Java tutorial
/************************************************************************* * * * This file is part of the 20n/act project. * * 20n/act enables DNA prediction for synthetic biology/bioengineering. * * Copyright (C) 2017 20n Labs, Inc. * * * * Please direct all queries to act@20n.com. * * * * 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/>. * * * *************************************************************************/ package act.installer; import act.installer.sequence.UniprotSeqEntry; import act.installer.sequence.UniprotSeqEntryFactory; import act.server.DBIterator; import act.server.MongoDB; import act.shared.Organism; import act.shared.Seq; import com.act.biointerpretation.Utils.OrgMinimalPrefixGenerator; import com.act.utils.parser.UniprotInterpreter; import com.mongodb.DBObject; import org.apache.commons.cli.CommandLine; import org.apache.commons.cli.CommandLineParser; import org.apache.commons.cli.DefaultParser; import org.apache.commons.cli.HelpFormatter; import org.apache.commons.cli.Option; import org.apache.commons.cli.Options; import org.apache.commons.cli.ParseException; import org.apache.commons.lang3.StringUtils; import org.apache.logging.log4j.LogManager; import org.apache.logging.log4j.Logger; import org.biojava.nbio.core.exceptions.CompoundNotFoundException; import org.json.JSONArray; import org.json.JSONObject; import org.xml.sax.SAXException; import javax.xml.parsers.ParserConfigurationException; import java.io.File; import java.io.IOException; import java.util.ArrayList; import java.util.HashMap; import java.util.HashSet; import java.util.Iterator; import java.util.List; import java.util.Map; import java.util.Set; import java.util.regex.Pattern; public class UniprotInstaller { private static final Logger LOGGER = LogManager.getFormatterLogger(UniprotInstaller.class); private static final UniprotSeqEntryFactory seqEntryFactory = new UniprotSeqEntryFactory(); private static final String OPTION_UNIPROT_PATH = "p"; private static final String OPTION_DB_NAME = "d"; private static final String NAME = "name"; private static final String ACCESSION = "accession"; private static final String SYNONYMS = "synonyms"; private static final String PRODUCT_NAMES = "product_names"; private static final String VAL = "val"; private static final String SRC = "src"; private static final String PMID = "PMID"; private static final String CATALYTIC_ACTIVITY = "catalytic_activity"; // http://www.uniprot.org/help/accession_numbers public static final Pattern UNIPROT_ACCESSION_PATTERN = Pattern .compile("[OPQ][0-9][A-Z0-9]{3}[0-9]|[A-NR-Z][0-9]([A-Z][A-Z0-9]{2}[0-9]){1,2}"); public static final String HELP_MESSAGE = StringUtils.join(new String[] { "This class is the driver to write sequence data from a Uniprot file to our database. It can be used on the ", "command line with a file path as a parameter." }, ""); public static final List<Option.Builder> OPTION_BUILDERS = new ArrayList<Option.Builder>() { { add(Option.builder(OPTION_UNIPROT_PATH).argName("uniprot file") .desc("uniprot file containing sequence and annotations").hasArg().longOpt("uniprot") .required()); add(Option.builder(OPTION_DB_NAME).argName("db name").desc("name of the database to be queried") .hasArg().longOpt("database").required()); add(Option.builder("h").argName("help").desc("Example of usage: -p filepath.gb -d marvin") .longOpt("help")); } }; public static final HelpFormatter HELP_FORMATTER = new HelpFormatter(); static { HELP_FORMATTER.setWidth(100); } File uniprotFile; MongoDB db; Map<String, String> minimalPrefixMapping; // the minimalPrefixMapping is generated by OrgMinimalPrefixGenerator public UniprotInstaller(File uniprotFile, MongoDB db, Map<String, String> minimalPrefixMapping) { this.uniprotFile = uniprotFile; this.db = db; this.minimalPrefixMapping = minimalPrefixMapping; } public void init() throws IOException, SAXException, ParserConfigurationException, CompoundNotFoundException { UniprotInterpreter uniprotInterpreter = new UniprotInterpreter(uniprotFile); uniprotInterpreter.init(); UniprotSeqEntry seqEntry = seqEntryFactory.createFromDocumentReference(uniprotInterpreter.getXmlDocument(), db, minimalPrefixMapping); addSeqEntryToDb(seqEntry, db); } /** * Verifies the accession string according to the standard Genbank/Uniprot accession qualifications * @param proteinAccession the accession string to be validated * @param accessionPattern the pattern that the accession string should match * @return */ private boolean verifyAccession(String proteinAccession, Pattern accessionPattern) { return accessionPattern.matcher(proteinAccession).matches(); } /** * Checks if the new value already exists in the field. If so, doesn't update the metadata. If it doesn't exist, * appends the new value to the data. * @param field the key referring to the array in the metadata we wish to update * @param value the value we wish to add to the array * @param data the metadata * @return the updated metadata JSONObject */ private JSONObject updateArrayField(String field, String value, JSONObject data) { if (value == null || value.isEmpty()) { return data; } if (data.has(field)) { JSONArray fieldData = data.getJSONArray(field); for (int i = 0; i < fieldData.length(); i++) { if (fieldData.get(i).toString().equals(value)) { return data; } } } return data.append(field, value); } /** * Updates the accession JSONObject for the given accessions type * @param newAccessionObject the new accession object to load in the new accessions of the given type * @param metadata contains the accession object to be updated * @param accType the type of accessions to update * @param accessionPattern the accession pattern to validate the accession string according to Genbank/Uniprot * standards * @return the metadata containing the updated accession mapping */ private JSONObject updateAccessions(JSONObject newAccessionObject, JSONObject metadata, Seq.AccType accType, Pattern accessionPattern) { JSONObject oldAccessionObject = metadata.getJSONObject(ACCESSION); if (newAccessionObject.has(accType.toString())) { JSONArray newAccTypeAccessions = newAccessionObject.getJSONArray(accType.toString()); for (int i = 0; i < newAccTypeAccessions.length(); i++) { if (!verifyAccession(newAccTypeAccessions.getString(i), accessionPattern)) { LOGGER.error("%s accession not the right format: %s\n", accType.toString(), newAccTypeAccessions.getString(i)); continue; } oldAccessionObject = updateArrayField(accType.toString(), newAccTypeAccessions.getString(i), oldAccessionObject); } } return metadata.put(ACCESSION, oldAccessionObject); } /** * Updates metadata and reference fields with the information extracted from file * @param se an instance of the UniprotSeqEntry class that extracts all the relevant information from a sequence * object * @param db reference to the database that should be queried and updated */ private void addSeqEntryToDb(UniprotSeqEntry se, MongoDB db) { List<Seq> seqs = se.getMatchingSeqs(); // no prior data on this sequence if (seqs.isEmpty()) { se.writeToDB(db, Seq.AccDB.uniprot); return; } // update prior data for (Seq seq : seqs) { JSONObject metadata = seq.getMetadata(); JSONObject accessions = se.getAccession(); if (!metadata.has(ACCESSION)) { metadata.put(ACCESSION, accessions); } else { metadata = updateAccessions(accessions, metadata, Seq.AccType.genbank_nucleotide, GenbankInstaller.NUCLEOTIDE_ACCESSION_PATTERN); metadata = updateAccessions(accessions, metadata, Seq.AccType.genbank_protein, GenbankInstaller.PROTEIN_ACCESSION_PATTERN); metadata = updateAccessions(accessions, metadata, Seq.AccType.uniprot, UNIPROT_ACCESSION_PATTERN); } List<String> geneSynonyms = se.getGeneSynonyms(); if (se.getGeneName() != null) { if (!metadata.has(NAME) || metadata.isNull(NAME)) { metadata.put(NAME, se.getGeneName()); } else if (!se.getGeneName().equals(metadata.get(NAME))) { geneSynonyms.add(se.getGeneName()); } } for (String geneSynonym : geneSynonyms) { if (!geneSynonym.equals(metadata.get(NAME))) { metadata = updateArrayField(SYNONYMS, geneSynonym, metadata); } } List<String> productNames = se.getProductName(); if (!productNames.isEmpty()) { for (int i = 0; i < productNames.size(); i++) { metadata = updateArrayField(PRODUCT_NAMES, productNames.get(i), metadata); } } if (se.getCatalyticActivity() != null) { metadata.put(CATALYTIC_ACTIVITY, se.getCatalyticActivity()); } seq.setMetadata(metadata); db.updateMetadata(seq); List<JSONObject> oldRefs = seq.getReferences(); List<JSONObject> newPmidRefs = se.getRefs(); if (!oldRefs.isEmpty()) { Set<String> oldPmids = new HashSet<>(); for (JSONObject oldRef : oldRefs) { if (oldRef.get(SRC).equals(PMID)) { oldPmids.add(oldRef.getString(VAL)); } } for (JSONObject newPmidRef : newPmidRefs) { if (!oldPmids.contains(newPmidRef.getString(VAL))) { oldRefs.add(newPmidRef); } } seq.setReferences(oldRefs); } else { seq.setReferences(se.getRefs()); } if (seq.getReferences() != null) { db.updateReferences(seq); } } } public static void main(String[] args) throws IOException, SAXException, ParserConfigurationException, CompoundNotFoundException { Options opts = new Options(); for (Option.Builder b : OPTION_BUILDERS) { opts.addOption(b.build()); } CommandLine cl = null; try { CommandLineParser parser = new DefaultParser(); cl = parser.parse(opts, args); } catch (ParseException e) { LOGGER.error("Argument parsing failed: %s", e.getMessage()); HELP_FORMATTER.printHelp(UniprotInstaller.class.getCanonicalName(), HELP_MESSAGE, opts, null, true); System.exit(1); } if (cl.hasOption("help")) { HELP_FORMATTER.printHelp(UniprotInstaller.class.getCanonicalName(), HELP_MESSAGE, opts, null, true); System.exit(1); } File uniprotFile = new File(cl.getOptionValue(OPTION_UNIPROT_PATH)); String dbName = cl.getOptionValue(OPTION_DB_NAME); if (!uniprotFile.exists()) { String msg = String.format("Uniprot file path is null"); LOGGER.error(msg); throw new RuntimeException(msg); } else { MongoDB db = new MongoDB("localhost", 27017, dbName); DBIterator iter = db.getDbIteratorOverOrgs(); Iterator<Organism> orgIterator = new Iterator<Organism>() { @Override public boolean hasNext() { boolean hasNext = iter.hasNext(); if (!hasNext) iter.close(); return hasNext; } @Override public Organism next() { DBObject o = iter.next(); return db.convertDBObjectToOrg(o); } }; OrgMinimalPrefixGenerator prefixGenerator = new OrgMinimalPrefixGenerator(orgIterator); Map<String, String> minimalPrefixMapping = prefixGenerator.getMinimalPrefixMapping(); UniprotInstaller installer = new UniprotInstaller(uniprotFile, db, minimalPrefixMapping); installer.init(); } } }