if(!(pro.getRDFId().startsWith("urn:miriam:") || pro.getRDFId().startsWith("http://identifiers.org/")) && pro.getName().isEmpty()) { if(log.isInfoEnabled()) log.info("Skipping: cannot normalize Provenance: " + pro.getRDFId()); if(pro.getRDFId().startsWith("urn:miriam:") || pro.getRDFId().startsWith("http://identifiers.org/")) { key = pro.getRDFId(); } else if (pro.getStandardName() != null) { key = pro.getStandardName(); } else { key = pro.getDisplayName(); // can be null try { names.addAll(Arrays.asList(MiriamLink.getNames(key))); pro.setStandardName(MiriamLink.getName(key)); String description = MiriamLink.getDataTypeDef(pro.getStandardName()); pro.addComment(description); } catch (IllegalArgumentException e) { for (String name : pro.getName()) { try { names.addAll(Arrays.asList(MiriamLink.getNames(name))); pro.setStandardName(MiriamLink .getName(names.iterator().next())); pro.addName(name);
Collection<Provenance> datasources = ((Entity)bpe).getDataSource(); for(Provenance pr : datasources) { if(pr.getComment() != null) sb.append(pr.getComment().toString()); sb.append(" : ").append(getNodeName(pr)).append(' ');
public void check(Provenance p, boolean fix) { // check standardName or displayName is valid String db = null; if(p.getStandardName() != null) db = xrefHelper.getPrimaryDbName(p.getStandardName()); if (db == null) { // was null or unknown name; try displayName - if(p.getDisplayName() != null) { db = xrefHelper.getPrimaryDbName(p.getDisplayName()); if (db == null) { error(p, "unknown.db", false, p.getDisplayName() + " or " + p.getStandardName()); } } else { error(p, "cardinality.violated", false, "standardName or displayName", 1); } } // check unif.xrefs for (Xref x : p.getXref()) { if (x instanceof UnificationXref) { error(x, "not.allowed.xref", false, x.getDb(), p, "Provenance", "- Miriam or PubMed but not a bioentities db!"); /* if(fix) { p.removeXref(x); } */ } } }
pro.setDisplayName(name); pro.addXref(px); pro.addXref(ux); pro.addComment(attr.toString()); pro.addComment("Release Date: " + ver);
sources.addAll(provenance.getName());
@Deprecated //does not worth it (Miriam cannot help with all DBs) private void normalizeProvenance(Model model) { // process the rest of utility classes (selectively though) for(Provenance pro : model.getObjects(Provenance.class)) { autoName(pro); // throws IAE (from MiriamLink) normalizeID(model, pro, pro.getStandardName(), null); } // replace/update elements in the model doSubs(model); }
sources.addAll(provenance.getName());