List of usage examples for java.io InputStream reset
public synchronized void reset() throws IOException
mark method was last called on this input stream. From source file:au.org.theark.lims.util.BioCollectionSpecimenUploader.java
/** * //w ww.j a va2 s.com * Upload the biocollection file data. * * Where N is any number of columns * * @param fileInputStream * is the input stream of a file * @param inLength * is the length of a file * @throws FileFormatException * file format Exception * @throws ArkBaseException * general ARK Exception * @return the upload report detailing the upload process */ public StringBuffer uploadAndReportMatrixBiocollectionFile(InputStream fileInputStream, long inLength, String inFileFormat, char inDelimChr) throws FileFormatException, ArkSystemException { delimiterCharacter = inDelimChr; uploadReport = new StringBuffer(); curPos = 0; InputStreamReader inputStreamReader = null; CsvReader csvReader = null; DecimalFormat decimalFormat = new DecimalFormat("0.00"); // If Excel, convert to CSV for validation if (inFileFormat.equalsIgnoreCase("XLS")) { Workbook w; try { w = Workbook.getWorkbook(fileInputStream); delimiterCharacter = ','; XLStoCSV xlsToCsv = new XLStoCSV(delimiterCharacter); fileInputStream = xlsToCsv.convertXlsToCsv(w); fileInputStream.reset(); } catch (BiffException e) { log.error(e.getMessage()); } catch (IOException e) { log.error(e.getMessage()); } } try { inputStreamReader = new InputStreamReader(fileInputStream); csvReader = new CsvReader(inputStreamReader, delimiterCharacter); srcLength = inLength; if (srcLength <= 0) { uploadReport.append("The input size was not greater than 0. Actual length reported: "); uploadReport.append(srcLength); uploadReport.append("\n"); throw new FileFormatException( "The input size was not greater than 0. Actual length reported: " + srcLength); } timer = new StopWatch(); timer.start(); csvReader.readHeaders(); srcLength = inLength - csvReader.getHeaders().toString().length(); log.debug("Header length: " + csvReader.getHeaders().toString().length()); // Loop through all rows in file while (csvReader.readRecord()) { log.info("At record: " + recordCount); String subjectUID = csvReader.get("SUBJECTUID"); String biocollectionUID = csvReader.get("BIOCOLLECTIONUID"); LinkSubjectStudy linkSubjectStudy = iArkCommonService.getSubjectByUIDAndStudy(subjectUID, study); //this is validated in prior step and should never happen if (linkSubjectStudy == null) { log.error( "\n\n\n\n\n\n\n\n\n\n\n\nUnexpected subject? a shouldnt happen...we should have errored this in validation"); break;//TODO : log appropriately or do some handling } BioCollection bioCollection = iLimsService.getBioCollectionForStudySubjectByUID(biocollectionUID, study, linkSubjectStudy); if (bioCollection == null) { bioCollection = new BioCollection(); if (study.getAutoGenerateBiocollectionUid()) { // if biocollection not in the system we have to create a new biocollection uid. bioCollection.setBiocollectionUid(iLimsService.getNextGeneratedBiospecimenUID(study)); } else { bioCollection.setBiocollectionUid(biocollectionUID); } } else {// if exsists we do not want to auto genetared the uid. bioCollection.setBiocollectionUid(biocollectionUID); } bioCollection.setStudy(study); bioCollection.setLinkSubjectStudy(linkSubjectStudy); if (csvReader.getIndex("NAME") > 0) { String name = csvReader.get("NAME"); bioCollection.setName(name); } if (csvReader.getIndex("COLLECTIONDATE") > 0) { String collectionDate = csvReader.get("COLLECTIONDATE"); bioCollection.setCollectionDate(simpleDateFormat.parse(collectionDate)); } if (csvReader.getIndex("COMMENTS") > 0) { String comments = csvReader.get("COMMENTS"); bioCollection.setComments(comments); } //validation SHOULD make sure these cases will work. TODO: test scripts if (bioCollection.getId() == null) { insertBiocollections.add(bioCollection); StringBuffer sb = new StringBuffer(); sb.append("BioCollectionUID: "); sb.append(bioCollection.getBiocollectionUid()); sb.append(" has been created successfully."); sb.append("\n"); uploadReport.append(sb); insertCount++; } else { updateBiocollections.add(bioCollection); StringBuffer sb = new StringBuffer(); sb.append("BioCollectionUID: "); sb.append(bioCollection.getBiocollectionUid()); sb.append(" has been updated successfully."); sb.append("\n"); uploadReport.append(sb); updateCount++; } recordCount++; } } catch (IOException ioe) { uploadReport.append("Unexpected I/O exception whilst reading the biospecimen data file\n"); log.error("processMatrixBiospecimenFile IOException stacktrace:", ioe); throw new ArkSystemException("Unexpected I/O exception whilst reading the biospecimen data file"); } catch (Exception ex) { uploadReport.append("Unexpected exception whilst reading the biospecimen data file\n"); log.error("processMatrixBiospecimenFile Exception stacktrace:", ex); throw new ArkSystemException( "Unexpected exception occurred when trying to process biospecimen data file"); } finally { // Clean up the IO objects timer.stop(); uploadReport.append("\n"); uploadReport.append("Total elapsed time: "); uploadReport.append(timer.getTime()); uploadReport.append(" ms or "); uploadReport.append(decimalFormat.format(timer.getTime() / 1000.0)); uploadReport.append(" s"); uploadReport.append("\n"); uploadReport.append("Total file size: "); uploadReport.append(inLength); uploadReport.append(" B or "); uploadReport.append(decimalFormat.format(inLength / 1024.0 / 1024.0)); uploadReport.append(" MB"); uploadReport.append("\n"); if (timer != null) timer = null; if (csvReader != null) { try { csvReader.close(); } catch (Exception ex) { log.error("Cleanup operation failed: csvRdr.close()", ex); } } if (inputStreamReader != null) { try { inputStreamReader.close(); } catch (Exception ex) { log.error("Cleanup operation failed: isr.close()", ex); } } // Restore the state of variables srcLength = -1; } uploadReport.append("Processed "); uploadReport.append(recordCount); uploadReport.append(" records."); uploadReport.append("\n"); uploadReport.append("Inserted "); uploadReport.append(insertCount); uploadReport.append(" records."); uploadReport.append("\n"); uploadReport.append("Updated "); uploadReport.append(updateCount); uploadReport.append(" records."); uploadReport.append("\n"); // Batch insert/update iLimsService.batchInsertBiocollections(insertBiocollections); iLimsService.batchUpdateBiocollections(updateBiocollections); return uploadReport; }
From source file:eu.medsea.mimeutil.detector.OpendesktopMimeDetector.java
private Collection lookupMimeTypesForMagicData(InputStream in) { int offset = 0; int len = getMaxExtents(); byte[] data = new byte[len]; // Mark the input stream in.mark(len);/*from w ww .ja v a2s . c o m*/ try { // Since an InputStream might return only some data (not all // requested), we have to read in a loop until // either EOF is reached or the desired number of bytes have been // read. int restBytesToRead = len; while (restBytesToRead > 0) { int bytesRead = in.read(data, offset, restBytesToRead); if (bytesRead < 0) break; // EOF offset += bytesRead; restBytesToRead -= bytesRead; } } catch (IOException ioe) { throw new MimeException(ioe); } finally { try { // Reset the input stream to where it was marked. in.reset(); } catch (Exception e) { throw new MimeException(e); } } return lookupMagicData(data); }
From source file:com.ksc.http.KSCHttpClient.java
/** * Used to perform a last reset on the content input stream (if mark-supported); this is so that, for backward * compatibility reason, any "blind" retry (ie without calling reset) by user of this library with the same input * stream (such as ByteArrayInputStream) could still succeed. * * @param t the failure/*from www . ja va 2 s . com*/ * @param req the request, if known; or null otherwise. * @return the failure as given */ private <T extends Throwable> T lastReset(final T t, final Request<?> req) { try { InputStream content = req.getContent(); if (content != null) { if (content.markSupported()) content.reset(); } } catch (Exception ex) { log.debug("FYI: failed to reset content inputstream before throwing up", ex); } return t; }
From source file:org.opendap.d1.DAPMNodeService.java
/** * Return the SDO, SMO or ORE document that matches the given D1/DAP server * PID. Note that this is used for both /object and /replica calls. * //from w ww. ja v a 2s.c o m * @param pid The D1 Persistent Identifier for the local object * @return An InputStream; read the object from this. * @see org.dataone.service.mn.tier1.v1.MNRead#get() */ @Override public InputStream get(Identifier pid) throws InvalidToken, NotAuthorized, NotImplemented, ServiceFailure, NotFound, InsufficientResources { // Query the database for the PID. If it is a SDO or SMO, then we must // access the DAP server and return the streamed object via the InputStream. // if the PID references an ORE document, we must build the ORE doc and // return it. log.debug("... in DAPMNodeService, get()..."); if (!db.isInMetadata(pid.getValue())) throw new NotFound("1020", "The PID '" + pid.getValue() + "' was not found on this server."); try { InputStream in = null; // Anything other than an ORE doc must be DAP URL for this server. if (db.isDAPURL(pid.getValue())) { // For a DAP URL (e.g., it's a .nc or .iso URL), dereference and // return the InputStream HttpClient client = new DefaultHttpClient(); HttpGet request = new HttpGet(db.getDAPURL(pid.getValue())); HttpResponse response = client.execute(request); // Get the response in = response.getEntity().getContent(); } else { String ore_doc = db.getOREDoc(pid.getValue()); in = new ByteArrayInputStream(ore_doc.getBytes()); log.debug("ORE doc: $${}$$", ore_doc); log.debug("ORE doc checksum: {}", ChecksumUtil.checksum(in, "SHA-1").getValue()); in.reset(); /* List<String> ids = db.getIdentifiersForORE(pid.getValue()); Identifier smoId = new Identifier(); smoId.setValue(ids.get(0)); List<Identifier> dataObjects = new Vector<Identifier>(); Identifier sdoId = new Identifier(); sdoId.setValue(ids.get(1)); dataObjects.add(sdoId); Map<Identifier, List<Identifier>> idMap = new HashMap<Identifier, List<Identifier>>(); idMap.put(smoId, dataObjects); ResourceMap rm = ResourceMapFactory.getInstance().createResourceMap(pid, idMap); String resourceMapXML = ResourceMapFactory.getInstance().serializeResourceMap(rm); in = new ByteArrayInputStream(resourceMapXML.getBytes()); */ } if (in == null) throw new NotFound("1020", "The PID '" + pid.getValue() + "' was not found."); return in; } catch (Exception e) { log.error(e.getMessage()); throw new ServiceFailure("1030", e.getMessage()); } }
From source file:org.lockss.plugin.atypon.BaseAtyponRisFilterFactory.java
public InputStream createFilteredInputStream(ArchivalUnit au, InputStream in, String encoding) throws PluginException { InputStream inBuf = null; // to make sure mark() is supported /* //w w w .j a v a 2s. c o m * RIS files are collected with content type text/plain (encoding) and so * we have to filter all text/plain and then determine if they're a RIS file * here. We are working on a different long-term solution by allowing us to verify * the URL against a regexp. */ BufferedReader bReader; if (in.markSupported() != true) { inBuf = new BufferedInputStream(in); //wrap the one that came in } else { inBuf = in; //use the one passed in } int BUF_LEN = 2000; inBuf.mark(BUF_LEN); // not sure about the limit...just reading far enough to identify file type try { //Now create a BoundedInputReader to make sure that we don't overstep our reset mark bReader = new BufferedReader(new InputStreamReader(new BoundedInputStream(inBuf, BUF_LEN), encoding)); String aLine = bReader.readLine(); // The first tag in a RIS file must be "TY - "; be nice about WS // The specification doesn't allow for comments or other preceding characters // isBlank() checks if whitespace, empty or null // keep initial null check or you'd never exit loop if you hit the end of input! while (aLine != null && StringUtils.isBlank(aLine)) { aLine = bReader.readLine(); // get the next line } // do NOT close bReader - it would also close underlying inBuf! inBuf.reset(); // if we have data, see if it matches the RIS pattern if (aLine != null && RIS_PATTERN.matcher(aLine).find()) { return new RisFilterInputStream(inBuf, encoding, "Y2"); } return inBuf; // If not a RIS file, just return reset file } catch (UnsupportedEncodingException e) { log.debug2("Internal error (unsupported encoding)", e); throw new PluginException("Unsupported encoding looking ahead in input stream", e); } catch (IOException e) { log.debug2("Internal error (IO exception)", e); throw new PluginException("IO exception looking ahead in input stream", e); } }
From source file:org.mifos.customers.client.struts.action.ClientCustAction.java
@TransactionDemarcate(joinToken = true) public ActionForward retrievePictureOnPreview(ActionMapping mapping, ActionForm form, @SuppressWarnings("unused") HttpServletRequest request, HttpServletResponse response) throws Exception { ClientCustActionForm actionForm = (ClientCustActionForm) form; InputStream in = actionForm.getPicture().getInputStream(); in.mark(0);//from www. j a va 2 s . c om response.setContentType("image/jpeg"); BufferedOutputStream out = new BufferedOutputStream(response.getOutputStream()); byte[] by = new byte[1024 * 4]; // 4K buffer buf, 0, buf.length int index = in.read(by, 0, 1024 * 4); while (index != -1) { out.write(by, 0, index); index = in.read(by, 0, 1024 * 4); } out.flush(); out.close(); in.reset(); String forward = ClientConstants.CUSTOMER_PICTURE_PAGE; return mapping.findForward(forward); }
From source file:org.collectionspace.services.common.config.TenantBindingConfigReaderImpl.java
private InputStream merge(File srcFile, File deltaFile) throws IOException { InputStream result = null; try {//from w ww. j a v a2 s . c o m FileInputStream srcStream = new FileInputStream(srcFile); FileInputStream deltaStream = new FileInputStream(deltaFile); InputStream[] inputStreamArray = { srcStream, deltaStream }; Configurer configurer = new AttributeMergeConfigurer(); result = new ConfigurableXmlMerge(configurer).merge(inputStreamArray); } catch (Exception e) { logger.error("Could not merge tenant configuration delta file: " + deltaFile.getAbsolutePath(), e); } // // Try to save the merge output to a file that is suffixed with ".merged.xml" in the same directory // as the delta file. // if (result != null) { File outputDir = deltaFile.getParentFile(); String mergedFileName = outputDir.getAbsolutePath() + File.separator + this.TENANT_BINDINGS_FILENAME_PREFIX + MERGED_SUFFIX; File mergedOutFile = new File(mergedFileName); try { FileUtils.copyInputStreamToFile(result, mergedOutFile); } catch (IOException e) { logger.warn("Could not create a copy of the merged tenant configuration at: " + mergedFileName, e); } result.reset(); //reset the stream even if the file create failed. } return result; }
From source file:au.org.theark.lims.util.BioCollectionSpecimenUploader.java
/** * //ww w . j a v a2s .co m * Upload the biospecimen file data. * * Where N is any number of columns * * @param fileInputStream * is the input stream of a file * @param inLength * is the length of a file * @throws FileFormatException * file format Exception * @throws ArkBaseException * general ARK Exception * @return the upload report detailing the upload process */ public StringBuffer uploadAndReportMatrixBiospecimenFile(InputStream fileInputStream, long inLength, String inFileFormat, char inDelimChr) throws FileFormatException, ArkSystemException { delimiterCharacter = inDelimChr; uploadReport = new StringBuffer(); curPos = 0; InputStreamReader inputStreamReader = null; CsvReader csvReader = null; DecimalFormat decimalFormat = new DecimalFormat("0.00"); // If Excel, convert to CSV for validation if (inFileFormat.equalsIgnoreCase("XLS")) { Workbook w; try { w = Workbook.getWorkbook(fileInputStream); delimiterCharacter = ','; XLStoCSV xlsToCsv = new XLStoCSV(delimiterCharacter); fileInputStream = xlsToCsv.convertXlsToCsv(w); fileInputStream.reset(); } catch (BiffException e) { log.error(e.getMessage()); } catch (IOException e) { log.error(e.getMessage()); } } try { inputStreamReader = new InputStreamReader(fileInputStream); csvReader = new CsvReader(inputStreamReader, delimiterCharacter); srcLength = inLength; if (srcLength <= 0) { uploadReport.append("The input size was not greater than 0. Actual length reported: "); uploadReport.append(srcLength); uploadReport.append("\n"); throw new FileFormatException( "The input size was not greater than 0. Actual length reported: " + srcLength); } timer = new StopWatch(); timer.start(); csvReader.readHeaders(); srcLength = inLength - csvReader.getHeaders().toString().length(); log.debug("Header length: " + csvReader.getHeaders().toString().length()); // Loop through all rows in file while (csvReader.readRecord()) { log.info("At record: " + recordCount); String subjectUID = csvReader.get("SUBJECTUID"); String biospecimenUID = csvReader.get("BIOSPECIMENUID"); LinkSubjectStudy linkSubjectStudy = iArkCommonService.getSubjectByUIDAndStudy(subjectUID, study); //this is validated in prior step and should never happen if (linkSubjectStudy == null) { log.error( "\n\n\n\n\n\n\n\n\n\n\n\n Unexpected subject? a shouldnt happen...we should have errored this in validation"); break;//TODO : log appropriately or do some handling } //Always create a new biospecimen in this time //exsisting biospecimen are not allow to update in here. Biospecimen biospecimen = iLimsService.getBiospecimenByUid(biospecimenUID, study); if (biospecimen == null) { biospecimen = new Biospecimen(); } else { log.error( "\n\n\n\n\n\n\n\n\n....We should NEVER have existing biospecimens this should be validated in prior step"); break; } biospecimen.setStudy(study); biospecimen.setLinkSubjectStudy(linkSubjectStudy); if (csvReader.getIndex("BIOCOLLECTIONUID") > 0) { String biocollectionUid = csvReader.get("BIOCOLLECTIONUID"); BioCollection bioCollection = iLimsService.getBioCollectionByUID(biocollectionUid, this.study.getId(), subjectUID); if (bioCollection == null) { log.error( "\n\n\n\n\n\n\n\n\n....We already validated for the exsisting biocollection and we never created " + "new one if it does not exsists."); break; } else { biospecimen.setBioCollection(bioCollection); } } if (csvReader.getIndex("SAMPLETYPE") > 0) { String name = csvReader.get("SAMPLETYPE"); BioSampletype sampleType = new BioSampletype(); sampleType = iLimsService.getBioSampleTypeByName(name); biospecimen.setSampleType(sampleType); } if (csvReader.getIndex("QUANTITY") > 0) { String quantity = csvReader.get("QUANTITY"); biospecimen.setQuantity(new Double(quantity)); } if (csvReader.getIndex("CONCENTRATION") > 0) { String concentration = csvReader.get("CONCENTRATION"); if (concentration != null && !concentration.isEmpty()) { try { biospecimen.setConcentration(Double.parseDouble(concentration)); } catch (NumberFormatException ne) { log.error("Already validated in the previous step and never happen the for error"); } } } if (csvReader.getIndex("UNITS") > 0) { String name = csvReader.get("UNITS"); Unit unit = iLimsService.getUnitByName(name); biospecimen.setUnit(unit); } if (csvReader.getIndex("TREATMENT") > 0) { String name = csvReader.get("TREATMENT"); TreatmentType treatmentType = iLimsService.getTreatmentTypeByName(name); biospecimen.setTreatmentType(treatmentType); } Set<BioTransaction> bioTransactions = new HashSet<BioTransaction>(0); // Inheriently create a transaction for the initial quantity BioTransaction bioTransaction = new BioTransaction(); bioTransaction.setBiospecimen(biospecimen); bioTransaction.setTransactionDate(Calendar.getInstance().getTime()); bioTransaction.setQuantity(biospecimen.getQuantity()); bioTransaction.setReason(au.org.theark.lims.web.Constants.BIOTRANSACTION_STATUS_INITIAL_QUANTITY); BioTransactionStatus initialStatus = iLimsService.getBioTransactionStatusByName( au.org.theark.lims.web.Constants.BIOTRANSACTION_STATUS_INITIAL_QUANTITY); bioTransaction.setStatus(initialStatus); //ensure that the initial transaction can be identified bioTransactions.add(bioTransaction); biospecimen.setBioTransactions(bioTransactions); //validation SHOULD make sure these cases will work. TODO: test scripts if (study.getAutoGenerateBiospecimenUid()) { biospecimen.setBiospecimenUid(iLimsService.getNextGeneratedBiospecimenUID(study)); } else { biospecimen.setBiospecimenUid(biospecimenUID); } insertBiospecimens.add(biospecimen); StringBuffer sb = new StringBuffer(); sb.append("Biospecimen UID: "); sb.append(biospecimen.getBiospecimenUid()); sb.append(" has been created successfully."); sb.append("\n"); uploadReport.append(sb); insertCount++; // Allocation details String siteName = csvReader.get("SITE"); String freezerName = csvReader.get("FREEZER"); String rackName = csvReader.get("RACK"); String boxName = csvReader.get("BOX"); String row = csvReader.get("ROW"); String column = csvReader.get("COLUMN"); InvCell invCell = iInventoryService.getInvCellByLocationNames(siteName, freezerName, rackName, boxName, row, column); //Biospecimen was supposed to locate in the following valid, empty inventory cell // inventory cell is not persist with biospeciman. So we have to update the valid inventory cell location with the //biospecimen uid which we will do it while bispecimen creates. biospecimen.setInvCell(invCell); recordCount++; } } catch (IOException ioe) { uploadReport.append("Unexpected I/O exception whilst reading the biospecimen data file\n"); log.error("processMatrixBiospecimenFile IOException stacktrace:", ioe); throw new ArkSystemException("Unexpected I/O exception whilst reading the biospecimen data file"); } catch (Exception ex) { uploadReport.append("Unexpected exception whilst reading the biospecimen data file\n"); log.error("processMatrixBiospecimenFile Exception stacktrace:", ex); throw new ArkSystemException( "Unexpected exception occurred when trying to process biospecimen data file"); } finally { // Clean up the IO objects timer.stop(); uploadReport.append("\n"); uploadReport.append("Total elapsed time: "); uploadReport.append(timer.getTime()); uploadReport.append(" ms or "); uploadReport.append(decimalFormat.format(timer.getTime() / 1000.0)); uploadReport.append(" s"); uploadReport.append("\n"); uploadReport.append("Total file size: "); uploadReport.append(inLength); uploadReport.append(" B or "); uploadReport.append(decimalFormat.format(inLength / 1024.0 / 1024.0)); uploadReport.append(" MB"); uploadReport.append("\n"); if (timer != null) timer = null; if (csvReader != null) { try { csvReader.close(); } catch (Exception ex) { log.error("Cleanup operation failed: csvRdr.close()", ex); } } if (inputStreamReader != null) { try { inputStreamReader.close(); } catch (Exception ex) { log.error("Cleanup operation failed: isr.close()", ex); } } // Restore the state of variables srcLength = -1; } uploadReport.append("Processed "); uploadReport.append(recordCount); uploadReport.append(" records."); uploadReport.append("\n"); uploadReport.append("Inserted "); uploadReport.append(insertCount); uploadReport.append(" records."); uploadReport.append("\n"); uploadReport.append("Updated "); uploadReport.append(updateCount); uploadReport.append(" records."); uploadReport.append("\n"); // Batch insert/update iLimsService.batchInsertBiospecimensAndUpdateInventoryCell(insertBiospecimens); return uploadReport; }
From source file:au.org.theark.lims.util.BioCollectionSpecimenUploader.java
/** * Upload Biospecimen Inventory location file. * * * Where N is any number of columns//w w w .j ava 2 s. c om * * @param fileInputStream * is the input stream of a file * @param inLength * is the length of a file * @throws FileFormatException * file format Exception * @throws ArkBaseException * general ARK Exception * @return the upload report detailing the upload process */ public StringBuffer uploadAndReportMatrixBiospecimenInventoryFile(InputStream fileInputStream, long inLength, String inFileFormat, char inDelimChr) throws FileFormatException, ArkSystemException { delimiterCharacter = inDelimChr; uploadReport = new StringBuffer(); curPos = 0; List<InvCell> cellsToUpdate = new ArrayList<InvCell>(); InputStreamReader inputStreamReader = null; CsvReader csvReader = null; DecimalFormat decimalFormat = new DecimalFormat("0.00"); // If Excel, convert to CSV for validation if (inFileFormat.equalsIgnoreCase("XLS")) { Workbook w; try { w = Workbook.getWorkbook(fileInputStream); delimiterCharacter = ','; XLStoCSV xlsToCsv = new XLStoCSV(delimiterCharacter); fileInputStream = xlsToCsv.convertXlsToCsv(w); fileInputStream.reset(); } catch (BiffException e) { log.error(e.getMessage()); } catch (IOException e) { log.error(e.getMessage()); } } try { inputStreamReader = new InputStreamReader(fileInputStream); csvReader = new CsvReader(inputStreamReader, delimiterCharacter); srcLength = inLength; if (srcLength <= 0) { uploadReport.append("The input size was not greater than 0. Actual length reported: "); uploadReport.append(srcLength); uploadReport.append("\n"); throw new FileFormatException( "The input size was not greater than 0. Actual length reported: " + srcLength); } timer = new StopWatch(); timer.start(); csvReader.readHeaders(); srcLength = inLength - csvReader.getHeaders().toString().length(); log.debug("Header length: " + csvReader.getHeaders().toString().length()); // Loop through all rows in file while (csvReader.readRecord()) { log.info("At record: " + recordCount); String biospecimenUID = csvReader.get("BIOSPECIMENUID"); Biospecimen biospecimen = iLimsService.getBiospecimenByUid(biospecimenUID, study); if (biospecimen == null) { log.error( "\n\n\n\n\n\n\n\n\n....We should NEVER have null biospecimens this should be validated in prior step"); break; } // Allocation details InvCell invCell; String siteName = null; String freezerName = null; String rackName = null; String boxName = null; String row = null; String column = null; if (csvReader.getIndex("SITE") > 0) { siteName = csvReader.get("SITE"); } if (csvReader.getIndex("FREEZER") > 0) { freezerName = csvReader.get("FREEZER"); } if (csvReader.getIndex("RACK") > 0) { rackName = csvReader.get("RACK"); } if (csvReader.getIndex("BOX") > 0) { boxName = csvReader.get("BOX"); } if (csvReader.getIndex("ROW") > 0) { row = csvReader.get("ROW"); } if (csvReader.getIndex("COLUMN") > 0) { column = csvReader.get("COLUMN"); } invCell = iInventoryService.getInvCellByLocationNames(siteName, freezerName, rackName, boxName, row, column); if (invCell != null && invCell.getId() != null) { if (invCell.getBiospecimen() != null) { log.error( "This should NEVER happen as validation should ensure no cell will wipte another"); break; } invCell.setBiospecimen(biospecimen); cellsToUpdate.add(invCell); updateCount++; } else { log.error("This should NEVER happen as validation should ensure all cells valid"); break; } recordCount++; } } catch (IOException ioe) { uploadReport.append("Unexpected I/O exception whilst reading the biospecimen data file\n"); log.error("processMatrixBiospecimenFile IOException stacktrace:", ioe); throw new ArkSystemException("Unexpected I/O exception whilst reading the biospecimen data file"); } catch (Exception ex) { uploadReport.append("Unexpected exception whilst reading the biospecimen data file\n"); log.error("processMatrixBiospecimenFile Exception stacktrace:", ex); throw new ArkSystemException( "Unexpected exception occurred when trying to process biospecimen data file"); } finally { // Clean up the IO objects timer.stop(); uploadReport.append("\n"); uploadReport.append("Total elapsed time: "); uploadReport.append(timer.getTime()); uploadReport.append(" ms or "); uploadReport.append(decimalFormat.format(timer.getTime() / 1000.0)); uploadReport.append(" s"); uploadReport.append("\n"); uploadReport.append("Total file size: "); uploadReport.append(inLength); uploadReport.append(" B or "); uploadReport.append(decimalFormat.format(inLength / 1024.0 / 1024.0)); uploadReport.append(" MB"); uploadReport.append("\n"); if (timer != null) timer = null; if (csvReader != null) { try { csvReader.close(); } catch (Exception ex) { log.error("Cleanup operation failed: csvRdr.close()", ex); } } if (inputStreamReader != null) { try { inputStreamReader.close(); } catch (Exception ex) { log.error("Cleanup operation failed: isr.close()", ex); } } // Restore the state of variables srcLength = -1; } uploadReport.append("Processed "); uploadReport.append(recordCount); uploadReport.append(" records."); uploadReport.append("\n"); uploadReport.append("Updated "); uploadReport.append(updateCount); uploadReport.append(" records."); uploadReport.append("\n"); iLimsService.batchUpdateInvCells(cellsToUpdate); return uploadReport; }
From source file:com.ksc.http.KSCHttpClient.java
/** * Reset the input stream of the request before a retry. * * @param request Request containing input stream to reset * @throws ResetException If Input Stream can't be reset which means the request can't be retried *//*from w ww. ja va 2 s . co m*/ private void resetRequestInputStream(final Request<?> request) throws ResetException { InputStream requestInputStream = request.getContent(); if (requestInputStream != null) { if (requestInputStream.markSupported()) { try { requestInputStream.reset(); } catch (IOException ex) { throw new ResetException("Failed to reset the request input stream", ex); } } } }