public void FromCataloguesExtractionRequestFulfiller_NormalMatching_SeriesInstanceUIDOnly(DatabaseType databaseType)
{
var db = GetCleanedServer(databaseType);
var dt = new DataTable();
dt.Columns.Add("SeriesInstanceUID");
dt.Columns.Add("Extractable", typeof(bool));
dt.Columns.Add(QueryToExecuteColumnSet.DefaultImagePathColumnName);
dt.Rows.Add("123", true, "/images/1.dcm");
dt.Rows.Add("123", false, "/images/2.dcm");
dt.Rows.Add("1234", false, "/images/3.dcm");
dt.Rows.Add("1234", true, "/images/4.dcm");
dt.SetDoNotReType(true);
var tbl = db.CreateTable("FromCataloguesExtractionRequestFulfillerTests", dt);
var catalogue = Import(tbl);
var fulfiller = new FromCataloguesExtractionRequestFulfiller(new[] { catalogue });
var matching = fulfiller.GetAllMatchingFiles(new ExtractionRequestMessage()
{
KeyTag = "SeriesInstanceUID",
ExtractionIdentifiers = new List <string>(new string[] { "123" }),
}, new NullAuditExtractions()).ToArray();
Assert.AreEqual(1, matching.Length);
Assert.AreEqual(2, matching[0].Accepted.Count());
Assert.AreEqual(1, matching[0].Accepted.Count(f => f.FilePathValue.Equals("/images/1.dcm")));
Assert.AreEqual(1, matching[0].Accepted.Count(f => f.FilePathValue.Equals("/images/2.dcm")));
}
public void Test_FromCataloguesExtractionRequestFulfiller_NoFilterExtraction(DatabaseType databaseType, bool isNoFiltersExtraction)
{
DiscoveredDatabase db = GetCleanedServer(databaseType);
var dt = new DataTable();
dt.Columns.Add("StudyInstanceUID");
dt.Columns.Add("SeriesInstanceUID");
dt.Columns.Add("SOPInstanceUID");
dt.Columns.Add("Extractable", typeof(bool));
dt.Columns.Add(QueryToExecuteColumnSet.DefaultImagePathColumnName);
dt.Rows.Add("1.1", "123.1", "1.1", true, "/images/1.dcm");
dt.SetDoNotReType(true);
DiscoveredTable tbl = db.CreateTable("FromCataloguesExtractionRequestFulfillerTests", dt);
ICatalogue catalogue = Import(tbl);
ExtractionInformation ei = catalogue.GetAllExtractionInformation(ExtractionCategory.Any).First();
var filter = new ExtractionFilter(CatalogueRepository, "Extractable only", ei)
{
IsMandatory = true,
WhereSQL = "Extractable = 1"
};
filter.SaveToDatabase();
var fulfiller = new FromCataloguesExtractionRequestFulfiller(new[] { catalogue });
fulfiller.Rejectors.Add(new RejectAll());
var message = new ExtractionRequestMessage
{
KeyTag = "SeriesInstanceUID",
ExtractionIdentifiers = new List <string>(new [] { "123.1" }),
IsNoFilterExtraction = isNoFiltersExtraction,
};
ExtractImageCollection[] matching = fulfiller.GetAllMatchingFiles(message, new NullAuditExtractions()).ToArray();
int expected = isNoFiltersExtraction ? 1 : 0;
Assert.AreEqual(1, matching.Length);
Assert.AreEqual(expected, matching[0].Accepted.Count);
}
public void FromCataloguesExtractionRequestFulfiller_MandatoryFilter(DatabaseType databaseType)
{
var db = GetCleanedServer(databaseType);
var dt = new DataTable();
dt.Columns.Add("StudyInstanceUID");
dt.Columns.Add("SeriesInstanceUID");
dt.Columns.Add("SOPInstanceUID");
dt.Columns.Add("Extractable", typeof(bool));
dt.Columns.Add(QueryToExecuteColumnSet.DefaultImagePathColumnName);
dt.Rows.Add("1.1", "123.1", "1.1", true, "/images/1.dcm");
dt.Rows.Add("1.1", "123.1", "2.1", false, "/images/2.dcm");
dt.Rows.Add("1.1", "1234.1", "3.1", false, "/images/3.dcm");
dt.Rows.Add("1.1", "1234.1", "4.1", true, "/images/4.dcm");
dt.SetDoNotReType(true);
var tbl = db.CreateTable("FromCataloguesExtractionRequestFulfillerTests", dt);
var catalogue = Import(tbl);
var ei = catalogue.GetAllExtractionInformation(ExtractionCategory.Any).First();
var filter = new ExtractionFilter(CatalogueRepository, "Extractable only", ei);
filter.IsMandatory = true;
filter.WhereSQL = "Extractable = 1";
filter.SaveToDatabase();
var fulfiller = new FromCataloguesExtractionRequestFulfiller(new[] { catalogue });
var matching = fulfiller.GetAllMatchingFiles(new ExtractionRequestMessage()
{
KeyTag = "SeriesInstanceUID",
ExtractionIdentifiers = new List <string>(new string[] { "123.1" }),
}, new NullAuditExtractions()).ToArray();
Assert.AreEqual(1, matching.Length);
Assert.AreEqual(1, matching[0].Accepted.Count);
Assert.AreEqual(1, matching[0].Accepted.Count(f => f.FilePathValue.Equals("/images/1.dcm")));
}
public void Test_OnlyExtractableImages(DatabaseType dbType, bool useDynamic)
{
var db = GetCleanedServer(dbType);
//create table with 300 rows to ensure at least two studies
const int testrows = 300;
var tbl = BuildExampleExtractionTable(db, "CT", testrows, true);
Assert.AreEqual(testrows, tbl.GetRowCount());
var cata = Import(tbl);
List <string> studies;
//fetch all unique studies from the database
using (var dt = tbl.GetDataTable())
studies = dt.Rows.Cast <DataRow>().Select(r => r["StudyInstanceUID"]).Cast <string>().Distinct().ToList();
Assert.GreaterOrEqual(studies.Count, 2, "Expected at least 2 studies to be randomly generated in database");
//Create message to extract all the studies by StudyInstanceUID
var msgIn = new ExtractionRequestMessage();
msgIn.KeyTag = DicomTag.StudyInstanceUID.DictionaryEntry.Keyword;
msgIn.ExtractionIdentifiers = studies;
int matches = 0;
//The strategy pattern implementation that goes to the database but also considers reason
var fulfiller = new FromCataloguesExtractionRequestFulfiller(new[] { cata });
fulfiller.Rejectors.Add(useDynamic? (IRejector) new DynamicRejector():new TestRejector());
foreach (ExtractImageCollection msgOut in fulfiller.GetAllMatchingFiles(msgIn, new NullAuditExtractions()))
{
matches += msgOut.Accepted.Count();
Assert.IsEmpty(msgOut.Rejected);
}
//currently all images are extractable
Assert.AreEqual(testrows, matches);
//now make 10 not extractable
using (var con = tbl.Database.Server.GetConnection())
{
con.Open();
string sql = GetUpdateTopXSql(tbl, 10, "Set IsExtractableToDisk=0, IsExtractableToDisk_Reason = 'We decided NO!'");
//make the top 10 not extractable
using (var cmd = tbl.Database.Server.GetCommand(sql, con))
{
cmd.ExecuteNonQuery();
}
}
matches = 0;
int rejections = 0;
foreach (ExtractImageCollection msgOut in fulfiller.GetAllMatchingFiles(msgIn, new NullAuditExtractions()))
{
matches += msgOut.Accepted.Count;
rejections += msgOut.Rejected.Count;
Assert.IsTrue(msgOut.Rejected.All(v => v.RejectReason.Equals("We decided NO!")));
}
Assert.AreEqual(testrows - 10, matches);
Assert.AreEqual(10, rejections);
}
public void Test_OnlyListedModalities(DatabaseType dbType)
{
var db = GetCleanedServer(dbType);
//create table with 100 rows
var tblCT = BuildExampleExtractionTable(db, "CT", 70, true);
var tblMR = BuildExampleExtractionTable(db, "MR", 30, true);
var cataCT = Import(tblCT);
var cataMR = Import(tblMR);
List <string> studies = new List <string>();
//fetch all unique studies from the database
using (var dt = tblCT.GetDataTable())
studies.AddRange(dt.Rows.Cast <DataRow>().Select(r => r["StudyInstanceUID"]).Cast <string>().Distinct());
using (var dt = tblMR.GetDataTable())
studies.AddRange(dt.Rows.Cast <DataRow>().Select(r => r["StudyInstanceUID"]).Cast <string>().Distinct());
//Create message to extract all the series by StudyInstanceUID
var msgIn = new ExtractionRequestMessage();
msgIn.KeyTag = DicomTag.StudyInstanceUID.DictionaryEntry.Keyword;
//extract only MR (this is what we are actually testing).
msgIn.Modality = "MR";
msgIn.ExtractionIdentifiers = studies;
int matches = 0;
//The strategy pattern implementation that goes to the database but also considers reason
var fulfiller = new FromCataloguesExtractionRequestFulfiller(new[] { cataCT, cataMR })
{
//Give it the default modality pattern (table prefix)
ModalityRoutingRegex = new Regex(new CohortExtractorOptions().ModalityRoutingRegex)
};
foreach (ExtractImageCollection msgOut in fulfiller.GetAllMatchingFiles(msgIn, new NullAuditExtractions()))
{
matches += msgOut.Accepted.Count();
Assert.IsEmpty(msgOut.Rejected);
}
//expect only the MR images to be returned
Assert.AreEqual(30, matches);
// Ask for something that doesn't exist
msgIn.Modality = "Hello";
var ex = Assert.Throws <Exception>(() => fulfiller.GetAllMatchingFiles(msgIn, new NullAuditExtractions()).ToArray());
StringAssert.Contains("Modality=Hello", ex.Message);
// Ask for all modalities at once by not specifying any
msgIn.Modality = null;
Assert.AreEqual(100, fulfiller.GetAllMatchingFiles(msgIn, new NullAuditExtractions()).Sum(r => r.Accepted.Count));
// Ask for both modalities specifically
msgIn.Modality = "CT,Hello";
Assert.AreEqual(70, fulfiller.GetAllMatchingFiles(msgIn, new NullAuditExtractions()).Sum(r => r.Accepted.Count));
// Ask for both modalities specifically
msgIn.Modality = "CT,MR";
Assert.AreEqual(100, fulfiller.GetAllMatchingFiles(msgIn, new NullAuditExtractions()).Sum(r => r.Accepted.Count));
//when we don't have that flag anymore the error should tell us that
tblCT.DropColumn(tblCT.DiscoverColumn("IsOriginal"));
msgIn.Modality = "CT,MR";
ex = Assert.Throws(Is.AssignableTo(typeof(Exception)), () => fulfiller.GetAllMatchingFiles(msgIn, new NullAuditExtractions()).ToArray());
StringAssert.Contains("IsOriginal", ex.Message);
}
