@Override
public ArticleMetadata extract(MetadataTarget target, CachedUrl cu) throws IOException {
log.debug3("Metadata - cachedurl cu:" + cu.getUrl());
ArticleMetadata am = super.extract(target, cu);
am.cook(tagMap);
return am;
} // extract
public void testDOIExtraction() throws Exception {
List<ArticleMetadata> mdlist =
setupContentForAU(bau1, ABS_URL, goodHtmlContentNoDOIorPublisher, true);
assertNotEmpty(mdlist);
ArticleMetadata md = mdlist.get(0);
assertNotNull(md);
// gets pulled from the URL if not set in the metadata
assertEquals("10.1175/2010WCAS1063.1", md.get(MetadataField.FIELD_DOI));
// gets set manually if not in the metadata
// first it would try the TDB
assertEquals(goodPublisher, md.get(MetadataField.FIELD_PUBLISHER));
}
@Override
public void extract(MetadataTarget target, CachedUrl cu, Emitter emitter) throws IOException {
ArticleMetadata am = new SimpleHtmlMetaTagMetadataExtractor().extract(target, cu);
am.cook(tagMap);
String url = am.get(MetadataField.FIELD_ACCESS_URL);
ArchivalUnit au = cu.getArchivalUnit();
if (url == null || url.isEmpty() || !au.makeCachedUrl(url).hasContent()) {
url = cu.getUrl();
}
am.replace(
MetadataField.FIELD_ACCESS_URL,
HttpToHttpsUtil.AuUtil.normalizeHttpHttpsFromBaseUrl(au, url));
emitter.emitMetadata(cu, am);
}
/*
* When testing no-pdf-check basic XML parsing, you will get partial MD records
* depending on whether the info comes from dataset.xml or from main.xml
*/
private void validateDatasetMetadataRecord(ArticleMetadata am) {
log.debug3("valideDatasetMetadatRecord");
String doi_val = am.get(MetadataField.FIELD_DOI);
assertEquals(common_issn, am.get(MetadataField.FIELD_ISSN));
log.debug3("doi val is: " + doi_val);
// The dataset doesn't set this value, it'll fail over the main.xml value
if (doi_val.equals("10.1016/S0140-1111(14)61865-1")) {
assertEquals(null, am.get(MetadataField.FIELD_DATE));
} else {
assertEquals(dateMap.get(doi_val), am.get(MetadataField.FIELD_DATE));
}
assertEquals(pubTitleMap.get(doi_val), am.get(MetadataField.FIELD_PUBLICATION_TITLE));
}
@Override
public ArticleMetadata extract(MetadataTarget target, CachedUrl cu) throws IOException {
ArticleMetadata am = super.extract(target, cu);
am.cook(tagMap);
String url = am.get(MetadataField.FIELD_ACCESS_URL);
if (url != null && !url.isEmpty()) {
CachedUrl val = cu.getArchivalUnit().makeCachedUrl(url);
if (!val.hasContent()) {
am.replace(MetadataField.FIELD_ACCESS_URL, cu.getUrl());
}
} else {
am.replace(MetadataField.FIELD_ACCESS_URL, cu.getUrl());
}
return am;
}
/*
* hasArticleMetadata(CachedUrl cu)
* Given the CachedUrl for the potential abstract file, using the existing
* SimpleHtmlMetaTagMetadataExtractor to parse the file and
* retrieve any contained metadata. If a doi or author exists, it's an article
* NOT defining the Metadata Extractor here!
*/
private boolean hasArticleMetadata(CachedUrl cu) {
MetadataTarget at = new MetadataTarget(MetadataTarget.PURPOSE_ARTICLE);
ArticleMetadata am;
SimpleHtmlMetaTagMetadataExtractor ext = new SimpleHtmlMetaTagMetadataExtractor();
if (cu != null && cu.hasContent()) {
try {
at.setFormat("text/html");
am = ext.extract(at, cu);
if ((am.containsRawKey("bepress_citation_journal_title"))
|| (am.containsRawKey("bepress_citation_abstract_html_url"))
|| (am.containsRawKey("bepress_citation_doi"))
|| (am.containsRawKey("bepress_citation_author"))) {
return true;
}
} catch (IOException e) {
e.printStackTrace();
}
}
return false; // no reasonable metadata, probably a toc
}
public void testExtractGoodHtmlContent() throws Exception {
List<ArticleMetadata> mdlist = setupContentForAU(bau1, ABS_URL, goodHtmlContent, true);
assertNotEmpty(mdlist);
ArticleMetadata md = mdlist.get(0);
assertNotNull(md);
assertEquals(goodPublisher, md.get(MetadataField.FIELD_PUBLISHER));
assertEquals(goodTitle, md.get(MetadataField.DC_FIELD_TITLE));
assertEquals(goodDate, md.get(MetadataField.FIELD_DATE));
assertEquals(goodFormat, md.get(MetadataField.DC_FIELD_FORMAT));
assertEquals(goodType, md.get(MetadataField.DC_FIELD_TYPE));
assertEquals(Arrays.asList(goodAuthors), md.getList(MetadataField.FIELD_AUTHOR));
assertEquals(goodAuthors[0], md.get(MetadataField.DC_FIELD_CREATOR));
}
/*
* You will have to tell it the DOI and the schema because those normally come from dataset
*/
private void validateSingleMainMetadataRecord(ArticleMetadata am, String doi_val, String schema) {
log.debug3("valideSingleMainMetadatRecord");
if ("simple-article".equals(schema)) {
assertEquals(common_simple_article_title, am.get(MetadataField.FIELD_ARTICLE_TITLE));
} else {
assertEquals(common_article_title, am.get(MetadataField.FIELD_ARTICLE_TITLE));
}
log.debug3("doi val is: " + doi_val);
assertEquals(authorMap.get(doi_val), am.getList(MetadataField.FIELD_AUTHOR));
assertEquals(volMap.get(doi_val), am.get(MetadataField.FIELD_VOLUME));
assertEquals(issueMap.get(doi_val), am.get(MetadataField.FIELD_ISSUE));
assertEquals("Comment", am.getRaw(ElsevierMainDTD5XmlSchemaHelper.common_dochead));
assertEquals(doi_val, am.getRaw(ElsevierMainDTD5XmlSchemaHelper.common_doi));
assertEquals("2014", am.getRaw(ElsevierMainDTD5XmlSchemaHelper.common_copyright));
}
/**
* Method that creates a simulated Cached URL from the source code provided by the goodContent
* String. It then asserts that the metadata extracted, by using the
* MetaPressRisMetadataExtractorFactory, match the metadata in the source code.
*
* @throws Exception
*/
public void testExtractAlternateRisContent() throws Exception {
String goodContent = createAlternateRisContent();
log.debug3(goodContent);
List<ArticleMetadata> mdlist = setupContentForAU(bau1, RIS_URL, goodContent, false);
assertNotEmpty(mdlist);
ArticleMetadata md = mdlist.get(0);
assertNotNull(md);
Iterator<String> actAuthIter = md.getList(MetadataField.FIELD_AUTHOR).iterator();
for (String expAuth : goodAuthors) {
assertEquals(expAuth, actAuthIter.next());
}
assertEquals(goodTitle, md.get(MetadataField.FIELD_ARTICLE_TITLE));
assertEquals(goodJournal, md.get(MetadataField.FIELD_PUBLICATION_TITLE));
assertEquals(goodDate, md.get(MetadataField.FIELD_DATE));
assertEquals(goodPublisher, md.get(MetadataField.FIELD_PUBLISHER));
}
/*
* The filename is the ProducID with either ".pdf" or ".epub" suffix.
* Tje content files live in a parallel directory
* <base>/<year>/Content/
* The XML file represented by the current cu would be something like:
* <base>/<year>/DataFeed/EBSCOhostGKB_20160205_DELTA.zip!/EBSCOhostGKB_20160205_DELTA.xml
* and the pdf would be
* <base>/<year>/Content/123456.pdf
*/
@Override
protected List<String> getFilenamesAssociatedWithRecord(
SourceXmlSchemaHelper helper, CachedUrl cu, ArticleMetadata oneAM) {
// this has been set to be the "ProductID" value
String filenameValue = oneAM.getRaw(helper.getFilenameXPathKey());
String cuBase = FilenameUtils.getFullPath(cu.getUrl());
int datafeed_dir_start = cuBase.lastIndexOf("/DataFeed/");
// This will leave the "/", so just add back on the sibling_dir and filename
String contentPath;
if (datafeed_dir_start < 0) {
// can't return null because that would make it okay to emit
// this will fail to emit, as it should - we don't know how to verify the PDF existence
log.siteWarning("The XML file lives at an unexpected location: " + cuBase);
contentPath = CONTENT_DIR; // invalid but will force failure
} else {
contentPath = cuBase.substring(0, datafeed_dir_start) + CONTENT_DIR;
}
List<String> returnList = new ArrayList<String>();
returnList.add(contentPath + filenameValue + ".pdf");
returnList.add(contentPath + filenameValue + ".epub");
return returnList;
}
/**
* Method that creates a simulated Cached URL from the source code provided by the goodContent
* String. It then asserts that the metadata extracted, by using the
* MetaPressRisMetadataExtractorFactory, match the metadata in the source code.
*
* @throws Exception
*/
public void testExtractGoodRisContent() throws Exception {
String goodContent = createGoodRisContent();
log.debug3(goodContent);
List<ArticleMetadata> mdlist = setupContentForAU(bau1, RIS_URL, goodContent, false);
assertNotEmpty(mdlist);
ArticleMetadata md = mdlist.get(0);
assertNotNull(md);
assertEquals(goodVolume, md.get(MetadataField.FIELD_VOLUME));
assertEquals(goodIssue, md.get(MetadataField.FIELD_ISSUE));
assertEquals(goodStartPage, md.get(MetadataField.FIELD_START_PAGE));
assertEquals(goodEndPage, md.get(MetadataField.FIELD_END_PAGE));
assertEquals(goodIssn, md.get(MetadataField.FIELD_ISSN));
Iterator<String> actAuthIter = md.getList(MetadataField.FIELD_AUTHOR).iterator();
for (String expAuth : goodAuthors) {
assertEquals(expAuth, actAuthIter.next());
}
assertEquals(goodTitle, md.get(MetadataField.FIELD_ARTICLE_TITLE));
assertEquals(goodJournal, md.get(MetadataField.FIELD_PUBLICATION_TITLE));
assertEquals(goodDate, md.get(MetadataField.FIELD_DATE));
assertEquals(goodPublisher, md.get(MetadataField.FIELD_PUBLISHER));
assertEquals(goodDOI, md.get(MetadataField.FIELD_DOI));
// This shouldn't get set. It will default later to fuill_text_cu
assertNotEquals(doiURL, md.get(MetadataField.FIELD_ACCESS_URL));
}
// override this to do some additional attempts to get valid data before emitting
@Override
public void extract(MetadataTarget target, CachedUrl cu, FileMetadataExtractor.Emitter emitter)
throws IOException, PluginException {
ArticleMetadata am = extract(target, cu);
/*
* if, due to overcrawl, we got to a page that didn't have anything
* valid, eg "this page not found" html page
* don't emit empty metadata (because defaults would get put in
* Must do this after cooking, because it checks size of cooked info
*/
if (am.isEmpty()) {
return;
}
/*
* RIS data can be variable. We don't have any way to add priority to
* the cooking of data, so fallback to alternate values manually
*
* There are differences between books and journals, so fork for titles
* and metadata check
*/
if (am.get(MetadataField.FIELD_DATE) == null) {
if (am.getRaw("Y1") != null) { // if DA wasn't there, use Y1
am.put(MetadataField.FIELD_DATE, am.getRaw("Y1"));
}
}
/*
* Determine if this is a book item or a journal item.
* set the appropriate article type once the daemon passes along the TY
*/
String ris_type = am.getRaw("TY");
if (ris_type == null) {
// pre 1.69, do an alternate check because TY wasn't passed through
ris_type = "JOUR"; // set a default
if (am.get(MetadataField.FIELD_ISBN) != null) {
// it is a bad value, but it was recognized as an isbn because of TY type
ris_type = "BOOK"; // it could be a chapter but until TY is passed through...
}
}
// Modify or try alternate RIS tag values based after cooking
postCookProcess(cu, am, ris_type);
// Only emit if this item is likely to be from this AU
// protect against counting overcrawled articles by checking against
// values from the TDB file - differentiate between book items and journal itesm
ArchivalUnit au = cu.getArchivalUnit();
if (ris_type.contains("BOOK") || ris_type.contains("CHAP")) {
if (!BaseAtyponMetadataUtil.metadataMatchesBookTdb(au, am)) {
return;
}
} else {
// JOURNAL default is to assume it's a journal for backwards compatibility
if (!BaseAtyponMetadataUtil.metadataMatchesTdb(au, am)) {
return;
}
}
/*
* Fill in DOI, publisher, other information available from
* the URL or TDB
* CORRECT the access.url if it is not in the AU
*/
BaseAtyponMetadataUtil.completeMetadata(cu, am);
emitter.emitMetadata(cu, am);
}
/*
* isolate the modifications done on the AM after the initial extraction
* in order to allow child plugins to do override this and do
* additional work before calling the pre-emit checking...
* ArticleMetadata - passed in information from extract/cook
* ris_type - the TY value or its inferred type (basically, book or journal)
*/
protected void postCookProcess(CachedUrl cu, ArticleMetadata am, String ris_type) {
/*
* RIS data can be variable. We don't have any way to add priority to
* the cooking of data, so fallback to alternate values manually
*/
if (am.get(MetadataField.FIELD_DATE) == null) {
if (am.getRaw("Y1") != null) { // if DA wasn't there, use Y1
am.put(MetadataField.FIELD_DATE, am.getRaw("Y1"));
}
}
/*
* There are differences between books and journals, so fork for titles
* and metadata check
*/
if (ris_type.contains("BOOK") || ris_type.contains("CHAP")) {
// BOOK in some form
// T1 is the primary title - of the chapter for a book chapter, or book for a complete book
// T2 is the next title up - of the book for a chapter, of the series for a book
// T3 is the uppermost - of the series for a chapter
// sometimes they use TI instead of T1...
if (am.get(MetadataField.FIELD_ARTICLE_TITLE) == null) {
if (am.getRaw("TI") != null) { // if T1 wasn't there, use TI
am.put(MetadataField.FIELD_ARTICLE_TITLE, am.getRaw("TI"));
}
}
if (ris_type.contains("CHAP")) {
// just one chapter - set the article type correctly
am.put(MetadataField.FIELD_ARTICLE_TYPE, MetadataField.ARTICLE_TYPE_BOOKCHAPTER);
if ((am.get(MetadataField.FIELD_PUBLICATION_TITLE) == null)
&& (am.getRaw("T2") != null)) {
// the publication and the article titles are just the name of the book
am.put(MetadataField.FIELD_PUBLICATION_TITLE, am.getRaw("T2"));
}
if ((am.get(MetadataField.FIELD_SERIES_TITLE) == null) && (am.getRaw("T3") != null)) {
// the publication and the article titles are just the name of the book
am.put(MetadataField.FIELD_SERIES_TITLE, am.getRaw("T3"));
}
} else {
// We're a full book volume - articletitle = publicationtitle
am.put(MetadataField.FIELD_ARTICLE_TYPE, MetadataField.ARTICLE_TYPE_BOOKVOLUME);
if (am.get(MetadataField.FIELD_PUBLICATION_TITLE) == null) {
// the publication and the article titles are just the name of the book
am.put(
MetadataField.FIELD_PUBLICATION_TITLE, am.get(MetadataField.FIELD_ARTICLE_TITLE));
}
// series title can be from T2
if ((am.get(MetadataField.FIELD_SERIES_TITLE) == null) && (am.getRaw("T2") != null)) {
// the publication and the article titles are just the name of the book
am.put(MetadataField.FIELD_SERIES_TITLE, am.getRaw("T2"));
}
}
} else {
// JOURNAL default is to assume it's a journal for backwards compatibility
if (am.get(MetadataField.FIELD_PUBLICATION_TITLE) == null) {
if (am.getRaw("T2") != null) {
am.put(MetadataField.FIELD_PUBLICATION_TITLE, am.getRaw("T2"));
} else if (am.getRaw("JO") != null) {
am.put(
MetadataField.FIELD_PUBLICATION_TITLE,
am.getRaw("JO")); // might be unabbreviated version
}
}
}
}
/*
* When testing a complete extraction out of the tarset, the MD record will be completely filled in
* and pdf-existence will get established
*/
private void validateCompleteMetadataRecord(ArticleMetadata am) {
log.debug3("valideCompleteMetadatRecord");
String doi_val = am.get(MetadataField.FIELD_DOI);
/* make sure we can pick up both types of xml article data */
log.debug3("doi val is: " + doi_val);
if ("JA 5.2.0 SIMPLE-ARTICLE"
.equals(am.getRaw(ElsevierDatasetXmlSchemaHelper.dataset_dtd_metadata))) {
log.debug3("simple-article");
assertEquals(common_simple_article_title, am.get(MetadataField.FIELD_ARTICLE_TITLE));
} else {
assertEquals(common_article_title, am.get(MetadataField.FIELD_ARTICLE_TITLE));
}
assertEquals(common_issn, am.get(MetadataField.FIELD_ISSN));
assertEquals(authorMap.get(doi_val), am.getList(MetadataField.FIELD_AUTHOR));
assertEquals(dateMap.get(doi_val), am.get(MetadataField.FIELD_DATE));
assertEquals(accessUrlMap.get(doi_val), am.get(MetadataField.FIELD_ACCESS_URL));
assertEquals(volMap.get(doi_val), am.get(MetadataField.FIELD_VOLUME));
assertEquals(issueMap.get(doi_val), am.get(MetadataField.FIELD_ISSUE));
assertEquals(pubTitleMap.get(doi_val), am.get(MetadataField.FIELD_PUBLICATION_TITLE));
assertEquals("Elsevier", am.get(MetadataField.FIELD_PROVIDER));
assertEquals("Elsevier", am.get(MetadataField.FIELD_PUBLISHER));
log.debug3(am.ppString(2));
}