| Age | Commit message (Expand) | Author |
|---|
| 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 |
| 2022-03-07 | Fix/caching (#679)...* unlink file for JSONDecodeError
* fix for avoiding caching empty dicts
* fix for checking null dicts | Alexander Kabui |
| 2022-02-28 | Fix fulltext search for certain searches...Hyphens in fulltext searches were causing problems, but a recent commit
I made to fix the issue apparently had some side effects for other types
of searches, in addition to make such searches someewhat slower
Apparently the issue wasn't just the hyphens, but also the text to
either side of the hyphen being lower than the minimum word length
(which is either 2 or 3 for us, can't remember). To try and address
this, I did a regular expression check for a pattern with text of <3
legnth to either side of a hyphen, and when that's the case I add quotes
from the search term plus an asterisk, which seeems to be necessary to
get it to not treat the hyphen as a delimiter and to correctly detect
the search term
| zsloan |
| 2022-02-28 | Add distinct to fix issue where GeneRIF search returns duplicates | zsloan |
| 2022-02-26 | Remove CSS from partial_correlations.css...This CSS is overwritten by CSS from trait_list.css and show_trait.css
| zsloan |
