Add ability to give local alias to genome sequences

Author: bbimber

SequenceAnalysis/resources/schemas/dbscripts/postgresql/SequenceAnalysis-12.324-12.325.sql

@@ -0,0 +1 @@
+ALTER TABLE sequenceanalysis.reference_library_members ADD alias VARCHAR(4000);

SequenceAnalysis/resources/schemas/dbscripts/sqlserver/SequenceAnalysis-12.324-12.325.sql

@@ -0,0 +1 @@
+ALTER TABLE sequenceanalysis.reference_library_members ADD alias VARCHAR(4000);

SequenceAnalysis/resources/schemas/sequenceanalysis.xml

@@ -2234,6 +2234,9 @@
                     <fkColumnName>rowid</fkColumnName>
                 </fk>
             </column>
+            <column columnName="alias">
+                <description>Optional.  Can be used to give the sequence a local name</description>
+            </column>
             <column columnName="start">
                 <description>Optional.  Can be used in conjunction with stop to select a subsequence of the reference.  If blank the region will begin at the first base of the reference</description>
             </column>

SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceAnalysisModule.java

@@ -178,7 +178,7 @@ public String getName()
     @Override
     public Double getSchemaVersion()
     {
-        return 12.324;
+        return 12.325;
     }
 
     @Override

SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/ImportGenomeTrackTask.java

@@ -357,6 +357,8 @@ private Map<String, Pair<String, Integer>> getNameTranslationMap(List<RefNtSeque
 
         getJob().getLogger().info("building list of chromosome name translations");
         Map<String, Pair<String, Integer>> ret = new CaseInsensitiveHashMap<>();
+
+        TableInfo rlm = SequenceAnalysisSchema.getTable(SequenceAnalysisSchema.TABLE_REF_LIBRARY_MEMBERS);
         for (RefNtSequenceModel m : refNtSequenceModels)
         {
             if (m.getOffsetsFile() != null && m.getOffsetsFile().exists())
@@ -446,6 +448,18 @@ private Map<String, Pair<String, Integer>> getNameTranslationMap(List<RefNtSeque
                         String strPart = m.getName().toLowerCase().replaceAll("^chr", "");
                         ret.put(strPart, Pair.of(m.getName(), 0));
                     }
+
+                    SimpleFilter filter = new SimpleFilter(FieldKey.fromString("library_id"), getPipelineJob().getLibraryId());
+                    filter.addCondition(FieldKey.fromString("ref_nt_id"), m.getRowid());
+                    TableSelector ts = new TableSelector(rlm, PageFlowUtil.set("alias"), filter, null);
+                    if (ts.exists())
+                    {
+                        String alias = ts.getObject(String.class);
+                        if (alias != null)
+                        {
+                            ret.put(alias, Pair.of(m.getName(), 0));
+                        }
+                    }
                 }
             }
         }

SequenceAnalysis/src/org/labkey/sequenceanalysis/util/ChainFileValidator.java

@@ -7,11 +7,19 @@
 import org.junit.Assert;
 import org.junit.Test;
 import org.labkey.api.collections.CaseInsensitiveHashMap;
+import org.labkey.api.data.CompareType;
 import org.labkey.api.data.DbScope;
+import org.labkey.api.data.Results;
 import org.labkey.api.data.SQLFragment;
 import org.labkey.api.data.Selector;
+import org.labkey.api.data.SimpleFilter;
 import org.labkey.api.data.SqlSelector;
+import org.labkey.api.data.TableSelector;
+import org.labkey.api.query.FieldKey;
+import org.labkey.api.sequenceanalysis.RefNtSequenceModel;
 import org.labkey.api.util.FileUtil;
+import org.labkey.api.util.PageFlowUtil;
+import org.labkey.sequenceanalysis.SequenceAnalysisSchema;
 
 import java.io.BufferedWriter;
 import java.io.File;
@@ -301,6 +309,23 @@ public void exec(ResultSet rs) throws SQLException
                 }
             });
 
+            SimpleFilter filter = new SimpleFilter(FieldKey.fromString("library_id"), genomeId);
+            filter.addCondition(FieldKey.fromString("alias"), null, CompareType.NONBLANK);
+            TableSelector ts = new TableSelector(SequenceAnalysisSchema.getTable(SequenceAnalysisSchema.TABLE_REF_LIBRARY_MEMBERS), PageFlowUtil.set("ref_nt_id", "alias"), filter, null);
+            if (ts.exists())
+            {
+                ts.forEachResults(new Selector.ForEachBlock<Results>()
+               {
+                   @Override
+                   public void exec(Results rs) throws SQLException
+                   {
+                       String name = RefNtSequenceModel.getForRowId(rs.getInt(FieldKey.fromString("ref_nt_id"))).getName();
+                       String alias = rs.getString(FieldKey.fromString("alias"));
+                       cachedReferences.put(alias, name);
+                   }
+               });
+            }
+
             _cachedReferencesByGenome.put(genomeId, cachedReferences);
         }