DO NOT MERGE - Just for comparison of latest updates#1
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All our changes were merged into the official OLS release. I created another PR to see what will happen if we just use that one.. |
(1) Fixes for the null-pointer exception and deadlock that slipped in as part of the implementation of ticket #241. (2) To pinpoint the errors encountered in (1), logging and exception handling has been improve slightly. (3) Ticket #236 has been address by not allowing any exception error messages to propagate to the front-end. (4) I introduced a typo in the API docs that I fixed. (5) Ticket #241 still has not been fixed.
for 404 errors to display sensible error message.
occurred` only for HTTP 500 status errors.
class renderer will handle when no language tag is present fixes #261
(1) Replaced log4j.xml with logback-test.xml since the code base is in actual fact using logback rather than log4j. (2) Loading of preferredRootTerms from an ontology has been added.
(1) Implementation (2) Simple integration test
Hard-incorporate Tommy's existing modified templates (from branch new-ui) over old-style html (with equivalent functionality), also adding new banner image. Fix a problem with Thymeleaf and self-closing tags. Implement dockerised solr and mongo instances: add appropriate dockerfile for OLS, plus bash scripts resprectively to create, and to run, the necessary docker image. Note that this is mostly untested: not only does the UI still require work, but functionality might also be broken.
Merge branch '3.x-dev'
…Displaying roots is working. What is not working consistently is displaying a specific term.
…You can also filter on ontology ids using the ids parameter fixes #275
…You can also filter on ontology ids using the ids parameter fixes #275
Depictions hotfix
…s inconsistent or has unsatisfiable classes. Ideally the pseudo reasoner should be used in these circumstances. For the test cases used efo, mondo - both the .obo and .owl and duo the Pseudo reasoner works well. However, for chebi it does not. The idea is to monitor use of the Structural Reasoner which will tell us which ontologies are incoherent. Then at a later stage we can test the Pseudo reasoner for these ontologies. Then there is also the possibility that the redesigned indexer may have less of a dependency on reasoners.
Pseudo reasoner
Pseudo reasoner
Fix a typo in the .m2 path
Add property information
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