genenetwork2 - GeneNetwork (2nd generation)

Age	Commit message (Collapse)	Author
2020-08-27	Replace mysqldb's "escape" with the one from utils.db_tools	BonfaceKilz
	Mysqldb's escape returns a binary string. Use utils.db_tools which adds an extra step of converting the binary string to a string.
2020-08-27	Remove redundant methods which are defined elsewhere	BonfaceKilz
	* wqflask/base/data_set.py: Delete "create_in_clause", and "mescape" which are defined in "utility.db_tools"
2020-08-27	Remove unused imports	BonfaceKilz

2020-08-27	Replace "string.split" & "string.join" with python's inbuilt methods	BonfaceKilz

2020-08-26	Remove "from __future__ import new_feature" statements	BonfaceKilz
	See: <https://docs.python.org/2/library/2to3.html#2to3fixer-future>
2020-08-26	Replace "__cmp__" with "__eq__" magic method	BonfaceKilz
	* 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>
2020-08-26	Rename "unicode" to "str"	BonfaceKilz
	See: <https://docs.python.org/2/library/2to3.html#2to3fixer-unicode>
2020-08-25	Fixed issue in DatasetType that caused an error when trying to load new	zsloan
	datasets * wqflask/base/data_set.py - Added fetchone() to g.db.execute() which is what was causing the error
2020-08-20	Handle module renames in the standard library	BonfaceKilz
	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>
2020-08-20	Disable python2 QTLReaper	BonfaceKilz
	* wqflask/base/data_set.py: Remove usage of "reaper" to load datasets
2020-08-20	Add backward support for urllib	BonfaceKilz
	* wqflask/base/trait.py: Remove unused imports * wqflask/db/call.py (Bench): Add urllib2 fallback for python2
2020-08-19	Remove extra whitespace(or add it) from comma separated items	BonfaceKilz
	See: <https://docs.python.org/2/library/2to3.html#2to3fixer-urllib>
2020-08-19	Make Python more idiomatic	BonfaceKilz
	Run `2to3-3.8 -f idioms -w .` See: <https://docs.python.org/2/library/2to3.html#2to3fixer-idioms>
2020-08-19	Handle the rename of urllib and urllib2 to the urllib package	BonfaceKilz
	See: <https://docs.python.org/2/library/2to3.html#2to3fixer-urllib>
2020-08-19	Replace backtick repr with the repr() function	BonfaceKilz
	* wqflask/base/trait.py: See <https://docs.python.org/2/library/2to3.html#2to3fixer-repr>
2020-08-19	Wrap `raise` statements in parenthesis	BonfaceKilz
	Run `2to3-3.8 -f raise -w .` See: <https://docs.python.org/2/library/2to3.html#2to3fixer-raise>
2020-08-19	Replace `izip` with python's built-in equivalent	BonfaceKilz
	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>
2020-08-19	Fix dictionary iteration methods	BonfaceKilz
	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>
2020-07-27	Clean up webqtlCaseData class	BonfaceKilz
	* 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
2020-07-27	Abstract away redundant code into set_dataset_key method	BonfaceKilz
	* wqflask/base/data_set.py (Dataset): - Add set_dataset_key - Remove __call__ method
2020-07-27	Use the correct redis instance inside object	BonfaceKilz
	* wqflask/base/data_set.py (DatasetType): Use object's redis instance
2020-07-25	Removing bimbam check. We'll get rid of bimbam anyway.	Pjotr Prins

2020-07-24	Merge pull request #409 from BonfaceKilz/Build/add-tests	zsloan
	Build/add tests
2020-07-24	Fixed queries that were wrongly returning Data IDs as Ns	zsloan

2020-07-24	Remove unreachable conditional	BonfaceKilz
	* wqflask/base/GeneralObject.py(__getattr__): remove if statement that is unreachable
2020-07-24	Inject redis instance into DatasetType class	BonfaceKilz
	* 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
2020-07-24	Apply autopep-8	BonfaceKilz
	* wqflask/base/data_set.py: Apply autopep-8
2020-07-24	Apply autopep-8	BonfaceKilz
	* wqflask/base/GeneralObject.py: Replace tabs with 4 spaces
2020-07-24	Remove unused import	BonfaceKilz

2020-07-24	Added binary casting to phenotype trait info query to fix unicode issue	zsloan

2020-07-21	Fixed issue that caused group codes to be wrong sometimes	zsloan

2020-07-14	Added binary casting to phenotype trait info query to fix unicode issue	zsloan

2020-07-08	Removed remaining unused references to the old qtlreaper	zsloan

2020-07-06	Temporarily commented out the line in trait.py doing the encoding until we ↵	zsloan
	figure out the real solution to that issue
2020-07-06	Fixed some of the logic with how traits are authenticated to avoid situation ↵	zsloan
	where a trait is authenticated twice
2020-06-29	Change that hopefully fixes some encoding stuff	zsloan

2020-06-24	Temporary partial fix to issue of resources without info; need to add ↵	zsloan
	something that automatically inserts resources with default privileges
2020-06-22	Fixed issue with temp traits not working for trait page functions like ↵	zsloan
	correlation or mapping
2020-06-20	Fixed ports for proxy (though I need to add the port to global variables) ↵	zsloan
	and also simplified the check_owner_or_admin function a little
2020-06-20	Added some admin functionality and fixed issue with temp traits	zsloan

2020-06-17	Adding all the authentication stuff	zsloan

2020-06-05	Commiting other current group/resource management code, plus the new files	zsloan

2020-06-04	Added back in trait info queries for situations where the proxy isn't running	zsloan

2020-06-04	Really should have split this into many more commits:	zsloan
	- 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
2020-05-28	Added lines calling proxy for publish datasets + added some resource redis ↵	zsloan
	queries and a missing import for the hmac functions
2020-05-21	Made search result table width variable again and fixed row highlighting, ↵	zsloan
	though later I need to go through and redo a bunch of CSS stuff
2020-05-07	Fixed blatseq issue and geno correlation issueblatseq_fix	zsloan

2020-05-07	Committing current progress on group manager + a minor fix in dataset.py	zsloan

2020-04-27	Added timeout for when/if it does the REST API query, so it doesn't hang ↵	zsloan
	indefinitely
2020-04-27	Made change that should allow dataset structure to be loaded from Redis ↵	zsloan
	instead of the JSON file without breaking things