private bool TryGetMongoExtractJobDoc(Guid extractionJobIdentifier, out MongoExtractJobDoc mongoExtractJobDoc)
{
mongoExtractJobDoc = _inProgressJobCollection
.Find(GetFilterForSpecificJob <MongoExtractJobDoc>(extractionJobIdentifier))
.SingleOrDefault();
return(mongoExtractJobDoc != null);
}
public void TestToExtractJobInfo()
{
Guid guid = Guid.NewGuid();
var message = new ExtractionRequestInfoMessage
{
ExtractionModality = "MR",
JobSubmittedAt = _dateTimeProvider.UtcNow(),
ProjectNumber = "1234",
ExtractionJobIdentifier = guid,
ExtractionDirectory = "test/directory",
KeyTag = "KeyTag",
KeyValueCount = 123,
IsIdentifiableExtraction = true,
IsNoFilterExtraction = true,
};
MongoExtractJobDoc doc = MongoExtractJobDoc.FromMessage(message, _messageHeader, _dateTimeProvider);
ExtractJobInfo extractJobInfo = doc.ToExtractJobInfo();
var expected = new ExtractJobInfo(
guid,
_dateTimeProvider.UtcNow(),
"1234",
"test/directory",
"KeyTag",
123,
"MR",
ExtractJobStatus.WaitingForCollectionInfo,
isIdentifiableExtraction: true,
isNoFilterExtraction: true
);
Assert.AreEqual(expected, extractJobInfo);
}
public void TestMongoExtractJobDoc_GetHashCode()
{
Guid guid = Guid.NewGuid();
var doc1 = new MongoExtractJobDoc(
guid,
MongoExtractionMessageHeaderDoc.FromMessageHeader(guid, _messageHeader, _dateTimeProvider),
"1234",
ExtractJobStatus.WaitingForCollectionInfo,
"test/directory",
_dateTimeProvider.UtcNow(),
"KeyTag",
123,
"MR",
isIdentifiableExtraction: true,
isNoFilterExtraction: true,
null);
var doc2 = new MongoExtractJobDoc(
guid,
MongoExtractionMessageHeaderDoc.FromMessageHeader(guid, _messageHeader, _dateTimeProvider),
"1234",
ExtractJobStatus.WaitingForCollectionInfo,
"test/directory",
_dateTimeProvider.UtcNow(),
"KeyTag",
123,
"MR",
isIdentifiableExtraction: true,
isNoFilterExtraction: true,
null);
Assert.AreEqual(doc1.GetHashCode(), doc2.GetHashCode());
}
public void TestMongoExtractJobDoc_Equality()
{
Guid guid = Guid.NewGuid();
var failedInfoDoc = new MongoFailedJobInfoDoc(new TestException("aaah"), _dateTimeProvider);
var doc1 = new MongoExtractJobDoc(
guid,
MongoExtractionMessageHeaderDoc.FromMessageHeader(guid, _messageHeader, _dateTimeProvider),
"1234",
ExtractJobStatus.WaitingForCollectionInfo,
"test/directory",
_dateTimeProvider.UtcNow(),
"KeyTag",
123,
"MR",
isIdentifiableExtraction: true,
isNoFilterExtraction: true,
failedInfoDoc);
var doc2 = new MongoExtractJobDoc(
guid,
MongoExtractionMessageHeaderDoc.FromMessageHeader(guid, _messageHeader, _dateTimeProvider),
"1234",
ExtractJobStatus.WaitingForCollectionInfo,
"test/directory",
_dateTimeProvider.UtcNow(),
"KeyTag",
123,
"MR",
isIdentifiableExtraction: true,
isNoFilterExtraction: true,
failedInfoDoc);
Assert.AreEqual(doc1, doc2);
}
protected override void PersistMessageToStoreImpl(ExtractionRequestInfoMessage message, IMessageHeader header)
{
if (InCompletedJobCollection(message.ExtractionJobIdentifier))
{
throw new ApplicationException("Received an ExtractionRequestInfoMessage for a job that is already completed");
}
MongoExtractJobDoc newJobInfo = MongoExtractJobDoc.FromMessage(message, header, _dateTimeProvider);
_inProgressJobCollection.InsertOne(newJobInfo);
}
public static ExtractJobInfo ToExtractJobInfo(this MongoExtractJobDoc mongoExtractJobDoc)
=> new ExtractJobInfo(
mongoExtractJobDoc.ExtractionJobIdentifier,
mongoExtractJobDoc.JobSubmittedAt,
mongoExtractJobDoc.ProjectNumber,
mongoExtractJobDoc.ExtractionDirectory,
mongoExtractJobDoc.KeyTag,
mongoExtractJobDoc.KeyCount,
mongoExtractJobDoc.ExtractionModality,
mongoExtractJobDoc.JobStatus,
mongoExtractJobDoc.IsIdentifiableExtraction,
mongoExtractJobDoc.IsNoFilterExtraction
);
public void TestPersistMessageToStoreImpl_ExtractionRequestInfoMessage()
{
Guid guid = Guid.NewGuid();
var testExtractionRequestInfoMessage = new ExtractionRequestInfoMessage
{
ExtractionJobIdentifier = guid,
ProjectNumber = "1234-5678",
ExtractionDirectory = "1234-5678/testExtract",
JobSubmittedAt = _dateTimeProvider.UtcNow(),
KeyTag = "StudyInstanceUID",
KeyValueCount = 1,
ExtractionModality = "CT",
IsIdentifiableExtraction = true,
IsNoFilterExtraction = true,
};
var testHeader = new MessageHeader
{
MessageGuid = Guid.NewGuid(),
OriginalPublishTimestamp = MessageHeader.UnixTime(_dateTimeProvider.UtcNow()),
Parents = new[] { Guid.NewGuid(), },
ProducerExecutableName = "MongoExtractStoreTests",
ProducerProcessID = 1234,
};
var client = new TestMongoClient();
var store = new MongoExtractJobStore(client, ExtractionDatabaseName, _dateTimeProvider);
store.PersistMessageToStore(testExtractionRequestInfoMessage, testHeader);
Dictionary <Guid, MongoExtractJobDoc> docs = client.ExtractionDatabase.InProgressCollection.Documents;
Assert.AreEqual(docs.Count, 1);
MongoExtractJobDoc extractJob = docs.Values.ToList()[0];
var expected = new MongoExtractJobDoc(
guid,
MongoExtractionMessageHeaderDoc.FromMessageHeader(guid, testHeader, _dateTimeProvider),
"1234-5678",
ExtractJobStatus.WaitingForCollectionInfo,
"1234-5678/testExtract",
_dateTimeProvider.UtcNow(),
"StudyInstanceUID",
1,
"CT",
isIdentifiableExtraction: true,
isNoFilterExtraction: true,
null);
Assert.AreEqual(expected, extractJob);
}
public void Test_MongoExtractJobDoc_CopyConstructor()
{
var jobid = Guid.NewGuid();
var original = new MongoExtractJobDoc(
jobid,
MongoExtractionMessageHeaderDoc.FromMessageHeader(jobid, _messageHeader, _dateTimeProvider),
"1234",
ExtractJobStatus.WaitingForCollectionInfo,
"test/directory",
_dateTimeProvider.UtcNow(),
"KeyTag",
123,
"MR",
isIdentifiableExtraction: true,
isNoFilterExtraction: true,
new MongoFailedJobInfoDoc(new Exception("foo"), _dateTimeProvider)
);
var copied = new MongoExtractJobDoc(original);
Assert.AreEqual(original, copied);
}
public void TestMarkJobFailedImpl()
{
Guid jobId = Guid.NewGuid();
var testJob = new MongoExtractJobDoc(
jobId,
MongoExtractionMessageHeaderDoc.FromMessageHeader(jobId, new MessageHeader(), _dateTimeProvider),
"1234",
ExtractJobStatus.Failed,
"test/dir",
_dateTimeProvider.UtcNow(),
"1.2.3.4",
123,
"MR",
isIdentifiableExtraction: true,
isNoFilterExtraction: true,
null);
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.MarkJobFailed(Guid.NewGuid(), new Exception()));
client.MockSessionHandle.Verify(x => x.AbortTransaction(It.IsAny <CancellationToken>()), Times.Once);
client.MockSessionHandle.Verify(x => x.CommitTransaction(It.IsAny <CancellationToken>()), Times.Never);
// Assert that a job can't be failed twice
client = new TestMongoClient();
store = new MongoExtractJobStore(client, ExtractionDatabaseName, _dateTimeProvider);
client.ExtractionDatabase.InProgressCollection.InsertOne(testJob);
client.MockSessionHandle.Reset();
Assert.Throws <ApplicationException>(() => store.MarkJobFailed(jobId, new Exception()));
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 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.MockSessionHandle.Reset();
Assert.Throws <ApplicationException>(() => store.MarkJobFailed(jobId, new Exception()));
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);
testJob.JobStatus = ExtractJobStatus.WaitingForCollectionInfo;
testJob.FailedJobInfoDoc = null;
client.ExtractionDatabase.InProgressCollection.InsertOne(testJob);
client.MockSessionHandle.Reset();
store.MarkJobFailed(jobId, new Exception("TestMarkJobFailedImpl"));
client.MockSessionHandle.Verify(x => x.AbortTransaction(It.IsAny <CancellationToken>()), Times.Never);
client.MockSessionHandle.Verify(x => x.CommitTransaction(It.IsAny <CancellationToken>()), Times.Once);
Dictionary <Guid, MongoExtractJobDoc> docs = client.ExtractionDatabase.InProgressCollection.Documents;
Assert.AreEqual(1, docs.Count);
MongoExtractJobDoc failedDoc = docs[jobId];
Assert.AreEqual(ExtractJobStatus.Failed, failedDoc.JobStatus);
Assert.NotNull(failedDoc.FailedJobInfoDoc);
Assert.AreEqual("TestMarkJobFailedImpl", failedDoc.FailedJobInfoDoc.ExceptionMessage);
}
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);
}
