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2020-11-12Merge branch 'testing' of github.com:genenetwork/genenetwork2 into ↵zsloan
feature/corr_table_changes
2020-11-11Merge branch 'testing' of github.com:genenetwork/genenetwork2 into testingzsloan
2020-11-11Added Bonface to the footerzsloan
2020-11-11Changed some column widths and removed the width for description so it can ↵zsloan
vary with page width
2020-11-11- Fixed an issue causing the phenotype abbreviation to not be displayed ↵zsloan
properly in correlation results - Set default description to N/A when there's no trait description for phenotype traits
2020-11-11Switched checking if a trait is confidential to checking if it has a pubmed ↵zsloan
ID for the purposes of showing pre-publication abbreviation/description
2020-11-11Merge branch 'testing' of github.com:genenetwork/genenetwork2 into ↵BonfaceKilz
feature/add-glossary-page
2020-11-11Update image widthBonfaceKilz
2020-11-11Add basic markdown stylingBonfaceKilz
* wqflask/wqflask/static/new/css/markdown.css: New file. * wqflask/wqflask/templates/glossary.html: add markdown id to markdown container.
2020-11-10Changed logic for creating temp trait SampleList to account for both traits ↵zsloan
encoded as bytes and traits encoded as strings, since temp traits created before and after the Python 3 switchover will have different encoding
2020-11-10* wqflask/wqflask/correlation/show_corr_results.py - Changed some of the ↵zsloan
parameters sent to the correlation table * wqflask/wqflask/templates_correlation_page.html - Fixed some column defs and removed unused table configuration code
2020-11-10Fixed issue where strain values in bytes needed to be decoded when loading a ↵zsloan
Temp trait
2020-11-10Changed "BXD-Harvested" to "BXD-Longevity" since that group was renamed and ↵zsloan
using the wrong name was causing correlations to not work.
2020-11-10Added CSS file for all pages that include a table of traitszsloan
2020-11-10Add missing links and some markdown formatting(underline, bold)BonfaceKilz
* wqflask/wqflask/static/markdown/glossary.md: Update file.
2020-11-06Removed the page selection from the top of the table because it created an ↵zsloan
awkward gap between the column show/hide buttons and the table, and this table will be changed to use Scroller instead of paging soon regardless
2020-11-06Changed the show/hide column buttons to use DataTables API + a few other ↵zsloan
changes (for some reason none of my changes could be pushed from one of my local branches to origin/testing, so they're combined in this commit) - Fixed a couple column header glossary links to point to GN1 - Added trait_list.css for styling a couple elements common to similar pages (like correlations or view collection)
2020-11-06Added min-width for the divs containing the analysis tools and table ↵zsloan
options, since they would look weird if the window shrunk below a certain width Also made some indentation more consistent
2020-11-06Added new css file for pages that have trait list tables (not sure what else ↵zsloan
to call them, but pages like search results, view collection, and correlation results)
2020-11-06Increased the min-width for the show_trait page container div for all the ↵zsloan
accordion sections, since previously it could get too narrow and cause text to extend beyong the borders of each accordion area
2020-11-06After I changed some class names in the trait page to use - instead of _ (to ↵zsloan
keep naming consistent) I forgot to change the references in show_trait_mapping_tools.js (which broke the functionality of clicking a tab doing mapping)
2020-11-05Converted correlation table for ProbeSet target datasets to use the JSON ↵zsloan
input and removed the unused table html
2020-11-05Added some additional necessary fields to generate_corr_json in ↵zsloan
show_corr_results.py
2020-11-05Removed html from generate_corr_json since that will be done by the column ↵zsloan
definitions after passing the data to DataTables as JSON
2020-11-05Imported Scroller and used it with correlation page tablezsloan
2020-11-04Changed numeric-html sorting for the Tissue/Lit r columns to ↵zsloan
natural-minus-na so it deals with the "--" values * wqflask/wqflask/templates/correlation_page.html - Replaced numeric-html sorting with natural-minus-na for the lit/tissue r columns
2020-11-04Use new glossary link from glossary_blueprint in html templatesBonfaceKilz
2020-11-04Add missing imageBonfaceKilz
2020-11-04Add link markers to elements which are referenced from elsewhereBonfaceKilz
2020-11-04Update test_markdown_routesBonfaceKilz
* wqflask/tests/unit/wqflask/test_markdown_routes.py (test_render_markdown_when_fetching_locally): Fix failing test.
2020-11-04Add an edit link button to glossary pageBonfaceKilz
2020-11-04Wrap rendered content in div containerBonfaceKilz
2020-11-04Update glossary markdown fileBonfaceKilz
2020-11-04Merge pull request #475 from Alexanderlacuna/test-showtraitBonfaceKilz
Add more tests for show trait module
2020-11-04correct a typoAlexanderlacuna
2020-11-04remove extra whitespaceAlexanderlacuna
2020-11-04remove whitespace in line 119-120Alexanderlacuna
2020-11-04remove whitespaceAlexanderlacuna
2020-11-04remove whitespace and assertIsAlexanderlacuna
2020-11-03Merge pull request #479 from zsloan/bug/haplotype_analyst_error_fixzsloan
Bug/haplotype analyst error fix
2020-11-03Changed the syntax for the "sort" function in the docstring of GeneralObject ↵zsloan
to be compatible with Python 3 syntax * wqflask/base/GeneralObject.py - edited docstring to be correct for Python 3
2020-11-03Fixed a sort used when doing the haplotype analysis to be compatible with ↵zsloan
Python 3 * wqflask/wqflask/marker_regression/display_mapping_results.py - The arguments for sort are different in Python 3, so it was changed to be compatible
2020-11-03Fix false-positive testsBonfaceKilz
* wqflask/tests/unit/wqflask/test_markdown_routes.py: (MockRequests404): Pass self in all properties. (MockRequests200): Ditto. (test_render_markdown): Rename to test_render_markdown_when_fetching_locally. (test_render_markdown_when_fetching_remotely): New test.
2020-11-03Merge pull request #478 from zsloan/loading_page_n_fixzsloan
Joined sample names in primary_samples and all_samples with commas be…
2020-11-03Joined sample names in primary_samples and all_samples with commas because ↵zsloan
this list was being split to get the N of samples; not sure why this was working before * wqflask/wqflask/show_trait/show_trait.py primary_samples and all_samples passed as hidden form inputs now have names split by commas so they can be counted correctly when displaying the N on the mapping loading screen
2020-11-03Delete fileBonfaceKilz
* wqflask/tests/integration/test_glossary.py: Delete it. Earlier renamed to test_markdown_routes.
2020-11-03Add basic tests for rendering_markdownBonfaceKilz
* wqflask/tests/unit/wqflask/test_markdown_routes.py: New tests.
2020-11-03Add basic structure for "/glossary" routes testBonfaceKilz
2020-11-03Move logic for fetching md files to it's own functionBonfaceKilz
* wqflask/wqflask/markdown_routes.py (render_markdown): New function. (glossary): use render_markdown function.
2020-11-03Add simple md content in glossary.mdBonfaceKilz
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