| Age | Commit message (Expand) | Author |
|---|
| 2020-09-30 | Changed the logic for adding 0 to the PCA results to do so when the...shared samples are < 2 instead of 0; this fixed the error when running
the correlation matrix, but results in the PCA traits having no values
* wqflask/wqflask/correlation_matrx/show_corr_matrix.py - changed
"if num_overlap == 0" to "if num_overlap < 2" because correlations can't
be run if there are fewer than 2 shared samples (and previously would
throw an error if there was exactly 1 shared sample)
| zsloan |
| 2020-09-30 | Added "natural-minus-na" sorting for relevant columns in the correlation...page
* wqflask/wqflask/templates/correlation_page.html - Added
natural-minus-na type to columns that can contain N/A values, since I
apparently forgot to add it to this table before
| zsloan |
| 2020-09-30 | Fixed issue where columns sorted by inner text (text inside link tags)...didn't sort all rows when a table is paginated and has more than one
page
* wqflask/wqflask/static/new/javascript/search_results.js - Added
"extract_inner_text" function for getting the inner text from a string
containing HTML in order to avoid using DataTables' orderDataType (which
can only fetch values directly from the DOM, which is why sorting wasn't
working with multiple pages), and also included this function in the
"natural-minus-na" data type (so columns can be sorted that contain both
HTML/links and N/A values)
* wqflask/wqflask/templates/collections/view.html - Changed record column
to use "natural-minus-na" sort method in order to fix the inner-text
sorting issue + added sorting to the checkbox column (in the same way as
it already works in the search result page)
* wqflask/wqflask/templates/search_results_page.html - Replaced the
columns that used orderDataType with using the updated
"natural-minus-na" data type
* wqflask/wqflask/templates/correlation_page.html - Fixed issue where
N/As in the Year column (for phenotype correlations) were still displayed as links
| zsloan |
| 2020-09-30 | Removed unused code from TempDataSet class...* wqflask/base/data_set.py - TempDataSet class contained some code
referring to the SQL DB, but temp traits aren't stored in the SQL DB anymore
| zsloan |
| 2020-09-30 | Add missing import...* wqflask/wqflask/correlation/show_corr_results.py: Add it.
| BonfaceKilz |
| 2020-09-30 | Apply pep 8 formatting...* wqflask/wqflask/correlation/show_corr_results.py
[imports]: Apply pep8 and remove unused imports.
| BonfaceKilz |
| 2020-09-30 | Fix StopIteration error thrown in view collections page...* wqflask/wqflask/user_session.py (user_id): Use byte-string when
fetching user_id. See:
https://github.com/genenetwork/genenetwork2/pull/422#issuecomment-701082458
| BonfaceKilz |
| 2020-09-30 | Fix import in tests | BonfaceKilz |
| 2020-09-29 | Trait page link-out buttons were previously inside <a> tags, but this...caused there to be a small line between buttons when hovering over them
(because the <a> tags were wider than the button itself); this was
changed to instead just be an "onclick" on the button (which is also a
bit more concise)
* wqflask/wqflask/templates/show_trait_details.html - Replaced <a> tags
with onclick for trait page link-out buttons
| zsloan |
| 2020-09-29 | Removed "Color By Trait" button from the Bar Chart, because it was meant...to work with the figure we used before switching to Plotly. This feature
will need to be redone to work with Plotly
* wqflask/wqflask/templates/show_trait_statistics.html - commented out
Color By Trait button until it's reimplemented
| zsloan |
| 2020-09-29 | Made a variety of changes to table pages...* wqflask/wqflask/static/new/css/show_trait.css - Adding position
relative and a 2px offset for glyphicons to make them better align with
button text
* wqflask/wqflask/templates/collections/view.html - Added glyphicon to
Download button, changed a couple head names (Peak Location and Effect
Size), made Location and Peak Location columns the same width, and made
the "?" glossary links a little larger and red
* wqflask/wqflask/templates/search_result_page.html - same as above
* wqflask/wqflask/templates/show_trait_edit_data.html - Added glyphicon
to Export button
| zsloan |
| 2020-09-29 | Remove undefined variable | BonfaceKilz |
| 2020-09-29 | Apply pep 8 to buffer...* wqflask/wqflask/user_manager.py:
Remove some stale comments.
(imports): Apply pep-8 and remove unused imports.
| BonfaceKilz |
| 2020-09-29 | Fixed issue where negative additive effect values weren't being...displayed in the "view collection" page
* wqflask/wqflask/templates/collections/view.html - Apparently the
correct way to check if a value can be cast to a float in Jinja2 is to
say "value != 0"; it previous said "value > 0" which exlcuded all
negative values
| zsloan |
| 2020-09-29 | Changed Add (to collection) button color to match other Add buttons and...changed the text for the GN1 link button
* wqflask/wqflask/templates/show_trait_details.html - Changed Add button
class to btn-success (to make it green like the other Add buttons) and
changed text from "View in GN1" to "Go to GN1"
| zsloan |
| 2020-09-29 | Changed the DataTables column sort arrows to a different color by...changing the image they're referencing
* wqflask/wqflask/templates/base.html - Added CSS changing the table
sort arrow image directly into
base.html because it requires using url_for to reference the images in
the GUIX profile (so it needs to be in the template and can't just be
added to a CSS file)
| zsloan |
| 2020-09-29 | Add check for bytes...* wqflask/wqflask/collect.py (process_traits): Check whether the
passed "unprocessed_traits" is a byte otherwise an error is generated
when bytes(the default) are passed.
| BonfaceKilz |
| 2020-09-29 | Add test for process_traits from collections.py...* wqflask/tests/wqflask/test_collect.py: Add it.
| BonfaceKilz |
| 2020-09-28 | Changed add to collection to open the collection in a new tab/page so...the results on the initial page aren't lost
* wqflask/wqflask/static/new/javascript/search_results.js - Changed the
add to collection method name to "add_to_collection" because it was
previously "add" which is a terrible method name
* wqflask/wqflask/templates/collections/add.html - Added target="_blank"
to the add to collection form so it will open in a new tab/window
| zsloan |
| 2020-09-28 | Fix failing test...* wqflask/tests/base/test_trait.py: Add app_context to test class,
otherwise an error related to working outside the app_context is
generated. Adding the app_context is required when mocking "Flask.g".
| BonfaceKilz |
| 2020-09-28 | Merge branch 'build/python3-migration' of github.com:BonfaceKilz/genenetwork2... | BonfaceKilz |
| 2020-09-28 | Fix casting error...* wqflask/base/trait.py (retrieve_trait_info): If the
description_string or discription_display value return a None object,
evaluate to an empty string. Fixes errors related to *len(None)*.
| BonfaceKilz |
| 2020-09-28 | Merge branch 'testing' into build/python3-migration | BonfaceKilz |
| 2020-09-28 | Fix casting error...* wqflask/base/trait.py (retrieve_trait_info): If the
description_string or discription_display value return a None object,
evaluate to an empty string. Fixes errors related to *len(None)*.
| BonfaceKilz |
| 2020-09-28 | Convert None to "" in if statement...* wqflask/base/trait.py: Fixes error parsing error: "(GeneNetwork
error: float argument required, not NoneType)"
| BonfaceKilz |
| 2020-09-28 | Update trait tests...* wqflask/tests/base/test_trait.py
(test_retrieve_trait_info_with_non_empty_lrs): Check
trait.LRS_score_repr is set correctly if trait.lrs is None.
(test_retrieve_trait_info_with_empty_lrs_field): Check
trait.LRS_score_repr and test_trait.LRS_location_repr is set correctly
if trait.lrs is None.
(test_retrieve_trait_info_with_empty_chr_field): Check
test_trait.LRS_score_repr and test_trait.LRS_location_repr is set
correctly if trait.locus is None.
| BonfaceKilz |
| 2020-09-26 | Fix failing tests by replacing mock with unittest.mock...* wqflask/tests/base/test_data_set.py (imports): Run:
`find . -type f -name "*py" -print0 | xargs -0 sed -i \
"s|import mock|from unittest import mock|g"`
* wqflask/tests/base/test_trait.py(imports): Ditto.
* wqflask/tests/utility/test_authentication_tools.py(imports): Ditto.
* wqflask/tests/utility/test_hmac.py(imports). Ditto.
* wqflask/tests/wqflask/api/test_gen_menu.py: Ditto
| BonfaceKilz |
| 2020-09-26 | Fix failing tests...* wqflask/tests/base/test_trait.py: Remove decode function call which
is no longer supported in python3.
| BonfaceKilz |
| 2020-09-26 | Apply PEP 8 to buffer...* wqflask/wqflask/db_info.py: Run pep8 through buffers. Fixes
inconsistent use of tabs and spaces in indentation which trips up
unittests.
| BonfaceKilz |
| 2020-09-26 | Run 2to3-8 tool through file...* wqflask/wqflask/db_info.py:
Run: 2to3-3.8 -w wqflask/wqflask/db_info.py
| BonfaceKilz |
| 2020-09-26 | Fix inconsistent line ending in file...* wqflask/wqflask/db_info.py: Replace ^M with proper unix line
endings. See <http://ergoemacs.org/emacs/emacs_line_ending_char.html>
| BonfaceKilz |
| 2020-09-26 | Merge branch 'testing' into build/python3-migration | BonfaceKilz |
| 2020-09-25 | Fixed issue where attribute columns' alignment was offset by 1...* wqflask/wqflask/static/new/javascript/initialize_show_trait_tables.js
- attribute cells' alignment and column names were wrong because they were referring to an attribute offset by 1 in the attribute list
-
| zsloan |
| 2020-09-25 | Changed edit_data_change and block_by_index to use DataTables API...* wqflask/wqflask/static/new/javascript/show_trait.js - Changed
edit_data_change to use DataTables API to fetch the list of names,
values, and (where applicable) standard errors in a way that just looks
at those columns (previously it iterated through all rows).
block_by_index was also changed to look just at columns
| zsloan |
| 2020-09-24 | Changed logic that defines the primary/other samplelists to be much more...efficient
* wqflask/wqflask/show_trait/show_trait.py - Add an "if" statement to
avoid unnecessarily running some code and changed a list to a set for
the purposes of searching if it contains an element
| zsloan |
| 2020-09-23 | Aligned relevant columns to right in mapping results table...* wqflask/wqflask/templates/mapping_results.html - aligned score,
position, additive effect, and dominance column headers to the right
| zsloan |
| 2020-09-23 | Fix failing builds...* wqflask/wqflask/__init__.py: Move imports from views.py to
"__init__.py". Fixes failing build.
* wqflask/wqflask/views.py: Ditto.
| BonfaceKilz |
| 2020-09-23 | Fix failing tests...* wqflask/tests/base/test_trait.py: In python2 it's necessary to
decode the utf-8 string.
| BonfaceKilz |
| 2020-09-22 | Merge branch 'testing' of github.com:genenetwork/genenetwork2 into testing | zsloan |
| 2020-09-22 | Fixed a pretty big mistake where user accounts would be saved even when...there was some mistake/error during registration
* wqflask/wqflask/user_login.py - Previously it would still save a user
even if there was some problem like their e-mail already being
associated with an account. It would display the error, but still run
save_user. I fixed this so that it no longer saves the user if there are
any errors
| zsloan |
| 2020-09-22 | Added something to the mapping result page CSS to change the highlight...color to match the high color in other tables
* wqflask/wqflask/static/new/css/marker_regression.css - changed
background color when selecting a row (i.e. "highlight color")
| zsloan |
| 2020-09-22 | Fixed a couple mistakes in the previous commit and changed the position...header on the mapping results page to include the mapping scale
* wqflask/wqflask/marker_regression/run_mapping.py - changed how
"display_pos" is defined for marker obs
* wqflask/wqflask/templates/mapping_results.html - Fixed issues with
last commit and changed position header name to include mapping scale
| zsloan |
| 2020-09-22 | Replaced Chr and Mb/cM columns with a single position column in mapping...results and also changes the -log(p) to use an endash instead
* wqflask/wqflask/marker_regression/run_mapping.py - added "display_pos"
to each marker object that is a combination of Chr and Mb/cM
* wqflask/wqflask/templates/mapping_results.html - Included
"display_pos" in results table and replaced -log(p) with using an endash
| zsloan |
| 2020-09-22 | Changed JS on trait page that updates basic stats and graphs/figures to...use the DataTables API to pull sample values
* wqflask/wqflask/static/new/javascript/show_trait.js - Changed the way
sample name/val/var are pulled from the table to instead use DataTables'
API + removed an unused event listener
* wqflask/wqflask/static/new/javascript/initialize_show_trait_tables.js
- added "var" before a defined variable for consistency
| zsloan |
| 2020-09-18 | Made some style changes with whitespace/line-breaks | zsloan |
| 2020-09-18 | Made a bunch of changes to move trait page DataTables initialization to...a separate file (initialize_show_trait_tables.js). The biggest
complication was getting the order of attributes in the rows to sync
with the order of atribute namees in the column headers. Previously this
logic was all in the template.
* wqflask/base/webqtlCaseData.py - added attribute first_attr_col as a
very awkward solution to passing the column position into the column
render function in situations where there are case attribute columns
(which can be variable in number)
* wqflask/wqflask/show_trait/show_trait.py - Replace "attribute_names"
in js_data with "attributes" (which allows the JS access to more
information) and also pass new se_exists and
has_num_cases variables with js_data, so the javascript has access to
whether or not those columns exist in the table
* wqflask/wqflask/static/new/javascript/show_trait.js - Change case
attribute-related logic to use js_data.attributes instead of
js_data.attribute_names
* wqflask/wqflask/templates/show_trait.html - Removed table
initialization from template
* wqflask/wqflask/static/new/javascript/initialize_show_trait_tables.js
- new file that initializes tables and reproduces what the template
logic used to do with JS logic
| zsloan |
| 2020-09-18 | Apply pep8 formatting | BonfaceKilz |
| 2020-09-17 | Convert "target_string" to a str type...* wqflask/base/trait.py (retrieve_trait_info): Convert "target_string"
to a str, otherwise an exception will be thrown if it's None.
| BonfaceKilz |
| 2020-09-17 | Merge branch 'testing' into build/python3-migration | BonfaceKilz |
| 2020-09-17 | Mock "SECRET_HMAC_CODE"...* wqflask/tests/utility/test_hmac.py: Mock app.config's
"SECRET_HMAC_CODE" value.
| BonfaceKilz |
