CNA long format (RFC 65)

core/src/main/java/org/mskcc/cbio/portal/dao/DaoCnaEvent.java

@@ -70,8 +70,11 @@ public static void addCaseCnaEvent(CnaEvent cnaEvent, boolean newCnaEvent) throw
                 || 
                 (cnaEvent.getDriverTiersFilter() != null
                 && !cnaEvent.getDriverTiersFilter().isEmpty()
-                && !cnaEvent.getDriverTiersFilter().toLowerCase().equals("na"))) {
-                MySQLbulkLoader.getMySQLbulkLoader("alteration_driver_annotation").insertRecord(
+                && !cnaEvent.getDriverTiersFilter().toLowerCase().equals("na"))
+            ) {
+                    MySQLbulkLoader
+                        .getMySQLbulkLoader("alteration_driver_annotation")
+                        .insertRecord(
                     Long.toString(eventId),
                     Integer.toString(cnaEvent.getCnaProfileId()),
                     Integer.toString(cnaEvent.getSampleId()),

core/src/main/java/org/mskcc/cbio/portal/dao/DaoGeneticProfile.java

@@ -173,6 +173,34 @@ public static boolean updateNameAndDescription (int geneticProfileId, String nam
             JdbcUtil.closeAll(DaoGeneticProfile.class, con, pstmt, rs);
         }
 
+        reCache();
+        return ret;
+    }    
+
+    /**
+     * Updates a Genetic Profile datatype
+     */
+    public static boolean updateDatatype(
+        int geneticProfileId,
+        String datatype
+    ) throws DaoException {
+        Connection con = null;
+        PreparedStatement pstmt = null;
+        ResultSet rs = null;
+        boolean ret;
+        try {
+            con = JdbcUtil.getDbConnection(DaoGeneticProfile.class);
+            pstmt = con.prepareStatement("UPDATE genetic_profile SET DATATYPE=? " +
+                "WHERE GENETIC_PROFILE_ID=?");
+            pstmt.setString(1, datatype);
+            pstmt.setInt(2, geneticProfileId);
+            ret = pstmt.executeUpdate() > 0;
+        } catch (SQLException e) {
+            throw new DaoException(e);
+        } finally {
+            JdbcUtil.closeAll(DaoGeneticProfile.class, con, pstmt, rs);
+        }
+
         reCache();
         return ret;
     }

core/src/main/java/org/mskcc/cbio/portal/dao/DaoGeneticProfileSamples.java

@@ -56,7 +56,7 @@ private DaoGeneticProfileSamples() {}
      * @return number of rows added.
      * @throws DaoException Data Access Exception.
      */
-    public static int addGeneticProfileSamples(int geneticProfileId, ArrayList<Integer> orderedSampleList)
+    public static int addGeneticProfileSamples(int geneticProfileId, List<Integer> orderedSampleList)
             throws DaoException {
         Connection con = null;
         PreparedStatement pstmt = null;

core/src/main/java/org/mskcc/cbio/portal/model/CanonicalGene.java

@@ -32,8 +32,6 @@
 
 package org.mskcc.cbio.portal.model;
 
-import org.mskcc.cbio.portal.dao.DaoException;
-
 import java.util.*;
 import java.io.Serializable;
 

core/src/main/java/org/mskcc/cbio/portal/model/CnaEvent.java

@@ -72,7 +72,7 @@ public void setGene(CanonicalGene gene) {
         public void setEntrezGeneId(long entrezGeneId) {
             setGene(DaoGeneOptimized.getInstance().getGene(entrezGeneId));
             if (gene == null) {
-                throw new IllegalArgumentException("Could not find entrez gene id: "+entrezGeneId);
+                throw new IllegalArgumentException("Could not find entrez gene id: " + entrezGeneId);
             } 
         }
 
@@ -99,6 +99,10 @@ public int hashCode() {
             return hash;
         }
 
+        /**
+         * Compare by gene and alteration, 
+         * but not by eventId 
+         */
         @Override
         public boolean equals(Object obj) {
             if (obj == null) {

core/src/main/java/org/mskcc/cbio/portal/scripts/GeneticAlterationImporter.java

@@ -0,0 +1,59 @@
+package org.mskcc.cbio.portal.scripts;
+
+import org.mskcc.cbio.portal.dao.DaoException;
+import org.mskcc.cbio.portal.dao.DaoGeneticAlteration;
+import org.mskcc.cbio.portal.model.CanonicalGene;
+import org.mskcc.cbio.portal.util.ProgressMonitor;
+
+import java.util.*;
+
+import static java.lang.String.format;
+
+public class GeneticAlterationImporter {
+
+    private final int geneticProfileId;
+    private Set<Long> importSetOfGenes = new HashSet<>();
+    private DaoGeneticAlteration daoGeneticAlteration;
+
+    public GeneticAlterationImporter(
+        int geneticProfileId, 
+        DaoGeneticAlteration daoGeneticAlteration
+    ) {
+        this.geneticProfileId = geneticProfileId;
+        this.daoGeneticAlteration = daoGeneticAlteration;
+    }
+
+    /**
+     * Check that we have not already imported information regarding this gene.
+     * This is an important check, because a GISTIC or RAE file may contain
+     * multiple rows for the same gene, and we only want to import the first row.
+     */
+    public boolean store(
+        String[] values,
+        CanonicalGene gene,
+        String geneSymbol
+    ) throws DaoException {
+        try {
+            if (importSetOfGenes.add(gene.getEntrezGeneId())) {
+                daoGeneticAlteration.addGeneticAlterations(geneticProfileId, gene.getEntrezGeneId(), values);
+                return true;
+            } else {
+                String geneSymbolMessage = "";
+                if (geneSymbol != null && !geneSymbol.equalsIgnoreCase(gene.getHugoGeneSymbolAllCaps())) {
+                    geneSymbolMessage = " (given as alias in your file as: " + geneSymbol + ")";
+                }
+                ProgressMonitor.logWarning(format(
+                    "Gene %s (%d)%s found to be duplicated in your file. Duplicated row will be ignored!",
+                    gene.getHugoGeneSymbolAllCaps(),
+                    gene.getEntrezGeneId(),
+                    geneSymbolMessage)
+                );
+                return false;
+            }
+        } catch (Exception e) {
+            throw new RuntimeException("Aborted: Error found for row starting with " + geneSymbol + ": " + e.getMessage());
+        }
+    }
+
+
+}