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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
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Use d3-tip from guix
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* wqflask/wqflask/templates/new_security/not_authenticated.html -
Changed "this" to "these" since "data" is plural
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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).
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* wqflask/wqflask/templates/correlation_matrix.html: Fetch chroma from guix
profile
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BonfaceKilz/chore/delete-datatables-extensions-from-guix
Delete dataTables and it's extensions from git
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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
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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
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* wqflask/wqflask/static/new/packages/DataTables/: Delete folder.
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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
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* wqflask/wqflask/user_login.py - Added send_invitation_email function,
which does what it says
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datasets
* wqflask/base/data_set.py - Added fetchone() to g.db.execute() which is
what was causing the error
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BonfaceKilz/Build/add-scientific-js-datatables-plugin
Build/add scientific js datatables plugin
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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)
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BonfaceKilz/refactor/extract-htmlgen-methods-to-wrapper-class
Refactor/extract htmlgen methods to wrapper class
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* wqflask/wqflask/marker_regression/display_mapping_results.py
(HtmlGenWrapper)[create_image_tag]: Remove "src" and "alt" as function
parameters.
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* wqflask/wqflask/marker_regression/display_mapping_results.py
(DisplayMappingResults): Replace direct calls to HtmlGen with methods from
the constructed wrapper class "HtmlGenWrapper".
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* wqflask/wqflask/marker_regression/display_mapping_results.py: Add new class
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* wqflask/tests/wqflask/marker_regression/test_display_mapping_results.py: Add
new tests
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* wqflask/wqflask/marker_regression/display_mapping_results.py: Remove unused
imports and add fix some pylint errors
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* 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.
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* wqflask/tests/wqflask/marker_regression/test_display_mapping_results.py:
Rename test_display_marking_results.py to test_display_mapping_results.py
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* wqflask/tests/wqflask/api/test_gen_menu.py: Update assertion. Result data
introduced in 092212df
Signed-off-by: BonfaceKilz <bonfacemunyoki@gmail.com>
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* wqflask/wqflask/marker_regression/display_mapping_results.py - defined
im_drawer in drawHaplotypeBand to fix errror and removed an unused
import
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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
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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
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drop-down on the home page
* wqflask/wqflask/api_gen_menu.py - Changed where Molecular Trait
Datasets was hardcoded to Molecular Traits
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* 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
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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
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* wqflask/wqflask/templates/correlation_matrix.html - remove display:
none for short label div
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