public void TestMongoExpectedFilesDoc_GetHashCode()
{
var expectedFiles = new HashSet <MongoExpectedFileInfoDoc>
{
new MongoExpectedFileInfoDoc(Guid.NewGuid(), "anon1.dcm"),
new MongoExpectedFileInfoDoc(Guid.NewGuid(), "anon2.dcm"),
};
Guid jobId = Guid.NewGuid();
var rejectedKeys = new MongoRejectedKeyInfoDoc(
MongoExtractionMessageHeaderDoc.FromMessageHeader(jobId, _testHeader, _dateTimeProvider),
new Dictionary <string, int>
{
{ "reject-1", 1 },
{ "reject-2", 2 },
}
);
var doc1 = new MongoExpectedFilesDoc(
MongoExtractionMessageHeaderDoc.FromMessageHeader(jobId, _testHeader, _dateTimeProvider),
"TestKey",
expectedFiles,
rejectedKeys);
var doc2 = new MongoExpectedFilesDoc(
MongoExtractionMessageHeaderDoc.FromMessageHeader(jobId, _testHeader, _dateTimeProvider),
"TestKey",
expectedFiles,
rejectedKeys);
Assert.AreEqual(doc1.GetHashCode(), doc2.GetHashCode());
}
protected override void PersistMessageToStoreImpl(ExtractFileCollectionInfoMessage message, IMessageHeader header)
{
if (InCompletedJobCollection(message.ExtractionJobIdentifier))
{
throw new ApplicationException("Received an ExtractFileCollectionInfoMessage for a job that is already completed");
}
MongoExpectedFilesDoc expectedFilesForKey = MongoExpectedFilesDoc.FromMessage(message, header, _dateTimeProvider);
_database
.GetCollection <MongoExpectedFilesDoc>(ExpectedFilesCollectionName(message.ExtractionJobIdentifier))
.InsertOne(expectedFilesForKey);
}
public void TestMongoExpectedFilesDoc_FromMessage()
{
var mockMessage = new Mock <ExtractFileCollectionInfoMessage>();
mockMessage.Object.KeyValue = "TestKey";
Guid jobId = Guid.NewGuid();
mockMessage.Object.ExtractionJobIdentifier = jobId;
var header1 = new MessageHeader();
var header2 = new MessageHeader();
mockMessage.Object.ExtractFileMessagesDispatched = new JsonCompatibleDictionary <MessageHeader, string>
{
{ header1, "AnonFile1.dcm" },
{ header2, "AnonFile2.dcm" },
};
mockMessage.Object.RejectionReasons = new Dictionary <string, int>
{
{ "Reject1", 1 },
{ "Reject2", 2 },
};
MongoExpectedFilesDoc doc = MongoExpectedFilesDoc.FromMessage(mockMessage.Object, _testHeader, _dateTimeProvider);
var expected = new MongoExpectedFilesDoc(
MongoExtractionMessageHeaderDoc.FromMessageHeader(jobId, _testHeader, _dateTimeProvider),
"TestKey",
new HashSet <MongoExpectedFileInfoDoc>
{
new MongoExpectedFileInfoDoc(header1.MessageGuid, "AnonFile1.dcm"),
new MongoExpectedFileInfoDoc(header2.MessageGuid, "AnonFile2.dcm"),
},
MongoRejectedKeyInfoDoc.FromMessage(mockMessage.Object, _testHeader, _dateTimeProvider));
Assert.AreEqual(expected, doc);
}
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);
}
public void TestPersistMessageToStoreImpl_ExtractFileCollectionInfoMessage()
{
Guid jobId = Guid.NewGuid();
var header1 = new MessageHeader();
var header2 = new MessageHeader();
var testExtractFileCollectionInfoMessage = new ExtractFileCollectionInfoMessage
{
ExtractionJobIdentifier = jobId,
ProjectNumber = "1234-5678",
RejectionReasons = new Dictionary <string, int>
{
{ "reject1", 1 },
{ "reject2", 2 },
},
JobSubmittedAt = DateTime.UtcNow,
ExtractionDirectory = "1234-5678/testExtract",
ExtractFileMessagesDispatched = new JsonCompatibleDictionary <MessageHeader, string>
{
{ header1, "file1" },
{ header2, "file2" }
},
KeyValue = "series-1",
};
var header = new MessageHeader
{
MessageGuid = Guid.NewGuid(),
OriginalPublishTimestamp = MessageHeader.UnixTimeNow(),
Parents = new[] { Guid.NewGuid(), },
ProducerExecutableName = "MongoExtractStoreTests",
ProducerProcessID = 1234,
};
var client = new TestMongoClient();
var store = new MongoExtractJobStore(client, ExtractionDatabaseName, _dateTimeProvider);
store.PersistMessageToStore(testExtractFileCollectionInfoMessage, header);
Dictionary <Guid, MongoExpectedFilesDoc> docs = client.ExtractionDatabase.ExpectedFilesCollections[$"expectedFiles_{jobId}"].Documents;
Assert.AreEqual(docs.Count, 1);
MongoExpectedFilesDoc extractJob = docs.Values.ToList()[0];
var expected = new MongoExpectedFilesDoc(
MongoExtractionMessageHeaderDoc.FromMessageHeader(jobId, header, _dateTimeProvider),
"series-1",
new HashSet <MongoExpectedFileInfoDoc>
{
new MongoExpectedFileInfoDoc(header1.MessageGuid, "file1"),
new MongoExpectedFileInfoDoc(header2.MessageGuid, "file2"),
},
new MongoRejectedKeyInfoDoc(
MongoExtractionMessageHeaderDoc.FromMessageHeader(jobId, header, _dateTimeProvider),
new Dictionary <string, int>
{
{ "reject1", 1 },
{ "reject2", 2 },
})
);
Assert.True(extractJob.Equals(expected));
}