Search Mailing List Archives


Limit search to: Subject & Body Subject Author
Sort by: Reverse Sort
Limit to: All This Week Last Week This Month Last Month
Select Date Range     through    

[bioontology-support] category list on BioPortal VM

Line Pouchard linepouchard at gmail.com
Thu Apr 26 14:49:09 PDT 2012


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
>>
>>
>>


More information about the bioontology-support mailing list