Java tutorial
/*Copyright 2013 Johns Hopkins University Institute for Computational Medicine Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at http://www.apache.org/licenses/LICENSE-2.0 Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License. */ /** * @author Shallon Brown 2014 * */ package edu.jhu.cvrg.ceptools.main; import java.io.BufferedInputStream; import java.io.BufferedOutputStream; import java.io.File; import java.io.FileInputStream; import java.io.FileNotFoundException; import java.io.FileOutputStream; import java.io.IOException; import java.io.InputStream; import java.io.OutputStream; import java.io.PrintWriter; import java.io.Serializable; import java.io.StringWriter; import java.util.ArrayList; import java.util.Collection; import java.util.Iterator; import java.util.List; import javax.faces.application.FacesMessage; import javax.faces.bean.ManagedBean; import javax.faces.bean.SessionScoped; import javax.faces.context.ExternalContext; import javax.faces.context.FacesContext; import javax.faces.event.ActionEvent; import javax.portlet.PortletResponse; import javax.servlet.http.HttpServletResponse; import org.apache.commons.io.FilenameUtils; import org.apache.log4j.Logger; import org.apache.solr.client.solrj.SolrQuery; import org.apache.solr.client.solrj.SolrServer; import org.apache.solr.client.solrj.impl.HttpSolrServer; import org.apache.solr.client.solrj.request.CoreAdminRequest; import org.apache.solr.client.solrj.response.QueryResponse; import org.apache.solr.common.SolrDocument; import org.apache.solr.common.SolrDocumentList; import org.apache.solr.common.SolrInputDocument; import org.apache.solr.common.params.CoreAdminParams.CoreAdminAction; import org.dom4j.Document; import org.dom4j.Element; import org.dom4j.Node; import org.dom4j.io.SAXReader; import org.primefaces.context.RequestContext; import org.primefaces.event.FileUploadEvent; import org.primefaces.model.UploadedFile; import com.liferay.faces.portal.context.LiferayFacesContext; import com.liferay.portal.kernel.util.PropsUtil; import com.liferay.portal.util.PortalUtil; import edu.jhu.cvrg.ceptools.controller.FileDownloadController; import edu.jhu.cvrg.ceptools.controller.FileUploadController; import edu.jhu.cvrg.ceptools.model.FileStorer; import edu.jhu.cvrg.ceptools.model.Publication; import edu.jhu.cvrg.ceptools.utility.ZipDirectory; @ManagedBean(name = "pubMedSearch") @SessionScoped public class PubMedSearch implements Serializable { private static final long serialVersionUID = 3L; private List<Publication> publications; private List<Publication> results; private List<Publication> checklist; private String pSearcher; private String searcher; private String url; private String savemsg; private String base; private String redostep1; private boolean redostep3; @SuppressWarnings("unused") private boolean redostep5; @SuppressWarnings("unused") private boolean redostep6; private String redostep3msg; private String redostep5msg; private String redostep6msg; @SuppressWarnings("unused") private boolean finalsave; public int counter; private int solrindex; private int recurpmid; private String buttonvalue; private String curruserid; private String userauthor; private String usertitle; private String jv, jn, ji, jd, jm, jy, jsp, authorfull, doi, epday, epmonth, epyear, epubsum, epubsum2; private String userpmid; private int selectedindex; private Publication selectedPub; private FileUploadController fchooser; private FileDownloadController fdownload; private FileStorer selecteddownloadfile; private String selecteddownloadfiletype; private String selecteddownloadfilename; private List<String> filesanddata; private boolean match; private String uploaderr; private HttpSolrServer server = new HttpSolrServer("http://localhost:8983/solr"); private boolean confirmed; private List<File> files; private List<String> filenames; private List<FileStorer> allfiles; private List<FileStorer> previousfiles; private List<FileStorer> newrefinedfiles; private FileStorer selectedfile; private int selectedpubpmid; //specifically for filechooser for storage private ZipDirectory zip; private int index; private int step; private String searchchoice; private List<Integer> pmidlist; private SolrInputDocument metadoc = new SolrInputDocument(); public boolean getMatch() { return match; } public void setMatch(boolean s) { match = s; } public List<FileStorer> getNewrefinedfiles() { return newrefinedfiles; } public void setNewrefinedfiles(List<FileStorer> n) { newrefinedfiles = n; } public String getSavemsg() { return savemsg; } public void setSavemsg(String s) { savemsg = s; } public String getUploaderr() { return uploaderr; } public void setUploaderr(String u) { uploaderr = u; } public void setRedostep1(String m) { redostep1 = m; } public String getRedostep1() { return redostep1; } public void setRedostep3msg(String m) { redostep3msg = m; } public String getRedostep3msg() { return redostep3msg; } public void setRedostep5msg(String m) { redostep5msg = m; } public String getRedostep5msg() { return redostep5msg; } public void setRedostep6msg(String m) { redostep6msg = m; } public String getRedostep6msg() { return redostep6msg; } public List<Publication> getResults() { return results; } public void setResults(List<Publication> re) { results = re; } public List<Publication> getChecklist() { return checklist; } public void setChecklist(List<Publication> re) { checklist = re; } public int getIndex() { return index; } public void setIndex(int i) { this.index = i; } public List<FileStorer> getAllfiles() { return allfiles; } public void setAllfiles(List<FileStorer> allfiles) { this.allfiles = allfiles; } public Publication getSelectedPub() { return selectedPub; } public void setSelectedPub(Publication spub) { this.selectedPub = spub; } public List<Publication> getPublications() { return publications; } public void setPublications(List<Publication> publist) { this.publications = publist; } public String getUserauthor() { return userauthor; } public String getUsertitle() { return usertitle; } public String getCurruserid() { return curruserid; } public String getUserpmid() { return userpmid; } public void setUserauthor(String u) { userauthor = u; } public void setUsertitle(String u) { usertitle = u; } public void setUserpmid(String u) { userpmid = u; } public String setButtonvalue() { return buttonvalue; } public void getButtonvalue(String b) { this.buttonvalue = b; } public void setStep(int currstep) { step = currstep; } public int getStep() { return step; } public void setSearchchoice(String currsearch) { searchchoice = currsearch; } public String getSearchchoice() { return searchchoice; } public void setFilestring() { for (File currfile : this.files) { filenames.add(currfile.getName()); } } public void setFilenames(List<String> filenames) { this.filenames = filenames; } public List<String> getFilenames() { return filenames; } public void setSelecteddownloadfile(FileStorer thefile) { this.selecteddownloadfile = thefile; } public FileStorer getSelecteddownloadfile() { return selecteddownloadfile; } public void setFdownload(FileDownloadController fdownload) { this.fdownload = fdownload; } public FileDownloadController getFdownload() { return fdownload; } public void setSelectedfile(FileStorer thefile) { selectedfile = thefile; } public FileStorer getSelectedfile() { return selectedfile; } public FileUploadController getFchooser() { return fchooser; } public void setFchooser(FileUploadController fchooser) { this.fchooser = fchooser; } public String editPSearcher(String pSearcher) { this.pSearcher = pSearcher; return pSearcher; } public void setPSearcher(String pSearcher) { this.pSearcher = pSearcher; } public String getPSearcher() { return pSearcher; } public String getSearcher() { return searcher; } public void setSearcher(String searcher) { this.searcher = searcher; } public void save(ActionEvent actionEvent) { //Persist user FacesMessage msg = new FacesMessage("Successful", "Welcome "); FacesContext.getCurrentInstance().addMessage(null, msg); } private static Logger logger = Logger.getLogger(PubMedSearch.class.getName()); public PubMedSearch() { step = 1; counter = 0; searcher = "title"; buttonvalue = ""; userauthor = usertitle = userpmid = url = searcher = pSearcher = ""; base = "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/"; publications = new ArrayList<Publication>(); results = new ArrayList<Publication>(); checklist = new ArrayList<Publication>(); selectedindex = -1; selectedPub = new Publication(); fchooser = new FileUploadController(); files = new ArrayList<File>(); filenames = new ArrayList<String>(); allfiles = new ArrayList<FileStorer>(); previousfiles = new ArrayList<FileStorer>(); selectedfile = null; zip = new ZipDirectory(); finalsave = false; fdownload = new FileDownloadController(); selecteddownloadfile = null; index = 0; jv = jn = ji = jd = jm = jy = jsp = authorfull = doi = epday = epmonth = epyear = epubsum = epubsum2 = ""; selecteddownloadfiletype = selecteddownloadfilename = ""; searchchoice = ""; searchchoice = "searchtitle"; newrefinedfiles = new ArrayList<FileStorer>(); pmidlist = new ArrayList<Integer>(); confirmed = false; redostep3 = redostep5 = redostep6 = false; redostep3msg = redostep5msg = redostep6msg = ""; uploaderr = savemsg = ""; curruserid = Long.toString(LiferayFacesContext.getInstance().getUser().getUserId()); filesanddata = new ArrayList<String>(); match = false; } public void checkUpload() { if (!fchooser.getAllfiles().isEmpty()) { moveStep(4); } } public void configDisplay2() { String tmpdis = ""; if (!selectedPub.getFstorefiles().isEmpty()) { for (FileStorer currfile : selectedPub.getFstorefiles()) { if (currfile.getFigure().length() > 0 && currfile.getPanel().length() > 0) { tmpdis = "Figure " + currfile.getFigure() + ", Panel " + currfile.getPanel(); currfile.setFigpandisplay(tmpdis); } else if (currfile.getFigure().length() > 0 && currfile.getPanel().length() < 1) { tmpdis = "Figure " + currfile.getFigure(); currfile.setFigpandisplay(tmpdis); } else { currfile.setFigpandisplay(""); } } } } public void configDisplay() { String tmpdis = ""; for (FileStorer currfile : allfiles) { if (currfile.getFigure().length() > 0 && currfile.getPanel().length() > 0) { tmpdis = "Figure " + currfile.getFigure() + ", Panel " + currfile.getPanel(); currfile.setFigpandisplay(tmpdis); } else if (currfile.getFigure().length() > 0 && currfile.getPanel().length() < 1) { tmpdis = "Figure " + currfile.getFigure(); currfile.setFigpandisplay(tmpdis); } else { currfile.setFigpandisplay(""); } } } public void cleanMutual() { counter = 0; searcher = "title"; buttonvalue = ""; pmidlist = new ArrayList<Integer>(); userauthor = userpmid = url = searcher = pSearcher = ""; base = "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/"; publications = new ArrayList<Publication>(); results = new ArrayList<Publication>(); checklist = new ArrayList<Publication>(); selectedindex = -1; selectedPub = new Publication(); fchooser = new FileUploadController(); files = new ArrayList<File>(); filenames = new ArrayList<String>(); allfiles = new ArrayList<FileStorer>(); usertitle = ""; selectedfile = null; zip = new ZipDirectory(); fdownload = new FileDownloadController(); selecteddownloadfile = null; index = 0; previousfiles = new ArrayList<FileStorer>(); jv = jn = ji = jd = jm = jy = jsp = doi = epday = epmonth = epyear = epubsum = epubsum2 = ""; selecteddownloadfiletype = selecteddownloadfilename = ""; searchchoice = "searchtitle"; newrefinedfiles = new ArrayList<FileStorer>(); finalsave = false; confirmed = false; redostep3 = redostep5 = redostep6 = false; redostep3msg = redostep5msg = redostep6msg = ""; uploaderr = ""; match = false; curruserid = Long.toString(LiferayFacesContext.getInstance().getUser().getUserId()); } public void moveStep(int nextstep) { int previousstep = step; savemsg = ""; if (nextstep < step && step != 99) { switch (nextstep) { case 0: step = 0; CleanFileStorage(); getStoredFiles(); deleteZipFromRecord(); break; case 1: cleanMutual(); step = 1; break; case 2: break; case 3: step = 3; break; case 4: step = 4; break; case 5: step = 5; reconcileDescriptions(); draftPointSave2(); break; default: step = 1; break; } } else { step = nextstep; switch (step) { case 3: if (usertitle.isEmpty()) { step = 1; redostep1 = "Please enter a valid search."; } else if (redostep3 == false) { if (searchchoice == "searchauthor" || searchchoice == "searchtitle" || searchchoice == "searchpmid") { try { processUrl(); syncResults(); } catch (Exception ex) { logger.info(ex); } } redostep3 = true; } else if (redostep3 == true && previousstep == 99) { step = 3; } else { step = 4; } break; case 4: redostep1 = ""; if (selectedPub != null) { if (selectedPub.getExists()) { logger.info("The stored pub id is: " + selectedPub.getUserid() + " and the current user id is: " + curruserid); if (curruserid.equals(String.valueOf(selectedPub.getUserid()))) { match = true; } step = 99; } else { step = 4; } } else { uploaderr = "Please select a citation below to proceed."; step = 3; } break; case 5: if (previousstep == 4) { step = 5; uploaderr = ""; setFchooservar(); redostep5 = true; } else if (!fchooser.getAllfiles().isEmpty()) { uploaderr = ""; redostep5 = true; draftPointSave1(); CleanFileStorage(); getStoredFiles(); deleteZipFromRecord(); step = 6; } else { uploaderr = "You must upload at least one file to proceed."; step = 5; } break; case 6: validateDesc(); if (confirmed == true) { step = 7; configDisplay(); draftPointSave3(); } else { step = 6; draftPointSave2(); } redostep6 = true; break; case 7: configDisplay(); draftPointSave3(); break; case 8: if (!fchooser.getAllfiles().isEmpty()) { savemsg = "Your data has been saved to your account. This record will remain hidden until you choose to make it visible. To do so, you may return to this record by selecting View My Publications in the top menu."; } cleanMutual(); step = 1; break; } } try { LiferayFacesContext portletFacesContext = LiferayFacesContext.getInstance(); portletFacesContext.getExternalContext().redirect("upload"); return; } catch (Exception ex) { logger.info(ex); } } public void reconcileDescriptions() { for (FileStorer pfiles : previousfiles) { for (FileStorer afiles : allfiles) { if (afiles.getFilename().equals(pfiles.getFilename())) { if (pfiles.getDescription().length() > 0) { afiles.setDescription(pfiles.getDescription()); } if (pfiles.getFigure().length() > 0) { afiles.setFigure(pfiles.getFigure()); } if (pfiles.getFilelocation().length() > 0) { afiles.setFilelocation(pfiles.getFilelocation()); } if (pfiles.getPanel().length() > 0) { afiles.setPanel(pfiles.getPanel()); } if (pfiles.getFigpandisplay().length() > 0) { afiles.setFigpandisplay(pfiles.getFigpandisplay()); } } } } } public void validateDesc() { boolean verify = true; for (FileStorer currfile : allfiles) { //Validate Panel if (currfile.getFigure().length() < 1 && currfile.getPanel().length() >= 1) { currfile.setMessage("You must enter a figure number to correspond to the panel entered."); verify = false; } //Validate Description else if (currfile.getFigure().length() < 1 && currfile.getPanel().length() < 1 && currfile.getDescription().length() < 1) { currfile.setMessage("You must enter a description if there is no figure number entered."); verify = false; } else { currfile.setMessage(""); } } if (verify == true) { confirmed = true; } } public void syncResults() { for (Publication currpub : publications) { recurpmid = currpub.getPmid(); pmidlist.add(recurpmid); } SearchSolrList(pmidlist); } public void SearchSolr(int mypmid) { int currpmid = mypmid; try { CoreAdminRequest adminRequest = new CoreAdminRequest(); adminRequest.setAction(CoreAdminAction.RELOAD); SolrServer solr = new HttpSolrServer("http://localhost:8983/solr"); String query; query = "pmid:" + currpmid; SolrQuery theq = new SolrQuery(); theq.setQuery(query); QueryResponse response = new QueryResponse(); response = solr.query(theq, org.apache.solr.client.solrj.SolrRequest.METHOD.POST); SolrDocumentList list = response.getResults(); for (SolrDocument doc : list) { Publication currlist = new Publication(); currlist.setTitle(doc.getFieldValue("ptitle").toString()); currlist.setAbstract(doc.getFieldValue("abstract").toString()); currlist.setPmid(Integer.valueOf(doc.getFieldValue("pmid").toString())); results.add(currlist); } } catch (Exception ex) { logger.info(ex); StringWriter stack = new StringWriter(); ex.printStackTrace(new PrintWriter(stack)); } } public void SearchSolrList(List<Integer> mypmids) { String querylist = "pmid:("; List<Publication> results2 = new ArrayList<Publication>(); for (Integer currint : mypmids) { querylist += currint + " OR "; } if (querylist.length() > 5) { querylist = querylist.substring(0, querylist.length() - 4); querylist += ")"; } try { CoreAdminRequest adminRequest = new CoreAdminRequest(); adminRequest.setAction(CoreAdminAction.RELOAD); SolrServer solr = new HttpSolrServer("http://localhost:8983/solr"); SolrQuery theq = new SolrQuery(); theq.setQuery(querylist); QueryResponse response = new QueryResponse(); response = solr.query(theq, org.apache.solr.client.solrj.SolrRequest.METHOD.POST); SolrDocumentList list = response.getResults(); for (SolrDocument doc : list) { Publication currlist = new Publication(); solrindex = 0; currlist.setTitle(doc.getFieldValue("ptitle").toString()); currlist.setAbstract(doc.getFieldValue("abstract").toString()); currlist.setPmid(Integer.valueOf(doc.getFieldValue("pmid").toString())); currlist.setCompleted(Boolean.valueOf(doc.getFieldValue("completion").toString())); if (doc.getFieldValue("lruid") != null) { currlist.setUserid(Integer.valueOf(doc.getFieldValue("lruid").toString())); } else { currlist.setUserid(0); } if (doc.getFieldValues("pfileinfo") != null) { Collection<Object> currcoll = doc.getFieldValues("pfileinfo"); for (Object currobj : currcoll) { currlist = convertStore(String.valueOf(currobj), currlist); } } results2.add(currlist); } int currcounter = 0; for (Publication solrmatch : results2) { currcounter = 0; for (Publication publistrecord : publications) { if (solrmatch.getPmid() == publistrecord.getPmid()) { publications.get(currcounter).setExists(true); publications.get(currcounter).setCompleted(solrmatch.getCompleted()); publications.get(currcounter).setFstorefiles(solrmatch.getFstorefiles()); publications.get(currcounter).setUserid(solrmatch.getUserid()); } currcounter++; } } } catch (Exception ex) { logger.error("Error : ", ex); } } public Publication convertStore(String fileinfo, Publication currlist) { int fname, fsize, ffigure, fpanel, fdescription = -1; String sname, ssize, sfigure, spanel, sdescription; sname = ssize = sfigure = spanel = sdescription = ""; fsize = fileinfo.indexOf("filesize:"); fdescription = fileinfo.indexOf(",filedescription:"); ffigure = fileinfo.indexOf(",filefigure:"); fpanel = fileinfo.indexOf(",filepanel:"); fname = fileinfo.indexOf(",filename:"); if (fsize != -1 && fdescription != -1) { ssize = (String) fileinfo.subSequence(fsize, fdescription); } if (ffigure != -1 && fdescription != -1) { sdescription = (String) fileinfo.subSequence(fdescription, ffigure); } if (ffigure != -1 && fpanel != -1) { sfigure = (String) fileinfo.subSequence(ffigure, fpanel); } if (fname != -1 && fpanel != -1) { spanel = (String) fileinfo.subSequence(fpanel, fname); } if (fname != -1) { sname = (String) fileinfo.subSequence(fname, fileinfo.length()); } ssize = ssize.replace("filesize:", ""); sname = sname.replace(",filename:", ""); sdescription = sdescription.replace(",filedescription:", ""); sfigure = sfigure.replace(",filefigure:", ""); spanel = spanel.replace(",filepanel:", ""); String fileloc = PropsUtil.get("data_store2") + currlist.getPmid() + "/"; FileStorer currfile = new FileStorer(); currfile.setDescription(sdescription); currfile.setFigure(sfigure); currfile.setFilesize(Long.valueOf(ssize)); currfile.setFilename(sname); currfile.setPanel(spanel); currfile.setIndex(solrindex); currfile.setFilelocation(fileloc); currfile.setLocalfilestore(fileloc); currlist.getFstorefiles().add(currfile); solrindex++; return currlist; } public void downloadPrep(FileStorer currfile) { String filename = currfile.getFilename(); if (selecteddownloadfile != null) { String filetype = filename.substring(filename.length() - 4, filename.length() - 1); currfile.setFiletype(filetype); try { fdownload.downloadFile(currfile); } catch (Exception ex) { logger.info(ex); } } } public boolean checkSubmit() { if ((this.getUserauthor().length() > 0) || (this.getUsertitle().length() > 0) || (this.getUserpmid().length() > 0)) { return true; } else { return false; } } public List<File> getFiles() { return files; } public void setFiles(List<File> files) { this.files = files; } public void setFchooservar() { selectedpubpmid = this.selectedPub.getPmid(); fchooser.setPmid(selectedpubpmid); } public void setSelectedindex(int si) { this.selectedindex = si; } public Publication identifyRecord() { return publications.get(this.selectedindex); } public void CleanFileStorage() { previousfiles.addAll(allfiles); allfiles = new ArrayList<FileStorer>(); files = new ArrayList<File>(); filenames = new ArrayList<String>(); selectedPub.setFiles(files); selectedPub.setFilenames(filenames); } public void getStoredFiles() { String currlocation = PropsUtil.get("data_store2") + this.selectedPub.getPmid() + "/"; String zipfilelocation = currlocation + this.selectedPub.getPmid() + ".zip"; File folder = new File(currlocation); for (File currfile : folder.listFiles()) { String absolutePath = currfile.getAbsolutePath(); FileStorer currfilestore = new FileStorer(); currfilestore.setFilename(currfile.getName()); currfilestore.setFilelocation(currfile.getPath()); if (currfile.length() / 1000 < 1) { currfilestore.setFilesize(1); } else { currfilestore.setFilesize(currfile.length() / 1000); } currfilestore.setFiletype(FilenameUtils.getExtension(currfile.getName())); currfilestore.setLocalfilestore(absolutePath.substring(0, absolutePath.lastIndexOf(File.separator))); allfiles.add(currfilestore); files.add(currfile); filenames.add(currfile.getName()); } selectedPub.setFiles(files); selectedPub.setFilenames(filenames); reconcileDescriptions(); if (step != 0) { try { zip.setPmid(this.selectedPub.getPmid()); zip.Zipfiles(currlocation, zipfilelocation); } catch (Exception ex) { logger.info(ex); } } } public void getStoredFilesforDraftPointOnly() { String currlocation = PropsUtil.get("data_store2") + this.selectedPub.getPmid() + "/"; File folder = new File(currlocation); allfiles = new ArrayList<FileStorer>(); for (File currfile : folder.listFiles()) { String absolutePath = currfile.getAbsolutePath(); FileStorer currfilestore = new FileStorer(); currfilestore.setFilename(currfile.getName()); currfilestore.setFilelocation(currfile.getPath()); if (currfile.length() / 1000 < 1) { currfilestore.setFilesize(1); } else { currfilestore.setFilesize(currfile.length() / 1000); } currfilestore.setFiletype(FilenameUtils.getExtension(currfile.getName())); currfilestore.setLocalfilestore(absolutePath.substring(0, absolutePath.lastIndexOf(File.separator))); if (!currfilestore.getFilename().equals(selectedPub.getPmid() + ".zip")) { allfiles.add(currfilestore); files.add(currfile); filenames.add(currfile.getName()); } } selectedPub.setFiles(files); selectedPub.setFilenames(filenames); reconcileDescriptions(); } public void sendtoSolr() { setSOLRVariables(); try { setSOLRMetadata(); metadoc.addField("completion", "false"); metadoc.addField("draftpoint", "1"); server.add(metadoc); server.commit(); } catch (Exception ex) { logger.info(ex); } } public void handleFileUpload(FileUploadEvent event) { if (event != null) { fchooser.setFile(event.getFile()); fchooser.setNewestfiles(new ArrayList<UploadedFile>()); if (fchooser.getFilesondrive().isEmpty()) { fchooser.RetrieveFiles(); } else { fchooser.setFilesondrive(new ArrayList<FileStorer>()); fchooser.RetrieveFiles(); } fchooser.getNewestfiles().add(event.getFile()); fchooser.checkUploads(); fchooser.getAllfiles().add(event.getFile()); fchooser.FileSave(); getStoredFilesforDraftPointOnly(); newrefinedfiles = allfiles; draftPointSave1(); setSavedMsg(); RequestContext.getCurrentInstance() .execute("jQuery(\"div.fileupload-content tr.ui-state-error\").remove();"); } } public void deleteZipFromRecord() { //making an artificially large number to ensure the index is found Iterator<FileStorer> myitr = allfiles.iterator(); while (myitr.hasNext()) { FileStorer currfile = (FileStorer) myitr.next(); if (currfile.getFilename().equals(selectedPub.getPmid() + ".zip")) { myitr.remove(); } } } public int getCounter() { return this.counter; } public void downloadRawFiles(FileStorer currfile) { selecteddownloadfile = currfile; if (selecteddownloadfile != null) { downloadInit(); } } public void downloadInit() { //Gather the content type and store selecteddownloadfilename = selecteddownloadfile.getFilename(); String currtype = FilenameUtils.getExtension(selecteddownloadfile.getFilename()); selecteddownloadfile.setFiletype(currtype); downloadFile(selecteddownloadfilename, selecteddownloadfiletype); //Begin the download process } public void downloadZipOnly() { if (step == 0) { selectedpubpmid = selectedPub.getPmid(); } selecteddownloadfile = new FileStorer(); String fileloc = PropsUtil.get("data_store2") + selectedpubpmid; String filen = selectedpubpmid + ".zip"; selecteddownloadfile.setFilelocation(fileloc); selecteddownloadfile.setFilename(filen); selecteddownloadfile.setIndex(0); selecteddownloadfile.setLocalfilestore(fileloc); selecteddownloadfile.setFiletype("zip"); downloadFile(filen, "zip"); } public void downloadFile(String filename, String filetype) { //The filetypes used are as follows- //doc|docx|xls|xlsx|pdf|abf|xml|pgf|pul|amp|dat|txt|zip|tar String contentType = ""; if (filetype.equals("zip")) { contentType = "application/zip"; } else if (filetype.equals("tar")) { contentType = "application/tar"; } else if (filetype.equals("xls") || filetype.equals("xlsx")) { contentType = "application/xls"; } else if (filetype.equals("doc") || filetype.equals("docx")) { contentType = "application/doc"; } else if (filetype.equals("pdf")) { contentType = "application/pdf"; } else if (filetype.equals("xml")) { contentType = "text/xml"; } else { contentType = "text/plain"; } FacesContext facesContext = (FacesContext) FacesContext.getCurrentInstance(); ExternalContext externalContext = facesContext.getExternalContext(); PortletResponse portletResponse = (PortletResponse) externalContext.getResponse(); HttpServletResponse response = PortalUtil.getHttpServletResponse(portletResponse); File file = new File(selecteddownloadfile.getLocalfilestore(), filename); BufferedInputStream input = null; BufferedOutputStream output = null; try { input = new BufferedInputStream(new FileInputStream(file), 10240); response.reset(); response.setHeader("Content-Type", contentType); response.setHeader("Content-Length", String.valueOf(file.length())); response.setHeader("Content-Disposition", "attachment; filename=\"" + filename + "\""); response.flushBuffer(); output = new BufferedOutputStream(response.getOutputStream(), 10240); byte[] buffer = new byte[10240]; int length; while ((length = input.read(buffer)) > 0) { output.write(buffer, 0, length); } output.flush(); } catch (FileNotFoundException e) { e.printStackTrace(); } catch (IOException e) { e.printStackTrace(); } finally { try { output.close(); input.close(); } catch (IOException e) { e.printStackTrace(); } } facesContext.responseComplete(); } public void FileSave() { String currpmid = String.valueOf(selectedPub.getPmid()); String currlocation = PropsUtil.get("data_store2") + currpmid; ArrayList<org.primefaces.model.UploadedFile> thefiles = new ArrayList<org.primefaces.model.UploadedFile>(); File thedir = new File(currlocation); if (!thedir.exists()) { thedir.mkdirs(); } //Now add files to it try { thefiles = fchooser.getNewestfiles(); OutputStream out = new FileOutputStream(thedir); for (org.primefaces.model.UploadedFile currfile : thefiles) { String fullfilelocation = currlocation + currfile.getFileName(); File myfile = new File(fullfilelocation); InputStream in = currfile.getInputstream(); out = new FileOutputStream(myfile); org.apache.commons.io.IOUtils.copy(in, out); } } catch (Exception ex) { logger.info(ex); } } public void initialProcess() throws Exception { String input = ""; if (this.getUsertitle().length() > 0) { input = this.getUsertitle(); } else if (this.getUserauthor().length() > 0) { input = this.getUserauthor(); } else if (this.getUserpmid().length() > 0) { input = this.getUserpmid(); } if (searcher.equalsIgnoreCase("title")) { input = input.replaceAll("\\s", "+"); if (input.charAt(input.length() - 1) == ((char) '+')) { input = input.substring(0, input.length() - 1); } url = base + "esearch.fcgi?db=pubmed&term=" + input + "&retmax=200&tool=ceptools"; } else if (searcher.equalsIgnoreCase("pmid")) { input = input.replaceAll("\\s", "+"); if (input.charAt(input.length() - 1) == ((char) '+')) { input = input.substring(0, input.length() - 1); } url = base + "efetch.fcgi?db=pubmed&id=" + input + "&retmode=xml&rettype=abstract"; } else if (searcher.equalsIgnoreCase("author")) { input = input.replaceAll("\\s", "+"); if (input.charAt(input.length() - 1) == ((char) '+')) { input = input.substring(0, input.length() - 1); } url = base + "esearch.fcgi?db=pubmed&term=" + input + "&retmax=200&tool=ceptools"; } } public void handleFileSavePoint1(ActionEvent event) { if (event != null) { if (fchooser.getAllfiles().isEmpty()) { FacesMessage msg1 = new FacesMessage( "You must upload at least 1 file before you can save this publication.", ""); FacesContext.getCurrentInstance().addMessage(null, msg1); } else { draftPointSave1(); setSavedMsg(); } } } public void setSavedMsg() { FacesMessage msg2 = new FacesMessage("Your progress is saved.", " You may access this record under 'View My Publications'."); FacesContext.getCurrentInstance().addMessage(null, msg2); } public void handleFileSavePoint2(ActionEvent event) { if (event != null) { draftPointSave2(); setSavedMsg(); } } //save and return upload public void handleFileSavePoint3(ActionEvent event) { if (event != null) { if (fchooser.getAllfiles().isEmpty()) { moveStep(8); } else { getStoredFilesforDraftPointOnly(); draftPointSave1(); setSavedMsg(); moveStep(8); } } } //save and return descriptions public void handleFileSavePoint4(ActionEvent event) { if (event != null) { FacesMessage msg1 = new FacesMessage("Saving your progress...please wait.", ""); FacesContext.getCurrentInstance().addMessage(null, msg1); draftPointSave2(); FacesMessage msg2 = new FacesMessage("Your progress is saved.", " You may access your draft under 'View My Publications'."); FacesContext.getCurrentInstance().addMessage(null, msg2); } moveStep(8); } public void setSOLRVariables() { filesanddata = new ArrayList<String>(); String allstrings = ""; for (FileStorer currfile : allfiles) { String cfilesize = "filesize:" + String.valueOf(currfile.getFilesize()); String cfiledescription = ",filedescription:" + currfile.getDescription(); String cfilefigure = ",filefigure:" + currfile.getFigure(); String cfilepanel = ",filepanel:" + currfile.getPanel(); String cfilename = ",filename:" + currfile.getFilename(); allstrings = cfilesize + cfiledescription + cfilefigure + cfilepanel + cfilename; filesanddata.add(allstrings); } } public void setSOLRMetadata() { server = new HttpSolrServer("http://localhost:8983/solr"); metadoc = new SolrInputDocument(); metadoc.addField("pmid", selectedPub.getPmid()); metadoc.addField("abstract", selectedPub.getAbstract()); metadoc.addField("publicationdate_year", selectedPub.getYear()); metadoc.addField("doi", selectedPub.getDoi()); metadoc.addField("journalvolume", selectedPub.getJournalvolume()); metadoc.addField("journalissue", selectedPub.getJournalissue()); metadoc.addField("journalmonth", selectedPub.getJournalmonth()); metadoc.addField("journalyear", selectedPub.getJournalyear()); metadoc.addField("journalday", selectedPub.getJournalday()); metadoc.addField("journalname", selectedPub.getJournalname()); metadoc.addField("journalpage", selectedPub.getJournalstartpg()); metadoc.addField("epubday", selectedPub.getEpubday()); metadoc.addField("epubmonth", selectedPub.getEpubmonth()); metadoc.addField("epubyear", selectedPub.getEpubyear()); metadoc.addField("author_fullname_list", selectedPub.getAuthorfull()); metadoc.addField("lruid", curruserid); metadoc.addField("ptitle", selectedPub.getTitle()); for (int i = 0; i < selectedPub.getFauthors().size(); i++) { metadoc.addField("author_firstname", selectedPub.getFauthors().get(i)); metadoc.addField("author_lastname", selectedPub.getLauthors().get(i)); } for (String currstring : filesanddata) { metadoc.addField("pfileinfo", currstring); } } //update SOLR with the user's draftpoint save point 1 public void draftPointSave1() { setSOLRVariables(); try { setSOLRMetadata(); metadoc.addField("completion", "false"); metadoc.addField("draftpoint", "1"); server.add(metadoc); server.commit(); } catch (Exception ex) { logger.info(ex); } } //update SOLR with the user's draftpoint save point 2 public void draftPointSave2() { setSOLRVariables(); try { setSOLRMetadata(); metadoc.addField("completion", "false"); metadoc.addField("draftpoint", "2"); server.add(metadoc); server.commit(); } catch (Exception ex) { logger.info(ex); } } public void draftPointSave3() { setSOLRVariables(); finalsave = true; try { setSOLRMetadata(); metadoc.addField("completion", "true"); metadoc.addField("draftpoint", "2"); server.add(metadoc); server.commit(); } catch (Exception ex) { logger.info(ex); } } public void processUrl() throws Exception { searcher = "title"; initialProcess(); SAXReader reader = new SAXReader(); SAXReader reader2 = new SAXReader(); Document document; String mytitle, myabstract, myyear, myfullname; Element journalname, journalyear, journalmonth, journalday, journalvolume, journalissue, journalpagestart, epubday, epubmonth, epubyear, pubdoi; int mypmid; List<String> mylauthors = new ArrayList<String>(); List<String> myfauthors = new ArrayList<String>(); List<String> myfnames = new ArrayList<String>(); //PubMed if (searcher.equalsIgnoreCase("title")) { int counter = 1; document = reader.read(url); @SuppressWarnings("rawtypes") List idlist = document.selectNodes("//IdList/Id"); @SuppressWarnings("rawtypes") Iterator iditer = idlist.iterator(); String pubmedlist = ""; int x = 0; this.counter = 0; while (iditer.hasNext()) { Element pelement = (Element) iditer.next(); if (x == 0) { pubmedlist += pelement.getText(); x += 1; } else { pubmedlist += "," + pelement.getText(); } } url = base + "efetch.fcgi?db=pubmed&id=" + pubmedlist + "&retmax=200&retmode=xml&rettype=abstract"; Document pubdoc = reader2.read(url); @SuppressWarnings("unchecked") List<Node> thelist = pubdoc.selectNodes("//PubmedArticle| //PubmedBookArticle"); Element abstractnode, titlenode, yearsnode, pmidnode; @SuppressWarnings("rawtypes") List firstnamenode; @SuppressWarnings("rawtypes") List lastnamenode; for (Node currnode : thelist) { mylauthors = new ArrayList<String>(); myfauthors = new ArrayList<String>(); myfnames = new ArrayList<String>(); epubsum = epubsum2 = authorfull = ""; titlenode = (Element) currnode.selectSingleNode(".//ArticleTitle | .//BookTitle"); yearsnode = (Element) currnode .selectSingleNode(".//PubDate/Year | .//DateCompleted/Year | .//DateCreated/Year"); journalname = (Element) currnode.selectSingleNode(".//Journal/Title"); journalyear = (Element) currnode.selectSingleNode(".//PubDate/Year"); journalmonth = (Element) currnode.selectSingleNode(".//PubDate/Month"); journalday = (Element) currnode.selectSingleNode(".//PubDate/Day"); journalvolume = (Element) currnode.selectSingleNode(".//JournalIssue/Volume"); journalissue = (Element) currnode.selectSingleNode(".//JournalIssue/Issue"); journalpagestart = (Element) currnode.selectSingleNode(".//Pagination/MedlinePgn"); epubday = (Element) document.selectSingleNode( ".//PubMedPubDate[@PubStatus='aheadofprint']/Day | .//PubMedPubDate[@PubStatus='epublish']/Day "); epubmonth = (Element) document.selectSingleNode( ".//PubMedPubDate[@PubStatus='aheadofprint']/Month | .//PubMedPubDate[@PubStatus='epublish']/Month"); epubyear = (Element) document.selectSingleNode( ".//PubMedPubDate[@PubStatus='aheadofprint']/Year | .//PubMedPubDate[@PubStatus='epublish']/Year"); pubdoi = (Element) currnode.selectSingleNode(".//ArticleId[@IdType='doi']"); firstnamenode = currnode.selectNodes(".//ForeName"); lastnamenode = currnode.selectNodes(".//LastName"); abstractnode = (Element) currnode.selectSingleNode(".//Abstract/AbstractText[1]"); pmidnode = (Element) currnode.selectSingleNode(".//PMID"); myfnames = new ArrayList<String>(); @SuppressWarnings("rawtypes") Iterator fiter = firstnamenode.iterator(); @SuppressWarnings("rawtypes") Iterator liter = lastnamenode.iterator(); if (journalname != null) { jn = journalname.getText(); } if (journalvolume != null) { jv = journalvolume.getText(); } if (journalissue != null) { ji = journalissue.getText(); } if (journalmonth != null) { jm = journalmonth.getText(); } if (journalyear != null) { jy = journalyear.getText(); } if (journalpagestart != null) { jsp = journalpagestart.getText(); } if (journalday != null) { jd = journalday.getText(); } if (epubday != null) { epday = epubday.getText(); } if (epubmonth != null) { epmonth = epubmonth.getText(); } if (epubyear != null) { epyear = epubyear.getText(); } if (pubdoi != null) { doi = "doi: " + pubdoi.getText(); } if (jv.length() > 0) { epubsum2 += jv; } if (ji.length() > 0) { epubsum2 += "(" + ji + ")" + ":"; } if (jsp.length() > 0) { epubsum2 += jsp + "."; } if (epmonth.length() < 1 && epyear.length() < 1 && epday.length() < 1) { epubsum = "[Epub ahead of print]"; } else if (epyear.length() > 0) { epubsum = "Epub " + epyear + " " + epmonth + " " + epday; } else { epubsum = ""; } mytitle = titlenode.getText(); myyear = yearsnode.getText(); mypmid = Integer.valueOf(pmidnode.getText()); while (fiter.hasNext()) { Element fname = (Element) fiter.next(); Element lname = (Element) liter.next(); myfauthors.add(fname.getText()); mylauthors.add(lname.getText()); myfullname = fname.getText() + " " + lname.getText(); myfnames.add(myfullname); if (fiter.hasNext()) { authorfull = authorfull + myfullname + ", "; } else { authorfull = authorfull + myfullname; } } if (abstractnode != null) { myabstract = abstractnode.getText(); } else { myabstract = "NO ABSTRACT FOUND."; } publications.add(new Publication(mytitle, myabstract, myyear, myfauthors, mylauthors, myfnames, jv, jn, jy, jm, jd, jsp, ji, epday, epmonth, epyear, doi, epubsum, epubsum2, authorfull, mypmid, counter)); counter++; } } } }