public void Init()
{
_settingsContext = TestInitializer.ServiceProvider.GetService <SettingsContext>();
_settingsContextMysql = TestInitializer.ServiceProviderMysql.GetService <SettingsContext>();
_iQtoolsDb = TestInitializer.IQtoolsDbProtocol;
_kenyaEmrDb = TestInitializer.KenyaEmrDbProtocol;
}
public int Find(DbProtocol protocol, DbExtract extract)
{
Log.Debug($"Finding {nameof(PsmartSource)}...");
_mapper = GetMapper(extract.Emr);
int extractCount = 0;
var connection = GetConnection(protocol);
using (connection)
{
if (connection.State != ConnectionState.Open)
{
connection.Open();
}
using (var command = connection.CreateCommand())
{
//Extract SQL
command.CommandText = extract.GetCountSQL();
int.TryParse(command.ExecuteScalar().ToString(), out extractCount);
}
}
Log.Debug($"Finding {nameof(PsmartSource)} Completed");
return(extractCount);
}
public void Init()
{
var extractIds = TestInitializer.Iqtools.Extracts.Where(x => x.DocketId.IsSameAs("NDWH")).Select(x => x.Id)
.ToList();
var cleaner = TestInitializer.ServiceProvider.GetService <IClearDwhExtracts>();
cleaner.Clear(extractIds);
var extractIdsMySql = TestInitializer.KenyaEmr.Extracts.Where(x => x.DocketId.IsSameAs("NDWH")).Select(x => x.Id)
.ToList();
var cleanerMySql = TestInitializer.ServiceProviderMysql.GetService <IClearDwhExtracts>();
cleanerMySql.Clear(extractIdsMySql);
_extractsContext = TestInitializer.ServiceProvider.GetService <ExtractsContext>();
_extractsContextMySql = TestInitializer.ServiceProviderMysql.GetService <ExtractsContext>();
_iQtoolsDb = TestInitializer.Iqtools.DatabaseProtocols.First(x => x.DatabaseName.ToLower().Contains("iqtools".ToLower()));
_iQtoolsDb.Host = ".\\Koske14";
_iQtoolsDb.Username = "******";
_iQtoolsDb.Password = "******";
_kenyaEmrDb = TestInitializer.KenyaEmr.DatabaseProtocols.First();
_kenyaEmrDb.Host = "127.0.0.1";
_kenyaEmrDb.Username = "******";
_kenyaEmrDb.Password = "******";
_kenyaEmrDb.DatabaseName = "openmrs";
}
public void Init()
{
TestInitializer.ClearDb();
TestInitializer.SeedData(TestData.GenerateEmrSystems(TestInitializer.EmrConnectionString));
_protocol = TestInitializer.Protocol;
_extracts = TestInitializer.Extracts.Where(x => x.DocketId.IsSameAs("NDWH")).ToList();
}
public IDbConnection GetConnection(DbProtocol databaseProtocol)
{
var connectionString = databaseProtocol.GetConnectionString();
Log.Debug(new string('+', 40));
Log.Debug(connectionString);
Log.Debug(new string('+', 40));
if (databaseProtocol.DatabaseType == DatabaseType.Sqlite)
{
return(new SqliteConnection(connectionString));
}
if (databaseProtocol.DatabaseType == DatabaseType.MicrosoftSQL)
{
return(new System.Data.SqlClient.SqlConnection(connectionString));
}
if (databaseProtocol.DatabaseType == DatabaseType.MySQL)
{
return(new MySqlConnection(connectionString));
}
return(null);
}
public void SetUp()
{
_extractsContext = TestInitializer.ServiceProvider.GetService <ExtractsContext>();
_extractsContextMySql = TestInitializer.ServiceProviderMysql.GetService <ExtractsContext>();
_iQtoolsDb = TestInitializer.IQtoolsDbProtocol;
_kenyaEmrDb = TestInitializer.KenyaEmrDbProtocol;
}
public void Init()
{
var extractId = TestInitializer.Iqtools.Extracts.First(x => x.Name.IsSameAs(nameof(MasterPatientIndex))).Id;
var cleaner = TestInitializer.ServiceProvider.GetService <ICleanCbsExtracts>();
cleaner.Clean(extractId);
var extractIdMySql = TestInitializer.KenyaEmr.Extracts.First(x => x.Name.IsSameAs(nameof(MasterPatientIndex))).Id;
var cleanerMySql = TestInitializer.ServiceProviderMysql.GetService <ICleanCbsExtracts>();
cleanerMySql.Clean(extractIdMySql);
_extractsContext = TestInitializer.ServiceProvider.GetService <ExtractsContext>();
_extractsContextMySql = TestInitializer.ServiceProviderMysql.GetService <ExtractsContext>();
_iQtoolsDb = TestInitializer.Iqtools.DatabaseProtocols.First(x => x.DatabaseName.ToLower().Contains("iqtools".ToLower()));
_iQtoolsDb.Host = ".\\Koske14";
_iQtoolsDb.Username = "******";
_iQtoolsDb.Password = "******";
_kenyaEmrDb = TestInitializer.KenyaEmr.DatabaseProtocols.First();
_kenyaEmrDb.Host = "127.0.0.1";
_kenyaEmrDb.Username = "******";
_kenyaEmrDb.Password = "******";
_kenyaEmrDb.DatabaseName = "openmrs";
}
public virtual Task <IDataReader> ExecuteReader(DbProtocol protocol, DbExtract extract)
{
var sourceConnection = GetConnection(protocol);
if (null == sourceConnection)
{
throw new Exception("Data connection not initialized");
}
if (null == extract)
{
throw new Exception("Extract settings not configured");
}
if (sourceConnection.State != ConnectionState.Open)
{
sourceConnection.Open();
}
Connection = sourceConnection;
var commandDefinition = new CommandDefinition(extract.ExtractSql, null, null, 0);
if (sourceConnection is SqliteConnection)
{
return(Task.FromResult <IDataReader>(sourceConnection.ExecuteReader(commandDefinition)));
}
return(sourceConnection.ExecuteReaderAsync(commandDefinition, CommandBehavior.CloseConnection));
}
public void Init()
{
var extractId = TestInitializer.Iqtools.Extracts.First(x => x.Name.IsSameAs(nameof(PatientVisitExtract))).Id;
var cleaner = TestInitializer.ServiceProvider.GetService <ICleanCbsExtracts>();
cleaner.Clean(extractId);
var extractIdMySql = TestInitializer.KenyaEmr.Extracts.First(x => x.Name.IsSameAs(nameof(PatientVisitExtract))).Id;
var cleanerMySql = TestInitializer.ServiceProviderMysql.GetService <ICleanCbsExtracts>();
cleanerMySql.Clean(extractIdMySql);
_extractsContext = TestInitializer.ServiceProvider.GetService <ExtractsContext>();
_extractsContextMySql = TestInitializer.ServiceProviderMysql.GetService <ExtractsContext>();
var tempMpis = Builder <TempPatientVisitExtract> .CreateListOfSize(2).All().With(x => x.CheckError = false).Build().ToList();
_extractsContext.TempPatientVisitExtracts.AddRange(tempMpis);
_extractsContext.SaveChanges();
_extractsContextMySql.TempPatientVisitExtracts.AddRange(tempMpis);
_extractsContextMySql.SaveChanges();
_iQtoolsDb = TestInitializer.Iqtools.DatabaseProtocols.First(x => x.DatabaseName.ToLower().Contains("iqtools".ToLower()));
_iQtoolsDb.Host = ".";
_iQtoolsDb.Username = "******";
_iQtoolsDb.Password = "******";
_kenyaEmrDb = TestInitializer.KenyaEmr.DatabaseProtocols.First();
_kenyaEmrDb.Host = "127.0.0.1";
_kenyaEmrDb.Username = "******";
_kenyaEmrDb.Password = "******";
_kenyaEmrDb.DatabaseName = "openmrs";
}
public void Init()
{
TestInitializer.ClearDb();
TestInitializer.SeedData(TestData.GenerateEmrSystems(TestInitializer.EmrConnectionString));
_protocol = TestInitializer.Protocol;
_extracts = TestInitializer.Extracts.Where(x => Extentions.IsSameAs(x.DocketId, "HTS")).ToList();
_extractsContext = TestInitializer.ServiceProvider.GetService <ExtractsContext>();
}
public void SetUp()
{
_dbManager = new DbManager();
_dbProtocol = new DbProtocol();
_dbProtocol.Database = "iqcare";
_dbProtocol.Password = "******";
_dbProtocol.User = "******";
_dbProtocol.Server = @"192.168.1.10\sqlexpress";
}
public async Task <int> Extract(DbExtract extract, DbProtocol dbProtocol)
{
int batch = 500;
var list = new List <TempPatientAdverseEventExtract>();
int count = 0;
int loaded = 0;
using (var rdr = await _reader.ExecuteReader(dbProtocol, extract))
{
while (rdr.Read())
{
count++;
// AutoMapper profiles
var extractRecord = Mapper.Map <IDataRecord, TempPatientAdverseEventExtract>(rdr);
extractRecord.Id = LiveGuid.NewGuid();
if (extractRecord.HasData())
{
loaded++;
list.Add(extractRecord);
}
if (count == batch)
{
_extractRepository.BatchInsert(list);
count = 0;
DomainEvents.Dispatch(
new ExtractActivityNotification(extract.Id, new DwhProgress(
nameof(PatientAdverseEventExtract),
nameof(ExtractStatus.Finding),
loaded, 0, 0, 0, 0)));
list = new List <TempPatientAdverseEventExtract>();
}
}
if (count > 0)
{
// save remaining list;
_extractRepository.BatchInsert(list);
}
_extractRepository.CloseConnection();
}
// TODO: Notify Completed;
DomainEvents.Dispatch(
new ExtractActivityNotification(extract.Id, new DwhProgress(
nameof(PatientAdverseEventExtract),
nameof(ExtractStatus.Found),
loaded, 0, 0, 0, 0)));
return(loaded);
}
public Task <int> Extract(DbExtract extract, DbProtocol dbProtocol)
{
var mapper = dbProtocol.SupportsDifferential ? ExtractDiffMapper.Instance : ExtractMapper.Instance;
int batch = 500;
var list = new List <TempCwcVisitExtract>();
int count = 0;
int loaded = 0;
using (var rdr = _reader.ExecuteReaderSync(dbProtocol, extract))
{
while (rdr.Read())
{
count++;
loaded++;
// AutoMapper profiles
var extractRecord = mapper.Map <IDataRecord, TempCwcVisitExtract>(rdr);
extractRecord.Id = LiveGuid.NewGuid();
list.Add(extractRecord);
if (count == batch)
{
_extractRepository.BatchInsert(list);
count = 0;
DomainEvents.Dispatch(
new MnchExtractActivityNotification(extract.Id, new DwhProgress(
nameof(CwcVisitExtract),
nameof(ExtractStatus.Finding),
loaded, 0, 0, 0, 0)));
list = new List <TempCwcVisitExtract>();
}
}
if (count > 0)
{
// save remaining list;
_extractRepository.BatchInsert(list);
}
_extractRepository.CloseConnection();
}
// TODO: Notify Completed;
DomainEvents.Dispatch(
new MnchExtractActivityNotification(extract.Id, new DwhProgress(
nameof(CwcVisitExtract),
nameof(ExtractStatus.Found),
loaded, 0, 0, 0, 0)));
return(Task.FromResult(loaded));
}
private void InitExtractor()
{
_protocol = TestInitializer.Protocol;
_extracts = TestInitializer.Extracts.Where(x => Extentions.IsSameAs(x.DocketId, "NDWH")).ToList();
_extractsContext = TestInitializer.ServiceProvider.GetService <ExtractsContext>();
var patientExtract = _extracts.First(x => x.Name.IsSameAs(nameof(PatientExtract)));
var patientLoader = TestInitializer.ServiceProvider.GetService <IPatientLoader>();
var patientSourceExtractor = TestInitializer.ServiceProvider.GetService <IPatientSourceExtractor>();
var tempCount = patientSourceExtractor.Extract(patientExtract, _protocol).Result;
var patientCount = patientLoader.Load(patientExtract.Id, tempCount, false).Result;
}
public void SetUp()
{
_mssql = new DbProtocol(DatabaseType.MicrosoftSQL, @".\koske14", "sa", "maun", "IQTools_KeHMIS");
_extractA = new DbExtract {
ExtractSql = @"select [Id],[shr],[date_created],[status],[status_date],[uuid] FROM psmart_store", Emr = "IQCare"
};
_mysql = new DbProtocol(DatabaseType.MySQL, @"localhost", "root", "test", "openmrs");
_extractB = new DbExtract {
ExtractSql = @"select id,shr,date_created,status,status_date,uuid FROM psmart_store", Emr = "KenyaEMR"
};
_psmartSourceReader = new PsmartSourceReader();
}
public IEnumerable <PsmartSource> Read(DbProtocol protocol, DbExtract extract)
{
_mapper = GetMapper(extract.Emr);
IList <PsmartSource> extracts = new List <PsmartSource>();
var connection = GetConnection(protocol);
using (connection)
{
if (connection.State != ConnectionState.Open)
{
connection.Open();
}
using (var command = connection.CreateCommand())
{
//Extract SQL
command.CommandText = extract.ExtractSql;
extracts = _mapper.Map <IDataReader, IList <PsmartSource> >(command.ExecuteReader());
}
}
if (extracts.Count > 0)
{
using (connection = GetConnection(protocol))
{
if (connection.State != ConnectionState.Open)
{
connection.Open();
}
using (var updateCommand = connection.CreateCommand())
{
StringBuilder stringBuilder = new StringBuilder();
for (int i = 0; i < extracts.Count; i++)
{
if (i == extracts.Count - 1)
{
stringBuilder.Append($"'{extracts[i].Uuid}'");
}
else
{
stringBuilder.Append($"'{extracts[i].Uuid}',");
}
}
updateCommand.CommandText = $"update psmart_store set Status = 'Collected', Status_date = '{DateTime.Now.Date:yyyy-MM-dd HH:mm:ss}' where UUID in ({stringBuilder.ToString()})";
updateCommand.ExecuteNonQuery();
}
}
}
return(extracts);
}
public string BuildConncetion(DbProtocol dbProtocol)
{
var sb = new SqlConnectionStringBuilder();
sb.DataSource = dbProtocol.Server;
sb.UserID = dbProtocol.User;
sb.Password = dbProtocol.Password;
sb.InitialCatalog = dbProtocol.Database;
sb.MultipleActiveResultSets = true;
sb.Pooling = true;
sb.PersistSecurityInfo = true;
return(sb.ConnectionString);
}
public void Init()
{
TestInitializer.ClearDb();
TestInitializer.SeedData(TestData.GenerateEmrSystems(TestInitializer.EmrConnectionString));
_protocol = TestInitializer.Protocol;
_extracts = TestInitializer.Extracts.Where(x => x.DocketId.IsSameAs("MNCH")).ToList();
_extractsContext = TestInitializer.ServiceProvider.GetService <ExtractsContext>();
var patientExtract = _extracts.First(x => x.Name.IsSameAs(nameof(PatientMnchExtract)));
var patientLoader = TestInitializer.ServiceProvider.GetService <IPatientMnchLoader>();
var patientSourceExtractor = TestInitializer.ServiceProvider.GetService <IPatientMnchSourceExtractor>();
var tempCount = patientSourceExtractor.Extract(patientExtract, _protocol).Result;
var patientCount = patientLoader.Load(patientExtract.Id, tempCount, false).Result;
}
public void Init()
{
TestInitializer.ClearDb();
TestInitializer.SeedData(TestData.GenerateEmrSystems(TestInitializer.EmrConnectionString));
_protocol = TestInitializer.Protocol;
_extracts = TestInitializer.Extracts.Where(x => x.DocketId.IsSameAs("HTS")).ToList();
_extractsContext = TestInitializer.ServiceProvider.GetService <ExtractsContext>();
var clientExtract = _extracts.First(x => x.Name.IsSameAs("HtsClient"));
var clientLoader = TestInitializer.ServiceProvider.GetService <IHtsClientsLoader>();
var clientsSourceExtractor = TestInitializer.ServiceProvider.GetService <IHtsClientsSourceExtractor>();
var tempCount = clientsSourceExtractor.Extract(clientExtract, _protocol).Result;
var patientCount = clientLoader.Load(clientExtract.Id, tempCount).Result;
}
public bool CheckDiffSupport(DbProtocol protocol)
{
if (!protocol.DiffSupport)
{
return(false);
}
var sourceConnection = GetConnection(protocol);
if (null == sourceConnection)
{
throw new Exception("Data connection not initialized");
}
using (sourceConnection)
{
if (sourceConnection.State != ConnectionState.Open)
{
sourceConnection.Open();
}
var commandDefinition = new CommandDefinition(protocol.DiffSqlCheck, null, null, 0);
try
{
if (sourceConnection is SqliteConnection)
{
using (var diffReader = sourceConnection.ExecuteReader(commandDefinition))
{
diffReader.Read();
}
}
else
{
using (var diffReader = sourceConnection.ExecuteReader(commandDefinition, CommandBehavior.CloseConnection))
{
diffReader.Read();
}
}
return(true);
}
catch (Exception e)
{
Log.Warning("Missing differential upload feature in EMR");
}
}
return(false);
}
public IActionResult SaveConnection([FromBody] DbProtocol dbProtocol)
{
if (null == dbProtocol)
{
return(BadRequest());
}
try
{
_options.Update(opt =>
{
opt.HapiConnection = _dbManager.BuildConncetion(dbProtocol);
});
return(Ok(true));
}
catch (Exception e)
{
Log.Error($"{e}");
return(StatusCode(500, $"{e.Message}"));
}
}
public void SetUp()
{
_context = new ExtractsContext(_options);
_context.Database.EnsureDeleted();
_context.Database.EnsureCreated();
_dbExtractProtocolDtos = new List <DbExtractProtocolDTO>();
_mssql = new DbProtocol(DatabaseType.MicrosoftSQL, @".\koske14", "sa", "maun", "IQTools_KeHMIS");
_extractA = new DbExtract {
Id = _iqcareId, Emr = "IQCare", ExtractSql = @" select [Id],[shr],[date_created],[status],[status_date],[uuid] FROM [psmart_store]"
};
_mysql = new DbProtocol(DatabaseType.MySQL, @"localhost", "root", "test", "openmrs");
_extractB = new DbExtract {
Id = _kenyaEmrId, Emr = "KenyaEMR", ExtractSql = @" select id,shr,date_created,status,status_date,uuid FROM psmart_store"
};
_dbExtractProtocolDtos.Add(new DbExtractProtocolDTO(_extractA, _mssql));
_dbExtractProtocolDtos.Add(new DbExtractProtocolDTO(_extractB, _mysql));
_extractHistoryRepository = new ExtractHistoryRepository(_context);
_psmartExtractService =
new PsmartExtractService(new PsmartSourceReader(), new PsmartStageRepository(_context), _extractHistoryRepository);
}
public void Init()
{
var extractIds = TestInitializer.Iqtools.Extracts.Where(x => x.DocketId.IsSameAs("NDWH")).Select(x => x.Id)
.ToList();
var cleaner = TestInitializer.ServiceProvider.GetService <IClearDwhExtracts>();
cleaner.Clear(extractIds);
var extractIdsMySql = TestInitializer.KenyaEmr.Extracts.Where(x => x.DocketId.IsSameAs("NDWH")).Select(x => x.Id)
.ToList();
var cleanerMySql = TestInitializer.ServiceProviderMysql.GetService <IClearDwhExtracts>();
cleanerMySql.Clear(extractIdsMySql);
_extractsContext = TestInitializer.ServiceProvider.GetService <ExtractsContext>();
_extractsContextMySql = TestInitializer.ServiceProviderMysql.GetService <ExtractsContext>();
var patients = Builder <PatientExtract> .CreateListOfSize(1).All().With(x => x.SiteCode = 1).With(x => x.PatientPK = 1).Build().ToList();
var tempMpis = Builder <TempPatientPharmacyExtract> .CreateListOfSize(1).All().With(x => x.SiteCode = 1).With(x => x.PatientPK = 1).With(x => x.CheckError = false).Build().ToList();
_extractsContext.PatientExtracts.AddRange(patients);
_extractsContext.TempPatientPharmacyExtracts.AddRange(tempMpis);
_extractsContext.SaveChanges();
_extractsContextMySql.PatientExtracts.AddRange(patients);
_extractsContextMySql.TempPatientPharmacyExtracts.AddRange(tempMpis);
_extractsContextMySql.SaveChanges();
_iQtoolsDb = TestInitializer.Iqtools.DatabaseProtocols.First(x => x.DatabaseName.ToLower().Contains("iqtools".ToLower()));
_iQtoolsDb.Host = ".";
_iQtoolsDb.Username = "******";
_iQtoolsDb.Password = "******";
_kenyaEmrDb = TestInitializer.KenyaEmr.DatabaseProtocols.First();
_kenyaEmrDb.Host = "127.0.0.1";
_kenyaEmrDb.Username = "******";
_kenyaEmrDb.Password = "******";
_kenyaEmrDb.DatabaseName = "openmrs";
}
public bool VerfiyServer(DbProtocol dbProtocol)
{
bool isConnected = false;
var sb = new SqlConnectionStringBuilder();
sb.DataSource = dbProtocol.Server;
sb.UserID = dbProtocol.User;
sb.Password = dbProtocol.Password;
sb.InitialCatalog = "master";
sb.MultipleActiveResultSets = true;
sb.PersistSecurityInfo = true;
sb.Pooling = true;
using (var cn = new SqlConnection(sb.ConnectionString))
{
cn.Open();
isConnected = cn.State == ConnectionState.Open;
}
return(isConnected);
}
public IActionResult VerifyDb([FromBody] DbProtocol dbProtocol)
{
if (null == dbProtocol)
{
return(BadRequest());
}
try
{
var connected = _dbManager.Verfiy(dbProtocol);
if (connected)
{
return(Ok(true));
}
throw new Exception("Database could not connect");
}
catch (Exception e)
{
Log.Error($"{e}");
return(StatusCode(500, $"{e.Message}"));
}
}
public async Task <int> Extract(DbExtract extract, DbProtocol dbProtocol)
{
int batch = 500;
DomainEvents.Dispatch(new MgsNotification(new ExtractProgress(nameof(MetricMigrationExtract), "extracting...")));
//DomainEvents.Dispatch(new CbsStatusNotification(extract.Id,ExtractStatus.Loading));
var list = new List <TempMetricMigrationExtract>();
int count = 0;
int totalCount = 0;
using (var rdr = await _reader.ExecuteReader(dbProtocol, extract))
{
while (rdr.Read())
{
totalCount++;
count++;
// AutoMapper profiles
var extractRecord = Mapper.Map <IDataRecord, TempMetricMigrationExtract>(rdr);
extractRecord.Id = LiveGuid.NewGuid();
list.Add(extractRecord);
if (count == batch)
{
// TODO: batch and save
_extractRepository.BatchInsert(list);
try
{
DomainEvents.Dispatch(new MgsNotification(new ExtractProgress(nameof(MetricMigrationExtract), "extracting...", totalCount, count, 0, 0, 0)));
}
catch (Exception e)
{
Log.Error(e, "Notification error");
}
count = 0;
list = new List <TempMetricMigrationExtract>();
}
// TODO: Notify progress...
}
if (count > 0)
{
_extractRepository.BatchInsert(list);
}
_extractRepository.CloseConnection();
}
try
{
DomainEvents.Dispatch(new MgsNotification(new ExtractProgress(nameof(MetricMigrationExtract), "extracted", totalCount, 0, 0, 0, 0)));
DomainEvents.Dispatch(new MgsStatusNotification(extract.Id, ExtractStatus.Found, totalCount));
DomainEvents.Dispatch(new MgsStatusNotification(extract.Id, ExtractStatus.Loaded, totalCount));
}
catch (Exception e)
{
Log.Error(e, "Notification error");
}
return(totalCount);
}
public int Find(DbProtocol protocol, DbExtract extract)
{
throw new NotImplementedException();
}
public Task <int> ReadExtract(DbExtract extract, DbProtocol dbProtocol)
{
throw new NotImplementedException();
}
public IEnumerable <PsmartSource> Extract(DbProtocol protocol, DbExtract extract)
{
_emr = extract.Emr;
return(_psmartSourceReader.Read(protocol, extract));
}
public bool CheckDiffSupport(DbProtocol protocol)
{
throw new NotImplementedException();
}
