Commits · release/76 · ensembl-gh-mirror / ensembl-rest

This project is mirrored from https://:*****@github.com/Ensembl/ensembl-rest. Pull mirroring updated Feb 03, 2023.

19 Sep, 2014 1 commit
- Create README.md · 09f022a8
  Magali Ruffier authored Sep 19, 2014
  
  09f022a8
05 Sep, 2014 3 commits
- Merge branch 'hotfix/badjsonpsequence' into release/76 · c03df68f
  Alessandro Vullo authored Sep 05, 2014
  
  c03df68f
- Merge branch 'release/76' into hotfix/badjsonpsequence · d770dfb1
  Alessandro Vullo authored Sep 05, 2014
  
  d770dfb1
- JSONP was specified as a output format causing documentation problems. · 830d6ff3
  Andy Yates authored Sep 05, 2014
```
We specified jsonp as an output format. This caused problems in the
documentation code which looked to see if JSONP was already specified as
an output format. It meant that callback was not added as a parameter
which is a bit poor. Removing jsonp as an output format fixes the error.
```
  830d6ff3
22 Aug, 2014 6 commits
- REST version now 3.0.1 to include bugfix and additional assembly_name field in output · e5fdb336
  Ensembl Admin authored Aug 22, 2014
  
  e5fdb336
- Adding tests for multiple sequences and text/plain. · c2d8977e
  Andy Yates authored Aug 21, 2014
```
Checking that the changes will not regress by adding two new tests. The
firsts makes a bad request for multiple sequences and makes sure we
correctly error. The second makes sure we have 1 sequence per line.
```
  c2d8977e
- Service printed line breaks between multiple sequences to STDOUT and not to the file handle · 32cb9023
  Andy Yates authored Aug 21, 2014
  
  32cb9023
- Support JSON as the default serialisation for errors. Bug found by Lel on dev · 132b92d9
  Andy Yates authored Aug 21, 2014
  
  132b92d9
- added assembly_info field for most endpoints · 144a325d
  Magali Ruffier authored Aug 21, 2014
```
useful for making sure this is the correct assembly you are fetching from
```
  144a325d
- use stash method rather than attempting to access hash attributes directly · f7bca596
  Magali Ruffier authored Aug 21, 2014
```
later versions of catalyst do not expose them
```
  f7bca596
14 Aug, 2014 1 commit
- check if there is an alignment before doing anything with it · 1592b613
  Magali Ruffier authored Aug 14, 2014
  
  1592b613
08 Aug, 2014 1 commit
- update contig example to contig in both GRCh37 and GRCh38 assemblies · f326a76a
  Ensembl Admin authored Aug 08, 2014
  
  f326a76a
04 Aug, 2014 1 commit
- correct configuration for content-type discovery · 2a62507d
  Alessandro Vullo authored Aug 04, 2014
  
  2a62507d
30 Jul, 2014 2 commits
- updated vep test output to match changes to variation checkout · 5448a9e1
  Magali Ruffier authored Jul 30, 2014
  
  5448a9e1
- deprecated method fetch_by_source_stable_id replaced with fetch_by_stable_id · be7a94be
  Magali Ruffier authored Jul 30, 2014
  
  be7a94be
29 Jul, 2014 1 commit
- beta.rest.ensembl.org url replaced with rest.ensembl.org · 2f53b257
  Magali Ruffier authored Jul 29, 2014
  
  2f53b257
23 Jul, 2014 3 commits
- updated info test to include dummy funcgen database · 1c3ecdda
  Magali Ruffier authored Jul 23, 2014
  
  1c3ecdda
- added fake funcgen database for vep compatibility · 73dc5393
  Magali Ruffier authored Jul 23, 2014
  
  73dc5393
- add all required adaptors for all methods · 52a68662
  Magali Ruffier authored Jul 23, 2014
```
required to work with direct database connection, which is all species but human
```
  52a68662
22 Jul, 2014 1 commit
- if species not human, use database connection, ie remove cache config · d42ade48
  Magali Ruffier authored Jul 22, 2014
  
  d42ade48
21 Jul, 2014 1 commit
- ontology database correctly patched to release 76 · c175a8cf
  Magali Ruffier authored Jul 21, 2014
  
  c175a8cf
18 Jul, 2014 17 commits
- replace deprecated fetch_by_source_stable_id method with fetch_by_stable_id · 448a9a3a
  Magali Ruffier authored Jul 18, 2014
  
  448a9a3a
- map from GRCH37, example region does not have mapping for NCBI36 · 2504fd3b
  Magali Ruffier authored Jul 18, 2014
  
  2504fd3b
- Set new rate limits to 15 req/s adn 55000 per hour. · ae4c6d15
  Alessandro Vullo authored Jul 18, 2014
```
Correct expire time for hour rate limit.
```
  ae4c6d15
- Closer to the settings used in our REST server environment. · 4ac7cc37
  Alessandro Vullo authored Jul 18, 2014
  
  4ac7cc37
- Support for YAML serialisation. · 60fcb8b0
  Alessandro Vullo authored Jul 18, 2014
```
Some Catalyst installations need this addition.
```
  60fcb8b0
- Merge branch 'release/76' of https://github.com/Ensembl/ensembl-rest into release/76 · 64926042
  Alessandro Vullo authored Jul 18, 2014
  
  64926042
- Start-up script based on ensembl git repositories. · 73bd0e47
  Alessandro Vullo authored Jul 18, 2014
```
HOME variable is user environ variable.
```
  73bd0e47
- Net:CDR is required for correct test running · 503e2cc4
  Magali Ruffier authored Jul 18, 2014
  
  503e2cc4
- Update .travis.yml · b8fd32d3
  Magali Ruffier authored Jul 18, 2014
  
  b8fd32d3
- all tables should be latin1 else keys can become too long · bd78a1e5
  Magali Ruffier authored Jul 18, 2014
  
  bd78a1e5
- added travis configuration for continuous integration · 06c4a88a
  Magali Ruffier authored Jul 18, 2014
  
  06c4a88a
- example for mapping updated to GRCh38 · a63793ac
  Magali Ruffier authored Jul 18, 2014
  
  a63793ac
- bugfix: keep the default aligned option in genomic alignment trees · d82fa6a9
  Miguel Pignatelli authored Jul 18, 2014
  
  d82fa6a9
- Converting gene tree to perl hash (TreeHash.pm) has been moved to ensembl-compara repo · eba0ad29
  Miguel Pignatelli authored Jul 18, 2014
  
  eba0ad29
- Updated PhyloXML writer modules used · dadbae5b
  Miguel Pignatelli authored Jul 17, 2014
  
  dadbae5b
- test databases patched for release 76 · ca565b28
  Magali Ruffier authored Jul 18, 2014
  
  ca565b28
- use software_version to get the release tag · 9b751c5c
  Magali Ruffier authored Jul 18, 2014
  
  9b751c5c
16 Jul, 2014 2 commits
- Merge pull request #9 from danstaines/master · b3aec9dd
  Magali Ruffier authored Jul 16, 2014
```
support for new Ensembl Genomes LookUp API
```
  b3aec9dd
- support for new Ensembl Genomes LookUp API · c2955b7e
  Dan Staines authored Jul 16, 2014
  
  c2955b7e