OBO PURLs

This repository provides tools for managing OBO Foundry Permanent URLs (PURLs). Like https://github.com/perma-id/w3id.org we use per-directory Apache configuration files (.htaccess files), each of which uses RedirectMatch directives to redirect PURL requests to their proper targets. Unlike w3id.org, we do not edit the Apache configuration files by hand. Instead we have a simple YAML configuration format, and scripts to translate the YAML configuration into Apache configuration. The YAML files are easier to read and write, and allow us to validate and test PURLs automatically.

Status

All http://purl.obolibrary.org/obo/ PURLs are now handled by this system, with the exception of some open issues. PURLs that do not match any rule in this system will fall back to the old PURL.org system.

Adding and Updating PURLs

Please use one of these four options to make changes to the PURLs:

1. Create a new issue describing the change you require.

2. Browse to the configuration file you want to change and click the "pencil" icon to edit it.

3. Add a new configuration file.

4. Fork this repository and make a pull request.

All changes are reviewed before they are merged into the master branch. Once merged, updated PURLs will be active within 20 minutes.

Configuration Format

Each OBO project using this service gets a YAML configuration file in config/. That YAML configuration file is used to generate an Apache .htaccess file for that ontology. That Apache configuration will apply to all PURLs for that project.

Every YAML configuration file must have these fields:

• idspace: the project's IDSPACE, case sensitive, usually uppercase
• base_url: the part of a PURL that comes after the domain, usually lowercase
• term_browser: usually ontobee or ols but can be custom (see below)
• products: a list of primary files for the ontology and the URLs to redirect them to; an .owl file is required, and an .obo file is optional

Optional fields include:

• example_terms: a list of one or more term IDs for automated testing
• base_redirect: If your project redirects its base_url, then you will need a base_redirect: entry. So base_redirect: http://obi-ontology.org will redirect http://purl.obolibrary.org/obo/obi to http://obi-ontology.org.
• entries: a list of other PURLs under the base_url, see below

Here's an example adapted from the config/obi.yml file:

idspace: OBI
base_url: /obo/obi

products:
- obi.owl: http://svn.code.sf.net/p/obi/code/releases/2015-09-15/obi.owl

term_browser: ontobee
example_terms:
- OBI_0000070

entries:
- exact: /wiki
  replacement: http://obi-ontology.org

Most of these fields are straightforward, but the entries: need some more explanation.

Entries

Each YAML configuration file contains the keyword entries: followed by a list of entries. Each entry defines an Apache RedirectMatch directive for matching URLs and redirecting to new URLs. Every entry begins with a - , followed by keywords and values on indented lines. There are three types of entries:

1. exact: The simplest entry matches an exact URL and returns an exact replacement
2. prefix: These entries match the first part of a URL and replace just that prefix part
3. regex: These entries use powerful regular expressions, and should be avoided unless absolutely necessary.

The # character indicates a comment, which is not considered part of the configuration.

See the tools/examples/test2/test2.yml and tools/examples/test2/test2.htaccess for examples.

Exact

In the most common case, your PURL should match a unique URL and redirect to a unique URL. Here's an example from the config/obi.yml file:

- exact: /obi.owl
  replacement: http://svn.code.sf.net/p/obi/code/releases/2015-10-20/obi.owl

This entry will match exactly the URL http://purl.obolibrary.org/obo/obi/obi.owl, and it will redirect to exactly http://svn.code.sf.net/p/obi/code/releases/2015-10-20/obi.owl. The matched domain name is fixed http://purl.obolibrary.org; the next part is project-specific /obo/obi/; the final part is taken from the entry /obi.owl. The replacement is expected to be a valid, absolute URL, starting with http.

Behind the scenes, the entry is translated into a case insensitive Apache RedirectMatch directive in obo/obi/.htaccess by escaping special characters and "anchoring" with initial ^, the project's base URL, and final $:

RedirectMatch temp "(?i)^/2015\-09\-15/obi\.owl$" "http://svn.code.sf.net/p/obi/code/releases/2015-09-15/obi.owl"

Prefix

You can also match and replace just the first part of a URL, leaving the rest unchanged. This allows you to define one entry that redirects many URLs matching a common prefix. Another example from config/obi.yml:

- prefix: /branches/
  replacement: http://obi.svn.sourceforge.net/svnroot/obi/trunk/src/ontology/branches/

This entry will match the URL http://purl.obolibrary.org/obo/obi/branches/obi.owl (for example), replace the first part http://purl.obolibrary.org/obo/obi/branches/ with http://obi.svn.sourceforge.net/svnroot/obi/trunk/src/ontology/branches/, resulting in http://obi.svn.sourceforge.net/svnroot/obi/trunk/src/ontology/branches/obi.owl. Effectively, the obi.owl is appended to the replacement.

The translation is similar, with the addition of (.*) wildcard and a $1 "backreference" at the ends of the given strings:

RedirectMatch temp "(?i)^/branches/(.*)$" "http://obi.svn.sourceforge.net/svnroot/obi/trunk/src/ontology/branches/$1"

Regex

Regular expression entries should only be needed very rarely, and should always be used very carefully.

For the regular expression type, the value of the regex: and replacement: keywords should contain regular expressions in exactly the format expected by Apache RedirectMatch. The values will be quoted, but no other changes will be made to them. Consider using (?i) to make the match case insensitive.

Tests

Every prefix or regex entry should also have a tests: keyword, with a list of additional URLs to check. Each test requires a from: value (like exact:) and a to: value (like replacement:). Here's an example:

- prefix: /branches/
  replacement: http://obi.svn.sourceforge.net/svnroot/obi/trunk/src/ontology/branches/
  tests:
  - from: /branches/obi.owl
    to: http://obi.svn.sourceforge.net/svnroot/obi/trunk/src/ontology/branches/obi.owl

Order of Entries

Apache RedirectMatch directives are processed in the order that they appear in the configuration file. Be careful that your prefix and regex entries do not conflict with your other entries. The YAML-to-Apache translation preserves the order of entries, so you can control the order of processing, but it's best to avoid conflicts.

Custom Term Browsers

If your project does not use Ontobee or OLS as a term browser, you must specify term_browser: custom in your project's YAML configuration file, and provide a regex entry in the config/obo.yml configuration file. Here's an example for ChEBI:

# Terms for CHEBI
- regex: ^/obo/CHEBI_(\d+)$
  replacement: http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:$1
  tests:
  - from: /CHEBI_15377
    to: http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:15377

Note that term redirect rules are case sensitive.

Since these are regex entries, and could affect multiple projects, we prefer that OBO admins are the only ones to edit obo.yml. If you need a change to the term redirect entry for your project, please create a new issue.

Development and Testing

The PURL system runs on Ubuntu Linux, but you can test your changes using a virtual machine (VM) that runs on Windows, Mac, or Linux. Your local development machine (Windows, Mac, or Linux) will be the "host" machine. The VM will be a copy of Ubuntu Linux that runs on your host, and can be thrown away when you're done testing.

You'll have to install these three tools on your host machine:

1. VirtualBox to run the VM
2. Vagrant to setting up the VM
3. Ansible to provisioning the VM with the right software

All of these tools are free for you to use. If you're using macOS with Homebrew, then you can install the three tools like this:

brew cask install Caskroom/cask/vagrant
brew cask install Caskroom/cask/virtualbox
brew install ansible

Once the three tools are installed, check out a copy of this repository and start the VM:

git clone https://github.com/OBOFoundry/purl.obolibrary.org.git
cd purl.obolibrary.org/tools
vagrant up

This will:

1. download an Ubuntu Linux virtual machine (using Vagrant and the tools/Vagrantfile)
2. run it (using VirtualBox)
3. configure it as a web server (using Ansible and the tools/site.yml file)

If something goes wrong with step 3, the vagrant provision command will run Ansible again. Please report any issues that you run into.

Use your favourite text editor on your host machine to make your changes to the files in the purl.obolibrary.org directory. That directory will be synchronized with the /var/www/purl.obolibrary.org directory inside the VM. When you're ready to test your changes, log in to the VM and rebuild the .htaccess files:

vagrant ssh
cd /var/www/purl.obolibrary.org
make clean all

You can use the web browser on the host machine to see the results, using URLs starting with http://172.16.100.10/obo/, such as http://172.16.100.10/obo/OBI_0000070. You can also run an automated tests. To check a single config/foo.yml configuration file, run one of these commands

make clean validate-foo
make clean build-foo

To update and test the whole system, run

make clean all test

Detailed test results will be listed in tests/development/*.tsv files, with their expected and actual values. If you're making changes to the project tools, you can test them against the tools/examples/ files with:

make clean test-examples

Expert users who have to run more extensive tests can consider (temporarily) modifying their hosts file to redirect purl.obolibrary.org to the test server.

When you're done with the VM, log out with exit. Then you can choose to suspend the VM with

vagrant suspend

or delete the VM with

vagrant destroy

You can test against the production PURL server using make test-production. We only make one request per second, to avoid abusing the server, so this can take along time.

Optional: Sync VirtualBox Guest Additions

If you keep your development VM for any length of time you may be presented with this message upon starting your VM:

==> default: A newer version of the box 'ubuntu/trusty64' is available! You currently
==> default: have version '20190122.1.1'. The latest is version '20190206.0.0'. Run
==> default: `vagrant box update` to update.

If you upgrade, then the next time you resume your box you may receive the warning:

[default] The guest additions on this VM do not match the install version of
VirtualBox! This may cause things such as forwarded ports, shared
folders, and more to not work properly. If any of those things fail on
this machine, please update the guest additions and repackage the
box.

To automatically sync with VirtualBox's Guest Additions at startup (and thus avoid this warning) you can install vagrant-vbguest like so:

• vagrant plugin install vagrant-vbguest (in the tools directory on the host machine)

Now, whenever you bring up your VM, it will check the version of the VM's guest additions and automatically bring them up to date whenever this is needed.

Deployment

Deployment is automated using Ansible, and targets a stock Ubuntu Linux server with Python installed. You should install on a fresh server, not one that's running other applications, unless you really know what you're doing.

Install Ansible on your local machine, add the IP address or hostname of your target server to tools/hosts, then run:

cd tools
ansible-playbook -i hosts site.yml

Ansible uses SSH to connect to the target server an execute the tasks defined in tools/site.yml. If you have trouble connecting, you may have to adjust your SSH configuration to be more automatic, say by editing your .ssh/config.

You can re-run Ansible as you make changes. Once the system is running, it will fetch changes from the master Git repository every 10 minutes. From your local machine, you can test all URLs against any target server, e.g.:

export PRODUCTION=url.ontodev.org; make clean test-production

The make safe-update task will check Travis-CI to ensure that the latest build on the master branch passed all automated tests, and that it is newer than the last time safe-update completed. Then it will pull from the Git repository and rebuild the site. This should be safe for a cron task to synchronize PURLs with the repository.

Copyright

The copyright for the OBO PURL code and documentation belongs to the respective authors. The code is distributed under a BSD3 license.