Peter, (01)
The steps to make user account an admin account do not seem to be
right. I tried making my account an admin account and it did not work. (02)
I used following steps:
bioportal databse, ncbo.l.role table, what is the id for
ROLE_ADMINISTRATOR (e.g., 2824). Then, look in the ncbo_user table for
your user (firstname and lastname col), and write down the user id
from the id column (e.g. 38312). Then go to ncbo_user_role table and
edit the row that contains your user id in the user_id column, and put
in the role_id column the administrator role id. E.g.
(user_id:38312,role_id:2824). Restart the backend and try to log into
the bioportal_admin (03)
Ken Baclawski, Mike Gruninger and Leo Obrst have not created account
on oor-01f.cim3.net sandbox yet. Once they create their accounts I can
make them admins. (04)
--Tejas (05)
On Tue, Jan 26, 2010 at 10:15 PM, Peter Yim <peter.yim@xxxxxxxx> wrote:
> Tejas,
>
> Thank you very much.
>
> Have you created accounts for me and Mike, or do we have to create our
> own. If the latter, please advise how.
>
> I actually already have an account ( username = PeterYim) created on
> oor-01, and it still works on oor-01f. However, when I use that set of
> credentials at the admin login, I am getting a "Invalid credentials
> supplied" error. ... Any idea?
>
> Also, please provide Ken Baclawski, Mike Gruninger and Leo Obrst with
> access the admin portal as well.
>
> Thanks & regards. =ppy
> --
>
>
> On Tue, Jan 26, 2010 at 7:03 PM, Tejas Parikh <tejas@xxxxxxxxxxxxxxx> wrote:
>> Enabled ontology parser.
>>
>> # Ontology Parse Scheduler properties
>> # Enable/Disable scheduler service flag
>> ontology.parse.scheduler.enabled=true
>> # Scheduler cron expression
>> # Fire once every hour, at 30 past the hour: 0 30 * * * ? *
>> ontology.parse.scheduler.cronexpression=0 30 * * * ? *
>>
>> Also installed BioPortal Admin. It can be accessed at
>> http://oor-01f.cim3.net:8080/bioportal_admin/login.jsf and made Mike
>> Dean and Peter Yim administrators using the steps given in the install
>> guide.
>>
>> Mike / Peter can you try to login and confirm that you are able to
>> access the bioportal admin portal.
>>
>> Thanks,
>> --Tejas
>
>
>> On Tue, Jan 26, 2010 at 3:57 PM, Michael Dorf <mdorf@xxxxxxxxxxxx> wrote:
>>> Just to add to Paul’s comment about the cron expression, make sure that
>the
>>> following property (in build.properties) is set to true:
>>>
>>>
>>>
>>> # Ontology Parse Scheduler properties
>>>
>>> # Enable/Disable scheduler service flag
>>>
>>> ontology.parse.scheduler.enabled=true
>>>
>>>
>>>
>>> Once ontologies have been successfully parsed, you should see the actual
>>> Lucene index file generated in your
>>> bioportal.search.indexpath=${bioportal.resource.path}/searchindex
>>> directory.
>>>
>>>
>>>
>>> Misha
>
>
>>> From: oor-dev-bounces@xxxxxxxxxxxxxxxx
>>> [mailto:oor-dev-bounces@xxxxxxxxxxxxxxxx] On Behalf Of Paul R Alexander
>>> Sent: Tuesday, January 26, 2010 12:28 PM
>>> To: OpenOntologyRepository-development
>>> Subject: Re: [oor-dev] browsing errors in new sandbox
>>>
>>>
>>>
>>> Mike,
>>>
>>> Search doesn't return results because I don't think that the parser has
>>> processed the ontologies that have been loaded. If you look at the REST
>>> service [1], you'll see that the statusId for ontology 10018 (Basic RDF Geo
>>> Vocabulary) is set to 1, which indicates the system is 'awaiting action'.
>>> There's a cron statement in the build.properties file on the BioPortal Core
>>> that allows you to configure how often the parser will run:
>>> ontology.parse.scheduler.cronexpression=0/10 * * * * ? *
>>>
>>> This does rely on cron to operate, so that needs to be available on the
>>> machine. Also, the bioportal_admin app can be used to parse ontologies in a
>>> one-off or batch process.
>>>
>>> As for the "Most popular search" problem, I'll have to check with out Flex
>>> developer and get back to you.
>>>
>>> Paul
>>>
>>> [1] http://oor-01f.cim3.net:8080/bioportal/ontologies/10018
>>>
>>> On 1/25/10 9:03 PM, Mike Dean wrote:
>>>
>>> Paul and Tejas,
>>>
>>>
>>>
>>> Thanks very much for identifying and correcting these problems. I can now
>>> Browse and start to Search in [1].
>>>
>>>
>>>
>>> However, Search doesn't seem to return any results and the Status column of
>>> Browse is always empty (while BioPortal [2] typically has an Explore link).
>>> Does this mean that the ontologies failed to load, or is there some other
>>> problem?
>>>
>>>
>>>
>>> Also, I notice that the Search page has populated boxes for "Most popular
>>> searches" and "Recent searches" that probably weren't (successfully)
>>> performed on this instance. They seem to be coming from BioPortal itself,
>>> i.e. if I perform a search at [2], it shows up in the Recent searches list
>>> at [1] and its results are shown under Matching Terms.
>>>
>>>
>>>
>>> Thanks!
>>>
>>>
>>>
>>> Mike
>>>
>>>
>>>
>>> [1] http://oor-01f.cim3.net
>>>
>>>
>>>
>>> [2] http://bioportal.bioontology.org
>>>
>>>
>>>
>>>
>>>
>>> On Jan 25, 2010, at 10:03 PM, Tejas Parikh wrote:
>>>
>>>
>>>
>>>
>>>
>>> I will go ahead and update the code for BioPortal UI on OOR sandbox.
>>>
>>>
>>>
>>> --Tejas
>
>
>>> On Mon, Jan 25, 2010 at 8:45 PM, Paul R Alexander
>>>
>>> <palexander@xxxxxxxxxxxx> wrote:
>>>
>>>
>>>
>>> Mike,
>>>
>>>
>>>
>>> This was a bug that had been fixed in the BioPortal UI trunk but not the
>>>
>>> branch that OOR has deployed. I just merged the changes from the trunk to
>>>
>>> the OOR branch and if the code is updated this should go away.
>>>
>>>
>>>
>>> Note: There are some config changes in the environment.rb file that will
>>>
>>> need to be made for this update to work.
>>>
>>>
>>>
>>> Please let me know if you have any problems or questions.
>>>
>>>
>>>
>>> Paul
>>>
>>>
>>>
>>> On 1/24/10 9:04 AM, Mike Dean wrote:
>>>
>>>
>>>
>>> I'm often but erratically getting the error below when I browse specific
>>>
>>> ontologies (i.e. click Browse and then the ontology name or abbreviation,
>>>
>>> e.g. [1]) using the new sandbox.
>>>
>>>
>>>
>>> I originally thought this was consistently happening with several small
>>>
>>> (less than 50K byte) ontologies/vocabularies I loaded on Friday, but it now
>>>
>>> seems to happen (somewhat intermittently) with other ontologies as well.
>>>
>>> Logging-in/out, restarting Safari, or switching to Firefox doesn't seem to
>>>
>>> make a significant difference.
>>>
>>>
>>>
>>> Mike
>>>
>>>
>>>
>>> [1] http://oor-01f.cim3.net/ontologies/10018
>>>
>>>
>>>
>>> [2] http://oor-01f.cim3.net
>>>
>>>
>>>
>>>
>>>
>>> ArgumentError in Ontologies#show
>>>
>>>
>>>
>>> Showing ontologies/show.html.erb where line #522 raised:
>>>
>>>
>>>
>>> undefined class/module OntologyMetricsWrapper
>>>
>>> Extracted source (around line #522):
>>>
>>>
>>>
>>> 519: for the most recent version are reflected.
>>>
>>> 520: <%= link_to "See metrics descriptions",
>>>
>>> "http://www.bioontology.org/wiki/index.php/Ontology_Metrics"; %>
>>>
>>> 521: </p>
>>>
>>> 522: <% if @ontology.metrics.empty? %>
>>>
>>> 523: <h2 style="padding-left: 1em;">We have not
>yet calculated
>>> metrics for
>>>
>>> this ontology.</h2>
>>>
>>> 524: <% else %>
>>>
>>> 525: <table class="form">
>>>
>>>
>>>
>>> RAILS_ROOT: /usr/local/bioportal/bioportalui_oor
>>>
>>>
>>>
>>> Application Trace | Framework Trace | Full Trace
>>>
>>> /usr/lib64/ruby/gems/1.8/gems/memcache-client-1.7.7/lib/memcache.rb:255:in
>>>
>>> `load'
>>>
>>> /usr/lib64/ruby/gems/1.8/gems/memcache-client-1.7.7/lib/memcache.rb:255:in
>>>
>>> `get'
>>>
>>> /usr/lib64/ruby/gems/1.8/gems/memcache-client-1.7.7/lib/memcache.rb:878:in
>>>
>>> `with_server'
>>>
>>> /usr/lib64/ruby/gems/1.8/gems/memcache-client-1.7.7/lib/memcache.rb:251:in
>>>
>>> `get'
>>>
>>> app/models/data_access.rb:168:in `getOntologyMetrics'
>>>
>>> app/models/ontology_wrapper.rb:160:in `metrics'
>>>
>>> app/views/ontologies/show.html.erb:522:in
>>>
>>> `_run_erb_47app47views47ontologies47show46html46erb'
>>>
>>> app/controllers/ontologies_controller.rb:66:in `show'
>>>
>>> /usr/bin/mongrel_rails:19:in `load'
>>>
>>> /usr/bin/mongrel_rails:19
>>>
>>>
>>>
>>> Request
>>>
>>>
>>>
>>> Parameters:
>>>
>>>
>>>
>>> {"id"=>"10018"}
>>>
>>> Show session dump
>>>
>>>
>>>
>>> Response
>>>
>>>
>>>
>>> Headers:
>>>
>>>
>>>
>>> {"cookie"=>[],
>>>
>>> "Cache-Control"=>"no-cache"}
>>>
>>>
>>>
>>>
>>>
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>>
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> (06)
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