Matthew Laird authored 9 years ago and Kieron Taylor committed 9 years ago

wekane doesn't like to be inline in this context, but I'm not positive this will actually get all the variation errors.

Speed up transcript_variation fetch (copy of master PR)

Use a hash instead of grepping loads, and assign the VF
properly to the TV so it doesn't go and load it again.

Also needs a fix to VariationFeatureOverlap.pm in
ensembl-variation to properly go faster.

some missing config variables

Enscoresw 1551

Introduce a custom logger middleware to forcibly replace the starman access logger. Allows us to provide file rotation amongst other logging features. Without it we can only amalgamate the logs together into a single handler.

Completed rate limiting override header, a custom header that removed the 429 responses for rate limiting can be set at startup now.
Added tests for the rate limiting override header.

Conflicts:
	lib/Plack/Middleware/EnsThrottle.pm

Change Retry-After resolution to round up to the nearest second, accuracy on some platforms is not sufficient for this to work reliably on some tests. Also, sub-second resolution for a header like this just doesn't feel very HTTPy.
Remove the skip for the ratelimit test in travis

Rate limiting whitelist based on headers provided by client. Stashing initial changes to switch to master branch.

ENSCORESW-1480

- Removed redundant code for calling _process_subseq()
- Fixed calculation error when translating from genomic space to protein space
- Added tests for single bp regions, both in direct sequences and translated sequence

- Allow users to specify start and end coordinates for a sequence when using the /sequence/id endpoint
- Testing for sub-sequence calls
- Added new tests to harness to check return code and do a regex test on the response regardless of return code (ie. text response on a 400)
- Modified tests to use these new test types for start/end coordinates beyond sequence boundaries

schema patch for release 83

Correct summary_as_hash key

Fixes so Conservation plugin works (master)

add variant set list

Feature/ld documentation

Replace Bio::DB::Fasta with faidx_xs