diff --git a/rtd_cina/source/java/ch/systemsx/cisd/cina/client/util/cli/AbstractCinaCommand.java b/rtd_cina/source/java/ch/systemsx/cisd/cina/client/util/cli/AbstractCinaCommand.java
index b0d6eb7cbcd5dc1697bcdb587c9c0a9a25fe1101..f27873f2e0b7accbe8bd0031af0dd65c40fd1c50 100644
--- a/rtd_cina/source/java/ch/systemsx/cisd/cina/client/util/cli/AbstractCinaCommand.java
+++ b/rtd_cina/source/java/ch/systemsx/cisd/cina/client/util/cli/AbstractCinaCommand.java
@@ -24,8 +24,7 @@ import ch.systemsx.cisd.openbis.dss.client.api.cli.GlobalArguments;
/**
* Superclass for cina command-line client commands.
* <p>
- * Provides services used by most subclasses. In order for the AbstractCommand to work, subclasses
- * must do the following:
+ * Provides services used by most subclasses. In order for the AbstractCommand to work, subclasses must do the following:
* <ul>
* <li>Set the parser ivar in their constructor
* </ul>
diff --git a/rtd_cina/source/java/ch/systemsx/cisd/cina/client/util/cli/BundleDownloader.java b/rtd_cina/source/java/ch/systemsx/cisd/cina/client/util/cli/BundleDownloader.java
index d0b56786eb13b78a98575b3f469c625e9d291a4c..ffe05f01355b31aaf2e0e80efc09370101ed8f39 100644
--- a/rtd_cina/source/java/ch/systemsx/cisd/cina/client/util/cli/BundleDownloader.java
+++ b/rtd_cina/source/java/ch/systemsx/cisd/cina/client/util/cli/BundleDownloader.java
@@ -106,8 +106,7 @@ class BundleDownloader
}
/**
- * Retrieve the raw data and current metadata for the replica sample as well as the current
- * metadata for the parent grid of the replica.
+ * Retrieve the raw data and current metadata for the replica sample as well as the current metadata for the parent grid of the replica.
*/
public void download()
{
diff --git a/rtd_cina/source/java/ch/systemsx/cisd/cina/client/util/cli/CinaCommandFactory.java b/rtd_cina/source/java/ch/systemsx/cisd/cina/client/util/cli/CinaCommandFactory.java
index d906a7316cdaa2bff90038b19ec8604fbc317ce5..1c415c9f9df7cf24bdd8ee987c016dceba6f3478 100644
--- a/rtd_cina/source/java/ch/systemsx/cisd/cina/client/util/cli/CinaCommandFactory.java
+++ b/rtd_cina/source/java/ch/systemsx/cisd/cina/client/util/cli/CinaCommandFactory.java
@@ -38,7 +38,7 @@ public class CinaCommandFactory extends AbstractCommandFactory
public List<String> getKnownCommands()
{
String[] commands =
- { "listsamps", "gencode", "listexps", "getreplica", "getbundle", "listprefs" };
+ { "listsamps", "gencode", "listexps", "getreplica", "getbundle", "listprefs" };
return Arrays.asList(commands);
}
diff --git a/rtd_cina/source/java/ch/systemsx/cisd/cina/client/util/cli/ReplicaDownloader.java b/rtd_cina/source/java/ch/systemsx/cisd/cina/client/util/cli/ReplicaDownloader.java
index 8250e91d5f1736d38f5806238a17120fe9cf33b2..de8cb327f95977d2233a9e986c2471bb29eae61f 100644
--- a/rtd_cina/source/java/ch/systemsx/cisd/cina/client/util/cli/ReplicaDownloader.java
+++ b/rtd_cina/source/java/ch/systemsx/cisd/cina/client/util/cli/ReplicaDownloader.java
@@ -91,8 +91,7 @@ class ReplicaDownloader
}
/**
- * Retrieve the raw data and current metadata for the replica sample as well as the current
- * metadata for the parent grid of the replica.
+ * Retrieve the raw data and current metadata for the replica sample as well as the current metadata for the parent grid of the replica.
*/
protected void download()
{
diff --git a/rtd_cina/source/java/ch/systemsx/cisd/cina/client/util/v1/CinaUtilitiesFacadeFactory.java b/rtd_cina/source/java/ch/systemsx/cisd/cina/client/util/v1/CinaUtilitiesFacadeFactory.java
index 5e338b7807699759c691173e12c53224d25781ee..2473b107a2b66f24786b315523f33eff6e40b21f 100644
--- a/rtd_cina/source/java/ch/systemsx/cisd/cina/client/util/v1/CinaUtilitiesFacadeFactory.java
+++ b/rtd_cina/source/java/ch/systemsx/cisd/cina/client/util/v1/CinaUtilitiesFacadeFactory.java
@@ -40,8 +40,7 @@ public class CinaUtilitiesFacadeFactory
}
/**
- * Public factory method for creating an ICinaUtilities for a user that has already been
- * authenticated.
+ * Public factory method for creating an ICinaUtilities for a user that has already been authenticated.
*
* @param sessionToken The session token provided by authentication
* @param openBISUrl The URL to openBIS
diff --git a/rtd_cina/source/java/ch/systemsx/cisd/cina/client/util/v1/ICinaUtilities.java b/rtd_cina/source/java/ch/systemsx/cisd/cina/client/util/v1/ICinaUtilities.java
index b4f23100744f8d65338052830edae490b219686d..81319e9df97f1f486347cc0f79c83b6b063527a7 100644
--- a/rtd_cina/source/java/ch/systemsx/cisd/cina/client/util/v1/ICinaUtilities.java
+++ b/rtd_cina/source/java/ch/systemsx/cisd/cina/client/util/v1/ICinaUtilities.java
@@ -47,8 +47,7 @@ public interface ICinaUtilities
* @param searchCriteria The criteria to search for
* @return A list of samples that match the criteria.
* @throws IllegalStateException Thrown if the user has not yet been authenticated.
- * @throws EnvironmentFailureException Thrown in cases where it is not possible to connect to
- * the server.
+ * @throws EnvironmentFailureException Thrown in cases where it is not possible to connect to the server.
*/
public List<Sample> searchForSamples(SearchCriteria searchCriteria)
throws IllegalStateException, EnvironmentFailureException;
@@ -59,8 +58,7 @@ public interface ICinaUtilities
* @param sampleTypeCode The sample type of the sample the generated identifier will belong to.
* @return A sample code for the provided sample type.
* @throws IllegalStateException Thrown if the user has not yet been authenticated.
- * @throws EnvironmentFailureException Thrown in cases where it is not possible to connect to
- * the server.
+ * @throws EnvironmentFailureException Thrown in cases where it is not possible to connect to the server.
*/
public String generateSampleCode(String sampleTypeCode) throws IllegalStateException,
EnvironmentFailureException;
@@ -71,8 +69,7 @@ public interface ICinaUtilities
* @param experimentType The type of experiment we want listed
* @return A list of experiments for the given experiment type
* @throws IllegalStateException Thrown if the user has not yet been authenticated.
- * @throws EnvironmentFailureException Thrown in cases where it is not possible to connect to
- * the server.
+ * @throws EnvironmentFailureException Thrown in cases where it is not possible to connect to the server.
*/
public List<Experiment> listVisibleExperiments(String experimentType)
throws IllegalStateException, EnvironmentFailureException;
@@ -83,8 +80,8 @@ public interface ICinaUtilities
* @param samples The samples we want to retrieve data sets for
* @return The data sets connected to the sample
* @throws IllegalStateException Thrown if the user has not yet been authenticated.
- * @throws EnvironmentFailureException Thrown in cases where it is not possible to connect to
- * the server or if there are multiple samples with the given code.
+ * @throws EnvironmentFailureException Thrown in cases where it is not possible to connect to the server or if there are multiple samples with the
+ * given code.
* @throws UserFailureException Thrown if no sample exists with the specified code.
*/
public List<DataSet> listDataSets(List<Sample> samples) throws IllegalStateException,
@@ -95,8 +92,8 @@ public interface ICinaUtilities
*
* @param dataSetCode The code of the data set to download
* @throws IllegalStateException Thrown if the user has not yet been authenticated.
- * @throws EnvironmentFailureException Thrown in cases where it is not possible to connect to
- * the server or if there are multiple samples with the given code.
+ * @throws EnvironmentFailureException Thrown in cases where it is not possible to connect to the server or if there are multiple samples with the
+ * given code.
* @throws UserFailureException Thrown if no sample exists with the specified code.
*/
public IDataSetDss getDataSet(String dataSetCode) throws IllegalStateException,
@@ -106,12 +103,12 @@ public interface ICinaUtilities
* Return a list of data sets for the sample specified by code.
*
* @param sample The sample we want to retrieve data sets for
- * @param areOnlyDirectlyConnectedIncluded If false, data sets for children of the sample are
- * included, o.w. only data sets directly connected to the sample are included.
+ * @param areOnlyDirectlyConnectedIncluded If false, data sets for children of the sample are included, o.w. only data sets directly connected to
+ * the sample are included.
* @return The data sets connected to the sample
* @throws IllegalStateException Thrown if the user has not yet been authenticated.
- * @throws EnvironmentFailureException Thrown in cases where it is not possible to connect to
- * the server or if there are multiple samples with the given code.
+ * @throws EnvironmentFailureException Thrown in cases where it is not possible to connect to the server or if there are multiple samples with the
+ * given code.
* @throws UserFailureException Thrown if no sample exists with the specified code.
*/
public List<DataSet> listDataSetsForSample(Sample sample,
diff --git a/rtd_cina/source/java/ch/systemsx/cisd/cina/client/util/v1/impl/CinaUtilitiesFacade.java b/rtd_cina/source/java/ch/systemsx/cisd/cina/client/util/v1/impl/CinaUtilitiesFacade.java
index 4ea02d92e9fd7cd7b42ce443a42e21b324916220..73245f55a4039f4e3b9642daa5a2b6ec7ccce57e 100644
--- a/rtd_cina/source/java/ch/systemsx/cisd/cina/client/util/v1/impl/CinaUtilitiesFacade.java
+++ b/rtd_cina/source/java/ch/systemsx/cisd/cina/client/util/v1/impl/CinaUtilitiesFacade.java
@@ -69,8 +69,7 @@ public class CinaUtilitiesFacade implements ICinaUtilities
}
/**
- * Public factory method for creating a DssComponent for a user that has already been
- * authenticated.
+ * Public factory method for creating a DssComponent for a user that has already been authenticated.
*
* @param sessionToken The session token provided by authentication
* @param openBISUrl The URL to openBIS
@@ -108,8 +107,8 @@ public class CinaUtilitiesFacade implements ICinaUtilities
/**
* Create a DSS component that connects to the openBIS instance specified by the URL.
* <p>
- * The DSS component needs to connect to openBIS to find out which DSS manages a given data set.
- * Once it has a connection to openBIS, it can figure out how to connect to DSS servers itself.
+ * The DSS component needs to connect to openBIS to find out which DSS manages a given data set. Once it has a connection to openBIS, it can
+ * figure out how to connect to DSS servers itself.
*/
private static IDssComponent createDssComponent(IServiceForDataStoreServer openbisService,
IGeneralInformationService generalInformationService, String sessionTokenOrNull,
@@ -131,12 +130,10 @@ public class CinaUtilitiesFacade implements ICinaUtilities
/**
* Internal constructor, also used for testing.
*
- * @param generalInformationService A proxy to the openBIS application server's general
- * information service
+ * @param generalInformationService A proxy to the openBIS application server's general information service
* @param openbisService A proxy to the openBIS application server's ETLLIMS Service
* @param dssComponent A dss component facade for interacting with dss services
- * @param sessionTokenOrNull A session token, if the user has already logged in, or null
- * otherwise.
+ * @param sessionTokenOrNull A session token, if the user has already logged in, or null otherwise.
*/
protected CinaUtilitiesFacade(IGeneralInformationService generalInformationService,
IServiceForDataStoreServer openbisService, IDssComponent dssComponent, String sessionTokenOrNull)
@@ -157,8 +154,7 @@ public class CinaUtilitiesFacade implements ICinaUtilities
/**
* FOR TESTING ONLY <br>
- * This method makes it possible to hand in a mocked dssComponent -- it should only be used for
- * testing and it therefore marked deprecated.
+ * This method makes it possible to hand in a mocked dssComponent -- it should only be used for testing and it therefore marked deprecated.
*
* @deprecated
*/
@@ -177,8 +173,7 @@ public class CinaUtilitiesFacade implements ICinaUtilities
* Authenticates the <code>user</code> with given <code>password</code>.
*
* @throws AuthorizationFailureException Thrown if the username / password do not authenticate.
- * @throws EnvironmentFailureException Thrown in cases where it is not possible to connect to
- * the server.
+ * @throws EnvironmentFailureException Thrown in cases where it is not possible to connect to the server.
*/
void login(String user, String password, long timeoutInMillis)
throws AuthorizationFailureException,
@@ -253,8 +248,7 @@ public class CinaUtilitiesFacade implements ICinaUtilities
/**
* Superclass for component states, which make the state machine of the Cina facade explicit.
* <p>
- * By default, all methods just throw an exception. Subclasses should override the methods they
- * accept.
+ * By default, all methods just throw an exception. Subclasses should override the methods they accept.
*
* @author Chandrasekhar Ramakrishnan
*/
@@ -319,8 +313,7 @@ abstract class AbstractCinaFacadeState implements ICinaUtilities
* Authenticates the <code>user</code> with given <code>password</code>.
*
* @throws AuthorizationFailureException Thrown if the username / password do not authenticate.
- * @throws EnvironmentFailureException Thrown in cases where it is not possible to connect to
- * the server.
+ * @throws EnvironmentFailureException Thrown in cases where it is not possible to connect to the server.
*/
abstract void login(final String user, final String password)
throws AuthorizationFailureException, EnvironmentFailureException;
@@ -333,8 +326,8 @@ abstract class AbstractCinaFacadeState implements ICinaUtilities
}
/**
- * An object representing an unauthenticated state. Being in this state implies that the user has
- * not yet logged in. Only login and logout are allowed in this state.
+ * An object representing an unauthenticated state. Being in this state implies that the user has not yet logged in. Only login and logout are allowed
+ * in this state.
*
* @author Chandrasekhar Ramakrishnan
*/
@@ -378,8 +371,8 @@ class UnauthenticatedState extends AbstractCinaFacadeState
}
/**
- * An object representing an authenticated state. Being in this state means that the user has logged
- * in and all operations are available, except login.
+ * An object representing an authenticated state. Being in this state means that the user has logged in and all operations are available, except
+ * login.
*
* @author Chandrasekhar Ramakrishnan
*/
diff --git a/rtd_cina/source/java/ch/systemsx/cisd/cina/dss/CinaImageDataSetInformation.java b/rtd_cina/source/java/ch/systemsx/cisd/cina/dss/CinaImageDataSetInformation.java
index 6c18d58b8f85faea12612bf4da75d5049a2f0e95..f9f3a3dac1e1daae933671fce8ec77c9f4e2f8ff 100644
--- a/rtd_cina/source/java/ch/systemsx/cisd/cina/dss/CinaImageDataSetInformation.java
+++ b/rtd_cina/source/java/ch/systemsx/cisd/cina/dss/CinaImageDataSetInformation.java
@@ -19,8 +19,7 @@ package ch.systemsx.cisd.cina.dss;
import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
/**
- * This class is simply used as a marker for deciding which storage processor to use. It serves no
- * other purpose.
+ * This class is simply used as a marker for deciding which storage processor to use. It serves no other purpose.
*
* @author Chandrasekhar Ramakrishnan
*/
diff --git a/rtd_cina/source/java/ch/systemsx/cisd/cina/dss/CinaImageStorageProcessor.java b/rtd_cina/source/java/ch/systemsx/cisd/cina/dss/CinaImageStorageProcessor.java
index 201f9273a2da458f7450b37c6dd07adbb82fae86..eaa442918f7a7e79919893aced2f407c3b126796 100644
--- a/rtd_cina/source/java/ch/systemsx/cisd/cina/dss/CinaImageStorageProcessor.java
+++ b/rtd_cina/source/java/ch/systemsx/cisd/cina/dss/CinaImageStorageProcessor.java
@@ -23,8 +23,7 @@ import ch.systemsx.cisd.openbis.dss.etl.MicroscopyBlackboxSeriesStorageProcessor
import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
/**
- * An extension of the {@link MicroscopyBlackboxSeriesStorageProcessor} that accepts a particular
- * subclass of DataSetInformation.
+ * An extension of the {@link MicroscopyBlackboxSeriesStorageProcessor} that accepts a particular subclass of DataSetInformation.
*
* @author Chandrasekhar Ramakrishnan
*/
diff --git a/rtd_cina/source/java/ch/systemsx/cisd/cina/dss/bundle/CinaBundleDataSetHandler.java b/rtd_cina/source/java/ch/systemsx/cisd/cina/dss/bundle/CinaBundleDataSetHandler.java
index c87fd35eabffbef89aa96b25dc05e3892ffd7d3e..404d663a623dbc8ac9f1cddbee5002a2fcb658e8 100644
--- a/rtd_cina/source/java/ch/systemsx/cisd/cina/dss/bundle/CinaBundleDataSetHandler.java
+++ b/rtd_cina/source/java/ch/systemsx/cisd/cina/dss/bundle/CinaBundleDataSetHandler.java
@@ -28,12 +28,10 @@ import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
/**
- * CINA registers data in the form of a bundle. A bundle contains several different kinds data sets.
- * The CinaBundleDataSetHandler breaks apart the data into several pieces and takes action on each
- * of those pieces.
+ * CINA registers data in the form of a bundle. A bundle contains several different kinds data sets. The CinaBundleDataSetHandler breaks apart the
+ * data into several pieces and takes action on each of those pieces.
* <p>
- * The structure of the bundle mirrors the structure of CINA experiments and is made up of the
- * following pieces:
+ * The structure of the bundle mirrors the structure of CINA experiments and is made up of the following pieces:
* <ul>
* <li>Grid Preparation (a template for grids which are imaged by microscopes)</li>
* <ul>
@@ -71,8 +69,7 @@ import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
* <li>Create datasets for each of the annotated images in the data set</li>
* </ul>
* </li>
- * <li>Create a bundle data set which points to the metadata and original data sets we registered
- * above</li>
+ * <li>Create a bundle data set which points to the metadata and original data sets we registered above</li>
* <li>Update the grid preparation's metadata</li>
* </ul>
*
diff --git a/rtd_cina/source/java/ch/systemsx/cisd/cina/dss/bundle/registrators/BundleDataSetHelper.java b/rtd_cina/source/java/ch/systemsx/cisd/cina/dss/bundle/registrators/BundleDataSetHelper.java
index 9a0d28bfe865cf8a91f3f0f9c810ba921e564e6a..c4b46d08e245d84cc2a86e59d956e0e8be7a62b6 100644
--- a/rtd_cina/source/java/ch/systemsx/cisd/cina/dss/bundle/registrators/BundleDataSetHelper.java
+++ b/rtd_cina/source/java/ch/systemsx/cisd/cina/dss/bundle/registrators/BundleDataSetHelper.java
@@ -52,8 +52,8 @@ abstract class BundleDataSetHelper
}
/**
- * Get all the data set information that has been created as a result of
- * {@link #registerDataSet}. Only makes sense to invoke after registerDataSet has been called
+ * Get all the data set information that has been created as a result of {@link #registerDataSet}. Only makes sense to invoke after
+ * registerDataSet has been called
*/
public ArrayList<DataSetInformation> getDataSetInformation()
{
@@ -77,8 +77,7 @@ abstract class BundleDataSetHelper
}
/**
- * Register a file which is already in the store as a data set and add it to the
- * dataSetInformation collection.
+ * Register a file which is already in the store as a data set and add it to the dataSetInformation collection.
* <p>
* Since the file is already in the store, the new data set contains a (hard) link to it.
*
diff --git a/rtd_cina/source/java/ch/systemsx/cisd/cina/shared/constants/BundleStructureConstants.java b/rtd_cina/source/java/ch/systemsx/cisd/cina/shared/constants/BundleStructureConstants.java
index 7cc3ac31ce8baffa1091271190f02d07df144d0a..31ef3170145f0ab062347f53bddf2d595673c70f 100644
--- a/rtd_cina/source/java/ch/systemsx/cisd/cina/shared/constants/BundleStructureConstants.java
+++ b/rtd_cina/source/java/ch/systemsx/cisd/cina/shared/constants/BundleStructureConstants.java
@@ -41,8 +41,7 @@ package ch.systemsx.cisd.cina.shared.constants;
* <li>Collection Folder</li>
* </ul>
* </ul>
- * A note for understanding the constants: Collections were once called replicas, and the old name
- * has not yet been removed everywere.
+ * A note for understanding the constants: Collections were once called replicas, and the old name has not yet been removed everywere.
*
* @author Chandrasekhar Ramakrishnan
*/
@@ -51,7 +50,7 @@ public class BundleStructureConstants
public static final String COLLECTIONS_FOLDER_NAME = "Collections";
public static final String METADATA_FOLDER_NAME = "Annotations";
-
+
public static final String RAW_IMAGES_FOLDER_NAME = "RawData";
public static final String ANNOTATED_IMAGES_FOLDER_NAME = "Representations";
@@ -59,9 +58,9 @@ public class BundleStructureConstants
public static final String BUNDLE_METADATA_FOLDER_NAME = "Annotations";
public static final String BUNDLE_METADATA_FILE_NAME = "CollectionMetadata.xml";
-
+
public static final String OLD_BUNDLE_METADATA_FILE_NAME = "BundleMetadata.xml";
-
+
public final static String IMAGE_METADATA_FILE_NAME = "metadata.xml";
public static final String GRID_PREP_SAMPLE_CODE_KEY = "database id";
diff --git a/rtd_cina/source/java/ch/systemsx/cisd/cina/shared/constants/CinaConstants.java b/rtd_cina/source/java/ch/systemsx/cisd/cina/shared/constants/CinaConstants.java
index b63d10895f28fc55246d3364e4f605d547e7bc3b..3421f6ed26d18d760c04edb7a14ec2aca6013279 100644
--- a/rtd_cina/source/java/ch/systemsx/cisd/cina/shared/constants/CinaConstants.java
+++ b/rtd_cina/source/java/ch/systemsx/cisd/cina/shared/constants/CinaConstants.java
@@ -17,8 +17,7 @@
package ch.systemsx.cisd.cina.shared.constants;
/**
- * A note for understanding the constants: Collections were once called replicas, and the old name
- * has not yet been removed everywere.
+ * A note for understanding the constants: Collections were once called replicas, and the old name has not yet been removed everywere.
*
* @author Chandrasekhar Ramakrishnan
*/
diff --git a/rtd_cina/source/java/ch/systemsx/cisd/cina/shared/labview/package-info.java b/rtd_cina/source/java/ch/systemsx/cisd/cina/shared/labview/package-info.java
index cb55cc2123d6c2ddf69a31b53c3d8ea385d4cc54..66a20f1ca3a19f3e63bdc61ddd00cf95722f3497 100644
--- a/rtd_cina/source/java/ch/systemsx/cisd/cina/shared/labview/package-info.java
+++ b/rtd_cina/source/java/ch/systemsx/cisd/cina/shared/labview/package-info.java
@@ -1,6 +1,6 @@
// Annotatations for the XML parser
@javax.xml.bind.annotation.XmlSchema(xmlns =
- {
- @javax.xml.bind.annotation.XmlNs(prefix = "lv", namespaceURI = "http://www.ni.com/LVData"),
- @javax.xml.bind.annotation.XmlNs(prefix = "xsd", namespaceURI = "http://www.w3.org/2001/XMLSchema") })
+{
+ @javax.xml.bind.annotation.XmlNs(prefix = "lv", namespaceURI = "http://www.ni.com/LVData"),
+ @javax.xml.bind.annotation.XmlNs(prefix = "xsd", namespaceURI = "http://www.w3.org/2001/XMLSchema") })
package ch.systemsx.cisd.cina.shared.labview;
\ No newline at end of file
diff --git a/rtd_cina/source/java/ch/systemsx/cisd/cina/shared/metadata/BundleMetadataExtractor.java b/rtd_cina/source/java/ch/systemsx/cisd/cina/shared/metadata/BundleMetadataExtractor.java
index a0bf2d3969b1349187047ed57197f838fac46133..1d4337e343d2ee1dd1315e8ad7783e9848b42ed2 100644
--- a/rtd_cina/source/java/ch/systemsx/cisd/cina/shared/metadata/BundleMetadataExtractor.java
+++ b/rtd_cina/source/java/ch/systemsx/cisd/cina/shared/metadata/BundleMetadataExtractor.java
@@ -32,7 +32,7 @@ public class BundleMetadataExtractor
{
private static final String COLLECTIONS_FOLDER_NAME =
BundleStructureConstants.COLLECTIONS_FOLDER_NAME;
-
+
private static final String METADATA_FOLDER_NAME =
BundleStructureConstants.METADATA_FOLDER_NAME;
@@ -89,8 +89,8 @@ public class BundleMetadataExtractor
}
/**
- * Get the metadata extractors for each of the replica files in this bundle. The method
- * {@link #prepare} must be called before getting the metadata extractors.
+ * Get the metadata extractors for each of the replica files in this bundle. The method {@link #prepare} must be called before getting the
+ * metadata extractors.
*/
public List<CollectionMetadataExtractor> getReplicaMetadataExtractors()
{
@@ -112,12 +112,12 @@ public class BundleMetadataExtractor
private void processDirectory(File file)
{
File annotationsDirectory = new File(file, METADATA_FOLDER_NAME);
-
+
if (false == annotationsDirectory.exists())
{
return;
}
-
+
if (false == annotationsDirectory.isDirectory())
{
return;
@@ -151,7 +151,7 @@ public class BundleMetadataExtractor
{
continue;
}
-
+
processDirectory(replicaFile);
}
}
diff --git a/rtd_cina/source/java/ch/systemsx/cisd/cina/shared/metadata/CollectionMetadataExtractor.java b/rtd_cina/source/java/ch/systemsx/cisd/cina/shared/metadata/CollectionMetadataExtractor.java
index d0473ca7bd1f09bd5c7a65a18d3e8431c9a4a158..5c41b486d9a59d1527914619c6b353833c350373 100644
--- a/rtd_cina/source/java/ch/systemsx/cisd/cina/shared/metadata/CollectionMetadataExtractor.java
+++ b/rtd_cina/source/java/ch/systemsx/cisd/cina/shared/metadata/CollectionMetadataExtractor.java
@@ -74,7 +74,7 @@ public class CollectionMetadataExtractor implements IMetadataExtractor
// We've already parsed this
return;
}
-
+
// First parse the metadata for the replica
File metadataFile = new File(folder, REPLICA_METADATA_FILE_NAME);
lvdata = LVDataParser.parse(metadataFile);
@@ -100,8 +100,7 @@ public class CollectionMetadataExtractor implements IMetadataExtractor
}
/**
- * Get the metadata extracted from the file in the form of a map. The method {@link #prepare}
- * must be called before getting the metadata map.
+ * Get the metadata extracted from the file in the form of a map. The method {@link #prepare} must be called before getting the metadata map.
*/
@Override
public Map<String, String> getMetadataMap()
@@ -111,8 +110,8 @@ public class CollectionMetadataExtractor implements IMetadataExtractor
}
/**
- * Get the metadata extractors for each of the image files for this replica. The method
- * {@link #prepare} must be called before getting the metadata extractors.
+ * Get the metadata extractors for each of the image files for this replica. The method {@link #prepare} must be called before getting the
+ * metadata extractors.
*/
public List<ImageMetadataExtractor> getImageMetadataExtractors()
{
diff --git a/rtd_cina/source/java/ch/systemsx/cisd/cina/shared/metadata/ImageMetadataExtractor.java b/rtd_cina/source/java/ch/systemsx/cisd/cina/shared/metadata/ImageMetadataExtractor.java
index 6dc37ac8484437dd54c6b4a4b17acafddd1c9892..b0198290fb9a1fa7174894068d6df76b8c08003f 100644
--- a/rtd_cina/source/java/ch/systemsx/cisd/cina/shared/metadata/ImageMetadataExtractor.java
+++ b/rtd_cina/source/java/ch/systemsx/cisd/cina/shared/metadata/ImageMetadataExtractor.java
@@ -73,8 +73,7 @@ public class ImageMetadataExtractor implements IMetadataExtractor
/**
* Read the files and fill the metadata map.
*
- * @throws IllegalArgumentException If there is not metadata.xml file in the folder or if the
- * file is faulty.
+ * @throws IllegalArgumentException If there is not metadata.xml file in the folder or if the file is faulty.
*/
public void prepare() throws IllegalArgumentException
{
@@ -102,8 +101,7 @@ public class ImageMetadataExtractor implements IMetadataExtractor
}
/**
- * Get the metadata extracted from the file in the form of a map. The method {@link #prepare}
- * must be called before getting the metadata map.
+ * Get the metadata extracted from the file in the form of a map. The method {@link #prepare} must be called before getting the metadata map.
*/
@Override
public Map<String, String> getMetadataMap()
diff --git a/rtd_cina/source/java/ch/systemsx/cisd/cina/shared/metadata/LabViewXMLToHashMap.java b/rtd_cina/source/java/ch/systemsx/cisd/cina/shared/metadata/LabViewXMLToHashMap.java
index 5f152c2bdfdded808ef8cfeb20acdd9ad2e49588..b8ecc487b8015d81705daf03942fd7bded9968a5 100644
--- a/rtd_cina/source/java/ch/systemsx/cisd/cina/shared/metadata/LabViewXMLToHashMap.java
+++ b/rtd_cina/source/java/ch/systemsx/cisd/cina/shared/metadata/LabViewXMLToHashMap.java
@@ -54,8 +54,7 @@ class LabViewXMLToHashMap
}
/**
- * Constructor for converting lvdata into the metadataMap, specifying a mapping from cluster
- * prefixes to key prefixes
+ * Constructor for converting lvdata into the metadataMap, specifying a mapping from cluster prefixes to key prefixes
*
* @param lvdata The XML Data
* @param metadataMap The map to append the converted content into
diff --git a/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/DependencyCheckingTest.java b/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/DependencyCheckingTest.java
index 8a2329d664a1cb50970549427f62e3b780daa368..63f5664fba797d45cf42f815d6c8a91090930eb2 100644
--- a/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/DependencyCheckingTest.java
+++ b/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/DependencyCheckingTest.java
@@ -17,8 +17,6 @@
package ch.systemsx.cisd.cina;
/**
- *
- *
* @author Franz-Josef Elmer
*/
public class DependencyCheckingTest extends ch.systemsx.cisd.common.test.DependencyCheckingTest
diff --git a/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/client/util/cli/CinaCommandFactoryTest.java b/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/client/util/cli/CinaCommandFactoryTest.java
index 77d79564e738054482c7eb1359cb5d280a9cf8c1..159ae501730cd77968d8a4bb65445c23998c197a 100644
--- a/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/client/util/cli/CinaCommandFactoryTest.java
+++ b/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/client/util/cli/CinaCommandFactoryTest.java
@@ -57,13 +57,13 @@ public class CinaCommandFactoryTest extends AssertJUnit
System.out.print("\n");
cmd = factory.tryCommandForName("help");
String[] lsArgs =
- { "preps" };
+ { "preps" };
cmd.execute(lsArgs);
System.out.print("\n");
cmd = factory.tryCommandForName("help");
String[] getArgs =
- { "genid" };
+ { "genid" };
cmd.execute(getArgs);
}
}
diff --git a/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/client/util/cli/CommandExperimentListerTest.java b/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/client/util/cli/CommandExperimentListerTest.java
index 8208cdbe30f738c619f9d49c0e3fac2557bbb474..5da16c833f5f4ed3ad04cb9e546d21d24b7e311d 100644
--- a/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/client/util/cli/CommandExperimentListerTest.java
+++ b/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/client/util/cli/CommandExperimentListerTest.java
@@ -122,7 +122,7 @@ public class CommandExperimentListerTest extends AssertJUnit
ICommand command = new MockCommandExperimentLister();
ResultCode exitCode = command.execute(new String[]
- { "-s", "url", "-u", USER_ID, "-p", PASSWORD, "EXP-TYPE" });
+ { "-s", "url", "-u", USER_ID, "-p", PASSWORD, "EXP-TYPE" });
assertEquals(ResultCode.OK, exitCode);
context.assertIsSatisfied();
@@ -150,7 +150,7 @@ public class CommandExperimentListerTest extends AssertJUnit
try
{
command.execute(new String[]
- { "-s", "url", "-u", USER_ID, "-p", PASSWORD, "EXP-TYPE" });
+ { "-s", "url", "-u", USER_ID, "-p", PASSWORD, "EXP-TYPE" });
fail("Command should throw an exception when run against an older version of the interface.");
} catch (EnvironmentFailureException e)
{
diff --git a/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/client/util/cli/CommandGenerateSampleCodeTest.java b/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/client/util/cli/CommandGenerateSampleCodeTest.java
index 19719710a04a7e1109dda118a0b8b859b38476d3..540f21746329ceab4c3b0954b04d1d970dd05ced 100644
--- a/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/client/util/cli/CommandGenerateSampleCodeTest.java
+++ b/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/client/util/cli/CommandGenerateSampleCodeTest.java
@@ -107,7 +107,7 @@ public class CommandGenerateSampleCodeTest extends AssertJUnit
ICommand command = new MockCommandGenerateSampleCode();
ResultCode exitCode = command.execute(new String[]
- { "-s", "url", "-u", USER_ID, "-p", PASSWORD, sampleTypeCode });
+ { "-s", "url", "-u", USER_ID, "-p", PASSWORD, sampleTypeCode });
assertEquals(ResultCode.OK, exitCode);
context.assertIsSatisfied();
@@ -125,7 +125,7 @@ public class CommandGenerateSampleCodeTest extends AssertJUnit
ICommand command = new MockCommandGenerateSampleCode();
ResultCode exitCode = command.execute(new String[]
- { "-s", "url", "-u", USER_ID, "-p", PASSWORD });
+ { "-s", "url", "-u", USER_ID, "-p", PASSWORD });
assertEquals(ResultCode.INVALID_ARGS, exitCode);
context.assertIsSatisfied();
diff --git a/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/client/util/cli/CommandGetBundleTest.java b/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/client/util/cli/CommandGetBundleTest.java
index 6b33754cfc664235f98fbb7504e62c653ec65ff8..23b0f6e97d61d6ddb35ab6c10b8629c4947f1872 100644
--- a/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/client/util/cli/CommandGetBundleTest.java
+++ b/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/client/util/cli/CommandGetBundleTest.java
@@ -365,7 +365,7 @@ public class CommandGetBundleTest extends AbstractFileSystemTestCase
{
String[] bundleContents = outputFolder.list();
Arrays.sort(bundleContents);
-
+
assertEquals(BundleStructureConstants.METADATA_FOLDER_NAME, bundleContents[0]);
assertEquals(BundleStructureConstants.OLD_BUNDLE_METADATA_FILE_NAME, bundleContents[1]);
assertEquals(BundleStructureConstants.RAW_IMAGES_FOLDER_NAME, bundleContents[2]);
@@ -385,8 +385,8 @@ public class CommandGetBundleTest extends AbstractFileSystemTestCase
ResultCode exitCode =
command.execute(new String[]
- { "-s", "url", "-u", USER_ID, "-p", PASSWORD, "-o", outputFolder.getPath(),
- "/SPACE/GRID-ID" });
+ { "-s", "url", "-u", USER_ID, "-p", PASSWORD, "-o", outputFolder.getPath(),
+ "/SPACE/GRID-ID" });
assertEquals(ResultCode.OK, exitCode);
@@ -403,15 +403,15 @@ public class CommandGetBundleTest extends AbstractFileSystemTestCase
{
setupAuthenticationExpectations();
List<String> sampleCodes = Arrays.asList(new String[]
- { "REPLICA-ID1", "REPLICA-ID2" });
+ { "REPLICA-ID1", "REPLICA-ID2" });
setupListDataSetsExpectations(sampleCodes);
setupDownloadDataSetExpectations(sampleCodes);
ICommand command = new MockCommandGetBundle();
File outputFolder = new File(workingDirectory, "Foo.bundle/");
ResultCode exitCode =
command.execute(new String[]
- { "-s", "url", "-u", USER_ID, "-p", PASSWORD, "-o", outputFolder.getPath(),
- "/SPACE/GRID-ID" });
+ { "-s", "url", "-u", USER_ID, "-p", PASSWORD, "-o", outputFolder.getPath(),
+ "/SPACE/GRID-ID" });
assertEquals(ResultCode.OK, exitCode); // Check the contents of the bundle
verifyBundleTopLevel(outputFolder);
verifyRawDataContents(outputFolder, 2);
@@ -424,15 +424,15 @@ public class CommandGetBundleTest extends AbstractFileSystemTestCase
{
setupAuthenticationExpectations();
List<String> sampleCodes = Arrays.asList(new String[]
- { "REPLICA-ID1", "REPLICA-ID2" });
+ { "REPLICA-ID1", "REPLICA-ID2" });
setupListDataSetsExpectations(sampleCodes);
setupDownloadDataSetExpectations("REPLICA-ID2");
ICommand command = new MockCommandGetBundle();
File outputFolder = new File(workingDirectory, "Foo.bundle/");
ResultCode exitCode =
command.execute(new String[]
- { "-s", "url", "-u", USER_ID, "-p", PASSWORD, "-o", outputFolder.getPath(),
- "/SPACE/GRID-ID", "/SPACE/REPLICA-ID2" });
+ { "-s", "url", "-u", USER_ID, "-p", PASSWORD, "-o", outputFolder.getPath(),
+ "/SPACE/GRID-ID", "/SPACE/REPLICA-ID2" });
assertEquals(ResultCode.OK, exitCode); // Check the contents of the bundle
verifyBundleTopLevel(outputFolder);
verifyRawDataContents(outputFolder, 1);
@@ -482,7 +482,7 @@ public class CommandGetBundleTest extends AbstractFileSystemTestCase
try
{
command.execute(new String[]
- { "-s", "url", "-u", USER_ID, "-p", PASSWORD, "GRID-ID", "REPLICA-ID" });
+ { "-s", "url", "-u", USER_ID, "-p", PASSWORD, "GRID-ID", "REPLICA-ID" });
fail("Command should throw an exception when run against an older version of the interface.");
} catch (EnvironmentFailureException e)
{
diff --git a/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/client/util/cli/CommandGetReplicaTest.java b/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/client/util/cli/CommandGetReplicaTest.java
index c990c5601ab9c2de8d7d7804831a739096b7f496..b239b44115bda1eb20ab38ab08cb29ad9ef5a235 100644
--- a/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/client/util/cli/CommandGetReplicaTest.java
+++ b/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/client/util/cli/CommandGetReplicaTest.java
@@ -341,8 +341,8 @@ public class CommandGetReplicaTest extends AbstractFileSystemTestCase
ResultCode exitCode =
command.execute(new String[]
- { "-s", "url", "-u", USER_ID, "-p", PASSWORD, "-o", outputFolder.getPath(),
- "/SPACE/REPLICA-ID" });
+ { "-s", "url", "-u", USER_ID, "-p", PASSWORD, "-o", outputFolder.getPath(),
+ "/SPACE/REPLICA-ID" });
assertEquals(ResultCode.OK, exitCode);
@@ -371,8 +371,8 @@ public class CommandGetReplicaTest extends AbstractFileSystemTestCase
ResultCode exitCode =
command.execute(new String[]
- { "-s", "url", "-u", USER_ID, "-p", PASSWORD, "-o", outputFolder.getPath(),
- "/SPACE/REPLICA-ID1", "/SPACE/REPLICA-ID2" });
+ { "-s", "url", "-u", USER_ID, "-p", PASSWORD, "-o", outputFolder.getPath(),
+ "/SPACE/REPLICA-ID1", "/SPACE/REPLICA-ID2" });
assertEquals(ResultCode.OK, exitCode);
@@ -406,7 +406,7 @@ public class CommandGetReplicaTest extends AbstractFileSystemTestCase
try
{
command.execute(new String[]
- { "-s", "url", "-u", USER_ID, "-p", PASSWORD, "/SPACE/REPLICA-ID" });
+ { "-s", "url", "-u", USER_ID, "-p", PASSWORD, "/SPACE/REPLICA-ID" });
fail("Command should throw an exception when run against an older version of the interface.");
} catch (EnvironmentFailureException e)
{
diff --git a/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/client/util/cli/CommandPreferencesListerTest.java b/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/client/util/cli/CommandPreferencesListerTest.java
index 06c605b635fed0c38fe7d0c501d800e36568aac9..89bb61a14a0ab825f7d40aaa20d305753e51e26f 100644
--- a/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/client/util/cli/CommandPreferencesListerTest.java
+++ b/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/client/util/cli/CommandPreferencesListerTest.java
@@ -119,7 +119,7 @@ public class CommandPreferencesListerTest extends AssertJUnit
ICommand command = new MockPreferencesList();
ResultCode exitCode = command.execute(new String[]
- { "-s", "url", "-u", USER_ID, "-p", PASSWORD });
+ { "-s", "url", "-u", USER_ID, "-p", PASSWORD });
assertEquals(ResultCode.OK, exitCode);
context.assertIsSatisfied();
@@ -160,8 +160,8 @@ public class CommandPreferencesListerTest extends AssertJUnit
ResultCode exitCode =
command.execute(new String[]
- { "-s", "url", "-u", USER_ID, "-p", PASSWORD,
- CinaConstants.CINA_BROWSER_PREFERENCES_TYPE_CODE });
+ { "-s", "url", "-u", USER_ID, "-p", PASSWORD,
+ CinaConstants.CINA_BROWSER_PREFERENCES_TYPE_CODE });
assertEquals(ResultCode.OK, exitCode);
context.assertIsSatisfied();
@@ -189,8 +189,8 @@ public class CommandPreferencesListerTest extends AssertJUnit
try
{
command.execute(new String[]
- { "-s", "url", "-u", USER_ID, "-p", PASSWORD,
- CinaConstants.COLLECTION_SAMPLE_TYPE_CODE });
+ { "-s", "url", "-u", USER_ID, "-p", PASSWORD,
+ CinaConstants.COLLECTION_SAMPLE_TYPE_CODE });
fail("Command should throw an exception when run against an older version of the interface.");
} catch (EnvironmentFailureException e)
{
diff --git a/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/client/util/cli/CommandSampleListerTest.java b/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/client/util/cli/CommandSampleListerTest.java
index ecc7b63eaf1fea56e1f04d4308e92d3f69c547c7..4d0f5c6749fbf6dc39b206488a126838bbd7d8fc 100644
--- a/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/client/util/cli/CommandSampleListerTest.java
+++ b/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/client/util/cli/CommandSampleListerTest.java
@@ -113,7 +113,7 @@ public class CommandSampleListerTest extends AssertJUnit
ICommand command = new MockCommandSampleLister();
ResultCode exitCode = command.execute(new String[]
- { "-s", "url", "-u", USER_ID, "-p", PASSWORD });
+ { "-s", "url", "-u", USER_ID, "-p", PASSWORD });
assertEquals(ResultCode.OK, exitCode);
context.assertIsSatisfied();
@@ -148,8 +148,8 @@ public class CommandSampleListerTest extends AssertJUnit
ResultCode exitCode =
command.execute(new String[]
- { "-s", "url", "-u", USER_ID, "-p", PASSWORD,
- CinaConstants.GRID_PREP_SAMPLE_TYPE_CODE });
+ { "-s", "url", "-u", USER_ID, "-p", PASSWORD,
+ CinaConstants.GRID_PREP_SAMPLE_TYPE_CODE });
assertEquals(ResultCode.OK, exitCode);
context.assertIsSatisfied();
@@ -177,8 +177,8 @@ public class CommandSampleListerTest extends AssertJUnit
try
{
command.execute(new String[]
- { "-s", "url", "-u", USER_ID, "-p", PASSWORD,
- CinaConstants.COLLECTION_SAMPLE_TYPE_CODE });
+ { "-s", "url", "-u", USER_ID, "-p", PASSWORD,
+ CinaConstants.COLLECTION_SAMPLE_TYPE_CODE });
fail("Command should throw an exception when run against an older version of the interface.");
} catch (EnvironmentFailureException e)
{
diff --git a/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/dss/bundle/CinaBundleDataSetHandlerTest.java b/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/dss/bundle/CinaBundleDataSetHandlerTest.java
index 0887af3aa7794c1f54b1065b4689a5f531dae0e7..9fcf806b0345fc764586349dc046d26344229dd5 100644
--- a/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/dss/bundle/CinaBundleDataSetHandlerTest.java
+++ b/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/dss/bundle/CinaBundleDataSetHandlerTest.java
@@ -31,8 +31,8 @@ public class CinaBundleDataSetHandlerTest extends CinaBundleRegistrationTest
private CinaBundleDataSetHandler handler;
/**
- * First set up expectations for the case that the entities do not exist, then set up the
- * expectations for existing entities to simulate registering new entities.
+ * First set up expectations for the case that the entities do not exist, then set up the expectations for existing entities to simulate
+ * registering new entities.
*/
@Test
public void testHandlingWithCreationOfNewEntities()
diff --git a/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/dss/bundle/registrators/GridPreparationRegistratorTest.java b/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/dss/bundle/registrators/GridPreparationRegistratorTest.java
index 979e32d4426073c14f30f090b579eb22751583e9..bb9e9b4ed4a88e2bfcf81ff5522904424592701d 100644
--- a/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/dss/bundle/registrators/GridPreparationRegistratorTest.java
+++ b/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/dss/bundle/registrators/GridPreparationRegistratorTest.java
@@ -31,7 +31,7 @@ public class GridPreparationRegistratorTest extends CinaBundleRegistrationTest
protected GridPreparationRegistrator registrator;
@Test(expectedExceptions =
- { AssertionError.class })
+ { AssertionError.class })
public void testRegistratorWithoutUserSuppliedExperiment()
{
setupOpenBisExpectations();
@@ -57,8 +57,8 @@ public class GridPreparationRegistratorTest extends CinaBundleRegistrationTest
}
/**
- * First set up expectations for the case that the entities do not exist, then set up the
- * expectations for existing entities to simulate registering new entities.
+ * First set up expectations for the case that the entities do not exist, then set up the expectations for existing entities to simulate
+ * registering new entities.
*/
@Test
public void testRegistratorForNewEntities()