mvdbeek
39e47c5145
Fix workflow editor save as functionality
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Fixes https://github.com/galaxyproject/galaxy/issues/9308
2020-02-04 19:46:22 +01:00
John Chilton
bd96d8d3c8
Merge pull request #9294 from dannon/no_cache_bootstrapped_client
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[20.01] Prevent caching of bootstrapped client data
2020-02-03 09:43:24 -05:00
Dannon Baker
0688ec88a6
Prevent caching of bootstrapped client data.
2020-01-31 17:21:06 -05:00
Nicola Soranzo
d525fd0913
Merge branch 'release_19.09' into release_20.01
2020-01-31 15:00:26 +00:00
Nicola Soranzo
44859c7d6d
Merge pull request #9290 from nsoranzo/release_19.09_fix_9178
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[19.09] Python3: don't check for has_key attribute
2020-01-31 14:51:53 +00:00
Nicola Soranzo
2e587f14a7
Python3: don't check for has_key attribute
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Also partially backport commit f892231b8bhttps://github.com/galaxyproject/galaxy/issues/9178 .
2020-01-31 01:17:02 +00:00
Nicola Soranzo
230900fe85
Merge branch 'release_19.09' into release_20.01
2020-01-30 11:36:31 +00:00
Wolfgang Maier
7135ab307b
Python3 compatible SnpEff and SnpSift metadata detection
2020-01-30 11:20:26 +00:00
mvdbeek
cc6e2aba83
Merge branch 'release_19.09' into release_20.01
2020-01-29 22:12:27 +01:00
John Chilton
0940b1ec26
Starting work on tool-util 20.1.0.dev6
2020-01-29 14:08:18 -05:00
John Chilton
948005e8d7
Merge pull request #9278 from mvdbeek/backwards_compatible_build_number_parsing
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[20.01] Backwards compatible build number parsing
2020-01-29 14:04:49 -05:00
mvdbeek
e7998dee41
Don't include build number 0 for single images
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And have conda build take precedence over image_build
for single target images.
If overriding the build suffix is really necessary one can
use the `name_override` column.
2020-01-29 17:36:10 +01:00
mvdbeek
9a4ff7fba1
Restore parsing build numbers separated with --
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I changed this in https://github.com/galaxyproject/galaxy/pull/9268/
but the alternative -- is also in used at https://github.com/BioContainers/multi-package-containers/blob/master/combinations/hash.tsv#L14
2020-01-29 17:34:38 +01:00
Nicola Soranzo
86b89ddae2
Merge pull request #9276 from dannon/email-notification-tweaks
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[20.01] Email notifications aren't used from just workflow steps anymore.
2020-01-29 14:02:57 +00:00
Dannon Baker
ba4e59d4ba
Email notifications aren't used from just workflow steps anymore.
2020-01-29 06:20:11 -05:00
Marius van den Beek
2797857cfb
Merge pull request #9170 from mvdbeek/try_sourcing_activate_d_scripts
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[20.01] source /usr/local/etc/conda/activate.d/*.sh files
2020-01-29 10:20:39 +01:00
Dannon
8e16fcb4cc
Merge pull request #9233 from dannon/external-auth-login-refinement
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[20.01] External auth login refinement
2020-01-28 13:22:55 -05:00
Nicola Soranzo
1ce75c8297
Merge pull request #9269 from mvdbeek/fix_target_str_to_targets
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[20.01] backport 9268: Fix target_str_to_targets
2020-01-27 18:41:19 +00:00
John Chilton
002964ee17
Merge pull request #9242 from mvdbeek/limit_dataid_in_incoming_special_case
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[19.09] Limit async hack to async tools
2020-01-27 09:52:23 -05:00
John Chilton
fdfdcc50b4
Starting work on tool-util 20.1.0.dev5
2020-01-27 09:41:11 -05:00
John Chilton
dbf6d3a565
Merge pull request #9234 from mvdbeek/mount_configs_rw
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[20.01] Mount job_working_directory/configs rw
2020-01-27 09:36:57 -05:00
mvdbeek
afc4ceb138
Fix target_str_to_targets
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This function is used to parse out Conda targets. The build part here is
wrong, a package build is specified like this:
`<package_name>=<version>=build`. This fixed building images as in https://github.com/BioContainers/multi-package-containers/pull/953
2020-01-26 20:53:10 +01:00
Björn Grüning
2e1c5e427e
Merge pull request #9267 from mvdbeek/mulled_build_image_name_fix
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[20.01] Fix suffix for single target mulled builds
2020-01-25 23:45:44 +01:00
mvdbeek
4448286a75
Fix suffix for single target builds
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Without this single target builds with explicit `iamge_build`
would be called quay.io/biocontainers/<package><image_build>,
which is not right.
2020-01-25 19:21:03 +01:00
Nicola Soranzo
6fbe8c9031
Merge branch 'release_19.09' into release_20.01
2020-01-24 17:08:02 +00:00
Nicola Soranzo
83bd84842e
Merge pull request #9266 from mvdbeek/fix_iteritems_in_workflow_extraction
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[19.09] Fix iteritems use in build_from_current_history.mako
2020-01-24 17:03:20 +00:00
Marius van den Beek
6bb6aa22b7
Merge pull request #9263 from nsoranzo/release_19.09_backport_9260
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[19.09] Backport #9260 plus refactor
2020-01-24 16:59:13 +01:00
mvdbeek
f405dbf719
Fix iteritems use in build_from_current_history.mako
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Fixes https://github.com/galaxyproject/galaxy/issues/9265
2020-01-24 15:24:51 +01:00
Nicola Soranzo
d67295162a
Simplify and refactor
2020-01-23 21:57:54 +00:00
mvdbeek
e227b1473f
Fix unselected select parameter comparison to empty string
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`$wrapper == ""` and `$wrapper == "None"` had been valid ways
to check for unselected / optional select parameters.
This restores the `$wrapper == ""` form as used by gffcompare
https://github.com/galaxyproject/tools-iuc/blob/master/tools/gffcompare/gffcompare.xml#L41
2020-01-23 19:24:52 +00:00
Björn Grüning
1a6d98d29d
Merge pull request #9260 from mvdbeek/fix_multi_select_equals_empty_string
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[20.01] Fix unselected select parameter comparison to empty string
2020-01-23 19:12:28 +01:00
mvdbeek
673f21f9b6
Merge branch 'release_19.09' into release_20.01
2020-01-23 17:00:38 +01:00
Marius van den Beek
fc0e31887f
Merge pull request #9253 from bernt-matthias/topic/fix-popen-py3-followup
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[19.09] fix bug introduced in https://github.com/galaxyproject/galaxy/pull/9246
2020-01-23 16:58:44 +01:00
Dannon Baker
0be9fd5e56
Fix test bit array length...
2020-01-23 10:28:46 -05:00
mvdbeek
5d379dc4a5
Fix unselected select parameter comparison to empty string
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`$wrapper == ""` and `$wrapper == "None"` had been valid ways
to check for unselected / optional select parameters.
This restores the `$wrapper == ""` form as used by gffcompare
https://github.com/galaxyproject/tools-iuc/blob/master/tools/gffcompare/gffcompare.xml#L41
2020-01-23 16:02:56 +01:00
Dannon Baker
4ddb038f3f
Drop authnz package; leave coupled with webapp
2020-01-23 09:54:40 -05:00
Dannon Baker
f041eb2190
Fix lint in custos test
2020-01-22 16:43:42 -05:00
Dannon Baker
1dd4a880b6
Add psa-specific user creation duplicate protection.
2020-01-22 15:57:14 -05:00
mvdbeek
b7e1c1bf08
Also mkdir -p configs
2020-01-22 21:43:39 +01:00
mvdbeek
60d8c4668e
Make tools that manipulate files in configs/ resubmittable
2020-01-22 19:02:23 +01:00
mvdbeek
96aabc1382
Make mounting configs dir conditional on tool profile
2020-01-22 19:02:23 +01:00
Dannon Baker
20a0777a25
Fix custos authnz tests. This should be swapped to use the standard mocked objects?
2020-01-22 11:44:27 -05:00
Dannon Baker
2a18857bba
Swap custos auth to use standard manager-based user creation.
2020-01-22 11:43:58 -05:00
mvdbeek
7bbdf83771
Mount job_working_directory/configs rw
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Many tools have this pattern where they move the config file somewhere,
which doesn't work if it is mounted read-only.
2020-01-22 17:40:22 +01:00
M Bernt and Marius van den Beek
c358e3ab69
remove space
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Co-Authored-By: Marius van den Beek <m.vandenbeek@gmail.com >
2020-01-22 16:54:48 +01:00
M Bernt
db5bd4fac3
fix bug introduced in https://github.com/galaxyproject/galaxy/pull/9246
2020-01-22 16:16:45 +01:00
mvdbeek
54d6bad26e
Merge branch 'release_19.09' into release_20.01
2020-01-22 16:08:45 +01:00
John Chilton
a52e24ee3a
Merge pull request #9245 from mvdbeek/fix_deletion_of_outputs_before_job
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[20.01] Fix deletion of outputs and working before job
2020-01-22 09:02:45 -05:00
John Chilton
d6a077c75e
Merge pull request #9243 from mvdbeek/fix_data_table_moving
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[19.09] Fix moving of data manager output for entries
2020-01-22 09:02:02 -05:00
Marius van den Beek
dc7e2e5f68
Merge pull request #9246 from bernt-matthias/topic/fix-popen-py3
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[19.09] python3 fixes for setups using drmaa and realuser setups
2020-01-22 13:28:53 +01:00
mvdbeek