obofoundry / purl.obolibrary.org Goto Github PK

As of c264b20 the validation requires that the replacement: be an absolute HTTP(S) or FTP URL.

When migrating from PURL.org, I've seen a few examples with relative redirects, e.g.

- exact: /ReleaseNotes
  replacement: /2012-07-20/ReleaseNotes

That's not a bad idea. But I'm worried about relaxing the validation too much. Do we allow any URL? Only absolute URLs and URLs that at relative to the same project? Suggestions are welcome.

Current PURLs redirect to Ontobee, but ontology does not exist in Ontobee or OLS.

Current PURLs redirect to Ontobee, but ontology is not in Ontobee or OLS.

Terms are redirecting to 404s: http://purl.obolibrary.org/obo/UPHENO_0000000

Ontology is not in Ontobee.

Current PURLs redirect to Ontobee, but the ontology is not in Ontobee or OLS.

Does not follow OBO ID policy.

Does not use OBO ID Policy. Example: http://purl.obolibrary.org/obo/geo.owl#GEO_000000102

Case sensitive: http://purl.obolibrary.org/obo/MmusDv_0000000

May be an Ontobee problem.

PURLs seem to work, but most of the content is missing from both Ontobee and OLS.

Problem with mixed case:

1. resolves: http://purl.obolibrary.org/obo/ExO_0000002
2. does not resolve: http://purl.obolibrary.org/obo/EXO_0000002

This could be an Ontobee problem.

http://purl.obolibrary.org/obo/dpo.owl does not resolve. BBOP redirects terms to Ontobee, but Ontobee does not include this ontology.

Case sensitive: http://purl.obolibrary.org/obo/HsapDv_0000174

See #17, #18.

Current PURLs redirect to Ontobee, but ontology is not loaded in Ontobee or OLS.

PURLs seem to work, but most of the content is missing from Ontobee.

Currently the exact entries are migrated in the order they appear in the XML, which I think is by creation date. It might be friendlier to sort them alphanumerically. It will not change behaviour of the system.

New ontology. I have to set up the PURLs.

PURLs redirect to Ontobee, but ontology is not in Ontobee or OLS.

Case sensitive: http://purl.obolibrary.org/obo/OlatDv_0000020

Do we need HTML pages to show on errors, and for the root page? Currently http://purl.obolibrary.org redirects to https://purl.org/docs/index.html.

PURLs seem to work, but most of the content is missing from both Ontobee and OLS.

Assuming we could write some kind of validator for the htaccess files, it should be easy to write a .travis.yml that can be used to assist with PR evaluation.

I see one entry in PURL.org: http://purl.obolibrary.org/obo/cheminf.owl

But otherwise they do not seem to use OBO PURLs for their terms.

I'm getting a 500. I think the BBOP redirect is circular.

Does not use OBO ID Policy. Example: http://identifiers.org/mamo/MAMO_0000003

Problems with Ontobee and missing from OLS.

I think that the Apache server should run directly against the master branch. So master can only contain vetted changes with updated .htaccess files that have passed the automatic tests (#2, #3).

From the user's perspective, easiest to hardest:

1. create a new issue with your request; an admin will make a pull request, test it automatically, then merge the PR
2. use GitHub to edit the config/foo.yml file in your browser; that should automatically make a pull request? somebody still has to update the .htaccess file
3. fork the repo, edit config/foo.yml, run a Python script, commit to the fork, and make a pull request with updated YAML and .htaccess files

Something is wrong on Ontobee, and terms are not appearing on OLS. Need to check again.

Something is wrong on Ontobee, and terms are not appearing on OLS. Need to check again.

Most content is missing from Ontobee. OLS has 404.

I'm getting a 500. I think the BBOP redirect is circular. @cmungall

Does not use OBO identifiers, example: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#BioAssay

Current PURLs redirect to Ontobee, but ontology is not loaded in Ontobee or OLS.

Does not use OBO ID Policy. Example: http://www.biomodels.net/kisao/KISAO#KISAO_0000000

Does not use OBO PURLs: http://www.ebi.ac.uk/swo/SWO_0000001

Current PURLs redirect to Ontobee, but ontology is not loaded in Ontobee or OLS.

Do not use OBO identifiers:

• NIF_Cell
• NIF_Dysfunction
• NIF_Grossanatomy

Current PURLs redirect to Ontobee, but ontology is not loaded in Ontobee or OLS.

Terms redirect to Ontobee, but ontology is not loaded in Ontobee or OLS.

http://purl.obolibrary.org/obo/dinto.owl points to a GitHub page, not an OWL file.

Currently BBOP redirects DINTO terms to Ontobee, but Ontobee does not include this ontology.

I couldn't find any content for this ontology in a quick search.

Current PURLs redirect to Ontobee, but ontology is not loaded in Ontobee or OLS.

For a given PURL there are two main things to check:

1. does the redirect work correctly, e.g. response code 302 with the correct Location header
2. does the target resolve, e.g. response code 200 with non-empty content

We could maintain a table of test data, with a selection of PURLs, and columns for source, redirect code, and target. Then we could have a script that uses the table to run these two types of test. Slightly more clever would be #TEST foo lines in the .htaccess files that would be assembled into a test suite.

We should also test some known-bad data, to ensure that the correct failure notifications are returned.

@cmungall: We may or may not want to run these tests with Travis, see #2.

Terms redirect to Ontobee, but the ontology is not loaded there.

ID is lowercase: http://purl.obolibrary.org/obo/sep_00073

Terms redirect to 404: http://purl.obolibrary.org/obo/TAXRANK_0000000 -> http://vertebrate-taxonomy-ontology.googlecode.com/svn/trunk/releases/about/TAXRANK_0000000

Mixed case problem:

1. resolves to a useful page: http://purl.obolibrary.org/obo/FBbi_00000001
2. does not resolve to a useful page: http://purl.obolibrary.org/obo/FBBI_00000001

Maybe an Ontobee problem.

Ontology exists in Ontobee with expected term IDs, but current PURLs redirect to OBA on Ontobee: http://www.ontobee.org/browser/rdf.php?o=OBA&iri=http://purl.obolibrary.org/obo/

To use this new system, we need to migrate our configuration from the current system. We should to be able to verify that migration is complete and correct (see also #3).

Given a copy of the current database table, a semi-automatic, one-time conversion should be pretty easy, and we can be pretty sure that we haven't missed anything. I don't know if this is possible.

Without a copy of the table, we can use the search interface: https://purl.org/docs/purl.html#search. The results can be scraped from the HTML, or we can fetch XML like this.

The search interface only returns 100 results at a time. This is enough for all the specific ontologies that I have checked: 44 for /obo/bfo/*, 66 for /obo/obi/*, 63 for /obo/iao/*, 1 for /obo/pro/*, 7 for /obo/go/*, 6 for /obo/chebi/*.

However, for the /obo/* path there are more than 100 results. Most of the results I see belong to PRO. And I think there might be other redirect magic going on for /obo/*. @cmungall?

Does not use OBO standard identifiers.