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Structured tool state #17393

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Structured tool state #17393

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b797090
tool input format test fixutre
jmchilton Oct 13, 2024
158620d
More tool tests.
jmchilton Oct 4, 2024
4f76561
Refactor Tool._populate for reuse of hook checks.
jmchilton Oct 1, 2024
7c79add
Spelling error.
jmchilton Sep 27, 2024
856001f
Refactor for reuse in galaxy.tool_util.parameters.
jmchilton Sep 27, 2024
fe39357
Refactor encode/decode for reuse.
jmchilton Sep 30, 2024
bc9cc92
Use get_color_value in basic.py.
jmchilton Oct 1, 2024
aca7b5c
models for tool landing request state...
jmchilton Sep 27, 2024
cc475aa
Pydantic models for parameter validators.
jmchilton Oct 7, 2024
66a1a3b
Fix param models for dynamic options and truevalue/falsevalue
jmchilton Oct 8, 2024
043181c
Update tool shed schema for parameter model changes.
jmchilton Oct 8, 2024
336d450
Cleanup stock tool sources parsed in galaxy.tools.stock.
jmchilton Oct 17, 2024
6cbe6f3
Refactor complex method for clarity.
jmchilton Oct 16, 2024
ea06e9f
Numerous fixes for 21.01 parameters.
jmchilton Oct 14, 2024
61c531b
Do not skip CI tests on missing tools.
jmchilton Oct 14, 2024
ac447e8
Cleaner startup when there are tool problems.
jmchilton Oct 9, 2024
23a9b10
Improved error messages when there are problems generating tool tests.
jmchilton Oct 9, 2024
b0a9f7c
Tool Request API...
jmchilton Oct 16, 2024
8bb1108
Refactoring that lets the tool request API work.
jmchilton Oct 7, 2024
5e882d4
Blah....
jmchilton Sep 18, 2024
1a2ec24
Rebuild schema for tool request APIs...
jmchilton Oct 16, 2024
bbbdc54
Tool Landing API...
jmchilton Sep 20, 2024
f3c9953
Regenerate schema
jmchilton Oct 7, 2024
640e0b7
More json schema API options...
jmchilton Sep 30, 2024
8c5e5c1
Update API schema for more tool state schema APIs...
jmchilton Sep 30, 2024
563de46
Latest prototype of a minimal workflow UI.
jmchilton Jun 27, 2024
d60fe61
gxformat2 abstraction layer...
jmchilton Aug 27, 2024
f03fd64
Named type for parsed tool versions.
jmchilton Jul 11, 2024
9fbbbd0
Workflow tool state validation plumbing.
jmchilton Jul 11, 2024
f940040
[WIP] Use tool request API from the tool form.
jmchilton Aug 28, 2024
c972feb
WIP: maybe dont want, more ps testing
jmchilton Oct 1, 2024
54e0da4
Extra debugging we dont' want
jmchilton Oct 18, 2024
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1 change: 1 addition & 0 deletions .github/workflows/api.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -18,6 +18,7 @@ env:
GALAXY_TEST_DBURI: 'postgresql://postgres:postgres@localhost:5432/galaxy?client_encoding=utf8'
GALAXY_TEST_RAISE_EXCEPTION_ON_HISTORYLESS_HDA: '1'
GALAXY_CONFIG_SQLALCHEMY_WARN_20: '1'
GALAXY_TEST_REQUIRE_ALL_NEEDED_TOOLS: '1'
concurrency:
group: ${{ github.workflow }}-${{ github.ref }}
cancel-in-progress: true
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3 changes: 2 additions & 1 deletion .github/workflows/framework_tools.yaml
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Expand Up @@ -26,6 +26,7 @@ jobs:
strategy:
matrix:
python-version: ['3.8']
use-legacy-api: ['if_needed', 'always']
services:
postgres:
image: postgres:13
Expand Down Expand Up @@ -63,7 +64,7 @@ jobs:
path: 'galaxy root/.venv'
key: gxy-venv-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('galaxy root/requirements.txt') }}-framework-tools
- name: Run tests
run: ./run_tests.sh --coverage --framework-tools
run: GALAXY_TEST_USE_LEGACY_TOOL_API="${{ matrix.use-legacy-api }}" ./run_tests.sh --coverage --framework-tools
working-directory: 'galaxy root'
- uses: codecov/codecov-action@v3
with:
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