Commits · ad051607e087b4c551c9cb18a16e63d836934040 · ensembl-gh-mirror / ensembl

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Dec 14, 2011
- fix usage of dry_run parameter · ad051607
  Monika Komorowska authored 13 years ago
  
  ad051607
Dec 13, 2011
- Don't pass null into a column that is not allowed to have null as value, · bc44e9db
  epaule authored 13 years ago
```
will use 0 instead
```
  bc44e9db
- don't use TYPE= that has been deprecated years ago and doesn't work anymore · 73e17e45
  epaule authored 13 years ago
  
  73e17e45
- Added new species, gaeumannomyces_graminis · adfad7be
  Arnaud Kerhornou authored 13 years ago
  
  adfad7be
- Documentation update · 4dfd9ecf
  Andy Yates authored 13 years ago
  
  4dfd9ecf
- use the default column value instead of an empty string as version · 6b4df2c3
  epaule authored 13 years ago
  
  6b4df2c3
- the BaseParser expects error_codes and no fatal errors to work around checking... · 537bf49e
  epaule authored 13 years ago
```
the BaseParser expects error_codes and no fatal errors to work around checking for existence of xrefs,
so I turned them off again
```
  537bf49e
Dec 12, 2011
- unique genes method (for assembly patches), interactive does have an argument,... · 0ce0ebf5
  Steve Trevanion authored 13 years ago
```
unique genes method (for assembly patches), interactive does have an argument, other binaries default to 1 if nothing specified
```
  0ce0ebf5
- * fixed the UniProt version parsing · 56da698e
  epaule authored 13 years ago
```
* reenabled text SQL error messages, as error codes make it impossible to find out which error happened in which statement
```
  56da698e
- added section counting the size and mapping percentage of continuous runs of projections · a6a7816b
  Monika Komorowska authored 13 years ago
  
  a6a7816b
Dec 09, 2011
- Typo in POD of get_Gene method. · 67a07432
  Kieron Taylor authored 13 years ago
  
  67a07432
Dec 08, 2011
- updated patch identifiers · 35efd363
  Monika Komorowska authored 13 years ago
  
  35efd363
- Reorder an index in unmapped_object · 021d2e8f
  Monika Komorowska authored 13 years ago
  
  021d2e8f
- external_db_id definition change · e6a65b25
  Monika Komorowska authored 13 years ago
  
  e6a65b25
- schema version update · 64776949
  Monika Komorowska authored 13 years ago
  
  64776949
- schema version update · 2195ced6
  Monika Komorowska authored 13 years ago
  
  2195ced6
- updated API version · 5cd0180f
  Monika Komorowska authored 13 years ago
  
  5cd0180f
- updated documentation for method get_all_DBEntries · 7b29ce83
  Monika Komorowska authored 13 years ago
  
  7b29ce83
- that readme is actually for the unmapped_reason table and *not* external_db · e61f0169
  epaule authored 13 years ago
  
  e61f0169
- Updated the help wrt the production database commandline arguments · eb827e26
  Arnaud Kerhornou authored 13 years ago
  
  eb827e26
- Added commandline arguments for connecting ensembl_production db · 827fd6c2
  Arnaud Kerhornou authored 13 years ago
  
  827fd6c2
- Fixed bug with the character ` in the input file · af49c477
  Laurent Gil authored 13 years ago
  
  af49c477
- Added a missung use statement for DBAdaptor.pm · 27304384
  Arnaud Kerhornou authored 13 years ago
  
  27304384
- added production database paramertes to make it work for Ensembl Genomes · 3c1bf83d
  Uma Maheswari authored 13 years ago
  
  3c1bf83d
Dec 07, 2011
- Checksums should be the other way around. It's checksum then file not file then checksum · e3233965
  Andy Yates authored 13 years ago
  
  e3233965
- Up-comming patches not live yet · e2e40b26
  Andy Yates authored 13 years ago
  
  e2e40b26
- Bugfixing the reactivaition of aliases and making sure we only do it if we need to · becad6a4
  Andy Yates authored 13 years ago
  
  becad6a4
- Alternative script which does processing based upon taxonomy databases · 134468c2
  Andy Yates authored 13 years ago
  
  134468c2
- fixed gene synonym xml bug · ef905951
  Nick Langridge authored 13 years ago
  
  ef905951
- First pass addition of this script · 44bf05a5
  Andy Yates authored 13 years ago
  
  44bf05a5
- added 'use' for missing module · a394cb34
  Nick Langridge authored 13 years ago
  
  a394cb34
Dec 06, 2011
- fixed GOA xrefs · 116d4975
  Nick Langridge authored 13 years ago
  
  116d4975
- the TYPE= is showing deprecation warnings since MySQL versions > 3.23 · 5ebff4eb
  epaule authored 13 years ago
```
and was finally removed in 5.1.47. Please use ENGINE= instead
```
  5ebff4eb
- changed mapping percentage calculation per alignment length bin to use non-N... · 991acfbc
  Monika Komorowska authored 13 years ago
```
changed mapping percentage calculation per alignment length bin to use non-N sequence length like the total mapping percentage per chromosome
```
  991acfbc
Dec 05, 2011
- Making sure that the views are defined with security set to the invoker and not the definer · 003e81c4
  Andy Yates authored 13 years ago
  
  003e81c4
- Un-used registry import removed · 7700373c
  Andy Yates authored 13 years ago
  
  7700373c
Dec 02, 2011
- Removing IO::File and going back to the old ways · 895117f4
  Andy Yates authored 13 years ago
  
  895117f4
Dec 01, 2011
- Adding a dry mode which just reports the databases it would have dumped · cd3d13a7
  Andy Yates authored 13 years ago
  
  cd3d13a7
Nov 30, 2011
- need to alter dumps to r/w for user, group & others · abaaf4cb
  Andy Yates authored 13 years ago
  
  abaaf4cb
- Changes to externalise more items and to make the program more configurable · 02a1bc7a
  Andy Yates authored 13 years ago
  
  02a1bc7a