public void CreateTask()
{
_lmd = new LoadMetadata(CatalogueRepository);
_dir = new DirectoryInfo(Path.Combine(TestContext.CurrentContext.TestDirectory, "ProcessTaskCheckingTests"));
_dir.Create();
var hicdir = LoadDirectory.CreateDirectoryStructure(_dir, "ProjDir", true);
_lmd.LocationOfFlatFiles = hicdir.RootPath.FullName;
_lmd.SaveToDatabase();
Catalogue c = new Catalogue(CatalogueRepository, "c");
CatalogueItem ci = new CatalogueItem(CatalogueRepository, c, "ci");
TableInfo t = new TableInfo(CatalogueRepository, "t");
t.Server = DiscoveredServerICanCreateRandomDatabasesAndTablesOn.Name;
t.Database = "mydb";
t.SaveToDatabase();
ColumnInfo col = new ColumnInfo(CatalogueRepository, "col", "bit", t);
ci.SetColumnInfo(col);
c.LoadMetadata_ID = _lmd.ID;
c.SaveToDatabase();
_task = new ProcessTask(CatalogueRepository, _lmd, LoadStage.GetFiles);
_checker = new ProcessTaskChecks(_lmd);
}
public void Check(ICheckNotifier notifier)
{
var catalogueLoadChecks = new CatalogueLoadChecks(LoadMetadata, _loadConfigurationFlags, _databaseConfiguration);
var metadataLoggingConfigurationChecks = new MetadataLoggingConfigurationChecks(LoadMetadata);
var processTaskChecks = new ProcessTaskChecks(LoadMetadata);
var preExecutionChecks = new PreExecutionChecker(LoadMetadata, _databaseConfiguration);
_mef.CheckForVersionMismatches(notifier);
//If the load is a progressable (loaded over time) then make sure any associated caches are compatible with the load ProcessTasks
foreach (ILoadProgress loadProgress in LoadMetadata.LoadProgresses)
{
loadProgress.Check(notifier);
var cp = loadProgress.CacheProgress;
if (cp != null)
{
try
{
var f = new CacheLayoutFactory();
f.CreateCacheLayout(loadProgress, LoadMetadata);
}
catch (Exception e)
{
notifier.OnCheckPerformed(new CheckEventArgs("Load contains a CacheProgress '" + cp + "' but we were unable to generate an ICacheLayout, see Inner Exception for details", CheckResult.Fail, e));
}
}
}
//Make sure there are some load tasks and they are valid
processTaskChecks.Check(notifier);
try
{
metadataLoggingConfigurationChecks.Check(notifier);
preExecutionChecks.Check(notifier);
if (!preExecutionChecks.HardFail)
{
catalogueLoadChecks.Check(notifier);
}
}
catch (Exception e)
{
notifier.OnCheckPerformed(new CheckEventArgs("Entire check process crashed in an unexpected way", CheckResult.Fail, e));
}
}
public void IntegrationTest_HappyPath_WithIsolation(DatabaseType databaseType, Type namerType)
{
var server = GetCleanedServer(databaseType, ScratchDatabaseName);
SetupSuite(server, false, "MR_");
//this ensures that the ExtractionConfiguration.ID and Project.ID properties are out of sync (they are automnums). Its just a precaution since we are using both IDs in places if we
//had any bugs where we used the wrong one but they were the same then it would be obscured until production
var p = new Project(DataExportRepository, "delme");
p.DeleteInDatabase();
_globals.DicomRelationalMapperOptions.Guid = new Guid("fc229fc3-f700-4515-86e8-e3d38b3d1823");
_globals.DicomRelationalMapperOptions.QoSPrefetchCount = 5000;
_globals.DicomRelationalMapperOptions.MinimumBatchSize = 3;
_globals.DicomRelationalMapperOptions.DatabaseNamerType = namerType.FullName;
_helper.TruncateTablesIfExists();
//Create test directory with a single image
var dir = new DirectoryInfo(Path.Combine(TestContext.CurrentContext.TestDirectory, nameof(IntegrationTest_HappyPath_WithIsolation)));
dir.Create();
var ptIsolation = new ProcessTask(CatalogueRepository, _helper.LoadMetadata, LoadStage.AdjustRaw);
ptIsolation.CreateArgumentsForClassIfNotExists <PrimaryKeyCollisionIsolationMutilation>();
ptIsolation.Path = typeof(PrimaryKeyCollisionIsolationMutilation).FullName;
ptIsolation.ProcessTaskType = ProcessTaskType.MutilateDataTable;
ptIsolation.SaveToDatabase();
var arg1 = _helper.LoadMetadata.ProcessTasks.SelectMany(a => a.ProcessTaskArguments).Single(a => a.Name.Equals("TablesToIsolate"));
arg1.SetValue(new[] { _helper.StudyTableInfo, _helper.SeriesTableInfo, _helper.ImageTableInfo });
arg1.SaveToDatabase();
var db = new ExternalDatabaseServer(CatalogueRepository, "IsolationDatabase(live)", null);
db.SetProperties(server);
var arg2 = _helper.LoadMetadata.ProcessTasks.SelectMany(a => a.ProcessTaskArguments).Single(a => a.Name.Equals("IsolationDatabase"));
arg2.SetValue(db);
arg2.SaveToDatabase();
var arg3 = _helper.LoadMetadata.ProcessTasks.SelectMany(a => a.ProcessTaskArguments).Single(a => a.Name.Equals("ModalityMatchingRegex"));
arg3.SetValue(new Regex("([A-z]*)_.*$"));
arg3.SaveToDatabase();
//build the joins
new JoinInfo(CatalogueRepository,
_helper.ImageTableInfo.ColumnInfos.Single(c => c.GetRuntimeName().Equals("SeriesInstanceUID")),
_helper.SeriesTableInfo.ColumnInfos.Single(c => c.GetRuntimeName().Equals("SeriesInstanceUID")),
ExtractionJoinType.Right, null);
new JoinInfo(CatalogueRepository,
_helper.SeriesTableInfo.ColumnInfos.Single(c => c.GetRuntimeName().Equals("StudyInstanceUID")),
_helper.StudyTableInfo.ColumnInfos.Single(c => c.GetRuntimeName().Equals("StudyInstanceUID")),
ExtractionJoinType.Right, null);
//start with Study table
_helper.StudyTableInfo.IsPrimaryExtractionTable = true;
_helper.StudyTableInfo.SaveToDatabase();
//clean up the directory
foreach (FileInfo f in dir.GetFiles())
{
f.Delete();
}
TestData.Create(new FileInfo(Path.Combine(dir.FullName, "MyTestFile.dcm")));
var ds1 = new DicomDataset();
ds1.Add(DicomTag.StudyInstanceUID, "1.2.3");
ds1.Add(DicomTag.SeriesInstanceUID, "1.2.2");
ds1.Add(DicomTag.SOPInstanceUID, "1.2.3");
ds1.Add(DicomTag.PatientAge, "030Y");
ds1.Add(DicomTag.PatientID, "123");
ds1.Add(DicomTag.SOPClassUID, "1");
ds1.Add(DicomTag.Modality, "MR");
new DicomFile(ds1).Save(Path.Combine(dir.FullName, "abc.dcm"));
var ds2 = new DicomDataset();
ds2.Add(DicomTag.StudyInstanceUID, "1.2.3");
ds2.Add(DicomTag.SeriesInstanceUID, "1.2.4");
ds2.Add(DicomTag.SOPInstanceUID, "1.2.7");
ds2.Add(DicomTag.PatientAge, "040Y"); //age is replicated but should be unique at study level so gets isolated
ds2.Add(DicomTag.PatientID, "123");
ds2.Add(DicomTag.SOPClassUID, "1");
ds2.Add(DicomTag.Modality, "MR");
new DicomFile(ds2).Save(Path.Combine(dir.FullName, "def.dcm"));
var checks = new ProcessTaskChecks(_helper.LoadMetadata);
checks.Check(new AcceptAllCheckNotifier());
RunTest(dir, 1);
Assert.AreEqual(1, _helper.ImageTable.GetRowCount());
var isoTable = server.ExpectTable(_helper.ImageTable.GetRuntimeName() + "_Isolation");
Assert.AreEqual(2, isoTable.GetRowCount());
}