From 5762d37e00652cbe507f88cf533d6dc38e96c3f1 Mon Sep 17 00:00:00 2001
From: kaloyane <kaloyane>
Date: Fri, 14 Jan 2011 13:01:31 +0000
Subject: [PATCH] [LMS-1929] added support for genes with multiple symbols
SVN: 19427
---
.../cisd/etlserver/PlateDimensionParser.java | 23 +-
.../server/business/bo/AttachmentBO.java | 2 +-
.../server/util/KeyExtractorFactory.java | 12 +-
.../generic/shared/util/EntityHelper.java | 40 +++
.../web/server/LibraryRegistrationTask.java | 133 ----------
.../web/server/ScreeningClientService.java | 20 +-
.../server/LibraryRegistrationTask.java | 245 ++++++++++++++++++
.../screening/server/ScreeningServer.java | 31 ++-
.../server/ScreeningServerLogger.java | 13 +-
.../screening/shared/IScreeningServer.java | 11 +
.../shared/dto/PlateDimensionParser.java | 23 +-
.../server/LibraryRegistrationTaskTest.java | 184 +++++++++++++
12 files changed, 540 insertions(+), 197 deletions(-)
delete mode 100644 screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/server/LibraryRegistrationTask.java
create mode 100644 screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/LibraryRegistrationTask.java
create mode 100644 screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/server/LibraryRegistrationTaskTest.java
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/PlateDimensionParser.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/PlateDimensionParser.java
index 9a02274cd00..a59141c3afc 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/PlateDimensionParser.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/PlateDimensionParser.java
@@ -17,7 +17,7 @@
package ch.systemsx.cisd.etlserver;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityProperty;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.PropertyType;
+import ch.systemsx.cisd.openbis.generic.shared.util.EntityHelper;
/**
* Extractor and parser of the plate geometry from an array of properties.
@@ -56,12 +56,13 @@ public class PlateDimensionParser
public static PlateDimension tryToGetPlateDimension(final IEntityProperty[] properties)
{
assert properties != null : "Unspecified properties";
- final String plateGeometryString =
- tryFindProperty(properties, PLATE_GEOMETRY_PROPERTY_NAME);
- if (plateGeometryString == null)
+ IEntityProperty plateGeometryProperty =
+ EntityHelper.tryFindProperty(properties, PLATE_GEOMETRY_PROPERTY_NAME);
+ if (plateGeometryProperty == null)
{
return null;
}
+ final String plateGeometryString = plateGeometryProperty.tryGetAsString();
final PlateDimension dimension = tryParsePlateDimension(plateGeometryString);
if (dimension == null)
{
@@ -103,18 +104,4 @@ public class PlateDimensionParser
}
}
- private static String tryFindProperty(final IEntityProperty[] properties,
- final String propertyCode)
- {
- for (final IEntityProperty property : properties)
- {
- final PropertyType propertyType = property.getPropertyType();
- if (propertyType.getCode().equals(propertyCode))
- {
- return property.tryGetAsString();
- }
- }
- return null;
- }
-
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/AttachmentBO.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/AttachmentBO.java
index 3ce8b79bc79..389e90215b0 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/AttachmentBO.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/AttachmentBO.java
@@ -26,10 +26,10 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Attachment;
import ch.systemsx.cisd.openbis.generic.shared.dto.AttachmentHolderPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.AttachmentPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.EventPE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.EventPE.EntityType;
import ch.systemsx.cisd.openbis.generic.shared.dto.EventType;
import ch.systemsx.cisd.openbis.generic.shared.dto.PersonPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.Session;
-import ch.systemsx.cisd.openbis.generic.shared.dto.EventPE.EntityType;
/**
* The only productive implementation of {@link IAttachmentBO}.
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/util/KeyExtractorFactory.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/util/KeyExtractorFactory.java
index 1123f8fe99e..a85afcc37f8 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/util/KeyExtractorFactory.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/util/KeyExtractorFactory.java
@@ -17,12 +17,12 @@
package ch.systemsx.cisd.openbis.generic.server.util;
import ch.systemsx.cisd.common.collections.IKeyExtractor;
+import ch.systemsx.cisd.openbis.generic.shared.basic.ICodeHolder;
import ch.systemsx.cisd.openbis.generic.shared.basic.IIdHolder;
import ch.systemsx.cisd.openbis.generic.shared.dto.AuthorizationGroupPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.DatabaseInstancePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.EntityTypePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.ExperimentPE;
-import ch.systemsx.cisd.openbis.generic.shared.dto.IIdAndCodeHolder;
import ch.systemsx.cisd.openbis.generic.shared.dto.MaterialPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.PersonPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.PropertyTypePE;
@@ -78,10 +78,9 @@ public final class KeyExtractorFactory
}
/**
- * Creates an <code>IKeyExtractor</code> implementation based on {@link IIdAndCodeHolder}
- * extension.
+ * Creates an <code>IKeyExtractor</code> implementation based on {@link ICodeHolder} extension.
*/
- public final static <T extends IIdAndCodeHolder> IKeyExtractor<String, T> createCodeKeyExtractor()
+ public final static <T extends ICodeHolder> IKeyExtractor<String, T> createCodeKeyExtractor()
{
return new CodeKeyExtractor<T>();
}
@@ -187,15 +186,14 @@ public final class KeyExtractorFactory
}
}
- private final static class CodeKeyExtractor<T extends IIdAndCodeHolder> implements
+ private final static class CodeKeyExtractor<T extends ICodeHolder> implements
IKeyExtractor<String, T>
{
-
//
// IKeyExtractor
//
- public final String getKey(final IIdAndCodeHolder id)
+ public final String getKey(final ICodeHolder id)
{
return id.getCode();
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/util/EntityHelper.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/util/EntityHelper.java
index 19b70f9f9c3..4fc488fb638 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/util/EntityHelper.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/util/EntityHelper.java
@@ -20,7 +20,9 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.EntityKind;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.EntityType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExperimentType;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityProperty;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.MaterialType;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.PropertyType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SampleType;
/**
@@ -53,4 +55,42 @@ public class EntityHelper
type.setCode(code);
return type;
}
+
+ /**
+ * @return finds and returns an {@link IEntityProperty} for a specified code. Returns
+ * <code>null</code> if no matching property is found.
+ */
+ public static IEntityProperty tryFindProperty(Iterable<IEntityProperty> properties,
+ final String propertyCode)
+ {
+ for (final IEntityProperty property : properties)
+ {
+ final PropertyType propertyType = property.getPropertyType();
+ if (propertyType.getCode().equalsIgnoreCase(propertyCode))
+ {
+ return property;
+ }
+ }
+ return null;
+ }
+
+ /**
+ * does the same as {@link #tryFindProperty(Iterable, String)} but with arrays.
+ */
+ // TODO 2011-01-13 KE : could we scratch the usage of arrays and only have lists ?
+ // if so, we could delete this method
+ public static IEntityProperty tryFindProperty(IEntityProperty[] properties,
+ final String propertyCode)
+ {
+ for (final IEntityProperty property : properties)
+ {
+ final PropertyType propertyType = property.getPropertyType();
+ // TODO KE : ugly, why is the extracting logic not uppercasing ??
+ if (propertyType.getCode().equalsIgnoreCase(propertyCode))
+ {
+ return property;
+ }
+ }
+ return null;
+ }
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/server/LibraryRegistrationTask.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/server/LibraryRegistrationTask.java
deleted file mode 100644
index cdad5cd61ac..00000000000
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/server/LibraryRegistrationTask.java
+++ /dev/null
@@ -1,133 +0,0 @@
-package ch.systemsx.cisd.openbis.plugin.screening.client.web.server;
-
-import java.util.Date;
-import java.util.List;
-
-import ch.systemsx.cisd.common.mail.IMailClient;
-import ch.systemsx.cisd.common.mail.MailClient;
-import ch.systemsx.cisd.common.mail.MailClientParameters;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewMaterial;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewSamplesWithTypes;
-import ch.systemsx.cisd.openbis.plugin.generic.shared.IGenericServer;
-import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ScreeningConstants;
-
-/**
- * Saves genes, oligos and plates. Sends an email to specified address upon error or completion.
- *
- * @author Izabela Adamczyk
- */
-class LibraryRegistrationTask implements Runnable
-{
-
- private static final String SUCCESSFUL_LIBRARY_REGISTARION_STATUS =
- "Library successfuly registered";
-
- private static final String UNSUCCESSFUL_LIBRARY_REGISTARION_STATUS =
- "Library registration failed";
-
- private final MailClientParameters mailClientParameters;
-
- private final String sessionToken;
-
- private final String email;
-
- private final List<NewMaterial> newGenesOrNull;
-
- private final List<NewMaterial> newOligosOrNull;
-
- private final List<NewSamplesWithTypes> newSamplesWithType;
-
- private final IGenericServer genericServer;
-
- public LibraryRegistrationTask(final String sessionToken, final String email,
- final List<NewMaterial> newGenesOrNull, final List<NewMaterial> newOligosOrNull,
- final List<NewSamplesWithTypes> newSamplesWithType, IGenericServer server,
- MailClientParameters mailClientParameters)
- {
- this.sessionToken = sessionToken;
- this.email = email;
- this.newGenesOrNull = newGenesOrNull;
- this.newOligosOrNull = newOligosOrNull;
- this.newSamplesWithType = newSamplesWithType;
- this.genericServer = server;
- this.mailClientParameters = mailClientParameters;
- }
-
- public void run()
- {
- Date startDate = new Date();
- StringBuilder message = new StringBuilder();
- try
- {
- if (newGenesOrNull != null)
- {
- genericServer.registerOrUpdateMaterials(sessionToken,
- ScreeningConstants.GENE_PLUGIN_TYPE_CODE, newGenesOrNull);
- message.append("Successfuly saved properties of " + newGenesOrNull.size()
- + " genes.\n");
- }
- } catch (Exception ex)
- {
- message.append("ERROR: Genes could not be saved!\n");
- message.append(ex.getMessage());
- sendErrorEmail(message, startDate, email);
- return;
- }
- try
- {
- if (newOligosOrNull != null)
- {
- genericServer.registerOrUpdateMaterials(sessionToken,
- ScreeningConstants.SIRNA_PLUGIN_TYPE_NAME, newOligosOrNull);
- message.append("Successfuly saved " + newOligosOrNull.size() + " siRNAs.\n");
- }
- } catch (Exception ex)
- {
- message.append("ERROR: siRNAs could not be saved!\n");
- message.append(ex.getMessage());
- sendErrorEmail(message, startDate, email);
- return;
- }
- try
- {
- genericServer.registerOrUpdateSamples(sessionToken, newSamplesWithType);
- for (NewSamplesWithTypes s : newSamplesWithType)
- {
- message.append("Successfuly saved " + s.getNewSamples().size()
- + " samples of type " + s.getSampleType() + ".\n");
- }
- } catch (Exception ex)
- {
- message.append("ERROR: Plates and wells could not be saved!\n");
- message.append(ex.getMessage());
- sendErrorEmail(message, startDate, email);
- return;
- }
- sendSuccessEmail(message, startDate, email);
-
- }
-
- private void sendErrorEmail(StringBuilder content, Date startDate, String recipient)
- {
- String subject = addDate(UNSUCCESSFUL_LIBRARY_REGISTARION_STATUS, startDate);
- sendEmail(subject, content.toString(), recipient);
- }
-
- private void sendSuccessEmail(StringBuilder content, Date startDate, String recipient)
- {
- String subject = addDate(SUCCESSFUL_LIBRARY_REGISTARION_STATUS, startDate);
- sendEmail(subject, content.toString(), recipient);
- }
-
- private static String addDate(String subject, Date startDate)
- {
- return subject + " (initiated at " + startDate + ")";
- }
-
- private void sendEmail(String subject, String content, String recipient)
- {
- final IMailClient mailClient = new MailClient(mailClientParameters);
- mailClient.sendMessage(subject, content, null, null, recipient);
- }
-
-}
\ No newline at end of file
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/server/ScreeningClientService.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/server/ScreeningClientService.java
index be0392b8664..4d4497a3b27 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/server/ScreeningClientService.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/server/ScreeningClientService.java
@@ -17,9 +17,6 @@
package ch.systemsx.cisd.openbis.plugin.screening.client.web.server;
import java.util.List;
-import java.util.concurrent.LinkedBlockingQueue;
-import java.util.concurrent.ThreadPoolExecutor;
-import java.util.concurrent.TimeUnit;
import javax.annotation.Resource;
import javax.servlet.http.HttpSession;
@@ -27,7 +24,6 @@ import javax.servlet.http.HttpSession;
import org.springframework.stereotype.Component;
import ch.rinn.restrictions.Private;
-import ch.systemsx.cisd.common.mail.MailClientParameters;
import ch.systemsx.cisd.common.servlet.IRequestContextProvider;
import ch.systemsx.cisd.common.spring.IUncheckedMultipartFile;
import ch.systemsx.cisd.openbis.generic.client.web.client.dto.IResultSetConfig;
@@ -50,7 +46,6 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SampleParentWithDerived
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TableModelRowWithObject;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Vocabulary;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifierFactory;
-import ch.systemsx.cisd.openbis.plugin.generic.shared.IGenericServer;
import ch.systemsx.cisd.openbis.plugin.screening.BuildAndEnvironmentInfo;
import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.IScreeningClientService;
import ch.systemsx.cisd.openbis.plugin.screening.shared.IScreeningServer;
@@ -81,15 +76,6 @@ public final class ScreeningClientService extends AbstractClientService implemen
@Resource(name = ResourceNames.SCREENING_PLUGIN_SERVER)
private IScreeningServer server;
- @Resource(name = ch.systemsx.cisd.openbis.plugin.generic.shared.ResourceNames.GENERIC_PLUGIN_SERVER)
- private IGenericServer genericServer;
-
- @Resource(name = ResourceNames.MAIL_CLIENT_PARAMETERS)
- private MailClientParameters mailClientParameters;
-
- private static ThreadPoolExecutor executor = new ThreadPoolExecutor(1, 10, 360,
- TimeUnit.SECONDS, new LinkedBlockingQueue<Runnable>());
-
public ScreeningClientService()
{
}
@@ -221,9 +207,9 @@ public final class ScreeningClientService extends AbstractClientService implemen
new LibraryExtractor(file.getInputStream(), details.getSeparator(),
experiment, space, details.getPlateGeometry(), details.getScope());
extractor.extract();
- executor.submit(new LibraryRegistrationTask(sessionToken, details.getUserEmail(),
- extractor.getNewGenes(), extractor.getNewOligos(), extractor
- .getNewSamplesWithType(), genericServer, mailClientParameters));
+ server.registerLibrary(sessionToken, details.getUserEmail(),
+ extractor.getNewGenes(), extractor.getNewOligos(),
+ extractor.getNewSamplesWithType());
}
} catch (final ch.systemsx.cisd.common.exceptions.UserFailureException e)
{
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/LibraryRegistrationTask.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/LibraryRegistrationTask.java
new file mode 100644
index 00000000000..40944dd1ff8
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/LibraryRegistrationTask.java
@@ -0,0 +1,245 @@
+package ch.systemsx.cisd.openbis.plugin.screening.server;
+
+import java.util.Date;
+import java.util.List;
+
+import ch.systemsx.cisd.common.collections.TableMap;
+import ch.systemsx.cisd.common.mail.IMailClient;
+import ch.systemsx.cisd.common.shared.basic.utils.StringUtils;
+import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDAOFactory;
+import ch.systemsx.cisd.openbis.generic.server.util.KeyExtractorFactory;
+import ch.systemsx.cisd.openbis.generic.shared.ICommonServer;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityProperty;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ListMaterialCriteria;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Material;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.MaterialType;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewMaterial;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewSamplesWithTypes;
+import ch.systemsx.cisd.openbis.generic.shared.dto.EntityTypePE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.properties.EntityKind;
+import ch.systemsx.cisd.openbis.generic.shared.translator.MaterialTypeTranslator;
+import ch.systemsx.cisd.openbis.generic.shared.util.EntityHelper;
+import ch.systemsx.cisd.openbis.plugin.generic.shared.IGenericServer;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ScreeningConstants;
+
+/**
+ * Saves genes, oligos and plates. Sends an email to specified address upon error or completion.
+ *
+ * @author Izabela Adamczyk
+ */
+class LibraryRegistrationTask implements Runnable
+{
+
+ private static final String SUCCESSFUL_LIBRARY_REGISTARION_STATUS =
+ "Library successfully registered";
+
+ private static final String UNSUCCESSFUL_LIBRARY_REGISTARION_STATUS =
+ "Library registration failed";
+
+
+ private final String sessionToken;
+
+ private final String email;
+
+ private final List<NewMaterial> newGenesOrNull;
+
+ private final List<NewMaterial> newOligosOrNull;
+
+ private final List<NewSamplesWithTypes> newSamplesWithType;
+
+ private final IGenericServer genericServer;
+
+ private final ICommonServer commonServer;
+
+ private final IDAOFactory daoFactory;
+
+ private final IMailClient mailClient;
+
+
+ public LibraryRegistrationTask(String sessionToken, String email,
+ List<NewMaterial> newGenesOrNull, List<NewMaterial> newOligosOrNull,
+ List<NewSamplesWithTypes> newSamplesWithType, ICommonServer commonServer,
+ IGenericServer server, IDAOFactory daoFactory, IMailClient mailClient)
+ {
+ this.sessionToken = sessionToken;
+ this.email = email;
+ this.newGenesOrNull = newGenesOrNull;
+ this.newOligosOrNull = newOligosOrNull;
+ this.newSamplesWithType = newSamplesWithType;
+ this.commonServer = commonServer;
+ this.genericServer = server;
+ this.daoFactory = daoFactory;
+ this.mailClient = mailClient;
+ }
+
+ public void run()
+ {
+ boolean success = true;
+ Date startDate = new Date();
+ StringBuilder message = new StringBuilder();
+
+ try
+ {
+ // when one of these methods fails it will throw an unchecked exception
+ registerOrUpdateGenes(message);
+ registerOrUpdateOligos(message);
+ registerOrUpdateSamples(message);
+ } catch (RuntimeException rex)
+ {
+ success = false;
+ }
+
+ sendEmail(message.toString(), startDate, email, success);
+ }
+
+ private void registerOrUpdateSamples(StringBuilder message)
+ {
+ try
+ {
+ if (newSamplesWithType != null)
+ {
+ genericServer.registerOrUpdateSamples(sessionToken, newSamplesWithType);
+ for (NewSamplesWithTypes s : newSamplesWithType)
+ {
+ message.append("Successfuly saved " + s.getNewSamples().size()
+ + " samples of type " + s.getSampleType() + ".\n");
+ }
+ }
+ } catch (RuntimeException ex)
+ {
+ message.append("ERROR: Plates and wells could not be saved!\n");
+ message.append(ex.getMessage());
+ throw ex;
+ }
+ }
+
+ private void registerOrUpdateOligos(StringBuilder message)
+ {
+ try
+ {
+ if (newOligosOrNull != null)
+ {
+ genericServer.registerOrUpdateMaterials(sessionToken,
+ ScreeningConstants.SIRNA_PLUGIN_TYPE_NAME, newOligosOrNull);
+ message.append("Successfuly saved " + newOligosOrNull.size() + " siRNAs.\n");
+ }
+ } catch (RuntimeException ex)
+ {
+ message.append("ERROR: siRNAs could not be saved!\n");
+ message.append(ex.getMessage());
+ throw ex;
+ }
+ }
+
+ private void registerOrUpdateGenes(StringBuilder message)
+ {
+ try
+ {
+ if (newGenesOrNull != null)
+ {
+ TableMap<String, Material> existingGenes = listExistingGenes();
+ for (NewMaterial newGene : newGenesOrNull)
+ {
+ Material existingGene = existingGenes.tryGet(newGene.getCode());
+ if (existingGene != null)
+ {
+ mergeGeneTypeCode(existingGene, newGene);
+ }
+ }
+
+ genericServer.registerOrUpdateMaterials(sessionToken,
+ ScreeningConstants.GENE_PLUGIN_TYPE_CODE, newGenesOrNull);
+ message.append("Successfuly saved properties of " + newGenesOrNull.size()
+ + " genes.\n");
+ }
+ } catch (RuntimeException ex)
+ {
+ message.append("ERROR: Genes could not be saved!\n");
+ message.append(ex.getMessage());
+ throw ex;
+ }
+ }
+
+ private TableMap<String, Material> listExistingGenes()
+ {
+ EntityTypePE entityTypePE =
+ daoFactory.getEntityTypeDAO(EntityKind.MATERIAL).tryToFindEntityTypeByCode(
+ ScreeningConstants.GENE_PLUGIN_TYPE_CODE);
+ MaterialType materialType = MaterialTypeTranslator.translateSimple(entityTypePE);
+ List<Material> materials =
+ commonServer.listMaterials(sessionToken, new ListMaterialCriteria(materialType),
+ true);
+
+ return new TableMap<String, Material>(materials,
+ KeyExtractorFactory.<Material> createCodeKeyExtractor());
+ }
+
+ /**
+ * when an existing gene is being updated, we merge the existing gene symbols with the newly
+ * specified into a space-separated new field. If the new gene does not contain new information
+ * i.e. its gene symbol is already present in the DB, the existing gene symbols are not altered.
+ * <p>
+ * For further information see LMS-1929.
+ */
+ private void mergeGeneTypeCode(Material existingMaterial, NewMaterial newMaterial)
+ {
+ IEntityProperty existingGeneProp =
+ EntityHelper.tryFindProperty(existingMaterial.getProperties(),
+ ScreeningConstants.GENE_SYMBOLS);
+ if (existingGeneProp == null)
+ {
+ return;
+ }
+
+ String existingGene = existingGeneProp.getValue();
+
+ IEntityProperty newGeneProp =
+ EntityHelper.tryFindProperty(newMaterial.getProperties(),
+ ScreeningConstants.GENE_SYMBOLS);
+
+ if (newGeneProp == null)
+ {
+ return;
+ }
+ String mergedGeneType = mergeGeneTypes(existingGene, newGeneProp.getValue());
+ newGeneProp.setValue(mergedGeneType);
+ }
+
+ private String mergeGeneTypes(String existingType, String newType)
+ {
+ if (StringUtils.isBlank(newType) || newType.equals(existingType))
+ {
+ return existingType;
+ }
+
+ boolean ignoreNewType =
+ existingType.startsWith(newType + " ") || existingType.endsWith(" " + newType)
+ || (existingType.indexOf(" " + newType + " ") > 0);
+
+ if (ignoreNewType)
+ {
+ return existingType;
+ } else
+ {
+ return existingType + " " + newType;
+ }
+ }
+
+
+ private void sendEmail(String content, Date startDate, String recipient,
+ boolean successful)
+ {
+ String status =
+ successful ? SUCCESSFUL_LIBRARY_REGISTARION_STATUS
+ : UNSUCCESSFUL_LIBRARY_REGISTARION_STATUS;
+
+ String subject = addDate(status, startDate);
+ mailClient.sendMessage(subject, content, null, null, recipient);
+ }
+
+ private static String addDate(String subject, Date startDate)
+ {
+ return subject + " (initiated at " + startDate + ")";
+ }
+
+}
\ No newline at end of file
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/ScreeningServer.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/ScreeningServer.java
index 415964c98ef..00fb39aa222 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/ScreeningServer.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/ScreeningServer.java
@@ -20,6 +20,9 @@ import java.sql.Connection;
import java.util.ArrayList;
import java.util.Collection;
import java.util.List;
+import java.util.concurrent.LinkedBlockingQueue;
+import java.util.concurrent.ThreadPoolExecutor;
+import java.util.concurrent.TimeUnit;
import javax.annotation.Resource;
@@ -31,6 +34,9 @@ import org.springframework.stereotype.Component;
import ch.rinn.restrictions.Private;
import ch.systemsx.cisd.authentication.ISessionManager;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
+import ch.systemsx.cisd.common.mail.IMailClient;
+import ch.systemsx.cisd.common.mail.MailClient;
+import ch.systemsx.cisd.common.mail.MailClientParameters;
import ch.systemsx.cisd.common.spring.IInvocationLoggerContext;
import ch.systemsx.cisd.openbis.generic.server.AbstractServer;
import ch.systemsx.cisd.openbis.generic.server.business.bo.ISampleBO;
@@ -46,6 +52,8 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExternalData;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ListMaterialCriteria;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Material;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.MaterialType;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewMaterial;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewSamplesWithTypes;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SampleParentWithDerived;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Vocabulary;
import ch.systemsx.cisd.openbis.generic.shared.dto.SamplePE;
@@ -54,6 +62,7 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.SessionContextDTO;
import ch.systemsx.cisd.openbis.generic.shared.dto.VocabularyPE;
import ch.systemsx.cisd.openbis.generic.shared.translator.SampleTranslator;
import ch.systemsx.cisd.openbis.generic.shared.translator.VocabularyTranslator;
+import ch.systemsx.cisd.openbis.plugin.generic.shared.IGenericServer;
import ch.systemsx.cisd.openbis.plugin.screening.server.dataaccess.IScreeningQuery;
import ch.systemsx.cisd.openbis.plugin.screening.server.logic.PlateContentLoader;
import ch.systemsx.cisd.openbis.plugin.screening.server.logic.ScreeningApiImpl;
@@ -94,11 +103,20 @@ public final class ScreeningServer extends AbstractServer<IScreeningServer> impl
*/
public static final int MINOR_VERSION = 4;
+ private static ThreadPoolExecutor executor = new ThreadPoolExecutor(1, 10, 360,
+ TimeUnit.SECONDS, new LinkedBlockingQueue<Runnable>());
+
@Resource(name = ResourceNames.SCREENING_BUSINESS_OBJECT_FACTORY)
private IScreeningBusinessObjectFactory businessObjectFactory;
@Resource(name = ch.systemsx.cisd.openbis.generic.shared.ResourceNames.COMMON_SERVER)
- protected ICommonServer commonServer;
+ private ICommonServer commonServer;
+
+ @Resource(name = ch.systemsx.cisd.openbis.plugin.generic.shared.ResourceNames.GENERIC_PLUGIN_SERVER)
+ private IGenericServer genericServer;
+
+ @Resource(name = ResourceNames.MAIL_CLIENT_PARAMETERS)
+ private MailClientParameters mailClientParameters;
public ScreeningServer()
{
@@ -198,6 +216,16 @@ public final class ScreeningServer extends AbstractServer<IScreeningServer> impl
return VocabularyTranslator.translate(vocabulary);
}
+ public void registerLibrary(String sessionToken, String userEmail,
+ List<NewMaterial> newGenesOrNull, List<NewMaterial> newOligosOrNull,
+ List<NewSamplesWithTypes> newSamplesWithType)
+ {
+ IMailClient mailClient = new MailClient(mailClientParameters);
+ executor.submit(new LibraryRegistrationTask(sessionToken, userEmail, newGenesOrNull,
+ newOligosOrNull, newSamplesWithType, commonServer, genericServer, getDAOFactory(),
+ mailClient));
+ }
+
// --------- IScreeningOpenbisServer - method signature should be changed with care
public List<FeatureVectorDatasetReference> listFeatureVectorDatasets(String sessionToken,
@@ -317,4 +345,5 @@ public final class ScreeningServer extends AbstractServer<IScreeningServer> impl
{
return MINOR_VERSION;
}
+
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/ScreeningServerLogger.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/ScreeningServerLogger.java
index 63749e23f33..eb38f03b670 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/ScreeningServerLogger.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/ScreeningServerLogger.java
@@ -29,7 +29,9 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExternalData;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Material;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.MaterialType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewAttachment;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewMaterial;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewSample;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewSamplesWithTypes;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SampleParentWithDerived;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TableModel;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Vocabulary;
@@ -244,8 +246,6 @@ final class ScreeningServerLogger extends AbstractServerLogger implements IScree
public List<Material> listExperimentMaterials(String sessionToken, TechId experimentId,
MaterialType materialType)
{
- logAccess(sessionToken, "listExperimentMaterials", "experimentId(%s), materialType(%s)",
- experimentId, materialType);
return null;
}
@@ -258,4 +258,13 @@ final class ScreeningServerLogger extends AbstractServerLogger implements IScree
{
return ScreeningServer.MINOR_VERSION;
}
+
+ public void registerLibrary(String sessionToken, String userEmail,
+ List<NewMaterial> newGenesOrNull, List<NewMaterial> newOligosOrNull,
+ List<NewSamplesWithTypes> newSamplesWithType)
+ {
+ logAccess(sessionToken, "registerLibrary",
+ "userEmail(%s), newGenesOrNull(%s), newOligosOrNull(%s), newSamplesWithType(%s)",
+ userEmail, newGenesOrNull, newOligosOrNull, newSamplesWithType);
+ }
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/IScreeningServer.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/IScreeningServer.java
index a0eb95d6dd8..d0d16455309 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/IScreeningServer.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/IScreeningServer.java
@@ -33,6 +33,8 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExternalData;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Material;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.MaterialType;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewMaterial;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewSamplesWithTypes;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.RoleWithHierarchy;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SampleParentWithDerived;
@@ -140,4 +142,13 @@ public interface IScreeningServer extends IServer
@Transactional
@RolesAllowed(RoleWithHierarchy.SPACE_OBSERVER)
public Vocabulary getVocabulary(String sessionToken, String code) throws UserFailureException;
+
+ /**
+ * registers the contents of an uploaded library.
+ */
+ @Transactional
+ @RolesAllowed(RoleWithHierarchy.SPACE_ADMIN)
+ public void registerLibrary(String sessionToken, String userEmail,
+ List<NewMaterial> newGenesOrNull, List<NewMaterial> newOligosOrNull,
+ List<NewSamplesWithTypes> newSamplesWithType);
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/dto/PlateDimensionParser.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/dto/PlateDimensionParser.java
index 48a2171d205..39c9343c846 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/dto/PlateDimensionParser.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/dto/PlateDimensionParser.java
@@ -19,7 +19,7 @@ package ch.systemsx.cisd.openbis.plugin.screening.shared.dto;
import java.util.List;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityProperty;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.PropertyType;
+import ch.systemsx.cisd.openbis.generic.shared.util.EntityHelper;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.Geometry;
/**
@@ -57,12 +57,13 @@ public class PlateDimensionParser
public static PlateDimension tryToGetPlateDimension(final IEntityProperty[] properties)
{
assert properties != null : "Unspecified properties";
- final String plateGeometryString =
- tryFindProperty(properties, PLATE_GEOMETRY_PROPERTY_NAME);
- if (plateGeometryString == null)
+ IEntityProperty plateGeometryProperty =
+ EntityHelper.tryFindProperty(properties, PLATE_GEOMETRY_PROPERTY_NAME);
+ if (plateGeometryProperty == null)
{
return null;
}
+ final String plateGeometryString = plateGeometryProperty.tryGetAsString();
final PlateDimension dimension = tryParsePlateDimension(plateGeometryString);
if (dimension == null)
{
@@ -104,20 +105,6 @@ public class PlateDimensionParser
}
}
- private static String tryFindProperty(final IEntityProperty[] properties,
- final String propertyCode)
- {
- for (final IEntityProperty property : properties)
- {
- final PropertyType propertyType = property.getPropertyType();
- if (propertyType.getCode().equals(propertyCode))
- {
- return property.tryGetAsString();
- }
- }
- return null;
- }
-
public static Geometry getPlateGeometry(List<IEntityProperty> properties)
{
return getPlateDimension(properties.toArray(new IEntityProperty[0])).getPlateGeometry();
diff --git a/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/server/LibraryRegistrationTaskTest.java b/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/server/LibraryRegistrationTaskTest.java
new file mode 100644
index 00000000000..70cc63560d1
--- /dev/null
+++ b/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/server/LibraryRegistrationTaskTest.java
@@ -0,0 +1,184 @@
+/*
+ * Copyright 2011 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.plugin.screening.server;
+
+import static org.hamcrest.text.StringContains.containsString;
+
+import java.util.Arrays;
+import java.util.List;
+
+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.mail.From;
+import ch.systemsx.cisd.common.mail.IMailClient;
+import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDAOFactory;
+import ch.systemsx.cisd.openbis.generic.server.dataaccess.IEntityTypeDAO;
+import ch.systemsx.cisd.openbis.generic.shared.ICommonServer;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataType;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataTypeCode;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.GenericEntityProperty;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityProperty;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ListMaterialCriteria;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Material;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.MaterialType;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewMaterial;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.PropertyType;
+import ch.systemsx.cisd.openbis.generic.shared.dto.MaterialTypePE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.properties.EntityKind;
+import ch.systemsx.cisd.openbis.generic.shared.util.EntityHelper;
+import ch.systemsx.cisd.openbis.plugin.generic.shared.IGenericServer;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ScreeningConstants;
+
+/**
+ * @author Kaloyan Enimanev
+ */
+public class LibraryRegistrationTaskTest extends AssertJUnit
+{
+ private static final String SESSION_TOKEN = "session";
+
+ private static final String USER_EMAIL = "micky.mouse@acme.org";
+
+ private Mockery context;
+
+ private ICommonServer commonServer;
+
+ private IGenericServer genericServer;
+
+ private IDAOFactory daoFactory;
+
+ private IEntityTypeDAO entityTypeDAO;
+
+ private IMailClient mailClient;
+
+ private LibraryRegistrationTask task;
+
+
+ @BeforeMethod
+ public void setUp()
+ {
+ context = new Mockery();
+ commonServer = context.mock(ICommonServer.class);
+ genericServer = context.mock(IGenericServer.class);
+ daoFactory = context.mock(IDAOFactory.class);
+ entityTypeDAO = context.mock(IEntityTypeDAO.class);
+ mailClient = context.mock(IMailClient.class);
+ }
+
+ @AfterMethod
+ public void tearDown()
+ {
+ context.assertIsSatisfied();
+ }
+
+ @Test
+ public void testUpdateGeneSymbols()
+ {
+ NewMaterial g1 = createNewGene("G1", "AB");
+ NewMaterial g2 = createNewGene("G2", "AB");
+ NewMaterial g3 = createNewGene("G3", "AB");
+ NewMaterial g4 = createNewGene("G4", "AB");
+ NewMaterial g5 = createNewGene("G5", "AB");
+
+ final List<NewMaterial> newGenes = Arrays.asList(g1, g2, g3, g4, g5);
+ final List<Material> existingGenes =
+ Arrays.asList(createExistingGene("G1", "ABC A"), createExistingGene("G2", "AB"),
+ createExistingGene("G3", "AB BC"), createExistingGene("G4", "XY AB"),
+ createExistingGene("G5", "XY AB YZ"));
+
+ task =
+ new LibraryRegistrationTask(SESSION_TOKEN, USER_EMAIL, newGenes, null, null,
+ commonServer, genericServer, daoFactory, mailClient);
+
+ context.checking(new Expectations()
+ {
+ {
+ one(daoFactory).getEntityTypeDAO(EntityKind.MATERIAL);
+ will(returnValue(entityTypeDAO));
+
+ one(entityTypeDAO).tryToFindEntityTypeByCode(
+ ScreeningConstants.GENE_PLUGIN_TYPE_CODE);
+ will(returnValue(new MaterialTypePE()));
+
+ one(commonServer).listMaterials(with(SESSION_TOKEN),
+ with(any(ListMaterialCriteria.class)), with(true));
+ will(returnValue(existingGenes));
+
+ one(genericServer).registerOrUpdateMaterials(SESSION_TOKEN,
+ ScreeningConstants.GENE_PLUGIN_TYPE_CODE, newGenes);
+
+ String[] emailTo = new String[]
+ { USER_EMAIL };
+ one(mailClient).sendMessage(with(containsString("success")),
+ with(any(String.class)),
+ with(aNull(String.class)), with(aNull(From.class)), with(emailTo));
+ }
+ });
+
+ task.run();
+
+ assertEquals("ABC A AB", extractGeneSymbol(g1));
+ assertEquals("AB", extractGeneSymbol(g2));
+ assertEquals("AB BC", extractGeneSymbol(g3));
+ assertEquals("XY AB", extractGeneSymbol(g4));
+ assertEquals("XY AB YZ", extractGeneSymbol(g5));
+ }
+
+ private NewMaterial createNewGene(String code, String geneSymbol)
+ {
+ IEntityProperty geneSymbolProperty = createGeneSymbolProperty(geneSymbol);
+ NewMaterial gene = new NewMaterial(code);
+ gene.setProperties(new IEntityProperty[]
+ { geneSymbolProperty });
+
+ return gene;
+ }
+
+ private Material createExistingGene(String code, String geneSymbol)
+ {
+ IEntityProperty geneSymbolProperty = createGeneSymbolProperty(geneSymbol);
+ Material gene = new Material();
+ gene.setCode(code);
+ gene.setMaterialType(new MaterialType());
+ gene.setProperties(Arrays.asList(geneSymbolProperty));
+ return gene;
+ }
+
+ private IEntityProperty createGeneSymbolProperty(String geneSymbol)
+ {
+ PropertyType propType = new PropertyType();
+ propType.setDataType(new DataType(DataTypeCode.MATERIAL));
+ propType.setCode(ScreeningConstants.GENE_SYMBOLS);
+
+ GenericEntityProperty entityProperty = new GenericEntityProperty();
+ entityProperty.setPropertyType(propType);
+ entityProperty.setValue(geneSymbol);
+ return entityProperty;
+ }
+
+ private String extractGeneSymbol(NewMaterial newMaterial)
+ {
+ IEntityProperty property =
+ EntityHelper.tryFindProperty(newMaterial.getProperties(),
+ ScreeningConstants.GENE_SYMBOLS);
+ return property.getValue();
+ }
+}
--
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