List of usage examples for org.apache.commons.csv CSVPrinter close
@Override
public void close() throws IOException
From source file:com.chargebee.CSV.RemovingDuplicateEntries.java
public static void main(String[] args) throws IOException, Exception { String source = System.getProperty("user.home") + "/input.csv"; String output = System.getProperty("user.home") + "/output.csv"; RemovingDuplicateEntries rde = new RemovingDuplicateEntries(); CSVParser parser = MethodBank.parserInitializer(source); CSVPrinter printer = MethodBank.printerInitializer(output); rde.remove(parser, printer);/* w ww .j a v a 2 s .co m*/ parser.close(); printer.close(); }
From source file:com.chargebee.Application.DateFormat.java
public static void main(String[] args) throws IOException, Exception { Scanner sc = new Scanner(System.in); System.out.println("Input CSV File: "); String source = sc.nextLine(); System.out.println("Input JSON File: "); String requirements = sc.nextLine(); System.out.println("Output CSV File: "); String output = sc.nextLine(); DateFormat df = new DateFormat(); JSONObject jobj = MethodBank.readJsonObjectData(requirements); CSVParser parser = MethodBank.parserInitializer(source); CSVPrinter printer = MethodBank.printerInitializer(output); df.formatter(parser, printer, jobj); parser.close();//from www. ja v a 2s .c o m printer.close(); }
From source file:com.chargebee.Application.Amountediting.java
public static void main(String[] args) throws IOException, Exception { Scanner sc = new Scanner(System.in); System.out.println("Input CSV File: "); String source = sc.nextLine(); System.out.println("Input JSON File: "); String requirements = sc.nextLine(); System.out.println("Output CSV File: "); String output = sc.nextLine(); Amountediting ae = new Amountediting(); JSONObject jobj = MethodBank.readJsonObjectData(requirements); CSVParser parser = MethodBank.parserInitializer(source); CSVPrinter printer = MethodBank.printerInitializer(output); ae.formatter(parser, printer, jobj); parser.close();/*from ww w . j a v a2 s. c om*/ printer.close(); }
From source file:com.chargebee.Application.MappingHeaders.java
public static void main(String[] args) throws Exception { String source1 = System.getProperty("user.home") + "/Output-3.csv"; // Source CSV file containing the customer details String source2 = System.getProperty("user.home") + "/header.json";//Json file containing the customer id and token String output = System.getProperty("user.home") + "/Output-4.csv";// The destination CSV file. // Scanner sc = new Scanner(System.in); // System.out.println("Input CSV File: "); // String source1 = sc.nextLine(); ////from w ww. j ava 2 s. c om // System.out.println("config File: "); // String source2 = sc.nextLine(); // // System.out.println("Output CSV File: "); // String output = sc.nextLine(); // MappingHeaders objHm = new MappingHeaders(); JSONObject jobj = objHm.readJsonData(source2); CSVPrinter printer = new CSVPrinter(new FileWriter(output), CSVFormat.EXCEL.withRecordSeparator("\n").withDelimiter(',')); CSVParser parser = new CSVParser(new FileReader(source1), CSVFormat.EXCEL.withHeader()); objHm.extractJsonData(jobj, printer, parser); parser.close(); printer.close(); }
From source file:com.act.lcms.db.analysis.StandardIonAnalysis.java
public static void main(String[] args) throws Exception { Options opts = new Options(); for (Option.Builder b : OPTION_BUILDERS) { opts.addOption(b.build());//from w w w .j a v a2 s. com } CommandLine cl = null; try { CommandLineParser parser = new DefaultParser(); cl = parser.parse(opts, args); } catch (ParseException e) { System.err.format("Argument parsing failed: %s\n", e.getMessage()); HELP_FORMATTER.printHelp(LoadPlateCompositionIntoDB.class.getCanonicalName(), HELP_MESSAGE, opts, null, true); System.exit(1); } if (cl.hasOption("help")) { HELP_FORMATTER.printHelp(LoadPlateCompositionIntoDB.class.getCanonicalName(), HELP_MESSAGE, opts, null, true); return; } File lcmsDir = new File(cl.getOptionValue(OPTION_DIRECTORY)); if (!lcmsDir.isDirectory()) { System.err.format("File at %s is not a directory\n", lcmsDir.getAbsolutePath()); HELP_FORMATTER.printHelp(LoadPlateCompositionIntoDB.class.getCanonicalName(), HELP_MESSAGE, opts, null, true); System.exit(1); } try (DB db = DB.openDBFromCLI(cl)) { ScanFile.insertOrUpdateScanFilesInDirectory(db, lcmsDir); StandardIonAnalysis analysis = new StandardIonAnalysis(); HashMap<Integer, Plate> plateCache = new HashMap<>(); String plateBarcode = cl.getOptionValue(OPTION_STANDARD_PLATE_BARCODE); String inputChemicals = cl.getOptionValue(OPTION_STANDARD_CHEMICAL); String medium = cl.getOptionValue(OPTION_MEDIUM); // If standard chemical is specified, do standard LCMS ion selection analysis if (inputChemicals != null && !inputChemicals.equals("")) { String[] chemicals; if (!inputChemicals.contains(",")) { chemicals = new String[1]; chemicals[0] = inputChemicals; } else { chemicals = inputChemicals.split(","); } String outAnalysis = cl.getOptionValue(OPTION_OUTPUT_PREFIX) + "." + CSV_FORMAT; String plottingDirectory = cl.getOptionValue(OPTION_PLOTTING_DIR); String[] headerStrings = { "Molecule", "Plate Bar Code", "LCMS Detection Results" }; CSVPrinter printer = new CSVPrinter(new FileWriter(outAnalysis), CSVFormat.DEFAULT.withHeader(headerStrings)); for (String inputChemical : chemicals) { List<StandardWell> standardWells; Plate queryPlate = Plate.getPlateByBarcode(db, cl.getOptionValue(OPTION_STANDARD_PLATE_BARCODE)); if (plateBarcode != null && medium != null) { standardWells = analysis.getStandardWellsForChemicalInSpecificPlateAndMedium(db, inputChemical, queryPlate.getId(), medium); } else if (plateBarcode != null) { standardWells = analysis.getStandardWellsForChemicalInSpecificPlate(db, inputChemical, queryPlate.getId()); } else { standardWells = analysis.getStandardWellsForChemical(db, inputChemical); } if (standardWells.size() == 0) { throw new RuntimeException("Found no LCMS wells for " + inputChemical); } // Sort in descending order of media where MeOH and Water related media are promoted to the top and // anything derived from yeast media are demoted. Collections.sort(standardWells, new Comparator<StandardWell>() { @Override public int compare(StandardWell o1, StandardWell o2) { if (StandardWell.doesMediaContainYeastExtract(o1.getMedia()) && !StandardWell.doesMediaContainYeastExtract(o2.getMedia())) { return 1; } else { return 0; } } }); Map<StandardWell, StandardIonResult> wellToIonRanking = StandardIonAnalysis .getBestMetlinIonsForChemical(inputChemical, lcmsDir, db, standardWells, plottingDirectory); if (wellToIonRanking.size() != standardWells.size() && !cl.hasOption(OPTION_OVERRIDE_NO_SCAN_FILE_FOUND)) { throw new Exception("Could not find a scan file associated with one of the standard wells"); } for (StandardWell well : wellToIonRanking.keySet()) { LinkedHashMap<String, XZ> snrResults = wellToIonRanking.get(well).getAnalysisResults(); String snrRankingResults = ""; int numResultsToShow = 0; Plate plateForWellToAnalyze = Plate.getPlateById(db, well.getPlateId()); for (Map.Entry<String, XZ> ionToSnrAndTime : snrResults.entrySet()) { if (numResultsToShow > 3) { break; } String ion = ionToSnrAndTime.getKey(); XZ snrAndTime = ionToSnrAndTime.getValue(); snrRankingResults += String.format(ion + " (%.2f SNR at %.2fs); ", snrAndTime.getIntensity(), snrAndTime.getTime()); numResultsToShow++; } String[] resultSet = { inputChemical, plateForWellToAnalyze.getBarcode() + " " + well.getCoordinatesString() + " " + well.getMedia() + " " + well.getConcentration(), snrRankingResults }; printer.printRecord(resultSet); } } try { printer.flush(); printer.close(); } catch (IOException e) { System.err.println("Error while flushing/closing csv writer."); e.printStackTrace(); } } else { // Get the set of chemicals that includes the construct and all it's intermediates Pair<ConstructEntry, List<ChemicalAssociatedWithPathway>> constructAndPathwayChems = analysis .getChemicalsForConstruct(db, cl.getOptionValue(OPTION_CONSTRUCT)); System.out.format("Construct: %s\n", constructAndPathwayChems.getLeft().getCompositionId()); for (ChemicalAssociatedWithPathway pathwayChem : constructAndPathwayChems.getRight()) { System.out.format(" Pathway chem %s\n", pathwayChem.getChemical()); // Get all the standard wells for the pathway chemicals. These wells contain only the // the chemical added with controlled solutions (ie no organism or other chemicals in the // solution) List<StandardWell> standardWells; if (plateBarcode != null) { Plate queryPlate = Plate.getPlateByBarcode(db, cl.getOptionValue(OPTION_STANDARD_PLATE_BARCODE)); standardWells = analysis.getStandardWellsForChemicalInSpecificPlate(db, pathwayChem.getChemical(), queryPlate.getId()); } else { standardWells = analysis.getStandardWellsForChemical(db, pathwayChem.getChemical()); } for (StandardWell wellToAnalyze : standardWells) { List<StandardWell> negativeControls = analysis.getViableNegativeControlsForStandardWell(db, wellToAnalyze); Map<StandardWell, List<ScanFile>> allViableScanFiles = analysis .getViableScanFilesForStandardWells(db, wellToAnalyze, negativeControls); List<String> primaryStandardScanFileNames = new ArrayList<>(); for (ScanFile scanFile : allViableScanFiles.get(wellToAnalyze)) { primaryStandardScanFileNames.add(scanFile.getFilename()); } Plate plate = plateCache.get(wellToAnalyze.getPlateId()); if (plate == null) { plate = Plate.getPlateById(db, wellToAnalyze.getPlateId()); plateCache.put(plate.getId(), plate); } System.out.format(" Standard well: %s @ %s, '%s'%s%s\n", plate.getBarcode(), wellToAnalyze.getCoordinatesString(), wellToAnalyze.getChemical(), wellToAnalyze.getMedia() == null ? "" : String.format(" in %s", wellToAnalyze.getMedia()), wellToAnalyze.getConcentration() == null ? "" : String.format(" @ %s", wellToAnalyze.getConcentration())); System.out.format(" Scan files: %s\n", StringUtils.join(primaryStandardScanFileNames, ", ")); for (StandardWell negCtrlWell : negativeControls) { plate = plateCache.get(negCtrlWell.getPlateId()); if (plate == null) { plate = Plate.getPlateById(db, negCtrlWell.getPlateId()); plateCache.put(plate.getId(), plate); } List<String> negativeControlScanFileNames = new ArrayList<>(); for (ScanFile scanFile : allViableScanFiles.get(negCtrlWell)) { negativeControlScanFileNames.add(scanFile.getFilename()); } System.out.format(" Viable negative: %s @ %s, '%s'%s%s\n", plate.getBarcode(), negCtrlWell.getCoordinatesString(), negCtrlWell.getChemical(), negCtrlWell.getMedia() == null ? "" : String.format(" in %s", negCtrlWell.getMedia()), negCtrlWell.getConcentration() == null ? "" : String.format(" @ %s", negCtrlWell.getConcentration())); System.out.format(" Scan files: %s\n", StringUtils.join(negativeControlScanFileNames, ", ")); // TODO: do something useful with the standard wells and their scan files, and then stop all the printing. } } } } } }
From source file:com.streamsets.pipeline.lib.util.CsvUtil.java
public static String csvRecordToString(Record r, CSVFormat csvFormat) throws IOException { StringWriter stringWriter = new StringWriter(); CSVPrinter csvPrinter = new CSVPrinter(stringWriter, csvFormat); csvPrinter.printRecord(CsvUtil.fieldToCsv(r.get())); csvPrinter.flush();//from w ww.jav a2s . c o m csvPrinter.close(); return stringWriter.toString(); }
From source file:com.siemens.sw360.exporter.CSVExport.java
@NotNull private static ByteArrayOutputStream getCSVOutputStream(Iterable<String> csvHeaderIterable, Iterable<Iterable<String>> inputIterable) throws IOException { final ByteArrayOutputStream outB = new ByteArrayOutputStream(); try (Writer out = new BufferedWriter(new OutputStreamWriter(outB));) { CSVPrinter csvPrinter = new CSVPrinter(out, CommonUtils.sw360CsvFormat); csvPrinter.printRecord(csvHeaderIterable); csvPrinter.printRecords(inputIterable); csvPrinter.flush();/* w w w. j av a 2 s . c o m*/ csvPrinter.close(); } catch (Exception e) { outB.close(); throw e; } return outB; }
From source file:de.tudarmstadt.ukp.experiments.argumentation.sequence.significance.SignificanceMain.java
/** * Prints table to output string as CSV//from ww w . j a v a 2s . com * * @param out output * @param <T> value type * @param table table * @throws IOException */ public static <T> String tableToCsv(Table<String, String, Boolean> table) throws IOException { StringWriter sw = new StringWriter(); CSVPrinter printer = new CSVPrinter(sw, CSVFormat.DEFAULT); List<String> firstRow = new ArrayList<>(); firstRow.add(" "); firstRow.addAll(table.columnKeySet()); printer.printRecord(firstRow); for (String rowKey : table.rowKeySet()) { printer.print(rowKey); for (String columnKey : table.columnKeySet()) { printer.print(table.get(rowKey, columnKey)); } printer.println(); } printer.close(); return sw.toString(); }
From source file:com.streamsets.pipeline.kafka.common.KafkaTestUtil.java
public static List<KeyedMessage<String, String>> produceCsvMessages(String topic, String partition, CSVFormat csvFormat, File csvFile) throws IOException { List<KeyedMessage<String, String>> messages = new ArrayList<>(); String line;// www. j av a 2 s . c o m BufferedReader bufferedReader = new BufferedReader( new FileReader(KafkaTestUtil.class.getClassLoader().getResource("testKafkaTarget.csv").getFile())); while ((line = bufferedReader.readLine()) != null) { String[] strings = line.split(","); StringWriter stringWriter = new StringWriter(); CSVPrinter csvPrinter = new CSVPrinter(stringWriter, csvFormat); csvPrinter.printRecord(strings); csvPrinter.flush(); csvPrinter.close(); messages.add(new KeyedMessage<>(topic, partition, stringWriter.toString())); } return messages; }
From source file:de.tudarmstadt.ukp.experiments.argumentation.sequence.evaluation.helpers.FinalTableExtractor.java
public static <T> String tableToCsv(Table<String, String, T> table) throws IOException { StringWriter sw = new StringWriter(); CSVPrinter printer = new CSVPrinter(sw, CSVFormat.DEFAULT); List<String> firstRow = new ArrayList<>(); firstRow.add(" "); firstRow.addAll(table.columnKeySet()); printer.printRecord(firstRow);// w ww .j a v a 2s . c om for (String rowKey : table.rowKeySet()) { printer.print(rowKey); for (String columnKey : table.columnKeySet()) { printer.print(table.get(rowKey, columnKey)); } printer.println(); } printer.close(); return sw.toString(); }