/**
* 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;
}