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:org.docx4j.openpackaging.parts.JaxbXmlPart.java
/** * Unmarshal XML data from the specified InputStream and return the * resulting content tree. Validation event location information may be * incomplete when using this form of the unmarshal API. * * <p>//from w ww . j av a2 s . com * Implements <a href="#unmarshalGlobal">Unmarshal Global Root Element</a>. * * @param is * the InputStream to unmarshal XML data from * @return the newly created root object of the java content tree * * @throws JAXBException * If any unexpected errors occur while unmarshalling */ public E unmarshal(java.io.InputStream is) throws JAXBException { try { /* To avoid possible XML External Entity Injection attack, * we need to configure the processor. * * We use STAX XMLInputFactory to do that. * * createXMLStreamReader(is) is 40% slower than unmarshal(is). * * But it seems to be the best we can do ... * * org.w3c.dom.Document doc = XmlUtils.getNewDocumentBuilder().parse(is) * unmarshal(doc) * * ie DOM is 5x slower than unmarshal(is) * */ XMLInputFactory xif = XMLInputFactory.newInstance(); xif.setProperty(XMLInputFactory.IS_SUPPORTING_EXTERNAL_ENTITIES, false); xif.setProperty(XMLInputFactory.SUPPORT_DTD, false); // a DTD is merely ignored, its presence doesn't cause an exception XMLStreamReader xsr = xif.createXMLStreamReader(is); Unmarshaller u = jc.createUnmarshaller(); JaxbValidationEventHandler eventHandler = new JaxbValidationEventHandler(); if (is.markSupported()) { // Only fail hard if we know we can restart eventHandler.setContinue(false); } u.setEventHandler(eventHandler); try { jaxbElement = (E) XmlUtils.unwrap(u.unmarshal(xsr)); } catch (UnmarshalException ue) { if (ue.getLinkedException() != null && ue.getLinkedException().getMessage().contains("entity")) { /* Caused by: javax.xml.stream.XMLStreamException: ParseError at [row,col]:[10,19] Message: The entity "xxe" was referenced, but not declared. at com.sun.org.apache.xerces.internal.impl.XMLStreamReaderImpl.next(Unknown Source) at com.sun.xml.internal.bind.v2.runtime.unmarshaller.StAXStreamConnector.bridge(Unknown Source) */ log.error(ue.getMessage(), ue); throw ue; } if (is.markSupported()) { // When reading from zip, we use a ByteArrayInputStream, // which does support this. log.info("encountered unexpected content; pre-processing"); eventHandler.setContinue(true); try { Templates mcPreprocessorXslt = JaxbValidationEventHandler.getMcPreprocessor(); is.reset(); JAXBResult result = XmlUtils.prepareJAXBResult(jc); XmlUtils.transform(new StreamSource(is), mcPreprocessorXslt, null, result); jaxbElement = (E) XmlUtils.unwrap(result.getResult()); } catch (Exception e) { throw new JAXBException("Preprocessing exception", e); } } else { log.error(ue.getMessage(), ue); log.error(".. and mark not supported"); throw ue; } } } catch (XMLStreamException e1) { log.error(e1.getMessage(), e1); throw new JAXBException(e1); } return jaxbElement; }
From source file:ca.sqlpower.architect.swingui.SwingUIProjectLoader.java
public void load(InputStream in, DataSourceCollection<? extends SPDataSource> dataSources, ArchitectSession messageDelegate) throws IOException, SQLObjectException { olapPaneLoadIdMap = new HashMap<String, OLAPPane<?, ?>>(); UnclosableInputStream uin = new UnclosableInputStream(in); olapObjectLoadIdMap = new HashMap<String, OLAPObject>(); // sqlObjectLoadIdMap is not ready yet when parsing the olap objects // so this keeps track of the id of the SQLDatabase that OLAPSessions reference. Map<OLAPSession, String> sessionDbMap = new HashMap<OLAPSession, String>(); try {//from ww w .j a v a 2 s .co m getSession().getUndoManager().setLoading(true); if (uin.markSupported()) { uin.mark(Integer.MAX_VALUE); } else { throw new IllegalStateException("Failed to load with an input stream that does not support mark!"); } // parse the Mondrian business model parts first because the olap id // map is needed in the digester for parsing the olap gui try { MondrianXMLReader.parse(uin, getSession().getOLAPRootObject(), sessionDbMap, olapObjectLoadIdMap); } catch (SAXException e) { logger.error("Error parsing project file's olap schemas!", e); throw new SQLObjectException("SAX Exception in project file olap schemas parse!", e); } catch (Exception ex) { logger.error("General Exception in project file olap schemas parse!", ex); throw new SQLObjectException("Unexpected Exception", ex); } in.reset(); super.load(in, dataSources, messageDelegate); } finally { getSession().getUndoManager().setLoading(false); uin.forceClose(); } // now that the sqlObjectLoadIdMap is populated, we can set the // OLAPSessions' database. for (Map.Entry<OLAPSession, String> entry : sessionDbMap.entrySet()) { OLAPSession oSession = entry.getKey(); SQLDatabase db = (SQLDatabase) sqlObjectLoadIdMap.get(entry.getValue()); oSession.setDatabase(db); } // set the view positions again in the case that the viewport was invalid earlier. getSession().getPlayPen().setInitialViewPosition(); for (OLAPEditSession editSession : getSession().getOLAPEditSessions()) { editSession.getOlapPlayPen().setInitialViewPosition(); } // TODO change this to load the undo history from a file getSession().getUndoManager().discardAllEdits(); }
From source file:org.codelibs.fess.crawler.extractor.impl.TikaExtractor.java
@Override public ExtractData getText(final InputStream inputStream, final Map<String, String> params) { if (inputStream == null) { throw new CrawlerSystemException("The inputstream is null."); }/* ww w .ja va 2 s .co m*/ final File tempFile; final boolean isByteStream = inputStream instanceof ByteArrayInputStream; if (isByteStream) { inputStream.mark(0); tempFile = null; } else { try { tempFile = File.createTempFile("tikaExtractor-", ".out"); } catch (final IOException e) { throw new ExtractException("Could not create a temp file.", e); } } try { final PrintStream originalOutStream = System.out; final ByteArrayOutputStream outStream = new ByteArrayOutputStream(); System.setOut(new PrintStream(outStream, true)); final PrintStream originalErrStream = System.err; final ByteArrayOutputStream errStream = new ByteArrayOutputStream(); System.setErr(new PrintStream(errStream, true)); try { final String resourceName = params == null ? null : params.get(TikaMetadataKeys.RESOURCE_NAME_KEY); final String contentType = params == null ? null : params.get(HttpHeaders.CONTENT_TYPE); String contentEncoding = params == null ? null : params.get(HttpHeaders.CONTENT_ENCODING); // password for pdf String pdfPassword = params == null ? null : params.get(ExtractData.PDF_PASSWORD); if (pdfPassword == null && params != null) { pdfPassword = getPdfPassword(params.get(ExtractData.URL), resourceName); } final Metadata metadata = createMetadata(resourceName, contentType, contentEncoding, pdfPassword); final Parser parser = new DetectParser(); final ParseContext parseContext = new ParseContext(); parseContext.set(Parser.class, parser); String content = getContent(writer -> { InputStream in = null; try { if (!isByteStream) { try (OutputStream out = new FileOutputStream(tempFile)) { CopyUtil.copy(inputStream, out); } in = new FileInputStream(tempFile); } else { in = inputStream; } parser.parse(in, new BodyContentHandler(writer), metadata, parseContext); } finally { IOUtils.closeQuietly(in); } }, contentEncoding); if (StringUtil.isBlank(content)) { if (resourceName != null) { if (logger.isDebugEnabled()) { logger.debug("retry without a resource name: {}", resourceName); } final Metadata metadata2 = createMetadata(null, contentType, contentEncoding, pdfPassword); content = getContent(writer -> { InputStream in = null; try { if (isByteStream) { inputStream.reset(); in = inputStream; } else { in = new FileInputStream(tempFile); } parser.parse(in, new BodyContentHandler(writer), metadata2, parseContext); } finally { IOUtils.closeQuietly(in); } }, contentEncoding); } if (StringUtil.isBlank(content) && contentType != null) { if (logger.isDebugEnabled()) { logger.debug("retry without a content type: {}", contentType); } final Metadata metadata3 = createMetadata(null, null, contentEncoding, pdfPassword); content = getContent(writer -> { InputStream in = null; try { if (isByteStream) { inputStream.reset(); in = inputStream; } else { in = new FileInputStream(tempFile); } parser.parse(in, new BodyContentHandler(writer), metadata3, parseContext); } finally { IOUtils.closeQuietly(in); } }, contentEncoding); } if (readAsTextIfFailed && StringUtil.isBlank(content)) { if (logger.isDebugEnabled()) { logger.debug("read the content as a text."); } if (contentEncoding == null) { contentEncoding = Constants.UTF_8; } final String enc = contentEncoding; content = getContent(writer -> { BufferedReader br = null; try { if (isByteStream) { inputStream.reset(); br = new BufferedReader(new InputStreamReader(inputStream, enc)); } else { br = new BufferedReader( new InputStreamReader(new FileInputStream(tempFile), enc)); } String line; while ((line = br.readLine()) != null) { writer.write(line); } } catch (final Exception e) { logger.warn( "Could not read " + (tempFile != null ? tempFile.getAbsolutePath() : "a byte stream"), e); } finally { IOUtils.closeQuietly(br); } }, contentEncoding); } } final ExtractData extractData = new ExtractData(content); final String[] names = metadata.names(); Arrays.sort(names); for (final String name : names) { extractData.putValues(name, metadata.getValues(name)); } if (logger.isDebugEnabled()) { logger.debug("Result: metadata: {}", metadata); } return extractData; } catch (final TikaException e) { if (e.getMessage().indexOf("bomb") >= 0) { throw e; } final Throwable cause = e.getCause(); if (cause instanceof SAXException) { final Extractor xmlExtractor = crawlerContainer.getComponent("xmlExtractor"); if (xmlExtractor != null) { InputStream in = null; try { if (isByteStream) { inputStream.reset(); in = inputStream; } else { in = new FileInputStream(tempFile); } return xmlExtractor.getText(in, params); } finally { IOUtils.closeQuietly(in); } } } throw e; } finally { if (originalOutStream != null) { System.setOut(originalOutStream); } if (originalErrStream != null) { System.setErr(originalErrStream); } try { if (logger.isInfoEnabled()) { final byte[] bs = outStream.toByteArray(); if (bs.length != 0) { logger.info(new String(bs, outputEncoding)); } } if (logger.isWarnEnabled()) { final byte[] bs = errStream.toByteArray(); if (bs.length != 0) { logger.warn(new String(bs, outputEncoding)); } } } catch (final Exception e) { // NOP } } } catch (final Exception e) { throw new ExtractException("Could not extract a content.", e); } finally { if (tempFile != null && !tempFile.delete()) { logger.warn("Failed to delete " + tempFile.getAbsolutePath()); } } }
From source file:au.org.theark.study.util.DataUploader.java
/** * Imports the subject data file to the database tables, and creates report on the process Assumes the file is in the default "matrix" file format: * SUBJECTUID,FIELD1,FIELD2,FIELDN... 1,01/01/1900,99.99,99.99,, ... * /*w w w. jav a 2s .c om*/ * 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 **/ @SuppressWarnings("unchecked") public StringBuffer uploadAndReportMatrixSubjectFile(InputStream fileInputStream, long inLength, String inFileFormat, char inDelimChr, List<String> uidsWhichNeedUpdating) throws FileFormatException, ArkSystemException { List<LinkSubjectStudy> insertSubjects = new ArrayList<LinkSubjectStudy>(); List<LinkSubjectStudy> updateSubjects = new ArrayList<LinkSubjectStudy>(); long rowCount = 0; long subjectCount = 0; long insertCount = 0; long updateCount = 0; long srcLength = -1; // -1 means nothing being processed delimiterCharacter = inDelimChr; uploadReport = new StringBuffer(); 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); String[] stringLineArray; // this is a list of all our somewhat enum-like reference tables... // much better to call this once than each one n times in the for loop...plus each ones default is n times // should save 200,000-250,000 selects for a 17K insert. may still wish to evaluate whats best here Collection<MaritalStatus> maritalStatiiPossible = iArkCommonService.getMaritalStatus(); Collection<EmailStatus> emailStatiiPossible = iArkCommonService.getAllEmailStatuses(); Collection<SubjectStatus> subjectStatiiPossible = iArkCommonService.getSubjectStatus(); Collection<GenderType> genderTypesPossible = iArkCommonService.getGenderTypes(); Collection<TitleType> titleTypesPossible = iArkCommonService.getTitleType(); List<AddressType> addressTypesPossible = iArkCommonService.getAddressTypes(); List<AddressStatus> addressStatiiPossible = iArkCommonService.getAddressStatuses(); List<PhoneType> phoneTypesPossible = iArkCommonService.getPhoneTypes(); List<PhoneStatus> phoneStatiiPossible = iArkCommonService.getPhoneStatuses(); List<Country> countriesPossible = iArkCommonService.getCountries(); // List<State> statesPossible = iArkCommonService.getStates(country); Collection<VitalStatus> vitalStatiiPossible = iArkCommonService.getVitalStatus(); Collection<PersonContactMethod> personContactMethodPossible = iArkCommonService .getPersonContactMethodList(); // Collection<MaritalStatus> yesNoList = iArkCommonService.getYesNoList(); //TODO would boolean not be better? YesNo yes = iArkCommonService.getYes();// TODO: boolean YesNo no = iArkCommonService.getNo(); // things inherant... "CONSENT_ID", "CONSENT_STUDY_ID", "CONSENT_LINK_SUBJECT_STUDY_ID", // things needed from file... "CONSENT_STUDY_COMP_ID", "CONSENT_STUDY_COMP_STATUS_ID", "CONSENT_CONSENT_STATUS_ID", // "CONSENT_CONSENT_TYPE_ID", "CONSENT_CONSENT_DATE", // "CONSENT_CONSENTED_BY", "CONSENT_COMMENTS", "CONSENT_REQUESTED_DATE", "CONSENT_RECEIVED_DATE", "CONSENT_COMPLETED_DATE", // "CONSENT_CONSENT_DOWNLOADED_ID"? /* * int consentComponentIndex = csvReader.getIndex("CONSENT_STUDY_COMP_ID"); int consentComponentStatusIndex = * csvReader.getIndex("CONSENT_STUDY_COMP_STATUS_ID"); int consentStatusIndex = csvReader.getIndex("CONSENT_CONSENT_STATUS_ID"); int * consentTypeIndex = csvReader.getIndex("CONSENT_CONSENT_TYPE_ID"); int consentDateIndex = csvReader.getIndex("CONSENT_CONSENT_DATE"); int * consentByIndex = csvReader.getIndex("CONSENT_CONSENTED_BY"); int consentCommentsIndex = csvReader.getIndex("CONSENT_COMMENTS"); int * consentRequestedDateIndex = csvReader.getIndex("CONSENT_REQUESTED_DATE"); int consentReceivedDateIndex = * csvReader.getIndex("CONSENT_RECEIVED_DATE"); int consentCompletedDateIndex = csvReader.getIndex("CONSENT_COMPLETED_DATE"); //??? * "CONSENT_CONSENT_DOWNLOADED_ID"; * * * * * "CONSENT_TO_ACTIVE_CONTACT_ID", "CONSENT_TO_PASSIVE_DATA_GATHERING_ID", "CONSENT_TO_USE_DATA_ID", "CONSENT_STATUS_ID", "CONSENT_TYPE_ID", * "CONSENT_DATE", "CONSENT_DOWNLOADED" consent_option c_o c_o c_status c_type date study.yes_no each of these appears to have a link to * consent_option table which has a number 1-6 for id each representing a status...there appears to be no default...therefore may need * validation * * the diffrence being consent statuys and consent type link to consent_status and consent_type tables...so look ups and validation needed */ boolean autoConsent = study.getAutoConsent(); SubjectStatus defaultSubjectStatus = iStudyService.getDefaultSubjectStatus(); TitleType defaultTitleType = iStudyService.getDefaultTitleType(); AddressType defaultAddressType = iStudyService.getDefaultAddressType(); AddressStatus defaultAddressStatus = iStudyService.getDefaultAddressStatus(); PhoneType defaultPhoneType = iStudyService.getDefaultPhoneType(); PhoneStatus defaultPhoneStatus = iStudyService.getDefaultPhoneStatus(); GenderType defaultGenderType = iStudyService.getDefaultGenderType(); VitalStatus defaultVitalStatus = iStudyService.getDefaultVitalStatus(); MaritalStatus defaultMaritalStatus = iStudyService.getDefaultMaritalStatus(); EmailStatus defaultEmailStatus = iStudyService.getDefaultEmailStatus(); ConsentOption concentOptionOfYes = iStudyService.getConsentOptionForBoolean(true);// sounds a lot like boolean blah = true???? ConsentStatus consentStatusOfConsented = iStudyService.getConsentStatusByName("Consented"); ConsentType consentTypeOfElectronic = iStudyService.getConsentTypeByName("Electronic"); List<ConsentOption> consentOptionsPossible = iStudyService.getConsentOptions(); List<ConsentStatus> consentStatusPossible = iStudyService.getConsentStatus(); List<ConsentType> consentTypePossible = iStudyService.getConsentType(); List<LinkSubjectStudy> allSubjectWhichWillBeUpdated = null; if (uidsWhichNeedUpdating.size() > 0) { // TODO analyse performance of bringing all back and having to iterate everytime, vs conditional query + looping through less // TODO analyze performance of getting that big list of UIDs and doing a .contains(subjectuid) VS getting all the entities and doing a // .getSubjectUID.equals(subjectUID) allSubjectWhichWillBeUpdated = iArkCommonService.getUniqueSubjectsWithTheseUIDs(study, uidsWhichNeedUpdating); } else { allSubjectWhichWillBeUpdated = new ArrayList(); } srcLength = inLength; if (srcLength <= 0) { uploadReport.append("ERROR: 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); } csvReader.readHeaders(); srcLength = inLength - csvReader.getHeaders().toString().length(); int firstNameIndex = csvReader.getIndex("FIRST_NAME"); int middleNameIndex = csvReader.getIndex("MIDDLE_NAME"); int lastNameIndex = csvReader.getIndex("LAST_NAME"); int previousLastNameIndex = csvReader.getIndex("PREVIOUS_LAST_NAME"); int preferredNameIndex = csvReader.getIndex("PREFERRED_NAME"); int preferredEmailIndex = csvReader.getIndex("EMAIL"); int preferredEmailStatusIndex = csvReader.getIndex("EMAIL_STATUS"); int otherEmailIndex = csvReader.getIndex("OTHER_EMAIL"); int otherEmailStatusIndex = csvReader.getIndex("OTHER_EMAIL_STATUS"); int heardAboutStudyIndex = csvReader.getIndex("HEARD_ABOUT_STUDY"); int commentsIndex = csvReader.getIndex("COMMENTS"); int titleIndex = csvReader.getIndex("TITLE"); int vitalStatusIndex = csvReader.getIndex("VITAL_STATUS"); int maritalStatusIndex = csvReader.getIndex("MARITAL_STATUS"); int statusIndex = csvReader.getIndex("STATUS"); int addressLine1Index = csvReader.getIndex("BUILDING_NAME"); int addressLine2Index = csvReader.getIndex("STREET_ADDRESS"); int suburbIndex = csvReader.getIndex("SUBURB"); int stateIndex = csvReader.getIndex("STATE"); int countryIndex = csvReader.getIndex("COUNTRY"); int postCodeIndex = csvReader.getIndex("POST_CODE"); int addressSourceIndex = csvReader.getIndex("ADDRESS_SOURCE"); int addressStatusIndex = csvReader.getIndex("ADDRESS_STATUS"); int addressTypeIndex = csvReader.getIndex("ADDRESS_TYPE"); int addressReceivedIndex = csvReader.getIndex("ADDRESS_DATE_RECEIVED"); int addressCommentsIndex = csvReader.getIndex("ADDRESS_COMMENTS"); int isPreferredMailingIndex = csvReader.getIndex("IS_PREFERRED_MAILING_ADDRESS"); int phoneNumberIndex = csvReader.getIndex("PHONE_NUMBER"); int areaCodeIndex = csvReader.getIndex("PHONE_AREA_CODE"); int phoneStatusIndex = csvReader.getIndex("PHONE_STATUS"); int phoneTypeIndex = csvReader.getIndex("PHONE_TYPE"); int phoneSourceIndex = csvReader.getIndex("PHONE_SOURCE"); int phoneCommentsIndex = csvReader.getIndex("PHONE_COMMENTS"); int phoneDateReceivedIndex = csvReader.getIndex("PHONE_DATE_RECEIVED"); int phoneSilentIndex = csvReader.getIndex("SILENT"); // if(PERSON_CONTACT_METHOD is in headers, use it, // else, if CONTACT_METHOD, us IT, else, just set to -1 int personContactIndex = ((csvReader.getIndex("PERSON_CONTACT_METHOD") > 0) ? csvReader.getIndex("PERSON_CONTACT_METHOD") : ((csvReader.getIndex("CONTACT_METHOD") > 0) ? csvReader.getIndex("CONTACT_METHOD") : -1)); int dateOfBirthIndex = ((csvReader.getIndex("DATE_OF_BIRTH") > 0) ? csvReader.getIndex("DATE_OF_BIRTH") : ((csvReader.getIndex("DOB") > 0) ? csvReader.getIndex("DOB") : -1)); int dateOfDeathIndex = ((csvReader.getIndex("DATE_OF_DEATH") > 0) ? csvReader.getIndex("DATE_OF_DEATH") : ((csvReader.getIndex("DODEATH") > 0) ? csvReader.getIndex("DODEATH") : -1)); int dateLastKnownAliveIndex = ((csvReader.getIndex("DATE_LAST_KNOWN_ALIVE") > 0) ? csvReader.getIndex("DATE_LAST_KNOWN_ALIVE") : ((csvReader.getIndex("LAST_KNOWN_ALIVE") > 0) ? csvReader.getIndex("LAST_KNOWN_ALIVE") : -1)); int causeOfDeathIndex = ((csvReader.getIndex("CAUSE_OF_DEATH") > 0) ? csvReader.getIndex("CAUSE_OF_DEATH") : ((csvReader.getIndex("CODEATH") > 0) ? csvReader.getIndex("CODEATH") : -1)); // in reality, validation doesnt permit this yet anyway...but probably not bad to align it over in validation int genderIndex = ((csvReader.getIndex("GENDER_TYPE") > 0) ? csvReader.getIndex("GENDER_TYPE") : ((csvReader.getIndex("GENDER") > 0) ? csvReader.getIndex("GENDER") : ((csvReader.getIndex("SEX") > 0) ? csvReader.getIndex("SEX") : -1))); boolean isAutoGen = study.getAutoGenerateSubjectUid(); while (csvReader.readRecord()) { rowCount++; LinkSubjectStudy subject = null; // Hack to ensure XLS rows contain all cells (ie empty strings for cells after the right-hand non-null value List<String> stringList = new ArrayList<String>(csvReader.getHeaders().length); for (int i = 0; i < csvReader.getHeaders().length; i++) { stringList.add(csvReader.get(i)); } stringLineArray = stringList.toArray(new String[csvReader.getHeaders().length]); String subjectUID = stringLineArray[0]; boolean hasSomeData = false; for (String next : stringLineArray) { if (next != null && !next.isEmpty()) { hasSomeData = true; } } if (!isAutoGen && (subjectUID == null || subjectUID.isEmpty())) { if (!hasSomeData) { uploadReport.append("Warning/Info: Row " + rowCount + ": There appeared to be no data on this row, so we ignored this line"); } else { // THIS SHOULD NEVER EVER HAPPEN IF VALIDATION IS CORRECT uploadReport.append("Error: Row " + rowCount + ": There is no subject UID on this row, " + "yet the study is not set up to auto generate subject UIDs. This line was ignored. Please remove this line or provide an ID"); } } else if (isAutoGen && (subjectUID == null || subjectUID.isEmpty()) && !hasSomeData) { uploadReport.append("Warning/Info: Row " + rowCount + ": There appeared to be no data on this row, so we ignored this line"); } else { subject = getSubjectByUIDFromExistList(allSubjectWhichWillBeUpdated, subjectUID); boolean thisSubjectAlreadyExists = (subject != null); Person person = null; if (thisSubjectAlreadyExists) { person = subject.getPerson(); } else { subject = new LinkSubjectStudy(); subject.setSubjectUID(subjectUID);// note: this will be overwritten IF study.isautogenerate subject.setStudy(study); person = new Person(); } if (firstNameIndex > 0) person.setFirstName(stringLineArray[firstNameIndex]); if (heardAboutStudyIndex > 0) subject.setHeardAboutStudy(stringLineArray[heardAboutStudyIndex]); if (commentsIndex > 0) subject.setComment(stringLineArray[commentsIndex]); if (middleNameIndex > 0) person.setMiddleName(stringLineArray[middleNameIndex]); if (lastNameIndex > 0) { String lastnameFromFile = stringLineArray[lastNameIndex]; if (thisSubjectAlreadyExists && lastnameFromFile != null && !lastnameFromFile.isEmpty() && !lastnameFromFile.equalsIgnoreCase(person.getLastName()) && person.getLastName() != null) { PersonLastnameHistory personLastNameHistory = new PersonLastnameHistory(); personLastNameHistory.setPerson(person); personLastNameHistory.setLastName(person.getLastName()); person.getPersonLastnameHistory().add(personLastNameHistory);// TODO analyze this } else if (!thisSubjectAlreadyExists) { if (previousLastNameIndex > 0) { String previousLastName = (stringLineArray[previousLastNameIndex]); if (previousLastName != null && !previousLastName.isEmpty()) { PersonLastnameHistory personLastNameHistory = new PersonLastnameHistory(); personLastNameHistory.setPerson(person); personLastNameHistory.setLastName(previousLastName); person.getPersonLastnameHistory().add(personLastNameHistory); } } } person.setLastName(lastnameFromFile); } else { // just in the odd instance of no last name but has previous lastname known if (!thisSubjectAlreadyExists) { if (previousLastNameIndex > 0) { String previousLastName = (stringLineArray[previousLastNameIndex]); if (previousLastName != null && !previousLastName.isEmpty()) { PersonLastnameHistory personLastNameHistory = new PersonLastnameHistory(); personLastNameHistory.setPerson(person); personLastNameHistory.setLastName(previousLastName); person.getPersonLastnameHistory().add(personLastNameHistory); } } } } if (preferredNameIndex > 0) { person.setPreferredName(stringLineArray[preferredNameIndex]); } if (genderIndex > 0) { if (stringLineArray[genderIndex] != null && stringLineArray[genderIndex].length() > 0) { for (GenderType boygirl : genderTypesPossible) { if (boygirl.getName().equalsIgnoreCase(stringLineArray[genderIndex])) { person.setGenderType(boygirl); } } } if (person.getGenderType() == null || StringUtils.isBlank(person.getGenderType().getName())) { person.setGenderType(defaultGenderType); } } if (person.getGenderType() == null) { person.setGenderType(defaultGenderType); } if (dateOfBirthIndex > 0) { Date dateOfBirth = new Date(); if (stringLineArray[dateOfBirthIndex] != null && stringLineArray[dateOfBirthIndex].length() > 0) { dateOfBirth = simpleDateFormat.parse(stringLineArray[dateOfBirthIndex]); person.setDateOfBirth(dateOfBirth); } } if (dateOfDeathIndex > 0) { Date dateOfDeath = new Date(); if (stringLineArray[dateOfDeathIndex] != null && stringLineArray[dateOfDeathIndex].length() > 0) { dateOfDeath = simpleDateFormat.parse(stringLineArray[dateOfDeathIndex]); person.setDateOfDeath(dateOfDeath); } } if (dateLastKnownAliveIndex > 0) { Date dateLastKnownAlive = new Date(); if (stringLineArray[dateLastKnownAliveIndex] != null && stringLineArray[dateLastKnownAliveIndex].length() > 0) { dateLastKnownAlive = simpleDateFormat.parse(stringLineArray[dateLastKnownAliveIndex]); person.setDateLastKnownAlive(dateLastKnownAlive); } } if (causeOfDeathIndex > 0) { if (stringLineArray[causeOfDeathIndex] != null && stringLineArray[causeOfDeathIndex].length() > 0) { person.setCauseOfDeath(stringLineArray[causeOfDeathIndex]); } } if (vitalStatusIndex > 0) { String vitalStatusStr = (stringLineArray[vitalStatusIndex]); for (VitalStatus vitalStat : vitalStatiiPossible) { if (vitalStat.getName().equalsIgnoreCase(vitalStatusStr)) { person.setVitalStatus(vitalStat); } } if (person.getVitalStatus() == null || StringUtils.isBlank(person.getVitalStatus().getName())) { person.setVitalStatus(defaultVitalStatus); } } if (person.getVitalStatus() == null) { person.setVitalStatus(defaultVitalStatus); } if (preferredEmailIndex > 0) { person.setPreferredEmail(stringLineArray[preferredEmailIndex]); } if (otherEmailIndex > 0) { person.setOtherEmail(stringLineArray[otherEmailIndex]); } if (preferredEmailStatusIndex > 0) { String preferredEmailStatusStr = (stringLineArray[preferredEmailStatusIndex]); for (EmailStatus possibleEmailStat : emailStatiiPossible) { if (possibleEmailStat.getName().equalsIgnoreCase(preferredEmailStatusStr)) { person.setPreferredEmailStatus(possibleEmailStat); } } if (person.getPreferredEmailStatus() == null || StringUtils.isBlank(person.getPreferredEmailStatus().getName())) { person.setPreferredEmailStatus(defaultEmailStatus); } } if (person.getPreferredEmailStatus() == null) { person.setPreferredEmailStatus(defaultEmailStatus); } if (otherEmailStatusIndex > 0) { String OtherEmailStatusStr = (stringLineArray[otherEmailStatusIndex]); for (EmailStatus possibleEmailStat : emailStatiiPossible) { if (possibleEmailStat.getName().equalsIgnoreCase(OtherEmailStatusStr)) { person.setOtherEmailStatus(possibleEmailStat); } } if (person.getOtherEmailStatus() == null || StringUtils.isBlank(person.getOtherEmailStatus().getName())) { person.setOtherEmailStatus(defaultEmailStatus); } } if (person.getOtherEmailStatus() == null) { person.setOtherEmailStatus(defaultEmailStatus); } if (titleIndex > 0) { String titleStr = (stringLineArray[titleIndex]); for (TitleType titleType : titleTypesPossible) { if (titleType.getName().equalsIgnoreCase(titleStr)) { person.setTitleType(titleType); } } if (person.getTitleType() == null || StringUtils.isBlank(person.getTitleType().getName())) { person.setTitleType(defaultTitleType); } } if (person.getTitleType() == null) { person.setTitleType(defaultTitleType); } if (maritalStatusIndex > 0) { String maritalStatusStr = (stringLineArray[maritalStatusIndex]); for (MaritalStatus maritalStat : maritalStatiiPossible) { if (maritalStat.getName().equalsIgnoreCase(maritalStatusStr)) { person.setMaritalStatus(maritalStat); } } if (person.getMaritalStatus() == null || StringUtils.isBlank(person.getMaritalStatus().getName())) { person.setMaritalStatus(defaultMaritalStatus); } } if (person.getMaritalStatus() == null) { person.setMaritalStatus(defaultMaritalStatus); } if (personContactIndex > 0) { String personContactMethodStr = null; personContactMethodStr = (stringLineArray[personContactIndex]); for (PersonContactMethod possibleMethod : personContactMethodPossible) { if (possibleMethod.getName().equalsIgnoreCase(personContactMethodStr)) { person.setPersonContactMethod(possibleMethod); } } // TODO if we get to the end and personcontactmethod doesnt exist...what do we do? do we want a default or does it get ignored } if (statusIndex > 0) { String statusStr = (stringLineArray[statusIndex]); for (SubjectStatus subjectStat : subjectStatiiPossible) { if (subjectStat.getName().equalsIgnoreCase(statusStr)) { subject.setSubjectStatus(subjectStat); } } if (subject.getSubjectStatus() == null || StringUtils.isBlank(subject.getSubjectStatus().getName())) { subject.setSubjectStatus(defaultSubjectStatus); } } else { subject.setSubjectStatus(defaultSubjectStatus); } // if the study is autoconsent...then there are some defaults we have to set TODO get rid of hardcoding subject.setUpdateConsent(false); if (autoConsent && subject.getSubjectStatus().getName().equalsIgnoreCase("Subject")) { subject.setConsentDate(new Date()); subject.setConsentStatus(consentStatusOfConsented); subject.setConsentType(consentTypeOfElectronic); ConsentOption defaultConsentOption = concentOptionOfYes; subject.setConsentToActiveContact(defaultConsentOption); subject.setConsentToPassiveDataGathering(defaultConsentOption); subject.setConsentToUseData(defaultConsentOption); } else { // Manual Consent details String consentDate = csvReader.get("CONSENT_DATE"); String consentStatusStr = csvReader.get("CONSENT_STATUS"); String consentTypeStr = csvReader.get("CONSENT_TYPE"); String passiveDataStr = csvReader.get("CONSENT_TO_PASSIVE_DATA_GATHERING"); String activeContactStr = csvReader.get("CONSENT_TO_ACTIVE_CONTACT"); String useDataStr = csvReader.get("CONSENT_TO_USE_DATA"); if (!consentDate.isEmpty() || !consentStatusStr.isEmpty() || !consentTypeStr.isEmpty() || !passiveDataStr.isEmpty() || !activeContactStr.isEmpty() || !useDataStr.isEmpty()) { LinkSubjectStudy newSubject = new LinkSubjectStudy(); if (!consentDate.isEmpty()) { newSubject.setConsentDate(simpleDateFormat.parse(consentDate)); } if (!consentStatusStr.isEmpty()) { for (ConsentStatus consentStatus : consentStatusPossible) { if (consentStatus.getName().equalsIgnoreCase(consentStatusStr)) { newSubject.setConsentStatus(consentStatus); } } } if (!consentTypeStr.isEmpty()) { for (ConsentType consentType : consentTypePossible) { if (consentType.getName().equalsIgnoreCase(consentTypeStr)) { newSubject.setConsentType(consentType); } } } if (!passiveDataStr.isEmpty() || !activeContactStr.isEmpty() || !useDataStr.isEmpty()) { for (ConsentOption consentOption : consentOptionsPossible) { if (consentOption.getName().equalsIgnoreCase(passiveDataStr)) { newSubject.setConsentToPassiveDataGathering(consentOption); } if (consentOption.getName().equalsIgnoreCase(activeContactStr)) { newSubject.setConsentToActiveContact(consentOption); } if (consentOption.getName().equalsIgnoreCase(useDataStr)) { newSubject.setConsentToUseData(consentOption); } } } if (thisSubjectAlreadyExists) { // Existing Subject to compare if consent actually changed (inherently handles when no consent previously) LinkSubjectStudyConsentHistoryComparator comparator = new LinkSubjectStudyConsentHistoryComparator(); if (comparator.compare(subject, newSubject) != 0) { subject.setUpdateConsent(true); subject.setConsentDate(newSubject.getConsentDate()); subject.setConsentStatus(newSubject.getConsentStatus()); subject.setConsentType(newSubject.getConsentType()); subject.setConsentToPassiveDataGathering( newSubject.getConsentToPassiveDataGathering()); subject.setConsentToActiveContact(newSubject.getConsentToActiveContact()); subject.setConsentToUseData(newSubject.getConsentToUseData()); } else { subject.setUpdateConsent(false); } } else { // New Subject with consent details subject.setConsentDate(newSubject.getConsentDate()); subject.setConsentStatus(newSubject.getConsentStatus()); subject.setConsentType(newSubject.getConsentType()); subject.setConsentToPassiveDataGathering( newSubject.getConsentToPassiveDataGathering()); subject.setConsentToActiveContact(newSubject.getConsentToActiveContact()); subject.setConsentToUseData(newSubject.getConsentToUseData()); } } } // if no address info - ignore if (addressLine1Index > 0 || addressLine1Index > 0) { boolean updateAddress = false; String address1String = stringLineArray[addressLine1Index]; String address2String = stringLineArray[addressLine2Index]; String suburb = stringLineArray[suburbIndex]; String countryString = stringLineArray[countryIndex]; String stateString = stringLineArray[stateIndex]; String postCode = stringLineArray[postCodeIndex]; if ((address1String == null || StringUtils.isBlank(address1String)) && (address2String == null || StringUtils.isBlank(address2String)) && (suburb == null || StringUtils.isBlank(suburb)) && (postCode == null || StringUtils.isBlank(postCode)) && (countryString == null || StringUtils.isBlank(countryString)) && (stateString == null || StringUtils.isBlank(stateString))) { // then lets just jump out as there is no address to validate. lay down to user that they must have data if they want an update } else { boolean usingDefaultType = false; boolean usingDefaultStatus = false; Address addressToAttachToPerson = null; if (thisSubjectAlreadyExists) { String typeString = null; String statusString = null; if (addressTypeIndex > 0) { typeString = stringLineArray[addressTypeIndex]; if (typeString == null || typeString.isEmpty()) { typeString = defaultAddressType.getName(); usingDefaultType = true; } } if (addressStatusIndex > 0) { statusString = stringLineArray[addressStatusIndex]; if (statusString == null || statusString.isEmpty()) { statusString = defaultPhoneStatus.getName(); usingDefaultStatus = true; } } for (Address a : person.getAddresses()) { if (a.getAddressStatus().getName().equalsIgnoreCase(statusString) && a.getAddressType().getName().equalsIgnoreCase(typeString)) { addressToAttachToPerson = a; updateAddress = true; } } } if (addressToAttachToPerson == null) { log.info("address was null"); addressToAttachToPerson = new Address(); } else { log.info("address was not null"); } AddressType type = findAddressType(addressTypesPossible, stringLineArray[addressTypeIndex]); if (type == null) { type = defaultAddressType; usingDefaultType = true; } AddressStatus status = findAddressStatus(addressStatiiPossible, stringLineArray[addressTypeIndex]); if (status == null) { status = defaultAddressStatus; usingDefaultStatus = true; } String addressComments = stringLineArray[addressCommentsIndex]; Country country = findCountry(countriesPossible, countryString); if (country != null) { addressToAttachToPerson.setCountry(country); // TODO one option: all possible states locally and test where it matches might work...or lets see how the entity goes first, // and if it hits db again! // State state = findState(statesPossible, stateString, country); State state = findStateWithinThisCountry(stateString, country); if (state == null) { uploadReport.append("Warning/Info: could not find a state named '" + stateString + "' in " + country.getName() + " for row " + rowCount + ", but will proceed.\n"); addressToAttachToPerson.setOtherState(stateString); } else { addressToAttachToPerson.setState(state); } } else { uploadReport.append("Warning/Info: Could not find country '" + countryString + " for row " + rowCount + ", but will proceed.\n"); } String addressSource = stringLineArray[addressSourceIndex]; String dateReceivedString = stringLineArray[addressReceivedIndex]; String isPreferredMailingString = stringLineArray[isPreferredMailingIndex]; addressToAttachToPerson.setAddressType(type); addressToAttachToPerson.setAddressStatus(status); if (postCode != null && !postCode.isEmpty()) addressToAttachToPerson.setPostCode(postCode); if (address1String != null && !address1String.isEmpty()) addressToAttachToPerson.setAddressLineOne(address1String); if (address2String != null && !address2String.isEmpty()) addressToAttachToPerson.setStreetAddress(address2String);// yeah.. if (dateReceivedString != null && !dateReceivedString.isEmpty()) { // TODO dateconvert and set Date dateReceived = new Date(); dateReceived = simpleDateFormat.parse(dateReceivedString); addressToAttachToPerson.setDateReceived(dateReceived); } if (suburb != null && !suburb.isEmpty()) addressToAttachToPerson.setCity(suburb); if (addressComments != null && !addressComments.isEmpty()) addressToAttachToPerson.setComments(addressComments); if (DataConversionAndManipulationHelper .isSomethingLikeABoolean(isPreferredMailingString)) { if (DataConversionAndManipulationHelper .isSomethingLikeTrue(isPreferredMailingString)) { // isPreferredMailingString!=null && // !isPreferredMailingString.isEmpty()){ addressToAttachToPerson.setPreferredMailingAddress(true); } else { addressToAttachToPerson.setPreferredMailingAddress(false); } } else { addressToAttachToPerson.setPreferredMailingAddress(false); } if (usingDefaultStatus && usingDefaultType) { uploadReport .append("Info: Using the default status '" + defaultAddressStatus.getName() + "' and the default type '" + defaultAddressType.getName() + " for row " + rowCount + ", but will proceed.\n"); } else if (usingDefaultType) { uploadReport.append("Info: Using the default type '" + defaultAddressType.getName() + "' for row " + rowCount + ", but will proceed.\n"); } else if (usingDefaultStatus) { uploadReport .append("Info: Using the default status '" + defaultAddressStatus.getName() + " for row " + rowCount + ", but will proceed.\n"); } if (addressSource != null && !addressSource.isEmpty()) addressToAttachToPerson.setSource(addressSource); if (!updateAddress) { // TODO check this works in all cases addressToAttachToPerson.setPerson(person); person.getAddresses().add(addressToAttachToPerson); } } } // if no address info - ignore if (phoneNumberIndex > 0) { boolean updatePhones = false; boolean usingDefaultType = false; boolean usingDefaultStatus = false; String phoneNumberString = stringLineArray[phoneNumberIndex]; if (phoneNumberString == null || StringUtils.isBlank(phoneNumberString)) { // then lets just jump out as there is no phone to validate. lay down to user that they must have data if they want an update } else { Phone phoneToAttachToPerson = null; if (thisSubjectAlreadyExists) { String typeString = null; String statusString = null; if (phoneTypeIndex > 0) { typeString = stringLineArray[phoneTypeIndex]; if (typeString == null || typeString.isEmpty()) { typeString = defaultPhoneType.getName(); usingDefaultType = true; } } if (phoneStatusIndex > 0) { statusString = stringLineArray[phoneStatusIndex]; if (statusString == null || statusString.isEmpty()) { statusString = defaultPhoneStatus.getName(); usingDefaultStatus = true; } } for (Phone phone : person.getPhones()) { if (phone.getPhoneStatus().getName().equalsIgnoreCase(statusString) && phone.getPhoneType().getName().equalsIgnoreCase(typeString)) { phoneToAttachToPerson = phone; updatePhones = true; } } } if (phoneToAttachToPerson == null) { phoneToAttachToPerson = new Phone(); } PhoneType type = findPhoneTypeOrSetDefault(phoneTypesPossible, defaultPhoneType, stringLineArray[phoneTypeIndex]); PhoneStatus status = findPhoneStatusOrSetDefault(phoneStatiiPossible, defaultPhoneStatus, stringLineArray[phoneTypeIndex]); String phoneComments = stringLineArray[phoneCommentsIndex]; String areaCode = stringLineArray[areaCodeIndex]; String silentString = stringLineArray[phoneSilentIndex]; String phoneSource = stringLineArray[phoneSourceIndex]; String phoneDateReceivedString = stringLineArray[phoneDateReceivedIndex]; // log.warn("phone Date Reveived = " + phoneDateReceivedString + " for index = " + phoneDateReceivedIndex); phoneToAttachToPerson.setPhoneType(type); phoneToAttachToPerson.setPhoneStatus(status); if (areaCode != null && !areaCode.isEmpty()) phoneToAttachToPerson.setAreaCode(areaCode); if (phoneNumberString != null && !phoneNumberString.isEmpty()) phoneToAttachToPerson.setPhoneNumber(phoneNumberString); if (phoneDateReceivedString != null && !phoneDateReceivedString.isEmpty()) { // TODO dateconvert and set Date dateReceived = new Date(); dateReceived = simpleDateFormat.parse(phoneDateReceivedString); phoneToAttachToPerson.setDateReceived(dateReceived); } if (DataConversionAndManipulationHelper.isSomethingLikeABoolean(silentString)) { if (DataConversionAndManipulationHelper.isSomethingLikeTrue(silentString)) { phoneToAttachToPerson.setSilentMode(yes); } else { phoneToAttachToPerson.setSilentMode(no); } } if (phoneComments != null && !phoneComments.isEmpty()) phoneToAttachToPerson.setComment(phoneComments); if (phoneSource != null && !phoneSource.isEmpty()) phoneToAttachToPerson.setSource(phoneSource); if (usingDefaultStatus && usingDefaultType) { uploadReport .append("Info: Using the default status '" + defaultAddressStatus.getName() + "' and the default type '" + defaultAddressType.getName() + " for row " + rowCount + ", but will proceed.\n"); } else if (usingDefaultType) { uploadReport.append("Info: Using the default type '" + defaultAddressType.getName() + "' for row " + rowCount + ", but will proceed.\n"); } else if (usingDefaultStatus) { uploadReport .append("Info: Using the default status '" + defaultAddressStatus.getName() + " for row " + rowCount + ", but will proceed.\n"); } if (!updatePhones) { // TODO check this works in all cases phoneToAttachToPerson.setPerson(person); person.getPhones().add(phoneToAttachToPerson); } } } /* * * * //if no address info - ignore if(consentByIndex >0 && consentCompletedDateIndex >0 && consentDateIndex >0 && * consentCompletedDateIndex >0 && consentCompletedDateIndex >0 && consentCompletedDateIndex >0 && consentCompletedDateIndex >0 && * consentCompletedDateIndex >0 ){ * * * * * boolean updatePhones= false; boolean usingDefaultType = false; boolean usingDefaultStatus = false; String phoneNumberString = * stringLineArray[phoneNumberIndex]; * * if(phoneNumberString == null || StringUtils.isBlank(phoneNumberString)){ //then lets just jump out as there is no phone to validate. * lay down to user that they must have data if they want an update } else{ Phone phoneToAttachToPerson = null; * if(thisSubjectAlreadyExists){ String typeString = null; String statusString = null; * * if (phoneTypeIndex > 0){ typeString = stringLineArray[phoneTypeIndex]; if(typeString==null || typeString.isEmpty()){ typeString = * defaultPhoneType.getName(); usingDefaultType = true; } } if (phoneStatusIndex > 0){ statusString = * stringLineArray[phoneStatusIndex]; if(statusString==null || statusString.isEmpty()){ statusString = defaultPhoneStatus.getName(); * usingDefaultStatus = true; } } for(Phone phone : person.getPhones()){ * if(phone.getPhoneStatus().getName().equalsIgnoreCase(statusString) && phone.getPhoneType().getName().equalsIgnoreCase(typeString)){ * phoneToAttachToPerson = phone; updatePhones = true; } } } if(phoneToAttachToPerson==null){ phoneToAttachToPerson = new Phone(); } * * PhoneType type = findPhoneTypeOrSetDefault(phoneTypesPossible, defaultPhoneType, stringLineArray[phoneTypeIndex]); PhoneStatus * status = findPhoneStatusOrSetDefault(phoneStatiiPossible, defaultPhoneStatus, stringLineArray[phoneTypeIndex]); String phoneComments * = stringLineArray[phoneCommentsIndex]; * * String areaCode = stringLineArray[areaCodeIndex]; String silentString = stringLineArray[phoneSilentIndex]; String phoneSource = * stringLineArray[phoneSourceIndex]; String phoneDateReceivedString = stringLineArray[phoneDateReceivedIndex]; * //log.warn("phone Date Reveived = " + phoneDateReceivedString + " for index = " + phoneDateReceivedIndex); * * phoneToAttachToPerson.setPhoneType(type); phoneToAttachToPerson.setPhoneStatus(status); if(areaCode!=null && !areaCode.isEmpty()) * phoneToAttachToPerson.setAreaCode(areaCode); if(phoneNumberString !=null && !phoneNumberString.isEmpty()) * phoneToAttachToPerson.setPhoneNumber(phoneNumberString); if(phoneDateReceivedString!=null && !phoneDateReceivedString.isEmpty()){ // * TODO dateconvert and set Date dateReceived = new Date(); dateReceived = simpleDateFormat.parse(phoneDateReceivedString); * phoneToAttachToPerson.setDateReceived(dateReceived); } * * if(DataConversionAndManipulationHelper.isSomethingLikeABoolean(silentString)){ * if(DataConversionAndManipulationHelper.isSomethingLikeTrue(silentString)){ phoneToAttachToPerson.setSilentMode(yes); } else{ * phoneToAttachToPerson.setSilentMode(no); } } if(phoneComments!=null && !phoneComments.isEmpty()) * phoneToAttachToPerson.setComment(phoneComments); if(phoneSource!=null && !phoneSource.isEmpty()) * phoneToAttachToPerson.setSource(phoneSource); * * * if(usingDefaultStatus && usingDefaultType){ uploadReport.append("Info: Using the default status '" + defaultAddressStatus.getName() * + "' and the default type '" + defaultAddressType.getName() + " for row " + rowCount + ", but will proceed.\n"); } else * if(usingDefaultType){ uploadReport.append("Info: Using the default type '" + defaultAddressType.getName() + "' for row " + rowCount * + ", but will proceed.\n"); } else if(usingDefaultStatus){ uploadReport.append("Info: Using the default status '" + * defaultAddressStatus.getName() + " for row " + rowCount + ", but will proceed.\n"); } * * if(!updatePhones){ //TODO check this works in all cases phoneToAttachToPerson.setPerson(person); * person.getPhones().add(phoneToAttachToPerson); } } } */ subject.setPerson(person); if (subject.getId() == null || subject.getPerson().getId() == 0) { insertSubjects.add(subject); /* * StringBuffer sb = new StringBuffer(); //does this report have to happen? ... and in reality it hasnt had success yet * sb.append("\nCreated subject from original Subject UID: "); sb.append(subject.getSubjectUID()); * //sb.append(" has been created successfully and linked to the study: "); //sb.append(study.getName()); //sb.append("\n"); * uploadReport.append(sb); */ insertCount++; } else { // iStudyService.updateSubject(subjectVo); updateSubjects.add(subject); /* * StringBuffer sb = new StringBuffer(); sb.append("\nUpdate subject with Subject UID: "); sb.append(subject.getSubjectUID()); * //sb.append(" has been updated successfully and linked to the study: "); //sb.append(study.getName()); //sb.append("\n"); * uploadReport.append(sb); */ updateCount++; } subjectCount++; } } } catch (IOException ioe) { uploadReport.append("System Error: Unexpected I/O exception whilst reading the subject data file\n"); log.error("processMatrixSubjectFile IOException stacktrace:", ioe); throw new ArkSystemException("Unexpected I/O exception whilst reading the subject data file"); } catch (Exception ex) { uploadReport.append("System Error: Unexpected exception whilst reading the subject data file\n"); log.error("processMatrixSubjectFile Exception stacktrace:", ex); throw new ArkSystemException("Unexpected exception occurred when trying to process subject data file"); } finally { uploadReport.append("Total file size: "); uploadReport.append(decimalFormat.format(inLength / 1024.0 / 1024.0)); uploadReport.append(" MB"); uploadReport.append("\n"); 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(subjectCount); uploadReport.append(" rows for "); uploadReport.append(subjectCount); * uploadReport.append(" subjects."); uploadReport.append("\n"); uploadReport.append(insertCount); * uploadReport.append(" fields were inserted."); uploadReport.append("\n"); uploadReport.append(updateCount); * uploadReport.append(" fields were updated."); uploadReport.append("\n"); */ uploadReport.append("Processed "); uploadReport.append(subjectCount); uploadReport.append(" rows."); uploadReport.append("\n"); uploadReport.append("Inserted "); uploadReport.append(insertCount); uploadReport.append(" subjects."); uploadReport.append("\n"); uploadReport.append("Updated "); uploadReport.append(updateCount); uploadReport.append(" subjects."); uploadReport.append("\n"); // TODO better exceptionhandling iStudyService.processBatch(insertSubjects, study, updateSubjects); return uploadReport; }
From source file:s3.com.qiniu.services.s3.AmazonS3Client.java
/** * Calculate the content length of a mark supported input stream. * * @param is input stream/*from w w w . j ava2 s .c o m*/ * @return length of the input stream */ private long calculateContentLength(InputStream is) { long len = 0; byte[] buf = new byte[8 * 1024]; int read; is.mark(-1); try { while ((read = is.read(buf)) != -1) { len += read; } is.reset(); } catch (IOException ioe) { throw new AmazonClientException("Could not calculate content length.", ioe); } return len; }
From source file:org.lockss.servlet.ServeContent.java
/** * Check whether the input stream is to a publisher's html permission page. * Throws a CacheExcepiton.PermissionException if so; otherwise returns an * input stream positioned at the same position. The original input stream * will be closed if a new one is created. * * @param input an input stream//from w ww . ja va 2 s .c o m * @param headers a set of header properties * @return an input stream positioned at the same position as the original * one if the original stream is not a login page * @throws CacheException.PermissionException if the connection is to a * login page or the LoginPageChecker for the plugin reported an error * @throws IOException if IO error while checking the stream */ private InputStream checkLoginPage(InputStream input, CIProperties headers) throws CacheException.PermissionException, IOException { LoginPageChecker checker = au.getLoginPageChecker(); if (checker != null) { InputStream oldInput = input; // buffer html page stream to allow login page checker to read it int limit = CurrentConfig.getIntParam(BaseUrlFetcher.PARAM_LOGIN_CHECKER_MARK_LIMIT, BaseUrlFetcher.DEFAULT_LOGIN_CHECKER_MARK_LIMIT); DeferredTempFileOutputStream dos = new DeferredTempFileOutputStream(limit); try { StreamUtil.copy(input, dos); if (dos.isInMemory()) { input = new ByteArrayInputStream(dos.getData()); } else { // create an input stream whose underlying file is deleted // when the input stream closes. File tempFile = dos.getFile(); try { input = new FileInputStream(tempFile); } catch (FileNotFoundException fnfe) { FileUtils.deleteQuietly(tempFile); throw fnfe; } } } finally { IOUtil.safeClose(oldInput); IOUtil.safeClose(dos); } // create reader for input stream String ctype = headers.getProperty("Content-Type"); String charset = HeaderUtil.getCharsetOrDefaultFromContentType(ctype); try { Reader reader = new InputStreamReader(input, charset); if (checker.isLoginPage(headers, reader)) { IOUtil.safeClose(input); input = null; throw new CacheException.PermissionException("Found a login page"); } } catch (PluginException e) { CacheException.PermissionException ex = new CacheException.PermissionException( "Error checking login page"); ex.initCause(e); IOUtil.safeClose(input); input = null; throw ex; } finally { if (input == null) { // delete the temp file immediately if not returning an input // stream open on it dos.deleteTempFile(); } else if (dos.isInMemory()) { input.reset(); } else { // special treatment because cannot reset FileInputStream, // so must close and re-open input stream from temp file IOUtil.safeClose(input); input = new DeleteFileOnCloseInputStream(dos.getFile()); } } } return input; }
From source file:org.sakaiproject.tool.assessment.facade.AssessmentGradingFacadeQueries.java
private byte[] getMediaStream(Long mediaId) { byte[] b = new byte[4000]; Session session = null;//from w w w . j a va 2 s.c o m Connection conn = null; InputStream in = null; ResultSet rs = null; PreparedStatement statement = null; try { session = getSessionFactory().openSession(); conn = session.connection(); log.debug("****Connection=" + conn); String query = "select MEDIA from SAM_MEDIA_T where MEDIAID=?"; statement = conn.prepareStatement(query); statement.setLong(1, mediaId.longValue()); rs = statement.executeQuery(); if (rs.next()) { java.lang.Object o = rs.getObject("MEDIA"); if (o != null) { in = rs.getBinaryStream("MEDIA"); in.mark(0); int ch; int len = 0; while ((ch = in.read()) != -1) { len++; } b = new byte[len]; in.reset(); in.read(b, 0, len); } } } catch (Exception e) { log.warn(e.getMessage()); } finally { if (session != null) { try { session.close(); } catch (Exception e1) { e1.printStackTrace(); } } if (rs != null) { try { rs.close(); } catch (Exception e1) { e1.printStackTrace(); } } if (statement != null) { try { statement.close(); } catch (Exception e1) { e1.printStackTrace(); } } if (in != null) { try { in.close(); } catch (Exception e1) { e1.printStackTrace(); } } if (conn != null) { try { conn.close(); } catch (Exception e1) { e1.printStackTrace(); } } } return b; }
From source file:org.regenstrief.util.Util.java
/** * Retrieves a Reader for the given InputStream, using the correct character encoding * // w w w . java 2s . c o m * @param is the InputStream * @return the Reader * @throws Exception if an I/O problem occurs **/ public static final Reader getReader(InputStream is) throws Exception { is = getMarkableInputStream(is, 11); final String enc = getEncoding(is, false); is.reset(); if (is instanceof LabeledInputStream) { return new LabeledReader((LabeledInputStream) is, enc); } return new BomReader(is, enc); }
From source file:org.docx4j.openpackaging.io3.Load3.java
/** * Get a Part (except a relationships part), but not its relationships part * or related parts. Useful if you need quick access to just this part. * This can be called directly from outside the library, in which case * the Part will not be owned by a Package until the calling code makes it so. * @see To get a Part and all its related parts, and add all to a package, use * getPart.//from w ww . j a v a 2s . c o m * @param partByteArrays * @param ctm * @param resolvedPartUri * @param rel * @return * @throws Docx4JException including if result is null */ public Part getRawPart(ContentTypeManager ctm, String resolvedPartUri, Relationship rel) throws Docx4JException { Part part = null; InputStream is = null; try { try { log.debug("resolved uri: " + resolvedPartUri); // Get a subclass of Part appropriate for this content type // This will throw UnrecognisedPartException in the absence of // specific knowledge. Hence it is important to get the is // first, as we do above. part = ctm.getPart("/" + resolvedPartUri, rel); log.debug("ctm returned " + part.getClass().getName()); if (part instanceof org.docx4j.openpackaging.parts.ThemePart || part instanceof org.docx4j.openpackaging.parts.DocPropsCorePart || part instanceof org.docx4j.openpackaging.parts.DocPropsCustomPart || part instanceof org.docx4j.openpackaging.parts.DocPropsExtendedPart || part instanceof org.docx4j.openpackaging.parts.CustomXmlDataStoragePropertiesPart || part instanceof org.docx4j.openpackaging.parts.digitalsignature.XmlSignaturePart || part instanceof org.docx4j.openpackaging.parts.JaxbXmlPart) { // Nothing to do here } else if (part instanceof org.docx4j.openpackaging.parts.WordprocessingML.BinaryPart) { log.debug("Detected BinaryPart " + part.getClass().getName()); // Note that this is done lazily, since the below lines are commented out // is = partStore.loadPart( resolvedPartUri); // ((BinaryPart)part).setBinaryData(is); } else if (part instanceof org.docx4j.openpackaging.parts.CustomXmlDataStoragePart) { // ContentTypeManager initially detects them as CustomXmlDataStoragePart; // the below changes as necessary // Is it a part we know? is = partStore.loadPart(resolvedPartUri); try { XMLInputFactory xif = XMLInputFactory.newInstance(); xif.setProperty(XMLInputFactory.IS_SUPPORTING_EXTERNAL_ENTITIES, false); xif.setProperty(XMLInputFactory.SUPPORT_DTD, false); // a DTD is merely ignored, its presence doesn't cause an exception XMLStreamReader xsr = xif.createXMLStreamReader(is); Unmarshaller u = Context.jc.createUnmarshaller(); Object o = u.unmarshal(xsr); log.debug(o.getClass().getName()); PartName name = part.getPartName(); if (o instanceof CoverPageProperties) { part = new DocPropsCoverPagePart(name); ((DocPropsCoverPagePart) part).setJaxbElement((CoverPageProperties) o); } else if (o instanceof org.opendope.conditions.Conditions) { part = new ConditionsPart(name); ((ConditionsPart) part).setJaxbElement((org.opendope.conditions.Conditions) o); } else if (o instanceof org.opendope.xpaths.Xpaths) { part = new XPathsPart(name); ((XPathsPart) part).setJaxbElement((org.opendope.xpaths.Xpaths) o); } else if (o instanceof org.opendope.questions.Questionnaire) { part = new QuestionsPart(name); ((QuestionsPart) part).setJaxbElement((org.opendope.questions.Questionnaire) o); } else if (o instanceof org.opendope.answers.Answers) { part = new StandardisedAnswersPart(name); ((StandardisedAnswersPart) part).setJaxbElement((org.opendope.answers.Answers) o); } else if (o instanceof org.opendope.components.Components) { part = new ComponentsPart(name); ((ComponentsPart) part).setJaxbElement((org.opendope.components.Components) o); } else if (o instanceof JAXBElement<?> && XmlUtils.unwrap(o) instanceof org.docx4j.bibliography.CTSources) { part = new BibliographyPart(name); ((BibliographyPart) part) .setJaxbElement((JAXBElement<org.docx4j.bibliography.CTSources>) o); } else { log.error("TODO: handle known CustomXmlPart part " + o.getClass().getName()); CustomXmlDataStorage data = getCustomXmlDataStorageClass().factory(); is.reset(); data.setDocument(is); // Not necessarily JAXB, that's just our method name ((org.docx4j.openpackaging.parts.CustomXmlDataStoragePart) part).setData(data); } } catch (javax.xml.bind.UnmarshalException ue) { log.warn("No JAXB model for this CustomXmlDataStorage part; " + ue.getMessage()); CustomXmlDataStorage data = getCustomXmlDataStorageClass().factory(); is.reset(); data.setDocument(is); // Not necessarily JAXB, that's just our method name ((org.docx4j.openpackaging.parts.CustomXmlDataStoragePart) part).setData(data); } } else if (part instanceof org.docx4j.openpackaging.parts.XmlPart) { is = partStore.loadPart(resolvedPartUri); // try { ((XmlPart) part).setDocument(is); // Experimental 22/6/2011; don't fall back to binary (which we used to) // } catch (Docx4JException d) { // // This isn't an XML part after all, // // even though ContentTypeManager detected it as such // // So get it as a binary part // part = getBinaryPart(partByteArrays, ctm, resolvedPartUri); // log.warn("Could not parse as XML, so using BinaryPart for " // + resolvedPartUri); // ((BinaryPart)part).setBinaryData(is); // } } else { // Shouldn't happen, since ContentTypeManagerImpl should // return an instance of one of the above, or throw an // Exception. log.error("No suitable part found for: " + resolvedPartUri); part = null; } } catch (PartUnrecognisedException e) { log.error("PartUnrecognisedException shouldn't happen anymore!", e); // Try to get it as a binary part part = getBinaryPart(ctm, resolvedPartUri); log.warn("Using BinaryPart for " + resolvedPartUri); // is = partStore.loadPart( resolvedPartUri); // ((BinaryPart)part).setBinaryData(is); } } catch (Exception ex) { // IOException, URISyntaxException ex.printStackTrace(); throw new Docx4JException("Failed to getPart", ex); } finally { IOUtils.closeQuietly(is); } if (part == null) { throw new Docx4JException( "cannot find part " + resolvedPartUri + " from rel " + rel.getId() + "=" + rel.getTarget()); } return part; }