Changeset 5934

Timestamp:

Jan 25, 2012, 1:52:40 PM (11 years ago)

Author:

Nicklas Nordborg

Message:

Merged patch release 3.0.2 to the trunk.

Location:

trunk

Files:

• . (modified) (1 prop)
• credits.txt (modified) (1 diff)
• src/clients/web/net/sf/basedb/clients/web/Base.java (modified) (2 diffs)
• src/core/net/sf/basedb/core/Keyring.java (modified) (4 diffs)
• src/plugins/core/net/sf/basedb/plugins/batchimport/AbstractItemImporter.java (modified) (1 diff)
• src/test/TestItemImporter.java (modified) (17 diffs)

trunk/credits.txt

@@ -1 +1 @@
 $Id$
 
-The current BASE team is (at BASE 3.0.1 release)
+The current BASE team is (at BASE 3.0.2 release)
 {{{
 Jari Häkkinen

trunk/src/clients/web/net/sf/basedb/clients/web/Base.java

@@ -560 +560 @@
       
       // Item permission
-      String permission = Values.getStringOrNull(request.getParameter("permission"));
+      String permission = request.getParameter("permission");
       if (permission != null)
       {
@@ -586 +586 @@
       {
         cc.removeAllPropertyFilters();
+        cc.setItemPermission(null);
         filterHasChanged = true;
       }

trunk/src/core/net/sf/basedb/core/Keyring.java

@@ -164 +164 @@
     TRUE if the Timer has signaled that it is time to reload the information.
   */
-  private boolean reload;
+  private volatile boolean reload;
 
   /**
@@ -263 +263 @@
   {
     if (!getReload()) return true;
+    setReload(false);
     org.hibernate.Session session = null;
     org.hibernate.Transaction tx = null;
@@ -284 +285 @@
         loadPluginPermissionKeys(session);
       }
-      setReload(false);
       // Schedule another reload as configured in base.config
       Application.getCoreTimer().schedule(new ReloadTask(), 
@@ -743 +743 @@
     else
     {
-      maxProjectPermission = IntegerUtil.getInt(projects.get(projectId));
+      maxProjectPermission = IntegerUtil.getInt(projects.get(projectId)) | getRolePermissions(Item.PROJECT);
     }
   }

trunk/src/plugins/core/net/sf/basedb/plugins/batchimport/AbstractItemImporter.java

@@ -605 +605 @@
       if (subtypes.size() == 1)
       {
-        selectedSubtype = subtypes.get(0);
+        selectedSubtype = ItemSubtype.getById(dc, subtypes.get(0).getId());
         itemQuery.restrict(Restrictions.eq(Hql.property("itemSubtype"), subtypeParameter));
         itemQuery.setEntityParameter("subtypes", selectedSubtype);

trunk/src/test/TestItemImporter.java

@@ -20 +20 @@
   along with BASE. If not, see <http://www.gnu.org/licenses/>.
 */
+
+import java.util.Collections;
 
 import net.sf.basedb.core.BaseException;
@@ -28 +30 @@
 import net.sf.basedb.core.Hardware;
 import net.sf.basedb.core.Item;
+import net.sf.basedb.core.ItemSubtype;
 import net.sf.basedb.core.Job;
 import net.sf.basedb.core.ParameterType;
@@ -81 +84 @@
     int freezerId = TestHardware.test_create(SystemItems.getId(Hardware.FREEZER), "Freezer", false);
     int childScanId = TestItemSubtype.test_create(Item.DERIVEDBIOASSAY, "ChildScan", SystemItems.getId(DerivedBioAssay.SCAN));
+    int allSamplesSubtypeId = TestItemSubtype.test_create(Item.SAMPLE, "All samples");
     
     TestProject.test_defaultItem(projectId, Item.PROTOCOL, defaultSamplingProtocolId);
@@ -89 +93 @@
     int bioPlateFileId = TestFile.test_create("data/test.batchimport.bioplates.txt", false, false);
     int bioPlateImporterId  = TestPluginDefinition.test_get("net.sf.basedb.plugins.batchimport.BioPlateImporter");
-    int bioPlateJobId = test_create_item_import_job(Item.BIOPLATE, bioPlateImporterId, bioPlateFileId);
+    int bioPlateJobId = test_create_item_import_job(Item.BIOPLATE, bioPlateImporterId, bioPlateFileId, 0);
     ok = ok & TestJob.test_execute(bioPlateJobId, false);
     ok = ok & TestBioPlate.test_list(2);
@@ -96 +100 @@
     int bioSourceFileId = TestFile.test_create("data/test.batchimport.biosources.txt", false, false);
     int bioSourceImporterId  = TestPluginDefinition.test_get("net.sf.basedb.plugins.batchimport.BioSourceImporter");
-    int bioSourceJobId = test_create_item_import_job(Item.BIOSOURCE, bioSourceImporterId, bioSourceFileId);
+    int bioSourceJobId = test_create_item_import_job(Item.BIOSOURCE, bioSourceImporterId, bioSourceFileId, 0);
     ok = ok & TestJob.test_execute(bioSourceJobId, false);
     ok = ok & TestBioSource.test_list(3);
@@ -103 +107 @@
     int sampleFileId = TestFile.test_create("data/test.batchimport.samples.txt", false, false);
     int sampleImporterId  = TestPluginDefinition.test_get("net.sf.basedb.plugins.batchimport.SampleImporter");
-    int sampleJobId = test_create_item_import_job(Item.SAMPLE, sampleImporterId, sampleFileId);
+    int sampleJobId = test_create_item_import_job(Item.SAMPLE, sampleImporterId, sampleFileId, allSamplesSubtypeId);
     ok = ok & TestJob.test_execute(sampleJobId, false);
     ok = ok & TestSample.test_list(4);
@@ -110 +114 @@
     int extractFileId = TestFile.test_create("data/test.batchimport.extracts.txt", false, false);
     int extractImporterId  = TestPluginDefinition.test_get("net.sf.basedb.plugins.batchimport.ExtractImporter");
-    int extractJobId = test_create_item_import_job(Item.EXTRACT, extractImporterId, extractFileId);
+    int extractJobId = test_create_item_import_job(Item.EXTRACT, extractImporterId, extractFileId, 0);
     ok = ok & TestJob.test_execute(extractJobId, false);
     ok = ok & TestExtract.test_list(0, 4);
@@ -117 +121 @@
     int labledExtractFileId = TestFile.test_create("data/test.batchimport.labeledextracts.txt", false, false);
     int labledExtractImporterId  = extractImporterId;
-    int labledExtractJobId = test_create_item_import_job(Item.EXTRACT, labledExtractImporterId, labledExtractFileId);
+    int labledExtractJobId = test_create_item_import_job(Item.EXTRACT, labledExtractImporterId, labledExtractFileId, 0);
     ok = ok & TestJob.test_execute(labledExtractJobId, false);
     ok = ok & TestExtract.test_list(SystemItems.getId(Extract.LABELED), 7);
@@ -128 +132 @@
     int designFileId = TestFile.test_create("data/test.batchimport.arraydesigns.txt", false, false);
     int designImporterId  = TestPluginDefinition.test_get("net.sf.basedb.plugins.batchimport.ArrayDesignImporter");
-    int designJobId = test_create_item_import_job(Item.ARRAYDESIGN, designImporterId, designFileId);
+    int designJobId = test_create_item_import_job(Item.ARRAYDESIGN, designImporterId, designFileId, 0);
     ok = ok & TestJob.test_execute(designJobId, false);
     ok = ok & TestArrayDesign.test_list(3);
@@ -135 +139 @@
     int arrayBatchFileId = TestFile.test_create("data/test.batchimport.arraybatches.txt", false, false);
     int arrayBatchImporterId  = TestPluginDefinition.test_get("net.sf.basedb.plugins.batchimport.ArrayBatchImporter");
-    int arrayBatchJobId = test_create_item_import_job(Item.ARRAYBATCH, arrayBatchImporterId, arrayBatchFileId);
+    int arrayBatchJobId = test_create_item_import_job(Item.ARRAYBATCH, arrayBatchImporterId, arrayBatchFileId, 0);
     ok = ok & TestJob.test_execute(arrayBatchJobId, false);
     ok = ok & TestArrayBatch.test_list(3);
@@ -142 +146 @@
     int arraySlideFileId = TestFile.test_create("data/test.batchimport.arrayslides.txt", false, false);
     int arraySlideImporterId  = TestPluginDefinition.test_get("net.sf.basedb.plugins.batchimport.ArraySlideImporter");
-    int arraySlideJobId = test_create_item_import_job(Item.ARRAYSLIDE, arraySlideImporterId, arraySlideFileId);
+    int arraySlideJobId = test_create_item_import_job(Item.ARRAYSLIDE, arraySlideImporterId, arraySlideFileId, 0);
     ok = ok & TestJob.test_execute(arraySlideJobId, false);
     ok = ok & TestArraySlide.test_list(5);
@@ -149 +153 @@
     int hybFileId = TestFile.test_create("data/test.batchimport.hybridizations.txt", false, false);
     int hybImporterId  = TestPluginDefinition.test_get("net.sf.basedb.plugins.batchimport.PhysicalBioAssayImporter");
-    int hybJobId = test_create_item_import_job(Item.PHYSICALBIOASSAY, hybImporterId, hybFileId);
+    int hybJobId = test_create_item_import_job(Item.PHYSICALBIOASSAY, hybImporterId, hybFileId, 0);
     ok = ok & TestJob.test_execute(hybJobId, false);
     ok = ok & TestPhysicalBioAssay.test_list(3);
@@ -158 +162 @@
     int scanFileId = TestFile.test_create("data/test.batchimport.scans.txt", false, false);
     int scanImporterId  = TestPluginDefinition.test_get("net.sf.basedb.plugins.batchimport.DerivedBioAssayImporter");
-    int scanJobId = test_create_item_import_job(Item.DERIVEDBIOASSAY, scanImporterId, scanFileId);
+    int scanJobId = test_create_item_import_job(Item.DERIVEDBIOASSAY, scanImporterId, scanFileId, 0);
     ok = ok & TestJob.test_execute(scanJobId, false);
     ok = ok & TestDerivedBioAssay.test_list(0, 4);
@@ -169 +173 @@
     int rbaFileId = TestFile.test_create("data/test.batchimport.rawbioassays.txt", false, false);
     int rbaImporterId  = TestPluginDefinition.test_get("net.sf.basedb.plugins.batchimport.RawBioAssayImporter");
-    int rbaJobId = test_create_item_import_job(Item.RAWBIOASSAY, rbaImporterId, rbaFileId);
+    int rbaJobId = test_create_item_import_job(Item.RAWBIOASSAY, rbaImporterId, rbaFileId, 0);
     ok = ok & TestJob.test_execute(rbaJobId, false);
     ok = ok & TestRawBioAssay.test_list(4);
@@ -252 +256 @@
     TestPlatform.test_delete_variant(variantId);
     TestItemSubtype.test_delete(childScanId);
+    TestItemSubtype.test_delete(allSamplesSubtypeId);
     TestProject.test_delete(projectId);
 
@@ -258 +263 @@
   }
 
-  static int test_create_item_import_job(Item itemType, int pluginDefinitionId, int fileId)
+  static int test_create_item_import_job(Item itemType, int pluginDefinitionId, int fileId, int subtypeId)
   {
     if (pluginDefinitionId == 0 || fileId == 0) return 0;
@@ -278 +283 @@
       setParserParameters(request);
       setColumnMappingParameters(request, itemType, file);
+      if (subtypeId != 0)
+      {
+        request.setParameterValues("itemSubtypes", Collections.singletonList(ItemSubtype.getById(dc, subtypeId)));
+      }
+      
+      
       PluginResponse response = request.invoke();
       if (response.getStatus() != Response.Status.CONTINUE)