/** Set the preferences for this import object. */ public void setPrefs(Prefs prefs, DataObject db) throws Exception { Errors.logInfo("ImportData.setPrefs(...) started"); this.pid = Integer.valueOf(prefs.pid).toString(); this.isid = Integer.valueOf(prefs.isid).toString(); this.ifid = Integer.valueOf(prefs.ifid).toString(); this.upPath = prefs.upPath; this.systemFileName = prefs.fileName; this.updateMethod = prefs.updateMethod; this.connection = prefs.connection; this.conn_viss = prefs.connViss; this.sampleUnitId = prefs.sampleUnitId; this.speciesId = prefs.speciesId; this.userId = prefs.userId; this.db = db; debug(); if (!updateMethod.equals("CREATE") && !updateMethod.equals("UPDATE") && !updateMethod.equals("CREATE_OR_UPDATE")) throw new Exception("UpdateMethod is not CREATE, UPDATE, CREATE_OR_UPDATE"); Errors.logInfo("ImportData.setPrefs(...) ended"); }
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; }
/** Prints a debug information about the knowledge of this import module. */ public void debug() { Errors.logInfo("ImportData.debug() started"); if (connection == null) Errors.logDebug("connection is null"); else Errors.logDebug("connection is not null"); if (conn_viss == null) Errors.logDebug("conn_viss is null"); else Errors.logDebug("conn_viss is not null"); if (pid == null) Errors.logDebug("pid is null"); else Errors.logDebug("pid=" + pid); if (isid == null) Errors.logDebug("isid is null"); else Errors.logDebug("isid=" + isid); if (upPath == null) Errors.logDebug("upPath is null"); else Errors.logDebug("upPath=" + upPath); Errors.logDebug("sampleUnitId=" + sampleUnitId); Errors.logDebug("speciesId=" + speciesId); if (userId == null) Errors.logDebug("userId is null"); else Errors.logDebug("userId=" + userId); Errors.logDebug("level=" + level); Errors.logDebug("maxDev=" + maxDev); if (updateMethod == null) Errors.logDebug("updateMethod is null"); else Errors.logDebug("updateMethod=" + updateMethod); Errors.logInfo("ImportData.debug() ended"); }
public boolean check() { Errors.logDebug("CheckVariables started"); boolean res = false; DbImportFile dbInFile = new DbImportFile(); String fullFileName = ""; String checkFileName = ""; String errMessage = null; try { // Create the variable DbVariable dbVariable = new DbVariable(); dbInFile.setStatus(conn_viss, ifid, "0%"); // Store the file on server filesystem fullFileName = dbInFile.storeImportFileBLOB(conn_viss, ifid); checkFileName = fullFileName + "_checked"; FileHeader header = FileParser.scanFileHeader(fullFileName); String type = header.formatTypeName().toUpperCase(); char delimiter = header.delimiter().charValue(); FileParser fileParser = new FileParser(fullFileName); fileParser.Parse( FileTypeDefinitionList.matchingDefinitions( FileTypeDefinition.VARIABLE, FileTypeDefinition.LIST)); // Write out the result to a new file FileWriter fileOut = new FileWriter(checkFileName); fileOut.write( header.objectTypeName() + "/" + header.formatTypeName() + "/" + header.version() + "/" + header.delimiter() + "\n"); String titles[] = fileParser.columnTitles(); for (int j = 0; j < titles.length; j++) { fileOut.write(titles[j] + delimiter); } fileOut.write("\n"); String errorMsg = ""; errorMsg = checkList(fileParser, fileOut, delimiter); fileOut.close(); /* * Save the file to database */ dbInFile.saveCheckedFile(conn_viss, ifid, checkFileName); if (errorMsg.startsWith("ERROR:")) { res = false; dbInFile.setStatus(conn_viss, ifid, "ERROR"); // Add a message to the log dbInFile.addErrMsg( conn_viss, ifid, "File checked failed for sampling unit " + DbSamplingUnit.getSUName(conn_viss, Integer.toString(sampleUnitId)) + ". <br>" + errorMsg); Errors.logDebug("ErrorMsg=" + errorMsg); } else if (errorMsg.startsWith("WARNING:")) { dbInFile.setStatus(conn_viss, ifid, "WARNING"); res = true; // Add a message to the log dbInFile.addErrMsg(conn_viss, ifid, "Warnings exists: " + errorMsg); } else { dbInFile.setStatus(conn_viss, ifid, "CHECKED"); res = true; // Add a message to the log dbInFile.addErrMsg( conn_viss, ifid, "File checked for sampling unit " + DbSamplingUnit.getSUName(conn_viss, Integer.toString(sampleUnitId)) + ".<br>" + errorMsg); } /* if (errorMsg.length()>0) { res = false; dbInFile.setStatus(conn_viss,ifid,"ERROR"); // Add a message to the log dbInFile.addErrMsg(conn_viss,ifid,"File failed the check for sampling unit "+DbSamplingUnit.getSUName(conn_viss,Integer.toString(sampleUnitId)) +"<br>"+errorMsg); } else { res = true; dbInFile.setStatus(conn_viss,ifid,"CHECKED"); // Add a message to the log dbInFile.addErrMsg(conn_viss,ifid,"File checked for sampling unit "+DbSamplingUnit.getSUName(conn_viss,Integer.toString(sampleUnitId)) +"<br>"+errorMsg); }*/ } catch (Exception e) { 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(); } } finally { try { /* * Delete files uploaded */ File tmp = new File(checkFileName); tmp.delete(); tmp = new File(fullFileName); tmp.delete(); } catch (Exception ignore) { } } Errors.logDebug("CheckVariables completed"); 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; }
public boolean check() { Errors.logDebug("CheckPhenotype started"); boolean res = false; String errMessage = null; FileWriter fileOut = null; DbImportFile dbInFile = new DbImportFile(); String fullFileName = ""; String checkFileName = ""; try { dbInFile.setStatus(conn_viss, ifid, "0%"); fullFileName = dbInFile.storeImportFileBLOB(conn_viss, ifid); checkFileName = fullFileName + "_checked"; // Create the Phenotype DbPhenotype dbPhenotype = new DbPhenotype(); FileHeader header = FileParser.scanFileHeader(fullFileName); String type = header.formatTypeName().toUpperCase(); char delimiter = header.delimiter().charValue(); // AbstractValueFileParser fp = null; FileParser fp = null; if (type.equals("LIST")) { fp = new FileParser(fullFileName); fp.Parse( FileTypeDefinitionList.matchingDefinitions( FileTypeDefinition.PHENOTYPE, FileTypeDefinition.LIST)); } else if (type.equals("MATRIX")) { fp = new FileParser(fullFileName); fp.Parse( FileTypeDefinitionList.matchingDefinitions( FileTypeDefinition.PHENOTYPE, FileTypeDefinition.MATRIX)); } // Write out the result to a new file fileOut = new FileWriter(checkFileName); fileOut.write( header.objectTypeName() + "/" + header.formatTypeName() + "/" + header.version() + "/" + header.delimiter() + "\n"); String titles[] = fp.columnTitles(); for (int j = 0; j < titles.length; j++) { fileOut.write(titles[j] + delimiter); } fileOut.write("\n"); // Garbage collect the unused variables header = null; // fullFileName = null; // checkFileName = null; // Fix to upper case updateMethod = updateMethod.toUpperCase(); Vector fatalErrors = new Vector(); if (type.equals("LIST")) checkListTitles(titles, fatalErrors); else checkMatrixTitles(titles, fatalErrors); writeTitleErrors(fileOut, fatalErrors); String indId; if (titles[0].equals("IDENTITY")) indId = "IDENTITY"; else indId = "Alias"; String errMsg = ""; if (type.equals("LIST")) errMsg = checkList((FileParser) fp, fileOut, delimiter, indId); // errMsg = checkList((FileParser)fp, fatalErrors,fileOut,delimiter,indId); else if (type.equals("MATRIX")) errMsg = checkMatrix((FileParser) fp, fatalErrors, fileOut, delimiter, indId); // Close the file fileOut.close(); /* * Save the file to database */ dbInFile.saveCheckedFile(conn_viss, ifid, checkFileName); // Get the error message from the database object. If it is set an // error occured during the operation so an error is thrown. // errMessage = dbIndividual.getErrorMessage(); // Assertion.assertMsg(errMessage == null || // errMessage.trim().equals(""), errMessage); if (errMsg.startsWith("ERROR:")) { dbInFile.setStatus(conn_viss, ifid, "ERROR"); res = false; } else if (errMsg.startsWith("WARNING:")) { dbInFile.setStatus(conn_viss, ifid, "WARNING"); res = true; } else { dbInFile.setStatus(conn_viss, ifid, "CHECKED"); res = true; } // Add a message to the log dbInFile.addErrMsg( conn_viss, ifid, "File checked for sampling unit " + DbSamplingUnit.getSUName(conn_viss, Integer.toString(sampleUnitId)) + "<br>\n" + errMsg); } catch (Exception e) { // Flag for error and set the errMessage if it has not been set // isOk = false; 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 temporary file */ File tmp = new File(fullFileName); tmp.delete(); tmp = null; tmp = new File(checkFileName); tmp.delete(); tmp = null; } catch (Exception ignore) { } } Errors.logDebug("CheckPhenotype completed"); return res; }