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Commit Graph
107 Commits
Author SHA1 Message Date
mvdbeek 0122cdb16e Merge branch 'release_24.0' into release_24.1 2024-06-05 17:43:18 +02:00
mvdbeek fed2294c1b Merge branch 'release_23.1' into release_23.2 2024-06-05 10:03:56 +02:00
mvdbeek 06b8db47ba Change hardcoded repo location in more place 2024-05-31 11:36:59 +02:00
Nicola Soranzo 8cdca0f343 Revert some requests import changes 
introduced in https://github.com/galaxyproject/galaxy/pull/18003 .
In particular, when using requests in the tests to connect to Galaxy
or the ToolShed it's not needed to use the modified headers.

Also:
- Move some imports after conditional imports.
- Fix type annotations in `lib/tool_shed/test/base/populators.py`
- Fix typo bug in `test/unit/util/test_get_url.py`
 2024-05-23 15:55:56 +01:00
John Chilton 2f43c32fd9 Merge pull request #18003 from mvdbeek/add_galaxy_to_user_agent 
Add galaxy to user agent
 2024-05-20 12:14:13 -04:00
Nicola Soranzo 534010a8cb Enable flake8-implicit-str-concat ruff rules 
See https://docs.astral.sh/ruff/rules/#flake8-implicit-str-concat-isc
 2024-04-29 13:37:54 +01:00
Nicola Soranzo 0629908541 Fix new UP031 errors from ruff 0.4.2 2024-04-29 00:09:38 +01:00
mvdbeek e8a3b8c0cd Create wrapper for requests with default user agent 2024-04-16 17:54:29 +02:00
John Davis 09fe7b9a54 Fix select stmts in scripts 2023-07-19 11:05:55 -04:00
John Davis 9ddaaf8d06 Wrap session.flush in tool_shed/* scripts 2023-06-09 13:05:26 -04:00
Nicola Soranzo c3139f246d Fix UP031 errors reported by ruff 2023-03-29 08:55:54 +01:00
John Davis e08e1aaa9f Drop tool shed bootstrapping scripts and references to them 2023-02-08 00:33:48 -05:00
Nicola Soranzo 14b1730eb2 Combine "as" imports with other "from" imports 2022-06-20 20:06:30 +01:00
John Chilton 4e01cfe3eb Merge pull request #13562 from ic4f/dev_sa20_3 
Misc. SQLAlchemy 2.0 upgrades
 2022-03-20 18:37:17 -04:00
Nicola Soranzo 00f7522e7e Merge branch 'release_22.01' into dev 2022-03-19 01:57:33 +00:00
mvdbeek 4c7bfd1032 Fix tool shed bootstrapping script 2022-03-17 19:34:43 +01:00
Sergey Golitsynskiy 09be05082f Wrap sql stmt in text() (tool_shed, exluding migrate/versions) 2022-03-17 12:41:47 -04:00
Sergey Golitsynskiy 3c992a608f Add create/migrate scripts for Alembic dbs (squashed) 
Also add exec permissions to create/migrate python scripts.
(not sure this is required, adding for consistency with previous
version)

+ A few fixes for TS scripts, tests

Squashed:
- pick b62443245e Add create/migrate scripts for Alembic dbs
- squash 06f0a923ca Fix integration test (test only relevant for TS)
 2022-03-09 18:41:02 -05:00
Dannon Baker 623a5e165a Apply black formatting. 
Apply isort.
 2022-02-03 07:42:20 -05:00
mvdbeek bab12662a9 Drop old sqlalchemy patterns 2021-12-16 12:30:49 +01:00
Nicola Soranzo 9d74bba7fb Drop support for retired Python 3.5 
Upgrade syntax using `pyupgrade --py36-plus` .

Manually drop several `six` imports.

Also:
- Remove broken pr_cache in scripts/bootstrap_history.py
- Fix broken prefix removal in lib/galaxy/tool_util/deps/mulled/mulled_build.py
 2020-10-07 11:52:13 +01:00
Nicola Soranzo 089e11ce65 Small refactor to `validate_password()`. Add back deleted line 
Follow-up on https://github.com/galaxyproject/galaxy/pull/9587
 2020-06-04 18:52:59 +01:00
Marius van den Beek 0fe6be60ea Merge pull request #9587 from nuwang/set_password_if_null 
[20.05] Assign random password in user manager if none specified
 2020-06-02 12:04:50 +02:00
Nuwan Goonasekera c9f29aa888 Refactor toolshed password validation 2020-05-25 23:39:52 +05:30
mvdbeek a36b4486bf Merge branch 'release_20.01' into dev 2020-03-26 10:51:46 +01:00
mvdbeek 7105de2fb0 Fix import order 2020-03-21 13:27:53 +01:00
mvdbeek 159a94b95d Move index logic to lib.tool_shed.util.shed_index 
Since we need the index for browsing repos in the new client
we should incrementally build the index with every repo update.
Having this in tool_shed will make re-use easier.
 2020-03-21 13:27:53 +01:00
mvdbeek afce65249f Implement incremental indexing 2020-03-21 13:27:53 +01:00
mvdbeek 2bb2f0989f Make build_ts_whoosh_index.py py3 compatible 2020-03-21 13:27:53 +01:00
Nicola Soranzo f5cd88465e Make str.join()s more efficient 
by using generator expressions and tuples instead of lists.
 2020-01-23 11:06:32 +00:00
Nicola Soranzo 2fcbe0afa3 changectx() method was dropped in mercurial 4.6 
in favour of `__getitem__()`.
 2019-12-05 18:31:26 +00:00
Martin Cech 5a18a486bd when building ts index log parse errors as debug level 2019-11-22 17:27:07 -05:00
Nicola Soranzo 72186b40a1 Merge branch 'release_19.09' into dev 2019-11-19 23:30:02 +01:00
Martin CechandMarius van den Beek fc8b832888 Apply suggestions from code review @mvdbeek 
Co-Authored-By: Marius van den Beek <m.vandenbeek@gmail.com>
 2019-11-19 09:32:15 -05:00
Martin Cech 0c075f73b4 set logging level according to the argument 
also report the run summary as 'info' level
 2019-11-18 12:05:02 -05:00
Martin Cech 5c495d6514 refactor logging 2019-11-18 11:25:47 -05:00
Martin Cech 19c56c725b add exec timer 2019-11-18 09:56:15 -05:00
Martin Cech c9d9009299 refactor and modernize toolshed search indexes build script 
mainly so it can read yml config
 2019-11-14 18:07:06 -05:00
John Chilton 559b664b07 Refactor tool_shed webapp out of Galaxy. 2019-11-11 12:32:19 -05:00
Martin Cech a48c7420d7 Merge pull request #8956 from jmchilton/remove_ts_api 
Remove tool shed API examples.
 2019-11-11 10:41:22 -05:00
Nicola Soranzo 6b1bacc2b8 Merge pull request #8957 from jmchilton/remove_legacy_shed 
Remove script for migrating tools to the tool shed...
 2019-11-11 10:54:27 +00:00
John Chilton d4196b61a4 Remove tool shed API examples. 
These aren't tested, bioblend likely has better documentation (https://bioblend.readthedocs.io/en/latest/api_docs/toolshed/all.html), and we should be encouraging TS interactions to be done through Planemo and not raw API calls.

Excluding scripts used by bootstrap.
 2019-11-11 02:55:26 -05:00
John Chilton a27beb0fd8 Remove script for migrating tools to the tool shed... 
from an older tool shed? I completely forgot there even was an older tool shed.
 2019-11-11 02:50:12 -05:00
John Chilton fbe21f94bf Remove tool dependency scripts. 2019-11-11 02:35:31 -05:00
Nicola Soranzo 85f7f91206 Fix script shebangs 
Improve tools.
 2019-10-26 20:20:01 +01:00
John Chilton 4287bb787f Merge pull request #8621 from martenson/ux-ts-installer 
[19.09] allow the TS search API to bypass wildcard search
 2019-09-12 13:35:01 -04:00
Martin Cech 99ec4ecf75 adjust indexing and searching of special keywords to be case-insensitive 2019-09-11 16:39:14 -04:00
Martin Cech 02a3342bd6 regenerate ts search indexes in tmp directory 2019-09-10 16:06:21 -04:00
Sergey Golitsynskiy 1694b79185 Update import paths for loader_directory 2019-07-06 00:52:45 +02:00
Nicola Soranzo 90a6c6d46b Fix issues reported by ShellCheck 2019-06-13 12:53:26 +01:00