| Age | Commit message (Expand) | Author |
|---|
| 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 | Use d3-tip from guix | 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 |
| 2020-08-25 | 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 |
| 2020-08-24 | Use natural.js dataTables extension plugin from guix | BonfaceKilz |
| 2020-08-24 | Remove non-keyword args•••* wqflask/wqflask/marker_regression/display_mapping_results.py
(HtmlGenWrapper)[create_image_tag]: Remove "src" and "alt" as function
parameters.
| BonfaceKilz |
| 2020-08-24 | Replace "HtmlGen" method calls with those from "HtmlGenWrapper"•••* wqflask/wqflask/marker_regression/display_mapping_results.py
(DisplayMappingResults): Replace direct calls to HtmlGen with methods from
the constructed wrapper class "HtmlGenWrapper".
| BonfaceKilz |
| 2020-08-24 | Add new wrapper class for HtmlGen method•••* wqflask/wqflask/marker_regression/display_mapping_results.py: Add new class
| BonfaceKilz |
| 2020-08-24 | Add tests for the HtmlGenWrapper class•••* wqflask/tests/wqflask/marker_regression/test_display_mapping_results.py: Add
new tests
| BonfaceKilz |
| 2020-08-24 | Fix some pylint errors•••* wqflask/wqflask/marker_regression/display_mapping_results.py: Remove unused
imports and add fix some pylint errors
| BonfaceKilz |
| 2020-08-24 | Remove unused imports•••* wqflask/utility/Plot.py: Remove unused imports like "numarray". "numarray" is
does not have py3 support so it's important to remove references to it.
| BonfaceKilz |
| 2020-08-24 | Rename file•••* wqflask/tests/wqflask/marker_regression/test_display_mapping_results.py:
Rename test_display_marking_results.py to test_display_mapping_results.py
| BonfaceKilz |
| 2020-08-24 | Fix failing test•••* wqflask/tests/wqflask/api/test_gen_menu.py: Update assertion. Result data
introduced in 092212df
Signed-off-by: BonfaceKilz <bonfacemunyoki@gmail.com>
| BonfaceKilz |
| 2020-08-24 | Fixed issue where im_drawer wasn't being set in drawHaplotypeBand•••* wqflask/wqflask/marker_regression/display_mapping_results.py - defined
im_drawer in drawHaplotypeBand to fix errror and removed an unused
import
| zsloan |
| 2020-08-24 | The function draw_rotated_text_ was writing an image to /tmp, which GN2•••user apparently doesn't have access to, so I replaced it with a link to
the dynamically set TEMPDIR
* wqflask/utility/pillow_utils.py - Replaced "/tmp/" in image location
with TEMPDIR
| zsloan |
| 2020-08-22 | Set min-width for search result table, since the description column•••often looks weird if it gets below a certain width
* wqflask/wqflask/templates/search_result_page.html - Set min-width of
table container div to 1500px since that seems to be a reasonable width
that prevents the description column from getting too narrow
| zsloan |
| 2020-08-20 | Changed Molecular Trait Datasets to Molecular Traits in the Type•••drop-down on the home page
* wqflask/wqflask/api_gen_menu.py - Changed where Molecular Trait
Datasets was hardcoded to Molecular Traits
| zsloan |
| 2020-08-20 | Merge branch 'testing' of github.com:genenetwork/genenetwork2 into testing | zsloan |
| 2020-08-20 | Use dataTables.colResize.js and naturalSort from guix | BonfaceKilz |
| 2020-08-20 | Use buttons.colVis.min.js from guix | BonfaceKilz |
| 2020-08-20 | Use buttons.bootstrap.css from guix | BonfaceKilz |
| 2020-08-20 | Use scroller.dataTables.min.css from guix | BonfaceKilz |
| 2020-08-20 | Use dataTables.colReorder.js from guix | BonfaceKilz |
| 2020-08-20 | Use jquery.dataTables.js from guix | BonfaceKilz |
| 2020-08-20 | Use dataTables.buttons.min.js from guix | BonfaceKilz |
| 2020-08-20 | Use buttons.dataTables.min.css from guix | BonfaceKilz |
| 2020-08-19 | Added Invert button to collection page•••* wqflask/wqflask/templates/collections/view.html - Added the Invert
button back to the collection page; it was removed in the past but Rob
decided it should be re-added
| zsloan |
| 2020-08-19 | Tools used from the collection page now use all traits if no rows are•••checked and there are fewer than 100 traits in the table
* wqflask/wqflask/static/new/javascript/search_results.js - Created
get_traits_from_table function to get the list of traits and check if
none are selected, and also renamed the previous function also called
get_traits_from_table to submit_traits_to_export_or_bnw since that
better describes what the function does
| zsloan |
| 2020-08-19 | Show short labels by default in Correlation Matrix•••* wqflask/wqflask/templates/correlation_matrix.html - remove display:
none for short label div
| zsloan |
| 2020-08-17 | Merge branch 'testing' of github.com:genenetwork/genenetwork2 into testing | zsloan |
| 2020-08-18 | Fix positioning for many instances of text in the mapping figure•••* wqflask/wqflask/marker_regression/display_mapping_results.py: Many text
instances had their positions changed by the switch from piddle to PIL. Change
various Y offsets and in some cases changing the logic of the way text is
positioned related to its length and font size.
* wqflask/wqflask/static/fonts/verdanab.ttf: Add bold Verdana, since there needs
to be a separate font file for bold text.
| zsloan |
| 2020-08-17 | Placed X/Y trait info before the table on the correlation scatterplot•••page
* wqflask/wqflask/templates/corr_scatterplot.html - reordered table and
X/Y trait info divs
| zsloan |
| 2020-08-10 | Add fonts for pillow•••* wqflask/wqflask/marker_regression/display_mapping_results.py: replace piddle
method with PIL.ImageFont
* wqflask/wqflask/static/fonts: Add fonts in path
| Pjotr Prins |
| 2020-08-08 | Add a basic test for test_display_marking_results.py•••* wqflask/tests/wqflask/marker_regression/__init__.py: Add it
* wqflask/tests/wqflask/marker_regression/test_display_marking_results.py: Check
that PIL colors are being used instead of the deprecated Piddle colors.
| BonfaceKilz |
| 2020-08-08 | Change Y Coodinate system•••* wqflask/wqflask/marker_regression/display_mapping_results.py: Piddle seemed to
centre text about the given Y coordinate, while Pillow requires specification to
top-left corner of the text. This slight change means text all over the image is
displaced somewhat, and this fixes the coordinate system for some of the text.
| Muriithi Frederick Muriuki |
| 2020-08-08 | Fix placement for axes labels•••* wqflask/wqflask/marker_regression/display_mapping_results.py: Fix the
placement for the axes labels.
| Muriithi Frederick Muriuki |
| 2020-08-08 | Use TEXT_Y_DISPLACEMENT instead of magic numbers•••* wqflask/wqflask/marker_regression/display_mapping_results.py: Use
TEXT_Y_DISPLACEMENT instead of magic numbers to help with making it clear that
the drawn text is displaced somewhat.
| Muriithi Frederick Muriuki |
| 2020-08-08 | Give rectangles black outlines•••* wqflask/wqflask/marker_regression/display_mapping_results.py: Give the
rectangles black outlines to correspond to earlier drawings.
| Muriithi Frederick Muriuki |
