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.IOException; import java.io.PrintWriter; import java.io.Serializable; import java.io.StringWriter; import java.util.ArrayList; import java.util.Collection; import java.util.List; import javax.faces.bean.ManagedBean; import javax.faces.bean.SessionScoped; import javax.faces.context.ExternalContext; import javax.faces.context.FacesContext; import javax.portlet.PortletResponse; import javax.servlet.http.HttpServletResponse; import org.apache.commons.io.FilenameUtils; import org.apache.log4j.Logger; import org.primefaces.event.FlowEvent; 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.response.QueryResponse; import org.apache.solr.common.SolrDocument; import org.apache.solr.common.SolrDocumentList; 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.FileStorer; import edu.jhu.cvrg.ceptools.controller.Publication; @ManagedBean(name = "searchPubs") @SessionScoped public class SearchPubs implements Serializable { private static final long serialVersionUID = 3L; private static Logger logger = Logger.getLogger(SearchPubs.class.getName()); List<Publication> results; private List<FileStorer> allfiles; private FileStorer selectedfile; private boolean redostep2; private String redostep2msg; private FileStorer selecteddownloadfile; Publication searchresultpub; String searchentry; private List<File> files; private List<String> filenames; private List<FileStorer> filesfromsolr; private String pmid; private String step1msg; private String selecteddownloadfiletype; private String selecteddownloadfilename; int step; int solrindex; private boolean match; public SearchPubs() { allfiles = new ArrayList<FileStorer>(); redostep2 = false; filesfromsolr = new ArrayList<FileStorer>(); searchentry = ""; selecteddownloadfile = null; searchresultpub = null; selectedfile = null; results = new ArrayList<Publication>(); files = new ArrayList<File>(); filenames = new ArrayList<String>(); solrindex = 0; pmid = ""; step = 1; selecteddownloadfiletype = selecteddownloadfilename = ""; redostep2 = false; step1msg = ""; redostep2msg = ""; match = false; } public void reassignStepsandSearch() { searchentry = ""; step = 1; } public void cleanMutual() { searchresultpub = null; results = new ArrayList<Publication>(); allfiles = new ArrayList<FileStorer>(); selecteddownloadfile = null; selectedfile = null; results = new ArrayList<Publication>(); files = new ArrayList<File>(); filenames = new ArrayList<String>(); solrindex = 0; step1msg = ""; redostep2 = false; redostep2msg = ""; pmid = ""; selecteddownloadfiletype = selecteddownloadfilename = ""; match = false; } public void setMatch(boolean m) { match = m; } public boolean getMatch() { return match; } public void setStep1msg(String m) { step1msg = m; } public String getStep1msg() { return step1msg; } public void setRedostep2msg(String m) { redostep2msg = m; } public String getRedostep2msg() { return redostep2msg; } public void setRedostep2(boolean m) { redostep2 = m; } public boolean getRedostep2() { return redostep2; } public int getSolrindex() { return solrindex; } public void setSolrIndex(int s) { solrindex = s; } public void setFilesfromsolr(List<FileStorer> f) { filesfromsolr = f; } public List<FileStorer> getFilesfromsolr() { return filesfromsolr; } public void setAllfiles(List<FileStorer> g) { allfiles = g; } public List<FileStorer> getAllfiles() { return allfiles; } public void setSelecteddownloadfile(FileStorer afiles) { selecteddownloadfile = afiles; } public FileStorer getSelecteddownloadfile() { return selecteddownloadfile; } public void setSelectedfile(FileStorer thefile) { selectedfile = thefile; } public FileStorer getSelectedfile() { return selectedfile; } public void setResults(List<Publication> re) { this.results = re; } public List<Publication> getResults() { return results; } public void setSearchresultpub(Publication pub) { this.searchresultpub = pub; } public Publication getSearchresultpub() { return searchresultpub; } public String getSearchentry() { return searchentry; } public void setSearchentry(String se) { this.searchentry = se; } public void setStep(int currstep) { step = currstep; } public int getStep() { return step; } public void moveStep(int nextstep) { int previousstep = step; step = nextstep; if (step == 1) { cleanMutual(); reassignStepsandSearch(); } if (step == 2) { if (previousstep == 1) { cleanMutual(); if (searchentry.isEmpty()) { step = 1; redostep2msg = "Please enter a valid search. Use * for wildcard searches."; } else { redostep2msg = ""; SearchSolr(); redostep2 = true; } } else if (redostep2 == true) { if (previousstep == 99 || previousstep == 3) { step = 2; } else if (searchresultpub != null) { step = 3; } else { step = 2; redostep2msg = "Please choose a single citation from the listing."; } } } if (step == 3) { if (!searchresultpub.getCompleted()) { match = false; String curruserid = Long.toString(LiferayFacesContext.getInstance().getUser().getUserId()); logger.info( "The current user is: " + curruserid + " one file id is: " + searchresultpub.getUserid()); if (curruserid.equals(searchresultpub.getUserid())) { match = true; } step = 99; } else { RetrieveFiles(); setDisplay(); } } try { LiferayFacesContext portletFacesContext = LiferayFacesContext.getInstance(); portletFacesContext.getExternalContext().redirect("search"); return; } catch (Exception ex) { logger.info(ex); } } public void downloadRawFiles(FileStorer currfile) { selecteddownloadfile = currfile; if (selecteddownloadfile != null) { downloadInit(); } } public void 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") + pmid + "/"; 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.addFile(currfile); //filesfromsolr.add(currfile); solrindex++; } public void downloadZipOnly() { selecteddownloadfile = new FileStorer(); String fileloc = PropsUtil.get("data_store2") + pmid + "/"; String filen = pmid + ".zip"; selecteddownloadfile.setFilelocation(fileloc); selecteddownloadfile.setFilename(filen); selecteddownloadfile.setIndex(0); selecteddownloadfile.setLocalfilestore(fileloc); selecteddownloadfile.setFiletype("zip"); downloadFile(filen, "zip"); } public void downloadInit() { //Gather the content type and store selecteddownloadfilename = selecteddownloadfile.getFilename(); String currtype = FilenameUtils.getExtension(selecteddownloadfile.getFilename()); selecteddownloadfile.setFiletype(currtype); //Begin the download process downloadFile(selecteddownloadfilename, selecteddownloadfiletype); } public String onFlowProcess(FlowEvent event) { if (event.getOldStep().equalsIgnoreCase("searchpubs")) { SearchSolr(); return "searchresultsofpubs"; } else if (event.getOldStep().equalsIgnoreCase("searchresultsofpubs")) { RetrieveFiles(); return "searchresultdisplay"; } else { cleanMutual(); reassignStepsandSearch(); return "searchpubs"; } } private void RetrieveFiles() { int currpmid = searchresultpub.getPmid(); pmid = String.valueOf(currpmid); String currlocation = PropsUtil.get("data_store2") + this.searchresultpub.getPmid() + "/"; File folder = new File(currlocation); for (File currfile : folder.listFiles()) { String absolutePath = currfile.getAbsolutePath(); FileStorer currfilestore = new FileStorer(); currfilestore.setFilename(currfile.getName()); currfilestore.setFilelocation(currlocation); 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()); } searchresultpub.setFiles(files); searchresultpub.setFilenames(filenames); } public void downloadFile(String filename, String filetype) { String contentType = "application/zip"; if (filetype.equals("abf")) { contentType = "text/abf"; } FacesContext facesContext = (FacesContext) FacesContext.getCurrentInstance(); ExternalContext externalContext = facesContext.getExternalContext(); PortletResponse portletResponse = (PortletResponse) externalContext.getResponse(); HttpServletResponse response = PortalUtil.getHttpServletResponse(portletResponse); File file = new File(selecteddownloadfile.getFilelocation(), 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(); } @SuppressWarnings("unchecked") public void SearchSolr() { try { // CoreAdminRequest adminRequest = new CoreAdminRequest(); // adminRequest.setAction(CoreAdminAction.RELOAD); SolrServer solr = new HttpSolrServer("http://localhost:8983/solr"); String query; query = "collector:" + searchentry; SolrQuery theq = new SolrQuery(); theq.setQuery(query); theq.setRows(1000); QueryResponse response = new QueryResponse(); response = solr.query(theq); SolrDocumentList list = response.getResults(); int docnum = 1; for (SolrDocument doc : list) { Publication currlist = new Publication(); List<String> fullnames = new ArrayList<String>(); String currepubsum1 = "", currepubsum2 = ""; currlist.setTitle(doc.getFieldValue("ptitle").toString()); currlist.setAbstract(doc.getFieldValue("abstract").toString()); currlist.setPmid(Integer.valueOf(doc.getFieldValue("pmid").toString())); pmid = String.valueOf(currlist.getPmid()); if (doc.getFieldValue("lruid") != null) { currlist.setUserid(doc.getFieldValue("lruid").toString()); } else { currlist.setUserid(""); } if (doc.getFieldValue("journalname") != null) { currlist.setJournalname(doc.getFieldValue("journalname").toString()); } if (doc.getFieldValue("completion") != null) { currlist.setCompleted(Boolean.valueOf(doc.getFieldValue("completion").toString())); } else { currlist.setCompleted(false); } if (doc.getFieldValue("journalyear") != null) { currlist.setJournalyear(doc.getFieldValue("journalyear").toString()); } if (doc.getFieldValue("journalday") != null) { currlist.setJournalday(doc.getFieldValue("journalday").toString()); } if (doc.getFieldValue("journalmonth") != null) { currlist.setJournalmonth(doc.getFieldValue("journalmonth").toString()); } if (doc.getFieldValue("journalpage") != null) { currlist.setJournalstartpg(doc.getFieldValue("journalpage").toString()); } if (doc.getFieldValue("journalissue") != null) { currlist.setJournalissue(doc.getFieldValue("journalissue").toString()); } if (doc.getFieldValue("journalvolume") != null) { currlist.setJournalvolume(doc.getFieldValue("journalvolume").toString()); } if (doc.getFieldValue("publication_year") != null) { currlist.setYear(doc.getFieldValue("publicationdate_year").toString()); } if (doc.getFieldValue("doi") != null) { currlist.setDoi(doc.getFieldValue("doi").toString()); } if (doc.getFieldValues("pfileinfo") != null) { Collection<Object> currcoll = doc.getFieldValues("pfileinfo"); for (Object currobj : currcoll) { convertStore(String.valueOf(currobj), currlist); } } List<String> fieldValue = (List<String>) doc.getFieldValue("author_firstname"); currlist.setFauthors(fieldValue); currlist.setLauthors((List<String>) doc.getFieldValue("author_lastname")); if (doc.getFieldValue("epubmonth") != null) { currlist.setEpubmonth(doc.getFieldValue("epubmonth").toString()); } if (doc.getFieldValue("epubyear") != null) { currlist.setEpubyear(doc.getFieldValue("epubyear").toString()); } if (doc.getFieldValue("epubday") != null) { currlist.setEpubday(doc.getFieldValue("epubday").toString()); } if (doc.getFieldValue("author_fullname_list") != null) { currlist.setAuthorfull(doc.getFieldValue("author_fullname_list").toString()); } int counter = 0; for (String currstring : currlist.getFauthors()) { currstring += " " + currlist.getLauthors().get(counter); fullnames.add(currstring); counter++; } currlist.setFullnames(fullnames); if (currlist.getJournalvolume().length() > 0) { currepubsum2 += currlist.getJournalvolume(); } if (currlist.getJournalissue().length() > 0) { currepubsum2 += "(" + currlist.getJournalissue() + ")" + ":"; } if (currlist.getJournalstartpg().length() > 0) { currepubsum2 += currlist.getJournalstartpg() + "."; } if (currlist.getEpubday().length() < 1 && currlist.getEpubmonth().length() < 1 && currlist.getEpubyear().length() < 1) { currepubsum1 = "[Epub ahead of print]"; } else if (currlist.getEpubyear().length() > 0) { currepubsum1 = "Epub " + currlist.getEpubyear() + " " + currlist.getEpubmonth() + " " + currlist.getEpubday(); } else { currepubsum1 = ""; } currlist.setEpubsum(currepubsum1); currlist.setEpubsum2(currepubsum2); currlist.setIndex(docnum); results.add(currlist); docnum++; } } catch (Exception ex) { logger.info(ex); StringWriter stack = new StringWriter(); ex.printStackTrace(new PrintWriter(stack)); } } public void setDisplay() { String tmpdis = ""; for (FileStorer currfile : searchresultpub.getPubfiles()) { 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(""); } } } }