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DaoClinicalAttributeMeta.java

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+/*
+ * Copyright (c) 2015 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 org.mskcc.cbio.portal.model.*;
+
+import com.google.inject.internal.Join;
+
+import edu.jhu.u01.DBProperties;
+
+import org.apache.commons.lang.StringUtils;
+
+import java.sql.*;
+import java.util.*;
+import org.mskcc.cbio.portal.util.InternalIdUtil;
+
+/**
+ * Data Access Object for `clinical_attribute_meta` table
+ *
+ * @author Gideon Dresdner
+ */
+public class DaoClinicalAttributeMeta {
+
+    public static int addDatum(ClinicalAttribute attr)  throws DaoException {
+        Connection con = null;
+        PreparedStatement pstmt = null;
+        ResultSet rs = null;
+        try {
+            con = JdbcUtil.getDbConnection(DaoClinicalAttributeMeta.class);
+            switch(DBProperties.getDBVendor()){
+            case mssql:
+                pstmt = con.prepareStatement
+                ("INSERT INTO clinical_attribute_meta(" +
+                        "[ATTR_ID]," +
+                        "[DISPLAY_NAME]," +
+                        "[DESCRIPTION]," +
+                        "[DATATYPE]," +
+                        "[PATIENT_ATTRIBUTE]," +
+                        "[PRIORITY]," +
+                        "[CANCER_STUDY_ID])" +
+                        " VALUES(?,?,?,?,?,?,?)");
+                break;
+            default:
+                pstmt = con.prepareStatement
+                ("INSERT INTO clinical_attribute_meta(" +
+                        "`ATTR_ID`," +
+                        "`DISPLAY_NAME`," +
+                        "`DESCRIPTION`," +
+                        "`DATATYPE`," +
+                        "`PATIENT_ATTRIBUTE`," +
+                        "`PRIORITY`," +
+                        "`CANCER_STUDY_ID`)" +
+                        " VALUES(?,?,?,?,?,?,?)");
+            	break;
+            }//JK-UPDATED
+
+            pstmt.setString(1, attr.getAttrId());
+            pstmt.setString(2, attr.getDisplayName());
+            pstmt.setString(3, attr.getDescription());
+            pstmt.setString(4, attr.getDatatype());
+            pstmt.setBoolean(5, attr.isPatientAttribute());
+            pstmt.setString(6, attr.getPriority());
+            pstmt.setInt(7, attr.getCancerStudyId());
+            return pstmt.executeUpdate();
+        } catch (SQLException e) {
+            throw new DaoException(e);
+        } finally {
+            JdbcUtil.closeAll(DaoClinicalAttributeMeta.class, con, pstmt, rs);
+        }
+    }
+
+    private static ClinicalAttribute unpack(ResultSet rs) throws SQLException {
+        return new ClinicalAttribute(rs.getString("ATTR_ID"),
+            rs.getString("DISPLAY_NAME"),
+            rs.getString("DESCRIPTION"),
+            rs.getString("DATATYPE"),
+            rs.getBoolean("PATIENT_ATTRIBUTE"),
+            rs.getString("PRIORITY"),
+            rs.getInt("CANCER_STUDY_ID"));//JK-UPDATED
+    }
+
+    public static ClinicalAttribute getDatum(String attrId, Integer cancerStudyId) throws DaoException {
+        List<ClinicalAttribute> attrs = getDatum(Arrays.asList(attrId), cancerStudyId);
+        if (attrs.isEmpty()) {
+            return null;
+        }
+
+        return attrs.get(0);
+    }
+
+    public static List<ClinicalAttribute> getDatum(Collection<String> attrIds, Integer cancerStudyId) throws DaoException {
+        if(attrIds == null || attrIds.isEmpty() ) {
+            return Collections.emptyList();
+        }
+        Connection con = null;
+        PreparedStatement pstmt = null;
+        ResultSet rs = null;
+        try {
+            con = JdbcUtil.getDbConnection(DaoClinicalAttributeMeta.class);
+
+            pstmt = con.prepareStatement("SELECT * FROM clinical_attribute_meta WHERE ATTR_ID IN ('"
+                    + StringUtils.join(attrIds,"','")+"')  AND CANCER_STUDY_ID=" + String.valueOf(cancerStudyId));//JK-UPDATED
+
+            rs = pstmt.executeQuery();
+
+            List<ClinicalAttribute> list = new ArrayList<ClinicalAttribute>();
+            while (rs.next()) {
+                list.add(unpack(rs));
+            }
+
+            return list;
+        } catch (SQLException e) {
+            throw new DaoException(e);
+        } finally {
+            JdbcUtil.closeAll(DaoClinicalAttributeMeta.class, con, pstmt, rs);
+        }
+    }
+
+    public static List<ClinicalAttribute> getDatum(Collection<String> attrIds) throws DaoException {
+        if(attrIds == null || attrIds.isEmpty() ) {
+            return Collections.emptyList();
+        }
+        Connection con = null;
+        PreparedStatement pstmt = null;
+        ResultSet rs = null;
+        try {
+            con = JdbcUtil.getDbConnection(DaoClinicalAttributeMeta.class);
+
+            pstmt = con.prepareStatement("SELECT * FROM clinical_attribute_meta WHERE ATTR_ID IN ('"
+                    + StringUtils.join(attrIds,"','")+"')");//JK-UPDATED
+
+            rs = pstmt.executeQuery();
+
+            List<ClinicalAttribute> list = new ArrayList<ClinicalAttribute>();
+            while (rs.next()) {
+                list.add(unpack(rs));
+            }
+
+            return list;
+        } catch (SQLException e) {
+            throw new DaoException(e);
+        } finally {
+            JdbcUtil.closeAll(DaoClinicalAttributeMeta.class, con, pstmt, rs);
+        }        
+    }
+
+    public static List<ClinicalAttribute> getDataByStudy(int cancerStudyId) throws DaoException
+    {
+        List<ClinicalAttribute> attrs = new ArrayList<ClinicalAttribute>();
+        attrs.addAll(getDataByCancerStudyId(cancerStudyId));
+
+        return attrs;
+    }
+
+    /**
+     * Gets all the clinical attributes for a particular set of samples
+     * Looks in the clinical table for all records associated with any of the samples, extracts and uniques
+     * the attribute ids, then finally uses the attribute ids to fetch the clinical attributes from the db.
+     *
+     * @param sampleIdSet
+     * @return
+     * @throws DaoException
+     */
+    private static List<ClinicalAttribute> getDataByCancerStudyId(int cancerStudyId) throws DaoException {
+
+        Connection con = null;
+        ResultSet rs = null;
+		PreparedStatement pstmt = null;
+
+        String sql = ("SELECT DISTINCT ATTR_ID FROM clinical_attribute_meta"
+                + " WHERE CANCER_STUDY_ID = " + String.valueOf(cancerStudyId));//JK-UPDATED
+
+        Set<String> attrIds = new HashSet<String>();
+        try {
+            con = JdbcUtil.getDbConnection(DaoClinicalAttributeMeta.class);
+            pstmt = con.prepareStatement(sql);
+            rs = pstmt.executeQuery();
+
+             while(rs.next()) {
+                attrIds.add(rs.getString("ATTR_ID"));
+            }
+
+        } catch (SQLException e) {
+            throw new DaoException(e);
+        } finally {
+            JdbcUtil.closeAll(DaoClinicalAttributeMeta.class, con, pstmt, rs);
+        }
+
+        return getDatum(attrIds, cancerStudyId);
+    }
+
+    private static Collection<ClinicalAttribute> getAll() throws DaoException {
+        Connection con = null;
+        PreparedStatement pstmt = null;
+        ResultSet rs = null;
+        Collection<ClinicalAttribute> all = new ArrayList<ClinicalAttribute>();
+
+        try {
+            con = JdbcUtil.getDbConnection(DaoClinicalAttributeMeta.class);
+            pstmt = con.prepareStatement("SELECT * FROM clinical_attribute_meta");
+            rs = pstmt.executeQuery();
+
+            while (rs.next()) {
+                all.add(unpack(rs));
+            }
+
+        } catch (SQLException e) {
+            throw new DaoException(e);
+        } finally {
+            JdbcUtil.closeAll(DaoClinicalAttributeMeta.class, con, pstmt, rs);
+        }
+        return all;
+    }
+
+	public static Map<String, String> getAllMap() throws DaoException {
+
+		HashMap<String, String> toReturn = new HashMap<String, String>();
+		for (ClinicalAttribute clinicalAttribute : DaoClinicalAttributeMeta.getAll()) {
+			toReturn.put(clinicalAttribute.getAttrId(), clinicalAttribute.getDisplayName());
+		}
+		return toReturn;
+	}
+
+    /**
+     * Deletes all Records.
+     * @throws DaoException DAO Error.
+     */
+    public static void deleteAllRecords() throws DaoException {
+        Connection con = null;
+        PreparedStatement pstmt = null;
+        ResultSet rs = null;
+        try {
+            con = JdbcUtil.getDbConnection(DaoClinicalAttributeMeta.class);
+            pstmt = con.prepareStatement("TRUNCATE TABLE clinical_attribute_meta");
+            pstmt.executeUpdate();
+        } catch (SQLException e) {
+            throw new DaoException(e);
+        } finally {
+            JdbcUtil.closeAll(DaoClinicalAttributeMeta.class, con, pstmt, rs);
+        }
+    }
+}