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

Example 71 with BibEntry

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

the class BibtexParser method parseEntry.

private BibEntry parseEntry(String entryType) throws IOException {
    BibEntry result = new BibEntry(entryType);
    skipWhitespace();
    consume('{', '(');
    int character = peek();
    if ((character != '\n') && (character != '\r')) {
        skipWhitespace();
    }
    String key = parseKey();
    result.setCiteKey(key);
    skipWhitespace();
    while (true) {
        character = peek();
        if ((character == '}') || (character == ')')) {
            break;
        }
        if (character == ',') {
            consume(',');
        }
        skipWhitespace();
        character = peek();
        if ((character == '}') || (character == ')')) {
            break;
        }
        parseField(result);
    }
    consume('}', ')');
    // Consume new line which signals end of entry
    skipOneNewline();
    return result;
}

Example 72 with BibEntry

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

the class CopacImporter method importDatabase.

@Override
public ParserResult importDatabase(BufferedReader reader) throws IOException {
    Objects.requireNonNull(reader);
    List<String> entries = new LinkedList<>();
    StringBuilder sb = new StringBuilder();
    // Preprocess entries
    String str;
    while ((str = reader.readLine()) != null) {
        if (str.length() < 4) {
            continue;
        }
        String code = str.substring(0, 4);
        if ("    ".equals(code)) {
            sb.append(' ').append(str.trim());
        } else {
            // begining of a new item
            if ("TI- ".equals(str.substring(0, 4))) {
                if (sb.length() > 0) {
                    entries.add(sb.toString());
                }
                sb = new StringBuilder();
            }
            sb.append('\n').append(str);
        }
    }
    if (sb.length() > 0) {
        entries.add(sb.toString());
    }
    List<BibEntry> results = new LinkedList<>();
    for (String entry : entries) {
        // Copac does not contain enough information on the type of the
        // document. A book is assumed.
        BibEntry b = new BibEntry("book");
        String[] lines = entry.split("\n");
        for (String line1 : lines) {
            String line = line1.trim();
            if (line.length() < 4) {
                continue;
            }
            String code = line.substring(0, 4);
            if ("TI- ".equals(code)) {
                setOrAppend(b, FieldName.TITLE, line.substring(4).trim(), ", ");
            } else if ("AU- ".equals(code)) {
                setOrAppend(b, FieldName.AUTHOR, line.substring(4).trim(), " and ");
            } else if ("PY- ".equals(code)) {
                setOrAppend(b, FieldName.YEAR, line.substring(4).trim(), ", ");
            } else if ("PU- ".equals(code)) {
                setOrAppend(b, FieldName.PUBLISHER, line.substring(4).trim(), ", ");
            } else if ("SE- ".equals(code)) {
                setOrAppend(b, FieldName.SERIES, line.substring(4).trim(), ", ");
            } else if ("IS- ".equals(code)) {
                setOrAppend(b, FieldName.ISBN, line.substring(4).trim(), ", ");
            } else if ("KW- ".equals(code)) {
                setOrAppend(b, FieldName.KEYWORDS, line.substring(4).trim(), ", ");
            } else if ("NT- ".equals(code)) {
                setOrAppend(b, FieldName.NOTE, line.substring(4).trim(), ", ");
            } else if ("PD- ".equals(code)) {
                setOrAppend(b, "physicaldimensions", line.substring(4).trim(), ", ");
            } else if ("DT- ".equals(code)) {
                setOrAppend(b, "documenttype", line.substring(4).trim(), ", ");
            } else {
                setOrAppend(b, code.substring(0, 2), line.substring(4).trim(), ", ");
            }
        }
        results.add(b);
    }
    return new ParserResult(results);
}

Example 73 with BibEntry

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

the class EndnoteImporter method importDatabase.

@Override
public ParserResult importDatabase(BufferedReader reader) throws IOException {
    List<BibEntry> bibitems = new ArrayList<>();
    StringBuilder sb = new StringBuilder();
    String str;
    boolean first = true;
    while ((str = reader.readLine()) != null) {
        str = str.trim();
        if (str.indexOf("%0") == 0) {
            if (first) {
                first = false;
            } else {
                sb.append(ENDOFRECORD);
            }
            sb.append(str);
        } else {
            sb.append(str);
        }
        sb.append('\n');
    }
    String[] entries = sb.toString().split(ENDOFRECORD);
    Map<String, String> hm = new HashMap<>();
    String author;
    String type;
    String editor;
    String artnum;
    for (String entry : entries) {
        hm.clear();
        author = "";
        type = BibEntry.DEFAULT_TYPE;
        editor = "";
        artnum = "";
        boolean isEditedBook = false;
        String[] fields = entry.trim().substring(1).split("\n%");
        for (String field : fields) {
            if (field.length() < 3) {
                continue;
            }
            /*
                 * Details of Refer format for Journal Article and Book:
                 *
                 * Generic Ref Journal Article Book Code Author %A Author Author Year %D
                 * Year Year Title %T Title Title Secondary Author %E Series Editor
                 * Secondary Title %B Journal Series Title Place Published %C City
                 * Publisher %I Publisher Volume %V Volume Volume Number of Volumes %6
                 * Number of Volumes Number %N Issue Pages %P Pages Number of Pages
                 * Edition %7 Edition Subsidiary Author %? Translator Alternate Title %J
                 * Alternate Journal Label %F Label Label Keywords %K Keywords Keywords
                 * Abstract %X Abstract Abstract Notes %O Notes Notes
                 */
            String prefix = field.substring(0, 1);
            String val = field.substring(2);
            if ("A".equals(prefix)) {
                if ("".equals(author)) {
                    author = val;
                } else {
                    author += " and " + val;
                }
            } else if ("E".equals(prefix)) {
                if ("".equals(editor)) {
                    editor = val;
                } else {
                    editor += " and " + val;
                }
            } else if ("T".equals(prefix)) {
                hm.put(FieldName.TITLE, val);
            } else if ("0".equals(prefix)) {
                if (val.indexOf("Journal") == 0) {
                    type = "article";
                } else if (val.indexOf("Book Section") == 0) {
                    type = "incollection";
                } else if (val.indexOf("Book") == 0) {
                    type = "book";
                } else if (val.indexOf("Edited Book") == 0) {
                    type = "book";
                    isEditedBook = true;
                } else if (val.indexOf("Conference") == 0) {
                    type = "inproceedings";
                } else if (val.indexOf("Report") == 0) {
                    type = "techreport";
                } else if (val.indexOf("Review") == 0) {
                    type = "article";
                } else if (val.indexOf("Thesis") == 0) {
                    type = "phdthesis";
                } else {
                    //
                    type = BibEntry.DEFAULT_TYPE;
                }
            } else if ("7".equals(prefix)) {
                hm.put(FieldName.EDITION, val);
            } else if ("C".equals(prefix)) {
                hm.put(FieldName.ADDRESS, val);
            } else if ("D".equals(prefix)) {
                hm.put(FieldName.YEAR, val);
            } else if ("8".equals(prefix)) {
                hm.put(FieldName.DATE, val);
            } else if ("J".equals(prefix)) {
                // "Alternate journal. Let's set it only if no journal
                // has been set with %B.
                hm.putIfAbsent(FieldName.JOURNAL, val);
            } else if ("B".equals(prefix)) {
                // "series" in a book entry.
                if ("article".equals(type)) {
                    hm.put(FieldName.JOURNAL, val);
                } else if ("book".equals(type) || "inbook".equals(type)) {
                    hm.put(FieldName.SERIES, val);
                } else {
                    /* type = inproceedings */
                    hm.put(FieldName.BOOKTITLE, val);
                }
            } else if ("I".equals(prefix)) {
                if ("phdthesis".equals(type)) {
                    hm.put(FieldName.SCHOOL, val);
                } else {
                    hm.put(FieldName.PUBLISHER, val);
                }
            } else // replace single dash page ranges (23-45) with double dashes (23--45):
            if ("P".equals(prefix)) {
                hm.put(FieldName.PAGES, val.replaceAll("([0-9]) *- *([0-9])", "$1--$2"));
            } else if ("V".equals(prefix)) {
                hm.put(FieldName.VOLUME, val);
            } else if ("N".equals(prefix)) {
                hm.put(FieldName.NUMBER, val);
            } else if ("U".equals(prefix)) {
                hm.put(FieldName.URL, val);
            } else if ("R".equals(prefix)) {
                String doi = val;
                if (doi.startsWith("doi:")) {
                    doi = doi.substring(4);
                }
                hm.put(FieldName.DOI, doi);
            } else if ("O".equals(prefix)) {
                // Notes may contain Article number
                if (val.startsWith("Artn")) {
                    String[] tokens = val.split("\\s");
                    artnum = tokens[1];
                } else {
                    hm.put(FieldName.NOTE, val);
                }
            } else if ("K".equals(prefix)) {
                hm.put(FieldName.KEYWORDS, val);
            } else if ("X".equals(prefix)) {
                hm.put(FieldName.ABSTRACT, val);
            } else if ("9".equals(prefix)) {
                if (val.indexOf("Ph.D.") == 0) {
                    type = "phdthesis";
                }
                if (val.indexOf("Masters") == 0) {
                    type = "mastersthesis";
                }
            } else if ("F".equals(prefix)) {
                hm.put(BibEntry.KEY_FIELD, BibtexKeyPatternUtil.checkLegalKey(val, preferences.getBibtexKeyPatternPreferences().isEnforceLegalKey()));
            }
        }
        // We want them in the editor field so that bibtex knows it's an edited book
        if (isEditedBook && "".equals(editor)) {
            editor = author;
            author = "";
        }
        //fixauthorscomma
        if (!"".equals(author)) {
            hm.put(FieldName.AUTHOR, fixAuthor(author));
        }
        if (!"".equals(editor)) {
            hm.put(FieldName.EDITOR, fixAuthor(editor));
        }
        //if pages missing and article number given, use the article number
        if (((hm.get(FieldName.PAGES) == null) || "-".equals(hm.get(FieldName.PAGES))) && !"".equals(artnum)) {
            hm.put(FieldName.PAGES, artnum);
        }
        BibEntry b = new BibEntry(type);
        b.setField(hm);
        if (!b.getFieldNames().isEmpty()) {
            bibitems.add(b);
        }
    }
    return new ParserResult(bibitems);
}

Example 74 with BibEntry

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

the class BibtexParser method parseAndAddEntry.

private void parseAndAddEntry(String type) {
    /**
         * Morten Alver 13 Aug 2006: Trying to make the parser more
         * robust. If an exception is thrown when parsing an entry,
         * drop the entry and try to resume parsing. Add a warning
         * for the user.
         */
    try {
        // collect all comments and the entry type definition in front of the actual entry
        // this is at least `@Type`
        String commentsAndEntryTypeDefinition = dumpTextReadSoFarToString();
        BibEntry entry = parseEntry(type);
        // store comments collected without type definition
        entry.setCommentsBeforeEntry(commentsAndEntryTypeDefinition.substring(0, commentsAndEntryTypeDefinition.lastIndexOf('@')));
        // store complete parsed serialization (comments, type definition + type contents)
        entry.setParsedSerialization(commentsAndEntryTypeDefinition + dumpTextReadSoFarToString());
        boolean duplicateKey = database.insertEntry(entry);
        if (duplicateKey) {
            parserResult.addDuplicateKey(entry.getCiteKey());
        }
    } catch (IOException ex) {
        LOGGER.debug("Could not parse entry", ex);
        parserResult.addWarning(Localization.lang("Error occurred when parsing entry") + ": '" + ex.getMessage() + "'. " + Localization.lang("Skipped entry."));
    }
}

Example 75 with BibEntry

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

the class MedlineFetcher method fetchMedline.

/**
     * Fetch and parse an medline item from eutils.ncbi.nlm.nih.gov.
     * The E-utilities generate a huge XML file containing all entries for the ids
     *
     * @param ids A list of IDs to search for.
     * @return Will return an empty list on error.
     */
private List<BibEntry> fetchMedline(List<String> ids) throws FetcherException {
    try {
        //Separate the IDs with a comma to search multiple entries
        URL fetchURL = getURLForID(String.join(",", ids));
        URLConnection data = fetchURL.openConnection();
        ParserResult result = new MedlineImporter().importDatabase(new BufferedReader(new InputStreamReader(data.getInputStream(), StandardCharsets.UTF_8)));
        if (result.hasWarnings()) {
            LOGGER.warn(result.getErrorMessage());
        }
        List<BibEntry> resultList = result.getDatabase().getEntries();
        resultList.forEach(this::doPostCleanup);
        return resultList;
    } catch (URISyntaxException | MalformedURLException e) {
        throw new FetcherException("Error while generating fetch URL", Localization.lang("Error while generating fetch URL"), e);
    } catch (IOException e) {
        throw new FetcherException("Error while fetching from Medline", Localization.lang("Error while fetching from %0", "Medline"), e);
    }
}