[bioontology-support] Fwd: OntoPortal Appliance 3.0.2

classic Classic list List threaded Threaded
1 message Options
Reply | Threaded
Open this post in threaded view

[bioontology-support] Fwd: OntoPortal Appliance 3.0.2

Michael Dorf
Hi Pierfrancesco,

You should be able to customize the Mapping Counts job in Cron by performing the following steps:

1. Login to VA as ontoportal User
[centos@localhost ~]$ sudo su - ontoportal
[ontoportal@localhost ~]$

2. Update NCBO Cron Configuration Files
Navigate to NCBO Cron config directory and open config.rb in your favorite Linux editor:

[ontoportal@localhost config]$ cd /srv/ontoportal/virtual_appliance/appliance_config/ncbo_cron/config/
[ontoportal@localhost config]$ nano config.rb

Add these lines inside the "NcboCron.config do |config|" block:

NcboCron.config do |config|
    # Mapping Counts config
    config.enable_mapping_counts = true
    config.cron_mapping_counts   = '30 0 * * 6'

Set your cron expression to the desired value, save the file and exit.

3. Restart NCBO Cron Service
[ontoportal@localhost config]$ exit
[centos@localhost ~]$ sudo systemctl stop ncbo_cron
[centos@localhost ~]$ sudo systemctl status ncbo_cron

Make sure you see these lines:

Dec 03 23:42:30 localhost.localdomain systemd[1]: Stopping ncbo_cron service...
Dec 03 23:42:30 localhost.localdomain systemd[1]: Stopped ncbo_cron service.

[centos@localhost ~]$ sudo systemctl start ncbo_cron
[centos@localhost ~]$ sudo systemctl status ncbo_cron

Make sure you see this line:

Dec 03 23:44:37 localhost.localdomain ncbo_cron[2544]: Daemon has started successfully

Your new Mapping Counts job schedule should now be in effect. Let us know if you run into any other issues.


Michael Dorf
Chief Software Architect
The National Center for Biomedical Ontology
Stanford Biomedical Informatics Research
[hidden email]
O: 650-723-0357
M: 650-995-4374

Begin forwarded message:

From: Pierfrancesco Tommasino <[hidden email]>
Subject: Re: OntoPortal Appliance 3.0.2
Date: November 25, 2020 at 5:18:04 AM PST
To: John Graybeal <[hidden email]>

Dear Jhon,
thank you very much for your valuable information.
Yes I can confirm that I have just analyzed the cron and the job that runs "create mapping counts" starts the "30 0 * * 6" which should coincide with "At 12:30 AM, only on Saturday" but through the documentation of the following link https://ontoportal.github.io/administration/management/reference_ncbo-cron/
i can't figure out how to customize the job launch.
Analyzing the ontoportal documentation, I also found some possible changes to be made in the future and I would be happy to help.
Thank you again for the help you are giving me.

Kind regards,


Il giorno 24 nov 2020, alle ore 19:07, John Graybeal <[hidden email]> ha scritto:

Hi Pierfrancesco,

It’s nice to hear from you! Let me first mention a few things I know for sure, see if that helps.

The global Mapping page should show a list of ontologies in a drop down selector, then a table of mapped ontologies for the selected ontology, then the mappings to the ontology you select in the table. Which are you not seeing?

You don’t need the license to make anything work, all features are fully functional.

There could be a cron-caused delay, I’m not sure. Normally it would not be longer than overnight.

If you can reply to support@ontoportal.org I can get more knowledgeable team members to have a look.


From: Pierfrancesco Tommasino <[hidden email]>
Sent: Tuesday, November 24, 2020 8:34:53 AM
To: John Graybeal <[hidden email]>
Subject: OntoPortal Appliance 3.0.2
Dear John,

nice to meet you, i'm pierfrancesco Tommasino a new research fellow of LifeWatch Italy, Nicola Fiore introduced me a few days ago.
Right now I am evaluating the portability from OntoPortal Appliance 2.5 on which Ecoportal is based to OntoPortal Appliance 3.0.2. After downloading the .ova OntoPortal Appliance 3.0.2 I am proceeding to a study of the various updates made, noting some extraordinary improvements.
I haven't asked for licenses yet because I'm just testing new features by creating various VMs in VMware.
The only thing I wanted to ask you is how Mappings works. After importing various ontologies into the mappings page it keeps telling me "No mappings available" and the same happens in the Mappings tab after selecting an ontology. The strange thing is that if instead I browse the classes of the ontology loaded inside the Class Mappings tab all the mappings for that specific class are shown and the LOOM algorithm works correctly. What are the steps for mappings to be shown, could it be that it escapes me that it is activated by the ncbo-cron job in a period of time that I cannot verify?
Or could it be that you need to activate the license to access the mappings functionality?
I look forward to hearing from you,
Kind regards,
Pierfrancesco Tommasino

John Graybeal
Technical Program Manager
Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal
Stanford Center for Biomedical Informatics Research
650-736-1632  | ORCID  0000-0001-6875-5360

bioontology-support mailing list
[hidden email]