Examples with IArticle eu.etaxonomy.cdm.model.reference.IArticle used on opensource projects

Example 6 with IArticle

use of eu.etaxonomy.cdm.model.reference.IArticle in project cdmlib by cybertaxonomy.

the class MarkupImportBase method handleNonCitationSpecific.

/**
 * Create reference for non nomenclatural references
 * @return
 */
protected Reference handleNonCitationSpecific(MarkupImportState state, String type, String authorStr, String titleStr, String titleCache, String volume, String issue, String edition, String editors, String pubName, String appendix, String pages, XMLEvent parentEvent) {
    Reference reference;
    // volume / issue
    if (isBlank(volume) && isNotBlank(issue)) {
        String message = "Issue ('" + issue + "') exists but no volume";
        fireWarningEvent(message, parentEvent, 4);
        volume = issue;
    } else if (isNotBlank(issue)) {
        volume = volume + "(" + issue + ")";
    }
    // pubName / appendix
    if (isNotBlank(appendix)) {
        pubName = pubName == null ? appendix : (pubName + " " + appendix).replaceAll("  ", " ");
    }
    if (isArticleNonCitation(type, pubName, volume, editors)) {
        IArticle article = ReferenceFactory.newArticle();
        if (pubName != null) {
            IJournal journal = ReferenceFactory.newJournal();
            journal.setTitle(pubName);
            article.setInJournal(journal);
        } else {
            fireWarningEvent("Article has no journal", parentEvent, 4);
        }
        reference = (Reference) article;
    } else {
        if (isBookSection(type, authorStr, titleStr, editors, pubName, volume)) {
            IBookSection bookSection = ReferenceFactory.newBookSection();
            if (pubName != null) {
                IBook book = ReferenceFactory.newBook();
                book.setTitle(pubName);
                bookSection.setInBook(book);
            }
            reference = (Reference) bookSection;
        } else {
            // ??
            Reference bookOrPartOf = ReferenceFactory.newGeneric();
            if (pubName != null && titleStr != null) {
                Reference inReference = ReferenceFactory.newGeneric();
                inReference.setTitle(pubName);
                bookOrPartOf.setInReference(inReference);
            }
            reference = bookOrPartOf;
        }
    }
    // author
    TeamOrPersonBase<?> author = createAuthor(state, authorStr);
    reference.setAuthorship(author);
    // title
    reference.setTitle(titleStr);
    if (StringUtils.isNotBlank(titleCache)) {
        reference.setTitleCache(titleCache, true);
    }
    // edition
    if (reference.getInReference() != null) {
        reference.getInReference().setEdition(edition);
        reference.getInReference().setEditor(editors);
    } else {
        // edition
        reference.setEdition(edition);
        reference.setEditor(editors);
    }
    // volume
    reference.setVolume(volume);
    // pages
    reference.setPages(pages);
    return reference;
}

Example 7 with IArticle

use of eu.etaxonomy.cdm.model.reference.IArticle in project cdmlib by cybertaxonomy.

the class NonViralNameParserImplTest method testParseReferencedName.

/**
 * Test method for {@link eu.etaxonomy.cdm.strategy.parser.NonViralNameParserImpl#parseReferencedName(NonViralName, java.lang.String, eu.etaxonomy.cdm.model.name.Rank, boolean)(, )}.
 */
@Test
public final void testParseReferencedName() {
    try {
        Method parseMethod = parser.getClass().getDeclaredMethod("parseReferencedName", String.class, NomenclaturalCode.class, Rank.class);
        testName_StringNomcodeRank(parseMethod);
    } catch (Exception e) {
        e.printStackTrace();
        assertTrue(false);
    }
    // null
    String strNull = null;
    Rank rankSpecies = Rank.SPECIES();
    INonViralName nameNull = parser.parseReferencedName(strNull, null, rankSpecies);
    assertNull(nameNull);
    // Empty
    String strEmpty = "";
    INonViralName nameEmpty = parser.parseReferencedName(strEmpty, null, rankSpecies);
    assertFalse(nameEmpty.hasProblem());
    assertEquals(strEmpty, nameEmpty.getFullTitleCache());
    assertNull(nameEmpty.getNomenclaturalMicroReference());
    // Whitespaces
    String strFullWhiteSpcaceAndDot = "Abies alba Mill.,  Sp.   Pl.  4:  455 .  1987 .";
    INonViralName namefullWhiteSpcaceAndDot = parser.parseReferencedName(strFullWhiteSpcaceAndDot, null, rankSpecies);
    assertFullRefStandard(namefullWhiteSpcaceAndDot);
    assertTrue(namefullWhiteSpcaceAndDot.getNomenclaturalReference().getType().equals(eu.etaxonomy.cdm.model.reference.ReferenceType.Book));
    assertEquals("Abies alba Mill., Sp. Pl. 4: 455. 1987", namefullWhiteSpcaceAndDot.getFullTitleCache());
    // Book
    String fullReference = "Abies alba Mill., Sp. Pl. 4: 455. 1987";
    INonViralName name1 = parser.parseReferencedName(fullReference, null, rankSpecies);
    assertFullRefStandard(name1);
    assertTrue(name1.getNomenclaturalReference().getType().equals(eu.etaxonomy.cdm.model.reference.ReferenceType.Book));
    assertEquals(fullReference, name1.getFullTitleCache());
    assertTrue("Name author and reference author should be the same", name1.getCombinationAuthorship() == name1.getNomenclaturalReference().getAuthorship());
    // Book Section
    fullReference = "Abies alba Mill. in Otto, Sp. Pl. 4(6): 455. 1987";
    INonViralName name2 = parser.parseReferencedName(fullReference + ".", null, rankSpecies);
    assertFullRefNameStandard(name2);
    assertEquals(fullReference, name2.getFullTitleCache());
    assertFalse(name2.hasProblem());
    INomenclaturalReference ref = name2.getNomenclaturalReference();
    assertEquals(ReferenceType.BookSection, ((Reference) ref).getType());
    IBookSection bookSection = (IBookSection) ref;
    IBook inBook = bookSection.getInBook();
    assertNotNull(inBook);
    assertNotNull(inBook.getAuthorship());
    assertEquals("Otto", inBook.getAuthorship().getTitleCache());
    assertEquals("Otto: Sp. Pl. 4(6)", inBook.getTitleCache());
    assertEquals("Sp. Pl.", inBook.getAbbrevTitle());
    assertEquals("4(6)", inBook.getVolume());
    assertTrue("Name author and reference author should be the same", name2.getCombinationAuthorship() == name2.getNomenclaturalReference().getAuthorship());
    // Article
    fullReference = "Abies alba Mill. in Sp. Pl. 4(6): 455. 1987";
    INonViralName name3 = parser.parseReferencedName(fullReference, null, rankSpecies);
    assertFullRefNameStandard(name3);
    name3.setTitleCache(null);
    assertEquals(fullReference, name3.getFullTitleCache());
    assertFalse(name3.hasProblem());
    ref = name3.getNomenclaturalReference();
    assertEquals(eu.etaxonomy.cdm.model.reference.ReferenceType.Article, ref.getType());
    // Article article = (Article)ref;
    IJournal journal = ((IArticle) ref).getInJournal();
    assertNotNull(journal);
    // assertEquals("Sp. Pl. 4(6)", inBook.getTitleCache());
    assertEquals("Sp. Pl.", ((Reference) journal).getTitleCache());
    assertEquals("Sp. Pl.", journal.getAbbrevTitle());
    assertEquals("4(6)", ((IArticle) ref).getVolume());
    assertTrue("Name author and reference author should be the same", name3.getCombinationAuthorship() == name3.getNomenclaturalReference().getAuthorship());
    // Article with volume range
    fullReference = "Abies alba Mill. in Sp. Pl. 4(1-2): 455. 1987";
    INonViralName name3a = parser.parseReferencedName(fullReference, null, rankSpecies);
    name3a.setTitleCache(null);
    assertEquals(fullReference, name3a.getFullTitleCache());
    assertFalse(name3a.hasProblem());
    ref = name3a.getNomenclaturalReference();
    assertEquals(eu.etaxonomy.cdm.model.reference.ReferenceType.Article, ref.getType());
    assertEquals("4(1-2)", ((IArticle) ref).getVolume());
    // SoftArticle - having "," on position > 4
    String journalTitle = "Bull. Soc. Bot.France. Louis., Roi";
    String yearPart = " 1987 - 1989";
    String parsedYearFormatted = "1987" + SEP + "1989";
    String fullReferenceWithoutYear = "Abies alba Mill. in " + journalTitle + " 4(6): 455.";
    fullReference = fullReferenceWithoutYear + yearPart;
    String fullReferenceWithEnd = fullReference + ".";
    INonViralName name4 = parser.parseReferencedName(fullReferenceWithEnd, null, rankSpecies);
    assertFalse(name4.hasProblem());
    assertFullRefNameStandard(name4);
    assertEquals(fullReferenceWithoutYear + " " + parsedYearFormatted, name4.getFullTitleCache());
    ref = name4.getNomenclaturalReference();
    assertEquals(ReferenceType.Article, ref.getType());
    // article = (Article)ref;
    assertEquals(parsedYearFormatted, ref.getYear());
    journal = ((IArticle) ref).getInJournal();
    assertNotNull(journal);
    assertEquals(journalTitle, ((Reference) journal).getTitleCache());
    assertEquals(journalTitle, journal.getAbbrevTitle());
    assertEquals("4(6)", ((IArticle) ref).getVolume());
    // Zoo name
    String strNotParsableZoo = "Abies alba M., 1923, Sp. P. xxwer4352, nom. inval.";
    IZoologicalName nameZooRefNotParsabel = parser.parseReferencedName(strNotParsableZoo, null, null);
    assertTrue(nameZooRefNotParsabel.hasProblem());
    List<ParserProblem> list = nameZooRefNotParsabel.getParsingProblems();
    assertTrue("List must contain detail and year warning ", list.contains(ParserProblem.CheckDetailOrYear));
    assertEquals(21, nameZooRefNotParsabel.getProblemStarts());
    assertEquals(37, nameZooRefNotParsabel.getProblemEnds());
    assertTrue(nameZooRefNotParsabel.getNomenclaturalReference().hasProblem());
    list = nameZooRefNotParsabel.getNomenclaturalReference().getParsingProblems();
    assertTrue("List must contain detail and year warning ", list.contains(ParserProblem.CheckDetailOrYear));
    assertEquals(NomenclaturalCode.ICZN, nameZooRefNotParsabel.getNameType());
    assertEquals(Integer.valueOf(1923), nameZooRefNotParsabel.getPublicationYear());
    assertEquals(1, nameZooRefNotParsabel.getStatus().size());
    String strZooNameSineYear = "Homo sapiens L., 1758, Sp. An. 3: 345";
    IZoologicalName nameZooNameSineYear = parser.parseReferencedName(strZooNameSineYear);
    assertFalse(nameZooNameSineYear.hasProblem());
    assertEquals("Name without reference year must have year", (Integer) 1758, nameZooNameSineYear.getPublicationYear());
    assertEquals("Name without reference year must have year", "1758", nameZooNameSineYear.getNomenclaturalReference().getYear());
    String strZooNameNewCombination = "Homo sapiens (L., 1758) Mill., 1830, Sp. An. 3: 345";
    IZoologicalName nameZooNameNewCombination = parser.parseReferencedName(strZooNameNewCombination);
    assertTrue(nameZooNameNewCombination.hasProblem());
    list = nameZooNameNewCombination.getParsingProblems();
    assertTrue("List must contain new combination has publication warning ", list.contains(ParserProblem.NewCombinationHasPublication));
    assertEquals(35, nameZooNameNewCombination.getProblemStarts());
    assertEquals(51, nameZooNameNewCombination.getProblemEnds());
    // Special MicroRefs
    String strSpecDetail1 = "Abies alba Mill. in Sp. Pl. 4(6): [455]. 1987";
    INonViralName nameSpecDet1 = parser.parseReferencedName(strSpecDetail1 + ".", null, rankSpecies);
    assertFalse(nameSpecDet1.hasProblem());
    assertEquals(strSpecDetail1, nameSpecDet1.getFullTitleCache());
    assertEquals("[455]", nameSpecDet1.getNomenclaturalMicroReference());
    // Special MicroRefs
    String strSpecDetail2 = "Abies alba Mill. in Sp. Pl. 4(6): couv. 2. 1987";
    INonViralName nameSpecDet2 = parser.parseReferencedName(strSpecDetail2 + ".", null, rankSpecies);
    assertFalse(nameSpecDet2.hasProblem());
    assertEquals(strSpecDetail2, nameSpecDet2.getFullTitleCache());
    assertEquals("couv. 2", nameSpecDet2.getNomenclaturalMicroReference());
    // Special MicroRefs
    String strSpecDetail3 = "Abies alba Mill. in Sp. Pl. 4(6): fig. 455. 1987";
    INonViralName nameSpecDet3 = parser.parseReferencedName(strSpecDetail3 + ".", null, rankSpecies);
    assertFalse(nameSpecDet3.hasProblem());
    assertEquals(strSpecDetail3, nameSpecDet3.getFullTitleCache());
    assertEquals("fig. 455", nameSpecDet3.getNomenclaturalMicroReference());
    // Special MicroRefs
    String strSpecDetail4 = "Abies alba Mill. in Sp. Pl. 4(6): fig. 455-567. 1987";
    fullReference = strSpecDetail4 + ".";
    INonViralName nameSpecDet4 = parser.parseReferencedName(fullReference, null, rankSpecies);
    assertFalse(nameSpecDet4.hasProblem());
    assertEquals(strSpecDetail4, nameSpecDet4.getFullTitleCache());
    assertEquals("fig. 455-567", nameSpecDet4.getNomenclaturalMicroReference());
    // Special MicroRefs
    String strSpecDetail5 = "Abies alba Mill. in Sp. Pl. 4(6): Gard n\u00B0 4. 1987";
    fullReference = strSpecDetail5 + ".";
    INonViralName nameSpecDet5 = parser.parseReferencedName(fullReference, null, rankSpecies);
    assertFalse(nameSpecDet5.hasProblem());
    assertEquals(strSpecDetail5, nameSpecDet5.getFullTitleCache());
    assertEquals("Gard n\u00B0 4", nameSpecDet5.getNomenclaturalMicroReference());
    // Special MicroRefs
    String strSpecDetail6 = "Abies alba Mill. in Sp. Pl. 4(6): 455a. 1987";
    fullReference = strSpecDetail6 + ".";
    INonViralName nameSpecDet6 = parser.parseReferencedName(fullReference, null, rankSpecies);
    assertFalse(nameSpecDet6.hasProblem());
    assertEquals(strSpecDetail6, nameSpecDet6.getFullTitleCache());
    assertEquals("455a", nameSpecDet6.getNomenclaturalMicroReference());
    // Special MicroRefs
    String strSpecDetail7 = "Abies alba Mill. in Sp. Pl. 4(6): pp.455-457. 1987";
    fullReference = strSpecDetail7 + ".";
    INonViralName nameSpecDet7 = parser.parseReferencedName(fullReference, null, rankSpecies);
    assertFalse(nameSpecDet7.hasProblem());
    assertEquals(strSpecDetail7, nameSpecDet7.getFullTitleCache());
    assertEquals("pp.455-457", nameSpecDet7.getNomenclaturalMicroReference());
    // Special MicroRefs
    String strSpecDetail8 = "Abies alba Mill. in Sp. Pl. 4(6): ppp.455-457. 1987";
    INonViralName nameSpecDet8 = parser.parseReferencedName(strSpecDetail8, null, rankSpecies);
    assertTrue(nameSpecDet8.hasProblem());
    // TODO better start behind :
    assertEquals(20, nameSpecDet8.getProblemStarts());
    // TODO better stop after -457
    assertEquals(51, nameSpecDet8.getProblemEnds());
    // Special MicroRefs
    String strSpecDetail9 = "Abies alba Mill. in Sp. Pl. 4(6): pp. 455 - 457. 1987";
    INonViralName nameSpecDet9 = parser.parseReferencedName(strSpecDetail9, null, rankSpecies);
    assertFalse(nameSpecDet9.hasProblem());
    assertEquals(strSpecDetail9, nameSpecDet9.getFullTitleCache());
    assertEquals("pp. 455 - 457", nameSpecDet9.getNomenclaturalMicroReference());
    // Special MicroRefs
    String strSpecDetail10 = "Abies alba Mill. in Sp. Pl. 4(6): p 455. 1987";
    INonViralName nameSpecDet10 = parser.parseReferencedName(strSpecDetail10, null, rankSpecies);
    assertFalse(nameSpecDet10.hasProblem());
    assertEquals(strSpecDetail10, nameSpecDet10.getFullTitleCache());
    assertEquals("p 455", nameSpecDet10.getNomenclaturalMicroReference());
    // Special MicroRefs
    String strSpecDetail11 = "Abies alba Mill. in Sp. Pl. 4(6): p. 455 - 457. 1987";
    INonViralName nameSpecDet11 = parser.parseReferencedName(strSpecDetail11, null, rankSpecies);
    assertTrue(nameSpecDet11.hasProblem());
    list = nameSpecDet11.getParsingProblems();
    assertTrue("Problem is Detail. Must be pp.", list.contains(ParserProblem.CheckDetailOrYear));
    // TODO better start behind :
    assertEquals(20, nameSpecDet8.getProblemStarts());
    // TODO better stop after - 457
    assertEquals(51, nameSpecDet8.getProblemEnds());
    // no volume, no edition
    String strNoVolume = "Abies alba Mill., Sp. Pl.: 455. 1987";
    INonViralName nameNoVolume = parser.parseReferencedName(strNoVolume, null, rankSpecies);
    assertFalse(nameNoVolume.hasProblem());
    assertEquals(strNoVolume, nameNoVolume.getFullTitleCache());
    assertEquals(null, ((IVolumeReference) (nameNoVolume.getNomenclaturalReference())).getVolume());
    assertEquals(null, ((IBook) nameNoVolume.getNomenclaturalReference()).getEdition());
    // volume, no edition
    strNoVolume = "Abies alba Mill., Sp. Pl. 2: 455. 1987";
    nameNoVolume = parser.parseReferencedName(strNoVolume, null, rankSpecies);
    assertFalse(nameNoVolume.hasProblem());
    assertEquals(strNoVolume, nameNoVolume.getFullTitleCache());
    assertEquals("2", ((IVolumeReference) (nameNoVolume.getNomenclaturalReference())).getVolume());
    assertEquals(null, ((IBook) (nameNoVolume.getNomenclaturalReference())).getEdition());
    // no volume, edition
    strNoVolume = "Abies alba Mill., Sp. Pl., ed. 3: 455. 1987";
    nameNoVolume = parser.parseReferencedName(strNoVolume, null, rankSpecies);
    assertFalse(nameNoVolume.hasProblem());
    assertEquals(strNoVolume, nameNoVolume.getFullTitleCache());
    assertEquals(null, ((IVolumeReference) (nameNoVolume.getNomenclaturalReference())).getVolume());
    assertEquals("3", ((IBook) (nameNoVolume.getNomenclaturalReference())).getEdition());
    // volume, edition
    strNoVolume = "Abies alba Mill., Sp. Pl. ed. 3, 4(5): 455. 1987";
    nameNoVolume = parser.parseReferencedName(strNoVolume, null, rankSpecies);
    assertFalse(nameNoVolume.hasProblem());
    assertEquals(strNoVolume.replace(" ed.", ", ed."), nameNoVolume.getFullTitleCache());
    assertEquals("4(5)", ((IVolumeReference) (nameNoVolume.getNomenclaturalReference())).getVolume());
    assertEquals("3", ((IBook) (nameNoVolume.getNomenclaturalReference())).getEdition());
    String strUnparsableInRef = "Abies alba Mill. in -er46: 455. 1987";
    INonViralName nameUnparsableInRef = parser.parseReferencedName(strUnparsableInRef, null, rankSpecies);
    assertTrue(nameUnparsableInRef.hasProblem());
    list = nameUnparsableInRef.getParsingProblems();
    assertTrue("Unparsable title", list.contains(ParserProblem.UnparsableReferenceTitle));
    assertEquals(strUnparsableInRef, nameUnparsableInRef.getFullTitleCache());
    assertEquals(20, nameUnparsableInRef.getProblemStarts());
    assertEquals(25, nameUnparsableInRef.getProblemEnds());
    // volume, edition
    String strNoSeparator = "Abies alba Mill. Sp. Pl. ed. 3, 4(5): 455. 1987";
    INonViralName nameNoSeparator = parser.parseReferencedName(strNoSeparator, ICNAFP, rankSpecies);
    assertTrue(nameNoSeparator.hasProblem());
    list = nameNoSeparator.getParsingProblems();
    assertTrue("Problem is missing name-reference separator", list.contains(ParserProblem.NameReferenceSeparation));
    assertEquals(strNoSeparator, nameNoSeparator.getFullTitleCache());
    // TODO better start behind Mill. (?)
    assertEquals(10, nameNoSeparator.getProblemStarts());
    // TODO better stop before :
    assertEquals(47, nameNoSeparator.getProblemEnds());
    String strUnparsableInRef2 = "Hieracium pepsicum L., My Bookkkk 1. 1903";
    INonViralName nameUnparsableInRef2 = parser.parseReferencedName(strUnparsableInRef2, null, rankSpecies);
    assertTrue(nameUnparsableInRef2.hasProblem());
    list = nameUnparsableInRef2.getParsingProblems();
    assertTrue("Problem detail", list.contains(ParserProblem.CheckDetailOrYear));
    assertEquals(strUnparsableInRef2, nameUnparsableInRef2.getFullTitleCache());
    assertEquals(23, nameUnparsableInRef2.getProblemStarts());
    assertEquals(41, nameUnparsableInRef2.getProblemEnds());
    String strUnparsableInRef3 = "Hieracium pespcim N., My Bookkkk 1. 1902";
    INonViralName nameUnparsableInRef3 = parser.parseReferencedName(strUnparsableInRef3, null, null);
    assertTrue(nameUnparsableInRef3.hasProblem());
    list = nameUnparsableInRef3.getParsingProblems();
    assertTrue("Problem detail", list.contains(ParserProblem.CheckDetailOrYear));
    assertEquals(strUnparsableInRef3, nameUnparsableInRef3.getFullTitleCache());
    assertEquals(22, nameUnparsableInRef3.getProblemStarts());
    assertEquals(40, nameUnparsableInRef3.getProblemEnds());
    String strUnparsableInRef4 = "Hieracium pepsicum (Hsllreterto) L., My Bookkkk 1. 1903";
    INonViralName nameUnparsableInRef4 = parser.parseReferencedName(strUnparsableInRef4, null, null);
    assertTrue(nameUnparsableInRef4.hasProblem());
    list = nameUnparsableInRef4.getParsingProblems();
    assertTrue("Problem detail", list.contains(ParserProblem.CheckDetailOrYear));
    assertEquals(strUnparsableInRef4, nameUnparsableInRef4.getFullTitleCache());
    assertEquals(37, nameUnparsableInRef4.getProblemStarts());
    assertEquals(55, nameUnparsableInRef4.getProblemEnds());
    String strSameName = "Hieracium pepcum (Hsllreterto) L., My Bokkk 1. 1903";
    INonViralName nameSameName = nameUnparsableInRef4;
    parser.parseReferencedName(nameSameName, strSameName, null, true);
    assertTrue(nameSameName.hasProblem());
    list = nameSameName.getParsingProblems();
    assertTrue("Problem detail", list.contains(ParserProblem.CheckDetailOrYear));
    assertEquals(strSameName, nameSameName.getFullTitleCache());
    assertEquals(35, nameSameName.getProblemStarts());
    assertEquals(51, nameSameName.getProblemEnds());
    String strGenusUnparse = "Hieracium L., jlklk";
    INonViralName nameGenusUnparse = parser.parseReferencedName(strGenusUnparse, null, null);
    assertTrue(nameGenusUnparse.hasProblem());
    list = nameGenusUnparse.getParsingProblems();
    assertTrue("Problem detail", list.contains(ParserProblem.CheckDetailOrYear));
    assertTrue("Problem uninomial", list.contains(ParserProblem.CheckRank));
    assertEquals(strGenusUnparse, nameGenusUnparse.getFullTitleCache());
    assertEquals(0, nameGenusUnparse.getProblemStarts());
    assertEquals(19, nameGenusUnparse.getProblemEnds());
    String strGenusUnparse2 = "Hieracium L., Per Luigi: 44. 1987";
    INonViralName nameGenusUnparse2 = parser.parseReferencedName(strGenusUnparse2, null, Rank.FAMILY());
    assertFalse(nameGenusUnparse2.hasProblem());
    assertEquals(strGenusUnparse2, nameGenusUnparse2.getFullTitleCache());
    assertEquals(-1, nameGenusUnparse2.getProblemStarts());
    assertEquals(-1, nameGenusUnparse2.getProblemEnds());
    String strBookSection2 = "Hieracium vulgatum subsp. acuminatum (Jord.) Zahn in Schinz & Keller, Fl. Schweiz, ed. 2, 2: 288. 1905-1907";
    String strBookSection2NoComma = "Hieracium vulgatum subsp. acuminatum (Jord.) Zahn in Schinz & Keller, Fl. Schweiz ed. 2, 2: 288. 1905-1907";
    INonViralName nameBookSection2 = parser.parseReferencedName(strBookSection2, null, null);
    assertFalse(nameBookSection2.hasProblem());
    nameBookSection2.setFullTitleCache(null, false);
    assertEquals(strBookSection2NoComma.replace(" ed.", ", ed.").replace("-", SEP), nameBookSection2.getFullTitleCache());
    assertEquals(-1, nameBookSection2.getProblemStarts());
    assertEquals(-1, nameBookSection2.getProblemEnds());
    assertNull((nameBookSection2.getNomenclaturalReference()).getDatePublished().getStart());
    assertEquals("1905" + SEP + "1907", ((IBookSection) nameBookSection2.getNomenclaturalReference()).getInBook().getDatePublished().getYear());
    String strBookSection = "Hieracium vulgatum subsp. acuminatum (Jord.) Zahn in Schinz & Keller, Fl. Schweiz ed. 2, 2: 288. 1905";
    INonViralName nameBookSection = parser.parseReferencedName(strBookSection, null, null);
    assertFalse(nameBookSection.hasProblem());
    assertEquals(strBookSection.replace(" ed.", ", ed."), nameBookSection.getFullTitleCache());
    assertEquals(-1, nameBookSection.getProblemStarts());
    assertEquals(-1, nameBookSection.getProblemEnds());
    assertNull(((IBookSection) nameBookSection.getNomenclaturalReference()).getInBook().getDatePublished().getStart());
    assertEquals("1905", ((IBookSection) nameBookSection.getNomenclaturalReference()).getDatePublished().getYear());
    String strXXXs = "Abies alba, Soer der 1987";
    INonViralName problemName = parser.parseReferencedName(strXXXs, null, null);
    assertTrue(problemName.hasProblem());
    list = problemName.getParsingProblems();
    assertTrue("Problem must be name-reference separation", list.contains(ParserProblem.NameReferenceSeparation));
    parser.parseReferencedName(problemName, strBookSection, null, true);
    assertFalse(problemName.hasProblem());
    problemName = parser.parseFullName(strXXXs, null, null);
    assertTrue(problemName.hasProblem());
    list = problemName.getParsingProblems();
    assertTrue("Name part must be unparsable", list.contains(ParserProblem.UnparsableNamePart));
    String testParsable = "Pithecellobium macrostachyum Benth.";
    assertTrue(isParsable(testParsable, ICNAFP));
    testParsable = "Pithecellobium macrostachyum (Benth.)";
    assertTrue(isParsable(testParsable, ICNAFP));
    testParsable = "Pithecellobium macrostachyum (Benth., 1845)";
    assertTrue(isParsable(testParsable, NomenclaturalCode.ICZN));
    // 00B0 is degree character
    testParsable = "Pithecellobium macrostachyum L., Sp. Pl. 3: n\u00B0 123. 1753.";
    assertTrue(isParsable(testParsable, ICNAFP));
    testParsable = "Hieracium lachenalii subsp. acuminatum (Jord.) Zahn in Hegi, Ill. Fl. Mitt.-Eur. 6: 1285. 1929";
    assertTrue("Reference title should support special characters as separators like - and &", isParsable(testParsable, ICNAFP));
    testParsable = "Hieracium lachenalii subsp. acuminatum (Jord.) Zahn in Hegi, Ill. Fl. Mitt.&Eur. 6: 1285. 1929";
    assertTrue("Reference title should support special characters as separators like - and &", isParsable(testParsable, ICNAFP));
    testParsable = "Hieracium lachenalii subsp. acuminatum (Jord.) Zahn in Hegi, Ill. Fl. Mitt.-Eur.& 6: 1285. 1929";
    assertFalse("Reference title should not support special characters like - and & at the end of the title", isParsable(testParsable, ICNAFP));
    assertTrue("Problem must be reference title", getProblems(testParsable, ICNAFP).contains(ParserProblem.UnparsableReferenceTitle));
    testParsable = "Hieracium lachenalii subsp. acuminatum (Jord.) Zahn in Hegi, Ill. Fl. Mitt.:Eur. 6: 1285. 1929";
    assertFalse("Reference title should not support detail separator", isParsable(testParsable, ICNAFP));
    assertTrue("Problem must be reference title", getProblems(testParsable, ICNAFP).contains(ParserProblem.UnparsableReferenceTitle));
    testParsable = "Hieracium lachenalii subsp. acuminatum (Jord.) Zahn in Hegi, Ill. Fl. (Mitt.) 6: 1285. 1929";
    assertTrue("Reference title should support brackets", isParsable(testParsable, ICNAFP));
    testParsable = "Hieracium lachenalii subsp. acuminatum (Jord.) Zahn in Hegi, Ill. Fl. (Mitt.) 6: 1285. 1929";
    assertTrue("Reference title should support brackets", isParsable(testParsable, ICNAFP));
    testParsable = "Hieracium lachenalii Zahn, nom. illeg.";
    assertTrue("Reference should not be obligatory if a nom status exist", isParsable(testParsable, ICNAFP));
    testParsable = "Hieracium lachenalii, nom. illeg.";
    assertTrue("Authorship should not be obligatory if followed by nom status", isParsable(testParsable, ICNAFP));
    testParsable = "Hieracium lachenalii, Ill. Fl. (Mitt.) 6: 1285. 1929";
    assertFalse("Author is obligatory if followed by reference", isParsable(testParsable, ICNAFP));
    assertTrue("Problem must be name-reference separation", getProblems(testParsable, ICNAFP).contains(ParserProblem.NameReferenceSeparation));
    testParsable = "Hieracium lachenalii in Hegi, Ill. Fl. (Mitt.) 6: 1285. 1929";
    assertFalse("Author is obligatory if followed by reference", isParsable(testParsable, ICNAFP));
    assertTrue("Problem must be name-reference separation", getProblems(testParsable, ICNAFP).contains(ParserProblem.NameReferenceSeparation));
    testParsable = "Abies alba Mill. var. alba";
    assertTrue("Autonym problem", isParsable(testParsable, ICNAFP));
    testParsable = "Scleroblitum abc Ulbr. in Engler & Prantl, Nat. Pflanzenfam., ed. 2, 16c: 495. 1934.";
    assertTrue("Volume with subdivision", isParsable(testParsable, ICNAFP));
    testParsable = "Hieracium antarcticum d'Urv. in M\u00E9m. Soc. Linn. Paris 4: 608. 1826";
    // testParsable = "Hieracium antarcticum Urv. in M\u00E9m. Soc. Linn. Paris 4: 608. 1826";
    assertTrue("Name with apostrophe is not parsable", isParsable(testParsable, ICNAFP));
    testParsable = "Cichorium intybus subsp. glaucum (Hoffmanns. & Link) Tzvelev in Komarov, Fl. SSSR 29: 17. 1964";
    assertTrue("Reference containing a word in uppercase is not parsable", isParsable(testParsable, ICNAFP));
    testParsable = "Silene broussonetiana Schott ex Webb & Berthel., Hist. Nat. Iles Canaries 3(2,1): 141. 1840";
    assertTrue("Reference with volume with 2 number in brackets is not parsable", isParsable(testParsable, ICNAFP));
    testParsable = "Silene broussonetiana Schott ex Webb & Berthel., Hist. Nat. Iles Canaries 3(2, 1): 141. 1840";
    assertTrue("Reference with volume with 2 number in brackets is not parsable", isParsable(testParsable, ICNAFP));
}

Example 8 with IArticle

use of eu.etaxonomy.cdm.model.reference.IArticle in project cdmlib by cybertaxonomy.

the class CacheStrategyGeneratorTest method testOnSaveOrUpdateReferences.

@Test
@DataSet("CacheStrategyGeneratorTest.xml")
@ExpectedDataSet
public // TODO correct abbrevTitleCache for article still unclear (open question: with or without article title ?)
void testOnSaveOrUpdateReferences() {
    // References
    IJournal journal1 = ReferenceFactory.newJournal();
    Person journalAuthor = makePerson1();
    journal1.setTitle("My journal");
    journal1.setUuid(UUID.fromString("a7fdf3b8-acd8-410a-afcd-1768d29d67e9"));
    journal1.setAbbrevTitle("M. Journ.");
    ((Reference) journal1).setAuthorship(journalAuthor);
    referenceDao.save((Reference) journal1);
    Person articleAuthor = makePerson2();
    IArticle article1 = ReferenceFactory.newArticle();
    article1.setUuid(UUID.fromString("eb090fbc-5895-405c-aba5-cac287efb128"));
    article1.setAbbrevTitle("M. Art.");
    article1.setVolume("1");
    article1.setDatePublished(VerbatimTimePeriod.NewVerbatimInstance(1972));
    article1.setInJournal(journal1);
    article1.setAuthorship(articleAuthor);
    article1.getAbbrevTitleCache();
    referenceDao.saveOrUpdate((Reference) article1);
    commit();
}

Example 9 with IArticle

use of eu.etaxonomy.cdm.model.reference.IArticle in project cdmlib by cybertaxonomy.

the class MatchStrategyFactoryTest method testParsedReference.

@Test
public void testParsedReference() throws MatchException {
    IParsedMatchStrategy matchStrategy = MatchStrategyFactory.NewParsedReferenceInstance();
    Assert.assertNotNull(matchStrategy);
    IArticle fullArticle;
    IArticle parsedArticle;
    fullArticle = getMatchingFullArticle();
    parsedArticle = getDefaultParsedArticle();
    Assert.assertTrue("Only author, book and date published should match", matchStrategy.invoke(parsedArticle, fullArticle).isSuccessful());
    // should match
    fullArticle = getDefaultFullArticle();
    Assert.assertFalse("Abbrev. title must be equal or null", matchStrategy.invoke(parsedArticle, fullArticle).isSuccessful());
    parsedArticle.setAbbrevTitle(fullArticle.getAbbrevTitle());
    Assert.assertFalse("Still not match because pages are not equal (parsed is null)", matchStrategy.invoke(parsedArticle, fullArticle).isSuccessful());
    parsedArticle.setPages(fullArticle.getPages());
    Assert.assertFalse("Now they should match", matchStrategy.invoke(parsedArticle, fullArticle).isSuccessful());
    // differing nom. title.
    parsedArticle.setAbbrevTitle("Wrong");
    Assert.assertFalse("Differing abbrev. title. should not match", matchStrategy.invoke(parsedArticle, fullArticle).isSuccessful());
    // differing family
    parsedArticle = getDefaultParsedArticle();
    parsedArticle.setTitle("Wrong title");
    Assert.assertFalse("Differing title should not match", matchStrategy.invoke(parsedArticle, fullArticle).isSuccessful());
    fullArticle.setTitle(null);
    Assert.assertFalse("Title only for parsed book should not match. Wrong direction.", matchStrategy.invoke(parsedArticle, fullArticle).isSuccessful());
    // change author
    fullArticle = getMatchingFullArticle();
    parsedArticle = getDefaultParsedArticle();
    fullArticle.getAuthorship().setNomenclaturalTitleCache("Wrong", true);
    Assert.assertFalse("Differing author in nomencl. title should not match", matchStrategy.invoke(parsedArticle, fullArticle).isSuccessful());
    // change author
    fullArticle = getMatchingFullArticle();
    parsedArticle = getDefaultParsedArticle();
    ((Team) fullArticle.getAuthorship()).getTeamMembers().get(0).setFamilyName("Changed");
    Assert.assertTrue("Full book family name author changed should still match", matchStrategy.invoke(parsedArticle, fullArticle).isSuccessful());
}

Example 10 with IArticle

use of eu.etaxonomy.cdm.model.reference.IArticle in project cdmlib by cybertaxonomy.

the class MatchStrategyFactoryTest method getDefaultParsedArticle.

/**
 * Article with {@link #getDefaultParsedTeam() parsed authorship},
 * {@link #getDefaultParsedJournal() parsed journal} and date published.
 */
private IArticle getDefaultParsedArticle() {
    IArticle article = ReferenceFactory.newArticle();
    article.setAuthorship(getDefaultParsedTeam());
    article.setInJournal(getDefaultParsedJournal());
    article.setDatePublished(TimePeriodParser.parseStringVerbatim("1950"));
    ((Reference) article).updateCaches();
    return article;
}