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2022-06-13Check for chromosome of 'Un' and print location as 'Not available' in such caseszsloan
2022-03-25Fix issues that prevented genotype traits from being added to collectionszsloan
Some of this was caused by heatmaps supporting code; that code should probably pass the traits differently than the way it does in the "trait_info_str" function
2021-10-22Replace hardcoded GN proxy URLs in trait.py with one pulled from settingszsloan
2021-08-20Fixed some logic in trait.py that could cause a problem if a dataset_name ↵zsloan
was passed that wasn't Temp
2021-06-16Changed the function jsonable in trait.py to return a couple extra fields + ↵zsloan
take dataset as an optional argument (to avoid having to pointlessly create it)
2021-04-30autopep8: Fix W504BonfaceKilz
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'
2021-04-29base: trait: Remove unused functionBonfaceKilz
* wqflask/base/trait.py (jsonable_table_row): Delete it.
2021-04-28Added something to jsonable in trait.py to account for temp traits (this is ↵zsloan
necessary for them to show up correctly when selecting traits from collections in pop-up windows, like when selecting cofactors for mapping)
2021-03-03Checked if pre_publication_description is NULL, because there was an error ↵zsloan
resulting from a trait missing both pre_publication_description and pubmed ID
2021-02-18Fixed missing colonzsloan
2021-02-18Fixed checking permissions in trait.pyzsloan
2021-02-11Ensure trait description_display is setzsloan
2020-12-07Changed the logic in create_trait so that permissions should always be set, ↵zsloan
and added an assert that 'name' is passed instead of using if/else, since it should always be passed
2020-12-01Merge pull request #482 from zsloan/feature/corr_table_changeszsloan
Feature/corr table changes
2020-11-18Fixed issue where the cofactor trait descriptions didn't work correctlyzsloan
for genotype/snp cofactors (the code previously only accounted for probeset/phenotype cofactors, so it was treating genotypes/snps like phenotype traits)
2020-11-18Fixed issue that was causing scatterplot cofactors to not work if thezsloan
cofactors were genotypes (because it tried to get the "description_display" which doesn't exist for genotype traits)
2020-11-11Switched checking if a trait is confidential to checking if it has a pubmed ↵zsloan
ID for the purposes of showing pre-publication abbreviation/description
2020-10-12Merge branch 'testing' into build/python3-migrationBonfaceKilz
2020-10-09Apply PEP 8 to bufferBonfaceKilz
* wqflask/wqflask/wgcna/wgcna_analysis.py: Apply pep8 * wqflask/wqflask/collect.py: Ditto * wqflask/base/trait.py: Ditto
2020-10-02Ignore utf-8 encoding errorsBonfaceKilz
* 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.
2020-10-01Convert trait attributes to utf-8 strings if they were bytesBonfaceKilz
2020-09-28Merge branch 'build/python3-migration' of ↵BonfaceKilz
github.com:BonfaceKilz/genenetwork2 into build/python3-migration
2020-09-28Fix casting errorBonfaceKilz
* 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)*.
2020-09-28Merge branch 'testing' into build/python3-migrationBonfaceKilz
2020-09-28Fix casting errorBonfaceKilz
* 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)*.
2020-09-28Convert None to "" in if statementBonfaceKilz
* wqflask/base/trait.py: Fixes error parsing error: "(GeneNetwork error: float argument required, not NoneType)"
2020-09-17Convert "target_string" to a str typeBonfaceKilz
* wqflask/base/trait.py (retrieve_trait_info): Convert "target_string" to a str, otherwise an exception will be thrown if it's None.
2020-09-17Apply pep8BonfaceKilz
* wqflask/base/trait.py: Apply pep8. * wqflask/utility/authentication_tools.py: Ditto.
2020-08-27Remove python2 string processing to utf-8BonfaceKilz
* wqflask/base/trait.py: Remove python2 codecs.BOM_UTF8 methods. * wqflask/wqflask/search_results.py: Remove utf-8 decode method on string.
2020-08-27Replace mysqldb's "escape" with the one from utils.db_toolsBonfaceKilz
Mysqldb's escape returns a binary string. Use utils.db_tools which adds an extra step of converting the binary string to a string.
2020-08-27Replace "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>
2020-08-26Rename "unicode" to "str"BonfaceKilz
See: <https://docs.python.org/2/library/2to3.html#2to3fixer-unicode>
2020-08-20Add backward support for urllibBonfaceKilz
* wqflask/base/trait.py: Remove unused imports * wqflask/db/call.py (Bench): Add urllib2 fallback for python2
2020-08-19Remove extra whitespace(or add it) from comma separated itemsBonfaceKilz
See: <https://docs.python.org/2/library/2to3.html#2to3fixer-urllib>
2020-08-19Handle the rename of urllib and urllib2 to the urllib packageBonfaceKilz
See: <https://docs.python.org/2/library/2to3.html#2to3fixer-urllib>
2020-08-19Replace backtick repr with the repr() functionBonfaceKilz
* wqflask/base/trait.py: See <https://docs.python.org/2/library/2to3.html#2to3fixer-repr>
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>
2020-08-19Fix 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>
2020-07-21Fixed 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
2020-06-20Fixed 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
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