John Chilton
4bd80ce6ef
Flush out documentation and service-info for DRS API a bit.
2022-12-08 10:08:01 -05:00
Uwe Winter
f24e55aa9f
Implement access_id method to resolve object with expensive url generation schema. See https://ga4gh.github.io/data-repository-service-schemas/preview/develop/docs/#tag/AccessMethodModel
2022-12-08 10:08:01 -05:00
John Chilton
8ff9fe2610
Implement initial GA4GH DRS Support.
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- Implement APIs for serving Galaxy's public datasets as DRS objects.
- Implement support in galaxy.files.uris for DRS URIs so that upload, etc... can use DRS URIs from other data repositories.
The ways this can be improved are endless:
- New object ID patterns can be implemented to allow access to composite data, metadata files from a bundle view of datasets.
- New object ID patterns can be implemented to allow access to collections as bundles of datasets.
- More auth types and AccessMethods could be implemented for loading datasets from clients.
- Some sort of scheme for providing authenticated URLs to non-public data could be implemented to provide access to more of Galaxy's data if user's can implement.
Despite all these limitations - I think having the guts in like this provide useful points for interested parties to go and add functionality to enable their desired usecases.
2022-12-08 10:07:11 -05:00
Nicola Soranzo
89273050f1
Merge branch 'release_22.05' into dev
2022-12-07 16:21:17 +00:00
Marius van den Beek
3158fbac21
Merge pull request #15119 from ElectronicBlueberry/composables-ts
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Fix and Convert composables to TypeScript
2022-12-07 10:40:10 +01:00
Marius van den Beek
2a6f9c2a29
Merge pull request #15017 from natefoo/gravity-1.0
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Update Gravity version to 1.0.0 pre-release
2022-12-07 07:37:59 +01:00
Marius van den Beek
fdc59a350d
Merge pull request #15130 from nsoranzo/fix_test_build_mulled
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Install involucro when resolvers are instantiated
2022-12-07 07:32:30 +01:00
Nicola Soranzo
7676afbf3b
Update minikube-setup-action and use more recent k8s version
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The older minikube/k8s fail to launch under Ubuntu 22.04, which
is being deployed on GitHub action workers:
2022-12-07 03:59:45 +00:00
Nicola Soranzo
f9daab77c3
Install involucro when resolvers are instantiated
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i.e. at Galaxy startup.
Also:
- Type annotations
- Code refactorings
2022-12-07 02:26:51 +00:00
Dannon
4390d3532d
Merge pull request #15125 from galaxyproject/martenson-patch-1
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update the workflow form language
2022-12-06 16:11:54 -05:00
Nicola Soranzo
f882d387d9
Fix resolved default value of `tool_dependency_dir and involucro_path` config options
2022-12-06 19:50:06 +00:00
Marius van den Beek
f2c221f484
Merge pull request #15122 from natefoo/gravity-0.13.6
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[22.05] Update gravity to 0.13.6
2022-12-06 20:40:00 +01:00
John Davis
da85409c97
Merge pull request #15123 from mschatz/patch-1
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Update to 2022 NAR paper
2022-12-06 13:56:57 -05:00
Martin Cech
d42b9a7d95
Merge pull request #15116 from dannon/convert-utcdate
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Convert UtcDate from options to composition+ts.
2022-12-06 19:55:47 +01:00
Martin Cech
f5a24f084b
Merge pull request #15121 from dannon/minor-tsconfig-tweaks
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TS config and linting tweaks
2022-12-06 19:54:33 +01:00
Martin Cech
24e2755ea1
update the workflow form language
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these are not stars anymore, they're checkboxes
2022-12-06 19:46:04 +01:00
Michael Schatz
9a87821c1c
Update to 2022 NAR paper
2022-12-06 12:04:29 -05:00
Nate Coraor
d30fd7bfc5
Update gravity to 0.13.6
2022-12-06 11:46:22 -05:00
Nate Coraor
fad0453e72
Update gravity section of sample config
2022-12-06 10:53:21 -05:00
Laila Los
ced9e3cef0
make index const
2022-12-06 16:26:02 +01:00
Aysam Guerler
be46794aa0
Merge pull request #14985 from itisAliRH/vuetify_published_histories
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Vuetify published histories
2022-12-06 10:16:59 -05:00
Laila Los
f2c5eb3496
fix typo
2022-12-06 15:59:00 +01:00
Laila Los
442e74ab47
remove var
2022-12-06 15:55:28 +01:00
Laila Los
b98481f484
remove unused import
2022-12-06 15:47:49 +01:00
Laila Los
07d33086bd
convert filter to ts
2022-12-06 15:46:40 +01:00
Laila Los
47f41efd9b
convert sensors to ts
2022-12-06 15:41:04 +01:00
Dannon Baker
3044722832
Drop explicit node_modules exclude -- this is already in the default setting
2022-12-06 09:35:35 -05:00
Dannon Baker
eab33026c1
Set an explicit outDir. We don't *use* this in our build process, but it prevents errors when vscode thinks it needs to overwrite js
2022-12-06 09:35:14 -05:00
Laila Los
4ae456b854
fix animation frame resize observer
2022-12-06 15:31:57 +01:00
Dannon Baker
576edb50fe
Flag explicit any as warning instead of masking
2022-12-06 09:31:09 -05:00
Laila Los
d739c7a24e
convert animationFrame to ts
2022-12-06 15:30:58 +01:00
Dannon Baker
8a6563f2bc
Add toplevel tsconfig // fixes precommit hook and might help vscode find settings better?
2022-12-06 09:30:35 -05:00
Dannon
6f836720c7
Merge pull request #15106 from mvdbeek/typescript_api_client
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Add autogenerated typescript API client & use it
2022-12-06 09:07:51 -05:00
Marius van den Beek and Laila Los
8e5a942c48
Drop unused paths type import
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Co-authored-by: Laila Los <44241786+ElectronicBlueberry@users.noreply.github.com >
2022-12-06 14:56:12 +01:00
Marius van den Beek
d689b79169
Merge pull request #15090 from davelopez/fix_task_history_export_ftp
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Fix export history to FTP using tasks
2022-12-06 14:51:49 +01:00
Marius van den Beek and Laila Los
0051281b1f
Use FetchArgType throughout
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Co-authored-by: Laila Los <44241786+ElectronicBlueberry@users.noreply.github.com >
2022-12-06 13:16:04 +01:00
mvdbeek
adac1f51d2
Use FetchArgType to extact types
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Thanks again Laila, very cool!
2022-12-06 13:16:04 +01:00
mvdbeek
55b6cc60f1
Type fixes for strict mode
2022-12-06 13:16:04 +01:00
mvdbeek
7cb88fa750
Move rethrowSimple into openapi-typescript-fetch middleware
2022-12-06 13:16:04 +01:00
mvdbeek
87e68c24e4
Convert Dataset/services.js to typescript and use typed client
2022-12-06 13:16:04 +01:00
mvdbeek
ee083cde3f
Only strip trailing slash for fetcher
2022-12-06 13:16:04 +01:00
mvdbeek
2c8cf98460
Strip trailing slash in getAppRoot
2022-12-06 13:16:04 +01:00
mvdbeek
d39dd525c9
Use autogenerated client in datatypes service
2022-12-06 13:16:03 +01:00
mvdbeek
1192bb5428
Add generated schema
2022-12-06 13:16:03 +01:00
mvdbeek
7b864a8c45
Add makefile target to update autogenerated client
2022-12-06 13:16:03 +01:00
mvdbeek
b7c62d0ac8
Add script that can dump openapi schema without a running galaxy
2022-12-06 12:59:01 +01:00
Marius van den Beek
1986e73841
Merge pull request #15105 from mvdbeek/model_class_fix
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Fix ``model_class`` field annotations
2022-12-06 11:50:42 +01:00
Dannon Baker
cc6402e135
Use type declaration for props.
2022-12-05 18:31:24 -05:00
Dannon Baker
8af76ab49f
Drop unused import from RuleDefinitions.test.ts
2022-12-05 18:31:23 -05:00
Dannon Baker
5b9a19c971
Overhaul utcdate test to toggle props and observe text instead of directly inspecting computeds
2022-12-05 18:31:22 -05:00
John Chilton