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Author SHA1 Message Date
Anthony Bretaudeau 47d0e6232b ignore empty lines 2021-12-14 13:04:31 +01:00
mvdbeek dd60630588 Merge branch 'release_21.05' into release_21.09 2021-12-13 15:20:05 +01:00
mvdbeek b4238f9717 Merge branch 'release_21.01' into release_21.05 2021-12-13 15:18:13 +01:00
Marius van den Beek 6928436125 Merge pull request #13055 from mvdbeek/lift_version_check_in_toolshed 
[21.01] Only check profile version in Galaxy
 2021-12-13 15:15:33 +01:00
mvdbeek b4a29f2600 Only check profile version in Galaxy 
Should fix https://github.com/galaxyproject/galaxy/issues/13008
 2021-12-13 12:49:50 +01:00
Marius van den Beek 8ec119eebb Merge pull request #13050 from cat-bro/add-to-implicitly-required-tool-files-for-pulsar 
add tools to IMPLICITLY_REQUIRED_TOOL_FILES in tools/__init__.py
 2021-12-12 17:39:02 +01:00
Björn Grüning d6e6235687 Merge pull request #13021 from mvdbeek/copy_hdas_within_hdcas_on_import 
[21.09] Copy HDCA member items to new history when copying history
 2021-12-11 22:41:23 +01:00
cat-bro 9a0978102e add tools to IMPLICITLY_REQUIRED_TOOL_FILES in tools/__init__.py 2021-12-08 20:30:56 +11:00
Dannon 7ef39f676d Merge pull request #12985 from OlegZharkov/fixhistoryerror 
[21.09] fix showing history error
 2021-12-07 10:09:05 -05:00
Oleg Zharkov dbcf1e8e98 expose api to expose api anonymous 2021-12-06 19:28:34 +01:00
Dannon 0afd730d33 Merge pull request #13024 from natefoo/display-anonymous-and-sessionless 
[21.09] Make dataset display route sessionless as well as anonymous
 2021-12-03 08:41:58 -05:00
Nicola Soranzo b779aeb21a Merge branch 'release_21.05' into release_21.09 2021-12-03 12:56:28 +00:00
Nicola Soranzo 35dda33fa6 Merge pull request #13028 from nsoranzo/release_21.05_min_pip_version 2021-12-03 12:49:44 +00:00
Nicola Soranzo 262ab8386c Increase pip minimum version in startup script 
Pip <19.0 cannot install abi3 wheels, so for example on Python >3.6 it
would (try to) build a cryptography wheel, which is not needed since
cp36-abi3 wheels are already available on PyPI:
https://cryptography.io/en/latest/faq/#why-are-there-no-wheels-for-my-python3-x-version

Fix https://github.com/galaxyproject/galaxy/issues/13023 .

xref: https://github.com/galaxyproject/planemo/issues/1208#issuecomment-984831111
 2021-12-03 11:02:20 +00:00
mvdbeek 5810adb3e6 Add minimize_copies mode for coying histories 2021-12-02 19:13:48 +01:00
Nate Coraor 9146fcc981 Make dataset display route sessionless as well as anonymous. 2021-12-02 12:29:42 -05:00
mvdbeek 483e5658c0 Use HDCA dataset instance hid to skip unnecesary new HDAs 2021-12-02 18:05:27 +01:00
mvdbeek dd806f0993 Copy HDCA member items to new history when copying history 2021-12-02 16:22:15 +01:00
Marius van den Beek 60ab1d5b7a Merge pull request #13010 from natefoo/sentry-ts 
[21.09] Refactor Sentry middleware/client changes for Tool Shed
 2021-12-02 10:21:47 +01:00
Nate Coraor 9b293ac438 Refactor Sentry middleware/client changes for Tool Shed 2021-11-30 15:04:32 -05:00
Björn Grüning 5793a1c325 Merge pull request #12989 from mvdbeek/install_model_sessionfactory 
[21.09] Reconstruct separate scoped session for ToolShedRepositoryCache
 2021-11-26 16:45:49 +01:00
Oleg Zharkov 499362f6a6 fix response formatting 2021-11-26 15:29:18 +01:00
Oleg Zharkov 1caa2b9c08 fix error message 2021-11-26 14:18:25 +01:00
Oleg Zharkov d1cfec038e drop local error handling and use @expose_api functionality 2021-11-26 14:01:11 +01:00
oleg c64d1bc200 fix history error 2021-11-26 13:31:28 +01:00
mvdbeek 4e17fcc851 Reconstructed separate scoped session for ToolShedRepositoryCache 
If we just construct a single session, but the underlying connection is
closed, we can't use the session anymore, at all.
 2021-11-26 10:05:47 +01:00
Marius van den Beek 760e77b5f7 Merge pull request #12973 from IslamHeggy/release_21.09 
[21.09] BugFix: Update social-auth-core library version to fix OIDC problem
 2021-11-25 15:50:35 +01:00
Nicola Soranzo 8045ee5b61 Update social-auth-core library also in requirements files 2021-11-24 17:46:09 +00:00
Islam Heggy cde79eef33 Update social-auth-core library version to fix OIDC problem 2021-11-24 05:00:28 +02:00
mvdbeek 512526a5f5 Version 21.9.2 of tool-util (tag galaxy-tool-util-21.9.2). galaxy-tool-util-21.9.2 2021-11-23 13:54:07 +01:00
Marius van den Beek 4110381645 Merge pull request #12968 from bernt-matthias/backport/lint-select-fix 
[21.09] Backport lint select fix #12920
 2021-11-23 13:46:15 +01:00
M BerntandNicola Soranzo c36ff1e2e7 simplify code 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2021-11-23 11:50:29 +01:00
Matthias Bernt fb86d06c55 fix linter for select inputs 
from the docs: `select parameters with multiple="true" are optional by default`
 2021-11-23 11:50:29 +01:00
Björn Grüning b183cd3141 Merge pull request #12906 from dannon/fix-menu-overflow 
Fix menu overflow in right panel
 2021-11-18 22:05:13 +01:00
Björn Grüning ff7b6c9fd7 Merge pull request #12915 from mvdbeek/add_ca_certificates 
[21.09] Fix containerized NCBI Datasets Genomes data source tool
 2021-11-18 22:04:53 +01:00
Marius van den Beek 90c2f31cb4 Don't add ca-ceritificates to tool requirements 
ca-certificates is now part of the ncbi-datasets-cli conda package
 2021-11-18 17:17:19 +01:00
Marius van den Beek 066b887574 Merge pull request #12936 from bernt-matthias/topic/validator_multiple 
[21.09] fix value_in_data_table validator for multiple selects
 2021-11-17 17:54:38 +01:00
M BerntandMarius van den Beek fe9b15752b Update lib/galaxy/tools/parameters/basic.py 
Co-authored-by: Marius van den Beek <m.vandenbeek@gmail.com>
 2021-11-17 15:55:02 +01:00
Matthias Bernt 8a39ae6bda update docs 2021-11-17 15:55:01 +01:00
Matthias Bernt 25c3c5bbc5 implement validation for multiple selects in SelectToolParamter 
instead of in the validator. then it also works for derived parameter
types
 2021-11-17 15:55:01 +01:00
Matthias Bernt 074b011b41 fix value_in_data_table validator for multiple selects 2021-11-17 15:55:01 +01:00
Marius van den BeekandHelena f1986a481f Export just once 
Thanks!

Co-authored-by: Helena <hxr@hx42.org>
 2021-11-17 15:28:07 +01:00
Nicola Soranzo 043ab2939a Merge branch 'release_21.05' into release_21.09 2021-11-17 12:33:58 +00:00
Nuwan Goonasekera 6c97e488a6 Merge pull request #12925 from nuwang/fix_docker_image_build_output_name 
Fix output step name in docker image build
 2021-11-16 08:24:22 +05:30
Nicola Soranzo cd99d1076a Merge branch 'release_21.05' into release_21.09 2021-11-16 01:33:45 +00:00
Nuwan Goonasekera 52cbc86102 Fix output step name in docker image build 2021-11-16 01:30:07 +05:30
Nuwan Goonasekera 55acdf9ba0 Merge pull request #12922 from nuwang/fix_docker_repo_names 
[21.05] Update docker autobuilds to use correct repos
 2021-11-16 00:38:00 +05:30
Marius van den Beek f01b44ccfd Merge pull request #12919 from mvdbeek/fix_install_of_tools_biotools 
[21.09] Fix installation of tools with biotools id
 2021-11-15 16:24:16 +01:00
Nuwan Goonasekera 3d7b713f75 Update docker autobuilds to use correct repos 2021-11-15 20:38:59 +05:30
Marius van den BeekandNicola Soranzo 29372686b2 Improve indentation consistency 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2021-11-15 13:18:34 +01:00