public Collection<EntityMetaData> loadOMX(RepositoryCollection omx) {
// extract attribute metadata
Map<String, AttributeMetaData> attributes = new LinkedHashMap<String, AttributeMetaData>();
for (Entity e : omx.getRepositoryByEntityName("observablefeature")) {
logger.debug("found observablefeature: " + e);
DefaultAttributeMetaData att = new DefaultAttributeMetaData(e.getString("name"));
if (e.get("dataType") != null)
att.setDataType(MolgenisFieldTypes.getType(e.getString("dataType")));
attributes.put(e.getString("identifier"), att);
if (e.get("description") != null) att.setDescription(e.getString("description"));
// TODO unit! if(e.get("unit") != null)
if ("xref".equals(e.get("dataType")) || "mref".equals(e.get("dataType"))) {
// TODO: cannot solve!!!
att.setRefEntity(omxEntities.get("Characteristic"));
}
if ("categorical".equals(e.get("dataType"))) {
att.setRefEntity(omxEntities.get("Category"));
}
}
// TODO: fix categorical!
// extract protocols as entities(abstract=true)
Map<String, EntityMetaData> entities = new LinkedHashMap<String, EntityMetaData>();
for (Entity e : omx.getRepositoryByEntityName("protocol")) {
// skip all null entities
if (hasValues(e)) {
logger.debug("found protocol: " + e);
DefaultEntityMetaData ent = new DefaultEntityMetaData(e.getString("identifier")); // alas
ent.setLabel(e.getString("name"));
ent.setAbstract(true);
// add attributes
if (e.get("features_identifier") != null)
for (String attIdentifier : e.getList("features_identifier")) {
if (attributes.get(attIdentifier) == null)
throw new RuntimeException("attribute '" + attIdentifier + "' unknown");
ent.addAttributeMetaData(attributes.get(attIdentifier));
}
entities.put(e.getString("identifier"), ent);
}
}
for (Entity e : omx.getRepositoryByEntityName("protocol")) {
// add subprotocols as compound
if (e.get("subprotocols_identifier") != null) {
for (String subProtocol : e.getList("subprotocols_identifier")) {
DefaultAttributeMetaData att = new DefaultAttributeMetaData(subProtocol);
att.setDataType(MolgenisFieldTypes.COMPOUND);
att.setRefEntity(entities.get(subProtocol));
((DefaultEntityMetaData) entities.get(e.get("identifier"))).addAttributeMetaData(att);
}
}
}
// create dataset as entities
for (Entity e : omx.getRepositoryByEntityName("dataset")) {
logger.debug("found dataset: " + e);
DefaultEntityMetaData ent = new DefaultEntityMetaData(e.getString("identifier"));
ent.setLabel(e.getString("name"));
// dataset 'extends' protocol
ent.setExtends(entities.get(e.getString("protocolused_identifier")));
entities.put(e.getString("identifier"), ent);
}
return entities.values();
}
