No db port exposed #137
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No db port exposed #137
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… 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
* Updated Demo DB to comply with pytest, also see issue #93 * Port 5432 (postgres) need to be open for pytest to work on docker DB app * PG DB needs to be 'phenopolis_db' for pytest to work with docker * Added comments, flake8 and blackened * CRITICAL: can only go ahead together with frontend issue #160 * Removed duplicated query_user_config() * New tests, using PyTest, at last, yet no 100% coverage yet * Commented out _get_hpo_ids_per_gene(), not used
Add dotenv to run tests.
Install pysam
Install pysam with sudo
Must be pysam for python3
pysam via pip
* add missing check_auth in change_password * adding variant search + some refactoring around conversion of results from postgres (#90) * Code tidy (#97) * 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 * 61 consanguinity editing (#101) * 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 * improve search with HGVS, Ensembl ids and HPO ids (#105) @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. * 44 create new patient (#109) * add endpoint for creating individuals * make authentication backwards compatible * add endpoint to create users (#114) * add 404s to individuals endpoints (#113) * add 404s to individuals endpoints * blackened * 89 create new user individuals (#116) * add endpoint to post user_individuals * blackened * add limit to the autocomplete query + change query type to a query param + remove best guess endpoint * blackened Co-authored-by: IsmailM <ismail.moghul@gmail.com> Co-authored-by: Alan <alanwilter@gmail.com>
* add missing check_auth in change_password * adding variant search + some refactoring around conversion of results from postgres (#90) * Code tidy (#97) * 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 * 61 consanguinity editing (#101) * 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 * improve search with HGVS, Ensembl ids and HPO ids (#105) @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. * 44 create new patient (#109) * add endpoint for creating individuals * make authentication backwards compatible * add endpoint to create users (#114) * add 404s to individuals endpoints (#113) * add 404s to individuals endpoints * blackened * 89 create new user individuals (#116) * add endpoint to post user_individuals * blackened * PyTest at last (#117) * Updated Demo DB to comply with pytest, also see issue #93 * Port 5432 (postgres) need to be open for pytest to work on docker DB app * PG DB needs to be 'phenopolis_db' for pytest to work with docker * Added comments, flake8 and blackened * CRITICAL: can only go ahead together with frontend issue #160 * Removed duplicated query_user_config() * New tests, using PyTest, at last, yet no 100% coverage yet * Commented out _get_hpo_ids_per_gene(), not used * copy config from admin user for new users (#118) * Updated tests after PR #118 (#119) * Update requirements.txt (#120) Add dotenv to run tests. * Fix db (#121) * Updated tests after PR #118 * Fixed a bug in DB:variant_pos_text_pattern_idx * Debugging for query_type searching. * Added a ugly function _search_variants_by_match_name to do pure string matching. * Removed Partial Match for Variant, changed return results. * Fix regex typo raised by Alan, but did NOT do pytest yet Co-authored-by: IsmailM <ismail.moghul@gmail.com> Co-authored-by: Pablo Riesgo Ferreiro <priesgoferreiro@gmail.com> Co-authored-by: Alan <alanwilter@gmail.com> Co-authored-by: Nikolas Pontikos <n.pontikos@gmail.com>
If the host has postgres installed that won't work.
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Closing because wrong target branch. |
IsmailM
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Nov 14, 2020
* 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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If there is the need to have the port open in other environment the thing can be done using two overlaying docker-compose files.