| Age | Commit message (Expand) | Author |
|---|
| 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 |
| 2022-02-26 | Add container div | zsloan |
| 2022-02-26 | Add checkbox and index columns | zsloan |
| 2022-02-26 | Include DataTables imports and necessary CSS | zsloan |
| 2022-02-26 | Add JS initializing DataTables | zsloan |
| 2022-02-24 | Fix ProbeSet query for aliases...ProbeSet queries previously weren't dealing with aliases correctly,
because it was doing a MATCH/AGAINST against the ProbeSet.alias field,
but that field usually contains a list of gene symbols separated by
semi-colons (so it wouldn't detect the alias unless there was only a
single alias.
To fix this, I added some LIKE conditions, searching for the possible
variations. This is a little awkward, because I needed to make sure to
avoid a situation where, for example, an alias like 'LPD-1' matches a
search for 'PD-1'. I don't think the way it currently works is
efficient, but I don't know of any good alternative without changing the
way we store aliases in the database.
| zsloan |
| 2022-02-24 | Fix alias query | zsloan |
| 2022-02-24 | Change parser.py to also detect hyphen in search terms | zsloan |
| 2022-02-23 | Fix Heatmap GN3 URL | zsloan |
| 2022-02-23 | Improve Heatmap options' appearance...Moved the Heatmap display area above the table selection options (since
it didn't make sense to have it below those)
Added a button for clearing the Heatmap area and hiding the Heatmap
options
Added some margins to the Heatmap options
| zsloan |
| 2022-02-23 | Show heatmap options when heatmap is run...Heatmap options are now shown after the user clicks the button
I also reordered the Heatmap and Partial Correlation buttons, since it's
awkward to get the Heatmap options to display well if its button is
second. We'll probably completely rework this later, but for now this
looks a little less ugly.
| zsloan |
| 2022-02-23 | Reposition Partial Correlations and Heatmap buttons...Moved Partial Correlations and Generate Heatmap buttons to be lined up
below the other buttons and hide the Heatmap orientation selection (JS
will be added to show it after Heatmap is run)
| zsloan |
| 2022-02-23 | Add top margin to Partial Correlations button...Later this button should just be included with the other function buttons.
There's no need for it to be in a separate form, since it should be able
to take the same trait list input as all the other collection page
functions (with just the action url for the form changing)
| zsloan |
| 2022-02-21 | Fix incorrect dataset trait data caching...Trait data caching wasn't working correctly because it didn't account
for the samplelist, causing caching to work incorrect in any situation
where the target dataset's samplelist wasn't the same as that of the
trait being correlated against. Trait data is stored as a dictionary
where the keys are trait IDs and values are *lists* of sample values.
This means that the caching needs to account for the exact same set of
samples; otherwise you'll end up with samples being mismatched (since
"the third sample with a value" for one dataset's trait might not be the
same as "the third sample with a value" for another dataset's trait).
To fix this, I added the samplelist to the functions that generate and
fetch the hash file. This will require more cache files, though, so this
should probably be reexamined later to make the code work with only a
single cache file for each dataset.
| zsloan |
| 2022-02-18 | wqflask: Remove python pre-2.2 checks....These checks are only relevant for python pre-2.2.
* wqflask/utility/svg.py: Remove python pre-2.2 checks.
| Arun Isaac |
| 2022-02-18 | README: Replace GitHub actions badge with Laminar CI badge....* README.md: Replace GitHub actions badge with Laminar CI badge.
| Arun Isaac |
| 2022-02-17 | bin: Allow for not starting redis....redis needs to be started and managed as a separate service. We create
a flag NO_REDIS so that it can be so. If NO_REDIS is not defined, the
present behavior of starting redis remains. Thus current use cases are
not broken.
* bin/genenetwork2: Allow for not starting redis with the NO_REDIS
flag.
| Arun Isaac |
| 2022-02-17 | etc: Close VERSION file after opening....Use a context manager so that the VERSION file is automatically closed
on exiting the block.
* etc/default_settings.py: Close VERSION file after opening.
| Arun Isaac |
| 2022-02-14 | Add search text for cis/transLRS/LOD searches...There wasn't any search text for cis/trans searches including both
chromosome and exclusion zone, so I added somee
| zsloan |
| 2022-02-14 | Fix CisTrans search bug...', Geno' was being added to the FROM clause, which is wrong becausee
Geno is included in the query via a JOIN (and caused an error making
those searches not work)
| zsloan |
| 2022-02-09 | doc: Document how to fetch case-attribute data from a sample-list | BonfaceKilz |
| 2022-02-09 | variable naming and docstrings fix | Alexander Kabui |
| 2022-02-09 | handle exceptions | Alexander Kabui |
| 2022-02-09 | autopep8 formatting | Alexander Kabui |
| 2022-02-09 | delete unused js packages | Alexander Kabui |
| 2022-02-09 | autopep8 formatting | Alexander Kabui |
| 2022-02-09 | fix for performing parametric analysis | Alexander Kabui |
| 2022-02-09 | minor template fixes | Alexander Kabui |
| 2022-02-09 | add trait lists and links to ctl plot | Alexander Kabui |
| 2022-02-09 | disabble autoslide | Alexander Kabui |
| 2022-02-09 | fix for ctl ui page | Alexander Kabui |
| 2022-02-09 | endpoint to download network files | Alexander Kabui |
| 2022-02-09 | btn download for network sif and node file | Alexander Kabui |
| 2022-02-09 | modify ctl endpoint | Alexander Kabui |
| 2022-02-09 | minor fixes for images | Alexander Kabui |
| 2022-02-09 | fix for dcor and LOD rounding | Alexander Kabui |
