| Age | Commit message (Expand) | Author |
|---|
| 2020-10-09 | Merge pull request #458 from BonfaceKilz/tests/add-extra-tests-for-collections...Tests/add extra tests for collections | BonfaceKilz |
| 2020-10-09 | Apply PEP 8 to buffer...* wqflask/wqflask/wgcna/wgcna_analysis.py: Apply pep8
* wqflask/wqflask/collect.py: Ditto
* wqflask/base/trait.py: Ditto
| BonfaceKilz |
| 2020-10-09 | Add test for process_traits from collections.py...* wqflask/tests/wqflask/test_collect.py: Add it.
| BonfaceKilz |
| 2020-10-08 | Merge pull request #457 from zsloan/bxd_longevity_search_error_fix...Fixed issue where new phenotype groups wouldn't be saved to the self.… | zsloan |
| 2020-10-08 | Fixed remaining issue that applies to all dataset types...* wqflask/base/data_set.py - Fixed issue where there was an error when trying to take the len of the query results when there were no results
| zsloan |
| 2020-10-08 | Fixed issue where new phenotype groups wouldn't be saved to the self.datasets......* wqflask/base/data_set.py - Set "group_name" as a separate variable from "name" to avoid it being used as the key in self.datasets
| zsloan |
| 2020-10-08 | Merge pull request #452 from zsloan/authentication_bug_fix...Checked if owner_id is "none" to avoid an error when trying to access… | zsloan |
| 2020-10-08 | Merge pull request #455 from zsloan/temp_trait_scatterplot_fix...Temp Trait Scatterplot Error Fix | zsloan |
| 2020-10-08 | When generating links to correlation scatterplots (in corr results and corr m......* wqflask/wqflask/correlation/corr_scatter_plot.py - Create the dataset object using the group name included with Temp dataset names (which take the form "Temp_(group_name)")
* wqflask/wqflask/templates/correlation_matrix.html - Change scatterplot links to include the group name if the dataset name is "Temp"
* wqflask/wqflask/templates/correlation_page.html - Change scatterplot links to include the group name if the dataset name is "Temp" + a couple minor style changes
| zsloan |
| 2020-10-06 | Merge pull request #454 from zsloan/update_docs_fix...Made change that should fix error when trying to change page text usi… | zsloan |
| 2020-10-06 | Made change that should fix error when trying to change page text using ckeditor...* wqflask/wqflask/docs.py - Changed query to include casting as binary to deal with certain unicode characters in ckeditor pages
* wqflask/wqflask/views.py - Imported update_text from Docs since it previously wasn't updated, causing an error when attempting to update text
| zsloan |
| 2020-10-06 | Merge pull request #453 from zsloan/index_page_textarea_fix...Index page dropdown/textarea fix | zsloan |
| 2020-10-06 | Fixed issue where drop-down arrows and textarea corners couldn't be clicked w......* wqflask/wqflask/templates/index_page_orig.html - Changed the left/right div's padding to prevent them from overlapping and changed the textareas' styles to make them only expandable vertically
| zsloan |
| 2020-10-02 | Checked if owner_id is "none" to avoid an error when trying to access the res......* wqflask/wqflask/resource_manager.py - Only get owner user info conditional on owner_id not being "none" (which it will be by default for newly added datasets). Previously it would throw an error due to "owner_info" being None
| zsloan |
| 2020-10-02 | Merge pull request #450 from zsloan/corr_matrix_error_fix...Corr matrix error fix | zsloan |
| 2020-10-01 | Merge branch 'testing' of github.com:genenetwork/genenetwork2 into corr_matri... | zsloan |
| 2020-09-30 | Merge pull request #449 from zsloan/table_sort_fix...Table sort error fix | zsloan |
| 2020-09-30 | Changed the logic for adding 0 to the PCA results to do so when the...shared samples are < 2 instead of 0; this fixed the error when running
the correlation matrix, but results in the PCA traits having no values
* wqflask/wqflask/correlation_matrx/show_corr_matrix.py - changed
"if num_overlap == 0" to "if num_overlap < 2" because correlations can't
be run if there are fewer than 2 shared samples (and previously would
throw an error if there was exactly 1 shared sample)
| 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 | Removed unused code from TempDataSet class...* wqflask/base/data_set.py - TempDataSet class contained some code
referring to the SQL DB, but temp traits aren't stored in the SQL DB anymore
| zsloan |
| 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 | 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 | 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 | 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 | 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 | 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 | Apply pep8 formatting | BonfaceKilz |
