diff --git a/bds/source/java/ch/systemsx/cisd/bds/Constants.java b/bds/source/java/ch/systemsx/cisd/bds/Constants.java
index 0e720d6c2c9b940776461897e17a6e354b578fcd..d04d9fbf6641911b6cb4f35497a39477e9e1ad17 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/Constants.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/Constants.java
@@ -17,6 +17,7 @@
package ch.systemsx.cisd.bds;
import java.text.SimpleDateFormat;
+import java.util.regex.Pattern;
import ch.systemsx.cisd.common.utilities.DateFormatThreadLocal;
@@ -38,6 +39,11 @@ public final class Constants
public static final ThreadLocal<SimpleDateFormat> DATE_FORMAT =
new DateFormatThreadLocal(DATE_FORMAT_PATTERN);
+ /** Regular expression pattern for <i>UUID</i>. */
+ public static final Pattern UUID_PATTERN =
+ Pattern.compile("^[0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12}$",
+ Pattern.CASE_INSENSITIVE);
+
private Constants()
{
// Can not be instantiated.
diff --git a/bds/source/java/ch/systemsx/cisd/bds/DataSet.java b/bds/source/java/ch/systemsx/cisd/bds/DataSet.java
index a85cf46ffb19f1a891d3e67aa8d074ee44726442..29a5ebb65616e42e07c6325ce83e24c62c187330 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/DataSet.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/DataSet.java
@@ -172,7 +172,7 @@ public final class DataSet implements IStorable
final String observableTypeCode = Utilities.getTrimmedString(idFolder, OBSERVABLE_TYPE);
final Boolean isMeasured = Utilities.getBoolean(idFolder, IS_MEASURED);
final Date productionTimestampOrNull =
- Utilities.getDateOrNull(idFolder, PRODUCTION_TIMESTAMP);
+ Utilities.tryGetDate(idFolder, PRODUCTION_TIMESTAMP);
final String producerCode = Utilities.getTrimmedString(idFolder, PRODUCER_CODE);
final List<String> parentCodes = Utilities.getStringList(idFolder, PARENT_CODES);
final String strIsComplete = Utilities.getTrimmedString(idFolder, IS_COMPLETE);
diff --git a/bds/source/java/ch/systemsx/cisd/bds/DataStructureV1_0.java b/bds/source/java/ch/systemsx/cisd/bds/DataStructureV1_0.java
index 5fb136cd34f5c5e662e9692b9fc3874e19bb74d8..0a9a55193f4d3886195020be5372471c2dac5eaa 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/DataStructureV1_0.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/DataStructureV1_0.java
@@ -168,7 +168,7 @@ public class DataStructureV1_0 extends AbstractDataStructure implements IDataStr
* @throws DataStructureException if the experiment identifier hasn't be loaded nor hasn't be
* set by {@link #setExperimentIdentifier(ExperimentIdentifier)}.
*/
- public final ExperimentIdentifier getExperimentIdentifier()
+ public ExperimentIdentifier getExperimentIdentifier()
{
assertOpenOrCreated();
return ExperimentIdentifier.loadFrom(getMetaDataDirectory());
@@ -177,7 +177,7 @@ public class DataStructureV1_0 extends AbstractDataStructure implements IDataStr
/**
* Sets the experiment identifier. Overwrites an already set or loaded value.
*/
- public final void setExperimentIdentifier(final ExperimentIdentifier experimentIdentifier)
+ public void setExperimentIdentifier(final ExperimentIdentifier experimentIdentifier)
{
assert experimentIdentifier != null : "Unspecified experiment identifier";
assertOpenOrCreated();
@@ -298,7 +298,7 @@ public class DataStructureV1_0 extends AbstractDataStructure implements IDataStr
{
throw new DataStructureException("Unspecified format.");
}
- if (metaDataDirectory.tryGetNode(ExperimentIdentifier.EXPERIMENT_IDENTIFIER) == null)
+ if (metaDataDirectory.tryGetNode(ExperimentIdentifier.FOLDER) == null)
{
throw new DataStructureException("Unspecified experiment identifier.");
}
diff --git a/bds/source/java/ch/systemsx/cisd/bds/DataStructureV1_1.java b/bds/source/java/ch/systemsx/cisd/bds/DataStructureV1_1.java
index c6952bd48aefe55f300267f267f79f2dd3c8d1c5..e037aad5b9879efc3e926df4ee2a880f0a086918 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/DataStructureV1_1.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/DataStructureV1_1.java
@@ -54,6 +54,26 @@ public final class DataStructureV1_1 extends DataStructureV1_0
return (SampleWithOwner) sample;
}
+ /**
+ * Returns the experiment identifier with the database instance <i>UUID</i>.
+ * <p>
+ * This is only available in version 1.1. Using this method with data structure version 1.0
+ * throws an exception.
+ * </p>
+ *
+ * @throws DataStructureException if trying to use this method with data structure of version
+ * 1.0.
+ */
+ public final ExperimentIdentifierWithUUID getExperimentIdentifierWithUUID()
+ {
+ final ExperimentIdentifier experimentIdentifier = getExperimentIdentifier();
+ if (experimentIdentifier instanceof ExperimentIdentifierWithUUID == false)
+ {
+ throw new DataStructureException("Can not be used in data structure v1.0.");
+ }
+ return (ExperimentIdentifierWithUUID) experimentIdentifier;
+ }
+
//
// DataStructureV1_0
//
@@ -104,16 +124,61 @@ public final class DataStructureV1_1 extends DataStructureV1_0
super.setSample(sample);
}
+ /**
+ * Sets the experiment identifier. Overwrites an already set or loaded value.
+ *
+ * @param experimentIdentifier Must be an instance of {@link ExperimentIdentifierWithUUID}.
+ */
@Override
- public final void performClosing()
+ public final void setExperimentIdentifier(final ExperimentIdentifier experimentIdentifier)
+ {
+ assert experimentIdentifier != null : "Unspecified experiment identifier.";
+ if (experimentIdentifier instanceof ExperimentIdentifierWithUUID == false)
+ {
+ throw new DataStructureException("Must be an instance of ExperimentIdentifierWithUUID.");
+ }
+ super.setExperimentIdentifier(experimentIdentifier);
+ }
+
+ /**
+ * Returns the experiment identifier.
+ * <p>
+ * For backward compatibility, loads a {@link ExperimentIdentifier} when no
+ * <code>ExperimentIdentifierWithUUID.INSTANCE_UUID</code> node could be found in experiment
+ * identifier directory.
+ * </p>
+ *
+ * @throws DataStructureException if the experiment identifier hasn't be loaded nor hasn't be
+ * set by {@link #setExperimentIdentifier(ExperimentIdentifier)}.
+ * @return a {@link Sample} or {@link SampleWithOwner} (if v1.1).
+ */
+ @Override
+ public final ExperimentIdentifier getExperimentIdentifier()
{
- if (getSample() instanceof SampleWithOwner)
+ assertOpenOrCreated();
+ final IDirectory metaDataDirectory = getMetaDataDirectory();
+ final IDirectory experimentIdentifierDirectory =
+ metaDataDirectory.tryGetNode(ExperimentIdentifier.FOLDER).tryAsDirectory();
+ if (experimentIdentifierDirectory.tryGetNode(ExperimentIdentifierWithUUID.INSTANCE_UUID) == null)
{
- super.performClosing();
- } else
+ return ExperimentIdentifier.loadFrom(metaDataDirectory);
+ }
+ return ExperimentIdentifierWithUUID.loadFrom(metaDataDirectory);
+ }
+
+ @Override
+ public final void performClosing()
+ {
+ if (getSample() instanceof SampleWithOwner == false)
{
throw new DataStructureException(
"The owner (group or database instance) has not been set.");
}
+ if (getExperimentIdentifier() instanceof ExperimentIdentifierWithUUID == false)
+ {
+ throw new DataStructureException(
+ "Instance UUID not specified for exeperiment identifier.");
+ }
+ super.performClosing();
}
}
diff --git a/bds/source/java/ch/systemsx/cisd/bds/ExperimentIdentifier.java b/bds/source/java/ch/systemsx/cisd/bds/ExperimentIdentifier.java
index ebe4309a1ed3d5cdad0905dbee81fa11a6e4b73b..44dc99374281ba14b6980611b8c98e979929f8b5 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/ExperimentIdentifier.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/ExperimentIdentifier.java
@@ -16,6 +16,9 @@
package ch.systemsx.cisd.bds;
+import org.apache.commons.lang.builder.EqualsBuilder;
+import org.apache.commons.lang.builder.HashCodeBuilder;
+
import ch.systemsx.cisd.bds.exception.DataStructureException;
import ch.systemsx.cisd.bds.storage.IDirectory;
@@ -27,12 +30,10 @@ import ch.systemsx.cisd.bds.storage.IDirectory;
*/
public class ExperimentIdentifier implements IStorable
{
- static final String EXPERIMENT_IDENTIFIER = "experiment_identifier";
+ static final String FOLDER = "experiment_identifier";
static final String INSTANCE_CODE = "instance_code";
- static final String INSTANCE_UUID = "instance_uuid";
-
static final String GROUP_CODE = "group_code";
static final String PROJECT_CODE = "project_code";
@@ -44,9 +45,9 @@ public class ExperimentIdentifier implements IStorable
*
* @throws DataStructureException if file missing.
*/
- final static ExperimentIdentifier loadFrom(final IDirectory directory)
+ static ExperimentIdentifier loadFrom(final IDirectory directory)
{
- final IDirectory idFolder = Utilities.getSubDirectory(directory, EXPERIMENT_IDENTIFIER);
+ final IDirectory idFolder = Utilities.getSubDirectory(directory, FOLDER);
final String instanceCode = Utilities.getTrimmedString(idFolder, INSTANCE_CODE);
final String groupCode = Utilities.getTrimmedString(idFolder, GROUP_CODE);
final String projectCode = Utilities.getTrimmedString(idFolder, PROJECT_CODE);
@@ -63,7 +64,8 @@ public class ExperimentIdentifier implements IStorable
private final String experimentCode;
/**
- * Creates an instance for the specified codes of group, project, and experiment.
+ * Creates an instance for the specified database instance and codes of group, project and
+ * experiment.
*
* @param instanceCode A non-empty string of the instance code.
* @param groupCode A non-empty string of the group code.
@@ -83,8 +85,38 @@ public class ExperimentIdentifier implements IStorable
this.experimentCode = experimentCode;
}
+ final ToStringBuilder createToStringBuilder()
+ {
+ final ToStringBuilder builder = new ToStringBuilder();
+ builder.append(INSTANCE_CODE, instanceCode);
+ builder.append(GROUP_CODE, groupCode);
+ builder.append(PROJECT_CODE, projectCode);
+ builder.append(EXPERIMENT_CODE, experimentCode);
+ return builder;
+ }
+
+ final EqualsBuilder createEqualsBuilder(final ExperimentIdentifier experimentIdentifier)
+ {
+ final EqualsBuilder builder = new EqualsBuilder();
+ builder.append(instanceCode, experimentIdentifier.instanceCode);
+ builder.append(groupCode, experimentIdentifier.groupCode);
+ builder.append(projectCode, experimentIdentifier.projectCode);
+ builder.append(experimentCode, experimentIdentifier.experimentCode);
+ return builder;
+ }
+
+ final HashCodeBuilder createHashCodeBuilder()
+ {
+ final HashCodeBuilder builder = new HashCodeBuilder();
+ builder.append(instanceCode);
+ builder.append(groupCode);
+ builder.append(projectCode);
+ builder.append(experimentCode);
+ return builder;
+ }
+
/**
- * Returns the instance code;
+ * Returns the instance code.
*/
public final String getInstanceCode()
{
@@ -92,7 +124,7 @@ public class ExperimentIdentifier implements IStorable
}
/**
- * Returns the group code;
+ * Returns the group code.
*/
public final String getGroupCode()
{
@@ -100,7 +132,7 @@ public class ExperimentIdentifier implements IStorable
}
/**
- * Returns the project code;
+ * Returns the project code.
*/
public final String getProjectCode()
{
@@ -108,7 +140,7 @@ public class ExperimentIdentifier implements IStorable
}
/**
- * Returns the experiment code;
+ * Returns the experiment code.
*/
public final String getExperimentCode()
{
@@ -122,9 +154,9 @@ public class ExperimentIdentifier implements IStorable
/**
* Saves this instance to the specified directory.
*/
- public final void saveTo(final IDirectory directory)
+ public void saveTo(final IDirectory directory)
{
- final IDirectory folder = directory.makeDirectory(EXPERIMENT_IDENTIFIER);
+ final IDirectory folder = directory.makeDirectory(FOLDER);
folder.addKeyValuePair(INSTANCE_CODE, instanceCode);
folder.addKeyValuePair(GROUP_CODE, groupCode);
folder.addKeyValuePair(PROJECT_CODE, projectCode);
@@ -146,31 +178,19 @@ public class ExperimentIdentifier implements IStorable
{
return false;
}
- final ExperimentIdentifier id = (ExperimentIdentifier) obj;
- return id.instanceCode.equals(instanceCode) && id.groupCode.equals(groupCode)
- && id.projectCode.equals(projectCode) && id.experimentCode.equals(experimentCode);
+ return createEqualsBuilder((ExperimentIdentifier) obj).isEquals();
}
@Override
public final int hashCode()
{
- int result = 17;
- result = 37 * result + instanceCode.hashCode();
- result = 37 * result + groupCode.hashCode();
- result = 37 * result + projectCode.hashCode();
- result = 37 * result + experimentCode.hashCode();
- return result;
+ return createHashCodeBuilder().toHashCode();
}
@Override
public final String toString()
{
- final ToStringBuilder builder = new ToStringBuilder();
- builder.append(INSTANCE_CODE, instanceCode);
- builder.append(GROUP_CODE, groupCode);
- builder.append(PROJECT_CODE, projectCode);
- builder.append(EXPERIMENT_CODE, experimentCode);
- return builder.toString();
+ return createToStringBuilder().toString();
}
}
diff --git a/bds/source/java/ch/systemsx/cisd/bds/ExperimentIdentifierWithUUID.java b/bds/source/java/ch/systemsx/cisd/bds/ExperimentIdentifierWithUUID.java
new file mode 100644
index 0000000000000000000000000000000000000000..03692c237e6d0d9d948de945d28d74a36ae8d047
--- /dev/null
+++ b/bds/source/java/ch/systemsx/cisd/bds/ExperimentIdentifierWithUUID.java
@@ -0,0 +1,109 @@
+/*
+ * Copyright 2008 ETH Zuerich, CISD
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package ch.systemsx.cisd.bds;
+
+import ch.systemsx.cisd.bds.exception.DataStructureException;
+import ch.systemsx.cisd.bds.storage.IDirectory;
+
+/**
+ * A small {@link ExperimentIdentifier} extension which adds the reading/writing of database
+ * instance <i>UUID</i>.
+ * <p>
+ * Does not override {@link #equals(Object)} resp. {@link #hashCode()} methods as equality for this
+ * class is based on the same rules.
+ * </p>
+ *
+ * @author Christian Ribeaud
+ */
+public final class ExperimentIdentifierWithUUID extends ExperimentIdentifier
+{
+ static final String INSTANCE_UUID = "instance_uuid";
+
+ private final String instanceUUID;
+
+ /**
+ * Creates an instance for the specified {@link ExperimentIdentifier} and given database
+ * instance <i>UUID</i>.
+ *
+ * @param instanceUUID A non-empty string of the instance <i>UUID</i>.
+ * @param experimentIdentifier A non-<code>null</code> experiment identifier.
+ */
+ public ExperimentIdentifierWithUUID(final ExperimentIdentifier experimentIdentifier,
+ final String instanceUUID)
+ {
+ this(experimentIdentifier.getInstanceCode(), instanceUUID, experimentIdentifier
+ .getGroupCode(), experimentIdentifier.getProjectCode(), experimentIdentifier
+ .getExperimentCode());
+ }
+
+ /**
+ * Creates an instance for the specified database instance and codes of group, project and
+ * experiment.
+ *
+ * @param instanceCode A non-empty string of the instance code.
+ * @param instanceUUID A non-empty string of the instance <i>UUID</i>.
+ * @param groupCode A non-empty string of the group code.
+ * @param projectCode A non-empty string of the project code.
+ * @param experimentCode A non-empty string of the experiment code.
+ */
+ public ExperimentIdentifierWithUUID(final String instanceCode, final String instanceUUID,
+ final String groupCode, final String projectCode, final String experimentCode)
+ {
+ super(instanceCode, groupCode, projectCode, experimentCode);
+ assert StringUtils.isEmpty(instanceUUID) == false : "Undefined instance UUID";
+ this.instanceUUID = instanceUUID;
+ }
+
+ /**
+ * Returns the instance <i>UUID</i>.
+ */
+ public final String getInstanceUUID()
+ {
+ return instanceUUID;
+ }
+
+ //
+ // ExperimentIdentifier
+ //
+
+ /**
+ * Loads the experiment identifier from the specified directory.
+ *
+ * @throws DataStructureException if file missing.
+ */
+ final static ExperimentIdentifierWithUUID loadFrom(final IDirectory directory)
+ {
+ final IDirectory idFolder = Utilities.getSubDirectory(directory, FOLDER);
+ final String instanceCode = Utilities.getTrimmedString(idFolder, INSTANCE_CODE);
+ final String groupCode = Utilities.getTrimmedString(idFolder, GROUP_CODE);
+ final String projectCode = Utilities.getTrimmedString(idFolder, PROJECT_CODE);
+ final String experimentCode = Utilities.getTrimmedString(idFolder, EXPERIMENT_CODE);
+ final String instanceUUID =
+ Utilities.getTrimmedString(idFolder, ExperimentIdentifierWithUUID.INSTANCE_UUID);
+ return new ExperimentIdentifierWithUUID(instanceCode, instanceUUID, groupCode, projectCode,
+ experimentCode);
+
+ }
+
+ @Override
+ public final void saveTo(final IDirectory directory)
+ {
+ super.saveTo(directory);
+ final IDirectory folder = directory.makeDirectory(FOLDER);
+ folder.addKeyValuePair(ExperimentIdentifierWithUUID.INSTANCE_UUID, instanceUUID);
+ }
+}
diff --git a/bds/source/java/ch/systemsx/cisd/bds/ExperimentRegistrationTimestamp.java b/bds/source/java/ch/systemsx/cisd/bds/ExperimentRegistrationTimestamp.java
index 00b5ae18761efe9c4d0b133d11c3ed05ef49c4b4..57631b8a227abb249d912b836ed1ddbc69fa1ba1 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/ExperimentRegistrationTimestamp.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/ExperimentRegistrationTimestamp.java
@@ -39,7 +39,7 @@ public final class ExperimentRegistrationTimestamp implements IStorable
final static ExperimentRegistrationTimestamp loadFrom(final IDirectory directory)
{
- return new ExperimentRegistrationTimestamp(Utilities.getDateOrNull(directory,
+ return new ExperimentRegistrationTimestamp(Utilities.tryGetDate(directory,
EXPERIMENT_REGISTRATION_TIMESTAMP));
}
diff --git a/bds/source/java/ch/systemsx/cisd/bds/SampleWithOwner.java b/bds/source/java/ch/systemsx/cisd/bds/SampleWithOwner.java
index 410a2c29f12800ab38f4486156c4bdfbe7547e24..051e25b96a91e99ed73fb53f32c307ea5f5c3371 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/SampleWithOwner.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/SampleWithOwner.java
@@ -34,7 +34,7 @@ public final class SampleWithOwner extends Sample
static final String INSTANCE_CODE = ExperimentIdentifier.INSTANCE_CODE;
- static final String INSTANCE_UUID = ExperimentIdentifier.INSTANCE_UUID;
+ static final String INSTANCE_UUID = ExperimentIdentifierWithUUID.INSTANCE_UUID;
private final String groupCode;
diff --git a/bds/source/java/ch/systemsx/cisd/bds/Utilities.java b/bds/source/java/ch/systemsx/cisd/bds/Utilities.java
index f99601db8498287d7f91e7b6ea9b6edcaeabd886..2bc4f3a28b10d1b92a2083b826f0472fb5ee5c62 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/Utilities.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/Utilities.java
@@ -196,7 +196,7 @@ public class Utilities
*
* @return the parsed date or <code>null</code> if the value is empty.
*/
- public final static Date getDateOrNull(final IDirectory directory, final String name)
+ public final static Date tryGetDate(final IDirectory directory, final String name)
throws DataStructureException
{
// No assertion here as 'getString(IDirectory, String)' already does it.
diff --git a/bds/source/java/ch/systemsx/cisd/bds/check/AbstractChecker.java b/bds/source/java/ch/systemsx/cisd/bds/check/AbstractChecker.java
index aefb7f619be46096907d09339f3e712de4230d85..44e4c9bec41c4a41b27a9fc805a28f6e459a0f3e 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/check/AbstractChecker.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/check/AbstractChecker.java
@@ -200,6 +200,8 @@ public abstract class AbstractChecker
private static final String IO_EXCEPTION_WHILE_COMPARING_FILES =
"I/O Exception while comparing file '%s' with file '%s': %s";
+ public static final String MSG_WRONG_UUID = "Value '%s' found in file '%s' is not a UUID";
+
protected static final String path(final String... args)
{
final String separator = "/";
diff --git a/bds/source/java/ch/systemsx/cisd/bds/check/StructureChecker.java b/bds/source/java/ch/systemsx/cisd/bds/check/StructureChecker.java
index 5ccb3ebb6340feecc498872230792d5815baee41..bfb8b4e94ac3df7a6a17fcdff5f4588b0afcd313 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/check/StructureChecker.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/check/StructureChecker.java
@@ -18,6 +18,7 @@ package ch.systemsx.cisd.bds.check;
import java.io.File;
+import ch.systemsx.cisd.bds.Constants;
import ch.systemsx.cisd.bds.StringUtils;
import ch.systemsx.cisd.bds.Utilities;
import ch.systemsx.cisd.bds.exception.DataStructureException;
@@ -151,7 +152,7 @@ public final class StructureChecker extends AbstractChecker
final IDirectory sample = Utilities.getSubDirectory(metadata, AbstractChecker.SAMPLE);
checkFileNotEmptyAndTrimmed(sample, AbstractChecker.GROUP_CODE);
checkFileNotEmptyAndTrimmed(sample, AbstractChecker.INSTANCE_CODE);
- checkFileNotEmptyAndTrimmed(sample, AbstractChecker.INSTANCE_UUID);
+ checkFileContainsUUID(sample, AbstractChecker.INSTANCE_UUID);
checkFileNotEmptyAndTrimmed(sample, AbstractChecker.TYPE_DESCRIPTION);
checkFileNotEmptyAndTrimmed(sample, AbstractChecker.TYPE_CODE);
checkFileNotEmptyAndTrimmed(sample, AbstractChecker.CODE);
@@ -188,6 +189,7 @@ public final class StructureChecker extends AbstractChecker
final IDirectory experimentIdentifier =
Utilities.getSubDirectory(metadata, AbstractChecker.EXPERIMENT_IDENTIFIER);
checkFileNotEmptyAndTrimmed(experimentIdentifier, AbstractChecker.INSTANCE_CODE);
+ checkFileContainsUUID(experimentIdentifier, AbstractChecker.INSTANCE_UUID);
checkFileNotEmptyAndTrimmed(experimentIdentifier, AbstractChecker.GROUP_CODE);
checkFileNotEmptyAndTrimmed(experimentIdentifier, AbstractChecker.PROJECT_CODE);
checkFileNotEmptyAndTrimmed(experimentIdentifier, AbstractChecker.EXPERIMENT_CODE);
@@ -266,7 +268,7 @@ public final class StructureChecker extends AbstractChecker
try
{
checkTrimmed(problemReport, dataDir, name);
- if (Utilities.getDateOrNull(dataDir, name) == null)
+ if (Utilities.tryGetDate(dataDir, name) == null)
{
throw new DataStructureException(String.format(
AbstractChecker.MSG_DOES_NOT_CONTAIN_TIMESTAMP, name));
@@ -277,7 +279,24 @@ public final class StructureChecker extends AbstractChecker
}
}
- private void checkFileNotEmpty(final IDirectory dataDir, final String name,
+ private final void checkFileContainsUUID(final IDirectory directory, final String name)
+ {
+ try
+ {
+ checkTrimmed(problemReport, directory, name);
+ final String value = Utilities.getTrimmedString(directory, name);
+ if (Constants.UUID_PATTERN.matcher(value).matches() == false)
+ {
+ throw new DataStructureException(String.format(AbstractChecker.MSG_WRONG_UUID,
+ value, name));
+ }
+ } catch (final Exception e)
+ {
+ problemReport.error(e.getMessage());
+ }
+ }
+
+ private final void checkFileNotEmpty(final IDirectory dataDir, final String name,
final boolean mustBeTrimmed)
{
try
diff --git a/bds/sourceTest/java/ch/systemsx/cisd/bds/DataSetFileSystemTestCase.java b/bds/sourceTest/java/ch/systemsx/cisd/bds/DataSetFileSystemTestCase.java
index d5ae579f6a97747bd3199b4d0d312113c6f82ce6..d50db73393a764266a671b2699bb2c3c9c30dcc2 100644
--- a/bds/sourceTest/java/ch/systemsx/cisd/bds/DataSetFileSystemTestCase.java
+++ b/bds/sourceTest/java/ch/systemsx/cisd/bds/DataSetFileSystemTestCase.java
@@ -53,7 +53,7 @@ public final class DataSetFileSystemTestCase extends AbstractFileSystemTestCase
assertEquals(0, Utilities.getStringList(folder, DataSet.PARENT_CODES).size());
assertEquals(StringUtils.EMPTY_STRING, Utilities.getTrimmedString(folder,
DataSet.PRODUCER_CODE));
- assertNull(Utilities.getDateOrNull(folder, DataSet.PRODUCTION_TIMESTAMP));
+ assertNull(Utilities.tryGetDate(folder, DataSet.PRODUCTION_TIMESTAMP));
assertEquals(StringUtils.EMPTY_STRING, Utilities.getTrimmedString(folder,
DataSet.PRODUCTION_TIMESTAMP));
}
@@ -82,7 +82,7 @@ public final class DataSetFileSystemTestCase extends AbstractFileSystemTestCase
checkBasicDataSet(folder, dataSetCode, observableType, Boolean.TRUE);
assertEquals(0, Utilities.getStringList(folder, DataSet.PARENT_CODES).size());
assertEquals(producerCode, Utilities.getTrimmedString(folder, DataSet.PRODUCER_CODE));
- assertEquals(productionTimestamp, Utilities.getDateOrNull(folder,
+ assertEquals(productionTimestamp, Utilities.tryGetDate(folder,
DataSet.PRODUCTION_TIMESTAMP));
}
@@ -114,7 +114,7 @@ public final class DataSetFileSystemTestCase extends AbstractFileSystemTestCase
assertEquals(parentCode, parentList.get(0));
assertEquals(StringUtils.EMPTY_STRING, Utilities.getTrimmedString(folder,
DataSet.PRODUCER_CODE));
- assertNull(Utilities.getDateOrNull(folder, DataSet.PRODUCTION_TIMESTAMP));
+ assertNull(Utilities.tryGetDate(folder, DataSet.PRODUCTION_TIMESTAMP));
assertEquals(StringUtils.EMPTY_STRING, Utilities.getTrimmedString(folder,
DataSet.PRODUCTION_TIMESTAMP));
}
diff --git a/bds/sourceTest/java/ch/systemsx/cisd/bds/DataStructureV1_0Test.java b/bds/sourceTest/java/ch/systemsx/cisd/bds/DataStructureV1_0Test.java
index 49cf8be238c5575ff31151ac4fbc4824869a6a84..ee4d83f580fc26176081960fa5d31c6bbd0c2d44 100644
--- a/bds/sourceTest/java/ch/systemsx/cisd/bds/DataStructureV1_0Test.java
+++ b/bds/sourceTest/java/ch/systemsx/cisd/bds/DataStructureV1_0Test.java
@@ -110,8 +110,7 @@ public final class DataStructureV1_0Test extends AbstractFileSystemTestCase
dataStructure.setExperimentIdentifier(id);
final IDirectory root = storage.getRoot();
final IDirectory metaData = Utilities.getSubDirectory(root, DataStructureV1_0.DIR_METADATA);
- final IDirectory idDir =
- Utilities.getSubDirectory(metaData, ExperimentIdentifier.EXPERIMENT_IDENTIFIER);
+ final IDirectory idDir = Utilities.getSubDirectory(metaData, ExperimentIdentifier.FOLDER);
assertEquals("i\n", Utilities.getString(idDir, ExperimentIdentifier.INSTANCE_CODE));
assertEquals("g\n", Utilities.getString(idDir, ExperimentIdentifier.GROUP_CODE));
assertEquals("p\n", Utilities.getString(idDir, ExperimentIdentifier.PROJECT_CODE));
@@ -127,8 +126,7 @@ public final class DataStructureV1_0Test extends AbstractFileSystemTestCase
dataStructure.setExperimentIdentifier(id);
final IDirectory root = storage.getRoot();
final IDirectory metaData = Utilities.getSubDirectory(root, DataStructureV1_0.DIR_METADATA);
- final IDirectory idDir =
- Utilities.getSubDirectory(metaData, ExperimentIdentifier.EXPERIMENT_IDENTIFIER);
+ final IDirectory idDir = Utilities.getSubDirectory(metaData, ExperimentIdentifier.FOLDER);
assertEquals("i\n", Utilities.getString(idDir, ExperimentIdentifier.INSTANCE_CODE));
assertEquals("g\n", Utilities.getString(idDir, ExperimentIdentifier.GROUP_CODE));
assertEquals("p\n", Utilities.getString(idDir, ExperimentIdentifier.PROJECT_CODE));
@@ -145,7 +143,7 @@ public final class DataStructureV1_0Test extends AbstractFileSystemTestCase
fail("DataStructureException expected.");
} catch (final DataStructureException e)
{
- assertPartOfString(ExperimentIdentifier.EXPERIMENT_IDENTIFIER, e.getMessage());
+ assertPartOfString(ExperimentIdentifier.FOLDER, e.getMessage());
}
}
diff --git a/bds/sourceTest/java/ch/systemsx/cisd/bds/DataStructureV1_1Test.java b/bds/sourceTest/java/ch/systemsx/cisd/bds/DataStructureV1_1Test.java
index 61a598b833b2e1d481a44af1af5ce7c714d24362..2ec7debc0b9ea531683f77198f83408b6e3eb2e9 100644
--- a/bds/sourceTest/java/ch/systemsx/cisd/bds/DataStructureV1_1Test.java
+++ b/bds/sourceTest/java/ch/systemsx/cisd/bds/DataStructureV1_1Test.java
@@ -40,10 +40,21 @@ public final class DataStructureV1_1Test extends AbstractFileSystemTestCase
{
private static final Sample SAMPLE = new Sample("a", "CELL_PLATE", "b");
+ private static final ExperimentIdentifier EXPERIMENT_IDENTIFIER =
+ new ExperimentIdentifier(SampleWithOwnerTest.INSTANCE_CODE,
+ SampleWithOwnerTest.GROUP_CODE, ExperimentIdentifierTest.PROJECT_CODE,
+ ExperimentIdentifierTest.EXPERMENT_CODE);
+
private FileStorage storage;
private DataStructureV1_1 dataStructure;
+ private final static SampleWithOwner createSampleWithOwner()
+ {
+ return new SampleWithOwner(SAMPLE, SampleWithOwnerTest.INSTANCE_UUID,
+ SampleWithOwnerTest.INSTANCE_CODE, "");
+ }
+
//
// AbstractFileSystemTestCase
//
@@ -76,17 +87,14 @@ public final class DataStructureV1_1Test extends AbstractFileSystemTestCase
{
// Nothing to do here.
}
- dataStructure.setSample(new SampleWithOwner(SAMPLE,
- SampleWithOwnerTest.INSTANCE_GLOBAL_CODE, SampleWithOwnerTest.INSTANCE_CODE, ""));
+ dataStructure.setSample(createSampleWithOwner());
}
@Test
public final void testGetSample()
{
dataStructure.create();
- final SampleWithOwner sampleWithOwner =
- new SampleWithOwner(SAMPLE, SampleWithOwnerTest.INSTANCE_GLOBAL_CODE,
- SampleWithOwnerTest.INSTANCE_CODE, "");
+ final SampleWithOwner sampleWithOwner = createSampleWithOwner();
dataStructure.setSample(sampleWithOwner);
final Sample sample = dataStructure.getSample();
assertTrue(sample instanceof SampleWithOwner);
@@ -96,7 +104,35 @@ public final class DataStructureV1_1Test extends AbstractFileSystemTestCase
}
@Test
- public void testOpenVersionV1_0()
+ public final void testGetExperimentIdentifier()
+ {
+ dataStructure.create();
+ final ExperimentIdentifierWithUUID experimentIdentifierWithUUID =
+ ExperimentIdentifierWithUUIDTest.createExperimentIdentifierWithUUID();
+ dataStructure.setExperimentIdentifier(experimentIdentifierWithUUID);
+ final ExperimentIdentifier experimentIdentifier = dataStructure.getExperimentIdentifier();
+ assertTrue(experimentIdentifier instanceof ExperimentIdentifierWithUUID);
+ assertEquals(SampleWithOwnerTest.INSTANCE_UUID,
+ ((ExperimentIdentifierWithUUID) experimentIdentifier).getInstanceUUID());
+ }
+
+ @Test
+ public final void testSetExperimentIdentifier()
+ {
+ dataStructure.create();
+ try
+ {
+ dataStructure.setExperimentIdentifier(EXPERIMENT_IDENTIFIER);
+ fail();
+ } catch (final DataStructureException ex)
+ {
+ // Nothing to do here.
+ }
+ dataStructure.setExperimentIdentifier(ExperimentIdentifierWithUUIDTest.createExperimentIdentifierWithUUID());
+ }
+
+ @Test
+ public final void testOpenVersionV1_0()
{
DataStructureV1_0Test.createExampleDataStructure(storage, new Version(1, 0));
storage.mount();
@@ -136,10 +172,8 @@ public final class DataStructureV1_1Test extends AbstractFileSystemTestCase
{
// Nothing to do here.
}
- final SampleWithOwner sampleWithOwner =
- new SampleWithOwner(SAMPLE, SampleWithOwnerTest.INSTANCE_GLOBAL_CODE,
- SampleWithOwnerTest.INSTANCE_CODE, "");
- dataStructure.setSample(sampleWithOwner);
+ dataStructure.setSample(createSampleWithOwner());
+ dataStructure.setExperimentIdentifier(ExperimentIdentifierWithUUIDTest.createExperimentIdentifierWithUUID());
dataStructure.close();
}
}
diff --git a/bds/sourceTest/java/ch/systemsx/cisd/bds/ExperimentIdentifierTest.java b/bds/sourceTest/java/ch/systemsx/cisd/bds/ExperimentIdentifierTest.java
index e9c27283f176ac6b70830e5e7449e893a314ceb8..e64ceab7faba1657752bca5d0b5a3ac73ec40e82 100644
--- a/bds/sourceTest/java/ch/systemsx/cisd/bds/ExperimentIdentifierTest.java
+++ b/bds/sourceTest/java/ch/systemsx/cisd/bds/ExperimentIdentifierTest.java
@@ -16,6 +16,8 @@
package ch.systemsx.cisd.bds;
+import static org.testng.AssertJUnit.assertFalse;
+
import org.testng.annotations.Test;
import ch.systemsx.cisd.common.test.EqualsHashCodeTestCase;
@@ -29,6 +31,35 @@ import ch.systemsx.cisd.common.test.EqualsHashCodeTestCase;
public final class ExperimentIdentifierTest extends EqualsHashCodeTestCase<ExperimentIdentifier>
{
+ static final String EXPERMENT_CODE = "EXP1";
+
+ static final String PROJECT_CODE = "PROJ1";
+
+ @Test
+ public final void testConstructor()
+ {
+ boolean fail = true;
+ try
+ {
+ new ExperimentIdentifier(SampleWithOwner.INSTANCE_CODE, SampleWithOwner.GROUP_CODE,
+ null, null);
+ } catch (final AssertionError ex)
+ {
+ fail = false;
+ }
+ assertFalse(fail);
+ fail = true;
+ try
+ {
+ new ExperimentIdentifier(SampleWithOwner.INSTANCE_CODE, SampleWithOwner.GROUP_CODE,
+ PROJECT_CODE, "");
+ } catch (final AssertionError ex)
+ {
+ fail = false;
+ }
+ assertFalse(fail);
+ }
+
//
// EqualsHashCodeTestCase
//
diff --git a/bds/sourceTest/java/ch/systemsx/cisd/bds/ExperimentIdentifierWithUUIDTest.java b/bds/sourceTest/java/ch/systemsx/cisd/bds/ExperimentIdentifierWithUUIDTest.java
new file mode 100644
index 0000000000000000000000000000000000000000..facb3f431dfe48b874c4d56ab27b48595f10afcf
--- /dev/null
+++ b/bds/sourceTest/java/ch/systemsx/cisd/bds/ExperimentIdentifierWithUUIDTest.java
@@ -0,0 +1,86 @@
+/*
+ * Copyright 2008 ETH Zuerich, CISD
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package ch.systemsx.cisd.bds;
+
+import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertFalse;
+import static org.testng.AssertJUnit.assertNotNull;
+
+import org.testng.annotations.Test;
+
+import ch.systemsx.cisd.bds.storage.IDirectory;
+import ch.systemsx.cisd.bds.storage.filesystem.NodeFactory;
+import ch.systemsx.cisd.common.filesystem.AbstractFileSystemTestCase;
+
+/**
+ * Test cases for corresponding {@link ExperimentIdentifierWithUUID} class.
+ *
+ * @author Christian Ribeaud
+ */
+public final class ExperimentIdentifierWithUUIDTest extends AbstractFileSystemTestCase
+{
+ final static ExperimentIdentifierWithUUID createExperimentIdentifierWithUUID()
+ {
+ return new ExperimentIdentifierWithUUID(SampleWithOwnerTest.INSTANCE_CODE,
+ SampleWithOwnerTest.INSTANCE_UUID, SampleWithOwnerTest.GROUP_CODE,
+ ExperimentIdentifierTest.PROJECT_CODE, ExperimentIdentifierTest.EXPERMENT_CODE);
+ }
+
+ @Test
+ public final void testConstructor()
+ {
+ boolean fail = true;
+ try
+ {
+ new ExperimentIdentifierWithUUID(SampleWithOwner.INSTANCE_CODE, null,
+ SampleWithOwner.GROUP_CODE, ExperimentIdentifierTest.PROJECT_CODE,
+ ExperimentIdentifierTest.EXPERMENT_CODE);
+ } catch (final AssertionError ex)
+ {
+ fail = false;
+ }
+ assertFalse(fail);
+ fail = true;
+ try
+ {
+ new ExperimentIdentifierWithUUID(SampleWithOwner.INSTANCE_CODE, "",
+ SampleWithOwner.GROUP_CODE, ExperimentIdentifierTest.PROJECT_CODE,
+ ExperimentIdentifierTest.EXPERMENT_CODE);
+ } catch (final AssertionError ex)
+ {
+ fail = false;
+ }
+ assertFalse(fail);
+ new ExperimentIdentifierWithUUID(SampleWithOwner.INSTANCE_CODE,
+ SampleWithOwner.INSTANCE_UUID, SampleWithOwner.GROUP_CODE,
+ ExperimentIdentifierTest.PROJECT_CODE, ExperimentIdentifierTest.EXPERMENT_CODE);
+ }
+
+ @Test
+ public final void testLoadFrom()
+ {
+ final IDirectory directory = NodeFactory.createDirectoryNode(workingDirectory);
+ final ExperimentIdentifierWithUUID experimentIdentifier =
+ createExperimentIdentifierWithUUID();
+ experimentIdentifier.saveTo(directory);
+ final ExperimentIdentifierWithUUID loaded =
+ ExperimentIdentifierWithUUID.loadFrom(directory);
+ assertEquals(experimentIdentifier, loaded);
+ assertNotNull(loaded.getInstanceUUID());
+ assertEquals(experimentIdentifier.getInstanceUUID(), loaded.getInstanceUUID());
+ }
+}
diff --git a/bds/sourceTest/java/ch/systemsx/cisd/bds/SampleWithOwnerTest.java b/bds/sourceTest/java/ch/systemsx/cisd/bds/SampleWithOwnerTest.java
index b5c5fa753ed543dccde726577afe5c6ac76e14ce..d5fb6de16ebcc9ea953d0d5a2718bf48ad4ca69d 100644
--- a/bds/sourceTest/java/ch/systemsx/cisd/bds/SampleWithOwnerTest.java
+++ b/bds/sourceTest/java/ch/systemsx/cisd/bds/SampleWithOwnerTest.java
@@ -42,7 +42,7 @@ public final class SampleWithOwnerTest extends AbstractFileSystemTestCase
static final String INSTANCE_CODE = "DB1";
- static final String INSTANCE_GLOBAL_CODE = "111-222";
+ static final String INSTANCE_UUID = "111-222";
static final String GROUP_CODE = "G1";
@@ -89,8 +89,8 @@ public final class SampleWithOwnerTest extends AbstractFileSystemTestCase
{
return new Object[][]
{
- { INSTANCE_GLOBAL_CODE, INSTANCE_CODE, GROUP_CODE },
- { INSTANCE_GLOBAL_CODE, INSTANCE_CODE, "" }, };
+ { INSTANCE_UUID, INSTANCE_CODE, GROUP_CODE },
+ { INSTANCE_UUID, INSTANCE_CODE, "" }, };
}
@Test(dataProvider = "getSampleData")
@@ -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.getInstanceUUID());
+ assertEquals(INSTANCE_UUID, newSample.getInstanceUUID());
} else
{
assertEquals("", newSample.getGroupCode());
assertEquals(INSTANCE_CODE, newSample.getInstanceCode());
- assertEquals(INSTANCE_GLOBAL_CODE, newSample.getInstanceUUID());
+ assertEquals(INSTANCE_UUID, newSample.getInstanceUUID());
}
}
}
diff --git a/bds/sourceTest/java/ch/systemsx/cisd/bds/check/StructureCheckerTest.java b/bds/sourceTest/java/ch/systemsx/cisd/bds/check/StructureCheckerTest.java
index 91aba071c6fd9905cf2033e8dabb9e2feb55c5bc..63063122f1018b9d4110a58619373662aa4d3c05 100644
--- a/bds/sourceTest/java/ch/systemsx/cisd/bds/check/StructureCheckerTest.java
+++ b/bds/sourceTest/java/ch/systemsx/cisd/bds/check/StructureCheckerTest.java
@@ -69,16 +69,17 @@ public class StructureCheckerTest extends AbstractCheckerTest
@Test
public final void testMissingFiles()
{
-
- assertEquals(new StructureChecker(verbose).getStructureConsistencyReport(
- new File("testdata/bds_missing_files")).numberOfProblems(), 22);
+ final ProblemReport report =
+ new StructureChecker(verbose).getStructureConsistencyReport(new File(
+ "testdata/bds_missing_files"));
+ assertEquals(report.numberOfProblems(), 23);
}
@Test
public final void testEmptyFiles()
{
assertEquals(new StructureChecker(verbose).getStructureConsistencyReport(
- new File("testdata/bds_empty_files")).numberOfProblems(), 26);
+ new File("testdata/bds_empty_files")).numberOfProblems(), 27);
}
@Test
@@ -87,7 +88,7 @@ public class StructureCheckerTest extends AbstractCheckerTest
final ProblemReport structureConsistencyReport =
new StructureChecker(verbose).getStructureConsistencyReport(new File(
"testdata/bds_wrong_values"));
- assertEquals(structureConsistencyReport.numberOfProblems(), 10);
+ assertEquals(structureConsistencyReport.numberOfProblems(), 11);
}
@Test
@@ -96,38 +97,32 @@ public class StructureCheckerTest extends AbstractCheckerTest
final File dir = new File("testdata/bds_new_lines");
final String path = dir.getAbsolutePath();
- 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"));
+ assertEquals(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, "instance_uuid", "/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"), new StructureChecker(
+ verbose).getStructureConsistencyReport(dir).toString());
}
}
diff --git a/bds/testdata/bds_empty_files/metadata/experiment_identifier/instance_uuid b/bds/testdata/bds_empty_files/metadata/experiment_identifier/instance_uuid
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/bds/testdata/bds_new_lines/metadata/experiment_identifier/instance_uuid b/bds/testdata/bds_new_lines/metadata/experiment_identifier/instance_uuid
new file mode 100644
index 0000000000000000000000000000000000000000..8d3164211f85087e9c63112efd0edf098a9b30c9
--- /dev/null
+++ b/bds/testdata/bds_new_lines/metadata/experiment_identifier/instance_uuid
@@ -0,0 +1,2 @@
+
+550E8400-E29B-41E4-A716-446655440000
diff --git a/bds/testdata/bds_new_lines/metadata/sample/instance_uuid b/bds/testdata/bds_new_lines/metadata/sample/instance_uuid
index df2eecf1f87a6e653d9687a0c6248ef1341e57a4..8d3164211f85087e9c63112efd0edf098a9b30c9 100644
--- a/bds/testdata/bds_new_lines/metadata/sample/instance_uuid
+++ b/bds/testdata/bds_new_lines/metadata/sample/instance_uuid
@@ -1,2 +1,2 @@
-3VCP1
+550E8400-E29B-41E4-A716-446655440000
diff --git a/bds/testdata/bds_ok/metadata/experiment_identifier/instance_uuid b/bds/testdata/bds_ok/metadata/experiment_identifier/instance_uuid
new file mode 100644
index 0000000000000000000000000000000000000000..f4b5f296ddffcccbdbc8d2b1aeca929e174a38d6
--- /dev/null
+++ b/bds/testdata/bds_ok/metadata/experiment_identifier/instance_uuid
@@ -0,0 +1 @@
+550E8400-E29B-41E4-A716-446655440000
\ No newline at end of file
diff --git a/bds/testdata/bds_ok/metadata/sample/instance_uuid b/bds/testdata/bds_ok/metadata/sample/instance_uuid
index d04cb00f615f617e91c77f5faa20858c4f7183e5..f4b5f296ddffcccbdbc8d2b1aeca929e174a38d6 100644
--- a/bds/testdata/bds_ok/metadata/sample/instance_uuid
+++ b/bds/testdata/bds_ok/metadata/sample/instance_uuid
@@ -1 +1 @@
-3VCP1
\ No newline at end of file
+550E8400-E29B-41E4-A716-446655440000
\ No newline at end of file
diff --git a/integration-tests/run.sh b/integration-tests/run.sh
index f8126a218a7cfae640ab0145e1f391d423c0cc7f..69b072637770575710547214135f1c43eb44ff22 100755
--- a/integration-tests/run.sh
+++ b/integration-tests/run.sh
@@ -663,6 +663,7 @@ function assert_correct_content_of_plate_3VCP1_in_store {
assert_equals_as_in_file CISD $metadata_dir/experiment_identifier/group_code
assert_equals_as_in_file NEMO $metadata_dir/experiment_identifier/project_code
assert_equals_as_in_file EXP1 $metadata_dir/experiment_identifier/experiment_code
+ assert_file_exists $metadata_dir/experiment_identifier/instance_uuid
# Experiment registration
assert_file_exists $metadata_dir/experiment_registration_timestamp
assert_file_exists $metadata_dir/experiment_registrator/email