Conversation
- when creating plates in Sequencescape using the Beckman destination plate creation endpoint - set phenotype instead to the 'result' in the MongoDB - use strip() and lower() because the equivalent Sentinel code (in 'create_post_body' method) does the same thing - also remove all references to FIELD_SS_RESULT (Result) because there is no such field on sample or sample_metadata in Sequencescape
…s_columns' method
Specify buster as the base image for Python 3.8 Slim
…code-result # Conflicts: # lighthouse/constants/fields.py
Beckman endpoint hardcoding phenotype / result
Bumps [black](https://github.com/psf/black) from 21.7b0 to 21.10b0. - [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>
Bumps [types-requests](https://github.com/python/typeshed) from 2.25.0 to 2.25.11. - [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>
Bumps [sqlalchemy](https://github.com/sqlalchemy/sqlalchemy) from 1.4.21 to 1.4.26. - [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>
Bumps [pytest](https://github.com/pytest-dev/pytest) from 6.2.4 to 6.2.5. - [Release notes](https://github.com/pytest-dev/pytest/releases) - [Changelog](https://github.com/pytest-dev/pytest/blob/main/CHANGELOG.rst) - [Commits](pytest-dev/pytest@6.2.4...6.2.5) --- updated-dependencies: - dependency-name: pytest dependency-type: direct:development update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <support@github.com>
Bumps [flake8](https://github.com/pycqa/flake8) from 3.9.2 to 4.0.1. - [Release notes](https://github.com/pycqa/flake8/releases) - [Commits](PyCQA/flake8@3.9.2...4.0.1) --- updated-dependencies: - dependency-name: flake8 dependency-type: direct:development update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com>
Bumps [flake8-bugbear](https://github.com/PyCQA/flake8-bugbear) from 21.4.3 to 21.9.2. - [Release notes](https://github.com/PyCQA/flake8-bugbear/releases) - [Commits](PyCQA/flake8-bugbear@21.4.3...21.9.2) --- 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 [pandas](https://github.com/pandas-dev/pandas) from 1.3.0 to 1.3.4. - [Release notes](https://github.com/pandas-dev/pandas/releases) - [Changelog](https://github.com/pandas-dev/pandas/blob/master/RELEASE.md) - [Commits](pandas-dev/pandas@v1.3.0...v1.3.4) --- updated-dependencies: - dependency-name: pandas dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <support@github.com>
Bumps [coverage](https://github.com/nedbat/coveragepy) from 5.5 to 6.1.1. - [Release notes](https://github.com/nedbat/coveragepy/releases) - [Changelog](https://github.com/nedbat/coveragepy/blob/master/CHANGES.rst) - [Commits](coveragepy/coveragepy@coverage-5.5...6.1.1) --- updated-dependencies: - dependency-name: coverage dependency-type: direct:development update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com>
Bumps [pytest-cov](https://github.com/pytest-dev/pytest-cov) from 2.12.1 to 3.0.0. - [Release notes](https://github.com/pytest-dev/pytest-cov/releases) - [Changelog](https://github.com/pytest-dev/pytest-cov/blob/master/CHANGELOG.rst) - [Commits](pytest-dev/pytest-cov@v2.12.1...v3.0.0) --- updated-dependencies: - dependency-name: pytest-cov dependency-type: direct:development update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com>
Bumps [python-dotenv](https://github.com/theskumar/python-dotenv) from 0.18.0 to 0.19.1. - [Release notes](https://github.com/theskumar/python-dotenv/releases) - [Changelog](https://github.com/theskumar/python-dotenv/blob/master/CHANGELOG.md) - [Commits](theskumar/python-dotenv@v0.18.0...v0.19.1) --- updated-dependencies: - dependency-name: python-dotenv dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com>
Bumps [types-requests](https://github.com/python/typeshed) from 2.25.12 to 2.26.0. - [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-minor ... Signed-off-by: dependabot[bot] <support@github.com>
Bump types-requests from 2.25.12 to 2.26.0
Bumps [coverage](https://github.com/nedbat/coveragepy) from 6.1.1 to 6.1.2. - [Release notes](https://github.com/nedbat/coveragepy/releases) - [Changelog](https://github.com/nedbat/coveragepy/blob/master/CHANGES.rst) - [Commits](coveragepy/coveragepy@6.1.1...6.1.2) --- updated-dependencies: - dependency-name: coverage dependency-type: direct:development update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <support@github.com>
Bump coverage from 6.1.1 to 6.1.2
They've fixed the new release.
Bumps [python-dotenv](https://github.com/theskumar/python-dotenv) from 0.19.1 to 0.19.2. - [Release notes](https://github.com/theskumar/python-dotenv/releases) - [Changelog](https://github.com/theskumar/python-dotenv/blob/master/CHANGELOG.md) - [Commits](theskumar/python-dotenv@v0.19.1...v0.19.2) --- updated-dependencies: - dependency-name: python-dotenv dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <support@github.com>
Bumps [sqlalchemy](https://github.com/sqlalchemy/sqlalchemy) from 1.4.26 to 1.4.27. - [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 python-dotenv from 0.19.1 to 0.19.2
Bump sqlalchemy from 1.4.26 to 1.4.27
Disable the last package deletion for the Docker registry
- When trying to follow it with Sangeetha, it was a little confusing, some steps seemed to be unnecessary or in the wrong order - Simplify - make two main sections, with Docker and without Docker, rather than interleaving the advice - Simplify - remove references to running Docker without using docker-compose - I think docker-compose gives a smoother experience, and it is too complicated to have 3 separate setup options (docker-compose, docker without compose, and local pipenv) - Remove references to using pipenv install and pipenv shell within the Docker container - this is not necessary as the dependencies are installed when the image is built
Bumps [responses](https://github.com/getsentry/responses) from 0.15.0 to 0.16.0. - [Release notes](https://github.com/getsentry/responses/releases) - [Changelog](https://github.com/getsentry/responses/blob/master/CHANGES) - [Commits](getsentry/responses@0.15.0...0.16.0) --- updated-dependencies: - dependency-name: responses dependency-type: direct:development update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com>
Bumps [black](https://github.com/psf/black) from 21.10b0 to 21.11b0. - [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>
Co-authored-by: Stuart McHattie <sm49@sanger.ac.uk>
Update readme
Bump responses from 0.15.0 to 0.16.0
Bump black from 21.10b0 to 21.11b0
Changes to update the updated_at timestamp in lighthouse_samples
Bumps [black](https://github.com/psf/black) from 21.11b0 to 21.11b1. - [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 21.11b0 to 21.11b1
Codecov Report
@@ Coverage Diff @@
## master #468 +/- ##
=======================================
Coverage 92.39% 92.39%
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Files 98 98
Lines 3223 3223
Branches 258 258
=======================================
Hits 2978 2978
Misses 200 200
Partials 45 45
Continue to review full report at Codecov.
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Closes DPL-012
Housekeeping - updated_at timestamp not updated (C=M, V=3*)