| Age | Commit message (Expand) | Author |
|---|
| 2022-03-17 | Set min-width for table container, so the table never ends up so narrow it lo... | zsloan |
| 2022-03-17 | Fix authentication for phenotype search results...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"
| zsloan |
| 2022-03-17 | Lint some test files | BonfaceKilz |
| 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 |
