Re: [oor-dev] browsing errors in new sandbox

["Michael Dorf" <mdorf@xxxxxxxxxxxx>]

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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