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- Oct 23, 2013
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Andy Yates authored
We now check the roundtripping of to_hash(). Should not have built this method without a test case. Would have fixed the issue long ago!
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- Oct 18, 2013
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Alessandro Vullo authored
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- Oct 17, 2013
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Andy Yates authored
Method in GeneAdaptor fetch_all_alt_alleles() was not working as it did prior to our changes. It normally returned everything bar itself. That has been fixed. Also stopped a warning which was driving the webteam mad.
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Andy Yates authored
[ENSCORESW-720] and [ENSCORESW-721]. Allowing default HashRef in execute() and sleep for less than a second. First issue raised by Lee from EG. He wanted to be able to work with hash refs in the same way you can do with ArrayRefs. Done and dusted. Second issue raised by me. Want to sleep for periods less than 1 second for the test suite sanity.
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- Oct 10, 2013
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Dan Staines authored
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- Oct 03, 2013
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Andy Yates authored
The code did not attempt to build the additional lookup before fetching from it. Our solution is to switch to requesting the cache in get_????_additional_lookup() which will trigger the building of the additional lookup.
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- Oct 02, 2013
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Magali Ruffier authored
added test for 'fetch_all_by_feature_class' with density features
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Andy Yates authored
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- Oct 01, 2013
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Andy Yates authored
Other schemas may need this which do not go through a process of removing old/retired seq region ids in favour of their new ids. When querying by a slice this is automatically delt with. When fetching by an ID you now need to force the search on.
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Andy Yates authored
It seems that $DBI::errstr has a very strange life. We can get the error message recived by incorrect connections or bad drivers (DBD::mysql is missing) when we just warn the error. However concatenating it into another string makes the message disapear. Even assignment and then concat will not work. Instead we have switched to using the $@. This has the error in it.
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- Sep 27, 2013
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Andy Yates authored
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Magali Ruffier authored
replaced ok tests with is where possible replaced core test database with patch database
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- Sep 23, 2013
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Magali Ruffier authored
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Magali Ruffier authored
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- Sep 19, 2013
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Magali Ruffier authored
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Magali Ruffier authored
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Magali Ruffier authored
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- Sep 18, 2013
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Andy Yates authored
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- Sep 17, 2013
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Andy Yates authored
We needed more methods to be able to handle alt allele group interactions. We also needed to make sure a single gene could not be added more than once. Think we got this one fixed
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- Sep 12, 2013
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Alessandro Vullo authored
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Alessandro Vullo authored
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Alessandro Vullo authored
Removed dependencies on non-core APIs.
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Andy Yates authored
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- Sep 11, 2013
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Alessandro Vullo authored
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Alessandro Vullo authored
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Alessandro Vullo authored
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Magali Ruffier authored
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Alessandro Vullo authored
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- Sep 06, 2013
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Alessandro Vullo authored
Added just a test for the new method filter_dir at the moment.
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- Sep 03, 2013
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Magali Ruffier authored
updated test cases to check integrity of api once deprecated tables, columns and methods have been removed test databases patched to schema 74
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- Aug 30, 2013
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Magali Ruffier authored
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- Aug 27, 2013
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Andy Yates authored
Committing since we are now beyond the branch point in the API. This allows a FullIdCache to key on various alternative identifiers/keys generated by the implementing class. It means that if you want this functionality you need to sub-class FullIdCache.
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Magali Ruffier authored
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Magali Ruffier authored
is not required for ontology database but allows for compatibility with metacontainer and schema version control like other databases
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Magali Ruffier authored
allows for future schema patching added single table.sql file, replaces the need for individual sql files for each table
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- Aug 22, 2013
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Magali Ruffier authored
also updated existing tests to use is rather than ok whenever possible
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- Aug 08, 2013
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Andy Yates authored
The test schema was out of sync for ages due to it never being patched using the patch sets. This is no longer the case. We needed a one shot resynchronisation between the live schema and this test schema. All test cases have been run and still pass. Assuming the processes has not destroyed data. Any data changes seem to be related to different levels of precision being emitted in the files. Meta coord was updated.
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Alessandro Vullo authored
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Alessandro Vullo authored
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Magali Ruffier authored
patch was mentioned in meta table but not actually applied
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