/// <summary>
/// Creates a new instance of the host with the given
/// </summary>
/// <param name="options">Settings for the microservice (location of rabbit, queue names etc)</param>
/// <param name="auditor">Optional override for the value specified in <see cref="GlobalOptions.CohortExtractorOptions"/></param>
/// <param name="fulfiller">Optional override for the value specified in <see cref="GlobalOptions.CohortExtractorOptions"/></param>
public CohortExtractorHost(GlobalOptions options, IAuditExtractions auditor, IExtractionRequestFulfiller fulfiller)
: base(options)
{
_consumerOptions = options.CohortExtractorOptions;
_consumerOptions.Validate();
_auditor = auditor;
_fulfiller = fulfiller;
}
public ExtractionRequestQueueConsumer(
CohortExtractorOptions options,
IExtractionRequestFulfiller fulfiller, IAuditExtractions auditor,
IProjectPathResolver pathResolver, IProducerModel fileMessageProducer,
IProducerModel fileMessageInfoProducer)
{
_options = options;
_fulfiller = fulfiller;
_auditor = auditor;
_resolver = pathResolver;
_fileMessageProducer = fileMessageProducer;
_fileMessageInfoProducer = fileMessageInfoProducer;
}
/// <summary>
/// Connects to RDMP platform databases to retrieve extractable catalogues and initializes the <see cref="IExtractionRequestFulfiller"/> (if none
/// was specified in the constructor override).
/// </summary>
/// <param name="repositoryLocator"></param>
private void InitializeExtractionSources(IRDMPPlatformRepositoryServiceLocator repositoryLocator)
{
// Get all extractable catalogues
ICatalogue[] catalogues = repositoryLocator
.DataExportRepository
.GetAllObjects <ExtractableDataSet>()
.Select(eds => eds.Catalogue)
.ToArray();
if (_auditor == null)
{
_auditor = ObjectFactory.CreateInstance <IAuditExtractions>(_consumerOptions.AuditorType, typeof(IAuditExtractions).Assembly,
repositoryLocator);
}
if (_auditor == null)
{
throw new Exception("No IAuditExtractions set");
}
if (!_consumerOptions.AllCatalogues)
{
catalogues = catalogues.Where(c => _consumerOptions.OnlyCatalogues.Contains(c.ID)).ToArray();
}
if (_fulfiller == null)
{
_fulfiller = ObjectFactory.CreateInstance <IExtractionRequestFulfiller>(_consumerOptions.RequestFulfillerType,
typeof(IExtractionRequestFulfiller).Assembly, new object[] { catalogues });
}
if (_fulfiller == null)
{
throw new Exception("No IExtractionRequestFulfiller set");
}
if (!string.IsNullOrWhiteSpace(_consumerOptions.ModalityRoutingRegex))
{
_fulfiller.ModalityRoutingRegex = new Regex(_consumerOptions.ModalityRoutingRegex);
}
if (!string.IsNullOrWhiteSpace(_consumerOptions.RejectorType))
{
_fulfiller.Rejectors.Add(ObjectFactory.CreateInstance <IRejector>(_consumerOptions.RejectorType, typeof(IRejector).Assembly));
}
if (_consumerOptions.RejectColumnInfos != null)
{
foreach (var id in _consumerOptions.RejectColumnInfos)
{
_fulfiller.Rejectors.Add(new ColumnInfoValuesRejector(repositoryLocator.CatalogueRepository.GetObjectByID <ColumnInfo>(id)));
}
}
if (_consumerOptions.Blacklists != null)
{
foreach (int id in _consumerOptions.Blacklists)
{
var cata = repositoryLocator.CatalogueRepository.GetObjectByID <Catalogue>(id);
var rejector = new BlacklistRejector(cata);
_fulfiller.Rejectors.Add(rejector);
}
}
if (!string.IsNullOrWhiteSpace(_consumerOptions.ProjectPathResolverType))
{
_pathResolver = ObjectFactory.CreateInstance <IProjectPathResolver>(_consumerOptions.ProjectPathResolverType, typeof(IProjectPathResolver).Assembly, repositoryLocator);
}
else
{
_pathResolver = new DefaultProjectPathResolver();
}
}
public IEnumerable <ExtractImageCollection> GetAllMatchingFiles(ExtractionRequestMessage message, IAuditExtractions auditor)
{
var queries = new List <QueryToExecute>();
foreach (var c in GetCataloguesFor(message))
{
var query = GetQueryToExecute(c, message);
if (query != null)
{
queries.Add(query);
auditor.AuditCatalogueUse(message, c.Catalogue);
}
}
Logger.Debug($"Found {queries.Count} Catalogues which support extracting based on '{message.KeyTag}'");
if (queries.Count == 0)
{
throw new Exception($"Couldn't find any compatible Catalogues to run extraction queries against for query {message}");
}
List <IRejector> rejectorsToUse = message.IsNoFilterExtraction ? new List <IRejector>() : Rejectors;
foreach (string valueToLookup in message.ExtractionIdentifiers)
{
var results = new ExtractImageCollection(valueToLookup);
foreach (QueryToExecute query in queries)
{
foreach (QueryToExecuteResult result in query.Execute(valueToLookup, rejectorsToUse))
{
if (!results.ContainsKey(result.SeriesTagValue))
{
results.Add(result.SeriesTagValue, new HashSet <QueryToExecuteResult>());
}
results[result.SeriesTagValue].Add(result);
}
}
yield return(results);
}
}
public IEnumerable <ExtractImageCollection> GetAllMatchingFiles(ExtractionRequestMessage message, IAuditExtractions auditor)
{
Logger.Debug("Found " + message.KeyTag);
foreach (string valueToLookup in message.ExtractionIdentifiers)
{
var results = new ExtractImageCollection(valueToLookup);
string filePathValue = valueToLookup; // "img001.dcm";
string studyTagValue = "2";
string seriesTagValue = "3";
string instanceTagValue = "4";
bool rejection = false;
string rejectionReason = "";
var result = new QueryToExecuteResult(filePathValue, studyTagValue, seriesTagValue, instanceTagValue, rejection, rejectionReason);
if (!results.ContainsKey(result.SeriesTagValue))
{
results.Add(result.SeriesTagValue, new HashSet <QueryToExecuteResult>());
}
results[result.SeriesTagValue].Add(result);
yield return(results);
}
}
