Merge develop into master by BenTopping · Pull Request #500 · sanger/lighthouse

BenTopping · 2022-01-12T10:33:46Z

Changes proposed in this pull request:

Added plates/cherrytrack endpoint as a way to query cherrytrack destination and source plates from lighthouse without being formatted
Dependency updates
Move hardcoded protocols for SS and Baracoda to deployment config rather than in the application config

DPL-126-plate-state

Bumps [flake8-bugbear](https://github.com/PyCQA/flake8-bugbear) from 21.9.2 to 21.11.28. - [Release notes](https://github.com/PyCQA/flake8-bugbear/releases) - [Commits](PyCQA/flake8-bugbear@21.9.2...21.11.28) --- updated-dependencies: - dependency-name: flake8-bugbear dependency-type: direct:development update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com>

Bumps [coverage](https://github.com/nedbat/coveragepy) from 6.1.2 to 6.2. - [Release notes](https://github.com/nedbat/coveragepy/releases) - [Changelog](https://github.com/nedbat/coveragepy/blob/master/CHANGES.rst) - [Commits](coveragepy/coveragepy@6.1.2...6.2) --- updated-dependencies: - dependency-name: coverage dependency-type: direct:development update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com>

Bump coverage from 6.1.2 to 6.2

Bumps [types-requests](https://github.com/python/typeshed) from 2.26.0 to 2.26.1. - [Release notes](https://github.com/python/typeshed/releases) - [Commits](https://github.com/python/typeshed/commits) --- updated-dependencies: - dependency-name: types-requests dependency-type: direct:development update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <support@github.com>

Bump types-requests from 2.26.0 to 2.26.1

…11.28 Bump flake8-bugbear from 21.9.2 to 21.11.28

Bumps [flake8-bugbear](https://github.com/PyCQA/flake8-bugbear) from 21.11.28 to 21.11.29. - [Release notes](https://github.com/PyCQA/flake8-bugbear/releases) - [Commits](PyCQA/flake8-bugbear@21.11.28...21.11.29) --- updated-dependencies: - dependency-name: flake8-bugbear dependency-type: direct:development update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <support@github.com>

…11.29 Bump flake8-bugbear from 21.11.28 to 21.11.29

Bumps [black](https://github.com/psf/black) from 21.11b1 to 21.12b0. - [Release notes](https://github.com/psf/black/releases) - [Changelog](https://github.com/psf/black/blob/main/CHANGES.md) - [Commits](https://github.com/psf/black/commits) --- updated-dependencies: - dependency-name: black dependency-type: direct:development ... Signed-off-by: dependabot[bot] <support@github.com>

Bump black from 21.11b1 to 21.12b0

Bumps [sqlalchemy](https://github.com/sqlalchemy/sqlalchemy) from 1.4.27 to 1.4.28. - [Release notes](https://github.com/sqlalchemy/sqlalchemy/releases) - [Changelog](https://github.com/sqlalchemy/sqlalchemy/blob/main/CHANGES) - [Commits](https://github.com/sqlalchemy/sqlalchemy/commits) --- updated-dependencies: - dependency-name: sqlalchemy dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <support@github.com>

Bump sqlalchemy from 1.4.27 to 1.4.28

Bumps [pandas](https://github.com/pandas-dev/pandas) from 1.3.4 to 1.3.5. - [Release notes](https://github.com/pandas-dev/pandas/releases) - [Changelog](https://github.com/pandas-dev/pandas/blob/master/RELEASE.md) - [Commits](pandas-dev/pandas@v1.3.4...v1.3.5) --- updated-dependencies: - dependency-name: pandas dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <support@github.com>

Bump pandas from 1.3.4 to 1.3.5

readme improvement

Bumps [mypy](https://github.com/python/mypy) from 0.910 to 0.920. - [Release notes](https://github.com/python/mypy/releases) - [Commits](python/mypy@v0.910...v0.920) --- updated-dependencies: - dependency-name: mypy dependency-type: direct:development update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com>

Bump mypy from 0.910 to 0.920

Bumps [flask-apscheduler](https://github.com/viniciuschiele/flask-apscheduler) from 1.12.2 to 1.12.3. - [Release notes](https://github.com/viniciuschiele/flask-apscheduler/releases) - [Changelog](https://github.com/viniciuschiele/flask-apscheduler/blob/master/CHANGELOG.md) - [Commits](viniciuschiele/flask-apscheduler@1.12.2...1.12.3) --- updated-dependencies: - dependency-name: flask-apscheduler dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <support@github.com>

This resolves an issue that causes CodeQL to fail to run correctly

…1.12.3 Bump flask-apscheduler from 1.12.2 to 1.12.3

Bumps [types-requests](https://github.com/python/typeshed) from 2.26.1 to 2.26.2. - [Release notes](https://github.com/python/typeshed/releases) - [Commits](https://github.com/python/typeshed/commits) --- updated-dependencies: - dependency-name: types-requests dependency-type: direct:development update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <support@github.com>

Bump types-requests from 2.26.1 to 2.26.2

Bumps [mypy](https://github.com/python/mypy) from 0.920 to 0.921. - [Release notes](https://github.com/python/mypy/releases) - [Commits](python/mypy@v0.920...v0.921) --- updated-dependencies: - dependency-name: mypy dependency-type: direct:development update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com>

Bump mypy from 0.920 to 0.921

Move protocol on baracoda and ss url to config

Rollback pymongo version to master

codecov · 2022-01-12T10:36:32Z

Codecov Report

Merging #500 (6d8fbef) into master (76cc779) will decrease coverage by 0.06%.
The diff coverage is 86.20%.

@@            Coverage Diff             @@
##           master     #500      +/-   ##
==========================================
- Coverage   92.39%   92.33%   -0.07%     
==========================================
  Files          98       98              
  Lines        3223     3247      +24     
  Branches      258      330      +72     
==========================================
+ Hits         2978     2998      +20     
- Misses        200      203       +3     
- Partials       45       46       +1

Impacted Files	Coverage Δ
lighthouse/routes/common/plates.py	`88.63% <81.81%> (-2.28%)`	⬇️
lighthouse/config/defaults.py	`100.00% <100.00%> (ø)`
lighthouse/helpers/plates.py	`93.75% <100.00%> (ø)`
lighthouse/routes/v1/routes.py	`100.00% <100.00%> (ø)`

Continue to review full report at Codecov.

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revert default ss and baracoda links to http

BenTopping and others added 30 commits November 15, 2021 16:15

added endpoint to access cherrytrack plates

cbf3027

adding unstaged changes required for last commit to work

855c4a2

updated debugger message and resolved merge conflicts

09fbd60

Merge pull request #462 from sanger/DPL-126-biosero-plate-state

7e104b7

DPL-126-plate-state

Merge pull request #471 from sanger/dependabot/pip/coverage-6.2

477f8df

Bump coverage from 6.1.2 to 6.2

Merge pull request #469 from sanger/dependabot/pip/types-requests-2.26.1

0c446fd

Bump types-requests from 2.26.0 to 2.26.1

Merge pull request #470 from sanger/dependabot/pip/flake8-bugbear-21.…

36c85e5

…11.28 Bump flake8-bugbear from 21.9.2 to 21.11.28

Merge pull request #472 from sanger/dependabot/pip/flake8-bugbear-21.…

f43be9c

…11.29 Bump flake8-bugbear from 21.11.28 to 21.11.29

Merge pull request #474 from sanger/dependabot/pip/black-21.12b0

c4bc6b2

Bump black from 21.11b1 to 21.12b0

Merge pull request #477 from sanger/dependabot/pip/sqlalchemy-1.4.28

a6726ef

Bump sqlalchemy from 1.4.27 to 1.4.28

Merge pull request #478 from sanger/dependabot/pip/pandas-1.3.5

0ed9c86

Bump pandas from 1.3.4 to 1.3.5

readme improvement

8019aa6

add option for background mode

209e419

Merge pull request #479 from sanger/readme-improvement

e0c8cea

readme improvement

Merge pull request #481 from sanger/dependabot/pip/mypy-0.920

26e5355

Bump mypy from 0.910 to 0.920

Set setuptools dependency to 60.0.3

d5c850e

This resolves an issue that causes CodeQL to fail to run correctly

Merge pull request #482 from sanger/dependabot/pip/flask-apscheduler-…

2f075e0

…1.12.3 Bump flask-apscheduler from 1.12.2 to 1.12.3

Merge pull request #483 from sanger/dependabot/pip/types-requests-2.26.2

5f2f280

Bump types-requests from 2.26.1 to 2.26.2

Merge pull request #484 from sanger/dependabot/pip/mypy-0.921

ded48ed

Bump mypy from 0.920 to 0.921

harrietc52 and others added 7 commits January 4, 2022 16:51

Rollback pymongo version to master

0a0d2c1

Move protocol on baracoda and ss url to config

5216f50

black reformat

5b878ca

remove branch

45df3ec

Merge pull request #492 from sanger/remove_hardcoded_protocols

f9f804a

Move protocol on baracoda and ss url to config

Merge branch 'develop' into rollback_pymongo_version_to_master

48e3d29

Merge pull request #490 from sanger/rollback_pymongo_version_to_master

8e65499

Rollback pymongo version to master

revert default ss and baracoda links to http

55a3aee

BenTopping requested a review from sdjmchattie January 12, 2022 14:22

Merge pull request #501 from sanger/revert-links-to-http

6dca94c

revert default ss and baracoda links to http

sdjmchattie previously approved these changes Jan 12, 2022

View reviewed changes

minor release version bump

6d8fbef

BenTopping dismissed sdjmchattie’s stale review via 6d8fbef January 17, 2022 10:15

BenTopping requested a review from harrietc52 January 17, 2022 10:31

harrietc52 approved these changes Jan 17, 2022

View reviewed changes

harrietc52 merged commit 929c1a3 into master Jan 17, 2022

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Merge develop into master#500

Merge develop into master#500
harrietc52 merged 40 commits intomasterfrom
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BenTopping commented Jan 12, 2022 •

edited by harrietc52

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BenTopping commented Jan 12, 2022 •

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