guerler
9e3a632eda
Use history component in history view route
2022-09-18 15:23:08 -04:00
guerler
6d003018ac
Remove legacy copy history modal from history grid, vue variant available in current history dropdown
2022-09-18 15:23:08 -04:00
guerler
d89c24ad00
Properly parse selected history id to collection builders
2022-09-18 15:23:08 -04:00
guerler
84f6da4574
Decouple data library from legacy history
2022-09-18 15:23:08 -04:00
Björn Grüning
8bcdff6f3a
Merge pull request #14642 from jmchilton/tool_shed_registry_refactor
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Refactor tool shed registry into utility code.
2022-09-17 19:23:16 +02:00
Nicola Soranzo
f9d0dabd2e
Merge pull request #14650 from galaxybot/dev_auto_update_dependencies
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Update Python dependencies
2022-09-17 07:35:38 +01:00
galaxybot
4899a6e3f5
Update Python dependencies
2022-09-17 03:58:36 +00:00
John Davis
fd13d1e750
Merge pull request #14648 from jdavcs/dev_config_tests
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Drop unnecessary config tests
2022-09-16 20:41:11 -04:00
John Chilton
44d6a34178
Remove repository review functionality from tool shed.
2022-09-16 20:25:37 -04:00
John Chilton
eb56507edc
Merge pull request #14645 from jmchilton/eliminate_configures_galaxy_mixin
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Eliminate configuresgalaxymixin.
2022-09-16 20:11:46 -04:00
John Chilton
d700581bd1
Eliminate configuresgalaxymixin.
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At this point it is only used in one place so just dump the methods into there.
2022-09-16 15:33:34 -04:00
John Davis
4c7d6805e7
Drop integration test for config defaults
2022-09-16 15:31:55 -04:00
John Davis
5236b66382
Improve test of assignment of default config values
2022-09-16 15:15:03 -04:00
John Davis
eb9dccef58
Drop unit tests for default config values
2022-09-16 15:05:20 -04:00
mvdbeek
ceea0a5dd5
Allow using simplified workflow run form with unconnected optional data input
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Fixes https://github.com/galaxyproject/galaxy/issues/13247 .
I'm not sure we need any other special treatment for optional data
inputs, just don't set them seems sufficient to me? I think that's the
natural course of action from the API consumer perspective.
Whether we want to track this more robsutly in the backend and whether
we want to require explicitly stating that optional data inputs must be
set as not specifyiable are separate questions IMO.
FWIW the best practices panel only checks for disconnected required data
inputs, so that brings the experience in line.
2022-09-16 19:17:53 +02:00
John Chilton
10dcf79157
Annotate tool shed registry in structured_app.
2022-09-16 13:05:39 -04:00
John Chilton
528bd5df5a
Refactor galaxy.tool_shed.tool_shed_registry -> galaxy.util.tool_shed.
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common_util makes heavy use of this implicitly so typing and designwise this will be better.
2022-09-16 13:03:41 -04:00
John Chilton
49c990a53b
Typing for tool shed registry.
2022-09-16 13:03:39 -04:00
David López
fa35e66709
Merge pull request #14639 from davelopez/fix_ro_crate_file_source_export
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Fix export RO-crate to file source
2022-09-16 18:47:41 +02:00
John Davis
39fee533a5
Point to init command as safer way to initialize empty database
2022-09-16 12:30:55 -04:00
John Davis
1c7e5fa13e
Split documentation into admin and dev sections
2022-09-16 12:17:21 -04:00
davelopez
0128e05a23
Fix export ro-crate to file source
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Write to the store the correct archive file
2022-09-16 17:19:49 +02:00
John Chilton
e1daab1768
Merge pull request #14629 from jmchilton/toolbox_typing
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Type annotations for base toolbox functionality.
2022-09-16 09:22:33 -04:00
John Chilton
b84076fa4a
Merge pull request #14609 from guerler/bundle_toolshed_js
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Place Toolshed JS modules into separate bundle
2022-09-16 09:21:58 -04:00
Björn Grüning
5d1a3e0b13
Merge pull request #14630 from guerler/remove_display_structured
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Remove outdated display structured history view
2022-09-16 15:10:14 +02:00
John Chilton
222fb13029
Merge pull request #14626 from jmchilton/mypy_infrastructure
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Improvements to mypy setup.
2022-09-16 08:58:13 -04:00
John Davis
6d1ee9d4f3
Remove duplication
2022-09-16 00:39:44 -04:00
John Davis
1eb4d15f38
Split script into admin and dev
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TODO: remove duplication between db.py and db_dev.py (split into
multiple commits is intentional)
2022-09-16 00:39:44 -04:00
John Davis
ad7f7f9268
Remove run_alembic.sh from root; user scripts/run_alembic.py instead.
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Rationale: move developer-focused scripts out of galaxy root.
2022-09-16 00:39:44 -04:00
John Davis
b6a5286487
Rename db.sh > manage_db.sh, following code review feedback
2022-09-16 00:39:44 -04:00
John Davis and Marius van den Beek
f54ffeaa86
Update lib/galaxy/model/migrations/README.md
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Co-authored-by: Marius van den Beek <m.vandenbeek@gmail.com >
2022-09-16 00:39:44 -04:00
John Davis and Marius van den Beek
76fa2de1f6
Update lib/galaxy/model/migrations/README.md
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Co-authored-by: Marius van den Beek <m.vandenbeek@gmail.com >
2022-09-16 00:39:44 -04:00
John Davis and Marius van den Beek
7e5fa1f1c8
Update lib/galaxy/model/migrations/README.md
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Co-authored-by: Marius van den Beek <m.vandenbeek@gmail.com >
2022-09-16 00:39:03 -04:00
John Davis and Marius van den Beek
766b4d8c7a
Update lib/galaxy/model/migrations/README.md
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Co-authored-by: Marius van den Beek <m.vandenbeek@gmail.com >
2022-09-16 00:39:03 -04:00
John Davis
78dc54e8c7
Rewrite migrations documentation
2022-09-16 00:39:03 -04:00
John Davis
2aaf6b8896
Override script name to display correct usage in cli help
2022-09-16 00:39:03 -04:00
John Davis
3c094790a1
Update test comments
2022-09-16 00:39:03 -04:00
John Davis
372d4af0b8
Add type hints
2022-09-16 00:39:03 -04:00
John Davis
9e7d82b295
Remove duplicate migration code
2022-09-16 00:39:03 -04:00
John Davis
1f5b0e6bba
Drop LegacyScripts: no longer used
2022-09-16 00:39:03 -04:00
John Davis
5b7d46efe6
Remove manage_db_adapter.py
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We no longer need to translate the arguments of manage_db.sh into
arguments for alembic. The new facade script for alembic (db.sh)
accesses the alembic api programmatically.
2022-09-16 00:39:03 -04:00
John Davis
9b66c57fe0
Rename migrate_db.py > run_alembic.py
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This is consistent with other similar pairs of files:
[script-name].sh invoking scripts/[script-name].py (check_model, create_roolshed_db, db)
Also, the python file does not require exec permissions.
2022-09-16 00:39:03 -04:00
John Davis
6bb29939e2
Drop create_db.sh, create_db.py (see note)
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For ToolShed, we have create_toolshed_db.sh.
For galaxy and toolshed install databases (gxy and tsi branches under
alembic), we use the `init` subcommand of the `db.sh` script (`./db.sh
init`), which has exactly the same functionality as these deleted
scripts.
To the best of my knowledge, these are not used anywhere else (unlike,
for example, scripts/manage_db.py, which is called from the
ansible-galaxy role).
2022-09-16 00:39:03 -04:00
John Davis
36850443f1
Rename manage_db.sh to manage_toolshed_db.sh. Limit to TS operations.
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Becuase everything else is handled via db.sh or run_alembic.sh
2022-09-16 00:39:03 -04:00
John Davis
dc89cf2b4f
Misc edits to db.sh
2022-09-16 00:39:03 -04:00
John Davis
7e238bf591
Add --raiseerr option; hide error traceback by default
2022-09-16 00:39:03 -04:00
John Davis
959bc49e66
Add missing tests
2022-09-16 00:39:03 -04:00
John Davis
330d2043c1
Revise db.sh cli command aliases
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1. Remove aliases from subcommands that change things (upgrade, downgrade,
revision, init) to reduce risk of accidental usage.
2. Add aliases to readonly subcommands (history, show, version,
dbversion)
3. Minor edits
2022-09-16 00:39:03 -04:00
John Davis
1f25c6ee96
Change parsing of --galaxy-config option
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Rationale: alternate config file applies to all subcommands, so, I
think, it is more correct to run this:
> ./db.sh -c mygalaxy.yml upgrade some-revision-id
than this:
> ./db.sh upgrade some-revision-id -c mygalaxy.yml
That's also consistent with how alembic handles this option.
2022-09-16 00:39:03 -04:00
John Davis
0745e2e05c
Fix mypy by asserting object before accessing its attributes
2022-09-16 00:39:03 -04:00
guerler