| Age | Commit message (Expand) | Author |
|---|
| 2020-10-09 | Replace "ncores" with "nthreads" param to r_CTLscan | BonfaceKilz |
| 2020-10-09 | Use built-in array as a named import...* wqflask/wqflask/wgcna/wgcna_analysis.py
(WGCNA.render_image): Use named import method. This is a workaround
for using explicitly using "array" which conflicts with something else
in the namespace.
| BonfaceKilz |
| 2020-10-09 | Update base64 conversion...* wqflask/wqflask/wgcna/wgcna_analysis.py
(WGCNA.render_image): Use Python3's base64 library from the stdlib to
perform conversion.
* wqflask/wqflask/ctl/ctl_analysis.py (CTL.loadImage): Ditto.
| BonfaceKilz |
| 2020-10-09 | Convert cmp function into a key function...* wqflask/wqflask/correlation_matrix/show_corr_matrix.py
(sortEigenVectors): Convert the comparison function into a key
function. See:
https://docs.python.org/3/howto/sorting.html#the-old-way-using-the-cmp-parameter
| BonfaceKilz |
| 2020-10-09 | Apply PEP-8 formatting | BonfaceKilz |
| 2020-10-02 | Ignore utf-8 encoding errors...* wqflask/base/trait.py (retrieve_trait_info): Add extra param to
ignore errors such as: "utf-8 codec can't decode byte 0xb5 in position
0: invalid start byte" thrown in Python3.
| BonfaceKilz |
| 2020-10-02 | Split author's list into it's own variable...* wqflask/wqflask/templates/correlation_page.html: Ditto. Prevents
jinja from throwing an error due to compaing a list type with an int.
| BonfaceKilz |
| 2020-10-02 | Merge branch 'testing' of github.com:genenetwork/genenetwork2 into build/pyth... | BonfaceKilz |
| 2020-10-02 | Apply PEP 8 formatting | BonfaceKilz |
| 2020-10-02 | Cast variable properly to avoid type exceptions...* wqflask/wqflask/marker_regression/run_mapping.py: See 94c36c8c.
| BonfaceKilz |
| 2020-10-02 | Replace is_integer with isinstance when checking for an int value | BonfaceKilz |
| 2020-10-02 | Update natural_sort function...* wqflask/wqflask/show_trait/SampleList.py
(natural_sort): Add new function.
(SampleList.get_attributes): Use new sort function to do natural_sort.
| BonfaceKilz |
| 2020-10-02 | Remove unnecessary commented out blocks...* wqflask/wqflask/show_trait/SampleList.py: See above.
| BonfaceKilz |
| 2020-10-02 | Cast "previous_chr" to an int...* wqflask/wqflask/marker_regression/gemma_mapping.py
(parse_loco_output): Cast "previous_chr" to an int which prevents the
error "Python typeerror: ‘>’ not supported between instances of ‘str’
and ‘int’" from being thrown. The error is **only** thrown in Python3.
| BonfaceKilz |
| 2020-10-01 | Convert trait attributes to utf-8 strings if they were bytes | BonfaceKilz |
| 2020-10-01 | Make object JSON serializable...* wqflask/wqflask/search_results.py
(SearchResultPage.gen_search_result): Some of the items is
self.trait_list are in bytes, and *json.loads* can't serialize bytes
into JSON.
| BonfaceKilz |
| 2020-09-30 | Merge pull request #449 from zsloan/table_sort_fix...Table sort error fix | 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 | 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 | Merge pull request #448 from zsloan/misc_rob_changes...Misc rob changes | zsloan |
| 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 | Merge pull request #446 from BonfaceKilz/Bug/Fix-casting-error...Bug/fix casting error | 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 | Use Python3 image to run tests | 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 |
