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Commit be253981 authored by vkovtun's avatar vkovtun
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Merge branch 'master' into ssdm-13253-dataset-creation-from-v3

parents 83d7b147 f2a448ca
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1 merge request!40SSDM-13578 : 2PT : Database and V3 Implementation - include the new AFS "free"...
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openbis/source/java/ch/systemsx/cisd/openbis/generic/server/CommonServiceProvider.java
+ 12
− 1
View file @ be253981
......@@ -16,6 +16,7 @@
package ch.systemsx.cisd.openbis.generic.server;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.db.DAOFactory;
import ch.systemsx.cisd.openbis.generic.shared.ISessionWorkspaceProvider;
import ch.systemsx.cisd.openbis.generic.shared.SessionWorkspaceProvider;
import org.springframework.context.ApplicationContext;
......@@ -41,6 +42,8 @@ public class CommonServiceProvider
{
private static ApplicationContext applicationContext;
private static IDAOFactory daoFactory;
public static void setApplicationContext(ApplicationContext context)
{
applicationContext = context;
......@@ -63,7 +66,15 @@ public class CommonServiceProvider
public static IDAOFactory getDAOFactory()
{
return (IDAOFactory) applicationContext.getBean("dao-factory");
if (daoFactory == null) {
daoFactory = (IDAOFactory) applicationContext.getBean("dao-factory");
}
return daoFactory;
}
public static void setDAOFactory(IDAOFactory daoFactory)
{
CommonServiceProvider.daoFactory = daoFactory;
}
public static ICommonBusinessObjectFactory getBusinessObjectFactory()
......
openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/AbstractServerTestCase.java
+ 8
− 9
View file @ be253981
......@@ -19,6 +19,8 @@ package ch.systemsx.cisd.openbis.generic.shared;
import java.util.ArrayList;
import java.util.Arrays;
import ch.systemsx.cisd.openbis.generic.server.CommonServiceProvider;
import ch.systemsx.cisd.openbis.generic.shared.dto.*;
import org.apache.log4j.Level;
import org.jmock.Expectations;
import org.jmock.Mockery;
......@@ -84,15 +86,6 @@ import ch.systemsx.cisd.openbis.generic.server.dataaccess.PersistencyResources;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.db.IPermIdDAO;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DisplaySettings;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewExperiment;
import ch.systemsx.cisd.openbis.generic.shared.dto.DataSetTypePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.DataStorePE;
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.ExternalDataPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.PersonPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.ProjectPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.Session;
import ch.systemsx.cisd.openbis.generic.shared.dto.SpacePE;
import ch.systemsx.cisd.openbis.generic.shared.util.MaterialConfigurationProvider;
import ch.systemsx.cisd.openbis.util.LogRecordingUtils;
......@@ -134,6 +127,8 @@ public abstract class AbstractServerTestCase extends AssertJUnit
protected ISampleDAO sampleDAO;
protected ISampleRelationshipDAO sampleRelationshipDAO;
protected ISpaceBO spaceBO;
protected ISampleBO sampleBO;
......@@ -236,10 +231,12 @@ public abstract class AbstractServerTestCase extends AssertJUnit
propertiesBatchManager = context.mock(IPropertiesBatchManager.class);
// DAO
daoFactory = context.mock(IDAOFactory.class);
CommonServiceProvider.setDAOFactory(daoFactory);
personDAO = context.mock(IPersonDAO.class);
groupDAO = context.mock(ISpaceDAO.class);
spaceDAO = groupDAO;
sampleDAO = context.mock(ISampleDAO.class);
sampleRelationshipDAO = context.mock(ISampleRelationshipDAO.class);
roleAssignmentDAO = context.mock(IRoleAssignmentDAO.class);
dataSetDAO = context.mock(IDataDAO.class);
permIdDAO = context.mock(IPermIdDAO.class);
......@@ -298,6 +295,8 @@ public abstract class AbstractServerTestCase extends AssertJUnit
will(returnValue(groupDAO));
allowing(daoFactory).getSampleDAO();
will(returnValue(sampleDAO));
allowing(daoFactory).getSampleRelationshipDAO();
will(returnValue(sampleRelationshipDAO));
allowing(daoFactory).getExperimentDAO();
will(returnValue(experimentDAO));
allowing(daoFactory).getRoleAssignmentDAO();
......
openbis_standard_technologies/dist/core-plugins/eln-lims/1/dss/reporting-plugins/exports-api/exportsApi.py
+ 22
− 20
View file @ be253981
......@@ -151,10 +151,12 @@ def validateDataSize(entitiesToExport, tr):
estimatedSizeInBytes += 12000; # AVG File Metadata size
estimatedSizeInMegabytes = estimatedSizeInBytes / 1000000;
operationLog.info(
"Size Limit check - limitDataSizeInBytes: " + str(limitDataSizeInBytes) + " > " + " estimatedSizeInBytes: " + str(estimatedSizeInBytes));
u"Size Limit check - limitDataSizeInBytes: " + str(limitDataSizeInBytes).encode('utf-8') +
u" > estimatedSizeInBytes: " + str(estimatedSizeInBytes).encode('utf-8'));
if estimatedSizeInBytes > limitDataSizeInBytes:
raise UserFailureException("The selected data is " + str(estimatedSizeInMegabytes) + " MB that is bigger than the configured limit of " + str(
limitDataSizeInMegabytes) + " MB");
raise UserFailureException(u"The selected data is " + estimatedSizeInMegabytes +
u" MB that is bigger than the configured limit of " +
limitDataSizeInMegabytes + u" MB");
def findEntitiesToExport(params):
......@@ -172,17 +174,17 @@ def findEntitiesToExport(params):
if entity.get("expand"):
entitiesToExpand.append(entityAsPythonMap);
operationLog.info("Found %d entities to expand." % len(entitiesToExpand))
operationLog.info(u"Found %d entities to expand." % len(entitiesToExpand))
while entitiesToExpand:
entityToExpand = entitiesToExpand.popleft();
type = entityToExpand["type"];
permId = entityToExpand["permId"];
operationLog.info("Expanding type: " + str(type) + " permId: " + str(permId));
operationLog.info(u"Expanding type: " + type.encode("utf-8") + u" permId: " + permId.encode("utf-8"));
if type == "ROOT":
criteria = SpaceSearchCriteria();
results = v3.searchSpaces(sessionToken, criteria, SpaceFetchOptions());
operationLog.info("Found: " + str(results.getTotalCount()) + " spaces");
operationLog.info(u"Found: %d spaces" % results.getTotalCount());
for space in results.getObjects():
entityFound = {"type": "SPACE", "permId": space.getCode(), "registrationDate": space.getRegistrationDate()};
addToExportWithoutRepeating(entitiesToExport, entityFound);
......@@ -191,7 +193,7 @@ def findEntitiesToExport(params):
criteria = ProjectSearchCriteria();
criteria.withSpace().withCode().thatEquals(permId);
results = v3.searchProjects(sessionToken, criteria, ProjectFetchOptions());
operationLog.info("Found: " + str(results.getTotalCount()) + " projects");
operationLog.info(u"Found: %d projects" % results.getTotalCount());
for project in results.getObjects():
entityFound = {"type": "PROJECT", "permId": project.getPermId().getPermId(), "registrationDate": project.getRegistrationDate()};
addToExportWithoutRepeating(entitiesToExport, entityFound);
......@@ -200,7 +202,7 @@ def findEntitiesToExport(params):
criteria = ExperimentSearchCriteria();
criteria.withProject().withPermId().thatEquals(permId);
results = v3.searchExperiments(sessionToken, criteria, ExperimentFetchOptions());
operationLog.info("Found: " + str(results.getTotalCount()) + " experiments");
operationLog.info(u"Found: %d experiments" % results.getTotalCount());
for experiment in results.getObjects():
entityFound = {"type": "EXPERIMENT", "permId": experiment.getPermId().getPermId(),
"registrationDate": experiment.getRegistrationDate()};
......@@ -210,7 +212,7 @@ def findEntitiesToExport(params):
criteria = SampleSearchCriteria();
criteria.withExperiment().withPermId().thatEquals(permId);
results = v3.searchSamples(sessionToken, criteria, SampleFetchOptions());
operationLog.info("Found: " + str(results.getTotalCount()) + " samples");
operationLog.info(u"Found: %d samples" % results.getTotalCount());
dCriteria = DataSetSearchCriteria();
dCriteria.withExperiment().withPermId().thatEquals(permId);
......@@ -218,13 +220,13 @@ def findEntitiesToExport(params):
fetchOptions = DataSetFetchOptions()
fetchOptions.withDataStore()
dResults = v3.searchDataSets(sessionToken, dCriteria, fetchOptions);
operationLog.info("Found: " + str(dResults.getTotalCount()) + " datasets");
operationLog.info(u"Found: %d datasets" % dResults.getTotalCount());
for dataset in dResults.getObjects():
entityFound = {"type": "DATASET", "permId": dataset.getPermId().getPermId(), "registrationDate": dataset.getRegistrationDate()};
addToExportWithoutRepeating(entitiesToExport, entityFound);
entitiesToExpand.append(entityFound);
operationLog.info("Found: " + str(results.getTotalCount()) + " samples");
operationLog.info(u"Found: %d samples" % results.getTotalCount());
for sample in results.getObjects():
entityFound = {"type": "SAMPLE", "permId": sample.getPermId().getPermId(), "registrationDate": sample.getRegistrationDate()};
addToExportWithoutRepeating(entitiesToExport, entityFound);
......@@ -235,7 +237,7 @@ def findEntitiesToExport(params):
fetchOptions = DataSetFetchOptions()
fetchOptions.withDataStore()
results = v3.searchDataSets(sessionToken, criteria, fetchOptions);
operationLog.info("Found: " + str(results.getTotalCount()) + " datasets");
operationLog.info(u"Found: %d datasets" % results.getTotalCount());
for dataset in results.getObjects():
entityFound = {"type": "DATASET", "permId": dataset.getPermId().getPermId(), "registrationDate": dataset.getRegistrationDate()};
addToExportWithoutRepeating(entitiesToExport, entityFound);
......@@ -244,7 +246,7 @@ def findEntitiesToExport(params):
criteria = DataSetFileSearchCriteria();
criteria.withDataSet().withPermId().thatEquals(permId);
results = v3d.searchFiles(sessionToken, criteria, DataSetFileFetchOptions());
operationLog.info("Found: " + str(results.getTotalCount()) + " files");
operationLog.info(u"Found: %d files" % results.getTotalCount());
for file in results.getObjects():
entityFound = {"type": "FILE", "permId": permId, "path": file.getPath(), "isDirectory": file.isDirectory(),
"length": file.getFileLength()};
......@@ -282,7 +284,7 @@ def generateFilesInZip(zos, entities, includeRoot, sessionToken, tempDirPath, de
for entity in entities:
type = entity["type"];
permId = entity["permId"];
operationLog.info("exporting type: " + str(type) + " permId: " + str(permId));
operationLog.info(u"exporting type: " + type.encode("utf-8") + u" permId: " + permId.encode("utf-8"));
entityObj = None;
entityFilePath = None;
......@@ -383,8 +385,7 @@ def generateFilesInZip(zos, entities, includeRoot, sessionToken, tempDirPath, de
if entityObj is not None:
objectCache[permId] = entityObj;
operationLog.info("--> Entity type: " + type + " permId: " + permId + " obj: " + str(entityObj is not None) + " path: " + str(
entityFilePath) + " before files.");
operationLog.info(u"--> Entity type: %s permId: %s obj: %s path: %s before files." % (type, permId, str(entityObj is not None), entityFilePath));
if entityObj is not None and entityFilePath is not None:
# JSON
entityJson = String(objectMapper.writerWithDefaultPrettyPrinter().writeValueAsString(entityObj));
......@@ -403,19 +404,20 @@ def generateFilesInZip(zos, entities, includeRoot, sessionToken, tempDirPath, de
entityHTML = getDOCX(entityObj, v3, sessionToken, True);
fileMetadatum = addFile(tempDirPath, entityFilePath, "html", entityHTML, zos, deflated=deflated);
fileMetadata.append(fileMetadatum)
operationLog.info("--> Entity type: " + type + " permId: " + permId + " post html.");
operationLog.info(u"--> Entity type: " + type.encode("utf-8") + u" permId: " + permId.encode("utf-8") +
u" post html.");
if emptyZip:
raise IOError('Nothing added to ZIP file.')
raise IOError("Nothing added to ZIP file.")
return fileMetadata
def generateDownloadUrl(sessionToken, tempZipFileName, tempZipFilePath):
# Store on workspace to be able to generate a download link
operationLog.info("Zip file can be found on the temporal directory: " + tempZipFilePath);
operationLog.info(u"Zip file can be found on the temporal directory: " + tempZipFilePath.encode("utf-8"));
dssService = ServiceProvider.getApplicationContext().getBean("dss-service-rpc-generic")
dssService.putFileToSessionWorkspace(sessionToken, tempZipFileName, FileInputStream(File(tempZipFilePath)))
tempZipFileWorkspaceURL = DataStoreServer.getConfigParameters().getDownloadURL() + "/datastore_server/session_workspace_file_download?sessionID=" + sessionToken + "&filePath=" + tempZipFileName;
operationLog.info("Zip file can be downloaded from the workspace: " + tempZipFileWorkspaceURL);
operationLog.info(u"Zip file can be downloaded from the workspace: " + tempZipFileWorkspaceURL.encode("utf-8"));
return tempZipFileWorkspaceURL
......
screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/server/ScreeningServerTest.java
+ 6
− 0
View file @ be253981
......@@ -17,6 +17,8 @@
package ch.systemsx.cisd.openbis.plugin.screening.server;
import java.lang.reflect.Method;
import java.util.Collections;
import java.util.List;
import org.jmock.Expectations;
import org.testng.annotations.AfterMethod;
......@@ -113,6 +115,8 @@ public class ScreeningServerTest extends AbstractServerTestCase
one(sampleBO).loadBySamplePermId(PERM_ID);
one(sampleBO).getSample();
will(returnValue(exampleSample));
one(sampleRelationshipDAO).listSampleParents(List.of(exampleSample.getId()));
will(returnValue(List.of()));
}
});
......@@ -143,6 +147,8 @@ public class ScreeningServerTest extends AbstractServerTestCase
SampleIdentifierFactory.parse(SAMPLE_IDENTIFIER));
one(sampleBO).getSample();
will(returnValue(exampleSample));
one(sampleRelationshipDAO).listSampleParents(List.of(exampleSample.getId()));
will(returnValue(List.of()));
}
});
......
screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/ScreeningApiImplTest.java
+ 4
− 0
View file @ be253981
......@@ -102,6 +102,8 @@ public class ScreeningApiImplTest extends AbstractServerTestCase
one(sampleBO).loadBySampleIdentifier(SampleIdentifierFactory.parse(identifier));
one(sampleBO).getSample();
will(returnValue(plate));
one(sampleRelationshipDAO).listSampleParents(List.of(plate.getId()));
will(returnValue(List.of()));
one(screeningBOFactory).createSampleLister(session);
will(returnValue(sampleLister));
......@@ -139,6 +141,8 @@ public class ScreeningApiImplTest extends AbstractServerTestCase
one(sampleBO).loadBySamplePermId(permId);
one(sampleBO).getSample();
will(returnValue(plate));
one(sampleRelationshipDAO).listSampleParents(List.of(plate.getId()));
will(returnValue(List.of()));
one(screeningBOFactory).createSampleLister(session);
will(returnValue(sampleLister));
......
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