public boolean imp() { boolean res = false; DbVariable dbVariable = null; String fullFileName = ""; String errMessage = null; DbImportFile dbInFile = new DbImportFile(); try { dbVariable = new DbVariable(); // Store the file on server filesystem fullFileName = dbInFile.storeImportFileBLOB(conn_viss, ifid); FileParser fileParser = new FileParser(fullFileName); fileParser.Parse( FileTypeDefinitionList.matchingDefinitions( FileTypeDefinition.VARIABLE, FileTypeDefinition.LIST)); dbVariable.CreateVariables(fileParser, connection, sampleUnitId, Integer.parseInt(userId)); errMessage = dbVariable.getErrorMessage(); Assertion.assertMsg(errMessage == null || errMessage.trim().equals(""), errMessage); dbInFile.setStatus(conn_viss, ifid, "IMPORTED"); // dbInFile.UpdateImportFile(connection,null,null,"Done",Integer.parseInt(ifid),Integer.parseInt(userId)); // Add a message to the log dbInFile.addErrMsg( conn_viss, ifid, "File imported to sampling unit " + DbSamplingUnit.getSUName(conn_viss, Integer.toString(sampleUnitId)) + "Note: Markers is always imported in Create mode."); res = true; } catch (Exception e) { Errors.logError("ImportVariables.imp(...)" + e.getMessage()); dbInFile.setStatus(conn_viss, ifid, "ERROR"); // dbInFile.UpdateImportFile(connection,null,null,e.getMessage(),Integer.parseInt(ifid),Integer.parseInt(userId)); // Add a message to the log dbInFile.addErrMsg(conn_viss, ifid, e.getMessage()); e.printStackTrace(System.err); if (errMessage == null) { errMessage = e.getMessage(); } } finally { try { /* * Delete files uploaded */ File tmp = new File(fullFileName); tmp.delete(); } catch (Exception ignore) { } } return res; }
public boolean imp() { boolean res = false; String errMessage = null; DbImportFile dbInFile = new DbImportFile(); DbPhenotype dbp = new DbPhenotype(); String fullFileName = null; try { Errors.logInfo("CheckPhenotype started"); // connection.setAutoCommit(false); dbInFile.setStatus(conn_viss, ifid, "0%"); fullFileName = dbInFile.storeImportFileBLOB(conn_viss, ifid); FileHeader header = FileParser.scanFileHeader(fullFileName); FileParser fileParser = new FileParser(fullFileName); // Set status dbInFile.setStatus(conn_viss, ifid, "10%"); // Ensure file format is list or matrix Assertion.assertMsg( header.formatTypeName().equalsIgnoreCase(FileTypeDefinition.LIST) || header.formatTypeName().equalsIgnoreCase(FileTypeDefinition.MATRIX), "Format type name should be list or matrix " + "but found found " + header.formatTypeName()); // If file is a list if (header.formatTypeName().equalsIgnoreCase(FileTypeDefinition.LIST)) { fileParser.Parse( FileTypeDefinitionList.matchingDefinitions( FileTypeDefinition.PHENOTYPE, FileTypeDefinition.LIST)); dbInFile.setStatus(conn_viss, ifid, "20%"); if (updateMethod.equals("CREATE")) { dbp.CreatePhenotypesList( fileParser, connection, sampleUnitId, Integer.valueOf(userId).intValue()); } else if (updateMethod.equals("UPDATE")) { dbp.UpdatePhenotypesList( fileParser, connection, sampleUnitId, Integer.valueOf(userId).intValue()); } else if (updateMethod.equals("CREATE_OR_UPDATE")) { dbp.CreateOrUpdatePhenotypesList( fileParser, connection, sampleUnitId, Integer.valueOf(userId).intValue()); } } // If file is a matrix else if (header.formatTypeName().equalsIgnoreCase(FileTypeDefinition.MATRIX)) { fileParser.Parse( FileTypeDefinitionList.matchingDefinitions( FileTypeDefinition.PHENOTYPE, FileTypeDefinition.MATRIX)); dbInFile.setStatus(conn_viss, ifid, "20%"); if (updateMethod.equals("CREATE")) { dbp.CreatePhenotypesMatrix( fileParser, connection, sampleUnitId, Integer.valueOf(userId).intValue()); } else if (updateMethod.equals("UPDATE")) { dbp.UpdatePhenotypesMatrix( fileParser, connection, sampleUnitId, Integer.valueOf(userId).intValue()); } else if (updateMethod.equals("CREATE_OR_UPDATE")) { dbp.CreateOrUpdatePhenotypesMatrix( fileParser, connection, sampleUnitId, Integer.valueOf(userId).intValue()); } } errMessage = dbp.getErrorMessage(); Assertion.assertMsg(errMessage == null || errMessage.trim().equals(""), errMessage); dbInFile.setStatus(conn_viss, ifid, "IMPORTED"); // Add a message to the log dbInFile.addErrMsg( conn_viss, ifid, "File imported for sampling unit " + DbSamplingUnit.getSUName(conn_viss, Integer.toString(sampleUnitId))); res = true; Errors.logInfo("Check Phenotype ended"); } catch (Exception e) { // Flag for error and set the errMessage if it has not been set // isOk = false; dbInFile.setStatus(conn_viss, ifid, "ERROR"); // Add a message to the log dbInFile.addErrMsg(conn_viss, ifid, e.getMessage()); e.printStackTrace(System.err); if (errMessage == null) { errMessage = e.getMessage(); } } return res; }