Commits · 5a091cadfe5f8508f4897f135edb862bbe1214e5 · ensembl-gh-mirror / ensembl-hive

This project is mirrored from https://:*****@github.com/Ensembl/ensembl-hive.git. Pull mirroring updated Feb 09, 2023.

22 May, 2015 10 commits
- updated schema/scripts/doxygen documentation · 5a091cad
  Leo Gordon authored May 22, 2015
  
  5a091cad
- updated schema diagram v.71 · 3d4850b7
  Leo Gordon authored May 22, 2015
  
  3d4850b7
- text_to_shell_lit has already moved to Utils.pm · 7bd3b031
  Matthieu Muffato authored May 22, 2015
  
  7bd3b031
- bugfix: force EHIVE_TMP_PASSWORD_* to be unquoted and thus substituted · 1dcd9016
  Matthieu Muffato authored May 22, 2015
  
  1dcd9016
- "append" parameters are now always appended to the end of the command · a382cb83
  Matthieu Muffato authored May 22, 2015
  
  a382cb83
- Moved Utils::dbc_to_cmd() (static method) to DBConnection::to_cmd() (instance method) · ca4171b2
  Matthieu Muffato authored May 21, 2015
  
  ca4171b2
- Safety measure to avoid resetting all the jobs inadvertently · cc0e3549
  Matthieu Muffato authored May 21, 2015
  
  cc0e3549
- Hide passwords when using DatabaseDumper and MySQLTransfer · 37738e4f
  Matthieu Muffato authored May 18, 2015
  
  37738e4f
- Standalone jobs have job_id=-1, and "-" is not allowed in parameter names · f66a8e1d
  Matthieu Muffato authored May 20, 2015
  
  f66a8e1d
- The input source is only needed for the default executable (i.e. the sql client) · adf4932c
  Matthieu Muffato authored May 19, 2015
  
  adf4932c
21 May, 2015 5 commits
- bugfix: prevent PostgreSQL from padding the test numbers with spaces (again) · 71d61abc
  Matthieu Muffato authored May 21, 2015
  
  71d61abc
- Merge remote-tracking branch 'ensembl-github/master' into python · bd2ebbd0
  Matthieu Muffato authored May 21, 2015
```
* ensembl-github/master:
  bugfix: round down the potentially non-integer hive_capacity-related limit
  bugfix: switching to using the newly created find_all_by_pattern() and collections in Worker to fix the -job_id bug
  find_all_by_pattern() is now supported on the collection level
```
  bd2ebbd0
- bugfix: round down the potentially non-integer hive_capacity-related limit · 9390d682
  Leo Gordon authored May 21, 2015
  
  9390d682
- bugfix: switching to using the newly created find_all_by_pattern() and... · 4da5806f
  Leo Gordon authored May 21, 2015
```
bugfix: switching to using the newly created find_all_by_pattern() and collections in Worker to fix the -job_id bug
```
  4da5806f
- find_all_by_pattern() is now supported on the collection level · 4dd351f0
  Leo Gordon authored May 21, 2015
  
  4dd351f0
20 May, 2015 5 commits

Now handles lost connection (aka broken-pipe) · 5f6535f6
Matthieu Muffato authored May 20, 2015

5f6535f6
Force dbID and retry_count to be numeric (not strings) · 1730faa0
Matthieu Muffato authored May 20, 2015

1730faa0
We need python3 to test the python modules · be379067
Matthieu Muffato authored May 20, 2015

be379067

Last merge before the pull-request · a174bbb6

Matthieu Muffato authored May 20, 2015

Merge remote-tracking branch 'ensembl-github/master' into python

* ensembl-github/master:
  moved mysql_use_result=>1 to the $sth_attribs hash
  allow capturing dataflow from a standaloneJob into a semaphored group
  Dataflow rules are stored in the Analysis, not the Job
  bugfix: make sure dataflown jobs are stored even in standalone mode
  generalized load_parameters() moved into AnalysisJob
  bugfix [to 97e17d94] : removed the leading zero from param_init call in gc_dataflow
  The $a syntax in #expr() has long gone, Should use #a# instead
  Deprecate --append in db_cmd.pl
  deprecated and removed support for strict_hash_format() method in Runnables
  We don't use $SKIP_TESTS in ensembl-hive

Conflicts:
	modules/Bio/EnsEMBL/Hive/Worker.pm
	t/10.pipeconfig/longmult.t

a174bbb6

moved mysql_use_result=>1 to the $sth_attribs hash · fa49be74
Leo Gordon authored May 20, 2015

fa49be74

19 May, 2015 2 commits
- allow capturing dataflow from a standaloneJob into a semaphored group · 7092520e
  Leo Gordon authored May 19, 2015
  
  7092520e
- Dataflow rules are stored in the Analysis, not the Job · f757c786
  Matthieu Muffato authored May 21, 2014
  
  f757c786
18 May, 2015 3 commits
- bugfix: make sure dataflown jobs are stored even in standalone mode · c07e4b5a
  Leo Gordon authored May 18, 2015
  
  c07e4b5a
- generalized load_parameters() moved into AnalysisJob · 179ee1e4
  Leo Gordon authored May 18, 2015
  
  179ee1e4
- bugfix [to 97e17d94 ] : removed the leading zero from param_init call in gc_dataflow · 241440c2
  Leo Gordon authored May 15, 2015
  
  241440c2
15 May, 2015 6 commits
- Updated the doc for the update of TestRunnable.py · f4816bec
  Matthieu Muffato authored May 15, 2015
  
  f4816bec
- The $a syntax in #expr() has long gone, Should use #a# instead · 98d93ceb
  Matthieu Muffato authored May 15, 2015
  
  98d93ceb
- Deprecate --append in db_cmd.pl · 596723eb
  Matthieu Muffato authored May 15, 2015
  
  596723eb
- Added a new "05.runnabledb" test for python · 65ca04b4
  Matthieu Muffato authored May 15, 2015
  
  65ca04b4
- Use a sub-test for standaloneJob · 04140725
  Matthieu Muffato authored May 15, 2015
  
  04140725
- We in fact only need lives_ok() here · 4368ea46
  Matthieu Muffato authored May 15, 2015
  
  4368ea46
14 May, 2015 9 commits
- Added references to the new Python doc · 5c775d05
  Matthieu Muffato authored May 14, 2015
  
  5c775d05
- Test Python in the test-suite · 337bf07c
  Matthieu Muffato authored May 14, 2015
  
  337bf07c
- Also generate Doxygen doc for Python · f8019ad4
  Matthieu Muffato authored May 14, 2015
  
  f8019ad4
- More documentation for Python · e63d87c7
  Matthieu Muffato authored May 14, 2015
  
  e63d87c7
- Updated the public/private status of several functions · 93216495
  Matthieu Muffato authored May 14, 2015
  
  93216495
- A bit more documentation · 1436ff0f
  Matthieu Muffato authored May 14, 2015
  
  1436ff0f
- Increased the length of the VARCHAR field to 255 (same as the other fields) · 6763f96f
  Matthieu Muffato authored May 14, 2015
  
  6763f96f
- Updated the public/private status of several variables · 052a334f
  Matthieu Muffato authored May 14, 2015
  
  052a334f
- deprecated and removed support for strict_hash_format() method in Runnables · 97e17d94
  Leo Gordon authored May 14, 2015
  
  97e17d94