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2021-04-30autopep8: Fix E20-E27BonfaceKilz
Run: python -m autopep8 --in-place --recrusive ./ --select\ E20,E211,E22,E224,E224,E225,E226,E227,E228,E231,E241,\ E242,E251,E252,E26,E265,E266,E27 -p 3
2021-04-29Merge branch 'testing' into Feature/Add-upload-data-formsBonfaceKilz
2021-04-29Run `sed -i 's/(object)//g'`BonfaceKilz
See: https://is.gd/pL7IJF Ran: find . \( -type d -name .git -prune \) -o -type f -print0 | xargs -0 sed -i 's/(object)//g'
2021-04-23Apply PEP-8BonfaceKilz
2021-04-23Move looped sql query into one statement in "get_species_groups"BonfaceKilz
It's in-efficient to have a sql query executed in a loop. As data grows, the query becomes slower. It's better to let sql handle such queries.
2021-04-23Remove stale commentsBonfaceKilz
2021-04-19Specify only getting the first two items after splitting the trait/dataset ↵zsloan
input string
2021-03-16Fixed encoding in load_json_from_redis to account for the first that column ↵zsloan
values are sometimes stored as bytes and sometimes as strings
2021-03-16Fixed encoding to make get_user_groups work properly, since the user IDs for ↵zsloan
groups in Redis are stored as strings
2021-03-16Removed unnecessary encoding of user_id from authentication_tools.pyzsloan
2021-02-18Remove the deocde since it was throwing an errorzsloan
2021-02-18Changed authentication_tools.py to account for encoding str as bytes and ↵zsloan
dealing with the permissions response either being a list or not a list (this should be temporary until I figure out what is going on here)
2021-02-17Fixed error caused by user IDs being encoded as byteszsloan
2021-01-06replace vars with vars_obj which is a function name in pythonAlexanderkabui
2020-12-18Added redirect_uri to the ORCID_AUTH_URL since it wasn't working due to ↵zsloan
missing this parameter
2020-11-02Created function for encoding the column value as bytes when fetching from ↵zsloan
the JSON-formatted string pulled from Redis (since this was needed after the Python 3 switchover) * wqflask/utility/redis_tools.py - Created function load_json_from_redis that encodes the key (column_value) when fetching a value from the JSON pulled from Redis
2020-10-28Use latin-1 encoding when converting hmac secret to bytesBonfaceKilz
* wqflask/utility/hmac.py (hmac_creation): Use latin-1 when serializing the hmac secret. This ensures that the behaviour of *verify_cookie* remains the same as in the python2 tip.
2020-09-26Merge branch 'testing' into build/python3-migrationBonfaceKilz
2020-09-18Apply pep8 formattingBonfaceKilz
2020-09-17Replace string arguments to "hmac.new" with bytearrayBonfaceKilz
Same as: https://github.com/genenetwork/genenetwork2/pull/422/commits/46443ec8d2cdfd7c60358a889d90a90e4f7daaf4
2020-09-17Apply pep8BonfaceKilz
* wqflask/base/trait.py: Apply pep8. * wqflask/utility/authentication_tools.py: Ditto.
2020-09-17Merge branch 'testing' into build/python3-migrationBonfaceKilz
2020-09-17Apply pep8BonfaceKilz
* wqflask/utility/hmac.py: Apply pep8 and fix typo.
2020-09-16Apply pep8BonfaceKilz
* wqflask/utility/authentication_tools.py: Apply pep8 formatting to file.
2020-09-16Remove unnecessary if branchBonfaceKilz
* wqflask/utility/authentication_tools.py (check_resource_availability): Combine if statements into one boolean check in one if branch.
2020-08-31Remove typo at beginning of lineBonfaceKilz
* wqflask/utility/authentication_tools.py: Remove accidental char at beginning of line.
2020-08-31Fixed issue that was causing updating resource default privileges to notzsloan
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).
2020-08-31Merge branch 'testing' into build/python3-migrationBonfaceKilz
2020-08-29Fixed issue where exporting traits would throw an error if a dataset'szsloan
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
2020-08-27Add check for empty group_code when adding a new resourceBonfaceKilz
* wqflask/utility/authentication_tools.py(add_new_resource): If group_code is "None", an error is thrown when you try to: `group_code + "_" + str(trait_id)`
2020-08-27Replace string arguments to "hmac.new" with bytearrayBonfaceKilz
See: <https://stackoverflow.com/questions/31848293/python3-and-hmac-how-to-handle-string-not-being-binary>
2020-08-27Add global method to convert binary string to plain stringBonfaceKilz
* wqflask/utility/db_tools.py: escape_string returns a binary string which introduces a bug when composing sql query string. The escaped strings have to be converted to plain text.
2020-08-27Replace "string.split" & "string.join" with python's inbuilt methodsBonfaceKilz
2020-08-26Remove "from __future__ import new_feature" statementsBonfaceKilz
See: <https://docs.python.org/2/library/2to3.html#2to3fixer-future>
2020-08-26Replace calls to "basestring with "str""BonfaceKilz
See: <https://docs.python.org/2/library/2to3.html#2to3fixer-basestring>
2020-08-26Update corestats importBonfaceKilz
* wqflask/utility/Plot.py: import corestats from the utility module.
2020-08-26Merge branch 'testing' into build/python3-migrationBonfaceKilz
2020-08-24Remove unused importsBonfaceKilz
* 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.
2020-08-24The function draw_rotated_text_ was writing an image to /tmp, which GN2zsloan
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
2020-08-23Use Python3 string methodsBonfaceKilz
* wqflask/utility/webqtlUtil.py (genRandStr): Replace "string.letters" with "string.ascii_letters".
2020-08-20Handle module renames in the standard libraryBonfaceKilz
Run: ``` 2to3-3.8 -f imports -w . && \ 2to3-3.8 -f imports2 -w . ``` See: <https://docs.python.org/2/library/2to3.html#2to3fixer-imports> and <https://docs.python.org/2/library/2to3.html#2to3fixer-imports2>
2020-08-19Remove extra whitespace(or add it) from comma separated itemsBonfaceKilz
See: <https://docs.python.org/2/library/2to3.html#2to3fixer-urllib>
2020-08-19Make Python more idiomaticBonfaceKilz
Run `2to3-3.8 -f idioms -w .` See: <https://docs.python.org/2/library/2to3.html#2to3fixer-idioms>
2020-08-19Rename xrange() to range() and wrap existing range() calls with listBonfaceKilz
See: <https://docs.python.org/2/library/2to3.html#2to3fixer-xrange>
2020-08-19Wrap `raise` statements in parenthesisBonfaceKilz
Run `2to3-3.8 -f raise -w .` See: <https://docs.python.org/2/library/2to3.html#2to3fixer-raise>
2020-08-19Convert the old not-equal syntax, <>, to !=BonfaceKilz
Run `2to3-3.8 -f ne -w .` See: <https://docs.python.org/2/library/2to3.html#2to3fixer-ne>
2020-08-19Fix dictionary iteration methodsBonfaceKilz
Run `2to3-3.8 -f dict -w .` See: <https://docs.python.org/2/library/2to3.html#2to3fixer-dict> and <https://stackoverflow.com/questions/17695456/why-does-python-3-need-dict-items-to-be-wrapped-with-list>
2020-08-19Remove erroneous `if .. else` branchBonfaceKilz
* wqflask/utility/svg.py [roct, ellipse, SVGelement]: Raise only a single value error if either height or width is not defined. Fixes parsing error when running `2to3-3.8 -f apply -w .`
2020-08-19Wrap `map()` in a `list` callBonfaceKilz
Run `2to3-3.8 -f map -w .` See: <https://docs.python.org/2/library/2to3.html#2to3fixer-map>
2020-08-18Apply pep8BonfaceKilz
* wqflask/utility/svg.py: Apply pep8 to fix indentation error when running `2to3-3.8 -w .`: ```` RefactoringTool: Can't parse ./wqflask/utility/svg.py: IndentationError: unindent does not match any outer indentation level (<tokenize>, line 403) ````
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