Nicklas Nordborg wrote: > Pawel Sztromwasser wrote: > > >>>> The second thing is transferring wizzzards. In our Base1 database those >>>> with /formatType=reportermap/, have column and row numbers in /mapping/ >>>> property proceeded by /_r_x /and/ _r_y/ respectively, not by /numCol/ >>>> and /numRow/ as WizzzardTransfer class expects. That causes the >>>> ReporterMapImporter plugin configuration to fail. I don't know if the >>>> mapping format has changed, but if the old one is still in use, the >>>> migration could support it. >>>> >>>> >>> BASE 2 supports the same mappings as BASE 1 (and some more). I think it >>> should be backwards slashes, eg. \_r_x\, etc. I am not sure what you >>> mean with that the WizzzardTransfer expects \numCol\. The migration >>> doesn't care about the mapping expressions. It should transfer them >>> exactly as they are. Please post any error messages/stack traces, etc. >>> >>> >>> >>> >> I am sorry, the backslashes were added by Thunderbird when changing from >> italic to text format. >> The wizzard transfer works like this (when comes to mapping): >> 1) it parses mapping string from Base1 database using regular expression >> looking for (key:value) pairs separated by comma (example part of a >> mapping string: >> _r_block:1,_r_x:\"Column"\,_r_y:\"Row"\,reporterId:\"Probe_ID"\, ...) >> 2) it puts the (key,value) pairs into HashMap >> 3) and uses this map when configuring import plugin. When getting those >> values, it looks for certain keys ('numCol' and 'numRow' are among them, >> explicitly coded around lines 130 and 140 in WizzzardTransfer.java). >> When there is no value in HashMap it returns null, so null is passed to >> plugin configuration. Then it complains: >> > > Hmm... it seems like the code transfering 'reportermap' file formats is > not correctly coded. It doesn't look for any coordinates mappings at > all. The 'numCol' and 'numRow' you are referring to are part of the > 'result' file formats, not 'reportermap' file formats. > > Good point. I missed that IF checking for formatType. Are you planning to fix that in 2.5?
> On the good side is that this doesn't stop the migration. The only > problem is that the file formats for reporter maps are not transfered. > > > >> My changes should work with MySql with no problems, but they are not >> 'nice-coded'. >> Failing method PreparedStatement.getParameterMetaData is used in three >> places in code : >> - run() : Transfer.java >> - runUnbatched() : Transfer.java >> - run() : SampleTissueTransfer.java >> Each time only for getting parameterCount from statement query (number >> of question marks in query in migration-queries.sql file). Only two >> queries have this value != 2 and none of the classes using those queries >> uses methods mentioned above. So what I did was just commenting this: >> //int parameters = ps.getParameterMetaData().getParameterCount(); >> and adding: >> int parameters = 2; >> in those methods. Not very nice-coded, but little change that makes it >> work. I am sure you will find better way to code that. I did not change >> the number of question marks in none of the queries so it should work >> with MySql as well. >> > > We will not do anything about the problem. Since Postgres has fixed it > in a later version our policy is that users should upgrade. The > hard-coded approach is not solid enough to make it into the main > distribution. > > It's OK with me. As long there is a simple workaround nobody will be upset I suppose. > /Nicklas > > ------------------------------------------------------------------------- > SF.Net email is sponsored by: The Future of Linux Business White Paper > from Novell. From the desktop to the data center, Linux is going > mainstream. Let it simplify your IT future. > http://altfarm.mediaplex.com/ad/ck/8857-50307-18918-4 > _______________________________________________ > The BASE general discussion mailing list > basedb-users@lists.sourceforge.net > unsubscribe: send a mail with subject "unsubscribe" to > [EMAIL PROTECTED] > ------------------------------------------------------------------------- SF.Net email is sponsored by: The Future of Linux Business White Paper from Novell. From the desktop to the data center, Linux is going mainstream. Let it simplify your IT future. http://altfarm.mediaplex.com/ad/ck/8857-50307-18918-4 _______________________________________________ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject "unsubscribe" to [EMAIL PROTECTED]