org.icgc.dcc.generator.utils.RegexMatches.java Source code

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Here is the source code for org.icgc.dcc.generator.utils.RegexMatches.java

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/*
 * Copyright (c) 2013 The Ontario Institute for Cancer Research. All rights reserved.                             
 *                                                                                                               
 * This program and the accompanying materials are made available under the terms of the GNU Public License v3.0.
 * You should have received a copy of the GNU General Public License along with                                  
 * this program. If not, see <http://www.gnu.org/licenses/>.                                                     
 *                                                                                                               
 * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY                           
 * EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES                          
 * OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT                           
 * SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT,                                
 * INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED                          
 * TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;                               
 * OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER                              
 * IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN                         
 * ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 */
package org.icgc.dcc.generator.utils;

import static lombok.AccessLevel.PRIVATE;
import static org.apache.commons.lang.StringEscapeUtils.escapeJava;
import static org.apache.commons.lang.StringUtils.isBlank;
import lombok.NoArgsConstructor;
import lombok.val;

import org.icgc.dcc.submission.dictionary.model.RestrictionType;

import com.google.common.base.Splitter;
import com.google.common.collect.ImmutableMap;
import com.google.common.collect.Maps;

/**
 * See https://wiki.oicr.on.ca/display/DCCSOFT/0.6c+to+0.6d.
 * <p>
 * Consider Xeger library to reverse regexes (beware of limitations).
 * <p>
 * TODO: Must support obtaining multiple and unique matches for a regex (DCC-1202).
 */
@NoArgsConstructor(access = PRIVATE)
public final class RegexMatches {

    /**
     * Keep track of corresponding dictionary version since regexes are version-dependent.
     */
    public static final String LATEST_KNOWN_DICTIONARY_VERSION = "0.7e";

    // @formatter:off
    public static final ImmutableMap<String, String> MATCHING_VALUES = new ImmutableMap.Builder<String, String>()
            .put("(?iu)^([ATGC\\-]+$){1,200}", "GA").put("(?iu)^([ATGC\\-]+(([,{1}][ATGC\\-]+){1,3})?+)$", "AC")
            .put("(?iu)^([ATGC\\-]+/[ATGC\\-]+(([/{1}][ATGC\\-]+){0,2})?+)$", "GA/-")
            .put("(?iu)^([ATGC\\-]+/[ATGC\\-]+)$", "GA/GA").put("(A|C|G|T|U)+", "AUGGUCGCCUUCCACC")
            .put("(^[\\w\\s_\\-\\.]+)((\\s)(http(s)?://|www[.])[-A-Za-z0-9+&@#/%?=~_()|!:,.;]*)?((\\s)[-A-Za-z0-9_\\s|><.]+)?",
                    "Paired End http://www.illumina.com/technology/paired_end_sequencing_assay.ilmn")
            .put("^(1)$", "1").put("^([\\w+\\-\\_]+)$", "LAML_PO_00445").put("^(\\w+)\\:(\\w+)$", "Ensembl:69")
            .put("^[\\w+\\-\\_]+$", "hnc_12").put("^\\d+$", "243198475").build();
    // @formatter:on

    /**
     * Utility to generate the code above.
     */
    public static void main(String... args) {
        // Set to remove duplicates, TreeSet to sort
        val regexes = Maps.<String, String>newTreeMap();
        val splitter = Splitter.on(",").trimResults();

        // Find all the unique regexes
        val fileSchemas = new FileSchemas();
        for (val fileSchema : fileSchemas.getSchemas()) {
            for (val field : fileSchema.getFields()) {
                for (val restriction : field.getRestrictions()) {
                    if (restriction.getType() == RestrictionType.REGEX) {
                        val config = restriction.getConfig();
                        val regex = (String) config.get("pattern");
                        val examples = (String) config.get("examples");

                        if (regexes.containsKey(regex) && !isBlank(examples)) {
                            continue;
                        }

                        val example = isBlank(examples) ? "" : splitter.splitToList(examples).get(0);
                        regexes.put(regex, example);
                    }
                }
            }
        }

        for (val entry : regexes.entrySet()) {
            val regex = entry.getKey();
            val example = entry.getValue();

            val line = "      .put(\"" + escapeJava(regex) + "\",\"" + example + "\")";
            System.out.println(line);
        }
    }
}