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path: root/wqflask/base/species.py
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2022-09-26Remove unused database_connection import from species.pyzsloan
2022-09-22Provide database cursor as argument for TheSpecies and ChromosomesFrederick Muriuki Muriithi
Provide the database cursor as an argument to the methods of the two classes: * wqflask.base.species.TheSpecies * wqflask.base.species.Chromosomes Also update dependent code to initialise and pass the cursor where these classes are used.
2022-09-20Revert "Use member variable `self.conn` to avoid test failure"Frederick Muriuki Muriithi
This reverts commit 4fafdfd8487ddf61105b2a5ca92534c8014c1db4. While using `self.conn.cursor()` works in the tests, it will not work in the application since the point of initialisation could be very different from the point where the 'property' is called.
2022-09-20Use member variable `self.conn` to avoid test failureFrederick Muriuki Muriithi
Use the `self.conn` variable to prevent test from failing.
2022-09-09Use `database_connection()`Frederick Muriuki Muriithi
Call the `database_connection()` function to get a connection to the database.
2022-09-08Simplify how chromosomes are fetchedMunyoki Kilyungi
* wqflask/base/species.py: Import "Any" and "Union". (TheSpecies): Add type hints. Get rid of redundant "if ... else" statement. (IndChromosome.mb_length): Add type hints. (Chromosomes): Inject conn and add type hints.
2022-09-08Replace g.db with database_connection() context managerMunyoki Kilyungi
* wqflask/base/mrna_assay_tissue_data.py: Replace "flask.g" with database_connection. (MrnaAssayTissueData.__init__): Use database_connection. (MrnaAssayTissueData.get_symbol_values_pairs): Ditto. * wqflask/base/species.py: Replace "Flask.g" imports with "database_connection". (Chromosomes.chromosomes): Use database_connection. * wqflask/base/trait.py: Import database_connection. (retrieve_trait_info): Use database_connection. * wqflask/utility/authentication_tools.py: Replace "flask.g" with database_connection. (get_group_code): Use database_connection. * wqflask/utility/helper_functions.py: Replace "flask.g" with "database_connection". (get_species_groups): Use database_connection. * wqflask/wqflask/db_info.py: Replace "Flask" and "g" with "database_connection". (InfoPage.get_info): Use database_connection. * wqflask/wqflask/do_search.py (DoSearch.execute): Use database_connection(). * wqflask/wqflask/external_tools/send_to_geneweaver.py: Replace "Flask" and "g" import with database_connection. (test_chip): Use database_connection. * wqflask/wqflask/external_tools/send_to_webgestalt.py: Replace "Flask, g" imports with database_connection. (test_chip): Use database_connection. * wqflask/wqflask/gsearch.py: Replace "Flask" and "g" import with database_connection. (GSearch.__init__): Use database_connection. * wqflask/wqflask/interval_analyst/GeneUtil.py (loadGenes): Use database_connection(). * wqflask/wqflask/show_trait/SampleList.py: Replace "flask.g import" with database_connection. (SampleList.get_attributes): Use database_connection. (SampleList.get_extra_attribute_values): Ditto. * wqflask/wqflask/show_trait/show_trait.py: Replace "Flask" and "g" import with database_connection. (ShowTrait.__init__): Use database_connection. (ShowTrait.get_external_links): Ditto. (get_nearest_marker): Ditto.
2021-05-05base: species: Remove redundant assignmentBonfaceKilz
2021-05-05base: chromosomes: Fetch the chromosomes lazilyBonfaceKilz
2021-05-05base: species: Rewrite Chromosomes using a dataclassBonfaceKilz
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: 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
2021-04-29Run `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'
2020-08-27Remove unused importsBonfaceKilz
2020-08-26Remove "from __future__ import new_feature" statementsBonfaceKilz
See: <https://docs.python.org/2/library/2to3.html#2to3fixer-future>
2018-10-11- Added fix for GEMMA LOCOzsloan
- Added all current SNP browser code (not complete yet) - Added change to convert_geno_to_bimbam that makes it ignore .geno files marked as "filler" (so ones where the .geno file is fake and we sometimes directly receive the genotypes as BIMBAM) - Changes TheSpecies object in species.py to accept species name as well as dataset name
2018-04-06Mapping figure output now gives more accurate informationzsloan
Committing partway through removing a bunch of unused code/files just in case something necessary gets removed
2016-06-23Logger: SQLPjotr Prins
2016-06-18Changed file permssions to non-executablePjotr Prins
2016-06-17Removed trailing spaces in .py and .js filesPjotr Prins
2014-06-25Added Karl's correlation matrix codeZachary Sloan
Improved the "scatterplot matrix" feature on the trait page so that it matches the chosen trait against every selected trait
2014-05-05Committing a bunch of changes related to integrating GEMMA andZachary Sloan
adding the correlation matrix page
2013-06-26Got code that creates DataSets object runningZachary Sloan
Fixed one genofile that had extra quotation marks in the comments that caused an error Defaults mb_graph_interval to 1 for species without chromosome lengths in megabases
2013-04-09Nick's code works fine with human dataZachary Sloan
Added option to limit results based on lod score (which also changes the y-axis of the plot)
2013-03-12Got cashing working with pickleZachary Sloan
2013-01-08Created IndChromosome class in species.py and wrote functions forZachary Sloan
chromosome-related attributes Began to try and pass qtlreaper results as js_data to use when drawing graphs
2013-01-08Deleted some unnecessary code in marker_regression.py and fixed some bugsZachary Sloan
Added a couple utility functions to the Chromosomes class in species.py
2013-01-03Began working on marker_regression.py and created Chromosomes classZachary Sloan
in species.py
2012-12-18Created new file species.py and species class object TheSpeciesZachary Sloan
Converted html for the mapping tabs to bootstrap and redid html inside of the Interval Mapping tab Added text input for # of permutation tests and bootstrap tests
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