| Age | Commit message (Expand) | Author |
|---|
| 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 |
| 2020-09-25 | Update docs on CI setup with docker...* doc/docker-container.org: Update it.
| BonfaceKilz |
| 2020-09-25 | Update github action...* .github/workflows/main.yml: Set up a mariadb and redis within the GH
action.
(services): Remove mariadb service.
| BonfaceKilz |
| 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 | Update github action to include mariadb service...* .github/workflows/main.yml: Add mariadb service. This makes the
build pass because somewhere(because of cyclic imports), a connection
to mariadb is required.
| 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 |
| 2020-09-22 | 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 |
| 2020-09-22 | Merge pull request #445 from BonfaceKilz/buid/add-ci...Buid/add ci | BonfaceKilz |
| 2020-09-22 | Add testing badge on README...* README.md: Badge becomes green on successful runs.
| BonfaceKilz |
| 2020-09-22 | Update documentation on testing and CI...* README.md: Update section on testing.
* doc/docker-container.org: Add it.
| BonfaceKilz |
| 2020-09-22 | Add unittesting github action...* .github/workflows/main.yml: Add it.
| BonfaceKilz |
| 2020-09-22 | Update Mechanical Rob...* test/requests/main_web_functionality.py (check_search_page):
Breaking change introduced by updating text in search page. See:
9f76abc95
| BonfaceKilz |
| 2020-09-22 | Update bug_report template...* .github/ISSUE_TEMPLATE/bug_report.md: Update environment setup
section
| BonfaceKilz |
| 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 | Update Mechanical Rob...* test/requests/link_checker.py (verify_static_file): Cast
result.content.find's args to bytes.
* test/requests/main_web_functionality.py (check_search_page): Update
text to search for in a successful result. This value changed in
2aac6a06.
| 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 | Merge pull request #443 from BonfaceKilz/tests/test-auth-and-utf8...Tests/test auth and utf8 | 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 | Changed references to se_exists to just get it as a property of...SampleList instead of calling the method
* wqflask/wqflask/show_trait/show_trait.py - see above
* wqflask/wqflask/templates/show_trait.html - see above + removed some
commented out code
| zsloan |
| 2020-09-16 | Changed se_exists to a property so the SampleList instance can include...that when converted to a dict (which is needed to use it in the
javascript)
* wqflask/wqflask/show_trait/SampleList.py - Directly set se_exists as a
property of SampleList instead of requiring a method be called; I could
have set self.se_exists by calling the se_exists method, but that would
have resulted in the convoluted line "self.se_exists = self.se_exists()"
and the se_exists method only consisted of one line anyways
| zsloan |
| 2020-09-16 | Applied PEP8 and removed commented out code | zsloan |
| 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 |
| 2020-09-15 | Added scroller to trait page and changed sample tables to use it...* wqflask/wqflask/templates/show_trait.html - Imported scroller (from
the Google cdn temporarily for testing) and activated it for the sample
tables, as well as disabled options that conflicted with it (like
paging: false)
| zsloan |
