Java tutorial
/* Copyright (c) 2014 "(IA)2 Research Group. Universidad de Mlaga" http://iaia.lcc.uma.es | http://www.uma.es This file is part of SISOB Data Extractor. SISOB Data Extractor is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. SISOB Data Extractor is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with SISOB Data Extractor. If not, see <http://www.gnu.org/licenses/>. */ package eu.sisob.uma.NPL.Researchers; import eu.sisob.uma.api.prototypetextmining.AnnotatorCollector; import eu.sisob.uma.api.prototypetextmining.MiddleData; import eu.sisob.uma.api.prototypetextmining.globals.CVItemExtracted; import eu.sisob.uma.api.prototypetextmining.globals.DataExchangeLiterals; import gate.Annotation; import gate.AnnotationSet; import gate.Document; import gate.FeatureMap; import java.io.File; import java.io.FileWriter; import java.io.IOException; import java.io.UnsupportedEncodingException; import java.net.URISyntaxException; import java.net.URL; import java.net.URLEncoder; import java.util.ArrayList; import java.util.HashMap; import java.util.HashSet; import java.util.List; import java.util.Set; import java.util.logging.Level; import org.apache.commons.io.FileUtils; import org.apache.log4j.Logger; /** * *** @author Daniel Lpez Gonzlez (dlopezgonzalez@gmail.com) for the SISOB PROJECT (http://sisob.lcc.uma.es/) */ public class GateResearcherAnnCollector extends AnnotatorCollector { /** * * @param type */ public GateResearcherAnnCollector(String type) { super(type); } /** * * @param doc * @param aoData */ @Override public void collect(Object doc, MiddleData aoData) { int n_expressions = 0; org.dom4j.Element eOut = org.dom4j.DocumentFactory.getInstance().createElement("blockinfo"); eOut.addAttribute(DataExchangeLiterals.MIDDLE_ELEMENT_XML_ID_ANNOTATIONRECOLLECTING, aoData.getId_annotationrecollecting()); // aoData[MiddleData.I_INDEX_DATA_TYPE].toString()); eOut.addAttribute(DataExchangeLiterals.MIDDLE_ELEMENT_XML_ID_ENTITY_ATT, aoData.getId_entity()); // aoData[MiddleData.I_INDEX_DATA_ID].toString()); gate.Document docGate = (gate.Document) doc; HashMap<String, String> extra_data = null; try { extra_data = (HashMap<String, String>) aoData.getData_extra(); } catch (Exception ex) { extra_data = null; } boolean collect_expressions = false; List<String> expression_to_collect = new ArrayList<String>(); if (extra_data != null) { if (extra_data.containsKey(DataExchangeLiterals.MIDDLE_ELEMENT_XML_EXTRADATA_BLOCK_TYPE)) { String block_type = extra_data.get(DataExchangeLiterals.MIDDLE_ELEMENT_XML_EXTRADATA_BLOCK_TYPE); if (block_type.equals(CVBlocks.CVBLOCK_REST.toString())) { expression_to_collect.add("ProfessionalActivityCurrent"); expression_to_collect.add("ProfessionalActivityNoCurrent"); expression_to_collect.add("AccreditedUniversityStudiesOtherPostGrade"); expression_to_collect.add("AccreditedUniversityStudiesDegree"); expression_to_collect.add("AccreditedUniversityStudiesPhDStudies"); collect_expressions = true; } else if (block_type.equals(CVBlocks.CVBLOCK_PROFESSIONAL_ACTIVITY.toString())) { expression_to_collect.add("ProfessionalActivityCurrent"); expression_to_collect.add("ProfessionalActivityNoCurrent"); collect_expressions = true; } else if (block_type.equals(CVBlocks.CVBLOCK_UNIVERSITY_STUDIES.toString())) { expression_to_collect.add("AccreditedUniversityStudiesOtherPostGrade"); expression_to_collect.add("AccreditedUniversityStudiesDegree"); expression_to_collect.add("AccreditedUniversityStudiesPhDStudies"); collect_expressions = true; } } else { expression_to_collect.add("ProfessionalActivityCurrent"); expression_to_collect.add("ProfessionalActivityNoCurrent"); expression_to_collect.add("AccreditedUniversityStudiesOtherPostGrade"); expression_to_collect.add("AccreditedUniversityStudiesDegree"); expression_to_collect.add("AccreditedUniversityStudiesPhDStudies"); collect_expressions = true; } } else { expression_to_collect.add("ProfessionalActivityCurrent"); expression_to_collect.add("ProfessionalActivityNoCurrent"); expression_to_collect.add("AccreditedUniversityStudiesOtherPostGrade"); expression_to_collect.add("AccreditedUniversityStudiesDegree"); expression_to_collect.add("AccreditedUniversityStudiesPhDStudies"); collect_expressions = true; } eOut.addAttribute("URL", docGate.getSourceUrl() != null ? docGate.getSourceUrl().toString() : ""); AnnotationSet annoset = docGate.getAnnotations(); if (collect_expressions) { List<Annotation> anns = new ArrayList<Annotation>(); for (String exp : expression_to_collect) anns.addAll(annoset.get(exp)); //Collections.sort(anns, new OffsetBeginEndComparator()); //need to bee order if (anns.size() > 0) { for (Annotation an : anns) { String cvnItemName = an.getType(); org.dom4j.Element eAux = new org.dom4j.DocumentFactory().createElement(cvnItemName); // eAux.addElement("Domain").addText(gate.Utils.stringFor(docGate, // an.getStartNode().getOffset() > 100 ? an.getStartNode().getOffset() - 100 : an.getStartNode().getOffset(), // an.getEndNode().getOffset() + 100 < docGate.getContent().size() ? an.getEndNode().getOffset() + 100 : an.getEndNode().getOffset())); eAux.addAttribute("action_mode", "add"); eAux.addElement("Content").addText(gate.Utils.stringFor(docGate, an)); FeatureMap fmap = an.getFeatures(); for (Object key : fmap.keySet()) { String fieldName = key.toString(); eAux.addElement(fieldName).addText(fmap.get(key).toString()); } eOut.add(eAux); } } n_expressions += eOut.elements().size(); } collect_expressions = false; if (extra_data != null) { if (extra_data.containsKey(DataExchangeLiterals.MIDDLE_ELEMENT_XML_EXTRADATA_BLOCK_TYPE)) { String block_type = extra_data.get(DataExchangeLiterals.MIDDLE_ELEMENT_XML_EXTRADATA_BLOCK_TYPE); if (block_type.equals(CVBlocks.CVBLOCK_REST.toString())) { collect_expressions = true; } else if (block_type.equals(CVBlocks.CVBLOCK_PERSONAL.toString())) { collect_expressions = true; } } else { collect_expressions = true; } } else { collect_expressions = true; } if (collect_expressions) { ArrayList<Annotation> anns = new ArrayList<Annotation>(); anns.addAll(annoset.get("AgentIdentification")); if (anns.size() > 0) { String lastname = ""; String initials = ""; String name = ""; String firstname = ""; if (extra_data != null) { lastname = extra_data.get(DataExchangeLiterals.MIDDLE_ELEMENT_XML_EXTRADATA_LASTNAME); initials = extra_data.get(DataExchangeLiterals.MIDDLE_ELEMENT_XML_EXTRADATA_INITIALS); name = extra_data.get(DataExchangeLiterals.MIDDLE_ELEMENT_XML_EXTRADATA_NAME); firstname = extra_data.get(DataExchangeLiterals.MIDDLE_ELEMENT_XML_EXTRADATA_FIRSTNAME); } if (firstname.equals("")) { firstname = initials; } for (Annotation an : anns) { String cvnItemName = an.getType(); org.dom4j.Element eAux = new org.dom4j.DocumentFactory().createElement(cvnItemName); // eAux.addElement("Domain").addText(gate.Utils.stringFor(docGate, // an.getStartNode().getOffset() > 100 ? an.getStartNode().getOffset() - 100 : an.getStartNode().getOffset(), // an.getEndNode().getOffset() + 100 < docGate.getContent().size() ? an.getEndNode().getOffset() + 100 : an.getEndNode().getOffset())); eAux.addAttribute("action_mode", "overwrite"); eAux.addAttribute("extra_gets", "getInformation"); eAux.addElement("Content").addText(gate.Utils.stringFor(docGate, an)); FeatureMap fmap = an.getFeatures(); for (Object key : fmap.keySet()) { String fieldName = key.toString(); eAux.addElement(fieldName).addText(fmap.get(key).toString()); } eAux.addElement(CVItemExtracted.AgentIdentification.GivenName).addText(firstname); eAux.addElement(CVItemExtracted.AgentIdentification.FirstFamilyName).addText(lastname); eOut.add(eAux); } } n_expressions += eOut.elements().size(); } ProjectLogger.LOGGER.info(String.format("%3d expressions in %s : ", n_expressions, docGate.getName())); // + docXML.asXML() if (eOut == null) ProjectLogger.LOGGER.info("Output is null"); // + docXML.asXML() aoData.setData_out(eOut); if (aoData.getVerbose()) { File dest_dir = aoData.getVerboseDir(); File path = null; String fileName = ""; if (extra_data != null && extra_data.containsKey(DataExchangeLiterals.MIDDLE_ELEMENT_XML_EXTRADATA_DOCUMENT_NAME)) { fileName = extra_data.get(DataExchangeLiterals.MIDDLE_ELEMENT_XML_EXTRADATA_DOCUMENT_NAME); } else { URL url = docGate.getSourceUrl(); try { path = new File(url.toURI()); fileName = path.getName(); } catch (Exception e) { String filename; try { filename = URLEncoder.encode(url.toString(), "UTF-8") + ".html"; } catch (Exception ex) { filename = docGate.getName() + ".html"; } path = new File(filename); fileName = path.getName(); } if (!fileName.equals("")) { fileName = fileName.substring(0, fileName.lastIndexOf(".")); } } File file_result = new File(dest_dir, fileName + "_verbose.html"); try { writeResultsInHTMLFile(docGate, file_result); } catch (Exception ex) { Logger.getRootLogger().error("Error writing verbose results. " + ex.toString()); } } } @SuppressWarnings("unchecked") private void writeResultsInHTMLFile(Document doc, File file_result) { String startTagPart_1 = "<br><span GateID=\""; String startTagPart_2 = "\" title=\""; String startTagPart_3 = "\" style=\"background:LightBlue;\">"; String endTag = "</span><br>"; AnnotationSet defaultAnnotSet = doc.getAnnotations(); Set annotTypesRequired = new HashSet(); annotTypesRequired.add("ProfessionalActivityCurrent"); annotTypesRequired.add("ProfessionalActivityNoCurrent"); annotTypesRequired.add("AccreditedUniversityStudiesOtherPostGrade"); annotTypesRequired.add("AccreditedUniversityStudiesDegree"); annotTypesRequired.add("AccreditedUniversityStudiesPhDStudies"); annotTypesRequired.add("AgentIdentification"); Set<Annotation> peopleAndPlaces = new HashSet<Annotation>(defaultAnnotSet.get(annotTypesRequired)); FeatureMap features = doc.getFeatures(); String originalContent = doc.getContent().toString(); //(String) features.get(GateConstants.ORIGINAL_DOCUMENT_CONTENT_FEATURE_NAME); //RepositioningInfo info = (RepositioningInfo) // features.get(GateConstants.DOCUMENT_REPOSITIONING_INFO_FEATURE_NAME); String xmlDocument = doc.toXml(peopleAndPlaces, true); String css_code = "<style type=\"text/css\">" + "span.AgentIdentification" + "{" + " background-color: #808080;" + "} " + "span.AccreditedUniversityStudiesPhDStudies" + "{" + " background-color: #FFFFCC;" + "} " + "span.AccreditedUniversityStudiesDegree" + "{" + " background-color: #CCFFCC;" + "} " + "span.AccreditedUniversityStudiesOtherPostGrade" + "{" + " background-color: #C17128;" + "} " + "span.ProfessionalActivityNoCurrent" + "{" + " background-color: #99CCCC;" + "} " + "span.ProfessionalActivityCurrent" + "{" + " background-color: #FF99CC;" + "} " + ".fixed {position:fixed !important; right:0px; top:0px; z-index:10 !important; background-color: #ffffff;} " + "</style>"; String legend = "<div class=\"fixed\">NOTES:<br>"; legend = legend + "|1| = <span class=\"AccreditedUniversityStudiesPhDStudies\">AccreditedUniversityStudiesPhDStudies"; legend = legend + "</span><br>"; legend = legend + "|2| = <span class=\"AccreditedUniversityStudiesDegree\">AccreditedUniversityStudiesDegree"; legend = legend + "</span><br>"; legend = legend + "|3| = <span class=\"AccreditedUniversityStudiesOtherPostGrade\">AccreditedUniversityStudiesOtherPostGrade"; legend = legend + "</span><br>"; legend = legend + "|4| = <span class=\"ProfessionalActivityNoCurrent\">ProfessionalActivityNoCurrent"; legend = legend + "</span><br>"; legend = legend + "|5| = <span class=\"ProfessionalActivityCurrent\">ProfessionalActivityCurrent"; legend = legend + "</span><br>"; legend = legend + "|6| = <span class=\"AgentIdentification\">AgentIdentification"; legend = legend + "</span></div><br><br><br><br><br>"; int index1 = xmlDocument.indexOf("</head>"); if (index1 > 0) { xmlDocument = xmlDocument.replace("</head>", "</head>" + css_code + legend); } else { xmlDocument = css_code + legend + xmlDocument; } { org.jsoup.nodes.Document docjsoup = org.jsoup.Jsoup.parse(xmlDocument); org.jsoup.select.Elements elements = docjsoup.select("AccreditedUniversityStudiesDegree"); if (elements != null) { for (org.jsoup.nodes.Element element : elements) { String s = element.html(); s = s; } } } // xmlDocument = xmlDocument.replace("<AccreditedUniversityStudiesPhDStudies","<b>#SP#</b><span class=\"AccreditedUniversityStudiesPhDStudies\""); // xmlDocument = xmlDocument.replace("</AccreditedUniversityStudiesPhDStudies>","</span><b>#SP#</b>"); // // xmlDocument = xmlDocument.replace("<AccreditedUniversityStudiesDegree","<b>#SD#</b><span class=\"AccreditedUniversityStudiesDegree\""); // xmlDocument = xmlDocument.replace("</AccreditedUniversityStudiesDegree>","</span><b>#SD#</b>"); // // xmlDocument = xmlDocument.replace("<AccreditedUniversityStudiesOtherPostGrade","<b>#SO#</b><span class=\"AccreditedUniversityStudiesPhDStudies\""); // xmlDocument = xmlDocument.replace("</AccreditedUniversityStudiesOtherPostGrade>","</span><b>#SO#</b>"); // // xmlDocument = xmlDocument.replace("<ProfessionalActivityNoCurrent","<b>#</b><span class=\"ProfessionalActivityNoCurrent\""); // xmlDocument = xmlDocument.replace("</ProfessionalActivityNoCurrent>","</span><b>#PN#</b>"); // // xmlDocument = xmlDocument.replace("<ProfessionalActivityCurrent","<b>#</b><span class=\"ProfessionalActivityCurrent\""); // xmlDocument = xmlDocument.replace("</ProfessionalActivityCurrent>","</span><b>#PC#</b>"); // xmlDocument = xmlDocument.replace("<AccreditedUniversityStudiesPhDStudies","<span class=\"AccreditedUniversityStudiesPhDStudies\""); // xmlDocument = xmlDocument.replace("</AccreditedUniversityStudiesPhDStudies>","</span>"); // // xmlDocument = xmlDocument.replace("<AccreditedUniversityStudiesDegree","<span class=\"AccreditedUniversityStudiesDegree\""); // xmlDocument = xmlDocument.replace("</AccreditedUniversityStudiesDegree>","</span>"); // // xmlDocument = xmlDocument.replace("<AccreditedUniversityStudiesOtherPostGrade","<span class=\"AccreditedUniversityStudiesPhDStudies\""); // xmlDocument = xmlDocument.replace("</AccreditedUniversityStudiesOtherPostGrade>","</span>"); // // xmlDocument = xmlDocument.replace("<ProfessionalActivityNoCurrent","<span class=\"ProfessionalActivityNoCurrent\""); // xmlDocument = xmlDocument.replace("</ProfessionalActivityNoCurrent>","</span>"); // // xmlDocument = xmlDocument.replace("<ProfessionalActivityCurrent","<span class=\"ProfessionalActivityCurrent\""); // xmlDocument = xmlDocument.replace("</ProfessionalActivityCurrent>","</span>"); xmlDocument = xmlDocument.replace("<AccreditedUniversityStudiesPhDStudies", "<b>|1|</b><span class=\"AccreditedUniversityStudiesPhDStudies\""); xmlDocument = xmlDocument.replace("</AccreditedUniversityStudiesPhDStudies>", "</span><b>|1|</b>"); xmlDocument = xmlDocument.replace("<AccreditedUniversityStudiesDegree", "<b>|2|</b><span class=\"AccreditedUniversityStudiesDegree\""); xmlDocument = xmlDocument.replace("</AccreditedUniversityStudiesDegree>", "</span><b>|2|</b>"); xmlDocument = xmlDocument.replace("<AccreditedUniversityStudiesOtherPostGrade", "<b>|3|</b><span class=\"AccreditedUniversityStudiesPhDStudies\""); xmlDocument = xmlDocument.replace("</AccreditedUniversityStudiesOtherPostGrade>", "</span><b>|3|</b>"); xmlDocument = xmlDocument.replace("<ProfessionalActivityNoCurrent", "<b>|4|</b><span class=\"ProfessionalActivityNoCurrent\""); xmlDocument = xmlDocument.replace("</ProfessionalActivityNoCurrent>", "</span><b>|4|</b>"); xmlDocument = xmlDocument.replace("<ProfessionalActivityCurrent", "<b>|5|</b><span class=\"ProfessionalActivityCurrent\""); xmlDocument = xmlDocument.replace("</ProfessionalActivityCurrent>", "</span><b>|5|</b>"); xmlDocument = xmlDocument.replace("<AgentIdentification", "<b>|6|</b><span class=\"AgentIdentification\""); xmlDocument = xmlDocument.replace("</AgentIdentification>", "</span><b>|6|</b>"); xmlDocument = xmlDocument.replace("\n", "<br>"); try { FileUtils.write(file_result, xmlDocument, "UTF-8"); } catch (IOException ex) { ProjectLogger.LOGGER.error("The verbose file can not be created " + file_result.getPath(), ex); } } }