| Age | Commit message (Expand) | Author |
|---|
| 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 |
| 2020-09-28 | 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 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 |
| 2020-09-25 | 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 | Mock "SECRET_HMAC_CODE"...* wqflask/tests/utility/test_hmac.py: Mock app.config's
"SECRET_HMAC_CODE" value.
| 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 |
| 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 |
| 2020-09-08 | Changed the Add button color for all the different pages that use it...* wqflask/wqflask/templates/collections/view.html - changed Add button
color
* wqflask/wqflask/templates/correlation_matrix.html - changed Add button
color
* wqflask/wqflask/templates/correlation_page.html - changed Add button
color
* wqflask/wqflask/templates/mapping_results.html - changed Add button
color
* wqflask/wqflask/templates/search_result_page.html - changed Add button
color
| zsloan |
