| Age | Commit message (Expand) | Author |
|---|
| 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 | Merge pull request #437 from BonfaceKilz/fix/use-correct-path-give-a-path-loc......Fix/use correct path give a path location | BonfaceKilz |
| 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 |
| 2020-09-04 | Fix false positive tests...* test/requests/link_checker.py:
(verify_static_file): Add it. Verify that a static link is fetched by checking
for the message "Error: 404 not Found" in page.
(check_package_js_files): Add appropriate 'js' or 'css' prefix.
| 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 | Merge pull request #434 from BonfaceKilz/Build/use-md5-js-from-guix...Build/use md5 js from guix | BonfaceKilz |
| 2020-09-01 | Add check for "md5.min.js" library...* test/requests/link_checker.py: Add it.
| BonfaceKilz |
| 2020-09-01 | Use "md5.min.js" from guix | BonfaceKilz |
| 2020-09-01 | Merge pull request #433 from BonfaceKilz/Build/remove-cdns...Build/remove cdns | BonfaceKilz |
| 2020-09-01 | Check availability of several js and css files...* test/requests/link_checker.py: Check availability of: chroma.min.js;
d3-tip.js; d3.min.js; underscore.min.js; nv.d3.min.css; and jquery.qtip.min.js
| 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 | Merge pull request #432 from BonfaceKilz/Fix/add-missing-apostrophe...Add missing apostrophe in url_for args | 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 | Add check for "d3-tip.js" js library...* test/requests/link_checker.py (check_packaged_js_files): Add it.
| BonfaceKilz |
| 2020-08-31 | Merge pull request #429 from BonfaceKilz/chore/add-gh-templates...Add github templates for filing bugs, user stories/ features and PRs | BonfaceKilz |
| 2020-08-31 | Use d3-tip from guix | BonfaceKilz |
| 2020-08-31 | Merge pull request #430 from BonfaceKilz/Build/add-chroma-js...Build/add chroma js | BonfaceKilz |
| 2020-08-31 | Add github templates for filing bugs, user stories/ features and PRs...* .github/ISSUE_TEMPLATE/bug_report.md : Add template for filing bug reports.
* .github/ISSUE_TEMPLATE/feature_request.md: Add template for filing a feature.
* .github/ISSUE_TEMPLATE/user_story.md: Add a template for creating a user story
for a feature.
* .github/PULL_REQUEST_TEMPLATE.md: Add a template for filing a PR.
| BonfaceKilz |
| 2020-08-31 | Add check for "chroma.js" dataTables extension plugin...* test/requests/link_checker.py (check_packaged_js_files): Add it.
| BonfaceKilz |
| 2020-08-31 | Use chroma from guix...* wqflask/wqflask/templates/correlation_matrix.html: Fetch chroma from guix
profile
| BonfaceKilz |
| 2020-08-31 | Merge pull request #428 from BonfaceKilz/chore/delete-datatables-extensions-f......Delete dataTables and it's extensions from git | BonfaceKilz |
| 2020-08-29 | Fixed issue where exporting traits would throw an error if a dataset's...group didn't have an InbredSetCode set in the DB
* wqflask/utility/authentication_tools.py - Changed get_group_code to
return an empty string instead of None if InbredSetCode doesn't exist
for a dataset group
* wqflask/wqflask/views.py - Changed zipped export filename to
"export_(datetime)" instead of "collection_(datetime)" since this export
can occur from both the collection page and the global search page
| zsloan |
| 2020-08-29 | Fixed issue with exporting traits from multiple different groups from...the collection page (the filename wasn't being set)
* wqflask/wqflask/views.py - Set filename to "collection_(datetime)" in
export_traits_csv because it wasn't being set before
| zsloan |
| 2020-08-28 | Delete dataTables and it's extensions from git...* wqflask/wqflask/static/new/packages/DataTables/: Delete folder.
| BonfaceKilz |
| 2020-08-27 | Added logic that creates a user account if an e-mail is added to a group...that isn't already associated with a GN2 account and sends the user an
e-mail; still need to test
* wqflask/wqflask/group_manager.py - Added logic sending an invitation
e-mail if user_details aren't found for any of the e-mails provided when
adding users to a group
| zsloan |
| 2020-08-27 | Added function for sending an invitation e-mail...* wqflask/wqflask/user_login.py - Added send_invitation_email function,
which does what it says
| zsloan |
| 2020-08-27 | Added manager_user.html because it was missing from git | zsloan |
| 2020-08-25 | Merge branch 'testing' of github.com:genenetwork/genenetwork2 into testing | zsloan |
| 2020-08-25 | Fixed issue in DatasetType that caused an error when trying to load new...datasets
* wqflask/base/data_set.py - Added fetchone() to g.db.execute() which is
what was causing the error
| zsloan |
| 2020-08-25 | Merge pull request #427 from BonfaceKilz/Build/add-scientific-js-datatables-p......Build/add scientific js datatables plugin | zsloan |
| 2020-08-26 | Add check for "scientific.js" dataTables extension plugin...* test/requests/link_checker.py (check_packaged_file): Add it.
| BonfaceKilz |
| 2020-08-25 | This should fix an issue where the new qtlreaper wouldn't work properlty...with genotypes that only have cM positions
* wqflask/wqflask/marker_regression/qtlreaper_mapping.py -
parse_reaper_output is changed to check if cM and Mb exist in output
when creating marker obs
* wqflask/wqflask/marker_regression/run_mapping.py - Changed
export_mapping_results to properly deal with all combinations of cM and
Mb positions (both and either/or)
| zsloan |
| 2020-08-25 | Merge pull request #425 from BonfaceKilz/refactor/extract-htmlgen-methods-to-......Refactor/extract htmlgen methods to wrapper class | zsloan |
| 2020-08-25 | Use scientific.js dataTables extension plugin from guix | BonfaceKilz |
| 2020-08-25 | Merge pull request #426 from BonfaceKilz/Build/use-naturaljs-datatables-exten......Build/use naturaljs datatables extensions | zsloan |
| 2020-08-24 | Add check for "natural.js" in Mechanical Rob...* test/requests/link_checker.py (check_packaged_file): Add it.
| BonfaceKilz |
