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2021-05-05base: species: Rewrite IndChromosome using a dataclassBonfaceKilz
2021-05-05base: trait: Remove logging informationBonfaceKilz
The log adds unnecessary noise in addition to creating unwanted side-effects.
2021-05-05base: species: Rewrite TheSpecies class using a dataclassBonfaceKilz
2021-05-05base: species: Remove unused importBonfaceKilz
2021-05-05base: species: Format SQL queriesBonfaceKilz
2021-04-30autopep8: Run autopep8 100 times with target rulesBonfaceKilz
Rules used are: E20,E211,E22,E224,E224,E225,E226,E227,E228,E231,E241,E242, E251,E252,E26,E265,E266,E27,E301,E302,E303,E304,E305,E306, E401,E501,E70,E701,W291,W292,W293,W391,W504,E101,E11,E121, E122,E123,E124,E125,E126,E127,E128,E129,E131,E133
2021-04-30autopep8: Fix E121,E122,E123,EI24,E125,E126,E127,E128,E129,E131,E133BonfaceKilz
2021-04-30autopep8: Fix W504BonfaceKilz
2021-04-30autopep8: Fix W291, W292, W293, W391BonfaceKilz
2021-04-30autopep8: Fix E501BonfaceKilz
2021-04-30autopep8: Fix E301,E302,E303,E304,E305,E306BonfaceKilz
2021-04-30autopep8: Fix E20-E27BonfaceKilz
Run: python -m autopep8 --in-place --recrusive ./ --select\ E20,E211,E22,E224,E224,E225,E226,E227,E228,E231,E241,\ E242,E251,E252,E26,E265,E266,E27 -p 3
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.
2021-04-29base: data_set: Remove unused methodBonfaceKilz
* wqflask/base/data_set.py (Dataset.get_accession_id): Delete it.
2021-04-29base: data_set: Apply pep-8BonfaceKilz
2021-04-29base: data_set: Remove unused methodBonfaceKilz
* wqflask/base/data_set.py (riset): Delete class method.
2021-04-29base: data_set: Rewrite data_set using @dataclassBonfaceKilz
@dataclasses should be used to hold only data. Since dataset only encapsulates data, re-writing it using a dataclass makes it more readable and easier to follow.
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)
2021-04-23Remove stale commentsBonfaceKilz
2021-04-19Removed unused codezsloan
2021-03-17Added the RRID urls for mouse and rat to webqtlConfigzsloan
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
2021-02-18Changed DEFAULT_PERMISSIONS AND SUPER_PERMISSIONS to not have permissions be ↵zsloan
lists (I think the proxy expects them to not be lists, but then returns them as lists; need to check about this)
2021-02-18Fixed missing colonzsloan
2021-02-18Fixed checking permissions in trait.pyzsloan
2021-02-18Fixed SUPER_PRIVILEGES and DEFAULT_PRIVILEGESzsloan
2021-02-11Removed some log statementszsloan
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
2020-11-03Changed the syntax for the "sort" function in the docstring of GeneralObject ↵zsloan
to be compatible with Python 3 syntax * wqflask/base/GeneralObject.py - edited docstring to be correct for Python 3
2020-10-27Get the "first_attr_start_pos" from a samplelist instead of from each ↵zsloan
individual sample, because it was previously causing problems when only some samples had an N * wqflask/base/webqtlCaseData.py - Removed code getting first_attr_start_pos * wqflask/wqflask/show_trait/SampleList.py - Added code getting first_attr_start_pos and assigning it to all samples + removing one unnecessary sort * wqflask/wqflask/static/new/javascript/initialize_show_trait_tables.js - Fixed issue that was causing the N column to not be displayed
2020-10-20Merge branch 'testing' into build/python3-migrationBonfaceKilz
2020-10-19Merge branch 'testing' into scroller_testingzsloan
2020-10-12Merge branch 'testing' into build/python3-migrationBonfaceKilz
2020-10-09Merge pull request #458 from BonfaceKilz/tests/add-extra-tests-for-collectionsBonfaceKilz
Tests/add extra tests for collections
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
2020-10-08Fixed remaining issue that applies to all dataset typeszsloan
* wqflask/base/data_set.py - Fixed issue where there was an error when trying to take the len of the query results when there were no results
2020-10-08Fixed issue where new phenotype groups wouldn't be saved to the ↵zsloan
self.datasets property because the group name was used as the key (instead of the group name + "Publish", which is the full dataset name for phenotypes) * wqflask/base/data_set.py - Set "group_name" as a separate variable from "name" to avoid it being used as the key in self.datasets
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
2020-09-30Removed unused code from TempDataSet classzsloan
* wqflask/base/data_set.py - TempDataSet class contained some code referring to the SQL DB, but temp traits aren't stored in the SQL DB anymore
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
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-25 17:59:45 +0000