From 45a004a1dd3c54c20357170d81719628750f7ec2 Mon Sep 17 00:00:00 2001
From: cramakri <cramakri>
Date: Mon, 11 Oct 2010 14:31:40 +0000
Subject: [PATCH] LMS-1811 Implemented generate sample code service, refactored
stuff.
SVN: 18246
---
...tCommand.java => AbstractCinaCommand.java} | 60 +---
.../client/util/cli/AbstractExecutor.java | 4 +-
.../client/util/cli/CinaCommandFactory.java | 10 +-
.../util/cli/CommandGenerateSampleCode.java | 99 +++++
.../client/util/cli/CommandSampleLister.java | 12 +-
.../cina/client/util/v1/ICinaUtilities.java | 14 +-
.../util/v1/impl/CinaUtilitiesFacade.java | 58 ++-
.../dss/info/CinaDataSetInfoExtractor.java | 176 ---------
.../cisd/cina/dss/info/CinaTypeExtractor.java | 118 ------
.../info/EntityRegistrationSuccessEmail.java | 289 ---------------
.../cisd/cina/dss/info/EntityTypes.java | 63 ----
...imentRegistrationInformationExtractor.java | 177 ---------
.../cisd/cina/dss/info/FolderOracle.java | 233 ------------
...ampleRegistrationInformationExtractor.java | 182 ----------
.../util/cli/CinaCommandFactoryTest.java | 2 +-
.../client/util/cli/CommandFactoryTest.java | 6 +-
.../cli/CommandGenerateSampleCodeTest.java | 129 +++++++
...Test.java => CommandSampleListerTest.java} | 19 +-
.../util/v1/impl/CinaUtilitiesFacadeTest.java | 55 ++-
.../cina/dss/MockDefaultStorageProcessor.java | 58 ---
.../cisd/cina/dss/StorageProcessorTest.java | 139 --------
.../info/CinaDataSetInfoExtractorTest.java | 133 -------
.../info/ExperimentMetadataExtractorTest.java | 237 ------------
.../cisd/cina/dss/info/FolderOracleTest.java | 88 -----
.../dss/info/SampleMetadataExtractorTest.java | 337 ------------------
.../ambiguous-data-folder/dataset.properties | 3 -
.../ambiguous-data-folder/sample.properties | 3 -
.../dataset-data-folder/dataset.properties | 3 -
.../dss/info/dataset-data-folder/metadata.xml | 63 ----
.../dss/info/empty-data-folder/.gitignore | 0
.../experiment.properties | 3 -
.../info/sample-data-folder/sample.properties | 3 -
32 files changed, 380 insertions(+), 2396 deletions(-)
rename rtd_cina/source/java/ch/systemsx/cisd/cina/client/util/cli/{AbstractCommand.java => AbstractCinaCommand.java} (53%)
create mode 100644 rtd_cina/source/java/ch/systemsx/cisd/cina/client/util/cli/CommandGenerateSampleCode.java
delete mode 100644 rtd_cina/source/java/ch/systemsx/cisd/cina/dss/info/CinaDataSetInfoExtractor.java
delete mode 100644 rtd_cina/source/java/ch/systemsx/cisd/cina/dss/info/CinaTypeExtractor.java
delete mode 100644 rtd_cina/source/java/ch/systemsx/cisd/cina/dss/info/EntityRegistrationSuccessEmail.java
delete mode 100644 rtd_cina/source/java/ch/systemsx/cisd/cina/dss/info/EntityTypes.java
delete mode 100644 rtd_cina/source/java/ch/systemsx/cisd/cina/dss/info/ExperimentRegistrationInformationExtractor.java
delete mode 100644 rtd_cina/source/java/ch/systemsx/cisd/cina/dss/info/FolderOracle.java
delete mode 100644 rtd_cina/source/java/ch/systemsx/cisd/cina/dss/info/SampleRegistrationInformationExtractor.java
create mode 100644 rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/client/util/cli/CommandGenerateSampleCodeTest.java
rename rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/client/util/cli/{SampleListerCommandTest.java => CommandSampleListerTest.java} (92%)
delete mode 100644 rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/dss/MockDefaultStorageProcessor.java
delete mode 100644 rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/dss/StorageProcessorTest.java
delete mode 100644 rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/dss/info/CinaDataSetInfoExtractorTest.java
delete mode 100644 rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/dss/info/ExperimentMetadataExtractorTest.java
delete mode 100644 rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/dss/info/FolderOracleTest.java
delete mode 100644 rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/dss/info/SampleMetadataExtractorTest.java
delete mode 100644 rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/dss/info/ambiguous-data-folder/dataset.properties
delete mode 100644 rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/dss/info/ambiguous-data-folder/sample.properties
delete mode 100644 rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/dss/info/dataset-data-folder/dataset.properties
delete mode 100644 rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/dss/info/dataset-data-folder/metadata.xml
delete mode 100644 rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/dss/info/empty-data-folder/.gitignore
delete mode 100644 rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/dss/info/experiment-data-folder/experiment.properties
delete mode 100644 rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/dss/info/sample-data-folder/sample.properties
diff --git a/rtd_cina/source/java/ch/systemsx/cisd/cina/client/util/cli/AbstractCommand.java b/rtd_cina/source/java/ch/systemsx/cisd/cina/client/util/cli/AbstractCinaCommand.java
similarity index 53%
rename from rtd_cina/source/java/ch/systemsx/cisd/cina/client/util/cli/AbstractCommand.java
rename to rtd_cina/source/java/ch/systemsx/cisd/cina/client/util/cli/AbstractCinaCommand.java
index 88540021853..b583ec0ccd7 100644
--- a/rtd_cina/source/java/ch/systemsx/cisd/cina/client/util/cli/AbstractCommand.java
+++ b/rtd_cina/source/java/ch/systemsx/cisd/cina/client/util/cli/AbstractCinaCommand.java
@@ -16,14 +16,10 @@
package ch.systemsx.cisd.cina.client.util.cli;
-import java.io.PrintStream;
-
-import ch.systemsx.cisd.args4j.CmdLineParser;
-import ch.systemsx.cisd.args4j.ExampleMode;
import ch.systemsx.cisd.cina.client.util.v1.CinaUtilitiesFacadeFactory;
import ch.systemsx.cisd.cina.client.util.v1.ICinaUtilities;
+import ch.systemsx.cisd.openbis.dss.client.api.cli.AbstractCommand;
import ch.systemsx.cisd.openbis.dss.client.api.cli.GlobalArguments;
-import ch.systemsx.cisd.openbis.dss.client.api.cli.ICommand;
/**
* Superclass for cina command-line client commands.
@@ -36,54 +32,20 @@ import ch.systemsx.cisd.openbis.dss.client.api.cli.ICommand;
*
* @author Chandrasekhar Ramakrishnan
*/
-abstract class AbstractCommand<T extends GlobalArguments> implements ICommand
+abstract class AbstractCinaCommand<T extends GlobalArguments> extends AbstractCommand<T>
{
- // The parser for command-line arguments; set by subclasses in the constructor.
- protected final CmdLineParser parser;
-
- // The object that describes and receives the value of the arguments
- protected final T arguments;
-
- protected AbstractCommand(T arguments)
- {
- this.parser = new CmdLineParser(arguments);
- this.arguments = arguments;
- }
-
- /**
- * Print usage information about the command.
- */
- public void printUsage(PrintStream out)
- {
- out.println(getUsagePrefixString() + " [options]");
- parser.printUsage(out);
- out.println(" Example : " + getCommandCallString() + " "
- + parser.printExample(ExampleMode.ALL) + "");
- }
-
- /**
- * How is this command invoked from the command line? This is the program call string + command
- * name
- */
- protected String getCommandCallString()
- {
- return getProgramCallString() + " " + getName();
- }
-
- /**
- * Used for displaying help.
- */
- protected String getUsagePrefixString()
+ protected AbstractCinaCommand(T arguments)
{
- return "usage: " + getCommandCallString();
+ super(arguments);
}
/**
* How is this program invoked from the command line?
*/
+ @Override
protected String getProgramCallString()
{
- return "cina_client.sh";
+ return CinaCommandFactory.PROGRAM_CALL_STRING;
}
/**
@@ -100,14 +62,4 @@ abstract class AbstractCommand<T extends GlobalArguments> implements ICommand
}
return component;
}
-
- CmdLineParser getParser()
- {
- return parser;
- }
-
- T getArguments()
- {
- return arguments;
- }
}
diff --git a/rtd_cina/source/java/ch/systemsx/cisd/cina/client/util/cli/AbstractExecutor.java b/rtd_cina/source/java/ch/systemsx/cisd/cina/client/util/cli/AbstractExecutor.java
index 1453784a21e..b370baa3bbd 100644
--- a/rtd_cina/source/java/ch/systemsx/cisd/cina/client/util/cli/AbstractExecutor.java
+++ b/rtd_cina/source/java/ch/systemsx/cisd/cina/client/util/cli/AbstractExecutor.java
@@ -29,9 +29,9 @@ abstract class AbstractExecutor<A extends GlobalArguments>
private final CmdLineParser parser;
- private final AbstractCommand<A> command;
+ private final AbstractCinaCommand<A> command;
- AbstractExecutor(AbstractCommand<A> command)
+ AbstractExecutor(AbstractCinaCommand<A> command)
{
this.command = command;
arguments = command.getArguments();
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 31fb6399b91..e3797d8e5fe 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
@@ -32,13 +32,13 @@ public class CinaCommandFactory extends AbstractCommandFactory
private static enum Command
{
- PREPS, GENID, HELP
+ LISTSAMPS, GENCODE, HELP
}
public List<String> getKnownCommands()
{
String[] commands =
- { "preps", "genid" };
+ { "listsamps", "gencode" };
return Arrays.asList(commands);
}
@@ -67,11 +67,11 @@ public class CinaCommandFactory extends AbstractCommandFactory
ICommand result;
switch (command)
{
- case PREPS:
+ case LISTSAMPS:
result = new CommandSampleLister();
break;
- case GENID:
- result = new CommandSampleLister();
+ case GENCODE:
+ result = new CommandGenerateSampleCode();
break;
case HELP:
result = new CommandHelp(this, PROGRAM_CALL_STRING);
diff --git a/rtd_cina/source/java/ch/systemsx/cisd/cina/client/util/cli/CommandGenerateSampleCode.java b/rtd_cina/source/java/ch/systemsx/cisd/cina/client/util/cli/CommandGenerateSampleCode.java
new file mode 100644
index 00000000000..8c52d14992e
--- /dev/null
+++ b/rtd_cina/source/java/ch/systemsx/cisd/cina/client/util/cli/CommandGenerateSampleCode.java
@@ -0,0 +1,99 @@
+/*
+ * Copyright 2010 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.cina.client.util.cli;
+
+import ch.systemsx.cisd.cina.client.util.v1.ICinaUtilities;
+import ch.systemsx.cisd.common.exceptions.EnvironmentFailureException;
+import ch.systemsx.cisd.common.exceptions.UserFailureException;
+import ch.systemsx.cisd.openbis.dss.client.api.cli.GlobalArguments;
+
+/**
+ * @author Chandrasekhar Ramakrishnan
+ */
+public class CommandGenerateSampleCode extends
+ AbstractCinaCommand<CommandGenerateSampleCode.CommandGenerateSampleCodeArguments>
+{
+ static class CommandGenerateSampleCodeArguments extends GlobalArguments
+ {
+ public String getSampleTypeCode()
+ {
+ return getArguments().get(0).toString().toUpperCase();
+ }
+
+ @Override
+ public boolean isComplete()
+ {
+ if (getArguments().size() < 1)
+ {
+ return false;
+ }
+ if (getSampleTypeCode().length() < 1)
+ {
+ return false;
+ }
+
+ if (false == super.isComplete())
+ return false;
+
+ return true;
+ }
+ }
+
+ private static class GenerateSampleIdExecutor extends
+ AbstractExecutor<CommandGenerateSampleCodeArguments>
+ {
+ /**
+ * @param command The parent command
+ */
+ GenerateSampleIdExecutor(CommandGenerateSampleCode command)
+ {
+ super(command);
+ }
+
+ @Override
+ protected int doExecute(ICinaUtilities component)
+ {
+ String sampleTypeCode = arguments.getSampleTypeCode();
+ String result = component.generateSampleCode(sampleTypeCode);
+ System.out.println(result);
+ return 0;
+ }
+
+ }
+
+ public CommandGenerateSampleCode()
+ {
+ super(new CommandGenerateSampleCodeArguments());
+ }
+
+ public int execute(String[] args) throws UserFailureException, EnvironmentFailureException
+ {
+ return new GenerateSampleIdExecutor(this).execute(args);
+ }
+
+ public String getName()
+ {
+ return "gencode";
+ }
+
+ @Override
+ protected String getRequiredArgumentsString()
+ {
+ return "<sample type code>";
+ }
+
+}
diff --git a/rtd_cina/source/java/ch/systemsx/cisd/cina/client/util/cli/CommandSampleLister.java b/rtd_cina/source/java/ch/systemsx/cisd/cina/client/util/cli/CommandSampleLister.java
index 19df328ef04..55c661f33d3 100644
--- a/rtd_cina/source/java/ch/systemsx/cisd/cina/client/util/cli/CommandSampleLister.java
+++ b/rtd_cina/source/java/ch/systemsx/cisd/cina/client/util/cli/CommandSampleLister.java
@@ -31,7 +31,7 @@ import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria.MatchCl
/**
* @author Chandrasekhar Ramakrishnan
*/
-public class CommandSampleLister extends AbstractCommand<GlobalArguments>
+public class CommandSampleLister extends AbstractCinaCommand<GlobalArguments>
{
private static class SampleListerExecutor extends AbstractExecutor<GlobalArguments>
{
@@ -42,7 +42,7 @@ public class CommandSampleLister extends AbstractCommand<GlobalArguments>
{
super(command);
}
-
+
@Override
protected int doExecute(ICinaUtilities component)
{
@@ -71,6 +71,12 @@ public class CommandSampleLister extends AbstractCommand<GlobalArguments>
public String getName()
{
- return "list-samples";
+ return "listsamps";
+ }
+
+ @Override
+ protected String getRequiredArgumentsString()
+ {
+ return "";
}
}
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 d600880d14b..40d819a9850 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
@@ -46,7 +46,19 @@ public interface ICinaUtilities
* @throws EnvironmentFailureException Thrown in cases where it is not possible to connect to
* the server.
*/
- public List<Sample> searchForSamples(SearchCriteria searchCriteria) throws IllegalStateException,
+ public List<Sample> searchForSamples(SearchCriteria searchCriteria)
+ throws IllegalStateException, EnvironmentFailureException;
+
+ /**
+ * Return a generated sample code for the provided sample type.
+ *
+ * @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.
+ */
+ public String generateSampleCode(String sampleTypeCode) throws IllegalStateException,
EnvironmentFailureException;
/**
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 1d5ccdb9ddb..a1d20e15410 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
@@ -24,9 +24,13 @@ import ch.systemsx.cisd.cina.client.util.v1.ICinaUtilities;
import ch.systemsx.cisd.common.api.client.ServiceFinder;
import ch.systemsx.cisd.common.exceptions.AuthorizationFailureException;
import ch.systemsx.cisd.common.exceptions.EnvironmentFailureException;
+import ch.systemsx.cisd.openbis.generic.shared.IETLLIMSService;
+import ch.systemsx.cisd.openbis.generic.shared.OpenBisServiceFactory;
+import ch.systemsx.cisd.openbis.generic.shared.ResourceNames;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.IGeneralInformationService;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Sample;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SampleType;
/**
* @author Chandrasekhar Ramakrishnan
@@ -34,7 +38,7 @@ import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria;
public class CinaUtilitiesFacade implements ICinaUtilities
{
/**
- * Public factory method for creating a DssComponent with a username and password.
+ * Public factory method for creating a CinaUtilitiesFacade with a username and password.
*
* @param user The user name
* @param password The user's password
@@ -77,9 +81,17 @@ public class CinaUtilitiesFacade implements ICinaUtilities
return service;
}
+ private static IETLLIMSService createOpenBisService(String openBISURL)
+ {
+ return new OpenBisServiceFactory(openBISURL, ResourceNames.ETL_SERVICE_URL).createService();
+ }
+
/** The interface for accessing the remote services. */
private final IGeneralInformationService generalInformationService;
+ /** The LIMS service. */
+ private final IETLLIMSService openbisService;
+
/** The current state of the facade */
private AbstractCinaFacadeState state;
@@ -95,7 +107,8 @@ public class CinaUtilitiesFacade implements ICinaUtilities
*/
private CinaUtilitiesFacade(String openBISURL, String sessionTokenOrNull)
{
- this(createGeneralInformationService(openBISURL), sessionTokenOrNull);
+ this(createGeneralInformationService(openBISURL), createOpenBisService(openBISURL),
+ sessionTokenOrNull);
}
/**
@@ -103,20 +116,24 @@ public class CinaUtilitiesFacade implements ICinaUtilities
*
* @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 sessionTokenOrNull A session token, if the user has already logged in, or null
* otherwise.
*/
protected CinaUtilitiesFacade(IGeneralInformationService generalInformationService,
- String sessionTokenOrNull)
+ IETLLIMSService openbisService, String sessionTokenOrNull)
{
this.generalInformationService = generalInformationService;
+ this.openbisService = openbisService;
if (sessionTokenOrNull == null)
{
this.state = new UnauthenticatedState(generalInformationService);
} else
{
- this.state = new AuthenticatedState(generalInformationService, sessionTokenOrNull);
+ this.state =
+ new AuthenticatedState(generalInformationService, openbisService,
+ sessionTokenOrNull);
}
}
@@ -132,7 +149,9 @@ public class CinaUtilitiesFacade implements ICinaUtilities
{
// login and transition to the authenticated state
state.login(user, password);
- state = new AuthenticatedState(generalInformationService, state.getSessionToken());
+ state =
+ new AuthenticatedState(generalInformationService, openbisService,
+ state.getSessionToken());
}
public void logout()
@@ -152,6 +171,12 @@ public class CinaUtilitiesFacade implements ICinaUtilities
{
return state.searchForSamples(searchCriteria);
}
+
+ public String generateSampleCode(String sampleTypeCode) throws IllegalStateException,
+ EnvironmentFailureException
+ {
+ return state.generateSampleCode(sampleTypeCode);
+ }
}
/**
@@ -182,6 +207,12 @@ abstract class AbstractCinaFacadeState implements ICinaUtilities
throw new IllegalStateException("Please log in");
}
+ public String generateSampleCode(String sampleTypeCode) throws IllegalStateException,
+ EnvironmentFailureException
+ {
+ throw new IllegalStateException("Please log in");
+ }
+
/**
* Authenticates the <code>user</code> with given <code>password</code>.
*
@@ -252,13 +283,17 @@ class AuthenticatedState extends AbstractCinaFacadeState
{
private final String sessionToken;
+ private final IETLLIMSService openbisService;
+
/**
* @param service
*/
- AuthenticatedState(IGeneralInformationService service, String sessionToken)
+ AuthenticatedState(IGeneralInformationService service, IETLLIMSService openbisService,
+ String sessionToken)
{
super(service);
this.sessionToken = sessionToken;
+ this.openbisService = openbisService;
}
@Override
@@ -291,4 +326,15 @@ class AuthenticatedState extends AbstractCinaFacadeState
{
return sessionToken;
}
+
+ @Override
+ public String generateSampleCode(String sampleTypeCode) throws IllegalStateException,
+ EnvironmentFailureException
+ {
+ SampleType replicaSampleType = openbisService.getSampleType(sessionToken, sampleTypeCode);
+ long sampleCodeSuffix = openbisService.drawANewUniqueID(sessionToken);
+ String sampleCode =
+ String.format("%s%d", replicaSampleType.getGeneratedCodePrefix(), sampleCodeSuffix);
+ return sampleCode;
+ }
}
\ No newline at end of file
diff --git a/rtd_cina/source/java/ch/systemsx/cisd/cina/dss/info/CinaDataSetInfoExtractor.java b/rtd_cina/source/java/ch/systemsx/cisd/cina/dss/info/CinaDataSetInfoExtractor.java
deleted file mode 100644
index f934c9ee9f3..00000000000
--- a/rtd_cina/source/java/ch/systemsx/cisd/cina/dss/info/CinaDataSetInfoExtractor.java
+++ /dev/null
@@ -1,176 +0,0 @@
-/*
- * Copyright 2010 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.cina.dss.info;
-
-import java.io.File;
-import java.io.FileInputStream;
-import java.io.FileNotFoundException;
-import java.io.IOException;
-import java.util.Calendar;
-import java.util.GregorianCalendar;
-import java.util.HashMap;
-import java.util.Properties;
-import java.util.Map.Entry;
-
-import ch.systemsx.cisd.cina.dss.info.FolderOracle.FolderMetadata;
-import ch.systemsx.cisd.cina.dss.info.FolderOracle.FolderType;
-import ch.systemsx.cisd.common.exceptions.EnvironmentFailureException;
-import ch.systemsx.cisd.common.exceptions.UserFailureException;
-import ch.systemsx.cisd.etlserver.IDataSetInfoExtractor;
-import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
-import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
-
-/**
- * TODO 2010-08-16, CR, This class is no longer used. It can be deleted.
- * <p>
- * CINA uses the data store server to register experiments and samples in addition to data sets. The
- * CinaBundleDataSetInfoExtractor follows the conventions agreed to by the CINA project to determine
- * if the file represents an experiment, sample, or data set and takes according action.
- * <p>
- * In the case of data representing experiments and samples, the extractor may need to register the
- * experiment/sample with openBIS before continuing to process the data set.
- *
- * @author Chandrasekhar Ramakrishnan
- */
-public class CinaDataSetInfoExtractor implements IDataSetInfoExtractor
-{
- // Keys used in the metadata file
- static final String DESCRIPTION_KEY = "DESCRIPTION";
-
- public CinaDataSetInfoExtractor(final Properties properties)
- {
-
- }
-
- public DataSetInformation getDataSetInformation(File incomingDataSetFile,
- IEncapsulatedOpenBISService openbisService) throws UserFailureException,
- EnvironmentFailureException
- {
- final DataSetInformation dataSetInformation = new DataSetInformation();
-
- final FolderOracle folderOracle = new FolderOracle();
- FolderMetadata metadata = folderOracle.getFolderMetadataForFolder(incomingDataSetFile);
- FolderType folderType = metadata.getType();
-
- switch (folderType)
- {
- case DATA_SET:
- processDataSetFolder(metadata, dataSetInformation, openbisService);
- break;
- case EXPERIMENT:
- processExperimentFolder(metadata, dataSetInformation, openbisService);
- break;
- case SAMPLE:
- processSampleFolder(metadata, dataSetInformation, openbisService);
- break;
- case UNKNOWN:
- // Ignore it
- break;
- }
-
- return dataSetInformation;
- }
-
- /**
- * See if the incoming data set folder is contains an experiment and, if so, register the
- * experiment.
- */
- private void processExperimentFolder(final FolderMetadata folderMetadata,
- final DataSetInformation dataSetInformation, IEncapsulatedOpenBISService openbisService)
- {
- final File markerFile = folderMetadata.tryGetMarkerFile();
- try
- {
- HashMap<String, String> metadata = new HashMap<String, String>();
- metadata = appendMarkerFileToMap(markerFile, metadata);
- ExperimentRegistrationInformationExtractor extractor =
- new ExperimentRegistrationInformationExtractor(dataSetInformation, metadata,
- getEntityCodeSuffix(), openbisService);
- extractor.processMetadataAndFillDataSetInformation();
- } catch (IOException ex)
- {
- UserFailureException userFailure =
- new UserFailureException("Could not register experiment", ex);
- throw userFailure;
- }
- }
-
- /**
- * See if the incoming data set folder is contains a sample and, if so, register the sample.
- */
- private void processSampleFolder(final FolderMetadata folderMetadata,
- final DataSetInformation dataSetInformation, IEncapsulatedOpenBISService openbisService)
- {
- final File markerFile = folderMetadata.tryGetMarkerFile();
- try
- {
- HashMap<String, String> metadata = new HashMap<String, String>();
- metadata = appendMarkerFileToMap(markerFile, metadata);
- SampleRegistrationInformationExtractor extractor =
- new SampleRegistrationInformationExtractor(dataSetInformation, metadata,
- getEntityCodeSuffix(), openbisService);
- extractor.processMetadataAndFillDataSetInformation();
- } catch (IOException ex)
- {
- UserFailureException userFailure =
- new UserFailureException("Could not register sample", ex);
- throw userFailure;
- }
- }
-
- /**
- * See if the incoming data set folder is contains a data set and, if so, register the data set.
- */
- private void processDataSetFolder(final FolderMetadata folderMetadata,
- final DataSetInformation dataSetInformation, IEncapsulatedOpenBISService openbisService)
- {
- }
-
- /**
- * Create a suffix for the entity code.
- */
- private String getEntityCodeSuffix()
- {
- Calendar now = GregorianCalendar.getInstance();
- StringBuffer sb = new StringBuffer();
- sb.append(now.get(Calendar.YEAR));
- sb.append(String.format("%02d", now.get(Calendar.MONTH) + 1));
- sb.append(String.format("%02d", now.get(Calendar.DAY_OF_MONTH)));
- sb.append("-");
- sb.append(now.get(Calendar.HOUR_OF_DAY));
- sb.append(now.get(Calendar.MINUTE));
- sb.append("-");
- sb.append(now.get(Calendar.MILLISECOND));
- return sb.toString();
- }
-
- /**
- * Parse the marker file and append it to hashmap.
- */
- private HashMap<String, String> appendMarkerFileToMap(File markerFile,
- HashMap<String, String> map) throws IOException, FileNotFoundException
- {
- Properties properties = new Properties();
- properties.load(new FileInputStream(markerFile));
-
- for (Entry<Object, Object> entry : properties.entrySet())
- {
- map.put((String) entry.getKey(), (String) entry.getValue());
- }
- return map;
- }
-}
diff --git a/rtd_cina/source/java/ch/systemsx/cisd/cina/dss/info/CinaTypeExtractor.java b/rtd_cina/source/java/ch/systemsx/cisd/cina/dss/info/CinaTypeExtractor.java
deleted file mode 100644
index f401a28f6a7..00000000000
--- a/rtd_cina/source/java/ch/systemsx/cisd/cina/dss/info/CinaTypeExtractor.java
+++ /dev/null
@@ -1,118 +0,0 @@
-/*
- * Copyright 2010 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.cina.dss.info;
-
-import java.io.File;
-import java.util.Properties;
-
-import ch.systemsx.cisd.cina.dss.info.FolderOracle.FolderType;
-import ch.systemsx.cisd.etlserver.ITypeExtractor;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetType;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.FileFormatType;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.LocatorType;
-
-/**
- * TODO 2010-08-16, CR, This class is no longer used. It can be deleted.
- * <p>
- * The extractor expects that certain things have been set up in the database. In particular:
- * <ul>
- * <li>A data set type with code CINA_EXP_PREP — this is the data set for preparation
- * information for an experiment</li>
- * <li>A data set type with code CINA_SAMPLE_PREP — this is the data set for preparation
- * information for a sample</li>
- * </ul>
- *
- * @author Chandrasekhar Ramakrishnan
- */
-public class CinaTypeExtractor implements ITypeExtractor
-{
-
- private final String EXPERIMENT_METADATA_DATASET_TYPE = "CINA_EXP_PREP";
-
- private final String SAMPLE_METADATA_DATASET_TYPE = "CINA_SAMPLE_PREP";
-
- private final String UNKNOWN_METADATA_DATASET_TYPE = "UNKNOWN";
-
- public CinaTypeExtractor(final Properties properties)
- {
-
- }
-
- public DataSetType getDataSetType(File incomingDataSetPath)
- {
- FolderOracle folderOracle = new FolderOracle();
- FolderType folderType = folderOracle.getTypeForFolder(incomingDataSetPath);
- DataSetType datasetType = null;
- switch (folderType)
- {
- case DATA_SET:
- datasetType = new DataSetType(UNKNOWN_METADATA_DATASET_TYPE);
- break;
- case EXPERIMENT:
- datasetType = new DataSetType(EXPERIMENT_METADATA_DATASET_TYPE);
- break;
- case SAMPLE:
- datasetType = new DataSetType(SAMPLE_METADATA_DATASET_TYPE);
- break;
- case UNKNOWN:
- datasetType = new DataSetType(UNKNOWN_METADATA_DATASET_TYPE);
- break;
-
- }
- return datasetType;
- }
-
- public FileFormatType getFileFormatType(File incomingDataSetPath)
- {
- return new FileFormatType("PROPRIETARY");
- }
-
- public LocatorType getLocatorType(File incomingDataSetPath)
- {
- return new LocatorType("RELATIVE_LOCATION");
- }
-
- public String getProcessorType(File incomingDataSetPath)
- {
- return null;
- }
-
- public boolean isMeasuredData(File incomingDataSetPath)
- {
- FolderOracle folderOracle = new FolderOracle();
- FolderType folderType = folderOracle.getTypeForFolder(incomingDataSetPath);
- boolean isMeasuredData = false;
- switch (folderType)
- {
- case DATA_SET:
- isMeasuredData = true;
- break;
- case EXPERIMENT:
- isMeasuredData = false;
- break;
- case SAMPLE:
- isMeasuredData = false;
- break;
- case UNKNOWN:
- isMeasuredData = false;
- break;
-
- }
- return isMeasuredData;
- }
-
-}
diff --git a/rtd_cina/source/java/ch/systemsx/cisd/cina/dss/info/EntityRegistrationSuccessEmail.java b/rtd_cina/source/java/ch/systemsx/cisd/cina/dss/info/EntityRegistrationSuccessEmail.java
deleted file mode 100644
index 795f105a013..00000000000
--- a/rtd_cina/source/java/ch/systemsx/cisd/cina/dss/info/EntityRegistrationSuccessEmail.java
+++ /dev/null
@@ -1,289 +0,0 @@
-/*
- * Copyright 2010 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.cina.dss.info;
-
-import java.io.File;
-
-import javax.activation.DataHandler;
-
-import ch.systemsx.cisd.cina.dss.info.FolderOracle.FolderType;
-import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
-
-/**
- * TODO 2010-08-16, CR, This class is no longer used. It can be deleted.
- *
- * Create the subject and content for an email that is sent when an experiment or sample is
- * registered.
- *
- * @author Chandrasekhar Ramakrishnan
- */
-class EntityRegistrationSuccessEmail
-{
- private static final String MARKER_FILE_MIME_TYPE = "application/octet-stream";
-
- private final DataSetInformation dataSetInformation;
-
- private final EntityEmailDetails entityEmailDetails;
-
- private static final String EMAIL_SUBJECT_PREFIX = "[CINA]";
-
- private static final String SAMPLE_CODE_PREFIX = "S";
-
- public EntityRegistrationSuccessEmail(DataSetInformation dataSetInformation,
- File incomingDataSetDirectory)
- {
- this.dataSetInformation = dataSetInformation;
-
- FolderType folderType = new FolderOracle().getTypeForFolder(incomingDataSetDirectory);
- switch (folderType)
- {
- case DATA_SET:
- entityEmailDetails = new DatasetEmailDetails();
- break;
- case EXPERIMENT:
- entityEmailDetails = new ExperimentEmailDetails();
- break;
- case SAMPLE:
- entityEmailDetails = new SampleEmailDetails();
- break;
- case UNKNOWN:
- entityEmailDetails = new UnknownEmailDetails();
- break;
- default:
- entityEmailDetails = new UnknownEmailDetails();
- break;
- }
- }
-
- /**
- * Return true if the incoming data set requires that an email be sent on registration.
- */
- public boolean shouldSendEmail()
- {
- return entityEmailDetails.shouldSendEmail();
- }
-
- /**
- * Return the subject of the email
- */
- public String getSubject()
- {
- StringBuffer subject = new StringBuffer();
- subject.append(EMAIL_SUBJECT_PREFIX);
- subject.append(" Registered ");
- entityEmailDetails.appendEntityName(subject);
- subject.append(" ");
- entityEmailDetails.appendSubjectDetails(subject);
- return subject.toString();
- }
-
- /**
- * Return the body of the email for a text-only (no attachments) email. Used if the mail client
- * does no support sending attachments.
- */
- public String getContentTextOnly()
- {
- StringBuffer content = new StringBuffer();
- entityEmailDetails.appendEntityName(content);
- content.append(" was successfully registered. Use the following metadata file to register");
- entityEmailDetails.appendFollowOnEntityName(content);
- content.append(":\n");
- content.append("------");
- entityEmailDetails.appendMarkerFileName(content);
- content.append("------");
- content.append("\n");
- entityEmailDetails.appendMarkerFileContent(content);
-
- return content.toString();
- }
-
- /**
- * Return the body of the email for a MIME email. In a MIME email, the marker file is sent as a
- * file attachment, not part of the text body of the email.
- */
- public String getContentMimeText()
- {
- StringBuffer content = new StringBuffer();
- entityEmailDetails.appendEntityName(content);
- content.append(" was successfully registered. Use the attached metadata file to register ");
- entityEmailDetails.appendFollowOnEntityName(content);
-
- return content.toString();
- }
-
- /**
- * Return the file name of the MIME file attachment.
- */
- public String getContentMimeAttachmentFileName()
- {
- StringBuffer content = new StringBuffer();
- entityEmailDetails.appendMarkerFileName(content);
-
- return content.toString();
- }
-
- public DataHandler getContentMimeAttachmentContent()
- {
- StringBuffer content = new StringBuffer();
- entityEmailDetails.appendMarkerFileContent(content);
- DataHandler attachment = new DataHandler(content.toString(), MARKER_FILE_MIME_TYPE);
-
- return attachment;
- }
-
- private abstract class EntityEmailDetails
- {
- boolean shouldSendEmail()
- {
- return false;
- }
-
- abstract void appendEntityName(StringBuffer sb);
-
- void appendFollowOnEntityName(StringBuffer sb)
- {
- }
-
- void appendSubjectDetails(StringBuffer subject)
- {
- }
-
- void appendMarkerFileName(StringBuffer sb)
- {
- }
-
- void appendMarkerFileContent(StringBuffer sb)
- {
-
- }
- }
-
- private class ExperimentEmailDetails extends EntityEmailDetails
- {
- @Override
- boolean shouldSendEmail()
- {
- return true;
- }
-
- @Override
- void appendEntityName(StringBuffer sb)
- {
- sb.append("Experiment");
- }
-
- @Override
- void appendFollowOnEntityName(StringBuffer sb)
- {
- sb.append("Samples");
- }
-
- @Override
- void appendSubjectDetails(StringBuffer subject)
- {
- subject.append(dataSetInformation.getExperimentIdentifier());
- }
-
- @Override
- void appendMarkerFileContent(StringBuffer sb)
- {
- sb.append(SampleRegistrationInformationExtractor.EXPERIMENT_IDENTIFIER_KEY);
- sb.append("=");
- sb.append(dataSetInformation.getExperimentIdentifier());
- sb.append("\n");
-
- sb.append(SampleRegistrationInformationExtractor.EXPERIMENT_OWNER_EMAIL_KEY);
- sb.append("=");
- sb.append(dataSetInformation.tryGetUploadingUserEmail());
- sb.append("\n");
-
- sb.append(SampleRegistrationInformationExtractor.SAMPLE_CODE_PREFIX_KEY);
- sb.append("=");
- sb.append(SAMPLE_CODE_PREFIX);
- sb.append("\n");
- }
-
- @Override
- void appendMarkerFileName(StringBuffer sb)
- {
- sb.append(FolderOracle.SAMPLE_MARKER_FILENAME);
-
- }
- }
-
- private class SampleEmailDetails extends EntityEmailDetails
- {
- @Override
- boolean shouldSendEmail()
- {
- return true;
- }
-
- @Override
- void appendEntityName(StringBuffer sb)
- {
- sb.append("Sample");
- }
-
- @Override
- void appendFollowOnEntityName(StringBuffer sb)
- {
- sb.append("Data Sets");
- }
-
- @Override
- void appendSubjectDetails(StringBuffer subject)
- {
- subject.append(dataSetInformation.getSampleIdentifier());
- }
-
- @Override
- void appendMarkerFileContent(StringBuffer sb)
- {
- }
-
- @Override
- void appendMarkerFileName(StringBuffer sb)
- {
- sb.append(FolderOracle.DATA_SET_MARKER_FILENAME);
- }
- }
-
- private class DatasetEmailDetails extends EntityEmailDetails
- {
- @Override
- void appendEntityName(StringBuffer sb)
- {
- sb.append("Data Set");
- }
-
- @Override
- void appendSubjectDetails(StringBuffer subject)
- {
- subject.append(dataSetInformation.getDataSetCode());
- }
- }
-
- private class UnknownEmailDetails extends EntityEmailDetails
- {
- @Override
- void appendEntityName(StringBuffer sb)
- {
- sb.append("Unknown");
- }
- }
-}
diff --git a/rtd_cina/source/java/ch/systemsx/cisd/cina/dss/info/EntityTypes.java b/rtd_cina/source/java/ch/systemsx/cisd/cina/dss/info/EntityTypes.java
deleted file mode 100644
index dd5bad9df16..00000000000
--- a/rtd_cina/source/java/ch/systemsx/cisd/cina/dss/info/EntityTypes.java
+++ /dev/null
@@ -1,63 +0,0 @@
-/*
- * Copyright 2010 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.cina.dss.info;
-
-/**
- * TODO 2010-08-16, CR, This class is no longer used. It can be deleted.
- * <p>
- * A registry for the different entity types CINA uses
- *
- * @author Chandrasekhar Ramakrishnan
- */
-public class EntityTypes
-{
- /**
- * CINA carries out the following kinds of experiment: electron microscopy, light microscopy,
- * mass spectrometry, tomography, and a non-specific CINA experiment type.
- *
- * @author Chandrasekhar Ramakrishnan
- */
- public static enum ExperimentTypes
- {
- ELECTRON_MICROSCOPY, LIGHT_MICROSCOPY, MASS_SPEC, TOMOGRAPHY, CINA_EXP_TYPE
- }
-
- /**
- * CINA utilizes the following sample types: original experimental sample, samples that result
- * from biochemical manipulation of the original, grid peperation, and non-specific CINA sample
- * type.
- *
- * @author Chandrasekhar Ramakrishnan
- */
- public static enum SampleTypes
- {
- ORIGINAL, BIOCHEMISTRY, GRID_PREP, CINA_SAMPLE_TYPE
- }
-
- /**
- * Results and by products of experiments in CINA are data sets types: electron microscope
- * images, light microscope images, mass spectrograms, tomograms, ยต-fluidics parameters, lab
- * notebooks, and a non-specific data set type.
- *
- * @author Chandrasekhar Ramakrishnan
- */
- public static enum DataSetTypes
- {
- EM_IMAGE, LM_IMAGE, MASS_SPECTROGRAM, TOMOGRAM, U_FLUIDICS_PARAMETERS, LAB_NOTEBOOK,
- UNKNOWN
- }
-}
diff --git a/rtd_cina/source/java/ch/systemsx/cisd/cina/dss/info/ExperimentRegistrationInformationExtractor.java b/rtd_cina/source/java/ch/systemsx/cisd/cina/dss/info/ExperimentRegistrationInformationExtractor.java
deleted file mode 100644
index 729debfb550..00000000000
--- a/rtd_cina/source/java/ch/systemsx/cisd/cina/dss/info/ExperimentRegistrationInformationExtractor.java
+++ /dev/null
@@ -1,177 +0,0 @@
-/*
- * Copyright 2010 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.cina.dss.info;
-
-import java.util.Map;
-
-import ch.systemsx.cisd.common.exceptions.EnvironmentFailureException;
-import ch.systemsx.cisd.common.exceptions.UserFailureException;
-import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
-import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Experiment;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewExperiment;
-import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifier;
-import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ProjectIdentifier;
-import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ProjectIdentifierFactory;
-
-/**
- * Package-visible helper class to extract information from the XML metadata file and register a new
- * experiment using this data.
- *
- * @author Chandrasekhar Ramakrishnan
- */
-class ExperimentRegistrationInformationExtractor
-{
- // Keys expected in metadata properties file
- public static final String PROJECT_IDENTIFIER_KEY = "project.identifier";
-
- public static final String EXPERIMENT_CODE_KEY = "experiment.code-prefix";
-
- public static final String EXPERIMENT_OWNER_EMAIL_KEY = "experiment.owner-email";
-
- // Instance state
- private final DataSetInformation dataSetInformation;
-
- private final Map<String, String> experimentMetadata;
-
- private final String experimentCodeSuffix;
-
- private final IEncapsulatedOpenBISService openbisService;
-
- // Internal state used during extraction
- private ProjectIdentifier projectIdentifier;
-
- private String experimentCodePrefix;
-
- private String emailAddress;
-
- ExperimentRegistrationInformationExtractor(DataSetInformation dataSetInformation,
- Map<String, String> experimentMetadata, String experimentCodeSuffix,
- IEncapsulatedOpenBISService openbisService)
- {
- this.dataSetInformation = dataSetInformation;
- this.experimentMetadata = experimentMetadata;
- this.experimentCodeSuffix = experimentCodeSuffix;
- this.openbisService = openbisService;
- }
-
- /**
- * Takes the project code, experiment code, and email address from the properties file and
- * creates a new experiment.
- * <p>
- * This method is package-visible for testing purposes.
- */
- void processMetadataAndFillDataSetInformation() throws UserFailureException
- {
- extractMetadata();
-
- // Set the email address as early as possible because it will be used later to notify the
- // user.
- dataSetInformation.setUploadingUserEmail(emailAddress);
-
- // Check that that the required data was specified in the properties file.
- verifyRequiredMetadataDataHasBeenProvided();
-
- ExperimentIdentifier experimentId = this.createExperiment();
- dataSetInformation.setExperimentIdentifier(experimentId);
- }
-
- private void extractMetadata()
- {
- String projectIdString = experimentMetadata.get(PROJECT_IDENTIFIER_KEY);
- if (projectIdString != null)
- {
- projectIdentifier = new ProjectIdentifierFactory(projectIdString).createIdentifier();
- }
- experimentCodePrefix = experimentMetadata.get(EXPERIMENT_CODE_KEY);
- emailAddress = experimentMetadata.get(EXPERIMENT_OWNER_EMAIL_KEY);
- }
-
- /**
- * Create a new experiment. If an experiment already exists, raise an error.
- */
- private ExperimentIdentifier createExperiment() throws EnvironmentFailureException
- {
- ExperimentIdentifier experimentIdentifier =
- new ExperimentIdentifier(projectIdentifier, experimentCodePrefix + "-"
- + experimentCodeSuffix);
-
- // Check that the identifier is unique
- Experiment experiment = openbisService.tryToGetExperiment(experimentIdentifier);
- if (experiment != null)
- {
- throw new EnvironmentFailureException(
- "The generated experiment identifer, which must be unique, is already in the database. This should not happen: Please contact the administrator.");
- }
-
- openbisService.registerExperiment(new NewExperiment(experimentIdentifier.toString(),
- EntityTypes.ExperimentTypes.CINA_EXP_TYPE.toString()));
-
- return experimentIdentifier;
- }
-
- /**
- * Ensure the required user-provided data has been specified. Throws an exception if this is not
- * the case.
- */
- private void verifyRequiredMetadataDataHasBeenProvided() throws UserFailureException
- {
- if (null == projectIdentifier)
- {
- throw new UserFailureException(
- "A project identifier must be specified to register an experiment.");
- }
-
- if (null == experimentCodePrefix)
- {
- throw new UserFailureException(
- "An experiment code prefix must be specified to register an experiment.");
- }
-
- if (null == emailAddress)
- {
- throw new UserFailureException(
- "An email address must be specified to register an experiment.");
- }
- }
- /**
- * Automatically generates the code.
- */
- // Need to use something like this.
- // public void generateCode()
- // {
- // viewContext.getCommonService().generateCode(codePrefix,
- // new GenerateCodeCallback(viewContext));
- // }
- //
- // private final class GenerateCodeCallback extends AbstractAsyncCallback<String>
- // {
- //
- // GenerateCodeCallback(final IViewContext<?> viewContext)
- // {
- // super(viewContext);
- // }
- //
- // @Override
- // protected final void process(final String result)
- // {
- // setValue(result);
- // }
- //
- // }
-
-}
\ No newline at end of file
diff --git a/rtd_cina/source/java/ch/systemsx/cisd/cina/dss/info/FolderOracle.java b/rtd_cina/source/java/ch/systemsx/cisd/cina/dss/info/FolderOracle.java
deleted file mode 100644
index 2b3901776b9..00000000000
--- a/rtd_cina/source/java/ch/systemsx/cisd/cina/dss/info/FolderOracle.java
+++ /dev/null
@@ -1,233 +0,0 @@
-/*
- * Copyright 2010 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.cina.dss.info;
-
-import java.io.File;
-import java.io.FilenameFilter;
-
-import ch.systemsx.cisd.common.exceptions.EnvironmentFailureException;
-import ch.systemsx.cisd.common.exceptions.UserFailureException;
-
-/**
- * The Folder Oracle knows the naming conventions for the different types of data provided by CINA
- * and can tell clients which of the types this data actually is.
- * <p>
- * Instances of this class are designed to be used within a single thread.
- *
- * @author Chandrasekhar Ramakrishnan
- */
-class FolderOracle
-{
- /**
- * The different kinds of metadata known to the oracle.
- *
- * @author Chandrasekhar Ramakrishnan
- */
- static enum FolderType
- {
- EXPERIMENT, SAMPLE, DATA_SET, UNKNOWN;
- }
-
- /**
- * A little helper class for storing the location and type of the sidecar files for a folder. If
- * the type is UNKNOWN, the files will be null. If the type is known, the marker file will be
- * non-null. The metadata file might still be null.
- *
- * @author Chandrasekhar Ramakrishnan
- */
- static class FolderMetadata
- {
- private final FolderType type;
-
- private final File markerFileOrNull;
-
- private final File metadataXMLFileOrNull;
-
- FolderMetadata(FolderType type, File markerFile, File metadataXMLFile)
- {
- this.type = type;
- this.markerFileOrNull = markerFile;
- this.metadataXMLFileOrNull = metadataXMLFile;
- }
-
- /**
- * The type of the folder.
- */
- FolderType getType()
- {
- return type;
- }
-
- /**
- * The marker file for this folder -- this is a properties file.
- */
- File tryGetMarkerFile()
- {
- return markerFileOrNull;
- }
-
- /**
- * The metadata file for this folder -- this is an XML file.
- */
- File tryGetMetadataXMLFile()
- {
- return metadataXMLFileOrNull;
- }
- }
-
- // The known conventions for naming metadata files. If a new metadata file is created, cases
- // should be added to getFilenameFilter() and getFolderMetadataForFile() as well.
- static String EXPERIMENT_MARKER_FILENAME = "experiment.properties";
-
- static String SAMPLE_MARKER_FILENAME = "sample.properties";
-
- static String DATA_SET_MARKER_FILENAME = "dataset.properties";
-
- static String METADATA_XML_FILENAME = "metadata.xml";
-
- FolderOracle()
- {
-
- }
-
- /**
- * Scan the folder and return the metadata file for the folder along with its associated type.
- * <p>
- * Returns type UNKNOWN if the folder cannot be identified and throws an error if the
- * identification is ambiguous.
- */
- FolderMetadata getFolderMetadataForFolder(File incomingDataSetFolder)
- throws UserFailureException
- {
- // Don't know what to do with this file
- if (!incomingDataSetFolder.isDirectory())
- {
- return new FolderMetadata(FolderType.UNKNOWN, null, null);
- }
-
- File[] metadata = incomingDataSetFolder.listFiles(getMarkerFilenameFilter());
-
- // Didn't find any metadata
- if (metadata.length < 1)
- {
- return new FolderMetadata(FolderType.UNKNOWN, null, null);
- }
-
- // Found too much metadata
- if (metadata.length > 1)
- {
- StringBuffer errorDescription = new StringBuffer();
- errorDescription.append("Folder (" + incomingDataSetFolder
- + ") contains multiple description files: ");
- for (File file : metadata)
- {
- errorDescription.append("\n\t");
- errorDescription.append(file);
- }
- throw new UserFailureException(errorDescription.toString());
- }
-
- return getFolderMetadataForFile(metadata[0]);
- }
-
- /**
- * Returns the type of data stored in the folder
- */
- FolderType getTypeForFolder(File incomingDataSetFolder) throws UserFailureException
- {
- FolderMetadata metadata = getFolderMetadataForFolder(incomingDataSetFolder);
- return metadata.getType();
- }
-
- /**
- * After it has been determined that the folder contains metadata for some known type, this
- * method can be invoked to return a folder metadata object.
- */
- private FolderMetadata getFolderMetadataForFile(File metadataFile)
- {
- String filename = metadataFile.getName();
- File parentDir = metadataFile.getParentFile();
- File metadataXMLFileOrNull = null;
- if (parentDir != null)
- {
-
- File[] metadataXMLFiles = parentDir.listFiles(getMetadataXMLFilenameFilter());
- if (metadataXMLFiles.length > 0)
- {
- metadataXMLFileOrNull = metadataXMLFiles[0];
- }
- }
-
- if (EXPERIMENT_MARKER_FILENAME.equals(filename))
- {
- return new FolderMetadata(FolderType.EXPERIMENT, metadataFile, metadataXMLFileOrNull);
- }
-
- if (SAMPLE_MARKER_FILENAME.equals(filename))
- {
- return new FolderMetadata(FolderType.SAMPLE, metadataFile, metadataXMLFileOrNull);
- }
-
- if (DATA_SET_MARKER_FILENAME.equals(filename))
- {
- return new FolderMetadata(FolderType.DATA_SET, metadataFile, metadataXMLFileOrNull);
- }
-
- throw new EnvironmentFailureException(
- "A metadata file convention was added without modifing getFolderMetadataForFile()");
- }
-
- private FilenameFilter getMarkerFilenameFilter()
- {
- return new FilenameFilter()
- {
- public boolean accept(File dir, String name)
- {
- if (EXPERIMENT_MARKER_FILENAME.equals(name))
- {
- return true;
- } else if (SAMPLE_MARKER_FILENAME.equals(name))
- {
- return true;
- } else if (DATA_SET_MARKER_FILENAME.equals(name))
- {
- return true;
- } else
- {
- return false;
- }
- }
- };
- }
-
- private FilenameFilter getMetadataXMLFilenameFilter()
- {
- return new FilenameFilter()
- {
- public boolean accept(File dir, String name)
- {
- if (METADATA_XML_FILENAME.equals(name))
- {
- return true;
- } else
- {
- return false;
- }
- }
- };
- }
-}
diff --git a/rtd_cina/source/java/ch/systemsx/cisd/cina/dss/info/SampleRegistrationInformationExtractor.java b/rtd_cina/source/java/ch/systemsx/cisd/cina/dss/info/SampleRegistrationInformationExtractor.java
deleted file mode 100644
index 45b04ebc48a..00000000000
--- a/rtd_cina/source/java/ch/systemsx/cisd/cina/dss/info/SampleRegistrationInformationExtractor.java
+++ /dev/null
@@ -1,182 +0,0 @@
-/*
- * Copyright 2010 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.cina.dss.info;
-
-import java.util.Map;
-
-import ch.systemsx.cisd.common.exceptions.EnvironmentFailureException;
-import ch.systemsx.cisd.common.exceptions.UserFailureException;
-import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
-import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Experiment;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewSample;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SampleType;
-import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifier;
-import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifierFactory;
-import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.GroupIdentifier;
-import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
-
-/**
- * TODO 2010-08-16, CR, This class is no longer used. It can be deleted.
- * <p>
- * Package-visible helper class to extract information from the XML metadata file and register a new
- * sample using this data.
- * <p>
- * This class assumes that the sample type CINA_SAMPLE_TYPE has been registered.
- *
- * @author Chandrasekhar Ramakrishnan
- */
-class SampleRegistrationInformationExtractor
-{
- // Keys expected in metadata properties file
-
- public static final String EXPERIMENT_IDENTIFIER_KEY = "experiment.identifier";
-
- public static final String EXPERIMENT_OWNER_EMAIL_KEY =
- ExperimentRegistrationInformationExtractor.EXPERIMENT_OWNER_EMAIL_KEY;
-
- public static final String SAMPLE_CODE_PREFIX_KEY = "sample.code-prefix";
-
- // Instance state
- private final DataSetInformation dataSetInformation;
-
- private final Map<String, String> sampleMetadata;
-
- private final String sampleCodeSuffix;
-
- private final IEncapsulatedOpenBISService openbisService;
-
- private ExperimentIdentifier experimentIdentifier;
-
- private String sampleCodePrefix;
-
- private String emailAddress;
-
- SampleRegistrationInformationExtractor(DataSetInformation dataSetInformation,
- Map<String, String> sampleMetadata, String sampleCodeSuffix,
- IEncapsulatedOpenBISService openbisService)
- {
- this.dataSetInformation = dataSetInformation;
- this.sampleMetadata = sampleMetadata;
- this.sampleCodeSuffix = sampleCodeSuffix;
- this.openbisService = openbisService;
- }
-
- /**
- * Takes the project code, experiment code, and email address from the properties file and
- * creates a new experiment.
- * <p>
- * This method is package-visible for testing purposes.
- */
- void processMetadataAndFillDataSetInformation()
- {
- extractMetadata();
-
- // Set the email address as early as possible because it will be used later to notify the
- // user.
- dataSetInformation.setUploadingUserEmail(emailAddress);
-
- // Check that that the required data was specified in the properties file.
- verifyRequiredMetadataDataHasBeenProvided();
-
- SampleIdentifier sampleId = this.createSample();
- dataSetInformation.setExperimentIdentifier(experimentIdentifier);
- dataSetInformation.setSpaceCode(sampleId.getSpaceLevel().getSpaceCode());
- dataSetInformation.setSampleCode(sampleId.getSampleCode());
- dataSetInformation.setUploadingUserEmail(emailAddress);
- }
-
- private void extractMetadata()
- {
- String experimentIdString = sampleMetadata.get(EXPERIMENT_IDENTIFIER_KEY);
- if (experimentIdString != null)
- experimentIdentifier =
- new ExperimentIdentifierFactory(experimentIdString).createIdentifier();
- sampleCodePrefix = sampleMetadata.get(SAMPLE_CODE_PREFIX_KEY);
- emailAddress = sampleMetadata.get(EXPERIMENT_OWNER_EMAIL_KEY);
- }
-
- /**
- * Create a new sample attached to the experiment identified by the identifier.
- * <p>
- * <ul>
- * <li>If the experiment the sample is supposed to be attached to does not exist, raise an
- * error.</li>
- * <li>If a sample with the desired identifier already exists, raise an error.</li>
- * </ul>
- */
- private SampleIdentifier createSample() throws UserFailureException,
- EnvironmentFailureException
- {
- Experiment experiment = openbisService.tryToGetExperiment(experimentIdentifier);
- if (null == experiment)
- {
- throw new UserFailureException(
- "The experiment with identifier ("
- + experimentIdentifier.toString()
- + ") does not exist. Please select an experiment to be the container for registered samples.");
- }
-
- SampleIdentifier sampleId =
- new SampleIdentifier(new GroupIdentifier((String) null, experimentIdentifier
- .getSpaceCode()), sampleCodePrefix + "-" + sampleCodeSuffix);
-
- NewSample sample = new NewSample();
- SampleType sampleType = new SampleType();
- sampleType.setCode(EntityTypes.SampleTypes.CINA_SAMPLE_TYPE.toString());
- sample.setSampleType(sampleType);
- sample.setExperimentIdentifier(experimentIdentifier.toString());
- sample.setIdentifier(sampleId.toString());
-
- Sample dbSample = openbisService.tryGetSampleWithExperiment(sampleId);
- if (dbSample != null)
- {
- throw new EnvironmentFailureException(
- "The generated sample identifer, which must be unique, is already in the database. This should not happen: Please contact the administrator.");
- }
-
- openbisService.registerSample(sample, null);
-
- return sampleId;
- }
-
- /**
- * Ensure the required user-provided data has been specified. Throws an exception if this is not
- * the case.
- */
- private void verifyRequiredMetadataDataHasBeenProvided() throws UserFailureException
- {
- if (null == experimentIdentifier)
- {
- throw new UserFailureException(
- "An experiment identifier must be specified to register an experiment.");
- }
-
- if (null == sampleCodePrefix)
- {
- throw new UserFailureException(
- "An sample code prefix must be specified to register an experiment.");
- }
-
- if (null == emailAddress)
- {
- throw new UserFailureException(
- "An email address must be specified to register an experiment.");
- }
- }
-}
\ No newline at end of file
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 35c16f7d2a9..5cfb0a4485e 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
@@ -39,7 +39,7 @@ public class CinaCommandFactoryTest extends AssertJUnit
public void testNameMapping()
{
ICommand cmd;
- cmd = factory.tryCommandForName("preps");
+ cmd = factory.tryCommandForName("listsamps");
assertEquals(CommandSampleLister.class, cmd.getClass());
cmd = factory.tryCommandForName("genid");
diff --git a/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/client/util/cli/CommandFactoryTest.java b/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/client/util/cli/CommandFactoryTest.java
index 38c2b8b9546..a9aeef38881 100644
--- a/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/client/util/cli/CommandFactoryTest.java
+++ b/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/client/util/cli/CommandFactoryTest.java
@@ -49,7 +49,7 @@ public class CommandFactoryTest extends AssertJUnit
public void testNameMapping()
{
ICommand cmd;
- cmd = factory.tryCommandForName("preps");
+ cmd = factory.tryCommandForName("listsamps");
assertEquals(CommandSampleLister.class, cmd.getClass());
cmd = factory.tryCommandForName("genid");
@@ -72,8 +72,8 @@ public class CommandFactoryTest extends AssertJUnit
cmd.printUsage(out);
String helpText =
"usage: cina_client.sh COMMAND [options...] <command arguments>\n" + "\n"
- + "Commands:\n" + " preps\n" + " genid\n" + " ls\n" + " get\n" + " put\n"
- + "\n" + "Options:\n"
+ + "Commands:\n" + " listsamps\n" + " genid\n" + " ls\n" + " get\n"
+ + " put\n" + "\n" + "Options:\n"
+ " [-p,--password] VAL : User login password\n"
+ " [-s,--server-base-url] VAL : URL for openBIS Server (required)\n"
+ " [-u,--username] VAL : User login name\n";
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
new file mode 100644
index 00000000000..7d47eb08ba7
--- /dev/null
+++ b/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/client/util/cli/CommandGenerateSampleCodeTest.java
@@ -0,0 +1,129 @@
+/*
+ * Copyright 2010 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.cina.client.util.cli;
+
+import org.jmock.Expectations;
+import org.jmock.Mockery;
+import org.testng.AssertJUnit;
+import org.testng.annotations.AfterMethod;
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
+
+import ch.systemsx.cisd.cina.client.util.v1.ICinaUtilities;
+import ch.systemsx.cisd.openbis.dss.client.api.cli.ICommand;
+import ch.systemsx.cisd.openbis.generic.shared.IETLLIMSService;
+import ch.systemsx.cisd.openbis.generic.shared.api.v1.IGeneralInformationService;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SampleType;
+
+/**
+ * @author Chandrasekhar Ramakrishnan
+ */
+public class CommandGenerateSampleCodeTest extends AssertJUnit
+{
+ private final class MockCommandGenerateSampleCode extends CommandGenerateSampleCode
+ {
+
+ @Override
+ protected ICinaUtilities login()
+ {
+ facade =
+ ch.systemsx.cisd.cina.client.util.v1.impl.CinaUtilitiesFacadeTest.createFacade(
+ service, openbisService, USER_ID, PASSWORD);
+ return facade;
+ }
+
+ }
+
+ private final static String USER_ID = "userid";
+
+ private final static String PASSWORD = "password";
+
+ private final static String SESSION_TOKEN = "sessionToken";
+
+ private Mockery context;
+
+ private ICinaUtilities facade;
+
+ private IGeneralInformationService service;
+
+ private IETLLIMSService openbisService;
+
+ @BeforeMethod
+ public void setUp()
+ {
+ context = new Mockery();
+ service = context.mock(IGeneralInformationService.class);
+ openbisService = context.mock(IETLLIMSService.class);
+ }
+
+ @AfterMethod
+ public void tearDown()
+ {
+ // To following line of code should also be called at the end of each test method.
+ // Otherwise one does not known which test failed.
+ context.assertIsSatisfied();
+ }
+
+ @Test
+ public void testCodePath()
+ {
+ final String sampleTypeCode = "SampleTypeCode";
+ final SampleType sampleType = new SampleType();
+ sampleType.setAutoGeneratedCode(true);
+ sampleType.setGeneratedCodePrefix("STC-");
+ context.checking(new Expectations()
+ {
+ {
+ one(service).tryToAuthenticateForAllServices(USER_ID, PASSWORD);
+ will(returnValue(SESSION_TOKEN));
+
+ one(openbisService).getSampleType(SESSION_TOKEN, sampleTypeCode.toUpperCase());
+ will(returnValue(sampleType));
+
+ one(openbisService).drawANewUniqueID(SESSION_TOKEN);
+ will(returnValue((long) 1));
+
+ one(service).logout(SESSION_TOKEN);
+ }
+ });
+ ICommand command = new MockCommandGenerateSampleCode();
+
+ int exitCode = command.execute(new String[]
+ { "-s", "url", "-u", USER_ID, "-p", PASSWORD, sampleTypeCode });
+
+ assertEquals(0, exitCode);
+ context.assertIsSatisfied();
+ }
+
+ @Test
+ public void testMissingArguments()
+ {
+ context.checking(new Expectations()
+ {
+ {
+
+ }
+ });
+ ICommand command = new MockCommandGenerateSampleCode();
+
+ int exitCode = command.execute(new String[]
+ { "-s", "url", "-u", USER_ID, "-p", PASSWORD });
+
+ assertEquals(1, exitCode);
+ context.assertIsSatisfied();
+ }
+}
diff --git a/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/client/util/cli/SampleListerCommandTest.java b/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/client/util/cli/CommandSampleListerTest.java
similarity index 92%
rename from rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/client/util/cli/SampleListerCommandTest.java
rename to rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/client/util/cli/CommandSampleListerTest.java
index c97bb090269..fd90d70bf03 100644
--- a/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/client/util/cli/SampleListerCommandTest.java
+++ b/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/client/util/cli/CommandSampleListerTest.java
@@ -30,6 +30,7 @@ import ch.systemsx.cisd.cina.client.util.v1.ICinaUtilities;
import ch.systemsx.cisd.cina.shared.constants.CinaConstants;
import ch.systemsx.cisd.common.exceptions.EnvironmentFailureException;
import ch.systemsx.cisd.openbis.dss.client.api.cli.ICommand;
+import ch.systemsx.cisd.openbis.generic.shared.IETLLIMSService;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.IGeneralInformationService;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Sample;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria;
@@ -39,17 +40,18 @@ import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria.MatchCl
/**
* @author Chandrasekhar Ramakrishnan
*/
-public class SampleListerCommandTest extends AssertJUnit
+public class CommandSampleListerTest extends AssertJUnit
{
private final class MockCommandSampleLister extends CommandSampleLister
{
-
@Override
protected ICinaUtilities login()
{
+ facade =
+ ch.systemsx.cisd.cina.client.util.v1.impl.CinaUtilitiesFacadeTest.createFacade(
+ service, openbisService, USER_ID, PASSWORD);
return facade;
}
-
}
private final static String USER_ID = "userid";
@@ -64,11 +66,14 @@ public class SampleListerCommandTest extends AssertJUnit
private IGeneralInformationService service;
+ private IETLLIMSService openbisService;
+
@BeforeMethod
public void setUp()
{
context = new Mockery();
service = context.mock(IGeneralInformationService.class);
+ openbisService = context.mock(IETLLIMSService.class);
}
@AfterMethod
@@ -103,9 +108,7 @@ public class SampleListerCommandTest extends AssertJUnit
one(service).logout(SESSION_TOKEN);
}
});
- facade =
- ch.systemsx.cisd.cina.client.util.v1.impl.CinaUtilitiesFacadeTest.createFacade(
- service, USER_ID, PASSWORD);
+
ICommand command = new MockCommandSampleLister();
int exitCode = command.execute(new String[]
@@ -135,9 +138,7 @@ public class SampleListerCommandTest extends AssertJUnit
one(service).logout(SESSION_TOKEN);
}
});
- facade =
- ch.systemsx.cisd.cina.client.util.v1.impl.CinaUtilitiesFacadeTest.createFacade(
- service, USER_ID, PASSWORD);
+
ICommand command = new MockCommandSampleLister();
try
diff --git a/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/client/util/v1/impl/CinaUtilitiesFacadeTest.java b/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/client/util/v1/impl/CinaUtilitiesFacadeTest.java
index cbdfb15401e..85548c9d7da 100644
--- a/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/client/util/v1/impl/CinaUtilitiesFacadeTest.java
+++ b/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/client/util/v1/impl/CinaUtilitiesFacadeTest.java
@@ -26,9 +26,11 @@ import org.testng.annotations.AfterMethod;
import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;
+import ch.systemsx.cisd.openbis.generic.shared.IETLLIMSService;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.IGeneralInformationService;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Sample;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SampleType;
/**
* @author Chandrasekhar Ramakrishnan
@@ -45,11 +47,14 @@ public class CinaUtilitiesFacadeTest extends AssertJUnit
private IGeneralInformationService service;
+ private IETLLIMSService openbisService;
+
@BeforeMethod
public void setUp()
{
context = new Mockery();
service = context.mock(IGeneralInformationService.class);
+ openbisService = context.mock(IETLLIMSService.class);
}
@AfterMethod
@@ -61,7 +66,7 @@ public class CinaUtilitiesFacadeTest extends AssertJUnit
}
@Test
- public void test()
+ public void testSearchForSamples()
{
final SearchCriteria searchCriteria = new SearchCriteria();
context.checking(new Expectations()
@@ -81,7 +86,8 @@ public class CinaUtilitiesFacadeTest extends AssertJUnit
one(service).logout(SESSION_TOKEN);
}
});
- CinaUtilitiesFacade facade = createFacade(service, USER_ID, PASSWORD);
+ CinaUtilitiesFacade facade = createFacade(service, openbisService);
+ facade.login(USER_ID, PASSWORD);
assertEquals(facade.getSessionToken(), SESSION_TOKEN);
List<Sample> result = facade.searchForSamples(searchCriteria);
assertEquals(0, result.size());
@@ -89,13 +95,54 @@ public class CinaUtilitiesFacadeTest extends AssertJUnit
context.assertIsSatisfied();
}
+ @Test
+ public void testGenerateSampleCode()
+ {
+ final String sampleTypeCode = "SampleTypeCode";
+ final SampleType sampleType = new SampleType();
+ sampleType.setAutoGeneratedCode(true);
+ sampleType.setGeneratedCodePrefix("STC-");
+ context.checking(new Expectations()
+ {
+ {
+ one(service).tryToAuthenticateForAllServices(USER_ID, PASSWORD);
+ will(returnValue(SESSION_TOKEN));
+
+ one(openbisService).getSampleType(SESSION_TOKEN, sampleTypeCode);
+ will(returnValue(sampleType));
+
+ one(openbisService).drawANewUniqueID(SESSION_TOKEN);
+ will(returnValue((long) 1));
+
+ one(service).logout(SESSION_TOKEN);
+ }
+ });
+ CinaUtilitiesFacade facade = createFacade(service, openbisService);
+ facade.login(USER_ID, PASSWORD);
+ assertEquals(facade.getSessionToken(), SESSION_TOKEN);
+ String result = facade.generateSampleCode(sampleTypeCode);
+ assertEquals("STC-1", result);
+ facade.logout();
+ context.assertIsSatisfied();
+ }
+
+ /**
+ * Utility method to create a CinaUtilitiesFacade object for testing.
+ */
+ public static CinaUtilitiesFacade createFacade(IGeneralInformationService service,
+ IETLLIMSService openbisService)
+ {
+ CinaUtilitiesFacade facade = new CinaUtilitiesFacade(service, openbisService, null);
+ return facade;
+ }
+
/**
* Utility method to create a CinaUtilitiesFacade object for testing.
*/
public static CinaUtilitiesFacade createFacade(IGeneralInformationService service,
- String userId, String password)
+ IETLLIMSService openbisService, String userId, String password)
{
- CinaUtilitiesFacade facade = new CinaUtilitiesFacade(service, null);
+ CinaUtilitiesFacade facade = new CinaUtilitiesFacade(service, openbisService, null);
facade.login(userId, password);
return facade;
}
diff --git a/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/dss/MockDefaultStorageProcessor.java b/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/dss/MockDefaultStorageProcessor.java
deleted file mode 100644
index 9308dbe7143..00000000000
--- a/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/dss/MockDefaultStorageProcessor.java
+++ /dev/null
@@ -1,58 +0,0 @@
-/*
- * Copyright 2010 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.cina.dss;
-
-import java.io.File;
-import java.util.Properties;
-
-import ch.systemsx.cisd.common.mail.IMailClient;
-import ch.systemsx.cisd.etlserver.AbstractStorageProcessor;
-import ch.systemsx.cisd.etlserver.ITypeExtractor;
-import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
-import ch.systemsx.cisd.openbis.generic.shared.dto.StorageFormat;
-
-public class MockDefaultStorageProcessor extends AbstractStorageProcessor
-{
-
- public MockDefaultStorageProcessor(final Properties properties)
- {
- super(properties);
- }
-
- public StorageFormat getStorageFormat()
- {
- return StorageFormat.PROPRIETARY;
- }
-
- public UnstoreDataAction rollback(File incomingDataSetDirectory, File storedDataDirectory,
- Throwable exception)
- {
- return null;
- }
-
- public File storeData(DataSetInformation dataSetInformation, ITypeExtractor typeExtractor,
- IMailClient mailClient, File incomingDataSetDirectory, File rootDir)
- {
- return null;
- }
-
- public File tryGetProprietaryData(File storedDataDirectory)
- {
- return null;
- }
-
-}
\ No newline at end of file
diff --git a/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/dss/StorageProcessorTest.java b/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/dss/StorageProcessorTest.java
deleted file mode 100644
index 03b98caa4f0..00000000000
--- a/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/dss/StorageProcessorTest.java
+++ /dev/null
@@ -1,139 +0,0 @@
-/*
- * Copyright 2010 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.cina.dss;
-
-import java.io.File;
-import java.io.IOException;
-import java.util.Properties;
-
-import org.jmock.Expectations;
-import org.jmock.Mockery;
-import org.testng.annotations.AfterMethod;
-import org.testng.annotations.BeforeMethod;
-import org.testng.annotations.Test;
-
-import ch.systemsx.cisd.base.tests.AbstractFileSystemTestCase;
-import ch.systemsx.cisd.cina.dss.info.CinaDataSetInfoExtractor;
-import ch.systemsx.cisd.cina.dss.info.CinaTypeExtractor;
-import ch.systemsx.cisd.common.mail.IMailClient;
-import ch.systemsx.cisd.common.mail.MailClient;
-import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
-import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewExperiment;
-import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifier;
-
-/**
- * @author Chandrasekhar Ramakrishnan
- */
-public class StorageProcessorTest extends AbstractFileSystemTestCase
-{
- Mockery context;
-
- IEncapsulatedOpenBISService openbisService;
-
- CinaDataSetInfoExtractor extractor;
-
- CinaTypeExtractor typeExtractor;
-
- StorageProcessor storageProcessor;
-
- IMailClient mailClient;
-
- File rootDir;
-
- File emailDir;
-
- private void initializeDSSInfrastructure()
- {
- context = new Mockery();
- openbisService = context.mock(IEncapsulatedOpenBISService.class);
- extractor = new CinaDataSetInfoExtractor(new Properties());
- typeExtractor = new CinaTypeExtractor(new Properties());
- rootDir = new File("sourceTest/java/ch/systemsx/cisd/cina/dss/info/");
- }
-
- private void initializeMailClient()
- {
- String emailFolderPath = workingDirectory.getPath() + "/emails";
- mailClient = new MailClient("sender", "file://" + emailFolderPath);
- emailDir = new File(emailFolderPath);
- }
-
- private void initializeStorageProcessor()
- {
- final Properties props = new Properties();
- props.setProperty("data-store-server-code", "DSS1");
- // Don't use this
- // props.setProperty("data-folder", "targets/playground/data") ;
- props.setProperty("storeroot-dir", "store");
- // workingDirectory
- props.setProperty("mail.smtp.host", emailDir.getPath());
- props.setProperty("mail.from", "datastore_server@localhost");
- props.setProperty("processor", "ch.systemsx.cisd.cina.dss.MockDefaultStorageProcessor");
- storageProcessor = new StorageProcessor(props);
- }
-
- @Override
- @BeforeMethod
- public void setUp() throws IOException
- {
- // Override setUp and call super first to make sure the working directory has been created
- super.setUp();
-
- // create openbis, extractor, other necessary infrastructure
- initializeDSSInfrastructure();
-
- initializeMailClient();
-
- initializeStorageProcessor();
- }
-
- @AfterMethod
- public void afterMethod()
- {
- // To following line of code should also be called at the end of each test method.
- // Otherwise one do not known which test failed.
- context.assertIsSatisfied();
- }
-
- @Test
- public void testRegisterExperiment()
- {
- // set up the expectations
- context.checking(new Expectations()
- {
- {
- one(openbisService).tryToGetExperiment(with(any(ExperimentIdentifier.class)));
- will(returnValue(null));
- one(openbisService).registerExperiment(with(any(NewExperiment.class)));
- }
- });
-
- // "store" the data set
- doStoreData(new File(
- "sourceTest/java/ch/systemsx/cisd/cina/dss/info/experiment-data-folder"));
- }
-
- private void doStoreData(File datasetFolder)
- {
- DataSetInformation dataSetInformation =
- extractor.getDataSetInformation(datasetFolder, openbisService);
-
- storageProcessor.storeData(dataSetInformation, typeExtractor, mailClient, datasetFolder,
- rootDir);
- }
-}
diff --git a/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/dss/info/CinaDataSetInfoExtractorTest.java b/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/dss/info/CinaDataSetInfoExtractorTest.java
deleted file mode 100644
index 047286c2edc..00000000000
--- a/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/dss/info/CinaDataSetInfoExtractorTest.java
+++ /dev/null
@@ -1,133 +0,0 @@
-/*
- * Copyright 2010 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.cina.dss.info;
-
-import java.io.File;
-import java.util.Properties;
-
-import org.jmock.Expectations;
-import org.jmock.Mockery;
-import org.testng.AssertJUnit;
-import org.testng.annotations.AfterMethod;
-import org.testng.annotations.BeforeMethod;
-import org.testng.annotations.Test;
-
-import ch.systemsx.cisd.common.exceptions.UserFailureException;
-import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
-import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Experiment;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewExperiment;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewSample;
-import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifier;
-import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
-
-/**
- * @author Chandrasekhar Ramakrishnan
- */
-public class CinaDataSetInfoExtractorTest extends AssertJUnit
-{
- Mockery context;
-
- IEncapsulatedOpenBISService openbisService;
-
- CinaDataSetInfoExtractor extractor;
-
- @BeforeMethod
- public void beforeMethod()
- {
- context = new Mockery();
- openbisService = context.mock(IEncapsulatedOpenBISService.class);
- extractor = new CinaDataSetInfoExtractor(new Properties());
- }
-
- @AfterMethod
- public void afterMethod()
- {
- // To following line of code should also be called at the end of each test method.
- // Otherwise one do not known which test failed.
- context.assertIsSatisfied();
- }
-
- @Test
- public void testRegisterExperiment()
- {
- context.checking(new Expectations()
- {
- {
- one(openbisService).tryToGetExperiment(with(any(ExperimentIdentifier.class)));
- will(returnValue(null));
- one(openbisService).registerExperiment(with(any(NewExperiment.class)));
- }
- });
-
- File experimentFolder =
- new File("sourceTest/java/ch/systemsx/cisd/cina/dss/info/experiment-data-folder");
- DataSetInformation dataSetInformation =
- extractor.getDataSetInformation(experimentFolder, openbisService);
-
- assertTrue("no-one@nowhere.ch".equals(dataSetInformation.tryGetUploadingUserEmail()));
- }
-
- @Test
- public void testRegisterSample()
- {
- final Experiment existingExperiment = new Experiment();
- context.checking(new Expectations()
- {
- {
- one(openbisService).tryToGetExperiment(with(any(ExperimentIdentifier.class)));
- will(returnValue(existingExperiment));
- one(openbisService).tryGetSampleWithExperiment(
- with(any(SampleIdentifier.class)));
- will(returnValue(null));
- one(openbisService).registerSample(with(any(NewSample.class)),
- with(aNull(String.class)));
- }
- });
-
- File sampleFolder =
- new File("sourceTest/java/ch/systemsx/cisd/cina/dss/info/sample-data-folder");
- DataSetInformation dataSetInformation =
- extractor.getDataSetInformation(sampleFolder, openbisService);
-
- assertTrue("no-one@nowhere.ch".equals(dataSetInformation.tryGetUploadingUserEmail()));
- }
-
- @Test
- public void testRegisterAmbiguousFolder()
- {
- File ambiguousDataFolder =
- new File("sourceTest/java/ch/systemsx/cisd/cina/dss/info/ambiguous-data-folder");
-
- try
- {
- extractor.getDataSetInformation(ambiguousDataFolder, openbisService);
- fail("An ambiguous data folder should result in a UserFailureException.");
- } catch (UserFailureException ex)
- {
-
- }
- }
-
- @Test
- public void testRegisterEmptyFolder()
- {
- File emptyDataFolder =
- new File("sourceTest/java/ch/systemsx/cisd/cina/dss/info/empty-data-folder");
- extractor.getDataSetInformation(emptyDataFolder, openbisService);
- }
-}
diff --git a/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/dss/info/ExperimentMetadataExtractorTest.java b/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/dss/info/ExperimentMetadataExtractorTest.java
deleted file mode 100644
index 94b1aaa2062..00000000000
--- a/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/dss/info/ExperimentMetadataExtractorTest.java
+++ /dev/null
@@ -1,237 +0,0 @@
-/*
- * Copyright 2010 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.cina.dss.info;
-
-import java.util.HashMap;
-
-import org.jmock.Expectations;
-import org.jmock.Mockery;
-import org.testng.AssertJUnit;
-import org.testng.annotations.AfterMethod;
-import org.testng.annotations.BeforeMethod;
-import org.testng.annotations.Test;
-
-import ch.systemsx.cisd.common.exceptions.EnvironmentFailureException;
-import ch.systemsx.cisd.common.exceptions.UserFailureException;
-import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
-import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Experiment;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewExperiment;
-import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifier;
-import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ProjectIdentifier;
-import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ProjectIdentifierFactory;
-
-/**
- * @author Chandrasekhar Ramakrishnan
- */
-public class ExperimentMetadataExtractorTest extends AssertJUnit
-{
- Mockery context;
-
- DataSetInformation dataSetInformation;
-
- IEncapsulatedOpenBISService openbisService;
-
- @BeforeMethod
- public void beforeMethod()
- {
- dataSetInformation = new DataSetInformation();
- context = new Mockery();
- openbisService = context.mock(IEncapsulatedOpenBISService.class);
- }
-
- @AfterMethod
- public void afterMethod()
- {
- // To following line of code should also be called at the end of each test method.
- // Otherwise one do not known which test failed.
- context.assertIsSatisfied();
- }
-
- /**
- * Creates dummy metadata and invokes the ExperimentMetadataExtrator.
- */
- @Test
- public void testSuccessfulExperimentRegistration()
- {
- final String projectIdString = "/CINA/CINA1";
- final String experimentCodePrefix = "EXP";
- final String experimentCodeSuffix = "SUFFIX";
- final String ownerEmail = "no-one@nowhere.ch";
-
- final HashMap<String, String> experimentMetadata = new HashMap<String, String>();
- experimentMetadata.put("project.identifier", projectIdString);
- experimentMetadata.put("experiment.code-prefix", experimentCodePrefix);
- experimentMetadata.put("experiment.owner-email", ownerEmail);
-
- final ProjectIdentifier projectIdentifier =
- new ProjectIdentifierFactory(projectIdString).createIdentifier();
-
- final ExperimentIdentifier identifier =
- new ExperimentIdentifier(projectIdentifier, experimentCodePrefix + "-"
- + experimentCodeSuffix);
- final NewExperiment newExperiment =
- new NewExperiment(identifier.toString(), "CINA_EXP_TYPE");
- context.checking(new Expectations()
- {
- {
- one(openbisService).tryToGetExperiment(identifier);
- will(returnValue(null));
- // TODO: This does not check the type of the new experiment -- it only tests
- // that the identifier of the new experiment is the one specified above.
- one(openbisService).registerExperiment(newExperiment);
- }
- });
-
- ExperimentRegistrationInformationExtractor extractor =
- new ExperimentRegistrationInformationExtractor(dataSetInformation, experimentMetadata,
- experimentCodeSuffix, openbisService);
- extractor.processMetadataAndFillDataSetInformation();
- assertEquals(ownerEmail, dataSetInformation.tryGetUploadingUserEmail());
-
- context.assertIsSatisfied();
- }
-
- /**
- * Tries to register an experiment that is already in the database (this should not happen in
- * practice)
- */
- @Test
- public void testDuplicateExperimentRegistration()
- {
- final String projectIdString = "/CINA/CINA1";
- final String experimentCodePrefix = "EXP";
- final String experimentCodeSuffix = "SUFFIX";
- final String ownerEmail = "no-one@nowhere.ch";
-
- final HashMap<String, String> experimentMetadata = new HashMap<String, String>();
- experimentMetadata.put("project.identifier", projectIdString);
- experimentMetadata.put("experiment.code-prefix", experimentCodePrefix);
- experimentMetadata.put("experiment.owner-email", ownerEmail);
-
- final ProjectIdentifier projectIdentifier =
- new ProjectIdentifierFactory(projectIdString).createIdentifier();
-
- final ExperimentIdentifier identifier =
- new ExperimentIdentifier(projectIdentifier, experimentCodePrefix + "-"
- + experimentCodeSuffix);
- final Experiment existingExperiment = new Experiment();
- context.checking(new Expectations()
- {
- {
- one(openbisService).tryToGetExperiment(identifier);
- will(returnValue(existingExperiment));
- }
- });
-
- ExperimentRegistrationInformationExtractor extractor =
- new ExperimentRegistrationInformationExtractor(dataSetInformation, experimentMetadata,
- experimentCodeSuffix, openbisService);
- try
- {
- extractor.processMetadataAndFillDataSetInformation();
- fail("Registering a duplicate experiment should throw an exception.");
- } catch (EnvironmentFailureException ex)
- {
- // this should happen
- }
- assertEquals(ownerEmail, dataSetInformation.tryGetUploadingUserEmail());
-
- context.assertIsSatisfied();
- }
-
- /**
- * Tries to register an experiment where required metadata is missing.
- */
- @Test
- public void testRegisterExperimentWithMissingProjectCode()
- {
- final String experimentCode = "EXP";
- final String experimentCodeSuffix = "SUFFIX";
- final String ownerEmail = "no-one@nowhere.ch";
-
- final HashMap<String, String> experimentMetadata = new HashMap<String, String>();
- experimentMetadata.put("experiment.code", experimentCode);
- experimentMetadata.put("experiment.owner-email", ownerEmail);
-
- ExperimentRegistrationInformationExtractor extractor =
- new ExperimentRegistrationInformationExtractor(dataSetInformation, experimentMetadata,
- experimentCodeSuffix, openbisService);
- try
- {
- extractor.processMetadataAndFillDataSetInformation();
- fail("Project code was not specified -- this should result in an exception");
- } catch (UserFailureException ex)
- {
- // This should happen
- }
- }
-
- /**
- * Tries to register an experiment where required metadata is missing.
- */
- @Test
- public void testRegisterExperimentWithMissingExperimentCodePrefix()
- {
- final String projectCode = "CINA1";
- final String experimentCodeSuffix = "SUFFIX";
- final String ownerEmail = "no-one@nowhere.ch";
-
- final HashMap<String, String> experimentMetadata = new HashMap<String, String>();
- experimentMetadata.put("project.code", projectCode);
- experimentMetadata.put("experiment.owner-email", ownerEmail);
-
- ExperimentRegistrationInformationExtractor extractor =
- new ExperimentRegistrationInformationExtractor(dataSetInformation, experimentMetadata,
- experimentCodeSuffix, openbisService);
- try
- {
- extractor.processMetadataAndFillDataSetInformation();
- fail("Experiment code prefix was not specified -- this should result in an exception");
- } catch (UserFailureException ex)
- {
- // This should happen
- }
- }
-
- /**
- * Tries to register an experiment where required metadata is missing.
- */
- @Test
- public void testRegisterExperimentWithMissingEmailAddress()
- {
- final String projectCode = "CINA1";
- final String experimentCode = "EXP";
- final String experimentCodeSuffix = "SUFFIX";
-
- final HashMap<String, String> experimentMetadata = new HashMap<String, String>();
- experimentMetadata.put("project.code", projectCode);
- experimentMetadata.put("experiment.code", experimentCode);
-
- ExperimentRegistrationInformationExtractor extractor =
- new ExperimentRegistrationInformationExtractor(dataSetInformation, experimentMetadata,
- experimentCodeSuffix, openbisService);
- try
- {
- extractor.processMetadataAndFillDataSetInformation();
- fail("Owner email address was not specified -- this should result in an exception");
- } catch (UserFailureException ex)
- {
- // This should happen
- }
- }
-}
diff --git a/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/dss/info/FolderOracleTest.java b/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/dss/info/FolderOracleTest.java
deleted file mode 100644
index 98638f0f596..00000000000
--- a/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/dss/info/FolderOracleTest.java
+++ /dev/null
@@ -1,88 +0,0 @@
-/*
- * Copyright 2010 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.cina.dss.info;
-
-import java.io.File;
-
-import org.testng.AssertJUnit;
-import org.testng.annotations.Test;
-
-import ch.systemsx.cisd.cina.dss.info.FolderOracle.FolderMetadata;
-import ch.systemsx.cisd.cina.dss.info.FolderOracle.FolderType;
-import ch.systemsx.cisd.common.exceptions.UserFailureException;
-
-/**
- * @author Chandrasekhar Ramakrishnan
- */
-public class FolderOracleTest extends AssertJUnit
-{
-
- @Test
- public void testExperimentFolder()
- {
- FolderOracle folderOracle = new FolderOracle();
- File experimentFolder =
- new File("sourceTest/java/ch/systemsx/cisd/cina/dss/info/experiment-data-folder");
- FolderMetadata metadata = folderOracle.getFolderMetadataForFolder(experimentFolder);
- assertEquals(metadata.getType(), FolderType.EXPERIMENT);
- assertEquals("experiment.properties", metadata.tryGetMarkerFile().getName());
- // The folder doesn't have an XML metadata file
- assertNull(metadata.tryGetMetadataXMLFile());
- }
-
- @Test
- public void testSampleFolder()
- {
- FolderOracle folderOracle = new FolderOracle();
- File sampleFolder =
- new File("sourceTest/java/ch/systemsx/cisd/cina/dss/info/sample-data-folder");
- FolderMetadata metadata = folderOracle.getFolderMetadataForFolder(sampleFolder);
- assertEquals(metadata.getType(), FolderType.SAMPLE);
- assertEquals("sample.properties", metadata.tryGetMarkerFile().getName());
- // The folder doesn't have an XML metadata file
- assertNull(metadata.tryGetMetadataXMLFile());
- }
-
- @Test
- public void testDataSetFolder()
- {
- FolderOracle folderOracle = new FolderOracle();
- File datasetFolder =
- new File("sourceTest/java/ch/systemsx/cisd/cina/dss/info/dataset-data-folder");
- FolderMetadata metadata = folderOracle.getFolderMetadataForFolder(datasetFolder);
- assertEquals(metadata.getType(), FolderType.DATA_SET);
- assertEquals("dataset.properties", metadata.tryGetMarkerFile().getName());
- assertNotNull(metadata.tryGetMetadataXMLFile());
- assertEquals("metadata.xml", metadata.tryGetMetadataXMLFile().getName());
- }
-
- @Test
- public void testAmbiguousFolder()
- {
- FolderOracle folderOracle = new FolderOracle();
- File ambiguousFolder =
- new File("sourceTest/java/ch/systemsx/cisd/cina/dss/info/ambiguous-data-folder");
- try
- {
- folderOracle.getFolderMetadataForFolder(ambiguousFolder);
- fail("The method getMetadataForFolder should throw an error on folder ambiguous-data-folder.");
- } catch (UserFailureException ex)
- {
- // This should happen
- }
- }
-}
diff --git a/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/dss/info/SampleMetadataExtractorTest.java b/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/dss/info/SampleMetadataExtractorTest.java
deleted file mode 100644
index 6232930ac6b..00000000000
--- a/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/dss/info/SampleMetadataExtractorTest.java
+++ /dev/null
@@ -1,337 +0,0 @@
-/*
- * Copyright 2010 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.cina.dss.info;
-
-import java.util.HashMap;
-
-import org.jmock.Expectations;
-import org.jmock.Mockery;
-import org.testng.AssertJUnit;
-import org.testng.annotations.AfterMethod;
-import org.testng.annotations.BeforeMethod;
-import org.testng.annotations.Test;
-
-import ch.systemsx.cisd.common.exceptions.EnvironmentFailureException;
-import ch.systemsx.cisd.common.exceptions.UserFailureException;
-import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
-import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Experiment;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewSample;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SampleType;
-import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifier;
-import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifierFactory;
-import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.GroupIdentifier;
-import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
-import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleOwnerIdentifier;
-
-/**
- * @author Chandrasekhar Ramakrishnan
- */
-public class SampleMetadataExtractorTest extends AssertJUnit
-{
- Mockery context;
-
- DataSetInformation dataSetInformation;
-
- IEncapsulatedOpenBISService openbisService;
-
- @BeforeMethod
- public void beforeMethod()
- {
- dataSetInformation = new DataSetInformation();
- context = new Mockery();
- openbisService = context.mock(IEncapsulatedOpenBISService.class);
- }
-
- @AfterMethod
- public void afterMethod()
- {
- // To following line of code should also be called at the end of each test method.
- // Otherwise one do not known which test failed.
- context.assertIsSatisfied();
- }
-
- /**
- * Creates dummy metadata and invokes the SampleMetadataExtrator.
- */
- @Test
- public void testSuccessfulSampleRegistration()
- {
- final String experimentId = "/CINA/CINA1/EXP1";
- final String sampleCodePrefix = "S";
- final String sampleCodeSuffix = "SUFFIX";
- final String ownerEmail = "no-one@nowhere.ch";
-
- final HashMap<String, String> sampleMetadata = new HashMap<String, String>();
- sampleMetadata.put("experiment.identifier", experimentId);
- sampleMetadata.put("sample.code-prefix", sampleCodePrefix);
- sampleMetadata.put("experiment.owner-email", ownerEmail);
-
- final ExperimentIdentifier experimentIdentifier =
- new ExperimentIdentifierFactory(experimentId).createIdentifier();
- final Experiment experiment = new Experiment();
- experiment.setIdentifier(experimentIdentifier.toString());
-
- final SampleIdentifier sampleIdentifier =
- new SampleIdentifier(new GroupIdentifier((String) null, "CINA"), sampleCodePrefix
- + "-" + sampleCodeSuffix);
-
- final NewSample newSample = new NewSample();
- SampleType sampleType = new SampleType();
- sampleType.setCode("CINA_SAMPLE_TYPE");
- newSample.setSampleType(sampleType);
- newSample.setExperimentIdentifier(experimentId.toString());
- newSample.setIdentifier(sampleIdentifier.toString());
- context.checking(new Expectations()
- {
- {
- one(openbisService).tryToGetExperiment(experimentIdentifier);
- will(returnValue(experiment));
- one(openbisService).tryGetSampleWithExperiment(sampleIdentifier);
- will(returnValue(null));
- one(openbisService).registerSample(newSample, null);
- }
- });
-
- SampleRegistrationInformationExtractor extractor =
- new SampleRegistrationInformationExtractor(dataSetInformation, sampleMetadata, sampleCodeSuffix,
- openbisService);
- extractor.processMetadataAndFillDataSetInformation();
- assertEquals(ownerEmail, dataSetInformation.tryGetUploadingUserEmail());
- assertEquals("/CINA/S-SUFFIX", dataSetInformation.getSampleIdentifier().toString());
-
- context.assertIsSatisfied();
- }
-
- /**
- * Tries to register a sample that is already in the database (this should not happen in
- * practice)
- */
- @Test
- public void testDuplicateSampleRegistration()
- {
- final String experimentId = "/CINA/CINA1/EXP1";
- final String sampleCodePrefix = "S";
- final String sampleCodeSuffix = "SUFFIX";
- final String ownerEmail = "no-one@nowhere.ch";
-
- final HashMap<String, String> sampleMetadata = new HashMap<String, String>();
- sampleMetadata.put("experiment.identifier", experimentId);
- sampleMetadata.put("sample.code-prefix", sampleCodePrefix);
- sampleMetadata.put("experiment.owner-email", ownerEmail);
-
- final ExperimentIdentifier experimentIdentifier =
- new ExperimentIdentifierFactory(experimentId).createIdentifier();
- final Experiment experiment = new Experiment();
- experiment.setIdentifier(experimentIdentifier.toString());
-
- final SampleIdentifier sampleIdentifier =
- new SampleIdentifier(new GroupIdentifier((String) null, "CINA"), sampleCodePrefix
- + "-" + sampleCodeSuffix);
-
- final Sample existingSample = new Sample();
- context.checking(new Expectations()
- {
- {
- one(openbisService).tryToGetExperiment(experimentIdentifier);
- will(returnValue(experiment));
- one(openbisService).tryGetSampleWithExperiment(sampleIdentifier);
- will(returnValue(existingSample));
- }
- });
-
- SampleRegistrationInformationExtractor extractor =
- new SampleRegistrationInformationExtractor(dataSetInformation, sampleMetadata, sampleCodeSuffix,
- openbisService);
-
- try
- {
- extractor.processMetadataAndFillDataSetInformation();
- fail("Registering a duplicate sample should throw an exception.");
- } catch (EnvironmentFailureException ex)
- {
- // this should happen
- }
- assertEquals(ownerEmail, dataSetInformation.tryGetUploadingUserEmail());
-
- context.assertIsSatisfied();
- }
-
- /**
- * Tries to register an sample where required metadata is missing.
- */
- @Test
- public void testRegisterExperimentWithMissingExperimentIdentifier()
- {
- final String sampleCodePrefix = "S";
- final String sampleCodeSuffix = "SUFFIX";
- final String ownerEmail = "no-one@nowhere.ch";
-
- final HashMap<String, String> sampleMetadata = new HashMap<String, String>();
- sampleMetadata.put("sample.code-prefix", sampleCodePrefix);
- sampleMetadata.put("experiment.owner-email", ownerEmail);
-
- SampleRegistrationInformationExtractor extractor =
- new SampleRegistrationInformationExtractor(dataSetInformation, sampleMetadata, sampleCodeSuffix,
- openbisService);
- try
- {
- extractor.processMetadataAndFillDataSetInformation();
- fail("Experiment identifier was not specified -- this should result in an exception");
- } catch (UserFailureException ex)
- {
- // This should happen
- }
- }
-
- /**
- * Tries to register an sample where required metadata is missing.
- */
- @Test
- public void testRegisterExperimentWithJunkExperimentIdentifier()
- {
- final String experimentId = "/CINA-adf-EXP1";
- final String sampleCodePrefix = "S";
- final String sampleCodeSuffix = "SUFFIX";
- final String ownerEmail = "no-one@nowhere.ch";
-
- final HashMap<String, String> sampleMetadata = new HashMap<String, String>();
- sampleMetadata.put("experiment.identifier", experimentId);
- sampleMetadata.put("sample.code-prefix", sampleCodePrefix);
- sampleMetadata.put("experiment.owner-email", ownerEmail);
-
- SampleRegistrationInformationExtractor extractor =
- new SampleRegistrationInformationExtractor(dataSetInformation, sampleMetadata, sampleCodeSuffix,
- openbisService);
- try
- {
- extractor.processMetadataAndFillDataSetInformation();
- fail("Experiment identifier was not in the correct format -- this should result in an exception");
- } catch (UserFailureException ex)
- {
- // This should happen
- }
- }
-
- /**
- * Tries to register an sample where required metadata is missing.
- */
- @Test
- public void testRegisterExperimentWithInvalidExperimentIdentifier()
- {
- final String experimentId = "/CINA/CINA1/EXP482";
- final String sampleCodePrefix = "S";
- final String sampleCodeSuffix = "SUFFIX";
- final String ownerEmail = "no-one@nowhere.ch";
-
- final HashMap<String, String> sampleMetadata = new HashMap<String, String>();
- sampleMetadata.put("experiment.identifier", experimentId);
- sampleMetadata.put("sample.code-prefix", sampleCodePrefix);
- sampleMetadata.put("experiment.owner-email", ownerEmail);
-
- final ExperimentIdentifier experimentIdentifier =
- new ExperimentIdentifierFactory(experimentId).createIdentifier();
-
- final SampleIdentifier sampleIdentifier =
- SampleIdentifier.createOwnedBy(new SampleOwnerIdentifier(experimentIdentifier),
- sampleCodePrefix + "-" + sampleCodeSuffix);
-
- final NewSample newSample = new NewSample();
- SampleType sampleType = new SampleType();
- sampleType.setCode("CINA_SAMPLE_TYPE");
- newSample.setSampleType(sampleType);
- newSample.setExperimentIdentifier(experimentId.toString());
- newSample.setIdentifier(sampleIdentifier.toString());
- context.checking(new Expectations()
- {
- {
- one(openbisService).tryToGetExperiment(experimentIdentifier);
- will(returnValue(null));
- }
- });
-
- SampleRegistrationInformationExtractor extractor =
- new SampleRegistrationInformationExtractor(dataSetInformation, sampleMetadata, sampleCodeSuffix,
- openbisService);
- try
- {
- extractor.processMetadataAndFillDataSetInformation();
- fail("There is no experiment with the provided identifier -- this should result in an exception");
- } catch (UserFailureException ex)
- {
- // This should happen
- }
- assertEquals(ownerEmail, dataSetInformation.tryGetUploadingUserEmail());
-
- context.assertIsSatisfied();
- }
-
- /**
- * Tries to register an sample where required metadata is missing.
- */
- @Test
- public void testRegisterSampleWithMissingSampleCodePrefix()
- {
- final String experimentId = "/CINA/CINA1/EXP1";
- final String sampleCodeSuffix = "SUFFIX";
- final String ownerEmail = "no-one@nowhere.ch";
-
- final HashMap<String, String> sampleMetadata = new HashMap<String, String>();
- sampleMetadata.put("experiment.identifier", experimentId);
- sampleMetadata.put("experiment.owner-email", ownerEmail);
-
- SampleRegistrationInformationExtractor extractor =
- new SampleRegistrationInformationExtractor(dataSetInformation, sampleMetadata, sampleCodeSuffix,
- openbisService);
- try
- {
- extractor.processMetadataAndFillDataSetInformation();
- fail("Sample code prefix was not specified -- this should result in an exception");
- } catch (UserFailureException ex)
- {
- // This should happen
- }
- }
-
- /**
- * Tries to register an sample where required metadata is missing.
- */
- @Test
- public void testRegisterSampleWithMissingEmailAddress()
- {
- final String experimentId = "/CINA/CINA1/EXP1";
- final String sampleCodePrefix = "S";
- final String sampleCodeSuffix = "SUFFIX";
-
- final HashMap<String, String> sampleMetadata = new HashMap<String, String>();
- sampleMetadata.put("experiment.identifier", experimentId);
- sampleMetadata.put("sample.code-prefix", sampleCodePrefix);
-
- SampleRegistrationInformationExtractor extractor =
- new SampleRegistrationInformationExtractor(dataSetInformation, sampleMetadata, sampleCodeSuffix,
- openbisService);
- try
- {
- extractor.processMetadataAndFillDataSetInformation();
- fail("Owner email address was not specified -- this should result in an exception");
- } catch (UserFailureException ex)
- {
- // This should happen
- }
- }
-}
diff --git a/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/dss/info/ambiguous-data-folder/dataset.properties b/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/dss/info/ambiguous-data-folder/dataset.properties
deleted file mode 100644
index 124fde3eff7..00000000000
--- a/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/dss/info/ambiguous-data-folder/dataset.properties
+++ /dev/null
@@ -1,3 +0,0 @@
-project.code = CINA1
-experiment.code = EXP
-experiment.owner-email = no-one@nowhere.ch
\ No newline at end of file
diff --git a/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/dss/info/ambiguous-data-folder/sample.properties b/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/dss/info/ambiguous-data-folder/sample.properties
deleted file mode 100644
index 124fde3eff7..00000000000
--- a/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/dss/info/ambiguous-data-folder/sample.properties
+++ /dev/null
@@ -1,3 +0,0 @@
-project.code = CINA1
-experiment.code = EXP
-experiment.owner-email = no-one@nowhere.ch
\ No newline at end of file
diff --git a/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/dss/info/dataset-data-folder/dataset.properties b/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/dss/info/dataset-data-folder/dataset.properties
deleted file mode 100644
index 124fde3eff7..00000000000
--- a/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/dss/info/dataset-data-folder/dataset.properties
+++ /dev/null
@@ -1,3 +0,0 @@
-project.code = CINA1
-experiment.code = EXP
-experiment.owner-email = no-one@nowhere.ch
\ No newline at end of file
diff --git a/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/dss/info/dataset-data-folder/metadata.xml b/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/dss/info/dataset-data-folder/metadata.xml
deleted file mode 100644
index e053af4a7e1..00000000000
--- a/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/dss/info/dataset-data-folder/metadata.xml
+++ /dev/null
@@ -1,63 +0,0 @@
-<?xml version="1.0" standalone="yes"?>
-<LVData xmlns="http://www.ni.com/LVData">
- <Version>8.6.1</Version>
- <Cluster>
- <Name>GeneralDatabaseEnty</Name>
- <NumElts>9</NumElts>
- <DBL>
- <Name>Experiment identifier</Name>
- <Val>0.00000000000000</Val>
- </DBL>
- <String>
- <Name>Operator</Name>
- <Val>dedeed</Val>
- </String>
- <Timestamp>
- <Name>Creation data</Name>
- <Cluster>
- <Name/>
- <NumElts>4</NumElts>
- <I32>
- <Name/>
- <Val>0</Val>
- </I32>
- <I32>
- <Name/>
- <Val>348413952</Val>
- </I32>
- <I32>
- <Name/>
- <Val>-946831183</Val>
- </I32>
- <I32>
- <Name/>
- <Val>0</Val>
- </I32>
- </Cluster>
- </Timestamp>
- <String>
- <Name>Description</Name>
- <Val>wqded ewdewdewd wedewdewd wedewdewd wedewdew §</Val>
- </String>
- <DBL>
- <Name>Sample identifier</Name>
- <Val>0.00000000000000</Val>
- </DBL>
- <Boolean>
- <Name>DBGetExpIndentifier</Name>
- <Val>0</Val>
- </Boolean>
- <Boolean>
- <Name>DBGetExpIndentifier 2</Name>
- <Val>0</Val>
- </Boolean>
- <Path>
- <Name>Bundle folder</Name>
- <Val>C:\Documents and Settings\tbraun\My Documents\CINA_Data_Container</Val>
- </Path>
- <String>
- <Name>Experiment name</Name>
- <Val>Wednesday10</Val>
- </String>
- </Cluster>
-</LVData>
diff --git a/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/dss/info/empty-data-folder/.gitignore b/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/dss/info/empty-data-folder/.gitignore
deleted file mode 100644
index e69de29bb2d..00000000000
diff --git a/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/dss/info/experiment-data-folder/experiment.properties b/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/dss/info/experiment-data-folder/experiment.properties
deleted file mode 100644
index f15a939bc1b..00000000000
--- a/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/dss/info/experiment-data-folder/experiment.properties
+++ /dev/null
@@ -1,3 +0,0 @@
-project.identifier = /CINA/CINA1
-experiment.code-prefix = EXP
-experiment.owner-email = no-one@nowhere.ch
\ No newline at end of file
diff --git a/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/dss/info/sample-data-folder/sample.properties b/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/dss/info/sample-data-folder/sample.properties
deleted file mode 100644
index 80ba74bf10f..00000000000
--- a/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/dss/info/sample-data-folder/sample.properties
+++ /dev/null
@@ -1,3 +0,0 @@
-experiment.identifier = /CINA/CINA1/EXP1
-experiment.owner-email = no-one@nowhere.ch
-sample.code-prefix = S
\ No newline at end of file
--
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