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* .github/ISSUE_TEMPLATE/bug_report.md: Update environment setup
section
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a separate file (initialize_show_trait_tables.js). The biggest
complication was getting the order of attributes in the rows to sync
with the order of atribute namees in the column headers. Previously this
logic was all in the template.
* wqflask/base/webqtlCaseData.py - added attribute first_attr_col as a
very awkward solution to passing the column position into the column
render function in situations where there are case attribute columns
(which can be variable in number)
* wqflask/wqflask/show_trait/show_trait.py - Replace "attribute_names"
in js_data with "attributes" (which allows the JS access to more
information) and also pass new se_exists and
has_num_cases variables with js_data, so the javascript has access to
whether or not those columns exist in the table
* wqflask/wqflask/static/new/javascript/show_trait.js - Change case
attribute-related logic to use js_data.attributes instead of
js_data.attribute_names
* wqflask/wqflask/templates/show_trait.html - Removed table
initialization from template
* wqflask/wqflask/static/new/javascript/initialize_show_trait_tables.js
- new file that initializes tables and reproduces what the template
logic used to do with JS logic
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* wqflask/tests/utility/test_hmac.py: Mock app.config's
"SECRET_HMAC_CODE" value.
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Tests/test auth and utf8
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* wqflask/utility/hmac.py: Apply pep8 and fix typo.
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* wqflask/tests/utility/test_hmac.py: New tests.
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SampleList instead of calling the method
* wqflask/wqflask/show_trait/show_trait.py - see above
* wqflask/wqflask/templates/show_trait.html - see above + removed some
commented out code
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that when converted to a dict (which is needed to use it in the
javascript)
* wqflask/wqflask/show_trait/SampleList.py - Directly set se_exists as a
property of SampleList instead of requiring a method be called; I could
have set self.se_exists by calling the se_exists method, but that would
have resulted in the convoluted line "self.se_exists = self.se_exists()"
and the se_exists method only consisted of one line anyways
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* wqflask/tests/base/test_trait.py: New tests.
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* wqflask/utility/authentication_tools.py: Apply pep8 formatting to
file.
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* wqflask/tests/utility/test_authentication_tools.py: Add them.
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* wqflask/utility/authentication_tools.py
(check_resource_availability): Combine if statements into one boolean
check in one if branch.
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Catches bugs in:
-
https://github.com/genenetwork/genenetwork2/pull/422/commits/70dbeeb5832711ed5271434e482c18bc7ea095b8
* wqflask/tests/utility/test_authentication_tools.py: New file. Add
tests for "check_resource_availability".
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* wqflask/tests/base/test_data_set.py: Update failing tests introduced
by the change in 301bdd2f4.
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* wqflask/wqflask/templates/show_trait.html - Imported scroller (from
the Google cdn temporarily for testing) and activated it for the sample
tables, as well as disabled options that conflicted with it (like
paging: false)
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authorization/security guide
* wqflask/wqflask/views.py - Added endpoint for info page and
authorization/security tutorial
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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
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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
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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
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* 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
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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
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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
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places N/As at the bottom regardless of search direction
* wqflask/wqflask/static/new/javascript/search_results.js - created
"natural-minus-na" sort
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BonfaceKilz/fix/use-correct-path-give-a-path-location
Fix/use correct path give a path location
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* 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>
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* 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.
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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
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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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Build/use md5 js from guix
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* test/requests/link_checker.py: Add it.
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Build/remove cdns
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* 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
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Add missing apostrophe in url_for args
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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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* test/requests/link_checker.py (check_packaged_js_files): Add it.
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Add github templates for filing bugs, user stories/ features and PRs
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Build/add chroma js
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