LMS-966 LMS-967 improved database model, handling sequences and database...

LMS-966 LMS-967 improved database model, handling sequences and database version in uploading. Show UniProt ID in protein browser.

SVN: 11644

rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/IProtDAO.java

@@ -21,8 +21,10 @@ import net.lemnik.eodsql.DataSet;
 import net.lemnik.eodsql.Select;
 import net.lemnik.eodsql.Update;
 
+import ch.systemsx.cisd.openbis.etlserver.phosphonetx.dto.Database;
 import ch.systemsx.cisd.openbis.etlserver.phosphonetx.dto.Experiment;
 import ch.systemsx.cisd.openbis.etlserver.phosphonetx.dto.ModificationType;
+import ch.systemsx.cisd.openbis.etlserver.phosphonetx.dto.ProteinReference;
 import ch.systemsx.cisd.openbis.etlserver.phosphonetx.dto.Sample;
 import ch.systemsx.cisd.openbis.etlserver.phosphonetx.dto.Sequence;
 
@@ -36,13 +38,6 @@ public interface IProtDAO extends BaseQuery
     @Select("select * from modification_types")
     public DataSet<ModificationType> listModificationTypes();
     
-    @Select("select * from sequences where amino_acid_sequence = ?{1}")
-    public Sequence tryToGetSequenceBySequenceString(String sequence);
-    
-    @Select("insert into sequences (amino_acid_sequence, checksum) "
-            + "values (?{1.sequence}, ?{1.checksum}) returning id")
-    public long createSequence(Sequence sequence);
-    
     @Select("select * from experiments where perm_id = ?{1}")
     public Experiment tryToGetExperimentByPermID(String permID);
     
@@ -55,11 +50,18 @@ public interface IProtDAO extends BaseQuery
     @Select("insert into samples (expe_id, perm_id) values (?{1}, ?{2}) returning id")
     public long createSample(long experimentID, String samplePermID);
     
+    @Select("select * from databases where name_and_version = ?{1}")
+    public Database tryToGetDatabaseByName(String name);
+    
+    @Select("insert into databases (name_and_version) values (?{1}) returning id")
+    public long createDatabase(String databaseName);
+    
     @Select("select * from data_sets where perm_id = ?{1}")
     public ch.systemsx.cisd.openbis.etlserver.phosphonetx.dto.DataSet tryToGetDataSetByPermID(String permID);
     
-    @Select("insert into data_sets (expe_id, samp_id, perm_id) values (?{1}, ?{2}, ?{3}) returning id")
-    public long createDataSet(long experimentID, Long sampleID, String dataSetPermID);
+    @Select("insert into data_sets (expe_id, samp_id, perm_id, db_id) "
+            + "values (?{1}, ?{2}, ?{3}, ?{4}) returning id")
+    public long createDataSet(long experimentID, Long sampleID, String dataSetPermID, long databaseID);
     
     @Update("insert into probability_fdr_mappings (dase_id, probability, false_discovery_rate) "
             + "values (?{1}, ?{2}, ?{3})")
@@ -75,7 +77,26 @@ public interface IProtDAO extends BaseQuery
     @Update("insert into modifications (pept_id, moty_id, pos, mass) values (?{1}, ?{2}, ?{3}, ?{4})")
     public void createModification(long peptideID, long modificationTypeID, int position,
             double mass);
+    
+    @Select("select * from protein_references where uniprot_id = ?{1}")
+    public ProteinReference tryToGetProteinReference(String uniprotID);
+    
+    @Select("insert into protein_references (uniprot_id, description) values (?{1}, ?{2}) returning id")
+    public long createProteinReference(String uniprotID, String description);
+    
+    @Update("update protein_references set description = ?{2} where id = ?{1}")
+    public void updateProteinReferenceDescription(long proteinReferenceID, String description);
+    
+    @Select("select * from sequences where prre_id = ?{1} and db_id = ?{2}")
+    public Sequence tryToGetSequenceByReferenceAndDatabase(long referenceID, long databaseID);
+
+    @Select("insert into sequences (db_id, prre_id, amino_acid_sequence, checksum) "
+            + "values (?{1.databaseID}, ?{1.proteinReferenceID}, ?{1.sequence}, ?{1.checksum}) "
+            + "returning id")
+    public long createSequence(Sequence sequence);
+    
+    @Update("insert into identified_proteins (prot_id, sequ_id) values (?{1}, ?{2})")
+    public void createIdentifiedProtein(long proteinID, long sequenceID);
 
-    @Update("insert into identified_proteins (prot_id, sequ_id, description) values (?{1}, ?{2}, ?{3})")
-    public void createIdentifiedProtein(long proteinID, Long sequenceID, String description);
 }
+

rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/ResultDataSetHandler.java

@@ -40,6 +40,7 @@ import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
 import ch.systemsx.cisd.openbis.etlserver.phosphonetx.dto.AminoAcidMass;
 import ch.systemsx.cisd.openbis.etlserver.phosphonetx.dto.AnnotatedProtein;
 import ch.systemsx.cisd.openbis.etlserver.phosphonetx.dto.DataSet;
+import ch.systemsx.cisd.openbis.etlserver.phosphonetx.dto.Database;
 import ch.systemsx.cisd.openbis.etlserver.phosphonetx.dto.Experiment;
 import ch.systemsx.cisd.openbis.etlserver.phosphonetx.dto.ModificationType;
 import ch.systemsx.cisd.openbis.etlserver.phosphonetx.dto.Peptide;
@@ -48,6 +49,7 @@ import ch.systemsx.cisd.openbis.etlserver.phosphonetx.dto.Protein;
 import ch.systemsx.cisd.openbis.etlserver.phosphonetx.dto.ProteinAnnotation;
 import ch.systemsx.cisd.openbis.etlserver.phosphonetx.dto.ProteinGroup;
 import ch.systemsx.cisd.openbis.etlserver.phosphonetx.dto.ProteinProphetDetails;
+import ch.systemsx.cisd.openbis.etlserver.phosphonetx.dto.ProteinReference;
 import ch.systemsx.cisd.openbis.etlserver.phosphonetx.dto.ProteinSummary;
 import ch.systemsx.cisd.openbis.etlserver.phosphonetx.dto.ProteinSummaryDataFilter;
 import ch.systemsx.cisd.openbis.etlserver.phosphonetx.dto.Sample;
@@ -67,6 +69,55 @@ public class ResultDataSetHandler implements IDataSetHandler
     private static final String DATABASE_OWNER = "database.owner";
     private static final String DATABASE_PASSWORD = "database.password";
     
+    private static final class ProteinDescription
+    {
+        private final String uniprotID;
+        private final String description;
+        private final String sequence;
+
+        public ProteinDescription(String proteinDescription)
+        {
+            String[] items = proteinDescription.split("\\\\");
+            uniprotID = tryToGetUniprotID(items);
+            description = tryToGetValue(items, "DE");
+            sequence = tryToGetValue(items, "SEQ");
+        }
+        
+        public final String getUniprotID()
+        {
+            return uniprotID;
+        }
+
+        public final String getDescription()
+        {
+            return description;
+        }
+
+        public final String getSequence()
+        {
+            return sequence;
+        }
+
+        private String tryToGetUniprotID(String[] items)
+        {
+            return items == null || items.length == 0 ? null : items[0].trim(); 
+        }
+        
+        private String tryToGetValue(String[] items, String key)
+        {
+            for (String item : items)
+            {
+                int indexOfEqualSign = item.indexOf('=');
+                if (indexOfEqualSign > 0
+                        && item.substring(0, indexOfEqualSign).trim().equalsIgnoreCase(key))
+                {
+                    return item.substring(indexOfEqualSign + 1).trim();
+                }
+            }
+            return null;
+        }
+    }
+    
     private final IDataSetHandler delegator;
     private final Unmarshaller unmarshaller;
     private final IProtDAO dao;
@@ -130,12 +181,35 @@ public class ResultDataSetHandler implements IDataSetHandler
         dataSetInfo.getSample().getPermId();
         Experiment experiment = getOrCreateExperiment(dataSetInfo.getExperiment().getPermId());
         Sample sample = getOrCreateSample(experiment, dataSetInfo.getSample().getPermId());
-        DataSet ds = getOrCreateDataSet(experiment, sample, dataSetInfo.getDataSetCode());
+        String referenceDatabase = summary.getSummaryHeader().getReferenceDatabase();
+        Database database = getOrGreateDatabase(referenceDatabase);
+        DataSet ds = getOrCreateDataSet(experiment, sample, database, dataSetInfo.getDataSetCode());
         addToDatabase(ds, summary);
         return dataSets;
     }
 
-    private DataSet getOrCreateDataSet(Experiment experiment, Sample sample, String dataSetPermID)
+    private Database getOrGreateDatabase(String databaseNameAndVersion)
+    {
+        int indexOfLastSlash = databaseNameAndVersion.lastIndexOf('/');
+        String nameOrVersion;
+        if (indexOfLastSlash < 0)
+        {
+            nameOrVersion = databaseNameAndVersion;
+        } else
+        {
+            nameOrVersion = databaseNameAndVersion.substring(indexOfLastSlash + 1);
+        }
+        Database database = dao.tryToGetDatabaseByName(nameOrVersion);
+        if (database == null)
+        {
+            database = new Database();
+            database.setNameAndVersion(nameOrVersion);
+            database.setId(dao.createDatabase(database.getNameAndVersion()));
+        }
+        return database;
+    }
+
+    private DataSet getOrCreateDataSet(Experiment experiment, Sample sample, Database database, String dataSetPermID)
     {
         DataSet dataSet = dao.tryToGetDataSetByPermID(dataSetPermID);
         if (dataSet == null)
@@ -144,7 +218,11 @@ public class ResultDataSetHandler implements IDataSetHandler
             dataSet.setPermID(dataSetPermID);
             long experimentID = experiment.getId();
             dataSet.setExperimentID(experimentID);
-            dataSet.setId(dao.createDataSet(experimentID, sample.getId(), dataSetPermID));
+            long sampleID = sample.getId();
+            dataSet.setSampleID(sampleID);
+            long databaseID = database.getId();
+            dataSet.setDatabaseID(databaseID);
+            dataSet.setId(dao.createDataSet(experimentID, sampleID, dataSetPermID, databaseID));
         }
         return dataSet;
     }
@@ -193,29 +271,26 @@ public class ResultDataSetHandler implements IDataSetHandler
     private void addToDatabase(DataSet dataSet, ProteinSummary summary)
     {
         long dataSetID = dataSet.getId();
+        Long databaseID = dataSet.getDatabaseID();
         createProbabilityToFDRMapping(dataSetID, summary);
         Iterable<ModificationType> modificationTypes = dao.listModificationTypes();
+        System.out.println(modificationTypes);
         List<ProteinGroup> proteinGroups = summary.getProteinGroups();
-        int maxGroupSize = 0;
-        String maxGroupName = null;
         for (ProteinGroup proteinGroup : proteinGroups)
         {
             double probability = proteinGroup.getProbability();
             List<Protein> proteins = proteinGroup.getProteins();
-            if (maxGroupSize < proteins.size())
-            {
-                maxGroupSize = proteins.size();
-                maxGroupName = proteinGroup.getGroupNumber();
-            }
-            for (Protein protein : proteins)
+            if  (proteins.isEmpty() == false)
             {
+                // only the first protein is added. All other proteins are ignored.
+                Protein protein = proteins.get(0);
                 ProteinAnnotation annotation = protein.getAnnotation();
                 long proteinID = dao.createProtein(dataSetID, probability);
-                dao.createIdentifiedProtein(proteinID, null, annotation.getDescription());
+                createIdentifiedProtein(proteinID, databaseID, annotation.getDescription());
                 for (AnnotatedProtein annotatedProtein : protein.getIndistinguishableProteins())
                 {
                     String description = annotatedProtein.getAnnotation().getDescription();
-                    dao.createIdentifiedProtein(proteinID, null, description);
+                    createIdentifiedProtein(proteinID, databaseID, description);
                 }
                 List<Peptide> peptides = protein.getPeptides();
                 for (Peptide peptide : peptides)
@@ -238,7 +313,6 @@ public class ResultDataSetHandler implements IDataSetHandler
                 }
             }
         }
-        System.out.println("maximum group size: " + maxGroupSize + ", name:" + maxGroupName);
     }
 
     private void createProbabilityToFDRMapping(long dataSetID, ProteinSummary summary)
@@ -264,20 +338,35 @@ public class ResultDataSetHandler implements IDataSetHandler
         }
         throw new UserFailureException("Missing Protein Prophet details.");
     }
-
-    private Sequence getOrCreateSequence(Peptide peptide)
+    
+    private void createIdentifiedProtein(long proteinID, long databaseID, String proteinDescription)
     {
-        String s = peptide.getSequence();
-        Sequence sequence = dao.tryToGetSequenceBySequenceString(s);
-        if (sequence == null)
+        ProteinDescription protDesc = new ProteinDescription(proteinDescription);
+        String uniprotID = protDesc.getUniprotID();
+        String description = protDesc.getDescription();
+        ProteinReference proteinReference = dao.tryToGetProteinReference(uniprotID);
+        if (proteinReference == null)
         {
-            sequence = new Sequence(s);
-            long id = dao.createSequence(sequence);
-            sequence.setId(id);
+            proteinReference = new ProteinReference();
+            proteinReference.setUniprotID(uniprotID);
+            proteinReference.setDescription(description);
+            proteinReference.setId(dao.createProteinReference(uniprotID, description));
+        } else if (description.equals(proteinReference.getDescription()) == false)
+        {
+            dao.updateProteinReferenceDescription(proteinReference.getId(), description);
+        }
+        Sequence sequence =
+                dao.tryToGetSequenceByReferenceAndDatabase(proteinReference.getId(), databaseID);
+        if (sequence == null || protDesc.getSequence().equals(sequence.getSequence()) == false)
+        {
+            sequence = new Sequence(protDesc.getSequence());
+            sequence.setDatabaseID(databaseID);
+            sequence.setProteinReferenceID(proteinReference.getId());
+            sequence.setId(dao.createSequence(sequence));
         }
-        return sequence;
+        dao.createIdentifiedProtein(proteinID, sequence.getId());
     }
-
+    
     private ModificationType findModificationType(Iterable<ModificationType> modificationTypes,
             double mass)
     {

rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/dto/DataSet.java

@@ -30,6 +30,9 @@ public class DataSet extends AbstractDTOWithIDAndPermID
     
     @ResultColumn("expe_id")
     private Long experimentID;
+    
+    @ResultColumn("db_id")
+    private Long databaseID;
 
     public final Long getSampleID()
     {
@@ -50,4 +53,14 @@ public class DataSet extends AbstractDTOWithIDAndPermID
     {
         this.experimentID = experimentID;
     }
+
+    public final Long getDatabaseID()
+    {
+        return databaseID;
+    }
+
+    public final void setDatabaseID(Long databaseID)
+    {
+        this.databaseID = databaseID;
+    }
 }

rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/dto/Database.java

+/*
+ * Copyright 2009 ETH Zuerich, CISD
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package ch.systemsx.cisd.openbis.etlserver.phosphonetx.dto;
+
+import net.lemnik.eodsql.ResultColumn;
+
+/**
+ * 
+ *
+ * @author Franz-Josef Elmer
+ */
+public class Database extends AbstractDTOWithID
+{
+    @ResultColumn("name_and_version")
+    private String nameAndVersion;
+
+    public final String getNameAndVersion()
+    {
+        return nameAndVersion;
+    }
+
+    public final void setNameAndVersion(String nameAndVersion)
+    {
+        this.nameAndVersion = nameAndVersion;
+    }
+
+}

rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/dto/ModificationType.java

@@ -27,9 +27,12 @@ public class ModificationType extends AbstractDTOWithID
 {
     private String code;
     
+    @ResultColumn("amino_acid")
+    private String aminoAcid;
+    
     private double mass;
     
-    @ResultColumn("delta_mass")
+    @ResultColumn("mass_tolerance")
     private double deltaMass;
 
     public final String getCode()
@@ -42,6 +45,16 @@ public class ModificationType extends AbstractDTOWithID
         this.code = code;
     }
 
+    public final String getAminoAcid()
+    {
+        return aminoAcid;
+    }
+
+    public final void setAminoAcid(String aminoAcid)
+    {
+        this.aminoAcid = aminoAcid;
+    }
+
     public final double getMass()
     {
         return mass;
@@ -70,7 +83,7 @@ public class ModificationType extends AbstractDTOWithID
     @Override
     public String toString()
     {
-        return code + "=(" + mass + "\u00b1" + deltaMass + ")";
+        return code + "=(" + aminoAcid + ":" + mass + "\u00b1" + deltaMass + ")";
     }
     
     

rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/dto/ProteinReference.java

+/*
+ * Copyright 2009 ETH Zuerich, CISD
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package ch.systemsx.cisd.openbis.etlserver.phosphonetx.dto;
+
+import net.lemnik.eodsql.ResultColumn;
+
+/**
+ * 
+ *
+ * @author Franz-Josef Elmer
+ */
+public class ProteinReference extends AbstractDTOWithID
+{
+    @ResultColumn("uniprot_id")
+    private String uniprotID;
+    
+    @ResultColumn("description")
+    private String description;
+
+    public final String getUniprotID()
+    {
+        return uniprotID;
+    }
+
+    public final void setUniprotID(String uniprotID)
+    {
+        this.uniprotID = uniprotID;
+    }
+
+    public final String getDescription()
+    {
+        return description;
+    }
+
+    public final void setDescription(String description)
+    {
+        this.description = description;
+    }
+}

rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/dto/Sequence.java

@@ -25,6 +25,12 @@ import net.lemnik.eodsql.ResultColumn;
  */
 public class Sequence extends AbstractDTOWithID
 {
+    @ResultColumn("database_id")
+    private long databaseID;
+    
+    @ResultColumn("protein_reference_id")
+    private long proteinReferenceID;
+    
     @ResultColumn("amino_acid_sequence")
     private String sequence;
     
@@ -42,6 +48,26 @@ public class Sequence extends AbstractDTOWithID
         calculateChecksum();
     }
     
+    public final long getDatabaseID()
+    {
+        return databaseID;
+    }
+
+    public final void setDatabaseID(long databaseID)
+    {
+        this.databaseID = databaseID;
+    }
+
+    public final long getProteinReferenceID()
+    {
+        return proteinReferenceID;
+    }
+
+    public final void setProteinReferenceID(long proteinDescriptionID)
+    {
+        this.proteinReferenceID = proteinDescriptionID;
+    }
+
     public final String getSequence()
     {
         return sequence;

rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/Dict.java

@@ -26,6 +26,7 @@ public class Dict
     public static final String QUERY_MENU_TITLE = "query_menu_title";
     public static final String SELECTED_EXPERIMENT_LABEL = "selected_experiment_label";
     
+    public static final String UNIPROT_ID = "uniprot_id";
     public static final String PROTEIN_DESCRIPTION = "protein_description";
     public static final String FALSE_DISCOVERY_RATE = "false_discovery_rate";
     public static final String DATA_SET = "data_set";

rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/ProteinByExperimentBrowserGrid.java

@@ -21,6 +21,7 @@ import java.util.List;
 import ch.systemsx.cisd.openbis.generic.client.web.client.application.AbstractAsyncCallback;
 import ch.systemsx.cisd.openbis.generic.client.web.client.application.GenericConstants;
 import ch.systemsx.cisd.openbis.generic.client.web.client.application.IViewContext;
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.framework.DispatcherHelper;
 import ch.systemsx.cisd.openbis.generic.client.web.client.application.renderer.LinkRenderer;
 import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.columns.framework.IColumnDefinitionKind;
 import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.grid.AbstractSimpleBrowserGrid;
@@ -73,11 +74,12 @@ class ProteinByExperimentBrowserGrid extends AbstractSimpleBrowserGrid<ProteinIn
         super(viewContext.getCommonViewContext(), BROWSER_ID, GRID_ID, false);
         specificViewContext = viewContext;
         setDisplayTypeIDGenerator(PhosphoNetXDisplayTypeIDGenerator.PROTEIN_BY_EXPERIMENT_BROWSER_GRID);
-        registerLinkClickListenerFor(ProteinColDefKind.DATA_SET.id(),
+        registerLinkClickListenerFor(ProteinColDefKind.DESCRIPTION.id(),
                 new ICellListener<ProteinInfo>()
                     {
                         public void handle(ProteinInfo rowItem)
                         {
+                            DispatcherHelper.dispatchNaviEvent(ProteinViewer.createTabItemFactory(viewContext, rowItem));
                             System.out.println(rowItem.getDataSetPermID());
                         }
                     });
@@ -100,7 +102,7 @@ class ProteinByExperimentBrowserGrid extends AbstractSimpleBrowserGrid<ProteinIn
     protected ColumnDefsAndConfigs<ProteinInfo> createColumnsDefinition()
     {
         ColumnDefsAndConfigs<ProteinInfo> definitions = super.createColumnsDefinition();
-        definitions.setGridCellRendererFor(ProteinColDefKind.DATA_SET.id(), LinkRenderer.createLinkRenderer());
+        definitions.setGridCellRendererFor(ProteinColDefKind.DESCRIPTION.id(), LinkRenderer.createLinkRenderer());
         return definitions;
     }
 

rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/ProteinViewer.java

+/*
+ * Copyright 2009 ETH Zuerich, CISD
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.application;
+
+import java.util.LinkedHashMap;
+import java.util.Map;
+import java.util.Set;
+
+import com.extjs.gxt.ui.client.widget.ContentPanel;
+
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.GenericConstants;
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.IViewContext;
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.framework.DatabaseModificationAwareComponent;
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.framework.DefaultTabItem;
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.framework.IDatabaseModificationObserver;
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.framework.ITabItem;
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.framework.ITabItemFactory;
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.AbstractViewer;
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.PropertyValueRenderers;
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.property.PropertyGrid;
+import ch.systemsx.cisd.openbis.generic.client.web.client.dto.Experiment;
+import ch.systemsx.cisd.openbis.generic.client.web.client.dto.Invalidation;
+import ch.systemsx.cisd.openbis.generic.client.web.client.dto.Sample;
+import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DatabaseModificationKind;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Person;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SampleProperty;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SampleType;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.IPhosphoNetXClientServiceAsync;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.dto.ProteinInfo;
+
+/**
+ * 
+ *
+ * @author Franz-Josef Elmer
+ */
+public class ProteinViewer extends ContentPanel implements IDatabaseModificationObserver
+{
+    private static final String PREFIX = "protein-viewer_";
+
+    public static final String ID_PREFIX = GenericConstants.ID_PREFIX + PREFIX;
+    
+    static ITabItemFactory createTabItemFactory(final IViewContext<IPhosphoNetXClientServiceAsync> viewContext, final ProteinInfo proteinInfo)
+    {
+        return new ITabItemFactory()
+            {
+                public String getId()
+                {
+                    return createWidgetID(proteinInfo.getId());
+                }
+        
+                public ITabItem create()
+                {
+                    ProteinViewer viewer = new ProteinViewer(viewContext, proteinInfo.getId());
+                    DatabaseModificationAwareComponent c = new DatabaseModificationAwareComponent(viewer, viewer);
+                    return DefaultTabItem.create("Protein: " + proteinInfo.getDescription(), c, viewContext, false);
+                }
+            };
+    }
+    
+    static String createWidgetID(TechId proteinID)
+    {
+        return ID_PREFIX + proteinID.getId();
+    }
+    
+    private final IViewContext<IPhosphoNetXClientServiceAsync> viewContext;
+    private final TechId proteinID;
+    private final String widgetID;
+    
+    private ProteinViewer(IViewContext<IPhosphoNetXClientServiceAsync> viewContext,
+            TechId proteinID)
+    {
+        widgetID = createWidgetID(proteinID);
+        this.viewContext = viewContext;
+        this.proteinID = proteinID;
+    }
+    
+    private void createUI()
+    {
+        final Map<String, Object> properties = new LinkedHashMap<String, Object>();
+        final PropertyGrid propertyGrid = new PropertyGrid(viewContext, properties.size());
+        properties.put("ID", proteinID);
+        add(propertyGrid);
+    }
+
+    public DatabaseModificationKind[] getRelevantModifications()
+    {
+        return new DatabaseModificationKind[0];
+    }
+
+    public void update(Set<DatabaseModificationKind> observedModifications)
+    {
+    }
+
+}

rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/columns/ProteinColDefKind.java

@@ -26,14 +26,22 @@ import ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.dto.Protein
  */
 public enum ProteinColDefKind implements IColumnDefinitionKind<ProteinInfo>
 {
-    DESCRIPTION(new AbstractColumnDefinitionKind<ProteinInfo>(Dict.PROTEIN_DESCRIPTION)
+    UNIPROT_ID(new AbstractColumnDefinitionKind<ProteinInfo>(Dict.UNIPROT_ID)
         {
             @Override
             public String tryGetValue(ProteinInfo entity)
             {
-                return entity.getDescription();
+                return entity.getUniprotID();
             }
         }), 
+    DESCRIPTION(new AbstractColumnDefinitionKind<ProteinInfo>(Dict.PROTEIN_DESCRIPTION)
+                {
+            @Override
+            public String tryGetValue(ProteinInfo entity)
+            {
+                return entity.getDescription();
+            }
+                }), 
     FALSE_DISCOVERY_RATE(new AbstractColumnDefinitionKind<ProteinInfo>(Dict.FALSE_DISCOVERY_RATE)
         {
             @Override
@@ -48,14 +56,6 @@ public enum ProteinColDefKind implements IColumnDefinitionKind<ProteinInfo>
                 return entity.getFalseDiscoveryRate();
             }
         }), 
-    DATA_SET(new AbstractColumnDefinitionKind<ProteinInfo>(Dict.DATA_SET)
-        {
-            @Override
-            public String tryGetValue(ProteinInfo entity)
-            {
-                return entity.getDataSetPermID();
-            }
-        }), 
     ;
 
     private final AbstractColumnDefinitionKind<ProteinInfo> columnDefinitionKind;

rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/dto/ProteinInfo.java

@@ -29,6 +29,8 @@ public class ProteinInfo implements IsSerializable
 {
     private TechId id;
     
+    private String uniprotID;
+    
     private String dataSetPermID;
     
     private String description;
@@ -65,6 +67,16 @@ public class ProteinInfo implements IsSerializable
         this.falseDiscoveryRate = falseDiscoveryRate;
     }
 
+    public final String getUniprotID()
+    {
+        return uniprotID;
+    }
+
+    public final void setUniprotID(String uniprotID)
+    {
+        this.uniprotID = uniprotID;
+    }
+
     public final String getDescription()
     {
         return description;

rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/public/phosphonetx-dictionary.js

@@ -6,6 +6,7 @@ var phosphonetx = {
   selected_experiment_label: "Experiment",
   
   // Protein grid
+  uniprot_id: "UniProt ID",
   protein_description: "Protein",
   false_discovery_rate: "FDR",
   

rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/server/ListProteinOriginalDataProvider.java

@@ -52,6 +52,7 @@ class ListProteinOriginalDataProvider implements IOriginalDataProvider<ProteinIn
         {
             ProteinInfo proteinInfo = new ProteinInfo();
             proteinInfo.setId(new TechId(protein.getId()));
+            proteinInfo.setUniprotID(protein.getUniprotID());
             proteinInfo.setDescription(protein.getDescription());
             proteinInfo.setFalseDiscoveryRate(protein.getFalseDiscoveryRate());
             proteinInfo.setDataSetPermID(protein.getDataSetPermID());

rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/dataaccess/IProteinQueryDAO.java

@@ -34,9 +34,11 @@ public interface IProteinQueryDAO extends BaseQuery
     public DataSet<ProbabilityFDRMapping> getProbabilityFDRMapping(long dataSetID);
     
     @Select("select ip.id as id, d.id as data_set_id, d.perm_id as data_set_perm_id, "
-            + "p.id as protein_id, p.probability, ip.description "
+            + "p.id as protein_id, p.probability, pr.uniprot_id, pr.description "
             + "from identified_proteins as ip left join proteins as p on ip.prot_id = p.id "
             + "left join data_sets as d on p.dase_id = d.id "
-            + "left join experiments as e on d.expe_id = e.id where e.perm_id = ?{1}")
+            + "left join experiments as e on d.expe_id = e.id, " 
+            + "sequences as s left join protein_references as pr on s.prre_id = pr.id "
+            + "where e.perm_id = ?{1} and ip.sequ_id = s.id")
     public DataSet<IdentifiedProtein> listProteinsByExperiment(String experimentPermID);
 }

rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/dto/IdentifiedProtein.java

@@ -37,6 +37,9 @@ public class IdentifiedProtein
     @ResultColumn("protein_id")
     private long proteinID;
     
+    @ResultColumn("uniprot_id")
+    private String uniprotID;
+    
     @ResultColumn("description")
     private String description;
     
@@ -65,6 +68,16 @@ public class IdentifiedProtein
         this.dataSetPermID = dataSetPermID;
     }
 
+    public final String getUniprotID()
+    {
+        return uniprotID;
+    }
+
+    public final void setUniprotID(String uniprotID)
+    {
+        this.uniprotID = uniprotID;
+    }
+
     public final String getDescription()
     {
         return description;

rtd_phosphonetx/source/sql/postgresql/001/data-001.sql

@@ -2,7 +2,7 @@ INSERT INTO MODIFICATION_TYPES
 (CODE
 ,DESCRIPTION
 ,MASS
-,DELTA_MASS)
+,MASS_TOLERANCE)
 values
 ('UNKNOWN'
 ,'Unknown mass'
@@ -13,11 +13,13 @@ values
 INSERT INTO MODIFICATION_TYPES
 (CODE
 ,DESCRIPTION
+,AMINO_ACID
 ,MASS
-,DELTA_MASS)
+,MASS_TOLERANCE)
 values
 ('115'
 ,'Mass around 115'
+,'N'
 ,115
 ,2
 );
@@ -25,11 +27,13 @@ values
 INSERT INTO MODIFICATION_TYPES
 (CODE
 ,DESCRIPTION
+,AMINO_ACID
 ,MASS
-,DELTA_MASS)
+,MASS_TOLERANCE)
 values
 ('147'
 ,'Mass around 147'
+,'M'
 ,147
 ,2
 );
@@ -37,11 +41,13 @@ values
 INSERT INTO MODIFICATION_TYPES
 (CODE
 ,DESCRIPTION
+,AMINO_ACID
 ,MASS
-,DELTA_MASS)
+,MASS_TOLERANCE)
 values
 ('160'
 ,'Mass around 160'
+,'C'
 ,160
 ,2
 );

rtd_phosphonetx/source/sql/postgresql/001/schema-001.sql

 /* ---------------------------------------------------------------------- */
 /* Script generated with: DeZign for Databases v5.2.2                     */
 /* Target DBMS:           PostgreSQL 8                                    */
-/* Project file:          phosphonetx.dez                                 */
+/* Project file:          schema-001.dez                                  */
 /* Project name:                                                          */
 /* Author:                                                                */
 /* Script type:           Database creation script                        */
-/* Created on:            2009-06-30 09:00                                */
-/* Model version:         Version 2009-06-30                              */
+/* Created on:            2009-07-06 13:30                                */
+/* Model version:         Version 2009-07-06 1                            */
 /* ---------------------------------------------------------------------- */
 
 
@@ -14,8 +14,6 @@
 /* Domains                                                                */
 /* ---------------------------------------------------------------------- */
 
-CREATE DOMAIN BINARY_DATA AS BYTEA;
-
 CREATE DOMAIN CHECKSUM AS CHARACTER VARYING(8);
 
 CREATE DOMAIN CODE AS CHARACTER VARYING(40);
@@ -34,6 +32,8 @@ CREATE DOMAIN TECH_ID AS BIGINT;
 
 CREATE DOMAIN SHORT_SEQUENCE AS CHARACTER VARYING(1000);
 
+CREATE DOMAIN UNIPROT_ACCESSION_NUMBER AS CHARACTER VARYING(40);
+
 /* ---------------------------------------------------------------------- */
 /* Tables                                                                 */
 /* ---------------------------------------------------------------------- */
@@ -69,6 +69,7 @@ CREATE TABLE DATA_SETS (
     ID BIGSERIAL  NOT NULL,
     EXPE_ID TECH_ID  NOT NULL,
     SAMP_ID TECH_ID  NOT NULL,
+    DB_ID TECH_ID  NOT NULL,
     PERM_ID CODE  NOT NULL,
     CONSTRAINT PK_DATA_SETS PRIMARY KEY (ID),
     CONSTRAINT TUC_DATA_SETS_1 UNIQUE (PERM_ID)
@@ -103,8 +104,9 @@ CREATE TABLE MODIFICATION_TYPES (
     ID BIGSERIAL  NOT NULL,
     CODE CODE  NOT NULL,
     DESCRIPTION SHORT_DESCRIPTION,
+    AMINO_ACID CHARACTER(1),
     MASS REAL_NUMBER,
-    DELTA_MASS REAL_NUMBER,
+    MASS_TOLERANCE REAL_NUMBER,
     CONSTRAINT PK_MODIFICATION_TYPES PRIMARY KEY (ID),
     CONSTRAINT TUC_MODIFICATION_TYPES_1 UNIQUE (CODE)
 );
@@ -154,6 +156,8 @@ CREATE TABLE SAMPLES (
 
 CREATE TABLE SEQUENCES (
     ID BIGSERIAL  NOT NULL,
+    DB_ID TECH_ID  NOT NULL,
+    PRRE_ID TECH_ID  NOT NULL,
     AMINO_ACID_SEQUENCE LONG_SEQUENCE  NOT NULL,
     CHECKSUM CHECKSUM  NOT NULL,
     CONSTRAINT PK_SEQUENCES PRIMARY KEY (ID)
@@ -166,8 +170,7 @@ CREATE TABLE SEQUENCES (
 CREATE TABLE IDENTIFIED_PROTEINS (
     ID BIGSERIAL  NOT NULL,
     PROT_ID TECH_ID  NOT NULL,
-    SEQU_ID TECH_ID,
-    DESCRIPTION DESCRIPTION  NOT NULL,
+    SEQU_ID TECH_ID  NOT NULL,
     CONSTRAINT PK_IDENTIFIED_PROTEINS PRIMARY KEY (ID)
 );
 
@@ -196,6 +199,31 @@ CREATE TABLE PROBABILITY_FDR_MAPPINGS (
     CONSTRAINT PK_PROBABILITY_FDR_MAPPINGS PRIMARY KEY (ID)
 );
 
+/* ---------------------------------------------------------------------- */
+/* Add table "PROTEIN_REFERENCES"                                         */
+/* ---------------------------------------------------------------------- */
+
+CREATE TABLE PROTEIN_REFERENCES (
+    ID BIGSERIAL  NOT NULL,
+    UNIPROT_ID UNIPROT_ACCESSION_NUMBER  NOT NULL,
+    DESCRIPTION DESCRIPTION,
+    CONSTRAINT PK_PROTEIN_REFERENCES PRIMARY KEY (ID),
+    CONSTRAINT TUC_PROTEIN_REFERENCES_1 UNIQUE (UNIPROT_ID)
+);
+
+CREATE INDEX IDX_PROTEIN_REFERENCES_1 ON PROTEIN_REFERENCES (UNIPROT_ID);
+
+/* ---------------------------------------------------------------------- */
+/* Add table "DATABASES"                                                  */
+/* ---------------------------------------------------------------------- */
+
+CREATE TABLE DATABASES (
+    ID BIGSERIAL  NOT NULL,
+    NAME_AND_VERSION SHORT_DESCRIPTION  NOT NULL,
+    CONSTRAINT PK_DATABASES PRIMARY KEY (ID),
+    CONSTRAINT TUC_DATABASES_1 UNIQUE (NAME_AND_VERSION)
+);
+
 /* ---------------------------------------------------------------------- */
 /* Foreign key constraints                                                */
 /* ---------------------------------------------------------------------- */
@@ -206,6 +234,9 @@ ALTER TABLE DATA_SETS ADD CONSTRAINT DA_EX_FK
 ALTER TABLE DATA_SETS ADD CONSTRAINT DA_SA_FK 
     FOREIGN KEY (SAMP_ID) REFERENCES SAMPLES (ID);
 
+ALTER TABLE DATA_SETS ADD CONSTRAINT DATABASES_DATA_SETS 
+    FOREIGN KEY (DB_ID) REFERENCES DATABASES (ID);
+
 ALTER TABLE MODIFICATIONS ADD CONSTRAINT MO_PE_FK 
     FOREIGN KEY (PEPT_ID) REFERENCES PEPTIDES (ID);
 
@@ -218,6 +249,12 @@ ALTER TABLE PEPTIDES ADD CONSTRAINT PE_PR_FK
 ALTER TABLE PROTEINS ADD CONSTRAINT DATA_SETS_PROTEINS 
     FOREIGN KEY (DASE_ID) REFERENCES DATA_SETS (ID);
 
+ALTER TABLE SEQUENCES ADD CONSTRAINT DATABASES_SEQUENCES 
+    FOREIGN KEY (DB_ID) REFERENCES DATABASES (ID);
+
+ALTER TABLE SEQUENCES ADD CONSTRAINT PROTEIN_REFERENCES_SEQUENCES 
+    FOREIGN KEY (PRRE_ID) REFERENCES PROTEIN_REFERENCES (ID);
+
 ALTER TABLE IDENTIFIED_PROTEINS ADD CONSTRAINT PROTEINS_IDENTIFIED_PROTEINS 
     FOREIGN KEY (PROT_ID) REFERENCES PROTEINS (ID);