public static String getCitationString(Citable citable, String prepend, String postpend) {
List<Citation> citations = citable.getCitations();
if (citations == null || citations.size() == 0) {
return null;
}
StringBuilder builder = new StringBuilder();
for (Citation citation : citations) {
builder.append(prepend);
builder.append(citation.toString());
builder.append(postpend);
}
return builder.toString();
}
/** {@inheritDoc} */
@Override
public Evidence[] mapEdgeToEvidence(Graph graph, Edge edge) {
if (graph == null) throw new NullPointerException("graph cannot be null");
if (edge == null) throw new NullPointerException("edge cannot be null");
if (edge.metadata == null) return new Evidence[0];
Object evidences = edge.metadata.get("evidences");
if (evidences == null || !(evidences instanceof List)) return new Evidence[0];
List<Map> evidenceMap = typedList(((List) evidences), Map.class);
List<Evidence> evidenceList = new ArrayList<Evidence>();
for (Map item : evidenceMap) {
@SuppressWarnings("unchecked")
Map<String, Object> evMap = (Map<String, Object>) item;
Evidence ev = new Evidence();
ev.belStatement = getOrEmptyString("bel_statement", evMap).replace("\\\"", "\"");
ev.summaryText = getOrEmptyString("summary_text", evMap);
Citation citation = new Citation();
@SuppressWarnings("unchecked")
Map<String, Object> citationMap = (Map<String, Object>) evMap.get("citation");
if (citationMap != null) {
citation.id = getOrEmptyString("id", citationMap);
citation.type = getOrEmptyString("type", citationMap);
citation.name = getOrEmptyString("name", citationMap);
}
ev.citation = citation;
BiologicalContext context = new BiologicalContext();
@SuppressWarnings("unchecked")
Map<String, Object> contextMap = (Map<String, Object>) evMap.get("biological_context");
if (contextMap != null) {
context.speciesCommonName = getOrEmptyString("species_common_name", contextMap);
context.ncbiTaxId = getOrZero("ncbi_tax_id", contextMap);
Set<String> varying = new HashSet<String>(contextMap.keySet());
varying.removeAll(asList("species_common_name", "ncbi_tax_id"));
for (String key : varying) {
context.variedAnnotations.put(key, contextMap.get(key));
}
ev.biologicalContext = context;
}
evidenceList.add(ev);
}
return evidenceList.toArray(new Evidence[evidenceList.size()]);
}
public GbifRacine parse(Element element, EmlData data) {
this.setDateStamp(element.getChildText("dateStamp"));
this.setHierarchyLevel(element.getChildText("hierarchyLevel"));
citation = new Citation();
this.setCitation(citation.parse(element.getChild("citation"), this));
if (element.getChild("bibliography") != null) {
bibliography = new ArrayList<Biblio>();
List<Element> bibliographyElement = element.getChild("bibliography").getChildren("citation");
for (int i = 0; i < bibliographyElement.size(); i++) {
Biblio cit = new Biblio();
this.addBibliography(cit.parse(bibliographyElement.get(i), this));
}
}
physicals = new ArrayList<Physical>();
List<Element> physicalsElement = element.getChildren("physical");
for (int i = 0; i < physicalsElement.size(); i++) {
Physical phys = new Physical();
this.addPhysical(phys.parse(physicalsElement.get(i), this));
}
this.setResourceLogoUrl(element.getChildText("resourceLogoUrl"));
collection = new GbifCollection();
this.setCollection(collection.parse(element.getChild("collection"), this));
this.setFormationPeriod(element.getChildText("formationPeriod"));
this.setSpecimenPreservationMethod(element.getChildText("specimenPreservationMethod"));
this.setLivingTimePeriod(element.getChildText("livingTimePeriod"));
jgtiCuratorialUnits = new ArrayList<JgtiCuratorialUnit>();
List<Element> jgtiElement = element.getChildren("jgtiCuratorialUnit");
for (int i = 0; i < jgtiElement.size(); i++) {
JgtiCuratorialUnit jgti = new JgtiCuratorialUnit();
this.addJgtiCuratorialUnits(jgti.parse(jgtiElement.get(i), this));
}
this.setEmlData(data);
return this;
}
