Dev live #103
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Dev live #103
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* fix #100 * Eslint Prettier * clean the code for style * Enslint Prettier. * fix #114, tried to add icon, but not very nice and seems need to overwrite a lot default metarial UI components. * Enslint Prettier. * fix #95 * Enslint Prettier. * Enslint Prettier. * Enslint Prettier. * Fixed bug that pages with tab panel show slightly bigger fontSize. * Enslint Prettier. * fix #71 * fix #71 * clean code a bit. * clean code a bit.
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Maybe the Logging level should be set by an env variable: e.g. |
alanwilter
reviewed
Jul 30, 2020
pontikos
approved these changes
Jul 31, 2020
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So shall we wait for the Logging issue - #107 Also, want to clarify here, if there needs to be any changes made to the DB? (If so, we should also update |
… from postgres (#90)
* Udated gitignore * Code tidied after Daniele's suggestions * Code tidied and improved autocomplete search * Introducing tox configuration * Flake8 and Black applied * Updated tox.ini and created pyproject.toml for Black code formatter * Files updated by Black new config in pyproject.toml * Refactored imports from db * To include Black and Flake8 for Tox * Commented out _gene_hpo_ids, not used
* reformat individual.py * fix the individual update (actually get) + some refactoring around the place * make good use of postgres API * black reformatting + excluding some folders from flake8 * controlling none result
@alanwilter @priesgo we should probably test the suggested search functionality using unit test. I'm going to merge this now into dev-live for testing on the dev website.
* add endpoint for creating individuals * make authentication backwards compatible
* add 404s to individuals endpoints * blackened
* add endpoint to post user_individuals * blackened
* Delete user #352 * Only Admin and User itself can delete user * Added button in each user profile to delete it, with a dialog warning. It works well. Co-authored-by: YuanTian1991 <[email protected]>
* Redesigned the Actionbar. * fix #293
* Created compact table, nearly done. * Compact Table Done, looks good.
…ading, they will only be loaded once when first time called, there is no way to replace them with skeleton I think. (#358)
* Updated demo db * Updated demo db * Using f-string * Using new _get_variants * Updated process_for_display HET and HOM * Refactored compact lists _individual_complete_view * _get_variants using new schema * Fixed duplicated gene_symbol in hpo view * Fixed a wrong test and updated others * Updated for new demo db * Removed redundant v["variant_id"] definition * Avoid None values in variant dict * Updated variant pytest * Updated pytest for variant * Skip empty genes * Refactored rare_comp_hets_variants and fixed duplicated genes * Updated demo db * updated tests for individuals * Only new schema now for individuals * The real fix for sex unknown * Reverting, the problem was not here * Text sex unknown * Add typing to Sex * API for version
* Just format * Using new schema for genes * Stats count genes for user * Handle transcripts and its canonicals * Fixed count genes * Reorganising some general parameters and function * Added /my_genes (get_all_genes) endpoint * Harmeless typo * To handle misisng transcripts * Updated demo db and pytest for gene and transcript * Added 'my_variants' endpoint * Refactored stats for variants in new schema * Improved 'my_genes' endpoint to render gene chips * Updated tests for new endpoints & refactored stats * To reset github action cache check_app_api2 * Reverting to check_app_api * Make peace with github actions
* Migrated _search_phenotypes to new schema * Updated tests for HPO autocomplete * Migrated _search_genes to new schema * Moved variants search to new schema but not hgvs * Skipping hgvs autocomplete tests, still old schema * Reviewed * NETLIFY_SITE_ID moved to private.env * HGVS now working but not with Gene Symbol yet * Bye old schema * Replace hardcoded GRCh37 with var HG_ASSEMBLY * Search with HGVs now completed, old schema gone * Removed netlify reference
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* Able to use either local or S3 remote vcf file * Improved pytest report * Rebranded from S3_VCF_FILE_URL to VCF_FILE
* Hide external_id for demo * Updated test_get_genotypes_exception * Another try with test_get_genotypes_exception * Silenced test_get_genotypes_exception * Typo * Freeze cyvcf2 0.30.12
* Use dynamic year for copyright * pallets/markupsafe#284
* Added and applied pre-commit * Typing
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@IsmailM what is the status of this draft? |
Bumps [black](https://github.com/psf/black) from 19.10b0 to 24.3.0. - [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/24.3.0) --- updated-dependencies: - dependency-name: black dependency-type: direct:production ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
✅ Deploy Preview for phenopolis-dev canceled.
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Shall we merge
dev-liveintoProd-live?cc'ed: @priesgo @alanwilter @YuanTian1991 @pontikos
Note when merging from
dev-livetoprod-live, it's best to merge with a rebase - as both branches have the same linear history... Happy to do this when we are ready :)