Code

Tool Shed 2.0#15639

Code

Merged

mvdbeek merged 73 commits intogalaxyproject:devgalaxyproject/galaxy:devfrom jmchilton:tool_shed_2jmchilton/galaxy:tool_shed_2Copy head branch name to clipboardOct 3, 2023

+23,815-5,737

Commits

Commits on Sep 26, 2023

• Cleanup method signature for uninstall_repository in twilltestcase.

  jmchilton

  committed
  d4dec27

• metadata_generator: initial typing for metadata_generator, no functional changes

  jmchilton

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  42b0d30

• metadata_generator: populate initial dict with helper (to split later)

  jmchilton

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  338dfe9

• metadata_generator: Spit into Base and Galaxy and ToolShed implementations...

  Show description for f000b83
  jmchilton

  committed
  f000b83

• metadata_generator: simplify NOT_TOOL_CONFIG handling

  jmchilton

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  3ba9888

• metadata_generator: split constructors into Galaxy and tool shed versions.

  Show description for f338fc7
  jmchilton

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  f338fc7

• metadata_generator: split initial_metadata_dict into Galaxy and TS implementations.

  jmchilton

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  cb8a7f4

• metadata_generator: split set_repository into Galaxy and TS implementations.

  jmchilton

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  ea74b1f

• metadata_generator: Split handle_repo_elem implementations into gx and ts versions.

  Show description for d22eb01
  jmchilton

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  d22eb01

• metadata_generator: protocols to better type repository abstractions...

  jmchilton

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  7c357d7

• metadata_generator: move tool shed impl into tool shed package

  Show description for 32b2d38
  jmchilton

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  32b2d38

• Remove metadata_generator from mypy exclusions...

  jmchilton

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  d0622fc

• metadata_generator: more typing fixes/annotations

  jmchilton

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  bac9fb8

• metadata_generator: only tool shed side uses sa_session.

  jmchilton

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  f0af1bf

• Refactor a tool_shed-only utility into tool shed code.

  jmchilton

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  10ce487

• Protocol to try to break up app for cleaner tool shed install typing.

  jmchilton

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  f1c2dde

• Better data managers interface?

  jmchilton

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  7f2bd72

• More typing around tool validator...

  jmchilton

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  dc047e8

• Additional debugging when handling API errors during repository upload.

  jmchilton

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  904a600

• Standalone app for installing tools...

  jmchilton

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  ca1e7e5

• Preparation for creating galaxy tool shed client package...

  jmchilton

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  179f592

• Make galaxy login logic in tool shed more uniform.

  Show description for 8c01410
  jmchilton

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  8c01410

• Improved error message for repository_util.

  jmchilton

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  691ba8d

• Setup abstraction in twilltestcase to allow for separate installation target backend.

  jmchilton

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  7cc01d3

• Abstraction for getting install object that can be swapped out.

  jmchilton

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  d729553

• Standalone implementation of tool shed client...

  jmchilton

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  ebf8e2b

• Decompose tool shed + schema package.

  Show description for 59cff45
  jmchilton

  committed
  59cff45

• metadata_generator: use TYPE_CHECKING to avoid dependency issues

  jmchilton

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  3c3e31e

• metadata_generator: mark cleanup_repository_metadata as private

  Show description for 43e1574
  jmchilton

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  43e1574

• metadata_generator: Small typing fixes for tool shed metadata_generator

  jmchilton

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  fca10e4

• Move generate_clone_url_for_repository_in_tool_shed into tool shed.

  jmchilton

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  e611a95

• Allow external shed testing.

  jmchilton

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  8910714

• Use repository manager to capture more of the upload process.

  jmchilton

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  2fa1657

• Remove unused repository manager code (hard to de-conflict with upload stuff).

  jmchilton

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  95b9c6c

• Integration-y unit tests for the core tool shed code.

  jmchilton

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  2c5f63a

• Fix API uploads to do more work that happens in web uploads.

  Show description for 7ba099a
  jmchilton

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  7ba099a

• Progress toward exercising less of the tool shed upload API.

  Show description for 8852f07
  jmchilton

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  8852f07

• More integration-y unit tests for tool shed...

  jmchilton

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  b66a0bc

• Remove upload controller - everything should come through the API now.

  jmchilton

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  e7353b7

• Remove upload_point upload logic in tool shed.

  Show description for 55564b6
  jmchilton

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  55564b6

• metadata_generator: no metadata for workflows and datatypes

  Show description for 122abb0
  jmchilton

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  122abb0

• metadata_generator: Typing has improved to the point that we can annotate this.

  jmchilton

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  5a4e950

• Bug fix: data manager changes misaligned...

  Show description for cdfdaaf
  jmchilton

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  cdfdaaf

• Refactor install manager a bit to isolate interaction.

  jmchilton

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  78b978e

• Remove contact owner functionality from the tool shed - use github please.

  jmchilton

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  9e7fafb

• Tool Shed API Modernization ahead of FastAPI

  Show description for 85100ed
  jmchilton

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  85100ed

• metadata_generator: mark private method as internal

  jmchilton

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  8f89935

• Less encoding in toolshed app to adapt to functions...

  jmchilton

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  bb468a2

• metadata_generator: refactor helper method out...

  jmchilton

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  9db5e9c

• More format fixes.

  jmchilton

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  68899ff

• repository_metadata_manager.py - linting fix

  jmchilton

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  688d237

• Remove admin mako helper that is unused.

  jmchilton

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  5b3c34d

• Improve tool shed API client schema.

  jmchilton

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  cdf8193

• Test setup for an allow push API (implement in v1?)

  jmchilton

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  f4031b7

• Reusable tool ID generation helper for TS API tests.

  jmchilton

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  4a5e355

• Refactor tool shed interactions for reuse outside of test framework.

  jmchilton

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  a46425c

• WIP: Implement dry_run in upload API.

  jmchilton

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  698d58e

• Formatting...

  jmchilton

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  bad135b

• ToolShed API 2.0

  jmchilton

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  d1d6290

• black formatting fix

  jmchilton

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  0772a51

• Refactor tool shed tests for injection of browser.

  jmchilton

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  b04c326

• Script for bootstrapping the tool shed.

  jmchilton

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  24b3abe

• Implement the GA4GH TRS API in the new tool shed.

  jmchilton

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  dd58bfc

• Category test stuff...

  jmchilton

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  b5fb7c0

• Category reworking..

  jmchilton

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  c98fa8c

• bismark populator improvement...

  jmchilton

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  0d42ad7

• Modernized framework to replace tool shed functional tests.

  Show description for 0666747
  jmchilton

  committed
  0666747

• Option config_hg_for_dev...

  jmchilton

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  04e7563

• DEBUG lint openapi CI

  jmchilton

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  e2e0d44

Commits on Sep 27, 2023

• WIP: modern tool shed frontend

  jmchilton

  committed
  7dc0b13

• More typing?

  jmchilton

  committed
  990f3dc

• Remove incorrect auto-generated readme for frontend.

  jmchilton

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  bb45581

• Fixes...

  jmchilton

  committed
  ec6d8fd