Ejemplo n.º 1
0
  /** {@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()]);
  }
Ejemplo n.º 2
0
  /** {@inheritDoc} */
  @Override
  public Evidence[] mapFromTable(CyEdge edge, CyTable table) {
    if (edge == null) throw new NullPointerException("edge cannot be null");
    if (table == null) throw new NullPointerException("table cannot be null");

    Set<String> nonAnnotationColumns =
        new HashSet<String>(
            asList(
                CyNetwork.SUID,
                NETWORK_SUID,
                NETWORK_NAME,
                EDGE_SUID,
                BEL_STATEMENT,
                SUMMARY_TEXT,
                CITATION_ID,
                CITATION_NAME,
                CITATION_TYPE,
                SPECIES));

    Collection<CyRow> evidenceRows = table.getMatchingRows(EDGE_SUID, edge.getSUID());
    List<Evidence> evidences = new ArrayList<Evidence>(evidenceRows.size());
    if (!evidenceRows.isEmpty()) {
      for (CyRow evRow : evidenceRows) {
        Evidence e = new Evidence();
        e.belStatement = evRow.get(BEL_STATEMENT, String.class);
        e.summaryText = evRow.get(SUMMARY_TEXT, String.class);
        e.citation = new Citation();
        e.citation.id = evRow.get(CITATION_ID, String.class);
        e.citation.name = evRow.get(CITATION_NAME, String.class);
        e.citation.type = evRow.get(CITATION_TYPE, String.class);
        e.biologicalContext = new BiologicalContext();
        e.biologicalContext.speciesCommonName = evRow.get(SPECIES, String.class);
        e.biologicalContext.variedAnnotations = new HashMap<String, Object>();
        for (Entry<String, Object> columnValue : evRow.getAllValues().entrySet()) {
          if (nonAnnotationColumns.contains(columnValue.getKey())) continue;
          e.biologicalContext.variedAnnotations.put(columnValue.getKey(), columnValue.getValue());
        }
        evidences.add(e);
      }
    }

    return evidences.toArray(new Evidence[evidences.size()]);
  }