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From: Stefan K. <sh...@us...> - 2006-10-26 17:18:58
|
Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/webservices In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv7406/src/java/org/openscience/nmrshiftdb/webservices Modified Files: NMRShiftDBServiceBindingImpl.java Log Message: the user order of the lab system works in non-java mode as well Index: NMRShiftDBServiceBindingImpl.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/webservices/NMRShiftDBServiceBindingImpl.java,v retrieving revision 1.33 retrieving revision 1.34 diff -C2 -r1.33 -r1.34 *** NMRShiftDBServiceBindingImpl.java 24 Oct 2006 14:30:56 -0000 1.33 --- NMRShiftDBServiceBindingImpl.java 26 Oct 2006 17:18:48 -0000 1.34 *************** *** 414,419 **** metadata.setContent(format.format(((Double)similarities.get(i)).doubleValue(), s, f) + " %"); CMLMetadata metadata2=new CMLMetadata(); ! metadata.setName("qname:name"); ! metadata.setContent(mol.getChemicalNamesAsOneStringWithFallback()); mdl.addMetadata(metadata); mdl.addMetadata(metadata2); --- 414,419 ---- metadata.setContent(format.format(((Double)similarities.get(i)).doubleValue(), s, f) + " %"); CMLMetadata metadata2=new CMLMetadata(); ! metadata2.setName("qname:name"); ! metadata2.setContent(mol.getChemicalNamesAsOneStringWithFallback()); mdl.addMetadata(metadata); mdl.addMetadata(metadata2); |
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From: Stefan K. <sh...@us...> - 2006-10-26 17:18:57
|
Update of /cvsroot/nmrshiftdb/nmrshiftdb/doc In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv7406/doc Modified Files: nmrshiftdbhelp.pdf nmrshiftdbhelp.xml Log Message: the user order of the lab system works in non-java mode as well Index: nmrshiftdbhelp.pdf =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/doc/nmrshiftdbhelp.pdf,v retrieving revision 1.68 retrieving revision 1.69 diff -C2 -r1.68 -r1.69 Binary files /tmp/cvsZWDIMf and /tmp/cvstGIdy1 differ Index: nmrshiftdbhelp.xml =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/doc/nmrshiftdbhelp.xml,v retrieving revision 1.83 retrieving revision 1.84 diff -C2 -r1.83 -r1.84 *** nmrshiftdbhelp.xml 24 Oct 2006 17:17:22 -0000 1.83 --- nmrshiftdbhelp.xml 26 Oct 2006 17:18:47 -0000 1.84 *************** *** 4,8 **** <sect1 id="about"><title>About NMRShiftDB</title> <sect2 id="whatis"><title>What is NMRShiftDB ?</title> ! <para>NMRShiftDB is a web database for organic structures and their nuclear magnetic resonance (nmr) spectra. It allows for spectrum prediction (currently only for carbon) as well as for searching spectra, structures and other properties. Last not least, it features peer-reviewed submission of datasets by its users. The NMRShiftDB software is open source, the data is published under an open content license. Currently, only 13C, 1H, 15N and 31P NMR shift data can be stored, but the architecture of the software allows for future extension to other nucleii, e.g., correlated 1H/13C data, 19F, etc. The implemented search algorithms can scan the database for example for the following items: substance name, formula, structure, substructures, chemical shifts, and a Hit List of best matches is generated. Furthermore, a shift prediction algorithm based on the molecular HOSE code and the measured shift data has been included. For proton spectra a prediction based on 3D molecular properties is available.</para> <para id="opencontent">It is the policy of NMRShiftDB to have its content freely available. This means that spectra in NMRShiftDB can be accessed and used without restrictions. Access to single items is possible via the software and we also make available the bunch data (without the personal data). Note that, according to our opinion, NMR spectra do not represent "literary and artistic works" as mentioned in Art. 2 (1) of the Berne Convention, the author of a spectrum is, so to say, nature, and that therefore there is no copyright in NMR data. NMRShiftDB as a database is a protected work in the sense of article 5 of the WIPO Copyright Convention, authored by its contributors and reviewers. It is available under the <ulink url="http://www.gnu.org/copyleft/fdl.html">GNU Free Documentation Licence</ulink>.</para> <para>The NMRShiftDB data are available as: --- 4,8 ---- <sect1 id="about"><title>About NMRShiftDB</title> <sect2 id="whatis"><title>What is NMRShiftDB ?</title> ! <para>NMRShiftDB is a web database for organic structures and their nuclear magnetic resonance (nmr) spectra. It allows for spectrum prediction as well as for searching spectra, structures and other properties. Last not least, it features peer-reviewed submission of datasets by its users. The NMRShiftDB software is open source, the data is published under an open content license. Currently, only 13C, 1H, 15N and 31P NMR shift data can be stored, but the architecture of the software allows for future extension to other nucleii, e.g., correlated 1H/13C data, 19F, etc. The implemented search algorithms can scan the database for example for the following items: substance name, formula, structure, substructures, chemical shifts, and a Hit List of best matches is generated. Furthermore, a shift prediction algorithm based on the molecular HOSE code and the measured shift data has been included. For proton spectra a prediction based on 3D molecular properties is available.</para> <para id="opencontent">It is the policy of NMRShiftDB to have its content freely available. This means that spectra in NMRShiftDB can be accessed and used without restrictions. Access to single items is possible via the software and we also make available the bunch data (without the personal data). Note that, according to our opinion, NMR spectra do not represent "literary and artistic works" as mentioned in Art. 2 (1) of the Berne Convention, the author of a spectrum is, so to say, nature, and that therefore there is no copyright in NMR data. NMRShiftDB as a database is a protected work in the sense of article 5 of the WIPO Copyright Convention, authored by its contributors and reviewers. It is available under the <ulink url="http://www.gnu.org/copyleft/fdl.html">GNU Free Documentation Licence</ulink>.</para> <para>The NMRShiftDB data are available as: |
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From: Stefan K. <sh...@us...> - 2006-10-26 17:18:57
|
Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/html In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv7406/src/html Modified Files: t1.html using.html Log Message: the user order of the lab system works in non-java mode as well Index: t1.html =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/t1.html,v retrieving revision 1.28 retrieving revision 1.29 diff -C2 -r1.28 -r1.29 *** t1.html 6 Sep 2005 22:01:29 -0000 1.28 --- t1.html 26 Oct 2006 17:18:48 -0000 1.29 *************** *** 36,40 **** ></H2 ><P ! >NMRShiftDB is a web database for organic structures and their nuclear magnetic resonance (nmr) spectra. It allows for spectrum prediction (currently only for carbon) as well as for searching spectra, structures and other properties. Last not least, it features peer-reviewed submission of datasets by its users. The NMRShiftDB software is open source, the data is published under an open content license. Currently, only 13C, 1H, 15N and 31P NMR shift data can be stored, but the architecture of the software allows for future extension to other nucleii, e.g., correlated 1H/13C data, 19F, etc. The implemented search algorithms can scan the database for example for the following items: substance name, formula, structure, substructures, chemical shifts, and a Hit List of best matches is generated. Furthermore, a shift prediction algorithm based on the molecular HOSE code and the measured shift data has been included. For proton spectra a prediction based on 3D molecular properties is available.</P ><P >It is the policy of NMRShiftDB to have its content freely available. This means that spectra in NMRShiftDB can be accessed and used without restrictions. Access to single items is possible via the software and we also make available the bunch data (without the personal data). Note that, according to our opinion, NMR spectra do not represent "literary and artistic works" as mentioned in Art. 2 (1) of the Berne Convention, the author of a spectrum is, so to say, nature, and that therefore there is no copyright in NMR data. NMRShiftDB as a database is a protected work in the sense of article 5 of the WIPO Copyright Convention, authored by its contributors and reviewers. It is available under the <A --- 36,40 ---- ></H2 ><P ! >NMRShiftDB is a web database for organic structures and their nuclear magnetic resonance (nmr) spectra. It allows for spectrum prediction as well as for searching spectra, structures and other properties. Last not least, it features peer-reviewed submission of datasets by its users. The NMRShiftDB software is open source, the data is published under an open content license. Currently, only 13C, 1H, 15N and 31P NMR shift data can be stored, but the architecture of the software allows for future extension to other nucleii, e.g., correlated 1H/13C data, 19F, etc. The implemented search algorithms can scan the database for example for the following items: substance name, formula, structure, substructures, chemical shifts, and a Hit List of best matches is generated. Furthermore, a shift prediction algorithm based on the molecular HOSE code and the measured shift data has been included. For proton spectra a prediction based on 3D molecular properties is available.</P ><P >It is the policy of NMRShiftDB to have its content freely available. This means that spectra in NMRShiftDB can be accessed and used without restrictions. Access to single items is possible via the software and we also make available the bunch data (without the personal data). Note that, according to our opinion, NMR spectra do not represent "literary and artistic works" as mentioned in Art. 2 (1) of the Berne Convention, the author of a spectrum is, so to say, nature, and that therefore there is no copyright in NMR data. NMRShiftDB as a database is a protected work in the sense of article 5 of the WIPO Copyright Convention, authored by its contributors and reviewers. It is available under the <A Index: using.html =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/using.html,v retrieving revision 1.50 retrieving revision 1.51 diff -C2 -r1.50 -r1.51 *** using.html 24 Oct 2006 10:48:44 -0000 1.50 --- using.html 26 Oct 2006 17:18:48 -0000 1.51 *************** *** 721,725 **** ></H2 ><P ! >NMRShiftdb can work as a user and order administration system for NMR labs. The concept of the lab system is centered around two roles, oooperator and user, and the concept of an order.</P ><P >Users can assign themself membership of a labgroup, either as operator or user. They need to be approved by the group leader. Once this is done, a user can submit orders and a operator can work on them.</P --- 721,725 ---- ></H2 ><P ! >NMRShiftdb can work as a user and order administration system for NMR labs. The concept of the lab system is centered around two roles, operator and user, and the concept of an order.</P ><P >Users can assign themself membership of a labgroup, either as operator or user. They need to be approved by the group leader. Once this is done, a user can submit orders and a operator can work on them.</P |
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From: Stefan K. <sh...@us...> - 2006-10-26 17:18:57
|
Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/modules/actions/portlets In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv7406/src/java/org/openscience/nmrshiftdb/modules/actions/portlets Modified Files: OrderAction.java Log Message: the user order of the lab system works in non-java mode as well Index: OrderAction.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/modules/actions/portlets/OrderAction.java,v retrieving revision 1.33 retrieving revision 1.34 diff -C2 -r1.33 -r1.34 *** OrderAction.java 24 Oct 2006 13:19:37 -0000 1.33 --- OrderAction.java 26 Oct 2006 17:18:48 -0000 1.34 *************** *** 5,8 **** --- 5,9 ---- import java.io.FileWriter; import java.io.StringReader; + import java.io.StringWriter; import java.text.SimpleDateFormat; import java.util.Collections; *************** *** 18,24 **** --- 19,28 ---- import org.apache.turbine.util.ServletUtils; import org.apache.turbine.util.db.Criteria; + import org.apache.turbine.util.upload.FileItem; import org.apache.velocity.context.Context; import org.openscience.cdk.Molecule; + import org.openscience.cdk.interfaces.IMolecule; import org.openscience.cdk.io.MDLReader; + import org.openscience.cdk.io.MDLWriter; import org.openscience.nmrshiftdb.om.DBCondition; import org.openscience.nmrshiftdb.om.DBConditionPeer; *************** *** 77,80 **** --- 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",this.WORKER); buildOrderContext(context,data); *************** *** 157,166 **** context.put("probablestructure",toshow.getProbableStructure()); //The mol is put into the MView applet via a file ! if(!new String(toshow.getProbableStructure()+"").equals("")){ ! File outputFile = new File(ServletUtils.expandRelative(data.getServletConfig(), "/nmrshiftdbhtml/" + System.currentTimeMillis() + "order.mol")); ! FileWriter out = new FileWriter(outputFile); ! out.write(toshow.getDBMolecule().getStructureFile(1,false)); ! out.close(); ! context.put("molfile", "/nmrshiftdbhtml/" + outputFile.getName()); } //this is for the self fullfill --- 167,184 ---- context.put("probablestructure",toshow.getProbableStructure()); //The mol is put into the MView applet via a file ! if(data.getSession().getAttribute("applet") !=null && data.getSession().getAttribute("applet").equals("applet")){ ! if(!new String(toshow.getProbableStructure()+"").equals("")){ ! File outputFile = new File(ServletUtils.expandRelative(data.getServletConfig(), "/nmrshiftdbhtml/" + System.currentTimeMillis() + "order.mol")); ! FileWriter out = new FileWriter(outputFile); ! out.write(toshow.getDBMolecule().getStructureFile(1,false)); ! out.close(); ! context.put("molfile", "/nmrshiftdbhtml/" + outputFile.getName()); ! } ! }else{ ! if(!new String(toshow.getProbableStructure()+"").equals("")){ ! String filename="/nmrshiftdbhtml/" + System.currentTimeMillis() + "userorder.jpg"; ! GeneralUtils.makeJpg(toshow.getDBMolecule().getStructureFile(1,false),filename,data.getServletConfig(),200,200,false); ! context.put("imagefile",filename); ! } } //this is for the self fullfill *************** *** 318,326 **** DBMachine fstrength=(DBMachine)DBMachinePeer.doSelect(crit).get(0); sample.setDBMachine(fstrength); ! String molecule = data.getParameters().get("MolTxt"); ! Molecule mol = (Molecule) new MDLReader(new StringReader(molecule)).read(new Molecule()); ! if(mol!= null && mol.getAtomCount()>0){ ! SubmittingData sd=new SubmittingData(ServletUtils.expandRelative(data.getServletConfig(), "/WEB-INF/conf/normalizer.xml")); ! sample.setProbableStructure(sd.saveMoleculeOnly(molecule, data, (NmrshiftdbUser)data.getUser())); } sample.setDate(new Date()); --- 336,365 ---- DBMachine fstrength=(DBMachine)DBMachinePeer.doSelect(crit).get(0); sample.setDBMachine(fstrength); ! IMolecule mol=null; ! if(data.getSession().getAttribute("applet") !=null && data.getSession().getAttribute("applet").equals("applet")){ ! String molecule = data.getParameters().get("MolTxt"); ! mol = (Molecule) new MDLReader(new StringReader(molecule)).read(new Molecule()); ! if(mol!= null && mol.getAtomCount()>0){ ! SubmittingData sd=new SubmittingData(ServletUtils.expandRelative(data.getServletConfig(), "/WEB-INF/conf/normalizer.xml")); ! sample.setProbableStructure(sd.saveMoleculeOnly(molecule, data, (NmrshiftdbUser)data.getUser())); ! } ! }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"); ! if(fi!=null){ ! StringBuffer messages=new StringBuffer(); ! GeneralUtils.processFileItem(fi[0],messages,data,"moltxt"); ! message+=messages.toString(); ! mol=(IMolecule)data.getSession().getAttribute("moltxt"); ! data.getSession().removeAttribute("moltxt"); ! if(mol!= null && mol.getAtomCount()>0){ ! SubmittingData sd=new SubmittingData(ServletUtils.expandRelative(data.getServletConfig(), "/WEB-INF/conf/normalizer.xml")); ! StringWriter sw = new StringWriter(); ! new MDLWriter(sw).writeMolecule(mol); ! sample.setProbableStructure(sd.saveMoleculeOnly(sw.toString(), data, (NmrshiftdbUser)data.getUser())); ! } ! } ! } } sample.setDate(new Date()); |
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From: Stefan K. <sh...@us...> - 2006-10-26 17:18:56
|
Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/conf/jetspeed/WEB-INF/templates/vm/layouts/html In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv7406/src/conf/jetspeed/WEB-INF/templates/vm/layouts/html Modified Files: default.vm Log Message: the user order of the lab system works in non-java mode as well Index: default.vm =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/conf/jetspeed/WEB-INF/templates/vm/layouts/html/default.vm,v retrieving revision 1.11 retrieving revision 1.12 diff -C2 -r1.11 -r1.12 *** default.vm 16 May 2006 10:58:41 -0000 1.11 --- default.vm 26 Oct 2006 17:18:48 -0000 1.12 *************** *** 3,7 **** <base href="$clink.External" /> <link href="$clink.setURI("css/default.css").Absolute" type="text/css" rel="stylesheet" /> ! <title>NMRShiftDB - nmr web database</title> <link rel="shortcut icon" href="/nmrshiftdbhtml/favicon.png"> <link rel="alternate" type="application/rss+xml" title="RSS for NMRShiftDB news" href="http://sourceforge.net/export/rss2_projnews.php?group_id=20485"> --- 3,7 ---- <base href="$clink.External" /> <link href="$clink.setURI("css/default.css").Absolute" type="text/css" rel="stylesheet" /> ! <title>NMRShiftDB - nmr database - open access via web</title> <link rel="shortcut icon" href="/nmrshiftdbhtml/favicon.png"> <link rel="alternate" type="application/rss+xml" title="RSS for NMRShiftDB news" href="http://sourceforge.net/export/rss2_projnews.php?group_id=20485"> |
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From: Stefan K. <sh...@us...> - 2006-10-26 17:18:56
|
Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/vmtemplates/portlets/html In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv7406/src/vmtemplates/portlets/html Modified Files: user-order.vm Log Message: the user order of the lab system works in non-java mode as well Index: user-order.vm =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/vmtemplates/portlets/html/user-order.vm,v retrieving revision 1.45 retrieving revision 1.46 diff -C2 -r1.45 -r1.46 *** user-order.vm 24 Oct 2006 10:48:45 -0000 1.45 --- user-order.vm 26 Oct 2006 17:18:48 -0000 1.46 *************** *** 113,121 **** <p style="color:red">$!message</p> #if($submitorshow=="submit") ! <form name="orderform" method="post" action="portal/pane0/NMR+lab+administration"> Here you can submit a <b>new order</b>:<br> I want this order to be processed by <input type="radio" name="process" #if($ordertype=="worker") checked #end value="worker"> a lab operator <input type="radio" name="process" #if($ordertype=="self") checked #end value="self"> myself <input type="radio" name="process" #if($ordertype=="robot") checked #end value="robot"> myself via sample changer<br> #elseif($submitorshow=="edit") ! <form name="orderform" method="post" action="portal/pane0/NMR+lab+administration"> Here you can edit your submit:<br> I want this order to be processed by <input type="radio" name="process" #if($ordertype=="worker") checked #end value="worker"> a lab operator <input type="radio" name="process" #if($ordertype=="self") checked #end value="self"> myself <input type="radio" name="process" #if($ordertype=="robot") checked #end value="robot"> myself via sample changer<br> --- 113,121 ---- <p style="color:red">$!message</p> #if($submitorshow=="submit") ! <form name="orderform" method="post" action="portal/pane0/NMR+lab+administration" enctype="multipart/form-data"> Here you can submit a <b>new order</b>:<br> I want this order to be processed by <input type="radio" name="process" #if($ordertype=="worker") checked #end value="worker"> a lab operator <input type="radio" name="process" #if($ordertype=="self") checked #end value="self"> myself <input type="radio" name="process" #if($ordertype=="robot") checked #end value="robot"> myself via sample changer<br> #elseif($submitorshow=="edit") ! <form name="orderform" method="post" action="portal/pane0/NMR+lab+administration" enctype="multipart/form-data"> Here you can edit your submit:<br> I want this order to be processed by <input type="radio" name="process" #if($ordertype=="worker") checked #end value="worker"> a lab operator <input type="radio" name="process" #if($ordertype=="self") checked #end value="self"> myself <input type="radio" name="process" #if($ordertype=="robot") checked #end value="robot"> myself via sample changer<br> *************** *** 142,145 **** --- 142,147 ---- #if($submitorshow=="show") #if($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"> *************** *** 153,197 **** mview_end(); </script> #else No probable structure suggested! #end #else ! Probable Structure (click the field to open a sketcher):<br> ! <script LANGUAGE="JavaScript1.1" SRC="nmrshiftdbhtml/marvin.js"></script> ! <script LANGUAGE="JavaScript1.1"> ! <!-- ! function exportMol() ! { ! if(document.JcpEditor != null) ! { ! var s = document.JcpEditor.getMolFile();; ! s = unix2local(s); ! document.orderform.MolTxt.value=s; ! } ! else ! { ! alert("Cannot import molecule: no JavaScript to Java communication in your browser."); ! } ! } ! function openStructureHistory(){ ! mywindow=window.open("/nmrshiftdbhtml/importfromstructureshistory.jsp;jsessionid=$data.getSession().getId()","molimport","height=200,width=900"); ! mywindow.focus(); ! } ! function openImport(){ ! mywindow=window.open("/nmrshiftdbhtml/import.htm","molimport","height=500,width=900"); ! mywindow.focus(); ! } ! msketch_mayscript = true; ! msketch_name = "JcpEditor"; ! msketch_begin("/nmrshiftdbhtml", 450, 400); ! #if($import=="true") ! msketch_param("load","$molfile"); ! #end ! msketch_end(); ! --> ! </script> ! <input type="hidden" name="MolTxt"> ! <input type="button" value="Clear" onClick="document.JcpEditor.clear();"> ! <input type="button" value="Import from structures history" onClick="openStructureHistory()"> #end <br> --- 155,208 ---- mview_end(); </script> + #else + <a href="$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> + <img src="$imagefile"> + #end #else No probable structure suggested! #end #else ! #if($data.getSession().getAttribute("applet")=="applet") ! Probable Structure: <a href="$data.getRequest().getRequestURI();jsessionid=$data.getSession().getId()?$data.getRequest().getQueryString()&applet=noapplet" title="Switch off Java applets" style="color:white"><img src="images/nojava.png"></a><br> ! <script LANGUAGE="JavaScript1.1" SRC="nmrshiftdbhtml/marvin.js"></script> ! <script LANGUAGE="JavaScript1.1"> ! <!-- ! function exportMol() ! { ! if(document.JcpEditor != null) ! { ! var s = document.JcpEditor.getMolFile();; ! s = unix2local(s); ! document.orderform.MolTxt.value=s; ! } ! else ! { ! alert("Cannot import molecule: no JavaScript to Java communication in your browser."); ! } ! } ! function openStructureHistory(){ ! mywindow=window.open("/nmrshiftdbhtml/importfromstructureshistory.jsp;jsessionid=$data.getSession().getId()","molimport","height=200,width=900"); ! mywindow.focus(); ! } ! function openImport(){ ! mywindow=window.open("/nmrshiftdbhtml/import.htm","molimport","height=500,width=900"); ! mywindow.focus(); ! } ! msketch_mayscript = true; ! msketch_name = "JcpEditor"; ! msketch_begin("/nmrshiftdbhtml", 450, 400); ! #if($import=="true") ! msketch_param("load","$molfile"); ! #end ! msketch_end(); ! --> ! </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> ! Choose a structure file for the probable structure: <input type="file" name="datei" size="40"> ! #end #end <br> |
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From: Stefan K. <sh...@us...> - 2006-10-25 10:51:13
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/om In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv29048/src/java/org/openscience/nmrshiftdb/om Modified Files: DBSpectrum.java Log Message: The rating now longer includes default mark Index: DBSpectrum.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/om/DBSpectrum.java,v retrieving revision 1.191 retrieving revision 1.192 diff -C2 -r1.191 -r1.192 *** DBSpectrum.java 24 Oct 2006 17:17:23 -0000 1.191 --- DBSpectrum.java 25 Oct 2006 10:51:09 -0000 1.192 *************** *** 1134,1143 **** usermark.setComment(comment); usermark.save(); ! crit = new Criteria(); crit.add(DBUserDBSpectrumMarkPeer.SPECTRUM_ID, getSpectrumId()); v = DBUserDBSpectrumMarkPeer.doSelect(crit); if (v.size() == 1) { addMark(10, NmrshiftdbUserPeer.getByName("admin"), "Default mark"); ! } if (getMark() < new Integer(GeneralUtils.getNmrshiftdbProperty("minimum.mark.prediction")).intValue()) { GeneralUtils.sendEmailToEventReceivers("Mark below threshold for prediction", "The mark of spectrum " + getSpectrumId() + " has fallen below the threshold.", runData, 0); --- 1134,1143 ---- usermark.setComment(comment); usermark.save(); ! /*crit = new Criteria(); crit.add(DBUserDBSpectrumMarkPeer.SPECTRUM_ID, getSpectrumId()); v = DBUserDBSpectrumMarkPeer.doSelect(crit); if (v.size() == 1) { addMark(10, NmrshiftdbUserPeer.getByName("admin"), "Default mark"); ! }*/ if (getMark() < new Integer(GeneralUtils.getNmrshiftdbProperty("minimum.mark.prediction")).intValue()) { GeneralUtils.sendEmailToEventReceivers("Mark below threshold for prediction", "The mark of spectrum " + getSpectrumId() + " has fallen below the threshold.", runData, 0); |
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From: Stefan K. <sh...@us...> - 2006-10-25 10:51:13
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Update of /cvsroot/nmrshiftdb/nmrshiftdb In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv29048 Modified Files: CHANGELOG Log Message: The rating now longer includes default mark Index: CHANGELOG =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/CHANGELOG,v retrieving revision 1.116 retrieving revision 1.117 diff -C2 -r1.116 -r1.117 *** CHANGELOG 10 Oct 2006 15:20:18 -0000 1.116 --- CHANGELOG 25 Oct 2006 10:51:09 -0000 1.117 *************** *** 7,10 **** --- 7,12 ---- * Expert/normal mode makes search interface clearer * Weight search/formula with(out) other elements integrated into general search + * Peak table/structure/peak view combinations highlight the rows in table as well + * The rating now longer includes default mark Fixes: |
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From: Stefan K. <sh...@us...> - 2006-10-24 17:17:28
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/util In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv22673/src/java/org/openscience/nmrshiftdb/util Modified Files: UrlTool.java Log Message: updated the cml generation code Index: UrlTool.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/util/UrlTool.java,v retrieving revision 1.18 retrieving revision 1.19 diff -C2 -r1.18 -r1.19 *** UrlTool.java 10 Oct 2006 15:20:31 -0000 1.18 --- UrlTool.java 24 Oct 2006 17:17:23 -0000 1.19 *************** *** 166,170 **** NmrshiftdbUserPeer.executeStatement("update JETSPEED_USER_PROFILE set PROFILE ='"+((Record)rs.get(0)).getValue(1)+"' where USER_NAME ='" + data.getUser().getUserName() + "' and MEDIA_TYPE='html';"); }else{ ! NmrshiftdbUserPeer.executeStatement("update JETSPEED_USER_PROFILE set PROFILE =(select DISTINCT PROFILE from JETSPEED_ANON_PROFILE where MEDIA_TYPE ='html' and LANGUAGE ='en' and PAGE='default.psml') where USER_NAME ='" + data.getUser().getUserName() + "' and MEDIA_TYPE='html';"); } return ("The user interface has been reset to initial configuration!"); --- 166,170 ---- NmrshiftdbUserPeer.executeStatement("update JETSPEED_USER_PROFILE set PROFILE ='"+((Record)rs.get(0)).getValue(1)+"' where USER_NAME ='" + data.getUser().getUserName() + "' and MEDIA_TYPE='html';"); }else{ ! NmrshiftdbUserPeer.executeStatement("update JETSPEED_USER_PROFILE set PROFILE =(select DISTINCT PROFILE from JETSPEED_ANON_PROFILE where MEDIA_TYPE ='html' and LANGUAGE ='en' and PAGE='default.psml' limit 1) where USER_NAME ='" + data.getUser().getUserName() + "' and MEDIA_TYPE='html';"); } return ("The user interface has been reset to initial configuration!"); |
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From: Stefan K. <sh...@us...> - 2006-10-24 17:17:28
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv22673/src/java/org/openscience/nmrshiftdb Modified Files: NmrshiftdbServlet.java Log Message: updated the cml generation code Index: NmrshiftdbServlet.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/NmrshiftdbServlet.java,v retrieving revision 1.94 retrieving revision 1.95 diff -C2 -r1.94 -r1.95 *** NmrshiftdbServlet.java 11 Oct 2006 16:54:34 -0000 1.94 --- NmrshiftdbServlet.java 24 Oct 2006 17:17:22 -0000 1.95 *************** *** 43,49 **** import javax.xml.transform.stream.StreamSource; import nu.xom.Element; import nu.xom.Node; - import nu.xom.Text; import org.apache.fop.apps.FOUserAgent; --- 43,49 ---- import javax.xml.transform.stream.StreamSource; + import nu.xom.Attribute; import nu.xom.Element; import nu.xom.Node; import org.apache.fop.apps.FOUserAgent; *************** *** 200,206 **** }else{ Element cmlElement = new Element("cml"); Element parent=((DBSpectrum)spectra.get(0)).getDBMolecule().getCML(1); nu.xom.Node cmldoc = parent.getChild(0); ! ((Element)cmldoc).setNamespaceURI("http://www.xml-cml.org/schema/cml2/core"); parent.removeChildren(); cmlElement.appendChild(cmldoc); --- 200,208 ---- }else{ Element cmlElement = new Element("cml"); + cmlElement.addAttribute(new Attribute("convention","nmrshiftdb-convention")); + cmlElement.setNamespaceURI("http://www.xml-cml.org/schema"); Element parent=((DBSpectrum)spectra.get(0)).getDBMolecule().getCML(1); nu.xom.Node cmldoc = parent.getChild(0); ! ((Element)cmldoc).setNamespaceURI("http://www.xml-cml.org/schema"); parent.removeChildren(); cmlElement.appendChild(cmldoc); *************** *** 210,214 **** parentspec.removeChildren(); cmlElement.appendChild(spectrumel); ! ((Element)spectrumel).setNamespaceURI("http://www.xml-cml.org/schema/cml2/spect"); } out.write(cmlElement.toXML()); --- 212,216 ---- parentspec.removeChildren(); cmlElement.appendChild(spectrumel); ! ((Element)spectrumel).setNamespaceURI("http://www.xml-cml.org/schema"); } out.write(cmlElement.toXML()); *************** *** 564,570 **** if(format.equals("cmlboth")){ Element cmlElement = new Element("cml"); Element parent=spectrum.getDBMolecule().getCML(1, spectrum.getDBSpectrumType().getName().equals("1H")); nu.xom.Node cmldoc = parent.getChild(0); ! ((Element)cmldoc).setNamespaceURI("http://www.xml-cml.org/schema/cml2/core"); parent.removeChildren(); cmlElement.appendChild(cmldoc); --- 566,574 ---- if(format.equals("cmlboth")){ Element cmlElement = new Element("cml"); + cmlElement.addAttribute(new Attribute("convention","nmrshiftdb-convention")); + cmlElement.setNamespaceURI("http://www.xml-cml.org/schema"); Element parent=spectrum.getDBMolecule().getCML(1, spectrum.getDBSpectrumType().getName().equals("1H")); nu.xom.Node cmldoc = parent.getChild(0); ! ((Element)cmldoc).setNamespaceURI("http://www.xml-cml.org/schema"); parent.removeChildren(); cmlElement.appendChild(cmldoc); *************** *** 573,577 **** parentspec.removeChildren(); cmlElement.appendChild(spectrumel); ! ((Element)spectrumel).setNamespaceURI("http://www.xml-cml.org/schema/cml2/spect"); out.write(cmlElement.toXML()); } --- 577,581 ---- parentspec.removeChildren(); cmlElement.appendChild(spectrumel); ! ((Element)spectrumel).setNamespaceURI("http://www.xml-cml.org/schema"); out.write(cmlElement.toXML()); } |
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From: Stefan K. <sh...@us...> - 2006-10-24 17:17:28
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/doc In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv22673/doc Modified Files: nmrshiftdbhelp.xml Log Message: updated the cml generation code Index: nmrshiftdbhelp.xml =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/doc/nmrshiftdbhelp.xml,v retrieving revision 1.82 retrieving revision 1.83 diff -C2 -r1.82 -r1.83 *** nmrshiftdbhelp.xml 24 Oct 2006 10:48:42 -0000 1.82 --- nmrshiftdbhelp.xml 24 Oct 2006 17:17:22 -0000 1.83 *************** *** 283,287 **** </sect2> <sect2 id="labadmin"><title>The Lab Amdinistration System</title> ! <para>NMRShiftdb can work as a user and order administration system for NMR labs. The concept of the lab system is centered around two roles, oooperator and user, and the concept of an order.</para> <para>Users can assign themself membership of a labgroup, either as operator or user. They need to be approved by the group leader. Once this is done, a user can submit orders and a operator can work on them.</para> <para>A user, when logged in, has an additional tab "NMR lab administration". Here, he has a form which he needs to fill out to submit an order. There are three possible ways to handle an order: --- 283,287 ---- </sect2> <sect2 id="labadmin"><title>The Lab Amdinistration System</title> ! <para>NMRShiftdb can work as a user and order administration system for NMR labs. The concept of the lab system is centered around two roles, operator and user, and the concept of an order.</para> <para>Users can assign themself membership of a labgroup, either as operator or user. They need to be approved by the group leader. Once this is done, a user can submit orders and a operator can work on them.</para> <para>A user, when logged in, has an additional tab "NMR lab administration". Here, he has a form which he needs to fill out to submit an order. There are three possible ways to handle an order: |
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From: Stefan K. <sh...@us...> - 2006-10-24 17:17:26
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/om In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv22673/src/java/org/openscience/nmrshiftdb/om Modified Files: DBSpectrum.java Log Message: updated the cml generation code Index: DBSpectrum.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/om/DBSpectrum.java,v retrieving revision 1.190 retrieving revision 1.191 diff -C2 -r1.190 -r1.191 *** DBSpectrum.java 10 Oct 2006 15:20:31 -0000 1.190 --- DBSpectrum.java 24 Oct 2006 17:17:23 -0000 1.191 *************** *** 866,870 **** spectrum.addMetadataList(ml); CMLSubstanceList sl=new CMLSubstanceList(); ! //spectrum.addSubstanceList(sl); TODO Vector v=this.getDBSpectrumDBConditions(); for(int i=0;i<v.size();i++){ --- 866,870 ---- spectrum.addMetadataList(ml); CMLSubstanceList sl=new CMLSubstanceList(); ! spectrum.appendChild(sl); Vector v=this.getDBSpectrumDBConditions(); for(int i=0;i<v.size();i++){ |
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From: Stefan K. <sh...@us...> - 2006-10-24 15:47:32
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/deploymentdescriptors In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv4706/src/deploymentdescriptors Modified Files: NMRShiftDB.wsdd Added Files: NMRShiftDB.wsdl NMRShiftDBTypes.xsd Removed Files: NMRShiftDBelucidate.wsdl NMRShiftDBpredict.wsdl NMRShiftDBrpc.wsdl NMRShiftDBsubmit.wsdl Log Message: all the webservices should now be in a single file --- NEW FILE: NMRShiftDBTypes.xsd --- <?xml version="1.0" encoding="UTF-8"?> <xsd:schema targetNamespace="http://www.nmrshiftdb.org/schemas/2006/10/NMRShiftDBTypes" xmlns:nsdt="http://www.nmrshiftdb.org/schemas/2006/10/NMRShiftDBTypes" xmlns:cml="http://www.xml-cml.org/schema" xmlns:xsd="http://www.w3.org/2001/XMLSchema" elementFormDefault="qualified"> <xsd:import namespace="http://www.xml-cml.org/schema" schemaLocation="http://almost.cubic.uni-koeln.de/schema.xsd" /> <!-- Elements --> <xsd:element name="doPredictionParameters" type="nsdt:DoPredictionParameters" /> <xsd:element name="doSubmitParameters" type="nsdt:DoSubmitParameters" /> <xsd:element name="getSpectrumTypesParameters" type="nsdt:GetSpectrumTypesParameters" /> <xsd:element name="doElucidateParameters" type="nsdt:DoElucidateParameters" /> <!-- Types --> <xsd:complexType name="DoPredictionParameters"> <xsd:sequence> <xsd:element ref="cml:molecule" minOccurs="1" maxOccurs="1" /> <xsd:element name="spectrumTypeName" type="xsd:string" minOccurs="1" maxOccurs="1" /> </xsd:sequence> </xsd:complexType> <xsd:complexType name="DoSubmitParameters"> <xsd:sequence> <xsd:element ref="cml:cml" minOccurs="1" maxOccurs="1" /> <xsd:element name="username" type="xsd:string" minOccurs="1" maxOccurs="1" /> <xsd:element name="password" type="xsd:string" minOccurs="1" maxOccurs="1" /> </xsd:sequence> </xsd:complexType> <xsd:complexType name="GetSpectrumTypesParameters"> <xsd:sequence> <xsd:element name="dummy" type="xsd:string" minOccurs="0" maxOccurs="0" /> </xsd:sequence> </xsd:complexType> <xsd:complexType name="DoElucidateParameters"> <xsd:sequence> <xsd:element ref="cml:spectrum" minOccurs="1" maxOccurs="1" /> <xsd:element name="suborwhole" type="xsd:string" /> </xsd:sequence> </xsd:complexType> </xsd:schema> Index: NMRShiftDB.wsdd =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/deploymentdescriptors/NMRShiftDB.wsdd,v retrieving revision 1.3 retrieving revision 1.4 diff -C2 -r1.3 -r1.4 *** NMRShiftDB.wsdd 4 Jul 2006 13:38:54 -0000 1.3 --- NMRShiftDB.wsdd 24 Oct 2006 15:47:23 -0000 1.4 *************** *** 4,8 **** <!-- Services from serviceName WSDL service -->; ! <service name="NMRShiftDBpredict" provider="java:MSG" use="literal"> <!-- Definitions for the SOAPMonitor (optional) --> <!--<requestFlow> --- 4,8 ---- <!-- Services from serviceName WSDL service -->; ! <service name="NMRShiftDB" provider="java:MSG" use="literal"> <!-- Definitions for the SOAPMonitor (optional) --> <!--<requestFlow> *************** *** 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> --- 15,20 ---- <parameter name="className" value="org.openscience.nmrshiftdb.webservices.NMRShiftDBServiceBindingImpl"/> ! <parameter name="allowedMethods" value="doPrediction doSubmit getSpectrumTypes doElucidate"/> ! <wsdlFile>NMRShiftDB.wsdl</wsdlFile> </service> </deployment> --- NMRShiftDBelucidate.wsdl DELETED --- --- NMRShiftDBpredict.wsdl DELETED --- --- NMRShiftDBrpc.wsdl DELETED --- --- NMRShiftDBsubmit.wsdl DELETED --- |
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From: Stefan K. <sh...@us...> - 2006-10-24 14:31:03
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/webservices In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv28810/src/java/org/openscience/nmrshiftdb/webservices Modified Files: NMRShiftDB.java NMRShiftDBServiceBindingImpl.java Log Message: more changes in web services Index: NMRShiftDB.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/webservices/NMRShiftDB.java,v retrieving revision 1.7 retrieving revision 1.8 diff -C2 -r1.7 -r1.8 *** NMRShiftDB.java 24 Oct 2006 13:19:37 -0000 1.7 --- NMRShiftDB.java 24 Oct 2006 14:30:56 -0000 1.8 *************** *** 8,12 **** throws java.rmi.RemoteException; ! public String getSpectrumTypes(Document dummy) throws java.rmi.RemoteException; --- 8,12 ---- throws java.rmi.RemoteException; ! public Document getSpectrumTypes(Document dummy) throws java.rmi.RemoteException; Index: NMRShiftDBServiceBindingImpl.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/webservices/NMRShiftDBServiceBindingImpl.java,v retrieving revision 1.32 retrieving revision 1.33 diff -C2 -r1.32 -r1.33 *** NMRShiftDBServiceBindingImpl.java 24 Oct 2006 13:19:37 -0000 1.32 --- NMRShiftDBServiceBindingImpl.java 24 Oct 2006 14:30:56 -0000 1.33 *************** *** 128,134 **** } ! public String getSpectrumTypes(org.w3c.dom.Document dummy) throws RemoteException { System.err.println("lkj"); StringBuffer sb=new StringBuffer(); try{ TurbineConfig tc = new TurbineConfig("", webinfdir+"conf/TurbineResources.properties"); --- 128,135 ---- } ! public org.w3c.dom.Document getSpectrumTypes(org.w3c.dom.Document dummy) throws RemoteException { System.err.println("lkj"); StringBuffer sb=new StringBuffer(); + org.w3c.dom.Document document = null; try{ TurbineConfig tc = new TurbineConfig("", webinfdir+"conf/TurbineResources.properties"); *************** *** 138,145 **** sb.append(((DBSpectrumType)v.get(i)).getName()+" "); } }catch(Exception ex){ throw new RemoteException(ex.getMessage(),ex); } ! return sb.toString().trim(); } --- 139,149 ---- sb.append(((DBSpectrumType)v.get(i)).getName()+" "); } + DocumentBuilder builder; + builder = DocumentBuilderFactory.newInstance().newDocumentBuilder(); + document = builder.parse(new ByteArrayInputStream(new String("<xml>"+sb.toString()+"</xml>").getBytes())); }catch(Exception ex){ throw new RemoteException(ex.getMessage(),ex); } ! return document; } |
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From: Stefan K. <sh...@us...> - 2006-10-24 13:19:42
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/webservices In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv25659/src/java/org/openscience/nmrshiftdb/webservices Modified Files: NMRShiftDB.java NMRShiftDBServiceBindingImpl.java Log Message: fixes bug in lab system Index: NMRShiftDB.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/webservices/NMRShiftDB.java,v retrieving revision 1.6 retrieving revision 1.7 diff -C2 -r1.6 -r1.7 *** NMRShiftDB.java 24 Oct 2006 12:41:10 -0000 1.6 --- NMRShiftDB.java 24 Oct 2006 13:19:37 -0000 1.7 *************** *** 8,12 **** throws java.rmi.RemoteException; ! public String getSpectrumTypes(String dummy) throws java.rmi.RemoteException; --- 8,12 ---- throws java.rmi.RemoteException; ! public String getSpectrumTypes(Document dummy) throws java.rmi.RemoteException; Index: NMRShiftDBServiceBindingImpl.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/webservices/NMRShiftDBServiceBindingImpl.java,v retrieving revision 1.31 retrieving revision 1.32 diff -C2 -r1.31 -r1.32 *** NMRShiftDBServiceBindingImpl.java 24 Oct 2006 12:41:10 -0000 1.31 --- NMRShiftDBServiceBindingImpl.java 24 Oct 2006 13:19:37 -0000 1.32 *************** *** 128,132 **** } ! public String getSpectrumTypes(String dummy) throws RemoteException { System.err.println("lkj"); StringBuffer sb=new StringBuffer(); --- 128,132 ---- } ! public String getSpectrumTypes(org.w3c.dom.Document dummy) throws RemoteException { System.err.println("lkj"); StringBuffer sb=new StringBuffer(); |
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From: Stefan K. <sh...@us...> - 2006-10-24 13:19:39
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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-serv25659/src/java/org/openscience/nmrshiftdb/modules/actions/portlets Modified Files: OrderAction.java OrderFullfillAction.java Log Message: fixes bug in lab system Index: OrderAction.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/modules/actions/portlets/OrderAction.java,v retrieving revision 1.32 retrieving revision 1.33 diff -C2 -r1.32 -r1.33 *** OrderAction.java 24 Oct 2006 10:48:44 -0000 1.32 --- OrderAction.java 24 Oct 2006 13:19:37 -0000 1.33 *************** *** 563,566 **** --- 563,567 ---- rawfile.setUrl(GeneralUtils.getNmrshiftdbProperty("urlcompressedfiles",data)+"/"+filename); rawfile.setContainedFiles(attachedfiles.toString()); + rawfile.setAssigned("false"); rawfile.save(); if(data.getParameters().get("finished")!=null && data.getParameters().get("finished").equals("finished")){ Index: OrderFullfillAction.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/modules/actions/portlets/OrderFullfillAction.java,v retrieving revision 1.24 retrieving revision 1.25 diff -C2 -r1.24 -r1.25 *** OrderFullfillAction.java 6 Oct 2006 20:12:10 -0000 1.24 --- OrderFullfillAction.java 24 Oct 2006 13:19:37 -0000 1.25 *************** *** 178,181 **** --- 178,182 ---- rawfile.setUrl(GeneralUtils.getNmrshiftdbProperty("urlcompressedfiles",data)+"/"+filename); rawfile.setContainedFiles(attachedfiles.toString()); + rawfile.setAssigned("false"); rawfile.save(); if(data.getParameters().get("finished")!=null && data.getParameters().get("finished").equals("finished")){ |
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From: Stefan K. <sh...@us...> - 2006-10-24 13:19:39
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/daemons In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv25659/src/java/org/openscience/nmrshiftdb/daemons Modified Files: AssignRobotDaemon.java Log Message: fixes bug in lab system Index: AssignRobotDaemon.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/daemons/AssignRobotDaemon.java,v retrieving revision 1.7 retrieving revision 1.8 diff -C2 -r1.7 -r1.8 *** AssignRobotDaemon.java 22 Sep 2006 16:30:35 -0000 1.7 --- AssignRobotDaemon.java 24 Oct 2006 13:19:36 -0000 1.8 *************** *** 48,51 **** --- 48,52 ---- rawfile.setUrl(GeneralUtils.getNmrshiftdbProperty("urlcompressedfiles",servcon)+"/"+usersid+".zip"); rawfile.setContainedFiles(attachedfiles.toString()); + rawfile.setAssigned("false"); rawfile.save(); DBSample sample=DBSamplePeer.retrieveByPK(new NumberKey(sampleid)); |
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From: Stefan K. <sh...@us...> - 2006-10-24 12:41:18
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/webservices In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv7137/src/java/org/openscience/nmrshiftdb/webservices Modified Files: NMRShiftDB.java NMRShiftDBServiceBindingImpl.java Log Message: change in webservices Index: NMRShiftDB.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/webservices/NMRShiftDB.java,v retrieving revision 1.5 retrieving revision 1.6 diff -C2 -r1.5 -r1.6 *** NMRShiftDB.java 18 Oct 2006 09:27:02 -0000 1.5 --- NMRShiftDB.java 24 Oct 2006 12:41:10 -0000 1.6 *************** *** 8,12 **** throws java.rmi.RemoteException; ! public String getSpectrumTypes() throws java.rmi.RemoteException; --- 8,12 ---- throws java.rmi.RemoteException; ! public String getSpectrumTypes(String dummy) throws java.rmi.RemoteException; Index: NMRShiftDBServiceBindingImpl.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/webservices/NMRShiftDBServiceBindingImpl.java,v retrieving revision 1.30 retrieving revision 1.31 diff -C2 -r1.30 -r1.31 *** NMRShiftDBServiceBindingImpl.java 23 Oct 2006 11:58:09 -0000 1.30 --- NMRShiftDBServiceBindingImpl.java 24 Oct 2006 12:41:10 -0000 1.31 *************** *** 128,132 **** } ! public String getSpectrumTypes() throws RemoteException { System.err.println("lkj"); StringBuffer sb=new StringBuffer(); --- 128,132 ---- } ! public String getSpectrumTypes(String dummy) throws RemoteException { System.err.println("lkj"); StringBuffer sb=new StringBuffer(); |
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From: Stefan K. <sh...@us...> - 2006-10-24 10:48:55
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/doc In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv10251/doc Modified Files: nmrshiftdbhelp.pdf nmrshiftdbhelp.xml Log Message: orders can be re-issued Index: nmrshiftdbhelp.pdf =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/doc/nmrshiftdbhelp.pdf,v retrieving revision 1.67 retrieving revision 1.68 diff -C2 -r1.67 -r1.68 Binary files /tmp/cvs7lYZhz and /tmp/cvsRBQsgH differ Index: nmrshiftdbhelp.xml =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/doc/nmrshiftdbhelp.xml,v retrieving revision 1.81 retrieving revision 1.82 diff -C2 -r1.81 -r1.82 *** nmrshiftdbhelp.xml 23 Oct 2006 11:58:08 -0000 1.81 --- nmrshiftdbhelp.xml 24 Oct 2006 10:48:42 -0000 1.82 *************** *** 290,294 **** <listitem>By the user via a sample changer: Here the user needs to put his probe into the sample changer and it will be measured during the next night. The data files get attached automatically and the order goes to the fullfilled orders list.</listitem> </itemizedlist> ! The user can delete (=cancel) orders which have not yet been processed. Once an order is processed (i. e. has files assigned to it) it can not be deleted, because it is needed for statistcs. It stays in the "done orders" till a peak assignment is done. If the user does not want to do a peak assignment, he can view the order by clicking it and choose "I do not want to assign th spectra", having checked "confirm" before, which will take the order from the list as well. If the user wants to see the the orders which either have a peak assignment or where the user decided not to do it, he can choose "Also show orders already assigned" and press "Change dates/show alreayd assigned".</para> <para>An operator, when logged in, also has the "NMR lab administration" tab. He sees a list of open orders. When clicking on one, he can assign raw data files to it and declare the order to be finished. It will then disappear from the list.</para> </sect2> --- 290,294 ---- <listitem>By the user via a sample changer: Here the user needs to put his probe into the sample changer and it will be measured during the next night. The data files get attached automatically and the order goes to the fullfilled orders list.</listitem> </itemizedlist> ! The user can delete (=cancel) orders which have not yet been processed. Once an order is processed (i. e. has files assigned to it) it can not be deleted, because it is needed for statistcs. It stays in the "done orders" till a peak assignment is done. If the user does not want to do a peak assignment, he can view the order by clicking it and choose "I do not want to assign th spectra", having checked "confirm" before, which will take the order from the list as well. If the user wants to see the the orders which either have a peak assignment or where the user decided not to do it, he can choose "Also show orders already assigned" and press "Change dates/show alreayd assigned". With "I want to measure this sample again" the order is marked as not to be assigned and the user gets the submit order form, with the data of the order filled in.</para> <para>An operator, when logged in, also has the "NMR lab administration" tab. He sees a list of open orders. When clicking on one, he can assign raw data files to it and declare the order to be finished. It will then disappear from the list.</para> </sect2> |
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From: Stefan K. <sh...@us...> - 2006-10-24 10:48:55
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/sql In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv10251/src/sql Modified Files: populate-mysql.sql Log Message: orders can be re-issued Index: populate-mysql.sql =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/sql/populate-mysql.sql,v retrieving revision 1.60 retrieving revision 1.61 diff -C2 -r1.60 -r1.61 *** populate-mysql.sql 23 Oct 2006 11:58:09 -0000 1.60 --- populate-mysql.sql 24 Oct 2006 10:48:44 -0000 1.61 *************** *** 143,147 **** alter table CONDITION_TYPE change CML_ENTRY_TYPE CML_ENTRY_TYPE enum("","metadata","substance","condition") not null default ""; alter table SAMPLE change PROCESS PROCESS enum("self","worker","robot") not null default "self"; ! alter table RAW_FILE change ASSIGNED ASSIGNED enum("self","worker","robot") not null default "self"; alter table MOLECULE change fp0 fp0 BIGINT UNSIGNED; alter table MOLECULE change fp1 fp1 BIGINT UNSIGNED; --- 143,147 ---- alter table CONDITION_TYPE change CML_ENTRY_TYPE CML_ENTRY_TYPE enum("","metadata","substance","condition") not null default ""; alter table SAMPLE change PROCESS PROCESS enum("self","worker","robot") not null default "self"; ! alter table RAW_FILE change ASSIGNED ASSIGNED enum("false","true") not null default "false"; alter table MOLECULE change fp0 fp0 BIGINT UNSIGNED; alter table MOLECULE change fp1 fp1 BIGINT UNSIGNED; |
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From: Stefan K. <sh...@us...> - 2006-10-24 10:48:48
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/vmtemplates/portlets/html In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv10251/src/vmtemplates/portlets/html Modified Files: user-order.vm Log Message: orders can be re-issued Index: user-order.vm =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/vmtemplates/portlets/html/user-order.vm,v retrieving revision 1.44 retrieving revision 1.45 diff -C2 -r1.44 -r1.45 *** user-order.vm 23 Oct 2006 11:58:09 -0000 1.44 --- user-order.vm 24 Oct 2006 10:48:45 -0000 1.45 *************** *** 244,247 **** --- 244,248 ---- #else <form name="orderform" method="post" action="portal/pane0/NMR+lab+administration"><input type="hidden" name="id" value="$sample.getSampleId()"><input type="submit" name="eventSubmit_doNoassignment" value="I do not want to assign the spectra"/> Confirm this by checking <input type="checkbox" name="confirm" value="confirm"></form> + <form name="orderform" method="post" action="portal/pane0/NMR+lab+administration"><input type="hidden" name="id" value="$sample.getSampleId()"><input type="submit" name="eventSubmit_doRemeasurement" value="I want to measure this sample again"/> Confirm this by checking <input type="checkbox" name="confirm" value="confirm"></form> #end #elseif($submitorshow=="edit") |
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From: Stefan K. <sh...@us...> - 2006-10-24 10:48:48
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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-serv10251/src/java/org/openscience/nmrshiftdb/modules/actions/portlets Modified Files: OrderAction.java Log Message: orders can be re-issued Index: OrderAction.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/modules/actions/portlets/OrderAction.java,v retrieving revision 1.31 retrieving revision 1.32 diff -C2 -r1.31 -r1.32 *** OrderAction.java 23 Oct 2006 11:58:09 -0000 1.31 --- OrderAction.java 24 Oct 2006 10:48:44 -0000 1.32 *************** *** 475,480 **** rf.save(); } - DBRawFilePeer.doDelete(crit); - DBSamplePeer.doDelete(crit); buildOrderContext(context,data); } --- 475,478 ---- *************** *** 486,490 **** ! public void doDeleteorder(RunData data, Context context) throws Exception { try{ if(data.getParameters().get("confirm")!=null && data.getParameters().get("confirm").equals("confirm")){ --- 484,527 ---- ! public void doRemeasurement(RunData data, Context context) throws Exception { ! try{ ! if(data.getParameters().get("confirm")!=null && data.getParameters().get("confirm").equals("confirm")){ ! Criteria crit=new Criteria(); ! crit.add(DBRawFilePeer.SAMPLE_ID,data.getParameters().get("id")); ! Vector v=DBRawFilePeer.doSelect(crit); ! for(int i=0;i<v.size();i++){ ! DBRawFile rf=(DBRawFile)v.get(i); ! rf.setAssigned("true"); ! rf.save(); ! } ! DBSample sample=DBSamplePeer.retrieveByPK(new NumberKey(data.getParameters().get("id"))); ! context.put("ordertype",sample.getProcess()); ! context.put("usersid",sample.getUsersId()+"-2"); ! context.put("solvent", sample.getDBCondition().getValue()); ! context.put("other",sample.getWishedSpectrum()); ! context.put("othernuc",sample.getOtherNuclei()); ! context.put("care",sample.getSpecialCare()); ! 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")); ! FileWriter out = new FileWriter(outputFile); ! out.write(sample.getDBMolecule().getStructureFile(1,false)); ! out.close(); ! context.put("molfile", "/nmrshiftdbhtml/" + outputFile.getName()); ! context.put("import","true"); ! } ! context.put("message","The new ID is a suggestion, you can change it, but it must be different from the old one"); ! buildOrderContext(context,data); ! } ! }catch(Exception ex){ ! ex.printStackTrace(); ! GeneralUtils.logError(ex,"guestbook/doentry",data,true); ! } ! } ! ! ! public void doDeleteorder(RunData data, Context context) throws Exception { try{ if(data.getParameters().get("confirm")!=null && data.getParameters().get("confirm").equals("confirm")){ |
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From: Stefan K. <sh...@us...> - 2006-10-24 10:48:48
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/html In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv10251/src/html Modified Files: using.html Log Message: orders can be re-issued Index: using.html =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/using.html,v retrieving revision 1.49 retrieving revision 1.50 diff -C2 -r1.49 -r1.50 *** using.html 23 Oct 2006 11:58:09 -0000 1.49 --- using.html 24 Oct 2006 10:48:44 -0000 1.50 *************** *** 737,741 **** ></UL > ! The user can delete (=cancel) orders which have not yet been processed. Once an order is processed (i. e. has files assigned to it) it can not be deleted, because it is needed for statistcs. It stays in the "done orders" till a peak assignment is done. If the user does not want to do a peak assignment, he can view the order by clicking it and choose "I do not want to assign th spectra", having checked "confirm" before, which will take the order from the list as well. If the user wants to see the the orders which either have a peak assignment or where the user decided not to do it, he can choose "Also show orders already assigned" and press "Change dates/show alreayd assigned".</P ><P >An operator, when logged in, also has the "NMR lab administration" tab. He sees a list of open orders. When clicking on one, he can assign raw data files to it and declare the order to be finished. It will then disappear from the list.</P --- 737,741 ---- ></UL > ! The user can delete (=cancel) orders which have not yet been processed. Once an order is processed (i. e. has files assigned to it) it can not be deleted, because it is needed for statistcs. It stays in the "done orders" till a peak assignment is done. If the user does not want to do a peak assignment, he can view the order by clicking it and choose "I do not want to assign th spectra", having checked "confirm" before, which will take the order from the list as well. If the user wants to see the the orders which either have a peak assignment or where the user decided not to do it, he can choose "Also show orders already assigned" and press "Change dates/show alreayd assigned". With "I want to measure this sample again" the order is marked as not to be assigned and the user gets the submit order form, with the data of the order filled in.</P ><P >An operator, when logged in, also has the "NMR lab administration" tab. He sees a list of open orders. When clicking on one, he can assign raw data files to it and declare the order to be finished. It will then disappear from the list.</P |
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From: Stefan K. <sh...@us...> - 2006-10-23 11:58:16
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/om In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv27992/src/java/org/openscience/nmrshiftdb/om Modified Files: BaseDBRawFile.java BaseDBRawFilePeer.java Log Message: changes in the lab system Index: BaseDBRawFile.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/om/BaseDBRawFile.java,v retrieving revision 1.4 retrieving revision 1.5 diff -C2 -r1.4 -r1.5 *** BaseDBRawFile.java 7 Jun 2006 19:13:50 -0000 1.4 --- BaseDBRawFile.java 23 Oct 2006 11:58:09 -0000 1.5 *************** *** 2,16 **** ! 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; *************** *** 30,33 **** --- 28,33 ---- /** the value for the contained_files field */ private String contained_files; + /** the value for the assigned field */ + private String assigned; *************** *** 177,180 **** --- 177,206 ---- + /** + * Get the Assigned + * @return String + */ + public String getAssigned() + { + return assigned; + } + + + /** + * Set the value of Assigned + */ + public void setAssigned(String v ) + { + + + + if ( !ObjectUtils.equals(this.assigned, v) ) + { + this.assigned = v; + setModified(true); + } + } + + *************** *** 423,426 **** --- 449,453 ---- fieldNames_.add("Url"); fieldNames_.add("ContainedFiles"); + fieldNames_.add("Assigned"); } return fieldNames_; *************** *** 449,452 **** --- 476,483 ---- return getContainedFiles(); } + if (name.equals("Assigned")) + { + return getAssigned(); + } return null; } *************** *** 474,477 **** --- 505,512 ---- return getContainedFiles(); } + if (name.equals(DBRawFilePeer.ASSIGNED )) + { + return getAssigned(); + } return null; } *************** *** 499,502 **** --- 534,541 ---- return getContainedFiles(); } + if ( pos == 4 ) + { + return getAssigned(); + } return null; } *************** *** 650,653 **** --- 689,693 ---- copyObj.setUrl(url); copyObj.setContainedFiles(contained_files); + copyObj.setAssigned(assigned); *************** *** 661,665 **** copyObj.setRawFileId((NumberKey)null); ! return copyObj; } } --- 701,705 ---- copyObj.setRawFileId((NumberKey)null); ! return copyObj; } } Index: BaseDBRawFilePeer.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/om/BaseDBRawFilePeer.java,v retrieving revision 1.4 retrieving revision 1.5 diff -C2 -r1.4 -r1.5 *** BaseDBRawFilePeer.java 7 Jun 2006 19:13:50 -0000 1.4 --- BaseDBRawFilePeer.java 23 Oct 2006 11:58:09 -0000 1.5 *************** *** 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.DBRawFileMapBuilder; ! 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.*; /** *************** *** 46,53 **** /** the column name for the CONTAINED_FILES field */ public static final String CONTAINED_FILES = mapBuilder.getDBRawFile_ContainedFiles(); /** number of columns for this peer */ ! public static final int numColumns = 4; /** A class that can be returned by this peer. */ --- 46,55 ---- /** the column name for the CONTAINED_FILES field */ public static final String CONTAINED_FILES = mapBuilder.getDBRawFile_ContainedFiles(); + /** the column name for the ASSIGNED field */ + public static final String ASSIGNED = mapBuilder.getDBRawFile_Assigned(); /** number of columns for this peer */ ! public static final int numColumns = 5; /** A class that can be returned by this peer. */ *************** *** 105,109 **** public static ObjectKey doInsert( Criteria criteria ) throws Exception { ! return BasePeer.doInsert( criteria ); } --- 107,111 ---- public static ObjectKey doInsert( Criteria criteria ) throws Exception { ! return BasePeer.doInsert( criteria ); } *************** *** 116,120 **** throws Exception { ! return BasePeer.doInsert( criteria, dbCon ); } --- 118,122 ---- throws Exception { ! return BasePeer.doInsert( criteria, dbCon ); } *************** *** 126,129 **** --- 128,132 ---- criteria.addSelectColumn( URL ); criteria.addSelectColumn( CONTAINED_FILES ); + criteria.addSelectColumn( ASSIGNED ); } *************** *** 165,168 **** --- 168,172 ---- obj.setUrl(row.getValue(offset+2).asString()); obj.setContainedFiles(row.getValue(offset+3).asString()); + obj.setAssigned(row.getValue(offset+4).asString()); } *************** *** 197,201 **** } ! // BasePeer returns a Vector of Value (Village) arrays. The array // order follows the order columns were placed in the Select clause. --- 201,205 ---- } ! // BasePeer returns a Vector of Value (Village) arrays. The array // order follows the order columns were placed in the Select clause. *************** *** 217,221 **** } ! // BasePeer returns a Vector of Value (Village) arrays. The array // order follows the order columns were placed in the Select clause. --- 221,225 ---- } ! // BasePeer returns a Vector of Value (Village) arrays. The array // order follows the order columns were placed in the Select clause. *************** *** 265,269 **** Criteria(mapBuilder.getDatabaseMap().getName(), 2); selectCriteria.put( RAW_FILE_ID, criteria.remove(RAW_FILE_ID) ); ! BasePeer.doUpdate( selectCriteria, criteria ); } --- 269,273 ---- Criteria(mapBuilder.getDatabaseMap().getName(), 2); selectCriteria.put( RAW_FILE_ID, criteria.remove(RAW_FILE_ID) ); ! BasePeer.doUpdate( selectCriteria, criteria ); } *************** *** 280,284 **** Criteria(mapBuilder.getDatabaseMap().getName(), 2); selectCriteria.put( RAW_FILE_ID, criteria.remove(RAW_FILE_ID) ); ! BasePeer.doUpdate( selectCriteria, criteria, dbCon ); } --- 284,288 ---- Criteria(mapBuilder.getDatabaseMap().getName(), 2); selectCriteria.put( RAW_FILE_ID, criteria.remove(RAW_FILE_ID) ); ! BasePeer.doUpdate( selectCriteria, criteria, dbCon ); } *************** *** 290,294 **** public static void doDelete(Criteria criteria) throws Exception { ! BasePeer.doDelete ( criteria ); } --- 294,298 ---- public static void doDelete(Criteria criteria) throws Exception { ! BasePeer.doDelete ( criteria ); } *************** *** 302,306 **** public static void doDelete(Criteria criteria, DBConnection dbCon) throws Exception { ! BasePeer.doDelete ( criteria, dbCon ); } --- 306,310 ---- public static void doDelete(Criteria criteria, DBConnection dbCon) throws Exception { ! BasePeer.doDelete ( criteria, dbCon ); } *************** *** 372,375 **** --- 376,380 ---- criteria.add( URL, obj.getUrl() ); criteria.add( CONTAINED_FILES, obj.getContainedFiles() ); + criteria.add( ASSIGNED, obj.getAssigned() ); return criteria; } *************** *** 452,456 **** ! Vector rows = BasePeer.doSelect(c); Vector results = new Vector(); --- 457,461 ---- ! Vector rows = BasePeer.doSelect(c); Vector results = new Vector(); |
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From: Stefan K. <sh...@us...> - 2006-10-23 11:58:16
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/webservices In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv27992/src/java/org/openscience/nmrshiftdb/webservices Modified Files: NMRShiftDBServiceBindingImpl.java Log Message: changes in the lab system Index: NMRShiftDBServiceBindingImpl.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/webservices/NMRShiftDBServiceBindingImpl.java,v retrieving revision 1.29 retrieving revision 1.30 diff -C2 -r1.29 -r1.30 *** NMRShiftDBServiceBindingImpl.java 20 Oct 2006 14:42:04 -0000 1.29 --- NMRShiftDBServiceBindingImpl.java 23 Oct 2006 11:58:09 -0000 1.30 *************** *** 358,362 **** public org.w3c.dom.Document doElucidate(org.w3c.dom.Document request) throws RemoteException { - StringBuffer sb=new StringBuffer(); org.w3c.dom.Document document; try{ --- 358,361 ---- *************** *** 385,389 **** } boolean sub = complete.getValue().equals("sub"); ! Vector v=new Vector(); if (sub) { v.add(new ValuesForVelocityBean(NmrshiftdbConstants.SUBSPECTRUM, "--", searchSpectrumBuffer.toString())); --- 384,388 ---- } boolean sub = complete.getValue().equals("sub"); ! Vector<ValuesForVelocityBean> v=new Vector<ValuesForVelocityBean>(); if (sub) { v.add(new ValuesForVelocityBean(NmrshiftdbConstants.SUBSPECTRUM, "--", searchSpectrumBuffer.toString())); |
