| Age | Commit message (Expand) | Author |
|---|
| 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 |
| 2020-09-23 | 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 |
| 2020-09-18 | 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 |
| 2020-09-17 | Replace string arguments to "hmac.new" with bytearray...Same as:
https://github.com/genenetwork/genenetwork2/pull/422/commits/46443ec8d2cdfd7c60358a889d90a90e4f7daaf4
| BonfaceKilz |
| 2020-09-17 | Fix errors in tests...* wqflask/tests/utility/test_authentication_tools.py
test_check_resource_availability_non_default_mask): Mock flask's
global 'g' variable properly.
* wqflask/tests/base/test_trait.py: Ditto.
* wqflask/tests/utility/test_authentication_tools.py: Ditto.
| BonfaceKilz |
| 2020-09-17 | Apply pep8...* wqflask/base/trait.py: Apply pep8.
* wqflask/utility/authentication_tools.py: Ditto.
| BonfaceKilz |
| 2020-09-17 | Merge branch 'testing' into build/python3-migration | BonfaceKilz |
| 2020-09-17 | Apply pep8...* wqflask/utility/hmac.py: Apply pep8 and fix typo.
| BonfaceKilz |
| 2020-09-17 | Add tests for hmac utility...* wqflask/tests/utility/test_hmac.py: New tests.
| BonfaceKilz |
| 2020-09-16 | Add new tests for "base/trait.py"...* wqflask/tests/base/test_trait.py: New tests.
| BonfaceKilz |
| 2020-09-16 | Apply pep8...* wqflask/utility/authentication_tools.py: Apply pep8 formatting to
file.
| BonfaceKilz |
| 2020-09-16 | Add tests for "add_new_resource" method...* wqflask/tests/utility/test_authentication_tools.py: Add them.
| BonfaceKilz |
| 2020-09-16 | Remove unnecessary if branch...* wqflask/utility/authentication_tools.py
(check_resource_availability): Combine if statements into one boolean
check in one if branch.
| BonfaceKilz |
| 2020-09-16 | Add tests for authentication tools...Catches bugs in:
-
https://github.com/genenetwork/genenetwork2/pull/422/commits/70dbeeb5832711ed5271434e482c18bc7ea095b8
* wqflask/tests/utility/test_authentication_tools.py: New file. Add
tests for "check_resource_availability".
| BonfaceKilz |
| 2020-09-15 | Fix failing tests...* wqflask/tests/base/test_data_set.py: Update failing tests introduced
by the change in 301bdd2f4.
| BonfaceKilz |
| 2020-09-14 | Merge branch 'scroller_testing' of github.com:zsloan/genenetwork2 into testing | zsloan |
| 2020-09-13 | Added in-progress info-page to views.py as well as in-progress...authorization/security guide
* wqflask/wqflask/views.py - Added endpoint for info page and
authorization/security tutorial
| zsloan |
| 2020-09-11 | Wrote code and template for reproducing GN1's Info Page (page that...displays info about a dataset + download links for its data)
* wqflask/wqflask/db_info.py - Python that pulls the info out of the DB
and parses the download links from the ipfs response
* wqflask/wqflask/templates/info_page.html - template for displaying
db info; need to make a lot of changes to its format/aesthetics
| zsloan |
| 2020-09-10 | Modified "natural-minus-na" sort function to treat an array of values...as equivalent to "N/A" (since different tables sometimes include other
values that imply there's no value) and applied it to some extra columns
in the Interval Analyst table
* wqflask/wqflask/static/new/javascript/search_results.js - Modified
sort_NAs function to take an array of "N/A"-equivalent values instead of
just comparing against the string "N/A"
* wqflask/wqflask/templates/mapping_results.html - Applied
"natural-minus-na" sort method to several columns that include "--" in
the Interval Analyst table
| zsloan |
| 2020-09-10 | Fixed several sorting issues and moved orderDataType definitions into...search_results.js since all the tables that use them import that file
(that file's name needs to be changed, though)
* wqflask/wqflask/static/new/javascript/search_results.js - Added the
dom-checkbox and dom-inner-text order types into this file; they were
previously duplicated across several template files
* wqflask/wqflask/templates/gsearch_gene.html - Added dom-inner-text
order type to relevant columns with hyperlink contents and disabled
deferRender since it conflicted with use of both pagination and
orderDataType for sorting
* wqflask/wqflask/templates/gsearch_pheno.html - Same as above
* wqflask/wqflask/templates/mapping_results.html - Added dom-inner-text
for a few columns that have hyperlink values - still need to modify
natural-minus-na to also include other "N/A"-equivalent values like "--"
* wqflask/wqflask/templates/search_result_page.html Removed the
dom-checkbox and dom-inner-text order types from this file since they
were moved to search_results.js
| zsloan |
