opensource/galaxy
3
0
Fork 0
mirror of https://github.com/galaxyproject/galaxy.git synced 2026-09-24 16:30:27 +08:00
Code Issues Packages Projects Releases Wiki Activity
23,395 Commits 69 Branches 243 Tags
f724e84fda22fb73042ea344ec00be86b3a7c564
Commit Graph
23395 Commits
This Branch
This Branch
All Branches
Author SHA1 Message Date
carlfeberhard f724e84fda API, users: use default to assign username 2016-07-07 11:20:02 -04:00
carlfeberhard 86a3531730 API, users: add deserializer to user manager 
- Adds deserialization method for usernames (note: still needs trans)
- Adds tests for deserializer in test_UserManager.py
 2016-07-07 10:38:08 -04:00
carlfeberhard 54e07906f5 User API tests: add update test 2016-07-06 14:10:14 -04:00
carlfeberhard aa69199bd1 User API tests: add show 2016-07-06 13:33:28 -04:00
Martin Cech a630c92df4 Merge pull request #2527 from dannon/fix_tabular_display_chunking 
Fix tabular display chunking
 2016-07-05 13:21:21 -04:00
Nicola Soranzo 3eeedc61e8 Merge pull request #2540 from zipho/dev 
Fix dataset matcher when no tool available.
 2016-07-05 15:49:11 +01:00
Dannon Baker dd12980777 Merge pull request #2486 from benfulton/ForcePasswordChange 
Add a password expiration config option (resolves #2485)
 2016-07-05 10:03:37 -04:00
Dannon Baker a946b04316 Merge pull request #2574 from bxlab/python3 
Python3: port 215 files
 2016-07-05 09:57:54 -04:00
Martin Cech 6c995f73fb Merge pull request #2534 from jmchilton/client-install-deps 
Add Makefile target for fetching updated bower dependencies.
 2016-07-03 14:21:06 -04:00
Martin Cech 00556bd912 Merge pull request #2553 from natefoo/user-purge-default 
Allow users to purge datasets by default
 2016-07-01 22:30:47 -04:00
Björn Grüning 537b917b4f Merge pull request #2578 from phnmnl/feature/serviceAccount 
Kubernetes runner: authenticate through service account
 2016-06-30 19:42:28 +02:00
Björn Grüning 05066ae655 Merge pull request #2572 from erasche/fix-2442 
Fixes #2442
 2016-06-30 19:07:35 +02:00
Pablo Moreno ef72b45320 Adds missing parameter specification for k8s_use_service_account 2016-06-30 00:25:26 +01:00
Nicola Soranzo 79bf27e7e8 Merge pull request #2528 from phnmnl/dev 
Writes Kubernetes logs files in UTF-8
 2016-06-29 17:52:12 -04:00
Pablo Moreno fe22e1ec44 Adds the ability to use the Kubernetes runner with Galaxy being executed inside Kubernetes (uses service account authentication). 2016-06-29 16:30:35 +01:00
Ben Fulton d9e3d69b78 Add password_expiration_period to toolshed config 
This is necessary as it shares the user class with the galaxy app.
 2016-06-29 10:57:00 -04:00
Pablo Moreno c9b7d9b68a Merge pull request #5 from galaxyproject/dev 
keeps up to date with main galaxy dev
 2016-06-29 13:40:24 +01:00
Nicola Soranzo 9a97a2952f Python3: test/unit/ 2016-06-29 01:55:44 -04:00
Eric Rasche f8fb69c81a All the binary datatypes 2016-06-28 21:02:00 +00:00
Eric Rasche b5468340ee Fixes #2442 2016-06-28 20:51:10 +00:00
John Chilton 097eb49f57 Merge pull request #2555 from jgoecks/trackster-nan-coverage-fix 
Fixes for showing min/max labels in Trackster.
 2016-06-28 12:13:18 -04:00
Martin Cech d944d3cd65 Merge pull request #2564 from NickSto/run_tests_documentation 
run_tests.sh: Clarify when/where the report file is created.
 2016-06-27 21:50:10 -04:00
Nicola Soranzo 40f85f2913 Python3: add missing print_function imports 2016-06-27 12:41:40 -04:00
Nicola Soranzo 5feefc73b3 Simplify .ci/py3_sources.txt 2016-06-27 10:52:25 -04:00
Nicola Soranzo 6a870a7345 Simplify .ci/py3_sources.txt 2016-06-26 18:22:53 -04:00
jgoecks 73b0ebfd27 Remove debugging statements. 2016-06-26 17:06:09 -04:00
Nick Stoler 834736946c Small run_tests.sh documentation updates. 
Make clear that run reports are created by default, print the filename.
 2016-06-26 16:08:04 -04:00
Eric Enns 9ad9c0c80a Python 3: remaining model migrations 2016-06-26 14:08:06 -05:00
Björn Grüning f280645ca2 Merge pull request #2552 from erasche/gie-proxy-issue 
More defensive GIE Proxying
 2016-06-26 18:28:28 +02:00
Timur Shtatland 005429acbb Python3: lib/galaxy/model/migrate/versions/0014..0023 
lib/galaxy/model/migrate/versions/0014_pages.py
lib/galaxy/model/migrate/versions/0015_tagging.py
lib/galaxy/model/migrate/versions/0016_v0015_mysql_index_fix.py
lib/galaxy/model/migrate/versions/0017_library_item_indexes.py
lib/galaxy/model/migrate/versions/0018_ordered_tags_and_page_tags.py
lib/galaxy/model/migrate/versions/0019_request_library_folder.py
lib/galaxy/model/migrate/versions/0020_library_upload_job.py
lib/galaxy/model/migrate/versions/0021_user_prefs.py
lib/galaxy/model/migrate/versions/0022_visualization_tables.py
lib/galaxy/model/migrate/versions/0023_page_published_and_deleted_columns.py
 2016-06-26 12:07:49 -04:00
Nicola Soranzo de99c7efe2 Python3: lib/galaxy/visualization/ 2016-06-26 12:03:49 -04:00
Timur Shtatland 2c67f1e7e5 Python3: lib/galaxy/model/migrate/versions/0006..0013 
lib/galaxy/model/migrate/versions/0006_change_qual_datatype.py
lib/galaxy/model/migrate/versions/0007_sharing_histories.py
lib/galaxy/model/migrate/versions/0008_galaxy_forms.py
lib/galaxy/model/migrate/versions/0009_request_table.py
lib/galaxy/model/migrate/versions/0010_hda_display_at_authz_table.py
lib/galaxy/model/migrate/versions/0011_v0010_mysql_index_fix.py
lib/galaxy/model/migrate/versions/0012_user_address.py
lib/galaxy/model/migrate/versions/0013_change_lib_item_templates_to_forms.py
 2016-06-26 11:51:30 -04:00
jgoecks babe85f3dc Fixes for showing min/max labels in Trackster. 2016-06-26 11:36:21 -04:00
Timur Shtatland 1b06c52e8d Python3: sort, remove dup in .ci/py3_sources.txt 2016-06-26 11:33:13 -04:00
Timur Shtatland 1fd6efcb0c Python3: the rest of lib/galaxy/datatypes/converters/ 
lib/galaxy/datatypes/converters/pbed_ldreduced_converter.py
lib/galaxy/datatypes/converters/pbed_to_lped_converter.py
lib/galaxy/datatypes/converters/picard_interval_list_to_bed6_converter.py
lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.py
lib/galaxy/datatypes/converters/wiggle_to_simple_converter.py
 2016-06-26 11:28:07 -04:00
Nicola Soranzo a8ac700318 Python3: lib/galaxy/model/__init__.py 2016-06-26 11:14:00 -04:00
Nate Coraor 3d688e6bcf Allow users to purge datasets by default 2016-06-26 10:17:53 -04:00
Nicola Soranzo 693e18cdc2 Fix the fix 2016-06-26 10:16:51 -04:00
Eric Rasche 26013f24e4 More defensive proxying 2016-06-26 13:44:12 +00:00
Björn Grüning b8fa771c4a Merge pull request #2548 from erasche/gie-uhoh 
Fix old bug in non-allowed_images.yml GIEs
 2016-06-26 14:07:24 +02:00
Nicola Soranzo cd13423953 Python3: small fixes to previous commits 2016-06-26 02:43:57 -04:00
Nicola Soranzo 440c9f66d7 Python3: lib/galaxy/managers/ 2016-06-26 00:24:08 -04:00
Eric Rasche 15fac1510f Fix old bug in non-allowed_images.yml GIEs 2016-06-26 02:44:54 +00:00
Junzhou Wang f68a8198da Python3: scripts/cleanup_datasets scripts/data_libraries 2016-06-25 21:49:25 -04:00
Nicola Soranzo 31c61caba3 Simplify .ci/py3_sources.txt 2016-06-25 21:27:09 -04:00
Nicola Soranzo 86a54452b3 Revert change to callable(), it has been brought back in Python 3.2 2016-06-25 21:24:20 -04:00
Nicola Soranzo ef33572167 Python3: lib/galaxy/datatypes/dataproviders/ 2016-06-25 21:24:20 -04:00
Timur Shtatland 3b31f02d07 Python 3: more lib/galaxy/datatypes/converters/ 
lib/galaxy/datatypes/converters/lped_to_fped_converter.py
lib/galaxy/datatypes/converters/lped_to_pbed_converter.py
lib/galaxy/datatypes/converters/maf_to_fasta_converter.py
lib/galaxy/datatypes/converters/maf_to_interval_converter.py
 2016-06-25 21:03:20 -04:00
John Chilton 48af26ebfb Merge pull request #2544 from dannon/fix_set_dataset_sizes_script 
Initialize objectstore for fix_set_dataset_sizes script
 2016-06-25 20:53:19 -04:00
John Chilton 6552bd71df Merge pull request #2545 from dpryan79/igv_bigwig 
bigWig files displayed in IGV
 2016-06-25 20:50:34 -04:00