| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 2021-04-30 | autopep8: Fix W504 | BonfaceKilz | |
| 2021-04-29 | Merge branch 'testing' into Feature/Add-upload-data-forms | BonfaceKilz | |
| 2021-04-29 | Run `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' | |||
| 2021-04-29 | base: trait: Remove unused function | BonfaceKilz | |
| * wqflask/base/trait.py (jsonable_table_row): Delete it. | |||
| 2021-04-28 | Added 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) | |||
| 2021-03-03 | Checked if pre_publication_description is NULL, because there was an error ↵ | zsloan | |
| resulting from a trait missing both pre_publication_description and pubmed ID | |||
| 2021-02-18 | Fixed missing colon | zsloan | |
| 2021-02-18 | Fixed checking permissions in trait.py | zsloan | |
| 2021-02-11 | Ensure trait description_display is set | zsloan | |
| 2020-12-07 | Changed 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 | |||
| 2020-12-01 | Merge pull request #482 from zsloan/feature/corr_table_changes | zsloan | |
| Feature/corr table changes | |||
| 2020-11-18 | Fixed issue where the cofactor trait descriptions didn't work correctly | zsloan | |
| for genotype/snp cofactors (the code previously only accounted for probeset/phenotype cofactors, so it was treating genotypes/snps like phenotype traits) | |||
| 2020-11-18 | Fixed issue that was causing scatterplot cofactors to not work if the | zsloan | |
| cofactors were genotypes (because it tried to get the "description_display" which doesn't exist for genotype traits) | |||
| 2020-11-11 | Switched checking if a trait is confidential to checking if it has a pubmed ↵ | zsloan | |
| ID for the purposes of showing pre-publication abbreviation/description | |||
| 2020-10-12 | Merge branch 'testing' into build/python3-migration | BonfaceKilz | |
| 2020-10-09 | Apply PEP 8 to buffer | BonfaceKilz | |
| * wqflask/wqflask/wgcna/wgcna_analysis.py: Apply pep8 * wqflask/wqflask/collect.py: Ditto * wqflask/base/trait.py: Ditto | |||
| 2020-10-02 | Ignore utf-8 encoding errors | BonfaceKilz | |
| * 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. | |||
| 2020-10-01 | Convert trait attributes to utf-8 strings if they were bytes | BonfaceKilz | |
| 2020-09-28 | Merge branch 'build/python3-migration' of ↵ | BonfaceKilz | |
| github.com:BonfaceKilz/genenetwork2 into build/python3-migration | |||
| 2020-09-28 | Fix casting error | BonfaceKilz | |
| * 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)*. | |||
| 2020-09-28 | Merge branch 'testing' into build/python3-migration | BonfaceKilz | |
| 2020-09-28 | Fix casting error | BonfaceKilz | |
| * 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)*. | |||
| 2020-09-28 | Convert None to "" in if statement | BonfaceKilz | |
| * wqflask/base/trait.py: Fixes error parsing error: "(GeneNetwork error: float argument required, not NoneType)" | |||
| 2020-09-17 | Convert "target_string" to a str type | BonfaceKilz | |
| * wqflask/base/trait.py (retrieve_trait_info): Convert "target_string" to a str, otherwise an exception will be thrown if it's None. | |||
| 2020-09-17 | Apply pep8 | BonfaceKilz | |
| * wqflask/base/trait.py: Apply pep8. * wqflask/utility/authentication_tools.py: Ditto. | |||
| 2020-08-27 | Remove python2 string processing to utf-8 | BonfaceKilz | |
| * wqflask/base/trait.py: Remove python2 codecs.BOM_UTF8 methods. * wqflask/wqflask/search_results.py: Remove utf-8 decode method on string. | |||
| 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 | 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 | Rename "unicode" to "str" | BonfaceKilz | |
| See: <https://docs.python.org/2/library/2to3.html#2to3fixer-unicode> | |||
| 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 | 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 | 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> | |||
| 2020-07-21 | 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 | |||
| 2020-06-20 | 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 | |||
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index : genenetwork2 | |
| GeneNetwork (2nd generation) |
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