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2022-03-18Apply "python-black" on fileBonfaceKilz
* test/requests/test-website.py: Run "black test/requests/test test-website.py".
2022-03-18Remove outdated integration tests on different login mechanismsBonfaceKilz
* test/requests/test-website.py: Delete parser option "-i" for running integration tests. (integration_tests): Delete it. (integration_suite): Ditto. (run_integration_tests): Ditto. * test/requests/test_registration.py: Delete it.
2022-03-18Delete deprecated modulesBonfaceKilz
* test/requests/test-website: These imports were deleted in an earlier PR here: <https://github.com/genenetwork/genenetwork2/pull/574>
2022-03-18Delete "app" import in MRBonfaceKilz
* test/requests/test-website.py: Delete "from wqflask import app". This has the undesired effect of starting an instance of Genenetwork2.
2022-03-18Document configurationsFrederick Muriuki Muriithi
Document the configurations for the service, and how to use them when invoking the service.
2022-03-17Fix/change Authors column in phenotype search resultszsloan
- Limit number of full names to 2 followed by "et al." - Fix wrong logic that was using the full length of the authors string instead of the truncated length when determining the width of the column, resulting in it always being at least 500px wide
2022-03-17Set min-width for table container, so the table never ends up so narrow it ↵zsloan
looks strange
2022-03-17Fix authentication for phenotype search resultszsloan
Previously authentication didn't work correctly if users had "edit" privileges, because the code specifically looked for just "view"; this changes it to check for either "view" or "edit"
2022-03-17Lint some test filesBonfaceKilz
2022-03-17Fix failing testBonfaceKilz
2022-03-17Create a db connection correctlyBonfaceKilz
* wqflask/maintenance/quantile_normalize.py: Fix how the cursor is created.
2022-03-17Skip unittestsBonfaceKilz
These tests touch on core data-structures in gn2; and there's a chance that refactoring said data-structures may break many things.
2022-03-17Replace "g.db" object with a proper database connectionBonfaceKilz
* wqflask/tests/unit/wqflask/api/test_correlation.py: Use proper database connection instead of the db connection attached at "g.db". * wqflask/tests/unit/wqflask/snp_browser/test_snp_browser.py: Ditto. * wqflask/wqflask/api/correlation.py: Ditto. * wqflask/wqflask/snp_browser/snp_browser.py: Ditto.
2022-03-17Delete dead codeBonfaceKilz
2022-03-17Delete unused "logger" importBonfaceKilz
* wqflask/wqflask/snp_browser/snp_browser.py: Remove "getLogger".
2022-03-17Document how to run testsFrederick Muriuki Muriithi
Add documentation on how to run the tests - this was no clear from the existing documentation up to this point.
2022-03-17Provide path to default settings/configuration file as a fallbackFrederick Muriuki Muriithi
If the GN2_SETTINGS environment variable, is for some reason, not set, and the application actually ever tries to get a connection to the database, then use the default settings/configuration file.
2022-03-16Remove unnecessary print statementzsloan
2022-03-16Replace top comment with docstringzsloan
2022-03-16Add code generating the new genotype fileszsloan
Also made a large number of other fixes that proved necessary during testing
2022-03-16Generate JSON file for target genotypeszsloan
Also store parents/type metadata from source genofiles
2022-03-16Fix the way target/source genofiles were being processed + some other changeszsloan
- I was mixing up source/target genofiles previously; the JSON file is for the source genofiles - references to the app context are removed in favor of just taking input as arguments or environment variables - Updated example commands
2022-03-16Add function for mapping strain to sample pos + begin creating ↵zsloan
generate_new_genofiles function
2022-03-16Add function for getting strain name from sample namezsloan
2022-03-16Change EOL from CRLF to LFzsloan
2022-03-16Minor changes/bug fixeszsloan
- Removed some unused code - Strip marker genotype to avoid newline character at end - Convert zip to list for marker genotypes - Add typing to group_samples - Rename strain_genofile to source_genofile
2022-03-16Add in-progress gen_ind_genofiles.pyzsloan
gen_ind_genofiles.py is a command line script to generate genotype files for groups of individuals/samples, taking a source .geno or .json file and a target 'dummy' .geno file as input
2022-03-16Delete unused issue templatesBonfaceKilz
* .github/ISSUE_TEMPLATE/: Delete this directory.
2022-03-16Delete GitHub CI runnerBonfaceKilz
We have moved to Laminar. See: <https://penguin2.genenetwork.org/> * .github/workflows/main.yml: Delete it.
2022-03-14instantiate plotly objectAlexander Kabui
2022-03-14add custom configs for scree plotAlexander Kabui
2022-03-14add scree plot dataAlexander Kabui
2022-03-14add scree plot layoutAlexander Kabui
2022-03-14add plotlyAlexander Kabui
2022-03-14init scree plot templateAlexander Kabui
2022-03-14Warn when someone uploads a csv file that has columns not in the dbBonfaceKilz
* wqflask/wqflask/metadata_edits.py: Import "extract_invalid_csv_headers" and "get_allowable_sampledata_headers". (display_phenotype_metadata): Pass the allowable headers to the template. (update_phenotype): If a user uploads data with a column header that's not in the db, don't upload the file, and send a warning message. * wqflask/wqflask/templates/edit_phenotype.html: List the allowable headers in the template.
2022-03-14Remove button for "Edit Privileges"BonfaceKilz
This is a WIP.
2022-03-14Reword link text for downloading csv sample dataBonfaceKilz
2022-03-12Use "database_connection" within a context-managerBonfaceKilz
Using "database_connection" within a context-manager makes sure that the SQL connection that is created is closed. * wqflask/wqflask/metadata_edits.py (display_probeset_metadata): Connect to the db within a context-manager. (update_phenotype): Ditto. (update_probeset): Ditto. (approve_data): Ditto.
2022-03-12Remove unused importsBonfaceKilz
2022-03-12Close a connection after it's useBonfaceKilz
* wqflask/wqflask/metadata_edits.py (approve_data): Explicitly close a connection after it is used.
2022-03-12Use updated `update_sample_data` from gn3BonfaceKilz
2022-03-12Use updated `delete_sample_data` from gn3BonfaceKilz
2022-03-12Use updated `insert_sample_data` from gn3BonfaceKilz
2022-03-12Fix broken f-stringsBonfaceKilz
* wqflask/wqflask/metadata_edits.py (approve_data): Update query strings.
2022-03-12Replace `db.traits` with `db.sample_data`BonfaceKilz
* wqflask/wqflask/metadata_edits.py: Replace imports that start with `db.traits` with `db.sample_data`.
2022-03-12display_diffs.html: Display the csv columns header in the diffs pageBonfaceKilz
2022-03-12metadata_edits.py: Use `csv_diff` and `remove_insignificant_edits`BonfaceKilz
* wqflask/wqflask/metadata_edits (update_phenotype): The logic was for generating csv_diff and removing insignificant values in the edits was moved to gn3; use those functions instead of the manual way.
2022-03-12metadata_edits.py: Use "create_dirs_if_not_exists" for creating dirsBonfaceKilz
2022-03-12doc: Update query for fetching case attribute dataBonfaceKilz
* doc/database.org: Also join on StrainId for case-attribute data.
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