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19792 Commits
Author SHA1 Message Date
Nicola Soranzo c560f673b6 Merge branch 'release_19.01' into dev 2019-03-12 00:40:32 +00:00
Nicola Soranzo 031a58bb27 Merge branch 'release_18.09' into release_19.01 2019-03-12 00:38:59 +00:00
Dannon 5d90d78d2c Merge pull request #7510 from martenson/rip-biostar 
remove biostar integrations
 2019-03-11 17:59:04 -04:00
mvdbeek 5522360953 Update to gxformat2 with change_datatype action 2019-03-11 21:48:10 +01:00
mvdbeek df8a4dcf16 Fix ChangeDatatypeAction for collections 2019-03-11 21:48:10 +01:00
mvdbeek 34725f61ac Consolidate hiding HDAs in DatabaseOperation tools 
This fixes dataset being added to histories when the source
HDA is visible.
 2019-03-11 21:48:10 +01:00
mvdbeek 4cceb67d62 Fix ChangeDatatype action for collection output 2019-03-11 21:48:10 +01:00
mvdbeek f26a1177b8 Fix delayed post jobs actions for DatabaseOperationTools 2019-03-11 21:48:09 +01:00
John Chilton cc62d06899 Merge pull request #7480 from mvdbeek/fix_build_list_pjas 
Fix post job actions for Database Operation tools, implement change_datatype for collection output
 2019-03-11 16:38:43 -04:00
Martin Cech 75ae68693f remove biostar integrations 
we stopped using it and this will lower our maintenance burden
 2019-03-11 15:51:41 -04:00
Martin Cech 8ae44cd8cb Merge pull request #7463 from VJalili/upgrade_psa_2 
Update to PSA 3.1 and support login with Globus identity
 2019-03-11 15:41:22 -04:00
vahid 81fbfdac4a Drop support for PixelPin IdP. 2019-03-11 12:39:41 -07:00
vahid 8e56a53a7b Drop support to Elixir IdP per missing ID token in authn response. 2019-03-11 10:05:03 -07:00
mvdbeek 48c303365c Update to gxformat2 with change_datatype action 2019-03-11 17:14:44 +01:00
Nicola Soranzo 7b316215f4 Merge pull request #7504 from mvdbeek/logging_fix 
[18.09] Fix warning message formatting in sharing controller
 2019-03-11 14:07:44 +00:00
John Chilton 1ca256aaba Merge pull request #7470 from jmchilton/portable_metadata 
Implement portable metadata generation.
 2019-03-11 09:57:13 -04:00
mvdbeek 98a189ceff Fix warning message formatting in sharing controller 
Reported by @erasche in https://github.com/galaxyproject/galaxy/issues/7503#issuecomment-471496500,
broken in https://github.com/galaxyproject/galaxy/commit/e4399021520440a8f58e33dbae161f031f8da9eb
 2019-03-11 13:25:54 +01:00
John Chilton f0912eb404 Fix set_metadata executing from wrong directory when using tool. 2019-03-10 21:15:56 -04:00
Nicola Soranzo 417292b501 Merge branch 'release_19.01' into dev 2019-03-10 21:44:29 +00:00
Nicola Soranzo aef53f6cde Merge branch 'release_18.09' into release_19.01 2019-03-10 21:39:24 +00:00
Nicola Soranzo 8e125b7698 Merge branch 'release_18.05' into release_18.09 2019-03-10 21:36:15 +00:00
Nicola Soranzo c1a9095ad4 Restrict loading of JSON files on the server via the workflow API to Galaxy admins 
Fix https://github.com/galaxyproject/security/issues/29
 2019-03-10 12:52:02 +00:00
vahid 06dd2f8bae Revert sqlalchemy version increment, since it breaks all the tests. 2019-03-08 13:20:50 -08:00
mvdbeek 377bffd3ae Fix ChangeDatatypeAction for collections 2019-03-08 16:59:05 +01:00
mvdbeek 199468e920 Consolidate hiding HDAs in DatabaseOperation tools 
This fixes dataset being added to histories when the source
HDA is visible.
 2019-03-08 16:17:15 +01:00
mvdbeek 54adb6e73a Fix ChangeDatatype action for collection output 2019-03-08 16:13:55 +01:00
John Chilton e767686816 Better I/O in metadata package. 2019-03-08 09:47:18 -05:00
John Chilton 395380fc66 Fix: Handle galaxy.json entries without dataset_id in galaxy.json. 2019-03-08 09:47:02 -05:00
John Chilton 17cb35bc25 Use ToolProvidedMetadata abstraction in set_metadata. 
There is are somethings that happen in set_metadata.py that assume the old style galaxy.json. This sets the stage for proper external metadata collection of newer style galaxy.json files.
 2019-03-08 09:47:02 -05:00
John Chilton 1d0e4bcb2c New, portable metadata generation. 
Variant of external metadata generation that doesn't use command-line arguments or absolute paths and simply takes operates on the current, job working directory and knows what to do.

- Uses relative paths allowing the directory to be staged elsewhere via Pulsar, Condor, or Docker for instance.
- Avoids DB objects for hard-coded paths making everything more robust.
- Avoids huge command-lines which for huge collection reduction jobs might hit system limits for command-line length.
- Uses JSON dicts to communicate parameters - meaning we can avoid awkward argument parsing as this evolves (see old max_metadata_value_size handling in set_metadata.py for instance).
- Uses output names instead of database IDs to key files - so file naming is consistent and human readable.
 2019-03-08 09:47:02 -05:00
John Chilton 676cdf7678 Log exception in set_metadata.py. 
We can finally do this as a result of #7095 I believe!
 2019-03-07 12:33:38 -05:00
Martin Cech c714b6e665 Merge pull request #7288 from fmareuil/dev 
Add a validator that ensures one metadata is between min and max values
 2019-03-07 12:17:17 -05:00
John Chilton 192a091d16 Merge pull request #7442 from VJalili/upgrade_psa 
Inform users if an exception has happened authenticating via OIDC
 2019-03-07 11:52:07 -05:00
mvdbeek 0951324aef Fix delayed post jobs actions for DatabaseOperationTools 2019-03-07 17:04:20 +01:00
Marius van den Beek a10813a4f8 Merge pull request #7457 from bensellak/dev 
Adding microarrays data types Gpr and Gal
 2019-03-07 16:27:23 +01:00
Nicola Soranzo cf2f192d1b No need to iterate 2019-03-07 12:47:25 +00:00
Nicola Soranzo 5f738d9503 Forgot to remove increment to count 
Introduced in commit d140178dc6
 2019-03-07 12:05:13 +00:00
Nicola Soranzo e101d14230 More dep updates 2019-03-07 12:00:48 +00:00
bensellak 9621900512 Update microarrays.py 2019-03-06 20:35:01 +00:00
Nicola Soranzo d140178dc6 Use `enumerate()` 2019-03-06 18:04:20 +00:00
Nicola Soranzo cfb854f6c7 Use `sniff_prefix()` 2019-03-06 17:40:18 +00:00
bensellak 7f25bb7874 Add files via upload 2019-03-06 18:25:57 +01:00
Marius van den Beek 8bc23e03e0 Merge pull request #7471 from jmchilton/model_free_job_refactor_0 
Collected Refactoring of Job Output Handling Code
 2019-03-06 17:52:48 +01:00
bensellak f47048bb9c Update microarrays.py 2019-03-06 15:55:01 +00:00
bensellak d3a7f383d9 Modified classes definition, metadata and sniffing 2019-03-06 15:18:10 +01:00
mvdbeek 9d4f857378 Fix workflow_building_mode typo 2019-03-05 21:47:06 +01:00
John Chilton 3077895b22 Relocate dynamic output metadata source code for clarity. 2019-03-05 11:46:55 -05:00
John Chilton 2841a3dc26 Refactor output_collect to use app less. 2019-03-05 11:46:55 -05:00
John Chilton df0e58ba11 Relocate job param code for clarity. 2019-03-05 11:16:22 -05:00
John Chilton 0967412e3f Refactor output discovery toward cohesiveness in Tool class. 2019-03-05 11:16:21 -05:00