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- Oct 09, 2013
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Arnaud Kerhornou authored
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James Allen authored
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Kieron Taylor authored
Reverted Production DB dependency in order to allow Xref pipeline to run. Changes can be reinstated once slightly more mature.
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- Oct 08, 2013
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Kieron Taylor authored
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Kieron Taylor authored
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Daniel Barrell authored
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- Oct 07, 2013
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Alessandro Vullo authored
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Magali Ruffier authored
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Steve Trevanion authored
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- Oct 04, 2013
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Andy Yates authored
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James Allen 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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Dan Sheppard authored
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Andy Yates authored
[ENSCORESW-577]. Fixing a logical hole where we reqiured a method to be defined but did nothing with it. Looks like I was between implementations. Now switched to requesting the additional lookup keys and if the hash was empty then skipping any additional work. Seems to behave a lot better and means users need only override one method in the object.
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Magali Ruffier authored
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Magali Ruffier authored
(ie, include the duplicated sequence Y has in common with X rather than the two sequences unique to Y)
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- Oct 02, 2013
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Magali Ruffier authored
DensityType is not a feature but is the object storing the analysis related to the DensityFeature
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Magali Ruffier authored
unlike other features, the related analysis is stored in the density type table
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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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Kieron Taylor authored
Fixed a warning that was testing the wrong value and failing to verify a store_alt_alleles call properly
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ens-carlos authored
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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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Andy Yates authored
The optimise tree step can take a very long time and cause web timeouts. We have added a time limit expressed in floting-point seconds. If an optimisation is taking longer than the specified time we will abort any more attempts.
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Andy Yates authored
The optimise tree step can take a very long time and cause web timeouts. We have added a time limit expressed in floting-point seconds. If an optimisation is taking longer than the specified time we will abort any more attempts.
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Andy Yates authored
The original code decalred a max of 2K ids because of max allowed packet concerns and wanted the packet to stay close to 256KB. However the actual figure was off by a factor of 8 as the max packet is 1MB not 1Mbit. We have increased the limit to 16K when working with numerics. Strings are still at 2K due to their possible large size.
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Andy Yates authored
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- Sep 30, 2013
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Andy Yates authored
Fixes for the alt alleles code. We needed to make sure we used the right variables in the code. Also needed to make sure an array is actually defined during construction
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Andy Yates authored
Fixing an issue raised by vega and non-standard DBAdaptor group names. Vega use ensembl to denote the ensembl db. We assumed incorrectly that core could always be used. That would always fail the moment a different group name was used
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Andreas Kusalananda Kähäri authored
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- Sep 27, 2013
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Andy Yates authored
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Andy Yates authored
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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 26, 2013
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Andreas Kusalananda Kähäri authored
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Andreas Kusalananda Kähäri authored
by farm3.
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Andreas Kusalananda Kähäri authored
small queue for exonerate to finish. Also added spaces after -R and -J switches.
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Andreas Kusalananda Kähäri authored
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Arnaud Kerhornou authored
Making consistent through plants species the use of ncRNA_EG source for maintaining ncRNA genes xrefs asscoiated with logic_name ncrna_eg
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