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); }