From 39dc72e1211e59b875910ea69aea3b4b9b36735d Mon Sep 17 00:00:00 2001
From: juanf <juanf@bsse-bs-dock-dhcp-358.ethz.ch>
Date: Tue, 25 Sep 2018 12:45:40 +0200
Subject: [PATCH] SSDM-7235 : Continuous sample codes, project samples support
---
.../parser/SampleUploadSectionsParser.java | 27 ++++++---
.../web/server/GenericClientService.java | 14 ++++-
.../plugin/generic/server/GenericServer.java | 57 +++++++++++++++----
3 files changed, 78 insertions(+), 20 deletions(-)
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/parser/SampleUploadSectionsParser.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/parser/SampleUploadSectionsParser.java
index ba0386f3962..45319af47c0 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/parser/SampleUploadSectionsParser.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/parser/SampleUploadSectionsParser.java
@@ -25,6 +25,8 @@ import java.util.Map;
import org.apache.commons.lang.StringUtils;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.project.id.ProjectIdentifier;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.sample.id.SampleIdentifier;
import ch.systemsx.cisd.common.io.DelegatedReader;
import ch.systemsx.cisd.common.parser.ExcelFileLoader;
import ch.systemsx.cisd.common.parser.IParserObjectFactory;
@@ -85,7 +87,9 @@ public class SampleUploadSectionsParser
List<String> generateCodes(int size);
}
- public static BatchSamplesOperation prepareSamples(final SampleType sampleType,
+ public static BatchSamplesOperation prepareSamples(
+ final boolean projectSamplesEnabled,
+ final SampleType sampleType,
final String spaceIdentifierSilentOverrideOrNull,
final String experimentIdentifierSilentOverrideOrNull,
final Collection<NamedInputStream> files, String defaultGroupIdentifier,
@@ -107,7 +111,7 @@ public class SampleUploadSectionsParser
case REGISTRATION:
if (isAutoGenerateCodes)
{
- generateIdentifiers(defaultGroupIdentifier, sampleCodeGeneratorOrNull,
+ generateIdentifiers(projectSamplesEnabled, defaultGroupIdentifier, sampleCodeGeneratorOrNull,
isAutoGenerateCodes, newSamples);
}
break;
@@ -332,7 +336,8 @@ public class SampleUploadSectionsParser
return results;
}
- private static void generateIdentifiers(String defaultGroupIdentifier,
+ private static void generateIdentifiers(boolean projectSamplesEnabled,
+ String defaultGroupIdentifier,
SampleCodeGenerator sampleCodeGenerator, boolean isAutoGenerateCodes,
List<NewSamplesWithTypes> newSamplesWithTypes)
{
@@ -344,14 +349,22 @@ public class SampleUploadSectionsParser
List<String> codes = sampleCodeGenerator.generateCodes(newSamples.size());
for (int i = 0; i < newSamples.size(); i++)
{
- if (newSamples.get(i).getDefaultSpaceIdentifier() == null || newSamples.get(i).getDefaultSpaceIdentifier().isEmpty())
+ String spaceCodeOrNull = null;
+ if (newSamples.get(i).getDefaultSpaceIdentifier() == null || newSamples.get(i).getDefaultSpaceIdentifier().isEmpty())
{
- newSamples.get(i).setIdentifier(defaultGroupIdentifier + "/" + codes.get(i));
+ spaceCodeOrNull = defaultGroupIdentifier;
} else
{
- newSamples.get(i).setIdentifier(
- newSamples.get(i).getDefaultSpaceIdentifier() + "/" + codes.get(i));
+ spaceCodeOrNull = newSamples.get(i).getDefaultSpaceIdentifier();
}
+ spaceCodeOrNull = spaceCodeOrNull.substring(1);
+ String projectCodeOrNull = null;
+ if(projectSamplesEnabled && newSamples.get(i).getExperimentIdentifier() != null && !newSamples.get(i).getExperimentIdentifier().isEmpty()) {
+ String[] experimentIdentifierParts = newSamples.get(i).getExperimentIdentifier().split("/");
+ projectCodeOrNull = experimentIdentifierParts[experimentIdentifierParts.length - 2];
+ }
+ SampleIdentifier identifier = new SampleIdentifier(spaceCodeOrNull, projectCodeOrNull, null, codes.get(i));
+ newSamples.get(i).setIdentifier(identifier.getIdentifier());
}
}
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/server/GenericClientService.java b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/server/GenericClientService.java
index 2e25dc08210..880f76470a7 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/server/GenericClientService.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/server/GenericClientService.java
@@ -26,6 +26,7 @@ import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
+import java.util.Properties;
import java.util.Set;
import javax.annotation.Resource;
@@ -39,6 +40,7 @@ import ch.systemsx.cisd.base.exceptions.CheckedExceptionTunnel;
import ch.systemsx.cisd.common.exceptions.ExceptionUtils;
import ch.systemsx.cisd.common.properties.PropertyUtils;
import ch.systemsx.cisd.common.servlet.IRequestContextProvider;
+import ch.systemsx.cisd.common.spring.ExposablePropertyPlaceholderConfigurer;
import ch.systemsx.cisd.openbis.common.spring.IUncheckedMultipartFile;
import ch.systemsx.cisd.openbis.generic.client.web.client.dto.DataSetUpdates;
import ch.systemsx.cisd.openbis.generic.client.web.client.dto.SampleUpdates;
@@ -114,6 +116,9 @@ import ch.systemsx.cisd.openbis.plugin.generic.shared.ResourceNames;
public class GenericClientService extends AbstractClientService implements IGenericClientService, IEntityImportService
{
+ @Resource(name = ExposablePropertyPlaceholderConfigurer.PROPERTY_CONFIGURER_BEAN_NAME)
+ private ExposablePropertyPlaceholderConfigurer configurer;
+
@Resource(name = ResourceNames.GENERIC_PLUGIN_SERVER)
private IGenericServerInternal genericServer;
@@ -592,9 +597,11 @@ public class GenericClientService extends AbstractClientService implements IGene
{
files.add(new NamedInputStream(f.getInputStream(), f.getOriginalFilename()));
}
-
+
+ boolean projectSamplesEnabled = PropertyUtils.getBoolean(configurer.getResolvedProps(), Constants.PROJECT_SAMPLES_ENABLED_KEY, false);
+
BatchSamplesOperation batchSamplesOperation =
- SampleUploadSectionsParser.prepareSamples(sampleType, spaceIdentifierSilentOverrideOrNull, experimentIdentifierSilentOverrideOrNull,
+ SampleUploadSectionsParser.prepareSamples(projectSamplesEnabled, sampleType, spaceIdentifierSilentOverrideOrNull, experimentIdentifierSilentOverrideOrNull,
files,
defaultGroupIdentifier, sampleCodeGeneratorOrNull, allowExperiments,
excelSheetName, operationKind);
@@ -1372,7 +1379,10 @@ public class GenericClientService extends AbstractClientService implements IGene
Map<String, Object> info = new HashMap<String, Object>();
try
{
+ boolean projectSamplesEnabled = PropertyUtils.getBoolean(configurer.getResolvedProps(), Constants.PROJECT_SAMPLES_ENABLED_KEY, false);
+
BatchSamplesOperation batchSamplesOperation = SampleUploadSectionsParser.prepareSamples(
+ projectSamplesEnabled,
sampleType,
null,
null,
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 fdb3181bd20..02fc32bdf6a 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
@@ -68,6 +68,7 @@ import ch.systemsx.cisd.openbis.generic.server.business.bo.SampleCodeGeneratorBy
import ch.systemsx.cisd.openbis.generic.server.business.bo.SampleCodeGeneratorForTempCodes;
import ch.systemsx.cisd.openbis.generic.server.business.bo.samplelister.ISampleLister;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDAOFactory;
+import ch.systemsx.cisd.openbis.generic.server.dataaccess.IProjectDAO;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.ISampleDAO;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.ISpaceDAO;
import ch.systemsx.cisd.openbis.generic.server.plugin.IDataSetTypeSlaveServerPlugin;
@@ -111,6 +112,7 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.ExperimentPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.ExperimentTypePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.ExperimentUpdatesDTO;
import ch.systemsx.cisd.openbis.generic.shared.dto.MetaprojectPE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.ProjectPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.SampleBatchUpdatesDTO;
import ch.systemsx.cisd.openbis.generic.shared.dto.SamplePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.SampleTypePE;
@@ -1041,9 +1043,12 @@ public final class GenericServer extends AbstractServer<IGenericServerInternal>
public void updateTemporaryCodes(String sessionToken, Map<String, List<String>> sampleTypeCodeToTemporaryIdentifiers)
{
ISpaceDAO spaceDAO = getDAOFactory().getSpaceDAO();
+ IProjectDAO projectDAO = getDAOFactory().getProjectDAO();
ISampleDAO sampleDAO = getDAOFactory().getSampleDAO();
Map<String, SpacePE> spaceCache = new HashMap<String, SpacePE>();
+ Map<String, ProjectPE> projectCache = new HashMap<String, ProjectPE>();
Map<String, List<String>> spaceToOldSampleCodes = new HashMap<String, List<String>>();
+ Map<String, List<String>> projectToOldSampleCodes = new HashMap<String, List<String>>();
Map<String, String> identifiersToNewSampleCodes = new HashMap<String, String>();
// Generate Updates for each space and build helper maps
@@ -1060,23 +1065,48 @@ public final class GenericServer extends AbstractServer<IGenericServerInternal>
String tempIdentifier = temporaryIdentifiers.get(tIdx);
String spaceCode = tempIdentifier.split("/")[1];
String tempSampleCode = tempIdentifier.substring(tempIdentifier.lastIndexOf('/') + 1, tempIdentifier.length());
- SpacePE spacePE = spaceCache.get(spaceCode);
- if (spacePE == null)
- {
- spacePE = spaceDAO.tryFindSpaceByCode(spaceCode);
- spaceCache.put(spaceCode, spacePE);
+ String[] tempIdentifierParts = tempIdentifier.split("/");
+ String projectIdentifier = null;
+ String projectCode = null;
+ if(tempIdentifierParts.length == 4) {
+ projectCode = tempIdentifierParts[2];
+ projectIdentifier = "/" + spaceCode + "/" + projectCode;
}
- List<String> oldSampleCodes = spaceToOldSampleCodes.get(spaceCode);
- if (oldSampleCodes == null)
- {
- oldSampleCodes = new ArrayList<String>();
- spaceToOldSampleCodes.put(spaceCode, oldSampleCodes);
+
+ List<String> oldSampleCodes = null;
+ if(projectIdentifier != null) {
+ ProjectPE projectPE = projectCache.get(projectIdentifier);
+ if(projectPE == null) {
+ projectPE = projectDAO.tryFindProject(spaceCode, projectCode);
+ projectCache.put(projectIdentifier, projectPE);
+ }
+
+ oldSampleCodes = projectToOldSampleCodes.get(projectIdentifier);
+ if (oldSampleCodes == null)
+ {
+ oldSampleCodes = new ArrayList<String>();
+ projectToOldSampleCodes.put(projectIdentifier, oldSampleCodes);
+ }
+ } else {
+ SpacePE spacePE = spaceCache.get(spaceCode);
+ if (spacePE == null)
+ {
+ spacePE = spaceDAO.tryFindSpaceByCode(spaceCode);
+ spaceCache.put(spaceCode, spacePE);
+ }
+
+ oldSampleCodes = spaceToOldSampleCodes.get(spaceCode);
+ if (oldSampleCodes == null)
+ {
+ oldSampleCodes = new ArrayList<String>();
+ spaceToOldSampleCodes.put(spaceCode, oldSampleCodes);
+ }
}
oldSampleCodes.add(tempSampleCode);
identifiersToNewSampleCodes.put(tempIdentifier, newCodes.get(tIdx));
}
}
-
+
// Retrieve all sample PE objects
List<SamplePE> allSamplesPE = new ArrayList<SamplePE>();
for (String spaceCode : spaceToOldSampleCodes.keySet())
@@ -1084,6 +1114,11 @@ public final class GenericServer extends AbstractServer<IGenericServerInternal>
List<SamplePE> samples = sampleDAO.listByCodesAndSpace(spaceToOldSampleCodes.get(spaceCode), null, spaceCache.get(spaceCode));
allSamplesPE.addAll(samples);
}
+ for (String projectIdentifier : projectToOldSampleCodes.keySet())
+ {
+ List<SamplePE> samples = sampleDAO.listByCodesAndProject(projectToOldSampleCodes.get(projectIdentifier), null, projectCache.get(projectIdentifier));
+ allSamplesPE.addAll(samples);
+ }
// Update all codes in sample PE objects
for (SamplePE samplePE : allSamplesPE)
{
--
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