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.

Testing and Deployment

We use Docker to test the PURL system locally and deploy it. See the docker/ directory for code and documentation. Test the system locally like so:

$ docker pull ubuntu:20.04
$ docker build -f docker/Dockerfile -t purl:latest .
$ docker run --rm -it -v "$(pwd)/config":/var/www/purl.obolibrary.org/config purl bash
# sudo su
# cd /var/www/purl.obolibrary.org
# make clean all test

To check a single config/foo.yml configuration file, run one of these commands

# make clean validate-foo
# make clean build-foo

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

Copyright

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