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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.
2022-03-11Add updated version of script for adding new expression sample datazsloan
2022-03-11Fix error with calling database_connection in gen_dropdown_menuzsloan
2022-03-11Add imports to database.py for 4a7e2c1602ed82aabd7d04953067ba49cb1cebffzsloan
2022-03-11Break dependence on `wqflask.utility.tools` to fix circular importsFrederick Muriuki Muriithi
Remove the `wqflask.utility.tools` and retrieve the `SQL_URI` setting directly from the environment or the settings file. This breaks the circular imports and makes the `wqflask.database` module standalone. Move the `parse_db_url` function to the `wqflask.database` module, where it is more sensible to be.
2022-03-10Use context manager with database connectionFrederick Muriuki Muriithi
Use the `with` context manager with database connections and cursors to ensure that they are closed once they are no longer needed. Where it was not feasible to use the `with` context manager without a huge refactor/rewrite, the cursors and connections are closed manually.
2022-03-10Use one-step process for the partial correlations computationspartial_corr_ui_reworkFrederick Muriuki Muriithi
This commit gets rid of the multi-step partial correlations process replacing it with a single-step process. Summary of changes: * wqflask/wqflask/collect.py: Add function to format the trait details in a format that is usable for the partial correlations system. * wqflask/wqflask/database.py: Provide function to create a connection to the database * wqflask/wqflask/partial_correlations_views.py: Rework the code to enable the one-step process for the partial correlations computations * wqflask/wqflask/static/new/javascript/partial_correlations.js: Get rid of code that supported the multi-step process * wqflask/wqflask/templates/collections/view.html: Remove inconsistent UI elements. Attach traits info in a form usable for the partial correlations * wqflask/wqflask/templates/partial_correlations.html: delete html template * wqflask/wqflask/templates/partial_correlations/pcorrs_error.html: provide a html template to display errors in the partial correlations computation process * wqflask/wqflask/templates/partial_correlations/pcorrs_poll_results.html: UI template to provide user with feedback as the computations continue in the background * wqflask/wqflask/templates/partial_correlations/pcorrs_results_presentation.html: UI template to present the results of successful computation * wqflask/wqflask/templates/partial_correlations/pcorrs_select_operations.html: UI template to trigger the partial correlations computations * wqflask/wqflask/templates/tool_buttons.html: Add the partial correlations button to the template to ensure a consistent look and feel
2022-03-07Fix/caching (#679)Alexander Kabui
* unlink file for JSONDecodeError * fix for avoiding caching empty dicts * fix for checking null dicts
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