Commits · 34f5699bf3e02aeab19b3a9ead02c172780dc5c6 · ensembl-gh-mirror / ensembl

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

11 Dec, 2015 4 commits
- ENSCORESW-1596 : longer synonym column · 34f5699b
  Magali Ruffier authored Dec 11, 2015
  
  34f5699b
- Merge pull request #105 from Ensembl/ENSCORESW-1381 · c7c63865
  Magali Ruffier authored Dec 11, 2015
```
Enscoresw 1381
```
  c7c63865
- Merge pull request #104 from ckongEbi/master · 1183566c
  Magali Ruffier authored Dec 11, 2015
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To use dbprimary_acc instead of display_id;Fix GO source duplication
```
  1183566c
- Merge branch 'master' of https://github.com/Ensembl/ensembl · c6dd98be
  Magali Ruffier authored Dec 11, 2015
  
  c6dd98be
04 Dec, 2015 5 commits
- Merge pull request #108 from nicklangridge/nicklangridge-patch-2 · 1c1d66f6
  Magali Ruffier authored Dec 04, 2015
```
Check that adaptor exists before trying to use dbc
```
  1c1d66f6
- Check that adaptor exists before trying to use dbc · 3cfb9269
  Nick Langridge authored Dec 04, 2015
  
  3cfb9269
- Merge pull request #107 from nicklangridge/nicklangridge-patch-1 · bca12541
  Magali Ruffier authored Dec 04, 2015
```
Check that adaptor exists before trying to use dbc
```
  bca12541
- Merge pull request #106 from Ensembl/bugfix/externaldbname · 0fbc0a35
  Alessandro Vullo authored Dec 04, 2015
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Bugfix/externaldbname
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  0fbc0a35
- Check that adaptor exists before trying to use dbc · 2e466009
  Nick Langridge authored Dec 04, 2015
  
  2e466009
03 Dec, 2015 2 commits
- To use infor from provider meta key to update annotation source · 005f2dee
  ChuangKee Ong authored Dec 03, 2015
  
  005f2dee
- Merge remote branch 'upstream/master' · 6a32827f
  ChuangKee Ong authored Dec 03, 2015
  
  6a32827f
02 Dec, 2015 8 commits
- Merge pull request #103 from ens-ma7/ens-ma7-patch-1 · 26abd369
  Magali Ruffier authored Dec 02, 2015
```
Do not gzip checksum
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  26abd369
- Jira ENSCORESW-1381 · a9ac8581
  Matthew Laird authored Dec 02, 2015
```
- Added fetch_by_stable_id_version to TranslationAdaptor for consistency
- Related tests for new function
```
  a9ac8581
- ENSCORESW-1349 : return slice if no offset · a7aab0be
  Magali Ruffier authored Dec 02, 2015
  
  a7aab0be
- patch test databases for 84 · 3c42736d
  Magali Ruffier authored Dec 02, 2015
  
  3c42736d
- update for release 84 · df58aad7
  Magali Ruffier authored Dec 02, 2015
  
  df58aad7
- ENSCORESW-1570 : only store unique alignments · 1452c722
  Magali Ruffier authored Dec 02, 2015
  
  1452c722
- ENSCORESW-1571 : xref default version is null · 9c4ab46c
  Magali Ruffier authored Dec 02, 2015
  
  9c4ab46c
- updated for release 84 · c74bc67f
  Magali Ruffier authored Dec 02, 2015
  
  c74bc67f
01 Dec, 2015 4 commits
- ENSCORESW-1584 : remove e84 deprecated methods · 661ec5c2
  Magali Ruffier authored Dec 01, 2015
  
  661ec5c2
- Jira ENSCORESW-1381 · 09abe4f6
  Matthew Laird authored Dec 01, 2015
```
- Ensire the "version" if tested for is digits only
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  09abe4f6
- Jira ENSCORESW-1381 · 61093b6e
  Matthew Laird authored Dec 01, 2015
```
- Added support in the Registry for version ids (\.\d+) support in stable_id when determining idenfitier type
- Added support to the ArchiveStableIdAdaptor for versions in stable_ids on object creation
- Test cases for identifiers with and without versions when doing lookups
```
  61093b6e
- ENSCORESW-1573 : score penalty if score 1 but version increment · afe187a1
  Magali Ruffier authored Dec 01, 2015
  
  afe187a1
30 Nov, 2015 2 commits

To use dbprimary_acc instead of display_id;Fix GO source duplication · c25dcd6d
ChuangKee Ong authored Nov 30, 2015

c25dcd6d

Jira · c5d6508b

Matthew Laird authored Nov 30, 2015

- handlers in Exon, Gene, Operon, OperonTranscript and Transcript Adaptors for a versions fetch_by_stable_id call and new handler for fetch_by_stable_id_version
- Translation is handled implicitly through calls to Transcript
- Test cases for the new handlers and functionality

c5d6508b

27 Nov, 2015 5 commits
- ENSCORESW-1583 : do not skip all dependent xrefs · 89f30aff
  Magali Ruffier authored Nov 27, 2015
  
  89f30aff
- Merge branch 'master' of https://github.com/Ensembl/ensembl · 2687dcfc
  Magali Ruffier authored Nov 27, 2015
  
  2687dcfc
- Update dump_mysql.pl · 8e01c3a6
  Ridwan Amode authored Nov 27, 2015
  
  8e01c3a6
- ENSCORESW-1573 : do not include PAR for duplicated genes · e47843db
  Magali Ruffier authored Nov 27, 2015
  
  e47843db
- Do not gzip checksum · f69687f2
  Ridwan Amode authored Nov 27, 2015
  
  f69687f2
26 Nov, 2015 2 commits
- Merge pull request #102 from willmclaren/fix/vf-fake-adaptor-circular · 0c98601e
  Dan Staines authored Nov 26, 2015
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fix for VariationFeatures using a fake adaptor on circular slices
```
  0c98601e
- couple more methods tested · be71197b
  Magali Ruffier authored Nov 25, 2015
  
  be71197b
25 Nov, 2015 3 commits
- Will this post notifications to slack? hope so · 2211c7ed
  Andy Yates authored Nov 25, 2015
  
  2211c7ed
- deal with situation where ensembl_taxonomy API is not available but the database is · 2efe4f22
  Dan Staines authored Nov 25, 2015
  
  2efe4f22
- couple more methods tested · 987d1b0d
  Magali Ruffier authored Nov 25, 2015
  
  987d1b0d
24 Nov, 2015 4 commits
- Merge pull request #101 from willmclaren/fix/vf-fake-adaptor-circular · b27c653a
  Magali Ruffier authored Nov 24, 2015
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fix for VariationFeatures using a fake adaptor on circular slices
```
  b27c653a
- update fix with suggestions · 959c5ac3
  William McLaren authored Nov 24, 2015
  
  959c5ac3
- changed package name for taxonomy · b89b3719
  Dan Staines authored Nov 24, 2015
  
  b89b3719
- more test for GeneAdaptor methods · 8bd313b7
  Magali Ruffier authored Nov 24, 2015
  
  8bd313b7
23 Nov, 2015 1 commit
- Merge pull request #99 from Ensembl/ENSCORESW-1454 · fb9becb3
  Magali Ruffier authored Nov 23, 2015
```
Enscoresw 1454
```
  fb9becb3