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From: Stefan K. <sh...@us...> - 2006-09-11 15:06:49
|
Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/vmtemplates In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv22034/src/vmtemplates Modified Files: confirm.vm Log Message: more chagnes for lab system Index: confirm.vm =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/vmtemplates/confirm.vm,v retrieving revision 1.56 retrieving revision 1.57 diff -C2 -r1.56 -r1.57 *** confirm.vm 16 May 2006 10:58:42 -0000 1.56 --- confirm.vm 11 Sep 2006 15:06:44 -0000 1.57 *************** *** 1,5 **** <table> <tr> ! <th colspan="3"><h2>Check your submitted data. Hover over the lines of the box on the right to check the assignments! <a href="portal/pane0/Help;jsessionid=$data.getSession().getId()?URL=using.html#submit">Help</a></h2></th> </tr> <tr> --- 1,5 ---- <table> <tr> ! <th colspan="3"><h2>Check your submitted data. Hover over the lines of the box on the right to check the assignments! <a href="portal/pane0/Help;jsessionid=$data.getSession().getId()?URL=using.html#submit" style="color:white"><img src="images/help.png"></a></h2></th> </tr> <tr> |
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From: Stefan K. <sh...@us...> - 2006-09-11 14:21:26
|
Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/om/map In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv3168/src/java/org/openscience/nmrshiftdb/om/map Modified Files: DBSampleMapBuilder.java Log Message: improved the lab system Index: DBSampleMapBuilder.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/om/map/DBSampleMapBuilder.java,v retrieving revision 1.5 retrieving revision 1.6 diff -C2 -r1.5 -r1.6 *** DBSampleMapBuilder.java 4 Aug 2005 21:55:24 -0000 1.5 --- DBSampleMapBuilder.java 11 Sep 2006 14:21:16 -0000 1.6 *************** *** 1,9 **** package org.openscience.nmrshiftdb.om.map; ! import java.util.Date; ! import org.apache.turbine.services.db.TurbineDB; - import org.apache.turbine.util.db.map.DatabaseMap; import org.apache.turbine.util.db.map.MapBuilder; import org.apache.turbine.util.db.map.TableMap; --- 1,10 ---- package org.openscience.nmrshiftdb.om.map; ! import java.util.*; ! import java.math.*; ! import org.apache.turbine.services.db.PoolBrokerService; import org.apache.turbine.services.db.TurbineDB; import org.apache.turbine.util.db.map.MapBuilder; + import org.apache.turbine.util.db.map.DatabaseMap; import org.apache.turbine.util.db.map.TableMap; *************** *** 88,91 **** --- 89,98 ---- } + /** SAMPLE.PROCESS */ + public static String getDBSample_Process() + { + return getTable() + ".PROCESS"; + } + /** the database map */ private DatabaseMap dbMap = null; *************** *** 116,120 **** tMap.setPrimaryKeyMethod(TableMap.IDBROKERTABLE); ! --- 123,127 ---- tMap.setPrimaryKeyMethod(TableMap.IDBROKERTABLE); ! *************** *** 141,144 **** --- 148,153 ---- tMap.addColumn ( getDBSample_Finished(), new String() ); + tMap.addColumn ( getDBSample_Process(), new String() ); + } |
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From: Stefan K. <sh...@us...> - 2006-09-11 14:21:26
|
Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/modules/actions/portlets In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv3168/src/java/org/openscience/nmrshiftdb/modules/actions/portlets Modified Files: OrderAction.java OrderFullfillAction.java Log Message: improved the lab system Index: OrderAction.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/modules/actions/portlets/OrderAction.java,v retrieving revision 1.16 retrieving revision 1.17 diff -C2 -r1.16 -r1.17 *** OrderAction.java 19 Oct 2005 13:45:19 -0000 1.16 --- OrderAction.java 11 Sep 2006 14:21:16 -0000 1.17 *************** *** 2,9 **** --- 2,11 ---- import java.io.File; + import java.io.FileOutputStream; import java.io.FileWriter; import java.io.StringReader; import java.util.Date; import java.util.Vector; + import java.util.zip.ZipOutputStream; import org.apache.jetspeed.modules.actions.portlets.VelocityPortletAction; *************** *** 18,21 **** --- 20,24 ---- import org.openscience.nmrshiftdb.om.DBCondition; import org.openscience.nmrshiftdb.om.DBConditionPeer; + import org.openscience.nmrshiftdb.om.DBRawFile; import org.openscience.nmrshiftdb.om.DBRawFilePeer; import org.openscience.nmrshiftdb.om.DBSample; *************** *** 34,37 **** --- 37,45 ---- */ public class OrderAction extends VelocityPortletAction { + + + public static String WORKER="worker"; + public static String ROBOT="robot"; + public static String SELF="self"; *************** *** 72,76 **** private void buildOrderContext(Context context, RunData data) throws Exception{ ! String sql="select SAMPLE.SAMPLE_ID from SAMPLE left join RAW_FILE using (SAMPLE_ID) where URL is null and USER_ID ="+((NmrshiftdbUser)data.getUser()).getUserId(); Vector v1=DBSamplePeer.executeQuery(sql); Vector v2=new Vector(); --- 80,85 ---- 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(); *************** *** 79,82 **** --- 88,92 ---- } context.put("samples",v2); + //done orders Criteria crit=new Criteria(); crit.add(DBSamplePeer.USER_ID, ((NmrshiftdbUser)data.getUser()).getUserId()); *************** *** 92,95 **** --- 102,113 ---- } 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(); + for(int i=0;i<v5.size();i++){ + v6.add(DBSamplePeer.retrieveByPK(new NumberKey(((Record) v5.get(i)).getValue(1).asInt()))); + } + context.put("samplesself",v6); context.put("data", data); if(data.getParameters().get("submitorshow")!=null && data.getParameters().get("submitorshow").equals("show")){ *************** *** 108,111 **** --- 126,178 ---- out.close(); context.put("molfile", "/nmrshiftdbhtml/" + outputFile.getName()); + //this is for the self fullfill + if(toshow.getProcess().equals(this.SELF) && toshow.getFinished().equals("false")){ + File rawfiledir=new File(GeneralUtils.getNmrshiftdbProperty("rawfiledirectoryuser",data)); + File currentraw=((File)data.getSession().getAttribute("currentraw")); + StringBuffer choosenfiles=new StringBuffer(); + if(data.getSession().getAttribute("choosenfiles")==null){ + data.getSession().setAttribute("choosenfiles", new Vector()); + } + v=(Vector)data.getSession().getAttribute("choosenfiles"); + if(data.getParameters().get("nmrshiftdbaction")!=null && data.getParameters().get("nmrshiftdbaction").equals("addtochoosenfiles")){ + if(!data.getParameters().get("filename").equals("..")){ + v.add(new File(currentraw+"/"+data.getParameters().get("filename"))); + }else{ + data.getSession().setAttribute("currentraw",new File(((File)data.getSession().getAttribute("currentraw"))+"/..")); + } + } + if(data.getSession().getAttribute("currentraw")==null) + data.getSession().setAttribute("currentraw",rawfiledir); + if(data.getParameters().get("nmrshiftdbaction")!=null && data.getParameters().get("nmrshiftdbaction").equals("browseto")){ + data.getSession().setAttribute("currentraw",new File(((File)data.getSession().getAttribute("currentraw"))+"/"+data.getParameters().get("filename"))); + } + for(int i=0;i<v.size();i++){ + choosenfiles.append(((File)v.get(i)).getName()+"\r\n"); + } + context.put("choosenfiles",choosenfiles); + Vector attachedfiles=toshow.getDBRawFiles(); + StringBuffer oldfiles=new StringBuffer(); + for(int i=0;i<attachedfiles.size();i++){ + oldfiles.append(((DBRawFile)attachedfiles.get(i)).getContainedFiles()); + } + context.put("oldfiles",oldfiles.toString()); + Vector files=new Vector(); + File[] filesindir=((File)data.getSession().getAttribute("currentraw")).listFiles(); + for(int i=0;i<filesindir.length;i++){ + Vector local=new Vector(); + local.add("portal/pane0/NMR+lab+administration?nmrshiftdbaction=addtochoosenfiles&filename="+filesindir[i].getName()+"&submitorshow=show&id="+toshow.getSampleId()); + local.add(filesindir[i].getName()); + local.add("portal/pane0/NMR+lab+administration?nmrshiftdbaction=browseto&filename="+filesindir[i].getName()+"&submitorshow=show&id="+toshow.getSampleId()); + files.add(local); + } + if(!((File)data.getSession().getAttribute("currentraw")).getCanonicalFile().equals(rawfiledir.getCanonicalFile())){ + Vector local=new Vector(); + local.add("portal/pane0/NMR+lab+administration?nmrshiftdbaction=addtochoosenfiles&filename=..&submitorshow=show&id="+toshow.getSampleId()); + local.add(".."); + local.add("portal/pane0/NMR+lab+administration?nmrshiftdbaction=browseto&filename=..&submitorshow=show&id="+toshow.getSampleId()); + files.add(local); + } + context.put("files",files); + } }else{ context.put("date", new Date()); *************** *** 169,172 **** --- 236,240 ---- sample.setSpecialCare(data.getParameters().get("specialcare")); sample.setFinished("false"); + sample.setProcess(data.getParameters().get("process")); String wishedSpectrum=""; if(data.getParameters().get("othertext")!=null && !data.getParameters().get("othertext").equals("")){ *************** *** 209,211 **** --- 277,311 ---- } } + + public void doFullfill(RunData data, Context context) throws Exception { + try{ + DBSample sample=DBSamplePeer.retrieveByPK(new NumberKey(data.getParameters().get("id"))); + Vector v=(Vector)data.getSession().getAttribute("choosenfiles"); + String filename=sample.getUsersId()+System.currentTimeMillis()+".zip"; + FileOutputStream baos=new FileOutputStream(GeneralUtils.getNmrshiftdbProperty("compressedfiledirectory",data)+"/"+filename); + ZipOutputStream zipout=new ZipOutputStream(baos); + StringBuffer attachedfiles=new StringBuffer(); + for(int i=0;i<v.size();i++){ + GeneralUtils.zipDir(((File)v.get(i)), zipout,new File(GeneralUtils.getNmrshiftdbProperty("rawfiledirectory",data))); + attachedfiles.append(((File)v.get(i)).getName()+"; "); + } + zipout.close(); + DBRawFile rawfile=new DBRawFile(); + rawfile.setSampleId(sample.getSampleId()); + rawfile.setUrl(GeneralUtils.getNmrshiftdbProperty("urlcompressedfiles",data)+"/"+filename); + rawfile.setContainedFiles(attachedfiles.toString()); + rawfile.save(); + if(data.getParameters().get("finished")!=null && data.getParameters().get("finished").equals("finished")){ + sample.setFinished("true"); + sample.save(); + } + data.getSession().removeAttribute("choosenfiles"); + data.getSession().setAttribute("currentraw",new File(GeneralUtils.getNmrshiftdbProperty("rawfiledirectory",data))); + buildOrderContext(context,data); + } + catch(Exception ex){ + 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 1.14 retrieving revision 1.15 diff -C2 -r1.14 -r1.15 *** OrderFullfillAction.java 19 Oct 2005 13:45:19 -0000 1.14 --- OrderFullfillAction.java 11 Sep 2006 14:21:16 -0000 1.15 *************** *** 49,52 **** --- 49,53 ---- crit.add(DBLabGroupPeer.LABGROUP_ID,((NmrshiftdbUser)data.getUser()).getLabGroup()); crit.add(DBSamplePeer.FINISHED, "false"); + crit.add(DBSamplePeer.PROCESS,OrderAction.WORKER); context.put("openorders",DBSamplePeer.doSelect(crit)); context.put("data", data); |
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From: Stefan K. <sh...@us...> - 2006-09-11 14:21:26
|
Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/om In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv3168/src/java/org/openscience/nmrshiftdb/om Modified Files: BaseDBSample.java BaseDBSamplePeer.java Log Message: improved the lab system Index: BaseDBSample.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/om/BaseDBSample.java,v retrieving revision 1.5 retrieving revision 1.6 diff -C2 -r1.5 -r1.6 *** BaseDBSample.java 4 Aug 2005 21:55:18 -0000 1.5 --- BaseDBSample.java 11 Sep 2006 14:21:16 -0000 1.6 *************** *** 2,17 **** ! import java.util.Date; ! import java.util.List; ! import java.util.Vector; ! ! import org.apache.turbine.om.BaseObject; ! import org.apache.turbine.om.NumberKey; ! import org.apache.turbine.om.ObjectKey; ! import org.apache.turbine.om.Persistent; ! import org.apache.turbine.om.Retrievable; import org.apache.turbine.om.peer.BasePeer; - import org.apache.turbine.util.ObjectUtils; import org.apache.turbine.util.db.Criteria; import org.apache.turbine.util.db.pool.DBConnection; --- 2,14 ---- ! import java.util.*; ! import java.math.*; ! import org.apache.turbine.om.*; import org.apache.turbine.om.peer.BasePeer; import org.apache.turbine.util.db.Criteria; + import org.apache.turbine.util.ObjectUtils; + import org.apache.turbine.util.StringUtils; + import org.apache.turbine.util.ParameterParser; + import org.apache.turbine.util.Log; import org.apache.turbine.util.db.pool.DBConnection; *************** *** 45,48 **** --- 42,47 ---- /** the value for the finished field */ private String finished; + /** the value for the process field */ + private String process; *************** *** 419,422 **** --- 418,447 ---- + /** + * Get the Process + * @return String + */ + public String getProcess() + { + return process; + } + + + /** + * Set the value of Process + */ + public void setProcess(String v ) + { + + + + if ( !ObjectUtils.equals(this.process, v) ) + { + this.process = v; + setModified(true); + } + } + + *************** *** 767,770 **** --- 792,796 ---- fieldNames_.add("WishedSpectrum"); fieldNames_.add("Finished"); + fieldNames_.add("Process"); } return fieldNames_; *************** *** 821,824 **** --- 847,854 ---- return getFinished(); } + if (name.equals("Process")) + { + return getProcess(); + } return null; } *************** *** 874,877 **** --- 904,911 ---- return getFinished(); } + if (name.equals(DBSamplePeer.PROCESS )) + { + return getProcess(); + } return null; } *************** *** 927,930 **** --- 961,968 ---- return getFinished(); } + if ( pos == 11 ) + { + return getProcess(); + } return null; } *************** *** 1085,1088 **** --- 1123,1127 ---- copyObj.setWishedSpectrum(wished_spectrum); copyObj.setFinished(finished); + copyObj.setProcess(process); *************** *** 1096,1100 **** copyObj.setSampleId((NumberKey)null); ! return copyObj; } } --- 1135,1139 ---- copyObj.setSampleId((NumberKey)null); ! return copyObj; } } Index: BaseDBSamplePeer.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/om/BaseDBSamplePeer.java,v retrieving revision 1.4 retrieving revision 1.5 diff -C2 -r1.4 -r1.5 *** BaseDBSamplePeer.java 4 Aug 2005 21:55:18 -0000 1.4 --- BaseDBSamplePeer.java 11 Sep 2006 14:21:16 -0000 1.5 *************** *** 1,19 **** package org.openscience.nmrshiftdb.om; ! import java.util.Vector; ! ! import org.apache.turbine.om.NumberKey; ! import org.apache.turbine.om.ObjectKey; ! import org.apache.turbine.om.peer.BasePeer; ! import org.apache.turbine.services.db.TurbineDB; ! import org.apache.turbine.util.Log; ! import org.apache.turbine.util.db.Criteria; ! import org.apache.turbine.util.db.map.MapBuilder; ! import org.apache.turbine.util.db.map.TableMap; import org.apache.turbine.util.db.pool.DBConnection; ! import org.openscience.nmrshiftdb.om.map.DBSampleMapBuilder; ! import com.workingdogs.village.QueryDataSet; ! import com.workingdogs.village.Record; /** --- 1,19 ---- package org.openscience.nmrshiftdb.om; ! import java.util.*; ! import java.math.*; ! import java.sql.*; ! import com.workingdogs.village.*; ! import org.apache.turbine.om.*; ! import org.apache.turbine.om.peer.*; ! import org.apache.turbine.util.*; ! import org.apache.turbine.util.db.*; ! import org.apache.turbine.util.db.map.*; import org.apache.turbine.util.db.pool.DBConnection; ! import org.apache.turbine.services.db.TurbineDB; ! import org.apache.turbine.util.TurbineException; ! // Local classes ! import org.openscience.nmrshiftdb.om.map.*; /** *************** *** 60,67 **** /** the column name for the FINISHED field */ public static final String FINISHED = mapBuilder.getDBSample_Finished(); /** number of columns for this peer */ ! public static final int numColumns = 11; /** A class that can be returned by this peer. */ --- 60,69 ---- /** the column name for the FINISHED field */ public static final String FINISHED = mapBuilder.getDBSample_Finished(); + /** the column name for the PROCESS field */ + public static final String PROCESS = mapBuilder.getDBSample_Process(); /** number of columns for this peer */ ! public static final int numColumns = 12; /** A class that can be returned by this peer. */ *************** *** 119,123 **** public static ObjectKey doInsert( Criteria criteria ) throws Exception { ! return BasePeer.doInsert( criteria ); } --- 121,125 ---- public static ObjectKey doInsert( Criteria criteria ) throws Exception { ! return BasePeer.doInsert( criteria ); } *************** *** 130,134 **** throws Exception { ! return BasePeer.doInsert( criteria, dbCon ); } --- 132,136 ---- throws Exception { ! return BasePeer.doInsert( criteria, dbCon ); } *************** *** 147,150 **** --- 149,153 ---- criteria.addSelectColumn( WISHED_SPECTRUM ); criteria.addSelectColumn( FINISHED ); + criteria.addSelectColumn( PROCESS ); } *************** *** 196,199 **** --- 199,203 ---- obj.setWishedSpectrum(row.getValue(offset+9).asString()); obj.setFinished(row.getValue(offset+10).asString()); + obj.setProcess(row.getValue(offset+11).asString()); } *************** *** 228,232 **** } ! // BasePeer returns a Vector of Value (Village) arrays. The array // order follows the order columns were placed in the Select clause. --- 232,236 ---- } ! // BasePeer returns a Vector of Value (Village) arrays. The array // order follows the order columns were placed in the Select clause. *************** *** 248,252 **** } ! // BasePeer returns a Vector of Value (Village) arrays. The array // order follows the order columns were placed in the Select clause. --- 252,256 ---- } ! // BasePeer returns a Vector of Value (Village) arrays. The array // order follows the order columns were placed in the Select clause. *************** *** 296,300 **** Criteria(mapBuilder.getDatabaseMap().getName(), 2); selectCriteria.put( SAMPLE_ID, criteria.remove(SAMPLE_ID) ); ! BasePeer.doUpdate( selectCriteria, criteria ); } --- 300,304 ---- Criteria(mapBuilder.getDatabaseMap().getName(), 2); selectCriteria.put( SAMPLE_ID, criteria.remove(SAMPLE_ID) ); ! BasePeer.doUpdate( selectCriteria, criteria ); } *************** *** 311,315 **** Criteria(mapBuilder.getDatabaseMap().getName(), 2); selectCriteria.put( SAMPLE_ID, criteria.remove(SAMPLE_ID) ); ! BasePeer.doUpdate( selectCriteria, criteria, dbCon ); } --- 315,319 ---- Criteria(mapBuilder.getDatabaseMap().getName(), 2); selectCriteria.put( SAMPLE_ID, criteria.remove(SAMPLE_ID) ); ! BasePeer.doUpdate( selectCriteria, criteria, dbCon ); } *************** *** 321,325 **** public static void doDelete(Criteria criteria) throws Exception { ! BasePeer.doDelete ( criteria ); } --- 325,329 ---- public static void doDelete(Criteria criteria) throws Exception { ! BasePeer.doDelete ( criteria ); } *************** *** 333,337 **** public static void doDelete(Criteria criteria, DBConnection dbCon) throws Exception { ! BasePeer.doDelete ( criteria, dbCon ); } --- 337,341 ---- public static void doDelete(Criteria criteria, DBConnection dbCon) throws Exception { ! BasePeer.doDelete ( criteria, dbCon ); } *************** *** 410,413 **** --- 414,418 ---- criteria.add( WISHED_SPECTRUM, obj.getWishedSpectrum() ); criteria.add( FINISHED, obj.getFinished() ); + criteria.add( PROCESS, obj.getProcess() ); return criteria; } *************** *** 490,494 **** ! Vector rows = BasePeer.doSelect(c); Vector results = new Vector(); --- 495,499 ---- ! Vector rows = BasePeer.doSelect(c); Vector results = new Vector(); *************** *** 557,561 **** ! Vector rows = BasePeer.doSelect(c); Vector results = new Vector(); --- 562,566 ---- ! Vector rows = BasePeer.doSelect(c); Vector results = new Vector(); *************** *** 624,628 **** ! Vector rows = BasePeer.doSelect(c); Vector results = new Vector(); --- 629,633 ---- ! Vector rows = BasePeer.doSelect(c); Vector results = new Vector(); *************** *** 691,695 **** ! Vector rows = BasePeer.doSelect(c); Vector results = new Vector(); --- 696,700 ---- ! Vector rows = BasePeer.doSelect(c); Vector results = new Vector(); *************** *** 762,766 **** DBMoleculePeer.addSelectColumns(c); int offset5 = offset4 + DBMoleculePeer.numColumns; ! Vector rows = BasePeer.doSelect(c); Vector results = new Vector(); --- 767,771 ---- DBMoleculePeer.addSelectColumns(c); int offset5 = offset4 + DBMoleculePeer.numColumns; ! Vector rows = BasePeer.doSelect(c); Vector results = new Vector(); *************** *** 883,887 **** DBMoleculePeer.addSelectColumns(c); int offset4 = offset3 + DBMoleculePeer.numColumns; ! Vector rows = BasePeer.doSelect(c); Vector results = new Vector(); --- 888,892 ---- DBMoleculePeer.addSelectColumns(c); int offset4 = offset3 + DBMoleculePeer.numColumns; ! Vector rows = BasePeer.doSelect(c); Vector results = new Vector(); *************** *** 980,984 **** DBMoleculePeer.addSelectColumns(c); int offset4 = offset3 + DBMoleculePeer.numColumns; ! Vector rows = BasePeer.doSelect(c); Vector results = new Vector(); --- 985,989 ---- DBMoleculePeer.addSelectColumns(c); int offset4 = offset3 + DBMoleculePeer.numColumns; ! Vector rows = BasePeer.doSelect(c); Vector results = new Vector(); *************** *** 1079,1083 **** int offset5 = offset4 + DBConditionPeer.numColumns; ! Vector rows = BasePeer.doSelect(c); Vector results = new Vector(); --- 1084,1088 ---- int offset5 = offset4 + DBConditionPeer.numColumns; ! Vector rows = BasePeer.doSelect(c); Vector results = new Vector(); |
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From: Stefan K. <sh...@us...> - 2006-09-11 14:21:25
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/conf/jetspeed/WEB-INF/conf In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv3168/src/conf/jetspeed/WEB-INF/conf Modified Files: JetspeedResources.properties NMRShiftDB.properties Log Message: improved the lab system Index: JetspeedResources.properties =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/conf/jetspeed/WEB-INF/conf/JetspeedResources.properties,v retrieving revision 1.22 retrieving revision 1.23 diff -C2 -r1.22 -r1.23 *** JetspeedResources.properties 1 Jun 2006 14:47:13 -0000 1.22 --- JetspeedResources.properties 11 Sep 2006 14:21:16 -0000 1.23 *************** *** 216,219 **** --- 216,220 ---- #daemon.entry=buildsdf daemon.entry=buildsvm + #daemon.entry=robotdaemon daemon.feeddaemon.classname=org.apache.jetspeed.daemon.impl.FeedDaemon *************** *** 257,260 **** --- 258,265 ---- daemon.buildsvm.onstartup=true + daemon.robotdaemon.classname=org.openscience.nmrshiftdb.daemons.AssignRobotDaemon + daemon.robotdaemon.interval=3600 + daemon.robotdaemon.onstartup=true + ######################################### # Jetspeed Content # Index: NMRShiftDB.properties =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/conf/jetspeed/WEB-INF/conf/NMRShiftDB.properties,v retrieving revision 1.49 retrieving revision 1.50 diff -C2 -r1.49 -r1.50 *** NMRShiftDB.properties 28 May 2006 15:27:09 -0000 1.49 --- NMRShiftDB.properties 11 Sep 2006 14:21:16 -0000 1.50 *************** *** 29,32 **** --- 29,36 ---- #A directory where raw files can be found, comment out if server is not for labgroup adminstration rawfiledirectory=/home/shk3 + #A directory where raw files can be found for user assignment + rawfiledirectoryuser=/home/shk3 + #A directory where raw files can be found for robot assignment + rawfiledirectoryrobot=/home/shk3 #A directoy where to put compressed raw files for download compressedfiledirectory=/home/shk3 |
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From: Stefan K. <sh...@us...> - 2006-09-11 14:21:25
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/sql In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv3168/src/sql Modified Files: nmrshiftdb-schema.sql populate-mysql.sql Log Message: improved the lab system Index: nmrshiftdb-schema.sql =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/sql/nmrshiftdb-schema.sql,v retrieving revision 1.78 retrieving revision 1.79 diff -C2 -r1.78 -r1.79 *** nmrshiftdb-schema.sql 8 Jun 2006 12:22:46 -0000 1.78 --- nmrshiftdb-schema.sql 11 Sep 2006 14:21:16 -0000 1.79 *************** *** 829,832 **** --- 829,833 ---- WISHED_SPECTRUM VARCHAR (50) NOT NULL, FINISHED VARCHAR (8) NOT NULL, + PROCESS VARCHAR (8) NOT NULL, PRIMARY KEY(SAMPLE_ID), FOREIGN KEY (USER_ID) REFERENCES TURBINE_USER (USER_ID), Index: populate-mysql.sql =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/sql/populate-mysql.sql,v retrieving revision 1.58 retrieving revision 1.59 diff -C2 -r1.58 -r1.59 *** populate-mysql.sql 14 Jul 2006 08:09:59 -0000 1.58 --- populate-mysql.sql 11 Sep 2006 14:21:16 -0000 1.59 *************** *** 142,145 **** --- 142,146 ---- alter table GUESTBOOK change VALID VALID enum("false","true") not null default "false"; alter table CONDITION_TYPE change CML_ENTRY_TYPE CML_ENTRY_TYPE enum("","metadata","substance","condition") not null default ""; + alter table SAMPLE change PROCESS PROCESS enum("self","worker","robot") not null default "self"; alter table MOLECULE change fp0 fp0 BIGINT UNSIGNED; alter table MOLECULE change fp1 fp1 BIGINT UNSIGNED; |
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From: Stefan K. <sh...@us...> - 2006-09-11 14:21:20
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/vmtemplates/portlets/html In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv3168/src/vmtemplates/portlets/html Modified Files: user-order.vm Log Message: improved the lab system Index: user-order.vm =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/vmtemplates/portlets/html/user-order.vm,v retrieving revision 1.28 retrieving revision 1.29 diff -C2 -r1.28 -r1.29 *** user-order.vm 17 May 2006 13:20:35 -0000 1.28 --- user-order.vm 11 Sep 2006 14:21:16 -0000 1.29 *************** *** 3,7 **** <tr><td><a href="portal/pane0/Help;jsessionid=$data.getSession().getId()?URL=using.html#labadmin">Help</a></td></tr> <tr> ! <td>You have the following <b>open orders</b>:</td><td width="50"></td><td>The following <b>orders have been (partly or fully) done</b> and wait for assignment:</td> </tr> <tr> --- 3,7 ---- <tr><td><a href="portal/pane0/Help;jsessionid=$data.getSession().getId()?URL=using.html#labadmin">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> </tr> <tr> *************** *** 24,27 **** --- 24,44 ---- <td width="50"></td> <td> + #if($samplesself.size()==0) + None + #else + <table> + #foreach($sample in $samplesself) + #set($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 *************** *** 48,51 **** --- 65,69 ---- <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 $sample.getUsersId()</b> has the following properties: *************** *** 174,177 **** --- 192,216 ---- </tr> </table> + #if($submitorshow=="show" && $sample.getProcess()=="self" && $sample.getFinished()=="false") + <table> + <tr> + <td> + The following files are already attached: $oldfiles + <form name="orderform" method="post" action="portal/pane0/NMR+lab+administration"> + <input type="hidden" name="id" value="$sample.getSampleId()"> + <textarea name="url" cols="20" rows="20">$choosenfiles</textarea><br> + <input type="checkbox" name="finished" value="finished">Check if you consider this order to be finished<br> + <input type="submit" name="eventSubmit_doFullfill" value="Attach these files to this order"/> + </form> + </td> + <td> + <b>Choose files/directories you want to attach to this order!</b><br> + #foreach($file in $files) + <a href="$file.get(0)">$file.get(1)</a> <a href="$file.get(2)">>>>></a><br> + #end + </td> + </tr> + </table> + #end #else You are not a user in any labgroup or not yet approved! |
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From: Stefan K. <sh...@us...> - 2006-09-01 21:05:38
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/doc In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv8518/doc Modified Files: ER-Diagram_for_NMRShiftDB.gd ER-Diagram_for_NMRShiftDB.pdf ER-Diagram_for_NMRShiftDB.ps Log Message: improved doc Index: ER-Diagram_for_NMRShiftDB.gd =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/doc/ER-Diagram_for_NMRShiftDB.gd,v retrieving revision 1.43 retrieving revision 1.44 diff -C2 -r1.43 -r1.44 *** ER-Diagram_for_NMRShiftDB.gd 19 Oct 2005 09:49:44 -0000 1.43 --- ER-Diagram_for_NMRShiftDB.gd 1 Sep 2006 21:05:27 -0000 1.44 *************** *** 1529,1548 **** } - GenericNode 1656 - { - { Name "" } - { Annotation "" } - { Parent 0 } - { Index "" } - } - - GenericNode 1657 - { - { Name "Canonical\rName" } - { Annotation "" } - { Parent 0 } - { Index "" } - } - GenericNode 1658 { --- 1529,1532 ---- *************** *** 1563,1591 **** GenericNode 1660 { ! { Name "" } ! { Annotation "" } ! { Parent 0 } ! { Index "" } ! } ! ! 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From: Stefan K. <sh...@us...> - 2006-08-31 15:45:40
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/webservices In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv19687/src/java/org/openscience/nmrshiftdb/webservices Modified Files: NMRShiftDBServiceBindingImpl.java Log Message: bug Index: NMRShiftDBServiceBindingImpl.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/webservices/NMRShiftDBServiceBindingImpl.java,v retrieving revision 1.17 retrieving revision 1.18 diff -C2 -r1.17 -r1.18 *** NMRShiftDBServiceBindingImpl.java 31 Aug 2006 14:54:23 -0000 1.17 --- NMRShiftDBServiceBindingImpl.java 31 Aug 2006 15:45:35 -0000 1.18 *************** *** 157,168 **** } CMLMolecule cmlmol=(CMLMolecule)cmlcml.getChildCMLElement("molecule",0); - boolean[] doublebondconfigurations=new boolean[cmlmol.getBondCount()]; - for(int i=0;i<cmlmol.getBondCount();i++){ - CMLBond bond=cmlmol.getBonds().get(i); - if(bond.getFirstChildElement("doublebondconfiguration")==null){ - doublebondconfigurations[i]=true; - } - - } Elements spectra=cmlcml.getChildCMLElements("spectrum"); if(spectra.size()==0){ --- 157,160 ---- *************** *** 201,204 **** --- 193,205 ---- mdlwriter.write(cdkmol); subData.setMol(writer.toString(),false,false,true); + 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; + } + + } + subData.setIsDoubleBondSpecified(doublebondconfigurations); for(int k=0;k<cmlmol.getAtomCount();k++){ subData.getMolWithH().getAtom(k).setID(cmlmol.getAtom(k).getId()); |
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From: Stefan K. <sh...@us...> - 2006-08-31 14:54:27
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/webservices In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv30605/src/java/org/openscience/nmrshiftdb/webservices Modified Files: NMRShiftDBServiceBindingImpl.java Log Message: extended web service Index: NMRShiftDBServiceBindingImpl.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/webservices/NMRShiftDBServiceBindingImpl.java,v retrieving revision 1.16 retrieving revision 1.17 diff -C2 -r1.16 -r1.17 *** NMRShiftDBServiceBindingImpl.java 31 Aug 2006 13:13:20 -0000 1.16 --- NMRShiftDBServiceBindingImpl.java 31 Aug 2006 14:54:23 -0000 1.17 *************** *** 49,52 **** --- 49,53 ---- import org.xmlcml.cml.base.CMLElements; import org.xmlcml.cml.base.CMLUtil; + import org.xmlcml.cml.element.CMLBond; import org.xmlcml.cml.element.CMLBuilder; import org.xmlcml.cml.element.CMLCml; *************** *** 156,159 **** --- 157,168 ---- } CMLMolecule cmlmol=(CMLMolecule)cmlcml.getChildCMLElement("molecule",0); + boolean[] doublebondconfigurations=new boolean[cmlmol.getBondCount()]; + for(int i=0;i<cmlmol.getBondCount();i++){ + CMLBond bond=cmlmol.getBonds().get(i); + if(bond.getFirstChildElement("doublebondconfiguration")==null){ + doublebondconfigurations[i]=true; + } + + } Elements spectra=cmlcml.getChildCMLElements("spectrum"); if(spectra.size()==0){ *************** *** 294,298 **** for(int i=0; i<elements.size(); i++) { Element elem = elements.get(i); ! if(!elem.getLocalName().equals("entry")){ elem.setNamespaceURI(CMLUtil.CML_NS); if (elem.getChildCount() != 0) { --- 303,307 ---- for(int i=0; i<elements.size(); i++) { Element elem = elements.get(i); ! if(!elem.getLocalName().equals("entry") && !elem.getLocalName().equals("doublebondconfiguration")){ elem.setNamespaceURI(CMLUtil.CML_NS); if (elem.getChildCount() != 0) { |
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From: Stefan K. <sh...@us...> - 2006-08-31 13:13:23
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/webservices In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv19089/src/java/org/openscience/nmrshiftdb/webservices Modified Files: NMRShiftDBServiceBindingImpl.java Log Message: extended submit service Index: NMRShiftDBServiceBindingImpl.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/webservices/NMRShiftDBServiceBindingImpl.java,v retrieving revision 1.15 retrieving revision 1.16 diff -C2 -r1.15 -r1.16 *** NMRShiftDBServiceBindingImpl.java 30 Aug 2006 18:37:34 -0000 1.15 --- NMRShiftDBServiceBindingImpl.java 31 Aug 2006 13:13:20 -0000 1.16 *************** *** 165,168 **** --- 165,169 ---- for(int i=0;i<spectra.size();i++){ CMLSpectrum spectrum=(CMLSpectrum)spectra.get(i); + CMLMolecule molecule=(CMLMolecule)cmlcml.getChildCMLElements("molecule").get(0); SubmittingData subData=new SubmittingData(webinfdir+"conf/normalizer.xml"); //is this an edit? *************** *** 174,177 **** --- 175,187 ---- } subData.setMeasured(); + StringBuffer names=new StringBuffer(); + for(int k=0;k<molecule.getNameElements().size();k++){ + if(molecule.getNameElements().get(k).getAttribute("convention")!=null && molecule.getNameElements().get(k).getAttribute("convention").getValue().equals("CAS")){ + subData.setCasNumber(molecule.getNameElements().get(k).getXMLContent()); + }else{ + names.append(molecule.getNameElements().get(k).getXMLContent()+"\r\n"); + } + } + subData.setChemName(names.toString()); DBSpectrumType type=DBSpectrumTypePeer.getByName(spectrum.getMetadataListElements().get(0).getMetadataDescendantsByName("nmr:OBSERVENUCLEUS").get(0).getContent()); subData.setChoosenSpectrumType(type); |
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From: Stefan K. <sh...@us...> - 2006-08-30 18:37:43
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/webservices In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv4251/src/java/org/openscience/nmrshiftdb/webservices Modified Files: NMRShiftDBServiceBindingImpl.java Log Message: minor changes Index: NMRShiftDBServiceBindingImpl.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/webservices/NMRShiftDBServiceBindingImpl.java,v retrieving revision 1.14 retrieving revision 1.15 diff -C2 -r1.14 -r1.15 *** NMRShiftDBServiceBindingImpl.java 29 Aug 2006 16:10:06 -0000 1.14 --- NMRShiftDBServiceBindingImpl.java 30 Aug 2006 18:37:34 -0000 1.15 *************** *** 6,10 **** import java.io.StringWriter; import java.rmi.RemoteException; - import java.sql.Statement; import java.util.Date; import java.util.HashMap; --- 6,9 ---- *************** *** 24,32 **** import org.apache.turbine.om.NumberKey; import org.apache.turbine.om.security.User; - import org.apache.turbine.services.db.TurbineDB; import org.apache.turbine.services.security.TurbineSecurity; import org.apache.turbine.util.TurbineConfig; import org.apache.turbine.util.db.Criteria; - import org.apache.turbine.util.db.pool.DBConnection; import org.openscience.cdk.ChemFile; import org.openscience.cdk.interfaces.IChemFile; --- 23,29 ---- *************** *** 44,47 **** --- 41,45 ---- import org.openscience.nmrshiftdb.om.NmrshiftdbUser; import org.openscience.nmrshiftdb.om.NmrshiftdbUserPeer; + import org.openscience.nmrshiftdb.portlets.SubmitPortlet; import org.openscience.nmrshiftdb.util.GeneralUtils; import org.openscience.nmrshiftdb.util.NmrshiftdbConstants; *************** *** 171,176 **** if(spectrum.getMetadataListElements().size()>0 && spectrum.getMetadataListElements().get(0).getMetadataDescendantsByName("nmr:nmrshiftdbid").size()>0){ if(spectrum.getMetadataListElements().get(0).getMetadataDescendantsByName("nmr:nmrshiftdbid").size()>0){ - DBConnection dbconn = TurbineDB.getConnection(); - Statement stmt = dbconn.createStatement(); List l=DBSpectrumPeer.executeQuery("select SPECTRUM_ID from SPECTRUM where NMRSHIFTDB_NUMBER='"+spectrum.getMetadataListElements().get(0).getMetadataDescendantsByName("nmr:nmrshiftdbid").get(0).getContent()+"'"); subData.setEditSpectrum(new NumberKey(((Record)l.get(0)).getValue(1).asInt())); --- 169,172 ---- *************** *** 207,211 **** if(((DBConditionType) subData.getConditions().get(l)).getConditionName().equals("Solvent")){ for(int k=0;k<els.size();k++){ ! if(els.get(k).getAttribute("dictRef")!=null && els.get(k).getAttribute("dictRef").getValue().equals("jcamp:.SOLVENTNAME")){ ((DBConditionType) subData.getConditions().get(l)).setCurrentValue(((CMLScalar)els.get(k)).getValue()); break; --- 203,207 ---- if(((DBConditionType) subData.getConditions().get(l)).getConditionName().equals("Solvent")){ for(int k=0;k<els.size();k++){ ! if(els.get(k).getAttribute("dictRef")!=null && els.get(k).getAttribute("dictRef").getValue().equals(NmrshiftdbConstants.solvent)){ ((DBConditionType) subData.getConditions().get(l)).setCurrentValue(((CMLScalar)els.get(k)).getValue()); break; *************** *** 215,219 **** if(((DBConditionType) subData.getConditions().get(l)).getConditionName().equals("Temperature [K]")){ for(int k=0;k<els.size();k++){ ! if(els.get(k).getAttribute("dictRef")!=null && els.get(k).getAttribute("dictRef").getValue().equals("jcamp:TEMPERATURE")){ ((DBConditionType) subData.getConditions().get(l)).setCurrentValue(((CMLScalar)els.get(k)).getValue()); break; --- 211,215 ---- if(((DBConditionType) subData.getConditions().get(l)).getConditionName().equals("Temperature [K]")){ for(int k=0;k<els.size();k++){ ! if(els.get(k).getAttribute("dictRef")!=null && els.get(k).getAttribute("dictRef").getValue().equals(NmrshiftdbConstants.temperature)){ ((DBConditionType) subData.getConditions().get(l)).setCurrentValue(((CMLScalar)els.get(k)).getValue()); break; *************** *** 223,227 **** if(((DBConditionType) subData.getConditions().get(l)).getConditionName().equals("Field Strength [MHz]")){ for(int k=0;k<els.size();k++){ ! if(els.get(k).getAttribute("dictRef")!=null && els.get(k).getAttribute("dictRef").getValue().equals("jcamp:.OBSERVE FREQUENCY")){ ((DBConditionType) subData.getConditions().get(l)).setCurrentValue(((CMLScalar)els.get(k)).getValue()); break; --- 219,223 ---- if(((DBConditionType) subData.getConditions().get(l)).getConditionName().equals("Field Strength [MHz]")){ for(int k=0;k<els.size();k++){ ! if(els.get(k).getAttribute("dictRef")!=null && els.get(k).getAttribute("dictRef").getValue().equals(NmrshiftdbConstants.frequency)){ ((DBConditionType) subData.getConditions().get(l)).setCurrentValue(((CMLScalar)els.get(k)).getValue()); break; *************** *** 230,234 **** } if(((DBConditionType) subData.getConditions().get(l)).getConditionName().equals("Assignment Method")){ ! ((DBConditionType) subData.getConditions().get(l)).setCurrentValue(spectrum.getMetadataListElements().get(0).getMetadataDescendantsByName("nmr:assignmentMethod").get(0).getContent()); } } --- 226,230 ---- } if(((DBConditionType) subData.getConditions().get(l)).getConditionName().equals("Assignment Method")){ ! ((DBConditionType) subData.getConditions().get(l)).setCurrentValue(spectrum.getMetadataListElements().get(0).getMetadataDescendantsByName(NmrshiftdbConstants.assignment).get(0).getContent()); } } *************** *** 270,273 **** --- 266,270 ---- subData.save(user.getUserId(),"false","bioclipse", new Date(),null,Integer.parseInt(GeneralUtils.getNmrshiftdbProperty("hosecode.spheres")), false); sb.append(subData.nmrshiftdbnr+" "); + SubmitPortlet.doReview(subData, new Date(), user, null); } DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance(); |
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From: Stefan K. <sh...@us...> - 2006-08-30 18:37:43
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/util In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv4251/src/java/org/openscience/nmrshiftdb/util Modified Files: NmrshiftdbConstants.java Log Message: minor changes Index: NmrshiftdbConstants.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/util/NmrshiftdbConstants.java,v retrieving revision 1.34 retrieving revision 1.35 diff -C2 -r1.34 -r1.35 *** NmrshiftdbConstants.java 24 Aug 2006 12:00:25 -0000 1.34 --- NmrshiftdbConstants.java 30 Aug 2006 18:37:34 -0000 1.35 *************** *** 70,73 **** --- 70,81 ---- public static String CONDITION="condition"; + //These are used for handling of properties in cml submits. need to duplicate the Bc_nmrshfitdbConstants in bc_nmrshiftdb of bioclipse + public static String frequency="jcamp:.OBSERVE FREQUENCY"; + public static String solvent="jcamp:.SOLVENTNAME"; + public static String temperature="jcamp:TEMPERATURE"; + public static String assignment="nmr:assignmentMethod"; + public static String nucleus="nmr:OBSERVENUCLEUS"; + public static String nmrid="nmr:nmrshiftdbid"; + //These are needed for velocity which cannot read attributes public String getSUBSPECTRUM(){ |
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From: Stefan K. <sh...@us...> - 2006-08-29 16:10:18
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/util In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv17360/src/java/org/openscience/nmrshiftdb/util Modified Files: GeneralUtils.java Log Message: improved web service Index: GeneralUtils.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/util/GeneralUtils.java,v retrieving revision 1.185 retrieving revision 1.186 diff -C2 -r1.185 -r1.186 *** GeneralUtils.java 28 Aug 2006 14:33:58 -0000 1.185 --- GeneralUtils.java 29 Aug 2006 16:10:05 -0000 1.186 *************** *** 820,824 **** StringBuffer buffer = new StringBuffer(); for (int i = 0; i < text.length(); i++) { ! if (text.charAt(i) == '\'' || text.charAt(i) == '\"' || text.charAt(i) == '\\' || text.charAt(i) == '%') { buffer.append('\\'); } --- 820,824 ---- StringBuffer buffer = new StringBuffer(); for (int i = 0; i < text.length(); i++) { ! if (text.charAt(i) == '\'' || text.charAt(i) == '\"' || text.charAt(i) == '\\' || text.charAt(i) == '%' || text.charAt(i) == '\'') { buffer.append('\\'); } |
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From: Stefan K. <sh...@us...> - 2006-08-29 16:10:15
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv17360/src/java/org/openscience/nmrshiftdb Modified Files: AdminPanel.java Log Message: improved web service Index: AdminPanel.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/AdminPanel.java,v retrieving revision 1.231 retrieving revision 1.232 diff -C2 -r1.231 -r1.232 *** AdminPanel.java 28 Aug 2006 14:33:58 -0000 1.231 --- AdminPanel.java 29 Aug 2006 16:10:04 -0000 1.232 *************** *** 994,998 **** DBConnection dbconn = TurbineDB.getConnection(); Statement stmt = dbconn.createStatement(); ! ResultSet rs = stmt.executeQuery("select MOLECULE_ID from MOLECULE;"); int errors=0; while (rs.next()) { --- 994,1004 ---- DBConnection dbconn = TurbineDB.getConnection(); Statement stmt = dbconn.createStatement(); ! ResultSet rs = stmt.executeQuery("select SPECTRUM_ID, COMMENT from SPECTRUM;"); ! FileOutputStream fos=new FileOutputStream("/tmp/gr.sql"); ! while (rs.next()) { ! fos.write(new String("update SPECTRUM set COMMENT='"+GeneralUtils.escape(rs.getString(2))+"' where SPECTRUM_ID="+rs.getInt(1)+";\r\n").getBytes()); ! } ! fos.close(); ! /*ResultSet rs = stmt.executeQuery("select MOLECULE_ID from MOLECULE;"); int errors=0; while (rs.next()) { *************** *** 1005,1015 **** errors++; } ! } //makes multis from h count ! /*for(int i=115962;i<=118436;i++){ System.err.println(i+""); ! ResultSet rs=stmt.executeQuery("select SIGNAL_ID from SIGNAL where SPECTRUM_ID="+i); ! while(rs.next()){ ! DBSignal signal=DBSignalPeer.retrieveByPK(new NumberKey(rs.getInt(1))); if(signal.getMultiplicity().equals("")){ if(((DBAtom)signal.getAtoms().get(0)).getHydrogenCount()==0) --- 1011,1024 ---- errors++; } ! }*/ //makes multis from h count ! /* ! ResultSet rs = stmt.executeQuery("select SIGNAL.SPECTRUM_ID, SPECTRUM.NMRSHIFTDB_NUMBER, count(*) as c from SIGNAL, SPECTRUM where MULTIPLICITY='' and SIGNAL.SPECTRUM_ID=SPECTRUM.SPECTRUM_ID and SPECTRUM.SPECTRUM_TYPE_ID=1 and SPECTRUM.REVIEW_FLAG='true' group by SIGNAL.SPECTRUM_ID having c>3"); ! while (rs.next()){ ! int i=rs.getInt(1); System.err.println(i+""); ! ResultSet rs2=stmt.executeQuery("select SIGNAL_ID from SIGNAL where SPECTRUM_ID="+i); ! while(rs2.next()){ ! DBSignal signal=DBSignalPeer.retrieveByPK(new NumberKey(rs2.getInt(1))); if(signal.getMultiplicity().equals("")){ if(((DBAtom)signal.getAtoms().get(0)).getHydrogenCount()==0) *************** *** 1063,1067 **** } }*/ ! System.err.println("There were "+errors+" errors"); } --- 1072,1076 ---- } }*/ ! //System.err.println("There were "+errors+" errors"); } |
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From: Stefan K. <sh...@us...> - 2006-08-29 16:10:15
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/om In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv17360/src/java/org/openscience/nmrshiftdb/om Modified Files: DBAtom.java Log Message: improved web service Index: DBAtom.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/om/DBAtom.java,v retrieving revision 1.53 retrieving revision 1.54 diff -C2 -r1.53 -r1.54 *** DBAtom.java 28 Aug 2006 14:33:58 -0000 1.53 --- DBAtom.java 29 Aug 2006 16:10:05 -0000 1.54 *************** *** 61,65 **** setAtomicMass(atom.getAtomicNumber()); setFormalCharge(atom.getFormalCharge()); ! if ((!Double.isNaN(atom.getPoint3d().z) && atom.getPoint3d().z != 0) || force3d) { coords3 = new DBCoordinateSet3d(atom.getPoint2d().x, atom.getPoint2d().y, atom.getPoint3d().z, 1); } else { --- 61,65 ---- setAtomicMass(atom.getAtomicNumber()); setFormalCharge(atom.getFormalCharge()); ! if (atom.getPoint3d()!=null && ((!Double.isNaN(atom.getPoint3d().z) && atom.getPoint3d().z != 0) || force3d)) { coords3 = new DBCoordinateSet3d(atom.getPoint2d().x, atom.getPoint2d().y, atom.getPoint3d().z, 1); } else { |
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From: Stefan K. <sh...@us...> - 2006-08-29 16:10:14
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/webservices In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv17360/src/java/org/openscience/nmrshiftdb/webservices Modified Files: NMRShiftDBServiceBindingImpl.java Log Message: improved web service Index: NMRShiftDBServiceBindingImpl.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/webservices/NMRShiftDBServiceBindingImpl.java,v retrieving revision 1.13 retrieving revision 1.14 diff -C2 -r1.13 -r1.14 *** NMRShiftDBServiceBindingImpl.java 28 Aug 2006 14:33:58 -0000 1.13 --- NMRShiftDBServiceBindingImpl.java 29 Aug 2006 16:10:06 -0000 1.14 *************** *** 6,11 **** --- 6,13 ---- import java.io.StringWriter; import java.rmi.RemoteException; + import java.sql.Statement; import java.util.Date; import java.util.HashMap; + import java.util.List; import java.util.Properties; import java.util.Vector; *************** *** 20,35 **** --- 22,43 ---- import nu.xom.converters.DOMConverter; + import org.apache.turbine.om.NumberKey; import org.apache.turbine.om.security.User; + import org.apache.turbine.services.db.TurbineDB; import org.apache.turbine.services.security.TurbineSecurity; import org.apache.turbine.util.TurbineConfig; import org.apache.turbine.util.db.Criteria; + import org.apache.turbine.util.db.pool.DBConnection; import org.openscience.cdk.ChemFile; import org.openscience.cdk.interfaces.IChemFile; import org.openscience.cdk.interfaces.IMolecule; import org.openscience.cdk.io.CMLReader; + import org.openscience.cdk.io.MDLWriter; + import org.openscience.cdk.io.cml.ChemFileCDO; import org.openscience.cdk.tools.manipulator.AtomContainerManipulator; import org.openscience.nmrshiftdb.PredictionTool; import org.openscience.nmrshiftdb.om.DBConditionType; import org.openscience.nmrshiftdb.om.DBLiterature; + import org.openscience.nmrshiftdb.om.DBSpectrumPeer; import org.openscience.nmrshiftdb.om.DBSpectrumType; import org.openscience.nmrshiftdb.om.DBSpectrumTypePeer; *************** *** 50,54 **** import org.xmlcml.cml.element.CMLScalar; import org.xmlcml.cml.element.CMLSpectrum; ! import org.xmlcml.cml.legacy.molecule.MDLConverter; public class NMRShiftDBServiceBindingImpl implements NMRShiftDB { --- 58,63 ---- import org.xmlcml.cml.element.CMLScalar; import org.xmlcml.cml.element.CMLSpectrum; ! ! import com.workingdogs.village.Record; public class NMRShiftDBServiceBindingImpl implements NMRShiftDB { *************** *** 159,169 **** CMLSpectrum spectrum=(CMLSpectrum)spectra.get(i); SubmittingData subData=new SubmittingData(webinfdir+"conf/normalizer.xml"); subData.setMeasured(); DBSpectrumType type=DBSpectrumTypePeer.getByName(spectrum.getMetadataListElements().get(0).getMetadataDescendantsByName("nmr:OBSERVENUCLEUS").get(0).getContent()); subData.setChoosenSpectrumType(type); StringWriter writer=new StringWriter(); ! MDLConverter mdlconv=new MDLConverter(); ! mdlconv.setVersion("V2000"); ! mdlconv.writeMOL(writer,cmlmol); subData.setMol(writer.toString(),false,false,true); for(int k=0;k<cmlmol.getAtomCount();k++){ --- 168,188 ---- CMLSpectrum spectrum=(CMLSpectrum)spectra.get(i); SubmittingData subData=new SubmittingData(webinfdir+"conf/normalizer.xml"); + //is this an edit? + if(spectrum.getMetadataListElements().size()>0 && spectrum.getMetadataListElements().get(0).getMetadataDescendantsByName("nmr:nmrshiftdbid").size()>0){ + if(spectrum.getMetadataListElements().get(0).getMetadataDescendantsByName("nmr:nmrshiftdbid").size()>0){ + DBConnection dbconn = TurbineDB.getConnection(); + Statement stmt = dbconn.createStatement(); + List l=DBSpectrumPeer.executeQuery("select SPECTRUM_ID from SPECTRUM where NMRSHIFTDB_NUMBER='"+spectrum.getMetadataListElements().get(0).getMetadataDescendantsByName("nmr:nmrshiftdbid").get(0).getContent()+"'"); + subData.setEditSpectrum(new NumberKey(((Record)l.get(0)).getValue(1).asInt())); + } + } subData.setMeasured(); DBSpectrumType type=DBSpectrumTypePeer.getByName(spectrum.getMetadataListElements().get(0).getMetadataDescendantsByName("nmr:OBSERVENUCLEUS").get(0).getContent()); subData.setChoosenSpectrumType(type); + CMLReader cmlreader=new CMLReader(new ByteArrayInputStream(cmlmol.toXML().getBytes())); + IMolecule cdkmol=((ChemFileCDO)cmlreader.read(new ChemFile())).getChemSequence(0).getChemModel(0).getSetOfMolecules().getMolecule(0); StringWriter writer=new StringWriter(); ! MDLWriter mdlwriter=new MDLWriter(writer); ! mdlwriter.write(cdkmol); subData.setMol(writer.toString(),false,false,true); for(int k=0;k<cmlmol.getAtomCount();k++){ *************** *** 250,254 **** } subData.save(user.getUserId(),"false","bioclipse", new Date(),null,Integer.parseInt(GeneralUtils.getNmrshiftdbProperty("hosecode.spheres")), false); ! sb.append(subData.spectrumid+" "); } DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance(); --- 269,273 ---- } subData.save(user.getUserId(),"false","bioclipse", new Date(),null,Integer.parseInt(GeneralUtils.getNmrshiftdbProperty("hosecode.spheres")), false); ! sb.append(subData.nmrshiftdbnr+" "); } DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance(); |
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From: Stefan K. <sh...@us...> - 2006-08-28 14:34:28
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/apache/jetspeed/modules/actions In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv32127/src/java/org/apache/jetspeed/modules/actions Modified Files: CreateNewUserAndConfirm.java Log Message: updated cdk Index: CreateNewUserAndConfirm.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/apache/jetspeed/modules/actions/CreateNewUserAndConfirm.java,v retrieving revision 1.29 retrieving revision 1.30 diff -C2 -r1.29 -r1.30 *** CreateNewUserAndConfirm.java 28 Feb 2006 11:49:46 -0000 1.29 --- CreateNewUserAndConfirm.java 28 Aug 2006 14:33:57 -0000 1.30 *************** *** 90,108 **** import org.openscience.nmrshiftdb.om.NmrshiftdbUserPeer; import org.openscience.nmrshiftdb.util.GeneralUtils; - /** - *This action validates the form input from the NewAccount Screen. - *If it is valid, then it will check to make sure that the user account - *does not already exist. If it does, then it will show the NewAccount - *screen again. If it doesn't alread exist, then it will create the new - *user and set the CONFIRM_VALUE to be the users session id. This part should - *probably be re-done to get a better less hackable CONFIRM_VALUE, but this - *should work for now. If everything goes well, this action will send the user - *a confirmation email and then show the ConfirmRegistration screen. - * - * @author Jon S. Stevens <a href="mailto:jo...@cl...">jo...@cl...</a> - * @author David S. Taylor <a href="mailto:da...@bl...">da...@bl...</a> - * @author Tom Adams <a href="mailto:to...@PI...">to...@PI...</a> - * @created April 29, 2002 - */ /** --- 90,93 ---- |
Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/om In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv32127/src/java/org/openscience/nmrshiftdb/om Modified Files: BaseDBConditionType.java BaseDBConditionTypePeer.java DBAtom.java DBMolecule.java DBSpectrum.java Log Message: updated cdk Index: BaseDBConditionType.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/om/BaseDBConditionType.java,v retrieving revision 1.6 retrieving revision 1.7 diff -C2 -r1.6 -r1.7 *** BaseDBConditionType.java 8 Jun 2006 12:22:45 -0000 1.6 --- BaseDBConditionType.java 28 Aug 2006 14:33:58 -0000 1.7 *************** *** 2,14 **** ! import java.util.*; ! import java.math.*; ! import org.apache.turbine.om.*; import org.apache.turbine.om.peer.BasePeer; - import org.apache.turbine.util.db.Criteria; import org.apache.turbine.util.ObjectUtils; ! import org.apache.turbine.util.StringUtils; ! import org.apache.turbine.util.ParameterParser; ! import org.apache.turbine.util.Log; import org.apache.turbine.util.db.pool.DBConnection; --- 2,16 ---- ! import java.util.List; ! import java.util.Vector; ! ! import org.apache.turbine.om.BaseObject; ! import org.apache.turbine.om.NumberKey; ! import org.apache.turbine.om.ObjectKey; ! import org.apache.turbine.om.Persistent; ! import org.apache.turbine.om.Retrievable; import org.apache.turbine.om.peer.BasePeer; import org.apache.turbine.util.ObjectUtils; ! import org.apache.turbine.util.db.Criteria; import org.apache.turbine.util.db.pool.DBConnection; Index: BaseDBConditionTypePeer.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/om/BaseDBConditionTypePeer.java,v retrieving revision 1.6 retrieving revision 1.7 diff -C2 -r1.6 -r1.7 *** BaseDBConditionTypePeer.java 8 Jun 2006 12:22:45 -0000 1.6 --- BaseDBConditionTypePeer.java 28 Aug 2006 14:33:58 -0000 1.7 *************** *** 1,19 **** package org.openscience.nmrshiftdb.om; ! import java.util.*; ! import java.math.*; ! import java.sql.*; ! import com.workingdogs.village.*; ! import org.apache.turbine.om.*; ! import org.apache.turbine.om.peer.*; ! import org.apache.turbine.util.*; ! import org.apache.turbine.util.db.*; ! import org.apache.turbine.util.db.map.*; ! import org.apache.turbine.util.db.pool.DBConnection; import org.apache.turbine.services.db.TurbineDB; ! import org.apache.turbine.util.TurbineException; ! // Local classes ! import org.openscience.nmrshiftdb.om.map.*; /** --- 1,19 ---- package org.openscience.nmrshiftdb.om; ! import java.util.Vector; ! ! import org.apache.turbine.om.NumberKey; ! import org.apache.turbine.om.ObjectKey; ! import org.apache.turbine.om.peer.BasePeer; import org.apache.turbine.services.db.TurbineDB; ! import org.apache.turbine.util.Log; ! import org.apache.turbine.util.db.Criteria; ! import org.apache.turbine.util.db.map.MapBuilder; ! import org.apache.turbine.util.db.map.TableMap; ! import org.apache.turbine.util.db.pool.DBConnection; ! import org.openscience.nmrshiftdb.om.map.DBConditionTypeMapBuilder; ! import com.workingdogs.village.QueryDataSet; ! import com.workingdogs.village.Record; /** Index: DBAtom.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/om/DBAtom.java,v retrieving revision 1.52 retrieving revision 1.53 diff -C2 -r1.52 -r1.53 *** DBAtom.java 30 May 2006 11:42:48 -0000 1.52 --- DBAtom.java 28 Aug 2006 14:33:58 -0000 1.53 *************** *** 61,68 **** setAtomicMass(atom.getAtomicNumber()); setFormalCharge(atom.getFormalCharge()); ! if ((!Double.isNaN(atom.getZ3d()) && atom.getZ3d() != 0) || force3d) { ! coords3 = new DBCoordinateSet3d(atom.getX2d(), atom.getY2d(), atom.getZ3d(), 1); } else { ! coords2 = new DBCoordinateSet2d(atom.getX2d(), atom.getY2d(), 1); } if (atom.getFlag(CDKConstants.ISAROMATIC)) { --- 61,68 ---- setAtomicMass(atom.getAtomicNumber()); setFormalCharge(atom.getFormalCharge()); ! if ((!Double.isNaN(atom.getPoint3d().z) && atom.getPoint3d().z != 0) || force3d) { ! coords3 = new DBCoordinateSet3d(atom.getPoint2d().x, atom.getPoint2d().y, atom.getPoint3d().z, 1); } else { ! coords2 = new DBCoordinateSet2d(atom.getPoint2d().x, atom.getPoint2d().y, 1); } if (atom.getFlag(CDKConstants.ISAROMATIC)) { *************** *** 130,134 **** for (int i = 0; i < dbatoms.length; i++) { if(this.getAtomId().equals(dbatoms[i].getAtomId())){ ! IAtom[] connectedatoms=mol.getConnectedAtoms(mol.getAtomAt(i)); for(int k=0;k<connectedatoms.length;k++){ connecteddbatoms.add(dbatoms[mol.getAtomNumber(connectedatoms[k])]); --- 130,134 ---- for (int i = 0; i < dbatoms.length; i++) { if(this.getAtomId().equals(dbatoms[i].getAtomId())){ ! IAtom[] connectedatoms=mol.getConnectedAtoms(mol.getAtom(i)); for(int k=0;k<connectedatoms.length;k++){ connecteddbatoms.add(dbatoms[mol.getAtomNumber(connectedatoms[k])]); *************** *** 257,261 **** for (int i = 0; i < atoms.length; i++) { if (atoms[i].equals(this)) { ! return (getDBMolecule().getAsCDKMolecule(1).getAtomAt(i)); } } --- 257,261 ---- for (int i = 0; i < atoms.length; i++) { if (atoms[i].equals(this)) { ! return (getDBMolecule().getAsCDKMolecule(1).getAtom(i)); } } *************** *** 275,279 **** for (int i = 0; i < atoms.length; i++) { if (atoms[i].equals(this)) { ! return (subData.getMolWithH().getAtomAt(i)); } } --- 275,279 ---- for (int i = 0; i < atoms.length; i++) { if (atoms[i].equals(this)) { ! return (subData.getMolWithH().getAtom(i)); } } Index: DBMolecule.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/om/DBMolecule.java,v retrieving revision 1.186 retrieving revision 1.187 diff -C2 -r1.186 -r1.187 *** DBMolecule.java 18 Aug 2006 10:45:24 -0000 1.186 --- DBMolecule.java 28 Aug 2006 14:33:58 -0000 1.187 *************** *** 223,227 **** } } ! IBond bond = new org.openscience.cdk.Bond(cdkMolecule.getAtomAt(((Integer) map.get(new NumberKey(mdl1))).intValue()), cdkMolecule.getAtomAt(((Integer) map.get(new NumberKey(mdl2))).intValue()), (double) order, stereo); if (thisBond.getIsAromatic().equals(NmrshiftdbConstants.TRUE)) { bond.setFlag(CDKConstants.ISAROMATIC, true); --- 223,227 ---- } } ! IBond bond = new org.openscience.cdk.Bond(cdkMolecule.getAtom(((Integer) map.get(new NumberKey(mdl1))).intValue()), cdkMolecule.getAtom(((Integer) map.get(new NumberKey(mdl2))).intValue()), (double) order, stereo); if (thisBond.getIsAromatic().equals(NmrshiftdbConstants.TRUE)) { bond.setFlag(CDKConstants.ISAROMATIC, true); *************** *** 294,298 **** IMolecule molgo = (IMolecule)AtomContainerManipulator.removeHydrogens(mol); for (int i = 0; i < molgo.getAtomCount(); i++) { ! molgo.getAtomAt(i).setHydrogenCount(0); } AllRingsFinder arf=new AllRingsFinder(); --- 294,298 ---- IMolecule molgo = (IMolecule)AtomContainerManipulator.removeHydrogens(mol); for (int i = 0; i < molgo.getAtomCount(); i++) { ! molgo.getAtom(i).setHydrogenCount(0); } AllRingsFinder arf=new AllRingsFinder(); *************** *** 767,771 **** for(int i=0;i<localmol.getAtomCount();i++){ DBCoordinateSet2d set2d=DBCoordinateSet2dPeer.retrieveByPK(new NumberKey(1), this.getAtomsAsArrayInMdlOrder()[i].getAtomId()); ! localmol.getAtomAt(i).setPoint2d(new Point2d(set2d.getXCoordinate(),set2d.getYCoordinate())); } return localmol; --- 767,771 ---- for(int i=0;i<localmol.getAtomCount();i++){ DBCoordinateSet2d set2d=DBCoordinateSet2dPeer.retrieveByPK(new NumberKey(1), this.getAtomsAsArrayInMdlOrder()[i].getAtomId()); ! localmol.getAtom(i).setPoint2d(new Point2d(set2d.getXCoordinate(),set2d.getYCoordinate())); } return localmol; *************** *** 887,891 **** cdkMoleculeWithoutHsAndCount = (IMolecule)AtomContainerManipulator.removeHydrogens(getAsCDKMolecule(1)); for (int i = 0; i < cdkMoleculeWithoutHsAndCount.getAtomCount(); i++) { ! cdkMoleculeWithoutHsAndCount.getAtomAt(i).setHydrogenCount(0); } } --- 887,891 ---- cdkMoleculeWithoutHsAndCount = (IMolecule)AtomContainerManipulator.removeHydrogens(getAsCDKMolecule(1)); for (int i = 0; i < cdkMoleculeWithoutHsAndCount.getAtomCount(); i++) { ! cdkMoleculeWithoutHsAndCount.getAtom(i).setHydrogenCount(0); } } *************** *** 1406,1410 **** for (int i = 0; i < atoms.length; i++) { if (atoms[i].getAnySignal(spectrum.getSpectrumId()) != null && !atoms[i].getAnySignal(spectrum.getSpectrumId()).getMultiplicity().equals("")) { ! subData.multis.put(subData.getMolWithH().getAtomAt(i), atoms[i].getAnySignal(spectrum.getSpectrumId()).getMultiplicity()); } } --- 1406,1410 ---- for (int i = 0; i < atoms.length; i++) { if (atoms[i].getAnySignal(spectrum.getSpectrumId()) != null && !atoms[i].getAnySignal(spectrum.getSpectrumId()).getMultiplicity().equals("")) { ! subData.multis.put(subData.getMolWithH().getAtom(i), atoms[i].getAnySignal(spectrum.getSpectrumId()).getMultiplicity()); } } *************** *** 1527,1534 **** IMolecule promol = new org.openscience.cdk.Molecule(); for (int i = 0; i < getAsCDKMolecule(setid).getAtomCount(); i++) { ! promol.addAtom(getAsCDKMolecule(setid).getAtomAt(i)); } for (int i = 0; i < getAsCDKMolecule(setid).getBondCount(); i++) { ! promol.addBond(getAsCDKMolecule(setid).getBondAt(i)); } DBAtom[] atoms = getAtomsAsArrayInMdlOrder(); --- 1527,1534 ---- IMolecule promol = new org.openscience.cdk.Molecule(); for (int i = 0; i < getAsCDKMolecule(setid).getAtomCount(); i++) { ! promol.addAtom(getAsCDKMolecule(setid).getAtom(i)); } for (int i = 0; i < getAsCDKMolecule(setid).getBondCount(); i++) { ! promol.addBond(getAsCDKMolecule(setid).getBond(i)); } DBAtom[] atoms = getAtomsAsArrayInMdlOrder(); *************** *** 1542,1553 **** promol.setProperty(CDKConstants.REMARK, "NMRShiftDB " + getMoleculeId()+" "+getNmrshiftdbNumber()); for(int i=0;i<promol.getAtomCount();i++){ ! promol.getAtomAt(i).setFlag(CDKConstants.ISAROMATIC, false); if(i<promol.getBondCount()) ! promol.getBondAt(i).setFlag(CDKConstants.ISAROMATIC, false); } new SaturationChecker().newSaturate(promol.getBonds(), promol); for (int i = promol.getAtomCount() - 1; i > -1; i--) { if (!visibility[i]) { ! promol.removeAtomAndConnectedElectronContainers(promol.getAtomAt(i)); } } --- 1542,1553 ---- promol.setProperty(CDKConstants.REMARK, "NMRShiftDB " + getMoleculeId()+" "+getNmrshiftdbNumber()); for(int i=0;i<promol.getAtomCount();i++){ ! promol.getAtom(i).setFlag(CDKConstants.ISAROMATIC, false); if(i<promol.getBondCount()) ! promol.getBond(i).setFlag(CDKConstants.ISAROMATIC, false); } new SaturationChecker().newSaturate(promol.getBonds(), promol); for (int i = promol.getAtomCount() - 1; i > -1; i--) { if (!visibility[i]) { ! promol.removeAtomAndConnectedElectronContainers(promol.getAtom(i)); } } *************** *** 1603,1607 **** public IMolecule addCdkCoords(DBConnection conn, IMolecule mol, NumberKey[] atoms) throws Exception{ for(int k=0;k<mol.getAtomCount();k++){ ! mol.getAtomAt(k).setFlag(CDKConstants.ISPLACED, false); } GeneralUtils.getModelBuilder("mm2").setMolecule(mol, false); --- 1603,1607 ---- public IMolecule addCdkCoords(DBConnection conn, IMolecule mol, NumberKey[] atoms) throws Exception{ for(int k=0;k<mol.getAtomCount();k++){ ! mol.getAtom(k).setFlag(CDKConstants.ISPLACED, false); } GeneralUtils.getModelBuilder("mm2").setMolecule(mol, false); *************** *** 1609,1613 **** IMolecule mol3d = GeneralUtils.getModelBuilder("mm2").getMolecule(); for(int k=0;k<mol3d.getAtomCount();k++){ ! DBCoordinateSet3d c3=new DBCoordinateSet3d(mol3d.getAtomAt(k).getPoint3d().x,mol3d.getAtomAt(k).getPoint3d().y,mol3d.getAtomAt(k).getPoint3d().z,3,atoms[k]); c3.save(conn); } --- 1609,1613 ---- IMolecule mol3d = GeneralUtils.getModelBuilder("mm2").getMolecule(); for(int k=0;k<mol3d.getAtomCount();k++){ ! DBCoordinateSet3d c3=new DBCoordinateSet3d(mol3d.getAtom(k).getPoint3d().x,mol3d.getAtom(k).getPoint3d().y,mol3d.getAtom(k).getPoint3d().z,3,atoms[k]); c3.save(conn); } Index: DBSpectrum.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/om/DBSpectrum.java,v retrieving revision 1.185 retrieving revision 1.186 diff -C2 -r1.185 -r1.186 *** DBSpectrum.java 23 Aug 2006 15:09:11 -0000 1.185 --- DBSpectrum.java 28 Aug 2006 14:33:58 -0000 1.186 *************** *** 267,271 **** }else{ StringBuffer comment=new StringBuffer(); ! prediction = AtomUtils.predictRange(getDBMolecule().getAsCDKMolecule(1), getDBMolecule().getAsCDKMolecule(1).getAtomAt(((DBAtom) neighbouringAtoms.get(l)).getMdlNumber()), false, true, null, comment, false, true, runData, null, -1, true,null, ((Boolean)runData.getSession().getAttribute("trueonly")).booleanValue()); searchShift.append(new String(format.format(prediction[0]) + "-<b>" + format.format(prediction[1]) + "</b>-" + format.format(prediction[2])) + "; " + comment); } --- 267,271 ---- }else{ StringBuffer comment=new StringBuffer(); ! prediction = AtomUtils.predictRange(getDBMolecule().getAsCDKMolecule(1), getDBMolecule().getAsCDKMolecule(1).getAtom(((DBAtom) neighbouringAtoms.get(l)).getMdlNumber()), false, true, null, comment, false, true, runData, null, -1, true,null, ((Boolean)runData.getSession().getAttribute("trueonly")).booleanValue()); searchShift.append(new String(format.format(prediction[0]) + "-<b>" + format.format(prediction[1]) + "</b>-" + format.format(prediction[2])) + "; " + comment); } *************** *** 328,332 **** l--; } ! double[] prediction = AtomUtils.predictRange(cdkMolWithOutH, cdkMolWithOutH.getAtomAt(l), false, true, null, comment, false, true, runData, null, -1, true,null, ((Boolean)runData.getSession().getAttribute("trueonly")).booleanValue()); if (prediction[0] > prediction[1]) { prediction[0] = prediction[1]; --- 328,332 ---- l--; } ! double[] prediction = AtomUtils.predictRange(cdkMolWithOutH, cdkMolWithOutH.getAtom(l), false, true, null, comment, false, true, runData, null, -1, true,null, ((Boolean)runData.getSession().getAttribute("trueonly")).booleanValue()); if (prediction[0] > prediction[1]) { prediction[0] = prediction[1]; |
Update of /cvsroot/nmrshiftdb/nmrshiftdb/lib In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv32127/lib Modified Files: cdk-builder3d.jar cdk-charges.jar cdk-core.jar cdk-data.jar cdk-extra.jar cdk-forcefield.jar cdk-interfaces.jar cdk-io.jar cdk-libio-cml.jar cdk-pdb-cml.jar cdk-pdb.jar cdk-qsar-cml.jar cdk-qsar.jar cdk-render.jar cdk-smiles.jar cdk-standard.jar cdk-valencycheck.jar Added Files: cdk-sdg.jar Log Message: updated cdk --- NEW FILE: cdk-sdg.jar --- PK *x×Ò µ¢>XB0MkÁTáyºepÙ%Û©Iÿñ¹/>¨ÑÃþ(ãH>t9·ïoÎýùëÛw 3 Xa?2 Ö¹`} ÃH ïa¦GÆèoÝ"1ÃD¿ÀU´QÃ6ÖñÑÁ^c{ ¯gjòÒÒ"®[[¢&¸ëôïæ}$<˸I=2)ï<ndQäÁ],$7¥&ñPK QÏü¬ÉÇ\·þG¤ò5×âVû ;¾îZ¼ýÒìÜsòø0þMÈ·L~ÞäLþO¿mòпcòwM~ÑädÅ7MþÉß ¸ùÂâÒú±É?ñò+üSæåãüªPþsaò/Mþ¼iyüZyÍäÿ6ù72¸×Í¿¡ßü{_7ù Áöf ¿Å0ù²åO&ÿÙä¿üWßµ3ù ÿnò?dí»&¿'?7M¥LeÊa*'+©Ünezé~åµÊµ*Ï«|* ¨×bÓk±õInU»UE¦'!g5ÞJÜÊÏäìlëídâMLùÍx* §Û±ÞÌä%:;#I¦Ù+ÉκDO$jFâíºö uéD"ª[5Ñxçz¼Ìc2»±H{o,ÂT7ì¦h< In·GRu+¤Ý87 Æ#Ilö.Y¿zÕy«ÏjYvÓç/ ×õ¦£±ºæDwO8N'dUU{,JÍò9ÈgùÌX¸/Ñ)x×ÄpH g¡ ãuͲ<ëúâé®H:Ú çGãÑôB&£¼¢ÉÑè n°ªìÒ!*o´#0Ø×÷Å#;[¢I WMú±<±ÆÔúDK2¼S¢C?× `)? 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From: Stefan K. <sh...@us...> - 2006-08-28 14:34:09
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv32127/src/java/org/openscience/nmrshiftdb Modified Files: AdminPanel.java NmrshiftdbServlet.java PredictionTool.java Log Message: updated cdk Index: AdminPanel.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/AdminPanel.java,v retrieving revision 1.230 retrieving revision 1.231 diff -C2 -r1.230 -r1.231 *** AdminPanel.java 4 Jul 2006 13:38:54 -0000 1.230 --- AdminPanel.java 28 Aug 2006 14:33:58 -0000 1.231 *************** *** 78,82 **** import org.openscience.nmrshiftdb.om.DBCoordinateSet3d; import org.openscience.nmrshiftdb.om.DBIsotopePeer; - import org.openscience.nmrshiftdb.om.DBLiterature; import org.openscience.nmrshiftdb.om.DBMolecule; import org.openscience.nmrshiftdb.om.DBMoleculeHyperlink; --- 78,81 ---- *************** *** 88,92 **** import org.openscience.nmrshiftdb.om.DBSignalPeer; import org.openscience.nmrshiftdb.om.DBSpectrum; - import org.openscience.nmrshiftdb.om.DBSpectrumDBLiterature; import org.openscience.nmrshiftdb.om.DBSpectrumPeer; import org.openscience.nmrshiftdb.om.DBSpectrumType; --- 87,90 ---- *************** *** 730,734 **** for(int l=0;l<signals.size();l++){ if(((ValueTriple)signals.get(l)).value1==value){ ! ((ValueTriple)signals.get(l)).atoms.add(subData.getMolWithH().getAtomAt(atom-1)); added=true; } --- 728,732 ---- for(int l=0;l<signals.size();l++){ if(((ValueTriple)signals.get(l)).value1==value){ ! ((ValueTriple)signals.get(l)).atoms.add(subData.getMolWithH().getAtom(atom-1)); added=true; } *************** *** 736,740 **** if(!added){ signals.add(new ValueTriple(value)); ! ((ValueTriple)signals.get(signals.size()-1)).atoms.add(subData.getMolWithH().getAtomAt(atom-1)); } } --- 734,738 ---- if(!added){ signals.add(new ValueTriple(value)); ! ((ValueTriple)signals.get(signals.size()-1)).atoms.add(subData.getMolWithH().getAtom(atom-1)); } } *************** *** 867,871 **** for(int l=0;l<signals.size();l++){ if(((ValueTriple)signals.get(l)).value1==value){ ! ((ValueTriple)signals.get(l)).atoms.add(subData.getMolWithH().getAtomAt(atom-1)); added=true; break; --- 865,869 ---- for(int l=0;l<signals.size();l++){ if(((ValueTriple)signals.get(l)).value1==value){ ! ((ValueTriple)signals.get(l)).atoms.add(subData.getMolWithH().getAtom(atom-1)); added=true; break; *************** *** 874,878 **** if(!added){ signals.add(new ValueTriple(value)); ! ((ValueTriple)signals.get(signals.size()-1)).atoms.add(subData.getMolWithH().getAtomAt(atom-1)); } }else{ --- 872,876 ---- if(!added){ signals.add(new ValueTriple(value)); ! ((ValueTriple)signals.get(signals.size()-1)).atoms.add(subData.getMolWithH().getAtom(atom-1)); } }else{ *************** *** 887,891 **** Vector signals=subData.getSignalstable(); boolean added=false; ! List connatoms=subData.getMolWithH().getConnectedAtomsVector(subData.getMolWithH().getAtomAt(atom-1));//H for(int l=0;l<signals.size();l++){ if(((ValueTriple)signals.get(l)).value1==value){ --- 885,889 ---- Vector signals=subData.getSignalstable(); boolean added=false; ! List connatoms=subData.getMolWithH().getConnectedAtomsVector(subData.getMolWithH().getAtom(atom-1));//H for(int l=0;l<signals.size();l++){ if(((ValueTriple)signals.get(l)).value1==value){ *************** *** 1125,1133 **** } if (bondorder == 4) { ! IBond bond = new org.openscience.cdk.Bond(atom, mol.getAtomAt(atomnumber), 1); bond.setFlag(CDKConstants.ISAROMATIC,true); mol.addBond(bond); atom.setFlag(CDKConstants.ISAROMATIC,true); ! mol.getAtomAt(atomnumber).setFlag(CDKConstants.ISAROMATIC,true); } } --- 1123,1131 ---- } if (bondorder == 4) { ! IBond bond = new org.openscience.cdk.Bond(atom, mol.getAtom(atomnumber), 1); bond.setFlag(CDKConstants.ISAROMATIC,true); mol.addBond(bond); atom.setFlag(CDKConstants.ISAROMATIC,true); ! mol.getAtom(atomnumber).setFlag(CDKConstants.ISAROMATIC,true); } } *************** *** 1238,1242 **** String x = st.nextToken(); if (!x.equals("0")) { ! ((ValueTriple) subdata.getSignalstable().get(counter3)).atoms.add(subdata.getMolWithH().getAtomAt(Integer.parseInt(x) - 1)); } counter3++; --- 1236,1240 ---- String x = st.nextToken(); if (!x.equals("0")) { ! ((ValueTriple) subdata.getSignalstable().get(counter3)).atoms.add(subdata.getMolWithH().getAtom(Integer.parseInt(x) - 1)); } counter3++; *************** *** 1470,1474 **** int corinanumber=((RMap) list.get(k)).getId1(); int atomid=dbmol.getAtomsAsArrayInMdlOrder()[numbernmrshiftdb].getAtomId().getBigDecimal().intValue(); ! DBCoordinateSet3d coords3d=new DBCoordinateSet3d(molWithHfromCorina.getAtomAt(corinanumber).getX3d(),molWithHfromCorina.getAtomAt(corinanumber).getY3d(),molWithHfromCorina.getAtomAt(corinanumber).getZ3d(),2); coords3d.setAtomId(new NumberKey(atomid)); try{ --- 1468,1472 ---- int corinanumber=((RMap) list.get(k)).getId1(); int atomid=dbmol.getAtomsAsArrayInMdlOrder()[numbernmrshiftdb].getAtomId().getBigDecimal().intValue(); ! DBCoordinateSet3d coords3d=new DBCoordinateSet3d(molWithHfromCorina.getAtom(corinanumber).getPoint3d().x,molWithHfromCorina.getAtom(corinanumber).getPoint3d().y,molWithHfromCorina.getAtom(corinanumber).getPoint3d().z,2); coords3d.setAtomId(new NumberKey(atomid)); try{ *************** *** 1555,1559 **** try{ String nmrshiftdbnr=(String)mol.getProperty(CDKConstants.TITLE); ! System.err.println(nmrshiftdbnr+" "+mol.getAtomAt(0).getPoint2d()+" "+mol.getAtomAt(0).getPoint3d()); MFAnalyser mfa=new MFAnalyser(mol); Vector elements=mfa.getElements(); --- 1553,1557 ---- try{ String nmrshiftdbnr=(String)mol.getProperty(CDKConstants.TITLE); ! System.err.println(nmrshiftdbnr+" "+mol.getAtom(0).getPoint2d()+" "+mol.getAtom(0).getPoint3d()); MFAnalyser mfa=new MFAnalyser(mol); Vector elements=mfa.getElements(); *************** *** 1583,1590 **** subData.setComment(files[i].getName()+"; "+mol.getProperty("Comment")); for(int l=0;l<mol.getAtomCount();l++){ ! if(mol.getAtomAt(l).getSymbol().equals(element)){ ! IAtom atom=mol.getAtomAt(l); ValueTriple vt=new ValueTriple(((Double)atom.getProperty("first shift")).floatValue(),0); ! vt.atoms.add(subData.getMolWithH().getAtomAt(l));; subData.getSignalstable().add(vt); } --- 1581,1588 ---- subData.setComment(files[i].getName()+"; "+mol.getProperty("Comment")); for(int l=0;l<mol.getAtomCount();l++){ ! if(mol.getAtom(l).getSymbol().equals(element)){ ! IAtom atom=mol.getAtom(l); ValueTriple vt=new ValueTriple(((Double)atom.getProperty("first shift")).floatValue(),0); ! vt.atoms.add(subData.getMolWithH().getAtom(l));; subData.getSignalstable().add(vt); } *************** *** 1670,1674 **** DBCondition solvent=spectrum.getMeasurementConditionWithName("Solvent",null); int protonclass=AtomUtils.getProtonClass(cdkmol, atomnumber, arf.findAllRings(cdkmol)); ! floats=AtomUtils.getDescriptorSet(temp, field,solvent, cdkmol, cdkmol.getAtomAt(atomnumber), AtomUtils.getAllRings(),protonclass); if(floats!=null){ if(first){ --- 1668,1672 ---- DBCondition solvent=spectrum.getMeasurementConditionWithName("Solvent",null); int protonclass=AtomUtils.getProtonClass(cdkmol, atomnumber, arf.findAllRings(cdkmol)); ! floats=AtomUtils.getDescriptorSet(temp, field,solvent, cdkmol, cdkmol.getAtom(atomnumber), AtomUtils.getAllRings(),protonclass); if(floats!=null){ if(first){ *************** *** 1778,1782 **** DBCondition solvent=spectrum.getMeasurementConditionWithName("Solvent",null); int protonclass=AtomUtils.getProtonClass(cdkmol, atomnumber, arf.findAllRings(cdkmol)); ! floats=AtomUtils.getDescriptorSet(temp, field,solvent, cdkmol, cdkmol.getAtomAt(atomnumber), AtomUtils.getAllRings(),protonclass); if(floats!=null){ StringBuffer sql=new StringBuffer("insert into DESCRIPTORS_ALL values("+((DBAtom)signal.getAtoms().get(h)).getAtomId()+","+signal.getSignalId()+","); --- 1776,1780 ---- DBCondition solvent=spectrum.getMeasurementConditionWithName("Solvent",null); int protonclass=AtomUtils.getProtonClass(cdkmol, atomnumber, arf.findAllRings(cdkmol)); ! floats=AtomUtils.getDescriptorSet(temp, field,solvent, cdkmol, cdkmol.getAtom(atomnumber), AtomUtils.getAllRings(),protonclass); if(floats!=null){ StringBuffer sql=new StringBuffer("insert into DESCRIPTORS_ALL values("+((DBAtom)signal.getAtoms().get(h)).getAtomId()+","+signal.getSignalId()+","); *************** *** 2036,2040 **** DBAtom[] dbatoms=mol.getAtomsAsArrayInMdlOrder(); for(int k=0;k<molWithH.getAtomCount();k++){ ! if(molWithH.getAtomAt(k).getFlag(CDKConstants.ISAROMATIC)) dbatoms[k].setIsAromatic(NmrshiftdbConstants.TRUE); else --- 2034,2038 ---- DBAtom[] dbatoms=mol.getAtomsAsArrayInMdlOrder(); for(int k=0;k<molWithH.getAtomCount();k++){ ! if(molWithH.getAtom(k).getFlag(CDKConstants.ISAROMATIC)) dbatoms[k].setIsAromatic(NmrshiftdbConstants.TRUE); else *************** *** 2044,2048 **** Vector bonds=mol.getBonds(); for(int k=0;k<molWithH.getBondCount();k++){ ! if(molWithH.getBondAt(k).getFlag(CDKConstants.ISAROMATIC)) ((DBBond)bonds.get(k)).setIsAromatic(NmrshiftdbConstants.TRUE); else --- 2042,2046 ---- Vector bonds=mol.getBonds(); for(int k=0;k<molWithH.getBondCount();k++){ ! if(molWithH.getBond(k).getFlag(CDKConstants.ISAROMATIC)) ((DBBond)bonds.get(k)).setIsAromatic(NmrshiftdbConstants.TRUE); else *************** *** 2365,2369 **** } for(int i=0;i<mol.getAtomCount();i++){ ! IAtom a=mol.getAtomAt(i); for(int k=1;k<7;k++){ if(a.getSymbol().equals("C")){ --- 2363,2367 ---- } for(int i=0;i<mol.getAtomCount();i++){ ! IAtom a=mol.getAtom(i); for(int k=1;k<7;k++){ if(a.getSymbol().equals("C")){ *************** *** 2404,2410 **** if(wishit && v.size()==0){ for(int i=0;i<mol.getAtomCount();i++){ ! IAtom a=mol.getAtomAt(i); ! a.setX2d(a.getX3d()); ! a.setY2d(a.getY3d()); a.setZ3d(0); } --- 2402,2408 ---- if(wishit && v.size()==0){ for(int i=0;i<mol.getAtomCount();i++){ ! IAtom a=mol.getAtom(i); ! a.setX2d(a.getPoint3d().x); ! a.setY2d(a.getPoint3d().y); a.setZ3d(0); } *************** *** 2579,2586 **** Vector signalstable = new Vector(); for (int i = 0; i < molWithH.getAtomCount(); i++) { ! if (molWithH.getAtomAt(i).getSymbol().equals("C")) { ValueTriple vt = new ValueTriple(); ! vt.value1 = (float)((java.lang.Math.floor(((Double) mol.getAtomAt(i).getProperty(CDKConstants.NMRSHIFT_CARBON)).floatValue() * 100)) / 100); ! vt.atoms.add(molWithH.getAtomAt(i)); signalstable.add(vt); } --- 2577,2584 ---- Vector signalstable = new Vector(); for (int i = 0; i < molWithH.getAtomCount(); i++) { ! if (molWithH.getAtom(i).getSymbol().equals("C")) { ValueTriple vt = new ValueTriple(); ! vt.value1 = (float)((java.lang.Math.floor(((Double) mol.getAtom(i).getProperty(CDKConstants.NMRSHIFT_CARBON)).floatValue() * 100)) / 100); ! vt.atoms.add(molWithH.getAtom(i)); signalstable.add(vt); } *************** *** 2643,2650 **** signalstable.removeAllElements(); for (int i = 0; i < mol.getAtomCount(); i++) { ! IAtom parent = mol.getAtomAt(i); if (parent.getHydrogenCount() == 1) { ValueTriple vt = new ValueTriple(); ! IAtom[] children = molWithH.getConnectedAtoms(molWithH.getAtomAt(i)); for (int k = 0; k < children.length; k++) { if (children[k].getSymbol().equals("H")) { --- 2641,2648 ---- signalstable.removeAllElements(); for (int i = 0; i < mol.getAtomCount(); i++) { ! IAtom parent = mol.getAtom(i); if (parent.getHydrogenCount() == 1) { ValueTriple vt = new ValueTriple(); ! IAtom[] children = molWithH.getConnectedAtoms(molWithH.getAtom(i)); for (int k = 0; k < children.length; k++) { if (children[k].getSymbol().equals("H")) { *************** *** 2656,2660 **** } if (parent.getHydrogenCount() == 2) { ! IAtom[] children = molWithH.getConnectedAtoms(molWithH.getAtomAt(i)); String appendix = ".1"; for (int k = 0; k < children.length; k++) { --- 2654,2658 ---- } if (parent.getHydrogenCount() == 2) { ! IAtom[] children = molWithH.getConnectedAtoms(molWithH.getAtom(i)); String appendix = ".1"; for (int k = 0; k < children.length; k++) { *************** *** 2671,2675 **** } if (parent.getHydrogenCount() > 2) { ! IAtom[] children = molWithH.getConnectedAtoms(molWithH.getAtomAt(i)); double altogether = 0; ValueTriple vt = new ValueTriple(); --- 2669,2673 ---- } if (parent.getHydrogenCount() > 2) { ! IAtom[] children = molWithH.getConnectedAtoms(molWithH.getAtom(i)); double altogether = 0; ValueTriple vt = new ValueTriple(); *************** *** 2743,2747 **** DBMolecule dbmol=atom.getDBMolecule(); float shift=signal.getFirstShift().getValue(); ! double predicted=PredictionTool.generalPredict(dbmol.getAsCDKMolecule(1), dbmol.getAsCDKMolecule(1).getAtomAt(atom.getMdlNumber()), true, true, -1, -1, new StringBuffer(""), false, false, null, new HashMap(), -1, false, new StringBuffer(), 6, true, true)[1]; shift=shift-(float)predicted+5; //System.err.println("Korrektur "+shift+" bei "+signal.getFirstShift().getValue()); --- 2741,2745 ---- DBMolecule dbmol=atom.getDBMolecule(); float shift=signal.getFirstShift().getValue(); ! double predicted=PredictionTool.generalPredict(dbmol.getAsCDKMolecule(1), dbmol.getAsCDKMolecule(1).getAtom(atom.getMdlNumber()), true, true, -1, -1, new StringBuffer(""), false, false, null, new HashMap(), -1, false, new StringBuffer(), 6, true, true)[1]; shift=shift-(float)predicted+5; //System.err.println("Korrektur "+shift+" bei "+signal.getFirstShift().getValue()); *************** *** 2797,2801 **** DBMolecule dbmol=atom.getDBMolecule(); float shift=signal.getFirstShift().getValue(); ! double predictedhose=PredictionTool.generalPredict(dbmol.getAsCDKMolecule(1), dbmol.getAsCDKMolecule(1).getAtomAt(atom.getMdlNumber()), true, true, -1, -1, new StringBuffer(""), false, false, null, new HashMap(), -1, false, new StringBuffer(), 6, true, true)[1]; System.err.println("hose "+predictedhose+" korrektur "+predicted); predicted=predicted+predictedhose; --- 2795,2799 ---- DBMolecule dbmol=atom.getDBMolecule(); float shift=signal.getFirstShift().getValue(); ! double predictedhose=PredictionTool.generalPredict(dbmol.getAsCDKMolecule(1), dbmol.getAsCDKMolecule(1).getAtom(atom.getMdlNumber()), true, true, -1, -1, new StringBuffer(""), false, false, null, new HashMap(), -1, false, new StringBuffer(), 6, true, true)[1]; System.err.println("hose "+predictedhose+" korrektur "+predicted); predicted=predicted+predictedhose; *************** *** 2860,2866 **** IMolecule cdkmol=mol.getAsCDKMolecule(1); for(int l=0;l<cdkmol.getAtomCount();l++){ ! if(cdkmol.getAtomAt(l).getSymbol().equals("H") && mol.getAtomsAsArrayInMdlOrder()[l].getDBSignalsBySpectrumType("1H").size()>0 && cdkmol.getConnectedAtoms(cdkmol.getAtomAt(l))[0].getSymbol().equals("C")){ try{ ! double predicted=PredictionTool.generalPredict(cdkmol, cdkmol.getAtomAt(l), true, true, startmol, endmol, new StringBuffer(""), false, false, null, new HashMap(), -1, false, new StringBuffer(), 6, true, true)[1]; double real=((DBSignal)mol.getAtomsAsArrayInMdlOrder()[l].getDBSignalsBySpectrumType("1H").get(0)).getFirstShift().getValue(); errors[i]+=(predicted-real)*(predicted-real); --- 2858,2864 ---- IMolecule cdkmol=mol.getAsCDKMolecule(1); for(int l=0;l<cdkmol.getAtomCount();l++){ ! if(cdkmol.getAtom(l).getSymbol().equals("H") && mol.getAtomsAsArrayInMdlOrder()[l].getDBSignalsBySpectrumType("1H").size()>0 && cdkmol.getConnectedAtoms(cdkmol.getAtom(l))[0].getSymbol().equals("C")){ try{ ! double predicted=PredictionTool.generalPredict(cdkmol, cdkmol.getAtom(l), true, true, startmol, endmol, new StringBuffer(""), false, false, null, new HashMap(), -1, false, new StringBuffer(), 6, true, true)[1]; double real=((DBSignal)mol.getAtomsAsArrayInMdlOrder()[l].getDBSignalsBySpectrumType("1H").get(0)).getFirstShift().getValue(); errors[i]+=(predicted-real)*(predicted-real); *************** *** 2977,2988 **** for(int k=0;k<mol4ring.getAtomCount();k++){ AnyOrderQueryBond q=new AnyOrderQueryBond(); ! q.setAtoms(mol4ring.getBondAt(k).getAtoms()); ! mol4ring.setElectronContainerAt(k,q); } QueryAtomContainer mol3ring=QueryAtomContainerCreator.createBasicQueryContainer(mol3ringc); for(int k=0;k<mol3ring.getAtomCount();k++){ AnyOrderQueryBond q=new AnyOrderQueryBond(); ! q.setAtoms(mol3ring.getBondAt(k).getAtoms()); ! mol3ring.setElectronContainerAt(k,q); } int rightmapping=1; --- 2975,2986 ---- for(int k=0;k<mol4ring.getAtomCount();k++){ AnyOrderQueryBond q=new AnyOrderQueryBond(); ! q.setAtoms(mol4ring.getBond(k).getAtoms()); ! mol4ring.setElectronContainer(k,q); } QueryAtomContainer mol3ring=QueryAtomContainerCreator.createBasicQueryContainer(mol3ringc); for(int k=0;k<mol3ring.getAtomCount();k++){ AnyOrderQueryBond q=new AnyOrderQueryBond(); ! q.setAtoms(mol3ring.getBond(k).getAtoms()); ! mol3ring.setElectronContainer(k,q); } int rightmapping=1; *************** *** 2995,3004 **** IAtom leftn=null; for(int k=0;k<sd.getMolWithH().getAtomCount();k++){ ! if(sd.getMolWithH().getAtomAt(k).getSymbol().equals("N")){ if(leftn==null){ ! leftn=sd.getMolWithH().getAtomAt(k); }else{ ! if(leftn.getX2d()>sd.getMolWithH().getAtomAt(k).getX2d()) ! leftn=sd.getMolWithH().getAtomAt(k); } } --- 2993,3002 ---- IAtom leftn=null; for(int k=0;k<sd.getMolWithH().getAtomCount();k++){ ! if(sd.getMolWithH().getAtom(k).getSymbol().equals("N")){ if(leftn==null){ ! leftn=sd.getMolWithH().getAtom(k); }else{ ! if(leftn.getPoint2d().x>sd.getMolWithH().getAtom(k).getPoint2d().x) ! leftn=sd.getMolWithH().getAtom(k); } } *************** *** 3048,3052 **** } if(Integer.parseInt(fn.substring(5))>0){ ! IAtom atom=sd.getMolWithH().getAtomAt(Integer.parseInt(fn.substring(5))-1); float shift=0; String mult=""; --- 3046,3050 ---- } if(Integer.parseInt(fn.substring(5))>0){ ! IAtom atom=sd.getMolWithH().getAtom(Integer.parseInt(fn.substring(5))-1); float shift=0; String mult=""; *************** *** 3083,3087 **** newatomnumber=((RMap)((Vector)l.get(rightmapping)).get(n)).getId1(); } ! ((ValueTriple)sd.getSignalstable().get(k)).atoms.add(sd.getMolWithH().getAtomAt(newatomnumber)); } } --- 3081,3085 ---- newatomnumber=((RMap)((Vector)l.get(rightmapping)).get(n)).getId1(); } ! ((ValueTriple)sd.getSignalstable().get(k)).atoms.add(sd.getMolWithH().getAtom(newatomnumber)); } } *************** *** 3098,3103 **** IRingSet sar=new AllRingsFinder().findAllRings(sd.getMolWithH()); for(int n=0;n<sd.getMolWithH().getAtomCount();n++){ ! if(sd.getMolWithH().getAtomAt(n).getSymbol().equals("C") && !sar.contains(sd.getMolWithH().getAtomAt(n))){ ! ((ValueTriple)sd.getSignalstable().get(unassigned)).atoms.add(sd.getMolWithH().getAtomAt(n)); break; } --- 3096,3101 ---- IRingSet sar=new AllRingsFinder().findAllRings(sd.getMolWithH()); for(int n=0;n<sd.getMolWithH().getAtomCount();n++){ ! if(sd.getMolWithH().getAtom(n).getSymbol().equals("C") && !sar.contains(sd.getMolWithH().getAtom(n))){ ! ((ValueTriple)sd.getSignalstable().get(unassigned)).atoms.add(sd.getMolWithH().getAtom(n)); break; } Index: NmrshiftdbServlet.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/NmrshiftdbServlet.java,v retrieving revision 1.91 retrieving revision 1.92 diff -C2 -r1.91 -r1.92 *** NmrshiftdbServlet.java 24 Aug 2006 12:00:24 -0000 1.91 --- NmrshiftdbServlet.java 28 Aug 2006 14:33:58 -0000 1.92 *************** *** 60,64 **** import org.openscience.cdk.interfaces.IMolecule; import org.openscience.cdk.io.RssWriter; - import org.openscience.nmrshiftdb.PredictionTool.ValueBean; import org.openscience.nmrshiftdb.om.DBCanonicalName; import org.openscience.nmrshiftdb.om.DBCanonicalNamePeer; --- 60,63 ---- Index: PredictionTool.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/PredictionTool.java,v retrieving revision 1.20 retrieving revision 1.21 diff -C2 -r1.20 -r1.21 *** PredictionTool.java 14 Jul 2006 08:09:58 -0000 1.20 --- PredictionTool.java 28 Aug 2006 14:33:58 -0000 1.21 *************** *** 2,6 **** import java.io.BufferedReader; - import java.io.FileInputStream; import java.io.FileReader; import java.io.IOException; --- 2,5 ---- *************** *** 8,17 **** import java.io.InputStreamReader; import java.text.DecimalFormat; - import java.util.ArrayList; import java.util.HashMap; - import java.util.Iterator; import java.util.List; import java.util.Map; - import java.util.Set; import java.util.StringTokenizer; --- 7,13 ---- *************** *** 29,33 **** import org.openscience.nmrshiftdb.om.DBMolecule; import org.openscience.nmrshiftdb.om.DBSpectrumPeer; - import org.openscience.nmrshiftdb.util.AtomUtils; import org.openscience.nmrshiftdb.util.GeneralUtils; --- 25,28 ---- *************** *** 88,97 **** new HydrogenAdder().addImplicitHydrogensToSatisfyValency(mol); for(int i=0;i<mol.getAtomCount();i++){ ! if(mol.getAtomAt(i).getHydrogenCount()<0) ! mol.getAtomAt(i).setHydrogenCount(0); } HueckelAromaticityDetector.detectAromaticity(mol, false); PredictionTool predictor = new PredictionTool(); ! double[] result = predictor.predict(mol, mol.getAtomAt(1)); System.err.println(result[0] + " " + result[1] + " " + result[2]); } --- 83,92 ---- new HydrogenAdder().addImplicitHydrogensToSatisfyValency(mol); for(int i=0;i<mol.getAtomCount();i++){ ! if(mol.getAtom(i).getHydrogenCount()<0) ! mol.getAtom(i).setHydrogenCount(0); } HueckelAromaticityDetector.detectAromaticity(mol, false); PredictionTool predictor = new PredictionTool(); ! double[] result = predictor.predict(mol, mol.getAtom(1)); System.err.println(result[0] + " " + result[1] + " " + result[2]); } |
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From: Stefan K. <sh...@us...> - 2006-08-28 14:34:07
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/tests In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv32127/src/java/org/openscience/nmrshiftdb/tests Modified Files: NMRShiftDBServicesTest.java Log Message: updated cdk Index: NMRShiftDBServicesTest.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/tests/NMRShiftDBServicesTest.java,v retrieving revision 1.6 retrieving revision 1.7 diff -C2 -r1.6 -r1.7 *** NMRShiftDBServicesTest.java 22 Jun 2006 16:33:24 -0000 1.6 --- NMRShiftDBServicesTest.java 28 Aug 2006 14:33:58 -0000 1.7 *************** *** 5,9 **** import java.util.Vector; - import javax.xml.namespace.QName; import javax.xml.parsers.DocumentBuilder; import javax.xml.parsers.DocumentBuilderFactory; --- 5,8 ---- |
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From: Stefan K. <sh...@us...> - 2006-08-28 14:34:06
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/webservices In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv32127/src/java/org/openscience/nmrshiftdb/webservices Modified Files: MyNmrshiftdbServices.java NMRShiftDB.java NMRShiftDBServiceBindingImpl.java Log Message: updated cdk Index: MyNmrshiftdbServices.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/webservices/MyNmrshiftdbServices.java,v retrieving revision 1.35 retrieving revision 1.36 diff -C2 -r1.35 -r1.36 *** MyNmrshiftdbServices.java 23 Nov 2005 10:28:36 -0000 1.35 --- MyNmrshiftdbServices.java 28 Aug 2006 14:33:58 -0000 1.36 *************** *** 66,71 **** DBSpectrumType type = DBSpectrumTypePeer.getByName(spectrumTypeName); for (int i = 0; i < mol.getAtomCount(); i++) { ! if (mol.getAtomAt(i).getSymbol().equals(type.getDBIsotope(1).getElementSymbol())) { ! returnValue.add(AtomUtils.predictRange(mol, mol.getAtomAt(i), false, true, null, new StringBuffer(), false, true, null, null, -1,true,null, true)); } } --- 66,71 ---- DBSpectrumType type = DBSpectrumTypePeer.getByName(spectrumTypeName); for (int i = 0; i < mol.getAtomCount(); i++) { ! if (mol.getAtom(i).getSymbol().equals(type.getDBIsotope(1).getElementSymbol())) { ! returnValue.add(AtomUtils.predictRange(mol, mol.getAtom(i), false, true, null, new StringBuffer(), false, true, null, null, -1,true,null, true)); } } Index: NMRShiftDB.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/webservices/NMRShiftDB.java,v retrieving revision 1.3 retrieving revision 1.4 diff -C2 -r1.3 -r1.4 *** NMRShiftDB.java 4 Jul 2006 13:38:55 -0000 1.3 --- NMRShiftDB.java 28 Aug 2006 14:33:58 -0000 1.4 *************** *** 1,6 **** package org.openscience.nmrshiftdb.webservices; - import java.rmi.RemoteException; - import org.w3c.dom.Document; --- 1,4 ---- Index: NMRShiftDBServiceBindingImpl.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/webservices/NMRShiftDBServiceBindingImpl.java,v retrieving revision 1.12 retrieving revision 1.13 diff -C2 -r1.12 -r1.13 *** NMRShiftDBServiceBindingImpl.java 28 Aug 2006 09:34:39 -0000 1.12 --- NMRShiftDBServiceBindingImpl.java 28 Aug 2006 14:33:58 -0000 1.13 *************** *** 9,13 **** import java.util.HashMap; import java.util.Properties; - import java.util.StringTokenizer; import java.util.Vector; --- 9,12 ---- *************** *** 83,89 **** spectrum.addPeakList(peakList); for(int i=0;i<mol.getAtomCount();i++){ ! if(spectype.equals("All") || dbspectype.getDBIsotope(1).getElementSymbol().equals(mol.getAtomAt(i).getSymbol())){ try{ ! double[] result=PredictionTool.generalPredict(mol,mol.getAtomAt(i),false,true,-1,-1,new StringBuffer(),false,false,null,new HashMap(),-1,true,new StringBuffer(),6,true,true); CMLPeak peak=new CMLPeak(); peak.setXMin(result[0]); --- 82,88 ---- spectrum.addPeakList(peakList); for(int i=0;i<mol.getAtomCount();i++){ ! if(spectype.equals("All") || dbspectype.getDBIsotope(1).getElementSymbol().equals(mol.getAtom(i).getSymbol())){ try{ ! double[] result=PredictionTool.generalPredict(mol,mol.getAtom(i),false,true,-1,-1,new StringBuffer(),false,false,null,new HashMap(),-1,true,new StringBuffer(),6,true,true); CMLPeak peak=new CMLPeak(); peak.setXMin(result[0]); *************** *** 92,96 **** peak.setXUnits("units:ppm"); peak.setId("p"+i); ! String[] atomrefs=new String[]{mol.getAtomAt(i).getID()}; peak.setAtomRefs(atomrefs); peakList.addPeak(peak); --- 91,95 ---- peak.setXUnits("units:ppm"); peak.setId("p"+i); ! String[] atomrefs=new String[]{mol.getAtom(i).getID()}; peak.setAtomRefs(atomrefs); peakList.addPeak(peak); *************** *** 169,175 **** subData.setMol(writer.toString(),false,false,true); for(int k=0;k<cmlmol.getAtomCount();k++){ ! subData.getMolWithH().getAtomAt(k).setID(cmlmol.getAtom(k).getId()); if(k<subData.getMolWithHCount().getAtomCount()) ! subData.getMolWithHCount().getAtomAt(k).setID(cmlmol.getAtom(k).getId()); } CMLElements<CMLPeak> peaks=spectrum.getPeakListElements().get(0).getPeakElements(); --- 168,174 ---- subData.setMol(writer.toString(),false,false,true); for(int k=0;k<cmlmol.getAtomCount();k++){ ! subData.getMolWithH().getAtom(k).setID(cmlmol.getAtom(k).getId()); if(k<subData.getMolWithHCount().getAtomCount()) ! subData.getMolWithHCount().getAtom(k).setID(cmlmol.getAtom(k).getId()); } CMLElements<CMLPeak> peaks=spectrum.getPeakListElements().get(0).getPeakElements(); |
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From: Stefan K. <sh...@us...> - 2006-08-28 14:34:05
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/om/map In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv32127/src/java/org/openscience/nmrshiftdb/om/map Modified Files: DBConditionTypeMapBuilder.java Log Message: updated cdk Index: DBConditionTypeMapBuilder.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/om/map/DBConditionTypeMapBuilder.java,v retrieving revision 1.8 retrieving revision 1.9 diff -C2 -r1.8 -r1.9 *** DBConditionTypeMapBuilder.java 8 Jun 2006 12:22:45 -0000 1.8 --- DBConditionTypeMapBuilder.java 28 Aug 2006 14:33:58 -0000 1.9 *************** *** 1,10 **** package org.openscience.nmrshiftdb.om.map; - import java.util.*; - import java.math.*; - import org.apache.turbine.services.db.PoolBrokerService; import org.apache.turbine.services.db.TurbineDB; - import org.apache.turbine.util.db.map.MapBuilder; import org.apache.turbine.util.db.map.DatabaseMap; import org.apache.turbine.util.db.map.TableMap; --- 1,7 ---- package org.openscience.nmrshiftdb.om.map; import org.apache.turbine.services.db.TurbineDB; import org.apache.turbine.util.db.map.DatabaseMap; + import org.apache.turbine.util.db.map.MapBuilder; import org.apache.turbine.util.db.map.TableMap; |
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From: Stefan K. <sh...@us...> - 2006-08-28 09:34:47
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/webservices In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv4643/src/java/org/openscience/nmrshiftdb/webservices Modified Files: NMRShiftDBServiceBindingImpl.java Log Message: more work on web services Index: NMRShiftDBServiceBindingImpl.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/webservices/NMRShiftDBServiceBindingImpl.java,v retrieving revision 1.11 retrieving revision 1.12 diff -C2 -r1.11 -r1.12 *** NMRShiftDBServiceBindingImpl.java 25 Aug 2006 19:32:54 -0000 1.11 --- NMRShiftDBServiceBindingImpl.java 28 Aug 2006 09:34:39 -0000 1.12 *************** *** 189,193 **** if(((DBConditionType) subData.getConditions().get(l)).getConditionName().equals("Solvent")){ for(int k=0;k<els.size();k++){ ! if(els.get(k).getAttribute("dictRef")!=null && els.get(k).getAttribute("dictRef").equals(".SOLVENTNAME")){ ((DBConditionType) subData.getConditions().get(l)).setCurrentValue(((CMLScalar)els.get(k)).getValue()); break; --- 189,193 ---- if(((DBConditionType) subData.getConditions().get(l)).getConditionName().equals("Solvent")){ for(int k=0;k<els.size();k++){ ! if(els.get(k).getAttribute("dictRef")!=null && els.get(k).getAttribute("dictRef").getValue().equals("jcamp:.SOLVENTNAME")){ ((DBConditionType) subData.getConditions().get(l)).setCurrentValue(((CMLScalar)els.get(k)).getValue()); break; *************** *** 197,201 **** if(((DBConditionType) subData.getConditions().get(l)).getConditionName().equals("Temperature [K]")){ for(int k=0;k<els.size();k++){ ! if(els.get(k).getAttribute("dictRef")!=null && els.get(k).getAttribute("dictRef").equals("TEMPERATURE")){ ((DBConditionType) subData.getConditions().get(l)).setCurrentValue(((CMLScalar)els.get(k)).getValue()); break; --- 197,201 ---- if(((DBConditionType) subData.getConditions().get(l)).getConditionName().equals("Temperature [K]")){ for(int k=0;k<els.size();k++){ ! if(els.get(k).getAttribute("dictRef")!=null && els.get(k).getAttribute("dictRef").getValue().equals("jcamp:TEMPERATURE")){ ((DBConditionType) subData.getConditions().get(l)).setCurrentValue(((CMLScalar)els.get(k)).getValue()); break; *************** *** 205,209 **** if(((DBConditionType) subData.getConditions().get(l)).getConditionName().equals("Field Strength [MHz]")){ for(int k=0;k<els.size();k++){ ! if(els.get(k).getAttribute("dictRef")!=null && els.get(k).getAttribute("dictRef").equals(".OBSERVE FREQUENCY")){ ((DBConditionType) subData.getConditions().get(l)).setCurrentValue(((CMLScalar)els.get(k)).getValue()); break; --- 205,209 ---- if(((DBConditionType) subData.getConditions().get(l)).getConditionName().equals("Field Strength [MHz]")){ for(int k=0;k<els.size();k++){ ! if(els.get(k).getAttribute("dictRef")!=null && els.get(k).getAttribute("dictRef").getValue().equals("jcamp:.OBSERVE FREQUENCY")){ ((DBConditionType) subData.getConditions().get(l)).setCurrentValue(((CMLScalar)els.get(k)).getValue()); break; *************** *** 217,236 **** Elements els=spectrum.getChildElements("entry","http://bibtexml.sf.net/"); for(int k=0;k<els.size();k++){ - Element el=els.get(k).getChildElements().get(0); DBLiterature lit=null; ! if(el.getValue().equals("article")){ ! lit=new DBLiterature(NmrshiftdbConstants.JOURNAL_ARTICLE); ! lit.setAuthor(el.getChildElements("author","http://bibtexml.sf.net/").get(0).getValue()); ! lit.setTitle(el.getChildElements("title","http://bibtexml.sf.net/").get(0).getValue()); ! lit.journaltitle=el.getChildElements("journal","http://bibtexml.sf.net/").get(0).getValue(); ! lit.year=Integer.parseInt(el.getChildElements("year","http://bibtexml.sf.net/").get(0).getValue()); ! lit.volume=Integer.parseInt(el.getChildElements("volume","http://bibtexml.sf.net/").get(0).getValue()); ! String pages=el.getChildElements("author","http://bibtexml.sf.net/").get(0).getValue(); ! StringTokenizer pagestokenizer=new StringTokenizer(pages,"-"); ! lit.from=Integer.parseInt(pagestokenizer.nextToken()); ! lit.to=Integer.parseInt(pagestokenizer.nextToken()); ! //TODO consistrency checks? } //TODO other types } subData.save(user.getUserId(),"false","bioclipse", new Date(),null,Integer.parseInt(GeneralUtils.getNmrshiftdbProperty("hosecode.spheres")), false); --- 217,252 ---- Elements els=spectrum.getChildElements("entry","http://bibtexml.sf.net/"); for(int k=0;k<els.size();k++){ DBLiterature lit=null; ! for(int m=0;m<els.get(k).getChildElements().size();m++){ ! Element el=els.get(k).getChildElements().get(m); ! if(el.getLocalName().equals("article")){ ! lit=new DBLiterature(NmrshiftdbConstants.JOURNAL_ARTICLE); ! lit.setAuthor(el.getChildElements("author","http://bibtexml.sf.net/").get(0).getValue()); ! lit.setTitle(el.getChildElements("title","http://bibtexml.sf.net/").get(0).getValue()); ! lit.journaltitle=el.getChildElements("journal","http://bibtexml.sf.net/").get(0).getValue(); ! lit.year=Integer.parseInt(el.getChildElements("year","http://bibtexml.sf.net/").get(0).getValue()); ! lit.volume=Integer.parseInt(el.getChildElements("volume","http://bibtexml.sf.net/").get(0).getValue()); ! String pages=el.getChildElements("pages","http://bibtexml.sf.net/").get(0).getValue(); ! StringBuffer sb1=new StringBuffer(); ! StringBuffer sb2=new StringBuffer(); ! boolean first=true; ! for(int o=0;o<pages.length();o++){ ! if(first && Character.isDigit(pages.charAt(o))){ ! sb1.append(pages.charAt(o)); ! }else if(first && !Character.isDigit(pages.charAt(o))){ ! first=false; ! }else{ ! sb2.append(pages.charAt(o)); ! } ! } ! lit.from=Integer.parseInt(sb1.toString()); ! lit.to=Integer.parseInt(sb2.toString()); ! //TODO consistrency checks? ! } } //TODO other types + if(lit!=null){ + subData.getLiterature().add(lit); + } } subData.save(user.getUserId(),"false","bioclipse", new Date(),null,Integer.parseInt(GeneralUtils.getNmrshiftdbProperty("hosecode.spheres")), false); *************** *** 253,259 **** for(int i=0; i<elements.size(); i++) { Element elem = elements.get(i); ! elem.setNamespaceURI(CMLUtil.CML_NS); ! if (elem.getChildCount() != 0) { ! namespaceThemAll(elem.getChildElements()); } } --- 269,277 ---- for(int i=0; i<elements.size(); i++) { Element elem = elements.get(i); ! if(!elem.getLocalName().equals("entry")){ ! elem.setNamespaceURI(CMLUtil.CML_NS); ! if (elem.getChildCount() != 0) { ! namespaceThemAll(elem.getChildElements()); ! } } } |
