From bfa79c39620d924a62fbbb967c9a10d8ffb23712 Mon Sep 17 00:00:00 2001
From: pkupczyk <pkupczyk>
Date: Mon, 1 Oct 2012 08:14:59 +0000
Subject: [PATCH] SP-282/BIS-179: Failure of Sample Registration with
automatically generated codes
SVN: 26862
---
.../server/EncapsulatedOpenBISService.java | 6 -
.../shared/IEncapsulatedOpenBISService.java | 9 +-
.../openbis/generic/server/CommonServer.java | 3 +-
.../openbis/generic/server/ETLService.java | 18 +--
.../generic/server/ETLServiceLogger.java | 8 --
.../business/bo/EntityCodeGenerator.java | 135 ++++++++++++++++++
.../generic/shared/IETLLIMSService.java | 8 --
.../plugin/generic/server/GenericServer.java | 9 +-
.../systemtest/CodeGenerationTest.java | 76 ++++++++--
...DataSetInfoExtractorForProteinResults.java | 52 ++++---
...SetInfoExtractorForProteinResultsTest.java | 58 ++++----
11 files changed, 271 insertions(+), 111 deletions(-)
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/EntityCodeGenerator.java
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/EncapsulatedOpenBISService.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/EncapsulatedOpenBISService.java
index 4d0b6e9348e..21908a7ec16 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/EncapsulatedOpenBISService.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/EncapsulatedOpenBISService.java
@@ -439,12 +439,6 @@ public final class EncapsulatedOpenBISService implements IEncapsulatedOpenBISSer
return service.drawANewUniqueID(session.getSessionToken());
}
- @Override
- public long drawANewUniqueID(EntityKind entityKind)
- {
- return service.drawANewUniqueID(session.getSessionToken(), entityKind);
- }
-
@Override
public ExternalData tryGetDataSet(String dataSetCode) throws UserFailureException
{
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/IEncapsulatedOpenBISService.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/IEncapsulatedOpenBISService.java
index 680b8a014ae..a6bd6e16471 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/IEncapsulatedOpenBISService.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/IEncapsulatedOpenBISService.java
@@ -313,13 +313,6 @@ public interface IEncapsulatedOpenBISService
@ManagedAuthentication
public long drawANewUniqueID();
- /**
- * Creates a new unique ID for the specified entity kind. It is guaranteed to be unique for that
- * entity kind.
- */
- @ManagedAuthentication
- public long drawANewUniqueID(EntityKind entityKind);
-
/**
* Creates a list of specified size with new unique ID for the specified entity kind.
*/
@@ -409,7 +402,7 @@ public interface IEncapsulatedOpenBISService
*/
@ManagedAuthentication
public SessionContextDTO tryGetSession(String sessionToken);
-
+
/**
* See @{link {@link IETLLIMSService#checkSession(String)}.
*/
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/CommonServer.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/CommonServer.java
index 5471b45a67b..dad0ccd151b 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/CommonServer.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/CommonServer.java
@@ -80,6 +80,7 @@ import ch.systemsx.cisd.openbis.generic.server.authorization.validator.SampleVal
import ch.systemsx.cisd.openbis.generic.server.authorization.validator.SpaceValidator;
import ch.systemsx.cisd.openbis.generic.server.business.IPropertiesBatchManager;
import ch.systemsx.cisd.openbis.generic.server.business.bo.DataAccessExceptionTranslator;
+import ch.systemsx.cisd.openbis.generic.server.business.bo.EntityCodeGenerator;
import ch.systemsx.cisd.openbis.generic.server.business.bo.EntityTypeBO;
import ch.systemsx.cisd.openbis.generic.server.business.bo.IAttachmentBO;
import ch.systemsx.cisd.openbis.generic.server.business.bo.IAuthorizationGroupBO;
@@ -2046,7 +2047,7 @@ public final class CommonServer extends AbstractCommonServer<ICommonServerForInt
public String generateCode(String sessionToken, String prefix, EntityKind entityKind)
{
checkSession(sessionToken);
- return prefix + getDAOFactory().getCodeSequenceDAO().getNextCodeSequenceId(entityKind);
+ return new EntityCodeGenerator(getDAOFactory()).generateCode(prefix, entityKind);
}
@Override
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/ETLService.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/ETLService.java
index fc548f5534c..95a8432b189 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/ETLService.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/ETLService.java
@@ -73,6 +73,7 @@ import ch.systemsx.cisd.openbis.generic.server.business.IDataStoreServiceFactory
import ch.systemsx.cisd.openbis.generic.server.business.IPropertiesBatchManager;
import ch.systemsx.cisd.openbis.generic.server.business.IServiceConversationClientManagerLocal;
import ch.systemsx.cisd.openbis.generic.server.business.IServiceConversationServerManagerLocal;
+import ch.systemsx.cisd.openbis.generic.server.business.bo.EntityCodeGenerator;
import ch.systemsx.cisd.openbis.generic.server.business.bo.ICommonBusinessObjectFactory;
import ch.systemsx.cisd.openbis.generic.server.business.bo.IDataBO;
import ch.systemsx.cisd.openbis.generic.server.business.bo.IDataSetTable;
@@ -371,16 +372,6 @@ public class ETLService extends AbstractCommonServer<IETLLIMSService> implements
return daoFactory.getCodeSequenceDAO().getNextCodeSequenceId();
}
- @Override
- @RolesAllowed(RoleWithHierarchy.SPACE_ETL_SERVER)
- public long drawANewUniqueID(String sessionToken,
- ch.systemsx.cisd.openbis.generic.shared.basic.dto.EntityKind entityKind)
- throws UserFailureException
- {
- checkSession(sessionToken);
- return daoFactory.getCodeSequenceDAO().getNextCodeSequenceId(entityKind);
- }
-
@Override
@RolesAllowed(
{ RoleWithHierarchy.SPACE_OBSERVER, RoleWithHierarchy.SPACE_ETL_SERVER })
@@ -1154,12 +1145,7 @@ public class ETLService extends AbstractCommonServer<IETLLIMSService> implements
ch.systemsx.cisd.openbis.generic.shared.basic.dto.EntityKind entityKind, int number)
{
checkSession(sessionToken);
- ArrayList<String> result = new ArrayList<String>();
- for (int i = 0; i < number; i++)
- {
- result.add(prefix + daoFactory.getCodeSequenceDAO().getNextCodeSequenceId(entityKind));
- }
- return result;
+ return new EntityCodeGenerator(daoFactory).generateCodes(prefix, entityKind, number);
}
@Override
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/ETLServiceLogger.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/ETLServiceLogger.java
index 947bb398f80..8739e429b87 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/ETLServiceLogger.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/ETLServiceLogger.java
@@ -102,14 +102,6 @@ public class ETLServiceLogger extends AbstractServerLogger implements IETLLIMSSe
return 0;
}
- @Override
- public long drawANewUniqueID(String sessionToken, EntityKind entityKind)
- throws UserFailureException
- {
- logTracking(sessionToken, "drawANewUniqueID", "ENTITY_KIND(%s)", entityKind);
- return 0;
- }
-
@Override
public DatabaseInstance getHomeDatabaseInstance(String sessionToken)
{
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/EntityCodeGenerator.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/EntityCodeGenerator.java
new file mode 100644
index 00000000000..8b2ebe4d21b
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/EntityCodeGenerator.java
@@ -0,0 +1,135 @@
+/*
+ * Copyright 2012 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.openbis.generic.server.business.bo;
+
+import java.util.Arrays;
+import java.util.List;
+
+import net.lemnik.eodsql.BaseQuery;
+import net.lemnik.eodsql.QueryTool;
+import net.lemnik.eodsql.Select;
+
+import ch.systemsx.cisd.openbis.generic.server.business.bo.common.DatabaseContextUtils;
+import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDAOFactory;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.EntityKind;
+import ch.systemsx.cisd.openbis.generic.shared.dto.TableNames;
+
+/**
+ * Generates unique codes for openBIS entities. It uses database sequences as a base for the code
+ * generation. Moreover it verifies that the generated codes are in fact unique (i.e. entities with
+ * such codes do not exist yet). If it finds that the new generated code is already used by an
+ * existing entity (e.g. the entity code was manually entered by a user) then it regenerates the
+ * code until it is unique.
+ *
+ * @author pkupczyk
+ */
+public class EntityCodeGenerator
+{
+
+ private IDAOFactory daoFactory;
+
+ private Query query;
+
+ public EntityCodeGenerator(IDAOFactory daoFactory)
+ {
+ this.daoFactory = daoFactory;
+ }
+
+ public String generateCode(String codePrefix, EntityKind entityKind)
+ {
+ return generateCodes(codePrefix, entityKind, 1).get(0);
+ }
+
+ /**
+ * Generate unique codes for openBIS entities.
+ *
+ * @param codePrefix Prefix for the generated codes (e.g. when "ABC-" then codes will be
+ * "ABC-1", "ABC-2", ...)
+ * @param entityKind Kind of an entity the codes should be generated for (different kinds of
+ * entities use different database sequences).
+ * @param numberOfCodes Number of codes to be generated.
+ */
+ public List<String> generateCodes(String codePrefix, EntityKind entityKind, int numberOfCodes)
+ {
+ String[] codes = new String[numberOfCodes];
+
+ query = QueryTool.getQuery(DatabaseContextUtils.getConnection(daoFactory), Query.class);
+
+ for (int i = 0; i < numberOfCodes; i++)
+ {
+ long sequenceValue;
+ String code;
+
+ do
+ {
+ sequenceValue = daoFactory.getCodeSequenceDAO().getNextCodeSequenceId(entityKind);
+ code = codePrefix + sequenceValue;
+
+ } while (isCodeUsed(code, entityKind));
+
+ codes[i] = code;
+ }
+
+ return Arrays.asList(codes);
+ }
+
+ private boolean isCodeUsed(String code, EntityKind entityKind)
+ {
+ int count;
+
+ if (EntityKind.EXPERIMENT.equals(entityKind))
+ {
+ count = query.getExperimentCount(code);
+ } else if (EntityKind.SAMPLE.equals(entityKind))
+ {
+ count = query.getSampleCount(code);
+ } else if (EntityKind.DATA_SET.equals(entityKind))
+ {
+ count = query.getDataSetCount(code);
+ } else if (EntityKind.MATERIAL.equals(entityKind))
+ {
+ count = query.getMaterialsCount(code);
+ } else
+ {
+ throw new IllegalArgumentException("Unsupported entity kind: " + entityKind);
+ }
+
+ return count > 0;
+ }
+
+ private interface Query extends BaseQuery
+ {
+
+ public final static String PREFIX = "SELECT count(*) FROM ";
+
+ public final static String SUFFIX = " WHERE code = ?{1}";
+
+ @Select(sql = PREFIX + TableNames.EXPERIMENTS_ALL_TABLE + SUFFIX)
+ public int getExperimentCount(String code);
+
+ @Select(sql = PREFIX + TableNames.SAMPLES_ALL_TABLE + SUFFIX)
+ public int getSampleCount(String code);
+
+ @Select(sql = PREFIX + TableNames.DATA_ALL_TABLE + SUFFIX)
+ public int getDataSetCount(String code);
+
+ @Select(sql = PREFIX + TableNames.MATERIALS_TABLE + SUFFIX)
+ public int getMaterialsCount(String code);
+
+ }
+
+}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/IETLLIMSService.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/IETLLIMSService.java
index 93444f92c7e..a35af5f43d8 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/IETLLIMSService.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/IETLLIMSService.java
@@ -331,14 +331,6 @@ public interface IETLLIMSService extends IServer, ISessionProvider
@Transactional
public long drawANewUniqueID(String sessionToken) throws UserFailureException;
- /**
- * Draw a new unique ID for the specified entity kind. The returned value is guaranteed to be
- * unique.
- */
- @Transactional
- public long drawANewUniqueID(String sessionToken, EntityKind entityKind)
- throws UserFailureException;
-
/**
* Lists samples codes filtered by specified criteria, see {@link ListSamplesByPropertyCriteria}
* to see the details.
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/server/GenericServer.java b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/server/GenericServer.java
index 4c43ca49159..128f1f42f2e 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/server/GenericServer.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/server/GenericServer.java
@@ -56,6 +56,7 @@ import ch.systemsx.cisd.openbis.generic.server.authorization.predicate.UpdatedEx
import ch.systemsx.cisd.openbis.generic.server.batch.BatchOperationExecutor;
import ch.systemsx.cisd.openbis.generic.server.batch.IBatchOperation;
import ch.systemsx.cisd.openbis.generic.server.business.IPropertiesBatchManager;
+import ch.systemsx.cisd.openbis.generic.server.business.bo.EntityCodeGenerator;
import ch.systemsx.cisd.openbis.generic.server.business.bo.IExperimentBO;
import ch.systemsx.cisd.openbis.generic.server.business.bo.IProjectBO;
import ch.systemsx.cisd.openbis.generic.server.business.bo.ISampleBO;
@@ -698,13 +699,7 @@ public final class GenericServer extends AbstractServer<IGenericServer> implemen
ch.systemsx.cisd.openbis.generic.shared.basic.dto.EntityKind entityKind, int number)
{
checkSession(sessionToken);
- ArrayList<String> result = new ArrayList<String>();
- for (int i = 0; i < number; i++)
- {
- result.add(prefix
- + getDAOFactory().getCodeSequenceDAO().getNextCodeSequenceId(entityKind));
- }
- return result;
+ return new EntityCodeGenerator(getDAOFactory()).generateCodes(prefix, entityKind, number);
}
@Override
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/CodeGenerationTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/CodeGenerationTest.java
index 6fbcc453e50..777a1dfd557 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/CodeGenerationTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/CodeGenerationTest.java
@@ -18,10 +18,13 @@ package ch.systemsx.cisd.openbis.systemtest;
import static org.testng.AssertJUnit.assertEquals;
+import java.util.Arrays;
import java.util.Collections;
import java.util.Comparator;
import java.util.List;
+import junit.framework.Assert;
+
import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;
@@ -44,9 +47,24 @@ public class CodeGenerationTest extends SystemTestCase
@BeforeMethod
public void setSequences()
{
- simpleJdbcTemplate.queryForLong("select setval('code_seq', 8)");
- simpleJdbcTemplate.queryForLong("select setval('experiment_code_seq', 100)");
- simpleJdbcTemplate.queryForLong("select setval('sample_code_seq', 200)");
+ setCodeSequence(8);
+ setExperimentCodeSequence(100);
+ setSampleCodeSequence(200);
+ }
+
+ private void setCodeSequence(int value)
+ {
+ simpleJdbcTemplate.queryForLong("select setval('code_seq', " + value + ")");
+ }
+
+ private void setExperimentCodeSequence(int value)
+ {
+ simpleJdbcTemplate.queryForLong("select setval('experiment_code_seq', " + value + ")");
+ }
+
+ private void setSampleCodeSequence(int value)
+ {
+ simpleJdbcTemplate.queryForLong("select setval('sample_code_seq', " + value + ")");
}
@Test
@@ -60,6 +78,34 @@ public class CodeGenerationTest extends SystemTestCase
assertEquals("S-202", commonClientService.generateCode("S-", EntityKind.SAMPLE));
}
+ @Test
+ public void testCommonClientServiceGenerateCodeWhenSomeCodesAreAlreadyUsed()
+ {
+ logIntoCommonClientService();
+
+ // Experiments EXP10 and EXP11 already exist
+ setExperimentCodeSequence(10);
+ assertEquals("EXP12", commonClientService.generateCode("EXP", EntityKind.EXPERIMENT));
+ assertEquals("EXP13", commonClientService.generateCode("EXP", EntityKind.EXPERIMENT));
+
+ // Samples A10 .. A22 already exist
+ setSampleCodeSequence(10);
+ assertEquals("A23", commonClientService.generateCode("A", EntityKind.SAMPLE));
+ assertEquals("A24", commonClientService.generateCode("A", EntityKind.SAMPLE));
+
+ // Materials AD3 and AD5 already exist
+ setCodeSequence(3);
+ assertEquals("AD4", commonClientService.generateCode("AD", EntityKind.MATERIAL));
+ assertEquals("AD6", commonClientService.generateCode("AD", EntityKind.MATERIAL));
+
+ // Data sets 20120628092259000-22 .. 20120628092259000-25 already exist
+ setCodeSequence(22);
+ assertEquals("20120628092259000-26",
+ commonClientService.generateCode("20120628092259000-", EntityKind.DATA_SET));
+ assertEquals("20120628092259000-27",
+ commonClientService.generateCode("20120628092259000-", EntityKind.DATA_SET));
+ }
+
@Test
public void testGenericServerGenerateCodes()
{
@@ -77,11 +123,21 @@ public class CodeGenerationTest extends SystemTestCase
.toString());
}
+ @Test(timeOut = 1000)
+ public void testGenericServerGenerateManyCodesWhenSomeCodesAreAlreadyUsed()
+ {
+ setSampleCodeSequence(10);
+ genericServer.generateCodes(systemSessionToken, "A", EntityKind.SAMPLE, 1000);
+ }
+
@Test
- public void testETLServiceDrawANewUniqueID()
+ public void testGenericServerGenerateCodesWhenSomeCodesAreAlreadyUsed()
{
- assertEquals(9, etlService.drawANewUniqueID(systemSessionToken));
- assertEquals(201, etlService.drawANewUniqueID(systemSessionToken, EntityKind.SAMPLE));
+ // Samples A10 .. A22 already exist
+ setSampleCodeSequence(10);
+ List<String> codes =
+ genericServer.generateCodes(systemSessionToken, "A", EntityKind.SAMPLE, 5);
+ Assert.assertEquals(Arrays.asList("A23", "A24", "A25", "A26", "A27"), codes);
}
@Test
@@ -95,11 +151,14 @@ public class CodeGenerationTest extends SystemTestCase
@Test
public void testAutomaticCreationOfSampleCodesInBatchSampleRegistration()
{
+ // Samples A10 .. A22 already exist
+ setSampleCodeSequence(10);
+
String sessionID = logIntoCommonClientService().getSessionID();
uploadFile("testAutomaticCreationOfSampleCodesInBatchSampleRegistration.txt",
"experiment\tCOMMENT\n" + "/CISD/NEMO/EXP1\tA\n" + "/CISD/NEMO/EXP1\tB\n");
SampleType sampleType = new SampleType();
- sampleType.setGeneratedCodePrefix("SAMPLE-");
+ sampleType.setGeneratedCodePrefix("A");
sampleType.setCode("CELL_PLATE");
genericClientService.registerSamples(sampleType, SESSION_KEY, "/CISD", false);
@@ -124,7 +183,6 @@ public class CodeGenerationTest extends SystemTestCase
builder.append(sample.getIdentifier()).append(":").append(sample.getProperties());
builder.append("\n");
}
- assertEquals("/CISD/SAMPLE-201:[COMMENT: A]\n" + "/CISD/SAMPLE-202:[COMMENT: B]\n",
- builder.toString());
+ assertEquals("/CISD/A23:[COMMENT: A]\n" + "/CISD/A24:[COMMENT: B]\n", builder.toString());
}
}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/DataSetInfoExtractorForProteinResults.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/DataSetInfoExtractorForProteinResults.java
index 016aa43ef68..477e1a547c5 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/DataSetInfoExtractorForProteinResults.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/DataSetInfoExtractorForProteinResults.java
@@ -41,25 +41,38 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifi
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ProjectIdentifier;
/**
- *
- *
* @author Franz-Josef Elmer
*/
public class DataSetInfoExtractorForProteinResults extends AbstractDataSetInfoExtractorWithService
{
- @Private static final String EXPERIMENT_TYPE_CODE_KEY = "experiment-type-code";
- @Private static final String EXPERIMENT_PROPERTIES_FILE_NAME_KEY = "experiment-properties-file-name";
- @Private static final String DEFAULT_EXPERIMENT_TYPE_CODE = "MS_SEARCH";
- @Private static final String SEPARATOR_KEY = "separator";
- @Private static final String DEFAULT_SEPARATOR = "&";
- @Private static final String DEFAULT_EXPERIMENT_PROPERTIES_FILE_NAME = "search.properties";
+ @Private
+ static final String EXPERIMENT_TYPE_CODE_KEY = "experiment-type-code";
+
+ @Private
+ static final String EXPERIMENT_PROPERTIES_FILE_NAME_KEY = "experiment-properties-file-name";
+
+ @Private
+ static final String DEFAULT_EXPERIMENT_TYPE_CODE = "MS_SEARCH";
+
+ @Private
+ static final String SEPARATOR_KEY = "separator";
+
+ @Private
+ static final String DEFAULT_SEPARATOR = "&";
+
+ @Private
+ static final String DEFAULT_EXPERIMENT_PROPERTIES_FILE_NAME = "search.properties";
+
static final String PARENT_DATA_SET_CODES = "parent-data-set-codes";
+
static final String EXPERIMENT_IDENTIFIER_KEY = "base-experiment";
-
+
private final String separator;
+
private final String experimentPropertiesFileName;
+
private final String experimentTypeCode;
-
+
public DataSetInfoExtractorForProteinResults(Properties properties)
{
this(properties, ServiceProvider.getOpenBISService());
@@ -72,7 +85,8 @@ public class DataSetInfoExtractorForProteinResults extends AbstractDataSetInfoEx
experimentPropertiesFileName =
properties.getProperty(EXPERIMENT_PROPERTIES_FILE_NAME_KEY,
DEFAULT_EXPERIMENT_PROPERTIES_FILE_NAME);
- experimentTypeCode = properties.getProperty(EXPERIMENT_TYPE_CODE_KEY, DEFAULT_EXPERIMENT_TYPE_CODE);
+ experimentTypeCode =
+ properties.getProperty(EXPERIMENT_TYPE_CODE_KEY, DEFAULT_EXPERIMENT_TYPE_CODE);
}
@Override
@@ -85,13 +99,13 @@ public class DataSetInfoExtractorForProteinResults extends AbstractDataSetInfoEx
if (items.length < 2)
{
throw new UserFailureException(
- "The name of the data set should have at least two parts separated by '" + separator
- + "': " + name);
+ "The name of the data set should have at least two parts separated by '"
+ + separator + "': " + name);
}
ProjectIdentifier projectIdentifier = new ProjectIdentifier(items[0], items[1]);
+ String experimentCode = service.generateCodes("E", EntityKind.EXPERIMENT, 1).get(0);
ExperimentIdentifier experimentIdentifier =
- new ExperimentIdentifier(projectIdentifier, "E"
- + service.drawANewUniqueID(EntityKind.EXPERIMENT));
+ new ExperimentIdentifier(projectIdentifier, experimentCode);
NewExperiment experiment =
new NewExperiment(experimentIdentifier.toString(), experimentTypeCode);
ExperimentType experimentType = service.getExperimentType(experimentTypeCode);
@@ -117,8 +131,8 @@ public class DataSetInfoExtractorForProteinResults extends AbstractDataSetInfoEx
}
/**
- * Returns data set codes either from the first argument or if <code>null</code> from
- * the data sets of the specified experiment.
+ * Returns data set codes either from the first argument or if <code>null</code> from the data
+ * sets of the specified experiment.
*/
static ParentDataSetCodes getParentDataSetCodes(String parentDataSetCodesOrNull,
String baseExperimentIdentifier, IEncapsulatedOpenBISService service)
@@ -160,7 +174,7 @@ public class DataSetInfoExtractorForProteinResults extends AbstractDataSetInfoEx
String errorMessage = builder.length() > 0 ? builder.toString() : null;
return new ParentDataSetCodes(parentDataSetCodes, errorMessage);
}
-
+
private String getProperty(Properties properties, String key)
{
String property = properties.getProperty(key);
@@ -170,7 +184,7 @@ public class DataSetInfoExtractorForProteinResults extends AbstractDataSetInfoEx
}
return property;
}
-
+
private Properties loadSearchProperties(File propertiesFile)
{
Properties properties;
diff --git a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/etlserver/proteomics/DataSetInfoExtractorForProteinResultsTest.java b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/etlserver/proteomics/DataSetInfoExtractorForProteinResultsTest.java
index ebb19d4b60d..b7d50683735 100644
--- a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/etlserver/proteomics/DataSetInfoExtractorForProteinResultsTest.java
+++ b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/etlserver/proteomics/DataSetInfoExtractorForProteinResultsTest.java
@@ -56,20 +56,20 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifi
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ProjectIdentifier;
/**
- *
- *
* @author Franz-Josef Elmer
*/
-@Friend(toClasses=DataSetInfoExtractorForProteinResults.class)
+@Friend(toClasses = DataSetInfoExtractorForProteinResults.class)
public class DataSetInfoExtractorForProteinResultsTest extends AbstractFileSystemTestCase
{
private static final String PARENT_DATA_SET_CODES_KEY =
DataSetInfoExtractorForProteinResults.PARENT_DATA_SET_CODES.toUpperCase();
private Mockery context;
+
private IEncapsulatedOpenBISService service;
+
private File dataSet;
-
+
@BeforeMethod
public void beforeMethod()
{
@@ -78,7 +78,7 @@ public class DataSetInfoExtractorForProteinResultsTest extends AbstractFileSyste
dataSet = new File(workingDirectory, "space1&project1");
dataSet.mkdirs();
}
-
+
@AfterMethod
public void afterMethod()
{
@@ -86,7 +86,7 @@ public class DataSetInfoExtractorForProteinResultsTest extends AbstractFileSyste
// Otherwise one do not known which test failed.
context.assertIsSatisfied();
}
-
+
@Test
public void testWithNonDefaultExperimentTypeAndPropertiesFileName()
{
@@ -111,14 +111,14 @@ public class DataSetInfoExtractorForProteinResultsTest extends AbstractFileSyste
});
IDataSetInfoExtractor extractor = createExtractor(properties);
-
+
DataSetInformation info = extractor.getDataSetInformation(dataSet, service);
-
+
assertEquals("/SPACE1/PROJECT1/E4711", info.getExperimentIdentifier().toString());
assertEquals("[1, 2, 3, 4]", info.getParentDataSetCodes().toString());
context.assertIsSatisfied();
}
-
+
@Test
public void testRegistrationWithOneMandatoryProperty()
{
@@ -142,8 +142,8 @@ public class DataSetInfoExtractorForProteinResultsTest extends AbstractFileSyste
if (item instanceof NewExperiment)
{
NewExperiment experiment = (NewExperiment) item;
- assertEquals(DEFAULT_EXPERIMENT_TYPE_CODE, experiment
- .getExperimentTypeCode());
+ assertEquals(DEFAULT_EXPERIMENT_TYPE_CODE,
+ experiment.getExperimentTypeCode());
IEntityProperty[] properties = experiment.getProperties();
assertEquals(1, properties.length);
assertEquals("answer", properties[0].getPropertyType()
@@ -174,7 +174,7 @@ public class DataSetInfoExtractorForProteinResultsTest extends AbstractFileSyste
public void testRegistrationWithMissingMandatoryProperty()
{
prepare(DEFAULT_EXPERIMENT_TYPE_CODE);
-
+
IDataSetInfoExtractor extractor = createExtractor(new Properties());
try
{
@@ -184,10 +184,10 @@ public class DataSetInfoExtractorForProteinResultsTest extends AbstractFileSyste
{
assertEquals("The following mandatory properties are missed: [answer]", ex.getMessage());
}
-
+
context.assertIsSatisfied();
}
-
+
@Test
public void testWithParentDataSetsDefinedByBaseExperiment()
{
@@ -207,25 +207,25 @@ public class DataSetInfoExtractorForProteinResultsTest extends AbstractFileSyste
"EXP1"));
Experiment experiment = new ExperimentBuilder().id(123789L).getExperiment();
will(returnValue(experiment));
-
+
one(service).listDataSetsByExperimentID(experiment.getId());
ExternalData ds1 = new DataSetBuilder().code("ds1").getDataSet();
ExternalData ds2 = new DataSetBuilder().code("ds2").getDataSet();
will(returnValue(Arrays.asList(ds1, ds2)));
-
+
one(service).registerExperiment(with(any(NewExperiment.class)));
}
});
IDataSetInfoExtractor extractor = createExtractor(properties);
-
+
DataSetInformation info = extractor.getDataSetInformation(dataSet, service);
-
+
assertEquals("/SPACE1/PROJECT1/E4711", info.getExperimentIdentifier().toString());
assertEquals("[ds1, ds2]", info.getParentDataSetCodes().toString());
context.assertIsSatisfied();
}
-
+
@Test
public void testWithUnkownBaseExperiment()
{
@@ -247,9 +247,9 @@ public class DataSetInfoExtractorForProteinResultsTest extends AbstractFileSyste
}
});
-
+
IDataSetInfoExtractor extractor = createExtractor(properties);
-
+
try
{
extractor.getDataSetInformation(dataSet, service);
@@ -260,7 +260,7 @@ public class DataSetInfoExtractorForProteinResultsTest extends AbstractFileSyste
}
context.assertIsSatisfied();
}
-
+
@Test
public void testWithUnkownParentDataSets()
{
@@ -289,7 +289,7 @@ public class DataSetInfoExtractorForProteinResultsTest extends AbstractFileSyste
}
context.assertIsSatisfied();
}
-
+
@Test
public void testWithParentDataSetsSeparatedBySpaces()
{
@@ -348,15 +348,15 @@ public class DataSetInfoExtractorForProteinResultsTest extends AbstractFileSyste
assertEquals("[ds1, ds2]", info.getParentDataSetCodes().toString());
context.assertIsSatisfied();
}
-
+
private void prepare(final String experimentType)
{
context.checking(new Expectations()
{
{
- one(service).drawANewUniqueID(EntityKind.EXPERIMENT);
+ one(service).generateCodes("E", EntityKind.EXPERIMENT, 1);
will(returnValue(4711L));
-
+
one(service).getExperimentType(experimentType);
ExperimentType type = new ExperimentType();
ExperimentTypePropertyType etpt = new ExperimentTypePropertyType();
@@ -369,12 +369,12 @@ public class DataSetInfoExtractorForProteinResultsTest extends AbstractFileSyste
}
});
}
-
+
private void prepareGetDataSet(final String dataSetCode)
{
prepareGetDataSet(dataSetCode, new DataSetBuilder().code(dataSetCode).getDataSet());
}
-
+
private void prepareGetDataSet(final String dataSetCode, final ExternalData data)
{
context.checking(new Expectations()
@@ -385,7 +385,7 @@ public class DataSetInfoExtractorForProteinResultsTest extends AbstractFileSyste
}
});
}
-
+
private IDataSetInfoExtractor createExtractor(Properties properties)
{
return new DataSetInfoExtractorForProteinResults(properties, service);
--
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