/**
* @param doc the article xml document in question
* @param authors list of article authors
* @return an xml-sorted map of article affiliates and their respective authors
*/
public Map<String, List<AuthorView>> getAuthorsByAffiliation(
Document doc, List<AuthorView> authors) throws RuntimeException {
Map<String, List<AuthorView>> authorsByAffiliation =
new LinkedHashMap<String, List<AuthorView>>();
try {
/*
<String, String> in the following case is, in xpath parlance, <//aff@id>,<//aff/addr-line/text() but
AuthorView cues on the //aff/addr-line/text() part, so we need to add a level of indirection
*/
Map<String, String> originalAffiliateMap =
AuthorsXmlExtractor.getAffiliateMap(doc, xPathUtil);
for (Map.Entry<String, String> entry : originalAffiliateMap.entrySet()) {
authorsByAffiliation.put(entry.getValue(), new ArrayList<AuthorView>());
}
for (AuthorView currentAuthorView : authors) {
for (String affiliate : currentAuthorView.getAffiliations()) {
List<AuthorView> authorList = authorsByAffiliation.get(affiliate);
if (authorList != null) {
authorsByAffiliation.get(affiliate).add(currentAuthorView);
} else {
log.error(
new StringBuilder("Could not associate ")
.append(currentAuthorView.getFullName())
.append(" with institution ")
.append(affiliate)
.toString());
}
}
}
} catch (XPathException e) {
throw new RuntimeException();
}
// make sure to return only non-empty lists
Map<String, List<AuthorView>> tempAuthorAffiliations =
new LinkedHashMap<String, List<AuthorView>>();
for (Map.Entry<String, List<AuthorView>> affiliationMapping : authorsByAffiliation.entrySet()) {
if (affiliationMapping.getValue().size() > 0) {
tempAuthorAffiliations.put(affiliationMapping.getKey(), affiliationMapping.getValue());
}
}
authorsByAffiliation = tempAuthorAffiliations;
return authorsByAffiliation;
}
protected void checkAnnotationProperties(AnnotationView result, Annotation expected) {
if (expected.getType() == AnnotationType.MINOR_CORRECTION) {
assertEquals(
result.getTitle(),
"Minor Correction: " + expected.getTitle(),
"Annotation view had incorrect title");
} else if (expected.getType() == AnnotationType.FORMAL_CORRECTION) {
assertEquals(
result.getTitle(),
"Formal Correction: " + expected.getTitle(),
"Annotation view had incorrect title");
} else if (expected.getType() == AnnotationType.RETRACTION) {
assertEquals(
result.getTitle(),
"Retraction: " + expected.getTitle(),
"Annotation view had incorrect title");
}
assertEquals(
result.getBody(),
"<p>" + expected.getBody() + "</p>",
"Annotation view had incorrect body");
assertEquals(
result.getCompetingInterestStatement(),
expected.getCompetingInterestBody() == null ? "" : expected.getCompetingInterestBody(),
"Annotation view had incorrect ci statement");
assertEquals(
result.getAnnotationUri(),
expected.getAnnotationUri(),
"Annotation view had incorrect annotation uri");
assertEquals(
result.getCreatorID(),
expected.getCreator().getID(),
"Annotation view had incorrect creator id");
assertEquals(
result.getCreatorDisplayName(),
expected.getCreator().getDisplayName(),
"Annotation view had incorrect creator name");
if (Arrays.asList(
AnnotationType.FORMAL_CORRECTION,
AnnotationType.MINOR_CORRECTION,
AnnotationType.RETRACTION)
.contains(expected.getType())) {
assertTrue(result.isCorrection(), "Result should have been created as a correction");
} else {
assertFalse(result.isCorrection(), "Result should not have been created as a correction");
}
if (expected.getAnnotationCitation() == null) {
assertNull(result.getCitation(), "returned non-null citation when null was expected");
} else {
assertNotNull(result.getCitation(), "returned null citation when non-null was expected");
assertEquals(
result.getCitation().getTitle(),
expected.getAnnotationCitation().getTitle(),
"Returned citation with incorrect title");
assertEquals(
result.getCitation().geteLocationId(),
expected.getAnnotationCitation().getELocationId(),
"Returned citation with incorrect eLocationId");
assertEquals(
result.getCitation().getJournal(),
expected.getAnnotationCitation().getJournal(),
"Returned citation with incorrect journal");
assertEquals(
result.getCitation().getYear(),
expected.getAnnotationCitation().getYear(),
"Returned citation with incorrect year");
assertEquals(
result.getCitation().getVolume(),
expected.getAnnotationCitation().getVolume(),
"Returned citation with incorrect volume");
assertEquals(
result.getCitation().getIssue(),
expected.getAnnotationCitation().getIssue(),
"Returned citation with incorrect issue");
assertEquals(
result.getCitation().getSummary(),
expected.getAnnotationCitation().getSummary(),
"Returned citation with incorrect summary");
assertEquals(
result.getCitation().getNote(),
expected.getAnnotationCitation().getNote(),
"Returned citation with incorrect note");
if (expected.getAnnotationCitation().getCollaborativeAuthors() != null) {
assertEqualsNoOrder(
result.getCitation().getCollabAuthors(),
expected.getAnnotationCitation().getCollaborativeAuthors().toArray(),
"Returned citation with incorrect collab authors");
} else {
assertTrue(
ArrayUtils.isEmpty(result.getCitation().getCollabAuthors()),
"Returned non-empty collab authors when empty was expected");
}
if (expected.getAnnotationCitation().getAuthors() != null) {
assertNotNull(
result.getCitation().getAuthors(), "Returned null authors when authors were expected");
assertEquals(
result.getCitation().getAuthors().length,
expected.getAnnotationCitation().getAuthors().size(),
"Returned incorrect number of authors");
for (int i = 0; i < result.getCitation().getAuthors().length; i++) {
AuthorView actualAuthor = result.getCitation().getAuthors()[i];
CorrectedAuthor expectedAuthor = expected.getAnnotationCitation().getAuthors().get(i);
assertEquals(
actualAuthor.getGivenNames(),
expectedAuthor.getGivenNames(),
"Author " + (i + 1) + " had incorrect given names");
assertEquals(
actualAuthor.getSurnames(),
expectedAuthor.getSurName(),
"Author " + (i + 1) + " had incorrect surnames");
assertEquals(
actualAuthor.getSuffix(),
expectedAuthor.getSuffix(),
"Author " + (i + 1) + " had incorrect suffix");
}
}
}
}