public void TestPersistMessageToStore_IsIdentifiableMessage()
{
var testExtractJobStore = new TestExtractJobStore();
var header = new MessageHeader();
// Must have AnonymisedFileName
var message = new ExtractedFileVerificationMessage();
message.OutputFilePath = "";
Assert.Throws <ApplicationException>(() => testExtractJobStore.PersistMessageToStore(message, header));
// Report shouldn't be an empty string or null
message = new ExtractedFileVerificationMessage();
message.OutputFilePath = "anon.dcm";
message.Report = "";
Assert.Throws <ApplicationException>(() => testExtractJobStore.PersistMessageToStore(message, header));
// Report needs to contain content if marked as IsIdentifiable
message = new ExtractedFileVerificationMessage();
message.OutputFilePath = "anon.dcm";
message.IsIdentifiable = true;
message.Report = "[]";
Assert.Throws <ApplicationException>(() => testExtractJobStore.PersistMessageToStore(message, header));
// NOTE(rkm 2020-07-23) The actual report content is verified to be valid the message consumer, so don't need to re-check here
message.Report = "['foo': 'bar']";
testExtractJobStore.PersistMessageToStore(message, header);
// Report can be empty if not marked as IsIdentifiable
message = new ExtractedFileVerificationMessage();
message.OutputFilePath = "anon.dcm";
message.IsIdentifiable = false;
message.Report = "[]";
testExtractJobStore.PersistMessageToStore(message, header);
}
public void Integration_HappyPath(ReportFormat reportFormat)
{
// Test messages:
// - series-1
// - series-1-anon-1.dcm -> valid
using var pf = new PathFixtures($"Integration_HappyPath_{reportFormat}");
var jobId = Guid.NewGuid();
var testExtractionRequestInfoMessage = new ExtractionRequestInfoMessage
{
JobSubmittedAt = _dateTimeProvider.UtcNow(),
ProjectNumber = "testProj1",
ExtractionJobIdentifier = jobId,
ExtractionDirectory = pf.ProjExtractDirRelative,
KeyTag = "SeriesInstanceUID",
KeyValueCount = 1,
};
var testExtractFileCollectionInfoMessage = new ExtractFileCollectionInfoMessage
{
JobSubmittedAt = _dateTimeProvider.UtcNow(),
ProjectNumber = "testProj1",
ExtractionJobIdentifier = jobId,
ExtractionDirectory = pf.ProjExtractDirRelative,
ExtractFileMessagesDispatched = new JsonCompatibleDictionary <MessageHeader, string>
{
{ new MessageHeader(), "series-1-anon-1.dcm" },
},
RejectionReasons = new Dictionary <string, int>
{
{ "rejected - blah", 1 },
},
KeyValue = "series-1",
};
var testIsIdentifiableMessage = new ExtractedFileVerificationMessage
{
JobSubmittedAt = _dateTimeProvider.UtcNow(),
OutputFilePath = "series-1-anon-1.dcm",
ProjectNumber = "testProj1",
ExtractionJobIdentifier = jobId,
ExtractionDirectory = pf.ProjExtractDirRelative,
IsIdentifiable = false,
Report = "[]",
DicomFilePath = "series-1-orig-1.dcm",
};
GlobalOptions globals = new GlobalOptionsFactory().Load();
VerifyReports(
globals,
pf,
reportFormat,
new[]
{
new Tuple <ConsumerOptions, IMessage>(globals.CohortPackagerOptions.ExtractRequestInfoOptions, testExtractionRequestInfoMessage),
new Tuple <ConsumerOptions, IMessage>(globals.CohortPackagerOptions.FileCollectionInfoOptions, testExtractFileCollectionInfoMessage),
new Tuple <ConsumerOptions, IMessage>(globals.CohortPackagerOptions.VerificationStatusOptions, testIsIdentifiableMessage),
}
);
}
public void PersistMessageToStore(
[NotNull] ExtractedFileVerificationMessage message,
[NotNull] IMessageHeader header)
{
if (string.IsNullOrWhiteSpace(message.OutputFilePath))
{
throw new ApplicationException("Received a verification message without the AnonymisedFileName set");
}
if (string.IsNullOrWhiteSpace(message.Report))
{
throw new ApplicationException("Null or empty report data");
}
if (message.IsIdentifiable && message.Report == "[]")
{
throw new ApplicationException("No report data for message marked as identifiable");
}
PersistMessageToStoreImpl(message, header);
}
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 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 Integration_BumpyRoad(ReportFormat reportFormat)
{
// Test messages:
// - series-1
// - series-1-anon-1.dcm -> valid
// - series-1-anon-2.dcm -> rejected
// - series-2
// - series-2-anon-1.dcm -> fails anonymisation
// - series-2-anon-2.dcm -> fails validation
using var pf = new PathFixtures($"Integration_BumpyRoad_{reportFormat}");
var jobId = Guid.NewGuid();
var testExtractionRequestInfoMessage = new ExtractionRequestInfoMessage
{
JobSubmittedAt = _dateTimeProvider.UtcNow(),
ProjectNumber = "testProj1",
ExtractionJobIdentifier = jobId,
ExtractionDirectory = pf.ProjExtractDirRelative,
KeyTag = "SeriesInstanceUID",
KeyValueCount = 2,
};
var testExtractFileCollectionInfoMessage1 = new ExtractFileCollectionInfoMessage
{
JobSubmittedAt = _dateTimeProvider.UtcNow(),
ProjectNumber = "testProj1",
ExtractionJobIdentifier = jobId,
ExtractionDirectory = pf.ProjExtractDirRelative,
ExtractFileMessagesDispatched = new JsonCompatibleDictionary <MessageHeader, string>
{
{ new MessageHeader(), "series-1-anon-1.dcm" },
},
RejectionReasons = new Dictionary <string, int>
{
{ "rejected - blah", 1 },
},
KeyValue = "series-1",
};
var testExtractFileCollectionInfoMessage2 = new ExtractFileCollectionInfoMessage
{
JobSubmittedAt = _dateTimeProvider.UtcNow(),
ProjectNumber = "testProj1",
ExtractionJobIdentifier = jobId,
ExtractionDirectory = pf.ProjExtractDirRelative,
ExtractFileMessagesDispatched = new JsonCompatibleDictionary <MessageHeader, string>
{
{ new MessageHeader(), "series-2-anon-1.dcm" },
{ new MessageHeader(), "series-2-anon-2.dcm" },
},
RejectionReasons = new Dictionary <string, int>(),
KeyValue = "series-2",
};
var testExtractFileStatusMessage = new ExtractedFileStatusMessage
{
JobSubmittedAt = _dateTimeProvider.UtcNow(),
OutputFilePath = "series-2-anon-1.dcm",
ProjectNumber = "testProj1",
ExtractionJobIdentifier = jobId,
ExtractionDirectory = pf.ProjExtractDirRelative,
Status = ExtractedFileStatus.ErrorWontRetry,
StatusMessage = "Couldn't anonymise",
DicomFilePath = "series-2-orig-1.dcm",
};
var testIsIdentifiableMessage1 = new ExtractedFileVerificationMessage
{
JobSubmittedAt = _dateTimeProvider.UtcNow(),
OutputFilePath = "series-1-anon-1.dcm",
ProjectNumber = "testProj1",
ExtractionJobIdentifier = jobId,
ExtractionDirectory = pf.ProjExtractDirRelative,
IsIdentifiable = false,
Report = "[]",
DicomFilePath = "series-1-orig-1.dcm",
};
const string failureReport = @"
[
{
'Parts': [],
'Resource': 'series-2-anon-2.dcm',
'ResourcePrimaryKey': '1.2.3.4',
'ProblemField': 'ScanOptions',
'ProblemValue': 'FOO'
}
]";
var testIsIdentifiableMessage2 = new ExtractedFileVerificationMessage
{
JobSubmittedAt = _dateTimeProvider.UtcNow(),
OutputFilePath = "series-2-anon-2.dcm",
ProjectNumber = "testProj1",
ExtractionJobIdentifier = jobId,
ExtractionDirectory = pf.ProjExtractDirRelative,
IsIdentifiable = true,
Report = failureReport,
DicomFilePath = "series-2-orig-2.dcm",
};
GlobalOptions globals = new GlobalOptionsFactory().Load();
VerifyReports(
globals,
pf,
reportFormat,
new[]
{
new Tuple <ConsumerOptions, IMessage>(globals.CohortPackagerOptions.ExtractRequestInfoOptions, testExtractionRequestInfoMessage),
new Tuple <ConsumerOptions, IMessage>(globals.CohortPackagerOptions.FileCollectionInfoOptions, testExtractFileCollectionInfoMessage1),
new Tuple <ConsumerOptions, IMessage>(globals.CohortPackagerOptions.FileCollectionInfoOptions, testExtractFileCollectionInfoMessage2),
new Tuple <ConsumerOptions, IMessage>(globals.CohortPackagerOptions.NoVerifyStatusOptions, testExtractFileStatusMessage),
new Tuple <ConsumerOptions, IMessage>(globals.CohortPackagerOptions.VerificationStatusOptions, testIsIdentifiableMessage1),
new Tuple <ConsumerOptions, IMessage>(globals.CohortPackagerOptions.VerificationStatusOptions, testIsIdentifiableMessage2),
}
);
}
protected override void PersistMessageToStoreImpl(ExtractedFileVerificationMessage message, IMessageHeader header)
{
}
protected abstract void PersistMessageToStoreImpl(ExtractedFileVerificationMessage message, IMessageHeader header);
