Mercurial > hg > anteater
view src/de/mpiwg/anteater/species/scientific/ScientificNameFindController.java @ 9:51ed79e28b45
annotate texts with results and build events with linnaeus
author | jdamerow |
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date | Mon, 19 Nov 2012 16:36:15 -0700 |
parents | dcc35f89dce3 |
children |
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package de.mpiwg.anteater.species.scientific; import java.io.File; import java.util.ArrayList; import java.util.List; import de.mpiwg.anteater.AnteaterConfiguration; import de.mpiwg.anteater.species.NameFinder; import de.mpiwg.anteater.species.scientific.impl.GNRDNameFinder; import de.mpiwg.anteater.text.TextInformation; import de.mpiwg.anteater.text.TextPart; import de.mpiwg.anteater.text.TextType; import de.mpiwg.anteater.xml.INameFinderParser; import de.mpiwg.anteater.xml.impl.AnalysisXMLManager; import de.mpiwg.anteater.xml.impl.GNRDXMLParser; public class ScientificNameFindController { public final static String COMPONENT_NAME = ScientificNameFindController.class.getSimpleName(); private AnteaterConfiguration configuration; public ScientificNameFindController(AnteaterConfiguration configuration) { this.configuration = configuration; } /** * Method for retrieving scientific names in a XML document. It tooks all summaries and all * suplementary informations and looks for names in them. * @param file * @return */ public List<ScientificNamesExtraction> findScientificNamesInXML(TextInformation info) { List<ScientificNamesExtraction> results = new ArrayList<ScientificNamesExtraction>(); List<String> summaryAnalysisResults = new ArrayList<String>(); List<String> supplinfAnalysisResults = new ArrayList<String>(); // check if there are already stored results AnalysisXMLManager analysisManager = null; if (configuration.getAnalysisPath() != null && !configuration.getAnalysisPath().isEmpty()) { File file = new File(info.getFilepath()); analysisManager = new AnalysisXMLManager(configuration.getAnalysisPath() + File.separator + file.getName()); configuration.getLogger().logMessageWithoutNewLine(COMPONENT_NAME, "Check analysis file for scientific names in summaries..."); summaryAnalysisResults = analysisManager.getSummaryNamesResults(); configuration.getLogger().logMessage("found " + summaryAnalysisResults.size() + " result(s)."); configuration.getLogger().logMessageWithoutNewLine(COMPONENT_NAME, "Check analysis file for scientific names in supplementary information..."); supplinfAnalysisResults = analysisManager.getSupplementaryInfoNamesResults(); configuration.getLogger().logMessage("found " + supplinfAnalysisResults.size() + " result(s)."); } IScientificNamesFinder nameFinder = new GNRDNameFinder(configuration.getLogger()); // if there are no results for summaries, ask GNRD name finding service. if (summaryAnalysisResults.size() == 0) { configuration.getLogger().logMessage(COMPONENT_NAME, "No results found for summaries, so will ask GNRDNameFinder."); for (TextPart sum : info.getSummaries()) { String sumResult = nameFinder.findScientificNames(sum.getText()); if (sumResult != null) { summaryAnalysisResults.add(sumResult); // if there is an analysis folder, add result to analysis file if (analysisManager != null) analysisManager.addSummaryNamesResult(sumResult); } } } // if there are no results for supplementary information, ask GNRD name fining service if (supplinfAnalysisResults.size() == 0) { configuration.getLogger().logMessage(COMPONENT_NAME, "No results found for supplementary information, so will ask GNRDNameFinder."); for (TextPart sInf : info.getSupplInfos()) { String supinfResult = nameFinder.findScientificNames(sInf.getText()); if (supinfResult != null) { supplinfAnalysisResults.add(supinfResult); // if there is an analysis folder, add result to analysis file if (analysisManager != null) analysisManager.addSupplInfNamesResult(supinfResult); } } } configuration.getLogger().logMessage(COMPONENT_NAME, "Creating analysis results..."); int idx = 0; for (String summaryResult : summaryAnalysisResults) { INameFinderParser nameParser = new GNRDXMLParser(summaryResult); List<ScientificName> scientificNames = nameParser.parseScientificNames(); ScientificNamesExtraction scientificNameResult = new ScientificNamesExtraction(); scientificNameResult.setType(TextType.TYPE_SUMMARY); scientificNameResult.setNames(scientificNames); scientificNameResult.setTextIdx(idx); scientificNameResult.setFoundBy(NameFinder.GNRD); results.add(scientificNameResult); idx++; } idx = 0; for (String suplinfResult : supplinfAnalysisResults) { INameFinderParser nameParser = new GNRDXMLParser(suplinfResult); List<ScientificName> scientificNames = nameParser.parseScientificNames(); ScientificNamesExtraction scientificNameResult = new ScientificNamesExtraction(); scientificNameResult.setType(TextType.TYPE_SUPLINF); scientificNameResult.setNames(scientificNames); scientificNameResult.setTextIdx(idx); scientificNameResult.setFoundBy(NameFinder.GNRD); results.add(scientificNameResult); idx++; } return results; } }