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Merge pull request #223 from cdk/patch/inchitimeout
Workaround for timeouts in JNI InChI - default timeout included of 5 …
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storage/inchi/src/main/java/org/openscience/cdk/inchi/JniInChIInputAdapter.java
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| /* | ||
| * Copyright (c) 2016 John May <jwmay@users.sf.net> | ||
| * | ||
| * Contact: cdk-devel@lists.sourceforge.net | ||
| * | ||
| * This program is free software; you can redistribute it and/or modify it | ||
| * under the terms of the GNU Lesser General Public License as published by | ||
| * the Free Software Foundation; either version 2.1 of the License, or (at | ||
| * your option) any later version. All we ask is that proper credit is given | ||
| * for our work, which includes - but is not limited to - adding the above | ||
| * copyright notice to the beginning of your source code files, and to any | ||
| * copyright notice that you may distribute with programs based on this work. | ||
| * | ||
| * 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 Lesser General Public | ||
| * License for more details. | ||
| * | ||
| * You should have received a copy of the GNU Lesser General Public License | ||
| * along with this program; if not, write to the Free Software | ||
| * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 U | ||
| */ | ||
|
|
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| package org.openscience.cdk.inchi; | ||
|
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| import net.sf.jniinchi.INCHI_OPTION; | ||
| import net.sf.jniinchi.JniInchiException; | ||
| import net.sf.jniinchi.JniInchiInput; | ||
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| import java.util.List; | ||
| import java.util.StringTokenizer; | ||
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| public class JniInChIInputAdapter extends JniInchiInput { | ||
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| public static final String FIVE_SECOND_TIMEOUT = "-W5"; | ||
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| public JniInChIInputAdapter(String options) throws JniInchiException { | ||
| this.options = options == null ? "" : checkOptions(options); | ||
| } | ||
|
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| public JniInChIInputAdapter(List<INCHI_OPTION> options) throws JniInchiException { | ||
| this.options = options == null ? "" : checkOptions(options); | ||
| } | ||
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| private static boolean isTimeoutOptions(String op) { | ||
| if (op == null || op.length() < 2) return false; | ||
| int pos = 0; | ||
| int len = op.length(); | ||
| if (op.charAt(pos) == 'W') | ||
| pos++; | ||
| while (pos < len && Character.isDigit(op.charAt(pos))) | ||
| pos++; | ||
| if (pos < len && op.charAt(pos) == '.') | ||
| pos++; | ||
| while (pos < len && Character.isDigit(op.charAt(pos))) | ||
| pos++; | ||
| return pos == len; | ||
| } | ||
|
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| private static String checkOptions(final String ops) throws JniInchiException { | ||
| if (ops == null) { | ||
| throw new IllegalArgumentException("Null options"); | ||
| } | ||
| StringBuilder sbOptions = new StringBuilder(); | ||
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| boolean hasUserSpecifiedTimeout = false; | ||
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| StringTokenizer tok = new StringTokenizer(ops); | ||
| while (tok.hasMoreTokens()) { | ||
| String op = tok.nextToken(); | ||
|
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| if (op.startsWith("-") || op.startsWith("/")) { | ||
| op = op.substring(1); | ||
| } | ||
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| INCHI_OPTION option = INCHI_OPTION.valueOfIgnoreCase(op); | ||
| if (option != null) { | ||
| sbOptions.append('-').append(option.name()); | ||
| if (tok.hasMoreTokens()) { | ||
| sbOptions.append(" "); | ||
| } | ||
| } else if (isTimeoutOptions(op)) { | ||
| sbOptions.append('-').append(op); | ||
| hasUserSpecifiedTimeout = true; | ||
| if (tok.hasMoreTokens()) { | ||
| sbOptions.append(" "); | ||
| } | ||
| } else { | ||
| throw new JniInchiException("Unrecognised InChI option"); | ||
| } | ||
| } | ||
|
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| if (!hasUserSpecifiedTimeout) { | ||
| if (sbOptions.length() > 0) | ||
| sbOptions.append(' '); | ||
| sbOptions.append(FIVE_SECOND_TIMEOUT); | ||
| } | ||
|
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| return sbOptions.toString(); | ||
| } | ||
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| private static String checkOptions(List<INCHI_OPTION> ops) throws JniInchiException { | ||
| if (ops == null) { | ||
| throw new IllegalArgumentException("Null options"); | ||
| } | ||
| StringBuilder sbOptions = new StringBuilder(); | ||
|
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| for (INCHI_OPTION op : ops) { | ||
| sbOptions.append('-').append(op.name()).append(" "); | ||
| } | ||
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| if (sbOptions.length() > 0) | ||
| sbOptions.append(' '); | ||
| sbOptions.append(FIVE_SECOND_TIMEOUT); | ||
|
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| return sbOptions.toString(); | ||
| } | ||
| } |
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