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Author SHA1 Message Date
Martin Cech 94e08ebb05 Merge pull request #8309 from cganote/purgegoodies 
Implement undelete and purge API for users
 2019-08-27 13:05:58 -04:00
Martin Cech bada84445f incorporate @nsoranzo's abstraction suggestions 2019-08-27 10:56:35 -04:00
Martin Cech b3e4abfd86 Merge pull request #8227 from veg/hyphyVision 
hyphy-vision
 2019-08-27 10:26:56 -04:00
John Chilton bd21368b27 Merge pull request #7913 from jmchilton/validation 
Datatype Validation and Tool-based QC
 2019-08-27 09:26:13 -04:00
Dannon 3b92741238 Merge pull request #8508 from selten/data-managers-update 
Documentation update
 2019-08-26 16:42:10 -04:00
Martin Cech addfeffb9e avoid calling superclass method for purging 
Because multiple inheritance will result in calling this class 'delete' method
which is not the correct target. This also avoid a database operation
I believe, since the PurgableManagerMixin.purge also calls delete before purging.
 2019-08-26 15:27:36 -04:00
Dannon aa5d47220a Merge pull request #8507 from martenson/update-sass 
update sass version to support node12
 2019-08-26 14:22:01 -04:00
John Chilton 613eb5daba Merge pull request #8515 from FredericBGA/async_mode 
Asynchronous data source: unable to create the file
 2019-08-26 12:24:02 -04:00
Marius van den Beek 7847ac1fa2 Merge pull request #8091 from nuwang/add_k8s_job_cleanup 
Added option to delete or preserve k8s pods after completion
 2019-08-26 16:53:34 +02:00
Frederic Sapet e18e0519d8 explicitly create the file with object_store.create function 2019-08-26 15:53:01 +02:00
mvdbeek bb832fbeaa Adjust testcase for new delete job behavior 2019-08-26 18:45:43 +05:30
mvdbeek fcd1c3bd3a Use set literal 2019-08-26 18:34:11 +05:30
mvdbeek 6d6e1a3e49 Fix watch_checked_item exception when deleting job externally 
Avoids:
```
galaxy.jobs.runners.kubernetes ERROR 2019-06-16 19:06:43,961 No Jobs are available under expected selector app=galaxy-gx-short-id-5
galaxy.jobs.runners ERROR 2019-06-16 19:06:43,962 Unhandled exception checking active jobs
Traceback (most recent call last):
  File "/Users/mvandenb/src/galaxy/lib/galaxy/jobs/runners/__init__.py", line 696, in monitor
    self.check_watched_items()
  File "/Users/mvandenb/src/galaxy/lib/galaxy/jobs/runners/__init__.py", line 723, in check_watched_items
    new_async_job_state = self.check_watched_item(async_job_state)
  File "/Users/mvandenb/src/galaxy/lib/galaxy/jobs/runners/kubernetes.py", line 447, in check_watched_item
    with open(job_state.error_file, 'w') as error_file:
FileNotFoundError: [Errno 2] No such file or directory: '/Users/mvandenb/temp/tmp1nx5r6_s/000/5/galaxy_5.e'
```
Can be tested with the `test_kill_process` testcase.
 2019-08-26 18:34:10 +05:30
Nuwan Goonasekera 4fd14946b3 Send DeleteOptions when deleting k8s jobs 2019-08-26 18:32:37 +05:30
Nuwan Goonasekera fc11f6608c Added option to delete or preserve k8s pods after completion 2019-08-26 18:31:35 +05:30
Björn Grüning a44f56480c Merge pull request #8506 from blankenberg/it-cleanup 
Little more RealTimeTools cleanup.
 2019-08-25 11:08:22 +02:00
Björn Grüning c8739a33b0 Merge pull request #8510 from jmchilton/job_metrics 
Fix default job metrics in dev/.
 2019-08-25 11:07:21 +02:00
John Chilton f50fafba5c Fix job metrics in dev/. 2019-08-24 11:50:33 -04:00
John Chilton a47742feb8 Merge pull request #8509 from ic4f/dev_config_refactor 
Factor out yaml read/write from config_manage.py
 2019-08-24 11:20:40 -04:00
selten 4d325460b0 Change 'ToolShed' to 'Tool Shed' 2019-08-24 12:14:21 +02:00
Peter Selten 53ad227750 Fix documentation more, spread data managers documentation over multiple lines so it's easier to read when editing. 2019-08-24 11:56:47 +02:00
Peter Selten d48d66644c Merge branch 'dev' of https://github.com/galaxyproject/galaxy into data-managers-update 2019-08-24 11:06:30 +02:00
Nicola Soranzo 28096601b2 Merge pull request #8497 from mvdbeek/fix_external_metadata 
Fix setting metadata externally
 2019-08-24 09:07:58 +01:00
Sergey Golitsynskiy 81bc4cc04a Fix linting errors (import stms order) 2019-08-23 18:01:57 -04:00
Nicola Soranzo 47ebdd8910 Remove some unnecessary casts 2019-08-23 22:22:53 +01:00
Sergey Golitsynskiy 9f999ea166 Factor out yaml processing out of config_manage 
- Create new utility module for processing yaml
- Move yaml processing into new utility module
- Factor out Schema classes out of config_manage into schema module
- Refactor yaml reading to accommodate a unit test (minor change)
- Add unit test for new schema module

Overall: this is first step towards refactoring config.
 2019-08-23 16:13:16 -04:00
selten 333950ec46 Update faq.rst 2019-08-23 21:28:03 +02:00
selten 9dc36d36c5 Update build runner documentation 2019-08-23 21:23:32 +02:00
selten 7448a11c39 Small changes to the data managers docs 2019-08-23 21:04:50 +02:00
Martin Cech 1846e74b20 update sass version to support node12 2019-08-23 14:01:15 -04:00
mvdbeek 14f6483378 Restore try/except around Biom2 metadata setting 2019-08-23 19:28:44 +02:00
John Chilton e9ee529aca Merge pull request #8502 from ic4f/dev_move_config_manage 
Move config_manage out of webapps/ into config/
 2019-08-23 12:02:28 -04:00
Daniel BlankenbergandNicola Soranzo a2199ee575 Update scripts/interactivetools/key_type_token_mapping.py 
Co-Authored-By: Nicola Soranzo <nicola.soranzo@gmail.com>
 2019-08-23 11:29:36 -04:00
rdvelazquez f1a5481316 add hyphy-vision visualization 2019-08-23 10:19:39 -04:00
Marius van den BeekandNicola Soranzo fa3e09b689 Update lib/galaxy/datatypes/binary.py 
Co-Authored-By: Nicola Soranzo <nicola.soranzo@gmail.com>
 2019-08-23 16:11:39 +02:00
John Chilton 54c77a22c9 Cleanup of validation PR. 2019-08-23 09:43:03 -04:00
Daniel Blankenberg 995fce6b9b Little more RealTimeTools cleanup. 2019-08-23 09:24:55 -04:00
mvdbeek f7caec54af Open h5py files in 'r' mode, drop redundant .get('x', None) 2019-08-23 15:15:05 +02:00
Björn Grüning 770416dfbb Merge pull request #8503 from selten/data-managers-update 
Documentation update for #8250
 2019-08-23 13:21:57 +02:00
selten f34b29fca3 Update documentation for clarity on docs.galaxyproject.org 2019-08-23 09:49:17 +02:00
selten cfe4422c26 Merge branch 'dev' of https://github.com/galaxyproject/galaxy into data-managers-update 2019-08-23 09:43:58 +02:00
Björn Grüning 1db199763f Merge pull request #8490 from jmchilton/fix_data_dir 
Fix some data_dir stuff in galaxy.config.
 2019-08-23 08:30:06 +02:00
Marius van den Beek 4b93b9fc0a Merge pull request #8440 from bgruening/n_lines_validation 
add assert for n_lines in tool output verifications
 2019-08-22 22:13:04 +02:00
John Chilton 08b39a2b7d Fix config.realtime_map for config.data_dir. 2019-08-22 15:55:22 -04:00
John ChiltonandNicola Soranzo 5d7cb8050c Apply suggestions from code review 
Co-Authored-By: Nicola Soranzo <nicola.soranzo@gmail.com>
 2019-08-22 15:54:43 -04:00
John Chilton d6865ac07d Fix some data_dir stuff in galaxy.config. 2019-08-22 15:54:43 -04:00
Martin Cech b218f36ba7 remove unused imports 2019-08-22 15:50:24 -04:00
Sergey Golitsynskiy fb98cf3585 Move config_manage out of webapps/ into config/ 
First pass.
 2019-08-22 15:46:08 -04:00
John ChiltonandMarius van den Beek 956bf8ab93 Apply suggestions from code review 
Co-Authored-By: Marius van den Beek <m.vandenbeek@gmail.com>
 2019-08-22 15:45:25 -04:00
John Chilton 55b384cc50 Add ability to collect QC from jobs. 2019-08-22 15:45:25 -04:00