Enabled ontology parser. (01)
# 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 * * * ? * (02)
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. (03)
Mike / Peter can you try to login and confirm that you are able to
access the bioportal admin portal. (04)
Thanks,
--Tejas (05)
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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> (06)
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