| Age | Commit message (Expand) | Author |
|---|---|---|
| 2022-03-17 | Fix failing test | BonfaceKilz |
| 2022-03-17 | Create a db connection correctly...* wqflask/maintenance/quantile_normalize.py: Fix how the cursor is created. | BonfaceKilz |
| 2022-03-17 | Skip unittests...These tests touch on core data-structures in gn2; and there's a chance that refactoring said data-structures may break many things. | BonfaceKilz |
| 2022-03-17 | Replace "g.db" object with a proper database connection...* 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. | BonfaceKilz |
| 2022-03-17 | Delete dead code | BonfaceKilz |
| 2022-03-17 | Delete unused "logger" import...* wqflask/wqflask/snp_browser/snp_browser.py: Remove "getLogger". | BonfaceKilz |
| 2022-03-17 | Document how to run tests...Add documentation on how to run the tests - this was no clear from the existing documentation up to this point. | Frederick Muriuki Muriithi |
| 2022-03-17 | Provide path to default settings/configuration file as a fallback...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. | Frederick Muriuki Muriithi |
| 2022-03-16 | Remove unnecessary print statement | zsloan |
| 2022-03-16 | Replace top comment with docstring | zsloan |
| 2022-03-16 | Add code generating the new genotype files...Also made a large number of other fixes that proved necessary during testing | zsloan |
| 2022-03-16 | Generate JSON file for target genotypes...Also store parents/type metadata from source genofiles | zsloan |
| 2022-03-16 | Fix the way target/source genofiles were being processed + some other changes...- 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 | zsloan |
| 2022-03-16 | Add function for mapping strain to sample pos + begin creating generate_new_g... | zsloan |
| 2022-03-16 | Add function for getting strain name from sample name | zsloan |
| 2022-03-16 | Change EOL from CRLF to LF | zsloan |
| 2022-03-16 | Minor changes/bug fixes...- 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 | zsloan |
| 2022-03-16 | Add in-progress gen_ind_genofiles.py...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 | zsloan |
| 2022-03-16 | Delete unused issue templates...* .github/ISSUE_TEMPLATE/: Delete this directory. | BonfaceKilz |
| 2022-03-16 | Delete GitHub CI runner...We have moved to Laminar. See: <https://penguin2.genenetwork.org/> * .github/workflows/main.yml: Delete it. | BonfaceKilz |
| 2022-03-14 | instantiate plotly object | Alexander Kabui |
| 2022-03-14 | add custom configs for scree plot | Alexander Kabui |
| 2022-03-14 | add scree plot data | Alexander Kabui |
| 2022-03-14 | add scree plot layout | Alexander Kabui |
| 2022-03-14 | add plotly | Alexander Kabui |
| 2022-03-14 | init scree plot template | Alexander Kabui |
| 2022-03-14 | Warn when someone uploads a csv file that has columns not in the db...* 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. | BonfaceKilz |
| 2022-03-14 | Remove button for "Edit Privileges"...This is a WIP. | BonfaceKilz |
| 2022-03-14 | Reword link text for downloading csv sample data | BonfaceKilz |
| 2022-03-12 | Use "database_connection" within a context-manager...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. | BonfaceKilz |
| 2022-03-12 | Remove unused imports | BonfaceKilz |
| 2022-03-12 | Close a connection after it's use...* wqflask/wqflask/metadata_edits.py (approve_data): Explicitly close a connection after it is used. | BonfaceKilz |
| 2022-03-12 | Use updated `update_sample_data` from gn3 | BonfaceKilz |
| 2022-03-12 | Use updated `delete_sample_data` from gn3 | BonfaceKilz |
| 2022-03-12 | Use updated `insert_sample_data` from gn3 | BonfaceKilz |
| 2022-03-12 | Fix broken f-strings...* wqflask/wqflask/metadata_edits.py (approve_data): Update query strings. | BonfaceKilz |
| 2022-03-12 | Replace `db.traits` with `db.sample_data`...* wqflask/wqflask/metadata_edits.py: Replace imports that start with `db.traits` with `db.sample_data`. | BonfaceKilz |
| 2022-03-12 | display_diffs.html: Display the csv columns header in the diffs page | BonfaceKilz |
| 2022-03-12 | metadata_edits.py: Use `csv_diff` and `remove_insignificant_edits`...* 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. | BonfaceKilz |
| 2022-03-12 | metadata_edits.py: Use "create_dirs_if_not_exists" for creating dirs | BonfaceKilz |
| 2022-03-12 | doc: Update query for fetching case attribute data...* doc/database.org: Also join on StrainId for case-attribute data. | BonfaceKilz |
| 2022-03-11 | Add updated version of script for adding new expression sample data | zsloan |
| 2022-03-11 | Fix error with calling database_connection in gen_dropdown_menu | zsloan |
| 2022-03-11 | Add imports to database.py for 4a7e2c1602ed82aabd7d04953067ba49cb1cebff | zsloan |
| 2022-03-11 | Break dependence on `wqflask.utility.tools` to fix circular imports...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. | Frederick Muriuki Muriithi |
| 2022-03-10 | Use context manager with database connection...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. | Frederick Muriuki Muriithi |
| 2022-03-10 | Use one-step process for the partial correlations computations...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 partial_corr_ui_rework | Frederick Muriuki Muriithi |
| 2022-03-08 | remove global variables;pep8 formatting | Alexander Kabui |
| 2022-03-08 | make fixes;variable names and kwargs | Alexander Kabui |
| 2022-03-07 | Fix/caching (#679)...* unlink file for JSONDecodeError * fix for avoiding caching empty dicts * fix for checking null dicts | Alexander Kabui |
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