()?URL=using.html#predict" title="Help for results"><img src="images/help.png" style="color:white"></a> ! <div style="color:red"> $messages ! </div> <table><tr> #if($method=="hose") <td> <form action="portal/pane0/Predict;jsessionid=$session.getId()"> *************** *** 68,75 **** #end <form action="portal/pane0/Predict;jsessionid=$session.getId()" enctype="multipart/form-data" name="uploadform" method="post"> ! Structure file (<a target="_new" href="nmrshiftdbhtml/formats.jsp">valid formats</a>): ! <input name="Datei" type="file" size="25" maxlength="100000" accept="text/*"> <input type="hidden" name="nmrshiftdbaction" value="upload"> ! <input TYPE="submit" VALUE="Import file"><br> </form> #if($session.getAttribute("applet")=="applet" || $showoldinput=="true") --- 68,75 ---- #end <form action="portal/pane0/Predict;jsessionid=$session.getId()" enctype="multipart/form-data" name="uploadform" method="post"> ! Structure file: ! <input style="font-size:smaller" name="Datei" type="file" size="25" maxlength="100000" accept="text/*"> <input type="hidden" name="nmrshiftdbaction" value="upload"> ! <input style="font-size:smaller" TYPE="submit" VALUE="Import file"><br> </form> #if($session.getAttribute("applet")=="applet" || $showoldinput=="true") *************** *** 78,86 **** <input type="hidden" name="nmrshiftdbaction" value="predict"> #if($session.getAttribute("applet")=="applet") ! <input type="button" value="Import text by copy & paste" onClick="openImport()"> ! <input type="button" value="Import from structures history" onClick="openStructureHistory()"><br> #end Use <input type="checkbox" name="measuredonly" value="true" checked>measured and/or <input type="checkbox" name="calculatedonly" value="true">calculated spectra<br> ! Spectrum to predict: <select size="1" name="spectrumType"> #foreach($spectrumtype in $types) <option value="$spectrumtype.getSpectrumTypeId()" --- 78,86 ---- <input type="hidden" name="nmrshiftdbaction" value="predict"> #if($session.getAttribute("applet")=="applet") ! <input style="font-size:smaller" type="button" value="Import text by copy & paste" onClick="openImport()"> ! <input style="font-size:smaller" type="button" value="Import from structures history" onClick="openStructureHistory()"><br> #end Use <input type="checkbox" name="measuredonly" value="true" checked>measured and/or <input type="checkbox" name="calculatedonly" value="true">calculated spectra<br> ! <select size="1" name="spectrumType"> #foreach($spectrumtype in $types) <option value="$spectrumtype.getSpectrumTypeId()" *************** *** 155,166 **** </tr> <tr> ! <td colspan="3"> ! <center> #if($linkmessage=="none") #else ! <a href="$linkmessage">This molecule is in the database. View it!</a> #end ! <a href="portal/pane0/Predict;jsessionid=$session.getId()?nmrshiftdbaction=newpredict">New prediction</a></center> #end </td> --- 155,169 ---- </tr> <tr> ! <td> #if($linkmessage=="none") #else ! <a href="$linkmessage">View structure in database</a> #end ! </td> ! <td></td> ! <td> ! <a href="portal/pane0/Predict;jsessionid=$session.getId()?nmrshiftdbaction=newpredict">New prediction</a> ! </td> #end </td> Index: results.vm =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/vmtemplates/results.vm,v retrieving revision 1.42 retrieving revision 1.43 diff -C2 -r1.42 -r1.43 *** results.vm 19 May 2006 15:21:22 -0000 1.42 --- results.vm 27 Jun 2006 14:29:17 -0000 1.43 *************** *** 49,52 **** --- 49,53 ---- Results: $numberofresults<br><br> Browse: $browsingline<br><br> + <hr> <table> #set ($text="2") *************** *** 155,159 **** #end </table> ! <a href="portal/pane0/Results?nmrshiftdbaction=showids">Get a list of IDs of all structures found</a> --- 156,161 ---- #end </table> ! <hr> ! <a href="portal/pane0/Results?nmrshiftdbaction=showids">Result IDs</a> Index: review.vm =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/vmtemplates/review.vm,v retrieving revision 1.72 retrieving revision 1.73 diff -C2 -r1.72 -r1.73 *** review.vm 8 Jun 2006 11:02:37 -0000 1.72 --- review.vm 27 Jun 2006 14:29:17 -0000 1.73 *************** *** 150,156 **** <td> <form action="portal/pane0/Review;jsessionid=$data.getSession().getId()" method="post"> ! You can send an email to the submitter (you can get a cc of the email). He might also edit the input prior to review via his personal page.<br> ! This comment will be included in the email:<br> ! I want this email to be CCed to me <input type="checkbox" name="cc" value="true"><br> <textarea cols="70" rows="5" name="comment"></textarea> <input type="hidden" name="nmrshiftdbaction" value="changeemail"> --- 150,155 ---- <td> <form action="portal/pane0/Review;jsessionid=$data.getSession().getId()" method="post"> ! Send email comment to the submitter.<br> ! I want this email to be CCed to me <input type="checkbox" name="cc" value="true"><br> <textarea cols="70" rows="5" name="comment"></textarea> <input type="hidden" name="nmrshiftdbaction" value="changeemail"> Index: searchBySpectrum.vm =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/vmtemplates/searchBySpectrum.vm,v retrieving revision 1.40 retrieving revision 1.41 diff -C2 -r1.40 -r1.41 *** searchBySpectrum.vm 30 May 2006 10:51:12 -0000 1.40 --- searchBySpectrum.vm 27 Jun 2006 14:29:17 -0000 1.41 *************** *** 40,46 **** <form action="portal/pane0/Search;jsessionid=$data.getSession().getId()" enctype="multipart/form-data" name="uploadform" method="post"> Or choose jcamp file:<br> ! <input name="Datei2" type="file" size="20" maxlength="100000" accept="text/*"> <input type="hidden" name="nmrshiftdbaction" value="uploadjcampsearch"> ! <input TYPE="submit" VALUE="Upload file"> </form> <br> --- 40,46 ---- <form action="portal/pane0/Search;jsessionid=$data.getSession().getId()" enctype="multipart/form-data" name="uploadform" method="post"> Or choose jcamp file:<br> ! <input style="font-size:smaller" name="Datei2" type="file" size="20" maxlength="100000" accept="text/*"> <input type="hidden" name="nmrshiftdbaction" value="uploadjcampsearch"> ! <input style="font-size:smaller" TYPE="submit" VALUE="Upload file"> </form> <br> Index: searchByStructure.vm =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/vmtemplates/searchByStructure.vm,v retrieving revision 1.62 retrieving revision 1.63 diff -C2 -r1.62 -r1.63 *** searchByStructure.vm 13 Jun 2006 08:53:00 -0000 1.62 --- searchByStructure.vm 27 Jun 2006 14:29:17 -0000 1.63 *************** *** 57,61 **** checked #end ! > Substructure Similarity Search<br> <input type="radio" value="$constants.getTOTALSTRUCTURE()" name="type" #if($sub=="$constants.getTOTALSTRUCTURE()") --- 57,61 ---- checked #end ! > Similarity Search<br> <input type="radio" value="$constants.getTOTALSTRUCTURE()" name="type" #if($sub=="$constants.getTOTALSTRUCTURE()") *************** *** 64,69 **** > Identity Search ?<br> #if($data.getSession().getAttribute("applet")=="applet") ! <input type="button" value="Clear" onClick="document.JcpEditor.clear();"> ! <input type="button" value="Import from structures history" onClick="openStructureHistory()"> #end <input type="submit" style="background-color:#0000AA; color:white" value="Search by structure" onClick="exportMol()"> --- 64,69 ---- > Identity Search ?<br> #if($data.getSession().getAttribute("applet")=="applet") ! <input style="font-size:smaller" type="button" value="Clear" onClick="document.JcpEditor.clear();"> ! <input style="font-size:smaller" type="button" value="Import from structures history" onClick="openStructureHistory()"> #end <input type="submit" style="background-color:#0000AA; color:white" value="Search by structure" onClick="exportMol()"> *************** *** 75,83 **** <form action="portal/pane0/Search;jsessionid=$data.getSession().getId()" enctype="multipart/form-data" name="uploadform" method="post"> Structure file<br> ! <input name="Datei" type="file" size="20" maxlength="100000" accept="text/*"> <input type="hidden" name="nmrshiftdbaction" value="upload"> ! <input TYPE="submit" VALUE="Import file"> <a href="portal/pane0/Help;jsessionid=$data.getSession().getId()?URL=using.html#sstruc" title="Help for structure search" style="color:white"><img src="images/help.png"></a><br> #if($data.getSession().getAttribute("applet")=="applet") ! <input type="button" value="Import text by copy & paste" onClick="openImport()"> #end </form> --- 75,83 ---- <form action="portal/pane0/Search;jsessionid=$data.getSession().getId()" enctype="multipart/form-data" name="uploadform" method="post"> Structure file<br> ! <input style="font-size:smaller" name="Datei" type="file" size="20" maxlength="100000" accept="text/*"> <input type="hidden" name="nmrshiftdbaction" value="upload"> ! <input style="font-size:smaller" TYPE="submit" VALUE="Import file"> <a href="portal/pane0/Help;jsessionid=$data.getSession().getId()?URL=using.html#sstruc" title="Help for structure search" style="color:white"><img src="images/help.png"></a><br> #if($data.getSession().getAttribute("applet")=="applet") ! <input style="font-size:smaller" type="button" value="Import text by copy & paste" onClick="openImport()"> #end </form> Index: searchhistory.vm =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/vmtemplates/searchhistory.vm,v retrieving revision 1.21 retrieving revision 1.22 diff -C2 -r1.21 -r1.22 *** searchhistory.vm 16 May 2006 10:58:42 -0000 1.21 --- searchhistory.vm 27 Jun 2006 14:29:17 -0000 1.22 *************** *** 26,30 **** </form> <form action="portal/pane0/Search;jsessionid=$data.getSession().getId()" method="post" name="$nmrshiftdbconstansts.DELETE_SEARCH_HISTORY"> ! <input type="hidden" name="nmrshiftdbaction" value="$nmrshiftdbconstants.DELETE_SEARCH_HISTORY"> <input type="submit" value="$nmrshiftdbconstants.getDELETE_SEARCH_HISTORY()"> </form> --- 26,30 ---- </form> <form action="portal/pane0/Search;jsessionid=$data.getSession().getId()" method="post" name="$nmrshiftdbconstansts.DELETE_SEARCH_HISTORY"> ! <input style="font-size:smaller" type="hidden" name="nmrshiftdbaction" value="$nmrshiftdbconstants.DELETE_SEARCH_HISTORY"> <input type="submit" value="$nmrshiftdbconstants.getDELETE_SEARCH_HISTORY()"> </form> Index: submit.vm =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/vmtemplates/submit.vm,v retrieving revision 1.154 retrieving revision 1.155 diff -C2 -r1.154 -r1.155 *** submit.vm 13 Jun 2006 08:53:00 -0000 1.154 --- submit.vm 27 Jun 2006 14:29:18 -0000 1.155 *************** *** 27,31 **** #if($recentliteratures) <form name="literatureform" action="portal/pane0/Submit?nmrshiftdbaction=usesessionliterature" method="post"> ! <input type="submit" value="Use literatures from last submit"></center> </form #end --- 27,31 ---- #if($recentliteratures) <form name="literatureform" action="portal/pane0/Submit?nmrshiftdbaction=usesessionliterature" method="post"> ! <input style="font-size:smaller" type="submit" value="Use literatures from last submit"></center> </form #end *************** *** 200,204 **** #if($literaturecomplete=="false") <form action="portal/pane0/Submit;jsessionid=$session.getId()?nmrshiftdbaction=literaturecomplete" method="post" NAME="MolForm" enctype="application/x-www-form-urlencoded"> ! <input TYPE="submit" VALUE="Enter more literature items including monographs"> </form> #end --- 200,204 ---- #if($literaturecomplete=="false") <form action="portal/pane0/Submit;jsessionid=$session.getId()?nmrshiftdbaction=literaturecomplete" method="post" NAME="MolForm" enctype="application/x-www-form-urlencoded"> ! <input style="font-size:smaller" TYPE="submit" VALUE="Enter more literature items including monographs"> </form> #end *************** *** 239,243 **** #end <form action="portal/pane0/Submit?nmrshiftdbaction=correctliteratures" name="correctliteraturesform" method="post"> ! <input type="submit" value="Correct literatures"> </form> #end --- 239,243 ---- #end <form action="portal/pane0/Submit?nmrshiftdbaction=correctliteratures" name="correctliteraturesform" method="post"> ! <input style="font-size:smaller" type="submit" value="Correct literatures"> </form> #end *************** *** 337,347 **** <form action="portal/pane0/Submit;jsessionid=$session.getId()" enctype="multipart/form-data" name="uploadform" method="post"> Structure file:<br> ! <input name="Datei" type="file" size="25" maxlength="100000" accept="text/*"> <input type="hidden" name="nmrshiftdbaction" value="upload"> ! <input TYPE="submit" VALUE="Import file"><br> </form> <br><form action="portal/pane0/Submit" method="post" NAME="MolForm2" enctype="application/x-www-form-urlencoded"> <input type="hidden" name="nmrshiftdbaction" value="importcopypaste"> ! <input type="submit" value="Import text by copy & paste" onClick="openImport()"> </form> #end --- 337,347 ---- <form action="portal/pane0/Submit;jsessionid=$session.getId()" enctype="multipart/form-data" name="uploadform" method="post"> Structure file:<br> ! <input style="font-size:smaller" name="Datei" type="file" size="25" maxlength="100000" accept="text/*"> <input type="hidden" name="nmrshiftdbaction" value="upload"> ! <input style="font-size:smaller" TYPE="submit" VALUE="Import file"><br> </form> <br><form action="portal/pane0/Submit" method="post" NAME="MolForm2" enctype="application/x-www-form-urlencoded"> <input type="hidden" name="nmrshiftdbaction" value="importcopypaste"> ! <input style="font-size:smaller" type="submit" value="Import text by copy & paste" onClick="openImport()"> </form> #end *************** *** 381,385 **** <input type="hidden" name="nmrshiftdbaction" value="submitMolecule"> <input type="button" value="Import from structures history" onClick="openStructureHistory()"><br> ! <input TYPE="submit" #if($subdata.getLevel()==1) style="background-color:#0000AA; color:white" #end VALUE="Submit molecule" onClick="exportMol()"> Input shifts as <input type="radio" name="shiftlist" value="0" checked> text list or for <input type="radio" name="shiftlist" value="1"> each atom #end </form> --- 381,385 ---- <input type="hidden" name="nmrshiftdbaction" value="submitMolecule"> <input type="button" value="Import from structures history" onClick="openStructureHistory()"><br> ! <input TYPE="submit" #if($subdata.getLevel()==1) style="background-color:#0000AA; color:white" #else style="font-size:smaller" #end VALUE="Submit molecule" onClick="exportMol()"> Input shifts as <input type="radio" name="shiftlist" value="0" checked> text list or for <input type="radio" name="shiftlist" value="1"> each atom #end </form> *************** *** 401,405 **** <form action="portal/pane0/Submit;jsessionid=$session.getId()" method="post" NAME="MolForm"> <input type="hidden" name="nmrshiftdbaction" value="correctMolecule"> ! <input TYPE="submit" VALUE="Modify molecule"> </form> #end --- 401,405 ---- <form action="portal/pane0/Submit;jsessionid=$session.getId()" method="post" NAME="MolForm"> <input type="hidden" name="nmrshiftdbaction" value="correctMolecule"> ! <input style="font-size:smaller" TYPE="submit" VALUE="Modify molecule"> </form> #end *************** *** 430,434 **** <INPUT TYPE="button" onClick="parent.location='portal/pane0/Home'" value="Abort this submit"> #end ! <input type="submit" #if($subdata.getLevel()==2) style="background-color:#0000AA; color:white" #end value="Submit signals"> </form> #if($shiftlist=="0") --- 430,434 ---- <INPUT TYPE="button" onClick="parent.location='portal/pane0/Home'" value="Abort this submit"> #end ! <input type="submit" #if($subdata.getLevel()==2) style="background-color:#0000AA; color:white" #else style="font-size:smaller" #end value="Submit signals"> </form> #if($shiftlist=="0") *************** *** 437,442 **** <input type="hidden" name="spectrumType" value=""> <input type="hidden" name="nmrshiftdbaction" value="uploadjcamp"> ! <input name="Datei2" type="file" size="25" maxlength="100000" accept="text/*"> ! <input TYPE="submit" VALUE="Import file" onClick="exchangeSpectrumType()"><br> </form> #end --- 437,442 ---- <input type="hidden" name="spectrumType" value=""> <input type="hidden" name="nmrshiftdbaction" value="uploadjcamp"> ! <input name="Datei2" style="font-size:smaller" type="file" size="25" maxlength="100000" accept="text/*"> ! <input TYPE="submit" style="font-size:smaller" VALUE="Import file" onClick="exchangeSpectrumType()"><br> </form> #end *************** *** 569,573 **** <INPUT TYPE="button" onClick="parent.location='portal/pane0/Home'" value="Abort this submit"> #end ! <input type="submit" #if($subdata.getLevel()==3) style="background-color:#0000AA; color:white" #end value="Submit assignments"> <a href="portal/pane0/Submit;jsessionid=$session.getId()?nmrshiftdbaction=enterconstants">I want to enter coupling constants</a> </td> --- 569,573 ---- <INPUT TYPE="button" onClick="parent.location='portal/pane0/Home'" value="Abort this submit"> #end ! <input type="submit" #if($subdata.getLevel()==3) style="background-color:#0000AA; color:white" #else style="font-size:smaller" #end value="Submit assignments"> <a href="portal/pane0/Submit;jsessionid=$session.getId()?nmrshiftdbaction=enterconstants">I want to enter coupling constants</a> </td> *************** *** 710,714 **** <INPUT TYPE="button" onClick="parent.location='portal/pane0/Home'" value="Abort this submit"> #end ! <input type="submit" #if($subdata.getLevel()==4) style="background-color:#0000AA; color:white" #end value="Write to Database"></center> </form> #end --- 710,714 ---- <INPUT TYPE="button" onClick="parent.location='portal/pane0/Home'" value="Abort this submit"> #end ! <input type="submit" #if($subdata.getLevel()==4) style="background-color:#0000AA; color:white" #else style="font-size:smaller" #end value="Write to Database"></center> </form> #end |
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From: Stefan K. <sh...@us...> - 2006-06-27 14:29:21
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/vmtemplates/portlets/html In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv25355/src/vmtemplates/portlets/html Modified Files: choose-types.vm Log Message: more redesign Index: choose-types.vm =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/vmtemplates/portlets/html/choose-types.vm,v retrieving revision 1.7 retrieving revision 1.8 diff -C2 -r1.7 -r1.8 *** choose-types.vm 16 May 2006 10:58:42 -0000 1.7 --- choose-types.vm 27 Jun 2006 14:29:18 -0000 1.8 *************** *** 1,3 **** - Here you can restrict your search to certain spectrum types. The choice is valid for all searches until changed. Check a spectrum type to include it in the search: <form name="orderform" method="post" action="$jlink.setPanel("Order handling")"> #foreach($spectrum in $spectra) --- 1,2 ---- |
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From: Stefan K. <sh...@us...> - 2006-06-27 14:29:20
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/om In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv25355/src/java/org/openscience/nmrshiftdb/om Modified Files: DBMolecule.java Log Message: more redesign Index: DBMolecule.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/om/DBMolecule.java,v retrieving revision 1.182 retrieving revision 1.183 diff -C2 -r1.182 -r1.183 *** DBMolecule.java 3 Mar 2006 16:30:57 -0000 1.182 --- DBMolecule.java 27 Jun 2006 14:29:17 -0000 1.183 *************** *** 659,667 **** Vector v = getDBCanonicalNames(); for (int i = 0; i < v.size(); i++) { ! name.append(((DBCanonicalName) v.get(i)).getName() + " (" + ((DBCanonicalName) v.get(i)).getDBCanonicalNameType().getCanonicalNameType() + "), "); } ! name.append(getSmilesStringStr() + " (SMILES), "); if (getSmilesStringChiral() != null) { ! name.append(getSmilesStringChiralStr() + " (chiral SMILES), "); } return (GeneralUtils.removeLastComma(name).toString()); --- 659,667 ---- Vector v = getDBCanonicalNames(); for (int i = 0; i < v.size(); i++) { ! name.append(GeneralUtils.getShort(((DBCanonicalName) v.get(i)).getName()) + " (" + ((DBCanonicalName) v.get(i)).getDBCanonicalNameType().getCanonicalNameType() + "), "); } ! name.append(GeneralUtils.getShort(getSmilesStringStr()) + " (SMILES), "); if (getSmilesStringChiral() != null) { ! name.append(GeneralUtils.getShort(getSmilesStringChiralStr()) + " (chiral SMILES), "); } return (GeneralUtils.removeLastComma(name).toString()); |
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From: Stefan K. <sh...@us...> - 2006-06-27 14:29:20
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/portlets In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv25355/src/java/org/openscience/nmrshiftdb/portlets Modified Files: DetailPortlet.java Log Message: more redesign Index: DetailPortlet.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/portlets/DetailPortlet.java,v retrieving revision 1.68 retrieving revision 1.69 diff -C2 -r1.68 -r1.69 *** DetailPortlet.java 7 Jun 2006 19:13:50 -0000 1.68 --- DetailPortlet.java 27 Jun 2006 14:29:17 -0000 1.69 *************** *** 208,211 **** --- 208,212 ---- context.put("random", new java.util.Random()); context.put("easylink",mol.getEasylink(req)); + context.put("genutil", GeneralUtils.getInstance()); if(action.equals("showDetailsFromHome")) context.put("lastaction",action); |
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From: Stefan K. <sh...@us...> - 2006-06-27 14:29:20
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/util In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv25355/src/java/org/openscience/nmrshiftdb/util Modified Files: GeneralUtils.java Log Message: more redesign Index: GeneralUtils.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/util/GeneralUtils.java,v retrieving revision 1.179 retrieving revision 1.180 diff -C2 -r1.179 -r1.180 *** GeneralUtils.java 9 Jun 2006 14:25:57 -0000 1.179 --- GeneralUtils.java 27 Jun 2006 14:29:17 -0000 1.180 *************** *** 147,150 **** --- 147,151 ---- static Vector atomsWithHoseCode = null; static HashMap mb3d = new HashMap(); + static GeneralUtils instance=new GeneralUtils(); /** *************** *** 152,155 **** --- 153,160 ---- */ private GeneralUtils() { } + + public static GeneralUtils getInstance(){ + return instance; + } *************** *** 169,172 **** --- 174,185 ---- } } + + public static String getShort(String input){ + if(input.length()<30){ + return input; + }else{ + return "<a href=\"javascript:alert('"+input+"')\""+input.substring(0,30)+"... (trunkated)</a>"; + } + } |
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From: Stefan K. <sh...@us...> - 2006-06-27 14:29:19
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/html In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv25355/src/html Modified Files: marvin.js Log Message: more redesign Index: marvin.js =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/marvin.js,v retrieving revision 1.23 retrieving revision 1.24 diff -C2 -r1.23 -r1.24 *** marvin.js 12 Jun 2006 10:51:16 -0000 1.23 --- marvin.js 27 Jun 2006 14:29:17 -0000 1.24 *************** *** 389,393 **** { applet_end(); ! document.write("<br><a href=\"javascript:showmol(document."+msketch_name+".getMolFile())\">Show editor content as mol file</a>"); msketch_name = ""; } --- 389,393 ---- { applet_end(); ! document.write("<br><a href=\"javascript:showmol(document."+msketch_name+".getMolFile())\">Get mol file</a>"); msketch_name = ""; } |
