obofoundry / purl.obolibrary.org Goto Github PK
View Code? Open in Web Editor NEWA system for managing OBO PURLs
License: BSD 3-Clause "New" or "Revised" License
A system for managing OBO PURLs
License: BSD 3-Clause "New" or "Revised" License
Does not use OBO identifiers, example: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#BioAssay
Does not use OBO ID Policy. Example: http://purl.obolibrary.org/obo/geo.owl#GEO_000000102
http://purl.obolibrary.org/obo/dpo.owl does not resolve. BBOP redirects terms to Ontobee, but Ontobee does not include this ontology.
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:
config/foo.yml
file in your browser; that should automatically make a pull request? somebody still has to update the .htaccess
fileconfig/foo.yml
, run a Python script, commit to the fork, and make a pull request with updated YAML and .htaccess filesPURLs redirect to Ontobee, but ontology is not 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.
Current PURLs redirect to Ontobee, but ontology is not loaded in Ontobee or OLS.
Does not use OBO PURLs: http://www.ebi.ac.uk/swo/SWO_0000001
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.
Does not use OBO ID Policy. Example: http://www.biomodels.net/kisao/KISAO#KISAO_0000000
Terms redirect to Ontobee, but the ontology is not loaded there.
Most content is missing from Ontobee. OLS has 404.
Do not use OBO identifiers:
PURLs seem to work, but most of the content is missing from both Ontobee and OLS.
Does not use OBO ID Policy. Example: http://identifiers.org/mamo/MAMO_0000003
I'm getting a 500. I think the BBOP redirect is circular.
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?
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.
Mixed case problem:
Maybe an Ontobee problem.
Case sensitive: http://purl.obolibrary.org/obo/MmusDv_0000000
May be an Ontobee problem.
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.
New ontology. I have to set up the PURLs.
Terms are redirecting to 404s: http://purl.obolibrary.org/obo/UPHENO_0000000
Ontology is not in Ontobee.
Case sensitive: http://purl.obolibrary.org/obo/HsapDv_0000174
Terms redirect to Ontobee, but ontology is not loaded in Ontobee or OLS.
Does not follow OBO ID policy.
Does not use OBO standard identifiers.
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.
PURLs seem to work, but most of the content is missing from both Ontobee and OLS.
Problems with Ontobee and missing from OLS.
Something is wrong on Ontobee, and terms are not appearing on OLS. Need to check again.
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.
Current PURLs redirect to Ontobee, but ontology is not loaded in Ontobee or OLS.
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.
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:
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.
Current PURLs redirect to Ontobee, but the ontology is not in Ontobee or OLS.
Current PURLs redirect to Ontobee, but ontology is not loaded in Ontobee or OLS.
I'm getting a 500. I think the BBOP redirect is circular. @cmungall
Something is wrong on Ontobee, and terms are not appearing on OLS. Need to check again.
Current PURLs redirect to Ontobee, but ontology does not exist in Ontobee or OLS.
ID is lowercase: http://purl.obolibrary.org/obo/sep_00073
Current PURLs redirect to Ontobee, but ontology is not in Ontobee or OLS.
I couldn't find any content for this ontology in a quick search.
Case sensitive: http://purl.obolibrary.org/obo/OlatDv_0000020
Problem with mixed case:
This could be 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/
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