Virtual Appliance FAQ

2023-03-23T22:53:20Z

Alexskr: update links

[[Category:NCBO Virtual Appliance]]
[[Category:Migrated to GitHub]]

This content has been moved! Please find the new content for the 3.0 version of the Virtual Appliance at our new [https://ontoportal.github.io/administration/ OntoPortal Virtual Appliance Administration pages].

In particular '''this content''' is mostly at the '''[https://https://ontoportal.github.io/documentation/administration/general/faq Frequently Asked Questions (FAQ) page]'''.

= '''ARCHIVAL''' ONTOPORTAL VIRTUAL APPLIANCE v2.5 FAQ '''ARCHIVAL''' =

This page is the archival FAQ for the the Ontoportal Virtual Appliance v2.5.

The FAQ for v1.0 is available in the [http://www.bioontology.org/wiki/index.php?title=Virtual_Appliance_FAQ&oldid=12621 archive]

= General =
== How do I access Virtual Appliance? ==

Virtual Appliance Web UI can be accessed by going to http://{your_appliance_ip_or_domain_name} on your web browser.<br>
API can be accessed at http://{your_appliance_ip_or_domain_name}:8080

You can get IP address of the Appliance with the following methods:
* Local IP Address from terminal:
<code>ip address show eth0 | awk '/inet / {print $2}' | cut -d/ -f1'</code>
* External IP address from the terminal:
<code>curl http://ipecho.net/plain; echo</code>
* Vmware Appliance:
Check 'IP Addresses' on the summary page of the appliance. Please note that Virtual Appliance does not come with vmware tools installed so IP Address would not be displayed until vmware tools are installed.
* Amazon AWS:
use Public IP Addresses or Public DNS listed in your EC2 management console.

== How can I enable emails for lost passwords, notes, and ontology processing? ==

Emails are sent via the ontologies_api project on the Appliance. You need to provide a valid mail server (smtp) configuration. The configuration should be provided in the /srv/ncbo/ontologies_api/current/config/environments/production.rb file.

Here are the available settings:
<code>
config.enable_notifications = true # Set to 'true' to send emails
config.email_sender = "admin@example.org" # Default sender for emails
config.email_disable_override = true # If this is set to 'false', all emails will be sent to the email configured in the 'email_override' setting
config.email_override = "admin@example.org"
config.smtp_host = "smtp.example.org"
config.smtp_port = 25
config.smtp_auth_type = :none # :none, :plain, :login, :cram_md5
config.smtp_user = "username" # only used if auth_type is not :none
config.smtp_password = "password" # only used if auth_type is not :none
config.smtp_domain = "example.org"
</code>

Once you have changed your settings, you will need to restart the server by running the command <code>/sbin/service unicorn restart</code>

== Can I use the Annotator and Recommender on their own? ==

Because services like the Annotator and Recommender depend on the Ontologies API in BioPortal, you can not usefully install those services in a stand-alone way without also installing the core BioPortal software and ontologies.

= Ontology Management =

== How do I add or change categories or groups? ==
There is currently no UI administrator interface. Categories and groups can be added using a console after logging into the Appliance as the ontoportal user.
<pre>
# from the bash shell:
cd /srv/ncbo/ncbo_cron
bin/ncbo_cron --console
# once in the ruby console:
category = LinkedData::Models::Category.new
category.name = "My Category"
category.acronym = "MY_CAT"
category.save
group = LinkedData::Models::Group.new
group.name = "My Group"
group.acronym = "MY_GRP"
group.save
</pre>

== How do I add or change slices? ==
There is currently no UI administrator interface. Slices can be added using a console after logging into the Appliance as the ontoportal user.
<pre>
# from the bash shell:
cd /srv/ncbo/ncbo_cron
bin/ncbo_cron --console
# once in the ruby console:
ont1 = LinkedData::Models::Ontology.find("ONT1").first
ont2 = LinkedData::Models::Ontology.find("ONT2").first
slice = LinkedData::Models::Slice.new
slice.name = "My Slice",
slice.description = "This is my custom slice",
slice.acronym = "my_slice",
slice.ontologies = [ont1, ont2]
slice.save
</pre>

== How do I delete an ontology? ==
Deleting can be done using a console after logging into the Appliance as the ontoportal user.
<pre>
# from the bash shell:
cd /srv/ncbo/ncbo_cron
bin/ncbo_cron --console
# once in the ruby console:
ontology = LinkedData::Models::Ontology.find("MY_ONTOLOGY_ACRONYM").first
ontology.delete
</pre>

== How can I migrate ontologies from BioPortal or previous NCBO Virtual Appliance versions into a new Appliance? ==

Programmatic migrations are not officially supported ("Ontologies can be manually downloaded and added using the Web UI") but we included a script for importing ontologies.

/srv/ncbo/virtual_appliance/deployment/utils/bioportal_ontologies_import.rb, you will need to modify SOURCE_API, SOURCE_APIKEY and ONTOLOGIES_TO_IMPORT variables.

== How can I restrict ontology downloads via the UI? ==

This line of code should be modified to include the acronyms of the ontologies for which you want to restrict downloads via the UI:

https://github.com/ncbo/bioportal_web_ui/blob/master/app/views/ontologies/_submissions.html.haml#L32

This will prevent the “Downloads” column in the Submissions table from appearing on ontology summary pages.

If you want to restrict download via the REST endpoint, you need to modify your environment configuration files (e.g., production.rb, staging.rb, etc.) in your ontologies_api project. The production.rb file should contain a “config.restrict_download” property -- there’s an example of what it should look like in the sample configuration file in GitHub:

https://github.com/ncbo/ontologies_api/blob/master/config/environments/config.rb.sample#L38

= Ontology Parsing =
== When are new ontologies parsed? ==
The ncbo_cron project uses a scheduler to run a process that collects new ontology submissions and parses them, adds them to the search index, calculates metrics, and processes them for use with the annotator. You can also parse ontologies manually.

== How do I manually parse an ontology? ==
To manually parse an ontology, you will need to interact with the code using the console after switching to ontoportal user:
<pre>
# from the bash shell:
cd /srv/ncbo/ncbo_cron
bin/ncbo_cron --console
# once in the ruby console:
ontology = LinkedData::Models::Ontology.find("MY_ACRONYM").first
submission = ontology.latest_submission(status: :any)
logger = Logger.new(STDOUT)
submission.process_submission(logger)
# make available in annotator
annotator = Annotator::Models::NcboAnnotator.new
annotator.create_term_cache_for_submission(logger, submission)
annotator.generate_dictionary_file()
</pre>

== How can I process a UMLS ontology? ==

UMLS ontologies can be processed to work with our system by converting them to RDF. There is no automated way to do this and you must have your own UMLS MySQL installation and an OSX/Linux/Unix machine with 8GB+ of RAM in order for the conversion process to work. The scripts to convert UMLS to RDF are available on [https://github.com/ncbo/umls2rdf Github].

Once you have converted UMLS to RDF, you will get Turtle (.ttl) files that can be uploaded using the BioPortal Web UI. Please select UMLS as the format for these ontologies.

== How do I know if an ontology has parsed? ==
The BioPortal Web UI will cache information about ontologies for 60 seconds. After parsing is complete, just refresh the ontology summary page to see the status for the most recent submission listed under the "Submissions" table.

In addition, you can look at the REST service directly, which will always give you the most updated information. To do this, visit the following URL:
* http://{your_appliance_ip_or_domain_name}:8080/ontologies/{ontology_acronym}/latest_submission?include=all
* You can look for the submissionStatus attribute to get the status

== Is there a log file for parsing? ==
Parsing progress is logged in the ontology submission repository folder:
/srv/ncbo/repository/{ontology acronym}/{submission id}

= Web User Interface =
== How can I clear the memcached-based UI cache? ==
* If you are logged in as the admin user, simply visit http://{your_appliance_ip_or_domain_name}/admin and click the "Flush Memcache" button. There should be a response indicating success or failure.

== How can I use widgets with my Virtual Appliance? ==
In addition to the [http://www.bioontology.org/wiki/index.php/NCBO_Widgets#How_to_use_NCBO_Widgets existing instructions], you must define an additional Javascript variable in order to have the widgets communicate with your instance of the Virtual Appliance.
<code>
var BP_SEARCH_SERVER = "http://{your_appliance_ip_or_domain_name}";
</code>
Replace the '{your_appliance_ip_or_domain_name}' text with the IP address or domain name that's assigned to your Virtual Appliance.

= Virtualization Environments =

== How can I use the OVF image with my virtualization software? <br/><span style="font-size: smaller;">(VMware, VirtualBox, KVM, Xen, etc)</span> ==

=== VMware ===
You can use [http://communities.vmware.com/community/vmtn/vsphere/automationtools/ovf VMware's ovftool] to convert the appliance to work with your VMware product. For example, to convert the appliance for use in VMware Player or Workstation, you would run the command:

<pre>
ovftool ncbo-appliance.ovf ncbo-appliance.vmx
</pre>

=== VirtualBox ===
VirtualBox supports importing OVF images directly. Simply start your VirtualBox software, then select '''File->Import Appliance''' and select the OVF file included in the NCBO Virtual Appliance download.

=== KVM ===
First, convert the OVF to VMX format as mentioned in the VMware section above.

Next, ensure that the <code>kvm-qemu-img</code> RPM (or <code>qemu-kvm</code> DEB) is installed. Then, convert the [new] VMDKs (from the VMX conversion step) to raw disk images via the following command:

<pre>for disk in `ls -1 *.vmdk`; do diskbase=`basename $disk .vmdk`; qemu-img convert -O raw ${diskbase}.vmdk ${diskbase}.img; done</pre>

Create <code>/etc/libvirt/qemu/ncbo-appliance.xml</code> with the following contents:

<pre>
<domain type='kvm'>
<name>ncbo-appliance</name>
<memory>4194304</memory>
<vcpu>2</vcpu>
<os>
<type arch='x86_64' machine='rhel5.4.0'>hvm</type>
<boot dev='hd'/>
</os>
<features>
<acpi/>
<apic/>
<pae/>
</features>
<clock offset='utc'>
<timer name='pit' tickpolicy='delay'/>
</clock>
<on_poweroff>destroy</on_poweroff>
<on_reboot>restart</on_reboot>
<on_crash>restart</on_crash>
<devices>
<emulator>/usr/libexec/qemu-kvm</emulator>
<disk type='file' device='disk'>
<driver name='qemu' type='raw'/>
<source file='/var/lib/libvirt/images/ncbo-appliance/ncbo-appliance-disk1.img'/>
<target dev='hda' bus='ide'/>
<address type='drive' controller='0' bus='0' unit='0'/>
</disk>
<disk type='file' device='disk'>
<driver name='qemu' type='raw'/>
<source file='/var/lib/libvirt/images/ncbo-appliance/ncbo-appliance-disk2.img'/>
<target dev='hdb' bus='ide'/>
<address type='drive' controller='0' bus='0' unit='1'/>
</disk>
<controller type='ide' index='0'/>
<interface type='network'>
<source network='default'/>
<model type='virtio'/>
</interface>
<serial type='pty'>
<target port='0'/>
</serial>
<console type='pty'>
<target port='0'/>
</console>
<input type='mouse' bus='ps2'/>
<graphics type='vnc' port='-1' autoport='yes' keymap='en-us'/>
<video>
<model type='cirrus' vram='9216' heads='1'/>
</video>
</devices>
</domain>
</pre>

Finally, make any necessary edits to the above file, and run:

<pre>
virsh start ncbo-appliance
</pre>

=== Xen ===
First, convert the VMDKs to raw disk images as mentioned in the KVM section above.

Create <code>/etc/xen/ncbo-appliance.cfg</code> with the following contents:

<pre>
name = "ncbo-appliance"
memory = 4096
vcpus = 2
builder = "hvm"
kernel = "/usr/lib/xen/boot/hvmloader"
boot = "c"
pae = 1
acpi = 1
apic = 1
localtime = 0
on_poweroff = "destroy"
on_reboot = "destroy"
on_crash = "destroy"
device_model = "/usr/lib64/xen/bin/qemu-dm"
sdl = 0
vnc = 1
vncunused = 1
keymap = "en-us"
disk = [ "file:/var/lib/xen/images/ncbo-appliance/ncbo-appliance-disk1.img,hda,w", "file:/var/lib/xen/images/ncbo-appliance/ncbo-appliance-disk2.img,hdb,w" ]
vif = [ "bridge=xenbr0,script=vif-bridge,vifname=vif41.0" ]
parallel = "none"
serial = "pty"
</pre>

Finally, make any necessary edits to the above file, and run:

<pre>
xm create ncbo-appliance
</pre>

== How can I use the Appliance on Amazon EC2? ==

Appliance is available on [https://aws.amazon.com/marketplace/pp/B00MX5YKVU Amazon Marketplace]

=== What is the admin password for the AWS Appliance? ===

The default application administrator is 'admin' and the initial password is the Instance ID (i-xxxxxxxx). Please change this as soon as you install the virtual appliance.

Importing UMLS To Virtual Appliance

2023-03-23T22:52:28Z

Alexskr:

Google Analytics

2023-03-23T22:47:53Z

Alexskr:

Advanced Administration

2023-03-23T22:47:00Z

Alexskr: update links

[[Category:NCBO Virtual Appliance]]
[[Category:Migrated to GitHub]]

This content has been moved! Please visit it at our new [https://ontoportal.github.io/documentation/administration OntoPortal Virtual Appliance Administration pages].

You can find Advanced content in each of the sections [https://ontoportal.github.io/documentation/administration/steps Installing OntoPortal], [https://ontoportal.github.io/documentation/administration/ontologies Managing Ontologies in OntoPortal], and [https://ontoportal.github.io/documentation/administration/management Managing Your System].

Annotator Documentation

2023-03-23T22:45:50Z

Alexskr:

Advanced Administration

2023-03-23T22:44:40Z

Alexskr:

[[Category:NCBO Virtual Appliance]]
[[Category:Migrated to GitHub]]

This content has been moved! Please visit it at our new [https://ontoportal.github.io/documentation/administration/ OntoPortal Virtual Appliance Administration pages].

You can find Advanced content in each of the sections [https://ontoportal.github.io/documentation/administration/steps/ Installing OntoPortal], [https://ontoportal.github.io/documentation/administration/ontologies/ Managing Ontologies in OntoPortal], and [https://ontoportal.github.io/documentation/administration/management/ Managing Your System].

Category:NCBO Virtual Appliance

2019-10-18T17:25:43Z

Alexskr: Undo revision 12996 by Alexskr (talk)

== OntoPortal Virtual Appliance version 3.0 coming soon ==

After briefly putting out a Release Candidate 1 for the v3.0 Virtual Appliance, we have identified a few more features that we want to complete before making the Appliance available.

We intend to release a Virtual Appliance 3.0 later this fall; watch this space for news.

== OntoPortal Virtual Appliance v2.5 is available ==

The OntoPortal Virtual Appliance is the (rebranded) update of the BioPortal Virtual Appliance originally developed by the National Center for Biomedical Ontologies (NCBO). Our current Virtual Appliance software is based on BioPortal's v5.x software infrastructure, including the use of an RDF triplestore as the primary data storage mechanism.

== Virtual Appliance Basics ==

The OntoPortal Virtual Appliance is a copy of the BioPortal software that you can run on your own Linux system. You have to install it following the instructions below, and upload your own ontologies (and/or copies of ours, if they are public).

The OntoPortal Virtual Appliance image contains a pre-installed, pre-configured version of commonly-used open source software running on a Linux operating system.

It is available as a VMWare Virtual Appliance OVF, as well as an Amazon Web Service AMI, and can be obtained by contacting us following the instructions under '''Getting Started''' below.

The following software is included on the image as of v2.5:
* Ontologies API (REST service)
* Annotator
* Recommender
* OntoPortal Web User Interface (including UIs for ontology browse, Annotator and Recommender, ontology tree visualization, graph visualization with BioMixer, and widgets)
* API services

Please see below for how-to documentation for managing the software and running data population for Annotator and Recommender.

You may also want to visit the [[Virtual Appliance FAQ]] for additional information on the Virtual Appliance, as well as the other pages in this category (bottom of the page).

== Getting Started ==
=== VMWare Virtual Appliance ===

To obtain the VMWare Virtual Appliance, contact [mailto:support@bioontology.org OntoPortal Support] to initiate your request. You'll then be asked privately for your BioPortal account username, project goals, and reason for preferring the local installation.
* If you don't have a BioPortal account, you can create one at: http://bit.ly/bioportal-account.
* If your email doesn't include your organization or other means of identifying you, we will ask for that as well.
* The overall transaction can take a few working days, depending on resource availability.

The download is provided as a zip archive containing several files. One of these is an Open Virtualization Format (OVF) file that may need to be [http://www.bioontology.org/wiki/index.php/Virtual_Appliance_FAQ#How_can_I_use_the_OVF_image_with_my_virtualization_software.3F_.28VMWare.2C_VirtualBox.2C_KVM.2C_Xen.2C_etc.29 converted to work in your virtualization environment].

* You can supply the hostname (machine name) for the virtual machine during the deployment process. Documentation will refer to this hostname as 'example'.
* '''Change default passwords'''
** Operating System
*** Username: <code>root</code>
*** Password: password is prompted on the first boot
** OntoPortal Admin User
*** Username: <code>admin</code>
*** Password: <code>changeme</code>

=== Amazon AWS AMI ===
For users who want to run their OntoPortal instance on Amazon Web Services, an Amazon Machine Instance (AMI) is available on the [https://aws.amazon.com/marketplace/seller-profile/ref=dtl_pcp_sold_by?ie=UTF8&id=76948a46-8f8a-4a68-9a5c-3e3ff6b82d10 BioOntology AWS Market Place]. Please contact [mailto:support@bioontology.org OntoPortal Support] for more information.

Once the instance is running, enter the public DNS provided by Amazon into your browser to access BioPortal web interface. The default application administrator is 'admin' and the initial password is the Instance ID. You can also SSH to the machine using the username 'ec2-user' and your Amazon private key.

=== General Instruction ===
Virtual Appliance Web UI can be accessed at http://{ip_address_of_appliance}. You can get IP address of the Appliance by using the following command in the terminal 'ip addr show eth0'
* Add an ontology using the OntoPortal Admin User here: http://{ip_address_of_appliance}/ontologies/new
** The ncbo_cron project is configured to automatically process new ontologies every 5 minutes (see [http://www.bioontology.org/wiki/index.php/Virtual_Appliance_FAQ#When_are_new_ontologies_parsed.3F documentation for enabling the scheduler]). This processing includes:
*** Parsing any new, unparsed ontologies
*** Calculating a set of metrics for these ontologies
*** Indexing these ontologies for use with search
*** Processing the ontology for use with the annotator
* REST services are available at the following location:
** http://{ip_address_of_appliance}:8080
** http://{ip_address_of_appliance}:8080/documentation

== System Requirements ==
The following requirements are for the resources that you devote to your Appliance instance, not for the machine running your host environment. For example, if you are using a system with 4GB of RAM, then you will need to devote all of that RAM to your guest Appliance.

'''Note: these requirements are for basic usage'''. System requirements will vary greatly depending on the size of the ontologies you work with, the number of ontologies in the system, and the number of concurrent requests that the system needs to respond to. It can also vary depending on how the ontologies are used. For example, the search index can be RAM-intensive but parsing ontologies can be CPU-intensive. You will need to experiment with your Appliance resource settings to find what works for your scenario.

* Minimum
** 2 CPU (2 GHz)
** 4GB RAM
** Hard disk space: 20GB

* Recommended for heavier usage
** 4 CPU (3 GHz)
** 8GB RAM (or more depending on the size/number of ontologies)
** Hard disk space: 20GB (or more depending on number/size of ontologies)

== Image Format and Operating System Details ==
The OntoPortal Virtual Appliance image was created using the [http://www.vmware.com/appliances/getting-started/learn/ovf.html Open Virtualization Format], which should allow the machine to be used in a variety of environments.

The operating system is CentOS 6.9 64-bit running:
*Tomcat 6.0.26
*Solr 6.6
*Java 8
*MySQL 5.1.x
*Rails 4.2.x
*Ruby 2.3.6
*memcached
*redis 2.3.11
*nginx 1.12.1
*4store
*Passenger/Apache

The following applications use these services/runtime environments:
* Sinatra, Ruby, 4store, redis
** Ontologies API
** Annotator
** Recommender
* Rails, Ruby, memcached, mysql
** BioPortal Web User Interface (including ontology visualization, Flex widgets, biomixer, Annotator)
* Tomcat, Solr
** Search index

== Basic System Administration ==
* Most of our administration scripts and build environment assume that you will be running as the root user.
* We assume familiarity with basic CentOS Linux administration
* 2 text editors are originally installed: nano and vim
* All services required for OntoPortal Stack are automatically started on boot. For troubleshooting purposes you can manually stop/start services:
** <code>bprestart</code>: manually restart services required for Ontoportal Stack.
** <code>bpstart</code>: manually start services.
** <code>bpstop</code>: manually stop services
* Start individual services:
** <code>/sbin/service httpd start</code>
** <code>/sbin/service memcached start</code>
** <code>/sbin/service tomcat6 start</code>
** <code>/sbin/service mgrep start</code>
** <code>/sbin/service 4s-httpd-ontologies_api start</code>
** <code>/sbin/service unicorn start</code>
* Stop individual services:
** <code>/sbin/service httpd stop</code>
** <code>/sbin/service memcached stop</code>
** <code>/sbin/service tomcat6 stop</code>
** <code>/sbin/service mgrep stop</code>
** <code>/sbin/service 4s-httpd-ontologies_api stop</code>
** <code>/sbin/service unicorn stop</code>

== License ==

The Virtual Appliance software is released with the 2-clause BSD license. Source code is included on the Virtual Appliance.

== Archival ==

For documentation of previous (v1.0) Virtual Appliances, please see our [http://www.bioontology.org/wiki/index.php?title=Category:NCBO_Virtual_Appliance&oldid=12610 archive].

Category:NCBO Virtual Appliance

2019-10-18T17:18:22Z

Alexskr: Reverted edits by Graybeal (talk) to last revision by Alexskr

== ONTOPORTAL VIRTUAL APPLIANCE v3.0 RC1 IS NOW AVAILABLE ==

The OntoPortal Virtual Appliance is the (rebranded) update of the BioPortal Virtual Appliance originally developed by the National Center for Biomedical Ontologies (NCBO). Our current Virtual Appliance software is based on BioPortal's v5.x software infrastructure, including the use of an RDF triplestore as the primary data storage mechanism.

== Virtual Appliance Basics ==

The OntoPortal Virtual Appliance is a copy of the BioPortal software that you can run on your own Linux system. You have to install it following the instructions below, and upload your own ontologies (and/or copies of ours, if they are public).

The OntoPortal Virtual Appliance image contains a pre-installed, pre-configured version of commonly-used open source software running on a Linux operating system.

It is available as a VMWare Virtual Appliance OVF, as well as an Amazon Web Service AMI, and can be obtained by contacting us following the instructions under '''Getting Started''' below.

The following software is included on the image as of v3.0 RC1:
* Ontologies API (REST service)
* Annotator
* Recommender
* OntoPortal Web User Interface (including UIs for ontology browse, Annotator, Annotator+ and Recommender, ontology tree visualization, graph visualization with BioMixer, and widgets)
* API services
* Annotator Plus Proxy

Please see below for how-to documentation for managing the software and running data population for Annotator and Recommender.

You may also want to visit the [[Virtual Appliance FAQ]] for additional information on the Virtual Appliance, as well as the other pages in this category (bottom of the page).

== Getting Started ==
=== VMWare Virtual Appliance ===

To obtain the VMWare Virtual Appliance, contact [mailto:support@bioontology.org OntoPortal Support] to initiate your request. You'll then be asked privately for your BioPortal account username, project goals, and reason for preferring the local installation.
* If you don't have a BioPortal account, you can create one at: http://bit.ly/bioportal-account.
* If your email doesn't include your organization or other means of identifying you, we will ask for that as well.
* The overall transaction can take a few working days, depending on resource availability.

The download is provided as a zip archive containing several files. One of these is an Open Virtualization Format (OVF) file that may need to be [http://www.bioontology.org/wiki/index.php/Virtual_Appliance_FAQ#How_can_I_use_the_OVF_image_with_my_virtualization_software.3F_.28VMWare.2C_VirtualBox.2C_KVM.2C_Xen.2C_etc.29 converted to work in your virtualization environment].

* You can supply the hostname (machine name) for the virtual machine during the deployment process. Documentation will refer to this hostname as 'example'.
* '''Change default passwords'''
** Operating System
*** Username: <code>root</code>
*** Password: <code>Ontoportal</code>
** OntoPortal Admin User
*** Username: <code>admin</code>
*** Password: <code>changeme</code>

=== Amazon AWS AMI ===
For users who want to run their OntoPortal instance on Amazon Web Services, an Amazon Machine Instance (AMI) is available on the [https://aws.amazon.com/marketplace/seller-profile/ref=dtl_pcp_sold_by?ie=UTF8&id=76948a46-8f8a-4a68-9a5c-3e3ff6b82d10 BioOntology AWS Market Place]. Please contact [mailto:support@bioontology.org OntoPortal Support] for more information.

Once the instance is running, enter the public DNS provided by Amazon into your browser to access BioPortal web interface. The default application administrator is 'admin' and the initial password is the Instance ID. You can also SSH to the machine using the username 'ec2-user' and your Amazon private key.

=== General Instruction ===
Virtual Appliance Web UI can be accessed at http://{ip_address_of_appliance}. You can get IP address of the Appliance by using the following command in the terminal 'ip addr show eth0'
* Add an ontology using the OntoPortal Admin User here: http://{ip_address_of_appliance}/ontologies/new
** The ncbo_cron project is configured to automatically process new ontologies every 5 minutes (see [http://www.bioontology.org/wiki/index.php/Virtual_Appliance_FAQ#When_are_new_ontologies_parsed.3F documentation for enabling the scheduler]). This processing includes:
*** Parsing any new, unparsed ontologies
*** Calculating a set of metrics for these ontologies
*** Indexing these ontologies for use with search
*** Processing the ontology for use with the annotator
* REST services are available at the following location:
** http://{ip_address_of_appliance}:8080
** http://{ip_address_of_appliance}:8080/documentation

== System Requirements ==
The following requirements are for the resources that you devote to your Appliance instance, not for the machine running your host environment. For example, if you are using a system with 4GB of RAM, then you will need to devote all of that RAM to your guest Appliance.

'''Note: these requirements are for basic usage'''. System requirements will vary greatly depending on the size of the ontologies you work with, the number of ontologies in the system, and the number of concurrent requests that the system needs to respond to. It can also vary depending on how the ontologies are used. For example, the search index can be RAM-intensive but parsing ontologies can be CPU-intensive. You will need to experiment with your Appliance resource settings to find what works for your scenario.

* Minimum
** 2 CPU (2 GHz)
** 4GB RAM
** Hard disk space: 20GB

* Recommended for heavier usage
** 4 CPU (3 GHz)
** 8GB RAM (or more depending on the size/number of ontologies)
** Hard disk space: 20GB (or more depending on number/size of ontologies)

== Image Format and Operating System Details ==
The OntoPortal Virtual Appliance image was created using the [http://www.vmware.com/appliances/getting-started/learn/ovf.html Open Virtualization Format], which should allow the machine to be used in a variety of environments.

The operating system is CentOS 7.6 64-bit running:
*Tomcat 7.0.x
*Solr 6.6
*Java 8
*MariaDB 5.5.x
*Rails 4.2.x
*Ruby 2.5.5
*memcached
*redis 3.2.12
*nginx 1.15.8
*4store
*Passenger/Apache

The following applications use these services/runtime environments:
* Sinatra, Ruby, 4store, redis
** Ontologies API
** Annotator
** Recommender
* Rails, Ruby, memcached, mysql
** BioPortal Web User Interface (including ontology visualization, Flex widgets, biomixer, Annotator)
* Tomcat, Solr
** Search index

== Basic System Administration ==
* Most of our administration scripts and build environment assume that you will be running as the root user.
* We assume familiarity with basic CentOS Linux administration
* 2 text editors are originally installed: nano and vim
* All services required for OntoPortal Stack are automatically started on boot. For troubleshooting purposes you can manually stop/start services:
** <code>sudo oprestart</code>: manually restart services required for Ontoportal Stack.
** <code>sudo opstart</code>: manually start services.
** <code>sudo opstop</code>: manually stop services
* Start individual services:
** <code>sudo systemctl start httpd</code>
** <code>sudo systemctl start memcached</code>
** <code>sudo systemctl start tomcat</code>
** <code>sudo systemctl start mgrep</code>
** <code>sudo systemctl start 4s-httpd</code>
** <code>sudo systemctl start start</code>
* Stop individual services:
** <code>sudo systemctl stop httpd</code>
** <code>sudo systemctl stop memcached</code>
** <code>sudo systemctl stop tomcat</code>
** <code>sudo systemctl stop mgrep</code>
** <code>sudo systemctl stop 4s-httpd</code>
** <code>sudo systemctl stop unicorn</code>

== License ==

The Virtual Appliance software is released with the 2-clause BSD license. Source code is included on the Virtual Appliance.

== Older Versions Documentation ==

For documentation of previous
(v2.5) Virtual Appliances, please see our [http://www.bioontology.org/wiki/index.php?title=Category:NCBO_Virtual_Appliance&oldid=12987 archive].
(v1.0) Virtual Appliances, please see our [http://www.bioontology.org/wiki/index.php?title=Category:NCBO_Virtual_Appliance&oldid=12610 archive].

2017-08-03T19:05:37Z

Alexskr: /* Changes */

2016-01-27T22:07:05Z

Alexskr: /* Basic System Administration */

== NCBO VIRTUAL APPLIANCE v2.4 IS NOW AVAILABLE ==
The NCBO Virtual Appliance has been updated to use NCBO's new v4.0 software infrastructure, including the use of an RDF triplestore as the primary data storage mechanism. Please read below as much of the Appliance workflow has changed.

For documentation of v1.0 Virtual Appliances, please see our [http://www.bioontology.org/wiki/index.php?title=Category:NCBO_Virtual_Appliance&oldid=12610 archive].

== Virtual Appliance Basics ==

The NCBO Virtual Appliance image contains a pre-installed, pre-configured version of commonly-used open source NCBO software running on a Linux operating system.

It is available as a VMWare Virtual Appliance OVF, as well as an Amazon Web Service AMI, and can be obtained by contacting us following the instructions under '''Getting Started''' below.

The following software is included on the image as of v2.4:
* Ontologies API (REST service)
* Annotator
* Recommender
* BioPortal Web User Interface (including ontology visualization, widgets, biomixer, and Annotator UI)

Please see below for how-to documentation for managing the software and running data population for Annotator.

== Getting Started ==
=== VMWare Virtual Appliance ===
* To obtain the VMWare Virtual Appliance, contact [mailto:support@bioontology.org NCBO Support] to initiate your request. You'll then be asked privately for your BioPortal account username. organizational goals, and reason for preferring the local installation. (If you don't have a BioPortal account, you can create one at: http://bit.ly/bioportal-account.) The overall transaction can take a few working days, depending on resource availability.
* The download is provided as a zip archive containing several files. One of these is an Open Virtualization Format (OVF) file that may need to be [http://www.bioontology.org/wiki/index.php/Virtual_Appliance_FAQ#How_can_I_use_the_OVF_image_with_my_virtualization_software.3F_.28VMWare.2C_VirtualBox.2C_KVM.2C_Xen.2C_etc.29 converted to work in your virtualization environment].
* You can supply the hostname (machine name) for the virtual machine during the deployment process. Documentation will refer to this hostname as 'example'.
* '''Change default passwords'''
** Operating System
*** Username: <code>root</code>
*** Password: password is prompted on the first boot
** BioPortal Admin User
*** Username: <code>admin</code>
*** Password: <code>changeme</code>

=== Amazon AWS AMI ===
Amazon AMI is available on the [https://aws.amazon.com/marketplace/seller-profile/ref=dtl_pcp_sold_by?ie=UTF8&id=76948a46-8f8a-4a68-9a5c-3e3ff6b82d10 AWS Market Place]. Please contact [mailto:support@bioontology.org NCBO Support] for more information.
Once the instance is running, enter the public DNS provided by Amazon into your browser to access BioPortal web interface. The default application administrator is 'admin' and the initial password is the Instance ID. You can also SSH to the machine using the username 'ec2-user' and your Amazon private key.

=== General Instruction ===
* Add an ontology using the BioPortal Admin User here: http://{YourDomainName}/ontologies/new
** The ncbo_cron project is configured to automatically process new ontologies every 5 minutes (see [http://www.bioontology.org/wiki/index.php/Virtual_Appliance_FAQ#When_are_new_ontologies_parsed.3F documentation for enabling the scheduler]). This processing includes:
*** Parsing any new, unparsed ontologies
*** Calculating a set of metrics for these ontologies
*** Indexing these ontologies for use with search
*** Processing the ontology for use with the annotator
* REST services are available at the following location:
** http://example:8080
** http://example:8080/documentation

== System Requirements ==
The following requirements are for the resources that you devote to your Appliance instance, not for the machine running your host environment. For example, if you are using a system with 4GB of RAM, then you will need to devote all of that RAM to your guest Appliance.

'''Note: these requirements are for basic usage'''. System requirements will vary greatly depending on the size of the ontologies you work with, the number of ontologies in the system, and the number of concurrent requests that the system needs to respond to. It can also vary depending on how the ontologies are used. For example, the search index can be RAM-intensive but parsing ontologies can be CPU-intensive. You will need to experiment with your Appliance resource settings to find what works for your scenario.

* Minimum
** 2 CPU (2 GHz)
** 4GB RAM
** Hard disk space: 20GB

* Recommended for heavier usage
** 4 CPU (3 GHz)
** 8GB RAM (or more depending on the size/number of ontologies)
** Hard disk space: 20GB (or more depending on number/size of ontologies)

== Image Format and Operating System Details ==
The NCBO Appliance image was created using the [http://www.vmware.com/appliances/getting-started/learn/ovf.html Open Virtualization Format], which should allow the machine to be used in a variety of environments.

The operating system is CentOS 6.6 64-bit running:
*Tomcat 6.0.26
*Solr 4.10.4
*Java 7
*MySQL 5.1.x
*Rails 3.2.x
*Ruby 2.1.5
*memcached
*redis 2.8.18
*nginx 1.6.3
*4store
*Passenger/Apache

The following applications use these services/runtime environments:
* Sinatra, Ruby, 4store, redis
** Ontologies API
** Annotator
** Recommender
* Rails, Ruby, memcached, mysql
** BioPortal Web User Interface (including ontology visualization, Flex widgets, biomixer, Annotator)
* Tomcat, Solr
** Search index

== Basic System Administration ==
* Most of our administration scripts and build environment assume that you will be running as the root user.
* We assume familiarity with basic CentOS Linux administration
* All services required for BioPortal Stack are automatically started on boot. For troubleshooting purposes you can manually stop/start services:
** <code>bprestart</code>: manually restart services required for BioPortal Stack.
** <code>bpstart</code>: manually start services.
** <code>bpstop</code>: manually stop services
* Start individual services:
** <code>/sbin/service httpd start</code>
** <code>/sbin/service memcached start</code>
** <code>/sbin/service tomcat6 start</code>
** <code>/sbin/service mgrep start</code>
** <code>/sbin/service 4s-httpd-ontologies_api start</code>
** <code>/sbin/service unicorn start</code>
* Stop individual services:
** <code>/sbin/service httpd stop</code>
** <code>/sbin/service memcached stop</code>
** <code>/sbin/service tomcat6 stop</code>
** <code>/sbin/service mgrep stop</code>
** <code>/sbin/service 4s-httpd-ontologies_api stop</code>
** <code>/sbin/service unicorn stop</code>

== License ==
All NCBO software is released with the 2-clause BSD license. Source code is included on the Virtual Appliance.

User talk:Vemonet

2016-01-27T18:41:19Z

Alexskr: Welcome!

'''Welcome to ''NCBO Wiki''!'''
We hope you will contribute much and well.
You will probably want to read the [[Help:Contents|help pages]].
Again, welcome and have fun! [[User:Alexskr|alexskr]] ([[User talk:Alexskr|talk]]) 10:41, 27 January 2016 (PST)

2014-11-26T23:53:11Z

Alexskr: /* Amazon AWS AMI */

== NCBO VIRTUAL APPLIANCE v2.2 IS NOW AVAILABLE ==
The NCBO Virtual Appliance has been updated to use NCBO's new v4.0 software infrastructure, including the use of an RDF triplestore as the primary data storage mechanism. Please read below as much of the Appliance workflow has changed.

For documentation of v1.0 Virtual Appliances, please see our [http://www.bioontology.org/wiki/index.php?title=Category:NCBO_Virtual_Appliance&oldid=12610 archive].

== Virtual Appliance Basics ==

The NCBO Virtual Appliance image contains a pre-installed, pre-configured version of commonly-used open source NCBO software running on a Linux operating system.

It is available as a VMWare Virtual Appliance OVF as well as Amazon AWS AMI and can be obtained by contacting support@bioontology.org.

The following software is included on the image as of v2.2:
* Ontologies API (REST service)
* Annotator
* Recommender
* BioPortal Web User Interface (including ontology visualization, widgets, biomixer, and Annotator UI)

Please see below for how-to documentation for managing the software and running data population for Annotator.

== Getting Started ==
=== VMWare Virtual Appliance ===
* To obtain the VMWare Virtual Appliance, contact [mailto:support@bioontology.org NCBO Support] and include your BioPortal account username. You can create a BioPortal account at: http://bit.ly/bioportal-account
* The download is provided as a zip archive containing several files. One of these is an Open Virtualization Format (OVF) file that may need to be [http://www.bioontology.org/wiki/index.php/Virtual_Appliance_FAQ#How_can_I_use_the_OVF_image_with_my_virtualization_software.3F_.28VMWare.2C_VirtualBox.2C_KVM.2C_Xen.2C_etc.29 converted to work in your virtualization environment].
* You can supply the hostname (machine name) for the virtual machine during the deployment process. Documentation will refer to this hostname as 'example'.
* '''Change default passwords'''
** Operating System
*** Username: <code>root</code>
*** Password: password is prompted on the first boot
** BioPortal Admin User
*** Username: <code>admin</code>
*** Password: <code>changeme</code>

=== Amazon AWS AMI ===
Amazon AMI is available on the [https://aws.amazon.com/marketplace/seller-profile/ref=dtl_pcp_sold_by?ie=UTF8&id=76948a46-8f8a-4a68-9a5c-3e3ff6b82d10 AWS Market Place]. Please contact [mailto:support@bioontology.org NCBO Support] for more information.
Once the instance is running, enter the public DNS provided by Amazon into your browser to access BioPortal web interface. The default application administrator is 'admin' and the initial password is the Instance ID. You can also SSH to the machine using the username 'ec2-user' and your Amazon private key.

=== General Instruction ===
* Add an ontology using the BioPortal Admin User here: http://{YourDomainName}/ontologies/new
** The ncbo_cron project is configured to automatically process new ontologies every 5 minutes (see [http://www.bioontology.org/wiki/index.php/Virtual_Appliance_FAQ#When_are_new_ontologies_parsed.3F documentation for enabling the scheduler]). This processing includes:
*** Parsing any new, unparsed ontologies
*** Calculating a set of metrics for these ontologies
*** Indexing these ontologies for use with search
*** Processing the ontology for use with the annotator
* REST services are available at the following location:
** http://example:8080
** http://example:8080/documentation

== System Requirements ==
The following requirements are for the resources that you devote to your Appliance instance, not for the machine running your host environment. For example, if you are using a system with 4GB of RAM, then you will need to devote all of that RAM to your guest Appliance.

'''Note: these requirements are for basic usage'''. System requirements will vary greatly depending on the size of the ontologies you work with, the number of ontologies in the system, and the number of concurrent requests that the system needs to respond to. It can also vary depending on how the ontologies are used. For example, the search index can be RAM-intensive but parsing ontologies can be CPU-intensive. You will need to experiment with your Appliance resource settings to find what works for your scenario.

* Minimum
** 2 CPU (2 GHz)
** 4GB RAM
** Hard disk space: 20GB

* Recommended for heavier usage
** 4 CPU (3 GHz)
** 8GB RAM
** Hard disk space: 20GB (or more depending on number/size of ontologies)

== Image Format and Operating System Details ==
The NCBO Appliance image was created using the [http://www.vmware.com/appliances/getting-started/learn/ovf.html Open Virtualization Format], which should allow the machine to be used in a variety of environments.

The operating system is CentOS 6.5 64-bit running:
*Tomcat 6.0.26
*Solr 4.7.2
*Java 7
*MySQL 5.1.x
*Rails 2.3.x
*Ruby 2.0.0p353
*memcached
*redis 2.6.14
*nginx 1.6.0
*4store
*Passenger/Apache

The following applications use these services/runtime environments:
* Sinatra, Ruby, 4store, redis
** Ontologies API
** Annotator
** Recommender
* Rails, Ruby, memcached, mysql
** BioPortal Web User Interface (including ontology visualization, Flex widgets, biomixer, Annotator)
* Tomcat, Solr
** Search index

== Basic System Administration ==
* Most of our administration scripts and build environment assume that you will be running as the root user.
* Helper commands:
** <code>bpstart</code>: the required services are started on boot automatically, but if they need to be started automatically
** <code>bpstop</code>: manually stop services
** <code>bprestart</code>: manually start/stop services
* Start individual services:
** <code>/sbin/service httpd start</code>
** <code>/sbin/service memcached start</code>
** <code>/sbin/service tomcat6 start</code>
** <code>/sbin/service mgrep start</code>
** <code>/sbin/service 4s-httpd-ontologies_api start</code>
** <code>/sbin/service unicorn start</code>
* Stop individual services:
** <code>/sbin/service httpd stop</code>
** <code>/sbin/service memcached stop</code>
** <code>/sbin/service tomcat6 stop</code>
** <code>/sbin/service mgrep stop</code>
** <code>/sbin/service 4s-httpd-ontologies_api stop</code>
** <code>/sbin/service unicorn stop</code>

== License ==
All NCBO software is released with the 2-clause BSD license. Source code is included on the Virtual Appliance.