protected override void PersistMessageToStoreImpl(ExtractedFileVerificationMessage message, IMessageHeader header)
{
if (InCompletedJobCollection(message.ExtractionJobIdentifier))
{
throw new ApplicationException("Received an ExtractedFileVerificationMessage for a job that is already completed");
}
var newStatus = new MongoFileStatusDoc(
MongoExtractionMessageHeaderDoc.FromMessageHeader(message.ExtractionJobIdentifier, header, _dateTimeProvider),
message.DicomFilePath,
message.OutputFilePath,
wasAnonymised: true,
isIdentifiable: message.IsIdentifiable,
ExtractedFileStatus.Anonymised,
statusMessage: message.Report);
_database
.GetCollection <MongoFileStatusDoc>(StatusCollectionName(message.ExtractionJobIdentifier))
.InsertOne(newStatus);
}
public void TestMongoFileStatusDoc_GetHashCode()
{
Guid guid = Guid.NewGuid();
var doc1 = new MongoFileStatusDoc(
MongoExtractionMessageHeaderDoc.FromMessageHeader(guid, _messageHeader, _dateTimeProvider),
"input.dcm",
"anon.dcm",
true,
false,
ExtractedFileStatus.Anonymised,
"anonymised");
var doc2 = new MongoFileStatusDoc(
MongoExtractionMessageHeaderDoc.FromMessageHeader(guid, _messageHeader, _dateTimeProvider),
"input.dcm",
"anon.dcm",
true,
false,
ExtractedFileStatus.Anonymised,
"anonymised");
Assert.AreEqual(doc1.GetHashCode(), doc2.GetHashCode());
}
public void TestPersistMessageToStoreImpl_IsIdentifiableMessage()
{
var client = new TestMongoClient();
var store = new MongoExtractJobStore(client, ExtractionDatabaseName, _dateTimeProvider);
Guid jobId = Guid.NewGuid();
var testIsIdentifiableMessage = new ExtractedFileVerificationMessage
{
OutputFilePath = "anon.dcm",
JobSubmittedAt = _dateTimeProvider.UtcNow(),
ProjectNumber = "1234",
ExtractionJobIdentifier = jobId,
ExtractionDirectory = "1234/test",
DicomFilePath = "original.dcm",
IsIdentifiable = false,
Report = "[]", // NOTE(rkm 2020-03-10) An "empty" report from IsIdentifiable
};
var header = new MessageHeader();
store.PersistMessageToStore(testIsIdentifiableMessage, header);
Dictionary <Guid, MongoFileStatusDoc> docs = client.ExtractionDatabase.StatusCollections[$"statuses_{jobId}"].Documents;
Assert.AreEqual(docs.Count, 1);
MongoFileStatusDoc statusDoc = docs.Values.ToList()[0];
var expected = new MongoFileStatusDoc(
MongoExtractionMessageHeaderDoc.FromMessageHeader(jobId, header, _dateTimeProvider),
"original.dcm",
"anon.dcm",
true,
false,
ExtractedFileStatus.Anonymised,
"[]");
Assert.True(statusDoc.Equals(expected));
}
public void TestPersistMessageToStoreImpl_ExtractFileStatusMessage()
{
var client = new TestMongoClient();
var store = new MongoExtractJobStore(client, ExtractionDatabaseName, _dateTimeProvider);
Guid jobId = Guid.NewGuid();
var testExtractFileStatusMessage = new ExtractedFileStatusMessage
{
OutputFilePath = "anon.dcm",
JobSubmittedAt = _dateTimeProvider.UtcNow(),
Status = ExtractedFileStatus.ErrorWontRetry,
ProjectNumber = "1234",
ExtractionJobIdentifier = jobId,
ExtractionDirectory = "1234/test",
StatusMessage = "Could not anonymise",
DicomFilePath = "original.dcm",
};
var header = new MessageHeader();
store.PersistMessageToStore(testExtractFileStatusMessage, header);
Dictionary <Guid, MongoFileStatusDoc> docs = client.ExtractionDatabase.StatusCollections[$"statuses_{jobId}"].Documents;
Assert.AreEqual(docs.Count, 1);
MongoFileStatusDoc statusDoc = docs.Values.ToList()[0];
var expected = new MongoFileStatusDoc(
MongoExtractionMessageHeaderDoc.FromMessageHeader(jobId, header, _dateTimeProvider),
"original.dcm",
"anon.dcm",
false,
true,
ExtractedFileStatus.ErrorWontRetry,
"Could not anonymise");
Assert.True(statusDoc.Equals(expected));
}
public void TestCompleteJobImpl()
{
Guid jobId = Guid.NewGuid();
var testJob = new MongoExtractJobDoc(
jobId,
MongoExtractionMessageHeaderDoc.FromMessageHeader(jobId, new MessageHeader(), _dateTimeProvider),
"1234",
ExtractJobStatus.Failed,
"test/dir",
_dateTimeProvider.UtcNow(),
"SeriesInstanceUID",
1,
"MR",
isIdentifiableExtraction: true,
isNoFilterExtraction: true,
null);
var testMongoExpectedFilesDoc = new MongoExpectedFilesDoc(
MongoExtractionMessageHeaderDoc.FromMessageHeader(jobId, new MessageHeader(), _dateTimeProvider),
"1.2.3.4",
new HashSet <MongoExpectedFileInfoDoc>
{
new MongoExpectedFileInfoDoc(Guid.NewGuid(), "anon1.dcm"),
},
new MongoRejectedKeyInfoDoc(
MongoExtractionMessageHeaderDoc.FromMessageHeader(jobId, new MessageHeader(), _dateTimeProvider),
new Dictionary <string, int>())
);
var testMongoFileStatusDoc = new MongoFileStatusDoc(
MongoExtractionMessageHeaderDoc.FromMessageHeader(jobId, new MessageHeader(), _dateTimeProvider),
"input.dcm",
"anon1.dcm",
true,
false,
ExtractedFileStatus.Anonymised,
"Verified");
var client = new TestMongoClient();
var store = new MongoExtractJobStore(client, ExtractionDatabaseName, _dateTimeProvider);
// Assert that an exception is thrown for a non-existent job
Assert.Throws <ApplicationException>(() => store.MarkJobCompleted(Guid.NewGuid()));
client.MockSessionHandle.Verify(x => x.AbortTransaction(It.IsAny <CancellationToken>()), Times.Once);
client.MockSessionHandle.Verify(x => x.CommitTransaction(It.IsAny <CancellationToken>()), Times.Never);
// Assert that an exception is thrown for a job which is marked as failed
client = new TestMongoClient();
store = new MongoExtractJobStore(client, ExtractionDatabaseName, _dateTimeProvider);
client.ExtractionDatabase.InProgressCollection.InsertOne(testJob);
client.MockSessionHandle.Reset();
Assert.Throws <ApplicationException>(() => store.MarkJobCompleted(Guid.NewGuid()));
client.MockSessionHandle.Verify(x => x.AbortTransaction(It.IsAny <CancellationToken>()), Times.Once);
client.MockSessionHandle.Verify(x => x.CommitTransaction(It.IsAny <CancellationToken>()), Times.Never);
// Check that we handle a failed insertion
client = new TestMongoClient();
store = new MongoExtractJobStore(client, ExtractionDatabaseName, _dateTimeProvider);
testJob.JobStatus = ExtractJobStatus.Completed;
client.ExtractionDatabase.InProgressCollection.InsertOne(testJob);
client.ExtractionDatabase.CompletedJobCollection.RejectChanges = true;
client.MockSessionHandle.Reset();
Assert.Throws <Exception>(() => store.MarkJobCompleted(jobId));
client.MockSessionHandle.Verify(x => x.AbortTransaction(It.IsAny <CancellationToken>()), Times.Once);
client.MockSessionHandle.Verify(x => x.CommitTransaction(It.IsAny <CancellationToken>()), Times.Never);
// Check we handle a bad DeleteResult
client = new TestMongoClient();
store = new MongoExtractJobStore(client, ExtractionDatabaseName, _dateTimeProvider);
client.ExtractionDatabase.InProgressCollection.RejectChanges = true;
client.MockSessionHandle.Reset();
Assert.Throws <ApplicationException>(() => store.MarkJobCompleted(jobId));
client.MockSessionHandle.Verify(x => x.AbortTransaction(It.IsAny <CancellationToken>()), Times.Once);
client.MockSessionHandle.Verify(x => x.CommitTransaction(It.IsAny <CancellationToken>()), Times.Never);
// Check we handle missing expectedFiles collection
client = new TestMongoClient();
store = new MongoExtractJobStore(client, ExtractionDatabaseName, _dateTimeProvider);
client.ExtractionDatabase.InProgressCollection.InsertOne(testJob);
client.MockSessionHandle.Reset();
Assert.Throws <ApplicationException>(() => store.MarkJobCompleted(jobId));
client.MockSessionHandle.Verify(x => x.AbortTransaction(It.IsAny <CancellationToken>()), Times.Once);
client.MockSessionHandle.Verify(x => x.CommitTransaction(It.IsAny <CancellationToken>()), Times.Never);
// Check we handle missing statuses collection
client = new TestMongoClient();
store = new MongoExtractJobStore(client, ExtractionDatabaseName, _dateTimeProvider);
client.ExtractionDatabase.InProgressCollection.InsertOne(testJob);
client.ExtractionDatabase.ExpectedFilesCollections[$"expectedFiles_{jobId}"] = new MockExtractCollection <Guid, MongoExpectedFilesDoc>();
client.ExtractionDatabase.ExpectedFilesCollections[$"expectedFiles_{jobId}"].InsertOne(testMongoExpectedFilesDoc);
client.MockSessionHandle.Reset();
Assert.Throws <ApplicationException>(() => store.MarkJobCompleted(jobId));
client.MockSessionHandle.Verify(x => x.AbortTransaction(It.IsAny <CancellationToken>()), Times.Once);
client.MockSessionHandle.Verify(x => x.CommitTransaction(It.IsAny <CancellationToken>()), Times.Never);
// Check happy path
client = new TestMongoClient();
store = new MongoExtractJobStore(client, ExtractionDatabaseName, _dateTimeProvider);
client.ExtractionDatabase.InProgressCollection.InsertOne(testJob);
client.ExtractionDatabase.ExpectedFilesCollections[$"expectedFiles_{jobId}"] = new MockExtractCollection <Guid, MongoExpectedFilesDoc>();
client.ExtractionDatabase.ExpectedFilesCollections[$"expectedFiles_{jobId}"].InsertOne(testMongoExpectedFilesDoc);
client.ExtractionDatabase.StatusCollections[$"statuses_{jobId}"] = new MockExtractCollection <Guid, MongoFileStatusDoc>();
client.ExtractionDatabase.StatusCollections[$"statuses_{jobId}"].InsertOne(testMongoFileStatusDoc);
client.MockSessionHandle.Reset();
store.MarkJobCompleted(jobId);
client.MockSessionHandle.Verify(x => x.AbortTransaction(It.IsAny <CancellationToken>()), Times.Never);
client.MockSessionHandle.Verify(x => x.CommitTransaction(It.IsAny <CancellationToken>()), Times.Once);
Assert.AreEqual(1, client.ExtractionDatabase.ExpectedFilesCollections.Count);
Assert.AreEqual(1, client.ExtractionDatabase.StatusCollections.Count);
}
public void TestGetReadJobsImpl()
{
Guid jobId = Guid.NewGuid();
var testJob = new MongoExtractJobDoc(
jobId,
MongoExtractionMessageHeaderDoc.FromMessageHeader(jobId, new MessageHeader(), _dateTimeProvider),
"1234",
ExtractJobStatus.Failed,
"test/dir",
_dateTimeProvider.UtcNow(),
"SeriesInstanceUID",
1,
"MR",
isIdentifiableExtraction: true,
isNoFilterExtraction: true,
null);
var testMongoExpectedFilesDoc = new MongoExpectedFilesDoc(
MongoExtractionMessageHeaderDoc.FromMessageHeader(jobId, new MessageHeader(), _dateTimeProvider),
"1.2.3.4",
new HashSet <MongoExpectedFileInfoDoc>
{
new MongoExpectedFileInfoDoc(Guid.NewGuid(), "anon1.dcm"),
},
new MongoRejectedKeyInfoDoc(
MongoExtractionMessageHeaderDoc.FromMessageHeader(jobId, new MessageHeader(), _dateTimeProvider),
new Dictionary <string, int>())
);
var testMongoFileStatusDoc = new MongoFileStatusDoc(
MongoExtractionMessageHeaderDoc.FromMessageHeader(jobId, new MessageHeader(), _dateTimeProvider),
"input.dcm",
"anon1.dcm",
true,
false,
ExtractedFileStatus.Anonymised,
"Verified");
var client = new TestMongoClient();
var store = new MongoExtractJobStore(client, ExtractionDatabaseName, _dateTimeProvider);
// Assert that jobs marked as failed are not returned
client.ExtractionDatabase.InProgressCollection.InsertOne(testJob);
client.ExtractionDatabase.InProgressCollection.RejectChanges = true;
Assert.AreEqual(0, store.GetReadyJobs().Count);
// Assert that an in progress job is not returned
client = new TestMongoClient();
store = new MongoExtractJobStore(client, ExtractionDatabaseName, _dateTimeProvider);
testJob.JobStatus = ExtractJobStatus.WaitingForCollectionInfo;
client.ExtractionDatabase.InProgressCollection.InsertOne(testJob);
client.ExtractionDatabase.InProgressCollection.RejectChanges = true;
Assert.AreEqual(0, store.GetReadyJobs().Count);
// Check we handle a bad ReplaceOneResult
client = new TestMongoClient();
store = new MongoExtractJobStore(client, ExtractionDatabaseName, _dateTimeProvider);
testJob.JobStatus = ExtractJobStatus.WaitingForCollectionInfo;
client.ExtractionDatabase.InProgressCollection.InsertOne(testJob);
client.ExtractionDatabase.InProgressCollection.RejectChanges = true;
client.ExtractionDatabase.ExpectedFilesCollections[$"expectedFiles_{jobId}"] = new MockExtractCollection <Guid, MongoExpectedFilesDoc>();
client.ExtractionDatabase.ExpectedFilesCollections[$"expectedFiles_{jobId}"].InsertOne(testMongoExpectedFilesDoc);
Assert.Throws <ApplicationException>(() => store.GetReadyJobs());
// Check happy path
client = new TestMongoClient();
store = new MongoExtractJobStore(client, ExtractionDatabaseName, _dateTimeProvider);
testJob.JobStatus = ExtractJobStatus.WaitingForCollectionInfo;
client.ExtractionDatabase.InProgressCollection.InsertOne(testJob);
client.ExtractionDatabase.ExpectedFilesCollections[$"expectedFiles_{jobId}"] = new MockExtractCollection <Guid, MongoExpectedFilesDoc>();
client.ExtractionDatabase.ExpectedFilesCollections[$"expectedFiles_{jobId}"].InsertOne(testMongoExpectedFilesDoc);
Assert.AreEqual(0, store.GetReadyJobs().Count);
Assert.AreEqual(ExtractJobStatus.WaitingForStatuses, client.ExtractionDatabase.InProgressCollection.Documents.Single().Value.JobStatus);
client.ExtractionDatabase.StatusCollections[$"statuses_{jobId}"] = new MockExtractCollection <Guid, MongoFileStatusDoc>();
client.ExtractionDatabase.StatusCollections[$"statuses_{jobId}"].InsertOne(testMongoFileStatusDoc);
ExtractJobInfo job = store.GetReadyJobs().Single();
Assert.AreEqual(ExtractJobStatus.ReadyForChecks, job.JobStatus);
Assert.AreEqual(ExtractJobStatus.ReadyForChecks, client.ExtractionDatabase.InProgressCollection.Documents.Single().Value.JobStatus);
}
