Examples with BibEntry org.jabref.model.entry.BibEntry used on opensource projects

Example 66 with BibEntry

use of org.jabref.model.entry.BibEntry in project jabref by JabRef.

the class CrossRef method extractIdentifier.

@Override
public Optional<DOI> extractIdentifier(BibEntry inputEntry, List<BibEntry> fetchedEntries) throws FetcherException {
    final String entryTitle = REMOVE_BRACES_FORMATTER.format(inputEntry.getLatexFreeField(FieldName.TITLE).orElse(""));
    final StringSimilarity stringSimilarity = new StringSimilarity();
    for (BibEntry fetchedEntry : fetchedEntries) {
        // currently only title-based comparison
        // title
        Optional<String> dataTitle = fetchedEntry.getField(FieldName.TITLE);
        if (OptionalUtil.isPresentAnd(dataTitle, title -> stringSimilarity.isSimilar(entryTitle, title))) {
            return fetchedEntry.getDOI();
        }
        // subtitle
        // additional check, as sometimes subtitle is needed but sometimes only duplicates the title
        Optional<String> dataSubtitle = fetchedEntry.getField(FieldName.SUBTITLE);
        Optional<String> dataWithSubTitle = OptionalUtil.combine(dataTitle, dataSubtitle, (title, subtitle) -> title + " " + subtitle);
        if (OptionalUtil.isPresentAnd(dataWithSubTitle, titleWithSubtitle -> stringSimilarity.isSimilar(entryTitle, titleWithSubtitle))) {
            return fetchedEntry.getDOI();
        }
    }
    return Optional.empty();
}

Example 67 with BibEntry

use of org.jabref.model.entry.BibEntry in project jabref by JabRef.

the class MrDLibFetcher method performSearch.

@Override
public List<BibEntry> performSearch(BibEntry entry) throws FetcherException {
    Optional<String> title = entry.getLatexFreeField(FieldName.TITLE);
    if (title.isPresent()) {
        String response = makeServerRequest(title.get());
        MrDLibImporter importer = new MrDLibImporter();
        ParserResult parserResult = new ParserResult();
        try {
            if (importer.isRecognizedFormat(new BufferedReader(new StringReader(response)))) {
                parserResult = importer.importDatabase(new BufferedReader(new StringReader(response)));
            } else {
                // For displaying An ErrorMessage
                BibEntry errorBibEntry = new BibEntry();
                errorBibEntry.setField("html_representation", Localization.lang("Error_while_fetching_from_%0", "Mr.DLib"));
                BibDatabase errorBibDataBase = new BibDatabase();
                errorBibDataBase.insertEntry(errorBibEntry);
                parserResult = new ParserResult(errorBibDataBase);
            }
        } catch (IOException e) {
            LOGGER.error(e.getMessage(), e);
            throw new FetcherException("XML Parser IOException.");
        }
        return parserResult.getDatabase().getEntries();
    } else {
        // without a title there is no reason to ask MrDLib
        return new ArrayList<>(0);
    }
}

Example 68 with BibEntry

use of org.jabref.model.entry.BibEntry in project jabref by JabRef.

the class MedlineImporter method parseArticle.

private void parseArticle(PubmedArticle article, List<BibEntry> bibItems) {
    Map<String, String> fields = new HashMap<>();
    if (article.getPubmedData() != null) {
        if (article.getMedlineCitation().getDateRevised() != null) {
            DateRevised dateRevised = article.getMedlineCitation().getDateRevised();
            addDateRevised(fields, dateRevised);
            putIfValueNotNull(fields, "pubstatus", article.getPubmedData().getPublicationStatus());
            if (article.getPubmedData().getArticleIdList() != null) {
                ArticleIdList articleIdList = article.getPubmedData().getArticleIdList();
                addArticleIdList(fields, articleIdList);
            }
        }
    }
    if (article.getMedlineCitation() != null) {
        MedlineCitation medlineCitation = article.getMedlineCitation();
        fields.put("status", medlineCitation.getStatus());
        DateCreated dateCreated = medlineCitation.getDateCreated();
        fields.put("created", convertToDateFormat(dateCreated.getYear(), dateCreated.getMonth(), dateCreated.getDay()));
        fields.put("pubmodel", medlineCitation.getArticle().getPubModel());
        if (medlineCitation.getDateCompleted() != null) {
            DateCompleted dateCompleted = medlineCitation.getDateCompleted();
            fields.put("completed", convertToDateFormat(dateCompleted.getYear(), dateCompleted.getMonth(), dateCompleted.getDay()));
        }
        fields.put(FieldName.PMID, medlineCitation.getPMID().getContent());
        fields.put(FieldName.OWNER, medlineCitation.getOwner());
        addArticleInformation(fields, medlineCitation.getArticle().getContent());
        MedlineJournalInfo medlineJournalInfo = medlineCitation.getMedlineJournalInfo();
        putIfValueNotNull(fields, "country", medlineJournalInfo.getCountry());
        putIfValueNotNull(fields, "journal-abbreviation", medlineJournalInfo.getMedlineTA());
        putIfValueNotNull(fields, "nlm-id", medlineJournalInfo.getNlmUniqueID());
        putIfValueNotNull(fields, "issn-linking", medlineJournalInfo.getISSNLinking());
        if (medlineCitation.getChemicalList() != null) {
            if (medlineCitation.getChemicalList().getChemical() != null) {
                addChemicals(fields, medlineCitation.getChemicalList().getChemical());
            }
        }
        if (medlineCitation.getCitationSubset() != null) {
            fields.put("citation-subset", join(medlineCitation.getCitationSubset(), ", "));
        }
        if (medlineCitation.getGeneSymbolList() != null) {
            addGeneSymbols(fields, medlineCitation.getGeneSymbolList());
        }
        if (medlineCitation.getMeshHeadingList() != null) {
            addMeashHeading(fields, medlineCitation.getMeshHeadingList());
        }
        putIfValueNotNull(fields, "references", medlineCitation.getNumberOfReferences());
        if (medlineCitation.getPersonalNameSubjectList() != null) {
            addPersonalNames(fields, medlineCitation.getPersonalNameSubjectList());
        }
        if (medlineCitation.getOtherID() != null) {
            addOtherId(fields, medlineCitation.getOtherID());
        }
        if (medlineCitation.getKeywordList() != null) {
            addKeyWords(fields, medlineCitation.getKeywordList());
        }
        if (medlineCitation.getSpaceFlightMission() != null) {
            fields.put("space-flight-mission", join(medlineCitation.getSpaceFlightMission(), ", "));
        }
        if (medlineCitation.getInvestigatorList() != null) {
            addInvestigators(fields, medlineCitation.getInvestigatorList());
        }
        if (medlineCitation.getGeneralNote() != null) {
            addNotes(fields, medlineCitation.getGeneralNote());
        }
    }
    BibEntry entry = new BibEntry("article");
    entry.setField(fields);
    bibItems.add(entry);
}

Example 69 with BibEntry

use of org.jabref.model.entry.BibEntry in project jabref by JabRef.

the class MedlineImporter method importDatabase.

@Override
public ParserResult importDatabase(BufferedReader reader) throws IOException {
    Objects.requireNonNull(reader);
    List<BibEntry> bibItems = new ArrayList<>();
    try {
        JAXBContext context = JAXBContext.newInstance("org.jabref.logic.importer.fileformat.medline");
        XMLInputFactory xmlInputFactory = XMLInputFactory.newFactory();
        XMLStreamReader xmlStreamReader = xmlInputFactory.createXMLStreamReader(reader);
        //go to the root element
        while (!xmlStreamReader.isStartElement()) {
            xmlStreamReader.next();
        }
        Unmarshaller unmarshaller = context.createUnmarshaller();
        Object unmarshalledObject = unmarshaller.unmarshal(xmlStreamReader);
        //check whether we have an article set, an article, a book article or a book article set
        if (unmarshalledObject instanceof PubmedArticleSet) {
            PubmedArticleSet articleSet = (PubmedArticleSet) unmarshalledObject;
            for (Object article : articleSet.getPubmedArticleOrPubmedBookArticle()) {
                if (article instanceof PubmedArticle) {
                    PubmedArticle currentArticle = (PubmedArticle) article;
                    parseArticle(currentArticle, bibItems);
                }
                if (article instanceof PubmedBookArticle) {
                    PubmedBookArticle currentArticle = (PubmedBookArticle) article;
                    parseBookArticle(currentArticle, bibItems);
                }
            }
        } else if (unmarshalledObject instanceof PubmedArticle) {
            PubmedArticle article = (PubmedArticle) unmarshalledObject;
            parseArticle(article, bibItems);
        } else if (unmarshalledObject instanceof PubmedBookArticle) {
            PubmedBookArticle currentArticle = (PubmedBookArticle) unmarshalledObject;
            parseBookArticle(currentArticle, bibItems);
        } else {
            PubmedBookArticleSet bookArticleSet = (PubmedBookArticleSet) unmarshalledObject;
            for (PubmedBookArticle bookArticle : bookArticleSet.getPubmedBookArticle()) {
                parseBookArticle(bookArticle, bibItems);
            }
        }
    } catch (JAXBException | XMLStreamException e) {
        LOGGER.debug("could not parse document", e);
        return ParserResult.fromError(e);
    }
    return new ParserResult(bibItems);
}

Example 70 with BibEntry

use of org.jabref.model.entry.BibEntry in project jabref by JabRef.

the class IsiImporter method importDatabase.

@Override
public ParserResult importDatabase(BufferedReader reader) throws IOException {
    Objects.requireNonNull(reader);
    List<BibEntry> bibitems = new ArrayList<>();
    StringBuilder sb = new StringBuilder();
    // Pattern fieldPattern = Pattern.compile("^AU |^TI |^SO |^DT |^C1 |^AB
    // |^ID |^BP |^PY |^SE |^PY |^VL |^IS ");
    String str;
    while ((str = reader.readLine()) != null) {
        if (str.length() < 3) {
            continue;
        }
        // beginning of a new item
        if ("PT ".equals(str.substring(0, 3))) {
            sb.append("::").append(str);
        } else {
            String beg = str.substring(0, 3).trim();
            // quick and dirty and it works!
            if (beg.length() == 2) {
                // mark the beginning of each field
                sb.append(" ## ");
                sb.append(str);
            } else {
                // mark the end of each line
                sb.append("EOLEOL");
                // remove the initial spaces
                sb.append(str.trim());
            }
        }
    }
    String[] entries = sb.toString().split("::");
    Map<String, String> hm = new HashMap<>();
    // skip the first entry as it is either empty or has document header
    for (String entry : entries) {
        String[] fields = entry.split(" ## ");
        if (fields.length == 0) {
            fields = entry.split("\n");
        }
        String Type = "";
        String PT = "";
        String pages = "";
        hm.clear();
        for (String field : fields) {
            // empty field don't do anything
            if (field.length() <= 2) {
                continue;
            }
            String beg = field.substring(0, 2);
            String value = field.substring(3);
            if (value.startsWith(" - ")) {
                value = value.substring(3);
            }
            value = value.trim();
            if ("PT".equals(beg)) {
                if (value.startsWith("J")) {
                    PT = "article";
                } else {
                    PT = value;
                }
                // make all of them PT?
                Type = "article";
            } else if ("TY".equals(beg)) {
                if ("JOUR".equals(value)) {
                    Type = "article";
                } else if ("CONF".equals(value)) {
                    Type = "inproceedings";
                }
            } else if ("JO".equals(beg)) {
                hm.put(FieldName.BOOKTITLE, value);
            } else if ("AU".equals(beg)) {
                String author = IsiImporter.isiAuthorsConvert(value.replace("EOLEOL", " and "));
                // if there is already someone there then append with "and"
                if (hm.get(FieldName.AUTHOR) != null) {
                    author = hm.get(FieldName.AUTHOR) + " and " + author;
                }
                hm.put(FieldName.AUTHOR, author);
            } else if ("TI".equals(beg)) {
                hm.put(FieldName.TITLE, value.replace("EOLEOL", " "));
            } else if ("SO".equals(beg) || "JA".equals(beg)) {
                hm.put(FieldName.JOURNAL, value.replace("EOLEOL", " "));
            } else if ("ID".equals(beg) || "KW".equals(beg)) {
                value = value.replace("EOLEOL", " ");
                String existingKeywords = hm.get(FieldName.KEYWORDS);
                if ((existingKeywords == null) || existingKeywords.contains(value)) {
                    existingKeywords = value;
                } else {
                    existingKeywords += ", " + value;
                }
                hm.put(FieldName.KEYWORDS, existingKeywords);
            } else if ("AB".equals(beg)) {
                hm.put(FieldName.ABSTRACT, value.replace("EOLEOL", " "));
            } else if ("BP".equals(beg) || "BR".equals(beg) || "SP".equals(beg)) {
                pages = value;
            } else if ("EP".equals(beg)) {
                int detpos = value.indexOf(' ');
                // tweak for IEEE Explore
                if ((detpos != -1) && !value.substring(0, detpos).trim().isEmpty()) {
                    value = value.substring(0, detpos);
                }
                pages = pages + "--" + value;
            } else if ("PS".equals(beg)) {
                pages = IsiImporter.parsePages(value);
            } else if ("AR".equals(beg)) {
                pages = value;
            } else if ("IS".equals(beg)) {
                hm.put(FieldName.NUMBER, value);
            } else if ("PY".equals(beg)) {
                hm.put(FieldName.YEAR, value);
            } else if ("VL".equals(beg)) {
                hm.put(FieldName.VOLUME, value);
            } else if ("PU".equals(beg)) {
                hm.put(FieldName.PUBLISHER, value);
            } else if ("DI".equals(beg)) {
                hm.put(FieldName.DOI, value);
            } else if ("PD".equals(beg)) {
                String month = IsiImporter.parseMonth(value);
                if (month != null) {
                    hm.put(FieldName.MONTH, month);
                }
            } else if ("DT".equals(beg)) {
                Type = value;
                if ("Review".equals(Type)) {
                    // set "Review" in Note/Comment?
                    Type = "article";
                } else if (Type.startsWith("Article") || Type.startsWith("Journal") || "article".equals(PT)) {
                    Type = "article";
                } else {
                    Type = BibEntry.DEFAULT_TYPE;
                }
            } else if ("CR".equals(beg)) {
                hm.put("CitedReferences", value.replace("EOLEOL", " ; ").trim());
            } else {
                // Preserve all other entries except
                if ("ER".equals(beg) || "EF".equals(beg) || "VR".equals(beg) || "FN".equals(beg)) {
                    continue;
                }
                hm.put(beg.toLowerCase(Locale.ROOT), value);
            }
        }
        if (!"".equals(pages)) {
            hm.put(FieldName.PAGES, pages);
        }
        // Skip empty entries
        if (hm.isEmpty()) {
            continue;
        }
        BibEntry b = new BibEntry(Type);
        // id assumes an existing database so don't
        // Remove empty fields:
        List<Object> toRemove = new ArrayList<>();
        for (Map.Entry<String, String> field : hm.entrySet()) {
            String content = field.getValue();
            if ((content == null) || content.trim().isEmpty()) {
                toRemove.add(field.getKey());
            }
        }
        for (Object aToRemove : toRemove) {
            hm.remove(aToRemove);
        }
        // Polish entries
        IsiImporter.processSubSup(hm);
        IsiImporter.processCapitalization(hm);
        b.setField(hm);
        bibitems.add(b);
    }
    return new ParserResult(bibitems);
}