Merge pull request #2641 from jjgao/merge-hotfix-to-master

release 1.6.3

OPEN-SOURCE-DOCUMENTATION

@@ -136,6 +136,7 @@ [email protected].
 * FileSaver.min
 * Font Awesome (CSS)
 * Font Awesome (Fonts)
+* clusterfck.min.js
 
 
 ant-1.7.0
@@ -19686,3 +19687,30 @@ INCLUDING ANY GENERAL, SPECIAL, INDIRECT, INCIDENTAL, OR CONSEQUENTIAL
 DAMAGES, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
 FROM, OUT OF THE USE OR INABILITY TO USE THE FONT SOFTWARE OR FROM
 OTHER DEALINGS IN THE FONT SOFTWARE.
+
+clusterfck.min.js
+-----------------
+From: https://github.com/tayden/clusterfck
+
+Available under license:
+
+Copyright (c) 2011 Heather Arthur <[email protected]>
+
+Permission is hereby granted, free of charge, to any person obtaining
+a copy of this software and associated documentation files (the
+"Software"), to deal in the Software without restriction, including
+without limitation the rights to use, copy, modify, merge, publish,
+distribute, sublicense, and/or sell copies of the Software, and to
+permit persons to whom the Software is furnished to do so, subject to
+the following conditions:
+
+The above copyright notice and this permission notice shall be
+included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
+LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
+WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

app.json

@@ -17,7 +17,7 @@
     },
     "MAVEN_CUSTOM_OPTS": {
         "description":"set heroku profile for mvn",
-        "value":"-Pheroku,public -DskipTests -Dfinal.war.name=cbioportal -Ddb.user=cbio_user -Ddb.password=cbio_pass -Ddb.portal_db_name=public_test -Dtomcat.catalina.scope=runtime -Ddb.connection_string=jdbc:mysql://sm4sa6ozhn5ya6.cuooweljyhix.us-east-1.rds.amazonaws.com:3306/ -Ddb.host=sm4sa6ozhn5ya6.cuooweljyhix.us-east-1.rds.amazonaws.com"
+        "value":"-Pheroku,public -DskipTests -Dfinal.war.name=cbioportal -Ddb.user=cbio_user -Ddb.password=cbio_pass -Ddb.portal_db_name=public_test_small -Dtomcat.catalina.scope=runtime -Ddb.connection_string=jdbc:mysql://sm4sa6ozhn5ya6.cuooweljyhix.us-east-1.rds.amazonaws.com:3306/ -Ddb.host=sm4sa6ozhn5ya6.cuooweljyhix.us-east-1.rds.amazonaws.com"
     }
   },
   "buildpacks": [

business/pom.xml

@@ -4,7 +4,7 @@
   <parent>
     <artifactId>master</artifactId>
     <groupId>org.mskcc.cbio</groupId>
-    <version>1.6.2</version>
+    <version>1.6.3</version>
   </parent>
   <modelVersion>4.0.0</modelVersion>
   <artifactId>business</artifactId>

business/src/main/java/org/mskcc/cbio/portal/repository/GenePanelMyBatisRepository.java

@@ -68,11 +68,6 @@ public List<GenePanel> getGenePanels() {
         return genePanelMapper.getGenePanels();
     }
 
-    @Override
-    public Sample getSampleByStableIdAndStudyId(String stableId, String studyId) {
-        return genePanelMapper.getSampleByStableIdAndStudyId(stableId, studyId);
-    }
-
     @Override
     public GeneticProfile getGeneticProfileByStableId(String stableId) {
         return genePanelMapper.getGeneticProfileByStableId(stableId);
@@ -138,11 +133,6 @@ public void insertGenePanelListByHugo(Map<String, Object> map) {
         genePanelMapper.insertGenePanelListByHugo(map);
     }
 
-    @Override
-    public void insertGenePanelSampleProfileMap(Map<String, Object> map) {
-        genePanelMapper.insertGenePanelSampleProfileMap(map);
-    }
-
     public void setGenePanelMapper(GenePanelMapper genePanelMapper) {
         this.genePanelMapper = genePanelMapper;
     }

business/src/main/java/org/mskcc/cbio/portal/repository/GenePanelRepository.java

@@ -50,7 +50,6 @@ public interface GenePanelRepository {
         // removed once a proper import solution is put in place.
         List<GenePanel> getGenePanelByStableId(String stableId);
         List<GenePanel> getGenePanels();
-        Sample getSampleByStableIdAndStudyId(String stableId, String studyId);
         GeneticProfile getGeneticProfileByStableId(String stableId);
         Gene getGeneByEntrezGeneId(Integer geneId);
         Gene getGeneByHugoSymbol(String symbol);
@@ -64,5 +63,4 @@ public interface GenePanelRepository {
         void deleteSampleProfileMappingByPanel(Integer panelId);
         void insertGenePanelList(Map<String, Object> map);
         void insertGenePanelListByHugo(Map<String, Object> map);
-        void insertGenePanelSampleProfileMap(Map<String, Object> map);
 }

business/src/main/resources/org/mskcc/cbio/portal/persistence/GenePanelMapper.xml

@@ -148,43 +148,6 @@
         from gene_panel
     </select>
 
-    <select id="getSampleByStableIdAndStudyId" resultMap="sampleResultMap">
-        select
-            sample.INTERNAL_ID,
-            sample.STABLE_ID,
-            sample.SAMPLE_TYPE,
-            sample.PATIENT_ID,
-            patient.INTERNAL_ID,
-            patient.STABLE_ID,
-            patient.CANCER_STUDY_ID,
-            sample.TYPE_OF_CANCER_ID,
-            type_of_cancer.TYPE_OF_CANCER_ID,
-            type_of_cancer.NAME,
-            type_of_cancer.CLINICAL_TRIAL_KEYWORDS,
-            type_of_cancer.DEDICATED_COLOR,
-            type_of_cancer.SHORT_NAME,
-            type_of_cancer.PARENT,
-            cancer_study.CANCER_STUDY_ID,
-            cancer_study.CANCER_STUDY_IDENTIFIER,
-            cancer_study.TYPE_OF_CANCER_ID,
-            cancer_study.NAME,
-            cancer_study.SHORT_NAME,
-            cancer_study.DESCRIPTION,
-            cancer_study.PUBLIC,
-            cancer_study.PMID,
-            cancer_study.CITATION,
-            cancer_study.GROUPS,
-            cancer_study.STATUS
-        from sample
-            inner join patient on sample.PATIENT_ID = patient.INTERNAL_ID
-            inner join type_of_cancer on sample.TYPE_OF_CANCER_ID = type_of_cancer.TYPE_OF_CANCER_ID
-            inner join cancer_study on patient.CANCER_STUDY_ID = cancer_study.CANCER_STUDY_ID
-        where
-            sample.STABLE_ID = #{stableId}
-            and
-            cancer_study.CANCER_STUDY_IDENTIFIER=#{studyId}
-    </select>
-
 <select id="getGeneByHugoSymbol" resultMap="geneResultMap">
         select
             gene.ENTREZ_GENE_ID,
@@ -313,8 +276,4 @@
             (#{panelId}, (select ENTREZ_GENE_ID from gene where HUGO_GENE_SYMBOL = #{gene}))
         </foreach>
     </insert>
-
-    <insert id="insertGenePanelSampleProfileMap" parameterType="map" useGeneratedKeys="false">
-        update sample_profile set PANEL_ID = #{panelId} where SAMPLE_ID = #{sampleId} and GENETIC_PROFILE_ID = #{profileId}
-    </insert>
 </mapper>

core/pom.xml

@@ -4,7 +4,7 @@
   <parent>
     <artifactId>master</artifactId>
     <groupId>org.mskcc.cbio</groupId>
-    <version>1.6.2</version>
+    <version>1.6.3</version>
   </parent>
   <modelVersion>4.0.0</modelVersion>
   <artifactId>core</artifactId>

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

@@ -0,0 +1,84 @@
+/*
+ * Copyright (c) 2017 Memorial Sloan-Kettering Cancer Center.
+ *
+ * This library is distributed in the hope that it will be useful, but WITHOUT
+ * ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF MERCHANTABILITY OR FITNESS
+ * FOR A PARTICULAR PURPOSE. The software and documentation provided hereunder
+ * is on an "as is" basis, and Memorial Sloan-Kettering Cancer Center has no
+ * obligations to provide maintenance, support, updates, enhancements or
+ * modifications. In no event shall Memorial Sloan-Kettering Cancer Center be
+ * liable to any party for direct, indirect, special, incidental or
+ * consequential damages, including lost profits, arising out of the use of this
+ * software and its documentation, even if Memorial Sloan-Kettering Cancer
+ * Center has been advised of the possibility of such damage.
+ */
+
+/*
+ * This file is part of cBioPortal.
+ *
+ * cBioPortal is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU Affero General Public License as
+ * published by the Free Software Foundation, either version 3 of the
+ * License.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU Affero General Public License for more details.
+ *
+ * You should have received a copy of the GNU Affero General Public License
+ * along with this program.  If not, see <http://www.gnu.org/licenses/>.
+*/
+
+package org.mskcc.cbio.portal.dao;
+
+import java.sql.Connection;
+import java.sql.PreparedStatement;
+import java.sql.ResultSet;
+import java.sql.SQLException;
+import java.util.*;
+import org.mskcc.cbio.portal.model.CancerStudy;
+import org.mskcc.cbio.portal.model.GenePanel;
+
+/**
+ *
+ * @author heinsz
+ */
+public class DaoGenePanel {
+    private static Map<String, GenePanel> genePanelMap = initMap();
+
+    public static GenePanel getGenePanelByStableId(String stableId) {
+        return genePanelMap.get(stableId);
+    }
+
+    private static Map<String, GenePanel> initMap() {
+        Map<String, GenePanel> genePanelMap = null;
+        Connection con = null;
+        PreparedStatement pstmt = null;
+        ResultSet rs = null;
+        try {
+            con = JdbcUtil.getDbConnection(DaoCancerStudy.class);
+            pstmt = con.prepareStatement("SELECT * FROM gene_panel");
+            rs = pstmt.executeQuery();
+            genePanelMap = extractGenePanelMap(rs);
+        } catch (SQLException e) {
+            e.printStackTrace();
+        } finally {
+            JdbcUtil.closeAll(DaoCancerStudy.class, con, pstmt, rs);
+        }
+        return genePanelMap;
+    }
+
+    private static Map<String, GenePanel> extractGenePanelMap(ResultSet rs) throws SQLException {
+        Map<String, GenePanel> genePanelMap = new HashMap<>();
+        while(rs.next()) {
+            GenePanel gp = new GenePanel();
+            gp.setInternalId(rs.getInt("INTERNAL_ID"));
+            gp.setStableId(rs.getString("STABLE_ID"));
+            gp.setDescription(rs.getString("DESCRIPTION"));
+            genePanelMap.put(gp.getStableId(), gp);
+        }
+        return genePanelMap;
+    }
+
+}

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

@@ -44,10 +44,24 @@
  */
 public final class DaoSampleProfile {
     private DaoSampleProfile() {}
-   
+
     private static final int NO_SUCH_PROFILE_ID = -1;
+    private static final String TABLE_NAME = "sample_profile";
 
-    public static int addSampleProfile(int sampleId, int geneticProfileId, Integer panelId) throws DaoException {
+    public static int addSampleProfile(Integer sampleId, Integer geneticProfileId, Integer panelId) throws DaoException {        
+        if (MySQLbulkLoader.isBulkLoad()) {
+            if (panelId != null) {
+                MySQLbulkLoader.getMySQLbulkLoader(TABLE_NAME).insertRecord(Integer.toString(sampleId),
+                    Integer.toString(geneticProfileId),
+                    Integer.toString(panelId));            
+            }
+            else {
+                MySQLbulkLoader.getMySQLbulkLoader(TABLE_NAME).insertRecord(Integer.toString(sampleId),
+                    Integer.toString(geneticProfileId), null);     
+            }
+
+            return 1;
+        }
 
         Connection con = null;
         PreparedStatement pstmt = null;
@@ -65,7 +79,7 @@ public static int addSampleProfile(int sampleId, int geneticProfileId, Integer p
                     pstmt.setInt(3, panelId);
                 }
                 else {
-                    pstmt.setNull(3, java.sql.Types.INTEGER);                    
+                    pstmt.setNull(3, java.sql.Types.INTEGER);
                 }
                 return pstmt.executeUpdate();
             } else {
@@ -102,7 +116,7 @@ public static boolean sampleExistsInGeneticProfile(int sampleId, int geneticProf
             JdbcUtil.closeAll(DaoSampleProfile.class, con, pstmt, rs);
         }
     }
-    
+
     public static int countSamplesInProfile(int geneticProfileId) throws DaoException {
         Connection con = null;
         PreparedStatement pstmt = null;
@@ -258,8 +272,8 @@ public static List<Map<String, Object>> metaData(List<CancerStudy> cancerStudies
         } finally {
             JdbcUtil.closeAll(DaoMutation.class, con, pstmt, rs);
         }
-        
-	return data;
+
+    return data;
     }
 
     public static void deleteAllRecords() throws DaoException {
@@ -276,4 +290,23 @@ public static void deleteAllRecords() throws DaoException {
             JdbcUtil.closeAll(DaoSampleProfile.class, con, pstmt, rs);
         }
     }
+
+    public static void deleteRecords(List<Integer> sampleIds, List<Integer> profileIds) throws DaoException {
+        Connection con = null;
+        PreparedStatement pstmt = null;
+        ResultSet rs = null;
+        try {
+            con = JdbcUtil.getDbConnection(DaoSampleProfile.class);
+            for (int i = 0; i < sampleIds.size(); i++) {
+                pstmt = con.prepareCall("DELETE FROM sample_profile WHERE sample_id = ? and genetic_profile_id = ?");
+                pstmt.setInt(1, sampleIds.get(i));
+                pstmt.setInt(2, profileIds.get(i));
+                pstmt.executeUpdate();
+            }
+        } catch (SQLException e) {
+            throw new DaoException(e);
+        } finally {
+            JdbcUtil.closeAll(DaoSampleProfile.class, con, pstmt, rs);
+        }
+    }
 }