Errors in the startup logs

[yfarjoun]

Hello,

Thanks for setting up your popular imputation server as a docker image! it's a great service and it's good to be able to use it in settings that require complete "privacy" for leagal reasons.

As I have been trying out the image, I ran it in non-daemon mode (i.e. without -d) and saw that the startup logs contains some errors and warnings. I wanted to be sure that they are OK:

org.h2.jdbc.JdbcSQLSyntaxErrorException: Syntax error in SQL statement "
            

ALTER TABLE DOWNLOADS MODIFY[*] PARAMETER_ID INTEGER;
CREATE INDEX IDX_DOWNLOADS_PARAMETER_ID ON DOWNLOADS(PARAMETER_ID);
CREATE INDEX IDX_PARAMETER_JOB_ID ON PARAMETER(JOB_ID,INPUT);
CREATE INDEX IDX_STEPS_JOB_ID ON STEPS(JOB_ID);
CREATE INDEX IDX_LOG_MESSAGES_STEP_ID ON LOG_MESSAGES(STEP_ID);
CREATE INDEX IDX_JOB_USER_ID ON JOB(USER_ID,STATE);
"; expected "., ADD, SET, RENAME, DROP, ALTER"; SQL statement:

-- 2.0.0-rc3

alter table downloads modify parameter_id INTEGER;
create index idx_downloads_parameter_id on downloads(parameter_id);
create index idx_parameter_job_id on parameter(job_id,input);
create index idx_steps_job_id on steps(job_id);
create index idx_log_messages_step_id on log_messages(step_id);
create index idx_job_user_id on job(user_id,state);
 [42001-200]
	at org.h2.message.DbException.getJdbcSQLException(DbException.java:453)
	at org.h2.message.DbException.getJdbcSQLException(DbException.java:429)
	at org.h2.message.DbException.getSyntaxError(DbException.java:243)
	at org.h2.command.Parser.getSyntaxError(Parser.java:1053)
	at org.h2.command.Parser.parseAlterTable(Parser.java:7705)
	at org.h2.command.Parser.parseAlter(Parser.java:6983)
	at org.h2.command.Parser.parsePrepared(Parser.java:887)
	at org.h2.command.Parser.parse(Parser.java:843)
	at org.h2.command.Parser.parse(Parser.java:819)
	at org.h2.command.Parser.prepareCommand(Parser.java:738)
	at org.h2.engine.Session.prepareLocal(Session.java:657)
	at org.h2.engine.Session.prepareCommand(Session.java:595)
	at org.h2.jdbc.JdbcConnection.prepareCommand(JdbcConnection.java:1235)
	at org.h2.jdbc.JdbcPreparedStatement.<init>(JdbcPreparedStatement.java:76)
	at org.h2.jdbc.JdbcConnection.prepareStatement(JdbcConnection.java:352)
	at org.apache.commons.dbcp.DelegatingConnection.prepareStatement(DelegatingConnection.java:281)
	at org.apache.commons.dbcp.PoolingDataSource$PoolGuardConnectionWrapper.prepareStatement(PoolingDataSource.java:313)
	at genepi.db.DatabaseUpdater.executeSQLFile(DatabaseUpdater.java:308)
	at genepi.db.DatabaseUpdater.readAndPrepareSqlClasspath(DatabaseUpdater.java:268)
	at genepi.db.DatabaseUpdater.update(DatabaseUpdater.java:132)
	at genepi.db.DatabaseUpdater.updateDB(DatabaseUpdater.java:98)
	at cloudgene.mapred.Main.runCloudgene(Main.java:165)
	at cloudgene.mapred.cli.StartServer.run(StartServer.java:51)
	at genepi.base.Tool.start(Tool.java:197)
	at genepi.base.Toolbox.start(Toolbox.java:44)
	at cloudgene.mapred.CommandLineInterface.main(CommandLineInterface.java:65)