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2020-10-08Merge branch 'testing' of github.com:genenetwork/genenetwork2 into testingzsloan
2020-10-08Merge pull request #455 from zsloan/temp_trait_scatterplot_fixzsloan
Temp Trait Scatterplot Error Fix
2020-10-08When generating links to correlation scatterplots (in corr results and corr ↵zsloan
matrix), append the group name to Temp dataset names so temp traits can be used in scatterplot * 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
2020-10-06Merge pull request #454 from zsloan/update_docs_fixzsloan
Made change that should fix error when trying to change page text usi…
2020-10-06Made change that should fix error when trying to change page text using ckeditorzsloan
* 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
2020-10-06Merge pull request #453 from zsloan/index_page_textarea_fixzsloan
Index page dropdown/textarea fix
2020-10-06Fixed issue where drop-down arrows and textarea corners couldn't be clicked ↵zsloan
with certain window widths * 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
2020-10-05Replaced "+" with "and" in transform textzsloan
* wqflask/wqflask/static/new/javascript/show_trait.js - Replaced "+" with "and" when Invert and another transform are combined and capitalized "Transform"
2020-10-05Changed the way tranform functions workzsloan
* wqflask/wqflask/static/new/javascript/show_trait.js - Changed transform options to only apply to original values, with the exception of the "invert" transform and rows where the value was set to "x" - Only run "check_if_zero_to_one_vals" once on page load instead of running it every time a transform is run - Changed Transform text to reflect when there's a combination of Invert and some other transform - Updated Reset function to use DataTables API
2020-10-05Simplified if statementszsloan
* wqflask/wqflask/static/new/javascript/initialize_show_trait_tables.js - simplified if statements to just say if(js_data.se_exists) instead of if(js_data.se_exists === true)
2020-10-05Changed order of JS imports to both make DataTables objects available to all ↵zsloan
other JS code and move all local JS code below third-party libraries * wqflask/wqflask/templates/show_trait.html - Changed order of JS imports
2020-10-05Added square root to the transform functions that are only active if there ↵zsloan
are no negative values * wqflask/wqflask/templates/show_trait_transform_and_filter.html - made sqrt option contingent on no negative values
2020-10-05Fixed issue that was causing SE column to not show up in the trait page tablezsloan
* wqflask/wqflask/static/new/javascript/initialize_show_trait_tables.js - Apparently "true" in js_data was a boolean instead of a string, so the previous if statements weren't working properly
2020-10-02Converted transform functions to use DataTables API to work with scroller + ↵zsloan
fixed them to take into account blocked samples * wqflask/wqflask/static/new/javascript/show_trait.js - Changed transform/normalize functions to use DataTables API to fetch and change values and also changed the way that code is structured to avoid a lot of duplicated code
2020-10-02Added function that pulls input data out of table and inserts it as hidden ↵zsloan
input elements in the form (so form submission can work with Scroller) * wqflask/wqflask/static/new/javascript/show_trait.js - Added function "get_table_contents_for_form_submit" that is called with submit_special (that is called for correlations and mapping from the trait page)
2020-10-02There were two copies of the "submit_special" function in both show_trait.js ↵zsloan
and show_trait_mapping_tools.js. The latter now just calls the function from the former * wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js - Everything in this file was previously inside its own function, which made its functions unable to access the functions from show_trait.js (and necessitated it having its own "copy" of the submit_special function
2020-10-02Checked if owner_id is "none" to avoid an error when trying to access the ↵zsloan
resource manager page with newly added datasets * 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
2020-10-02Merge pull request #450 from zsloan/corr_matrix_error_fixzsloan
Corr matrix error fix
2020-10-02Ignore utf-8 encoding errorsBonfaceKilz
* wqflask/base/trait.py (retrieve_trait_info): Add extra param to ignore errors such as: "utf-8 codec can't decode byte 0xb5 in position 0: invalid start byte" thrown in Python3.
2020-10-02Split author's list into it's own variableBonfaceKilz
* wqflask/wqflask/templates/correlation_page.html: Ditto. Prevents jinja from throwing an error due to compaing a list type with an int.
2020-10-02Merge branch 'testing' of github.com:genenetwork/genenetwork2 into ↵BonfaceKilz
build/python3-migration
2020-10-02Apply PEP 8 formattingBonfaceKilz
2020-10-02Cast variable properly to avoid type exceptionsBonfaceKilz
* wqflask/wqflask/marker_regression/run_mapping.py: See 94c36c8c.
2020-10-02Replace is_integer with isinstance when checking for an int valueBonfaceKilz
2020-10-02Update natural_sort functionBonfaceKilz
* wqflask/wqflask/show_trait/SampleList.py (natural_sort): Add new function. (SampleList.get_attributes): Use new sort function to do natural_sort.
2020-10-02Remove unnecessary commented out blocksBonfaceKilz
* wqflask/wqflask/show_trait/SampleList.py: See above.
2020-10-02Cast "previous_chr" to an intBonfaceKilz
* wqflask/wqflask/marker_regression/gemma_mapping.py (parse_loco_output): Cast "previous_chr" to an int which prevents the error "Python typeerror: ‘>’ not supported between instances of ‘str’ and ‘int’" from being thrown. The error is **only** thrown in Python3.
2020-10-01Merge branch 'testing' of github.com:genenetwork/genenetwork2 into ↵zsloan
corr_matrix_error_fix
2020-10-01Convert trait attributes to utf-8 strings if they were bytesBonfaceKilz
2020-10-01Make object JSON serializableBonfaceKilz
* wqflask/wqflask/search_results.py (SearchResultPage.gen_search_result): Some of the items is self.trait_list are in bytes, and *json.loads* can't serialize bytes into JSON.
2020-09-30Merge pull request #449 from zsloan/table_sort_fixzsloan
Table sort error fix
2020-09-30Changed the logic for adding 0 to the PCA results to do so when thezsloan
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)
2020-09-30Added "natural-minus-na" sorting for relevant columns in the correlationzsloan
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
2020-09-30Fixed issue where columns sorted by inner text (text inside link tags)zsloan
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
2020-09-30Removed unused code from TempDataSet classzsloan
* 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
2020-09-30Add missing importBonfaceKilz
* wqflask/wqflask/correlation/show_corr_results.py: Add it.
2020-09-30Apply pep 8 formattingBonfaceKilz
* wqflask/wqflask/correlation/show_corr_results.py [imports]: Apply pep8 and remove unused imports.
2020-09-30Fix StopIteration error thrown in view collections pageBonfaceKilz
* wqflask/wqflask/user_session.py (user_id): Use byte-string when fetching user_id. See: https://github.com/genenetwork/genenetwork2/pull/422#issuecomment-701082458
2020-09-30Fix import in testsBonfaceKilz
2020-09-29Merge pull request #448 from zsloan/misc_rob_changeszsloan
Misc rob changes
2020-09-29Trait page link-out buttons were previously inside <a> tags, but thiszsloan
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
2020-09-29Removed "Color By Trait" button from the Bar Chart, because it was meantzsloan
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
2020-09-29Made a variety of changes to table pageszsloan
* 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
2020-09-29Remove undefined variableBonfaceKilz
2020-09-29Apply pep 8 to bufferBonfaceKilz
* wqflask/wqflask/user_manager.py: Remove some stale comments. (imports): Apply pep-8 and remove unused imports.
2020-09-29Fixed issue where negative additive effect values weren't beingzsloan
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
2020-09-29Changed Add (to collection) button color to match other Add buttons andzsloan
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"
2020-09-29Changed the DataTables column sort arrows to a different color byzsloan
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)
2020-09-29Add check for bytesBonfaceKilz
* 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.
2020-09-29Add test for process_traits from collections.pyBonfaceKilz
* wqflask/tests/wqflask/test_collect.py: Add it.
generated by cgit v1.2.3 (git 2.44.0) at 2024-12-12 05:03:22 +0000