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2020-08-27Replace mysqldb's "escape" with the one from utils.db_tools...Mysqldb's escape returns a binary string. Use utils.db_tools which adds an extra step of converting the binary string to a string. BonfaceKilz
2020-08-27Remove redundant methods which are defined elsewhere...* wqflask/base/data_set.py: Delete "create_in_clause", and "mescape" which are defined in "utility.db_tools" BonfaceKilz
2020-08-27Remove unused importsBonfaceKilz
2020-08-27Replace "string.split" & "string.join" with python's inbuilt methodsBonfaceKilz
2020-08-26Remove "from __future__ import new_feature" statements...See: <https://docs.python.org/2/library/2to3.html#2to3fixer-future> BonfaceKilz
2020-08-26Replace "__cmp__" with "__eq__" magic method...* wqflask/base/GeneralObject.py: "__cmp__" is no longer used in python3. See: <https://stackoverflow.com/questions/8276983/why-cant-i-use-the-method-cmp-in-python-3-as-for-python-2> BonfaceKilz
2020-08-26Rename "unicode" to "str"...See: <https://docs.python.org/2/library/2to3.html#2to3fixer-unicode> BonfaceKilz
2020-08-25Fixed 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
2020-08-20Handle module renames in the standard library...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> BonfaceKilz
2020-08-20Disable python2 QTLReaper...* wqflask/base/data_set.py: Remove usage of "reaper" to load datasets BonfaceKilz
2020-08-20Add backward support for urllib...* wqflask/base/trait.py: Remove unused imports * wqflask/db/call.py (Bench): Add urllib2 fallback for python2 BonfaceKilz
2020-08-19Remove extra whitespace(or add it) from comma separated items...See: <https://docs.python.org/2/library/2to3.html#2to3fixer-urllib> BonfaceKilz
2020-08-19Make Python more idiomatic...Run `2to3-3.8 -f idioms -w .` See: <https://docs.python.org/2/library/2to3.html#2to3fixer-idioms> BonfaceKilz
2020-08-19Handle the rename of urllib and urllib2 to the urllib package...See: <https://docs.python.org/2/library/2to3.html#2to3fixer-urllib> BonfaceKilz
2020-08-19Replace backtick repr with the repr() function...* wqflask/base/trait.py: See <https://docs.python.org/2/library/2to3.html#2to3fixer-repr> BonfaceKilz
2020-08-19Wrap `raise` statements in parenthesis...Run `2to3-3.8 -f raise -w .` See: <https://docs.python.org/2/library/2to3.html#2to3fixer-raise> BonfaceKilz
2020-08-19Replace `izip` with python's built-in equivalent...Run `2to3-3.8 -f itertools -w . && 2to3-3.8 -f itertools_imports -w .` See: <https://docs.python.org/2/library/2to3.html#2to3fixer-itertools_imports> and <https://docs.python.org/2/library/2to3.html#2to3fixer-itertools> BonfaceKilz
2020-08-19Fix dictionary iteration methods...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> BonfaceKilz
2020-07-27Clean up webqtlCaseData class...* wqflask/base/webqtlCaseData.py (webqtlCaseData): - Remove obsolete 'Object' from Class inheritance - Replace 'str' with 'case_data_string' variable- it collides with python in-builts - Use pythonic 'is Not None' form - Remove redundancy in 'if' forms - Update copyright header BonfaceKilz
2020-07-27Abstract away redundant code into set_dataset_key method...* wqflask/base/data_set.py (Dataset): - Add set_dataset_key - Remove __call__ method BonfaceKilz
2020-07-27Use the correct redis instance inside object...* wqflask/base/data_set.py (DatasetType): Use object's redis instance BonfaceKilz
2020-07-25Removing bimbam check. We'll get rid of bimbam anyway.Pjotr Prins
2020-07-24Merge pull request #409 from BonfaceKilz/Build/add-tests...Build/add testszsloan
2020-07-24Fixed queries that were wrongly returning Data IDs as Nszsloan
2020-07-24Remove unreachable conditional...* wqflask/base/GeneralObject.py(__getattr__): remove if statement that is unreachable BonfaceKilz
2020-07-24Inject redis instance into DatasetType class...* wqflask/base/data_set.py(DatasetType): - Rename Redis instance to r to avoid confusion and name collisions - Inject the redis instance into Dataset_Types class to make it easier to test - Rename Dataset_Types class to DatasetType class BonfaceKilz
2020-07-24Apply autopep-8...* wqflask/base/data_set.py: Apply autopep-8 BonfaceKilz
2020-07-24Apply autopep-8...* wqflask/base/GeneralObject.py: Replace tabs with 4 spaces BonfaceKilz
2020-07-24Remove unused importBonfaceKilz
2020-07-24Added binary casting to phenotype trait info query to fix unicode issuezsloan
2020-07-21Fixed issue that caused group codes to be wrong sometimeszsloan
2020-07-14Added binary casting to phenotype trait info query to fix unicode issuezsloan
2020-07-08Removed remaining unused references to the old qtlreaperzsloan
2020-07-06Temporarily commented out the line in trait.py doing the encoding until we fi...zsloan
2020-07-06Fixed some of the logic with how traits are authenticated to avoid situation ...zsloan
2020-06-29Change that hopefully fixes some encoding stuffzsloan
2020-06-24Temporary partial fix to issue of resources without info; need to add somethi...zsloan
2020-06-22Fixed issue with temp traits not working for trait page functions like correl...zsloan
2020-06-20Fixed ports for proxy (though I need to add the port to global variables) and...zsloan
2020-06-20Added some admin functionality and fixed issue with temp traitszsloan
2020-06-17Adding all the authentication stuffzsloan
2020-06-05Commiting other current group/resource management code, plus the new fileszsloan
2020-06-04Added back in trait info queries for situations where the proxy isn't runningzsloan
2020-06-04Really should have split this into many more commits:...- Now use proxy to pull trait data and hide traits/results that the user doesn't have view permission for - Created a factory method for creating trait ob so it can return None when user doesn't have view permissions (this is why such a large number of files are changed) - Added metadata to permutation export - Added current group management code - Added fixed password verification e-mail code zsloan
2020-05-28Added lines calling proxy for publish datasets + added some resource redis qu...zsloan
2020-05-21Made search result table width variable again and fixed row highlighting, tho...zsloan
2020-05-07Fixed blatseq issue and geno correlation issueblatseq_fixzsloan
2020-05-07Committing current progress on group manager + a minor fix in dataset.pyzsloan
2020-04-27Added timeout for when/if it does the REST API query, so it doesn't hang inde...zsloan
2020-04-27Made change that should allow dataset structure to be loaded from Redis inste...zsloan
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