Difference between revisions of "Virtual Appliance FAQ"

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[[Category:NCBO Virtual Appliance]]
 
[[Category:NCBO Virtual Appliance]]
 +
[[Category:Migrated to GitHub]]
  
= NCBO VIRTUAL APPLIANCE v2.0 FAQ =
+
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].  
This FAQ now covers the NCBO Virtual Appliance v2.0. The FAQ for v1.0 is available in the [http://www.bioontology.org/wiki/index.php?title=Virtual_Appliance_FAQ&oldid=12621 archive]
 
  
 +
In particular '''this content''' is mostly at the '''[https://https://ontoportal.github.io/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 =
 
= Ontology Management =
  
 
== How do I add or change categories or groups? ==
 
== How do I add or change categories or groups? ==
There is currently no UI administrator interface (though this will likely be added in future versions). Categories and groups can be added using a console after logging into the Appliance as the root user.
+
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>
 
<pre>
 
# from the bash shell:
 
# from the bash shell:
Line 22: Line 71:
 
group.acronym = "MY_GRP"
 
group.acronym = "MY_GRP"
 
group.save
 
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>
 
</pre>
  
 
== How can I migrate ontologies from BioPortal or previous NCBO Virtual Appliance versions into a new Appliance? ==
 
== How can I migrate ontologies from BioPortal or previous NCBO Virtual Appliance versions into a new Appliance? ==
Programmatic migrations are currently unsupported. Ontologies can be manually downloaded and added using the Web UI.
+
 
 +
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 =
 
= Ontology Parsing =
Line 32: Line 124:
  
 
== How do I manually parse an ontology? ==
 
== How do I manually parse an ontology? ==
To manually parse an ontology, you will need to interact with the code using the console:
+
To manually parse an ontology, you will need to interact with the code using the console after switching to ontoportal user:
 
<pre>
 
<pre>
 
# from the bash shell:
 
# from the bash shell:
Line 42: Line 134:
 
logger = Logger.new(STDOUT)
 
logger = Logger.new(STDOUT)
 
submission.process_submission(logger)
 
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>
 
</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? ==
 
== How do I know if an ontology has parsed? ==
Line 48: Line 150:
  
 
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:
 
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://example:8080/ontologies/{ontology_acronym}/latest_submission?include=all
+
* 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
 
* You can look for the submissionStatus attribute to get the status
  
Line 57: Line 159:
 
= Web User Interface =
 
= Web User Interface =
 
== How can I clear the memcached-based UI cache? ==
 
== How can I clear the memcached-based UI cache? ==
* If you are logged in as the admin user, simply visit http://example/admin and click the "Flush Memcache" button. There should be a response indicating success or failure.
+
* 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? ==
 
== How can I use widgets with my Virtual Appliance? ==
Line 186: Line 288:
  
 
== How can I use the Appliance on Amazon EC2? ==
 
== How can I use the Appliance on Amazon EC2? ==
The NCBO Virtual Appliance can be deployed in Amazon EC2. The AMI is available in US West (Northern California) region, has the id '''ami-f7e8c7b2''' and is built on the EBS-backed 64-bit Amazon Linux AMI 2013.03
+
 
* https://aws.amazon.com/amis/ncbo-bioportal-appliance-v1-1
+
Appliance is available on [https://aws.amazon.com/marketplace/pp/B00MX5YKVU Amazon Marketplace]
=== Installation Instructions ===
+
 
* Login to AWS Console: https://console.aws.amazon.com/ec2/home?region=us-west-1
+
=== What is the admin password for the AWS Appliance? ===
* Click on Instances → Launch Instance → Classic Wizard → Community AMIs → Choose an AMI:
+
 
** Search for “NCBO Appliance” and choose the latest version
+
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.
** Click '''Continue'''
 
* Instance Details:
 
** Instance Type = m1.large (or any other type with at least 2 cores and ~8 GB of RAM)
 
** Availability Zone = No preference
 
** Click '''Continue'''
 
* Advanced Instance Options:
 
** Termination Protection = Prevention against accidental termination
 
** Shutdown Behavior = Stop
 
** Click '''Continue'''
 
* Instance Tags:
 
** Name = Name this instance something meaningful
 
** Click '''Continue'''
 
* Key Pairs:
 
** Choose from your Existing Key Pairs or Create a Key Pair
 
** Click '''Continue'''
 
* Configure Firewall:
 
** Choose (you may need to create one first) a Security Group that has ports 22, 80, and 8080 open. It is recommended that you only allow the networks you need. We accept no responsibility/liability for machines getting compromised.
 
** Click '''Continue'''
 
* Review Instance Details:
 
** Make sure your settings are correct
 
** Click '''Launch'''
 
** Click '''Close'''
 
* Click on Instances (left hand side of the screen):
 
** Once the instance State has changed from Pending to Running and Status Checks is “2/2 checks passed”, login to the instance via the public hostname provided.
 
** Now you can SSH into the machine using your key-pair and '''ec2-user''' as the user name:
 
***  <code>ssh -i yourkey_pair ec2-user@{amazon public domain name}</code>
 
** The domain name can be retrieved by clicking on the instance and looking at the details that appear at the bottom of the screen. It should look similar to this but with a different set of numbers in the subdomain: ec2-10-0-0-1.us-west-1.compute.amazonaws.com
 

Latest revision as of 20:26, 12 June 2020


This content has been moved! Please find the new content for the 3.0 version of the Virtual Appliance at our new OntoPortal Virtual Appliance Administration pages.

In particular this content is mostly at the 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 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.
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:

ip address show eth0 | awk '/inet / {print $2}' | cut -d/ -f1'

  • External IP address from the terminal:

curl http://ipecho.net/plain; echo

  • 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:

 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"

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

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.

# 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

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.

# 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

How do I delete an ontology?

Deleting can be done using a console after logging into the Appliance as the ontoportal user.

# 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

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:

# 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()

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 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:

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?

How can I use widgets with my Virtual Appliance?

In addition to the existing instructions, you must define an additional Javascript variable in order to have the widgets communicate with your instance of the Virtual Appliance.

 var BP_SEARCH_SERVER = "http://{your_appliance_ip_or_domain_name}";

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?
(VMware, VirtualBox, KVM, Xen, etc)

VMware

You can use 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:

ovftool ncbo-appliance.ovf ncbo-appliance.vmx

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

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

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

<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>

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

virsh start ncbo-appliance

Xen

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

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

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"

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

xm create ncbo-appliance

How can I use the Appliance on Amazon EC2?

Appliance is available on 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.