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2022-02-11sql: Remove database mapping code.Arun Isaac
These tools have been greatly improved and moved to a new home at https://git.genenetwork.org/arunisaac/dump-genenetwork-database * sql/map-database.sh, sql/schema-from-in-db-documentation.org, sql/schema-original.sql, sql/schema.png, sql/schema.sql, sql/schema.svg: New files.
2022-02-11Add scaffolding to run different types of testsFrederick Muriuki Muriithi
Enable running commands: - `python3 setup.py unit_check`: run the unit tests - `python3 setup.py integration_check`: run integration tests - `python3 setup.py performance_check`: run performance tests
2022-02-11Quote shell variables to prevent globbingFrederick Muriuki Muriithi
Quote the shell variables to prevent globbing and word splitting. Deactivate this check for the specific lines that require intentional word splitting
2022-02-09github: Remove GitHub actions.Arun Isaac
We have our own laminar CI and no longer need GitHub actions. * .github/workflows: Delete directory.
2022-02-09Remove obsolete `PublishFreeze` tableFrederick Muriuki Muriithi
2022-02-08Merge iterations to remove unnecessary computationsFrederick Muriuki Muriithi
Do all the work in a single iteration to avoid unnecessary iterations that hamper performance.
2022-02-08Remove multiprocessing for stabilityFrederick Muriuki Muriithi
Web servers are long-running processes, and python is not very good at cleaning up after itself especially in forked processes - this leads to memory errors in the web-server after a while. This commit removes the use of multiprocessing to avoid such failures.
2022-02-08Give sorting functions more descriptive namesFrederick Muriuki Muriithi
2022-02-08Use multiprocessing to speed up computationFrederick Muriuki Muriithi
This commit refactors the code to make it possible to use multiprocessing to speed up the computation of the partial correlations. The major refactor is to move the `__compute_trait_info__` function to the top-level of the module, and provide to it all the other necessary context via the new args.
2022-02-08Remove unnecessary computationFrederick Muriuki Muriithi
In Python3 when slicing, seq[:min(some_val, len(seq))] == seq[:some_val] because Python3 will just return a copy of the entire sequence if `some_val` happens to be larger/greater than the length of the sequence. This commit removes the unnecessary call to `min()`
2022-02-08db: traits: Enable deletion of individual sample valuesBonfaceKilz
If a user replaces an individual value with an "x", delete that date entry from the respective table. Deletion here is the only option since by default the Nstrain, PublishData and PublishSE don't accept null values. Note that deleting all 3 values is equivalent to removing the sample from the CSV file. * gn3/db/traits.py (update_sample_data): If a value is "x", delete it from the respective table.
2022-02-08db: traits: Allow insertions of "0" in resp. sample values tablesBonfaceKilz
When editing values from "x" to "0"(or any other value) when editing data, an "update" statement was being run; thereby no new value was being inserted. To the end user, modifying an "x" value to something else meant that no value was being inserted. This commit fixes that by doing an insert whenever a change from "x" to "0" is performed. * gn3/db/traits.py (update_sample_data): Add insert statements whenever an "update" statement returns a 0 row-count.
2022-02-08db: traits: Insert "count" instead of "error" in "NStrain" tableBonfaceKilz
2022-02-03db: Fetch correct sample dataBonfaceKilz
2022-02-02Fix R/qtl covar bugzsloan
The rqtl_wrapper script was throwing an error when only a single categorical covariate was used. This is apparently because "covars[,name]" throws an error in such a situation. Using just "covars" in such a situation prevents the error. So I just added an if statement checking the number of covariates. There might be some better way to deal with this in R, but this is the best I could come up with.
2022-02-02Remove PublishFreeze from retrieve_publish_trait_info queryzsloan
The PublishFreeze table isn't necessary in phenotype queries, since PublishFreeze.Id = InbredSet.Id (for the purposes of identifying traits, at least)
2022-02-02Fix bug where sample values of 0 were being treated as Falsezsloan
In line 91 of gn3/db/traits.py, there was an if statement "if record[key] else 'x'" that was treating values of 0 as False, so I changed it to explicitly check that values aren't None
2022-02-02Fix retrieve_publish_trait_data queryzsloan
The PublishFreeeze table is actually unnecessary for this query, since the group ID (inbred_set_id) should be passed in and that ID is in the PublishXRef table (so no neeed to join with PublishFreeze)
2022-02-02response object error fixAlexander Kabui
2022-02-02pep8 formattingAlexander Kabui
2022-02-02remove commentsAlexander Kabui
2022-02-02return 401 on request failAlexander Kabui
2022-02-02refactor code for invoking ctl scriptAlexander Kabui
2022-02-02pep8 formattingAlexander Kabui
2022-02-02match case string input to booleanAlexander Kabui
2022-02-02fix for parametric inputAlexander Kabui
2022-02-02use user input significanceAlexander Kabui
2022-02-02new line fixAlexander Kabui
2022-02-02add new json outputAlexander Kabui
2022-02-02fix comprehension listAlexander Kabui
2022-02-02Revert "Use guix shell shortcut with guix.scm file"BonfaceKilz
This reverts commit f676c291967f8a81836b73c5a5dcd3c65e02552c.
2022-01-27Use guix shell shortcut with guix.scm filejgart
2022-01-24README: Add pylint and mypy CI badges.Arun Isaac
We now have separate CI jobs for the pylint and mypy tests. * README.md: Add pylint and mypy CI badges.
2022-01-22minor refactoringAlexander Kabui
2022-01-22function override:fix target specific output file for networkAlexander Kabui
2022-01-22generate networkAlexander Kabui
2022-01-22process ctl plot data imgAlexander Kabui
2022-01-22generate ctl plots for each traitAlexander Kabui
2022-01-22read stdout data;handle exceptionsAlexander Kabui
2022-01-22generate required json data for ctl apiAlexander Kabui
2022-01-22fixes for ctl script:generate ctl ctl_significant jsonAlexander Kabui
2022-01-22bugfixes for script;create pheno and geno objectsAlexander Kabui
2022-01-22add endpoint for ctlAlexander Kabui
2022-01-22init file to call ctl scriptAlexander Kabui
2022-01-22generate lineplotAlexander Kabui
2022-01-22minor fix:read input data from json fileAlexander Kabui
2022-01-22export json dataAlexander Kabui
2022-01-22get significant interactionsAlexander Kabui
2022-01-22perform the ctl scanAlexander Kabui
2022-01-22fetch genotypes and phenotype filesAlexander Kabui