[Biojava-dev] Re: [Biojava-l] ontology exception, addSequence & BioSQLSequenceD B

[Simon Foote]

Changes have now been checked in.

Note to BioSQL users/developers, the cvs version now uses the Jakarata 
commons-dbcp & commons-pool packages to provide connection pooling.  The 
2 packages must be in your classpath to use BioSQLSequenceDB.

Cheers,
Simon

-- 
Bioinformatics Programmer
Institute for Biological Sciences
National Research Council of Canada
[T] 613-990-0561  [F] 613-952-9092
simon.foote at nrc-cnrc.gc.ca



Matthew Pocock wrote:

> S. Foote wrote:
>
>> I've tested out my mods and everything appears to work as expected.
>>
> great
>
>> Unfortunately, I'm away until Monday, so I will do the checkin on 
>> Monday morning.
>> Should I use the ant-lib dir for the 2 jar files and put an ant-task 
>> in the build file for it, as it
>> needs those 2 in the classpath for it to compile.
>>
> No; ant-lib is for ant tasks (junit, sablecc etc.), not for 
> dependancies. Put the jars in the root directory as usual. If they are 
> needed at run-time, then you could modify the Class-Path entry of the 
> biojava.jar manifest to pull them in.
>
> Best,
>
> Matthew
>
>>
>> Maybe if you could give me a pointer on what has to be added.  I 
>> checked the 2 jar files in previously,
>> but there in the top dir, so maybe we can get them moved to the 
>> ant-lib dir, if necessary.
>>
>> Cheers,
>> Simon
>>
>> According to Matthew Pocock:
>>  
>>
>>> Simon Foote wrote:
>>>
>>>   
>>>
>>>> Hi Mathew,
>>>>
>>>> That would be it.     
>>>
>>> Cool.
>>>
>>>   
>>>
>>>> Ran into that problem bringing in Genbank files where the feature 
>>>> keys could be organism or ORGANISM
>>>> I've also solved it. In MySQL, the varchar field type is compared 
>>>> in a case-insensitive fashion, but if you add the attribute BINARY 
>>>> to the field, then it compares in a case-sensitive fashion and 
>>>> everything works.     
>>>
>>> So we are ready to go for updating biojava with your mods then?
>>>
>>>   
>>>
>>>> I also cc'd Hilmar, for possibly changing this in the biosql schema 
>>>> for MySQL.  I far as I can tell it doesn't cause any problems with 
>>>> existing databases as it only effects sorting and comparing of the 
>>>> field.     
>>>
>>> Wonderful. Fingers crossed.
>>>
>>> Matthew
>>>
>>>   
>>>
>>>> Cheers,
>>>> Simon
>>>>
>>>> Matthew Pocock wrote:
>>>>
>>>>     
>>>>
>>>>> I wonder if it is a case thing - we persist _c:81, and then it 
>>>>> fails for _C:18. You are using MySQL? I tested on postgresql, 
>>>>> which is more case sensetive. Any ideas where I should begin?
>>>>>
>>>>> Simon Foote wrote:
>>>>>
>>>>>
>>>>>
>>>>>       
>>>>>
>>>>>> Attached is the complete error.log for this.
>>>>>>
>>>>>> Simon
>>>>>>
>>>>>> Matthew Pocock wrote:
>>>>>>  
>>>>>>         
>>>>>
>>>>>
>>>>>
>>>>>       
>>>>
>>
>>  
>>
>