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Author SHA1 Message Date
selten 42ff20f6a0 Minor spelling error fix 
Fixes a minor spelling error.
 2021-01-14 17:43:35 +01:00
mvdbeek 40a7cd8f3c Don't attempt to use docker cli if it is not available 
This fixes https://github.com/galaxyproject/galaxy/issues/11125, which
became a problem with https://github.com/galaxyproject/galaxy/pull/10814
and the recent removal of the docker runtime from kubernetes.

This is the quick fix, but I don't like the guessing and disabling
that we do if docker is not available or not functional.

I'm hesitating between adding a config option for the resolver
(`docker_cli_available` or `docker_list_images` + `docker_pull_images`)
and adding a `KubernetesContainerResolver` / `RemoteContainerResolver`
class that doesn't assume docker is available for listing and pulling
iages.

Not wanting to list/pull images on the Galaxy node is probably a
reasonable thing outside of kubernetes as well, so I tend to
go with a `RemoteContainerResolver` class in dev ?
 2021-01-14 17:43:25 +01:00
davelopez 970edcd8c3 Ignore mypy error with Union in response_model 2021-01-14 15:30:28 +01:00
Dannon e8af1abbfc Merge pull request #11128 from jmchilton/revert_10 
Revert "Make all fastapi methods async (for consistency)."
 2021-01-14 08:32:23 -05:00
Nicola Soranzo f05584e427 Merge pull request #11115 from jmchilton/api_guidelines 2021-01-14 12:06:37 +00:00
Marius van den Beek 2757d7b3b7 Merge pull request #11116 from jmchilton/uvicorn_factory 
uvicorn-compatible factory function for fastapi.
 2021-01-14 12:50:14 +01:00
John Chilton 5543ddf728 Revert "Make all fastapi methods async (for consistency)." 
This reverts commit 8c7d74cb10.
 2021-01-14 06:45:20 -05:00
Dannon 9ab56a2954 Merge pull request #11124 from jmchilton/more_framework 
Dynamic discovery of FastAPI routers.
 2021-01-13 21:07:07 -05:00
John Chilton 8c7d74cb10 Make all fastapi methods async (for consistency). 2021-01-13 18:55:43 -05:00
John Chilton a43e9820ed Auto-discover fastapi controllers. 2021-01-13 18:54:30 -05:00
John Chilton 37f8684582 Extract code for walking controller modules. 2021-01-13 18:54:07 -05:00
John Chilton 42bd3b269e Remove unused, deprecated ControllerUnavailable. 2021-01-13 18:42:44 -05:00
John Chilton 5e011fa82e Merge pull request #11098 from davelopez/fastapi-migration-datatypes 
Add FastAPI routes for datatypes
 2021-01-13 18:23:53 -05:00
John ChiltonandNicola Soranzo 400da5d677 Apply suggestions from code review 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2021-01-13 18:19:29 -05:00
John Chilton 21f06bafef API design guidelines. 2021-01-13 18:18:39 -05:00
John Chilton 58620c0602 Merge pull request #11113 from jmchilton/types_and_trans 
Establish a best practice for trans dependency management.
 2021-01-13 18:11:57 -05:00
Dannon 539d4d6773 Merge pull request #11122 from mvdbeek/version-21.05.dev 
Version 21.05.dev
 2021-01-13 16:12:39 -05:00
Dannon 461cfdc122 Merge pull request #11123 from mvdbeek/version-21.01 
Update version to 21.01.rc1
 2021-01-13 15:14:27 -05:00
mvdbeek d12671d86e Merge branch 'version-21.01' into version-21.05.dev 2021-01-13 21:11:32 +01:00
mvdbeek e5e7b6258d Update version to 21.01.rc1 2021-01-13 21:11:32 +01:00
mvdbeek 0492602e80 Update version to 21.05.dev 2021-01-13 21:11:32 +01:00
Dannon 5d1d29d838 Merge pull request #9873 from juleengraham/fav-tool-version 
Show favourited tools independent of version
 2021-01-13 14:19:03 -05:00
Dannon d4f5a93027 Merge pull request #10524 from OlegZharkov/proper-error 
informative error message on /api/authenticate/baseauth
 2021-01-13 12:57:38 -05:00
John Chilton fa685e4fd0 uvicorn-compatible factory function for fastapi. 2021-01-13 11:34:19 -05:00
Marius van den Beek eec72b2e24 Merge pull request #10984 from davebx/stc_sections 
Put new toolshed tools in existing tool panel sections if the ID matches
 2021-01-13 15:17:09 +01:00
davelopez e91e754ac8 Add pydantic to the packages/data/requirements.txt 2021-01-13 14:31:16 +01:00
davelopez 02e9f02db9 Refactor move pydantic model to datatypes/_schema.py 2021-01-13 14:04:14 +01:00
Marius van den Beek c148445e6c Merge pull request #10880 from bernt-matthias/topic/options-fallback-name 
Dynamic select parameters: also allow to choose legal options by name
 2021-01-13 12:00:08 +01:00
Sergey Golitsynskiy 882ad635d8 Merge pull request #11089 from ic4f/dev_fastapi_tours 
Add FastAPI routes for tours
 2021-01-12 22:08:47 -05:00
Sergey Golitsynskiy 2a2559812c Define __all__ list for tours package 2021-01-12 20:45:19 -05:00
John Chilton 1341c879dd Establish a best practice for trans type annotations. 
Provide justification and information in docstrings also.
 2021-01-12 20:22:54 -05:00
Sergey Golitsynskiy 8f3e5921e9 Work around limitations of mypy 2021-01-12 19:51:36 -05:00
Dannon 4d985e2a3d Merge pull request #11035 from bgruening/nora 
[WIP] NORA's image viewer. A medical image viewer and annotation tool
 2021-01-12 15:41:18 -05:00
John Chilton 6246cf94a4 Cleanup some docstring comments. 
- Fix spelling.
- Drop a way pre-jmchilton deprecation notice.
 2021-01-12 15:40:26 -05:00
Sergey Golitsynskiy dcaa04b690 Refactor tours module implemantation 2021-01-12 15:31:55 -05:00
Marius van den Beek a4bed8e5a6 Merge pull request #11026 from bernt-matthias/topic/xsd_doc_section_refs 
Document how parameters in sections are referenced
 2021-01-12 20:22:48 +01:00
Dave Bouvier 3c8da66593 Merge branch 'dev' of ssh://github.com/galaxyproject/galaxy into stc_sections 2021-01-12 14:16:00 -05:00
Dave BandMarius van den Beek b21f657761 Update lib/galaxy/tool_shed/galaxy_install/tools/tool_panel_manager.py 
Co-authored-by: Marius van den Beek <m.vandenbeek@gmail.com>
 2021-01-12 14:13:16 -05:00
Sergey Golitsynskiy d90b4d24a2 Refactor tours package organization 2021-01-12 13:46:11 -05:00
Matthias Bernt 5f67c2075b fix name and value column in select_from_dataset.xml 2021-01-12 19:27:07 +01:00
Matthias Bernt 07aa0fa271 improve legal value check 2021-01-12 19:27:00 +01:00
Marius van den Beek 0a81e25273 Merge pull request #10981 from kxk302/empty-file 
If input file is empty, and you are trying to access anything but column 1 of the input file
 2021-01-12 19:24:35 +01:00
Marius van den Beek 2aaea427c6 Merge pull request #10522 from dannon/get-or-create-api-key 
Simpler API for getting user API key
 2021-01-12 19:22:53 +01:00
Nicola Soranzo e225de9b00 Merge pull request #11103 from jmchilton/more_docs_stuff_3 2021-01-12 17:58:24 +00:00
Sergey Golitsynskiy f9b4862c3d Merge pull request #11104 from ic4f/dev_writing_tests 
Make minor improvements, add ToC
 2021-01-12 12:43:40 -05:00
John Chilton 0e3a55fa91 Merge pull request #10681 from nuwang/add_dockerfile 
Added dockerfile [biohackathon]
 2021-01-12 12:16:25 -05:00
M BerntandMarius van den Beek 975a6e72c8 make example valid 
Co-authored-by: Marius van den Beek <m.vandenbeek@gmail.com>
 2021-01-12 17:45:55 +01:00
kxk302andMarius van den Beek a310047bd3 Update lib/galaxy/tools/parameters/basic.py 
Co-authored-by: Marius van den Beek <m.vandenbeek@gmail.com>
 2021-01-12 11:00:26 -05:00
Marius van den Beek 5a954cba51 Merge pull request #11078 from nuwang/add_extra_k8s_job_metadata 
Allow extra job metadata to be specified for k8s
 2021-01-12 16:51:37 +01:00
Marius van den Beek 520e097771 Merge pull request #11063 from bernt-matthias/topic/validate-collections 
add validation for collection parameters
 2021-01-12 16:40:06 +01:00