/// <summary>
/// Processing Test ID 001, 002, and 003
/// Register Items with Repository
/// </summary>
/// <returns></returns>
public static async Task RegisterItems(IVersionable item)
{
// First find all the items that should be registered.
// The dirty item finder can collect new and changed items in a model
var dirtyItemGatherer = new DirtyItemGatherer();
item.Accept(dirtyItemGatherer);
// Get an API client, windows or username
var api = GetRepositoryApiWindows();
// start a transaction
var transaction = await api.CreateTransactionAsync();
// Add all of the items to register to a transaction
var addItemsRequest = new RepositoryTransactionAddItemsRequest();
foreach (var itemToRegister in dirtyItemGatherer.DirtyItems)
{
addItemsRequest.Items.Add(VersionableToRepositoryItem(itemToRegister));
}
// commit the transaction, the Repository will handle the versioning
var options = new RepositoryTransactionCommitOptions()
{
TransactionId = transaction.TransactionId,
TransactionType = RepositoryTransactionType.CommitAsLatestWithLatestChildrenAndPropagateVersions
};
var results = await api.CommitTransactionAsync(options);
}
public void RewriteCCS()
{
MultilingualString.CurrentCulture = "en-GB";
VersionableBase.DefaultAgencyId = "example.org";
var client = RepositoryIntro.GetClient();
var instance = client.GetItem(new Guid("b9ee3aa5-5bc5-43ed-a24e-f560abb30801"), "example.org", 2)
as DdiInstance;
//DDIWorkflowDeserializer deserializer = new DDIWorkflowDeserializer();
//var instance = deserializer.LoadDdiFile(@"D:\Downloads\filesforMinneapolis\filesforMinneapolis\bcs08v08.xml");
GraphPopulator populator = new GraphPopulator(client);
populator.ChildProcessing = ChildReferenceProcessing.Populate;
instance.Accept(populator);
var resourcePackage = instance.ResourcePackages[0];
var instrument = instance.ResourcePackages[0].DataCollections[0].Instruments[0];
//var topLevelSequence = client.GetLatestItem(new Guid("ceaa9acf-2b2f-4c41-b298-b9f419412586"), "cls")
// as CustomSequenceActivity;
var topLevelSequence = instrument.Sequence;
var moduleSequences = topLevelSequence.Activities;
foreach (CustomSequenceActivity module in moduleSequences.OfType <CustomSequenceActivity>())
{
DirtyItemGatherer gatherer = new DirtyItemGatherer(true);
module.Accept(gatherer);
var allChildren = gatherer.DirtyItems;
ControlConstructScheme ccs = new ControlConstructScheme();
ccs.ItemName.Copy(module.ItemName);
foreach (var child in allChildren.OfType <ActivityBase>())
{
ccs.ControlConstructs.Add(child);
}
//client.RegisterItem(ccs, new CommitOptions());
resourcePackage.ControlConstructSchemes.Add(ccs);
}
DDIWorkflowSerializer serializer = new DDIWorkflowSerializer();
serializer.UseConciseBoundedDescription = false;
var doc = serializer.Serialize(instance);
doc.Save(@"d:\ColecticaOutput\bcsv8.xml");
}
public void RewriteCCS()
{
MultilingualString.CurrentCulture = "en-GB";
VersionableBase.DefaultAgencyId = "example.org";
var client = RepositoryIntro.GetClient();
var instance = client.GetItem(new Guid("b9ee3aa5-5bc5-43ed-a24e-f560abb30801"), "example.org", 2)
as DdiInstance;
//DDIWorkflowDeserializer deserializer = new DDIWorkflowDeserializer();
//var instance = deserializer.LoadDdiFile(@"D:\Downloads\filesforMinneapolis\filesforMinneapolis\bcs08v08.xml");
GraphPopulator populator = new GraphPopulator(client);
populator.ChildProcessing = ChildReferenceProcessing.Populate;
instance.Accept(populator);
var resourcePackage = instance.ResourcePackages[0];
var instrument = instance.ResourcePackages[0].DataCollections[0].Instruments[0];
//var topLevelSequence = client.GetLatestItem(new Guid("ceaa9acf-2b2f-4c41-b298-b9f419412586"), "cls")
// as CustomSequenceActivity;
var topLevelSequence = instrument.Sequence;
var moduleSequences = topLevelSequence.Activities;
foreach (CustomSequenceActivity module in moduleSequences.OfType<CustomSequenceActivity>())
{
DirtyItemGatherer gatherer = new DirtyItemGatherer(true);
module.Accept(gatherer);
var allChildren = gatherer.DirtyItems;
ControlConstructScheme ccs = new ControlConstructScheme();
ccs.ItemName.Copy(module.ItemName);
foreach (var child in allChildren.OfType<ActivityBase>())
{
ccs.ControlConstructs.Add(child);
}
//client.RegisterItem(ccs, new CommitOptions());
resourcePackage.ControlConstructSchemes.Add(ccs);
}
DDIWorkflowSerializer serializer = new DDIWorkflowSerializer();
serializer.UseConciseBoundedDescription = false;
var doc = serializer.Serialize(instance);
doc.Save(@"d:\ColecticaOutput\bcsv8.xml");
}
public void IngestIntoRepository(Group group)
{
// Register every DDI item in the repository.
var client = new LocalRepositoryClient();
var options = new CommitOptions();
var gatherer = new DirtyItemGatherer(true);
group.Accept(gatherer);
options.NamedOptions.Add("RegisterOrReplace");
client.RegisterItems(gatherer.DirtyItems, options);
}
public void GetItemChangeChildAndReregister()
{
VersionableBase.DefaultAgencyId = "int.example";
var client = GetClient();
// Get a ConceptScheme from the repository,
// and populate the member concepts.
// Note that you probably have to change the UUID here
// to represent one that is in your repository.
var scheme = client.GetItem(
new Guid("0cc13be5-3c89-4d1a-927f-ac7634d0c05a"),
"int.example", 2,
ChildReferenceProcessing.Populate) as ConceptScheme;
if (scheme == null || scheme.Concepts.Count < 3)
{
Console.WriteLine("No scheme, or not enough items in the scheme.");
return;
}
// Grab the second concept and add a description to it.
var concept = scheme.Concepts[2];
concept.Description.Current = "This is the fourth concept";
// When we change a property on the Concept, the concept's
// IsDirty property is automatically set to true, indicating
// that it has unsaved changes.
Console.WriteLine("IsDirty: ", concept.IsDirty);
// The DirtyItemGatherer will walk a set of objects and create
// a list of all objects that are dirty.
DirtyItemGatherer gatherer = new DirtyItemGatherer(
gatherEvenIfNotDirty: false,
markParentsDirty: true);
scheme.Accept(gatherer);
var options = new CommitOptions();
// For every changed item, increase the version and
// register the new version with the repository.
foreach (var item in gatherer.DirtyItems)
{
item.Version++;
client.RegisterItem(item, options);
}
}
public void IncrementDityItemAndParents(IVersionable item)
{
Dig(item);
var dirtyGthr = new DirtyItemGatherer();
item.Accept(dirtyGthr);
foreach (var dirtyItem in dirtyGthr.DirtyItems)
{
Increment(dirtyItem);
var allParents = GetAllParents(dirtyItem);
foreach (var parent in allParents)
{
Increment(parent);
}
}
}
/// <summary>
/// Load the sample DDI 3.1 file and register all its items with the Repository.
/// </summary>
public void RegisterFile()
{
// Load the sample data file.
DDIWorkflowDeserializer deserializer = new DDIWorkflowDeserializer();
string directory = Path.GetDirectoryName(Assembly.GetExecutingAssembly().Location);
var instance = deserializer.LoadDdiFile(Path.Combine(directory, "sample.xml"));
// Gather all items instance in the DdiInstance we just loaded.
// We need to do this to get the items in a flat list.
DirtyItemGatherer gatherer = new DirtyItemGatherer(gatherEvenIfNotDirty: true);
instance.Accept(gatherer);
// Grab a client to communicate with the Repository.
var client = GetClient();
// Register each item with the Repository.
foreach (var item in gatherer.DirtyItems)
{
client.RegisterItem(item, new CommitOptions());
}
}
/// <summary>
/// Load the sample DDI 3.1 file and register all its items with the Repository.
/// </summary>
public void RegisterFile()
{
// Load the sample data file.
DDIWorkflowDeserializer deserializer = new DDIWorkflowDeserializer();
string directory = Path.GetDirectoryName(Assembly.GetExecutingAssembly().Location);
var instance = deserializer.LoadDdiFile(Path.Combine(directory, "sample.xml"));
// Gather all items instance in the DdiInstance we just loaded.
// We need to do this to get the items in a flat list.
DirtyItemGatherer gatherer = new DirtyItemGatherer(gatherEvenIfNotDirty:true);
instance.Accept(gatherer);
// Grab a client to communicate with the Repository.
var client = GetClient();
// Register each item with the Repository.
foreach (var item in gatherer.DirtyItems)
{
client.RegisterItem(item, new CommitOptions());
}
}
public void GetItemChangeChildAndReregister()
{
VersionableBase.DefaultAgencyId = "int.example";
var client = GetClient();
// Get a ConceptScheme from the repository,
// and populate the member concepts.
// Note that you probably have to change the UUID here
// to represent one that is in your repository.
var scheme = client.GetItem(
new Guid("0cc13be5-3c89-4d1a-927f-ac7634d0c05a"),
"int.example", 2,
ChildReferenceProcessing.Populate) as ConceptScheme;
if (scheme == null || scheme.Concepts.Count < 3)
{
Console.WriteLine("No scheme, or not enough items in the scheme.");
return;
}
// Grab the second concept and add a description to it.
var concept = scheme.Concepts[2];
concept.Description.Current = "This is the fourth concept";
// When we change a property on the Concept, the concept's
// IsDirty property is automatically set to true, indicating
// that it has unsaved changes.
Console.WriteLine("IsDirty: ", concept.IsDirty);
// The DirtyItemGatherer will walk a set of objects and create
// a list of all objects that are dirty.
DirtyItemGatherer gatherer = new DirtyItemGatherer(
gatherEvenIfNotDirty: false,
markParentsDirty: true);
scheme.Accept(gatherer);
var options = new CommitOptions();
// For every changed item, increase the version and
// register the new version with the repository.
foreach (var item in gatherer.DirtyItems)
{
item.Version++;
client.RegisterItem(item, options);
}
}
public static string CreateOrUpdatePhysicalInstanceForFile <TImporter>(Guid fileId, string filePath, string agencyId, PhysicalInstance existingPhysicalInstance)
where TImporter : IDataImporter, new()
{
var logger = LogManager.GetLogger("Curation");
logger.Debug("File import: " + fileId);
IDataImporter importer = new TImporter();
var client = RepositoryHelper.GetClient();
PhysicalInstance physicalInstance = existingPhysicalInstance;
// For PhysicalInstances that do not exist yet, create from scratch.
if (physicalInstance == null)
{
// Extract metadata.
ResourcePackage rp = importer.Import(filePath, agencyId);
logger.Debug("Imported metadata from data file.");
if (rp.PhysicalInstances.Count == 0)
{
logger.Debug("No dataset could be extracted from SPSS");
return(string.Empty);
}
physicalInstance = rp.PhysicalInstances[0];
physicalInstance.Identifier = fileId;
}
else
{
// If there is an existing PhysicalInstance, update it from the data file.
var updateCommand = new UpdatePhysicalInstanceFromFile();
updateCommand.DataImporters = new List <IDataImporter>();
updateCommand.DataImporters.Add(new SpssImporter());
updateCommand.DataImporters.Add(new StataImporter());
updateCommand.DataImporters.Add(new SasImporter());
updateCommand.DataImporters.Add(new RDataImporter());
updateCommand.DataImporters.Add(new CsvImporter());
var context = new Algenta.Colectica.ViewModel.Commands.VersionableCommandContext();
// Update the PhysicalInstance from the data file.
var repoNode = new RepositoryNode(client, null);
var repoItemNode = new RepositoryItemNode(existingPhysicalInstance.GetMetadata(), repoNode, client);
context.Node = repoItemNode;
context.Item = physicalInstance;
try
{
updateCommand.Execute(context);
physicalInstance.Version++;
foreach (var item in updateCommand.Result.ModifiedItems)
{
item.Version++;
}
}
catch (Exception ex)
{
logger.Error("Problem updating PhysicalInstance.", ex);
return("Problem updating PhysicalInstance. " + ex.Message);
}
}
// Calculate summary statistics, for both new and updated files.
try
{
logger.Debug("Calculating summary statistics");
var calculator = new PhysicalInstanceSummaryStatisticComputer();
SummaryStatisticsOptions options = new SummaryStatisticsOptions()
{
CalculateQuartiles = true
};
var stats = calculator.ComputeStatistics(importer, filePath, physicalInstance,
physicalInstance.FileStructure.CaseQuantity, options, (percent, message) => { });
logger.Debug("Done calculating summary statistics");
if (stats != null)
{
physicalInstance.Statistics.Clear();
foreach (VariableStatistic stat in stats)
{
physicalInstance.Statistics.Add(stat);
}
}
}
catch (Exception ex)
{
logger.Error("Problem calculating summary statistics.", ex);
return("Problem calculating summary statistics. " + ex.Message);
}
// Register all items that were created with the repository.
DirtyItemGatherer visitor = new DirtyItemGatherer(false, true);
physicalInstance.Accept(visitor);
logger.Debug("Setting agency IDs");
// The static default agency id is not thread safe, so set it explicitly here
foreach (var item in visitor.DirtyItems)
{
item.AgencyId = agencyId;
}
logger.Debug("Done setting agency IDs");
logger.Debug("Registering items with the repository");
var repoOptions = new Algenta.Colectica.Model.Repository.CommitOptions();
repoOptions.NamedOptions.Add("RegisterOrReplace");
client.RegisterItems(visitor.DirtyItems, repoOptions);
logger.Debug("Done registering items with the repository");
logger.Debug("Done with CreatePhysicalInstanceForFile");
return(string.Empty);
}
public static void UpdateRepositoryItemFromModel(CatalogRecord record)
{
var client = RepositoryHelper.GetClient();
var logger = LogManager.GetLogger("Curation");
long version = 0;
try
{
version = client.GetLatestVersionNumber(record.Id, record.Organization.AgencyID);
}
catch
{
// StudyUnit does not exist yet. That is okay, because we are making one from
// scratch anyway.
logger.Debug("StudyUnit does not yet exist in the repository");
}
var study = new StudyUnit()
{
Identifier = record.Id,
AgencyId = record.Organization.AgencyID,
Version = version + 1
};
var studyMapper = new CatalogRecordToStudyUnitMapper();
studyMapper.Map(record, study);
// Add each file as either a PhysicalInstance or an OtherMaterial.
foreach (var file in record.Files.Where(x => x.Status != FileStatus.Removed))
{
if (file.IsStatisticalDataFile())
{
try
{
var pi = client.GetLatestItem(file.Id, record.Organization.AgencyID)
as PhysicalInstance;
if (pi != null)
{
var mapper = new ManagedFileToPhysicalInstanceMapper();
mapper.Map(file, pi);
pi.Version++;
// Make sure the file is added to the StudyUnit.
if (!study.PhysicalInstances.Any(x => x.Identifier == pi.Identifier))
{
study.PhysicalInstances.Add(pi);
}
}
}
catch (Exception ex)
{
logger.Warn("Could not attach PhysicalInstance to StudyUnit", ex);
}
}
else
{
var material = study.OtherMaterials.Where(x => x.DublinCoreMetadata.Title.Current == file.PublicName)
.FirstOrDefault();
// If this material is not already on the study, add it.
if (material == null)
{
material = new OtherMaterial();
study.OtherMaterials.Add(material);
}
// Perform the mapping.
var mapper = new ManagedFileToOtherMaterialMapper();
mapper.Map(file, material);
material.Version++;
}
}
// Register the updated item with the repository.
var commitOptions = new CommitOptions();
commitOptions.NamedOptions.Add("RegisterOrReplace");
var dirty = new DirtyItemGatherer();
study.Accept(dirty);
foreach (var dirtyItem in dirty.DirtyItems)
{
client.RegisterItem(dirtyItem, commitOptions);
}
}
