| Age | Commit message (Expand) | Author |
|---|
| 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 | 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 |
| 2020-09-28 | 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 | 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 |
| 2020-09-23 | 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 | Mock "SECRET_HMAC_CODE"...* wqflask/tests/utility/test_hmac.py: Mock app.config's
"SECRET_HMAC_CODE" value.
| 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 |
| 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 |
| 2020-09-08 | Search code now checks if there are more than 50,000 results before...running the code that queries the DB for max LRS locus information
(which is what takes the most time to run) and sets a variable that
indicates to the template (search_results.html) that it shouldn't show
the results
* wqflask/wqflask/search_results.py - Check number of results from base
query in order to prevent certain searches from running too long
| zsloan |
| 2020-09-08 | Changed regular and global search results table to use the new sort...method that always places NAs at bottom, changed the Add to Collection
button's color, and added something to the regular search page template
to display alternative text if there are more than 50000 results
* wqflask/wqflask/templates/gsearch_gene.html - Added natural-minus-na
sort to certain columns and changed Add button color
* wqflask/wqflask/templates/gsearch_pheno.html - Added natural-minus-na
sort to certain columns and changed Add button color
* wqflask/wqflask/templates/search_result_page.html - Added
natural-minus-na sort to certain columns, changed Add button color, and
added template logic that shows alternative text if there are more than
50,000 results
| zsloan |
| 2020-09-08 | Added a sort function (derived from the natural sort import) that always...places N/As at the bottom regardless of search direction
* wqflask/wqflask/static/new/javascript/search_results.js - created
"natural-minus-na" sort
| zsloan |
| 2020-09-04 | Update how static js/ css files are fetched...* wqflask/wqflask/views.p:(css, js) Add "css" router decorator. Also, if
"js_alt" is in path, fetch the file from "GUIX_PROFILE/share/javascript" instead
of the default directory: "GUIX_PROFILE/share/genenetwork2/javascript"
See: <https://github.com/genenetwork/genenetwork2/issues/436>
| BonfaceKilz |
| 2020-09-01 | There was a missing quote in one of the javascript imports added by the...PR changing them to get fetched from GUIX; I need to check and see if
there are other situations like this
* wqflask/wqflask/templates/mapping_results.html - Added missing quote
| zsloan |
| 2020-09-01 | Merge branch 'testing' of github.com:genenetwork/genenetwork2 into testing | zsloan |
| 2020-09-01 | Fixed indent issue that could cause error when showing the haplotype...analyst in the mapping chromosome view
* wqflask/wqflask/marker_regression/display_mapping_results.py -
Indented a bit of code that was wrongly indented in such a way that the
variable "ind" wasn't set if "plotbxd" is 0
| zsloan |
| 2020-09-01 | Use "md5.min.js" from guix | BonfaceKilz |
| 2020-09-01 | Remove commented out script tags that references CDNs | BonfaceKilz |
| 2020-09-01 | Replace CDNs with packages from guix | BonfaceKilz |
| 2020-09-01 | Add missing apostrophe in url_for args | BonfaceKilz |
| 2020-08-31 | Merge pull request #431 from BonfaceKilz/Build/add-d3-tip...Use d3-tip from guix | BonfaceKilz |
| 2020-08-31 | Fixed text on not_authenticated to use proper grammar...* wqflask/wqflask/templates/new_security/not_authenticated.html -
Changed "this" to "these" since "data" is plural
| zsloan |
| 2020-08-31 | Merge branch 'testing' of github.com:genenetwork/genenetwork2 into testing | zsloan |
| 2020-08-31 | Fixed issue that was causing updating resource default privileges to not...work
* wqflask/utility/redis_tools.py - There was an issue where resources
wouldn't be updated if they already existed. This is because the code
didn't yet account for the "update" tag (that is meant to give the
option of preventing updating resources when running the script to enter
all resources into Redis). I changed the logic to add a resource if
"update" is True or the resource doesn't already exist (so it won't if
update is False and the resource exists).
| zsloan |
| 2020-08-31 | Use d3-tip from guix | BonfaceKilz |
| 2020-08-31 | Use chroma from guix...* wqflask/wqflask/templates/correlation_matrix.html: Fetch chroma from guix
profile
| BonfaceKilz |
