Java tutorial
/** * ============================================================================= * * ORCID (R) Open Source * http://orcid.org * * Copyright (c) 2012-2014 ORCID, Inc. * Licensed under an MIT-Style License (MIT) * http://orcid.org/open-source-license * * This copyright and license information (including a link to the full license) * shall be included in its entirety in all copies or substantial portion of * the software. * * ============================================================================= */ package org.orcid.api.common.writer.citeproc; import java.io.IOException; import java.lang.reflect.Field; import java.util.ArrayList; import java.util.Arrays; import java.util.List; import java.util.Map; import org.apache.commons.io.IOUtils; import org.apache.commons.lang.StringUtils; import org.jbibtex.BibTeXDatabase; import org.jbibtex.ParseException; import org.orcid.jaxb.model.common.Contributor; import org.orcid.jaxb.model.record_rc1.CitationType; import org.orcid.jaxb.model.record_rc1.Work; import org.orcid.jaxb.model.record_rc1.WorkExternalIdentifier; import org.orcid.jaxb.model.record_rc1.WorkExternalIdentifierType; import org.springframework.util.ReflectionUtils; import com.google.common.base.Joiner; import de.undercouch.citeproc.bibtex.BibTeXConverter; import de.undercouch.citeproc.csl.CSLItemData; import de.undercouch.citeproc.csl.CSLItemDataBuilder; import de.undercouch.citeproc.csl.CSLName; import de.undercouch.citeproc.csl.CSLNameBuilder; import de.undercouch.citeproc.csl.CSLType; public class WorkToCiteprocTranslator { private final Field authorField = ReflectionUtils.findField(CSLItemData.class, "author"); private final Field literalField = ReflectionUtils.findField(CSLName.class, "literal"); private final Field doiField = ReflectionUtils.findField(CSLItemData.class, "DOI"); private final Field urlField = ReflectionUtils.findField(CSLItemData.class, "URL"); /** * Turn a work into Citeproc JSON. Uses bibtex citation if present, * otherwise attempts to map ORCID metadata * * @param work the work to translate * @param creditName name to use as author if no bibtex found * @param abreviate if true, will shorten bibtex derived authorship to 200 characters or 20 authors * @return the JSON as a String. */ public CSLItemData toCiteproc(Work work, String creditName, boolean abreviate) { if (work.getWorkCitation() != null && work.getWorkCitation().getWorkCitationType() != null && work.getWorkCitation().getWorkCitationType().equals(CitationType.BIBTEX)) { return translateFromBibtexCitation(work, abreviate); } return translateFromWorkMetadata(work, creditName); } /** * Extract the bibtex and turn into CSL Adds in DOI and URL from metadata if * missing Horrible use of reflection to shorten hyperauthorship. It will * strip anything above 20 authors down to the primary author and 'et all'. * * @param work * @param abreviate * @return */ private CSLItemData translateFromBibtexCitation(Work work, boolean abreviate) { try { System.out.println("----"); System.out.println(work.getWorkCitation().getCitation()); System.out.println("----"); BibTeXConverter conv = new BibTeXConverter(); BibTeXDatabase db = conv.loadDatabase(IOUtils.toInputStream(work.getWorkCitation().getCitation())); Map<String, CSLItemData> cids = conv.toItemData(db); if (cids.size() == 1) { CSLItemData item = cids.values().iterator().next(); // FOR REASONS UNKNOWN, CITEPROC WILL SOMETIMES generate // multiple authors not a literal. if (abreviate) { if (item.getAuthor().length > 20) { CSLName[] abrev = Arrays.copyOf(item.getAuthor(), 1); abrev[0] = new CSLNameBuilder() .literal(abrev[0].getGiven() + " " + abrev[0].getFamily() + " " + "et all.") .build(); ReflectionUtils.makeAccessible(authorField); ReflectionUtils.setField(authorField, item, abrev); } for (int i = 0; i < item.getAuthor().length; i++) { if (item.getAuthor()[i].getLiteral() != null && item.getAuthor()[i].getLiteral().length() > 200) { ReflectionUtils.makeAccessible(literalField); ReflectionUtils.setField(literalField, item.getAuthor()[i], StringUtils.abbreviate(item.getAuthor()[i].getLiteral(), 200)); } } } if (item.getDOI() == null) { String doi = extractID(work, WorkExternalIdentifierType.DOI); if (doi != null) { ReflectionUtils.makeAccessible(doiField); ReflectionUtils.setField(doiField, item, doi); } } if (item.getURL() == null) { if (extractID(work, WorkExternalIdentifierType.URI) != null) { ReflectionUtils.makeAccessible(urlField); ReflectionUtils.setField(urlField, item, extractID(work, WorkExternalIdentifierType.URI)); } else if (item.getDOI() != null) { ReflectionUtils.makeAccessible(urlField); ReflectionUtils.setField(urlField, item, item.getDOI()); } else if (extractID(work, WorkExternalIdentifierType.HANDLE) != null) { ReflectionUtils.makeAccessible(urlField); ReflectionUtils.setField(urlField, item, extractID(work, WorkExternalIdentifierType.HANDLE)); } } return item; } else throw new ParseException("Invalid Citation count"); } catch (IOException | ParseException e) { return null; } } /** * Use the ORCID work metadata to generate a *limited* citation. You'll most * likely get a title, doi, url, date and author. * * Translates type according to https://docs.google.com/spreadsheets/d/ * 1h4nTF6DKNEpWcGNQVMDwt0ea09qmkBnkWisxkJE-li4/edit#gid=754644608 * * Informed by mendley tranforms at * http://support.mendeley.com/customer/portal/articles/364144-csl-type- * mapping * * See also: * http://docs.citationstyles.org/en/stable/specification.html#appendix-iii- * types http://members.orcid.org/api/supported-work-types datacite and * crossref mappings here: * https://github.com/lagotto/lagotto/blob/master/config/initializers/ * constants.rb * @param creditName * * @param worktype * @return a CSLItemData, default CSLType.ARTICLE if cannot map type */ private CSLItemData translateFromWorkMetadata(Work work, String creditName) { CSLItemDataBuilder builder = new CSLItemDataBuilder(); builder.title((work.getWorkTitle() != null) ? work.getWorkTitle().getTitle().getContent() : "No Title"); String doi = extractID(work, WorkExternalIdentifierType.DOI); String url = extractID(work, WorkExternalIdentifierType.URI); if (doi != null) { builder.DOI(doi); } if (url != null) { builder.URL(url); } else if (doi != null) { builder.URL("http://doi.org/" + doi); } else { url = extractID(work, WorkExternalIdentifierType.HANDLE); if (url != null) { builder.URL(url); } } if (work.getJournalTitle() != null) { builder.containerTitle(work.getJournalTitle().getContent()); } List<String> names = new ArrayList<String>(); // TODO: Pass in credit name names.add(creditName); if (work.getWorkContributors() != null && work.getWorkContributors().getContributor() != null) { for (Contributor c : work.getWorkContributors().getContributor()) { names.add(c.getCreditName().getContent()); } } CSLNameBuilder name = new CSLNameBuilder(); name.literal(Joiner.on(" and ").skipNulls().join(names)); builder.author(name.build()); // TODO: make it work with "Spring", "August", whatever... if (work.getPublicationDate() != null) { int year = 0; int month = 0; int day = 0; try { year = Integer.parseInt(work.getPublicationDate().getYear().getValue()); month = Integer.parseInt(work.getPublicationDate().getMonth().getValue()); day = Integer.parseInt(work.getPublicationDate().getDay().getValue()); } catch (Exception e) { } if (year > 0 && month > 0 && day > 0) { builder.issued(year, month, day); } else if (year > 0 && month > 0) { builder.issued(year, month); } else if (year > 0) { builder.issued(year); } } switch (work.getWorkType()) { case ARTISTIC_PERFORMANCE: break; case BOOK: builder.type(CSLType.BOOK); break; case BOOK_CHAPTER: builder.type(CSLType.CHAPTER); break; case BOOK_REVIEW: builder.type(CSLType.REVIEW_BOOK); break; case CONFERENCE_ABSTRACT: builder.type(CSLType.PAPER_CONFERENCE); break; case CONFERENCE_PAPER: builder.type(CSLType.PAPER_CONFERENCE); break; case CONFERENCE_POSTER: builder.type(CSLType.PAPER_CONFERENCE); break; case DATA_SET: builder.type(CSLType.DATASET); break; case DICTIONARY_ENTRY: builder.type(CSLType.ENTRY_DICTIONARY); break; case DISSERTATION: builder.type(CSLType.THESIS); break; case ENCYCLOPEDIA_ENTRY: builder.type(CSLType.ENTRY_ENCYCLOPEDIA); break; case JOURNAL_ARTICLE: builder.type(CSLType.ARTICLE_JOURNAL); break; case MAGAZINE_ARTICLE: builder.type(CSLType.ARTICLE_MAGAZINE); break; case NEWSLETTER_ARTICLE: builder.type(CSLType.ARTICLE_NEWSPAPER); break; case NEWSPAPER_ARTICLE: builder.type(CSLType.ARTICLE_NEWSPAPER); break; case ONLINE_RESOURCE: builder.type(CSLType.WEBPAGE); break; case REPORT: builder.type(CSLType.REPORT); break; case WEBSITE: builder.type(CSLType.WEBPAGE); break; case WORKING_PAPER: builder.type(CSLType.ARTICLE); break; case DISCLOSURE: case EDITED_BOOK: case INVENTION: case JOURNAL_ISSUE: case LECTURE_SPEECH: case LICENSE: case MANUAL: case OTHER: case PATENT: case REGISTERED_COPYRIGHT: case RESEARCH_TECHNIQUE: case RESEARCH_TOOL: case SPIN_OFF_COMPANY: case STANDARDS_AND_POLICY: case SUPERVISED_STUDENT_PUBLICATION: case TECHNICAL_STANDARD: case TEST: case TRADEMARK: case TRANSLATION: case UNDEFINED: default: // TODO: do we want a default type? Datacite defaults to no type. // builder.type(CSLType.ARTICLE); break; } return builder.build(); } /** * Merges in the DOI from a work into a CSLItemdata (if found and not * already present) * * @param work * @param item */ private String extractID(Work work, WorkExternalIdentifierType type) { if (work.getExternalIdentifiers() != null && work.getExternalIdentifiers().getExternalIdentifier() != null && work.getExternalIdentifiers().getExternalIdentifier().size() > 0) { for (WorkExternalIdentifier id : work.getExternalIdentifiers().getExternalIdentifier()) { if (id.getWorkExternalIdentifierType().equals(type)) { return id.getWorkExternalIdentifierId().getContent(); } } } return null; } }