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Create a new class of static method, IDRangeHelper, and move all the code needed to deal with ID range files to that class. That code will later be reused by another command.
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robot/src/main/java/org/incenp/obofoundry/kgcl/robot/IDRangeHelper.java
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| /* | ||
| * KGCL-Java - KGCL library for Java | ||
| * Copyright © 2024 Damien Goutte-Gattat | ||
| * | ||
| * This program 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. | ||
| * | ||
| * This program 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 this program. If not, see <http://www.gnu.org/licenses/>. | ||
| */ | ||
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| package org.incenp.obofoundry.kgcl.robot; | ||
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| import java.io.File; | ||
| import java.io.FilenameFilter; | ||
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| import org.incenp.obofoundry.idrange.IDRange; | ||
| import org.incenp.obofoundry.idrange.IDRangePolicyException; | ||
| import org.incenp.obofoundry.idrange.IDRangePolicyParser; | ||
| import org.incenp.obofoundry.idrange.IIDRangePolicy; | ||
| import org.incenp.obofoundry.kgcl.IAutoIDGenerator; | ||
| import org.incenp.obofoundry.kgcl.RandomizedIDGenerator; | ||
| import org.incenp.obofoundry.kgcl.SequentialIDGenerator; | ||
| import org.semanticweb.owlapi.model.OWLOntology; | ||
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| /* | ||
| * Helper methods to work with OBO-style ID range policy files. | ||
| */ | ||
| public class IDRangeHelper { | ||
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| /** | ||
| * Finds an ID range policy file in the current directory. This methods looks | ||
| * for a single file whose name ends with {@code -idranges.owl} in the current | ||
| * directory. | ||
| * | ||
| * @return The name of the ID range policy file, if such a file exists; | ||
| * otherwise {@code null}. | ||
| */ | ||
| public static String findIDRangeFile() { | ||
| FilenameFilter idRangeFilter = new FilenameFilter() { | ||
| @Override | ||
| public boolean accept(File file, String name) { | ||
| return name.endsWith("-idranges.owl"); | ||
| } | ||
| }; | ||
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| File cwd = new File("."); | ||
| String[] rangeFiles = cwd.list(idRangeFilter); | ||
| if ( rangeFiles.length == 1 ) { | ||
| return rangeFiles[0]; | ||
| } | ||
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| return null; | ||
| } | ||
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| /** | ||
| * Gets an ID generator initialised with data from the specified range file. | ||
| * | ||
| * @param ontology The ontology to generate IDs for. | ||
| * @param rangeFile The range file to initialise the generator with. | ||
| * @param rangeName The name of the range to use. This should match the | ||
| * {@code allocatedto} annotation of one of the ranges in the | ||
| * file. May be {@code null}, in which case the method will | ||
| * look for a range that matches one of the alternative names | ||
| * instead. If not {@code null} and a corresponding range | ||
| * cannot be found, an exception will be thrown. | ||
| * @param altNames A list of default range names to use if {@code rangeName} is | ||
| * {@code null}. | ||
| * @param random If {@code true}, the generator will produce IDs picked at | ||
| * random within the target range; otherwise, IDs will be | ||
| * picked sequentially. | ||
| * @return A newly initialised ID generator. | ||
| * @throws IDRangePolicyException If the range file cannot be read for any | ||
| * reason, if the requested {@code rangeName} | ||
| * cannot be found, or if none of the default | ||
| * ranges can be found. | ||
| */ | ||
| public static IAutoIDGenerator getIDGenerator(OWLOntology ontology, String rangeFile, String rangeName, | ||
| String[] altNames, boolean random) throws IDRangePolicyException { | ||
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| IDRangePolicyParser parser = new IDRangePolicyParser(rangeFile); | ||
| IIDRangePolicy policy = parser.parse(); | ||
| IDRange range = null; | ||
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| if ( rangeName != null ) { | ||
| range = policy.getRange(rangeName); | ||
| if ( range == null ) { | ||
| throw new IDRangePolicyException("Requested range not found in ID range file"); | ||
| } | ||
| } | ||
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| int i = 0; | ||
| while ( range == null && altNames != null && i < altNames.length ) { | ||
| range = policy.getRange(altNames[i++]); | ||
| } | ||
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| if ( range == null ) { | ||
| throw new IDRangePolicyException("Not suitable range found in ID range file"); | ||
| } | ||
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| String format = String.format("%s%%0%dd", policy.getPrefix(), policy.getWidth()); | ||
| if ( random ) { | ||
| return new RandomizedIDGenerator(ontology, format, range.getLowerBound(), range.getUpperBound()); | ||
| } else { | ||
| return new SequentialIDGenerator(ontology, format, range.getLowerBound(), range.getUpperBound()); | ||
| } | ||
| } | ||
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| /** | ||
| * Gets an ID generator initialised with data from the specified range file, or | ||
| * a default file. This method is similar to | ||
| * {@link #getIDGenerator(OWLOntology, String, String, String[], boolean)}, | ||
| * except that if the {@code rangeFile} parameter is {@code null}, it tries to | ||
| * find a default range file (using the {@link #findIDRangeFile()} method); in | ||
| * that case, no exception will be thrown. | ||
| * | ||
| * @param ontology The ontology to generate IDs for. | ||
| * @param rangeFile The range file to initialise the generator with. If | ||
| * {@code null}, the method will try to find a default file. | ||
| * @param rangeName The name of the range to use. This should match the | ||
| * {@code allocatedto} annotation of one of the ranges in the | ||
| * file. May be {@code null}, in which case the method will | ||
| * look for a range that matches one of the alternative names | ||
| * instead. | ||
| * @param altNames A list of default range names to use if {@code rangeName} is | ||
| * {@code null}. | ||
| * @param random If {@code true}, the generator will produce IDs picked at | ||
| * random within the target range; otherwise, IDs will be | ||
| * picked sequentially. | ||
| * @return A newly initialised ID generator or {@code null} if no range file has | ||
| * been specified and no suitable default file was found. | ||
| * @throws IDRangePolicyException Only if {@code rangeFile} is not {@code null}: | ||
| * iIf the range file cannot be read for any | ||
| * reason, if the requested {@code rangeName} | ||
| * cannot be found, or if none of the default | ||
| * ranges can be found. | ||
| */ | ||
| public static IAutoIDGenerator maybeGetIDGenerator(OWLOntology ontology, String rangeFile, String rangeName, | ||
| String[] altNames, boolean random) throws IDRangePolicyException { | ||
| boolean silent = false; | ||
| IAutoIDGenerator generator = null; | ||
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| if ( rangeFile == null ) { | ||
| rangeFile = findIDRangeFile(); | ||
| if ( rangeFile == null ) { | ||
| return null; | ||
| } | ||
| silent = true; | ||
| } | ||
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| try { | ||
| generator = getIDGenerator(ontology, rangeFile, rangeName, altNames, random); | ||
| } catch ( IDRangePolicyException e ) { | ||
| if ( !silent ) { | ||
| throw e; | ||
| } | ||
| } | ||
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| return generator; | ||
| } | ||
| } |