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- Aug 07, 2013
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Andy Yates authored
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Andy Yates authored
After talking to Compara we found the need to support additional lookups with the full id cache. Since all values are stored in memory the lookup is very easy to compute.
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Andy Yates authored
The production and web teams have reported odd going ons when people copy from staging onto another server. This is because this script optimises databases before copying. These DBs should already be optimised so there is no need to do this stage. In fact it can alter the checksums of the MYI files which causes the webteam to wonder if data has been switched out without them knowing.
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Andy Yates authored
Leo submitted patch. We support pgsql as a way of defining the driver. This is inline with us accepting sqlite as a valid synonym for DBD::SQLite.
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Andy Yates authored
To provide improved querying of caches we now support SQL statements. These queries return a list of keys (normally primary key db identifiers) defining a list of objects to return. It is up to sub-BaseCache implementations to deal with the nitty gritty of cache mis-hits (something they need to do anyway).
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- Aug 06, 2013
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Alessandro Vullo authored
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Alessandro Vullo authored
- seq: pass defined slice intervals to trigger the correct program flow in SequenceAdaptor - project: removed since believed to have bugs - project_org: removed since it's not used anywhere
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Kieron Taylor authored
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Andy Yates authored
The code previously allowed bogus numbers through into the final slice which caused errors in later methods. The website crashed because of this. We will reject anything that was not an integer if the start or end was defined.
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Alessandro Vullo authored
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Andy Yates authored
Nathan requested methods which can perform this kind of task (assert the contents of a data structure). We support 1 level of arrays and hashes. All test cases pass at time of writing. Methods for capturing method returns were not implemented. They do not fit into the Utils way of doing (no method actually performs a task on an object they just report what it is).
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- Aug 05, 2013
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Magali Ruffier authored
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Magali Ruffier authored
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Magali Ruffier authored
also some ergonomical changes: - get a count+ is test replaced by is_count method - variable names declared at the top of the modules, so can easily change gene/dbid/db used if the test database changes
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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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Alessandro Vullo authored
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Alessandro Vullo authored
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Alessandro Vullo authored
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- Aug 02, 2013
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Magali Ruffier authored
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Magali Ruffier authored
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Alessandro Vullo authored
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Alessandro Vullo authored
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Alessandro Vullo authored
Changed expected GTF in some cases: the start/stop codons should not have been there (incomplete CDS annotation)
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- Jul 31, 2013
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Alessandro Vullo authored
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James Allen authored
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Alessandro Vullo authored
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Alessandro Vullo authored
Removed get_all_ExternalFeatures method, now borrowed from parent where the corresponding adaptor handle the circular slice case
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Alessandro Vullo authored
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Alessandro Vullo authored
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Alessandro Vullo authored
Removed some Slice overridden get_all_(Feature) methods since features/slices spanning the origin of replication are handled the corresponding feature adaptor
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Alessandro Vullo authored
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- Jul 30, 2013
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Andy Yates authored
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Magali Ruffier authored
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Magali Ruffier authored
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Andy Yates authored
Modified the enum on object_xref from 72->73 patch c and the redump re-did some data. Such as choosing a different encoding for some very small values. All changes are small though.
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Andy Yates authored
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Andy Yates authored
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Magali Ruffier authored
now fully testing patches and haplotypes
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