Examples with BibliographicReferenceService ubic.gemma.core.annotation.reference.BibliographicReferenceService used on opensource projects

Example 1 with BibliographicReferenceService

use of ubic.gemma.core.annotation.reference.BibliographicReferenceService in project Gemma by PavlidisLab.

the class BibRefUpdaterCli method doWork.

@Override
protected Exception doWork(String[] args) {
    Exception ex = super.processCommandLine(args);
    if (ex != null)
        return ex;
    BibliographicReferenceService bibliographicReferenceService = this.getBean(BibliographicReferenceService.class);
    Collection<Long> bibrefIds = new ArrayList<>();
    if (this.hasOption("pmids")) {
        for (String s : StringUtils.split(this.getOptionValue("pmids"), ",")) {
            BibliographicReference found = bibliographicReferenceService.findByExternalId(s);
            if (found == null) {
                log.warn("Did not find " + s);
                continue;
            }
            bibrefIds.add(found.getId());
        }
    } else {
        log.info("Updating all bibrefs in the system ...");
        bibrefIds = bibliographicReferenceService.listAll();
    }
    log.info("There are " + bibrefIds.size() + " to update");
    for (Long id : bibrefIds) {
        BibliographicReference bibref = bibliographicReferenceService.load(id);
        if (bibref == null) {
            log.info("No reference with id=" + id);
            continue;
        }
        bibref = bibliographicReferenceService.thaw(bibref);
        try {
            BibliographicReference updated = bibliographicReferenceService.refresh(bibref.getPubAccession().getAccession());
            log.info(updated);
        } catch (Exception e) {
            log.info("Failed to update: " + bibref + " (" + e.getMessage() + ")");
        }
        try {
            Thread.sleep(RandomUtils.nextInt(1000));
        } catch (InterruptedException e) {
            return e;
        }
    }
    return null;
}