Examples with MalformedDOIException org.globalbioticinteractions.doi.MalformedDOIException used on opensource projects

Example 6 with MalformedDOIException

use of org.globalbioticinteractions.doi.MalformedDOIException in project eol-globi-data by jhpoelen.

the class CitationUtil method getDOI.

public static DOI getDOI(Dataset dataset) {
    String doi = dataset.getOrDefault("doi", "");
    DOI doiObj = null;
    URI archiveURI = dataset.getArchiveURI();
    if (StringUtils.isBlank(doi)) {
        String recordZenodo = StringUtils.replace(archiveURI.toString(), ZENODO_URL_PREFIX, "");
        String[] split = recordZenodo.split("/");
        if (split.length > 0) {
            doiObj = new DOI("5281", "zenodo." + split[0]);
        }
    }
    try {
        doiObj = doiObj == null ? DOI.create(doi) : doiObj;
    } catch (MalformedDOIException e) {
        LOG.warn("found malformed doi [" + doi + "]", e);
    }
    return doiObj;
}

Example 7 with MalformedDOIException

use of org.globalbioticinteractions.doi.MalformedDOIException in project eol-globi-data by jhpoelen.

the class DOIResolverImpl method requestLinks.

private Map<String, DOI> requestLinks(Collection<String> references) throws IOException {
    Map<String, DOI> doiMap = new TreeMap<>();
    for (String reference : references) {
        try {
            URIBuilder builder = new URIBuilder(baseURL + "/works");
            builder.addParameter("sort", "score");
            builder.addParameter("order", "desc");
            builder.addParameter("rows", "1");
            builder.addParameter("select", "DOI,score");
            builder.addParameter("query.bibliographic", reference);
            HttpGet get = new HttpGet(builder.build());
            get.setHeader("Content-Type", "application/json");
            doiMap.put(reference, getMostRelevantDOIMatch(get));
        } catch (URISyntaxException e) {
            LOG.warn("unexpected malformed URI on resolving crossref dois", e);
        } catch (MalformedDOIException e) {
            LOG.warn("received malformed doi from cross ref", e);
        }
    }
    return doiMap;
}

Example 8 with MalformedDOIException

use of org.globalbioticinteractions.doi.MalformedDOIException in project eol-globi-data by jhpoelen.

the class DOIResolverCache method init.

public void init(final Reader reader) throws PropertyEnricherException, IOException {
    DB db = initDb("doiCache");
    StopWatch watch = new StopWatch();
    watch.start();
    final CSVParse parser = CSVTSVUtil.createTSVParser(reader);
    if (db.exists("doiCache")) {
        LOG.info("reusing existing doi cache...");
    } else {
        LOG.info("doi cache building...");
        doiCitationMap = db.createTreeMap("doiCache").pumpPresort(300000).pumpIgnoreDuplicates().pumpSource(new Iterator<Fun.Tuple2<String, DOI>>() {

            private String[] line = null;

            final AtomicBoolean nextLineParsed = new AtomicBoolean(false);

            String getCitation(String[] line) {
                return line != null && line.length > 1 ? line[1] : null;
            }

            DOI getDOI(String[] line) {
                String doiString = line[0];
                try {
                    return StringUtils.isBlank(doiString) ? null : DOI.create(doiString);
                } catch (MalformedDOIException e) {
                    LOG.warn("skipping malformed doi [" + doiString + "]", e);
                    return null;
                }
            }

            @Override
            public boolean hasNext() {
                try {
                    while (!nextLineParsed.get()) {
                        line = parser.getLine();
                        if (line == null) {
                            break;
                        }
                        nextLineParsed.set(getDOI(line) != null && StringUtils.isNotBlank(getCitation(line)));
                    }
                    return line != null && nextLineParsed.get();
                } catch (IOException e) {
                    LOG.error("problem reading", e);
                    return false;
                }
            }

            @Override
            public Fun.Tuple2<String, DOI> next() {
                String citationString = StringUtils.defaultString(getCitation(line), "");
                DOI doi = getDOI(line);
                nextLineParsed.set(false);
                return new Fun.Tuple2<>(citationString, doi);
            }
        }).make();
        db.commit();
        watch.stop();
        LOG.info("doi cache built in [" + watch.getTime(TimeUnit.SECONDS) + "] s.");
    }
}

Example 9 with MalformedDOIException

use of org.globalbioticinteractions.doi.MalformedDOIException in project eol-globi-data by jhpoelen.

the class DatasetImporterForPensoft method findCitation.

private static String findCitation(SparqlClient openBiodivClient, String bindStatement) throws IOException {
    String sparql = "PREFIX fabio: <http://purl.org/spar/fabio/>\n" + "PREFIX prism: <http://prismstandard.org/namespaces/basic/2.0/>\n" + "PREFIX doco: <http://purl.org/spar/doco/>\n" + "PREFIX dc: <http://purl.org/dc/elements/1.1/>\n" + "SELECT " + "   ?article " + "   ?title " + "   ?doi " + "   (group_concat(distinct ?authorName; separator=\", \") as ?authorsList)  " + "   ( REPLACE(str(?pubDate), \"(\\\\d*)-.*\", \"$1\") as ?pubYear) " + "   ?journalName " + "WHERE { \n" + bindStatement + "    ?article a fabio:JournalArticle.\n" + "    ?article prism:doi ?doi.\n" + "    ?article dc:title ?title.\n" + "    ?article prism:publicationDate ?pubDate.\n" + "    ?article <http://purl.org/vocab/frbr/core#realizationOf> ?paper.\n" + "    ?paper dc:creator ?author.\n" + "    ?journal <http://purl.org/vocab/frbr/core#part> ?article.\n" + "    ?journal a fabio:Journal.\n" + "    ?journal <http://www.w3.org/2004/02/skos/core#prefLabel> ?journalName.\n" + "    ?author <http://www.w3.org/2000/01/rdf-schema#label> ?authorName.\n" + "}   GROUP BY ?article ?title ?doi ?pubDate ?journalName \n" + " LIMIT 1";
    try {
        String citation = null;
        final LabeledCSVParser parser = openBiodivClient.query(sparql);
        parser.getLine();
        String doi = parser.getValueByLabel("doi");
        if (StringUtils.isNotBlank(doi)) {
            final String doiURIString = DOI.create(doi).toURI().toString();
            citation = StringUtils.join(Arrays.asList(parser.getValueByLabel("authorsList"), parser.getValueByLabel("pubYear"), parser.getValueByLabel("title"), parser.getValueByLabel("journalName"), doiURIString), ". ");
        }
        return citation;
    } catch (MalformedDOIException e) {
        throw new IOException("marlformed uri", e);
    }
}