public int typeId(String cvName, String cvTermName) {
Integer result = idByCvNameAndTermName.get(cvName, cvTermName);
if (result == null)
throw new IllegalArgumentException(
String.format("Term '%s' not found in CV '%s'", cvTermName, cvName));
return result;
}
/**
* Fetch a synonym from the local cache. Failing that, create a new one.
*
* @param synonymType the synonym type (should be a term in the <code>genedb_synonym_type</code>
* CV).
* @param synonymString the actual synonym
* @return the cached or newly-created synonym object
*/
public synchronized Synonym getSynonym(String synonymType, String synonymString) {
logger.debug(String.format("Looking for synonym '%s:%s'", synonymType, synonymString));
if (session == null) {
throw new IllegalStateException("getSynonym called with no session");
}
if (synonymsByType.containsKey(synonymType, synonymString)) {
logger.debug("Synonym found in cache");
return synonymsByType.get(synonymType, synonymString);
}
if (detachedSynonymsByType.containsKey(synonymType, synonymString)) {
logger.debug("Synonym found in detached cache. Merging");
Synonym mergedSynonym =
(Synonym) session.merge(detachedSynonymsByType.get(synonymType, synonymString));
detachedSynonymsByType.remove(synonymType, synonymString);
synonymsByType.put(synonymType, synonymString, mergedSynonym);
return mergedSynonym;
}
logger.debug(String.format("Synonym '%s:%s' not found in cache", synonymType, synonymString));
CvTerm synonymTypeCvTerm =
(CvTerm)
session.load(
CvTerm.class,
objectManager.getIdOfExistingCvTerm("genedb_synonym_type", synonymType));
Synonym synonym = new Synonym(synonymTypeCvTerm, synonymString, synonymString);
synonymsByType.put(synonymType, synonymString, synonym);
return synonym;
}
public TypeCodes(Connection conn) throws SQLException {
PreparedStatement st =
conn.prepareStatement(
"select cvterm_id"
+ " , cv.name as cv_name"
+ " , cvterm.name as cvterm_name"
+ " from cvterm"
+ " join cv using (cv_id)"
+ " join ("
+ " select distinct type_id as cvterm_id from feature"
+ " union"
+ " select distinct type_id as cvterm_id from organismprop"
+ " union"
+ " select distinct type_id as cvterm_id from featureprop"
+ ") feature_types using (cvterm_id)");
try {
ResultSet rs = st.executeQuery();
logger.trace("Loading CV terms from database");
while (rs.next()) {
int cvTermId = rs.getInt("cvterm_id");
String cvName = rs.getString("cv_name");
String cvTermName = rs.getString("cvterm_name");
idByCvNameAndTermName.put(cvName, cvTermName, cvTermId);
cvNameById.put(cvTermId, cvName);
termNameById.put(cvTermId, cvTermName);
}
logger.trace("CV terms loaded");
} finally {
try {
st.close();
} catch (SQLException e) {
System.err.println("SQLException from close(), probably caused by a previous exception");
e.printStackTrace(System.err);
}
}
}