Changeset 5930
- Timestamp:
- Jan 20, 2012, 8:17:31 AM (11 years ago)
- Location:
- branches/3.0-stable/src
- Files:
-
- 2 edited
Legend:
- Unmodified
- Added
- Removed
-
branches/3.0-stable/src/plugins/core/net/sf/basedb/plugins/batchimport/AbstractItemImporter.java
r5719 r5930 598 598 if (subtypes.size() == 1) 599 599 { 600 selectedSubtype = subtypes.get(0);600 selectedSubtype = ItemSubtype.getById(dc, subtypes.get(0).getId()); 601 601 itemQuery.restrict(Restrictions.eq(Hql.property("itemSubtype"), subtypeParameter)); 602 602 itemQuery.setEntityParameter("subtypes", selectedSubtype); -
branches/3.0-stable/src/test/TestItemImporter.java
r5696 r5930 20 20 along with BASE. If not, see <http://www.gnu.org/licenses/>. 21 21 */ 22 23 import java.util.Collections; 22 24 23 25 import net.sf.basedb.core.BaseException; … … 28 30 import net.sf.basedb.core.Hardware; 29 31 import net.sf.basedb.core.Item; 32 import net.sf.basedb.core.ItemSubtype; 30 33 import net.sf.basedb.core.Job; 31 34 import net.sf.basedb.core.ParameterType; … … 76 79 int freezerId = TestHardware.test_create(SystemItems.getId(Hardware.FREEZER), "Freezer", false); 77 80 int childScanId = TestItemSubtype.test_create(Item.DERIVEDBIOASSAY, "ChildScan", SystemItems.getId(DerivedBioAssay.SCAN)); 81 int allSamplesSubtypeId = TestItemSubtype.test_create(Item.SAMPLE, "All samples"); 78 82 79 83 // Import bioplates 80 84 int bioPlateFileId = TestFile.test_create("data/test.batchimport.bioplates.txt", false, false); 81 85 int bioPlateImporterId = TestPluginDefinition.test_get("net.sf.basedb.plugins.batchimport.BioPlateImporter"); 82 int bioPlateJobId = test_create_item_import_job(Item.BIOPLATE, bioPlateImporterId, bioPlateFileId );86 int bioPlateJobId = test_create_item_import_job(Item.BIOPLATE, bioPlateImporterId, bioPlateFileId, 0); 83 87 ok = ok & TestJob.test_execute(bioPlateJobId, false); 84 88 ok = ok & TestBioPlate.test_list(2); … … 87 91 int bioSourceFileId = TestFile.test_create("data/test.batchimport.biosources.txt", false, false); 88 92 int bioSourceImporterId = TestPluginDefinition.test_get("net.sf.basedb.plugins.batchimport.BioSourceImporter"); 89 int bioSourceJobId = test_create_item_import_job(Item.BIOSOURCE, bioSourceImporterId, bioSourceFileId );93 int bioSourceJobId = test_create_item_import_job(Item.BIOSOURCE, bioSourceImporterId, bioSourceFileId, 0); 90 94 ok = ok & TestJob.test_execute(bioSourceJobId, false); 91 95 ok = ok & TestBioSource.test_list(3); … … 94 98 int sampleFileId = TestFile.test_create("data/test.batchimport.samples.txt", false, false); 95 99 int sampleImporterId = TestPluginDefinition.test_get("net.sf.basedb.plugins.batchimport.SampleImporter"); 96 int sampleJobId = test_create_item_import_job(Item.SAMPLE, sampleImporterId, sampleFileId );100 int sampleJobId = test_create_item_import_job(Item.SAMPLE, sampleImporterId, sampleFileId, allSamplesSubtypeId); 97 101 ok = ok & TestJob.test_execute(sampleJobId, false); 98 102 ok = ok & TestSample.test_list(4); … … 101 105 int extractFileId = TestFile.test_create("data/test.batchimport.extracts.txt", false, false); 102 106 int extractImporterId = TestPluginDefinition.test_get("net.sf.basedb.plugins.batchimport.ExtractImporter"); 103 int extractJobId = test_create_item_import_job(Item.EXTRACT, extractImporterId, extractFileId );107 int extractJobId = test_create_item_import_job(Item.EXTRACT, extractImporterId, extractFileId, 0); 104 108 ok = ok & TestJob.test_execute(extractJobId, false); 105 109 ok = ok & TestExtract.test_list(0, 4); … … 108 112 int labledExtractFileId = TestFile.test_create("data/test.batchimport.labeledextracts.txt", false, false); 109 113 int labledExtractImporterId = extractImporterId; 110 int labledExtractJobId = test_create_item_import_job(Item.EXTRACT, labledExtractImporterId, labledExtractFileId );114 int labledExtractJobId = test_create_item_import_job(Item.EXTRACT, labledExtractImporterId, labledExtractFileId, 0); 111 115 ok = ok & TestJob.test_execute(labledExtractJobId, false); 112 116 ok = ok & TestExtract.test_list(SystemItems.getId(Extract.LABELED), 7); … … 119 123 int designFileId = TestFile.test_create("data/test.batchimport.arraydesigns.txt", false, false); 120 124 int designImporterId = TestPluginDefinition.test_get("net.sf.basedb.plugins.batchimport.ArrayDesignImporter"); 121 int designJobId = test_create_item_import_job(Item.ARRAYDESIGN, designImporterId, designFileId );125 int designJobId = test_create_item_import_job(Item.ARRAYDESIGN, designImporterId, designFileId, 0); 122 126 ok = ok & TestJob.test_execute(designJobId, false); 123 127 ok = ok & TestArrayDesign.test_list(3); … … 126 130 int arrayBatchFileId = TestFile.test_create("data/test.batchimport.arraybatches.txt", false, false); 127 131 int arrayBatchImporterId = TestPluginDefinition.test_get("net.sf.basedb.plugins.batchimport.ArrayBatchImporter"); 128 int arrayBatchJobId = test_create_item_import_job(Item.ARRAYBATCH, arrayBatchImporterId, arrayBatchFileId );132 int arrayBatchJobId = test_create_item_import_job(Item.ARRAYBATCH, arrayBatchImporterId, arrayBatchFileId, 0); 129 133 ok = ok & TestJob.test_execute(arrayBatchJobId, false); 130 134 ok = ok & TestArrayBatch.test_list(3); … … 133 137 int arraySlideFileId = TestFile.test_create("data/test.batchimport.arrayslides.txt", false, false); 134 138 int arraySlideImporterId = TestPluginDefinition.test_get("net.sf.basedb.plugins.batchimport.ArraySlideImporter"); 135 int arraySlideJobId = test_create_item_import_job(Item.ARRAYSLIDE, arraySlideImporterId, arraySlideFileId );139 int arraySlideJobId = test_create_item_import_job(Item.ARRAYSLIDE, arraySlideImporterId, arraySlideFileId, 0); 136 140 ok = ok & TestJob.test_execute(arraySlideJobId, false); 137 141 ok = ok & TestArraySlide.test_list(5); … … 140 144 int hybFileId = TestFile.test_create("data/test.batchimport.hybridizations.txt", false, false); 141 145 int hybImporterId = TestPluginDefinition.test_get("net.sf.basedb.plugins.batchimport.PhysicalBioAssayImporter"); 142 int hybJobId = test_create_item_import_job(Item.PHYSICALBIOASSAY, hybImporterId, hybFileId );146 int hybJobId = test_create_item_import_job(Item.PHYSICALBIOASSAY, hybImporterId, hybFileId, 0); 143 147 ok = ok & TestJob.test_execute(hybJobId, false); 144 148 ok = ok & TestPhysicalBioAssay.test_list(3); … … 149 153 int scanFileId = TestFile.test_create("data/test.batchimport.scans.txt", false, false); 150 154 int scanImporterId = TestPluginDefinition.test_get("net.sf.basedb.plugins.batchimport.DerivedBioAssayImporter"); 151 int scanJobId = test_create_item_import_job(Item.DERIVEDBIOASSAY, scanImporterId, scanFileId );155 int scanJobId = test_create_item_import_job(Item.DERIVEDBIOASSAY, scanImporterId, scanFileId, 0); 152 156 ok = ok & TestJob.test_execute(scanJobId, false); 153 157 ok = ok & TestDerivedBioAssay.test_list(0, 4); … … 160 164 int rbaFileId = TestFile.test_create("data/test.batchimport.rawbioassays.txt", false, false); 161 165 int rbaImporterId = TestPluginDefinition.test_get("net.sf.basedb.plugins.batchimport.RawBioAssayImporter"); 162 int rbaJobId = test_create_item_import_job(Item.RAWBIOASSAY, rbaImporterId, rbaFileId );166 int rbaJobId = test_create_item_import_job(Item.RAWBIOASSAY, rbaImporterId, rbaFileId, 0); 163 167 ok = ok & TestJob.test_execute(rbaJobId, false); 164 168 ok = ok & TestRawBioAssay.test_list(4); … … 242 246 TestPlatform.test_delete_variant(variantId); 243 247 TestItemSubtype.test_delete(childScanId); 248 TestItemSubtype.test_delete(allSamplesSubtypeId); 244 249 245 250 write("++Testing item import using plugin "+(ok ? "OK" : "Failed")+"\n"); … … 247 252 } 248 253 249 static int test_create_item_import_job(Item itemType, int pluginDefinitionId, int fileId )254 static int test_create_item_import_job(Item itemType, int pluginDefinitionId, int fileId, int subtypeId) 250 255 { 251 256 if (pluginDefinitionId == 0 || fileId == 0) return 0; … … 267 272 setParserParameters(request); 268 273 setColumnMappingParameters(request, itemType, file); 274 if (subtypeId != 0) 275 { 276 request.setParameterValues("itemSubtypes", Collections.singletonList(ItemSubtype.getById(dc, subtypeId))); 277 } 278 279 269 280 PluginResponse response = request.invoke(); 270 281 if (response.getStatus() != Response.Status.CONTINUE)
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