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] Issues bringing up the NCBO Virtual Appliance: mgrep does not start

Stephen Granite sgranite at jhu.edu
Thu Apr 11 07:14:05 PDT 2013


Paul,

 

Thanks for all your previous help.  We were able to get the script to run
after incrementing the space available to 100GB.  Actually 30GB was used.
However, we received a number of parsing errors on ontologies and ran into a
DataFactory out of memory error.  We have 6GB RAM allocated on the VM and
2GB min/4GB max allocated to tomcat.  We're thinking that we're going to
start from scratch and attempt to run the script under the admin API key
account (we had done this under my account on our appliance instance, which
may have caused the errors, but we are unsure).  As a side question, once
all the ontologies are loaded, how does one make them publicly available on
the appliance instance?

 

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: Paul R Alexander [mailto:palexander at stanford.edu] 
Sent: Friday, March 22, 2013 2:02 PM
To: Stephen Granite
Cc: 'Kyle Reynolds'; 'Trish Whetzel'; 'NCBO User Support'
Subject: Re: [bioontology-support] Issues bringing up the NCBO Virtual
Appliance: mgrep does not start

 

Stephen,

 

Size requirements are completely dependent on which ontologies you are
trying to import and how many versions each of them has. Our total storage
for ontology files (taking into account multiple versions) is around 100GB.
The search index takes about 18GB. The databases containing the parsed
ontologies is even larger.

 

Again, this is for our entire production system, which contains multiple
versions of many ontologies. However, it gives you a rough idea of the
scale.

 

For $INCLUDE_ONTOLOGIES you can just list the ontologyIds (aka virtual ids)
as comma-seperated integers.

 

Paul

 

 

On Mar 22, 2013, at 5:28 AM, "Stephen Granite" <sgranite at jhu.edu> wrote:





Paul,

 

Thanks again for your previous guidance.  We attempted to use the
import_ontologies script, but have run into space issues in the virtual
appliance.  The original VM is 8 GB and we expanded it to 20GB, but still
ran into a space issue.  What is a reasonable size to place the VM at, to
handle importing ontologies?

 

Also, the directions say that $INCLUDE_ONTOLOGIES can be uncommented and
used to import specific ontologies. What is meant to be entered in the
$INCLUDE_ONTOLOGIES parameter?

 

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: Paul R Alexander [mailto:palexander@ <http://stanford.edu>
stanford.edu] 
Sent: Thursday, March 14, 2013 2:19 PM
To: Stephen Granite
Cc: 'Kyle Reynolds'; 'Trish Whetzel';  <mailto:ksr at jhu.edu> ksr at jhu.edu;
'NCBO User Support'
Subject: Re: [bioontology-support] Issues bringing up the NCBO Virtual
Appliance: mgrep does not start

 

The user id number.

 

Paul

 

 

On Mar 14, 2013, at 11:18 AM, "Stephen Granite" < <mailto:sgranite at jhu.edu>
sgranite at jhu.edu> wrote:






Paul,

 

Thanks for the guidance.  We'll give it a shot.  One last question, is the
user id for $ONTOLOGY_OWNER my username or the id number?

 

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: Paul R Alexander [mailto:palexander@ <http://stanford.edu>
stanford.edu] 
Sent: Thursday, March 14, 2013 1:47 PM
To: Stephen Granite
Cc: 'Kyle Reynolds'; 'Trish Whetzel';  <mailto:ksr at jhu.edu> ksr at jhu.edu;
'NCBO User Support'
Subject: Re: [bioontology-support] Issues bringing up the NCBO Virtual
Appliance: mgrep does not start

 

Ok, so my guess is that the lack of ontologies in the system is causing the
error you are seeing. As you can imagine, we don't have many situations
where we have to handle a completely empty ontology library, so there are
possibilities for errors when the Appliance is in this state. I've filed a
bug report so we can investigate this further.

 

As for the migration, you will want two api keys from two different systems.
The first should be from an account you have with us on the BioPortal site:
<http://bioportal.bioontology.org/account>
http://bioportal.bioontology.org/account. This is what you would use in the
"FROM" option.

 

The other should be a key from your Appliance, either from the admin user or
a user who you have created. This would be used in the "TO" option.

 

Let me know if you have any other questions.

 

Paul

 

 

On Mar 14, 2013, at 10:21 AM, "Stephen Granite" < <mailto:sgranite at jhu.edu>
sgranite at jhu.edu> wrote:







Paul,

 

We had not put any ontologies in yet because we were trying to follow the
instructions in the Appliance FAQ for ontology migration:
<http://www.bioontology.org/wiki/index.php/Virtual_Appliance_FAQ#How_can_I_m
igrate_ontologies_from_BioPortal_or_previous_NCBO_Virtual_Appliance_versions
_into_a_new_Appliance.3F>
http://www.bioontology.org/wiki/index.php/Virtual_Appliance_FAQ#How_can_I_mi
grate_ontologies_from_BioPortal_or_previous_NCBO_Virtual_Appliance_versions_
into_a_new_Appliance.3F

I may have confused things slightly by thinking that the API key referenced
in those instructions was my user API key, rather than the system API key.
So in order to migrate ontologies into our instance of the NCBO appliance,
what are the values that we need for the "FROM" and "TO" API Keys?  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

 

From: Paul R Alexander [mailto:palexander@ <http://stanford.edu>
stanford.edu] 
Sent: Thursday, March 14, 2013 12:47 PM
To: Stephen Granite
Cc: 'Kyle Reynolds'; 'Trish Whetzel';  <mailto:ksr at jhu.edu> ksr at jhu.edu;
'NCBO User Support'
Subject: Re: [bioontology-support] Issues bringing up the NCBO Virtual
Appliance: mgrep does not start

 

Stephen,

 

Are there any ontologies submitted to your system?

 

 

On Mar 14, 2013, at 6:34 AM, "Stephen Granite" < <mailto:sgranite at jhu.edu>
sgranite at jhu.edu> wrote:








Paul,

 

We followed your instructions and the previous errors have disappeared.
However, when I attempted to update my account (sgranite) to see my API key
or make a new account (sjagranite), I received stack traces in the browser
and the script/server log.  I've attached the log and html pages from the
browser views of the same errors.  As a separate test, instead of using the
update button on my account, I went to reset my password.  After I reset my
password, I did get back the proper API key screen.  I've included just the
HTML from that, as the last attachment.

 

Is there anything else we need to change?

 

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: Paul R Alexander [mailto:palexander@ <http://stanford.edu>
stanford.edu] 
Sent: Wednesday, March 13, 2013 6:52 PM
To: Stephen Granite
Cc: 'Kyle Reynolds'; 'Trish Whetzel';  <mailto:ksr at jhu.edu> ksr at jhu.edu;
'NCBO User Support'
Subject: Re: [bioontology-support] Issues bringing up the NCBO Virtual
Appliance: mgrep does not start

 

Stephen,

 

Sorry, one more modification. You'll need to stop running the server
(ctrl+c), then modify this file:

/srv/ncbo/rails/BioPortal/current/config/database.yml

 

Replace the contents of the 'development' section with the contents from the
'production' section.

 

Then, restart the server with script/server and the error you sent me should
go away.

 

Paul

 

 

On Mar 13, 2013, at 11:18 AM, Stephen Granite < <mailto:sgranite at jhu.edu>
sgranite at jhu.edu> wrote:









Paul,

 

Attached is the spool of the output we received when following your
instructions.  We ran the script in /srv/ncbo/rails/BioPortal/current.  It
looks like it is having issues connecting to the mySQL database, but that is
just a guess on my part, based upon the error shown.

 

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: Paul R Alexander [mailto:palexander@ <http://stanford.edu>
stanford.edu] 
Sent: Tuesday, March 12, 2013 7:18 PM
To: Stephen Granite
Cc: 'Kyle Reynolds'; 'Trish Whetzel';  <mailto:ksr at jhu.edu> ksr at jhu.edu;
'NCBO User Support'
Subject: Re: [bioontology-support] Issues bringing up the NCBO Virtual
Appliance: mgrep does not start

 

No, the UI and REST services are designed to run on separate ports.
Unfortunately, I can't venture a guess as to why the account
creation/display process seems to be failing, especially given that they
work on my version of the Appliance.

 

One more thing you could try is shutting down apache httpd on the machine
and running the Rails app directly by doing the following while logged in as
root:

service httpd stop

cd /srv/rails/BioPortal/current

script/server -p 80

 

Then, visit the account page. When you get a failure, the stack trace should
get output to the terminal where you ran the script/server command. Using
that we might be able to figure it out.

 

Paul

 

 

On Mar 11, 2013, at 11:59 AM, Stephen Granite < <mailto:sgranite at jhu.edu>
sgranite at jhu.edu> wrote:










Paul,

 

Sorry for the confusion.  We took the OVF from bioportal and
converted/implemented it in VMware, with no changes except for IP address.
<http://%7byour> http://{your appliance IP or domain} responds and presents
the web UI.   <http://%7byour> http://{your appliance IP or
domain}:8080/bioportal/auth?username. responds fine with the API key
information.

 

The question I posed is whether the UI and the REST services should both be
running out of port 8080.  I ask because I'm confused as to why I can sign
into BioPortal on 80 and the UI seems to be working, but none of the account
capabilities provided by the UI (i.e., account creation, obtaining the API
key, etc.) seem to be working, even though the REST services are operational
and functioning.  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

 

From: Paul R Alexander [mailto:palexander@ <http://stanford.edu>
stanford.edu] 
Sent: Monday, March 11, 2013 2:50 PM
To: Stephen Granite
Cc: 'Kyle Reynolds'; 'Trish Whetzel';  <mailto:ksr at jhu.edu> ksr at jhu.edu;
'NCBO User Support'
Subject: Re: [bioontology-support] Issues bringing up the NCBO Virtual
Appliance: mgrep does not start

 

Sorry, I'm confused. Which portion of the infrastructure is running on port
80? The web UI? Or the REST services? Or both on separate machines?

 

If the REST service is not running on port 8080, then you will need to
modify the UI's configuration file in order to have things work properly.
You want to replace instances of 8080 with 80. The file is located here:

/srv/ncbo/src/config/bioportalui/BioPortal/config/bioportal_config.rb

 

After saving, you'll need to do a `bpdeploy deployui` command to have it
take effect.

 

Paul

 

 

On Mar 11, 2013, at 11:12 AM, "Stephen Granite" < <mailto:sgranite at jhu.edu>
sgranite at jhu.edu> wrote:











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> <mailto:sgranite at jhu.edu> 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@ <http://jhu.edu> jhu.edu] 
Sent: Monday, March 11, 2013 2:06 PM
To: 'Paul R Alexander'; Stephen Granite
Cc: 'Trish Whetzel';  <mailto:ksr at jhu.edu> 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>
mailto:palexander at stanford.edu] 
Sent: Monday, March 11, 2013 12:59 PM
To: Stephen Granite
Cc: 'Trish Whetzel';  <mailto:ksr at jhu.edu> 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://%7byour> http://{your 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" < <mailto:sgranite at jhu.edu>
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

 

 

 

_______________________________________________
bioontology-support mailing list
 <mailto:bioontology-support at lists.stanford.edu>
bioontology-support at lists.stanford.edu
 <https://mailman.stanford.edu/mailman/listinfo/bioontology-support>
https://mailman.stanford.edu/mailman/listinfo/bioontology-support

 

 

<NCBO_Error.txt>

 

<NCBO_Error_20130313.txt><Action_Controller_Exception_caught_create.htm><Act
ion_Controller_  Exception_caught_update.htm><Account Information   NCBO
BioPortal.htm>

 

 

 

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.stanford.edu/pipermail/bioontology-support/attachments/20130411/de1ecf08/attachment-0001.html>


More information about the bioontology-support mailing list