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[bioontology-support] category list on BioPortal VM

Paul R Alexander palexander at stanford.edu
Thu Apr 26 15:00:07 PDT 2012


Line,

It looks like version 2 should work, you just need one more step that I 
just added to the instructions. To fix the problem, please download the 
MySQL connector jar here 
<http://smi-protege.stanford.edu/repos/protege/protege-core/trunk/dbdrivers/>. 
You will need to rename this file to 'driver.jar' and place it in the 
Protégé installation directory.

Paul R Alexander
Web / UI Developer
NCBO BioPortal
Stanford Center for Biomedical Informatics Research


On 4/26/12 2:49 PM, Line Pouchard wrote:
> Hi Paul:
>
> I have been running 2 instances of Protege client and get two
> different kinds of exceptions (quoted below):
> 1) downloaded with the VM and runs on the same host:
> 2) protege 3.4.4 as stated in the "doc"
>
> Any suggestions?
>
> 1) exceptions
> [7lp at mercury-ncbo ~]$ WARNING: Look and feel not found:
> com.jgoodies.looks.plastic.PlasticLookAndFeel --
> SystemUtilities.setLookAndFeel()
> WARNING: missing bundle: protege_text -- BundleHelper.<init>()
> WARNING: no such class:
> edu.stanford.smi.protegex.owl.database.OWLDatabaseKnowledgeBaseFactory
> -- SystemUtilities.newInstance()
> SEVERE: Cannot find knowledgebase factory:
> edu.stanford.smi.protegex.owl.database.OWLDatabaseKnowledgeBaseFactory
> Please check that you have the required plug-in. -- Project.createDomainKB()
> Project load time for file:/home/7lp/bioportal_metadata.pprj: 2 sec
>
>
> 2) The Protege 3.4.4 just gives me another exception:
> WARNING: Unable to load knowledgebase
> jdbc:mysql://mercury-ncbo.ornl.gov/bioportal_protege --
> java.lang.RuntimeException: class not found: com.mysql.jdbc.Driver
>         at edu.stanford.smi.protege.storage.database.pool.ConnectionPool.<init>(Unknown
> Source)
>         at edu.stanford.smi.protege.storage.database.pool.ConnectionPool.getConnectionPool(Unknown
> Source)
>         at edu.stanford.smi.protege.storage.database.RobustConnection.<init>(Unknown
> Source)
>         at edu.stanford.smi.protege.storage.database.AbstractDatabaseFrameDb.createConnection(Unknown
> Source)
>         at edu.stanford.smi.protege.storage.database.AbstractDatabaseFrameDb.initialize(Unknown
> Source)
>         at edu.stanford.smi.protegex.owl.database.OWLDatabaseKnowledgeBaseFactory.initializeKB(Unknown
> Source)
>         at edu.stanford.smi.protege.storage.database.DatabaseKnowledgeBaseFactory.loadKnowledgeBase(Unknown
> Source)
>         at edu.stanford.smi.protege.storage.database.DatabaseKnowledgeBaseFactory.loadKnowledgeBase(Unknown
> Source)
>         at edu.stanford.smi.protegex.owl.database.OWLDatabaseKnowledgeBaseFactory.loadKnowledgeBase(Unknown
> Source)
>         at edu.stanford.smi.protege.model.Project.loadDomainKB(Unknown Source)
>         at edu.stanford.smi.protege.model.Project.createDomainKnowledgeBase(Unknown
> Source)
>
>
> On Thu, Apr 26, 2012 at 3:34 PM, Line Pouchard <linepouchard at gmail.com> wrote:
>> Hi Paul:
>>
>> Is there documentation on setting up a connection between the Protege
>> client and the VM?
>> Line
>>
>> On Thu, Apr 26, 2012 at 2:59 PM, Paul R Alexander
>> <palexander at stanford.edu> wrote:
>>> You can run the Protege client on any machine that has access to the Virtual
>>> Appliance. It does not need to be run on the Appliance itself.
>>>
>>> Paul R Alexander
>>> Web / UI Developer
>>> NCBO BioPortal
>>> Stanford Center for Biomedical Informatics Research
>>>
>>>
>>> On 4/26/12 11:55 AM, Line Pouchard wrote:
>>>> Hi Paul:
>>>>
>>>> Is there any other way than using a local Protege client?  This is not
>>>> really an option for our install where I only use cli.
>>>>
>>>> Line
>>>>
>>>> On Thu, Apr 26, 2012 at 2:41 PM, Paul R Alexander
>>>> <palexander at stanford.edu> wrote:
>>>>> On 4/26/12 11:36 AM, Line Pouchard wrote:
>>>>>>> Instructions say: modify the Bioportal_protege project file.
>>>>>> 1) if I download from the support page and modify using my own protege
>>>>>> copy, which resides on a different machine than the VM, where do I
>>>>>> place the modified copy in the VM tree?
>>>>> You need to use a local Protege client to connect to the Virtual
>>>>> Appliance.
>>>>> You won't need to store the project file on the server at all, it is only
>>>>> for local use in connecting to the Appliance.
>>>>>> and 2)
>>>>>> Where in the tree do I find my VM original?
>>>>>> just want to cut and paste the correct ip and domain
>>>>> There is no original file on the Appliance, this is a totally separate
>>>>> process.
>>>>>
>>>>> Modifying the Protege project file will not change the categories, follow
>>>>> steps 3-8 after modifying the file and opening it in your local copy of
>>>>> Protege in order to actually make changes.
>>>>>
>>>>>   I don't know what the IP or domain for your Appliance is, but it should
>>>>> be
>>>>> the same as whatever you use to access the UI or REST services.
>>>>>
>>>>> Steps 3-8 on the instructions require you to be running Protege locally
>>>>> on
>>>>> your machine in order to connect to the Appliance, where you can then use
>>>>> Protege to modify the available categories. Changes will be made
>>>>> instantly
>>>>> (though may take a while to show up on the UI due to caching) and you
>>>>> won't
>>>>> need to upload anything to the Appliance in order to make the change.
>>>>>
>>>>> Paul R Alexander
>>>>> Web / UI Developer
>>>>> NCBO BioPortal
>>>>> Stanford Center for Biomedical Informatics Research
>>>
>>>


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