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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>
2020-08-19Replace `izip` with python's built-in equivalentBonfaceKilz
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>
2020-08-19Fix 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>
2020-07-27Clean up webqtlCaseData classBonfaceKilz
* 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
2020-07-27Abstract away redundant code into set_dataset_key methodBonfaceKilz
* wqflask/base/data_set.py (Dataset): - Add set_dataset_key - Remove __call__ method
2020-07-27Use the correct redis instance inside objectBonfaceKilz
* wqflask/base/data_set.py (DatasetType): Use object's redis instance
2020-07-25Removing bimbam check. We'll get rid of bimbam anyway.Pjotr Prins
2020-07-24Merge pull request #409 from BonfaceKilz/Build/add-testszsloan
Build/add tests
2020-07-24Fixed queries that were wrongly returning Data IDs as Nszsloan
2020-07-24Remove unreachable conditionalBonfaceKilz
* wqflask/base/GeneralObject.py(__getattr__): remove if statement that is unreachable
2020-07-24Inject redis instance into DatasetType classBonfaceKilz
* 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
2020-07-24Apply autopep-8BonfaceKilz
* wqflask/base/data_set.py: Apply autopep-8
2020-07-24Apply autopep-8BonfaceKilz
* wqflask/base/GeneralObject.py: Replace tabs with 4 spaces
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 ↵zsloan
figure out the real solution to that issue
2020-07-06Fixed some of the logic with how traits are authenticated to avoid situation ↵zsloan
where a trait is authenticated twice
2020-06-29Change that hopefully fixes some encoding stuffzsloan
2020-06-24Temporary partial fix to issue of resources without info; need to add ↵zsloan
something that automatically inserts resources with default privileges
2020-06-22Fixed issue with temp traits not working for trait page functions like ↵zsloan
correlation or mapping
2020-06-20Fixed 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
2020-06-20Added 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: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
2020-05-28Added lines calling proxy for publish datasets + added some resource redis ↵zsloan
queries and a missing import for the hmac functions
2020-05-21Made 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
2020-05-07Fixed 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 ↵zsloan
indefinitely
2020-04-27Made change that should allow dataset structure to be loaded from Redis ↵zsloan
instead of the JSON file without breaking things
2020-04-26Removed the code that was still writing the database menu JSONzsloan
2020-04-24Replaced hard-coded instances of GN2 urls with ones pulled from settings filezsloan
2020-04-24Made a fix that should prevent the issue where new datasets cause an error ↵zsloan
when they're in search results
2020-04-06Added Mean column for phenotype traits in search and global search result tableszsloan
2020-03-27Fixed issue where GEMMA wasn't showing up for certain groupszsloan
2020-03-27Added integration for using RData files with R/qtl, plus some other changes ↵zsloan
to how it decides which mapping methods to display on the trait page
2020-03-09I think this should complete consolidating all the collections code.zsloan
2020-03-03Forgot to replace code referring to hmac function user_managerzsloan
2020-02-07Users can now add and do mapping on genotype files that only include a ↵zsloan
subset of samples/strains Also filtered the results used by Christian's genome browser, so now it should have an easier time loading when dealing with larger numbers of markers
2020-02-06Fixed encoding issuezsloan
2020-01-22Fixed issue that caused submitting temp traits to not workzsloan
2020-01-08Made change that I think should fix the unicode stuff once and for allzsloan
2019-12-17Added RGD link to trait page and removed Genotation link since it isn't workingzsloan
2019-12-04Added M to the possible non-number 'chromosome' nameszsloan
2019-12-04Fixed error that sometimes occurs if there's no mean expression and changed ↵zsloan
index page header style a little
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