List of usage examples for org.joda.time.format DateTimeFormatter parseDateTime
public DateTime parseDateTime(String text)
From source file:org.dllearner.utilities.OWLAPIUtils.java
License:Open Source License
/** * Checks whether the given value is in the closed interval [min,max], i.e. * the value is greater than min and lower than max. * @param value the value// w ww . j a v a 2 s. c om * @param min the lower interval endpoint * @param max the upper interval endpoint * @return whether the given value is in the closed interval [min,max] */ public static boolean inRange(OWLLiteral value, OWLLiteral min, OWLLiteral max) { OWLDatatype datatype = value.getDatatype(); if (OWLAPIUtils.dtDatatypes.contains(datatype)) { DateTimeFormatter parser = OWLAPIUtils.dateTimeParsers.get(datatype); // parse min DateTime minDateTime = null; if (min != null) { minDateTime = parser.parseDateTime(min.getLiteral()); } // parse max DateTime maxDateTime = null; if (max != null) { maxDateTime = parser.parseDateTime(max.getLiteral()); } // parse value DateTime dateTime = parser.parseDateTime(value.getLiteral()); if ((minDateTime == null || (dateTime.isEqual(minDateTime) || dateTime.isAfter(minDateTime))) && (maxDateTime == null || (dateTime.isEqual(maxDateTime) || dateTime.isBefore(maxDateTime)))) { return true; } } return false; }
From source file:org.dllearner.utilities.split.DefaultDateTimeValuesSplitter.java
License:Open Source License
@Override public List<OWLLiteral> computeSplits(OWLDataProperty dp) { List<OWLLiteral> splitLiterals = new ArrayList<>(); Map<OWLIndividual, SortedSet<OWLLiteral>> ind2Values = reasoner.getDatatypeMembers(dp); OWLDatatype datatype = reasoner.getDatatype(dp); DateTimeFormatter parser = OWLAPIUtils.dateTimeParsers.get(datatype); DateTimeFormatter formatter = OWLAPIUtils.dateTimeFormatters.get(datatype); List<DateTime> values = new LinkedList<>(); for (Entry<OWLIndividual, SortedSet<OWLLiteral>> entry : ind2Values.entrySet()) { for (OWLLiteral value : entry.getValue()) { DateTime dateTime = parser.parseDateTime(value.getLiteral()); values.add(dateTime);//from w ww . j av a 2s .c o m } } List<DateTime> splitValues = simpleListSplitter(values, maxNrOfSplits); for (DateTime value : splitValues) { OWLLiteral literal = dataFactory.getOWLLiteral(value.toString(formatter), reasoner.getDatatype(dp)); splitLiterals.add(literal); } return splitLiterals; }
From source file:org.dmb.trueprice.utils.internal.ServletUtils.java
/** * Renvoie la priode de temps ecoule depuis <param>fromDate</param> * en un String formatte en FR//from w w w .j a v a 2 s. co m * @param fromDate * @return la priode de temps ecoule formattee en FR */ public static String getFormattedTimeElapsed(String fromDate) { /* Rcupration de la date courante */ DateTime dtCourante = new DateTime(); /* Rcupration de la date prsente dans le cookie */ DateTimeFormatter formatter = DateTimeFormat.forPattern(FORMAT_DATE); DateTime dtDerniereConnexion = formatter.parseDateTime(fromDate); /* Calcul de la dure de l'intervalle */ Period periode = new Period(dtDerniereConnexion, dtCourante); /* Formatage de la dure de l'intervalle */ PeriodFormatter periodFormatter = new PeriodFormatterBuilder().appendYears().appendSuffix(" an ", " ans ") .appendMonths().appendSuffix(" mois ").appendDays().appendSuffix(" jour ", " jours ").appendHours() .appendSuffix(" heure ", " heures ").appendMinutes().appendSuffix(" minute ", "minutes ") .appendSeparator(" et ").appendSeconds().appendSuffix(" seconde ", " secondes ").toFormatter(); String intervalleConnexions = periodFormatter.print(periode); return intervalleConnexions; }
From source file:org.drftpd.commands.tvmaze.TvMazeUtils.java
License:Open Source License
public static ReplacerEnvironment getShowEnv(TvMazeInfo tvShow) { ReplacerEnvironment env = new ReplacerEnvironment(SiteBot.GLOBAL_ENV); DateTimeFormatter df = DateTimeFormat.forPattern(TvMazeConfig.getInstance().getDateFormat()); DateTimeFormatter tf = DateTimeFormat.forPattern(TvMazeConfig.getInstance().getTimeFormat()); env.add("id", tvShow.getID()); env.add("url", tvShow.getURL()); env.add("name", tvShow.getName()); env.add("type", tvShow.getType()); env.add("language", tvShow.getLanguage()); env.add("genres", StringUtils.join(tvShow.getGenres(), " | ")); env.add("status", tvShow.getStatus()); env.add("runtime", tvShow.getRuntime()); DateTimeFormatter dtf = DateTimeFormat.forPattern("yyyy-MM-dd"); env.add("premiered", df.withZone(TvMazeConfig.getInstance().getTimezone()) .print(dtf.parseDateTime(tvShow.getPremiered()))); env.add("network", tvShow.getNetwork()); env.add("country", tvShow.getCountry()); env.add("summary", StringUtils.abbreviate(tvShow.getSummary(), 250)); if (tvShow.getPreviousEP() != null) { env.add("prevepid", tvShow.getPreviousEP().getID()); env.add("prevepurl", tvShow.getPreviousEP().getURL()); env.add("prevepname", tvShow.getPreviousEP().getName()); env.add("prevepseason", tvShow.getPreviousEP().getSeason()); env.add("prevepnumber", String.format("%02d", tvShow.getPreviousEP().getNumber())); env.add("prevepairdate", df.withZone(TvMazeConfig.getInstance().getTimezone()) .print(new DateTime(tvShow.getPreviousEP().getAirDate()))); env.add("prevepairtime", tf.withZone(TvMazeConfig.getInstance().getTimezone()) .print(new DateTime(tvShow.getPreviousEP().getAirDate()))); env.add("prevepruntime", tvShow.getPreviousEP().getRuntime()); env.add("prevepsummary", StringUtils.abbreviate(tvShow.getPreviousEP().getSummary(), 250)); env.add("prevepage", calculateAge(new DateTime(tvShow.getPreviousEP().getAirDate()))); }//from w w w . jav a 2 s . com if (tvShow.getNextEP() != null) { env.add("nextepid", tvShow.getNextEP().getID()); env.add("nextepurl", tvShow.getNextEP().getURL()); env.add("nextepname", tvShow.getNextEP().getName()); env.add("nextepseason", tvShow.getNextEP().getSeason()); env.add("nextepnumber", String.format("%02d", tvShow.getNextEP().getNumber())); env.add("nextepairdate", df.withZone(TvMazeConfig.getInstance().getTimezone()) .print(new DateTime(tvShow.getNextEP().getAirDate()))); env.add("nextepairtime", tf.withZone(TvMazeConfig.getInstance().getTimezone()) .print(new DateTime(tvShow.getNextEP().getAirDate()))); env.add("nextepruntime", tvShow.getNextEP().getRuntime()); env.add("nextepsummary", StringUtils.abbreviate(tvShow.getNextEP().getSummary(), 250)); env.add("nextepage", calculateAge(new DateTime(tvShow.getNextEP().getAirDate()))); } return env; }
From source file:org.drftpd.commands.tvmaze.TvMazeUtils.java
License:Open Source License
public static ReplacerEnvironment getEPEnv(TvMazeInfo tvShow, TvEpisode tvEP) { ReplacerEnvironment env = new ReplacerEnvironment(SiteBot.GLOBAL_ENV); DateTimeFormatter df = DateTimeFormat.forPattern(TvMazeConfig.getInstance().getDateFormat()); DateTimeFormatter tf = DateTimeFormat.forPattern(TvMazeConfig.getInstance().getTimeFormat()); env.add("id", tvShow.getID()); env.add("url", tvShow.getURL()); env.add("name", tvShow.getName()); env.add("type", tvShow.getType()); env.add("language", tvShow.getLanguage()); env.add("genres", StringUtils.join(tvShow.getGenres(), " | ")); env.add("status", tvShow.getStatus()); env.add("runtime", tvShow.getRuntime()); DateTimeFormatter dtf = DateTimeFormat.forPattern("yyyy-MM-dd"); env.add("premiered", df.withZone(TvMazeConfig.getInstance().getTimezone()) .print(dtf.parseDateTime(tvShow.getPremiered()))); env.add("network", tvShow.getNetwork()); env.add("country", tvShow.getCountry()); env.add("summary", StringUtils.abbreviate(tvShow.getSummary(), 250)); env.add("epid", tvEP.getID()); env.add("epurl", tvEP.getURL()); env.add("epname", tvEP.getName()); env.add("epseason", tvEP.getSeason()); env.add("epnumber", String.format("%02d", tvEP.getNumber())); env.add("epairdate", df.withZone(TvMazeConfig.getInstance().getTimezone()).print(new DateTime(tvEP.getAirDate()))); env.add("epairtime", tf.withZone(TvMazeConfig.getInstance().getTimezone()).print(new DateTime(tvEP.getAirDate()))); env.add("epruntime", tvEP.getRuntime()); env.add("epsummary", StringUtils.abbreviate(tvEP.getSummary(), 250)); env.add("epage", calculateAge(new DateTime(tvEP.getAirDate()))); return env;//from www . java 2 s. co m }
From source file:org.dspace.authority.AuthorityValue.java
License:BSD License
public Date stringToDate(String date) { Date result = null;/*from ww w .j a v a2s .c o m*/ if (StringUtils.isNotBlank(date)) { List<DateTimeFormatter> dateFormatters = getDateFormatters(); boolean converted = false; int formatter = 0; while (!converted) { try { DateTimeFormatter dateTimeFormatter = dateFormatters.get(formatter); DateTime dateTime = dateTimeFormatter.parseDateTime(date); result = dateTime.toDate(); converted = true; } catch (IllegalArgumentException e) { formatter++; if (formatter > dateFormatters.size()) { converted = true; } log.error("Could not find a valid date format for: \"" + date + "\"", e); } } } return result; }
From source file:org.dspace.search.IndexDenIndex.java
License:BSD License
/** * Helper function to retrieve a date using a best guess of the potential date encodings on a field * /*from w w w.j a v a 2 s. c om*/ * @param t * @return */ private static Date toDate(String t) { List<String> fmts = new ArrayList<String>(); // Choose the likely date formats based on string length switch (t.length()) { case 4: fmts.add("yyyy"); break; case 6: fmts.add("yyyyMM"); break; case 7: fmts.add("yyyy-MM"); break; case 8: fmts.add("yyyyMMdd"); fmts.add("yyyy MMM"); break; case 10: fmts.add("yyyy-MM-dd"); break; case 11: fmts.add("yyyy MM dd"); break; case 20: fmts.add("yyyy-MM-dd'T'HH:mm:ss'Z'"); break; default: fmts.add("yyyy-MM-dd'T'HH:mm:ss.SSS'Z'"); break; } for (String fmt : fmts) { try { // Parse the date DateTimeFormatter formatter = DateTimeFormat.forPattern(fmt); DateTime dt = formatter.parseDateTime(t); return dt.toDate(); } catch (IllegalArgumentException pe) { log.error("Unable to parse date format", pe); } } return null; }
From source file:org.ecocean.servlet.importer.ImportExcelMetadata.java
License:Open Source License
public void doPost(HttpServletRequest request, HttpServletResponse response) throws ServletException, IOException { //set up for response response.setContentType("text/html"); PrintWriter out = response.getWriter(); boolean locked = false; String context = "context0"; context = ServletUtilities.getContext(request); Shepherd myShepherd = new Shepherd(context); myShepherd.beginDBTransaction();/*from ww w . j a v a2 s . c o m*/ AssetStore assetStore = AssetStore.getDefault(myShepherd); myShepherd.commitDBTransaction(); System.out.println("\n\nStarting ImportExcelMetadata servlet..."); //setup data dir String rootWebappPath = getServletContext().getRealPath("/"); File webappsDir = new File(rootWebappPath).getParentFile(); File shepherdDataDir = new File(webappsDir, CommonConfiguration.getDataDirectoryName(context)); if (!shepherdDataDir.exists()) { shepherdDataDir.mkdirs(); } File tempSubdir = new File(webappsDir, "temp"); if (!tempSubdir.exists()) { tempSubdir.mkdirs(); } System.out.println("\n\n Finished directory creation..."); String fileName = "None"; StringBuffer messages = new StringBuffer(); boolean successfullyWroteFile = false; File finalFile = new File(tempSubdir, "temp.csv"); try { MultipartParser mp = new MultipartParser(request, (CommonConfiguration.getMaxMediaSizeInMegabytes(context) * 1048576)); Part part; while ((part = mp.readNextPart()) != null) { String name = part.getName(); if (part.isParam()) { // it's a parameter part ParamPart paramPart = (ParamPart) part; String value = paramPart.getStringValue(); } if (part.isFile()) { FilePart filePart = (FilePart) part; fileName = ServletUtilities.cleanFileName(filePart.getFileName()); if (fileName != null) { System.out.println("ImportExcelMetadata is trying to upload file " + fileName); //File thisSharkDir = new File(encountersDir.getAbsolutePath() +"/"+ encounterNumber); //if(!thisSharkDir.exists()){thisSharkDir.mkdirs();} finalFile = new File(tempSubdir, fileName); filePart.writeTo(finalFile); successfullyWroteFile = true; System.out.println("\n\nImportExcelMetadata successfully uploaded the file!"); } } } try { if (successfullyWroteFile) { System.out.println("\n\n Starting Excel Metadata content import"); //OK, we have our CSV file //let's import CSVReader reader = new CSVReader(new FileReader(finalFile)); List<String[]> allLines = reader.readAll(); System.out.println("\n\n Read in the file!"); //let's detect the size of this array by reading the number of header columns in row 0 String[] headerNames = allLines.get(0); int numColumns = headerNames.length; int numRows = allLines.size(); //determine the Occurrence_ID column as it is at the end int occurrenceIDColumnNumber = -1; for (int g = 0; g < numColumns; g++) { if (headerNames[g].equals("Occurrence_ID")) { occurrenceIDColumnNumber = g; } } for (int i = 1; i < numRows; i++) { System.out.println("\n\n Processing row " + i); boolean newEncounter = true; boolean newShark = true; String[] line = allLines.get(i); boolean ok2import = true; Encounter enc = new Encounter(); myShepherd.beginDBTransaction(); //line[0] is the sample_ID String encNumber = line[0].trim(); if ((encNumber != null) && (!encNumber.equals(""))) { if (myShepherd.isEncounter(encNumber)) { enc = myShepherd.getEncounter(encNumber); newEncounter = false; } else { enc.setCatalogNumber(encNumber); enc.setState("approved"); } } else { ok2import = false; messages.append("<li>Row " + i + ": could not find sample/encounter ID in the first column of row " + i + ".</li>"); System.out.println( " Could not find sample/encounter ID in the first column of row " + i + "."); } //line[1] is the IndividualID String individualID = line[1].trim(); if (individualID != null) { enc.addComments("<p><em>" + request.getRemoteUser() + " on " + (new java.util.Date()).toString() + "</em><br>" + "Import SRGD process set marked individual to " + individualID + ".</p>"); //enc.setIndividualID(individualID); System.out.println( " Setting Individual ID for row " + i + ". Value: " + individualID); } //line[2] is the latitude String latitude = line[2].trim(); if ((latitude != null) && (!latitude.equals(""))) { try { enc.addComments("<p><em>" + request.getRemoteUser() + " on " + (new java.util.Date()).toString() + "</em><br>" + "Import SRGD process set latitude to " + latitude + ".</p>"); Double lat = new Double(latitude); enc.setDecimalLatitude(lat); System.out.println( " Setting latitude for row " + i + ". Value: " + latitude); } catch (NumberFormatException nfe) { messages.append("<li>Row " + i + " for sample ID " + enc.getCatalogNumber() + ": Latitude hit a NumberFormatException in row " + i + " and could not be imported. The listed value was: " + latitude + "</li>"); } } //line[3] is the latitude String longitude = line[3].trim(); if ((longitude != null) && (!longitude.equals(""))) { try { enc.addComments("<p><em>" + request.getRemoteUser() + " on " + (new java.util.Date()).toString() + "</em><br>" + "Import SRGD process set longitude to " + longitude + ".</p>"); Double longie = new Double(longitude); enc.setDecimalLongitude(longie); System.out.println( " Setting longitude for row " + i + ". Value: " + longitude); } catch (NumberFormatException nfe) { nfe.printStackTrace(); messages.append("<li>Row " + i + " for sample ID " + enc.getCatalogNumber() + ": Longitude hit a NumberFormatException in row " + i + " and could not be imported. The listed value was: " + longitude + "</li>"); } } //line[4] is the date_time String isoDate = line[4].trim(); if ((isoDate != null) && (!isoDate.equals(""))) { StringTokenizer tks = new StringTokenizer(isoDate, "-"); int numTokens = tks.countTokens(); DateTimeFormatter parser2 = ISODateTimeFormat.dateTimeParser(); enc.setMonth(-1); enc.setDay(-1); enc.setYear(-1); enc.setHour(-1); enc.setMinutes("00"); try { DateTime time = parser2.parseDateTime(isoDate); enc.setYear(time.getYear()); if (numTokens >= 2) { enc.setMonth(time.getMonthOfYear()); } if (numTokens >= 3) { enc.setDay(time.getDayOfMonth()); } if (isoDate.indexOf("T") != -1) { int minutes = time.getMinuteOfHour(); String minutes2 = (new Integer(minutes)).toString(); if ((time.getHourOfDay() != 0) && (minutes != 0)) { enc.setHour(time.getHourOfDay()); if (isoDate.indexOf(":") != -1) { enc.setMinutes(minutes2); } } } enc.addComments("<p><em>" + request.getRemoteUser() + " on " + (new java.util.Date()).toString() + "</em><br>" + "Import SRGD process set date to " + enc.getDate() + ".</p>"); System.out.println(" Set date for encounter: " + enc.getDate()); } catch (IllegalArgumentException iae) { iae.printStackTrace(); messages.append("<li>Row " + i + ": could not import the date and time for row: " + i + ". Cancelling the import for this row.</li>"); ok2import = false; } } //line[5] get locationID String locationID = line[5].trim(); if (line.length >= 6) { if ((locationID != null) && (!locationID.equals(""))) { enc.setLocationID(locationID); enc.addComments("<p><em>" + request.getRemoteUser() + " on " + (new java.util.Date()).toString() + "</em><br>" + "Import SRGD process set location ID to " + locationID + ".</p>"); System.out.println( " Setting location ID for row " + i + ". Value: " + locationID); } } //line[6] get sex String sex = line[6].trim(); if (line.length >= 7) { if ((sex != null) && (!sex.equals(""))) { if (sex.equals("M")) { enc.setSex("male"); } else if (sex.equals("F")) { enc.setSex("female"); } else { enc.setSex("unknown"); } System.out.println(" Setting sex for row " + i + ". Value: " + sex); enc.addComments("<p><em>" + request.getRemoteUser() + " on " + (new java.util.Date()).toString() + "</em><br>" + "Import SRGD process set sex to " + enc.getSex() + ".</p>"); } //line[occurrenceIDColumnNumber] get Occurrence_ID Occurrence occur = new Occurrence(); if (occurrenceIDColumnNumber != -1) { String occurID = line[occurrenceIDColumnNumber]; if (myShepherd.isOccurrence(occurID)) { occur = myShepherd.getOccurrence(occurID); boolean isNew = occur.addEncounter(enc); if (isNew) { occur.addComments("<p><em>" + request.getRemoteUser() + " on " + (new java.util.Date()).toString() + "</em><br>" + "Import SRGD process added encounter " + enc.getCatalogNumber() + ".</p>"); } } else { occur = new Occurrence(occurID, enc); occur.addComments("<p><em>" + request.getRemoteUser() + " on " + (new java.util.Date()).toString() + "</em><br>" + "Import SRGD process added encounter " + enc.getCatalogNumber() + ".</p>"); myShepherd.getPM().makePersistent(occur); } } } if (ok2import) { System.out.println(" ok2import"); myShepherd.commitDBTransaction(); if (newEncounter) { myShepherd.storeNewEncounter(enc, enc.getCatalogNumber()); } //before proceeding with haplotype and loci importing, we need to create the tissue sample myShepherd.beginDBTransaction(); Encounter enc3 = myShepherd.getEncounter(encNumber); TissueSample ts = new TissueSample(encNumber, ("sample_" + encNumber)); if (myShepherd.isTissueSample(("sample_" + encNumber), encNumber)) { ts = myShepherd.getTissueSample(("sample_" + encNumber), encNumber); } else { myShepherd.getPM().makePersistent(ts); enc3.addTissueSample(ts); } System.out.println(" Added TissueSample."); //let's set genetic Sex if ((sex != null) && (!sex.equals(""))) { SexAnalysis sexDNA = new SexAnalysis( ("analysis_" + enc3.getCatalogNumber() + "_sex"), sex, enc3.getCatalogNumber(), ("sample_" + enc3.getCatalogNumber())); if (myShepherd.isGeneticAnalysis(ts.getSampleID(), encNumber, ("analysis_" + enc3.getCatalogNumber() + "_sex"), "SexAnalysis")) { sexDNA = myShepherd.getSexAnalysis(ts.getSampleID(), encNumber, ("analysis_" + enc3.getCatalogNumber() + "_sex")); sexDNA.setSex(sex); } else { ts.addGeneticAnalysis(sexDNA); myShepherd.getPM().makePersistent(sexDNA); } enc3.addComments("<p><em>" + request.getRemoteUser() + " on " + (new java.util.Date()).toString() + "</em><br />" + "Import SRGD process added or updated genetic sex analysis " + sexDNA.getAnalysisID() + " for tissue sample " + ts.getSampleID() + ".<br />" + sexDNA.getHTMLString()); } System.out.println(" Added genetic sex."); //line[7] get haplotype if (line.length >= 8) { String haplo = line[7].trim(); if ((haplo != null) && (!haplo.equals(""))) { //TBD check id this analysis already exists System.out.println(" Starting haplotype."); MitochondrialDNAAnalysis mtDNA = new MitochondrialDNAAnalysis( ("analysis_" + enc3.getCatalogNumber()), haplo, enc3.getCatalogNumber(), ("sample_" + enc3.getCatalogNumber())); if (myShepherd.isGeneticAnalysis(ts.getSampleID(), encNumber, ("analysis_" + enc3.getCatalogNumber()), "MitochondrialDNA")) { mtDNA = myShepherd.getMitochondrialDNAAnalysis(ts.getSampleID(), encNumber, ("analysis_" + enc3.getCatalogNumber())); mtDNA.setHaplotype(haplo); System.out.println(" Haplotype reset."); } else { ts.addGeneticAnalysis(mtDNA); myShepherd.getPM().makePersistent(mtDNA); System.out.println(" Added new haplotype."); } enc3.addComments("<p><em>" + request.getRemoteUser() + " on " + (new java.util.Date()).toString() + "</em><br />" + "Import SRGD process added or updated mitochondrial DNA analysis (haplotype) " + mtDNA.getAnalysisID() + " for tissue sample " + ts.getSampleID() + ".<br />" + mtDNA.getHTMLString()); System.out.println(" Added haplotype."); } else { System.out.println(" Did NOT add haplotype."); } } ArrayList<Locus> loci = new ArrayList<Locus>(); //loci value import if (line.length >= 9) { for (int f = 8; f < numColumns; f++) { if (line.length > (f + 2)) { String l1 = line[f].trim(); String l2 = line[f + 1].trim(); String locusName = headerNames[f].replaceAll("L_", ""); System.out.println(" Loaded loci name."); //verify that we're looking at the right loci and everything matches up nicely if ((l1 != null) && (l2 != null) && (!l1.equals("")) && (!l2.equals("")) && (!locusName.equals("")) && (headerNames[f].trim().toLowerCase().startsWith("l_")) && (headerNames[f + 1].trim().toLowerCase().startsWith("l_")) && (headerNames[f].trim().toLowerCase() .equals(headerNames[f + 1].trim().toLowerCase()))) { //get allele values Integer intA = new Integer(l1); Integer intB = new Integer(l2); Locus myLocus = new Locus(locusName, intA, intB); loci.add(myLocus); } f++; } } } //TBD check if this analysis already exists if (loci.size() > 0) { System.out.println(" Found msMarkers!!!!!!!!!!!!1"); MicrosatelliteMarkersAnalysis microAnalysis = new MicrosatelliteMarkersAnalysis( (ts.getSampleID() + "_msMarkerAnalysis"), ts.getSampleID(), enc.getCatalogNumber(), loci); if (myShepherd.isGeneticAnalysis(ts.getSampleID(), encNumber, (ts.getSampleID() + "_msMarkerAnalysis"), "MicrosatelliteMarkers")) { microAnalysis = myShepherd.getMicrosatelliteMarkersAnalysis(ts.getSampleID(), encNumber, (ts.getSampleID() + "_msMarkerAnalysis")); microAnalysis.setLoci(loci); } else { ts.addGeneticAnalysis(microAnalysis); myShepherd.getPM().makePersistent(microAnalysis); } System.out.println(" Added ms markers."); enc3.addComments("<p><em>" + request.getRemoteUser() + " on " + (new java.util.Date()).toString() + "</em><br />" + "Import SRGD process added or updated microsatellite markers of analysis " + microAnalysis.getAnalysisID() + " for tissue sample " + ts.getSampleID() + ".<br />" + microAnalysis.getHTMLString()); } myShepherd.commitDBTransaction(); if (!individualID.equals("")) { MarkedIndividual indie = new MarkedIndividual(); myShepherd.beginDBTransaction(); Encounter enc2 = myShepherd.getEncounter(encNumber); if (myShepherd.isMarkedIndividual(individualID)) { indie = myShepherd.getMarkedIndividual(individualID); newShark = false; } else { //indie.setIndividualID(individualID); FIXME !!! } //OK to generically add it as the addEncounter() method will ignore it if already added to marked individual indie.addEncounter(enc2); if ((indie.getSex() == null) || ((enc2.getSex() != null) && (indie.getSex() != enc2.getSex()))) { indie.setSex(enc2.getSex()); indie.addComments("<p><em>" + request.getRemoteUser() + " on " + (new java.util.Date()).toString() + "</em><br>" + "Import SRGD process set sex to " + enc2.getSex() + ".</p>"); } if ((indie.getHaplotype() == null) && (enc2.getHaplotype() != null)) { indie.doNotSetLocalHaplotypeReflection(enc2.getHaplotype()); } indie.refreshDependentProperties(); indie.addComments("<p><em>" + request.getRemoteUser() + " on " + (new java.util.Date()).toString() + "</em><br>" + "Import SRGD process added encounter " + enc2.getCatalogNumber() + ".</p>"); myShepherd.commitDBTransaction(); if (newShark) { myShepherd.storeNewMarkedIndividual(indie); } } } else { myShepherd.rollbackDBTransaction(); } //out.println("Imported row: "+line); } } else { locked = true; System.out.println("ImportSRGD: For some reason the import failed without exception."); } } catch (Exception le) { locked = true; myShepherd.rollbackDBTransaction(); myShepherd.closeDBTransaction(); le.printStackTrace(); } if (!locked) { myShepherd.commitDBTransaction(); myShepherd.closeDBTransaction(); out.println(ServletUtilities.getHeader(request)); out.println( "<p><strong>Success!</strong> I have successfully uploaded and imported your SRGD CSV file.</p>"); if (messages.toString().equals("")) { messages.append("None"); } out.println("<p>The following error messages were reported during the import process:<br /><ul>" + messages + "</ul></p>"); out.println("<p><a href=\"appadmin/import.jsp\">Return to the import page</a></p>"); out.println(ServletUtilities.getFooter(context)); } } catch (IOException lEx) { lEx.printStackTrace(); out.println(ServletUtilities.getHeader(request)); out.println( "<strong>Error:</strong> I was unable to upload your SRGD CSV. Please contact the webmaster about this message."); out.println(ServletUtilities.getFooter(context)); } catch (NullPointerException npe) { npe.printStackTrace(); out.println(ServletUtilities.getHeader(request)); out.println("<strong>Error:</strong> I was unable to import SRGD data as no file was specified."); out.println(ServletUtilities.getFooter(context)); } out.close(); }
From source file:org.ecocean.servlet.importer.ImportSRGD.java
License:Open Source License
public void doPost(HttpServletRequest request, HttpServletResponse response) throws ServletException, IOException { String context = "context0"; context = ServletUtilities.getContext(request); Shepherd myShepherd = new Shepherd(context); myShepherd.setAction("ImportSRGD"); System.out.println("\n\nStarting ImportSRGD servlet..."); //setup data dir String rootWebappPath = getServletContext().getRealPath("/"); File webappsDir = new File(rootWebappPath).getParentFile(); File shepherdDataDir = new File(webappsDir, CommonConfiguration.getDataDirectoryName(context)); if (!shepherdDataDir.exists()) { shepherdDataDir.mkdirs();/*from w ww . ja v a2s. c om*/ } File tempSubdir = new File(webappsDir, "temp"); if (!tempSubdir.exists()) { tempSubdir.mkdirs(); } System.out.println("\n\n Finished directory creation..."); //set up for response response.setContentType("text/html"); PrintWriter out = response.getWriter(); boolean locked = false; String fileName = "None"; StringBuffer messages = new StringBuffer(); boolean successfullyWroteFile = false; File finalFile = new File(tempSubdir, "temp.csv"); try { MultipartParser mp = new MultipartParser(request, (CommonConfiguration.getMaxMediaSizeInMegabytes(context) * 1048576)); Part part; while ((part = mp.readNextPart()) != null) { String name = part.getName(); if (part.isParam()) { // it's a parameter part ParamPart paramPart = (ParamPart) part; String value = paramPart.getStringValue(); } if (part.isFile()) { FilePart filePart = (FilePart) part; fileName = ServletUtilities.cleanFileName(filePart.getFileName()); if (fileName != null) { System.out.println(" Trying to upload file: " + fileName); //File thisSharkDir = new File(encountersDir.getAbsolutePath() +"/"+ encounterNumber); //if(!thisSharkDir.exists()){thisSharkDir.mkdirs();} finalFile = new File(tempSubdir, fileName); filePart.writeTo(finalFile); successfullyWroteFile = true; System.out.println("\n\n I successfully uploaded the file!"); } } } try { if (successfullyWroteFile) { System.out.println("\n\n Starting CSV content import..."); //OK, we have our CSV file //let's import CSVReader reader = new CSVReader(new FileReader(finalFile)); List<String[]> allLines = reader.readAll(); System.out.println("\n\n Read in the CSV file!"); //let's detect the size of this array by reading the number of header columns in row 0 String[] headerNames = allLines.get(0); int numColumns = headerNames.length; int numRows = allLines.size(); //determine the Occurrence_ID column as it is at the end int occurrenceIDColumnNumber = -1; for (int g = 0; g < numColumns; g++) { if (headerNames[g].equals("Occurrence_ID")) { occurrenceIDColumnNumber = g; } } for (int i = 1; i < numRows; i++) { System.out.println("\n\n Processing row " + i); boolean newEncounter = true; boolean newShark = true; String[] line = allLines.get(i); boolean ok2import = true; Encounter enc = new Encounter(); myShepherd.beginDBTransaction(); //line[0] is the sample_ID String encNumber = line[0].trim(); if ((encNumber != null) && (!encNumber.equals(""))) { if (myShepherd.isEncounter(encNumber)) { enc = myShepherd.getEncounter(encNumber); newEncounter = false; } else { enc.setCatalogNumber(encNumber); enc.setState("approved"); } } else { ok2import = false; messages.append("<li>Row " + i + ": could not find sample/encounter ID in the first column of row " + i + ".</li>"); System.out.println( " Could not find sample/encounter ID in the first column of row " + i + "."); } //line[1] is the IndividualID String individualID = line[1].trim(); if (individualID != null) { enc.addComments("<p><em>" + request.getRemoteUser() + " on " + (new java.util.Date()).toString() + "</em><br>" + "Import SRGD process set marked individual to " + individualID + ".</p>"); //enc.setIndividualID(individualID); System.out.println( " Setting Individual ID for row " + i + ". Value: " + individualID); } //line[2] is the latitude String latitude = line[2].trim(); if ((latitude != null) && (!latitude.equals(""))) { try { enc.addComments("<p><em>" + request.getRemoteUser() + " on " + (new java.util.Date()).toString() + "</em><br>" + "Import SRGD process set latitude to " + latitude + ".</p>"); Double lat = new Double(latitude); enc.setDecimalLatitude(lat); System.out.println( " Setting latitude for row " + i + ". Value: " + latitude); } catch (NumberFormatException nfe) { messages.append("<li>Row " + i + " for sample ID " + enc.getCatalogNumber() + ": Latitude hit a NumberFormatException in row " + i + " and could not be imported. The listed value was: " + latitude + "</li>"); } } //line[3] is the latitude String longitude = line[3].trim(); if ((longitude != null) && (!longitude.equals(""))) { try { enc.addComments("<p><em>" + request.getRemoteUser() + " on " + (new java.util.Date()).toString() + "</em><br>" + "Import SRGD process set longitude to " + longitude + ".</p>"); Double longie = new Double(longitude); enc.setDecimalLongitude(longie); System.out.println( " Setting longitude for row " + i + ". Value: " + longitude); } catch (NumberFormatException nfe) { nfe.printStackTrace(); messages.append("<li>Row " + i + " for sample ID " + enc.getCatalogNumber() + ": Longitude hit a NumberFormatException in row " + i + " and could not be imported. The listed value was: " + longitude + "</li>"); } } //line[4] is the date_time String isoDate = line[4].trim(); if ((isoDate != null) && (!isoDate.equals(""))) { StringTokenizer tks = new StringTokenizer(isoDate, "-"); int numTokens = tks.countTokens(); DateTimeFormatter parser2 = ISODateTimeFormat.dateTimeParser(); enc.setMonth(-1); enc.setDay(-1); enc.setYear(-1); enc.setHour(-1); enc.setMinutes("00"); try { DateTime time = parser2.parseDateTime(isoDate); enc.setYear(time.getYear()); if (numTokens >= 2) { enc.setMonth(time.getMonthOfYear()); } if (numTokens >= 3) { enc.setDay(time.getDayOfMonth()); } if (isoDate.indexOf("T") != -1) { int minutes = time.getMinuteOfHour(); String minutes2 = (new Integer(minutes)).toString(); if ((time.getHourOfDay() != 0) && (minutes != 0)) { enc.setHour(time.getHourOfDay()); if (isoDate.indexOf(":") != -1) { enc.setMinutes(minutes2); } } } enc.addComments("<p><em>" + request.getRemoteUser() + " on " + (new java.util.Date()).toString() + "</em><br>" + "Import SRGD process set date to " + enc.getDate() + ".</p>"); System.out.println(" Set date for encounter: " + enc.getDate()); } catch (IllegalArgumentException iae) { iae.printStackTrace(); messages.append("<li>Row " + i + ": could not import the date and time for row: " + i + ". Cancelling the import for this row.</li>"); ok2import = false; } } //line[5] get locationID String locationID = line[5].trim(); if (line.length >= 6) { if ((locationID != null) && (!locationID.equals(""))) { enc.setLocationID(locationID); enc.addComments("<p><em>" + request.getRemoteUser() + " on " + (new java.util.Date()).toString() + "</em><br>" + "Import SRGD process set location ID to " + locationID + ".</p>"); System.out.println( " Setting location ID for row " + i + ". Value: " + locationID); } } //line[6] get sex String sex = line[6].trim(); if (line.length >= 7) { if ((sex != null) && (!sex.equals(""))) { if (sex.equals("M")) { enc.setSex("male"); } else if (sex.equals("F")) { enc.setSex("female"); } else { enc.setSex("unknown"); } System.out.println(" Setting sex for row " + i + ". Value: " + sex); enc.addComments("<p><em>" + request.getRemoteUser() + " on " + (new java.util.Date()).toString() + "</em><br>" + "Import SRGD process set sex to " + enc.getSex() + ".</p>"); } //line[occurrenceIDColumnNumber] get Occurrence_ID Occurrence occur = new Occurrence(); if (occurrenceIDColumnNumber != -1) { String occurID = line[occurrenceIDColumnNumber]; if (myShepherd.isOccurrence(occurID)) { occur = myShepherd.getOccurrence(occurID); boolean isNew = occur.addEncounter(enc); if (isNew) { occur.addComments("<p><em>" + request.getRemoteUser() + " on " + (new java.util.Date()).toString() + "</em><br>" + "Import SRGD process added encounter " + enc.getCatalogNumber() + ".</p>"); } } else { occur = new Occurrence(occurID, enc); occur.addComments("<p><em>" + request.getRemoteUser() + " on " + (new java.util.Date()).toString() + "</em><br>" + "Import SRGD process added encounter " + enc.getCatalogNumber() + ".</p>"); myShepherd.getPM().makePersistent(occur); } } } if (ok2import) { System.out.println(" ok2import"); myShepherd.commitDBTransaction(); if (newEncounter) { myShepherd.storeNewEncounter(enc, enc.getCatalogNumber()); } //before proceeding with haplotype and loci importing, we need to create the tissue sample myShepherd.beginDBTransaction(); Encounter enc3 = myShepherd.getEncounter(encNumber); TissueSample ts = new TissueSample(encNumber, ("sample_" + encNumber)); if (myShepherd.isTissueSample(("sample_" + encNumber), encNumber)) { ts = myShepherd.getTissueSample(("sample_" + encNumber), encNumber); } else { myShepherd.getPM().makePersistent(ts); enc3.addTissueSample(ts); } System.out.println(" Added TissueSample."); //let's set genetic Sex if ((sex != null) && (!sex.equals(""))) { SexAnalysis sexDNA = new SexAnalysis( ("analysis_" + enc3.getCatalogNumber() + "_sex"), sex, enc3.getCatalogNumber(), ("sample_" + enc3.getCatalogNumber())); if (myShepherd.isGeneticAnalysis(ts.getSampleID(), encNumber, ("analysis_" + enc3.getCatalogNumber() + "_sex"), "SexAnalysis")) { sexDNA = myShepherd.getSexAnalysis(ts.getSampleID(), encNumber, ("analysis_" + enc3.getCatalogNumber() + "_sex")); sexDNA.setSex(sex); } else { ts.addGeneticAnalysis(sexDNA); myShepherd.getPM().makePersistent(sexDNA); } enc3.addComments("<p><em>" + request.getRemoteUser() + " on " + (new java.util.Date()).toString() + "</em><br />" + "Import SRGD process added or updated genetic sex analysis " + sexDNA.getAnalysisID() + " for tissue sample " + ts.getSampleID() + ".<br />" + sexDNA.getHTMLString()); } System.out.println(" Added genetic sex."); //line[7] get haplotype if (line.length >= 8) { String haplo = line[7].trim(); if ((haplo != null) && (!haplo.equals(""))) { //TBD check id this analysis already exists System.out.println(" Starting haplotype."); MitochondrialDNAAnalysis mtDNA = new MitochondrialDNAAnalysis( ("analysis_" + enc3.getCatalogNumber()), haplo, enc3.getCatalogNumber(), ("sample_" + enc3.getCatalogNumber())); if (myShepherd.isGeneticAnalysis(ts.getSampleID(), encNumber, ("analysis_" + enc3.getCatalogNumber()), "MitochondrialDNA")) { mtDNA = myShepherd.getMitochondrialDNAAnalysis(ts.getSampleID(), encNumber, ("analysis_" + enc3.getCatalogNumber())); mtDNA.setHaplotype(haplo); System.out.println(" Haplotype reset."); } else { ts.addGeneticAnalysis(mtDNA); myShepherd.getPM().makePersistent(mtDNA); System.out.println(" Added new haplotype."); } enc3.addComments("<p><em>" + request.getRemoteUser() + " on " + (new java.util.Date()).toString() + "</em><br />" + "Import SRGD process added or updated mitochondrial DNA analysis (haplotype) " + mtDNA.getAnalysisID() + " for tissue sample " + ts.getSampleID() + ".<br />" + mtDNA.getHTMLString()); System.out.println(" Added haplotype."); } else { System.out.println(" Did NOT add haplotype."); } } ArrayList<Locus> loci = new ArrayList<Locus>(); //loci value import if (line.length >= 9) { for (int f = 8; f < numColumns; f++) { if (line.length > (f + 2)) { String l1 = line[f].trim(); String l2 = line[f + 1].trim(); String locusName = headerNames[f].replaceAll("L_", ""); System.out.println(" Loaded loci name."); //verify that we're looking at the right loci and everything matches up nicely if ((l1 != null) && (l2 != null) && (!l1.equals("")) && (!l2.equals("")) && (!locusName.equals("")) && (headerNames[f].trim().toLowerCase().startsWith("l_")) && (headerNames[f + 1].trim().toLowerCase().startsWith("l_")) && (headerNames[f].trim().toLowerCase() .equals(headerNames[f + 1].trim().toLowerCase()))) { //get allele values Integer intA = new Integer(l1); Integer intB = new Integer(l2); Locus myLocus = new Locus(locusName, intA, intB); loci.add(myLocus); } f++; } } } //TBD check if this analysis already exists if (loci.size() > 0) { System.out.println(" Found msMarkers!!!!!!!!!!!!1"); MicrosatelliteMarkersAnalysis microAnalysis = new MicrosatelliteMarkersAnalysis( (ts.getSampleID() + "_msMarkerAnalysis"), ts.getSampleID(), enc.getCatalogNumber(), loci); if (myShepherd.isGeneticAnalysis(ts.getSampleID(), encNumber, (ts.getSampleID() + "_msMarkerAnalysis"), "MicrosatelliteMarkers")) { microAnalysis = myShepherd.getMicrosatelliteMarkersAnalysis(ts.getSampleID(), encNumber, (ts.getSampleID() + "_msMarkerAnalysis")); microAnalysis.setLoci(loci); } else { ts.addGeneticAnalysis(microAnalysis); myShepherd.getPM().makePersistent(microAnalysis); } System.out.println(" Added ms markers."); enc3.addComments("<p><em>" + request.getRemoteUser() + " on " + (new java.util.Date()).toString() + "</em><br />" + "Import SRGD process added or updated microsatellite markers of analysis " + microAnalysis.getAnalysisID() + " for tissue sample " + ts.getSampleID() + ".<br />" + microAnalysis.getHTMLString()); } myShepherd.commitDBTransaction(); if (!individualID.equals("")) { MarkedIndividual indie = new MarkedIndividual(); myShepherd.beginDBTransaction(); Encounter enc2 = myShepherd.getEncounter(encNumber); if (myShepherd.isMarkedIndividual(individualID)) { indie = myShepherd.getMarkedIndividual(individualID); newShark = false; } else { //indie.setIndividualID(individualID); } //OK to generically add it as the addEncounter() method will ignore it if already added to marked individual indie.addEncounter(enc2); if ((indie.getSex() == null) || ((enc2.getSex() != null) && (indie.getSex() != enc2.getSex()))) { indie.setSex(enc2.getSex()); indie.addComments("<p><em>" + request.getRemoteUser() + " on " + (new java.util.Date()).toString() + "</em><br>" + "Import SRGD process set sex to " + enc2.getSex() + ".</p>"); } if ((indie.getHaplotype() == null) && (enc2.getHaplotype() != null)) { indie.doNotSetLocalHaplotypeReflection(enc2.getHaplotype()); } indie.refreshDependentProperties(); indie.addComments("<p><em>" + request.getRemoteUser() + " on " + (new java.util.Date()).toString() + "</em><br>" + "Import SRGD process added encounter " + enc2.getCatalogNumber() + ".</p>"); myShepherd.commitDBTransaction(); if (newShark) { myShepherd.storeNewMarkedIndividual(indie); } } } else { myShepherd.rollbackDBTransaction(); } //out.println("Imported row: "+line); } } else { locked = true; System.out.println("ImportSRGD: For some reason the import failed without exception."); } } catch (Exception le) { locked = true; myShepherd.rollbackDBTransaction(); myShepherd.closeDBTransaction(); le.printStackTrace(); } if (!locked) { myShepherd.commitDBTransaction(); myShepherd.closeDBTransaction(); out.println(ServletUtilities.getHeader(request)); out.println( "<p><strong>Success!</strong> I have successfully uploaded and imported your SRGD CSV file.</p>"); if (messages.toString().equals("")) { messages.append("None"); } out.println("<p>The following error messages were reported during the import process:<br /><ul>" + messages + "</ul></p>"); out.println("<p><a href=\"appadmin/import.jsp\">Return to the import page</a></p>"); out.println(ServletUtilities.getFooter(context)); } } catch (IOException lEx) { lEx.printStackTrace(); out.println(ServletUtilities.getHeader(request)); out.println( "<strong>Error:</strong> I was unable to upload your SRGD CSV. Please contact the webmaster about this message."); out.println(ServletUtilities.getFooter(context)); } catch (NullPointerException npe) { npe.printStackTrace(); out.println(ServletUtilities.getHeader(request)); out.println("<strong>Error:</strong> I was unable to import SRGD data as no file was specified."); out.println(ServletUtilities.getFooter(context)); } out.close(); }
From source file:org.efaps.ui.wicket.util.DateUtil.java
License:Apache License
/** * Convert a date from a parameter into a <code>DateTime</code>. * * @param _value value to be converted/*from ww w . j a va2 s. co m*/ * @return DateTime * @throws EFapsException on error */ public static DateTime getDateFromParameter(final String _value) throws EFapsException { final StyleDateConverter styledate = new StyleDateConverter(false); final DateTimeFormatter fmt = DateTimeFormat .forPattern(styledate.getDatePattern(Context.getThreadContext().getLocale())); fmt.withLocale(Context.getThreadContext().getLocale()); final DateTime dt = fmt.parseDateTime(_value); return dt; }