/
BiblioItem.java
executable file
·4638 lines (4093 loc) · 170 KB
/
BiblioItem.java
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package org.grobid.core.data;
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.collections4.CollectionUtils;
import org.grobid.core.data.util.AuthorEmailAssigner;
import org.grobid.core.data.util.ClassicAuthorEmailAssigner;
import org.grobid.core.data.util.EmailSanitizer;
import org.grobid.core.document.*;
import org.grobid.core.engines.config.GrobidAnalysisConfig;
import org.grobid.core.exceptions.GrobidException;
import org.grobid.core.lang.Language;
import org.grobid.core.layout.BoundingBox;
import org.grobid.core.layout.LayoutToken;
import org.grobid.core.tokenization.TaggingTokenCluster;
import org.grobid.core.tokenization.TaggingTokenClusteror;
import org.grobid.core.engines.label.TaggingLabel;
import org.grobid.core.lexicon.Lexicon;
import org.grobid.core.utilities.LanguageUtilities;
import org.grobid.core.utilities.TextUtilities;
import org.grobid.core.utilities.KeyGen;
import org.grobid.core.GrobidModels;
import java.net.URLEncoder;
import java.util.*;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
import java.util.stream.Collectors;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
/**
* Class for representing and exchanging a bibliographical item.
*
* @author Patrice Lopez
*/
public class BiblioItem {
protected static final Logger LOGGER = LoggerFactory.getLogger(BiblioItem.class);
private LanguageUtilities languageUtilities = LanguageUtilities.getInstance();
private AuthorEmailAssigner authorEmailAssigner = new ClassicAuthorEmailAssigner();
private EmailSanitizer emailSanitizer = new EmailSanitizer();
private String teiId;
//TODO: keep in sync with teiId - now teiId is generated in many different places
private Integer ordinal;
private List<BoundingBox> coordinates = null;
// map of labels (e.g. <title> or <abstract>) to LayoutToken
private Map<String, List<LayoutToken>> labeledTokens;
/**
* The following are internal working structures not meant to be used outside.
* For collecting layout tokens of the various bibliographical component,
* please refers to @See(getLayoutTokens(TaggingLabels label)
*/
private List<LayoutToken> authorsTokensWorkingCopy = new ArrayList<>();
private List<LayoutToken> abstractTokensWorkingCopy = new ArrayList<>();
@Override
public String toString() {
return "BiblioItem{" +
"submission_date='" + submission_date + '\'' +
", download_date='" + download_date + '\'' +
", server_date='" + server_date + '\'' +
", languageUtilities=" + languageUtilities +
", item=" + item +
", parentItem=" + parentItem +
", ISBN13='" + ISBN13 + '\'' +
", ISBN10='" + ISBN10 + '\'' +
", title='" + title + '\'' +
", publisher='" + publisher + '\'' +
", nbPages=" + nbPages +
", edition='" + edition + '\'' +
", language='" + language + '\'' +
", subtitle='" + subtitle + '\'' +
", publication_date='" + publication_date + '\'' +
", normalized_publication_date=" + normalized_publication_date +
", editors='" + editors + '\'' +
", publisher_website='" + publisher_website + '\'' +
", serie='" + serie + '\'' +
", ISSN='" + ISSN + '\'' +
", ISSNe='" + ISSNe + '\'' +
", volume='" + volume + '\'' +
", number='" + number + '\'' +
", month='" + month + '\'' +
", support_type='" + support_type + '\'' +
", version='" + version + '\'' +
", smallImageURL='" + smallImageURL + '\'' +
", largeImageURL='" + largeImageURL + '\'' +
", publisherPlace='" + publisherPlace + '\'' +
", review='" + review + '\'' +
", keywords=" + keywords +
", subjects=" + subjects +
", categories='" + categories + '\'' +
", type='" + type + '\'' +
", typeDescription='" + typeDescription + '\'' +
", book_type='" + book_type + '\'' +
", DOI='" + doi + '\'' +
", arXivId='" + arXivId + '\'' +
", PMID='" + PMID + '\'' +
", PMCID='" + PMCID + '\'' +
", PII='" + PII + '\'' +
", ark='" + ark + '\'' +
", istexId='" + istexId + '\'' +
", inDOI='" + inDOI + '\'' +
", abstract_='" + abstract_ + '\'' +
", authors='" + authors + '\'' +
", firstAuthorSurname='" + firstAuthorSurname + '\'' +
", location='" + location + '\'' +
", bookTitle='" + bookTitle + '\'' +
", serieTitle='" + serieTitle + '\'' +
", pageRange='" + pageRange + '\'' +
", journal='" + journal + '\'' +
", volumeBlock='" + volumeBlock + '\'' +
", institution='" + institution + '\'' +
", note='" + note + '\'' +
", affiliation='" + affiliation + '\'' +
", address='" + address + '\'' +
", country='" + country + '\'' +
", town='" + town + '\'' +
", email='" + email + '\'' +
", pubnum='" + pubnum + '\'' +
", keyword='" + keyword + '\'' +
", phone='" + phone + '\'' +
", degree='" + degree + '\'' +
", web='" + web + '\'' +
", issue='" + issue + '\'' +
", journal_abbrev='" + journal_abbrev + '\'' +
", event='" + event + '\'' +
", abstractHeader='" + abstractHeader + '\'' +
", day='" + day + '\'' +
", locationPublisher='" + locationPublisher + '\'' +
", dedication='" + dedication + '\'' +
", submission='" + submission + '\'' +
", english_title='" + english_title + '\'' +
", url='" + url + '\'' +
", oaUrl='" + oaUrl + '\'' +
", uri='" + uri + '\'' +
", confidence='" + confidence + '\'' +
", conf=" + conf +
", e_year='" + e_year + '\'' +
", e_month='" + e_month + '\'' +
", e_day='" + e_day + '\'' +
", s_year='" + s_year + '\'' +
", s_month='" + s_month + '\'' +
", s_day='" + s_day + '\'' +
", d_year='" + d_year + '\'' +
", d_month='" + d_month + '\'' +
", d_day='" + d_day + '\'' +
", a_year='" + a_year + '\'' +
", a_month='" + a_month + '\'' +
", a_day='" + a_day + '\'' +
", authorList=" + authorList +
", editorList=" + editorList +
", affiliationList=" + affiliationList +
", addressList=" + addressList +
", emailList=" + emailList +
", webList=" + webList +
", phoneList=" + phoneList +
", markers=" + markers +
", fullAuthors=" + fullAuthors +
", fullEditors=" + fullEditors +
", fullAffiliations=" + fullAffiliations +
", reference='" + reference + '\'' +
", copyright='" + copyright + '\'' +
", funding='" + funding + '\'' +
", affiliationAddressBlock='" + affiliationAddressBlock + '\'' +
", articleTitle='" + articleTitle + '\'' +
", beginPage=" + beginPage +
", endPage=" + endPage +
", year='" + year + '\'' +
", authorString='" + authorString + '\'' +
", path='" + path + '\'' +
", collaboration='" + collaboration + '\'' +
", postProcessEditors=" + postProcessEditors +
", crossrefError=" + crossrefError +
", normalized_submission_date=" + normalized_submission_date +
", normalized_download_date=" + normalized_download_date +
", originalAffiliation='" + originalAffiliation + '\'' +
", originalAbstract='" + originalAbstract + '\'' +
", originalTitle='" + originalTitle + '\'' +
", originalAuthors='" + originalAuthors + '\'' +
", originalEditors='" + originalEditors + '\'' +
", originalAddress='" + originalAddress + '\'' +
", originalNote='" + originalNote + '\'' +
", originalKeyword='" + originalKeyword + '\'' +
", originalVolumeBlock='" + originalVolumeBlock + '\'' +
", originalJournal='" + originalJournal + '\'' +
", workingGroup='" + workingGroup + '\'' +
", documentType='" + documentType + '\'' +
'}';
}
public int item = -1;
public static final int Book = 0; // the whole book
public static final int Periodical = 1; // the journal or magazine item
public static final int Digital_support = 2;
public static final int Article = 3; // of a journal or magazine
public static final int Unknown = 4;
public static final int InBook = 5;
public static final int InProceedings = 6;
public static final int InCollection = 7;
public static final int Manual = 8;
public static final int TechReport = 9;
public static final int MasterThesis = 10;
public static final int PhdThesis = 11;
public static final int Unpublished = 12;
public static final int Proceedings = 13;
public static final int Serie = 14;
private BiblioItem parentItem = null; // the bibliographic item "container", i.e.
// the book for a chapter
// the journal for a journal article, etc.
private String ISBN13 = null;
private String ISBN10 = null;
private String title = null;
private String publisher = null;
private int nbPages = -1;
private String edition = null;
private String language = null;
private String subtitle = null;
private String publication_date = null;
private Date normalized_publication_date = null;
private String editors = null;
private String publisher_website = null;
private String serie = null;
private String ISSN = null; // print/default
private String ISSNe = null; // electronic
private String volume = null;
private String number = null;
private String month = null;
private String support_type = null;
private String version = null;
private String smallImageURL = null;
private String largeImageURL = null;
private String publisherPlace = null;
private String review = null;
private List<Keyword> keywords;
private List<String> subjects;
private List<String> categories;
private String type = null; // book, journal, proceedings, in book, etc
private String typeDescription = null;
private String book_type = null;
private String doi = null;
private String inDOI = null;
private String arXivId = null;
private String PMID = null;
private String PMCID = null;
private String PII = null;
private String ark = null;
private String istexId = null;
private String abstract_ = null;
private String collaboration = null;
private String documentType = null;
// for convenience GROBIDesque
private String authors = null;
//private List<LayoutToken> authorsTokens = new ArrayList<>();
private String firstAuthorSurname = null;
private String location = null;
private String bookTitle = null;
private String serieTitle = null;
private String pageRange = null;
private String journal = null;
private String volumeBlock = null;
private String institution = null;
private String note = null;
private String affiliation = null;
private String address = null;
private String country = null;
private String town = null;
private String email = null;
private String pubnum = null;
private String keyword = null;
private String phone = null;
private String degree = null;
private String web = null;
private String issue = null;
private String journal_abbrev = null;
private String event = null;
private String abstractHeader = null;
private String day = null;
private String locationPublisher = null;
private String dedication = null;
private String submission = null;
private String english_title = null;
private String url = null;
private String oaUrl = null;
private String uri = null;
private String confidence = null;
private double conf = 0.0;
// abstract labeled featured sequence (to produce a structured abstract with, in particular, reference callout)
private String labeledAbstract = null;
// date for electronic publishing
private String e_year = null;
private String e_month = null;
private String e_day = null;
// date of submission
private String s_year = null;
private String s_month = null;
private String s_day = null;
// date of acceptance
private String a_year = null;
private String a_month = null;
private String a_day = null;
// date of download
private String d_year = null;
private String d_month = null;
private String d_day = null;
// advanced grobid recognitions
private List<String> authorList;
private List<String> editorList;
private List<String> affiliationList;
private List<String> addressList;
private List<String> emailList;
private List<String> webList;
private List<String> phoneList;
private List<String> markers;
private List<Person> fullAuthors = null;
private List<Person> fullEditors = null;
private List<Affiliation> fullAffiliations = null;
private String reference = null;
private String copyright = null;
private String funding = null;
//public List<String> affiliationAddressBlock = null;
public String affiliationAddressBlock = null;
// just for articles
private String articleTitle = null;
private int beginPage = -1;
private int endPage = -1;
private String year = null; // default is publication date on print media
private String authorString = null;
private String path = "";
private boolean postProcessEditors = false;
private boolean crossrefError = true;
private String submission_date = null;
private Date normalized_submission_date = null;
private String download_date = null;
private Date normalized_download_date = null;
private String server_date = null;
private Date normalized_server_date = null;
// for OCR post-corrections
private String originalAffiliation = null;
private String originalAbstract = null;
private String originalTitle = null;
private String originalAuthors = null;
private String originalEditors = null;
private String originalAddress = null;
private String originalNote = null;
private String originalKeyword = null;
private String originalVolumeBlock = null;
private String originalJournal = null;
private String workingGroup = null;
private String rawMeeting = null;
public static final List<String> confPrefixes = Arrays.asList("Proceedings of", "proceedings of",
"In Proceedings of the", "In: Proceeding of", "In Proceedings, ", "In Proceedings of",
"In Proceeding of", "in Proceeding of", "in Proceeding", "In Proceeding", "Proceedings",
"proceedings", "In Proc", "in Proc", "In Proc.", "in Proc.", "In proc.", "in proc", "in proc.",
"In proc", "Proc", "proc", "Proc.", "proc.", "Acte de la", "Acte de", "Acte", "acte de la",
"acte de", "acte");
public BiblioItem() {
}
public void setParentItem(BiblioItem bi) {
parentItem = bi;
}
public BiblioItem getParentItem() {
return parentItem;
}
public int getItem() {
return item;
}
public void setItem(int type) {
item = type;
}
public String getISBN13() {
return this.ISBN13;
}
public String getISBN10() {
return this.ISBN10;
}
public String getTitle() {
return this.title;
}
public String getPublisher() {
return this.publisher;
}
public String getEdition() {
return this.edition;
}
public String getLanguage() {
return this.language;
}
public String getSubtitle() {
if (subtitle != null)
if (subtitle.length() != 0)
if (!subtitle.equals("null"))
return this.subtitle;
return null;
}
public String getPublicationDate() {
return this.publication_date;
}
public Date getNormalizedPublicationDate() {
return normalized_publication_date;
}
public String getEditors() {
return this.editors;
}
public String getPublisherWebsite() {
return this.publisher_website;
}
public String getSerie() {
return this.serie;
}
public String getISSN() {
return this.ISSN;
}
public String getISSNe() {
return this.ISSNe;
}
public String getVolume() {
return this.volume;
}
public String getNumber() {
return this.number;
}
public String getMonth() {
return this.month;
}
public String getSupportType() {
return this.support_type;
}
public String getVersion() {
return this.version;
}
public String getSmallImageURL() {
return this.smallImageURL;
}
public String getLargeImageURL() {
return this.largeImageURL;
}
public String getPublisherPlace() {
return publisherPlace;
}
public String getReview() {
return this.review;
}
public List<String> getCategories() {
return this.categories;
}
public int getNbPages() {
return nbPages;
}
public String getType() {
return type;
}
public String getTypeDescription() {
return typeDescription;
}
public String getBookType() {
return book_type;
}
public String getDOI() {
return doi;
}
public String getArk() {
return ark;
}
public String getIstexId() {
return istexId;
}
public String getInDOI() {
return inDOI;
}
public String getArXivId() {
return arXivId;
}
public String getPMID() {
return PMID;
}
public String getPMCID() {
return PMCID;
}
public String getPII() {
return PII;
}
public String getArticleTitle() {
return articleTitle;
}
public int getBeginPage() {
return beginPage;
}
public int getEndPage() {
return endPage;
}
public String getYear() {
return year;
}
public String getAbstract() {
return abstract_;
}
public String getLabeledAbstract() {
return labeledAbstract;
}
public String getEmail() {
return email;
}
public String getPubnum() {
return pubnum;
}
public String getCollaboration() {
return collaboration;
}
public String getSerieTitle() {
return serieTitle;
}
public String getURL() {
return url;
}
public String getOAURL() {
return oaUrl;
}
public String getURI() {
return uri;
}
public String getConfidence() {
return confidence;
}
// temp
public String getAuthors() {
return authors;
}
public String getLocation() {
return location;
}
public String getBookTitle() {
return bookTitle;
}
public String getPageRange() {
if (pageRange != null)
return pageRange;
else if ((beginPage != -1) && (endPage != -1))
return "" + beginPage + "--" + endPage;
else
return null;
}
public String getJournal() {
return journal;
}
public String getVolumeBlock() {
return volumeBlock;
}
public String getInstitution() {
return institution;
}
public String getNote() {
return note;
}
public String getAffiliation() {
return affiliation;
}
public String getAddress() {
return address;
}
public String getCountry() {
return country;
}
public String getTown() {
return town;
}
public String getKeyword() {
return keyword;
}
public List<Keyword> getKeywords() {
return keywords;
}
public List<String> getSubjects() {
return subjects;
}
public String getPhone() {
return phone;
}
public String getDegree() {
return degree;
}
public String getWeb() {
return web;
}
public String getIssue() {
return issue;
}
public String getJournalAbbrev() {
return journal_abbrev;
}
public String getEvent() {
return event;
}
public boolean getError() {
return crossrefError;
}
public String getAbstractHeader() {
return abstractHeader;
}
public String getDay() {
return day;
}
public String getLocationPublisher() {
return locationPublisher;
}
public String getAuthorString() {
return authorString;
}
public String getE_Year() {
return e_year;
}
public String getE_Month() {
return e_month;
}
public String getE_Day() {
return e_day;
}
public String getS_Year() {
return s_year;
}
public String getS_Month() {
return s_month;
}
public String getS_Day() {
return s_day;
}
public String getA_Year() {
return a_year;
}
public String getA_Month() {
return a_month;
}
public String getA_Day() {
return a_day;
}
public String getD_Year() {
return d_year;
}
public String getD_Month() {
return d_month;
}
public String getD_Day() {
return d_day;
}
public String getDedication() {
return dedication;
}
public String getSubmission() {
return submission;
}
public String getEnglishTitle() {
return english_title;
}
public String getSubmissionDate() {
return submission_date;
}
public Date getNormalizedSubmissionDate() {
return normalized_submission_date;
}
public String getDownloadDate() {
return download_date;
}
public Date getNormalizedDownloadDate() {
return normalized_download_date;
}
public String getServerDate() {
return server_date;
}
public Date getNormalizedServerDate() {
return normalized_server_date;
}
public String getOriginalAffiliation() {
return originalAffiliation;
}
public String getOriginalAbstract() {
return originalAbstract;
}
public String getOriginalAuthors() {
return originalAuthors;
}
public String getOriginalEditors() {
return originalEditors;
}
public String getOriginalTitle() {
return originalTitle;
}
public String getOriginalAddress() {
return originalAddress;
}
public String getOriginalNote() {
return originalNote;
}
public String getOriginalKeyword() {
return originalKeyword;
}
public String getOriginalVolumeBlock() {
return originalVolumeBlock;
}
public String getOriginalJournal() {
return originalJournal;
}
public List<org.grobid.core.data.Person> getFullAuthors() {
return fullAuthors;
}
public List<org.grobid.core.data.Person> getFullEditors() {
return fullEditors;
}
public List<org.grobid.core.data.Affiliation> getFullAffiliations() {
return fullAffiliations;
}
public String getReference() {
return reference;
}
public String getCopyright() {
return copyright;
}
public String getFunding() {
return funding;
}
public String getWorkingGroup() {
return workingGroup;
}
public String getDocumentType() {
return documentType;
}
public void setISBN13(String isbn) {
/* some cleaning... */
this.ISBN13 = StringUtils.normalizeSpace(cleanISBNString(isbn));
}
public void setISBN10(String isbn) {
/* some cleaning... */
this.ISBN10 = StringUtils.normalizeSpace(isbn);
}
public void setTitle(String theTitle) {
this.title = StringUtils.normalizeSpace(theTitle);
}
public void setPublisher(String thePublisher) {
this.publisher = StringUtils.normalizeSpace(thePublisher);
}
public void setEdition(String theEdition) {
if (theEdition != null) {
if (theEdition.length() > 10) {
theEdition = theEdition.substring(0, 9);
}
}
this.edition = StringUtils.normalizeSpace(theEdition);
}
public void setLanguage(String theLanguage) {
this.language = StringUtils.normalizeSpace(theLanguage);
}
public void setSubtitle(String theSubtitle) {
this.subtitle = StringUtils.normalizeSpace(theSubtitle);
}
public void setPublicationDate(String theDate) {
this.publication_date = StringUtils.normalizeSpace(theDate);
}
public void setNormalizedPublicationDate(Date theDate) {
this.normalized_publication_date = theDate;
}
public void setEditors(String theEditors) {
this.editors = StringUtils.normalizeSpace(theEditors);
}
public void setPublisherWebsite(String theWebsite) {
this.publisher_website = StringUtils.normalizeSpace(theWebsite);
}
public void setSerie(String theSerie) {
this.serie = StringUtils.normalizeSpace(theSerie);
}
public void setISSN(String theISSN) {
this.ISSN = StringUtils.normalizeSpace(theISSN);
}
public void setISSNe(String theISSN) {
this.ISSNe = StringUtils.normalizeSpace(theISSN);
}
public void setVolume(String theVolume) {
this.volume = StringUtils.normalizeSpace(theVolume);
}
public void setNumber(String theNumber) {
this.number = StringUtils.normalizeSpace(theNumber);
}
public void setMonth(String theMonth) {
this.month = StringUtils.normalizeSpace(theMonth);
}
public void setSupportType(String theType) {
this.support_type = StringUtils.normalizeSpace(theType);
}
public void setVersion(String theVersion) {
this.version = StringUtils.normalizeSpace(theVersion);
}
public void setSmallImageURL(String url) {
this.smallImageURL = url;
}
public void setLargeImageURL(String url) {
this.largeImageURL = url;
}
public void setPublisherPlace(String p) {
this.publisherPlace = StringUtils.normalizeSpace(p);
}
public void setCategories(List<String> cat) {
this.categories = cat;
}
public void addCategory(String cat) {
if (categories == null) {
categories = new ArrayList<String>();
}
categories.add(cat);
}
public void setNbPages(int nb) {
this.nbPages = nb;
}
public void setReview(String rev) {
this.review = rev;
}
public void setType(String t) {
this.type = t;
}
public void setTypeDescription(String t) {
typeDescription = t;
}
public void setBookType(String bt) {
this.book_type = StringUtils.normalizeSpace(bt);
}
public void setDOI(String id) {
if (id == null)
return;
this.doi = cleanDOI(id);
}
public void setInDOI(String id) {
if (id != null) {