/**
* {@inheritDoc}
*
* @return
*/
@Override
public ReturnValue clean_up() {
try {
writer.flush();
writer.close();
if (options.has("stdout")) {
Log.stdout(writer.toString());
}
} catch (IOException ex) {
Log.error("Writer is already closed.", ex);
}
return ret;
}
/**
* {@inheritDoc}
*
* @return
*/
@Override
public ReturnValue do_run() {
ReturnValue ret = new ReturnValue();
ResultSet rs = null;
MetadataDB mdb = null;
PreparedStatement prepareStatement = null;
try {
String query =
new StringBuilder()
.append(
"select w.sw_accession, w.workflow_run_id, w.status, f.* FROM workflow_run w LEFT OUTER JOIN workflow_run_input_files f ")
.append(
"ON w.workflow_run_id = f.workflow_run_id WHERE (status = 'completed' OR status= 'failed') AND ")
.append("f.workflow_run_id IS NULL ORDER BY w.sw_accession;")
.toString();
Log.info("Executing query: " + query);
mdb = DBAccess.get();
List<int[]> ids =
mdb.executeQuery(
query,
new ResultSetHandler<List<int[]>>() {
@Override
public List<int[]> handle(ResultSet rs) throws SQLException {
List<int[]> ids = new ArrayList<>();
while (rs.next()) {
ids.add(new int[] {rs.getInt("sw_accession"), rs.getInt("workflow_run_id")});
}
return ids;
}
});
mdb.getDb().setAutoCommit(false);
prepareStatement =
mdb.getDb()
.prepareStatement(
"INSERT INTO workflow_run_input_files (workflow_run_id, file_id) VALUES(?,?)");
for (int[] i : ids) {
int workflowSWID = i[0];
int workflowRunID = i[1];
Log.stdout("Working on workflow_run " + workflowSWID);
// populate input files
List<Integer> listOfFiles = this.getListOfFiles(workflowSWID);
Log.stdout("Found " + listOfFiles.size() + " input files for workflow_run " + workflowSWID);
// insert into new workflow_run_input_files table
for (Integer fSWID : listOfFiles) {
Integer fileID = this.metadata.getFile(fSWID).getFileId();
prepareStatement.setInt(1, workflowRunID);
prepareStatement.setInt(2, fileID);
prepareStatement.executeUpdate();
}
}
Log.stdout("Success!");
mdb.getDb().commit();
return ret;
} catch (SQLException ex) {
Log.fatal("Population failed, aborting.");
Logger.getLogger(WorkflowRunFilesInitialPopulationPlugin.class.getName())
.log(Level.SEVERE, null, ex);
ret.setExitStatus(ReturnValue.FAILURE);
} finally {
if (mdb != null) {
DbUtils.closeQuietly(mdb.getDb(), mdb.getSql(), rs);
}
DBAccess.close();
DbUtils.closeQuietly(prepareStatement);
}
ret.setExitStatus(ReturnValue.FAILURE);
return ret;
}
