[LMS-557] add: - Database schema 24 and its migration script.

change: - Global code renamed in UUID all over the code.

SVN: 7925

bds/source/java/ch/systemsx/cisd/bds/ExperimentIdentifier.java

@@ -31,7 +31,7 @@ public class ExperimentIdentifier implements IStorable
 
     static final String INSTANCE_CODE = "instance_code";
 
-    static final String INSTANCE_GLOBAL_CODE = "instance_global_code";
+    static final String INSTANCE_UUID = "instance_uuid";
 
     static final String GROUP_CODE = "group_code";
 

bds/source/java/ch/systemsx/cisd/bds/SampleWithOwner.java

@@ -34,13 +34,13 @@ public final class SampleWithOwner extends Sample
 
     static final String INSTANCE_CODE = ExperimentIdentifier.INSTANCE_CODE;
 
-    static final String INSTANCE_GLOBAL_CODE = ExperimentIdentifier.INSTANCE_GLOBAL_CODE;
+    static final String INSTANCE_UUID = ExperimentIdentifier.INSTANCE_UUID;
 
     private final String groupCode;
 
     private final String instanceCode;
 
-    private final String instanceGlobalCode;
+    private final String instanceUUID;
 
     /**
      * Creates an instance for the specified {@link Sample}, group code and database instance code
@@ -49,14 +49,13 @@ public final class SampleWithOwner extends Sample
      * @param groupCode A non-<code>null</code> string of the group code. Could be empty.
      * @param instanceCode A non-<code>null</code> string of the database instance code. Could
      *            not be empty.
-     * @param instanceGlobalCode A non-<code>null</code> string of the database instance global
-     *            code (aka <i>UUID</i>). Could not be empty.
+     * @param instanceUUID the database instance <i>UUID</i>. Could not be empty.
      */
-    public SampleWithOwner(final Sample sample, final String instanceGlobalCode,
+    public SampleWithOwner(final Sample sample, final String instanceUUID,
             final String instanceCode, final String groupCode)
     {
-        this(sample.getCode(), sample.getTypeCode(), sample.getTypeDescription(),
-                instanceGlobalCode, instanceCode, groupCode);
+        this(sample.getCode(), sample.getTypeCode(), sample.getTypeDescription(), instanceUUID,
+                instanceCode, groupCode);
     }
 
     /**
@@ -66,32 +65,32 @@ public final class SampleWithOwner extends Sample
      * @param groupCode A non-<code>null</code> string of the group code. Could be empty.
      * @param instanceCode A non-<code>null</code> string of the database instance code. Could
      *            not be empty.
-     * @param instanceGlobalCode A non-<code>null</code> string of the database instance global
-     *            code (aka <i>UUID</i>). Could not be empty.
+     * @param instanceUUID A non-<code>null</code> string of the database instance <i>UUID</i>.
+     *            Could not be empty.
      */
     public SampleWithOwner(final String code, final String typeCode, final String typeDescription,
-            final String instanceGlobalCode, final String instanceCode, final String groupCode)
+            final String instanceUUID, final String instanceCode, final String groupCode)
     {
         super(code, typeCode, typeDescription);
         assert groupCode != null : "Undefined group code.";
         assert instanceCode != null : "Undefined database instance code.";
-        assert instanceGlobalCode != null : "Undefined database instance global code.";
-        assertNonEmptyInstanceCodes(instanceGlobalCode, instanceCode);
-        this.instanceGlobalCode = instanceGlobalCode;
+        assert instanceUUID != null : "Undefined database instance UUID.";
+        assertNonEmptyInstanceCodes(instanceUUID, instanceCode);
+        this.instanceUUID = instanceUUID;
         this.instanceCode = instanceCode;
         this.groupCode = groupCode;
     }
 
-    private final static void assertNonEmptyInstanceCodes(final String instanceGlobalCode,
+    private final static void assertNonEmptyInstanceCodes(final String instanceUUID,
             final String instanceCode)
     {
         if (instanceCode.length() == 0)
         {
             throw new DataStructureException("Empty database instance code.");
         }
-        if (instanceGlobalCode.length() == 0)
+        if (instanceUUID.length() == 0)
         {
-            throw new DataStructureException("Empty database instance global code.");
+            throw new DataStructureException("Empty database instance UUID.");
         }
     }
 
@@ -105,9 +104,9 @@ public final class SampleWithOwner extends Sample
         return instanceCode;
     }
 
-    public final String getInstanceGlobalCode()
+    public final String getInstanceUUID()
     {
-        return instanceGlobalCode;
+        return instanceUUID;
     }
 
     //
@@ -128,9 +127,9 @@ public final class SampleWithOwner extends Sample
         final String typeCode = Utilities.getTrimmedString(folder, TYPE_CODE);
         final String groupCode = Utilities.getTrimmedString(folder, GROUP_CODE);
         final String instanceCode = Utilities.getTrimmedString(folder, INSTANCE_CODE);
-        final String instanceGlobalCode = Utilities.getTrimmedString(folder, INSTANCE_GLOBAL_CODE);
-        return new SampleWithOwner(code, typeCode, typeDescription, instanceGlobalCode,
-                instanceCode, groupCode);
+        final String instanceUUID = Utilities.getTrimmedString(folder, INSTANCE_UUID);
+        return new SampleWithOwner(code, typeCode, typeDescription, instanceUUID, instanceCode,
+                groupCode);
     }
 
     @Override
@@ -140,14 +139,14 @@ public final class SampleWithOwner extends Sample
         final IDirectory folder = directory.makeDirectory(FOLDER);
         folder.addKeyValuePair(GROUP_CODE, groupCode);
         folder.addKeyValuePair(INSTANCE_CODE, instanceCode);
-        folder.addKeyValuePair(INSTANCE_GLOBAL_CODE, instanceGlobalCode);
+        folder.addKeyValuePair(INSTANCE_UUID, instanceUUID);
     }
 
     @Override
     public final String toString()
     {
         final ToStringBuilder builder = createToStringBuilder();
-        builder.append(INSTANCE_GLOBAL_CODE, instanceGlobalCode);
+        builder.append(INSTANCE_UUID, instanceUUID);
         builder.append(INSTANCE_CODE, instanceCode);
         if (groupCode.length() > 0)
         {
@@ -175,7 +174,7 @@ public final class SampleWithOwner extends Sample
             builder.append(that.groupCode, groupCode);
         } else
         {
-            builder.append(that.instanceGlobalCode, instanceGlobalCode);
+            builder.append(that.instanceUUID, instanceUUID);
         }
         return builder.isEquals();
     }
@@ -190,7 +189,7 @@ public final class SampleWithOwner extends Sample
             builder.append(groupCode);
         } else
         {
-            builder.append(instanceGlobalCode);
+            builder.append(instanceUUID);
         }
         return builder.toHashCode();
     }

bds/source/java/ch/systemsx/cisd/bds/check/AbstractChecker.java

@@ -87,6 +87,8 @@ public abstract class AbstractChecker
 
     public static final String INSTANCE_CODE = "instance_code";
 
+    public static final String INSTANCE_UUID = "instance_uuid";
+
     public static final String IS_COMPLETE = "is_complete";
 
     public static final String IS_MEASURED = "is_measured";

bds/source/java/ch/systemsx/cisd/bds/check/StructureChecker.java

@@ -149,6 +149,9 @@ public final class StructureChecker extends AbstractChecker
         try
         {
             final IDirectory sample = Utilities.getSubDirectory(metadata, AbstractChecker.SAMPLE);
+            checkFileNotEmptyAndTrimmed(sample, AbstractChecker.GROUP_CODE);
+            checkFileNotEmptyAndTrimmed(sample, AbstractChecker.INSTANCE_CODE);
+            checkFileNotEmptyAndTrimmed(sample, AbstractChecker.INSTANCE_UUID);
             checkFileNotEmptyAndTrimmed(sample, AbstractChecker.TYPE_DESCRIPTION);
             checkFileNotEmptyAndTrimmed(sample, AbstractChecker.TYPE_CODE);
             checkFileNotEmptyAndTrimmed(sample, AbstractChecker.CODE);

bds/sourceTest/java/ch/systemsx/cisd/bds/SampleWithOwnerTest.java

@@ -94,12 +94,12 @@ public final class SampleWithOwnerTest extends AbstractFileSystemTestCase
     }
 
     @Test(dataProvider = "getSampleData")
-    public final void testLoadFrom(final String instanceGlobalCode, final String instanceCode,
+    public final void testLoadFrom(final String instanceUUID, final String instanceCode,
             final String groupCode)
     {
         final IDirectory directory = NodeFactory.createDirectoryNode(workingDirectory);
         final Sample sample =
-                new SampleWithOwner(CODE, TYPE_CODE, TYPE_DESCRIPTION, instanceGlobalCode,
+                new SampleWithOwner(CODE, TYPE_CODE, TYPE_DESCRIPTION, instanceUUID,
                         instanceCode, groupCode);
         sample.saveTo(directory);
         final SampleWithOwner newSample = SampleWithOwner.loadFrom(directory);
@@ -107,12 +107,12 @@ public final class SampleWithOwnerTest extends AbstractFileSystemTestCase
         {
             assertEquals(GROUP_CODE, newSample.getGroupCode());
             assertEquals(INSTANCE_CODE, newSample.getInstanceCode());
-            assertEquals(INSTANCE_GLOBAL_CODE, newSample.getInstanceGlobalCode());
+            assertEquals(INSTANCE_GLOBAL_CODE, newSample.getInstanceUUID());
         } else
         {
             assertEquals("", newSample.getGroupCode());
             assertEquals(INSTANCE_CODE, newSample.getInstanceCode());
-            assertEquals(INSTANCE_GLOBAL_CODE, newSample.getInstanceGlobalCode());
+            assertEquals(INSTANCE_GLOBAL_CODE, newSample.getInstanceUUID());
         }
     }
 }

bds/sourceTest/java/ch/systemsx/cisd/bds/check/StructureCheckerTest.java

@@ -16,10 +16,11 @@
 
 package ch.systemsx.cisd.bds.check;
 
+import static org.testng.AssertJUnit.assertEquals;
+
 import java.io.File;
 import java.io.IOException;
 
-import org.testng.Assert;
 import org.testng.annotations.Test;
 
 /**
@@ -38,8 +39,8 @@ public class StructureCheckerTest extends AbstractCheckerTest
         final ProblemReport structureConsistencyReport =
                 new StructureChecker(verbose).getStructureConsistencyReport(new File(
                         "testdata/bds_ok"));
-        Assert.assertEquals(structureConsistencyReport.toString(), "");
-        Assert.assertEquals(structureConsistencyReport.noProblemsFound(), true);
+        assertEquals(structureConsistencyReport.toString(), "");
+        assertEquals(structureConsistencyReport.noProblemsFound(), true);
 
     }
 
@@ -53,7 +54,7 @@ public class StructureCheckerTest extends AbstractCheckerTest
     public final void testEmptyContainer()
     {
 
-        Assert.assertEquals(new StructureChecker(verbose).getStructureConsistencyReport(
+        assertEquals(new StructureChecker(verbose).getStructureConsistencyReport(
                 new File("testdata/bds_empty")).numberOfProblems(), 4);
     }
 
@@ -61,7 +62,7 @@ public class StructureCheckerTest extends AbstractCheckerTest
     public final void testEmptyDirectories()
     {
 
-        Assert.assertEquals(new StructureChecker(verbose).getStructureConsistencyReport(
+        assertEquals(new StructureChecker(verbose).getStructureConsistencyReport(
                 new File("testdata/bds_empty_dirs")).numberOfProblems(), 13);
     }
 
@@ -69,16 +70,15 @@ public class StructureCheckerTest extends AbstractCheckerTest
     public final void testMissingFiles()
     {
 
-        Assert.assertEquals(new StructureChecker(verbose).getStructureConsistencyReport(
-                new File("testdata/bds_missing_files")).numberOfProblems(), 19);
+        assertEquals(new StructureChecker(verbose).getStructureConsistencyReport(
+                new File("testdata/bds_missing_files")).numberOfProblems(), 22);
     }
 
     @Test
     public final void testEmptyFiles()
     {
-
-        Assert.assertEquals(new StructureChecker(verbose).getStructureConsistencyReport(
-                new File("testdata/bds_empty_files")).numberOfProblems(), 23);
+        assertEquals(new StructureChecker(verbose).getStructureConsistencyReport(
+                new File("testdata/bds_empty_files")).numberOfProblems(), 26);
     }
 
     @Test
@@ -87,7 +87,7 @@ public class StructureCheckerTest extends AbstractCheckerTest
         final ProblemReport structureConsistencyReport =
                 new StructureChecker(verbose).getStructureConsistencyReport(new File(
                         "testdata/bds_wrong_values"));
-        Assert.assertEquals(structureConsistencyReport.numberOfProblems(), 7);
+        assertEquals(structureConsistencyReport.numberOfProblems(), 10);
     }
 
     @Test
@@ -96,28 +96,38 @@ public class StructureCheckerTest extends AbstractCheckerTest
         final File dir = new File("testdata/bds_new_lines");
         final String path = dir.getAbsolutePath();
 
-        Assert.assertEquals(new StructureChecker(verbose).getStructureConsistencyReport(dir)
-                .toString(), errorFoundNotTrimmed(path, "major", "/version")
-                + errorFoundNotTrimmed(path, "minor", "/version")
-                + errorFoundNotTrimmed(path, "code", "/metadata/data_set")
-                + errorFoundNotTrimmed(path, "production_timestamp", "/metadata/data_set")
-                + errorFoundNotTrimmed(path, "producer_code", "/metadata/data_set")
-                + errorFoundNotTrimmed(path, "observable_type", "/metadata/data_set")
-                + errorFoundNotTrimmed(path, "is_measured", "/metadata/data_set")
-                + errorFoundNotTrimmed(path, "is_complete", "/metadata/data_set")
-                + errorFoundNotTrimmed(path, "major", "/metadata/format/version")
-                + errorFoundNotTrimmed(path, "minor", "/metadata/format/version")
-                + errorFoundNotTrimmed(path, "code", "/metadata/format")
-                + errorFoundNotTrimmed(path, "instance_code", "/metadata/experiment_identifier")
-                + errorFoundNotTrimmed(path, "group_code", "/metadata/experiment_identifier")
-                + errorFoundNotTrimmed(path, "project_code", "/metadata/experiment_identifier")
-                + errorFoundNotTrimmed(path, "experiment_code", "/metadata/experiment_identifier")
-                + errorFoundNotTrimmed(path, "experiment_registration_timestamp", "/metadata")
-                + errorFoundNotTrimmed(path, "first_name", "/metadata/experiment_registrator")
-                + errorFoundNotTrimmed(path, "last_name", "/metadata/experiment_registrator")
-                + errorFoundNotTrimmed(path, "email", "/metadata/experiment_registrator")
-                + errorFoundNotTrimmed(path, "type_description", "/metadata/sample")
-                + errorFoundNotTrimmed(path, "type_code", "/metadata/sample")
-                + errorFoundNotTrimmed(path, "code", "/metadata/sample"));
+        assertEquals(new StructureChecker(verbose).getStructureConsistencyReport(dir).toString(),
+                errorFoundNotTrimmed(path, "major", "/version")
+                        + errorFoundNotTrimmed(path, "minor", "/version")
+                        + errorFoundNotTrimmed(path, "code", "/metadata/data_set")
+                        + errorFoundNotTrimmed(path, "production_timestamp", "/metadata/data_set")
+                        + errorFoundNotTrimmed(path, "producer_code", "/metadata/data_set")
+                        + errorFoundNotTrimmed(path, "observable_type", "/metadata/data_set")
+                        + errorFoundNotTrimmed(path, "is_measured", "/metadata/data_set")
+                        + errorFoundNotTrimmed(path, "is_complete", "/metadata/data_set")
+                        + errorFoundNotTrimmed(path, "major", "/metadata/format/version")
+                        + errorFoundNotTrimmed(path, "minor", "/metadata/format/version")
+                        + errorFoundNotTrimmed(path, "code", "/metadata/format")
+                        + errorFoundNotTrimmed(path, "instance_code",
+                                "/metadata/experiment_identifier")
+                        + errorFoundNotTrimmed(path, "group_code",
+                                "/metadata/experiment_identifier")
+                        + errorFoundNotTrimmed(path, "project_code",
+                                "/metadata/experiment_identifier")
+                        + errorFoundNotTrimmed(path, "experiment_code",
+                                "/metadata/experiment_identifier")
+                        + errorFoundNotTrimmed(path, "experiment_registration_timestamp",
+                                "/metadata")
+                        + errorFoundNotTrimmed(path, "first_name",
+                                "/metadata/experiment_registrator")
+                        + errorFoundNotTrimmed(path, "last_name",
+                                "/metadata/experiment_registrator")
+                        + errorFoundNotTrimmed(path, "email", "/metadata/experiment_registrator")
+                        + errorFoundNotTrimmed(path, "group_code", "/metadata/sample")
+                        + errorFoundNotTrimmed(path, "instance_code", "/metadata/sample")
+                        + errorFoundNotTrimmed(path, "instance_uuid", "/metadata/sample")
+                        + errorFoundNotTrimmed(path, "type_description", "/metadata/sample")
+                        + errorFoundNotTrimmed(path, "type_code", "/metadata/sample")
+                        + errorFoundNotTrimmed(path, "code", "/metadata/sample"));
     }
 }

bds/testdata/bds_new_lines/metadata/sample/group_code

+
+3VCP1

bds/testdata/bds_new_lines/metadata/sample/instance_code

+
+3VCP1

bds/testdata/bds_new_lines/metadata/sample/instance_uuid

+
+3VCP1

bds/testdata/bds_ok/metadata/sample/group_code

+3VCP1
\ No newline at end of file

bds/testdata/bds_ok/metadata/sample/instance_code

+3VCP1
\ No newline at end of file

bds/testdata/bds_ok/metadata/sample/instance_uuid

+3VCP1
\ No newline at end of file