Commits · 15dad152dcee58ff8b0198218bdb1372b16fd74a · ensembl-gh-mirror / ensembl-hive

This project is mirrored from https://:*****@github.com/Ensembl/ensembl-hive.git. Pull mirroring updated Jan 29, 2023.

02 Dec, 2016 1 commit
- The LSF meadow can now detect workers that are not properly named · 15dad152
  Matthieu Muffato authored Dec 02, 2016
  
  15dad152
30 Nov, 2016 1 commit
- (1) protect the pre-locking itself from dead-locks and (2) do not perform... · 75c58b1f
  Leo Gordon authored Nov 30, 2016
```
(1) protect the pre-locking itself from dead-locks and (2) do not perform pre-locking when not needed
```
  75c58b1f
25 Nov, 2016 2 commits
- bugfix: make sure -pipeline_name ends up without any whitespace · b488e2b6
  Leo Gordon authored Nov 25, 2016
  
  b488e2b6
- sprintf real numbers used in test comparisons · 4938870a
  Brandon Walts authored Nov 25, 2016
  
  4938870a
24 Nov, 2016 2 commits
- bugfix [to previous] : make sure both X_job and X_job_id are deleted, to... · 42700f22
  Leo Gordon authored Nov 24, 2016
```
bugfix [to previous] : make sure both X_job and X_job_id are deleted, to prevent automatic cross-generation
```
  42700f22
- bugfix [to 3863666b and b7668259 ] - prevent automatic loading of all jobs into the collection · 294adc04
  Leo Gordon authored Nov 24, 2016
  
  294adc04
23 Nov, 2016 17 commits
- perlcritic doesn't like variables declared in conditional statement · 78a94b1a
  Matthieu Muffato authored Nov 23, 2016
  
  78a94b1a
- Added tests for the reset options of beekeeper · e30847c8
  Matthieu Muffato authored Nov 23, 2016
  
  e30847c8
- Added beekeeper comands to forgive failed jobs and discard ready jobs · 123840bf
  Matthieu Muffato authored Nov 23, 2016
  
  123840bf
- Code factorization: synchronize_hive() is needed in several tasks · c79f9bd0
  Matthieu Muffato authored Nov 23, 2016
  
  c79f9bd0
- bugfix: do is a DBConnection method · 57a1ab2c
  Matthieu Muffato authored Nov 23, 2016
  
  57a1ab2c
- Added a TAP-compatible wrapper around system()+beekeeper.pl · f9e2d873
  Matthieu Muffato authored Nov 23, 2016
  
  f9e2d873
- Run this in a transaction to ensure consistency · 92e5cb32
  Matthieu Muffato authored Nov 22, 2016
  
  92e5cb32
- Run this in a transaction to ensure consistency · 7200ae00
  Matthieu Muffato authored Nov 22, 2016
  
  7200ae00
- Added an option in beekeeper to set the SEMAPHORED jobs to READY · 30ed88c4
  Matthieu Muffato authored Mar 04, 2016
  
  30ed88c4
- Added a -reset_done_jobs option to beekeeper · c179e37a
  Matthieu Muffato authored Mar 04, 2016
  
  c179e37a
- When resetting jobs, also mark their funnels as SEMAPHORED · dc6581f2
  Matthieu Muffato authored Mar 04, 2016
  
  dc6581f2
- Code refactorization: extracted a method to cast a job status in a SQL query for Postgres only · 77cec776
  Matthieu Muffato authored Nov 23, 2016
  
  77cec776
- Comply with the new reset_jobs_for_analysis_id() interface · d3b5853b
  Matthieu Muffato authored Sep 15, 2016
  
  d3b5853b
- POD update · 1a8afecc
  Matthieu Muffato authored Sep 15, 2016
  
  1a8afecc
- Quick exit if there is nothing to update · 97c25586
  Matthieu Muffato authored Sep 15, 2016
  
  97c25586
- Do not reset the status of live jobs, workers may be harmed · cc5413e2
  Matthieu Muffato authored Mar 04, 2016
  
  cc5413e2
- It is more useful to show the content of the event we've received · 61eb65c2
  Matthieu Muffato authored Sep 09, 2016
  
  61eb65c2
22 Nov, 2016 4 commits
- rename FK constrain names while renaming the table name · d4c0ba0b
  Wasiu Akanni authored Nov 22, 2016
  
  d4c0ba0b
- bugfix: default_insertion_method becomes INSERT (INSERT_IGNORE for Jobs only)... · e2d4a4d0
  Leo Gordon authored Nov 22, 2016
```
bugfix: default_insertion_method becomes INSERT (INSERT_IGNORE for Jobs only) to avoid masking FK collisions in mysql 5.6
```
  e2d4a4d0
- bugfix: only 3 tests have to be skipped · e836196d
  Leo Gordon authored Nov 22, 2016
  
  e836196d
- bugfix: be more careful when treating structures as TRUE values · b55efa53
  Leo Gordon authored Nov 22, 2016
  
  b55efa53
21 Nov, 2016 9 commits
- getting rid of the mysql v5.5+ warnings about passwords · cd3c47cd
  Leo Gordon authored Nov 21, 2016
  
  cd3c47cd
- Be nice to PostgreSQL and disconnect from the database before dropping it · e1c618b0
  Matthieu Muffato authored Nov 21, 2016
  
  e1c618b0
- New unit-test to check that the behaviour of INSERT IGNORE is correctly mimicked under Postgre · 3799f023
  Matthieu Muffato authored Nov 21, 2016
  
  3799f023
- Added a rule at the PostgreSQL level to mimic INSERT IGNORE · 715ddfb7
  Matthieu Muffato authored May 11, 2016
  
  715ddfb7
- Lighter version of init_pipeline (when we don't require any jobs, analyses etc added to the tables) · 6f669216
  Matthieu Muffato authored Nov 21, 2016
  
  6f669216
- 1 test database is enough for this test · d5e14d2e
  Matthieu Muffato authored Nov 21, 2016
  
  d5e14d2e
- Enclose each test URL in its own subtest · edb24d43
  Matthieu Muffato authored Nov 21, 2016
  
  edb24d43
- Added methods to ease the creation of custom databases and run SQL on arbitrary URLs · 3384a7ab
  Matthieu Muffato authored Nov 21, 2016
  
  3384a7ab
- Added more documentation on the test methods · 1aa9b85f
  Matthieu Muffato authored Nov 21, 2016
  
  1aa9b85f
19 Nov, 2016 4 commits

Merge branch 'version/2.4' · 55662aaa
Matthieu Muffato authored Nov 19, 2016
```
* version/2.4:
  bugfix: $PWD/perl5 was incorrectly listed
```
55662aaa
bugfix: $PWD/perl5 was incorrectly listed · 007ec1a5
Matthieu Muffato authored Nov 19, 2016

007ec1a5

Matthieu Muffato authored Nov 19, 2016

* version/2.4:
  Added a test for the "take_time" parameter of Dummy
  Unneeded dependency
  Trivial test to complete the coverage of Bio::EnsEMBL::Hive::Version
  "prove" itself should not be listed in Coveralls
  Also test the dark collection
  Added tests for the remaining patterns
  Added documentation about the Params interface, and the changed made in 2.4
  bugfix: use varchar, otherwise Postgre pads the strings with whitespace

aaa641b7

And we also need the command-line tools · 086aeed3
Matthieu Muffato authored Nov 18, 2016

086aeed3