164 lines
9.4 KiB
Java
164 lines
9.4 KiB
Java
package org.gcube.dataanalysis.executor.nodes.transducers.bionym.abstracts;
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import java.io.File;
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import java.security.Permission;
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import java.util.HashMap;
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import java.util.UUID;
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import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger;
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import org.gcube.dataanalysis.executor.nodes.transducers.bionym.implementations.matchers.LevensteinMatcher;
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import org.gcube.dataanalysis.executor.nodes.transducers.bionym.interfaces.Matcher;
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import org.gcube.dataanalysis.executor.nodes.transducers.bionym.utils.YasmeenFileTools;
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import org.gcube.dataanalysis.executor.nodes.transducers.bionym.utils.YasmeenGlobalParameters;
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public abstract class YasmeenMatcher implements Matcher {
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public static String matcherLib = "YASMEEN-matcher-1.2.0.1.jar";
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protected String sandBoxFolder = "./";
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public double threshold = 0.4;
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public int maxResults = 10;
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public HashMap<String, String> parameters;
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HashMap<String, String> urlsmap = createReferenceMap();
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static HashMap<String, String> performancemap = createPerformanceMap();
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protected static HashMap<String, String> createReferenceMap() {
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HashMap<String, String> urlsMaps = new HashMap<String, String>();
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urlsMaps.put(YasmeenGlobalParameters.BuiltinDataSources.ASFIS.name(), "http://goo.gl/qfeTp7");
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urlsMaps.put(YasmeenGlobalParameters.BuiltinDataSources.FISHBASE.name(), "http://goo.gl/FcnUc0");
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urlsMaps.put(YasmeenGlobalParameters.BuiltinDataSources.OBIS.name(), "http://goo.gl/AUcUXt");
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urlsMaps.put(YasmeenGlobalParameters.BuiltinDataSources.OBIS_ANIMALIA.name(), "http://goo.gl/mW1fvb");
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urlsMaps.put(YasmeenGlobalParameters.BuiltinDataSources.OBIS_CNIDARIA.name(), "http://goo.gl/N6vCq8");
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urlsMaps.put(YasmeenGlobalParameters.BuiltinDataSources.OBIS_ECHINODERMATA.name(), "http://goo.gl/2qQThI");
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urlsMaps.put(YasmeenGlobalParameters.BuiltinDataSources.OBIS_PLATYHELMINTHES.name(), "http://goo.gl/RLmCn2");
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urlsMaps.put(YasmeenGlobalParameters.BuiltinDataSources.COL_FULL.name(), "http://goo.gl/fJ9feg");
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urlsMaps.put(YasmeenGlobalParameters.BuiltinDataSources.COL_CHORDATA.name(), "http://goo.gl/11upZC");
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urlsMaps.put(YasmeenGlobalParameters.BuiltinDataSources.COL_MAMMALIA.name(), "http://goo.gl/J4fga6");
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urlsMaps.put(YasmeenGlobalParameters.BuiltinDataSources.IRMNG_ACTINOPTERYGII.name(), "http://goo.gl/Z8eRly");
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urlsMaps.put(YasmeenGlobalParameters.BuiltinDataSources.WORMS_ANIMALIA.name(), "http://goo.gl/XRMWgr");
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urlsMaps.put(YasmeenGlobalParameters.BuiltinDataSources.WORMS_PISCES.name(), "http://goo.gl/OdPRiA");
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return urlsMaps;
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}
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protected HashMap<String, String> createReferenceMapFile(String localFolder) {
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HashMap<String, String> urlsMaps = new HashMap<String, String>();
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urlsMaps.put(YasmeenGlobalParameters.BuiltinDataSources.ASFIS.name(), new File(localFolder, "ASFIS_taxa.taf").getAbsolutePath());
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urlsMaps.put(YasmeenGlobalParameters.BuiltinDataSources.FISHBASE.name(), new File(localFolder, "FISHBASE_taxa.taf").getAbsolutePath());
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urlsMaps.put(YasmeenGlobalParameters.BuiltinDataSources.OBIS.name(), new File(localFolder, "OBIS_taxa.taf").getAbsolutePath());
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urlsMaps.put(YasmeenGlobalParameters.BuiltinDataSources.OBIS_ANIMALIA.name(), new File(localFolder, "OBIS_Animalia_taxa.taf").getAbsolutePath());
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urlsMaps.put(YasmeenGlobalParameters.BuiltinDataSources.OBIS_CNIDARIA.name(), new File(localFolder, "OBIS_Cnidaria_taxa.taf").getAbsolutePath());
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urlsMaps.put(YasmeenGlobalParameters.BuiltinDataSources.OBIS_ECHINODERMATA.name(), new File(localFolder, "OBIS_Echinodermata_taxa.taf").getAbsolutePath());
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urlsMaps.put(YasmeenGlobalParameters.BuiltinDataSources.OBIS_PLATYHELMINTHES.name(), new File(localFolder, "OBIS_Platyhelminthes_taxa.taf").getAbsolutePath());
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urlsMaps.put(YasmeenGlobalParameters.BuiltinDataSources.COL_FULL.name(), new File(localFolder, "COL_FULL_taxa.taf").getAbsolutePath());
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urlsMaps.put(YasmeenGlobalParameters.BuiltinDataSources.COL_CHORDATA.name(), new File(localFolder, "COL_Chordata_taxa.taf").getAbsolutePath());
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urlsMaps.put(YasmeenGlobalParameters.BuiltinDataSources.COL_MAMMALIA.name(), new File(localFolder, "COL_Mammalia_taxa.taf").getAbsolutePath());
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urlsMaps.put(YasmeenGlobalParameters.BuiltinDataSources.IRMNG_ACTINOPTERYGII.name(), new File(localFolder, "IRMNG_Actinopterygii_taxa.taf").getAbsolutePath());
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urlsMaps.put(YasmeenGlobalParameters.BuiltinDataSources.WORMS_ANIMALIA.name(), new File(localFolder, "WORMS_Animalia_taxa.taf").getAbsolutePath());
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urlsMaps.put(YasmeenGlobalParameters.BuiltinDataSources.WORMS_PISCES.name(), new File(localFolder, "WoRMS_Pisces_taxa.taf").getAbsolutePath());
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return urlsMaps;
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}
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protected static HashMap<String, String> createPerformanceMap() {
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HashMap<String, String> performanceMap = new HashMap<String, String>();
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performanceMap.put(YasmeenGlobalParameters.Performance.MAX_ACCURACY.name(), "");
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performanceMap.put(YasmeenGlobalParameters.Performance.LOW_SPEED.name(), "-dpt 10");
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performanceMap.put(YasmeenGlobalParameters.Performance.MEDIUM_SPEED.name(), "-dpt 6");
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performanceMap.put(YasmeenGlobalParameters.Performance.HIGH_SPEED.name(), "-dpt 2");
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performanceMap.put(YasmeenGlobalParameters.Performance.MAX_SPEED.name(), "-dpt 0");
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return performanceMap;
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}
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protected abstract String getMatchlets();
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protected abstract String getLexicalDistancesWeights();
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protected abstract String getStemming();
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public YasmeenMatcher(String sandboxfolder, double threshold, int maxResults, HashMap<String, String> parameters) {
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init(sandboxfolder, threshold, maxResults, parameters);
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}
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@Override
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public void init(String sandboxfolder, double threshold, int maxResults, HashMap<String, String> parameters) {
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this.sandBoxFolder = sandboxfolder;
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this.parameters = parameters;
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this.threshold = threshold;
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this.maxResults = maxResults;
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}
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@Override
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public MatcherOutput match(MatcherInput inputName) throws Exception {
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String inputFileName = parameters.get(YasmeenGlobalParameters.parserOutputFileParam);
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String uuid = ("" + UUID.randomUUID()).replace("-", "");
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String outputFileName = "matcherOutput" + uuid + ".csv";
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File outfile = new File(sandBoxFolder, outputFileName);
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if (outfile.exists()) {
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outfile.delete();
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}
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// String outputFileName = parameters.get(YasmeenGlobalParameters.parserOutputFileParam);
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String taxaAuthorityFile = parameters.get(YasmeenGlobalParameters.taxaAuthorityFileParam);
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String performanceMap = parameters.get(YasmeenGlobalParameters.performanceParam);
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String performanceCommand = performancemap.get(performanceMap);
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if (performanceCommand == null)
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performanceCommand = "";
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boolean stemmit = Boolean.parseBoolean(parameters.get(YasmeenGlobalParameters.useStemmedGenusAndSpecies));
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String normalizeMatchlets = "";
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String standardMatchlets = "";
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if (stemmit)
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normalizeMatchlets = getStemming();
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else
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standardMatchlets = getMatchlets();
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/* ENABLE LOCAL FILES USAGE */
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/*
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* String localFilesFolder = parameters.get(YasmeenGlobalParameters.staticFilesFolderParam); if (localFilesFolder==null){ localFilesFolder=""; urlsmap=createReferenceMap(); } else urlsmap=createReferenceMapFile(localFilesFolder);
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*/
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// java -jar YASMEEN-matcher-1.1.1.jar -inFile output.csv -refData ASFIS@https://dl.dropboxusercontent.com/u/12809149/ASFIS_taxa.taf.gz -outFile matchout.csv -man -may -mSn -mt -mc 10 -ps -pt 1.5x -xml -xslTemplate csv -law 90:30:60
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// YasmeenFileTools.writeYasmeenMatcherInput(sandBoxFolder, inputFileName, parser, inputName);
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// org.fao.fi.comet.domain.species.tools.process.matching.cli.MatchingEngine
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String localFilesFolder = parameters.get(YasmeenGlobalParameters.staticFilesFolderParam);
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if ((localFilesFolder != null) && (localFilesFolder.length() > 0)
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&& (taxaAuthorityFile.equals(YasmeenGlobalParameters.BuiltinDataSources.FISHBASE.name()))
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&& (this instanceof LevensteinMatcher)
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&& new File(createReferenceMapFile(localFilesFolder).get(taxaAuthorityFile)).exists()) {
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RealTimeMatcher rm = new RealTimeMatcher();
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HashMap<String, String> filesMap = createReferenceMapFile(localFilesFolder);
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rm.match(filesMap.get(taxaAuthorityFile), taxaAuthorityFile, new File(sandBoxFolder, inputFileName).getAbsolutePath(), outfile.getAbsolutePath(), threshold, maxResults);
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}
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else {
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String execution = "java -Xmx512m -Xmx1024m -jar " + new File(sandBoxFolder, matcherLib).getAbsolutePath() + " -inFile " + new File(sandBoxFolder, inputFileName).getAbsolutePath() + " -refData " + taxaAuthorityFile + "@" + urlsmap.get(taxaAuthorityFile) + " -outFile " + outfile.getAbsolutePath() + " " + normalizeMatchlets + " -mc " + maxResults + " -mst " + threshold + " -pt 1x -xml -xslTemplate csv" + " " + getLexicalDistancesWeights() + " " + standardMatchlets + " " + performanceCommand;
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AnalysisLogger.getLogger().debug(execution);
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YasmeenFileTools.callYasmeen(execution.trim());
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}
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MatcherOutput mo = YasmeenFileTools.getYasmeenMatcherOutput(sandBoxFolder, outputFileName);
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outfile.delete();
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return mo;
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}
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private static class NoExitSecurityManager extends SecurityManager {
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@Override
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public void checkPermission(Permission perm) {
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// allow anything.
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}
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@Override
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public void checkPermission(Permission perm, Object context) {
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// allow anything.
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}
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@Override
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public void checkExit(int status) {
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super.checkExit(status);
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throw new RuntimeException("exit status is "+status);
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}
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}
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}
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