Updated tests after PR #118 #119
Merged
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
pontikos
approved these changes
Aug 3, 2020
IsmailM
pushed a commit
that referenced
this pull request
Aug 4, 2020
pontikos
added a commit
that referenced
this pull request
Aug 8, 2020
* 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>
IsmailM
pushed a commit
that referenced
this pull request
Nov 14, 2020
* Fixed phenopolis reference, and footer. * Fixed phenopolis reference, and footer.
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Just updating one line in tests after PR #118