eu.project.ttc.tools.cli.TermSuiteTerminoCLI Maven / Gradle / Ivy
/*
* Licensed to the Apache Software Foundation (ASF) under one
* or more contributor license agreements. See the NOTICE file
* distributed with this work for additional information
* regarding copyright 2, 2015nership. The ASF licenses this file
* to you 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.
*/
package eu.project.ttc.tools.cli;
import java.io.File;
import java.io.IOException;
import java.io.PrintStream;
import java.io.UnsupportedEncodingException;
import java.nio.file.Paths;
import java.text.SimpleDateFormat;
import java.util.Date;
import java.util.List;
import java.util.regex.Pattern;
import org.apache.commons.cli.CommandLine;
import org.apache.commons.cli.Options;
import org.apache.commons.cli.ParseException;
import org.apache.commons.cli.PosixParser;
import org.apache.uima.fit.factory.JCasFactory;
import org.apache.uima.jcas.JCas;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import com.google.common.base.Joiner;
import com.google.common.base.Optional;
import com.google.common.base.Preconditions;
import com.google.common.base.Splitter;
import com.google.common.base.Stopwatch;
import com.google.common.collect.Lists;
import eu.project.ttc.engines.cleaner.TermProperty;
import eu.project.ttc.engines.desc.Lang;
import eu.project.ttc.engines.desc.TermSuiteCollection;
import eu.project.ttc.models.OccurrenceType;
import eu.project.ttc.models.TermIndex;
import eu.project.ttc.resources.MemoryTermIndexManager;
import eu.project.ttc.tools.TermSuitePipeline;
import eu.project.ttc.utils.TermUtils;
/**
* Command line interface for the Terminology extraction (Spotter+Indexer) engines.
*
* @author Damien Cram
*/
public class TermSuiteTerminoCLI {
private static final Logger LOGGER = LoggerFactory.getLogger(TermSuiteTerminoCLI.class);
/** Short usage description of the CLI */
private static final String USAGE = "java [-DconfigFile=] -Xms1g -Xmx2g -cp termsuite-core-x.x.jar eu.project.ttc.tools.cli.TermSuiteTerminoCLI";
/// Parameter names
/** Name of the example limit parament */
private static final String TEXT = "text";
/** Name of the watch parameter */
private static final String WATCH = "watch";
/** Name of the corpus parameter */
private static final String PATH_TO_CORPUS = "corpus-home";
/** Name of the resource path parameter */
private static final String PATH_TO_RESOURCE_PACK = "resource-pack";
/** Name of the corpus format parameter */
private static final String CORPUS_FORMAT = "corpus-format";
/** Name of the parameter that must be set to the tt dir */
public static final String P_TAGGER_HOME_DIRECTORY = "tagger-home";
/** Name of the parameter that must be set to disable graphical variants */
private static final String GRAPHICAL_SIMILARITY = "graphical-similarity-th";
/** Name of the paramter that shows tree tagger tags**/
private static final String SHOW_TAGGER_TAGS = "tags";
/** Compost configuration parameters **/
private static final String COMPOST_COEFF = "compost-coeff";
private static final String COMPOST_MIN_COMPONENT_SIZE = "compost-min-component-size";
private static final String COMPOST_MAX_COMPONENT_NUM = "compost-max-component-num";
private static final String COMPOST_SIMILARITY_THRESHOLD = "compost-similarity-threshold";
private static final String COMPOST_SCORE_THRESHOLD = "compost-score-threshold";
/** deactivate the occurrences saving in memory while indexing **/
private static final String NO_OCCURRENCE = "no-occurrence";
/** MongoDB parameters **/
private static final String MONGODB_STORE = "mongodb-store";
private static final String MONGODB_SOFT_LINK = "json-mongodb-soft-link";
/*
* The mongo db options
*/
private static Optional mongoStoreDBURL = Optional.absent();
private static boolean mongoStoreSoftLinked = false;
/** Mate tagger parameter **/
private static final String MATE = "mate";
/*
* With Mate
*/
private static enum Tagger{Mate, TreeTagger};
/*
* Logging arguments
*/
private static final String DEBUG = "debug";
private static final String TRACE = "trace";
private static final String NO_LOGGING = "no-logging";
/*
* Contextualizer
*/
private static final String CONTEXTUALIZE = "contextualize";
private static final String CONTEXTUALIZE_ALL_TERMS = "contextualize-all-terms";
private static final String CONTEXT_SCOPE = "context-scope";
private static final String ALLOW_MWT_IN_CONTEXTS = "allow-mwts-in-contexts";
/*
* Cleaning arguments
*/
private static final String CLEAN_THRESHOLD = "filter-th";
private static final String CLEAN_TOP_N = "filter-top-n";
private static final String CLEAN_PROPERTY = "filter-property";
private static final String CLEAN_FILTER_VARIANTS = "filter-variants";
/*
* Max size filtering
*/
private static final String PERIODIC_FILTER_PROPERTY = "periodic-filter-property";
private static final String PERIODIC_FILTER_MAX_SIZE = "periodic-filter-max-size";
// the tsv file path argument
private static final String TSV = "tsv";
private static final String TSV_PROPERTIES = "tsv-properties";
private static final String TSV_VARIANT_SCORES = "tsv-show-scores";
// the json file path argument
private static final String JSON = "json";
// the tbx file path argument
private static final String TBX = "tbx";
// the jsonCAS file path argument
private static final String JSCASFILE = "jsonCasFile";
// tagger argument
private static Tagger tagger = Tagger.TreeTagger;
private static String resourcePack = null;
private static String corpusPath = null;
private static Lang language = null;
private static String encoding = "UTF-8";
// private static String pipelineCRInputDirectory = null;
private static String taggerHome = "";
private static String inlineText = null;
private static TermSuiteCollection corpusType = TermSuiteCollection.TXT;
private static float graphicalSimilarityThreshold = 0.9f;
/*
* contetxualizer
*/
private static boolean contextualize = false;
private static boolean contextualizeAllTerms = false;
private static boolean allowMWTInContexts = false;
private static int contextScope = 3;
/*
* Cleaning parameters
*/
private static Optional cleaningThreshold = Optional.of(2f);
private static Optional cleaningTopN = Optional.absent();
private static Optional cleaningProperty = Optional.of(TermProperty.WR_LOG);
private static boolean keepVariantsWhileCleaning = true;
/*
* Max size periodic filtering
*/
private static Optional periodicFilteringProperty = Optional.absent();
private static int maxSizeFilteringMaxSize = 20000;
/*
* Spotter params
*/
private static boolean spotWithOccurrences = true;
/*
* Export params
*/
private static Optional tsvFile = Optional.absent();
private static Optional tsvProperties = Optional.absent();
private static boolean tsvShowVariantScores = false;
private static Optional jsonFile = Optional.absent();
private static Optional tbxFile = Optional.absent();
private static Optional jsonCasFile = Optional.absent();
/*
* compost params
*/
private static Optional compostAlpha = Optional.absent();
private static Optional compostBeta = Optional.absent();
private static Optional compostGamma = Optional.absent();
private static Optional compostDelta = Optional.absent();
private static Optional compostMinComponentSize = Optional.absent();
private static Optional compostMaxComponentNum = Optional.absent();
private static Optional compostSimilarityThreshold = Optional.of(1f);
private static Optional compostScoreThreshold = Optional.absent();
/*
* Ouput and display params
*/
private static Optional watch = Optional.absent();
/**
* Application entry point
*
* @param args
* Command line arguments
* @throws UnsupportedEncodingException
*/
public static void main(String[] args) throws UnsupportedEncodingException {
File logDir = new File("logs");
if(!logDir.exists())
logDir.mkdir();
String logPath = Paths.get("logs", "termsuite-" + new SimpleDateFormat("yyyyMMdd-HHmmss").format(new Date()) +".log").toAbsolutePath().toString();
TermSuiteCLIUtils.logToFile(logPath);
Stopwatch sw = Stopwatch.createStarted();
LOGGER.info("Logging to {}", logPath);
try {
// usage
// java -DconfigFile=myPropertiesFileName -Xms1g -Xmx2g -cp ttc-term-suite-1.3.jar eu.project.ttc.tools.cli.TermSuiteSpotterCLI
// if the option -DconfigFile is missing preferencesFileName is set to TermSuiteCLIUtils.USER_HOME+PREFERENCES_FILE_NAME
// create the command line parser
PosixParser parser = new PosixParser();
// create the Options
Options options = declareOptions();
try {
// Parse and set CL options
CommandLine line = parser.parse(options, args, false);
readArguments(line);
if(line.hasOption(NO_LOGGING))
TermSuiteCLIUtils.disableLogging();
else if(line.hasOption(DEBUG))
TermSuiteCLIUtils.setGlobalLogLevel("debug");
else if(line.hasOption(TRACE))
TermSuiteCLIUtils.setGlobalLogLevel("trace");
else
TermSuiteCLIUtils.setGlobalLogLevel("info");
TermSuiteCLIUtils.logCommandLineOptions(line);
TermSuitePipeline pipeline = TermSuitePipeline.create(language.getCode());
if(isInlineMode()) {
pipeline.setInlineString(inlineText);
} else {
pipeline.setCollection(corpusType, corpusPath, encoding);
}
// resource
pipeline.setResourcePath(resourcePack);
// mongodb
if(mongoStoreDBURL.isPresent())
pipeline.setMongoDBOccurrenceStore(mongoStoreDBURL.get());
// tokenizer
pipeline.aeWordTokenizer();
// tagger
if(tagger == Tagger.TreeTagger)
pipeline.setTreeTaggerHome(taggerHome)
.aeTreeTagger();
else if(tagger == Tagger.Mate)
pipeline.setMateModelPath(taggerHome)
.aeMateTaggerLemmatizer();
// Filter urlsFilter
pipeline.aeUrlFilter();
// stemmer
pipeline.aeStemmer();
// regex spotter
pipeline.setSpotWithOccurrences(spotWithOccurrences);
pipeline.aeRegexSpotter();
//export Json CAS spotter
if(jsonCasFile.isPresent())
pipeline.haeJsonCasExporter(jsonCasFile.get());
// filter stop words
pipeline.aeStopWordsFilter();
// specificity computer
pipeline.aeSpecificityComputer();
// compost (morphology)
if(compostAlpha.isPresent())
pipeline.setCompostCoeffs(compostAlpha.get(), compostBeta.get(), compostGamma.get(), compostDelta.get());
if(compostMinComponentSize.isPresent())
pipeline.setCompostMinComponentSize(compostMinComponentSize.get());
if(compostMaxComponentNum.isPresent())
pipeline.setCompostMaxComponentNum(compostMaxComponentNum.get());
if(compostScoreThreshold.isPresent())
pipeline.setCompostScoreThreshold(compostScoreThreshold.get());
if(compostSimilarityThreshold.isPresent())
pipeline.setCompostSegmentSimilarityThreshold(compostSimilarityThreshold.get());
pipeline.aeCompostSplitter();
// syntactic variant gathering
pipeline.aeSyntacticVariantGatherer();
// graphical variant gathering
pipeline.setGraphicalVariantSimilarityThreshold(graphicalSimilarityThreshold);
pipeline.aeGraphicalVariantGatherer();
// filtering
if(cleaningThreshold.isPresent()) {
pipeline.setKeepVariantsWhileCleaning(keepVariantsWhileCleaning);
pipeline.aeThresholdCleaner(
cleaningProperty.get(), cleaningThreshold.get());
} else if(cleaningTopN.isPresent()) {
pipeline.setKeepVariantsWhileCleaning(keepVariantsWhileCleaning);
pipeline.aeTopNCleaner(cleaningProperty.get(), cleaningTopN.get());
}
if(periodicFilteringProperty.isPresent())
pipeline.aeMaxSizeThresholdCleaner(periodicFilteringProperty.get(), maxSizeFilteringMaxSize);
// contextualize
if(contextualize) {
pipeline
.setContextualizeCoTermsType(allowMWTInContexts ? OccurrenceType.ALL : OccurrenceType.SINGLE_WORD)
.aeContextualizer(contextScope, contextualizeAllTerms);
}
// stats
pipeline.haeCasStatCounter("at end of pipeline");
// Export
if(tsvFile.isPresent()) {
if(tsvProperties.isPresent()) {
pipeline.setTsvExportProperties(tsvProperties.get());
pipeline.setTsvShowScores(tsvShowVariantScores);
} else
pipeline.setTsvExportProperties(
TermProperty.PILOT,
TermProperty.FREQUENCY
);
pipeline.haeTsvExporter(tsvFile.get());
}
if(tbxFile.isPresent())
pipeline.haeTbxExporter(tbxFile.get());
if(jsonFile.isPresent()) {
pipeline.setExportJsonWithContext(contextualize);
pipeline.setExportJsonWithOccurrences(true);
if(mongoStoreSoftLinked)
pipeline.linkMongoStore();
pipeline.haeJsonExporter(jsonFile.get());
}
// run the pipeline
final String termIndexName = "ScriptTermIndex_" + System.currentTimeMillis();
if(isInlineMode()) {
LOGGER.info("Running TermSuite pipeline (inline mode)");
JCas cas = JCasFactory.createJCas();
cas.setDocumentText(inlineText);
cas.setDocumentLanguage(language.getCode());
pipeline.run(cas);
System.err.flush();
System.out.println("Term index: ");
TermIndex index = MemoryTermIndexManager.getInstance().getIndex(termIndexName);
TermUtils.showIndex(index, System.out, watch);
} else {
LOGGER.info("Running TermSuite pipeline in corpus mode");
pipeline.run();
if(watch.isPresent())
TermUtils.showIndex(
MemoryTermIndexManager.getInstance().getIndex(termIndexName),
new PrintStream(System.err, true, "UTF-8"),
watch);
}
LOGGER.info("Script executed in " + sw.toString());
} catch (ParseException e) {
TermSuiteCLIUtils.printUsage(e, USAGE, options);
}
} catch (Exception e) {
e.printStackTrace(System.err);
LOGGER.error(e.getMessage());
}
}
private static boolean isInlineMode() {
return inlineText != null && inlineText.trim().length() > 0;
}
private static Options declareOptions() {
Options options = new Options();
options.addOption(TermSuiteCLIUtils.createOption(
null,
NO_OCCURRENCE,
false,
"Deactivate the occurrence store in memory (recommended for big corpus).",
false));
options.addOption(TermSuiteCLIUtils.createOption(
null,
PERIODIC_FILTER_PROPERTY,
true,
"Activate a periodic cleaning of the on-going terminology by a given property.",
false));
options.addOption(TermSuiteCLIUtils.createOption(
null,
PERIODIC_FILTER_MAX_SIZE,
true,
"The maximum allowed size of the on-going terminology in memory.",
false));
options.addOption(TermSuiteCLIUtils.createOption(
null,
MATE,
false,
"Use Mate tagger instead of TreeTagger.",
false));
options.addOption(TermSuiteCLIUtils.createOption(
null,
TEXT,
true,
"The text to analyze",
false));
options.addOption(TermSuiteCLIUtils.createOption(
null,
COMPOST_MAX_COMPONENT_NUM,
true,
"The maximum number of components that a compound can have",
false));
options.addOption(TermSuiteCLIUtils.createOption(
null,
COMPOST_MIN_COMPONENT_SIZE,
true,
"The minimum size allowed in a component",
false));
options.addOption(TermSuiteCLIUtils.createOption(
null,
COMPOST_SCORE_THRESHOLD,
true,
"The segmentation score threshold of COMPOST algo.",
false));
options.addOption(TermSuiteCLIUtils.createOption(
null,
COMPOST_SIMILARITY_THRESHOLD,
true,
"The segment similarity threshold above which an existing string in COMPOST index is considered as recognized.",
false));
options.addOption(TermSuiteCLIUtils.createOption(
null,
COMPOST_COEFF,
true,
"COMPOST alpha, beta, gamma and delta parameters, separated with a hyphen \"-\". Sum must be 1",
false));
options.addOption(TermSuiteCLIUtils.createOption(
null,
NO_LOGGING,
false,
"Disable logging",
false));
options.addOption(TermSuiteCLIUtils.createOption(
null,
DEBUG,
false,
"fine-grained logging",
false));
options.addOption(TermSuiteCLIUtils.createOption(
null,
TRACE,
false,
"very fine grained logging",
false));
options.addOption(TermSuiteCLIUtils.createOption(
null,
CONTEXTUALIZE,
false,
"Enable the contextualizer. Compute a context vector for each SWT term.",
false));
options.addOption(TermSuiteCLIUtils.createOption(
null,
CONTEXTUALIZE_ALL_TERMS,
false,
"Compute a context vector for MWTs too.",
false));
options.addOption(TermSuiteCLIUtils.createOption(
null,
ALLOW_MWT_IN_CONTEXTS,
false,
"Allow to set MWTs as cooccurrences in context vectors.",
false));
options.addOption(TermSuiteCLIUtils.createOption(
null,
CONTEXT_SCOPE,
true,
"The window size for term contexts capture",
false));
options.addOption(TermSuiteCLIUtils.createOption(
null,
CORPUS_FORMAT,
true,
"The file format in the input corpus. txt and tei supported",
false));
options.addOption(TermSuiteCLIUtils.createOption(
"c",
PATH_TO_CORPUS,
true,
"Path to the corpus",
false));
options.addOption(TermSuiteCLIUtils.createOption(
"r",
PATH_TO_RESOURCE_PACK,
true,
"Path to the TermSuite resource pack",
false));
options.addOption(TermSuiteCLIUtils.createOption(
"l",
TermSuiteCLIUtils.P_LANGUAGE,
true,
"language of the input files: fr/en/etc.",
true));
options.addOption(TermSuiteCLIUtils.createOption(
null,
TermSuiteCLIUtils.P_ENCODING,
true,
"encoding of the input files",
false));
options.addOption(TermSuiteCLIUtils.createOption(
"t",
P_TAGGER_HOME_DIRECTORY,
true,
"TreeTagger home directory or Mate model directory",
true));
options.addOption(TermSuiteCLIUtils.createOption(
null,
GRAPHICAL_SIMILARITY,
false,
"The similarity threshold (a value between 0 and 1, 0.9 advised) for graphical variant gathering.",
false));
options.addOption(TermSuiteCLIUtils.createOption(
null,
SHOW_TAGGER_TAGS,
false,
"Show tree tagger tags",
false));
options.addOption(
null,
WATCH,
true,
"Show infos about terms matching this string");
options.addOption(
null,
CLEAN_PROPERTY,
true,
"The name of the term property used for cleaning filtering the term index");
options.addOption(
null,
CLEAN_FILTER_VARIANTS,
false,
"Also filter variants with terms.");
options.addOption(
null,
CLEAN_THRESHOLD,
true,
"The filtering threshold");
options.addOption(
null,
CLEAN_TOP_N,
true,
"The number of terms to keep after filtering");
options.addOption(
null,
TSV,
true,
"The tsv file path where to export the term index");
options.addOption(
null,
TSV_PROPERTIES,
true,
"comma-separated list of term properties to export as a column in TSV file");
options.addOption(
null,
TSV_VARIANT_SCORES,
false,
"shows variant scores next to the \"V\" label");
options.addOption(
null,
TBX,
true,
"The tbx file path where to export the term index");
options.addOption(
null,
JSON,
true,
"The json file path where to export the term index");
options.addOption(
null,
JSCASFILE,
true,
"The directory path where to export the TreeTagger token of each files give in entry of TermSuite in " +
"Json Format");
options.addOption(
null,
MONGODB_STORE,
true,
"The mongo db url of the database where to store the occurrences");
options.addOption(
null,
MONGODB_SOFT_LINK,
false,
"shows variant scores next to the \"V\" label");
return options;
}
public static void readArguments(CommandLine line) throws IOException {
if(line.hasOption(NO_OCCURRENCE))
spotWithOccurrences = false;
inlineText = line.getOptionValue(TEXT);
if(inlineText == null)
inlineText = TermSuiteCLIUtils.readIn(encoding);
corpusPath = line.getOptionValue(PATH_TO_CORPUS);
if(inlineText == null && corpusPath == null)
TermSuiteCLIUtils.exitWithErrorMessage("Either the argument --" + TEXT + " or --" + PATH_TO_CORPUS + " must be set.");
resourcePack = line.getOptionValue(PATH_TO_RESOURCE_PACK);
language = Lang.forName(line.getOptionValue(TermSuiteCLIUtils.P_LANGUAGE));
encoding = line.getOptionValue(TermSuiteCLIUtils.P_ENCODING, "UTF-8");
taggerHome = line.getOptionValue(P_TAGGER_HOME_DIRECTORY);
if(line.hasOption(CORPUS_FORMAT)) {
if(line.getOptionValue(CORPUS_FORMAT).equals(TermSuiteCollection.TEI.name())) {
corpusType = TermSuiteCollection.TEI;
} else if(line.getOptionValue(CORPUS_FORMAT).equals(TermSuiteCollection.TXT.name())) {
corpusType = TermSuiteCollection.TXT;
} else
TermSuiteCLIUtils.exitWithErrorMessage("Unknown corpus format: " + line.getOptionValue(CORPUS_FORMAT) + ". Supported formats: " + Joiner.on(',').join(TermSuiteCollection.values()));
}
// pipelineCRInputDirectory = TermSuiteCLIUtils.getCorpusLanguagePath(corpusPath, language, corpusType.name().toLowerCase());
if(line.hasOption(GRAPHICAL_SIMILARITY))
graphicalSimilarityThreshold = Float.parseFloat(line.getOptionValue(GRAPHICAL_SIMILARITY));
if(line.hasOption(COMPOST_MIN_COMPONENT_SIZE))
compostMinComponentSize = Optional.of(Integer.parseInt(line.getOptionValue(COMPOST_MIN_COMPONENT_SIZE)));
if(line.hasOption(COMPOST_MAX_COMPONENT_NUM))
compostMaxComponentNum = Optional.of(Integer.parseInt(line.getOptionValue(COMPOST_MAX_COMPONENT_NUM)));
if(line.hasOption(COMPOST_SCORE_THRESHOLD))
compostScoreThreshold = Optional.of(Float.parseFloat(line.getOptionValue(COMPOST_SCORE_THRESHOLD)));
if(line.hasOption(WATCH))
watch = Optional.of(Pattern.compile(line.getOptionValue(WATCH)));
if(line.hasOption(COMPOST_SIMILARITY_THRESHOLD))
compostSimilarityThreshold = Optional.of(Float.parseFloat(line.getOptionValue(COMPOST_SIMILARITY_THRESHOLD)));
if(line.hasOption(COMPOST_COEFF)) {
List strings = Splitter.on('-').splitToList(line.getOptionValue(COMPOST_COEFF));
compostAlpha = Optional.of(Float.parseFloat(strings.get(0)));
compostBeta = Optional.of(Float.parseFloat(strings.get(1)));
compostGamma = Optional.of(Float.parseFloat(strings.get(2)));
compostDelta = Optional.of(Float.parseFloat(strings.get(3)));
Preconditions.checkArgument(
1.0f == compostAlpha.get() + compostBeta.get() + compostGamma.get() + compostDelta.get(),
String.format("The sum of Compost coeffs must be 1 (%3.2f+%3.2f+%3.2f+%3.2f=%3.2f)",
compostAlpha.get(),
compostBeta.get(),
compostGamma.get(),
compostDelta.get(),
compostAlpha.get() + compostBeta.get() + compostGamma.get() + compostDelta.get()
)
);
}
/*
* Contextualizer
*/
contextualize = line.hasOption(CONTEXTUALIZE);
allowMWTInContexts = line.hasOption(ALLOW_MWT_IN_CONTEXTS);
contextualizeAllTerms = line.hasOption(CONTEXTUALIZE_ALL_TERMS);
if(line.hasOption(CONTEXT_SCOPE)) {
contextScope = Integer.parseInt(line.getOptionValue(CONTEXT_SCOPE));
}
if(line.hasOption(CLEAN_THRESHOLD))
cleaningThreshold = Optional.of(Float.parseFloat(line.getOptionValue(CLEAN_THRESHOLD)));
if(line.hasOption(CLEAN_TOP_N))
cleaningTopN = Optional.of(Integer.parseInt(line.getOptionValue(CLEAN_TOP_N)));
if(line.hasOption(CLEAN_PROPERTY)) {
cleaningProperty = Optional.of(TermProperty.forName(line.getOptionValue(CLEAN_PROPERTY)));
}
if(line.hasOption(CLEAN_FILTER_VARIANTS))
keepVariantsWhileCleaning = false;
if(line.hasOption(PERIODIC_FILTER_PROPERTY)) {
periodicFilteringProperty = Optional.of(TermProperty.forName(line.getOptionValue(PERIODIC_FILTER_PROPERTY)));
if(line.hasOption(PERIODIC_FILTER_MAX_SIZE))
maxSizeFilteringMaxSize = Integer.parseInt(line.getOptionValue(PERIODIC_FILTER_MAX_SIZE).trim());
}
if(line.hasOption(TSV))
tsvFile = Optional.of(line.getOptionValue(TSV));
if(line.hasOption(TSV_PROPERTIES)) {
List list = Lists.newArrayList();
for(String pName:Splitter.on(",").split(line.getOptionValue(TSV_PROPERTIES))) {
list.add(TermProperty.forName(pName));
}
TermProperty[] ary = new TermProperty[list.size()];
tsvProperties = Optional.of(list.toArray(ary));
}
if(line.hasOption(TSV_VARIANT_SCORES))
tsvShowVariantScores = true;
if(line.hasOption(TBX))
tbxFile = Optional.of(line.getOptionValue(TBX));
if(line.hasOption(JSON))
jsonFile = Optional.of(line.getOptionValue(JSON));
if(line.hasOption(JSCASFILE))
jsonCasFile = Optional.of(line.getOptionValue(JSCASFILE));
if(line.hasOption(MATE))
tagger = Tagger.Mate;
if(line.hasOption(MONGODB_STORE))
mongoStoreDBURL = Optional.of(line.getOptionValue(MONGODB_STORE));
if(line.hasOption(MONGODB_SOFT_LINK)) {
Preconditions.checkArgument(line.hasOption(MONGODB_STORE), "The option %s requires the option %s", MONGODB_SOFT_LINK, MONGODB_STORE);
mongoStoreSoftLinked = true;
}
}
}
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