nmrshiftdb-devel — For developers of the NMRShiftDB software and admins of an NMRShiftDB node

[Nmrshiftdb-devel] CVS: nmrshiftdb/src/java/org/openscience/nmrshiftdb/daemons AssignRobotDaemon.java, 1.3, 1.4

[Stefan K. <sh...@us...>]

Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/daemons
In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv30884/src/java/org/openscience/nmrshiftdb/daemons

Modified Files:
	AssignRobotDaemon.java 
Log Message:
this should assign directories to the robot orders as well


Index: AssignRobotDaemon.java
===================================================================
RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/daemons/AssignRobotDaemon.java,v
retrieving revision 1.3
retrieving revision 1.4
diff -C2 -r1.3 -r1.4
*** AssignRobotDaemon.java	22 Sep 2006 08:22:15 -0000	1.3
--- AssignRobotDaemon.java	22 Sep 2006 09:26:28 -0000	1.4
***************
*** 64,70 ****
      private void searchfiles(File tolookin, String usersid, ZipOutputStream zipoutputstream, StringBuffer attachedfiles, File dirtoignore) throws IOException{
      	File[] filesindir=tolookin.listFiles();
      	for(int i=0;i<filesindir.length;i++){
!     		if(filesindir[i].isDirectory() && !filesindir[i].getName().equals(".") && !filesindir[i].getName().equals("..") && !filesindir[i].equals(dirtoignore)){
      			searchfiles(filesindir[i],usersid,zipoutputstream,attachedfiles, dirtoignore);
      		}else{
      			if(filesindir[i].getName().indexOf(usersid)==0){
--- 64,73 ----
      private void searchfiles(File tolookin, String usersid, ZipOutputStream zipoutputstream, StringBuffer attachedfiles, File dirtoignore) throws IOException{
      	File[] filesindir=tolookin.listFiles();
+     	System.err.println("search "+tolookin+"  "+usersid+"  "+filesindir[0].getName());
      	for(int i=0;i<filesindir.length;i++){
!     		if(filesindir[i].isDirectory() && filesindir[i].getName().indexOf(usersid)!=0 && !filesindir[i].getName().equals(".") && !filesindir[i].getName().equals("..") && !filesindir[i].equals(dirtoignore)){
      			searchfiles(filesindir[i],usersid,zipoutputstream,attachedfiles, dirtoignore);
+     		}else if(filesindir[i].isDirectory() && filesindir[i].getName().indexOf(usersid)==0){
+     			addfiles(filesindir[i], zipoutputstream, attachedfiles);
      		}else{
      			if(filesindir[i].getName().indexOf(usersid)==0){
***************
*** 81,84 ****
      	}
      }
! 
  }
--- 84,105 ----
      	}
      }
!     
!     private void addfiles(File toadd, ZipOutputStream zipoutputstream, StringBuffer attachedfiles) throws IOException{
!     	System.err.println("add "+toadd);
!     	File[] filesindir=toadd.listFiles();
!     	for(int i=0;i<filesindir.length;i++){
!     		if(filesindir[i].isDirectory() && !filesindir[i].getName().equals(".") && !filesindir[i].getName().equals("..")){
!     			addfiles(filesindir[i],zipoutputstream,attachedfiles);
!     		}else{
!     				zipoutputstream.putNextEntry(new ZipEntry(filesindir[i].getName()));
!     				FileInputStream fis=new FileInputStream(filesindir[i]);
!     				int read=0;
!     				while((read=fis.read())!=-1){
!     					zipoutputstream.write(read);
!     				}
!     				attachedfiles.append(filesindir[i]+"; ");
!     				zipoutputstream.closeEntry();
!     		}
!     	}
!     }
  }

[Nmrshiftdb-devel] CVS: nmrshiftdb/src/java/org/openscience/nmrshiftdb/daemons AssignRobotDaemon.java, 1.2, 1.3

[Stefan K. <sh...@us...>]

Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/daemons
In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv4603/src/java/org/openscience/nmrshiftdb/daemons

Modified Files:
	AssignRobotDaemon.java 
Log Message:
fixes bug with robot file change


Index: AssignRobotDaemon.java
===================================================================
RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/daemons/AssignRobotDaemon.java,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -r1.2 -r1.3
*** AssignRobotDaemon.java	15 Sep 2006 09:38:11 -0000	1.2
--- AssignRobotDaemon.java	22 Sep 2006 08:22:15 -0000	1.3
***************
*** 41,45 ****
              	File rawfiledir=new File(GeneralUtils.getNmrshiftdbProperty("rawfiledirectoryrobot",servcon));
              	StringBuffer attachedfiles=new StringBuffer();
!             	searchfiles(rawfiledir,usersid,zipout,attachedfiles);
              	if(!attachedfiles.toString().equals("")){
              		zipout.close();
--- 41,45 ----
              	File rawfiledir=new File(GeneralUtils.getNmrshiftdbProperty("rawfiledirectoryrobot",servcon));
              	StringBuffer attachedfiles=new StringBuffer();
!             	searchfiles(rawfiledir,usersid,zipout,attachedfiles, new File(GeneralUtils.getNmrshiftdbProperty("compressedfiledirectory",servcon)));
              	if(!attachedfiles.toString().equals("")){
              		zipout.close();
***************
*** 62,70 ****
      }
      
!     private void searchfiles(File tolookin, String usersid, ZipOutputStream zipoutputstream, StringBuffer attachedfiles) throws IOException{
      	File[] filesindir=tolookin.listFiles();
      	for(int i=0;i<filesindir.length;i++){
!     		if(filesindir[i].isDirectory() && !filesindir[i].getName().equals(".") && !filesindir[i].getName().equals("..")){
!     			searchfiles(filesindir[i],usersid,zipoutputstream,attachedfiles);
      		}else{
      			if(filesindir[i].getName().indexOf(usersid)==0){
--- 62,70 ----
      }
      
!     private void searchfiles(File tolookin, String usersid, ZipOutputStream zipoutputstream, StringBuffer attachedfiles, File dirtoignore) throws IOException{
      	File[] filesindir=tolookin.listFiles();
      	for(int i=0;i<filesindir.length;i++){
!     		if(filesindir[i].isDirectory() && !filesindir[i].getName().equals(".") && !filesindir[i].getName().equals("..") && !filesindir[i].equals(dirtoignore)){
!     			searchfiles(filesindir[i],usersid,zipoutputstream,attachedfiles, dirtoignore);
      		}else{
      			if(filesindir[i].getName().indexOf(usersid)==0){

[Nmrshiftdb-devel] CVS: nmrshiftdb/src/java/org/apache/jetspeed/modules/actions CreateNewUserAndConfirm.java, 1.30, 1.31

[Stefan K. <sh...@us...>]

Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/apache/jetspeed/modules/actions
In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv4603/src/java/org/apache/jetspeed/modules/actions

Modified Files:
	CreateNewUserAndConfirm.java 
Log Message:
fixes bug with robot file change


Index: CreateNewUserAndConfirm.java
===================================================================
RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/apache/jetspeed/modules/actions/CreateNewUserAndConfirm.java,v
retrieving revision 1.30
retrieving revision 1.31
diff -C2 -r1.30 -r1.31
*** CreateNewUserAndConfirm.java	28 Aug 2006 14:33:57 -0000	1.30
--- CreateNewUserAndConfirm.java	22 Sep 2006 08:22:15 -0000	1.31
***************
*** 309,312 ****
--- 309,313 ----
            NmrshiftdbUserPeer.executeStatement(sql);
            if(data.getParameters().getString("labgroup")!=null && !data.getParameters().getString("labgroup").equals("-1")){
+         	  JetspeedSecurity.grant(user,JetspeedSecurity.getGroup("Jetspeed"),JetspeedSecurity.getRole("contributor"));
            if(data.getParameters().getString("groupmember").equals("coworker")){
              JetspeedSecurity.grant(user,JetspeedSecurity.getGroup("Jetspeed"),JetspeedSecurity.getRole("labgroup_worker")); 

[Nmrshiftdb-devel] CVS: nmrshiftdb CHANGELOG,1.114,1.115

[Stefan K. <sh...@us...>]

Update of /cvsroot/nmrshiftdb/nmrshiftdb
In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv7898

Modified Files:
	CHANGELOG 
Log Message:
delete only for open orders, design stuff


Index: CHANGELOG
===================================================================
RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/CHANGELOG,v
retrieving revision 1.114
retrieving revision 1.115
diff -C2 -r1.114 -r1.115
*** CHANGELOG	24 Aug 2006 12:00:20 -0000	1.114
--- CHANGELOG	21 Sep 2006 12:22:11 -0000	1.115
***************
*** 10,13 ****
--- 10,14 ----
  Fixes:
  * The CML export now contains Hs if exported with a proton spectrum
+ * Saving multiple bookmarks for the same molecule no longer gives an exception
  
  1.2.1 Release

[Nmrshiftdb-devel] CVS: nmrshiftdb/src/html using.html,1.47,1.48

[Stefan K. <sh...@us...>]

Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/html
In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv7898/src/html

Modified Files:
	using.html 
Log Message:
delete only for open orders, design stuff


Index: using.html
===================================================================
RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/using.html,v
retrieving revision 1.47
retrieving revision 1.48
diff -C2 -r1.47 -r1.48
*** using.html	15 Sep 2006 13:33:46 -0000	1.47
--- using.html	21 Sep 2006 12:22:11 -0000	1.48
***************
*** 736,742 ****
  >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.</LI
  ></UL
! ></P
  ><P
! >A 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
  ></DIV
  ></DIV
--- 736,743 ----
  >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.</LI
  ></UL
! >
! The user can delete orders which have not yet been processed.</P
  ><P
! >An operator, when logged in, also has the "NMR lab administration" tab. He sees a list of open orders. When clicking on one, he can assign raw data files to it and declare the order to be finished. It will then disappear from the list.</P
  ></DIV
  ></DIV

[Nmrshiftdb-devel] CVS: nmrshiftdb/src/java/org/openscience/nmrshiftdb/modules/actions/portlets OrderAction.java, 1.24, 1.25 OrderFullfillAction.java, 1.20, 1.21

[Stefan K. <sh...@us...>]

Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/modules/actions/portlets
In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv7898/src/java/org/openscience/nmrshiftdb/modules/actions/portlets

Modified Files:
	OrderAction.java OrderFullfillAction.java 
Log Message:
delete only for open orders, design stuff


Index: OrderAction.java
===================================================================
RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/modules/actions/portlets/OrderAction.java,v
retrieving revision 1.24
retrieving revision 1.25
diff -C2 -r1.24 -r1.25
*** OrderAction.java	20 Sep 2006 12:50:04 -0000	1.24
--- OrderAction.java	21 Sep 2006 12:22:11 -0000	1.25
***************
*** 84,88 ****
    private void buildOrderContext(Context context, RunData data) throws Exception{
  	//open worker orders
!     String sql="select SAMPLE.SAMPLE_ID from SAMPLE left join RAW_FILE using (SAMPLE_ID) where URL is null and PROCESS=\""+this.WORKER+"\" and USER_ID ="+((NmrshiftdbUser)data.getUser()).getUserId();
      Vector v1=DBSamplePeer.executeQuery(sql);
      Vector v2=new Vector();
--- 84,88 ----
    private void buildOrderContext(Context context, RunData data) throws Exception{
  	//open worker orders
!     String sql="select SAMPLE.SAMPLE_ID from SAMPLE left join RAW_FILE using (SAMPLE_ID) where URL is null and PROCESS=\""+this.WORKER+"\" and USER_ID ="+((NmrshiftdbUser)data.getUser()).getUserId()+" order by SAMPLE.DATE";
      Vector v1=DBSamplePeer.executeQuery(sql);
      Vector v2=new Vector();
***************
*** 96,99 ****
--- 96,100 ----
      crit.addJoin(DBSamplePeer.SAMPLE_ID,DBRawFilePeer.SAMPLE_ID);
      crit.setDistinct();
+     crit.addDescendingOrderByColumn(DBSamplePeer.DATE);
      Vector v=DBSamplePeer.doSelect(crit);
      Vector v3=new Vector();
***************
*** 106,110 ****
      context.put("samplesdone",v3);
      //open self orders
!     String sql3="select SAMPLE.SAMPLE_ID from SAMPLE left join RAW_FILE using (SAMPLE_ID) where URL is null and PROCESS=\""+this.SELF+"\" and USER_ID ="+((NmrshiftdbUser)data.getUser()).getUserId();
      Vector v5=DBSamplePeer.executeQuery(sql3);
      Vector v6=new Vector();
--- 107,111 ----
      context.put("samplesdone",v3);
      //open self orders
!     String sql3="select SAMPLE.SAMPLE_ID from SAMPLE left join RAW_FILE using (SAMPLE_ID) where URL is null and PROCESS=\""+this.SELF+"\" and USER_ID ="+((NmrshiftdbUser)data.getUser()).getUserId()+" order by SAMPLE.DATE";
      Vector v5=DBSamplePeer.executeQuery(sql3);
      Vector v6=new Vector();
***************
*** 114,118 ****
      context.put("samplesself",v6);
      //open robot orders
!     String sql4="select SAMPLE.SAMPLE_ID from SAMPLE left join RAW_FILE using (SAMPLE_ID) where URL is null and PROCESS=\""+this.ROBOT+"\" and USER_ID ="+((NmrshiftdbUser)data.getUser()).getUserId();
      Vector v7=DBSamplePeer.executeQuery(sql4);
      Vector v8=new Vector();
--- 115,119 ----
      context.put("samplesself",v6);
      //open robot orders
!     String sql4="select SAMPLE.SAMPLE_ID from SAMPLE left join RAW_FILE using (SAMPLE_ID) where URL is null and PROCESS=\""+this.ROBOT+"\" and USER_ID ="+((NmrshiftdbUser)data.getUser()).getUserId()+" order by SAMPLE.DATE";
      Vector v7=DBSamplePeer.executeQuery(sql4);
      Vector v8=new Vector();

Index: OrderFullfillAction.java
===================================================================
RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/modules/actions/portlets/OrderFullfillAction.java,v
retrieving revision 1.20
retrieving revision 1.21
diff -C2 -r1.20 -r1.21
*** OrderFullfillAction.java	20 Sep 2006 12:50:04 -0000	1.20
--- OrderFullfillAction.java	21 Sep 2006 12:22:11 -0000	1.21
***************
*** 59,62 ****
--- 59,63 ----
      crit.add(DBConditionPeer.CONDITION_TYPE_ID,"3");
      crit.add(DBConditionPeer.VALUE,"250");
+     crit.addDescendingOrderByColumn(DBSamplePeer.DATE);
      context.put("openorders250",DBSamplePeer.doSelect(crit));
      crit.add(DBConditionPeer.VALUE,"300");

[Nmrshiftdb-devel] CVS: nmrshiftdb/src/java/org/openscience/nmrshiftdb/om DBSample.java, 1.4, 1.5

[Stefan K. <sh...@us...>]

Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/om
In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv7898/src/java/org/openscience/nmrshiftdb/om

Modified Files:
	DBSample.java 
Log Message:
delete only for open orders, design stuff


Index: DBSample.java
===================================================================
RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/om/DBSample.java,v
retrieving revision 1.4
retrieving revision 1.5
diff -C2 -r1.4 -r1.5
*** DBSample.java	4 Aug 2005 21:55:20 -0000	1.4
--- DBSample.java	21 Sep 2006 12:22:12 -0000	1.5
***************
*** 3,7 ****
--- 3,10 ----
  
  // JDK classes
+ import java.util.Vector;
+ 
  import org.apache.turbine.om.Persistent;
+ import org.apache.turbine.util.db.Criteria;
  
  /** 
***************
*** 14,17 ****
--- 17,27 ----
      implements Persistent
  {
+ 	
+ 	public boolean isDeletable() throws Exception{
+ 		Criteria crit=new Criteria();
+ 		crit.add(DBRawFilePeer.SAMPLE_ID,this.getSampleId());
+ 		Vector v=DBRawFilePeer.doSelect(crit);
+ 		return v.size()==0;
+ 	}
  }
  

[Nmrshiftdb-devel] CVS: nmrshiftdb/src/vmtemplates/portlets/html user-order.vm, 1.36, 1.37 worker-order.vm, 1.16, 1.17

[Stefan K. <sh...@us...>]

Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/vmtemplates/portlets/html
In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv7898/src/vmtemplates/portlets/html

Modified Files:
	user-order.vm worker-order.vm 
Log Message:
delete only for open orders, design stuff


Index: user-order.vm
===================================================================
RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/vmtemplates/portlets/html/user-order.vm,v
retrieving revision 1.36
retrieving revision 1.37
diff -C2 -r1.36 -r1.37
*** user-order.vm	20 Sep 2006 12:50:04 -0000	1.36
--- user-order.vm	21 Sep 2006 12:22:12 -0000	1.37
***************
*** 1,10 ****
  #if($data.User.isLabgroupUser($data))
!   <table align="center">
!   	<tr><td><a href="portal/pane0/Help;jsessionid=$data.getSession().getId()?URL=using.html#labadmin" style="color:white"><img src="images/help.png"></a></td></tr>
      <tr>
!       <td>You have the following <b>open orders for labgroup operators</b>:</td><td width="50"></td><td>You have the following <b>open orders for self processing</b>:</td><td width="50"></td><td>You have the following <b>open orders for processing by sample changer</b>:</td><td width="50"></td><td>The following <b>orders have been (partly or fully) done</b> and wait for assignment:</td>
      </tr>
      <tr>
!       <td>
          #if($samples.size()==0)
            None
--- 1,10 ----
+ <a href="portal/pane0/Help;jsessionid=$data.getSession().getId()?URL=using.html#labadmin" style="color:white"><img src="images/help.png"></a>
  #if($data.User.isLabgroupUser($data))
!   <table align="center" border="3" rules="cols">
      <tr>
!       <td>You have the following <b>open orders for labgroup operators</b>:</td><td>You have the following <b>open orders for self processing</b>:</td><td>You have the following <b>open orders for processing by sample changer</b>:</td><td>The following <b>orders have been (partly or fully) done</b> and wait for assignment:</td>
      </tr>
      <tr>
!       <td align="left" valign="top">
          #if($samples.size()==0)
            None
***************
*** 22,27 ****
          #end
        </td>
!       <td width="50"></td>
!       <td>
          #if($samplesself.size()==0)
            None
--- 22,26 ----
          #end
        </td>
!       <td align="left" valign="top">
          #if($samplesself.size()==0)
            None
***************
*** 39,44 ****
          #end
        </td>
!       <td width="50"></td>
!       <td>
          #if($samplesrobot.size()==0)
            None
--- 38,42 ----
          #end
        </td>
!       <td align="left" valign="top">
          #if($samplesrobot.size()==0)
            None
***************
*** 56,61 ****
          #end
        </td>
!       <td width="50"></td>
!       <td>
          #if($samplesdone.size()==0)
            None
--- 54,58 ----
          #end
        </td>
!       <td align="left" valign="top">
          #if($samplesdone.size()==0)
            None
***************
*** 82,86 ****
            <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($ordertype=="worker") checked #end value="worker"> a lab worker <input type="radio" name="process" #if($ordertype=="self") checked #end value="self"> myself <input type="radio" name="process" #if($ordertype=="robot") checked #end value="robot"> myself via sample changer<br>
          #else
            <b>Order $sample.getUsersId()</b> has the following properties:
--- 79,83 ----
            <form name="orderform" method="post" action="portal/pane0/NMR+lab+administration">
            Here you can submit a <b>new order</b>:<br>
!           I want this order to be processed by <input type="radio" name="process" #if($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>
          #else
            <b>Order $sample.getUsersId()</b> has the following properties:
***************
*** 203,207 ****
            </form>
          #else
!           <form name="orderform" method="post" action="portal/pane0/NMR+lab+administration"><input type="hidden" name="id" value="$sample.getSampleId()"><input type="submit" name="eventSubmit_doDeleteorder" value="Delete order"/> Confirm deletion by checking <input type="checkbox" name="confirm" value="confirm"></form>
          #end
        </td>
--- 200,206 ----
            </form>
          #else
!           #if($sample.isDeletable())
! 	        <form name="orderform" method="post" action="portal/pane0/NMR+lab+administration"><input type="hidden" name="id" value="$sample.getSampleId()"><input type="submit" name="eventSubmit_doDeleteorder" value="Delete order"/> Confirm deletion by checking <input type="checkbox" name="confirm" value="confirm"></form>
! 	      #end
          #end
        </td>

Index: worker-order.vm
===================================================================
RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/vmtemplates/portlets/html/worker-order.vm,v
retrieving revision 1.16
retrieving revision 1.17
diff -C2 -r1.16 -r1.17
*** worker-order.vm	20 Sep 2006 11:35:47 -0000	1.16
--- worker-order.vm	21 Sep 2006 12:22:13 -0000	1.17
***************
*** 8,12 ****
          #else
            The following orders for your labgroup wait to be fullfilled:
!           <table><tr><td>
            <table>
            	<tr><th>250 MHz</th></tr>
--- 8,12 ----
          #else
            The following orders for your labgroup wait to be fullfilled:
!           <table border="3" rules="cols">><tr><td align="left" valign="top">
            <table>
            	<tr><th>250 MHz</th></tr>
***************
*** 19,23 ****
                ><td><a href="portal/pane0/NMR+lab+administration?submitorshow=show&id=$sample.getSampleId()">$sample.getUsersId()</a></td></tr>
              #end
!           </table></td><td>
            <table>
            	<tr><th>300 MHz</th></tr>
--- 19,23 ----
                ><td><a href="portal/pane0/NMR+lab+administration?submitorshow=show&id=$sample.getSampleId()">$sample.getUsersId()</a></td></tr>
              #end
!           </table></td><td align="left" valign="top">
            <table>
            	<tr><th>300 MHz</th></tr>
***************
*** 30,34 ****
                ><td><a href="portal/pane0/NMR+lab+administration?submitorshow=show&id=$sample.getSampleId()">$sample.getUsersId()</a></td></tr>
              #end
!           </table></td><td>
            <table>
            	<tr><th>400 MHz</th></tr>
--- 30,34 ----
                ><td><a href="portal/pane0/NMR+lab+administration?submitorshow=show&id=$sample.getSampleId()">$sample.getUsersId()</a></td></tr>
              #end
!           </table></td><td align="left" valign="top">
            <table>
            	<tr><th>400 MHz</th></tr>
***************
*** 41,45 ****
                ><td><a href="portal/pane0/NMR+lab+administration?submitorshow=show&id=$sample.getSampleId()">$sample.getUsersId()</a></td></tr>
              #end
!           </table></td><td>
            <table>
            	<tr><th>500 MHz</th></tr>
--- 41,45 ----
                ><td><a href="portal/pane0/NMR+lab+administration?submitorshow=show&id=$sample.getSampleId()">$sample.getUsersId()</a></td></tr>
              #end
!           </table></td><td align="left" valign="top">
            <table>
            	<tr><th>500 MHz</th></tr>
***************
*** 52,56 ****
                ><td><a href="portal/pane0/NMR+lab+administration?submitorshow=show&id=$sample.getSampleId()">$sample.getUsersId()</a></td></tr>
              #end
!           </table></td><td>
            <table>
            	<tr><th>600 MHz</th></tr>
--- 52,56 ----
                ><td><a href="portal/pane0/NMR+lab+administration?submitorshow=show&id=$sample.getSampleId()">$sample.getUsersId()</a></td></tr>
              #end
!           </table></td><td align="left" valign="top">
            <table>
            	<tr><th>600 MHz</th></tr>

[Nmrshiftdb-devel] CVS: nmrshiftdb/doc nmrshiftdbhelp.pdf, 1.65, 1.66 nmrshiftdbhelp.xml, 1.79, 1.80

[Stefan K. <sh...@us...>]

Update of /cvsroot/nmrshiftdb/nmrshiftdb/doc
In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv7898/doc

Modified Files:
	nmrshiftdbhelp.pdf nmrshiftdbhelp.xml 
Log Message:
delete only for open orders, design stuff


Index: nmrshiftdbhelp.pdf
===================================================================
RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/doc/nmrshiftdbhelp.pdf,v
retrieving revision 1.65
retrieving revision 1.66
diff -C2 -r1.65 -r1.66
Binary files /tmp/cvsaFpyYI and /tmp/cvszqXOkg differ

Index: nmrshiftdbhelp.xml
===================================================================
RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/doc/nmrshiftdbhelp.xml,v
retrieving revision 1.79
retrieving revision 1.80
diff -C2 -r1.79 -r1.80
*** nmrshiftdbhelp.xml	15 Sep 2006 13:33:46 -0000	1.79
--- nmrshiftdbhelp.xml	21 Sep 2006 12:22:11 -0000	1.80
***************
*** 289,294 ****
  <listitem>By the user himself: Here the user needs to do the measurement. When he clicks on the order on the open orders list, he can browse through the data files and attach them to the order. Once this is done, the procedure is the same as above.</listitem>
  <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></para>
! <para>A 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>
  </sect1>
--- 289,295 ----
  <listitem>By the user himself: Here the user needs to do the measurement. When he clicks on the order on the open orders list, he can browse through the data files and attach them to the order. Once this is done, the procedure is the same as above.</listitem>
  <listitem>By the user via a sample changer: Here the user needs to put his probe into the sample changer and it will be measured during the next night. The data files get attached automatically and the order goes to the fullfilled orders list.</listitem>
! </itemizedlist>
! The user can delete orders which have not yet been processed.</para>
! <para>An operator, when logged in, also has the "NMR lab administration" tab. He sees a list of open orders. When clicking on one, he can assign raw data files to it and declare the order to be finished. It will then disappear from the list.</para>
  </sect2>
  </sect1>

[Nmrshiftdb-devel] CVS: nmrshiftdb/src/java/org/openscience/nmrshiftdb/om DBBookmark.java, 1.2, 1.3 DBSpectrum.java, 1.187, 1.188

[Stefan K. <sh...@us...>]

Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/om
In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv16807/src/java/org/openscience/nmrshiftdb/om

Modified Files:
	DBBookmark.java DBSpectrum.java 
Log Message:
this avoids excpetion if multiple bookmarks for the same molecule are saved



Index: DBBookmark.java
===================================================================
RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/om/DBBookmark.java,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -r1.2 -r1.3
*** DBBookmark.java	4 Aug 2005 21:55:20 -0000	1.2
--- DBBookmark.java	21 Sep 2006 07:24:23 -0000	1.3
***************
*** 2,7 ****
--- 2,10 ----
  
  // JDK classes
+ import java.util.Vector;
+ 
  import org.apache.turbine.om.NumberKey;
  import org.apache.turbine.om.Persistent;
+ import org.apache.turbine.util.db.Criteria;
  
  /**
***************
*** 37,40 ****
--- 40,59 ----
      super();
    }
+   
+   /**
+    * Stores the object in the database.  If the object is new and not yet existing,
+    * it inserts it; otherwise an update is performed.
+    */
+   public void save() throws Exception{
+ 	  if(this.isNew()){
+ 	      Criteria criteria=new Criteria();
+ 	      criteria.add(DBBookmarkPeer.MOLECULE_ID, this.getMoleculeId());
+ 	      criteria.add(DBBookmarkPeer.USER_ID, this.getUserId());
+ 	      Vector v = DBBookmarkPeer.doSelect(criteria);
+ 	      if ( v.size() >0)
+ 	    	  return;
+ 	  }
+   	  super.save();
+   }
  }
  

Index: DBSpectrum.java
===================================================================
RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/om/DBSpectrum.java,v
retrieving revision 1.187
retrieving revision 1.188
diff -C2 -r1.187 -r1.188
*** DBSpectrum.java	12 Sep 2006 14:08:43 -0000	1.187
--- DBSpectrum.java	21 Sep 2006 07:24:23 -0000	1.188
***************
*** 913,916 ****
--- 913,919 ----
            peak.setPeakHeight(((DBSignal) signals.get(i)).getIntensity());
          }
+         if(!signal.getMultiplicity().equals("")){
+         	peak.setPeakMultiplicity(signal.getMultiplicity());
+         }
          peak.setId("p" + i);
          Vector atoms = signal.getAtoms();
***************
*** 924,929 ****
                CMLPeakStructure peakStructure=new CMLPeakStructure();
                peakStructure.setType("coupling");
!               peakStructure.setPeakMultiplicity(signal.getMultiplicity());
!         	  peakStructure.setAtomRefs(new String[]{((Record) l.get(m)).getValue(2).asInt()==((DBAtom) atoms.get(k)).getAtomId().getBigDecimal().intValue() ? "a"+DBAtomPeer.retrieveByPK(new NumberKey(((Record) l.get(m)).getValue(1).asInt())).getMdlNumberPlus1() : "a"+DBAtomPeer.retrieveByPK(new NumberKey(((Record) l.get(m)).getValue(2).asInt())).getMdlNumberPlus1()});
          	  peakStructure.setUnits("unit:hertz");
          	  peakStructure.setCMLValue(((Record) l.get(m)).getValue(3).asDouble()+"");
--- 927,931 ----
                CMLPeakStructure peakStructure=new CMLPeakStructure();
                peakStructure.setType("coupling");
!               peakStructure.setAtomRefs(new String[]{((Record) l.get(m)).getValue(2).asInt()==((DBAtom) atoms.get(k)).getAtomId().getBigDecimal().intValue() ? "a"+DBAtomPeer.retrieveByPK(new NumberKey(((Record) l.get(m)).getValue(1).asInt())).getMdlNumberPlus1() : "a"+DBAtomPeer.retrieveByPK(new NumberKey(((Record) l.get(m)).getValue(2).asInt())).getMdlNumberPlus1()});
          	  peakStructure.setUnits("unit:hertz");
          	  peakStructure.setCMLValue(((Record) l.get(m)).getValue(3).asDouble()+"");

[Nmrshiftdb-devel] CVS: nmrshiftdb/src/vmtemplates/portlets/html user-order.vm, 1.35, 1.36

[Stefan K. <sh...@us...>]

Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/vmtemplates/portlets/html
In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv4184/src/vmtemplates/portlets/html

Modified Files:
	user-order.vm 
Log Message:
multiple ids not possible


Index: user-order.vm
===================================================================
RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/vmtemplates/portlets/html/user-order.vm,v
retrieving revision 1.35
retrieving revision 1.36
diff -C2 -r1.35 -r1.36
*** user-order.vm	19 Sep 2006 14:28:56 -0000	1.35
--- user-order.vm	20 Sep 2006 12:50:04 -0000	1.36
***************
*** 176,185 ****
          #if($submitorshow=="submit")
            #foreach($type in $typesc)
!             $type <input type="checkbox" name="$type" value="$type"><br>
            #end
            </td>
            <td>
            #foreach($type in $typesh)
!             $type <input type="checkbox" name="$type" value="$type"><br>
            #end
          </td>
--- 176,185 ----
          #if($submitorshow=="submit")
            #foreach($type in $typesc)
!             $type <input type="checkbox" name="$type" value="$type" #if($nuclei.indexOf($type)>-1) checked #end><br>
            #end
            </td>
            <td>
            #foreach($type in $typesh)
!             $type <input type="checkbox" name="$type" value="$type" #if($nuclei.indexOf($type)>-1) checked #end><br>
            #end
          </td>

[Nmrshiftdb-devel] CVS: nmrshiftdb/src/java/org/openscience/nmrshiftdb/modules/actions/portlets OrderAction.java, 1.23, 1.24 OrderFullfillAction.java, 1.19, 1.20

[Stefan K. <sh...@us...>]

Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/modules/actions/portlets
In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv4184/src/java/org/openscience/nmrshiftdb/modules/actions/portlets

Modified Files:
	OrderAction.java OrderFullfillAction.java 
Log Message:
multiple ids not possible


Index: OrderAction.java
===================================================================
RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/modules/actions/portlets/OrderAction.java,v
retrieving revision 1.23
retrieving revision 1.24
diff -C2 -r1.23 -r1.24
*** OrderAction.java	20 Sep 2006 11:35:46 -0000	1.23
--- OrderAction.java	20 Sep 2006 12:50:04 -0000	1.24
***************
*** 265,288 ****
        }
        sample.setWishedSpectrum(wishedSpectrum);
        if(wishedSpectrum.equals("")){
          message+="You did not enter a spectrum type!";
!         context.put("ordertype",data.getParameters().get("process"));
!         context.put("usersid",data.getParameters().get("sampleid"));
!         context.put("solvent", solvent.getValue());
!         context.put("other",data.getParameters().get("othertext"));
!         context.put("othernuc",sample.getOtherNuclei());
!         context.put("care",sample.getSpecialCare());
!         if(mol!= null && mol.getAtomCount()>0){
! 	        //The mol is put into the MView applet via a file
! 	        File outputFile = new File(ServletUtils.expandRelative(data.getServletConfig(), "/nmrshiftdbhtml/" + System.currentTimeMillis() + "order.mol"));
! 	        FileWriter out = new FileWriter(outputFile);
! 	        out.write(sample.getDBMolecule().getStructureFile(1,false));
! 	        out.close();
! 	        context.put("molfile", "/nmrshiftdbhtml/" + outputFile.getName());
! 	        context.put("import","true");
!         }
        }else{
          sample.save();
        }
        context.put("message",message);
        buildOrderContext(context,data);
--- 265,296 ----
        }
        sample.setWishedSpectrum(wishedSpectrum);
+       Criteria crit2=new Criteria();
+       crit2.add(DBSamplePeer.USERS_ID,sample.getUsersId());
+       Vector oldsamples=DBSamplePeer.doSelect(crit2);
        if(wishedSpectrum.equals("")){
          message+="You did not enter a spectrum type!";
!       }else if(oldsamples.size()>0){
!     	  message+="Your id has already been used. Choose a different one!";
        }else{
          sample.save();
        }
+       if(!message.equals("")){
+           context.put("ordertype",data.getParameters().get("process"));
+           context.put("usersid",data.getParameters().get("sampleid"));
+           context.put("solvent", solvent.getValue());
+           context.put("other",data.getParameters().get("othertext"));
+           context.put("othernuc",sample.getOtherNuclei());
+           context.put("care",sample.getSpecialCare());
+           context.put("nuclei",wishedSpectrum);
+           if(mol!= null && mol.getAtomCount()>0){
+   	        //The mol is put into the MView applet via a file
+   	        File outputFile = new File(ServletUtils.expandRelative(data.getServletConfig(), "/nmrshiftdbhtml/" + System.currentTimeMillis() + "order.mol"));
+   	        FileWriter out = new FileWriter(outputFile);
+   	        out.write(sample.getDBMolecule().getStructureFile(1,false));
+   	        out.close();
+   	        context.put("molfile", "/nmrshiftdbhtml/" + outputFile.getName());
+   	        context.put("import","true");
+           }
+       }
        context.put("message",message);
        buildOrderContext(context,data);

Index: OrderFullfillAction.java
===================================================================
RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/modules/actions/portlets/OrderFullfillAction.java,v
retrieving revision 1.19
retrieving revision 1.20
diff -C2 -r1.19 -r1.20
*** OrderFullfillAction.java	20 Sep 2006 11:35:46 -0000	1.19
--- OrderFullfillAction.java	20 Sep 2006 12:50:04 -0000	1.20
***************
*** 140,144 ****
  	    		String sql="update TURBINE_USER set LABGROUP=0 where LOGIN_NAME='"+data.getParameters().getString("username")+"'";
  	    		BasePeer.executeStatement(sql);
! 	    		if(NmrshiftdbUserPeer.getByName(data.getParameters().getString("username")).getDBSpectrums().size()==0.){
  	            	User user = JetspeedSecurity.getUser(data.getParameters().getString("username"));
  	            	JetspeedSecurity.removeUser(user, data);
--- 140,144 ----
  	    		String sql="update TURBINE_USER set LABGROUP=0 where LOGIN_NAME='"+data.getParameters().getString("username")+"'";
  	    		BasePeer.executeStatement(sql);
! 	    		if(NmrshiftdbUserPeer.getByName(data.getParameters().getString("username")).getDBSpectrums().size()==0 && NmrshiftdbUserPeer.getByName(data.getParameters().getString("username")).getDBSamples().size()==0){
  	            	User user = JetspeedSecurity.getUser(data.getParameters().getString("username"));
  	            	JetspeedSecurity.removeUser(user, data);

[Nmrshiftdb-devel] CVS: nmrshiftdb/src/java/org/openscience/nmrshiftdb/modules/actions/portlets OrderAction.java, 1.22, 1.23 OrderFullfillAction.java, 1.18, 1.19

[Stefan K. <sh...@us...>]

Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/modules/actions/portlets
In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv3312/src/java/org/openscience/nmrshiftdb/modules/actions/portlets

Modified Files:
	OrderAction.java OrderFullfillAction.java 
Log Message:
admin can view and delete users from his labgroup


Index: OrderAction.java
===================================================================
RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/modules/actions/portlets/OrderAction.java,v
retrieving revision 1.22
retrieving revision 1.23
diff -C2 -r1.22 -r1.23
*** OrderAction.java	19 Sep 2006 14:28:56 -0000	1.22
--- OrderAction.java	20 Sep 2006 11:35:46 -0000	1.23
***************
*** 22,25 ****
--- 22,26 ----
  import org.openscience.nmrshiftdb.om.DBConditionPeer;
  import org.openscience.nmrshiftdb.om.DBRawFile;
+ import org.openscience.nmrshiftdb.om.DBRawFileDBSpectrumPeer;
  import org.openscience.nmrshiftdb.om.DBRawFilePeer;
  import org.openscience.nmrshiftdb.om.DBSample;
***************
*** 298,305 ****
--- 299,315 ----
          Criteria crit=new Criteria();
          crit.add(DBSamplePeer.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);
+             Criteria crit2=new Criteria();
+             crit2.add(DBRawFilePeer.RAW_FILE_ID,rf.getRawFileId());
+             DBRawFileDBSpectrumPeer.doDelete(crit);        	
+         }
+         DBRawFilePeer.doDelete(crit);
          DBSamplePeer.doDelete(crit);
          buildOrderContext(context,data);
        }
      }catch(Exception ex){
+     	ex.printStackTrace();
        GeneralUtils.logError(ex,"guestbook/doentry",data,true);
      }

Index: OrderFullfillAction.java
===================================================================
RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/modules/actions/portlets/OrderFullfillAction.java,v
retrieving revision 1.18
retrieving revision 1.19
diff -C2 -r1.18 -r1.19
*** OrderFullfillAction.java	15 Sep 2006 11:57:00 -0000	1.18
--- OrderFullfillAction.java	20 Sep 2006 11:35:46 -0000	1.19
***************
*** 11,15 ****
--- 11,18 ----
  import org.apache.jetspeed.modules.actions.portlets.VelocityPortletAction;
  import org.apache.jetspeed.portal.portlets.VelocityPortlet;
+ import org.apache.jetspeed.services.JetspeedSecurity;
  import org.apache.turbine.om.NumberKey;
+ import org.apache.turbine.om.peer.BasePeer;
+ import org.apache.turbine.om.security.User;
  import org.apache.turbine.util.RunData;
  import org.apache.turbine.util.db.Criteria;
***************
*** 132,135 ****
--- 135,155 ----
    }
    
+   public void doSubmitdelete(RunData data, Context context) throws Exception {
+ 	    try{
+ 	    	if(data.getParameters().getString("deleteconfirm").equals("true")){
+ 	    		String sql="update TURBINE_USER set LABGROUP=0 where LOGIN_NAME='"+data.getParameters().getString("username")+"'";
+ 	    		BasePeer.executeStatement(sql);
+ 	    		if(NmrshiftdbUserPeer.getByName(data.getParameters().getString("username")).getDBSpectrums().size()==0.){
+ 	            	User user = JetspeedSecurity.getUser(data.getParameters().getString("username"));
+ 	            	JetspeedSecurity.removeUser(user, data);
+ 	    		}
+ 			    buildOrderContext(context,data);
+ 	    	}
+ 	    }
+ 	    catch(Exception ex){
+ 	    	ex.printStackTrace();
+ 	      GeneralUtils.logError(ex,"guestbook/doentry",data,true);
+ 	    }
+ 	}
    
      /**

[Nmrshiftdb-devel] CVS: nmrshiftdb/src/java/org/openscience/nmrshiftdb/om DBLabGroup.java, 1.2, 1.3

[Stefan K. <sh...@us...>]

Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/om
In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv3312/src/java/org/openscience/nmrshiftdb/om

Modified Files:
	DBLabGroup.java 
Log Message:
admin can view and delete users from his labgroup


Index: DBLabGroup.java
===================================================================
RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/om/DBLabGroup.java,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -r1.2 -r1.3
*** DBLabGroup.java	4 Aug 2005 21:55:20 -0000	1.2
--- DBLabGroup.java	20 Sep 2006 11:35:47 -0000	1.3
***************
*** 4,7 ****
--- 4,10 ----
  // JDK classes
  import org.apache.turbine.om.Persistent;
+ import org.apache.turbine.util.db.Criteria;
+ 
+ import java.util.Vector;
  
  /** 
***************
*** 14,17 ****
--- 17,25 ----
      implements Persistent
  {
+ 	public Vector getMembers() throws Exception{
+ 		Criteria crit=new Criteria();
+ 		crit.add(NmrshiftdbUserPeer.LABGROUP,this.getLabgroupId());
+ 		return NmrshiftdbUserPeer.doSelect(crit);
+ 	}
  }
  

[Nmrshiftdb-devel] CVS: nmrshiftdb/src/vmtemplates/portlets/html worker-order.vm, 1.15, 1.16

[Stefan K. <sh...@us...>]

Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/vmtemplates/portlets/html
In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv3312/src/vmtemplates/portlets/html

Modified Files:
	worker-order.vm 
Log Message:
admin can view and delete users from his labgroup


Index: worker-order.vm
===================================================================
RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/vmtemplates/portlets/html/worker-order.vm,v
retrieving revision 1.15
retrieving revision 1.16
diff -C2 -r1.15 -r1.16
*** worker-order.vm	15 Sep 2006 13:33:46 -0000	1.15
--- worker-order.vm	20 Sep 2006 11:35:47 -0000	1.16
***************
*** 108,111 ****
--- 108,126 ----
      </tr>
    </table>
+   #if($data.User.getUserId()==$data.User.getDBLabGroup().getLeader())
+   	<br><br>
+   	Users in your labgroup
+   	<table>
+   	<tr><th>Username</th><th>First name</th><th>Last name</th><th colspan="">Check and click to delete user from labgroup</th></tr>
+   	#foreach($member in $data.User.getDBLabGroup().getMembers())
+   		<tr><td>$member.getUserName()</td><td>$member.getFirstName()</td><td>$member.getLastName()</td><td>
+   			<form name="deleteform$member.getUserName()" method="post" action="portal/pane0/NMR+lab+administration">
+   				<input type="checkbox" name="deleteconfirm" value="true">
+   				<input type="hidden" name="username" value="$member.getUserName()">
+   				<input type="submit" name="eventSubmit_doSubmitdelete" value="Delete this user"/>
+   			</form>
+   		</td></tr>
+   	#end
+   #end
  #else
    You are not an operator in any labgroup or not yet approved!

[Nmrshiftdb-devel] CVS: nmrshiftdb/src/vmtemplates/portlets/html user-order.vm, 1.34, 1.35

[Stefan K. <sh...@us...>]

Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/vmtemplates/portlets/html
In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv368/src/vmtemplates/portlets/html

Modified Files:
	user-order.vm 
Log Message:
improvements in lab system


Index: user-order.vm
===================================================================
RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/vmtemplates/portlets/html/user-order.vm,v
retrieving revision 1.34
retrieving revision 1.35
diff -C2 -r1.34 -r1.35
*** user-order.vm	15 Sep 2006 13:33:46 -0000	1.34
--- user-order.vm	19 Sep 2006 14:28:56 -0000	1.35
***************
*** 82,86 ****
            <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" checked value="worker"> a lab worker <input type="radio" name="process" value="self"> myself <input type="radio" name="process" value="robot"> myself via sample changer<br>
          #else
            <b>Order $sample.getUsersId()</b> has the following properties:
--- 82,86 ----
            <form name="orderform" method="post" action="portal/pane0/NMR+lab+administration">
            Here you can submit a <b>new order</b>:<br>
!           I want this order to be processed by <input type="radio" name="process" #if($ordertype=="worker") checked #end value="worker"> a lab worker <input type="radio" name="process" #if($ordertype=="self") checked #end value="self"> myself <input type="radio" name="process" #if($ordertype=="robot") checked #end value="robot"> myself via sample changer<br>
          #else
            <b>Order $sample.getUsersId()</b> has the following properties:
***************
*** 88,97 ****
          Name: $data.getUser().getFirstName() $data.getUser().getLastName()<br>
          Workgroup: $data.getUser().getAffiliation()<br>
!         Sample I. D.: #if($submitorshow=="submit")<input name="sampleid" type="text" size="30">#else $sample.getUsersId() #end <br>
          Date: $date<br>
          <br>
          Solvent 
          #if($submitorshow=="submit")
!           (enter or choose): <input type="text" name="solvent" size="15">
                      <select name="solvents" size="1" onChange="document.restform.elements['solvent'].value=''">
                      #foreach($existingcondition in $solvents)
--- 88,97 ----
          Name: $data.getUser().getFirstName() $data.getUser().getLastName()<br>
          Workgroup: $data.getUser().getAffiliation()<br>
!         Sample I. D.: #if($submitorshow=="submit")<input name="sampleid" type="text" size="30" value="$!usersid">#else $sample.getUsersId() #end <br>
          Date: $date<br>
          <br>
          Solvent 
          #if($submitorshow=="submit")
!           (enter or choose): <input type="text" name="solvent" size="15" value="$!solvent">
                      <select name="solvents" size="1" onChange="document.restform.elements['solvent'].value=''">
                      #foreach($existingcondition in $solvents)
***************
*** 163,167 ****
            : <select name="fstrengths" size="1" onChange="document.restform.elements['fstrength'].value=''">
            #foreach($existingcondition in $fstrengths)
!             <option value="$existingcondition.getConditionId()">$existingcondition.getValue()</option>
            #end
            </select>
--- 163,167 ----
            : <select name="fstrengths" size="1" onChange="document.restform.elements['fstrength'].value=''">
            #foreach($existingcondition in $fstrengths)
!             <option value="$existingcondition.getConditionId()" #if($strength==$existingcondition.getValue()) selected #end>$existingcondition.getValue()</option>
            #end
            </select>
***************
*** 185,189 ****
          </td>
        </tr>
!       <tr><td>other<input name="othertext" type="text" size="30"></td>
          #else
            $sample.getWishedSpectrum()
--- 185,189 ----
          </td>
        </tr>
!       <tr><td>other<input name="othertext" type="text" size="30" value="$!other"></td>
          #else
            $sample.getWishedSpectrum()
***************
*** 193,198 ****
      <tr>
        <td colspan="2">
!         Other nuclei (please specify): #if($submitorshow=="submit") <input name="othernuc" type="text" size="30"> #else $sample.getOtherNuclei() #end <br>
!         Special care for sample: #if($submitorshow=="submit") <input name="specialcare" type="text" size="30"> #else $sample.getSpecialCare() #end <br>
          #foreach($sample in $sample.getDBRawFiles())
            <a href="$sample.getUrl()">Download the raw NMR file here</a>
--- 193,198 ----
      <tr>
        <td colspan="2">
!         Other nuclei (please specify): #if($submitorshow=="submit") <input name="othernuc" type="text" size="30" value="$!othernuc"> #else $sample.getOtherNuclei() #end <br>
!         Special care for sample: #if($submitorshow=="submit") <input name="specialcare" type="text" size="30" value="$!care"> #else $sample.getSpecialCare() #end <br>
          #foreach($sample in $sample.getDBRawFiles())
            <a href="$sample.getUrl()">Download the raw NMR file here</a>

[Nmrshiftdb-devel] CVS: nmrshiftdb/src/java/org/openscience/nmrshiftdb/modules/actions/portlets OrderAction.java, 1.21, 1.22

[Stefan K. <sh...@us...>]

Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/modules/actions/portlets
In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv368/src/java/org/openscience/nmrshiftdb/modules/actions/portlets

Modified Files:
	OrderAction.java 
Log Message:
improvements in lab system


Index: OrderAction.java
===================================================================
RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/modules/actions/portlets/OrderAction.java,v
retrieving revision 1.21
retrieving revision 1.22
diff -C2 -r1.21 -r1.22
*** OrderAction.java	15 Sep 2006 11:57:00 -0000	1.21
--- OrderAction.java	19 Sep 2006 14:28:56 -0000	1.22
***************
*** 72,76 ****
  	protected void buildNormalContext(VelocityPortlet portlet, Context context, RunData data) {
      try{
!       buildOrderContext(context,data);
      }
      catch(Exception ex){
--- 72,77 ----
  	protected void buildNormalContext(VelocityPortlet portlet, Context context, RunData data) {
      try{
!     	context.put("ordertype",this.WORKER);
!     	buildOrderContext(context,data);
      }
      catch(Exception ex){
***************
*** 240,244 ****
        String molecule = data.getParameters().get("MolTxt");
        Molecule mol = (Molecule) new MDLReader(new StringReader(molecule)).read(new Molecule());
!       if(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()));
--- 241,245 ----
        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()));
***************
*** 265,268 ****
--- 266,284 ----
        if(wishedSpectrum.equals("")){
          message+="You did not enter a spectrum type!";
+         context.put("ordertype",data.getParameters().get("process"));
+         context.put("usersid",data.getParameters().get("sampleid"));
+         context.put("solvent", solvent.getValue());
+         context.put("other",data.getParameters().get("othertext"));
+         context.put("othernuc",sample.getOtherNuclei());
+         context.put("care",sample.getSpecialCare());
+         if(mol!= null && mol.getAtomCount()>0){
+ 	        //The mol is put into the MView applet via a file
+ 	        File outputFile = new File(ServletUtils.expandRelative(data.getServletConfig(), "/nmrshiftdbhtml/" + System.currentTimeMillis() + "order.mol"));
+ 	        FileWriter out = new FileWriter(outputFile);
+ 	        out.write(sample.getDBMolecule().getStructureFile(1,false));
+ 	        out.close();
+ 	        context.put("molfile", "/nmrshiftdbhtml/" + outputFile.getName());
+ 	        context.put("import","true");
+         }
        }else{
          sample.save();

[Nmrshiftdb-devel] CVS: nmrshiftdb/src/conf/jetspeed/WEB-INF/templates/vm/screens/html NewAccount.vm, 1.13, 1.14

[Stefan K. <sh...@us...>]

Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/conf/jetspeed/WEB-INF/templates/vm/screens/html
In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv2187/src/conf/jetspeed/WEB-INF/templates/vm/screens/html

Modified Files:
	NewAccount.vm 
Log Message:
better to use new user form


Index: NewAccount.vm
===================================================================
RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/conf/jetspeed/WEB-INF/templates/vm/screens/html/NewAccount.vm,v
retrieving revision 1.13
retrieving revision 1.14
diff -C2 -r1.13 -r1.14
*** NewAccount.vm	15 Sep 2006 13:33:46 -0000	1.13
--- NewAccount.vm	15 Sep 2006 14:06:40 -0000	1.14
***************
*** 44,48 ****
              <td align=right><input name="firstname" type="TEXT" value="$!data.Parameters.getString("firstname")" /> </td> 
            </tr>
!           <tr>
              <td> $l10n.USERFORM_LASTNAMEMSG </td>
              <td align=right><input name="lastname" type="TEXT" value="$!data.Parameters.getString("lastname")" /> </td>
--- 44,48 ----
              <td align=right><input name="firstname" type="TEXT" value="$!data.Parameters.getString("firstname")" /> </td> 
            </tr>
!           <tr bgcolor="#F8F8F8">
              <td> $l10n.USERFORM_LASTNAMEMSG </td>
              <td align=right><input name="lastname" type="TEXT" value="$!data.Parameters.getString("lastname")" /> </td>
***************
*** 52,56 ****
              <td align=right><input name="title" type="TEXT" value="$!data.Parameters.getString("title")" /> </td>
            </tr>
! 	  <tr>
              <td> Address: </td>
              <td align=right><input name="address" type="TEXT" value="$!data.Parameters.getString("address")" /> </td>
--- 52,56 ----
              <td align=right><input name="title" type="TEXT" value="$!data.Parameters.getString("title")" /> </td>
            </tr>
! 	  <tr bgcolor="#F8F8F8">
              <td> Address: </td>
              <td align=right><input name="address" type="TEXT" value="$!data.Parameters.getString("address")" /> </td>
***************
*** 60,64 ****
              <td align=right><input name="city" type="TEXT" value="$!data.Parameters.getString("city")" /> </td>
            </tr>
! 	  <tr>
              <td> State: </td>
              <td align=right><input name="state" type="TEXT" value="$!data.Parameters.getString("state")" /> </td>
--- 60,64 ----
              <td align=right><input name="city" type="TEXT" value="$!data.Parameters.getString("city")" /> </td>
            </tr>
! 	  <tr bgcolor="#F8F8F8">
              <td> State: </td>
              <td align=right><input name="state" type="TEXT" value="$!data.Parameters.getString("state")" /> </td>
***************
*** 68,72 ****
              <td align=right><input name="zipcode" type="TEXT" value="$!data.Parameters.getString("zipcode")" /> </td>
            </tr>
! 	  <tr>
              <td> Country: </td>
              <td align=right><input name="country" type="TEXT" value="$!data.Parameters.getString("country")" /> </td>
--- 68,72 ----
              <td align=right><input name="zipcode" type="TEXT" value="$!data.Parameters.getString("zipcode")" /> </td>
            </tr>
! 	  <tr bgcolor="#F8F8F8">
              <td> Country: </td>
              <td align=right><input name="country" type="TEXT" value="$!data.Parameters.getString("country")" /> </td>
***************
*** 76,80 ****
              <td align=right><input name="email" type="TEXT" value="$!data.Parameters.getString("email")" /> </td>
            </tr>
! 	  <tr>
              <td> Web Page: </td>
              <td align=right><input name="webpage" type="TEXT" value="$!data.Parameters.getString("webpage")" /> </td>
--- 76,80 ----
              <td align=right><input name="email" type="TEXT" value="$!data.Parameters.getString("email")" /> </td>
            </tr>
! 	  <tr bgcolor="#F8F8F8">
              <td> Web Page: </td>
              <td align=right><input name="webpage" type="TEXT" value="$!data.Parameters.getString("webpage")" /> </td>
***************
*** 84,88 ****
              <td align=right><input name="affiliation" type="TEXT" value="$!data.Parameters.getString("affiliation")" /> </td>
            </tr>
! 	  <tr>
              <td> I want to become a contributor </td>
              <td align=right><input name="contributor" type="checkbox" value="contributor" checked> </td>
--- 84,88 ----
              <td align=right><input name="affiliation" type="TEXT" value="$!data.Parameters.getString("affiliation")" /> </td>
            </tr>
! 	  <tr bgcolor="#F8F8F8">
              <td> I want to become a contributor </td>
              <td align=right><input name="contributor" type="checkbox" value="contributor" checked> </td>
***************
*** 92,96 ****
              <td align=right><input name="realname" type="checkbox" value="realname" checked> </td>
            </tr>
!           <tr>
              <td> I want to become a member of the following lab group, meaning I am either working there or want my compounds<br>
              to be measured there (use this only if you have spoken to a group leader of an actual NMRShiftDB lab group,<br>
--- 92,96 ----
              <td align=right><input name="realname" type="checkbox" value="realname" checked> </td>
            </tr>
!           <tr bgcolor="#F8F8F8">
              <td> I want to become a member of the following lab group, meaning I am either working there or want my compounds<br>
              to be measured there (use this only if you have spoken to a group leader of an actual NMRShiftDB lab group,<br>
***************
*** 103,107 ****
              </select> </td>
            </tr>
!           <tr>
              <td colspan=2> I am an <input type="radio" name="groupmember" value="coworker">operator in this lab group or <input type="radio" name="groupmember" value="user" checked>want to get my compounds measured there.</td>
            </tr>          
--- 103,107 ----
              </select> </td>
            </tr>
!           <tr bgcolor="#F8F8F8">
              <td colspan=2> I am an <input type="radio" name="groupmember" value="coworker">operator in this lab group or <input type="radio" name="groupmember" value="user" checked>want to get my compounds measured there.</td>
            </tr>          

[Nmrshiftdb-devel] CVS: nmrshiftdb/src/html using.html,1.46,1.47

[Stefan K. <sh...@us...>]

Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/html
In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv21180/src/html

Modified Files:
	using.html 
Log Message:
corrected typos


Index: using.html
===================================================================
RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/using.html,v
retrieving revision 1.46
retrieving revision 1.47
diff -C2 -r1.46 -r1.47
*** using.html	12 Sep 2006 08:56:24 -0000	1.46
--- using.html	15 Sep 2006 13:33:46 -0000	1.47
***************
*** 502,506 ****
  >After submitting the signals, you will see an additional area for submitting the assignments. Here you have got one line per atom, showing a drop-down box for the shifts and the expected range for the shift. These predictions are calculated based on HOSE codes, as in the prediction function. Additionally there is a range for the signal given. In some rare cases the predicted value will be identical with one of the limits of the range. Blue figures indicate that your value is inside this range, red means outside. Choose a shift for every atom. The atoms are identified by the figures and will be marked when you go over a line. If you have chosen a literature for entering identifiers, you can enter these here or they are displayed in case somebody else already entered identifiers for this literature and this molecule. Shifts not assigned will be lost - this is also a way to get rid of mistyped shifts. After you assigned all signals, press the "Submit assignments" button. If you forgot to submit a signal, you can just put that in the signals box and submit this. It will be added to the signals you can choose for the atoms.</P
  ><P
! >You then need to enter the additional data. Please choose first if the spectrum is measured or calculated. Then enter the chemical names, any links to web-literature about the molecule and the CASNumber and autonom name of the molecule, if known (you do not need to do that if the molecule is already in the database). From time to time IUPAC and index names for molecules in NMRShiftDB will be autor-created, so you do not need to enter them. You can also enter literature and web pages about the spectrum. Further more, you can give keywords for the molecule and categories for the spectrum - either existing ones or new ones. Molecule keywords should be compund-specific, e. g. alcaloids. The spectrum categories, on the other hand, should refer to the spectrum, e. g. a certain institution they have been measured at. Here you can also enter multiplicities for atoms (except for proton spectra, the default is calculated by the proton count of an atom) and coupling constants for every atom-atom combination.</P
  ><P
  >NMRShiftDB stores both experimental and calculated NMR spectra together 
--- 502,506 ----
  >After submitting the signals, you will see an additional area for submitting the assignments. Here you have got one line per atom, showing a drop-down box for the shifts and the expected range for the shift. These predictions are calculated based on HOSE codes, as in the prediction function. Additionally there is a range for the signal given. In some rare cases the predicted value will be identical with one of the limits of the range. Blue figures indicate that your value is inside this range, red means outside. Choose a shift for every atom. The atoms are identified by the figures and will be marked when you go over a line. If you have chosen a literature for entering identifiers, you can enter these here or they are displayed in case somebody else already entered identifiers for this literature and this molecule. Shifts not assigned will be lost - this is also a way to get rid of mistyped shifts. After you assigned all signals, press the "Submit assignments" button. If you forgot to submit a signal, you can just put that in the signals box and submit this. It will be added to the signals you can choose for the atoms.</P
  ><P
! >You then need to enter the additional data. Please choose first if the spectrum is measured or calculated. Then enter the chemical names, any links to web-literature about the molecule and the CASNumber and autonom name of the molecule, if known (you do not need to do that if the molecule is already in the database). From time to time IUPAC and index names for molecules in NMRShiftDB will be auto-created, so you do not need to enter them. You can also enter literature and web pages about the spectrum. Further more, you can give keywords for the molecule and categories for the spectrum - either existing ones or new ones. Molecule keywords should be compund-specific, e. g. alcaloids. The spectrum categories, on the other hand, should refer to the spectrum, e. g. a certain institution they have been measured at. Here you can also enter multiplicities for atoms (except for proton spectra, the default is calculated by the proton count of an atom) and coupling constants for every atom-atom combination.</P
  ><P
  >NMRShiftDB stores both experimental and calculated NMR spectra together 
***************
*** 515,519 ****
  of the chemical element type for which the experiment has been performed.</P
  ><P
! >While physicist use the SI unit "Tesla" as the correct unit for magnet 
  strength, NMR spectroscopists traditionally use the resonance frequency 
  of protons, which depends on the magnet strength, to denominate the 
--- 515,519 ----
  of the chemical element type for which the experiment has been performed.</P
  ><P
! >While physicists use the SI unit "Tesla" as the correct unit for magnet 
  strength, NMR spectroscopists traditionally use the resonance frequency 
  of protons, which depends on the magnet strength, to denominate the 
***************
*** 532,536 ****
  ><LI
  ><P
! >Field Strenght [MHz] (example value: 500)</P
  ></LI
  ><LI
--- 532,536 ----
  ><LI
  ><P
! >Field Strength [MHz] (example value: 500)</P
  ></LI
  ><LI
***************
*** 629,633 ****
  >After inserting all data, click the "Submit for database" button.</P
  ><P
! >You will then be presented with your data check their validity and press the appropriate button. You can also view and download the molecule and/or spectrum you entered in various formats, e. g. pdf, rtf or jpeg. Choose a format and click the button "Request" for that.  Your data will not be available immediately, but after they have been confirmed by a reviewer (you will get an email telling you who is your reviewer). To check the status of your contributions, use the "Show all my contributions" link on the Search pane. If for some reasons your submit is interrupted, you can continue that when you log in next time. You will see a blue box on top of the submit page where you can choose to continue or to discard the broken submit. If you get the message "There was delay ..." after you submitted the spectrum, this simply means you spectrum will be added later. You will be informed about this by email and you should not enter the same spectrum again.</P
  ><P
  >If you are logged in, you can edit molecules you have entered. In the details portlet, you will see a button "Edit this spectrum". If you click this, you can follow the submit procedure and change anything you like. The changes need to be approved by the reviewer of the original spectrum.</P
--- 629,633 ----
  >After inserting all data, click the "Submit for database" button.</P
  ><P
! >You will then be presented with your data: check their validity and press the appropriate button. You can also view and download the molecule and/or spectrum you entered in various formats, e. g. pdf, rtf or jpeg. Choose a format and click the button "Request" for that.  Your data will not be available immediately, but after they have been confirmed by a reviewer (you will get an email telling you who is your reviewer). To check the status of your contributions, use the "Show all my contributions" link on the Search pane. If for some reasons your submit is interrupted, you can continue that when you log in next time. You will see a blue box on top of the submit page where you can choose to continue or to discard the broken submit. If you get the message "There was delay ..." after you submitted the spectrum, this simply means your spectrum will be added later. You will be informed about this by email and you should not enter the same spectrum again.</P
  ><P
  >If you are logged in, you can edit molecules you have entered. In the details portlet, you will see a button "Edit this spectrum". If you click this, you can follow the submit procedure and change anything you like. The changes need to be approved by the reviewer of the original spectrum.</P
***************
*** 683,687 ****
  ></H2
  ><P
! >In the guestbook, our visitors can leave informal comments. The wishlist is a facility to request spectra. For requesting a specctrum, enter the structure (about entering molecules see <A
  HREF="using.html#submit"
  >Submitting Spectra</A
--- 683,687 ----
  ></H2
  ><P
! >In the guestbook, our visitors can leave informal comments. The wishlist is a facility to request spectra. For requesting a spectrum, enter the structure (about entering molecules see <A
  HREF="using.html#submit"
  >Submitting Spectra</A
***************
*** 708,714 ****
  ></H2
  ><P
! >NMRShiftdb automatically collects the last 20 structures you painted in search by structure, predict or submit. You can load one of theses structeres at any time by clicking the "Import from structures history" button next to a sketcher. You get a window where you can choose a structure. Clicking "Import" imports this and closes the import window.</P
  ><P
! >The collection of structures is session-based, which means that structures are lost if you log in, log out or close the browser window. This is not true for registered and logged in users - they will find their old structures history if they log in againg.</P
  ></DIV
  ><DIV
--- 708,714 ----
  ></H2
  ><P
! >NMRShiftdb automatically collects the last 20 structures you painted in search by structure, predict or submit. You can load one of these structeres at any time by clicking the "Import from structures history" button next to a sketcher. You get a window where you can choose a structure. Clicking "Import" imports this and closes the import window.</P
  ><P
! >The collection of stcructures is session-based, which means that structures are lost if you log in, log out or close the browser window. This is not true for registered and logged in users - they will find their old structures history if they log in again.</P
  ></DIV
  ><DIV
***************
*** 721,727 ****
  ></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, coworker and user, and the concept of an order.</P
  ><P
! >Users can assign themself membership of a labgroup, either as coworker or user. They need to be approved by the group leader. Once this is done, a user can submit orders and a coworker can work on them.</P
  ><P
  >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:
--- 721,727 ----
  ></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
  ><P
  >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:
***************
*** 730,742 ****
  ><UL
  ><LI
! >By an operator: This means a lab operator will handle the order. After the submit, this will show up in the list of open orders. If a coworker has dealt with this, it goes to the fullfilled orders list. The user can click on a fullfilled order and can download the raw data files then. He can also start an assignment of peaks here, which is done via the normal NRMShiftDB input.</LI
  ><LI
! >By the user himself: Here the user needs to do the measurement. When he clicks on the order on the open orders list, he can browse through the data files and attach them to the order. Once this is done, the procdure is the same as above.</LI
  ><LI
! >By the user via a robot: Here the user needs to put his probe into the robot and it will be measured during the next night. The data files get attached automatically and the order goes to the fullfilled orders lis.</LI
  ></UL
  ></P
  ><P
! >A coworker, when logged in, also has teh "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
  ></DIV
  ></DIV
--- 730,742 ----
  ><UL
  ><LI
! >By an operator: This means a lab operator will handle the order. After the submission, it will show up in the list of open orders. If a operator has dealt with this, it goes to the fullfilled orders list. The user can click on a fullfilled order and can download the raw data files then. He can also start an assignment of peaks here, which is done via the normal NRMShiftDB input.</LI
  ><LI
! >By the user himself: Here the user needs to do the measurement. When he clicks on the order on the open orders list, he can browse through the data files and attach them to the order. Once this is done, the procedure is the same as above.</LI
  ><LI
! >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.</LI
  ></UL
  ></P
  ><P
! >A 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
  ></DIV
  ></DIV

[Nmrshiftdb-devel] CVS: nmrshiftdb/doc nmrshiftdbhelp.pdf, 1.64, 1.65 nmrshiftdbhelp.xml, 1.78, 1.79

[Stefan K. <sh...@us...>]

Update of /cvsroot/nmrshiftdb/nmrshiftdb/doc
In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv21180/doc

Modified Files:
	nmrshiftdbhelp.pdf nmrshiftdbhelp.xml 
Log Message:
corrected typos


Index: nmrshiftdbhelp.pdf
===================================================================
RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/doc/nmrshiftdbhelp.pdf,v
retrieving revision 1.64
retrieving revision 1.65
diff -C2 -r1.64 -r1.65
Binary files /tmp/cvsXBKAbH and /tmp/cvsaxO1oE differ

Index: nmrshiftdbhelp.xml
===================================================================
RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/doc/nmrshiftdbhelp.xml,v
retrieving revision 1.78
retrieving revision 1.79
diff -C2 -r1.78 -r1.79
*** nmrshiftdbhelp.xml	12 Sep 2006 08:56:24 -0000	1.78
--- nmrshiftdbhelp.xml	15 Sep 2006 13:33:46 -0000	1.79
***************
*** 189,193 ****
  <para>Here you also need to choose the spectrum type.</para>
  <para>After submitting the signals, you will see an additional area for submitting the assignments. Here you have got one line per atom, showing a drop-down box for the shifts and the expected range for the shift. These predictions are calculated based on HOSE codes, as in the prediction function. Additionally there is a range for the signal given. In some rare cases the predicted value will be identical with one of the limits of the range. Blue figures indicate that your value is inside this range, red means outside. Choose a shift for every atom. The atoms are identified by the figures and will be marked when you go over a line. If you have chosen a literature for entering identifiers, you can enter these here or they are displayed in case somebody else already entered identifiers for this literature and this molecule. Shifts not assigned will be lost - this is also a way to get rid of mistyped shifts. After you assigned all signals, press the "Submit assignments" button. If you forgot to submit a signal, you can just put that in the signals box and submit this. It will be added to the signals you can choose for the atoms.</para>
! <para>You then need to enter the additional data. Please choose first if the spectrum is measured or calculated. Then enter the chemical names, any links to web-literature about the molecule and the CASNumber and autonom name of the molecule, if known (you do not need to do that if the molecule is already in the database). From time to time IUPAC and index names for molecules in NMRShiftDB will be autor-created, so you do not need to enter them. You can also enter literature and web pages about the spectrum. Further more, you can give keywords for the molecule and categories for the spectrum - either existing ones or new ones. Molecule keywords should be compund-specific, e. g. alcaloids. The spectrum categories, on the other hand, should refer to the spectrum, e. g. a certain institution they have been measured at. Here you can also enter multiplicities for atoms (except for proton spectra, the default is calculated by the proton count of an atom) and coupling constants for every atom-atom combination.</para>
  <para>NMRShiftDB stores both experimental and calculated NMR spectra together 
  with their associated molecular structures. The experimental spectra are 
--- 189,193 ----
  <para>Here you also need to choose the spectrum type.</para>
  <para>After submitting the signals, you will see an additional area for submitting the assignments. Here you have got one line per atom, showing a drop-down box for the shifts and the expected range for the shift. These predictions are calculated based on HOSE codes, as in the prediction function. Additionally there is a range for the signal given. In some rare cases the predicted value will be identical with one of the limits of the range. Blue figures indicate that your value is inside this range, red means outside. Choose a shift for every atom. The atoms are identified by the figures and will be marked when you go over a line. If you have chosen a literature for entering identifiers, you can enter these here or they are displayed in case somebody else already entered identifiers for this literature and this molecule. Shifts not assigned will be lost - this is also a way to get rid of mistyped shifts. After you assigned all signals, press the "Submit assignments" button. If you forgot to submit a signal, you can just put that in the signals box and submit this. It will be added to the signals you can choose for the atoms.</para>
! <para>You then need to enter the additional data. Please choose first if the spectrum is measured or calculated. Then enter the chemical names, any links to web-literature about the molecule and the CASNumber and autonom name of the molecule, if known (you do not need to do that if the molecule is already in the database). From time to time IUPAC and index names for molecules in NMRShiftDB will be auto-created, so you do not need to enter them. You can also enter literature and web pages about the spectrum. Further more, you can give keywords for the molecule and categories for the spectrum - either existing ones or new ones. Molecule keywords should be compund-specific, e. g. alcaloids. The spectrum categories, on the other hand, should refer to the spectrum, e. g. a certain institution they have been measured at. Here you can also enter multiplicities for atoms (except for proton spectra, the default is calculated by the proton count of an atom) and coupling constants for every atom-atom combination.</para>
  <para>NMRShiftDB stores both experimental and calculated NMR spectra together 
  with their associated molecular structures. The experimental spectra are 
***************
*** 200,204 ****
  collection of signals at a particular radio frequency, one for each atom 
  of the chemical element type for which the experiment has been performed.</para>
! <para>While physicist use the SI unit "Tesla" as the correct unit for magnet 
  strength, NMR spectroscopists traditionally use the resonance frequency 
  of protons, which depends on the magnet strength, to denominate the 
--- 200,204 ----
  collection of signals at a particular radio frequency, one for each atom 
  of the chemical element type for which the experiment has been performed.</para>
! <para>While physicists use the SI unit "Tesla" as the correct unit for magnet 
  strength, NMR spectroscopists traditionally use the resonance frequency 
  of protons, which depends on the magnet strength, to denominate the 
***************
*** 208,212 ****
  conditions under which a spectrum has been recorded are:</para>
  <itemizedlist><listitem><para>Temperature [K] (example value: 298)</para></listitem>
! <listitem><para>Field Strenght [MHz] (example value: 500)</para></listitem>
  <listitem><para>Solvent (example value: CDCl3)</para></listitem>
  <listitem><para>Assignment method (example value: longrange Hetcor)</para></listitem>
--- 208,212 ----
  conditions under which a spectrum has been recorded are:</para>
  <itemizedlist><listitem><para>Temperature [K] (example value: 298)</para></listitem>
! <listitem><para>Field Strength [MHz] (example value: 500)</para></listitem>
  <listitem><para>Solvent (example value: CDCl3)</para></listitem>
  <listitem><para>Assignment method (example value: longrange Hetcor)</para></listitem>
***************
*** 259,263 ****
  actualy compound in question.</para></listitem></itemizedlist>
  <para>After inserting all data, click the "Submit for database" button.</para>
! <para>You will then be presented with your data check their validity and press the appropriate button. You can also view and download the molecule and/or spectrum you entered in various formats, e. g. pdf, rtf or jpeg. Choose a format and click the button "Request" for that.  Your data will not be available immediately, but after they have been confirmed by a reviewer (you will get an email telling you who is your reviewer). To check the status of your contributions, use the "Show all my contributions" link on the Search pane. If for some reasons your submit is interrupted, you can continue that when you log in next time. You will see a blue box on top of the submit page where you can choose to continue or to discard the broken submit. If you get the message "There was delay ..." after you submitted the spectrum, this simply means you spectrum will be added later. You will be informed about this by email and you should not enter the same spectrum again.</para>
  <para>If you are logged in, you can edit molecules you have entered. In the details portlet, you will see a button "Edit this spectrum". If you click this, you can follow the submit procedure and change anything you like. The changes need to be approved by the reviewer of the original spectrum.</para></sect2>
  <sect2 id="review"><title>Review</title>
--- 259,263 ----
  actualy compound in question.</para></listitem></itemizedlist>
  <para>After inserting all data, click the "Submit for database" button.</para>
! <para>You will then be presented with your data: check their validity and press the appropriate button. You can also view and download the molecule and/or spectrum you entered in various formats, e. g. pdf, rtf or jpeg. Choose a format and click the button "Request" for that.  Your data will not be available immediately, but after they have been confirmed by a reviewer (you will get an email telling you who is your reviewer). To check the status of your contributions, use the "Show all my contributions" link on the Search pane. If for some reasons your submit is interrupted, you can continue that when you log in next time. You will see a blue box on top of the submit page where you can choose to continue or to discard the broken submit. If you get the message "There was delay ..." after you submitted the spectrum, this simply means your spectrum will be added later. You will be informed about this by email and you should not enter the same spectrum again.</para>
  <para>If you are logged in, you can edit molecules you have entered. In the details portlet, you will see a button "Edit this spectrum". If you click this, you can follow the submit procedure and change anything you like. The changes need to be approved by the reviewer of the original spectrum.</para></sect2>
  <sect2 id="review"><title>Review</title>
***************
*** 273,277 ****
  </sect2>
  <sect2 id="guest"><title>Guestbook / Wishlist</title>
! <para>In the guestbook, our visitors can leave informal comments. The wishlist is a facility to request spectra. For requesting a specctrum, enter the structure (about entering molecules see <link linkend="submit">Submitting Spectra</link>) and choose the spectrum type, then write it to the wishlist. Any contributor can choose a structure from the wishlist by clicking on it. Pressing "Submit spectrum" takes the conributor to the submit page. The stucture will disappear from the wishlist if a spectrum of the requested type has been entered for the structure, no matter if using the wishlist or not. If the person who requested a spectrum was logged in when adding something to the wishlist, she/he gets notified via email about this.</para>
  </sect2>
  <sect2 id="rating"><title>The rating system</title>
--- 273,277 ----
  </sect2>
  <sect2 id="guest"><title>Guestbook / Wishlist</title>
! <para>In the guestbook, our visitors can leave informal comments. The wishlist is a facility to request spectra. For requesting a spectrum, enter the structure (about entering molecules see <link linkend="submit">Submitting Spectra</link>) and choose the spectrum type, then write it to the wishlist. Any contributor can choose a structure from the wishlist by clicking on it. Pressing "Submit spectrum" takes the conributor to the submit page. The stucture will disappear from the wishlist if a spectrum of the requested type has been entered for the structure, no matter if using the wishlist or not. If the person who requested a spectrum was logged in when adding something to the wishlist, she/he gets notified via email about this.</para>
  </sect2>
  <sect2 id="rating"><title>The rating system</title>
***************
*** 279,294 ****
  </sect2>
  <sect2 id="struchistory"><title>The structures history</title>
! <para>NMRShiftdb automatically collects the last 20 structures you painted in search by structure, predict or submit. You can load one of theses structeres at any time by clicking the "Import from structures history" button next to a sketcher. You get a window where you can choose a structure. Clicking "Import" imports this and closes the import window.</para>
! <para>The collection of structures is session-based, which means that structures are lost if you log in, log out or close the browser window. This is not true for registered and logged in users - they will find their old structures history if they log in againg.</para>
  </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, coworker and user, and the concept of an order.</para>
! <para>Users can assign themself membership of a labgroup, either as coworker or user. They need to be approved by the group leader. Once this is done, a user can submit orders and a coworker 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:
! <itemizedlist><listitem>By an operator: This means a lab operator will handle the order. After the submit, this will show up in the list of open orders. If a coworker has dealt with this, it goes to the fullfilled orders list. The user can click on a fullfilled order and can download the raw data files then. He can also start an assignment of peaks here, which is done via the normal NRMShiftDB input.</listitem>
! <listitem>By the user himself: Here the user needs to do the measurement. When he clicks on the order on the open orders list, he can browse through the data files and attach them to the order. Once this is done, the procdure is the same as above.</listitem>
! <listitem>By the user via a robot: Here the user needs to put his probe into the robot and it will be measured during the next night. The data files get attached automatically and the order goes to the fullfilled orders lis.</listitem>
  </itemizedlist></para>
! <para>A coworker, when logged in, also has teh "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>
  </sect1>
--- 279,294 ----
  </sect2>
  <sect2 id="struchistory"><title>The structures history</title>
! <para>NMRShiftdb automatically collects the last 20 structures you painted in search by structure, predict or submit. You can load one of these structeres at any time by clicking the "Import from structures history" button next to a sketcher. You get a window where you can choose a structure. Clicking "Import" imports this and closes the import window.</para>
! <para>The collection of stcructures is session-based, which means that structures are lost if you log in, log out or close the browser window. This is not true for registered and logged in users - they will find their old structures history if they log in again.</para>
  </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:
! <itemizedlist><listitem>By an operator: This means a lab operator will handle the order. After the submission, it will show up in the list of open orders. If a operator has dealt with this, it goes to the fullfilled orders list. The user can click on a fullfilled order and can download the raw data files then. He can also start an assignment of peaks here, which is done via the normal NRMShiftDB input.</listitem>
! <listitem>By the user himself: Here the user needs to do the measurement. When he clicks on the order on the open orders list, he can browse through the data files and attach them to the order. Once this is done, the procedure is the same as above.</listitem>
! <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></para>
! <para>A 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>
  </sect1>

[Nmrshiftdb-devel] CVS: nmrshiftdb/src/vmtemplates/portlets/html user-order.vm, 1.33, 1.34 worker-order.vm, 1.14, 1.15

[Stefan K. <sh...@us...>]

Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/vmtemplates/portlets/html
In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv21180/src/vmtemplates/portlets/html

Modified Files:
	user-order.vm worker-order.vm 
Log Message:
corrected typos


Index: user-order.vm
===================================================================
RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/vmtemplates/portlets/html/user-order.vm,v
retrieving revision 1.33
retrieving revision 1.34
diff -C2 -r1.33 -r1.34
*** user-order.vm	15 Sep 2006 11:57:00 -0000	1.33
--- user-order.vm	15 Sep 2006 13:33:46 -0000	1.34
***************
*** 3,7 ****
    	<tr><td><a href="portal/pane0/Help;jsessionid=$data.getSession().getId()?URL=using.html#labadmin" style="color:white"><img src="images/help.png"></a></td></tr>
      <tr>
!       <td>You have the following <b>open orders for labgroup operators</b>:</td><td width="50"></td><td>You have the following <b>open orders for self processing</b>:</td><td width="50"></td><td>You have the following <b>open orders for processing by robot</b>:</td><td width="50"></td><td>The following <b>orders have been (partly or fully) done</b> and wait for assignment:</td>
      </tr>
      <tr>
--- 3,7 ----
    	<tr><td><a href="portal/pane0/Help;jsessionid=$data.getSession().getId()?URL=using.html#labadmin" style="color:white"><img src="images/help.png"></a></td></tr>
      <tr>
!       <td>You have the following <b>open orders for labgroup operators</b>:</td><td width="50"></td><td>You have the following <b>open orders for self processing</b>:</td><td width="50"></td><td>You have the following <b>open orders for processing by sample changer</b>:</td><td width="50"></td><td>The following <b>orders have been (partly or fully) done</b> and wait for assignment:</td>
      </tr>
      <tr>
***************
*** 82,86 ****
            <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" checked value="worker"> a lab worker <input type="radio" name="process" value="self"> myself <input type="radio" name="process" value="robot"> myself via robot<br>
          #else
            <b>Order $sample.getUsersId()</b> has the following properties:
--- 82,86 ----
            <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" checked value="worker"> a lab worker <input type="radio" name="process" value="self"> myself <input type="radio" name="process" value="robot"> myself via sample changer<br>
          #else
            <b>Order $sample.getUsersId()</b> has the following properties:

Index: worker-order.vm
===================================================================
RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/vmtemplates/portlets/html/worker-order.vm,v
retrieving revision 1.14
retrieving revision 1.15
diff -C2 -r1.14 -r1.15
*** worker-order.vm	15 Sep 2006 11:57:00 -0000	1.14
--- worker-order.vm	15 Sep 2006 13:33:46 -0000	1.15
***************
*** 109,112 ****
    </table>
  #else
!   You are not a coworker in any labgroup or not yet approved!
  #end
--- 109,112 ----
    </table>
  #else
!   You are not an operator in any labgroup or not yet approved!
  #end

[Nmrshiftdb-devel] CVS: nmrshiftdb/src/conf/jetspeed/WEB-INF/templates/vm/screens/html NewAccount.vm, 1.12, 1.13

[Stefan K. <sh...@us...>]

Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/conf/jetspeed/WEB-INF/templates/vm/screens/html
In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv21180/src/conf/jetspeed/WEB-INF/templates/vm/screens/html

Modified Files:
	NewAccount.vm 
Log Message:
corrected typos


Index: NewAccount.vm
===================================================================
RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/conf/jetspeed/WEB-INF/templates/vm/screens/html/NewAccount.vm,v
retrieving revision 1.12
retrieving revision 1.13
diff -C2 -r1.12 -r1.13
*** NewAccount.vm	14 Sep 2006 14:40:16 -0000	1.12
--- NewAccount.vm	15 Sep 2006 13:33:46 -0000	1.13
***************
*** 104,108 ****
            </tr>
            <tr>
!             <td colspan=2> I am a <input type="radio" name="groupmember" value="coworker">coworker in this lab group or <input type="radio" name="groupmember" value="user" checked>want to get my compounds measured there.</td>
            </tr>          
            <tr>
--- 104,108 ----
            </tr>
            <tr>
!             <td colspan=2> I am an <input type="radio" name="groupmember" value="coworker">operator in this lab group or <input type="radio" name="groupmember" value="user" checked>want to get my compounds measured there.</td>
            </tr>          
            <tr>

[Nmrshiftdb-devel] CVS: nmrshiftdb/src/java/org/openscience/nmrshiftdb/portlets SubmitPortlet.java, 1.420, 1.421

[Stefan K. <sh...@us...>]

Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/portlets
In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv19240/src/java/org/openscience/nmrshiftdb/portlets

Modified Files:
	SubmitPortlet.java 
Log Message:
submit in labgroup does not need to be reviewed


Index: SubmitPortlet.java
===================================================================
RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/portlets/SubmitPortlet.java,v
retrieving revision 1.420
retrieving revision 1.421
diff -C2 -r1.420 -r1.421
*** SubmitPortlet.java	15 Sep 2006 10:32:47 -0000	1.420
--- SubmitPortlet.java	15 Sep 2006 12:08:32 -0000	1.421
***************
*** 333,336 ****
--- 333,337 ----
          subData.setSpectrumKeywords(((NmrshiftdbUser)runData.getUser()).getDBLabGroup().getLabgroupName());
          subData.fullfillsOrder=new NumberKey(runData.getParameters().get("id"));
+         subData.noreview=true;
        } catch (Exception ex) {
          return new StringElement(GeneralUtils.logError(ex, "SubmitPortlet/Edit/populate subData", runData,true));
***************
*** 1491,1495 ****
            subData.save(saveUser, DBSpectrumPeer.retrieveByPK(subData.getEditSpectrum()).getReviewFlag(), url, now, runData, Integer.parseInt(GeneralUtils.getNmrshiftdbProperty("hosecode.spheres", runData)), false);
          } else {
!           subData.save(saveUser, NmrshiftdbConstants.FALSE, url, now, runData, Integer.parseInt(GeneralUtils.getNmrshiftdbProperty("hosecode.spheres", runData)), false);
          }
          now=new Date();
--- 1492,1496 ----
            subData.save(saveUser, DBSpectrumPeer.retrieveByPK(subData.getEditSpectrum()).getReviewFlag(), url, now, runData, Integer.parseInt(GeneralUtils.getNmrshiftdbProperty("hosecode.spheres", runData)), false);
          } else {
!           subData.save(saveUser, subData.noreview? NmrshiftdbConstants.TRUE : NmrshiftdbConstants.FALSE, url, now, runData, Integer.parseInt(GeneralUtils.getNmrshiftdbProperty("hosecode.spheres", runData)), false);
          }
          now=new Date();
***************
*** 1531,1535 ****
            session.removeAttribute("onesubmit");
          }
!         showMessageWithReviewer = doReview(subData, now, user, runData);
          //We need to remove some flags
          if (session.getAttribute("contributoredit") != null) {
--- 1532,1537 ----
            session.removeAttribute("onesubmit");
          }
!         if(!subData.noreview)
!         	showMessageWithReviewer = doReview(subData, now, user, runData);
          //We need to remove some flags
          if (session.getAttribute("contributoredit") != null) {

[Nmrshiftdb-devel] CVS: nmrshiftdb/src/java/org/openscience/nmrshiftdb/util SubmittingData.java, 1.281, 1.282

[Stefan K. <sh...@us...>]

Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/util
In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv19240/src/java/org/openscience/nmrshiftdb/util

Modified Files:
	SubmittingData.java 
Log Message:
submit in labgroup does not need to be reviewed


Index: SubmittingData.java
===================================================================
RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/util/SubmittingData.java,v
retrieving revision 1.281
retrieving revision 1.282
diff -C2 -r1.281 -r1.282
*** SubmittingData.java	28 Aug 2006 14:33:58 -0000	1.281
--- SubmittingData.java	15 Sep 2006 12:08:33 -0000	1.282
***************
*** 164,167 ****
--- 164,168 ----
    public int coordinatesetid3=-1;
    public IMolecule molcoord=null;
+   public boolean noreview=false;
    int level = 0;
    String keepAssignmentEntries = "";

[Nmrshiftdb-devel] CVS: nmrshiftdb/src/vmtemplates/portlets/html user-order.vm, 1.32, 1.33 worker-order.vm, 1.13, 1.14

[Stefan K. <sh...@us...>]

Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/vmtemplates/portlets/html
In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv14857/src/vmtemplates/portlets/html

Modified Files:
	user-order.vm worker-order.vm 
Log Message:
separate listing of orders for different frequencies


Index: user-order.vm
===================================================================
RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/vmtemplates/portlets/html/user-order.vm,v
retrieving revision 1.32
retrieving revision 1.33
diff -C2 -r1.32 -r1.33
*** user-order.vm	15 Sep 2006 11:17:31 -0000	1.32
--- user-order.vm	15 Sep 2006 11:57:00 -0000	1.33
***************
*** 161,166 ****
          Field Strength
          #if($submitorshow=="submit")
!           (enter or choose): <input type="text" name="fstrength" size="15">
!           <select name="fstrengths" size="1" onChange="document.restform.elements['fstrength'].value=''">
            #foreach($existingcondition in $fstrengths)
              <option value="$existingcondition.getConditionId()">$existingcondition.getValue()</option>
--- 161,165 ----
          Field Strength
          #if($submitorshow=="submit")
!           : <select name="fstrengths" size="1" onChange="document.restform.elements['fstrength'].value=''">
            #foreach($existingcondition in $fstrengths)
              <option value="$existingcondition.getConditionId()">$existingcondition.getValue()</option>

Index: worker-order.vm
===================================================================
RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/vmtemplates/portlets/html/worker-order.vm,v
retrieving revision 1.13
retrieving revision 1.14
diff -C2 -r1.13 -r1.14
*** worker-order.vm	14 Sep 2006 16:24:01 -0000	1.13
--- worker-order.vm	15 Sep 2006 11:57:00 -0000	1.14
***************
*** 8,13 ****
          #else
            The following orders for your labgroup wait to be fullfilled:
            <table>
!             #foreach($sample in $openorders)
                #set($greyorwhite=$velocityCount%2)
                <tr 
--- 8,59 ----
          #else
            The following orders for your labgroup wait to be fullfilled:
+           <table><tr><td>
+           <table>
+           	<tr><th>250 MHz</th></tr>
+             #foreach($sample in $openorders250)
+               #set($greyorwhite=$velocityCount%2)
+               <tr 
+               #if($greyorwhite==0)
+                 bgcolor="#D3D3D3" 
+               #end
+               ><td><a href="portal/pane0/NMR+lab+administration?submitorshow=show&id=$sample.getSampleId()">$sample.getUsersId()</a></td></tr>
+             #end
+           </table></td><td>
+           <table>
+           	<tr><th>300 MHz</th></tr>
+             #foreach($sample in $openorders300)
+               #set($greyorwhite=$velocityCount%2)
+               <tr 
+               #if($greyorwhite==0)
+                 bgcolor="#D3D3D3" 
+               #end
+               ><td><a href="portal/pane0/NMR+lab+administration?submitorshow=show&id=$sample.getSampleId()">$sample.getUsersId()</a></td></tr>
+             #end
+           </table></td><td>
+           <table>
+           	<tr><th>400 MHz</th></tr>
+             #foreach($sample in $openorders400)
+               #set($greyorwhite=$velocityCount%2)
+               <tr 
+               #if($greyorwhite==0)
+                 bgcolor="#D3D3D3" 
+               #end
+               ><td><a href="portal/pane0/NMR+lab+administration?submitorshow=show&id=$sample.getSampleId()">$sample.getUsersId()</a></td></tr>
+             #end
+           </table></td><td>
+           <table>
+           	<tr><th>500 MHz</th></tr>
+             #foreach($sample in $openorders500)
+               #set($greyorwhite=$velocityCount%2)
+               <tr 
+               #if($greyorwhite==0)
+                 bgcolor="#D3D3D3" 
+               #end
+               ><td><a href="portal/pane0/NMR+lab+administration?submitorshow=show&id=$sample.getSampleId()">$sample.getUsersId()</a></td></tr>
+             #end
+           </table></td><td>
            <table>
!           	<tr><th>600 MHz</th></tr>
!             #foreach($sample in $openorders600)
                #set($greyorwhite=$velocityCount%2)
                <tr 
***************
*** 17,21 ****
                ><td><a href="portal/pane0/NMR+lab+administration?submitorshow=show&id=$sample.getSampleId()">$sample.getUsersId()</a></td></tr>
              #end
!           </table>
          #end
        </td>
--- 63,67 ----
                ><td><a href="portal/pane0/NMR+lab+administration?submitorshow=show&id=$sample.getSampleId()">$sample.getUsersId()</a></td></tr>
              #end
!           </table></td></tr></table>
          #end
        </td>