Commits · 536bd1eea584aae9cfb5cddb26f9b04ef7a4a619 · ensembl-gh-mirror / ensembl

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May 27, 2009
- relation_type.name needs to be longer. · 536bd1ee
  Andreas Kusalananda Kähäri authored 15 years ago
  
  536bd1ee
- New external_db used for getting stable id bits · 84ba2bde
  Ian Longden authored 15 years ago
  
  84ba2bde
- staging databases changed · 37460027
  Ian Longden authored 15 years ago
  
  37460027
- Spelling. · 8db495a1
  Andreas Kusalananda Kähäri authored 15 years ago
  
  8db495a1
- NO_DISPLAY added to object_xref status · 01ad933f
  Ian Longden authored 15 years ago
  
  01ad933f
- Add comment at the head of the code to say what the program is doing. · c26dd3dd
  Andreas Kusalananda Kähäri authored 15 years ago
  
  c26dd3dd
- ignore now used properly · e1346692
  Ian Longden authored 15 years ago
  
  e1346692
- KNOWN bug · 23ed8a6f
  Ian Longden authored 15 years ago
  
  23ed8a6f
May 26, 2009
- Demonstration program for the Ensembl ontology database and API: · 0ad1438d
  Andreas Kusalananda Kähäri authored 15 years ago
```
Fetching a GO term and then displaying its ancestors recursively using
the information fetched from _fetch_ancestor_chart().
```
  0ad1438d
- Throw an exception in _fetch_ancestor_chart() if argument is not an · 02765bbf
  Andreas Kusalananda Kähäri authored 15 years ago
```
ontology term.
```
  02765bbf
- Demonstration program for the Ensembl ontology database and API: · ea05c40a
  Andreas Kusalananda Kähäri authored 15 years ago
```
Fetching a GO term and then using it to get genes.
```
  ea05c40a
- Documentation for the ontology database and API. · 4f413d7f
  Andreas Kusalananda Kähäri authored 15 years ago
  
  4f413d7f
- In fetch_all_by_GOTerm(), throw exception if the argument is not a GO · 18ed30d1
  Andreas Kusalananda Kähäri authored 15 years ago
```
term.
```
  18ed30d1
- Add ability to query an ontology term for its ontology. · f451aefc
  Andreas Kusalananda Kähäri authored 15 years ago
  
  f451aefc
May 22, 2009
- store meta values and set some data in it after parsing · 898d6960
  Ian Longden authored 15 years ago
  
  898d6960
- meta table added · 29838034
  Ian Longden authored 15 years ago
  
  29838034
- samll bug fix and storign object_xrefs for dependents and store dependent_xrefs · 6b75344e
  Ian Longden authored 15 years ago
  
  6b75344e
- verbose set to be default · db5370e2
  Ian Longden authored 15 years ago
  
  db5370e2
- verbose set to be defualt and full and part modes introduced · bf288d2a
  Ian Longden authored 15 years ago
  
  bf288d2a
- Unigene added for a couple of species · 244893c0
  Ian Longden authored 15 years ago
  
  244893c0
- New fast calulations of the gene and transcript attributes · ebf4e29c
  Ian Longden authored 15 years ago
  
  ebf4e29c
- get core info on status of the external databases · a5ff0956
  Ian Longden authored 15 years ago
  
  a5ff0956
- store and retrieve meta pair vlaues · dac53213
  Ian Longden authored 15 years ago
  
  dac53213
May 21, 2009
- added indexes in bak tables · 0025f167
  Daniel Rios authored 15 years ago
  
  0025f167
- Proper check for HGNC_* when deciding whether to overwrite XP-named genes in target. · ceb7bf0a
  Glenn Proctor authored 15 years ago
  
  ceb7bf0a
May 20, 2009
- allow linkage_type in go_xref to be null · 781acc12
  Ian Longden authored 15 years ago
  
  781acc12
- patch to set to NULL version column in coord_system table instead of blank · b3b69be2
  Daniel Rios authored 15 years ago
  
  b3b69be2
May 19, 2009
- store: added undef check for db_release for is NULL clause · 53595c66
  Nathan Johnson authored 15 years ago
  
  53595c66
May 15, 2009

Edited to remove syntax complaint - ERROR 1064 (42000) at line 10: You have an... · af9dc3e1

Susan Fairley authored 15 years ago

Edited to remove syntax complaint - ERROR 1064 (42000) at line 10: You have an error in your SQL syntax; check the manual that corresponds to your MySQL server version for the right syntax to use near ''is_constitutive' BOOLEAN NOT NULL DEFAULT 0' at line 1.

af9dc3e1

May 13, 2009
- Fixed a misspeling. · d2769e29
  Amonida Zadissa authored 15 years ago
  
  d2769e29
May 12, 2009
- Don't use 'Bio::EnsEMBL::Utils::Argument'. · 4edafe91
  Andreas Kusalananda Kähäri authored 15 years ago
  
  4edafe91
- Exit when we try to load a newer version of a file. The database will · bc950ff0
  Andreas Kusalananda Kähäri authored 15 years ago
```
need to be cleaned manually or by using the -t (truncate) option to the
script.
```
  bc950ff0
- The get_db_privs() did not parse all GRANTS returned from "SHOW GRANTS · 7f7ac046
  Andreas Kusalananda Kähäri authored 15 years ago
```
FOR <user>".  Now it does.  This stopped the stable ID mapping from
running correctly for a while.
```
  7f7ac046
May 11, 2009
- Add patch file for the 'is_constitutive' patch, adding a column to the · f2104dc5
  Andreas Kusalananda Kähäri authored 15 years ago
```
exon table.
```
  f2104dc5
- Add the 'is_constitutive' column to the exon table. · 6b7f8f72
  Andreas Kusalananda Kähäri authored 15 years ago
  
  6b7f8f72
- Small fixes. · 86fcb2ef
  Andreas Kusalananda Kähäri authored 15 years ago
  
  86fcb2ef
- small fix. · a338b239
  Andreas Kusalananda Kähäri authored 15 years ago
  
  a338b239
- Add code to write the OBO file name, and the date stored withing the · d472204d
  Andreas Kusalananda Kähäri authored 15 years ago
```
file, to the meta table with the key 'OBO_file_date'.  Also store the
file name and the load date with key 'OBO_load_date'.

Add a boolean command line flag -t/--truncate.  Using this flag will
truncate (empty) the various tables before loading data into them.
```
  d472204d
- Add a meta table. · d714e02f
  Andreas Kusalananda Kähäri authored 15 years ago
  
  d714e02f
- Script to calculate the constitutive exons and add the information to the is_constitutive · d06660d6
  Rhoda Kinsella authored 15 years ago
```
column in the core exon table for each species.
```
  d06660d6