/// <summary>
/// Writes current data to a mzid file
/// </summary>
/// <param name="xml">
/// A <see cref="System.String"/> with the output file name
/// </param>
public void Save(string xml)
{
Data.creationDate = DateTime.UtcNow;
// CommonOntology
Data.cvList = ListOntology.ToArray();
// AnalysisSoftwareList
Data.AnalysisSoftwareList = ListSW.ToArray();
// Provider
Data.Provider = Provider;
// AuditCollection
Data.AuditCollection = new FuGECollectionAuditCollectionType();
Data.AuditCollection.Person = ListPeople.ToArray();
Data.AuditCollection.Organization = ListOrganizations.ToArray();
// SequenceCollection
SequenceCollectionType seq = new SequenceCollectionType();
seq.DBSequence = ListProteins.ToArray();
seq.Peptide = ListPeptides.ToArray();
Data.SequenceCollection = seq;
// Serialization
XmlSerializer serializer = new XmlSerializer(typeof(PSIPIMainmzIdentMLType));
TextWriter writer = new StreamWriter(xml);
serializer.Serialize(writer, Data);
writer.Close();
System.GC.Collect();
}
/// <summary>
/// Reads data from a mzid file
/// </summary>
/// <param name="xml">
/// A <see cref="System.String"/> with the input file name
/// </param>
public void Load(string xml)
{
Default();
// Deserialization
XmlSerializer serializer = new XmlSerializer(typeof(MzIdentMLType));
TextReader reader = new StreamReader(xml);
Data = (MzIdentMLType)serializer.Deserialize(reader);
reader.Close();
//Data = MzIdentMLType.LoadFromFile( xml );
// Parse data
if (Data.AnalysisSoftwareList != null)
{
ListSW = new List <AnalysisSoftwareType>(Data.AnalysisSoftwareList);
}
if (Data.AuditCollection != null)
{
ListOrganizations.Clear();
ListPeople.Clear();
foreach (IdentifiableType contact in Data.AuditCollection)
{
if (contact is OrganizationType)
{
ListOrganizations.Add(contact as OrganizationType);
}
else if (contact is PersonType)
{
ListPeople.Add(contact as PersonType);
}
}
}
if (Data.SequenceCollection == null || Data.SequenceCollection.DBSequence == null ||
Data.SequenceCollection.Peptide == null || Data.SequenceCollection.PeptideEvidence == null)
{
throw new ApplicationException("mzIdentML file without identification sequences");
}
ListProteins = new List <DBSequenceType>(Data.SequenceCollection.DBSequence);
ListPeptides = new List <PeptideType>(Data.SequenceCollection.Peptide);
ListEvidences = new List <PeptideEvidenceType>(Data.SequenceCollection.PeptideEvidence);
System.GC.Collect();
}
public Task <IEnumerable <Organization> > Execute(ListOrganizations query,
CancellationToken cancellationToken = new CancellationToken())
{
if (query == null)
{
throw new ArgumentNullException("query");
}
if (string.IsNullOrWhiteSpace(query.UserId))
{
throw new AggregateException("UserId must be specfiied");
}
CloudTable cloudTable = _tableProvider.GetTable(_settings.UserOrganizationIndexTableName);
TableQuery <UserOrganizationIndexEntity> indexQuery = new TableQuery <UserOrganizationIndexEntity>()
.Where(TableQuery.GenerateFilterCondition("PartitionKey", QueryComparisons.Equal, query.UserId));
return(cloudTable.ExecuteQueryAsync(indexQuery, x => (Organization) new OrganizationResult(x.OrganizationId, x.OrganizationName),
cancellationToken));
}
