Examples with MedlineImporter org.jabref.logic.importer.fileformat.MedlineImporter used on opensource projects

Example 1 with MedlineImporter

use of org.jabref.logic.importer.fileformat.MedlineImporter 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);
    }
}

Example 2 with MedlineImporter

use of org.jabref.logic.importer.fileformat.MedlineImporter in project jabref by JabRef.

the class ImporterTest method instancesToTest.

@Parameters(name = "{index}: {0}")
public static Collection<Object[]> instancesToTest() {
    // all classes implementing {@link Importer}
    // sorted alphabetically
    ImportFormatPreferences importFormatPreferences = mock(ImportFormatPreferences.class);
    XMPPreferences xmpPreferences = mock(XMPPreferences.class);
    // @formatter:off
    return Arrays.asList(new Object[] { new BiblioscapeImporter() }, new Object[] { new BibtexImporter(importFormatPreferences) }, new Object[] { new BibTeXMLImporter() }, new Object[] { new CopacImporter() }, new Object[] { new EndnoteImporter(importFormatPreferences) }, new Object[] { new FreeCiteImporter(importFormatPreferences) }, new Object[] { new InspecImporter() }, new Object[] { new IsiImporter() }, new Object[] { new MedlineImporter() }, new Object[] { new MedlinePlainImporter() }, new Object[] { new ModsImporter() }, new Object[] { new MsBibImporter() }, new Object[] { new OvidImporter() }, new Object[] { new PdfContentImporter(importFormatPreferences) }, new Object[] { new PdfXmpImporter(xmpPreferences) }, new Object[] { new RepecNepImporter(importFormatPreferences) }, new Object[] { new RisImporter() }, new Object[] { new SilverPlatterImporter() });
// @formatter:on
}

Example 3 with MedlineImporter

use of org.jabref.logic.importer.fileformat.MedlineImporter in project jabref by JabRef.

the class ImportFormatReader method resetImportFormats.

public void resetImportFormats(ImportFormatPreferences newImportFormatPreferences, XMPPreferences xmpPreferences) {
    this.importFormatPreferences = newImportFormatPreferences;
    formats.clear();
    formats.add(new BiblioscapeImporter());
    formats.add(new BibtexImporter(importFormatPreferences));
    formats.add(new BibTeXMLImporter());
    formats.add(new CopacImporter());
    formats.add(new EndnoteImporter(importFormatPreferences));
    formats.add(new FreeCiteImporter(importFormatPreferences));
    formats.add(new InspecImporter());
    formats.add(new IsiImporter());
    formats.add(new MedlineImporter());
    formats.add(new MedlinePlainImporter());
    formats.add(new ModsImporter());
    formats.add(new MsBibImporter());
    formats.add(new OvidImporter());
    formats.add(new PdfContentImporter(importFormatPreferences));
    formats.add(new PdfXmpImporter(xmpPreferences));
    formats.add(new RepecNepImporter(importFormatPreferences));
    formats.add(new RisImporter());
    formats.add(new SilverPlatterImporter());
    // Get custom import formats
    for (CustomImporter importer : importFormatPreferences.getCustomImportList()) {
        formats.add(importer);
    }
}