protected Item createRSSItem(SyndEntry sEntry) { Item item = super.createRSSItem(sEntry); SyndContent sContent = sEntry.getDescription(); if (sContent != null) { item.setDescription(createItemDescription(sContent)); } List contents = sEntry.getContents(); if (contents != null && contents.size() > 0) { SyndContent syndContent = (SyndContent) contents.get(0); Content cont = new Content(); cont.setValue(syndContent.getValue()); cont.setType(syndContent.getType()); item.setContent(cont); } return item; }
private void generateItem(Element conflictElement, Item item) { if (item != null) { Element itemElement = new Element("item"); parentGenerator.populateItem(item, itemElement, 0); parentGenerator.generateItemModules(item.getModules(), itemElement); conflictElement.addContent(itemElement); } }
protected Item parseItem(Element rssRoot, Element eItem) { Item item = super.parseItem(rssRoot, eItem); Element e = eItem.getChild("pubDate", getRSSNamespace()); if (e != null) { item.setPubDate(DateParser.parseDate(e.getText())); } e = eItem.getChild("expirationDate", getRSSNamespace()); if (e != null) { item.setExpirationDate(DateParser.parseDate(e.getText())); } e = eItem.getChild("description", getRSSNamespace()); if (e != null) { String type = e.getAttributeValue("type"); if (type != null) { item.getDescription().setType(type); } } return item; }
protected SyndEntry createSyndEntry(Item item) { SyndEntry syndEntry = super.createSyndEntry(item); Description desc = item.getDescription(); if (desc != null) { SyndContent descContent = new SyndContentImpl(); descContent.setType(desc.getType()); descContent.setValue(desc.getValue()); syndEntry.setDescription(descContent); } Content cont = item.getContent(); if (cont != null) { SyndContent content = new SyndContentImpl(); content.setType(cont.getType()); content.setValue(cont.getValue()); List syndContents = new ArrayList(); syndContents.add(content); syndEntry.setContents(syndContents); } return syndEntry; }
/** * download the rss file from the remote server and populate a list of zeprs id's * * @param urlString * @return a list of zeprs id's on remote site * @throws Exception * @throws ConnectException * @throws NoRouteToHostException */ public static ArrayList<String> populateRemotePatientIdList(String urlString) throws Exception, ConnectException, NoRouteToHostException { // download the rss file from the remote server ArrayList<String> remotePatients = new ArrayList<String>(); URL feedUrl = new URL(urlString); HttpURLConnection httpcon = (HttpURLConnection) feedUrl.openConnection(); boolean isProxied = httpcon.usingProxy(); if (isProxied) { log.debug(" Proxied: " + isProxied); } String encoding = new sun.misc.BASE64Encoder().encode("zepadmin:zepadmin11".getBytes()); httpcon.setRequestProperty("Authorization", "Basic " + encoding); final WireFeedInput input = new WireFeedInput(); WireFeed rssFeed = null; XmlReader reader = null; String message = null; Channel channel = null; try { reader = new XmlReader(httpcon); rssFeed = input.build(reader); rssFeed.setFeedType("rss_2.0"); channel = (Channel) rssFeed; List items = channel.getItems(); for (int i = 0; i < items.size(); i++) { Item item = (Item) items.get(i); String link = item.getLink(); String fileName = item.getTitle(); String zeprsId = fileName.replace(".xml", ""); remotePatients.add(zeprsId); } } catch (SocketException e1) { message = "Unable to connect to host for feed: " + urlString; log.debug(message); } return remotePatients; }
protected Item createRSSItem(SyndEntry sEntry) { Item item = new Item(); item.setModules(ModuleUtils.cloneModules(sEntry.getModules())); item.setTitle(sEntry.getTitle()); item.setLink(sEntry.getLink()); item.setUri(sEntry.getUri()); if (sEntry.getDescription() != null) { Description description = new Description(); description.setValue(sEntry.getDescription().getValue()); item.setDescription(description); } return item; }
protected SyndEntry createSyndEntry(Item item) { SyndEntry syndEntry = new SyndEntryImpl(); syndEntry.setModules(ModuleUtils.cloneModules(item.getModules())); if (((List) item.getForeignMarkup()).size() > 0) { syndEntry.setForeignMarkup(item.getForeignMarkup()); } syndEntry.setUri(item.getUri()); syndEntry.setLink(item.getLink()); syndEntry.setTitle(item.getTitle()); if (item.getDescription() != null) { SyndContent description = new SyndContentImpl(); description.setValue(item.getDescription().getValue()); syndEntry.setDescription(description); } if (item.getAuthor() != null) syndEntry.setAuthor(item.getAuthor()); if (item.getPubDate() != null) syndEntry.setPublishedDate(item.getPubDate()); syndEntry.setCategories(item.getCategories()); return syndEntry; }
/** * Imports patient records from remote pc. * * @param conn * @param urlString - url of feed * @param view - if not 0, simply parses rss feed and provides output. * @param comments - messages generated during import process * @param start - indicates if this is the first time this feed has been imported. * @param siteId - id of site being imported. * @param reload * @param refreshPatientZeprsId * @return status message * @throws Exception */ public static String importFeed( Connection conn, String urlString, Boolean view, StringBuffer comments, Long start, Long siteId, Long reload, String refreshPatientZeprsId) throws Exception, ConnectException, NoRouteToHostException { // download the rss file from the remote server URL feedUrl = new URL(urlString); HttpURLConnection httpcon = (HttpURLConnection) feedUrl.openConnection(); boolean isProxied = httpcon.usingProxy(); if (isProxied) { log.debug(" Proxied: " + isProxied); } // BASE64Encoder is Sun proprietary encoder. Use Apache commons Base64 codec instead. String credentials = new sun.misc.BASE64Encoder().encode("zepadmin:zepadmin11".getBytes()); /*String encodeString = "zepadmin:zepadmin11"; Base64 encoder = new Base64(); String encoding = String.valueOf(encoder.encode(encodeString.getBytes()));*/ httpcon.setRequestProperty("Authorization", "Basic " + credentials); final WireFeedInput input = new WireFeedInput(); WireFeed rssFeed = null; XmlReader reader = null; String message = null; String siteAbbrev = null; Channel channel = null; java.util.Date lastBuildDate = null; Site site = (Site) DynaSiteObjects.getClinicMap().get(siteId); siteAbbrev = site.getAbbreviation(); try { String importFilePath = org.cidrz.webapp.dynasite.Constants.ARCHIVE_PATH + siteAbbrev + Constants.pathSep + "import" + Constants.pathSep; // Save the feed to the local filesystem. This will be used to help the master create its own // feed for this site. BufferedInputStream in = null; in = new BufferedInputStream(httpcon.getInputStream()); String importedRssPath = importFilePath + "rss.xml"; Writer writer = new FileWriter(importedRssPath); for (int c = in.read(); c != -1; c = in.read()) { writer.write(c); } writer.close(); // make a hashmap of zeprs id's:last_modified from database HashMap<String, Timestamp> localPatientMap = new HashMap<String, Timestamp>(); ResultSet updatedPatients = PatientDAO.getAllRS(conn); while (updatedPatients.next()) { String zeprsId = updatedPatients.getString("district_patient_id"); Timestamp lastModified = updatedPatients.getTimestamp("last_modified"); // Long site_id = updatedPatients.getLong("site_id"); String fileName = zeprsId + ".xml"; localPatientMap.put(fileName, lastModified); } int changes = 0; // check what site this pc is publishing Long publisherSiteId = null; Publisher publisher = null; String publisherFile = Constants.ARCHIVE_PATH + "publisher.xml"; try { publisher = (Publisher) XmlUtils.getOne(publisherFile); publisherSiteId = publisher.getSiteId(); } catch (FileNotFoundException e) { // it's ok - file not created yet. } boolean process = true; Timestamp buildDate = null; try { UpdateLog updateLog = (UpdateLog) UpdateLogDAO.getLastUpdate(conn, siteAbbrev); buildDate = updateLog.getBuilddate(); } catch (SQLException e) { e.printStackTrace(); } catch (ServletException e) { e.printStackTrace(); } catch (ObjectNotFoundException e) { // log.debug("No entries in updateLog - this must be a new site subscription for " + // siteAbbrev + ". Forcing import of records for this site. "); log.debug( "No entries in updateLog - this must be a new site subscription for " + siteAbbrev + ". "); // cekelley May 28, 2009 - disabled forced import (reload) of records. Unnecessary and // time-consuming. // reload = Long.valueOf("1"); comments.append("Subscribed to site: " + siteAbbrev + ". "); } File importedRssFile = new File(importedRssPath); reader = new XmlReader(importedRssFile); rssFeed = input.build(reader); rssFeed.setFeedType("rss_2.0"); channel = (Channel) rssFeed; List items = channel.getItems(); siteAbbrev = channel.getTitle(); lastBuildDate = channel.getLastBuildDate(); String previousSiteAbbrev = null; for (int i = 0; i < items.size(); i++) { process = true; Item item = (Item) items.get(i); String link = item.getLink(); String fileName = item.getTitle(); Long clinicHomeId = null; if (item.getAuthor() != null) { clinicHomeId = Long.valueOf(item.getAuthor()); } if (publisherSiteId != null && (publisherSiteId.longValue() != clinicHomeId.longValue()) && !publisher.getSite().getSiteAlphaId().equals("MST")) { process = false; } else if (publisher.getSite().getSiteAlphaId().equals("MST")) { process = true; // MST site will update no matter the sites conti } java.util.Date pubDate = item.getPubDate(); Timestamp lastModifiedTimestamp = localPatientMap.get(fileName); java.util.Date currentLastModified = null; if (lastModifiedTimestamp != null) { currentLastModified = DateUtils.toDate(lastModifiedTimestamp); } if ((DynaSiteObjects.getStatusMap().get("Halt-Feed-Imports") != null) && (DynaSiteObjects.getStatusMap().get("Halt-Feed-Imports").equals("true"))) { log.debug("Halting Feed Imports: Halt-Feed-Imports = true"); break; } site = (Site) DynaSiteObjects.getClinicMap().get(clinicHomeId); try { siteAbbrev = site.getAbbreviation(); previousSiteAbbrev = siteAbbrev; } catch (NullPointerException e) { log.debug( "Site not found for " + fileName + " Setting siteAbbrev to " + previousSiteAbbrev); } URL patientUrl = new URL(link); // if (view == 0) { if (process) { // If imported record's pubDate > most recent buildDate, process. Previously we only // checked if // currentLastModified != pubdate, but that would cause every out-of-date record to be // imported. if (refreshPatientZeprsId != null && (refreshPatientZeprsId.concat(".xml").equals(fileName))) { try { importPatientRecord( currentLastModified, fileName, pubDate, importFilePath, patientUrl, credentials, conn, comments, Long.valueOf(1), siteAbbrev, view); } catch (Exception e) { log.debug(e); } } else { if ((reload != null) || (view) || (currentLastModified == null) || (buildDate == null) || (buildDate != null && pubDate.getTime() > buildDate.getTime())) { changes++; try { importPatientRecord( currentLastModified, fileName, pubDate, importFilePath, patientUrl, credentials, conn, comments, reload, siteAbbrev, view); } catch (Exception e) { log.debug(e); e.printStackTrace(); } } } } // } } } catch (SocketException e1) { message = "Unable to connect to host for feed: " + urlString; log.debug(message); } if (!view) { if (comments.toString().equals("")) { message = "No records to update."; } else { Timestamp updated = new Timestamp(System.currentTimeMillis()); // reset siteAbbrev to channel siteAbbrev = channel.getTitle(); String commentsString = null; if (comments.toString().length() > 500) { commentsString = comments.toString().substring(0, 500); } else { commentsString = comments.toString(); } UpdateLogDAO.save( conn, updated, new Timestamp(lastBuildDate.getTime()), siteAbbrev, commentsString); Subscription subscription = (Subscription) SubscriptionDAO.getOne(conn, urlString); // this is getting imported for the first time either manually or via a scheduled job. if (start != null || subscription.getDatesubscribed() == null) { Timestamp datesubscribed = new Timestamp(System.currentTimeMillis()); SubscriptionDAO.updateSite(conn, subscription.getId(), siteAbbrev, datesubscribed); } // log.debug(comments); } } return message; }
/** * Exports a list of patients at the clinic and their records. Compare a list of all patients in * the rss file last published by the server with a list of patients in the system. Publish any * changed records if they are not equal If site is the master data center (such as ZEPRS), loops * through each site's patient list and creates RSS file for each site. Note that a patient's xml * record could be listed in more than one site - The patient listing for each site selects from * patient_status.site_id. Download the remote site listing and see if there are adidtional * patients who may have been transferred to another site - UTH for instance. This enables sites * to see records of their regular patients who were referred to another site. Also creates an * index which is used on remote sites for finding patient records within the imported archive. * * @param conn * @param siteAbbrev - if siteabbrev = ZEP,, export all sites w/ their own rss feed. * @param siteId * @param checkXml - true if you want to check if xml files have been generated. * @return * @throws SQLException * @throws ServletException * @throws ObjectNotFoundException * @throws IOException * @throws ClassNotFoundException * @throws IllegalAccessException * @throws PersistenceException * @throws InvocationTargetException * @throws FeedException */ public static String createSiteRssFiles( Connection conn, String siteAbbrev, Long siteId, Boolean checkXml) throws SQLException, ServletException, ObjectNotFoundException, IOException, ClassNotFoundException, IllegalAccessException, PersistenceException, InvocationTargetException, FeedException { String message = null; StringBuffer sbuf = new StringBuffer(); Timestamp beginDate = null; Timestamp endDate = new Timestamp(System.currentTimeMillis()); Map statusMap = DynaSiteObjects.getStatusMap(); Publisher publisher = null; String publisherFile = Constants.ARCHIVE_PATH + "publisher.xml"; String ipAddress = null; Boolean renderAllSites = false; try { publisher = (Publisher) XmlUtils.getOne(publisherFile); ipAddress = publisher.getUrl(); } catch (FileNotFoundException e) { log.debug("publisher.xml not available - cannot render site rss files."); } if (publisher != null) { // check the db for the date of the last archive. // Fetch list of updated patients. This list is used to generate each patient's updated xml // file ResultSet updatedPatients = null; try { ArchiveLog mostRecentArchive = (ArchiveLog) ArchiveDAO.getOne(conn); beginDate = mostRecentArchive.getArchived(); updatedPatients = PatientDAO.getAllDate(conn, beginDate, endDate); } catch (SQLException e) { e.printStackTrace(); } catch (ServletException e) { e.printStackTrace(); } catch (ObjectNotFoundException e) { // This is the first time this has been run - archive all. updatedPatients = PatientDAO.getAllRS(conn); renderAllSites = true; } // update date of last archive before any more records get updated. Long archiveId = (Long) ArchiveDAO.save(conn, endDate, (long) 1); HashMap updatedMap = new HashMap(); while (updatedPatients.next()) { Long updatedId = updatedPatients.getLong("id"); updatedMap.put(updatedId, updatedId); } List<Site> clinics = null; if (siteAbbrev.equals("ZEP")) { // loop thorough all of the sites and render an rss file for each one. clinics = DynaSiteObjects.getClinics(); // todo: reset to the big list - preset to KAL and AIR /*clinics = new ArrayList<Site>(); Site site = (Site) DynaSiteObjects.getClinicMap().get(Long.valueOf(16)); clinics.add(site); site = (Site) DynaSiteObjects.getClinicMap().get(Long.valueOf(1)); clinics.add(site);*/ } else { clinics = new ArrayList<Site>(); Site site = (Site) DynaSiteObjects.getClinicMap().get(siteId); clinics.add(site); } // create the archive listing // StringBuffer indexBuffer = new StringBuffer(); HashMap<String, String> indexMap = new HashMap<String, String>(); int currentSiteNum = 0; int archivedPatientsAllSites = 0; for (Site site : clinics) { currentSiteNum++; int archivedPatientsThisSite = 0; siteAbbrev = site.getAbbreviation(); siteId = site.getId(); String rssFileName = org.cidrz.webapp.dynasite.Constants.ARCHIVE_PATH + siteAbbrev + Constants.pathSep + "rss.xml"; Timestamp lastBuildDate = new Timestamp(System.currentTimeMillis()); Channel feed = new Channel(); String feedType = "rss_2.0"; feed.setFeedType(feedType); feed.setDescription(siteAbbrev + " Patients"); String port = Constants.APP_PORT; feed.setLink( "http://" + ipAddress + ":" + port + "/" + "archive/" + siteAbbrev + "/rss.xml"); feed.setTitle(siteAbbrev); // Title is used to identify which site the feed is from. feed.setLastBuildDate(lastBuildDate); List entries = new ArrayList(); // Loop through the list of all patients and see if their id exists in the updatedMap ResultSet patientListResultSet = PatientDAO.getAllSiteRS(conn, siteId); ArrayList<Patient> patientRssList = new ArrayList<Patient>(); while (patientListResultSet.next()) { Long patientId = patientListResultSet.getLong("id"); String zeprsId = patientListResultSet.getString("district_patient_id"); String surname = patientListResultSet.getString("surname"); Timestamp lastModified = patientListResultSet.getTimestamp("last_modified"); Long clinicId = patientListResultSet.getLong( "site_id"); // clinic the patient belongs to - should be the same as the site // feed. Patient rssPatient = new Patient(); rssPatient.setId(patientId); rssPatient.setDistrictPatientid(zeprsId); rssPatient.setSurname(surname); rssPatient.setLastModified(lastModified); rssPatient.setSiteId(clinicId); patientRssList.add(rssPatient); } HashMap<String, String> patientRssMap = new HashMap<String, String>(); // loop through the patientRssList to weed out duplicates for (Patient patient : patientRssList) { String zeprsId = patient.getDistrictPatientid(); patientRssMap.put(zeprsId, zeprsId); } String rssMessage = "Generating RSS and Patient Xml for " + siteAbbrev + " :" + currentSiteNum + " out of " + clinics.size() + " sites. " + updatedMap.size() + " patient records to be generated."; statusMap.put("RSS-message", rssMessage); if (renderAllSites == true) { log.debug(rssMessage); } // see if there is already a subscription to this site. String importFilePath = org.cidrz.webapp.dynasite.Constants.ARCHIVE_PATH + siteAbbrev + Constants.pathSep + "import" + Constants.pathSep; String importedRssPath = importFilePath + "rss.xml"; // Reader reader = new BufferedReader((new FileReader(importedRssPath))); File importedRssFile = new File(importedRssPath); if (importedRssFile.exists() && importedRssFile.length() > 0) { final WireFeedInput input = new WireFeedInput(); WireFeed rssFeed = null; XmlReader reader = null; Channel channel = null; reader = new XmlReader(importedRssFile); try { rssFeed = input.build(reader); rssFeed.setFeedType("rss_2.0"); channel = (Channel) rssFeed; List items = channel.getItems(); // siteAbbrev = channel.getTitle(); // Create a list of patients the remote site is "interested" in. // ArrayList<String> subscribedPatientList = new ArrayList<String>(); ArrayList<Patient> subscribedPatientList = new ArrayList<Patient>(); for (int i = 0; i < items.size(); i++) { Item item = (Item) items.get(i); // String link = item.getLink(); String fileName = item.getTitle(); String zeprsId = fileName.replace(".xml", ""); try { Patient rssPatient = PatientDAO.getOneFromZeprsId(conn, zeprsId); // check if the patient is not already in the patientRssList if (patientRssMap.get(zeprsId) == null) { subscribedPatientList.add(rssPatient); } } catch (ObjectNotFoundException e) { // Patient may not yet be in system. It should be OK. } } patientRssList.addAll(subscribedPatientList); } catch (ParsingFeedException e1) { log.debug("Unable to parse RSS feed at " + importedRssPath); } reader.close(); } // while (patientListResultSet.next()) { for (Patient rssPatient : patientRssList) { Long patientId = rssPatient.getId(); String zeprsId = rssPatient.getDistrictPatientid(); String surname = rssPatient.getSurname(); Timestamp lastModified = rssPatient.getLastModified(); Long clinicId = rssPatient .getSiteId(); // clinic the patient belongs to - should be the same as the site // feed. // get the siteAbbrev from the parent's record only // no longer need this part. /*try { site = (Site) DynaSiteObjects.getClinicMap().get(clinicId); siteAbbrev = site.getAbbreviation(); } catch (Exception e) { log.error("Incorrect site data for patient: " + zeprsId + " clinicId: " + clinicId); }*/ String filePath = org.cidrz.webapp.dynasite.Constants.ARCHIVE_PATH + siteAbbrev + Constants.pathSep + "local" + Constants.pathSep; String fileName = getPatientFilename(zeprsId, surname, patientId); // write to the index // String indexValue = zeprsId + ":" + siteAbbrev + Constants.pathSep + "local" + // Constants.pathSep + fileName + "\n"; // indexBuffer.append(indexValue); indexMap.put( zeprsId, siteAbbrev + Constants.pathSep + "local" + Constants.pathSep + fileName); // check if the xml file exists. This is useful when testing - you may not have all of the // xml files generated yet. boolean forceXml = false; if (checkXml != null) { File filecheck = new File(filePath + fileName); if (filecheck.length() == 0) { log.debug("Re-rendering file for : " + fileName + " in " + siteAbbrev + "/local."); forceXml = true; } } if (updatedMap.get(patientId) != null || forceXml) { PatientRecordUtils.archivePatient(conn, patientId, siteAbbrev, filePath, fileName); archivedPatientsThisSite++; archivedPatientsAllSites++; rssMessage = "Generating RSS and Patient Xml for " + siteAbbrev + ": " + currentSiteNum + " out of " + clinics.size() + " sites. " + archivedPatientsAllSites + " out of " + updatedMap.size() + " patient records have been generated. " + "Current file: " + filePath + fileName; statusMap.put("RSS-message", rssMessage); // don't remove from the list because this patient may also be at another site // (referral). // updatedMap.remove(patientId); } if (lastModified == null) { lastModified = DateUtils.generateTimestamp(); log.debug("Null lastModified for patient: " + zeprsId); } java.util.Date pubDate = new Date(lastModified.getTime()); Item item; Description description; String url = "http://" + ipAddress + ":" + port + "/archive/" + siteAbbrev + "/local/" + fileName; item = new Item(); item.setTitle(fileName); item.setLink(url); item.setPubDate(pubDate); item.setAuthor(clinicId.toString()); Guid gd = new Guid(); gd.setPermaLink(true); gd.setValue(url); item.setGuid(gd); description = new Description(); description.setType("text/plain"); description.setValue(clinicId.toString()); item.setDescription(description); entries.add(item); } // Open the remote site RSS file and add patients who may have been transferred // ArrayList<String> remotePatientIdList = populateRemotePatientIdList(urlString); // log.debug("RSS feed being generated for " + siteAbbrev + " has " + entries.size() + " // patients. URL: " + rssFileName); sbuf.append(entries.size() + " patients added to " + siteAbbrev + "<br/>"); feed.setItems(entries); Writer writer = new FileWriter(rssFileName); WireFeedOutput output = new WireFeedOutput(); output.output(feed, writer); writer.close(); entries.clear(); } // create the archive listing /*Writer indexWriter = new FileWriter(Constants.MASTER_ARCHIVE_INDEX); indexWriter.write(indexBuffer.toString()); indexWriter.flush(); indexWriter.close();*/ XmlUtils.save(indexMap, Constants.MASTER_ARCHIVE_INDEX_XML); // log.debug("writing index file to " + Constants.MASTER_ARCHIVE_INDEX_JS); // XmlUtils.saveJson(indexMap, Constants.MASTER_ARCHIVE_INDEX_JS); updatedMap.clear(); indexMap.clear(); String rssMessage = "Completed RSS and patient XML generation task"; statusMap.put("RSS-message", rssMessage); } // Create the archive // Compress.zipDirectory(Constants.ARCHIVE_PATH, Constants.MASTER_ARCHIVE_ZIP); // Zip.zip(Constants.ARCHIVE_PATH, Constants.MASTER_ARCHIVE_ZIP, // Constants.MASTER_ARCHIVE_CHECKSUM); // Zip.CreateZipFile(new File(Constants.MASTER_ARCHIVE_ZIP), new File[]{new // File(Constants.ARCHIVE_PATH)}, false); message = sbuf.toString(); return message; }