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[bioontology-support] Issues bringing up the NCBO Virtual Appliance: mgrep does not start

Stephen Granite sgranite at jhu.edu
Mon Mar 11 11:12:10 PDT 2013


Paul,

 

Thanks for your help and guidance.  I ran the REST command below (edited for
our IP and my account) and received this back:

 

<success>

<accessedResource>/bioportal/auth</accessedResource>

<accessDate>2013-03-11 11:09:22.628 PDT</accessDate>

<data>

<session>

<attributes>

<entry>

<string>SECURITY_CONTEXT</string>

<securityContext>

<apiKey>6ef75be7-3571-4b7b-8d75-b51e0168270d</apiKey>

<userBean>

<id>16</id>

<username>sgranite</username>

<email>sgranite at jhu.edu</email>

<firstname>Stephen</firstname>

<lastname>Granite</lastname>

<dateCreated class="sql-timestamp">2013-03-11 11:07:55.0</dateCreated>

<roles>

<string>ROLE_LIBRARIAN</string>

</roles>

<ontologyAcl/>

<ontologyLicenses/>

</userBean>

</securityContext>

</entry>

</attributes>

<creationTime>0</creationTime>

<id>6ef75be7-3571-4b7b-8d75-b51e0168270d</id>

<lastAccessedTime>0</lastAccessedTime>

<isNew>false</isNew>

<isValid>true</isValid>

<lastUsedTime>0</lastUsedTime>

</session>

</data>

</success>

 

While it is good that I got this back, I will note that we are running the
BioPortal on port 80, rather than 8080, on the implementation of the
appliance.  Should we be running everything through 8080?  Would that
explain why I am getting the error messages?

 

Stephen J. Granite, MS, MBA

Director of Database and Software Development 

Center for Cardiovascular Bioinformatics and Modeling 

Institute for Computational Medicine 

The Johns Hopkins University 

3400 North Charles Street 

Hackerman Hall 312 

Baltimore, MD 21218-2686

phone: 410-516-8849

fax: 410-516-5294

 

From: Kyle Reynolds [mailto:kyle.reynolds at jhu.edu] 
Sent: Monday, March 11, 2013 2:06 PM
To: 'Paul R Alexander'; Stephen Granite
Cc: 'Trish Whetzel'; ksr at jhu.edu; 'NCBO User Support'
Subject: RE: [bioontology-support] Issues bringing up the NCBO Virtual
Appliance: mgrep does not start

 

FYI, I took a look for the log and there was nothing there. The directory
structure exists, but no production log was created yet. 

-Kyle

 

From: Paul R Alexander [mailto:palexander at stanford.edu] 
Sent: Monday, March 11, 2013 12:59 PM
To: Stephen Granite
Cc: 'Trish Whetzel'; ksr at jhu.edu; 'NCBO User Support'
Subject: Re: [bioontology-support] Issues bringing up the NCBO Virtual
Appliance: mgrep does not start

 

Unfortunately, I cannot reproduce either the error you get when creating an
account or the error you get when trying to view the API key. Here is the
log location on the Appliance. If you can see an error there I may be able
to help figure it out:

/var/log/rails/BioPortal/production.log

 

There is also a workaround. You can authorize an account using the REST
service:

http://{your <http://%7byour>  appliance IP or
domain}:8080//bioportal/auth?username={your username}&password={your
password}&apikey=11111111-9dd1-11e0-a996-115056bd0024

 

Just replace the brackets with your information. The API key in the URL is
the one included on the Appliance by default.

 

Paul

 

 

On Mar 11, 2013, at 6:53 AM, "Stephen Granite" <sgranite at jhu.edu> wrote:

 

Trish,

 

In order for us to load ontologies in, I need an API key for both Bioportal
and the appliance here.  As I said before, the account here exists.
However, when I go to get the API key, I receive the same message I got when
I tried to make the account in the first place: We're sorry but something
has gone wrong. We have been notified of this error. 

 

What should we be checking for regarding this?  Is this meant to spool out
in an error log somewhere?

 

Stephen J. Granite, MS, MBA

Director of Database and Software Development

Center for Cardiovascular Bioinformatics and Modeling

Institute for Computational Medicine

The Johns Hopkins University

3400 North Charles Street

Hackerman Hall 312

Baltimore, MD 21218-2686

phone: 410-516-8849

fax: 410-516-5294

 

From: Trish Whetzel [mailto:whetzel@ <http://stanford.edu> stanford.edu] 
Sent: Friday, March 08, 2013 5:11 PM
To: Stephen Granite
Cc: 'Paul R Alexander'; 'NCBO User Support';  <mailto:ksr at jhu.edu>
ksr at jhu.edu
Subject: Re: Issues bringing up the NCBO Virtual Appliance: mgrep does not
start

 

Yes, however I do not know if that was a one-time submit web service error
or a general bug in the create new user function included in that release.

 

Trish 

 

 

On Mar 8, 2013, at 9:05 AM, Stephen Granite wrote:





Trish and Paul,

 

On a tangential note, I had tried to make an account in the BioPortal
instance, but the interface said there was an error.  However, when I tried
to make the same account again, the interface came back saying that the
account in error existed.  I was then able to sign in with the account.
Does that make sense?

 

Stephen J. Granite, MS, MBA

Director of Database and Software Development

Center for Cardiovascular Bioinformatics and Modeling

Institute for Computational Medicine

The Johns Hopkins University

3400 North Charles Street

Hackerman Hall 312

Baltimore, MD 21218-2686

phone: 410-516-8849

fax: 410-516-5294

 

From: Trish Whetzel [ <mailto:whetzel at stanford.edu>
mailto:whetzel at stanford.edu] 
Sent: Friday, March 08, 2013 11:58 AM
To: Stephen Granite; Paul R Alexander
Cc: NCBO User Support;  <mailto:ksr at jhu.edu> ksr at jhu.edu
Subject: Re: Issues bringing up the NCBO Virtual Appliance: mgrep does not
start

 

Mgrep is used by the Annotator, however I do not know if having this start
successfully is dependent on having ontologies populated in the Annotator
database. Have you also populated ontologies in the Annotator database? As
for the dependency, Paul can you comment on this?

 

Trish 

 

 

On Mar 8, 2013, at 5:57 AM, Stephen Granite wrote:






In the CVRG, we are interested in bringing up an instance of the NCBO
applicance, to serve as a sandbox for ontologies we develop, to harden them
prior to submission to NCBO.  We downloaded a copy of the version 1.0 OVF
and were able to get the BioPortal web interface to come up without much
effort.  However, in the startup, one service fails to start properly:
mgrep.  mgrep is supposed to start from init.d, but when we execute "service
mgrep status," the response says the service is dead and the subsystem is
locked.  We don't see anything showing up in logs about mgrep.  What would
you advise that we do?  Thanks.

 

Stephen J. Granite, MS, MBA

Director of Database and Software Development

Center for Cardiovascular Bioinformatics and Modeling

Institute for Computational Medicine

The Johns Hopkins University

3400 North Charles Street

Hackerman Hall 312

Baltimore, MD 21218-2686

phone: 410-516-8849

fax: 410-516-5294

 

 

 

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