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From: Stefan K. <sh...@us...> - 2006-09-15 11:57:02
|
Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/modules/actions/portlets In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv14857/src/java/org/openscience/nmrshiftdb/modules/actions/portlets Modified Files: OrderAction.java OrderFullfillAction.java Log Message: separate listing of orders for different frequencies Index: OrderAction.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/modules/actions/portlets/OrderAction.java,v retrieving revision 1.20 retrieving revision 1.21 diff -C2 -r1.20 -r1.21 *** OrderAction.java 15 Sep 2006 11:26:59 -0000 1.20 --- OrderAction.java 15 Sep 2006 11:57:00 -0000 1.21 *************** *** 234,249 **** } sample.setDBConditionRelatedBySolvent(solvent); ! DBCondition fstrength; ! if(data.getParameters().get("fstrength")!=null && !data.getParameters().get("fstrength").equals("")){ ! fstrength = new DBCondition(); ! fstrength.setDBConditionTypeKey(new NumberKey(3)); ! fstrength.setValue(data.getParameters().get("fstrength")); ! fstrength.setNmrshiftdbUser((NmrshiftdbUser)data.getUser()); ! fstrength.save(); ! }else{ ! Criteria crit=new Criteria(); ! crit.add(DBConditionPeer.CONDITION_ID,data.getParameters().get("fstrengths")); ! fstrength=(DBCondition)DBConditionPeer.doSelect(crit).get(0); ! } sample.setDBConditionRelatedByFieldStrength(fstrength); String molecule = data.getParameters().get("MolTxt"); --- 234,240 ---- } sample.setDBConditionRelatedBySolvent(solvent); ! Criteria crit=new Criteria(); ! crit.add(DBConditionPeer.CONDITION_ID,data.getParameters().get("fstrengths")); ! DBCondition fstrength=(DBCondition)DBConditionPeer.doSelect(crit).get(0); sample.setDBConditionRelatedByFieldStrength(fstrength); String molecule = data.getParameters().get("MolTxt"); Index: OrderFullfillAction.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/modules/actions/portlets/OrderFullfillAction.java,v retrieving revision 1.17 retrieving revision 1.18 diff -C2 -r1.17 -r1.18 *** OrderFullfillAction.java 14 Sep 2006 16:24:01 -0000 1.17 --- OrderFullfillAction.java 15 Sep 2006 11:57:00 -0000 1.18 *************** *** 15,18 **** --- 15,19 ---- import org.apache.turbine.util.db.Criteria; import org.apache.velocity.context.Context; + import org.openscience.nmrshiftdb.om.DBConditionPeer; import org.openscience.nmrshiftdb.om.DBLabGroupPeer; import org.openscience.nmrshiftdb.om.DBRawFile; *************** *** 52,56 **** crit.add(DBSamplePeer.FINISHED, "false"); crit.add(DBSamplePeer.PROCESS,OrderAction.WORKER); ! context.put("openorders",DBSamplePeer.doSelect(crit)); context.put("data", data); context.put("submitorshow","submit"); --- 53,68 ---- crit.add(DBSamplePeer.FINISHED, "false"); crit.add(DBSamplePeer.PROCESS,OrderAction.WORKER); ! crit.addJoin(DBSamplePeer.FIELD_STRENGTH, DBConditionPeer.CONDITION_ID); ! crit.add(DBConditionPeer.CONDITION_TYPE_ID,"3"); ! crit.add(DBConditionPeer.VALUE,"250"); ! context.put("openorders250",DBSamplePeer.doSelect(crit)); ! crit.add(DBConditionPeer.VALUE,"300"); ! context.put("openorders300",DBSamplePeer.doSelect(crit)); ! crit.add(DBConditionPeer.VALUE,"400"); ! context.put("openorders400",DBSamplePeer.doSelect(crit)); ! crit.add(DBConditionPeer.VALUE,"500"); ! context.put("openorders500",DBSamplePeer.doSelect(crit)); ! crit.add(DBConditionPeer.VALUE,"600"); ! context.put("openorders600",DBSamplePeer.doSelect(crit)); context.put("data", data); context.put("submitorshow","submit"); |
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From: Stefan K. <sh...@us...> - 2006-09-15 11:27:01
|
Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/modules/actions/portlets In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv3222/src/java/org/openscience/nmrshiftdb/modules/actions/portlets Modified Files: OrderAction.java Log Message: restricts frequencies to common ones Index: OrderAction.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/modules/actions/portlets/OrderAction.java,v retrieving revision 1.19 retrieving revision 1.20 diff -C2 -r1.19 -r1.20 *** OrderAction.java 15 Sep 2006 11:17:31 -0000 1.19 --- OrderAction.java 15 Sep 2006 11:26:59 -0000 1.20 *************** *** 191,196 **** crit.add(DBConditionPeer.CONDITION_TYPE_ID,"2"); context.put("solvents", DBConditionPeer.doSelect(crit)); crit.add(DBConditionPeer.CONDITION_TYPE_ID,"3"); ! context.put("fstrengths", DBConditionPeer.doSelect(crit)); context.put("data",data); context.put("typesc",getTypesC()); --- 191,207 ---- crit.add(DBConditionPeer.CONDITION_TYPE_ID,"2"); context.put("solvents", DBConditionPeer.doSelect(crit)); + Vector strengths=new Vector(); crit.add(DBConditionPeer.CONDITION_TYPE_ID,"3"); ! crit.add(DBConditionPeer.VALUE,"250"); ! strengths.addAll(DBConditionPeer.doSelect(crit)); ! crit.add(DBConditionPeer.VALUE,"300"); ! strengths.addAll(DBConditionPeer.doSelect(crit)); ! crit.add(DBConditionPeer.VALUE,"400"); ! strengths.addAll(DBConditionPeer.doSelect(crit)); ! crit.add(DBConditionPeer.VALUE,"500"); ! strengths.addAll(DBConditionPeer.doSelect(crit)); ! crit.add(DBConditionPeer.VALUE,"600"); ! strengths.addAll(DBConditionPeer.doSelect(crit)); ! context.put("fstrengths", strengths); context.put("data",data); context.put("typesc",getTypesC()); |
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From: Stefan K. <sh...@us...> - 2006-09-15 11:17:33
|
Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/modules/actions/portlets In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv32102/src/java/org/openscience/nmrshiftdb/modules/actions/portlets Modified Files: OrderAction.java Log Message: extra column for robot orders Index: OrderAction.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/modules/actions/portlets/OrderAction.java,v retrieving revision 1.18 retrieving revision 1.19 diff -C2 -r1.18 -r1.19 *** OrderAction.java 14 Sep 2006 16:24:01 -0000 1.18 --- OrderAction.java 15 Sep 2006 11:17:31 -0000 1.19 *************** *** 111,114 **** --- 111,122 ---- } 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(); + for(int i=0;i<v7.size();i++){ + v8.add(DBSamplePeer.retrieveByPK(new NumberKey(((Record) v7.get(i)).getValue(1).asInt()))); + } + context.put("samplesrobot",v8); context.put("data", data); if(data.getParameters().get("submitorshow")!=null && data.getParameters().get("submitorshow").equals("show")){ |
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From: Stefan K. <sh...@us...> - 2006-09-15 11:17:33
|
Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/vmtemplates/portlets/html In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv32102/src/vmtemplates/portlets/html Modified Files: user-order.vm Log Message: extra column for robot orders Index: user-order.vm =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/vmtemplates/portlets/html/user-order.vm,v retrieving revision 1.31 retrieving revision 1.32 diff -C2 -r1.31 -r1.32 *** user-order.vm 14 Sep 2006 16:24:01 -0000 1.31 --- user-order.vm 15 Sep 2006 11:17:31 -0000 1.32 *************** *** 3,7 **** <tr><td><a href="portal/pane0/Help;jsessionid=$data.getSession().getId()?URL=using.html#labadmin" style="color:white"><img src="images/help.png"></a></td></tr> <tr> ! <td>You have the following <b>open orders</b> for labgroup operators:</td><td width="50"></td><td>You have the following <b>open orders</b> for self processing:</td><td width="50"></td><td>The following <b>orders have been (partly or fully) done</b> and wait for assignment:</td> </tr> <tr> --- 3,7 ---- <tr><td><a href="portal/pane0/Help;jsessionid=$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 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> *************** *** 41,44 **** --- 41,61 ---- <td width="50"></td> <td> + #if($samplesrobot.size()==0) + None + #else + <table> + #foreach($sample in $samplesrobot) + #set($greyorwhite=$velocityCount%2) + <tr + #if($greyorwhite==0) + bgcolor="#D3D3D3" + #end + ><td><a href="portal/pane0/NMR+lab+administration;jsessionid=$data.getSession().getId()?submitorshow=show&id=$sample.getSampleId()">$sample.getUsersId()</a></td></tr> + #end + </table> + #end + </td> + <td width="50"></td> + <td> #if($samplesdone.size()==0) None |
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From: Stefan K. <sh...@us...> - 2006-09-15 10:32:50
|
Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/portlets In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv14441/src/java/org/openscience/nmrshiftdb/portlets Modified Files: SubmitPortlet.java Log Message: bold atom numbers Index: SubmitPortlet.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/portlets/SubmitPortlet.java,v retrieving revision 1.419 retrieving revision 1.420 diff -C2 -r1.419 -r1.420 *** SubmitPortlet.java 15 Sep 2006 09:38:11 -0000 1.419 --- SubmitPortlet.java 15 Sep 2006 10:32:47 -0000 1.420 *************** *** 1748,1759 **** twoHs = true; if (v.size() > 0) { ! elementsOfChoosenType.add(new ValuesForVelocityBean(new Float(i + ".1"), i + "001", prediction.length==20 ? 0 : prediction[0], prediction.length==20 ? 1000 : prediction[2], prediction.length==20 ? new String("No data available") : new String(format.format(prediction[0], s, f) + "-<b>" + format.format(prediction[1], s3, f) + "</b>-" + format.format(prediction[2], s2, f)) + "; " + comment, new String((i + 1) + "-H<sub>a</sub> (H " + (Integer) v.get(0) + ")" + (dbatoms != null && !dbatoms[i].getIdentifier(spectrumWithIdentifiers).equals("") ? " (" + dbatoms[i].getIdentifier(spectrumWithIdentifiers) + ")" : "")), mol.getAtom(((Integer) v.get(0)).intValue() - 1))); } else { ! elementsOfChoosenType.add(new ValuesForVelocityBean(new Float(i + ".1"), i + "001", prediction.length==20 ? 0 : prediction[0], prediction.length==20 ? 1000 : prediction[2], prediction.length==20 ? new String("No data available") : new String(format.format(prediction[0], s, f) + "-<b>" + format.format(prediction[1], s3, f) + "</b>-" + format.format(prediction[2], s2, f)) + "; " + comment, new String((i + 1) + "-H<sub>a</sub>" + (dbatoms != null && !dbatoms[i].getIdentifier(spectrumWithIdentifiers).equals("") ? " (" + dbatoms[i].getIdentifier(spectrumWithIdentifiers) + ")" : "")), mol.getAtom(((Integer) v.get(0)).intValue() - 1))); } if (v.size() > 1) { ! elementsOfChoosenType.add(new ValuesForVelocityBean(new Float(i + ".2"), i + "002", prediction.length==20 ? 0 : prediction[0], prediction.length==20 ? 1000 : prediction[2], prediction.length==20 ? new String("No data available") : new String(format.format(prediction[0], s, f) + "-<b>" + format.format(prediction[1], s3, f) + "</b>-" + format.format(prediction[2], s2, f)) + "; " + comment, new String((i + 1) + "-H<sub>b</sub> (H " + (Integer) v.get(1) + ")" + (dbatoms != null && !dbatoms[i].getIdentifier(spectrumWithIdentifiers).equals("") ? " (" + dbatoms[i].getIdentifier(spectrumWithIdentifiers) + ")" : "")), mol.getAtom(((Integer) v.get(1)).intValue() - 1))); } else { ! elementsOfChoosenType.add(new ValuesForVelocityBean(new Float(i + ".2"), i + "002", prediction.length==20 ? 0 : prediction[0], prediction.length==20 ? 1000 : prediction[2], prediction.length==20 ? new String("No data available") : new String(format.format(prediction[0], s, f) + "-<b>" + format.format(prediction[1], s3, f) + "</b>-" + format.format(prediction[2], s2, f)) + "; " + comment, new String((i + 1) + "-H<sub>b</sub>" + (dbatoms != null && !dbatoms[i].getIdentifier(spectrumWithIdentifiers).equals("") ? " (" + dbatoms[i].getIdentifier(spectrumWithIdentifiers) + ")" : "")), mol.getAtom(((Integer) v.get(1)).intValue() - 1))); } predictions.add(new Float(-1)); --- 1748,1759 ---- twoHs = true; if (v.size() > 0) { ! elementsOfChoosenType.add(new ValuesForVelocityBean(new Float(i + ".1"), i + "001", prediction.length==20 ? 0 : prediction[0], prediction.length==20 ? 1000 : prediction[2], prediction.length==20 ? new String("No data available") : new String(format.format(prediction[0], s, f) + "-<b>" + format.format(prediction[1], s3, f) + "</b>-" + format.format(prediction[2], s2, f)) + "; " + comment, new String("<b>"+(i + 1) + "</b>-H<sub>a</sub> (H " + (Integer) v.get(0) + ")" + (dbatoms != null && !dbatoms[i].getIdentifier(spectrumWithIdentifiers).equals("") ? " (" + dbatoms[i].getIdentifier(spectrumWithIdentifiers) + ")" : "")), mol.getAtom(((Integer) v.get(0)).intValue() - 1))); } else { ! elementsOfChoosenType.add(new ValuesForVelocityBean(new Float(i + ".1"), i + "001", prediction.length==20 ? 0 : prediction[0], prediction.length==20 ? 1000 : prediction[2], prediction.length==20 ? new String("No data available") : new String(format.format(prediction[0], s, f) + "-<b>" + format.format(prediction[1], s3, f) + "</b>-" + format.format(prediction[2], s2, f)) + "; " + comment, new String("<b>"+(i + 1) + "</b>-H<sub>a</sub>" + (dbatoms != null && !dbatoms[i].getIdentifier(spectrumWithIdentifiers).equals("") ? " (" + dbatoms[i].getIdentifier(spectrumWithIdentifiers) + ")" : "")), mol.getAtom(((Integer) v.get(0)).intValue() - 1))); } if (v.size() > 1) { ! elementsOfChoosenType.add(new ValuesForVelocityBean(new Float(i + ".2"), i + "002", prediction.length==20 ? 0 : prediction[0], prediction.length==20 ? 1000 : prediction[2], prediction.length==20 ? new String("No data available") : new String(format.format(prediction[0], s, f) + "-<b>" + format.format(prediction[1], s3, f) + "</b>-" + format.format(prediction[2], s2, f)) + "; " + comment, new String("<b>"+(i + 1) + "</b>-H<sub>b</sub> (H " + (Integer) v.get(1) + ")" + (dbatoms != null && !dbatoms[i].getIdentifier(spectrumWithIdentifiers).equals("") ? " (" + dbatoms[i].getIdentifier(spectrumWithIdentifiers) + ")" : "")), mol.getAtom(((Integer) v.get(1)).intValue() - 1))); } else { ! elementsOfChoosenType.add(new ValuesForVelocityBean(new Float(i + ".2"), i + "002", prediction.length==20 ? 0 : prediction[0], prediction.length==20 ? 1000 : prediction[2], prediction.length==20 ? new String("No data available") : new String(format.format(prediction[0], s, f) + "-<b>" + format.format(prediction[1], s3, f) + "</b>-" + format.format(prediction[2], s2, f)) + "; " + comment, new String("<b>"+(i + 1) + "</b>-H<sub>b</sub>" + (dbatoms != null && !dbatoms[i].getIdentifier(spectrumWithIdentifiers).equals("") ? " (" + dbatoms[i].getIdentifier(spectrumWithIdentifiers) + ")" : "")), mol.getAtom(((Integer) v.get(1)).intValue() - 1))); } predictions.add(new Float(-1)); *************** *** 1764,1768 **** } GeneralUtils.removeLastComma(hnumbers); ! elementsOfChoosenType.add(new ValuesForVelocityBean(new Float(i), "" + i, prediction.length==20 ? 0 : prediction[0], prediction.length==20 ? 1000 : prediction[2], prediction.length==20 ? new String("No data available") : new String(format.format(prediction[0], s, f) + "-<b>" + format.format(prediction[1], s3, f) + "</b>-" + format.format(prediction[2], s2, f)) + "; " + comment, new String((i + 1) + "-H (" + hnumbers + ")" + (dbatoms != null && !dbatoms[i].getIdentifier(spectrumWithIdentifiers).equals("") ? " (" + dbatoms[i].getIdentifier(spectrumWithIdentifiers) + ")" : "")), mol.getAtom(((Integer) v.get(0)).intValue() - 1))); predictions.add(new Float(-1)); } --- 1764,1768 ---- } GeneralUtils.removeLastComma(hnumbers); ! elementsOfChoosenType.add(new ValuesForVelocityBean(new Float(i), "" + i, prediction.length==20 ? 0 : prediction[0], prediction.length==20 ? 1000 : prediction[2], prediction.length==20 ? new String("No data available") : new String(format.format(prediction[0], s, f) + "-<b>" + format.format(prediction[1], s3, f) + "</b>-" + format.format(prediction[2], s2, f)) + "; " + comment, new String("<b>"+(i + 1) + "</b>-H (" + hnumbers + ")" + (dbatoms != null && !dbatoms[i].getIdentifier(spectrumWithIdentifiers).equals("") ? " (" + dbatoms[i].getIdentifier(spectrumWithIdentifiers) + ")" : "")), mol.getAtom(((Integer) v.get(0)).intValue() - 1))); predictions.add(new Float(-1)); } |
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From: Stefan K. <sh...@us...> - 2006-09-15 09:38:15
|
Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/portlets In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv24576/src/java/org/openscience/nmrshiftdb/portlets Modified Files: SubmitPortlet.java Log Message: should solve some problems with lab system Index: SubmitPortlet.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/portlets/SubmitPortlet.java,v retrieving revision 1.418 retrieving revision 1.419 diff -C2 -r1.418 -r1.419 *** SubmitPortlet.java 28 Aug 2006 14:33:58 -0000 1.418 --- SubmitPortlet.java 15 Sep 2006 09:38:11 -0000 1.419 *************** *** 1780,1784 **** predictions.add(new Object()); } ! multiheaders.add(new String((i + 1) + "-H (" + hnumbers + ")" + (dbatoms != null && !dbatoms[i].getIdentifier(spectrumWithIdentifiers).equals("") ? " (" + dbatoms[i].getIdentifier(spectrumWithIdentifiers) + ")" : ""))); } else { boolean rightAtom = mol.getAtom(i).getSymbol().equals(subData.getChoosenSpectrumType().getElementSymbol()); --- 1780,1784 ---- predictions.add(new Object()); } ! multiheaders.add("<b>"+new String((i + 1) + "</b>-H (" + hnumbers + ")" + (dbatoms != null && !dbatoms[i].getIdentifier(spectrumWithIdentifiers).equals("") ? " (" + dbatoms[i].getIdentifier(spectrumWithIdentifiers) + ")" : ""))); } else { boolean rightAtom = mol.getAtom(i).getSymbol().equals(subData.getChoosenSpectrumType().getElementSymbol()); |
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From: Stefan K. <sh...@us...> - 2006-09-15 09:38:15
|
Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/vmtemplates In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv24576/src/vmtemplates Modified Files: predict.vm Log Message: should solve some problems with lab system Index: predict.vm =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/vmtemplates/predict.vm,v retrieving revision 1.83 retrieving revision 1.84 diff -C2 -r1.83 -r1.84 *** predict.vm 14 Sep 2006 17:08:26 -0000 1.83 --- predict.vm 15 Sep 2006 09:38:11 -0000 1.84 *************** *** 108,112 **** <!-- #end - <span style="color:#0000AA">Double click to get resizeable window!</span><br> mview_name = "JcpViewer"; mview_begin("/nmrshiftdbhtml", 300, 300); --- 108,111 ---- |
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From: Stefan K. <sh...@us...> - 2006-09-15 09:38:15
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/daemons In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv24576/src/java/org/openscience/nmrshiftdb/daemons Modified Files: AssignRobotDaemon.java Log Message: should solve some problems with lab system Index: AssignRobotDaemon.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/daemons/AssignRobotDaemon.java,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -r1.1 -r1.2 *** AssignRobotDaemon.java 11 Sep 2006 15:06:44 -0000 1.1 --- AssignRobotDaemon.java 15 Sep 2006 09:38:11 -0000 1.2 *************** *** 13,16 **** --- 13,17 ---- import org.apache.jetspeed.daemon.Daemon; + import org.apache.turbine.om.NumberKey; import org.apache.turbine.services.db.TurbineDB; import org.apache.turbine.util.Log; *************** *** 18,21 **** --- 19,24 ---- import org.openscience.nmrshiftdb.modules.actions.portlets.OrderAction; import org.openscience.nmrshiftdb.om.DBRawFile; + import org.openscience.nmrshiftdb.om.DBSample; + import org.openscience.nmrshiftdb.om.DBSamplePeer; import org.openscience.nmrshiftdb.util.GeneralUtils; *************** *** 25,29 **** Log.info("running robot stuff"); DBConnection dbconn=null; ! String query="select distinct SAMPLE.SAMPLE_ID, USERS_ID from SAMPLE left join RAW_FILE using (SAMPLE_ID) where URL is null and PROCESS=\""+OrderAction.ROBOT+"\""; try{ dbconn = TurbineDB.getConnection(); --- 28,32 ---- Log.info("running robot stuff"); DBConnection dbconn=null; ! String query="select distinct SAMPLE.SAMPLE_ID, USERS_ID from SAMPLE left join RAW_FILE using (SAMPLE_ID) where URL is null and FINISHED=\"false\" and PROCESS=\""+OrderAction.ROBOT+"\""; try{ dbconn = TurbineDB.getConnection(); *************** *** 39,48 **** StringBuffer attachedfiles=new StringBuffer(); searchfiles(rawfiledir,usersid,zipout,attachedfiles); ! zipout.close(); ! DBRawFile rawfile=new DBRawFile(); rawfile.setSampleId(sampleid); rawfile.setUrl(GeneralUtils.getNmrshiftdbProperty("urlcompressedfiles",servcon)+"/"+usersid+".zip"); rawfile.setContainedFiles(attachedfiles.toString()); rawfile.save(); } dbconn.close(); --- 42,56 ---- StringBuffer attachedfiles=new StringBuffer(); searchfiles(rawfiledir,usersid,zipout,attachedfiles); ! if(!attachedfiles.toString().equals("")){ ! zipout.close(); ! DBRawFile rawfile=new DBRawFile(); rawfile.setSampleId(sampleid); rawfile.setUrl(GeneralUtils.getNmrshiftdbProperty("urlcompressedfiles",servcon)+"/"+usersid+".zip"); rawfile.setContainedFiles(attachedfiles.toString()); rawfile.save(); + DBSample sample=DBSamplePeer.retrieveByPK(new NumberKey(sampleid)); + sample.setFinished("true"); + sample.save(); + } } dbconn.close(); |
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From: Stefan K. <sh...@us...> - 2006-09-14 17:08:38
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/vmtemplates In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv16813/src/vmtemplates Modified Files: predict.vm Log Message: some more changes from sab Index: predict.vm =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/vmtemplates/predict.vm,v retrieving revision 1.82 retrieving revision 1.83 diff -C2 -r1.82 -r1.83 *** predict.vm 22 Aug 2006 12:58:17 -0000 1.82 --- predict.vm 14 Sep 2006 17:08:26 -0000 1.83 *************** *** 108,111 **** --- 108,112 ---- <!-- #end + <span style="color:#0000AA">Double click to get resizeable window!</span><br> mview_name = "JcpViewer"; mview_begin("/nmrshiftdbhtml", 300, 300); |
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From: Stefan K. <sh...@us...> - 2006-09-14 17:08:28
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/portlets In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv16813/src/java/org/openscience/nmrshiftdb/portlets Modified Files: PredictPortlet.java Log Message: some more changes from sab Index: PredictPortlet.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/portlets/PredictPortlet.java,v retrieving revision 1.172 retrieving revision 1.173 diff -C2 -r1.172 -r1.173 *** PredictPortlet.java 28 Aug 2006 14:33:58 -0000 1.172 --- PredictPortlet.java 14 Sep 2006 17:08:26 -0000 1.173 *************** *** 568,575 **** context.put("horiorverti", session.getAttribute("horiorverti")); context.put("typeid", request.getParameter("spectrumType")); context.put("selectedType", session.getAttribute("spectype")); Criteria crit = new Criteria(); Vector v=DBSpectrumTypePeer.doSelect(crit); - v.insertElementAt(new DBSpectrumType(101,"All heavy atoms",1),0); for(int i=0;i<v.size();i++){ if(((DBSpectrumType)v.get(i)).getName().equals("1H")){ --- 568,576 ---- context.put("horiorverti", session.getAttribute("horiorverti")); context.put("typeid", request.getParameter("spectrumType")); + if(session.getAttribute("spectype")==null) + session.setAttribute("spectype","13C"); context.put("selectedType", session.getAttribute("spectype")); Criteria crit = new Criteria(); Vector v=DBSpectrumTypePeer.doSelect(crit); for(int i=0;i<v.size();i++){ if(((DBSpectrumType)v.get(i)).getName().equals("1H")){ *************** *** 578,581 **** --- 579,583 ---- } } + v.insertElementAt(new DBSpectrumType(101,"All heavy atoms",1),0); v.add(new DBSpectrumType(100,"1H (using support vector machine)",1)); context.put("types", v); |
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From: Stefan K. <sh...@us...> - 2006-09-14 16:24:17
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/modules/actions/portlets In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv31234/src/java/org/openscience/nmrshiftdb/modules/actions/portlets Modified Files: OrderAction.java OrderFullfillAction.java Log Message: some cleanup of the labgroup interface Index: OrderAction.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/modules/actions/portlets/OrderAction.java,v retrieving revision 1.17 retrieving revision 1.18 diff -C2 -r1.17 -r1.18 *** OrderAction.java 11 Sep 2006 14:21:16 -0000 1.17 --- OrderAction.java 14 Sep 2006 16:24:01 -0000 1.18 *************** *** 5,8 **** --- 5,9 ---- import java.io.FileWriter; import java.io.StringReader; + import java.util.Collections; import java.util.Date; import java.util.Vector; *************** *** 166,169 **** --- 167,171 ---- files.add(local); } + Collections.sort(files, new OrderFullfillAction.LocalComparator()); if(!((File)data.getSession().getAttribute("currentraw")).getCanonicalFile().equals(rawfiledir.getCanonicalFile())){ Vector local=new Vector(); Index: OrderFullfillAction.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/modules/actions/portlets/OrderFullfillAction.java,v retrieving revision 1.16 retrieving revision 1.17 diff -C2 -r1.16 -r1.17 *** OrderFullfillAction.java 14 Sep 2006 14:40:17 -0000 1.16 --- OrderFullfillAction.java 14 Sep 2006 16:24:01 -0000 1.17 *************** *** 156,160 **** } ! class LocalComparator implements Comparator{ public int compare(Object o1, Object o2){ return ((String)((Vector)o1).get(1)).compareTo(((String)((Vector)o2).get(1))); --- 156,160 ---- } ! public static class LocalComparator implements Comparator{ public int compare(Object o1, Object o2){ return ((String)((Vector)o1).get(1)).compareTo(((String)((Vector)o2).get(1))); |
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From: Stefan K. <sh...@us...> - 2006-09-14 16:24:09
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/vmtemplates/portlets/html In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv31234/src/vmtemplates/portlets/html Modified Files: user-order.vm worker-order.vm Log Message: some cleanup of the labgroup interface Index: user-order.vm =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/vmtemplates/portlets/html/user-order.vm,v retrieving revision 1.30 retrieving revision 1.31 diff -C2 -r1.30 -r1.31 *** user-order.vm 11 Sep 2006 15:06:44 -0000 1.30 --- user-order.vm 14 Sep 2006 16:24:01 -0000 1.31 *************** *** 58,62 **** </tr> </table><br><br> ! <table align="center" border="3" rules="none"> <tr> <td colspan="2"> --- 58,62 ---- </tr> </table><br><br> ! <table border="3" rules="none"> <tr> <td colspan="2"> *************** *** 193,197 **** </table> #if($submitorshow=="show" && $sample.getProcess()=="self" && $sample.getFinished()=="false") ! <table> <tr> <td> --- 193,197 ---- </table> #if($submitorshow=="show" && $sample.getProcess()=="self" && $sample.getFinished()=="false") ! <table border="3" rules="none"> <tr> <td> *************** *** 206,212 **** --- 206,218 ---- <td> <b>Choose files/directories you want to attach to this order!</b><br> + <table><tr><td> #foreach($file in $files) <a href="$file.get(0)">$file.get(1)</a> <a href="$file.get(2)">>>>></a><br> + #set($test=$velocityCount % 50) + #if($test==0) + </td><td> + #end #end + </td></tr></table> </td> </tr> Index: worker-order.vm =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/vmtemplates/portlets/html/worker-order.vm,v retrieving revision 1.12 retrieving revision 1.13 diff -C2 -r1.12 -r1.13 *** worker-order.vm 14 Sep 2006 14:40:17 -0000 1.12 --- worker-order.vm 14 Sep 2006 16:24:01 -0000 1.13 *************** *** 50,62 **** <b>Choose files/directories you want to attach to this order!</b><br> <table><tr><td> ! #foreach($file in $files) ! <a href="$file.get(0)">$file.get(1)</a> <a href="$file.get(2)">>>>></a><br> ! #set($test=$velocityCountM1%30) ! #if($test==0) ! </td></tr><tr><td> ! #end ! #end ! </td></tr></table> ! </td></tr></table> #end </td> --- 50,61 ---- <b>Choose files/directories you want to attach to this order!</b><br> <table><tr><td> ! #foreach($file in $files) ! <a href="$file.get(0)">$file.get(1)</a> <a href="$file.get(2)">>>>></a><br> ! #set($test=$velocityCount % 50) ! #if($test==0) ! </td><td> ! #end ! #end ! </td></tr></table> #end </td> |
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From: Stefan K. <sh...@us...> - 2006-09-14 14:40:19
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/vmtemplates/portlets/html In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv19345/src/vmtemplates/portlets/html Modified Files: worker-order.vm Log Message: better layout for the lab stuff Index: worker-order.vm =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/vmtemplates/portlets/html/worker-order.vm,v retrieving revision 1.11 retrieving revision 1.12 diff -C2 -r1.11 -r1.12 *** worker-order.vm 11 Sep 2006 15:06:44 -0000 1.11 --- worker-order.vm 14 Sep 2006 14:40:17 -0000 1.12 *************** *** 49,55 **** --- 49,61 ---- <td> <b>Choose files/directories you want to attach to this order!</b><br> + <table><tr><td> #foreach($file in $files) <a href="$file.get(0)">$file.get(1)</a> <a href="$file.get(2)">>>>></a><br> + #set($test=$velocityCountM1%30) + #if($test==0) + </td></tr><tr><td> + #end #end + </td></tr></table> </td></tr></table> #end |
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From: Stefan K. <sh...@us...> - 2006-09-14 14:40:19
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/modules/actions/portlets In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv19345/src/java/org/openscience/nmrshiftdb/modules/actions/portlets Modified Files: OrderFullfillAction.java Log Message: better layout for the lab stuff Index: OrderFullfillAction.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/modules/actions/portlets/OrderFullfillAction.java,v retrieving revision 1.15 retrieving revision 1.16 diff -C2 -r1.15 -r1.16 *** OrderFullfillAction.java 11 Sep 2006 14:21:16 -0000 1.15 --- OrderFullfillAction.java 14 Sep 2006 14:40:17 -0000 1.16 *************** *** 4,7 **** --- 4,9 ---- import java.io.FileOutputStream; import java.io.StringWriter; + import java.util.Collections; + import java.util.Comparator; import java.util.Vector; import java.util.zip.ZipOutputStream; *************** *** 106,109 **** --- 108,112 ---- files.add(local); } + Collections.sort(files, new LocalComparator()); if(!((File)data.getSession().getAttribute("currentraw")).getCanonicalFile().equals(rawfiledir.getCanonicalFile())){ Vector local=new Vector(); *************** *** 152,154 **** --- 155,163 ---- } } + + class LocalComparator implements Comparator{ + public int compare(Object o1, Object o2){ + return ((String)((Vector)o1).get(1)).compareTo(((String)((Vector)o2).get(1))); + } + } } |
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From: Stefan K. <sh...@us...> - 2006-09-14 14:40:19
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/conf/jetspeed/WEB-INF/templates/vm/screens/html In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv19345/src/conf/jetspeed/WEB-INF/templates/vm/screens/html Modified Files: NewAccount.vm Log Message: better layout for the lab stuff Index: NewAccount.vm =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/conf/jetspeed/WEB-INF/templates/vm/screens/html/NewAccount.vm,v retrieving revision 1.11 retrieving revision 1.12 diff -C2 -r1.11 -r1.12 *** NewAccount.vm 23 Feb 2006 10:58:02 -0000 1.11 --- NewAccount.vm 14 Sep 2006 14:40:16 -0000 1.12 *************** *** 104,108 **** </tr> <tr> ! <td colspan=2> I am a <input type="radio" name="groupmember" value="coworker" checked>coworker in this lab group or <input type="radio" name="groupmember" value="user">want to get my compounds measured there.</td> </tr> <tr> --- 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> |
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From: Stefan K. <sh...@us...> - 2006-09-12 14:30:48
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/webservices In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv30021/src/java/org/openscience/nmrshiftdb/webservices Modified Files: NMRShiftDBServiceBindingImpl.java Log Message: this should be better Index: NMRShiftDBServiceBindingImpl.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/webservices/NMRShiftDBServiceBindingImpl.java,v retrieving revision 1.20 retrieving revision 1.21 diff -C2 -r1.20 -r1.21 *** NMRShiftDBServiceBindingImpl.java 12 Sep 2006 14:08:43 -0000 1.20 --- NMRShiftDBServiceBindingImpl.java 12 Sep 2006 14:30:42 -0000 1.21 *************** *** 199,220 **** } } for(int k=0;k<cdkmol.getBondCount();k++){ IAtom atom1=cdkmol.getBond(k).getAtoms()[0]; if(!doublebondconfigurationsprov[k] && !BondTools.isStereo(cdkmol, atom1)){ ! IAtom[] conn=cdkmol.getConnectedAtoms(atom1); ! for(int l=0;l<conn.length;l++){ ! if(conn[l].getSymbol().equals("H")) ! cdkmol.removeAtomAndConnectedElectronContainers(conn[l]); ! } } ! IAtom atom2=cdkmol.getBond(k).getAtoms()[0]; if(!doublebondconfigurationsprov[k] && !BondTools.isStereo(cdkmol, atom2)){ ! IAtom[] conn=cdkmol.getConnectedAtoms(atom2); ! for(int l=0;l<conn.length;l++){ ! if(conn[l].getSymbol().equals("H")) ! cdkmol.removeAtomAndConnectedElectronContainers(conn[l]); ! } } } StringWriter writer=new StringWriter(); MDLWriter mdlwriter=new MDLWriter(writer); --- 199,220 ---- } } + Vector toremove=new Vector(); for(int k=0;k<cdkmol.getBondCount();k++){ IAtom atom1=cdkmol.getBond(k).getAtoms()[0]; if(!doublebondconfigurationsprov[k] && !BondTools.isStereo(cdkmol, atom1)){ ! toremove.add(atom1); } ! IAtom atom2=cdkmol.getBond(k).getAtoms()[1]; if(!doublebondconfigurationsprov[k] && !BondTools.isStereo(cdkmol, atom2)){ ! toremove.add(atom2); } } + for(int k=0;k<toremove.size();k++){ + IAtom[] conn=cdkmol.getConnectedAtoms((IAtom)toremove.get(k)); + for(int l=0;l<conn.length;l++){ + if(conn[l].getSymbol().equals("H")) + cdkmol.removeAtomAndConnectedElectronContainers(conn[l]); + } + } StringWriter writer=new StringWriter(); MDLWriter mdlwriter=new MDLWriter(writer); |
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From: Stefan K. <sh...@us...> - 2006-09-12 14:08:46
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/webservices In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv20944/src/java/org/openscience/nmrshiftdb/webservices Modified Files: NMRShiftDBServiceBindingImpl.java Log Message: this is for proton submit Index: NMRShiftDBServiceBindingImpl.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/webservices/NMRShiftDBServiceBindingImpl.java,v retrieving revision 1.19 retrieving revision 1.20 diff -C2 -r1.19 -r1.20 *** NMRShiftDBServiceBindingImpl.java 12 Sep 2006 08:56:24 -0000 1.19 --- NMRShiftDBServiceBindingImpl.java 12 Sep 2006 14:08:43 -0000 1.20 *************** *** 27,30 **** --- 27,31 ---- import org.apache.turbine.util.db.Criteria; import org.openscience.cdk.ChemFile; + import org.openscience.cdk.geometry.BondTools; import org.openscience.cdk.interfaces.IAtom; import org.openscience.cdk.interfaces.IChemFile; *************** *** 190,193 **** --- 191,220 ---- CMLReader cmlreader=new CMLReader(new ByteArrayInputStream(cmlmol.toXML().getBytes())); IMolecule cdkmol=((ChemFileCDO)cmlreader.read(new ChemFile())).getChemSequence(0).getChemModel(0).getSetOfMolecules().getMolecule(0); + //we remove all explicit Hs not around stereo centers/double bond configurations + boolean[] doublebondconfigurationsprov=new boolean[cdkmol.getBondCount()]; + for(int k=0;k<cdkmol.getBondCount();k++){ + CMLBond bond=cmlmol.getBonds().get(k); + if(bond.getFirstChildElement("doublebondconfiguration")!=null){ + doublebondconfigurationsprov[k]=true; + } + } + for(int k=0;k<cdkmol.getBondCount();k++){ + IAtom atom1=cdkmol.getBond(k).getAtoms()[0]; + if(!doublebondconfigurationsprov[k] && !BondTools.isStereo(cdkmol, atom1)){ + IAtom[] conn=cdkmol.getConnectedAtoms(atom1); + for(int l=0;l<conn.length;l++){ + if(conn[l].getSymbol().equals("H")) + cdkmol.removeAtomAndConnectedElectronContainers(conn[l]); + } + } + IAtom atom2=cdkmol.getBond(k).getAtoms()[0]; + if(!doublebondconfigurationsprov[k] && !BondTools.isStereo(cdkmol, atom2)){ + IAtom[] conn=cdkmol.getConnectedAtoms(atom2); + for(int l=0;l<conn.length;l++){ + if(conn[l].getSymbol().equals("H")) + cdkmol.removeAtomAndConnectedElectronContainers(conn[l]); + } + } + } StringWriter writer=new StringWriter(); MDLWriter mdlwriter=new MDLWriter(writer); *************** *** 196,201 **** boolean[] doublebondconfigurations=new boolean[subData.getMolWithH().getBondCount()]; for(int k=0;k<cmlmol.getBondCount();k++){ ! CMLBond bond=cmlmol.getBonds().get(k); ! if(bond.getFirstChildElement("doublebondconfiguration")!=null){ doublebondconfigurations[k]=true; } --- 223,227 ---- boolean[] doublebondconfigurations=new boolean[subData.getMolWithH().getBondCount()]; for(int k=0;k<cmlmol.getBondCount();k++){ ! if(doublebondconfigurationsprov.length>k && doublebondconfigurationsprov[k]==true){ doublebondconfigurations[k]=true; } *************** *** 215,226 **** vt.value2=(float)peak.getYValue(); String[] atomrefs=peak.getAtomRefs(); ! for(int l=0;l<atomrefs.length;l++){ ! IAtom atom=AtomContainerManipulator.getAtomById(subData.getMolWithH(),atomrefs[l]); ! if(atom.getSymbol().equals("H")){ ! atom=subData.getMolWithH().getConnectedAtoms(atom)[0]; ! } ! vt.atoms.add(atom); ! } ! subData.getSignalstable().add(vt); } for (int l = 0; l < subData.getConditions().size(); l++) { --- 241,251 ---- vt.value2=(float)peak.getYValue(); String[] atomrefs=peak.getAtomRefs(); ! if(atomrefs!=null){ ! for(int l=0;l<atomrefs.length;l++){ ! IAtom atom=AtomContainerManipulator.getAtomById(subData.getMolWithH(),atomrefs[l]); ! vt.atoms.add(atom); ! } ! subData.getSignalstable().add(vt); ! } } for (int l = 0; l < subData.getConditions().size(); l++) { |
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From: Stefan K. <sh...@us...> - 2006-09-12 14:08:45
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/om In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv20944/src/java/org/openscience/nmrshiftdb/om Modified Files: DBSpectrum.java Log Message: this is for proton submit Index: DBSpectrum.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/om/DBSpectrum.java,v retrieving revision 1.186 retrieving revision 1.187 diff -C2 -r1.186 -r1.187 *** DBSpectrum.java 28 Aug 2006 14:33:58 -0000 1.186 --- DBSpectrum.java 12 Sep 2006 14:08:43 -0000 1.187 *************** *** 294,298 **** } GeneralUtils.removeLastComma(displayString); ! if (runData == null) { GeneralUtils.removeLastComma(searchShift); v.add(new ValuesForVelocityBean(new Float(atomnumber), searchShift.toString(), 0, 0, displayString.toString(), (atomnumber + 1) + (isHSpectrum ? "-H" : ""), delta.toString(), GeneralUtils.removeLastComma(multis).toString())); --- 294,298 ---- } GeneralUtils.removeLastComma(displayString); ! if (runData == null || searchSignalMap == null) { GeneralUtils.removeLastComma(searchShift); v.add(new ValuesForVelocityBean(new Float(atomnumber), searchShift.toString(), 0, 0, displayString.toString(), (atomnumber + 1) + (isHSpectrum ? "-H" : ""), delta.toString(), GeneralUtils.removeLastComma(multis).toString())); |
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From: Stefan K. <sh...@us...> - 2006-09-12 08:56:31
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/webservices In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv20379/src/java/org/openscience/nmrshiftdb/webservices Modified Files: NMRShiftDBServiceBindingImpl.java Log Message: submit of H spectra via web services should be possible Index: NMRShiftDBServiceBindingImpl.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/webservices/NMRShiftDBServiceBindingImpl.java,v retrieving revision 1.18 retrieving revision 1.19 diff -C2 -r1.18 -r1.19 *** NMRShiftDBServiceBindingImpl.java 31 Aug 2006 15:45:35 -0000 1.18 --- NMRShiftDBServiceBindingImpl.java 12 Sep 2006 08:56:24 -0000 1.19 *************** *** 27,30 **** --- 27,31 ---- import org.apache.turbine.util.db.Criteria; import org.openscience.cdk.ChemFile; + import org.openscience.cdk.interfaces.IAtom; import org.openscience.cdk.interfaces.IChemFile; import org.openscience.cdk.interfaces.IMolecule; *************** *** 196,200 **** for(int k=0;k<cmlmol.getBondCount();k++){ CMLBond bond=cmlmol.getBonds().get(k); ! if(bond.getFirstChildElement("doublebondconfiguration")==null){ doublebondconfigurations[k]=true; } --- 197,201 ---- for(int k=0;k<cmlmol.getBondCount();k++){ CMLBond bond=cmlmol.getBonds().get(k); ! if(bond.getFirstChildElement("doublebondconfiguration")!=null){ doublebondconfigurations[k]=true; } *************** *** 215,219 **** String[] atomrefs=peak.getAtomRefs(); for(int l=0;l<atomrefs.length;l++){ ! vt.atoms.add(AtomContainerManipulator.getAtomById(subData.getMolWithH(),atomrefs[l])); } subData.getSignalstable().add(vt); --- 216,224 ---- String[] atomrefs=peak.getAtomRefs(); for(int l=0;l<atomrefs.length;l++){ ! IAtom atom=AtomContainerManipulator.getAtomById(subData.getMolWithH(),atomrefs[l]); ! if(atom.getSymbol().equals("H")){ ! atom=subData.getMolWithH().getConnectedAtoms(atom)[0]; ! } ! vt.atoms.add(atom); } subData.getSignalstable().add(vt); |
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From: Stefan K. <sh...@us...> - 2006-09-12 08:56:31
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/html In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv20379/src/html Modified Files: using.html Log Message: submit of H spectra via web services should be possible Index: using.html =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/using.html,v retrieving revision 1.45 retrieving revision 1.46 diff -C2 -r1.45 -r1.46 *** using.html 11 Sep 2006 15:06:44 -0000 1.45 --- using.html 12 Sep 2006 08:56:24 -0000 1.46 *************** *** 276,280 **** CLASS="inlinemediaobject" ><IMG ! SRC="../images/mug.gif"></SPAN > symbol. You can then use the JChemPaint applet to interactivly paint structues. You can also import a file by Copy & Paste via the "Import text by copy &paste button".</P ><P --- 276,280 ---- CLASS="inlinemediaobject" ><IMG ! SRC="../images/java.png"></SPAN > symbol. You can then use the JChemPaint applet to interactivly paint structues. You can also import a file by Copy & Paste via the "Import text by copy &paste button".</P ><P *************** *** 471,475 **** CLASS="inlinemediaobject" ><IMG ! SRC="../images/mug.gif"></SPAN > symbol. You can then use the JChemPaint applet to interactivly paint structues. You can also import a file by Copy & Paste via the "Import text by copy &paste button". You do not need to (but you may) draw implicit hydrogens. After you drew or imported your structure, submit it by clicking the submit button. Your structures are collected in the <A HREF="using.html#struchistory" --- 471,475 ---- CLASS="inlinemediaobject" ><IMG ! SRC="../images/java.png"></SPAN > symbol. You can then use the JChemPaint applet to interactivly paint structues. You can also import a file by Copy & Paste via the "Import text by copy &paste button". You do not need to (but you may) draw implicit hydrogens. After you drew or imported your structure, submit it by clicking the submit button. Your structures are collected in the <A HREF="using.html#struchistory" |
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From: Stefan K. <sh...@us...> - 2006-09-12 08:56:27
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/doc In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv20379/doc Modified Files: nmrshiftdbhelp.pdf nmrshiftdbhelp.xml Log Message: submit of H spectra via web services should be possible Index: nmrshiftdbhelp.pdf =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/doc/nmrshiftdbhelp.pdf,v retrieving revision 1.63 retrieving revision 1.64 diff -C2 -r1.63 -r1.64 Binary files /tmp/cvsWvU76h and /tmp/cvsP3ZQyO differ Index: nmrshiftdbhelp.xml =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/doc/nmrshiftdbhelp.xml,v retrieving revision 1.77 retrieving revision 1.78 diff -C2 -r1.77 -r1.78 *** nmrshiftdbhelp.xml 11 Sep 2006 15:06:43 -0000 1.77 --- nmrshiftdbhelp.xml 12 Sep 2006 08:56:24 -0000 1.78 *************** *** 130,134 **** </sect3> <sect3 id="sstruc"><title>Search by Structure</title> ! <para>In order to search the database for molecular structures, it is first necessary to create or input a structure in an appropriate encoding format which NMRShiftDB understands. You can either upload a file in common formats (<ulink url="nmrshiftdbhtml/formats.jsp">valid formats</ulink>) via the "Browse" button or activate the Java based version via the <inlinemediaobject><imageobject> <imagedata fileref="../images/mug.gif" format="GIF"></imagedata></imageobject></inlinemediaobject> symbol. You can then use the JChemPaint applet to interactivly paint structues. You can also import a file by Copy & Paste via the "Import text by copy &paste button".</para> <para>You can enter stereochemical configurations by using solid (up) and dashed (down) wedged bonds. These will be used for total structure search, but currentliy not for the substructure search. If the total structure search finds nothing with respecting stereochemistry, it "falls back" to not using stereochemistry.</para> <para>Once the desired structure has been drawn or loaded into the Marvin Sketch window, the type of search to be performed can be selected by clicking the check box next to "substructure search" (look for structures containing the input structure), "similarity search" (look for structures with a similar substructure) or "identity search" (look for structures identical to the input structure). Note that the similarity search will always be a superset of the substructure search. Click on "Search by structure" to start the search. The results are displayed on the "Results" tab. For more information about viewing results see <link linkend="browse">Browsing the Results</link>.</para> --- 130,134 ---- </sect3> <sect3 id="sstruc"><title>Search by Structure</title> ! <para>In order to search the database for molecular structures, it is first necessary to create or input a structure in an appropriate encoding format which NMRShiftDB understands. You can either upload a file in common formats (<ulink url="nmrshiftdbhtml/formats.jsp">valid formats</ulink>) via the "Browse" button or activate the Java based version via the <inlinemediaobject><imageobject> <imagedata fileref="../images/java.png" format="GIF"></imagedata></imageobject></inlinemediaobject> symbol. You can then use the JChemPaint applet to interactivly paint structues. You can also import a file by Copy & Paste via the "Import text by copy &paste button".</para> <para>You can enter stereochemical configurations by using solid (up) and dashed (down) wedged bonds. These will be used for total structure search, but currentliy not for the substructure search. If the total structure search finds nothing with respecting stereochemistry, it "falls back" to not using stereochemistry.</para> <para>Once the desired structure has been drawn or loaded into the Marvin Sketch window, the type of search to be performed can be selected by clicking the check box next to "substructure search" (look for structures containing the input structure), "similarity search" (look for structures with a similar substructure) or "identity search" (look for structures identical to the input structure). Note that the similarity search will always be a superset of the substructure search. Click on "Search by structure" to start the search. The results are displayed on the "Results" tab. For more information about viewing results see <link linkend="browse">Browsing the Results</link>.</para> *************** *** 180,184 **** </sect2> <sect2 id="submit"><title>Submit</title> ! <para>In order to submit data for NMRShiftDB, you need to be a <link linkend="register">registered user</link>. Please do not use the "back" and "forward" button of your browser while doing a submit. To do a submit, click on the "Submit molecule" tab. In the first step, you may enter literature references for your data. If custom identifiers (e. g. letters) for atoms are used in the literature you want to enter, mark this literature in the first colum. Then press "Submit literatures". You then need to enter the strucure for your spectrum. You can either upload a file in common formats (<ulink url="nmrshiftdbhtml/formats.jsp">valid formats</ulink>) via the "Choose file..." button or activate the Java based version via the <inlinemediaobject><imageobject> <imagedata fileref="../images/mug.gif" format="GIF"></imagedata></imageobject></inlinemediaobject> symbol. You can then use the JChemPaint applet to interactivly paint structues. You can also import a file by Copy & Paste via the "Import text by copy &paste button". You do not need to (but you may) draw implicit hydrogens. After you drew or imported your structure, submit it by clicking the submit button. Your structures are collected in the <link linkend="struchistory">structures history</link>. If you want to correct the molecule you can do this by clicking the "Correct molecule" button.</para> <para>After submitting the structure, you will see an additional text field, which allows you to enter your spectrum. You need to give one signal per line, shift and intensity separated by ; or ,. Example:</para> <simplelist> --- 180,184 ---- </sect2> <sect2 id="submit"><title>Submit</title> ! <para>In order to submit data for NMRShiftDB, you need to be a <link linkend="register">registered user</link>. Please do not use the "back" and "forward" button of your browser while doing a submit. To do a submit, click on the "Submit molecule" tab. In the first step, you may enter literature references for your data. If custom identifiers (e. g. letters) for atoms are used in the literature you want to enter, mark this literature in the first colum. Then press "Submit literatures". You then need to enter the strucure for your spectrum. You can either upload a file in common formats (<ulink url="nmrshiftdbhtml/formats.jsp">valid formats</ulink>) via the "Choose file..." button or activate the Java based version via the <inlinemediaobject><imageobject> <imagedata fileref="../images/java.png" format="GIF"></imagedata></imageobject></inlinemediaobject> symbol. You can then use the JChemPaint applet to interactivly paint structues. You can also import a file by Copy & Paste via the "Import text by copy &paste button". You do not need to (but you may) draw implicit hydrogens. After you drew or imported your structure, submit it by clicking the submit button. Your structures are collected in the <link linkend="struchistory">structures history</link>. If you want to correct the molecule you can do this by clicking the "Correct molecule" button.</para> <para>After submitting the structure, you will see an additional text field, which allows you to enter your spectrum. You need to give one signal per line, shift and intensity separated by ; or ,. Example:</para> <simplelist> |
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From: Stefan K. <sh...@us...> - 2006-09-11 15:06:59
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/daemons In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv22034/src/java/org/openscience/nmrshiftdb/daemons Added Files: AssignRobotDaemon.java Log Message: more chagnes for lab system --- NEW FILE: AssignRobotDaemon.java --- package org.openscience.nmrshiftdb.daemons; import java.io.File; import java.io.FileInputStream; import java.io.FileOutputStream; import java.io.IOException; import java.sql.ResultSet; import java.sql.Statement; import java.util.zip.ZipEntry; import java.util.zip.ZipOutputStream; import javax.servlet.ServletConfig; import org.apache.jetspeed.daemon.Daemon; import org.apache.turbine.services.db.TurbineDB; import org.apache.turbine.util.Log; import org.apache.turbine.util.db.pool.DBConnection; import org.openscience.nmrshiftdb.modules.actions.portlets.OrderAction; import org.openscience.nmrshiftdb.om.DBRawFile; import org.openscience.nmrshiftdb.util.GeneralUtils; public class AssignRobotDaemon extends AbstractDaemonWithServletConfig { public void run(ServletConfig servcon) throws Exception{ this.setResult( Daemon.RESULT_PROCESSING ); Log.info("running robot stuff"); DBConnection dbconn=null; String query="select distinct SAMPLE.SAMPLE_ID, USERS_ID from SAMPLE left join RAW_FILE using (SAMPLE_ID) where URL is null and PROCESS=\""+OrderAction.ROBOT+"\""; try{ dbconn = TurbineDB.getConnection(); Statement stmt = dbconn.createStatement(); ResultSet rs = stmt.executeQuery(query); while(rs.next()){ String sampleid=rs.getString(1); String usersid=rs.getString(2); File zipfile = new File(GeneralUtils.getNmrshiftdbProperty("compressedfiledirectory",servcon)+"/"+usersid+".zip"); FileOutputStream baos=new FileOutputStream(zipfile); ZipOutputStream zipout=new ZipOutputStream(baos); File rawfiledir=new File(GeneralUtils.getNmrshiftdbProperty("rawfiledirectoryrobot",servcon)); StringBuffer attachedfiles=new StringBuffer(); searchfiles(rawfiledir,usersid,zipout,attachedfiles); zipout.close(); DBRawFile rawfile=new DBRawFile(); rawfile.setSampleId(sampleid); rawfile.setUrl(GeneralUtils.getNmrshiftdbProperty("urlcompressedfiles",servcon)+"/"+usersid+".zip"); rawfile.setContainedFiles(attachedfiles.toString()); rawfile.save(); } dbconn.close(); this.setResult( Daemon.RESULT_SUCCESS ); }catch(Exception ex){ dbconn.close(); GeneralUtils.logError(ex,"robot daemon",null,true); } } 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){ 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(); } } } } } |
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From: Stefan K. <sh...@us...> - 2006-09-11 15:06:55
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/doc In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv22034/doc Modified Files: nmrshiftdbhelp.pdf nmrshiftdbhelp.xml Log Message: more chagnes for lab system Index: nmrshiftdbhelp.pdf =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/doc/nmrshiftdbhelp.pdf,v retrieving revision 1.62 retrieving revision 1.63 diff -C2 -r1.62 -r1.63 Binary files /tmp/cvs76xNV8 and /tmp/cvsny0wEZ differ Index: nmrshiftdbhelp.xml =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/doc/nmrshiftdbhelp.xml,v retrieving revision 1.76 retrieving revision 1.77 diff -C2 -r1.76 -r1.77 *** nmrshiftdbhelp.xml 13 Jun 2006 08:53:00 -0000 1.76 --- nmrshiftdbhelp.xml 11 Sep 2006 15:06:43 -0000 1.77 *************** *** 285,289 **** <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. 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.</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> --- 285,293 ---- <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> |
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From: Stefan K. <sh...@us...> - 2006-09-11 15:06:53
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/html In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv22034/src/html Modified Files: using.html Log Message: more chagnes for lab system Index: using.html =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/using.html,v retrieving revision 1.44 retrieving revision 1.45 diff -C2 -r1.44 -r1.45 *** using.html 13 Jun 2006 08:53:00 -0000 1.44 --- using.html 11 Sep 2006 15:06:44 -0000 1.45 *************** *** 725,729 **** >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. 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.</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 --- 725,740 ---- >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: ! <P ! ></P ! ><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 |
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From: Stefan K. <sh...@us...> - 2006-09-11 15:06:53
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/vmtemplates/portlets/html In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv22034/src/vmtemplates/portlets/html Modified Files: user-order.vm worker-order.vm Log Message: more chagnes for lab system Index: user-order.vm =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/vmtemplates/portlets/html/user-order.vm,v retrieving revision 1.29 retrieving revision 1.30 diff -C2 -r1.29 -r1.30 *** user-order.vm 11 Sep 2006 14:21:16 -0000 1.29 --- user-order.vm 11 Sep 2006 15:06:44 -0000 1.30 *************** *** 1,5 **** #if($data.User.isLabgroupUser($data)) <table align="center"> ! <tr><td><a href="portal/pane0/Help;jsessionid=$data.getSession().getId()?URL=using.html#labadmin">Help</a></td></tr> <tr> <td>You have the following <b>open orders</b> for labgroup operators:</td><td width="50"></td><td>You have the following <b>open orders</b> for self processing:</td><td width="50"></td><td>The following <b>orders have been (partly or fully) done</b> and wait for assignment:</td> --- 1,5 ---- #if($data.User.isLabgroupUser($data)) <table align="center"> ! <tr><td><a href="portal/pane0/Help;jsessionid=$data.getSession().getId()?URL=using.html#labadmin" style="color:white"><img src="images/help.png"></a></td></tr> <tr> <td>You have the following <b>open orders</b> for labgroup operators:</td><td width="50"></td><td>You have the following <b>open orders</b> for self processing:</td><td width="50"></td><td>The following <b>orders have been (partly or fully) done</b> and wait for assignment:</td> Index: worker-order.vm =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/vmtemplates/portlets/html/worker-order.vm,v retrieving revision 1.10 retrieving revision 1.11 diff -C2 -r1.10 -r1.11 *** worker-order.vm 22 Feb 2006 16:15:53 -0000 1.10 --- worker-order.vm 11 Sep 2006 15:06:44 -0000 1.11 *************** *** 1,5 **** #if($data.User.isLabgroupWorker($data)) <table> ! <tr><td><a href="portal/pane0/Help;jsessionid=$data.getSession().getId()?URL=using.html#labadmin">Help</a></td></tr> <tr> <td> --- 1,5 ---- #if($data.User.isLabgroupWorker($data)) <table> ! <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> |
