From 59fbdef3b1cfc36c7fe45b5eb92921ed4cf9dba0 Mon Sep 17 00:00:00 2001
From: jakubs <jakubs>
Date: Wed, 3 Oct 2012 11:06:49 +0000
Subject: [PATCH] SP-299 BIS-211 add filter for storage confirmed datasets in
general information service
SVN: 26947
---
.../api/v1/GeneralInformationService.java | 5 +++--
...DataSetByExperimentIdentifierValidator.java | 18 ++++++++++--------
.../StorageConfirmedForAdminValidator.java | 11 ++++++++---
.../datasetlister/DataSetLister.java | 5 +++++
.../datasetlister/DataSetRecord.java | 2 ++
.../datasetlister/IDataSetListingQuery.java | 2 ++
.../generic/shared/api/v1/Translator.java | 2 ++
.../GeneralInformationServiceJsonApiTest.java | 17 +++++++++++++++++
.../sql/postgresql/122/030=external_data.tsv | 2 +-
9 files changed, 50 insertions(+), 14 deletions(-)
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/api/v1/GeneralInformationService.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/api/v1/GeneralInformationService.java
index ad3415a3007..77a9be667a8 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/api/v1/GeneralInformationService.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/api/v1/GeneralInformationService.java
@@ -864,12 +864,13 @@ public class GeneralInformationService extends AbstractServer<IGeneralInformatio
// filter by user
final PersonPE person = getDAOFactory().getPersonDAO().tryFindPersonByUserId(userId);
- final DataSetByExperimentIdentifierValidator validator =
+ final DataSetByExperimentIdentifierValidator experimentIdentifierValidator =
new DataSetByExperimentIdentifierValidator();
+
final ArrayList<DataSet> dataSets = new ArrayList<DataSet>(allDataSets.size());
for (DataSet dataSet : allDataSets)
{
- if (validator.doValidation(person, dataSet))
+ if (experimentIdentifierValidator.doValidation(person, dataSet))
{
dataSets.add(dataSet);
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/validator/DataSetByExperimentIdentifierValidator.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/validator/DataSetByExperimentIdentifierValidator.java
index 4556eff6263..2507f9e9bca 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/validator/DataSetByExperimentIdentifierValidator.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/validator/DataSetByExperimentIdentifierValidator.java
@@ -32,14 +32,16 @@ public class DataSetByExperimentIdentifierValidator extends AbstractValidator<Da
@Override
public boolean doValidation(PersonPE person, final DataSet value)
{
- return validator.isValid(person, new IIdentifierHolder()
- {
- @Override
- public String getIdentifier()
- {
- return value.getExperimentIdentifier();
- }
- });
+
+ return StorageConfirmedForAdminValidator.isValid(person, value.isStorageConfirmed())
+ && validator.isValid(person, new IIdentifierHolder()
+ {
+ @Override
+ public String getIdentifier()
+ {
+ return value.getExperimentIdentifier();
+ }
+ });
}
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/validator/StorageConfirmedForAdminValidator.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/validator/StorageConfirmedForAdminValidator.java
index 52a86b7f003..07cf24091a9 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/validator/StorageConfirmedForAdminValidator.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/validator/StorageConfirmedForAdminValidator.java
@@ -21,13 +21,13 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.PersonPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.RoleAssignmentPE;
/**
- * @author Franz-Josef Elmer
+ * @author Jakub Straszewski
*/
public class StorageConfirmedForAdminValidator extends
AbstractValidator<ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExternalData>
{
- private boolean isPersonAllowedForNotConfirmed(PersonPE person)
+ private static boolean isPersonAllowedForNotConfirmed(PersonPE person)
{
for (RoleAssignmentPE role : person.getAllPersonRoles())
{
@@ -39,10 +39,15 @@ public class StorageConfirmedForAdminValidator extends
return false;
}
+ public static boolean isValid(PersonPE person, boolean isStorageConfirmed)
+ {
+ return isStorageConfirmed || isPersonAllowedForNotConfirmed(person);
+ }
+
@Override
public boolean doValidation(PersonPE person,
ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExternalData value)
{
- return value.isStorageConfirmation() || isPersonAllowedForNotConfirmed(person);
+ return isValid(person, value.isStorageConfirmation());
}
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/fetchoptions/datasetlister/DataSetLister.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/fetchoptions/datasetlister/DataSetLister.java
index 958f643f9ee..bc1aab89116 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/fetchoptions/datasetlister/DataSetLister.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/fetchoptions/datasetlister/DataSetLister.java
@@ -173,6 +173,11 @@ public class DataSetLister implements IDataSetLister
initializer.setDataSetTypeCode(dataSet.dt_code);
initializer.setContainerDataSet(DataSetKind.CONTAINER.name().equals(
dataSet.dt_data_set_kind));
+ initializer.setStorageConfirmed(dataSet.ed_sc == null || dataSet.ed_sc); // if there's no
+ // external data
+ // than the storage
+ // is considered
+ // confirmed
initializer.setLinkDataSet(DataSetKind.LINK.name().equals(dataSet.dt_data_set_kind));
if (initializer.isLinkDataSet())
{
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/fetchoptions/datasetlister/DataSetRecord.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/fetchoptions/datasetlister/DataSetRecord.java
index ed9c22a20cd..515920cd652 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/fetchoptions/datasetlister/DataSetRecord.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/fetchoptions/datasetlister/DataSetRecord.java
@@ -36,6 +36,8 @@ public class DataSetRecord
public String dt_data_set_kind;
+ public Boolean ed_sc;
+
public String ex_code;
public String sa_code;
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/fetchoptions/datasetlister/IDataSetListingQuery.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/fetchoptions/datasetlister/IDataSetListingQuery.java
index 67ee0e2aab0..1870ea93c6d 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/fetchoptions/datasetlister/IDataSetListingQuery.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/fetchoptions/datasetlister/IDataSetListingQuery.java
@@ -37,6 +37,7 @@ public interface IDataSetListingQuery extends BaseQuery
+ " ds.modification_timestamp as ds_modification_timestamp,"
+ " dt.code as dt_code, dt.data_set_kind as dt_data_set_kind,"
+ " ex.code as ex_code, "
+ + " ed.storage_confirmation as ed_sc,"
+ " sa.code as sa_code, sa.dbin_id as sa_dbin_id, sac.code as sac_code,"
+ " pe.first_name as pe_first_name, pe.last_name as pe_last_name, pe.email as pe_email, pe.user_id as pe_user_id,"
+ " mod.first_name as mod_first_name, mod.last_name as mod_last_name, mod.email as mod_email, mod.user_id as mod_user_id,"
@@ -45,6 +46,7 @@ public interface IDataSetListingQuery extends BaseQuery
+ " ld.external_code as ld_external_code, edms.id as edms_id, edms.code as edms_code, edms.label as edms_label, edms.url_template as edms_url_template, edms.is_openbis as edms_is_openbis"
+ " from data ds inner join data_set_types dt on ds.dsty_id = dt.id"
+ " inner join experiments ex on ds.expe_id = ex.id"
+ + " left outer join external_data ed on ds.id = ed.data_id"
+ " left outer join link_data ld on ds.id = ld.data_id"
+ " left outer join external_data_management_systems edms on ld.edms_id = edms.id"
+ " left outer join samples sa on ds.samp_id = sa.id"
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/Translator.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/Translator.java
index 87a8c6831fa..75bca955dac 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/Translator.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/Translator.java
@@ -342,6 +342,8 @@ public class Translator
initializer.setExperimentIdentifier(externalDatum.getExperiment().getIdentifier());
initializer.setSampleIdentifierOrNull(externalDatum.getSampleIdentifier());
initializer.setDataSetTypeCode(externalDatum.getDataSetType().getCode());
+ initializer.setStorageConfirmed(externalDatum.isStorageConfirmation());
+
List<IEntityProperty> properties = externalDatum.getProperties();
for (IEntityProperty prop : properties)
{
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/remoteapitest/api/v1/GeneralInformationServiceJsonApiTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/remoteapitest/api/v1/GeneralInformationServiceJsonApiTest.java
index 4cfffcdcceb..743daa4b38b 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/remoteapitest/api/v1/GeneralInformationServiceJsonApiTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/remoteapitest/api/v1/GeneralInformationServiceJsonApiTest.java
@@ -68,6 +68,8 @@ public class GeneralInformationServiceJsonApiTest extends RemoteApiTestCase
protected String sessionToken;
+ protected String userSessionToken;
+
protected IGeneralInformationService createService()
{
return TestJsonServiceFactory.createGeneralInfoService();
@@ -78,6 +80,8 @@ public class GeneralInformationServiceJsonApiTest extends RemoteApiTestCase
{
generalInformationService = createService();
sessionToken = generalInformationService.tryToAuthenticateForAllServices("test", "a");
+ userSessionToken =
+ generalInformationService.tryToAuthenticateForAllServices("test_role", "a");
}
@AfterMethod
@@ -327,6 +331,19 @@ public class GeneralInformationServiceJsonApiTest extends RemoteApiTestCase
assertEquals(true, result.size() > 0);
}
+ @Test
+ public void testListDataSetsForSampleForRegularUserDoesntIncludeStorageNonConfirmed()
+ {
+ // Search for Samples first
+ SearchCriteria sc = new SearchCriteria();
+ sc.addMatchClause(MatchClause.createPropertyMatch("ORGANISM", "HUMAN"));
+ List<Sample> samples = generalInformationService.searchForSamples(userSessionToken, sc);
+ List<DataSet> result =
+ generalInformationService.listDataSetsForSample(userSessionToken, samples.get(0),
+ true);
+ assertEquals(0, result.size());
+ }
+
@Test
public void testListDataSetsForEmptySampleList()
{
diff --git a/openbis/sourceTest/sql/postgresql/122/030=external_data.tsv b/openbis/sourceTest/sql/postgresql/122/030=external_data.tsv
index 62d8e8972a9..3b5f306416e 100644
--- a/openbis/sourceTest/sql/postgresql/122/030=external_data.tsv
+++ b/openbis/sourceTest/sql/postgresql/122/030=external_data.tsv
@@ -1,6 +1,6 @@
2 xxx/yyy/zzz 1 1 4 U \N AVAILABLE \N \N f -50 t
4 analysis/result 2 1 4 U \N AVAILABLE \N \N f -50 t
-5 a/1 1 1 4 U \N AVAILABLE 42 4711 f 42 t
+5 a/1 1 1 4 U \N AVAILABLE 42 4711 f 42 f
6 a/2 2 1 4 U \N AVAILABLE \N \N f -50 t
7 a/3 3 1 4 U \N AVAILABLE \N \N f -50 t
8 xml/result-8 8 1 4 U \N AVAILABLE \N \N f -50 t
--
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