Changeset 554 for trunk/org.bridgedb.tools.qc

Timestamp:

12/04/11 13:10:15 (6 months ago)

Author:

martijn

Message:

QC on database capabilities

Files:

• trunk/org.bridgedb.tools.qc/src/org/bridgedb/tools/qc/BridgeQC.java (modified) (4 diffs)

trunk/org.bridgedb.tools.qc/src/org/bridgedb/tools/qc/BridgeQC.java

@@ -3 +3 @@
 import java.sql.Connection;
 import java.sql.SQLException;
+import java.text.ParseException;
+import java.text.SimpleDateFormat;
+import java.util.Date;
 import java.util.HashMap;
 import java.util.Map;
@@ -10 +13 @@
 import org.bridgedb.IDMapperException;
 import org.bridgedb.bio.BioDataSource;
+import org.bridgedb.bio.Organism;
 import org.bridgedb.rdb.SimpleGdb;
 import org.bridgedb.rdb.SimpleGdbFactory;
@@ -133 +137 @@
         }
 
+        public static boolean safeEquals (Object a, Object b)
+        {
+                return a == null ? b == null : a.equals(b);
+        }
+
+        public interface PropertyChecker
+        {
+                abstract void check(String oldVal, String newVal);
+        }
+        
+        enum Props implements PropertyChecker
+        {
+                ORGANISM (true, false) {
+                        public void check(String oldVal, String newVal) 
+                        {
+                                if (newVal != null)
+                                {
+                                        Organism o = Organism.fromLatinName(newVal);
+                                        if (o == null) System.out.println ("WARNING: species '" + newVal + "' is not a recognized latin name");
+                                }
+                        }
+                },
+                DATASOURCENAME (true, true) {
+                        public void check(String oldVal, String newVal) {}
+                },
+                SERIES (true, true) {
+                        public void check(String oldVal, String newVal) {}
+                },
+                DATATYPE (true, true) {
+                        public void check(String oldVal, String newVal) {}
+                },
+                DATASOURCEVERSION (false, true) {
+                        public void check(String oldVal, String newVal) {}
+                },
+                BUILDDATE (false, true) {
+                        public void check(String oldVal, String newVal) {
+                                SimpleDateFormat sft = new SimpleDateFormat("yyyyMMdd");
+                                Date oldDate = null;
+                                Date newDate = null;
+                                try
+                                {
+                                        if (oldVal != null)
+                                                oldDate = sft.parse(oldVal);
+                                }
+                                catch (ParseException e)
+                                {
+                                        System.out.println ("ERROR: " + oldVal + " does not match pattern yyyymmdd"); 
+                                }
+                                try
+                                {
+                                        if (newVal != null)
+                                                newDate = sft.parse(newVal);
+                                }
+                                catch (ParseException e)
+                                {
+                                        System.out.println ("ERROR: " + oldVal + " does not match pattern yyyymmdd"); 
+                                }
+                                if (oldDate != null && newDate != null && oldDate.after(newDate))
+                                {
+                                        System.out.println ("ERROR: new date " + newVal + " is older than old date " + oldVal); 
+                                }
+                        }
+                },
+                SCHEMAVERSION (false, true) {
+                        public void check(String oldVal, String newVal) {}
+                },
+                ;
+                
+                private boolean mustBeSame;
+                private boolean mustBeDefined;
+                
+                Props(boolean mustBeSame, boolean mustBeDefined)
+                {
+                        this.mustBeSame = mustBeSame;
+                        this.mustBeDefined = mustBeDefined;
+                }
+                
+                public void checkWrap(String oldVal, String newVal)
+                {
+                        if (mustBeSame && !safeEquals (oldVal, newVal))
+                                System.out.println ("WARNING: old " + name() + "'" + oldVal + "' doesn\'t match new " + name() + " '" + newVal + "'");
+                        if (mustBeDefined && (newVal == null || newVal.equals("")))
+                                System.out.println ("WARNING: property " + name() + " is undefined");
+                        check(oldVal, newVal);
+                }
+        }
+        
+        public void compareInfo()
+        {
+                for (Props p : Props.values())
+                {
+                        p.checkWrap(oldGdb.getCapabilities().getProperty(p.name()),
+                                        newGdb.getCapabilities().getProperty(p.name()));
+                }
+        }
+        
         public void run() throws IDMapperException, SQLException
         {
                 initDatabases();
+                compareInfo();
                 compareDataSources();
 
@@ -141 +242 @@
                 
                 compareAttributes();
-                compareFileSizes();
+                compareFileSizes();             
         }