| Age | Commit message (Expand) | Author |
|---|
| 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 |
| 2020-10-09 | Fix export function on traits and analysis page...* wqflask/wqflask/views.py (export_trait_excel): Write data as bytes
instead of strings. See:
https://stackoverflow.com/questions/32075135/python-3-in-memory-zipfile-error-string-argument-expected-got-bytes
* wqflask/wqflask/show_trait/export_trait_data.py: Convert cmp
function into a key function.
| BonfaceKilz |
| 2020-10-09 | Update base64 conversion | BonfaceKilz |
| 2020-10-09 | Replace string concat("+") with python3's f-string | BonfaceKilz |
| 2020-10-09 | Replace "ncores" with "nthreads" param to r_CTLscan | BonfaceKilz |
| 2020-10-09 | Use built-in array as a named import...* wqflask/wqflask/wgcna/wgcna_analysis.py
(WGCNA.render_image): Use named import method. This is a workaround
for using explicitly using "array" which conflicts with something else
in the namespace.
| BonfaceKilz |
| 2020-10-09 | Update base64 conversion...* wqflask/wqflask/wgcna/wgcna_analysis.py
(WGCNA.render_image): Use Python3's base64 library from the stdlib to
perform conversion.
* wqflask/wqflask/ctl/ctl_analysis.py (CTL.loadImage): Ditto.
| BonfaceKilz |
| 2020-10-09 | Convert cmp function into a key function...* wqflask/wqflask/correlation_matrix/show_corr_matrix.py
(sortEigenVectors): Convert the comparison function into a key
function. See:
https://docs.python.org/3/howto/sorting.html#the-old-way-using-the-cmp-parameter
| BonfaceKilz |
| 2020-10-09 | Apply PEP-8 formatting | BonfaceKilz |
| 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 | Allowed mapping method description text to shrink with screen size...* wqflask/wqflask/templates/show_trait_mapping_tools.html - Removed the "col-xs-_" class to allow the div containing mapping description text to shrink with screen size
| zsloan |
| 2020-10-08 | Adjusted some widths/classes to allow correlation description text to expand/......* wqflask/wqflask/templates/show_trait_calculate_correlations.html - Adjusted widths of drop-down divs and removed the col-width class from the description div (the right side) so it can shrink wqwith screen size
| zsloan |
| 2020-10-08 | Changed the min-width of trait page main div in order to allow trait descript......* wqflask/wqflask/templates/show_trait.html - Changed width of main container div to 700px
| zsloan |
| 2020-10-08 | Merge branch 'testing' of github.com:genenetwork/genenetwork2 into testing | 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 branch 'testing' of github.com:genenetwork/genenetwork2 into testing | 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 |
| 2020-10-05 | Replaced "+" with "and" in transform text...* wqflask/wqflask/static/new/javascript/show_trait.js - Replaced "+" with "and" when Invert and another transform are combined and capitalized "Transform"
| zsloan |
| 2020-10-05 | Changed the way tranform functions work...* 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
| zsloan |
| 2020-10-05 | Simplified if statements...* 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)
| zsloan |
| 2020-10-05 | Changed order of JS imports to both make DataTables objects available to all ......* wqflask/wqflask/templates/show_trait.html - Changed order of JS imports
| zsloan |
| 2020-10-05 | Added square root to the transform functions that are only active if there ar......* wqflask/wqflask/templates/show_trait_transform_and_filter.html - made sqrt option contingent on no negative values
| zsloan |
| 2020-10-05 | Fixed issue that was causing SE column to not show up in the trait page table...* 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
| zsloan |
| 2020-10-02 | Converted transform functions to use DataTables API to work with scroller + f......* 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
| zsloan |
| 2020-10-02 | Added function that pulls input data out of table and inserts it as hidden in......* 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)
| zsloan |
| 2020-10-02 | There were two copies of the "submit_special" function in both show_trait.js ......* 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
| 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 | Ignore utf-8 encoding errors...* 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.
| BonfaceKilz |
| 2020-10-02 | Split author's list into it's own variable...* wqflask/wqflask/templates/correlation_page.html: Ditto. Prevents
jinja from throwing an error due to compaing a list type with an int.
| BonfaceKilz |
| 2020-10-02 | Merge branch 'testing' of github.com:genenetwork/genenetwork2 into build/pyth... | BonfaceKilz |
| 2020-10-02 | Apply PEP 8 formatting | BonfaceKilz |
| 2020-10-02 | Cast variable properly to avoid type exceptions...* wqflask/wqflask/marker_regression/run_mapping.py: See 94c36c8c.
| BonfaceKilz |
| 2020-10-02 | Replace is_integer with isinstance when checking for an int value | BonfaceKilz |
| 2020-10-02 | Update natural_sort function...* wqflask/wqflask/show_trait/SampleList.py
(natural_sort): Add new function.
(SampleList.get_attributes): Use new sort function to do natural_sort.
| BonfaceKilz |
| 2020-10-02 | Remove unnecessary commented out blocks...* wqflask/wqflask/show_trait/SampleList.py: See above.
| BonfaceKilz |
| 2020-10-02 | Cast "previous_chr" to an int...* 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.
| BonfaceKilz |
| 2020-10-01 | Merge branch 'testing' of github.com:genenetwork/genenetwork2 into corr_matri... | zsloan |
| 2020-10-01 | Convert trait attributes to utf-8 strings if they were bytes | BonfaceKilz |
| 2020-10-01 | Make object JSON serializable...* 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.
| BonfaceKilz |
| 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 |
