@Override public void process(JCas jCas) throws AnalysisEngineProcessException { int pmId = getHeaderIntDocId(jCas); try { if (PubmedArticleEntity.findFirst(PUBMED_ID + " = ?", pmId) == null) { PubmedArticleEntity a = new PubmedArticleEntity(); a.set(PUBMED_ID, pmId); a.set(ABSTRACT, jCas.getDocumentText()); try { Date date = JCasUtil.selectSingle(jCas, Date.class); a.set(PUBLISHED_DATE, date.getYear() + "-" + date.getMonth() + "-" + date.getDay()); } catch (Exception e) {// nope LOG.warn("could not add date to " + pmId, e); } a.set(TITLE, StringUtils.snippetizeAtSpace(getTitle(jCas), 510)); a.saveIt(); inserted++; if (processed++ % 10000 == 0) LOG.debug("processed {}\tinserted {}", processed, inserted); } } catch (Exception e) { LOG.error("could not insert " + pmId, e); } }