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take dataset as an optional argument (to avoid having to pointlessly create it)
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See: https://is.gd/pL7IJF
Ran:
find . \( -type d -name .git -prune \) -o -type f -print0 | xargs -0 sed -i 's/(object)//g'
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* wqflask/base/trait.py (jsonable_table_row): Delete it.
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necessary for them to show up correctly when selecting traits from collections in pop-up windows, like when selecting cofactors for mapping)
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resulting from a trait missing both pre_publication_description and pubmed ID
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and added an assert that 'name' is passed instead of using if/else, since it should always be passed
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Feature/corr table changes
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for genotype/snp cofactors (the code previously only accounted for
probeset/phenotype cofactors, so it was treating genotypes/snps like
phenotype traits)
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cofactors were genotypes (because it tried to get the
"description_display" which doesn't exist for genotype traits)
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ID for the purposes of showing pre-publication abbreviation/description
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* wqflask/wqflask/wgcna/wgcna_analysis.py: Apply pep8
* wqflask/wqflask/collect.py: Ditto
* wqflask/base/trait.py: Ditto
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* wqflask/base/trait.py (retrieve_trait_info): Add extra param to
ignore errors such as: "utf-8 codec can't decode byte 0xb5 in position
0: invalid start byte" thrown in Python3.
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github.com:BonfaceKilz/genenetwork2 into build/python3-migration
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* wqflask/base/trait.py (retrieve_trait_info): If the
description_string or discription_display value return a None object,
evaluate to an empty string. Fixes errors related to *len(None)*.
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* wqflask/base/trait.py (retrieve_trait_info): If the
description_string or discription_display value return a None object,
evaluate to an empty string. Fixes errors related to *len(None)*.
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* wqflask/base/trait.py: Fixes error parsing error: "(GeneNetwork
error: float argument required, not NoneType)"
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* wqflask/base/trait.py (retrieve_trait_info): Convert "target_string"
to a str, otherwise an exception will be thrown if it's None.
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* wqflask/base/trait.py: Apply pep8.
* wqflask/utility/authentication_tools.py: Ditto.
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* wqflask/base/trait.py: Remove python2 codecs.BOM_UTF8 methods.
* wqflask/wqflask/search_results.py: Remove utf-8 decode method on string.
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Mysqldb's escape returns a binary string. Use utils.db_tools which adds an extra
step of converting the binary string to a string.
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See: <https://docs.python.org/2/library/2to3.html#2to3fixer-future>
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See: <https://docs.python.org/2/library/2to3.html#2to3fixer-unicode>
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* wqflask/base/trait.py: Remove unused imports
* wqflask/db/call.py (Bench): Add urllib2 fallback for python2
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See: <https://docs.python.org/2/library/2to3.html#2to3fixer-urllib>
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See: <https://docs.python.org/2/library/2to3.html#2to3fixer-urllib>
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* wqflask/base/trait.py: See
<https://docs.python.org/2/library/2to3.html#2to3fixer-repr>
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Run `2to3-3.8 -f raise -w .`
See: <https://docs.python.org/2/library/2to3.html#2to3fixer-raise>
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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>
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figure out the real solution to that issue
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where a trait is authenticated twice
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something that automatically inserts resources with default privileges
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and also simplified the check_owner_or_admin function a little
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- 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
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