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
>
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