/**
* get.
*
* @return a {@link net.sourceforge.seqware.common.metadata.MetadataDB} object.
*/
public static synchronized MetadataDB get() {
try {
if (metadataDBWrapper.get() != null
&& ((metadataDBWrapper.get().getDb() != null
&& metadataDBWrapper.get().getDb().isClosed())))
// || db.getSql()!=null && db.getSql().isClosed()))
{
metadataDBWrapper.get().clean_up();
metadataDBWrapper.set(null);
// db = null;
}
} catch (SQLException ex) {
Log.error("Closing DB connection and creating a new one failed", ex);
}
if (metadataDBWrapper.get() == null) {
metadataDBWrapper.set(new MetadataDB());
// Log.debug("DBAccess is using " + user + " " + pass + " on " + connection);
DataSource ds = null;
try {
InitialContext initCtx = new InitialContext();
ds = (DataSource) initCtx.lookup("java:comp/env/jdbc/SeqWareMetaDB");
} catch (NamingException ex) {
Log.fatal(ex);
ex.printStackTrace();
}
if (ds != null) {
Log.debug("init via db.init(ds), datasource is " + ds.getClass());
metadataDBWrapper.get().init(ds);
} else {
Log.debug("init via init(user,pass,connection)");
Map<String, String> settings = null;
try {
settings = ConfigTools.getSettings();
String connection =
"jdbc:postgresql://" + settings.get("SW_DB_SERVER") + "/" + settings.get("SW_DB");
String user = settings.get("SW_DB_USER");
String pass = settings.get("SW_DB_PASS");
Log.debug("DBAccess is using " + user + " " + pass + " on " + connection);
metadataDBWrapper.get().init(connection, user, pass);
} catch (Exception ex) {
Log.fatal("get() could not init ", ex);
Logger.getLogger(DBAccess.class.getName()).log(Level.SEVERE, null, ex);
}
}
}
Log.debug(metadataDBWrapper.get().toString() + " was returned ");
return metadataDBWrapper.get();
}
/** close. */
public static synchronized void close() {
if (metadataDBWrapper.get() != null) {
Log.debug(metadataDBWrapper.get().toString() + " was closed ");
metadataDBWrapper.get().clean_up();
metadataDBWrapper.set(null);
// db = null;
}
}
/**
* Given a workflowRunAcc returns a list of file paths that were used in that run using
* effectively, the workflow run reporter.
*
* <p>Hopefully, this is the last we'll use this approach!
*
* @param workflowRunAcc
* @param filesToRun
* @return
*/
private List<Integer> getListOfFiles(int workflowRunAcc) {
Map<String, String> map = generateWorkflowRunMap(workflowRunAcc);
List<Integer> ranOnList = new ArrayList<>();
if (map.isEmpty()) {
return ranOnList;
}
String ranOnString = map.get("Immediate Input File SWIDs");
if (ranOnString == null) {
return ranOnList;
}
String[] ranOnArr = ranOnString.split(",");
if (ranOnString.isEmpty()) {
return ranOnList;
}
for (String i : ranOnArr) {
ranOnList.add(Integer.valueOf(i.trim()));
Log.trace("Adding item: " + i);
}
Log.debug("Got list of files: " + StringUtils.join(ranOnList, ','));
return ranOnList;
}
